From dd4059191eeb500cd7a18a831e10cf9d56a331e2 Mon Sep 17 00:00:00 2001 From: kaeldai Date: Tue, 28 Jan 2025 09:53:29 -0800 Subject: [PATCH 1/3] updating tests and fixing some dep warnings --- bmtk/builder/index_builders.py | 9 +++++---- bmtk/builder/network_adaptors/nxnetwork.py | 2 +- bmtk/utils/sonata/edge_stats.py | 4 ++-- {bmtk/tests => tests}/__init__.py | 0 {bmtk/tests => tests}/builder/__init__.py | 0 {bmtk/tests => tests}/builder/auxi/__init__.py | 0 .../tests => tests}/builder/auxi/structure_721.nrrd | Bin .../builder/auxi/test_edge_connectors.py | 0 .../builder/auxi/test_node_params.py | 0 {bmtk/tests => tests}/builder/bionet/__init__.py | 0 .../builder/bionet/test_swc_reader.py | 0 .../tests => tests}/builder/test_connection_map.py | 0 {bmtk/tests => tests}/builder/test_connector.py | 0 {bmtk/tests => tests}/builder/test_densenetwork.py | 0 {bmtk/tests => tests}/builder/test_edge_iterator.py | 0 {bmtk/tests => tests}/builder/test_edges_sorter.py | 0 {bmtk/tests => tests}/builder/test_id_generator.py | 0 .../tests => tests}/builder/test_index_builders.py | 0 {bmtk/tests => tests}/builder/test_iterator.py | 0 {bmtk/tests => tests}/builder/test_network.py | 0 {bmtk/tests => tests}/builder/test_network_mpi.py | 0 {bmtk/tests => tests}/builder/test_node_pool.py | 0 {bmtk/tests => tests}/builder/test_node_set.py | 0 {bmtk/tests => tests}/builder/test_save_network.py | 0 {bmtk/tests => tests}/simulator/__init__.py | 0 {bmtk/tests => tests}/simulator/bionet/__init__.py | 0 .../simulator/bionet/bionet_virtual_files.py | 0 .../components/mechanisms/modfiles/vecevent.mod | 0 .../morphology/rorb_480169178_morphology.swc | 0 {bmtk/tests => tests}/simulator/bionet/conftest.py | 0 .../simulator/bionet/set_cell_params.py | 0 .../simulator/bionet/set_syn_params.py | 0 .../tests => tests}/simulator/bionet/set_weights.py | 0 .../simulator/bionet/test_biograph.py | 0 {bmtk/tests => tests}/simulator/bionet/test_gids.py | 0 .../tests => tests}/simulator/bionet/test_iclamp.py | 0 .../simulator/bionet/test_morphology.py | 0 {bmtk/tests => tests}/simulator/bionet/test_nrn.py | 0 .../simulator/bionet/test_virtualcell.py | 0 .../simulator/core/test_ecephys_module.py | 0 {bmtk/tests => tests}/simulator/core/test_iclamp.py | 0 .../tests => tests}/simulator/core/test_io_tools.py | 0 .../simulator/core/test_pyfunction_cache.py | 0 .../simulator/core/test_simulation_config.py | 0 .../core/test_simulation_config_validator.py | 0 .../filternet/data/network/LGN_node_types.csv | 0 .../simulator/filternet/data/network/LGN_nodes.h5 | Bin .../simulator/filternet/lgnmodel/test_kernels.py | 0 .../simulator/filternet/lgnmodel/test_movie.py | 0 .../filternet/lgnmodel/test_subclass_metrics.py | 0 .../filternet/lgnmodel/test_transferfunction.py | 0 .../simulator/filternet/lgnmodel/test_units.py | 0 .../simulator/filternet/lgnmodel/test_utils.py | 0 .../simulator/filternet/test_default_setters.py | 0 .../simulator/filternet/test_filternet_movies.py | 0 .../tests => tests}/simulator/pointnet/__init__.py | 0 .../tests => tests}/simulator/pointnet/conftest.py | 0 .../pointnet/glif_models/637930677_lif.json | 0 .../pointnet/glif_models/637930677_lif_asc.json | 0 .../pointnet/glif_models/637930677_lif_r.json | 0 .../pointnet/glif_models/637930677_lif_r_asc.json | 0 .../pointnet/glif_models/637930677_lif_r_asc_a.json | 0 .../simulator/pointnet/pointnet_virtual_files.py | 0 .../simulator/pointnet/test_glif_utils.py | 0 .../simulator/pointnet/test_multimeter_report.py | 0 .../simulator/pointnet/test_pointgraph.py | 0 .../simulator/pointnet/test_pointnetwork.py | 0 {bmtk/tests => tests}/simulator/popnet/__init__.py | 0 .../simulator/popnet/popnet_virtual_files.py | 0 .../simulator/popnet/test_popgraph.py | 0 .../simulator/utils/test_simulation_inputs.py | 0 .../simulator/utils/test_simulation_reports.py | 0 {bmtk/tests => tests}/utils/__init__.py | 0 {bmtk/tests => tests}/utils/reports/__init__.py | 0 .../utils/reports/compartment/__init__.py | 0 .../compartment_files/multi_population_report.h5 | Bin .../reports/compartment/test_compartment_reader.py | 0 .../reports/compartment/test_compartment_report.py | 0 .../reports/compartment/test_compartment_writer.py | 0 .../utils/reports/compartment/test_plotting.py | 0 .../utils/reports/spike_trains/__init__.py | 0 .../spike_trains/benchmark_spikes_buffers.py | 0 .../utils/reports/spike_trains/test_csv_adaptor.py | 0 .../reports/spike_trains/test_csv_adaptor_mpi.py | 0 .../utils/reports/spike_trains/test_plotting.py | 0 .../reports/spike_trains/test_sonata_adaptor.py | 0 .../reports/spike_trains/test_sonata_adaptor_mpi.py | 0 .../reports/spike_trains/test_spikes_buffer.py | 0 .../reports/spike_trains/test_spikes_buffer_mpi.py | 0 .../utils/reports/spike_trains/test_spikes_core.py | 0 {bmtk/tests => tests}/utils/sonata/__init__.py | 0 {bmtk/tests => tests}/utils/sonata/test_config.py | 0 .../utils/sonata/test_config_validator.py | 0 .../tests => tests}/utils/sonata/test_edge_stats.py | 0 94 files changed, 8 insertions(+), 7 deletions(-) rename {bmtk/tests => tests}/__init__.py (100%) rename {bmtk/tests => tests}/builder/__init__.py (100%) rename {bmtk/tests => tests}/builder/auxi/__init__.py (100%) rename {bmtk/tests => tests}/builder/auxi/structure_721.nrrd (100%) rename {bmtk/tests => tests}/builder/auxi/test_edge_connectors.py (100%) rename {bmtk/tests => tests}/builder/auxi/test_node_params.py (100%) rename {bmtk/tests => tests}/builder/bionet/__init__.py (100%) rename {bmtk/tests => tests}/builder/bionet/test_swc_reader.py (100%) rename {bmtk/tests => tests}/builder/test_connection_map.py (100%) rename {bmtk/tests => tests}/builder/test_connector.py (100%) rename {bmtk/tests => tests}/builder/test_densenetwork.py (100%) rename {bmtk/tests => tests}/builder/test_edge_iterator.py (100%) rename {bmtk/tests => tests}/builder/test_edges_sorter.py (100%) rename {bmtk/tests => tests}/builder/test_id_generator.py (100%) rename {bmtk/tests => tests}/builder/test_index_builders.py (100%) rename {bmtk/tests => tests}/builder/test_iterator.py (100%) rename {bmtk/tests => tests}/builder/test_network.py (100%) rename {bmtk/tests => tests}/builder/test_network_mpi.py (100%) rename {bmtk/tests => tests}/builder/test_node_pool.py (100%) rename {bmtk/tests => tests}/builder/test_node_set.py (100%) rename {bmtk/tests => tests}/builder/test_save_network.py (100%) rename {bmtk/tests => tests}/simulator/__init__.py (100%) rename {bmtk/tests => tests}/simulator/bionet/__init__.py (100%) rename {bmtk/tests => tests}/simulator/bionet/bionet_virtual_files.py (100%) rename {bmtk/tests => tests}/simulator/bionet/components/mechanisms/modfiles/vecevent.mod (100%) rename {bmtk/tests => tests}/simulator/bionet/components/morphology/rorb_480169178_morphology.swc (100%) rename {bmtk/tests => tests}/simulator/bionet/conftest.py (100%) rename {bmtk/tests => tests}/simulator/bionet/set_cell_params.py (100%) rename {bmtk/tests => tests}/simulator/bionet/set_syn_params.py (100%) rename {bmtk/tests => tests}/simulator/bionet/set_weights.py (100%) rename {bmtk/tests => tests}/simulator/bionet/test_biograph.py (100%) rename {bmtk/tests => tests}/simulator/bionet/test_gids.py (100%) rename {bmtk/tests => tests}/simulator/bionet/test_iclamp.py (100%) rename {bmtk/tests => tests}/simulator/bionet/test_morphology.py (100%) rename {bmtk/tests => tests}/simulator/bionet/test_nrn.py (100%) rename {bmtk/tests => tests}/simulator/bionet/test_virtualcell.py (100%) rename {bmtk/tests => tests}/simulator/core/test_ecephys_module.py (100%) rename {bmtk/tests => tests}/simulator/core/test_iclamp.py (100%) rename {bmtk/tests => tests}/simulator/core/test_io_tools.py (100%) rename {bmtk/tests => tests}/simulator/core/test_pyfunction_cache.py (100%) rename {bmtk/tests => tests}/simulator/core/test_simulation_config.py (100%) rename {bmtk/tests => tests}/simulator/core/test_simulation_config_validator.py (100%) rename {bmtk/tests => tests}/simulator/filternet/data/network/LGN_node_types.csv (100%) rename {bmtk/tests => tests}/simulator/filternet/data/network/LGN_nodes.h5 (100%) rename {bmtk/tests => tests}/simulator/filternet/lgnmodel/test_kernels.py (100%) rename {bmtk/tests => tests}/simulator/filternet/lgnmodel/test_movie.py (100%) rename {bmtk/tests => tests}/simulator/filternet/lgnmodel/test_subclass_metrics.py (100%) rename {bmtk/tests => tests}/simulator/filternet/lgnmodel/test_transferfunction.py (100%) rename {bmtk/tests => tests}/simulator/filternet/lgnmodel/test_units.py (100%) rename {bmtk/tests => tests}/simulator/filternet/lgnmodel/test_utils.py (100%) rename {bmtk/tests => tests}/simulator/filternet/test_default_setters.py (100%) rename {bmtk/tests => tests}/simulator/filternet/test_filternet_movies.py (100%) rename {bmtk/tests => tests}/simulator/pointnet/__init__.py (100%) rename {bmtk/tests => tests}/simulator/pointnet/conftest.py (100%) rename {bmtk/tests => tests}/simulator/pointnet/glif_models/637930677_lif.json (100%) rename {bmtk/tests => tests}/simulator/pointnet/glif_models/637930677_lif_asc.json (100%) rename {bmtk/tests => tests}/simulator/pointnet/glif_models/637930677_lif_r.json (100%) rename {bmtk/tests => tests}/simulator/pointnet/glif_models/637930677_lif_r_asc.json (100%) rename {bmtk/tests => tests}/simulator/pointnet/glif_models/637930677_lif_r_asc_a.json (100%) rename {bmtk/tests => tests}/simulator/pointnet/pointnet_virtual_files.py (100%) rename {bmtk/tests => tests}/simulator/pointnet/test_glif_utils.py (100%) rename {bmtk/tests => tests}/simulator/pointnet/test_multimeter_report.py (100%) rename {bmtk/tests => tests}/simulator/pointnet/test_pointgraph.py (100%) rename {bmtk/tests => tests}/simulator/pointnet/test_pointnetwork.py (100%) rename {bmtk/tests => tests}/simulator/popnet/__init__.py (100%) rename {bmtk/tests => tests}/simulator/popnet/popnet_virtual_files.py (100%) rename {bmtk/tests => tests}/simulator/popnet/test_popgraph.py (100%) rename {bmtk/tests => tests}/simulator/utils/test_simulation_inputs.py (100%) rename {bmtk/tests => tests}/simulator/utils/test_simulation_reports.py (100%) rename {bmtk/tests => tests}/utils/__init__.py (100%) rename {bmtk/tests => tests}/utils/reports/__init__.py (100%) rename {bmtk/tests => tests}/utils/reports/compartment/__init__.py (100%) rename {bmtk/tests => tests}/utils/reports/compartment/compartment_files/multi_population_report.h5 (100%) rename {bmtk/tests => tests}/utils/reports/compartment/test_compartment_reader.py (100%) rename {bmtk/tests => tests}/utils/reports/compartment/test_compartment_report.py (100%) rename {bmtk/tests => tests}/utils/reports/compartment/test_compartment_writer.py (100%) rename {bmtk/tests => tests}/utils/reports/compartment/test_plotting.py (100%) rename {bmtk/tests => tests}/utils/reports/spike_trains/__init__.py (100%) rename {bmtk/tests => tests}/utils/reports/spike_trains/benchmark_spikes_buffers.py (100%) rename {bmtk/tests => tests}/utils/reports/spike_trains/test_csv_adaptor.py (100%) rename {bmtk/tests => tests}/utils/reports/spike_trains/test_csv_adaptor_mpi.py (100%) rename {bmtk/tests => tests}/utils/reports/spike_trains/test_plotting.py (100%) rename {bmtk/tests => tests}/utils/reports/spike_trains/test_sonata_adaptor.py (100%) rename {bmtk/tests => tests}/utils/reports/spike_trains/test_sonata_adaptor_mpi.py (100%) rename {bmtk/tests => tests}/utils/reports/spike_trains/test_spikes_buffer.py (100%) rename {bmtk/tests => tests}/utils/reports/spike_trains/test_spikes_buffer_mpi.py (100%) rename {bmtk/tests => tests}/utils/reports/spike_trains/test_spikes_core.py (100%) rename {bmtk/tests => tests}/utils/sonata/__init__.py (100%) rename {bmtk/tests => tests}/utils/sonata/test_config.py (100%) rename {bmtk/tests => tests}/utils/sonata/test_config_validator.py (100%) rename {bmtk/tests => tests}/utils/sonata/test_edge_stats.py (100%) diff --git a/bmtk/builder/index_builders.py b/bmtk/builder/index_builders.py index 375f673cd..1bc9beba0 100644 --- 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 index 30879b2a5..296c81933 100644 --- 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 index 764f41931..fa3c3e8c4 100644 --- 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(copy=False).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(copy=False).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 b/tests/__init__.py similarity index 100% rename from bmtk/tests/__init__.py rename to tests/__init__.py diff --git a/bmtk/tests/builder/__init__.py b/tests/builder/__init__.py similarity index 100% rename from bmtk/tests/builder/__init__.py rename to tests/builder/__init__.py diff --git a/bmtk/tests/builder/auxi/__init__.py b/tests/builder/auxi/__init__.py similarity index 100% rename from bmtk/tests/builder/auxi/__init__.py rename to tests/builder/auxi/__init__.py diff --git a/bmtk/tests/builder/auxi/structure_721.nrrd b/tests/builder/auxi/structure_721.nrrd similarity index 100% rename from bmtk/tests/builder/auxi/structure_721.nrrd rename to tests/builder/auxi/structure_721.nrrd diff --git a/bmtk/tests/builder/auxi/test_edge_connectors.py b/tests/builder/auxi/test_edge_connectors.py similarity index 100% rename from bmtk/tests/builder/auxi/test_edge_connectors.py rename to tests/builder/auxi/test_edge_connectors.py diff --git a/bmtk/tests/builder/auxi/test_node_params.py b/tests/builder/auxi/test_node_params.py similarity index 100% rename from bmtk/tests/builder/auxi/test_node_params.py rename to tests/builder/auxi/test_node_params.py diff --git a/bmtk/tests/builder/bionet/__init__.py b/tests/builder/bionet/__init__.py similarity index 100% rename from bmtk/tests/builder/bionet/__init__.py rename to tests/builder/bionet/__init__.py diff --git a/bmtk/tests/builder/bionet/test_swc_reader.py b/tests/builder/bionet/test_swc_reader.py similarity index 100% rename from bmtk/tests/builder/bionet/test_swc_reader.py rename to tests/builder/bionet/test_swc_reader.py diff --git a/bmtk/tests/builder/test_connection_map.py b/tests/builder/test_connection_map.py similarity index 100% rename from bmtk/tests/builder/test_connection_map.py rename to tests/builder/test_connection_map.py diff --git a/bmtk/tests/builder/test_connector.py b/tests/builder/test_connector.py similarity index 100% rename from bmtk/tests/builder/test_connector.py rename to tests/builder/test_connector.py diff --git a/bmtk/tests/builder/test_densenetwork.py b/tests/builder/test_densenetwork.py similarity index 100% rename from bmtk/tests/builder/test_densenetwork.py rename to tests/builder/test_densenetwork.py diff --git a/bmtk/tests/builder/test_edge_iterator.py b/tests/builder/test_edge_iterator.py similarity index 100% rename from bmtk/tests/builder/test_edge_iterator.py rename to tests/builder/test_edge_iterator.py diff --git a/bmtk/tests/builder/test_edges_sorter.py b/tests/builder/test_edges_sorter.py similarity index 100% rename from bmtk/tests/builder/test_edges_sorter.py rename to tests/builder/test_edges_sorter.py diff --git a/bmtk/tests/builder/test_id_generator.py b/tests/builder/test_id_generator.py similarity index 100% rename from bmtk/tests/builder/test_id_generator.py rename to tests/builder/test_id_generator.py diff --git a/bmtk/tests/builder/test_index_builders.py b/tests/builder/test_index_builders.py similarity index 100% rename from bmtk/tests/builder/test_index_builders.py rename to tests/builder/test_index_builders.py diff --git a/bmtk/tests/builder/test_iterator.py b/tests/builder/test_iterator.py similarity index 100% rename from bmtk/tests/builder/test_iterator.py rename to tests/builder/test_iterator.py diff --git a/bmtk/tests/builder/test_network.py b/tests/builder/test_network.py similarity index 100% rename from bmtk/tests/builder/test_network.py rename to tests/builder/test_network.py diff --git a/bmtk/tests/builder/test_network_mpi.py b/tests/builder/test_network_mpi.py similarity index 100% rename from bmtk/tests/builder/test_network_mpi.py rename to tests/builder/test_network_mpi.py diff --git a/bmtk/tests/builder/test_node_pool.py b/tests/builder/test_node_pool.py similarity index 100% rename from bmtk/tests/builder/test_node_pool.py rename to tests/builder/test_node_pool.py diff --git a/bmtk/tests/builder/test_node_set.py b/tests/builder/test_node_set.py similarity index 100% rename from bmtk/tests/builder/test_node_set.py rename to tests/builder/test_node_set.py diff --git a/bmtk/tests/builder/test_save_network.py b/tests/builder/test_save_network.py similarity index 100% rename from bmtk/tests/builder/test_save_network.py rename to tests/builder/test_save_network.py diff --git a/bmtk/tests/simulator/__init__.py b/tests/simulator/__init__.py similarity index 100% rename from bmtk/tests/simulator/__init__.py rename to tests/simulator/__init__.py diff --git a/bmtk/tests/simulator/bionet/__init__.py b/tests/simulator/bionet/__init__.py similarity index 100% rename from bmtk/tests/simulator/bionet/__init__.py rename to tests/simulator/bionet/__init__.py diff --git a/bmtk/tests/simulator/bionet/bionet_virtual_files.py b/tests/simulator/bionet/bionet_virtual_files.py similarity index 100% rename from bmtk/tests/simulator/bionet/bionet_virtual_files.py rename to tests/simulator/bionet/bionet_virtual_files.py diff --git a/bmtk/tests/simulator/bionet/components/mechanisms/modfiles/vecevent.mod b/tests/simulator/bionet/components/mechanisms/modfiles/vecevent.mod similarity index 100% rename from bmtk/tests/simulator/bionet/components/mechanisms/modfiles/vecevent.mod rename to tests/simulator/bionet/components/mechanisms/modfiles/vecevent.mod diff --git a/bmtk/tests/simulator/bionet/components/morphology/rorb_480169178_morphology.swc b/tests/simulator/bionet/components/morphology/rorb_480169178_morphology.swc similarity index 100% rename from bmtk/tests/simulator/bionet/components/morphology/rorb_480169178_morphology.swc rename to tests/simulator/bionet/components/morphology/rorb_480169178_morphology.swc diff --git a/bmtk/tests/simulator/bionet/conftest.py b/tests/simulator/bionet/conftest.py similarity index 100% rename from bmtk/tests/simulator/bionet/conftest.py rename to tests/simulator/bionet/conftest.py diff --git a/bmtk/tests/simulator/bionet/set_cell_params.py b/tests/simulator/bionet/set_cell_params.py similarity index 100% rename from bmtk/tests/simulator/bionet/set_cell_params.py rename to tests/simulator/bionet/set_cell_params.py diff --git a/bmtk/tests/simulator/bionet/set_syn_params.py b/tests/simulator/bionet/set_syn_params.py similarity index 100% rename from bmtk/tests/simulator/bionet/set_syn_params.py rename to tests/simulator/bionet/set_syn_params.py diff --git a/bmtk/tests/simulator/bionet/set_weights.py b/tests/simulator/bionet/set_weights.py similarity index 100% rename from bmtk/tests/simulator/bionet/set_weights.py rename to tests/simulator/bionet/set_weights.py diff --git a/bmtk/tests/simulator/bionet/test_biograph.py b/tests/simulator/bionet/test_biograph.py similarity index 100% rename from bmtk/tests/simulator/bionet/test_biograph.py rename to tests/simulator/bionet/test_biograph.py diff --git a/bmtk/tests/simulator/bionet/test_gids.py b/tests/simulator/bionet/test_gids.py similarity index 100% rename from bmtk/tests/simulator/bionet/test_gids.py rename to tests/simulator/bionet/test_gids.py diff --git a/bmtk/tests/simulator/bionet/test_iclamp.py b/tests/simulator/bionet/test_iclamp.py similarity index 100% rename from bmtk/tests/simulator/bionet/test_iclamp.py rename to tests/simulator/bionet/test_iclamp.py diff --git a/bmtk/tests/simulator/bionet/test_morphology.py b/tests/simulator/bionet/test_morphology.py similarity index 100% rename from bmtk/tests/simulator/bionet/test_morphology.py rename to tests/simulator/bionet/test_morphology.py diff --git a/bmtk/tests/simulator/bionet/test_nrn.py b/tests/simulator/bionet/test_nrn.py similarity index 100% rename from bmtk/tests/simulator/bionet/test_nrn.py rename to tests/simulator/bionet/test_nrn.py diff --git a/bmtk/tests/simulator/bionet/test_virtualcell.py b/tests/simulator/bionet/test_virtualcell.py similarity index 100% rename from bmtk/tests/simulator/bionet/test_virtualcell.py rename to tests/simulator/bionet/test_virtualcell.py diff --git a/bmtk/tests/simulator/core/test_ecephys_module.py b/tests/simulator/core/test_ecephys_module.py similarity index 100% rename from bmtk/tests/simulator/core/test_ecephys_module.py rename to tests/simulator/core/test_ecephys_module.py diff --git a/bmtk/tests/simulator/core/test_iclamp.py b/tests/simulator/core/test_iclamp.py similarity index 100% rename from bmtk/tests/simulator/core/test_iclamp.py rename to tests/simulator/core/test_iclamp.py diff --git a/bmtk/tests/simulator/core/test_io_tools.py b/tests/simulator/core/test_io_tools.py similarity index 100% rename from bmtk/tests/simulator/core/test_io_tools.py rename to tests/simulator/core/test_io_tools.py diff --git a/bmtk/tests/simulator/core/test_pyfunction_cache.py b/tests/simulator/core/test_pyfunction_cache.py similarity index 100% rename from bmtk/tests/simulator/core/test_pyfunction_cache.py rename to tests/simulator/core/test_pyfunction_cache.py diff --git a/bmtk/tests/simulator/core/test_simulation_config.py b/tests/simulator/core/test_simulation_config.py similarity index 100% rename from bmtk/tests/simulator/core/test_simulation_config.py rename to tests/simulator/core/test_simulation_config.py diff --git a/bmtk/tests/simulator/core/test_simulation_config_validator.py b/tests/simulator/core/test_simulation_config_validator.py similarity index 100% rename from bmtk/tests/simulator/core/test_simulation_config_validator.py rename to tests/simulator/core/test_simulation_config_validator.py diff --git a/bmtk/tests/simulator/filternet/data/network/LGN_node_types.csv b/tests/simulator/filternet/data/network/LGN_node_types.csv similarity index 100% rename from bmtk/tests/simulator/filternet/data/network/LGN_node_types.csv rename to 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b/tests/simulator/filternet/lgnmodel/test_subclass_metrics.py similarity index 100% rename from bmtk/tests/simulator/filternet/lgnmodel/test_subclass_metrics.py rename to tests/simulator/filternet/lgnmodel/test_subclass_metrics.py diff --git a/bmtk/tests/simulator/filternet/lgnmodel/test_transferfunction.py b/tests/simulator/filternet/lgnmodel/test_transferfunction.py similarity index 100% rename from bmtk/tests/simulator/filternet/lgnmodel/test_transferfunction.py rename to tests/simulator/filternet/lgnmodel/test_transferfunction.py diff --git a/bmtk/tests/simulator/filternet/lgnmodel/test_units.py b/tests/simulator/filternet/lgnmodel/test_units.py similarity index 100% rename from bmtk/tests/simulator/filternet/lgnmodel/test_units.py rename to tests/simulator/filternet/lgnmodel/test_units.py diff --git a/bmtk/tests/simulator/filternet/lgnmodel/test_utils.py b/tests/simulator/filternet/lgnmodel/test_utils.py similarity index 100% rename from bmtk/tests/simulator/filternet/lgnmodel/test_utils.py rename to tests/simulator/filternet/lgnmodel/test_utils.py diff --git a/bmtk/tests/simulator/filternet/test_default_setters.py b/tests/simulator/filternet/test_default_setters.py similarity index 100% rename from bmtk/tests/simulator/filternet/test_default_setters.py rename to tests/simulator/filternet/test_default_setters.py diff --git a/bmtk/tests/simulator/filternet/test_filternet_movies.py b/tests/simulator/filternet/test_filternet_movies.py similarity index 100% rename from bmtk/tests/simulator/filternet/test_filternet_movies.py rename to tests/simulator/filternet/test_filternet_movies.py diff --git a/bmtk/tests/simulator/pointnet/__init__.py b/tests/simulator/pointnet/__init__.py similarity index 100% rename from bmtk/tests/simulator/pointnet/__init__.py rename to tests/simulator/pointnet/__init__.py diff --git a/bmtk/tests/simulator/pointnet/conftest.py b/tests/simulator/pointnet/conftest.py similarity index 100% rename from bmtk/tests/simulator/pointnet/conftest.py rename to tests/simulator/pointnet/conftest.py diff --git a/bmtk/tests/simulator/pointnet/glif_models/637930677_lif.json b/tests/simulator/pointnet/glif_models/637930677_lif.json similarity index 100% rename from bmtk/tests/simulator/pointnet/glif_models/637930677_lif.json rename to tests/simulator/pointnet/glif_models/637930677_lif.json diff --git a/bmtk/tests/simulator/pointnet/glif_models/637930677_lif_asc.json b/tests/simulator/pointnet/glif_models/637930677_lif_asc.json similarity index 100% rename from bmtk/tests/simulator/pointnet/glif_models/637930677_lif_asc.json rename to tests/simulator/pointnet/glif_models/637930677_lif_asc.json diff --git a/bmtk/tests/simulator/pointnet/glif_models/637930677_lif_r.json b/tests/simulator/pointnet/glif_models/637930677_lif_r.json similarity index 100% rename from bmtk/tests/simulator/pointnet/glif_models/637930677_lif_r.json rename to tests/simulator/pointnet/glif_models/637930677_lif_r.json diff --git a/bmtk/tests/simulator/pointnet/glif_models/637930677_lif_r_asc.json b/tests/simulator/pointnet/glif_models/637930677_lif_r_asc.json similarity index 100% rename from bmtk/tests/simulator/pointnet/glif_models/637930677_lif_r_asc.json rename to tests/simulator/pointnet/glif_models/637930677_lif_r_asc.json diff --git a/bmtk/tests/simulator/pointnet/glif_models/637930677_lif_r_asc_a.json b/tests/simulator/pointnet/glif_models/637930677_lif_r_asc_a.json similarity index 100% rename from bmtk/tests/simulator/pointnet/glif_models/637930677_lif_r_asc_a.json rename to tests/simulator/pointnet/glif_models/637930677_lif_r_asc_a.json diff --git a/bmtk/tests/simulator/pointnet/pointnet_virtual_files.py b/tests/simulator/pointnet/pointnet_virtual_files.py similarity index 100% rename from bmtk/tests/simulator/pointnet/pointnet_virtual_files.py rename to tests/simulator/pointnet/pointnet_virtual_files.py diff --git a/bmtk/tests/simulator/pointnet/test_glif_utils.py b/tests/simulator/pointnet/test_glif_utils.py similarity index 100% rename from bmtk/tests/simulator/pointnet/test_glif_utils.py rename to tests/simulator/pointnet/test_glif_utils.py diff --git a/bmtk/tests/simulator/pointnet/test_multimeter_report.py b/tests/simulator/pointnet/test_multimeter_report.py similarity index 100% rename from bmtk/tests/simulator/pointnet/test_multimeter_report.py rename to tests/simulator/pointnet/test_multimeter_report.py diff --git a/bmtk/tests/simulator/pointnet/test_pointgraph.py b/tests/simulator/pointnet/test_pointgraph.py similarity index 100% rename from bmtk/tests/simulator/pointnet/test_pointgraph.py rename to tests/simulator/pointnet/test_pointgraph.py diff --git a/bmtk/tests/simulator/pointnet/test_pointnetwork.py b/tests/simulator/pointnet/test_pointnetwork.py similarity index 100% rename from bmtk/tests/simulator/pointnet/test_pointnetwork.py rename to tests/simulator/pointnet/test_pointnetwork.py diff --git a/bmtk/tests/simulator/popnet/__init__.py b/tests/simulator/popnet/__init__.py similarity index 100% rename from bmtk/tests/simulator/popnet/__init__.py rename to tests/simulator/popnet/__init__.py diff --git a/bmtk/tests/simulator/popnet/popnet_virtual_files.py b/tests/simulator/popnet/popnet_virtual_files.py similarity index 100% rename from bmtk/tests/simulator/popnet/popnet_virtual_files.py rename to tests/simulator/popnet/popnet_virtual_files.py diff --git a/bmtk/tests/simulator/popnet/test_popgraph.py b/tests/simulator/popnet/test_popgraph.py similarity index 100% rename from bmtk/tests/simulator/popnet/test_popgraph.py rename to tests/simulator/popnet/test_popgraph.py diff --git a/bmtk/tests/simulator/utils/test_simulation_inputs.py b/tests/simulator/utils/test_simulation_inputs.py similarity index 100% rename from bmtk/tests/simulator/utils/test_simulation_inputs.py rename to tests/simulator/utils/test_simulation_inputs.py diff --git a/bmtk/tests/simulator/utils/test_simulation_reports.py b/tests/simulator/utils/test_simulation_reports.py similarity index 100% rename from bmtk/tests/simulator/utils/test_simulation_reports.py rename to tests/simulator/utils/test_simulation_reports.py diff --git a/bmtk/tests/utils/__init__.py b/tests/utils/__init__.py similarity index 100% rename from bmtk/tests/utils/__init__.py rename to tests/utils/__init__.py diff --git a/bmtk/tests/utils/reports/__init__.py b/tests/utils/reports/__init__.py similarity index 100% rename from bmtk/tests/utils/reports/__init__.py rename to tests/utils/reports/__init__.py diff --git a/bmtk/tests/utils/reports/compartment/__init__.py b/tests/utils/reports/compartment/__init__.py similarity index 100% rename from bmtk/tests/utils/reports/compartment/__init__.py rename to tests/utils/reports/compartment/__init__.py diff --git a/bmtk/tests/utils/reports/compartment/compartment_files/multi_population_report.h5 b/tests/utils/reports/compartment/compartment_files/multi_population_report.h5 similarity index 100% rename from bmtk/tests/utils/reports/compartment/compartment_files/multi_population_report.h5 rename to tests/utils/reports/compartment/compartment_files/multi_population_report.h5 diff --git a/bmtk/tests/utils/reports/compartment/test_compartment_reader.py b/tests/utils/reports/compartment/test_compartment_reader.py similarity index 100% rename from bmtk/tests/utils/reports/compartment/test_compartment_reader.py rename to tests/utils/reports/compartment/test_compartment_reader.py diff --git a/bmtk/tests/utils/reports/compartment/test_compartment_report.py b/tests/utils/reports/compartment/test_compartment_report.py similarity index 100% rename from bmtk/tests/utils/reports/compartment/test_compartment_report.py rename to tests/utils/reports/compartment/test_compartment_report.py diff --git a/bmtk/tests/utils/reports/compartment/test_compartment_writer.py b/tests/utils/reports/compartment/test_compartment_writer.py similarity index 100% rename from bmtk/tests/utils/reports/compartment/test_compartment_writer.py rename to tests/utils/reports/compartment/test_compartment_writer.py diff --git a/bmtk/tests/utils/reports/compartment/test_plotting.py b/tests/utils/reports/compartment/test_plotting.py similarity index 100% rename from bmtk/tests/utils/reports/compartment/test_plotting.py rename to tests/utils/reports/compartment/test_plotting.py diff --git a/bmtk/tests/utils/reports/spike_trains/__init__.py b/tests/utils/reports/spike_trains/__init__.py similarity index 100% rename from bmtk/tests/utils/reports/spike_trains/__init__.py rename to tests/utils/reports/spike_trains/__init__.py diff --git a/bmtk/tests/utils/reports/spike_trains/benchmark_spikes_buffers.py b/tests/utils/reports/spike_trains/benchmark_spikes_buffers.py similarity index 100% rename from bmtk/tests/utils/reports/spike_trains/benchmark_spikes_buffers.py rename to tests/utils/reports/spike_trains/benchmark_spikes_buffers.py diff --git a/bmtk/tests/utils/reports/spike_trains/test_csv_adaptor.py b/tests/utils/reports/spike_trains/test_csv_adaptor.py similarity index 100% rename from bmtk/tests/utils/reports/spike_trains/test_csv_adaptor.py rename to tests/utils/reports/spike_trains/test_csv_adaptor.py diff --git a/bmtk/tests/utils/reports/spike_trains/test_csv_adaptor_mpi.py b/tests/utils/reports/spike_trains/test_csv_adaptor_mpi.py similarity index 100% rename from bmtk/tests/utils/reports/spike_trains/test_csv_adaptor_mpi.py rename to tests/utils/reports/spike_trains/test_csv_adaptor_mpi.py diff --git a/bmtk/tests/utils/reports/spike_trains/test_plotting.py b/tests/utils/reports/spike_trains/test_plotting.py similarity index 100% rename from bmtk/tests/utils/reports/spike_trains/test_plotting.py rename to tests/utils/reports/spike_trains/test_plotting.py diff --git a/bmtk/tests/utils/reports/spike_trains/test_sonata_adaptor.py b/tests/utils/reports/spike_trains/test_sonata_adaptor.py similarity index 100% rename from bmtk/tests/utils/reports/spike_trains/test_sonata_adaptor.py rename to tests/utils/reports/spike_trains/test_sonata_adaptor.py diff --git a/bmtk/tests/utils/reports/spike_trains/test_sonata_adaptor_mpi.py b/tests/utils/reports/spike_trains/test_sonata_adaptor_mpi.py similarity index 100% rename from bmtk/tests/utils/reports/spike_trains/test_sonata_adaptor_mpi.py rename to tests/utils/reports/spike_trains/test_sonata_adaptor_mpi.py diff --git a/bmtk/tests/utils/reports/spike_trains/test_spikes_buffer.py b/tests/utils/reports/spike_trains/test_spikes_buffer.py similarity index 100% rename from bmtk/tests/utils/reports/spike_trains/test_spikes_buffer.py rename to tests/utils/reports/spike_trains/test_spikes_buffer.py diff --git a/bmtk/tests/utils/reports/spike_trains/test_spikes_buffer_mpi.py b/tests/utils/reports/spike_trains/test_spikes_buffer_mpi.py similarity index 100% rename from bmtk/tests/utils/reports/spike_trains/test_spikes_buffer_mpi.py rename to tests/utils/reports/spike_trains/test_spikes_buffer_mpi.py diff --git a/bmtk/tests/utils/reports/spike_trains/test_spikes_core.py b/tests/utils/reports/spike_trains/test_spikes_core.py similarity index 100% rename from bmtk/tests/utils/reports/spike_trains/test_spikes_core.py rename to tests/utils/reports/spike_trains/test_spikes_core.py diff --git a/bmtk/tests/utils/sonata/__init__.py b/tests/utils/sonata/__init__.py similarity index 100% rename from bmtk/tests/utils/sonata/__init__.py rename to tests/utils/sonata/__init__.py diff --git a/bmtk/tests/utils/sonata/test_config.py b/tests/utils/sonata/test_config.py similarity index 100% rename from bmtk/tests/utils/sonata/test_config.py rename to tests/utils/sonata/test_config.py diff --git a/bmtk/tests/utils/sonata/test_config_validator.py b/tests/utils/sonata/test_config_validator.py similarity index 100% rename from bmtk/tests/utils/sonata/test_config_validator.py rename to tests/utils/sonata/test_config_validator.py diff --git a/bmtk/tests/utils/sonata/test_edge_stats.py b/tests/utils/sonata/test_edge_stats.py similarity index 100% rename from bmtk/tests/utils/sonata/test_edge_stats.py rename to tests/utils/sonata/test_edge_stats.py From 4165d29ea4fabc4a6dd1bfcf26e07b0fab076964 Mon Sep 17 00:00:00 2001 From: kaeldai Date: Tue, 28 Jan 2025 10:02:20 -0800 Subject: [PATCH 2/3] fixing ghactions to new dir of tests --- .github/workflows/validate-pull-request.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/validate-pull-request.yaml b/.github/workflows/validate-pull-request.yaml index ac177e707..a665434fe 100644 --- 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 }} From acfdbcbd14bd306da1d626a170e0c4805fe60761 Mon Sep 17 00:00:00 2001 From: kaeldai Date: Tue, 28 Jan 2025 10:21:58 -0800 Subject: [PATCH 3/3] error with old version of pandas infer_objects call --- bmtk/utils/sonata/edge_stats.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bmtk/utils/sonata/edge_stats.py b/bmtk/utils/sonata/edge_stats.py index fa3c3e8c4..03f950b70 100644 --- 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].infer_objects(copy=False).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'].infer_objects(copy=False).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)