Merge branch 'graded-electrode-example' of github.com:pybamm-team/PyB…

…aMM into graded-electrode-example
MarcBerliner · Sep 7, 2024 · b3aeaf1 · b3aeaf1
2 parents f28e687 + d43142b
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diff --git a/.all-contributorsrc b/.all-contributorsrc
@@ -960,6 +960,15 @@
         "code",
         "test"
       ]
+    },
+    {
+      "login": "medha-14",
+      "name": "Medha Bhardwaj",
+      "avatar_url": "https://avatars.githubusercontent.com/u/143182673?v=4",
+      "profile": "https://github.com/medha-14",
+      "contributions": [
+        "code"
+      ]
     }
   ],
   "contributorsPerLine": 7,

diff --git a/.github/release_reminder.md b/.github/release_reminder.md
diff --git a/.github/release_workflow.md b/.github/release_workflow.md
@@ -1,10 +1,13 @@
 # Release workflow
 
-This file contains the workflow required to make a `PyBaMM` release on GitHub, PyPI, and conda-forge by the maintainers.
+This file contains the workflow required to make a `PyBaMM` release on
+GitHub, PyPI, and conda-forge by the maintainers.
 
-## rc0 releases (automated)
+## Initial release (automated)
 
-1. The `update_version.yml` workflow will run on every 1st of January, May and September, updating incrementing the version to `vYY.MMrc0` by running `scripts/update_version.py` in the following files -
+1. The `update_version.yml` workflow will run on every 1st of January, May
+   and September, updating incrementing the version to `vYY.MM.0` by running
+   `scripts/update_version.py` in the following files:
 
    - `pybamm/version.py`
    - `docs/conf.py`
@@ -13,21 +16,27 @@ This file contains the workflow required to make a `PyBaMM` release on GitHub, P
    - `vcpkg.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).
+   These changes will be automatically pushed to a new branch `vYY.MM`
+   and a PR from `vYY.MM` to `main` will be created.
 
-2. Create a new GitHub _pre-release_ with the tag `vYY.MMrc0` from the `vYY.MM` branch and a description copied from `CHANGELOG.md`.
+2. Create a new GitHub _release_ with the tag `vYY.MM.0` from the `vYY.MM`
+   branch and a description copied from `CHANGELOG.md`.
 
-3. This release will automatically trigger `publish_pypi.yml` and create a _pre-release_ on PyPI.
+3. This release will automatically trigger `publish_pypi.yml` and create a
+   _release_ on PyPI.
 
-## rcX releases (manual)
+## Bug fix releases (manual)
 
-If a new release candidate is required after the release of `rc{X-1}` -
+If a new release is required after the release of `vYY.MM.{x-1}` -
 
-1. Cherry-pick the bug fix (no new features should be added to `vYY.MM` once `rc{X-1}` is released) commit to `vYY.MM` branch once the fix is merged into `develop`. The CHANGELOG entry for such fixes should go under the `rc{X-1}` heading in `CHANGELOG.md`
+1. Create a new branch for the `vYY.MM.x` release using the `vYY.MM.{x-1}` tag.
 
-2. Run `update_version.yml` manually while using `append_to_tag` to specify the release candidate version number (`rc1`, `rc2`, ...).
+2. Cherry-pick the bug fixes to `vYY.MM.x` branch once the fix is
+   merged into `develop`. The CHANGELOG entry for such fixes should go under the
+   `YY.MM.x` heading in `CHANGELOG.md`
 
-3. This will increment the version to `vYY.MMrcX` by running `scripts/update_version.py` in the following files -
+3. Run `scripts/update_version.py` manually while setting `VERSION=vYY.MM.x`
+   in your environment. This will update the version in the following files:
 
    - `pybamm/version.py`
    - `docs/conf.py`
@@ -36,45 +45,41 @@ If a new release candidate is required after the release of `rc{X-1}` -
    - `vcpkg.json`
    - `CHANGELOG.md`
 
-      These changes will be automatically pushed to the existing `vYY.MM` branch and a PR will be created to update version strings in `develop`.
+   Commit the changes to your release branch.
 
-4. Create a new GitHub _pre-release_ with the same tag (`vYY.MMrcX`) from the `vYY.MM` branch and a description copied from `CHANGELOG.md`.
+4. Create a PR for the release and configure it to merge into the `main` branch.
 
-5. This release will automatically trigger `publish_pypi.yml` and create a _pre-release_ on PyPI.
-
-## Actual release (manual)
-
-Once satisfied with the release candidates -
-
-1. Run `update_version.yml` manually, leaving the `append_to_tag` field blank ("") for an actual release.
-
-2. This will increment the version to `vYY.MMrcX` by running `scripts/update_version.py` in the following files -
-
-   - `pybamm/version.py`
-   - `docs/conf.py`
-   - `CITATION.cff`
-   - `pyproject.toml`
-   - `vcpkg.json`
-   - `CHANGELOG.md`
-
-      These changes will be automatically pushed to the existing `vYY.MM` branch and a PR will be created to update version strings in `develop`.
-
-3. Next, a PR from `vYY.MM` to `main` will be generated that should be merged once all the tests pass.
-
-4. Create a new GitHub _release_ with the same tag from the `main` branch and a description copied from `CHANGELOG.md`.
-
-5. This release will automatically trigger `publish_pypi.yml` and create a _release_ on PyPI.
+5. Create a new GitHub release with the same tag (`YY.MM.x`) from the `main`
+   branch and a description copied from `CHANGELOG.md`. This release will
+   automatically trigger `publish_pypi.yml` and create a _release_ on PyPI.
 
 ## Other checks
 
 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 `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>
-  git push -f <pybamm-team/PyBaMM_remote_name> <tag_name>  # can only be carried out by the maintainers
-  ```
-- If changes are made to the API, console scripts, entry points, new optional dependencies are added, support for major Python versions is dropped or added, or core project information and metadata are modified at the time of the release, make sure to update the `meta.yaml` file in the `recipe/` folder of the [conda-forge/pybamm-feedstock](https://github.com/conda-forge/pybamm-feedstock) repository accordingly by following the instructions in the [conda-forge documentation](https://conda-forge.org/docs/maintainer/updating_pkgs.html#updating-the-feedstock-repository) and re-rendering the recipe
-- The conda-forge release workflow will automatically be triggered following a stable PyPI release, and the aforementioned updates should be carried out directly in the main repository by pushing changes to the automated PR created by the conda-forge-bot. A manual PR can also be created if the updates are not included in the automated PR for some reason. This manual PR **must** bump the build number in `meta.yaml` and **must** be from a personal fork of the repository.
+- If updating our custom vcpkg registry entries
+  [sundials-vcpkg-registry][SUNDIALS_VCPKG]
+  or [casadi-vcpkg-registry][CASADI_VCPKG] (used to build Windows
+  wheels), make sure to update the baseline of the registries in
+  vcpkg-configuration.json to the latest commit id.
+- Update jax and jaxlib to the latest version in `pybamm.util` and
+  `pyproject.toml`, fixing any bugs that arise.
+- If changes are made to the API, console scripts, entry points, new optional
+  dependencies are added, support for major Python versions is dropped or
+  added, or core project information and metadata are modified at the time
+  of the release, make sure to update the `meta.yaml` file in the `recipe/`
+  folder of the [pybamm-feedstock][PYBAMM_FEED] repository accordingly by
+  following the instructions in the [conda-forge documentation][FEED_GUIDE] and
+  re-rendering the recipe.
+- The conda-forge release workflow will automatically be triggered following
+  a stable PyPI release, and the aforementioned updates should be carried
+  out directly in the main repository by pushing changes to the automated PR
+  created by the conda-forge-bot. A manual PR can also be created if the
+  updates are not included in the automated PR for some reason. This manual
+  PR **must** bump the build number in `meta.yaml` and **must** be from a
+  personal fork of the repository.
+
+[SUNDIALS_VCPKG]: https://github.com/pybamm-team/sundials-vcpkg-registry
+[CASADI_VCPKG]: https://github.com/pybamm-team/casadi-vcpkg-registry
+[PYBAMM_FEED]: https://github.com/conda-forge/pybamm-feedstock
+[FEED_GUIDE]: https://conda-forge.org/docs/maintainer/updating_pkgs.html#updating-the-feedstock-repository
diff --git a/.github/workflows/benchmark_on_push.yml b/.github/workflows/benchmark_on_push.yml
@@ -23,10 +23,13 @@ jobs:
           sudo apt-get update
           sudo apt install gfortran gcc libopenblas-dev
 
+      - name: Set up uv
+        run: python -m pip install uv
+
       - name: Install python dependencies
         run: |
-          python -m pip install --upgrade pip wheel setuptools wget cmake casadi numpy
-          python -m pip install asv[virtualenv]
+          python -m uv pip install --upgrade pip wheel setuptools wget cmake casadi numpy
+          python -m uv pip install asv[virtualenv]
 
       - name: Install SuiteSparse and SUNDIALS
         run: python scripts/install_KLU_Sundials.py

diff --git a/.github/workflows/periodic_benchmarks.yml b/.github/workflows/periodic_benchmarks.yml
@@ -31,10 +31,13 @@ jobs:
           sudo apt-get update
           sudo apt-get install gfortran gcc libopenblas-dev
 
+      - name: Set up uv
+        run: python -m pip install uv
+
       - name: Install python dependencies
         run: |
-          python -m pip install --upgrade pip wheel setuptools wget cmake casadi numpy
-          python -m pip install asv[virtualenv]
+          python -m uv pip install --upgrade pip wheel setuptools wget cmake casadi numpy
+          python -m uv pip install asv[virtualenv]
 
       - name: Install SuiteSparse and SUNDIALS
         run: python scripts/install_KLU_Sundials.py
@@ -48,7 +51,7 @@ jobs:
           LD_LIBRARY_PATH: $HOME/.local/lib
 
       - name: Upload results as artifact
-        uses: actions/upload-artifact@v4.3.6
+        uses: actions/upload-artifact@v4.4.0
         with:
           name: asv_periodic_results
           path: results

diff --git a/.github/workflows/publish_pypi.yml b/.github/workflows/publish_pypi.yml
@@ -84,13 +84,15 @@ jobs:
             CMAKE_BUILD_PARALLEL_LEVEL=${{ steps.get_num_cores.outputs.count }}
           CIBW_ARCHS: AMD64
           CIBW_BEFORE_BUILD: python -m pip install setuptools wheel delvewheel # skip CasADi and CMake
-          CIBW_REPAIR_WHEEL_COMMAND: delvewheel repair -w {dest_dir} {wheel}
+          # Fix access violation because GHA runners have modified PATH that picks wrong
+          # msvcp140.dll, see https://github.com/adang1345/delvewheel/issues/54
+          CIBW_REPAIR_WHEEL_COMMAND: delvewheel repair --add-path C:/Windows/System32 -w {dest_dir} {wheel}
           CIBW_TEST_EXTRAS: "all,dev,jax"
           CIBW_TEST_COMMAND: |
             python -c "import pybamm; print(pybamm.IDAKLUSolver())"
             python -m pytest -m cibw {project}/tests/unit
       - name: Upload Windows wheels
-        uses: actions/upload-artifact@v4.3.6
+        uses: actions/upload-artifact@v4.4.0
         with:
           name: wheels_windows
           path: ./wheelhouse/*.whl
@@ -127,7 +129,7 @@ jobs:
             python -m pytest -m cibw {project}/tests/unit
 
       - name: Upload wheels for Linux
-        uses: actions/upload-artifact@v4.3.6
+        uses: actions/upload-artifact@v4.4.0
         with:
           name: wheels_manylinux
           path: ./wheelhouse/*.whl
@@ -149,9 +151,6 @@ jobs:
       - name: Clone pybind11 repo (no history)
         run: git clone --depth 1 --branch v2.12.0 https://github.com/pybind/pybind11.git -c advice.detachedHead=false
 
-      - name: Set macOS-specific environment variables
-        run: echo "MACOSX_DEPLOYMENT_TARGET=11.0" >> $GITHUB_ENV
-
       - name: Install cibuildwheel
         run: python -m pip install cibuildwheel
 
@@ -243,13 +242,15 @@ jobs:
             python scripts/install_KLU_Sundials.py
             python -m cibuildwheel --output-dir wheelhouse
         env:
+          # 10.13 for Intel (macos-12/macos-13), 11.0 for Apple Silicon (macos-14 and macos-latest)
+          MACOSX_DEPLOYMENT_TARGET: ${{ matrix.os == 'macos-14' && '11.0' || '10.13' }}
           CIBW_ARCHS_MACOS: auto
           CIBW_BEFORE_BUILD: python -m pip install cmake casadi setuptools wheel delocate
           CIBW_REPAIR_WHEEL_COMMAND: |
             if [[ $(uname -m) == "x86_64" ]]; then
               delocate-listdeps {wheel} && delocate-wheel -v -w {dest_dir} {wheel}
             elif [[ $(uname -m) == "arm64" ]]; then
-              # Use higher macOS target for now: https://github.com/casadi/casadi/issues/3698
+              # Use higher macOS target for now since casadi/libc++.1.0.dylib is still not fixed
               delocate-listdeps {wheel} && delocate-wheel -v -w {dest_dir} {wheel} --require-target-macos-version 11.1
               for file in {dest_dir}/*.whl; do mv "$file" "${file//macosx_11_1/macosx_11_0}"; done
             fi
@@ -260,7 +261,7 @@ jobs:
             python -m pytest -m cibw {project}/tests/unit
 
       - name: Upload wheels for macOS (amd64, arm64)
-        uses: actions/upload-artifact@v4.3.6
+        uses: actions/upload-artifact@v4.4.0
         with:
           name: wheels_${{ matrix.os }}
           path: ./wheelhouse/*.whl
@@ -280,7 +281,7 @@ jobs:
         run: pipx run build --sdist
 
       - name: Upload SDist
-        uses: actions/upload-artifact@v4.3.6
+        uses: actions/upload-artifact@v4.4.0
         with:
           name: sdist
           path: ./dist/*.tar.gz

diff --git a/.github/workflows/release_reminder.yml b/.github/workflows/release_reminder.yml
diff --git a/.github/workflows/run_benchmarks_over_history.yml b/.github/workflows/run_benchmarks_over_history.yml
@@ -46,7 +46,7 @@ jobs:
           ${{ github.event.inputs.commit_start }}..${{ github.event.inputs.commit_end }}
 
       - name: Upload results as artifact
-        uses: actions/upload-artifact@v4.3.6
+        uses: actions/upload-artifact@v4.4.0
         with:
           name: asv_over_history_results
           path: results

diff --git a/.github/workflows/run_periodic_tests.yml b/.github/workflows/run_periodic_tests.yml
@@ -68,8 +68,11 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
+      - name: Set up uv
+        run: python -m pip install uv
+
       - name: Install nox
-        run: python -m pip install nox
+        run: python -m uv pip install nox[uv]
 
       - name: Install SuiteSparse and SUNDIALS on GNU/Linux and macOS
         timeout-minutes: 10
@@ -114,8 +117,11 @@ jobs:
         with:
           python-version: 3.11
 
+      - name: Set up uv
+        run: python -m pip install uv
+
       - name: Install nox
-        run: python -m pip install nox
+        run: python -m uv pip install nox[uv]
 
       - name: Install docs dependencies and run doctests for GNU/Linux
         run: python -m nox -s doctests
@@ -141,8 +147,11 @@ jobs:
         with:
           python-version: 3.12
 
+      - name: Set up uv
+        run: python -m pip install uv
+
       - name: Install nox
-        run: python -m pip install nox
+        run: python -m uv pip install nox[uv]
 
       - name: Install SuiteSparse and SUNDIALS on GNU/Linux
         timeout-minutes: 10
@@ -169,8 +178,11 @@ jobs:
         with:
           python-version: 3.12
 
+      - name: Set up uv
+        run: python -m pip install uv
+
       - name: Install nox
-        run: python -m pip install nox
+        run: python -m uv pip install nox[uv]
 
       - name: Install SuiteSparse and SUNDIALS on GNU/Linux
         timeout-minutes: 10

diff --git a/.github/workflows/scorecard.yml b/.github/workflows/scorecard.yml
@@ -59,7 +59,7 @@ jobs:
       # Upload the results as artifacts (optional). Commenting out will disable uploads of run results in SARIF
       # format to the repository Actions tab.
       - name: "Upload artifact"
-        uses: actions/upload-artifact@834a144ee995460fba8ed112a2fc961b36a5ec5a # v4.3.6
+        uses: actions/upload-artifact@50769540e7f4bd5e21e526ee35c689e35e0d6874 # v4.4.0
         with:
           name: SARIF file
           path: results.sarif
@@ -68,6 +68,6 @@ jobs:
       # Upload the results to GitHub's code scanning dashboard (optional).
       # Commenting out will disable upload of results to your repo's Code Scanning dashboard
       - name: "Upload to code-scanning"
-        uses: github/codeql-action/upload-sarif@2c779ab0d087cd7fe7b826087247c2c81f27bfa6 # v3.26.5
+        uses: github/codeql-action/upload-sarif@4dd16135b69a43b6c8efb853346f8437d92d3c93 # v3.26.6
         with:
           sarif_file: results.sarif