Merge branch 'develop' into expression-tree-typing

pybamm-team · Feb 21, 2024 · eeceaa7 · eeceaa7
2 parents ea03b4f + cf686e7
commit eeceaa7
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diff --git a/.all-contributorsrc b/.all-contributorsrc
@@ -215,7 +215,8 @@
       "profile": "https://github.com/jonchapman1",
       "contributions": [
         "ideas",
-        "fundingFinding"
+        "fundingFinding",
+        "doc"
       ]
     },
     {
@@ -772,7 +773,9 @@
       "avatar_url": "https://avatars.githubusercontent.com/u/99216956?v=4",
       "profile": "https://github.com/prady0t",
       "contributions": [
-        "infra"
+        "infra",
+        "code",
+        "test"
       ]
     },
     {

diff --git a/.github/workflows/lychee_url_checker.yml b/.github/workflows/lychee_url_checker.yml
@@ -28,7 +28,7 @@ jobs:
 
       # use stable version for now to avoid breaking changes
       - name: Lychee URL checker
-        uses: lycheeverse/[email protected].1
+        uses: lycheeverse/[email protected].3
         with:
           # arguments with file types to check
           args: >-

diff --git a/.github/workflows/publish_pypi.yml b/.github/workflows/publish_pypi.yml
@@ -133,7 +133,7 @@ jobs:
           CIBW_REPAIR_WHEEL_COMMAND_LINUX: auditwheel repair -w {dest_dir} {wheel}
           CIBW_TEST_COMMAND: python -c "import pybamm; pybamm.IDAKLUSolver()"
 
-      - name: Build wheels on macOS
+      - name: Build wheels on macOS amd64
         if: matrix.os == 'macos-latest'
         run: pipx run cibuildwheel --output-dir wheelhouse
         env:
@@ -150,11 +150,45 @@ jobs:
           path: ./wheelhouse/*.whl
           if-no-files-found: error
 
-      - name: Upload wheels for macOS
+      - name: Upload wheels for macOS amd64
         uses: actions/upload-artifact@v4
         if: matrix.os == 'macos-latest'
         with:
-          name: macos_wheels
+          name: macos_amd64_wheels
+          path: ./wheelhouse/*.whl
+          if-no-files-found: error
+
+  build_macos_arm64_wheels:
+    name: Wheels (macos-arm64)
+    # Current runner is macOS X 14+ on GitHub-hosted runners
+    runs-on: macos-14
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+
+      - name: Clone pybind11 repo (no history)
+        run: git clone --depth 1 --branch v2.11.1 https://github.com/pybind/pybind11.git
+
+      - name: Install SuiteSparse and SUNDIALS on macOS
+        run: |
+          brew install graphviz openblas libomp
+          brew reinstall gcc
+          python -m pip install cmake pipx
+          python scripts/install_KLU_Sundials.py
+
+      - name: Build wheels on macOS arm64
+        run: python -m pipx run cibuildwheel --output-dir wheelhouse
+        env:
+          CIBW_BEFORE_BUILD: python -m pip install cmake casadi setuptools wheel delocate
+          CIBW_REPAIR_WHEEL_COMMAND: delocate-listdeps {wheel} && delocate-wheel -v -w {dest_dir} {wheel}
+          CIBW_TEST_COMMAND: python -c "import pybamm; pybamm.IDAKLUSolver()"
+
+      - name: Upload wheels for macOS arm64
+        uses: actions/upload-artifact@v4
+        with:
+          name: macos_arm64_wheels
           path: ./wheelhouse/*.whl
           if-no-files-found: error
 
@@ -182,7 +216,7 @@ jobs:
     # This job is only of value to PyBaMM and would always be skipped in forks
     if: github.event_name != 'schedule' && github.repository == 'pybamm-team/PyBaMM'
     name: Upload package to PyPI
-    needs: [build_macos_and_linux_wheels, build_windows_wheels, build_sdist]
+    needs: [build_macos_and_linux_wheels, build_macos_arm64_wheels, build_windows_wheels, build_sdist]
     runs-on: ubuntu-latest
     steps:
       - name: Download all artifacts
@@ -191,7 +225,7 @@ jobs:
       - name: Move all package files to files/
         run: |
           mkdir files
-          mv windows_wheels/* linux_wheels/* macos_wheels/* sdist/* files/
+          mv windows_wheels/* linux_wheels/* macos_amd64_wheels/* macos_arm64_wheels/* sdist/* files/
 
       - name: Publish on PyPI
         if: github.event.inputs.target == 'pypi' || github.event_name == 'release'

diff --git a/.github/workflows/run_periodic_tests.yml b/.github/workflows/run_periodic_tests.yml
@@ -46,9 +46,21 @@ jobs:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
         python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        # Include macOS M1 runners
+        include:
+          - os: macos-14
+            python-version: "3.10"
+          - os: macos-14
+            python-version: "3.11"
+          - os: macos-14
+            python-version: "3.12"
 
     steps:
-      - uses: actions/checkout@v4
+      - 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:
@@ -62,7 +74,7 @@ jobs:
           sudo apt install texlive-full
 
       - name: Install macOS system dependencies
-        if: matrix.os == 'macos-latest'
+        if: matrix.os == 'macos-latest' || matrix.os == 'macos-14'
         run: |
           brew analytics off
           brew install graphviz openblas libomp
@@ -76,6 +88,7 @@ jobs:
         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
 
@@ -89,7 +102,9 @@ jobs:
 
       - name: Upload coverage report
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
-        uses: codecov/[email protected]
+        uses: codecov/[email protected]
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
 
       - name: Run integration tests
         run: python -m nox -s integration
@@ -110,42 +125,54 @@ jobs:
         if: matrix.os == 'ubuntu-latest'
         run: python -m nox -s scripts
 
-  #M-series Mac Mini
+  # 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}
+      LD_LIBRARY_PATH: $HOME/.local/lib
     strategy:
       fail-fast: false
       matrix:
         python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
 
     steps:
       - uses: actions/checkout@v4
-      - name: Install python & create virtualenv
+      - name: Install Python & create virtualenv
         shell: bash
         run: |
           eval "$(pyenv init -)"
           pyenv install ${{ matrix.python-version }} -s
           pyenv virtualenv ${{ matrix.python-version }} pybamm-${{ matrix.python-version }}
 
-      - name: Install dependencies & run unit tests for Windows and MacOS
+      - name: Install build-time dependencies & run unit tests for M-series macOS runner
         shell: bash
+        env:
+          # Point scikits.odes to the correct SUNDIALS installation
+          SUNDIALS_INST: $HOME/.local/lib
+          # Homebrew environment variables
+          HOMEBREW_NO_INSTALL_CLEANUP: 1
+          NONINTERACTIVE: 1
         run: |
           eval "$(pyenv init -)"
           pyenv activate pybamm-${{ matrix.python-version }}
-          python -m pip install --upgrade pip wheel setuptools nox
+          python -m pip install --upgrade pip nox
+          # Don't use Homebrew to install SUNDIALS because scikits.odes looks for
+          # in Homebrew folders instead, which we don't want
+          brew uninstall sundials --force
+          pip cache remove scikits.odes
+          python -m nox -s pybamm-requires -- --force
           python -m nox -s unit
 
-      - name: Run integration tests for Windows and MacOS
+      - name: Run integration tests for M-series macOS runner
         run: |
           eval "$(pyenv init -)"
           pyenv activate pybamm-${{ matrix.python-version }}
           python -m nox -s integration
 
-      - name: Uninstall pyenv-virtualenv & python
+      - name: Uninstall pyenv-virtualenv & Python
         if: always()
         shell: bash
         run: |
@@ -159,8 +186,18 @@ jobs:
         matrix:
             os: [ubuntu-latest, macos-latest]
             python-version: ["3.8", "3.9", "3.10", "3.11"]
+          # Include macOS M1 runners
+            include:
+              - os: macos-14
+                python-version: "3.10"
+              - os: macos-14
+                python-version: "3.11"
+              # scikits.odes is not available on Python 3.12 yet
+              # See https://github.com/bmcage/odes/issues/162
+              # - os: macos-14
+              #  python-version: "3.12"
         fail-fast: false
-    name: Test pybamm_install_odes on ${{ matrix.os }}
+    name: Test pybamm_install_odes (${{ matrix.os }} / Python ${{ matrix.python-version }})
 
     steps:
       - name: Check out PyBaMM repository
@@ -172,7 +209,7 @@ jobs:
           sudo apt-get update
           sudo apt-get install gfortran gcc libopenblas-dev
       - name: Install macOS system dependencies
-        if: matrix.os == 'macos-latest'
+        if: matrix.os == 'macos-latest' || matrix.os == 'macos-14'
         env:
           # Homebrew environment variables
           HOMEBREW_NO_INSTALL_CLEANUP: 1

diff --git a/.github/workflows/test_on_push.yml b/.github/workflows/test_on_push.yml
@@ -43,6 +43,14 @@ jobs:
         exclude:
           - os: ubuntu-latest
             python-version: "3.11"
+        # Include macOS M1 runners
+        include:
+          - os: macos-14
+            python-version: "3.10"
+          - os: macos-14
+            python-version: "3.11"
+          - os: macos-14
+            python-version: "3.12"
     name: Unit tests (${{ matrix.os }} / Python ${{ matrix.python-version }})
 
     steps:
@@ -51,7 +59,7 @@ jobs:
 
       # Install and cache apt packages
       - name: Install Linux system dependencies
-        uses: awalsh128/cache-apt-pkgs-action@v1.3.1
+        uses: awalsh128/cache-apt-pkgs-action@v1.4.1
         if: matrix.os == 'ubuntu-latest'
         with:
           packages: gfortran gcc graphviz pandoc
@@ -66,7 +74,7 @@ jobs:
           sudo apt-get install libopenblas-dev texlive-latex-extra dvipng
 
       - name: Install macOS system dependencies
-        if: matrix.os == 'macos-latest'
+        if: matrix.os == 'macos-latest' || matrix.os == 'macos-14'
         env:
           # Homebrew environment variables
           HOMEBREW_NO_INSTALL_CLEANUP: 1
@@ -108,6 +116,7 @@ jobs:
           key: nox-${{ matrix.os }}-pybamm-requires-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/install_KLU_Sundials.py', '**/noxfile.py', '**/test_on_push.yml') }}
 
       - 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
 
@@ -129,7 +138,7 @@ jobs:
 
       # Install and cache apt packages
       - name: Install Linux system dependencies
-        uses: awalsh128/cache-apt-pkgs-action@v1.3.1
+        uses: awalsh128/cache-apt-pkgs-action@v1.4.1
         with:
           packages: gfortran gcc graphviz pandoc
           execute_install_scripts: true
@@ -164,13 +173,16 @@ jobs:
           key: nox-${{ matrix.os }}-pybamm-requires-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/install_KLU_Sundials.py', '**/noxfile.py', '**/test_on_push.yml') }}
 
       - 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 3.11 and generate coverage report
         run: python -m nox -s coverage
 
       - name: Upload coverage report
-        uses: codecov/[email protected]
+        uses: codecov/[email protected]
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
 
   run_integration_tests:
     needs: style
@@ -180,6 +192,14 @@ jobs:
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
         python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        # Include macOS M1 runners
+        include:
+          - os: macos-14
+            python-version: "3.10"
+          - os: macos-14
+            python-version: "3.11"
+          - os: macos-14
+            python-version: "3.12"
     name: Integration tests (${{ matrix.os }} / Python ${{ matrix.python-version }})
 
     steps:
@@ -188,7 +208,7 @@ jobs:
 
       # Install and cache apt packages
       - name: Install Linux system dependencies
-        uses: awalsh128/cache-apt-pkgs-action@v1.3.1
+        uses: awalsh128/cache-apt-pkgs-action@v1.4.1
         if: matrix.os == 'ubuntu-latest'
         with:
           packages: gfortran gcc graphviz pandoc
@@ -203,7 +223,7 @@ jobs:
           sudo apt-get install libopenblas-dev texlive-latex-extra dvipng
 
       - name: Install macOS system dependencies
-        if: matrix.os == 'macos-latest'
+        if: matrix.os == 'macos-latest' || matrix.os == 'macos-14'
         env:
           # Homebrew environment variables
           HOMEBREW_NO_INSTALL_CLEANUP: 1
@@ -245,6 +265,7 @@ jobs:
           key: nox-${{ matrix.os }}-pybamm-requires-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/install_KLU_Sundials.py', '**/noxfile.py', '**/test_on_push.yml') }}
 
       - 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
 
@@ -268,7 +289,7 @@ jobs:
 
       # Install and cache apt packages
       - name: Install Linux system dependencies
-        uses: awalsh128/cache-apt-pkgs-action@v1.3.1
+        uses: awalsh128/cache-apt-pkgs-action@v1.4.1
         with:
           packages: graphviz pandoc
           execute_install_scripts: true
@@ -310,7 +331,7 @@ jobs:
 
       # Install and cache apt packages
       - name: Install Linux system dependencies
-        uses: awalsh128/cache-apt-pkgs-action@v1.3.1
+        uses: awalsh128/cache-apt-pkgs-action@v1.4.1
         with:
           packages: gfortran gcc graphviz pandoc
           execute_install_scripts: true
@@ -345,6 +366,7 @@ jobs:
           key: nox-${{ matrix.os }}-pybamm-requires-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/install_KLU_Sundials.py', '**/noxfile.py', '**/test_on_push.yml') }}
 
       - 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
@@ -364,7 +386,7 @@ jobs:
 
       # Install and cache apt packages
       - name: Install Linux system dependencies
-        uses: awalsh128/cache-apt-pkgs-action@v1.3.1
+        uses: awalsh128/cache-apt-pkgs-action@v1.4.1
         with:
           packages: gfortran gcc graphviz
           execute_install_scripts: true
@@ -399,6 +421,7 @@ jobs:
           key: nox-${{ matrix.os }}-pybamm-requires-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/install_KLU_Sundials.py', '**/noxfile.py', '**/test_on_push.yml') }}
 
       - 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