Pytom-match-pick

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

What has changed
* The name has changed to pytom-match-pick for easy distinguishing!
* Installation has been changed to use entry-points instead of bin scripts.
* Small fixes for template generation to prevent some nasty artifacts. It can improve results for EM map generated templates.
* Small improvements to the repository to continuous testing.
* Coverage reports are now generated for pull requests!

List of PR's
* Convert bin scripts to entry points by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/109
* small fixes for template generation and preparation by McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/114
* initual guess for github workflow by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/115
* get gh workflows working by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/116
* Add test badge to README.md by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/117
* add coverage reporting by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/118
* Update coverage.yml by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/120
* Update unit-tests.yml by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/121
* Update coverage.yml by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/122
* test 80% coverage failing by McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/123
* and back to 75! by McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/124
* enable coverage of the multiprocess code by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/125
* changing name to pytom-match-pick from pytom-template-matching-gpu by McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/126
* add tests for missing libraries by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/127
* remove unnecessary 'if __name__==__main__:unittest.main()' from testfiles by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/130
* get tests to 100% coverage by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/131
* readme update pytom-match-pick by McHaillet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/132
* Update main branch version to 0.4.0 by sroet in https://github.com/SBC-Utrecht/pytom-match-pick/pull/133


**Full Changelog**: https://github.com/SBC-Utrecht/pytom-match-pick/compare/0.3.5...0.4.0

Updates
* The calculation of standard deviation over the template matching search has been updated, which means the default extraction mode of `pytom_extract_candidates.py` should work better. This is especially the case for jobs that split the search into subvolumes.
* Quality of life improvement, but does not change any results: whitening filter is no longer recalculated everytime the TMJob class is initialized, which saves unnecessary calculation for extraction jobs.

List of PRs
* Slicing for std calculation by McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/110
* Prevent whitening for extraction by McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/112


**Full Changelog**: https://github.com/SBC-Utrecht/pytom-template-matching-gpu/compare/0.3.4...0.3.5

Major points
* We fixed a bug where in template matching the combination of a restricted search in xyz (`--search-x` option, etc.) and volume split would lead to incorrect merging of subvolumes.
* Installation instructions favor building cupy against local cuda-toolkit, but for robustness also highlight the option to put a cuda-toolkit with prebuild cupy in the conda environment. However, building cupy can provide almost 2x better performance on our systems.
* We added a workaround for cupy 13.0.0 which currently broke a custom kernel.

List of PRs
* Improved installation instructions by thorstenwagner in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/69
* Update install instruction p2 by McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/71
* Terminate other processes if one breaks by McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/75
* parallel manager in a separate test file by McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/78
* unittest discover requirest testfiles to start with 'test' by sroet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/79
* calculate spectrum whitening filter only in the search region by McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/81
* Standard deviation cut-off lower threshold by McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/82
* Subvolume indexing bug by McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/83
* Add scipy to requirements in setup.py by sroet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/87
* Add tutorial wiki link to the README.md by sroet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/86
* make json writing OS agnostic in tmjob.py by sroet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/90
* Template.py: make filter warnings conditional and allow for no ctf_params by sroet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/98
* experimental tophat filtering for constraining score volume peaks at extraction by McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/91
* add docstrings to all functions by McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/100
* Convert to pyproject.toml by sroet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/104
* Cupy13 workaround by McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/107
* update install instructions to prefer building cupy by McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/108

New Contributors
* thorstenwagner made their first contribution in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/69

**Full Changelog**: https://github.com/SBC-Utrecht/pytom-template-matching-gpu/compare/0.3.3...0.3.4

What's Changed
* update to minimal cutoff value in estimate_roc by McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/65
* Patch unittest inconsistency by McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/66
* Patch single radial average function by McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/67
* Bump version to 0.3.3 by McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/68


**Full Changelog**: https://github.com/SBC-Utrecht/pytom-template-matching-gpu/compare/0.3.2...0.3.3

What's Changed
* Patch for failing extraction at volume edges by McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/60
* Patch band pass unassigned by McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/62
* improve radial average speed with nimdage.mean() by McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/63
* add check for equal scores in merging sub jobs to prevent race condition by McHaillet in https://github.com/SBC-Utrecht/pytom-template-matching-gpu/pull/64


**Full Changelog**: https://github.com/SBC-Utrecht/pytom-template-matching-gpu/compare/0.3.1...0.3.2