Merge pull request #322 from GC-repeat/iss313_pylinting

Fix #313

.github/workflows/python_linter.yaml

@@ -29,7 +29,7 @@ jobs:
           find . -type f -name "*.py" |
           xargs pylint
           --max-line-length=120
-          --disable=C0103,C0114,C0115,C0116,C0201,C0206,C0301,C0303,C0325,C0411
+          --disable=C0103,C0114,C0115,C0116,C0201,C0206,C0325,C0411
           --disable=E0611
           --disable=R0402,R0801,R0903,R0912,R0914,R0915,R1702,R1705,R1720,R1721,R1724
           --disable=W0212,W0511,W0611,W0612,W0622,W1309,W1203,W1512,W1514
@@ -48,4 +48,4 @@ jobs:
           path: "."
           max-line-length: 120
           update-pip: TRUE
-          ignore: E121,E203,E226,E231,E251,E265,E302,E305,E501,F401,F403,F541,W291,W503
+          ignore: E121,F401,F403,F541,W503

scripts/scriptutils/conversions.py

@@ -19,9 +19,11 @@ def convert_package_sbol2_files(package: str) -> dict[str, str]:
     mappings = {}
 
     # import SBOL2
-    for file in itertools.chain(*(glob.glob(os.path.join(package, f'*{ext}')) for ext in GENETIC_DESIGN_FILE_TYPES['SBOL2'])):
+    for file in itertools.chain(
+        *(glob.glob(os.path.join(package, f'*{ext}')) for ext in GENETIC_DESIGN_FILE_TYPES['SBOL2'])
+    ):
         print(f'Attempting to convert SBOL2 file {file}')
-        file3 = os.path.splitext(file)[0]+'.nt'  # make an SBOL3 version of the file name
+        file3 = os.path.splitext(file)[0] + '.nt'  # make an SBOL3 version of the file name
         doc2 = sbol2.Document()
         doc2.read(file)  # confirm that it is, in fact, an SBOL2 file
         doc3 = convert2to3(file)

scripts/scriptutils/helpers.py

@@ -20,7 +20,7 @@ def vector_to_insert(component: sbol3.Component) -> sbol3.Component:
     if len(subvectors) == 0 and not is_plasmid(component):
         return component
     # otherwise, if there's precisely one non-vector subcomponent, return the Component it points to
-    inserts = {f for f in set(component.features)-subvectors if isinstance(f, sbol3.SubComponent)}
+    inserts = {f for f in set(component.features) - subvectors if isinstance(f, sbol3.SubComponent)}
     if len(inserts) == 1:
         return inserts.pop().instance_of.lookup()
     elif len(inserts) == 0:
@@ -54,11 +54,11 @@ def remove_duplicate_prefix(name: str) -> str:
     """
     components = name.split('_')
     # check from largest possible repeated block to smallest
-    for i in reversed(range(1, math.floor(len(components)/2)+1)):
+    for i in reversed(range(1, math.floor(len(components) / 2) + 1)):
         # Check if there is a repeated block at the front
-        if components[0:i] == components[i:(2*i)]:
-            if components[2*i] == 'ins':  # also remove insertion markers
-                ins_less = "_".join(name.split("_")[0:i] + [name.split("_", (2*i)+1)[-1]])
+        if components[0:i] == components[i:(2 * i)]:
+            if components[2 * i] == 'ins':  # also remove insertion markers
+                ins_less = "_".join(name.split("_")[0:i] + [name.split("_", (2 * i) + 1)[-1]])
                 return ins_less
             else:
                 return name.split('_', i)[-1]
@@ -77,7 +77,7 @@ def truncate_by_underscores(name: str, max_len: int) -> str:
         if len(components) > 1:
             name = components[-1]
         else:
-            name = name[(len(name)-max_len):]
+            name = name[(len(name) - max_len):]
     return name
 
 

scripts/scriptutils/package_specification.py

@@ -79,7 +79,8 @@ def export_sbol(package: str) -> sbol3.Document:
     """
     # get workbook and perform conversion
     excel_file = package_excel(package)
-    sbol3.set_namespace(package_stem(package))  # TODO: update after resolution of https://github.com/SynBioDex/pySBOL3/issues/288
+    sbol3.set_namespace(package_stem(package))  # TODO: update after resolution of https://github.com/SynBioDex/pySBOL3/issues/288 # pylint: disable=C0301 # noqa: E501
+
     with warnings.catch_warnings():
         warnings.simplefilter("ignore", category=UserWarning)  # filter the "data validation not supported" warning
         wb = openpyxl.open(excel_file, data_only=True)

scripts/test/helpers.py

@@ -5,7 +5,7 @@
 from scripts.scriptutils import EXPORT_DIRECTORY
 
 
-def copy_to_tmp(package: list[str] = None, exports: list[str] = None, renames: dict[str,str] = None) -> str:
+def copy_to_tmp(package: list[str] = None, exports: list[str] = None, renames: dict[str, str] = None) -> str:
     """Copy test files into a temporary package directory
 
     :param package: list of files to go into the package directory
@@ -31,6 +31,6 @@ def copy_to_tmp(package: list[str] = None, exports: list[str] = None, renames: d
         copy(os.path.join(test_dir, 'test_files', f), tmp_sub)
     for f in exports:
         copy(os.path.join(test_dir, 'test_files', EXPORT_DIRECTORY, f), tmp_export)
-    for old_f,new_f in renames.items():
+    for old_f, new_f in renames.items():
         copy(os.path.join(test_dir, 'test_files', old_f), os.path.join(tmp_sub, new_f))
     return tmp_sub

scripts/test/test_conversion.py

@@ -9,7 +9,7 @@
 class Test2To3Conversion(unittest.TestCase):
     def test_2to3_package_conversion(self):
         """Test ability to convert parts already in a directory"""
-        tmpsub = copy_to_tmp(package = ['test_sequence.fasta', 'two_sequences.gb', 'BBa_J23101.xml'])
+        tmpsub = copy_to_tmp(package=['test_sequence.fasta', 'two_sequences.gb', 'BBa_J23101.xml'])
         mappings = scripts.scriptutils.convert_package_sbol2_files(tmpsub)
         expected = {os.path.join(tmpsub, 'BBa_J23101.xml'): os.path.join(tmpsub, 'BBa_J23101.nt')}
         assert mappings == expected, f'Conversion mappings do not match expected value: {mappings}'
@@ -21,8 +21,8 @@ def test_2to3_package_conversion(self):
 
     def test_2to3_package_merge(self):
         """Test ability to convert parts already in a directory"""
-        tmpsub = copy_to_tmp(package = ['test_sequence.fasta', 'two_sequences.gb', 'BBa_J23101.xml'],
-                             renames = {'BBa_J23101_and_J23102.nt': 'BBa_J23101.nt'})
+        tmpsub = copy_to_tmp(package=['test_sequence.fasta', 'two_sequences.gb', 'BBa_J23101.xml'],
+                             renames={'BBa_J23101_and_J23102.nt': 'BBa_J23101.nt'})
         mappings = scripts.scriptutils.convert_package_sbol2_files(tmpsub)
         expected = {os.path.join(tmpsub, 'BBa_J23101.xml'): os.path.join(tmpsub, 'BBa_J23101.nt')}
         assert mappings == expected, f'Conversion mappings do not match expected value: {mappings}'
@@ -32,5 +32,6 @@ def test_2to3_package_merge(self):
         assert filecmp.cmp(os.path.join(tmpsub, 'BBa_J23101.nt'), comparison_file), \
             f'Converted file {comparison_file} is not identical'
 
+
 if __name__ == '__main__':
     unittest.main()

scripts/test/test_helpers.py

@@ -12,22 +12,22 @@ def test_duplicate_name_removal(self):
         self.assertEqual(helpers.remove_duplicate_prefix('foo_bar_baz'), 'foo_bar_baz')
         self.assertEqual(helpers.remove_duplicate_prefix('foo_foo_bar'), 'foo_bar')
         self.assertEqual(helpers.remove_duplicate_prefix('foo_foo_bar_baz'), 'foo_bar_baz')
-        self.assertEqual(helpers.remove_duplicate_prefix('foo_foo_foo_foo_bar_baz'), 
+        self.assertEqual(helpers.remove_duplicate_prefix('foo_foo_foo_foo_bar_baz'),
                          'foo_foo_bar_baz')
-        self.assertEqual(helpers.remove_duplicate_prefix('foo_qux_foo_qux_bar_baz'), 
+        self.assertEqual(helpers.remove_duplicate_prefix('foo_qux_foo_qux_bar_baz'),
                          'foo_qux_bar_baz')
-        self.assertEqual(helpers.remove_duplicate_prefix('foo_qux_zap_foo_qux_zap_bar_baz'), 
+        self.assertEqual(helpers.remove_duplicate_prefix('foo_qux_zap_foo_qux_zap_bar_baz'),
                          'foo_qux_zap_bar_baz')
         # removing insert markers when appropriate
         self.assertEqual(helpers.remove_duplicate_prefix('foo_ins_bar'), 'foo_ins_bar')
         self.assertEqual(helpers.remove_duplicate_prefix('foo_ins_bar_baz'), 'foo_ins_bar_baz')
         self.assertEqual(helpers.remove_duplicate_prefix('foo_foo_ins_bar'), 'foo_bar')
         self.assertEqual(helpers.remove_duplicate_prefix('foo_foo_ins_bar_baz'), 'foo_bar_baz')
-        self.assertEqual(helpers.remove_duplicate_prefix('foo_foo_foo_foo_ins_bar_baz'), 
+        self.assertEqual(helpers.remove_duplicate_prefix('foo_foo_foo_foo_ins_bar_baz'),
                          'foo_foo_bar_baz')
-        self.assertEqual(helpers.remove_duplicate_prefix('foo_qux_foo_qux_ins_bar_baz'), 
+        self.assertEqual(helpers.remove_duplicate_prefix('foo_qux_foo_qux_ins_bar_baz'),
                          'foo_qux_bar_baz')
-        self.assertEqual(helpers.remove_duplicate_prefix('foo_qux_zap_foo_qux_zap_ins_bar_baz'), 
+        self.assertEqual(helpers.remove_duplicate_prefix('foo_qux_zap_foo_qux_zap_ins_bar_baz'),
                          'foo_qux_zap_bar_baz')
 
     def test_name_truncation(self):

scripts/test/test_import.py

@@ -68,8 +68,9 @@ def test_all_import_types(self):
 
         # first round of import should obtain all but one missing part
         retrieved = part_retrieval.import_parts(tmp_sub)
-        #assert len(retrieved) == 7  # all but the local file and LCP SynBioHub
-        github_prefix = 'https://raw.githubusercontent.com/iGEM-Engineering/iGEM-distribution/develop/scripts/test/test_files'
+        # assert len(retrieved) == 7  # all but the local file and LCP SynBioHub
+        github_prefix = ('https://raw.githubusercontent.com/'
+                         'iGEM-Engineering/iGEM-distribution/develop/scripts/test/test_files')
         expected = ['https://www.ncbi.nlm.nih.gov/nuccore/JWYZ01000115_1',  # NCBI
                     'http://parts.igem.org/BBa_J364007',  # iGEM FASTA
                     'http://parts.igem.org/J23100',  # iGEM SynBioHub

scripts/test/test_markdown_generation.py

@@ -44,5 +44,6 @@ def test_distribution_readme_generation(self):
         comparison_file = os.path.join(test_dir, 'test_files', 'distribution', DISTRIBUTION_SUMMARY)
         assert filecmp.cmp(generated_file, comparison_file), f'Generated file {generated_file} is not identical'
 
+
 if __name__ == '__main__':
     unittest.main()