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katiebreivikkatiebreivik
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Meson (#627)
- changes the repository structure to COSMIC/src/cosmic instead of COSMIC/cosmic - changes the build from numpy.distutils since we cannot compile modern fortran with distutils - updated the action yaml accordingly. For new installs we recommend: python -m pip install .
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‎.github/workflows/python-package.yml

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name: Unit Test COSMIC
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on: [pull_request, push]
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on: [pull_request]
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jobs:
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build:
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runs-on: ubuntu-latest
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strategy:
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fail-fast: false
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restore-keys: |
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${{ runner.os }}-pip-
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${{ runner.os }}-
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- name: Install dependencies
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- name: Install dependencies and package
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run: |
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sudo apt-get update
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sudo apt-get install gfortran swig libhdf5-serial-dev
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pip install numpy
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sudo apt-get install gfortran swig libhdf5-serial-dev meson python3-dev
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pip install numpy ninja pytest
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pip install -r requirements.txt
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pip install .
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python -m pip install .
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- name: Lint with flake8
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run: |
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# stop the build if there are Python syntax errors or undefined names
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flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics --exclude docs
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# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
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flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics --exclude docs,versioneer.py,cosmic/_version.py,cosmic/tests,cosmic/*/__init__.py
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- name: Test with pytest
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run: |
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bash ci/compile_benchmark.sh
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export PYTHONPATH=$(meson introspect --install-dir)
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pytest --cov=./cosmic --cov-report=xml
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pytest --cov=./src/cosmic --cov-report=xml
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- name: Upload coverage to Codecov
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uses: codecov/codecov-action@v1

‎ci/compile_benchmark.sh

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gfortran -coverage -fprofile-arcs -ftest-coverage -O0 ./cosmic/src/assign_remnant.f ./cosmic/src/benchmarkevolv2.f ./cosmic/src/comenv.f ./cosmic/src/corerd.f ./cosmic/src/deltat.f ./cosmic/src/dgcore.f ./cosmic/src/evolv2.f ./cosmic/src/gntage.f ./cosmic/src/hrdiag.f ./cosmic/src/hrdiag_remnant.f ./cosmic/src/instar.f ./cosmic/src/kick.f ./cosmic/src/mix.f ./cosmic/src/mlwind.f ./cosmic/src/mrenv.f ./cosmic/src/ran3.f ./cosmic/src/rl.f ./cosmic/src/star.f ./cosmic/src/zcnsts.f ./cosmic/src/zfuncs.f ./cosmic/src/concatkstars.f ./cosmic/src/bpp_array.f ./cosmic/src/checkstate.f -o benchmarkevolv2.exe -I cosmic/src -Wl,-rpath,${CONDA_PREFIX}/lib
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gfortran -coverage -fprofile-arcs -ftest-coverage -O0 src/cosmic/src/assign_remnant.f src/cosmic/src/benchmarkevolv2.f src/cosmic/src/comenv.f src/cosmic/src/corerd.f src/cosmic/src/deltat.f src/cosmic/src/dgcore.f src/cosmic/src/evolv2.f src/cosmic/src/gntage.f src/cosmic/src/hrdiag.f src/cosmic/src/hrdiag_remnant.f src/cosmic/src/instar.f src/cosmic/src/kick.f src/cosmic/src/mix.f src/cosmic/src/mlwind.f src/cosmic/src/mrenv.f src/cosmic/src/ran3.f src/cosmic/src/rl.f src/cosmic/src/star.f src/cosmic/src/zcnsts.f src/cosmic/src/zfuncs.f src/cosmic/src/concatkstars.f src/cosmic/src/bpp_array.f src/cosmic/src/checkstate.f -o benchmarkevolv2.exe -I src/cosmic/src -Wl,-rpath,${CONDA_PREFIX}/lib
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./benchmarkevolv2.exe

‎cosmic/tests/__init__.py

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‎docs/Makefile

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.PHONY: apidoc
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apidoc:
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sphinx-apidoc -o api/ ../cosmic ../cosmic/tests --no-toc --separate --no-headings --force
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sphinx-apidoc -o api/ ../src/cosmic ../src/cosmic/tests --no-toc --separate --no-headings --force
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@echo
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@echo "APIdoc run is complete."

‎docs/install/index.rst

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@@ -45,15 +45,3 @@ Installation Notes/FAQ
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``pip install jupyter ipython``
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.. note::
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USING COMSIC WHEN BUILT FROM SOURCE
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If you want import the fortran wrapped library
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from the GITHUB folder itself, i.e.
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``from cosmic import _evolvebin``
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then you must build the extension locally
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``python setup.py build_ext --inplace``

‎meson.build

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project('cosmic',
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'c',
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'fortran',
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version : '3.4.10',
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default_options: ['warning_level=0', 'optimization=3'],
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)
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# Enable fortran and check arguments
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# add_languages('fortran', native: false)
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ff = meson.get_compiler('fortran')
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f_args = ff.get_supported_arguments('-fPIC')
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add_project_arguments(f_args, language: 'fortran')
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py3 = import('python').find_installation()
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numpy_include_dir = run_command(py3, ['-c', 'import numpy; print(numpy.get_include())'], check: true).stdout().strip()
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f2py_include_dir = run_command(py3, ['-c', 'import numpy.f2py; print(numpy.f2py.get_include())'], check: true).stdout().strip()
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inc_np = include_directories(numpy_include_dir, f2py_include_dir)
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f2py_source = custom_target(
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'evolvebin-target',
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input : ['src/cosmic/src/evolv2.f', 'src/cosmic/src/comprad.f'],
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output : ['_evolvebinmodule.c', '_evolvebin-f2pywrappers.f'],
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command : [py3, '-m', 'numpy.f2py', '@INPUT@', '-m', '_evolvebin', '--lower', '@OUTDIR']
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)
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lib_source = [
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'src/cosmic/src/hrdiag_remnant.f',
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'src/cosmic/src/assign_remnant.f',
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'src/cosmic/src/benchmarkevolv2.f',
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'src/cosmic/src/corerd.f',
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'src/cosmic/src/comenv.f',
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'src/cosmic/src/dgcore.f',
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'src/cosmic/src/evolv2.f',
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'src/cosmic/src/gntage.f',
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'src/cosmic/src/instar.f',
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'src/cosmic/src/kick.f',
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'src/cosmic/src/mix.f',
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'src/cosmic/src/mrenv.f',
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'src/cosmic/src/ran3.f',
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'src/cosmic/src/rl.f',
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'src/cosmic/src/concatkstars.f',
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'src/cosmic/src/comprad.f',
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'src/cosmic/src/bpp_array.f',
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'src/cosmic/src/checkstate.f',
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'src/cosmic/src/deltat.f',
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'src/cosmic/src/mlwind.f',
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'src/cosmic/src/hrdiag.f',
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'src/cosmic/src/star.f',
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'src/cosmic/src/zcnsts.f',
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'src/cosmic/src/deltat.f',
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'src/cosmic/src/mlwind.f',
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'src/cosmic/src/hrdiag.f',
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'src/cosmic/src/star.f',
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'src/cosmic/src/zcnsts.f',
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'src/cosmic/src/zfuncs.f',]
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# Detect operating system and set appropriate linker flags
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host_system = host_machine.system()
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if host_system == 'darwin'
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ldflags = ['-Wl,-no_compact_unwind']
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else
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ldflags = [] # No special flags for other systems
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endif
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evolvebin_module = py3.extension_module('_evolvebin',
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f2py_source,
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lib_source,
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f2py_include_dir / 'fortranobject.c',
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include_directories: inc_np,
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link_args: ldflags,
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install : true,
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install_dir : py3.get_install_dir() / 'cosmic'
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)
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module_dirs = ['src/cosmic', 'src/cosmic/bse_utils',
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'src/cosmic/sample', 'src/cosmic/tests']
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# Install modules
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foreach mod_dir: module_dirs
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install_subdir(mod_dir,
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install_dir: py3.get_install_dir())
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endforeach
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python_script = 'bin/cosmic-pop'
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install_data(python_script, install_dir: get_option('bindir'))

‎pyproject.toml

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[project]
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name = "cosmic"
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distname = "cosmic-popsynth"
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description = "a Python-interfaced binary population synthesis suite"
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authors = [
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{ name="Katelyn Breivik", email="katie.breivik@gmail.com" },
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{ name="Scott Coughlin" },
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{ name="Michael Zevin" },
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{ name="Carl L. Rodriguez" },
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]
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readme = "README.md"
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requires-python = ">=3.7"
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license = { text = "MIT License" }
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classifiers = [
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"Development Status :: 5 - Production/Stable",
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"Intended Audience :: Developers",
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"Intended Audience :: Science/Research",
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"License :: OSI Approved :: MIT License",
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"Operating System :: OS Independent",
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"Programming Language :: Python",
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]
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dynamic = ["version"]
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dependencies = ["numpy", "scipy", "astropy", "configparser",
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"tqdm", "pandas", "tables", "h5py", "schwimmbad",
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"matplotlib", "importlib-metadata"]
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[project.optional-dependencies]
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test = ["pytest", "pytest-xdist", "pytest-cov", "flake8", "coverage"]
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docs = ["sphinx", "numpydoc", "sphinx-bootstrap-theme",
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"sphinxcontrib-programoutput", "sphinx-automodapi",
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"ipython", "sphinx_rtd_theme", "pickleshare"]
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[build-system]
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requires = ["meson", "meson-python", "wheel", "numpy", "setuptools"]
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build-backend = 'mesonpy'
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# pyproject.toml
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[tool.setuptools]
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write_to = "src/cosmic/_version.py"

‎setup.cfg

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