PyCosmo 2.0.3__tar.gz → 2.1.1__tar.gz

{PyCosmo-2.0.3/PyCosmo.egg-info → PyCosmo-2.1.1}/PKG-INFO

@@ -1,23 +1,27 @@
 Metadata-Version: 2.1
 Name: PyCosmo
-Version: 2.0.3
+Version: 2.1.1
 Summary: A multi-purpose cosmology calculation tool
-Home-page: https://cosmo-docs.phys.ethz.ch/PyCosmo
-Author: Institute for Cosmology
-Author-email: pycosmo@lists.phys.ethz.ch
+Author: Uwe Schmitt et al
+Author-email: uwe.schmitt@id.ethz.ch
 License: GPLv3
-Platform: UNKNOWN
+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 :: Python
 Classifier: Programming Language :: C
-Classifier: Topic :: Scientific/Engineering :: Astronomy
-Classifier: Programming Language :: Python :: 3.7
-Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Topic :: Scientific/Engineering :: Astronomy
+Requires-Python: >=3.8
+Description-Content-Type: text/x-rst; charset=UTF-8
+Provides-Extra: dev
+Provides-Extra: docs
 License-File: LICENSE
 License-File: AUTHORS.rst
 
@@ -39,5 +43,3 @@ The code includes calculations of:
 The code documentation can be found at `<https://cosmo-docs.phys.ethz.ch/PyCosmo/>`_ or created by typing make docs from the PyCosmo folder in your terminal.
 
 Interactive tutorial notebooks are available on the PyCosmoHUB `<https://pycosmohub.com/>`_.
-
-

PyCosmo-2.1.1/pyproject.toml

@@ -0,0 +1,45 @@
+[build-system]
+requires = ["setuptools >= 40.6.0", "wheel", "numpy", "Cython"]
+build-backend = "setuptools.build_meta"
+
+
+[tool.black]
+include = '\.pyi?$'
+exclude = '''
+(
+    \.eggs
+  | \.git
+  | \.mypy_cache
+  | \.tox
+  | \.venv
+  | venv
+  | _build/
+  | build/
+  | dist
+)
+'''
+
+[tool.pytest.ini_options]
+addopts = "-v -ra"
+testpaths = ["tests"]
+filterwarnings = ["ignore:invalid"]
+
+[tool.tox]
+legacy_tox_ini = '''
+[tox]
+isolated_build = true
+envlist = py39,py310,py311
+package = sdist
+setenv =
+    PIP_EXTRA_INDEX_URL=https://cosmo-pypi.phys.ethz.ch/simple
+    HTTP_PROXY=http://proxy.ethz.ch:3128
+    HTTPS_PROXY=http://proxy.ethz.ch:3128
+
+[testenv]
+skip_install = false
+passenv = *
+allowlist_externals = pytest
+extras = dev
+commands =
+    pytest --runslow -v -ra tests
+'''

PyCosmo-2.1.1/setup.cfg

@@ -0,0 +1,79 @@
+[metadata]
+name = PyCosmo
+version = 2.1.1
+license = GPLv3
+description = A multi-purpose cosmology calculation tool
+long_description = file: README.rst
+long_description_content_type = text/x-rst; charset=UTF-8
+author = Uwe Schmitt et al
+author_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 :: 3.10
+	Programming Language :: Python :: 3.9
+	Programming Language :: Python :: 3.8
+	Topic :: Scientific/Engineering :: Astronomy
+project_urls = 
+	Source = https://cosmo-docs.phys.ethz.ch/PyCosmo
+
+[options]
+install_requires = 
+	numpy
+	recfast4py>=0.2.3
+	dill
+	matplotlib
+	numba>=0.57.0rc1
+	sympy2c>=2.2.2
+	numexpr
+	scipy
+packages = find:
+package_dir = 
+	=src
+zip_safe = False
+python_requires = >=3.8
+
+[options.packages.find]
+where = src
+
+[options.package_data]
+* = 
+	*.pyx
+	*.c
+	*.h
+	config/*.ini
+
+[options.entry_points]
+console_scripts = 
+	recompile = PyCosmo:Cosmo.recompile_from_cli
+
+[options.extras_require]
+dev = 
+	Cython
+	twine
+	pytest<7.2.0
+	pytest-cov
+	pytest-regtest
+	tox
+	flake8
+	black
+	isort
+	sphinx
+	sphinx-pynpoint-theme
+	myst-parser
+	memray
+docs = 
+	sphinx
+	sphinx-pynpoint-theme
+	myst-parser
+
+[egg_info]
+tag_build = 
+tag_date = 0
+

PyCosmo-2.1.1/setup.py

@@ -0,0 +1,30 @@
+#!/usr/bin/env python
+import numpy
+from Cython.Build import cythonize
+from setuptools import Extension, setup
+
+files = [
+    "const.c",
+    "main.c",
+    "halo_integral.c",
+    "polevl.c",
+    "sici.c",
+    "sicif.c",
+    "polevlf.c",
+    "logf.c",
+    "sinf.c",
+    "constf.c",
+    "mtherr.c",
+]
+ext_modules = [
+    Extension(
+        name="PyCosmo.cython.halo_integral",
+        ext_modules=cythonize("src/PyCosmo/cython/halo_integral.pyx"),
+        sources=["src/PyCosmo/cython/" + file for file in files],
+        include_dirs=[numpy.get_include()],
+    )
+]
+
+setup(
+    ext_modules=ext_modules,
+)

{PyCosmo-2.0.3 → PyCosmo-2.1.1/src}/PyCosmo/Background.py

@@ -16,6 +16,7 @@
 
 import numpy as np
 from scipy import integrate
+from scipy.interpolate import interp1d
 
 
 def _call(wrapper, function, a=None):
@@ -26,8 +27,7 @@ def _call(wrapper, function, a=None):
     elif isinstance(a, list):
         a = np.array(a)
     assert isinstance(a, np.ndarray)
-    a = a.astype(float)
-    return getattr(wrapper, function + "_ufunc")(a)
+    return getattr(wrapper, function)(a.astype(float))
 
 
 class Background(object):
@@ -46,6 +46,18 @@ class Background(object):
         self._params = params
         self._rec = rec
         self._wrapper = wrapper
+        self._eta_to_a = None
+
+    def _setup_eta_to_a(self):
+        a = np.logspace(-100, 0.0, 1000)
+        eta = self.eta(a)
+        a = a[eta > 0]
+        eta = eta[eta > 0]
+        self._eta_to_a = interp1d(
+            eta, a, "cubic", bounds_error=False, fill_value="extrapolate"
+        )
+        self._eta_min = np.min(eta)
+        self._eta_max = np.max(eta)
 
     def H(self, a):
         """
@@ -67,12 +79,11 @@ class Background(object):
     _hubble = H
 
     def _H2_H02_a(self, a=1.0):
-        return (
-            self._H2_H02_Omegar_a(a=a)
-            + self._H2_H02_Omegam_a(a=a)
-            + self._H2_H02_Omegak_a(a=a)
-            + self._H2_H02_Omegal_a(a=a)
-        )
+        result = self._H2_H02_Omegar_a(a=a)
+        result += self._H2_H02_Omegam_a(a=a)
+        result += self._H2_H02_Omegak_a(a=a)
+        result += self._H2_H02_Omegal_a(a=a)
+        return result
 
     def _H2_H02_Omegar_a(self, a=1.0):
         return self._params.omega_r / a**4
@@ -96,6 +107,7 @@ class Background(object):
         return _call(self._wrapper, "omega_nu_m", a) / a**4
 
     def _w_a(self, a=1.0):
+        self._cosmo.reset_wrapper_globals()
         return self._params.w0 + (1.0 - a) * self._params.wa
 
     #########################################################
@@ -131,7 +143,6 @@ class Background(object):
         :param a: scale factor [1]
         :return: Radial comoving horizon, :math:`\chi(a)`, in :math:`[Mpc s/km]`.
         """
-        self._cosmo.reset_wrapper_globals()
         return _call(self._wrapper, "chi", a)
 
     def dist_trans_a(self, a=1.0):
@@ -198,16 +209,30 @@ class Background(object):
 
         return self.dist_trans_a(a) / a
 
-    def eta(self, a):
-        r"""
-        Calculates conformal time :math:`\eta` to a given scale factor.
+    def eta_to_a(self, eta):
+        if self._eta_to_a is None:
+            self._setup_eta_to_a()
+        eta = np.atleast_1d(eta)
+        if np.any(eta < 0.95 * self._eta_min) or np.any(eta > self._eta_max * 1.05):
+            raise ValueError(
+                f"eta value(s) outside of range {self._eta_min:e} .. "
+                f" {self._eta_max:e}"
+            )
+        return self._eta_to_a(eta)
 
-        :param a: scale factor [1]
-        :return: :math:`\eta` conformal time [:math:`\mathrm{Mpc}/h`]
-        """
+    def eta(self, a):
         a = np.atleast_1d(a)
-        self._cosmo.reset_wrapper_globals()
-        return _call(self._wrapper, "eta", a)  # Mpc/h
+        af = a[a > 1e-100]
+        af = np.concatenate(([1e-100], af))
+        y, meta = self._wrapper.solve_fast_eta(
+            np.array((0.0,)),
+            af,
+            1e-8,
+            1e-8,
+        )
+        eta = np.zeros_like(a)
+        eta[a > 1e-100] = y.flatten()[1:]
+        return eta
 
     #########################################################
     # A series of functions to compute thermodynamical      #
@@ -267,7 +292,12 @@ class Background(object):
         """
         a = np.atleast_1d(a)
         return np.array(
-            [integrate.quadrature(self._tau_intgd, np.log(aa), 0.0)[0] for aa in a]
+            [
+                integrate.quadrature(
+                    self._tau_intgd, np.log(aa), 0.0, rtol=1e-6, maxiter=100
+                )[0]
+                for aa in a
+            ]
         )
 
     def _tau_intgd(self, lna):
@@ -408,7 +438,9 @@ class Background(object):
         input: a - scale factor [1]
         output: [1]
         """
-        return self._H2_H02_Omegal_a(a=a) / self._H2_H02_a(a=a)
+        result = self._H2_H02_Omegal_a(a=a)
+        result /= self._H2_H02_a(a=a)
+        return result
 
     def _omega_nu_m_a(self, a=1.0):
         """

{PyCosmo-2.0.3 → PyCosmo-2.1.1/src}/PyCosmo/BoltzmannSolver/Fields.py

@@ -37,7 +37,7 @@ class Fields(object):
         self.lna = None
         self._offsets = defaultdict(list)
 
-    def set_results(self, lna, solver_result, keep_lna0):
+    def set_results(self, lna, solver_result):
         self.lna = lna
 
         fields_map = self._wrapper.fields(lna, solver_result, self._cosmology)
@@ -61,10 +61,6 @@ class Fields(object):
         assert self._y.shape[1] == len(lna), "fields and lna vector mismatch"
         self._offsets = offsets
 
-        if not keep_lna0:
-            self._y = self._y[:, 1:]
-            self.lna = self.lna[1:]
-
     def __dir__(self):
         return super().__dir__() + list(map(str, self._symbols))