Modernize infrastructure

.github/workflows/main.yml

@@ -17,38 +17,34 @@ jobs:
       matrix:
         include:
           - name: Python 3.6
-            os: ubuntu-latest
+            os: ubuntu-20.04
             python: '3.6'
           - name: Python 3.7
-            os: ubuntu-latest
+            os: ubuntu-20.04
             python: '3.7'
           - name: Python 3.8
-            os: ubuntu-latest
+            os: ubuntu-20.04
             python: '3.8'
           - name: Python 3.9
-            os: ubuntu-latest
+            os: ubuntu-20.04
             python: '3.9'
           - name: Python 3.10
-            os: ubuntu-latest
+            os: ubuntu-20.04
             python: '3.10'
     steps:
     - name: Checkout code
       uses: actions/checkout@v2
       with:
         submodules: 'true'
+        fetch-depth: 0
     - name: Set up Python
       uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python }}
     - name: Install HDF5 and MPI
       if: startsWith(matrix.os, 'ubuntu')
       run: sudo apt-get install libhdf5-serial-dev libmpich-dev
-    - name: Install Hyperion Fortran executables
-      run: |
-        ./configure
-        make serial
-        sudo make install
-    - name: Install Hyperion Python package
-      run: pip install -e .[test]
+    - name: Install tox
+      run: pip install tox
     - name: Run tests
-      run: pytest hyperion
+      run: tox -e test-bitlevel

hyperion/__init__.py

@@ -2,22 +2,6 @@
 
 from .version import __version__
 
-try:
-    _HYPERION_SETUP_
-except NameError:  # we are not currently running setup.py
-    try:
-        from .util import integrate
-    except ImportError:  # indicates the C extension failed to build
-        import os
-        import sys
-        if os.path.exists('setup.py'):
-            print("\nYou appear to be importing Hyperion from the source code "
-                  "directory. Try changing to a different directory and try "
-                  "importing Hyperion again.\n")
-            sys.exit(0)
-        else:
-            raise
-
 # Set up the test function
 _test_runner = None
 

hyperion/conftest.py

@@ -1,23 +1,7 @@
 import warnings
 
-import pytest
-
 from .util.nans import NaNWarning
 
 
-def pytest_addoption(parser):
-    parser.addoption('--generate-reference', help="generate reference results for bit-level tests", type="string")
-    parser.addoption('--enable-bit-level-tests', help="enable bit-level tests", action="store_true")
-
-
 def pytest_configure(config):
     warnings.simplefilter('error', NaNWarning)
-
-
-def pytest_collection_modifyitems(config, items):
-    if config.getoption("--enable-bit-level-tests"):
-        return
-    skip_bit_level = pytest.mark.skip(reason="need --enable-bit-level-tests option to run")
-    for item in items:
-        if "bitlevel" in item.keywords:
-            item.add_marker(skip_bit_level)

hyperion/testing/pytest_plugin.py

@@ -0,0 +1,15 @@
+import pytest
+
+
+def pytest_addoption(parser):
+    parser.addoption('--generate-reference', help="generate reference results for bit-level tests", type="string")
+    parser.addoption('--enable-bit-level-tests', help="enable bit-level tests", action="store_true")
+
+
+def pytest_collection_modifyitems(config, items):
+    if config.getoption("--enable-bit-level-tests"):
+        return
+    skip_bit_level = pytest.mark.skip(reason="need --enable-bit-level-tests option to run")
+    for item in items:
+        if "bitlevel" in item.keywords:
+            item.add_marker(skip_bit_level)

hyperion/version.py

@@ -1,2 +1,2 @@
-__version__ = '1.0.0'
-__dev__ = True
+from hyperion._version import version as __version__
+__dev__ = 'dev' in __version__

pyproject.toml

@@ -0,0 +1,9 @@
+[build-system]
+requires = ["setuptools",
+            "setuptools_scm>=6.2",
+            "wheel",
+            "oldest-supported-numpy"]
+build-backend = 'setuptools.build_meta'
+
+[tool.setuptools_scm]
+write_to = "hyperion/_version.py"

setup.cfg

@@ -9,8 +9,6 @@ description = Monte-Carlo Radiative Transfer Code
 [options]
 zip_safe = True
 packages = find:
-include_package_data = True
-setup_requires = oldest-supported-numpy
 install_requires =
     numpy>=1.11
     matplotlib>=1.5
@@ -31,3 +29,7 @@ hyperion.model.tests = data/*.rtout, data/*.hdf5
 hyperion.importers.tests = data/*.hdf5
 hyperion.grid.tests = data/*.hdf5, data/DD0010/*
 hyperion.testing = coveragerc
+
+[options.entry_points]
+pytest11 =
+    hyperion = hyperion.testing.pytest_plugin

setup.py

@@ -1,87 +1,36 @@
 #!/usr/bin/env python
 
-import sys
-
-if sys.version_info[0] >= 3:
-    import builtins
-else:
-    import __builtin__ as builtins
-builtins._HYPERION_SETUP_ = True
-
-from setuptools import setup, Extension, find_packages
-from distutils.command.sdist import sdist
-from distutils.command.build_py import build_py
-from distutils.command.build_ext import build_ext
-
-from hyperion.testing.helper import HyperionTest
-from hyperion.version import __version__
-
-
-class custom_sdist(sdist):
-
-    user_options = sdist.user_options + [('unstable', None, "make an unstable release (keep __dev__=True)")]
-
-    def __init__(self, *args, **kwargs):
-        sdist.__init__(self, *args, **kwargs)
-        self.unstable = False
-
-    def run(self):
-        if not self.unstable:
-            version_file = 'hyperion/version.py'
-            content = open(version_file, 'r').read()
-            open(version_file, 'w').write(content.replace('__dev__ = True', "__dev__ = False"))
-        try:
-            sdist.run(self)
-        finally:
-            if not self.unstable:
-                open(version_file, 'w').write(content)
-
-
-class NumpyBuildExt(build_ext):
-    def run(self):
-        import numpy
-        self.include_dirs.append(numpy.get_include())
-        build_ext.run(self)
-
-
-cmdclass = {}
-cmdclass['build_py'] = build_py
-cmdclass['test'] = HyperionTest
-cmdclass['sdist'] = custom_sdist
-cmdclass['build_ext'] = NumpyBuildExt
-
-if 'egg_info' in sys.argv:
-
-    ext_modules = []
-
-else:
-
-    ext_modules = [Extension("hyperion.util._integrate_core",
-                             ['hyperion/util/_integrate_core.c'],
-                             extra_compile_args=['-Wno-error=declaration-after-statement']),
-                   Extension("hyperion.util._interpolate_core",
-                             ['hyperion/util/_interpolate_core.c'],
-                             extra_compile_args=['-Wno-error=declaration-after-statement']),
-                   Extension("hyperion.importers._discretize_sph",
-                             ['hyperion/importers/_discretize_sph.c'],
-                             extra_compile_args=['-Wno-error=declaration-after-statement']),
-                   Extension("hyperion.grid._voronoi_core",
-                             ['hyperion/grid/_voronoi_core.c',
-                              'hyperion/grid/voropp_wrap.cc',
-                              'hyperion/grid/voro++/c_loops.cc',
-                              'hyperion/grid/voro++/cell.cc',
-                              'hyperion/grid/voro++/common.cc',
-                              'hyperion/grid/voro++/container.cc',
-                              'hyperion/grid/voro++/container_prd.cc',
-                              'hyperion/grid/voro++/pre_container.cc',
-                              'hyperion/grid/voro++/unitcell.cc',
-                              'hyperion/grid/voro++/v_base.cc',
-                              'hyperion/grid/voro++/v_compute.cc',
-                              'hyperion/grid/voro++/wall.cc'],
-                             extra_compile_args = ['-O2', '-Wno-error=declaration-after-statement'],
-                             extra_link_args=['-lstdc++'])]
-
-setup(version=__version__,
-      scripts=['scripts/hyperion', 'scripts/hyperion2fits'],
-      cmdclass=cmdclass,
+import numpy
+from setuptools import setup, Extension
+
+ext_modules = [Extension("hyperion.util._integrate_core",
+                         ['hyperion/util/_integrate_core.c'],
+                         include_dirs=[numpy.get_include()],
+                         extra_compile_args=['-Wno-error=declaration-after-statement']),
+               Extension("hyperion.util._interpolate_core",
+                         ['hyperion/util/_interpolate_core.c'],
+                         include_dirs=[numpy.get_include()],
+                         extra_compile_args=['-Wno-error=declaration-after-statement']),
+               Extension("hyperion.importers._discretize_sph",
+                         ['hyperion/importers/_discretize_sph.c'],
+                         include_dirs=[numpy.get_include()],
+                         extra_compile_args=['-Wno-error=declaration-after-statement']),
+               Extension("hyperion.grid._voronoi_core",
+                         ['hyperion/grid/_voronoi_core.c',
+                          'hyperion/grid/voropp_wrap.cc',
+                          'hyperion/grid/voro++/c_loops.cc',
+                          'hyperion/grid/voro++/cell.cc',
+                          'hyperion/grid/voro++/common.cc',
+                          'hyperion/grid/voro++/container.cc',
+                          'hyperion/grid/voro++/container_prd.cc',
+                          'hyperion/grid/voro++/pre_container.cc',
+                          'hyperion/grid/voro++/unitcell.cc',
+                          'hyperion/grid/voro++/v_base.cc',
+                          'hyperion/grid/voro++/v_compute.cc',
+                          'hyperion/grid/voro++/wall.cc'],
+                         include_dirs=[numpy.get_include()],
+                         extra_compile_args = ['-O2', '-Wno-error=declaration-after-statement'],
+                         extra_link_args=['-lstdc++'])]
+
+setup(scripts=['scripts/hyperion', 'scripts/hyperion2fits'],
       ext_modules=ext_modules)

tox.ini

@@ -0,0 +1,22 @@
+[tox]
+envlist =
+    py{36,37,38,39,310}-test{,-bitlevel}
+requires =
+    setuptools >= 30.3.0
+    pip >= 19.3.1
+isolated_build = true
+
+[testenv]
+changedir = .tmp/{envname}
+extras =
+    test: test
+allowlist_externals =
+    make
+commands =
+    pip freeze
+    {toxinidir}/configure --prefix={envdir}
+    mv Makefile {toxinidir}/
+    make -C {toxinidir} serial
+    make -C {toxinidir} install
+    !bitlevel: pytest --pyargs hyperion
+    bitlevel: pytest --pyargs hyperion --enable-bit-level-tests