From d247549e39a2e8e87d85d5f6733c6abf63c2cddf Mon Sep 17 00:00:00 2001 From: Najib Ishaq Date: Wed, 14 Feb 2024 12:49:20 -0500 Subject: [PATCH 1/8] chore: added plugin suffix to all things --- .../.bumpversion.cfg | 0 .../Dockerfile | 0 .../README.md | 0 .../VERSION | 0 .../build-docker.sh | 0 .../plugin.cwl | 0 .../plugin.json | 0 .../pyproject.toml | 0 .../run-plugin.sh | 0 .../features/feature_segmentation_eval/__init__.py | 0 .../features/feature_segmentation_eval/__main__.py | 0 .../feature_segmentation_eval/feature_evaluation.py | 0 .../features/feature_segmentation_eval/metrics.py | 0 .../tests/__init__.py | 0 .../tests/conftest.py | 0 .../tests/test_cli.py | 0 .../tests/test_feature_single.py | 0 .../.bumpversion.cfg | 0 .../.gitignore | 0 .../CHANGELOG.md | 0 .../Dockerfile | 0 .../README.md | 0 .../VERSION | 0 .../build-docker.sh | 0 .../plugin.json | 0 .../pyproject.toml | 0 .../run-plugin.sh | 0 .../features/pixel_segmentation_eval/__init__.py | 0 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rename to visualization/ome-to-microjson-plugin/tests/__init__.py diff --git a/visualization/ome-to-microjson/tests/conftest.py b/visualization/ome-to-microjson-plugin/tests/conftest.py similarity index 100% rename from visualization/ome-to-microjson/tests/conftest.py rename to visualization/ome-to-microjson-plugin/tests/conftest.py diff --git a/visualization/ome-to-microjson/tests/test_cli.py b/visualization/ome-to-microjson-plugin/tests/test_cli.py similarity index 100% rename from visualization/ome-to-microjson/tests/test_cli.py rename to visualization/ome-to-microjson-plugin/tests/test_cli.py diff --git a/visualization/ome-to-microjson/tests/test_ome_micojson.py b/visualization/ome-to-microjson-plugin/tests/test_ome_micojson.py similarity index 100% rename from visualization/ome-to-microjson/tests/test_ome_micojson.py rename to visualization/ome-to-microjson-plugin/tests/test_ome_micojson.py diff --git a/visualization/tabular-to-microjson/.bumpversion.cfg b/visualization/tabular-to-microjson-plugin/.bumpversion.cfg similarity index 100% rename from visualization/tabular-to-microjson/.bumpversion.cfg rename to visualization/tabular-to-microjson-plugin/.bumpversion.cfg diff --git a/visualization/tabular-to-microjson/Dockerfile b/visualization/tabular-to-microjson-plugin/Dockerfile similarity index 100% rename from visualization/tabular-to-microjson/Dockerfile rename to visualization/tabular-to-microjson-plugin/Dockerfile diff --git a/visualization/tabular-to-microjson/README.md b/visualization/tabular-to-microjson-plugin/README.md similarity index 100% rename from visualization/tabular-to-microjson/README.md rename to visualization/tabular-to-microjson-plugin/README.md diff --git a/visualization/tabular-to-microjson/VERSION b/visualization/tabular-to-microjson-plugin/VERSION similarity index 100% rename from visualization/tabular-to-microjson/VERSION rename to visualization/tabular-to-microjson-plugin/VERSION diff --git a/visualization/tabular-to-microjson/build-docker.sh b/visualization/tabular-to-microjson-plugin/build-docker.sh similarity index 100% rename from visualization/tabular-to-microjson/build-docker.sh rename to visualization/tabular-to-microjson-plugin/build-docker.sh diff --git a/visualization/tabular-to-microjson/examples/example_overlay_Point.json b/visualization/tabular-to-microjson-plugin/examples/example_overlay_Point.json similarity index 100% rename from visualization/tabular-to-microjson/examples/example_overlay_Point.json rename to visualization/tabular-to-microjson-plugin/examples/example_overlay_Point.json diff --git a/visualization/tabular-to-microjson/examples/example_overlay_Polygon.json b/visualization/tabular-to-microjson-plugin/examples/example_overlay_Polygon.json similarity index 100% rename from visualization/tabular-to-microjson/examples/example_overlay_Polygon.json rename to visualization/tabular-to-microjson-plugin/examples/example_overlay_Polygon.json diff --git a/visualization/tabular-to-microjson/plugin.json b/visualization/tabular-to-microjson-plugin/plugin.json similarity index 100% rename from visualization/tabular-to-microjson/plugin.json rename to visualization/tabular-to-microjson-plugin/plugin.json diff --git a/visualization/tabular-to-microjson/pyproject.toml b/visualization/tabular-to-microjson-plugin/pyproject.toml similarity index 100% rename from visualization/tabular-to-microjson/pyproject.toml rename to visualization/tabular-to-microjson-plugin/pyproject.toml diff --git a/visualization/tabular-to-microjson/run-plugin.sh b/visualization/tabular-to-microjson-plugin/run-plugin.sh similarity index 100% rename from visualization/tabular-to-microjson/run-plugin.sh rename to visualization/tabular-to-microjson-plugin/run-plugin.sh diff --git a/visualization/tabular-to-microjson/src/polus/plugins/visualization/tabular_to_microjson/__init__.py b/visualization/tabular-to-microjson-plugin/src/polus/plugins/visualization/tabular_to_microjson/__init__.py similarity index 100% rename from visualization/tabular-to-microjson/src/polus/plugins/visualization/tabular_to_microjson/__init__.py rename to visualization/tabular-to-microjson-plugin/src/polus/plugins/visualization/tabular_to_microjson/__init__.py diff --git a/visualization/tabular-to-microjson/src/polus/plugins/visualization/tabular_to_microjson/__main__.py b/visualization/tabular-to-microjson-plugin/src/polus/plugins/visualization/tabular_to_microjson/__main__.py similarity index 100% rename from visualization/tabular-to-microjson/src/polus/plugins/visualization/tabular_to_microjson/__main__.py rename to visualization/tabular-to-microjson-plugin/src/polus/plugins/visualization/tabular_to_microjson/__main__.py diff --git a/visualization/tabular-to-microjson/src/polus/plugins/visualization/tabular_to_microjson/microjson_overlay.py b/visualization/tabular-to-microjson-plugin/src/polus/plugins/visualization/tabular_to_microjson/microjson_overlay.py similarity index 100% rename from visualization/tabular-to-microjson/src/polus/plugins/visualization/tabular_to_microjson/microjson_overlay.py rename to visualization/tabular-to-microjson-plugin/src/polus/plugins/visualization/tabular_to_microjson/microjson_overlay.py diff --git a/visualization/tabular-to-microjson/tests/__init__.py b/visualization/tabular-to-microjson-plugin/tests/__init__.py similarity index 100% rename from visualization/tabular-to-microjson/tests/__init__.py rename to visualization/tabular-to-microjson-plugin/tests/__init__.py diff --git a/visualization/tabular-to-microjson/tests/test_microjson_overlay.py b/visualization/tabular-to-microjson-plugin/tests/test_microjson_overlay.py similarity index 100% rename from visualization/tabular-to-microjson/tests/test_microjson_overlay.py rename to visualization/tabular-to-microjson-plugin/tests/test_microjson_overlay.py From 54179d10ebe084e25c58e8f9c2936c8b52cded35 Mon Sep 17 00:00:00 2001 From: Najib Ishaq Date: Wed, 14 Feb 2024 13:41:47 -0500 Subject: [PATCH 2/8] chore: added build-docker scripts where missing --- .../theia-bleedthrough-estimation-plugin/build-docker.sh | 4 ++++ regression/theia-bleedthrough-estimation-plugin/plugin.json | 2 +- transforms/images/binary-operations-plugin/build-docker.sh | 4 ++++ transforms/images/image-calculator-plugin/build-docker.sh | 4 ++++ .../lumos-bleedthrough-correction-plugin/build-docker.sh | 4 ++++ transforms/images/montage-plugin/build-docker.sh | 4 ++++ 6 files changed, 21 insertions(+), 1 deletion(-) create mode 100755 regression/theia-bleedthrough-estimation-plugin/build-docker.sh create mode 100755 transforms/images/binary-operations-plugin/build-docker.sh create mode 100755 transforms/images/image-calculator-plugin/build-docker.sh create mode 100755 transforms/images/lumos-bleedthrough-correction-plugin/build-docker.sh create mode 100755 transforms/images/montage-plugin/build-docker.sh diff --git a/regression/theia-bleedthrough-estimation-plugin/build-docker.sh b/regression/theia-bleedthrough-estimation-plugin/build-docker.sh new file mode 100755 index 000000000..57d156094 --- /dev/null +++ b/regression/theia-bleedthrough-estimation-plugin/build-docker.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +version=$( Date: Wed, 14 Feb 2024 13:53:08 -0500 Subject: [PATCH 3/8] chore: added missing b2v config --- .../outlier-removal-plugin/.bumpversion.cfg | 29 +++++++++++++++++++ .../outlier-removal-plugin/CHANGELOG.md | 9 ++++-- clustering/outlier-removal-plugin/README.md | 16 ++++++---- clustering/outlier-removal-plugin/VERSION | 2 +- clustering/outlier-removal-plugin/plugin.json | 4 +-- .../outlier-removal-plugin/pyproject.toml | 2 +- .../clustering/outlier_removal/__init__.py | 3 +- 7 files changed, 51 insertions(+), 14 deletions(-) create mode 100644 clustering/outlier-removal-plugin/.bumpversion.cfg diff --git a/clustering/outlier-removal-plugin/.bumpversion.cfg b/clustering/outlier-removal-plugin/.bumpversion.cfg new file mode 100644 index 000000000..fc7c07790 --- /dev/null +++ b/clustering/outlier-removal-plugin/.bumpversion.cfg @@ -0,0 +1,29 @@ +[bumpversion] +current_version = 0.2.6-dev0 +commit = True +tag = False +parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? +serialize = + {major}.{minor}.{patch}-{release}{dev} + {major}.{minor}.{patch} + +[bumpversion:part:release] +optional_value = _ +first_value = dev +values = + dev + _ + +[bumpversion:part:dev] + +[bumpversion:file:pyproject.toml] +search = version = "{current_version}" +replace = version = "{new_version}" + +[bumpversion:file:VERSION] + +[bumpversion:file:README.md] + +[bumpversion:file:plugin.json] + +[bumpversion:file:src/polus/plugins/clustering/outlier_removal/__init__.py] diff --git a/clustering/outlier-removal-plugin/CHANGELOG.md b/clustering/outlier-removal-plugin/CHANGELOG.md index ac903bf17..59c463e1e 100644 --- a/clustering/outlier-removal-plugin/CHANGELOG.md +++ b/clustering/outlier-removal-plugin/CHANGELOG.md @@ -1,10 +1,13 @@ -## [0.2.6-dev] - 2024-01-12 -### Added +# [0.2.6-dev0] - 2024-01-12 + +## Added + - Pytests to test this plugin - This plugin is now installable with pip. - Added support for arrow file format in addition to csv -### Changed +## Changed + - Updated dependencies (bfio, filepattern, preadator) to latest - Argparse package is replaced with Typer package for command line arguments - Replaced docker base image with latest container image with pre-installed bfio diff --git a/clustering/outlier-removal-plugin/README.md b/clustering/outlier-removal-plugin/README.md index 273c95e89..ce1f6b427 100644 --- a/clustering/outlier-removal-plugin/README.md +++ b/clustering/outlier-removal-plugin/README.md @@ -1,20 +1,23 @@ -# Outlier removal +# Outlier removal (v0.2.6-dev0) + The outlier removal plugin removes the outliers from the data based on the method selected and outputs csv file. The output will have separate csv files for inliers and outliers. The input file should be in csv format. The plugin support vaex supported input csv file that need outliers to be removed. The file should be in csv format. This is a required parameter for the plugin. -## Methods: +## Methods + Choose any one of the methods mentioned to remove outliers from the data. ### Isolation Forest + Ensemble-based unsupervised method for outlier detection. The algorithm isolates outliers instead of normal instances. It works based on the principle that outliers are few and different and hence, the outliers can be identified easier than the normal points. The score is calculated as the path length to isolate the observation. These two methods can be selected to detect outliers> -1. `IsolationForest` -Detect outliers globally that deviates significantly from the rest of the datapoints -2. `IForest` -Detect local outliers that are distinct when compared to those of its neighbors. + +1. `IsolationForest` Detect outliers globally that deviates significantly from the rest of the datapoints +2. `IForest` Detect local outliers that are distinct when compared to those of its neighbors. ### Global + ### Local @@ -22,6 +25,7 @@ Detect local outliers that are distinct when compared to those of its neighbors. ## Outputs: + Select the output file by passing value to `outputType`. User can select from following options `inlier`, `oulier` or `combined`. The combined file contains `anomaly` column which score each datapoint if it is inlier or outlier. ## Building diff --git a/clustering/outlier-removal-plugin/VERSION b/clustering/outlier-removal-plugin/VERSION index aebc71f7a..fccaf8bba 100644 --- a/clustering/outlier-removal-plugin/VERSION +++ b/clustering/outlier-removal-plugin/VERSION @@ -1 +1 @@ -0.2.6-dev +0.2.6-dev0 diff --git a/clustering/outlier-removal-plugin/plugin.json b/clustering/outlier-removal-plugin/plugin.json index 0c22727f0..4142b51e2 100644 --- a/clustering/outlier-removal-plugin/plugin.json +++ b/clustering/outlier-removal-plugin/plugin.json @@ -1,6 +1,6 @@ { "name": "Outlier Removal", - "version": "0.2.6-dev", + "version": "0.2.6-dev0", "title": "Outlier Removal", "description": "Remove outliers from the data.", "author": "Jayapriya Nagarajan (github.com/Priyaaxle) and Hamdah Shafqat Abbasi (hamdahshafqat.abbasi@nih.gov)", @@ -8,7 +8,7 @@ "repository": "https://github.com/PolusAI/polus-plugins", "website": "https://ncats.nih.gov/preclinical/core/informatics", "citation": "", - "containerId": "polusai/outlier-removal-plugin:0.2.6-dev", + "containerId": "polusai/outlier-removal-plugin:0.2.6-dev0", "baseCommand": [ "python3", "-m", diff --git a/clustering/outlier-removal-plugin/pyproject.toml b/clustering/outlier-removal-plugin/pyproject.toml index e4a4dc15c..7761561cb 100644 --- a/clustering/outlier-removal-plugin/pyproject.toml +++ b/clustering/outlier-removal-plugin/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "polus-plugins-clustering-outlier-removal" -version = "0.2.6-dev" +version = "0.2.6-dev0" description = "Remove outliers from the data." authors = [ "Jayapriya Nagarajan ", diff --git a/clustering/outlier-removal-plugin/src/polus/plugins/clustering/outlier_removal/__init__.py b/clustering/outlier-removal-plugin/src/polus/plugins/clustering/outlier_removal/__init__.py index a0942d54d..14d087030 100644 --- a/clustering/outlier-removal-plugin/src/polus/plugins/clustering/outlier_removal/__init__.py +++ b/clustering/outlier-removal-plugin/src/polus/plugins/clustering/outlier_removal/__init__.py @@ -1,2 +1,3 @@ """Outlier Removal Plugin.""" -__version__ = "0.2.6-dev" \ No newline at end of file + +__version__ = "0.2.6-dev0" From c97cd0e87d1be00b6eaf8e99460fd7b885990a6d Mon Sep 17 00:00:00 2001 From: Najib Ishaq Date: Wed, 14 Feb 2024 14:13:09 -0500 Subject: [PATCH 4/8] build: renamed everything and bumped all versions --- clustering/k-means-clustering-plugin/VERSION | 1 - .../k-means-clustering-plugin/build-docker.sh | 4 --- .../.bumpversion.cfg | 4 +-- .../CHANGELOG.md | 2 +- .../Dockerfile | 2 +- .../README.md | 2 +- clustering/k-means-clustering-tool/VERSION | 1 + .../k-means-clustering-tool/build-docker.sh | 4 +++ .../plugin.json | 6 ++-- .../pyproject.toml | 4 +-- .../run-plugin.sh | 0 .../images}/clustering/k_means/__init__.py | 2 +- .../images}/clustering/k_means/__main__.py | 4 +-- .../images}/clustering/k_means/k_means.py | 0 .../polus/images}/clustering/k_means/utils.py | 0 .../tests/__init__.py | 0 .../tests/conftest.py | 0 .../tests/test_main.py | 4 +-- .../outlier-removal-plugin/build-docker.sh | 4 --- .../images/requirements.txt | 3 -- .../outlier-removal-tool}/.bumpversion.cfg | 8 ++--- .../.dockerignore | 0 .../.gitignore | 0 .../CHANGELOG.md | 0 .../Dockerfile | 2 +- .../README.md | 2 +- clustering/outlier-removal-tool/VERSION | 1 + .../outlier-removal-tool/build-docker.sh | 4 +++ .../bumpversion.cfg | 0 .../images/Global.PNG | Bin .../images/Local.PNG | Bin .../package-release.sh | 0 .../plugin.json | 6 ++-- .../pyproject.toml | 4 +-- .../run-docker.sh | 0 .../clustering/outlier_removal/__init__.py | 2 +- .../clustering/outlier_removal/__main__.py | 4 +-- .../outlier_removal/outlier_removal.py | 0 .../tests/__init__.py | 0 .../tests/conftest.py | 0 .../tests/test_cli.py | 2 +- .../tests/test_outlier_removal.py | 2 +- .../.bumpversion.cfg | 27 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/dev/null @@ -1 +0,0 @@ -0.3.4-dev2 diff --git a/clustering/k-means-clustering-plugin/build-docker.sh b/clustering/k-means-clustering-plugin/build-docker.sh deleted file mode 100644 index 7376ef14d..000000000 --- a/clustering/k-means-clustering-plugin/build-docker.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -version=$(\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? @@ -28,4 +28,4 @@ replace = version = "{new_version}" [bumpversion:file:CHANGELOG.md] -[bumpversion:file:src/polus/plugins/clustering/k_means/__init__.py] +[bumpversion:file:src/polus/images/clustering/k_means/__init__.py] diff --git a/clustering/k-means-clustering-plugin/CHANGELOG.md b/clustering/k-means-clustering-tool/CHANGELOG.md similarity index 96% rename from clustering/k-means-clustering-plugin/CHANGELOG.md rename to clustering/k-means-clustering-tool/CHANGELOG.md index 50df09118..92dfa02fd 100644 --- a/clustering/k-means-clustering-plugin/CHANGELOG.md +++ b/clustering/k-means-clustering-tool/CHANGELOG.md @@ -1,4 +1,4 @@ -# K-Means Clustering(0.3.4-dev2) +# K-Means Clustering(0.3.5-dev0) 1. This plugin is updated only to the new plugin standards 2. Before plugin support only `.csv` as an input files supported `.csv` and `.feather` file formats. Now this plugin support other vaex supported file formats both as inputs and outputs. diff --git a/clustering/k-means-clustering-plugin/Dockerfile b/clustering/k-means-clustering-tool/Dockerfile similarity index 86% rename from clustering/k-means-clustering-plugin/Dockerfile rename to clustering/k-means-clustering-tool/Dockerfile index fdf6d5a06..6d8db17a8 100644 --- a/clustering/k-means-clustering-plugin/Dockerfile +++ b/clustering/k-means-clustering-tool/Dockerfile @@ -16,5 +16,5 @@ COPY src ${EXEC_DIR}/src RUN pip3 install ${EXEC_DIR} --no-cache-dir -ENTRYPOINT ["python3", "-m", "polus.plugins.clustering.k_means"] +ENTRYPOINT ["python3", "-m", "polus.images.clustering.k_means"] CMD ["--help"] diff --git a/clustering/k-means-clustering-plugin/README.md b/clustering/k-means-clustering-tool/README.md similarity index 99% rename from clustering/k-means-clustering-plugin/README.md rename to clustering/k-means-clustering-tool/README.md index e3cb4baf4..e85b9d892 100644 --- a/clustering/k-means-clustering-plugin/README.md +++ b/clustering/k-means-clustering-tool/README.md @@ -1,4 +1,4 @@ -# K-Means Clustering(v0.3.4-dev2) +# K-Means Clustering(v0.3.5-dev0) The K-Means Clustering plugin clusters the data using Scikit-learn K-Means clustering algorithm and outputs csv file. Each instance(row) in the input csv file is assigned to one of the clusters. The output csv file contains the column 'Cluster' that shows which cluster the instance belongs to. diff --git a/clustering/k-means-clustering-tool/VERSION b/clustering/k-means-clustering-tool/VERSION new file mode 100644 index 000000000..fb9e21ef3 --- /dev/null +++ b/clustering/k-means-clustering-tool/VERSION @@ -0,0 +1 @@ +0.3.5-dev0 diff --git a/clustering/k-means-clustering-tool/build-docker.sh b/clustering/k-means-clustering-tool/build-docker.sh new file mode 100644 index 000000000..275ef5941 --- /dev/null +++ b/clustering/k-means-clustering-tool/build-docker.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +version=$(", diff --git a/clustering/k-means-clustering-plugin/run-plugin.sh b/clustering/k-means-clustering-tool/run-plugin.sh similarity index 100% rename from clustering/k-means-clustering-plugin/run-plugin.sh rename to clustering/k-means-clustering-tool/run-plugin.sh diff --git a/clustering/k-means-clustering-plugin/src/polus/plugins/clustering/k_means/__init__.py b/clustering/k-means-clustering-tool/src/polus/images/clustering/k_means/__init__.py similarity index 50% rename from clustering/k-means-clustering-plugin/src/polus/plugins/clustering/k_means/__init__.py rename to clustering/k-means-clustering-tool/src/polus/images/clustering/k_means/__init__.py index 0262b3179..2415b1e24 100644 --- a/clustering/k-means-clustering-plugin/src/polus/plugins/clustering/k_means/__init__.py +++ b/clustering/k-means-clustering-tool/src/polus/images/clustering/k_means/__init__.py @@ -1,3 +1,3 @@ """K_means clustering.""" -__version__ = "0.3.4-dev2" +__version__ = "0.3.5-dev0" diff --git a/clustering/k-means-clustering-plugin/src/polus/plugins/clustering/k_means/__main__.py b/clustering/k-means-clustering-tool/src/polus/images/clustering/k_means/__main__.py similarity index 96% rename from clustering/k-means-clustering-plugin/src/polus/plugins/clustering/k_means/__main__.py rename to clustering/k-means-clustering-tool/src/polus/images/clustering/k_means/__main__.py index 3fd0a43e3..ab977b429 100644 --- a/clustering/k-means-clustering-plugin/src/polus/plugins/clustering/k_means/__main__.py +++ b/clustering/k-means-clustering-tool/src/polus/images/clustering/k_means/__main__.py @@ -11,14 +11,14 @@ import filepattern as fp import typer -from polus.plugins.clustering.k_means import k_means as km +from polus.images.clustering.k_means import k_means as km # Initialize the logger logging.basicConfig( format="%(asctime)s - %(name)-8s - %(levelname)-8s - %(message)s", datefmt="%d-%b-%y %H:%M:%S", ) -logger = logging.getLogger("polus.plugins.clustering.k_means") +logger = logging.getLogger("polus.images.clustering.k_means") logger.setLevel(os.environ.get("POLUS_LOG", logging.INFO)) POLUS_TAB_EXT = os.environ.get("POLUS_TAB_EXT", ".arrow") diff --git a/clustering/k-means-clustering-plugin/src/polus/plugins/clustering/k_means/k_means.py b/clustering/k-means-clustering-tool/src/polus/images/clustering/k_means/k_means.py similarity index 100% rename from clustering/k-means-clustering-plugin/src/polus/plugins/clustering/k_means/k_means.py rename to clustering/k-means-clustering-tool/src/polus/images/clustering/k_means/k_means.py diff --git a/clustering/k-means-clustering-plugin/src/polus/plugins/clustering/k_means/utils.py b/clustering/k-means-clustering-tool/src/polus/images/clustering/k_means/utils.py similarity index 100% rename from clustering/k-means-clustering-plugin/src/polus/plugins/clustering/k_means/utils.py rename to clustering/k-means-clustering-tool/src/polus/images/clustering/k_means/utils.py diff --git a/clustering/k-means-clustering-plugin/tests/__init__.py b/clustering/k-means-clustering-tool/tests/__init__.py similarity index 100% rename from clustering/k-means-clustering-plugin/tests/__init__.py rename to clustering/k-means-clustering-tool/tests/__init__.py diff --git a/clustering/k-means-clustering-plugin/tests/conftest.py b/clustering/k-means-clustering-tool/tests/conftest.py similarity index 100% rename from clustering/k-means-clustering-plugin/tests/conftest.py rename to clustering/k-means-clustering-tool/tests/conftest.py diff --git a/clustering/k-means-clustering-plugin/tests/test_main.py b/clustering/k-means-clustering-tool/tests/test_main.py similarity index 96% rename from clustering/k-means-clustering-plugin/tests/test_main.py rename to clustering/k-means-clustering-tool/tests/test_main.py index c445172c2..7c516c759 100644 --- a/clustering/k-means-clustering-plugin/tests/test_main.py +++ b/clustering/k-means-clustering-tool/tests/test_main.py @@ -5,8 +5,8 @@ import filepattern as fp import pytest import vaex -from polus.plugins.clustering.k_means import k_means as km -from polus.plugins.clustering.k_means.__main__ import app +from polus.images.clustering.k_means import k_means as km +from polus.images.clustering.k_means.__main__ import app from typer.testing import CliRunner from .conftest import Generatedata diff --git a/clustering/outlier-removal-plugin/build-docker.sh b/clustering/outlier-removal-plugin/build-docker.sh deleted file mode 100644 index 9da675202..000000000 --- a/clustering/outlier-removal-plugin/build-docker.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -version=$(=1.2.3 -scikit-learn==0.24.1 -pyod==0.8.7 \ No newline at end of file diff --git a/transforms/images/montage-plugin/.bumpversion.cfg b/clustering/outlier-removal-tool/.bumpversion.cfg similarity index 85% rename from transforms/images/montage-plugin/.bumpversion.cfg rename to clustering/outlier-removal-tool/.bumpversion.cfg index d9a682f59..1a4319f1c 100644 --- a/transforms/images/montage-plugin/.bumpversion.cfg +++ b/clustering/outlier-removal-tool/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.5.0 +current_version = 0.2.7-dev0 commit = True tag = False parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? @@ -20,10 +20,10 @@ values = search = version = "{current_version}" replace = version = "{new_version}" -[bumpversion:file:plugin.json] - [bumpversion:file:VERSION] [bumpversion:file:README.md] -[bumpversion:file:src/polus/plugins/transforms/images/montage/__init__.py] +[bumpversion:file:plugin.json] + +[bumpversion:file:src/polus/images/clustering/outlier_removal/__init__.py] diff --git a/clustering/outlier-removal-plugin/.dockerignore b/clustering/outlier-removal-tool/.dockerignore similarity index 100% rename from clustering/outlier-removal-plugin/.dockerignore rename to clustering/outlier-removal-tool/.dockerignore diff --git a/clustering/outlier-removal-plugin/.gitignore b/clustering/outlier-removal-tool/.gitignore similarity index 100% rename from clustering/outlier-removal-plugin/.gitignore rename to clustering/outlier-removal-tool/.gitignore diff --git a/clustering/outlier-removal-plugin/CHANGELOG.md b/clustering/outlier-removal-tool/CHANGELOG.md similarity index 100% rename from clustering/outlier-removal-plugin/CHANGELOG.md rename to clustering/outlier-removal-tool/CHANGELOG.md diff --git a/clustering/outlier-removal-plugin/Dockerfile b/clustering/outlier-removal-tool/Dockerfile similarity index 83% rename from clustering/outlier-removal-plugin/Dockerfile rename to clustering/outlier-removal-tool/Dockerfile index d4c515b72..da498532b 100644 --- a/clustering/outlier-removal-plugin/Dockerfile +++ b/clustering/outlier-removal-tool/Dockerfile @@ -16,5 +16,5 @@ COPY README.md ${EXEC_DIR} RUN pip3 install ${EXEC_DIR} --no-cache -ENTRYPOINT ["python3", "-m", "polus.plugins.clustering.outlier_removal"] +ENTRYPOINT ["python3", "-m", "polus.images.clustering.outlier_removal"] CMD ["--help"] diff --git a/clustering/outlier-removal-plugin/README.md b/clustering/outlier-removal-tool/README.md similarity index 98% rename from clustering/outlier-removal-plugin/README.md rename to clustering/outlier-removal-tool/README.md index ce1f6b427..9b39a9a63 100644 --- a/clustering/outlier-removal-plugin/README.md +++ b/clustering/outlier-removal-tool/README.md @@ -1,4 +1,4 @@ -# Outlier removal (v0.2.6-dev0) +# Outlier removal (v0.2.7-dev0) The outlier removal plugin removes the outliers from the data based on the method selected and outputs csv file. The output will have separate csv files for inliers and outliers. The input file should be in csv format. diff --git a/clustering/outlier-removal-tool/VERSION b/clustering/outlier-removal-tool/VERSION new file mode 100644 index 000000000..c9f43e05d --- /dev/null +++ b/clustering/outlier-removal-tool/VERSION @@ -0,0 +1 @@ +0.2.7-dev0 diff --git a/clustering/outlier-removal-tool/build-docker.sh b/clustering/outlier-removal-tool/build-docker.sh new file mode 100644 index 000000000..be64f7228 --- /dev/null +++ b/clustering/outlier-removal-tool/build-docker.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +version=$(", diff --git a/clustering/outlier-removal-plugin/run-docker.sh b/clustering/outlier-removal-tool/run-docker.sh similarity index 100% rename from clustering/outlier-removal-plugin/run-docker.sh rename to clustering/outlier-removal-tool/run-docker.sh diff --git a/clustering/outlier-removal-plugin/src/polus/plugins/clustering/outlier_removal/__init__.py b/clustering/outlier-removal-tool/src/polus/images/clustering/outlier_removal/__init__.py similarity index 53% rename from clustering/outlier-removal-plugin/src/polus/plugins/clustering/outlier_removal/__init__.py rename to clustering/outlier-removal-tool/src/polus/images/clustering/outlier_removal/__init__.py index 14d087030..d41a2977f 100644 --- a/clustering/outlier-removal-plugin/src/polus/plugins/clustering/outlier_removal/__init__.py +++ b/clustering/outlier-removal-tool/src/polus/images/clustering/outlier_removal/__init__.py @@ -1,3 +1,3 @@ """Outlier Removal Plugin.""" -__version__ = "0.2.6-dev0" +__version__ = "0.2.7-dev0" diff --git a/clustering/outlier-removal-plugin/src/polus/plugins/clustering/outlier_removal/__main__.py b/clustering/outlier-removal-tool/src/polus/images/clustering/outlier_removal/__main__.py similarity index 95% rename from clustering/outlier-removal-plugin/src/polus/plugins/clustering/outlier_removal/__main__.py rename to clustering/outlier-removal-tool/src/polus/images/clustering/outlier_removal/__main__.py index 92196454b..35ce74195 100644 --- a/clustering/outlier-removal-plugin/src/polus/plugins/clustering/outlier_removal/__main__.py +++ b/clustering/outlier-removal-tool/src/polus/images/clustering/outlier_removal/__main__.py @@ -8,7 +8,7 @@ from typing import Optional import filepattern as fp -import polus.plugins.clustering.outlier_removal.outlier_removal as rm +import polus.images.clustering.outlier_removal.outlier_removal as rm import preadator import typer @@ -21,7 +21,7 @@ format="%(asctime)s - %(name)-8s - %(levelname)-8s - %(message)s", datefmt="%d-%b-%y %H:%M:%S", ) -logger = logging.getLogger("polus.plugins.clustering.outlier_removal") +logger = logging.getLogger("polus.images.clustering.outlier_removal") @app.command() diff --git a/clustering/outlier-removal-plugin/src/polus/plugins/clustering/outlier_removal/outlier_removal.py b/clustering/outlier-removal-tool/src/polus/images/clustering/outlier_removal/outlier_removal.py similarity index 100% rename from clustering/outlier-removal-plugin/src/polus/plugins/clustering/outlier_removal/outlier_removal.py rename to clustering/outlier-removal-tool/src/polus/images/clustering/outlier_removal/outlier_removal.py diff --git a/clustering/outlier-removal-plugin/tests/__init__.py b/clustering/outlier-removal-tool/tests/__init__.py similarity index 100% rename from clustering/outlier-removal-plugin/tests/__init__.py rename to clustering/outlier-removal-tool/tests/__init__.py diff --git a/clustering/outlier-removal-plugin/tests/conftest.py b/clustering/outlier-removal-tool/tests/conftest.py similarity index 100% rename from clustering/outlier-removal-plugin/tests/conftest.py rename to clustering/outlier-removal-tool/tests/conftest.py diff --git a/clustering/outlier-removal-plugin/tests/test_cli.py b/clustering/outlier-removal-tool/tests/test_cli.py similarity index 95% rename from clustering/outlier-removal-plugin/tests/test_cli.py rename to clustering/outlier-removal-tool/tests/test_cli.py index 93910779a..c303a5d54 100644 --- a/clustering/outlier-removal-plugin/tests/test_cli.py +++ b/clustering/outlier-removal-tool/tests/test_cli.py @@ -1,6 +1,6 @@ """Test Command line Tool.""" from typer.testing import CliRunner -from polus.plugins.clustering.outlier_removal.__main__ import app +from polus.images.clustering.outlier_removal.__main__ import app import shutil from pathlib import Path diff --git a/clustering/outlier-removal-plugin/tests/test_outlier_removal.py b/clustering/outlier-removal-tool/tests/test_outlier_removal.py similarity index 95% rename from clustering/outlier-removal-plugin/tests/test_outlier_removal.py rename to clustering/outlier-removal-tool/tests/test_outlier_removal.py index e28617b49..5f90fb01c 100644 --- a/clustering/outlier-removal-plugin/tests/test_outlier_removal.py +++ b/clustering/outlier-removal-tool/tests/test_outlier_removal.py @@ -4,7 +4,7 @@ import filepattern as fp import numpy as np -import polus.plugins.clustering.outlier_removal.outlier_removal as rm +import polus.images.clustering.outlier_removal.outlier_removal as rm import vaex diff --git a/features/feature-segmentation-eval-tool/.bumpversion.cfg b/features/feature-segmentation-eval-tool/.bumpversion.cfg new file mode 100644 index 000000000..24647bf21 --- /dev/null +++ b/features/feature-segmentation-eval-tool/.bumpversion.cfg @@ -0,0 +1,27 @@ +[bumpversion] +current_version = 0.2.6-dev0 +commit = True +tag = False +parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? +serialize = + {major}.{minor}.{patch}-{release}{dev} + {major}.{minor}.{patch} + +[bumpversion:part:release] +optional_value = _ +first_value = dev +values = + dev + _ + +[bumpversion:part:dev] + +[bumpversion:file:pyproject.toml] +search = version = "{current_version}" +replace = version = "{new_version}" + +[bumpversion:file:plugin.json] + +[bumpversion:file:VERSION] + +[bumpversion:file:src/polus/images/features/feature_segmentation_eval/__init__.py] diff --git a/features/feature-segmentation-eval-plugin/Dockerfile b/features/feature-segmentation-eval-tool/Dockerfile similarity index 83% rename from features/feature-segmentation-eval-plugin/Dockerfile rename to features/feature-segmentation-eval-tool/Dockerfile index 843787cb2..73d0b9f5d 100644 --- a/features/feature-segmentation-eval-plugin/Dockerfile +++ b/features/feature-segmentation-eval-tool/Dockerfile @@ -16,5 +16,5 @@ COPY src ${EXEC_DIR}/src RUN pip3 install ${EXEC_DIR} --no-cache-dir -ENTRYPOINT ["python3", "-m", "polus.plugins.features.feature_segmentation_eval"] +ENTRYPOINT ["python3", "-m", "polus.images.features.feature_segmentation_eval"] CMD ["--help"] diff --git a/features/feature-segmentation-eval-plugin/README.md b/features/feature-segmentation-eval-tool/README.md similarity index 100% rename from features/feature-segmentation-eval-plugin/README.md rename to features/feature-segmentation-eval-tool/README.md diff --git a/clustering/outlier-removal-plugin/VERSION b/features/feature-segmentation-eval-tool/VERSION similarity index 100% rename from clustering/outlier-removal-plugin/VERSION rename to features/feature-segmentation-eval-tool/VERSION diff --git a/features/feature-segmentation-eval-plugin/build-docker.sh b/features/feature-segmentation-eval-tool/build-docker.sh similarity index 100% rename from features/feature-segmentation-eval-plugin/build-docker.sh rename to features/feature-segmentation-eval-tool/build-docker.sh diff --git a/features/feature-segmentation-eval-plugin/plugin.cwl b/features/feature-segmentation-eval-tool/plugin.cwl similarity index 100% rename from features/feature-segmentation-eval-plugin/plugin.cwl rename to features/feature-segmentation-eval-tool/plugin.cwl diff --git a/features/feature-segmentation-eval-plugin/plugin.json b/features/feature-segmentation-eval-tool/plugin.json similarity index 94% rename from features/feature-segmentation-eval-plugin/plugin.json rename to features/feature-segmentation-eval-tool/plugin.json index 6a3c3ae35..6267b9431 100644 --- a/features/feature-segmentation-eval-plugin/plugin.json +++ b/features/feature-segmentation-eval-tool/plugin.json @@ -1,6 +1,6 @@ { "name": "Feature Segmentation Eval", - "version": "0.2.5-dev0", + "version": "0.2.6-dev0", "title": "Feature Segmentation Eval", "description": "Plugin to generate evaluation metrics for feature comparison of ground truth and predicted images.", "author": "Vishakha Goyal (vishakha.goyal@nih.gov), Hamdah Shafqat Abbasi (hamdahshafqat.abbasi@nih.gov)", @@ -8,11 +8,11 @@ "repository": "https://github.com/labshare/polus-plugins", "website": "https://ncats.nih.gov/preclinical/core/informatics", "citation": "", - "containerId": "polusai/feature-segmentation-eval:0.2.5-dev0", + "containerId": "polusai/feature-segmentation-eval:0.2.6-dev0", "baseCommand": [ "python3", "-m", - "polus.plugins.features.feature_segmentation_eval" + "polus.images.features.feature_segmentation_eval" ], "inputs": [ { diff --git a/features/feature-segmentation-eval-plugin/pyproject.toml b/features/feature-segmentation-eval-tool/pyproject.toml similarity index 90% rename from features/feature-segmentation-eval-plugin/pyproject.toml rename to features/feature-segmentation-eval-tool/pyproject.toml index b6c237f4b..e6452c702 100644 --- a/features/feature-segmentation-eval-plugin/pyproject.toml +++ b/features/feature-segmentation-eval-tool/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] -name = "polus-plugins-features-feature-segmentation-eval" -version = "0.2.5-dev0" +name = "polus-images-features-feature-segmentation-eval" +version = "0.2.6-dev0" description = "Feature segmentation eval" authors = [ "Vishakha Goyal ", diff --git a/features/feature-segmentation-eval-plugin/run-plugin.sh b/features/feature-segmentation-eval-tool/run-plugin.sh similarity index 100% rename from features/feature-segmentation-eval-plugin/run-plugin.sh rename to features/feature-segmentation-eval-tool/run-plugin.sh diff --git a/features/feature-segmentation-eval-plugin/src/polus/plugins/features/feature_segmentation_eval/__init__.py b/features/feature-segmentation-eval-tool/src/polus/images/features/feature_segmentation_eval/__init__.py similarity index 79% rename from features/feature-segmentation-eval-plugin/src/polus/plugins/features/feature_segmentation_eval/__init__.py rename to features/feature-segmentation-eval-tool/src/polus/images/features/feature_segmentation_eval/__init__.py index 9efb8204b..b81e99792 100644 --- a/features/feature-segmentation-eval-plugin/src/polus/plugins/features/feature_segmentation_eval/__init__.py +++ b/features/feature-segmentation-eval-tool/src/polus/images/features/feature_segmentation_eval/__init__.py @@ -1,4 +1,4 @@ """Feature segmentation evaluation package.""" -__version__ = "0.2.5-dev0" +__version__ = "0.2.6-dev0" from . import feature_evaluation from . import metrics diff --git a/features/feature-segmentation-eval-plugin/src/polus/plugins/features/feature_segmentation_eval/__main__.py b/features/feature-segmentation-eval-tool/src/polus/images/features/feature_segmentation_eval/__main__.py similarity index 95% rename from features/feature-segmentation-eval-plugin/src/polus/plugins/features/feature_segmentation_eval/__main__.py rename to features/feature-segmentation-eval-tool/src/polus/images/features/feature_segmentation_eval/__main__.py index bab8e4e0e..909ecd530 100644 --- a/features/feature-segmentation-eval-plugin/src/polus/plugins/features/feature_segmentation_eval/__main__.py +++ b/features/feature-segmentation-eval-tool/src/polus/images/features/feature_segmentation_eval/__main__.py @@ -7,7 +7,7 @@ from typing import Any import filepattern as fp -import polus.plugins.features.feature_segmentation_eval.feature_evaluation as fs +import polus.images.features.feature_segmentation_eval.feature_evaluation as fs import typer logging.basicConfig( @@ -15,7 +15,7 @@ datefmt="%d-%b-%y %H:%M:%S", ) POLUS_LOG = getattr(logging, environ.get("POLUS_LOG", "INFO")) -logger = logging.getLogger("polus.plugins.features.feature_segmentation_eval") +logger = logging.getLogger("polus.images.features.feature_segmentation_eval") logger.setLevel(POLUS_LOG) logging.getLogger("bfio").setLevel(POLUS_LOG) # Set number of threads for scalability diff --git a/features/feature-segmentation-eval-plugin/src/polus/plugins/features/feature_segmentation_eval/feature_evaluation.py b/features/feature-segmentation-eval-tool/src/polus/images/features/feature_segmentation_eval/feature_evaluation.py similarity index 100% rename from features/feature-segmentation-eval-plugin/src/polus/plugins/features/feature_segmentation_eval/feature_evaluation.py rename to features/feature-segmentation-eval-tool/src/polus/images/features/feature_segmentation_eval/feature_evaluation.py diff --git a/features/feature-segmentation-eval-plugin/src/polus/plugins/features/feature_segmentation_eval/metrics.py b/features/feature-segmentation-eval-tool/src/polus/images/features/feature_segmentation_eval/metrics.py similarity index 100% rename from features/feature-segmentation-eval-plugin/src/polus/plugins/features/feature_segmentation_eval/metrics.py rename to features/feature-segmentation-eval-tool/src/polus/images/features/feature_segmentation_eval/metrics.py diff --git a/features/feature-segmentation-eval-plugin/tests/__init__.py b/features/feature-segmentation-eval-tool/tests/__init__.py similarity index 100% rename from features/feature-segmentation-eval-plugin/tests/__init__.py rename to features/feature-segmentation-eval-tool/tests/__init__.py diff --git a/features/feature-segmentation-eval-plugin/tests/conftest.py b/features/feature-segmentation-eval-tool/tests/conftest.py similarity index 100% rename from features/feature-segmentation-eval-plugin/tests/conftest.py rename to features/feature-segmentation-eval-tool/tests/conftest.py diff --git a/features/feature-segmentation-eval-plugin/tests/test_cli.py b/features/feature-segmentation-eval-tool/tests/test_cli.py similarity index 92% rename from features/feature-segmentation-eval-plugin/tests/test_cli.py rename to features/feature-segmentation-eval-tool/tests/test_cli.py index d9c6255c6..c92f8ea9e 100644 --- a/features/feature-segmentation-eval-plugin/tests/test_cli.py +++ b/features/feature-segmentation-eval-tool/tests/test_cli.py @@ -3,7 +3,7 @@ from pathlib import Path from typing import Union -from polus.plugins.features.feature_segmentation_eval.__main__ import app +from polus.images.features.feature_segmentation_eval.__main__ import app from typer.testing import CliRunner diff --git a/features/feature-segmentation-eval-plugin/tests/test_feature_single.py b/features/feature-segmentation-eval-tool/tests/test_feature_single.py similarity index 93% rename from features/feature-segmentation-eval-plugin/tests/test_feature_single.py rename to features/feature-segmentation-eval-tool/tests/test_feature_single.py index 1f0c2782d..505b8c486 100644 --- a/features/feature-segmentation-eval-plugin/tests/test_feature_single.py +++ b/features/feature-segmentation-eval-tool/tests/test_feature_single.py @@ -3,7 +3,7 @@ from pathlib import Path from typing import Union -import polus.plugins.features.feature_segmentation_eval.feature_evaluation as fs +import polus.images.features.feature_segmentation_eval.feature_evaluation as fs import pytest import vaex diff --git a/features/nyxus-plugin/VERSION b/features/nyxus-plugin/VERSION deleted file mode 100755 index c946ee616..000000000 --- a/features/nyxus-plugin/VERSION +++ /dev/null @@ -1 +0,0 @@ -0.1.6 diff --git a/features/nyxus-plugin/build-docker.sh b/features/nyxus-plugin/build-docker.sh deleted file mode 100755 index 5a8d510d6..000000000 --- a/features/nyxus-plugin/build-docker.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -version=$(\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? @@ -26,4 +26,4 @@ replace = version = "{new_version}" [bumpversion:file:README.md] -[bumpversion:file:src/polus/plugins/formats/ome_converter/__init__.py] +[bumpversion:file:src/polus/images/features/nyxus_plugin/__init__.py] diff --git a/features/nyxus-plugin/.gitignore b/features/nyxus-tool/.gitignore similarity index 100% rename from features/nyxus-plugin/.gitignore rename to features/nyxus-tool/.gitignore diff --git a/features/nyxus-plugin/CHANGELOG.md b/features/nyxus-tool/CHANGELOG.md similarity index 100% rename from features/nyxus-plugin/CHANGELOG.md rename to features/nyxus-tool/CHANGELOG.md diff --git a/features/nyxus-plugin/Dockerfile b/features/nyxus-tool/Dockerfile similarity index 85% rename from features/nyxus-plugin/Dockerfile rename to features/nyxus-tool/Dockerfile index cc541f99a..172618817 100755 --- a/features/nyxus-plugin/Dockerfile +++ b/features/nyxus-tool/Dockerfile @@ -15,5 +15,5 @@ COPY src ${EXEC_DIR}/src RUN pip3 install ${EXEC_DIR} --no-cache-dir -ENTRYPOINT ["python3", "-m", "polus.plugins.features.nyxus_plugin"] +ENTRYPOINT ["python3", "-m", "polus.images.features.nyxus_plugin"] CMD ["--help"] diff --git a/features/nyxus-plugin/README.md b/features/nyxus-tool/README.md similarity index 99% rename from features/nyxus-plugin/README.md rename to features/nyxus-tool/README.md index cefa84a50..e3f82b7e2 100755 --- a/features/nyxus-plugin/README.md +++ b/features/nyxus-tool/README.md @@ -1,4 +1,4 @@ -# Nyxus-Plugin(v0.1.6) +# Nyxus-Plugin(v0.1.7-dev0) Nyxus plugin uses parallel processing of [Nyxus python package](https://pypi.org/project/nyxus/) to extract nyxus features from intensity-label image data. Especially useful when processing high throughput screens. diff --git a/features/nyxus-tool/VERSION b/features/nyxus-tool/VERSION new file mode 100755 index 000000000..be8ec7f46 --- /dev/null +++ b/features/nyxus-tool/VERSION @@ -0,0 +1 @@ +0.1.7-dev0 diff --git a/features/nyxus-tool/build-docker.sh b/features/nyxus-tool/build-docker.sh new file mode 100755 index 000000000..c7a24dddd --- /dev/null +++ b/features/nyxus-tool/build-docker.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +version=$(", diff --git a/features/nyxus-plugin/run-plugin.sh b/features/nyxus-tool/run-plugin.sh similarity index 100% rename from features/nyxus-plugin/run-plugin.sh rename to features/nyxus-tool/run-plugin.sh diff --git a/features/nyxus-tool/src/polus/images/features/nyxus_plugin/__init__.py b/features/nyxus-tool/src/polus/images/features/nyxus_plugin/__init__.py new file mode 100644 index 000000000..4f6db49b1 --- /dev/null +++ b/features/nyxus-tool/src/polus/images/features/nyxus_plugin/__init__.py @@ -0,0 +1,2 @@ +"""Nyxus Plugin.""" +__version__ = "0.1.7-dev0" diff --git a/features/nyxus-plugin/src/polus/plugins/features/nyxus_plugin/__main__.py b/features/nyxus-tool/src/polus/images/features/nyxus_plugin/__main__.py similarity index 94% rename from features/nyxus-plugin/src/polus/plugins/features/nyxus_plugin/__main__.py rename to features/nyxus-tool/src/polus/images/features/nyxus_plugin/__main__.py index 032b2aff4..073aabe77 100644 --- a/features/nyxus-plugin/src/polus/plugins/features/nyxus_plugin/__main__.py +++ b/features/nyxus-tool/src/polus/images/features/nyxus_plugin/__main__.py @@ -12,10 +12,10 @@ import filepattern as fp import preadator import typer -from polus.plugins.features.nyxus_plugin.nyxus_func import nyxus_func -from polus.plugins.features.nyxus_plugin.utils import FEATURE_GROUP -from polus.plugins.features.nyxus_plugin.utils import FEATURE_LIST -from polus.plugins.features.nyxus_plugin.utils import Extension +from polus.images.features.nyxus_plugin.nyxus_func import nyxus_func +from polus.images.features.nyxus_plugin.utils import FEATURE_GROUP +from polus.images.features.nyxus_plugin.utils import FEATURE_LIST +from polus.images.features.nyxus_plugin.utils import Extension from tqdm import tqdm # #Import environment variables @@ -28,7 +28,7 @@ format="%(asctime)s - %(name)-8s - %(levelname)-8s - %(message)s", datefmt="%d-%b-%y %H:%M:%S", ) -logger = logging.getLogger("polus.plugins.features.nyxus_plugin") +logger = logging.getLogger("polus.images.features.nyxus_plugin") @app.command() diff --git a/features/nyxus-plugin/src/polus/plugins/features/nyxus_plugin/nyxus_func.py b/features/nyxus-tool/src/polus/images/features/nyxus_plugin/nyxus_func.py similarity index 100% rename from features/nyxus-plugin/src/polus/plugins/features/nyxus_plugin/nyxus_func.py rename to features/nyxus-tool/src/polus/images/features/nyxus_plugin/nyxus_func.py diff --git a/features/nyxus-plugin/src/polus/plugins/features/nyxus_plugin/utils.py b/features/nyxus-tool/src/polus/images/features/nyxus_plugin/utils.py similarity index 100% rename from features/nyxus-plugin/src/polus/plugins/features/nyxus_plugin/utils.py rename to features/nyxus-tool/src/polus/images/features/nyxus_plugin/utils.py diff --git a/features/nyxus-plugin/tests/__init__.py b/features/nyxus-tool/tests/__init__.py similarity index 100% rename from features/nyxus-plugin/tests/__init__.py rename to features/nyxus-tool/tests/__init__.py diff --git a/features/nyxus-plugin/tests/conftest.py b/features/nyxus-tool/tests/conftest.py similarity index 100% rename from features/nyxus-plugin/tests/conftest.py rename to features/nyxus-tool/tests/conftest.py diff --git a/features/nyxus-plugin/tests/test_main.py b/features/nyxus-tool/tests/test_main.py similarity index 97% rename from features/nyxus-plugin/tests/test_main.py rename to features/nyxus-tool/tests/test_main.py index 529801ede..6ac27e94e 100755 --- a/features/nyxus-plugin/tests/test_main.py +++ b/features/nyxus-tool/tests/test_main.py @@ -11,8 +11,8 @@ from skimage import filters, io, measure from typer.testing import CliRunner -from polus.plugins.features.nyxus_plugin.__main__ import app as app -from polus.plugins.features.nyxus_plugin.nyxus_func import nyxus_func +from polus.images.features.nyxus_plugin.__main__ import app as app +from polus.images.features.nyxus_plugin.nyxus_func import nyxus_func runner = CliRunner() diff --git a/features/pixel-segmentation-eval-plugin/VERSION b/features/pixel-segmentation-eval-plugin/VERSION deleted file mode 100644 index dfacca8f8..000000000 --- a/features/pixel-segmentation-eval-plugin/VERSION +++ /dev/null @@ -1 +0,0 @@ -0.1.11-dev1 diff --git a/features/pixel-segmentation-eval-plugin/.bumpversion.cfg b/features/pixel-segmentation-eval-tool/.bumpversion.cfg similarity index 83% rename from features/pixel-segmentation-eval-plugin/.bumpversion.cfg rename to features/pixel-segmentation-eval-tool/.bumpversion.cfg index 2f4542e27..8622f5d32 100644 --- a/features/pixel-segmentation-eval-plugin/.bumpversion.cfg +++ b/features/pixel-segmentation-eval-tool/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.1.11-dev1 +current_version = 0.1.12-dev0 commit = True tag = False parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? @@ -28,4 +28,4 @@ replace = version = "{new_version}" [bumpversion:file:CHANGELOG.md] -[bumpversion:file:src/polus/plugins/features/pixel_segmentation_eval/__init__.py] +[bumpversion:file:src/polus/images/features/pixel_segmentation_eval/__init__.py] diff --git a/features/pixel-segmentation-eval-plugin/.gitignore b/features/pixel-segmentation-eval-tool/.gitignore similarity index 100% rename from features/pixel-segmentation-eval-plugin/.gitignore rename to features/pixel-segmentation-eval-tool/.gitignore diff --git a/features/pixel-segmentation-eval-plugin/CHANGELOG.md b/features/pixel-segmentation-eval-tool/CHANGELOG.md similarity index 94% rename from features/pixel-segmentation-eval-plugin/CHANGELOG.md rename to features/pixel-segmentation-eval-tool/CHANGELOG.md index 767b2d178..8a1911e70 100644 --- a/features/pixel-segmentation-eval-plugin/CHANGELOG.md +++ b/features/pixel-segmentation-eval-tool/CHANGELOG.md @@ -1,4 +1,4 @@ -# pixel-segmentation-eval(v0.1.11-dev1) +# pixel-segmentation-eval(v0.1.12-dev0) 1. This plugin is updated only to the new plugin standards 2. `csv` python packages is replaced with vaex for adding support for additional tabular file formats `.arrow`, `.feather`. diff --git a/features/region-segmentation-eval-plugin/Dockerfile b/features/pixel-segmentation-eval-tool/Dockerfile similarity index 83% rename from features/region-segmentation-eval-plugin/Dockerfile rename to features/pixel-segmentation-eval-tool/Dockerfile index b1fa15196..578bc68bd 100644 --- a/features/region-segmentation-eval-plugin/Dockerfile +++ b/features/pixel-segmentation-eval-tool/Dockerfile @@ -15,5 +15,5 @@ COPY src ${EXEC_DIR}/src RUN pip3 install ${EXEC_DIR} --no-cache-dir -ENTRYPOINT ["python3", "-m", "polus.plugins.features.region_segmentation_eval"] +ENTRYPOINT ["python3", "-m", "polus.images.features.pixel_segmentation_eval"] CMD ["--help"] diff --git a/features/pixel-segmentation-eval-plugin/README.md b/features/pixel-segmentation-eval-tool/README.md similarity index 97% rename from features/pixel-segmentation-eval-plugin/README.md rename to features/pixel-segmentation-eval-tool/README.md index a82a10c6e..bb34ae562 100644 --- a/features/pixel-segmentation-eval-plugin/README.md +++ b/features/pixel-segmentation-eval-tool/README.md @@ -1,4 +1,4 @@ -# Pixel segmentation eval (v0.1.11-dev1) +# Pixel segmentation eval (v0.1.12-dev0) Plugin to generate evaluation metrics for pixel-wise comparison of ground truth and predicted images. Contact [Vishakha Goyal](mailto:vishakha.goyal@nih.gov) , [Hamdah Shafqat Abbasi](mailto:hamdahshafqat.abbasi@nih.gov) for more information. diff --git a/features/pixel-segmentation-eval-tool/VERSION b/features/pixel-segmentation-eval-tool/VERSION new file mode 100644 index 000000000..2155fe166 --- /dev/null +++ b/features/pixel-segmentation-eval-tool/VERSION @@ -0,0 +1 @@ +0.1.12-dev0 diff --git a/features/pixel-segmentation-eval-plugin/build-docker.sh b/features/pixel-segmentation-eval-tool/build-docker.sh similarity index 100% rename from features/pixel-segmentation-eval-plugin/build-docker.sh rename to features/pixel-segmentation-eval-tool/build-docker.sh diff --git a/features/pixel-segmentation-eval-plugin/plugin.json b/features/pixel-segmentation-eval-tool/plugin.json similarity index 94% rename from features/pixel-segmentation-eval-plugin/plugin.json rename to features/pixel-segmentation-eval-tool/plugin.json index 8552359ea..d569a160a 100644 --- a/features/pixel-segmentation-eval-plugin/plugin.json +++ b/features/pixel-segmentation-eval-tool/plugin.json @@ -1,6 +1,6 @@ { "name": "Pixel Segmentation Eval", - "version": "0.1.11-dev1", + "version": "0.1.12-dev0", "title": "Pixel Segmentation Eval", "description": "Plugin to generate evaluation metrics for pixel-wise comparison of ground truth and predicted images.", "author": "Vishakha Goyal (vishakha.goyal@nih.gov)", @@ -8,11 +8,11 @@ "repository": "https://github.com/polusai/polus-plugins", "website": "https://ncats.nih.gov/preclinical/core/informatics", "citation": "", - "containerId": "polusai/pixel-segmentation-eval:0.1.11-dev1", + "containerId": "polusai/pixel-segmentation-eval:0.1.12-dev0", "baseCommand": [ "python3", "-m", - "polus.plugins.features.pixel_segmentation_eval" + "polus.images.features.pixel_segmentation_eval" ], "inputs": [ { diff --git a/features/pixel-segmentation-eval-plugin/pyproject.toml b/features/pixel-segmentation-eval-tool/pyproject.toml similarity index 90% rename from features/pixel-segmentation-eval-plugin/pyproject.toml rename to features/pixel-segmentation-eval-tool/pyproject.toml index fbd1acc24..a80081258 100644 --- a/features/pixel-segmentation-eval-plugin/pyproject.toml +++ b/features/pixel-segmentation-eval-tool/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] -name = "polus-plugins-features-pixel-segmentation-eval" -version = "0.1.11-dev1" +name = "polus-images-features-pixel-segmentation-eval" +version = "0.1.12-dev0" description = "" authors = [ "Vishakha Goyal ", diff --git a/features/pixel-segmentation-eval-plugin/run-plugin.sh b/features/pixel-segmentation-eval-tool/run-plugin.sh similarity index 100% rename from features/pixel-segmentation-eval-plugin/run-plugin.sh rename to features/pixel-segmentation-eval-tool/run-plugin.sh diff --git a/features/pixel-segmentation-eval-plugin/src/polus/plugins/features/pixel_segmentation_eval/__init__.py b/features/pixel-segmentation-eval-tool/src/polus/images/features/pixel_segmentation_eval/__init__.py similarity index 58% rename from features/pixel-segmentation-eval-plugin/src/polus/plugins/features/pixel_segmentation_eval/__init__.py rename to features/pixel-segmentation-eval-tool/src/polus/images/features/pixel_segmentation_eval/__init__.py index 39065ae2a..cdad65018 100644 --- a/features/pixel-segmentation-eval-plugin/src/polus/plugins/features/pixel_segmentation_eval/__init__.py +++ b/features/pixel-segmentation-eval-tool/src/polus/images/features/pixel_segmentation_eval/__init__.py @@ -1,3 +1,3 @@ """Pixel segmentation eval package.""" -__version__ = "0.1.11-dev1" +__version__ = "0.1.12-dev0" diff --git a/features/pixel-segmentation-eval-plugin/src/polus/plugins/features/pixel_segmentation_eval/__main__.py b/features/pixel-segmentation-eval-tool/src/polus/images/features/pixel_segmentation_eval/__main__.py similarity index 95% rename from features/pixel-segmentation-eval-plugin/src/polus/plugins/features/pixel_segmentation_eval/__main__.py rename to features/pixel-segmentation-eval-tool/src/polus/images/features/pixel_segmentation_eval/__main__.py index 4183ec286..beeb3e955 100644 --- a/features/pixel-segmentation-eval-plugin/src/polus/plugins/features/pixel_segmentation_eval/__main__.py +++ b/features/pixel-segmentation-eval-tool/src/polus/images/features/pixel_segmentation_eval/__main__.py @@ -6,7 +6,7 @@ import filepattern as fp import typer -from polus.plugins.features.pixel_segmentation_eval.evaluate import ( +from polus.images.features.pixel_segmentation_eval.evaluate import ( evaluation, POLUS_TAB_EXT ) @@ -16,7 +16,7 @@ format="%(asctime)s - %(name)-8s - %(levelname)-8s - %(message)s", datefmt="%d-%b-%y %H:%M:%S", ) -logger = logging.getLogger("polus.plugins.features.pixel_segmentation_eval") +logger = logging.getLogger("polus.images.features.pixel_segmentation_eval") app = typer.Typer() diff --git a/features/pixel-segmentation-eval-plugin/src/polus/plugins/features/pixel_segmentation_eval/evaluate.py b/features/pixel-segmentation-eval-tool/src/polus/images/features/pixel_segmentation_eval/evaluate.py similarity index 100% rename from features/pixel-segmentation-eval-plugin/src/polus/plugins/features/pixel_segmentation_eval/evaluate.py rename to features/pixel-segmentation-eval-tool/src/polus/images/features/pixel_segmentation_eval/evaluate.py diff --git a/features/pixel-segmentation-eval-plugin/tests/__init__.py b/features/pixel-segmentation-eval-tool/tests/__init__.py similarity index 100% rename from features/pixel-segmentation-eval-plugin/tests/__init__.py rename to features/pixel-segmentation-eval-tool/tests/__init__.py diff --git a/features/pixel-segmentation-eval-plugin/tests/test_pixel_seg.py b/features/pixel-segmentation-eval-tool/tests/test_pixel_seg.py similarity index 95% rename from features/pixel-segmentation-eval-plugin/tests/test_pixel_seg.py rename to features/pixel-segmentation-eval-tool/tests/test_pixel_seg.py index 6fe2788be..d7f9e0126 100644 --- a/features/pixel-segmentation-eval-plugin/tests/test_pixel_seg.py +++ b/features/pixel-segmentation-eval-tool/tests/test_pixel_seg.py @@ -9,8 +9,8 @@ import pytest import skimage import vaex -from polus.plugins.features.pixel_segmentation_eval.__main__ import app -from polus.plugins.features.pixel_segmentation_eval.evaluate import evaluation +from polus.images.features.pixel_segmentation_eval.__main__ import app +from polus.images.features.pixel_segmentation_eval.evaluate import evaluation from skimage import io from typer.testing import CliRunner diff --git a/features/feature-segmentation-eval-plugin/.bumpversion.cfg b/features/region-segmentation-eval-tool/.bumpversion.cfg similarity index 86% rename from features/feature-segmentation-eval-plugin/.bumpversion.cfg rename to features/region-segmentation-eval-tool/.bumpversion.cfg index c8a261f23..4f87883eb 100644 --- a/features/feature-segmentation-eval-plugin/.bumpversion.cfg +++ b/features/region-segmentation-eval-tool/.bumpversion.cfg @@ -24,4 +24,4 @@ replace = version = "{new_version}" [bumpversion:file:VERSION] -[bumpversion:file:src/polus/plugins/features/feature_segmentation_eval/__init__.py] +[bumpversion:file:src/polus/images/features/region_segmentation_eval/__init__.py] diff --git a/features/region-segmentation-eval-plugin/.gitignore b/features/region-segmentation-eval-tool/.gitignore similarity index 100% rename from features/region-segmentation-eval-plugin/.gitignore rename to features/region-segmentation-eval-tool/.gitignore diff --git a/features/region-segmentation-eval-plugin/CHANGELOG.md b/features/region-segmentation-eval-tool/CHANGELOG.md similarity index 100% rename from features/region-segmentation-eval-plugin/CHANGELOG.md rename to features/region-segmentation-eval-tool/CHANGELOG.md diff --git a/features/pixel-segmentation-eval-plugin/Dockerfile b/features/region-segmentation-eval-tool/Dockerfile similarity index 86% rename from features/pixel-segmentation-eval-plugin/Dockerfile rename to features/region-segmentation-eval-tool/Dockerfile index d66ef97ec..9a32afb4c 100644 --- a/features/pixel-segmentation-eval-plugin/Dockerfile +++ b/features/region-segmentation-eval-tool/Dockerfile @@ -15,5 +15,5 @@ COPY src ${EXEC_DIR}/src RUN pip3 install ${EXEC_DIR} --no-cache-dir -ENTRYPOINT ["python3", "-m", "polus.plugins.features.pixel_segmentation_eval"] +ENTRYPOINT ["python3", "-m", "polus.images.features.region_segmentation_eval"] CMD ["--help"] diff --git a/features/region-segmentation-eval-plugin/README.md b/features/region-segmentation-eval-tool/README.md similarity index 100% rename from features/region-segmentation-eval-plugin/README.md rename to features/region-segmentation-eval-tool/README.md diff --git a/features/feature-segmentation-eval-plugin/VERSION b/features/region-segmentation-eval-tool/VERSION similarity index 100% rename from features/feature-segmentation-eval-plugin/VERSION rename to features/region-segmentation-eval-tool/VERSION diff --git a/features/region-segmentation-eval-plugin/build-docker.sh b/features/region-segmentation-eval-tool/build-docker.sh similarity index 100% rename from features/region-segmentation-eval-plugin/build-docker.sh rename to features/region-segmentation-eval-tool/build-docker.sh diff --git a/features/region-segmentation-eval-plugin/plugin.cwl b/features/region-segmentation-eval-tool/plugin.cwl similarity index 100% rename from features/region-segmentation-eval-plugin/plugin.cwl rename to features/region-segmentation-eval-tool/plugin.cwl diff --git a/features/region-segmentation-eval-plugin/plugin.json b/features/region-segmentation-eval-tool/plugin.json similarity index 96% rename from features/region-segmentation-eval-plugin/plugin.json rename to features/region-segmentation-eval-tool/plugin.json index 80fcd19fa..771966018 100644 --- a/features/region-segmentation-eval-plugin/plugin.json +++ b/features/region-segmentation-eval-tool/plugin.json @@ -1,6 +1,6 @@ { "name": "Region Segmentation Eval", - "version": "0.2.4-dev0", + "version": "0.2.5-dev0", "title": "Region Segmentation Eval", "description": "Plugin to generate evaluation metrics for region-wise comparison of ground truth and predicted images.", "author": "Vishakha Goyal (vishakha.goyal@nih.gov), Hamdah Shafqat Abbasi (hamdahshafqat.abbasi@nih.gov),", @@ -8,11 +8,11 @@ "repository": "https://github.com/polusai/polus-plugins", "website": "https://ncats.nih.gov/preclinical/core/informatics", "citation": "", - "containerId": "polusai/region-segmentation-eval:0.2.4-dev0", + "containerId": "polusai/region-segmentation-eval:0.2.5-dev0", "baseCommand": [ "python3", "-m", - "polus.plugins.features.region_segmentation_eval" + "polus.images.features.region_segmentation_eval" ], "inputs": [ { diff --git a/features/region-segmentation-eval-plugin/pyproject.toml b/features/region-segmentation-eval-tool/pyproject.toml similarity index 91% rename from features/region-segmentation-eval-plugin/pyproject.toml rename to features/region-segmentation-eval-tool/pyproject.toml index 2b562ad20..ad3423286 100644 --- a/features/region-segmentation-eval-plugin/pyproject.toml +++ b/features/region-segmentation-eval-tool/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] -name = "polus-plugins-features-region-segmentation-eval" -version = "0.2.4-dev0" +name = "polus-images-features-region-segmentation-eval" +version = "0.2.5-dev0" description = "" authors = [ "Vishakha Goyal ", diff --git a/features/region-segmentation-eval-plugin/run-plugin.sh b/features/region-segmentation-eval-tool/run-plugin.sh similarity index 100% rename from features/region-segmentation-eval-plugin/run-plugin.sh rename to features/region-segmentation-eval-tool/run-plugin.sh diff --git a/features/region-segmentation-eval-plugin/src/polus/plugins/features/region_segmentation_eval/__init__.py b/features/region-segmentation-eval-tool/src/polus/images/features/region_segmentation_eval/__init__.py similarity index 59% rename from features/region-segmentation-eval-plugin/src/polus/plugins/features/region_segmentation_eval/__init__.py rename to features/region-segmentation-eval-tool/src/polus/images/features/region_segmentation_eval/__init__.py index 138a5f4f8..a50fd899c 100644 --- a/features/region-segmentation-eval-plugin/src/polus/plugins/features/region_segmentation_eval/__init__.py +++ b/features/region-segmentation-eval-tool/src/polus/images/features/region_segmentation_eval/__init__.py @@ -1,2 +1,2 @@ """Region segmentation eval package.""" -__version__ = "0.2.4-dev0" +__version__ = "0.2.5-dev0" diff --git a/features/region-segmentation-eval-plugin/src/polus/plugins/features/region_segmentation_eval/__main__.py b/features/region-segmentation-eval-tool/src/polus/images/features/region_segmentation_eval/__main__.py similarity index 94% rename from features/region-segmentation-eval-plugin/src/polus/plugins/features/region_segmentation_eval/__main__.py rename to features/region-segmentation-eval-tool/src/polus/images/features/region_segmentation_eval/__main__.py index 61de07a5c..3c6812ee6 100644 --- a/features/region-segmentation-eval-plugin/src/polus/plugins/features/region_segmentation_eval/__main__.py +++ b/features/region-segmentation-eval-tool/src/polus/images/features/region_segmentation_eval/__main__.py @@ -6,15 +6,15 @@ import filepattern as fp import typer -from polus.plugins.features.region_segmentation_eval.evaluate import POLUS_TAB_EXT -from polus.plugins.features.region_segmentation_eval import evaluate as evaluate +from polus.images.features.region_segmentation_eval.evaluate import POLUS_TAB_EXT +from polus.images.features.region_segmentation_eval import evaluate as evaluate # Initialize the logger logging.basicConfig( format="%(asctime)s - %(name)-8s - %(levelname)-8s - %(message)s", datefmt="%d-%b-%y %H:%M:%S", ) -logger = logging.getLogger("polus.plugins.features.region_segmentation_eval") +logger = logging.getLogger("polus.images.features.region_segmentation_eval") app = typer.Typer() diff --git a/features/region-segmentation-eval-plugin/src/polus/plugins/features/region_segmentation_eval/evaluate.py b/features/region-segmentation-eval-tool/src/polus/images/features/region_segmentation_eval/evaluate.py similarity index 100% rename from features/region-segmentation-eval-plugin/src/polus/plugins/features/region_segmentation_eval/evaluate.py rename to features/region-segmentation-eval-tool/src/polus/images/features/region_segmentation_eval/evaluate.py diff --git a/features/region-segmentation-eval-plugin/tests/__init__.py b/features/region-segmentation-eval-tool/tests/__init__.py similarity index 100% rename from features/region-segmentation-eval-plugin/tests/__init__.py rename to features/region-segmentation-eval-tool/tests/__init__.py diff --git a/features/region-segmentation-eval-plugin/tests/test_main.py b/features/region-segmentation-eval-tool/tests/test_main.py similarity index 95% rename from features/region-segmentation-eval-plugin/tests/test_main.py rename to features/region-segmentation-eval-tool/tests/test_main.py index 076aeb075..fc526ec32 100644 --- a/features/region-segmentation-eval-plugin/tests/test_main.py +++ b/features/region-segmentation-eval-tool/tests/test_main.py @@ -9,8 +9,8 @@ import pytest import skimage import vaex -from polus.plugins.features.region_segmentation_eval.__main__ import app as app -from polus.plugins.features.region_segmentation_eval.evaluate import evaluation +from polus.images.features.region_segmentation_eval.__main__ import app as app +from polus.images.features.region_segmentation_eval.evaluate import evaluation from skimage import io from typer.testing import CliRunner diff --git a/formats/arrow-to-tabular-plugin/build-docker.sh b/formats/arrow-to-tabular-plugin/build-docker.sh deleted file mode 100755 index 5516c50ce..000000000 --- a/formats/arrow-to-tabular-plugin/build-docker.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -version=$(\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? @@ -24,4 +24,4 @@ replace = version = "{new_version}" [bumpversion:file:VERSION] -[bumpversion:file:src/polus/plugins/formats/file_renaming/__init__.py] +[bumpversion:file:src/polus/images/formats/arrow_to_tabular/__init__.py] diff --git a/formats/arrow-to-tabular-plugin/.gitignore b/formats/arrow-to-tabular-tool/.gitignore similarity index 100% rename from formats/arrow-to-tabular-plugin/.gitignore rename to formats/arrow-to-tabular-tool/.gitignore diff --git a/formats/arrow-to-tabular-plugin/Dockerfile b/formats/arrow-to-tabular-tool/Dockerfile similarity index 87% rename from formats/arrow-to-tabular-plugin/Dockerfile rename to formats/arrow-to-tabular-tool/Dockerfile index b969a44c5..210b38a63 100644 --- a/formats/arrow-to-tabular-plugin/Dockerfile +++ b/formats/arrow-to-tabular-tool/Dockerfile @@ -16,5 +16,5 @@ COPY src ${EXEC_DIR}/src RUN pip3 install ${EXEC_DIR} --no-cache-dir -ENTRYPOINT ["python3", "-m", "polus.plugins.formats.arrow_to_tabular"] +ENTRYPOINT ["python3", "-m", "polus.images.formats.arrow_to_tabular"] CMD ["--help"] diff --git a/formats/arrow-to-tabular-plugin/README.md b/formats/arrow-to-tabular-tool/README.md similarity index 100% rename from formats/arrow-to-tabular-plugin/README.md rename to formats/arrow-to-tabular-tool/README.md diff --git a/segmentation/cell-border-segmentation-plugin/VERSION b/formats/arrow-to-tabular-tool/VERSION similarity index 100% rename from segmentation/cell-border-segmentation-plugin/VERSION rename to formats/arrow-to-tabular-tool/VERSION diff --git a/formats/arrow-to-tabular-tool/build-docker.sh b/formats/arrow-to-tabular-tool/build-docker.sh new file mode 100755 index 000000000..b1ddde0d0 --- /dev/null +++ b/formats/arrow-to-tabular-tool/build-docker.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +version=$(","Hamdah Shafqat abbasi "] readme = "README.md" diff --git a/formats/arrow-to-tabular-plugin/run-plugin.sh b/formats/arrow-to-tabular-tool/run-plugin.sh similarity index 100% rename from formats/arrow-to-tabular-plugin/run-plugin.sh rename to formats/arrow-to-tabular-tool/run-plugin.sh diff --git a/formats/arrow-to-tabular-plugin/src/polus/plugins/formats/arrow_to_tabular/__init__.py b/formats/arrow-to-tabular-tool/src/polus/images/formats/arrow_to_tabular/__init__.py similarity index 79% rename from formats/arrow-to-tabular-plugin/src/polus/plugins/formats/arrow_to_tabular/__init__.py rename to formats/arrow-to-tabular-tool/src/polus/images/formats/arrow_to_tabular/__init__.py index 87a6748ae..79e509ac6 100644 --- a/formats/arrow-to-tabular-plugin/src/polus/plugins/formats/arrow_to_tabular/__init__.py +++ b/formats/arrow-to-tabular-tool/src/polus/images/formats/arrow_to_tabular/__init__.py @@ -1,4 +1,4 @@ """Arrow to Tabular.""" -__version__ = "0.2.2-dev0" +__version__ = "0.2.3-dev0" from polus.plugins.formats.arrow_to_tabular.arrow_to_tabular import arrow_tabular diff --git a/formats/arrow-to-tabular-plugin/src/polus/plugins/formats/arrow_to_tabular/__main__.py b/formats/arrow-to-tabular-tool/src/polus/images/formats/arrow_to_tabular/__main__.py similarity index 96% rename from formats/arrow-to-tabular-plugin/src/polus/plugins/formats/arrow_to_tabular/__main__.py rename to formats/arrow-to-tabular-tool/src/polus/images/formats/arrow_to_tabular/__main__.py index c50ea441f..dc6040323 100644 --- a/formats/arrow-to-tabular-plugin/src/polus/plugins/formats/arrow_to_tabular/__main__.py +++ b/formats/arrow-to-tabular-tool/src/polus/images/formats/arrow_to_tabular/__main__.py @@ -11,7 +11,7 @@ import typer from tqdm import tqdm -from polus.plugins.formats.arrow_to_tabular.arrow_to_tabular import ( +from polus.images.formats.arrow_to_tabular.arrow_to_tabular import ( Format, arrow_tabular, ) @@ -24,7 +24,7 @@ format="%(asctime)s - %(name)-8s - %(levelname)-8s - %(message)s", datefmt="%d-%b-%y %H:%M:%S", ) -logger = logging.getLogger("polus.plugins.formats.arrow_to_tabular") +logger = logging.getLogger("polus.images.formats.arrow_to_tabular") def main( diff --git a/formats/arrow-to-tabular-plugin/src/polus/plugins/formats/arrow_to_tabular/arrow_to_tabular.py b/formats/arrow-to-tabular-tool/src/polus/images/formats/arrow_to_tabular/arrow_to_tabular.py similarity index 100% rename from formats/arrow-to-tabular-plugin/src/polus/plugins/formats/arrow_to_tabular/arrow_to_tabular.py rename to formats/arrow-to-tabular-tool/src/polus/images/formats/arrow_to_tabular/arrow_to_tabular.py diff --git a/formats/arrow-to-tabular-plugin/tests/__init__.py b/formats/arrow-to-tabular-tool/tests/__init__.py similarity index 100% rename from formats/arrow-to-tabular-plugin/tests/__init__.py rename to formats/arrow-to-tabular-tool/tests/__init__.py diff --git a/formats/arrow-to-tabular-plugin/tests/test_main.py b/formats/arrow-to-tabular-tool/tests/test_main.py similarity index 96% rename from formats/arrow-to-tabular-plugin/tests/test_main.py rename to formats/arrow-to-tabular-tool/tests/test_main.py index d22d407c6..9dd214714 100644 --- a/formats/arrow-to-tabular-plugin/tests/test_main.py +++ b/formats/arrow-to-tabular-tool/tests/test_main.py @@ -8,7 +8,7 @@ import numpy as np import pandas as pd import pytest -from polus.plugins.formats.arrow_to_tabular.arrow_to_tabular import arrow_tabular +from polus.images.formats.arrow_to_tabular.arrow_to_tabular import arrow_tabular @pytest.fixture() diff --git a/formats/file-renaming-plugin/VERSION b/formats/file-renaming-plugin/VERSION deleted file mode 100644 index 717903969..000000000 --- a/formats/file-renaming-plugin/VERSION +++ /dev/null @@ -1 +0,0 @@ -0.2.3 diff --git a/formats/file-renaming-plugin/build-docker.sh b/formats/file-renaming-plugin/build-docker.sh deleted file mode 100644 index f5a953304..000000000 --- a/formats/file-renaming-plugin/build-docker.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash -version=$(", diff --git a/formats/file-renaming-plugin/run-plugin.sh b/formats/file-renaming-tool/run-plugin.sh similarity index 100% rename from formats/file-renaming-plugin/run-plugin.sh rename to formats/file-renaming-tool/run-plugin.sh diff --git a/formats/file-renaming-plugin/src/polus/plugins/formats/file_renaming/__init__.py b/formats/file-renaming-tool/src/polus/images/formats/file_renaming/__init__.py similarity index 80% rename from formats/file-renaming-plugin/src/polus/plugins/formats/file_renaming/__init__.py rename to formats/file-renaming-tool/src/polus/images/formats/file_renaming/__init__.py index 09ecedb95..bca53865e 100644 --- a/formats/file-renaming-plugin/src/polus/plugins/formats/file_renaming/__init__.py +++ b/formats/file-renaming-tool/src/polus/images/formats/file_renaming/__init__.py @@ -1,4 +1,4 @@ """File Renaming.""" -__version__ = "0.2.3" +__version__ = "0.2.4-dev0" from polus.plugins.formats.file_renaming import file_renaming as file_renaming # noqa diff --git a/formats/file-renaming-plugin/src/polus/plugins/formats/file_renaming/__main__.py b/formats/file-renaming-tool/src/polus/images/formats/file_renaming/__main__.py similarity index 97% rename from formats/file-renaming-plugin/src/polus/plugins/formats/file_renaming/__main__.py rename to formats/file-renaming-tool/src/polus/images/formats/file_renaming/__main__.py index 41b96d27a..38e377782 100644 --- a/formats/file-renaming-plugin/src/polus/plugins/formats/file_renaming/__main__.py +++ b/formats/file-renaming-tool/src/polus/images/formats/file_renaming/__main__.py @@ -9,7 +9,7 @@ from typing import Optional import typer -from polus.plugins.formats.file_renaming import file_renaming as fr +from polus.images.formats.file_renaming import file_renaming as fr app = typer.Typer() @@ -18,7 +18,7 @@ format="%(asctime)s - %(name)-8s - %(levelname)-8s - %(message)s", datefmt="%d-%b-%y %H:%M:%S", ) -logger = logging.getLogger("polus.plugins.formats.file_renaming") +logger = logging.getLogger("polus.images.formats.file_renaming") logger.setLevel(os.environ.get("POLUS_LOG", logging.INFO)) diff --git a/formats/file-renaming-plugin/src/polus/plugins/formats/file_renaming/file_renaming.py b/formats/file-renaming-tool/src/polus/images/formats/file_renaming/file_renaming.py similarity index 100% rename from formats/file-renaming-plugin/src/polus/plugins/formats/file_renaming/file_renaming.py rename to formats/file-renaming-tool/src/polus/images/formats/file_renaming/file_renaming.py diff --git a/formats/file-renaming-plugin/tests/__init__.py b/formats/file-renaming-tool/tests/__init__.py similarity index 100% rename from formats/file-renaming-plugin/tests/__init__.py rename to formats/file-renaming-tool/tests/__init__.py diff --git a/formats/file-renaming-plugin/tests/file_rename_test.json b/formats/file-renaming-tool/tests/file_rename_test.json similarity index 100% rename from formats/file-renaming-plugin/tests/file_rename_test.json rename to formats/file-renaming-tool/tests/file_rename_test.json diff --git a/formats/file-renaming-plugin/tests/test_main.py b/formats/file-renaming-tool/tests/test_main.py similarity index 99% rename from formats/file-renaming-plugin/tests/test_main.py rename to formats/file-renaming-tool/tests/test_main.py index eb36ec361..a9102061a 100644 --- a/formats/file-renaming-plugin/tests/test_main.py +++ b/formats/file-renaming-tool/tests/test_main.py @@ -10,8 +10,8 @@ import pytest from typer.testing import CliRunner -from polus.plugins.formats.file_renaming import file_renaming as fr -from polus.plugins.formats.file_renaming.__main__ import app as app +from polus.images.formats.file_renaming import file_renaming as fr +from polus.images.formats.file_renaming.__main__ import app as app runner = CliRunner() diff --git a/formats/label-to-vector-plugin/VERSION b/formats/label-to-vector-plugin/VERSION deleted file mode 100644 index faef31a43..000000000 --- a/formats/label-to-vector-plugin/VERSION +++ /dev/null @@ -1 +0,0 @@ -0.7.0 diff --git a/formats/label-to-vector-plugin/build-docker.sh b/formats/label-to-vector-plugin/build-docker.sh deleted file mode 100755 index 9dfa5eade..000000000 --- a/formats/label-to-vector-plugin/build-docker.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -version=$(\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? @@ -26,4 +26,4 @@ replace = version = "{new_version}" [bumpversion:file:README.md] -[bumpversion:file:src/polus/plugins/formats/label_to_vector/__init__.py] +[bumpversion:file:src/polus/images/formats/label_to_vector/__init__.py] diff --git a/formats/label-to-vector-plugin/Dockerfile b/formats/label-to-vector-tool/Dockerfile similarity index 88% rename from formats/label-to-vector-plugin/Dockerfile rename to formats/label-to-vector-tool/Dockerfile index 33345aaa5..c2a4931f4 100644 --- a/formats/label-to-vector-plugin/Dockerfile +++ b/formats/label-to-vector-tool/Dockerfile @@ -19,5 +19,5 @@ COPY src ${EXEC_DIR}/src RUN pip3 install ${EXEC_DIR} --no-cache-dir -ENTRYPOINT ["python3", "-m", "polus.plugins.formats.label_to_vector"] +ENTRYPOINT ["python3", "-m", "polus.images.formats.label_to_vector"] CMD ["--help"] diff --git a/formats/label-to-vector-plugin/README.md b/formats/label-to-vector-tool/README.md similarity index 99% rename from formats/label-to-vector-plugin/README.md rename to formats/label-to-vector-tool/README.md index 9ecc0cff0..1b3027262 100644 --- a/formats/label-to-vector-plugin/README.md +++ b/formats/label-to-vector-tool/README.md @@ -1,4 +1,4 @@ -# Label To Vector (v0.7.0) +# Label To Vector (v0.7.1-dev0) Here we provide the label-to-vector plugin to convert labeled images to vector fields. We have new algorithms for this conversion that are more accurate than the ones used in the [Cellpose](https://www.nature.com/articles/s41592-020-01018-x.epdf?sharing_token=yrCA1mB-y9TR8-RC8w_CPdRgN0jAjWel9jnR3ZoTv0Ms-A3TbUG5N7s_6d3I7lMImMDE6cyl-17ubiknffX50r-dX1un0XSIQ2PGYWsCV1du16fIaipcHNxste8FMByEL75Ek_S2_UEVkSk7lCFllWEVogGWJwmQkBC9uKq9UEA%3D) [(github)](https://github.com/MouseLand/cellpose). diff --git a/formats/label-to-vector-tool/VERSION b/formats/label-to-vector-tool/VERSION new file mode 100644 index 000000000..d77b40d91 --- /dev/null +++ b/formats/label-to-vector-tool/VERSION @@ -0,0 +1 @@ +0.7.1-dev0 diff --git a/formats/label-to-vector-plugin/benches/__init__.py b/formats/label-to-vector-tool/benches/__init__.py similarity index 100% rename from formats/label-to-vector-plugin/benches/__init__.py rename to formats/label-to-vector-tool/benches/__init__.py diff --git a/formats/label-to-vector-tool/build-docker.sh b/formats/label-to-vector-tool/build-docker.sh new file mode 100755 index 000000000..8723ec346 --- /dev/null +++ b/formats/label-to-vector-tool/build-docker.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +version=$(", diff --git a/formats/label-to-vector-plugin/run-plugin.sh b/formats/label-to-vector-tool/run-plugin.sh similarity index 100% rename from formats/label-to-vector-plugin/run-plugin.sh rename to formats/label-to-vector-tool/run-plugin.sh diff --git a/formats/label-to-vector-plugin/src/polus/plugins/formats/label_to_vector/__init__.py b/formats/label-to-vector-tool/src/polus/images/formats/label_to_vector/__init__.py similarity index 83% rename from formats/label-to-vector-plugin/src/polus/plugins/formats/label_to_vector/__init__.py rename to formats/label-to-vector-tool/src/polus/images/formats/label_to_vector/__init__.py index ef3663656..42efb94d4 100644 --- a/formats/label-to-vector-plugin/src/polus/plugins/formats/label_to_vector/__init__.py +++ b/formats/label-to-vector-tool/src/polus/images/formats/label_to_vector/__init__.py @@ -4,4 +4,4 @@ from . import utils from .dynamics.label_to_vector import convert -__version__ = "0.7.0" +__version__ = "0.7.1-dev0" diff --git a/formats/label-to-vector-plugin/src/polus/plugins/formats/label_to_vector/__main__.py b/formats/label-to-vector-tool/src/polus/images/formats/label_to_vector/__main__.py similarity index 96% rename from formats/label-to-vector-plugin/src/polus/plugins/formats/label_to_vector/__main__.py rename to formats/label-to-vector-tool/src/polus/images/formats/label_to_vector/__main__.py index 6cc1c8e40..841f2c7c2 100644 --- a/formats/label-to-vector-plugin/src/polus/plugins/formats/label_to_vector/__main__.py +++ b/formats/label-to-vector-tool/src/polus/images/formats/label_to_vector/__main__.py @@ -11,15 +11,15 @@ import tqdm import typer import zarr -from polus.plugins.formats.label_to_vector.dynamics.label_to_vector import convert -from polus.plugins.formats.label_to_vector.utils import constants -from polus.plugins.formats.label_to_vector.utils import helpers +from polus.images.formats.label_to_vector.dynamics.label_to_vector import convert +from polus.images.formats.label_to_vector.utils import constants +from polus.images.formats.label_to_vector.utils import helpers logging.basicConfig( format="%(asctime)s - %(name)-8s - %(levelname)-8s - %(message)s", datefmt="%d-%b-%y %H:%M:%S", ) -logger = helpers.make_logger("polus.plugins.formats.label_to_vector") +logger = helpers.make_logger("polus.images.formats.label_to_vector") app = typer.Typer() diff --git a/formats/label-to-vector-plugin/src/polus/plugins/formats/label_to_vector/dynamics/__init__.py b/formats/label-to-vector-tool/src/polus/images/formats/label_to_vector/dynamics/__init__.py similarity index 100% rename from formats/label-to-vector-plugin/src/polus/plugins/formats/label_to_vector/dynamics/__init__.py rename to formats/label-to-vector-tool/src/polus/images/formats/label_to_vector/dynamics/__init__.py diff --git a/formats/label-to-vector-plugin/src/polus/plugins/formats/label_to_vector/dynamics/common.py b/formats/label-to-vector-tool/src/polus/images/formats/label_to_vector/dynamics/common.py similarity index 100% rename from formats/label-to-vector-plugin/src/polus/plugins/formats/label_to_vector/dynamics/common.py rename to formats/label-to-vector-tool/src/polus/images/formats/label_to_vector/dynamics/common.py diff --git a/formats/label-to-vector-plugin/src/polus/plugins/formats/label_to_vector/dynamics/label_to_vector.py b/formats/label-to-vector-tool/src/polus/images/formats/label_to_vector/dynamics/label_to_vector.py similarity index 100% rename from formats/label-to-vector-plugin/src/polus/plugins/formats/label_to_vector/dynamics/label_to_vector.py rename to formats/label-to-vector-tool/src/polus/images/formats/label_to_vector/dynamics/label_to_vector.py diff --git a/formats/label-to-vector-plugin/src/polus/plugins/formats/label_to_vector/utils/__init__.py b/formats/label-to-vector-tool/src/polus/images/formats/label_to_vector/utils/__init__.py similarity index 100% rename from formats/label-to-vector-plugin/src/polus/plugins/formats/label_to_vector/utils/__init__.py rename to formats/label-to-vector-tool/src/polus/images/formats/label_to_vector/utils/__init__.py diff --git a/formats/label-to-vector-plugin/src/polus/plugins/formats/label_to_vector/utils/constants.py b/formats/label-to-vector-tool/src/polus/images/formats/label_to_vector/utils/constants.py similarity index 100% rename from formats/label-to-vector-plugin/src/polus/plugins/formats/label_to_vector/utils/constants.py rename to formats/label-to-vector-tool/src/polus/images/formats/label_to_vector/utils/constants.py diff --git a/formats/label-to-vector-plugin/src/polus/plugins/formats/label_to_vector/utils/helpers.py b/formats/label-to-vector-tool/src/polus/images/formats/label_to_vector/utils/helpers.py similarity index 100% rename from formats/label-to-vector-plugin/src/polus/plugins/formats/label_to_vector/utils/helpers.py rename to formats/label-to-vector-tool/src/polus/images/formats/label_to_vector/utils/helpers.py diff --git a/formats/label-to-vector-plugin/tests/__init__.py b/formats/label-to-vector-tool/tests/__init__.py similarity index 100% rename from formats/label-to-vector-plugin/tests/__init__.py rename to formats/label-to-vector-tool/tests/__init__.py diff --git a/formats/label-to-vector-plugin/tests/test_l2v.py b/formats/label-to-vector-tool/tests/test_l2v.py similarity index 95% rename from formats/label-to-vector-plugin/tests/test_l2v.py rename to formats/label-to-vector-tool/tests/test_l2v.py index c460870d1..16e9cd7cf 100644 --- a/formats/label-to-vector-plugin/tests/test_l2v.py +++ b/formats/label-to-vector-tool/tests/test_l2v.py @@ -8,9 +8,9 @@ import numpy import pytest import typer.testing -from polus.plugins.formats.label_to_vector import convert -from polus.plugins.formats.label_to_vector.__main__ import app -from polus.plugins.formats.label_to_vector.utils import helpers +from polus.images.formats.label_to_vector import convert +from polus.images.formats.label_to_vector.__main__ import app +from polus.images.formats.label_to_vector.utils import helpers from skimage import data as sk_data from skimage.measure import label as sk_label diff --git a/formats/ome-converter-plugin/VERSION b/formats/ome-converter-plugin/VERSION deleted file mode 100644 index 9e11b32fc..000000000 --- a/formats/ome-converter-plugin/VERSION +++ /dev/null @@ -1 +0,0 @@ -0.3.1 diff --git a/formats/ome-converter-plugin/build-docker.sh b/formats/ome-converter-plugin/build-docker.sh deleted file mode 100755 index ff13fb3a5..000000000 --- a/formats/ome-converter-plugin/build-docker.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -version=$(\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? @@ -26,4 +26,4 @@ replace = version = "{new_version}" [bumpversion:file:README.md] -[bumpversion:file:src/polus/plugins/features/nyxus_plugin/__init__.py] +[bumpversion:file:src/polus/images/formats/ome_converter/__init__.py] diff --git a/formats/ome-converter-plugin/Dockerfile b/formats/ome-converter-tool/Dockerfile similarity index 86% rename from formats/ome-converter-plugin/Dockerfile rename to formats/ome-converter-tool/Dockerfile index 344e17193..e35be14c9 100644 --- a/formats/ome-converter-plugin/Dockerfile +++ b/formats/ome-converter-tool/Dockerfile @@ -16,5 +16,5 @@ COPY src ${EXEC_DIR}/src RUN pip3 install ${EXEC_DIR} --no-cache-dir -ENTRYPOINT ["python3", "-m", "polus.plugins.formats.ome_converter"] +ENTRYPOINT ["python3", "-m", "polus.images.formats.ome_converter"] CMD ["--help"] diff --git a/formats/ome-converter-plugin/README.md b/formats/ome-converter-tool/README.md similarity index 98% rename from formats/ome-converter-plugin/README.md rename to formats/ome-converter-tool/README.md index 1b6109dc1..a0f310196 100644 --- a/formats/ome-converter-plugin/README.md +++ b/formats/ome-converter-tool/README.md @@ -1,4 +1,4 @@ -# OME Converter (v0.3.1) +# OME Converter (v0.3.2-dev0) This WIPP plugin converts BioFormats supported data types to the OME Zarr or OME TIF file format. This is not a complete implementation, rather it implements a file diff --git a/formats/ome-converter-tool/VERSION b/formats/ome-converter-tool/VERSION new file mode 100644 index 000000000..6084d5650 --- /dev/null +++ b/formats/ome-converter-tool/VERSION @@ -0,0 +1 @@ +0.3.2-dev0 diff --git a/formats/ome-converter-tool/build-docker.sh b/formats/ome-converter-tool/build-docker.sh new file mode 100755 index 000000000..5d3ba149e --- /dev/null +++ b/formats/ome-converter-tool/build-docker.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +version=$(", diff --git a/formats/ome-converter-plugin/run-plugin.sh b/formats/ome-converter-tool/run-plugin.sh similarity index 100% rename from formats/ome-converter-plugin/run-plugin.sh rename to formats/ome-converter-tool/run-plugin.sh diff --git a/formats/ome-converter-plugin/src/polus/plugins/formats/ome_converter/__init__.py b/formats/ome-converter-tool/src/polus/images/formats/ome_converter/__init__.py similarity index 86% rename from formats/ome-converter-plugin/src/polus/plugins/formats/ome_converter/__init__.py rename to formats/ome-converter-tool/src/polus/images/formats/ome_converter/__init__.py index a0d5a39a3..ae8527c5f 100644 --- a/formats/ome-converter-plugin/src/polus/plugins/formats/ome_converter/__init__.py +++ b/formats/ome-converter-tool/src/polus/images/formats/ome_converter/__init__.py @@ -1,6 +1,6 @@ """Ome Converter.""" -__version__ = "0.3.1" +__version__ = "0.3.2-dev0" from polus.plugins.formats.ome_converter.image_converter import batch_convert from polus.plugins.formats.ome_converter.image_converter import convert_image diff --git a/formats/ome-converter-plugin/src/polus/plugins/formats/ome_converter/__main__.py b/formats/ome-converter-tool/src/polus/images/formats/ome_converter/__main__.py similarity index 90% rename from formats/ome-converter-plugin/src/polus/plugins/formats/ome_converter/__main__.py rename to formats/ome-converter-tool/src/polus/images/formats/ome_converter/__main__.py index 506cc2517..7c4c36559 100644 --- a/formats/ome-converter-plugin/src/polus/plugins/formats/ome_converter/__main__.py +++ b/formats/ome-converter-tool/src/polus/images/formats/ome_converter/__main__.py @@ -10,9 +10,9 @@ import filepattern as fp import preadator import typer -from polus.plugins.formats.ome_converter.image_converter import NUM_THREADS -from polus.plugins.formats.ome_converter.image_converter import Extension -from polus.plugins.formats.ome_converter.image_converter import convert_image +from polus.images.formats.ome_converter.image_converter import NUM_THREADS +from polus.images.formats.ome_converter.image_converter import Extension +from polus.images.formats.ome_converter.image_converter import convert_image from tqdm import tqdm app = typer.Typer() @@ -22,7 +22,7 @@ format="%(asctime)s - %(name)-8s - %(levelname)-8s - %(message)s", datefmt="%d-%b-%y %H:%M:%S", ) -logger = logging.getLogger("polus.plugins.formats.ome_converter") +logger = logging.getLogger("polus.images.formats.ome_converter") logger.setLevel(os.environ.get("POLUS_LOG", logging.INFO)) diff --git a/formats/ome-converter-plugin/src/polus/plugins/formats/ome_converter/image_converter.py b/formats/ome-converter-tool/src/polus/images/formats/ome_converter/image_converter.py similarity index 100% rename from formats/ome-converter-plugin/src/polus/plugins/formats/ome_converter/image_converter.py rename to formats/ome-converter-tool/src/polus/images/formats/ome_converter/image_converter.py diff --git a/formats/ome-converter-plugin/tests/__init__.py b/formats/ome-converter-tool/tests/__init__.py similarity index 100% rename from formats/ome-converter-plugin/tests/__init__.py rename to formats/ome-converter-tool/tests/__init__.py diff --git a/formats/ome-converter-plugin/tests/conftest.py b/formats/ome-converter-tool/tests/conftest.py similarity index 100% rename from formats/ome-converter-plugin/tests/conftest.py rename to formats/ome-converter-tool/tests/conftest.py diff --git a/formats/ome-converter-plugin/tests/test_main.py b/formats/ome-converter-tool/tests/test_main.py similarity index 91% rename from formats/ome-converter-plugin/tests/test_main.py rename to formats/ome-converter-tool/tests/test_main.py index b6b22c930..027a4a1a6 100644 --- a/formats/ome-converter-plugin/tests/test_main.py +++ b/formats/ome-converter-tool/tests/test_main.py @@ -5,9 +5,9 @@ import numpy as np import pytest from bfio import BioReader -from polus.plugins.formats.ome_converter.__main__ import app -from polus.plugins.formats.ome_converter.image_converter import batch_convert -from polus.plugins.formats.ome_converter.image_converter import convert_image +from polus.images.formats.ome_converter.__main__ import app +from polus.images.formats.ome_converter.image_converter import batch_convert +from polus.images.formats.ome_converter.image_converter import convert_image from typer.testing import CliRunner runner = CliRunner() diff --git a/formats/tabular-converter-plugin/VERSION b/formats/tabular-converter-plugin/VERSION deleted file mode 100644 index 44bf4db83..000000000 --- a/formats/tabular-converter-plugin/VERSION +++ /dev/null @@ -1 +0,0 @@ -0.1.1-dev0 diff --git a/formats/tabular-converter-plugin/build-docker.sh b/formats/tabular-converter-plugin/build-docker.sh deleted file mode 100644 index 37bf0a257..000000000 --- a/formats/tabular-converter-plugin/build-docker.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -version=$(\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? @@ -24,4 +24,4 @@ replace = version = "{new_version}" [bumpversion:file:VERSION] -[bumpversion:file:src/polus/plugins/formats/tabular_to_arrow/__init__.py] +[bumpversion:file:src/polus/images/formats/tabular_converter/__init__.py] diff --git a/formats/tabular-converter-plugin/.gitignore b/formats/tabular-converter-tool/.gitignore similarity index 100% rename from formats/tabular-converter-plugin/.gitignore rename to formats/tabular-converter-tool/.gitignore diff --git a/formats/tabular-converter-plugin/Dockerfile b/formats/tabular-converter-tool/Dockerfile similarity index 86% rename from formats/tabular-converter-plugin/Dockerfile rename to formats/tabular-converter-tool/Dockerfile index 12aa7991c..3c3fd17e4 100644 --- a/formats/tabular-converter-plugin/Dockerfile +++ b/formats/tabular-converter-tool/Dockerfile @@ -16,5 +16,5 @@ COPY src ${EXEC_DIR}/src RUN pip3 install ${EXEC_DIR} --no-cache-dir -ENTRYPOINT ["python3", "-m", "polus.plugins.formats.tabular_converter"] +ENTRYPOINT ["python3", "-m", "polus.images.formats.tabular_converter"] CMD ["--help"] diff --git a/formats/tabular-converter-plugin/README.md b/formats/tabular-converter-tool/README.md similarity index 100% rename from formats/tabular-converter-plugin/README.md rename to formats/tabular-converter-tool/README.md diff --git a/formats/tabular-converter-tool/VERSION b/formats/tabular-converter-tool/VERSION new file mode 100644 index 000000000..9d8d2c119 --- /dev/null +++ b/formats/tabular-converter-tool/VERSION @@ -0,0 +1 @@ +0.1.2-dev0 diff --git a/formats/tabular-converter-tool/build-docker.sh b/formats/tabular-converter-tool/build-docker.sh new file mode 100644 index 000000000..fed7c5a74 --- /dev/null +++ b/formats/tabular-converter-tool/build-docker.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +version=$(", diff --git a/formats/tabular-converter-plugin/run-plugin.sh b/formats/tabular-converter-tool/run-plugin.sh similarity index 100% rename from formats/tabular-converter-plugin/run-plugin.sh rename to formats/tabular-converter-tool/run-plugin.sh diff --git a/formats/tabular-converter-plugin/src/polus/plugins/formats/tabular_converter/__init__.py b/formats/tabular-converter-tool/src/polus/images/formats/tabular_converter/__init__.py similarity index 87% rename from formats/tabular-converter-plugin/src/polus/plugins/formats/tabular_converter/__init__.py rename to formats/tabular-converter-tool/src/polus/images/formats/tabular_converter/__init__.py index 05dc245d8..c5c6c1a30 100644 --- a/formats/tabular-converter-plugin/src/polus/plugins/formats/tabular_converter/__init__.py +++ b/formats/tabular-converter-tool/src/polus/images/formats/tabular_converter/__init__.py @@ -1,5 +1,5 @@ """Tabular Converter.""" -__version__ = "0.1.1-dev0" +__version__ = "0.1.2-dev0" from polus.plugins.formats.tabular_converter.tabular_converter import ConvertTabular from polus.plugins.formats.tabular_converter.tabular_converter import Extensions diff --git a/formats/tabular-converter-plugin/src/polus/plugins/formats/tabular_converter/__main__.py b/formats/tabular-converter-tool/src/polus/images/formats/tabular_converter/__main__.py similarity index 95% rename from formats/tabular-converter-plugin/src/polus/plugins/formats/tabular_converter/__main__.py rename to formats/tabular-converter-tool/src/polus/images/formats/tabular_converter/__main__.py index 356a21884..1801d0012 100644 --- a/formats/tabular-converter-plugin/src/polus/plugins/formats/tabular_converter/__main__.py +++ b/formats/tabular-converter-tool/src/polus/images/formats/tabular_converter/__main__.py @@ -10,7 +10,7 @@ import typer from tqdm import tqdm -from polus.plugins.formats.tabular_converter import tabular_converter as tc +from polus.images.formats.tabular_converter import tabular_converter as tc app = typer.Typer() # Set number of processors for scalability @@ -21,7 +21,7 @@ format="%(asctime)s - %(name)-8s - %(levelname)-8s - %(message)s", datefmt="%d-%b-%y %H:%M:%S", ) -logger = logging.getLogger("polus.plugins.formats.tabular_converter") +logger = logging.getLogger("polus.images.formats.tabular_converter") logger.setLevel(logging.INFO) diff --git a/formats/tabular-converter-plugin/src/polus/plugins/formats/tabular_converter/tabular_converter.py b/formats/tabular-converter-tool/src/polus/images/formats/tabular_converter/tabular_converter.py similarity index 100% rename from formats/tabular-converter-plugin/src/polus/plugins/formats/tabular_converter/tabular_converter.py rename to formats/tabular-converter-tool/src/polus/images/formats/tabular_converter/tabular_converter.py diff --git a/formats/tabular-converter-plugin/tests/__init__.py b/formats/tabular-converter-tool/tests/__init__.py similarity index 100% rename from formats/tabular-converter-plugin/tests/__init__.py rename to formats/tabular-converter-tool/tests/__init__.py diff --git a/formats/tabular-converter-plugin/tests/test_main.py b/formats/tabular-converter-tool/tests/test_main.py similarity index 98% rename from formats/tabular-converter-plugin/tests/test_main.py rename to formats/tabular-converter-tool/tests/test_main.py index fc11d05af..b512a83f4 100644 --- a/formats/tabular-converter-plugin/tests/test_main.py +++ b/formats/tabular-converter-tool/tests/test_main.py @@ -12,7 +12,7 @@ import pytest import vaex from astropy.table import Table -from polus.plugins.formats.tabular_converter import tabular_converter as tc +from polus.images.formats.tabular_converter import tabular_converter as tc class Generatedata: diff --git a/formats/tabular-to-arrow-plugin/VERSION b/formats/tabular-to-arrow-plugin/VERSION deleted file mode 100644 index 5fe8c3768..000000000 --- a/formats/tabular-to-arrow-plugin/VERSION +++ /dev/null @@ -1 +0,0 @@ -0.2.2-dev0 diff --git a/formats/tabular-to-arrow-plugin/build-docker.sh b/formats/tabular-to-arrow-plugin/build-docker.sh deleted file mode 100755 index 054f2d00b..000000000 --- a/formats/tabular-to-arrow-plugin/build-docker.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -version=$(\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? @@ -24,4 +24,4 @@ replace = version = "{new_version}" [bumpversion:file:VERSION] -[bumpversion:file:src/polus/plugins/formats/arrow_to_tabular/__init__.py] +[bumpversion:file:src/polus/images/formats/tabular_to_arrow/__init__.py] diff --git a/formats/tabular-to-arrow-plugin/.gitignore b/formats/tabular-to-arrow-tool/.gitignore similarity index 100% rename from formats/tabular-to-arrow-plugin/.gitignore rename to formats/tabular-to-arrow-tool/.gitignore diff --git a/formats/tabular-to-arrow-plugin/Dockerfile b/formats/tabular-to-arrow-tool/Dockerfile similarity index 87% rename from formats/tabular-to-arrow-plugin/Dockerfile rename to formats/tabular-to-arrow-tool/Dockerfile index a3f56a09f..aab61fb38 100644 --- a/formats/tabular-to-arrow-plugin/Dockerfile +++ b/formats/tabular-to-arrow-tool/Dockerfile @@ -16,5 +16,5 @@ COPY src ${EXEC_DIR}/src RUN pip3 install ${EXEC_DIR} --no-cache-dir -ENTRYPOINT ["python3", "-m", "polus.plugins.formats.tabular_to_arrow"] +ENTRYPOINT ["python3", "-m", "polus.images.formats.tabular_to_arrow"] CMD ["--help"] diff --git a/formats/tabular-to-arrow-plugin/README.md b/formats/tabular-to-arrow-tool/README.md similarity index 100% rename from formats/tabular-to-arrow-plugin/README.md rename to formats/tabular-to-arrow-tool/README.md diff --git a/formats/tabular-to-arrow-tool/VERSION b/formats/tabular-to-arrow-tool/VERSION new file mode 100644 index 000000000..398833448 --- /dev/null +++ b/formats/tabular-to-arrow-tool/VERSION @@ -0,0 +1 @@ +0.2.3-dev0 diff --git a/formats/tabular-to-arrow-tool/build-docker.sh b/formats/tabular-to-arrow-tool/build-docker.sh new file mode 100755 index 000000000..194e8432c --- /dev/null +++ b/formats/tabular-to-arrow-tool/build-docker.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +version=$(","hamshkhawar "] readme = "README.md" diff --git a/formats/tabular-to-arrow-plugin/run-plugin.sh b/formats/tabular-to-arrow-tool/run-plugin.sh similarity index 100% rename from formats/tabular-to-arrow-plugin/run-plugin.sh rename to formats/tabular-to-arrow-tool/run-plugin.sh diff --git a/formats/tabular-to-arrow-plugin/src/polus/plugins/formats/tabular_to_arrow/__init__.py b/formats/tabular-to-arrow-tool/src/polus/images/formats/tabular_to_arrow/__init__.py similarity index 93% rename from formats/tabular-to-arrow-plugin/src/polus/plugins/formats/tabular_to_arrow/__init__.py rename to formats/tabular-to-arrow-tool/src/polus/images/formats/tabular_to_arrow/__init__.py index de5966237..c87dbdab0 100644 --- a/formats/tabular-to-arrow-plugin/src/polus/plugins/formats/tabular_to_arrow/__init__.py +++ b/formats/tabular-to-arrow-tool/src/polus/images/formats/tabular_to_arrow/__init__.py @@ -1,5 +1,5 @@ """Tabular to Arrow.""" -__version__ = "0.2.2-dev0" +__version__ = "0.2.3-dev0" from polus.plugins.formats.tabular_to_arrow.tabular_arrow_converter import binary_to_df from polus.plugins.formats.tabular_to_arrow.tabular_arrow_converter import csv_to_df diff --git a/formats/tabular-to-arrow-plugin/src/polus/plugins/formats/tabular_to_arrow/__main__.py b/formats/tabular-to-arrow-tool/src/polus/images/formats/tabular_to_arrow/__main__.py similarity index 94% rename from formats/tabular-to-arrow-plugin/src/polus/plugins/formats/tabular_to_arrow/__main__.py rename to formats/tabular-to-arrow-tool/src/polus/images/formats/tabular_to_arrow/__main__.py index 5b29b6503..69a418a74 100644 --- a/formats/tabular-to-arrow-plugin/src/polus/plugins/formats/tabular_to_arrow/__main__.py +++ b/formats/tabular-to-arrow-tool/src/polus/images/formats/tabular_to_arrow/__main__.py @@ -11,7 +11,7 @@ import typer from tqdm import tqdm -from polus.plugins.formats.tabular_to_arrow import tabular_arrow_converter as tb +from polus.images.formats.tabular_to_arrow import tabular_arrow_converter as tb app = typer.Typer() # Set number of processors for scalability @@ -22,7 +22,7 @@ format="%(asctime)s - %(name)-8s - %(levelname)-8s - %(message)s", datefmt="%d-%b-%y %H:%M:%S", ) -logger = logging.getLogger("polus.plugins.formats.tabular_to_arrow") +logger = logging.getLogger("polus.images.formats.tabular_to_arrow") logger.setLevel(logging.INFO) POLUS_TAB_EXT = os.environ.get("POLUS_TAB_EXT", ".arrow") diff --git a/formats/tabular-to-arrow-plugin/src/polus/plugins/formats/tabular_to_arrow/tabular_arrow_converter.py b/formats/tabular-to-arrow-tool/src/polus/images/formats/tabular_to_arrow/tabular_arrow_converter.py similarity index 100% rename from formats/tabular-to-arrow-plugin/src/polus/plugins/formats/tabular_to_arrow/tabular_arrow_converter.py rename to formats/tabular-to-arrow-tool/src/polus/images/formats/tabular_to_arrow/tabular_arrow_converter.py diff --git a/formats/tabular-to-arrow-plugin/tests/__init__.py b/formats/tabular-to-arrow-tool/tests/__init__.py similarity index 100% rename from formats/tabular-to-arrow-plugin/tests/__init__.py rename to formats/tabular-to-arrow-tool/tests/__init__.py diff --git a/formats/tabular-to-arrow-plugin/tests/test_main.py b/formats/tabular-to-arrow-tool/tests/test_main.py similarity index 98% rename from formats/tabular-to-arrow-plugin/tests/test_main.py rename to formats/tabular-to-arrow-tool/tests/test_main.py index 01f2f2a01..b2ca21867 100644 --- a/formats/tabular-to-arrow-plugin/tests/test_main.py +++ b/formats/tabular-to-arrow-tool/tests/test_main.py @@ -13,7 +13,7 @@ import pytest import vaex from astropy.table import Table -from polus.plugins.formats.tabular_to_arrow import tabular_arrow_converter as tb +from polus.images.formats.tabular_to_arrow import tabular_arrow_converter as tb class Generatedata: diff --git a/formats/vector-to-label-plugin/VERSION b/formats/vector-to-label-plugin/VERSION deleted file mode 100644 index 99d54ff32..000000000 --- a/formats/vector-to-label-plugin/VERSION +++ /dev/null @@ -1 +0,0 @@ -0.7.0-dev34 diff --git a/formats/vector-to-label-plugin/build-docker.sh b/formats/vector-to-label-plugin/build-docker.sh deleted file mode 100755 index 334b2973d..000000000 --- a/formats/vector-to-label-plugin/build-docker.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -version=$(\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? @@ -26,4 +26,4 @@ replace = version = "{new_version}" [bumpversion:file:README.md] -[bumpversion:file:src/polus/plugins/formats/vector_to_label/__init__.py] +[bumpversion:file:src/polus/images/formats/vector_to_label/__init__.py] diff --git a/formats/vector-to-label-plugin/Dockerfile b/formats/vector-to-label-tool/Dockerfile similarity index 88% rename from formats/vector-to-label-plugin/Dockerfile rename to formats/vector-to-label-tool/Dockerfile index 4a897924d..37c55784a 100644 --- a/formats/vector-to-label-plugin/Dockerfile +++ b/formats/vector-to-label-tool/Dockerfile @@ -21,5 +21,5 @@ COPY src ${EXEC_DIR}/src RUN pip3 install ${EXEC_DIR} --no-cache-dir -ENTRYPOINT ["python3", "-m", "polus.plugins.formats.vector_to_label"] +ENTRYPOINT ["python3", "-m", "polus.images.formats.vector_to_label"] CMD ["--help"] diff --git a/formats/vector-to-label-plugin/README.md b/formats/vector-to-label-tool/README.md similarity index 99% rename from formats/vector-to-label-plugin/README.md rename to formats/vector-to-label-tool/README.md index 817cfe0de..97275d2f8 100644 --- a/formats/vector-to-label-plugin/README.md +++ b/formats/vector-to-label-tool/README.md @@ -1,4 +1,4 @@ -# Vector to Label (v0.7.0-dev34) +# Vector to Label (v0.7.1-dev0) Here we provide the vector-to-label plugin to convert vector fields to labeled images. We have new algorithms for this conversion that are more accurate than the ones used in the [CellPose](https://www.nature.com/articles/s41592-020-01018-x.epdf?sharing_token=yrCA1mB-y9TR8-RC8w_CPdRgN0jAjWel9jnR3ZoTv0Ms-A3TbUG5N7s_6d3I7lMImMDE6cyl-17ubiknffX50r-dX1un0XSIQ2PGYWsCV1du16fIaipcHNxste8FMByEL75Ek_S2_UEVkSk7lCFllWEVogGWJwmQkBC9uKq9UEA%3D) [(github)](https://github.com/MouseLand/cellpose). diff --git a/formats/vector-to-label-tool/VERSION b/formats/vector-to-label-tool/VERSION new file mode 100644 index 000000000..d77b40d91 --- /dev/null +++ b/formats/vector-to-label-tool/VERSION @@ -0,0 +1 @@ +0.7.1-dev0 diff --git a/formats/vector-to-label-tool/build-docker.sh b/formats/vector-to-label-tool/build-docker.sh new file mode 100755 index 000000000..30e968b5d --- /dev/null +++ b/formats/vector-to-label-tool/build-docker.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +version=$(", diff --git a/formats/vector-to-label-plugin/run-plugin.sh b/formats/vector-to-label-tool/run-plugin.sh similarity index 100% rename from formats/vector-to-label-plugin/run-plugin.sh rename to formats/vector-to-label-tool/run-plugin.sh diff --git a/formats/vector-to-label-plugin/src/polus/plugins/formats/vector_to_label/__init__.py b/formats/vector-to-label-tool/src/polus/images/formats/vector_to_label/__init__.py similarity index 76% rename from formats/vector-to-label-plugin/src/polus/plugins/formats/vector_to_label/__init__.py rename to formats/vector-to-label-tool/src/polus/images/formats/vector_to_label/__init__.py index fab7341bd..e89b9f8ba 100644 --- a/formats/vector-to-label-plugin/src/polus/plugins/formats/vector_to_label/__init__.py +++ b/formats/vector-to-label-tool/src/polus/images/formats/vector_to_label/__init__.py @@ -3,4 +3,4 @@ from . import dynamics from . import helpers -__version__ = "0.7.0-dev34" +__version__ = "0.7.1-dev0" diff --git a/formats/vector-to-label-plugin/src/polus/plugins/formats/vector_to_label/__main__.py b/formats/vector-to-label-tool/src/polus/images/formats/vector_to_label/__main__.py similarity index 96% rename from formats/vector-to-label-plugin/src/polus/plugins/formats/vector_to_label/__main__.py rename to formats/vector-to-label-tool/src/polus/images/formats/vector_to_label/__main__.py index e1484f5b9..020fbb08e 100644 --- a/formats/vector-to-label-plugin/src/polus/plugins/formats/vector_to_label/__main__.py +++ b/formats/vector-to-label-tool/src/polus/images/formats/vector_to_label/__main__.py @@ -11,17 +11,17 @@ import tqdm import typer import zarr -from polus.plugins.formats.label_to_vector.utils import constants -from polus.plugins.formats.label_to_vector.utils import helpers as l2v_helpers -from polus.plugins.formats.vector_to_label import helpers -from polus.plugins.formats.vector_to_label.dynamics import convert -from polus.plugins.formats.vector_to_label.dynamics import reconcile_overlap +from polus.images.formats.label_to_vector.utils import constants +from polus.images.formats.label_to_vector.utils import helpers as l2v_helpers +from polus.images.formats.vector_to_label import helpers +from polus.images.formats.vector_to_label.dynamics import convert +from polus.images.formats.vector_to_label.dynamics import reconcile_overlap logging.basicConfig( format="%(asctime)s - %(name)-8s - %(levelname)-8s - %(message)s", datefmt="%d-%b-%y %H:%M:%S", ) -logger = l2v_helpers.make_logger("polus.plugins.formats.vector_to_label") +logger = l2v_helpers.make_logger("polus.images.formats.vector_to_label") app = typer.Typer() diff --git a/formats/vector-to-label-plugin/src/polus/plugins/formats/vector_to_label/dynamics/__init__.py b/formats/vector-to-label-tool/src/polus/images/formats/vector_to_label/dynamics/__init__.py similarity index 100% rename from formats/vector-to-label-plugin/src/polus/plugins/formats/vector_to_label/dynamics/__init__.py rename to formats/vector-to-label-tool/src/polus/images/formats/vector_to_label/dynamics/__init__.py diff --git a/formats/vector-to-label-plugin/src/polus/plugins/formats/vector_to_label/dynamics/vector_to_label.py b/formats/vector-to-label-tool/src/polus/images/formats/vector_to_label/dynamics/vector_to_label.py similarity index 100% rename from formats/vector-to-label-plugin/src/polus/plugins/formats/vector_to_label/dynamics/vector_to_label.py rename to formats/vector-to-label-tool/src/polus/images/formats/vector_to_label/dynamics/vector_to_label.py diff --git a/formats/vector-to-label-plugin/src/polus/plugins/formats/vector_to_label/helpers.py b/formats/vector-to-label-tool/src/polus/images/formats/vector_to_label/helpers.py similarity index 100% rename from formats/vector-to-label-plugin/src/polus/plugins/formats/vector_to_label/helpers.py rename to formats/vector-to-label-tool/src/polus/images/formats/vector_to_label/helpers.py diff --git a/formats/vector-to-label-plugin/tests/__init__.py b/formats/vector-to-label-tool/tests/__init__.py similarity index 100% rename from formats/vector-to-label-plugin/tests/__init__.py rename to formats/vector-to-label-tool/tests/__init__.py diff --git a/formats/vector-to-label-plugin/tests/test_v2l.py b/formats/vector-to-label-tool/tests/test_v2l.py similarity index 92% rename from formats/vector-to-label-plugin/tests/test_v2l.py rename to formats/vector-to-label-tool/tests/test_v2l.py index c25e6a71e..66d8b8291 100644 --- a/formats/vector-to-label-plugin/tests/test_v2l.py +++ b/formats/vector-to-label-tool/tests/test_v2l.py @@ -8,11 +8,11 @@ import numpy import pytest import typer.testing -from polus.plugins.formats.label_to_vector.__main__ import main as l2v_main -from polus.plugins.formats.vector_to_label.__main__ import app -from polus.plugins.formats.vector_to_label import helpers -from polus.plugins.formats.vector_to_label.dynamics import convert -from polus.plugins.formats.label_to_vector.dynamics.label_to_vector import ( +from polus.images.formats.label_to_vector.__main__ import main as l2v_main +from polus.images.formats.vector_to_label.__main__ import app +from polus.images.formats.vector_to_label import helpers +from polus.images.formats.vector_to_label.dynamics import convert +from polus.images.formats.label_to_vector.dynamics.label_to_vector import ( convert as l2v_convert, ) from skimage import data as sk_data diff --git a/regression/basic-flatfield-estimation-plugin/VERSION b/regression/basic-flatfield-estimation-plugin/VERSION deleted file mode 100644 index 3e3c2f1e5..000000000 --- a/regression/basic-flatfield-estimation-plugin/VERSION +++ /dev/null @@ -1 +0,0 @@ -2.1.1 diff --git a/regression/basic-flatfield-estimation-plugin/build-docker.sh b/regression/basic-flatfield-estimation-plugin/build-docker.sh deleted file mode 100755 index f1967ff52..000000000 --- a/regression/basic-flatfield-estimation-plugin/build-docker.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -version=$(\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? +serialize = + {major}.{minor}.{patch}-{release}{dev} + {major}.{minor}.{patch} + +[bumpversion:part:release] +optional_value = _ +first_value = dev +values = + dev + _ + +[bumpversion:part:dev] + +[bumpversion:file:pyproject.toml] +search = version = "{current_version}" +replace = version = "{new_version}" + +[bumpversion:file:plugin.json] + +[bumpversion:file:VERSION] + +[bumpversion:file:README.md] + +[bumpversion:file:src/polus/images/regression/basic_flatfield_estimation/__init__.py] diff --git a/regression/basic-flatfield-estimation-plugin/.dockerignore b/regression/basic-flatfield-estimation-tool/.dockerignore similarity index 100% rename from regression/basic-flatfield-estimation-plugin/.dockerignore rename to regression/basic-flatfield-estimation-tool/.dockerignore diff --git a/regression/basic-flatfield-estimation-plugin/.gitignore b/regression/basic-flatfield-estimation-tool/.gitignore similarity index 100% rename from regression/basic-flatfield-estimation-plugin/.gitignore rename to regression/basic-flatfield-estimation-tool/.gitignore diff --git a/regression/basic-flatfield-estimation-plugin/Dockerfile b/regression/basic-flatfield-estimation-tool/Dockerfile similarity index 94% rename from regression/basic-flatfield-estimation-plugin/Dockerfile rename to regression/basic-flatfield-estimation-tool/Dockerfile index 1e073f3e4..36884685d 100644 --- a/regression/basic-flatfield-estimation-plugin/Dockerfile +++ b/regression/basic-flatfield-estimation-tool/Dockerfile @@ -49,5 +49,5 @@ COPY src ${EXEC_DIR}/src # Install the python package RUN pip3 install ${EXEC_DIR} --no-cache-dir -ENTRYPOINT ["python3", "-m", "polus.plugins.regression.basic_flatfield_estimation"] +ENTRYPOINT ["python3", "-m", "polus.images.regression.basic_flatfield_estimation"] CMD ["--help"] diff --git a/regression/basic-flatfield-estimation-plugin/README.md b/regression/basic-flatfield-estimation-tool/README.md similarity index 98% rename from regression/basic-flatfield-estimation-plugin/README.md rename to regression/basic-flatfield-estimation-tool/README.md index 72c351398..f61c346e7 100644 --- a/regression/basic-flatfield-estimation-plugin/README.md +++ b/regression/basic-flatfield-estimation-tool/README.md @@ -1,4 +1,4 @@ -# BaSiC Flatfield Correction (v2.1.1) +# BaSiC Flatfield Correction (v2.1.2-dev0) This WIPP plugin will take a collection of images and use the BaSiC flatfield correction algorithm to generate a flatfield image, a darkfield image, and a diff --git a/regression/basic-flatfield-estimation-tool/VERSION b/regression/basic-flatfield-estimation-tool/VERSION new file mode 100644 index 000000000..47e1d8bb2 --- /dev/null +++ b/regression/basic-flatfield-estimation-tool/VERSION @@ -0,0 +1 @@ +2.1.2-dev0 diff --git a/regression/basic-flatfield-estimation-tool/build-docker.sh b/regression/basic-flatfield-estimation-tool/build-docker.sh new file mode 100755 index 000000000..28fe53cce --- /dev/null +++ b/regression/basic-flatfield-estimation-tool/build-docker.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +version=$(", diff --git a/regression/basic-flatfield-estimation-plugin/run-plugin.sh b/regression/basic-flatfield-estimation-tool/run-plugin.sh similarity index 100% rename from regression/basic-flatfield-estimation-plugin/run-plugin.sh rename to regression/basic-flatfield-estimation-tool/run-plugin.sh diff --git a/regression/basic-flatfield-estimation-plugin/src/polus/plugins/regression/basic_flatfield_estimation/__init__.py b/regression/basic-flatfield-estimation-tool/src/polus/images/regression/basic_flatfield_estimation/__init__.py similarity index 98% rename from regression/basic-flatfield-estimation-plugin/src/polus/plugins/regression/basic_flatfield_estimation/__init__.py rename to regression/basic-flatfield-estimation-tool/src/polus/images/regression/basic_flatfield_estimation/__init__.py index df500e571..10883784f 100644 --- a/regression/basic-flatfield-estimation-plugin/src/polus/plugins/regression/basic_flatfield_estimation/__init__.py +++ b/regression/basic-flatfield-estimation-tool/src/polus/images/regression/basic_flatfield_estimation/__init__.py @@ -10,7 +10,7 @@ __all__ = ["estimate", "__version__"] -__version__ = "2.1.1" +__version__ = "2.1.2-dev0" # Set the basicpy logger to warning logging.getLogger("basicpy.basicpy").setLevel(logging.WARNING) diff --git a/regression/basic-flatfield-estimation-plugin/src/polus/plugins/regression/basic_flatfield_estimation/__main__.py b/regression/basic-flatfield-estimation-tool/src/polus/images/regression/basic_flatfield_estimation/__main__.py similarity index 93% rename from regression/basic-flatfield-estimation-plugin/src/polus/plugins/regression/basic_flatfield_estimation/__main__.py rename to regression/basic-flatfield-estimation-tool/src/polus/images/regression/basic_flatfield_estimation/__main__.py index d04d5da8b..ae07143a0 100644 --- a/regression/basic-flatfield-estimation-plugin/src/polus/plugins/regression/basic_flatfield_estimation/__main__.py +++ b/regression/basic-flatfield-estimation-tool/src/polus/images/regression/basic_flatfield_estimation/__main__.py @@ -5,15 +5,15 @@ import filepattern import typer -from polus.plugins.regression.basic_flatfield_estimation import estimate -from polus.plugins.regression.basic_flatfield_estimation import utils +from polus.images.regression.basic_flatfield_estimation import estimate +from polus.images.regression.basic_flatfield_estimation import utils # Initialize the logger logging.basicConfig( format="%(asctime)s - %(name)s - %(levelname)s - %(message)s", datefmt="%d-%b-%y %H:%M:%S", ) -logger = logging.getLogger("polus.plugins.regression.basic_flatfield_estimation") +logger = logging.getLogger("polus.images.regression.basic_flatfield_estimation") logger.setLevel(utils.POLUS_LOG) app = typer.Typer() diff --git a/regression/basic-flatfield-estimation-plugin/src/polus/plugins/regression/basic_flatfield_estimation/utils.py b/regression/basic-flatfield-estimation-tool/src/polus/images/regression/basic_flatfield_estimation/utils.py similarity index 100% rename from regression/basic-flatfield-estimation-plugin/src/polus/plugins/regression/basic_flatfield_estimation/utils.py rename to regression/basic-flatfield-estimation-tool/src/polus/images/regression/basic_flatfield_estimation/utils.py diff --git a/regression/basic-flatfield-estimation-plugin/tests/__init__.py b/regression/basic-flatfield-estimation-tool/tests/__init__.py similarity index 100% rename from regression/basic-flatfield-estimation-plugin/tests/__init__.py rename to regression/basic-flatfield-estimation-tool/tests/__init__.py diff --git a/regression/basic-flatfield-estimation-plugin/tests/test_plugin.py b/regression/basic-flatfield-estimation-tool/tests/test_plugin.py similarity index 94% rename from regression/basic-flatfield-estimation-plugin/tests/test_plugin.py rename to regression/basic-flatfield-estimation-tool/tests/test_plugin.py index 04a9bc1c9..3b0fea3de 100644 --- a/regression/basic-flatfield-estimation-plugin/tests/test_plugin.py +++ b/regression/basic-flatfield-estimation-tool/tests/test_plugin.py @@ -15,9 +15,9 @@ import numpy import pytest import typer.testing -from polus.plugins.regression.basic_flatfield_estimation import estimate -from polus.plugins.regression.basic_flatfield_estimation import utils -from polus.plugins.regression.basic_flatfield_estimation.__main__ import app +from polus.images.regression.basic_flatfield_estimation import estimate +from polus.images.regression.basic_flatfield_estimation import utils +from polus.images.regression.basic_flatfield_estimation.__main__ import app fixture_params = [ ( diff --git a/regression/theia-bleedthrough-estimation-plugin/.bumpversion.cfg b/regression/theia-bleedthrough-estimation-plugin/.bumpversion.cfg deleted file mode 100644 index 98f67dbdb..000000000 --- a/regression/theia-bleedthrough-estimation-plugin/.bumpversion.cfg +++ /dev/null @@ -1,29 +0,0 @@ -[bumpversion] -current_version = 0.5.1-dev1 -commit = True -tag = False -parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? -serialize = - {major}.{minor}.{patch}-{release}{dev} - {major}.{minor}.{patch} - -[bumpversion:part:release] -optional_value = _ -first_value = dev -values = - dev - _ - -[bumpversion:part:dev] - -[bumpversion:file:pyproject.toml] -search = version = "{current_version}" -replace = version = "{new_version}" - -[bumpversion:file:plugin.json] - -[bumpversion:file:VERSION] - -[bumpversion:file:README.md] - -[bumpversion:file:src/polus/plugins/regression/theia_bleedthrough_estimation/__init__.py] diff --git a/regression/theia-bleedthrough-estimation-plugin/VERSION b/regression/theia-bleedthrough-estimation-plugin/VERSION deleted file mode 100644 index 7385f4f0d..000000000 --- a/regression/theia-bleedthrough-estimation-plugin/VERSION +++ /dev/null @@ -1 +0,0 @@ -0.5.1-dev1 diff --git a/regression/theia-bleedthrough-estimation-plugin/build-docker.sh b/regression/theia-bleedthrough-estimation-plugin/build-docker.sh deleted file mode 100755 index 57d156094..000000000 --- a/regression/theia-bleedthrough-estimation-plugin/build-docker.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -version=$(\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? +serialize = + {major}.{minor}.{patch}-{release}{dev} + {major}.{minor}.{patch} + +[bumpversion:part:release] +optional_value = _ +first_value = dev +values = + dev + _ + +[bumpversion:part:dev] + +[bumpversion:file:pyproject.toml] +search = version = "{current_version}" +replace = version = "{new_version}" + +[bumpversion:file:plugin.json] + +[bumpversion:file:VERSION] + +[bumpversion:file:README.md] + +[bumpversion:file:src/polus/images/regression/theia_bleedthrough_estimation/__init__.py] diff --git a/regression/theia-bleedthrough-estimation-plugin/.dockerignore b/regression/theia-bleedthrough-estimation-tool/.dockerignore similarity index 100% rename from regression/theia-bleedthrough-estimation-plugin/.dockerignore rename to regression/theia-bleedthrough-estimation-tool/.dockerignore diff --git a/regression/theia-bleedthrough-estimation-plugin/.gitignore b/regression/theia-bleedthrough-estimation-tool/.gitignore similarity index 100% rename from regression/theia-bleedthrough-estimation-plugin/.gitignore rename to regression/theia-bleedthrough-estimation-tool/.gitignore diff --git a/regression/theia-bleedthrough-estimation-plugin/Dockerfile b/regression/theia-bleedthrough-estimation-tool/Dockerfile similarity index 94% rename from regression/theia-bleedthrough-estimation-plugin/Dockerfile rename to regression/theia-bleedthrough-estimation-tool/Dockerfile index 8ddc4c47d..fb7e555c2 100644 --- a/regression/theia-bleedthrough-estimation-plugin/Dockerfile +++ b/regression/theia-bleedthrough-estimation-tool/Dockerfile @@ -49,5 +49,5 @@ COPY src ${EXEC_DIR}/src # Install the python package RUN pip3 install ${EXEC_DIR} --no-cache-dir -ENTRYPOINT ["python3", "-m", "polus.plugins.regression.theia_bleedthrough_estimation"] +ENTRYPOINT ["python3", "-m", "polus.images.regression.theia_bleedthrough_estimation"] CMD ["--help"] diff --git a/regression/theia-bleedthrough-estimation-plugin/README.md b/regression/theia-bleedthrough-estimation-tool/README.md similarity index 99% rename from regression/theia-bleedthrough-estimation-plugin/README.md rename to regression/theia-bleedthrough-estimation-tool/README.md index 724e4c49c..b62120c18 100644 --- a/regression/theia-bleedthrough-estimation-plugin/README.md +++ b/regression/theia-bleedthrough-estimation-tool/README.md @@ -1,4 +1,4 @@ -# Theia Bleedthrough Estimation (v0.5.1-dev1) +# Theia Bleedthrough Estimation (v0.5.2-dev0) This WIPP plugin estimates the bleed-through in a collection of 2d images. It uses the Theia algorithm from [this repo](https://github.com/PolusAI/theia). diff --git a/transforms/images/binary-operations-plugin/VERSION b/regression/theia-bleedthrough-estimation-tool/VERSION similarity index 100% rename from transforms/images/binary-operations-plugin/VERSION rename to regression/theia-bleedthrough-estimation-tool/VERSION diff --git a/regression/theia-bleedthrough-estimation-tool/build-docker.sh b/regression/theia-bleedthrough-estimation-tool/build-docker.sh new file mode 100755 index 000000000..42f27930f --- /dev/null +++ b/regression/theia-bleedthrough-estimation-tool/build-docker.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +version=$(", diff --git a/regression/theia-bleedthrough-estimation-plugin/run-plugin.sh b/regression/theia-bleedthrough-estimation-tool/run-plugin.sh similarity index 100% rename from regression/theia-bleedthrough-estimation-plugin/run-plugin.sh rename to regression/theia-bleedthrough-estimation-tool/run-plugin.sh diff --git a/regression/theia-bleedthrough-estimation-plugin/src/polus/plugins/regression/theia_bleedthrough_estimation/__init__.py b/regression/theia-bleedthrough-estimation-tool/src/polus/images/regression/theia_bleedthrough_estimation/__init__.py similarity index 80% rename from regression/theia-bleedthrough-estimation-plugin/src/polus/plugins/regression/theia_bleedthrough_estimation/__init__.py rename to regression/theia-bleedthrough-estimation-tool/src/polus/images/regression/theia_bleedthrough_estimation/__init__.py index 0b660c630..ed888635f 100644 --- a/regression/theia-bleedthrough-estimation-plugin/src/polus/plugins/regression/theia_bleedthrough_estimation/__init__.py +++ b/regression/theia-bleedthrough-estimation-tool/src/polus/images/regression/theia_bleedthrough_estimation/__init__.py @@ -3,4 +3,4 @@ from . import tile_selectors from . import utils -__version__ = "0.5.1-dev1" +__version__ = "0.5.2-dev0" diff --git a/regression/theia-bleedthrough-estimation-plugin/src/polus/plugins/regression/theia_bleedthrough_estimation/__main__.py b/regression/theia-bleedthrough-estimation-tool/src/polus/images/regression/theia_bleedthrough_estimation/__main__.py similarity index 91% rename from regression/theia-bleedthrough-estimation-plugin/src/polus/plugins/regression/theia_bleedthrough_estimation/__main__.py rename to regression/theia-bleedthrough-estimation-tool/src/polus/images/regression/theia_bleedthrough_estimation/__main__.py index 29ae030b7..634680a8a 100644 --- a/regression/theia-bleedthrough-estimation-plugin/src/polus/plugins/regression/theia_bleedthrough_estimation/__main__.py +++ b/regression/theia-bleedthrough-estimation-tool/src/polus/images/regression/theia_bleedthrough_estimation/__main__.py @@ -8,16 +8,16 @@ import filepattern import tqdm import typer -from polus.plugins.regression.theia_bleedthrough_estimation import model -from polus.plugins.regression.theia_bleedthrough_estimation import tile_selectors -from polus.plugins.regression.theia_bleedthrough_estimation.utils import constants -from polus.plugins.regression.theia_bleedthrough_estimation.utils import helpers +from polus.images.regression.theia_bleedthrough_estimation import model +from polus.images.regression.theia_bleedthrough_estimation import tile_selectors +from polus.images.regression.theia_bleedthrough_estimation.utils import constants +from polus.images.regression.theia_bleedthrough_estimation.utils import helpers logging.basicConfig( format="%(asctime)s - %(name)s - %(levelname)s - %(message)s", datefmt="%d-%b-%y %H:%M:%S", ) -logger = helpers.make_logger("polus.plugins.regression.theia_bleedthrough_estimation") +logger = helpers.make_logger("polus.images.regression.theia_bleedthrough_estimation") app = typer.Typer() diff --git a/regression/theia-bleedthrough-estimation-plugin/src/polus/plugins/regression/theia_bleedthrough_estimation/model.py b/regression/theia-bleedthrough-estimation-tool/src/polus/images/regression/theia_bleedthrough_estimation/model.py similarity index 100% rename from regression/theia-bleedthrough-estimation-plugin/src/polus/plugins/regression/theia_bleedthrough_estimation/model.py rename to regression/theia-bleedthrough-estimation-tool/src/polus/images/regression/theia_bleedthrough_estimation/model.py diff --git a/regression/theia-bleedthrough-estimation-plugin/src/polus/plugins/regression/theia_bleedthrough_estimation/tile_selectors/__init__.py b/regression/theia-bleedthrough-estimation-tool/src/polus/images/regression/theia_bleedthrough_estimation/tile_selectors/__init__.py similarity index 100% rename from regression/theia-bleedthrough-estimation-plugin/src/polus/plugins/regression/theia_bleedthrough_estimation/tile_selectors/__init__.py rename to regression/theia-bleedthrough-estimation-tool/src/polus/images/regression/theia_bleedthrough_estimation/tile_selectors/__init__.py diff --git a/regression/theia-bleedthrough-estimation-plugin/src/polus/plugins/regression/theia_bleedthrough_estimation/tile_selectors/selector.py b/regression/theia-bleedthrough-estimation-tool/src/polus/images/regression/theia_bleedthrough_estimation/tile_selectors/selector.py similarity index 100% rename from regression/theia-bleedthrough-estimation-plugin/src/polus/plugins/regression/theia_bleedthrough_estimation/tile_selectors/selector.py rename to regression/theia-bleedthrough-estimation-tool/src/polus/images/regression/theia_bleedthrough_estimation/tile_selectors/selector.py diff --git a/regression/theia-bleedthrough-estimation-plugin/src/polus/plugins/regression/theia_bleedthrough_estimation/utils/__init__.py b/regression/theia-bleedthrough-estimation-tool/src/polus/images/regression/theia_bleedthrough_estimation/utils/__init__.py similarity index 100% rename from regression/theia-bleedthrough-estimation-plugin/src/polus/plugins/regression/theia_bleedthrough_estimation/utils/__init__.py rename to regression/theia-bleedthrough-estimation-tool/src/polus/images/regression/theia_bleedthrough_estimation/utils/__init__.py diff --git a/regression/theia-bleedthrough-estimation-plugin/src/polus/plugins/regression/theia_bleedthrough_estimation/utils/constants.py b/regression/theia-bleedthrough-estimation-tool/src/polus/images/regression/theia_bleedthrough_estimation/utils/constants.py similarity index 100% rename from regression/theia-bleedthrough-estimation-plugin/src/polus/plugins/regression/theia_bleedthrough_estimation/utils/constants.py rename to regression/theia-bleedthrough-estimation-tool/src/polus/images/regression/theia_bleedthrough_estimation/utils/constants.py diff --git a/regression/theia-bleedthrough-estimation-plugin/src/polus/plugins/regression/theia_bleedthrough_estimation/utils/helpers.py b/regression/theia-bleedthrough-estimation-tool/src/polus/images/regression/theia_bleedthrough_estimation/utils/helpers.py similarity index 100% rename from regression/theia-bleedthrough-estimation-plugin/src/polus/plugins/regression/theia_bleedthrough_estimation/utils/helpers.py rename to regression/theia-bleedthrough-estimation-tool/src/polus/images/regression/theia_bleedthrough_estimation/utils/helpers.py diff --git a/regression/theia-bleedthrough-estimation-plugin/tests/__init__.py b/regression/theia-bleedthrough-estimation-tool/tests/__init__.py similarity index 100% rename from regression/theia-bleedthrough-estimation-plugin/tests/__init__.py rename to regression/theia-bleedthrough-estimation-tool/tests/__init__.py diff --git a/regression/theia-bleedthrough-estimation-plugin/tests/conftest.py b/regression/theia-bleedthrough-estimation-tool/tests/conftest.py similarity index 100% rename from regression/theia-bleedthrough-estimation-plugin/tests/conftest.py rename to regression/theia-bleedthrough-estimation-tool/tests/conftest.py diff --git a/regression/theia-bleedthrough-estimation-plugin/tests/test_theia.py b/regression/theia-bleedthrough-estimation-tool/tests/test_theia.py similarity index 95% rename from regression/theia-bleedthrough-estimation-plugin/tests/test_theia.py rename to regression/theia-bleedthrough-estimation-tool/tests/test_theia.py index 25a886481..5b2191108 100644 --- a/regression/theia-bleedthrough-estimation-plugin/tests/test_theia.py +++ b/regression/theia-bleedthrough-estimation-tool/tests/test_theia.py @@ -16,9 +16,9 @@ import pytest import skimage.data import typer.testing -from polus.plugins.regression.theia_bleedthrough_estimation import model as theia -from polus.plugins.regression.theia_bleedthrough_estimation import tile_selectors -from polus.plugins.regression.theia_bleedthrough_estimation.__main__ import app +from polus.images.regression.theia_bleedthrough_estimation import model as theia +from polus.images.regression.theia_bleedthrough_estimation import tile_selectors +from polus.images.regression.theia_bleedthrough_estimation.__main__ import app PATTERN = "blobs_c{c:d}.ome.tif" NUM_FLUOROPHORES = [2, 4] @@ -219,7 +219,7 @@ def test_cli() -> None: """ -python -m src.polus.plugins.regression.theia_bleedthrough_estimation \ +python -m src.polus.images.regression.theia_bleedthrough_estimation \ --inpDir ./data/input \ --filePattern "blobs_c{c:d}.ome.tif" \ --groupBy "" \ diff --git a/segmentation/cell-border-segmentation-plugin/.bumpversion.cfg b/segmentation/cell-border-segmentation-plugin/.bumpversion.cfg deleted file mode 100644 index 113fad554..000000000 --- a/segmentation/cell-border-segmentation-plugin/.bumpversion.cfg +++ /dev/null @@ -1,29 +0,0 @@ -[bumpversion] -current_version = 0.2.3-dev0 -commit = True -tag = False -parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? -serialize = - {major}.{minor}.{patch}-{release}{dev} - {major}.{minor}.{patch} - -[bumpversion:part:release] -optional_value = _ -first_value = dev -values = - dev - _ - -[bumpversion:part:dev] - -[bumpversion:file:pyproject.toml] -search = version = "{current_version}" -replace = version = "{new_version}" - -[bumpversion:file:VERSION] - -[bumpversion:file:README.md] - -[bumpversion:file:plugin.json] - -[bumpversion:file:src/polus/plugins/segmentation/cell_border_segmentation/__init__.py] diff --git a/segmentation/cell-border-segmentation-plugin/build-docker.sh b/segmentation/cell-border-segmentation-plugin/build-docker.sh deleted file mode 100755 index 785e6f23d..000000000 --- a/segmentation/cell-border-segmentation-plugin/build-docker.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -version=$(", diff --git a/segmentation/cell-border-segmentation-plugin/run-plugin.sh b/segmentation/cell-border-segmentation-tool/run-plugin.sh similarity index 100% rename from segmentation/cell-border-segmentation-plugin/run-plugin.sh rename to segmentation/cell-border-segmentation-tool/run-plugin.sh diff --git a/segmentation/cell-border-segmentation-plugin/src/polus/plugins/segmentation/cell_border_segmentation/__init__.py b/segmentation/cell-border-segmentation-tool/src/polus/images/segmentation/cell_border_segmentation/__init__.py similarity index 60% rename from segmentation/cell-border-segmentation-plugin/src/polus/plugins/segmentation/cell_border_segmentation/__init__.py rename to segmentation/cell-border-segmentation-tool/src/polus/images/segmentation/cell_border_segmentation/__init__.py index 6c5c0016c..003cb7a5f 100644 --- a/segmentation/cell-border-segmentation-plugin/src/polus/plugins/segmentation/cell_border_segmentation/__init__.py +++ b/segmentation/cell-border-segmentation-tool/src/polus/images/segmentation/cell_border_segmentation/__init__.py @@ -1,3 +1,3 @@ """Cell border segmentation package.""" -__version__ = "0.2.3-dev0" +__version__ = "0.2.4-dev0" diff --git a/segmentation/cell-border-segmentation-plugin/src/polus/plugins/segmentation/cell_border_segmentation/__main__.py b/segmentation/cell-border-segmentation-tool/src/polus/images/segmentation/cell_border_segmentation/__main__.py similarity index 95% rename from segmentation/cell-border-segmentation-plugin/src/polus/plugins/segmentation/cell_border_segmentation/__main__.py rename to segmentation/cell-border-segmentation-tool/src/polus/images/segmentation/cell_border_segmentation/__main__.py index 6d2214928..60489f5d0 100644 --- a/segmentation/cell-border-segmentation-plugin/src/polus/plugins/segmentation/cell_border_segmentation/__main__.py +++ b/segmentation/cell-border-segmentation-tool/src/polus/images/segmentation/cell_border_segmentation/__main__.py @@ -7,7 +7,7 @@ from typing import Any import filepattern as fp -import polus.plugins.segmentation.cell_border_segmentation.segment as zs +import polus.images.segmentation.cell_border_segmentation.segment as zs import typer from tensorflow import keras from tqdm import tqdm @@ -17,7 +17,7 @@ datefmt="%d-%b-%y %H:%M:%S", ) POLUS_LOG = getattr(logging, environ.get("POLUS_LOG", "INFO")) -logger = logging.getLogger("polus.plugins.segmentation.zo1_segmentation") +logger = logging.getLogger("polus.images.segmentation.zo1_segmentation") logger.setLevel(POLUS_LOG) logging.getLogger("bfio").setLevel(POLUS_LOG) diff --git a/segmentation/cell-border-segmentation-plugin/src/polus/plugins/segmentation/cell_border_segmentation/cnn/saved_model.pb b/segmentation/cell-border-segmentation-tool/src/polus/images/segmentation/cell_border_segmentation/cnn/saved_model.pb similarity index 100% rename from segmentation/cell-border-segmentation-plugin/src/polus/plugins/segmentation/cell_border_segmentation/cnn/saved_model.pb rename to segmentation/cell-border-segmentation-tool/src/polus/images/segmentation/cell_border_segmentation/cnn/saved_model.pb diff --git a/segmentation/cell-border-segmentation-plugin/src/polus/plugins/segmentation/cell_border_segmentation/cnn/variables/variables.data-00000-of-00001 b/segmentation/cell-border-segmentation-tool/src/polus/images/segmentation/cell_border_segmentation/cnn/variables/variables.data-00000-of-00001 similarity index 100% rename from segmentation/cell-border-segmentation-plugin/src/polus/plugins/segmentation/cell_border_segmentation/cnn/variables/variables.data-00000-of-00001 rename to segmentation/cell-border-segmentation-tool/src/polus/images/segmentation/cell_border_segmentation/cnn/variables/variables.data-00000-of-00001 diff --git a/segmentation/cell-border-segmentation-plugin/src/polus/plugins/segmentation/cell_border_segmentation/cnn/variables/variables.index b/segmentation/cell-border-segmentation-tool/src/polus/images/segmentation/cell_border_segmentation/cnn/variables/variables.index similarity index 100% rename from segmentation/cell-border-segmentation-plugin/src/polus/plugins/segmentation/cell_border_segmentation/cnn/variables/variables.index rename to segmentation/cell-border-segmentation-tool/src/polus/images/segmentation/cell_border_segmentation/cnn/variables/variables.index diff --git a/segmentation/cell-border-segmentation-plugin/src/polus/plugins/segmentation/cell_border_segmentation/segment.py b/segmentation/cell-border-segmentation-tool/src/polus/images/segmentation/cell_border_segmentation/segment.py similarity index 100% rename from segmentation/cell-border-segmentation-plugin/src/polus/plugins/segmentation/cell_border_segmentation/segment.py rename to segmentation/cell-border-segmentation-tool/src/polus/images/segmentation/cell_border_segmentation/segment.py diff --git a/segmentation/cell-border-segmentation-plugin/tests/__init__.py b/segmentation/cell-border-segmentation-tool/tests/__init__.py similarity index 100% rename from segmentation/cell-border-segmentation-plugin/tests/__init__.py rename to segmentation/cell-border-segmentation-tool/tests/__init__.py diff --git a/segmentation/cell-border-segmentation-plugin/tests/conftest.py b/segmentation/cell-border-segmentation-tool/tests/conftest.py similarity index 100% rename from segmentation/cell-border-segmentation-plugin/tests/conftest.py rename to segmentation/cell-border-segmentation-tool/tests/conftest.py diff --git a/segmentation/cell-border-segmentation-plugin/tests/test_cli.py b/segmentation/cell-border-segmentation-tool/tests/test_cli.py similarity index 93% rename from segmentation/cell-border-segmentation-plugin/tests/test_cli.py rename to segmentation/cell-border-segmentation-tool/tests/test_cli.py index 5725b869b..fa784bc32 100644 --- a/segmentation/cell-border-segmentation-plugin/tests/test_cli.py +++ b/segmentation/cell-border-segmentation-tool/tests/test_cli.py @@ -2,7 +2,7 @@ import shutil from pathlib import Path -from polus.plugins.segmentation.cell_border_segmentation.__main__ import app +from polus.images.segmentation.cell_border_segmentation.__main__ import app from typer.testing import CliRunner diff --git a/segmentation/cell-border-segmentation-plugin/tests/test_segment.py b/segmentation/cell-border-segmentation-tool/tests/test_segment.py similarity index 96% rename from segmentation/cell-border-segmentation-plugin/tests/test_segment.py rename to segmentation/cell-border-segmentation-tool/tests/test_segment.py index 5af23105e..2bab224d8 100644 --- a/segmentation/cell-border-segmentation-plugin/tests/test_segment.py +++ b/segmentation/cell-border-segmentation-tool/tests/test_segment.py @@ -4,7 +4,7 @@ from pathlib import Path import numpy as np -import polus.plugins.segmentation.cell_border_segmentation.segment as zs +import polus.images.segmentation.cell_border_segmentation.segment as zs from bfio import BioReader from bfio import BioWriter from tensorflow import keras diff --git a/segmentation/mesmer-inference-plugin/CHANGELOG.md b/segmentation/mesmer-inference-plugin/CHANGELOG.md deleted file mode 100644 index 67bcdde5c..000000000 --- a/segmentation/mesmer-inference-plugin/CHANGELOG.md +++ /dev/null @@ -1 +0,0 @@ -# MESMER Inference(v0.0.8-dev0) diff --git a/segmentation/mesmer-inference-plugin/VERSION b/segmentation/mesmer-inference-plugin/VERSION deleted file mode 100644 index 5bb9d6ad4..000000000 --- a/segmentation/mesmer-inference-plugin/VERSION +++ /dev/null @@ -1 +0,0 @@ -0.0.8-dev0 diff --git a/segmentation/mesmer-inference-plugin/src/polus/plugins/segmentation/mesmer_inference/__init__.py b/segmentation/mesmer-inference-plugin/src/polus/plugins/segmentation/mesmer_inference/__init__.py deleted file mode 100644 index 7780471c6..000000000 --- a/segmentation/mesmer-inference-plugin/src/polus/plugins/segmentation/mesmer_inference/__init__.py +++ /dev/null @@ -1,3 +0,0 @@ -"""Mesmer Inference.""" - -__version__ = "0.0.8-dev0" diff --git a/segmentation/mesmer-training-plugin/.bumpversion.cfg b/segmentation/mesmer-inference-tool/.bumpversion.cfg similarity index 85% rename from segmentation/mesmer-training-plugin/.bumpversion.cfg rename to segmentation/mesmer-inference-tool/.bumpversion.cfg index 1d8498cf7..d64a75e13 100644 --- a/segmentation/mesmer-training-plugin/.bumpversion.cfg +++ b/segmentation/mesmer-inference-tool/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.0.6-dev0 +current_version = 0.0.9-dev0 commit = True tag = False parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? @@ -28,4 +28,4 @@ replace = version = "{new_version}" [bumpversion:file:CHANGELOG.md] -[bumpversion:file:src/polus/plugins/segmentation/mesmer_training/__init__.py] +[bumpversion:file:src/polus/images/segmentation/mesmer_inference/__init__.py] diff --git a/segmentation/mesmer-inference-plugin/.gitignore b/segmentation/mesmer-inference-tool/.gitignore similarity index 100% rename from segmentation/mesmer-inference-plugin/.gitignore rename to segmentation/mesmer-inference-tool/.gitignore diff --git a/segmentation/mesmer-inference-tool/CHANGELOG.md b/segmentation/mesmer-inference-tool/CHANGELOG.md new file mode 100644 index 000000000..949533556 --- /dev/null +++ b/segmentation/mesmer-inference-tool/CHANGELOG.md @@ -0,0 +1 @@ +# MESMER Inference(v0.0.9-dev0) diff --git a/segmentation/mesmer-inference-plugin/Dockerfile b/segmentation/mesmer-inference-tool/Dockerfile similarity index 93% rename from segmentation/mesmer-inference-plugin/Dockerfile rename to segmentation/mesmer-inference-tool/Dockerfile index 427d76445..d58828934 100644 --- a/segmentation/mesmer-inference-plugin/Dockerfile +++ b/segmentation/mesmer-inference-tool/Dockerfile @@ -31,5 +31,5 @@ RUN pip3 install ${EXEC_DIR} --no-cache-dir # Fix for cudnn error on RTX gpus ENV TF_FORCE_GPU_ALLOW_GROWTH=true RUN python3 -c "import deepcell;from deepcell.applications import Mesmer; app = Mesmer()" -ENTRYPOINT ["python3", "-m", "polus.plugins.segmentation.mesmer_inference"] +ENTRYPOINT ["python3", "-m", "polus.images.segmentation.mesmer_inference"] CMD ["--help"] diff --git a/segmentation/mesmer-inference-plugin/README.md b/segmentation/mesmer-inference-tool/README.md similarity index 98% rename from segmentation/mesmer-inference-plugin/README.md rename to segmentation/mesmer-inference-tool/README.md index dacbefa53..46489daa1 100644 --- a/segmentation/mesmer-inference-plugin/README.md +++ b/segmentation/mesmer-inference-tool/README.md @@ -1,4 +1,4 @@ -# MESMER Inference(v0.0.8-dev0) +# MESMER Inference(v0.0.9-dev0) This WIPP plugin segments images using PanopticNet model. diff --git a/segmentation/mesmer-inference-tool/VERSION b/segmentation/mesmer-inference-tool/VERSION new file mode 100644 index 000000000..cefaa5c7a --- /dev/null +++ b/segmentation/mesmer-inference-tool/VERSION @@ -0,0 +1 @@ +0.0.9-dev0 diff --git a/segmentation/mesmer-inference-plugin/build-docker.sh b/segmentation/mesmer-inference-tool/build-docker.sh similarity index 100% rename from segmentation/mesmer-inference-plugin/build-docker.sh rename to segmentation/mesmer-inference-tool/build-docker.sh diff --git a/segmentation/mesmer-inference-plugin/plugin.json b/segmentation/mesmer-inference-tool/plugin.json similarity index 95% rename from segmentation/mesmer-inference-plugin/plugin.json rename to segmentation/mesmer-inference-tool/plugin.json index da457b320..83b8e9789 100644 --- a/segmentation/mesmer-inference-plugin/plugin.json +++ b/segmentation/mesmer-inference-tool/plugin.json @@ -1,6 +1,6 @@ { "name": "Mesmer Inference", - "version": "0.0.8-dev0", + "version": "0.0.9-dev0", "title": "Mesmer Inference", "description": "WIPP plugin to run inference using MESMER.", "author": "Vishakha Goyal (vishakha.goyal@nih.gov), Hamdah Shafqat Abbasi (hamdahshafqat.abbasi@nih.gov)", @@ -8,11 +8,11 @@ "repository": "https://github.com/polusai/polus-plugins", "website": "https://ncats.nih.gov/preclinical/core/informatics", "citation": "", - "containerId": "polusai/mesmer-inference-plugin:0.0.8-dev0", + "containerId": "polusai/mesmer-inference-tool:0.0.9-dev0", "baseCommand": [ "python3", "-m", - "polus.plugins.segmentation.mesmer_inference" + "polus.images.segmentation.mesmer_inference" ], "inputs": [ { diff --git a/segmentation/mesmer-inference-plugin/pyproject.toml b/segmentation/mesmer-inference-tool/pyproject.toml similarity index 89% rename from segmentation/mesmer-inference-plugin/pyproject.toml rename to segmentation/mesmer-inference-tool/pyproject.toml index a9c920d2e..54ce91bc8 100644 --- a/segmentation/mesmer-inference-plugin/pyproject.toml +++ b/segmentation/mesmer-inference-tool/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] -name = "polus-plugins-segmentation-mesmer-inference" -version = "0.0.8-dev0" +name = "polus-images-segmentation-mesmer-inference" +version = "0.0.9-dev0" description = "" authors = [ "Vishakha Goyal ", diff --git a/segmentation/mesmer-inference-plugin/run-plugin.sh b/segmentation/mesmer-inference-tool/run-plugin.sh similarity index 100% rename from segmentation/mesmer-inference-plugin/run-plugin.sh rename to segmentation/mesmer-inference-tool/run-plugin.sh diff --git a/segmentation/mesmer-inference-tool/src/polus/images/segmentation/mesmer_inference/__init__.py b/segmentation/mesmer-inference-tool/src/polus/images/segmentation/mesmer_inference/__init__.py new file mode 100644 index 000000000..b93f5f02f --- /dev/null +++ b/segmentation/mesmer-inference-tool/src/polus/images/segmentation/mesmer_inference/__init__.py @@ -0,0 +1,3 @@ +"""Mesmer Inference.""" + +__version__ = "0.0.9-dev0" diff --git a/segmentation/mesmer-inference-plugin/src/polus/plugins/segmentation/mesmer_inference/__main__.py b/segmentation/mesmer-inference-tool/src/polus/images/segmentation/mesmer_inference/__main__.py similarity index 94% rename from segmentation/mesmer-inference-plugin/src/polus/plugins/segmentation/mesmer_inference/__main__.py rename to segmentation/mesmer-inference-tool/src/polus/images/segmentation/mesmer_inference/__main__.py index 7d067279c..2e241d0ca 100644 --- a/segmentation/mesmer-inference-plugin/src/polus/plugins/segmentation/mesmer_inference/__main__.py +++ b/segmentation/mesmer-inference-tool/src/polus/images/segmentation/mesmer_inference/__main__.py @@ -7,14 +7,14 @@ import filepattern as fp import typer -from polus.plugins.segmentation.mesmer_inference.padded import Extension, Model, run +from polus.images.segmentation.mesmer_inference.padded import Extension, Model, run # Initialize the logger logging.basicConfig( format="%(asctime)s - %(name)-8s - %(levelname)-8s - %(message)s", datefmt="%d-%b-%y %H:%M:%S", ) -logger = logging.getLogger("polus.plugins.segmentation.mesmer_inference") +logger = logging.getLogger("polus.images.segmentation.mesmer_inference") logger.setLevel(logging.INFO) diff --git a/segmentation/mesmer-inference-plugin/src/polus/plugins/segmentation/mesmer_inference/padded.py b/segmentation/mesmer-inference-tool/src/polus/images/segmentation/mesmer_inference/padded.py similarity index 100% rename from segmentation/mesmer-inference-plugin/src/polus/plugins/segmentation/mesmer_inference/padded.py rename to segmentation/mesmer-inference-tool/src/polus/images/segmentation/mesmer_inference/padded.py diff --git a/segmentation/mesmer-inference-plugin/tests/__init__.py b/segmentation/mesmer-inference-tool/tests/__init__.py similarity index 100% rename from segmentation/mesmer-inference-plugin/tests/__init__.py rename to segmentation/mesmer-inference-tool/tests/__init__.py diff --git a/segmentation/mesmer-inference-plugin/tests/conftest.py b/segmentation/mesmer-inference-tool/tests/conftest.py similarity index 100% rename from segmentation/mesmer-inference-plugin/tests/conftest.py rename to segmentation/mesmer-inference-tool/tests/conftest.py diff --git a/segmentation/mesmer-inference-plugin/tests/test_mesmer.py b/segmentation/mesmer-inference-tool/tests/test_mesmer.py similarity index 92% rename from segmentation/mesmer-inference-plugin/tests/test_mesmer.py rename to segmentation/mesmer-inference-tool/tests/test_mesmer.py index 793416061..67fe8df1f 100644 --- a/segmentation/mesmer-inference-plugin/tests/test_mesmer.py +++ b/segmentation/mesmer-inference-tool/tests/test_mesmer.py @@ -8,10 +8,10 @@ import pytest from bfio import BioReader from deepcell.applications import Mesmer -from polus.plugins.segmentation.mesmer_inference.__main__ import app -from polus.plugins.segmentation.mesmer_inference.padded import get_data -from polus.plugins.segmentation.mesmer_inference.padded import padding -from polus.plugins.segmentation.mesmer_inference.padded import run +from polus.images.segmentation.mesmer_inference.__main__ import app +from polus.images.segmentation.mesmer_inference.padded import get_data +from polus.images.segmentation.mesmer_inference.padded import padding +from polus.images.segmentation.mesmer_inference.padded import run from typer.testing import CliRunner from .conftest import DIR_RETURN_TYPE diff --git a/segmentation/mesmer-training-plugin/VERSION b/segmentation/mesmer-training-plugin/VERSION deleted file mode 100644 index 79b17e654..000000000 --- a/segmentation/mesmer-training-plugin/VERSION +++ /dev/null @@ -1 +0,0 @@ -0.0.6-dev0 diff --git a/segmentation/mesmer-inference-plugin/.bumpversion.cfg b/segmentation/mesmer-training-tool/.bumpversion.cfg similarity index 83% rename from segmentation/mesmer-inference-plugin/.bumpversion.cfg rename to segmentation/mesmer-training-tool/.bumpversion.cfg index 305bdf1f6..8d3792686 100644 --- a/segmentation/mesmer-inference-plugin/.bumpversion.cfg +++ b/segmentation/mesmer-training-tool/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.0.8-dev0 +current_version = 0.0.7-dev0 commit = True tag = False parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? @@ -28,4 +28,4 @@ replace = version = "{new_version}" [bumpversion:file:CHANGELOG.md] -[bumpversion:file:src/polus/plugins/segmentation/mesmer_inference/__init__.py] +[bumpversion:file:src/polus/images/segmentation/mesmer_training/__init__.py] diff --git a/segmentation/mesmer-training-plugin/CHANGELOG.md b/segmentation/mesmer-training-tool/CHANGELOG.md similarity index 94% rename from segmentation/mesmer-training-plugin/CHANGELOG.md rename to segmentation/mesmer-training-tool/CHANGELOG.md index d84d52fbb..cc544d5d7 100644 --- a/segmentation/mesmer-training-plugin/CHANGELOG.md +++ b/segmentation/mesmer-training-tool/CHANGELOG.md @@ -1,4 +1,4 @@ -# mesmer-training-plugin(v0.0.6-dev0) +# mesmer-training-plugin(v0.0.7-dev0) 1. This plugin is updated only to the new plugin standards 2. `--filePattern` is added as an input argument to parse image files. diff --git a/segmentation/mesmer-training-plugin/Dockerfile b/segmentation/mesmer-training-tool/Dockerfile similarity index 93% rename from segmentation/mesmer-training-plugin/Dockerfile rename to segmentation/mesmer-training-tool/Dockerfile index 142ea6e12..713942067 100644 --- a/segmentation/mesmer-training-plugin/Dockerfile +++ b/segmentation/mesmer-training-tool/Dockerfile @@ -30,5 +30,5 @@ COPY src ${EXEC_DIR}/src RUN pip3 install ${EXEC_DIR} --no-cache-dir # Fix for cudnn error on RTX gpus ENV TF_FORCE_GPU_ALLOW_GROWTH=true -ENTRYPOINT ["python3", "-m", "polus.plugins.segmentation.mesmer_training"] +ENTRYPOINT ["python3", "-m", "polus.images.segmentation.mesmer_training"] CMD ["--help"] diff --git a/segmentation/mesmer-training-plugin/README.md b/segmentation/mesmer-training-tool/README.md similarity index 98% rename from segmentation/mesmer-training-plugin/README.md rename to segmentation/mesmer-training-tool/README.md index 6b05127da..3f7272782 100644 --- a/segmentation/mesmer-training-plugin/README.md +++ b/segmentation/mesmer-training-tool/README.md @@ -1,4 +1,4 @@ -# MESMER Training(v0.0.6-dev0) +# MESMER Training(v0.0.7-dev0) This WIPP Plugin trains PanopticNet using MESMER Pipeline. diff --git a/segmentation/mesmer-training-tool/VERSION b/segmentation/mesmer-training-tool/VERSION new file mode 100644 index 000000000..b6d143eb7 --- /dev/null +++ b/segmentation/mesmer-training-tool/VERSION @@ -0,0 +1 @@ +0.0.7-dev0 diff --git a/segmentation/mesmer-training-plugin/build-docker.sh b/segmentation/mesmer-training-tool/build-docker.sh similarity index 100% rename from segmentation/mesmer-training-plugin/build-docker.sh rename to segmentation/mesmer-training-tool/build-docker.sh diff --git a/segmentation/mesmer-training-plugin/plugin.json b/segmentation/mesmer-training-tool/plugin.json similarity index 96% rename from segmentation/mesmer-training-plugin/plugin.json rename to segmentation/mesmer-training-tool/plugin.json index d803033dd..f7cd2de97 100644 --- a/segmentation/mesmer-training-plugin/plugin.json +++ b/segmentation/mesmer-training-tool/plugin.json @@ -1,6 +1,6 @@ { "name": "MESMER Training", - "version": "0.0.6-dev0", + "version": "0.0.7-dev0", "title": "MESMER Training", "description": "WIPP plugin to train PanopticNet model.", "author": "Vishakha Goyal (vishakha.goyal@nih.gov), Hamdah Shafqat Abbasi (hamdahshafqat.abbasi@nih.gov)", @@ -8,11 +8,11 @@ "repository": "https://github.com/polusai/polus-plugins", "website": "https://ncats.nih.gov/preclinical/core/informatics", "citation": "", - "containerId": "polusai/mesmer-training-plugin:0.0.6-dev0", + "containerId": "polusai/mesmer-training-tool:0.0.7-dev0", "baseCommand": [ "python3", "-m", - "polus.plugins.segmentation.mesmer_training" + "polus.images.segmentation.mesmer_training" ], "inputs": [ { diff --git a/segmentation/mesmer-training-plugin/pyproject.toml b/segmentation/mesmer-training-tool/pyproject.toml similarity index 90% rename from segmentation/mesmer-training-plugin/pyproject.toml rename to segmentation/mesmer-training-tool/pyproject.toml index dd6bc4cdd..6510cb13f 100644 --- a/segmentation/mesmer-training-plugin/pyproject.toml +++ b/segmentation/mesmer-training-tool/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] -name = "polus-plugins-segmentation-mesmer-training" -version = "0.0.6-dev0" +name = "polus-images-segmentation-mesmer-training" +version = "0.0.7-dev0" description = "" authors = [ "Vishakha Goyal ", diff --git a/segmentation/mesmer-training-plugin/run-plugin.sh b/segmentation/mesmer-training-tool/run-plugin.sh similarity index 100% rename from segmentation/mesmer-training-plugin/run-plugin.sh rename to segmentation/mesmer-training-tool/run-plugin.sh diff --git a/segmentation/mesmer-training-plugin/src/polus/plugins/segmentation/mesmer_training/__init__.py b/segmentation/mesmer-training-tool/src/polus/images/segmentation/mesmer_training/__init__.py similarity index 79% rename from segmentation/mesmer-training-plugin/src/polus/plugins/segmentation/mesmer_training/__init__.py rename to segmentation/mesmer-training-tool/src/polus/images/segmentation/mesmer_training/__init__.py index c68d25e94..50ab6629d 100644 --- a/segmentation/mesmer-training-plugin/src/polus/plugins/segmentation/mesmer_training/__init__.py +++ b/segmentation/mesmer-training-tool/src/polus/images/segmentation/mesmer_training/__init__.py @@ -1,5 +1,5 @@ """Mesmer Training.""" -__version__ = "0.0.6-dev0" +__version__ = "0.0.7-dev0" from polus.plugins.segmentation.mesmer_training import train as train # noqa diff --git a/segmentation/mesmer-training-plugin/src/polus/plugins/segmentation/mesmer_training/__main__.py b/segmentation/mesmer-training-tool/src/polus/images/segmentation/mesmer_training/__main__.py similarity index 96% rename from segmentation/mesmer-training-plugin/src/polus/plugins/segmentation/mesmer_training/__main__.py rename to segmentation/mesmer-training-tool/src/polus/images/segmentation/mesmer_training/__main__.py index 888e6595d..87f9da9f1 100644 --- a/segmentation/mesmer-training-plugin/src/polus/plugins/segmentation/mesmer_training/__main__.py +++ b/segmentation/mesmer-training-tool/src/polus/images/segmentation/mesmer_training/__main__.py @@ -7,14 +7,14 @@ import typer -from polus.plugins.segmentation.mesmer_training import train as train +from polus.images.segmentation.mesmer_training import train as train # Initialize the logger logging.basicConfig( format="%(asctime)s - %(name)-8s - %(levelname)-8s - %(message)s", datefmt="%d-%b-%y %H:%M:%S", ) -logger = logging.getLogger("polus.plugins.segmentation.mesmer_training") +logger = logging.getLogger("polus.images.segmentation.mesmer_training") logger.setLevel(os.environ.get("POLUS_LOG", logging.INFO)) diff --git a/segmentation/mesmer-training-plugin/src/polus/plugins/segmentation/mesmer_training/train.py b/segmentation/mesmer-training-tool/src/polus/images/segmentation/mesmer_training/train.py similarity index 100% rename from segmentation/mesmer-training-plugin/src/polus/plugins/segmentation/mesmer_training/train.py rename to segmentation/mesmer-training-tool/src/polus/images/segmentation/mesmer_training/train.py diff --git a/segmentation/mesmer-training-plugin/tests/__init__.py b/segmentation/mesmer-training-tool/tests/__init__.py similarity index 100% rename from segmentation/mesmer-training-plugin/tests/__init__.py rename to segmentation/mesmer-training-tool/tests/__init__.py diff --git a/segmentation/mesmer-training-plugin/tests/test_cli.py b/segmentation/mesmer-training-tool/tests/test_cli.py similarity index 98% rename from segmentation/mesmer-training-plugin/tests/test_cli.py rename to segmentation/mesmer-training-tool/tests/test_cli.py index cc3293d04..8258bbf6e 100644 --- a/segmentation/mesmer-training-plugin/tests/test_cli.py +++ b/segmentation/mesmer-training-tool/tests/test_cli.py @@ -6,7 +6,7 @@ import numpy as np import pytest -from polus.plugins.segmentation.mesmer_training.__main__ import app +from polus.images.segmentation.mesmer_training.__main__ import app from skimage import filters from skimage import io from skimage import measure diff --git a/transforms/images/apply-flatfield-plugin/VERSION b/transforms/images/apply-flatfield-plugin/VERSION deleted file mode 100644 index b2484da91..000000000 --- a/transforms/images/apply-flatfield-plugin/VERSION +++ /dev/null @@ -1 +0,0 @@ -2.0.0-dev9 diff --git a/transforms/images/apply-flatfield-plugin/build-docker.sh b/transforms/images/apply-flatfield-plugin/build-docker.sh deleted file mode 100644 index df2cdd207..000000000 --- a/transforms/images/apply-flatfield-plugin/build-docker.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -version=$(\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? @@ -26,4 +26,4 @@ replace = version = "{new_version}" [bumpversion:file:README.md] -[bumpversion:file:src/polus/plugins/transforms/images/image_calculator/__init__.py] +[bumpversion:file:src/polus/images/transforms/images/apply_flatfield/__init__.py] diff --git a/transforms/images/apply-flatfield-plugin/Dockerfile b/transforms/images/apply-flatfield-tool/Dockerfile similarity index 83% rename from transforms/images/apply-flatfield-plugin/Dockerfile rename to transforms/images/apply-flatfield-tool/Dockerfile index 97ef35df9..4e3be68d8 100644 --- a/transforms/images/apply-flatfield-plugin/Dockerfile +++ b/transforms/images/apply-flatfield-tool/Dockerfile @@ -16,5 +16,5 @@ COPY src ${EXEC_DIR}/src RUN pip3 install ${EXEC_DIR} --no-cache-dir -ENTRYPOINT ["python3", "-m", "polus.plugins.transforms.images.apply_flatfield"] +ENTRYPOINT ["python3", "-m", "polus.images.transforms.images.apply_flatfield"] CMD ["--help"] diff --git a/transforms/images/apply-flatfield-plugin/README.md b/transforms/images/apply-flatfield-tool/README.md similarity index 99% rename from transforms/images/apply-flatfield-plugin/README.md rename to transforms/images/apply-flatfield-tool/README.md index 37b07eaf0..aa08fb55e 100644 --- a/transforms/images/apply-flatfield-plugin/README.md +++ b/transforms/images/apply-flatfield-tool/README.md @@ -1,4 +1,4 @@ -# Apply Flatfield Plugin (v2.0.0-dev9) +# Apply Flatfield Plugin (v2.0.1-dev0) This WIPP plugin applies a flatfield operation on every image in a collection. The algorithm used to apply the flatfield is as follows: diff --git a/transforms/images/apply-flatfield-tool/VERSION b/transforms/images/apply-flatfield-tool/VERSION new file mode 100644 index 000000000..804166851 --- /dev/null +++ b/transforms/images/apply-flatfield-tool/VERSION @@ -0,0 +1 @@ +2.0.1-dev0 diff --git a/transforms/images/apply-flatfield-tool/build-docker.sh b/transforms/images/apply-flatfield-tool/build-docker.sh new file mode 100644 index 000000000..3d0ade47b --- /dev/null +++ b/transforms/images/apply-flatfield-tool/build-docker.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +version=$(", diff --git a/transforms/images/apply-flatfield-plugin/run-plugin.sh b/transforms/images/apply-flatfield-tool/run-plugin.sh similarity index 100% rename from transforms/images/apply-flatfield-plugin/run-plugin.sh rename to transforms/images/apply-flatfield-tool/run-plugin.sh diff --git a/transforms/images/apply-flatfield-plugin/src/polus/plugins/transforms/images/apply_flatfield/__init__.py b/transforms/images/apply-flatfield-tool/src/polus/images/transforms/images/apply_flatfield/__init__.py similarity index 78% rename from transforms/images/apply-flatfield-plugin/src/polus/plugins/transforms/images/apply_flatfield/__init__.py rename to transforms/images/apply-flatfield-tool/src/polus/images/transforms/images/apply_flatfield/__init__.py index 7d298350f..e1924973d 100644 --- a/transforms/images/apply-flatfield-plugin/src/polus/plugins/transforms/images/apply_flatfield/__init__.py +++ b/transforms/images/apply-flatfield-tool/src/polus/images/transforms/images/apply_flatfield/__init__.py @@ -3,4 +3,4 @@ from . import utils from .apply_flatfield import apply -__version__ = "2.0.0-dev9" +__version__ = "2.0.1-dev0" diff --git a/transforms/images/apply-flatfield-plugin/src/polus/plugins/transforms/images/apply_flatfield/__main__.py b/transforms/images/apply-flatfield-tool/src/polus/images/transforms/images/apply_flatfield/__main__.py similarity index 92% rename from transforms/images/apply-flatfield-plugin/src/polus/plugins/transforms/images/apply_flatfield/__main__.py rename to transforms/images/apply-flatfield-tool/src/polus/images/transforms/images/apply_flatfield/__main__.py index 7dac49e72..87b57e2c4 100644 --- a/transforms/images/apply-flatfield-plugin/src/polus/plugins/transforms/images/apply_flatfield/__main__.py +++ b/transforms/images/apply-flatfield-tool/src/polus/images/transforms/images/apply_flatfield/__main__.py @@ -6,15 +6,15 @@ import typing import typer -from polus.plugins.transforms.images.apply_flatfield import apply -from polus.plugins.transforms.images.apply_flatfield import utils +from polus.images.transforms.images.apply_flatfield import apply +from polus.images.transforms.images.apply_flatfield import utils # Initialize the logger logging.basicConfig( format="%(asctime)s - %(name)-8s - %(levelname)-8s - %(message)s", datefmt="%d-%b-%y %H:%M:%S", ) -logger = logging.getLogger("polus.plugins.transforms.images.apply_flatfield") +logger = logging.getLogger("polus.images.transforms.images.apply_flatfield") logger.setLevel(utils.POLUS_LOG) app = typer.Typer() diff --git a/transforms/images/apply-flatfield-plugin/src/polus/plugins/transforms/images/apply_flatfield/apply_flatfield.py b/transforms/images/apply-flatfield-tool/src/polus/images/transforms/images/apply_flatfield/apply_flatfield.py similarity index 100% rename from transforms/images/apply-flatfield-plugin/src/polus/plugins/transforms/images/apply_flatfield/apply_flatfield.py rename to transforms/images/apply-flatfield-tool/src/polus/images/transforms/images/apply_flatfield/apply_flatfield.py diff --git a/transforms/images/apply-flatfield-plugin/src/polus/plugins/transforms/images/apply_flatfield/utils.py b/transforms/images/apply-flatfield-tool/src/polus/images/transforms/images/apply_flatfield/utils.py similarity index 100% rename from transforms/images/apply-flatfield-plugin/src/polus/plugins/transforms/images/apply_flatfield/utils.py rename to transforms/images/apply-flatfield-tool/src/polus/images/transforms/images/apply_flatfield/utils.py diff --git a/transforms/images/apply-flatfield-plugin/tests/test_plugin.py b/transforms/images/apply-flatfield-tool/tests/test_plugin.py similarity index 96% rename from transforms/images/apply-flatfield-plugin/tests/test_plugin.py rename to transforms/images/apply-flatfield-tool/tests/test_plugin.py index 8bf296a08..d0faea18c 100644 --- a/transforms/images/apply-flatfield-plugin/tests/test_plugin.py +++ b/transforms/images/apply-flatfield-tool/tests/test_plugin.py @@ -10,8 +10,8 @@ import numpy import pytest import typer.testing -from polus.plugins.transforms.images.apply_flatfield import apply -from polus.plugins.transforms.images.apply_flatfield.__main__ import app +from polus.images.transforms.images.apply_flatfield import apply +from polus.images.transforms.images.apply_flatfield.__main__ import app logger = logging.getLogger(__name__) logger.setLevel(logging.DEBUG) diff --git a/transforms/images/binary-operations-plugin/build-docker.sh b/transforms/images/binary-operations-plugin/build-docker.sh deleted file mode 100755 index 4a49de945..000000000 --- a/transforms/images/binary-operations-plugin/build-docker.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -version=$(\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? @@ -24,7 +24,7 @@ replace = version = "{new_version}" [bumpversion:file:VERSION] -[bumpversion:file:src/polus/plugins/transforms/images/binary_operations/__init__.py] +[bumpversion:file:src/polus/images/transforms/images/binary_operations/__init__.py] [bumpversion:file:README.md] search = v{current_version} diff --git a/transforms/images/binary-operations-plugin/Dockerfile b/transforms/images/binary-operations-tool/Dockerfile similarity index 88% rename from transforms/images/binary-operations-plugin/Dockerfile rename to transforms/images/binary-operations-tool/Dockerfile index 10cd763f1..8db44f987 100644 --- a/transforms/images/binary-operations-plugin/Dockerfile +++ b/transforms/images/binary-operations-tool/Dockerfile @@ -19,5 +19,5 @@ COPY src ${EXEC_DIR}/src RUN pip3 install ${EXEC_DIR} --no-cache-dir -ENTRYPOINT ["python3", "-m", "polus.plugins.transforms.images.binary_operations"] +ENTRYPOINT ["python3", "-m", "polus.images.transforms.images.binary_operations"] CMD ["--help"] diff --git a/transforms/images/binary-operations-plugin/README.md b/transforms/images/binary-operations-tool/README.md similarity index 98% rename from transforms/images/binary-operations-plugin/README.md rename to transforms/images/binary-operations-tool/README.md index 4a8a8e901..9d032630f 100644 --- a/transforms/images/binary-operations-plugin/README.md +++ b/transforms/images/binary-operations-tool/README.md @@ -1,4 +1,4 @@ -# Binary Operations Plugin (v0.5.2-dev0) +# Binary Operations Plugin (v0.5.3-dev0) This WIPP plugin does Morphological Image Processing on binary and instance labelled images. The operations available are: diff --git a/transforms/images/binary-operations-tool/VERSION b/transforms/images/binary-operations-tool/VERSION new file mode 100644 index 000000000..a5fea336e --- /dev/null +++ b/transforms/images/binary-operations-tool/VERSION @@ -0,0 +1 @@ +0.5.3-dev0 diff --git a/transforms/images/binary-operations-tool/build-docker.sh b/transforms/images/binary-operations-tool/build-docker.sh new file mode 100755 index 000000000..73642e7d6 --- /dev/null +++ b/transforms/images/binary-operations-tool/build-docker.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +version=$(", "Madhuri Vihani"] readme = "README.md" diff --git a/transforms/images/binary-operations-plugin/run-plugin.sh b/transforms/images/binary-operations-tool/run-plugin.sh similarity index 100% rename from transforms/images/binary-operations-plugin/run-plugin.sh rename to transforms/images/binary-operations-tool/run-plugin.sh diff --git a/transforms/images/binary-operations-plugin/src/polus/plugins/transforms/images/binary_operations/__init__.py b/transforms/images/binary-operations-tool/src/polus/images/transforms/images/binary_operations/__init__.py similarity index 95% rename from transforms/images/binary-operations-plugin/src/polus/plugins/transforms/images/binary_operations/__init__.py rename to transforms/images/binary-operations-tool/src/polus/images/transforms/images/binary_operations/__init__.py index 49fef7078..f9e259477 100644 --- a/transforms/images/binary-operations-plugin/src/polus/plugins/transforms/images/binary_operations/__init__.py +++ b/transforms/images/binary-operations-tool/src/polus/images/transforms/images/binary_operations/__init__.py @@ -1,5 +1,5 @@ """Binary operations tool.""" -__version__ = "0.5.2-dev0" +__version__ = "0.5.3-dev0" from . import utils from .binops import Operation diff --git a/transforms/images/binary-operations-plugin/src/polus/plugins/transforms/images/binary_operations/__main__.py b/transforms/images/binary-operations-tool/src/polus/images/transforms/images/binary_operations/__main__.py similarity index 95% rename from transforms/images/binary-operations-plugin/src/polus/plugins/transforms/images/binary_operations/__main__.py rename to transforms/images/binary-operations-tool/src/polus/images/transforms/images/binary_operations/__main__.py index 702a0d27e..204705a9a 100644 --- a/transforms/images/binary-operations-plugin/src/polus/plugins/transforms/images/binary_operations/__main__.py +++ b/transforms/images/binary-operations-tool/src/polus/images/transforms/images/binary_operations/__main__.py @@ -8,7 +8,7 @@ import typer from filepattern import FilePattern -from polus.plugins.transforms.images.binary_operations import ( +from polus.images.transforms.images.binary_operations import ( Operation, StructuringShape, __version__, @@ -22,7 +22,7 @@ format="%(asctime)s - %(name)-8s - %(levelname)-8s - %(message)s", datefmt="%d-%b-%y %H:%M:%S", ) -logger = logging.getLogger("polus.plugins.transforms.images.binary_operations") +logger = logging.getLogger("polus.images.transforms.images.binary_operations") logger.setLevel(os.environ.get("POLUS_LOG", logging.INFO)) diff --git a/transforms/images/binary-operations-plugin/src/polus/plugins/transforms/images/binary_operations/binops.py b/transforms/images/binary-operations-tool/src/polus/images/transforms/images/binary_operations/binops.py similarity index 100% rename from transforms/images/binary-operations-plugin/src/polus/plugins/transforms/images/binary_operations/binops.py rename to transforms/images/binary-operations-tool/src/polus/images/transforms/images/binary_operations/binops.py diff --git a/transforms/images/binary-operations-plugin/src/polus/plugins/transforms/images/binary_operations/utils.py b/transforms/images/binary-operations-tool/src/polus/images/transforms/images/binary_operations/utils.py similarity index 100% rename from transforms/images/binary-operations-plugin/src/polus/plugins/transforms/images/binary_operations/utils.py rename to transforms/images/binary-operations-tool/src/polus/images/transforms/images/binary_operations/utils.py diff --git a/transforms/images/binary-operations-plugin/tests/__init__.py b/transforms/images/binary-operations-tool/tests/__init__.py similarity index 100% rename from transforms/images/binary-operations-plugin/tests/__init__.py rename to transforms/images/binary-operations-tool/tests/__init__.py diff --git a/transforms/images/binary-operations-plugin/tests/plugin_test.py b/transforms/images/binary-operations-tool/tests/plugin_test.py similarity index 99% rename from transforms/images/binary-operations-plugin/tests/plugin_test.py rename to transforms/images/binary-operations-tool/tests/plugin_test.py index ea7bfa482..c0808d20e 100644 --- a/transforms/images/binary-operations-plugin/tests/plugin_test.py +++ b/transforms/images/binary-operations-tool/tests/plugin_test.py @@ -8,10 +8,10 @@ import numpy as np from bfio import BioReader from bfio import BioWriter -from polus.plugins.transforms.images.binary_operations import ( +from polus.images.transforms.images.binary_operations import ( binary_op as binary_operation, ) -from polus.plugins.transforms.images.binary_operations import utils +from polus.images.transforms.images.binary_operations import utils class PluginData: # noqa diff --git a/transforms/images/binary-operations-plugin/tests/version_test.py b/transforms/images/binary-operations-tool/tests/version_test.py similarity index 100% rename from transforms/images/binary-operations-plugin/tests/version_test.py rename to transforms/images/binary-operations-tool/tests/version_test.py diff --git a/transforms/images/image-assembler-plugin/.bumpversion.cfg b/transforms/images/image-assembler-plugin/.bumpversion.cfg deleted file mode 100644 index 3f82046e5..000000000 --- a/transforms/images/image-assembler-plugin/.bumpversion.cfg +++ /dev/null @@ -1,29 +0,0 @@ -[bumpversion] -current_version = 1.4.0-dev0 -commit = True -tag = False -parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? -serialize = - {major}.{minor}.{patch}-{release}{dev} - {major}.{minor}.{patch} - -[bumpversion:part:release] -optional_value = _ -first_value = dev -values = - dev - _ - -[bumpversion:part:dev] - -[bumpversion:file:pyproject.toml] -search = version = "{current_version}" -replace = version = "{new_version}" - -[bumpversion:file:VERSION] - -[bumpversion:file:README.md] - -[bumpversion:file:plugin.json] - -[bumpversion:file:src/polus/plugins/transforms/images/image_assembler/__init__.py] diff --git a/transforms/images/image-assembler-plugin/VERSION b/transforms/images/image-assembler-plugin/VERSION deleted file mode 100644 index 016826dc5..000000000 --- a/transforms/images/image-assembler-plugin/VERSION +++ /dev/null @@ -1 +0,0 @@ -1.4.0-dev0 diff --git a/transforms/images/image-assembler-plugin/build-docker.sh b/transforms/images/image-assembler-plugin/build-docker.sh deleted file mode 100755 index b85732419..000000000 --- a/transforms/images/image-assembler-plugin/build-docker.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -version=$(\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? @@ -20,10 +20,10 @@ values = search = version = "{current_version}" replace = version = "{new_version}" -[bumpversion:file:plugin.json] - [bumpversion:file:VERSION] [bumpversion:file:README.md] -[bumpversion:file:src/polus/plugins/regression/basic_flatfield_estimation/__init__.py] +[bumpversion:file:plugin.json] + +[bumpversion:file:src/polus/images/transforms/images/image_assembler/__init__.py] diff --git a/transforms/images/image-assembler-plugin/.dockerignore b/transforms/images/image-assembler-tool/.dockerignore similarity index 100% rename from transforms/images/image-assembler-plugin/.dockerignore rename to transforms/images/image-assembler-tool/.dockerignore diff --git a/transforms/images/image-assembler-plugin/.gitignore b/transforms/images/image-assembler-tool/.gitignore similarity index 100% rename from transforms/images/image-assembler-plugin/.gitignore rename to transforms/images/image-assembler-tool/.gitignore diff --git a/transforms/images/image-assembler-plugin/CHANGELOG.md b/transforms/images/image-assembler-tool/CHANGELOG.md similarity index 100% rename from transforms/images/image-assembler-plugin/CHANGELOG.md rename to transforms/images/image-assembler-tool/CHANGELOG.md diff --git a/transforms/images/image-assembler-plugin/Dockerfile b/transforms/images/image-assembler-tool/Dockerfile similarity index 88% rename from transforms/images/image-assembler-plugin/Dockerfile rename to transforms/images/image-assembler-tool/Dockerfile index a9388b5ce..f3dc7bccc 100644 --- a/transforms/images/image-assembler-plugin/Dockerfile +++ b/transforms/images/image-assembler-tool/Dockerfile @@ -23,5 +23,5 @@ COPY src ${EXEC_DIR}/src RUN pip3 install ${EXEC_DIR} --no-cache-dir # Default command. Additional arguments are provided through the command line -ENTRYPOINT ["python3", "-m", "polus.plugins.transforms.images.image_assembler"] +ENTRYPOINT ["python3", "-m", "polus.images.transforms.images.image_assembler"] CMD ["--help"] diff --git a/transforms/images/image-assembler-plugin/README.md b/transforms/images/image-assembler-tool/README.md similarity index 98% rename from transforms/images/image-assembler-plugin/README.md rename to transforms/images/image-assembler-tool/README.md index b2bfc3168..1fbc564df 100644 --- a/transforms/images/image-assembler-plugin/README.md +++ b/transforms/images/image-assembler-tool/README.md @@ -1,4 +1,4 @@ -# Image Assembler (1.4.0-dev0) +# Image Assembler (1.4.1-dev0) This WIPP plugin assembles images into a stitched image using an image stitching vector. It can assemble 2d and z-stacked images. When assembling z-stacked images, diff --git a/transforms/images/image-assembler-tool/VERSION b/transforms/images/image-assembler-tool/VERSION new file mode 100644 index 000000000..675e6f04f --- /dev/null +++ b/transforms/images/image-assembler-tool/VERSION @@ -0,0 +1 @@ +1.4.1-dev0 diff --git a/transforms/images/image-assembler-tool/build-docker.sh b/transforms/images/image-assembler-tool/build-docker.sh new file mode 100755 index 000000000..1b491d1d9 --- /dev/null +++ b/transforms/images/image-assembler-tool/build-docker.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +version=$(", "Antoine Gerardin "] readme = "README.md" diff --git a/transforms/images/image-assembler-plugin/run-plugin.sh b/transforms/images/image-assembler-tool/run-plugin.sh similarity index 100% rename from transforms/images/image-assembler-plugin/run-plugin.sh rename to transforms/images/image-assembler-tool/run-plugin.sh diff --git a/transforms/images/image-assembler-plugin/src/polus/plugins/transforms/images/image_assembler/__init__.py b/transforms/images/image-assembler-tool/src/polus/images/transforms/images/image_assembler/__init__.py similarity index 89% rename from transforms/images/image-assembler-plugin/src/polus/plugins/transforms/images/image_assembler/__init__.py rename to transforms/images/image-assembler-tool/src/polus/images/transforms/images/image_assembler/__init__.py index 0b49c1e0d..f373d3d52 100644 --- a/transforms/images/image-assembler-plugin/src/polus/plugins/transforms/images/image_assembler/__init__.py +++ b/transforms/images/image-assembler-tool/src/polus/images/transforms/images/image_assembler/__init__.py @@ -1,6 +1,6 @@ """Image Assembler Plugin.""" -__version__ = "1.4.0-dev0" +__version__ = "1.4.1-dev0" from polus.plugins.transforms.images.image_assembler.image_assembler import ( # noqa assemble_images, diff --git a/transforms/images/image-assembler-plugin/src/polus/plugins/transforms/images/image_assembler/__main__.py b/transforms/images/image-assembler-tool/src/polus/images/transforms/images/image_assembler/__main__.py similarity index 97% rename from transforms/images/image-assembler-plugin/src/polus/plugins/transforms/images/image_assembler/__main__.py rename to transforms/images/image-assembler-tool/src/polus/images/transforms/images/image_assembler/__main__.py index 68b46cb96..73c050ea9 100644 --- a/transforms/images/image-assembler-plugin/src/polus/plugins/transforms/images/image_assembler/__main__.py +++ b/transforms/images/image-assembler-tool/src/polus/images/transforms/images/image_assembler/__main__.py @@ -15,7 +15,7 @@ datefmt="%d-%b-%y %H:%M:%S", ) POLUS_LOG = getattr(logging, environ.get("POLUS_LOG", "INFO")) -logger = logging.getLogger("polus.plugins.transforms.images.image_assembler") +logger = logging.getLogger("polus.images.transforms.images.image_assembler") logger.setLevel(POLUS_LOG) logging.getLogger("bfio").setLevel(POLUS_LOG) diff --git a/transforms/images/image-assembler-plugin/src/polus/plugins/transforms/images/image_assembler/image_assembler.py b/transforms/images/image-assembler-tool/src/polus/images/transforms/images/image_assembler/image_assembler.py similarity index 100% rename from transforms/images/image-assembler-plugin/src/polus/plugins/transforms/images/image_assembler/image_assembler.py rename to transforms/images/image-assembler-tool/src/polus/images/transforms/images/image_assembler/image_assembler.py diff --git a/transforms/images/image-assembler-plugin/tests/__init__.py b/transforms/images/image-assembler-tool/tests/__init__.py similarity index 100% rename from transforms/images/image-assembler-plugin/tests/__init__.py rename to transforms/images/image-assembler-tool/tests/__init__.py diff --git a/transforms/images/image-assembler-plugin/tests/conftest.py b/transforms/images/image-assembler-tool/tests/conftest.py similarity index 100% rename from transforms/images/image-assembler-plugin/tests/conftest.py rename to transforms/images/image-assembler-tool/tests/conftest.py diff --git a/transforms/images/image-assembler-plugin/tests/test_cli.py b/transforms/images/image-assembler-tool/tests/test_cli.py similarity index 96% rename from transforms/images/image-assembler-plugin/tests/test_cli.py rename to transforms/images/image-assembler-tool/tests/test_cli.py index d56e5855c..7dfea1868 100644 --- a/transforms/images/image-assembler-plugin/tests/test_cli.py +++ b/transforms/images/image-assembler-tool/tests/test_cli.py @@ -4,7 +4,7 @@ import json from pathlib import Path -from polus.plugins.transforms.images.image_assembler.__main__ import app +from polus.images.transforms.images.image_assembler.__main__ import app from typer.testing import CliRunner faulthandler.enable() diff --git a/transforms/images/image-assembler-plugin/tests/test_image_assembler.py b/transforms/images/image-assembler-tool/tests/test_image_assembler.py similarity index 92% rename from transforms/images/image-assembler-plugin/tests/test_image_assembler.py rename to transforms/images/image-assembler-tool/tests/test_image_assembler.py index 75aa89c68..03327aae7 100644 --- a/transforms/images/image-assembler-plugin/tests/test_image_assembler.py +++ b/transforms/images/image-assembler-tool/tests/test_image_assembler.py @@ -5,7 +5,7 @@ import numpy from bfio import BioReader -from polus.plugins.transforms.images.image_assembler.image_assembler import ( +from polus.images.transforms.images.image_assembler.image_assembler import ( assemble_images, ) diff --git a/transforms/images/image-assembler-plugin/tests/test_nist.py b/transforms/images/image-assembler-tool/tests/test_nist.py similarity index 92% rename from transforms/images/image-assembler-plugin/tests/test_nist.py rename to transforms/images/image-assembler-tool/tests/test_nist.py index 646658bd5..8af93b84f 100644 --- a/transforms/images/image-assembler-plugin/tests/test_nist.py +++ b/transforms/images/image-assembler-tool/tests/test_nist.py @@ -4,7 +4,7 @@ import numpy import pytest -from polus.plugins.transforms.images.image_assembler.image_assembler import ( +from polus.images.transforms.images.image_assembler.image_assembler import ( assemble_images, ) diff --git a/transforms/images/image-calculator-plugin/VERSION b/transforms/images/image-calculator-plugin/VERSION deleted file mode 100644 index 0c62199f1..000000000 --- a/transforms/images/image-calculator-plugin/VERSION +++ /dev/null @@ -1 +0,0 @@ -0.2.1 diff --git a/transforms/images/image-calculator-plugin/build-docker.sh b/transforms/images/image-calculator-plugin/build-docker.sh deleted file mode 100755 index 57b6a5ca4..000000000 --- a/transforms/images/image-calculator-plugin/build-docker.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -version=$(\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? @@ -26,4 +26,4 @@ replace = version = "{new_version}" [bumpversion:file:README.md] -[bumpversion:file:src/polus/plugins/transforms/images/apply_flatfield/__init__.py] +[bumpversion:file:src/polus/images/transforms/images/image_calculator/__init__.py] diff --git a/transforms/images/image-calculator-plugin/Dockerfile b/transforms/images/image-calculator-tool/Dockerfile similarity index 85% rename from transforms/images/image-calculator-plugin/Dockerfile rename to transforms/images/image-calculator-tool/Dockerfile index d2bfbdf49..4f96ca9cd 100644 --- a/transforms/images/image-calculator-plugin/Dockerfile +++ b/transforms/images/image-calculator-tool/Dockerfile @@ -19,5 +19,5 @@ COPY src ${EXEC_DIR}/src RUN pip3 install ${EXEC_DIR} --no-cache-dir -ENTRYPOINT ["python3", "-m", "polus.plugins.transforms.images.image_calculator"] +ENTRYPOINT ["python3", "-m", "polus.images.transforms.images.image_calculator"] CMD ["--help"] diff --git a/transforms/images/image-calculator-plugin/README.md b/transforms/images/image-calculator-tool/README.md similarity index 98% rename from transforms/images/image-calculator-plugin/README.md rename to transforms/images/image-calculator-tool/README.md index 82d83eb50..1a4f6d8f6 100644 --- a/transforms/images/image-calculator-plugin/README.md +++ b/transforms/images/image-calculator-tool/README.md @@ -1,4 +1,4 @@ -# Image Calculator (v0.2.1) +# Image Calculator (v0.2.2-dev0) This plugin performs pixel-wise operations between two image collections. For example, images in one image collection can be subtracted from images in another collection. diff --git a/formats/arrow-to-tabular-plugin/VERSION b/transforms/images/image-calculator-tool/VERSION similarity index 100% rename from formats/arrow-to-tabular-plugin/VERSION rename to transforms/images/image-calculator-tool/VERSION diff --git a/transforms/images/image-calculator-tool/build-docker.sh b/transforms/images/image-calculator-tool/build-docker.sh new file mode 100755 index 000000000..01d49cdfe --- /dev/null +++ b/transforms/images/image-calculator-tool/build-docker.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +version=$(", diff --git a/transforms/images/image-calculator-plugin/run-plugin.sh b/transforms/images/image-calculator-tool/run-plugin.sh similarity index 100% rename from transforms/images/image-calculator-plugin/run-plugin.sh rename to transforms/images/image-calculator-tool/run-plugin.sh diff --git a/transforms/images/image-calculator-plugin/src/polus/plugins/transforms/images/image_calculator/__init__.py b/transforms/images/image-calculator-tool/src/polus/images/transforms/images/image_calculator/__init__.py similarity index 89% rename from transforms/images/image-calculator-plugin/src/polus/plugins/transforms/images/image_calculator/__init__.py rename to transforms/images/image-calculator-tool/src/polus/images/transforms/images/image_calculator/__init__.py index 6f571ef90..06f6b7f4d 100644 --- a/transforms/images/image-calculator-plugin/src/polus/plugins/transforms/images/image_calculator/__init__.py +++ b/transforms/images/image-calculator-tool/src/polus/images/transforms/images/image_calculator/__init__.py @@ -6,4 +6,4 @@ from .calculator import Operation from .calculator import process_image -__version__ = "0.2.1" +__version__ = "0.2.2-dev0" diff --git a/transforms/images/image-calculator-plugin/src/polus/plugins/transforms/images/image_calculator/__main__.py b/transforms/images/image-calculator-tool/src/polus/images/transforms/images/image_calculator/__main__.py similarity index 96% rename from transforms/images/image-calculator-plugin/src/polus/plugins/transforms/images/image_calculator/__main__.py rename to transforms/images/image-calculator-tool/src/polus/images/transforms/images/image_calculator/__main__.py index 3db4bb9c5..3e2927a56 100644 --- a/transforms/images/image-calculator-plugin/src/polus/plugins/transforms/images/image_calculator/__main__.py +++ b/transforms/images/image-calculator-tool/src/polus/images/transforms/images/image_calculator/__main__.py @@ -7,14 +7,14 @@ import filepattern import preadator import typer -from polus.plugins.transforms.images import image_calculator +from polus.images.transforms.images import image_calculator # Initialize the logger logging.basicConfig( format="%(asctime)s - %(name)-8s - %(levelname)-8s - %(message)s", datefmt="%d-%b-%y %H:%M:%S", ) -logger = logging.getLogger("polus.plugins.transforms.images.image_calculator") +logger = logging.getLogger("polus.images.transforms.images.image_calculator") logger.setLevel(image_calculator.POLUS_LOG) app = typer.Typer() diff --git a/transforms/images/image-calculator-plugin/src/polus/plugins/transforms/images/image_calculator/calculator.py b/transforms/images/image-calculator-tool/src/polus/images/transforms/images/image_calculator/calculator.py similarity index 100% rename from transforms/images/image-calculator-plugin/src/polus/plugins/transforms/images/image_calculator/calculator.py rename to transforms/images/image-calculator-tool/src/polus/images/transforms/images/image_calculator/calculator.py diff --git a/transforms/images/image-calculator-plugin/tests/__init__.py b/transforms/images/image-calculator-tool/tests/__init__.py similarity index 100% rename from transforms/images/image-calculator-plugin/tests/__init__.py rename to transforms/images/image-calculator-tool/tests/__init__.py diff --git a/transforms/images/image-calculator-plugin/tests/conftest.py b/transforms/images/image-calculator-tool/tests/conftest.py similarity index 100% rename from transforms/images/image-calculator-plugin/tests/conftest.py rename to transforms/images/image-calculator-tool/tests/conftest.py diff --git a/transforms/images/image-calculator-plugin/tests/test_operations.py b/transforms/images/image-calculator-tool/tests/test_operations.py similarity index 95% rename from transforms/images/image-calculator-plugin/tests/test_operations.py rename to transforms/images/image-calculator-tool/tests/test_operations.py index 58592cafb..1359f79c7 100644 --- a/transforms/images/image-calculator-plugin/tests/test_operations.py +++ b/transforms/images/image-calculator-tool/tests/test_operations.py @@ -10,8 +10,8 @@ import numpy import pytest import typer.testing -from polus.plugins.transforms.images import image_calculator -from polus.plugins.transforms.images.image_calculator.__main__ import app +from polus.images.transforms.images import image_calculator +from polus.images.transforms.images.image_calculator.__main__ import app def _make_random_image( diff --git a/transforms/images/lumos-bleedthrough-correction-plugin/.bumpversion.cfg b/transforms/images/lumos-bleedthrough-correction-plugin/.bumpversion.cfg deleted file mode 100644 index 1b14ace83..000000000 --- a/transforms/images/lumos-bleedthrough-correction-plugin/.bumpversion.cfg +++ /dev/null @@ -1,29 +0,0 @@ -[bumpversion] -current_version = 0.1.1-dev0 -commit = True -tag = False -parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? -serialize = - {major}.{minor}.{patch}-{release}{dev} - {major}.{minor}.{patch} - -[bumpversion:part:release] -optional_value = _ -first_value = dev -values = - dev - _ - -[bumpversion:part:dev] - -[bumpversion:file:pyproject.toml] -search = version = "{current_version}" -replace = version = "{new_version}" - -[bumpversion:file:plugin.json] - -[bumpversion:file:VERSION] - -[bumpversion:file:README.md] - -[bumpversion:file:src/polus/plugins/transforms/images/lumos_bleedthrough_correction/__init__.py] diff --git a/transforms/images/lumos-bleedthrough-correction-plugin/VERSION b/transforms/images/lumos-bleedthrough-correction-plugin/VERSION deleted file mode 100644 index 44bf4db83..000000000 --- a/transforms/images/lumos-bleedthrough-correction-plugin/VERSION +++ /dev/null @@ -1 +0,0 @@ -0.1.1-dev0 diff --git a/transforms/images/lumos-bleedthrough-correction-plugin/build-docker.sh b/transforms/images/lumos-bleedthrough-correction-plugin/build-docker.sh deleted file mode 100755 index 677b3b1be..000000000 --- a/transforms/images/lumos-bleedthrough-correction-plugin/build-docker.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -version=$(\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? +serialize = + {major}.{minor}.{patch}-{release}{dev} + {major}.{minor}.{patch} + +[bumpversion:part:release] +optional_value = _ +first_value = dev +values = + dev + _ + +[bumpversion:part:dev] + +[bumpversion:file:pyproject.toml] +search = version = "{current_version}" +replace = version = "{new_version}" + +[bumpversion:file:plugin.json] + +[bumpversion:file:VERSION] + +[bumpversion:file:README.md] + +[bumpversion:file:src/polus/images/transforms/images/lumos_bleedthrough_correction/__init__.py] diff --git a/transforms/images/lumos-bleedthrough-correction-plugin/Dockerfile b/transforms/images/lumos-bleedthrough-correction-tool/Dockerfile similarity index 84% rename from transforms/images/lumos-bleedthrough-correction-plugin/Dockerfile rename to transforms/images/lumos-bleedthrough-correction-tool/Dockerfile index 8276be765..30a5adad9 100644 --- a/transforms/images/lumos-bleedthrough-correction-plugin/Dockerfile +++ b/transforms/images/lumos-bleedthrough-correction-tool/Dockerfile @@ -19,5 +19,5 @@ COPY src ${EXEC_DIR}/src RUN pip3 install ${EXEC_DIR} --no-cache-dir -ENTRYPOINT ["python3", "-m", "polus.plugins.transforms.images.lumos_bleedthrough_correction"] +ENTRYPOINT ["python3", "-m", "polus.images.transforms.images.lumos_bleedthrough_correction"] CMD ["--help"] diff --git a/transforms/images/lumos-bleedthrough-correction-plugin/README.md b/transforms/images/lumos-bleedthrough-correction-tool/README.md similarity index 98% rename from transforms/images/lumos-bleedthrough-correction-plugin/README.md rename to transforms/images/lumos-bleedthrough-correction-tool/README.md index a21f736d1..a105d242d 100644 --- a/transforms/images/lumos-bleedthrough-correction-plugin/README.md +++ b/transforms/images/lumos-bleedthrough-correction-tool/README.md @@ -1,4 +1,4 @@ -# LUMoS Bleedthrough Correction Plugin (v0.1.1-dev0) +# LUMoS Bleedthrough Correction Plugin (v0.1.2-dev0) This WIPP plugin will take a collection of images and use the LUMoS [1] bleedthrough correction algorithm to separate out the signal for each fluorophore. This is a reimplementation, in Python, of the authors' original [Java](https://github.com/tristan-mcrae-rochester/Multiphoton-Image-Analysis/blob/master/Spectral%20Unmixing/Code/ImageJ-FIJI/LUMoS_Spectral_Unmixing.java) and [Matlab](https://github.com/tristan-mcrae-rochester/Multiphoton-Image-Analysis/blob/master/Spectral%20Unmixing/Code/k_means_unmixing_circ/KMeansUnmixing.m) versions. diff --git a/transforms/images/lumos-bleedthrough-correction-tool/VERSION b/transforms/images/lumos-bleedthrough-correction-tool/VERSION new file mode 100644 index 000000000..9d8d2c119 --- /dev/null +++ b/transforms/images/lumos-bleedthrough-correction-tool/VERSION @@ -0,0 +1 @@ +0.1.2-dev0 diff --git a/transforms/images/lumos-bleedthrough-correction-tool/build-docker.sh b/transforms/images/lumos-bleedthrough-correction-tool/build-docker.sh new file mode 100755 index 000000000..3deeda1de --- /dev/null +++ b/transforms/images/lumos-bleedthrough-correction-tool/build-docker.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +version=$("] readme = "README.md" diff --git a/transforms/images/lumos-bleedthrough-correction-plugin/run-plugin.sh b/transforms/images/lumos-bleedthrough-correction-tool/run-plugin.sh similarity index 100% rename from transforms/images/lumos-bleedthrough-correction-plugin/run-plugin.sh rename to transforms/images/lumos-bleedthrough-correction-tool/run-plugin.sh diff --git a/transforms/images/lumos-bleedthrough-correction-plugin/src/polus/plugins/transforms/images/lumos_bleedthrough_correction/__init__.py b/transforms/images/lumos-bleedthrough-correction-tool/src/polus/images/transforms/images/lumos_bleedthrough_correction/__init__.py similarity index 76% rename from transforms/images/lumos-bleedthrough-correction-plugin/src/polus/plugins/transforms/images/lumos_bleedthrough_correction/__init__.py rename to transforms/images/lumos-bleedthrough-correction-tool/src/polus/images/transforms/images/lumos_bleedthrough_correction/__init__.py index ffc6d0a24..c77ffdc87 100644 --- a/transforms/images/lumos-bleedthrough-correction-plugin/src/polus/plugins/transforms/images/lumos_bleedthrough_correction/__init__.py +++ b/transforms/images/lumos-bleedthrough-correction-tool/src/polus/images/transforms/images/lumos_bleedthrough_correction/__init__.py @@ -3,4 +3,4 @@ from . import lumos from . import utils -__version__ = "0.1.1-dev0" +__version__ = "0.1.2-dev0" diff --git a/transforms/images/lumos-bleedthrough-correction-plugin/src/polus/plugins/transforms/images/lumos_bleedthrough_correction/__main__.py b/transforms/images/lumos-bleedthrough-correction-tool/src/polus/images/transforms/images/lumos_bleedthrough_correction/__main__.py similarity index 93% rename from transforms/images/lumos-bleedthrough-correction-plugin/src/polus/plugins/transforms/images/lumos_bleedthrough_correction/__main__.py rename to transforms/images/lumos-bleedthrough-correction-tool/src/polus/images/transforms/images/lumos_bleedthrough_correction/__main__.py index 86b9bc383..966a34a7d 100644 --- a/transforms/images/lumos-bleedthrough-correction-plugin/src/polus/plugins/transforms/images/lumos_bleedthrough_correction/__main__.py +++ b/transforms/images/lumos-bleedthrough-correction-tool/src/polus/images/transforms/images/lumos_bleedthrough_correction/__main__.py @@ -8,8 +8,8 @@ import filepattern import tqdm import typer -from polus.plugins.transforms.images.lumos_bleedthrough_correction import lumos -from polus.plugins.transforms.images.lumos_bleedthrough_correction import utils +from polus.images.transforms.images.lumos_bleedthrough_correction import lumos +from polus.images.transforms.images.lumos_bleedthrough_correction import utils # Initialize the logger logging.basicConfig( @@ -17,7 +17,7 @@ datefmt="%d-%b-%y %H:%M:%S", ) logger = logging.getLogger( - "polus.plugins.transforms.images.lumos_bleedthrough_correction", + "polus.images.transforms.images.lumos_bleedthrough_correction", ) logger.setLevel(utils.POLUS_LOG) diff --git a/transforms/images/lumos-bleedthrough-correction-plugin/src/polus/plugins/transforms/images/lumos_bleedthrough_correction/lumos.py b/transforms/images/lumos-bleedthrough-correction-tool/src/polus/images/transforms/images/lumos_bleedthrough_correction/lumos.py similarity index 100% rename from transforms/images/lumos-bleedthrough-correction-plugin/src/polus/plugins/transforms/images/lumos_bleedthrough_correction/lumos.py rename to transforms/images/lumos-bleedthrough-correction-tool/src/polus/images/transforms/images/lumos_bleedthrough_correction/lumos.py diff --git a/transforms/images/lumos-bleedthrough-correction-plugin/src/polus/plugins/transforms/images/lumos_bleedthrough_correction/utils.py b/transforms/images/lumos-bleedthrough-correction-tool/src/polus/images/transforms/images/lumos_bleedthrough_correction/utils.py similarity index 100% rename from transforms/images/lumos-bleedthrough-correction-plugin/src/polus/plugins/transforms/images/lumos_bleedthrough_correction/utils.py rename to transforms/images/lumos-bleedthrough-correction-tool/src/polus/images/transforms/images/lumos_bleedthrough_correction/utils.py diff --git a/transforms/images/lumos-bleedthrough-correction-plugin/tests/__init__.py b/transforms/images/lumos-bleedthrough-correction-tool/tests/__init__.py similarity index 100% rename from transforms/images/lumos-bleedthrough-correction-plugin/tests/__init__.py rename to transforms/images/lumos-bleedthrough-correction-tool/tests/__init__.py diff --git a/transforms/images/lumos-bleedthrough-correction-plugin/tests/test_lumos.py b/transforms/images/lumos-bleedthrough-correction-tool/tests/test_lumos.py similarity index 94% rename from transforms/images/lumos-bleedthrough-correction-plugin/tests/test_lumos.py rename to transforms/images/lumos-bleedthrough-correction-tool/tests/test_lumos.py index 2fbb825e0..b2d9cef3e 100644 --- a/transforms/images/lumos-bleedthrough-correction-plugin/tests/test_lumos.py +++ b/transforms/images/lumos-bleedthrough-correction-tool/tests/test_lumos.py @@ -10,9 +10,9 @@ import numpy import pytest import typer.testing -from polus.plugins.transforms.images.lumos_bleedthrough_correction import lumos -from polus.plugins.transforms.images.lumos_bleedthrough_correction import utils -from polus.plugins.transforms.images.lumos_bleedthrough_correction.__main__ import app +from polus.images.transforms.images.lumos_bleedthrough_correction import lumos +from polus.images.transforms.images.lumos_bleedthrough_correction import utils +from polus.images.transforms.images.lumos_bleedthrough_correction.__main__ import app from skimage import data diff --git a/transforms/images/montage-plugin/VERSION b/transforms/images/montage-plugin/VERSION deleted file mode 100644 index 8f0916f76..000000000 --- a/transforms/images/montage-plugin/VERSION +++ /dev/null @@ -1 +0,0 @@ -0.5.0 diff --git a/transforms/images/montage-plugin/build-docker.sh b/transforms/images/montage-plugin/build-docker.sh deleted file mode 100755 index 3f7bf57c0..000000000 --- a/transforms/images/montage-plugin/build-docker.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -version=$(\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? @@ -20,10 +20,10 @@ values = search = version = "{current_version}" replace = version = "{new_version}" +[bumpversion:file:plugin.json] + [bumpversion:file:VERSION] [bumpversion:file:README.md] -[bumpversion:file:plugin.json] - -[bumpversion:file:src/polus/plugins/clustering/outlier_removal/__init__.py] +[bumpversion:file:src/polus/images/transforms/images/montage/__init__.py] diff --git a/transforms/images/montage-plugin/Dockerfile b/transforms/images/montage-tool/Dockerfile similarity index 88% rename from transforms/images/montage-plugin/Dockerfile rename to transforms/images/montage-tool/Dockerfile index a630034bd..73179903f 100644 --- a/transforms/images/montage-plugin/Dockerfile +++ b/transforms/images/montage-tool/Dockerfile @@ -18,5 +18,5 @@ COPY src ${EXEC_DIR}/src RUN pip3 install ${EXEC_DIR} --no-cache-dir -ENTRYPOINT ["python3", "-m", "polus.plugins.transforms.images.montage"] +ENTRYPOINT ["python3", "-m", "polus.images.transforms.images.montage"] CMD ["--help"] diff --git a/transforms/images/montage-plugin/README.md b/transforms/images/montage-tool/README.md similarity index 99% rename from transforms/images/montage-plugin/README.md rename to transforms/images/montage-tool/README.md index a02cfbc32..5f05d1e3d 100644 --- a/transforms/images/montage-plugin/README.md +++ b/transforms/images/montage-tool/README.md @@ -1,4 +1,4 @@ -# Montage (v0.5.0) +# Montage (v0.5.1-dev0) This plugin generates a stitching vector that will montage images together. The inputs are an image collection, a file pattern, and a layout array that diff --git a/transforms/images/montage-tool/VERSION b/transforms/images/montage-tool/VERSION new file mode 100644 index 000000000..6f9bb2cc0 --- /dev/null +++ b/transforms/images/montage-tool/VERSION @@ -0,0 +1 @@ +0.5.1-dev0 diff --git a/transforms/images/montage-tool/build-docker.sh b/transforms/images/montage-tool/build-docker.sh new file mode 100755 index 000000000..4ba1d08b4 --- /dev/null +++ b/transforms/images/montage-tool/build-docker.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +version=$("] readme = "README.md" diff --git a/transforms/images/montage-plugin/run-plugin.sh b/transforms/images/montage-tool/run-plugin.sh similarity index 100% rename from transforms/images/montage-plugin/run-plugin.sh rename to transforms/images/montage-tool/run-plugin.sh diff --git a/transforms/images/montage-plugin/src/polus/plugins/transforms/images/montage/__init__.py b/transforms/images/montage-tool/src/polus/images/transforms/images/montage/__init__.py similarity index 96% rename from transforms/images/montage-plugin/src/polus/plugins/transforms/images/montage/__init__.py rename to transforms/images/montage-tool/src/polus/images/transforms/images/montage/__init__.py index 99723ba22..61175c547 100644 --- a/transforms/images/montage-plugin/src/polus/plugins/transforms/images/montage/__init__.py +++ b/transforms/images/montage-tool/src/polus/images/transforms/images/montage/__init__.py @@ -1,6 +1,6 @@ """The image montaging tool.""" -__version__ = "0.5.0" +__version__ = "0.5.1-dev0" from polus.plugins.transforms.images.montage.montage import ( # noqa diff --git a/transforms/images/montage-plugin/src/polus/plugins/transforms/images/montage/__main__.py b/transforms/images/montage-tool/src/polus/images/transforms/images/montage/__main__.py similarity index 92% rename from transforms/images/montage-plugin/src/polus/plugins/transforms/images/montage/__main__.py rename to transforms/images/montage-tool/src/polus/images/transforms/images/montage/__main__.py index 89d27ed86..86bbab010 100644 --- a/transforms/images/montage-plugin/src/polus/plugins/transforms/images/montage/__main__.py +++ b/transforms/images/montage-tool/src/polus/images/transforms/images/montage/__main__.py @@ -7,12 +7,12 @@ import typer -from polus.plugins.transforms.images.montage import ( +from polus.images.transforms.images.montage import ( __version__, generate_montage_patterns, montage_all, ) -from polus.plugins.transforms.images.montage.montage import MULTIPLIER, SPACING +from polus.images.transforms.images.montage.montage import MULTIPLIER, SPACING app = typer.Typer() @@ -21,7 +21,7 @@ format="%(asctime)s - %(name)-8s - %(levelname)-8s - %(message)s", datefmt="%d-%b-%y %H:%M:%S", ) -logger = logging.getLogger("polus.plugins.transforms.images.montage") +logger = logging.getLogger("polus.images.transforms.images.montage") logger.setLevel(os.environ.get("POLUS_LOG", logging.INFO)) diff --git a/transforms/images/montage-plugin/src/polus/plugins/transforms/images/montage/montage.py b/transforms/images/montage-tool/src/polus/images/transforms/images/montage/montage.py similarity index 100% rename from transforms/images/montage-plugin/src/polus/plugins/transforms/images/montage/montage.py rename to transforms/images/montage-tool/src/polus/images/transforms/images/montage/montage.py diff --git a/transforms/images/montage-plugin/src/polus/plugins/transforms/images/montage/utils.py b/transforms/images/montage-tool/src/polus/images/transforms/images/montage/utils.py similarity index 100% rename from transforms/images/montage-plugin/src/polus/plugins/transforms/images/montage/utils.py rename to transforms/images/montage-tool/src/polus/images/transforms/images/montage/utils.py diff --git a/transforms/images/montage-plugin/tests/__init__.py b/transforms/images/montage-tool/tests/__init__.py similarity index 100% rename from transforms/images/montage-plugin/tests/__init__.py rename to transforms/images/montage-tool/tests/__init__.py diff --git a/transforms/images/montage-plugin/tests/test_montage.py b/transforms/images/montage-tool/tests/test_montage.py similarity index 93% rename from transforms/images/montage-plugin/tests/test_montage.py rename to transforms/images/montage-tool/tests/test_montage.py index dd8c54b1d..2786ce5ac 100644 --- a/transforms/images/montage-plugin/tests/test_montage.py +++ b/transforms/images/montage-tool/tests/test_montage.py @@ -8,9 +8,9 @@ from bfio import BioWriter as BioWriter from typer.testing import CliRunner -from polus.plugins.transforms.images.montage import montage as montage -from polus.plugins.transforms.images.montage import subpattern as subpattern -from polus.plugins.transforms.images.montage.__main__ import app as app +from polus.images.transforms.images.montage import montage as montage +from polus.images.transforms.images.montage import subpattern as subpattern +from polus.images.transforms.images.montage.__main__ import app as app test_data_path = Path(__file__).parent.joinpath("data") diff --git a/transforms/images/roi-relabel-plugin/build-docker.sh b/transforms/images/roi-relabel-plugin/build-docker.sh deleted file mode 100755 index 0481444ef..000000000 --- a/transforms/images/roi-relabel-plugin/build-docker.sh +++ /dev/null @@ -1,5 +0,0 @@ -#!/bin/bash - -version=$(\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? +serialize = + {major}.{minor}.{patch}-{release}{dev} + {major}.{minor}.{patch} + +[bumpversion:part:release] +optional_value = _ +first_value = dev +values = + dev + _ + +[bumpversion:part:dev] + +[bumpversion:file:pyproject.toml] +search = version = "{current_version}" +replace = version = "{new_version}" + +[bumpversion:file:plugin.json] + +[bumpversion:file:VERSION] + +[bumpversion:file:README.md] + +[bumpversion:file:src/polus/images/transforms/images/roi_relabel/__init__.py] diff --git a/transforms/images/roi-relabel-plugin/.dockerignore b/transforms/images/roi-relabel-tool/.dockerignore similarity index 100% rename from transforms/images/roi-relabel-plugin/.dockerignore rename to transforms/images/roi-relabel-tool/.dockerignore diff --git a/transforms/images/roi-relabel-plugin/.gitignore b/transforms/images/roi-relabel-tool/.gitignore similarity index 100% rename from transforms/images/roi-relabel-plugin/.gitignore rename to transforms/images/roi-relabel-tool/.gitignore diff --git a/transforms/images/roi-relabel-plugin/Dockerfile b/transforms/images/roi-relabel-tool/Dockerfile similarity index 87% rename from transforms/images/roi-relabel-plugin/Dockerfile rename to transforms/images/roi-relabel-tool/Dockerfile index b63a0dcff..79fbeb8be 100644 --- a/transforms/images/roi-relabel-plugin/Dockerfile +++ b/transforms/images/roi-relabel-tool/Dockerfile @@ -18,5 +18,5 @@ COPY src ${EXEC_DIR}/src RUN pip3 install ${EXEC_DIR} --no-cache-dir -ENTRYPOINT ["python3", "-m", "polus.plugins.transforms.images.roi_relabel"] +ENTRYPOINT ["python3", "-m", "polus.images.transforms.images.roi_relabel"] CMD ["--help"] diff --git a/transforms/images/roi-relabel-plugin/README.md b/transforms/images/roi-relabel-tool/README.md similarity index 99% rename from transforms/images/roi-relabel-plugin/README.md rename to transforms/images/roi-relabel-tool/README.md index 7ea7832e5..0e35e2b79 100644 --- a/transforms/images/roi-relabel-plugin/README.md +++ b/transforms/images/roi-relabel-tool/README.md @@ -1,4 +1,4 @@ -# ROI Relabel Plugin (v0.2.4-dev0) +# ROI Relabel Plugin (v0.2.5-dev0) This WIPP plugin relabels and consolidates Regions of Interest (RoIs) in a segmented or hand-labeled image. diff --git a/transforms/images/roi-relabel-tool/VERSION b/transforms/images/roi-relabel-tool/VERSION new file mode 100644 index 000000000..0eac58ed7 --- /dev/null +++ b/transforms/images/roi-relabel-tool/VERSION @@ -0,0 +1 @@ +0.2.5-dev0 diff --git a/transforms/images/roi-relabel-tool/build-docker.sh b/transforms/images/roi-relabel-tool/build-docker.sh new file mode 100755 index 000000000..ab3559ce1 --- /dev/null +++ b/transforms/images/roi-relabel-tool/build-docker.sh @@ -0,0 +1,5 @@ +#!/bin/bash + +version=$("] readme = "README.md" diff --git a/transforms/images/roi-relabel-plugin/run-plugin.sh b/transforms/images/roi-relabel-tool/run-plugin.sh similarity index 100% rename from transforms/images/roi-relabel-plugin/run-plugin.sh rename to transforms/images/roi-relabel-tool/run-plugin.sh diff --git a/transforms/images/roi-relabel-plugin/src/polus/plugins/transforms/images/roi_relabel/__init__.py b/transforms/images/roi-relabel-tool/src/polus/images/transforms/images/roi_relabel/__init__.py similarity index 80% rename from transforms/images/roi-relabel-plugin/src/polus/plugins/transforms/images/roi_relabel/__init__.py rename to transforms/images/roi-relabel-tool/src/polus/images/transforms/images/roi_relabel/__init__.py index dc4848b79..33f190cb2 100644 --- a/transforms/images/roi-relabel-plugin/src/polus/plugins/transforms/images/roi_relabel/__init__.py +++ b/transforms/images/roi-relabel-tool/src/polus/images/transforms/images/roi_relabel/__init__.py @@ -4,4 +4,4 @@ from .methods import relabel from .utils import helpers -__version__ = "0.2.4-dev0" +__version__ = "0.2.5-dev0" diff --git a/transforms/images/roi-relabel-plugin/src/polus/plugins/transforms/images/roi_relabel/__main__.py b/transforms/images/roi-relabel-tool/src/polus/images/transforms/images/roi_relabel/__main__.py similarity index 93% rename from transforms/images/roi-relabel-plugin/src/polus/plugins/transforms/images/roi_relabel/__main__.py rename to transforms/images/roi-relabel-tool/src/polus/images/transforms/images/roi_relabel/__main__.py index 65b69254f..6dd73ca17 100644 --- a/transforms/images/roi-relabel-plugin/src/polus/plugins/transforms/images/roi_relabel/__main__.py +++ b/transforms/images/roi-relabel-tool/src/polus/images/transforms/images/roi_relabel/__main__.py @@ -8,14 +8,14 @@ import filepattern as fp import typer -from polus.plugins.transforms.images.roi_relabel import methods -from polus.plugins.transforms.images.roi_relabel import utils +from polus.images.transforms.images.roi_relabel import methods +from polus.images.transforms.images.roi_relabel import utils logging.basicConfig( format="%(asctime)s - %(levelname)s - %(name)s - %(funcName)s - %(message)s", datefmt="%d-%b-%y %H:%M:%S", ) -logger = logging.getLogger("polus.plugins.transforms.images.roi_relabel") +logger = logging.getLogger("polus.images.transforms.images.roi_relabel") logger.setLevel(utils.constants.POLUS_LOG) app = typer.Typer() diff --git a/transforms/images/roi-relabel-plugin/src/polus/plugins/transforms/images/roi_relabel/methods/__init__.py b/transforms/images/roi-relabel-tool/src/polus/images/transforms/images/roi_relabel/methods/__init__.py similarity index 100% rename from transforms/images/roi-relabel-plugin/src/polus/plugins/transforms/images/roi_relabel/methods/__init__.py rename to transforms/images/roi-relabel-tool/src/polus/images/transforms/images/roi_relabel/methods/__init__.py diff --git a/transforms/images/roi-relabel-plugin/src/polus/plugins/transforms/images/roi_relabel/methods/graph.py b/transforms/images/roi-relabel-tool/src/polus/images/transforms/images/roi_relabel/methods/graph.py similarity index 100% rename from transforms/images/roi-relabel-plugin/src/polus/plugins/transforms/images/roi_relabel/methods/graph.py rename to transforms/images/roi-relabel-tool/src/polus/images/transforms/images/roi_relabel/methods/graph.py diff --git a/transforms/images/roi-relabel-plugin/src/polus/plugins/transforms/images/roi_relabel/methods/roi.py b/transforms/images/roi-relabel-tool/src/polus/images/transforms/images/roi_relabel/methods/roi.py similarity index 100% rename from transforms/images/roi-relabel-plugin/src/polus/plugins/transforms/images/roi_relabel/methods/roi.py rename to transforms/images/roi-relabel-tool/src/polus/images/transforms/images/roi_relabel/methods/roi.py diff --git a/transforms/images/roi-relabel-plugin/src/polus/plugins/transforms/images/roi_relabel/utils/__init__.py b/transforms/images/roi-relabel-tool/src/polus/images/transforms/images/roi_relabel/utils/__init__.py similarity index 100% rename from transforms/images/roi-relabel-plugin/src/polus/plugins/transforms/images/roi_relabel/utils/__init__.py rename to transforms/images/roi-relabel-tool/src/polus/images/transforms/images/roi_relabel/utils/__init__.py diff --git a/transforms/images/roi-relabel-plugin/src/polus/plugins/transforms/images/roi_relabel/utils/constants.py b/transforms/images/roi-relabel-tool/src/polus/images/transforms/images/roi_relabel/utils/constants.py similarity index 100% rename from transforms/images/roi-relabel-plugin/src/polus/plugins/transforms/images/roi_relabel/utils/constants.py rename to transforms/images/roi-relabel-tool/src/polus/images/transforms/images/roi_relabel/utils/constants.py diff --git a/transforms/images/roi-relabel-plugin/src/polus/plugins/transforms/images/roi_relabel/utils/helpers.py b/transforms/images/roi-relabel-tool/src/polus/images/transforms/images/roi_relabel/utils/helpers.py similarity index 100% rename from transforms/images/roi-relabel-plugin/src/polus/plugins/transforms/images/roi_relabel/utils/helpers.py rename to transforms/images/roi-relabel-tool/src/polus/images/transforms/images/roi_relabel/utils/helpers.py diff --git a/transforms/images/roi-relabel-plugin/src/polus/plugins/transforms/images/roi_relabel/utils/types.py b/transforms/images/roi-relabel-tool/src/polus/images/transforms/images/roi_relabel/utils/types.py similarity index 100% rename from transforms/images/roi-relabel-plugin/src/polus/plugins/transforms/images/roi_relabel/utils/types.py rename to transforms/images/roi-relabel-tool/src/polus/images/transforms/images/roi_relabel/utils/types.py diff --git a/transforms/images/roi-relabel-plugin/tests/__init__.py b/transforms/images/roi-relabel-tool/tests/__init__.py similarity index 100% rename from transforms/images/roi-relabel-plugin/tests/__init__.py rename to transforms/images/roi-relabel-tool/tests/__init__.py diff --git a/transforms/images/roi-relabel-plugin/tests/test_relabel.py b/transforms/images/roi-relabel-tool/tests/test_relabel.py similarity index 97% rename from transforms/images/roi-relabel-plugin/tests/test_relabel.py rename to transforms/images/roi-relabel-tool/tests/test_relabel.py index 4cf88c532..72b220057 100644 --- a/transforms/images/roi-relabel-plugin/tests/test_relabel.py +++ b/transforms/images/roi-relabel-tool/tests/test_relabel.py @@ -13,8 +13,8 @@ from skimage.measure import label from skimage.segmentation import relabel_sequential -from polus.plugins.transforms.images.roi_relabel import methods, relabel -from polus.plugins.transforms.images.roi_relabel.__main__ import app +from polus.images.transforms.images.roi_relabel import methods, relabel +from polus.images.transforms.images.roi_relabel.__main__ import app runner = typer.testing.CliRunner() diff --git a/transforms/tabular/tabular-merger-plugin/.bumpversion.cfg b/transforms/tabular/tabular-merger-plugin/.bumpversion.cfg deleted file mode 100644 index 37dd699ec..000000000 --- a/transforms/tabular/tabular-merger-plugin/.bumpversion.cfg +++ /dev/null @@ -1,27 +0,0 @@ -[bumpversion] -current_version = 0.1.1-dev0 -commit = True -tag = False -parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? -serialize = - {major}.{minor}.{patch}-{release}{dev} - {major}.{minor}.{patch} - -[bumpversion:part:release] -optional_value = _ -first_value = dev -values = - dev - _ - -[bumpversion:part:dev] - -[bumpversion:file:pyproject.toml] -search = version = "{current_version}" -replace = version = "{new_version}" - -[bumpversion:file:plugin.json] - -[bumpversion:file:VERSION] - -[bumpversion:file:src/polus/plugins/transforms/tabular/tabular_merger/__init__.py] diff --git a/transforms/tabular/tabular-merger-plugin/VERSION b/transforms/tabular/tabular-merger-plugin/VERSION deleted file mode 100644 index 44bf4db83..000000000 --- a/transforms/tabular/tabular-merger-plugin/VERSION +++ /dev/null @@ -1 +0,0 @@ -0.1.1-dev0 diff --git a/transforms/tabular/tabular-merger-plugin/build-docker.sh b/transforms/tabular/tabular-merger-plugin/build-docker.sh deleted file mode 100755 index 1dbbf889a..000000000 --- a/transforms/tabular/tabular-merger-plugin/build-docker.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -version=$(\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? @@ -24,4 +24,4 @@ replace = version = "{new_version}" [bumpversion:file:VERSION] -[bumpversion:file:src/polus/plugins/formats/tabular_converter/__init__.py] +[bumpversion:file:src/polus/images/transforms/tabular/tabular_merger/__init__.py] diff --git a/transforms/tabular/tabular-merger-plugin/Dockerfile b/transforms/tabular/tabular-merger-tool/Dockerfile similarity index 86% rename from transforms/tabular/tabular-merger-plugin/Dockerfile rename to transforms/tabular/tabular-merger-tool/Dockerfile index 73c12405f..a851ae274 100755 --- a/transforms/tabular/tabular-merger-plugin/Dockerfile +++ b/transforms/tabular/tabular-merger-tool/Dockerfile @@ -17,5 +17,5 @@ COPY src ${EXEC_DIR}/src RUN pip3 install ${EXEC_DIR} --no-cache-dir -ENTRYPOINT ["python3", "-m", "polus.plugins.transforms.tabular.tabular_merger"] +ENTRYPOINT ["python3", "-m", "polus.images.transforms.tabular.tabular_merger"] CMD ["--help"] diff --git a/transforms/tabular/tabular-merger-plugin/README.md b/transforms/tabular/tabular-merger-tool/README.md similarity index 100% rename from transforms/tabular/tabular-merger-plugin/README.md rename to transforms/tabular/tabular-merger-tool/README.md diff --git a/transforms/tabular/tabular-merger-tool/VERSION b/transforms/tabular/tabular-merger-tool/VERSION new file mode 100644 index 000000000..9d8d2c119 --- /dev/null +++ b/transforms/tabular/tabular-merger-tool/VERSION @@ -0,0 +1 @@ +0.1.2-dev0 diff --git a/transforms/tabular/tabular-merger-tool/build-docker.sh b/transforms/tabular/tabular-merger-tool/build-docker.sh new file mode 100755 index 000000000..c2f27e88c --- /dev/null +++ b/transforms/tabular/tabular-merger-tool/build-docker.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +version=$(", diff --git a/transforms/tabular/tabular-merger-plugin/run-plugin.sh b/transforms/tabular/tabular-merger-tool/run-plugin.sh similarity index 100% rename from transforms/tabular/tabular-merger-plugin/run-plugin.sh rename to transforms/tabular/tabular-merger-tool/run-plugin.sh diff --git a/transforms/tabular/tabular-merger-plugin/src/polus/plugins/transforms/tabular/tabular_merger/__init__.py b/transforms/tabular/tabular-merger-tool/src/polus/images/transforms/tabular/tabular_merger/__init__.py similarity index 78% rename from transforms/tabular/tabular-merger-plugin/src/polus/plugins/transforms/tabular/tabular_merger/__init__.py rename to transforms/tabular/tabular-merger-tool/src/polus/images/transforms/tabular/tabular_merger/__init__.py index 7d8148ce0..665b22bd0 100644 --- a/transforms/tabular/tabular-merger-plugin/src/polus/plugins/transforms/tabular/tabular_merger/__init__.py +++ b/transforms/tabular/tabular-merger-tool/src/polus/images/transforms/tabular/tabular_merger/__init__.py @@ -1,4 +1,4 @@ """Tabular Merger.""" -__version__ = "0.1.1-dev0" +__version__ = "0.1.2-dev0" from polus.plugins.transforms.tabular.tabular_merger import tabular_merger diff --git a/transforms/tabular/tabular-merger-plugin/src/polus/plugins/transforms/tabular/tabular_merger/__main__.py b/transforms/tabular/tabular-merger-tool/src/polus/images/transforms/tabular/tabular_merger/__main__.py similarity index 95% rename from transforms/tabular/tabular-merger-plugin/src/polus/plugins/transforms/tabular/tabular_merger/__main__.py rename to transforms/tabular/tabular-merger-tool/src/polus/images/transforms/tabular/tabular_merger/__main__.py index da5fae6ce..01b74212b 100644 --- a/transforms/tabular/tabular-merger-plugin/src/polus/plugins/transforms/tabular/tabular_merger/__main__.py +++ b/transforms/tabular/tabular-merger-tool/src/polus/images/transforms/tabular/tabular_merger/__main__.py @@ -9,7 +9,7 @@ import filepattern as fp import typer -from polus.plugins.transforms.tabular.tabular_merger import tabular_merger as tm +from polus.images.transforms.tabular.tabular_merger import tabular_merger as tm app = typer.Typer() @@ -18,7 +18,7 @@ format="%(asctime)s - %(name)-8s - %(levelname)-8s - %(message)s", datefmt="%d-%b-%y %H:%M:%S", ) -logger = logging.getLogger("polus.plugins.transforms.tabular_merger") +logger = logging.getLogger("polus.images.transforms.tabular_merger") logger.setLevel(os.environ.get("POLUS_LOG", logging.INFO)) POLUS_TAB_EXT = os.environ.get("POLUS_TAB_EXT", ".arrow") diff --git a/transforms/tabular/tabular-merger-plugin/src/polus/plugins/transforms/tabular/tabular_merger/tabular_merger.py b/transforms/tabular/tabular-merger-tool/src/polus/images/transforms/tabular/tabular_merger/tabular_merger.py similarity index 100% rename from transforms/tabular/tabular-merger-plugin/src/polus/plugins/transforms/tabular/tabular_merger/tabular_merger.py rename to transforms/tabular/tabular-merger-tool/src/polus/images/transforms/tabular/tabular_merger/tabular_merger.py diff --git a/transforms/tabular/tabular-merger-plugin/tests/__init__.py b/transforms/tabular/tabular-merger-tool/tests/__init__.py similarity index 100% rename from transforms/tabular/tabular-merger-plugin/tests/__init__.py rename to transforms/tabular/tabular-merger-tool/tests/__init__.py diff --git a/transforms/tabular/tabular-merger-plugin/tests/test_main.py b/transforms/tabular/tabular-merger-tool/tests/test_main.py similarity index 98% rename from transforms/tabular/tabular-merger-plugin/tests/test_main.py rename to transforms/tabular/tabular-merger-tool/tests/test_main.py index 30b26cf5b..5b8bdffdd 100644 --- a/transforms/tabular/tabular-merger-plugin/tests/test_main.py +++ b/transforms/tabular/tabular-merger-tool/tests/test_main.py @@ -10,7 +10,7 @@ import pandas as pd import pytest import vaex -from polus.plugins.transforms.tabular.tabular_merger import tabular_merger as tm +from polus.images.transforms.tabular.tabular_merger import tabular_merger as tm class Generatedata: diff --git a/transforms/tabular/tabular-thresholding-plugin/.bumpversion.cfg b/transforms/tabular/tabular-thresholding-plugin/.bumpversion.cfg deleted file mode 100644 index ceedd52f3..000000000 --- a/transforms/tabular/tabular-thresholding-plugin/.bumpversion.cfg +++ /dev/null @@ -1,27 +0,0 @@ -[bumpversion] -current_version = 0.1.5-dev0 -commit = True -tag = False -parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? -serialize = - {major}.{minor}.{patch}-{release}{dev} - {major}.{minor}.{patch} - -[bumpversion:part:release] -optional_value = _ -first_value = dev -values = - dev - _ - -[bumpversion:part:dev] - -[bumpversion:file:pyproject.toml] -search = version = "{current_version}" -replace = version = "{new_version}" - -[bumpversion:file:plugin.json] - -[bumpversion:file:VERSION] - -[bumpversion:file:src/polus/plugins/transforms/tabular/tabular_thresholding/__init__.py] diff --git a/transforms/tabular/tabular-thresholding-plugin/build-docker.sh b/transforms/tabular/tabular-thresholding-plugin/build-docker.sh deleted file mode 100644 index c433ba1ed..000000000 --- a/transforms/tabular/tabular-thresholding-plugin/build-docker.sh +++ /dev/null @@ -1,2 +0,0 @@ -version=$(\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? +serialize = + {major}.{minor}.{patch}-{release}{dev} + {major}.{minor}.{patch} + +[bumpversion:part:release] +optional_value = _ +first_value = dev +values = + dev + _ + +[bumpversion:part:dev] + +[bumpversion:file:pyproject.toml] +search = version = "{current_version}" +replace = version = "{new_version}" + +[bumpversion:file:plugin.json] + +[bumpversion:file:VERSION] + +[bumpversion:file:src/polus/images/transforms/tabular/tabular_thresholding/__init__.py] diff --git a/transforms/tabular/tabular-thresholding-plugin/.gitignore b/transforms/tabular/tabular-thresholding-tool/.gitignore similarity index 100% rename from transforms/tabular/tabular-thresholding-plugin/.gitignore rename to transforms/tabular/tabular-thresholding-tool/.gitignore diff --git a/transforms/tabular/tabular-thresholding-plugin/Dockerfile b/transforms/tabular/tabular-thresholding-tool/Dockerfile similarity index 84% rename from transforms/tabular/tabular-thresholding-plugin/Dockerfile rename to transforms/tabular/tabular-thresholding-tool/Dockerfile index 874631a8a..9943e2eac 100644 --- a/transforms/tabular/tabular-thresholding-plugin/Dockerfile +++ b/transforms/tabular/tabular-thresholding-tool/Dockerfile @@ -16,5 +16,5 @@ COPY src ${EXEC_DIR}/src RUN pip3 install ${EXEC_DIR} --no-cache-dir -ENTRYPOINT ["python3", "-m", "polus.plugins.transforms.tabular.tabular_thresholding"] +ENTRYPOINT ["python3", "-m", "polus.images.transforms.tabular.tabular_thresholding"] CMD ["--help"] diff --git a/transforms/tabular/tabular-thresholding-plugin/README.md b/transforms/tabular/tabular-thresholding-tool/README.md similarity index 100% rename from transforms/tabular/tabular-thresholding-plugin/README.md rename to transforms/tabular/tabular-thresholding-tool/README.md diff --git a/transforms/tabular/tabular-thresholding-tool/VERSION b/transforms/tabular/tabular-thresholding-tool/VERSION new file mode 100644 index 000000000..951891996 --- /dev/null +++ b/transforms/tabular/tabular-thresholding-tool/VERSION @@ -0,0 +1 @@ +0.1.6-dev0 diff --git a/transforms/tabular/tabular-thresholding-tool/build-docker.sh b/transforms/tabular/tabular-thresholding-tool/build-docker.sh new file mode 100644 index 000000000..45824a87f --- /dev/null +++ b/transforms/tabular/tabular-thresholding-tool/build-docker.sh @@ -0,0 +1,2 @@ +version=$(", diff --git a/transforms/tabular/tabular-thresholding-plugin/run-plugin.sh b/transforms/tabular/tabular-thresholding-tool/run-plugin.sh similarity index 100% rename from transforms/tabular/tabular-thresholding-plugin/run-plugin.sh rename to transforms/tabular/tabular-thresholding-tool/run-plugin.sh diff --git a/transforms/tabular/tabular-thresholding-plugin/src/polus/plugins/transforms/tabular/tabular_thresholding/__init__.py b/transforms/tabular/tabular-thresholding-tool/src/polus/images/transforms/tabular/tabular_thresholding/__init__.py similarity index 81% rename from transforms/tabular/tabular-thresholding-plugin/src/polus/plugins/transforms/tabular/tabular_thresholding/__init__.py rename to transforms/tabular/tabular-thresholding-tool/src/polus/images/transforms/tabular/tabular_thresholding/__init__.py index 9b88f9bcf..6312f93d3 100644 --- a/transforms/tabular/tabular-thresholding-plugin/src/polus/plugins/transforms/tabular/tabular_thresholding/__init__.py +++ b/transforms/tabular/tabular-thresholding-tool/src/polus/images/transforms/tabular/tabular_thresholding/__init__.py @@ -1,4 +1,4 @@ """Tabular Thresholding.""" -__version__ = "0.1.5-dev0" +__version__ = "0.1.6-dev0" from polus.plugins.transforms.tabular.tabular_thresholding import tabular_thresholding diff --git a/transforms/tabular/tabular-thresholding-plugin/src/polus/plugins/transforms/tabular/tabular_thresholding/__main__.py b/transforms/tabular/tabular-thresholding-tool/src/polus/images/transforms/tabular/tabular_thresholding/__main__.py similarity index 97% rename from transforms/tabular/tabular-thresholding-plugin/src/polus/plugins/transforms/tabular/tabular_thresholding/__main__.py rename to transforms/tabular/tabular-thresholding-tool/src/polus/images/transforms/tabular/tabular_thresholding/__main__.py index 87b89c10c..c88c2aa90 100644 --- a/transforms/tabular/tabular-thresholding-plugin/src/polus/plugins/transforms/tabular/tabular_thresholding/__main__.py +++ b/transforms/tabular/tabular-thresholding-tool/src/polus/images/transforms/tabular/tabular_thresholding/__main__.py @@ -12,7 +12,7 @@ import filepattern as fp import typer -from polus.plugins.transforms.tabular.tabular_thresholding import ( +from polus.images.transforms.tabular.tabular_thresholding import ( tabular_thresholding as tt, ) @@ -22,7 +22,7 @@ datefmt="%d-%b-%y %H:%M:%S", level=logging.INFO, ) -logger = logging.getLogger("polus.plugins.transforms.tabular.tabular_thresholding") +logger = logging.getLogger("polus.images.transforms.tabular.tabular_thresholding") logger.setLevel(os.environ.get("POLUS_LOG", logging.INFO)) app = typer.Typer() diff --git a/transforms/tabular/tabular-thresholding-plugin/src/polus/plugins/transforms/tabular/tabular_thresholding/tabular_thresholding.py b/transforms/tabular/tabular-thresholding-tool/src/polus/images/transforms/tabular/tabular_thresholding/tabular_thresholding.py similarity index 100% rename from transforms/tabular/tabular-thresholding-plugin/src/polus/plugins/transforms/tabular/tabular_thresholding/tabular_thresholding.py rename to transforms/tabular/tabular-thresholding-tool/src/polus/images/transforms/tabular/tabular_thresholding/tabular_thresholding.py diff --git a/transforms/tabular/tabular-thresholding-plugin/src/polus/plugins/transforms/tabular/tabular_thresholding/thresholding/__init__.py b/transforms/tabular/tabular-thresholding-tool/src/polus/images/transforms/tabular/tabular_thresholding/thresholding/__init__.py similarity index 100% rename from transforms/tabular/tabular-thresholding-plugin/src/polus/plugins/transforms/tabular/tabular_thresholding/thresholding/__init__.py rename to transforms/tabular/tabular-thresholding-tool/src/polus/images/transforms/tabular/tabular_thresholding/thresholding/__init__.py diff --git a/transforms/tabular/tabular-thresholding-plugin/src/polus/plugins/transforms/tabular/tabular_thresholding/thresholding/custom_fpr.py b/transforms/tabular/tabular-thresholding-tool/src/polus/images/transforms/tabular/tabular_thresholding/thresholding/custom_fpr.py similarity index 100% rename from transforms/tabular/tabular-thresholding-plugin/src/polus/plugins/transforms/tabular/tabular_thresholding/thresholding/custom_fpr.py rename to transforms/tabular/tabular-thresholding-tool/src/polus/images/transforms/tabular/tabular_thresholding/thresholding/custom_fpr.py diff --git a/transforms/tabular/tabular-thresholding-plugin/src/polus/plugins/transforms/tabular/tabular_thresholding/thresholding/n_sigma.py b/transforms/tabular/tabular-thresholding-tool/src/polus/images/transforms/tabular/tabular_thresholding/thresholding/n_sigma.py similarity index 100% rename from transforms/tabular/tabular-thresholding-plugin/src/polus/plugins/transforms/tabular/tabular_thresholding/thresholding/n_sigma.py rename to transforms/tabular/tabular-thresholding-tool/src/polus/images/transforms/tabular/tabular_thresholding/thresholding/n_sigma.py diff --git a/transforms/tabular/tabular-thresholding-plugin/src/polus/plugins/transforms/tabular/tabular_thresholding/thresholding/otsu.py b/transforms/tabular/tabular-thresholding-tool/src/polus/images/transforms/tabular/tabular_thresholding/thresholding/otsu.py similarity index 100% rename from transforms/tabular/tabular-thresholding-plugin/src/polus/plugins/transforms/tabular/tabular_thresholding/thresholding/otsu.py rename to transforms/tabular/tabular-thresholding-tool/src/polus/images/transforms/tabular/tabular_thresholding/thresholding/otsu.py diff --git a/transforms/tabular/tabular-thresholding-plugin/tests/__init_.py b/transforms/tabular/tabular-thresholding-tool/tests/__init_.py similarity index 100% rename from transforms/tabular/tabular-thresholding-plugin/tests/__init_.py rename to transforms/tabular/tabular-thresholding-tool/tests/__init_.py diff --git a/transforms/tabular/tabular-thresholding-plugin/tests/test_main.py b/transforms/tabular/tabular-thresholding-tool/tests/test_main.py similarity index 98% rename from transforms/tabular/tabular-thresholding-plugin/tests/test_main.py rename to transforms/tabular/tabular-thresholding-tool/tests/test_main.py index 49c8dbaf5..9b5f85903 100644 --- a/transforms/tabular/tabular-thresholding-plugin/tests/test_main.py +++ b/transforms/tabular/tabular-thresholding-tool/tests/test_main.py @@ -11,7 +11,7 @@ import pandas as pd import pytest import vaex -from polus.plugins.transforms.tabular.tabular_thresholding import ( +from polus.images.transforms.tabular.tabular_thresholding import ( tabular_thresholding as tt, ) diff --git a/visualization/microjson-to-ome-plugin/.bumpversion.cfg b/visualization/microjson-to-ome-plugin/.bumpversion.cfg deleted file mode 100644 index 2cfc4b7da..000000000 --- a/visualization/microjson-to-ome-plugin/.bumpversion.cfg +++ /dev/null @@ -1,29 +0,0 @@ -[bumpversion] -current_version = 0.1.4-dev0 -commit = True -tag = False -parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? -serialize = - {major}.{minor}.{patch}-{release}{dev} - {major}.{minor}.{patch} - -[bumpversion:part:release] -optional_value = _ -first_value = dev -values = - dev - _ - -[bumpversion:part:dev] - -[bumpversion:file:pyproject.toml] -search = version = "{current_version}" -replace = version = "{new_version}" - -[bumpversion:file:VERSION] - -[bumpversion:file:README.md] - -[bumpversion:file:plugin.json] - -[bumpversion:file:src/polus/plugins/visualization/microjson_to_ome/__init__.py] diff --git a/visualization/microjson-to-ome-plugin/VERSION b/visualization/microjson-to-ome-plugin/VERSION deleted file mode 100644 index 197c2b5ee..000000000 --- a/visualization/microjson-to-ome-plugin/VERSION +++ /dev/null @@ -1 +0,0 @@ -0.1.4-dev0 diff --git a/visualization/microjson-to-ome-plugin/build-docker.sh b/visualization/microjson-to-ome-plugin/build-docker.sh deleted file mode 100644 index e9440cc5f..000000000 --- a/visualization/microjson-to-ome-plugin/build-docker.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -version=$(\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? +serialize = + {major}.{minor}.{patch}-{release}{dev} + {major}.{minor}.{patch} + +[bumpversion:part:release] +optional_value = _ +first_value = dev +values = + dev + _ + +[bumpversion:part:dev] + +[bumpversion:file:pyproject.toml] +search = version = "{current_version}" +replace = version = "{new_version}" + +[bumpversion:file:VERSION] + +[bumpversion:file:README.md] + +[bumpversion:file:plugin.json] + +[bumpversion:file:src/polus/images/visualization/microjson_to_ome/__init__.py] diff --git a/visualization/microjson-to-ome-plugin/.dockerignore b/visualization/microjson-to-ome-tool/.dockerignore similarity index 100% rename from visualization/microjson-to-ome-plugin/.dockerignore rename to visualization/microjson-to-ome-tool/.dockerignore diff --git a/visualization/microjson-to-ome-plugin/.gitignore b/visualization/microjson-to-ome-tool/.gitignore similarity index 100% rename from visualization/microjson-to-ome-plugin/.gitignore rename to visualization/microjson-to-ome-tool/.gitignore diff --git a/visualization/microjson-to-ome-plugin/CHANGELOG.md b/visualization/microjson-to-ome-tool/CHANGELOG.md similarity index 100% rename from visualization/microjson-to-ome-plugin/CHANGELOG.md rename to visualization/microjson-to-ome-tool/CHANGELOG.md diff --git a/visualization/microjson-to-ome-plugin/Dockerfile b/visualization/microjson-to-ome-tool/Dockerfile similarity index 89% rename from visualization/microjson-to-ome-plugin/Dockerfile rename to visualization/microjson-to-ome-tool/Dockerfile index fe1b34efd..c06c538a4 100644 --- a/visualization/microjson-to-ome-plugin/Dockerfile +++ b/visualization/microjson-to-ome-tool/Dockerfile @@ -22,5 +22,5 @@ COPY src ${EXEC_DIR}/src RUN pip3 install ${EXEC_DIR} --no-cache-dir # Default command. Additional arguments are provided through the command line -ENTRYPOINT ["python3", "-m", "polus.plugins.visualization.microjson_to_ome"] +ENTRYPOINT ["python3", "-m", "polus.images.visualization.microjson_to_ome"] CMD ["--help"] diff --git a/visualization/microjson-to-ome-plugin/README.md b/visualization/microjson-to-ome-tool/README.md similarity index 98% rename from visualization/microjson-to-ome-plugin/README.md rename to visualization/microjson-to-ome-tool/README.md index 51c22aed1..643d681f8 100644 --- a/visualization/microjson-to-ome-plugin/README.md +++ b/visualization/microjson-to-ome-tool/README.md @@ -1,4 +1,4 @@ -# Microjson To Ome(v0.1.4-dev0) +# Microjson To Ome(v0.1.5-dev0) This plugin reconstructs binary image from polygon coordinates reserved in microjson file format diff --git a/transforms/tabular/tabular-thresholding-plugin/VERSION b/visualization/microjson-to-ome-tool/VERSION similarity index 100% rename from transforms/tabular/tabular-thresholding-plugin/VERSION rename to visualization/microjson-to-ome-tool/VERSION diff --git a/visualization/microjson-to-ome-tool/build-docker.sh b/visualization/microjson-to-ome-tool/build-docker.sh new file mode 100644 index 000000000..cea40fddb --- /dev/null +++ b/visualization/microjson-to-ome-tool/build-docker.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +version=$("] readme = "README.md" diff --git a/visualization/microjson-to-ome-plugin/run-plugin.sh b/visualization/microjson-to-ome-tool/run-plugin.sh similarity index 100% rename from visualization/microjson-to-ome-plugin/run-plugin.sh rename to visualization/microjson-to-ome-tool/run-plugin.sh diff --git a/visualization/microjson-to-ome-tool/src/polus/images/visualization/microjson_to_ome/__init__.py b/visualization/microjson-to-ome-tool/src/polus/images/visualization/microjson_to_ome/__init__.py new file mode 100644 index 000000000..4fd285458 --- /dev/null +++ b/visualization/microjson-to-ome-tool/src/polus/images/visualization/microjson_to_ome/__init__.py @@ -0,0 +1,2 @@ +"""Micojson to Ome.""" +__version__ = "0.1.5-dev0" diff --git a/visualization/microjson-to-ome-plugin/src/polus/plugins/visualization/microjson_to_ome/__main__.py b/visualization/microjson-to-ome-tool/src/polus/images/visualization/microjson_to_ome/__main__.py similarity index 95% rename from visualization/microjson-to-ome-plugin/src/polus/plugins/visualization/microjson_to_ome/__main__.py rename to visualization/microjson-to-ome-tool/src/polus/images/visualization/microjson_to_ome/__main__.py index f761d6256..207fe064a 100644 --- a/visualization/microjson-to-ome-plugin/src/polus/plugins/visualization/microjson_to_ome/__main__.py +++ b/visualization/microjson-to-ome-tool/src/polus/images/visualization/microjson_to_ome/__main__.py @@ -10,7 +10,7 @@ from typing import Any import filepattern as fp -import polus.plugins.visualization.microjson_to_ome.microjson_ome as mo +import polus.images.visualization.microjson_to_ome.microjson_ome as mo import typer from tqdm import tqdm @@ -19,7 +19,7 @@ datefmt="%d-%b-%y %H:%M:%S", ) POLUS_LOG = getattr(logging, os.environ.get("POLUS_LOG", "INFO")) -logger = logging.getLogger("polus.plugins.visualization.micojson_to_ome") +logger = logging.getLogger("polus.images.visualization.micojson_to_ome") logger.setLevel(POLUS_LOG) # Set number of threads for scalability diff --git a/visualization/microjson-to-ome-plugin/src/polus/plugins/visualization/microjson_to_ome/microjson_ome.py b/visualization/microjson-to-ome-tool/src/polus/images/visualization/microjson_to_ome/microjson_ome.py similarity index 100% rename from visualization/microjson-to-ome-plugin/src/polus/plugins/visualization/microjson_to_ome/microjson_ome.py rename to visualization/microjson-to-ome-tool/src/polus/images/visualization/microjson_to_ome/microjson_ome.py diff --git a/visualization/microjson-to-ome-plugin/tests/__init__.py b/visualization/microjson-to-ome-tool/tests/__init__.py similarity index 100% rename from visualization/microjson-to-ome-plugin/tests/__init__.py rename to visualization/microjson-to-ome-tool/tests/__init__.py diff --git a/visualization/microjson-to-ome-plugin/tests/conftest.py b/visualization/microjson-to-ome-tool/tests/conftest.py similarity index 100% rename from visualization/microjson-to-ome-plugin/tests/conftest.py rename to visualization/microjson-to-ome-tool/tests/conftest.py diff --git a/visualization/microjson-to-ome-plugin/tests/test_cli.py b/visualization/microjson-to-ome-tool/tests/test_cli.py similarity index 94% rename from visualization/microjson-to-ome-plugin/tests/test_cli.py rename to visualization/microjson-to-ome-tool/tests/test_cli.py index aa45864ab..457ec13aa 100644 --- a/visualization/microjson-to-ome-plugin/tests/test_cli.py +++ b/visualization/microjson-to-ome-tool/tests/test_cli.py @@ -2,7 +2,7 @@ import shutil from pathlib import Path -from polus.plugins.visualization.microjson_to_ome.__main__ import app +from polus.images.visualization.microjson_to_ome.__main__ import app from typer.testing import CliRunner diff --git a/visualization/microjson-to-ome-plugin/tests/test_micojson_ome.py b/visualization/microjson-to-ome-tool/tests/test_micojson_ome.py similarity index 90% rename from visualization/microjson-to-ome-plugin/tests/test_micojson_ome.py rename to visualization/microjson-to-ome-tool/tests/test_micojson_ome.py index d35aae4e6..578950b4d 100644 --- a/visualization/microjson-to-ome-plugin/tests/test_micojson_ome.py +++ b/visualization/microjson-to-ome-tool/tests/test_micojson_ome.py @@ -4,7 +4,7 @@ import numpy as np from bfio import BioReader -from polus.plugins.visualization.microjson_to_ome.microjson_ome import MicrojsonOmeModel +from polus.images.visualization.microjson_to_ome.microjson_ome import MicrojsonOmeModel def clean_directories() -> None: diff --git a/visualization/ome-to-microjson-plugin/.bumpversion.cfg b/visualization/ome-to-microjson-plugin/.bumpversion.cfg deleted file mode 100644 index 84a88c1bb..000000000 --- a/visualization/ome-to-microjson-plugin/.bumpversion.cfg +++ /dev/null @@ -1,29 +0,0 @@ -[bumpversion] -current_version = 0.1.4-dev0 -commit = True -tag = False -parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? -serialize = - {major}.{minor}.{patch}-{release}{dev} - {major}.{minor}.{patch} - -[bumpversion:part:release] -optional_value = _ -first_value = dev -values = - dev - _ - -[bumpversion:part:dev] - -[bumpversion:file:pyproject.toml] -search = version = "{current_version}" -replace = version = "{new_version}" - -[bumpversion:file:VERSION] - -[bumpversion:file:README.md] - -[bumpversion:file:plugin.json] - -[bumpversion:file:src/polus/plugins/visualization/ome_to_microjson/__init__.py] diff --git a/visualization/ome-to-microjson-plugin/VERSION b/visualization/ome-to-microjson-plugin/VERSION deleted file mode 100644 index 197c2b5ee..000000000 --- a/visualization/ome-to-microjson-plugin/VERSION +++ /dev/null @@ -1 +0,0 @@ -0.1.4-dev0 diff --git a/visualization/ome-to-microjson-plugin/build-docker.sh b/visualization/ome-to-microjson-plugin/build-docker.sh deleted file mode 100755 index a7b937041..000000000 --- a/visualization/ome-to-microjson-plugin/build-docker.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -version=$(\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? +serialize = + {major}.{minor}.{patch}-{release}{dev} + {major}.{minor}.{patch} + +[bumpversion:part:release] +optional_value = _ +first_value = dev +values = + dev + _ + +[bumpversion:part:dev] + +[bumpversion:file:pyproject.toml] +search = version = "{current_version}" +replace = version = "{new_version}" + +[bumpversion:file:VERSION] + +[bumpversion:file:README.md] + +[bumpversion:file:plugin.json] + +[bumpversion:file:src/polus/images/visualization/ome_to_microjson/__init__.py] diff --git a/visualization/ome-to-microjson-plugin/.dockerignore b/visualization/ome-to-microjson-tool/.dockerignore similarity index 100% rename from visualization/ome-to-microjson-plugin/.dockerignore rename to visualization/ome-to-microjson-tool/.dockerignore diff --git a/visualization/ome-to-microjson-plugin/.gitignore b/visualization/ome-to-microjson-tool/.gitignore similarity index 100% rename from visualization/ome-to-microjson-plugin/.gitignore rename to visualization/ome-to-microjson-tool/.gitignore diff --git a/visualization/ome-to-microjson-plugin/CHANGELOG.md b/visualization/ome-to-microjson-tool/CHANGELOG.md similarity index 100% rename from visualization/ome-to-microjson-plugin/CHANGELOG.md rename to visualization/ome-to-microjson-tool/CHANGELOG.md diff --git a/visualization/ome-to-microjson-plugin/Dockerfile b/visualization/ome-to-microjson-tool/Dockerfile similarity index 87% rename from visualization/ome-to-microjson-plugin/Dockerfile rename to visualization/ome-to-microjson-tool/Dockerfile index 653bff0ef..37941c5dd 100644 --- a/visualization/ome-to-microjson-plugin/Dockerfile +++ b/visualization/ome-to-microjson-tool/Dockerfile @@ -18,5 +18,5 @@ COPY src ${EXEC_DIR}/src RUN pip3 install ${EXEC_DIR} --no-cache-dir # Default command. Additional arguments are provided through the command line -ENTRYPOINT ["python3", "-m", "polus.plugins.visualization.ome_to_microjson"] +ENTRYPOINT ["python3", "-m", "polus.images.visualization.ome_to_microjson"] CMD ["--help"] diff --git a/visualization/ome-to-microjson-plugin/README.md b/visualization/ome-to-microjson-tool/README.md similarity index 96% rename from visualization/ome-to-microjson-plugin/README.md rename to visualization/ome-to-microjson-tool/README.md index fec6fab95..1613284af 100644 --- a/visualization/ome-to-microjson-plugin/README.md +++ b/visualization/ome-to-microjson-tool/README.md @@ -1,4 +1,4 @@ -# Ome-to-microjson-plugin(v0.1.4-dev0) +# Ome-to-microjson-plugin(v0.1.5-dev0) This plugin generate a microjson of polygon coordinates of binary or label segmentations @@ -50,7 +50,7 @@ This plugin can take four input arguments and one output argument: ### Run the Docker Container ```bash -docker run -v /data:/data polusai/ome-to-microjson-plugin:0.1.4-dev0-dev \ +docker run -v /data:/data polusai/ome-to-microjson-plugin:0.1.5-dev0-dev \ --inpDir /data/input \ --filePattern ".*.ome.tif" \ --polygonType "encoding" \ diff --git a/visualization/ome-to-microjson-tool/VERSION b/visualization/ome-to-microjson-tool/VERSION new file mode 100644 index 000000000..731bd3966 --- /dev/null +++ b/visualization/ome-to-microjson-tool/VERSION @@ -0,0 +1 @@ +0.1.5-dev0 diff --git a/visualization/ome-to-microjson-tool/build-docker.sh b/visualization/ome-to-microjson-tool/build-docker.sh new file mode 100755 index 000000000..016d91348 --- /dev/null +++ b/visualization/ome-to-microjson-tool/build-docker.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +version=$("] readme = "README.md" diff --git a/visualization/ome-to-microjson-plugin/run-plugin.sh b/visualization/ome-to-microjson-tool/run-plugin.sh similarity index 100% rename from visualization/ome-to-microjson-plugin/run-plugin.sh rename to visualization/ome-to-microjson-tool/run-plugin.sh diff --git a/visualization/ome-to-microjson-plugin/src/polus/plugins/visualization/ome_to_microjson/__init__.py b/visualization/ome-to-microjson-tool/src/polus/images/visualization/ome_to_microjson/__init__.py similarity index 51% rename from visualization/ome-to-microjson-plugin/src/polus/plugins/visualization/ome_to_microjson/__init__.py rename to visualization/ome-to-microjson-tool/src/polus/images/visualization/ome_to_microjson/__init__.py index 55e449407..eae797d35 100644 --- a/visualization/ome-to-microjson-plugin/src/polus/plugins/visualization/ome_to_microjson/__init__.py +++ b/visualization/ome-to-microjson-tool/src/polus/images/visualization/ome_to_microjson/__init__.py @@ -1,3 +1,3 @@ """Ome micojson package.""" -__version__ = "0.1.4-dev0" +__version__ = "0.1.5-dev0" diff --git a/visualization/ome-to-microjson-plugin/src/polus/plugins/visualization/ome_to_microjson/__main__.py b/visualization/ome-to-microjson-tool/src/polus/images/visualization/ome_to_microjson/__main__.py similarity index 95% rename from visualization/ome-to-microjson-plugin/src/polus/plugins/visualization/ome_to_microjson/__main__.py rename to visualization/ome-to-microjson-tool/src/polus/images/visualization/ome_to_microjson/__main__.py index 6feece230..977b67242 100644 --- a/visualization/ome-to-microjson-plugin/src/polus/plugins/visualization/ome_to_microjson/__main__.py +++ b/visualization/ome-to-microjson-tool/src/polus/images/visualization/ome_to_microjson/__main__.py @@ -8,7 +8,7 @@ from pathlib import Path import filepattern as fp -import polus.plugins.visualization.ome_to_microjson.ome_microjson as sm +import polus.images.visualization.ome_to_microjson.ome_microjson as sm import typer from tqdm import tqdm @@ -19,7 +19,7 @@ datefmt="%d-%b-%y %H:%M:%S", ) POLUS_LOG = getattr(logging, environ.get("POLUS_LOG", "INFO")) -logger = logging.getLogger("polus.plugins.visualization.ome_to_micojson") +logger = logging.getLogger("polus.images.visualization.ome_to_micojson") logger.setLevel(POLUS_LOG) logging.getLogger("bfio").setLevel(POLUS_LOG) diff --git a/visualization/ome-to-microjson-plugin/src/polus/plugins/visualization/ome_to_microjson/ome_microjson.py b/visualization/ome-to-microjson-tool/src/polus/images/visualization/ome_to_microjson/ome_microjson.py similarity index 100% rename from visualization/ome-to-microjson-plugin/src/polus/plugins/visualization/ome_to_microjson/ome_microjson.py rename to visualization/ome-to-microjson-tool/src/polus/images/visualization/ome_to_microjson/ome_microjson.py diff --git a/visualization/ome-to-microjson-plugin/tests/__init__.py b/visualization/ome-to-microjson-tool/tests/__init__.py similarity index 100% rename from visualization/ome-to-microjson-plugin/tests/__init__.py rename to visualization/ome-to-microjson-tool/tests/__init__.py diff --git a/visualization/ome-to-microjson-plugin/tests/conftest.py b/visualization/ome-to-microjson-tool/tests/conftest.py similarity index 97% rename from visualization/ome-to-microjson-plugin/tests/conftest.py rename to visualization/ome-to-microjson-tool/tests/conftest.py index 4be4f2e2c..f69de7ba2 100644 --- a/visualization/ome-to-microjson-plugin/tests/conftest.py +++ b/visualization/ome-to-microjson-tool/tests/conftest.py @@ -9,7 +9,7 @@ import numpy as np import pytest import skimage as sk -from polus.plugins.visualization.ome_to_microjson.ome_microjson import PolygonType +from polus.images.visualization.ome_to_microjson.ome_microjson import PolygonType from skimage import io TILE_SIZE = 1024 diff --git a/visualization/ome-to-microjson-plugin/tests/test_cli.py b/visualization/ome-to-microjson-tool/tests/test_cli.py similarity index 94% rename from visualization/ome-to-microjson-plugin/tests/test_cli.py rename to visualization/ome-to-microjson-tool/tests/test_cli.py index 22da5264d..250a7df39 100644 --- a/visualization/ome-to-microjson-plugin/tests/test_cli.py +++ b/visualization/ome-to-microjson-tool/tests/test_cli.py @@ -2,7 +2,7 @@ import shutil from pathlib import Path -from polus.plugins.visualization.ome_to_microjson.__main__ import app +from polus.images.visualization.ome_to_microjson.__main__ import app from typer.testing import CliRunner diff --git a/visualization/ome-to-microjson-plugin/tests/test_ome_micojson.py b/visualization/ome-to-microjson-tool/tests/test_ome_micojson.py similarity index 96% rename from visualization/ome-to-microjson-plugin/tests/test_ome_micojson.py rename to visualization/ome-to-microjson-tool/tests/test_ome_micojson.py index bd9634e66..2f49c5da2 100644 --- a/visualization/ome-to-microjson-plugin/tests/test_ome_micojson.py +++ b/visualization/ome-to-microjson-tool/tests/test_ome_micojson.py @@ -8,8 +8,8 @@ import pytest from bfio import BioReader from memory_profiler import profile -from polus.plugins.visualization.ome_to_microjson.ome_microjson import OmeMicrojsonModel -from polus.plugins.visualization.ome_to_microjson.ome_microjson import PolygonType +from polus.images.visualization.ome_to_microjson.ome_microjson import OmeMicrojsonModel +from polus.images.visualization.ome_to_microjson.ome_microjson import PolygonType from skimage import morphology diff --git a/visualization/precompute-slide-plugin/VERSION b/visualization/precompute-slide-plugin/VERSION deleted file mode 100644 index bd8bf882d..000000000 --- a/visualization/precompute-slide-plugin/VERSION +++ /dev/null @@ -1 +0,0 @@ -1.7.0 diff --git a/visualization/precompute-slide-plugin/.bumpversion.cfg b/visualization/precompute-slide-tool/.bumpversion.cfg similarity index 94% rename from visualization/precompute-slide-plugin/.bumpversion.cfg rename to visualization/precompute-slide-tool/.bumpversion.cfg index 204c818b7..47f72449f 100644 --- a/visualization/precompute-slide-plugin/.bumpversion.cfg +++ b/visualization/precompute-slide-tool/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 1.7.0 +current_version = 1.7.1-dev0 commit = False tag = False parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? diff --git a/visualization/precompute-slide-plugin/.dockerignore b/visualization/precompute-slide-tool/.dockerignore similarity index 100% rename from visualization/precompute-slide-plugin/.dockerignore rename to visualization/precompute-slide-tool/.dockerignore diff --git a/visualization/precompute-slide-plugin/.gitignore b/visualization/precompute-slide-tool/.gitignore similarity index 100% rename from visualization/precompute-slide-plugin/.gitignore rename to visualization/precompute-slide-tool/.gitignore diff --git a/visualization/precompute-slide-plugin/CHANGELOG.md b/visualization/precompute-slide-tool/CHANGELOG.md similarity index 100% rename from visualization/precompute-slide-plugin/CHANGELOG.md rename to visualization/precompute-slide-tool/CHANGELOG.md diff --git a/visualization/precompute-slide-plugin/Dockerfile b/visualization/precompute-slide-tool/Dockerfile similarity index 89% rename from visualization/precompute-slide-plugin/Dockerfile rename to visualization/precompute-slide-tool/Dockerfile index 8ccba1c43..3e6515211 100644 --- a/visualization/precompute-slide-plugin/Dockerfile +++ b/visualization/precompute-slide-tool/Dockerfile @@ -21,5 +21,5 @@ RUN pip3 install ${EXEC_DIR} --no-cache-dir RUN python3 -c "import imageio; imageio.plugins.freeimage.download()" # Default command. Additional arguments are provided through the command line -ENTRYPOINT ["python3", "-m", "polus.plugins.visualization.precompute_slide"] +ENTRYPOINT ["python3", "-m", "polus.images.visualization.precompute_slide"] CMD ["--help"] diff --git a/visualization/precompute-slide-plugin/README.md b/visualization/precompute-slide-tool/README.md similarity index 97% rename from visualization/precompute-slide-plugin/README.md rename to visualization/precompute-slide-tool/README.md index 2e3a37984..5f76ff8f2 100644 --- a/visualization/precompute-slide-plugin/README.md +++ b/visualization/precompute-slide-tool/README.md @@ -1,4 +1,4 @@ -# Polus Precompute Slide Plugin (1.7.0) +# Polus Precompute Slide Plugin (1.7.1-dev0) This WIPP plugin generates image pyramids in multiple viewing formats. Each output has a special filepattern variable that will be used to combine images diff --git a/visualization/precompute-slide-tool/VERSION b/visualization/precompute-slide-tool/VERSION new file mode 100644 index 000000000..4866b4cb5 --- /dev/null +++ b/visualization/precompute-slide-tool/VERSION @@ -0,0 +1 @@ +1.7.1-dev0 diff --git a/visualization/precompute-slide-plugin/build-docker.sh b/visualization/precompute-slide-tool/build-docker.sh similarity index 56% rename from visualization/precompute-slide-plugin/build-docker.sh rename to visualization/precompute-slide-tool/build-docker.sh index cd27b7e8b..9b67f655b 100755 --- a/visualization/precompute-slide-plugin/build-docker.sh +++ b/visualization/precompute-slide-tool/build-docker.sh @@ -1,14 +1,14 @@ #!/bin/bash version=$(", diff --git a/visualization/precompute-slide-plugin/run-plugin.sh b/visualization/precompute-slide-tool/run-plugin.sh similarity index 100% rename from visualization/precompute-slide-plugin/run-plugin.sh rename to visualization/precompute-slide-tool/run-plugin.sh diff --git a/visualization/precompute-slide-plugin/src/polus/plugins/visualization/precompute_slide/__init__.py b/visualization/precompute-slide-tool/src/polus/images/visualization/precompute_slide/__init__.py similarity index 100% rename from visualization/precompute-slide-plugin/src/polus/plugins/visualization/precompute_slide/__init__.py rename to visualization/precompute-slide-tool/src/polus/images/visualization/precompute_slide/__init__.py diff --git a/visualization/precompute-slide-plugin/src/polus/plugins/visualization/precompute_slide/__main__.py b/visualization/precompute-slide-tool/src/polus/images/visualization/precompute_slide/__main__.py similarity index 97% rename from visualization/precompute-slide-plugin/src/polus/plugins/visualization/precompute_slide/__main__.py rename to visualization/precompute-slide-tool/src/polus/images/visualization/precompute_slide/__main__.py index baace97ff..c8af0a455 100644 --- a/visualization/precompute-slide-plugin/src/polus/plugins/visualization/precompute_slide/__main__.py +++ b/visualization/precompute-slide-tool/src/polus/images/visualization/precompute_slide/__main__.py @@ -16,7 +16,7 @@ datefmt="%d-%b-%y %H:%M:%S", ) -logger = logging.getLogger("polus.plugins.visualization.precompute_slide") +logger = logging.getLogger("polus.images.visualization.precompute_slide") POLUS_LOG = getattr(logging, environ.get("POLUS_LOG", "INFO")) logger.setLevel(POLUS_LOG) diff --git a/visualization/precompute-slide-plugin/src/polus/plugins/visualization/precompute_slide/chunk_encoder.py b/visualization/precompute-slide-tool/src/polus/images/visualization/precompute_slide/chunk_encoder.py similarity index 100% rename from visualization/precompute-slide-plugin/src/polus/plugins/visualization/precompute_slide/chunk_encoder.py rename to visualization/precompute-slide-tool/src/polus/images/visualization/precompute_slide/chunk_encoder.py diff --git a/visualization/precompute-slide-plugin/src/polus/plugins/visualization/precompute_slide/precompute_slide.py b/visualization/precompute-slide-tool/src/polus/images/visualization/precompute_slide/precompute_slide.py similarity index 100% rename from visualization/precompute-slide-plugin/src/polus/plugins/visualization/precompute_slide/precompute_slide.py rename to visualization/precompute-slide-tool/src/polus/images/visualization/precompute_slide/precompute_slide.py diff --git a/visualization/precompute-slide-plugin/src/polus/plugins/visualization/precompute_slide/pyramid_writer.py b/visualization/precompute-slide-tool/src/polus/images/visualization/precompute_slide/pyramid_writer.py similarity index 100% rename from visualization/precompute-slide-plugin/src/polus/plugins/visualization/precompute_slide/pyramid_writer.py rename to visualization/precompute-slide-tool/src/polus/images/visualization/precompute_slide/pyramid_writer.py diff --git a/visualization/precompute-slide-plugin/src/polus/plugins/visualization/precompute_slide/utils.py b/visualization/precompute-slide-tool/src/polus/images/visualization/precompute_slide/utils.py similarity index 100% rename from visualization/precompute-slide-plugin/src/polus/plugins/visualization/precompute_slide/utils.py rename to visualization/precompute-slide-tool/src/polus/images/visualization/precompute_slide/utils.py diff --git a/visualization/precompute-slide-plugin/tests/__init__.py b/visualization/precompute-slide-tool/tests/__init__.py similarity index 100% rename from visualization/precompute-slide-plugin/tests/__init__.py rename to visualization/precompute-slide-tool/tests/__init__.py diff --git a/visualization/precompute-slide-plugin/tests/conftest.py b/visualization/precompute-slide-tool/tests/conftest.py similarity index 100% rename from visualization/precompute-slide-plugin/tests/conftest.py rename to visualization/precompute-slide-tool/tests/conftest.py diff --git a/visualization/precompute-slide-plugin/tests/helpers.py b/visualization/precompute-slide-tool/tests/helpers.py similarity index 98% rename from visualization/precompute-slide-plugin/tests/helpers.py rename to visualization/precompute-slide-tool/tests/helpers.py index 3529eff3f..9b0a3c2e1 100644 --- a/visualization/precompute-slide-plugin/tests/helpers.py +++ b/visualization/precompute-slide-tool/tests/helpers.py @@ -6,8 +6,8 @@ import bfio import numpy import pytest -from polus.plugins.visualization.precompute_slide.utils import ImageType -from polus.plugins.visualization.precompute_slide.utils import PyramidType +from polus.images.visualization.precompute_slide.utils import ImageType +from polus.images.visualization.precompute_slide.utils import PyramidType FixtureReturnType = tuple[ pathlib.Path, # input dir diff --git a/visualization/precompute-slide-plugin/tests/test_zarr_filepattern_option.py b/visualization/precompute-slide-tool/tests/test_zarr_filepattern_option.py similarity index 89% rename from visualization/precompute-slide-plugin/tests/test_zarr_filepattern_option.py rename to visualization/precompute-slide-tool/tests/test_zarr_filepattern_option.py index c77551c1e..1dedc09e1 100644 --- a/visualization/precompute-slide-plugin/tests/test_zarr_filepattern_option.py +++ b/visualization/precompute-slide-tool/tests/test_zarr_filepattern_option.py @@ -9,9 +9,9 @@ from pathlib import Path import pytest -from polus.plugins.visualization.precompute_slide import precompute_slide -from polus.plugins.visualization.precompute_slide.utils import ImageType -from polus.plugins.visualization.precompute_slide.utils import PyramidType +from polus.images.visualization.precompute_slide import precompute_slide +from polus.images.visualization.precompute_slide.utils import ImageType +from polus.images.visualization.precompute_slide.utils import PyramidType from . import helpers diff --git a/visualization/precompute-slide-plugin/tests/test_zarr_pyramids.py b/visualization/precompute-slide-tool/tests/test_zarr_pyramids.py similarity index 96% rename from visualization/precompute-slide-plugin/tests/test_zarr_pyramids.py rename to visualization/precompute-slide-tool/tests/test_zarr_pyramids.py index 37be9ffd2..f0db9ac47 100644 --- a/visualization/precompute-slide-plugin/tests/test_zarr_pyramids.py +++ b/visualization/precompute-slide-tool/tests/test_zarr_pyramids.py @@ -11,9 +11,9 @@ import numpy import pytest import zarr -from polus.plugins.visualization.precompute_slide import precompute_slide -from polus.plugins.visualization.precompute_slide.utils import ImageType -from polus.plugins.visualization.precompute_slide.utils import PyramidType +from polus.images.visualization.precompute_slide import precompute_slide +from polus.images.visualization.precompute_slide.utils import ImageType +from polus.images.visualization.precompute_slide.utils import PyramidType from . import helpers diff --git a/visualization/tabular-to-microjson-plugin/.bumpversion.cfg b/visualization/tabular-to-microjson-plugin/.bumpversion.cfg deleted file mode 100644 index 9ced00cae..000000000 --- a/visualization/tabular-to-microjson-plugin/.bumpversion.cfg +++ /dev/null @@ -1,27 +0,0 @@ -[bumpversion] -current_version = 0.1.1 -commit = True -tag = False -parse = (?P\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? -serialize = - {major}.{minor}.{patch}-{release}{dev} - {major}.{minor}.{patch} - -[bumpversion:part:release] -optional_value = _ -first_value = dev -values = - dev - _ - -[bumpversion:part:dev] - -[bumpversion:file:pyproject.toml] -search = version = "{current_version}" -replace = version = "{new_version}" - -[bumpversion:file:plugin.json] - -[bumpversion:file:VERSION] - -[bumpversion:file:src/polus/plugins/visualization/tabular_to_microjson/__init__.py] diff --git a/visualization/tabular-to-microjson-plugin/VERSION b/visualization/tabular-to-microjson-plugin/VERSION deleted file mode 100644 index 17e51c385..000000000 --- a/visualization/tabular-to-microjson-plugin/VERSION +++ /dev/null @@ -1 +0,0 @@ -0.1.1 diff --git a/visualization/tabular-to-microjson-plugin/build-docker.sh b/visualization/tabular-to-microjson-plugin/build-docker.sh deleted file mode 100644 index 8b79e3744..000000000 --- a/visualization/tabular-to-microjson-plugin/build-docker.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -version=$(\d+)\.(?P\d+)\.(?P\d+)(\-(?P[a-z]+)(?P\d+))? +serialize = + {major}.{minor}.{patch}-{release}{dev} + {major}.{minor}.{patch} + +[bumpversion:part:release] +optional_value = _ +first_value = dev +values = + dev + _ + +[bumpversion:part:dev] + +[bumpversion:file:pyproject.toml] +search = version = "{current_version}" +replace = version = "{new_version}" + +[bumpversion:file:plugin.json] + +[bumpversion:file:VERSION] + +[bumpversion:file:src/polus/images/visualization/tabular_to_microjson/__init__.py] diff --git a/visualization/tabular-to-microjson-plugin/Dockerfile b/visualization/tabular-to-microjson-tool/Dockerfile similarity index 84% rename from visualization/tabular-to-microjson-plugin/Dockerfile rename to visualization/tabular-to-microjson-tool/Dockerfile index f4f078ec3..4b00db308 100644 --- a/visualization/tabular-to-microjson-plugin/Dockerfile +++ b/visualization/tabular-to-microjson-tool/Dockerfile @@ -16,5 +16,5 @@ COPY README.md ${EXEC_DIR} COPY src ${EXEC_DIR}/src RUN pip3 install ${EXEC_DIR} --no-cache-dir -ENTRYPOINT ["python3", "-m", "polus.plugins.visualization.tabular_to_microjson"] +ENTRYPOINT ["python3", "-m", "polus.images.visualization.tabular_to_microjson"] CMD ["--help"] diff --git a/visualization/tabular-to-microjson-plugin/README.md b/visualization/tabular-to-microjson-tool/README.md similarity index 100% rename from visualization/tabular-to-microjson-plugin/README.md rename to visualization/tabular-to-microjson-tool/README.md diff --git a/visualization/tabular-to-microjson-tool/VERSION b/visualization/tabular-to-microjson-tool/VERSION new file mode 100644 index 000000000..9d8d2c119 --- /dev/null +++ b/visualization/tabular-to-microjson-tool/VERSION @@ -0,0 +1 @@ +0.1.2-dev0 diff --git a/visualization/tabular-to-microjson-tool/build-docker.sh b/visualization/tabular-to-microjson-tool/build-docker.sh new file mode 100644 index 000000000..c63f2c211 --- /dev/null +++ b/visualization/tabular-to-microjson-tool/build-docker.sh @@ -0,0 +1,4 @@ +#!/bin/bash + +version=$("] readme = "README.md" diff --git a/visualization/tabular-to-microjson-plugin/run-plugin.sh b/visualization/tabular-to-microjson-tool/run-plugin.sh similarity index 100% rename from visualization/tabular-to-microjson-plugin/run-plugin.sh rename to visualization/tabular-to-microjson-tool/run-plugin.sh diff --git a/visualization/tabular-to-microjson-plugin/src/polus/plugins/visualization/tabular_to_microjson/__init__.py b/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/__init__.py similarity index 57% rename from visualization/tabular-to-microjson-plugin/src/polus/plugins/visualization/tabular_to_microjson/__init__.py rename to visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/__init__.py index a79cf7967..48c3937ea 100644 --- a/visualization/tabular-to-microjson-plugin/src/polus/plugins/visualization/tabular_to_microjson/__init__.py +++ b/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/__init__.py @@ -1,2 +1,2 @@ """Tabular to microjson package.""" -__version__ = "0.1.1" +__version__ = "0.1.2-dev0" diff --git a/visualization/tabular-to-microjson-plugin/src/polus/plugins/visualization/tabular_to_microjson/__main__.py b/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/__main__.py similarity index 95% rename from visualization/tabular-to-microjson-plugin/src/polus/plugins/visualization/tabular_to_microjson/__main__.py rename to visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/__main__.py index 6dab1a0a7..9aced4ee6 100644 --- a/visualization/tabular-to-microjson-plugin/src/polus/plugins/visualization/tabular_to_microjson/__main__.py +++ b/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/__main__.py @@ -10,7 +10,7 @@ import filepattern as fp import typer -from polus.plugins.visualization.tabular_to_microjson import microjson_overlay as mo +from polus.images.visualization.tabular_to_microjson import microjson_overlay as mo from tqdm import tqdm app = typer.Typer() @@ -21,7 +21,7 @@ format="%(asctime)s - %(name)-8s - %(levelname)-8s - %(message)s", datefmt="%d-%b-%y %H:%M:%S", ) -logger = logging.getLogger("polus.plugins.visualization.tabular_to_microjson") +logger = logging.getLogger("polus.images.visualization.tabular_to_microjson") logger.setLevel(os.environ.get("POLUS_LOG", logging.INFO)) # Set number of processors for scalability num_workers = max(cpu_count() // 2, 2) diff --git a/visualization/tabular-to-microjson-plugin/src/polus/plugins/visualization/tabular_to_microjson/microjson_overlay.py b/visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/microjson_overlay.py similarity index 100% rename from visualization/tabular-to-microjson-plugin/src/polus/plugins/visualization/tabular_to_microjson/microjson_overlay.py rename to visualization/tabular-to-microjson-tool/src/polus/images/visualization/tabular_to_microjson/microjson_overlay.py diff --git a/visualization/tabular-to-microjson-plugin/tests/__init__.py b/visualization/tabular-to-microjson-tool/tests/__init__.py similarity index 100% rename from visualization/tabular-to-microjson-plugin/tests/__init__.py rename to visualization/tabular-to-microjson-tool/tests/__init__.py diff --git a/visualization/tabular-to-microjson-plugin/tests/test_microjson_overlay.py b/visualization/tabular-to-microjson-tool/tests/test_microjson_overlay.py similarity index 97% rename from visualization/tabular-to-microjson-plugin/tests/test_microjson_overlay.py rename to visualization/tabular-to-microjson-tool/tests/test_microjson_overlay.py index 898155c19..7e8d7d88d 100644 --- a/visualization/tabular-to-microjson-plugin/tests/test_microjson_overlay.py +++ b/visualization/tabular-to-microjson-tool/tests/test_microjson_overlay.py @@ -9,8 +9,8 @@ import pandas as pd import pytest import vaex -from polus.plugins.visualization.tabular_to_microjson import microjson_overlay as mo -from polus.plugins.visualization.tabular_to_microjson.__main__ import app +from polus.images.visualization.tabular_to_microjson import microjson_overlay as mo +from polus.images.visualization.tabular_to_microjson.__main__ import app from typer.testing import CliRunner runner = CliRunner() From 941899ac6ee226ce47e1d1cde189026a8b612a31 Mon Sep 17 00:00:00 2001 From: Najib Ishaq Date: Wed, 14 Feb 2024 14:31:32 -0500 Subject: [PATCH 5/8] fix: updated imports and fixed tests --- .../images/clustering/k_means/k_means.py | 3 +-- .../feature_evaluation.py | 3 ++- .../features/nyxus_plugin/nyxus_func.py | 3 ++- .../formats/arrow_to_tabular/__init__.py | 2 +- .../images/formats/file_renaming/__init__.py | 2 +- .../images/formats/ome_converter/__init__.py | 4 ++-- .../formats/tabular_converter/__init__.py | 4 ++-- .../formats/tabular_to_arrow/__init__.py | 8 +++---- formats/vector-to-label-tool/pyproject.toml | 2 +- .../dynamics/vector_to_label.py | 4 ++-- .../images/formats/vector_to_label/helpers.py | 2 +- .../segmentation/mesmer_training/__init__.py | 2 +- .../images/binary_operations/binops.py | 2 +- .../images/image_assembler/__init__.py | 2 +- .../transforms/images/montage/__init__.py | 22 +++++-------------- .../tabular/tabular_merger/__init__.py | 2 +- .../tabular/tabular_thresholding/__init__.py | 2 +- 17 files changed, 30 insertions(+), 39 deletions(-) diff --git a/clustering/k-means-clustering-tool/src/polus/images/clustering/k_means/k_means.py b/clustering/k-means-clustering-tool/src/polus/images/clustering/k_means/k_means.py index 7844b92e9..3e58f8a33 100644 --- a/clustering/k-means-clustering-tool/src/polus/images/clustering/k_means/k_means.py +++ b/clustering/k-means-clustering-tool/src/polus/images/clustering/k_means/k_means.py @@ -11,8 +11,7 @@ from sklearn.cluster import KMeans from sklearn.metrics import calinski_harabasz_score, davies_bouldin_score - -from polus.plugins.clustering.k_means.utils import Methods +from .utils import Methods # Initialize the logger logging.basicConfig( diff --git a/features/feature-segmentation-eval-tool/src/polus/images/features/feature_segmentation_eval/feature_evaluation.py b/features/feature-segmentation-eval-tool/src/polus/images/features/feature_segmentation_eval/feature_evaluation.py index ca8a916b9..5726dad7c 100644 --- a/features/feature-segmentation-eval-tool/src/polus/images/features/feature_segmentation_eval/feature_evaluation.py +++ b/features/feature-segmentation-eval-tool/src/polus/images/features/feature_segmentation_eval/feature_evaluation.py @@ -12,9 +12,10 @@ import pandas as pd import scipy.stats import vaex -from polus.plugins.features.feature_segmentation_eval.metrics import evaluate_all from scipy.spatial import distance +from .metrics import evaluate_all + logger = logging.getLogger(__name__) logger.setLevel(logging.INFO) diff --git a/features/nyxus-tool/src/polus/images/features/nyxus_plugin/nyxus_func.py b/features/nyxus-tool/src/polus/images/features/nyxus_plugin/nyxus_func.py index 5a9833df6..a63bc247c 100644 --- a/features/nyxus-tool/src/polus/images/features/nyxus_plugin/nyxus_func.py +++ b/features/nyxus-tool/src/polus/images/features/nyxus_plugin/nyxus_func.py @@ -7,7 +7,8 @@ import vaex from nyxus import Nyxus -from polus.plugins.features.nyxus_plugin.utils import Extension + +from .utils import Extension logger = logging.getLogger(__name__) diff --git a/formats/arrow-to-tabular-tool/src/polus/images/formats/arrow_to_tabular/__init__.py b/formats/arrow-to-tabular-tool/src/polus/images/formats/arrow_to_tabular/__init__.py index 79e509ac6..3ac05503f 100644 --- a/formats/arrow-to-tabular-tool/src/polus/images/formats/arrow_to_tabular/__init__.py +++ b/formats/arrow-to-tabular-tool/src/polus/images/formats/arrow_to_tabular/__init__.py @@ -1,4 +1,4 @@ """Arrow to Tabular.""" __version__ = "0.2.3-dev0" -from polus.plugins.formats.arrow_to_tabular.arrow_to_tabular import arrow_tabular +from .arrow_to_tabular import arrow_tabular diff --git a/formats/file-renaming-tool/src/polus/images/formats/file_renaming/__init__.py b/formats/file-renaming-tool/src/polus/images/formats/file_renaming/__init__.py index bca53865e..95da50b49 100644 --- a/formats/file-renaming-tool/src/polus/images/formats/file_renaming/__init__.py +++ b/formats/file-renaming-tool/src/polus/images/formats/file_renaming/__init__.py @@ -1,4 +1,4 @@ """File Renaming.""" __version__ = "0.2.4-dev0" -from polus.plugins.formats.file_renaming import file_renaming as file_renaming # noqa +from .file_renaming import file_renaming diff --git a/formats/ome-converter-tool/src/polus/images/formats/ome_converter/__init__.py b/formats/ome-converter-tool/src/polus/images/formats/ome_converter/__init__.py index ae8527c5f..2e82db97b 100644 --- a/formats/ome-converter-tool/src/polus/images/formats/ome_converter/__init__.py +++ b/formats/ome-converter-tool/src/polus/images/formats/ome_converter/__init__.py @@ -2,5 +2,5 @@ __version__ = "0.3.2-dev0" -from polus.plugins.formats.ome_converter.image_converter import batch_convert -from polus.plugins.formats.ome_converter.image_converter import convert_image +from .image_converter import batch_convert +from .image_converter import convert_image diff --git a/formats/tabular-converter-tool/src/polus/images/formats/tabular_converter/__init__.py b/formats/tabular-converter-tool/src/polus/images/formats/tabular_converter/__init__.py index c5c6c1a30..1c0f1aab8 100644 --- a/formats/tabular-converter-tool/src/polus/images/formats/tabular_converter/__init__.py +++ b/formats/tabular-converter-tool/src/polus/images/formats/tabular_converter/__init__.py @@ -1,5 +1,5 @@ """Tabular Converter.""" __version__ = "0.1.2-dev0" -from polus.plugins.formats.tabular_converter.tabular_converter import ConvertTabular -from polus.plugins.formats.tabular_converter.tabular_converter import Extensions +from .tabular_converter import ConvertTabular +from .tabular_converter import Extensions diff --git a/formats/tabular-to-arrow-tool/src/polus/images/formats/tabular_to_arrow/__init__.py b/formats/tabular-to-arrow-tool/src/polus/images/formats/tabular_to_arrow/__init__.py index c87dbdab0..86caa18d0 100644 --- a/formats/tabular-to-arrow-tool/src/polus/images/formats/tabular_to_arrow/__init__.py +++ b/formats/tabular-to-arrow-tool/src/polus/images/formats/tabular_to_arrow/__init__.py @@ -1,7 +1,7 @@ """Tabular to Arrow.""" __version__ = "0.2.3-dev0" -from polus.plugins.formats.tabular_to_arrow.tabular_arrow_converter import binary_to_df -from polus.plugins.formats.tabular_to_arrow.tabular_arrow_converter import csv_to_df -from polus.plugins.formats.tabular_to_arrow.tabular_arrow_converter import df_to_arrow -from polus.plugins.formats.tabular_to_arrow.tabular_arrow_converter import fcs_to_arrow +from .tabular_arrow_converter import binary_to_df +from .tabular_arrow_converter import csv_to_df +from .tabular_arrow_converter import df_to_arrow +from .tabular_arrow_converter import fcs_to_arrow diff --git a/formats/vector-to-label-tool/pyproject.toml b/formats/vector-to-label-tool/pyproject.toml index 87432f4b0..3dc080fcb 100644 --- a/formats/vector-to-label-tool/pyproject.toml +++ b/formats/vector-to-label-tool/pyproject.toml @@ -11,7 +11,7 @@ packages = [{include = "polus", from = "src"}] [tool.poetry.dependencies] python = ">=3.9,<3.12" -polus-plugins-formats-label-to-vector = { path = "../label-to-vector-plugin/", develop = true } +polus-images-formats-label-to-vector = { path = "../label-to-vector-tool/", develop = true } bfio = {version = "2.1.9", extras = ["all"]} filepattern = "^2.0.1" numpy = "~1.24.4" diff --git a/formats/vector-to-label-tool/src/polus/images/formats/vector_to_label/dynamics/vector_to_label.py b/formats/vector-to-label-tool/src/polus/images/formats/vector_to_label/dynamics/vector_to_label.py index 3e614dfaa..0cb9dcc43 100644 --- a/formats/vector-to-label-tool/src/polus/images/formats/vector_to_label/dynamics/vector_to_label.py +++ b/formats/vector-to-label-tool/src/polus/images/formats/vector_to_label/dynamics/vector_to_label.py @@ -6,8 +6,8 @@ import numpy import scipy.ndimage -from polus.plugins.formats.label_to_vector.dynamics import common -from polus.plugins.formats.label_to_vector.utils import helpers as l2v_helpers +from polus.images.formats.label_to_vector.dynamics import common +from polus.images.formats.label_to_vector.utils import helpers as l2v_helpers logger = l2v_helpers.make_logger(__file__) diff --git a/formats/vector-to-label-tool/src/polus/images/formats/vector_to_label/helpers.py b/formats/vector-to-label-tool/src/polus/images/formats/vector_to_label/helpers.py index c40f4f033..46f1963d0 100644 --- a/formats/vector-to-label-tool/src/polus/images/formats/vector_to_label/helpers.py +++ b/formats/vector-to-label-tool/src/polus/images/formats/vector_to_label/helpers.py @@ -6,7 +6,7 @@ import bfio import numpy -from polus.plugins.formats.label_to_vector.utils import constants +from polus.images.formats.label_to_vector.utils import constants def init_zarr_file( diff --git a/segmentation/mesmer-training-tool/src/polus/images/segmentation/mesmer_training/__init__.py b/segmentation/mesmer-training-tool/src/polus/images/segmentation/mesmer_training/__init__.py index 50ab6629d..eff2efd67 100644 --- a/segmentation/mesmer-training-tool/src/polus/images/segmentation/mesmer_training/__init__.py +++ b/segmentation/mesmer-training-tool/src/polus/images/segmentation/mesmer_training/__init__.py @@ -2,4 +2,4 @@ __version__ = "0.0.7-dev0" -from polus.plugins.segmentation.mesmer_training import train as train # noqa +from . import train diff --git a/transforms/images/binary-operations-tool/src/polus/images/transforms/images/binary_operations/binops.py b/transforms/images/binary-operations-tool/src/polus/images/transforms/images/binary_operations/binops.py index 5ed517f59..ab981db66 100644 --- a/transforms/images/binary-operations-tool/src/polus/images/transforms/images/binary_operations/binops.py +++ b/transforms/images/binary-operations-tool/src/polus/images/transforms/images/binary_operations/binops.py @@ -11,7 +11,7 @@ from filepattern import FilePattern from preadator import ProcessManager -from polus.plugins.transforms.images.binary_operations.utils import ( +from .utils import ( TileTuple, blackhat, close_, diff --git a/transforms/images/image-assembler-tool/src/polus/images/transforms/images/image_assembler/__init__.py b/transforms/images/image-assembler-tool/src/polus/images/transforms/images/image_assembler/__init__.py index f373d3d52..d34d7ca74 100644 --- a/transforms/images/image-assembler-tool/src/polus/images/transforms/images/image_assembler/__init__.py +++ b/transforms/images/image-assembler-tool/src/polus/images/transforms/images/image_assembler/__init__.py @@ -2,7 +2,7 @@ __version__ = "1.4.1-dev0" -from polus.plugins.transforms.images.image_assembler.image_assembler import ( # noqa +from .image_assembler import ( # noqa assemble_images, generate_output_filepaths, ) diff --git a/transforms/images/montage-tool/src/polus/images/transforms/images/montage/__init__.py b/transforms/images/montage-tool/src/polus/images/transforms/images/montage/__init__.py index 61175c547..b18f33254 100644 --- a/transforms/images/montage-tool/src/polus/images/transforms/images/montage/__init__.py +++ b/transforms/images/montage-tool/src/polus/images/transforms/images/montage/__init__.py @@ -3,19 +3,9 @@ __version__ = "0.5.1-dev0" -from polus.plugins.transforms.images.montage.montage import ( # noqa - generate_montage_patterns as generate_montage_patterns, -) -from polus.plugins.transforms.images.montage.montage import montage as montage # noqa -from polus.plugins.transforms.images.montage.montage import ( # noqa - montage_all as montage_all, -) -from polus.plugins.transforms.images.montage.utils import ( # noqa - DictWriter as DictWriter, -) -from polus.plugins.transforms.images.montage.utils import ( # noqa - VectorWriter as VectorWriter, -) -from polus.plugins.transforms.images.montage.utils import ( # noqa - subpattern as subpattern, -) +from .montage import generate_montage_patterns +from .montage import montage +from .montage import montage_all +from .utils import DictWriter +from .utils import VectorWriter +from .utils import subpattern diff --git a/transforms/tabular/tabular-merger-tool/src/polus/images/transforms/tabular/tabular_merger/__init__.py b/transforms/tabular/tabular-merger-tool/src/polus/images/transforms/tabular/tabular_merger/__init__.py index 665b22bd0..0add1266f 100644 --- a/transforms/tabular/tabular-merger-tool/src/polus/images/transforms/tabular/tabular_merger/__init__.py +++ b/transforms/tabular/tabular-merger-tool/src/polus/images/transforms/tabular/tabular_merger/__init__.py @@ -1,4 +1,4 @@ """Tabular Merger.""" __version__ = "0.1.2-dev0" -from polus.plugins.transforms.tabular.tabular_merger import tabular_merger +from . import tabular_merger diff --git a/transforms/tabular/tabular-thresholding-tool/src/polus/images/transforms/tabular/tabular_thresholding/__init__.py b/transforms/tabular/tabular-thresholding-tool/src/polus/images/transforms/tabular/tabular_thresholding/__init__.py index 6312f93d3..cc71cde64 100644 --- a/transforms/tabular/tabular-thresholding-tool/src/polus/images/transforms/tabular/tabular_thresholding/__init__.py +++ b/transforms/tabular/tabular-thresholding-tool/src/polus/images/transforms/tabular/tabular_thresholding/__init__.py @@ -1,4 +1,4 @@ """Tabular Thresholding.""" __version__ = "0.1.6-dev0" -from polus.plugins.transforms.tabular.tabular_thresholding import tabular_thresholding +from . import tabular_thresholding From 589846cc1d730fda4d1cabb3827ade2b631325a5 Mon Sep 17 00:00:00 2001 From: Najib Ishaq Date: Wed, 14 Feb 2024 14:40:10 -0500 Subject: [PATCH 6/8] fix: more import fixes --- .../polus/images/formats/file_renaming/__init__.py | 2 +- .../images/transforms/images/montage/montage.py | 2 +- .../tabular_thresholding/tabular_thresholding.py | 12 +++--------- .../tabular_thresholding/thresholding/__init__.py | 12 +++--------- 4 files changed, 8 insertions(+), 20 deletions(-) diff --git a/formats/file-renaming-tool/src/polus/images/formats/file_renaming/__init__.py b/formats/file-renaming-tool/src/polus/images/formats/file_renaming/__init__.py index 95da50b49..89439693d 100644 --- a/formats/file-renaming-tool/src/polus/images/formats/file_renaming/__init__.py +++ b/formats/file-renaming-tool/src/polus/images/formats/file_renaming/__init__.py @@ -1,4 +1,4 @@ """File Renaming.""" __version__ = "0.2.4-dev0" -from .file_renaming import file_renaming +from . import file_renaming diff --git a/transforms/images/montage-tool/src/polus/images/transforms/images/montage/montage.py b/transforms/images/montage-tool/src/polus/images/transforms/images/montage/montage.py index 5eb26a266..8b79ae3d6 100644 --- a/transforms/images/montage-tool/src/polus/images/transforms/images/montage/montage.py +++ b/transforms/images/montage-tool/src/polus/images/transforms/images/montage/montage.py @@ -7,7 +7,7 @@ from bfio import BioReader from filepattern import FilePattern -from polus.plugins.transforms.images.montage.utils import ( +from .utils import ( DictWriter, VectorWriter, subpattern, diff --git a/transforms/tabular/tabular-thresholding-tool/src/polus/images/transforms/tabular/tabular_thresholding/tabular_thresholding.py b/transforms/tabular/tabular-thresholding-tool/src/polus/images/transforms/tabular/tabular_thresholding/tabular_thresholding.py index 75ca41964..d00ec2bd8 100644 --- a/transforms/tabular/tabular-thresholding-tool/src/polus/images/transforms/tabular/tabular_thresholding/tabular_thresholding.py +++ b/transforms/tabular/tabular-thresholding-tool/src/polus/images/transforms/tabular/tabular_thresholding/tabular_thresholding.py @@ -10,15 +10,9 @@ import numpy as np import vaex -from polus.plugins.transforms.tabular.tabular_thresholding.thresholding import ( # noqa - custom_fpr as custom_fpr, -) -from polus.plugins.transforms.tabular.tabular_thresholding.thresholding import ( # noqa - n_sigma as n_sigma, -) -from polus.plugins.transforms.tabular.tabular_thresholding.thresholding import ( # noqa - otsu as otsu, -) +from .thresholding import custom_fpr +from.thresholding import n_sigma +from .thresholding import otsu logger = logging.getLogger(__name__) diff --git a/transforms/tabular/tabular-thresholding-tool/src/polus/images/transforms/tabular/tabular_thresholding/thresholding/__init__.py b/transforms/tabular/tabular-thresholding-tool/src/polus/images/transforms/tabular/tabular_thresholding/thresholding/__init__.py index d3412dcad..5e67d641c 100644 --- a/transforms/tabular/tabular-thresholding-tool/src/polus/images/transforms/tabular/tabular_thresholding/thresholding/__init__.py +++ b/transforms/tabular/tabular-thresholding-tool/src/polus/images/transforms/tabular/tabular_thresholding/thresholding/__init__.py @@ -1,12 +1,6 @@ """Tabular Thresholding.""" __version__ = "0.1.3" -from polus.plugins.transforms.tabular.tabular_thresholding.thresholding import ( # noqa - custom_fpr as custom_fpr, -) -from polus.plugins.transforms.tabular.tabular_thresholding.thresholding import ( # noqa - n_sigma as n_sigma, -) -from polus.plugins.transforms.tabular.tabular_thresholding.thresholding import ( # noqa - otsu as otsu, -) +from . import custom_fpr +from . import n_sigma +from . import otsu From a50341d8a33fb819ee456d95e4312bbad7e51726 Mon Sep 17 00:00:00 2001 From: Najib Ishaq Date: Fri, 16 Feb 2024 10:40:30 -0500 Subject: [PATCH 7/8] fix: tool suffixes --- .../build-docker.sh | 2 +- .../feature-segmentation-eval-tool/plugin.cwl | 44 -------------- .../plugin.json | 2 +- .../pixel-segmentation-eval-tool/plugin.json | 2 +- .../build-docker.sh | 2 +- .../region-segmentation-eval-tool/plugin.cwl | 60 ------------------- .../region-segmentation-eval-tool/plugin.json | 2 +- muck.sh | 37 ------------ 8 files changed, 5 insertions(+), 146 deletions(-) delete mode 100644 features/feature-segmentation-eval-tool/plugin.cwl delete mode 100644 features/region-segmentation-eval-tool/plugin.cwl delete mode 100755 muck.sh diff --git a/features/feature-segmentation-eval-tool/build-docker.sh b/features/feature-segmentation-eval-tool/build-docker.sh index 629a59b56..9ba5a2d33 100644 --- a/features/feature-segmentation-eval-tool/build-docker.sh +++ b/features/feature-segmentation-eval-tool/build-docker.sh @@ -1,4 +1,4 @@ #!/bin/bash version=$( Date: Fri, 16 Feb 2024 11:34:10 -0500 Subject: [PATCH 8/8] fix: apply flatfield uses pinned filepattern version --- transforms/images/apply-flatfield-tool/pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/transforms/images/apply-flatfield-tool/pyproject.toml b/transforms/images/apply-flatfield-tool/pyproject.toml index 081f5951a..93ff18c35 100644 --- a/transforms/images/apply-flatfield-tool/pyproject.toml +++ b/transforms/images/apply-flatfield-tool/pyproject.toml @@ -12,7 +12,7 @@ packages = [{include = "polus", from = "src"}] [tool.poetry.dependencies] python = ">=3.9,<3.12" bfio = { version = "^2.3.3", extras = ["all"] } -filepattern = "^2.0.4" +filepattern = "2.0.4" typer = { version = "^0.7.0", extras = ["all"] } numpy = "^1.24.3" tqdm = "^4.65.0"