Update to match neurodatascience/nipoppy:main #92
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* switch from sphinx-autoapi to sphinx-autodoc2 extension to use markdown syntax in docstrings * add installation instructions * add Contributing guide and include README in index page * add notes about associated workflow class in CLI subcommand pages * add preliminary work on Quickstart page * add schema reference and link to it from Quickstart page * add tests/docs sections to contribution guide * minor changes * rename nipoppy_new -> nipoppy_cli * rename sample_data -> examples * update gitignore after rename * remove old files that didn't get merged correctly * add Codecov badge to README * move docs to correct directory * more fixes * revert back to sphinx-autoapi since sphinx-autodoc2 does not seem maintained anymore * add additional schemas (LayoutConfig, BoutiquesConfig) * add description string to all Pydantic model fields * update/move README * make README images appear correctly in both GitHub repo and Sphinx website * modify README text to match figure * remove empty tutorial section * mention "nipoppy_cli" in install instructions and add next steps in some pages * move images under docs/source/_static/img * reduce term references in installation instructions, and point to GitHub issues under Troubleshooting * set up ReadtheDocs * delete old README * fix ReadtheDocs config and move new README file to top * update path to README in pyproject.toml * update ReadtheDocs config to install the package so that the CLI reference works * fix typo in .readthedocs.yml and clean up .gitignore * update README after Nikhil comments * minor change
bcmcpher
approved these changes
May 7, 2024
make install command more robust
* unpin doc dependencies * add details furo config * maybe if I commited my stash things would show up in the PR * Apply suggestions from code review Co-authored-by: Michelle Wang <[email protected]> * Update nipoppy_cli/docs/source/conf.py --------- Co-authored-by: Michelle Wang <[email protected]>
…poppy#218) * build schema before doc * fail on warnings * ignore warnings
…oppy#196) * moving sample_global_configs.json and tree.json to the nipoppy subdir * fixed import paths after refactor * fixed import paths after refactor * refactored and cleaned up mriqc run script * refactored and cleaned up mriqc run script * Started tracker refactoring to use doughnut * added a catalog function to identify new proc-participants from bagel and doughnut * added a catalog function to identify new proc-participants from bagel and doughnut * added custom (new subjects only) pybids layout (sqldb) generation * fixed sessions loop and incorporated utils.load_status into run_tracker.py * fixed import path errors and incorporated tracker.py for status flags * fixed global var imports and logging levels * updated sample_run_nipoppy to set log-level and prototypical mriqc run with tracker * updated bids_tracker to match proc_pipe tracker schema * minor fixes and comments * fixed Pandas future warning on setting an item of incompatible dtype * fixed another Pandas future warning on setting an item of incompatible dtype * 1) Updated mriqc and fmirpre run scripts to bind complete bids_dir path, 2) added sqldb generation with ignore list for subjects and datatype+acq, 3) updated sample_run_nipoppy.py to show the these two functionalities. * fixed fmriprep pytest * fixed codespell * fixed NM filename pattern * added functionality to custom map participant_id to bids_id * fixed minor codespell errors * fixed errors from previous merge conflict resolution * updated sample_run_nipoppy to run tractoflow, renamed and moved check_dicom_status, and fixed minor bugs and logging in run_tracker * fixed session_id typo and optimized tracker runs * fixed FS utils function * added acq option to all trackers * added acq option to all trackers (fixed merge conflict) * fixed typos and added support for acq tag in mriqc tracker * fixed tractoflow subject dir path issues and added INCOMPLETE status * refactored FS extraction using brainload package * fixed hemisphere naming * fixed aseg extraction * remove version (i.e. v) prefix from run scripts to match trackers * fixed a typo and removed legacy FS extractor script * fixed bugs related to maget-brain data prep and tracking options * minor changes to extractor scripts * minor changes to extractor scripts
use official fids
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PR created/updated automatically by create-pull-request GitHub action. Will be merged automatically by automerge-action if there are no merge conflicts.
Closes #93.