Merge branch 'develop' into docker-ci

.all-contributorsrc

@@ -674,6 +674,27 @@
         "ideas",
         "bug"
       ]
+    },
+    {
+      "login": "bobonice",
+      "name": "bobonice",
+      "avatar_url": "https://avatars.githubusercontent.com/u/22030806?v=4",
+      "profile": "https://github.com/bobonice",
+      "contributions": [
+        "bug",
+        "code"
+      ]
+    },
+    {
+      "login": "kratman",
+      "name": "Eric G. Kratz",
+      "avatar_url": "https://avatars.githubusercontent.com/u/10170302?v=4",
+      "profile": "https://github.com/kratman",
+      "contributions": [
+        "doc",
+        "infra",
+        "bug"
+      ]
     }
   ],
   "contributorsPerLine": 7,

.github/release_reminder.md

@@ -0,0 +1,9 @@
+---
+title: Create {{ date | date('YY.MM') }} (final or rc0) release
+---
+Quarterly reminder to create a -
+
+1. pre-release if the month has just started.
+2. non-pre-release if the month is about to end (**before the end of the month**).
+
+See [Release Workflow](./release_workflow.md) for more information.

.github/release_workflow.md

@@ -0,0 +1,74 @@
+# Release workflow
+
+This file contains the workflow required to make a `PyBaMM` release on GitHub and PyPI by the maintainers.
+
+## rc0 releases (automated)
+
+1. The `update_version.yml` workflow will run on every 1st of January, May and September, updating incrementing the version to `YY.MMrc0` by running `scripts/update_version.py` in the following files -
+
+   - `pybamm/version.py`
+   - `docs/conf.py`
+   - `CITATION.cff`
+   - `vcpkg.json`
+   - `docs/_static/versions.json`
+   - `CHANGELOG.md`
+
+      These changes will be automatically pushed to a new branch `YY.MM`.
+
+2. Create a new GitHub _pre-release_ with the tag `YY.MMrc0` from the `YY.MM` branch and a description copied from `CHANGELOG.md`.
+
+3. This release will automatically trigger `publish_pypi.yml` and create a _pre-release_ on PyPI.
+
+## rcX releases (manual)
+
+If a new release candidate is required after the release of `rc0` -
+
+1. Fix a bug in `YY.MM` (no new features should be added to `YY.MM` once `rc0` is released) and `develop` individually.
+
+2. Run `update_version.yml` manually while using `append_to_tag` to specify the release candidate version number (`rc1`, `rc2`, ...).
+
+3. This will increment the version to `YY.MMrcX` by running `scripts/update_version.py` in the following files -
+
+   - `pybamm/version.py`
+   - `docs/conf.py`
+   - `CITATION.cff`
+   - `vcpkg.json`
+   - `docs/_static/versions.json`
+   - `CHANGELOG.md`
+
+      These changes will be automatically pushed to the existing branch `YY.MM`.
+
+4. Create a new GitHub _pre-release_ with the same tag (`YY.MMrcX`) from the `YY.MM` branch and a description copied from `CHANGELOG.md`.
+
+5. This release will automatically trigger `publish_pypi.yml` and create a _pre-release_ on PyPI.
+
+## Actual release (manual)
+
+Once satisfied with the release candidates -
+
+1. Run `update_version.yml` manually, leaving the `append_to_tag` field blank ("") for an actual release.
+
+2. This will increment the version to `YY.MMrcX` by running `scripts/update_version.py` in the following files -
+
+   - `pybamm/version.py`
+   - `docs/conf.py`
+   - `CITATION.cff`
+   - `vcpkg.json`
+   - `docs/_static/versions.json`
+   - `CHANGELOG.md`
+
+      These changes will be automatically pushed to the existing branch `YY.MM`.
+
+3. Next, a PR from `YY.MM` to `main` will be generated that should be merged once all the tests pass.
+
+4. Create a new GitHub _release_ with the same tag from the `main` branch and a description copied from `CHANGELOG.md`.
+
+5. This release will automatically trigger `publish_pypi.yml` and create a _release_ on PyPI.
+
+## Other checks
+
+Some other essential things to check throughout the release process -
+
+- If updating our custom vcpkg registory entries [pybamm-team/sundials-vcpkg-registry](https://github.com/pybamm-team/sundials-vcpkg-registry) or [pybamm-team/casadi-vcpkg-registry](https://github.com/pybamm-team/casadi-vcpkg-registry) (used to build Windows wheels), make sure to update the baseline of the registories in vcpkg-configuration.json to the latest commit id.
+- Update jax and jaxlib to the latest version in `pybamm.util` and `setup.py`, fixing any bugs that arise
+- Make sure the URLs in `docs/_static/versions.json` are valid

.github/workflows/lychee_url_checker.yml

@@ -45,6 +45,7 @@ jobs:
             --accept 200,429
             --exclude-path ./CHANGELOG.md
             --exclude-path ./scripts/update_version.py
+            --exclude-path docs/conf.py
             './**/*.rst'
             './**/*.md'
             './**/*.py'

.github/workflows/publish_pypi.yml

@@ -1,18 +1,18 @@
 name: Build and publish package to PyPI
 
 on:
-  push:
-    branches: main
+  release:
+    types: [published]
   workflow_dispatch:
     inputs:
       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
+        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:
@@ -130,15 +130,12 @@ jobs:
   build_sdist:
     name: Build sdist
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: [3.8]
 
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: 3.8
 
       - name: Install dependencies
         run: pip install wheel

.github/workflows/release_reminder.yml

@@ -0,0 +1,21 @@
+name: Create a release reminder
+
+on:
+  schedule:
+     # Run at 10 am UTC on days-of-month 1 and 28 in January, May, and September.
+     - cron: "0 10 1,28 1,5,9 *"
+
+permissions:
+  contents: read
+  issues: write
+
+jobs:
+  remind:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: JasonEtco/create-an-issue@v2
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          filename: .github/release_reminder.md

.github/workflows/run_periodic_tests.yml

@@ -115,6 +115,10 @@ jobs:
         if: matrix.os == 'ubuntu-latest'
         run: nox -s examples
 
+      - name: Run example scripts tests
+        if: matrix.os == 'ubuntu-latest'
+        run: nox -s scripts
+
   #M-series Mac Mini
   build-apple-mseries:
     needs: style

.github/workflows/update_version.yml

@@ -2,51 +2,73 @@ name: Update version
 
 on:
   workflow_dispatch:
+    inputs:
+      append_to_tag:
+        description: 'Leave blank for an actual release or "rc1", "rc2", ..., for release candidates."'
+        default: ""
+  schedule:
+     # Run at 10 am UTC on day-of-month 1 in January, May, and September.
+     - cron: "0 10 1 1,5,9 *"
 
 jobs:
   update-version:
     # This workflow is only of value to PyBaMM and would always be skipped in forks
     if: github.repository_owner == 'pybamm-team'
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: [3.8]
 
     steps:
+      - name: Get current date for the first release candidate
+        if: github.event_name == 'schedule'
+        run: |
+          echo "VERSION=$(date +'v%y.%-m')rc0" >> $GITHUB_ENV
+          echo "NON_RC_VERSION=$(date +'v%y.%-m')" >> $GITHUB_ENV
+
+      - name: Get current date for a manual release
+        if: github.event_name == 'workflow_dispatch'
+        run: |
+          echo "VERSION=$(date +'v%y.%-m')${{ github.event.inputs.append_to_tag }}" >> $GITHUB_ENV
+          echo "NON_RC_VERSION=$(date +'v%y.%-m')" >> $GITHUB_ENV
+
+      - uses: actions/checkout@v4
+        if: github.event_name == 'schedule'
+        with:
+          ref: 'develop'
+
       - uses: actions/checkout@v4
+        if: github.event_name == 'workflow_dispatch'
+        with:
+          ref: '${{ env.NON_RC_VERSION }}'
 
-      - name: Set up Python ${{ matrix.python-version }}
+      - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: 3.8
 
       - name: Install dependencies
         run: |
           pip install wheel
-          pip install --editable .
-
-      - name: Get current date
-        run: echo "VERSION=$(date +'v%y.%-m')" >> $GITHUB_ENV
+          pip install --editable ".[all]"
 
       - name: Update version
         run: python scripts/update_version.py
 
-      - name: Create Pull Request
-        id: version_pr
-        uses: peter-evans/create-pull-request@v5
+      - uses: EndBug/add-and-commit@v9
+        if: github.event_name == 'schedule'
         with:
-          delete-branch: true
-          branch-suffix: short-commit-hash
-          commit-message: Update version to ${{ env.VERSION }}
-          title: Update to ${{ env.VERSION }}
-          body: |
-            - [x] Update to ${{ env.VERSION }}
-            - [ ] Check the [release checklist](https://github.com/pybamm-team/PyBaMM/blob/develop/.github/release_checklist.md)
-
-      - name: Make a PR from develop to main
+          message: 'Bump to ${{ env.VERSION }}'
+          new_branch: '${{ env.NON_RC_VERSION }}'
+
+      - uses: EndBug/add-and-commit@v9
+        if: github.event_name == 'workflow_dispatch'
+        with:
+          message: 'Bump to ${{ env.VERSION }}'
+
+      - name: Make a PR from ${{ env.NON_RC_VERSION }} to main
+        if: github.event_name == 'workflow_dispatch' && !startsWith(github.event.inputs.append_to_tag, 'rc')
         uses: repo-sync/pull-request@v2
         with:
+          source_branch: '${{ env.NON_RC_VERSION }}'
           destination_branch: "main"
-          pr_title: "Make release ${{ env.VERSION }}"
-          pr_body: "**DO NOT MERGE UNTIL #${{ steps.version_pr.outputs.pull-request-number }} IS MERGED.**<br><br>Make release ${{ env.VERSION }}"
+          pr_title: "Make release ${{ env.NON_RC_VERSION }}"
+          pr_body: "**Check the [release workflow](https://github.com/pybamm-team/PyBaMM/blob/develop/.github/release_workflow.md)**"
           github_token: ${{ secrets.GITHUB_TOKEN }}

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.0.284"
+    rev: "v0.0.290"
     hooks:
       - id: ruff
         args: [--fix, --ignore=E741, --exclude=__init__.py]
@@ -17,7 +17,7 @@ repos:
         args: ["--fix","--ignore=E501,E402"]
 
   - repo: https://github.com/adamchainz/blacken-docs
-    rev: "1.15.0"
+    rev: "1.16.0"
     hooks:
        - id: blacken-docs
          additional_dependencies: [black==22.12.0]