Merge pull request #307 from Clinical-Genomics/fix_deprecated_action

Updated version of external images used in GitHub actions

.github/workflows/black.yml

@@ -6,6 +6,8 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
       - uses: psf/black@stable

.github/workflows/build_and_push_docker_stage.yml

@@ -7,22 +7,22 @@ jobs:
     runs-on: ubuntu-latest
     steps:
      - name: Check out git repository
-       uses: actions/checkout@v3
+       uses: actions/checkout@v4
 
      - name: Extract branch name and remove illegal chars
        id: get_branch_name
        shell: bash
        run: echo "branch=$(echo "$(tr "/" "-" <<<${GITHUB_REF#refs/heads/})")" >>$GITHUB_OUTPUT
 
      - name: Login to Docker Hub
-       uses: docker/login-action@v2
+       uses: docker/login-action@v3
        with:
          username: ${{ secrets.DOCKER_USERNAME }}
          password: ${{ secrets.DOCKER_PASSWORD }}
 
      - name: Set up Docker Buildx
        id: buildx
-       uses: docker/setup-buildx-action@v2
+       uses: docker/setup-buildx-action@v3
 
      - name: Build and push
        id: docker_build

.github/workflows/docker_build_on_release.yml

@@ -12,17 +12,17 @@ jobs:
     steps:
 
      - name: Check Out Repo
-       uses: actions/checkout@v3
+       uses: actions/checkout@v4
 
      - name: Login to Docker Hub
-       uses: docker/login-action@v2
+       uses: docker/login-action@v3
        with:
          username: ${{ secrets.DOCKER_USERNAME }}
          password: ${{ secrets.DOCKER_PASSWORD }}
 
      - name: Set up Docker Buildx
        id: buildx
-       uses: docker/setup-buildx-action@v2
+       uses: docker/setup-buildx-action@v3
 
      - name: Build and push
        id: docker_build

.github/workflows/mkdocs_publishing.yml

@@ -9,12 +9,12 @@ jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: 3.x
       - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV
-      - uses: actions/cache@v3
+      - uses: actions/cache@v4
         with:
           key: mkdocs-material-${{ env.cache_id }}
           path: .cache

.github/workflows/pypi_build_and_publish.yml

@@ -11,15 +11,15 @@ jobs:
   runs-on: ubuntu-latest
   steps:
    - name: Check out git repository
-     uses: actions/checkout@v3
+     uses: actions/checkout@v4
 
    - name: Set up Python 3.9
-     uses: actions/setup-python@v4
+     uses: actions/setup-python@v5
      with:
       python-version: 3.9
 
    - name: Install poetry
-     uses: abatilo/actions-poetry@v2
+     uses: abatilo/actions-poetry@v3
 
    - name: Build and publish to PYPI
      run: |

.github/workflows/vulture.yml

@@ -7,7 +7,7 @@ jobs:
     name: vulture
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Find changed Python files
         id: files

.github/workflows/woke.yml

@@ -7,7 +7,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: woke
         uses: get-woke/woke-action@v0

CHANGELOG.md

@@ -1,3 +1,7 @@
+## [unreleased]
+### Fixed
+- Updated version of external images used in GitHub actions
+
 ## [1.7]
 ### Added
 - An environment.yml with the minimum supported python version (3.8) and the installed libs