chores: fix ruff check messages

Author: ecarrenolozano

notebooks/graphblas_usecase_1.ipynb

@@ -1918,6 +1918,7 @@
    "source": [
     "from typing import Set, List\n",
     "\n",
+    "\n",
     "class QueryEngine:\n",
     "    def __init__(self, graph):\n",
     "        \"\"\"Initialize the QueryEngine with a Graph instance.\n",

notebooks/query_graphblas.ipynb

@@ -1019,6 +1019,7 @@
     "import re\n",
     "from typing import Set, List\n",
     "\n",
+    "\n",
     "class QueryEngine:\n",
     "    def __init__(self, graph):\n",
     "        self.graph = graph  # Graph must contain lookup_tables\n",
@@ -1350,6 +1351,7 @@
    "source": [
     "from typing import Set, List\n",
     "\n",
+    "\n",
     "class QueryEngine:\n",
     "    def __init__(self, graph):\n",
     "        \"\"\"Initialize the QueryEngine with a Graph instance.\n",

ontograph/client.py

@@ -35,8 +35,14 @@
 )
 from ontograph.downloader import DownloaderPort
 from ontograph.config.settings import DEFAULT_CACHE_DIR
-from ontograph.queries.navigator import NavigatorPronto, NavigatorGraphblas
-from ontograph.queries.relations import RelationsPronto, RelationsGraphblas
+from ontograph.queries.navigator import (
+    NavigatorPronto,
+    NavigatorGraphblas,
+)
+from ontograph.queries.relations import (
+    RelationsPronto,
+    RelationsGraphblas,
+)
 from ontograph.utils.pronto_utils import extract_terms
 from ontograph.queries.introspection import (
     IntrospectionPronto,
@@ -225,7 +231,9 @@ def __init__(self, cache_dir: str = DEFAULT_CACHE_DIR) -> None:
         self._relations = None
         self._introspection = None
 
-    def __create_graphblas_ontology(self, ontology, include_obsolete=False):
+    def __create_graphblas_ontology(
+        self, ontology: Ontology, include_obsolete: bool = False
+    ) -> tuple[LookUpTables, Graph]:
         terms = extract_terms(
             ontology=ontology, include_obsolete=include_obsolete
         )
@@ -263,11 +271,30 @@ def __create_graphblas_ontology(self, ontology, include_obsolete=False):
         return lookup_tables, graph
 
     def _detect_source_type(self, source: str) -> str:
-        """Determine whether 'source' is a file, an OBO Foundry ID, or a URL.
-        Priority order:
-            1. Local file path
-            2. OBO Foundry identifier
-            3. Other URL
+        """Detect the type of ontology source: file path, OBO Foundry ID, or URL.
+
+        This method checks the input string and determines its type in the following priority order:
+        1. Local file path
+        2. OBO Foundry identifier (alphanumeric, underscore, or hyphen; no slashes or dots)
+        3. HTTP/HTTPS URL
+
+        Args:
+            source (str): The ontology source string to check. Can be a file path, OBO Foundry ID, or URL.
+
+        Returns:
+            str: The detected source type. One of 'file', 'obo', or 'url'.
+
+        Raises:
+            ValueError: If the source type cannot be determined.
+
+        Example:
+            >>> client = ClientOntology()
+            >>> client._detect_source_type("./ontology.obo")
+            'file'
+            >>> client._detect_source_type("go")
+            'obo'
+            >>> client._detect_source_type("https://example.com/ontology.obo")
+            'url'
         """
         path = Path(source)
 
@@ -364,9 +391,35 @@ def load(
         self,
         source: str,
         downloader: DownloaderPort = None,
-        include_obsolete=False,
-        backend='pronto',
-    ):
+        include_obsolete: bool = False,
+        backend: str = 'pronto',
+    ) -> None:
+        """Load an ontology from a file path, URL, or OBO Foundry catalog.
+
+        This method detects the source type and loads the ontology using the appropriate strategy:
+        - Local file path
+        - URL
+        - OBO Foundry catalog identifier
+
+        It also initializes query adapters for navigation, relations, and introspection based on the selected backend.
+
+        Args:
+            source (str): Path to the ontology file, URL, or OBO Foundry identifier.
+            downloader (DownloaderPort, optional): Downloader adapter for remote files. Defaults to None.
+            include_obsolete (bool, optional): If True, include obsolete terms when building GraphBLAS structures. Defaults to False.
+            backend (str, optional): Backend for queries ('pronto' or 'graphblas'). Defaults to 'pronto'.
+
+        Raises:
+            FileNotFoundError: If the ontology source cannot be found as a file, URL, or catalog entry.
+            ValueError: If an unknown backend is specified.
+
+        Returns:
+            None
+
+        Example:
+            >>> client = ClientOntology()
+            >>> client.load(source="./tests/resources/dummy_ontology.obo")
+        """
         logger.info(f'Loading ontology from source: {source} ...')
         loader = ProntoLoaderAdapter(cache_dir=self._cache_dir)
 
@@ -431,8 +484,16 @@ def load(
 
         logger.info('Ontology loading complete.')
 
-    def _initialize_queries(self, backend) -> None:
-        """Initialize query adapters for navigation, relations, and introspection."""
+    def _initialize_queries(self, backend: str) -> None:
+        """Initializes query adapters for navigation, relations, and introspection based on the specified backend.
+
+        Args:
+            backend (str): The backend to use for query adapters. Supported values are 'pronto' and 'graphblas'.
+
+        Raises:
+            KeyError: If the specified backend is not supported.
+
+        """
 
         if backend == 'pronto':
             self._navigator = NavigatorPronto(ontology=self._get_ontology)

ontograph/loader.py

@@ -156,7 +156,15 @@ def _extract_ontology_id(self, ontology: pronto.Ontology) -> str | None:
             )
             return None
 
-    def find_file_encoding(self, file):
+    def find_file_encoding(self, file: str | Path) -> str | None:
+        """Detect the encoding of a file.
+
+        Args:
+            file (str | Path): Path to the file whose encoding should be detected.
+
+        Returns:
+            str | None: The detected encoding, or None if it cannot be determined.
+        """
         result = from_path(file).best()
         return result.encoding
 

ontograph/queries/introspection.py

@@ -2,11 +2,12 @@
 import logging
 from collections import deque
 
-from ontograph.queries.navigator import NavigatorPronto
-from ontograph.queries.relations import RelationsPronto
+from ontograph.models import LookUpTables
+from ontograph.queries.navigator import NavigatorOntology
+from ontograph.queries.relations import RelationsPronto, RelationsOntology
 
 __all__ = [
-    'OntologyIntrospection',
+    'IntrospectionOntology',
 ]
 
 logger = logging.getLogger(__name__)
@@ -16,10 +17,12 @@
 # ------------------------------------------------------------
 # ----     OntologyIntrospection Port (abstract class)    ----
 # ------------------------------------------------------------
-class OntologyIntrospection(ABC):
+class IntrospectionOntology(ABC):
     """Abstract class for ontology introspection utilities."""
 
-    def __init__(self, navigator, relations) -> None:
+    def __init__(
+        self, navigator: NavigatorOntology, relations: RelationsOntology
+    ) -> None:
         self._navigator = navigator
         self._relations = relations
 
@@ -60,14 +63,14 @@ def print_term_trajectories_tree(trajectories: list[dict]) -> None:
 # -------------------------------------------------------------
 # ----     IntrospectionPronto adapter (concrete class)    ----
 # -------------------------------------------------------------
-class IntrospectionPronto(OntologyIntrospection):
+class IntrospectionPronto(IntrospectionOntology):
     """Provides introspection utilities for ontology graphs.
 
     Includes methods for calculating distances, paths, and ancestor trajectories.
     """
 
     def __init__(
-        self, navigator: NavigatorPronto, relations: RelationsPronto
+        self, navigator: NavigatorOntology, relations: RelationsPronto
     ) -> None:
         """Initialize the introspection utility.
 
@@ -242,8 +245,8 @@ def print_term_trajectories_tree(trajectories: list[dict]) -> None:
                 print(f'{node["id"]}: {node["name"]}')
             return
         # Otherwise, use tree printing
-        root = OntologyIntrospection._build_tree_from_trajectories(trajectories)
-        OntologyIntrospection._print_ascii_tree(root)
+        root = IntrospectionOntology._build_tree_from_trajectories(trajectories)
+        IntrospectionOntology._print_ascii_tree(root)
 
     @staticmethod
     def _build_tree_from_trajectories(trajectories: list[dict]) -> object:
@@ -306,30 +309,31 @@ def print_ascii_tree(
             print_ascii_tree(child, '', is_last_child)
 
 
-class IntrospectionGraphblas(OntologyIntrospection):
+class IntrospectionGraphblas(IntrospectionOntology):
     """Provides introspection utilities for ontology graphs using GraphBLAS.
 
     Includes methods for calculating distances, paths, and ancestor trajectories.
     """
 
     def __init__(
         self,
-        navigator: NavigatorPronto,
-        relations: RelationsPronto,
-        lookup_tables,
+        navigator: NavigatorOntology,
+        relations: RelationsOntology,
+        lookup_tables: LookUpTables,
     ) -> None:
         """Initialize the introspection utility.
 
         Args:
-            navigator (OntologyNavigator): The ontology navigator.
-            relations (OntologyRelations): The ontology relations.
+            navigator (NavigatorPronto): The ontology navigator.
+            relations (RelationsPronto): The ontology relations.
+            lookup_tables (LookUpTables): Lookup tables for term/index/description mapping.
         """
         self.__navigator = navigator
         self.__relations = relations
         self.lookup_tables = lookup_tables
         self.matrices_container = navigator.matrices_container
 
-    def get_distance_from_root(self, term_id):
+    def get_distance_from_root(self, term_id: str) -> int:
         """Calculate the distance from the given term to the root node(s) of the ontology.
 
         Parameters
@@ -361,7 +365,7 @@ def get_distance_from_root(self, term_id):
 
         return max_distance
 
-    def get_path_between(self, node_a, node_b):
+    def get_path_between(self, node_a: str, node_b: str) -> list:
         """Find the shortest path between two nodes in the ontology.
 
         Parameters
@@ -403,7 +407,7 @@ def get_path_between(self, node_a, node_b):
         # BFS to find shortest path
 
         queue = deque([[start_idx]])
-        visited = set([start_idx])
+        visited = {start_idx}
 
         while queue:
             path = queue.popleft()

ontograph/queries/navigator.py

@@ -9,7 +9,7 @@
 from ontograph.models import Ontology, LookUpTables
 
 __all__ = [
-    'NavigatorPronto',
+    'NavigatorOntology',
 ]
 
 logger = logging.getLogger(__name__)
@@ -19,7 +19,7 @@
 # --------------------------------------------------------
 # ----     OntologyNavigator Port (abstract class)    ----
 # --------------------------------------------------------
-class NavigatorPronto(ABC):
+class NavigatorOntology(ABC):
     """Abstract navigator for traversing and querying ontology term relationships."""
 
     def __init__(self, ontology: 'Ontology') -> None:
@@ -90,7 +90,7 @@ def get_root(self) -> list:
 # ---------------------------------------------------------
 # ----     NavigatorPronto adapter (concrete class)    ----
 # ---------------------------------------------------------
-class NavigatorPronto(NavigatorPronto):
+class NavigatorPronto(NavigatorOntology):
     """Navigator for traversing and querying ontology term relationships.
 
     This class provides methods to retrieve parent, ancestor, descendant, sibling, and root terms
@@ -431,7 +431,7 @@ def get_root(self) -> list:
 # ------------------------------------------------------------
 # ----     NavigatorGraphblas adapter (concrete class)    ----
 # ------------------------------------------------------------
-class NavigatorGraphblas(NavigatorPronto):
+class NavigatorGraphblas(NavigatorOntology):
     def __init__(self, ontology: Ontology, lookup_tables: LookUpTables) -> None:
         self.__ontology = ontology
 

ontograph/queries/relations.py

@@ -2,10 +2,10 @@
 import logging
 from collections import deque
 
-from ontograph.queries.navigator import NavigatorPronto as _OntologyNavigator
+from ontograph.queries.navigator import NavigatorOntology as _OntologyNavigator
 
 __all__ = [
-    'RelationsPronto',
+    'RelationsOntology',
 ]
 
 logger = logging.getLogger(__name__)
@@ -15,7 +15,7 @@
 # --------------------------------------------------------
 # ----     OntologyRelations Port (abstract class)    ----
 # --------------------------------------------------------
-class RelationsPronto(ABC):
+class RelationsOntology(ABC):
     """Abstract class for querying relationships between ontology terms."""
 
     def __init__(self, navigator: _OntologyNavigator) -> None:
@@ -50,7 +50,7 @@ def get_lowest_common_ancestors(self, node_ids: list[str]) -> set:
 # ---------------------------------------------------------
 # ----     RelationsPronto adapter (abstract class)    ----
 # ---------------------------------------------------------
-class RelationsPronto(RelationsPronto):
+class RelationsPronto(RelationsOntology):
     """Provides methods for querying relationships between ontology terms.
 
     Includes ancestor, descendant, sibling checks, and common ancestor computations.
@@ -256,7 +256,7 @@ def get_lowest_common_ancestors(self, node_ids: list[str]) -> set:
 # ------------------------------------------------------------
 # ----     RelationsGraphblas adapter (abstract class)    ----
 # ------------------------------------------------------------
-class RelationsGraphblas(RelationsPronto):
+class RelationsGraphblas(RelationsOntology):
     def __init__(
         self, navigator: _OntologyNavigator, lookup_tables: object
     ) -> None:

ontograph/utils/pronto_utils.py

@@ -1,5 +1,10 @@
+import logging
+
 from pronto import Ontology
 
+logger = logging.getLogger(__name__)
+logger.addHandler(logging.NullHandler())
+
 
 def extract_terms(ontology: Ontology, include_obsolete: bool = False) -> list:
     """Single-pass extraction of pronto.Term objects, sorted by term.id."""

pyproject.toml

@@ -159,7 +159,11 @@ exclude = [
     "docs/_build",
     "tests/",
     "test_*.py",
-    "*/test_*.py"
+    "*/test_*.py",
+    "notebooks/",
+    "examples/",
+    "*.ipynb",
+    "**/*.ipynb"
 ]
 ignore = [
     # flake8-bugbear (B)