def test_export(tmpdir):
"""Test the export functionality
"""
tmpdir = "/tmp/test/"
# makefile
env, env_file = export_env(["rbp_eclip/UPF1"], env_dir=str(tmpdir))
env_dict = read_yaml(env_file)
assert env_dict['channels'] == ['bioconda', 'conda-forge', 'defaults']
pip_idx = [
i for i, x in enumerate(env_dict['dependencies'])
if isinstance(x, dict)
][0]
assert [
p for p in env_dict['dependencies'][pip_idx]['pip']
if "tensorflow=" in p or "tensorflow>=" in p
]
for dep in ['concise']:
assert [
p for p in env_dict['dependencies'][pip_idx]['pip'] if dep in p
]
# gpu version
env, env_file = export_env(["rbp_eclip/UPF1"],
env_dir=str(tmpdir),
gpu=True)
env_dict = read_yaml(env_file)
assert env_dict['channels'] == ['bioconda', 'conda-forge', 'defaults']
assert [
p for p in env_dict['dependencies'][pip_idx]['pip']
if "tensorflow-gpu=" in p or "tensorflow-gpu>=" in p
]
# vep
env, env_file = export_env(
["rbp_eclip/UPF1"],
env_dir=str(tmpdir),
gpu=True,
vep=True,
)
env_dict = read_yaml(env_file)
assert env_dict['channels'] == ['bioconda', 'conda-forge', 'defaults']
assert [p for p in env_dict['dependencies'] if "cyvcf2" in p]
assert env_dict['name'] == env
def test_export_multiple(tmpdir):
"""Test the export functionality
"""
tmpdir = "/tmp/test/"
# makefile
env, env_file = export_env(["rbp_eclip/UPF1", "rbp_eclip/XRN2"],
env_dir=str(tmpdir))
env_dict = read_yaml(env_file)
del env_dict['name']
env, env_file = export_env(["rbp_eclip/UPF1"], env_dir=str(tmpdir))
env_dict2 = read_yaml(env_file)
del env_dict2['name']
assert env_dict == env_dict2
env, env_file = export_env(["rbp_eclip/UPF1", "HAL"], env_dir=str(tmpdir))
env_dict2 = read_yaml(env_file)
del env_dict2['name']
assert env_dict != env_dict2
def test_cli(tmpdir):
env_file = os.path.join(str(tmpdir), "env.yml")
args = ["python", os.path.abspath("./kipoi/__main__.py"), "env", "export",
"rbp_eclip/UPF1",
"-o", env_file]
returncode = subprocess.call(args=args)
assert returncode == 0
env_dict = read_yaml(env_file)
env, env_file2 = export_env(["rbp_eclip/UPF1"],
env_dir=str(tmpdir))
env_dict2 = read_yaml(env_file2)
assert env_dict == env_dict2
