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bidspath example contains runtimewarning #829

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sappelhoff opened this issue Jul 6, 2021 · 3 comments · Fixed by #831
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bidspath example contains runtimewarning #829

sappelhoff opened this issue Jul 6, 2021 · 3 comments · Fixed by #831
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0.8

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@sappelhoff
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https://mne.tools/mne-bids/dev/auto_examples/bidspath.html#bidspath-example

/home/circleci/project/mne_bids/path.py:587: RuntimeWarning: Could not locate a data file of a supported format. This is likely a problem with your BIDS dataset. Please run the BIDS validator on your data. (root=my_bids_root, basename=sub-123_ses-test). []
warn(msg)

and there are 2 more of those. At least it should be discussed in the example why there is such a warning.
@sappelhoff sappelhoff added the doc label Jul 6, 2021
@sappelhoff sappelhoff added this to the 0.8 milestone Jul 8, 2021
@sappelhoff
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this is related to #712 #721 and the fetching behavior of BIDSPath.fpath

@hoechenberger
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Shall we finally kill off all the BIDSPath "trying to guess what the user meant" magic? :)

@sappelhoff sappelhoff mentioned this issue Jul 9, 2021
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@sappelhoff
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Shall we finally kill off all the BIDSPath "trying to guess what the user meant" magic? :)

yes 💯 Let's do it in 0.9 🙏

sappelhoff added a commit to sappelhoff/mne-bids that referenced this issue Jul 13, 2021
@sappelhoff
use tiny_bids in bidspath example, fix mne-tools#829
0067d11
@sappelhoff sappelhoff mentioned this issue Jul 13, 2021
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hoechenberger pushed a commit that referenced this issue Jul 14, 2021
@sappelhoff
[MRG] Add tiny BIDS test dataset, fix doctests, and run it in CI (#831)
0db039f 
* fix doctests in path.py

* test: use pytest --doctest-modules

* fix some more examples

* make use of _write_json instead of json.dump

* fix fine-calib and crosstalk doctest

* DATA: add tiny_bids test dataset ~800kb

* fix all doctests using new test ds

* add code for generating tiny_bids

* fix example, sphinx warning

* use tiny_bids in bidspath example, fix #829

* write TSV files with newline character

* add missing newlines at end of files

* do not run pytest on examples

we did not do that before either, but --doctest-modules is now ON

and that option apparently also runs the examples

* add whatsnew for TSV line end

* properly ignore examples in pytest

* fix head_to_mri upstream API change

* xfail doctest on windows due to / vs \

* BIDSPath __str__ always .as_posix()

* fix op.join -> Path

* root in __repr__ --> posix path or None

* circumvent bids_path.root __str__

* 1) fix pep, 2) fix type hints, 3) fix example ds

* fix type hint

* I should run make pep before pushing
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[MRG] Add tiny BIDS test dataset, fix doctests, and run it in CI sappelhoff/mne-bids
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@hoechenberger @sappelhoff