Dimension Stacking: Fixed Dockerfile and build script (PolusAI#554)

* chore: some initial cleanup

* ci: updated Dockerfile and build script

* Bump version: 0.1.1-dev0 → 0.1.1-dev1

* build: updated bfio to 2.3.6

* Bump version: 0.1.1-dev1 → 0.1.1-dev2

formats/image-dimension-stacking-tool/.bumpversion.cfg

@@ -1,6 +1,6 @@
 [bumpversion]
-current_version = 0.1.1-dev
-commit = False
+current_version = 0.1.1-dev2
+commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?
 serialize = 

formats/image-dimension-stacking-tool/Dockerfile

@@ -9,13 +9,17 @@ ENV POLUS_LOG="INFO"
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-COPY pyproject.toml ${EXEC_DIR}
-COPY VERSION ${EXEC_DIR}
-COPY README.md ${EXEC_DIR}
-COPY src ${EXEC_DIR}/src
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="formats/image-dimension-stacking-tool"
 
-RUN pip3 install ${EXEC_DIR} --no-cache-dir
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-# Default command. Additional arguments are provided through the command line
+# Install the tool
+RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
+
+# Set the entrypoint
+# TODO: Change the entrypoint to the tool entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.formats.image_dimension_stacking"]
 CMD ["--help"]

formats/image-dimension-stacking-tool/README.md

@@ -1,4 +1,4 @@
-# Image dimension stacking(0.1.1-dev)
+# Image dimension stacking(0.1.1-dev2)
 
 This plugin leverages the [filepattern](https://filepattern2.readthedocs.io/en/latest/Home.html) library and employs the filepattern `groupBy` functionality to enable the matching of image filenames, facilitating their stacking into multi-dimensional images.
 

formats/image-dimension-stacking-tool/VERSION

@@ -1 +1 @@
-0.1.1-dev
+0.1.1-dev2

formats/image-dimension-stacking-tool/build-docker.sh

@@ -1,4 +1,22 @@
 #!/bin/bash
 
+# TODO: Change the name of the tool here
+tool_dir="formats"
+tool_name="image-dimension-stacking-tool"
+
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/image-dimension-stacking-tool:${version}
+tag="polusai/${tool_name}:${version}"
+echo "Building docker image with tag: ${tag}"
+
+# The current directory and the repository root are saved in variables
+cur_dir=$(pwd)
+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
+docker build . -t ${tag}
+rm Dockerfile .dockerignore
+cd ${cur_dir}

formats/image-dimension-stacking-tool/plugin.json

@@ -1,13 +1,13 @@
 {
   "name": "Image Dimension Stacking",
-  "version": "0.1.1-dev",
+  "version": "0.1.1-dev2",
   "title": "Stacking of image dimensions (c, z, t) to create a multidimensional image.",
   "description": "Stacking of image dimensions (c, z, t) to create a multidimensional image.",
   "author": "Nick Schaub (nick.schaub@nih.gov), Hamdah Shafqat Abbasi (hamdahshafqat.abbasi@nih.gov)",
   "institution": "National Center for Advancing Translational Sciences, National Institutes of Health",
   "repository": "https://github.com/PolusAI/image-tools",
   "website": "https://ncats.nih.gov/preclinical/core/informatics",
-  "containerId": "polusai/image-dimension-stacking-tool:0.1.1-dev",
+  "containerId": "polusai/image-dimension-stacking-tool:0.1.1-dev2",
   "baseCommand": [
     "python3",
     "-m",

formats/image-dimension-stacking-tool/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "polus-images-formats-image-dimension-stacking"
-version = "0.1.1-dev"
+version = "0.1.1-dev2"
 description = "Stacking multi-dimensional images"
 authors = [
            "Nick Schaub <nick.schaub@nih.gov>",
@@ -12,19 +12,13 @@ packages = [{include = "polus", from = "src"}]
 
 [tool.poetry.dependencies]
 python = ">=3.9,<3.12"
-bfio = {version = "2.3.3", extras = ["all"]}
+bfio = {version = "^2.3.6", extras = ["all"]}
 typer = "^0.7.0"
 tqdm = "^4.66.1"
 filepattern = "^2.0.4"
 pydantic = "^1.10.4"
 preadator="0.4.0.dev2"
-
-
-[[tool.poetry.source]]
-name = "test"
-url = "https://test.pypi.org/simple/"
-default = false
-secondary = true
+numpy = "<2.0.0"
 
 [tool.poetry.group.dev.dependencies]
 bump2version = "^1.0.1"

formats/image-dimension-stacking-tool/src/polus/images/formats/image_dimension_stacking/__init__.py

@@ -1,2 +1,3 @@
 """Image dimension stacking package."""
-__version__ = "0.1.1-dev"
+
+__version__ = "0.1.1-dev2"

formats/image-dimension-stacking-tool/tests/conftest.py

@@ -2,6 +2,7 @@
 
 Set up all data used in tests.
 """
+
 import shutil
 import tempfile
 from pathlib import Path

formats/image-dimension-stacking-tool/tests/test_cli.py

@@ -1,9 +1,11 @@
 """Test Command line Tool."""
-from typer.testing import CliRunner
-from polus.images.formats.image_dimension_stacking.__main__ import app
+
 from pathlib import Path
 from typing import Union
+
+from typer.testing import CliRunner
 import pytest
+from polus.images.formats.image_dimension_stacking.__main__ import app
 
 
 def test_cli(synthetic_images: tuple[Union[str, Path]], output_directory: Path) -> None:

formats/image-dimension-stacking-tool/tests/test_dimension_stacking.py

@@ -1,4 +1,5 @@
 """Testing of image dimension stacking."""
+
 from pathlib import Path
 from typing import Union