Switch Python build system to use mesonpy instead of setuptools (#24)

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.

.github/workflows/tests.yml

@@ -12,12 +12,12 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest]
-        build: [meson, setuptools]
+        build: [meson, pyproject]
         include:
           - os: ubuntu-latest
             python-version: "3.10"
           - os: macos-latest
-            python-version: "3.11"
+            python-version: "3.12"
     steps:
       - name: Checkout nuflux
         uses: actions/checkout@v2
@@ -31,24 +31,24 @@ jobs:
           sudo apt-get update
           sudo apt-get install ninja-build gcovr libcfitsio-dev python-is-python3 libboost-python-dev doxygen
           sudo dpkg -r lcov
-          curl -L https://github.com/icecube/photospline/archive/refs/tags/v2.1.0.tar.gz | tar xz
-          cmake -S photospline-2.1.0 -B photospline -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr
+          curl -L https://github.com/icecube/photospline/archive/refs/tags/v2.2.1.tar.gz | tar xz
+          cmake -S photospline-2.2.1 -B photospline -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr
           sudo make install -C photospline
       - name: HomeBrew Install Dependencies
         if: startsWith( matrix.os, 'macos') 
         run: |
           brew tap icecube/icecube
           brew install boost-python3 ninja doxygen cfitsio gcovr icecube/icecube/photospline
-      - name: Build nuflux with setuptools
-        if: matrix.build == 'setuptools'
+      - name: Build nuflux with pyproject
+        if: matrix.build == 'pyproject'
         run: |
           python3 -m pip install .[test]
           python3 -m pytest
       - name: Build nuflux with Meson
         if: matrix.build == 'meson'
         run: |
           python3 -m pip install meson numpy sphinx breathe sphinx_rtd_theme pytest pytest-subtests
-          meson setup build . -D b_coverage=true
+          meson setup build . -D b_coverage=true --prefix=${HOME}/inst/
           ninja -C build test
       - name: Generate Coverage Report and Docs
         if: matrix.build == 'meson' && startsWith( matrix.os, 'ubuntu')
@@ -72,7 +72,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        cvmfs: [py3-v4.0.1, py3-v4.1.1, py3-v4.2.1, py3-v4.3.0]
+        cvmfs: [py3-v4.1.1, py3-v4.2.1, py3-v4.3.0]
     steps:
       - uses: cvmfs-contrib/github-action-cvmfs@v3
       - name: Checkout nuflux
@@ -89,25 +89,25 @@ jobs:
             pip install --user meson ninja pytest pytest-subtests
             CMAKE_PREFIX_PATH=${SROOT} BOOST_ROOT=${SROOT} meson setup build /nuflux
             ninja -Cbuild test
-  cvmfs_setuptools_tests:
-    name: cvmfs setuptools tests ${{matrix.cvmfs}}
+  cvmfs_pyproject_tests:
+    name: cvmfs pyproject tests ${{matrix.cvmfs}}
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        cvmfs: [py3-v4.0.1, py3-v4.1.1, py3-v4.2.1, py3-v4.3.0]
+        cvmfs: [py3-v4.1.1, py3-v4.3.0]
     steps:
       - uses: cvmfs-contrib/github-action-cvmfs@v3
       - name: Checkout nuflux
         uses: actions/checkout@v2
       - name: Build and Run Tests in Docker
         uses: addnab/docker-run-action@v3
         with:
-          options: -v /cvmfs/icecube.opensciencegrid.org/:/cvmfs/icecube.opensciencegrid.org/ -v /home/runner/work/nuflux/nuflux:/nuflux
+          options: -v /cvmfs/icecube.opensciencegrid.org/:/cvmfs/icecube.opensciencegrid.org/ -v /home/runner/work/nuflux/nuflux:/nf
           image: centos:centos7.9.2009
           run: |
             yum -y install glibc-headers glibc-devel
             eval $(/cvmfs/icecube.opensciencegrid.org/${{matrix.cvmfs}}/setup.sh)
-            pip install --user wheel pytest pytest-subtests
-            PREFIX=${SROOT} pip install --user --no-build-isolation /nuflux
-            python3 -m pytest /nuflux
+            python3 -m pip install --user pip pytest pytest-subtests
+            BOOST_ROOT=${SROOT} python3 -m pip install --user --verbose /nf
+            python3 -m pytest /nf

README.md

@@ -30,14 +30,14 @@ If you only need to use python you can install it directly through pip:
 
     pip install --user git+https://github.com/icecube/nuflux
 
-Note that this may fail if photospline and boost_python are installed in nonstandard locations, e.g. headers in /opt/toolsets/mystuff/include, libraries in /opt/toolsets/mystuff/lib. In this case, set the `PREFIX` environment variable to the root of your toolset installation:
+Note that this may fail if photospline and boost_python are installed in nonstandard locations, e.g. headers in /opt/toolsets/photospline/include, libraries in /opt/toolsets/photospline/lib. In this case, set the `CMAKE_PREFIX_PATH` environment variable to the root of your photospline installation and `BOOST_ROOT` to the root of your boost installation:
 
-    PREFIX=/opt/toolsets/mystuff pip install --user git+https://github.com/icecube/nuflux
+    CMAKE_PREFIX_PATH=/opt/toolsets/photospline BOOST_ROOT=/opt/toolsets/boost pip install --user git+https://github.com/icecube/nuflux
 
-If you are running it in IceCube's cvmfs environment you will want to set `PREFIX` to the base of the cvmfs envionment which is stored in the envionment variable `SROOT`:
+If you are running it in IceCube's cvmfs environment you will want to set `CMAKE_PREFIX_PATH` and `BOOST_ROOT` to the base of the cvmfs envionment which is stored in the environment variable `SROOT`:
 
-    eval `/cvmfs/icecube.opensciencegrid.org/py3-v4.1.1/setup.sh`
-    PREFIX=${SROOT} pip install --user git+https://github.com/icecube/nuflux
+    eval `/cvmfs/icecube.opensciencegrid.org/py3-v4.3.0/setup.sh`
+    CMAKE_PREFIX_PATH=${SROOT} BOOST_ROOT=${SROOT} pip install --user git+https://github.com/icecube/nuflux
 
 #### Meson
 
@@ -55,11 +55,11 @@ For example, in IceCube's cvmfs envionment you should do:
 
      CMAKE_PREFIX_PATH=${SROOT} BOOST_ROOT=${SROOT} meson setup build . --prefix=/path/to/instal/to
 
-the option -Ddata_path can be used to install to a directory outside of the PREFIX directory.
+the option -Ddata_path can be used to install the raw flux tables to a directory outside of the PREFIX directory.
 
 If you want to install to a read-only file system you can pass -Dinstall_data=False
 
-You may also use the environment variable `NUFLUX_DATA` to specify the path of the nuflux data tables if they are in a
+You may also use the environment variable `NUFLUX_DATA` to specify the path of the raw flux tables if they are in a
 place other than where they were installed to.
 
 ## Documentation

docs/installation.rst

@@ -53,11 +53,11 @@ Here are some errors that have been encountered with Python and Meson installati
 
 * **photospline and boost are installed in non-standard locations**
 
-  The Python installation may fail if photospline and boost_python are installed in non-standard locations, e.g. headers in ``/opt/toolsets/mystuff/include``, libraries in ``/opt/toolsets/mystuff/lib``. In this case, set the `PREFIX` environment variable to the root of your toolset installation:
+  The Python installation may fail if photospline and boost_python are installed in non-standard locations, e.g. headers in ``/opt/toolsets/mystuff/include``, libraries in ``/opt/toolsets/mystuff/lib``. In this case, set the `CMAKE_PREFIX_PATH` and `BOOST_ROOT` environment variables to the root of your toolset installation:
 
   ::
 
-    PREFIX=/opt/toolsets/mystuff pip install --user git+https://github.com/icecube/nuflux
+    CMAKE_PREFIX_PATH=/opt/toolsets/photospline and `BOOST_ROOT`=/opt/toolsets/boost pip install --user git+https://github.com/icecube/nuflux
 
 
 * **Meson is out of date**

meson.build

@@ -1,102 +1,29 @@
 project('nuflux', 'cpp',
-        version : '2.0.4',
-        default_options : ['cpp_std=c++17'])
+        version: '2.0.4',
+        default_options: ['cpp_std=c++17'])
 
 cfitsio = dependency('cfitsio')
 photospline = dependency('photospline', method : 'cmake')
 
-datadir = get_option('data_path')
-if datadir == ''
-  datadir = get_option('prefix') / get_option('datadir') / meson.project_name()
-endif
 conf_data = configuration_data()
-conf_data.set_quoted('DATA_DIR',datadir)
-configure_file(output : 'config.h',
-               configuration : conf_data)
-if get_option('install_data')
-  install_subdir('nuflux/data/',
-                 install_dir:datadir,
-                 strip_directory:true)
+conf_data.set_quoted('NUFLUX_VERSION',meson.project_version())
+if not get_option('pymodule')
+  datadir = get_option('data_path')
+  if datadir == ''
+    datadir = get_option('prefix') / get_option('datadir') / meson.project_name()
+  endif
+  conf_data.set_quoted('DATA_DIR',datadir)
 endif
-
-subdir('src/include/nuflux')
+configure_file(
+  output: 'config.h',
+  configuration: conf_data)
+configuration_inc = include_directories('.')
 
 inc = include_directories('src/include')
-libnuflux = library(
-  'nuflux',
-  'src/library/ANFlux.cpp',
-  'src/library/IPLEFlux.cpp',
-  'src/library/LegacyConventionalFlux.cpp',
-  'src/library/SplineFlux.cpp',
-  'src/library/SplineFlux2.cpp',
-  'src/library/FluxFunction.cpp',
-  'src/library/LegacyPromptFlux.cpp',
-  'src/library/detail.cpp',
-  include_directories : inc,
-  dependencies : [photospline,cfitsio],
-  install : true)
-
+init_file = files('src/nuflux/__init__.py')
+subdir('src/include/nuflux')
+subdir('src/library')
+subdir('src/pybindings')
+subdir('src/nuflux/data')
 subdir('tests')
-
-pkg_mod = import('pkgconfig')
-pkg_mod.generate(
-  libraries : libnuflux,
-  version : meson.project_version(),
-  name : meson.project_name(),
-  filebase :  meson.project_name(),
-  url : 'https://github.com/IceCubeOpenSource/nuflux',
-  description : 'A library for calculating atmospheric neutrino fluxes')
-
-cppcomp = meson.get_compiler('cpp')
-pymod = import('python')
-python = pymod.find_installation(get_option('python'),required: false)
-
-if not python.found()
-  warning('Can\'t find python: "'+get_option('python')+'", skipping python build')
-else
-  pydep = python.dependency()
-
-  # Find numpy
-  numpy = run_command(python,'-c',
-    'import importlib.util,os;print(os.path.join(importlib.util.find_spec("numpy").submodule_search_locations[0],"core","include"))',
-    check: true,
-    )
-  if numpy.returncode()==0
-    pybind_inc = include_directories(numpy.stdout().strip())
-    message ('Numpy found: '+ numpy.stdout().strip())
-  else
-    warning ('Numpy not found: building without arrays')
-    pybind_inc = include_directories()
-  endif
-
-  python_name = 'python'+''.join(python.language_version().split('.'))
-  boost = dependency('boost'      , modules : [python_name])
-
-  if not boost.found()
-    warning( 'Can\'t find boost python, Skipping python build')
-  else
-    message('Building package for python version ' +
-            python.language_version() + ': ' + python.get_install_dir())
-    python.install_sources('nuflux/__init__.py',
-                           subdir: 'nuflux',
-                           )
-
-    python.extension_module(
-      '_nuflux',
-      ['src/pybindings/module.cxx'],
-      include_directories : [inc,pybind_inc],
-      dependencies : [photospline,pydep, boost],
-      link_with : libnuflux,
-      install:true)
-
-    pytest_env = environment(test_env)
-    pytest_env.append('PYTHONPATH',meson.current_source_dir())
-    pytest_env.append('PYTHONPATH',meson.current_build_dir())
-    test('test_fluxes',find_program('tests/test_fluxes.py'), env: pytest_env)
-    test('doctest',python,args: ['-m','doctest',files('README.md')],env: pytest_env)
-    meson.add_devenv(pytest_env)
-  endif
-
-endif
-
 subdir('docs')

meson_options.txt

@@ -1,3 +1,4 @@
-option('python', type : 'string', value : 'python3', description : 'python path to compile against')
-option('data_path', type: 'string', value : '', description: 'absolute path to where to install data files, will overrede --datadir Default will be PREFIX/share/nuflux')
-option('install_data', type: 'boolean', value : true, description: 'can be set to false if installing on a readonly filesystem')
+option('python', type : 'string', value: 'python3', description : 'python path to compile against')
+option('data_path', type: 'string', value: '', description: 'absolute path to where to install the raw flux tables, will override --datadir Default will be PREFIX/share/nuflux')
+option('install_data', type: 'boolean', value: true, description: 'can be set to false if installing on a readonly filesystem')
+option('pymodule', type: 'boolean', value: false, description: 'install as a python module, no shared library, and with the data files as part of the python module' )

pyproject.toml

@@ -1,10 +1,10 @@
 [build-system]
-requires = ["setuptools", "oldest-supported-numpy"]
-build-backend = "setuptools.build_meta"
+build-backend = 'mesonpy'
+requires = ['meson-python', 'oldest-supported-numpy']
 
 [project]
 name = "nuflux"
-version = "2.0.4"
+dynamic = ["version"]
 description = "A library for calculating atmospheric neutrino fluxes"
 readme = "README.md"
 requires-python = "~=3.7"
@@ -37,6 +37,9 @@ doi = "https://doi.org/10.5281/zenodo.8180337"
 [project.optional-dependencies]
 test = ["pytest","pytest-subtests"]
 
+[tool.meson-python.args]
+setup = ['-Dpymodule=true']
+
 [tool.pytest.ini_options]
 addopts = "--doctest-glob='README.md'"
 testpaths = ["tests", "README.md"]

src/include/nuflux/SplineFlux.h

@@ -8,7 +8,7 @@ namespace nuflux{
 
   class SimpleSplineFlux : public FluxFunction{
   private:
-    std::map<ParticleType,boost::shared_ptr<photospline::splinetable<>> > components;
+    boost::shared_ptr<photospline::splinetable<>> spline;
   public:
     SimpleSplineFlux(const std::string& fluxName);
     static boost::shared_ptr<FluxFunction> makeFlux(const std::string& fluxName);

src/include/nuflux/nuflux.h

@@ -22,6 +22,9 @@ namespace nuflux{
 
   ///Print an listing of all supported models
   void printModels();
+
+  ///Return the current nuflux version
+  std::string getVersion();
 
 } //namespace nuflux