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Hotfix: Invalid python version specified in .mypy.ini
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dule1322 committed Sep 15, 2023
1 parent 0e2aa03 commit c3b752e
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Showing 4 changed files with 9 additions and 9 deletions.
2 changes: 1 addition & 1 deletion .mypy.ini
Original file line number Diff line number Diff line change
@@ -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
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6 changes: 3 additions & 3 deletions coretex/bioinformatics/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -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


Expand Down Expand Up @@ -64,7 +64,7 @@ def cutadaptTrim(
if isinstance(reverseOutput, Path):
reverseOutput = str(reverseOutput)

args: list[str] = [
args: List[str] = [
"cutadapt",
"-o", forwardOutput,
"-g", forwardAdapter,
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8 changes: 4 additions & 4 deletions coretex/bioinformatics/sequence_alignment/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -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()),
Expand Down Expand Up @@ -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()
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Original file line number Diff line number Diff line change
Expand Up @@ -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"):
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