fixed merge conflict in changelog

.all-contributorsrc

@@ -793,6 +793,18 @@
       "contributions": [
         "code"
       ]
+    },
+    {
+      "login": "AlessioBugetti",
+      "name": "Alessio Bugetti",
+      "avatar_url": "https://avatars.githubusercontent.com/u/38499721?v=4",
+      "profile": "https://github.com/AlessioBugetti",
+      "contributions": [
+        "infra",
+        "code",
+        "doc",
+        "test"
+      ]
     }
   ],
   "contributorsPerLine": 7,

.github/release_reminder.md

@@ -1,6 +1,6 @@
 ---
 title: Create {{ date | date('YY.MM') }} (final or rc0) release
-labels: priority:high
+labels: "priority: high"
 ---
 Quarterly reminder to create a -
 

.github/release_workflow.md

@@ -21,9 +21,9 @@ This file contains the workflow required to make a `PyBaMM` release on GitHub, P
 
 ## rcX releases (manual)
 
-If a new release candidate is required after the release of `rc0` -
+If a new release candidate is required after the release of `rc{X-1}` -
 
-1. Fix a bug in `vYY.MM` (no new features should be added to `vYY.MM` once `rc0` is released) and `develop` individually.
+1. Cherry-pick the bug fix (no new features should be added to `vYY.MM` once `rc{X-1}` is released) commit to `vYY.MM` branch once the fix is merged into `develop`. The CHANGELOG entry for such fixes should go under the `rc{X-1}` heading in `CHANGELOG.md`
 
 2. Run `update_version.yml` manually while using `append_to_tag` to specify the release candidate version number (`rc1`, `rc2`, ...).
 
@@ -36,7 +36,7 @@ If a new release candidate is required after the release of `rc0` -
    - `vcpkg.json`
    - `CHANGELOG.md`
 
-      These changes will be automatically pushed to the existing `vYY.MM` branch and a PR from `vvYY.MM` to `develop` will be created (to sync the branches).
+      These changes will be automatically pushed to the existing `vYY.MM` branch and a PR will be created to update version strings in `develop`.
 
 4. Create a new GitHub _pre-release_ with the same tag (`vYY.MMrcX`) from the `vYY.MM` branch and a description copied from `CHANGELOG.md`.
 
@@ -57,7 +57,7 @@ Once satisfied with the release candidates -
    - `vcpkg.json`
    - `CHANGELOG.md`
 
-      These changes will be automatically pushed to the existing `vYY.MM` branch and a PR from `vvYY.MM` to `develop` will be created (to sync the branches).
+      These changes will be automatically pushed to the existing `vYY.MM` branch and a PR will be created to update version strings in `develop`.
 
 3. Next, a PR from `vYY.MM` to `main` will be generated that should be merged once all the tests pass.
 

.github/wheel_failure.md

@@ -1,6 +1,6 @@
 ---
 title: Fortnightly build for wheels failed
-labels: priority:high, bug
+labels: "priority: high, bug"
 ---
 
 The build is failing with the following logs - {{ env.LOGS }}

.github/workflows/lychee_url_checker.yml

@@ -28,7 +28,7 @@ jobs:
 
       # use stable version for now to avoid breaking changes
       - name: Lychee URL checker
-        uses: lycheeverse/lychee-action@v1.8.0
+        uses: lycheeverse/lychee-action@v1.9.1
         with:
           # arguments with file types to check
           args: >-

.github/workflows/publish_pypi.yml

@@ -16,16 +16,37 @@ on:
         required: false
         default: false
 
+# Set options available for all jobs that use cibuildwheel
+env:
+  # Increase pip debugging output, equivalent to `pip -vv`
+  CIBW_BUILD_VERBOSITY: 2
+  # Disable build isolation to allow pre-installing build-time dependencies.
+  # Note: CIBW_BEFORE_BUILD must be present in all jobs using cibuildwheel.
+  CIBW_BUILD_FRONTEND: "pip; args: --no-build-isolation"
+  # Skip PyPy and MUSL builds in any and all jobs
+  CIBW_SKIP: "pp* *musllinux*"
+  FORCE_COLOR: 3
+
 jobs:
   build_windows_wheels:
-    name: Build wheels on windows-latest
+    name: Wheels (windows-latest)
     runs-on: windows-latest
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
           python-version: 3.8
 
+      - name: Get number of cores on Windows
+        id: get_num_cores
+        shell: python
+        run: |
+          from os import environ, cpu_count
+          num_cpus = cpu_count()
+          output_file = environ['GITHUB_OUTPUT']
+          with open(output_file, "a", encoding="utf-8") as output_stream:
+              output_stream.write(f"count={num_cpus}\n")
+
       - name: Clone pybind11 repo (no history)
         run: git clone --depth 1 --branch v2.11.1 https://github.com/pybind/pybind11.git
 
@@ -53,8 +74,17 @@ jobs:
       - name: Build 64-bit wheels on Windows
         run: pipx run cibuildwheel --output-dir wheelhouse
         env:
-          CIBW_ENVIRONMENT: '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'
-          CIBW_ARCHS: "AMD64"
+          CIBW_ENVIRONMENT: >
+            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=${{ steps.get_num_cores.outputs.count }}
+          CIBW_ARCHS: AMD64
+          CIBW_BEFORE_BUILD: python -m pip install setuptools wheel # skip CasADi and CMake
+          CIBW_TEST_COMMAND: python -c "import pybamm; pybamm.IDAKLUSolver()"
 
       - name: Upload Windows wheels
         uses: actions/upload-artifact@v4
@@ -63,16 +93,19 @@ jobs:
           path: ./wheelhouse/*.whl
           if-no-files-found: error
 
-  build_wheels:
-    name: Build wheels on ${{ matrix.os }}
+  build_macos_and_linux_wheels:
+    name: Wheels (${{ matrix.os }})
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest]
     steps:
       - uses: actions/checkout@v4
+        name: Check out PyBaMM repository
+
       - uses: actions/setup-python@v5
+        name: Set up Python
         with:
           python-version: 3.8
 
@@ -88,26 +121,26 @@ jobs:
           python -m pip install cmake wget
           python scripts/install_KLU_Sundials.py
 
-      - name: Build wheels on ${{ matrix.os }}
+      - name: Build wheels on Linux
         run: pipx run cibuildwheel --output-dir wheelhouse
+        if: matrix.os == 'ubuntu-latest'
         env:
           CIBW_ARCHS_LINUX: x86_64
           CIBW_BEFORE_ALL_LINUX: >
             yum -y install openblas-devel lapack-devel &&
             bash scripts/install_sundials.sh 6.0.3 6.5.0
-          CIBW_BEFORE_BUILD_LINUX: >
-            python -m pip install cmake casadi numpy
-          # override; point to casadi install path so that it can be found by the repair command
-          CIBW_REPAIR_WHEEL_COMMAND_LINUX: >
-            LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:$(python -c 'import casadi; print(casadi.__path__[0])')" auditwheel repair -w {dest_dir} {wheel}
+          CIBW_BEFORE_BUILD_LINUX: python -m pip install cmake casadi setuptools wheel
+          CIBW_REPAIR_WHEEL_COMMAND_LINUX: auditwheel repair -w {dest_dir} {wheel}
+          CIBW_TEST_COMMAND: python -c "import pybamm; pybamm.IDAKLUSolver()"
+
+      - name: Build wheels on macOS
+        if: matrix.os == 'macos-latest'
+        run: pipx run cibuildwheel --output-dir wheelhouse
+        env:
           CIBW_BEFORE_BUILD_MACOS: >
-            python -m pip
-            install cmake casadi numpy &&
-            python scripts/fix_casadi_rpath_mac.py && scripts/fix_suitesparse_rpath_mac.sh
-          CIBW_REPAIR_WHEEL_COMMAND_MACOS: >
-            delocate-listdeps {wheel} &&
-            delocate-wheel -v -w {dest_dir} {wheel}
-          CIBW_SKIP: "pp* *musllinux*"
+            python -m pip install --upgrade cmake casadi setuptools wheel
+          CIBW_REPAIR_WHEEL_COMMAND_MACOS: delocate-listdeps {wheel} && delocate-wheel -v -w {dest_dir} {wheel}
+          CIBW_TEST_COMMAND: python -c "import pybamm; pybamm.IDAKLUSolver()"
 
       - name: Upload wheels for Linux
         uses: actions/upload-artifact@v4
@@ -135,9 +168,6 @@ jobs:
         with:
           python-version: 3.12
 
-      - name: Install dependencies
-        run: pip install --upgrade pip setuptools wheel
-
       - name: Build SDist
         run: pipx run build --sdist
 
@@ -149,9 +179,10 @@ jobs:
           if-no-files-found: error
 
   publish_pypi:
-    if: github.event_name != 'schedule' && github.repository_owner == 'pybamm-team'
+    # This job is only of value to PyBaMM and would always be skipped in forks
+    if: github.event_name != 'schedule' && github.repository == 'pybamm-team/PyBaMM'
     name: Upload package to PyPI
-    needs: [build_wheels, build_windows_wheels, build_sdist]
+    needs: [build_macos_and_linux_wheels, build_windows_wheels, build_sdist]
     runs-on: ubuntu-latest
     steps:
       - name: Download all artifacts
@@ -180,9 +211,9 @@ jobs:
           repository-url: https://test.pypi.org/legacy/
 
   open_failure_issue:
-    needs: [build_windows_wheels, build_wheels, build_sdist]
+    needs: [build_windows_wheels, build_macos_and_linux_wheels, build_sdist]
     name: Open an issue if build fails
-    if: ${{ always() && contains(needs.*.result, 'failure') }}
+    if: ${{ always() && contains(needs.*.result, 'failure') && github.repository_owner == 'pybamm-team'}}
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4

.github/workflows/run_periodic_tests.yml

@@ -36,8 +36,7 @@ jobs:
       - name: Check style
         run: |
           python -m pip install pre-commit
-          git add .
-          pre-commit run ruff
+          pre-commit run -a
 
   build:
     needs: style
@@ -153,3 +152,50 @@ jobs:
           eval "$(pyenv init -)"
           pyenv activate pybamm-${{ matrix.python-version }}
           pyenv uninstall -f $( python --version )
+
+  test_install_odes:
+    runs-on: ${{ matrix.os }}
+    strategy:
+        matrix:
+            os: [ubuntu-latest, macos-latest]
+            python-version: ["3.8", "3.9", "3.10", "3.11"]
+        fail-fast: false
+    name: Test pybamm_install_odes on ${{ matrix.os }}
+
+    steps:
+      - name: Check out PyBaMM repository
+        uses: actions/checkout@v4
+
+      - name: Install Linux system dependencies
+        if: matrix.os == 'ubuntu-latest'
+        run: |
+          sudo apt-get update
+          sudo apt-get install gfortran gcc libopenblas-dev
+      - name: Install macOS system dependencies
+        if: matrix.os == 'macos-latest'
+        env:
+          # Homebrew environment variables
+          HOMEBREW_NO_INSTALL_CLEANUP: 1
+          HOMEBREW_NO_AUTO_UPDATE: 1
+          HOMEBREW_NO_COLOR: 1
+          # Speed up CI
+          NONINTERACTIVE: 1
+        run: |
+          brew analytics off
+          brew install openblas
+          brew reinstall gcc gfortran
+
+      - name: Set up Python ${{ matrix.python-version }}
+        id: setup-python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install PyBaMM
+        run: python -m pip install -e .
+
+      - name: Test pybamm_install_odes on ${{ matrix.os }}
+        run: |
+          python -m pip cache purge
+          python -m pip install wget cmake
+          pybamm_install_odes

.github/workflows/test_on_push.yml

@@ -28,8 +28,7 @@ jobs:
       - name: Check style
         run: |
           python -m pip install pre-commit
-          git add .
-          pre-commit run ruff
+          pre-commit run -a
 
   run_unit_tests:
     needs: style
@@ -106,8 +105,7 @@ jobs:
             # Headers and dynamic library files for SuiteSparse and SUNDIALS
             ${{ env.HOME }}/.local/lib/
             ${{ env.HOME }}/.local/include/
-            ${{ env.HOME }}/.local/examples/
-          key: nox-${{ matrix.os }}-pybamm-requires-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/install_KLU_Sundials.py', '**/noxfile.py') }}
+          key: nox-${{ matrix.os }}-pybamm-requires-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/install_KLU_Sundials.py', '**/noxfile.py', '**/test_on_push.yml') }}
 
       - name: Install SuiteSparse and SUNDIALS on GNU/Linux and macOS
         if: matrix.os != 'windows-latest'
@@ -163,8 +161,7 @@ jobs:
             # Headers and dynamic library files for SuiteSparse and SUNDIALS
             ${{ env.HOME }}/.local/lib/
             ${{ env.HOME }}/.local/include/
-            ${{ env.HOME }}/.local/examples/
-          key: nox-${{ matrix.os }}-pybamm-requires-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/install_KLU_Sundials.py', '**/noxfile.py') }}
+          key: nox-${{ matrix.os }}-pybamm-requires-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/install_KLU_Sundials.py', '**/noxfile.py', '**/test_on_push.yml') }}
 
       - name: Install SuiteSparse and SUNDIALS on GNU/Linux
         run: python -m nox -s pybamm-requires
@@ -245,8 +242,7 @@ jobs:
             # Headers and dynamic library files for SuiteSparse and SUNDIALS
             ${{ env.HOME }}/.local/lib/
             ${{ env.HOME }}/.local/include/
-            ${{ env.HOME }}/.local/examples/
-          key: nox-${{ matrix.os }}-pybamm-requires-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/install_KLU_Sundials.py', '**/noxfile.py') }}
+          key: nox-${{ matrix.os }}-pybamm-requires-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/install_KLU_Sundials.py', '**/noxfile.py', '**/test_on_push.yml') }}
 
       - name: Install SuiteSparse and SUNDIALS on GNU/Linux and macOS
         if: matrix.os != 'windows-latest'
@@ -344,8 +340,7 @@ jobs:
             # Headers and dynamic library files for SuiteSparse and SUNDIALS
             ${{ env.HOME }}/.local/lib/
             ${{ env.HOME }}/.local/include/
-            ${{ env.HOME }}/.local/examples/
-          key: nox-${{ matrix.os }}-pybamm-requires-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/install_KLU_Sundials.py', '**/noxfile.py') }}
+          key: nox-${{ matrix.os }}-pybamm-requires-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/install_KLU_Sundials.py', '**/noxfile.py', '**/test_on_push.yml') }}
 
       - name: Install SuiteSparse and SUNDIALS on GNU/Linux
         run: python -m nox -s pybamm-requires
@@ -399,8 +394,7 @@ jobs:
             # Headers and dynamic library files for SuiteSparse and SUNDIALS
             ${{ env.HOME }}/.local/lib/
             ${{ env.HOME }}/.local/include/
-            ${{ env.HOME }}/.local/examples/
-          key: nox-${{ matrix.os }}-pybamm-requires-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/install_KLU_Sundials.py', '**/noxfile.py') }}
+          key: nox-${{ matrix.os }}-pybamm-requires-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/install_KLU_Sundials.py', '**/noxfile.py', '**/test_on_push.yml') }}
 
       - name: Install SuiteSparse and SUNDIALS on GNU/Linux
         run: python -m nox -s pybamm-requires