Issue 4082 Documentation CI Fix (pybamm-team#4102)

* add temporary fix to doctests session * parallelize all jobs in scheduled workflow * style corrections * separated openblas installation in jobs * commented github.repo line to test workflow locally * fix logic: remove 'if' statements in certain jobs * install setuptools in run_doctests * remove the comment if statement in build-apple-mseries * style changes * add temporary fix to docs session * resolved conversations * style changes * removed style job and all instances of it * modified incorrect name of dvipng * Apply suggestions from code review resolve conversations --------- Co-authored-by: Agriya Khetarpal <[email protected]>
agriyakhetarpal · May 22, 2024 · 5f35628 · 5f35628
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diff --git a/.github/workflows/run_periodic_tests.yml b/.github/workflows/run_periodic_tests.yml
@@ -6,7 +6,7 @@ on:
   workflow_dispatch:
   pull_request:
     branches:
-    - main
+      - main
 
   # Run every day at 3 am UTC
   schedule:
@@ -24,22 +24,98 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  style:
+  run_unit_tests:
+    name: Unit tests (${{ matrix.os }} / Python ${{ matrix.python-version }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-12, macos-14, windows-latest]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        # Exclude Python 3.12 from unit tests since we run it in the coverage jobs
+        exclude:
+          - os: ubuntu-latest
+            python-version: "3.12"
+    steps:
+      - name: Check out PyBaMM repository
+        uses: actions/checkout@v4
+
+      - name: Install Linux system dependencies
+        if: matrix.os == 'ubuntu-latest'
+        run: |
+          sudo apt-get update
+          sudo apt-get install gfortran gcc graphviz pandoc libopenblas-dev texlive-latex-extra dvipng
+
+      - name: Install macOS system dependencies
+        if: matrix.os == 'macos-12' || matrix.os == 'macos-14'
+        env:
+          HOMEBREW_NO_INSTALL_CLEANUP: 1
+          HOMEBREW_NO_AUTO_UPDATE: 1
+          HOMEBREW_NO_COLOR: 1
+          # Speed up CI
+          NONINTERACTIVE: 1
+        # sometimes gfortran cannot be found, so reinstall gcc just to be sure
+        run: |
+          brew analytics off
+          brew install graphviz
+          brew reinstall gcc
+
+      - name: Install Windows system dependencies
+        if: matrix.os == 'windows-latest'
+        run: choco install graphviz --version=8.0.5
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install nox
+        run: python -m pip install nox
+
+      - name: Install SuiteSparse and SUNDIALS on GNU/Linux and macOS
+        timeout-minutes: 10
+        if: matrix.os != 'windows-latest'
+        run: python -m nox -s pybamm-requires
+
+      - name: Run unit tests for ${{ matrix.os }} with Python ${{ matrix.python-version }}
+        run: python -m nox -s unit
+
+  check_coverage:
     runs-on: ubuntu-latest
+    name: Coverage tests (ubuntu-latest / Python 3.12)
+
     steps:
-      - uses: actions/checkout@v4
-      - name: Setup python
+      - name: Check out PyBaMM repository
+        uses: actions/checkout@v4
+
+      - name: Install Linux system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install gfortran gcc graphviz pandoc libopenblas-dev texlive-latex-extra dvipng
+
+      - name: Set up Python 3.12
         uses: actions/setup-python@v5
         with:
           python-version: 3.12
 
-      - name: Check style
-        run: |
-          python -m pip install pre-commit
-          pre-commit run -a
+      - name: Install nox
+        run: python -m pip install nox
 
-  build:
-    needs: style
+      - name: Install SuiteSparse and SUNDIALS on GNU/Linux
+        timeout-minutes: 10
+        run: python -m nox -s pybamm-requires
+
+      - name: Run unit tests for Ubuntu with Python 3.12 and generate coverage report
+        run: python -m nox -s coverage
+
+      - name: Upload coverage report
+        uses: codecov/[email protected]
+        if: github.repository == 'pybamm-team/PyBaMM'
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+  run_integration_tests:
+    name: Integration tests (${{ matrix.os }} / Python ${{ matrix.python-version }})
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
@@ -49,31 +125,35 @@ jobs:
     steps:
       - name: Check out PyBaMM repository
         uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
-
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
 
       - name: Install Linux system dependencies
         if: matrix.os == 'ubuntu-latest'
         run: |
           sudo apt-get update
-          sudo apt install gfortran gcc libopenblas-dev graphviz pandoc
-          sudo apt install texlive-full
+          sudo apt-get install gfortran gcc graphviz pandoc libopenblas-dev texlive-latex-extra dvipng
 
       - name: Install macOS system dependencies
         if: matrix.os == 'macos-12' || matrix.os == 'macos-14'
+        env:
+          HOMEBREW_NO_INSTALL_CLEANUP: 1
+          HOMEBREW_NO_AUTO_UPDATE: 1
+          HOMEBREW_NO_COLOR: 1
+          # Speed up CI
+          NONINTERACTIVE: 1
+        # sometimes gfortran cannot be found, so reinstall gcc just to be sure
         run: |
           brew analytics off
           brew install graphviz
           brew reinstall gcc
 
       - name: Install Windows system dependencies
         if: matrix.os == 'windows-latest'
-        run: choco install graphviz --version=2.38.0.20190211
+        run: choco install graphviz --version=8.0.5
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
 
       - name: Install nox
         run: python -m pip install nox
@@ -83,43 +163,97 @@ jobs:
         if: matrix.os != 'windows-latest'
         run: python -m nox -s pybamm-requires
 
-      - name: Run unit tests for GNU/Linux, macOS, and Windows with all Python versions
-        if: (matrix.os == 'ubuntu-latest' && matrix.python-version != 3.11) || (matrix.os != 'ubuntu-latest')
-        run: python -m nox -s unit
+      - name: Run integration tests for ${{ matrix.os }} with Python ${{ matrix.python-version }}
+        run: python -m nox -s integration
 
-      - name: Run unit tests for GNU/Linux with Python 3.11 and generate coverage report
-        if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
-        run: python -m nox -s coverage
+  # Skips IDAKLU module compilation for speedups, which is already tested in other jobs.
+  run_doctests:
+    runs-on: ubuntu-latest
+    name: Doctests (ubuntu-latest / Python 3.11)
+    steps:
+      - name: Check out PyBaMM repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
 
-      - name: Upload coverage report
-        if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
-        uses: codecov/[email protected]
+      - name: Install Linux system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install graphviz pandoc libopenblas-dev texlive-latex-extra dvipng
+
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
         with:
-          token: ${{ secrets.CODECOV_TOKEN }}
+          python-version: 3.11
 
-      - name: Run integration tests
-        run: python -m nox -s integration
+      - name: Install nox
+        run: python -m pip install nox
 
-      - name: Install docs dependencies and run doctests
-        if: matrix.os == 'ubuntu-latest'
+      - name: Install docs dependencies and run doctests for GNU/Linux
         run: python -m nox -s doctests
 
-      - name: Check if the documentation can be built
-        if: matrix.os == 'ubuntu-latest'
+      - name: Check if the documentation can be built for GNU/Linux
         run: python -m nox -s docs
 
-      - name: Install dev dependencies and run example tests
-        if: matrix.os == 'ubuntu-latest'
+  run_example_tests:
+    runs-on: ubuntu-latest
+    name: Example notebooks (ubuntu-latest / Python 3.12)
+
+    steps:
+      - name: Check out PyBaMM repository
+        uses: actions/checkout@v4
+
+      - name: Install Linux system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install gfortran gcc graphviz pandoc libopenblas-dev texlive-latex-extra dvipng
+
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.12
+
+      - name: Install nox
+        run: python -m pip install nox
+
+      - name: Install SuiteSparse and SUNDIALS on GNU/Linux
+        timeout-minutes: 10
+        run: python -m nox -s pybamm-requires
+
+      - name: Run example notebooks tests for GNU/Linux with Python 3.12
         run: python -m nox -s examples
 
-      - name: Run example scripts tests
-        if: matrix.os == 'ubuntu-latest'
+  run_scripts_tests:
+    runs-on: ubuntu-latest
+    name: Example scripts (ubuntu-latest / Python 3.12)
+
+    steps:
+      - name: Check out PyBaMM repository
+        uses: actions/checkout@v4
+
+      - name: Install Linux system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt install gfortran gcc graphviz libopenblas-dev texlive-latex-extra dvipng
+
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.12
+
+      - name: Install nox
+        run: python -m pip install nox
+
+      - name: Install SuiteSparse and SUNDIALS on GNU/Linux
+        timeout-minutes: 10
+        run: python -m nox -s pybamm-requires
+
+      - name: Run example scripts tests for GNU/Linux with Python 3.12
         run: python -m nox -s scripts
 
   # M-series Mac Mini
   build-apple-mseries:
     if: github.repository_owner == 'pybamm-team'
-    needs: style
     runs-on: [self-hosted, macOS, ARM64]
     env:
       GITHUB_PATH: ${PYENV_ROOT/bin:$PATH}
@@ -130,7 +264,9 @@ jobs:
         python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
-      - uses: actions/checkout@v4
+      - name: Check out PyBaMM repository
+        uses: actions/checkout@v4
+
       - name: Install Python & create virtualenv
         shell: bash
         run: |

diff --git a/noxfile.py b/noxfile.py
@@ -77,6 +77,9 @@ def run_integration(session):
 @nox.session(name="doctests")
 def run_doctests(session):
     """Run the doctests and generate the output(s) in the docs/build/ directory."""
+    # TODO: Temporary fix for Python 3.12 CI.
+    # See: https://bitbucket.org/pybtex-devs/pybtex/issues/169/
+    session.install("setuptools", silent=False)
     session.install("-e", ".[all,dev,docs]", silent=False)
     session.run("python", "run-tests.py", "--doctest")
 
@@ -144,6 +147,9 @@ def run_tests(session):
 def build_docs(session):
     """Build the documentation and load it in a browser tab, rebuilding on changes."""
     envbindir = session.bin
+    # TODO: Temporary fix for Python 3.12 CI.
+    # See: https://bitbucket.org/pybtex-devs/pybtex/issues/169/
+    session.install("setuptools", silent=False)
     session.install("-e", ".[all,docs]", silent=False)
     session.chdir("docs")
     # Local development