Merge pull request #1140 from astropy/np_isin

np.in1d --> np.isin

Author: aphearin

CHANGES.rst

@@ -1,24 +1,28 @@
+0.9.4 (unreleased)
+------------------
+
+
 0.9.3 (2025-02-10)
 ------------------
- 
+
  - Compatibility with Numpy 2.0 (https://github.com/astropy/halotools/pull/1114)
 
 
 0.9.2 (2024-12-02)
 ------------------
- 
+
  - Compatibility with Astropy 7 (https://github.com/astropy/halotools/pull/1107)
 
 
 0.9.1 (2024-09-11)
 ------------------
- 
+
  - Repackage halotools according to pyproject.toml (https://github.com/astropy/halotools/pull/1093)
 
 
 0.9.0 (2024-09-06)
 ------------------
- 
+
  - Add models and mock observations of intrinsic alignments (https://github.com/astropy/halotools/pull/1056)
 
 

halotools/empirical_models/phase_space_models/analytic_models/profile_model_template.py

@@ -3,17 +3,17 @@
 a container class for the distribution of mass and/or galaxies
 within dark matter halos.
 """
-from __future__ import division, print_function, absolute_import, unicode_literals
+
+from __future__ import absolute_import, division, print_function, unicode_literals
 
 import numpy as np
-from scipy.integrate import quad as quad_integration
-from scipy.optimize import minimize as scipy_minimize
 from astropy import units as u
 from astropy.constants import G
-
-from . import halo_boundary_functions
+from scipy.integrate import quad as quad_integration
+from scipy.optimize import minimize as scipy_minimize
 
 from ... import model_defaults
+from . import halo_boundary_functions
 
 newtonG = G.to(u.km * u.km * u.Mpc / (u.Msun * u.s * u.s))
 
@@ -223,17 +223,20 @@ def cumulative_mass_PDF(self, scaled_radius, *prof_params):
         x = np.atleast_1d(scaled_radius).astype(np.float64)
         enclosed_mass = np.zeros_like(x)
 
+        def _scalar_integrand(*args, **kwargs):
+            return self._enclosed_dimensionless_mass_integrand(*args, **kwargs)[0]
+
         for i in range(len(x)):
             enclosed_mass[i], _ = quad_integration(
-                self._enclosed_dimensionless_mass_integrand,
+                _scalar_integrand,
                 0.0,
                 x[i],
                 epsrel=1e-5,
                 args=prof_params,
             )
 
         total, _ = quad_integration(
-            self._enclosed_dimensionless_mass_integrand,
+            _scalar_integrand,
             0.0,
             1.0,
             epsrel=1e-5,

halotools/empirical_models/phase_space_models/analytic_models/satellites/nfw/kernels/biased_isotropic_velocity.py

@@ -1,11 +1,10 @@
-"""
-"""
+""" """
+
 import numpy as np
 from scipy.integrate import quad as quad_integration
 
 from .mass_profile import _g_integral
 
-
 __all__ = ("dimensionless_radial_velocity_dispersion",)
 
 
@@ -58,21 +57,25 @@ def dimensionless_radial_velocity_dispersion(
         gal_conc * gal_conc * x * (1.0 + gal_conc * x) ** 2 / _g_integral(halo_conc)
     )
     extra_args = halo_conc / np.atleast_1d(gal_conc).astype("f4")
+    assert extra_args.shape == (1,)
+    extra_args = float(extra_args[0])
 
     lower_limit = gal_conc * x
     upper_limit = float("inf")
     for i in range(len(x)):
+        a = lower_limit[i]
+        b = upper_limit
         term1, _ = quad_integration(
             _jeans_integrand_term1,
-            lower_limit[i],
-            upper_limit,
+            a,
+            b,
             epsrel=profile_integration_tol,
             args=extra_args,
         )
         term2, _ = quad_integration(
             _jeans_integrand_term2,
-            lower_limit[i],
-            upper_limit,
+            a,
+            b,
             epsrel=profile_integration_tol,
             args=extra_args,
         )

halotools/empirical_models/phase_space_models/analytic_models/satellites/nfw/kernels/mass_profile.py

@@ -1,5 +1,5 @@
-"""
-"""
+""" """
+
 import numpy as np
 
 __all__ = ("cumulative_mass_PDF", "dimensionless_mass_density")

halotools/empirical_models/phase_space_models/analytic_models/satellites/nfw/kernels/tests/test_biased_isotropic_velocity.py

@@ -1,13 +1,16 @@
-"""
-"""
+""" """
+
 import numpy as np
 from astropy.utils.data import get_pkg_data_filename
 
-from ..unbiased_isotropic_velocity import dimensionless_radial_velocity_dispersion as unbiased_dimless_vel_rad_disp
-from ..biased_isotropic_velocity import dimensionless_radial_velocity_dispersion as biased_dimless_vel_rad_disp
-
+from ..biased_isotropic_velocity import (
+    dimensionless_radial_velocity_dispersion as biased_dimless_vel_rad_disp,
+)
+from ..unbiased_isotropic_velocity import (
+    dimensionless_radial_velocity_dispersion as unbiased_dimless_vel_rad_disp,
+)
 
-__all__ = ('test_unbiased_vel_rad_disp1', )
+__all__ = ("test_unbiased_vel_rad_disp1",)
 
 
 def test_unbiased_vel_rad_disp1():
@@ -25,14 +28,14 @@ def test_unbiased_vel_rad_disp2():
     halo_conc = 5
     unbiased_result = unbiased_dimless_vel_rad_disp(scaled_radius, halo_conc)
 
-    gal_conc = 2*halo_conc
+    gal_conc = 2 * halo_conc
     biased_result = biased_dimless_vel_rad_disp(scaled_radius, halo_conc, gal_conc)
     assert not np.allclose(unbiased_result, biased_result)
 
 
 def test_unbiased_vel_rad_disp_external_ch10_cg5():
     halo_conc, gal_conc = 10, 5
-    fname = get_pkg_data_filename('data/van_den_bosch_nfw_vr_disp_ch10_cg5.dat')
+    fname = get_pkg_data_filename("data/van_den_bosch_nfw_vr_disp_ch10_cg5.dat")
     x = np.loadtxt(fname)
     frank_r_by_Rvir = x[:, 1]
     frank_dimless_sigma_rad = x[:, 2]
@@ -42,7 +45,7 @@ def test_unbiased_vel_rad_disp_external_ch10_cg5():
 
 def test_unbiased_vel_rad_disp_external_ch5_cg10():
     halo_conc, gal_conc = 5, 10
-    fname = get_pkg_data_filename('data/van_den_bosch_nfw_vr_disp_ch5_cg10.dat')
+    fname = get_pkg_data_filename("data/van_den_bosch_nfw_vr_disp_ch5_cg10.dat")
     x = np.loadtxt(fname)
     frank_r_by_Rvir = x[:, 1]
     frank_dimless_sigma_rad = x[:, 2]

halotools/empirical_models/phase_space_models/analytic_models/satellites/nfw/kernels/unbiased_isotropic_velocity.py

@@ -1,11 +1,10 @@
-"""
-"""
+""" """
+
 import numpy as np
 from scipy.integrate import quad as quad_integration
 
 from .mass_profile import _g_integral
 
-
 __all__ = ("dimensionless_radial_velocity_dispersion",)
 
 

halotools/empirical_models/phase_space_models/analytic_models/satellites/nfw/nfw_phase_space.py

@@ -1,5 +1,5 @@
-"""
-"""
+""" """
+
 from __future__ import absolute_import, division, print_function
 
 import numpy as np

halotools/empirical_models/phase_space_models/analytic_models/satellites/nfw/nfw_profile.py

@@ -5,20 +5,20 @@
 Navarry, Frenk and White (1995), `arXiv:9508025 <http://arxiv.org/abs/astro-ph/9508025/>`_.
 a sub-class of `~halotools.empirical_models.AnalyticDensityProf`.
 """
-from __future__ import division, print_function, absolute_import, unicode_literals
 
-import numpy as np
-
-from .conc_mass import direct_from_halo_catalog, dutton_maccio14
-from .kernels import nfw_dimensionless_mass_density, nfw_cumulative_mass_PDF
-from .kernels import standalone_mc_generate_nfw_radial_positions
+from __future__ import absolute_import, division, print_function, unicode_literals
 
-from ...profile_model_template import AnalyticDensityProf
-
-from ..... import model_defaults
+import numpy as np
 
 from ......sim_manager import sim_defaults
-
+from ..... import model_defaults
+from ...profile_model_template import AnalyticDensityProf
+from .conc_mass import direct_from_halo_catalog, dutton_maccio14
+from .kernels import (
+    nfw_cumulative_mass_PDF,
+    nfw_dimensionless_mass_density,
+    standalone_mc_generate_nfw_radial_positions,
+)
 
 __all__ = ("NFWProfile",)
 __author__ = ("Andrew Hearin", "Benedikt Diemer")
@@ -44,7 +44,7 @@ def __init__(
         conc_mass_model=model_defaults.conc_mass_model,
         concentration_key=model_defaults.concentration_key,
         halo_boundary_key=None,
-        **kwargs
+        **kwargs,
     ):
         r"""
         Parameters