#1100 merge develop

Author: valentinsulzer

.all-contributorsrc

@@ -290,7 +290,9 @@
       "avatar_url": "https://avatars.githubusercontent.com/u/64051212?v=4",
       "profile": "https://github.com/priyanshuone6",
       "contributions": [
-        "test"
+        "test",
+        "code",
+        "bug"
       ]
     },
     {
@@ -312,7 +314,8 @@
       "profile": "https://github.com/Saransh-cpp",
       "contributions": [
         "code",
-        "test"
+        "test",
+        "doc"
       ]
     },
     {
@@ -321,7 +324,36 @@
       "avatar_url": "https://avatars.githubusercontent.com/u/10965193?v=4",
       "profile": "https://github.com/DavidMStraub",
       "contributions": [
-        "bug"
+        "bug",
+        "code"
+      ]
+    },
+    {
+      "login": "maurosgroi",
+      "name": "maurosgroi",
+      "avatar_url": "https://avatars.githubusercontent.com/u/37576773?v=4",
+      "profile": "https://github.com/maurosgroi",
+      "contributions": [
+        "ideas"
+      ]
+    },
+    {
+      "login": "asinghgaba",
+      "name": "Amarjit Singh Gaba",
+      "avatar_url": "https://avatars.githubusercontent.com/u/77078706?v=4",
+      "profile": "https://github.com/asinghgaba",
+      "contributions": [
+        "code"
+      ]
+    },
+    {
+      "login": "KennethNwanoro",
+      "name": "KennethNwanoro",
+      "avatar_url": "https://avatars.githubusercontent.com/u/78538806?v=4",
+      "profile": "https://github.com/KennethNwanoro",
+      "contributions": [
+        "code",
+        "test"
       ]
     }
   ],

.github/PULL_REQUEST_TEMPLATE.md

@@ -6,7 +6,7 @@ Fixes # (issue)
 
 ## Type of change
 
-Please add a line in the relevant section of [CHANGELOG.md](https://github.com/pybamm-team/PyBaMM/blob/master/CHANGELOG.md) to document the change (include PR #) - note reverse order of PR #s. If necessary, also add to the list of breaking changes.
+Please add a line in the relevant section of [CHANGELOG.md](https://github.com/pybamm-team/PyBaMM/blob/develop/CHANGELOG.md) to document the change (include PR #) - note reverse order of PR #s. If necessary, also add to the list of breaking changes.
 
 - [ ] New feature (non-breaking change which adds functionality)
 - [ ] Optimization (back-end change that speeds up the code)

.github/workflows/benchmark_on_PR.yml .github/workflows/benchmark_on_push.yml

@@ -15,8 +15,13 @@ jobs:
         run: pip install -U pip virtualenv asv
       - name: Fetch base branch
         run: |
-          git fetch origin $GITHUB_BASE_REF:$GITHUB_BASE_REF
-          git fetch origin $GITHUB_HEAD_REF:$GITHUB_HEAD_REF
+          # This workflow also runs for merge commits
+          # on develop. In this case, we don't want to be
+          # fetching the develop branch.
+          current_branch=$(git rev-parse --abbrev-ref HEAD)
+          if [ $current_branch != "develop" ]; then
+              git fetch origin develop:develop
+          fi
       - name: Run benchmarks
         run: |
           asv machine --machine "GitHubRunner"

.github/workflows/build_wheels.yml

@@ -0,0 +1,82 @@
+name: Build
+
+on:
+  push:
+    branches: main
+  workflow_dispatch:
+    inputs:
+      target:
+        description: 'Deployment target. Can be "pypi" or "testpypi"'
+        default: 'pypi'
+
+jobs:
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [macOS-10.15, ubuntu-20.04, windows-2019]
+
+    steps:
+      - uses: actions/checkout@v2
+
+      # Used to host cibuildwheel
+      - uses: actions/setup-python@v2
+
+      - name: Install cibuildwheel
+        run: python -m pip install cibuildwheel==1.9.0
+
+      - name: Install sundials on macOS
+        if: matrix.os == 'macOS-10.15'
+        run: |
+          brew update
+          brew install sundials
+
+      - name: Clone pybind11 repo
+        run: git clone https://github.com/pybind/pybind11.git
+
+      - name: Build wheels on manylinux and macos
+        if: matrix.os != 'windows-2019'
+        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"
+          CIBW_BEFORE_BUILD_LINUX: "python -m pip install cmake"
+
+      - name: Build wheels on windows
+        if: matrix.os == 'windows-2019'
+        run: |
+          python -m pip install wheel
+          python -m pip wheel --no-deps --wheel-dir wheelhouse .
+
+      - uses: actions/upload-artifact@v2
+        with:
+          name: wheels
+          path: ./wheelhouse/*.whl
+
+
+  publish-pypi:
+    name: Upload wheels to PyPI
+    needs: build_wheels
+    runs-on: ubuntu-latest
+    steps:
+      - name: Download wheels
+        uses: actions/download-artifact@v1
+        with:
+          name: wheels
+
+      - name: Publish wheels on PyPI
+        if: github.events.inputs.target == 'pypi'
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_TOKEN }}
+          packages_dir: wheels/
+
+      - name: Publish wheels on TestPyPI
+        if: github.events.inputs.target == 'testpypi'
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          user: __token__
+          password: ${{ secrets.TESTPYPI_TOKEN }}
+          packages_dir: wheels/
+          repository_url: https://test.pypi.org/legacy/

.github/workflows/build_wheels_and_publish.yml

@@ -11,6 +11,10 @@ on:
   # Everyday at 3 am UTC
   schedule:
     - cron: "0 3 * * *"
+  # Make it possible to trigger the
+  # workflow manually
+  workflow_dispatch:
+
 jobs:
   benchmarks:
     runs-on: ubuntu-latest
@@ -22,12 +26,6 @@ jobs:
           python-version: 3.8
       - name: Install tox and asv
         run: pip install -U pip tox asv
-      - name: Fetch develop branch
-        # Not required when worklow trigerred
-        # on develop, but useful when
-        # experimenting/developing on another one.
-        run: |
-          git fetch origin develop:develop
       - name: Run benchmarks
         run: |
           asv machine --machine "GitHubRunner"
@@ -60,10 +58,13 @@ jobs:
           name: asv_new_results
           path: new_results
       - name: Copy new results and push to pybamm-bench repo
+        env:
+          PUSH_BENCH_EMAIL: ${{ secrets.PUSH_BENCH_EMAIL }}
+          PUSH_BENCH_NAME: ${{ secrets.PUSH_BENCH_NAME }}
         run: |
           cp -vr new_results/* results
-          git config --global user.email ${{ secrets.PUSH_BENCH_EMAIL }}
-          git config --global user.name ${{ secrets.PUSH_BENCH_NAME }}
+          git config --global user.email "$PUSH_BENCH_EMAIL"
+          git config --global user.name "$PUSH_BENCH_NAME"
           git add results
           git commit -am "Add new results"
           git push

.github/workflows/periodic_benchmarks.yml

@@ -32,7 +32,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: [3.6, 3.7, 3.8]
+        python-version: [3.7, 3.8, 3.9]
 
     steps:
     - uses: actions/checkout@v2
@@ -45,7 +45,6 @@ jobs:
       if: matrix.os == 'ubuntu-latest'
       run: |
         sudo apt install gfortran gcc libopenblas-dev graphviz
-        sudo apt install python${{ matrix.python-version }}.dev
     
     - name: Install MacOS system dependencies
       if: matrix.os == 'macos-latest'
@@ -84,10 +83,10 @@ jobs:
       run: tox -e examples
 
     - name: Install and run coverage
-      if: success() && (matrix.os == 'ubuntu-latest' && matrix.python-version == 3.7)
+      if: success() && (matrix.os == 'ubuntu-latest' && matrix.python-version == 3.9)
       run: tox -e coverage
 
     - name: Upload coverage report
-      if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.7
+      if: matrix.os == 'ubuntu-latest' && matrix.python-version == 3.9
       uses: codecov/codecov-action@v1
 

.github/workflows/test_on_push.yml

@@ -0,0 +1,43 @@
+name: Update parameter_sets.py docstring
+
+on:
+  push:
+    branches:
+    - develop
+    paths:
+    - 'pybamm/parameters/parameter_sets.py'
+    - 'pybamm/parameters/CITATIONS.txt'
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.8]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install wheel
+        pip install --editable .
+        pip install pybtex
+    - name: Update docstring
+      run: python pybamm/parameters/update_parameter_sets_doc.py
+    - name: Create Pull Request
+      uses: peter-evans/create-pull-request@v3
+      with:
+        delete-branch: true
+        branch-suffix: short-commit-hash
+        commit-message: update parameter_sets docstring
+        title: Update parameter_sets.py docstring
+        body: |
+            Update docstring of parameter_sets.py
+
+            Auto-generated pull request