Merge pull request #3538 from pybamm-team/v23.9

Make release v23.9

.all-contributorsrc

@@ -331,7 +331,8 @@
         "example",
         "doc",
         "test",
-        "tutorial"
+        "tutorial",
+        "review"
       ]
     },
     {
@@ -530,7 +531,8 @@
       "contributions": [
         "infra",
         "code",
-        "doc"
+        "doc",
+        "review"
       ]
     },
     {
@@ -610,7 +612,10 @@
       "avatar_url": "https://avatars.githubusercontent.com/u/104268427?v=4",
       "profile": "https://github.com/arjxn-py",
       "contributions": [
-        "infra"
+        "infra",
+        "code",
+        "doc",
+        "review"
       ]
     },
     {
@@ -629,7 +634,8 @@
       "profile": "https://www.aboutenergy.io/",
       "contributions": [
         "code",
-        "bug"
+        "bug",
+        "ideas"
       ]
     },
     {
@@ -640,6 +646,68 @@
       "contributions": [
         "code"
       ]
+    },
+    {
+      "login": "js1tr3",
+      "name": "Jason Siegel",
+      "avatar_url": "https://avatars.githubusercontent.com/u/633873?v=4",
+      "profile": "https://batterycontrolgroup.engin.umich.edu/",
+      "contributions": [
+        "code",
+        "ideas"
+      ]
+    },
+    {
+      "login": "tommaull",
+      "name": "Tom Maull",
+      "avatar_url": "https://avatars.githubusercontent.com/u/101814207?v=4",
+      "profile": "https://github.com/tommaull",
+      "contributions": [
+        "code",
+        "test"
+      ]
+    },
+    {
+      "login": "ejfdickinson",
+      "name": "ejfdickinson",
+      "avatar_url": "https://avatars.githubusercontent.com/u/116663050?v=4",
+      "profile": "https://github.com/ejfdickinson",
+      "contributions": [
+        "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"
+      ]
+    },
+    {
+      "login": "aitorres",
+      "name": "Andrés Ignacio Torres",
+      "avatar_url": "https://avatars.githubusercontent.com/u/26191851?v=4",
+      "profile": "https://aitorres.com",
+      "contributions": [
+        "infra"
+      ]
     }
   ],
   "contributorsPerLine": 7,

.coveragerc

@@ -0,0 +1,3 @@
+[run]
+source = pybamm
+concurrency = multiprocessing

.git-blame-ignore-revs

@@ -1,2 +1,6 @@
 # activated pre-commit - https://github.com/pybamm-team/PyBaMM/pull/2272
 0054efe388d2d17301f7e0554449eac9a7d3b7fc
+# activated pre-commit for notebooks - https://github.com/pybamm-team/PyBaMM/pull/3110
+a63e49ece0f9336d1f5c2562f7459e555c6e6693
+# activated standard pre-commits - https://github.com/pybamm-team/PyBaMM/pull/3192
+5273214b585c5a4286609aed40e0b092d0e05f42

.github/ISSUE_TEMPLATE/new_parameter_set.yml

@@ -6,7 +6,7 @@ body:
       value: |
         Third-party parameter sets can be added to PyBaMM by registering an entry
         point with `pybamm-parameter-sets` as described in our
-        [documentation](https://pybamm.readthedocs.io/en/latest/source/api/parameters/parameter_sets.html).
+        [documentation](https://docs.pybamm.org/en/latest/source/api/parameters/parameter_sets.html).
   - type: input
     id: parameter-set-url
     attributes:

.github/PULL_REQUEST_TEMPLATE.md

@@ -14,11 +14,11 @@ Please add a line in the relevant section of [CHANGELOG.md](https://github.com/p
 
 # Key checklist:
 
-- [ ] No style issues: `$ pre-commit run` (see [CONTRIBUTING.md](https://github.com/pybamm-team/PyBaMM/blob/develop/CONTRIBUTING.md#installing-and-using-pre-commit) for how to set this up to run automatically when committing locally, in just two lines of code)
-- [ ] All tests pass: `$ python run-tests.py --all`
-- [ ] The documentation builds: `$ python run-tests.py --doctest`
+- [ ] No style issues: `$ pre-commit run` (or `$ nox -s pre-commit`) (see [CONTRIBUTING.md](https://github.com/pybamm-team/PyBaMM/blob/develop/CONTRIBUTING.md#installing-and-using-pre-commit) for how to set this up to run automatically when committing locally, in just two lines of code)
+- [ ] All tests pass: `$ python run-tests.py --all` (or `$ nox -s tests`)
+- [ ] The documentation builds: `$ python run-tests.py --doctest` (or `$ nox -s doctests`)
 
-You can run unit and doctests together at once, using `$ python run-tests.py --quick`.
+You can run integration tests, unit tests, and doctests together at once, using `$ python run-tests.py --quick` (or `$ nox -s quick`).
 
 ## Further checks:
 

.github/dependabot.yml

@@ -0,0 +1,7 @@
+version: 2
+updates:
+  # Maintain dependencies for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/release_reminder.md

@@ -0,0 +1,10 @@
+---
+title: Create {{ date | date('YY.MM') }} (final or rc0) release
+labels: priority:high
+---
+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](https://github.com/pybamm-team/PyBaMM/blob/develop/.github/release_workflow.md) for more information.

.github/release_workflow.md

@@ -0,0 +1,79 @@
+# 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 `vYY.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 `vYY.MM` and a PR from `vvYY.MM` to `develop` will be created (to sync the branches).
+
+2. Create a new GitHub _pre-release_ with the tag `vYY.MMrc0` from the `vYY.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 `vYY.MM` (no new features should be added to `vYY.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 `vYY.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 `vYY.MM` branch and a PR from `vvYY.MM` to `develop` will be created (to sync the branches).
+
+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`.
+
+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 `vYY.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 `vYY.MM` branch and a PR from `vvYY.MM` to `develop` will be created (to sync the branches).
+
+3. Next, a PR from `vYY.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
+- As the release workflow is initiated by the `release` event, it's important to note that the default `GITHUB_REF` used by `actions/checkout` during the checkout process will correspond to the tag created during the release process. Consequently, the workflows will consistently build PyBaMM based on the commit associated with this tag. Should new commits be introduced to the `vYY.MM` branch, such as those addressing build issues, it becomes necessary to manually update this tag to point to the most recent commit -
+  ```
+  git tag -f <tag_name> <commit_hash>
+  git push origin <tag_name>  # can only be carried out by the maintainers
+  ```

.github/wheel_failure.md

@@ -0,0 +1,6 @@
+---
+title: Fortnightly build for wheels failed
+labels: priority:high, bug
+---
+
+The build is failing with the following logs - {{ env.LOGS }}

.github/workflows/benchmark_on_push.yml

@@ -1,26 +1,37 @@
 name: Run benchmarks on push
 on:
   push:
+    branches: [main, develop]
   pull_request:
 
+concurrency:
+  # Cancel intermediate builds always
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 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:
           python-version: 3.8
+
       - name: Install Linux system dependencies
         run: |
           sudo apt-get update
           sudo apt install gfortran gcc libopenblas-dev
+
       - name: Install python dependencies
         run: |
-          python -m pip install --upgrade pip wheel setuptools virtualenv asv wget cmake casadi numpy
-      - name: Install SuiteSparse and Sundials
+          python -m pip install --upgrade pip wheel setuptools wget cmake casadi numpy
+          python -m pip install asv[virtualenv]
+
+      - name: Install SuiteSparse and SUNDIALS
         run: python scripts/install_KLU_Sundials.py
+
       - name: Fetch base branch
         run: |
           # This workflow also runs for merge commits
@@ -42,7 +53,8 @@ jobs:
           HEAD_COMMIT=$(git rev-parse HEAD)
           echo $BASE_COMMIT | tee commits_to_compare.txt
           echo $HEAD_COMMIT | tee -a commits_to_compare.txt
-          asv run HASHFILE:commits_to_compare.txt --m "GitHubRunner" --show-stderr --strict -v
+          asv run HASHFILE:commits_to_compare.txt --m "GitHubRunner" --show-stderr -v
+
       - name: Compare commits' benchmark results
         run: |
           BASE_COMMIT=$(head -1 commits_to_compare.txt)