0.6.0

What's Changed

• change default mrc permissive to false, try to autorecover, remove userfacing 'permissive' argument by @sroet in #140
• don't make plots for particle extraction in estimate_roc by @sroet in #147
• change 'ptm' to 'rln' in the extraction star file by @sroet in #149
• README.md now points to GitHub Discussions for usage questions by @sroet in #154

Full Changelog: 0.5.0...0.6.0

0.5.0

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 #138
• update readme to point to pip install instead of source by @sroet in #139
• ctf model ramp weighting correction and updated interpolation center by @McHaillet in #141

Full Changelog: 0.4.3...0.5.0

0.4.3

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

What's Changed

• Fix release workflow by @sroet in #137

Full Changelog: 0.4.2...0.4.3

0.4.2

second try for pypi release

What's Changed

• Update pyproject.toml by @sroet in #136

Full Changelog: 0.4.1...0.4.2

0.4.1

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 #134
• test updated version by @sroet in #135

Full Changelog: 0.4.0...0.4.1

0.4.0

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

Full Changelog: 0.3.5...0.4.0

0.3.5

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 #110
• Prevent whitening for extraction by @McHaillet in #112

Full Changelog: 0.3.4...0.3.5

0.3.4

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

New Contributors

• @thorstenwagner made their first contribution in #69

Full Changelog: 0.3.3...0.3.4

0.3.3

What's Changed

• update to minimal cutoff value in estimate_roc by @McHaillet in #65
• Patch unittest inconsistency by @McHaillet in #66
• Patch single radial average function by @McHaillet in #67
• Bump version to 0.3.3 by @McHaillet in #68

Full Changelog: 0.3.2...0.3.3

0.3.2

What's Changed

• Patch for failing extraction at volume edges by @McHaillet in #60
• Patch band pass unassigned by @McHaillet in #62
• improve radial average speed with nimdage.mean() by @McHaillet in #63
• add check for equal scores in merging sub jobs to prevent race condition by @McHaillet in #64

Full Changelog: 0.3.1...0.3.2