Black formatting

Makefile

@@ -76,13 +76,11 @@ servedocs: docs ## compile the docs watching for changes
 	watchmedo shell-command -p '*.md|*.rst' -c '$(MAKE) -C docs html' -R -D .
 
 release: dist ## package and upload a release
-	python setup.py sdist
-	python setup.py bdist_wheel
+	python -m build
 	twine upload dist/*
 
 dist: clean ## builds source and wheel package
-	python setup.py sdist
-	python setup.py bdist_wheel
+	python -m build
 	ls -l dist
 
 install: clean ## install the package to the active Python's site-packages

pysradb/cli.py

@@ -1,5 +1,6 @@
 """Command line interface for pysradb
 """
+
 import argparse
 import os
 import re

pysradb/filter_attrs.py

@@ -108,9 +108,9 @@ def expand_sample_attribute_columns(metadata_df):
         if sample_attribute_keys:
             sample_attribute_keys = list(
                 map(
-                    lambda x: x
-                    if x not in metadata_df.columns.tolist()
-                    else x + "_expanded",
+                    lambda x: (
+                        x if x not in metadata_df.columns.tolist() else x + "_expanded"
+                    ),
                     sample_attribute_keys,
                 )
             )

pysradb/search.py

@@ -1,5 +1,6 @@
 """This file contains the search classes for the search feature.
 """
+
 import os
 import re
 import sys

pysradb/sraweb.py

@@ -71,15 +71,15 @@ def __init__(self, api_key=None):
                  API key for ncbi eutils.
         """
         self.base_url = dict()
-        self.base_url[
-            "esummary"
-        ] = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi"
-        self.base_url[
-            "esearch"
-        ] = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"
-        self.base_url[
-            "efetch"
-        ] = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi"
+        self.base_url["esummary"] = (
+            "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi"
+        )
+        self.base_url["esearch"] = (
+            "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"
+        )
+        self.base_url["efetch"] = (
+            "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi"
+        )
 
         self.ena_fastq_search_url = "https://www.ebi.ac.uk/ena/portal/api/filereport"
         self.ena_params = [("result", "read_run"), ("fields", "fastq_ftp")]
@@ -411,7 +411,7 @@ def sra_metadata(
         detailed=False,
         expand_sample_attributes=False,
         output_read_lengths=False,
-        **kwargs
+        **kwargs,
     ):
         esummary_result = self.get_esummary_response("sra", srp)
         try: