ci: Updated actions, dockerfiles, and build-docker scripts

Bump version: 0.5.0 → 0.5.1-dev0

fix: CI bump version before building docker image

ci: ict.yml/yaml in tests actions

wip: updated docker files and build scripts

ci: removing manual filter from release actions

fix: installing iamgej in dockerfiles

fix: removing imagej stuff from non-imagej tools

fix: dockerfile for theia

build: pinning numpy under 2.0 for some tools

chore: deleted tools that have been moved into tabulsr-tools

.github/workflows/package-release.yml

@@ -129,6 +129,21 @@ jobs:
           fetch-depth: 0
           ref: ${{ github.event.inputs.branch }}
           persist-credentials: false
+      - name: Python | Setup
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.9'
+      - name: Python | Install bump2version
+        run: |
+          python -m pip install --upgrade pip
+          pip install bump2version
+      - name: Python | Bump Version Release
+        id: bump_version
+        run: |
+          cur_dir=$GITHUB_WORKSPACE
+          cd ${{ matrix.package_dir }}
+          bump2version release --no-commit --allow-dirty
+          cd ${cur_dir}
       - name: Docker | Tag
         id: docker_tag
         run: |

.github/workflows/pre-release-filter.yml

@@ -37,9 +37,6 @@ jobs:
           PACKAGE_DIRS=""
           COMPANION_FILES="VERSION .bumpversion.cfg"
 
-          # TODO: Remove this line and its effects after debugging
-          ALLOWED_DIRS="segmentation/imagej-threshold-apply-tool segmentation/imagej-threshold-huang-tool"
-
           # Get the names of all the files tracked by git in the repo
           ALL_FILES=$(git ls-tree --full-tree -r --name-only HEAD)
 
@@ -54,13 +51,6 @@ jobs:
               continue
             fi
 
-            # Check if the package directory is allowed
-            if [[ ! "$ALLOWED_DIRS" == *"$pkg_dir"* ]]
-            then
-              echo "Skipping $pkg_dir"
-              continue
-            fi
-
             # Check if the file is a pyproject.toml file
             if [[ "$(basename ${file})" = *"pyproject"* ]]
             then

clustering/k-means-clustering-tool/Dockerfile

@@ -9,12 +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="clustering/k-means-clustering-tool"
 
-RUN pip3 install ${EXEC_DIR} --no-cache-dir
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-ENTRYPOINT ["python3", "-m", "polus.images.clustering.k_means"]
+# 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.clustering.k_means_clustering"]
 CMD ["--help"]

clustering/k-means-clustering-tool/build-docker.sh

@@ -1,4 +1,23 @@
+
 #!/bin/bash
 
+# Change the name of the tool here
+tool_dir="clustering"
+tool_name="k-means-clustering-tool"
+
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/k-means-clustering-tool:${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}

clustering/outlier-removal-tool/Dockerfile

@@ -4,17 +4,22 @@ FROM polusai/bfio:2.3.3
 ENV EXEC_DIR="/opt/executables"
 ENV POLUS_IMG_EXT=".ome.tif"
 ENV POLUS_TAB_EXT=".arrow"
-
+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}
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="clustering/outlier-removal-tool"
 
-RUN pip3 install ${EXEC_DIR} --no-cache
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
+# 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.clustering.outlier_removal"]
 CMD ["--help"]

clustering/outlier-removal-tool/build-docker.sh

@@ -1,4 +1,23 @@
+
 #!/bin/bash
 
+# Change the name of the tool here
+tool_dir="clustering"
+tool_name="outlier-removal-tool"
+
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/outlier-removal-tool:${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}

features/nyxus-tool/Dockerfile

@@ -4,16 +4,22 @@ FROM polusai/bfio:2.3.3
 ENV EXEC_DIR="/opt/executables"
 ENV POLUS_IMG_EXT=".ome.tif"
 ENV POLUS_TAB_EXT=".csv"
+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="features/nyxus-tool"
 
-RUN pip3 install ${EXEC_DIR} --no-cache-dir
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-ENTRYPOINT ["python3", "-m", "polus.images.features.nyxus_plugin"]
+# 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.features.nyxus"]
 CMD ["--help"]

features/nyxus-tool/build-docker.sh

@@ -1,4 +1,23 @@
+
 #!/bin/bash
 
+# Change the name of the tool here
+tool_dir="features"
+tool_name="nyxus-tool"
+
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/nyxus-tool:${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}

features/pixel-segmentation-eval-tool/Dockerfile

@@ -4,16 +4,22 @@ FROM polusai/bfio:2.1.9
 ENV EXEC_DIR="/opt/executables"
 ENV POLUS_IMG_EXT=".ome.tif"
 ENV POLUS_TAB_EXT=".csv"
+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="features/pixel-segmentation-eval-tool"
 
-RUN pip3 install ${EXEC_DIR} --no-cache-dir
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
+# 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.features.pixel_segmentation_eval"]
 CMD ["--help"]

features/pixel-segmentation-eval-tool/build-docker.sh

@@ -1,4 +1,23 @@
+
 #!/bin/bash
 
+# Change the name of the tool here
+tool_dir="features"
+tool_name="pixel-segmentation-eval-tool"
+
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/pixel-segmentation-eval-tool:${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}

features/region-segmentation-eval-tool/Dockerfile

@@ -4,16 +4,22 @@ FROM polusai/bfio:2.1.9
 ENV EXEC_DIR="/opt/executables"
 ENV POLUS_IMG_EXT=".ome.tif"
 ENV POLUS_TAB_EXT=".csv"
+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="features/region-segmentation-eval-tool"
 
-RUN pip3 install ${EXEC_DIR} --no-cache-dir
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
+# 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.features.region_segmentation_eval"]
 CMD ["--help"]

features/region-segmentation-eval-tool/build-docker.sh

@@ -1,4 +1,23 @@
+
 #!/bin/bash
 
+# Change the name of the tool here
+tool_dir="features"
+tool_name="region-segmentation-eval-tool"
+
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/region-segmentation-eval-tool:${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/arrow-to-tabular-tool/Dockerfile

@@ -4,17 +4,22 @@ FROM polusai/bfio:2.1.9
 ENV EXEC_DIR="/opt/executables"
 ENV POLUS_IMG_EXT=".ome.tif"
 ENV POLUS_TAB_EXT=".csv"
+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}
-RUN pip3 install --index-url https://test.pypi.org/simple/ filepattern==2.2.7
-COPY src ${EXEC_DIR}/src
+# TODO: Change the tool_dir to the tool directory
+ENV TOOL_DIR="formats/arrow-to-tabular-tool"
 
-RUN pip3 install ${EXEC_DIR} --no-cache-dir
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
+# 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.arrow_to_tabular"]
 CMD ["--help"]

formats/arrow-to-tabular-tool/build-docker.sh

@@ -1,4 +1,23 @@
+
 #!/bin/bash
 
+# Change the name of the tool here
+tool_dir="formats"
+tool_name="arrow-to-tabular-tool"
+
+# The version is read from the VERSION file
 version=$(<VERSION)
-docker build . -t polusai/arrow-to-tabular-tool:${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/file-renaming-tool/Dockerfile

@@ -2,19 +2,24 @@ FROM polusai/bfio:2.1.9
 
 # environment variables defined in polusai/bfio
 ENV EXEC_DIR="/opt/executables"
-ENV POLUS_LOG="INFO"
 ENV POLUS_IMG_EXT=".ome.tif"
 ENV POLUS_TAB_EXT=".csv"
+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/file-renaming-tool"
+
+# Copy the repository into the container
+RUN mkdir image-tools
+COPY . ${EXEC_DIR}/image-tools
 
-RUN pip3 install ${EXEC_DIR} --no-cache-dir
+# Install the tool
+RUN pip3 install "${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.file_renaming"]
 CMD ["--help"]