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Recent Releases of Giga Connectome

Giga Connectome - 0.6.0

What's Changed

  • [MAINT] Post release 0.5.0 by @htwangtw in https://github.com/bids-apps/giga_connectome/pull/133
  • [BOT] update pre-commit hooks by @github-actions in https://github.com/bids-apps/giga_connectome/pull/134
  • [BOT] update pre-commit hooks by @github-actions in https://github.com/bids-apps/giga_connectome/pull/137
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/bids-apps/giga_connectome/pull/138
  • Bump actions/upload-artifact from 1 to 4 by @dependabot in https://github.com/bids-apps/giga_connectome/pull/139
  • Bump docker/login-action from 2.1.0 to 3.1.0 by @dependabot in https://github.com/bids-apps/giga_connectome/pull/140
  • EHN save denoising details into meta data by @htwangtw in https://github.com/bids-apps/giga_connectome/pull/145
  • [BOT] update pre-commit hooks by @github-actions in https://github.com/bids-apps/giga_connectome/pull/148
  • Update subject segmentation outputs by @htwangtw in https://github.com/bids-apps/giga_connectome/pull/146
  • FIX when renaming the files, only include entity res when it's present by @htwangtw in https://github.com/bids-apps/giga_connectome/pull/149
  • FIX reuse pregenerated subject segmentation or masks by @htwangtw in https://github.com/bids-apps/giga_connectome/pull/150
  • Fix/reuse subj mask by @htwangtw in https://github.com/bids-apps/giga_connectome/pull/152
  • When re-runing with the same atlases, load segmentations by @htwangtw in https://github.com/bids-apps/giga_connectome/pull/153
  • Bump docker/login-action from 3.1.0 to 3.2.0 by @dependabot in https://github.com/bids-apps/giga_connectome/pull/155
  • FIX Address the case of no volumes to scrub when given the scrubbing strategy by @htwangtw in https://github.com/bids-apps/giga_connectome/pull/156
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/bids-apps/giga_connectome/pull/158
  • [BOT] update pre-commit hooks by @github-actions in https://github.com/bids-apps/giga_connectome/pull/160
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/bids-apps/giga_connectome/pull/165
  • Bump docker/login-action from 3.2.0 to 3.3.0 by @dependabot in https://github.com/bids-apps/giga_connectome/pull/162
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/bids-apps/giga_connectome/pull/167
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/bids-apps/giga_connectome/pull/170
  • [FIX] Make sure version docker images matches version of package in the image by @Remi-Gau in https://github.com/bids-apps/giga_connectome/pull/169
  • [ENH] set pybids config by @Remi-Gau in https://github.com/bids-apps/giga_connectome/pull/174
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/bids-apps/giga_connectome/pull/178
  • [MAINT] drop python 3.8 and support 3.13 by @Remi-Gau in https://github.com/bids-apps/giga_connectome/pull/179
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/bids-apps/giga_connectome/pull/180
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/bids-apps/giga_connectome/pull/182
  • Bump codecov/codecov-action from 4 to 5 by @dependabot in https://github.com/bids-apps/giga_connectome/pull/183
  • [DOC] some edits of the docs by @jdkent in https://github.com/bids-apps/giga_connectome/pull/187
  • FIX mypy type on mask array for sanity check by @htwangtw in https://github.com/bids-apps/giga_connectome/pull/189
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/bids-apps/giga_connectome/pull/188
  • Add all contributor bots by @htwangtw in https://github.com/bids-apps/giga_connectome/pull/192
  • docs: add htwangtw as a contributor for ideas, research, and 2 more by @allcontributors in https://github.com/bids-apps/giga_connectome/pull/193
  • docs: add Hyedryn as a contributor for userTesting by @allcontributors in https://github.com/bids-apps/giga_connectome/pull/194
  • FIX QD contribution by @htwangtw in https://github.com/bids-apps/giga_connectome/pull/197
  • Fix/contributor by @htwangtw in https://github.com/bids-apps/giga_connectome/pull/198
  • docs: add Remi-Gau as a contributor for infra, and maintenance by @allcontributors in https://github.com/bids-apps/giga_connectome/pull/199
  • docs: add pbellec as a contributor for ideas, and financial by @allcontributors in https://github.com/bids-apps/giga_connectome/pull/201
  • docs: add shnizzedy as a contributor for bug by @allcontributors in https://github.com/bids-apps/giga_connectome/pull/202
  • docs: add emullier as a contributor for bug by @allcontributors in https://github.com/bids-apps/giga_connectome/pull/203
  • docs: add jdkent as a contributor for bug, and doc by @allcontributors in https://github.com/bids-apps/giga_connectome/pull/204
  • FIX underscore -> hyphen in CLI by @htwangtw in https://github.com/bids-apps/giga_connectome/pull/190
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/bids-apps/giga_connectome/pull/206
  • FIX use types-setuptools as types-all is deprecated by @htwangtw in https://github.com/bids-apps/giga_connectome/pull/191
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/bids-apps/giga_connectome/pull/207
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/bids-apps/giga_connectome/pull/208
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/bids-apps/giga_connectome/pull/209
  • Bump docker/login-action from 3.3.0 to 3.4.0 by @dependabot in https://github.com/bids-apps/giga_connectome/pull/210
  • Improve documention for both contributors and user by @htwangtw in https://github.com/bids-apps/giga_connectome/pull/205
  • DOCS/FIX typo in docstrings by @htwangtw in https://github.com/bids-apps/giga_connectome/pull/214
  • JOSS - Improvement on advance usages examples by @htwangtw in https://github.com/bids-apps/giga_connectome/pull/215
  • FIX ICA-AROMA implementation by @htwangtw in https://github.com/bids-apps/giga_connectome/pull/216
  • docs: add mstimberg as a contributor for userTesting, doc, and bug by @allcontributors in https://github.com/bids-apps/giga_connectome/pull/218
  • MAINT fix precommit badge by @htwangtw in https://github.com/bids-apps/giga_connectome/pull/219
  • Minor edits on docs by @htwangtw in https://github.com/bids-apps/giga_connectome/pull/222
  • Editing fixes for JOSS paper by @mstimberg in https://github.com/bids-apps/giga_connectome/pull/223
  • [JOSS] update affiliations by @htwangtw in https://github.com/bids-apps/giga_connectome/pull/224
  • DOCS add fmriprep version details by @htwangtw in https://github.com/bids-apps/giga_connectome/pull/227
  • REL 0.6.0 by @htwangtw in https://github.com/bids-apps/giga_connectome/pull/226
  • update orcid as JOSS requirement by @htwangtw in https://github.com/bids-apps/giga_connectome/pull/228

New Contributors

  • @jdkent made their first contribution in https://github.com/bids-apps/giga_connectome/pull/187
  • @allcontributors made their first contribution in https://github.com/bids-apps/giga_connectome/pull/193
  • @mstimberg made their first contribution in https://github.com/bids-apps/giga_connectome/pull/223

Full Changelog: https://github.com/bids-apps/giga_connectome/compare/0.5.0...0.6.0

Scientific Software - Peer-reviewed - Python
Published by htwangtw 8 months ago

Giga Connectome - 0.5.0

What's Changed

  • [MAINT] add citation.cff file and validation workflow by @Remi-Gau in https://github.com/bids-apps/giga_connectome/pull/55
  • [MAINT] add workflow to update precommit hooks by @Remi-Gau in https://github.com/bids-apps/giga_connectome/pull/56
  • [MAINT] run test suite with python 3.12 by @Remi-Gau in https://github.com/bids-apps/giga_connectome/pull/57
  • [MAINT] pin dependencies for docker build by @Remi-Gau in https://github.com/bids-apps/giga_connectome/pull/59
  • Bump actions/setup-python from 4 to 5 by @dependabot in https://github.com/bids-apps/giga_connectome/pull/60
  • Bump actions/checkout from 2 to 4 by @dependabot in https://github.com/bids-apps/giga_connectome/pull/61
  • [MAINT] use sphinx argparse to automatically render the cli arguments doc by @Remi-Gau in https://github.com/bids-apps/giga_connectome/pull/71
  • [MAINT] run pre-commit in CI to check style by @Remi-Gau in https://github.com/bids-apps/giga_connectome/pull/72
  • [MAINT] use tox to install test data by @Remi-Gau in https://github.com/bids-apps/giga_connectome/pull/73
  • [MAINT] bump nilearn version to 0.10.2 by @Remi-Gau in https://github.com/bids-apps/giga_connectome/pull/67
  • [ENH] use logger instead of print statements by @Remi-Gau in https://github.com/bids-apps/giga_connectome/pull/74
  • [DOC] add badges to readme by @Remi-Gau in https://github.com/bids-apps/giga_connectome/pull/85
  • [ENH] rerunning the app overrides old files and logs a warning by @Remi-Gau in https://github.com/bids-apps/giga_connectome/pull/83
  • [BOT] update pre-commit hooks by @github-actions in https://github.com/bids-apps/giga_connectome/pull/87
  • [STY] apply pre-commit hooks by @Remi-Gau in https://github.com/bids-apps/giga_connectome/pull/88
  • [BOT] update pre-commit hooks by @github-actions in https://github.com/bids-apps/giga_connectome/pull/90
  • [BOT] update pre-commit hooks by @github-actions in https://github.com/bids-apps/giga_connectome/pull/93
  • [DOC] update changelog by @Remi-Gau in https://github.com/bids-apps/giga_connectome/pull/84
  • [ENH] add methods section by @Remi-Gau in https://github.com/bids-apps/giga_connectome/pull/77
  • update the commit hash of mist2templateflow by @htwangtw in https://github.com/bids-apps/giga_connectome/pull/98
  • [BOT] update pre-commit hooks by @github-actions in https://github.com/bids-apps/giga_connectome/pull/99
  • [STY] apply the new black by @Remi-Gau in https://github.com/bids-apps/giga_connectome/pull/100
  • Bump codecov/codecov-action from 3 to 4 by @dependabot in https://github.com/bids-apps/giga_connectome/pull/101
  • Bump peter-evans/create-pull-request from 5 to 6 by @dependabot in https://github.com/bids-apps/giga_connectome/pull/102
  • Bump actions/cache from 3 to 4 by @dependabot in https://github.com/bids-apps/giga_connectome/pull/103
  • Bump pre-commit/action from 3.0.0 to 3.0.1 by @dependabot in https://github.com/bids-apps/giga_connectome/pull/105
  • [BOT] update pre-commit hooks by @github-actions in https://github.com/bids-apps/giga_connectome/pull/104
  • [MAINT] follow several recommendations from the Scientific Python Library Development Guide by @Remi-Gau in https://github.com/bids-apps/giga_connectome/pull/58
  • [ENH] switch tqdm for rich progress bar by @Remi-Gau in https://github.com/bids-apps/giga_connectome/pull/95
  • [MAINT] bump all artifact actions at once by @Remi-Gau in https://github.com/bids-apps/giga_connectome/pull/107
  • Bump actions/upload-artifact from 3 to 4 by @dependabot in https://github.com/bids-apps/giga_connectome/pull/91
  • Bump actions/download-artifact from 3 to 4 by @dependabot in https://github.com/bids-apps/giga_connectome/pull/92
  • [ENH] start using mypy and updating types by @Remi-Gau in https://github.com/bids-apps/giga_connectome/pull/86
  • change the default atlas to Schaefer20187Networks by @htwangtw in https://github.com/bids-apps/giga_connectome/pull/110
  • Remove all group level related process from the workflow by @htwangtw in https://github.com/bids-apps/giga_connectome/pull/112
  • Improve documentation on customised atlas and denoising strategy by @htwangtw in https://github.com/bids-apps/giga_connectome/pull/108
  • DOCS gigaconnectome workflow with flow chart by @htwangtw in https://github.com/bids-apps/giga_connectome/pull/114
  • [ENH] start bidsifying output by @Remi-Gau in https://github.com/bids-apps/giga_connectome/pull/80
  • remove psc as an option for standardising output by @htwangtw in https://github.com/bids-apps/giga_connectome/pull/113
  • [ENH] add HTML reports for each atlas / masked image by @Remi-Gau in https://github.com/bids-apps/giga_connectome/pull/115
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/bids-apps/giga_connectome/pull/122
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/bids-apps/giga_connectome/pull/125
  • [MAINT] add docker GHA worklow by @htwangtw in https://github.com/bids-apps/giga_connectome/pull/126
  • [MAINT] update codecov badge by @Remi-Gau in https://github.com/bids-apps/giga_connectome/pull/128
  • [DOC] add docker badge and update docs and links by @Remi-Gau in https://github.com/bids-apps/giga_connectome/pull/130
  • ENH harvard oxford atlas by @htwangtw in https://github.com/bids-apps/giga_connectome/pull/132
  • JOSS submision by @htwangtw in https://github.com/bids-apps/giga_connectome/pull/118
  • REL-0.5.0 by @htwangtw in https://github.com/bids-apps/giga_connectome/pull/131

New Contributors

  • @Remi-Gau made their first contribution in https://github.com/bids-apps/giga_connectome/pull/55
  • @dependabot made their first contribution in https://github.com/bids-apps/giga_connectome/pull/60
  • @github-actions made their first contribution in https://github.com/bids-apps/giga_connectome/pull/87
  • @pre-commit-ci made their first contribution in https://github.com/bids-apps/giga_connectome/pull/122

Full Changelog: https://github.com/bids-apps/giga_connectome/compare/0.4.1...0.5.0

Scientific Software - Peer-reviewed - Python
Published by htwangtw over 1 year ago