Add support for pyproject.toml

.github/workflows/lychee_url_checker.yml

@@ -45,13 +45,18 @@ jobs:
             --accept 200,429
             --exclude-path ./CHANGELOG.md
             --exclude-path ./scripts/update_version.py
+            --exclude-path asv.conf.json
             --exclude-path docs/conf.py
             './**/*.rst'
             './**/*.md'
             './**/*.py'
             './**/*.ipynb'
+            './**/*.json'
+            './**/*.toml'
           # fail the action on broken links
           fail: true
+          jobSummary: true
+          format: markdown
         env:
           # to be used in case rate limits are surpassed
           GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}

.github/workflows/publish_pypi.yml

@@ -1,13 +1,16 @@
-name: Build and publish package to PyPI
-
+# name: Build and publish package to PyPI
+name: Test building wheels
+# Temporarily disable publishing to PyPI and enable
+# building wheels on pull requests
 on:
   release:
     types: [published]
+  pull_request:
   workflow_dispatch:
     inputs:
-      target:
-        description: 'Deployment target. Can be "pypi" or "testpypi"'
-        default: "pypi"
+      # target:
+      #   description: 'Deployment target. Can be "pypi" or "testpypi"'
+      #   default: "pypi"
       debug_enabled:
         type: boolean
         description: 'Run the build with tmate debugging enabled (https://github.com/marketplace/actions/debugging-with-tmate)'
@@ -24,9 +27,6 @@ jobs:
         with:
           python-version: 3.8
 
-      - name: Install cibuildwheel
-        run: python -m pip install cibuildwheel==2.12.3
-
       - name: Clone pybind11 repo (no history)
         run: git clone --depth 1 --branch v2.10.4 https://github.com/pybind/pybind11.git
 
@@ -53,8 +53,7 @@ jobs:
         if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled }}
 
       - name: Build 64 bits wheels on Windows
-        run: |
-          python -m cibuildwheel --output-dir wheelhouse
+        run: pipx run cibuildwheel --output-dir wheelhouse
         env:
           CIBW_ENVIRONMENT: 'PYBAMM_USE_VCPKG=ON VCPKG_ROOT_DIR=C:\vcpkg VCPKG_DEFAULT_TRIPLET=x64-windows-static-md VCPKG_FEATURE_FLAGS=manifests,registries CMAKE_GENERATOR="Visual Studio 17 2022" CMAKE_GENERATOR_PLATFORM=x64'
           CIBW_ARCHS: "AMD64"
@@ -79,40 +78,37 @@ jobs:
         with:
           python-version: 3.8
 
-      - name: Install cibuildwheel
-        run: python -m pip install cibuildwheel==2.12.3
-
       - name: Clone pybind11 repo (no history)
-        run: git clone --depth 1 --branch v2.10.4 https://github.com/pybind/pybind11.git
+        run: git clone --depth 1 --branch v2.11.1 https://github.com/pybind/pybind11.git
 
-      - name: Install SUNDIALS on macOS
+      # sometimes gfortran cannot be found, so reinstall gcc just to be sure
+      - name: Install SuiteSparse and SUNDIALS on macOS
         if: matrix.os == 'macos-latest'
         run: |
-          # https://github.com/actions/virtual-environments/issues/1280
-          rm -f /usr/local/bin/2to3*
-          rm -f /usr/local/bin/idle3*
-          rm -f /usr/local/bin/pydoc3*
-          rm -f /usr/local/bin/python3*
           brew update
+          brew install gcc gfortran libomp graphviz openblas
           brew reinstall gcc
-          brew install libomp
           python -m pip install cmake wget
           python scripts/install_KLU_Sundials.py
 
-      - name: Build wheels on Linux and MacOS
-        run: python -m cibuildwheel --output-dir wheelhouse
+      - name: Build wheels on ${{ matrix.os }}
+        run: pipx run cibuildwheel --output-dir wheelhouse
         env:
+          # NumPy requires BLAS now which is no longer available on manylinux2014 i686, so skip it
+          CIBW_ARCHS_LINUX: x86_64
           # TODO: openblas no longer available on centos 7 i686 image, use blas instead for now
           CIBW_BEFORE_ALL_LINUX: >
             yum -y install blas-devel lapack-devel &&
             bash build_manylinux_wheels/install_sundials.sh 5.8.1 6.5.0
-
-          CIBW_BEFORE_BUILD_LINUX: "python -m pip install cmake casadi numpy"
+          CIBW_BEFORE_BUILD_LINUX: >
+            python -m pip install cmake casadi numpy
+          # override; point to casadi install path so that it can be found by the repair command
+          CIBW_REPAIR_WHEEL_COMMAND_LINUX: >
+            LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:$(python -c 'import casadi; print(casadi.__path__[0])')" auditwheel repair -w {dest_dir} {wheel}
           CIBW_BEFORE_BUILD_MACOS: >
             python -m pip
             install cmake casadi numpy &&
-            python scripts/fix_casadi_rpath_mac.py &&
-            scripts/fix_suitesparse_rpath_mac.sh
+            python scripts/fix_casadi_rpath_mac.py && scripts/fix_suitesparse_rpath_mac.sh
           # got error "re.error: multiple repeat at position 104" on python 3.7 when --require-archs added, so remove
           # it for mac
           CIBW_REPAIR_WHEEL_COMMAND_MACOS: >
@@ -128,56 +124,56 @@ jobs:
           if-no-files-found: error
 
   build_sdist:
-    name: Build sdist
+    name: Build SDist
     runs-on: ubuntu-latest
 
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: 3.11
 
       - name: Install dependencies
-        run: pip install wheel
+        run: pip install --upgrade pip setuptools wheel
 
-      - name: Build sdist
-        run: python setup.py sdist --formats=gztar
+      - name: Build SDist
+        run: pipx run build --sdist
 
-      - name: Upload sdist
+      - name: Upload SDist
         uses: actions/upload-artifact@v3
         with:
           name: sdist
           path: ./dist/*.tar.gz
           if-no-files-found: error
 
-  publish_pypi:
-    name: Upload package to PyPI
-    needs: [build_wheels, build_windows_wheels, build_sdist]
-    runs-on: ubuntu-latest
-    steps:
-      - name: Download all artifacts
-        uses: actions/download-artifact@v3
-
-      - name: Move all package files to files/
-        run: |
-          mkdir files
-          mv windows_wheels/* wheels/* sdist/* files/
-
-      - name: Publish on PyPI
-        if: |
-          github.event.inputs.target == 'pypi' ||
-          (github.event_name == 'push' && github.ref == 'refs/heads/main')
-        uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          user: __token__
-          password: ${{ secrets.PYPI_TOKEN }}
-          packages_dir: files/
-
-      - name: Publish on TestPyPI
-        if: github.event.inputs.target == 'testpypi'
-        uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          user: __token__
-          password: ${{ secrets.TESTPYPI_TOKEN }}
-          packages_dir: files/
-          repository_url: https://test.pypi.org/legacy/
+  # publish_pypi:
+  #   name: Upload package to PyPI
+  #   needs: [build_wheels, build_windows_wheels, build_sdist]
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #     - name: Download all artifacts
+  #       uses: actions/download-artifact@v3
+
+  #     - name: Move all package files to files/
+  #       run: |
+  #         mkdir files
+  #         mv windows_wheels/* wheels/* sdist/* files/
+
+  #     - name: Publish on PyPI
+  #       if: |
+  #         github.event.inputs.target == 'pypi' ||
+  #         (github.event-name == 'push' && github.ref == 'refs/heads/main')
+  #       uses: pypa/gh-action-pypi-publish@release/v1
+  #       with:
+  #         user: __token__
+  #         password: ${{ secrets.PYPI_TOKEN }}
+  #         packages_dir: files/
+
+  #     - name: Publish on TestPyPI
+  #       if: github.event.inputs.target == 'testpypi'
+  #       uses: pypa/gh-action-pypi-publish@release/v1
+  #       with:
+  #         user: __token__
+  #         password: ${{ secrets.TESTPYPI_TOKEN }}
+  #         packages-dir: files/
+  #         repository-url: https://test.pypi.org/legacy/

.github/workflows/run_periodic_tests.yml

@@ -12,24 +12,19 @@ on:
   schedule:
     - cron: "0 3 * * *"
 
-jobs:
-  pre_job:
-    runs-on: ubuntu-latest
-    # Map a step output to a job output
-    outputs:
-      should_skip: ${{ steps.skip_check.outputs.should_skip }}
-    steps:
-      - id: skip_check
-        uses: fkirc/skip-duplicate-actions@master
-        with:
-          # All of these options are optional, so you can remove them if you are happy with the defaults
-          concurrent_skipping: "never"
-          cancel_others: "true"
-          paths_ignore: '["**/README.md"]'
+env:
+  FORCE_COLOR: 3
+
+concurrency:
+  # github.workflow: name of the workflow, so that we don't cancel other workflows
+  # github.event.pull_request.number || github.ref: pull request number or branch name if not a pull request
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  # Cancel in-progress runs when a new workflow with the same group name is triggered
+  # This avoids workflow runs on both pushes and PRs
+  cancel-in-progress: true
 
+jobs:
   style:
-    needs: pre_job
-    if: ${{ needs.pre_job.outputs.should_skip != 'true' }}
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
@@ -66,58 +61,47 @@ jobs:
           sudo apt install gfortran gcc libopenblas-dev graphviz pandoc
           sudo apt install texlive-full
 
-      # Added fixes to homebrew installs:
-      # rm -f /usr/local/bin/2to3
-      # (see https://github.com/actions/virtual-environments/issues/2322)
       - name: Install MacOS system dependencies
         if: matrix.os == 'macos-latest'
         run: |
-          rm -f /usr/local/bin/2to3*
-          rm -f /usr/local/bin/idle3*
-          rm -f /usr/local/bin/pydoc3*
-          rm -f /usr/local/bin/python3*
+          brew analytics off
           brew update
-          brew install graphviz
-          brew install openblas
+          brew install graphviz openblas gcc gfortran libomp
 
       - name: Install Windows system dependencies
         if: matrix.os == 'windows-latest'
         run: choco install graphviz --version=2.38.0.20190211
 
-      - name: Install standard python dependencies
-        run: |
-          python -m pip install --upgrade pip wheel setuptools nox
-
-      - name: Install SuiteSparse and SUNDIALS on GNU/Linux
-        if: matrix.os == 'ubuntu-latest'
-        run: nox -s pybamm-requires
+      - name: Install SuiteSparse and SUNDIALS on GNU/Linux and macOS
+        if: matrix.os != 'windows-latest'
+        run: pipx run nox -s pybamm-requires
 
       - name: Run unit tests for GNU/Linux with Python 3.8, 3.9, and 3.10, and for macOS and Windows with all Python versions
         if: (matrix.os == 'ubuntu-latest' && matrix.python-version != 3.11) || (matrix.os != 'ubuntu-latest')
-        run: nox -s unit
+        run: pipx run nox -s unit
 
       - 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: nox -s coverage
+        run: pipx run nox -s coverage
 
       - name: Upload coverage report
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
         uses: codecov/[email protected]
 
       - name: Run integration tests
-        run: nox -s integration
+        run: pipx run nox -s integration
 
       - name: Install docs dependencies and run doctests
         if: matrix.os == 'ubuntu-latest'
-        run: nox -s doctests
+        run: pipx run nox -s doctests
 
       - name: Check if the documentation can be built
         if: matrix.os == 'ubuntu-latest'
         run: nox -s docs
 
       - name: Install dev dependencies and run example tests
         if: matrix.os == 'ubuntu-latest'
-        run: nox -s examples
+        run: pipx run nox -s examples
 
       - name: Run example scripts tests
         if: matrix.os == 'ubuntu-latest'