Switch Python build system to use mesonpy instead of setuptools

[kjmeagher]

This PR solves a couple of problems at once. I got an email from a user complaining that the setuptools build system couldn't handle multiple photospline and boost being in different directories. Meson's pkg-config dependency detection is far superior to anything you can ad hoc program in setuptools. This allowed some cleanup that I had wanted to do regarding the meson build file. Also, one of the reasons that I gave up on making wheels for nuflux was that setuptools couldn't figure out how to include header files while mesonpy does this automatically. The files changed looks big but that is just because I also moved the python source directory to /src/.

The only change from the user perspective is that when compiling you now use exactly the same env vars for both meson and python. Documentation has been updated to reflect this. cvmfs target py3-v4.0.1 was dropped because the last version of meson that worked with python 3.6 doesn't support the pure option for python. And py3-v4.2.1 was dropped because mesonpy doesn't play well with the python misconfiguration present in that version of cvmfs.

[codecov]

Codecov Report

Attention: 7 lines in your changes are missing coverage. Please review.

Comparison is base (07ab4b1) 56.36% compared to head (a7973b4) 56.94%.

Files	Patch %	Lines
src/library/SplineFlux.cpp	37.50%	2 Missing and 3 partials ⚠️
src/library/ANFlux.cpp	0.00%	0 Missing and 2 partials ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #24      +/-   ##
==========================================
+ Coverage   56.36%   56.94%   +0.57%     
==========================================
  Files          13       13              
  Lines         715      713       -2     
  Branches      326      323       -3     
==========================================
+ Hits          403      406       +3     
+ Misses        130      128       -2     
+ Partials      182      179       -3     

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[mjlarson]

Things seem reasonable enough here, although I'm not an expert on meson. Pip works and building from source seems to generally result in a functional build. I did receive some warnings when building on cobalt with py3-v4.3.0:

(test_venv) mlarson@cobalt01 /tmp/mlarson/nuflux/nuflux $ ninja -C build                            
ninja: Entering directory `build'
[16/17] Compiling C++ object src/pybindings/_nuflux.cpython-311-x86_64-linux-gnu.so.p/module.cxx.o
In file included from /cvmfs/icecube.opensciencegrid.org/py3-v4.3.0/RHEL_7_x86_64/include/boost/python/detail/is_xxx.hpp:8,
                 from /cvmfs/icecube.opensciencegrid.org/py3-v4.3.0/RHEL_7_x86_64/include/boost/python/detail/is_auto_ptr.hpp:9,
                 from /cvmfs/icecube.opensciencegrid.org/py3-v4.3.0/RHEL_7_x86_64/include/boost/python/detail/copy_ctor_mutates_rhs.hpp:8,
                 from /cvmfs/icecube.opensciencegrid.org/py3-v4.3.0/RHEL_7_x86_64/include/boost/python/detail/value_arg.hpp:7,
                 from /cvmfs/icecube.opensciencegrid.org/py3-v4.3.0/RHEL_7_x86_64/include/boost/python/object/forward.hpp:10,
                 from /cvmfs/icecube.opensciencegrid.org/py3-v4.3.0/RHEL_7_x86_64/include/boost/python/object/pointer_holder.hpp:16,
                 from /cvmfs/icecube.opensciencegrid.org/py3-v4.3.0/RHEL_7_x86_64/include/boost/python/to_python_indirect.hpp:10,
                 from /cvmfs/icecube.opensciencegrid.org/py3-v4.3.0/RHEL_7_x86_64/include/boost/python/converter/arg_to_python.hpp:10,
                 from /cvmfs/icecube.opensciencegrid.org/py3-v4.3.0/RHEL_7_x86_64/include/boost/python/call.hpp:15,
                 from /cvmfs/icecube.opensciencegrid.org/py3-v4.3.0/RHEL_7_x86_64/include/boost/python/object_core.hpp:14,
                 from /cvmfs/icecube.opensciencegrid.org/py3-v4.3.0/RHEL_7_x86_64/include/boost/python/args.hpp:22,
                 from /cvmfs/icecube.opensciencegrid.org/py3-v4.3.0/RHEL_7_x86_64/include/boost/python.hpp:11,
                 from ../src/pybindings/module.cxx:4:
/cvmfs/icecube.opensciencegrid.org/py3-v4.3.0/RHEL_7_x86_64/include/boost/python/detail/is_auto_ptr.hpp:17:40: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   17 | BOOST_PYTHON_IS_XXX_DEF(auto_ptr, std::auto_ptr, 1)
      |                                        ^~~~~~~~
/cvmfs/icecube.opensciencegrid.org/py3-v4.3.0/RHEL_7_x86_64/include/boost/detail/is_xxx.hpp:20:4: note: in definition of macro 'BOOST_DETAIL_IS_XXX_DEF'
   20 |    qualified_name< BOOST_PP_ENUM_PARAMS_Z(1, nargs, T) >        \
      |    ^~~~~~~~~~~~~~
/cvmfs/icecube.opensciencegrid.org/py3-v4.3.0/RHEL_7_x86_64/include/boost/python/detail/is_auto_ptr.hpp:17:1: note: in expansion of macro 'BOOST_PYTHON_IS_XXX_DEF'
   17 | BOOST_PYTHON_IS_XXX_DEF(auto_ptr, std::auto_ptr, 1)
      | ^~~~~~~~~~~~~~~~~~~~~~~
In file included from /cvmfs/icecube.opensciencegrid.org/py3-v4.3.0/RHEL_7_x86_64/spack/opt/spack/linux-centos7-x86_64_v2/gcc-4.8.5/gcc-13.1.0-5camztap56edgn7uluhb44htpco7ijzc/lib/gcc/x86_64-pc-linux-gnu/13.1.0/../../../../include/c++/13.1.0/memory:78,
                 from /cvmfs/icecube.opensciencegrid.org/py3-v4.3.0/RHEL_7_x86_64/include/boost/function/function_base.hpp:33,
                 from /cvmfs/icecube.opensciencegrid.org/py3-v4.3.0/RHEL_7_x86_64/include/boost/function/detail/prologue.hpp:18,
                 from /cvmfs/icecube.opensciencegrid.org/py3-v4.3.0/RHEL_7_x86_64/include/boost/function/function_template.hpp:13,
                 from /cvmfs/icecube.opensciencegrid.org/py3-v4.3.0/RHEL_7_x86_64/include/boost/function/detail/maybe_include.hpp:15,
                 from /cvmfs/icecube.opensciencegrid.org/py3-v4.3.0/RHEL_7_x86_64/include/boost/function/function0.hpp:11,
                 from /cvmfs/icecube.opensciencegrid.org/py3-v4.3.0/RHEL_7_x86_64/include/boost/python/errors.hpp:13,
                 from /cvmfs/icecube.opensciencegrid.org/py3-v4.3.0/RHEL_7_x86_64/include/boost/python/handle.hpp:11,
                 from /cvmfs/icecube.opensciencegrid.org/py3-v4.3.0/RHEL_7_x86_64/include/boost/python/args_fwd.hpp:10,
                 from /cvmfs/icecube.opensciencegrid.org/py3-v4.3.0/RHEL_7_x86_64/include/boost/python/args.hpp:10:
/cvmfs/icecube.opensciencegrid.org/py3-v4.3.0/RHEL_7_x86_64/spack/opt/spack/linux-centos7-x86_64_v2/gcc-4.8.5/gcc-13.1.0-5camztap56edgn7uluhb44htpco7ijzc/lib/gcc/x86_64-pc-linux-gnu/13.1.0/../../../../include/c++/13.1.0/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
[17/17] Linking target src/pybindings/_nuflux.cpython-311-x86_64-linux-gnu.so

and when running ninja,

...
Installing subdir /tmp/mlarson/nuflux/nuflux/src/nuflux/data/SplineFlux to /tmp/mlarson/nuflux/test_venv/share/nuflux/SplineFlux
Installing /tmp/mlarson/nuflux/nuflux/src/nuflux/data/SplineFlux/BERSS_H3p_central_nue.fits to /tmp/mlarson/nuflux/test_venv/share/nuflux/SplineFlux
Warning: trying to copy a symlink that points to a file. This will copy the file,
but this will be changed in a future version of Meson to copy the symlink as is. Please update your
build definitions so that it will not break when the change happens.
Installing /tmp/mlarson/nuflux/nuflux/src/nuflux/data/SplineFlux/BERSS_H3p_central_numu.fits to /tmp/mlarson/nuflux/test_venv/share/nuflux/SplineFlux
Warning: trying to copy a symlink that points to a file. This will copy the file,
but this will be changed in a future version of Meson to copy the symlink as is. Please update your
build definitions so that it will not break when the change happens.
Installing /tmp/mlarson/nuflux/nuflux/src/nuflux/data/SplineFlux/BERSS_H3p_upper_numubar.fits to /tmp/mlarson/nuflux/test_venv/share/nuflux/SplineFlux
Warning: trying to copy a symlink that points to a file. This will copy the file,
but this will be changed in a future version of Meson to copy the symlink as is. Please update your
build definitions so that it will not break when the change happens.
Installing /tmp/mlarson/nuflux/nuflux/src/nuflux/data/SplineFlux/BERSS_H3a_central.fits to /tmp/mlarson/nuflux/test_venv/share/nuflux/SplineFlux
Installing /tmp/mlarson/nuflux/nuflux/src/nuflux/data/SplineFlux/BERSS_H3p_upper_nuebar.fits to /tmp/mlarson/nuflux/test_venv/share/nuflux/SplineFlux
Warning: trying to copy a symlink that points to a file. This will copy the file,
but this will be changed in a future version of Meson to copy the symlink as is. Please update your
build definitions so that it will not break when the change happens.
Installing /tmp/mlarson/nuflux/nuflux/src/nuflux/data/SplineFlux/BERSS_H3a_central_nuebar.fits to /tmp/mlarson/nuflux/test_venv/share/nuflux/SplineFlux
Warning: trying to copy a symlink that points to a file. This will copy the file,
but this will be changed in a future version of Meson to copy the symlink as is. Please update your
build definitions so that it will not break when the change happens.
Installing /tmp/mlarson/nuflux/nuflux/src/nuflux/data/SplineFlux/BERSS_H3p_central_numubar.fits to /tmp/mlarson/nuflux/test_venv/share/nuflux/SplineFlux
Warning: trying to copy a symlink that points to a file. This will copy the file,
but this will be changed in a future version of Meson to copy the symlink as is. Please update your
build definitions so that it will not break when the change happens.
Installing /tmp/mlarson/nuflux/nuflux/src/nuflux/data/SplineFlux/BERSS_H3p_lower_nuebar.fits to /tmp/mlarson/nuflux/test_venv/share/nuflux/SplineFlux
Warning: trying to copy a symlink that points to a file. This will copy the file,
but this will be changed in a future version of Meson to copy the symlink as is. Please update your
build definitions so that it will not break when the change happens.
Installing /tmp/mlarson/nuflux/nuflux/src/nuflux/data/SplineFlux/BERSS_H3p_lower.fits to /tmp/mlarson/nuflux/test_venv/share/nuflux/SplineFlux
Installing /tmp/mlarson/nuflux/nuflux/src/nuflux/data/SplineFlux/BERSS_H3p_lower_numu.fits to /tmp/mlarson/nuflux/test_venv/share/nuflux/SplineFlux
Warning: trying to copy a symlink that points to a file. This will copy the file,
but this will be changed in a future version of Meson to copy the symlink as is. Please update your
build definitions so that it will not break when the change happens.
Installing /tmp/mlarson/nuflux/nuflux/src/nuflux/data/SplineFlux/BERSS_H3p_upper_nue.fits to /tmp/mlarson/nuflux/test_venv/share/nuflux/SplineFlux
Warning: trying to copy a symlink that points to a file. This will copy the file,
but this will be changed in a future version of Meson to copy the symlink as is. Please update your
build definitions so that it will not break when the change happens.
Installing /tmp/mlarson/nuflux/nuflux/src/nuflux/data/SplineFlux/BERSS_H3p_upper.fits to /tmp/mlarson/nuflux/test_venv/share/nuflux/SplineFlux
Installing /tmp/mlarson/nuflux/nuflux/src/nuflux/data/SplineFlux/BERSS_H3p_upper_numu.fits to /tmp/mlarson/nuflux/test_venv/share/nuflux/SplineFlux
Warning: trying to copy a symlink that points to a file. This will copy the file,
but this will be changed in a future version of Meson to copy the symlink as is. Please update your
build definitions so that it will not break when the change happens.
Installing /tmp/mlarson/nuflux/nuflux/src/nuflux/data/SplineFlux/BERSS_H3p_lower_nue.fits to /tmp/mlarson/nuflux/test_venv/share/nuflux/SplineFlux
Warning: trying to copy a symlink that points to a file. This will copy the file,
but this will be changed in a future version of Meson to copy the symlink as is. Please update your
build definitions so that it will not break when the change happens.
Installing /tmp/mlarson/nuflux/nuflux/src/nuflux/data/SplineFlux/BERSS_H3a_central_numu.fits to /tmp/mlarson/nuflux/test_venv/share/nuflux/SplineFlux
Warning: trying to copy a symlink that points to a file. This will copy the file,
but this will be changed in a future version of Meson to copy the symlink as is. Please update your
build definitions so that it will not break when the change happens.
Installing /tmp/mlarson/nuflux/nuflux/src/nuflux/data/SplineFlux/BERSS_H3a_central_nue.fits to /tmp/mlarson/nuflux/test_venv/share/nuflux/SplineFlux
Warning: trying to copy a symlink that points to a file. This will copy the file,
but this will be changed in a future version of Meson to copy the symlink as is. Please update your
build definitions so that it will not break when the change happens.
Installing /tmp/mlarson/nuflux/nuflux/src/nuflux/data/SplineFlux/BERSS_H3p_central.fits to /tmp/mlarson/nuflux/test_venv/share/nuflux/SplineFlux
Installing /tmp/mlarson/nuflux/nuflux/src/nuflux/data/SplineFlux/BERSS_H3p_lower_numubar.fits to /tmp/mlarson/nuflux/test_venv/share/nuflux/SplineFlux
Warning: trying to copy a symlink that points to a file. This will copy the file,
but this will be changed in a future version of Meson to copy the symlink as is. Please update your
build definitions so that it will not break when the change happens.
Installing /tmp/mlarson/nuflux/nuflux/src/nuflux/data/SplineFlux/BERSS_H3a_central_numubar.fits to /tmp/mlarson/nuflux/test_venv/share/nuflux/SplineFlux
Warning: trying to copy a symlink that points to a file. This will copy the file,
but this will be changed in a future version of Meson to copy the symlink as is. Please update your
build definitions so that it will not break when the change happens.
Installing /tmp/mlarson/nuflux/nuflux/src/nuflux/data/SplineFlux/BERSS_H3p_central_nuebar.fits to /tmp/mlarson/nuflux/test_venv/share/nuflux/SplineFlux
Warning: trying to copy a symlink that points to a file. This will copy the file,
but this will be changed in a future version of Meson to copy the symlink as is. Please update your
build definitions so that it will not break when the change happens.
Installing subdir /tmp/mlarson/nuflux/nuflux/src/nuflux/data/SplineFlux2 to /tmp/mlarson/nuflux/test_venv/share/nuflux/SplineFlux2
...

It may be worth checking these to see if they can be handled better to avoid worrying users.

[kjmeagher]

The deprication warnings were from code in boost python. The only way to get rid of them is adding -Wno-deprecated which I did. The install warnings were coming from symlinks wich were unnescessary so I removed them. The readme and meson_options were updated to be more clear that the data directory is where the raw flux tables are stored and a issue was submitted to cmvfs about adding the needed envvars.