[ENH] Remove pipeline configs from global config #503
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* Create dependabot.yml * add "bot" label * fix indentation * change schedule interval to monthly
* add new workflow and remove old ones * add required `enable-versioned-regex` field * try to fix labeler.yml * add write permissions for PRs * fix typo? * use pull_request_target insteade of pull_request event trigger
…ow (nipoppy#508) use bot instead of PAT
….cff` version after release (nipoppy#512) * add DOI and update contact/authors in CITATION.cff * rename validation workflow * add initial version of update workflow * update workflow * update names * exclude `nipoppy-bot` PRs from changelog
Bumps [actions/stale](https://github.com/actions/stale) from 9.0.0 to 9.1.0. - [Release notes](https://github.com/actions/stale/releases) - [Changelog](https://github.com/actions/stale/blob/main/CHANGELOG.md) - [Commits](actions/stale@v9.0.0...v9.1.0) --- updated-dependencies: - dependency-name: actions/stale dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v3...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@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> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Bump codecov/codecov-action from 4 to 5 Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 4 to 5. - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](codecov/codecov-action@v4...v5) --- updated-dependencies: - dependency-name: codecov/codecov-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * use `files` instead of deprecated `file` * add prefix to PR titles --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Michelle Wang <tomichellewang@gmail.com>
* clean up .gitignore * add entries for Python venvs
* add "how-to" guide for dataset init * address PR comments * split init doc in multiple pages for non-bids vs. bids start * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix error heading * fix heading and paths * fix header bids.md * update index and beginning of each page * update titles * minor changes --------- Co-authored-by: julia-pfarr <juliakatharina.pfarr@gmx.de> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Julia-Katharina Pfarr <111446107+julia-pfarr@users.noreply.github.com>
updates: - [github.com/pycqa/isort: 6.0.0 → 6.0.1](PyCQA/isort@6.0.0...6.0.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* add "nipoppy status" page to docs * import StatusWorkflow in workflows module init
try adding tooltip for glossary terms
do not include extractor scripts in autodocs (fix issue nipoppy#502)
…ipoppy#524) * add linkcheck in Makefile * add linkcheck to readthedocs config * try to fix readthedocs config * fix broken links * add comment * address PR review comment * increase timeout limit
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@mathdugre did you want to take a look at this again? |
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* Merge `main` -> `dev-catalog` (#535) * [MAINT] Add dependabot for GitHub actions (#511) * Create dependabot.yml * add "bot" label * fix indentation * change schedule interval to monthly * [MAINT] Fix/update issue labeller (#509) * add new workflow and remove old ones * add required `enable-versioned-regex` field * try to fix labeler.yml * add write permissions for PRs * fix typo? * use pull_request_target insteade of pull_request event trigger * [MAINT] Use Nipoppy bot instead of PAT for projects automation workflow (#508) use bot instead of PAT * [MAINT] Add GitHub Actions workflow to automatically update `CITATION.cff` version after release (#512) * add DOI and update contact/authors in CITATION.cff * rename validation workflow * add initial version of update workflow * update workflow * update names * exclude `nipoppy-bot` PRs from changelog * Bump actions/stale from 9.0.0 to 9.1.0 (#515) Bumps [actions/stale](https://github.com/actions/stale) from 9.0.0 to 9.1.0. - [Release notes](https://github.com/actions/stale/releases) - [Changelog](https://github.com/actions/stale/blob/main/CHANGELOG.md) - [Commits](actions/stale@v9.0.0...v9.1.0) --- updated-dependencies: - dependency-name: actions/stale dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/checkout from 3 to 4 (#514) Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v3...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/setup-python from 4 to 5 (#516) Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@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> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [MAINT] Bump codecov/codecov-action from 4 to 5 (#513) * Bump codecov/codecov-action from 4 to 5 Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 4 to 5. - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](codecov/codecov-action@v4...v5) --- updated-dependencies: - dependency-name: codecov/codecov-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * use `files` instead of deprecated `file` * add prefix to PR titles --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * [MAINT] Clean up `.gitignore` (#521) * clean up .gitignore * add entries for Python venvs * [DOC] Add "how-to" guide for dataset initialization (#489) * add "how-to" guide for dataset init * address PR comments * split init doc in multiple pages for non-bids vs. bids start * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix error heading * fix heading and paths * fix header bids.md * update index and beginning of each page * update titles * minor changes --------- Co-authored-by: julia-pfarr <juliakatharina.pfarr@gmx.de> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Julia-Katharina Pfarr <111446107+julia-pfarr@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#527) updates: - [github.com/pycqa/isort: 6.0.0 → 6.0.1](PyCQA/isort@6.0.0...6.0.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [DOC] Add a CLI reference page for `nipoppy status` (#529) * add "nipoppy status" page to docs * import StatusWorkflow in workflows module init * [DOC] Add tooltips for glossary terms (#526) try adding tooltip for glossary terms * [DOC] Do not include extractor scripts in autodocs (#525) do not include extractor scripts in autodocs (fix issue #502) * [DOC] Add external link checking for docs build + fix broken links (#524) * add linkcheck in Makefile * add linkcheck to readthedocs config * try to fix readthedocs config * fix broken links * add comment * address PR review comment * increase timeout limit --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: julia-pfarr <juliakatharina.pfarr@gmx.de> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Julia-Katharina Pfarr <111446107+julia-pfarr@users.noreply.github.com> * [ENH] Remove pipeline configs from global config (#503) * add path to pipeline config in layout * remove pipeline configs from global config and put them in pipeline bundle directories instead * update PipelineWorkflow (and subclasses) to handle new config file location * refactor get_pipeline_version to get dpath input instead of list * fix PipelineWorkflow tests * fix PipelineRunner tests * fix bug in _get_pipeline_config() * fix InitWorkflow tests * fix tests for BidsConversionRunner * fix tests for ExtractionRunner * fix TrackerWorkflow test * fix docs (?) * add/update tests * [MAINT] Add dependabot for GitHub actions (#511) * Create dependabot.yml * add "bot" label * fix indentation * change schedule interval to monthly * [MAINT] Fix/update issue labeller (#509) * add new workflow and remove old ones * add required `enable-versioned-regex` field * try to fix labeler.yml * add write permissions for PRs * fix typo? * use pull_request_target insteade of pull_request event trigger * [MAINT] Use Nipoppy bot instead of PAT for projects automation workflow (#508) use bot instead of PAT * [MAINT] Add GitHub Actions workflow to automatically update `CITATION.cff` version after release (#512) * add DOI and update contact/authors in CITATION.cff * rename validation workflow * add initial version of update workflow * update workflow * update names * exclude `nipoppy-bot` PRs from changelog * Bump actions/stale from 9.0.0 to 9.1.0 (#515) Bumps [actions/stale](https://github.com/actions/stale) from 9.0.0 to 9.1.0. - [Release notes](https://github.com/actions/stale/releases) - [Changelog](https://github.com/actions/stale/blob/main/CHANGELOG.md) - [Commits](actions/stale@v9.0.0...v9.1.0) --- updated-dependencies: - dependency-name: actions/stale dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/checkout from 3 to 4 (#514) Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v3...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/setup-python from 4 to 5 (#516) Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@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> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [MAINT] Bump codecov/codecov-action from 4 to 5 (#513) * Bump codecov/codecov-action from 4 to 5 Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 4 to 5. - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](codecov/codecov-action@v4...v5) --- updated-dependencies: - dependency-name: codecov/codecov-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * use `files` instead of deprecated `file` * add prefix to PR titles --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * [MAINT] Clean up `.gitignore` (#521) * clean up .gitignore * add entries for Python venvs * [DOC] Add "how-to" guide for dataset initialization (#489) * add "how-to" guide for dataset init * address PR comments * split init doc in multiple pages for non-bids vs. bids start * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix error heading * fix heading and paths * fix header bids.md * update index and beginning of each page * update titles * minor changes --------- Co-authored-by: julia-pfarr <juliakatharina.pfarr@gmx.de> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Julia-Katharina Pfarr <111446107+julia-pfarr@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#527) updates: - [github.com/pycqa/isort: 6.0.0 → 6.0.1](PyCQA/isort@6.0.0...6.0.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [DOC] Add a CLI reference page for `nipoppy status` (#529) * add "nipoppy status" page to docs * import StatusWorkflow in workflows module init * [DOC] Add tooltips for glossary terms (#526) try adding tooltip for glossary terms * [DOC] Do not include extractor scripts in autodocs (#525) do not include extractor scripts in autodocs (fix issue #502) * [DOC] Add external link checking for docs build + fix broken links (#524) * add linkcheck in Makefile * add linkcheck to readthedocs config * try to fix readthedocs config * fix broken links * add comment * address PR review comment * increase timeout limit * fix typo * fix paths --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: julia-pfarr <juliakatharina.pfarr@gmx.de> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Julia-Katharina Pfarr <111446107+julia-pfarr@users.noreply.github.com> * [ENH] Add `PIPELINE_VARIABLES` to global config (#548) * add `PIPELINE_VARIABLES` field to global config * add PIPELINE_TYPE: PipelineTypeEnum in pipeline configs * use pipeline variables instead of substitutions for replacement in pipeline files * increase test coverage * address PR review comments * [ENH] Deprecate `DATASET_NAME`, `VISIT_IDS` and `SESSION_IDS` fields from `Config` (#553) * deprecate field from Config class * update StatusWorkflow and fix tests * rename test file * clean up BaseWorkflow tests * clean up DicomReorgWorkflow tests * clean up DoughnutWorkflow tests * fix autodoc warning * increase linkcheck timeout limit * [ENH] Rename pipeline store subdirectories (#561) * rename directories * fix tests * fix docs * [ENH] Force pipeline step config files to only have relative paths (#560) * Remove TRACKER_CONFIG_FILE from ProcPipelineConfig (should only be in ProcPipelineStepConfig) * update validation for BasePipelineStepConfig * update test for invocation/descriptor file fields * add tests for absolute path check and fix bug * update sample config files * refactor pipeline config loading + update relevant tests * handle relative paths in BasePipelineWorkflow * revert pipeline store directory names * fix some tests * fix remaining tests * fix doc warnings * increase test coverage + add test case * fix test * add helper function for getting pipeline bundle path * rename "proc" -> "processing" in test * [ENH] Split `BaseWorkflow` into `BaseWorkflow` and `BaseDatasetWorkflow` (#556) * rename `BaseWorkflow` -> `BaseDatasetWorkflow` * Extract `BaseWorkflow` from `BaseDatasetWorkflow` * move/fix tests * make validate_layout an init argument instead of class attribute * rename _skip_logging -> _skip_logfile * [ENH] Add `nipoppy pipeline validate` command (#558) * [ENH] Add `nipoppy pipeline install` command (#566) * add core validation functions + tests * Remove TRACKER_CONFIG_FILE from ProcPipelineConfig (should only be in ProcPipelineStepConfig) * add CLI command and substitutions * add substitutions test * add CLI test * rename test file * fix docs warnings * add test for PipelineValidateWorkflow * update validation for BasePipelineStepConfig * update test for invocation/descriptor file fields * add tests for absolute path check and fix bug * update sample config files * refactor pipeline config loading + update relevant tests * handle relative paths in BasePipelineWorkflow * revert pipeline store directory names * fix some tests * fix remaining tests * fix doc warnings * increase test coverage + add test case * fix test * adapt for pending relative path change * update log messages * fix test broken by merge * add helper function for getting pipeline bundle path * add base "pipeline install" functionality * Squashed commit of the following: commit e922f12 Merge: 788d3f1 5444535 Author: Michelle Wang <tomichellewang@gmail.com> Date: Mon Mar 24 14:01:07 2025 -0400 Merge remote-tracking branch 'upstream/dev-catalog' into pipeline_step_paths commit 5444535 Author: Michelle Wang <tomichellewang@gmail.com> Date: Sat Mar 22 13:04:20 2025 -0400 [ENH] Rename pipeline store subdirectories (#561) * rename directories * fix tests * fix docs * Squashed commit of the following: commit 853be29 Author: Michelle Wang <tomichellewang@gmail.com> Date: Mon Mar 24 13:53:19 2025 -0400 minor update to CLI * add CLI command and update logging * add variables to global config * add check that pipeline vars are not null * make sure existing fields in global config are not changed * add VARIABLES to default pipeline configs and add test * Squashed commit of the following: commit 34a5ddd Author: Michelle Wang <tomichellewang@gmail.com> Date: Fri Mar 28 11:15:59 2025 -0400 fix CLI test commit 8d17a8b Author: Michelle Wang <tomichellewang@gmail.com> Date: Thu Mar 27 16:51:37 2025 -0400 fix typo commit 7975bb4 Author: Michelle Wang <tomichellewang@gmail.com> Date: Thu Mar 27 16:33:59 2025 -0400 try to fix Pydantic deprecation errors commit c51fe30 Author: Michelle Wang <tomichellewang@gmail.com> Date: Thu Mar 27 16:25:09 2025 -0400 remove things related to dataset layout commit 3229e46 Merge: 9e75942 f437b59 Author: Michelle Wang <tomichellewang@gmail.com> Date: Thu Mar 27 15:59:53 2025 -0400 Merge remote-tracking branch 'upstream/dev-catalog' into 557/pipeline_validate commit 9e75942 Author: Michelle Wang <tomichellewang@gmail.com> Date: Thu Mar 27 11:17:46 2025 -0400 address most PR review comments commit 2e87f8d Merge: 9391ded fac5d2b Author: Michelle Wang <tomichellewang@gmail.com> Date: Thu Mar 27 11:06:40 2025 -0400 Merge remote-tracking branch 'upstream/dev-catalog' into 557/pipeline_validate commit 9391ded Author: Michelle Wang <tomichellewang@gmail.com> Date: Tue Mar 25 14:52:15 2025 -0400 make sure pipeline bundle content is flat list of file (no subdirectories) commit 42e904a Author: Michelle Wang <tomichellewang@gmail.com> Date: Tue Mar 25 12:40:06 2025 -0400 handle edge case with relative parent directories commit 853be29 Author: Michelle Wang <tomichellewang@gmail.com> Date: Mon Mar 24 13:53:19 2025 -0400 minor update to CLI * fix merge * fix PipelineInstallWorkflow * address PR review comments * fix CLI argument order * fix test * fix test again * do not catch exceptions * [ENH] api to download and upload pipelines from zenodo. (#506) * [ENH] api to download files from zenodo. * [FIX] add httpx dependency * [MAINT] remove requests dependency * [FIX] remove tqdm for now * [MAINT] Add dependabot for GitHub actions (#511) * Create dependabot.yml * add "bot" label * fix indentation * change schedule interval to monthly * [MAINT] Fix/update issue labeller (#509) * add new workflow and remove old ones * add required `enable-versioned-regex` field * try to fix labeler.yml * add write permissions for PRs * fix typo? * use pull_request_target insteade of pull_request event trigger * [MAINT] Use Nipoppy bot instead of PAT for projects automation workflow (#508) use bot instead of PAT * [MAINT] Add GitHub Actions workflow to automatically update `CITATION.cff` version after release (#512) * add DOI and update contact/authors in CITATION.cff * rename validation workflow * add initial version of update workflow * update workflow * update names * exclude `nipoppy-bot` PRs from changelog * Bump actions/stale from 9.0.0 to 9.1.0 (#515) Bumps [actions/stale](https://github.com/actions/stale) from 9.0.0 to 9.1.0. - [Release notes](https://github.com/actions/stale/releases) - [Changelog](https://github.com/actions/stale/blob/main/CHANGELOG.md) - [Commits](actions/stale@v9.0.0...v9.1.0) --- updated-dependencies: - dependency-name: actions/stale dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/checkout from 3 to 4 (#514) Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v3...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/setup-python from 4 to 5 (#516) Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@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> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [MAINT] Bump codecov/codecov-action from 4 to 5 (#513) * Bump codecov/codecov-action from 4 to 5 Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 4 to 5. - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](codecov/codecov-action@v4...v5) --- updated-dependencies: - dependency-name: codecov/codecov-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * use `files` instead of deprecated `file` * add prefix to PR titles --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * [MAINT] Clean up `.gitignore` (#521) * clean up .gitignore * add entries for Python venvs * [DOC] Add "how-to" guide for dataset initialization (#489) * add "how-to" guide for dataset init * address PR comments * split init doc in multiple pages for non-bids vs. bids start * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix error heading * fix heading and paths * fix header bids.md * update index and beginning of each page * update titles * minor changes --------- Co-authored-by: julia-pfarr <juliakatharina.pfarr@gmx.de> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Julia-Katharina Pfarr <111446107+julia-pfarr@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#527) updates: - [github.com/pycqa/isort: 6.0.0 → 6.0.1](PyCQA/isort@6.0.0...6.0.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [DOC] Add a CLI reference page for `nipoppy status` (#529) * add "nipoppy status" page to docs * import StatusWorkflow in workflows module init * [DOC] Add tooltips for glossary terms (#526) try adding tooltip for glossary terms * [DOC] Do not include extractor scripts in autodocs (#525) do not include extractor scripts in autodocs (fix issue #502) * [DOC] Add external link checking for docs build + fix broken links (#524) * add linkcheck in Makefile * add linkcheck to readthedocs config * try to fix readthedocs config * fix broken links * add comment * address PR review comment * increase timeout limit * Update tests/test_zenodo.py Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * Update nipoppy/zenodo.py Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * Improve error message, no longer required access tokekn for download, improve test * add cli for downloading pipelines from zenodo * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update nipoppy/zenodo.py Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * [ENH] Prototype for Zenodo upload * [TMP] started working on tests for upload. * Rename nipoppy pipeline add subcommand to install * add tests for authentication * Test for upload pipeline * Integrate new change for PR - Use new pipeline config for test - rename nipoppy pipeline add to download - Enforce nipoppy keywords on zenodo * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * pre-commit-ci modified the zenodo.json file for the example pipeline. * [no ci] cleanup gitignore conflict * Triger CI after adding secret to GH * Update nipoppy/cli.py Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * Update nipoppy/zenodo.py Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * fix pr comments * Seperated ZenodoAPI from workflow + tests for download workflow. * test get zenodo metadata from local pipeline. * test for zenodo upload workflow * rename zenodo_id to record_id * Add ZENODO as github variable * Remove and Prevent log file in history * Update nipoppy/workflows/zenodo.py Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * pr comments * Fix PR comments * Fix env var name for zenodo ID * Handle empty ZENODO_TOKEN GitHub secret seems to be empty on PR * Update nipoppy/zenodo_api.py Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix after merge * try to fix failing test (Zenodo record not matching sample pipeline anymore) * fix new failing test * pre-commit fix * update test data directory name * fix again --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Michelle Wang <tomichellewang@gmail.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: julia-pfarr <juliakatharina.pfarr@gmx.de> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Julia-Katharina Pfarr <111446107+julia-pfarr@users.noreply.github.com> * fix tests * [FIX] Fix Zenodo keywords not being set correctly (#598) * fix tests * remove docs file * use "subjects" metadata field instead of "keywords" * use "Nipoppy user" as default creator name * fix test * fix other tests * add pipeline name and version as keywords * [ENH] Add schema version to Zenodo record keywords (and pipeline config files) (#602) * fix tests * remove docs file * use "subjects" metadata field instead of "keywords" * use "Nipoppy user" as default creator name * fix test * fix other tests * add pipeline name and version as keywords * add mandatory schema version field and fix tests * [ENH] Implement `nipoppy pipeline search` (#599) * add search function and tests * add debug message * add search workflow and tests * add CLI command and test * minor changes * minor improvements * increase test coverage * address PR review comments * [ENH] Merge `nipoppy pipeline download` into `nipoppy pipeline install` (#594) * Merge `main` -> `dev-catalog` (#563) * [MAINT] Add dependabot for GitHub actions (#511) * Create dependabot.yml * add "bot" label * fix indentation * change schedule interval to monthly * [MAINT] Fix/update issue labeller (#509) * add new workflow and remove old ones * add required `enable-versioned-regex` field * try to fix labeler.yml * add write permissions for PRs * fix typo? * use pull_request_target insteade of pull_request event trigger * [MAINT] Use Nipoppy bot instead of PAT for projects automation workflow (#508) use bot instead of PAT * [MAINT] Add GitHub Actions workflow to automatically update `CITATION.cff` version after release (#512) * add DOI and update contact/authors in CITATION.cff * rename validation workflow * add initial version of update workflow * update workflow * update names * exclude `nipoppy-bot` PRs from changelog * Bump actions/stale from 9.0.0 to 9.1.0 (#515) Bumps [actions/stale](https://github.com/actions/stale) from 9.0.0 to 9.1.0. - [Release notes](https://github.com/actions/stale/releases) - [Changelog](https://github.com/actions/stale/blob/main/CHANGELOG.md) - [Commits](actions/stale@v9.0.0...v9.1.0) --- updated-dependencies: - dependency-name: actions/stale dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/checkout from 3 to 4 (#514) Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v3...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/setup-python from 4 to 5 (#516) Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@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> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [MAINT] Bump codecov/codecov-action from 4 to 5 (#513) * Bump codecov/codecov-action from 4 to 5 Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 4 to 5. - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](codecov/codecov-action@v4...v5) --- updated-dependencies: - dependency-name: codecov/codecov-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * use `files` instead of deprecated `file` * add prefix to PR titles --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * [MAINT] Clean up `.gitignore` (#521) * clean up .gitignore * add entries for Python venvs * [DOC] Add "how-to" guide for dataset initialization (#489) * add "how-to" guide for dataset init * address PR comments * split init doc in multiple pages for non-bids vs. bids start * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix error heading * fix heading and paths * fix header bids.md * update index and beginning of each page * update titles * minor changes --------- Co-authored-by: julia-pfarr <juliakatharina.pfarr@gmx.de> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Julia-Katharina Pfarr <111446107+julia-pfarr@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#527) updates: - [github.com/pycqa/isort: 6.0.0 → 6.0.1](PyCQA/isort@6.0.0...6.0.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [DOC] Add a CLI reference page for `nipoppy status` (#529) * add "nipoppy status" page to docs * import StatusWorkflow in workflows module init * [DOC] Add tooltips for glossary terms (#526) try adding tooltip for glossary terms * [DOC] Do not include extractor scripts in autodocs (#525) do not include extractor scripts in autodocs (fix issue #502) * [DOC] Add external link checking for docs build + fix broken links (#524) * add linkcheck in Makefile * add linkcheck to readthedocs config * try to fix readthedocs config * fix broken links * add comment * address PR review comment * increase timeout limit * [MAINT] Add CI workflow for Read the docs preview link (#536) add Read the docs preview workflow * [ENH] Add `bids-validator` `2.0.3` (#534) * add `bids-validator` 2.0.3 * simplify container config * expose schema version field (use latest by default) in invocation * [ENH] group options in cli help. (#491) * [ENH] group options in cli help. * remove duplicate entry for --force flag * Update nipoppy/cli.py Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * Remove redundant "options" suffix --------- Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * [ENH] Remove Boutiques descriptor/invocation file content dumps (#542) * add `quiet` arg to `run_command` * silence bosh command * also overwrite subprocess error message * update error messages * fix regex in test * [ENH] Print container-pulling command and change global config container substitution (#540) * add test * add "apptainer pull" command to error message if URI is available * update default container store path * update container pull message * fix exception message in test * [BUG] Add validation for non-alphanumeric characters in `participant_id` and `session_id` in manifest (#546) * add failing tests * add validation * add test case with non-alphanumeric character in `visit_id` * clarify docstrings * update container path substitution pattern * [ENH] Improve `fs_stats` extractor pipeline (#550) * fix escape sequence warnings * make script crash if no subjects found + add troubleshooting suggestions for when FreeSurfer stats commands fail * make the default invocation have `"verbose": true` * rename script.py to fs_stats.py * update script * bump version to 0.2.1 * [MAINT] Fix Pydantic `model_fields` deprecations (#576) fix Pydantic `model_fields` deprecations * fix fs_stats version change * fix tests * fix test --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: julia-pfarr <juliakatharina.pfarr@gmx.de> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Julia-Katharina Pfarr <111446107+julia-pfarr@users.noreply.github.com> Co-authored-by: Mathieu Dugré <16450132+mathdugre@users.noreply.github.com> * more Zenodo workflow file into pipeline_store subdirectory * merge pipeline download with pipeline install * move tests * fix CLI tests * fix tests failing in 3.9 * increase test coverage * improve error message when Zenodo record doesn't have expected config file * address PR review comments * fix Zenodo ID for tests --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: julia-pfarr <juliakatharina.pfarr@gmx.de> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Julia-Katharina Pfarr <111446107+julia-pfarr@users.noreply.github.com> Co-authored-by: Mathieu Dugré <16450132+mathdugre@users.noreply.github.com> * [ENH] Automatically impute Zenodo record creator information (#601) * allow record_id in upload_pipeline() to start with "zenodo." * dynamically get creator info if user does not provide it * fix test * [ENH] Add `nipoppy pipeline list` command (#570) * Remove TRACKER_CONFIG_FILE from ProcPipelineConfig (should only be in ProcPipelineStepConfig) * update validation for BasePipelineStepConfig * update test for invocation/descriptor file fields * add tests for absolute path check and fix bug * update sample config files * refactor pipeline config loading + update relevant tests * handle relative paths in BasePipelineWorkflow * revert pipeline store directory names * fix some tests * fix remaining tests * fix doc warnings * increase test coverage + add test case * fix test * add helper function for getting pipeline bundle path * refactor test function args * add workflow and tests * fix failing tests * add CLI and test * switch to BaseDatasetWorkflow * update type annotation and refactor variable name * fix tests * fix tests * use defaultdict * reorder CLI subcommands * [BUG] delete --regenerate flag from rich_click.OPTION_GROUPS (#609) * delete --regenerate flag from rich_click.OPTION_GROUPS * move option groups on top of file * [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> * Fixing merge conflict to merge dev-catalog into main (#612) * Implement RABIES (#264) * Add and edits to global_configs file * delete unused global configs file * created rabies boutiques descriptor * add bid dir and output to boutique descriptor * auto generate boutique for RABIES * adding optional arg descriptors for RABIES * all optional args added to rabies boutiques json * create boutiques descriptor for each Rabies command * add output and input for RAbies analysis boutique descriptor * finish primary section of preprocess boutique descriptors * finish boutique desc for preprocess * fix boutiques descriptors * correct value key quotations * fix value key * add optional desc to confound correct boutique file * adding boutique desc for rabies analysis * added input and output to confound correction and analysis * generate invocation schema for rabies preprocess * generate innvocation schemas for analysis and confound-correction * remove extra data_diagnosis tag * correcting types in descriptors * renameupdate descriptors est Rabies version * fix rabies preprocess descriptor * remove default values from confound_correction * describe certain tags as type FLAG * correct confound-correction with Flag type * fix command line order in analysis descriptor * remove analysis default values * set confound input default a bids dir * fix descriptor typo * reorder confound_correciton descriptor and remove data_diagnosis tag * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * conf_list now list object in descriptor * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * correct spelling to make codespell happy :) * changed confound-correction default input value to derivatives * added sample innvocation files for RABIES steps * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add RABIES to sample global config files * edits to RABIES in sample configs * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * addition or RABIES to sample global config files * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * remove scan_list arg from RABIES analysis * fix verbose descriptions * fix uri for rabies sample config * empty tracker config for rabies * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * rename tracker file * set preprocess invocation file to defaults * added default local threads * replace variables with default values * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add descriptor files again * add rabies files to their own sample_pipelines folders * add descriptor and invocation to rabies sample pipeline files * add rabies config to global config files * remove out of data 0.4.8 rabies files * add rabies parameters to test config file * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add rabies tracker config file * make edits to descriptor via boutiques suggestions * fix pathing for rabies steps config * set proper naming convention for rabies pipeline files * full refactor to most up to date rabies descriptors * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix input/output dir paths in rabies invocation files * fix codespell issues/typos * remove default input/output for descriptor, use pipeline_output in invocation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix more codespell typos * add desciptions to all descriptor files from rabies docs * code spell fix * fix command-line-flag for verbose * add list attribute to proper analysis arguments * add value choices for detrending_order arg * adding select value choices and list attribute to args when needed * fix verbose description * remove deprecated nipoppy_cli folder * fix brackets in analysis invocation * add rabies pipelines steps to test_pipeline_runner test * input/output paths now stated in invocation files * Update nipoppy/data/examples/sample_pipelines/rabies-0.5.1/tracker_config.json Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * set data_diagnosis tag as true by default * add data_diagnosis files from analysis step as tracked outputs * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update nipoppy/data/examples/sample_global_config-all_pipelines.json Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * add version number to rabies container_info * Update nipoppy/data/examples/sample_global_config-all_pipelines.json Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * change input_dir to bids_dir for preprocess invocation * add analysis and generate pybids status to rabies steps * remove initial `/` from track config paths * switch analysis step to participant_session level, move tracker_config_file notation into analysis step * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * moving tracker to strictly analysis step * adding separate tracking files and steps in config * create tracker config files for each step * add confound correction image path to track * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add separate tracker configs for each step * tracking anatomical image files from preprocess outputs * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * rename all tracker config files to include step name * remove extra [ from preprocess invocation files * remove extra [ from confound-correciton invocation files * remove redundant tracker descriptor/innvocation files * remove descriptor and invocation lines from tracker steps in global config * remove unused tracker config files * add * to filepaths to improve flexibility * set "acq-rare" to * in preprocess tracker config paths * Add session number variable to session section of paths * remove non-image files from tracking * fix ses- and sub- labeling in tracker config file * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * remove ses- and sub- tags from preprocess tracking file paths --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * Add back rabies config. + Move to sample_pipelines/preprocessing/rabies-0.5.1 * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add shcema version * Add pipeline type --------- Co-authored-by: David Roper <60201980+david-roper@users.noreply.github.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> * Ignore zenodo_api.py Low coverage on response error code. --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Michelle Wang <tomichellewang@gmail.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: julia-pfarr <juliakatharina.pfarr@gmx.de> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Julia-Katharina Pfarr <111446107+julia-pfarr@users.noreply.github.com> Co-authored-by: David Roper <60201980+david-roper@users.noreply.github.com>
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* Merge `main` -> `dev-catalog` (#535) * [MAINT] Add dependabot for GitHub actions (#511) * Create dependabot.yml * add "bot" label * fix indentation * change schedule interval to monthly * [MAINT] Fix/update issue labeller (#509) * add new workflow and remove old ones * add required `enable-versioned-regex` field * try to fix labeler.yml * add write permissions for PRs * fix typo? * use pull_request_target insteade of pull_request event trigger * [MAINT] Use Nipoppy bot instead of PAT for projects automation workflow (#508) use bot instead of PAT * [MAINT] Add GitHub Actions workflow to automatically update `CITATION.cff` version after release (#512) * add DOI and update contact/authors in CITATION.cff * rename validation workflow * add initial version of update workflow * update workflow * update names * exclude `nipoppy-bot` PRs from changelog * Bump actions/stale from 9.0.0 to 9.1.0 (#515) Bumps [actions/stale](https://github.com/actions/stale) from 9.0.0 to 9.1.0. - [Release notes](https://github.com/actions/stale/releases) - [Changelog](https://github.com/actions/stale/blob/main/CHANGELOG.md) - [Commits](actions/stale@v9.0.0...v9.1.0) --- updated-dependencies: - dependency-name: actions/stale dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/checkout from 3 to 4 (#514) Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v3...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/setup-python from 4 to 5 (#516) Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@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> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [MAINT] Bump codecov/codecov-action from 4 to 5 (#513) * Bump codecov/codecov-action from 4 to 5 Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 4 to 5. - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](codecov/codecov-action@v4...v5) --- updated-dependencies: - dependency-name: codecov/codecov-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * use `files` instead of deprecated `file` * add prefix to PR titles --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * [MAINT] Clean up `.gitignore` (#521) * clean up .gitignore * add entries for Python venvs * [DOC] Add "how-to" guide for dataset initialization (#489) * add "how-to" guide for dataset init * address PR comments * split init doc in multiple pages for non-bids vs. bids start * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix error heading * fix heading and paths * fix header bids.md * update index and beginning of each page * update titles * minor changes --------- Co-authored-by: julia-pfarr <juliakatharina.pfarr@gmx.de> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Julia-Katharina Pfarr <111446107+julia-pfarr@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#527) updates: - [github.com/pycqa/isort: 6.0.0 → 6.0.1](PyCQA/isort@6.0.0...6.0.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [DOC] Add a CLI reference page for `nipoppy status` (#529) * add "nipoppy status" page to docs * import StatusWorkflow in workflows module init * [DOC] Add tooltips for glossary terms (#526) try adding tooltip for glossary terms * [DOC] Do not include extractor scripts in autodocs (#525) do not include extractor scripts in autodocs (fix issue #502) * [DOC] Add external link checking for docs build + fix broken links (#524) * add linkcheck in Makefile * add linkcheck to readthedocs config * try to fix readthedocs config * fix broken links * add comment * address PR review comment * increase timeout limit --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: julia-pfarr <juliakatharina.pfarr@gmx.de> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Julia-Katharina Pfarr <111446107+julia-pfarr@users.noreply.github.com> * [ENH] Remove pipeline configs from global config (#503) * add path to pipeline config in layout * remove pipeline configs from global config and put them in pipeline bundle directories instead * update PipelineWorkflow (and subclasses) to handle new config file location * refactor get_pipeline_version to get dpath input instead of list * fix PipelineWorkflow tests * fix PipelineRunner tests * fix bug in _get_pipeline_config() * fix InitWorkflow tests * fix tests for BidsConversionRunner * fix tests for ExtractionRunner * fix TrackerWorkflow test * fix docs (?) * add/update tests * [MAINT] Add dependabot for GitHub actions (#511) * Create dependabot.yml * add "bot" label * fix indentation * change schedule interval to monthly * [MAINT] Fix/update issue labeller (#509) * add new workflow and remove old ones * add required `enable-versioned-regex` field * try to fix labeler.yml * add write permissions for PRs * fix typo? * use pull_request_target insteade of pull_request event trigger * [MAINT] Use Nipoppy bot instead of PAT for projects automation workflow (#508) use bot instead of PAT * [MAINT] Add GitHub Actions workflow to automatically update `CITATION.cff` version after release (#512) * add DOI and update contact/authors in CITATION.cff * rename validation workflow * add initial version of update workflow * update workflow * update names * exclude `nipoppy-bot` PRs from changelog * Bump actions/stale from 9.0.0 to 9.1.0 (#515) Bumps [actions/stale](https://github.com/actions/stale) from 9.0.0 to 9.1.0. - [Release notes](https://github.com/actions/stale/releases) - [Changelog](https://github.com/actions/stale/blob/main/CHANGELOG.md) - [Commits](actions/stale@v9.0.0...v9.1.0) --- updated-dependencies: - dependency-name: actions/stale dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/checkout from 3 to 4 (#514) Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v3...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/setup-python from 4 to 5 (#516) Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@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> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [MAINT] Bump codecov/codecov-action from 4 to 5 (#513) * Bump codecov/codecov-action from 4 to 5 Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 4 to 5. - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](codecov/codecov-action@v4...v5) --- updated-dependencies: - dependency-name: codecov/codecov-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * use `files` instead of deprecated `file` * add prefix to PR titles --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * [MAINT] Clean up `.gitignore` (#521) * clean up .gitignore * add entries for Python venvs * [DOC] Add "how-to" guide for dataset initialization (#489) * add "how-to" guide for dataset init * address PR comments * split init doc in multiple pages for non-bids vs. bids start * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix error heading * fix heading and paths * fix header bids.md * update index and beginning of each page * update titles * minor changes --------- Co-authored-by: julia-pfarr <juliakatharina.pfarr@gmx.de> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Julia-Katharina Pfarr <111446107+julia-pfarr@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#527) updates: - [github.com/pycqa/isort: 6.0.0 → 6.0.1](PyCQA/isort@6.0.0...6.0.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [DOC] Add a CLI reference page for `nipoppy status` (#529) * add "nipoppy status" page to docs * import StatusWorkflow in workflows module init * [DOC] Add tooltips for glossary terms (#526) try adding tooltip for glossary terms * [DOC] Do not include extractor scripts in autodocs (#525) do not include extractor scripts in autodocs (fix issue #502) * [DOC] Add external link checking for docs build + fix broken links (#524) * add linkcheck in Makefile * add linkcheck to readthedocs config * try to fix readthedocs config * fix broken links * add comment * address PR review comment * increase timeout limit * fix typo * fix paths --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: julia-pfarr <juliakatharina.pfarr@gmx.de> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Julia-Katharina Pfarr <111446107+julia-pfarr@users.noreply.github.com> * [ENH] Add `PIPELINE_VARIABLES` to global config (#548) * add `PIPELINE_VARIABLES` field to global config * add PIPELINE_TYPE: PipelineTypeEnum in pipeline configs * use pipeline variables instead of substitutions for replacement in pipeline files * increase test coverage * address PR review comments * [ENH] Deprecate `DATASET_NAME`, `VISIT_IDS` and `SESSION_IDS` fields from `Config` (#553) * deprecate field from Config class * update StatusWorkflow and fix tests * rename test file * clean up BaseWorkflow tests * clean up DicomReorgWorkflow tests * clean up DoughnutWorkflow tests * fix autodoc warning * increase linkcheck timeout limit * [ENH] Rename pipeline store subdirectories (#561) * rename directories * fix tests * fix docs * [ENH] Force pipeline step config files to only have relative paths (#560) * Remove TRACKER_CONFIG_FILE from ProcPipelineConfig (should only be in ProcPipelineStepConfig) * update validation for BasePipelineStepConfig * update test for invocation/descriptor file fields * add tests for absolute path check and fix bug * update sample config files * refactor pipeline config loading + update relevant tests * handle relative paths in BasePipelineWorkflow * revert pipeline store directory names * fix some tests * fix remaining tests * fix doc warnings * increase test coverage + add test case * fix test * add helper function for getting pipeline bundle path * rename "proc" -> "processing" in test * [ENH] Split `BaseWorkflow` into `BaseWorkflow` and `BaseDatasetWorkflow` (#556) * rename `BaseWorkflow` -> `BaseDatasetWorkflow` * Extract `BaseWorkflow` from `BaseDatasetWorkflow` * move/fix tests * make validate_layout an init argument instead of class attribute * rename _skip_logging -> _skip_logfile * [ENH] Add `nipoppy pipeline validate` command (#558) * [ENH] Add `nipoppy pipeline install` command (#566) * add core validation functions + tests * Remove TRACKER_CONFIG_FILE from ProcPipelineConfig (should only be in ProcPipelineStepConfig) * add CLI command and substitutions * add substitutions test * add CLI test * rename test file * fix docs warnings * add test for PipelineValidateWorkflow * update validation for BasePipelineStepConfig * update test for invocation/descriptor file fields * add tests for absolute path check and fix bug * update sample config files * refactor pipeline config loading + update relevant tests * handle relative paths in BasePipelineWorkflow * revert pipeline store directory names * fix some tests * fix remaining tests * fix doc warnings * increase test coverage + add test case * fix test * adapt for pending relative path change * update log messages * fix test broken by merge * add helper function for getting pipeline bundle path * add base "pipeline install" functionality * Squashed commit of the following: commit e922f12 Merge: 788d3f1 5444535 Author: Michelle Wang <tomichellewang@gmail.com> Date: Mon Mar 24 14:01:07 2025 -0400 Merge remote-tracking branch 'upstream/dev-catalog' into pipeline_step_paths commit 5444535 Author: Michelle Wang <tomichellewang@gmail.com> Date: Sat Mar 22 13:04:20 2025 -0400 [ENH] Rename pipeline store subdirectories (#561) * rename directories * fix tests * fix docs * Squashed commit of the following: commit 853be29 Author: Michelle Wang <tomichellewang@gmail.com> Date: Mon Mar 24 13:53:19 2025 -0400 minor update to CLI * add CLI command and update logging * add variables to global config * add check that pipeline vars are not null * make sure existing fields in global config are not changed * add VARIABLES to default pipeline configs and add test * Squashed commit of the following: commit 34a5ddd Author: Michelle Wang <tomichellewang@gmail.com> Date: Fri Mar 28 11:15:59 2025 -0400 fix CLI test commit 8d17a8b Author: Michelle Wang <tomichellewang@gmail.com> Date: Thu Mar 27 16:51:37 2025 -0400 fix typo commit 7975bb4 Author: Michelle Wang <tomichellewang@gmail.com> Date: Thu Mar 27 16:33:59 2025 -0400 try to fix Pydantic deprecation errors commit c51fe30 Author: Michelle Wang <tomichellewang@gmail.com> Date: Thu Mar 27 16:25:09 2025 -0400 remove things related to dataset layout commit 3229e46 Merge: 9e75942 f437b59 Author: Michelle Wang <tomichellewang@gmail.com> Date: Thu Mar 27 15:59:53 2025 -0400 Merge remote-tracking branch 'upstream/dev-catalog' into 557/pipeline_validate commit 9e75942 Author: Michelle Wang <tomichellewang@gmail.com> Date: Thu Mar 27 11:17:46 2025 -0400 address most PR review comments commit 2e87f8d Merge: 9391ded fac5d2b Author: Michelle Wang <tomichellewang@gmail.com> Date: Thu Mar 27 11:06:40 2025 -0400 Merge remote-tracking branch 'upstream/dev-catalog' into 557/pipeline_validate commit 9391ded Author: Michelle Wang <tomichellewang@gmail.com> Date: Tue Mar 25 14:52:15 2025 -0400 make sure pipeline bundle content is flat list of file (no subdirectories) commit 42e904a Author: Michelle Wang <tomichellewang@gmail.com> Date: Tue Mar 25 12:40:06 2025 -0400 handle edge case with relative parent directories commit 853be29 Author: Michelle Wang <tomichellewang@gmail.com> Date: Mon Mar 24 13:53:19 2025 -0400 minor update to CLI * fix merge * fix PipelineInstallWorkflow * address PR review comments * fix CLI argument order * fix test * fix test again * do not catch exceptions * [ENH] api to download and upload pipelines from zenodo. (#506) * [ENH] api to download files from zenodo. * [FIX] add httpx dependency * [MAINT] remove requests dependency * [FIX] remove tqdm for now * [MAINT] Add dependabot for GitHub actions (#511) * Create dependabot.yml * add "bot" label * fix indentation * change schedule interval to monthly * [MAINT] Fix/update issue labeller (#509) * add new workflow and remove old ones * add required `enable-versioned-regex` field * try to fix labeler.yml * add write permissions for PRs * fix typo? * use pull_request_target insteade of pull_request event trigger * [MAINT] Use Nipoppy bot instead of PAT for projects automation workflow (#508) use bot instead of PAT * [MAINT] Add GitHub Actions workflow to automatically update `CITATION.cff` version after release (#512) * add DOI and update contact/authors in CITATION.cff * rename validation workflow * add initial version of update workflow * update workflow * update names * exclude `nipoppy-bot` PRs from changelog * Bump actions/stale from 9.0.0 to 9.1.0 (#515) Bumps [actions/stale](https://github.com/actions/stale) from 9.0.0 to 9.1.0. - [Release notes](https://github.com/actions/stale/releases) - [Changelog](https://github.com/actions/stale/blob/main/CHANGELOG.md) - [Commits](actions/stale@v9.0.0...v9.1.0) --- updated-dependencies: - dependency-name: actions/stale dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/checkout from 3 to 4 (#514) Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v3...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/setup-python from 4 to 5 (#516) Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@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> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [MAINT] Bump codecov/codecov-action from 4 to 5 (#513) * Bump codecov/codecov-action from 4 to 5 Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 4 to 5. - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](codecov/codecov-action@v4...v5) --- updated-dependencies: - dependency-name: codecov/codecov-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * use `files` instead of deprecated `file` * add prefix to PR titles --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * [MAINT] Clean up `.gitignore` (#521) * clean up .gitignore * add entries for Python venvs * [DOC] Add "how-to" guide for dataset initialization (#489) * add "how-to" guide for dataset init * address PR comments * split init doc in multiple pages for non-bids vs. bids start * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix error heading * fix heading and paths * fix header bids.md * update index and beginning of each page * update titles * minor changes --------- Co-authored-by: julia-pfarr <juliakatharina.pfarr@gmx.de> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Julia-Katharina Pfarr <111446107+julia-pfarr@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#527) updates: - [github.com/pycqa/isort: 6.0.0 → 6.0.1](PyCQA/isort@6.0.0...6.0.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [DOC] Add a CLI reference page for `nipoppy status` (#529) * add "nipoppy status" page to docs * import StatusWorkflow in workflows module init * [DOC] Add tooltips for glossary terms (#526) try adding tooltip for glossary terms * [DOC] Do not include extractor scripts in autodocs (#525) do not include extractor scripts in autodocs (fix issue #502) * [DOC] Add external link checking for docs build + fix broken links (#524) * add linkcheck in Makefile * add linkcheck to readthedocs config * try to fix readthedocs config * fix broken links * add comment * address PR review comment * increase timeout limit * Update tests/test_zenodo.py Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * Update nipoppy/zenodo.py Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * Improve error message, no longer required access tokekn for download, improve test * add cli for downloading pipelines from zenodo * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update nipoppy/zenodo.py Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * [ENH] Prototype for Zenodo upload * [TMP] started working on tests for upload. * Rename nipoppy pipeline add subcommand to install * add tests for authentication * Test for upload pipeline * Integrate new change for PR - Use new pipeline config for test - rename nipoppy pipeline add to download - Enforce nipoppy keywords on zenodo * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * pre-commit-ci modified the zenodo.json file for the example pipeline. * [no ci] cleanup gitignore conflict * Triger CI after adding secret to GH * Update nipoppy/cli.py Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * Update nipoppy/zenodo.py Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * fix pr comments * Seperated ZenodoAPI from workflow + tests for download workflow. * test get zenodo metadata from local pipeline. * test for zenodo upload workflow * rename zenodo_id to record_id * Add ZENODO as github variable * Remove and Prevent log file in history * Update nipoppy/workflows/zenodo.py Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * pr comments * Fix PR comments * Fix env var name for zenodo ID * Handle empty ZENODO_TOKEN GitHub secret seems to be empty on PR * Update nipoppy/zenodo_api.py Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix after merge * try to fix failing test (Zenodo record not matching sample pipeline anymore) * fix new failing test * pre-commit fix * update test data directory name * fix again --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Michelle Wang <tomichellewang@gmail.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: julia-pfarr <juliakatharina.pfarr@gmx.de> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Julia-Katharina Pfarr <111446107+julia-pfarr@users.noreply.github.com> * fix tests * [FIX] Fix Zenodo keywords not being set correctly (#598) * fix tests * remove docs file * use "subjects" metadata field instead of "keywords" * use "Nipoppy user" as default creator name * fix test * fix other tests * add pipeline name and version as keywords * [ENH] Add schema version to Zenodo record keywords (and pipeline config files) (#602) * fix tests * remove docs file * use "subjects" metadata field instead of "keywords" * use "Nipoppy user" as default creator name * fix test * fix other tests * add pipeline name and version as keywords * add mandatory schema version field and fix tests * [ENH] Implement `nipoppy pipeline search` (#599) * add search function and tests * add debug message * add search workflow and tests * add CLI command and test * minor changes * minor improvements * increase test coverage * address PR review comments * [ENH] Merge `nipoppy pipeline download` into `nipoppy pipeline install` (#594) * Merge `main` -> `dev-catalog` (#563) * [MAINT] Add dependabot for GitHub actions (#511) * Create dependabot.yml * add "bot" label * fix indentation * change schedule interval to monthly * [MAINT] Fix/update issue labeller (#509) * add new workflow and remove old ones * add required `enable-versioned-regex` field * try to fix labeler.yml * add write permissions for PRs * fix typo? * use pull_request_target insteade of pull_request event trigger * [MAINT] Use Nipoppy bot instead of PAT for projects automation workflow (#508) use bot instead of PAT * [MAINT] Add GitHub Actions workflow to automatically update `CITATION.cff` version after release (#512) * add DOI and update contact/authors in CITATION.cff * rename validation workflow * add initial version of update workflow * update workflow * update names * exclude `nipoppy-bot` PRs from changelog * Bump actions/stale from 9.0.0 to 9.1.0 (#515) Bumps [actions/stale](https://github.com/actions/stale) from 9.0.0 to 9.1.0. - [Release notes](https://github.com/actions/stale/releases) - [Changelog](https://github.com/actions/stale/blob/main/CHANGELOG.md) - [Commits](actions/stale@v9.0.0...v9.1.0) --- updated-dependencies: - dependency-name: actions/stale dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/checkout from 3 to 4 (#514) Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v3...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/setup-python from 4 to 5 (#516) Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@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> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [MAINT] Bump codecov/codecov-action from 4 to 5 (#513) * Bump codecov/codecov-action from 4 to 5 Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 4 to 5. - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](codecov/codecov-action@v4...v5) --- updated-dependencies: - dependency-name: codecov/codecov-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * use `files` instead of deprecated `file` * add prefix to PR titles --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * [MAINT] Clean up `.gitignore` (#521) * clean up .gitignore * add entries for Python venvs * [DOC] Add "how-to" guide for dataset initialization (#489) * add "how-to" guide for dataset init * address PR comments * split init doc in multiple pages for non-bids vs. bids start * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix error heading * fix heading and paths * fix header bids.md * update index and beginning of each page * update titles * minor changes --------- Co-authored-by: julia-pfarr <juliakatharina.pfarr@gmx.de> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Julia-Katharina Pfarr <111446107+julia-pfarr@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#527) updates: - [github.com/pycqa/isort: 6.0.0 → 6.0.1](PyCQA/isort@6.0.0...6.0.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [DOC] Add a CLI reference page for `nipoppy status` (#529) * add "nipoppy status" page to docs * import StatusWorkflow in workflows module init * [DOC] Add tooltips for glossary terms (#526) try adding tooltip for glossary terms * [DOC] Do not include extractor scripts in autodocs (#525) do not include extractor scripts in autodocs (fix issue #502) * [DOC] Add external link checking for docs build + fix broken links (#524) * add linkcheck in Makefile * add linkcheck to readthedocs config * try to fix readthedocs config * fix broken links * add comment * address PR review comment * increase timeout limit * [MAINT] Add CI workflow for Read the docs preview link (#536) add Read the docs preview workflow * [ENH] Add `bids-validator` `2.0.3` (#534) * add `bids-validator` 2.0.3 * simplify container config * expose schema version field (use latest by default) in invocation * [ENH] group options in cli help. (#491) * [ENH] group options in cli help. * remove duplicate entry for --force flag * Update nipoppy/cli.py Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * Remove redundant "options" suffix --------- Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * [ENH] Remove Boutiques descriptor/invocation file content dumps (#542) * add `quiet` arg to `run_command` * silence bosh command * also overwrite subprocess error message * update error messages * fix regex in test * [ENH] Print container-pulling command and change global config container substitution (#540) * add test * add "apptainer pull" command to error message if URI is available * update default container store path * update container pull message * fix exception message in test * [BUG] Add validation for non-alphanumeric characters in `participant_id` and `session_id` in manifest (#546) * add failing tests * add validation * add test case with non-alphanumeric character in `visit_id` * clarify docstrings * update container path substitution pattern * [ENH] Improve `fs_stats` extractor pipeline (#550) * fix escape sequence warnings * make script crash if no subjects found + add troubleshooting suggestions for when FreeSurfer stats commands fail * make the default invocation have `"verbose": true` * rename script.py to fs_stats.py * update script * bump version to 0.2.1 * [MAINT] Fix Pydantic `model_fields` deprecations (#576) fix Pydantic `model_fields` deprecations * fix fs_stats version change * fix tests * fix test --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: julia-pfarr <juliakatharina.pfarr@gmx.de> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Julia-Katharina Pfarr <111446107+julia-pfarr@users.noreply.github.com> Co-authored-by: Mathieu Dugré <16450132+mathdugre@users.noreply.github.com> * more Zenodo workflow file into pipeline_store subdirectory * merge pipeline download with pipeline install * move tests * fix CLI tests * fix tests failing in 3.9 * increase test coverage * improve error message when Zenodo record doesn't have expected config file * address PR review comments * fix Zenodo ID for tests --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: julia-pfarr <juliakatharina.pfarr@gmx.de> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Julia-Katharina Pfarr <111446107+julia-pfarr@users.noreply.github.com> Co-authored-by: Mathieu Dugré <16450132+mathdugre@users.noreply.github.com> * [ENH] Automatically impute Zenodo record creator information (#601) * allow record_id in upload_pipeline() to start with "zenodo." * dynamically get creator info if user does not provide it * fix test * [ENH] Add `nipoppy pipeline list` command (#570) * Remove TRACKER_CONFIG_FILE from ProcPipelineConfig (should only be in ProcPipelineStepConfig) * update validation for BasePipelineStepConfig * update test for invocation/descriptor file fields * add tests for absolute path check and fix bug * update sample config files * refactor pipeline config loading + update relevant tests * handle relative paths in BasePipelineWorkflow * revert pipeline store directory names * fix some tests * fix remaining tests * fix doc warnings * increase test coverage + add test case * fix test * add helper function for getting pipeline bundle path * refactor test function args * add workflow and tests * fix failing tests * add CLI and test * switch to BaseDatasetWorkflow * update type annotation and refactor variable name * fix tests * fix tests * use defaultdict * reorder CLI subcommands * restore substitutions behaviour for backward-compatibility * fix test * [BUG] delete --regenerate flag from rich_click.OPTION_GROUPS (#609) * delete --regenerate flag from rich_click.OPTION_GROUPS * move option groups on top of file * [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> * Fixing merge conflict to merge dev-catalog into main (#612) * Implement RABIES (#264) * Add and edits to global_configs file * delete unused global configs file * created rabies boutiques descriptor * add bid dir and output to boutique descriptor * auto generate boutique for RABIES * adding optional arg descriptors for RABIES * all optional args added to rabies boutiques json * create boutiques descriptor for each Rabies command * add output and input for RAbies analysis boutique descriptor * finish primary section of preprocess boutique descriptors * finish boutique desc for preprocess * fix boutiques descriptors * correct value key quotations * fix value key * add optional desc to confound correct boutique file * adding boutique desc for rabies analysis * added input and output to confound correction and analysis * generate invocation schema for rabies preprocess * generate innvocation schemas for analysis and confound-correction * remove extra data_diagnosis tag * correcting types in descriptors * renameupdate descriptors est Rabies version * fix rabies preprocess descriptor * remove default values from confound_correction * describe certain tags as type FLAG * correct confound-correction with Flag type * fix command line order in analysis descriptor * remove analysis default values * set confound input default a bids dir * fix descriptor typo * reorder confound_correciton descriptor and remove data_diagnosis tag * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * conf_list now list object in descriptor * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * correct spelling to make codespell happy :) * changed confound-correction default input value to derivatives * added sample innvocation files for RABIES steps * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add RABIES to sample global config files * edits to RABIES in sample configs * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * addition or RABIES to sample global config files * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * remove scan_list arg from RABIES analysis * fix verbose descriptions * fix uri for rabies sample config * empty tracker config for rabies * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * rename tracker file * set preprocess invocation file to defaults * added default local threads * replace variables with default values * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add descriptor files again * add rabies files to their own sample_pipelines folders * add descriptor and invocation to rabies sample pipeline files * add rabies config to global config files * remove out of data 0.4.8 rabies files * add rabies parameters to test config file * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add rabies tracker config file * make edits to descriptor via boutiques suggestions * fix pathing for rabies steps config * set proper naming convention for rabies pipeline files * full refactor to most up to date rabies descriptors * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix input/output dir paths in rabies invocation files * fix codespell issues/typos * remove default input/output for descriptor, use pipeline_output in invocation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix more codespell typos * add desciptions to all descriptor files from rabies docs * code spell fix * fix command-line-flag for verbose * add list attribute to proper analysis arguments * add value choices for detrending_order arg * adding select value choices and list attribute to args when needed * fix verbose description * remove deprecated nipoppy_cli folder * fix brackets in analysis invocation * add rabies pipelines steps to test_pipeline_runner test * input/output paths now stated in invocation files * Update nipoppy/data/examples/sample_pipelines/rabies-0.5.1/tracker_config.json Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * set data_diagnosis tag as true by default * add data_diagnosis files from analysis step as tracked outputs * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update nipoppy/data/examples/sample_global_config-all_pipelines.json Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * add version number to rabies container_info * Update nipoppy/data/examples/sample_global_config-all_pipelines.json Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * change input_dir to bids_dir for preprocess invocation * add analysis and generate pybids status to rabies steps * remove initial `/` from track config paths * switch analysis step to participant_session level, move tracker_config_file notation into analysis step * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * moving tracker to strictly analysis step * adding separate tracking files and steps in config * create tracker config files for each step * add confound correction image path to track * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add separate tracker configs for each step * tracking anatomical image files from preprocess outputs * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * rename all tracker config files to include step name * remove extra [ from preprocess invocation files * remove extra [ from confound-correciton invocation files * remove redundant tracker descriptor/innvocation files * remove descriptor and invocation lines from tracker steps in global config * remove unused tracker config files * add * to filepaths to improve flexibility * set "acq-rare" to * in preprocess tracker config paths * Add session number variable to session section of paths * remove non-image files from tracking * fix ses- and sub- labeling in tracker config file * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * remove ses- and sub- tags from preprocess tracking file paths --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * Add back rabies config. + Move to sample_pipelines/preprocessing/rabies-0.5.1 * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add shcema version * Add pipeline type --------- Co-authored-by: David Roper <60201980+david-roper@users.noreply.github.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> * Ignore zenodo_api.py Low coverage on response error code. * fix broken link in docs --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: julia-pfarr <juliakatharina.pfarr@gmx.de> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Julia-Katharina Pfarr <111446107+julia-pfarr@users.noreply.github.com> Co-authored-by: Mathieu Dugré <16450132+mathdugre@users.noreply.github.com> Co-authored-by: David Roper <60201980+david-roper@users.noreply.github.com>
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* Merge `main` -> `dev-catalog` (#535) * [MAINT] Add dependabot for GitHub actions (#511) * Create dependabot.yml * add "bot" label * fix indentation * change schedule interval to monthly * [MAINT] Fix/update issue labeller (#509) * add new workflow and remove old ones * add required `enable-versioned-regex` field * try to fix labeler.yml * add write permissions for PRs * fix typo? * use pull_request_target insteade of pull_request event trigger * [MAINT] Use Nipoppy bot instead of PAT for projects automation workflow (#508) use bot instead of PAT * [MAINT] Add GitHub Actions workflow to automatically update `CITATION.cff` version after release (#512) * add DOI and update contact/authors in CITATION.cff * rename validation workflow * add initial version of update workflow * update workflow * update names * exclude `nipoppy-bot` PRs from changelog * Bump actions/stale from 9.0.0 to 9.1.0 (#515) Bumps [actions/stale](https://github.com/actions/stale) from 9.0.0 to 9.1.0. - [Release notes](https://github.com/actions/stale/releases) - [Changelog](https://github.com/actions/stale/blob/main/CHANGELOG.md) - [Commits](actions/stale@v9.0.0...v9.1.0) --- updated-dependencies: - dependency-name: actions/stale dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/checkout from 3 to 4 (#514) Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v3...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/setup-python from 4 to 5 (#516) Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@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> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [MAINT] Bump codecov/codecov-action from 4 to 5 (#513) * Bump codecov/codecov-action from 4 to 5 Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 4 to 5. - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](codecov/codecov-action@v4...v5) --- updated-dependencies: - dependency-name: codecov/codecov-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * use `files` instead of deprecated `file` * add prefix to PR titles --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * [MAINT] Clean up `.gitignore` (#521) * clean up .gitignore * add entries for Python venvs * [DOC] Add "how-to" guide for dataset initialization (#489) * add "how-to" guide for dataset init * address PR comments * split init doc in multiple pages for non-bids vs. bids start * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix error heading * fix heading and paths * fix header bids.md * update index and beginning of each page * update titles * minor changes --------- Co-authored-by: julia-pfarr <juliakatharina.pfarr@gmx.de> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Julia-Katharina Pfarr <111446107+julia-pfarr@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#527) updates: - [github.com/pycqa/isort: 6.0.0 → 6.0.1](PyCQA/isort@6.0.0...6.0.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [DOC] Add a CLI reference page for `nipoppy status` (#529) * add "nipoppy status" page to docs * import StatusWorkflow in workflows module init * [DOC] Add tooltips for glossary terms (#526) try adding tooltip for glossary terms * [DOC] Do not include extractor scripts in autodocs (#525) do not include extractor scripts in autodocs (fix issue #502) * [DOC] Add external link checking for docs build + fix broken links (#524) * add linkcheck in Makefile * add linkcheck to readthedocs config * try to fix readthedocs config * fix broken links * add comment * address PR review comment * increase timeout limit --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: julia-pfarr <juliakatharina.pfarr@gmx.de> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Julia-Katharina Pfarr <111446107+julia-pfarr@users.noreply.github.com> * [ENH] Remove pipeline configs from global config (#503) * add path to pipeline config in layout * remove pipeline configs from global config and put them in pipeline bundle directories instead * update PipelineWorkflow (and subclasses) to handle new config file location * refactor get_pipeline_version to get dpath input instead of list * fix PipelineWorkflow tests * fix PipelineRunner tests * fix bug in _get_pipeline_config() * fix InitWorkflow tests * fix tests for BidsConversionRunner * fix tests for ExtractionRunner * fix TrackerWorkflow test * fix docs (?) * add/update tests * [MAINT] Add dependabot for GitHub actions (#511) * Create dependabot.yml * add "bot" label * fix indentation * change schedule interval to monthly * [MAINT] Fix/update issue labeller (#509) * add new workflow and remove old ones * add required `enable-versioned-regex` field * try to fix labeler.yml * add write permissions for PRs * fix typo? * use pull_request_target insteade of pull_request event trigger * [MAINT] Use Nipoppy bot instead of PAT for projects automation workflow (#508) use bot instead of PAT * [MAINT] Add GitHub Actions workflow to automatically update `CITATION.cff` version after release (#512) * add DOI and update contact/authors in CITATION.cff * rename validation workflow * add initial version of update workflow * update workflow * update names * exclude `nipoppy-bot` PRs from changelog * Bump actions/stale from 9.0.0 to 9.1.0 (#515) Bumps [actions/stale](https://github.com/actions/stale) from 9.0.0 to 9.1.0. - [Release notes](https://github.com/actions/stale/releases) - [Changelog](https://github.com/actions/stale/blob/main/CHANGELOG.md) - [Commits](actions/stale@v9.0.0...v9.1.0) --- updated-dependencies: - dependency-name: actions/stale dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/checkout from 3 to 4 (#514) Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v3...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/setup-python from 4 to 5 (#516) Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@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> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [MAINT] Bump codecov/codecov-action from 4 to 5 (#513) * Bump codecov/codecov-action from 4 to 5 Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 4 to 5. - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](codecov/codecov-action@v4...v5) --- updated-dependencies: - dependency-name: codecov/codecov-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * use `files` instead of deprecated `file` * add prefix to PR titles --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * [MAINT] Clean up `.gitignore` (#521) * clean up .gitignore * add entries for Python venvs * [DOC] Add "how-to" guide for dataset initialization (#489) * add "how-to" guide for dataset init * address PR comments * split init doc in multiple pages for non-bids vs. bids start * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix error heading * fix heading and paths * fix header bids.md * update index and beginning of each page * update titles * minor changes --------- Co-authored-by: julia-pfarr <juliakatharina.pfarr@gmx.de> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Julia-Katharina Pfarr <111446107+julia-pfarr@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#527) updates: - [github.com/pycqa/isort: 6.0.0 → 6.0.1](PyCQA/isort@6.0.0...6.0.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [DOC] Add a CLI reference page for `nipoppy status` (#529) * add "nipoppy status" page to docs * import StatusWorkflow in workflows module init * [DOC] Add tooltips for glossary terms (#526) try adding tooltip for glossary terms * [DOC] Do not include extractor scripts in autodocs (#525) do not include extractor scripts in autodocs (fix issue #502) * [DOC] Add external link checking for docs build + fix broken links (#524) * add linkcheck in Makefile * add linkcheck to readthedocs config * try to fix readthedocs config * fix broken links * add comment * address PR review comment * increase timeout limit * fix typo * fix paths --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: julia-pfarr <juliakatharina.pfarr@gmx.de> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Julia-Katharina Pfarr <111446107+julia-pfarr@users.noreply.github.com> * [ENH] Add `PIPELINE_VARIABLES` to global config (#548) * add `PIPELINE_VARIABLES` field to global config * add PIPELINE_TYPE: PipelineTypeEnum in pipeline configs * use pipeline variables instead of substitutions for replacement in pipeline files * increase test coverage * address PR review comments * [ENH] Deprecate `DATASET_NAME`, `VISIT_IDS` and `SESSION_IDS` fields from `Config` (#553) * deprecate field from Config class * update StatusWorkflow and fix tests * rename test file * clean up BaseWorkflow tests * clean up DicomReorgWorkflow tests * clean up DoughnutWorkflow tests * fix autodoc warning * increase linkcheck timeout limit * [ENH] Rename pipeline store subdirectories (#561) * rename directories * fix tests * fix docs * [ENH] Force pipeline step config files to only have relative paths (#560) * Remove TRACKER_CONFIG_FILE from ProcPipelineConfig (should only be in ProcPipelineStepConfig) * update validation for BasePipelineStepConfig * update test for invocation/descriptor file fields * add tests for absolute path check and fix bug * update sample config files * refactor pipeline config loading + update relevant tests * handle relative paths in BasePipelineWorkflow * revert pipeline store directory names * fix some tests * fix remaining tests * fix doc warnings * increase test coverage + add test case * fix test * add helper function for getting pipeline bundle path * rename "proc" -> "processing" in test * [ENH] Split `BaseWorkflow` into `BaseWorkflow` and `BaseDatasetWorkflow` (#556) * rename `BaseWorkflow` -> `BaseDatasetWorkflow` * Extract `BaseWorkflow` from `BaseDatasetWorkflow` * move/fix tests * make validate_layout an init argument instead of class attribute * rename _skip_logging -> _skip_logfile * [ENH] Add `nipoppy pipeline validate` command (#558) * [ENH] Add `nipoppy pipeline install` command (#566) * add core validation functions + tests * Remove TRACKER_CONFIG_FILE from ProcPipelineConfig (should only be in ProcPipelineStepConfig) * add CLI command and substitutions * add substitutions test * add CLI test * rename test file * fix docs warnings * add test for PipelineValidateWorkflow * update validation for BasePipelineStepConfig * update test for invocation/descriptor file fields * add tests for absolute path check and fix bug * update sample config files * refactor pipeline config loading + update relevant tests * handle relative paths in BasePipelineWorkflow * revert pipeline store directory names * fix some tests * fix remaining tests * fix doc warnings * increase test coverage + add test case * fix test * adapt for pending relative path change * update log messages * fix test broken by merge * add helper function for getting pipeline bundle path * add base "pipeline install" functionality * Squashed commit of the following: commit e922f12 Merge: 788d3f1 5444535 Author: Michelle Wang <tomichellewang@gmail.com> Date: Mon Mar 24 14:01:07 2025 -0400 Merge remote-tracking branch 'upstream/dev-catalog' into pipeline_step_paths commit 5444535 Author: Michelle Wang <tomichellewang@gmail.com> Date: Sat Mar 22 13:04:20 2025 -0400 [ENH] Rename pipeline store subdirectories (#561) * rename directories * fix tests * fix docs * Squashed commit of the following: commit 853be29 Author: Michelle Wang <tomichellewang@gmail.com> Date: Mon Mar 24 13:53:19 2025 -0400 minor update to CLI * add CLI command and update logging * add variables to global config * add check that pipeline vars are not null * make sure existing fields in global config are not changed * add VARIABLES to default pipeline configs and add test * Squashed commit of the following: commit 34a5ddd Author: Michelle Wang <tomichellewang@gmail.com> Date: Fri Mar 28 11:15:59 2025 -0400 fix CLI test commit 8d17a8b Author: Michelle Wang <tomichellewang@gmail.com> Date: Thu Mar 27 16:51:37 2025 -0400 fix typo commit 7975bb4 Author: Michelle Wang <tomichellewang@gmail.com> Date: Thu Mar 27 16:33:59 2025 -0400 try to fix Pydantic deprecation errors commit c51fe30 Author: Michelle Wang <tomichellewang@gmail.com> Date: Thu Mar 27 16:25:09 2025 -0400 remove things related to dataset layout commit 3229e46 Merge: 9e75942 f437b59 Author: Michelle Wang <tomichellewang@gmail.com> Date: Thu Mar 27 15:59:53 2025 -0400 Merge remote-tracking branch 'upstream/dev-catalog' into 557/pipeline_validate commit 9e75942 Author: Michelle Wang <tomichellewang@gmail.com> Date: Thu Mar 27 11:17:46 2025 -0400 address most PR review comments commit 2e87f8d Merge: 9391ded fac5d2b Author: Michelle Wang <tomichellewang@gmail.com> Date: Thu Mar 27 11:06:40 2025 -0400 Merge remote-tracking branch 'upstream/dev-catalog' into 557/pipeline_validate commit 9391ded Author: Michelle Wang <tomichellewang@gmail.com> Date: Tue Mar 25 14:52:15 2025 -0400 make sure pipeline bundle content is flat list of file (no subdirectories) commit 42e904a Author: Michelle Wang <tomichellewang@gmail.com> Date: Tue Mar 25 12:40:06 2025 -0400 handle edge case with relative parent directories commit 853be29 Author: Michelle Wang <tomichellewang@gmail.com> Date: Mon Mar 24 13:53:19 2025 -0400 minor update to CLI * fix merge * fix PipelineInstallWorkflow * address PR review comments * fix CLI argument order * fix test * fix test again * do not catch exceptions * [ENH] api to download and upload pipelines from zenodo. (#506) * [ENH] api to download files from zenodo. * [FIX] add httpx dependency * [MAINT] remove requests dependency * [FIX] remove tqdm for now * [MAINT] Add dependabot for GitHub actions (#511) * Create dependabot.yml * add "bot" label * fix indentation * change schedule interval to monthly * [MAINT] Fix/update issue labeller (#509) * add new workflow and remove old ones * add required `enable-versioned-regex` field * try to fix labeler.yml * add write permissions for PRs * fix typo? * use pull_request_target insteade of pull_request event trigger * [MAINT] Use Nipoppy bot instead of PAT for projects automation workflow (#508) use bot instead of PAT * [MAINT] Add GitHub Actions workflow to automatically update `CITATION.cff` version after release (#512) * add DOI and update contact/authors in CITATION.cff * rename validation workflow * add initial version of update workflow * update workflow * update names * exclude `nipoppy-bot` PRs from changelog * Bump actions/stale from 9.0.0 to 9.1.0 (#515) Bumps [actions/stale](https://github.com/actions/stale) from 9.0.0 to 9.1.0. - [Release notes](https://github.com/actions/stale/releases) - [Changelog](https://github.com/actions/stale/blob/main/CHANGELOG.md) - [Commits](actions/stale@v9.0.0...v9.1.0) --- updated-dependencies: - dependency-name: actions/stale dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/checkout from 3 to 4 (#514) Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v3...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/setup-python from 4 to 5 (#516) Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@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> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [MAINT] Bump codecov/codecov-action from 4 to 5 (#513) * Bump codecov/codecov-action from 4 to 5 Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 4 to 5. - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](codecov/codecov-action@v4...v5) --- updated-dependencies: - dependency-name: codecov/codecov-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * use `files` instead of deprecated `file` * add prefix to PR titles --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * [MAINT] Clean up `.gitignore` (#521) * clean up .gitignore * add entries for Python venvs * [DOC] Add "how-to" guide for dataset initialization (#489) * add "how-to" guide for dataset init * address PR comments * split init doc in multiple pages for non-bids vs. bids start * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix error heading * fix heading and paths * fix header bids.md * update index and beginning of each page * update titles * minor changes --------- Co-authored-by: julia-pfarr <juliakatharina.pfarr@gmx.de> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Julia-Katharina Pfarr <111446107+julia-pfarr@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#527) updates: - [github.com/pycqa/isort: 6.0.0 → 6.0.1](PyCQA/isort@6.0.0...6.0.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [DOC] Add a CLI reference page for `nipoppy status` (#529) * add "nipoppy status" page to docs * import StatusWorkflow in workflows module init * [DOC] Add tooltips for glossary terms (#526) try adding tooltip for glossary terms * [DOC] Do not include extractor scripts in autodocs (#525) do not include extractor scripts in autodocs (fix issue #502) * [DOC] Add external link checking for docs build + fix broken links (#524) * add linkcheck in Makefile * add linkcheck to readthedocs config * try to fix readthedocs config * fix broken links * add comment * address PR review comment * increase timeout limit * Update tests/test_zenodo.py Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * Update nipoppy/zenodo.py Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * Improve error message, no longer required access tokekn for download, improve test * add cli for downloading pipelines from zenodo * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update nipoppy/zenodo.py Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * [ENH] Prototype for Zenodo upload * [TMP] started working on tests for upload. * Rename nipoppy pipeline add subcommand to install * add tests for authentication * Test for upload pipeline * Integrate new change for PR - Use new pipeline config for test - rename nipoppy pipeline add to download - Enforce nipoppy keywords on zenodo * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * pre-commit-ci modified the zenodo.json file for the example pipeline. * [no ci] cleanup gitignore conflict * Triger CI after adding secret to GH * Update nipoppy/cli.py Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * Update nipoppy/zenodo.py Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * fix pr comments * Seperated ZenodoAPI from workflow + tests for download workflow. * test get zenodo metadata from local pipeline. * test for zenodo upload workflow * rename zenodo_id to record_id * Add ZENODO as github variable * Remove and Prevent log file in history * Update nipoppy/workflows/zenodo.py Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * pr comments * Fix PR comments * Fix env var name for zenodo ID * Handle empty ZENODO_TOKEN GitHub secret seems to be empty on PR * Update nipoppy/zenodo_api.py Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix after merge * try to fix failing test (Zenodo record not matching sample pipeline anymore) * fix new failing test * pre-commit fix * update test data directory name * fix again --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Michelle Wang <tomichellewang@gmail.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: julia-pfarr <juliakatharina.pfarr@gmx.de> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Julia-Katharina Pfarr <111446107+julia-pfarr@users.noreply.github.com> * fix tests * [FIX] Fix Zenodo keywords not being set correctly (#598) * fix tests * remove docs file * use "subjects" metadata field instead of "keywords" * use "Nipoppy user" as default creator name * fix test * fix other tests * add pipeline name and version as keywords * [ENH] Add schema version to Zenodo record keywords (and pipeline config files) (#602) * fix tests * remove docs file * use "subjects" metadata field instead of "keywords" * use "Nipoppy user" as default creator name * fix test * fix other tests * add pipeline name and version as keywords * add mandatory schema version field and fix tests * [ENH] Implement `nipoppy pipeline search` (#599) * add search function and tests * add debug message * add search workflow and tests * add CLI command and test * minor changes * minor improvements * increase test coverage * address PR review comments * [ENH] Merge `nipoppy pipeline download` into `nipoppy pipeline install` (#594) * Merge `main` -> `dev-catalog` (#563) * [MAINT] Add dependabot for GitHub actions (#511) * Create dependabot.yml * add "bot" label * fix indentation * change schedule interval to monthly * [MAINT] Fix/update issue labeller (#509) * add new workflow and remove old ones * add required `enable-versioned-regex` field * try to fix labeler.yml * add write permissions for PRs * fix typo? * use pull_request_target insteade of pull_request event trigger * [MAINT] Use Nipoppy bot instead of PAT for projects automation workflow (#508) use bot instead of PAT * [MAINT] Add GitHub Actions workflow to automatically update `CITATION.cff` version after release (#512) * add DOI and update contact/authors in CITATION.cff * rename validation workflow * add initial version of update workflow * update workflow * update names * exclude `nipoppy-bot` PRs from changelog * Bump actions/stale from 9.0.0 to 9.1.0 (#515) Bumps [actions/stale](https://github.com/actions/stale) from 9.0.0 to 9.1.0. - [Release notes](https://github.com/actions/stale/releases) - [Changelog](https://github.com/actions/stale/blob/main/CHANGELOG.md) - [Commits](actions/stale@v9.0.0...v9.1.0) --- updated-dependencies: - dependency-name: actions/stale dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/checkout from 3 to 4 (#514) Bumps [actions/checkout](https://github.com/actions/checkout) from 3 to 4. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v3...v4) --- updated-dependencies: - dependency-name: actions/checkout dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump actions/setup-python from 4 to 5 (#516) Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@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> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [MAINT] Bump codecov/codecov-action from 4 to 5 (#513) * Bump codecov/codecov-action from 4 to 5 Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 4 to 5. - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](codecov/codecov-action@v4...v5) --- updated-dependencies: - dependency-name: codecov/codecov-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * use `files` instead of deprecated `file` * add prefix to PR titles --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * [MAINT] Clean up `.gitignore` (#521) * clean up .gitignore * add entries for Python venvs * [DOC] Add "how-to" guide for dataset initialization (#489) * add "how-to" guide for dataset init * address PR comments * split init doc in multiple pages for non-bids vs. bids start * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix error heading * fix heading and paths * fix header bids.md * update index and beginning of each page * update titles * minor changes --------- Co-authored-by: julia-pfarr <juliakatharina.pfarr@gmx.de> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Julia-Katharina Pfarr <111446107+julia-pfarr@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#527) updates: - [github.com/pycqa/isort: 6.0.0 → 6.0.1](PyCQA/isort@6.0.0...6.0.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * [DOC] Add a CLI reference page for `nipoppy status` (#529) * add "nipoppy status" page to docs * import StatusWorkflow in workflows module init * [DOC] Add tooltips for glossary terms (#526) try adding tooltip for glossary terms * [DOC] Do not include extractor scripts in autodocs (#525) do not include extractor scripts in autodocs (fix issue #502) * [DOC] Add external link checking for docs build + fix broken links (#524) * add linkcheck in Makefile * add linkcheck to readthedocs config * try to fix readthedocs config * fix broken links * add comment * address PR review comment * increase timeout limit * [MAINT] Add CI workflow for Read the docs preview link (#536) add Read the docs preview workflow * [ENH] Add `bids-validator` `2.0.3` (#534) * add `bids-validator` 2.0.3 * simplify container config * expose schema version field (use latest by default) in invocation * [ENH] group options in cli help. (#491) * [ENH] group options in cli help. * remove duplicate entry for --force flag * Update nipoppy/cli.py Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * Remove redundant "options" suffix --------- Co-authored-by: Michelle Wang <tomichellewang@gmail.com> * [ENH] Remove Boutiques descriptor/invocation file content dumps (#542) * add `quiet` arg to `run_command` * silence bosh command * also overwrite subprocess error message * update error messages * fix regex in test * [ENH] Print container-pulling command and change global config container substitution (#540) * add test * add "apptainer pull" command to error message if URI is available * update default container store path * update container pull message * fix exception message in test * [BUG] Add validation for non-alphanumeric characters in `participant_id` and `session_id` in manifest (#546) * add failing tests * add validation * add test case with non-alphanumeric character in `visit_id` * clarify docstrings * update container path substitution pattern * [ENH] Improve `fs_stats` extractor pipeline (#550) * fix escape sequence warnings * make script crash if no subjects found + add troubleshooting suggestions for when FreeSurfer stats commands fail * make the default invocation have `"verbose": true` * rename script.py to fs_stats.py * update script * bump version to 0.2.1 * [MAINT] Fix Pydantic `model_fields` deprecations (#576) fix Pydantic `model_fields` deprecations * fix fs_stats version change * fix tests * fix test --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: julia-pfarr <juliakatharina.pfarr@gmx.de> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Julia-Katharina Pfarr <111446107+julia-pfarr@users.noreply.github.com> Co-authored-by: Mathieu Dugré <16450132+mathdugre@users.noreply.github.com> * more Zenodo workflow file into pipeline_store subdirectory * merge pipeline download with pipeline install * move tests * fix CLI tests * fix tests failing in 3.9 * increase test coverage * improve error message when Zenodo record doesn't have expected config file * address PR review comments * fix Zenodo ID for tests --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: julia-pfarr <juliakatharina.pfarr@gmx.de> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Julia-Katharina Pfarr <111446107+julia-pfarr@users.noreply.github.com> Co-authored-by: Mathieu Dugré <16450132+mathdugre@users.noreply.github.com> * [ENH] Automatically impute Zenodo record creator information (#601) * allow record_id in upload_pipeline() to start with "zenodo." * dynamically get creator info if user does not provide it * fix test * [ENH] Add `nipoppy pipeline list` command (#570) * Remove TRACKER_CONFIG_FILE from ProcPipelineConfig (should only be in ProcPipelineStepConfig) * update validation for BasePipelineStepConfig * update test for invocation/descriptor file fields * add tests for absolute path check and fix bug * update sample config files * refactor pipeline config loading + update relevant tests * handle relative paths in BasePipelineWorkflow * revert pipeline store directory names * fix some tests * fix remaining tests * fix doc warnings * increase test coverage + add test case * fix test * add helper function for getting pipeline bundle path * refactor test function args * add workflow and tests * fix failing tests * add CLI and test * switch to BaseDatasetWorkflow * update type annotation and refactor variable name * fix tests * fix tests * use defaultdict * reorder CLI subcommands * clean up sample global config * remove all sample pipeline files * remove default config tests * update init workflow * make tests pass * fix docs --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: julia-pfarr <juliakatharina.pfarr@gmx.de> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Julia-Katharina Pfarr <111446107+julia-pfarr@users.noreply.github.com> Co-authored-by: Mathieu Dugré <16450132+mathdugre@users.noreply.github.com>
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Changes proposed in this pull request:
<DATASET_ROOT>/pipelines/{bids,proc,extraction}/config.jsonChecklist (for reviewers)
This section is for the PR reviewer
[BUG],[DOC],[ENH],[MAINT])Refer to NumPy Development Guide for a full list
Closes #XXXXFor new features:
For bug fixes: