Update to match neurodatascience/nipoppy:main #98
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* add NAME, VERSION, and VARIANT to PipelineConfig * remove VARIANT and add BidsPipelineConfig (with STEP) * apply new pipeline config schemas to Config * apply changes to workflows and workflow tests * improve test for duplicate pipelines * rename BIDS -> BIDS_PIPELINES * add GLOBALS field to config to minimize repetition * make sample global config file only contain the "latest" version of each supported pipelines * rename global_configs.json -> global_config.json (singular) * update config file insert in docs (quickstart) * rename global_configs.json -> global_config.json in documentation and test files too * increase test coverage * fix tests so that dummy Templateflow file is written in tmp_path * put CONTAINER and URI inside CONTAINER_INFO in PipelineConfig * implement pipeline steps with INVOCATION_FILE/DESCRIPTOR_FILE instead of INVOCATION/DESCRIPTOR (non-config tests failing) * make workflows use pipeline steps with invocation/descriptor files (all tests pass except test_supported_pipelines.py) * make supported pipeline tests pass * rename GLOBALS field to SUBSTITUTIONS * apply substitutions to descriptor/invocation file content * make `nipoppy init` copy sample invocation files * apply layout path replacement right after loading config file * add `--pipeline-step` argument to `nipoppy run` * make `pipeline_version` argument optional * do not propagate container configs on load (fix triple --cleanenv issue) * move container subcommand field to Boutiques descriptor instead of CONTAINER_CONFIG * make ContainerConfig propagation optionally include COMMAND propagation * move manifest and config file to dataset root directory * use PYBIDS_IGNORE_FILE instead of PYBIDS_IGNORE * move tracker config(s) to separate file too * add "CUSTOM" field to Config and do not allow extra fields * update file schemas doc page * fix path in docs * uncomment caplog assert statements now that caplog is working * add "container store" substitution by default * add [[NIPOPPY_PIPELINE_VERSION]] and [[NIPOPPY_PIPELINE_NAME]] substitutions to config * fix incorrect freesurfer output paths * add descriptor file paths to global config and move descriptors in DatasetInitWorkflow * remove flaky test_capture_warnings test * fix dcm2bids/heudiconv default value for sourcedata directory * fix DICOM_DIR_MAP_FILE validation error caused by substitution logic * fix typo * make default values explicit for container command and CUSTOM field * rename CONTAINER_INFO.PATH -> CONTAINER_INFO.FILE * turn get_boutiques_config() into a cached property boutiques_config * make sure highlighted lines in docs are correct * add second visit/session example to sample global config * add note in tabular model classes about "model" terminology * update highlighted lines in example config in docs
bcmcpher
approved these changes
Jun 7, 2024
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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.