Merge branch 'paddy/issue-358' into saransh/test_points

.git-blame-ignore-revs

@@ -4,3 +4,4 @@ b42067f6776dcd763827000d585a88e071b78af3
 f9bac62f497a7288aa71fd4dbd948945c37f854e
 # applied ruff-linting - https://github.com/glass-dev/glass/pull/232
 e58d8616c03b8447aba90996905a98b42f18ba0a
+# added static typing - https://github.com/glass-dev/glass/pull/368

.gitignore

@@ -9,3 +9,4 @@ dist
 .env
 .coverage*
 coverage*
+.ipynb_checkpoints

.pre-commit-config.yaml

@@ -33,12 +33,12 @@ repos:
         args:
           - --strict
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.0
+    rev: v0.7.2
     hooks:
       - id: ruff
       - id: ruff-format
   - repo: https://github.com/adamchainz/blacken-docs
-    rev: 1.19.0
+    rev: 1.19.1
     hooks:
       - id: blacken-docs
         additional_dependencies:
@@ -62,11 +62,11 @@ repos:
     hooks:
       - id: forbid-tabs
   - repo: https://github.com/rhysd/actionlint
-    rev: v1.7.3
+    rev: v1.7.4
     hooks:
       - id: actionlint
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.12.1
+    rev: v1.13.0
     hooks:
       - id: mypy
         additional_dependencies:

docs/conf.py

@@ -54,7 +54,7 @@
 
 html_logo = "_static/logo.png"
 html_favicon = "_static/favicon.ico"
-html_css_files = []  # type: ignore[var-annotated]
+html_css_files: list[str] = []
 
 
 # -- Intersphinx -------------------------------------------------------------

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/core/algorithm.py

@@ -7,12 +7,12 @@
 
 
 def nnls(
-    a: npt.ArrayLike,
-    b: npt.ArrayLike,
+    a: npt.NDArray[np.float64],
+    b: npt.NDArray[np.float64],
     *,
     tol: float = 0.0,
     maxiter: int | None = None,
-) -> npt.ArrayLike:
+) -> npt.NDArray[np.float64]:
     """
     Compute a non-negative least squares solution.
 

glass/core/array.py

@@ -1,18 +1,32 @@
 """Module for array utilities."""
 
+from __future__ import annotations
+
+import typing
 from functools import partial
 
 import numpy as np
+import numpy.typing as npt
 
 
-def broadcast_first(*arrays):  # type: ignore[no-untyped-def]
+def broadcast_first(
+    *arrays: npt.NDArray[np.float64],
+) -> tuple[npt.NDArray[np.float64], ...]:
     """Broadcast arrays, treating the first axis as common."""
     arrays = tuple(np.moveaxis(a, 0, -1) if np.ndim(a) else a for a in arrays)
     arrays = np.broadcast_arrays(*arrays)
     return tuple(np.moveaxis(a, -1, 0) if np.ndim(a) else a for a in arrays)
 
 
-def broadcast_leading_axes(*args):  # type: ignore[no-untyped-def]
+def broadcast_leading_axes(
+    *args: tuple[
+        float | npt.NDArray[np.float64],
+        int,
+    ],
+) -> tuple[
+    tuple[int, ...],
+    typing.Unpack[tuple[npt.NDArray[np.float64], ...]],
+]:
     """
     Broadcast all but the last N axes.
 
@@ -49,7 +63,15 @@ def broadcast_leading_axes(*args):  # type: ignore[no-untyped-def]
     return (dims, *arrs)
 
 
-def ndinterp(x, xp, fp, axis=-1, left=None, right=None, period=None):  # type: ignore[no-untyped-def] # noqa: PLR0913
+def ndinterp(  # noqa: PLR0913
+    x: float | npt.NDArray[np.float64],
+    xp: npt.NDArray[np.float64],
+    fp: npt.NDArray[np.float64],
+    axis: int = -1,
+    left: float | None = None,
+    right: float | None = None,
+    period: float | None = None,
+) -> npt.NDArray[np.float64]:
     """Interpolate multi-dimensional array over axis."""
     return np.apply_along_axis(
         partial(np.interp, x, xp),
@@ -61,8 +83,16 @@ def ndinterp(x, xp, fp, axis=-1, left=None, right=None, period=None):  # type: i
     )
 
 
-def trapz_product(f, *ff, axis=-1):  # type: ignore[no-untyped-def]
+def trapz_product(
+    f: tuple[npt.NDArray[np.float64], npt.NDArray[np.float64]],
+    *ff: tuple[
+        npt.NDArray[np.float64],
+        npt.NDArray[np.float64],
+    ],
+    axis: int = -1,
+) -> npt.NDArray[np.float64]:
     """Trapezoidal rule for a product of functions."""
+    x: npt.NDArray[np.float64]
     x, _ = f
     for x_, _ in ff:
         x = np.union1d(
@@ -72,10 +102,19 @@ def trapz_product(f, *ff, axis=-1):  # type: ignore[no-untyped-def]
     y = np.interp(x, *f)
     for f_ in ff:
         y *= np.interp(x, *f_)
-    return np.trapz(y, x, axis=axis)  # type: ignore[attr-defined]
+    return np.trapz(  # type: ignore[attr-defined]
+        y,
+        x,
+        axis=axis,
+    )
 
 
-def cumtrapz(f, x, dtype=None, out=None):  # type: ignore[no-untyped-def]
+def cumtrapz(
+    f: npt.NDArray[np.int_] | npt.NDArray[np.float64],
+    x: npt.NDArray[np.int_] | npt.NDArray[np.float64],
+    dtype: npt.DTypeLike | None = None,
+    out: npt.NDArray[np.float64] | None = None,
+) -> npt.NDArray[np.float64]:
     """Cumulative trapezoidal rule along last axis."""
     if out is None:
         out = np.empty_like(f, dtype=dtype)

glass/ext/__init__.py

@@ -7,7 +7,7 @@
 """
 
 
-def _extend_path(path, name) -> list:  # type: ignore[no-untyped-def, type-arg]
+def _extend_path(path: list[str], name: str) -> list[str]:
     import os.path
     from pkgutil import extend_path
 
@@ -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
-        )
+        ),
     )