Re-enable anat fasttrack for dataset without t1w #3202
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Codecov ReportAttention:
Additional details and impacted files@@ Coverage Diff @@
## master #3202 +/- ##
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- Coverage 72.36% 72.35% -0.01%
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Files 55 55
Lines 4103 4106 +3
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+ Hits 2969 2971 +2
- Misses 1134 1135 +1 ☔ View full report in Codecov by Sentry. |
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Question for CircleCI experts: is there an easy way to run part of the tests locally? |
Not really. You need to set up the test data in the same way as the workflow. |
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After a lot of mistakes I managed to get the added circleci test to work. 🤦🏼 It still raises coverage issue, should I expand coverage for this usecase? |
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Coverage is always a pain, please don't worry about it. I'll have a look at this today. |
effigies
reviewed
Jan 16, 2024
effigies
reviewed
Jan 16, 2024
Co-authored-by: Chris Markiewicz <effigies@gmail.com>
effigies
reviewed
Jan 16, 2024
effigies
reviewed
Jan 16, 2024
Co-authored-by: Chris Markiewicz <effigies@gmail.com>
effigies
reviewed
Jan 17, 2024
trying to reuse the workdir, IIRC it gave me errors before Co-authored-by: Chris Markiewicz <effigies@gmail.com>
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Thanks @effigies for all your help in making this PR merged on a short time! |
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Jun 17, 2024
24.0.0 (June 17, 2024) New feature release in the 24.0.x series. This release is an incremental improvement on 23.2.x, with some fixes for bugs discovered in the updated workflow. New features include separation of HTML reports by session for subjects with many BOLD runs, a new ``--fs-no-resume`` option to improve interoperability with less typical FreeSurfer directories, such as those generated by longitudinal FreeSurfer or FastSurfer, and adoption of DatasetLinks and BIDS-URIs, to follow the recommendations of recent versions of BIDS. With thanks to Dimitri Papadopoulos, Basile Pinsard, Celine Provins, Taylor Salo and Wang Hao-Ting for their contributions! * FIX: Add "double" type to allowed DisplacementFieldTransform (#3287) * FIX: Require recent templateflow, select correct aparc dseg.tsv (#3256) * FIX: Ensure proper templates are retrieved with sloppy (#3251) * FIX: Delete summary from functional report when separated by sessions (#3223) * FIX: Support lists in bids filter file containing ``null`` or ``*`` (#3215) * FIX: Re-enable anat fasttrack for dataset without t1w (#3202) * ENH: Use BIDSURI in init_ds_boldmask_wf (#3297) * ENH: Add templateflow to DatasetLinks (#3267) * ENH: Track proximal sources of functional GIFTIs (#3263) * ENH: Support named derivative paths (#3264) * ENH: Track Sources for standard-space outputs (#3262) * ENH: Add --fs-no-resume option to reuse existing FreeSurfer outputs without resuming (#3142) * ENH: Use BIDS URIs to track Sources in sidecars (#3255) * ENH: Ignore unselected subjects in BIDSLayoutIndexer (#3236) * ENH: Add metadata for motion parameters (#3245) * ENH: Separate anatomical and functional reports per session for densely sampled dataset (#3191) * ENH: Leverage T2w if available for BOLD -> anat coregistration (#3208) * RF: Fix ITK warp conversion to nitransforms format (#3300) * RF: Load report assembler from nireports (#3177) * DOC: Clarify ``--dvars-spike-threshold`` uses standardized DVARS (#3205) * TST: Update test to reflect new report generation behavior (#3210) * STY: Manual conversions to f-strings (#3241) * STY: Apply ruff/pyupgrade rule UP031 (#3280) * STY: Lint and style check full repository (#3221) * STY: Adopt ruff for linting and formatting (#3206) * MNT: Pin libitk 5.3 and note dependencies (#3298) * MNT: Upgrade ruff pre-commit, add fixing checks (#3283) * MNT: Complete transition from flake8/black to ruff (#3279) * MNT: Apply Repo-Review suggestions (#3194) * MNT: Verbatim copy of Apache license 2.0 (#3259) * MNT: Bump cryptography from 41.0.7 to 42.0.4 (#3234) * MNT: Drop copyright year, unused dunder fields (#3247) * MNT: Update environment pins (#3226) * MNT: Bump codecov/codecov-action from 3 to 4 (#3219) * DOCKER: Restore mincinfo binary (#3249) * CI: Move to new circle machine tags (#3248) * CI: Avoid ruff warning (#3244) * CI: Pass ruff tests (#3243)
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Changes proposed in this pull request
fixes #3201
Re-enables the possibility to run fMRIPrep on a fMRI only dataset using anat derivatives from another (anatomical) dataset with the same participant.
Tries to implement integration test for that feature.
related to #2201
Documentation that should be reviewed
NA