Mne-bids

What's Changed
* Start 0.11 dev cycle by hoechenberger in https://github.com/mne-tools/mne-bids/pull/985
* FIX: zenodo metadata by sappelhoff in https://github.com/mne-tools/mne-bids/pull/986
* [MAINT, MRG] remove voxels from example by alexrockhill in https://github.com/mne-tools/mne-bids/pull/988
* [BUG, MRG] Fix ACPC Coordinates in surface RAS when they should be in scanner RAS by alexrockhill in https://github.com/mne-tools/mne-bids/pull/990
* [MRG] FIX: BrainProducts -> Brain Products by sappelhoff in https://github.com/mne-tools/mne-bids/pull/993
* [MRG] bump BIDS_VERSION to 1.7.0 by sappelhoff in https://github.com/mne-tools/mne-bids/pull/997
* [MRG] update make_dataset_description by sappelhoff in https://github.com/mne-tools/mne-bids/pull/996
* MRG: Simplify storage of empty-room data by hoechenberger in https://github.com/mne-tools/mne-bids/pull/998
* MRG: Suppress MaxShield warning in many places by hoechenberger in https://github.com/mne-tools/mne-bids/pull/1000
* [MRG] Update installation documentation by hoechenberger in https://github.com/mne-tools/mne-bids/pull/1001
* MRG: Make Inspector work even if mne-qt-browser is installed by hoechenberger in https://github.com/mne-tools/mne-bids/pull/1007
* [MRG] allow copyfile_brainvision to work with .dat extension by dominikwelke in https://github.com/mne-tools/mne-bids/pull/1008
* MRG: Remove deprecated mark_bad_channels() by hoechenberger in https://github.com/mne-tools/mne-bids/pull/1009
* follow up: allow copyfile_brainvision to work with .dat extension by dominikwelke in https://github.com/mne-tools/mne-bids/pull/1010
* [MRG] Bump to pybv 0.7.3 by sappelhoff in https://github.com/mne-tools/mne-bids/pull/1011
* MRG: Make print_dir_tree expand ~ by hoechenberger in https://github.com/mne-tools/mne-bids/pull/1013
* ci: add dependabot workflow to update github actions by sappelhoff in https://github.com/mne-tools/mne-bids/pull/1015
* Bump actions/cache from 2 to 3 by dependabot in https://github.com/mne-tools/mne-bids/pull/1016
* Bump actions/checkout from 2 to 3 by dependabot in https://github.com/mne-tools/mne-bids/pull/1017
* Bump codecov/codecov-action from 2 to 3 by dependabot in https://github.com/mne-tools/mne-bids/pull/1018
* Bump actions/setup-python from 2 to 4 by dependabot in https://github.com/mne-tools/mne-bids/pull/1019
* DOC: Document make_dataset_description by larsoner in https://github.com/mne-tools/mne-bids/pull/1029
* amended `_write_electrodes_tsv` to exclude writing stim channels to electrodes.tsv by scott-huberty in https://github.com/mne-tools/mne-bids/pull/1023
* MRG: In BIDSPath, don't infer the datatype from the suffix by hoechenberger in https://github.com/mne-tools/mne-bids/pull/1030
* [MRG, DOC] Fix whats_new.rst link by mscheltienne in https://github.com/mne-tools/mne-bids/pull/1032
* MRG: Don't store invalid weight and height in info['subject_info']; write weight and height to participants.tsv by hoechenberger in https://github.com/mne-tools/mne-bids/pull/1031
* Add EGI as manufacturer by anandsaini024 in https://github.com/mne-tools/mne-bids/pull/1006
* [MRG] Complete .zenodo.json for contributor credit by sappelhoff in https://github.com/mne-tools/mne-bids/pull/1028
* [MRG] FIX: Use os.replace instead of os.rename when copying CTF files (needed for windows) by sappelhoff in https://github.com/mne-tools/mne-bids/pull/1035
* [MRG] migrate from `.zenodo.json` to `CITATION.cff` by sappelhoff in https://github.com/mne-tools/mne-bids/pull/1037
* [MRG] Raise an error message when src==dest in write_raw_bids by adam2392 in https://github.com/mne-tools/mne-bids/pull/889
* [MRG] handle empty TSVs robustly and warn by sappelhoff in https://github.com/mne-tools/mne-bids/pull/1038
* Fixes for EEGLAB: do not 'simplify cells' when loading. by sappelhoff in https://github.com/mne-tools/mne-bids/pull/1039
* [MRG] Improve check of scans.tsv for BrainVision files by teonbrooks in https://github.com/mne-tools/mne-bids/pull/1034
* try fix for docs (nirs example) by sappelhoff in https://github.com/mne-tools/mne-bids/pull/1050
* MRG: Set channel type to misc if we cannot perform a proper conversion from BIDS to MNE channel types by hoechenberger in https://github.com/mne-tools/mne-bids/pull/1052
* MRG: Fix doc build for sphinx-gallery >=0.11.1 by hoechenberger in https://github.com/mne-tools/mne-bids/pull/1055
* Deprecate write_raw_bids()'s events_data parameter in favor of "events" by hoechenberger in https://github.com/mne-tools/mne-bids/pull/1054
* Doc Smallfix: Updated the BIDSPath in-place update method example by bhvieira in https://github.com/mne-tools/mne-bids/pull/1026
* [MRG] MAINT: Use new GitHub issue forms (yml) by sappelhoff in https://github.com/mne-tools/mne-bids/pull/1056
* Move emojis in issue templates to the titles by hoechenberger in https://github.com/mne-tools/mne-bids/pull/1058
* MRG: Add "description" entity to BIDSPath by hoechenberger in https://github.com/mne-tools/mne-bids/pull/1057
* MRG: Add support for GSR and temperature channels by hoechenberger in https://github.com/mne-tools/mne-bids/pull/1059
* MRG: Deprecate silently adding a leading period to an extension in BIDSPath by hoechenberger in https://github.com/mne-tools/mne-bids/pull/1061
* MRG: Remove special-casing for NIRS bids-validator by hoechenberger in https://github.com/mne-tools/mne-bids/pull/1063
* Fix chpi write by eort in https://github.com/mne-tools/mne-bids/pull/1067
* [MRG] Suggest alternatives when value not found in list by larsoner in https://github.com/mne-tools/mne-bids/pull/1066
* Fix Inspector tests for Matplotlib 3.6 compatibility by hoechenberger in https://github.com/mne-tools/mne-bids/pull/1069
* MAINT: Ensure we dont download without permission by larsoner in https://github.com/mne-tools/mne-bids/pull/1073
* fix CI after upstream changes by sappelhoff in https://github.com/mne-tools/mne-bids/pull/1071
* [MRG]: Add support for reading curry EEG files by dengemann in https://github.com/mne-tools/mne-bids/pull/1072
* MAINT: Tolerate new MNE behavior by larsoner in https://github.com/mne-tools/mne-bids/pull/1076
* Provide more helpful error messages when trying to write non-prelaoded concatenated data by hoechenberger in https://github.com/mne-tools/mne-bids/pull/1075
* REL: v0.11 by sappelhoff in https://github.com/mne-tools/mne-bids/pull/1077

New Contributors
* dependabot made their first contribution in https://github.com/mne-tools/mne-bids/pull/1016
* scott-huberty made their first contribution in https://github.com/mne-tools/mne-bids/pull/1023
* mscheltienne made their first contribution in https://github.com/mne-tools/mne-bids/pull/1032
* anandsaini024 made their first contribution in https://github.com/mne-tools/mne-bids/pull/1006
* bhvieira made their first contribution in https://github.com/mne-tools/mne-bids/pull/1026
* dengemann made their first contribution in https://github.com/mne-tools/mne-bids/pull/1072

**Full Changelog**: https://github.com/mne-tools/mne-bids/compare/v0.10...v0.11

Major enhancements
* We now have experimental support for fNIRS data (SNIRF format). This is still super fresh, and the respective BIDS enhancement proposal (BEP) has not yet been finalized & accepted into the standard. However, we’re excitied to be able to do this first step towards fNIRS support!
* Numerous improvements have been added to enhance our support for various coordinate frames, including those that are not yet supported by MNE-BIDS. These changes are mostly relevant to iEEG users. Please see the detailed list of changes below.
* We have added support for storing and reading multiple anatomical landmarks (“fiducials”) for the same participant. This makes it possible, for example, to store different sets of landmarks for each recording session.
It’s now possible to store Neuroscan (CNT) files with MNE-BIDS.


What's Changed
* MRG: Start 0.10 dev cycle by hoechenberger in https://github.com/mne-tools/mne-bids/pull/920
* doc: update dependencies by sappelhoff in https://github.com/mne-tools/mne-bids/pull/921
* [BUG] Add overwrite to export_raw for EDF conversions by adam2392 in https://github.com/mne-tools/mne-bids/pull/930
* [MRG] fix loading without age information / single-column .tsv by skjerns in https://github.com/mne-tools/mne-bids/pull/912
* MRG: Rework CI test matrix by hoechenberger in https://github.com/mne-tools/mne-bids/pull/934
* MRG: Don't store age, sex, handedness for empty-room in participants.tsv by hoechenberger in https://github.com/mne-tools/mne-bids/pull/935
* MRG: Fix handling of n/a event values when auto-renaming events on read by hoechenberger in https://github.com/mne-tools/mne-bids/pull/937
* Bump openneuro-py dep to 2022.1+ & Fix doc build for MNE-Python 1.0 by hoechenberger in https://github.com/mne-tools/mne-bids/pull/942
* Neuroscan Support by yjmantilla in https://github.com/mne-tools/mne-bids/pull/924
* MRG: Migrate report to Jinja2 by hoechenberger in https://github.com/mne-tools/mne-bids/pull/944
* MAINT: Fix setup by larsoner in https://github.com/mne-tools/mne-bids/pull/945
* bump cache, install with deps by sappelhoff in https://github.com/mne-tools/mne-bids/pull/951
* FIX: make update unalter the path instance if check fails by agramfort in https://github.com/mne-tools/mne-bids/pull/950
* [MRG] explicitly declare pymatreader an optional dep for EEGLAB by sappelhoff in https://github.com/mne-tools/mne-bids/pull/952
* [MRG] add metadata to ZENODO core archive by sappelhoff in https://github.com/mne-tools/mne-bids/pull/953
* ENH : add support for landmarks as dict in write_anat and kind param … by agramfort in https://github.com/mne-tools/mne-bids/pull/955
* MRG: Add "kind" kwarg to update_anat_landmarks() by hoechenberger in https://github.com/mne-tools/mne-bids/pull/957
* CI: Add concurrency by larsoner in https://github.com/mne-tools/mne-bids/pull/959
* doc: remove sphinx gallery css (now handled upstream); fix: testing split file by sappelhoff in https://github.com/mne-tools/mne-bids/pull/964
* DOC: fix author list rendering by Swastyy in https://github.com/mne-tools/mne-bids/pull/971
* MAINT: Report all unit test coverage by larsoner in https://github.com/mne-tools/mne-bids/pull/974
* MRG: Make get_head_mri_trans() respect datatype and suffix attributes of MEG BIDSPath by hoechenberger in https://github.com/mne-tools/mne-bids/pull/969
* [BUG, ENH, MRG] Pixels by alexrockhill in https://github.com/mne-tools/mne-bids/pull/976
* [ENH, MRG] Clarify intracranial narrative for why individual coordinates are preferred by alexrockhill in https://github.com/mne-tools/mne-bids/pull/975
* MRG: Initial support for NIRS data by rob-luke in https://github.com/mne-tools/mne-bids/pull/406
* MRG: Make update_anat_landmarks() accept fiducials file by hoechenberger in https://github.com/mne-tools/mne-bids/pull/977
* [ENH, MRG] Simplify reading dig by alexrockhill in https://github.com/mne-tools/mne-bids/pull/979
* [ENH, MRG] Allow template coordinate frame writing by alexrockhill in https://github.com/mne-tools/mne-bids/pull/980
* [BUG, MRG] Fix coordinate frames by alexrockhill in https://github.com/mne-tools/mne-bids/pull/982
* [ENH, MRG] Add BIDS Standard Template Transformations by alexrockhill in https://github.com/mne-tools/mne-bids/pull/983
* Prepare 0.10 release by hoechenberger in https://github.com/mne-tools/mne-bids/pull/984

New Contributors
* skjerns made their first contribution in https://github.com/mne-tools/mne-bids/pull/912
* yjmantilla made their first contribution in https://github.com/mne-tools/mne-bids/pull/924
* Swastyy made their first contribution in https://github.com/mne-tools/mne-bids/pull/971

**Full Changelog**: https://github.com/mne-tools/mne-bids/compare/v0.9...v0.10

Notable changes


- 🧠 Compatibility with MNE-Python 0.24!
- 👻 Anonymize an entire BIDS dataset via `mne_bids.anonymize_dataset`!
- 🏝 Conveniently turn a path into a `BIDSPath` via
`get_bids_path_from_fname`!
- 🏎 :func:`mne_bids.stats.count_events` and `mne_bids.BIDSPath.match`
are operating **much** faster now!
- 🔍 `write_raw_bids` now stores the names of the input files in the
``source`` column of ``*_scans.tsv``, making it easier for you to
*go back to the source* should you ever need to!

Notable changes

- You can now write preloaded and potentially modified data with
`mne_bids.write_raw_bids` by passing `allow_preload=True`. This is
a first step towards supporting derivative files.
- `mne_bids.BIDSPath` now has property getters and setters for all BIDS
entities. What this means is that you can now do things like
`bids_path.subject = '01'` instead of `bids_path.update(subject='01')`.
- We now support Deep Brain Stimulation (DBS) data.
- The way we handle anatomical landmarks was greatly revamped to ensure we're
always using the correct coordinate systems. A new function,
`mne_bids.get_anat_landmarks`, helps with extracting fiducial points from
anatomical scans.
- When creating a BIDS dataset from FIFF files on macOS and Linux, MNE-BIDS
can now optionally generate symbolic links to the original files instead of
copies. Simply pass `symlink=True` to
`mne_bids.write_raw_bids`. This can massively reduce the storage space
requirements.

Notable changes

- Channel names in ``*_channels.tsv`` and ``*_electrodes.tsv`` files now always take precedence over the names stored in the raw files.
- When reading data where the same trial type refers to different trigger values, we will now automatically create hierarchical event names in the form of ``trial_type/value1``, `trial_type/value2`` etc.
- :func:`mne_bids.write_raw_bids` now allows users to specify a format conversion via the new ``format`` parameter.
- Various improvements to data reading and :class:`mne_bids.BIDSPath` make working with real-life data easier.
- Many bug fixes in :func:`mne_bids.write_raw_bids` and in the MNE-BIDS Inspector.

These are challenging days for many of us, and to make your lives ever so slightly easier, we've been working hard to deliver this early
Christmas present 🎁 And even if you do not celebrate Christmas, we are quite certain you will like what we got for you! So – what are you waiting for? It's time to unwrap!

Notable changes

- The new Inspector, which can be invoked via :func:`mne_bids.inspect_dataset`, allows you to interactively explore your raw data,
change the bad channels selection, and edit :class:`mne.Annotations`. It also performs automated detection of flat data segments
or channels, to assist you during visual inspection. The capabilities of the inspector will be further expanded in upcoming releases of
MNE-BIDS.

- To further assist you during data inspection, we have added a function to summarize all events present in a dataset,
:func:`mne_bids.stats.count_events`.

- Sidecar JSON files can now be updated using a template via :func:`mne_bids.update_sidecar_json`.

- You can now read and write FLASH MRI images using :func:`mne_bids.write_anat`. We also fixed some issues with MRI defacing
along the way.

- Event durations are now preserved upon reading and writing data (we used to set all event durations to zero before).