tests: remove test that use read_network

hnn_core/tests/test_io.py

@@ -3,12 +3,10 @@
 #          Rajat Partani <[email protected]>
 
 from pathlib import Path
-from numpy.testing import assert_allclose
-from h5io import write_hdf5, read_hdf5
 import pytest
 import numpy as np
 
-from hnn_core import (read_network, simulate_dipole, read_params,
+from hnn_core import (simulate_dipole, read_params,
                       jones_2009_model, calcium_model,
                       )
 
@@ -314,43 +312,6 @@ def test_read_configuration_json(jones_2009_network):
     assert net == jones_2009_network
 
 
-def test_read_hdf5_with_simulation(jones_2009_network):
-    """ Read-in of a hdf5 file with simulation"""
-    # Test reading a network with simulation
-    net_sim = read_network(
-        Path(assets_path, 'jones2009_3x3_drives_simulated.hdf5')
-    )
-    assert net_sim.rec_arrays['el1'].voltages.size != 0
-    assert len(net_sim.external_drives['evdist1']['events']) > 0
-
-    # Test reading file without simulation information
-    net_sim_output_false = read_network(
-        Path(assets_path, 'jones2009_3x3_drives_simulated.hdf5'),
-        read_output=False
-    )
-    assert net_sim_output_false.rec_arrays['el1'].voltages.size == 0
-    assert len(net_sim_output_false.external_drives['evdist1']['events']) == 0
-
-    # Test reading file with simulation and without drive information
-    net_sim_drives_false = read_network(
-        Path(assets_path, 'jones2009_3x3_drives_simulated.hdf5'),
-        read_output=True,
-        read_drives=False
-    )
-    assert net_sim_drives_false.rec_arrays['el1'].voltages.size != 0
-    assert not bool(net_sim_drives_false.external_drives)
-
-    # Test reading file without simulation and drive information
-    net_sim_output_false_drives_false = read_network(
-        Path(assets_path, 'jones2009_3x3_drives_simulated.hdf5'),
-        read_output=False,
-        read_drives=False
-    )
-    assert (net_sim_output_false_drives_false
-            .rec_arrays['el1'].voltages.size == 0)
-    assert not bool(net_sim_output_false_drives_false.external_drives)
-
-
 def test_read_incorrect_format(tmp_path):
     """Test that error raise when the json do not have a Network label."""
 
@@ -365,24 +326,3 @@ def test_read_incorrect_format(tmp_path):
     with pytest.raises(ValueError,
                        match="The json should encode a Network object."):
         read_network_configuration(file_path)
-
-
-def test_simulate_from_read(jones_2009_network):
-    """
-    Tests a simulation from a read-in network creates a similar simulation to
-    the reference network the input file was created from.
-    """
-    net = jones_2009_network
-    dpls1 = simulate_dipole(net, tstop=2, n_trials=1, dt=0.5)
-
-    net_read = read_network(Path(assets_path, 'jones2009_3x3_drives.hdf5'))
-    dpls2 = simulate_dipole(net_read, tstop=2, n_trials=1, dt=0.5)
-
-    for dpl1, dpl2 in zip(dpls1, dpls2):
-        assert_allclose(dpl1.times, dpl2.times, rtol=0.00051, atol=0)
-        for dpl_key in dpl1.data.keys():
-            assert_allclose(dpl1.data[dpl_key],
-                            dpl2.data[dpl_key], rtol=0.000051, atol=0)
-
-    # Smoke test
-    net_read.plot_cells(show=False)

hnn_core/tests/test_params.py

@@ -8,9 +8,7 @@
 
 import pytest
 
-from hnn_core import (read_params, Params, jones_2009_model, convert_to_hdf5,
-                      Network)
-from hnn_core.hnn_io import read_network
+from hnn_core import read_params, Params, jones_2009_model, convert_to_hdf5
 
 hnn_core_root = Path(__file__).parents[1]
 
@@ -76,57 +74,6 @@ def test_base_params():
     assert params == params_base
 
 
-def test_convert_to_hdf5(tmp_path):
-    """Tests conversion of a json file to hdf5"""
-    # Download params
-    param_url = ('https://raw.githubusercontent.com/hnn-core/'
-                 'hnn_core/param/default.json')
-    params_base_fname = Path(hnn_core_root, 'param', 'default.json')
-    if not op.exists(params_base_fname):
-        urlretrieve(param_url, params_base_fname)
-    net_params = Network(read_params(params_base_fname),
-                         add_drives_from_params=True,
-                         )
-
-    # Write hdf5 and check if constructed network is equal
-    outpath = Path(tmp_path, 'default.hdf5')
-    convert_to_hdf5(params_base_fname, outpath)
-    net_hdf5 = read_network(outpath)
-    assert net_hdf5 == net_params
-
-    # Write hdf5 without drives
-    outpath_no_drives = Path(tmp_path, 'default_no_drives.hdf5')
-    convert_to_hdf5(params_base_fname, outpath_no_drives, include_drives=False)
-    net_hdf5_no_drives = read_network(outpath_no_drives)
-    assert net_hdf5_no_drives != net_hdf5
-    assert bool(net_hdf5_no_drives.external_drives) is False
-
-    # Check that writing with no extension will add one
-    outpath_no_ext = Path(tmp_path, 'default_no_ext')
-    convert_to_hdf5(params_base_fname, outpath_no_ext)
-    assert outpath_no_ext.with_suffix('.hdf5').exists()
-
-
-def test_convert_to_hdf5_legacy(tmp_path):
-    """Tests conversion of a param legacy file to hdf5"""
-    # Download params
-    param_url = ('https://raw.githubusercontent.com/hnnsolver/'
-                 'hnn-core/test_data/default.param')
-    params_base_fname = Path(hnn_core_root, 'param', 'default.param')
-    if not op.exists(params_base_fname):
-        urlretrieve(param_url, params_base_fname)
-    net_params = Network(read_params(params_base_fname),
-                         add_drives_from_params=True,
-                         legacy_mode=True
-                         )
-
-    # Write hdf5 and check if constructed network is equal
-    outpath = Path(tmp_path, 'default.hdf5')
-    convert_to_hdf5(params_base_fname, outpath)
-    net_hdf5 = read_network(outpath)
-    assert net_hdf5 == net_params
-
-
 def test_convert_to_hdf5_bad_type():
     """Tests type validation in convert_to_hdf5 function"""
     good_path = hnn_core_root