hoechenberger / openneuro-py

A client for accessing OpenNeuro datasets, written in Python.
GNU General Public License v3.0
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Tests in dev don't appear to work as expected #36

Closed ktavabi closed 1 year ago

ktavabi commented 3 years ago

Running the following tests: ds000246


datalad installing "ds000246" [INFO ] Scanning for unlocked files (this may take some time)
[INFO ] Remote origin not usable by git-annex; setting annex-ignore
[INFO ] access to 1 dataset sibling s3-PRIVATE not auto-enabled, enable with: | datalad siblings -d "/Users/ktavabi/mne_data/ds000246" enable -s s3-PRIVATE datalad get data "sub-0001/meg/sub-0001_task-AEF_run-01_meg.ds" for "ds000246" datalad get data "sub-0001/meg/sub-0001_task-AEF_run-01_meg.json" for "ds000246"
datalad get data "sub-0001/meg/sub-0001_task-AEF_run-01_channels.tsv" for "ds000246"
2021-03-26 00:17:49 INFO Now running: 01-import_and_maxfilter.py 00:17:49 Using custom configuration: /Users/ktavabi/Github/mne-study-template/tests/configs/config_ds000246.py 00:17:49 [Step-01] Initializing dataset. 00:17:49 [Step-01] Running Step 1: Data import and Maxwell filtering 00:18:00 [Step-01][sub-0001] Not applying Maxwell filter. If you wish to apply it, set use_maxwell_filter=True in your configuration. 00:18:00 A critical error occurred. Traceback (most recent call last): File "/Users/ktavabi/Github/mne-study-template/config.py", line 1187, in wrapper return func(*args, **kwargs) File "/Users/ktavabi/Github/mne-study-template/scripts/01-import_and_maxfilter.py", line 420, in main parallel(run_func(subject, session) for subject, session in File "/Users/ktavabi/Github/mne-study-template/scripts/01-import_and_maxfilter.py", line 420, in parallel(run_func(subject, session) for subject, session in File "/Users/ktavabi/Github/mne-study-template/scripts/01-import_and_maxfilter.py", line 338, in run_maxwell_filter raw_out.save(raw_fname_out, picks=chs_to_include, overwrite=True, File "", line 21, in save File "/Users/ktavabi/Github/mne-python/mne/io/base.py", line 1405, in save _write_raw(fname, self, info, picks, fmt, data_type, reset_range, File "/Users/ktavabi/Github/mne-python/mne/io/base.py", line 1864, in _write_raw use_fname = _construct_bids_filename(base, ext, part_idx) File "/Users/ktavabi/Github/mne-python/mne/io/utils.py", line 309, in _construct_bids_filename use_fname = '{}split-{:02}{}{}'.format(base, part_idx, modality, ext) UnboundLocalError: local variable 'modality' referenced before assignment /Users/ktavabi/Github/mne-python/mne/io/utils.py(309)_construct_bids_filename() use_fname = '{}split-{:02}{}{}'.format(base, part_idx, modality, ext)

(Pdb) mne.sys_info()...

Platform:      macOS-11.2.3-x86_64-i386-64bit
Python:        3.9.2 | packaged by conda-forge | (default, Feb 21 2021, 05:02:20)  [Clang 11.0.1 ]
Executable:    /Users/ktavabi/opt/miniconda3/envs/obiwan/bin/python
CPU:           i386: 12 cores
Memory:        32.0 GB

mne:           0.22.dev0
numpy:         1.20.1 {blas=NO_ATLAS_INFO, lapack=lapack}
scipy:         1.6.1
matplotlib:    3.3.4 {backend=MacOSX}

sklearn:       0.24.1
numba:         0.53.1
nibabel:       3.2.1
cupy:          Not found
pandas:        1.2.3
dipy:          1.4.0
mayavi:        4.7.2
pyvista:       0.29.0 {pyvistaqt=0.3.0, OpenGL 4.1 ATI-4.2.15 via AMD Radeon Pro Vega 16 OpenGL Engine}
vtk:           9.0.1
PyQt5:         5.12.3

PS datalad is not getting installed as a dependent of mne-study-template? nor openneuro?

hoechenberger commented 3 years ago

I think this is something we should address in MNE-BIDS-Pipeline, moving the issue once I'm back at my desktop computer