Issue/654/redshift to utils

.github/workflows/build_check.yml

@@ -16,7 +16,7 @@ jobs:
     - name: Install prereq and NumCosmo using conda
       run: |
         echo "$CONDA/bin" >> $GITHUB_PATH
-        conda install -c conda-forge gobject-introspection pygobject numcosmo cmake swig setuptools_scm sphinx sphinx_rtd_theme nbconvert pandoc ipython
+        conda install -c conda-forge gobject-introspection pygobject 'numcosmo<=0.22.0' cmake swig setuptools_scm sphinx sphinx_rtd_theme nbconvert pandoc ipython
     - name: Install prereq using pip
       run: |
         pip install -r requirements.txt

clmm/cosmology/cluster_toolkit.py

@@ -6,7 +6,7 @@
 from astropy import units
 from astropy.cosmology import LambdaCDM, FlatLambdaCDM
 
-from ..constants import Constants as const
+from ..utils.constants import Constants as const
 
 from .parent_class import CLMMCosmology
 

clmm/cosmology/parent_class.py

@@ -3,9 +3,8 @@
 """
 # CLMM Cosmology object abstract superclass
 import numpy as np
-from ..utils import validate_argument
-from ..redshift import compute_for_good_redshifts
-from ..constants import Constants as const
+from ..utils import validate_argument, compute_for_good_redshifts
+from ..utils.constants import Constants as const
 
 
 class CLMMCosmology:

clmm/dataops/__init__.py

@@ -14,8 +14,8 @@
     _validate_dec,
     _validate_is_deltasigma_sigma_c,
     _validate_coordinate_system,
+    _integ_pzfuncs,
 )
-from ..redshift import _integ_pzfuncs
 
 
 def compute_tangential_and_cross_components(

clmm/galaxycluster.py

@@ -12,14 +12,14 @@
     compute_background_probability,
 )
 from .theory import compute_critical_surface_density_eff
-from .plotting import plot_profiles
 from .utils import (
     validate_argument,
     _validate_ra,
     _validate_dec,
     _draw_random_points_from_tab_distribution,
     _validate_coordinate_system,
 )
+from .utils.plotting import plot_profiles
 
 
 class GalaxyCluster:

clmm/support/mock_data.py

@@ -17,8 +17,8 @@
     _draw_random_points_from_distribution,
     gaussian,
     _validate_coordinate_system,
+    redshift_distributions as zdist,
 )
-from ..redshift import distributions as zdist
 
 
 def generate_galaxy_catalog(

clmm/theory/parent_class.py

@@ -21,8 +21,6 @@
 from ..utils import (
     validate_argument,
     compute_beta_s_func,
-)
-from ..redshift import (
     _integ_pzfuncs,
     compute_for_good_redshifts,
 )

clmm/utils/__init__.py

@@ -1,5 +1,7 @@
 """General utility functions that are used in multiple modules"""
 
+from . import redshift_distributions, constants, plotting
+
 from .beta_lens import (
     compute_beta,
     compute_beta_s,
@@ -33,6 +35,11 @@
     gaussian,
 )
 
+from .redshift_tools import (
+    _integ_pzfuncs,
+    compute_for_good_redshifts,
+)
+
 from .validation import (
     arguments_consistency,
     _patch_rho_crit_to_cd2018,

clmm/utils/beta_lens.py

@@ -2,7 +2,7 @@
 import numpy as np
 from scipy.integrate import quad
 
-from ..redshift import distributions as zdist
+from . import redshift_distributions as zdist
 
 
 def compute_beta(z_src, z_cl, cosmo):

clmm/utils/validation.py

@@ -1,7 +1,7 @@
 """General utility functions that are used in multiple modules"""
 
 import numpy as np
-from ..constants import Constants as const
+from ..utils.constants import Constants as const
 
 
 def arguments_consistency(arguments, names=None, prefix=""):
@@ -226,6 +226,7 @@ def _validate_is_deltasigma_sigma_c(is_deltasigma, sigma_c):
     if not is_deltasigma and sigma_c is not None:
         raise TypeError(f"sigma_c (={sigma_c}) must be None when is_deltasigma=False")
 
+
 def _validate_coordinate_system(loc, coordinate_system, valid_type):
     r"""Validate the coordinate system.
 
@@ -245,6 +246,7 @@ def _validate_coordinate_system(loc, coordinate_system, valid_type):
     if loc[coordinate_system] not in ["celestial", "euclidean"]:
         raise ValueError(f"{coordinate_system} must be 'celestial' or 'euclidean'.")
 
+
 class DiffArray:
     """Array where arr1==arr2 is actually all(arr1==arr)"""
 

docs/doc-config.ini

@@ -1,13 +1,10 @@
 APIDOC
 clusterensemble
-constants
 cosmology
 dataops
 galaxycluster
 gcdata
-redshift
 theory
-plotting
 utils
 support
 

examples/demo_theory_functionality.ipynb

@@ -111,7 +111,7 @@
     "\n",
     "# source properties\n",
     "z_src = 2.0  # all sources in the same plan\n",
-    "z_distrib_func = clmm.redshift.distributions.chang2013  # sources redshift following a distribution\n",
+    "z_distrib_func = clmm.utils.redshift_distributions.chang2013  # sources redshift following a distribution\n",
     "alpha = [2, -0.5]"
    ]
   },

examples/demo_theory_functionality_diff_z_types.ipynb

@@ -90,7 +90,7 @@
    "source": [
     "from clmm.support import mock_data as mock\n",
     "from clmm import Cosmology\n",
-    "from clmm.redshift.distributions import *"
+    "from clmm.utils.redshift_distributions import *"
    ]
   },
   {

examples/demo_theory_functionality_oo.ipynb

@@ -106,7 +106,7 @@
     "\n",
     "# source properties\n",
     "z_src = 2.0  # all sources in the same plane\n",
-    "z_distrib_func = clmm.redshift.distributions.chang2013  # sources redshift following a distribution\n",
+    "z_distrib_func = clmm.utils.redshift_distributions.chang2013  # sources redshift following a distribution\n",
     "alpha = [2, -0.5]"
    ]
   },

examples/mass_fitting/Example3_Fit_Halo_Mass_to_Shear_Catalog.ipynb

@@ -453,7 +453,7 @@
     "        #'delta_z_cut': delta_z_cut,\n",
     "        #'zmin': None,\n",
     "        # We provide the redshift distribution (default: Chang et al. 2013) for calculating the beta_s statistics\n",
-    "        \"z_distrib_func\": clmm.redshift.distributions.chang2013,\n",
+    "        \"z_distrib_func\": clmm.utils.redshift_distributions.chang2013,\n",
     "    }\n",
     "    beta_s_mean = clmm.utils.compute_beta_s_mean_from_distribution(**beta_kwargs)\n",
     "    beta_s_square_mean = clmm.utils.compute_beta_s_square_mean_from_distribution(**beta_kwargs)\n",

tests/test_cosmo_parent.py

@@ -4,7 +4,7 @@
 from numpy.testing import assert_raises, assert_allclose, assert_equal
 import clmm.theory as theo
 from clmm.cosmology.parent_class import CLMMCosmology
-from clmm.constants import Constants as const
+from clmm.utils.constants import Constants as const
 
 # ----------- Some Helper Functions for the Validation Tests ---------------
 

tests/test_mockdata.py

@@ -7,7 +7,7 @@
 import clmm.dataops as da
 from clmm.support import mock_data as mock
 from clmm.support.sampler import fitters
-from clmm.redshift import distributions as zdist
+from clmm.utils import redshift_distributions as zdist
 
 TOLERANCE = {"rtol": 5.0e-4, "atol": 1.0e-4}
 
@@ -257,17 +257,13 @@ def test_shapenoise():
 
     # Verify that the shape noise is Gaussian around 0 (for the very small shear here)
     sigma = 0.25
-    data = mock.generate_galaxy_catalog(
-        10**12.0, 0.3, 4, cosmo, 0.8, ngals=50000, shapenoise=sigma
-    )
+    data = mock.generate_galaxy_catalog(10**12.0, 0.3, 4, cosmo, 0.8, ngals=50000, shapenoise=sigma)
     # Check that there are no galaxies with |e|>1
     assert_equal(np.count_nonzero((data["e1"] > 1) | (data["e1"] < -1)), 0)
     assert_equal(np.count_nonzero((data["e2"] > 1) | (data["e2"] < -1)), 0)
     # Check that shape noise is Guassian with correct std dev
     bins = np.arange(-1, 1.1, 0.1)
-    gauss = (
-        5000 * np.exp(-0.5 * (bins[:-1] + 0.05) ** 2 / sigma**2) / (sigma * np.sqrt(2 * np.pi))
-    )
+    gauss = 5000 * np.exp(-0.5 * (bins[:-1] + 0.05) ** 2 / sigma**2) / (sigma * np.sqrt(2 * np.pi))
     assert_allclose(np.histogram(data["e1"], bins=bins)[0], gauss, atol=50, rtol=0.05)
     assert_allclose(np.histogram(data["e2"], bins=bins)[0], gauss, atol=50, rtol=0.05)
 

tests/test_theory.py

@@ -1,18 +1,19 @@
 """Tests for theory/"""
+
 import json
 import numpy as np
 from numpy.testing import assert_raises, assert_allclose, assert_equal
 from astropy.cosmology import FlatLambdaCDM, LambdaCDM
 import clmm.theory as theo
-from clmm.constants import Constants as clc
+from clmm.utils.constants import Constants as clc
 from clmm.galaxycluster import GalaxyCluster
 from clmm import GCData
 from clmm.utils import (
     compute_beta_s_square_mean_from_distribution,
     compute_beta_s_mean_from_distribution,
     compute_beta_s_func,
+    redshift_distributions as zdist,
 )
-from clmm.redshift.distributions import chang2013, desc_srd
 
 TOLERANCE = {"rtol": 1.0e-8}
 
@@ -565,8 +566,8 @@ def test_shear_convergence_unittests(modeling_data, profile_init):
         gammat_inf = theo.compute_tangential_shear(cosmo=cosmo, **cfg_inf["GAMMA_PARAMS"])
         kappa_inf = theo.compute_convergence(cosmo=cosmo, **cfg_inf["GAMMA_PARAMS"])
 
-        # test z_src = chang2013 distribution
-        cfg_inf["GAMMA_PARAMS"]["z_src"] = chang2013
+        # test z_src = zdist.chang2013 distribution
+        cfg_inf["GAMMA_PARAMS"]["z_src"] = zdist.chang2013
         cfg_inf["GAMMA_PARAMS"]["z_src_info"] = "distribution"
 
         # store original values

tests/test_utils.py

@@ -12,8 +12,8 @@
     arguments_consistency,
     validate_argument,
     DiffArray,
+    redshift_distributions as zdist,
 )
-from clmm.redshift import distributions as zdist
 
 
 TOLERANCE = {"rtol": 1.0e-6, "atol": 0}
@@ -90,9 +90,7 @@ def test_correct_with_boost_model():
         )
 
     # Test requesting unsupported boost model
-    assert_raises(
-        KeyError, utils.correct_with_boost_model, rvals, sigma_vals, "glue", boost_rscale
-    )
+    assert_raises(KeyError, utils.correct_with_boost_model, rvals, sigma_vals, "glue", boost_rscale)
 
 
 def test_compute_radial_averages():
@@ -578,7 +576,7 @@ def test_beta_functions(modeling_data):
     # beta mean from distributions
 
     for model in (None, zdist.chang2013, zdist.desc_srd):
-        # None defaults to chang2013 for compute_beta* functions
+        # None defaults to chang2013 for compute_beta* functions.
 
         if model is None:
             model = zdist.chang2013