Merge pull request #3047 from pybamm-team/v23.5

Make release v23.5

Author: brosaplanella

.all-contributorsrc

@@ -441,7 +441,7 @@
       "login": "wigging",
       "name": "Gavin Wiggins",
       "avatar_url": "https://avatars.githubusercontent.com/u/6828967?v=4",
-      "profile": "https://gavinw.me",
+      "profile": "https://wigging.me",
       "contributions": [
         "bug",
         "code"
@@ -570,7 +570,8 @@
       "avatar_url": "https://avatars.githubusercontent.com/u/31622972?v=4",
       "profile": "https://aniketsinghrawat.vercel.app/",
       "contributions": [
-        "code"
+        "code",
+        "doc"
       ]
     },
     {
@@ -611,6 +612,34 @@
       "contributions": [
         "infra"
       ]
+    },
+    {
+      "login": "chenzhao-py",
+      "name": "CHEN ZHAO",
+      "avatar_url": "https://avatars.githubusercontent.com/u/75906533?v=4",
+      "profile": "https://github.com/chenzhao-py",
+      "contributions": [
+        "bug"
+      ]
+    },
+    {
+      "login": "darryl-ad",
+      "name": "darryl-ad",
+      "avatar_url": "https://avatars.githubusercontent.com/u/91731499?v=4",
+      "profile": "https://www.aboutenergy.io/",
+      "contributions": [
+        "code",
+        "bug"
+      ]
+    },
+    {
+      "login": "julian-evers",
+      "name": "julian-evers",
+      "avatar_url": "https://avatars.githubusercontent.com/u/133691040?v=4",
+      "profile": "https://github.com/julian-evers",
+      "contributions": [
+        "code"
+      ]
     }
   ],
   "contributorsPerLine": 7,
@@ -619,5 +648,6 @@
   "repoType": "github",
   "repoHost": "https://github.com",
   "skipCi": true,
-  "commitConvention": "angular"
+  "commitConvention": "angular",
+  "commitType": "docs"
 }

.github/workflows/benchmark_on_push.yml

@@ -1,6 +1,7 @@
 name: Run benchmarks on push
 on:
   push:
+  pull_request:
 
 jobs:
   benchmarks:
@@ -26,8 +27,11 @@ jobs:
           # on develop. In this case, we don't want to be
           # fetching the develop branch.
           current_branch=$(git rev-parse --abbrev-ref HEAD)
+          # This workflow should also run on forks; hence,
+          # we should fetch the upstream develop branch.
+          git remote add upstream https://github.com/pybamm-team/PyBaMM/
           if [ $current_branch != "develop" ]; then
-              git fetch origin develop:develop
+              git fetch upstream develop:develop
           fi
 
       - name: Run benchmarks

.github/workflows/need_reply_remove.yml

@@ -10,7 +10,8 @@ jobs:
     runs-on: ubuntu-latest
     if: |
       github.event.comment.author_association != 'OWNER' &&
-      github.event.comment.author_association != 'COLLABORATOR'
+      github.event.comment.author_association != 'COLLABORATOR' &&
+      github.repository-owner == 'pybamm-team'
     steps:
       - name: Remove needs-reply label
         uses: octokit/[email protected]

.github/workflows/needs_reply.yml

@@ -7,6 +7,7 @@ on:
 jobs:
   build:
     runs-on: ubuntu-latest
+    if: github.repository-owner == 'pybamm-team'
     steps:
       - name: Close old issues that need reply
         uses: dwieeb/needs-reply@v2

.github/workflows/periodic_benchmarks.yml

@@ -27,7 +27,7 @@ jobs:
       - name: Install Linux system dependencies
         run: |
           sudo apt-get update
-          sudo apt install gfortran gcc libopenblas-dev
+          sudo apt-get install gfortran gcc libopenblas-dev
       - name: Install python dependencies
         run: |
           python -m pip install --upgrade pip wheel setuptools virtualenv asv wget cmake casadi numpy

.github/workflows/publish_pypi.yml

@@ -8,6 +8,11 @@ on:
       target:
         description: 'Deployment target. Can be "pypi" or "testpypi"'
         default: "pypi"
+      debug_enabled:
+          type: boolean
+          description: 'Run the build with tmate debugging enabled (https://github.com/marketplace/actions/debugging-with-tmate)'
+          required: false
+          default: false
 
 jobs:
   build_windows_wheels:
@@ -20,10 +25,10 @@ jobs:
           python-version: 3.8
 
       - name: Install cibuildwheel
-        run: python -m pip install cibuildwheel==1.9.0
+        run: python -m pip install cibuildwheel==2.12.3
 
       - name: Clone pybind11 repo (no history)
-        run: git clone --depth 1 --branch v2.6.2 https://github.com/pybind/pybind11.git
+        run: git clone --depth 1 --branch v2.10.4 https://github.com/pybind/pybind11.git
 
       # remove when a new vcpkg version is released
       - name: Install the latest commit of vcpkg on windows
@@ -35,18 +40,23 @@ jobs:
           .\bootstrap-vcpkg.bat
 
       - name: Cache packages installed through vcpkg on windows
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         env:
           cache-name: vckpg_binary_cache
         with:
           path: C:\Users\runneradmin\AppData\Local\vcpkg\archives
           key: ${{ runner.os }}-build-VS2022-${{ env.cache-name }}-${{ hashFiles('vcpkg*.json') }}
 
+      # Enable tmate debugging of manually-triggered workflows if the input option was provided
+      - name: Setup tmate session
+        uses: mxschmitt/action-tmate@v3
+        if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled }}
+
       - name: Build 64 bits wheels on Windows
         run: |
           python -m cibuildwheel --output-dir wheelhouse
         env:
-          CIBW_ENVIRONMENT: 'PYBAMM_USE_VCPKG=ON VCPKG_ROOT_DIR=$cd/vcpkg VCPKG_DEFAULT_TRIPLET=x64-windows-static-md VCPKG_FEATURE_FLAGS=manifests,registries CMAKE_GENERATOR="Visual Studio 17 2022" CMAKE_GENERATOR_PLATFORM=x64'
+          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"
 
       - name: Upload windows wheels
@@ -70,12 +80,12 @@ jobs:
           python-version: 3.8
 
       - name: Install cibuildwheel
-        run: python -m pip install cibuildwheel==1.9.0
+        run: python -m pip install cibuildwheel==2.12.3
 
       - name: Clone pybind11 repo (no history)
-        run: git clone --depth 1 --branch v2.6.2 https://github.com/pybind/pybind11.git
+        run: git clone --depth 1 --branch v2.10.4 https://github.com/pybind/pybind11.git
 
-      - name: Install sundials on macOS
+      - name: Install SUNDIALS on macOS
         if: matrix.os == 'macos-latest'
         run: |
           # https://github.com/actions/virtual-environments/issues/1280
@@ -85,19 +95,30 @@ jobs:
           rm -f /usr/local/bin/python3*
           brew update
           brew reinstall gcc
+          brew install libomp
           python -m pip install cmake wget
           python scripts/install_KLU_Sundials.py
 
       - name: Build wheels on Linux and MacOS
         run: python -m cibuildwheel --output-dir wheelhouse
         env:
-          CIBW_BEFORE_ALL_LINUX: "bash build_manylinux_wheels/install_sundials.sh 5.8.1 5.7.0"
+          # TODO: openblas no longer available on centos 7 i686 image, use blas instead for now
+          CIBW_BEFORE_ALL_LINUX: >
+            yum -y install blas-devel lapack-devel &&
+            bash build_manylinux_wheels/install_sundials.sh 5.8.1 6.5.0
+
           CIBW_BEFORE_BUILD_LINUX: "python -m pip install cmake casadi numpy"
-          CIBW_BEFORE_BUILD_MACOS: "python -m pip install cmake casadi numpy && python scripts/fix_casadi_rpath_mac.py"
+          CIBW_BEFORE_BUILD_MACOS: >
+            python -m pip
+            install cmake casadi numpy &&
+            python scripts/fix_casadi_rpath_mac.py &&
+            scripts/fix_suitesparse_rpath_mac.sh
           # got error "re.error: multiple repeat at position 104" on python 3.7 when --require-archs added, so remove
           # it for mac
-          CIBW_REPAIR_WHEEL_COMMAND_MACOS: "delocate-listdeps {wheel} && delocate-wheel -v -w {dest_dir} {wheel}"
-          CIBW_SKIP: pp*
+          CIBW_REPAIR_WHEEL_COMMAND_MACOS: >
+            delocate-listdeps {wheel} &&
+            delocate-wheel -v -w {dest_dir} {wheel}
+          CIBW_SKIP: "pp* *musllinux*"
 
       - name: Upload wheels
         uses: actions/upload-artifact@v3

.github/workflows/run_periodic_tests.yml

@@ -0,0 +1,131 @@
+# Run all unit tests and integration tests for all Python versions 
+# and platforms at 3am UTC every day and on PRs to the main branch
+name: Scheduled
+
+on:
+  workflow_dispatch:
+  pull_request:
+    branches: 
+    - main
+
+  # Run everyday at 3 am UTC
+  schedule:
+    - cron: "0 3 * * *"
+
+jobs:
+  pre_job:
+    runs-on: ubuntu-latest
+    # Map a step output to a job output
+    outputs:
+      should_skip: ${{ steps.skip_check.outputs.should_skip }}
+    steps:
+      - id: skip_check
+        uses: fkirc/skip-duplicate-actions@master
+        with:
+          # All of these options are optional, so you can remove them if you are happy with the defaults
+          concurrent_skipping: "never"
+          cancel_others: "true"
+          paths_ignore: '["**/README.md"]'
+
+  style:
+    needs: pre_job
+    if: ${{ needs.pre_job.outputs.should_skip != 'true' }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Setup python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.11
+
+      - name: Check style
+        run: |
+          python -m pip install pre-commit
+          pre-commit run ruff
+
+  build:
+    needs: style
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install Linux system dependencies
+        if: matrix.os == 'ubuntu-latest'
+        run: |
+          sudo apt-get update
+          sudo apt install gfortran gcc libopenblas-dev graphviz
+          sudo apt install texlive-full
+
+      # Added fixes to homebrew installs:
+      # rm -f /usr/local/bin/2to3
+      # (see https://github.com/actions/virtual-environments/issues/2322)
+      - name: Install MacOS system dependencies
+        if: matrix.os == 'macos-latest'
+        run: |
+          rm -f /usr/local/bin/2to3*
+          rm -f /usr/local/bin/idle3*
+          rm -f /usr/local/bin/pydoc3*
+          rm -f /usr/local/bin/python3*
+          brew update
+          brew install graphviz
+          brew install openblas
+
+      - name: Install Windows system dependencies
+        if: matrix.os == 'windows-latest'
+        run: choco install graphviz --version=2.38.0.20190211
+
+      - name: Install standard python dependencies
+        run: |
+          python -m pip install --upgrade pip wheel setuptools
+          python -m pip install "tox<4"
+
+      - name: Install SuiteSparse and Sundials
+        if: matrix.os == 'ubuntu-latest'
+        run: tox -e pybamm-requires
+
+      - name: Run unit tests for GNU/Linux with Python 3.8, 3.9, and 3.10
+        if: matrix.os == 'ubuntu-latest' && matrix.python-version != 3.11
+        run: python -m tox -e unit
+
+      - name: Run unit tests for GNU/Linux with Python 3.11 and generate coverage report
+        if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
+        run: python -m tox -e coverage
+
+      - name: Upload coverage report
+        if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.11
+        uses: codecov/[email protected]
+
+      - name: Run integration tests for GNU/Linux
+        if: matrix.os == 'ubuntu-latest'
+        run: python -m tox -e integration
+
+      - name: Run unit tests for Windows and MacOS
+        if: matrix.os != 'ubuntu-latest'
+        run: python -m tox -e mac-windows-unit
+
+      - name: Run integration tests for Windows and MacOS
+        if: matrix.os != 'ubuntu-latest'
+        run: python -m tox -e mac-windows-integration
+
+      - name: Install docs dependencies and run doctests
+        if: matrix.os == 'ubuntu-latest'
+        run: tox -e doctests
+
+      - name: Install dev dependencies and run example tests
+        if: matrix.os == 'ubuntu-latest'
+        run: tox -e examples
+
+      - name: Install scikits.odes and test pybamm_install_odes
+        if: matrix.os == 'ubuntu-latest'
+        run: |
+          tox -e odes