def test_conda_wrapper_verify_environment(self):
"""
CondaWrapper: verify environment can be activated
"""
self._make_mock_conda()
os.makedirs(os.path.join(self.conda_env_dir,'[email protected]'))
conda = CondaWrapper(conda=self.conda)
self.assertTrue(conda.verify_env("[email protected]"))
def test_conda_wrapper_verify_fails_for_bad_environment(self):
"""
CondaWrapper: verify fails for 'bad' environment
"""
self._make_mock_conda(activate_fails=True)
os.makedirs(os.path.join(self.conda_env_dir,'[email protected]'))
conda = CondaWrapper(conda=self.conda)
self.assertFalse(conda.verify_env("[email protected]"))
def test_conda_wrapper_activate_command(self):
"""
CondaWrapper: check environment activation command
"""
self._make_mock_conda()
conda = CondaWrapper(conda=self.conda)
self.assertEqual(conda.activate_env_cmd("[email protected]").command_line,
Command(
'source',
os.path.join(self.conda_bin_dir,'activate'),
'[email protected]').command_line)
def test_conda_wrapper_conda_version(self):
"""
CondaWrapper: get conda version
"""
self._make_mock_conda()
conda = CondaWrapper(conda=self.conda)
self.assertEqual(conda.version,"4.10.3")
def test_conda_wrapper_create_env(self):
"""
CondaWrapper: check create new environment
"""
self._make_mock_conda()
conda = CondaWrapper(conda=self.conda)
conda.create_env("qc",
"fastqc=0.11.3",
"fastq-screen=0.14.0",
"bowtie=1.2.3")
env_dir = os.path.join(self.conda_env_dir,"qc")
self.assertTrue(os.path.exists(env_dir))
packages = os.path.join(env_dir,"packages.txt")
self.assertTrue(os.path.exists(packages))
with open(packages,'rt') as fp:
contents = fp.read().strip()
self.assertEqual(contents,
"fastqc=0.11.3 fastq-screen=0.14.0 bowtie=1.2.3")
def test_conda_wrapper_conda_defaults(self):
"""
CondaWrapper: check properties for default env dir
"""
self._make_mock_conda()
conda = CondaWrapper(conda=self.conda)
self.assertEqual(conda.conda,self.conda)
self.assertTrue(conda.is_installed)
self.assertEqual(conda.env_dir,self.conda_env_dir)
self.assertEqual(conda.list_envs,[])
def test_conda_wrapper_conda_not_specified(self):
"""
CondaWrapper: check properties when conda exe not specified
"""
self._make_mock_conda()
print(os.environ['PATH'])
conda = CondaWrapper()
self.assertEqual(conda.conda,self.conda)
self.assertTrue(conda.is_installed)
self.assertEqual(conda.env_dir,self.conda_env_dir)
self.assertEqual(conda.list_envs,[])
def test_conda_wrapper_create_env_raise_exception_on_error(self):
"""
CondaWrapper: raise exception on error when creating environment
"""
self._make_mock_conda(create_fails=True)
conda = CondaWrapper(conda=self.conda)
self.assertRaises(CondaCreateEnvError,
conda.create_env,
"qc",
"fastqc=0.11.3",
"fastq-screen=0.14.0",
"bowtie=1.2.3")
def test_conda_wrapper_missing_conda_executable(self):
"""
CondaWrapper: check properties when conda is missing
"""
conda = CondaWrapper(
conda="/usr/local/missing/conda/bin/conda")
self.assertEqual(conda.conda,
"/usr/local/missing/conda/bin/conda")
self.assertFalse(conda.is_installed)
self.assertEqual(conda.env_dir,
"/usr/local/missing/conda/envs")
self.assertEqual(conda.list_envs,[])
self.assertEqual(conda.version,None)
def test_conda_wrapper_null_wrapper(self):
"""
CondaWrapper: check properties for 'null' wrapper
"""
save_path = os.environ['PATH']
os.environ['PATH'] = ''
conda = CondaWrapper()
self.assertEqual(conda.conda,None)
self.assertFalse(conda.is_installed)
self.assertEqual(conda.env_dir,None)
self.assertEqual(conda.list_envs,[])
self.assertEqual(conda.version,None)
os.environ['PATH'] = save_path
def test_conda_wrapper_conda_custom_env_dir(self):
"""
CondaWrapper: check properties for custom env dir
"""
self._make_mock_conda()
custom_env_dir = os.path.join(self.working_dir,
"local_conda_envs")
os.makedirs(custom_env_dir)
conda = CondaWrapper(conda=self.conda,
env_dir=custom_env_dir)
self.assertEqual(conda.conda,self.conda)
self.assertTrue(conda.is_installed)
self.assertEqual(conda.env_dir,custom_env_dir)
self.assertEqual(conda.list_envs,[])
def test_conda_wrapper_list_envs(self):
"""
CondaWrapper: check listing environments
"""
self._make_mock_conda()
# Default env dir
conda = CondaWrapper(conda=self.conda)
self.assertEqual(conda.list_envs,[])
for env in ('fastqc','picard','star'):
os.makedirs(os.path.join(self.conda_env_dir,env))
self.assertEqual(conda.list_envs,
['fastqc','picard','star'])
# Custom env dir
custom_env_dir = os.path.join(self.working_dir,
"local_conda_envs")
os.makedirs(custom_env_dir)
conda = CondaWrapper(conda=self.conda,
env_dir=custom_env_dir)
self.assertEqual(conda.list_envs,[])
for env in ('fastqc','picard','star'):
os.makedirs(os.path.join(custom_env_dir,env))
self.assertEqual(conda.list_envs,
['fastqc','picard','star'])