Upgrade GitHub workflows (#1397)

* chore: upgrade GitHub workflows * chore: accept jinja2 vulnerability * docs: update readme badge * fix numpy 2 deprecation --------- Co-authored-by: Christian Diener <[email protected]>
opencobra · Aug 6, 2024 · 5bc58c9 · 5bc58c9
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diff --git a/.github/workflows/cron.yml b/.github/workflows/cron.yml
@@ -0,0 +1,11 @@
+name: Cron Test
+
+on:
+  schedule:
+  # Run every Tuesday at 10:30.
+  - cron: '30 10 * * 2'
+
+jobs:
+  prerequisites:
+    uses: ./.github/workflows/test.yml
+
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -1,89 +1,15 @@
-name: CI-CD
+name: CI
 
 on:
   push:
     branches:
       - stable
       - devel
-    tags:
-      - "[0-9]+.[0-9]+.[0-9]+"
-      - "[0-9]+.[0-9]+.[0-9]+a[0-9]+"
   pull_request:
     branches:
       - stable
       - devel
 
 jobs:
-  test:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.8", "3.11"]
-    timeout-minutes: 360
-
-    steps:
-      - 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: github.ref_type == 'tag'
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        os: [ubuntu-latest]
-        python-version: ["3.11"]
-    permissions:
-      contents: write
-
-    steps:
-      - 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 }}
+  prerequisites:
+    uses: ./.github/workflows/test.yml
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -0,0 +1,60 @@
+name: CD
+
+on:
+  push:
+    tags:
+    - "[0-9]+.[0-9]+.[0-9]+"
+    - "[0-9]+.[0-9]+.[0-9]+(a|b|rc|post|dev)[0-9]+"
+
+jobs:
+  prerequisites:
+    uses: ./.github/workflows/test.yml
+
+  release:
+    needs: [prerequisites]
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.11"]
+    runs-on: ${{ matrix.os }}
+    permissions:
+      # Write permissions are needed to create OIDC tokens.
+      id-token: write
+      # Write permissions are needed to make GitHub releases.
+      contents: write
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools wheel
+        python -m pip install build
+
+    - name: Build package
+      run: python -m build
+
+    # We rely on a trusted publisher configuration being present on PyPI,
+    # see https://docs.pypi.org/trusted-publishers/.
+    - name: Publish to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+
+    - name: GH release
+      uses: softprops/action-gh-release@v2
+      with:
+        body_path: "release-notes/${{ 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
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -0,0 +1,71 @@
+name: Test Suite
+
+on:
+  workflow_dispatch: {}
+  workflow_call: {}
+
+jobs:
+  lint:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ["3.11"]
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 60
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        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
+
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.8", "3.11"]
+    timeout-minutes: 360
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      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
+
+    - name: Test with tox
+      run: tox -- --benchmark-skip
+      timeout-minutes: 60
+
+    - name: Report coverage
+      shell: bash
+      run: bash <(curl -s https://codecov.io/bash)
+
diff --git a/README.rst b/README.rst
@@ -18,8 +18,8 @@ COBRApy - Constraint-Based Reconstruction and Analysis in Python
    :target: https://github.com/opencobra/cobrapy/blob/devel/.github/CODE_OF_CONDUCT.md
    :alt: Code of Conduct
 
-.. image:: https://github.com/opencobra/cobrapy/workflows/CI-CD/badge.svg
-   :target: https://github.com/opencobra/cobrapy/workflows/CI-CD
+.. image:: https://github.com/opencobra/cobrapy/actions/workflows/main.yml/badge.svg
+   :target: https://github.com/opencobra/cobrapy/actions/workflows/main.yml
    :alt: GitHub Actions CI/CD Status
 
 .. image:: https://codecov.io/gh/opencobra/cobrapy/branch/master/graph/badge.svg

diff --git a/src/cobra/io/mat.py b/src/cobra/io/mat.py
@@ -875,7 +875,7 @@ def from_mat_struct(
         # RECON3.0 mat has an array within an array for subsystems.
         # If we find a model that has multiple subsytems per reaction, this should be
         # modified
-        if np.sctype2char(m["subSystems"][0, 0][0][0]) == "O" and isinstance(
+        if m["subSystems"][0, 0][0][0].dtype.char == "O" and isinstance(
             m["subSystems"][0, 0][0][0][0], np.ndarray
         ):
             rxn_subsystems = [

diff --git a/tox.ini b/tox.ini
@@ -63,7 +63,7 @@ commands=
 deps=
     safety
 commands=
-    safety check --full-report
+    safety check --full-report -i 70612
 
 [testenv:install]
 skip_install = True