Cylindra

What's Changed
* Write IMOD mod file without IMOD command by hanjinliu in https://github.com/hanjinliu/cylindra/pull/97
* Fix FutureWarnings by hanjinliu in https://github.com/hanjinliu/cylindra/pull/98
* Plugin system by hanjinliu in https://github.com/hanjinliu/cylindra/pull/100
* Fix coverage not correctly calculated by hanjinliu in https://github.com/hanjinliu/cylindra/pull/101
* Improve coverage by hanjinliu in https://github.com/hanjinliu/cylindra/pull/102
* Cookiecutter template for creating plugins by hanjinliu in https://github.com/hanjinliu/cylindra/pull/103
* implement drop_molecules by hanjinliu in https://github.com/hanjinliu/cylindra/pull/104
* Refactoring and new implementation of landscape/annealing methods by hanjinliu in https://github.com/hanjinliu/cylindra/pull/106
* Use evaluable string for distance parameters of constrained alignment by hanjinliu in https://github.com/hanjinliu/cylindra/pull/107
* Find image by relative path by hanjinliu in https://github.com/hanjinliu/cylindra/pull/109
* fix some CLI by hanjinliu in https://github.com/hanjinliu/cylindra/pull/110
* Spherical mask creation by hanjinliu in https://github.com/hanjinliu/cylindra/pull/111
* Fix the behavior of `id` argument by hanjinliu in https://github.com/hanjinliu/cylindra/pull/112
* update show_reconstruction by hanjinliu in https://github.com/hanjinliu/cylindra/pull/113
* Bump actions/download-artifact from 3 to 4.1.7 in /.github/workflows by dependabot in https://github.com/hanjinliu/cylindra/pull/115
* Update bounding_box design and fix related bugs by hanjinliu in https://github.com/hanjinliu/cylindra/pull/114
* fix rise angle null values of `calculate_lattice_structure` by hanjinliu in https://github.com/hanjinliu/cylindra/pull/117
* Fix molecule positions when scales mismatch between projects by hanjinliu in https://github.com/hanjinliu/cylindra/pull/119
* Updates for the latest `acryo` by hanjinliu in https://github.com/hanjinliu/cylindra/pull/120
* View up-sampled cylindrical power spectrum by hanjinliu in https://github.com/hanjinliu/cylindra/pull/118
* Add NCC alignment option by hanjinliu in https://github.com/hanjinliu/cylindra/pull/116
* Add a SplineFitter method to auto-center along spline by hanjinliu in https://github.com/hanjinliu/cylindra/pull/121
* Fixes for polars=1.7.0 by hanjinliu in https://github.com/hanjinliu/cylindra/pull/122

New Contributors
* dependabot made their first contribution in https://github.com/hanjinliu/cylindra/pull/115

**Full Changelog**: https://github.com/hanjinliu/cylindra/compare/v1.0.0.b4...v1.0.0.b5

This is a small bug-fix release.

What's Changed
* Initialize visibility of project viewer by hanjinliu in https://github.com/hanjinliu/cylindra/pull/93
* Updates for latest `griffe` by hanjinliu in https://github.com/hanjinliu/cylindra/pull/95
* Fix simulated annealer construction with non-regular shape by hanjinliu in https://github.com/hanjinliu/cylindra/pull/96


**Full Changelog**: https://github.com/hanjinliu/cylindra/compare/v1.0.0.b3...v1.0.0.b4

What's Changed
* Fix undo operation of `align_averaged` by hanjinliu in https://github.com/hanjinliu/cylindra/pull/91
* minor updates for napari=0.5 by hanjinliu in https://github.com/hanjinliu/cylindra/pull/92


**Full Changelog**: https://github.com/hanjinliu/cylindra/compare/v1.0.0.b2...v1.0.0.b3

Highlights
- The spectra inspector widget is implemented in 78 90, as described in the [documentation](https://hanjinliu.github.io/cylindra/inspect_results/). This widget is useful for manually checking the cylindric power spectra to confirm that the analysis went well.
- The Rust implementation of RMA was optimized in 87 so its performance was greatly improved. The calculation time is nearly the half of the previous versions.

What's Changed
* Widget for validation of CFT by hanjinliu in https://github.com/hanjinliu/cylindra/pull/78
* fix symbols for orientation by hanjinliu in https://github.com/hanjinliu/cylindra/pull/79
* Add max_radius arguments by hanjinliu in https://github.com/hanjinliu/cylindra/pull/80
* Update PyO3 and polars by hanjinliu in https://github.com/hanjinliu/cylindra/pull/82
* support int8 and int16 by hanjinliu in https://github.com/hanjinliu/cylindra/pull/84
* Optimize the performance of lazy-loading projects by hanjinliu in https://github.com/hanjinliu/cylindra/pull/85
* Add `bin_size` parameter to landscape functions by hanjinliu in https://github.com/hanjinliu/cylindra/pull/86
* Use `Array2` instead of `HashMap` to speed up RMA by hanjinliu in https://github.com/hanjinliu/cylindra/pull/87
* Fix random seed problem by hanjinliu in https://github.com/hanjinliu/cylindra/pull/88
* Fix inspector by hanjinliu in https://github.com/hanjinliu/cylindra/pull/90


**Full Changelog**: https://github.com/hanjinliu/cylindra/compare/v1.0.0.b1...v1.0.0.b2

What's Changed
* Open as a napari plugin by hanjinliu in https://github.com/hanjinliu/cylindra/pull/75
* Improve coverage by hanjinliu in https://github.com/hanjinliu/cylindra/pull/76
* Simulate projection by hanjinliu in https://github.com/hanjinliu/cylindra/pull/77


**Full Changelog**: https://github.com/hanjinliu/cylindra/compare/v1.0.0.b0...v1.0.0.b1

What's Changed
* Update docs by hanjinliu in https://github.com/hanjinliu/cylindra/pull/59
* Disconnect close/hide button events by hanjinliu in https://github.com/hanjinliu/cylindra/pull/62
* Update Rust crate versions by hanjinliu in https://github.com/hanjinliu/cylindra/pull/61
* Use pydantic v2 by hanjinliu in https://github.com/hanjinliu/cylindra/pull/64
* Better UI/UX by hanjinliu in https://github.com/hanjinliu/cylindra/pull/66
* Allow reading projects with image path that doesn't exist. by hanjinliu in https://github.com/hanjinliu/cylindra/pull/67
* Support IO for RELION by hanjinliu in https://github.com/hanjinliu/cylindra/pull/65
* Read pdb/csv by hanjinliu in https://github.com/hanjinliu/cylindra/pull/72
* Implement alignment function to extend protofilaments by hanjinliu in https://github.com/hanjinliu/cylindra/pull/73


**Full Changelog**: https://github.com/hanjinliu/cylindra/compare/v1.0.0.a9...v1.0.0.b0