Merge branch 'develop' into serialisation

pybamm-team · Nov 27, 2023 · 95935a0 · 95935a0
2 parents 92e7c90 + 6ece7a1
commit 95935a0
Show file tree

Hide file tree

Showing 48 changed files with 727 additions and 4,951 deletions.
diff --git a/.github/release_workflow.md b/.github/release_workflow.md
@@ -9,8 +9,8 @@ This file contains the workflow required to make a `PyBaMM` release on GitHub, P
    - `pybamm/version.py`
    - `docs/conf.py`
    - `CITATION.cff`
+   - `pyproject.toml`
    - `vcpkg.json`
-   - `docs/_static/versions.json`
    - `CHANGELOG.md`
 
       These changes will be automatically pushed to a new branch `vYY.MM` and a PR from `vvYY.MM` to `develop` will be created (to sync the branches).
@@ -32,8 +32,8 @@ If a new release candidate is required after the release of `rc0` -
    - `pybamm/version.py`
    - `docs/conf.py`
    - `CITATION.cff`
+   - `pyproject.toml`
    - `vcpkg.json`
-   - `docs/_static/versions.json`
    - `CHANGELOG.md`
 
       These changes will be automatically pushed to the existing `vYY.MM` branch and a PR from `vvYY.MM` to `develop` will be created (to sync the branches).
@@ -53,8 +53,8 @@ Once satisfied with the release candidates -
    - `pybamm/version.py`
    - `docs/conf.py`
    - `CITATION.cff`
+   - `pyproject.toml`
    - `vcpkg.json`
-   - `docs/_static/versions.json`
    - `CHANGELOG.md`
 
       These changes will be automatically pushed to the existing `vYY.MM` branch and a PR from `vvYY.MM` to `develop` will be created (to sync the branches).
@@ -70,8 +70,7 @@ Once satisfied with the release candidates -
 Some other essential things to check throughout the release process -
 
 - If updating our custom vcpkg registory entries [pybamm-team/sundials-vcpkg-registry](https://github.com/pybamm-team/sundials-vcpkg-registry) or [pybamm-team/casadi-vcpkg-registry](https://github.com/pybamm-team/casadi-vcpkg-registry) (used to build Windows wheels), make sure to update the baseline of the registories in vcpkg-configuration.json to the latest commit id.
-- Update jax and jaxlib to the latest version in `pybamm.util` and `setup.py`, fixing any bugs that arise
-- Make sure the URLs in `docs/_static/versions.json` are valid
+- Update jax and jaxlib to the latest version in `pybamm.util` and `pyproject.toml`, fixing any bugs that arise
 - As the release workflow is initiated by the `release` event, it's important to note that the default `GITHUB_REF` used by `actions/checkout` during the checkout process will correspond to the tag created during the release process. Consequently, the workflows will consistently build PyBaMM based on the commit associated with this tag. Should new commits be introduced to the `vYY.MM` branch, such as those addressing build issues, it becomes necessary to manually update this tag to point to the most recent commit -
   ```
   git tag -f <tag_name> <commit_hash>

diff --git a/.github/workflows/lychee_url_checker.yml b/.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}}
diff --git a/.github/workflows/publish_pypi.yml b/.github/workflows/publish_pypi.yml
@@ -1,5 +1,4 @@
 name: Build and publish package to PyPI
-
 on:
   release:
     types: [published]
@@ -27,22 +26,18 @@ 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
 
-      # remove when a new vcpkg version is released
-      - name: Install the latest commit of vcpkg on windows
+      - name: Install vcpkg on Windows
         run: |
           cd C:\
           rm -r -fo 'C:\vcpkg'
           git clone https://github.com/microsoft/vcpkg
           cd vcpkg
           .\bootstrap-vcpkg.bat
 
-      - name: Cache packages installed through vcpkg on windows
+      - name: Cache packages installed through vcpkg on Windows
         uses: actions/cache@v3
         env:
           cache-name: vckpg_binary_cache
@@ -55,14 +50,13 @@ jobs:
         uses: mxschmitt/action-tmate@v3
         if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled }}
 
-      - name: Build 64 bits wheels on Windows
-        run: |
-          python -m cibuildwheel --output-dir wheelhouse
+      - name: Build 64-bit wheels on Windows
+        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"
 
-      - name: Upload windows wheels
+      - name: Upload Windows wheels
         uses: actions/upload-artifact@v3
         with:
           name: windows_wheels
@@ -82,42 +76,34 @@ 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 graphviz openblas libomp
           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 ${{ matrix.os }}
+        run: pipx run cibuildwheel --output-dir wheelhouse
         env:
           CIBW_ARCHS_LINUX: x86_64
           CIBW_BEFORE_ALL_LINUX: >
             yum -y install openblas-devel lapack-devel &&
-            bash build_manylinux_wheels/install_sundials.sh 6.0.3 6.5.0
-
-          CIBW_BEFORE_BUILD_LINUX: "python -m pip install cmake casadi numpy"
+            bash scripts/install_sundials.sh 6.0.3 6.5.0
+          CIBW_BEFORE_BUILD_LINUX: >
+            python -m pip install cmake casadi numpy
+          # override; point to casadi install path so that it can be found by the repair command
+          CIBW_REPAIR_WHEEL_COMMAND_LINUX: >
+            LD_LIBRARY_PATH="${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
-          # got error "re.error: multiple repeat at position 104" on python 3.7 when --require-archs added, so remove
-          # it for mac
+            python scripts/fix_casadi_rpath_mac.py && scripts/fix_suitesparse_rpath_mac.sh
           CIBW_REPAIR_WHEEL_COMMAND_MACOS: >
             delocate-listdeps {wheel} &&
             delocate-wheel -v -w {dest_dir} {wheel}
@@ -131,7 +117,7 @@ jobs:
           if-no-files-found: error
 
   build_sdist:
-    name: Build sdist
+    name: Build SDist
     runs-on: ubuntu-latest
 
     steps:
@@ -141,12 +127,12 @@ jobs:
           python-version: 3.11
 
       - name: Install dependencies
-        run: pip install --upgrade pip setuptools wheel build
+        run: pip install --upgrade pip setuptools wheel
 
-      - name: Build sdist
-        run: python -m build --sdist
+      - name: Build SDist
+        run: pipx run build --sdist
 
-      - name: Upload sdist
+      - name: Upload SDist
         uses: actions/upload-artifact@v3
         with:
           name: sdist

diff --git a/.github/workflows/run_periodic_tests.yml b/.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
@@ -66,62 +61,54 @@ 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
+      - 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 update
-          brew install graphviz
-          brew install openblas
+          brew analytics off
+          brew install graphviz openblas libomp
+          brew reinstall gcc
 
       - 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
+      - name: Install nox
+        run: python -m pip install nox
 
-      - name: Install SuiteSparse and SUNDIALS on GNU/Linux
-        if: matrix.os == 'ubuntu-latest'
-        run: pipx run nox -s pybamm-requires
+      - name: Install SuiteSparse and SUNDIALS on GNU/Linux and macOS
+        if: matrix.os != 'windows-latest'
+        run: python -m 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: pipx run nox -s unit
+        run: python -m 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: pipx run nox -s coverage
+        run: python -m 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: pipx run nox -s integration
+        run: python -m nox -s integration
 
       - name: Install docs dependencies and run doctests
         if: matrix.os == 'ubuntu-latest'
-        run: pipx run nox -s doctests
+        run: python -m nox -s doctests
 
       - name: Check if the documentation can be built
         if: matrix.os == 'ubuntu-latest'
-        run: pipx run nox -s docs
+        run: python -m nox -s docs
 
       - name: Install dev dependencies and run example tests
         if: matrix.os == 'ubuntu-latest'
-        run: pipx run nox -s examples
+        run: python -m nox -s examples
 
       - name: Run example scripts tests
         if: matrix.os == 'ubuntu-latest'
-        run: pipx run nox -s scripts
+        run: python -m nox -s scripts
 
   #M-series Mac Mini
   build-apple-mseries: