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czbiohub-sf / iohub

Pythonic and parallelizable I/O for N-dimensional imaging data with OME metadata
https://czbiohub-sf.github.io/iohub/
BSD 3-Clause "New" or "Revised" License
29 stars 7 forks source link

Test failing on Windows #111

Closed ziw-liu closed 1 year ago

ziw-liu commented 1 year ago

Cross-platform CI workflow on main was added in #107 for macOS and Windows in addition to existing Ubuntu PR tests. Windows tests are failing: https://github.com/czbiohub/iohub/actions/runs/4701735753/jobs/8338150267

Looks like another path separator issue.

ziw-liu commented 1 year ago

Failing test cases are all CLI stuff:

tests/cli/test_cli.py::test_cli_info_mock FAILED                         [  8%]
tests/cli/test_cli.py::test_cli_info_ndtiff FAILED                       [  9%]
tests/cli/test_cli.py::test_cli_info_ome_zarr FAILED                     [ 10%]
tests/cli/test_cli.py::test_cli_convert_ome_tiff FAILED                  [ 12%]

So more like terminal discrepancy when shell is not available.

ziw-liu commented 1 year ago

Tested locally on a Windows 10 VM. The same tests fail but CLI functions normally. So not a high priority then.

Integration test in PowerShell ```text > iohub info .\pytest_temp\test_data\MM20_ome-tiffs\mm2.0-20201209_100t_5z_3c_512k_1_nopositions\ Reading file: .\pytest_temp\test_data\MM20_ome-tiffs\mm2.0-20201209_100t_5z_3c_512k_1_nopositions\ === Summary === Format: ometiff Positions: 1 Time points: 100 Channels: 3 Channel names: ['Cy5', 'DAPI', 'FITC'] (Z, Y, X): (5, 128, 128) Z step (um): 1.75 > iohub info .\pytest_temp\test_data\MM20_pycromanager\mm2.0-20210713_pm0.13.2_2c_1\ Reading file: .\pytest_temp\test_data\MM20_pycromanager\mm2.0-20210713_pm0.13.2_2c_1\ Dataset opened === Summary === Format: ndtiff Positions: 1 Time points: 1 Channels: 2 Channel names: ['DAPI', 'FITC'] (Z, Y, X): (1, 128, 128) (iohub-dev) PS C:\Users\ziwen.liu\Projects\iohub> iohub info .\pytest_temp\test_data\20200812-CardiomyocyteDifferentiation14-Cycle1.zarr\ Reading file: .\pytest_temp\test_data\20200812-CardiomyocyteDifferentiation14-Cycle1.zarr\ === Summary === Format: omezarr v0.4 Axes: c (channel); z (space); y (space); x (space); Channel names: ['DAPI'] Row names: ['B'] Column names: ['03'] Wells: 1 > iohub convert -i .\pytest_temp\test_data\MM20_ome-tiffs\mm2.0-20201209_4p_20t_5z_3c_512k_1_multipositions\ -o test.hcs.ome.zarr Status: |████████████████|1200/1200 (Time Remaining: 00:00), 176.15it/s] > iohub info .\test.hcs.ome.zarr\ Reading file: .\test.hcs.ome.zarr\ === Summary === Format: omezarr v0.4 Axes: T (time); C (channel); Z (space); Y (space); X (space); Channel names: ['Cy5', 'DAPI', 'FITC'] Row names: ['0'] Column names: ['0', '1', '2', '3'] Wells: 4 ```