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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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1 change: 1 addition & 0 deletions doc/authors.rst
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Expand Up @@ -39,3 +39,4 @@
.. _Denis Engemann: https://github.com/dengemann
.. _Bruno Hebling Vieira: https://bhvieira.github.io/
.. _Daniel McCloy: http://dan.mccloy.info
.. _Moritz Gerster: http://moritz-gerster.com
1 change: 1 addition & 0 deletions doc/whats_new.rst
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Expand Up @@ -44,6 +44,7 @@ Detailed list of changes
- Add :meth:`mne_bids.BIDSPath.find_matching_sidecar` to find the sidecar file associated with a given file path by `Eric Larson`_ (:gh:`1093`)
- When writing data via :func:`~mne_bids.write_raw_bids`, it is now possible to specify a custom mapping of :class:`mne.Annotations` descriptions to event codes via the ``event_id`` parameter. Previously, passing this parameter would always require to also pass ``events``, and using a custom event code mapping for annotations was impossible, by `Richard Höchenberger`_ (:gh:`1084`)
- Improve error message when :obj:`~mne_bids.BIDSPath.fpath` cannot be uniquely resolved by `Eric Larson`_ (:gh:`1097`)
- Add :func:`mne_bids.find_matching_paths` to get all bids paths that match the requirements by :newcontrib:`Moritz Gerster` (:gh:`1103`)
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Is this correct @hoechenberger? In the mne_bids contribution guide it is not described how to add lines so I followed the mne contributing guide.

Here I didn't add my name because I guess this works automatically?

The following authors contributed for the first time. Thank you so much! 🤩

* ...

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I guess this works automatically

unfortunately not :-)

I followed the mne contributing guide.

it's a bit different here. You just add your name to the list you quoted above, and we don't have the sphinx role ":new_contrib:", so you can just follow the style of previous changelog entries.

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Nevermind, I checked the old versions of whats_new.rst and understood that you don't have :newcontrib: as in mne.

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if you want the function to be available as mne_bids.find_matching_paths, for example, you'd need to make additions here:

mne-bids/mne_bids/__init__.py

Lines 4 to 18 in b97ce0b

from mne_bids import commands
from mne_bids.report import make_report
from mne_bids.path import (BIDSPath, get_datatypes, get_entity_vals,
print_dir_tree, get_entities_from_fname,
search_folder_for_text, get_bids_path_from_fname)
from mne_bids.read import get_head_mri_trans, read_raw_bids
from mne_bids.utils import get_anonymization_daysback
from mne_bids.write import (make_dataset_description, write_anat,
write_raw_bids, mark_channels,
write_meg_calibration, write_meg_crosstalk,
get_anat_landmarks, anonymize_dataset)
from mne_bids.sidecar_updates import update_sidecar_json, update_anat_landmarks
from mne_bids.inspect import inspect_dataset
from mne_bids.dig import (template_to_head, convert_montage_to_ras,
convert_montage_to_mri)

for example look at BIDSPath in that file --> if it weren't where it is, you would always need to do mne_bids.path.BIDSPath.

And for the API docs, you need to add it here (provided you followed the above):

mne-bids/doc/api.rst

Lines 19 to 22 in b97ce0b

.. autosummary::
:toctree: generated/
write_raw_bids

Thanks @sappelhoff! Added with 1bc097e.


🧐 API and behavior changes
^^^^^^^^^^^^^^^^^^^^^^^^^^^
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