updated the rest of the imports after module renames

networkcommons/_data/omics/_moon.py

@@ -21,7 +21,7 @@
 
 import pandas as pd
 
-from . import _common
+from . import common
 
 __all__ = ['moon']
 

networkcommons/_methods/moon.py

@@ -25,7 +25,7 @@
 import decoupler as dc
 import numpy as np
 
-from networkcommons._methods import graph
+from networkcommons._methods import graph as _graph
 from networkcommons._session import _log
 
 __all__ = [
@@ -233,7 +233,7 @@ def keep_controllable_neighbours(source_dict, graph):
     - A dictionary of source nodes that are observable from the graph.
     """
 
-    return graph.run_reachability_filter(graph, source_dict)
+    return _graph.run_reachability_filter(graph, source_dict)
 
 
 def keep_observable_neighbours(target_dict, graph):
@@ -249,7 +249,7 @@ def keep_observable_neighbours(target_dict, graph):
     - A dictionary of target nodes that are observable from the graph.
     """
 
-    subnetwork = graph.run_reachability_filter(graph.reverse(), target_dict)
+    subnetwork = _graph.run_reachability_filter(graph.reverse(), target_dict)
 
     return subnetwork.reverse()
 

tests/test_eval_graph.py

@@ -3,7 +3,7 @@
 import networkx as nx
 import pandas as pd
 
-import networkcommons._eval.metrics as metrics
+import networkcommons._eval.metrics as _metrics
 
 
 @pytest.fixture
@@ -23,40 +23,40 @@ def network():
 
 def test_get_number_nodes():
 
-    assert metrics.get_number_nodes(nx.Graph()) == 0
-    assert metrics.get_number_nodes(nx.Graph([(1, 2)])) == 2
-    assert metrics.get_number_nodes(nx.Graph([(1, 2), (2, 3)])) == 3
+    assert _metrics.get_number_nodes(nx.Graph()) == 0
+    assert _metrics.get_number_nodes(nx.Graph([(1, 2)])) == 2
+    assert _metrics.get_number_nodes(nx.Graph([(1, 2), (2, 3)])) == 3
 
 
 def test_get_number_edges():
 
-    assert metrics.get_number_edges(nx.Graph()) == 0
-    assert metrics.get_number_edges(nx.Graph([(1, 2)])) == 1
-    assert metrics.get_number_edges(nx.Graph([(1, 2), (2, 3)])) == 2
+    assert _metrics.get_number_edges(nx.Graph()) == 0
+    assert _metrics.get_number_edges(nx.Graph([(1, 2)])) == 1
+    assert _metrics.get_number_edges(nx.Graph([(1, 2), (2, 3)])) == 2
 
 
 def test_get_mean_degree(network):
 
-    assert metrics.get_mean_degree(network) == 7/3
+    assert _metrics.get_mean_degree(network) == 7/3
 
 
 def test_get_mean_betweenness(network):
 
-    assert metrics.get_mean_betweenness(network) == 0.05833333333333334
+    assert _metrics.get_mean_betweenness(network) == 0.05833333333333334
 
 
 def test_get_mean_closeness(network):
 
-    assert metrics.get_mean_closeness(network) == 0.29444444444444445
+    assert _metrics.get_mean_closeness(network) == 0.29444444444444445
 
 
 def test_get_connected_targets(network):
 
     target_dict = {'D': 1, 'F': 1, 'W': 1}
 
-    assert metrics.get_connected_targets(network, target_dict) == 2
+    assert _metrics.get_connected_targets(network, target_dict) == 2
     assert (
-        metrics.get_connected_targets(network, target_dict, percent=True) ==
+        _metrics.get_connected_targets(network, target_dict, percent=True) ==
         2 / 3 * 100
     )
 
@@ -65,9 +65,9 @@ def test_get_recovered_offtargets(network):
 
     offtargets = ['B', 'D', 'W']
 
-    assert metrics.get_recovered_offtargets(network, offtargets) == 2
+    assert _metrics.get_recovered_offtargets(network, offtargets) == 2
     assert (
-        metrics.get_recovered_offtargets(network, offtargets, percent=True) ==
+        _metrics.get_recovered_offtargets(network, offtargets, percent=True) ==
         2 / 3 * 100
     )# noqa: E501
 
@@ -85,4 +85,4 @@ def test_get_graph_metrics(network):
         'Connected targets': 2
     }, index=[0])
 
-    assert metrics.get_graph_metrics(network, target_dict).equals(metrics)
+    assert _metrics.get_graph_metrics(network, target_dict).equals(metrics)

tests/test_omics.py

@@ -7,7 +7,7 @@
 
 def test_datasets():
 
-    dsets = omics._common._datasets()
+    dsets = omics.common._datasets()
 
     assert 'baseurl' in dsets
     assert isinstance(dsets['datasets'], dict)
@@ -16,23 +16,23 @@ def test_datasets():
 
 def test_datasets_2():
 
-    dsets = omics._common.datasets()
+    dsets = omics.common.datasets()
 
     assert 'decryptm' in dsets
 
 
 def test_commons_url():
 
-    url = omics._common._commons_url('test', table = 'meta')
+    url = omics.common._commons_url('test', table = 'meta')
 
     assert 'metadata' in url
 
 
 def test_download(tmp_path):
 
-    url = omics._common._commons_url('test', table = 'meta')
+    url = omics.common._commons_url('test', table = 'meta')
     path = tmp_path / 'test_download.tsv'
-    omics._common._download(url, path)
+    omics.common._download(url, path)
 
     assert path.exists()
 
@@ -45,9 +45,9 @@ def test_download(tmp_path):
 
 def test_open():
 
-    url = omics._common._commons_url('test', table = 'meta')
+    url = omics.common._commons_url('test', table = 'meta')
 
-    with omics._common._open(url) as fp:
+    with omics.common._open(url) as fp:
 
         line = next(fp)
 
@@ -56,8 +56,8 @@ def test_open():
 
 def test_open_df():
 
-    url = omics._common._commons_url('test', table = 'meta')
-    df = omics._common._open(url, df = {'sep': '\t'})
+    url = omics.common._commons_url('test', table = 'meta')
+    df = omics.common._open(url, df = {'sep': '\t'})
 
     assert isinstance(df, pd.DataFrame)
     assert df.shape == (4, 2)
@@ -78,9 +78,9 @@ def decryptm_args():
     return 'KDAC_Inhibitors', 'Acetylome', 'curves_CUDC101.txt'
 
 
-def test_decryptm(decryptm_args):
+def test_decryptm_table(decryptm_args):
 
-    df = omics.decryptm.decryptm(*decryptm_args)
+    df = omics.decryptm.decryptm_table(*decryptm_args)
 
     assert isinstance(df, pd.DataFrame)
     assert df.shape == (18007, 65)
@@ -100,7 +100,7 @@ def test_decryptm_experiment(decryptm_args):
 
 def test_panacea():
 
-    dfs = omics.panacea.panacea()
+    dfs = omics.panacea()
 
     assert isinstance(dfs, tuple)
     assert len(dfs) == 2