gh-248: fix all remaining possible ruff # noqa statements (#394)

examples/1-basic/density.ipynb

@@ -177,12 +177,12 @@
     "        z1 = gal_z * np.cos(np.deg2rad(gal_lon)) * np.cos(np.deg2rad(gal_lat))\n",
     "        z2 = gal_z * np.sin(np.deg2rad(gal_lon)) * np.cos(np.deg2rad(gal_lat))\n",
     "        z3 = gal_z * np.sin(np.deg2rad(gal_lat))\n",
-    "        (i, j, k), c = np.unique(  # noqa: PLW2901\n",
+    "        indices, count = np.unique(\n",
     "            np.searchsorted(zcub[1:], [z1, z2, z3]),\n",
     "            axis=1,\n",
     "            return_counts=True,\n",
     "        )\n",
-    "        cube[i, j, k] += c"
+    "        cube[*indices] += count"
    ]
   },
   {

examples/1-basic/lensing.ipynb

@@ -279,9 +279,9 @@
     "pw = hp.pixwin(nside, lmax=lmax)\n",
     "\n",
     "# plot the realised and expected cls\n",
-    "l = np.arange(lmax + 1)  # noqa: E741\n",
-    "plt.plot(l, sim_cls[0], \"-k\", lw=2, label=\"simulation\")\n",
-    "plt.plot(l, theory_cls[\"W1xW1\"] * pw**2, \"-r\", lw=2, label=\"expectation\")\n",
+    "ell = np.arange(lmax + 1)\n",
+    "plt.plot(ell, sim_cls[0], \"-k\", lw=2, label=\"simulation\")\n",
+    "plt.plot(ell, theory_cls[\"W1xW1\"] * pw**2, \"-r\", lw=2, label=\"expectation\")\n",
     "plt.xscale(\"symlog\", linthresh=10, linscale=0.5, subs=[2, 3, 4, 5, 6, 7, 8, 9])\n",
     "plt.yscale(\"symlog\", linthresh=1e-9, linscale=0.5, subs=[2, 3, 4, 5, 6, 7, 8, 9])\n",
     "plt.xlabel(r\"angular mode number $l$\")\n",

examples/2-advanced/cosmic_shear.ipynb

@@ -297,22 +297,23 @@
     "theory_cls = camb.get_results(pars).get_source_cls_dict(lmax=lmax, raw_cl=True)\n",
     "\n",
     "# factor transforming convergence to shear\n",
-    "l = np.arange(lmax + 1)  # noqa: E741\n",
-    "fl = (l + 2) * (l + 1) * l * (l - 1) / np.clip(l**2 * (l + 1) ** 2, 1, None)\n",
+    "ell = np.arange(lmax + 1)\n",
+    "fl = (ell + 2) * (ell + 1) * ell * (ell - 1) / np.clip(ell**2 * (ell + 1) ** 2, 1, None)\n",
     "\n",
     "# the noise level from discrete observations with shape noise\n",
-    "nl = 4 * np.pi / (nbar * npix) * sigma_e**2 * (l >= 2)\n",
+    "ntot = nbar * npix\n",
+    "nl = 4 * np.pi / ntot * sigma_e**2 * (ell >= 2)\n",
     "\n",
     "# mixing matrix for uniform distribution of points\n",
-    "mm = (1 - 1 / (nbar * npix)) * np.eye(lmax + 1, lmax + 1) + (l + 1 / 2) / (nbar * npix)\n",
+    "mm = (1 - 1 / ntot) * np.eye(lmax + 1, lmax + 1) + (ell + 1 / 2) / ntot\n",
     "mm[:2, :] = mm[:, :2] = 0\n",
     "\n",
     "# the shear pixel window function for HEALPix\n",
     "_, pw = hp.pixwin(nside, lmax=lmax, pol=True)\n",
     "\n",
     "# plot the realised and expected cls\n",
-    "plt.plot(l, cls[1] - nl, \"-k\", lw=2, label=\"simulation\")\n",
-    "plt.plot(l, pw**2 * mm @ (fl * theory_cls[\"W1xW1\"]), \"-r\", lw=2, label=\"expectation\")\n",
+    "plt.plot(ell, cls[1] - nl, \"-k\", lw=2, label=\"simulation\")\n",
+    "plt.plot(ell, pw**2 * mm @ (fl * theory_cls[\"W1xW1\"]), \"-r\", lw=2, label=\"expectation\")\n",
     "plt.xscale(\"symlog\", linthresh=10, linscale=0.5, subs=[2, 3, 4, 5, 6, 7, 8, 9])\n",
     "plt.yscale(\"symlog\", linthresh=1e-9, linscale=0.5, subs=[2, 3, 4, 5, 6, 7, 8, 9])\n",
     "plt.xlabel(\"angular mode number $l$\")\n",

glass/lensing.py

@@ -168,13 +168,13 @@ def from_convergence(  # noqa: PLR0913
     alm = hp.map2alm(kappa, lmax=lmax, pol=False, use_pixel_weights=True)
 
     # mode number; all conversions are factors of this
-    l = np.arange(lmax + 1)  # noqa: E741
+    ell = np.arange(lmax + 1)
 
     # this tuple will be returned
     results: tuple[npt.NDArray[np.float64], ...] = ()
 
     # convert convergence to potential
-    fl = np.divide(-2, l * (l + 1), where=(l > 0), out=np.zeros(lmax + 1))
+    fl = np.divide(-2, ell * (ell + 1), where=(ell > 0), out=np.zeros(lmax + 1))
     hp.almxfl(alm, fl, inplace=True)
 
     # if potential is requested, compute map and add to output
@@ -190,9 +190,8 @@ def from_convergence(  # noqa: PLR0913
     blm = np.zeros_like(alm)
 
     # compute deflection alms in place
-    fl = np.sqrt(l * (l + 1))
-    # TODO(ntessore): missing spin-1 pixel window function here # noqa: FIX002
-    # https://github.com/glass-dev/glass/issues/243
+    fl = np.sqrt(ell * (ell + 1))
+    # missing spin-1 pixel window function here
     hp.almxfl(alm, fl, inplace=True)
 
     # if deflection is requested, compute spin-1 maps and add to output
@@ -207,7 +206,7 @@ def from_convergence(  # noqa: PLR0913
 
     # compute shear alms in place
     # if discretised, factor out spin-0 kernel and apply spin-2 kernel
-    fl = np.sqrt((l - 1) * (l + 2), where=(l > 0), out=np.zeros(lmax + 1))
+    fl = np.sqrt((ell - 1) * (ell + 2), where=(ell > 0), out=np.zeros(lmax + 1))
     fl /= 2
     if discretized:
         pw0, pw2 = hp.pixwin(nside, lmax=lmax, pol=True)
@@ -250,9 +249,9 @@ def shear_from_convergence(
     blm = np.zeros_like(alm)
 
     # factor to convert convergence alm to shear alm
-    l = np.arange(lmax + 1)  # noqa: E741
-    fl = np.sqrt((l + 2) * (l + 1) * l * (l - 1))
-    fl /= np.clip(l * (l + 1), 1, None)
+    ell = np.arange(lmax + 1)
+    fl = np.sqrt((ell + 2) * (ell + 1) * ell * (ell - 1))
+    fl /= np.clip(ell * (ell + 1), 1, None)
     fl *= -1
 
     # if discretised, factor out spin-0 kernel and apply spin-2 kernel

glass/observations.py

@@ -23,7 +23,6 @@
 
 .. autofunction:: vmap_galactic_ecliptic
 
-
 """  # noqa: D205, D400
 
 from __future__ import annotations

glass/shapes.py

@@ -86,13 +86,13 @@ def triaxial_axis_ratio(
     x2 = np.square(xi)
 
     # eq. (11) multiplied by xi^2 zeta^2
-    A = (1 + z2m1 * sin2_phi) * cos2_theta + x2 * sin2_theta  # noqa: N806
-    B2 = 4 * z2m1**2 * cos2_theta * sin2_phi * cos2_phi  # noqa: N806
-    C = 1 + z2m1 * cos2_phi  # noqa: N806
+    a = (1 + z2m1 * sin2_phi) * cos2_theta + x2 * sin2_theta
+    b2 = 4 * z2m1**2 * cos2_theta * sin2_phi * cos2_phi
+    c = 1 + z2m1 * cos2_phi
 
     # eq. (12)
     return np.sqrt(  # type: ignore[no-any-return]
-        (A + C - np.sqrt((A - C) ** 2 + B2)) / (A + C + np.sqrt((A - C) ** 2 + B2)),
+        (a + c - np.sqrt((a - c) ** 2 + b2)) / (a + c + np.sqrt((a - c) ** 2 + b2)),
     )
 
 

glass/shells.py

@@ -40,6 +40,7 @@
 .. autofunction:: distance_weight
 .. autofunction:: volume_weight
 .. autofunction:: density_weight
+
 """  # noqa: D205, D400
 
 from __future__ import annotations

pyproject.toml

@@ -131,6 +131,10 @@ show-fixes = true
 src = [
     "glass",
 ]
+lint.allowed-confusables = [
+    "α",
+    "γ",
+]
 lint.ignore = [
     "COM812", # missing-trailing-comma (ruff-format recommended)
     "D203", # one-blank-line-before-class

tests/test_fits.py

@@ -60,32 +60,51 @@ def _test_append(
 
 @pytest.mark.skipif(not HAVE_FITSIO, reason="test requires fitsio")
 def test_write_exception(tmp_path: pathlib.Path) -> None:
+    class TestWriteError(Exception):
+        """Custom exception for controlled testing."""
+
+    def raise_error(msg: str) -> None:
+        """Raise a custom exception for controlled testing.
+
+        Parameters
+        ----------
+        msg
+            A message to be passed to the exception.
+
+        Raises
+        ------
+        TestWriteError
+            A custom exception for controlled testing.
+
+        """
+        raise TestWriteError(msg)
+
     try:
         with user.write_catalog(tmp_path / filename, ext="CATALOG") as out:
             for i in range(my_max):
                 if i == except_int:
                     msg = "Unhandled exception"
-                    raise Exception(msg)  # noqa: TRY002, TRY301
+                    raise_error(msg)
                 array = np.arange(i, i + 1, delta)  # array of size 1/delta
                 array2 = np.arange(i + 1, i + 2, delta)  # array of size 1/delta
                 out.write(RA=array, RB=array2)
 
-    except Exception:  # noqa: BLE001
+    except TestWriteError:
         import fitsio
 
         with fitsio.FITS(tmp_path / filename) as hdul:
             data = hdul[1].read()
             assert data["RA"].size == except_int / delta
             assert data["RB"].size == except_int / delta
 
-            fitsMat = data["RA"].reshape(except_int, int(1 / delta))  # noqa: N806
-            fitsMat2 = data["RB"].reshape(except_int, int(1 / delta))  # noqa: N806
+            fits_mat = data["RA"].reshape(except_int, int(1 / delta))
+            fits_mat2 = data["RB"].reshape(except_int, int(1 / delta))
             for i in range(except_int):
                 array = np.arange(
                     i,
                     i + 1,
                     delta,
                 )  # re-create array to compare to read data
                 array2 = np.arange(i + 1, i + 2, delta)
-                assert array.tolist() == fitsMat[i].tolist()
-                assert array2.tolist() == fitsMat2[i].tolist()
+                assert array.tolist() == fits_mat[i].tolist()
+                assert array2.tolist() == fits_mat2[i].tolist()