From dc69e02c142d740b5c78ac33ce0e352b4a1e670a Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 30 Sep 2024 14:09:59 +0000
Subject: [PATCH] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 geneplexus/_geneplexus.py |  2 +-
 geneplexus/download.py    | 19 ++++++++++---------
 geneplexus/geneplexus.py  |  2 +-
 3 files changed, 12 insertions(+), 11 deletions(-)

diff --git a/geneplexus/_geneplexus.py b/geneplexus/_geneplexus.py
index 152b211..31e3868 100644
--- a/geneplexus/_geneplexus.py
+++ b/geneplexus/_geneplexus.py
@@ -70,7 +70,7 @@ def _initial_id_convert(input_genes, file_loc, species):
                     agene,
                     converted_gene or "Could Not be mapped to Entrez",
                     converted_gene_name or "Could Not be mapped to Entrez",
-                ]
+                ],
             )
 
     column_names = ["Original ID", "Entrez ID", "Gene Name"]
diff --git a/geneplexus/download.py b/geneplexus/download.py
index e79cb38..7fa5eb9 100755
--- a/geneplexus/download.py
+++ b/geneplexus/download.py
@@ -2,6 +2,7 @@
 import io
 import os
 import os.path as osp
+import tarfile
 import time
 from concurrent.futures import ThreadPoolExecutor
 from itertools import repeat
@@ -11,7 +12,6 @@
 from typing import Union
 from urllib.parse import urljoin
 from zipfile import ZipFile
-import tarfile
 
 import requests
 from requests.sessions import Session
@@ -19,10 +19,10 @@
 from . import util
 from ._config import logger
 from ._config.config import ALL_SPECIES
-from ._config.config import SPECIES_SELECTION_TYPE
-from ._config.config import SPECIES_TYPE
 from ._config.config import LOG_LEVEL_TYPE
 from ._config.config import MAX_RETRY
+from ._config.config import SPECIES_SELECTION_TYPE
+from ._config.config import SPECIES_TYPE
 from ._config.config import URL_DICT
 from ._config.logger_util import file_handler_context
 from ._config.logger_util import stream_level_context
@@ -66,7 +66,6 @@ def download_select_data(
                 logger.warn(
                     f"Files already downloaded for {aspecies}",
                 )
-                
 
 
 def _get_species_list(
@@ -83,13 +82,14 @@ def _get_species_list(
         if i not in ALL_SPECIES:
             raise ValueError(f"Unexpected species {i!r}")
     return species
-    
+
+
 def _check_all_files(
     data_dir: str,
     aspecies: str,
 ):
     fn_end = f"data_filenames_{aspecies}.txt"
-    fn_full = osp.join(data_dir,fn_end)
+    fn_full = osp.join(data_dir, fn_end)
     # check if filenames file is present
     if not osp.exists(fn_full):
         return False
@@ -102,7 +102,8 @@ def _check_all_files(
         if len(files_missing) > 0:
             return False
         else:
-            return True 
+            return True
+
 
 def _download_and_extract(data_dir, aspecies, fn_download, data_loc, retry):
     session = requests.Session()
@@ -116,9 +117,9 @@ def _download_and_extract(data_dir, aspecies, fn_download, data_loc, retry):
                 with tarfile.open(fileobj=io.BytesIO(r.content), mode="r:gz") as tf:
                     for member in tf.getmembers():
                         member.name = os.path.basename(member.name)
-                        tf.extract(member,data_dir)    
+                        tf.extract(member, data_dir)
                         logger.info(f"Downloaded {member.name}")
-                if _check_all_files(data_dir, aspecies):    
+                if _check_all_files(data_dir, aspecies):
                     break
                 else:
                     logger.warning(f"Not all files downloaded, trying again")
diff --git a/geneplexus/geneplexus.py b/geneplexus/geneplexus.py
index 82d31e9..e8b5450 100755
--- a/geneplexus/geneplexus.py
+++ b/geneplexus/geneplexus.py
@@ -87,7 +87,7 @@ def __init__(
         elif self.auto_download:
             download_select_data(
                 self.file_loc,
-                list(set([self.sp_trn,self.sp_tst])),
+                list({self.sp_trn, self.sp_tst}),
                 log_level=log_level,
             )