Merge branch 'main' into consider-using-get

Author: tcmitchell

sbol3/document.py

@@ -4,13 +4,12 @@
 import logging
 import os
 import posixpath
-import warnings
-from pathlib import Path
-from typing import Dict, Callable, List, Optional, Any, Union, Iterable
-
 # import typing for typing.Sequence, which we don't want to confuse
 # with sbol3.Sequence
 import typing as pytyping
+import warnings
+from pathlib import Path
+from typing import Any, Callable, Dict, Iterable, List, Optional, Union
 
 import pyshacl
 import rdflib
@@ -124,7 +123,7 @@ def _build_extension_object(self, identity: str, sbol_type: str,
                 build_type = type_uri
                 break
             except KeyError:
-                logging.warning(f'No builder found for {type_uri}')
+                logging.warning('No builder for %s', type_uri)
         if builder is None:
             builder = custom_types[sbol_type]
             build_type = types[0]
@@ -162,7 +161,7 @@ def _build_object(self, identity: str, types: List[str]) -> Optional[Identified]
             try:
                 builder = self._uri_type_map[sbol_type]
             except KeyError:
-                logging.warning(f'No builder found for {sbol_type}')
+                logging.warning('No builder found for %s', sbol_type)
                 raise SBOLError(f'Unknown type {sbol_type}')
             result = builder(identity=identity, type_uri=sbol_type)
         # Fix https://github.com/SynBioDex/pySBOL3/issues/264

sbol3/object.py

@@ -3,8 +3,8 @@
 import uuid
 import warnings
 from collections import defaultdict
+from typing import Callable, Dict, Optional, Union
 from urllib.parse import urlparse
-from typing import Dict, Callable, Optional, Union
 
 from . import *
 
@@ -115,7 +115,7 @@ def copy(self, target_doc=None, target_namespace=None):
         try:
             builder = BUILDER_REGISTER[self.type_uri]
         except KeyError:
-            logging.warning(f'No builder found for {self.type_uri}; assuming {self.__class__.__name__}')
+            logging.warning('No builder found for %s; assuming %s', self.type_uri, self.__class__.__name__)
             builder = self.__class__
         new_obj = builder(**dict(identity=new_uri, type_uri=self.type_uri))
 

sbol3/toplevel.py

@@ -3,11 +3,11 @@
 import copy
 import math
 import posixpath
+import typing
 import urllib.parse
 import uuid
 import warnings
-from typing import Dict, Callable, Optional, Any
-import typing
+from typing import Any, Callable, Dict, Optional
 
 from . import *
 from .typing import *
@@ -234,8 +234,8 @@ def update_references_traverser(x):
             if v.property_uri not in x._properties:
                 continue
             items = x._properties[v.property_uri]
-            for i in range(len(items)):
-                str_item = str(items[i])
+            for i, item in enumerate(items):
+                str_item = str(item)
                 if str_item in identity_map:
                     new_reference = identity_map[str_item].identity
                     # The item is probably an rdflib.URIRef. We take

setup.cfg

@@ -14,12 +14,8 @@ max-line-length = 119
 disable = abstract-class-instantiated,
           attribute-defined-outside-init,
           catching-non-exception,
-          consider-using-generator,
           disallowed-name,
-          implicit-str-concat,
           import-outside-toplevel,
-          logging-not-lazy,
-          consider-using-enumerate,
           consider-using-f-string,
           cyclic-import,
           duplicate-code,
@@ -29,7 +25,6 @@ disable = abstract-class-instantiated,
           inconsistent-return-statements,
           invalid-name,
           isinstance-second-argument-not-valid-type,
-          logging-fstring-interpolation,
           missing-class-docstring,
           missing-function-docstring,
           missing-module-docstring,

test/test_component.py

@@ -148,8 +148,7 @@ def test_cloning_references(self):
         doc2 = sbol3.Document()
         doc2.add(toggle_clone)
         self.assertEqual(len(toggle.constraints), len(toggle_clone.constraints))
-        for i in range(len(toggle.constraints)):
-            c = toggle.constraints[i]
+        for i, c in enumerate(toggle.constraints):
             c_clone = toggle_clone.constraints[i]
             self.assertNotEqual(c.identity, c_clone.identity)
             s = c.subject.lookup()

test/test_document.py

@@ -125,15 +125,15 @@ def test_add_iterable(self):
         sbol3.set_namespace('https://github.com/synbiodex/pysbol3')
         doc = sbol3.Document()
         objects = [sbol3.Component(name, types=[sbol3.SBO_DNA])
-                   for name in ['foo', 'bar', 'baz' 'quux']]
+                   for name in ['foo', 'bar', 'baz', 'quux']]
         result = doc.add(objects)
         self.assertEqual(len(objects), len(result))
         self.assertListEqual(objects, result)
         #
         # Test adding a non-TopLevel in a list
         doc = sbol3.Document()
         objects = [sbol3.Component(name, types=[sbol3.SBO_DNA])
-                   for name in ['foo', 'bar', 'baz' 'quux']]
+                   for name in ['foo', 'bar', 'baz', 'quux']]
         objects.insert(2, 'non-TopLevel')
         with self.assertRaises(TypeError):
             doc.add(objects)
@@ -736,14 +736,14 @@ def test_ntriples_blank_line(self):
         doc.add(c1)
         output = doc.write_string(file_format=sbol3.NTRIPLES)
         lines = output.splitlines()
-        num_blanks = sum([1 for line in lines if not line])
+        num_blanks = sum(1 for line in lines if not line)
         # Expecting no blank lines
         self.assertEqual(0, num_blanks)
 
         # Now test sorted n-triples
         sorted_output = doc.write_string(file_format=sbol3.SORTED_NTRIPLES)
         sorted_lines = sorted_output.splitlines()
-        num_blanks = sum([1 for line in sorted_lines if not line])
+        num_blanks = sum(1 for line in sorted_lines if not line)
         # Expecting no blank lines
         self.assertEqual(0, num_blanks)
 

test/test_examples.py

@@ -1,10 +1,11 @@
 import logging
 import os
+import shutil
 import subprocess
 import sys
-import unittest
 import tempfile
-import shutil
+import unittest
+
 import rdflib
 import rdflib.compare
 
@@ -48,8 +49,8 @@ def test_circuit_example(self):
         expected_iso = rdflib.compare.to_isomorphic(expected_graph)
         rdf_diff = rdflib.compare.graph_diff(expected_iso, actual_iso)
         if rdf_diff[1] or rdf_diff[2]:
-            self.logger.warning('Detected %d different RDF triples in %s' %
-                                (len(rdf_diff[1]) + len(rdf_diff[2]), out_path))
+            self.logger.warning('Detected %d different RDF triples in %s',
+                                len(rdf_diff[1]) + len(rdf_diff[2]), out_path)
             for stmt in rdf_diff[1]:
                 self.logger.warning('Only in expected: %r', stmt)
             for stmt in rdf_diff[2]:

test/test_roundtrip.py

@@ -147,8 +147,11 @@ def run_round_trip_file(self, test_path, file_format):
         iso2 = rdflib.compare.to_isomorphic(g2)
         rdf_diff = rdflib.compare.graph_diff(iso1, iso2)
         if rdf_diff[1] or rdf_diff[2]:
-            self.logger.warning('Detected %d different RDF triples in %s' %
-                                (len(rdf_diff[1]) + len(rdf_diff[2]), test_path))
+            self.logger.warning(
+                'Detected %d different RDF triples in %s',
+                len(rdf_diff[1]) + len(rdf_diff[2]), test_path
+            )
+
             if not self.logger.isEnabledFor(logging.DEBUG):
                 self.logger.warning('Set environment variable %s to see details',
                                     DEBUG_ENV_VAR)
@@ -165,7 +168,7 @@ def test_sbol3_files(self):
             for test_file in self.find_all_files(test_dir):
                 basename = os.path.basename(test_file)
                 if os.path.splitext(basename)[0] in skip_list:
-                    self.logger.debug(f'Skipping {test_file}')
+                    self.logger.debug('Skipping %s', test_file)
                     continue
                 file_format = self.rdf_type(test_file)
                 if not file_format: