Update to python 3.10

.github/workflows/codeql-analysis.yml

@@ -12,7 +12,7 @@ on:
     # The branches below must be a subset of the branches above
     branches: [master]
   schedule:
-    - cron: '0 19 * * 3'
+    - cron: "0 19 * * 3"
 
 jobs:
   analyze:
@@ -24,48 +24,48 @@ jobs:
       matrix:
         # Override automatic language detection by changing the below list
         # Supported options are ['csharp', 'cpp', 'go', 'java', 'javascript', 'python']
-        language: ['python']
+        language: ["python"]
         # Learn more...
         # https://docs.github.com/en/github/finding-security-vulnerabilities-and-errors-in-your-code/configuring-code-scanning#overriding-automatic-language-detection
 
     steps:
-    - name: Checkout repository
-      uses: actions/checkout@v3
-      with:
-        # We must fetch at least the immediate parents so that if this is
-        # a pull request then we can checkout the head.
-        fetch-depth: 2
+      - name: Checkout repository
+        uses: actions/checkout@v3
+        with:
+          # We must fetch at least the immediate parents so that if this is
+          # a pull request then we can checkout the head.
+          fetch-depth: 2
 
-    # If this run was triggered by a pull request event, then checkout
-    # the head of the pull request instead of the merge commit.
-    - run: git checkout HEAD^2
-      if: ${{ github.event_name == 'pull_request' }}
+      # If this run was triggered by a pull request event, then checkout
+      # the head of the pull request instead of the merge commit.
+      - run: git checkout HEAD^2
+        if: ${{ github.event_name == 'pull_request' }}
 
-    # Initializes the CodeQL tools for scanning.
-    - name: Initialize CodeQL
-      uses: github/codeql-action/init@v2
-      with:
-        languages: ${{ matrix.language }}
-        # If you wish to specify custom queries, you can do so here or in a config file.
-        # By default, queries listed here will override any specified in a config file. 
-        # Prefix the list here with "+" to use these queries and those in the config file.
-        # queries: ./path/to/local/query, your-org/your-repo/queries@main
+      # Initializes the CodeQL tools for scanning.
+      - name: Initialize CodeQL
+        uses: github/codeql-action/init@v2
+        with:
+          languages: ${{ matrix.language }}
+          # If you wish to specify custom queries, you can do so here or in a config file.
+          # By default, queries listed here will override any specified in a config file.
+          # Prefix the list here with "+" to use these queries and those in the config file.
+          # queries: ./path/to/local/query, your-org/your-repo/queries@main
 
-    # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
-    # If this step fails, then you should remove it and run the build manually (see below)
-    - name: Autobuild
-      uses: github/codeql-action/autobuild@v2
+      # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
+      # If this step fails, then you should remove it and run the build manually (see below)
+      - name: Autobuild
+        uses: github/codeql-action/autobuild@v2
 
-    # ℹ️ Command-line programs to run using the OS shell.
-    # 📚 https://git.io/JvXDl
+      # ℹ️ Command-line programs to run using the OS shell.
+      # 📚 https://git.io/JvXDl
 
-    # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
-    #    and modify them (or add more) to build your code if your project
-    #    uses a compiled language
+      # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines
+      #    and modify them (or add more) to build your code if your project
+      #    uses a compiled language
 
-    #- run: |
-    #   make bootstrap
-    #   make release
+      #- run: |
+      #   make bootstrap
+      #   make release
 
-    - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v2
+      - name: Perform CodeQL Analysis
+        uses: github/codeql-action/analyze@v2

.github/workflows/dependabot-auto-merge.yml

@@ -22,7 +22,7 @@ jobs:
         with:
           github-token: "${{ secrets.GITHUB_TOKEN }}"
       - name: Enable auto-merge for Dependabot PRs
-        if:  ${{ steps.metadata.outputs.package-ecosystem == 'pip' || steps.metadata.outputs.package-ecosystem == 'github_actions' }}
+        if: ${{ steps.metadata.outputs.package-ecosystem == 'pip' || steps.metadata.outputs.package-ecosystem == 'github_actions' }}
         run: gh pr review --approve "$PR_URL" && gh pr merge --auto --merge "$PR_URL"
         env:
           PR_URL: ${{github.event.pull_request.html_url}}

.github/workflows/dependency-review.yml

@@ -4,7 +4,7 @@
 #
 # Source repository: https://github.com/actions/dependency-review-action
 # Public documentation: https://docs.github.com/en/code-security/supply-chain-security/understanding-your-software-supply-chain/about-dependency-review#dependency-review-enforcement
-name: 'Dependency Review'
+name: "Dependency Review"
 on: [pull_request]
 
 permissions:
@@ -14,9 +14,9 @@ jobs:
   dependency-review:
     runs-on: ubuntu-latest
     steps:
-      - name: 'Checkout Repository'
+      - name: "Checkout Repository"
         uses: actions/checkout@v3
-      - name: 'Dependency Review'
+      - name: "Dependency Review"
         uses: actions/dependency-review-action@v3
         with:
           fail-on-severity: moderate

.github/workflows/docs.yml

@@ -8,33 +8,32 @@ jobs:
       max-parallel: 4
       matrix:
         os: [ubuntu-latest]
-    
+
     runs-on: ${{ matrix.os }}
 
     steps:
-    - uses: actions/checkout@v3
-    - uses: rojopolis/spellcheck-github-actions@0.33.0
-      name: Spellcheck
+      - uses: actions/checkout@v3
+      - uses: rojopolis/spellcheck-github-actions@0.33.1
+        name: Spellcheck
 
   code_docs:
     strategy:
       max-parallel: 4
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.8]
-    
+        python-version: ["3.10"]
+
     runs-on: ${{ matrix.os }}
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install tox tox-gh-actions
-    - name: Run docs tests
-      run: tox -e docs
-
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install tox tox-gh-actions
+      - name: Run docs tests
+        run: tox -e docs

.github/workflows/int.yml

@@ -9,8 +9,8 @@ jobs:
       max-parallel: 4
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.8]
-    
+        python-version: ["3.10"]
+
     runs-on: ${{ matrix.os }}
 
     name: Integration Tests
@@ -20,54 +20,54 @@ jobs:
         image: registry:2
         ports:
           - 5000:5000
-    
+
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python-version }}
-
-    - name: Install requirements
-      run: |
-        pip install aiohttp
-        pip install requests
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install requirements
+        run: |
+          pip install aiohttp
+          pip install requests
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+        with:
+          driver-opts: network=host
+
+      - name: Build
+        uses: docker/build-push-action@v4
+        with:
+          context: .
+          push: true
+          file: ./Dockerfile
+          tags: localhost:5000/beacon-python:latest
+          cache-from: localhost:5000/beacon-python:latest
+          cache-to: type=local,dest=/tmp/.buildx-cache
 
-    - name: Set up Docker Buildx
-      uses: docker/setup-buildx-action@v2
-      with:
-        driver-opts: network=host
-
-    - name: Build
-      uses: docker/build-push-action@v4
-      with:
-        context: .
-        push: true
-        file: ./Dockerfile
-        tags: localhost:5000/beacon-python:latest
-        cache-from: localhost:5000/beacon-python:latest
-        cache-to: type=local,dest=/tmp/.buildx-cache
-
-    - name: Start Services
-      run: |
-        docker-compose -f deploy/test/docker-compose.yml up -d
-        sleep 10
-        docker exec test_beacon_1 beacon_init /exdata/ALL.chrMT.phase3_callmom-v0_4.20130502.genotypes.vcf.gz /exdata/example_metadata.json
-        docker exec test_beacon_1 beacon_init /exdata/ALL.chrMT.phase3_callmom-v0_4.20130502.genotypes.vcf.gz /exdata/example_metadata_registered.json
-        docker exec test_beacon_1 beacon_init /exdata/ALL.chrMT.phase3_callmom-v0_4.20130502.genotypes.vcf.gz /exdata/example_metadata_controlled.json
-        docker exec test_beacon_1 beacon_init /exdata/ALL.chrMT.phase3_callmom-v0_4.20130502.genotypes.vcf.gz /exdata/example_metadata_controlled1.json
+      - name: Start Services
+        run: |
+          docker-compose -f deploy/test/docker-compose.yml up -d
+          sleep 10
+          docker exec test_beacon_1 beacon_init /exdata/ALL.chrMT.phase3_callmom-v0_4.20130502.genotypes.vcf.gz /exdata/example_metadata.json
+          docker exec test_beacon_1 beacon_init /exdata/ALL.chrMT.phase3_callmom-v0_4.20130502.genotypes.vcf.gz /exdata/example_metadata_registered.json
+          docker exec test_beacon_1 beacon_init /exdata/ALL.chrMT.phase3_callmom-v0_4.20130502.genotypes.vcf.gz /exdata/example_metadata_controlled.json
+          docker exec test_beacon_1 beacon_init /exdata/ALL.chrMT.phase3_callmom-v0_4.20130502.genotypes.vcf.gz /exdata/example_metadata_controlled1.json
 
-    - name: Run Integration test
-      run: |
-        python deploy/test/run_tests.py
+      - name: Run Integration test
+        run: |
+          python deploy/test/run_tests.py
 
-    - name: Collect logs from docker
-      if: ${{ failure() }}
-      run: cd deploy && docker-compose logs --no-color -t > ../tests/dockerlogs || true
+      - name: Collect logs from docker
+        if: ${{ failure() }}
+        run: cd deploy && docker-compose logs --no-color -t > ../tests/dockerlogs || true
 
-    - name: Persist log files
-      if: ${{ failure() }}
-      uses: actions/upload-artifact@v3
-      with:
-        name: test_debugging_help
-        path: tests
+      - name: Persist log files
+        if: ${{ failure() }}
+        uses: actions/upload-artifact@v3
+        with:
+          name: test_debugging_help
+          path: tests

.github/workflows/publish.yml

@@ -6,7 +6,7 @@ on:
   push:
     branches: [master]
     tags:
-      - 'v*'
+      - "v*"
 
 jobs:
   push_to_registry:
@@ -18,10 +18,10 @@ jobs:
 
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v2
-      
+
       - name: Login to DockerHub
         if: github.event_name != 'pull_request'
-        uses: docker/login-action@v2 
+        uses: docker/login-action@v2
         with:
           username: ${{ secrets.DOCKER_USERNAME }}
           password: ${{ secrets.DOCKER_PASSWORD }}
@@ -35,7 +35,7 @@ jobs:
             type=raw,value=latest,enable=${{ github.ref == format('refs/heads/{0}', 'master') }}
             type=raw,value=stage,enable=${{ github.ref == format('refs/heads/{0}', 'dev') }}
             type=ref,event=tag
-      
+
       - name: Build and push
         uses: docker/build-push-action@v4
         with:

.github/workflows/s2i-build.yml

@@ -8,19 +8,19 @@ jobs:
       max-parallel: 4
       matrix:
         os: [ubuntu-latest]
-    
+
     runs-on: ${{ matrix.os }}
 
     name: Integration Tests
-    
+
     steps:
-    - uses: actions/checkout@v3
+      - uses: actions/checkout@v3
 
-    - name: Install requirements
-      run: |
-        wget https://github.com/openshift/source-to-image/releases/download/v1.3.1/source-to-image-v1.3.1-a5a77147-linux-amd64.tar.gz
-        tar -xvf source-to-image-v1.3.1-a5a77147-linux-amd64.tar.gz
-        sudo cp s2i /usr/local/bin
-    - name: Build image
-      run:  |
-        s2i build . centos/python-38-centos7 cscfi/beacon-python
+      - name: Install requirements
+        run: |
+          wget https://github.com/openshift/source-to-image/releases/download/v1.3.1/source-to-image-v1.3.1-a5a77147-linux-amd64.tar.gz
+          tar -xvf source-to-image-v1.3.1-a5a77147-linux-amd64.tar.gz
+          sudo cp s2i /usr/local/bin
+      - name: Build image
+        run: |
+          s2i build . centos/python-38-centos7 cscfi/beacon-python