Sourcery refactored main branch

skm_tools/ckn_utils.py

@@ -26,11 +26,7 @@ def filter_ckn_edges(g, keep_edge_ranks, remove_isolates=True):
     if isinstance(keep_edge_ranks, int):
         keep_edge_ranks = [keep_edge_ranks]
 
-    to_remove_ranks = []
-    for r in ckn_ranks:
-        if not (r in keep_edge_ranks):
-            to_remove_ranks.append(r)
-
+    to_remove_ranks = [r for r in ckn_ranks if r not in keep_edge_ranks]
     to_remove = []
     for r in to_remove_ranks:
         to_remove += [(u,v) for u, v, d in g.edges(data=True,) if d["rank"]==r]
@@ -62,23 +58,38 @@ def filter_ckn_nodes(
 
     if species:
         no_species = [
-            n for n, data in g.nodes(data=True) if not (
-                data['species'] in species
-            )
+            n
+            for n, data in g.nodes(data=True)
+            if data['species'] not in species
         ]
         to_remove.update(no_species)
-        reasons = {**reasons, **{n:"wrong species" for n in no_species if not n in reasons}}
+        reasons = reasons | {
+            n: "wrong species" for n in no_species if n not in reasons
+        }
 
     if node_types:
         # nodes not in keep_types
-        wrong_type = [n for n, data in g.nodes(data=True) if not (data['node_type'] in node_types)]
+        wrong_type = [
+            n
+            for n, data in g.nodes(data=True)
+            if data['node_type'] not in node_types
+        ]
         to_remove.update(wrong_type)
-        reasons = {**reasons, **{n:"wrong node type" for n in wrong_type if not n in reasons}}
+        reasons = reasons | {
+            n: "wrong node type" for n in wrong_type if n not in reasons
+        }
 
     if tissues:
-        wrong_tissue = [n for n, data in g.nodes(data=True) if ( not data['tissue'] ) or ( not (len([aa for aa in data['tissue'] if aa in tissues])>0) )]
+        wrong_tissue = [
+            n
+            for n, data in g.nodes(data=True)
+            if not data['tissue']
+            or not [aa for aa in data['tissue'] if aa in tissues]
+        ]
         to_remove.update(wrong_tissue)
-        reasons = {**reasons, **{n:"wrong tissue type" for n in wrong_tissue if not n in reasons}}
+        reasons = reasons | {
+            n: "wrong tissue type" for n in wrong_tissue if n not in reasons
+        }
 
 
     # now remove complexes that contain any nodes to be removed entities
@@ -94,9 +105,14 @@ def complex_to_remove(x):
         for n in x.split("|"):
             if n in as_components:
                 return True
+
     complex_component_missing = [n for n in g.nodes() if complex_to_remove(n)]
     to_remove.update(complex_component_missing)
-    reasons = {**reasons, **{n:"complex component removed" for n in complex_component_missing if not n in reasons}}
+    reasons = reasons | {
+        n: "complex component removed"
+        for n in complex_component_missing
+        if n not in reasons
+    }
 
     # remove the nodes
     g.remove_nodes_from(to_remove)
@@ -105,7 +121,7 @@ def complex_to_remove(x):
     if remove_isolates:
         isolates = list(nx.isolates(g))
         g.remove_nodes_from(isolates)
-        reasons = {**reasons, **{n:"isolate" for n in isolates if not n in reasons}}
+        reasons = reasons | {n: "isolate" for n in isolates if n not in reasons}
 
     now_size = g.number_of_nodes()
     print(f"Removed {og_size - now_size} nodes from network.")

skm_tools/cuts.py

@@ -3,7 +3,7 @@
 
 def get_cutset(sources, targets, g):
     source_sink_graph = g.copy()
-    
+
     source_sink_graph.add_node("source")
     for node in sources:
         if source_sink_graph.has_node(node):
@@ -15,23 +15,23 @@ def get_cutset(sources, targets, g):
 
     source_sink_graph.add_node('sink')
     for node in targets:
-        if source_sink_graph.has_node(node) and not (node in sources):
+        if source_sink_graph.has_node(node) and node not in sources:
             c = 99999
     #         c = 0
     #         for n in [x for x in source_sink_graph.predecessors(node)]:
     #             c += source_sink_graph.get_edge_data(n, node)['capacity']                
             source_sink_graph.add_edge(node, 'sink', capacity=c)
-    
+
     r = nx.flow.edmonds_karp(source_sink_graph, 'source', 'sink')
     print(f"max_flow = {r.graph['flow_value']}")    
-    
+
     cut_value, partition = nx.minimum_cut(source_sink_graph, 'source', 'sink', flow_func=nx.flow.edmonds_karp)
     reachable, non_reachable = partition
-    
+
     cutset = set()
     for u, nbrs in ((n, source_sink_graph[n]) for n in reachable):
         cutset.update((u, v) for v in nbrs if v in non_reachable)
 
     print(cut_value == sum(source_sink_graph.edges[u, v]["capacity"] for (u, v) in cutset)   )
-    
+
     return sorted(cutset)

skm_tools/cytoscape_utils.py

@@ -16,15 +16,15 @@ def _cytoscape_safe_names(names):
 def apply_builtin_style(suid, style):
     style = style.lower()
 
-    if not (style in resources.BUILTIN_STYLES):
+    if style not in resources.BUILTIN_STYLES:
         raise ValueError(f"apply_builtin_style expects a value in {resources.BUILTIN_STYLES}.")
 
     style_name = {
         'ckn':resources.CKN_DEFAULT_STYLE,
         'pss':resources.PSS_DEFAULT_STYLE
     }[style]
 
-    if not style_name in p4c.styles.get_visual_style_names():
+    if style_name not in p4c.styles.get_visual_style_names():
         p4c.import_visual_styles(resources.get_style_xml_path())
 
     p4c.styles.set_visual_style(style_name, network=suid)
@@ -90,7 +90,7 @@ def highlight_path(node_names, colour, skip_nodes=None, skip_edges=None, label_c
     '''
 
     if isinstance(skip_nodes, Sequence) and not isinstance(skip_nodes, str):
-        node_names = [n for n in node_names if not n in skip_nodes]
+        node_names = [n for n in node_names if n not in skip_nodes]
 
     if len(node_names) == 0:
         print("No more nodes to colour")
@@ -108,9 +108,7 @@ def highlight_path(node_names, colour, skip_nodes=None, skip_edges=None, label_c
         network=network
     )
 
-    edge_pairs = []
-    for s, t in zip(node_names, node_names[1:]):
-        edge_pairs.append((s, t))
+    edge_pairs = list(zip(node_names, node_names[1:]))
     edges = highlight_edges(edge_pairs, colour, skip_edges=skip_edges, edge_line_width=edge_line_width, network=network)
 
     return node_names, edges
@@ -123,7 +121,7 @@ def highlight_edges(edge_pairs, colour, skip_edges=None, edge_line_width=10, net
     edges = []
     for s, t in edge_pairs:
         e = f"{s} (interacts with) {t}"
-        if not (e in skip_edges):
+        if e not in skip_edges:
             edges.append(e)
 
     escaped_names = _cytoscape_safe_names(set(edges))
@@ -180,17 +178,15 @@ def subnetwork_edge_induced_from_paths(paths, g, parent_suid, name="subnetwork (
 
     _, cytoscape_edges = get_path_edges(paths, g)
 
-    network_suid = p4c.networks.create_subnetwork(
+    return p4c.networks.create_subnetwork(
         nodes=all_path_nodes,
         edges=cytoscape_edges,
         subnetwork_name=name,
         network=parent_suid,
         exclude_edges=True,
-        edges_by_col="shared name"
+        edges_by_col="shared name",
     )
 
-    return network_suid
-
 def subnetwork_node_induced(nodes, parent_suid, name="subnetwork (node induced)"):
     '''Subnetwork from existing Cystoscape network.
     '''
@@ -203,14 +199,10 @@ def subnetwork_node_induced(nodes, parent_suid, name="subnetwork (node induced)"
         network=parent_suid
     )
 
-    network_suid = p4c.networks.create_subnetwork(
-        nodes=select_result['nodes'],
-        subnetwork_name=name,
-        network=parent_suid
+    return p4c.networks.create_subnetwork(
+        nodes=select_result['nodes'], subnetwork_name=name, network=parent_suid
     )
 
-    return network_suid
-
 def subnetwork_neighbours(nodes, parent_suid, name="subnetwork (1st neighbours)"):
     ''' Node-induced neighbourhood of `nodes`.
     '''
@@ -225,14 +217,10 @@ def subnetwork_neighbours(nodes, parent_suid, name="subnetwork (1st neighbours)"
 
     neighbours = p4c.select_first_neighbors(network=parent_suid)
 
-    network_suid = p4c.networks.create_subnetwork(
-        nodes=neighbours['nodes'],
-        subnetwork_name=name,
-        network=parent_suid
+    return p4c.networks.create_subnetwork(
+        nodes=neighbours['nodes'], subnetwork_name=name, network=parent_suid
     )
 
-    return network_suid
-
 def contrast_colour(colour):
     '''To contrast label to node colours'''
     rgb = int(colour.lstrip('#'), 16)
@@ -275,13 +263,13 @@ def apply_shortest_paths_style(sources, path_lists, target, g, edge_colors=None,
         for node in nodes:
             d = len(nx.shortest_path(g, source=node, target=target)) -1
             path_searches_attributes[node]['distance-to-target'] = d
-            if not (node in skip_source):
+            if node not in skip_source:
                 path_searches_attributes[node]['node-path-source'] = source
                 skip_source.update([node])
 
         _, cytoscape_edges = get_path_edges(paths, g)
         for e in cytoscape_edges:
-            if not e in edge_priority:
+            if e not in edge_priority:
                 edge_priority[e] = {'edge-priority': f"direct path ({source})"}
 
     p4c.tables.load_table_data(
@@ -301,8 +289,10 @@ def apply_shortest_paths_style(sources, path_lists, target, g, edge_colors=None,
     )
 
     if node_colors:
-        max_len = max([path_searches_attributes[x]['distance-to-target'] \
-                       for x in path_searches_attributes])
+        max_len = max(
+            path_searches_attributes[x]['distance-to-target']
+            for x in path_searches_attributes
+        )
         node_color_mapping_range = range(0, max_len+1, int(max_len / (len(node_colors)-1)))
 
         p4c.style_mappings.set_node_color_mapping(
@@ -376,8 +366,7 @@ def add_custom_png(network, create_png, style=None):
 
     node_pngs = {}
     for node in nodes:
-        node_png_fname = create_png(node)
-        if node_png_fname:
+        if node_png_fname := create_png(node):
             node_pngs[node] = {'fig_location':f"file:{str(node_png_fname.absolute())}"}
 
     table = pd.DataFrame.from_dict(node_pngs, orient='index')

skm_tools/load_networks.py

@@ -58,9 +58,7 @@ def pss_to_networkx(edge_path=None, node_path=None):
     node_df.set_index("name", inplace=True, drop=False)
 
     def to_list(x):
-        if isinstance(x, str):
-            return x.split(',')
-        return None
+        return x.split(',') if isinstance(x, str) else None
 
     for c in [
         'ath_homologues',

skm_tools/pss_utils.py

@@ -16,20 +16,29 @@ def filter_pss_nodes(g, node_types=None, species=None, remove_isolates=True):
         # and do not have required homologues
         homologue_properties = [f"{sp}_homologues" for sp in species]
         no_species = [
-            n for n, data in g.nodes(data=True) if not (
-                 len([h for h in homologue_properties if data[h]])>0
-                 or
-                 not (data['node_type'] in ['PlantCoding', 'PlantNonCoding'])
+            n
+            for n, data in g.nodes(data=True)
+            if not (
+                [h for h in homologue_properties if data[h]]
+                or data['node_type'] not in ['PlantCoding', 'PlantNonCoding']
             )
         ]
         to_remove.update(no_species)
-        reasons = {**reasons, **{n:"species missing" for n in no_species if not n in reasons}}
+        reasons = reasons | {
+            n: "species missing" for n in no_species if n not in reasons
+        }
 
     if node_types:
         # nodes not in keep_types
-        wrong_type = [n for n, data in g.nodes(data=True) if not (data['node_type'] in node_types)]
+        wrong_type = [
+            n
+            for n, data in g.nodes(data=True)
+            if data['node_type'] not in node_types
+        ]
         to_remove.update(wrong_type)
-        reasons = {**reasons, **{n:"wrong node type" for n in wrong_type if not n in reasons}}
+        reasons = reasons | {
+            n: "wrong node type" for n in wrong_type if n not in reasons
+        }
 
     # now remove complexes that contain any nodes to be removed entities
     as_components = []
@@ -44,9 +53,14 @@ def complex_to_remove(x):
         for n in x.split("|"):
             if n in as_components:
                 return True
+
     complex_component_missing = [n for n in g.nodes() if complex_to_remove(n)]
     to_remove.update(complex_component_missing)
-    reasons = {**reasons, **{n:"complex component removed" for n in complex_component_missing if not n in reasons}}
+    reasons = reasons | {
+        n: "complex component removed"
+        for n in complex_component_missing
+        if n not in reasons
+    }
 
     # remove the nodes
     g.remove_nodes_from(to_remove)
@@ -55,7 +69,7 @@ def complex_to_remove(x):
     if remove_isolates:
         isolates = list(nx.isolates(g))
         g.remove_nodes_from(isolates)
-        reasons = {**reasons, **{n:"isolate" for n in isolates if not n in reasons}}
+        reasons = reasons | {n: "isolate" for n in isolates if n not in reasons}
 
     now_size = g.number_of_nodes()
     print(f"Removed {og_size - now_size} nodes from network.")

skm_tools/resources/__init__.py

@@ -11,5 +11,4 @@
 def get_style_xml_path():
     '''file path on disk '''
     module_path = os.path.abspath(__file__)
-    resource_path = os.path.join(os.path.dirname(module_path), STYLE_XML)
-    return resource_path
+    return os.path.join(os.path.dirname(module_path), STYLE_XML)