Update all actions (#347)

* Update all actions * Fix action version * Fix action version * Fix tests action * typo * ehatever * Fix broken action * typo in changelog --------- Co-authored-by: Chiara Rasi <rasi.chiara@gmacil.com>
Clinical-Genomics · Sep 4, 2024 · 8165ce1 · 8165ce1
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commit 8165ce1
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Showing 11 changed files with 39 additions and 32 deletions.
diff --git a/.github/workflows/autodeploy_mkdocs.yml b/.github/workflows/autodeploy_mkdocs.yml
@@ -11,9 +11,9 @@ jobs:
    runs-on: ubuntu-latest
    steps:
     - name: Checkout repo
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
     - name: Setup environment for docs deployment
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: 3.x
     - name: Install mkdocs

diff --git a/.github/workflows/black.yml b/.github/workflows/black.yml
@@ -7,9 +7,9 @@ jobs:
     runs-on: ubuntu-latest
     name: black
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@master
+        uses: actions/setup-python@v5
         with:
           python-version: 3.8
       - name: install black

diff --git a/.github/workflows/docker_build_n_publish.yml b/.github/workflows/docker_build_n_publish.yml
@@ -11,7 +11,7 @@ jobs:
    runs-on: ubuntu-latest
    steps:
     - name: Check out git repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
 
     - name: Publish main image (Dockerfile) to Registry
       uses: elgohr/Publish-Docker-Github-Action@master

diff --git a/.github/workflows/docker_build_n_publish_stage.yml b/.github/workflows/docker_build_n_publish_stage.yml
@@ -11,25 +11,25 @@ jobs:
     runs-on: ubuntu-latest
     steps:
      - name: Check out git repository
-       uses: actions/checkout@v2
+       uses: actions/checkout@v4
 
      - name: Get branch name
        id: branch-name
-       uses: tj-actions/branch-names@v7.0.7
+       uses: tj-actions/branch-names@v8
 
      - name: Login to Docker Hub
-       uses: docker/login-action@v1
+       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@v1
+       uses: docker/setup-buildx-action@v3
 
      - name: Build and push
        if: steps.branch-name.outputs.is_default == 'false'
-       uses: docker/build-push-action@v2
+       uses: docker/build-push-action@v6
        with:
          context: ./
          file: ./Dockerfile-server

diff --git a/.github/workflows/flake8.yml b/.github/workflows/flake8.yml
@@ -7,9 +7,9 @@ jobs:
     runs-on: ubuntu-latest
     name: Flake8
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@master
+        uses: actions/setup-python@v5
         with:
           python-version: 3.8
       - name: install flake8

diff --git a/.github/workflows/pypi_publish.yml b/.github/workflows/pypi_publish.yml
@@ -11,12 +11,12 @@ jobs:
   runs-on: ubuntu-latest
   steps:
    - name: Check out git repository
-     uses: actions/checkout@v2
+     uses: actions/checkout@v4
 
-   - name: Set up Python 3.7
-     uses: actions/setup-python@v2
+   - name: Set up Python 3.8
+     uses: actions/setup-python@v5
      with:
-      python-version: 3.7
+      python-version: 3.8
 
    - name: Install build tools
      run: >-

diff --git a/.github/workflows/pytest_codecov.yml b/.github/workflows/pytest_codecov.yml
@@ -11,10 +11,10 @@ jobs:
   setup:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: Set up Python 3.8
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: 3.8
 
@@ -24,7 +24,7 @@ jobs:
           pip check
 
         # Cache package installation step to speed up the following step
-      - uses: actions/cache@v2
+      - uses: actions/cache@v4
         with:
           path: ${{ env.pythonLocation }}
           key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }}-${{ hashFiles('requirements-dev.txt') }}
@@ -40,19 +40,19 @@ jobs:
       PMATCHER_CONFIG: ../instance/config.py
     steps:
       - name: Start MongoDB
-        uses: supercharge/mongodb-github-action@1.7.0
+        uses: supercharge/mongodb-github-action@1.11.0
         with:
          mongodb-version: ${{ matrix.mongodb-version }}
 
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - name: Set up Python 3.8
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: 3.8
 
         # Cache package installation step to speed up the following step
-      - uses: actions/cache@v2
+      - uses: actions/cache@v4
         with:
           path: ${{ env.pythonLocation }}
           key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }}-${{ hashFiles('requirements-dev.txt') }}
@@ -65,18 +65,19 @@ jobs:
         run: pytest --cov --test-group-count 3 --test-group=${{ matrix.group }} --test-group-random-seed=12345
 
       - name: Upload coverage
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: coverage${{ matrix.group }}
           path: .coverage
+          include-hidden-files: true
 
   coverage:
     needs: test
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up Python 3.8
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: 3.8
       - name: Install deps
@@ -85,10 +86,10 @@ jobs:
           pip install coverage
       - name: Download all artifacts
         # Download and combine coverage1, coverage2, etc.
-        uses: actions/download-artifact@v2
+        uses: actions/download-artifact@v4
       - name: Run coverage
         run: |
           coverage combine coverage*/.coverage*
           coverage report
           coverage xml
-      - uses: codecov/codecov-action@v2
+      - uses: codecov/codecov-action@v4
diff --git a/.github/workflows/vulture.yml b/.github/workflows/vulture.yml
@@ -7,11 +7,11 @@ jobs:
     name: vulture
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
       - name: Find changed Python files
         id: files
-        uses: Ana06/get-changed-files@v2.0.0
+        uses: Ana06/get-changed-files@v2.3.0
         with:
           filter: "*.py"
 

diff --git a/.github/workflows/woke.yaml b/.github/workflows/woke.yaml
@@ -7,7 +7,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
 
       - name: woke
         uses: get-woke/woke-action@v0

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,9 @@
+## [4.5.1] - 2024-09-04
+### Fixed
+- Bump actions/download-artifact from 2 to 4 in /.github/workflows (recommended by security advisory)
+- Update version of other actions
+- Broken upload to Codecov step in Tests & Coverage GitHub action
+
 ## [4.5] - 2023-11-07
 ## Changed
 - Unfreeze PyMongo dependency

diff --git a/patientMatcher/__version__.py b/patientMatcher/__version__.py
@@ -1 +1 @@
-__version__ = "4.5"
+__version__ = "4.5.1"