.dockerignore
.env.run-docker
.env.run-local
.env.test-docker
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CONTRIBUTING.md
Dockerfile
LICENSE
Makefile
README.md
docker-cmd.sh
docker-compose.run.yml
docker-compose.test.yml
docker-compose.yml
pyproject.toml
uv.lock
.github/workflows/publish-pypi.yml
.github/workflows/publish.yml
.github/workflows/run-tests.yml
app/__init__.py
app/__main__.py
app/application.py
app/config.py
app/errors.py
app/logger.py
app/dependencies/__init__.py
app/dependencies/auth.py
app/dependencies/entitysdk.py
app/endpoints/__init__.py
app/endpoints/circuit_connectivity.py
app/endpoints/circuit_properties.py
app/endpoints/count_scan_coordinates.py
app/endpoints/ephys_metrics.py
app/endpoints/morphology_metrics.py
app/endpoints/morphology_validation.py
app/endpoints/multi_values.py
app/endpoints/scan_config.py
app/schemas/__init__.py
app/schemas/auth.py
app/schemas/base.py
app/utils/__init__.py
app/utils/common.py
app/utils/http.py
examples/A_service_and_entitycore/circuit_simulation/entitysdk_circuit_simulations.ipynb
examples/A_service_and_entitycore/deserialize/deserialize_example.ipynb
examples/A_service_and_entitycore/ion_channel_modeling/ion_channel_modeling_example.ipynb
examples/A_service_and_entitycore/obi_one_entity_tools/entitysdk_example.ipynb
examples/A_service_and_entitycore/test_endpoints/test_endpoints.ipynb
examples/B_blocks/afferent_synapse_set_example.ipynb
examples/B_blocks/morphology_locations_example.ipynb
examples/B_blocks/motif_neuron_set_example.ipynb
examples/B_blocks/neuron_set_example.ipynb
examples/C_forms/basic_connectivity_plots/basic_connetivity_plots_example.ipynb
examples/C_forms/basic_connectivity_plots/colors_tab10.csv
examples/C_forms/circuit_extraction/circuit_extraction_example.ipynb
examples/C_forms/circuit_simulation/circuit_simulations_example.ipynb
examples/C_forms/circuit_simulation/circuit_simulations_with_manipulations_example.ipynb
examples/C_forms/connectivity_matrix_extraction/connectivity_matrix_extraction_example.ipynb
examples/C_forms/unsupported/validation/reconstruction_morphology_validation_example.ipynb
examples/D_blueetl_example/analysis_config_01_relative_with_soma.yaml
examples/D_blueetl_example/blueetl_example.ipynb
examples/E_run_small_microcircuit/run_circuit_simulation.ipynb
examples/F_single_cell_simulations/entitysdk_memodel_simulation.ipynb
examples/G_circuit_metrics/circuit_metrics_example.ipynb
examples/G_circuit_metrics/connectivity_metrics_example.ipynb
examples/Z_currently_not_supported/morphology_metrics_example.ipynb
examples/Z_currently_not_supported/simulation_schema_testing.ipynb
examples/Z_currently_not_supported/multiservice_launch/multiservice_launch.py
examples/data/blueetl_data/analysis/analysis_config_01_relative.yaml
examples/data/blueetl_data/circuit/README
examples/data/blueetl_data/circuit/sonata/circuit_config.json
examples/data/blueetl_data/circuit/sonata/node_sets.json
examples/data/blueetl_data/circuit/sonata/node_sets_extra.json
examples/data/blueetl_data/circuit/sonata/nodes.h5
examples/data/blueetl_data/simulation/README
examples/data/blueetl_data/simulation/sonata/simulation_config.json
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examples/data/blueetl_data/simulation/sonata/reporting/create_reports.py
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examples/data/blueetl_data/simulation/sonata/reporting/soma_report.h5
examples/data/blueetl_data/simulation/sonata/reporting/spikes.h5
examples/data/blueetl_data/simulation_campaign/config_01_relative_bbp_workflow.json
examples/data/blueetl_data/simulation_campaign/config_02_relative_blueetl.yaml
examples/data/blueetl_data/simulation_campaign/0/simulation_config.json
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examples/data/blueetl_data/simulation_campaign/0/reporting/soma_report.h5
examples/data/blueetl_data/simulation_campaign/0/reporting/spikes.h5
examples/data/connectivity_matrices/N_10__top_nodes_dim6/connectivity_matrix.h5
examples/data/connectivity_matrices/N_10__top_rc_nodes_dim2_rc/connectivity_matrix.h5
examples/data/morphologies/L5_TPC:A_MusMusculus_PrimarySomatosensory_C060114A5/C060114A5.asc
examples/data/morphologies/L5_TPC:A_MusMusculus_PrimarySomatosensory_C060114A5/C060114A5.h5
examples/data/morphologies/L5_TPC:A_MusMusculus_PrimarySomatosensory_C060114A5/C060114A5.swc
examples/data/single_neuron_circuits/SingleNeuronCircuit__top_nodes_dim6__IDX0/circuit_config.json
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obi_one/core/block_reference.py
obi_one/core/constants.py
obi_one/core/entity_from_id.py
obi_one/core/exception.py
obi_one/core/info.py
obi_one/core/param.py
obi_one/core/parametric_multi_values.py
obi_one/core/path.py
obi_one/core/run_tasks.py
obi_one/core/scan_config.py
obi_one/core/scan_generation.py
obi_one/core/serialization.py
obi_one/core/single.py
obi_one/core/task.py
obi_one/core/tuple.py
obi_one/core/unsupported/__init__.py
obi_one/core/unsupported/validation.py
obi_one/scientific/__init__.py
obi_one/scientific/blocks/__init__.py
obi_one/scientific/blocks/afferent_synapses.py
obi_one/scientific/blocks/extracellular_locations.py
obi_one/scientific/blocks/ion_channel_equations.py
obi_one/scientific/blocks/manipulations.py
obi_one/scientific/blocks/recording.py
obi_one/scientific/blocks/stimulus.py
obi_one/scientific/blocks/timestamps.py
obi_one/scientific/blocks/morphology_locations/__init__.py
obi_one/scientific/blocks/morphology_locations/base.py
obi_one/scientific/blocks/morphology_locations/clustered.py
obi_one/scientific/blocks/morphology_locations/path_distance.py
obi_one/scientific/blocks/morphology_locations/random.py
obi_one/scientific/blocks/neuron_sets/__init__.py
obi_one/scientific/blocks/neuron_sets/base.py
obi_one/scientific/blocks/neuron_sets/combined.py
obi_one/scientific/blocks/neuron_sets/id.py
obi_one/scientific/blocks/neuron_sets/pair.py
obi_one/scientific/blocks/neuron_sets/predefined.py
obi_one/scientific/blocks/neuron_sets/property.py
obi_one/scientific/blocks/neuron_sets/simplex.py
obi_one/scientific/blocks/neuron_sets/specific.py
obi_one/scientific/blocks/neuron_sets/volumetric.py
obi_one/scientific/from_id/__init__.py
obi_one/scientific/from_id/cell_morphology_from_id.py
obi_one/scientific/from_id/circuit_from_id.py
obi_one/scientific/from_id/ion_channel_recording_from_id.py
obi_one/scientific/from_id/memodel_from_id.py
obi_one/scientific/library/__init__.py
obi_one/scientific/library/basic_connectivity_plots_helpers.py
obi_one/scientific/library/cell_template_neurodamus.jinja2
obi_one/scientific/library/cell_template_neurodamus_obi.jinja2
obi_one/scientific/library/circuit.py
obi_one/scientific/library/circuit_metrics.py
obi_one/scientific/library/connectivity_metrics.py
obi_one/scientific/library/entity_property_types.py
obi_one/scientific/library/ephys_extraction.py
obi_one/scientific/library/find_afferent_synapses.py
obi_one/scientific/library/memodel_circuit.py
obi_one/scientific/library/morphology_locations.py
obi_one/scientific/library/morphology_metrics.py
obi_one/scientific/library/simplex_extractors.py
obi_one/scientific/library/simulation_execution.py
obi_one/scientific/library/sonata_circuit_helpers.py
obi_one/scientific/tasks/__init__.py
obi_one/scientific/tasks/basic_connectivity_plots.py
obi_one/scientific/tasks/circuit_extraction.py
obi_one/scientific/tasks/connectivity_matrix_extraction.py
obi_one/scientific/tasks/contribute.py
obi_one/scientific/tasks/ephys_extraction.py
obi_one/scientific/tasks/folder_compression.py
obi_one/scientific/tasks/generate_simulation_configs.py
obi_one/scientific/tasks/generate_simulation_task.py
obi_one/scientific/tasks/ion_channel_modeling.py
obi_one/scientific/tasks/morphology_containerization.py
obi_one/scientific/tasks/morphology_decontainerization.py
obi_one/scientific/tasks/morphology_locations.py
obi_one/scientific/tasks/morphology_metrics.py
obi_one/scientific/tasks/unsupported/__init__.py
obi_one/scientific/tasks/unsupported/cell_morphology_validation.py
obi_one/scientific/unions/__init__.py
obi_one/scientific/unions/aliases.py
obi_one/scientific/unions/block_references.py
obi_one/scientific/unions/config_task_map.py
obi_one/scientific/unions/unions_extracellular_locations.py
obi_one/scientific/unions/unions_manipulations.py
obi_one/scientific/unions/unions_morphology_locations.py
obi_one/scientific/unions/unions_neuron_sets.py
obi_one/scientific/unions/unions_recordings.py
obi_one/scientific/unions/unions_scan_configs.py
obi_one/scientific/unions/unions_stimuli.py
obi_one/scientific/unions/unions_synapse_set.py
obi_one/scientific/unions/unions_tasks.py
obi_one/scientific/unions/unions_timestamps.py
projects/EM_circuits/check_circuits.ipynb
projects/EM_circuits/check_unused_morphologies.ipynb
projects/EM_circuits/create_node_sets.ipynb
projects/EM_circuits/folder_compression.ipynb
projects/EM_circuits/morphology_containerization.ipynb
projects/EM_circuits/patch_edge_files.ipynb
projects/circuits_for_explore/basic_plots_all_connectomes.py
projects/circuits_for_explore/basic_plots_all_small_connectomes.py
projects/circuits_for_explore/circuit_extraction.ipynb
projects/circuits_for_explore/connectivity_matrix_extraction.ipynb
projects/circuits_for_explore/folder_compression.ipynb
projects/circuits_for_explore/morphology_containerization.ipynb
projects/circuits_for_explore/nodeset_generator.py
projects/circuits_for_explore/tests/circuit_extraction_test.ipynb
projects/circuits_for_explore/tests/connectivity_matrix_extraction_test.ipynb
projects/circuits_for_explore/tests/folder_compression_test.ipynb
projects/circuits_for_explore/tests/morphology_containerization_dev.ipynb
projects/circuits_for_explore/tests/morphology_containerization_test.ipynb
projects/tiny_circuits/Top10CentralNeurons_Layer_Hex.pkl
projects/tiny_circuits/Top10CentralNeurons_Layer_Hex_OptIDX.pkl
projects/tiny_circuits/check_mod_files.ipynb
projects/tiny_circuits/circuit_extraction.ipynb
projects/tiny_circuits/circuit_extraction_hippocampus.ipynb
projects/tiny_circuits/circuit_extraction_motif.ipynb
projects/tiny_circuits/circuit_extraction_simplex.ipynb
projects/tiny_circuits/circuit_extraction_volumetric.ipynb
projects/tiny_circuits/circuit_simulations.ipynb
projects/tiny_circuits/connectivity_matrix_extraction.ipynb
projects/tiny_circuits/folder_compression.ipynb
projects/tiny_circuits/hippocampus_cylinder_example.ipynb
projects/tiny_circuits/morphology_decontainerization.ipynb
projects/tiny_circuits/patch_circuits.ipynb
projects/tiny_circuits/selection1.csv
projects/tiny_circuits/selection2.csv
projects/tiny_circuits/single_neuron_extraction.ipynb
projects/tiny_circuits/top_nodes_dim6.csv
projects/tiny_circuits/top_rc_nodes_dim2_rc.csv
tests/__init__.py
tests/conftest.py
tests/test_auth.py
tests/test_example.py
tests/utils.py
tests/blocks/__init__.py
tests/blocks/test_neuron_set.py
tests/data/S1FL_L5_DBC_cIR_4.nwb
tests/data/cell_morphology.asc
tests/data/cell_morphology.json
tests/data/cell_morphology.swc
tests/data/electrical_cell_recording.json
tests/data/model_dumps/circuit_simulation_single_config_serialization.json
tests/data/model_dumps/deprecated_simulation_serialization.json
tests/data/model_dumps/grid_scan_simulations_form.json
tests/data/model_dumps/grid_scan_task_serialization.json
tests/deserialization/__init__.py
tests/deserialization/test_deserialization.py
tests/routers/__init__.py
tests/routers/test_root.py
tests/routers/declared/__init__.py
tests/routers/declared/test_neuron_electrophysiology_metrics.py
tests/routers/declared/test_neuron_morphology_metrics.py
tests/simulation/__init__.py
tests/simulation/test_execution.py
tests/tasks/__init__.py
tests/tasks/test_basic_connectivity_plots.py
tests/tasks/test_circuit_extraction.py
tests/tasks/test_connectivity_matrix_extraction.py
tests/tasks/test_folder_compression.py
tests/tasks/test_morphology_containerization.py
tests/tasks/test_morphology_decontainerization.py
tests/tasks/test_simulation_campaign_generation.py