Flake8 Round 2: We have to go deeper

setup.cfg

@@ -146,13 +146,10 @@ ignore =
     S318 # don't worry about unsafe xml
     S310 # TODO remove this later and switch to using requests
     # The following are documentation things (remove one at a time in future PRs)
+    BLK100
     D100
     D101
     D102
-    D103
-    D104
-    D105
-    D107
 exclude =
     sssom/sssom_datamodel.py
     sssom/cliquesummary.py

sssom/cliques.py

@@ -1,6 +1,6 @@
 import hashlib
 import statistics
-from typing import Any, Dict
+from typing import Any, Dict, List
 
 import networkx as nx
 import pandas as pd
@@ -59,7 +59,17 @@ def to_networkx(msdf: MappingSetDataFrame) -> nx.DiGraph:
     return g
 
 
-def split_into_cliques(msdf: MappingSetDataFrame):
+def split_into_cliques(msdf: MappingSetDataFrame) -> List[MappingSetDocument]:
+    """Split MappingSetDataFrames into cliques.
+
+    :param msdf: MappingSetDataFrame object
+    :type msdf: MappingSetDataFrame
+    :raises TypeError: If Mappings is not of type List
+    :raises TypeError: If each mapping is not of type Mapping
+    :raises TypeError: If Mappings is not of type List
+    :return: List of MappingSetDocument objects
+    :rtype: List[MappingSetDocument]
+    """
     doc = to_mapping_set_document(msdf)
     g = to_networkx(msdf)
     gen = nx.algorithms.components.strongly_connected_components(g)
@@ -87,6 +97,13 @@ def split_into_cliques(msdf: MappingSetDataFrame):
 
 
 def invert_dict(d: Dict[str, str]) -> Dict[str, str]:
+    """Invert Dictionary.
+
+    :param d: Dictionary
+    :type d: Dict[str, str]
+    :return: Dictionary with keys and values interchanged
+    :rtype: Dict[str, str]
+    """
     invdict: Dict[str, Any] = {}
     for k, v in d.items():
         if v not in invdict:
@@ -95,7 +112,16 @@ def invert_dict(d: Dict[str, str]) -> Dict[str, str]:
     return invdict
 
 
-def get_src(src, cid):
+def get_src(src: str, cid: str):
+    """Get source.
+
+    :param src: Source
+    :type src: str
+    :param cid: CURIE
+    :type cid: str
+    :return: Source
+    :rtype: [type]
+    """
     if src is None:
         return cid.split(":")[0]
     else:

sssom/context.py

@@ -15,14 +15,29 @@
 
 
 def get_jsonld_context():
+    """Get JSON-LD context.
+
+    :return: JSON-LD context
+    :rtype: Any
+    """
     return json.loads(sssom_context, strict=False)
 
 
 def get_external_jsonld_context():
+    """Get JSON-LD context.
+
+    :return: JSON-LD context
+    :rtype: Any
+    """
     return json.loads(sssom_external_context, strict=False)
 
 
 def get_built_in_prefix_map() -> PrefixMap:
+    """Get built-in prefix map.
+
+    :return: Prefix map
+    :rtype: PrefixMap
+    """
     contxt = get_jsonld_context()
     prefix_map = {}
     for key in contxt["@context"]:
@@ -36,6 +51,13 @@ def get_built_in_prefix_map() -> PrefixMap:
 def add_built_in_prefixes_to_prefix_map(
     prefix_map: Optional[PrefixMap] = None,
 ) -> PrefixMap:
+    """Add built-in prefix map.
+
+    :param prefix_map: Prefix map, defaults to None
+    :type prefix_map: Optional[PrefixMap], optional
+    :return: Prefix map
+    :rtype: PrefixMap
+    """
     builtinmap = get_built_in_prefix_map()
     if not prefix_map:
         prefix_map = builtinmap
@@ -51,6 +73,11 @@ def add_built_in_prefixes_to_prefix_map(
 
 
 def get_default_metadata() -> Metadata:
+    """Get Default metadata.
+
+    :return: Metadata
+    :rtype: Metadata
+    """
     contxt = get_jsonld_context()
     contxt_external = get_external_jsonld_context()
     prefix_map = {}

sssom/parsers.py

@@ -3,7 +3,7 @@
 import re
 import typing
 from collections import Counter
-from typing import Any, Dict, List, Optional, Set, TextIO, Union, cast
+from typing import Any, Callable, Dict, List, Optional, Set, TextIO, Union, cast
 from urllib.request import urlopen
 from xml.dom import Node, minidom
 from xml.dom.minidom import Document
@@ -294,6 +294,17 @@ def from_sssom_json(
     prefix_map: Dict[str, str],
     meta: Dict[str, str] = None,
 ) -> MappingSetDataFrame:
+    """Get data from JSON.
+
+    :param jsondoc: JSON document
+    :type jsondoc: Union[str, dict, TextIO]
+    :param prefix_map: Prefix map
+    :type prefix_map: Dict[str, str]
+    :param meta: metadata, defaults to None
+    :type meta: Dict[str, str], optional
+    :return: MappingSetDataFrame object
+    :rtype: MappingSetDataFrame
+    """
     prefix_map = _ensure_prefix_map(prefix_map)
     mapping_set = cast(
         MappingSet, JSONLoader().load(source=jsondoc, target_class=MappingSet)
@@ -452,7 +463,17 @@ def from_obographs(
 # All read_* take as an input a a file handle and return a MappingSetDataFrame (usually wrapping a from_* method)
 
 
-def get_parsing_function(input_format, filename):
+def get_parsing_function(input_format: str, filename: str) -> Callable:
+    """Return appropriate function based on input format of file.
+
+    :param input_format: File format
+    :type input_format: str
+    :param filename: Filename
+    :type filename: str
+    :raises Exception: Unknown file format
+    :return: Appropriate 'read' function
+    :rtype: function
+    """
     if input_format is None:
         input_format = get_file_extension(filename)
     if input_format == "tsv":
@@ -633,6 +654,14 @@ def to_mapping_set_document(msdf: MappingSetDataFrame) -> MappingSetDocument:
 def split_dataframe(
     msdf: MappingSetDataFrame,
 ) -> typing.Mapping[str, MappingSetDataFrame]:
+    """Split DataFrame.
+
+    :param msdf: MappingSetDataFrame object
+    :type msdf: MappingSetDataFrame
+    :raises RuntimeError: Object is None
+    :return: Mapping object
+    :rtype: typing.Mapping[str, MappingSetDataFrame]
+    """
     if msdf.df is None:
         raise RuntimeError
     subject_prefixes = set(msdf.df["subject_id"].str.split(":", 1, expand=True)[0])

sssom/sparql_util.py

@@ -84,10 +84,28 @@ def query_mappings(config: EndpointConfig) -> MappingSetDataFrame:
 
 
 def curiefy_row(row: Mapping[str, str], config: EndpointConfig) -> Dict[str, str]:
+    """CURIE-fy row.
+
+    :param row: Mapping object row
+    :type row: Mapping[str, str]
+    :param config: Configuration
+    :type config: EndpointConfig
+    :return: Dictionary of CURIEs
+    :rtype: Dict[str, str]
+    """
     return {k: contract_uri(v, config) for k, v in row.items()}
 
 
 def contract_uri(uristr: str, config: EndpointConfig) -> str:
+    """Contract URI.
+
+    :param uristr: URI string
+    :type uristr: str
+    :param config: Configuration
+    :type config: EndpointConfig
+    :return: URI string (contracted)
+    :rtype: str
+    """
     if config.prefix_map is None:
         return uristr
     for k, v in config.prefix_map.items():
@@ -97,6 +115,15 @@ def contract_uri(uristr: str, config: EndpointConfig) -> str:
 
 
 def expand_curie(curie: str, config: EndpointConfig) -> URIRef:
+    """Expand CURIE.
+
+    :param curie: CURIE
+    :type curie: str
+    :param config: Configuration
+    :type config: EndpointConfig
+    :return: URI of CURIE
+    :rtype: URIRef
+    """
     if config.prefix_map is None:
         return URIRef(curie)
     for k, v in config.prefix_map.items():