def create_model_env(model_name,
source_name,
env_name,
vep=False,
verbose=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 verbose:
args.append("--verbose")
if vep:
# Add --vep to environment installation
args.insert(-1, "--vep")
returncode = _call_command(cmd, args, use_stdout=True)
assert returncode == 0
def delete_envs(to_delete):
db = get_model_env_db()
for e in to_delete:
try:
kipoi_conda.remove_env(e.create_args.env)
db.remove(e)
db.save()
except Exception as err:
logger.warning(
"Conda delete of environment {0} failed with error: {1}. This environment entry was not "
"removed from the database.".format(e.create_args.env,
str(err)))
def rm_env(env_name):
"""Alias for remove_env
"""
from kipoi.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, 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']
