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GitHub pipeline test #407

Closed
wants to merge 54 commits into from
Closed

GitHub pipeline test #407

wants to merge 54 commits into from

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Lilferrit
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Just opening this PR to examine the Github actions Ubuntu run time issue.

Daniela Klaproth-Andrade and others added 30 commits November 19, 2024 12:57
@Lilferrit
migration to depthcharge v0.4.8
6826a1c
@Lilferrit
shuffling training set by default
8c8dc61
@wfondrie @Lilferrit
Reformat with Black
70cdea6
@wfondrie @Lilferrit
Fix formatting again after merge
8771d78
@Lilferrit
Resolve requested changes
7984bdc
@wfondrie @Lilferrit
Reformat with Black
f4b6ec6
@Lilferrit
removed invalid imports
4ec36b3
@Lilferrit
removed to be added functionality (for now)
355edc6
@Lilferrit
tensorboard logger
d224011
@Lilferrit
circular import bug
e6ac94e
@Lilferrit
removed tensorboard unit tests
39de098
@Lilferrit
beam search decode unit tests (IP)
97b8de7
@Lilferrit
teast_beam_search decode test update
2ee2845
@Lilferrit
test_eval_metrics test update
9b9349d
@Lilferrit
unit tests updates
0295493
@Lilferrit
spectrum id unit tests
3d1c20f
@Lilferrit
integration test fix
3ec8d7c
@Lilferrit
model prediction io flow fixes
9b8efea
@Lilferrit
PyLightning logging refactor
47df27e
@Lilferrit
mgf file reader title field formatting
45b3e26
@Lilferrit
integration tests fix
a1b42af
@Lilferrit
integration tests
261f63c
@Lilferrit
test_initialize_model fix
e3e8456
@Lilferrit
test_save_and_load_weights fix
0fb6692
@Lilferrit
test_save_and_load_weights_deprecated fix
5594bf8
@Lilferrit
test_evaluate fix, evaluate unnanotated peak file error handling
7bd2b5e
@Lilferrit
test_evaluate fix, evaluate unnanotated peak file error handling
d178860
@Lilferrit
test_eval_metrics fix
340695a
@Lilferrit
test_spectrum_id tests fix
e4d93f9
@Lilferrit
unit tests fixes
eb4af71
@Lilferrit Lilferrit marked this pull request as draft December 3, 2024 20:07
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codecov bot commented Dec 3, 2024 •
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Codecov Report

Attention: Patch coverage is 53.31126% with 141 lines in your changes missing coverage. Please review.

Project coverage is 38.02%. Comparing base (17bb3f2) to head (e2f9fb8).
Report is 6 commits behind head on dev.

Files with missing lines Patch % Lines
casanovo/denovo/model.py 38.40% 77 Missing ⚠️
casanovo/denovo/model_runner.py 48.27% 45 Missing ⚠️
casanovo/denovo/dataloaders.py 81.13% 10 Missing ⚠️
casanovo/data/ms_io.py 0.00% 4 Missing ⚠️
casanovo/casanovo.py 0.00% 2 Missing ⚠️
casanovo/data/db_utils.py 60.00% 2 Missing ⚠️
casanovo/version.py 50.00% 1 Missing ⚠️

❗ There is a different number of reports uploaded between BASE (17bb3f2) and HEAD (e2f9fb8). Click for more details.

HEAD has 1 upload less than BASE
Flag BASE (17bb3f2) HEAD (e2f9fb8)
3 2
Additional details and impacted files 
@@             Coverage Diff             @@
##              dev     #407       +/-   ##
===========================================
- Coverage   94.61%   38.02%   -56.59%     
===========================================
  Files          14       14               
  Lines        1282     1349       +67     
===========================================
- Hits         1213      513      -700     
- Misses         69      836      +767

☔ View full report in Codecov by Sentry.
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@bittremieux bittremieux linked an issue Dec 13, 2024 that may be closed by this pull request
Extremely long run time on unit tests in GitHub actions Ubuntu environment. #409
Open
@Lilferrit Lilferrit closed this Feb 26, 2025
@bittremieux bittremieux deleted the gh-pipeline-test branch February 26, 2025 22:15
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Extremely long run time on unit tests in GitHub actions Ubuntu environment.
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@Lilferrit @wfondrie