[BUG] keep working directory on failed run / flag to keep pipeline working directory on success #345

bcmcpher · 2024-08-30T21:37:41Z

Closes Pipeline runner removes work directory regardless of job success / fail #297

Changes proposed in this pull request:

Modified .run_cleanup() method to not remove working files in failed processes to facilitate resuming / restarting.
Added additional flag to PipelineRunner() to optionally keep working files even on success.

Checklist (for reviewers)

PR has an interpretable title with a prefix (e.g. [BUG], [DOC], [ENH], [MAINT])\
PR links to GitHub issue with mention Closes #XXXX
Tests pass
Checks pass

For bug fixes:

There is at least one test that would fail under the original bug conditions

… runs - TODO write test

for more information, see https://pre-commit.ci

codecov · 2024-08-30T21:40:22Z

Codecov Report

All modified and coverable lines are covered by tests ✅

Files with missing lines	Coverage Δ
nipoppy/cli/parser.py	`100.00% <100.00%> (ø)`
nipoppy/cli/run.py	`95.74% <ø> (ø)`
nipoppy/workflows/runner.py	`100.00% <100.00%> (ø)`

michellewang

This looks good overall. The main thing would be to add a test that checks if the directories are kept when there are failures (even if keep_workdir is False). Otherwise minor comments about log message being redundant with other parts of the code.

michellewang · 2024-08-30T22:05:18Z

nipoppy/cli/parser.py

+def add_arg_keepworkdir(parser: _ActionsContainer) -> _ActionsContainer:
+    """Add a --keep_workdir argument to the parser."""
+    parser.add_argument(
+        "--keep_workdir",


Use kebab-style to be consistent with other CLI args

Suggested change

"--keep_workdir",

"--keep-workdir",

Also should update docstring after this change is made

michellewang · 2024-08-30T22:10:32Z

nipoppy/workflows/runner.py

-            if dpath.exists():
-                self.rm(dpath)
+        if self.n_success == self.n_total:
+            self.logger.info("All pipeline segments completed successfully.")


Don't think this is needed since there is already a feedback message printed (from here)

michellewang · 2024-08-30T22:15:13Z

nipoppy/workflows/runner.py

+        if self.n_success == self.n_total:
+            self.logger.info("All pipeline segments completed successfully.")
+            if not self.keep_workdir:
+                self.logger.info("Removing working / intermediary files.")


Log message probably not needed since BaseWorkflow.rm() already prints a log message (see here)

michellewang · 2024-08-30T22:18:54Z

tests/test_workflow_runner.py


-def test_run_cleanup(tmp_path: Path):
+@pytest.mark.parametrize("keep_workdir", [True, False])
+def test_run_cleanup(tmp_path: Path, keep_workdir):


This looks good but we should also include another test for different values of n_success and n_total (this is also what CodeCov is complaining about. See e.g. this test which sets n_success and n_total to different values with different expected results for each pair

michellewang · 2024-08-30T22:27:41Z

nipoppy/cli/parser.py

+        "--keep_workdir",
+        type=str,
+        required=False,
+        help="Keep pipeline working directory upon success (default: False).",


Instead of (default: False), I would put something like `(default: working directory deleted unless a run failed)".

Also ideally mention that this applies to the pyBIDS database too (if it was created)

…test variable for clarity

michellewang

Thanks @bcmcpher!🧑‍🍳

* [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>

* [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>

bcmcpher and others added 7 commits August 29, 2024 15:15

added method / test for flag to clear working directory

5e24867

added --keep_workdir argument to parser; fixed bad spacing in test

00488aa

removed dev comments

7d79542

added pipeline runner arg to parser / cli invocation

f86e635

added logic to run_cleanup for keeping intermediary files from failed…

f010653

… runs - TODO write test

finalized cleanup fix and unit test

67f0bd8

[pre-commit.ci] auto fixes from pre-commit.com hooks

14e7b1a

for more information, see https://pre-commit.ci

github-actions bot added the T.0 - Bug Something isn't working label Aug 30, 2024

michellewang self-requested a review August 30, 2024 22:03

michellewang requested changes Aug 30, 2024

View reviewed changes

bcmcpher self-assigned this Oct 3, 2024

bcmcpher added 2 commits October 3, 2024 13:44

added unit test for codecov, addressed log feedback

aa58094

Merge remote-tracking branch 'upstream/main' into wd-clean

9356bf9

bcmcpher force-pushed the wd-clean branch from c279cf9 to 9356bf9 Compare October 4, 2024 20:29

bcmcpher added 2 commits October 4, 2024 16:35

added pre-commit to env

594e9d3

added config saving to test from new api; renamed fail to success in …

d0f8a2d

…test variable for clarity

michellewang approved these changes Oct 4, 2024

View reviewed changes

bcmcpher merged commit 33961a1 into nipoppy:main Oct 4, 2024
10 checks passed

bcmcpher deleted the wd-clean branch October 4, 2024 20:51

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[BUG] keep working directory on failed run / flag to keep pipeline working directory on success #345

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[BUG] keep working directory on failed run / flag to keep pipeline working directory on success #345

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bcmcpher commented Aug 30, 2024

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