Release v26.3

.github/workflows/draft-pdf.yml

@@ -0,0 +1,33 @@
+name: JossPaperCompilation
+
+on:
+  push:
+    paths:
+      - papers/joss/**
+  pull_request:
+    paths:
+    - 'papers/joss/**'
+  workflow_dispatch:
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        with:
+          persist-credentials: false
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@85a18372e48f551d8af9ddb7a747de685fbbb01c # v1.0
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: papers/joss/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@b7c566a772e6b6bfb58ed0dc250532a479d7789f # v6.0.0
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: papers/joss/paper.pdf

.github/workflows/lychee_links.yaml

@@ -15,17 +15,19 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v5
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        with:
+          persist-credentials: false
 
       - name: Restore lychee cache
-        uses: actions/cache@v4
+        uses: actions/cache@cdf6c1fa76f9f475f3d7449005a359c84ca0f306 # v5.0.3
         with:
           path: .lycheecache
           key: cache-lychee-${{ github.sha }}
           restore-keys: cache-lychee-
 
       - name: Run lychee
-        uses: lycheeverse/lychee-action@v2
+        uses: lycheeverse/lychee-action@a8c4c7cb88f0c7386610c35eb25108e448569cb0 # v2.7.0
         with:
           args: >-
             --cache

.github/workflows/nightly_dependency_tests.yaml

@@ -1,4 +1,4 @@
-name: Nightly dependencies at develop
+name: Nightly dependencies
 
 on:
   workflow_dispatch:
@@ -14,39 +14,82 @@ concurrency:
   # Cancel in-progress runs when a new workflow with the same group name is triggered
   cancel-in-progress: true
 
+permissions: {}
+
 jobs:
-  nightly_tests:
+  check_dependencies:
+    name: Test-${{ matrix.dep-type }}-${{ matrix.os }}-py-${{ matrix.python-version }}-${{ matrix.suite }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-14]
-        python-version: ["3.12"]
+        os: [ubuntu-latest, macos-latest]
         suite: ["unit", "integration", "examples", "notebooks"]
-
-    name: Test-${{ matrix.os }}-py-${{ matrix.python-version }}-${{ matrix.suite }})
+        dep-type: ["latest", "lowest"]
+        # The following must remain in sync with our Python version support as defined in pyproject.toml
+        include:
+          # Latest dependencies with Python 3.13 (our maximum supported Python version)
+          - dep-type: latest
+            python-version: "3.13"
+          # Lowest dependencies with Python 3.10 (our minimum supported Python version)
+          - dep-type: lowest
+            python-version: "3.10"
+    permissions:
+      contents: read
+      issues: write # for creating issues when tests fail
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        with:
+          persist-credentials: false
+
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: astral-sh/setup-uv@eac588ad8def6316056a12d4907a9d4d84ff7a3b # v7.3.0
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Install dependencies
+          activate-environment: "true"
+
+      - name: Install dependencies (latest)
+        if: matrix.dep-type == 'latest'
+        # uv pip install pip needed to allow %pip install within notebooks
         run: |
-          python -m pip install -e .[all,dev]
-          python -m pip uninstall -y pybamm
-          python -m pip install "pybamm[all] @ git+https://github.com/pybamm-team/PyBaMM@develop"
+          uv pip install pip
+          uv pip install -e .[all]
+          uv pip install --group dev
+          uv pip uninstall pybamm
+          uv pip install "pybamm[all] @ git+https://github.com/pybamm-team/PyBaMM@main"
+          uv pip install pytest-reportlog
 
+      - name: Install dependencies (lowest)
+        if: matrix.dep-type == 'lowest'
+        run: |
+          uv pip install pip
+          uv pip install --group dev
+          uv pip install --resolution lowest-direct -e .[all]
+          uv pip install pytest-reportlog
 
       - name: Run ${{ matrix.suite }} tests
+        id: pytest
+        env:
+          PYTEST: "pytest --report-log=pytest-log.jsonl"
         run: |
           if [[ "${{ matrix.suite }}" == "unit" ]]; then
-              python -m pytest --unit
+              python -m $PYTEST --unit
           elif [[ "${{ matrix.suite }}" == "integration" ]]; then
-              python -m pytest --integration
+              python -m $PYTEST --integration
           elif [[ "${{ matrix.suite }}" == "examples" ]]; then
-              python -m pytest --examples
+              python -m $PYTEST --examples
           elif [[ "${{ matrix.suite }}" == "notebooks" ]]; then
-              python -m pytest --notebooks --nbmake --nbmake-timeout=1000 examples/
+              python -m $PYTEST --notebooks --nbmake --nbmake-timeout=1000 examples/
           fi
+
+      - name: Create issues from pytest logs
+        uses: scientific-python/issue-from-pytest-log-action@8e905db353437cda1d6a773de245343fbfc940dd # v1.5.0
+        if: |
+          failure()
+          && steps.pytest.outcome == 'failure'
+          && github.repository == 'pybop-team/PyBOP'
+          && github.event_name == 'schedule'
+        with:
+          log-path: pytest-log.jsonl
+          issue-title: "Nightly ${{ matrix.dep-type }} dependencies ${{ matrix.suite }} tests failed (${{ matrix.os }} Python ${{ matrix.python-version }})"

.github/workflows/periodic_benchmarks.yaml

@@ -27,7 +27,9 @@ jobs:
           rm -rf ./* || true
           rm -rf ./.??* || true
 
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        with:
+          persist-credentials: false
 
       - name: Install python & create virtualenv
         shell: bash
@@ -41,13 +43,15 @@ jobs:
         run: |
             eval "$(pyenv init -)"
             pyenv activate pybop-312-bench
-            python -m pip install -e .[all,dev]
+            python -m pip install --upgrade pip
+            python -m pip install -e .[all]
+            python -m pip install --group dev
             python -m pip install asv[virtualenv]
             python -m asv machine --machine "SelfHostedRunner"
             python -m asv run --machine "SelfHostedRunner" NEW --show-stderr -v
 
       - name: Upload results as artifact
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@b7c566a772e6b6bfb58ed0dc250532a479d7789f # v6.0.0
         with:
           name: asv_periodic_results
           path: results
@@ -67,21 +71,21 @@ jobs:
     if: github.repository == 'pybop-team/PyBOP'
     steps:
       - name: Set up Python 3.12
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
         with:
           python-version: 3.12
 
       - name: Install asv
         run: pip install asv
 
       - name: Checkout pybop-bench repo
-        uses: actions/checkout@v4
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
         with:
           repository: pybop-team/pybop-bench
           token: ${{ secrets.PUSH_BENCH_TOKEN }}
 
       - name: Download results artifact
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@37930b1c2abaa49bbe596cd826c3c89aef350131 # v7.0.0
         with:
           name: asv_periodic_results
           path: new_results

.github/workflows/release_action.yaml

@@ -11,15 +11,17 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+      with:
+        persist-credentials: false
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
       with:
         python-version: "3.12"
     - name: Build a source tarball and a wheel from it
       run: pipx run build
     - name: Store the distribution packages
-      uses: actions/upload-artifact@v4
+      uses: actions/upload-artifact@b7c566a772e6b6bfb58ed0dc250532a479d7789f # v6.0.0
       with:
         name: python-package-distributions
         path: dist/
@@ -40,13 +42,13 @@ jobs:
 
     steps:
     - name: Download all the dists
-      uses: actions/download-artifact@v4
+      uses: actions/download-artifact@37930b1c2abaa49bbe596cd826c3c89aef350131 # v7.0.0
       with:
         name: python-package-distributions
         path: dist/
         merge-multiple: true
     - name: Publish distribution 📦 to PyPI
-      uses: pypa/gh-action-pypi-publish@release/v1
+      uses: pypa/gh-action-pypi-publish@ed0c53931b1dc9bd32cbe73a98c7f6766f8a527e # v1.13.0
 
   github-release:
     name: >-
@@ -62,19 +64,19 @@ jobs:
 
     steps:
     - name: Download all the dists
-      uses: actions/download-artifact@v4
+      uses: actions/download-artifact@37930b1c2abaa49bbe596cd826c3c89aef350131 # v7.0.0
       with:
         name: python-package-distributions
         path: dist/
         merge-multiple: true
     - name: Sign the dists with Sigstore
-      uses: sigstore/gh-action-sigstore-python@v1.2.3
+      uses: sigstore/gh-action-sigstore-python@a5caf349bc536fbef3668a10ed7f5cd309a4b53d # v3.2.0
       with:
         inputs: >-
           ./dist/*.tar.gz
           ./dist/*.whl
     - name: Publish artifacts and signatures to GitHub Releases
-      uses: softprops/action-gh-release@v2
+      uses: softprops/action-gh-release@a06a81a03ee405af7f2048a818ed3f03bbf83c7b # v2.5.0
       with:
         # `dist/` contains the built packages, and the
         # sigstore-produced signatures and certificates.
@@ -97,12 +99,12 @@ jobs:
 
     steps:
     - name: Download all the dists
-      uses: actions/download-artifact@v4
+      uses: actions/download-artifact@37930b1c2abaa49bbe596cd826c3c89aef350131 # v7.0.0
       with:
         name: python-package-distributions
         path: dist/
         merge-multiple: true
     - name: Publish distribution 📦 to TestPyPI
-      uses: pypa/gh-action-pypi-publish@release/v1
+      uses: pypa/gh-action-pypi-publish@ed0c53931b1dc9bd32cbe73a98c7f6766f8a527e # v1.13.0
       with:
         repository-url: https://test.pypi.org/legacy/

.github/workflows/scheduled_tests.yaml

@@ -22,8 +22,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out PyBOP repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
         with:
+          persist-credentials: false
           sparse-checkout-cone-mode: false
           sparse-checkout: |
             scripts/ci/build_matrix.sh
@@ -36,7 +37,7 @@ jobs:
       pybop_matrix: ${{ steps.set-matrix.outputs.matrix }}
 
   # Filter the matrix to only include Python and PyBaMM versions. This job
-  # is used for the self-hosted macOS-14 (arm64) runner at this time.
+  # is used for the self-hosted macOS (arm64) runner at this time.
   filter_pybamm_matrix:
     name: Filter the matrix for OS and Python version
     needs: [create_pybamm_matrix]
@@ -56,8 +57,8 @@ jobs:
           matrix = json.loads(matrix_json)
 
           # Filter the matrix to include just the Python version and PyBaMM version
-          # First filter the matrix to only include macOS-14 entries
-          filtered_entries = [entry for entry in matrix['include'] if entry['os'] == 'macos-14']
+          # First filter the matrix to only include macOS (arm64) entries
+          filtered_entries = [entry for entry in matrix['include'] if entry['os'] == 'macos-latest']
           # Then remove the os key from the entries
           for entry in filtered_entries:
               entry.pop('os')
@@ -82,9 +83,11 @@ jobs:
       PYBAMM_VERSION: ${{ matrix.pybamm_version }}
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        with:
+          persist-credentials: false
       - name: Set up Python ${{ matrix.python_version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
         with:
           python-version: ${{ matrix.python_version }}
 
@@ -107,7 +110,7 @@ jobs:
   # M-series Mac Mini
   build-apple-mseries:
     # This job filters the matrix JSON created in build_matrix.sh to provide
-    # a matrix of only macOS-14 (arm64) entries
+    # a matrix of only macOS (arm64) entries
     needs: [filter_pybamm_matrix]
     name: Build (MacOS M-series, Python ${{ matrix.python_version }}, PyBaMM ${{ matrix.pybamm_version }})
     runs-on: [self-hosted, macOS, ARM64]
@@ -125,7 +128,10 @@ jobs:
           rm -rf ./* || true
           rm -rf ./.??* || true
 
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        with:
+          persist-credentials: false
+
       - name: Install python & create virtualenv
         shell: bash
         run: |