Issue/592/ccl v3 (#595)

* Update for CCL v3 * Fix docs compiling * Remove warning filter * Update generate_einasto_hernquist_benchmarks_fromNC.ipynb * Remove concentration from MassDef * Fix profile name validation * Add virial massdef properly * Add use_projected_quad * Remove virial massdef from CT backend * Use --override-channels in build_check.yml * Update version to 1.9.0 --------- Co-authored-by: m-aguena <aguena@if.usp.br>
LSSTDESC · Sep 18, 2023 · 8e97b4a · 8e97b4a
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diff --git a/.github/workflows/build_check.yml b/.github/workflows/build_check.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - uses: conda-incubator/setup-miniconda@v2
     - name: Install prereq using conda
       run: |
@@ -33,10 +33,10 @@ jobs:
         pip install .
     - name: Install CCL from source
       run: |
-        conda install -c conda-forge cmake swig
+        conda install -c conda-forge cmake swig --override-channels
         git clone https://github.com/LSSTDESC/CCL
         cd CCL
-        git checkout 1a351df
+        git checkout v3.0.0
         pip install .
     - name: Analysing the code with pylint
       run: |

diff --git a/INSTALL.md b/INSTALL.md
@@ -18,7 +18,7 @@ To create a specific conda environment for CLMM, we recommend you to check the b
 
 ### Theory backend installation
 First, choose and install a theory backend for CLMM.
-This can be CCL (versions between 2.6.0 and 2.7.1.dev9+g1a351df6),
+This can be CCL (versions between 2.7.1.dev10+gf81b59a4 and 3),
 NumCosmo (v0.15 or later),
 or cluster_toolkit and they are installable as follows.
 

diff --git a/README.md b/README.md
@@ -35,7 +35,7 @@ CLMM requires Python version 3.8 or later.  CLMM has the following dependencies:
 For the theoretical predictions of the signal, CLMM relies on existing libraries and **at least one of the following must be installed as well**:
 
 - [cluster-toolkit](https://cluster-toolkit.readthedocs.io/en/latest/)
-- [CCL](https://ccl.readthedocs.io/en/latest/) (versions between 2.6.0 and 2.7.1.dev9+g1a351df6)
+- [CCL](https://ccl.readthedocs.io/en/latest/) (versions between 2.7.1.dev10+gf81b59a4 and 3)
 - [NumCosmo](https://numcosmo.github.io/) (v0.15 or later)
 
 

diff --git a/clmm/__init__.py b/clmm/__init__.py
@@ -26,4 +26,4 @@
 )
 from . import support
 
-__version__ = "1.8.2"
+__version__ = "1.9.0"
diff --git a/clmm/cosmology/ccl.py b/clmm/cosmology/ccl.py
@@ -113,7 +113,7 @@ def _eval_sigma_crit_core(self, z_len, z_src):
         a_len = self.get_a_from_z(z_len)
         a_src = self.get_a_from_z(z_src)
 
-        return self.be_cosmo.sigma_critical(a_len, a_src) * self.cor_factor
+        return self.be_cosmo.sigma_critical(a_lens=a_len, a_source=a_src) * self.cor_factor
 
     def _eval_linear_matter_powerspectrum(self, k_vals, redshift):
         return ccl.linear_matter_power(self.be_cosmo, k_vals, self.get_a_from_z(redshift))
diff --git a/clmm/theory/_ccl_supported_versions.py b/clmm/theory/_ccl_supported_versions.py
@@ -1,5 +1,5 @@
 """@file _ccl_supported_versions.py
 Versions of CCL supported by the current CLMM version
 """
-VMIN = '2.6.0'
-VMAX = '2.7.1.dev9+g1a351df6'
+VMIN = "2.7.1.dev10+gf81b59a4"
+VMAX = "3"
diff --git a/clmm/theory/ccl.py b/clmm/theory/ccl.py
@@ -30,11 +30,11 @@ class CCLCLMModeling(CLMModeling):
     backend: str
         Name of the backend being used
     massdef : str
-        Profile mass definition (`mean`, `critical`, `virial` - letter case independent)
+        Profile mass definition ("mean", "critical", "virial" - letter case independent)
     delta_mdef : int
         Mass overdensity definition.
     halo_profile_model : str
-        Profile model parameterization (`nfw`, `einasto`, `hernquist` - letter case independent)
+        Profile model parameterization ("nfw", "einasto", "hernquist" - letter case independent)
     cosmo: Cosmology
         Cosmology object
     hdpm: Object
@@ -94,12 +94,22 @@ def __init__(
         self.set_halo_density_profile(halo_profile_model, massdef, delta_mdef)
         self.set_cosmo(None)
 
+    def _set_projected_quad(self, use_projected_quad):
+        if hasattr(self.hdpm, "projected_quad"):
+            self.hdpm_opts["einasto"]["projected_quad"] = use_projected_quad
+            self._update_halo_density_profile()
+        else:
+            raise NotImplementedError("projected_quad is not available on this version of CCL.")
+
     # Functions implemented by child class
 
     def _update_halo_density_profile(self):
         """updates halo density profile with set internal properties"""
         # prepare mdef object
-        self.mdef = ccl.halos.MassDef(self.delta_mdef, self.mdef_dict[self.massdef])
+        if self.massdef == "virial":
+            self.mdef = ccl.halos.MassDef("vir", self.mdef_dict[self.massdef])
+        else:
+            self.mdef = ccl.halos.MassDef(self.delta_mdef, self.mdef_dict[self.massdef])
         # setting concentration (also updates hdpm)
         self.cdelta = self.cdelta if self.hdpm else 4.0  # ccl always needs an input concentration
 
@@ -113,13 +123,9 @@ def _get_mass(self):
 
     def _set_concentration(self, cdelta):
         """set concentration. Also sets/updates hdpm"""
-        # pylint: disable=protected-access
-        self.conc = ccl.halos.ConcentrationConstant(c=cdelta, mdef=self.mdef)
-        if hasattr(ccl, 'UnlockInstance'):
-            ccl.UnlockInstance.Funlock(type(self.mdef), "_concentration_init", True)
-        self.mdef._concentration_init(self.conc)
+        self.conc = ccl.halos.ConcentrationConstant(c=cdelta, mass_def=self.mdef)
         self.hdpm = self.hdpm_dict[self.halo_profile_model](
-            self.conc, **self.hdpm_opts[self.halo_profile_model]
+            concentration=self.conc, mass_def=self.mdef, **self.hdpm_opts[self.halo_profile_model]
         )
         self.hdpm.update_precision_fftlog(padding_lo_fftlog=1e-4, padding_hi_fftlog=1e3)
 
@@ -140,7 +146,7 @@ def _get_einasto_alpha(self, z_cl=None):
             a_cl = 1  # a_cl does not matter in this case
         else:
             a_cl = self.cosmo.get_a_from_z(z_cl)
-        return self.hdpm._get_alpha(self.cosmo.be_cosmo, self.__mdelta_cor, a_cl, self.mdef)
+        return self.hdpm._get_alpha(self.cosmo.be_cosmo, self.__mdelta_cor, a_cl)
 
     def _eval_3d_density(self, r3d, z_cl):
         """eval 3d density"""
@@ -188,7 +194,6 @@ def _call_ccl_profile_lens(self, ccl_hdpm_func, radius, z_lens, ndim=2):
                 radius / a_lens,
                 self.__mdelta_cor,
                 a_lens,
-                self.mdef,
             )
             * self.cor_factor
             / a_lens**ndim
@@ -203,9 +208,8 @@ def _call_ccl_profile_lens_src(self, ccl_hdpm_func, radius, z_lens, z_src):
             self.cosmo.be_cosmo,
             radius / a_lens,
             self.__mdelta_cor,
-            a_lens,
-            a_src,
-            self.mdef,
+            a_lens=a_lens,
+            a_source=a_src,
         )
 
 

diff --git a/clmm/theory/cluster_toolkit.py b/clmm/theory/cluster_toolkit.py
@@ -25,7 +25,7 @@ def _assert_correct_type_ct(arg):
 
     Returns
     -------
-    scale_factor : array_like
+    scale_factor : numpy.ndarray
         Scale factor
     """
     if np.isscalar(arg):
@@ -41,11 +41,11 @@ class CTCLMModeling(CLMModeling):
     backend: str
         Name of the backend being used
     massdef : str
-        Profile mass definition (`mean`, `critical`, `virial` - letter case independent)
+        Profile mass definition ("mean", "critical" - letter case independent)
     delta_mdef : int
         Mass overdensity definition.
     halo_profile_model : str
-        Profile model parameterization (`nfw`, `einasto`, `hernquist` - letter case independent)
+        Profile model parameterization ("nfw" - letter case independent)
     cosmo: Cosmology
         Cosmology object
     hdpm: Object
@@ -85,7 +85,6 @@ def __init__(
         self.mdef_dict = {
             "mean": self.cosmo.get_E2Omega_m,
             "critical": self.cosmo.get_E2,
-            "virial": self.cosmo.get_E2,
         }
 
         self.set_halo_density_profile(halo_profile_model, massdef, delta_mdef)
@@ -145,7 +144,7 @@ def _eval_surface_density(self, r_proj, z_cl):
         )  # pc**-2 to Mpc**-2
 
     def _eval_mean_surface_density(self, r_proj, z_cl):
-        r"""Computes the mean value of surface density inside radius r_proj
+        r"""Computes the mean value of surface density inside radius `r_proj`
 
         Parameters
         ----------
@@ -156,7 +155,7 @@ def _eval_mean_surface_density(self, r_proj, z_cl):
 
         Returns
         -------
-        array_like, float
+        numpy.ndarray, float
             Excess surface density in units of :math:`M_\odot\ Mpc^{-2}`.
 
         Note

diff --git a/clmm/theory/func_layer.py b/clmm/theory/func_layer.py
@@ -5,7 +5,7 @@
 # pylint: disable=invalid-name
 # Thin functonal layer on top of the class implementation of CLMModeling .
 # The functions expect a global instance of the actual CLMModeling named
-# `_modeling_object'.
+# "_modeling_object".
 
 import numpy as np
 
@@ -109,6 +109,7 @@ def compute_surface_density(
     massdef="mean",
     alpha_ein=None,
     verbose=False,
+    use_projected_quad=False,
     validate_input=True,
 ):
     r"""Computes the surface mass density
@@ -154,6 +155,10 @@ def compute_surface_density(
     verbose : boolean, optional
         If True, the Einasto slope (alpha_ein) is printed out. Only available for the NC and CCL
         backends.
+    use_projected_quad : bool
+        Only available for Einasto profile with CCL as the backend. If True, CCL will use
+        quad_vec instead of default FFTLog to calculate the surface density profile.
+        Default: False
     validate_input : bool, optional
         If True (default), the types of the arguments are checked before proceeding.
 
@@ -176,6 +181,8 @@ def compute_surface_density(
     _modeling_object.set_mass(mdelta)
     if halo_profile_model == "einasto" or alpha_ein is not None:
         _modeling_object.set_einasto_alpha(alpha_ein)
+    if halo_profile_model == "einasto" and _modeling_object.backend=="ccl":
+        _modeling_object.set_projected_quad(use_projected_quad)
 
     sigma = _modeling_object.eval_surface_density(r_proj, z_cl, verbose=verbose)
 
@@ -358,7 +365,7 @@ def compute_excess_surface_density_2h(
 
     .. math::
         \Delta\Sigma_{\text{2h}}(R) = \frac{\rho_m(z)b(M)}{(1 + z)^3D_A(z)^2}
-        \int\frac{ldl}{(2\pi)} P_{\rm mm}(k_l, z)J_2(l\theta)
+        \int\frac{ldl}{(2\pi)} P_{\text{mm}}(k_l, z)J_2(l\theta)
 
     where
 
@@ -424,13 +431,13 @@ def compute_surface_density_2h(
     r"""Computes the 2-halo term surface density from eq.(13) of Oguri & Hamana (2011)
 
     .. math::
-        \Sigma_{\rm 2h}(R) = \frac{\rho_m(z)b(M)}{(1 + z)^3D_A(z)^2} \int\frac{ldl}{(2\pi)}
-        P_{\rm mm}(k_l, z)J_0(l\theta)
+        \Sigma_{\text{2h}}(R) = \frac{\rho_\text{m}(z)b(M)}{(1 + z)^3D_A(z)^2}
+        \int\frac{ldl}{(2\pi)}P_{\text{mm}}(k_l, z)J_0(l\theta)
 
     where
 
     .. math::
-        k_l = \frac{l}{D_A(z)(1 +z)}
+        k_l = \frac{l}{D_A(z)(1 + z)}
 
     and :math:`b(M)` is the halo bias
 
@@ -481,14 +488,14 @@ def compute_critical_surface_density_eff(cosmo, z_cluster, pzbins, pzpdf, valida
     r"""Computes the 'effective critical surface density'
 
     .. math::
-        \langle \Sigma_{\rm crit}^{-1}\rangle^{-1} = \left(\int \frac{1}{\Sigma_{\rm crit}(z)}
-        p(z) dz\right)^{-1}
+        \langle \Sigma_{\text{crit}}^{-1}\rangle^{-1} =
+        \left(\int \frac{1}{\Sigma_{\text{crit}}(z)}p(z) \mathrm{d}z\right)^{-1}
 
     where :math:`p(z)` is the source photoz probability density function.
     This comes from the maximum likelihood estimator for evaluating a :math:`\Delta\Sigma`
     profile.
 
-    For the standard :math:`\Sigma_{\rm crit}(z)` definition, use the `eval_sigma_crit` method of
+    For the standard :math:`\Sigma_{\text{crit}}(z)` definition, use the `eval_sigma_crit` method of
     the CLMM cosmology object.
 
     Parameters
@@ -841,9 +848,9 @@ def compute_reduced_tangential_shear(
     massdef : str, optional
         Profile mass definition, with the following supported options (letter case independent):
 
-            * `mean` (default);
-            * `critical` - not in cluster_toolkit;
-            * `virial` - not in cluster_toolkit;
+            * 'mean' (default);
+            * 'critical' - not in cluster_toolkit;
+            * 'virial' - not in cluster_toolkit;
 
     alpha_ein : float, None, optional
         If `halo_profile_model=='einasto'`, set the value of the Einasto slope.

diff --git a/clmm/theory/generic.py b/clmm/theory/generic.py
@@ -85,7 +85,7 @@ def compute_rdelta(mdelta, redshift, cosmo, massdef="mean", delta_mdef=200):
     cosmo : clmm.Cosmology
         Cosmology object
     massdef : str, None
-        Profile mass definition (`mean`, `critical`, `virial`).
+        Profile mass definition ("mean", "critical", "virial").
     delta_mdef : int, None
         Mass overdensity definition.
 
@@ -151,11 +151,11 @@ def compute_profile_mass_in_radius(
     cdelta : float
         Concentration of the profile.
     massdef : str, None
-        Profile mass definition (`mean`, `critical`, `virial`).
+        Profile mass definition ("mean", "critical", "virial").
     delta_mdef : int, None
         Mass overdensity definition.
     halo_profile_model : str
-        Profile model parameterization (`nfw`, `einasto`, `hernquist`).
+        Profile model parameterization ("nfw", "einasto", "hernquist").
     alpha : float, None
         Einasto slope, required when `halo_profile_model='einasto'`.
 
@@ -209,19 +209,19 @@ def convert_profile_mass_concentration(
     cosmo : clmm.Cosmology
         Cosmology object
     massdef : str, None
-        Input profile mass definition (`mean`, `critical`, `virial`).
+        Input profile mass definition ("mean", "critical", "virial").
     delta_mdef : int, None
         Input mass overdensity definition.
     halo_profile_model : str, None
-        Input profile model parameterization (`nfw`, `einasto`, `hernquist`).
+        Input profile model parameterization ("nfw", "einasto", "hernquist").
     massdef2 : str, None
-        Profile mass definition to convert to (`mean`, `critical`, `virial`).
+        Profile mass definition to convert to ("mean", "critical", "virial").
         If None, `massdef2=massdef`.
     delta_mdef2 : int, None
         Mass overdensity definition to convert to.
         If None, `delta_mdef2=delta_mdef`.
     halo_profile_model2 : str, None
-        Profile model parameterization to convert to (`nfw`, `einasto`, `hernquist`).
+        Profile model parameterization to convert to ("nfw", "einasto", "hernquist").
         If None, `halo_profile_model2=halo_profile_model`.
     alpha : float, None
         Input Einasto slope when `halo_profile_model='einasto'`.

diff --git a/clmm/theory/numcosmo.py b/clmm/theory/numcosmo.py
@@ -23,11 +23,11 @@ class NumCosmoCLMModeling(CLMModeling):
     backend: str
         Name of the backend being used
     massdef : str
-        Profile mass definition (`mean`, `critical`, `virial` - letter case independent)
+        Profile mass definition ("mean", "critical", "virial" - letter case independent)
     delta_mdef : int
         Mass overdensity definition.
     halo_profile_model : str
-        Profile model parameterization (`nfw`, `einasto`, `hernquist` - letter case independent)
+        Profile model parameterization ("nfw", "einasto", "hernquist" - letter case independent)
     cosmo: Cosmology
         Cosmology object
     hdpm: Object