chore(ci): Add Windows test job #1113

effigies · 2024-12-13T21:45:48Z

No idea how tied we are to posix. Probably pretty tightly, but there's no reason in principle it couldn't be undone.

effigies · 2024-12-13T21:54:46Z

Looks like actually a fairly manageable job. @kaare-mikkelsen, would you be interested in having a go at adding Windows support?

kaare-mikkelsen · 2024-12-15T21:52:32Z

Hi @effigies
Well, yes and no :) I would like it to happen, and am not averse to contributing to a good tool. But I would probably also have to learn a bit more about how to contribute to pybids, and would have to find the time. I doubt that I will have much opportunity until end of january (I'm heading into exams season, and am presently buried in reports that need grading).
It sounded like you already looked at what would likely need to be done. Can you add a few pointers here?

Remi-Gau · 2024-12-16T09:44:52Z

@kaare-mikkelsen

My approach at this would be to first fix the failing tests from this run: https://github.com/bids-standard/pybids/actions/runs/12323508594/job/34399274262?pr=1113

I listed them below

  FAILED src/bids/layout/tests/test_layout.py::test_nested_include_exclude_with_regex - AssertionError: assert not <BIDSJSONFile filename='D:\a\pybids\pybids\tests...
  FAILED src/bids/layout/tests/test_layout.py::test_get_metadata_error - assert "Metadata term 'Missing' unavailable for file D:\\a\\pybids\\pybids\...
  FAILED src/bids/layout/tests/test_layout.py::test_ignore_files - AssertionError: assert 'D:\\a\\pybids\\pybids\\tests\\data\\ds005\\models\\...
  FAILED src/bids/layout/tests/test_layout.py::test_nested_include_exclude - re.error: bad escape \e at position 8
  FAILED src/bids/layout/tests/test_layout.py::test_indexed_file_associations - AssertionError: assert {'D:\\a\\pybi...hysio.tsv.gz'} == {'D:\\a\\pybi...hy...
  FAILED src/bids/layout/tests/test_layout.py::test_indexer_patterns[sub-01/anat/sub-01_T1w.nii.gz] - ValueError: 'D:\\home\\user\\.cache\\data\\sub-01\\anat\\sub-01_T1w.nii.gz'...
  FAILED src/bids/layout/tests/test_layout.py::test_indexer_patterns[.datalad] - ValueError: 'D:\\home\\user\\.cache\\data\\.datalad' is not in the subpath ...
  FAILED src/bids/layout/tests/test_layout.py::test_indexer_patterns[code] - ValueError: 'D:\\home\\user\\.cache\\data\\code' is not in the subpath of '...
  FAILED src/bids/layout/tests/test_layout.py::test_indexer_patterns[sub-01/.datalad] - ValueError: 'D:\\home\\user\\.cache\\data\\sub-01\\.datalad' is not in the ...
  FAILED src/bids/layout/tests/test_models.py::test_tag_init - assert (True and 'C:\\Users\\runneradmin\\AppData\\Local\\Temp\\pytest-of-r...
  FAILED src/bids/layout/tests/test_path_building.py::test_path_building_in_raw_scope[micr_SPIM] - AssertionError: assert 'D:/a/pybids/...-A_photo.json' == 'D:\\a\\pybid...-A...
  FAILED src/bids/layout/tests/test_path_building.py::test_path_building_in_raw_scope[asl001] - AssertionError: assert 'D:/a/pybids/...b103_T1w.json' == 'D:\\a\\pybid...b1...
  FAILED src/bids/layout/tests/test_path_building.py::test_path_building_in_raw_scope[asl002] - AssertionError: assert 'D:/a/pybids/...b103_T1w.json' == 'D:\\a\\pybid...b1...
  FAILED src/bids/layout/tests/test_path_building.py::test_path_building_in_raw_scope[asl003] - AssertionError: assert 'D:/a/pybids/...Sub1_T1w.json' == 'D:\\a\\pybid...Su...
  FAILED src/bids/layout/tests/test_path_building.py::test_path_building_in_raw_scope[asl004] - AssertionError: assert 'D:/a/pybids/...Sub1_T1w.json' == 'D:\\a\\pybid...Su...
  FAILED src/bids/layout/tests/test_path_building.py::test_path_building_in_raw_scope[asl005] - AssertionError: assert 'D:/a/pybids/...b103_T1w.json' == 'D:\\a\\pybid...b1...
  FAILED src/bids/layout/tests/test_path_building.py::test_path_building_in_raw_scope[pet001] - AssertionError: assert 'D:/a/pybids/...s-01_T1w.json' == 'D:\\a\\pybid...s-...
  FAILED src/bids/layout/tests/test_path_building.py::test_path_building_in_raw_scope[pet002] - AssertionError: assert 'D:/a/pybids/...line_T1w.json' == 'D:\\a\\pybid...li...
  FAILED src/bids/layout/tests/test_path_building.py::test_path_building_in_raw_scope[pet003] - AssertionError: assert 'D:/a/pybids/...es-01_T1w.nii' == 'D:\\a\\pybid...es...
  FAILED src/bids/layout/tests/test_path_building.py::test_path_building_in_raw_scope[pet004] - AssertionError: assert 'D:/a/pybids/...b-01_pet.json' == 'D:\\a\\pybid...b-...
  FAILED src/bids/layout/tests/test_path_building.py::test_path_building_in_raw_scope[pet005] - AssertionError: assert 'D:/a/pybids/...line_T1w.json' == 'D:\\a\\pybid...li...
  FAILED src/bids/layout/tests/test_path_building.py::test_path_building_in_raw_scope[qmri_megre] - AssertionError: assert 'D:/a/pybids/...01_MEGRE.json' == 'D:\\a\\pybid...01...
  FAILED src/bids/layout/tests/test_path_building.py::test_path_building_in_raw_scope[qmri_tb1tfl] - AssertionError: assert 'D:/a/pybids/...t_TB1TFL.json' == 'D:\\a\\pybid...t_...
  FAILED src/bids/layout/tests/test_path_building.py::test_path_building_in_raw_scope[eeg_cbm] - AssertionError: assert 'D:/a/pybids/..._channels.tsv' == 'D:\\a\\pybid..._c...
  FAILED src/bids/layout/tests/test_path_building.py::test_path_building_in_raw_scope[ieeg_filtered_speech] - AssertionError: assert 'D:/a/pybids/...rdsystem.json' == 'D:\\a\\pybid...rd...
  FAILED src/bids/layout/tests/test_path_building.py::test_path_building_in_raw_scope[ieeg_visual_multimodal] - AssertionError: assert 'D:/a/pybids/...3t01_T1w.json' == 'D:\\a\\pybid...3t...
  FAILED src/bids/layout/tests/test_path_building.py::test_bold_construction - AssertionError: assert 'sub-01/func/...1_bold.nii.gz' == 'sub-01\\func...1_...
  FAILED src/bids/layout/tests/test_path_building.py::test_path_building_in_raw_scope[ds000248] - AssertionError: assert 'D:/a/pybids/...01_FLASH.json' == 'D:\\a\\pybid...01...
  FAILED src/bids/layout/tests/test_path_building.py::test_path_building_on_derivative_examples[qmri_irt1] - AssertionError: assert 'D:/a/pybids/...01_M0map.json' == 'D:\\a\\pybid...01...
  FAILED src/bids/layout/tests/test_path_building.py::test_path_building_on_derivative_examples[qmri_mese] - AssertionError: assert 'D:/a/pybids/...01_M0map.json' == 'D:\\a\\pybid...01...
  FAILED src/bids/layout/tests/test_layout.py::test_get_file - AssertionError: assert None
  FAILED src/bids/layout/tests/test_path_building.py::test_path_building_on_derivative_examples[qmri_mp2rage] - AssertionError: assert 'D:/a/pybids/...-1_T1map.json' == 'D:\\a\\pybid...-1...
  FAILED src/bids/layout/tests/test_path_building.py::test_path_building_on_derivative_examples[qmri_mp2rageme] - AssertionError: assert 'D:/a/pybids/...2starmap.json' == 'D:\\a\\pybid...2s...
  FAILED src/bids/layout/tests/test_path_building.py::test_path_building_on_derivative_examples[qmri_mtsat] - AssertionError: assert 'D:/a/pybids/...01_M0map.json' == 'D:\\a\\pybid...01...
  FAILED src/bids/layout/tests/test_layout_on_examples.py::test_layout_on_examples_no_derivatives[ieeg_visual_multimodal-148] - AssertionError: assert 364 == 148
  FAILED src/bids/layout/tests/test_path_building.py::test_path_building_on_derivative_examples[qmri_sa2rage] - AssertionError: assert 'D:/a/pybids/...1_TB1map.json' == 'D:\\a\\pybid...1_...
  FAILED src/bids/layout/tests/test_path_building.py::test_path_building_in_raw_scope[ds001] - AssertionError: assert 'D:/a/pybids/...laneT2.nii.gz' == 'D:\\a\\pybid...la...
  FAILED src/bids/layout/tests/test_path_building.py::test_path_building_on_derivative_examples[qmri_vfa] - AssertionError: assert 'D:/a/pybids/...01_M0map.json' == 'D:\\a\\pybid...01...
  FAILED src/bids/layout/tests/test_path_building.py::test_path_building_in_raw_scope[ds114] - AssertionError: assert 'D:/a/pybids/...st_T1w.nii.gz' == 'D:\\a\\pybid...st...
  FAILED src/bids/layout/tests/test_path_building.py::test_path_building_in_raw_scope[qmri_irt1] - AssertionError: assert 'D:/a/pybids/...-01_IRT1.json' == 'D:\\a\\pybid...-0...
  FAILED src/bids/layout/tests/test_path_building.py::test_path_building_in_raw_scope[qmri_mese] - AssertionError: assert 'D:/a/pybids/...-01_MESE.json' == 'D:\\a\\pybid...-0...
  FAILED src/bids/layout/tests/test_path_building.py::test_path_building_in_raw_scope[qmri_mp2rage] - AssertionError: assert 'D:/a/pybids/..._MP2RAGE.json' == 'D:\\a\\pybid..._M...
  FAILED src/bids/layout/tests/test_path_building.py::test_path_building_in_raw_scope[qmri_mp2rageme] - AssertionError: assert 'D:/a/pybids/..._MP2RAGE.json' == 'D:\\a\\pybid..._M...
  FAILED src/bids/layout/tests/test_path_building.py::test_path_building_in_raw_scope[qmri_mtsat] - AssertionError: assert 'D:/a/pybids/...-off_MTS.json' == 'D:\\a\\pybid...-o...
  FAILED src/bids/layout/tests/test_path_building.py::test_path_building_in_raw_scope[qmri_sa2rage] - AssertionError: assert 'D:/a/pybids/..._TB1SRGE.json' == 'D:\\a\\pybid..._T...
  FAILED src/bids/layout/tests/test_path_building.py::test_path_building_on_derivative_examples[synthetic] - AssertionError: assert 'D:/a/pybids/...roc_bold.json' == 'D:\\a\\pybid...ro...
  FAILED src/bids/layout/tests/test_path_building.py::test_path_building_in_raw_scope[qmri_vfa] - AssertionError: assert 'D:/a/pybids/...ip-1_VFA.json' == 'D:\\a\\pybid...ip...
  FAILED src/bids/layout/tests/test_writing.py::TestWritableFile::test_build_file - AssertionError: assert 'A file at pa...writing file.' == 'A file at pa...wr...
  FAILED src/bids/layout/tests/test_path_building.py::test_path_building_in_raw_scope[micr_SEM] - AssertionError: assert 'D:/a/pybids/...e-A_photo.jpg' == 'D:\\a\\pybid...e-...
  FAILED src/bids/layout/tests/test_writing.py::TestWritableLayout::test_build_file_from_layout - AssertionError: assert 'C:/Users/run...01/r-1.nii.gz' == 'C:\\Users\\r...01...
  FAILED src/bids/layout/tests/test_path_building.py::test_path_building_in_raw_scope[ds000117] - AssertionError: assert 'D:/a/pybids/...on_events.tsv' == 'D:\\a\\pybid...on...
  FAILED src/bids/layout/tests/test_path_building.py::test_path_building_on_examples_with_derivatives_meg_ds_folder[ds000247-raw] - AssertionError: assert 'D:/a/pybids/...01_T1w.nii.gz' == 'D:\\a\\pybid...01...
  FAILED src/bids/layout/tests/test_path_building.py::test_path_building_on_examples_with_derivatives_meg_ds_folder[ds000246-raw] - AssertionError: assert 'D:/a/pybids/...01_T1w.nii.gz' == 'D:\\a\\pybid...01...
  FAILED src/bids/modeling/tests/test_transformations.py::test_orthogonalize_dense - ValueError: No variable named 'trial_type/parametric gain' found in this co...
  FAILED src/bids/reports/tests/test_parameters.py::test_describe_sequence[NONE-no sequence variant-SE_EP-spin echo and echo planar (SE/EP)] - AssertionError: assert 'spin echo an...anar (SE\\EP)' == 'spin echo an...la...
  FAILED src/bids/reports/tests/test_parameters.py::test_describe_sequence[SS-steady state-SE_EP-spin echo and echo planar (SE/EP)] - AssertionError: assert 'spin echo an...anar (SE\\EP)' == 'spin echo an...la...
  FAILED src/bids/reports/tests/test_parameters.py::test_describe_sequence[TRSS-time reversed steady state-SE_EP-spin echo and echo planar (SE/EP)] - AssertionError: assert 'spin echo an...anar (SE\\EP)' == 'spin echo an...la...
  FAILED src/bids/reports/tests/test_parameters.py::test_describe_sequence[MP_SS-MAG prepared and steady state-SE_EP-spin echo and echo planar (SE/EP)] - AssertionError: assert 'spin echo an...anar (SE\\EP)' == 'spin echo an...la...
  FAILED src/bids/reports/tests/test_parameters.py::test_describe_sequence[OSP-oversampling phase-SE_EP-spin echo and echo planar (SE/EP)] - AssertionError: assert 'spin echo an...anar (SE\\EP)' == 'spin echo an...la...
  FAILED src/bids/reports/tests/test_parameters.py::test_describe_sequence[SK-segmented k-space-SE_EP-spin echo and echo planar (SE/EP)] - AssertionError: assert 'spin echo an...anar (SE\\EP)' == 'spin echo an...la...
  FAILED src/bids/reports/tests/test_parameters.py::test_describe_sequence[MP-MAG prepared-SE_EP-spin echo and echo planar (SE/EP)] - AssertionError: assert 'spin echo an...anar (SE\\EP)' == 'spin echo an...la...
  FAILED src/bids/reports/tests/test_parameters.py::test_describe_sequence[MTC-magnetization transfer contrast-SE_EP-spin echo and echo planar (SE/EP)] - AssertionError: assert 'spin echo an...anar (SE\\EP)' == 'spin echo an...la...

I would :

fork the pybids repo
clone your fork
install tox (see the readme)
pick one test that fails in CI:
- let's say src/bids/layout/tests/test_path_building.py::test_path_building_in_raw_scope
Make sure the test fails locally using :
- tox run -e full -- src/bids/layout/tests/test_path_building.py::test_path_building_in_raw_scope
update the pybids code to make the test pass (the failing test should print the stack trace of the failure so it should leave a lot of breadcrumbs to find where to start looking at).

kaare-mikkelsen · 2024-12-16T10:01:04Z

@Remi-Gau that sounds pretty straight forward :) I will look into this when I get the time again, but also won't be in any way upset if someone solves it before then.

codecov · 2025-03-13T19:05:48Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 89.44%. Comparing base (8895e28) to head (5f71947).

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1113      +/-   ##
==========================================
+ Coverage   89.33%   89.44%   +0.11%     
==========================================
  Files          66       66              
  Lines        7259     7259              
  Branches     1149     1149              
==========================================
+ Hits         6485     6493       +8     
+ Misses        565      558       -7     
+ Partials      209      208       -1

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effigies added the windows label Dec 13, 2024

effigies marked this pull request as draft March 13, 2025 18:58

effigies force-pushed the windows branch from ed7cd2b to dd15002 Compare March 13, 2025 18:59

effigies force-pushed the windows branch from dd15002 to 75e132f Compare May 24, 2025 14:18

chore(ci): Add Windows test job

5f71947

effigies force-pushed the windows branch from 75e132f to 5f71947 Compare September 23, 2025 18:20

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