General bugfixes & enhancements. (#925)

* wrong Pk2D type should return TypeError

* cosmetics

* x_out in GNFW profile should trigger interp recomputation

* enable flake for constants.py

* comprehensive imports & specified __all__ for star-imports

* E402 is all over CCL and we silence it every time; get rid of it

* fixed typos

* document x_out behavior

* removed spurious import

* remove huge mamba banner from installation output

* temporary bugfix for rho0 in HMCalculator

* enable func_from_name --> Func.from_name

* implemented MassDef.from_name

* HMCalculator from strings

* removed  anti-patterns

* clear all temporary vars in Cosmology

* combined type checking for

* tests for all new features & few fixes

* don't even store fastpt; reload time is negligible

* more useful error when cosmicemu fails

* improved coverage

* Address Issue 805.

* needs a copy of ccl_params stored in cosmo

* removed repeated code

* added new func to __all__

* forgot parens

* flake

* ImportError --> ModuleNotFoundError

* make mass_def a required argument

* make mass_def a required argument (tests)

* reverted integ_interp in HaloProfileGNFW

* make mass_def a required argument (more funcs)

* bugfix in profiles.py

* make sure changes don't break API

* flake explicit exception

* flake explicit exception

* move rho_x calculation one indentation inward

* remove checks for Gaussian and PowerLaw profiles

Co-authored-by: David Alonso <dam.phys@gmail.com>

.github/workflows/ci.yml

@@ -49,6 +49,7 @@ jobs:
 
       - name: lint
         run: |
+          export MAMBA_NO_BANNER=1
           mamba install flake8
           flake8 pyccl
           flake8 --exclude=data benchmarks

pyccl/__init__.py

@@ -1,73 +1,178 @@
-# flake8: noqa
+# flake8: noqa E402
 from pkg_resources import get_distribution, DistributionNotFound
 try:
     __version__ = get_distribution(__name__).version
 except DistributionNotFound:
     # package is not installed
     pass
+del get_distribution, DistributionNotFound
 
-# Sets the environment variable for default config path if it does not
-# exist yet
+# Set the environment variable for default config path
 from os import environ, path
 if environ.get("CLASS_PARAM_DIR") is None:
     environ["CLASS_PARAM_DIR"] = path.dirname(path.abspath(__file__))
+del environ, path
 
+# SWIG-generated
 from . import ccllib as lib
-from . import core, constants, background, power, halomodel, pk2d, tk3d, haloprofile, halos, massfunction, nl_pt
+
+# Errors
+from .errors import (
+    CCLError,
+    CCLWarning,
+)
 
 # Core data structures
-from .core import Cosmology, CosmologyVanillaLCDM, CosmologyCalculator
+from .core import (
+    Cosmology,
+    CosmologyVanillaLCDM,
+    CosmologyCalculator,
+)
 
 # Background cosmology functions and growth functions
-from .background import growth_factor, growth_factor_unnorm, \
-    growth_rate, comoving_radial_distance, angular_diameter_distance, comoving_angular_distance, \
-    h_over_h0, luminosity_distance, distance_modulus, scale_factor_of_chi, \
-    omega_x, rho_x
+from .background import (
+    growth_factor,
+    growth_factor_unnorm,
+    growth_rate,
+    comoving_radial_distance,
+    angular_diameter_distance,
+    comoving_angular_distance,
+    luminosity_distance,
+    distance_modulus,
+    h_over_h0,
+    scale_factor_of_chi,
+    omega_x,
+    rho_x,
+    sigma_critical,
+)
 
 # Boltzmann solvers
-from .boltzmann import get_camb_pk_lin, get_isitgr_pk_lin, get_class_pk_lin
+from .boltzmann import (
+    get_camb_pk_lin,
+    get_isitgr_pk_lin,
+    get_class_pk_lin,
+)
 
 # Generalized power spectra
-from .pk2d import Pk2D, parse_pk2d
+from .pk2d import (
+    Pk2D,
+    parse_pk2d,
+)
 
 # Generalized connected trispectra
 from .tk3d import Tk3D
 
 # Power spectrum calculations, sigma8 and kNL
-from .power import linear_power, nonlin_power, linear_matter_power, nonlin_matter_power, \
-    sigmaR, sigmaV, sigma8, sigmaM, kNL
-
-# BCM stuff
-from .bcm import bcm_model_fka, bcm_correct_pk2d
-
-# Old halo mass function
-from .massfunction import massfunc, halo_bias, massfunc_m2r
-
-# Cl's and tracers
-from .tracers import Tracer, NumberCountsTracer, WeakLensingTracer, CMBLensingTracer, \
-    tSZTracer, CIBTracer, ISWTracer, get_density_kernel, get_kappa_kernel, get_lensing_kernel
+from .power import (
+    linear_power,
+    nonlin_power,
+    linear_matter_power,
+    nonlin_matter_power,
+    sigmaR,
+    sigmaV,
+    sigma8,
+    sigmaM,
+    kNL,
+)
+
+# Baryons & Neutrinos
+from .bcm import (
+    bcm_model_fka,
+    bcm_correct_pk2d,
+)
+
+from .neutrinos import (
+    Omeganuh2,
+    nu_masses,
+)
+
+# Cells & Tracers
 from .cls import angular_cl
-from .covariances import angular_cl_cov_cNG, angular_cl_cov_SSC, sigma2_B_disc, sigma2_B_from_mask
-
-# Useful constants and unit conversions
-physical_constants = lib.cvar.constants
-
+from .tracers import (
+    Tracer,
+    NumberCountsTracer,
+    WeakLensingTracer,
+    CMBLensingTracer,
+    tSZTracer,
+    CIBTracer,
+    ISWTracer,
+    get_density_kernel,
+    get_kappa_kernel,
+    get_lensing_kernel,
+)
+
+# Correlations & Covariances
 from .correlations import (
-    correlation, correlation_3d, correlation_multipole, correlation_3dRsd,
-    correlation_3dRsd_avgmu, correlation_pi_sigma)
-
-# Properties of haloes
-from .halomodel import (
-    halomodel_matter_power, halo_concentration,
-    onehalo_matter_power, twohalo_matter_power)
-
-# Halo density profiles
-from .haloprofile import nfw_profile_3d, einasto_profile_3d, hernquist_profile_3d, nfw_profile_2d
-
-# Specific to massive neutrinos
-from .neutrinos import Omeganuh2, nu_masses
+    correlation,
+    correlation_3d,
+    correlation_multipole,
+    correlation_3dRsd,
+    correlation_3dRsd_avgmu,
+    correlation_pi_sigma,
+)
+
+from .covariances import (
+    angular_cl_cov_cNG,
+    angular_cl_cov_SSC,
+    sigma2_B_disc,
+    sigma2_B_from_mask,
+)
+
+# Parameters
+physical_constants = lib.cvar.constants
 
-# Expose function to toggle debug mode
+# Miscellaneous
 from .pyutils import debug_mode, resample_array
 
-from .errors import CCLError, CCLWarning
+# Deprecated & Renamed modules
+from .halomodel import (
+    halomodel_matter_power,
+    halo_concentration,
+    onehalo_matter_power,
+    twohalo_matter_power,
+)
+
+from .massfunction import (
+    massfunc,
+    halo_bias,
+    massfunc_m2r,
+)
+
+from .haloprofile import (
+    nfw_profile_3d,
+    einasto_profile_3d,
+    hernquist_profile_3d,
+    nfw_profile_2d,
+)
+
+
+__all__ = (
+    'lib',
+    'physical_constants',
+    'CCLError', 'CCLWarning',
+    'Cosmology', 'CosmologyVanillaLCDM', 'CosmologyCalculator',
+    'growth_factor', 'growth_factor_unnorm', 'growth_rate',
+    'comoving_radial_distance', 'angular_diameter_distance',
+    'comoving_angular_distance', 'luminosity_distance', 'distance_modulus',
+    'h_over_h0', 'scale_factor_of_chi', 'omega_x', 'rho_x', 'sigma_critical',
+    'get_camb_pk_lin', 'get_isitgr_pk_lin', 'get_class_pk_lin',
+    'Pk2D', 'parse_pk2d', 'Tk3D',
+    'linear_power', 'nonlin_power',
+    'linear_matter_power', 'nonlin_matter_power',
+    'sigmaR', 'sigmaV', 'sigma8', 'sigmaM', 'kNL',
+    'bcm_model_fka', 'bcm_correct_pk2d',
+    'Omeganuh2', 'nu_masses',
+    'angular_cl',
+    'Tracer', 'NumberCountsTracer', 'WeakLensingTracer', 'CMBLensingTracer',
+    'tSZTracer', 'CIBTracer', 'ISWTracer',
+    'get_density_kernel', 'get_kappa_kernel', 'get_lensing_kernel',
+    'correlation', 'correlation_3d', 'correlation_multipole',
+    'correlation_3dRsd', 'correlation_3dRsd_avgmu', 'correlation_pi_sigma',
+    'angular_cl_cov_cNG', 'angular_cl_cov_SSC',
+    'sigma2_B_disc', 'sigma2_B_from_mask',
+    'debug_mode', 'resample_array',
+    'halomodel_matter_power', 'halo_concentration',
+    'onehalo_matter_power', 'twohalo_matter_power',
+    'massfunc', 'halo_bias', 'massfunc_m2r', 'nfw_profile_3d',
+    'einasto_profile_3d', 'hernquist_profile_3d', 'nfw_profile_2d',
+)

pyccl/background.py

@@ -137,7 +137,7 @@ def angular_diameter_distance(cosmo, a1, a2=None):
                               lib.angular_diameter_distance_vec,
                               cosmo, a1, a2)
     else:
-        if(isinstance(a1, float) or isinstance(a1, int)):
+        if isinstance(a1, (int, float)):
             return _vectorize_fn5(lib.angular_diameter_distance,
                                   lib.angular_diameter_distance_vec,
                                   cosmo, 1., a1)

pyccl/bcm.py

@@ -43,7 +43,7 @@ def bcm_correct_pk2d(cosmo, pk2d):
         pk2d (:class:`~pyccl.pk2d.Pk2D`): power spectrum.
     """
     if not isinstance(pk2d, Pk2D):
-        raise ValueError("pk2d must be a Pk2D object")
+        raise TypeError("pk2d must be a Pk2D object")
     status = 0
     status = lib.bcm_correct(cosmo.cosmo, pk2d.psp, status)
     check(status, cosmo)

pyccl/boltzmann.py

@@ -1,21 +1,8 @@
 import numpy as np
 
-try:
-    import classy
-    HAVE_CLASS = True
-except ImportError:
-    HAVE_CLASS = False
-
-try:
-    import camb
-    import camb.model
-    HAVE_CAMB = True
-except ImportError:
-    HAVE_CAMB = False
-
 try:
     import isitgr  # noqa: F401
-except ImportError:
+except ModuleNotFoundError:
     pass  # prevent nans from isitgr
 
 from . import ccllib as lib
@@ -39,12 +26,8 @@ def get_camb_pk_lin(cosmo, nonlin=False):
             spectrum. If ``nonlin=True``, returns a tuple \
             ``(pk_lin, pk_nonlin)``.
     """
-
-    # Comment from Jarvis: TODO clean up this and other assert
-    # anti-patterns in this file
-    assert HAVE_CAMB, (
-        "You must have the `camb` python package "
-        "installed to run CCL with CAMB!")
+    import camb
+    import camb.model
 
     # Get extra CAMB parameters that were specified
     extra_camb_params = {}
@@ -256,16 +239,8 @@ def get_isitgr_pk_lin(cosmo):
         :class:`~pyccl.pk2d.Pk2D`: Power spectrum \
             object. The linear power spectrum.
     """
-
-    try:
-        import isitgr  # noqa: F811
-        import isitgr.model
-    except ImportError as e:
-        e.args = (
-            "You must have the `isitgr` python package "
-            "installed to run CCL with ISiTGR-CAMB!",
-            *e.args)
-        raise
+    import isitgr  # noqa: F811
+    import isitgr.model
 
     # Get extra CAMB parameters that were specified
     extra_camb_params = {}
@@ -442,10 +417,7 @@ def get_class_pk_lin(cosmo):
         :class:`~pyccl.pk2d.Pk2D`: Power spectrum object.\
             The linear power spectrum.
     """
-
-    assert HAVE_CLASS, (
-        "You must have the python wrapper for CLASS "
-        "installed to run CCL with CLASS!")
+    import classy
 
     params = {
         "output": "mPk",

pyccl/ccl_core.i

@@ -4,7 +4,7 @@
 /* put additional #include here */
 %}
 
-// SWIG black magic. Change the behaviour of setting A_SPLINE_MAX to thowing an
+// SWIG black magic. Change the behaviour of setting A_SPLINE_MAX to throwing an
 // error.
 %typemap(memberin) double A_SPLINE_MAX {
     if($input) {
@@ -46,7 +46,7 @@ ccl_parameters parameters_create_nu(
     return ccl_parameters_create(
                         Omega_c, Omega_b, Omega_k, Neff, m_nu, n_m,
                         w0, wa, h, norm_pk, n_s, bcm_log10Mc, bcm_etab,
-                        bcm_ks, mu_0, sigma_0, c1_mg, c2_mg, lambda_mg, 
+                        bcm_ks, mu_0, sigma_0, c1_mg, c2_mg, lambda_mg,
                         -1, NULL, NULL, status );
 }
 
@@ -72,7 +72,7 @@ ccl_parameters parameters_create_nu_vec(
     return ccl_parameters_create(
                         Omega_c, Omega_b, Omega_k, Neff, m_nu, n_m,
                         w0, wa, h, norm_pk, n_s, bcm_log10Mc, bcm_etab, bcm_ks,
-                        mu_0, sigma_0, c1_mg, c2_mg, lambda_mg, 
+                        mu_0, sigma_0, c1_mg, c2_mg, lambda_mg,
                         nz, zarr, dfarr, status);
 }
 

pyccl/constants.py

@@ -1,7 +1,12 @@
-"""This file exposes constants present in CCL."""
-# flake8: noqa
 from .ccllib import (
     CCL_ERROR_CLASS, CCL_ERROR_INCONSISTENT, CCL_ERROR_INTEG,
     CCL_ERROR_LINSPACE, CCL_ERROR_MEMORY, CCL_ERROR_ROOT, CCL_ERROR_SPLINE,
     CCL_ERROR_SPLINE_EV, CCL_CORR_FFTLOG, CCL_CORR_BESSEL, CCL_CORR_LGNDRE,
     CCL_CORR_GG, CCL_CORR_GL, CCL_CORR_LP, CCL_CORR_LM)
+
+
+__all__ = ('CCL_ERROR_CLASS', 'CCL_ERROR_INCONSISTENT', 'CCL_ERROR_INTEG',
+           'CCL_ERROR_LINSPACE', 'CCL_ERROR_MEMORY', 'CCL_ERROR_ROOT',
+           'CCL_ERROR_SPLINE', 'CCL_ERROR_SPLINE_EV', 'CCL_CORR_FFTLOG',
+           'CCL_CORR_BESSEL', 'CCL_CORR_LGNDRE', 'CCL_CORR_GG', 'CCL_CORR_GL',
+           'CCL_CORR_LP', 'CCL_CORR_LM')