Fix what was that?

Author: Christian Fufezan

pymzml/regex_patterns.py

@@ -1,4 +1,5 @@
 """Collection of regular expressions to catch spectrum XML-tags."""
+
 import re
 import regex
 

pymzml/run.py

@@ -84,7 +84,7 @@ def __init__(
         build_index_from_scratch=False,
         skip_chromatogram=True,
         index_regex=None,
-        **kwargs
+        **kwargs,
     ):
         """Initialize and set required attributes."""
         self.index_regex = index_regex
@@ -296,7 +296,7 @@ def _obo_version_validator(version):
             2018: "4.1.10",
             2019: "4.1.22",
             2024: "4.1.79",
-            2025: "4.1.188"
+            2025: "4.1.188",
         }
         version_fixed = None
         if obo_rgx.match(version):
@@ -406,8 +406,8 @@ def _init_iter(self):
                 self.info["data_processing_list"] = True
                 self.info["data_processing_list_element"] = element
             elif element.tag.endswith("}cvParam"):
-                if self.term_is_a_member(element.attrib.get('accession'), "MS:1000494"):
-                    self.info["instrument_name"] = element.attrib.get('name')
+                if self.term_is_a_member(element.attrib.get("accession"), "MS:1000494"):
+                    self.info["instrument_name"] = element.attrib.get("name")
 
             elif element.tag.endswith("}spectrumList"):
                 spec_cnt = element.attrib.get("count")
@@ -470,9 +470,9 @@ def term_is_a_member(self, tested_term, member_of_term):
         try:
             term_in = self.OT[tested_term]
             if term_in:
-                is_member = self.OT.id[tested_term]['is_a'].startswith(member_of_term)
+                is_member = self.OT.id[tested_term]["is_a"].startswith(member_of_term)
         except KeyError:
-            print(f'term not found ({tested_term})')
+            print(f"term not found ({tested_term})")
         return is_member
 
 

pymzml/utils/GSGW.py

@@ -256,7 +256,7 @@ def _write_identifier(self, identifier):
         Arguments:
             identifier (str or int): identifier to write into index
         """
-        id_format = "{0:\xAC>" + str(self.max_idx_len) + "}"
+        id_format = "{0:\xac>" + str(self.max_idx_len) + "}"
         identifier = str(identifier)
         identifier = id_format.format(identifier).encode("latin-1")
         self.file_out.write(identifier)
@@ -270,7 +270,7 @@ def _write_offset(self, offset):
             offset (int): offset which will be formatted and written
                 into file index
         """
-        offset_format = "{0:\xAC>" + str(self.max_offset_len) + "}"
+        offset_format = "{0:\xac>" + str(self.max_offset_len) + "}"
         offset = str(offset)
         offset = offset_format.format(offset).encode("latin-1")
         self.file_out.write(offset)

tests/main_reader_test.py

@@ -30,7 +30,7 @@ def setUp(self):
         self.reader_uncompressed_unindexed = run.Reader(file_uncompressed_unindexed)
         self.reader_bad_obo_version = run.Reader(file_bad_obo_version)
         self.reader_set_obo_version = run.Reader(
-            file_bad_obo_version, obo_version="3.25.0"
+            file_bad_obo_version, obo_version="4.1.79"
         )
         self.reader_set_year_obo_version = run.Reader(
             file_uncompressed_indexed, obo_version="23:06:2017"
@@ -76,7 +76,7 @@ def test_init_iter(self):
         run_id = self.reader_uncompressed_unindexed.info["run_id"]
         start_time = self.reader_uncompressed_unindexed.info["start_time"]
         self.assertEqual(mzml_version, "1.1.0")
-        self.assertEqual(obo_version, "3.25.0")
+        self.assertEqual(obo_version, "4.1.79")
         self.assertIsInstance(spec_count, int)
         self.assertEqual(run_id, "exp105-01-ds5562-Pos")
         self.assertEqual(start_time, "2013-09-10T10:31:08Z")
@@ -87,7 +87,7 @@ def test_init_iter(self):
         run_id = self.reader_uncompressed_unindexed.info["run_id"]
         start_time = self.reader_uncompressed_unindexed.info["start_time"]
         self.assertEqual(mzml_version, "1.1.0")
-        self.assertEqual(obo_version, "3.25.0")
+        self.assertEqual(obo_version, "4.1.79")
         self.assertIsInstance(spec_count, int)
         self.assertEqual(run_id, "exp105-01-ds5562-Pos")
         self.assertEqual(start_time, "2013-09-10T10:31:08Z")
@@ -98,7 +98,7 @@ def test_init_iter(self):
         run_id = self.reader_uncompressed_unindexed.info["run_id"]
         start_time = self.reader_uncompressed_unindexed.info["start_time"]
         self.assertEqual(mzml_version, "1.1.0")
-        self.assertEqual(obo_version, "3.25.0")
+        self.assertEqual(obo_version, "4.1.79")
         self.assertIsInstance(spec_count, int)
         self.assertEqual(run_id, "exp105-01-ds5562-Pos")
         self.assertEqual(start_time, "2013-09-10T10:31:08Z")
@@ -110,7 +110,7 @@ def test_init_iter(self):
         start_time = self.reader_uncompressed_unindexed.info["start_time"]
 
         self.assertEqual(mzml_version, "1.1.0")
-        self.assertEqual(obo_version, "3.25.0")
+        self.assertEqual(obo_version, "4.1.79")
         self.assertIsInstance(spec_count, int)
         self.assertEqual(run_id, "exp105-01-ds5562-Pos")
         self.assertEqual(start_time, "2013-09-10T10:31:08Z")
@@ -135,7 +135,7 @@ def test_init_iter(self):
         start_time = self.reader_set_obo_version.info["start_time"]
 
         self.assertEqual(mzml_version, "1.1.0")
-        self.assertEqual(obo_version, "3.25.0")
+        self.assertEqual(obo_version, "4.1.79")
         self.assertIsInstance(spec_count, int)
         self.assertEqual(run_id, "exp105-01-ds5562-Pos")
         self.assertEqual(start_time, "2013-09-10T10:31:08Z")