Merge pull request #1363 from opencobra/chore-actions

chore: update actions
opencobra · Oct 21, 2023 · c9f428a · c9f428a
2 parents a2339c5 + 020a928
commit c9f428a
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Showing 4 changed files with 108 additions and 108 deletions.
diff --git a/.github/workflows/biosimulators_dispatch.yml b/.github/workflows/biosimulators_dispatch.yml
@@ -9,14 +9,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - name: Get tag
-        id: tag
-        run: echo "::set-output name=version::${GITHUB_REF#refs/tags/}"
       - name: Dispatch new release version to BioSimulators
         uses: benc-uk/workflow-dispatch@v1
         with:
           workflow: Continuous integration
           repo: biosimulators/Biosimulators_COBRApy
           ref: dev
           token: ${{ secrets.BIOSIM_DISPATCH_TOKEN }}
-          inputs: '{ "simulatorVersion": "${{ steps.tag.outputs.version }}", "simulatorVersionLatest": "true" }'
+          inputs: '{ "simulatorVersion": "${{ github.ref_name }}", "simulatorVersionLatest": "true" }'
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
@@ -3,15 +3,15 @@ name: Lint
 on:
   push:
     branches:
-    - stable
-    - devel
+      - stable
+      - devel
     tags:
-    - '[0-9]+.[0-9]+.[0-9]+'
-    - '[0-9]+.[0-9]+.[0-9]+a[0-9]+'
+      - "[0-9]+.[0-9]+.[0-9]+"
+      - "[0-9]+.[0-9]+.[0-9]+a[0-9]+"
   pull_request:
     branches:
-    - stable
-    - devel
+      - stable
+      - devel
 
 jobs:
   lint:
@@ -20,25 +20,27 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.10']
+        python-version: ["3.11"]
     timeout-minutes: 60
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip setuptools wheel
-        python -m pip install tox tox-gh-actions
-    - name: isort
-      run:
-        tox -e isort
-    - name: black
-      run:
-        tox -e black
-    - name: flake8
-      run:
-        tox -e flake8
+      - uses: actions/checkout@v4
+
+      - 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 setuptools wheel
+          python -m pip install tox tox-gh-actions
+
+      - name: isort
+        run: tox -e isort
+
+      - name: black
+        run: tox -e black
+
+      - name: flake8
+        run: tox -e flake8
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -3,15 +3,15 @@ name: CI-CD
 on:
   push:
     branches:
-    - stable
-    - devel
+      - stable
+      - devel
     tags:
-    - '[0-9]+.[0-9]+.[0-9]+'
-    - '[0-9]+.[0-9]+.[0-9]+a[0-9]+'
+      - "[0-9]+.[0-9]+.[0-9]+"
+      - "[0-9]+.[0-9]+.[0-9]+a[0-9]+"
   pull_request:
     branches:
-    - stable
-    - devel
+      - stable
+      - devel
 
 jobs:
   test:
@@ -20,71 +20,70 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ["3.8", "3.11"]
     timeout-minutes: 360
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip setuptools wheel
-        python -m pip install tox tox-gh-actions
-    - name: Test with tox
-      run:
-        tox -- --benchmark-skip
-      timeout-minutes: 60
-    - name: Report coverage
-      shell: bash
-      run: bash <(curl -s https://codecov.io/bash)
+      - uses: actions/checkout@v4
+      - 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 setuptools wheel
+          python -m pip install tox tox-gh-actions
+      - name: Test with tox
+        run: tox -- --benchmark-skip
+        timeout-minutes: 60
+      - name: Report coverage
+        shell: bash
+        run: bash <(curl -s https://codecov.io/bash)
 
   release:
     needs: test
-    if: startsWith(github.ref, 'refs/tags')
+    if: github.ref_type == 'tag'
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.8]
+        python-version: ["3.11"]
+    permissions:
+      contents: write
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Get tag
-      id: tag
-      run: echo "::set-output name=version::${GITHUB_REF#refs/tags/}"
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip setuptools wheel
-        python -m pip install build twine
-    - name: Build package
-      run: python -m build
-    - name: Publish to PyPI
-      env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-      run:
-        twine upload --skip-existing --non-interactive dist/*
-    - name: Create GitHub release
-      uses: actions/create-release@v1
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      with:
-        tag_name: ${{ github.ref }}
-        release_name: ${{ github.ref }}
-        body_path: "release-notes/${{ steps.tag.outputs.version }}.md"
-        draft: false
-        prerelease: false
-    - name: Publish to website
-      run: ./scripts/deploy_website.sh
-      shell: bash
-      env:
-        TAG: ${{ steps.tag.outputs.version }}
-        WORKSPACE: ${{ github.workspace }}
-        WEBSITE_DEPLOY_TOKEN: ${{ secrets.WEBSITE_DEPLOY_TOKEN }}
+      - uses: actions/checkout@v4
+
+      - 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 setuptools wheel
+          python -m pip install build twine
+
+      - name: Build package
+        run: python -m build
+
+      - name: Publish to PyPI
+        env:
+          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+        run: twine upload --skip-existing --non-interactive dist/*
+
+      - name: GH release
+        uses: softprops/action-gh-release@v1
+        with:
+          body_path: "release-notes/${{ github.ref_name }}.md"
+          draft: false
+          prerelease: false
+
+      - name: Publish to website
+        run: ./scripts/deploy_website.sh
+        shell: bash
+        env:
+          TAG: ${{ github.ref_name }}
+          WORKSPACE: ${{ github.workspace }}
+          WEBSITE_DEPLOY_TOKEN: ${{ secrets.WEBSITE_DEPLOY_TOKEN }}
diff --git a/.github/workflows/safety.yml b/.github/workflows/safety.yml
@@ -3,11 +3,11 @@ name: Safety
 on:
   push:
     branches:
-    - stable
-    - devel
+      - stable
+      - devel
     tags:
-    - '[0-9]+.[0-9]+.[0-9]+'
-    - '[0-9]+.[0-9]+.[0-9]+a[0-9]+'
+      - "[0-9]+.[0-9]+.[0-9]+"
+      - "[0-9]+.[0-9]+.[0-9]+a[0-9]+"
 
 jobs:
   safety:
@@ -16,19 +16,21 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
     timeout-minutes: 120
 
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip setuptools wheel
-        python -m pip install tox tox-gh-actions
-    - name: safety
-      run:
-        tox -e safety
+      - uses: actions/checkout@v4
+
+      - 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 setuptools wheel
+          python -m pip install tox tox-gh-actions
+
+      - name: safety
+        run: tox -e safety