Use setup.cfg for setup metadata

.circleci/config.yml

@@ -21,6 +21,9 @@ jobs:
               HYPERION_HDF5_VERSION=18 ./configure
               make
               make install
+      - run:
+          name: Upgrade setuptools and pip
+          command: pip install setuptools pip --upgrade
       - run:
           name: Installing Numpy
           command: pip install numpy==1.11.3
@@ -29,10 +32,10 @@ jobs:
           command: pip install Cython==0.24.1
       - run:
           name: Installing Python package
-          command: pip install .[test] matplotlib==1.5.3 astropy==1.2.2 h5py==2.4.0 yt==3.2.3
+          command: pip install -e .[test] matplotlib==1.5.3 astropy==1.2.2 h5py==2.4.0 yt==3.2.3
       - run:
           name: Run full test suite (including bit-level tests)
-          command: python setup.py test --enable-bit-level-tests
+          command: pytest hyperion --enable-bit-level-tests
 
   # Build with HDF5 1.8
   hdf5-18:
@@ -51,15 +54,21 @@ jobs:
               HYPERION_HDF5_VERSION=18 ./configure
               make
               make install
+      - run:
+          name: Upgrade setuptools and pip
+          command: pip install setuptools pip --upgrade
       - run:
           name: Installing Numpy
-          command: pip install numpy
+          command: pip install numpy Cython
       - run:
           name: Installing Python package
-          command: pip install .[test]
+          command: pip install -e .[test]
+      - run:
+          name: Ensure an old version of pytest is available
+          command: pip install "pytest<3.7,>=2.8"
       - run:
           name: Run full test suite (including bit-level tests)
-          command: python setup.py test --enable-bit-level-tests
+          command: pytest hyperion --enable-bit-level-tests
 
   # Build with HDF5 1.10
   hdf5-110:
@@ -83,10 +92,10 @@ jobs:
           command: pip3 install numpy
       - run:
           name: Installing Python package
-          command: pip3 install .[test]
+          command: pip3 install -e .[test]
       - run:
           name: Run full test suite (including bit-level tests)
-          command: python3 setup.py test --enable-bit-level-tests
+          command: pytest hyperion --enable-bit-level-tests
 
 workflows:
   version: 2

.travis.yml

@@ -8,7 +8,7 @@ env:
     global:
         - SETUP_XVFB=True
         - CONDA_CHANNELS='conda-forge'
-        - CONDA_DEPENDENCIES='numpy astropy h5py matplotlib yt mpich hdf5'
+        - CONDA_DEPENDENCIES='numpy astropy h5py matplotlib yt mpich hdf5 hdf5-static'
         - SETUP_CMD='test'
         - MPLBACKEND='Agg'
     matrix:
@@ -23,8 +23,9 @@ install:
     - if [[ $TRAVIS_OS_NAME == osx ]]; then conda install clang_osx-64 clangxx_osx-64 gfortran_osx-64; fi
 
 script:
+   - set -e
    - ./configure
    - make serial
    - sudo make install
-   - python setup.py install  # to get the hyperion script installed
-   - python setup.py $SETUP_CMD
+   - pip install -e .[test]
+   - pytest hyperion

Makefile.in

@@ -294,6 +294,6 @@ vor_mpi:	$(OBJECTS_VOR_MPI)
 
 install:	bin/hyperion_*
 		mkdir -p @prefix@/bin
-		cp bin/hyperion_* @prefix@/bin/
+		cp -r bin/hyperion_* @prefix@/bin/
 
 clean:;		rm *.mod src/*.mod src/*/*.mod *.o */*.o bin/* *~ */*~ fort.* ; echo "This file can be deleted." > bin/empty.txt ; echo "This file can be deleted." > src/modules/empty.txt

hyperion/conftest.py

@@ -5,11 +5,19 @@
 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)
+    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/model/tests/test_bit_level.py

@@ -9,10 +9,8 @@
 import shutil
 import itertools
 
-try:
-    import pytest
-except:
-    from astropy.tests.helper import pytest
+import pytest
+
 import numpy as np
 
 from six import StringIO
@@ -26,7 +24,6 @@
 
 DATA = os.path.join(os.path.dirname(__file__), 'data')
 
-bit_level = pytest.mark.skipif(str(not pytest.config.getoption('enable_bit_level_tests')))
 
 @pytest.fixture(scope="module")
 def generate(request):
@@ -137,7 +134,7 @@ def setup_class(self):
         setup_all_grid_types(self, pc, 1.e-20)
         self.dust_file = os.path.join(DATA, 'kmh_lite.hdf5')
 
-    @bit_level
+    @pytest.mark.bitlevel
     @pytest.mark.parametrize(('grid_type', 'sample_sources_evenly', 'multiple_densities'), list(itertools.product(GRID_TYPES, [False, True], [False, True])))
     def test_specific_energy(self, tmpdir, grid_type, sample_sources_evenly, multiple_densities, generate):
 
@@ -175,7 +172,7 @@ def test_specific_energy(self, tmpdir, grid_type, sample_sources_evenly, multipl
             reference_file = os.path.join(DATA, function_name() + ".rtout")
             assert_identical_results(output_file, reference_file)
 
-    @bit_level
+    @pytest.mark.bitlevel
     @pytest.mark.parametrize(('grid_type', 'raytracing', 'sample_sources_evenly'), list(itertools.product(GRID_TYPES, [False, True], [False, True])))
     def test_peeloff(self, tmpdir, grid_type, raytracing, sample_sources_evenly, generate):
 
@@ -339,7 +336,7 @@ def setup_class(self):
     def teardown_class(self):
         shutil.rmtree(self.tmpdir)
 
-    @bit_level
+    @pytest.mark.bitlevel
     @pytest.mark.parametrize(('tau'), [0.1, 1, 10, 100])
     def test_pascucci(self, tmpdir, tau, generate):
 
@@ -445,7 +442,7 @@ class TestPinteBenchmark(object):
     The current tests do not test the imaging part of the Pinte benchmark.
     '''
 
-    @bit_level
+    @pytest.mark.bitlevel
     @pytest.mark.parametrize(('tau'), [1000, 10000, 100000, 1000000])
     def test_pinte_seds(self, tmpdir, tau, generate):
 
@@ -547,7 +544,7 @@ def test_pinte_seds(self, tmpdir, tau, generate):
             reference_file = os.path.join(DATA, function_name() + ".rtout")
             assert_identical_results(output_file, reference_file)
 
-    @bit_level
+    @pytest.mark.bitlevel
     @pytest.mark.parametrize(('tau'), [1000, 10000, 100000, 1000000])
     def test_pinte_images(self, tmpdir, tau, generate):
 
@@ -638,7 +635,7 @@ def test_pinte_images(self, tmpdir, tau, generate):
             reference_file = os.path.join(DATA, function_name() + ".rtout")
             assert_identical_results(output_file, reference_file)
 
-    @bit_level
+    @pytest.mark.bitlevel
     @pytest.mark.parametrize(('tau'), [1000, 10000, 100000, 1000000])
     def test_pinte_specific_energy(self, tmpdir, tau, generate):
 

setup.cfg

@@ -0,0 +1,33 @@
+[metadata]
+name = Hyperion
+url = http://www.hyperion-rt.org
+author = Thomas Robitaille
+author_email = thomas.robitaille@gmail.com
+license = BSD
+description = Monte-Carlo Radiative Transfer Code
+
+[options]
+zip_safe = True
+packages = find:
+include_package_data = True
+setup_requires = numpy>=1.11
+install_requires =
+    numpy>=1.11
+    matplotlib>=1.5
+    astropy>=1.2
+    h5py>=2.4
+    yt>=3.2
+    six
+
+[options.extras_require]
+docs =
+    sphinx
+    numpydoc
+test =
+    pytest
+
+[options.package_data]
+hyperion.model.tests = data/*.rtout, data/*.hdf5
+hyperion.importers.tests = data/*.hdf5
+hyperion.grid.tests = data/*.hdf5, data/DD0010/*
+hyperion.testing = coveragerc

setup.py

@@ -14,7 +14,7 @@
 from distutils.command.build_ext import build_ext
 
 from hyperion.testing.helper import HyperionTest
-from hyperion.version import __version__, __dev__
+from hyperion.version import __version__
 
 
 class custom_sdist(sdist):
@@ -81,25 +81,7 @@ def run(self):
                              extra_compile_args = ['-O2', '-Wno-error=declaration-after-statement'],
                              extra_link_args=['-lstdc++'])]
 
-scripts = ['hyperion', 'hyperion2fits']
-
-setup(name='Hyperion',
-      version=__version__,
-      url='http://www.hyperion-rt.org',
-      description='Monte-Carlo Radiative Transfer Code',
-      long_description='Monte-Carlo Radiative Transfer Code',
-      author='Thomas Robitaille',
-      author_email='thomas.robitaille@gmail.com',
-      license='BSD',
-      packages=find_packages(),
-      package_data={'hyperion.model.tests': ['data/*.rtout', 'data/*.hdf5'],
-                    'hyperion.importers.tests': ['data/*.hdf5'],
-                    'hyperion.grid.tests': ['data/*.hdf5', 'data/DD0010/*'],
-                    'hyperion.testing': ['coveragerc']},
-      scripts=['scripts/' + x for x in scripts],
+setup(version=__version__,
+      scripts=['scripts/hyperion', 'scripts/hyperion2fits'],
       cmdclass=cmdclass,
-      ext_modules=ext_modules,
-      setup_requires=['numpy>=1.11'],
-      install_requires=['numpy>=1.11', 'matplotlib>=1.5', 'astropy>=1.2', 'h5py>=2.4', 'yt>=3.2', 'six'],
-      extras_require={'test': ['pytest'],
-                      'docs': ['sphinx', 'numpydoc']})
+      ext_modules=ext_modules)