Merge branch 'develop' into Saswatsusmoy-pybamm-team#3441-Call-proces…

…sed-variables-with-custom-spatial-coordinates

.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"
       ]
     },
     {

.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'

.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:
@@ -89,7 +101,9 @@ jobs:
 
       - name: Upload coverage report
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
-        uses: codecov/codecov-action@v3.1.5
+        uses: codecov/codecov-action@v4.0.1
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
 
       - name: Run integration tests
         run: python -m nox -s integration
@@ -110,42 +124,54 @@ 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 +185,16 @@ 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"
+              - 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

.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:
@@ -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
@@ -170,7 +178,9 @@ jobs:
         run: python -m nox -s coverage
 
       - name: Upload coverage report
-        uses: codecov/codecov-action@v3.1.5
+        uses: codecov/codecov-action@v4.0.1
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
 
   run_integration_tests:
     needs: style
@@ -180,6 +190,14 @@ 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:
@@ -203,7 +221,7 @@ 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

.github/workflows/update_version.yml

@@ -82,7 +82,7 @@ jobs:
       # create a pull request updating versions in develop
       - name: Create Pull Request
         id: version_pr
-        uses: peter-evans/create-pull-request@v5
+        uses: peter-evans/create-pull-request@v6
         with:
           delete-branch: true
           branch-suffix: short-commit-hash

.github/workflows/work_precision_sets.yml

@@ -27,7 +27,7 @@ jobs:
           python benchmarks/work_precision_sets/time_vs_reltols.py
           python benchmarks/work_precision_sets/time_vs_abstols.py
       - name: Create Pull Request
-        uses: peter-evans/create-pull-request@v5
+        uses: peter-evans/create-pull-request@v6
         with:
           delete-branch: true
           branch-suffix: short-commit-hash

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.1.14"
+    rev: "v0.2.0"
     hooks:
       - id: ruff
         args: [--fix, --show-fixes]

CHANGELOG.md

@@ -2,6 +2,7 @@
 
 ## Features
 
+- Added support for macOS arm64 (M-series) platforms. ([#3789](https://github.com/pybamm-team/PyBaMM/pull/3789))
 - Renamed "electrode diffusivity" to "particle diffusivity" as a non-breaking change with a deprecation warning ([#3624](https://github.com/pybamm-team/PyBaMM/pull/3624))
 - Add support for BPX version 0.4.0 which allows for blended electrodes and user-defined parameters in BPX([#3414](https://github.com/pybamm-team/PyBaMM/pull/3414))
 - Added the ability to specify a custom solver tolerance in `get_initial_stoichiometries` and related functions ([#3714](https://github.com/pybamm-team/PyBaMM/pull/3714))

README.md

@@ -205,7 +205,7 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
     </tr>
     <tr>
       <td align="center" valign="top" width="14.28%"><a href="https://www.rse.ox.ac.uk/"><img src="https://avatars3.githubusercontent.com/u/3770306?v=4?s=100" width="100px;" alt="Fergus Cooper"/><br /><sub><b>Fergus Cooper</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=fcooper8472" title="Code">💻</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=fcooper8472" title="Tests">⚠️</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/jonchapman1"><img src="https://avatars1.githubusercontent.com/u/28925818?v=4?s=100" width="100px;" alt="jonchapman1"/><br /><sub><b>jonchapman1</b></sub></a><br /><a href="#ideas-jonchapman1" title="Ideas, Planning, & Feedback">🤔</a> <a href="#fundingFinding-jonchapman1" title="Funding Finding">🔍</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/jonchapman1"><img src="https://avatars1.githubusercontent.com/u/28925818?v=4?s=100" width="100px;" alt="jonchapman1"/><br /><sub><b>jonchapman1</b></sub></a><br /><a href="#ideas-jonchapman1" title="Ideas, Planning, & Feedback">🤔</a> <a href="#fundingFinding-jonchapman1" title="Funding Finding">🔍</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=jonchapman1" title="Documentation">📖</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/colinplease"><img src="https://avatars3.githubusercontent.com/u/44977104?v=4?s=100" width="100px;" alt="Colin Please"/><br /><sub><b>Colin Please</b></sub></a><br /><a href="#ideas-colinplease" title="Ideas, Planning, & Feedback">🤔</a> <a href="#fundingFinding-colinplease" title="Funding Finding">🔍</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/cwmonroe"><img src="https://avatars.githubusercontent.com/u/92099819?v=4?s=100" width="100px;" alt="cwmonroe"/><br /><sub><b>cwmonroe</b></sub></a><br /><a href="#ideas-cwmonroe" title="Ideas, Planning, & Feedback">🤔</a> <a href="#fundingFinding-cwmonroe" title="Funding Finding">🔍</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/gjo97"><img src="https://avatars.githubusercontent.com/u/18349157?v=4?s=100" width="100px;" alt="Greg"/><br /><sub><b>Greg</b></sub></a><br /><a href="#ideas-gjo97" title="Ideas, Planning, & Feedback">🤔</a> <a href="#fundingFinding-gjo97" title="Funding Finding">🔍</a></td>
@@ -276,7 +276,7 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/jlauber18"><img src="https://avatars.githubusercontent.com/u/28939653?v=4?s=100" width="100px;" alt="Jonathan Lauber"/><br /><sub><b>Jonathan Lauber</b></sub></a><br /><a href="#infra-jlauber18" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a></td>
     </tr>
     <tr>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/prady0t"><img src="https://avatars.githubusercontent.com/u/99216956?v=4?s=100" width="100px;" alt="Pradyot Ranjan"/><br /><sub><b>Pradyot Ranjan</b></sub></a><br /><a href="#infra-prady0t" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/prady0t"><img src="https://avatars.githubusercontent.com/u/99216956?v=4?s=100" width="100px;" alt="Pradyot Ranjan"/><br /><sub><b>Pradyot Ranjan</b></sub></a><br /><a href="#infra-prady0t" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=prady0t" title="Code">💻</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=prady0t" title="Tests">⚠️</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/XuboGU"><img src="https://avatars.githubusercontent.com/u/53944452?v=4?s=100" width="100px;" alt="XuboGU"/><br /><sub><b>XuboGU</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=XuboGU" title="Code">💻</a> <a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3AXuboGU" title="Bug reports">🐛</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/cringeyburger"><img src="https://avatars.githubusercontent.com/u/121183876?v=4?s=100" width="100px;" alt="Ankit Meda"/><br /><sub><b>Ankit Meda</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=cringeyburger" title="Code">💻</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/AlessioBugetti"><img src="https://avatars.githubusercontent.com/u/38499721?v=4?s=100" width="100px;" alt="Alessio Bugetti"/><br /><sub><b>Alessio Bugetti</b></sub></a><br /><a href="#infra-AlessioBugetti" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=AlessioBugetti" title="Code">💻</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=AlessioBugetti" title="Documentation">📖</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=AlessioBugetti" title="Tests">⚠️</a></td>

pybamm/batch_study.py

@@ -196,7 +196,8 @@ def create_gif(self, number_of_images=80, duration=0.1, output_filename="plot.gi
             Name of the generated GIF file.
 
         """
-
+        if not hasattr(self, "sims"):
+            raise ValueError("The simulations have not been solved yet.")
         if self.quick_plot is None:
             self.quick_plot = pybamm.QuickPlot(self.sims)
 

pybamm/experiment/experiment.py

@@ -133,6 +133,21 @@ def __repr__(self):
     def read_termination(termination):
         """
         Read the termination reason. If this condition is hit, the experiment will stop.
+
+        Parameters
+        ----------
+        termination : str or list[str], optional
+           A single string, or a list of strings, representing the conditions to terminate the experiment.
+           Only capacity or voltage can be provided as a termination reason.
+           e.g. '4 Ah capacity' or ['80% capacity', '2.5 V']
+
+        Returns
+        -------
+        dict
+           A dictionary of the termination conditions.
+           e.g. {'capacity': (4.0, 'Ah')} or
+           {'capacity': (80.0, '%'), 'voltage': (2.5, 'V')}
+
         """
         if termination is None:
             return {}

pybamm/install_odes.py

@@ -191,6 +191,11 @@ def main(arguments=None):
     os.environ["SUNDIALS_INST"] = SUNDIALS_LIB_DIR
     env = os.environ.copy()
     logger.info("Installing scikits.odes via pip")
+    logger.info("Purging scikits.odes whels from pip cache if present")
+    subprocess.run(
+        [f"{sys.executable}", "-m", "pip", "cache", "remove", "scikits.odes"],
+        check=True,
+    )
     subprocess.run(
         [f"{sys.executable}", "-m", "pip", "install", "scikits.odes", "--verbose"],
         env=env,

pybamm/simulation.py

@@ -1072,6 +1072,8 @@ def create_gif(self, number_of_images=80, duration=0.1, output_filename="plot.gi
             Name of the generated GIF file.
 
         """
+        if self.solution is None:
+            raise ValueError("The simulation has not been solved yet.")
         if self.quick_plot is None:
             self.quick_plot = pybamm.QuickPlot(self._solution)
 

tests/unit/test_batch_study.py

@@ -93,6 +93,12 @@ def test_solve(self):
     def test_create_gif(self):
         with TemporaryDirectory() as dir_name:
             bs = pybamm.BatchStudy({"spm": pybamm.lithium_ion.SPM()})
+            with self.assertRaisesRegex(
+                ValueError, "The simulations have not been solved yet."
+            ):
+                pybamm.BatchStudy(
+                    models={"SPM": spm, "SPM uniform": spm_uniform}
+                ).create_gif()
             bs.solve([0, 10])
 
             # Create a temporary file name

tests/unit/test_simulation.py

@@ -396,6 +396,10 @@ def test_plot(self):
     def test_create_gif(self):
         with TemporaryDirectory() as dir_name:
             sim = pybamm.Simulation(pybamm.lithium_ion.SPM())
+            with self.assertRaisesRegex(
+                ValueError, "The simulation has not been solved yet."
+            ):
+                sim.create_gif()
             sim.solve(t_eval=[0, 10])
 
             # Create a temporary file name