.gitignore
CLAUDE.md
CONTRACT.md
LICENSE
MANIFEST.in
README.md
pyproject.toml
stages.yml
eval/README.md
eval/qsm_eval.py
eval/requirements.txt
eval/test_metrics.py
examples/workflow-engines/README.md
examples/workflow-engines/Snakefile
examples/workflow-engines/nipype_pipeline.py
examples/workflow-engines/pipeline.cwl
examples/workflow-engines/pipeline.nf
examples/workflow-engines/pydra_pipeline.py
qsm_ci/__init__.py
qsm_ci/cli.py
qsm_ci/containers.py
qsm_ci/interfaces.py
qsm_ci/nipype.py
qsm_ci/params.py
qsm_ci/pydra.py
qsm_ci/qsm_eval.py
qsm_ci/registry.json
qsm_ci/registry.py
qsm_ci/resources.py
qsm_ci/runner.py
qsm_ci/scaffold.py
qsm_ci/stages.py
qsm_ci/submit.py
qsm_ci/templates.py
qsm_ci.egg-info/PKG-INFO
qsm_ci.egg-info/SOURCES.txt
qsm_ci.egg-info/dependency_links.txt
qsm_ci.egg-info/entry_points.txt
qsm_ci.egg-info/requires.txt
qsm_ci.egg-info/scm_file_list.json
qsm_ci.egg-info/scm_version.json
qsm_ci.egg-info/top_level.txt
tests/conftest.py
tests/make_fixtures.py
tests/test_ci_eval_targets.py
tests/test_cli_errors.py
tests/test_datasets.py
tests/test_dedupe_hf_truth.py
tests/test_doc_slugs.py
tests/test_full_mask_scoring.py
tests/test_harness_smoke.py
tests/test_hc_chisep.py
tests/test_index_consistency.py
tests/test_interfaces.py
tests/test_intermediates.py
tests/test_manifest.py
tests/test_merge_index.py
tests/test_pipeline.py
tests/test_prune_stale_tuned.py
tests/test_publish_volumes.py
tests/test_publish_zenodo.py
tests/test_registry.py
tests/test_resource_sampler.py
tests/test_run_parser.py
tests/test_runner_help.py
tests/test_score_plan.py
tests/test_score_scheduling.py
tests/test_score_state.py
tests/test_scoring.py
tests/test_scoring_state_tracked.py
tests/test_stages_sync.py
tests/test_submissions.py
tests/test_web_sri.py
tests/methods/cp-bfr/algorithm.yml
tests/methods/cp-bfr/run.sh
tests/methods/cp-method/algorithm.yml
tests/methods/cp-method/run.sh
tests/methods/fail-bfr/algorithm.yml
tests/methods/fail-bfr/run.sh
tests/methods/needs-magnitude/algorithm.yml
tests/methods/needs-magnitude/run.sh
tests/methods/scale-method/algorithm.yml
tests/methods/scale-method/recon.py
tests/methods/scale-method/run.sh