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The tests and pycache are packaged

Open Helveg opened this issue 5 years ago • 0 comments

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
  bmtk\simulator\filternet\filternetwork.py
  bmtk\simulator\filternet\filters.py
  bmtk\simulator\filternet\filtersimulator.py
  bmtk\simulator\filternet\io_tools.py
  bmtk\simulator\filternet\lgnmodel\__init__.py
  bmtk\simulator\filternet\lgnmodel\__pycache__\__init__.cpython-39.pyc
  bmtk\simulator\filternet\lgnmodel\__pycache__\cellmodel.cpython-39.pyc
  bmtk\simulator\filternet\lgnmodel\__pycache__\cursor.cpython-39.pyc
  bmtk\simulator\filternet\lgnmodel\__pycache__\fitfuns.cpython-39.pyc
  bmtk\simulator\filternet\lgnmodel\__pycache__\kernel.cpython-39.pyc
  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
  bmtk\simulator\filternet\lgnmodel\cell_metrics\sOFF_cell_data.csv
  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
  bmtk\simulator\filternet\lgnmodel\transferfunction.py
  bmtk\simulator\filternet\lgnmodel\util_fns.py
  bmtk\simulator\filternet\lgnmodel\utilities.py
  bmtk\simulator\filternet\modules\__init__.py
  bmtk\simulator\filternet\modules\__pycache__\__init__.cpython-39.pyc
  bmtk\simulator\filternet\modules\__pycache__\base.cpython-39.pyc
  bmtk\simulator\filternet\modules\__pycache__\create_spikes.cpython-39.pyc
  bmtk\simulator\filternet\modules\__pycache__\record_rates.cpython-39.pyc
  bmtk\simulator\filternet\modules\base.py
  bmtk\simulator\filternet\modules\create_spikes.py
  bmtk\simulator\filternet\modules\record_rates.py
  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
  bmtk\simulator\mintnet\__init__.py
  bmtk\simulator\mintnet\__pycache__\Image_Library.cpython-39.pyc
  bmtk\simulator\mintnet\__pycache__\Image_Library_Supervised.cpython-39.pyc
  bmtk\simulator\mintnet\__pycache__\__init__.cpython-39.pyc
  bmtk\simulator\mintnet\analysis\LocallySparseNoise.py
  bmtk\simulator\mintnet\analysis\StaticGratings.py
  bmtk\simulator\mintnet\analysis\__init__.py
  bmtk\simulator\mintnet\analysis\__pycache__\LocallySparseNoise.cpython-39.pyc
  bmtk\simulator\mintnet\analysis\__pycache__\StaticGratings.cpython-39.pyc
  bmtk\simulator\mintnet\analysis\__pycache__\__init__.cpython-39.pyc
  bmtk\simulator\mintnet\hmax\C_Layer.py
  bmtk\simulator\mintnet\hmax\Readout_Layer.py
  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
  bmtk\simulator\mintnet\hmax\__init__.py
  bmtk\simulator\mintnet\hmax\__pycache__\C_Layer.cpython-39.pyc
  bmtk\simulator\mintnet\hmax\__pycache__\Readout_Layer.cpython-39.pyc
  bmtk\simulator\mintnet\hmax\__pycache__\S1_Layer.cpython-39.pyc
  bmtk\simulator\mintnet\hmax\__pycache__\S_Layer.cpython-39.pyc
  bmtk\simulator\mintnet\hmax\__pycache__\Sb_Layer.cpython-39.pyc
  bmtk\simulator\mintnet\hmax\__pycache__\ViewTunedLayer.cpython-39.pyc
  bmtk\simulator\mintnet\hmax\__pycache__\__init__.cpython-39.pyc
  bmtk\simulator\mintnet\hmax\__pycache__\hmax.cpython-39.pyc
  bmtk\simulator\mintnet\hmax\hmax.py
  bmtk\simulator\pointnet\__init__.py
  bmtk\simulator\pointnet\__pycache__\__init__.cpython-39.pyc
  bmtk\simulator\pointnet\__pycache__\config.cpython-39.pyc
  bmtk\simulator\pointnet\__pycache__\glif_utils.cpython-39.pyc
  bmtk\simulator\pointnet\__pycache__\io_tools.cpython-39.pyc
  bmtk\simulator\pointnet\__pycache__\pointnetwork.cpython-39.pyc
  bmtk\simulator\pointnet\__pycache__\pointsimulator.cpython-39.pyc
  bmtk\simulator\pointnet\__pycache__\property_map.cpython-39.pyc
  bmtk\simulator\pointnet\__pycache__\pyfunction_cache.cpython-39.pyc
  bmtk\simulator\pointnet\__pycache__\sonata_adaptors.cpython-39.pyc
  bmtk\simulator\pointnet\__pycache__\utils.cpython-39.pyc
  bmtk\simulator\pointnet\config.py
  bmtk\simulator\pointnet\default_setters\__init__.py
  bmtk\simulator\pointnet\default_setters\__pycache__\__init__.cpython-39.pyc
  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
  bmtk\simulator\popnet\__pycache__\popedge.cpython-39.pyc
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Helveg avatar Dec 17 '20 18:12 Helveg