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Bugfix uv in benchmark CI#5288

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martinjrobins merged 1 commit intopybamm-team:developfrom
pipliggins:ci-benchmarks
Nov 20, 2025
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Bugfix uv in benchmark CI#5288
martinjrobins merged 1 commit intopybamm-team:developfrom
pipliggins:ci-benchmarks

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@pipliggins pipliggins commented Nov 20, 2025 •
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Fixes #5287

@pipliggins pipliggins requested a review from a team as a code owner November 20, 2025 14:56
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codecov Bot commented Nov 20, 2025 •
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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 98.77%. Comparing base (af64ddd) to head (9efb965).

Additional details and impacted files 
@@           Coverage Diff            @@
##           develop    #5288   +/-   ##
========================================
  Coverage    98.77%   98.77%           
========================================
  Files          321      321           
  Lines        27727    27727           
========================================
  Hits         27387    27387           
  Misses         340      340

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martinjrobins
martinjrobins approved these changes Nov 20, 2025
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thanks @pipliggins

@martinjrobins martinjrobins merged commit 385ae7b into pybamm-team:develop Nov 20, 2025
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BradyPlanden pushed a commit that referenced this pull request Dec 8, 2025
@pipliggins @BradyPlanden
fix: instruct uv to install into system for CI (#5288)
65f3326
rtimms added a commit that referenced this pull request Dec 16, 2025
@rtimms @agriyakhetarpal
@swastim01 @valentinsulzer @cnaples79 @gregordecristoforo @pipliggins @MarcBerliner @BradyPlanden @pre-commit-ci
#5299 add inverse linear kinetics (#5303)
a0b2614 
* Don't be too strict with func_args longer than symbol.children

* Add a test

* Add support for uniform grid sizing across subdomains (#720) (#5253)

Co-authored-by: Valentin Sulzer <valentinsulzer@hotmail.com>

* Fix typo in Butler-Volmer equation docstring (#5279)

* fix bug with bulk ocp lithiation (#5280)

* doc: fix typo in concentration description in notebook (#5284)

* Fix typo in concentration description in notebook

* Add CHANGELOG.md entry for typo fix

* Remove unneccesary changelog entry

Co-authored-by: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>

---------

Co-authored-by: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>

* fix: instruct uv to install into system for CI (#5288)

* Fix `InputParameter` serialisation (#5289)

* fix `InputParameter` serialisation

* Update CHANGELOG.md

* Bugfix: inputs for `initial_conditions_from` scale evaluation (#5285)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Add `silence_sundials_errors` solver option (#5290)

* feat: add`silence_sundial_warnings` solver option

* refactor: `silence_sundials_warnings` -> `silence_sundials_errors`

* Update C-Rate current for changing nominal capacity (#5286)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Update `IDAKLUSolver` error handling (#5291)

* raise `SolverError` at failure to init sundials

* Update simulation.py

* Update idaklu_solver.py

* reuse `pybammsolvers` error messages

* Update test_idaklu_solver.py

* bump `pybammsolvers`

* Update CHANGELOG.md

* Update CHANGELOG.md

Update CHANGELOG.md

* #5299 add inverse linear kinetics

* #5299 check domain options for inverse kinetics

* update notebook

* #5299 brady comments

* #5299 fix composite total kinetics

---------

Co-authored-by: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Co-authored-by: Swasti Mishra <140950062+swastim01@users.noreply.github.com>
Co-authored-by: Valentin Sulzer <valentinsulzer@hotmail.com>
Co-authored-by: Chase Naples <cnaples79@gmail.com>
Co-authored-by: Gregor Decristoforo <gregor.decristoforo@gmail.com>
Co-authored-by: Pip Liggins <philippa.liggins@dtc.ox.ac.uk>
Co-authored-by: Marc Berliner <34451391+MarcBerliner@users.noreply.github.com>
Co-authored-by: Brady Planden <55357039+BradyPlanden@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
MarcBerliner added a commit that referenced this pull request Dec 17, 2025
@MarcBerliner @agriyakhetarpal
@swastim01 @valentinsulzer @cnaples79 @rtimms @gregordecristoforo @pipliggins @BradyPlanden @pre-commit-ci
Observe custom variables after solving + faster simulation build time (…
6ff7848 
…#5308)

* Don't be too strict with func_args longer than symbol.children

* Add a test

* Add support for uniform grid sizing across subdomains (#720) (#5253)

Co-authored-by: Valentin Sulzer <valentinsulzer@hotmail.com>

* Fix typo in Butler-Volmer equation docstring (#5279)

* fix bug with bulk ocp lithiation (#5280)

* doc: fix typo in concentration description in notebook (#5284)

* Fix typo in concentration description in notebook

* Add CHANGELOG.md entry for typo fix

* Remove unneccesary changelog entry

Co-authored-by: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>

---------

Co-authored-by: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>

* fix: instruct uv to install into system for CI (#5288)

* Fix `InputParameter` serialisation (#5289)

* fix `InputParameter` serialisation

* Update CHANGELOG.md

* Bugfix: inputs for `initial_conditions_from` scale evaluation (#5285)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Add `silence_sundials_errors` solver option (#5290)

* feat: add`silence_sundial_warnings` solver option

* refactor: `silence_sundials_warnings` -> `silence_sundials_errors`

* Update C-Rate current for changing nominal capacity (#5286)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Update `IDAKLUSolver` error handling (#5291)

* raise `SolverError` at failure to init sundials

* Update simulation.py

* Update idaklu_solver.py

* reuse `pybammsolvers` error messages

* Update test_idaklu_solver.py

* bump `pybammsolvers`

* Update CHANGELOG.md

* Update CHANGELOG.md

Update CHANGELOG.md

* revive `SymbolReplacer`

* add `VariableReplacementMap`

* Create replace_symbols.rst

* Update index.rst

* cleanup

* attach `parameter_values` to model for lazy post-processing

* update `model.parameter_values` serialization

* Update test_serialisation.py

* Update test_parameter_values.py

* add `observe` to solution for lazy evaluation of discretized symbols

* Update test_solution.py

* style

* Update CHANGELOG.md

* fix docstrings

* docs

* docs2

* Update replace_symbols.py

* Update replace_symbols.py

* remove `SymbolReplacer`

* add slots to `SpatialMethod` for memory

* add `SymbolProcessor` for `BaseModel` symbol eval

* add `ModelSolutionObservability` enums for `BaseModel`

* parameter_values: delay variable processing

* fix stale symbol id: use `scale` and `reference` setters

* discretisation delayed var processing, don't overwrite `model.variables`

* pass `delayed_variable_processing` args through `process_model`

* add `DUMMY_INPUT_PARAMETER_VALUE` const

* Update __init__.py

* Update index.rst

* Delete replace_symbols.py

* update symbol `scale` and `reference` setters

* update variable hash

* explicit `_variables_processed` base model attribute

* use `get_processed_variable_or_event` getter

* copy model in `Simulation`

* disable observability with `output_variables`

* delay variable processing in `Simulation` build

* add `Solution.observe(symbol)`

* update serialization

* update examples

* Update CONTRIBUTING.md

* Update CHANGELOG.md

* add observe tests

* update serialization tests

* Update test_base_model.py

* update symbol processor getters

* add model observability tests

* update symbol and base variable id setters

* Update symbol_processor.py

* Update CHANGELOG.md

* fix model serialization notebook

* Update symbol_processor.py

* remove unused serialisation methods

* remove debug statement

* update observe test comments

* add observe test failure for new parameters

* remove `_solution_observable` from custom model serialization

* fix observe test error

* set `DUMMY_INPUT_PARAMETER_VALUE = np.nan` to make errors more obvious

---------

Co-authored-by: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Co-authored-by: Swasti Mishra <140950062+swastim01@users.noreply.github.com>
Co-authored-by: Valentin Sulzer <valentinsulzer@hotmail.com>
Co-authored-by: Chase Naples <cnaples79@gmail.com>
Co-authored-by: Robert Timms <43040151+rtimms@users.noreply.github.com>
Co-authored-by: Gregor Decristoforo <gregor.decristoforo@gmail.com>
Co-authored-by: Pip Liggins <philippa.liggins@dtc.ox.ac.uk>
Co-authored-by: Brady Planden <55357039+BradyPlanden@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
martinjrobins added a commit that referenced this pull request Jan 31, 2026
@pipliggins @agriyakhetarpal
@swastim01 @valentinsulzer @cnaples79 @rtimms @gregordecristoforo @MarcBerliner @BradyPlanden @pre-commit-ci @martinjrobins
feat: Add informative error message to simulation (#5226)
c9121be 
* Add error

* Add test

* Add to changelog, edit message

* Don't be too strict with func_args longer than symbol.children

* Add a test

* Add support for uniform grid sizing across subdomains (#720) (#5253)

Co-authored-by: Valentin Sulzer <valentinsulzer@hotmail.com>

* Fix typo in Butler-Volmer equation docstring (#5279)

* fix bug with bulk ocp lithiation (#5280)

* doc: fix typo in concentration description in notebook (#5284)

* Fix typo in concentration description in notebook

* Add CHANGELOG.md entry for typo fix

* Remove unneccesary changelog entry

Co-authored-by: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>

---------

Co-authored-by: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>

* fix: instruct uv to install into system for CI (#5288)

* Fix `InputParameter` serialisation (#5289)

* fix `InputParameter` serialisation

* Update CHANGELOG.md

* Bugfix: inputs for `initial_conditions_from` scale evaluation (#5285)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

---------

Co-authored-by: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Co-authored-by: Swasti Mishra <140950062+swastim01@users.noreply.github.com>
Co-authored-by: Valentin Sulzer <valentinsulzer@hotmail.com>
Co-authored-by: Chase Naples <cnaples79@gmail.com>
Co-authored-by: Robert Timms <43040151+rtimms@users.noreply.github.com>
Co-authored-by: Gregor Decristoforo <gregor.decristoforo@gmail.com>
Co-authored-by: Marc Berliner <34451391+MarcBerliner@users.noreply.github.com>
Co-authored-by: Brady Planden <55357039+BradyPlanden@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Martin Robinson <martinjrobins@gmail.com>
AlessioBugetti pushed a commit to AlessioBugetti/PyBaMM that referenced this pull request Feb 2, 2026
@pipliggins @agriyakhetarpal
@swastim01 @valentinsulzer @cnaples79 @rtimms @gregordecristoforo @MarcBerliner @BradyPlanden @pre-commit-ci @martinjrobins @AlessioBugetti
feat: Add informative error message to simulation (pybamm-team#5226)
c686623 
* Add error

* Add test

* Add to changelog, edit message

* Don't be too strict with func_args longer than symbol.children

* Add a test

* Add support for uniform grid sizing across subdomains (pybamm-team#720) (pybamm-team#5253)

Co-authored-by: Valentin Sulzer <valentinsulzer@hotmail.com>

* Fix typo in Butler-Volmer equation docstring (pybamm-team#5279)

* fix bug with bulk ocp lithiation (pybamm-team#5280)

* doc: fix typo in concentration description in notebook (pybamm-team#5284)

* Fix typo in concentration description in notebook

* Add CHANGELOG.md entry for typo fix

* Remove unneccesary changelog entry

Co-authored-by: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>

---------

Co-authored-by: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>

* fix: instruct uv to install into system for CI (pybamm-team#5288)

* Fix `InputParameter` serialisation (pybamm-team#5289)

* fix `InputParameter` serialisation

* Update CHANGELOG.md

* Bugfix: inputs for `initial_conditions_from` scale evaluation (pybamm-team#5285)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

---------

Co-authored-by: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Co-authored-by: Swasti Mishra <140950062+swastim01@users.noreply.github.com>
Co-authored-by: Valentin Sulzer <valentinsulzer@hotmail.com>
Co-authored-by: Chase Naples <cnaples79@gmail.com>
Co-authored-by: Robert Timms <43040151+rtimms@users.noreply.github.com>
Co-authored-by: Gregor Decristoforo <gregor.decristoforo@gmail.com>
Co-authored-by: Marc Berliner <34451391+MarcBerliner@users.noreply.github.com>
Co-authored-by: Brady Planden <55357039+BradyPlanden@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Martin Robinson <martinjrobins@gmail.com>
martinjrobins added a commit that referenced this pull request Mar 7, 2026
@martinjrobins @agriyakhetarpal
@swastim01 @valentinsulzer @cnaples79 @rtimms @gregordecristoforo @pipliggins @MarcBerliner @BradyPlanden @pre-commit-ci
feat: add DiffSL export functionality (#5370)
11cba76 
* Don't be too strict with func_args longer than symbol.children

* Add a test

* Add support for uniform grid sizing across subdomains (#720) (#5253)

Co-authored-by: Valentin Sulzer <valentinsulzer@hotmail.com>

* Fix typo in Butler-Volmer equation docstring (#5279)

* fix bug with bulk ocp lithiation (#5280)

* doc: fix typo in concentration description in notebook (#5284)

* Fix typo in concentration description in notebook

* Add CHANGELOG.md entry for typo fix

* Remove unneccesary changelog entry

Co-authored-by: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>

---------

Co-authored-by: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>

* fix: instruct uv to install into system for CI (#5288)

* Fix `InputParameter` serialisation (#5289)

* fix `InputParameter` serialisation

* Update CHANGELOG.md

* Bugfix: inputs for `initial_conditions_from` scale evaluation (#5285)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Add `silence_sundials_errors` solver option (#5290)

* feat: add`silence_sundial_warnings` solver option

* refactor: `silence_sundials_warnings` -> `silence_sundials_errors`

* Update C-Rate current for changing nominal capacity (#5286)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Update `IDAKLUSolver` error handling (#5291)

* raise `SolverError` at failure to init sundials

* Update simulation.py

* Update idaklu_solver.py

* reuse `pybammsolvers` error messages

* Update test_idaklu_solver.py

* bump `pybammsolvers`

* Update CHANGELOG.md

* Update CHANGELOG.md

Update CHANGELOG.md

* implement heat equation export

* Move DiffslExport to evaluate_python.py

Co-authored-by: martinjrobins <martinjrobins@gmail.com>

* add tests for DiffSLExport

* rename DiffslExport to DiffSLExport

* consider both options for heat flux output

* move diffsl code to new file

* add spm, spme and dfn tests, apply fixes for these

* can export dfn and spme, but output is incorrect

* new input syntax

* move model export to integration, tidy up float formattting

* update changelog

* update to new delayed variable pipeline

* minor fixes, remove dead code

* turn off pydiffsol dep for mac intel

* don't use inplace for integration tests

* improve coverage

* fix: reg functions

* doc: minor comment to explain function fallback

* refactor: eqn -> eqn_str

* refactor: use ordered dict, remove unnecessary code

* test: remove diffsl integration tests

* test: add snapshot tests for unit diffsl export tests

* test: reg_power and arcsinh2

* dep: remove pydiffsol

---------

Co-authored-by: Agriya Khetarpal <74401230+agriyakhetarpal@users.noreply.github.com>
Co-authored-by: Swasti Mishra <140950062+swastim01@users.noreply.github.com>
Co-authored-by: Valentin Sulzer <valentinsulzer@hotmail.com>
Co-authored-by: Chase Naples <cnaples79@gmail.com>
Co-authored-by: Robert Timms <43040151+rtimms@users.noreply.github.com>
Co-authored-by: Gregor Decristoforo <gregor.decristoforo@gmail.com>
Co-authored-by: Pip Liggins <philippa.liggins@dtc.ox.ac.uk>
Co-authored-by: Marc Berliner <34451391+MarcBerliner@users.noreply.github.com>
Co-authored-by: Brady Planden <55357039+BradyPlanden@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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