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[ENH] Add function to enable smart path search #1098 #1103

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merged 22 commits into from
Nov 22, 2022
Merged

[ENH] Add function to enable smart path search #1098 #1103

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22a13b8
Enable matching json files
moritz-gerster Nov 21, 2022
16d06a4
correct entity order
moritz-gerster Nov 21, 2022
3eafc58
Enable list[str] input for _filter_fnames
moritz-gerster Nov 21, 2022
14109a4
Add find_matching_paths
moritz-gerster Nov 21, 2022
29ee7df
refactor to make DRY
moritz-gerster Nov 21, 2022
b31d5d9
misc
moritz-gerster Nov 21, 2022
16e2df1
add tests
moritz-gerster Nov 21, 2022
6af83c5
pep8
moritz-gerster Nov 21, 2022
240dba1
docstring flake8
moritz-gerster Nov 21, 2022
8f4862b
delete coverage file
moritz-gerster Nov 21, 2022
304c313
Merge branch 'main' into main
hoechenberger Nov 21, 2022
6cddad7
Add name + what's new
moritz-gerster Nov 21, 2022
cf9773a
Merge branch 'main' of https://github.com/moritz-gerster/mne-bids int…
moritz-gerster Nov 21, 2022
64ec45e
fix doc?
moritz-gerster Nov 21, 2022
1bc097e
add the function to the API docs
moritz-gerster Nov 21, 2022
e9eb927
Don't check BIDS conformity in _filter_fnames
moritz-gerster Nov 22, 2022
5ecf658
make sure .match() and find_matching_paths() use same default kwarg c…
moritz-gerster Nov 22, 2022
f88128b
add example in doc
moritz-gerster Nov 22, 2022
d472d02
pep8
moritz-gerster Nov 22, 2022
7b8064a
add another example applying 'ignore'
moritz-gerster Nov 22, 2022
2bbf6a4
Update doc/whats_new.rst
moritz-gerster Nov 22, 2022
2e000ba
add name
moritz-gerster Nov 22, 2022
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6 changes: 3 additions & 3 deletions mne_bids/path.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1927,7 +1927,7 @@ def _filter_fnames(fnames, *, subject=None, session=None, task=None,
recording = _ensure_tuple(recording)
split = _ensure_tuple(split)
description = _ensure_tuple(description)
suffixe = _ensure_tuple(suffix)
suffix = _ensure_tuple(suffix)
extension = _ensure_tuple(extension)

leading_path_str = r'.*\/?' # nothing or something ending with a `/`
Expand All @@ -1951,8 +1951,8 @@ def _filter_fnames(fnames, *, subject=None, session=None, task=None,
if split else r'(|_split-([^_]+))')
desc_str = (r'_desc-(' + '|'.join(description) + ')'
if description else r'(|_desc-([^_]+))')
suffix_str = (r'_(' + '|'.join(suffixe) + ')' if suffix
else (r'_(' + '|'.join(ALLOWED_FILENAME_SUFFIX) + ')'))
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I noticed that the function _filter_fnames() only returns paths with valid BIDS suffixes even if the two mother functions find_matching_paths() and BIDSPath.match() have the keyword argument check=False.

In theory, one could add the argument check=False to _filter_fnames(check=False) and then code

    if suffix:
        suffix_str = r'_(' + '|'.join(suffix) + ')'
    elif suffix is None and check:
        # only return files with suffixes that are valid in BIDS
        suffix_str = (r'_(' + '|'.join(ALLOWED_FILENAME_SUFFIX) + ')'))
    elif suffix is None and not check:
        suffix_str = r'_([^_]+)'

However, this seems overkill to me since the BIDS conformity is checked afterwards using _fnames_to_bidspaths(check=check).

suffix_str = (r'_(' + '|'.join(suffix) + ')' if suffix
else r'_([^_]+)')
ext_str = r'(' + '|'.join(extension) + ')' if extension else r'.([^_]+)'

regexp = (
Expand Down