Merge branch 'develop' of github.com:kratman/PyBaMM into feat/removeIDAKLU

Author: kratman

.github/workflows/scorecard.yml

@@ -68,6 +68,6 @@ jobs:
       # Upload the results to GitHub's code scanning dashboard (optional).
       # Commenting out will disable upload of results to your repo's Code Scanning dashboard
       - name: "Upload to code-scanning"
-        uses: github/codeql-action/upload-sarif@f779452ac5af1c261dce0346a8f964149f49322b # v3.26.13
+        uses: github/codeql-action/upload-sarif@662472033e021d55d94146f66f6058822b0b39fd # v3.27.0
         with:
           sarif_file: results.sarif

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.6.9"
+    rev: "v0.7.2"
     hooks:
       - id: ruff
         args: [--fix, --show-fixes]
@@ -13,7 +13,7 @@ repos:
         types_or: [python, pyi, jupyter]
 
   - repo: https://github.com/adamchainz/blacken-docs
-    rev: "1.19.0"
+    rev: "1.19.1"
     hooks:
        - id: blacken-docs
          additional_dependencies: [black==23.*]

CHANGELOG.md

@@ -2,6 +2,7 @@
 
 ## Features
 
+- Adds support to `pybamm.Experiment` for the `output_variables` option in the `IDAKLUSolver`. ([#4534](https://github.com/pybamm-team/PyBaMM/pull/4534))
 - Adds an option "voltage as a state" that can be "false" (default) or "true". If "true" adds an explicit algebraic equation for the voltage. ([#4507](https://github.com/pybamm-team/PyBaMM/pull/4507))
 - Improved `QuickPlot` accuracy for simulations with Hermite interpolation. ([#4483](https://github.com/pybamm-team/PyBaMM/pull/4483))
 - Added Hermite interpolation to the (`IDAKLUSolver`) that improves the accuracy and performance of post-processing variables. ([#4464](https://github.com/pybamm-team/PyBaMM/pull/4464))
@@ -20,7 +21,7 @@
 - Removed the `start_step_offset` setting and disabled minimum `dt` warnings for drive cycles with the (`IDAKLUSolver`). ([#4416](https://github.com/pybamm-team/PyBaMM/pull/4416))
 
 ## Bug Fixes
-
+- Fixed bug in post-processing solutions with infeasible experiments using the (`IDAKLUSolver`). ([#4541](https://github.com/pybamm-team/PyBaMM/pull/4541))
 - Disabled IREE on MacOS due to compatibility issues and added the CasADI
   path to the environment to resolve issues on MacOS and Linux. Windows
   users may still experience issues with interpolation. ([#4528](https://github.com/pybamm-team/PyBaMM/pull/4528))

CONTRIBUTING.md

@@ -44,7 +44,7 @@ You now have everything you need to start making changes!
 
 ### B. Writing your code
 
-6. PyBaMM is developed in [Python](https://www.python.org)), and makes heavy use of [NumPy](https://numpy.org/) (see also [NumPy for MatLab users](https://numpy.org/doc/stable/user/numpy-for-matlab-users.html) and [Python for R users](https://www.rebeccabarter.com/blog/2023-09-11-from_r_to_python)).
+6. PyBaMM is developed in [Python](https://www.python.org), and makes heavy use of [NumPy](https://numpy.org/).
 7. Make sure to follow our [coding style guidelines](#coding-style-guidelines).
 8. Commit your changes to your branch with [useful, descriptive commit messages](https://chris.beams.io/posts/git-commit/): Remember these are
    publicly visible and should still make sense a few months ahead in time.
@@ -116,8 +116,8 @@ PyBaMM provides a utility function `import_optional_dependency`, to check for th
 
 Optional dependencies should never be imported at the module level, but always inside methods. For example:
 
-```
-def use_pybtex(x,y,z):
+```python
+def use_pybtex(x, y, z):
     pybtex = import_optional_dependency("pybtex")
     ...
 ```

docs/source/api/index.rst

@@ -9,10 +9,10 @@ API documentation
 :Release: |version|
 :Date: |today|
 
-This reference manual details functions, modules, and objects
-included in PyBaMM, describing what they are and what they do.
+This reference manual details the classes, functions, modules, and objects included in PyBaMM, describing what they are and what they do.
 For a high-level introduction to PyBaMM, see the :ref:`user guide <user_guide>` and the :ref:`examples <pybamm_examples>`.
 
+
 .. toctree::
    :maxdepth: 2
 

docs/source/api/util.rst

@@ -19,3 +19,5 @@ Utility functions
 .. autofunction:: pybamm.has_jax
 
 .. autofunction:: pybamm.is_jax_compatible
+
+.. autofunction:: pybamm.set_logging_level

docs/source/examples/index.rst

@@ -87,6 +87,7 @@ The notebooks are organised into subfolders, and can be viewed in the galleries
     notebooks/parameterization/change-input-current.ipynb
     notebooks/parameterization/parameter-values.ipynb
     notebooks/parameterization/parameterization.ipynb
+    notebooks/parameterization/sensitivities_and_data_fitting.ipynb
 
 .. nbgallery::
     :caption: Simulations and Experiments