[REL] Fix merge conflict for REL 0.3.0 #417
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* [MAINT] Only move PRs to pending review. The PR states is then handled by the project workflows. * cleanup file from removed workflow.
…rking directory on success (nipoppy#345) * added method / test for flag to clear working directory * added --keep_workdir argument to parser; fixed bad spacing in test * removed dev comments * added pipeline runner arg to parser / cli invocation * added logic to run_cleanup for keeping intermediary files from failed runs - TODO write test * finalized cleanup fix and unit test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * added unit test for codecov, addressed log feedback * added pre-commit to env * added config saving to test from new api; renamed fail to success in test variable for clarity --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
updates: - [github.com/pre-commit/pre-commit-hooks: v4.6.0 → v5.0.0](pre-commit/pre-commit-hooks@v4.6.0...v5.0.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…eline configs (nipoppy#391) * refactor get_pipeline_version to take a list of pipeline configs * refactor get_pipeline_config to take a list of pipeline configs * add tests for BidsConversionWorkflow * fix sphinx xref warning * remove old nitpick-ignores
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* [ENH] Add `_id` suffix to `bids_participant` and `bids_session` (#382) * rename bids_participant -> bids_participant_id * rename bids_session -> bids_session_id * [ENH] Make `TRACKER_CONFIG_FILE` part of pipeline step config instead of pipeline config (#352) * set default step name * put tracker config file under PipelineStepConfig instead of PipelineConfig (no longer a list) * add pipeline_step column to bagel * use pipeline step config attributes directly instead of getters * improve pipeline step type annotation and refactor validation * update CLI * update tracking-related docs * Revert "improve pipeline step type annotation and refactor validation" This reverts commit aa2e621. * Revert "use pipeline step config attributes directly instead of getters" This reverts commit 6b2821f. * remove pipeline_step_config and check_pipeline_step * move redundant change * fix tests after merge * only allow tracking at participant-session level * address PR review comment * [API] make --dataset-root and positional arg. (#390) * [API] make --dataset-root and positional arg. * [MAINT] Only move PRs to pending review. (#389) * [MAINT] Only move PRs to pending review. The PR states is then handled by the project workflows. * cleanup file from removed workflow. * positional arg should not hae hyphen. Fixed to pass tests. * [ENH] Update pipeline config layout (#383) * move descriptors * move sample invocations * move tracker files * move sample_pipelines inside examples * update layout * update sample global configs * update dataset init and tests * rename proc -> pipelines in layout * fix docs * [ENH] Use TSV instead of CSV for tabular files (#381) * update JSON files * update loading/saving function calls * rename CSV files to TSV * convert to TSV * fix tests * rename remaining csv file * complete CSV -> TSV conversion * update docs * renamed "comma-separated" to "tab-separated" in docs * add check for CSV input and update tests * fix failing test * explicitly set separator as '\t' in BaseTabular instead of relying on default * [ENH] Update layout (#379) * remove releases and demographics directories * rename bids directory * Revert "rename bids directory" This reverts commit 0ff17c9. * move logs directory * rename sourcedata -> to_bidsify * rename raw_imaging -> to_reorg * change fpath_doughnut * move pybids_db file * move pybids_ignore_patterns directory * move downloads under sourcedata/imaging * add new paths for sourcedata directories * add code directory * move containers directory directly under root * add demographics.csv file to layout * move working directories under scratch/work * rename to_reorg -> pre_reorg * rename to_bidsify -> post_reorg * address PR comments * forgot to save before committing * remove missed mentions of "raw"... * rename bagel.tsv -> imaging_bagel.tsv * [ENH] Rename doughnut columns (#404) rename in_raw_imaging -> in_pre_reorg and in_sourcedata -> in_post_reorg * [DOC] Update file trees in user guide page for DICOM reorg (#408) update file trees * [DOC] Update dataset layout figure (#412) * update layout in figure * update figure based on feedback * remove subdirectories/files under pre-/post-reorg * remove trailing slashes, rename idps, etc. * [ENH] Update bagel columns (#354) * remove `pipeline_starttime` column * rename `session` -> `bids_session` * make tracker robust to bad/incompatible existing bagel * rename bids_session -> bids_session_id * fix MRIQC bagel example and add tests for valid/invalid bagels * csv -> tsv * make bids_participant_id and bids_session_id required by the schema * address comment for test --------- Co-authored-by: Sebastian Urchs <surchs@users.noreply.github.com> * [REL] Fix merge conflict for REL 0.3.0 (#417) * [MAINT] Only move PRs to pending review. (#389) * [MAINT] Only move PRs to pending review. The PR states is then handled by the project workflows. * cleanup file from removed workflow. * [BUG] keep working directory on failed run / flag to keep pipeline working directory on success (#345) * added method / test for flag to clear working directory * added --keep_workdir argument to parser; fixed bad spacing in test * removed dev comments * added pipeline runner arg to parser / cli invocation * added logic to run_cleanup for keeping intermediary files from failed runs - TODO write test * finalized cleanup fix and unit test * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * added unit test for codecov, addressed log feedback * added pre-commit to env * added config saving to test from new api; renamed fail to success in test variable for clarity --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#398) updates: - [github.com/pre-commit/pre-commit-hooks: v4.6.0 → v5.0.0](pre-commit/pre-commit-hooks@v4.6.0...v5.0.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [BUG] Do not pool BIDS and PROC pipelines together when searching pipeline configs (#391) * refactor get_pipeline_version to take a list of pipeline configs * refactor get_pipeline_config to take a list of pipeline configs * add tests for BidsConversionWorkflow * fix sphinx xref warning * remove old nitpick-ignores * [ENH] make fmriprep `--fs-no-reconall` value-key and id more intuitive. (#406) --------- Co-authored-by: Brent McPherson <bcmcpher@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Michelle Wang <tomichellewang@gmail.com> --------- Co-authored-by: Michelle Wang <tomichellewang@gmail.com> Co-authored-by: Sebastian Urchs <surchs@users.noreply.github.com> Co-authored-by: Brent McPherson <bcmcpher@gmail.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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[BUG],[DOC],[ENH],[MAINT])Refer to NumPy Development Guide for a full list
Closes #XXXXFor new features:
For bug fixes: