Bidsmreye

Added

* [ENH] Extra metadata have been added to the output of the `generalize` step to better align with BIDS BEP20 by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/232

Changed

* [ENH] Output filenames of the prepare step has been changed to use the `timeseries` suffix and the output of the `generalize` step now include the name of the Deepmreye model used to compute them by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/232

* [ENH] use non-linear alignment as default by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/234

Removed

* [ENH] the `--non_linear_coreg` CLI argument was replaced by the `--linear_coreg` by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/234

Fixed

* [FIX] do not apply `run` found for one task to all tasks by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/228


**Full Changelog**: https://github.com/cpp-lln-lab/bidsMReye/compare/0.4.0...0.5.0

What's Changed

* [FIX] update file naming when run indices are padded by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/146
* [MAINT] move most of the config to pyproject.toml by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/147
* [MAINT] update packaging by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/165
* [MAINT] pin pooch dependency by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/166
* [STY] use isort by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/191
* [FIX] pin keras and fix make file by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/197
* [FIX] fix deploy to github on Circle CI by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/210
* [ENH] improve error messages for invalid input data by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/150
* [ENH] turn `--action` into subcommands by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/215
* [ENH] Skip prepare and QC if output already exists by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/216
* [FIX] handle exceptions for QC at group level when participants are missing QC data by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/217
* [FIX] Use repetition time from BIDS metadata instead of nifti header by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/218
* [FIX] save models in output dir by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/219
* [FIX] improve help for missing subject / task by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/220

**Full Changelog**: https://github.com/cpp-lln-lab/bidsMReye/compare/0.3.1...0.4.0

What's Changed

* [ENH] update config by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/126
* [MNT] update docker and doc by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/118
* [FMT] format yml by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/120
* [INFRA] improve docker by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/122
* [DOC] update FAQ by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/121
* [INFRA] use code cov token by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/125
* [INFRA] verbose in ci by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/127
* [DOC] add CLI info for group level by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/128
* [INFRA] do not fail CI when coverage cannot be uploaded by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/129

**Full Changelog**: https://github.com/cpp-lln-lab/bidsMReye/compare/0.3.0...0.4.0

What's Changed
* [ENH] run QC on input data by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/113
* [ENH] add group level QA plot and table by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/115


**Full Changelog**: https://github.com/cpp-lln-lab/bidsMReye/compare/0.2.0...0.3.0

What's Changed

* [DOC] add logo by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/89
* [MISC] by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/92
* [MNT] add workflow to run on openneuro data by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/90
* [ENH] improve log and change verbosity parameter by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/96
* [ENH] improve model download by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/97
* [ENH] improve methods by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/98
* [ENH] add CCO license by default by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/99
* [ENH] add possibility to used ANTs non linear registration by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/100
* [ENH] add basic QC by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/102
* [ENH] add basic QC (Sourcery refactored) by sourcery-ai in https://github.com/cpp-lln-lab/bidsMReye/pull/104
* [MNT] update badge by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/105
* [FIX] fix typo in import by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/107
* [MNT] add release drafter - skip-ci by Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/108


**Full Changelog**: https://github.com/cpp-lln-lab/bidsMReye/compare/0.1.2...0.2.0