Ruff format fix

analysis/parse-opensnp-files/parse_opensnp_files.py

@@ -29,7 +29,7 @@
 
 # setup logger to output to file in output directory
 logging.basicConfig(
-    filename=f'{os.path.join(OUTPUT_DIR, "parse-opensnp-files.txt")}',
+    filename=f"{os.path.join(OUTPUT_DIR, 'parse-opensnp-files.txt')}",
     format="%(asctime)s: %(message)s",
     filemode="w",
     level=logging.INFO,

analysis/xy-chrom-snp-ratios/xy-chrom-snp-ratios.py

@@ -185,7 +185,7 @@ def create_analysis_plot(
         va="top",
     )
     ax_scatter.annotate(
-        f"n={ len(df_ratios.loc[(df_ratios.heterozygous_x_snps_ratio < heterozygous_x_snps_threshold)& (df_ratios.y_snps_not_null_ratio >= y_snps_not_null_threshold)])}",
+        f"n={len(df_ratios.loc[(df_ratios.heterozygous_x_snps_ratio < heterozygous_x_snps_threshold) & (df_ratios.y_snps_not_null_ratio >= y_snps_not_null_threshold)])}",
         (
             heterozygous_x_snps_threshold - x_offset,
             y_snps_not_null_threshold + y_offset,
@@ -194,7 +194,7 @@ def create_analysis_plot(
         va="bottom",
     )
     ax_scatter.annotate(
-        f"n={len(df_ratios.loc[ (df_ratios.heterozygous_x_snps_ratio >= heterozygous_x_snps_threshold) & (df_ratios.y_snps_not_null_ratio >= y_snps_not_null_threshold)])}",
+        f"n={len(df_ratios.loc[(df_ratios.heterozygous_x_snps_ratio >= heterozygous_x_snps_threshold) & (df_ratios.y_snps_not_null_ratio >= y_snps_not_null_threshold)])}",
         (
             heterozygous_x_snps_threshold + x_offset,
             y_snps_not_null_threshold + y_offset,

src/snps/io/writer.py

@@ -124,7 +124,7 @@ def _write_csv(self):
         comment = [
             f"# Source(s): {self._snps.source}",
             f"# Build: {self._snps.build}",
-            f"# Build Detected: { self._snps.build_detected}",
+            f"# Build Detected: {self._snps.build_detected}",
             f"# Phased: {self._snps.phased}",
             f"# SNPs: {self._snps.count}",
             f"# Chromosomes: {self._snps.chromosomes_summary}",
@@ -166,7 +166,7 @@ def _write_vcf(self):
 
         comment = [
             "##fileformat=VCFv4.3",
-            f'##fileDate={get_utc_now().strftime("%Y%m%d")}',
+            f"##fileDate={get_utc_now().strftime('%Y%m%d')}",
             f'##source="snps v{snps.__version__}; https://pypi.org/project/snps/"',
             f'##detectedCompany="{self._snps.source}"',
         ]

src/snps/utils.py

@@ -147,7 +147,7 @@ def save_df_as_csv(
         if prepend_info:
             s = (
                 f"# Generated by snps v{snps.__version__}, https://pypi.org/project/snps/\n"
-                f'# Generated at {get_utc_now().strftime("%Y-%m-%d %H:%M:%S")} UTC\n'
+                f"# Generated at {get_utc_now().strftime('%Y-%m-%d %H:%M:%S')} UTC\n"
             )
         else:
             s = ""

tests/io/test_reader.py

@@ -174,7 +174,7 @@ def test_read_ftdna_concat_gzip_extra_data(self):
         # generate content of second file
         s2 = "RSID,CHROMOSOME,POSITION,RESULT\r\n"
         for i in range(0, total_snps2):
-            s2 += f'"rs{total_snps1 + 1 + i}","1","{ total_snps1 + 101 + i}","AA"\r\n'
+            s2 += f'"rs{total_snps1 + 1 + i}","1","{total_snps1 + 101 + i}","AA"\r\n'
         snps_df = self.create_snp_df(
             rsid=[f"rs{1 + i}" for i in range(0, total_snps1 + total_snps2)],
             chrom="1",

tests/test_resources.py

@@ -184,7 +184,7 @@ def f():
             self.assertEqual(
                 seqs["MT"].path,
                 os.path.relpath(
-                    f'{os.path.join(self.resource._resources_dir,"fasta", assembly_expect,os.path.basename(url_expect))}'
+                    f"{os.path.join(self.resource._resources_dir, 'fasta', assembly_expect, os.path.basename(url_expect))}"
                 ),
             )
             self.assertTrue(os.path.exists(seqs["MT"].path))
@@ -261,7 +261,7 @@ def f():
             self.assertEqual(
                 seqs["MT"].path,
                 os.path.relpath(
-                    f'{os.path.join(self.resource._resources_dir,"fasta", "GRCh37","Homo_sapiens.GRCh37.dna.chromosome.MT.fa.gz")}'
+                    f"{os.path.join(self.resource._resources_dir, 'fasta', 'GRCh37', 'Homo_sapiens.GRCh37.dna.chromosome.MT.fa.gz')}"
                 ),
             )
             self.assertTrue(os.path.exists(seqs["MT"].path))

versioneer.py

@@ -1837,9 +1837,9 @@ def get_versions(verbose: bool = False) -> Dict[str, Any]:
     handlers = HANDLERS.get(cfg.VCS)
     assert handlers, "unrecognized VCS '%s'" % cfg.VCS
     verbose = verbose or bool(cfg.verbose)  # `bool()` used to avoid `None`
-    assert (
-        cfg.versionfile_source is not None
-    ), "please set versioneer.versionfile_source"
+    assert cfg.versionfile_source is not None, (
+        "please set versioneer.versionfile_source"
+    )
     assert cfg.tag_prefix is not None, "please set versioneer.tag_prefix"
 
     versionfile_abs = os.path.join(root, cfg.versionfile_source)