Merge branch 'main' into saransh/test_fields

glass/__init__.py

@@ -1,5 +1,60 @@
 """GLASS package."""
 
+__all__ = [
+    "cls2cov",
+    "combine",
+    "cubic_windows",
+    "deflect",
+    "density_weight",
+    "discretized_cls",
+    "distance_grid",
+    "distance_weight",
+    "effective_bias",
+    "effective_cls",
+    "ellipticity_gaussian",
+    "ellipticity_intnorm",
+    "ellipticity_ryden04",
+    "equal_dens_zbins",
+    "fixed_zbins",
+    "from_convergence",
+    "galaxy_shear",
+    "gaussian_nz",
+    "gaussian_phz",
+    "generate_gaussian",
+    "generate_lognormal",
+    "getcl",
+    "iternorm",
+    "linear_bias",
+    "linear_windows",
+    "load_cls",
+    "loglinear_bias",
+    "lognormal_gls",
+    "multalm",
+    "multi_plane_matrix",
+    "multi_plane_weights",
+    "MultiPlaneConvergence",
+    "partition",
+    "position_weights",
+    "positions_from_delta",
+    "RadialWindow",
+    "redshift_grid",
+    "redshifts",
+    "redshifts_from_nz",
+    "restrict",
+    "save_cls",
+    "shear_from_convergence",
+    "smail_nz",
+    "tomo_nz_gausserr",
+    "tophat_windows",
+    "transform_cls",
+    "triaxial_axis_ratio",
+    "uniform_positions",
+    "vmap_galactic_ecliptic",
+    "volume_weight",
+    "write_catalog",
+]
+
+
 import contextlib
 from importlib.metadata import PackageNotFoundError
 
@@ -19,7 +74,6 @@
     transform_cls,
 )
 from glass.galaxies import (
-    _kappa_ia_nla,
     galaxy_shear,
     gaussian_phz,
     redshifts,

glass/core/array.py

@@ -131,7 +131,7 @@ def ndinterp(  # noqa: PLR0913
     )
 
 
-def trapz_product(
+def trapezoid_product(
     f: tuple[npt.NDArray[np.float64], npt.NDArray[np.float64]],
     *ff: tuple[
         npt.NDArray[np.float64],
@@ -169,7 +169,7 @@ def trapz_product(
     return np.trapezoid(y, x, axis=axis)  # type: ignore[no-any-return]
 
 
-def cumtrapz(
+def cumulative_trapezoid(
     f: npt.NDArray[np.int_] | npt.NDArray[np.float64],
     x: npt.NDArray[np.int_] | npt.NDArray[np.float64],
     dtype: npt.DTypeLike | None = None,

glass/galaxies.py

@@ -26,7 +26,7 @@
 import numpy as np
 import numpy.typing as npt
 
-from glass.core.array import broadcast_leading_axes, cumtrapz
+from glass.core.array import broadcast_leading_axes, cumulative_trapezoid
 
 if typing.TYPE_CHECKING:
     from cosmology import Cosmology
@@ -129,7 +129,7 @@ def redshifts_from_nz(
     # go through extra dimensions; also works if dims is empty
     for k in np.ndindex(dims):
         # compute the CDF of each galaxy population
-        cdf = cumtrapz(nz_out[k], z_out[k], dtype=float)
+        cdf = cumulative_trapezoid(nz_out[k], z_out[k], dtype=float)
         cdf /= cdf[-1]
 
         # sample redshifts and store result

glass/observations.py

@@ -34,7 +34,7 @@
 import numpy as np
 import numpy.typing as npt
 
-from glass.core.array import cumtrapz
+from glass.core.array import cumulative_trapezoid
 
 
 def vmap_galactic_ecliptic(
@@ -225,8 +225,8 @@ def fixed_zbins(
     """
     if nbins is not None and dz is None:
         zbinedges = np.linspace(zmin, zmax, nbins + 1)
-    if nbins is None and dz is not None:
-        zbinedges = np.arange(zmin, zmax, dz)
+    elif nbins is None and dz is not None:
+        zbinedges = np.arange(zmin, np.nextafter(zmax + dz, zmax), dz)
     else:
         msg = "exactly one of nbins and dz must be given"
         raise ValueError(msg)
@@ -263,7 +263,7 @@ def equal_dens_zbins(
     # first compute the cumulative integral (by trapezoidal rule)
     # then normalise: the first z is at CDF = 0, the last z at CDF = 1
     # interpolate to find the z values at CDF = i/nbins for i = 0, ..., nbins
-    cuml_nz = cumtrapz(nz, z)
+    cuml_nz = cumulative_trapezoid(nz, z)
     cuml_nz /= cuml_nz[[-1]]
     zbinedges = np.interp(np.linspace(0, 1, nbins + 1), cuml_nz, z)
 

glass/points.py

@@ -37,7 +37,7 @@
 import numpy as np
 import numpy.typing as npt
 
-from glass.core.array import broadcast_first, broadcast_leading_axes, trapz_product
+from glass.core.array import broadcast_first, broadcast_leading_axes, trapezoid_product
 
 if typing.TYPE_CHECKING:
     import collections.abc
@@ -85,7 +85,7 @@ def effective_bias(
 
     """
     norm = np.trapezoid(w.wa, w.za)
-    return trapz_product((z, bz), (w.za, w.wa)) / norm
+    return trapezoid_product((z, bz), (w.za, w.wa)) / norm
 
 
 def linear_bias(

tests/conftest.py

@@ -4,6 +4,4 @@
 
 @pytest.fixture(scope="session")
 def rng() -> np.random.Generator:
-    import numpy as np
-
     return np.random.default_rng(seed=42)

tests/core/test_array.py

@@ -7,9 +7,9 @@
 from glass.core.array import (
     broadcast_first,
     broadcast_leading_axes,
-    cumtrapz,
+    cumulative_trapezoid,
     ndinterp,
-    trapz_product,
+    trapezoid_product,
 )
 
 # check if scipy is available for testing
@@ -144,21 +144,21 @@ def test_ndinterp() -> None:
     )
 
 
-def test_trapz_product() -> None:
+def test_trapezoid_product() -> None:
     x1 = np.linspace(0, 2, 100)
     f1 = np.full_like(x1, 2.0)
 
     x2 = np.linspace(1, 2, 10)
     f2 = np.full_like(x2, 0.5)
 
-    s = trapz_product((x1, f1), (x2, f2))
+    s = trapezoid_product((x1, f1), (x2, f2))
 
     np.testing.assert_allclose(s, 1.0)
 
 
 @pytest.mark.skipif(not HAVE_SCIPY, reason="test requires SciPy")
-def test_cumtrapz() -> None:
-    from scipy.integrate import cumulative_trapezoid
+def test_cumulative_trapezoid() -> None:
+    import scipy.integrate as spi
 
     # 1D f and x
 
@@ -167,19 +167,19 @@ def test_cumtrapz() -> None:
 
     # default dtype (int - not supported by scipy)
 
-    glass_ct = cumtrapz(f, x)
+    glass_ct = cumulative_trapezoid(f, x)
     np.testing.assert_allclose(glass_ct, np.array([0, 1, 4, 7]))
 
     # explicit dtype (float)
 
-    glass_ct = cumtrapz(f, x, dtype=float)
-    scipy_ct = cumulative_trapezoid(f, x, initial=0)
+    glass_ct = cumulative_trapezoid(f, x, dtype=float)
+    scipy_ct = spi.cumulative_trapezoid(f, x, initial=0)
     np.testing.assert_allclose(glass_ct, scipy_ct)
 
     # explicit return array
 
-    result = cumtrapz(f, x, dtype=float, out=np.zeros((4,)))
-    scipy_ct = cumulative_trapezoid(f, x, initial=0)
+    result = cumulative_trapezoid(f, x, dtype=float, out=np.zeros((4,)))
+    scipy_ct = spi.cumulative_trapezoid(f, x, initial=0)
     np.testing.assert_allclose(result, scipy_ct)
 
     # 2D f and 1D x
@@ -189,17 +189,17 @@ def test_cumtrapz() -> None:
 
     # default dtype (int - not supported by scipy)
 
-    glass_ct = cumtrapz(f, x)
+    glass_ct = cumulative_trapezoid(f, x)
     np.testing.assert_allclose(glass_ct, np.array([[0, 2, 12, 31], [0, 2, 8, 17]]))
 
     # explicit dtype (float)
 
-    glass_ct = cumtrapz(f, x, dtype=float)
-    scipy_ct = cumulative_trapezoid(f, x, initial=0)
+    glass_ct = cumulative_trapezoid(f, x, dtype=float)
+    scipy_ct = spi.cumulative_trapezoid(f, x, initial=0)
     np.testing.assert_allclose(glass_ct, scipy_ct)
 
     # explicit return array
 
-    glass_ct = cumtrapz(f, x, dtype=float, out=np.zeros((2, 4)))
-    scipy_ct = cumulative_trapezoid(f, x, initial=0)
+    glass_ct = cumulative_trapezoid(f, x, dtype=float, out=np.zeros((2, 4)))
+    scipy_ct = spi.cumulative_trapezoid(f, x, initial=0)
     np.testing.assert_allclose(glass_ct, scipy_ct)

tests/test_fields.py

@@ -2,7 +2,7 @@
 import numpy as np
 import pytest
 
-from glass.fields import (
+from glass import (
     cls2cov,
     discretized_cls,
     effective_cls,

tests/test_fits.py

@@ -5,7 +5,7 @@
 import numpy.typing as npt
 import pytest
 
-from glass import user
+from glass import write_catalog
 
 # check if fitsio is available for testing
 HAVE_FITSIO = importlib.util.find_spec("fitsio") is not None
@@ -37,7 +37,7 @@ def _test_append(
             hdu.write(data, names=names, firstrow=hdu.get_nrows())
 
     with (
-        user.write_catalog(tmp_path / filename_gfits, ext="CATALOG") as out,
+        write_catalog(tmp_path / filename_gfits, ext="CATALOG") as out,
         fitsio.FITS(tmp_path / filename_tfits, "rw", clobber=True) as my_fits,
     ):
         for i in range(my_max):
@@ -80,7 +80,7 @@ def raise_error(msg: str) -> None:
         raise TestWriteError(msg)
 
     try:
-        with user.write_catalog(tmp_path / filename, ext="CATALOG") as out:
+        with write_catalog(tmp_path / filename, ext="CATALOG") as out:
             for i in range(my_max):
                 if i == except_int:
                     msg = "Unhandled exception"

tests/test_galaxies.py

@@ -3,7 +3,12 @@
 import pytest
 import pytest_mock
 
-from glass.galaxies import galaxy_shear, gaussian_phz, redshifts, redshifts_from_nz
+from glass import (
+    galaxy_shear,
+    gaussian_phz,
+    redshifts,
+    redshifts_from_nz,
+)
 
 
 def test_redshifts(mocker: pytest_mock.MockerFixture) -> None:

tests/test_lensing.py

@@ -7,13 +7,13 @@
 import numpy.typing as npt
 import pytest
 
-from glass.lensing import (
+from glass import (
     MultiPlaneConvergence,
+    RadialWindow,
     deflect,
     multi_plane_matrix,
     multi_plane_weights,
 )
-from glass.shells import RadialWindow
 
 if typing.TYPE_CHECKING:
     from cosmology import Cosmology

tests/test_points.py

@@ -6,7 +6,7 @@
 import numpy.typing as npt
 import pytest
 
-from glass.points import (
+from glass import (
     effective_bias,
     linear_bias,
     loglinear_bias,

tests/test_shapes.py

@@ -1,7 +1,7 @@
 import numpy as np
 import pytest
 
-from glass.shapes import (
+from glass import (
     ellipticity_gaussian,
     ellipticity_intnorm,
     ellipticity_ryden04,

tests/test_shells.py

@@ -1,7 +1,12 @@
 import numpy as np
 import pytest
 
-from glass.shells import RadialWindow, partition, restrict, tophat_windows
+from glass import (
+    RadialWindow,
+    partition,
+    restrict,
+    tophat_windows,
+)
 
 
 def test_tophat_windows() -> None: