fix meson options (#18)

* fix meson options

fixes  #17
also add pyproject.toml so that numpy can be a build dependency
also add run_commnad check=True to squash warnings
fix GitHub actions

.github/workflows/tests.yml

@@ -1,80 +1,78 @@
 name: Tests
-on: [push, pull_request] 
+on:
+  push:
+    branches: 
+      - main
+  pull_request: 
 jobs:
   Tests:
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest]
-        build: ["meson", "setuptools"]
+        build: [meson, setuptools]
+        include:
+          - os: ubuntu-latest
+            python-version: "3.10"
+          - os: macos-latest
+            python-version: "3.11"
     steps:
+      - name: Checkout nuflux
+        uses: actions/checkout@v2
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
       - name: Apt-Get Install Dependencies
-        if: ${{ matrix.os == 'ubuntu-latest' }}
+        if: matrix.os == 'ubuntu-latest'
         run: |
           sudo apt-get update
-          sudo apt-get install ninja-build gcovr libcfitsio-dev python-is-python3 libboost-python-dev python3-numpy doxygen
-          sudo python3 -m pip install meson sphinx breathe sphinx_rtd_theme
+          sudo apt-get install ninja-build gcovr libcfitsio-dev python-is-python3 libboost-python-dev doxygen
+          python3 -m pip install sphinx breathe sphinx_rtd_theme meson numpy
+          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
+          sudo make install -C photospline
       - name: HomeBrew Install Dependencies
-        if: ${{ matrix.os == 'macos-latest' }}
-        run: |
-          brew install boost-python3 numpy ninja doxygen cfitsio gcovr
-          sudo python3 -m pip install meson sphinx breathe sphinx_rtd_theme
-      - name: Checkout Photospline
-        uses: actions/checkout@v2
-        with:
-          repository: icecube/photospline
-          ref: v2.0.7
-          path: photospline
-      - name: Build Photospline
+        if: matrix.os == 'macos-latest'
         run: |
-          cmake .
-          make
-          sudo make install
-        working-directory: photospline
-      - name: Checkout nuflux
-        uses: actions/checkout@v2
+          brew tap icecube/icecube
+          brew install boost-python3 ninja doxygen cfitsio gcovr icecube/icecube/photospline
+          python3 -m pip install sphinx breathe sphinx_rtd_theme meson numpy
       - name: Build nuflux with Meson
-        if: ${{ matrix.build == 'meson' }}
+        if: matrix.build == 'meson'
         run: |
-          mkdir build
-          meson build . -D b_coverage=true
+          meson setup build . -D b_coverage=true --libdir=lib
           ninja -C build
           sudo ninja -C build install
       - name: Build nuflux with setuptools
-        if: ${{ matrix.build == 'setuptools' }}
-        run: sudo python3 -m pip install .
+        if: matrix.build == 'setuptools'
+        run: python3 -m pip install --user .
       - name: Run Python Tests
         working-directory: tests        
         env:
-          LD_LIBRARY_PATH: /usr/local/lib/:/usr/local/lib/x86_64-linux-gnu
-          PYTHONPATH: /usr/local/lib/python3/dist-packages
+          LD_LIBRARY_PATH: /usr/local/lib/
+          PYTHONPATH: /usr/local/lib/python${{matrix.python-version}}/site-packages
         run: |
           ./test_fluxes.py
           python3 -m doctest -v ../README.md
       - name: Generate Coverage Report
-        if: ${{ matrix.build == 'meson' && matrix.os == 'ubuntu-latest' }}
+        if: matrix.build == 'meson' && startsWith( matrix.os, 'ubuntu') 
         run: ninja -C build coverage
       - name: Upload Coverage to Codecov
-        if: ${{ matrix.build == 'meson' && matrix.os == 'ubuntu-latest' }}
+        if: matrix.build == 'meson' && startsWith( matrix.os, 'ubuntu') 
         uses: codecov/codecov-action@v1
         with:
           fail_ci_if_error: false
           verbose: true
       - name: Build Documentation
-        if: ${{ matrix.build == 'meson' }}
-        run: ninja -C build docs/html
+        if: matrix.build == 'meson'
         env:
-          LD_LIBRARY_PATH: /usr/local/lib/:/usr/local/lib/x86_64-linux-gnu
-          PYTHONPATH: /usr/local/lib/python3/dist-packages
+          LD_LIBRARY_PATH: /usr/local/lib/
+          PYTHONPATH: /usr/local/lib/python${{matrix.python-version}}/site-packages
+        run: ninja -C build docs/html
       - name: Upload Documentation
-        if: ${{ matrix.build == 'meson' &&  matrix.os == 'ubuntu-latest' }}
+        if: matrix.build == 'meson' &&  matrix.os == 'ubuntu-latest' && github.ref == 'refs/heads/master'
         run: docs/docs-upload.sh
         env:
-          ICECUBE_PASSWORD: ${{ secrets.ICECUBE_PASSWORD }}
-      - name: Check Documentation Links
-        if: ${{ matrix.build == 'meson' }}
-        run: sphinx-build -c build/docs/ docs/ . -b linkcheck
-        env:
-          LD_LIBRARY_PATH: /usr/local/lib/:/usr/local/lib/x86_64-linux-gnu
-          PYTHONPATH: /usr/local/lib/python3/dist-packages
+          ICECUBE_PASSWORD: ${{ secrets.ICECUBE_PASSWORD }}

docs/cppapi.rst

@@ -1,4 +1,4 @@
 C++ API Reference
 =================
 
-.. doxygenindex::
+.. .. doxygenindex::

docs/development.rst

@@ -42,7 +42,7 @@ In Python::
 Creating new fluxes
 -------------------
 
-| Since the main purpose of nuflux is to provide atmospheric fluxes to analysers in an easy and simple-to-use manner, the introduction of new models and fluxes is the major part of developing it. This section is about creating new fluxes by means of `MCEq <https://github.com/afedynitch/MCEq>`_ and `photospline <https://github.com/icecube/photospline>`_, with the example of a specific combination of models.
+| Since the main purpose of nuflux is to provide atmospheric fluxes to analysers in an easy and simple-to-use manner, the introduction of new models and fluxes is the major part of developing it. This section is about creating new fluxes by means of `MCEq <https://github.com/mceq-project/MCEq>`_ and `photospline <https://github.com/icecube/photospline>`_, with the example of a specific combination of models.
 | Note that not all fluxes are created this way. This is just to give you an idea of how it might work. If you already have ready-to-go flux tables or splines and are curious on how to integrate them into the project, see :ref:`Storing new fluxes<Storing_new_fluxes>` instead.
 
 1) **Choose your weapon**: To make a new flux, there are three ingredients you need to get started: A primary cosmic ray (CR) model, a hadronic interaction (HI) model, and the type of particle (i.e. atmospheric lepton) you want to make the flux for. In this example, we choose ``HillasGaisser2012 (H3a)``, ``SIBYLL23C``, and ``NuMu``.
@@ -62,7 +62,7 @@ Creating new fluxes
     energy = mceq.e_grid
 
   | And obtain an array ``solutions``; one value for each value in the ``energy`` array. And that's basically it! We can now repeat this for several zenith angles, to have a 2D solution array (one dimension being energy, the other being zenith angle).
-  | **Remark:** MCEq can do a lot more than what is currently part of these instructions. For more information and options, please visit `https://github.com/afedynitch/MCEq <https://github.com/afedynitch/MCEq>`_.
+  | **Remark:** MCEq can do a lot more than what is currently part of these instructions. For more information and options, please visit `MCEq's GitHub <https://github.com/mceq-project/MCEq>`_.
 
 3) **Interpolate the solutions with photospline**: The photospline software is using B-splining as interpolation method. It can turn our 2D solution array into a spline surface that can be evaluated at any desired point on the surface. The splining process is pretty neat but may require some practice. The spline surface is stored in a FITS file, that, if correctly formatted, can be integrated into nuflux.
 

docs/fluxes.rst

@@ -64,7 +64,7 @@ Variants: ``CORSIKA_GaisserH3a_QGSJET-II``, ``CORSIKA_GaisserH3a_SIBYLL-2.1``, `
 
 This flux is the atmospheric neutrino flux (ANFlux) from direct CORSIKA calculation. A large Monte Carlo set of a modified verison of CORSIKA (v. 7.4003), to allow for the shower output to be serialized into ROOT files, was run for different hadronic interaction models. The neutrino flux at various directions was histogramed and then weighted to the Gaisser H3a cosmic-ray flux. Then these histogram were splined using photospline.
 
-Schöneberg, Sebastian, The spectrum of atmospheric neutrinos above GeV energies, `PhD Thesis, Ruhr Universität Bochum, 2016 <https://nbn-resolving.org/urn:nbn:de:hbz:294-52689>`_.
+Schöneberg, Sebastian, The spectrum of atmospheric neutrinos above GeV energies, `PhD Thesis, Ruhr Universität Bochum, 2016 <https://hss-opus.ub.ruhr-uni-bochum.de/opus4/frontdoor/index/index/docId/5268>`_.
 
 
 IPhonda2006_sno_solmin, IPhonda2014_spl_solmin, IPhonda2014_spl_solmax, IPhonda2014_sk_solmin, IPhonda2014_sk_solmax
@@ -79,7 +79,7 @@ Despite being continuous across energy, azimuth angle, and zenith angle, the flu
 
 The tables presented here are based on Honda 2006 location at SNO during the solar minimum/ Honda 2014 location at South Pole and Kamioka during the solar minimum and maximum.
 
-Wren, Steven, "Neutrino Mass Ordering Studies with IceCube-DeepCore", `PhD Thesis, University of Manchester, 2018. <https://www.research.manchester.ac.uk/portal/en/theses/neutrino-mass-ordering-studies-with-icecubedeepcore(70414fde-3bef-4028-877b-5e1e86b2165d).html>`_.
+Wren, Steven, "Neutrino Mass Ordering Studies with IceCube-DeepCore", `PhD Thesis, University of Manchester, 2018. <https://research.manchester.ac.uk/en/studentTheses/neutrino-mass-ordering-studies-with-icecube-deepcore>`_.
 
 
 bartol
@@ -98,7 +98,7 @@ honda2006
 
 Alternative Knee Models: ``gaisserH3a_elbert``, ``gaisserH4a_elbert``, ``gst13_elbert``, ``gst13star_elbert``, ``polygonato_mod_elbert``
 
-Original tables from `Honda's web page <https://www.icrr.u-tokyo.ac.jp/~mhonda/>`_.
+Original tables from Honda's web page (Dead link: ``https://www.icrr.u-tokyo.ac.jp/~mhonda/``).
 
 Honda *et al.*, Phys. Rev. D **75**, 043006 (2007).
 `astro-ph/0611418 <https://arxiv.org/abs/astro-ph/0611418>`_.

docs/meson.build

@@ -3,7 +3,7 @@ sphinx_build = find_program('sphinx-build',required:false)
 
 if sphinx_build.found() and doxygen.found()
 
-  version = run_command('git', 'describe', '--tags').stdout().strip()
+  version = run_command('git', 'describe', '--tags', '--always', check:true).stdout().strip()
   docs_config = {
     'CPP_SOURCE_DIR' : meson.project_source_root() + '/src',
     'DOCS_SOURCE_DIR' : meson.current_source_dir(),

meson.build

@@ -63,7 +63,10 @@ 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"))')
+  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())
@@ -78,12 +81,10 @@ else
   if not boost.found()
     warning( 'Can\'t find boost python, Skipping python build')
   else
-    py_install_dir = python.get_install_dir() / 'nuflux'
-    message( 'Building package for python version ' +
-             python.language_version() + ': ' + py_install_dir)
-
+    message('Building package for python version ' +
+            python.language_version() + ': ' + python.get_install_dir())
     python.install_sources('nuflux/__init__.py',
-                           subdir: py_install_dir,
+                           subdir: 'nuflux',
                            )
 
     python.extension_module(
@@ -92,7 +93,6 @@ else
       include_directories : [inc,pybind_inc],
       dependencies : [photospline,pydep, boost],
       link_with : libnuflux,
-      install_dir : py_install_dir,
       install:true)
 
     test('test_fluxes',find_program('tests/test_fluxes.py'))

meson_options.txt

@@ -1,3 +1,3 @@
 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('install_data', type: 'boolean', value : 'true', description: 'can be set to false if installing on a readonly filesystem')

nuflux/__init__.py

@@ -3,7 +3,7 @@
            'PionKaonAdjustable', 'SplineFlux', 'SplineFlux2', 'availableFluxes',
            'kneesForFlux', 'makeFlux', 'printModels', 'stand_alone']
 
-from ._nuflux import FluxFunction, KneeReweightable, LegacyConventionalFlux, LegacyPromptFlux
-from ._nuflux import NuE, NuEBar, NuMu, NuMuBar, NuTau, NuTauBar, ParticleType
-from ._nuflux import PionKaonAdjustable, SplineFlux, SplineFlux2, availableFluxes, kneesForFlux
-from ._nuflux import makeFlux, printModels, stand_alone
+from _nuflux import FluxFunction, KneeReweightable, LegacyConventionalFlux, LegacyPromptFlux
+from _nuflux import NuE, NuEBar, NuMu, NuMuBar, NuTau, NuTauBar, ParticleType
+from _nuflux import PionKaonAdjustable, SplineFlux, SplineFlux2, availableFluxes, kneesForFlux
+from _nuflux import makeFlux, printModels, stand_alone

pyproject.toml

@@ -0,0 +1,29 @@
+[build-system]
+requires = ["setuptools", "oldest-supported-numpy"]
+build_backend = "setuptools.build_meta"
+
+[project]
+name = "nuflux"
+version = "2.0.3"
+description = "A library for calculating atmospheric neutrino fluxes"
+readme = "README.md"
+#requires_python = "~=3.8"
+dependencies = ['numpy']
+license = {file = "LICENCE"}
+keywords = ["python", "science", "astronomy", "astrophysics", "IceCube", "atmospheric", "neutrino"]
+classifiers = [
+    'Development Status :: 4 - Beta',
+    'Intended Audience :: Developers',
+    'Intended Audience :: Science/Research',
+    'License :: OSI Approved :: GNU Lesser General Public License v3 or later (LGPLv3+)',
+    'Operating System :: MacOS :: MacOS X',
+    'Operating System :: POSIX :: Linux',
+    'Programming Language :: C++',
+    'Programming Language :: Python',
+    'Programming Language :: Python :: 3.8',
+    'Programming Language :: Python :: 3.9',
+    'Programming Language :: Python :: 3.10',
+    'Programming Language :: Python :: 3.11',
+    'Topic :: Scientific/Engineering :: Astronomy',
+    'Topic :: Scientific/Engineering :: Physics',
+    ]

scripts/create_fluxes/create_fluxes.py

@@ -97,7 +97,7 @@ def Solve_mceqs():
     ### This function solves matrix cascade equations using MCEq. Please
     ### note that MCEq can do a lot more than what is currently used
     ### in this script. For more information and options, visit:
-    ### https://github.com/afedynitch/MCEq
+    ### https://github.com/mceq-project/MCEq
 
     import crflux.models as crf
     from MCEq.core import config, MCEqRun

setup.py

@@ -7,7 +7,7 @@
 prefix = os.environ.get('PREFIX', '/usr/local')
 
 extension = Extension(
-    'nuflux._nuflux', [
+    '_nuflux', [
      'src/library/logging.cpp',
      'src/library/SplineFlux.cpp',
      'src/library/SplineFlux2.cpp',
@@ -26,25 +26,7 @@
     )
 
 setup(
-    name = "nuflux",
-    version = "2.0.3",
-    packages = find_packages(),
+    packages = ['nuflux'],
     ext_modules = [extension],
     package_data = {"nuflux":["data/*/*.fits",'data/*/*.dat']},
-    test_suite = "tests.test_fluxes",
-    zip_safe = False,
-    keywords = [
-        'neutrino', 'cosmic rays', 'atmospheric neutrinos',
-    ],
-    classifiers = [
-        'Development Status :: 3 - Alpha',
-        'Intended Audience :: Developers',
-        'Intended Audience :: Science/Research',
-        'Operating System :: MacOS :: MacOS X',
-        'Operating System :: POSIX :: Linux',
-        'Programming Language :: C++',
-        'Programming Language :: Python',
-        'Topic :: Scientific/Engineering :: Astronomy',
-        'Topic :: Scientific/Engineering :: Physics',
-    ],
 )