def test_build_from_source_github(self):
# TODO: expand on tests for building ANTs from source. It probably
# will not be possible to build ANTs in Travic because of the 50 min
# time limit. It takes about 45 minutes to compile ANTs.
ants = ANTs(version='latest', pkg_manager='apt', use_binaries=False)
assert "git checkout" not in ants.cmd
ants = ANTs(version='2.2.0', pkg_manager='yum', use_binaries=False)
assert ants.cmd
ants = ANTs(version='arbitrary', pkg_manager='apt', use_binaries=False,
git_hash='12345')
assert 'git checkout 12345' in ants.cmd
def setup(self, tmpdir):
self.tmpdir = tmpdir
self.specs = {'pkg_manager': 'apt',
'check_urls': False,
'instructions': [
('base', 'ubuntu:17.04'),
('afni', {'version': 'latest'}),
('mrtrix3', {}),
('miniconda', {'env_name': 'default',
'conda_install': 'python=3.5.1 numpy',
'pip_install': 'pandas'}),
('ants', {'version': '2.1.0', 'use_binaries': True}),
('freesurfer', {'version': '6.0.0', 'min': True}),
('fsl', {'version': '5.0.10', 'use_binaries': True}),
('spm', {'version': 12, 'matlab_version': 'R2017a'}),
('instruction', "RUN ls"),
]
}
inst = self.specs['instructions']
self.base = "FROM {}".format(_get_val_in_list_of_tuple(inst, 'base'))
self.noninteractive = "ARG DEBIAN_FRONTEND=noninteractive"
self.miniconda = Miniconda(pkg_manager='apt', check_urls=False, **_get_val_in_list_of_tuple(inst, 'miniconda')).cmd
Miniconda.clear_memory()
self.ants = ANTs(pkg_manager='apt', check_urls=False, **_get_val_in_list_of_tuple(inst, 'ants')).cmd
self.fsl = FSL(pkg_manager='apt', check_urls=False, **_get_val_in_list_of_tuple(inst, 'fsl')).cmd
self.spm = SPM(pkg_manager='apt', check_urls=False, **_get_val_in_list_of_tuple(inst, 'spm')).cmd
def test_invalid_binaries(self):
with pytest.raises(ValueError):
ANTs(version='fakeversion', pkg_manager='apt', check_urls=False)