Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

change default mrc permissive to false, try to autorecover, remove userfacing 'permissive' argument #140

Merged
merged 18 commits into from
Mar 26, 2024

Conversation

sroet
Copy link
Collaborator

@sroet sroet commented Mar 5, 2024

closes #39

Done:

  • make a test with an unrecoverable mrc file
  • remove permissive from read_mrc and read_mrc_meta_data
  • update version for API break

Copy link

github-actions bot commented Mar 5, 2024

File Coverage Missing
All files 80%
src/pytom_tm/angles.py 94% 44
src/pytom_tm/correlation.py 85% 94-95 126
src/pytom_tm/entry_points.py 68% 27 104-121 283-342 431-445 542-557 791-858 899-910
src/pytom_tm/extract.py 73% 107-118 170-176 202-205 277-295
src/pytom_tm/io.py 48% 15-19 25-28 34-37 43-46 52-55 62-66 74-87 93-100 107-114 129-131 184 218-219 261-263 279 295 312-321 341-346
src/pytom_tm/mask.py 80% 70 85 94-95
src/pytom_tm/matching.py 95% 186-196 340
src/pytom_tm/parallel.py 84% 14-15 81-87 95-97 104 109 148
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/template.py 57% 57-58 67 76-87 92-97 107-112 114
src/pytom_tm/tmjob.py 96% 170-171 183 189-191 194 327 367
src/pytom_tm/utils.py 78% 16-18
src/pytom_tm/weights.py 96% 61 292-293 300 479 482 485

Minimum allowed coverage is 79%

Generated by 🐒 cobertura-action against a444948

@sroet
Copy link
Collaborator Author

sroet commented Mar 5, 2024

@McHaillet Did you have some example failing MRCs as were mentioned in #35 ?

@sroet sroet changed the title change default mrc permissive to false change default mrc permissive to false, try to autorecover, remove userfacing 'permissive' argument Mar 25, 2024
@sroet sroet marked this pull request as ready for review March 25, 2024 16:24
@sroet sroet requested a review from McHaillet March 25, 2024 16:24
@sroet
Copy link
Collaborator Author

sroet commented Mar 25, 2024

@McHaillet It took a while, but this is ready for a round of review 😄 Feel free to throw some other files at it to see if you like/dislike the behavior

Copy link
Collaborator

@McHaillet McHaillet left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Looks very solid too me, really nothing to too comments 👍

Don't really have any more examples of corrupt mrcs, so nothing to further test from my side. Feel free to merge!

@sroet sroet merged commit 87a6f4f into SBC-Utrecht:main Mar 26, 2024
2 checks passed
@sroet sroet deleted the change_mrc_permission_to_strict branch March 26, 2024 10:54
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

MRC reading permissiveness needs to be strict and tested
2 participants