Fix import and formatting issues in multiple files (#11)

* Fix import and formatting issues in multiple files

* updates

* style(pre-commit.ci): auto fixes [...]

* unsafe fixes

* upda

* fix test

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.github/workflows/ci.yml

@@ -9,13 +9,18 @@ on:
   pull_request:
   workflow_dispatch:
   schedule:
+    # run every week (for --pre release tests)
     - cron: "0 0 * * 0"
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   check-manifest:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - run: pipx run check-manifest
 
   test:
@@ -24,16 +29,11 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
         platform: [ubuntu-latest, macos-latest, windows-latest]
 
     steps:
-      - name: 🛑 Cancel Previous Runs
-        uses: styfle/[email protected]
-        with:
-          access_token: ${{ github.token }}
-
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: 🐍 Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4
@@ -51,7 +51,6 @@ jobs:
       - name: 🧪 Run Tests
         run: pytest --color=yes --cov --cov-report=xml --cov-report=term-missing
 
-      # If something goes wrong with --pre tests, we can open an issue in the repo
       - name: 📝 Report --pre Failures
         if: failure() && github.event_name == 'schedule'
         uses: JasonEtco/create-an-issue@v2
@@ -74,8 +73,12 @@ jobs:
     if: success() && startsWith(github.ref, 'refs/tags/') && github.event_name != 'schedule'
     runs-on: ubuntu-latest
 
+    permissions:
+      id-token: write
+      contents: write
+
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -91,9 +94,8 @@ jobs:
 
       - name: 🚢 Publish to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          password: ${{ secrets.TWINE_API_KEY }}
 
       - uses: softprops/action-gh-release@v1
         with:
           generate_release_notes: true
+          files: './dist/*'

.pre-commit-config.yaml

@@ -5,23 +5,24 @@ ci:
 
 repos:
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.12.2
+    rev: v0.16
     hooks:
       - id: validate-pyproject
 
+  # - repo: https://github.com/crate-ci/typos
+  #   rev: v1.20.4
+  #   hooks:
+  #     - id: typos
+
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.265
+    rev: v0.3.5
     hooks:
       - id: ruff
-        args: [--fix]
-
-  - repo: https://github.com/psf/black
-    rev: 23.3.0
-    hooks:
-      - id: black
+        args: [--fix, --unsafe-fixes]
+      - id: ruff-format
 
   # - repo: https://github.com/pre-commit/mirrors-mypy
-  #   rev: v1.2.0
+  #   rev: v1.9.0
   #   hooks:
   #     - id: mypy
   #       files: "^src/"

examples/illum_widget.py

@@ -1,5 +1,6 @@
 import napari
 from magicgui import magicgui
+
 from microsim.models._illum import structillum_2d
 
 v = napari.Viewer()

pyproject.toml

@@ -6,6 +6,11 @@ build-backend = "hatchling.build"
 [tool.hatch.version]
 source = "vcs"
 
+# https://hatch.pypa.io/latest/config/build/
+[tool.hatch.build.targets.wheel]
+only-include = ["src"]
+sources = ["src"]
+
 # [tool.hatch.build.targets.wheel.hooks.mypyc]
 # mypy-args = ["--ignore-missing-imports"]
 # dependencies = ["hatch-mypyc>=0.13.0"]
@@ -22,12 +27,13 @@ license = { text = "BSD-3-Clause" }
 authors = [{ name = "Talley Lambert", email = "[email protected]" }]
 classifiers = [
     "Development Status :: 2 - Pre-Alpha",
+    "License :: OSI Approved :: BSD License",
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
-    "License :: OSI Approved :: BSD License",
+    "Programming Language :: Python :: 3.12",
     "Typing :: Typed",
 ]
 # add your package dependencies here
@@ -44,14 +50,7 @@ dependencies = [
 # https://peps.python.org/pep-0621/#dependencies-optional-dependencies
 [project.optional-dependencies]
 test = ["pytest", "pytest-cov"]
-dev = [
-    "black",
-    "ipython",
-    "mypy",
-    "pdbpp",   # https://github.com/pdbpp/pdbpp
-    "rich",    # https://github.com/Textualize/rich
-    "ruff",
-]
+dev = ["ipython", "mypy", "pdbpp", "rich", "ruff", "pre-commit"]
 
 [project.urls]
 homepage = "https://github.com/tlambert03/microsim"
@@ -60,35 +59,35 @@ repository = "https://github.com/tlambert03/microsim"
 [tool.ruff]
 line-length = 88
 target-version = "py38"
-# https://beta.ruff.rs/docs/rules/
+src = ["src"]
+
+[tool.ruff.lint]
+pydocstyle = { convention = "numpy" }
 select = [
-    "E", # style errors
-    "W", # style warnings
-    "F", # flakes
-    # "D",    # pydocstyle
+    "E",    # style errors
+    "W",    # style warnings
+    "F",    # flakes
+    "D",    # pydocstyle
+    "D417", # Missing argument descriptions in Docstrings
     "I",    # isort
-    "S",
     "UP",   # pyupgrade
     "C4",   # flake8-comprehensions
     "B",    # flake8-bugbear
     "A001", # flake8-builtins
     "RUF",  # ruff-specific rules
+    "TCH",  # flake8-type-checking
+    "TID",  # flake8-tidy-imports
 ]
 ignore = [
-    "D100", # Missing docstring in public module
-    "D107", # Missing docstring in __init__
-    "D203", # 1 blank line required before class docstring
-    "D212", # Multi-line docstring summary should start at the first line
-    "D213", # Multi-line docstring summary should start at the second line
+    "D10", # Missing docstring in public ...
     "D401", # First line should be in imperative mood
-    "D413", # Missing blank line after last section
-    "D416", # Section name should end with a colon
 ]
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 "tests/*.py" = ["D", "S"]
 "setup.py" = ["D"]
 
+
 # https://mypy.readthedocs.io/en/stable/config_file.html
 [tool.mypy]
 files = "src/**/"
@@ -97,14 +96,15 @@ disallow_any_generics = false
 disallow_subclassing_any = false
 show_error_codes = true
 pretty = true
+plugins = "pydantic.mypy"
 
 # [[tool.mypy.overrides]]
 # module = ["numpy.*",]
 # ignore_errors = true
 
 # https://docs.pytest.org/en/6.2.x/customize.html
 [tool.pytest.ini_options]
-minversion = "6.0"
+minversion = "7.0"
 testpaths = ["tests"]
 filterwarnings = ["error"]
 
@@ -117,9 +117,11 @@ exclude_lines = [
     "except ImportError",
     "\\.\\.\\.",
     "raise NotImplementedError()",
+    "pass"
 ]
+
 [tool.coverage.run]
-source = ["src"]
+source = ["microsim"]
 
 # https://github.com/mgedmin/check-manifest#configuration
 # add files that you want check-manifest to explicitly ignore here

src/microsim/__init__.py

@@ -1,4 +1,5 @@
 """Light microscopy simulation in python."""
+
 from importlib.metadata import PackageNotFoundError, version
 
 try:

src/microsim/_operator.py

@@ -1,5 +1,7 @@
-from .models._renderable import Renderable
+from typing import TYPE_CHECKING
 
+if TYPE_CHECKING:
+    from microsim.models._renderable import Renderable
 
-def convolve(a, b) -> "Renderable":
-    ...
+
+def convolve(a, b) -> "Renderable": ...

src/microsim/illum/_sim.py

@@ -2,7 +2,7 @@
 
 from functools import lru_cache
 from itertools import product
-from typing import TYPE_CHECKING, Sequence
+from typing import TYPE_CHECKING, Any, Iterable, Sequence
 
 import numpy as np
 from tqdm import tqdm
@@ -123,7 +123,9 @@ def create(self, shape: tuple[int, int, int], dz: float, dx: float) -> np.ndarra
         print(out.shape, "out")
         return out
 
-    def _render_plane(self, sim_plane, coords, theta, phase):
+    def _render_plane(
+        self, sim_plane: NDArray, coords: NDArray, theta: float, phase: float
+    ) -> NDArray:
         if map_coordinates.__module__.startswith("cupy"):
             _i = []
             CHUNKSIZE = 128  # TODO: determine better strategy
@@ -136,11 +138,11 @@ def _render_plane(self, sim_plane, coords, theta, phase):
             img = map_coordinates(sim_plane, new_coords, order=1)
         return img
 
-    def _map_coords(self, coords: np.ndarray, theta: float, phase: float) -> NDArray:
-        """Map a set of image coordinates to new coords after phaseshift and rotation"""
+    def _map_coords(self, coords: NDArray, theta: float, phase: float) -> NDArray:
+        """Map a set of img coordinates to new coords after phaseshift and rotation."""
         matrix = self._get_matrix(theta, phase)
         new_coordinates = (matrix[:-1, :-1] @ coords)[:2]
-        return new_coordinates + xp.expand_dims(xp.asarray(matrix[:2, -1]), -1)
+        return new_coordinates + xp.expand_dims(xp.asarray(matrix[:2, -1]), -1)  # type: ignore
 
     def _get_matrix(self, theta: float, phase: float) -> NDArray:
         """Get matrix to transform output coordinates to axial sim plane.
@@ -172,7 +174,7 @@ def _get_matrix(self, theta: float, phase: float) -> NDArray:
             ]
         )
 
-        return scale @ translate @ rotate
+        return scale @ translate @ rotate  # type: ignore
 
 
 class SIMIllum3D(SIMIllum2D):
@@ -183,8 +185,8 @@ class SIMIllum3D(SIMIllum2D):
 TAU = 1j * 2 * np.pi
 
 
-def efield(kvec: tuple[float, float], zarr: NDArray, xarr: NDArray):
-    return xp.exp(TAU * (kvec[0] * xarr + kvec[1] * zarr))
+def efield(kvec: tuple[float, float], zarr: NDArray, xarr: NDArray) -> NDArray:
+    return xp.exp(TAU * (kvec[0] * xarr + kvec[1] * zarr))  # type: ignore
 
 
 @lru_cache(maxsize=128)
@@ -313,5 +315,7 @@ def structillum_2d(
     return intensity
 
 
-def _enumerated_product(*args):
+def _enumerated_product(
+    *args: Any,
+) -> Iterable[tuple[tuple[int, int], tuple[Any, ...]]]:
     yield from zip(product(*(range(len(x)) for x in args)), product(*args))

src/microsim/illum/_widefield.py

@@ -1,4 +1,4 @@
-from ..models import Illumination
+from microsim.models import Illumination
 
 
 class Widefield(Illumination):

src/microsim/models/_camera.py

@@ -44,7 +44,7 @@ def simulate(
         add_poisson : bool, optional
             _description_, by default True
         """
-        from ..simulate import simulate_camera
+        from microsim.simulate import simulate_camera
 
         return simulate_camera(
             self, image, exposure, binning=binning, add_poisson=add_poisson
@@ -64,8 +64,7 @@ def quantize_electrons(self, total_electrons: np.ndarray) -> np.ndarray:
         return np.round((voltage / self.adc_gain) + self.offset)
 
 
-class CameraCCD(Camera):
-    ...
+class CameraCCD(Camera): ...
 
 
 class CameraEMCCD(Camera):
@@ -86,8 +85,7 @@ def apply_em_gain(self, electron_image):
         return np.minimum(electron_image, self.em_full_well)
 
 
-class CameraCMOS(Camera):
-    ...
+class CameraCMOS(Camera): ...
 
 
 ICX285 = CameraCCD(