Cylindra

This is the version used for the biorxiv preprint.

What's Changed
* Refactor spline properties to the property `props` by hanjinliu in https://github.com/hanjinliu/cylindra/pull/54
* Implement regionprops functions by hanjinliu in https://github.com/hanjinliu/cylindra/pull/55
* Add a global variable to define the sign of rise angle by hanjinliu in https://github.com/hanjinliu/cylindra/pull/56
* Improve spline fitting by hanjinliu in https://github.com/hanjinliu/cylindra/pull/58


**Full Changelog**: https://github.com/hanjinliu/cylindra/compare/v0.13.3...v1.0.0.a9

Changes
----------
- Save script as a runnable file.
- Add `update_variable` method to global variable widget.
- Fix workflow normalization to allow tab.

New Features
--------------
- Implement `overwrite_project`
- Implement workflow (custom runnable functions) architecture.
- Functions to measure local radii.
- Record monomer mapping offsets after calling `align_averaged`.
- Implement some specific widgets (CheckBoxes, RandomSeedEdit etc).
- New methods for analysis with project object.
- Improvement of binding potential model. Add angle constraint to annealing model.
- Implement backend low-level API for Viterbi alignment and annealing.

Changed
----------
- fix workflow.
- Refactor config.
- Refactor non-recordable methods to child widgets.
- Do not use projection to determine peaks in local DFT.
- Calculate projection images lazily for performance improvement.
- Use `list[T]()` since python<3.8 is dropped.
- Record window size of local properties.
- Mask irrelevant requency during `infer_polarity`.

Bug Fixes
-----------
- Project description was not initialized.
- Fix displacement of cylinder model.

Bug Fixes
----------
- Fix `save_project` when some of the spline properties are missing and add tests for this.
- Fix the output of `align_averaged`.

Changes
---------
- Keep source spline object in each molecules layer.
- Don't rely on reshaping if possible (29).
- Refactoring using latest `acryo`.
- Reimplement all the intensive functions in Rust (39).
- Implement simulated annealing.
- Renew simulator widget (41).
- Change the default project structure (42).
- Refactor `impl_preview` and `setup_function_gui` in a separate file.
- Spline linear extrapolation (44).
- Make the `tilt_range` parameter tomogram specific, not to reside in the subtomogram analysis widget (45).
- Make the spline orientation and molecules orientation consistent.
- Add 2D plotting.
- Batchize alignment methods.
- Use ColormapEdit.
- Change spline properties architecture.
- Change global variable architecture.
- More comprehensive tests.
- Implement undo/redo.
- Make spline semi-immutable.

Bug Fixes
----------
- Fix plain clip widget.
- Fix conversion from molecules to IMOD mod file (31).
- Cylindric monomor mapping had subtle error.
- Fix spline shortening on fitting after clipping.
- Fix recursion error of `alleviate()`.

New Features
---------------
- Protofilament-wise extend molecules.
- Update command palette.

Bug Fixes
----------
- Fix `polars` dtype casting errors.
- Spline-fitter widget was not reproducible (28).
- Fix `open_logger`.
- Fix Viterbi alignment.
- Fix seam search without mask images.