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AUTHORS.md
CHANGELOG.md
CONTRIBUTING.md
LICENSE.txt
MANIFEST.in
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codecov.yml
commitlint.config.js
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pyproject.toml
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tox.ini
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docs/Makefile
docs/environment.yml
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docs/source/changelog.rst
docs/source/cli.rst
docs/source/conf.py
docs/source/config_files.rst
docs/source/contributing.rst
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docs/source/synthesis_methodology.rst
examples/O1_example/logging.conf
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examples/O1_example/run.sh
examples/morphval_config/config_L23_PC.yaml
examples/morphval_config/config_bio.yaml
examples/parameter_update/compare.py
examples/parameter_update/logging.conf
examples/parameter_update/luigi.cfg
examples/parameter_update/run.sh
examples/rat_vaccum/logging.conf
examples/rat_vaccum/luigi.cfg
examples/rat_vaccum/run.sh
examples/trunk_validation/logging.conf
examples/trunk_validation/luigi.cfg
examples/trunk_validation/run.sh
requirements/base.pip
requirements/doc.pip
requirements/test.pip
src/version.py
src/morphval/__init__.py
src/morphval/cli.py
src/morphval/common.py
src/morphval/config.py
src/morphval/validation.py
src/morphval/validation_main.py
src/morphval/templates/report_summary_template.jinja2
src/morphval/templates/report_template.jinja2
src/morphval/templates/scripts.js
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src/synthesis_workflow/__init__.py
src/synthesis_workflow/circuit.py
src/synthesis_workflow/fit_utils.py
src/synthesis_workflow/synthesis.py
src/synthesis_workflow/tools.py
src/synthesis_workflow/utils.py
src/synthesis_workflow/vacuum_synthesis.py
src/synthesis_workflow/validation.py
src/synthesis_workflow.egg-info/PKG-INFO
src/synthesis_workflow.egg-info/SOURCES.txt
src/synthesis_workflow.egg-info/dependency_links.txt
src/synthesis_workflow.egg-info/entry_points.txt
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src/synthesis_workflow.egg-info/top_level.txt
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src/synthesis_workflow/defaults/morphval_default_config.yaml
src/synthesis_workflow/defaults/score_matrix_default_config.json
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src/synthesis_workflow/extra/insitu_validation.py
src/synthesis_workflow/extra/make_map.py
src/synthesis_workflow/tasks/__init__.py
src/synthesis_workflow/tasks/circuit.py
src/synthesis_workflow/tasks/cli.py
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src/synthesis_workflow/tasks/diametrizer.py
src/synthesis_workflow/tasks/synthesis.py
src/synthesis_workflow/tasks/vacuum_synthesis.py
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tests/conftest.py
tests/test_O1_workflow.py
tests/test_cli.py
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tests/test_utils.py
tests/test_vacuum_workflow.py
tests/data/.gitignore
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tests/data/luigi_tools.cfg
tests/data/raw_tmd_parameters.json
tests/data/in_small_O1/luigi.cfg
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tests/data/in_small_O1/out/atlas/atlas_planes_O0.npz
tests/data/in_small_O1/out/atlas/layer_annotation.nrrd
tests/data/in_small_O1/out/atlas/layer_annotation_layer_mapping.yaml
tests/data/in_small_O1/out/circuit/circuit_somata.mvd3
tests/data/in_small_O1/out/circuit/sliced_circuit_somata.mvd3
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tests/data/in_small_O1/out/morphs_df/synth_morphs_df.csv
tests/data/in_small_O1/out/synthesis/apical_points.yaml
tests/data/in_small_O1/out/synthesis/circuit.mvd3
tests/data/in_small_O1/out/synthesis/neurots_input/tmd_distributions.json
tests/data/in_small_O1/out/synthesis/neurots_input/tmd_parameters.json
tests/data/in_small_O1/out/validation/path_distance_fit.pdf
tests/data/in_small_O1/out/validation/score_matrix_reports.pdf
tests/data/in_small_O1/out/validation/morphology_validation_reports/validation_config.json
tests/data/in_small_O1/out/validation/morphology_validation_reports/validation_results.json
tests/data/in_small_O1/out/validation/scales/statistics.pdf
tests/data/in_vacuum/luigi.cfg
tests/data/in_vacuum/out/morphs_df/morphs_df.csv
tests/data/in_vacuum/out/morphs_df/substituted_morphs_df.csv
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tests/data/in_vacuum/out/synthesis/neurots_input/tmd_distributions.json
tests/data/in_vacuum/out/synthesis/neurots_input/tmd_parameters.json
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tests/data/in_vacuum/out/validation/morphometrics/morphometrics_apical_dendrite.pdf
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tests/data/input_cells/C170797A-P2.h5
tests/data/input_cells/C270106A.h5
tests/data/input_cells/neuronDB.xml
tests/data/input_cells/rat_20160908_E3_LH2_cell2.h5
tests/data/input_cells/sm080625a1-6_idD.h5
tests/data/synthesis_input/cell_composition.yaml
tests/data/synthesis_input/custom_parameters.csv
tests/data/synthesis_input/mtype_taxonomy.tsv
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tests/data/synthesis_input/scaling_rules.yaml
tests/data/synthesis_input/substitution_rules.yaml
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tests/morphval/test_validation.py
tests/morphval/test_validation_main.py