def rm_env(env_name):
"""Alias for remove_env
"""
if env_exists(env_name):
logger.info("Removing environment: {0}".
format(env_name))
remove_env(env_name)
def test_model(model_name, source_name, env_name, batch_size, vep=False):
"""kipoi test ...
Args:
model_name (str)
source_name: source name
"""
if env_exists(env_name):
logger.info("Environment {0} exists. Removing it.".format(env_name))
remove_env(env_name)
# TODO - if the model is a Keras model, print the Keras config file
# and note which config file got used
# create the model test environment
cmd = "kipoi"
args = ["env", "create",
"--source", source_name,
"--env", env_name,
model_name]
if vep:
# Add --vep to environment installation
args.insert(-1, "--vep")
returncode = _call_command(cmd, args, use_stdout=True)
assert returncode == 0
# run the tests in the environment
cmd = get_kipoi_bin(env_name)
args = ["test",
"--batch_size", str(batch_size),
"--source", source_name,
model_name]
# New, modified path for conda. Source activate namely does the following:
# - CONDA_DEFAULT_ENV=${env_name}
# - CONDA_PREFIX=${env_path}
# - PATH=$conda_bin:$PATH
new_env = os.environ.copy()
new_env['PATH'] = os.path.dirname(cmd) + os.pathsep + new_env['PATH']
returncode, logs = _call_command(cmd, args, use_stdout=True,
return_logs_with_stdout=True,
env=new_env
)
assert returncode == 0
# detect WARNING in the output log
warn = 0
for line in logs:
warn_start = escape_codes[default_log_colors['WARNING']] + \
'WARNING' + escape_codes['reset']
if line.startswith(warn_start):
logger.error("Warning present: {0}".format(line))
warn += 1
if warn > 0:
raise ValueError("{0} warnings were observed for model {1}".
format(warn, model_name))
def rm_env(env_name):
"""Alias for remove_env
"""
from kipoi.conda.env_db import get_model_env_db
if env_exists(env_name):
logger.info("Removing environment: {0}".format(env_name))
remove_env(env_name)
# remove from db
db = get_model_env_db()
db_entries = [e for e in db.get_all() if e.create_args.env == env_name]
[db.remove(e) for e in db_entries]
db.save()
def test_model(model_name, source_name, env_name, batch_size):
"""kipoi test ...
Args:
model_name (str)
source_name: source name
"""
if env_exists(env_name):
logger.info("Environment {0} exists. Removing it.".format(env_name))
remove_env(env_name)
# TODO - if the model is a Keras model, print the Keras config file
# and note which config file got used
# create the model test environment
cmd = "kipoi"
args = ["env", "create",
"--source", source_name,
"--env", env_name,
model_name]
returncode = _call_command(cmd, args, use_stdout=True)
assert returncode == 0
# run the tests in the environment
cmd = get_kipoi_bin(env_name)
args = ["test",
"--batch_size", str(batch_size),
"--source", source_name,
model_name]
returncode, logs = _call_command(cmd, args, use_stdout=True,
return_logs_with_stdout=True)
assert returncode == 0
# detect WARNING in the output log
warn = 0
for line in logs:
warn_start = escape_codes[default_log_colors['WARNING']] + \
'WARNING' + escape_codes['reset']
if line.startswith(warn_start):
logger.error("Warning present: {0}".format(line))
warn += 1
if warn > 0:
raise ValueError("{0} warnings were observed for model {1}".
format(warn, model_name))
def test_model(model_name, caplog):
"""kipoi test ...
"""
caplog.set_level(logging.INFO)
source_name = "kipoi"
assert source_name == "kipoi"
env_name = conda_env_name(model_name, model_name, source_name)
env_name = "test-" + env_name # prepend "test-"
# if environment already exists, remove it
if env_exists(env_name):
print("Removing the environment: {0}".format(env_name))
remove_env(env_name)
# create the model test environment
args = ["kipoi", "env", "create",
"--source", source_name,
"--env", env_name,
model_name]
returncode = subprocess.call(args=args)
assert returncode == 0
if model_name == "basenji":
batch_size = str(2)
else:
batch_size = str(4)
# run the tests in the environment
args = [get_kipoi_bin(env_name), "test",
"--batch_size", batch_size,
"--source", source_name,
model_name]
returncode = subprocess.call(args=args)
assert returncode == 0
for record in caplog.records:
# there shoudn't be any warning
assert record.levelname not in ['WARN', 'WARNING', 'ERROR', 'CRITICAL']
def create_model_env(model_name, source_name, env_name, vep=False):
"""kipoi test ...
Args:
model_name (str)
source_name: source name
"""
if env_exists(env_name):
logger.info("Environment {0} exists. Removing it.".format(env_name))
remove_env(env_name)
# TODO - if the model is a Keras model, print the Keras config file
# and note which config file got used
# create the model test environment
cmd = "kipoi"
args = [
"env", "create", "--source", source_name, "--env", env_name, model_name
]
if vep:
# Add --vep to environment installation
args.insert(-1, "--vep")
returncode = _call_command(cmd, args, use_stdout=True)
assert returncode == 0