added new graph metrics

tests/analysis/test_graphs.py

@@ -2,7 +2,12 @@ import networkx as nx
 import pytest
 
 from lang_main.analysis import graphs
-from lang_main.errors import EmptyEdgesError, EmptyGraphError, EdgePropertyNotContainedError
+from lang_main.errors import (
+    EdgePropertyNotContainedError,
+    EmptyEdgesError,
+    EmptyGraphError,
+    NodePropertyNotContainedError,
+)
 
 TK_GRAPH_NAME = 'TEST_TOKEN_GRAPH'
 
@@ -231,6 +236,49 @@ def test_add_weighted_degree():
     assert graph_obj.nodes[3][property_name] == 6
 
 
+def test_add_betweenness_centrality():
+    graph_obj = build_init_graph(token_graph=False)
+    property_name = 'betweenness_centrality'
+    graphs.add_betweenness_centrality(graph_obj, property_name=property_name)
+    assert round(graph_obj.nodes[1][property_name], 4) == pytest.approx(0.1667)
+    assert graph_obj.nodes[2][property_name] == 0
+    assert graph_obj.nodes[3][property_name] == 0
+
+
+def test_add_importance_metric():
+    graph_obj = build_init_graph(token_graph=False)
+    property_name_WD = 'degree_weighted'
+    graphs.add_weighted_degree(graph_obj, 'weight', property_name_WD)
+    property_name_BC = 'betweenness_centrality'
+    graphs.add_betweenness_centrality(graph_obj, property_name=property_name_BC)
+    property_name = 'importance'
+    graphs.add_importance_metric(
+        graph_obj,
+        property_name=property_name,
+        property_name_weighted_degree=property_name_WD,
+        property_name_betweenness=property_name_BC,
+    )
+    assert round(graph_obj.nodes[1][property_name], 4) == pytest.approx(2.3333)
+    assert graph_obj.nodes[2][property_name] == 0
+    assert graph_obj.nodes[3][property_name] == 0
+
+    with pytest.raises(NodePropertyNotContainedError):
+        graphs.add_importance_metric(
+            graph_obj,
+            property_name=property_name,
+            property_name_weighted_degree='prop_not_contained',
+            property_name_betweenness=property_name_BC,
+        )
+
+    with pytest.raises(NodePropertyNotContainedError):
+        graphs.add_importance_metric(
+            graph_obj,
+            property_name=property_name,
+            property_name_weighted_degree=property_name_WD,
+            property_name_betweenness='prop_not_contained',
+        )
+
+
 def test_static_graph_analysis():
     graph_obj = build_init_graph(token_graph=True)
     (graph_obj,) = graphs.static_graph_analysis(graph_obj)  # type: ignore
@@ -254,6 +302,20 @@ def test_pipe_add_graph_metrics():
     assert graph_collection[1].nodes[1][property_name] == 14
     assert graph_collection[1].nodes[2][property_name] == 10
     assert graph_collection[1].nodes[3][property_name] == 6
+    property_name = 'betweenness_centrality'
+    assert round(graph_collection[0].nodes[1][property_name], 4) == pytest.approx(0.1667)
+    assert graph_collection[0].nodes[2][property_name] == 0
+    assert graph_collection[0].nodes[3][property_name] == 0
+    assert round(graph_collection[1].nodes[1][property_name], 4) == pytest.approx(0.1667)
+    assert graph_collection[1].nodes[2][property_name] == 0
+    assert graph_collection[1].nodes[3][property_name] == 0
+    property_name = 'importance'
+    assert round(graph_collection[0].nodes[1][property_name], 4) == pytest.approx(2.3333)
+    assert graph_collection[0].nodes[2][property_name] == 0
+    assert graph_collection[0].nodes[3][property_name] == 0
+    assert round(graph_collection[1].nodes[1][property_name], 4) == pytest.approx(2.3333)
+    assert graph_collection[1].nodes[2][property_name] == 0
+    assert graph_collection[1].nodes[3][property_name] == 0
 
 
 def test_pipe_rescale_graph_edge_weights(tk_graph):

tests/pipelines/test_base.py

@@ -121,6 +121,7 @@ def test_pipeline_valid(pipeline, alter_content):
     assert len(pipe.actions) == 1
     assert len(pipe.action_names) == 1
     assert len(pipe.actions_kwargs) == 1
+    assert len(pipe.action_skip) == 1
     assert len(pipe.save_results) == 1
     assert len(pipe.load_results) == 1
     assert pipe.save_results[0] == (False, None)
@@ -166,7 +167,7 @@ def test_pipeline_valid_action_load(pipeline, working_dir):
     test_string = 'test'
 
     # action preparation
-    def valid_action(string, add_content=False):
+    def valid_action(string, add_content=False):  # pragma: no cover
         if add_content:
             string += '_2'
         return string
@@ -175,6 +176,7 @@ def test_pipeline_valid_action_load(pipeline, working_dir):
     assert len(pipe.actions) == 1
     assert len(pipe.action_names) == 1
     assert len(pipe.actions_kwargs) == 1
+    assert len(pipe.action_skip) == 1
     assert len(pipe.save_results) == 1
     assert len(pipe.load_results) == 1
     assert pipe.save_results[0] == (False, None)
@@ -209,19 +211,28 @@ def test_pipeline_multiple_actions(pipeline):
             string += '_3'
         return string
 
+    pipe.add(valid_action, {'add_content': True}, skip=True)
     pipe.add(valid_action, {'add_content': True})
     pipe.add(valid_action_2)
-    assert len(pipe.actions) == 2
-    assert len(pipe.action_names) == 2
-    assert len(pipe.actions_kwargs) == 2
-    assert len(pipe.save_results) == 2
-    assert len(pipe.load_results) == 2
+    assert len(pipe.actions) == 3
+    assert len(pipe.action_names) == 3
+    assert len(pipe.actions_kwargs) == 3
+    assert len(pipe.action_skip) == 3
+    assert len(pipe.save_results) == 3
+    assert len(pipe.load_results) == 3
     assert pipe.save_results[1] == (False, None)
     assert pipe.load_results[1] == (False, None)
 
     ret = pipe.run(starting_values=(test_string,))
     assert isinstance(ret, tuple)
     assert pipe._intermediate_result == ret
-    assert pipe.curr_proc_idx == 3
+    assert pipe.curr_proc_idx == 4
     assert ret is not None
     assert ret[0] == 'test_2_3'
+
+
+def test_pipeline_invalid_action(pipeline):
+    test_string = 'test'
+
+    with pytest.raises(WrongActionTypeError):
+        pipeline.add(test_string, skip=False)

tests/render/test_import.py

@@ -0,0 +1,54 @@
+import builtins
+import importlib.util
+from importlib import reload
+
+import pytest
+
+from lang_main.errors import DependencyMissingError
+
+
+@pytest.fixture(scope='function')
+def no_dep(monkeypatch):
+    import_orig = builtins.__import__
+
+    def mocked_import(name, globals, locals, fromlist, level):
+        if name == 'py4cytoscape':
+            raise ImportError()
+        return import_orig(name, locals, fromlist, level)
+
+    monkeypatch.setattr(builtins, '__import__', mocked_import)
+
+
+@pytest.fixture(scope='function')
+def patch_find_spec(monkeypatch):
+    find_spec_orig = importlib.util.find_spec
+
+    def mocked_find_spec(*args, **kwargs):
+        if args[0] == 'py4cytoscape':
+            return None
+        else:
+            return find_spec_orig(*args, **kwargs)
+
+    monkeypatch.setattr(importlib.util, 'find_spec', mocked_find_spec)
+
+
+def test_p4c_available():
+    import lang_main.constants
+
+    reload(lang_main.constants)
+
+    assert lang_main.constants.Dependencies.PY4C.value
+
+
+@pytest.mark.usefixtures('patch_find_spec')
+def test_p4c_missing(monkeypatch):
+    import lang_main.constants
+
+    reload(lang_main.constants)
+
+    assert not lang_main.constants.Dependencies.PY4C.value
+
+    with pytest.raises(DependencyMissingError):
+        from lang_main import render
+
+        reload(render)

tests/test_config.py

@@ -16,7 +16,7 @@ def test_p4c_dependency():
 def test_load_config():
     toml_path = config.PKG_DIR / 'lang_main_config.toml'
     loaded_cfg = config.load_toml_config(toml_path)
-    assert loaded_cfg['info']['pkg'] == 'lang_main_internal'
+    assert loaded_cfg['paths']['models'] == './lang-models'
 
 
 def test_get_config_path():
@@ -36,7 +36,7 @@ def test_get_config_path():
     assert cyto_internal == cyto_cfg_pth
 
 
-def test_load_cfg(monkeypatch, tmp_path):
+def test_load_cfg_func(monkeypatch, tmp_path):
     monkeypatch.setattr(Path, 'cwd', lambda: tmp_path)
     pkg_dir = config.PKG_DIR
     filename = config.CONFIG_FILENAME
@@ -44,21 +44,20 @@ def test_load_cfg(monkeypatch, tmp_path):
 
     cfg_pth_internal = (pkg_dir / filename).resolve()
     ref_config = config.load_toml_config(cfg_pth_internal)
+    assert ref_config['paths']['models'] == './lang-models'
 
-    assert ref_config['info']['pkg'] == 'lang_main_internal'
     loaded_cfg = config.load_cfg(
         starting_path=pkg_dir,
         glob_pattern=filename,
         stop_folder_name=stop_folder,
-        cfg_path_internal=cfg_pth_internal,
-        prefer_internal_config=True,
+        lookup_cwd=False,
     )
-    assert loaded_cfg['info']['pkg'] == 'lang_main_internal'
+    assert loaded_cfg['paths']['models'] == '../lang-models'
+
     loaded_cfg = config.load_cfg(
         starting_path=pkg_dir,
         glob_pattern=filename,
         stop_folder_name=stop_folder,
-        cfg_path_internal=cfg_pth_internal,
-        prefer_internal_config=False,
+        lookup_cwd=True,
     )
-    assert loaded_cfg['info']['pkg'] == 'lang_main'
+    assert loaded_cfg['paths']['models'] == '../lang-models'

tests/test_model_loader.py

@@ -4,12 +4,12 @@ from spacy.language import Language
 
 from lang_main import model_loader
 from lang_main.constants import (
-    STFR_MODEL_ARGS_ONNX,
     SimilarityFunction,
     SpacyModelTypes,
     STFRBackends,
     STFRDeviceTypes,
     STFRModelTypes,
+    stfr_model_args_onnx,
 )
 from lang_main.errors import LanguageModelNotFoundError
 from lang_main.types import LanguageModels
@@ -69,7 +69,7 @@ def test_load_sentence_transformer_onnx(model_name, similarity_func) -> None:
         similarity_func=similarity_func,
         backend=STFRBackends.ONNX,
         device=STFRDeviceTypes.CPU,
-        model_kwargs=STFR_MODEL_ARGS_ONNX,  # type: ignore
+        model_kwargs=stfr_model_args_onnx,  # type: ignore
     )
     assert isinstance(model, SentenceTransformer)