renamed utils module due to inconsistent behaviour in docs

docs/src/vignettes/1_simple_example.ipynb

@@ -525,7 +525,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "decoupler_input = nc._utils.decoupler_formatter(results, 'stat')\n",
+    "decoupler_input = nc.utils.decoupler_formatter(results, 'stat')\n",
     "collectri_net = dc.get_collectri()\n",
     "dc_estimates, dc_pvals = dc.run_ulm(decoupler_input, collectri_net)"
    ]

networkcommons/__init__.py

@@ -39,7 +39,7 @@
 from ._session import log, _log, session
 from ._conf import config, setup
 
-from . import _utils as utils
+from . import utils as utils
 
 
 _MODULES = [

networkcommons/data/network/_moon.py

@@ -23,7 +23,7 @@
 import numpy as np
 import pandas as pd
 
-from networkcommons import _utils
+from networkcommons import utils
 from . import _omnipath
 from . import _liana
 

networkcommons/eval/_metrics.py

@@ -41,7 +41,7 @@
 import decoupler as dc
 import numpy as np
 
-import networkcommons._utils as utils
+import networkcommons.utils as utils
 
 import random
 

networkcommons/methods/_causal.py

@@ -30,7 +30,7 @@
 import corneto as cn
 import corneto.contrib.networkx as cn_nx
 
-from .. import _utils
+from .. import utils
 
 
 def run_corneto_carnival(network,
@@ -53,7 +53,7 @@ def run_corneto_carnival(network,
         nx.Graph: The subnetwork containing the paths found by CARNIVAL.
         list: A list containing the paths found by CARNIVAL.
     """
-    corneto_net = _utils.to_cornetograph(network)
+    corneto_net = utils.to_cornetograph(network)
 
     problem, graph = cn.methods.runVanillaCarnival(
         perturbations=source_dict,
@@ -68,7 +68,7 @@ def run_corneto_carnival(network,
         cn.methods.carnival.get_selected_edges(problem, graph),
     )
 
-    network_nx = _utils.to_networkx(network_sol, skip_unsupported_edges=True)
+    network_nx = utils.to_networkx(network_sol, skip_unsupported_edges=True)
 
     network_nx.remove_nodes_from(['_s', '_pert_c0', '_meas_c0'])
 

networkcommons/methods/_graph.py

@@ -32,7 +32,7 @@
 import networkx as nx
 import numpy as np
 
-from networkcommons import _utils
+from networkcommons import utils
 from networkcommons._session import session as _session
 
 from collections import defaultdict, Counter
@@ -75,7 +75,7 @@ def run_shortest_paths(network, source_dict, target_dict, verbose=False):
                 # _session.log_traceback(console = verbose)
                 pass
 
-    subnetwork = _utils.get_subnetwork(network, shortest_paths_res)
+    subnetwork = utils.get_subnetwork(network, shortest_paths_res)
 
     return subnetwork, shortest_paths_res
 
@@ -148,7 +148,7 @@ def run_sign_consistency(network, paths, source_dict, target_dict=None):
             if np.sign(source_sign * product_sign) == np.sign(target_sign):
                 sign_consistency_res.append(path)
 
-    subnetwork = _utils.get_subnetwork(network, sign_consistency_res)
+    subnetwork = utils.get_subnetwork(network, sign_consistency_res)
 
     if not target_dict:
         return subnetwork, sign_consistency_res, inferred_target_sign
@@ -215,7 +215,7 @@ def run_all_paths(network,
             # _session.log_traceback(console = verbose)
             pass
 
-    subnetwork = _utils.get_subnetwork(network, all_paths_res)
+    subnetwork = utils.get_subnetwork(network, all_paths_res)
 
     return subnetwork, all_paths_res
 

networkcommons/network/_network.py

@@ -33,7 +33,7 @@
 from networkcommons.data import _network as _universe
 from networkcommons.noi._noi import Noi
 
-from networkcommons import _utils
+from networkcommons import utils
 
 
 class Network:
@@ -92,21 +92,21 @@ def _from_corneto(self):
 
     def _from_networkx(self):
 
-        self._co = _utils.to_cornetograph(self.universe)
+        self._co = utils.to_cornetograph(self.universe)
         self._attrs_from_corneto()
 
 
     def _from_pandas(self):
 
-        nxgraph = _utils.network_from_df(self.universe)
-        self._co = _utils.to_cornetograph(nxgraph)
+        nxgraph = utils.network_from_df(self.universe)
+        self._co = utils.to_cornetograph(nxgraph)
         self._attrs_from_corneto()
 
 
     def _attrs_from_corneto(self):
 
-        self._nodes = _utils.node_attrs_from_corneto(self._co)
-        self._edges = _utils.edge_attrs_from_corneto(self._co)
+        self._nodes = utils.node_attrs_from_corneto(self._co)
+        self._edges = utils.edge_attrs_from_corneto(self._co)
 
 
     def as_igraph(self, attrs: str | list[str]) -> "igraph.Graph":

networkcommons/visual/_rnaseq.py

@@ -38,7 +38,7 @@
 import matplotlib.pyplot as plt
 import seaborn as sns
 from sklearn import decomposition as sklearn_decomp
-from networkcommons._utils import handle_missing_values
+from networkcommons.utils import handle_missing_values
 
 
 def plot_density(df,

tests/test_utils.py

@@ -4,7 +4,7 @@
 import corneto as cn
 from unittest.mock import patch
 import pytest
-import networkcommons._utils as utils
+import networkcommons.utils as utils
 import pygraphviz as pgv
 
 
@@ -107,7 +107,7 @@ def test_to_networkx_when_not_supported():
 
 
 def test_read_network_from_file():
-    with patch('pandas.read_csv') as mock_read_csv, patch('networkcommons._utils.network_from_df') as mock_network_from_df:
+    with patch('pandas.read_csv') as mock_read_csv, patch('networkcommons.utils.network_from_df') as mock_network_from_df:
         mock_read_csv.return_value = pd.DataFrame({'source': ['a'], 'target': ['b']})
         utils.read_network_from_file('dummy_path')
         mock_network_from_df.assert_called_once()