Pytom-match-pick

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

Third (and hopefully last) release to try to get automatic pypi working

What's Changed
* Fix release workflow by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/137


**Full Changelog**: https://github.com/SBC-Utrecht/pytom-match-pick/compare/0.4.2...0.4.3

second try for pypi release
What's Changed
* Update pyproject.toml by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/136


**Full Changelog**: https://github.com/SBC-Utrecht/pytom-match-pick/compare/0.4.1...0.4.2

This is a (of hopefully not too many) test release to see if we can automagickally publish to pypi

What's Changed
* Enable auto pypi publishing by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/134
* test updated version by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/135


**Full Changelog**: https://github.com/SBC-Utrecht/pytom-match-pick/compare/0.4.0...0.4.1