Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]

Added

Changed

Deprecated

Removed

Fixed

Security

[0.5.0] - 2023-08-12

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

[0.4.0] - 20234-08-05

  • [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

[0.3.1] - 2023-01-23

  • [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

  • [DOC] add CLI info for group level by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/128

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

[0.3.0] - 2022-12-29

  • [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

[0.2.0] - 2022-12-19

  • [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

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

[0.1.0] - 2022-12-08

  • [MNT] coverage, doc, config by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/20

  • [ENH] save one output per subject by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/26

  • [ENH] add CLI by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/28

  • [REF] use Path instead of os.path by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/31

  • [MNT] set up dev docker by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/32

  • [ENH] use logging by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/34

  • [ENH] Dockerfile make by @WeeXee in https://github.com/cpp-lln-lab/bidsMReye/pull/40

  • [ENH] method section and vscode extensions by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/45

  • [ENH] set up config class (Sourcery refactored) by @sourcery-ai in https://github.com/cpp-lln-lab/bidsMReye/pull/50

  • [ENH] set up config class by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/48

  • [ENH] run on several files by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/52

  • [MISC] openneuro demo, add run argument, use pybids database… by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/58

  • [ENH] downloads all models by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/60

  • [FIX] do not specify nb args in argparse of CLI as leads to failure of constructing the config by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/63

  • [MNT] prepare for pypi release by @Remi-Gau in https://github.com/cpp-lln-lab/bidsMReye/pull/85

New Contributors

  • @pre-commit-ci made their first contribution in https://github.com/cpp-lln-lab/bidsMReye/pull/1

  • @Remi-Gau made their first contribution in https://github.com/cpp-lln-lab/bidsMReye/pull/20

  • @sourcery-ai made their first contribution in https://github.com/cpp-lln-lab/bidsMReye/pull/27

  • @WeeXee made their first contribution in https://github.com/cpp-lln-lab/bidsMReye/pull/40

  • @allcontributors made their first contribution in https://github.com/cpp-lln-lab/bidsMReye/pull/46

  • @Naubody made their first contribution in https://github.com/cpp-lln-lab/bidsMReye/pull/66

  • @dependabot made their first contribution in https://github.com/cpp-lln-lab/bidsMReye/pull/70

Full Changelog: https://github.com/cpp-lln-lab/bidsMReye/commits/0.1.0