Restore custom isort section sorting (#299)

* Add classifiers

* Combine optional dependencies

* Fix target version sorting

* Bump pre-commit

* Remove isort section

* Add custom isort section sorting

* Update `pre-commit`

* Run `ruff` on all code

* Fix `pyproject.toml`

.pre-commit-config.yaml

@@ -1,10 +1,10 @@
 repos:
     - repo: https://github.com/charliermarsh/ruff-pre-commit
-      rev: v0.0.257
+      rev: v0.0.262
       hooks:
         - id: ruff
     - repo: https://github.com/Lucas-C/pre-commit-hooks
-      rev: v1.4.2
+      rev: v1.5.1
       hooks:
         - id: remove-tabs
           exclude: Makefile|docs/Makefile|\.bat$
@@ -23,7 +23,7 @@ repos:
           - id: trailing-whitespace
             args: [--markdown-linebreak-ext=md]
     - repo: https://github.com/psf/black
-      rev: 23.1.0
+      rev: 23.3.0
       hooks:
           - id: black
     - repo: https://github.com/pappasam/toml-sort

btrack/btypes.py

@@ -160,7 +160,7 @@ def to_dict(self) -> Dict[str, Any]:
     def from_dict(properties: Dict[str, Any]) -> PyTrackObject:
         """Build an object from a dictionary."""
         obj = PyTrackObject()
-        fields = {k: kt for k, kt in PyTrackObject._fields_}
+        fields = dict(PyTrackObject._fields_)
         attr = [k for k in fields if k in properties]
         for key in attr:
             new_data = properties[key]
@@ -362,7 +362,7 @@ def __init__(
         children: Optional[List[int]] = None,
         fate: constants.Fates = constants.Fates.UNDEFINED,
     ):
-        assert all([isinstance(o, PyTrackObject) for o in data])
+        assert all(isinstance(o, PyTrackObject) for o in data)
 
         self.ID = ID
         self._data = data

btrack/io/hdf.py

@@ -249,7 +249,7 @@ def filtered_objects(
                 )
             )
             properties = {k: grp["properties"][k][:] for k in p_keys}
-            assert all([len(p) == len(txyz) for p in properties.values()])
+            assert all(len(p) == len(txyz) for p in properties.values())
 
         # note that this doesn't do much error checking at the moment
         # TODO(arl): this should now reference the `properties`

btrack/io/utils.py

@@ -63,7 +63,7 @@ def objects_from_dict(objects_dict: dict) -> List[btypes.PyTrackObject]:
     objects = []
     n_objects = int(objects_dict["t"].shape[0])
 
-    assert all([v.shape[0] == n_objects for k, v in objects_dict.items()])
+    assert all(v.shape[0] == n_objects for k, v in objects_dict.items())
 
     for i in range(n_objects):
         data = {k: v[i] for k, v in objects_dict.items()}

btrack/napari/main.py

@@ -4,16 +4,18 @@
 
 if TYPE_CHECKING:
     import numpy.typing as npt
+
     from magicgui.widgets import Container
 
     from btrack.config import TrackerConfig
     from btrack.napari.config import TrackerConfigs
 
 import logging
 
+import qtpy.QtWidgets
+
 import magicgui.widgets
 import napari
-import qtpy.QtWidgets
 
 import btrack
 import btrack.napari.config

btrack/napari/reader.py

@@ -4,9 +4,10 @@
 import os
 from typing import Callable, List, Optional, Sequence, Union
 
-from napari.types import LayerDataTuple
 from napari_plugin_engine import napari_hook_implementation
 
+from napari.types import LayerDataTuple
+
 from btrack.io import HDF5FileHandler
 from btrack.utils import tracks_to_napari
 

btrack/utils.py

@@ -88,7 +88,7 @@ def crop_volume(objects, volume=constants.VOLUME):
 
     def within(o):
         return all(
-            [getattr(o, a) >= v[0] and getattr(o, a) <= v[1] for a, v in axes]
+            getattr(o, a) >= v[0] and getattr(o, a) <= v[1] for a, v in axes
         )
 
     return [o for o in objects if within(o)]
@@ -103,7 +103,7 @@ def _cat_tracks_as_dict(
     tracks: list[btypes.Tracklet], properties: List[str]
 ) -> dict:
     """Concatenate all tracks as dictionary."""
-    assert all([isinstance(t, btypes.Tracklet) for t in tracks])
+    assert all(isinstance(t, btypes.Tracklet) for t in tracks)
 
     data: dict = {}
 

pyproject.toml

@@ -16,6 +16,8 @@ classifiers = [
     "License :: OSI Approved :: MIT License",
     "Operating System :: OS Independent",
     "Programming Language :: C++",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3 :: Only",
     "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
@@ -29,36 +31,32 @@ dynamic = [
     "version",
 ]
 name = "btrack"
-readme = "README.md"
-requires-python = ">=3.8"
-entry-points."napari.manifest".btrack = "btrack:napari.yaml"
-license.file = "LICENSE.md"
-optional-dependencies.docs = [
+optional-dependencies = {docs = [
     "numpydoc",
     "pytz",
-    "sphinx_rtd_theme",
+    "sphinx",
     "sphinx-automodapi",
     "sphinx-panels",
-    "sphinx",
-]
-optional-dependencies.napari = [
+    "sphinx_rtd_theme",
+], napari = [
     "magicgui>=0.5.0",
     "napari-plugin-engine>=0.1.4",
     "napari>=0.4.16",
     "qtpy",
-]
-optional-dependencies.pyqt = [
-    "btrack[napari]",
+], pyqt = [
     "PyQt5 >= 5.12.3, != 5.15.0",
-]
-optional-dependencies.pyside = [
     "btrack[napari]",
+], pyside = [
     "PySide2 >= 5.13.2, != 5.15.0 ; python_version != '3.8'",
     "PySide2 >= 5.14.2, != 5.15.0 ; python_version == '3.8'",
-]
-optional-dependencies.qt = [
+    "btrack[napari]",
+], qt = [
     "btrack[pyside]",
-]
+]}
+readme = "README.md"
+requires-python = ">=3.8"
+entry-points."napari.manifest".btrack = "btrack:napari.yaml"
+license.file = "LICENSE.md"
 urls.bugtracker = "https://github.com/quantumjot/btrack/issues"
 urls.documentation = "https://btrack.readthedocs.io"
 urls.homepage = "https://github.com/quantumjot/btrack"
@@ -82,20 +80,22 @@ exclude = '''
 )
 '''
 line-length = 79
-target-version = ["py38", "py39", "py310"]
+target-version = [
+    "py38",
+    "py39",
+    "py310",
+]
 
 [tool.coverage]
 report = {skip_covered = true, sort = "cover"}
-run = {branch = true, parallel = true, source = ["btrack"]}
+run = {branch = true, parallel = true, source = [
+    "btrack",
+]}
 paths.source = [
     "btrack",
     ".tox*/*/lib/python*/site-packages",
 ]
 
-[tool.isort]
-line_length = 79
-profile = "black"
-
 [tool.pytest.ini_options]
 addopts = "--color=yes -ra -v"
 testpaths = [
@@ -150,7 +150,21 @@ select = [
     "YTT",
 ]
 target-version = "py38"
-isort.known-first-party = ["btrack"]
+isort.known-first-party = [
+    "black",
+]
+isort.section-order = [
+    "future",
+    "standard-library",
+    "third-party",
+    "napari",
+    "first-party",
+    "local-folder",
+]
+isort.sections.napari = [
+    "magicgui",
+    "napari",
+]
 mccabe.max-complexity = 18
 pep8-naming.classmethod-decorators = [
     "classmethod",
@@ -167,11 +181,13 @@ local_scheme = "no-local-version"
 write_to = "btrack/_version.py"
 
 [tool.tomlsort]
-sort_inline_arrays = false
-sort_inline_tables = true
-sort_table_keys = true
+all = true
 spaces_indent_inline_array = 4
 trailing_comma_inline_array = true
+overrides."project.classifiers".inline_arrays = false
+overrides."tool.black.target-version".inline_arrays = false
+overrides."tool.coverage.paths.source".inline_arrays = false
+overrides."tool.ruff.isort.section-order".inline_arrays = false
 
 [tool.tox]
 legacy_tox_ini = """

tests/napari/test_dock_widget.py

@@ -8,11 +8,12 @@
 import json
 from unittest.mock import patch
 
-import napari
 import numpy as np
 import numpy.typing as npt
 import pytest
 
+import napari
+
 import btrack
 import btrack.napari
 import btrack.napari.main

tests/test_utils.py

@@ -49,14 +49,14 @@ def test_segmentation_to_objects_type():
     """Test that btrack objects are returned."""
     img, centroids = create_test_image()
     objects = utils.segmentation_to_objects(img[np.newaxis, ...])
-    assert all([isinstance(o, btypes.PyTrackObject) for o in objects])
+    assert all(isinstance(o, btypes.PyTrackObject) for o in objects)
 
 
 def test_segmentation_to_objects_type_generator():
     """Test generator as input."""
     generator = _example_segmentation_generator()
     objects = utils.segmentation_to_objects(generator)
-    assert all([isinstance(o, btypes.PyTrackObject) for o in objects])
+    assert all(isinstance(o, btypes.PyTrackObject) for o in objects)
 
 
 @pytest.mark.parametrize("ndim", [2, 3])
@@ -231,7 +231,7 @@ def test_tracks_to_napari(ndim: int):
     # keys that start with the property key, e.g. `nD` is replaced with `nD-0`
     # and so forth
     for key in tracks[0].properties:
-        assert any([k.startswith(key) for k in properties])
+        assert any(k.startswith(key) for k in properties)
 
 
 @pytest.mark.parametrize("ndim", [1, 4])