Bagel update #111
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Bagel update #111
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delete update_dataset_repos.yml and check_changed_files.yml
* add scaffolding for user guide * add links to User guide at the end of Quickstart page * add page for "Populating an empty dataset" * rename organization.md -> organization_imaging.md * add tabular organization page and add link to populate page in quickstart guide * pin sphinx-autoapi to 3.0.0 for now to silence warnings * update "Populating an empty dataset" page * add mostly complete DICOM reorg page * add note on supported operating systems * make minor changes to dataset population page * fix `nipoppy reorg` not passing `--check-dicoms` flag to workflow * add instructions for customizing DICOM reorganization * rename organization_* files to organizing_* * add summary section in BIDS conversion page * add remaining content in BIDS conversion page * add processing pipeline page * add user guide page for trackers * add workflow descriptions * add more information about doughnut file * add notes about Boutiques * add empty "global configs" page + other small changes * write user guide for global config * remove references that cause warnings... * link to other template string replacement sections in tracker config file description * show example input/output for DICOM reorg * add box about logfile directory for each command in CLI reference * expose DICOM_DIR_PARTICIPANT_FIRST default value in sample global config * update paths in DICOM reorg page * update dicom_dir_map (tests failing) * fix attribute name in conf.py * update BIDS conversion page to include BIDScoin * update template string patterns after participant/session variable rename * address PR review comments * make tests run again * update directory tree figure * update README and figure * update URLs to GitHub repo
change linting config and apply pre-commit
…t counts in pheno analysis
* [pre-commit.ci] pre-commit autoupdate updates: - [github.com/pre-commit/pre-commit-hooks: v4.5.0 → v4.6.0](pre-commit/pre-commit-hooks@v4.5.0...v4.6.0) - [github.com/psf/black-pre-commit-mirror: 23.12.1 → 24.4.2](psf/black-pre-commit-mirror@23.12.1...24.4.2) - [github.com/pyCQA/flake8: 7.0.0 → 7.1.1](PyCQA/flake8@7.0.0...7.1.1) - [github.com/codespell-project/codespell: v2.2.6 → v2.3.0](codespell-project/codespell@v2.2.6...v2.3.0) * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* update version number * update CITATION.cff * add build_and_publish.yml workflow * fix codecov badge in README * fix ORCID * fix TestPyPI URL * update workflow * use GitHub URLs for README images * add dynamic version * [MAINT] change linting config and apply pre-commit (nipoppy#311) change linting config and apply pre-commit * do not publish to TestPyPI on every push (for now) --------- Co-authored-by: Remi Gau <[email protected]>
…y#261) * add success message for InitWorkflow * add success message for DoughnutWorkflow * add summary message for DicomReorgWorkflow * remove kwargs arguments from run_* functions * slightly update message in DicomReorgWorkflow * add summary message for BasePipelineWorkflow * make the CLI return a non-zero exit code if run_single fails at least once * try to increase test coverage * fix bad merge * refactor return codes into nipoppy.env * use class instead of enum and add color class * address some of the PR comments * commit for release 0.2.0 * address more PR comments
* add version to cli * add test
updates: - [github.com/psf/black-pre-commit-mirror: 24.4.2 → 24.8.0](psf/black-pre-commit-mirror@24.4.2...24.8.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
remove restriction to main branch
* apply substitutions based on pipeline config name/version instead of CLI argument * add test checking for existence of pipeline config files (descriptor/invocation/tracker/pybids) * add similar substitution for step name * address PR review comments
* add workflow for new issues * try a projects automation workflow * fix wrong column for new issues * change trigger to `pull_request_target` * fix if conditions * don't run on PR being opened/reopened * [MAINT] automatically label stale issues and PRs. --------- Co-authored-by: Mathieu Dugré <[email protected]>
* restore jobs->steps change * comment out steps that run after pull_request_review events since they do not work
* delete nipoppy folder * remove tests, pyproject.toml and other files * move nipoppy_cli/* files to root * fix flake8 and pre-commit * fix paths and other mentions of `nipoppy_cli` * remove old test workflow * fix path in README * fix README path * fix readthedocs path * make isort and black work more nicely together
* [DOC] Revise installation steps for PyPI. Also shortened some parts to be less verbose for new users. * [DOC] add PyPI badge to readme. * Update nipoppy_cli/docs/source/installation.md Co-authored-by: Michelle Wang <[email protected]> * [ENH] make PyPI badge clickable. * [BUG] fix the url formatting for PyPI badge. * [DOC] Revise installation steps for PyPI. Also shortened some parts to be less verbose for new users. * [DOC] add PyPI badge to readme. * Update nipoppy_cli/docs/source/installation.md Co-authored-by: Michelle Wang <[email protected]> * [ENH] make PyPI badge clickable. * [REV] add back the venv instruction. * [DOC] Clean-up README after removing the legacy package. * [FIX] michelle fixed something... --------- Co-authored-by: Michelle Wang <[email protected]>
remove step that added software label
…roup-level processing (nipoppy#341) * add "ANALYSIS_LEVEL" to pipeline step configs * restore pybids ignore test... * use BasePipelineConfig instead of ProcPipelineConfig in tests whenever possible * implement analysis level in BasePipelineWorkflow * update BIDSCOIN global config * add newlines * raise a warning when replacing a template string with None * modify log message in run_cleanup to take analysis level into account * fix warning due to missing return statement in Pydantic validator * address PR review comments
* exclude pydicom version 3.0.0 * prevent loggers from propagating to root logger * add test checking for unexpected logs entries
* add auto-generated changelog * add comment for PAT config
* refactor pipeline_step_config in workflows * fix tests * add back check_pipeline_step * address PR review comments
* first extract from datalad PR * drop datalad install * add comment * do not use distutil * fix * Apply suggestions from code review Co-authored-by: Michelle Wang <[email protected]> * fixes * add test dry run * download bids readme template --------- Co-authored-by: Michelle Wang <[email protected]>
* relax doc dependency versions and update autoapi configs/template * silence warnings
* work in progress * add sections for PR review process and other * fix emojis
* add logo to README and docs website * do not use logo image in README because of padding issues/mobile view concerns * add poppy icon with the text
test with 3.13 Co-authored-by: Mathieu Dugré <[email protected]>
* [BUG] Fix logo path * Update README.md
…ipoppy#371) * Pybids database creation toggle * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * missing test change * Update nipoppy/config/pipeline_step.py Co-authored-by: Michelle Wang <[email protected]> * Update nipoppy/workflows/runner.py Co-authored-by: Michelle Wang <[email protected]> * Update test_workflow_runner.py * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * try to fix pre-commit * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * actually fix pre-commit --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Michelle Wang <[email protected]>
* [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
…related to subprocesses (nipoppy#410) * remove markup in logging related to subprocesses * add comments * clean up run_command
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