From 0cd809ee7d8c8808214c09b27bac6bde3abf44c4 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 22 Mar 2024 07:30:56 +0000
Subject: [PATCH 1/2] Bump pytest-mock from 3.11.1 to 3.14.0

Bumps [pytest-mock](https://github.com/pytest-dev/pytest-mock) from 3.11.1 to 3.14.0.
- [Release notes](https://github.com/pytest-dev/pytest-mock/releases)
- [Changelog](https://github.com/pytest-dev/pytest-mock/blob/main/CHANGELOG.rst)
- [Commits](https://github.com/pytest-dev/pytest-mock/compare/v3.11.1...v3.14.0)

---
updated-dependencies:
- dependency-name: pytest-mock
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 requirements-dev.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements-dev.txt b/requirements-dev.txt
index d7eba41..8f10c7e 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -4,4 +4,4 @@ pytest-cov==4.1.0
 pytest-order==1.1.0
 parameterized==0.9.0
 requests-mock==1.11.0
-pytest-mock==3.11.1
+pytest-mock==3.14.0

From 191c83434dd2340ead1f1fe8213736b81cf78632 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 22 Mar 2024 07:31:12 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 example/example_run.py   | 18 +++++++++---------
 geneplexus/geneplexus.py |  6 +++---
 2 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/example/example_run.py b/example/example_run.py
index 7f415eb..3fcfe6e 100755
--- a/example/example_run.py
+++ b/example/example_run.py
@@ -41,20 +41,20 @@
     tasks="All",
     networks="STRING",
     features="SixSpeciesN2V",
-    sp_trn = "Human",
-    sp_tst = "Mouse",
-    gsc= "GO",
+    sp_trn="Human",
+    sp_tst="Mouse",
+    gsc="GO",
 )
 
 # Run through the pipeline
 # First initialize the geneplexus object
 myclass = geneplexus.GenePlexus(
-    file_loc = fp_data,
-    gsc = "Combined",
-    features = "SixSpeciesN2V",
-    net_type = "STRING",
-    sp_trn = "Human",
-    sp_tst = "Mouse",
+    file_loc=fp_data,
+    gsc="Combined",
+    features="SixSpeciesN2V",
+    net_type="STRING",
+    sp_trn="Human",
+    sp_tst="Mouse",
 )
 
 # Load the input genes into the class and set up positives/negatives
diff --git a/geneplexus/geneplexus.py b/geneplexus/geneplexus.py
index e6144dd..8204ce2 100755
--- a/geneplexus/geneplexus.py
+++ b/geneplexus/geneplexus.py
@@ -16,7 +16,8 @@
 from ._config import logger
 from ._config.logger_util import set_stream_level
 from .download import download_select_data
-from .exception import CustomDataError, ZebrafishBioGRIDError
+from .exception import CustomDataError
+from .exception import ZebrafishBioGRIDError
 
 
 class GenePlexus:
@@ -88,14 +89,13 @@ def __init__(
 
         if input_genes is not None:
             self.load_genes(input_genes)
-               
+
         if ("Zebrafish" == (self.sp_trn or self.sp_tst)) and (self.net_type == "BioGRID"):
             raise ZebrafishBioGRIDError(
                 f"The BioGRID network for Zebrafish is not "
                 "included due to it not having enough nodes "
                 "so this combination is not allowed.",
             )
-            
 
     @property
     def _params(self) -> List[str]: