removed cytoscape tests

PyEED · May 22, 2024 · a3ed6eb · a3ed6eb
1 parent 540ca68
commit a3ed6eb
Showing 1 changed file with 3 additions and 38 deletions.
diff --git a/tests/unit/network_tests/test_newtork_graph_build.py b/tests/unit/network_tests/test_newtork_graph_build.py
@@ -1,12 +1,8 @@
-import json
-
-import pytest
-
 from pyeed.core import ProteinRecord
 from pyeed.network import SequenceNetwork
 
-class TestNetworkGraphBuild:
 
+class TestNetworkGraphBuild:
     def test_general_build_networkx(self):
         # check if it can be created and does the basic job
         # Accessions from different methionine adenyltransferases
@@ -22,39 +18,13 @@ def test_general_build_networkx(self):
         ]
         mats = ProteinRecord.get_ids(mat_accessions)
         # Create a network
-        network = SequenceNetwork(
-            sequences=mats,
-            weight="identity",
-            dimensions=2,
-        )    
-
-    def test_graph_build(self):
-
-        mat_accessions = [
-            "MBP1912539.1",
-            "SEV92896.1",
-            "MBO8174569.1",
-            "WP_042680787.1",
-        ]
-        mats = ProteinRecord.get_ids(mat_accessions)
-        # Create a network
         network = SequenceNetwork(
             sequences=mats,
             weight="identity",
             dimensions=2,
         )
-        threshhold = 0.85
-        # now create a cytoscape graph
-        network.create_cytoscape_graph(collection="tests", title="test_cytoscape", threshold=threshhold)
-        # check if each degree is correct
-        # it shoudl be at 1
-        assert network.network.nodes["MBP1912539.1"]["degree_with_threshold_{}".format(threshhold)] == 1
-        assert network.network.nodes["SEV92896.1"]["degree_with_threshold_{}".format(threshhold)] == 1
-        assert network.network.nodes["MBO8174569.1"]["degree_with_threshold_{}".format(threshhold)] == 1
-        assert network.network.nodes["WP_042680787.1"]["degree_with_threshold_{}".format(threshhold)] == 1
 
-
-    def test_cytoscape_nodes_size(self):
+    def test_graph_build(self):
         mat_accessions = [
             "MBP1912539.1",
             "SEV92896.1",
@@ -66,10 +36,5 @@ def test_cytoscape_nodes_size(self):
         network = SequenceNetwork(
             sequences=mats,
             weight="identity",
-            dimensions=2,
         )
-        threshhold = 0.85
-        # now create a cytoscape graph
-        network.create_cytoscape_graph(collection="tests", title="test_cytoscape", threshold=threshhold)
-        network.set_nodes_size(column_name="degree_with_threshold_{}".format(threshhold), min_size=20, max_size=100)
-        network.color_nodes(column_name='species')
+        assert len(list(network.network.nodes)) == len(mats)