Fix isort pre-commit hooks (#61)

* Exclude import sorting in `ruff`

As of now, `ruff` does not allow custom sorting and ordering of imports.
See astral-sh/ruff#2419.

* Run pre-commit hooks

Apply `isort` changes.

.pre-commit-config.yaml

@@ -14,6 +14,10 @@ repos:
       rev: 1.13.0
       hooks:
           - id: blacken-docs
+    - repo: https://github.com/PyCQA/isort
+      rev: 5.12.0
+      hooks:
+          - id: isort
     - repo: https://github.com/pre-commit/mirrors-prettier
       rev: v3.0.0-alpha.4
       hooks:

pyproject.toml

@@ -27,7 +27,9 @@ use_parentheses = true
 known_num = "networkx,numpy,pandas,scipy,sklearn,statmodels"
 known_plot = "matplotlib,mpl_toolkits,seaborn"
 known_bio = "anndata"
-sections = "FUTURE,STDLIB,THIRDPARTY,NUM,PLOT,BIO,FIRSTPARTY,LOCALFOLDER"
+known_r = "rpy2"
+known_firstparty = "tradeseq"
+sections = "FUTURE,STDLIB,THIRDPARTY,NUM,PLOT,R,BIO,FIRSTPARTY,LOCALFOLDER"
 no_lines_before = "LOCALFOLDER"
 balanced_wrapping = true
 length_sort = "0"
@@ -43,7 +45,6 @@ select = [
     "F",  # Errors detected by Pyflakes
     "E",  # Error detected by Pycodestyle
     "W",  # Warning detected by Pycodestyle
-    "I",  # isort
     "D",  # pydocstyle
     "B",  # flake8-bugbear
     "TID",  # flake8-tidy-imports
@@ -89,10 +90,9 @@ ignore = [
 ]
 
 [tool.ruff.per-file-ignores]
-"docs/*" = ["I", "BLE001"]
+"docs/*" = ["BLE001"]
 "tests/*" = ["D"]
 "*/__init__.py" = ["F401"]
-"scvelo/__init__.py" = ["I"]
 
 [tool.jupytext]
 formats = "ipynb,md"

tests/core/test_base.py

@@ -1,11 +1,13 @@
 from typing import Optional
 
 import hypothesis.strategies as st
-import numpy as np
-from anndata import AnnData
 from hypothesis.extra.numpy import arrays
+
+import numpy as np
 from scipy.sparse import csr_matrix
 
+from anndata import AnnData
+
 from tradeseq.gam import GAM
 
 MAX_INT_VALUE = 100

tests/core/tradeseq_r.py

@@ -1,4 +1,5 @@
 import numpy as np
+
 import rpy2.robjects as ro
 from rpy2.robjects import default_converter, numpy2ri
 from rpy2.robjects.conversion import localconverter

tests/de_tests/test_association.py

@@ -1,9 +1,10 @@
 from typing import Literal
 
-import numpy as np
 from hypothesis import given, settings
 from hypothesis import strategies as st
 
+import numpy as np
+
 from tests.core.test_base import get_gam
 from tradeseq.de_tests._association_test import AssociationTest
 from tradeseq.gam import GAM

tests/de_tests/test_diff_end.py

@@ -1,7 +1,8 @@
-import numpy as np
 from hypothesis import given, settings
 from hypothesis import strategies as st
 
+import numpy as np
+
 from tests.core.test_base import get_gam
 from tradeseq.de_tests._diff_end_test import DiffEndTest
 from tradeseq.gam import GAM

tests/de_tests/test_pattern.py

@@ -1,7 +1,8 @@
-import numpy as np
 from hypothesis import given, settings
 from hypothesis import strategies as st
 
+import numpy as np
+
 from tests.core.test_base import get_gam
 from tradeseq.de_tests._pattern_test import PatternTest
 from tradeseq.gam import GAM

tests/de_tests/test_start_vs_end.py

@@ -1,7 +1,8 @@
-import numpy as np
 from hypothesis import given, settings
 from hypothesis import strategies as st
 
+import numpy as np
+
 from tests.core.test_base import get_gam
 from tradeseq.de_tests._start_vs_end_test import StartVsEndTest
 from tradeseq.gam import GAM

tests/gam/test_fit.py

@@ -1,11 +1,13 @@
-import anndata as ad
-import numpy as np
 from hypothesis import given, settings
 from hypothesis import strategies as st
 
+import numpy as np
+
+import anndata as ad
+
 from tests.core.test_base import get_gam
 from tests.core.tradeseq_r import TradeseqR
-from tradeseq.gam._gam import GAM, _calculate_offset
+from tradeseq.gam._gam import _calculate_offset, GAM
 
 
 class TestGAMFitting:

tests/gam/test_getters.py

@@ -1,10 +1,11 @@
-import numpy as np
 import pytest
 from hypothesis import assume, given, settings
 from hypothesis import strategies as st
 from hypothesis.extra.numpy import arrays
 
-from tests.core.test_base import MAX_INT_VALUE, get_gam
+import numpy as np
+
+from tests.core.test_base import get_gam, MAX_INT_VALUE
 from tradeseq.gam._gam import GAM
 
 

tradeseq/_backend/_base.py

@@ -1,23 +1,25 @@
 from abc import ABC, abstractmethod
 from typing import (
-    TYPE_CHECKING,
     Any,
     Callable,
     Dict,
     Literal,
     Optional,
     Tuple,
     Type,
+    TYPE_CHECKING,
     Union,
 )
 
+from packaging.version import LegacyVersion, parse, Version
+
 import pandas as pd
+
 import rpy2.robjects as ro
-from packaging.version import LegacyVersion, Version, parse
 from rpy2.rinterface_lib.embedded import RRuntimeError
 from rpy2.robjects import pandas2ri
 from rpy2.robjects.conversion import localconverter
-from rpy2.robjects.packages import InstalledSTPackage, PackageNotInstalledError, importr
+from rpy2.robjects.packages import importr, InstalledSTPackage, PackageNotInstalledError
 
 __all__ = ("TradeSeqTest", "register")
 

tradeseq/_backend/_test.py

@@ -1,11 +1,13 @@
 from abc import ABC
 from typing import Any, Literal, Optional, Sequence
 
+from packaging.version import parse
+
 import pandas as pd
+
 import rpy2.robjects as ro
-from packaging.version import parse
 
-from tradeseq._backend._base import TradeSeqTest, _load_library, register
+from tradeseq._backend._base import _load_library, register, TradeSeqTest
 
 
 # TODO: Add docstrings

tradeseq/_base.py

@@ -3,19 +3,21 @@
 from abc import ABC, abstractmethod
 from contextlib import redirect_stderr
 from io import StringIO
-from typing import TYPE_CHECKING, Any, Literal, Optional, Sequence, Sized, Tuple, Union
+from typing import Any, Literal, Optional, Sequence, Sized, Tuple, TYPE_CHECKING, Union
 
 import numpy as np
 import pandas as pd
+from scipy.sparse import issparse
+
 import rpy2.robjects as ro
-from anndata import AnnData
 from rpy2.rinterface_lib.embedded import RRuntimeError
 from rpy2.robjects import numpy2ri, pandas2ri
 from rpy2.robjects.conversion import localconverter
 from rpy2.robjects.packages import importr
-from scipy.sparse import issparse
 
-from tradeseq._backend._base import TradeSeqTest, _load_library
+from anndata import AnnData
+
+from tradeseq._backend._base import _load_library, TradeSeqTest
 
 _PARALLEL = importr("BiocParallel")
 

tradeseq/gam/_backend.py

@@ -2,6 +2,7 @@
 
 import numpy as np
 import pandas as pd
+
 import rpy2.robjects as ro
 from rpy2.robjects import default_converter, numpy2ri, pandas2ri
 from rpy2.robjects.conversion import localconverter

tradeseq/gam/_gam.py

@@ -1,13 +1,16 @@
 import warnings
 from typing import List, Optional, Tuple, Union
 
-import matplotlib.pyplot as plt
+from conorm import tmm_norm_factors
+
 import numpy as np
 import pandas as pd
+from scipy.sparse import issparse
+
+import matplotlib.pyplot as plt
 import seaborn as sns
+
 from anndata import AnnData
-from conorm import tmm_norm_factors
-from scipy.sparse import issparse
 
 from tradeseq.gam import _backend