Merge branch 'develop' into v24.3.1_into_develop

pybop-team · Jun 18, 2024 · 025d60f · 025d60f
2 parents 2a588e0 + 4dfdd1d
commit 025d60f
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diff --git a/.all-contributorsrc b/.all-contributorsrc
@@ -61,13 +61,25 @@
       "avatar_url": "https://avatars.githubusercontent.com/u/28443643?v=4",
       "profile": "https://www.brosaplanella.xyz",
       "contributions": [
+        "review",
+        "code"
+      ]
+    },
+    {
+      "login": "agriyakhetarpal",
+      "name": "Agriya Khetarpal",
+      "avatar_url": "https://avatars.githubusercontent.com/u/74401230?v=4",
+      "profile": "https://github.com/agriyakhetarpal",
+      "contributions": [
+        "code",
+        "infra",
         "review"
       ]
     },
     {
       "login": "FaradayInstitution",
       "name": "Faraday Institution",
-      "avatar_url": "/assets/UKRI.svg",
+      "avatar_url": "assets/faraday-logo.jpg",
       "profile": "https://faraday.ac.uk",
       "contributions": [
         "financial"
@@ -76,20 +88,28 @@
     {
       "login": "UKRI",
       "name": "UK Research and Innovation",
-      "avatar_url": "/assets/UKRI.svg",
+      "avatar_url": "assets/UKRI.png",
       "profile": "https://www.ukri.org/",
       "contributions": [
         "financial"
       ]
     },
     {
-      "login": "agriyakhetarpal",
-      "name": "Agriya Khetarpal",
-      "avatar_url": "https://avatars.githubusercontent.com/u/74401230?v=4",
-      "profile": "https://github.com/agriyakhetarpal",
+      "login": "IntelLiGent",
+      "name": "Horizon Europe IntelLiGent Consortium",
+      "avatar_url": "assets/logo-farger.pdf",
+      "profile": "https://heuintelligent.eu/",
       "contributions": [
-        "code",
-        "infra"
+        "financial"
+      ]
+    },
+    {
+      "login": "muhammedsogut",
+      "name": "Muhammed Nedim Sogut",
+      "avatar_url": "https://avatars.githubusercontent.com/u/34511375?v=4",
+      "profile": "https://www.linkedin.com/in/muhammedsogut/",
+      "contributions": [
+        "code"
       ]
     }
   ],

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -13,6 +13,7 @@ Before you mark your PR as ready for review, please ensure that you've considere
 ## Type of change
 - [ ] New Feature: A non-breaking change that adds new functionality.
 - [ ] Optimization: A code change that improves performance.
+- [ ] Examples: A change to existing or additional examples.
 - [ ] Bug Fix: A non-breaking change that addresses an issue.
 - [ ] Documentation: Updates to documentation or new documentation for new features.
 - [ ] Refactoring: Non-functional changes that improve the codebase.
@@ -24,7 +25,7 @@ Before you mark your PR as ready for review, please ensure that you've considere
 
 - [ ] No style issues: `$ pre-commit run` (or `$ nox -s pre-commit`) (see [CONTRIBUTING.md](https://github.com/pybop-team/PyBOP/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 unit tests pass: `$ nox -s tests`
-- [ ] The documentation builds: `$ nox -s docs`
+- [ ] The documentation builds: `$ nox -s doctest`
 
 You can run integration tests, unit tests, and doctests together at once, using `$ nox -s quick`.
 

diff --git a/.github/release_workflow.md b/.github/release_workflow.md
@@ -9,7 +9,7 @@ To create a new release, follow these steps:
 1. **Prepare the Release:**
    -  Create a new branch for the release (i.e. `v24.XX`) from `develop`.
    -  Increment the following;
-         -  The version number in the `pyproject.toml` file following CalVer versioning.
+         -  The version number in the `pyproject.toml` and `CITATION.cff` files following CalVer versioning.
          -  The`CHANGELOG.md` version with the changes for the new version.
    -  Open a PR to the `main` branch. Once the PR is merged, proceed to the next step.
 

diff --git a/.github/workflows/nightly_dependency_tests.yaml b/.github/workflows/nightly_dependency_tests.yaml
@@ -0,0 +1,48 @@
+name: Nightly dependencies at develop
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: "0 23 * * 1"
+
+concurrency:
+  # github.workflow: name of the workflow, so that we don't cancel other workflows
+  # github.run_id || github.event_name: either the unique identifier for the job or the event that triggered it
+  group: ${{ github.workflow }}-${{ github.run_id || github.event_name }}
+  # Cancel in-progress runs when a new workflow with the same group name is triggered
+  cancel-in-progress: true
+
+jobs:
+  nightly_tests:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-14]
+        python-version: ["3.12"]
+        suite: ["unit", "integration", "examples"]
+
+    name: Test-${{ matrix.os }}-py-${{ matrix.python-version }}-${{ matrix.suite }})
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        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"
+
+
+      - name: Run ${{ matrix.suite }} tests
+        run: |
+          if [[ "${{ matrix.suite }}" == "unit" ]]; then
+              python -m pytest --unit
+          elif [[ "${{ matrix.suite }}" == "integration" ]]; then
+              python -m pytest --integration
+          elif [[ "${{ matrix.suite }}" == "examples" ]]; then
+              python -m pytest --nbmake --examples
+          fi
diff --git a/.github/workflows/periodic_benchmarks.yaml b/.github/workflows/periodic_benchmarks.yaml
@@ -10,9 +10,9 @@
 # - Publish website
 name: Benchmarks
 on:
-  # Everyday at 12 pm UTC
+  # Every Monday and Thursday at 12 pm UTC
   schedule:
-    - cron: "0 12 * * *"
+    - cron: "0 12 * * 1,4"
   # Make it possible to trigger the
   # workflow manually
   workflow_dispatch:

diff --git a/.github/workflows/release_action.yaml b/.github/workflows/release_action.yaml
@@ -16,14 +16,8 @@ jobs:
       uses: actions/setup-python@v4
       with:
         python-version: "3.12"
-    - name: Install pypa/build
-      run: >-
-        python3 -m
-        pip install
-        build
-        --user
-    - name: Build a binary wheel and a source tarball
-      run: python -m build
+    - name: Build a source tarball and a wheel from it
+      run: pipx run build
     - name: Store the distribution packages
       uses: actions/upload-artifact@v3
       with:
@@ -77,20 +71,17 @@ jobs:
         inputs: >-
           ./dist/*.tar.gz
           ./dist/*.whl
-    - name: Upload artifact signatures to GitHub Release
-      env:
-        GITHUB_TOKEN: ${{ github.token }}
-      # Upload to GitHub Release using the `gh` CLI.
-      # `dist/` contains the built packages, and the
-      # sigstore-produced signatures and certificates.
-      run: >-
-        gh release upload
-        '${{ github.ref_name }}' dist/**
-        --repo '${{ github.repository }}'
+    - name: Publish artifacts and signatures to GitHub Releases
+      uses: softprops/action-gh-release@9d7c94cfd0a1f3ed45544c887983e9fa900f0564  # v2.0.4
+      with:
+        # `dist/` contains the built packages, and the
+        # sigstore-produced signatures and certificates.
+        files: dist/*
 
   publish-to-testpypi:
     name: Publish Python 🐍 distribution 📦 to TestPyPI
-    if: contains(github.ref, 'rc') && github.repository == github.event.repository  # only publish to TestPyPI for rc tags
+    # only publish to TestPyPI for rc tags
+    if: contains(github.ref, 'rc') && github.repository == 'pybop-team/PyBOP'
     needs:
     - build
     runs-on: ubuntu-latest

diff --git a/.github/workflows/scheduled_tests.yaml b/.github/workflows/scheduled_tests.yaml
@@ -6,10 +6,9 @@ on:
     branches:
       - main
 
-  # runs every day at 09:00 and 15:00 UTC
+  # runs every day at 09:00 UTC
   schedule:
     - cron: '0 9 * * *'
-    - cron: '0 15 * * *'
 
 # Check noxfile.py for associated environment variables
 env:
@@ -35,10 +34,12 @@ jobs:
     outputs:
       pybop_matrix: ${{ steps.set-matrix.outputs.matrix }}
 
-  # filter the matrix to only include the macOS-latest entries
+  # 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.
   filter_pybamm_matrix:
-    name: Filter the matrix for macOS-latest entries
+    name: Filter the matrix for OS and Python version
     needs: [create_pybamm_matrix]
+    if: github.repository == 'pybop-team/PyBOP'
     runs-on: ubuntu-latest
     outputs:
       filtered_pybop_matrix: ${{ steps.set-matrix.outputs.matrix }}
@@ -53,8 +54,12 @@ jobs:
           matrix_json = '${{ needs.create_pybamm_matrix.outputs.pybop_matrix }}'
           matrix = json.loads(matrix_json)
 
-          # Filter the matrix for macOS-latest entries only
-          filtered_entries = [entry for entry in matrix['include'] if entry['os'] == 'macos-latest']
+          # 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']
+          # Then remove the os key from the entries
+          for entry in filtered_entries:
+              entry.pop('os')
           filtered_matrix = {'include': filtered_entries}
 
           # Set the output variable for other jobs to use
@@ -63,6 +68,8 @@ jobs:
               output_stream.write(f"matrix={json.dumps(filtered_matrix)}\n")
         shell: python
 
+  # This job is dependent on filter_pybamm_matrix so that the self-hosted runner starts
+  # as soon as the matrix is filtered (i.e. the runners don't get tied up with build below).
   build:
     needs: [create_pybamm_matrix, filter_pybamm_matrix]
     name: Build (${{ matrix.os }}, Python ${{ matrix.python_version }}, PyBaMM ${{ matrix.pybamm_version }})
@@ -82,16 +89,18 @@ jobs:
 
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip nox
+          python -m pip install --upgrade pip nox[uv]
 
       - name: Unit tests with nox
         run: python -m nox -s coverage
 
-      - name: Run notebooks with nox
-        run: python -m nox -s notebooks
+      - name: Run examples with nox
+        run: python -m nox -s examples
 
   # 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
     needs: [filter_pybamm_matrix]
     name: Build (MacOS M-series, Python ${{ matrix.python_version }}, PyBaMM ${{ matrix.pybamm_version }})
     runs-on: [self-hosted, macOS, ARM64]
@@ -112,14 +121,14 @@ jobs:
           pyenv install ${{ matrix.python_version }} -s
           pyenv virtualenv ${{ matrix.python_version }} pybop-${{ matrix.python_version }}-${{ matrix.pybamm_version }}
 
-      - name: Install dependencies & run unit + notebook tests
+      - name: Install dependencies & run tests
         shell: bash
         run: |
           eval "$(pyenv init -)"
           pyenv activate pybop-${{ matrix.python_version }}-${{ matrix.pybamm_version }}
-          python -m pip install --upgrade pip nox
+          python -m pip install --upgrade pip nox[uv]
           python -m nox -s coverage
-          python -m nox -s notebooks
+          python -m nox -s examples
 
       - name: Uninstall pyenv-virtualenv & python
         if: always()

diff --git a/.github/workflows/test_on_push.yaml b/.github/workflows/test_on_push.yaml
@@ -1,4 +1,4 @@
-name: PyBOP
+name: Pull Request
 
 on:
   workflow_dispatch:
@@ -33,7 +33,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest, macos-14]
+        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
         python-version: ["3.12"]
 
     name: Integration tests (${{ matrix.os }} / Python ${{ matrix.python-version }})
@@ -46,7 +46,7 @@ jobs:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip nox
+          python -m pip install --upgrade pip nox[uv]
 
       - name: Integration tests
         run: |
@@ -58,17 +58,9 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
-        exclude: # We run the coverage tests on Ubuntu with Python 3.12
-          - os: ubuntu-latest
-            python-version: "3.12"
-        # Include MacOS M-series Runners
-        include:
-          - os: macos-14
-            python-version: "3.10"
-          - os: macos-14
-            python-version: "3.11"
+        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        exclude: # We run the coverage tests on macos-14 with Python 3.12
           - os: macos-14
             python-version: "3.12"
 
@@ -82,7 +74,7 @@ jobs:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip nox
+          python -m pip install --upgrade pip nox[uv]
 
       - name: Unit tests
         run: |
@@ -94,7 +86,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest, macos-14]
+        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
         python-version: ["3.12"]
 
     name: Test examples (${{ matrix.os }} / Python ${{ matrix.python-version }})
@@ -107,23 +99,19 @@ jobs:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip nox
+          python -m pip install --upgrade pip nox[uv]
 
       - name: Run examples
         run: |
           nox -s examples
 
-      - name: Run notebooks
-        run: |
-          nox -s notebooks
-
-  # Runs only on Ubuntu with Python 3.12
+  # Runs only on macos-14 with Python 3.12
   check_coverage:
     needs: style
-    runs-on: ubuntu-latest
+    runs-on: macos-14
     strategy:
       fail-fast: false
-    name: Coverage tests (ubuntu-latest / Python 3.12)
+    name: Coverage tests (macos-14 / Python 3.12)
 
     steps:
       - name: Check out PyBOP repository
@@ -137,12 +125,14 @@ jobs:
           cache-dependency-path: setup.py
 
       - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip nox
-      - name: Run coverage tests for Ubuntu with Python 3.12 and generate report
+        run: python -m pip install --upgrade pip nox[uv]
+
+      - name: Run coverage tests for macos-14 with Python 3.12 and generate report
         run: nox -s coverage
 
       - name: Upload coverage report
-        uses: codecov/codecov-action@v3
-        env:
-          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+        uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: true
+          verbose: true
+          token: ${{ secrets.CODECOV_TOKEN }}