AllenInstitute · kaeldai · Jan 28, 2025 · Jan 28, 2025 · Jan 28, 2025 · Jan 28, 2025
diff --git a/.github/workflows/validate-pull-request.yaml b/.github/workflows/validate-pull-request.yaml
@@ -34,17 +34,17 @@ jobs:
         id: has_mechanisms_dir
         uses: andstor/file-existence-action@v1
         with:
-          files: bmtk/tests/simulator/bionet/components/mechanisms
+          files: tests/simulator/bionet/components/mechanisms
 
       - name: Setup NEURON
         if: steps.has_mechanisms_dir.outputs.files_exists == 'true'
         run: |
-          cd bmtk/tests/simulator/bionet/components/mechanisms
+          cd tests/simulator/bionet/components/mechanisms
           nrnivmodl modfiles
 
       - name: Run Tests
         run: |
-          pytest --cov=bmtk --cov-report=html bmtk/tests
+          pytest --cov=bmtk --cov-report=html tests
 
   linter:
     runs-on: ${{ matrix.os }}

diff --git a/bmtk/builder/index_builders.py b/bmtk/builder/index_builders.py
@@ -48,7 +48,7 @@ def create_index_in_memory(edges_file, edges_population, index_type, force_rebui
                 del edges_pop_grp[index_grp_name]
 
         index_grp = edges_pop_grp.create_group(index_grp_name)
-        ids_array = np.array(edges_pop_grp[col_to_index])  # ids to be indexed
+        ids_array = np.array(edges_pop_grp[col_to_index][()])  # ids to be indexed
         total_edges = len(edges_pop_grp[col_to_index])
 
         if total_edges == 0:
@@ -202,11 +202,12 @@ def create_index_on_disk(edges_file, edges_population, index_type, force_rebuild
 
             # fill in missing ids and foward fill Nans with the last previous index index
             i2r_table_df = i2r_table_df.reindex(pd.RangeIndex(i2r_table_df.index.max() + 1))
-            i2r_table_df['range_end'] = i2r_table_df['range_end'].fillna(method='ffill')
-            i2r_table_df['range_end'].fillna(0, inplace=True)
+            i2r_table_df['range_end'] = i2r_table_df['range_end'].ffill()
+            i2r_table_df.fillna({'range_end': 0}, inplace=True)
 
             nans_mask = i2r_table_df['range_beg'].isna()
-            i2r_table_df['range_beg'][nans_mask] = i2r_table_df['range_end'][nans_mask]
+            # i2r_table_df['range_beg'][nans_mask] = i2r_table_df['range_end'][nans_mask]
+            i2r_table_df.loc[nans_mask, 'range_beg'] = i2r_table_df['range_end'][nans_mask]
 
             # Save partition to disk
             partition_grp = cache_grp.create_group(partition_grp_name)

diff --git a/bmtk/builder/network_adaptors/nxnetwork.py b/bmtk/builder/network_adaptors/nxnetwork.py
@@ -25,7 +25,7 @@
 from .network import Network
 
 
-class NxNetwork(Network):
+class NxNetwork(Network): # pragma: no cover
     def __init__(self, name, **network_props):
         super(NxNetwork, self).__init__(name, **network_props or {})
 

diff --git a/bmtk/utils/sonata/edge_stats.py b/bmtk/utils/sonata/edge_stats.py
@@ -279,7 +279,7 @@ def edge_props_distribution(edge_files, edge_prop, populations=None,
             edges_df = pd.merge(edges_df, trg_nodes_df, how='left', on='target_node_id')
 
         if fill_val is not False:
-            edges_df[edge_prop] = fill_val if edge_prop not in edges_df.columns else edges_df[edge_prop].fillna(fill_val)
+            edges_df[edge_prop] = fill_val if edge_prop not in edges_df.columns else edges_df[edge_prop].infer_objects().fillna(fill_val)
 
         grouping_cols = edge_props_grouping + source_props_grouping + target_props_grouping
         if not grouping_cols:
@@ -431,7 +431,7 @@ def edge_stats_table(edges_data):
         n_trg_nodes = edges_df['target_node_id'].nunique()
         n_edge_types = edges_df.pop('edge_type_id').nunique()
 
-        edges_df['nsyns'] = 1 if 'nsyns' not in edges_df.columns else edges_df['nsyns'].fillna(1)
+        edges_df['nsyns'] = 1 if 'nsyns' not in edges_df.columns else edges_df['nsyns'].infer_objects().fillna(1)
         conns_se = edges_df.groupby(['source_node_id', 'target_node_id'])['nsyns'].agg('sum')
         n_conns = len(conns_se)
         n_syns = np.sum(conns_se.values)

diff --git a/bmtk/tests/__init__.py → tests/__init__.py b/bmtk/tests/__init__.py → tests/__init__.py
diff --git a/bmtk/tests/builder/__init__.py → tests/builder/__init__.py b/bmtk/tests/builder/__init__.py → tests/builder/__init__.py
diff --git a/bmtk/tests/builder/auxi/__init__.py → tests/builder/auxi/__init__.py b/bmtk/tests/builder/auxi/__init__.py → tests/builder/auxi/__init__.py
diff --git a/bmtk/tests/builder/auxi/structure_721.nrrd → tests/builder/auxi/structure_721.nrrd b/bmtk/tests/builder/auxi/structure_721.nrrd → tests/builder/auxi/structure_721.nrrd
diff --git a/...ests/builder/auxi/test_edge_connectors.py → tests/builder/auxi/test_edge_connectors.py b/...ests/builder/auxi/test_edge_connectors.py → tests/builder/auxi/test_edge_connectors.py
diff --git a/bmtk/tests/builder/auxi/test_node_params.py → tests/builder/auxi/test_node_params.py b/bmtk/tests/builder/auxi/test_node_params.py → tests/builder/auxi/test_node_params.py
diff --git a/bmtk/tests/builder/bionet/__init__.py → tests/builder/bionet/__init__.py b/bmtk/tests/builder/bionet/__init__.py → tests/builder/bionet/__init__.py
diff --git a/bmtk/tests/builder/bionet/test_swc_reader.py → tests/builder/bionet/test_swc_reader.py b/bmtk/tests/builder/bionet/test_swc_reader.py → tests/builder/bionet/test_swc_reader.py
diff --git a/bmtk/tests/builder/test_connection_map.py → tests/builder/test_connection_map.py b/bmtk/tests/builder/test_connection_map.py → tests/builder/test_connection_map.py
diff --git a/bmtk/tests/builder/test_connector.py → tests/builder/test_connector.py b/bmtk/tests/builder/test_connector.py → tests/builder/test_connector.py
diff --git a/bmtk/tests/builder/test_densenetwork.py → tests/builder/test_densenetwork.py b/bmtk/tests/builder/test_densenetwork.py → tests/builder/test_densenetwork.py
diff --git a/bmtk/tests/builder/test_edge_iterator.py → tests/builder/test_edge_iterator.py b/bmtk/tests/builder/test_edge_iterator.py → tests/builder/test_edge_iterator.py
diff --git a/bmtk/tests/builder/test_edges_sorter.py → tests/builder/test_edges_sorter.py b/bmtk/tests/builder/test_edges_sorter.py → tests/builder/test_edges_sorter.py
diff --git a/bmtk/tests/builder/test_id_generator.py → tests/builder/test_id_generator.py b/bmtk/tests/builder/test_id_generator.py → tests/builder/test_id_generator.py
diff --git a/bmtk/tests/builder/test_index_builders.py → tests/builder/test_index_builders.py b/bmtk/tests/builder/test_index_builders.py → tests/builder/test_index_builders.py
diff --git a/bmtk/tests/builder/test_iterator.py → tests/builder/test_iterator.py b/bmtk/tests/builder/test_iterator.py → tests/builder/test_iterator.py
diff --git a/bmtk/tests/builder/test_network.py → tests/builder/test_network.py b/bmtk/tests/builder/test_network.py → tests/builder/test_network.py
diff --git a/bmtk/tests/builder/test_network_mpi.py → tests/builder/test_network_mpi.py b/bmtk/tests/builder/test_network_mpi.py → tests/builder/test_network_mpi.py
diff --git a/bmtk/tests/builder/test_node_pool.py → tests/builder/test_node_pool.py b/bmtk/tests/builder/test_node_pool.py → tests/builder/test_node_pool.py
diff --git a/bmtk/tests/builder/test_node_set.py → tests/builder/test_node_set.py b/bmtk/tests/builder/test_node_set.py → tests/builder/test_node_set.py
diff --git a/bmtk/tests/builder/test_save_network.py → tests/builder/test_save_network.py b/bmtk/tests/builder/test_save_network.py → tests/builder/test_save_network.py
diff --git a/bmtk/tests/simulator/__init__.py → tests/simulator/__init__.py b/bmtk/tests/simulator/__init__.py → tests/simulator/__init__.py
diff --git a/bmtk/tests/simulator/bionet/__init__.py → tests/simulator/bionet/__init__.py b/bmtk/tests/simulator/bionet/__init__.py → tests/simulator/bionet/__init__.py
diff --git a/.../simulator/bionet/bionet_virtual_files.py → .../simulator/bionet/bionet_virtual_files.py b/.../simulator/bionet/bionet_virtual_files.py → .../simulator/bionet/bionet_virtual_files.py
diff --git a/...mponents/mechanisms/modfiles/vecevent.mod → ...mponents/mechanisms/modfiles/vecevent.mod b/...mponents/mechanisms/modfiles/vecevent.mod → ...mponents/mechanisms/modfiles/vecevent.mod
diff --git a/.../morphology/rorb_480169178_morphology.swc → .../morphology/rorb_480169178_morphology.swc b/.../morphology/rorb_480169178_morphology.swc → .../morphology/rorb_480169178_morphology.swc
diff --git a/bmtk/tests/simulator/bionet/conftest.py → tests/simulator/bionet/conftest.py b/bmtk/tests/simulator/bionet/conftest.py → tests/simulator/bionet/conftest.py
diff --git a/...tests/simulator/bionet/set_cell_params.py → tests/simulator/bionet/set_cell_params.py b/...tests/simulator/bionet/set_cell_params.py → tests/simulator/bionet/set_cell_params.py
diff --git a/.../tests/simulator/bionet/set_syn_params.py → tests/simulator/bionet/set_syn_params.py b/.../tests/simulator/bionet/set_syn_params.py → tests/simulator/bionet/set_syn_params.py
diff --git a/bmtk/tests/simulator/bionet/set_weights.py → tests/simulator/bionet/set_weights.py b/bmtk/tests/simulator/bionet/set_weights.py → tests/simulator/bionet/set_weights.py
diff --git a/bmtk/tests/simulator/bionet/test_biograph.py → tests/simulator/bionet/test_biograph.py b/bmtk/tests/simulator/bionet/test_biograph.py → tests/simulator/bionet/test_biograph.py
diff --git a/bmtk/tests/simulator/bionet/test_gids.py → tests/simulator/bionet/test_gids.py b/bmtk/tests/simulator/bionet/test_gids.py → tests/simulator/bionet/test_gids.py
diff --git a/bmtk/tests/simulator/bionet/test_iclamp.py → tests/simulator/bionet/test_iclamp.py b/bmtk/tests/simulator/bionet/test_iclamp.py → tests/simulator/bionet/test_iclamp.py
diff --git a/...tests/simulator/bionet/test_morphology.py → tests/simulator/bionet/test_morphology.py b/...tests/simulator/bionet/test_morphology.py → tests/simulator/bionet/test_morphology.py
diff --git a/bmtk/tests/simulator/bionet/test_nrn.py → tests/simulator/bionet/test_nrn.py b/bmtk/tests/simulator/bionet/test_nrn.py → tests/simulator/bionet/test_nrn.py
diff --git a/...ests/simulator/bionet/test_virtualcell.py → tests/simulator/bionet/test_virtualcell.py b/...ests/simulator/bionet/test_virtualcell.py → tests/simulator/bionet/test_virtualcell.py
diff --git a/...sts/simulator/core/test_ecephys_module.py → tests/simulator/core/test_ecephys_module.py b/...sts/simulator/core/test_ecephys_module.py → tests/simulator/core/test_ecephys_module.py
diff --git a/bmtk/tests/simulator/core/test_iclamp.py → tests/simulator/core/test_iclamp.py b/bmtk/tests/simulator/core/test_iclamp.py → tests/simulator/core/test_iclamp.py
diff --git a/bmtk/tests/simulator/core/test_io_tools.py → tests/simulator/core/test_io_tools.py b/bmtk/tests/simulator/core/test_io_tools.py → tests/simulator/core/test_io_tools.py
diff --git a/...s/simulator/core/test_pyfunction_cache.py → ...s/simulator/core/test_pyfunction_cache.py b/...s/simulator/core/test_pyfunction_cache.py → ...s/simulator/core/test_pyfunction_cache.py
diff --git a/.../simulator/core/test_simulation_config.py → .../simulator/core/test_simulation_config.py b/.../simulator/core/test_simulation_config.py → .../simulator/core/test_simulation_config.py
diff --git a/.../core/test_simulation_config_validator.py → .../core/test_simulation_config_validator.py b/.../core/test_simulation_config_validator.py → .../core/test_simulation_config_validator.py
diff --git a/...filternet/data/network/LGN_node_types.csv → ...filternet/data/network/LGN_node_types.csv b/...filternet/data/network/LGN_node_types.csv → ...filternet/data/network/LGN_node_types.csv
diff --git a/...lator/filternet/data/network/LGN_nodes.h5 → ...lator/filternet/data/network/LGN_nodes.h5 b/...lator/filternet/data/network/LGN_nodes.h5 → ...lator/filternet/data/network/LGN_nodes.h5
diff --git a/...ulator/filternet/lgnmodel/test_kernels.py → ...ulator/filternet/lgnmodel/test_kernels.py b/...ulator/filternet/lgnmodel/test_kernels.py → ...ulator/filternet/lgnmodel/test_kernels.py
diff --git a/...imulator/filternet/lgnmodel/test_movie.py → ...imulator/filternet/lgnmodel/test_movie.py b/...imulator/filternet/lgnmodel/test_movie.py → ...imulator/filternet/lgnmodel/test_movie.py
diff --git a/...lternet/lgnmodel/test_subclass_metrics.py → ...lternet/lgnmodel/test_subclass_metrics.py b/...lternet/lgnmodel/test_subclass_metrics.py → ...lternet/lgnmodel/test_subclass_metrics.py
diff --git a/...lternet/lgnmodel/test_transferfunction.py → ...lternet/lgnmodel/test_transferfunction.py b/...lternet/lgnmodel/test_transferfunction.py → ...lternet/lgnmodel/test_transferfunction.py
diff --git a/...imulator/filternet/lgnmodel/test_units.py → ...imulator/filternet/lgnmodel/test_units.py b/...imulator/filternet/lgnmodel/test_units.py → ...imulator/filternet/lgnmodel/test_units.py
diff --git a/...imulator/filternet/lgnmodel/test_utils.py → ...imulator/filternet/lgnmodel/test_utils.py b/...imulator/filternet/lgnmodel/test_utils.py → ...imulator/filternet/lgnmodel/test_utils.py
diff --git a/...mulator/filternet/test_default_setters.py → ...mulator/filternet/test_default_setters.py b/...mulator/filternet/test_default_setters.py → ...mulator/filternet/test_default_setters.py
diff --git a/...ulator/filternet/test_filternet_movies.py → ...ulator/filternet/test_filternet_movies.py b/...ulator/filternet/test_filternet_movies.py → ...ulator/filternet/test_filternet_movies.py
diff --git a/bmtk/tests/simulator/pointnet/__init__.py → tests/simulator/pointnet/__init__.py b/bmtk/tests/simulator/pointnet/__init__.py → tests/simulator/pointnet/__init__.py
diff --git a/bmtk/tests/simulator/pointnet/conftest.py → tests/simulator/pointnet/conftest.py b/bmtk/tests/simulator/pointnet/conftest.py → tests/simulator/pointnet/conftest.py
diff --git a/...r/pointnet/glif_models/637930677_lif.json → ...r/pointnet/glif_models/637930677_lif.json b/...r/pointnet/glif_models/637930677_lif.json → ...r/pointnet/glif_models/637930677_lif.json
diff --git a/...intnet/glif_models/637930677_lif_asc.json → ...intnet/glif_models/637930677_lif_asc.json b/...intnet/glif_models/637930677_lif_asc.json → ...intnet/glif_models/637930677_lif_asc.json
diff --git a/...pointnet/glif_models/637930677_lif_r.json → ...pointnet/glif_models/637930677_lif_r.json b/...pointnet/glif_models/637930677_lif_r.json → ...pointnet/glif_models/637930677_lif_r.json
diff --git a/...tnet/glif_models/637930677_lif_r_asc.json → ...tnet/glif_models/637930677_lif_r_asc.json b/...tnet/glif_models/637930677_lif_r_asc.json → ...tnet/glif_models/637930677_lif_r_asc.json
diff --git a/...et/glif_models/637930677_lif_r_asc_a.json → ...et/glif_models/637930677_lif_r_asc_a.json b/...et/glif_models/637930677_lif_r_asc_a.json → ...et/glif_models/637930677_lif_r_asc_a.json
diff --git a/...ulator/pointnet/pointnet_virtual_files.py → ...ulator/pointnet/pointnet_virtual_files.py b/...ulator/pointnet/pointnet_virtual_files.py → ...ulator/pointnet/pointnet_virtual_files.py
diff --git a/...sts/simulator/pointnet/test_glif_utils.py → tests/simulator/pointnet/test_glif_utils.py b/...sts/simulator/pointnet/test_glif_utils.py → tests/simulator/pointnet/test_glif_utils.py
diff --git a/...ulator/pointnet/test_multimeter_report.py → ...ulator/pointnet/test_multimeter_report.py b/...ulator/pointnet/test_multimeter_report.py → ...ulator/pointnet/test_multimeter_report.py
diff --git a/...sts/simulator/pointnet/test_pointgraph.py → tests/simulator/pointnet/test_pointgraph.py b/...sts/simulator/pointnet/test_pointgraph.py → tests/simulator/pointnet/test_pointgraph.py
diff --git a/...s/simulator/pointnet/test_pointnetwork.py → ...s/simulator/pointnet/test_pointnetwork.py b/...s/simulator/pointnet/test_pointnetwork.py → ...s/simulator/pointnet/test_pointnetwork.py
diff --git a/bmtk/tests/simulator/popnet/__init__.py → tests/simulator/popnet/__init__.py b/bmtk/tests/simulator/popnet/__init__.py → tests/simulator/popnet/__init__.py
diff --git a/.../simulator/popnet/popnet_virtual_files.py → .../simulator/popnet/popnet_virtual_files.py b/.../simulator/popnet/popnet_virtual_files.py → .../simulator/popnet/popnet_virtual_files.py
diff --git a/bmtk/tests/simulator/popnet/test_popgraph.py → tests/simulator/popnet/test_popgraph.py b/bmtk/tests/simulator/popnet/test_popgraph.py → tests/simulator/popnet/test_popgraph.py
diff --git a/...simulator/utils/test_simulation_inputs.py → ...simulator/utils/test_simulation_inputs.py b/...simulator/utils/test_simulation_inputs.py → ...simulator/utils/test_simulation_inputs.py
diff --git a/...imulator/utils/test_simulation_reports.py → ...imulator/utils/test_simulation_reports.py b/...imulator/utils/test_simulation_reports.py → ...imulator/utils/test_simulation_reports.py
diff --git a/bmtk/tests/utils/__init__.py → tests/utils/__init__.py b/bmtk/tests/utils/__init__.py → tests/utils/__init__.py
diff --git a/bmtk/tests/utils/reports/__init__.py → tests/utils/reports/__init__.py b/bmtk/tests/utils/reports/__init__.py → tests/utils/reports/__init__.py
diff --git a/...sts/utils/reports/compartment/__init__.py → tests/utils/reports/compartment/__init__.py b/...sts/utils/reports/compartment/__init__.py → tests/utils/reports/compartment/__init__.py
diff --git a/...partment_files/multi_population_report.h5 → ...partment_files/multi_population_report.h5 b/...partment_files/multi_population_report.h5 → ...partment_files/multi_population_report.h5
diff --git a/...ts/compartment/test_compartment_reader.py → ...ts/compartment/test_compartment_reader.py b/...ts/compartment/test_compartment_reader.py → ...ts/compartment/test_compartment_reader.py
diff --git a/...ts/compartment/test_compartment_report.py → ...ts/compartment/test_compartment_report.py b/...ts/compartment/test_compartment_report.py → ...ts/compartment/test_compartment_report.py
diff --git a/...ts/compartment/test_compartment_writer.py → ...ts/compartment/test_compartment_writer.py b/...ts/compartment/test_compartment_writer.py → ...ts/compartment/test_compartment_writer.py
diff --git a/...tils/reports/compartment/test_plotting.py → ...tils/reports/compartment/test_plotting.py b/...tils/reports/compartment/test_plotting.py → ...tils/reports/compartment/test_plotting.py
diff --git a/...ts/utils/reports/spike_trains/__init__.py → tests/utils/reports/spike_trains/__init__.py b/...ts/utils/reports/spike_trains/__init__.py → tests/utils/reports/spike_trains/__init__.py
diff --git a/.../spike_trains/benchmark_spikes_buffers.py → .../spike_trains/benchmark_spikes_buffers.py b/.../spike_trains/benchmark_spikes_buffers.py → .../spike_trains/benchmark_spikes_buffers.py
diff --git a/.../reports/spike_trains/test_csv_adaptor.py → .../reports/spike_trains/test_csv_adaptor.py b/.../reports/spike_trains/test_csv_adaptor.py → .../reports/spike_trains/test_csv_adaptor.py
diff --git a/...orts/spike_trains/test_csv_adaptor_mpi.py → ...orts/spike_trains/test_csv_adaptor_mpi.py b/...orts/spike_trains/test_csv_adaptor_mpi.py → ...orts/spike_trains/test_csv_adaptor_mpi.py
diff --git a/...ils/reports/spike_trains/test_plotting.py → ...ils/reports/spike_trains/test_plotting.py b/...ils/reports/spike_trains/test_plotting.py → ...ils/reports/spike_trains/test_plotting.py
diff --git a/...ports/spike_trains/test_sonata_adaptor.py → ...ports/spike_trains/test_sonata_adaptor.py b/...ports/spike_trains/test_sonata_adaptor.py → ...ports/spike_trains/test_sonata_adaptor.py
diff --git a/...s/spike_trains/test_sonata_adaptor_mpi.py → ...s/spike_trains/test_sonata_adaptor_mpi.py b/...s/spike_trains/test_sonata_adaptor_mpi.py → ...s/spike_trains/test_sonata_adaptor_mpi.py
diff --git a/...eports/spike_trains/test_spikes_buffer.py → ...eports/spike_trains/test_spikes_buffer.py b/...eports/spike_trains/test_spikes_buffer.py → ...eports/spike_trains/test_spikes_buffer.py
diff --git a/...ts/spike_trains/test_spikes_buffer_mpi.py → ...ts/spike_trains/test_spikes_buffer_mpi.py b/...ts/spike_trains/test_spikes_buffer_mpi.py → ...ts/spike_trains/test_spikes_buffer_mpi.py
diff --git a/.../reports/spike_trains/test_spikes_core.py → .../reports/spike_trains/test_spikes_core.py b/.../reports/spike_trains/test_spikes_core.py → .../reports/spike_trains/test_spikes_core.py
diff --git a/bmtk/tests/utils/sonata/__init__.py → tests/utils/sonata/__init__.py b/bmtk/tests/utils/sonata/__init__.py → tests/utils/sonata/__init__.py
diff --git a/bmtk/tests/utils/sonata/test_config.py → tests/utils/sonata/test_config.py b/bmtk/tests/utils/sonata/test_config.py → tests/utils/sonata/test_config.py
diff --git a/...sts/utils/sonata/test_config_validator.py → tests/utils/sonata/test_config_validator.py b/...sts/utils/sonata/test_config_validator.py → tests/utils/sonata/test_config_validator.py
diff --git a/bmtk/tests/utils/sonata/test_edge_stats.py → tests/utils/sonata/test_edge_stats.py b/bmtk/tests/utils/sonata/test_edge_stats.py → tests/utils/sonata/test_edge_stats.py