Merge branch 'pybamm-team:develop' into scheduled-scripts-fix

.all-contributorsrc

@@ -692,7 +692,8 @@
       "profile": "https://github.com/kratman",
       "contributions": [
         "doc",
-        "infra"
+        "infra",
+        "bug"
       ]
     }
   ],

.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/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/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: "v0.0.288"
+    rev: "v0.0.290"
     hooks:
       - id: ruff
         args: [--fix, --ignore=E741, --exclude=__init__.py]

CHANGELOG.md

@@ -11,6 +11,7 @@
 - Fixed a bug that caused incorrect results of “{Domain} electrode thickness change [m]” due to the absence of dimension for the variable `electrode_thickness_change`([#3329](https://github.com/pybamm-team/PyBaMM/pull/3329)).
 - Fixed a bug that occured in `check_ys_are_not_too_large` when trying to reference `y-slice` where the referenced variable was not a `pybamm.StateVector` ([#3313](https://github.com/pybamm-team/PyBaMM/pull/3313)
 - Fixed a bug with `_Heaviside._evaluate_for_shape` which meant some expressions involving heaviside function and subtractions did not work ([#3306](https://github.com/pybamm-team/PyBaMM/pull/3306))
+- Fixed bug causing incorrect activation energies using `create_from_bpx()` ([#3242](https://github.com/pybamm-team/PyBaMM/pull/3242))
 - The `OneDimensionalX` thermal model has been updated to account for edge/tab cooling and account for the current collector volumetric heat capacity. It now gives the correct behaviour compared with a lumped model with the correct total heat transfer coefficient and surface area for cooling. ([#3042](https://github.com/pybamm-team/PyBaMM/pull/3042))
 - Fixed a bug where the "basic" lithium-ion models gave incorrect results when using nonlinear particle diffusivity ([#3207](https://github.com/pybamm-team/PyBaMM/pull/3207))
 - Particle size distributions now work with SPMe and NewmanTobias models ([#3207](https://github.com/pybamm-team/PyBaMM/pull/3207))
@@ -22,12 +23,15 @@
 - Error generated when invalid parameter values are passed ([#3132](https://github.com/pybamm-team/PyBaMM/pull/3132))
 - Parameters in `Prada2013` have been updated to better match those given in the paper, which is a 2.3 Ah cell, instead of the mix-and-match with the 1.1 Ah cell from Lain2019 ([#3096](https://github.com/pybamm-team/PyBaMM/pull/3096))
 
+## Optimizations
 
+- Improved how steps are processed in simulations to reduce memory usage ([#3261](https://github.com/pybamm-team/PyBaMM/pull/3261))
 
 ## Breaking changes
 
 - The class `pybamm.thermal.OneDimensionalX` has been moved to `pybamm.thermal.pouch_cell.OneDimensionalX` to reflect the fact that the model formulation implicitly assumes a pouch cell geometry ([#3257](https://github.com/pybamm-team/PyBaMM/pull/3257))
 - The "lumped" thermal option now always used the parameters "Cell cooling surface area [m2]", "Cell volume [m3]" and "Total heat transfer coefficient [W.m-2.K-1]" to compute the cell cooling regardless of the chosen "cell geometry" option. The user must now specify the correct values for these parameters instead of them being calculated based on e.g. a pouch cell. An `OptionWarning` is raised to let users know to update their parameters ([#3257](https://github.com/pybamm-team/PyBaMM/pull/3257))
+- Numpy functions now work with PyBaMM symbols (e.g. `np.exp(pybamm.Symbol("a"))` returns `pybamm.Exp(pybamm.Symbol("a"))`). This means that parameter functions can be specified using numpy functions instead of pybamm functions. Additionally, combining numpy arrays with pybamm objects now works (the numpy array is converted to a pybamm array) ([#3205](https://github.com/pybamm-team/PyBaMM/pull/3205))
 - Added option to use an empirical hysteresis model for the diffusivity and exchange-current density ([#3194](https://github.com/pybamm-team/PyBaMM/pull/3194))
 - Double-layer capacity can now be provided as a function of temperature ([#3174](https://github.com/pybamm-team/PyBaMM/pull/3174))
 - `pybamm_install_jax` is deprecated. It is now replaced with `pip install pybamm[jax]` ([#3163](https://github.com/pybamm-team/PyBaMM/pull/3163))

README.md

@@ -14,7 +14,7 @@
 [![code style](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/charliermarsh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 
 <!-- ALL-CONTRIBUTORS-BADGE:START - Do not remove or modify this section -->
-[![All Contributors](https://img.shields.io/badge/all_contributors-62-orange.svg)](#-contributors)
+[![All Contributors](https://img.shields.io/badge/all_contributors-63-orange.svg)](#-contributors)
 <!-- ALL-CONTRIBUTORS-BADGE:END -->
 
 </div>
@@ -264,7 +264,7 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/tommaull"><img src="https://avatars.githubusercontent.com/u/101814207?v=4?s=100" width="100px;" alt="Tom Maull"/><br /><sub><b>Tom Maull</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=tommaull" title="Code">💻</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=tommaull" title="Tests">⚠️</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/ejfdickinson"><img src="https://avatars.githubusercontent.com/u/116663050?v=4?s=100" width="100px;" alt="ejfdickinson"/><br /><sub><b>ejfdickinson</b></sub></a><br /><a href="#ideas-ejfdickinson" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3Aejfdickinson" title="Bug reports">🐛</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/bobonice"><img src="https://avatars.githubusercontent.com/u/22030806?v=4?s=100" width="100px;" alt="bobonice"/><br /><sub><b>bobonice</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3Abobonice" title="Bug reports">🐛</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=bobonice" title="Code">💻</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/kratman"><img src="https://avatars.githubusercontent.com/u/10170302?v=4?s=100" width="100px;" alt="Eric G. Kratz"/><br /><sub><b>Eric G. Kratz</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=kratman" title="Documentation">📖</a> <a href="#infra-kratman" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/kratman"><img src="https://avatars.githubusercontent.com/u/10170302?v=4?s=100" width="100px;" alt="Eric G. Kratz"/><br /><sub><b>Eric G. Kratz</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=kratman" title="Documentation">📖</a> <a href="#infra-kratman" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3Akratman" title="Bug reports">🐛</a></td>
     </tr>
   </tbody>
 </table>