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
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 get_environments(source): """Cache for kipoi's environments""" import os from kipoi.utils import read_yaml src = kipoi.get_source(source) environments = read_yaml( os.path.join(src.local_path, 'shared/envs/models.yaml')) return environments
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