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Fix relion5 compat #220

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merged 3 commits into from
Aug 14, 2024
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McHaillet
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Fixes some of the problems addressed in #214 .

  • starfiles are now written with data_particles instead of data_ by providing a block name to the starfile package
  • a column name in relion5 compat mode has been updated from rlnDetectorPixelSize to rlnTomoTiltSeriesPixelSize

@McHaillet McHaillet marked this pull request as ready for review August 14, 2024 11:05
@McHaillet McHaillet requested a review from sroet August 14, 2024 11:05
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File Coverage Missing
All files 87%
src/pytom_tm/correlation.py 85% 98-99 131
src/pytom_tm/entry_points.py 79% 28 111-128 231-276 379-398 532-550 1000-1011
src/pytom_tm/extract.py 76% 127-138 205-212 256-261 354-372
src/pytom_tm/io.py 80% 20 40 58 76 89 110-116 133-137 144 150 162 169 216-218 288 325-328 433-441 466
src/pytom_tm/mask.py 80% 76 94 104-105
src/pytom_tm/parallel.py 89% 14-15 93 104-105 111 176
src/pytom_tm/plotting.py 16% 19-21 24-31 35-43 47-50 53-69 72-73 76-77 97-102 118-126 132-149 164-172 176-193 197-205 209-216 222 228 233 247-397
src/pytom_tm/tmjob.py 97% 309-310 326 336-341 420 542 591
src/pytom_tm/utils.py 78% 18-20
src/pytom_tm/weights.py 96% 59 314-318 325 535 540 545

Minimum allowed coverage is 86%

Generated by 🐒 cobertura-action against 2beb502

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@sroet sroet left a comment

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would these starfile still be readable in RELION 4 (as RELION 5 is technically still in public beta)? LGTM otherwise

@McHaillet
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Yes, already from 3.1 they changed to the data_particles notation, but I guess were still excepting just data_ (https://relion.readthedocs.io/en/release-4.0/Whats-new.html#release-3-1). So this is a safe fix for compatibility with the older version as well.

@McHaillet McHaillet merged commit 8133e9a into SBC-Utrecht:main Aug 14, 2024
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@McHaillet McHaillet deleted the fix_relion5_compat branch August 14, 2024 12:00
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2 participants