Add flake8 and isort to precommit

.pre-commit-config.yaml

@@ -1,5 +1,14 @@
 repos:
--   repo: https://github.com/psf/black
+  - repo: https://github.com/psf/black
     rev: 22.3.0
     hooks:
-    -   id: black
+      - id: black
+  - repo: https://github.com/pycqa/flake8
+    rev: 4.0.1
+    hooks:
+      - id: flake8
+  - repo: https://github.com/pycqa/isort
+    rev: 5.10.1
+    hooks:
+      - id: isort
+        name: isort (python)

case_utils/__init__.py

@@ -13,4 +13,4 @@
 
 __version__ = "0.5.0"
 
-from . import local_uuid
+from . import local_uuid  # noqa: F401

case_utils/case_file/__init__.py

@@ -28,7 +28,14 @@
 import rdflib  # type: ignore
 
 import case_utils
-from case_utils.namespace import *
+from case_utils.namespace import (
+    NS_RDF,
+    NS_UCO_CORE,
+    NS_UCO_OBSERVABLE,
+    NS_UCO_TYPES,
+    NS_UCO_VOCABULARY,
+    NS_XSD,
+)
 
 DEFAULT_PREFIX = "http://example.org/kb/"
 
@@ -147,7 +154,7 @@ def create_file_node(
                     sha1obj.update(buf)
                     sha256obj.update(buf)
                     sha512obj.update(buf)
-            if not stashed_error is None:
+            if stashed_error is not None:
                 raise stashed_error
             current_hashdict = HashDict(
                 byte_tally,
@@ -182,7 +189,7 @@ def create_file_node(
 
         # Add confirmed hashes into graph.
         for key in successful_hashdict._fields:
-            if not key in ("md5", "sha1", "sha256", "sha512"):
+            if key not in ("md5", "sha1", "sha256", "sha512"):
                 continue
             n_hash = rdflib.BNode()
             graph.add((n_contentdata_facet, NS_UCO_OBSERVABLE.hash, n_hash))
@@ -247,7 +254,7 @@ def main() -> None:
         serialize_kwargs["context"] = context_dictionary
 
     node_iri = NS_BASE["file-" + case_utils.local_uuid.local_uuid()]
-    n_file = create_file_node(
+    create_file_node(
         graph,
         args.in_file,
         node_iri=node_iri,

case_utils/case_sparql_construct/__init__.py

@@ -26,8 +26,10 @@
 import rdflib.plugins.sparql  # type: ignore
 
 import case_utils.ontology
-
-from case_utils.ontology.version_info import *
+from case_utils.ontology.version_info import (
+    CURRENT_CASE_VERSION,
+    built_version_choices_list,
+)
 
 _logger = logging.getLogger(os.path.basename(__file__))
 
@@ -81,7 +83,7 @@ def main() -> None:
     construct_query_text = None
     with open(args.in_sparql, "r") as in_fh:
         construct_query_text = in_fh.read().strip()
-    assert not construct_query_text is None
+    assert construct_query_text is not None
 
     if "subClassOf" in construct_query_text:
         case_utils.ontology.load_subclass_hierarchy(

case_utils/case_sparql_select/__init__.py

@@ -30,7 +30,6 @@
 
 import argparse
 import binascii
-import importlib.resources
 import logging
 import os
 import sys
@@ -39,8 +38,10 @@
 import rdflib.plugins.sparql  # type: ignore
 
 import case_utils.ontology
-
-from case_utils.ontology.version_info import *
+from case_utils.ontology.version_info import (
+    CURRENT_CASE_VERSION,
+    built_version_choices_list,
+)
 
 NS_XSD = rdflib.XSD
 

case_utils/case_validate/__init__.py

@@ -35,16 +35,17 @@
 import importlib.resources
 import logging
 import os
-import pathlib
 import sys
 import typing
 
-import rdflib.util  # type: ignore
 import pyshacl  # type: ignore
+import rdflib.util  # type: ignore
 
 import case_utils.ontology
-
-from case_utils.ontology.version_info import *
+from case_utils.ontology.version_info import (
+    CURRENT_CASE_VERSION,
+    built_version_choices_list,
+)
 
 _logger = logging.getLogger(os.path.basename(__file__))
 

case_utils/local_uuid.py

@@ -22,8 +22,8 @@
 import pathlib
 import sys
 import typing
-import warnings
 import uuid
+import warnings
 
 DEMO_UUID_BASE: typing.Optional[str] = None
 

case_utils/ontology/__init__.py

@@ -22,7 +22,7 @@
 # Yes, this next import is self-referential (/circular).  But, it does work with importlib.
 import case_utils.ontology
 
-from .version_info import *
+from .version_info import CURRENT_CASE_VERSION
 
 _logger = logging.getLogger(os.path.basename(__file__))
 

setup.cfg

@@ -37,3 +37,14 @@ console_scripts =
 [options.package_data]
 case_utils = py.typed
 case_utils.ontology = *.ttl
+
+[flake8]
+# https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#flake8
+extend-ignore =
+  E203
+  E302
+  E501
+
+[isort]
+# https://pycqa.github.io/isort/docs/configuration/black_compatibility.html
+profile = black

tests/case_utils/case_file/test_case_file.py

@@ -19,7 +19,7 @@
 import rdflib.plugins.sparql  # type: ignore
 
 import case_utils.ontology
-from case_utils.namespace import *
+from case_utils.namespace import NS_UCO_CORE, NS_UCO_OBSERVABLE, NS_UCO_TYPES
 
 _logger = logging.getLogger(os.path.basename(__file__))
 
@@ -117,12 +117,12 @@ def test_confirm_mtime(
     for result in graph_case_file_disable_hashes.query(query_object):
         (n_observable_object,) = result
     assert (
-        not n_observable_object is None
+        n_observable_object is not None
     ), "File object with expected mtime not found in hashless graph."
 
     n_observable_object = None
     for result in graph_case_file.query(query_object):
         (n_observable_object,) = result
     assert (
-        not n_observable_object is None
+        n_observable_object is not None
     ), "File object with expected mtime not found in fuller graph."

tests/case_utils/case_sparql_construct/test_case_sparql_construct.py

@@ -15,8 +15,6 @@
 
 import rdflib.plugins.sparql  # type: ignore
 
-import case_utils
-
 
 def _test_subclass_templates_result(filename: str, expected: typing.Set[str]) -> None:
     computed: typing.Set[str] = set()
@@ -38,8 +36,7 @@ def _test_subclass_templates_result(filename: str, expected: typing.Set[str]) ->
 
 
 def _test_w3_templates_with_blank_nodes_result(filename: str) -> None:
-    ground_truth_positive = {("Alice", "Hacker"), ("Bob", "Hacker")}
-    ground_truth_negative: typing.Set[str] = set()
+    expected = {("Alice", "Hacker"), ("Bob", "Hacker")}
 
     graph = rdflib.Graph()
     graph.parse(filename)
@@ -59,7 +56,7 @@ def _test_w3_templates_with_blank_nodes_result(filename: str) -> None:
     for result in graph.query(query_string):
         (l_given_name, l_family_name) = result
         computed.add((l_given_name.toPython(), l_family_name.toPython()))
-    assert computed == ground_truth_positive
+    assert expected == computed
 
 
 def test_w3_templates_with_blank_nodes_result_json() -> None:

tests/case_utils/case_validate/cli/test_format_output_flags.py

@@ -81,7 +81,7 @@ def test_format_jsonld_output_jsonld() -> None:
     subject_file = "format_jsonld_output_jsonld.jsonld"
     asserted_format = _guess_format(subject_file)
     assert asserted_format == "json-ld"
-    graph = _parse_graph(subject_file, asserted_format)
+    _parse_graph(subject_file, asserted_format)
 
 
 @pytest.mark.xfail(
@@ -107,7 +107,7 @@ def test_format_jsonld_output_unspecified() -> None:
     subject_file = "format_jsonld_output_unspecified.jsonld"
     asserted_format = _guess_format(subject_file)
     assert asserted_format == "json-ld"
-    graph = _parse_graph(subject_file, asserted_format)
+    _parse_graph(subject_file, asserted_format)
 
 
 @pytest.mark.xfail(
@@ -124,7 +124,7 @@ def test_format_turtle_output_turtle() -> None:
     subject_file = "format_turtle_output_turtle.ttl"
     asserted_format = _guess_format(subject_file)
     assert asserted_format == "turtle"
-    graph = _parse_graph(subject_file, asserted_format)
+    _parse_graph(subject_file, asserted_format)
 
 
 def test_format_turtle_output_txt() -> None:
@@ -138,7 +138,7 @@ def test_format_turtle_output_unspecified() -> None:
     subject_file = "format_turtle_output_unspecified.ttl"
     asserted_format = _guess_format(subject_file)
     assert asserted_format == "turtle"
-    graph = _parse_graph(subject_file, asserted_format)
+    _parse_graph(subject_file, asserted_format)
 
 
 @pytest.mark.xfail(

tests/case_utils/ontology/test_version_info.py

@@ -18,8 +18,10 @@
 import rdflib  # type: ignore
 
 import case_utils.ontology
-
-from case_utils.ontology.version_info import *
+from case_utils.ontology.version_info import (
+    CURRENT_CASE_VERSION,
+    built_version_choices_list,
+)
 
 NS_OWL = rdflib.OWL
 
@@ -30,7 +32,7 @@ def test_built_version_choices_list() -> None:
             continue
         ttl_filename = built_version_choice + ".ttl"
         with importlib.resources.open_text(case_utils.ontology, ttl_filename) as tmp_fh:
-            pass
+            assert tmp_fh
 
 
 def test_case_ontology_version_info_versus_monolithic() -> None:
@@ -49,7 +51,7 @@ def test_case_ontology_version_info_versus_monolithic() -> None:
         )
     ):
         version_info = str(triple[2])
-    assert not version_info is None, "Failed to retrieve owl:versionInfo"
+    assert version_info is not None, "Failed to retrieve owl:versionInfo"
 
     assert (
         CURRENT_CASE_VERSION == version_info
@@ -79,7 +81,7 @@ def test_case_ontology_version_info_versus_submodule() -> None:
         )
     ):
         version_info = str(triple[2])
-    assert not version_info is None, "Failed to retrieve owl:versionInfo"
+    assert version_info is not None, "Failed to retrieve owl:versionInfo"
 
     assert (
         CURRENT_CASE_VERSION == version_info

tests/case_utils/test_guess_format.py

@@ -14,8 +14,6 @@
 import pytest
 import rdflib  # type: ignore
 
-import case_utils
-
 PATH_TO_TTL = "/nonexistent/foo.ttl"
 PATH_TO_JSON = "/nonexistent/foo.json"
 PATH_TO_JSONLD = "/nonexistent/foo.jsonld"

tests/case_utils/test_local_uuid.py

@@ -11,8 +11,6 @@
 #
 # We would appreciate acknowledgement if the software is used.
 
-import os
-
 import pytest
 
 import case_utils.local_uuid

tests/src/compact.py

@@ -20,9 +20,9 @@
 
 __version__ = "0.2.0"
 
+import json
 import logging
 import os
-import json
 import typing
 
 import pyld  # type: ignore
@@ -35,7 +35,7 @@ def main() -> None:
         doc = None
         with open(args.in_json, "r") as in_fh:
             doc = json.load(in_fh)
-        assert not doc is None
+        assert doc is not None
         assert isinstance(
             doc, (dict, list)
         ), "JSON parsed top-level type assumption invalidated"
@@ -46,7 +46,7 @@ def main() -> None:
         def _accrue_local_context(doc_object: typing.Dict[str, typing.Any]) -> None:
             local_context = doc_object.get("@context", dict())
             for key in local_context.keys():
-                if not key in total_context:
+                if key not in total_context:
                     # Accrue new key.
                     total_context[key] = local_context[key]
 

tests/src/glom_graph.py

@@ -19,8 +19,6 @@
 
 import rdflib  # type: ignore
 
-import case_utils
-
 
 def main() -> None:
     g = rdflib.Graph()

tests/src/isomorphic_diff.py

@@ -36,8 +36,6 @@
 
 import rdflib.compare  # type: ignore
 
-import case_utils
-
 _logger = logging.getLogger(os.path.basename(__file__))