PyCosmo 2.2.0__tar.gz → 2.2.1__tar.gz

pycosmo-2.2.1/MANIFEST.in

@@ -0,0 +1 @@
+prune tests

pycosmo-2.2.1/PKG-INFO

@@ -0,0 +1,55 @@
+Metadata-Version: 2.4
+Name: PyCosmo
+Version: 2.2.1
+Summary: A multi-purpose cosmology calculation tool
+Author-email: Uwe Schmitt et al <uwe.schmitt@id.ethz.ch>
+License: GPLv3
+Project-URL: Source, https://cosmo-docs.phys.ethz.ch/PyCosmo
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
+Classifier: Natural Language :: English
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: C
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Topic :: Scientific/Engineering :: Astronomy
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown; charset=UTF-8
+License-File: LICENSE
+License-File: AUTHORS.rst
+Requires-Dist: numpy>=2
+Requires-Dist: recfast4py>=0.2.3
+Requires-Dist: dill
+Requires-Dist: matplotlib
+Requires-Dist: numba>=0.60
+Requires-Dist: sympy2c>=2.3.1
+Requires-Dist: numexpr>=2.10
+Requires-Dist: scipy
+Requires-Dist: setuptools>=75.6.0
+Requires-Dist: mpmath==1.3
+Dynamic: license-file
+
+# PyCosmo
+
+PyCosmo is a multi-purpose cosmology calculation tool in Python. It is
+designed to be interactive and user friendly.
+
+The code includes calculations of:
+  - Background
+  - Linear perturbations (incl. fitting functions and a Boltzmann solver)
+  - Non-linear perturbations
+  - Series of observables (e.g., weak lensing and galaxy clustering
+    power spectrum, ...)
+  - Several model extensions (massive neutrinos, wCDM, ...)
+
+
+The code documentation can be found at
+[https://cosmo-docs.phys.ethz.ch/PyCosmo](https://cosmo-docs.phys.ethz.ch/PyCosmo)
+
+Interactive tutorial notebooks are available on the
+[PyCosmoHUB](https://pycosmohub.com).

pycosmo-2.2.1/README.md

@@ -0,0 +1,19 @@
+# PyCosmo
+
+PyCosmo is a multi-purpose cosmology calculation tool in Python. It is
+designed to be interactive and user friendly.
+
+The code includes calculations of:
+  - Background
+  - Linear perturbations (incl. fitting functions and a Boltzmann solver)
+  - Non-linear perturbations
+  - Series of observables (e.g., weak lensing and galaxy clustering
+    power spectrum, ...)
+  - Several model extensions (massive neutrinos, wCDM, ...)
+
+
+The code documentation can be found at
+[https://cosmo-docs.phys.ethz.ch/PyCosmo](https://cosmo-docs.phys.ethz.ch/PyCosmo)
+
+Interactive tutorial notebooks are available on the
+[PyCosmoHUB](https://pycosmohub.com).

pycosmo-2.2.1/pyproject.toml

@@ -0,0 +1,113 @@
+[build-system]
+requires = ["setuptools >= 64", "numpy", "Cython"]
+build-backend = "setuptools.build_meta"
+
+
+[project]
+name = "PyCosmo"
+version = "2.2.1"
+license = {text = "GPLv3"}
+description = "A multi-purpose cosmology calculation tool"
+authors = [{name = "Uwe Schmitt et al", email = "uwe.schmitt@id.ethz.ch"}]
+classifiers = [
+    "Development Status :: 4 - Beta",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
+    "Natural Language :: English",
+    "Operating System :: OS Independent",
+    "Programming Language :: C",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.9",
+    "Topic :: Scientific/Engineering :: Astronomy",
+]
+
+urls = {Source = "https://cosmo-docs.phys.ethz.ch/PyCosmo"}
+requires-python = ">=3.10"
+dependencies = [
+    "numpy>=2",
+    "recfast4py>=0.2.3",
+    "dill",
+    "matplotlib",
+    "numba>=0.60",
+    "sympy2c>=2.3.1",
+    "numexpr>=2.10",
+    "scipy",
+    "setuptools>=75.6.0",
+    "mpmath==1.3",
+]
+
+[project.readme]
+file = "README.md"
+content-type = "text/markdown; charset=UTF-8"
+
+[dependency-groups]
+dev = [
+    "Cython",
+    "twine",
+    "pytest",
+    "pytest-cov",
+    "pytest-regtest>=2.2.0a2",
+    "ruff",
+    "isort",
+    "pre-commit",
+    "pdbp>=1.7.1",
+]
+
+docs = [
+    "sphinx < 7",
+    "sphinx-pynpoint-theme",
+    "myst-parser",
+]
+
+[project.scripts]
+recompile = "PyCosmo:Cosmo.recompile_from_cli"
+
+[tool.setuptools]
+zip-safe = false
+include-package-data = true
+
+[tool.setuptools.package-data]
+"*" = [
+    "*.pyx",
+    "*.c",
+    "*.h",
+    "config/*.ini",
+]
+
+
+[tool.ruff]
+line-length    = 88
+extend-exclude = ["benchmarks/", "*.ipynb"]
+
+    [tool.ruff.format]
+    quote-style           = "double"
+    line-ending           = "lf"
+    docstring-code-format = false
+
+    [tool.ruff.lint]
+    extend-select = [
+        "RUF100",             # unnecessary `noqa` directives
+    ]
+    ignore = [
+        "E501",
+        "E731",               # lambda assignment
+        "E741",               # ambiguous variable name
+    ]
+
+    [tool.ruff.lint.per-file-ignores]
+    '__init__.py' = [
+        "F401",               # imported but unused
+    ]
+
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+addopts = ["--verbose", "--durations=0", "--durations-min=5"]
+markers = [
+    "slow: Marks tests as slow to run. Pass `--runslow` to include them."
+]
+console_output_style = "count"

pycosmo-2.2.1/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

{pycosmo-2.2.0 → pycosmo-2.2.1}/src/PyCosmo/BoltzmannSolver/LinearPerturbationBoltzmann.py

@@ -16,7 +16,6 @@
 
 import itertools
 import warnings
-from datetime import datetime
 from functools import lru_cache
 from multiprocessing import current_process
 
@@ -28,7 +27,7 @@ from .LsodaSolver import LsodaSolver
 
 
 # use decorator to print messages only once per model:
-@lru_cache(maxsize=1)  # noqa: E302
+@lru_cache(maxsize=1)
 def print_new_traces(cache_file):
     print()
     print("new traces detected! you might want to run")
@@ -39,36 +38,6 @@ def print_new_traces(cache_file):
 proc_name = current_process().name
 
 
-def trace_call(frame, event, arg):
-    if proc_name.endswith("-2"):
-        return trace_call
-    if event in ("line",):
-        return trace_call
-    fname = frame.f_code.co_filename
-    if any(
-        n in fname
-        for n in (
-            "pprint",
-            "dill",
-            "pickle",
-            "numba",
-            "logging",
-            "ini_handling",
-            "llvmlite",
-            "traceback",
-            "weakref",
-        )
-    ):
-        return trace_call
-    print(datetime.now(), end=" ")
-    fr = frame
-    print(proc_name, f"{event:8s}", end="")
-    while (fr := fr.f_back) is not None:
-        print("  ", end="")
-    print(fname, frame.f_code.co_name, frame.f_lineno, flush=True)
-    return trace_call
-
-
 class LinearPerturbationBoltzmann(LinearPerturbationBase):
     """
     Class for computing linear perturbations by solving the Einstein-Boltzmann ODE
@@ -362,9 +331,9 @@ class LinearPerturbationBoltzmann(LinearPerturbationBase):
 
         :return: D(a): growth factor normalised to 1 at a=1 [1]
         """
-        assert (
-            k is not None
-        ), "growth factor of Einstein-Boltzmann model requires a k value"
+        assert k is not None, (
+            "growth factor of Einstein-Boltzmann model requires a k value"
+        )
         # TODO: add option where D is normalised to a in matter dominated era
         grid = np.log(np.atleast_1d(a))
         if grid[-1] != 0.0:

{pycosmo-2.2.0 → pycosmo-2.2.1}/src/PyCosmo/BoltzmannSolver/ScipySolver.py

@@ -300,7 +300,7 @@ def merge(wrapper, t_0, t_switch, t_1, y_0, y_1):  # pragma: no cover
         + a
         * H_Mpc
         * wrapper.taudot_interp_ufunc(a)
-        / k**2
+        / k** 2
         * (
             u_b
             - k / (a * H_Mpc) * wrapper.c_s_interp_ufunc(a) ** 2 * delta_b

{pycosmo-2.2.0 → pycosmo-2.2.1}/src/PyCosmo/CosmologyCore.py

@@ -16,6 +16,8 @@
 
 # pragma: no cover
 
+# ruff: noqa
+
 import sympy as sp
 from sympy2c import (
     ERROR,

{pycosmo-2.2.0 → pycosmo-2.2.1}/src/PyCosmo/CosmologyCore_massivenu.py

@@ -15,6 +15,9 @@
 # program.  If not, see <http://www.gnu.org/licenses/>.
 
 
+# pragma: no cover
+# ruff: noqa
+
 import numpy as np
 import sympy as sp
 from sympy2c import (

{pycosmo-2.2.0 → pycosmo-2.2.1}/src/PyCosmo/CosmologyCore_massivenu_rsa.py

@@ -14,6 +14,10 @@
 # You should have received a copy of the GNU General Public License along with this
 # program.  If not, see <http://www.gnu.org/licenses/>.
 
+
+# pragma: no cover
+# ruff: noqa
+
 from CosmologyCore_massivenu import *
 from sympy2c import OdeCombined
 

{pycosmo-2.2.0 → pycosmo-2.2.1}/src/PyCosmo/CosmologyCore_massivenu_wcdm.py

@@ -14,6 +14,8 @@
 # You should have received a copy of the GNU General Public License along with this
 # program.  If not, see <http://www.gnu.org/licenses/>.
 
+# pragma: no cover
+# ruff: noqa
 
 import numpy as np
 import sympy as sp

{pycosmo-2.2.0 → pycosmo-2.2.1}/src/PyCosmo/CosmologyCore_massivenu_wcdm_rsa.py

@@ -14,6 +14,9 @@
 # You should have received a copy of the GNU General Public License along with this
 # program.  If not, see <http://www.gnu.org/licenses/>.
 
+# pragma: no cover
+# ruff: noqa
+
 from CosmologyCore_massivenu_wcdm import *
 from sympy2c import OdeCombined
 

{pycosmo-2.2.0 → pycosmo-2.2.1}/src/PyCosmo/CosmologyCore_rsa.py

@@ -15,6 +15,7 @@
 # program.  If not, see <http://www.gnu.org/licenses/>.
 
 # pragma: no cover
+# ruff: noqa
 
 from CosmologyCore import *
 from sympy2c import OdeCombined

{pycosmo-2.2.0 → pycosmo-2.2.1}/src/PyCosmo/CosmologyCore_wcdm.py

@@ -15,6 +15,7 @@
 # program.  If not, see <http://www.gnu.org/licenses/>.
 
 # pragma: no cover
+# ruff: noqa
 
 import sympy as sp
 from sympy2c import (

{pycosmo-2.2.0 → pycosmo-2.2.1}/src/PyCosmo/CosmologyCore_wcdm_rsa.py

@@ -15,6 +15,7 @@
 # program.  If not, see <http://www.gnu.org/licenses/>.
 
 # pragma: no cover
+# ruff: noqa
 
 from CosmologyCore_wcdm import *
 from sympy2c import OdeCombined

{pycosmo-2.2.0 → pycosmo-2.2.1}/src/PyCosmo/LinearPerturbationApprox.py

@@ -169,9 +169,10 @@ class LinearPerturbationApprox(LinearPerturbationBase):
 
         _dlnh_dlna = self._background._dlnh_dlna(a=a_temp)[0]
 
-        f2 = -(4.0 + _dlnh_dlna) * y[1] - (
-            3.0 + _dlnh_dlna - 1.5 * self._background._omega_m_a(a=a_temp)
-        ) * y[0]
+        f2 = (
+            -(4.0 + _dlnh_dlna) * y[1]
+            - (3.0 + _dlnh_dlna - 1.5 * self._background._omega_m_a(a=a_temp)) * y[0]
+        )
         return [f1, f2]
 
     def _growth_derivs_nu(self, y, x):
@@ -186,9 +187,10 @@ class LinearPerturbationApprox(LinearPerturbationBase):
 
         _dlnh_dlna = self._background._dlnh_dlna_massive_nu(a=a_temp)
 
-        f2 = -(4.0 + _dlnh_dlna) * y[1] - (
-            3.0 + _dlnh_dlna - 1.5 * self._background._omega_m_a(a=a_temp)
-        ) * y[0]
+        f2 = (
+            -(4.0 + _dlnh_dlna) * y[1]
+            - (3.0 + _dlnh_dlna - 1.5 * self._background._omega_m_a(a=a_temp)) * y[0]
+        )
         return [f1, f2]
 
     def _growth_hyper_a(self, a=1.0):  # , Om=0.25,z=0):

{pycosmo-2.2.0 → pycosmo-2.2.1}/src/PyCosmo/LinearPerturbationBase.py

@@ -58,7 +58,7 @@ class LinearPerturbationBase(object):
                 3.0 / (k * ri) ** 2 * (np.sin(k * ri) / (k * ri) - np.cos(k * ri))
             )  # top hat window function
             pk = self.powerspec_a_k(a=1.0, k=k)
-            res[i] = np.trapz(k**3 * pk[0] * w**2, lnk)
+            res[i] = np.trapezoid(k**3 * pk[0] * w**2, lnk)
 
         return np.sqrt(1.0 / (2.0 * np.pi**2) * res)
 
@@ -107,7 +107,7 @@ class LinearPerturbationBase(object):
                 return k**3 * w**2 * pk_interpolated(np.log(k))
 
             with warnings.catch_warnings():
-                integral = np.trapz(integrand(k_fine), np.log(k_fine))
+                integral = np.trapezoid(integrand(k_fine), np.log(k_fine))
             res[i] = integral
 
         result = np.sqrt(1.0 / (2.0 * np.pi**2) * res)
@@ -116,16 +116,13 @@ class LinearPerturbationBase(object):
         return result
 
     @abc.abstractmethod
-    def growth_a(self, a=1.0, k=None, norm=0, diag_only=True):
-        ...
+    def growth_a(self, a=1.0, k=None, norm=0, diag_only=True): ...
 
     @abc.abstractmethod
-    def transfer_k(self, k):
-        ...
+    def transfer_k(self, k): ...
 
     @abc.abstractmethod
-    def powerspec_a_k(self, a=1.0, k=0.1, diag_only=False):
-        ...
+    def powerspec_a_k(self, a=1.0, k=0.1, diag_only=False): ...
 
     @abc.abstractmethod
     def max_redshift(self, k):

{pycosmo-2.2.0 → pycosmo-2.2.1}/src/PyCosmo/NonLinearPerturbationHaloFit.py

@@ -253,7 +253,7 @@ class NonLinearPerturbationHaloFit(NonLinearPerturbationBase):
 
         kseek = np.logspace(logkmin, logkmax, nk)
 
-        sig2gauss = np.trapz(
+        sig2gauss = np.trapezoid(
             np.exp(-(np.outer(1 / kseek, k) ** 2)) * Dlin / k, x=k, axis=1
         )
 
@@ -272,14 +272,14 @@ class NonLinearPerturbationHaloFit(NonLinearPerturbationBase):
         # Effective index, equation (C7)
         # n = -3 - dlnsig^2/dlnR
         #   = -3 + 2 int dlnk Dlin (k/ksig)^2 Wgauss(k/ksig) ** 2
-        np3 = 2.0 * np.trapz(y**2 * np.exp(-(y**2)) * Dlin / k, x=k)
+        np3 = 2.0 * np.trapezoid(y**2 * np.exp(-(y**2)) * Dlin / k, x=k)
         # Spectral curvature, equation (C8)
         # C = - d^2lnsig^2/dlnR^2
         #   = 2(n+3) + (n+3)^2 - 4 int dlnk Dlin (k/ksig)^4 Wgauss(k/ksig) ** 2
         C = (
             (np3 + 1.0) ** 2
             - 1.0
-            - 4.0 * np.trapz(y**4 * np.exp(-(y**2)) * Dlin / k, x=k)
+            - 4.0 * np.trapezoid(y**4 * np.exp(-(y**2)) * Dlin / k, x=k)
         )
 
         return ksig, np3, C
@@ -304,12 +304,12 @@ class NonLinearPerturbationHaloFit(NonLinearPerturbationBase):
         # Effective index, equation (C7)
         # n = -3 - dlnsig^2/dlnR
         #   = -3 + 2 int dlnk Dlin (k/ksig)^2 Wgauss(k/ksig) ** 2
-        # np3 = 2*np.trapz(ysq*np.exp(-ysq)*Dlin/k,x=k)
+        # np3 = 2*np.trapezoid(ysq*np.exp(-ysq)*Dlin/k,x=k)
         n = np3 - 3.0
         # Spectral curvature, equation (C8)
         # C = - d^2lnsig^2/dlnR^2
         #   = 2(n+3) + (n+3)^2 - 4 int dlnk Dlin (k/ksig)^4 Wgauss(k/ksig) ** 2
-        # C = (np3+1) ** 2 - 1 - 4*np.trapz(ysq ** 2*np.exp(-ysq)*Dlin/k,x=k)
+        # C = (np3+1) ** 2 - 1 - 4*np.trapezoid(ysq ** 2*np.exp(-ysq)*Dlin/k,x=k)
 
         # omega_m_z dependent functions
         # 1st case: Matter dominated universe
@@ -447,7 +447,7 @@ class NonLinearPerturbationHaloFit(NonLinearPerturbationBase):
         :param Dlin: P(k) linear-theory matter power spectrum P(k) [Mpc^3]
         :return: 1D linear displacement variance, as defined in eq.4 in Mead et al, 2015
         """
-        integr = 1.0 / 3 * np.trapz(Dlin / (k**3), x=k, axis=1)
+        integr = 1.0 / 3 * np.trapezoid(Dlin / (k**3), x=k, axis=1)
         sigmav = np.sqrt(integr)
         return np.sqrt(sigmav)
 
@@ -462,7 +462,7 @@ class NonLinearPerturbationHaloFit(NonLinearPerturbationBase):
         R = 100.0 / self._params.h
         T = 3 / ((k * R) ** 3) * (np.sin(k * R) - np.cos(k * R))
         # T = self.T(k * R)
-        integr = 1.0 / 3 * np.trapz((Dlin / (k**3)) * (T**2), x=k, axis=1)
+        integr = 1.0 / 3 * np.trapezoid((Dlin / (k**3)) * (T**2), x=k, axis=1)
         sigma_d100 = np.sqrt(integr)
         return sigma_d100
 
@@ -480,7 +480,7 @@ class NonLinearPerturbationHaloFit(NonLinearPerturbationBase):
         w = (
             3 / ((k * R) ** 3) * (np.sin(k * R) - np.cos(k * R))
         )  # top hat window function
-        res = np.trapz(k**3 * Dlin[0] * w**2, lnk)
+        res = np.trapezoid(k**3 * Dlin[0] * w**2, lnk)
         sig8z = np.sqrt(1.0 / (2.0 * np.pi**2) * res)
 
         return sig8z

{pycosmo-2.2.0 → pycosmo-2.2.1}/src/PyCosmo/NonLinearPerturbationMead.py

@@ -382,8 +382,8 @@ class NonLinearPerturbationMead(NonLinearPerturbationBase):
         # n = -3 - dlnsig^2/dlnR|R=1/ksig
         # The division by sigma^2(1/ksig) is needed because sigma^2(1/ksig) is not 1
 
-        i1 = np.trapz(Tksig * Tksig_deriv * Dlin, x=k_temp, axis=0)
-        i2 = np.trapz(
+        i1 = np.trapezoid(Tksig * Tksig_deriv * Dlin, x=k_temp, axis=0)
+        i2 = np.trapezoid(
             self.T(1.0 / ksig * k_temp).T ** 2 * Dlin / k_temp[:, None],
             x=k_temp,
             axis=0,
@@ -409,7 +409,7 @@ class NonLinearPerturbationMead(NonLinearPerturbationBase):
         pklin = self._lin_pert.powerspec_a_k(k=k, a=a)
         Dlin = self._pk_to_D(pklin, k)
 
-        res = np.trapz(Dlin / k[:, None] ** 3, k, axis=0)
+        res = np.trapezoid(Dlin / k[:, None] ** 3, k, axis=0)
         sigv = np.sqrt(res / 3.0)
         assert sigv.shape == (len(a),)
         return sigv
@@ -429,7 +429,7 @@ class NonLinearPerturbationMead(NonLinearPerturbationBase):
         Dlin = self._pk_to_D(pklin, k)
         T = self.T(k * R)
 
-        res = np.trapz(T[:, None] ** 2 * Dlin / k[:, None] ** 3, x=k, axis=0)
+        res = np.trapezoid(T[:, None] ** 2 * Dlin / k[:, None] ** 3, x=k, axis=0)
 
         sigv = np.sqrt(res / 3.0)
         return sigv
@@ -450,7 +450,7 @@ class NonLinearPerturbationMead(NonLinearPerturbationBase):
 
         w = self.T(k * r)  # top hat window function
         pk = self._lin_pert.powerspec_a_k(a=a, k=k)
-        res = np.trapz(k[:, None] ** 3 * pk * w[:, None] ** 2, lnk, axis=0)
+        res = np.trapezoid(k[:, None] ** 3 * pk * w[:, None] ** 2, lnk, axis=0)
 
         sig8z = np.sqrt(1.0 / (2.0 * np.pi**2) * res)
         return sig8z
@@ -484,7 +484,7 @@ class NonLinearPerturbationMead(NonLinearPerturbationBase):
         assert t.shape == (nk, nm, na)
         integrand_mpc = ps * t**2.0 * k[:, None, None] ** 3.0
 
-        integral = np.trapz(integrand_mpc, np.log(k), axis=0)
+        integral = np.trapezoid(integrand_mpc, np.log(k), axis=0)
 
         return integral.flatten()
 
@@ -853,5 +853,5 @@ def integral_halo(k, m_msun, nu_range, rv_mpc, c, a, f, eta):
     nufuncs = m_msun[:, None, :].T * nu_range[:, None, None] * f[:, None, None]
     u_km = _u_km_slow(k, a, c, rv_mpc, nu_range, eta)
     integrand_1halo = nufuncs * u_km**2.0
-    integral_1halo = np.trapz(integrand_1halo, np.log(nu_range), axis=0)
+    integral_1halo = np.trapezoid(integrand_1halo, np.log(nu_range), axis=0)
     return integral_1halo

{pycosmo-2.2.0 → pycosmo-2.2.1}/src/PyCosmo/NonLinearPerturbation_HI.py

@@ -155,7 +155,7 @@ class NonLinearPerturbation_HI(NonLinearPerturbation_HaloModel):
         # corrections such that int(f dnu)=1. But just if we integrate below one solar mass.
         if self._params.min_halo_mass <= 1.0:
             delta_nu = nu_range[:, 1] - nu_range[:, 0]
-            diff_f = 1 - np.trapz(f, nu_range)
+            diff_f = 1 - np.trapezoid(f, nu_range)
             const_f = diff_f / delta_nu * 2.0
             f[:, 0] += const_f
 
@@ -224,7 +224,7 @@ class NonLinearPerturbation_HI(NonLinearPerturbation_HaloModel):
         # corrections such that int(f dnu)=1. But just for if we integrate below one solar mass.
         if self._params.min_halo_mass <= 1.0:
             delta_nu = nu_range[:, 1] - nu_range[:, 0]
-            diff_f = 1 - np.trapz(f, nu_range)
+            diff_f = 1 - np.trapezoid(f, nu_range)
             const_f = diff_f / delta_nu * 2.0
             f[:, 0] += const_f
 
@@ -305,11 +305,11 @@ class NonLinearPerturbation_HI(NonLinearPerturbation_HaloModel):
         # corrections such that int(f dnu)=1 and int(f*b dnu)=1. But just for if we integrate below one solar mass.
         if self._params.min_halo_mass <= 1.0:
             delta_nu = nu_range[:, 1] - nu_range[:, 0]
-            diff_f = 1 - np.trapz(f, nu_range)
+            diff_f = 1 - np.trapezoid(f, nu_range)
             const_f = diff_f / delta_nu * 2.0
             f[:, 0] += const_f
 
-            diff_bf = 1 - np.trapz(f * bias, nu_range)
+            diff_bf = 1 - np.trapezoid(f * bias, nu_range)
             const_b = diff_bf / (delta_nu * f[:, 0]) * 2.0
             bias[:, 0] += const_b
 

{pycosmo-2.2.0 → pycosmo-2.2.1}/src/PyCosmo/NonLinearPerturbation_HaloModel.py

@@ -416,7 +416,7 @@ class NonLinearPerturbation_HaloModel(NonLinearPerturbationBase):
 
         w = self.T(k * r)  # top hat window function
         pk = self._lin_pert.powerspec_a_k(a=a, k=k)
-        res = np.trapz(k[:, None] ** 3 * pk * w[:, None] ** 2, lnk, axis=0)
+        res = np.trapezoid(k[:, None] ** 3 * pk * w[:, None] ** 2, lnk, axis=0)
 
         sig8z = np.sqrt(1.0 / (2.0 * np.pi**2) * res)
         return sig8z
@@ -453,7 +453,7 @@ class NonLinearPerturbation_HaloModel(NonLinearPerturbationBase):
         assert t.shape == (nk, nm, na)
         integrand_mpc = ps * t**2.0 * k[:, None, None] ** 3.0
 
-        integral = np.trapz(integrand_mpc, np.log(k), axis=0)
+        integral = np.trapezoid(integrand_mpc, np.log(k), axis=0)
 
         return integral.flatten()
 
@@ -1031,7 +1031,7 @@ class NonLinearPerturbation_HaloModel(NonLinearPerturbationBase):
         # dnu)=1. But just if we integrate below one solar mass.
         if self._params.min_halo_mass <= 1.0:
             delta_nu = nu_range[:, 1] - nu_range[:, 0]
-            diff_f = 1 - np.trapz(f, nu_range)
+            diff_f = 1 - np.trapezoid(f, nu_range)
             const_f = diff_f / delta_nu * 2.0
             f[:, 0] += const_f
 
@@ -1094,7 +1094,7 @@ class NonLinearPerturbation_HaloModel(NonLinearPerturbationBase):
         # dnu)=1. But just for if we integrate below one solar mass.
         if self._params.min_halo_mass <= 1.0:
             delta_nu = nu_range[:, 1] - nu_range[:, 0]
-            diff_f = 1 - np.trapz(f, nu_range)
+            diff_f = 1 - np.trapezoid(f, nu_range)
             const_f = diff_f / delta_nu * 2.0
             f[:, 0] += const_f
 
@@ -1162,11 +1162,11 @@ class NonLinearPerturbation_HaloModel(NonLinearPerturbationBase):
         # corrections such that int(f dnu)=1 and int(f*b dnu)=1. But just for if we integrate below one solar mass.
         if self._params.min_halo_mass <= 1.0:
             delta_nu = nu_range[:, 1] - nu_range[:, 0]
-            diff_f = 1 - np.trapz(f, nu_range)
+            diff_f = 1 - np.trapezoid(f, nu_range)
             const_f = diff_f / delta_nu * 2.0
             f[:, 0] += const_f
 
-            diff_bf = 1 - np.trapz(f * bias, nu_range)
+            diff_bf = 1 - np.trapezoid(f * bias, nu_range)
             const_b = diff_bf / (delta_nu * f[:, 0]) * 2.0
             bias[:, 0] += const_b
 
@@ -1261,6 +1261,6 @@ class NonLinearPerturbation_HaloModel(NonLinearPerturbationBase):
             cosmo.nonlin_pert.print_params()
         """
 
-        print("The halomodel has been initialised with the" " following attributes:")
+        print("The halomodel has been initialised with the following attributes:")
         for key in self._params.keys():
             print("{}={}".format(key, self._params[key]))

{pycosmo-2.2.0 → pycosmo-2.2.1}/src/PyCosmo/PerturbationTable.py

@@ -147,7 +147,7 @@ class PerturbationTable:
         if np.max(k_grid) < max_k:
             warnings.warn(
                 f"ignore tabulation_max_k value {max_k} which is beyond the largest"
-                " value {np.max(k_grid)} in the chosen k grid"
+                f" value {np.max(k_grid)} in the chosen k grid"
             )
 
         k_grid = k_grid[k_grid >= min_k]

{pycosmo-2.2.0 → pycosmo-2.2.1}/src/PyCosmo/_RecombinationCosmics.py

@@ -35,9 +35,9 @@ class RecombinationCosmics:
         # call RECFAST++ to compute reionisation history tables
         print("Reading COSMICS recombination file")
 
-        assert (
-            self._params.recomb_filename is None
-        ), "for cosmics setting the file name is not supported"
+        assert self._params.recomb_filename is None, (
+            "for cosmics setting the file name is not supported"
+        )
 
         tab_cosmics = cosmics(self._params.recomb_dir)