Merge pull request #2905 from pybamm-team/develop

Make release v23.4

Author: brosaplanella

.github/workflows/benchmark_on_push.yml

@@ -38,7 +38,7 @@ jobs:
           HEAD_COMMIT=$(git rev-parse HEAD)
           echo $BASE_COMMIT | tee commits_to_compare.txt
           echo $HEAD_COMMIT | tee -a commits_to_compare.txt
-          asv run HASHFILE:commits_to_compare.txt --m "GitHubRunner" --show-stderr -v
+          asv run HASHFILE:commits_to_compare.txt --m "GitHubRunner" --show-stderr --strict -v
       - name: Compare commits' benchmark results
         run: |
           BASE_COMMIT=$(head -1 commits_to_compare.txt)

.github/workflows/need_reply_remove.yml

@@ -0,0 +1,24 @@
+name: Remove needs-reply label
+
+on:
+  issue_comment:
+    types:
+      - created
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    if: |
+      github.event.comment.author_association != 'OWNER' &&
+      github.event.comment.author_association != 'COLLABORATOR'
+    steps:
+      - name: Remove needs-reply label
+        uses: octokit/[email protected]
+        continue-on-error: true
+        with:
+          route: DELETE /repos/:repository/issues/:issue/labels/:label
+          repository: ${{ github.repository }}
+          issue: ${{ github.event.issue.number }}
+          label: needs-reply
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/needs_reply.yml

@@ -0,0 +1,15 @@
+name: Close old issues that need reply
+
+on:
+  schedule:
+    - cron: "0 0 * * *"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Close old issues that need reply
+        uses: dwieeb/needs-reply@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          issue-label: needs-reply

.github/workflows/periodic_benchmarks.yml

@@ -24,12 +24,22 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: 3.8
-      - name: Install tox and asv
-        run: pip install -U pip "tox<4" asv
+      - 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
+        run: python scripts/install_KLU_Sundials.py
       - name: Run benchmarks
         run: |
           asv machine --machine "GitHubRunner"
-          asv run --machine "GitHubRunner" NEW
+          asv run --machine "GitHubRunner" NEW --show-stderr --strict -v
+        env:
+          SUNDIALS_INST: $HOME/.local
+          LD_LIBRARY_PATH: $HOME/.local/lib
       - name: Upload results as artifact
         uses: actions/upload-artifact@v2
         with:

.github/workflows/test_on_push.yml

@@ -46,7 +46,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: [3.8, 3.9]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
 
     steps:
       - uses: actions/checkout@v3
@@ -89,7 +89,7 @@ jobs:
         if: matrix.os == 'ubuntu-latest'
         run: tox -e pybamm-requires
 
-      - name: Run unit tests for GNU/Linux with Python 3.8
+      - name: Run unit tests for GNU/Linux with Python 3.8, 3.10, and 3.11
         if: matrix.os == 'ubuntu-latest' && matrix.python-version != 3.9
         run: python -m tox -e unit
 

.pre-commit-config.yaml

@@ -4,12 +4,12 @@ ci:
 
 repos:
   - repo: https://github.com/psf/black
-    rev: 23.1.0
+    rev: 23.3.0
     hooks:
       - id: black
 
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: "v0.0.259"
+    rev: "v0.0.262"
     hooks:
       - id: ruff
         args: [--ignore=E741, --exclude=__init__.py]

CHANGELOG.md

@@ -1,5 +1,28 @@
 # [Unreleased](https://github.com/pybamm-team/PyBaMM/)
 
+# [v23.4](https://github.com/pybamm-team/PyBaMM/tree/v23.4) - 2023-04-30
+
+# Features
+
+- Added verbose logging to `pybamm.print_citations()` and citation tags for the `pybamm.Citations` class so that users can now see where the citations were registered when running simulations ([#2862](https://github.com/pybamm-team/PyBaMM/pull/2862))
+- PyBaMM is now natively supported on Apple silicon chips (`M1/M2`) ([#2435](https://github.com/pybamm-team/PyBaMM/pull/2435))
+- PyBaMM is now supported on Python `3.10` and `3.11` ([#2435](https://github.com/pybamm-team/PyBaMM/pull/2435))
+- Updated to casadi 3.6, which required some changes to the casadi integrator. ([#2859](https://github.com/pybamm-team/PyBaMM/pull/2859))
+
+# Optimizations
+
+- Fixed deprecated `interp2d` method by switching to `xarray.DataArray` as the backend for `ProcessedVariable` ([#2907](https://github.com/pybamm-team/PyBaMM/pull/2907))
+
+## Bug fixes
+
+- Parameter sets can now contain the key "chemistry", and will ignore its value (this previously would give errors in some cases) ([#2901](https://github.com/pybamm-team/PyBaMM/pull/2901))
+- Fixed a bug in the discretisation of initial conditions of a scaled variable ([#2856](https://github.com/pybamm-team/PyBaMM/pull/2856))
+- Fixed keyerror on "all" when getting sensitivities from IDAKLU solver([#2883](https://github.com/pybamm-team/PyBaMM/pull/2883))
+
+# Breaking changes
+
+- Made `Jupyter` a development only dependency. Now `Jupyter` would not be a required dependency for users while installing `PyBaMM`. ([#2846](https://github.com/pybamm-team/PyBaMM/pull/2846))
+
 # [v23.3](https://github.com/pybamm-team/PyBaMM/tree/v23.3) - 2023-03-31
 
 ## Features
@@ -14,12 +37,13 @@
 
 ## Bug fixes
 
+- Fix non-deteministic outcome of some tests in the test suite ([#2844](https://github.com/pybamm-team/PyBaMM/pull/2844))
 - Fixed excessive RAM consumption when running multiple simulations ([#2823](https://github.com/pybamm-team/PyBaMM/pull/2823))
+- Fixed use of last_state as starting_solution in Simulation.solve() ([#2822](https://github.com/pybamm-team/PyBaMM/pull/2822))
 - Fixed a bug where variable bounds could not contain `InputParameters` ([#2795](https://github.com/pybamm-team/PyBaMM/pull/2795))
 - Improved `model.latexify()` to have a cleaner and more readable output ([#2764](https://github.com/pybamm-team/PyBaMM/pull/2764))
 - Fixed electrolyte conservation in the case of concentration-dependent transference number ([#2758](https://github.com/pybamm-team/PyBaMM/pull/2758))
 - Fixed `plot_voltage_components` so that the sum of overpotentials is now equal to the voltage ([#2740](https://github.com/pybamm-team/PyBaMM/pull/2740))
-- Fixed use of last_state as starting_solution in Simulation.solve() ([#2822](https://github.com/pybamm-team/PyBaMM/pull/2822))
 
 ## Optimizations
 

CITATION.cff

@@ -24,6 +24,6 @@ keywords:
   - "expression tree"
   - "python"
   - "symbolic differentiation"
-version: "23.3"
+version: "23.4"
 repository-code: "https://github.com/pybamm-team/PyBaMM"
 title: "Python Battery Mathematical Modelling (PyBaMM)"

README.md

@@ -229,7 +229,7 @@ Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/d
     <tr>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/chuckliu1979"><img src="https://avatars.githubusercontent.com/u/13491954?v=4?s=100" width="100px;" alt="Chuck Liu"/><br /><sub><b>Chuck Liu</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3Achuckliu1979" title="Bug reports">🐛</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=chuckliu1979" title="Code">💻</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/partben"><img src="https://avatars.githubusercontent.com/u/88316576?v=4?s=100" width="100px;" alt="partben"/><br /><sub><b>partben</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=partben" title="Documentation">📖</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://gavinw.me"><img src="https://avatars.githubusercontent.com/u/6828967?v=4?s=100" width="100px;" alt="Gavin Wiggins"/><br /><sub><b>Gavin Wiggins</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3Awigging" title="Bug reports">🐛</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=wigging" title="Code">💻</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://wigging.me"><img src="https://avatars.githubusercontent.com/u/6828967?v=4?s=100" width="100px;" alt="Gavin Wiggins"/><br /><sub><b>Gavin Wiggins</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3Awigging" title="Bug reports">🐛</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=wigging" title="Code">💻</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/dion-w"><img src="https://avatars.githubusercontent.com/u/91852142?v=4?s=100" width="100px;" alt="Dion Wilde"/><br /><sub><b>Dion Wilde</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3Adion-w" title="Bug reports">🐛</a> <a href="https://github.com/pybamm-team/PyBaMM/commits?author=dion-w" title="Code">💻</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://www.ehtec.co"><img src="https://avatars.githubusercontent.com/u/48386220?v=4?s=100" width="100px;" alt="Elias Hohl"/><br /><sub><b>Elias Hohl</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/commits?author=ehtec" title="Code">💻</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/KAschad"><img src="https://avatars.githubusercontent.com/u/93784399?v=4?s=100" width="100px;" alt="KAschad"/><br /><sub><b>KAschad</b></sub></a><br /><a href="https://github.com/pybamm-team/PyBaMM/issues?q=author%3AKAschad" title="Bug reports">🐛</a></td>

asv.conf.json

@@ -24,6 +24,7 @@
   // "install_command": ["in-dir={env_dir} python -mpip install {wheel_file}"],
   // "uninstall_command": ["return-code=any python -mpip uninstall -y {project}"],
   "build_command": [
+    "/bin/rm -rf pybind11",
     "/usr/bin/git clone --depth 1 --branch v2.6.2 https://github.com/pybind/pybind11.git",
     "python setup.py build",
     "PIP_NO_BUILD_ISOLATION=false python -mpip wheel --no-deps --no-index -w {build_cache_dir} {build_dir}"