Pytom-match-pick

Major updates
* pytom_match_template.py now supports relion5 metadata input via the `--relion5-tomograms-star` option. You can provide a tomograms.star file from a tomogram reconstruction job and pytom-match-pick will fetch the necessary CTF and dose data by the tomogram id.
* Some small fixes were also made to relion5-style star file particle list to make reading back easier.

PR's
* deal with new ruff version and next try for tutorial-test.yml by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/224
* Update tutorial-tests.yml by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/225
* Get tutorial-tests.yml working by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/226
* Add bins option to both the tophat and extraction plot by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/227
* add check on input gpu indices by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/228
* Drop py 39 and upgrade by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/230
* Relion5 input by McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/229


**Full Changelog**: https://github.com/SBC-Utrecht/pytom-match-pick/compare/0.7.2...0.7.4

Major changes
* We have a site! (It's automatically deployed with changes to the main branch)
* The tomogram mask supplied to match_template can now be ignored upon extraction to prevent unnecessary recalculation.
* After some initial issues, reading of starfiles by RELION5 should be fixed when using relion5-compat mode in extract_candidates.
* Score maps can be written out in float16 mode to save some disk space.
* Defocus handedness can be specified in match_template and will calculate defocus offsets for each subvolume. The site got a new 'Benchmarks' tab where a post is added that illustrates the effects of specifying defocus handedness ([check it out here](https://sbc-utrecht.github.io/pytom-match-pick/benchmarks/defocus_handedness/)).

PR overview
* fix defocus help unit by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/197
* mkdocs site for pytom-match-pick by McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/199
* fix: strings signs in deploy docs workflow by McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/203
* Update README.md by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/202
* update workflow permission to write github pages by McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/204
* Update Developers.md by McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/205
* Add ignore tomo mask option by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/209
* add check on tomo mask shape by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/210
* site updates: fix some usage informations, make authorship clear, add logo by McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/212
* add E501 check by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/216
* Create CITATION.cff by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/218
* Fix relion5 compat by McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/220
* logging.warn will be deprecated by McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/223
* add comment to entry_points that tells developers not to use line bre… by McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/219
* feature: calculate subvolume defocus values by McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/217
* Enable 16 bit output by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/222


**Full Changelog**: https://github.com/SBC-Utrecht/pytom-match-pick/compare/0.7.1...0.7.2

What's Changed
* Add DOI badge to readme.md by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/186
* add tutorial test yml by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/187
* Update pyproject.toml by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/188
* fix: make output directories for tutorial tests by McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/189
* revert healpix workaround by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/193
* bug fix: add int type for rng seed by McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/192


**Full Changelog**: https://github.com/SBC-Utrecht/pytom-match-pick/compare/0.7.0...0.7.1

This is a big one! And probably containts the last major api changes before the 1.0.0 release.

Wiki/tutorial will soon be updated to correspond with latest changes.

Main updates
* Thanks to sroet the package now supports arbitrary angular sampling generation via healpix. This now makes it possible to provide a particle diameter as input and let pytom-match-pick figure out the correct angular sampling!
* A bug was fixed in the particle symmetry option as it was not applied to the correct euler angle.
* CTF parameters can now only be applied in `pytom_match_template.py` and no longer for template creation. This makes input more consistent.
* Particle lists can be written out to be Relion5 compatible: centered coordinates in angstrom and proper star file column names.
* A tomogram mask can be provided during template matching and will skip subvolumes where the mask is empty.

PRs
* Readme illustration by McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/156
* Phase plate ctf and argparse grouping by McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/157
* default value phase shift entry point by McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/159
* Update cupy requirements by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/167
* wait longer to prevent leaked processes by McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/168
* small speedboost by precalculating conjugation by McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/165
* expose tophat kernel connectivity and make n-false-postives a float by McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/166
* make template non-symmetrical for template matching test to prevent race condition by McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/169
* refactor volume splitting by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/170
* auto generate sampling angles by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/163
* Ctf rework by McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/174
* Relion5 compatibility by McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/178
* Center of mass fix by McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/179
* calculate angular search from particle diameter by McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/181
* fix symmetry bug by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/184
* phase randomization score map correction by McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/182
* pre-commit with ruff by McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/183
* Add tomogram mask option for template matching by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/185


**Full Changelog**: https://github.com/SBC-Utrecht/pytom-match-pick/compare/0.6.0...0.7.0

What's Changed
* change default mrc permissive to false, try to autorecover, remove userfacing 'permissive' argument by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/140
* don't make plots for particle extraction in estimate_roc by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/147
* change 'ptm' to 'rln' in the extraction star file by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/149
* README.md now points to GitHub Discussions for usage questions by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/154


**Full Changelog**: https://github.com/SBC-Utrecht/pytom-match-pick/compare/0.5.0...0.6.0

What's changed
* summations of tilts in the per-tilt weighted wedge has been improved leading to less aliasing
* center of tilt rotation is updated to properly correspond to Fourier space origin
* install instructions now point to the pip install from pypi!

Pull requests
* Try to fix race condition in testing by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/138
* update readme to point to pip install instead of source by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/139
* ctf model ramp weighting correction and updated interpolation center by McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/141


**Full Changelog**: https://github.com/SBC-Utrecht/pytom-match-pick/compare/0.4.3...0.5.0