Mne-bids-pipeline

What's Changed

👁️ User-visible changes
* Add number of subjects to grand-average report by SophieHerbst in https://github.com/mne-tools/mne-bids-pipeline/pull/902, https://github.com/mne-tools/mne-bids-pipeline/pull/910
* Drop `Optional` and `Union` from type hints by hoechenberger in https://github.com/mne-tools/mne-bids-pipeline/pull/908
* Drop support for `loose=None` by hoechenberger in https://github.com/mne-tools/mne-bids-pipeline/pull/915
* Streamline ICA reporting by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/899
* Support variable time windows for epochs metadata creation by hoechenberger in https://github.com/mne-tools/mne-bids-pipeline/pull/874
* Raise a more helpful error message when requested subjects are missing from the dataset by hoechenberger in https://github.com/mne-tools/mne-bids-pipeline/pull/928
* In the report TOC, don't put the run numbers in quotation marks by hoechenberger in https://github.com/mne-tools/mne-bids-pipeline/pull/933
* Rename `ica_ctps_ecg_threshold` to `ica_ecg_threshold` by hoechenberger in https://github.com/mne-tools/mne-bids-pipeline/pull/935
* Improve logging output when rejecting epochs; and log number of reconstructed ICA and SSP epochs by hoechenberger in https://github.com/mne-tools/mne-bids-pipeline/pull/936
* Improve logging during ICA artifact discovery and rejection by hoechenberger in https://github.com/mne-tools/mne-bids-pipeline/pull/937
* Save ECG and EOG evokeds created during ICA artifact detection to disk by hoechenberger in https://github.com/mne-tools/mne-bids-pipeline/pull/938
* Provide a cleaner traceback on error by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/951
* Rework how we apply EEG montages by hoechenberger in https://github.com/mne-tools/mne-bids-pipeline/pull/960

📦 Dependencies
* Drop support for Python 3.9 by hoechenberger in https://github.com/mne-tools/mne-bids-pipeline/pull/908

🐛 Bug fixes
* Change default for info to use for inverse by SophieHerbst in https://github.com/mne-tools/mne-bids-pipeline/pull/919
* Fix report section on original raw data (didn't contain bad channels and subject or experimenter name) by hoechenberger in https://github.com/mne-tools/mne-bids-pipeline/pull/931

📚 Documentation
* Restructure configuration options documentation sections by hoechenberger in https://github.com/mne-tools/mne-bids-pipeline/pull/914
* Enhance documentation of caching by SophieHerbst in https://github.com/mne-tools/mne-bids-pipeline/pull/918
* Improve documentation and config validation of `loose` and `depth` parameters by hoechenberger in https://github.com/mne-tools/mne-bids-pipeline/pull/915
* Render type annotations in the documentation again by hoechenberger in https://github.com/mne-tools/mne-bids-pipeline/pull/909
* Do not show `Annotated` types in configuration options documentation by hoechenberger in https://github.com/mne-tools/mne-bids-pipeline/pull/911, https://github.com/mne-tools/mne-bids-pipeline/pull/913
*Fix typo by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/940

⛑️ Code health
* Ensure input changes cause output changes by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/904
* Cleaner hook into `mkdocstrings-python` by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/943
* Remove `ref-names` from `.git_archival.txt` by sappelhoff in https://github.com/mne-tools/mne-bids-pipeline/pull/948
* Switch to trusted publishing by tsbinns in https://github.com/mne-tools/mne-bids-pipeline/pull/957
* Set up Dependabot to automatically keep GitHub Actions up-to-date by hoechenberger in https://github.com/mne-tools/mne-bids-pipeline/pull/893

🤖 Automated infrastructure updates
* [dependabot]: Bump actions/setup-python from 4 to 5 by dependabot in https://github.com/mne-tools/mne-bids-pipeline/pull/894
* [dependabot]: Bump actions/download-artifact from 3 to 4 by dependabot in https://github.com/mne-tools/mne-bids-pipeline/pull/895
* [dependabot]: Bump actions/upload-artifact from 3 to 4 by dependabot in https://github.com/mne-tools/mne-bids-pipeline/pull/896
* [dependabot]: Bump codecov/codecov-action from 3 to 4 by dependabot in https://github.com/mne-tools/mne-bids-pipeline/pull/898
* [dependabot]: Bump actions/checkout from 3 to 4 by dependabot in https://github.com/mne-tools/mne-bids-pipeline/pull/897
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/mne-tools/mne-bids-pipeline/pull/903
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/mne-tools/mne-bids-pipeline/pull/917
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/mne-tools/mne-bids-pipeline/pull/923
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/mne-tools/mne-bids-pipeline/pull/929
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/mne-tools/mne-bids-pipeline/pull/942
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/mne-tools/mne-bids-pipeline/pull/945
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/mne-tools/mne-bids-pipeline/pull/947
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/mne-tools/mne-bids-pipeline/pull/953
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/mne-tools/mne-bids-pipeline/pull/954
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/mne-tools/mne-bids-pipeline/pull/955
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/mne-tools/mne-bids-pipeline/pull/959

👩‍💻New Contributors
* dependabot made their first contribution in https://github.com/mne-tools/mne-bids-pipeline/pull/894
* tsbinns made their first contribution in https://github.com/mne-tools/mne-bids-pipeline/pull/957

**Full Changelog**: https://github.com/mne-tools/mne-bids-pipeline/compare/v1.8.0...v1.9.0

What's Changed

👁️ User-visible changes
* We fixed a crash that was affecting users running CSP on Maxwell-filtered data by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/890
* Print longer tracebacks in case of a crash while saving a report file by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/892


📦 Dependencies
* Explicitly depend on `annotated-types` by hoechenberger in https://github.com/mne-tools/mne-bids-pipeline/pull/886

📚 Documentation
* Add missing release dates to changelog by hoechenberger in https://github.com/mne-tools/mne-bids-pipeline/pull/887

⛑️ Code health
* We removed the unused settings `shortest_event` and `study_name`. They were relics of the early days of the pipeline and haven't been in use for a long time by hoechenberger and larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/888, https://github.com/mne-tools/mne-bids-pipeline/pull/889
* We now internally check that all generated configuration options are actually used somewhere by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/889

🤖 Automated infrastructure updates
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/mne-tools/mne-bids-pipeline/pull/891


**Full Changelog**: https://github.com/mne-tools/mne-bids-pipeline/compare/v1.7.0...v1.8.0

👁️ User-visible changes
* Improve logging during cache invalidation by hoechenberger in https://github.com/mne-tools/mne-bids-pipeline/pull/877
* Fix handling of `analyze_channels` for EEG data, where some steps (like ERP calculation) would previously fail by hoechenberger in https://github.com/mne-tools/mne-bids-pipeline/pull/883

📚 Documentation
* Update contributing instructions and remove outdated building instructions by hoechenberger in https://github.com/mne-tools/mne-bids-pipeline/pull/875
* Fix a typo in the readme by hoechenberger in https://github.com/mne-tools/mne-bids-pipeline/pull/871

⛑️ Code health
* Enable stricter linting by hoechenberger in https://github.com/mne-tools/mne-bids-pipeline/pull/872

🤖 Automated infrastructure updates
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/mne-tools/mne-bids-pipeline/pull/885


**Full Changelog**: https://github.com/mne-tools/mne-bids-pipeline/compare/v1.6.0...v1.7.0

What's Changed

* The "Behavior changes" heading was incorrectly commented out in the changelog by hoechenberger in https://github.com/mne-tools/mne-bids-pipeline/pull/823
* MAINT: Fix CIs by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/824
* Switch build backend to hatchling by hoechenberger in https://github.com/mne-tools/mne-bids-pipeline/pull/825
* FIX: Paths and pyarrow by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/834
* MAINT: Test result caching by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/836
* MAINT: Enable more ruff rules by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/838
* ENH: Add artifact regression by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/837
* BUG: Fix several bugs by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/839
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/mne-tools/mne-bids-pipeline/pull/843
* ENH: Write out raw data and SSP events by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/840
* BUG: Fix bug with Maxwell step when find_noise_channels_meg=False by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/847
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/mne-tools/mne-bids-pipeline/pull/851
* BUG: Fix bug with multichannel classification by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/853
* ENH: Better event count rep and noise_cov_method by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/854
* BUG: Fix bug with split epochs and ICA by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/855
* [pre-commit.ci] pre-commit autoupdate by pre-commit-ci in https://github.com/mne-tools/mne-bids-pipeline/pull/856
* DOC: Automatic flowchart by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/860
* DOC: Automatically document settings by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/863
* add image_kwargs to report by SophieHerbst in https://github.com/mne-tools/mne-bids-pipeline/pull/859
* MAINT: Remove datalad by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/867
* ENH: Split ICA into multiple steps by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/865
* ENH: Document relevant steps by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/866
* ENH: Doc config in sheet by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/869

**Full Changelog**: https://github.com/mne-tools/mne-bids-pipeline/compare/v1.5.0...v1.6.0

What's Changed
* MAINT: Cleanup dependencies and doc build by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/755
* ENH: Add annotation of head velocity by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/757
* BUG: Fix bug with cache invalidation by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/756
* ENH: Add T1 and FLASH BEM to website by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/758
* BUG: Fix bug with empty room processing by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/761
* ENH: More compact logging by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/764
* ENH: Add eSSS by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/762
* ENH: Cache grand-average steps by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/765
* MAINT: Test MD5 hashing too by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/768
* ENH: Better logging of distances by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/769
* MAINT: pre-commit.ci by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/774
* Added deriv_root argument to CLI by vferat in https://github.com/mne-tools/mne-bids-pipeline/pull/773
* MAINT: Use pooch for downloading web data by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/775
* API: Change default to _cache by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/778
* ENH: Validate inputs with pydantic by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/779
* TST: Rerun CIs by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/781
* BUG: Fix bug where individual invs were not rendered by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/782
* MAINT: Fix bug with item by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/791
* Ensure link in "You're not viewing the latest stable version" banner is readable in light and dark theme by hoechenberger in https://github.com/mne-tools/mne-bids-pipeline/pull/793
* Reduce logging output when creating and saving reports by hoechenberger in https://github.com/mne-tools/mne-bids-pipeline/pull/799
* Use inst.pick() instead of inst.pick_types() by hoechenberger in https://github.com/mne-tools/mne-bids-pipeline/pull/800
* Use cleaned epochs for sensor-space decoding, time-frequency analysis, and covariance calculation by hoechenberger in https://github.com/mne-tools/mne-bids-pipeline/pull/796
* Add "picard-extended_infomax" ICA algorithm by hoechenberger in https://github.com/mne-tools/mne-bids-pipeline/pull/801
* Do not reject epochs based on PTP threshold before ICA cleaning by hoechenberger in https://github.com/mne-tools/mne-bids-pipeline/pull/806
* Add `"autoreject_local"` as new option for `preprocessing/ptp_reject` by hoechenberger in https://github.com/mne-tools/mne-bids-pipeline/pull/807
* ENH: Table sorting and ds004229 updates by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/809
* Add support for `autoreject` (local) before running ICA by hoechenberger in https://github.com/mne-tools/mne-bids-pipeline/pull/810
* BUG: Fix bug with verbosity by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/813
* Do not interpolate bad segments using autoreject before ICA by hoechenberger in https://github.com/mne-tools/mne-bids-pipeline/pull/816
* Omit bad channels when gathering data used for decoding by hoechenberger in https://github.com/mne-tools/mne-bids-pipeline/pull/817
* Allow decoding using epochs at different stages of pre-processing by hoechenberger in https://github.com/mne-tools/mne-bids-pipeline/pull/819
* Prepare for 1.5.0 release by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/821
* FIX: PyQt6 by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/822

New Contributors
* vferat made their first contribution in https://github.com/mne-tools/mne-bids-pipeline/pull/773

**Full Changelog**: https://github.com/mne-tools/mne-bids-pipeline/compare/v1.4.0...v1.5.0

What's Changed

🆕 New features
* ENH: Add movement compensation by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/747

🐛 Bug fixes
* BUG: Fix bug with `mf_reference_run` by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/742
* Fix bug with too many JSON files found during empty room matching by allermat in https://github.com/mne-tools/mne-bids-pipeline/pull/743
* Fix documentation examples for `ch_types` configuration option by allermat in https://github.com/mne-tools/mne-bids-pipeline/pull/745
* Fix for documentation issue related to processing EEG separately in a combined M/EEG dataset by allermat in https://github.com/mne-tools/mne-bids-pipeline/pull/751

⚕ Code health & maintenance
* MAINT: Refactor `_get_raw_paths` by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/749
* MAINT: DRY kwarg passing by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/746
* MAINT: Use a large resource class to speed up build by larsoner in https://github.com/mne-tools/mne-bids-pipeline/pull/741
* Prepare for 1.4.0 release by hoechenberger in https://github.com/mne-tools/mne-bids-pipeline/pull/753

New Contributors
* allermat made their first contribution in https://github.com/mne-tools/mne-bids-pipeline/pull/743

**Full Changelog**: https://github.com/mne-tools/mne-bids-pipeline/compare/v1.3.0...v1.4.0