.auto-changelog
.auto-changelog-template.hbs
.coveragerc
.gitignore
.readthedocs.yml
AUTHORS.md
CHANGELOG.md
CONTRIBUTING.md
LICENSE.txt
MANIFEST.in
README.md
codecov.yml
commitlint.config.js
pyproject.toml
setup.py
tox.ini
doc/.gitignore
doc/Makefile
doc/environment.yml
doc/source/.gitignore
doc/source/api_ref.rst
doc/source/changelog.rst
doc/source/cli.rst
doc/source/conf.py
doc/source/contributing.rst
doc/source/index.rst
doc/source/luigi_cfg.rst
doc/source/logo/BBP-Morphology-Workflows.jpg
examples/get_dataset.py
examples/logging.conf
examples/luigi.cfg
examples/run.sh
src/morphology_workflows/__init__.py
src/morphology_workflows/annotation.py
src/morphology_workflows/curation.py
src/morphology_workflows/marker_helper.py
src/morphology_workflows/placeholders.py
src/morphology_workflows/repair.py
src/morphology_workflows/utils.py
src/morphology_workflows.egg-info/PKG-INFO
src/morphology_workflows.egg-info/SOURCES.txt
src/morphology_workflows.egg-info/dependency_links.txt
src/morphology_workflows.egg-info/entry_points.txt
src/morphology_workflows.egg-info/requires.txt
src/morphology_workflows.egg-info/top_level.txt
src/morphology_workflows/_data/default_placeholders.csv
src/morphology_workflows/_templates/config_templates/default.cfg
src/morphology_workflows/_templates/config_templates/example_template_curate_dataset.cfg
src/morphology_workflows/_templates/source_report/conf.py
src/morphology_workflows/tasks/__init__.py
src/morphology_workflows/tasks/annotation.py
src/morphology_workflows/tasks/cli.py
src/morphology_workflows/tasks/curation.py
src/morphology_workflows/tasks/fetch.py
src/morphology_workflows/tasks/placeholders.py
src/morphology_workflows/tasks/repair.py
src/morphology_workflows/tasks/workflows.py
tests/__init__.py
tests/conftest.py
tests/test_cli.py
tests/test_curation.py
tests/test_download_morphs.py
tests/test_example_1.py
tests/test_placeholders.py
tests/data/allen_config_download.json
tests/data/mouselight_config_download.json
tests/data/neuromorpho_config_download.json
tests/data/placeholders.csv
tests/data/test_example_1/out_annotated/annotated_dataset.csv
tests/data/test_example_1/out_annotated/Annotate/report.csv
tests/data/test_example_1/out_annotated/ApicalPoint/report.csv
tests/data/test_example_1/out_annotated/CollectCurated/report.csv
tests/data/test_example_1/out_annotated/CutLeaves/report.csv
tests/data/test_example_1/out_annotated/HardLimit/report.csv
tests/data/test_example_1/out_annotated/MType/report.csv
tests/data/test_example_1/out_annotated/PlotApicalPoint/report.csv
tests/data/test_example_1/out_annotated/PlotCutLeaves/report.csv
tests/data/test_example_1/out_annotated/PlotHardLimit/report.csv
tests/data/test_example_1/out_curated/curated_dataset.csv
tests/data/test_example_1/out_curated/Align/report.csv
tests/data/test_example_1/out_curated/CheckNeurites/report.csv
tests/data/test_example_1/out_curated/Collect/report.csv
tests/data/test_example_1/out_curated/Curate/report.csv
tests/data/test_example_1/out_curated/DetectErrors/report.csv
tests/data/test_example_1/out_curated/EnsureNeuritesOutsideSoma/report.csv
tests/data/test_example_1/out_curated/ExtractMarkers/report.csv
tests/data/test_example_1/out_curated/Orient/report.csv
tests/data/test_example_1/out_curated/PlotErrors/report.csv
tests/data/test_example_1/out_curated/PlotMarkers/report.csv
tests/data/test_example_1/out_curated/PlotMorphologies/report.csv
tests/data/test_example_1/out_curated/Recenter/report.csv
tests/data/test_example_1/out_curated/Sanitize/report.csv
tests/data/test_example_1/out_repaired/repaired_dataset.csv
tests/data/test_example_1/out_repaired/CollectAnnotated/report.csv
tests/data/test_example_1/out_repaired/FixZeroDiameters/report.csv
tests/data/test_example_1/out_repaired/MakeCollage/report.csv
tests/data/test_example_1/out_repaired/MakeRelease/report.csv
tests/data/test_example_1/out_repaired/PlotRepair/report.csv
tests/data/test_example_1/out_repaired/Repair/report.csv
tests/data/test_example_1/out_repaired/RepairNeurites/report.csv
tests/data/test_example_1/out_repaired/Unravel/report.csv
tests/data/test_report/report_latexpdf.pdf
tests/data/test_report/report_no_exception_rst2pdf.pdf
tests/data/test_report/report_rst2pdf.pdf
tests/data/test_report_before_run/report_latexpdf.pdf
tests/data/test_report_before_run/report_rst2pdf.pdf
tests/examples_test/builder_recipe.xml
tests/examples_test/dataset.csv
tests/examples_test/get_dataset.py
tests/examples_test/logging.conf
tests/examples_test/luigi.cfg
tests/examples_test/mouse_dataset.csv
tests/examples_test/placement_rules.xml
tests/examples_test/report_CurateDataset.pdf
tests/examples_test/report_example.pdf
tests/examples_test/run_curation.sh
tests/examples_test/transform_rules.xml
tests/examples_test/morphologies/C060114A5.asc
tests/examples_test/morphologies/C270106A.asc
tests/examples_test/morphologies/README
tests/examples_test/morphologies/astrocyte.h5
tests/examples_test/morphologies/circle_contour.asc
tests/examples_test/morphologies/complexe.swc
tests/examples_test/morphologies/disconnected_neurite.swc
tests/examples_test/morphologies/iterators.asc
tests/examples_test/morphologies/mono-type.asc
tests/examples_test/morphologies/multiple_point_section.asc
tests/examples_test/morphologies/multiple_soma.swc
tests/examples_test/morphologies/nested_single_children.asc
tests/examples_test/morphologies/neurite_wrong_root_point.swc
tests/examples_test/morphologies/nrn-order-already-sorted.h5
tests/examples_test/morphologies/nrn_ordering.swc
tests/examples_test/morphologies/pia.asc
tests/examples_test/morphologies/reversed_NRN_neurite_order.swc
tests/examples_test/morphologies/rp100427-123_idC.asc
tests/examples_test/morphologies/sections-block.asc
tests/examples_test/morphologies/simple-with-font.asc
tests/examples_test/morphologies/simple-with-image-coord.asc
tests/examples_test/morphologies/simple.asc
tests/examples_test/morphologies/simple.swc
tests/examples_test/morphologies/simple2.asc
tests/examples_test/morphologies/soma_cylinders.swc
tests/examples_test/morphologies/soma_multiple_frustums.swc
tests/examples_test/morphologies/soma_single_frustum.swc
tests/examples_test/morphologies/soma_three_points_cylinder.swc
tests/examples_test/morphologies/spine.asc
tests/examples_test/morphologies/three_point_soma.swc