gh-362: review the ruff-format recommended rules

Closes #362. When you first run `ruff-format` it only warns about
`COM812` and `ISC001`. This PR just reduces the others which technically
also in conflict to just these two. I have used these extensively and
have had no issues.

examples/2-advanced/cosmic_shear.ipynb

@@ -225,7 +225,12 @@
     "\n",
     "        # apply the shear fields to the ellipticities\n",
     "        gal_she = glass.galaxy_shear(\n",
-    "            gal_lon, gal_lat, gal_eps, kappa_i, gamm1_i, gamm2_i\n",
+    "            gal_lon,\n",
+    "            gal_lat,\n",
+    "            gal_eps,\n",
+    "            kappa_i,\n",
+    "            gamm1_i,\n",
+    "            gamm2_i,\n",
     "        )\n",
     "\n",
     "        # map the galaxy shears to a HEALPix map; this is opaque but works\n",

examples/2-advanced/stage_4_galaxies.ipynb

@@ -281,7 +281,10 @@
     "\n",
     "    # generate galaxy positions from the matter density contrast\n",
     "    for gal_lon, gal_lat, gal_count in glass.positions_from_delta(\n",
-    "        ngal[i], delta_i, bias, vis\n",
+    "        ngal[i],\n",
+    "        delta_i,\n",
+    "        bias,\n",
+    "        vis,\n",
     "    ):\n",
     "        # generate random redshifts over the given shell\n",
     "        gal_z = glass.redshifts(gal_count, ws[i])\n",
@@ -297,7 +300,12 @@
     "\n",
     "        # apply the shear fields to the ellipticities\n",
     "        gal_she = glass.galaxy_shear(\n",
-    "            gal_lon, gal_lat, gal_eps, kappa_i, gamm1_i, gamm2_i\n",
+    "            gal_lon,\n",
+    "            gal_lat,\n",
+    "            gal_eps,\n",
+    "            kappa_i,\n",
+    "            gamm1_i,\n",
+    "            gamm2_i,\n",
     "        )\n",
     "\n",
     "        # make a mini-catalogue for the new rows\n",

glass/ext/__init__.py

@@ -17,7 +17,7 @@ def _extend_path(path, name) -> list:  # type: ignore[no-untyped-def, type-arg]
         filter(
             os.path.isdir,
             (os.path.join(p, _mod) for p in extend_path(path, _pkg)),  # noqa: PTH118
-        )
+        ),
     )
 
 

glass/fields.py

@@ -39,7 +39,8 @@
 Size = typing.Optional[typing.Union[int, tuple[int, ...]]]
 Iternorm = tuple[typing.Optional[int], npt.NDArray[typing.Any], npt.NDArray[typing.Any]]
 ClTransform = typing.Union[
-    str, typing.Callable[[npt.NDArray[typing.Any]], npt.NDArray[typing.Any]]
+    str,
+    typing.Callable[[npt.NDArray[typing.Any]], npt.NDArray[typing.Any]],
 ]
 Cls = collections.abc.Sequence[
     typing.Union[npt.NDArray[typing.Any], collections.abc.Sequence[float]]
@@ -110,7 +111,10 @@ def iternorm(
 
 
 def cls2cov(
-    cls: Cls, nl: int, nf: int, nc: int
+    cls: Cls,
+    nl: int,
+    nf: int,
+    nc: int,
 ) -> collections.abc.Generator[npt.NDArray[typing.Any], None, None]:
     """Return array of cls as a covariance matrix for iterative sampling."""
     cov = np.zeros((nl, nc + 1))
@@ -149,7 +153,8 @@ def transform_cls(cls: Cls, tfm: ClTransform, pars: tuple[typing.Any, ...] = ())
             gl, info, _, _ = gaussiancl(cl, tfm, pars, monopole=monopole)
             if info == 0:
                 warnings.warn(
-                    "Gaussian cl did not converge, inexact transform", stacklevel=2
+                    "Gaussian cl did not converge, inexact transform",
+                    stacklevel=2,
                 )
         else:
             gl = []
@@ -352,7 +357,11 @@ def getcl(cls, i, j, lmax=None):  # type: ignore[no-untyped-def]
 
 
 def effective_cls(  # type: ignore[no-untyped-def]
-    cls, weights1, weights2=None, *, lmax=None
+    cls,
+    weights1,
+    weights2=None,
+    *,
+    lmax=None,
 ) -> npt.NDArray[np.float64]:
     r"""
     Compute effective angular power spectra from weights.

glass/lensing.py

@@ -298,7 +298,10 @@ def add_window(self, delta: npt.NDArray[typing.Any], w: RadialWindow) -> None:
         self.add_plane(delta, zsrc, lens_weight)
 
     def add_plane(
-        self, delta: npt.NDArray[typing.Any], zsrc: float, wlens: float = 1.0
+        self,
+        delta: npt.NDArray[typing.Any],
+        zsrc: float,
+        wlens: float = 1.0,
     ) -> None:
         """Add a mass plane at redshift ``zsrc`` to the convergence."""
         if zsrc <= self.z3:
@@ -417,7 +420,9 @@ def multi_plane_weights(
 
 
 def deflect(
-    lon: npt.ArrayLike, lat: npt.ArrayLike, alpha: npt.ArrayLike
+    lon: npt.ArrayLike,
+    lat: npt.ArrayLike,
+    alpha: npt.ArrayLike,
 ) -> npt.NDArray[typing.Any]:
     r"""
     Apply deflections to positions.

glass/shells.py

@@ -165,7 +165,8 @@ def tophat_windows(
         raise ValueError(msg)
     if zbins[0] != 0:
         warnings.warn(
-            "first tophat window does not start at redshift zero", stacklevel=2
+            "first tophat window does not start at redshift zero",
+            stacklevel=2,
         )
 
     wht: WeightFunc

noxfile.py

@@ -50,7 +50,10 @@ def examples(session: nox.Session) -> None:
     """Run the example notebooks."""
     session.install("-e", ".[examples]")
     session.run(
-        "jupyter", "execute", *Path().glob("examples/**/*.ipynb"), *session.posargs
+        "jupyter",
+        "execute",
+        *Path().glob("examples/**/*.ipynb"),
+        *session.posargs,
     )
 
 

pyproject.toml

@@ -136,23 +136,11 @@ lint.ignore = [
     "ANN003", # TODO: missing-type-kwargs
     "ANN201", # TODO: missing-return-type-undocumented-public-function
     "COM812", # missing-trailing-comma (ruff-format recommended)
-    "COM819", # prohibited-trailing-comma (ruff-format recommended)
     "D203", # one-blank-line-before-class
-    "D206", # indent-with-spaces (ruff-format recommended)
     "D212", # blank-line-before-class
-    "D300", # triple-single-quotes (ruff-format recommended)
-    "E111", # indentation-with-invalid-multiple (ruff-format recommended)
-    "E114", # indentation-with-invalid-multiple-comment (ruff-format recommended)
-    "E117", # over-indented (ruff-format recommended)
     "ISC001", # single-line-implicit-string-concatenation (ruff-format recommended)
-    "ISC002", # multi-line-implicit-string-concatenation (ruff-format recommended)
     "NPY201", # TODO: numpy2-deprecation
-    "Q000", # bad-quotes-inline-string (ruff-format recommended)
-    "Q001", # bad-quotes-multiline-string (ruff-format recommended)
-    "Q002", # bad-quotes-docstring (ruff-format recommended)
-    "Q003", # avoidable-escaped-quote (ruff-format recommended)
     "RUF003", # ambiguous-unicode-character-comment
-    "W191", # tab-indentation (ruff-format recommended)
 ]
 lint.isort = {known-first-party = [
     "glass",

tests/test_galaxies.py

@@ -39,7 +39,11 @@ def test_redshifts_from_nz(rng: np.random.Generator) -> None:
     # test with rng
 
     redshifts = redshifts_from_nz(
-        10, [0, 1, 2, 3, 4], [0, 0, 1, 1, 1], warn=False, rng=rng
+        10,
+        [0, 1, 2, 3, 4],
+        [0, 0, 1, 1, 1],
+        warn=False,
+        rng=rng,
     )
     assert not np.any(redshifts <= 1)
 
@@ -130,7 +134,13 @@ def test_galaxy_shear(rng):  # type: ignore[no-untyped-def]
         rng.normal(size=(512,)),
     )
     shear = galaxy_shear(
-        gal_lon, gal_lat, gal_eps, kappa, gamma1, gamma2, reduced_shear=False
+        gal_lon,
+        gal_lat,
+        gal_eps,
+        kappa,
+        gamma1,
+        gamma2,
+        reduced_shear=False,
     )
     assert np.shape(shear) == (512,)