Meson

.github/workflows/python-package.yml

@@ -3,11 +3,11 @@
 
 name: Unit Test COSMIC
 
-on: [pull_request, push]
+on: [pull_request]
 
 jobs:
   build:
-
+  
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
@@ -30,23 +30,25 @@ jobs:
         restore-keys: |
           ${{ runner.os }}-pip-
           ${{ runner.os }}-
-    - name: Install dependencies
+    - name: Install dependencies and package
       run: |
         sudo apt-get update
-        sudo apt-get install gfortran swig libhdf5-serial-dev
-        pip install numpy
+        sudo apt-get install gfortran swig libhdf5-serial-dev meson python3-dev
+        pip install numpy ninja pytest
         pip install -r requirements.txt
-        pip install .
+        python -m pip install .
+
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics --exclude docs
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics --exclude docs,versioneer.py,cosmic/_version.py,cosmic/tests,cosmic/*/__init__.py
+
     - name: Test with pytest
       run: |
         bash ci/compile_benchmark.sh
-        export PYTHONPATH=$(meson introspect --install-dir)
-        pytest --cov=./cosmic --cov-report=xml
+        pytest --cov=./src/cosmic --cov-report=xml
+
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v1

ci/compile_benchmark.sh

@@ -1,2 +1,2 @@
-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,${CONDA_PREFIX}/lib
+gfortran -coverage -fprofile-arcs -ftest-coverage -O0 src/cosmic/src/assign_remnant.f src/cosmic/src/benchmarkevolv2.f src/cosmic/src/comenv.f src/cosmic/src/corerd.f src/cosmic/src/deltat.f src/cosmic/src/dgcore.f src/cosmic/src/evolv2.f src/cosmic/src/gntage.f src/cosmic/src/hrdiag.f src/cosmic/src/hrdiag_remnant.f src/cosmic/src/instar.f src/cosmic/src/kick.f src/cosmic/src/mix.f src/cosmic/src/mlwind.f src/cosmic/src/mrenv.f src/cosmic/src/ran3.f src/cosmic/src/rl.f src/cosmic/src/star.f src/cosmic/src/zcnsts.f src/cosmic/src/zfuncs.f src/cosmic/src/concatkstars.f src/cosmic/src/bpp_array.f src/cosmic/src/checkstate.f  -o benchmarkevolv2.exe -I src/cosmic/src -Wl,-rpath,${CONDA_PREFIX}/lib
 ./benchmarkevolv2.exe

docs/Makefile

@@ -225,6 +225,6 @@ pseudoxml:
 
 .PHONY: apidoc
 apidoc:
-	sphinx-apidoc -o api/ ../cosmic ../cosmic/tests --no-toc --separate --no-headings --force
+	sphinx-apidoc -o api/ ../src/cosmic ../src/cosmic/tests --no-toc --separate --no-headings --force
 	@echo
 	@echo "APIdoc run is complete."

docs/install/index.rst

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

meson.build

@@ -0,0 +1,89 @@
+project('cosmic', 
+    'c',
+    'fortran',
+    version : '3.4.10',
+    default_options: ['warning_level=0', 'optimization=3'],
+)
+
+# Enable fortran and check arguments
+# add_languages('fortran', native: false)
+ff = meson.get_compiler('fortran')
+f_args = ff.get_supported_arguments('-fPIC')
+add_project_arguments(f_args, language: 'fortran')
+
+py3 = import('python').find_installation()
+
+numpy_include_dir = run_command(py3, ['-c', 'import numpy; print(numpy.get_include())'], check: true).stdout().strip()
+f2py_include_dir = run_command(py3, ['-c', 'import numpy.f2py; print(numpy.f2py.get_include())'], check: true).stdout().strip()
+inc_np = include_directories(numpy_include_dir, f2py_include_dir)
+
+f2py_source = custom_target(
+    'evolvebin-target',
+    input : ['src/cosmic/src/evolv2.f', 'src/cosmic/src/comprad.f'],
+    output : ['_evolvebinmodule.c', '_evolvebin-f2pywrappers.f'],
+    command : [py3, '-m', 'numpy.f2py', '@INPUT@', '-m', '_evolvebin', '--lower', '@OUTDIR']
+)
+
+lib_source = [
+    'src/cosmic/src/hrdiag_remnant.f',
+    'src/cosmic/src/assign_remnant.f',
+    'src/cosmic/src/benchmarkevolv2.f',
+    'src/cosmic/src/corerd.f',
+    'src/cosmic/src/comenv.f',
+    'src/cosmic/src/dgcore.f',
+    'src/cosmic/src/evolv2.f',
+    'src/cosmic/src/gntage.f',
+    'src/cosmic/src/instar.f',
+    'src/cosmic/src/kick.f',
+    'src/cosmic/src/mix.f',
+    'src/cosmic/src/mrenv.f',
+    'src/cosmic/src/ran3.f',
+    'src/cosmic/src/rl.f',
+    'src/cosmic/src/concatkstars.f',
+    'src/cosmic/src/comprad.f',
+    'src/cosmic/src/bpp_array.f',
+    'src/cosmic/src/checkstate.f',
+    'src/cosmic/src/deltat.f',
+    'src/cosmic/src/mlwind.f',
+    'src/cosmic/src/hrdiag.f',
+    'src/cosmic/src/star.f',
+    'src/cosmic/src/zcnsts.f',
+    'src/cosmic/src/deltat.f',
+    'src/cosmic/src/mlwind.f',
+    'src/cosmic/src/hrdiag.f',
+    'src/cosmic/src/star.f',
+    'src/cosmic/src/zcnsts.f',
+    'src/cosmic/src/zfuncs.f',]
+
+# Detect operating system and set appropriate linker flags
+host_system = host_machine.system()
+
+if host_system == 'darwin'
+  ldflags = ['-Wl,-no_compact_unwind']
+else
+  ldflags = []  # No special flags for other systems
+endif
+
+evolvebin_module = py3.extension_module('_evolvebin',
+  f2py_source,
+  lib_source,
+  f2py_include_dir / 'fortranobject.c',
+  include_directories: inc_np,
+  link_args: ldflags,
+  install : true,
+  install_dir : py3.get_install_dir() / 'cosmic'
+)
+
+
+module_dirs = ['src/cosmic', 'src/cosmic/bse_utils', 
+               'src/cosmic/sample', 'src/cosmic/tests']
+
+# Install modules
+foreach mod_dir: module_dirs
+    install_subdir(mod_dir,
+                  install_dir: py3.get_install_dir())
+endforeach
+
+
+python_script = 'bin/cosmic-pop'
+install_data(python_script, install_dir: get_option('bindir'))

pyproject.toml

@@ -0,0 +1,45 @@
+[project]
+name = "cosmic"
+distname = "cosmic-popsynth"
+description = "a Python-interfaced binary population synthesis suite"
+authors = [
+    { name="Katelyn Breivik", email="katie.breivik@gmail.com" },
+    { name="Scott Coughlin" },
+    { name="Michael Zevin" },
+    { name="Carl L. Rodriguez" },
+]
+readme = "README.md"
+
+
+requires-python = ">=3.7"
+license = { text = "MIT License" }
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Programming Language :: Python",
+]
+dynamic = ["version"]
+dependencies = ["numpy", "scipy", "astropy", "configparser", 
+                "tqdm", "pandas", "tables", "h5py", "schwimmbad", 
+                "matplotlib", "importlib-metadata"]
+
+
+[project.optional-dependencies]
+test = ["pytest", "pytest-xdist", "pytest-cov", "flake8", "coverage"]
+docs = ["sphinx", "numpydoc", "sphinx-bootstrap-theme", 
+        "sphinxcontrib-programoutput", "sphinx-automodapi",
+        "ipython", "sphinx_rtd_theme", "pickleshare"]
+
+
+
+[build-system]
+requires = ["meson", "meson-python", "wheel", "numpy", "setuptools"]
+build-backend = 'mesonpy'
+
+
+# pyproject.toml
+[tool.setuptools]
+write_to = "src/cosmic/_version.py"