Fix linting issues

.github/workflows/ci.yml

@@ -117,7 +117,7 @@ jobs:
       run: |
         pytest --cov=snps tests
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
 
   test-extras:
     needs: [lint-format, build-docs]

analysis/parse-opensnp-files/get_file.py

@@ -3,6 +3,7 @@
 import os
 
 from atomicwrites import atomic_write
+
 from snps.resources import Resources
 from snps.utils import create_dir
 

analysis/parse-opensnp-files/parse_opensnp_files.py

@@ -13,6 +13,7 @@
 
 import pandas as pd
 from atomicwrites import atomic_write
+
 from snps import SNPs
 from snps.resources import Resources
 from snps.utils import Parallelizer, clean_str, create_dir, save_df_as_csv

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

@@ -7,6 +7,7 @@
 import pandas as pd
 from atomicwrites import atomic_write
 from matplotlib import patches
+
 from snps import SNPs
 from snps.resources import Resources
 from snps.utils import Parallelizer, create_dir, save_df_as_csv

tests/__init__.py

@@ -7,6 +7,7 @@
 import numpy as np
 import pandas as pd
 from pandas.api.types import is_object_dtype, is_unsigned_integer_dtype
+
 from snps import SNPs
 from snps.utils import gzip_file, zip_file
 

tests/io/test_reader.py

@@ -2,9 +2,9 @@
 import tempfile
 
 from atomicwrites import atomic_write
+
 from snps.resources import Resources
 from snps.utils import gzip_file
-
 from tests import BaseSNPsTestCase
 
 

tests/io/test_writer.py

@@ -3,10 +3,10 @@
 
 import numpy as np
 import pandas as pd
+
 from snps import SNPs
 from snps.resources import ReferenceSequence, Resources
 from snps.utils import gzip_file
-
 from tests import BaseSNPsTestCase
 
 

tests/test_resources.py

@@ -10,10 +10,10 @@
 import numpy as np
 import pandas as pd
 from atomicwrites import atomic_write
+
 from snps import SNPs
 from snps.resources import ReferenceSequence, Resources
 from snps.utils import gzip_file
-
 from tests import BaseSNPsTestCase
 
 

tests/test_snps.py

@@ -9,9 +9,9 @@
 
 import numpy as np
 import pandas as pd
+
 from snps import SNPs
 from snps.io import get_empty_snps_dataframe
-
 from tests import BaseSNPsTestCase