Merge pull request #4756 from pybamm-team/release/v25.1

Release 25.1.0

Author: kratman

.all-contributorsrc

@@ -1,7 +1,7 @@
 {
+  "skipCi": false,
   "files": [
-    "all_contributors.md",
-    "README.md"
+    "all_contributors.md"
   ],
   "imageSize": 100,
   "commit": false,
@@ -517,10 +517,10 @@
       ]
     },
     {
-      "login": "abillscmu",
+      "login": "aabills",
       "name": "Alec Bills",
       "avatar_url": "https://avatars.githubusercontent.com/u/48105066?v=4",
-      "profile": "https://github.com/abillscmu",
+      "profile": "https://github.com/aabills",
       "contributions": [
         "code"
       ]
@@ -991,14 +991,50 @@
       "contributions": [
         "test"
       ]
+    },
+    {
+      "login": "isaacbasil",
+      "name": "isaacbasil",
+      "avatar_url": "https://avatars.githubusercontent.com/u/123981577?v=4",
+      "profile": "https://github.com/isaacbasil",
+      "contributions": [
+        "doc"
+      ]
+    },
+    {
+      "login": "AndEsterson",
+      "name": "Andrew Esterson",
+      "avatar_url": "https://avatars.githubusercontent.com/u/55912083?v=4",
+      "profile": "https://github.com/AndEsterson",
+      "contributions": [
+        "infra"
+      ]
+    },
+    {
+      "login": "ahamed24",
+      "name": "ahamed24",
+      "avatar_url": "https://avatars.githubusercontent.com/u/153092659?v=4",
+      "profile": "https://github.com/ahamed24",
+      "contributions": [
+        "infra"
+      ]
+    },
+    {
+      "login": "RohitP2005",
+      "name": "RohitP2005",
+      "avatar_url": "https://avatars.githubusercontent.com/u/122815777?v=4",
+      "profile": "https://github.com/RohitP2005",
+      "contributions": [
+        "doc",
+        "infra"
+      ]
     }
   ],
   "contributorsPerLine": 7,
   "projectName": "PyBaMM",
   "projectOwner": "pybamm-team",
   "repoType": "github",
   "repoHost": "https://github.com",
-  "skipCi": true,
   "commitConvention": "angular",
   "commitType": "docs"
 }

.github/PULL_REQUEST_TEMPLATE.md

@@ -15,10 +15,10 @@ Please add a line in the relevant section of [CHANGELOG.md](https://github.com/p
 # 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 run-tests.py --all` (or `$ nox -s tests`)
-- [ ] The documentation builds: `$ python run-tests.py --doctest` (or `$ nox -s doctests`)
+- [ ] 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 `$ python run-tests.py --quick` (or `$ nox -s quick`).
+You can run integration tests, unit tests, and doctests together at once, using `$ nox -s quick`.
 
 ## Further checks:
 

.github/release_workflow.md

@@ -13,7 +13,6 @@ GitHub, PyPI, and conda-forge by the maintainers.
    - `docs/conf.py`
    - `CITATION.cff`
    - `pyproject.toml`
-   - `vcpkg.json`
    - `CHANGELOG.md`
 
    These changes will be automatically pushed to a new branch `vYY.MM`
@@ -42,7 +41,6 @@ If a new release is required after the release of `vYY.MM.{x-1}` -
    - `docs/conf.py`
    - `CITATION.cff`
    - `pyproject.toml`
-   - `vcpkg.json`
    - `CHANGELOG.md`
 
    Commit the changes to your release branch.
@@ -57,11 +55,6 @@ If a new release is required after the release of `vYY.MM.{x-1}` -
 
 Some other essential things to check throughout the release process -
 
-- 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
@@ -79,7 +72,5 @@ Some other essential things to check throughout the release process -
   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

.github/wheel_failure.md

@@ -15,9 +15,9 @@ jobs:
   benchmarks:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
       - name: Set up Python 3.12
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5.3.0
         with:
           python-version: 3.12
 
@@ -31,12 +31,8 @@ jobs:
 
       - name: Install python dependencies
         run: |
-          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
-
       - name: Fetch base branch
         run: |
           # This workflow also runs for merge commits

.github/workflows/benchmark_on_push.yml

@@ -0,0 +1,18 @@
+name: Discussion Autoresponder
+
+on:
+  discussion:
+    types: [created]
+
+jobs:
+  autorespond:
+    name: Autorespond to New Discussions
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Run Discussion Autoresponder
+        uses: wesleyscholl/[email protected]
+        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."
+          delay_milliseconds: 0

.github/workflows/discussion_autoresponder.yml

@@ -15,22 +15,22 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
 
       - name: Set up QEMU
-        uses: docker/setup-qemu-action@v3
+        uses: docker/setup-qemu-action@53851d14592bedcffcf25ea515637cff71ef929a # v3.3.0
 
       - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3
+        uses: docker/setup-buildx-action@6524bf65af31da8d45b59e8c27de4bd072b392f5 # v3.8.0
 
       - name: Login to Docker Hub
-        uses: docker/login-action@v3
+        uses: docker/login-action@9780b0c442fbb1117ed29e0efdff1e18412f7567 # v3.3.0
         with:
             username: ${{ secrets.DOCKERHUB_USERNAME }}
             password: ${{ secrets.DOCKERHUB_TOKEN }}
 
       - name: Build and push Docker image to Docker Hub
-        uses: docker/build-push-action@v6
+        uses: docker/build-push-action@b32b51a8eda65d6793cd0494a773d4f6bcef32dc # v6.11.0
         with:
           context: .
           file: scripts/Dockerfile

.github/workflows/docker.yml

@@ -17,18 +17,18 @@ jobs:
 
       # cache Lychee results to avoid hitting rate limits
       - name: Restore lychee cache
-        uses: actions/cache@v4
+        uses: actions/cache@1bd1e32a3bdc45362d1e726936510720a7c30a57 # v4.2.0
         with:
           path: .lycheecache
           key: cache-lychee-${{ github.sha }}
           restore-keys: cache-lychee-
 
       # check URLs with Lychee
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
 
       # use stable version for now to avoid breaking changes
       - name: Lychee URL checker
-        uses: lycheeverse/lychee-action@v2.1.0
+        uses: lycheeverse/lychee-action@f796c8b7d468feb9b8c0a46da3fac0af6874d374 # v2.2.0
         with:
           # arguments with file types to check
           args: >-

.github/workflows/lychee_url_checker.yml

@@ -17,7 +17,7 @@ jobs:
       github.event_name != 'pull_request'
     steps:
       - name: Remove needs-reply label
-        uses: octokit/request-action@v2.x
+        uses: octokit/request-action@dad4362715b7fb2ddedf9772c8670824af564f0d # v2.4.0
         continue-on-error: true
         with:
           route: DELETE /repos/:repository/issues/:issue/labels/:label

.github/workflows/need_reply_remove.yml

@@ -10,7 +10,7 @@ jobs:
     if: github.repository_owner == 'pybamm-team'
     steps:
       - name: Close old issues that need reply
-        uses: dwieeb/needs-reply@v2
+        uses: dwieeb/needs-reply@71e8d5144caa0d4a1e292348bfafa3866d08c855 # v2.0.0
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           issue-label: needs-reply

.github/workflows/needs_reply.yml

@@ -22,10 +22,10 @@ jobs:
   benchmarks:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
 
       - name: Set up Python 3.12
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5.3.0
         with:
           python-version: 3.12
 
@@ -39,22 +39,15 @@ jobs:
 
       - name: Install python dependencies
         run: |
-          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
-
       - name: Run benchmarks
         run: |
           asv machine --machine "GitHubRunner"
           asv run --machine "GitHubRunner" NEW --show-stderr -v
-        env:
-          SUNDIALS_INST: $HOME/.local
-          LD_LIBRARY_PATH: $HOME/.local/lib
 
       - name: Upload results as artifact
-        uses: actions/upload-artifact@v4.4.3
+        uses: actions/upload-artifact@65c4c4a1ddee5b72f698fdd19549f0f0fb45cf08 # v4.6.0
         with:
           name: asv_periodic_results
           path: results
@@ -67,21 +60,21 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Set up Python 3.12
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5.3.0
         with:
           python-version: 3.12
 
       - name: Install asv
         run: pip install asv
 
       - name: Checkout pybamm-bench repo
-        uses: actions/checkout@v4
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
         with:
           repository: pybamm-team/pybamm-bench
           token: ${{ secrets.BENCH_PAT }}
 
       - name: Download results artifact(s)
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4.1.8
         with:
           path: results
           merge-multiple: true