Merge pull request #4950 from pybamm-team/release/v25.4.0

Release v25.4.0

Author: kratman

.all-contributorsrc

@@ -1028,6 +1028,53 @@
         "doc",
         "infra"
       ]
+    },
+    {
+      "login": "vidipsingh",
+      "name": "Vidip Singh",
+      "avatar_url": "https://avatars.githubusercontent.com/u/112854574?v=4",
+      "profile": "https://github.com/vidipsingh",
+      "contributions": [
+        "infra"
+      ]
+    },
+    {
+      "login": "chtamar",
+      "name": "chtamar",
+      "avatar_url": "https://avatars.githubusercontent.com/u/196436685?v=4",
+      "profile": "https://github.com/chtamar",
+      "contributions": [
+        "code",
+        "doc",
+        "test"
+      ]
+    },
+    {
+      "login": "d-cogswell",
+      "name": "Dan Cogswell",
+      "avatar_url": "https://avatars.githubusercontent.com/u/51965251?v=4",
+      "profile": "https://dancogswell.com",
+      "contributions": [
+        "code"
+      ]
+    },
+    {
+      "login": "Prtm2110",
+      "name": "Pratham Hole",
+      "avatar_url": "https://avatars.githubusercontent.com/u/139000226?v=4",
+      "profile": "https://github.com/Prtm2110",
+      "contributions": [
+        "test"
+      ]
+    },
+    {
+      "login": "JC230903",
+      "name": "JC_005",
+      "avatar_url": "https://avatars.githubusercontent.com/u/152909047?v=4",
+      "profile": "https://github.com/JC230903",
+      "contributions": [
+        "infra"
+      ]
     }
   ],
   "contributorsPerLine": 7,

.github/CODEOWNERS

@@ -1,34 +1,2 @@
 # Automatically request reviews from maintainers
-
-# Package
-src/pybamm/discretisations/ @martinjrobins @rtimms @valentinsulzer
-src/pybamm/experiment/ @brosaplanella @martinjrobins @rtimms @valentinsulzer @TomTranter
-src/pybamm/expression_tree/ @martinjrobins @rtimms @valentinsulzer
-src/pybamm/geometry/ @martinjrobins @rtimms @valentinsulzer
-src/pybamm/input/ @brosaplanella @DrSOKane @rtimms @valentinsulzer @TomTranter @kratman
-src/pybamm/meshes/ @martinjrobins @rtimms @valentinsulzer @rtimms
-src/pybamm/models/ @brosaplanella @DrSOKane @rtimms @valentinsulzer @TomTranter @rtimms
-src/pybamm/parameters/ @brosaplanella @DrSOKane @rtimms @valentinsulzer @TomTranter @rtimms  @kratman
-src/pybamm/plotting/ @martinjrobins @rtimms @Saransh-cpp @valentinsulzer @rtimms  @kratman @agriyakhetarpal
-src/pybamm/solvers/ @martinjrobins @rtimms @valentinsulzer @TomTranter @rtimms @MarcBerliner
-src/pybamm/spatial_methods/ @martinjrobins @rtimms @valentinsulzer @rtimms
-src/pybamm/* @pybamm-team/maintainers # the files directly under /pybamm/, will not recurse
-
-# CI/CD workflows
-/.github/ @martinjrobins @Saransh-cpp @agriyakhetarpal @kratman @arjxn-py
-
-# Benchmarks
-/benchmarks/ @brosaplanella @Saransh-cpp @agriyakhetarpal @arjxn-py
-
-# Documentation
-/docs/ @kratman @arjxn-py @agriyakhetarpal @Saransh-cpp
-
-# Example scripts
-/examples/ @kratman @agriyakhetarpal @Saransh-cpp
-
-# Installation and other scripts
-/scripts/ @martinjrobins @Saransh-cpp @agriyakhetarpal @kratman @arjxn-py
-
-# Files in the root directory
-/* @martinjrobins @Saransh-cpp @agriyakhetarpal @kratman @arjxn-py
-/CHANGELOG.md # no owner (almost every PR edits the CHANGELOG)
+* @pybamm-team/maintainers

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,26 +1,18 @@
 # Description
 
-Please include a summary of the change and which issue is fixed. Please also include relevant motivation and context. List any dependencies that are required for this change.
+Please include a summary of the change and which issue is fixed. Please also include relevant motivation and context.
 
 Fixes # (issue)
 
 ## Type of change
 
-Please add a line in the relevant section of [CHANGELOG.md](https://github.com/pybamm-team/PyBaMM/blob/develop/CHANGELOG.md) to document the change (include PR #) - note reverse order of PR #s. If necessary, also add to the list of breaking changes.
+Please add a line in the relevant section of [CHANGELOG.md](https://github.com/pybamm-team/PyBaMM/blob/develop/CHANGELOG.md) to document the change (include PR #)
 
-- [ ] New feature (non-breaking change which adds functionality)
-- [ ] Optimization (back-end change that speeds up the code)
-- [ ] Bug fix (non-breaking change which fixes an issue)
+# Important checks:
 
-# Key checklist:
-
-- [ ] No style issues: `$ pre-commit run` (or `$ nox -s pre-commit`) (see [CONTRIBUTING.md](https://github.com/pybamm-team/PyBaMM/blob/develop/CONTRIBUTING.md#installing-and-using-pre-commit) for how to set this up to run automatically when committing locally, in just two lines of code)
-- [ ] All tests pass: `$ python -m pytest` (or `$ nox -s tests`)
-- [ ] The documentation builds: `$ python -m pytest --doctest-plus src` (or `$ nox -s doctests`)
-
-You can run integration tests, unit tests, and doctests together at once, using `$ nox -s quick`.
-
-## Further checks:
-
-- [ ] Code is commented, particularly in hard-to-understand areas
-- [ ] Tests added that prove fix is effective or that feature works
+Please confirm the following before marking the PR as ready for review:
+- No style issues: `nox -s pre-commit`
+- All tests pass: `nox -s tests`
+- The documentation builds: `nox -s doctests`
+- Code is commented for hard-to-understand areas
+- Tests added that prove fix is effective or that feature works

.github/release_workflow.md

@@ -3,44 +3,41 @@
 This file contains the workflow required to make a `PyBaMM` release on
 GitHub, PyPI, and conda-forge by the maintainers.
 
-## Initial release (automated)
+## Creating a release
 
-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:
+1. Checkout the latest develop branch, then create a local tag `vYY.MM.0`
+   with the new version. The year and month are taken from the date of the
+   release. The final number represents the bug fix version, which is zero for
+   a new release.
+
+2. Run `scripts/update_version.py` to update the following files:
 
-   - `pybamm/version.py`
-   - `docs/conf.py`
    - `CITATION.cff`
-   - `pyproject.toml`
    - `CHANGELOG.md`
 
-   These changes will be automatically pushed to a new branch `vYY.MM`
-   and a PR from `vYY.MM` to `main` will be created.
+   These changes should be pushed to a release branch `vYY.MM.0`
+   and a PR from `vYY.MM.0` to `main` needs to be created.
 
-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. After the release PR has been merged, 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
+4. This release will automatically trigger `publish_pypi.yml` and create a
    _release_ on PyPI.
 
-## Bug fix releases (manual)
+## Bug fix releases
 
-If a new release is required after the release of `vYY.MM.{x-1}` -
+If a new bugfix release is required after the release of `vYY.MM.{x-1}` -
 
 1. Create a new branch for the `vYY.MM.x` release using the `vYY.MM.{x-1}` tag.
 
 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. Run `scripts/update_version.py` manually while setting `VERSION=vYY.MM.x`
-   in your environment. This will update the version in the following files:
+3. Run `scripts/update_version.py` manually to update:
 
-   - `pybamm/version.py`
-   - `docs/conf.py`
    - `CITATION.cff`
-   - `pyproject.toml`
    - `CHANGELOG.md`
 
    Commit the changes to your release branch.

.github/workflows/benchmark_on_push.yml

@@ -3,6 +3,9 @@ on:
   push:
     branches: [main, develop]
 
+
+permissions: {}
+
 concurrency:
   # Cancel intermediate builds always
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -14,13 +17,18 @@ env:
 jobs:
   benchmarks:
     runs-on: ubuntu-latest
+    permissions:
+      contents: read
     steps:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        with:
+          persist-credentials: false
       - name: Set up Python 3.12
-        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5.3.0
+        uses: actions/setup-python@8d9ed9ac5c53483de85588cdf95a591a75ab9f55 # v5.5.0
         with:
           python-version: 3.12
 
+
       - name: Install Linux system dependencies
         run: |
           sudo apt-get update

.github/workflows/discussion_autoresponder.yml

@@ -4,14 +4,20 @@ on:
   discussion:
     types: [created]
 
+
+permissions: {}
+
 jobs:
   autorespond:
     name: Autorespond to New Discussions
     runs-on: ubuntu-latest
+    permissions:
+      discussions: write
+      contents: read
 
     steps:
       - name: Run Discussion Autoresponder
-        uses: wesleyscholl/[email protected]
+        uses: wesleyscholl/discussion-auto-responder@b1a3c1b9a1e3d1b1a3c1b9a1e3d1b1a3c1b9a1e3 # v1.0.8
         with:
           GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
           comment_body: "Hi! We have now moved our discussions to [Discourse](https://pybamm.discourse.group/). Please post your question there."

.github/workflows/docker.yml

@@ -6,37 +6,47 @@ on:
     branches:
     - develop
 
+permissions: {}
+
 jobs:
   build_docker_image:
     # This workflow is only of value to PyBaMM and would always be skipped in forks
-    if: github.repository_owner == 'pybamm-team'
+    if: github.repository == 'pybamm-team/PyBaMM'
     name: Build image
     runs-on: ubuntu-latest
+    permissions:
+      contents: read
 
     steps:
       - name: Checkout
         uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        with:
+          persist-credentials: false
 
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@53851d14592bedcffcf25ea515637cff71ef929a # v3.3.0
+        uses: docker/setup-qemu-action@29109295f81e9208d7d86ff1c6c12d2833863392 # v3.6.0
 
-      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@6524bf65af31da8d45b59e8c27de4bd072b392f5 # v3.8.0
 
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@b5ca514318bd6ebac0fb2aedd5d36ec1b5c232a2 # v3.10.0
+        with:
+          cache-binary: false
       - name: Login to Docker Hub
-        uses: docker/login-action@9780b0c442fbb1117ed29e0efdff1e18412f7567 # v3.3.0
+        uses: docker/login-action@74a5d142397b4f367a81961eba4e8cd7edddf772 # v3.4.0
         with:
             username: ${{ secrets.DOCKERHUB_USERNAME }}
             password: ${{ secrets.DOCKERHUB_TOKEN }}
 
+
       - name: Build and push Docker image to Docker Hub
-        uses: docker/build-push-action@67a2d409c0a876cbe6b11854e3e25193efe4e62d # v6.12.0
+        uses: docker/build-push-action@471d1dc4e07e5cdedd4c2171150001c434f0b7a4 # v6.15.0
         with:
           context: .
           file: scripts/Dockerfile
           tags: pybamm/pybamm:latest
           push: true
           platforms: linux/amd64, linux/arm64
+          no-cache: true
 
       - name: List built image(s)
         run: docker images

.github/workflows/lychee_url_checker.yml

@@ -10,25 +10,33 @@ on:
     # Run everyday at 3 am UTC
     - cron: "0 3 * * *"
 
+
+permissions: {}
+
 jobs:
   linkChecker:
     runs-on: ubuntu-latest
+    permissions:
+      contents: read
+
     steps:
 
       # cache Lychee results to avoid hitting rate limits
       - name: Restore lychee cache
-        uses: actions/cache@1bd1e32a3bdc45362d1e726936510720a7c30a57 # v4.2.0
+        uses: actions/cache@5a3ec84eff668545956fd18022155c47e93e2684 # v4.2.3
         with:
           path: .lycheecache
           key: cache-lychee-${{ github.sha }}
           restore-keys: cache-lychee-
 
       # check URLs with Lychee
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        with:
+          persist-credentials: false
 
       # use stable version for now to avoid breaking changes
       - name: Lychee URL checker
-        uses: lycheeverse/lychee-action@f796c8b7d468feb9b8c0a46da3fac0af6874d374 # v2.2.0
+        uses: lycheeverse/lychee-action@1d97d84f0bc547f7b25f4c2170d87d810dc2fb2c # v2.4.0
         with:
           # arguments with file types to check
           args: >-

.github/workflows/need_reply_remove.yml

@@ -7,13 +7,18 @@ on:
     types:
       - created
 
+permissions: {}
+
 jobs:
   build:
     runs-on: ubuntu-latest
+    permissions:
+      issues: read
+      contents: read
     if: |
       github.event.comment.author_association != 'OWNER' &&
       github.event.comment.author_association != 'COLLABORATOR' &&
-      github.repository_owner == 'pybamm-team' &&
+      github.repository == 'pybamm-team/PyBaMM' &&
       github.event_name != 'pull_request'
     steps:
       - name: Remove needs-reply label

.github/workflows/needs_reply.yml

@@ -4,10 +4,16 @@ on:
   schedule:
     - cron: "0 0 * * *"
 
+
+permissions: {}
+
 jobs:
   build:
     runs-on: ubuntu-latest
-    if: github.repository_owner == 'pybamm-team'
+    permissions:
+      issues: read
+      contents: read
+    if: github.repository == 'pybamm-team/PyBaMM'
     steps:
       - name: Close old issues that need reply
         uses: dwieeb/needs-reply@71e8d5144caa0d4a1e292348bfafa3866d08c855 # v2.0.0