Merge changes from develop

.all-contributorsrc

@@ -674,6 +674,29 @@
         "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",
+        "code",
+        "test"
+      ]
     }
   ],
   "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/benchmark_on_push.yml

@@ -13,7 +13,7 @@ jobs:
   benchmarks:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python 3.8
         uses: actions/setup-python@v4
         with:
@@ -23,8 +23,9 @@ jobs:
           sudo apt-get update
           sudo apt install gfortran gcc libopenblas-dev
       - name: Install python dependencies
+      # Pin asv==0.5.1 to fix failing benchmarks. Related to https://github.com/airspeed-velocity/asv/issues/1323
         run: |
-          python -m pip install --upgrade pip wheel setuptools virtualenv asv wget cmake casadi numpy
+          python -m pip install --upgrade pip wheel setuptools virtualenv asv==0.5.1 wget cmake casadi numpy
       - name: Install SuiteSparse and Sundials
         run: python scripts/install_KLU_Sundials.py
       - name: Fetch base branch

.github/workflows/lychee_url_checker.yml

@@ -24,7 +24,7 @@ jobs:
           restore-keys: cache-lychee-
 
       # check URLs with Lychee
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       # use stable version for now to avoid breaking changes
       - name: Lychee URL checker
@@ -46,6 +46,7 @@ jobs:
             --exclude-path ./CHANGELOG.md
             --exclude-path ./scripts/update_version.py
             --exclude-path asv.conf.json
+            --exclude-path docs/conf.py
             './**/*.rst'
             './**/*.md'
             './**/*.py'

.github/workflows/periodic_benchmarks.yml

@@ -19,7 +19,7 @@ jobs:
   benchmarks:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python 3.8
         uses: actions/setup-python@v4
         with:
@@ -58,7 +58,7 @@ jobs:
       - name: Install asv
         run: pip install asv
       - name: Checkout pybamm-bench repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           repository: pybamm-team/pybamm-bench
           token: ${{ secrets.BENCH_PAT }}

.github/workflows/publish_pypi.yml

@@ -3,26 +3,26 @@ name: Test building wheels
 # Temporarily disable publishing to PyPI and enable
 # building wheels on pull requests
 on:
-  # push:
-  #   branches: main
+  release:
+    types: [published]
   pull_request:
   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:
     name: Build wheels on windows-latest
     runs-on: windows-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with:
           python-version: 3.8
@@ -73,7 +73,7 @@ jobs:
       matrix:
         os: [ubuntu-latest, macos-latest]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with:
           python-version: 3.8
@@ -125,15 +125,12 @@ jobs:
   build_sdist:
     name: Build sdist
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-version: [3.8]
 
     steps:
-      - uses: actions/checkout@v3
+      - 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@v4
+      - uses: JasonEtco/create-an-issue@v2
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          filename: .github/release_reminder.md

.github/workflows/run_benchmarks_over_history.yml

@@ -22,7 +22,7 @@ jobs:
   benchmarks:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python 3.8
         uses: actions/setup-python@v4
         with:
@@ -59,7 +59,7 @@ jobs:
       - name: Install asv
         run: pip install asv
       - name: Checkout pybamm-bench repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           repository: pybamm-team/pybamm-bench
           token: ${{ secrets.BENCH_PAT }}

.github/workflows/run_periodic_tests.yml

@@ -27,7 +27,7 @@ jobs:
   style:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Setup python
         uses: actions/setup-python@v4
         with:
@@ -48,7 +48,7 @@ jobs:
         python-version: ["3.8", "3.9", "3.10", "3.11"]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4
         with:
@@ -99,6 +99,10 @@ jobs:
         if: matrix.os == 'ubuntu-latest'
         run: pipx 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
@@ -111,7 +115,7 @@ jobs:
         python-version: ["3.8", "3.9", "3.10", "3.11"]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Install python & create virtualenv
         shell: bash
         run: |