fix typing python 3.7 & add isort

Signed-off-by: zethson <[email protected]>

.isort.cfg

@@ -0,0 +1,4 @@
+[settings]
+multi_line_output=3
+include_trailing_comma=True
+line_length=120

.pre-commit-config.yaml

@@ -36,12 +36,6 @@ repos:
             types: [python]
             require_serial: true
             exclude: templates
-          - id: reorder-python-imports
-            name: Reorder python imports
-            entry: reorder-python-imports
-            language: system
-            types: [python]
-            args: [--application-directories=src]
           - id: trailing-whitespace
             name: Trim Trailing Whitespace
             entry: trailing-whitespace-fixer
@@ -53,3 +47,14 @@ repos:
       hooks:
           - id: prettier
             exclude: templates
+    - repo: https://github.com/pycqa/isort
+      rev: 5.8.0
+      hooks:
+          - id: isort
+            name: isort (python)
+          - id: isort
+            name: isort (cython)
+            types: [cython]
+          - id: isort
+            name: isort (pyi)
+            types: [pyi]

noxfile.py

@@ -8,8 +8,7 @@
 from rich import print
 
 try:
-    from nox_poetry import Session
-    from nox_poetry import session
+    from nox_poetry import Session, session
 except ImportError:
     print("[bold red]Did not found nox-poetry installed in your current environment!")
     print("[bold blue]Try installing it using [bold green]pip install nox-poetry [bold blue]! ")

pyproject.toml

@@ -30,6 +30,7 @@ seaborn = "^0.11.1"
 pandas = "^1.2.4"
 scipy = "^1.6.3"
 scikit-learn = "^0.24.1"
+typing-extensions = "^3.10.0"
 
 [tool.poetry.dev-dependencies]
 pytest = "^6.2.4"

sc_toolbox/__init__.py

@@ -4,6 +4,4 @@
 __email__ = "[email protected]"
 __version__ = "0.6.0"
 
-from sc_toolbox.api import plot
-from sc_toolbox.api import calc
-from sc_toolbox.api import util
+from sc_toolbox.api import calc, plot, util

sc_toolbox/__main__.py

@@ -6,8 +6,8 @@
 
 import click
 import rich.logging
-from rich import print
-from rich import traceback
+from rich import print, traceback
+
 from sc_toolbox.cli.commands.create import ProjectCreator
 from sc_toolbox.cli.commands.upgrade import UpgradeCommand
 

sc_toolbox/api/calc/__init__.py

@@ -1,6 +1,11 @@
 import os
 from typing import List
-from typing import Literal
+
+try:
+    from typing import Literal
+except ImportError:
+    from typing_extensions import Literal  # type: ignore
+
 from typing import Optional
 
 import numpy as np
@@ -206,8 +211,8 @@ def remove_outliers(cords, eps: int = 1, min_samples: int = 2):
         Pandas DataFrame of clusters
 
     """
-    from sklearn.cluster import DBSCAN
     from natsort import natsorted
+    from sklearn.cluster import DBSCAN
 
     clustering = DBSCAN(eps=eps, min_samples=min_samples).fit(cords)
     cluster = clustering.labels_.astype("U")

sc_toolbox/api/plot/__init__.py

@@ -1,9 +1,5 @@
 from enum import Enum
-from typing import Dict
-from typing import List
-from typing import Sequence
-from typing import Tuple
-from typing import Union
+from typing import Dict, List, Sequence, Tuple, Union
 
 import matplotlib.pyplot as plt
 import numpy as np

sc_toolbox/api/util/__init__.py

@@ -46,8 +46,9 @@ def read_concatenate_to_adata(file_paths: List[str]) -> AnnData:
     Returns:
         Single AnnData object containing all concatenated files
     """
-    import anndata as ad
     import gc
+
+    import anndata as ad
     import scipy.sparse
 
     for index, file_name in enumerate(file_paths):

sc_toolbox/cli/commands/create.py

@@ -1,9 +1,9 @@
 import logging
 import os
-from dataclasses import asdict
-from dataclasses import dataclass
+from dataclasses import asdict, dataclass
 
 from cookiecutter.main import cookiecutter
+
 from sc_toolbox.cli.questionary import sc_toolbox_questionary
 
 log = logging.getLogger(__name__)

sc_toolbox/cli/commands/upgrade.py

@@ -1,16 +1,13 @@
 import json
 import sys
-from subprocess import check_call
-from subprocess import PIPE
-from subprocess import Popen
-from urllib.error import HTTPError
-from urllib.error import URLError
-from urllib.request import Request
-from urllib.request import urlopen
+from subprocess import PIPE, Popen, check_call
+from urllib.error import HTTPError, URLError
+from urllib.request import Request, urlopen
 
-import sc_toolbox
 from pkg_resources import parse_version
 from rich import print
+
+import sc_toolbox
 from sc_toolbox.cli.questionary import sc_toolbox_questionary
 
 

tests/test_main.py

@@ -1,6 +1,7 @@
 """Test cases for the __main__ module."""
 import pytest
 from click.testing import CliRunner
+
 from sc_toolbox import __main__