https://github.com/poldracklab/mriqc

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4d96184 rel(23.1.1): Update CHANGES [skip ci] 20 March 2024, 11:15:20 UTC
907fc1c Merge pull request #1207 from nipreps/fix/dwi-pipeline-hmc-input FIX: Missing conection to head-motion estimation node in DWI workflow 20 March 2024, 11:06:44 UTC
1ad39fc Merge pull request #1208 from nipreps/fix/ruff-edits-side-effects MAINT: Add ``pytest-env`` as a dependency 20 March 2024, 10:40:12 UTC
af7dfee fix: add ``pytest-env`` as a dependency 20 March 2024, 10:37:29 UTC
17910cc fix: missing conection to head-motion estimation node in DWI workflow 20 March 2024, 10:33:41 UTC
a902225 rel(23.1.1): Update CONTRIBUTORS [skip ci] 20 March 2024, 09:23:13 UTC
fbbd916 rel(23.1.1): remove link dependency on *NiWorkflows* 20 March 2024, 09:18:37 UTC
5de1e08 rel(23.1.1): Update CHANGES [skip ci] 20 March 2024, 09:18:37 UTC
6c5c03d Merge pull request #1205 from DimitriPapadopoulos/CONTRIBUTORS MAINT: Update contributor details in ``CONTRIBUTORS.md`` 20 March 2024, 09:18:19 UTC
61d964d Merge pull request #1206 from nipreps/dependabot/github_actions/actions/setup-python-5 MAINT: Bump ``actions/setup-python`` from 4 to 5 20 March 2024, 09:04:22 UTC
8440c45 chore(deps): bump actions/setup-python from 4 to 5 Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](https://github.com/actions/setup-python/compare/v4...v5) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> 20 March 2024, 08:55:55 UTC
7aba220 Update my details in CONTRIBUTORS.md 20 March 2024, 08:55:38 UTC
a2cfa10 Merge pull request #1204 from DimitriPapadopoulos/ruff Start fixing Repo-Review issues 20 March 2024, 08:54:47 UTC
8aebe5d MAINT: remove isort config It has been recently replaced by ruff/isort rules. 20 March 2024, 08:31:33 UTC
6138332 MAINT: apply Repo-Review ruff rules RF201: Avoid using deprecated config settings extend-ignore deprecated, use ignore instead (identical) 20 March 2024, 08:31:33 UTC
7b456b1 MAINT: apply Repo-Review Dependabot rules GH200: Maintained by Dependabot All projects should have a .github/dependabot.yml file to support at least GitHub Actions regular updates. Copied from: https://github.com/dependabot/demo/ 20 March 2024, 08:31:33 UTC
7bfa637 MAINT: apply Repo-Review pytest rules PP302: Sets a minimum pytest to at least 6 Must have a minversion=, and must be at least 6 (first version to support pyproject.toml configuration). PP304: Sets the log level in pytest log_cli_level should be set. This will allow logs to be displayed on failures. PP305: Specifies xfail_strict xfail_strict should be set. You can manually specify if a check should be strict when setting each xfail. PP306: Specifies strict config --strict-config should be in addopts = [...]. This forces an error if a config setting is misspelled. PP307: Specifies strict markers --strict-markers should be in addopts = [...]. This forces all markers to be specified in config, avoiding misspellings. PP308: Specifies useful pytest summary An explicit summary flag like -ra should be in addopts = [...] (print summary of all fails/errors). 20 March 2024, 08:31:33 UTC
20a2d56 STY: apply ruff/refurb rules FURB148 `enumerate` index is unused, use `for x in y` instead 20 March 2024, 08:31:33 UTC
3127cc0 rel(23.1.1): Update CONTRIBUTORS [skip ci] Please @yibeichan, @neurorepro, and @DimitriPapadopoulos confirm you are okay with *officially* becoming MRIQC contributors and check your details on the ``.maint/CONTRIBUTORS.md`` table. Thanks for your contributions! 20 March 2024, 08:27:13 UTC
98638e9 rel(23.1.1): Update CHANGES [skip ci] 20 March 2024, 08:06:46 UTC
b5ae766 Merge pull request #1156 from DimitriPapadopoulos/3.12 MAINT: Test on Python 3.12 20 March 2024, 07:50:31 UTC
4a6c2f8 Merge branch 'master' into 3.12 20 March 2024, 06:15:19 UTC
544a505 Merge pull request #1203 from nipreps/sty/ruff STY: Add *Ruff* config and fix all warnings and errors 19 March 2024, 23:22:40 UTC
4d76600 sty: apply unsafe ruff fixes 19 March 2024, 22:49:05 UTC
9876ac4 sty: automatic changes by ruff 19 March 2024, 22:39:53 UTC
46c67a3 sty: configure and run ruff 19 March 2024, 22:39:53 UTC
7bc9ece Merge pull request #1202 from nipreps/maint/skip-flaky-test MAINT: Disable flaky T1w test on CircleCI 19 March 2024, 22:21:58 UTC
bacf330 main: disable flaky test 19 March 2024, 22:00:36 UTC
7921651 Merge pull request #1201 from nipreps/fix/sloppy-last-merges-2 HOTFIX: Revise porting to Loader 19 March 2024, 17:15:04 UTC
21cc46c hotfix: revise porting to Loader 19 March 2024, 17:13:40 UTC
a833602 Merge pull request #1200 from nipreps/fix/sloppy-last-merges FIX: Revise the last two sloppy merges 19 March 2024, 16:38:14 UTC
1d993d8 fix: variable name 19 March 2024, 16:33:59 UTC
26bfaf4 fix: wrong package string for Loaders 19 March 2024, 16:31:59 UTC
e57973e Merge pull request #1199 from nipreps/fix/move-to-loader FIX: Move from ``pkg_resources`` to ``niworkflows.data.Loader`` 19 March 2024, 14:48:15 UTC
3e26dfa Merge pull request #1198 from nipreps/enh/better-logging ENH: Improved logging and optimize early checkpoint on subjects 19 March 2024, 14:48:01 UTC
eca27e4 fix: move from ``pkg_resources`` to ``niworkflows.data.Loader`` 19 March 2024, 14:37:12 UTC
1108879 ENH: Improved logging and optimize early checkpoint on subjects This improves the initial logging so that the first message doesn't take a long while to signal MRIQC started. 19 March 2024, 14:34:37 UTC
b8f21ab Merge pull request #1197 from oesteban/fix/dipy-missing FIX: DIPY not listed as a dependency 19 March 2024, 13:08:18 UTC
56b4543 fix: DIPY not listed as a dependency 19 March 2024, 13:06:39 UTC
48a8154 Merge pull request #1196 from nipreps/fix/dwidenoise-missing FIX: Include ``dwidenoise`` within docker image 19 March 2024, 12:58:17 UTC
4c97bb6 fix: include ``dwidenoise`` within docker image Implements [@effigies' solution](https://github.com/nipreps/mriqc/issues/1175#issuecomment-1917588140) leveraging Docker multi-staged builds. Checked linked libraries within the Docker container: ``` $ ldd /usr/local/bin/dwidenoise linux-vdso.so.1 (0x00007fff6db65000) libmrtrix.so => /usr/local/bin/../lib/libmrtrix.so (0x00007f4e2b757000) libstdc++.so.6 => /opt/conda/lib/libstdc++.so.6 (0x00007f4e2b574000) libm.so.6 => /usr/lib/x86_64-linux-gnu/libm.so.6 (0x00007f4e2b48d000) libgcc_s.so.1 => /opt/conda/lib/libgcc_s.so.1 (0x00007f4e2b472000) libpthread.so.0 => /usr/lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f4e2b46d000) libc.so.6 => /usr/lib/x86_64-linux-gnu/libc.so.6 (0x00007f4e2b242000) /lib64/ld-linux-x86-64.so.2 (0x00007f4e2bac2000) libz.so.1 => /opt/conda/lib/libz.so.1 (0x00007f4e2b227000) libtiff.so.5 => /usr/lib/x86_64-linux-gnu/libtiff.so.5 (0x00007f4e2b19f000) libpng16.so.16 => /opt/conda/lib/libpng16.so.16 (0x00007f4e2b162000) librt.so.1 => /usr/lib/x86_64-linux-gnu/librt.so.1 (0x00007f4e2b15d000) libwebp.so.7 => /opt/conda/lib/libwebp.so.7 (0x00007f4e2b0bb000) libzstd.so.1 => /opt/conda/lib/libzstd.so.1 (0x00007f4e2afa7000) liblzma.so.5 => /opt/conda/lib/liblzma.so.5 (0x00007f4e2af7e000) libjbig.so.0 => /usr/lib/x86_64-linux-gnu/libjbig.so.0 (0x00007f4e2af6d000) libjpeg.so.8 => /opt/conda/lib/libjpeg.so.8 (0x00007f4e2ae87000) libdeflate.so.0 => /opt/conda/lib/libdeflate.so.0 (0x00007f4e2ae71000) libsharpyuv.so.0 => /opt/conda/lib/./libsharpyuv.so.0 (0x00007f4e2ae65000) ldd /usr/local/lib/libmrtrix.so linux-vdso.so.1 (0x00007ffc0a0b6000) libz.so.1 => /opt/conda/lib/libz.so.1 (0x00007f431b203000) libtiff.so.5 => /usr/lib/x86_64-linux-gnu/libtiff.so.5 (0x00007f431b17b000) libpng16.so.16 => /opt/conda/lib/libpng16.so.16 (0x00007f431b13e000) libstdc++.so.6 => /opt/conda/lib/libstdc++.so.6 (0x00007f431af5b000) libm.so.6 => /usr/lib/x86_64-linux-gnu/libm.so.6 (0x00007f431ae74000) libgcc_s.so.1 => /opt/conda/lib/libgcc_s.so.1 (0x00007f431ae57000) libpthread.so.0 => /usr/lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f431ae52000) libc.so.6 => /usr/lib/x86_64-linux-gnu/libc.so.6 (0x00007f431ac29000) /lib64/ld-linux-x86-64.so.2 (0x00007f431b4d5000) libwebp.so.7 => /opt/conda/lib/libwebp.so.7 (0x00007f431ab89000) libzstd.so.1 => /opt/conda/lib/libzstd.so.1 (0x00007f431aa75000) liblzma.so.5 => /opt/conda/lib/liblzma.so.5 (0x00007f431aa4c000) libjbig.so.0 => /usr/lib/x86_64-linux-gnu/libjbig.so.0 (0x00007f431aa39000) libjpeg.so.8 => /opt/conda/lib/libjpeg.so.8 (0x00007f431a953000) libdeflate.so.0 => /opt/conda/lib/libdeflate.so.0 (0x00007f431a93d000) librt.so.1 => /usr/lib/x86_64-linux-gnu/librt.so.1 (0x00007f431a938000) libsharpyuv.so.0 => /opt/conda/lib/./libsharpyuv.so.0 (0x00007f431a92e000) ``` And also tested *MRIQC* locally on DWI data. Resolves: #1175. 19 March 2024, 12:51:26 UTC
a188da5 Merge pull request #1195 from oesteban/maint/dockerfile-update MAINT: Overhaul of the ``Dockerfile`` 19 March 2024, 11:09:01 UTC
0b7c8dc enh: pacify datalad within docker 19 March 2024, 11:08:28 UTC
1cd0a88 fix: add missing AFNI program 19 March 2024, 10:36:33 UTC
1e8292d fix: missing AFNI program and circle pytest build 19 March 2024, 09:12:20 UTC
e4ccb5a fix(dockerimage): add missing AFNI program 19 March 2024, 08:39:34 UTC
d03c783 fix(dockerfile): do not remove necessary AFNI program 19 March 2024, 08:10:48 UTC
d5854c8 fix(circleci): make sourcecode available where needed 19 March 2024, 08:10:28 UTC
f4e70a2 fix: do not remove afni binary, fix tests build 18 March 2024, 23:04:13 UTC
b7283c8 fix: update circleci settings 18 March 2024, 22:17:42 UTC
3a9a69d fix: afni environment 18 March 2024, 21:52:29 UTC
e717df1 enh: update to latest miniconda image 18 March 2024, 17:36:50 UTC
ed700ef MAINT: Overhaul of the ``Dockerfile`` Update the docker build procedure to leverage multi-stage builds and lay the ground for #1175. 18 March 2024, 14:07:43 UTC
b16bfcb Merge pull request #1194 from nipreps/maint/revise-package-extra-deps MAINT: Revise package's extra dependencies 18 March 2024, 10:56:07 UTC
7347d59 Merge pull request #1193 from nipreps/maint/cleanup-setuptools-scm-remnants MAINT: Clean up some ``setuptools_scm`` remnants 18 March 2024, 10:55:51 UTC
2fa2d83 fix(circleci): documentation build 18 March 2024, 10:34:51 UTC
6d3a24f fix: git-archival and other minour issues 18 March 2024, 10:31:45 UTC
fda0c15 maint(deps): revise package's extra dependencies 18 March 2024, 10:22:24 UTC
c3dba83 maint(CircleCI): clean up some setuptools_scm remnants 18 March 2024, 10:19:24 UTC
2a6793e Merge pull request #1187 from celprov/fix/derivative_name_json FIX: copy name attribute of dataset_description.json from input dataset 18 March 2024, 10:17:09 UTC
9fcebc5 Merge pull request #1179 from celprov/fix/fd_is_not_iterfield FIX: Remove FD as an ``iterfield`` in ``MapNode`` causing crash with ME-BOLD 18 March 2024, 10:16:32 UTC
3b512df Merge pull request #1192 from nipreps/docs/fix-sphinx-pin DOC: Update sphinx pinned version to 5 18 March 2024, 10:14:18 UTC
ab1bd01 docs: update sphinx pinned version to 5 18 March 2024, 09:57:09 UTC
63f9b70 CI: Test on Python 3.12 18 March 2024, 09:16:02 UTC
fa714a3 Merge branch 'master' into fix/fd_is_not_iterfield 18 March 2024, 09:14:15 UTC
9050c05 Merge pull request #1186 from DimitriPapadopoulos/extraneous_parenthese STY: Remove extraneous parentheses 18 March 2024, 09:13:39 UTC
1fddcfc Update mriqc/utils/bids.py 18 March 2024, 09:13:01 UTC
3266559 Merge pull request #1188 from nipreps/oesteban-patch-1 FIX: Incorrect plugin metadata passed to Report assembler 08 March 2024, 08:38:46 UTC
4352183 fix: incorrect plugin metadata passed to Report assembler Resolves: #1127. 06 March 2024, 11:07:02 UTC
0af7a17 fix: precise MRIQC derivatives in the derivatives description name 05 March 2024, 17:20:59 UTC
9e5cfe8 fix: setup name attribute in derivative description from the dataset dataset_description.json 05 March 2024, 16:30:34 UTC
911430d STY: Remove extraneous parentheses https://docs.astral.sh/ruff/rules/extraneous-parentheses/ 01 March 2024, 09:43:30 UTC
4ccc5d8 Merge branch 'master' into fix/fd_is_not_iterfield 30 January 2024, 13:12:06 UTC
fef7289 Merge pull request #1174 from celprov/fix/dwi-key-missing FIX: temporary fix of the missing dwi key 29 January 2024, 15:30:08 UTC
095dca9 fix: remove fd as an iterfield in mapnode 29 January 2024, 15:26:05 UTC
ee51436 fix: missing dwi key in QCGROUPS dictionary 29 January 2024, 15:18:02 UTC
24f786a Merge pull request #1164 from celprov/fix/multi-echo-report FIX: Rearrange multi-echo report 15 December 2023, 17:06:42 UTC
9cb24e0 Merge branch 'master' into fix/multi-echo-report 14 December 2023, 23:59:33 UTC
d10c981 Merge pull request #1167 from celprov/maint/move-fmrisummary-to-nireports MAINT: load FMRISummary from nireports rather than niworkflows 07 December 2023, 23:09:28 UTC
b3be14c maint: load FMRISummary from nireports rather than niworkflows 07 December 2023, 21:55:25 UTC
41fdc70 Merge pull request #1166 from psadil/enh/store-qc-timeseries ENH: store confound timeseries data 06 December 2023, 21:26:34 UTC
337f892 Merge branch 'master' into fix/multi-echo-report 06 December 2023, 19:29:02 UTC
0cf2543 sty: reformat to pep8 05 December 2023, 19:45:12 UTC
92cb229 Avoid exists=True on output file; describe returned dictionary Co-authored-by: Chris Markiewicz <effigies@gmail.com> 05 December 2023, 19:42:17 UTC
8aba7a5 Return absolute path based on `runtime.cwd` Co-authored-by: Chris Markiewicz <effigies@gmail.com> 05 December 2023, 19:41:42 UTC
c1fa19b Favor `TraitedSpec` over unnecessary use of `BaseInterfaceInputSpec` Co-authored-by: Chris Markiewicz <effigies@gmail.com> 05 December 2023, 19:14:07 UTC
c6fab96 fix new flake8 issues after rebase on clean commit 05 December 2023, 18:09:59 UTC
ff1d686 store confound timeseries data 05 December 2023, 17:51:31 UTC
db3d3cb Merge pull request #1165 from celprov/fix/typo-in-diffusion-wf FIX: Typo in inputnode field for dmri mask workflow 05 December 2023, 01:39:20 UTC
22106d9 fix: typo in diffusion wf 05 December 2023, 00:32:34 UTC
8dd4801 enh: promote background viz to base report fix: reinstate the zoomed-in avg viz to base report enh: reverse order of extended echo-wise and extended share across echos section fix: adapt workflow accordingly, so that necessary plots are computed before the return if not verbose 04 December 2023, 18:41:30 UTC
8ceadba Merge pull request #1160 from mgxd/chore/migas MAINT: update to latest migas API 27 November 2023, 14:08:46 UTC
89fedbe Merge pull request #1162 from DimitriPapadopoulos/refurb STY: Apply a few refurb suggestions 27 November 2023, 14:07:26 UTC
85565e4 Merge pull request #1161 from DimitriPapadopoulos/codespell STY: Fix typo found by codespell 27 November 2023, 14:05:47 UTC
d41e41f STY: directly iterate over OrderedDict - No need for an intermediate list when iterating over keys() or items(). - Iterating over keys() is the same as iterating over the OrderedDict. 21 November 2023, 21:55:50 UTC
82383b2 STY: Apply a few refurb suggestions [FURB109]: Replace `in [x, y, z]` with `in (x, y, z)` [FURB110]: Replace `x if x else y` with `x or y` [FURB138]: Consider using list comprehension 21 November 2023, 21:46:32 UTC
f3ff572 STY: Fix typo found by codespell 21 November 2023, 21:31:05 UTC
7d3909d Update mriqc/cli/run.py 21 November 2023, 16:41:28 UTC
5c8d8f7 chore: update to latest migas api 21 November 2023, 05:18:38 UTC
3752c5d Merge pull request #1155 from nipreps/fix/multi-echo-bold ENH: Large overhaul of the functional workflow w/focus on ME-EPI 19 November 2023, 16:46:13 UTC
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