The tests and pycache are packaged

Start by reproducing the reported package contents with pip show -f bmtk, then inspect the repository's packaging configuration to find why tests and __pycache__ files are included. Done means a fresh pip install bmtk no longer installs those files while the package's runtime files remain available.

The tests and pycaches are unconventionally placed inside the source directory and as such are packaged and installed with every pip install bmtk:

PS C:\Users\robin> pip show -f bmtk
Name: bmtk
Version: 0.0.7
Summary: Brain Modeling Toolkit
Home-page: https://github.com/AllenInstitute/bmtk
Author: Kael Dai
Author-email: [email protected]
License: UNKNOWN
Location: c:\users\robin\appdata\local\programs\python\python39\lib\site-packages
Requires: matplotlib, h5py, jsonschema, six, numpy, pandas
Required-by:
Files:
  bmtk-0.0.7.dist-info\INSTALLER
  bmtk-0.0.7.dist-info\LICENSE.txt
  bmtk-0.0.7.dist-info\METADATA
  bmtk-0.0.7.dist-info\RECORD
  bmtk-0.0.7.dist-info\REQUESTED
  bmtk-0.0.7.dist-info\WHEEL
  bmtk-0.0.7.dist-info\top_level.txt
  bmtk\__init__.py
  bmtk\__pycache__\__init__.cpython-36.pyc
  bmtk\__pycache__\__init__.cpython-39.pyc
  bmtk\analyzer\__init__.py
  bmtk\analyzer\__pycache__\__init__.cpython-39.pyc
  bmtk\analyzer\__pycache__\cell_vars.cpython-39.pyc
  bmtk\analyzer\__pycache__\firing_rates.cpython-39.pyc
  bmtk\analyzer\__pycache__\io_tools.cpython-39.pyc
  bmtk\analyzer\__pycache__\spike_trains.cpython-39.pyc
  bmtk\analyzer\__pycache__\spikes_analyzer.cpython-39.pyc
  bmtk\analyzer\__pycache__\spikes_loader.cpython-39.pyc
  bmtk\analyzer\__pycache__\utils.cpython-39.pyc
  bmtk\analyzer\cell_vars.py
  bmtk\analyzer\firing_rates.py
  bmtk\analyzer\io_tools.py
  bmtk\analyzer\spike_trains.py
  bmtk\analyzer\spikes_analyzer.py
  bmtk\analyzer\spikes_loader.py
  bmtk\analyzer\utils.py
  bmtk\analyzer\visualization\__init__.py
  bmtk\analyzer\visualization\__pycache__\__init__.cpython-39.pyc
  bmtk\analyzer\visualization\__pycache__\rasters.cpython-39.pyc
  bmtk\analyzer\visualization\__pycache__\spikes.cpython-39.pyc
  bmtk\analyzer\visualization\__pycache__\widgets.cpython-39.pyc
  bmtk\analyzer\visualization\rasters.py
  bmtk\analyzer\visualization\spikes.py
  bmtk\analyzer\visualization\widgets.py
  bmtk\builder\__init__.py
  bmtk\builder\__pycache__\__init__.cpython-39.pyc
  bmtk\builder\__pycache__\connection_map.cpython-39.pyc
  bmtk\builder\__pycache__\connector.cpython-39.pyc
  bmtk\builder\__pycache__\edge.cpython-39.pyc
  bmtk\builder\__pycache__\functor_cache.cpython-39.pyc
  bmtk\builder\__pycache__\id_generator.cpython-39.pyc
  bmtk\builder\__pycache__\iterator.cpython-39.pyc
  bmtk\builder\__pycache__\network.cpython-39.pyc
  bmtk\builder\__pycache__\node.cpython-39.pyc
  bmtk\builder\__pycache__\node_pool.cpython-39.pyc
  bmtk\builder\__pycache__\node_set.cpython-39.pyc
  bmtk\builder\auxi\__init__.py
  bmtk\builder\auxi\__pycache__\__init__.cpython-39.pyc
  bmtk\builder\auxi\__pycache__\edge_connectors.cpython-39.pyc
  bmtk\builder\auxi\__pycache__\node_params.cpython-39.pyc
  bmtk\builder\auxi\edge_connectors.py
  bmtk\builder\auxi\node_params.py
  bmtk\builder\bionet\__init__.py
  bmtk\builder\bionet\__pycache__\__init__.cpython-39.pyc
  bmtk\builder\bionet\__pycache__\swc_reader.cpython-39.pyc
  bmtk\builder\bionet\swc_reader.py
  bmtk\builder\connection_map.py
  bmtk\builder\connector.py
  bmtk\builder\edge.py
  bmtk\builder\formats\__init__.py
  bmtk\builder\formats\__pycache__\__init__.cpython-39.pyc
  bmtk\builder\formats\__pycache__\hdf5_format.cpython-39.pyc
  bmtk\builder\formats\__pycache__\iformats.cpython-39.pyc
  bmtk\builder\formats\hdf5_format.py
  bmtk\builder\formats\iformats.py
  bmtk\builder\functor_cache.py
  bmtk\builder\id_generator.py
  bmtk\builder\io\__init__.py
  bmtk\builder\io\__pycache__\__init__.cpython-39.pyc
  bmtk\builder\iterator.py
  bmtk\builder\network.py
  bmtk\builder\networks\__init__.py
  bmtk\builder\networks\__pycache__\__init__.cpython-39.pyc
  bmtk\builder\networks\__pycache__\dm_network.cpython-39.pyc
  bmtk\builder\networks\__pycache__\input_network.cpython-39.pyc
  bmtk\builder\networks\__pycache__\mpi_network.cpython-39.pyc
  bmtk\builder\networks\__pycache__\nxnetwork.cpython-39.pyc
  bmtk\builder\networks\__pycache__\sparse_network.cpython-39.pyc
  bmtk\builder\networks\dm_network.py
  bmtk\builder\networks\input_network.py
  bmtk\builder\networks\mpi_network.py
  bmtk\builder\networks\nxnetwork.py
  bmtk\builder\networks\sparse_network.py
  bmtk\builder\node.py
  bmtk\builder\node_pool.py
  bmtk\builder\node_set.py
  bmtk\simulator\__init__.py
  bmtk\simulator\__pycache__\__init__.cpython-39.pyc
  bmtk\simulator\bionet\README.md
  bmtk\simulator\bionet\__init__.py
  bmtk\simulator\bionet\__pycache__\__init__.cpython-39.pyc
  bmtk\simulator\bionet\__pycache__\biocell.cpython-39.pyc
  bmtk\simulator\bionet\__pycache__\bionetwork.cpython-39.pyc
  bmtk\simulator\bionet\__pycache__\biosimulator.cpython-39.pyc
  bmtk\simulator\bionet\__pycache__\cell.cpython-39.pyc
  bmtk\simulator\bionet\__pycache__\config.cpython-39.pyc
  bmtk\simulator\bionet\__pycache__\iclamp.cpython-39.pyc
  bmtk\simulator\bionet\__pycache__\io_tools.cpython-39.pyc
  bmtk\simulator\bionet\__pycache__\morphology.cpython-39.pyc
  bmtk\simulator\bionet\__pycache__\nml_reader.cpython-39.pyc
  bmtk\simulator\bionet\__pycache__\nrn.cpython-39.pyc
  bmtk\simulator\bionet\__pycache__\pointprocesscell.cpython-39.pyc
  bmtk\simulator\bionet\__pycache__\pointsomacell.cpython-39.pyc
  bmtk\simulator\bionet\__pycache__\pyfunction_cache.cpython-39.pyc
  bmtk\simulator\bionet\__pycache__\sonata_adaptors.cpython-39.pyc
  bmtk\simulator\bionet\__pycache__\utils.cpython-39.pyc
  bmtk\simulator\bionet\__pycache__\virtualcell.cpython-39.pyc
  bmtk\simulator\bionet\biocell.py
  bmtk\simulator\bionet\bionetwork.py
  bmtk\simulator\bionet\biosimulator.py
  bmtk\simulator\bionet\cell.py
  bmtk\simulator\bionet\config.py
  bmtk\simulator\bionet\default_setters\__init__.py
  bmtk\simulator\bionet\default_setters\__pycache__\__init__.cpython-39.pyc
  bmtk\simulator\bionet\default_setters\__pycache__\cell_models.cpython-39.pyc
  bmtk\simulator\bionet\default_setters\__pycache__\synapse_models.cpython-39.pyc
  bmtk\simulator\bionet\default_setters\__pycache__\synaptic_weights.cpython-39.pyc
  bmtk\simulator\bionet\default_setters\cell_models.py
  bmtk\simulator\bionet\default_setters\synapse_models.py
  bmtk\simulator\bionet\default_setters\synaptic_weights.py
  bmtk\simulator\bionet\default_templates\BioAxonStub.hoc
  bmtk\simulator\bionet\default_templates\Biophys1.hoc
  bmtk\simulator\bionet\default_templates\advance.hoc
  bmtk\simulator\bionet\iclamp.py
  bmtk\simulator\bionet\import3d.hoc
  bmtk\simulator\bionet\import3d\import3d_gui.hoc
  bmtk\simulator\bionet\import3d\import3d_sec.hoc
  bmtk\simulator\bionet\import3d\read_morphml.hoc
  bmtk\simulator\bionet\import3d\read_nlcda.hoc
  bmtk\simulator\bionet\import3d\read_nlcda3.hoc
  bmtk\simulator\bionet\import3d\read_nts.hoc
  bmtk\simulator\bionet\import3d\read_swc.hoc
  bmtk\simulator\bionet\io_tools.py
  bmtk\simulator\bionet\modules\__init__.py
  bmtk\simulator\bionet\modules\__pycache__\__init__.cpython-39.pyc
  bmtk\simulator\bionet\modules\__pycache__\ecp.cpython-39.pyc
  bmtk\simulator\bionet\modules\__pycache__\record_cellvars.cpython-39.pyc
  bmtk\simulator\bionet\modules\__pycache__\record_netcons.cpython-39.pyc
  bmtk\simulator\bionet\modules\__pycache__\record_spikes.cpython-39.pyc
  bmtk\simulator\bionet\modules\__pycache__\save_synapses.cpython-39.pyc
  bmtk\simulator\bionet\modules\__pycache__\sim_module.cpython-39.pyc
  bmtk\simulator\bionet\modules\__pycache__\xstim.cpython-39.pyc
  bmtk\simulator\bionet\modules\__pycache__\xstim_waveforms.cpython-39.pyc
  bmtk\simulator\bionet\modules\ecp.py
  bmtk\simulator\bionet\modules\record_cellvars.py
  bmtk\simulator\bionet\modules\record_netcons.py
  bmtk\simulator\bionet\modules\record_spikes.py
  bmtk\simulator\bionet\modules\save_synapses.py
  bmtk\simulator\bionet\modules\sim_module.py
  bmtk\simulator\bionet\modules\xstim.py
  bmtk\simulator\bionet\modules\xstim_waveforms.py
  bmtk\simulator\bionet\morphology.py
  bmtk\simulator\bionet\nml_reader.py
  bmtk\simulator\bionet\nrn.py
  bmtk\simulator\bionet\pointprocesscell.py
  bmtk\simulator\bionet\pointsomacell.py
  bmtk\simulator\bionet\pyfunction_cache.py
  bmtk\simulator\bionet\schemas\config_schema.json
  bmtk\simulator\bionet\schemas\csv_edge_types.json
  bmtk\simulator\bionet\schemas\csv_node_types_external.json
  bmtk\simulator\bionet\schemas\csv_node_types_internal.json
  bmtk\simulator\bionet\schemas\csv_nodes_external.json
  bmtk\simulator\bionet\schemas\csv_nodes_internal.json
  bmtk\simulator\bionet\sonata_adaptors.py
  bmtk\simulator\bionet\utils.py
  bmtk\simulator\bionet\virtualcell.py
  bmtk\simulator\core\__init__.py
  bmtk\simulator\core\__pycache__\__init__.cpython-39.pyc
  bmtk\simulator\core\__pycache__\config.cpython-39.pyc
  bmtk\simulator\core\__pycache__\edge_population.cpython-39.pyc
  bmtk\simulator\core\__pycache__\graph.cpython-39.pyc
  bmtk\simulator\core\__pycache__\io_tools.cpython-39.pyc
  bmtk\simulator\core\__pycache__\network_reader.cpython-39.pyc
  bmtk\simulator\core\__pycache__\node_population.cpython-39.pyc
  bmtk\simulator\core\__pycache__\node_sets.cpython-39.pyc
  bmtk\simulator\core\__pycache__\simulator.cpython-39.pyc
  bmtk\simulator\core\__pycache__\simulator_network.cpython-39.pyc
  bmtk\simulator\core\config.py
  bmtk\simulator\core\edge_population.py
  bmtk\simulator\core\graph.py
  bmtk\simulator\core\io_tools.py
  bmtk\simulator\core\network_reader.py
  bmtk\simulator\core\node_population.py
  bmtk\simulator\core\node_sets.py
  bmtk\simulator\core\simulator.py
  bmtk\simulator\core\simulator_network.py
  bmtk\simulator\core\sonata_reader\__init__.py
  bmtk\simulator\core\sonata_reader\__pycache__\__init__.cpython-39.pyc
  bmtk\simulator\core\sonata_reader\__pycache__\edge_adaptor.cpython-39.pyc
  bmtk\simulator\core\sonata_reader\__pycache__\network_reader.cpython-39.pyc
  bmtk\simulator\core\sonata_reader\__pycache__\node_adaptor.cpython-39.pyc
  bmtk\simulator\core\sonata_reader\edge_adaptor.py
  bmtk\simulator\core\sonata_reader\network_reader.py
  bmtk\simulator\core\sonata_reader\node_adaptor.py
  bmtk\simulator\filternet\__init__.py
  bmtk\simulator\filternet\__pycache__\__init__.cpython-39.pyc
  bmtk\simulator\filternet\__pycache__\cell.cpython-39.pyc
  bmtk\simulator\filternet\__pycache__\cell_models.cpython-39.pyc
  bmtk\simulator\filternet\__pycache__\config.cpython-39.pyc
  bmtk\simulator\filternet\__pycache__\filternetwork.cpython-39.pyc
  bmtk\simulator\filternet\__pycache__\filters.cpython-39.pyc
  bmtk\simulator\filternet\__pycache__\filtersimulator.cpython-39.pyc
  bmtk\simulator\filternet\__pycache__\io_tools.cpython-39.pyc
  bmtk\simulator\filternet\__pycache__\pyfunction_cache.cpython-39.pyc
  bmtk\simulator\filternet\__pycache__\sonata_adaptors.cpython-39.pyc
  bmtk\simulator\filternet\__pycache__\transfer_functions.cpython-39.pyc
  bmtk\simulator\filternet\__pycache__\utils.cpython-39.pyc
  bmtk\simulator\filternet\cell.py
  bmtk\simulator\filternet\cell_models.py
  bmtk\simulator\filternet\config.py
  bmtk\simulator\filternet\default_setters\__init__.py
  bmtk\simulator\filternet\default_setters\__pycache__\__init__.cpython-39.pyc
  bmtk\simulator\filternet\default_setters\__pycache__\cell_loaders.cpython-39.pyc
  bmtk\simulator\filternet\default_setters\cell_loaders.py
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  bmtk\simulator\filternet\filtersimulator.py
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  bmtk\simulator\filternet\lgnmodel\__pycache__\__init__.cpython-39.pyc
  bmtk\simulator\filternet\lgnmodel\__pycache__\cellmodel.cpython-39.pyc
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  bmtk\simulator\filternet\lgnmodel\__pycache__\lattice_unit_constructor.cpython-39.pyc
  bmtk\simulator\filternet\lgnmodel\__pycache__\lgnmodel1.cpython-39.pyc
  bmtk\simulator\filternet\lgnmodel\__pycache__\linearfilter.cpython-39.pyc
  bmtk\simulator\filternet\lgnmodel\__pycache__\lnunit.cpython-39.pyc
  bmtk\simulator\filternet\lgnmodel\__pycache__\make_cell_list.cpython-39.pyc
  bmtk\simulator\filternet\lgnmodel\__pycache__\movie.cpython-39.pyc
  bmtk\simulator\filternet\lgnmodel\__pycache__\poissongeneration.cpython-39.pyc
  bmtk\simulator\filternet\lgnmodel\__pycache__\singleunitcell.cpython-39.pyc
  bmtk\simulator\filternet\lgnmodel\__pycache__\spatialfilter.cpython-39.pyc
  bmtk\simulator\filternet\lgnmodel\__pycache__\temporalfilter.cpython-39.pyc
  bmtk\simulator\filternet\lgnmodel\__pycache__\transferfunction.cpython-39.pyc
  bmtk\simulator\filternet\lgnmodel\__pycache__\util_fns.cpython-39.pyc
  bmtk\simulator\filternet\lgnmodel\__pycache__\utilities.cpython-39.pyc
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  bmtk\simulator\filternet\lgnmodel\cell_metrics\sON_cell_data.csv
  bmtk\simulator\filternet\lgnmodel\cell_metrics\sus_sus_cells_v3.csv
  bmtk\simulator\filternet\lgnmodel\cell_metrics\tOFF_cell_data.csv
  bmtk\simulator\filternet\lgnmodel\cell_metrics\tON_cell_data.csv
  bmtk\simulator\filternet\lgnmodel\cell_metrics\trans_sus_cells_v3.csv
  bmtk\simulator\filternet\lgnmodel\cellmodel.py
  bmtk\simulator\filternet\lgnmodel\cursor.py
  bmtk\simulator\filternet\lgnmodel\fitfuns.py
  bmtk\simulator\filternet\lgnmodel\kernel.py
  bmtk\simulator\filternet\lgnmodel\lattice_unit_constructor.py
  bmtk\simulator\filternet\lgnmodel\lgnmodel1.py
  bmtk\simulator\filternet\lgnmodel\linearfilter.py
  bmtk\simulator\filternet\lgnmodel\lnunit.py
  bmtk\simulator\filternet\lgnmodel\make_cell_list.py
  bmtk\simulator\filternet\lgnmodel\movie.py
  bmtk\simulator\filternet\lgnmodel\poissongeneration.py
  bmtk\simulator\filternet\lgnmodel\singleunitcell.py
  bmtk\simulator\filternet\lgnmodel\spatialfilter.py
  bmtk\simulator\filternet\lgnmodel\temporalfilter.py
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  bmtk\simulator\filternet\lgnmodel\util_fns.py
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  bmtk\simulator\filternet\modules\create_spikes.py
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  bmtk\simulator\filternet\pyfunction_cache.py
  bmtk\simulator\filternet\sonata_adaptors.py
  bmtk\simulator\filternet\transfer_functions.py
  bmtk\simulator\filternet\utils.py
  bmtk\simulator\mintnet\Image_Library.py
  bmtk\simulator\mintnet\Image_Library_Supervised.py
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  bmtk\simulator\mintnet\__pycache__\Image_Library.cpython-39.pyc
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  bmtk\simulator\mintnet\hmax\S1_Layer.py
  bmtk\simulator\mintnet\hmax\S_Layer.py
  bmtk\simulator\mintnet\hmax\Sb_Layer.py
  bmtk\simulator\mintnet\hmax\ViewTunedLayer.py
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  bmtk\simulator\pointnet\__pycache__\utils.cpython-39.pyc
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  bmtk\simulator\pointnet\default_setters\__pycache__\synapse_models.cpython-39.pyc
  bmtk\simulator\pointnet\default_setters\__pycache__\synaptic_weights.cpython-39.pyc
  bmtk\simulator\pointnet\default_setters\synapse_models.py
  bmtk\simulator\pointnet\default_setters\synaptic_weights.py
  bmtk\simulator\pointnet\glif_utils.py
  bmtk\simulator\pointnet\io_tools.py
  bmtk\simulator\pointnet\modules\__init__.py
  bmtk\simulator\pointnet\modules\__pycache__\__init__.cpython-39.pyc
  bmtk\simulator\pointnet\modules\__pycache__\multimeter_reporter.cpython-39.pyc
  bmtk\simulator\pointnet\modules\__pycache__\record_spikes.cpython-39.pyc
  bmtk\simulator\pointnet\modules\multimeter_reporter.py
  bmtk\simulator\pointnet\modules\record_spikes.py
  bmtk\simulator\pointnet\pointnetwork.py
  bmtk\simulator\pointnet\pointsimulator.py
  bmtk\simulator\pointnet\property_map.py
  bmtk\simulator\pointnet\pyfunction_cache.py
  bmtk\simulator\pointnet\sonata_adaptors.py
  bmtk\simulator\pointnet\utils.py
  bmtk\simulator\popnet\__init__.py
  bmtk\simulator\popnet\__pycache__\__init__.cpython-39.pyc
  bmtk\simulator\popnet\__pycache__\config.cpython-39.pyc
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