Testing github actions

.github/workflows/package-filter.yml

@@ -8,6 +8,11 @@ on:
         required: true
         default: 0
         type: number
+      ignore-missing-dev:
+        description: "If true, the action will ignore packages that do not have a dev version. Otherwise, the action will fail if any package does not have a dev version."
+        required: true
+        default: false
+        type: boolean
     outputs:
       matrix:
         description: "The directories containing the updated packages"
@@ -81,7 +86,8 @@ jobs:
               # Check that the version is a dev version
               if [[ "$(cat ${pkg_dir}/VERSION)" != *"dev"* ]]
               then
-                echo "::error::${pkg_dir} does not have a dev version" && exit 1
+                msg="${pkg_dir} does not have a dev version"
+                ${{ inputs.ignore-missing-dev }} && echo "::warning::${msg}" || $(echo "::error::${msg}" && exit 1)
               fi
 
               PACKAGE_DIRS="$PACKAGE_DIRS ${pkg_dir}"

.github/workflows/package-release.yml

@@ -12,22 +12,32 @@ on:
         required: true
         default: 1
         type: number
+      ignore-missing-dev:
+        description: "If true, the action will ignore packages that do not have a dev version. Otherwise, the action will fail if any package does not have a dev version."
+        required: true
+        default: true
+        type: boolean
       repo_name:
         description: 'Name of the base repository. The user can ignore this input if the action is triggered from the base repository.'
         required: true
         type: string
         default: 'image-tools'
   workflow_call:
     inputs:
-      repo_name:
-        description: 'Name of the base repository'
-        required: true
-        type: string
       num-commits:
         description: "The of commits to check for updated packages. If 0, the action will check all commits on the master branch. For any larger value, the action will check the last n commits for any updated packages."
         required: true
         default: 1
         type: number
+      ignore-missing-dev:
+        description: "If true, the action will ignore packages that do not have a dev version. Otherwise, the action will fail if any package does not have a dev version."
+        required: true
+        default: true
+        type: boolean
+      repo_name:
+        description: 'Name of the base repository'
+        required: true
+        type: string
     secrets:
       DOCKER_USERNAME:
         description: 'Docker Hub username'
@@ -41,19 +51,20 @@ permissions:
 
 jobs:
   package-filter:
-    name: Filter for updated package
+    name: Filter for updated packages
     if: github.repository == 'polusai/${{ github.event.inputs.repo_name }}'
     uses: ./.github/workflows/package-filter.yml
     with:
       num-commits: ${{ fromJson(github.event.inputs.num-commits) }}
+      ignore-missing-dev: ${{ fromJson(github.event.inputs.ignore-missing-dev) }}
 
   package-release:
-    name: Release "${{ matrix.package_name }}"
+    name: Release | ${{ matrix.package_name }}
     if: github.repository == 'polusai/${{ github.event.inputs.repo_name }}'
     needs: package-filter
     strategy:
       fail-fast: false
-      matrix: ${{fromJson(needs.package-filter.outputs.matrix)}}
+      matrix: ${{ fromJson(needs.package-filter.outputs.matrix) }}
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
@@ -62,51 +73,78 @@ jobs:
           fetch-depth: 0
           ref: ${{ github.event.inputs.branch }}
           persist-credentials: false
-      - name: Generate a token
+      - name: Token | Generate
         id: generate_token
         uses: actions/create-github-app-token@v1
         with:
           app-id: ${{ secrets.APP_ID }}
           private-key: ${{ secrets.APP_PRIVATE_KEY }}
-      - name: Use the token
+      - name: Token | Use the token
         env:
           GH_TOKEN: ${{ steps.generate_token.outputs.token }}
         run: |
           gh api octocat
-      - name: Set up Python
+      - name: Python | Setup
         uses: actions/setup-python@v5
         with:
           python-version: '3.9'
-      - name: Install bump2version
+      - name: Python | Install bump2version
         run: |
           python -m pip install --upgrade pip
           pip install bump2version
-      - name: Bump Version
+      - name: Python | Bump Version Release
+        id: bump_version
         run: |
-          cd "${{ matrix.package_dir }}"
-          bump2version release --no-commit
-      - name: Commit all changed files
+          pkg_dir=${{ matrix.package_dir }}
+          cd "${pkg_dir}"
+          # check if the package has a dev version
+          if [[ "$(cat VERSION)" != *dev* ]]
+          then
+            msg="${pkg_dir} does not have a dev version"
+            ${{ github.event.inputs.ignore-missing-dev }} && echo "::warning::${msg}" || $(echo "::error::${msg}" && exit 1)
+          else
+            bump2version release --no-commit
+          fi
+          echo "released=$(git status --porcelain)" >> $GITHUB_output
+      - name: Git | Commit
+        if: steps.bump_version.outputs.released == 'true'
         env:
           CI_COMMIT_AUTHOR: polusai-auth-helper[bot]
           CI_COMMIT_EMAIL: ${{ secrets.APP_ID }}+polusai-auth-helper[bot]@users.noreply.github.com
         run: |
           git config --global user.name "${{ env.CI_COMMIT_AUTHOR }}"
           git config --global user.email "${{ env.CI_COMMIT_EMAIL }}"
           git commit -a -m "build: Bumped release version for ${{ matrix.package_name }}"
-      - name: Push changes
+      - name: Git | Push
+        if: steps.bump_version.outputs.released == 'true'
         uses: ad-m/github-push-action@master
         with:
           force: true
           github_token: ${{ steps.generate_token.outputs.token }}
-
-  docker:
-    name: Build Docker images
-    if: github.repository == 'polusai/${{ github.event.inputs.repo_name }}'
-    needs: [package-filter, package-release]
-    uses: ./.github/workflows/docker.yml
-    with:
-      matrix: ${{ needs.package-filter.outputs.matrix }}
-      push: true
-    secrets:
-      DOCKER_USERNAME: ${{ secrets.DOCKER_USERNAME }}
-      DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
+      - name: Docker | Tag
+        id: docker_tag
+        run: |
+          package_dir="${{ matrix.package_dir }}"
+          cp .gitignore ${package_dir}/.dockerignore
+          version=$(cat ${package_dir}/VERSION)
+          tag=polusai/${{ matrix.package_name }}:${version}
+          echo "tag=${tag}" >> $GITHUB_OUTPUT
+      - name: Docker | Setup Buildx
+        uses: docker/setup-buildx-action@v3
+      - name: Docker | Login DockerHub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_TOKEN }}
+      - name: Docker | Check if Image exists
+        run: |
+          tag=${{ steps.docker_tag.outputs.tag }}
+          docker pull ${tag} > /dev/null \
+              && $(echo "::error::${tag} already exists on DockerHub" && exit 1) \
+              || echo "success"
+      - name: Docekr | Push Image
+        uses: docker/build-push-action@v5
+        with:
+          context: "{{defaultContext}}:${{ matrix.package_dir }}"
+          push: true
+          tags: ${{ steps.docker_tag.outputs.tag }}

.github/workflows/tests.yml → .github/workflows/package-tests.yml

@@ -1,9 +1,5 @@
 name: Package tests
 
-env:
-  DOCKER_USERNAME: ${{ secrets.DOCKER_USERNAME }}
-  DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
-
 on:
   pull_request:
     branches:
@@ -16,13 +12,6 @@ on:
       - master
       - dev
   workflow_call:
-    secrets:
-      DOCKER_USERNAME:
-        description: 'Docker Hub username'
-        required: true
-      DOCKER_TOKEN:
-        description: 'Docker Hub password'
-        required: true
 
 permissions:
   contents: read
@@ -33,13 +22,14 @@ jobs:
     uses: ./.github/workflows/package-filter.yml
     with:
       num-commits: 0
+      ignore-missing-dev: false
 
   tests:
-    name: Test "${{ matrix.package_name }}"
+    name: Test | ${{ matrix.package_name }}
     needs: package-filter
     strategy:
       fail-fast: false
-      matrix: ${{fromJson(needs.package-filter.outputs.matrix)}}
+      matrix: ${{ fromJson(needs.package-filter.outputs.matrix) }}
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
@@ -69,14 +59,26 @@ jobs:
 
           poetry install
           poetry run pytest -v
-
-  docker:
-    name: Build Docker images
-    needs: [package-filter, tests]
-    uses: ./.github/workflows/docker.yml
-    with:
-      matrix: ${{ needs.package-filter.outputs.matrix }}
-      push: false
-    secrets:
-      DOCKER_USERNAME: ${{ secrets.DOCKER_USERNAME }}
-      DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
+      - name: Docker | Tag
+        id: docker_tag
+        run: |
+          package_dir="${{ matrix.package_dir }}"
+          version=$(cat ${package_dir}/VERSION)
+          tag=polusai/${{ matrix.package_name }}:${version}
+          echo "tag will be ${tag}"
+          echo "tag=${tag}" >> $GITHUB_OUTPUT
+      - name: Docker | Setup Buildx
+        uses: docker/setup-buildx-action@v3
+      - name: Docker | Check if Image exists
+        run: |
+          tag=${{ steps.docker_tag.outputs.tag }}
+          docker pull ${tag} > /dev/null \
+              && $(echo "::error::${tag} already exists on DockerHub" && exit 1) \
+              || echo "success"
+      - name: Docker | Build Image
+        run: |
+          cp .gitignore ${{ matrix.package_dir }}/.dockerignore
+          cd "${{ matrix.package_dir }}"
+          tag=${{ steps.docker_tag.outputs.tag }}
+          docker build . -t ${tag}
+        # docker buildx build --platform linux/amd64,linux/arm64 -t ${tag} --push .

regression/basic-flatfield-estimation-plugin/.bumpversion.cfg

@@ -1,6 +1,6 @@
 [bumpversion]
-current_version = 2.1.0
-commit = False
+current_version = 2.1.1-dev0
+commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?
 serialize = 

regression/basic-flatfield-estimation-plugin/README.md

@@ -1,4 +1,4 @@
-# BaSiC Flatfield Correction (v2.1.0)
+# BaSiC Flatfield Correction (v2.1.1-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

regression/basic-flatfield-estimation-plugin/VERSION

@@ -1 +1 @@
-2.1.0
+2.1.1-dev0

regression/basic-flatfield-estimation-plugin/plugin.json

@@ -1,14 +1,14 @@
 {
   "name": "BaSiC Flatfield Estimation",
-  "version": "2.1.0",
+  "version": "2.1.1-dev0",
   "title": "Flatfield Estimation using BaSiC algorithm.",
   "description": "Generates images used for flatfield correction using the BaSiC algorithm.",
   "author": "Nick Schaub (nick.schaub@nih.gov), Najib Ishaq (najib.ishaq@nih.gov)",
   "institution": "National Center for the Advancing Translational Sciences, National Institutes of Health",
   "repository": "https://github.com/polusai/polus-plugins",
   "website": "https://ncats.nih.gov/preclinical/core/informatics",
   "citation": "Peng et al. \"A BaSiC tool for background and shading correction of optical microscopy images\" Nature Communications (2017)",
-  "containerId": "polusai/basic-flatfield-estimation-plugin:2.1.0",
+  "containerId": "polusai/basic-flatfield-estimation-plugin:2.1.1-dev0",
   "baseCommand": [
     "python3",
     "-m",