Fixed typo in docker build script (PolusAI#556)

* fix: typo in docker build script * fix: ci TODO and ftl ignore * fix: removing extraneous deps in image-assembler * Bump version: 1.4.1 → 1.4.2-dev0 * build: removed dep on tifffile in pixel-segmentation-eval * Bump version: 0.1.13 → 0.1.14-dev0 * build: removed dep on tifffile in mesmer-training * Bump version: 0.0.7 → 0.0.8-dev0 * build: allowing looser bfio versions in label-to-vector * Bump version: 0.7.1 → 0.7.2-dev0 * build: allowing looser bfio versions in vector-to-label * Bump version: 0.7.1 → 0.7.2-dev0
hamshkhawar · Aug 15, 2024 · 0353540 · 0353540
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diff --git a/.github/workflows/find-all-tools.yml b/.github/workflows/find-all-tools.yml
@@ -26,9 +26,8 @@ jobs:
         id: set-matrix
         run: |
           # List of directories to ignore
-          ignored_dirs="polus-python-template .venv"
+          ignored_dirs="polus-python-template ftl-label .venv"
 
-          # TODO: Remove these after merging PR #547
           # List of tools that are broken for known reasons
           broken_tools="binary-operations precompute-slide microjson-to-ome region-segmentation-eval basic-flatfield-estimation ftl-label cell-border-segmentation"
           # Reasons:

diff --git a/features/nyxus-tool/build-docker.sh b/features/nyxus-tool/build-docker.sh
@@ -1,4 +1,3 @@
-
 #!/bin/bash
 
 # Change the name of the tool here
@@ -17,7 +16,7 @@ repo_root=$(git rev-parse --show-toplevel)
 # The Dockerfile and .dockerignore files are copied to the repository root before building the image
 cd ${repo_root}
 cp ./${tool_dir}/${tool_name}/Dockerfile .
-cp .gitingore .dockerignore
+cp .gitignore .dockerignore
 docker build . -t ${tag}
 rm Dockerfile .dockerignore
 cd ${cur_dir}
diff --git a/features/pixel-segmentation-eval-tool/.bumpversion.cfg b/features/pixel-segmentation-eval-tool/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.1.13
+current_version = 0.1.14-dev0
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?

diff --git a/features/pixel-segmentation-eval-tool/CHANGELOG.md b/features/pixel-segmentation-eval-tool/CHANGELOG.md
@@ -1,4 +1,4 @@
-# pixel-segmentation-eval(v0.1.13)
+# pixel-segmentation-eval(v0.1.14-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/pixel-segmentation-eval-tool/README.md b/features/pixel-segmentation-eval-tool/README.md
@@ -1,4 +1,4 @@
-# Pixel segmentation eval (v0.1.13)
+# Pixel segmentation eval (v0.1.14-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
@@ -1 +1 @@
-0.1.13
+0.1.14-dev0
diff --git a/features/pixel-segmentation-eval-tool/build-docker.sh b/features/pixel-segmentation-eval-tool/build-docker.sh
@@ -1,4 +1,3 @@
-
 #!/bin/bash
 
 # Change the name of the tool here
@@ -17,7 +16,7 @@ repo_root=$(git rev-parse --show-toplevel)
 # The Dockerfile and .dockerignore files are copied to the repository root before building the image
 cd ${repo_root}
 cp ./${tool_dir}/${tool_name}/Dockerfile .
-cp .gitingore .dockerignore
+cp .gitignore .dockerignore
 docker build . -t ${tag}
 rm Dockerfile .dockerignore
 cd ${cur_dir}
diff --git a/features/pixel-segmentation-eval-tool/plugin.json b/features/pixel-segmentation-eval-tool/plugin.json
@@ -1,14 +1,14 @@
 {
   "name": "Pixel Segmentation Eval",
-  "version": "0.1.13",
+  "version": "0.1.14-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)",
   "institution": "National Center for Advancing Translational Sciences, National Institutes of Health",
   "repository": "https://github.com/polusai/polus-plugins",
   "website": "https://ncats.nih.gov/preclinical/core/informatics",
   "citation": "",
-  "containerId": "polusai/pixel-segmentation-eval-tool:0.1.13",
+  "containerId": "polusai/pixel-segmentation-eval-tool:0.1.14-dev0",
   "baseCommand": [
     "python3",
     "-m",

diff --git a/features/pixel-segmentation-eval-tool/pyproject.toml b/features/pixel-segmentation-eval-tool/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "polus-images-features-pixel-segmentation-eval"
-version = "0.1.13"
+version = "0.1.14-dev0"
 description = ""
 authors = [
            "Vishakha Goyal <vishakha.goyal@nih.gov>",
@@ -15,7 +15,6 @@ bfio = {version = "2.1.9", extras = ["all"]}
 filepattern = "^2.0.1"
 typer = "^0.7.0"
 tqdm = "^4.64.1"
-tifffile="^2020.10.1"
 vaex = "^4.7.0"
 scipy = "1.9.3"
 pyarrow = ">=16.0,<17.0"

diff --git a/...ixel-segmentation-eval-tool/src/polus/images/features/pixel_segmentation_eval/__init__.py b/...ixel-segmentation-eval-tool/src/polus/images/features/pixel_segmentation_eval/__init__.py
@@ -1,3 +1,3 @@
 """Pixel segmentation eval package."""
 
-__version__ = "0.1.13"
+__version__ = "0.1.14-dev0"
diff --git a/features/region-segmentation-eval-tool/build-docker.sh b/features/region-segmentation-eval-tool/build-docker.sh
@@ -1,4 +1,3 @@
-
 #!/bin/bash
 
 # Change the name of the tool here
@@ -17,7 +16,7 @@ repo_root=$(git rev-parse --show-toplevel)
 # The Dockerfile and .dockerignore files are copied to the repository root before building the image
 cd ${repo_root}
 cp ./${tool_dir}/${tool_name}/Dockerfile .
-cp .gitingore .dockerignore
+cp .gitignore .dockerignore
 docker build . -t ${tag}
 rm Dockerfile .dockerignore
 cd ${cur_dir}
diff --git a/formats/file-renaming-tool/build-docker.sh b/formats/file-renaming-tool/build-docker.sh
@@ -1,4 +1,3 @@
-
 #!/bin/bash
 
 # Change the name of the tool here
@@ -17,7 +16,7 @@ repo_root=$(git rev-parse --show-toplevel)
 # The Dockerfile and .dockerignore files are copied to the repository root before building the image
 cd ${repo_root}
 cp ./${tool_dir}/${tool_name}/Dockerfile .
-cp .gitingore .dockerignore
+cp .gitignore .dockerignore
 docker build . -t ${tag}
 rm Dockerfile .dockerignore
 cd ${cur_dir}
diff --git a/formats/label-to-vector-tool/.bumpversion.cfg b/formats/label-to-vector-tool/.bumpversion.cfg
@@ -1,6 +1,6 @@
 [bumpversion]
-current_version = 0.7.1
-commit = False
+current_version = 0.7.2-dev0
+commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?
 serialize = 

diff --git a/formats/label-to-vector-tool/Dockerfile b/formats/label-to-vector-tool/Dockerfile
@@ -1,4 +1,4 @@
-FROM polusai/bfio:2.1.9
+FROM polusai/bfio:2.4.1
 
 # environment variables defined in polusai/bfio
 ENV EXEC_DIR="/opt/executables"

diff --git a/formats/label-to-vector-tool/README.md b/formats/label-to-vector-tool/README.md
@@ -1,4 +1,4 @@
-# Label To Vector (v0.7.1)
+# Label To Vector (v0.7.2-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
@@ -1 +1 @@
-0.7.1
+0.7.2-dev0
diff --git a/formats/label-to-vector-tool/build-docker.sh b/formats/label-to-vector-tool/build-docker.sh
@@ -1,4 +1,3 @@
-
 #!/bin/bash
 
 # Change the name of the tool here
@@ -17,7 +16,7 @@ repo_root=$(git rev-parse --show-toplevel)
 # The Dockerfile and .dockerignore files are copied to the repository root before building the image
 cd ${repo_root}
 cp ./${tool_dir}/${tool_name}/Dockerfile .
-cp .gitingore .dockerignore
+cp .gitignore .dockerignore
 docker build . -t ${tag}
 rm Dockerfile .dockerignore
 cd ${cur_dir}
diff --git a/formats/label-to-vector-tool/plugin.json b/formats/label-to-vector-tool/plugin.json
@@ -1,14 +1,14 @@
 {
   "name": "Label to Vector",
-  "version": "0.7.1",
+  "version": "0.7.2-dev0",
   "title": "Label to Vector",
   "description": "Convert labelled masks to flow-field vectors.",
   "author": "Najib Ishaq (najib.ishaq@nih.gov), Nick Schaub (nick.schaub@nih.gov)",
   "institution": "National Center for Advancing Translational Sciences, National Institutes of Health",
   "repository": "https://github.com/PolusAI/polus-plugins/tree/dev/formats/polus-vector-converter-plugins",
   "website": "https://ncats.nih.gov/preclinical/core/informatics",
   "citation": "https://www.biorxiv.org/content/10.1101/2020.02.02.931238v1",
-  "containerId": "polusai/label-to-vector-tool:0.7.1",
+  "containerId": "polusai/label-to-vector-tool:0.7.2-dev0",
   "inputs": [
     {
       "name": "inpDir",

diff --git a/formats/label-to-vector-tool/pyproject.toml b/formats/label-to-vector-tool/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "polus-images-formats-label-to-vector"
-version = "0.7.1"
+version = "0.7.2-dev0"
 description = ""
 authors = [
     "Najib Ishaq <najib.ishaq@nih.gov>",
@@ -12,7 +12,7 @@ packages = [{include = "polus", from = "src"}]
 [tool.poetry.dependencies]
 python = ">=3.9,<3.12"
 numpy = "~1.24.4"
-bfio = { version = "2.1.9", extras = ["all"] }
+bfio = { version = "^2.1", extras = ["all"] }
 typer = "^0.7.0"
 filepattern = "^2.0.1"
 tqdm = "^4.66.1"

diff --git a/formats/label-to-vector-tool/src/polus/images/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__ = "0.7.1"
+__version__ = "0.7.2-dev0"
diff --git a/formats/ome-converter-tool/build-docker.sh b/formats/ome-converter-tool/build-docker.sh
@@ -1,4 +1,3 @@
-
 #!/bin/bash
 
 # Change the name of the tool here
@@ -17,7 +16,7 @@ repo_root=$(git rev-parse --show-toplevel)
 # The Dockerfile and .dockerignore files are copied to the repository root before building the image
 cd ${repo_root}
 cp ./${tool_dir}/${tool_name}/Dockerfile .
-cp .gitingore .dockerignore
+cp .gitignore .dockerignore
 docker build . -t ${tag}
 rm Dockerfile .dockerignore
 cd ${cur_dir}
diff --git a/formats/vector-to-label-tool/.bumpversion.cfg b/formats/vector-to-label-tool/.bumpversion.cfg
@@ -1,6 +1,6 @@
 [bumpversion]
-current_version = 0.7.1
-commit = False
+current_version = 0.7.2-dev0
+commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?
 serialize = 

diff --git a/formats/vector-to-label-tool/Dockerfile b/formats/vector-to-label-tool/Dockerfile
@@ -1,4 +1,4 @@
-FROM polusai/label-to-vector-plugin:0.7.0-dev30
+FROM polusai/bfio:2.4.1
 
 # environment variables defined in polusai/bfio
 ENV EXEC_DIR="/opt/executables"

diff --git a/formats/vector-to-label-tool/README.md b/formats/vector-to-label-tool/README.md
@@ -1,4 +1,4 @@
-# Vector to Label (v0.7.1)
+# Vector to Label (v0.7.2-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
@@ -1 +1 @@
-0.7.1
+0.7.2-dev0
diff --git a/formats/vector-to-label-tool/build-docker.sh b/formats/vector-to-label-tool/build-docker.sh
@@ -1,4 +1,3 @@
-
 #!/bin/bash
 
 # Change the name of the tool here
@@ -17,7 +16,7 @@ repo_root=$(git rev-parse --show-toplevel)
 # The Dockerfile and .dockerignore files are copied to the repository root before building the image
 cd ${repo_root}
 cp ./${tool_dir}/${tool_name}/Dockerfile .
-cp .gitingore .dockerignore
+cp .gitignore .dockerignore
 docker build . -t ${tag}
 rm Dockerfile .dockerignore
 cd ${cur_dir}
diff --git a/formats/vector-to-label-tool/plugin.json b/formats/vector-to-label-tool/plugin.json
@@ -1,14 +1,14 @@
 {
   "name": "Vector to Label",
-  "version": "0.7.1",
+  "version": "0.7.2-dev0",
   "title": "Vector to Label",
   "description": "Create labelled masks from flow-field vectors.",
   "author": "Nick Schaub (nick.schaub@nih.gov), Najib Ishaq (najib.ishaq@nih.gov)",
   "institution": "National Center for Advancing Translational Sciences, National Institutes of Health",
   "repository": "https://github.com/PolusAI/polus-plugins/tree/dev/formats/polus-vector-converter-plugin",
   "website": "https://ncats.nih.gov/preclinical/core/informatics",
   "citation": "https://www.biorxiv.org/content/10.1101/2020.02.02.931238v1",
-  "containerId": "polusai/vector-to-label-tool:0.7.1",
+  "containerId": "polusai/vector-to-label-tool:0.7.2-dev0",
   "inputs": [
     {
       "name": "inpDir",

diff --git a/formats/vector-to-label-tool/pyproject.toml b/formats/vector-to-label-tool/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "polus-images-formats-vector-to-label"
-version = "0.7.1"
+version = "0.7.2-dev0"
 description = ""
 authors = [
     "Najib Ishaq <najib.ishaq@nih.gov>",
@@ -12,7 +12,7 @@ packages = [{include = "polus", from = "src"}]
 [tool.poetry.dependencies]
 python = ">=3.9,<3.12"
 polus-images-formats-label-to-vector = { path = "../label-to-vector-tool/", develop = true }
-bfio = {version = "2.1.9", extras = ["all"]}
+bfio = {version = "^2.1", extras = ["all"]}
 filepattern = "^2.0.1"
 numpy = "~1.24.4"
 tqdm = "^4.66.1"

diff --git a/formats/vector-to-label-tool/src/polus/images/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__ = "0.7.1"
+__version__ = "0.7.2-dev0"
diff --git a/regression/basic-flatfield-estimation-tool/build-docker.sh b/regression/basic-flatfield-estimation-tool/build-docker.sh
@@ -1,4 +1,3 @@
-
 #!/bin/bash
 
 # Change the name of the tool here
@@ -17,7 +16,7 @@ repo_root=$(git rev-parse --show-toplevel)
 # The Dockerfile and .dockerignore files are copied to the repository root before building the image
 cd ${repo_root}
 cp ./${tool_dir}/${tool_name}/Dockerfile .
-cp .gitingore .dockerignore
+cp .gitignore .dockerignore
 docker build . -t ${tag}
 rm Dockerfile .dockerignore
 cd ${cur_dir}
diff --git a/regression/theia-bleedthrough-estimation-tool/build-docker.sh b/regression/theia-bleedthrough-estimation-tool/build-docker.sh
@@ -1,4 +1,3 @@
-
 #!/bin/bash
 
 # Change the name of the tool here
@@ -17,7 +16,7 @@ repo_root=$(git rev-parse --show-toplevel)
 # The Dockerfile and .dockerignore files are copied to the repository root before building the image
 cd ${repo_root}
 cp ./${tool_dir}/${tool_name}/Dockerfile .
-cp .gitingore .dockerignore
+cp .gitignore .dockerignore
 docker build . -t ${tag}
 rm Dockerfile .dockerignore
 cd ${cur_dir}
diff --git a/segmentation/cell-border-segmentation-tool/build-docker.sh b/segmentation/cell-border-segmentation-tool/build-docker.sh
@@ -1,4 +1,3 @@
-
 #!/bin/bash
 
 # Change the name of the tool here
@@ -17,7 +16,7 @@ repo_root=$(git rev-parse --show-toplevel)
 # The Dockerfile and .dockerignore files are copied to the repository root before building the image
 cd ${repo_root}
 cp ./${tool_dir}/${tool_name}/Dockerfile .
-cp .gitingore .dockerignore
+cp .gitignore .dockerignore
 docker build . -t ${tag}
 rm Dockerfile .dockerignore
 cd ${cur_dir}
diff --git a/segmentation/imagej-threshold-apply-tool/build-docker.sh b/segmentation/imagej-threshold-apply-tool/build-docker.sh
@@ -1,4 +1,3 @@
-
 #!/bin/bash
 
 # Change the name of the tool here
@@ -17,7 +16,7 @@ repo_root=$(git rev-parse --show-toplevel)
 # The Dockerfile and .dockerignore files are copied to the repository root before building the image
 cd ${repo_root}
 cp ./${tool_dir}/${tool_name}/Dockerfile .
-cp .gitingore .dockerignore
+cp .gitignore .dockerignore
 docker build . -t ${tag}
 rm Dockerfile .dockerignore
 cd ${cur_dir}
diff --git a/segmentation/imagej-threshold-huang-tool/build-docker.sh b/segmentation/imagej-threshold-huang-tool/build-docker.sh
@@ -1,4 +1,3 @@
-
 #!/bin/bash
 
 # Change the name of the tool here
@@ -17,7 +16,7 @@ repo_root=$(git rev-parse --show-toplevel)
 # The Dockerfile and .dockerignore files are copied to the repository root before building the image
 cd ${repo_root}
 cp ./${tool_dir}/${tool_name}/Dockerfile .
-cp .gitingore .dockerignore
+cp .gitignore .dockerignore
 docker build . -t ${tag}
 rm Dockerfile .dockerignore
 cd ${cur_dir}
diff --git a/segmentation/imagej-threshold-ij1-tool/build-docker.sh b/segmentation/imagej-threshold-ij1-tool/build-docker.sh
@@ -1,4 +1,3 @@
-
 #!/bin/bash
 
 # Change the name of the tool here
@@ -17,7 +16,7 @@ repo_root=$(git rev-parse --show-toplevel)
 # The Dockerfile and .dockerignore files are copied to the repository root before building the image
 cd ${repo_root}
 cp ./${tool_dir}/${tool_name}/Dockerfile .
-cp .gitingore .dockerignore
+cp .gitignore .dockerignore
 docker build . -t ${tag}
 rm Dockerfile .dockerignore
 cd ${cur_dir}
diff --git a/segmentation/imagej-threshold-intermodes-tool/build-docker.sh b/segmentation/imagej-threshold-intermodes-tool/build-docker.sh
@@ -1,4 +1,3 @@
-
 #!/bin/bash
 
 # Change the name of the tool here
@@ -17,7 +16,7 @@ repo_root=$(git rev-parse --show-toplevel)
 # The Dockerfile and .dockerignore files are copied to the repository root before building the image
 cd ${repo_root}
 cp ./${tool_dir}/${tool_name}/Dockerfile .
-cp .gitingore .dockerignore
+cp .gitignore .dockerignore
 docker build . -t ${tag}
 rm Dockerfile .dockerignore
 cd ${cur_dir}