Add PyBaMM IDAKLU solver, compiled from source

.all-contributorsrc

@@ -50,7 +50,9 @@
       "contributions": [
         "ideas",
         "mentoring",
-        "review"
+        "review",
+        "code",
+        "test"
       ]
     },
     {
@@ -79,6 +81,16 @@
       "contributions": [
         "financial"
       ]
+    },
+    {
+      "login": "agriyakhetarpal",
+      "name": "Agriya Khetarpal",
+      "avatar_url": "https://avatars.githubusercontent.com/u/74401230?v=4",
+      "profile": "https://github.com/agriyakhetarpal",
+      "contributions": [
+        "code",
+        "infra"
+      ]
     }
   ],
   "contributorsPerLine": 7,

.github/workflows/scheduled_tests.yaml

@@ -10,54 +10,113 @@ on:
   schedule:
     - cron: '0 9 * * *'
 
+# Check noxfile.py for associated environment variables
+env:
+  PYBOP_SCHEDULED: 1
+
 jobs:
+  # Dynamically create a matrix of OS, Python, and PyBaMM versions
+  create_pybamm_matrix:
+    name: Dynamically create GitHub Actions matrix
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out PyBOP repository
+        uses: actions/checkout@v4
+        with:
+          sparse-checkout-cone-mode: false
+          sparse-checkout: |
+            scripts/ci/build_matrix.sh
+
+      - name: Run script to create matrix
+        id: set-matrix
+        run: |
+          echo "matrix=$(bash scripts/ci/build_matrix.sh)" >> "$GITHUB_OUTPUT"
+    outputs:
+      pybop_matrix: ${{ steps.set-matrix.outputs.matrix }}
+
+  # filter the matrix to only include the macOS-latest entries
+  filter_pybamm_matrix:
+    name: Filter the matrix for macOS-latest entries
+    needs: [create_pybamm_matrix]
+    runs-on: ubuntu-latest
+    outputs:
+      filtered_pybop_matrix: ${{ steps.set-matrix.outputs.matrix }}
+    steps:
+      - name: Filter pybop matrix
+        id: set-matrix
+        run: |
+          import json
+          import os
+
+          # Get the matrix
+          matrix_json = '${{ 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']
+          filtered_matrix = {'include': filtered_entries}
+
+          # Set the output variable for other jobs to use
+          output_file = os.environ['GITHUB_OUTPUT']
+          with open(output_file, "a", encoding="utf-8") as output_stream:
+              output_stream.write(f"matrix={json.dumps(filtered_matrix)}\n")
+        shell: python
+
   build:
+    needs: [create_pybamm_matrix, filter_pybamm_matrix]
+    name: Build (${{ matrix.os }}, Python ${{ matrix.python_version }}, PyBaMM ${{ matrix.pybamm_version }})
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
-      matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+      matrix: ${{fromJson(needs.create_pybamm_matrix.outputs.pybop_matrix)}}
+    env:
+      PYBAMM_VERSION: ${{ matrix.pybamm_version }}
 
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python ${{ matrix.python-version }}
+      - name: Set up Python ${{ matrix.python_version }}
         uses: actions/setup-python@v4
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: ${{ matrix.python_version }}
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip nox
+
       - name: Unit tests with nox
-        run: |
-          python -m nox -s unit
-          python -m nox -s notebooks
+        run: python -m nox -s unit
 
-  #M-series Mac Mini
+      - name: Run notebooks with nox
+        run: python -m nox -s notebooks
+
+  # M-series Mac Mini
   build-apple-mseries:
+    needs: [filter_pybamm_matrix]
+    name: Build (MacOS M-series, Python ${{ matrix.python_version }}, PyBaMM ${{ matrix.pybamm_version }})
     runs-on: [self-hosted, macOS, ARM64]
+    if: github.repository == 'pybop-team/PyBOP'
     env:
       GITHUB_PATH: ${PYENV_ROOT/bin:$PATH}
+      PYBAMM_VERSION: ${{ matrix.pybamm_version }}
     strategy:
       fail-fast: false
-      matrix:
-        python-version: ["3.10"]
+      matrix: ${{fromJson(needs.filter_pybamm_matrix.outputs.filtered_pybop_matrix)}}
 
     steps:
       - uses: actions/checkout@v4
       - name: Install python & create virtualenv
         shell: bash
         run: |
           eval "$(pyenv init -)"
-          pyenv install ${{ matrix.python-version }} -s
-          pyenv virtualenv ${{ matrix.python-version }} pybop-${{ matrix.python-version }}
+          pyenv install ${{ matrix.python_version }} -s
+          pyenv virtualenv ${{ matrix.python_version }} pybop-${{ matrix.python_version }}-${{ matrix.pybamm_version }}
 
-      - name: Install dependencies & run unit tests
+      - name: Install dependencies & run unit + notebook tests
         shell: bash
         run: |
           eval "$(pyenv init -)"
-          pyenv activate pybop-${{ matrix.python-version }}
-          python -m pip install --upgrade pip wheel setuptools nox
+          pyenv activate pybop-${{ matrix.python_version }}-${{ matrix.pybamm_version }}
+          python -m pip install --upgrade pip nox
           python -m nox -s unit
           python -m nox -s notebooks
 
@@ -66,5 +125,5 @@ jobs:
         shell: bash
         run: |
           eval "$(pyenv init -)"
-          pyenv activate pybop-${{ matrix.python-version }}
+          pyenv activate pybop-${{ matrix.python_version }}-${{ matrix.pybamm_version }}
           pyenv uninstall -f $( python --version )

.github/workflows/test_on_push.yaml

@@ -29,26 +29,96 @@ jobs:
 
 
   build:
+    needs: style
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        exclude: # We run the coverage tests on Ubuntu with Python 3.11
+          - os: ubuntu-latest
+            python-version: "3.11"
+        # Include MacOS M-series Runners
+        include:
+          - os: macos-14
+            python-version: "3.10"
+          - os: macos-14
+            python-version: "3.11"
+          - os: macos-14
+            python-version: "3.12"
 
     steps:
-      - uses: actions/checkout@v4
+      - name: Check out PyBOP repository
+        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 --upgrade pip nox
+
+      - name: Check out PyBaMM v24.1
+        uses: actions/checkout@v4
+        with:
+          repository: pybamm-team/PyBaMM
+          ref: v24.1
+          path: pybamm
+
+      - name: Compile PyBaMM from source with IDAKLU solver (ubuntu-latest)
+        if: matrix.os == 'ubuntu-latest'
+        run: |
+          cd pybamm
+          sudo apt-get update && sudo apt-get install -y libopenblas-dev
+          python -m nox -s pybamm-requires
+          python -m pip install .[all]
+          cd ..
+
+      - name: Compile PyBaMM from source with IDAKLU solver (macos-latest)
+        if: matrix.os == 'macos-latest'
+        run: |
+          brew reinstall gcc
+          brew install libomp
+          cd pybamm
+          python -m nox -s pybamm-requires
+          python -m pip install .[all]
+          cd ..
+
+      - name: Compile PyBaMM from source with IDAKLU solver (macos-14)
+        if: matrix.os == 'macos-14'
+        run: |
+          brew reinstall gcc
+          brew install libomp
+          cd pybamm
+          python -m nox -s pybamm-requires
+          python -m pip install .[all]
+          cd ..
+
+      # TODO: remove later, temporary addition to test Windows build
+      - name: Compile PyBaMM from source with IDAKLU solver (windows-latest)
+        if: matrix.os == 'windows-latest'
+        env:
+          PYBAMM_USE_VCPKG: "ON"
+          VCPKG_ROOT_DIR: C:\vcpkg
+          VCPKG_DEFAULT_TRIPLET: x64-windows-static-md
+          VCPKG_FEATURE_FLAGS: manifests,registries
+          CMAKE_GENERATOR: "Visual Studio 17 2022"
+          CMAKE_GENERATOR_PLATFORM: x64
+          CMAKE_BUILD_PARALLEL_LEVEL: 4
+        run: |
+          cd pybamm
+          git clone --depth 1 --branch v2.11.1 https://github.com/pybind/pybind11.git
+          python -m pip install .[all]
+          cd ..
+
       - name: Unit and notebook tests with nox
         run: |
-          nox -s unit
-          nox -s notebooks
+          pip install -e .[all,dev]
+          python -m pytest --unit
+          python -m pytest --nbmake --examples examples/
 
   # Runs only on Ubuntu with Python 3.11
   check_coverage:
@@ -60,6 +130,7 @@ jobs:
     steps:
       - name: Check out PyBOP repository
         uses: actions/checkout@v4
+
       - name: Set up Python 3.11
         id: setup-python
         uses: actions/setup-python@v4
@@ -71,8 +142,28 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip nox
+
+      - name: Check out PyBaMM v24.1
+        uses: actions/checkout@v4
+        with:
+          repository: pybamm-team/PyBaMM
+          ref: v24.1
+          path: pybamm
+
+      - name: Compile PyBaMM from source with IDAKLU solver (ubuntu-latest)
+        run: |
+          cd pybamm
+          sudo apt-get update
+          sudo apt-get install -y libopenblas-dev
+          python -m nox -s pybamm-requires
+          python -m pip install .[all]
+          rm -rf pybind11/
+          cd ..
+
       - name: Run coverage tests for Ubuntu with Python 3.11 and generate report
-        run: nox -s coverage
+        run: |
+            pip install -e .[all,dev]
+            python -m pytest --unit --examples --cov --cov-report=xml
 
       - name: Upload coverage report
         uses: codecov/codecov-action@v3

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.1.14"
+    rev: "v0.2.2"
     hooks:
       - id: ruff
         args: [--fix, --show-fixes]

CHANGELOG.md

@@ -2,15 +2,25 @@
 
 ## Features
 
+- [#206](https://github.com/pybop-team/PyBOP/pull/206) - Adds Python 3.12 support with corresponding github actions changes.
+- [#18](https://github.com/pybop-team/PyBOP/pull/18) - Adds geometric parameter fitting capability, via `model.rebuild()` with `model.rebuild_parameters`.
+- [#203](https://github.com/pybop-team/PyBOP/pull/203) - Adds support for modern Python packaging via a `pyproject.toml` file and configures the `pytest` test runner and `ruff` linter to use their configurations stored as declarative metadata.
+- [#123](https://github.com/pybop-team/PyBOP/issues/123) - Configures scheduled tests to run against the last three PyPI releases of PyBaMM via dynamic GitHub Actions matrix generation.
+- [#187](https://github.com/pybop-team/PyBOP/issues/187) - Adds M1 Github runner to `test_on_push` workflow, updt. self-hosted supported python versions in scheduled tests.
 - [#118](https://github.com/pybop-team/PyBOP/issues/118) - Adds example jupyter notebooks.
 - [#151](https://github.com/pybop-team/PyBOP/issues/151) - Adds a standalone version of the Problem class.
+- [#12](https://github.com/pybop-team/PyBOP/issues/12) - Adds initial implementation of an Observer class and an unscented Kalman filter.
+- [#190](https://github.com/pybop-team/PyBOP/issues/190) - Adds a second example design cost, namely the VolumetricEnergyDensity.
 
 ## Bug Fixes
 
+- [#123](https://github.com/pybop-team/PyBOP/issues/123) - Reinstates check for availability of parameter sets via PyBaMM upon retrieval by `pybop.ParameterSet.pybamm()`.
+- [#196](https://github.com/pybop-team/PyBOP/issues/196) - Fixes failing observer cost tests.
 - [#63](https://github.com/pybop-team/PyBOP/issues/63) - Removes NLOpt Optimiser from future releases. This is to support deployment to the Apple M-Series platform.
 - [#164](https://github.com/pybop-team/PyBOP/issues/164) - Fixes convergence issues with gradient-based optimisers, changes default `model.check_params()` to allow infeasible solutions during optimisation iterations. Adds a feasibility check on the optimal parameters.
 
 # [v23.12](https://github.com/pybop-team/PyBOP/tree/v23.12) - 2023-12-19
+
 ## Features
 
 - [#141](https://github.com/pybop-team/PyBOP/pull/141) - Adds documentation with Sphinx and PyData Sphinx Theme. Updates docstrings across package, relocates `costs` and `dataset` to top-level of package. Adds noxfile session and deployment workflow for docs.
@@ -28,6 +38,8 @@
 
 ## Bug Fixes
 
+- [#182](https://github.com/pybop-team/PyBOP/pull/182) - Allow square-brackets indexing of Dataset
+
 # [v23.11](https://github.com/pybop-team/PyBOP/releases/tag/v23.11)
 - Initial release
 - Adds Pints, NLOpt, and SciPy optimisers