diff --git a/.travis.yml b/.travis.yml index 91b2b513..81c24268 100644 --- a/.travis.yml +++ b/.travis.yml @@ -32,7 +32,7 @@ env: - GROMACS_VERSION=4.6.5 PYTHON_VERSION=3.6 - GROMACS_VERSION=2018.6 PYTHON_VERSION=3.6 - GROMACS_VERSION=2019.1 PYTHON_VERSION=3.6 - - GROMACS_VERSION=2019.1 PYTHON_VERSION=3.7 + - GROMACS_VERSION=2019.1 PYTHON_VERSION=3.7 # Test "append_suffix" implementation - GROMACS_VERSION=2018.6 PYTHON_VERSION=3.6 SETUP_CMD="${SETUP_CMD} --link-gmx-mpi --no-append-suffix" @@ -44,7 +44,7 @@ matrix: include: # see Gromacs packages on bioconda https://anaconda.org/bioconda/gromacs/files - os: osx - env: GROMACS_VERSION=4.6.5 PYTHON_VERSION=3.6 + env: GROMACS_VERSION=4.6.5 PYTHON_VERSION=3.6 - os: osx env: GROMACS_VERSION=2019.1 PYTHON_VERSION=2.7 NUMPY_VERSION=1.16 - os: osx diff --git a/setup.py b/setup.py index b76713d0..b57df831 100644 --- a/setup.py +++ b/setup.py @@ -35,31 +35,24 @@ 'Topic :: Scientific/Engineering :: Chemistry', 'Topic :: Software Development :: Libraries :: Python Modules', ], - packages=find_packages(exclude=['tests','scripts','extras','doc/examples']), - scripts = [ - 'scripts/gw-join_parts.py', - 'scripts/gw-merge_topologies.py', - 'scripts/gw-forcefield.py', - 'scripts/gw-partial_tempering.py', - ], + packages=find_packages( + exclude=['scripts', 'tests', 'tests.*', 'extras', 'doc/examples']), + scripts=[ + 'scripts/gw-join_parts.py', + 'scripts/gw-merge_topologies.py', + 'scripts/gw-forcefield.py', + 'scripts/gw-partial_tempering.py', + ], package_data={'gromacs': ['templates/*.sge', 'templates/*.pbs', # template files 'templates/*.ll', 'templates/*.sh', - 'templates/*.mdp', 'templates/*.cfg', - 'tests/data/fileformats/top/*.mdp', # test data - 'tests/data/fileformats/top/*.bz2', - 'tests/data/fileformats/top/*/*.top', - 'tests/data/fileformats/top/*/*.gro', - 'tests/data/*.log', - 'tests/data/*.ndx', + 'templates/*.mdp', 'templates/*.cfg' ], }, - install_requires = ['numpy>=1.0', - 'six', # towards py 3 compatibility - 'numkit', # numerical helpers - 'matplotlib', - ], - tests_require = ['pytest', 'numpy>=1.0', 'pandas>=0.17'], - zip_safe = True, -) - - + install_requires=['numpy>=1.0', + 'six', # towards py 3 compatibility + 'numkit', # numerical helpers + 'matplotlib', + ], + tests_require=['pytest', 'numpy>=1.0', 'pandas>=0.17'], + zip_safe=True, + ) diff --git a/tests/fileformats/__init__.py b/tests/fileformats/__init__.py index d639b535..ccc39f61 100644 --- a/tests/fileformats/__init__.py +++ b/tests/fileformats/__init__.py @@ -2,4 +2,3 @@ # Copyright (c) 2009 Oliver Beckstein # Released under the GNU Public License 3 (or higher, your choice) # See the file COPYING for details. - diff --git a/tests/fileformats/top/__init__.py b/tests/fileformats/top/__init__.py index d639b535..ccc39f61 100644 --- a/tests/fileformats/top/__init__.py +++ b/tests/fileformats/top/__init__.py @@ -2,4 +2,3 @@ # Copyright (c) 2009 Oliver Beckstein # Released under the GNU Public License 3 (or higher, your choice) # See the file COPYING for details. - diff --git a/tests/test_cbook.py b/tests/test_cbook.py index 9ec3825d..57506659 100644 --- a/tests/test_cbook.py +++ b/tests/test_cbook.py @@ -12,12 +12,13 @@ from .datafiles import datafile + def test_grompp_qtot(tmpdir): pdb = datafile("1ake_A.pdb") top = tmpdir.mkdir("top") with top.as_cwd(): f = gromacs.setup.topology(struct=pdb, ff="oplsaa", water="tip4p") - with open('none.mdp','w') as mdp: + with open('none.mdp', 'w') as mdp: mdp.write('; empty mdp file\nrcoulomb = 1\nrvdw = 1\nrlist = 1\n') qtot = cbook.grompp_qtot(f="none.mdp", c=f['struct'], p=f['top'], stdout=False, maxwarn=10)