chores: resolve minor suggestions given by GitHub copilot

Author: ecarrenolozano

ontograph/downloader.py

@@ -218,44 +218,3 @@ class DownloadManagerAdapter(DownloaderPort):
     """
 
     pass
-
-
-# -------------------------------------------------------------------------
-# ----        MAIN FUNTION  (mini-sandbox to try functionalities)      ----
-# -------------------------------------------------------------------------
-if __name__ == '__main__':
-    # Configure logging
-    logging.basicConfig(level=logging.DEBUG)
-
-    # Define a directory to store all the downloads
-    cache = Path('./data/in')
-
-    # Initialize a downloader object
-    downloader = PoochDownloaderAdapter(cache_dir=cache)
-
-    # Functionality 1. Download from a URL
-    path_single_download = downloader.fetch_from_url(
-        url_ontology='https://purl.obolibrary.org/obo/ado.owl',
-        filename='adosdsdsds.owl',
-    )
-    print(f'Path single download: {path_single_download}')
-
-    # Functionality 2. Download several resources from a catalog.
-    from ontograph.models import CatalogOntologies
-
-    # Download automatically the catalog
-    catalog = CatalogOntologies(cache_dir=cache)
-    resources = [
-        {'name_id': 'go', 'format': 'obo'},
-        {'name_id': 'ado', 'format': 'owl'},
-    ]
-
-    catalog = CatalogOntologies(cache_dir=cache)
-    paths_resources = downloader.fetch_from_catalog(
-        resources=resources, catalog=catalog
-    )
-    print(f'\nPaths multiple resources: {paths_resources}')
-
-    print('\nPrint all the resources downloaded by the downloader')
-    for name_id, path_resource in downloader.get_paths().items():
-        print(f'\t{name_id}: {path_resource}')

ontograph/loader.py

@@ -378,45 +378,3 @@ class FastoboAdapter(OntologyLoaderPort):
     """
 
     pass
-
-
-if __name__ == '__main__':
-    """Example usage and testing for loader adapters."""
-    # Configure logging
-    logging.basicConfig(level=logging.INFO)
-
-    # Define a directory to store all the downloads
-    cache = Path('./data/out')
-
-    # Creates an object that will load the ontology
-    adapter = ProntoLoaderAdapter(cache_dir=cache)
-
-    # ----  Functionality 1. load_from_file()
-    path_test = './data/in/go_version1.obo'
-    print(f'Testing load_from_file with: {path_test}')
-    onto_file = adapter.load_from_file(file_path_ontology=path_test)
-
-    print(f'Loaded ontology: {onto_file._ontology_id}')
-    print(f'Number of terms: {len(onto_file._ontology.terms())}')
-
-    # ----  Functionality 2. load_from_catalog()
-    ontology_id = 'ado'  # Use a valid ontology ID
-    format = 'owl'
-
-    print(f'Testing load_from_catalog() with: {ontology_id}.{format}')
-    onto_catalog = adapter.load_from_catalog(ontology_id, format)
-    print(f'Loaded ontology: {ontology_id}.{format}')
-    print(f'Number of terms: {len(onto_catalog._ontology.terms())}')
-
-    # ----  Functionality 3. load_from_url()
-    url_chebi_ontology = 'https://purl.obolibrary.org/obo/chebi.owl'
-    filename = 'chebi.owl'
-    onto_url = adapter.load_from_url(
-        url_ontology=url_chebi_ontology,
-        filename=filename,
-        downloader=PoochDownloaderAdapter(
-            cache_dir=cache
-        ),  # By Dependency Injection
-    )
-    print(f'Loaded ontology: {filename}')
-    print(f'Number of terms: {len(onto_url._ontology.terms())}')

ontograph/queries/introspection.py

@@ -223,10 +223,10 @@ def insert_branch(root: Node, branch: list) -> None:
                 node = node.children[key]
 
         # All branches are sorted from term to root, so reverse to root-to-term
-        sorted_branches = [list(branch) for branch in trajectories]
-        root_info = sorted_branches[0][0]
+        branch_lists = [list(branch) for branch in trajectories]
+        root_info = branch_lists[0][0]
         root = Node(root_info['id'], root_info['name'], root_info['distance'])
-        for branch in sorted_branches:
+        for branch in branch_lists:
             insert_branch(root, branch[1:])  # skip root itself, already created
         return root
 

ontograph/queries/navigator.py

@@ -333,11 +333,6 @@ def get_root(self) -> list:
             Exception: If an error occurs during root term retrieval.
         """
         try:
-            # root_terms = [
-            #     term
-            #     for term in self.__ontology.terms()
-            #     if not any(term.superclasses(distance=1, with_self=False))
-            # ]
             root_terms = []
 
             for term in self.__ontology.terms():

ontograph/queries/relations.py

@@ -83,18 +83,9 @@ def is_sibling(self, nodeA: str, nodeB: str) -> bool:
             Exception: If an error occurs during parent lookup.
         """
         try:
-            parentsA = {
-                parent.id
-                for parent in self.__navigator.get_term(nodeA).superclasses(
-                    distance=1, with_self=False
-                )
-            }
-            parentsB = {
-                parent.id
-                for parent in self.__navigator.get_term(nodeB).superclasses(
-                    distance=1, with_self=False
-                )
-            }
+            parentsA = set(self.__navigator.get_parents(term_id=nodeA))
+            parentsB = set(self.__navigator.get_parents(term_id=nodeB))
+
             # Siblings must not be the same node and must share at least one parent
             return nodeA != nodeB and bool(parentsA & parentsB)
         except Exception as e: