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Relion5 compatibility #178

Merged

McHaillet merged 3 commits into SBC-Utrecht:main from McHaillet:relion5_compat

Jun 6, 2024

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McHaillet commented Jun 5, 2024

closes #177

Coordinates are written relative to the tomogram center and in Angstrom (instead of nr of voxels). Some star file column header names also changed.

I checked with relion what definition if of the tomogram center: 3dem/relion#1137

McHaillet added 3 commits

June 5, 2024 14:30


          add CLI argument

97bab80


          add relion5 support

e8bba65


          add comment to docstring of tomogram center definition

2cd53ab

github-actions bot commented Jun 5, 2024

File	Coverage		Missing
All files	`86%`	✅
src/pytom_tm/correlation.py	`85%`	✅	`94-95` `126`
src/pytom_tm/entry_points.py	`78%`	❌	`27` `104-121` `217-262` `351-366` `483-500` `879-890`
src/pytom_tm/extract.py	`74%`	❌	`110-121` `179-186` `212-215` `303-321`
src/pytom_tm/io.py	`80%`	❌	`16` `26` `35` `44` `53` `62-66` `75-79` `83` `87` `95` `98` `144-146` `199` `233-234` `333-336` `361`
src/pytom_tm/mask.py	`80%`	❌	`70` `85` `94-95`
src/pytom_tm/parallel.py	`89%`	✅	`14-15` `83` `95-97` `104` `148`
src/pytom_tm/plotting.py	`16%`	❌	`20-22` `25-32` `36-44` `48-51` `54-70` `73-74` `77-78` `98-103` `119-127` `133-150` `165-173` `177-194` `198-206` `210-217` `223` `229` `234` `248-398`
src/pytom_tm/tmjob.py	`97%`	✅	`276-277` `289` `295-297` `432` `472`
src/pytom_tm/utils.py	`78%`	❌	`16-18`
src/pytom_tm/weights.py	`96%`	✅	`61` `292-293` `300` `492` `495` `498`

Minimum allowed coverage is 85%

Generated by 🐒 cobertura-action against 2cd53ab

McHaillet requested a review from sroet

June 5, 2024 13:41

sroet approved these changes

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sroet left a comment

LGTM! feel free to merge!

McHaillet merged commit b80967b into SBC-Utrecht:main

2 checks passed

McHaillet deleted the relion5_compat branch

June 6, 2024 10:21

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