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a lightweight Python binding of the CLASS CMB Boltzmann code

Home Page: http://classylss.rtfd.io

License: GNU General Public License v3.0

Python 97.79% Shell 0.68% Makefile 1.53%

cosmology large-scale-structure cmb python boltzmann-code cosmic-microwave-background class

classylss's Introduction

Hello there 👋

I am currently a technologist at the Consumer Finance Protection Bureau working to detect and prevent unfair, deceptive, and abusive practices in consumer financial services. I also teach a Python geospatial data science course in the Masters of Urban Spatial Analytics program at the University of Pennsylvania. Prior to working at the CFPB, I was the Finance, Policy, and Data director for the City of Philadelphia's @PhilaController and

I'm a former academic with a Ph.D. in astrophysics from UC Berkeley. I am passionate about data visualization, predictive analytics, and effective communication of complex ideas to a broad audience. I am a strong supporter of transparency in government, open-source software, and the open science framework.

I live in the Wissahickon neighborhood of Philadelphia, PA, with my wife, young daughter, and rescue dog.

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classylss's Issues

wget not found.

When building on circle-ci for conda-forge, I get a 'wget' not found error.

What about building in a class source code zip file in the source code tarball? Does this violate the copy right of class?

N_ur is not automatically corrected when a different m_ncdm is set via clone

I guess this is by definition the correct behavior (though surprising ). perhaps we shall add m_ncdm to 'match'.

classylss does not read sigma8

If one uses the class command line binary, one can specify the power spectrum amplitude either as:
A_s = 2.215e-9
or as
sigma8 = 0.8607
and class will automatically find the right A_s to match sigma8.

With classylss this does not work: one gets
UserWarning: Class did not read input parameter(s): sigma8

and the output Sigma8/A_s are the defaults.

It would be nice if this did work!

add some simple tests

Does not build with python 3.12

numpy.distutils has been removed, see here:
https://numpy.org/doc/stable/reference/distutils_status_migration.html

Simply replacing numpy.distutils with distutils does not quite work:

[spb41]~/codes/classylss% python setup.py install
/usr/lib/python3.12/site-packages/setuptools/_distutils/cmd.py:66: SetuptoolsDeprecationWarning: setup.py install is deprecated.
!!

    ********************************************************************************
    Please avoid running ``setup.py`` directly.
    Instead, use pypa/build, pypa/installer or other
    standards-based tools.

    See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
    ********************************************************************************

!!
self.initialize_options()
/usr/lib/python3.12/site-packages/setuptools/_distutils/cmd.py:66: EasyInstallDeprecationWarning: easy_install command is deprecated.
!!

    ********************************************************************************
    Please avoid running ``setup.py`` and ``easy_install``.
    Instead, use pypa/build, pypa/installer or other
    standards-based tools.

    See https://github.com/pypa/setuptools/issues/917 for details.
    ********************************************************************************

!!
self.initialize_options()
error: in 'libraries' option (library 'class'), 'sources' must be present and must be a list of source filenames

Add `mode=` in most functions to capture the class out of bounds errors.

Currently if we evaluate outside of the bounds an exception is raised. We can do better by handling this like scipy function, mode='raise'/'constant'/'nearest', and set the value accordingly without raising an exception. This becomes handy in interactive plotting.

Add readthedocs?

Roadmap to turn classylss into a CLASS binding.

Here is what I propose as a roadmap.

Implement pure python classylss.cosmology that can be constructed from Astropy cosmology objects, and yet delegates to CLASS for all function evaluation,
Reimplement a classylss.lss module that contains original functionalities of classylss.legacy, but in pure python, using mcfit.
migrate classylss.cosmology and lss to nbodykit. Now classylss contains only class binding, and nbodykit doesn't contain any compiled code.
Move the original lss routines to a classylss.legacy module. We break all code that uses classylss at this step, such that they can be clearly grepped and switch to nbodykit when necessary.

Suddenly stopped working.

MPITest(commsize=1):test_fftpower ... FlatLambdaCDM(name="Planck15", H0=67.7 km / (Mpc s), Om0=0.307, Tcmb0=2.725 K, Neff=3.05, m_nu=[ 0.    0.    0.06] eV, Ob0=0.0486)


Error in thermodynamics_init 
=>thermodynamics_init(L:301) :error in thermodynamics_helium_from_bbn(ppr,pba,pth);
=>thermodynamics_helium_from_bbn(L:1112) :could not open fA with name /usr/lib64/python2.7/site-packages/classylss/class/bbn/sBBN.dat and mode "r"
ERROR

    compile options: '-Iclassylss/_gcl/include -I/usr/lib64/python2.7/site-packages/numpy/core/include -Ibuild/temp.linux-x86_64-2.7/include -c'
    extra options: '-fopenmp -O2 -std=c++11'
    g++: classylss/_gcl/cpp/PowerSpectrum.cpp
    g++: classylss/_gcl/cpp/ClassParams.cpp
    g++: classylss/_gcl/cpp/Tools.cpp
    g++: classylss/_gcl/cpp/parray.cpp
    g++: classylss/_gcl/cpp/ZeldovichPS.cpp
    g++: classylss/_gcl/cpp/Common.cpp
    classylss/_gcl/cpp/Common.cpp: In function ‘void Common::write(FILE*, const char*, ...)’:
    classylss/_gcl/cpp/Common.cpp:64:25: error: format not a string literal and no format arguments [-Werror=format-security]
         fprintf(stream, dest);
                             ^
    cc1plus: some warnings being treated as errors
    classylss/_gcl/cpp/Common.cpp: In function ‘void Common::write(FILE*, const char*, ...)’:
    classylss/_gcl/cpp/Common.cpp:64:25: error: format not a string literal and no format arguments [-Werror=format-security]
         fprintf(stream, dest);
                             ^
    cc1plus: some warnings being treated as errors
    error: Command "g++ -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -Iclassylss/_gcl/include -I/usr/lib64/python2.7/site-packages/numpy/core/include -Ibuild/temp.linux-x86_64-2.7/include -c classylss/_gcl/cpp/Common.cpp -o build/temp.linux-x86_64-2.7/classylss/_gcl/cpp/Common.o -fopenmp -O2 -std=c++11" failed with exit status 1

    ----------------------------------------
Command "/usr/bin/python -c "import setuptools, tokenize;__file__='/tmp/pip-build-K8J8zE/classylss/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-pVSOf4-record/install-record.txt --single-version-externally-managed --compile --user --prefix=" failed with error code 1 in /tmp/pip-build-K8J8zE/classylss
You are using pip version 7.1.2, however version 8.1.2 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.