Merge branch 'develop' into bump-jax-jaxlib-versions

Author: agriyakhetarpal

.all-contributorsrc

@@ -727,6 +727,34 @@
         "code",
         "test"
       ]
+    },
+    {
+      "login": "chmabaur",
+      "name": "chmabaur",
+      "avatar_url": "https://avatars.githubusercontent.com/u/127507466?v=4",
+      "profile": "https://github.com/chmabaur",
+      "contributions": [
+        "bug",
+        "code"
+      ]
+    },
+    {
+      "login": "AbhishekChaudharii",
+      "name": "Abhishek Chaudhari",
+      "avatar_url": "https://avatars.githubusercontent.com/u/91185083?v=4",
+      "profile": "https://github.com/AbhishekChaudharii",
+      "contributions": [
+        "doc"
+      ]
+    },
+    {
+      "login": "shubhambhar007",
+      "name": "Shubham Bhardwaj",
+      "avatar_url": "https://avatars.githubusercontent.com/u/32607282?v=4",
+      "profile": "https://github.com/shubhambhar007",
+      "contributions": [
+        "infra"
+      ]
     }
   ],
   "contributorsPerLine": 7,

.coveragerc

@@ -4,3 +4,5 @@
 a63e49ece0f9336d1f5c2562f7459e555c6e6693
 # activated standard pre-commits - https://github.com/pybamm-team/PyBaMM/pull/3192
 5273214b585c5a4286609aed40e0b092d0e05f42
+# migrate config to pyproject.toml - https://github.com/pybamm-team/PyBaMM/pull/3557
+12c5d77203bd93542785d237bac00bad5ed5469a

.git-blame-ignore-revs

@@ -11,7 +11,6 @@ This file contains the workflow required to make a `PyBaMM` release on GitHub, P
    - `CITATION.cff`
    - `pyproject.toml`
    - `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).
@@ -35,7 +34,6 @@ If a new release candidate is required after the release of `rc0` -
    - `CITATION.cff`
    - `pyproject.toml`
    - `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).
@@ -57,7 +55,6 @@ Once satisfied with the release candidates -
    - `CITATION.cff`
    - `pyproject.toml`
    - `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).
@@ -74,7 +71,6 @@ 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 `pyproject.toml`, 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>

.github/release_workflow.md

@@ -36,6 +36,7 @@ jobs:
       - name: Check style
         run: |
           python -m pip install pre-commit
+          git add .
           pre-commit run ruff
 
   build:

.github/workflows/run_periodic_tests.yml

@@ -28,6 +28,7 @@ jobs:
       - name: Check style
         run: |
           python -m pip install pre-commit
+          git add .
           pre-commit run ruff
 
   run_unit_tests:

.github/workflows/test_on_push.yml

@@ -138,6 +138,7 @@ results/
 # do not ignore images in _static folder in docs
 !docs/_static/favicon/favicon.png
 !docs/_static/pybamm_logo.png
+!docs/_static/pybamm_logo_whitetext.png
 
 # tests
 test_callback.log

.gitignore

@@ -1,7 +1,15 @@
 # [Unreleased](https://github.com/pybamm-team/PyBaMM/)
 
+## Features
+
+- Added a new unary operator, `EvaluateAt`, that evaluates a spatial variable at a given position ([#3573](https://github.com/pybamm-team/PyBaMM/pull/3573))
+- Added a method, `insert_reference_electrode`, to `pybamm.lithium_ion.BaseModel` that insert a reference electrode to measure the electrolyte potential at a given position in space and adds new variables that mimic a 3E cell setup. ([#3573](https://github.com/pybamm-team/PyBaMM/pull/3573))
+- Serialisation added so models can be written to/read from JSON ([#3397](https://github.com/pybamm-team/PyBaMM/pull/3397))
+- Mechanical parameters are now a function of stoichiometry and temperature ([#3576](https://github.com/pybamm-team/PyBaMM/pull/3576))
+
 ## Bug fixes
 
+- Fixed a bug where simulations using the CasADi-based solvers would fail randomly with the half-cell model ([#3494](https://github.com/pybamm-team/PyBaMM/pull/3494))
 - Fixed bug that made identical Experiment steps with different end times crash ([#3516](https://github.com/pybamm-team/PyBaMM/pull/3516))
 - Fixed bug in calculation of theoretical energy that made it very slow ([#3506](https://github.com/pybamm-team/PyBaMM/pull/3506))
 - The irreversible plating model now increments `f"{Domain} dead lithium concentration [mol.m-3]"`, not `f"{Domain} lithium plating concentration [mol.m-3]"` as it did previously. ([#3485](https://github.com/pybamm-team/PyBaMM/pull/3485))

CHANGELOG.md

@@ -2,6 +2,6 @@ graft pybamm
 include CITATION.cff
 prune tests
 
-exclude CHANGELOG.md CODE-OF-CONDUCT.md CONTRIBUTING.md GOVERNANCE.md CMakeLists.txt
+exclude CHANGELOG.md CODE-OF-CONDUCT.md CONTRIBUTING.md CMakeLists.txt
 
 global-exclude __pycache__ *.py[cod] .venv