Py-pde

What's Changed
* Fixed documentation and convert input to array by david-zwicker in https://github.com/zwicker-group/py-pde/pull/569
* Restrict numpy to version <2 by david-zwicker in https://github.com/zwicker-group/py-pde/pull/571
* Simple check for numpy 2.0 compatbility by david-zwicker in https://github.com/zwicker-group/py-pde/pull/570


**Full Changelog**: https://github.com/zwicker-group/py-pde/compare/0.39.0...0.40.0

This release adds the `GeometricInterrupts` class to provide logarithmically spaced time interrupts for trackers. We also improved multiple smaller aspects of the package and removed features that have been deprecated for more than a year.

What's Changed
* Rename workflow jobs for clarity and update pip installation command by david-zwicker in https://github.com/zwicker-group/py-pde/pull/656
* Refactor code: remove deprecated interval parameter, clean up unused classes, and improve import statements by david-zwicker in https://github.com/zwicker-group/py-pde/pull/657
* Enhance test script: add memory tracing with memray, update ignore rules, and clean up imports by david-zwicker in https://github.com/zwicker-group/py-pde/pull/658
* Disable multithreading on HPC by default by david-zwicker in https://github.com/zwicker-group/py-pde/pull/659
* Refactor boundary condition handling: update test cases and examples to use dictionary format for boundary conditions by david-zwicker in https://github.com/zwicker-group/py-pde/pull/660
* Removed a number of deprecated methods by david-zwicker in https://github.com/zwicker-group/py-pde/pull/661
* Update test coverage script to append reports and fixed a test by david-zwicker in https://github.com/zwicker-group/py-pde/pull/663
* Enhance numba_dict function to accept additional keyword arguments and update documentation; refactor related code for consistency by david-zwicker in https://github.com/zwicker-group/py-pde/pull/664
* Update numba_dict function to enforce positional-only parameters and add edge case test by david-zwicker in https://github.com/zwicker-group/py-pde/pull/665
* Add new functions to documentation and enhance autosummary in multiple modules by david-zwicker in https://github.com/zwicker-group/py-pde/pull/666
* Add GeometricInterrupts class and update documentation for interrupt classes by david-zwicker in https://github.com/zwicker-group/py-pde/pull/667
* Add logarithmic kymograph example and enhance GeometricInterrupts parsing with validation by david-zwicker in https://github.com/zwicker-group/py-pde/pull/668
* Fix typos and improve clarity in logarithmic kymograph example documentation by david-zwicker in https://github.com/zwicker-group/py-pde/pull/669
* Enhance interrupt data handling by allowing integers in InterruptData type and updating parse_interrupt logic; remove unnecessary nbconvert skip in tests by david-zwicker in https://github.com/zwicker-group/py-pde/pull/670
* Support Parameterized class from modelrunner in Sphinx documentation processing by david-zwicker in https://github.com/zwicker-group/py-pde/pull/671
* Enhance expression parsing by adding complex number support and improving local variable handling in parse_expr_guarded; update tests for constant expressions to include complex cases. by david-zwicker in https://github.com/zwicker-group/py-pde/pull/672
* Add pydot to requirements and update ignore rules in linter configuration by david-zwicker in https://github.com/zwicker-group/py-pde/pull/673


**Full Changelog**: https://github.com/zwicker-group/py-pde/compare/0.43.0...0.44.0

Added support for python 3.13

What's Changed
* Add synonym support for axis names in boundary conditions and update tests by david-zwicker in https://github.com/zwicker-group/py-pde/pull/645
* Add return type annotation for FieldCollection constructor by david-zwicker in https://github.com/zwicker-group/py-pde/pull/647
* Refactor boundary index handling to improve clarity and support new index formats by david-zwicker in https://github.com/zwicker-group/py-pde/pull/648
* Add corner weight parameter for 2D Laplacian and update performance script by david-zwicker in https://github.com/zwicker-group/py-pde/pull/649
* Improve input shape validation in GridBase methods and update performance script documentation by david-zwicker in https://github.com/zwicker-group/py-pde/pull/650
* Add ffmpeg version retrieval and update environment information by david-zwicker in https://github.com/zwicker-group/py-pde/pull/651
* Fixed 9-point stencil in Cartesian coordinates by david-zwicker in https://github.com/zwicker-group/py-pde/pull/652
* Update maximal Python version to 3.13 in workflows and configuration files by david-zwicker in https://github.com/zwicker-group/py-pde/pull/653


**Full Changelog**: https://github.com/zwicker-group/py-pde/compare/0.42.2...0.43.0

What's Changed
* Fix description of heterogeneous BC example by david-zwicker in https://github.com/zwicker-group/py-pde/pull/636
* Fix figure retrieval in BasicPlottingContext for root figures by david-zwicker in https://github.com/zwicker-group/py-pde/pull/637
* Fix typos in comments and add tests for vector_to_cartesian function by david-zwicker in https://github.com/zwicker-group/py-pde/pull/638
* Improve string representations in various files by david-zwicker in https://github.com/zwicker-group/py-pde/pull/640
* Update boundary conditions format in PDE tutorial notebook by david-zwicker in https://github.com/zwicker-group/py-pde/pull/641
* Update py-modelrunner version to 0.18.3 in requirements files and scripts by david-zwicker in https://github.com/zwicker-group/py-pde/pull/642
* Handle special case for identical boundary conditions in get_boundary_axis function and add corresponding test by david-zwicker in https://github.com/zwicker-group/py-pde/pull/644


**Full Changelog**: https://github.com/zwicker-group/py-pde/compare/0.42.1...0.42.2

This release fixes a number of minor bugs and improves the documentation.

What's Changed
* Improved codestyle and added checks by david-zwicker in https://github.com/zwicker-group/py-pde/pull/622
* Added argument `post_step_hook` to `PDE` class by david-zwicker in https://github.com/zwicker-group/py-pde/pull/623
* Split examples into different categories by david-zwicker in https://github.com/zwicker-group/py-pde/pull/625
* Removed `pyupgrade` since it is contained in `ruff` by david-zwicker in https://github.com/zwicker-group/py-pde/pull/626
* Fix GridBase by david-zwicker in https://github.com/zwicker-group/py-pde/pull/628
* Refactored logging by david-zwicker in https://github.com/zwicker-group/py-pde/pull/630
* Added config option to affect how operators are implemented by david-zwicker in https://github.com/zwicker-group/py-pde/pull/632
* Prevent usage of adaptive steppers with stochastic PDEs by david-zwicker in https://github.com/zwicker-group/py-pde/pull/633


**Full Changelog**: https://github.com/zwicker-group/py-pde/compare/0.42.0...test

This release changes the way in which boundary conditions should be normally set. In particular, it deprecates the nested list approach, where conditions were set for each side of all axes in a more flexible, dictionary-based approach. In the new approach, conditions are directly specified for entire axes (`x`) or for one side (`x+`).

Moreover, we refactored the `Boundaries` class, introducing a new base class and added the `BoundariesSetter` class, so ghost points can be set directly using a callback function.

We also cleaned up some code and moved around some classes, so this might break old code!

What's Changed
* Slightly improved documentation by david-zwicker in https://github.com/zwicker-group/py-pde/pull/618
* Refactored boundary conditions by david-zwicker in https://github.com/zwicker-group/py-pde/pull/619


**Full Changelog**: https://github.com/zwicker-group/py-pde/compare/0.41.1...0.42.0