From c3b752e48a42ee91b9987eaa3bcce527d00ea9b8 Mon Sep 17 00:00:00 2001
From: Dusko Mirkovic <dmirkovic@biomech.us>
Date: Fri, 15 Sep 2023 09:32:30 +0200
Subject: [PATCH] Hotfix: Invalid python version specified in .mypy.ini

---
 .mypy.ini                                                 | 2 +-
 coretex/bioinformatics/__init__.py                        | 6 +++---
 coretex/bioinformatics/sequence_alignment/__init__.py     | 8 ++++----
 .../sample/sequence_sample/local_sequence_sample.py       | 2 +-
 4 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/.mypy.ini b/.mypy.ini
index 7248bb12..c8f6d734 100644
--- a/.mypy.ini
+++ b/.mypy.ini
@@ -1,7 +1,7 @@
 # Global options:
 
 [mypy]
-python_version = 3.9
+python_version = 3.8
 pretty = True
 warn_return_any = True
 warn_no_return = True
diff --git a/coretex/bioinformatics/__init__.py b/coretex/bioinformatics/__init__.py
index 36d2c9ee..8d551661 100644
--- a/coretex/bioinformatics/__init__.py
+++ b/coretex/bioinformatics/__init__.py
@@ -15,10 +15,10 @@
 #     You should have received a copy of the GNU Affero General Public License
 #     along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
-from typing import Optional, Union
+from typing import Optional, Union, List
 from pathlib import Path
 
-from .utils import CommandException, command
+from .utils import command
 from ..coretex import CustomDataset
 
 
@@ -64,7 +64,7 @@ def cutadaptTrim(
     if isinstance(reverseOutput, Path):
         reverseOutput = str(reverseOutput)
 
-    args: list[str] = [
+    args: List[str] = [
         "cutadapt",
         "-o", forwardOutput,
         "-g", forwardAdapter,
diff --git a/coretex/bioinformatics/sequence_alignment/__init__.py b/coretex/bioinformatics/sequence_alignment/__init__.py
index d1072f70..4d985eb0 100644
--- a/coretex/bioinformatics/sequence_alignment/__init__.py
+++ b/coretex/bioinformatics/sequence_alignment/__init__.py
@@ -187,9 +187,9 @@ def extractData(samtoolsPath: Path, file: Path) -> Tuple[List[int], List[int], L
         Link to samtools: http://htslib.org/
     """
 
-    scores: list[int] = []
-    positions: list[int] = []
-    sequenceLengths: list[int] = []
+    scores: List[int] = []
+    positions: List[int] = []
+    sequenceLengths: List[int] = []
 
     args = [
         str(samtoolsPath.absolute()),
@@ -238,7 +238,7 @@ def chmodX(file: Path) -> None:
 
 
 def loadFa(dataset: CustomDataset) -> List[Path]:
-    inputFiles: list[Path] = []
+    inputFiles: List[Path] = []
 
     for sample in dataset.samples:
         sample.unzip()
diff --git a/coretex/coretex/sample/sequence_sample/local_sequence_sample.py b/coretex/coretex/sample/sequence_sample/local_sequence_sample.py
index edb598a9..39a7557f 100644
--- a/coretex/coretex/sample/sequence_sample/local_sequence_sample.py
+++ b/coretex/coretex/sample/sequence_sample/local_sequence_sample.py
@@ -129,7 +129,7 @@ def isPairedEnd(self) -> bool:
             sampleContent = archive.namelist()
 
         for extension in self.supportedExtensions():
-            fileNames: list[str] = []
+            fileNames: List[str] = []
 
             for fileName in sampleContent:
                 if fileName.endswith(extension) or fileName.endswith(f"{extension}.gz"):