def cli_create(cmd, raw_args):
"""Create a conda environment for a model
"""
from kipoi.conda import get_kipoi_bin
import uuid
parser = argparse.ArgumentParser(
'kipoi env {}'.format(cmd),
description='Create a conda environment for a specific model.')
add_env_args(parser)
parser.add_argument(
'-e',
'--env',
default=None,
help="Special environment name. default: kipoi-<model>[-<dataloader>]")
parser.add_argument(
'-t',
'--tmpdir',
default=None,
help=
"Temporary directory path where to create the conda environment file" +
"Defaults to /tmp/kipoi/envfiles/<uuid>/")
args = parser.parse_args(raw_args)
# create the tmp dir
if args.tmpdir is None:
tmpdir = "/tmp/kipoi/envfiles/" + str(uuid.uuid4())[:8]
else:
tmpdir = args.tmpdir
if not os.path.exists(tmpdir):
os.makedirs(tmpdir)
# write the env file
logger.info("Writing environment file: {0}".format(tmpdir))
env, env_file = export_env(args.model,
args.dataloader,
args.source,
env_file=None,
env_dir=tmpdir,
env=args.env,
vep=args.vep,
gpu=args.gpu)
env_db_entry = generate_env_db_entry(args, args_env_overload=env)
envdb = get_model_env_db()
envdb.append(env_db_entry)
envdb.save()
# setup the conda env from file
logger.info("Creating conda env from file: {0}".format(env_file))
kipoi.conda.create_env_from_file(env_file)
env_db_entry.successful = True
# env is environment name
env_db_entry.cli_path = get_kipoi_bin(env)
get_model_env_db().save()
logger.info("Done!")
print("\nActivate the environment via:")
print("source activate {0}".format(env))
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 test_model(model_name,
source_name,
env_name,
batch_size,
vep=False,
create_env=True):
"""kipoi test ...
Args:
model_name (str)
source_name: source name
"""
if create_env:
create_model_env(model_name, source_name, env_name, vep)
# 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 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 cli_create(cmd, raw_args):
"""Create a conda environment for a model
"""
from kipoi.conda import get_kipoi_bin
import uuid
parser = argparse.ArgumentParser(
'kipoi env {}'.format(cmd),
description='Create a conda environment for a specific model.')
add_env_args(parser)
parser.add_argument(
'-e',
'--env',
default=None,
help="Special environment name. default: kipoi-<model>[-<dataloader>]")
parser.add_argument('--dry-run',
action='store_true',
help="Don't actually create the environment")
parser.add_argument(
'-t',
'--tmpdir',
default=None,
help=
"Temporary directory path where to create the conda environment file" +
"Defaults to /tmp/kipoi/envfiles/<uuid>/")
args = parser.parse_args(raw_args)
# create the tmp dir
if args.tmpdir is None:
tmpdir = "/tmp/kipoi/envfiles/" + str(uuid.uuid4())[:8]
else:
tmpdir = args.tmpdir
if not os.path.exists(tmpdir):
os.makedirs(tmpdir)
# write the env file
logger.info("Writing environment file: {0}".format(tmpdir))
if args.model == ['all']:
from kipoi.cli.source_test import get_common_env
src = kipoi.get_source(args.source)
model_envs = yaml.load(
open(
os.path.join(src.local_path, SPECIAL_ENV_PREFIX,
"models.yaml")))
# TODO - test this by mocking up the CLI command execution
# setup the args for all the models
df = kipoi.list_models()
dfg = list_models_by_group(df, "")
for model_group in dfg.group.unique().tolist():
existing_envs = get_envs_by_model(model_group,
args.source,
only_valid=True)
if existing_envs or existing_envs is None:
# No need to create the environment
existing_envs_str = "\n".join(
[e.create_args.env for e in existing_envs])
logger.info(
"Environment for {} already exists ({}). Skipping installation"
.format(model_group, existing_envs_str))
continue
logger.info(
"Environment doesn't exists for model group {}. Installing it".
format(model_group))
# Figure out which <model> to use for installation
common_env = get_common_env(model_group, model_envs)
if common_env is not None:
# common environment exists for the model. Use it
logger.info("Using common environment: {}".format(common_env))
model_group = os.path.join(SPECIAL_ENV_PREFIX, common_env)
# Run cli_create
def optional_replace(x, ref, alt):
if x == ref:
return alt
else:
return x
new_raw_args = [
optional_replace(x, 'all', model_group) for x in raw_args
if x is not None
]
cli_create(cmd, new_raw_args)
logger.info("Done installing all environments!")
return None
env, env_file = export_env(args.model,
args.dataloader,
args.source,
env_file=None,
env_dir=tmpdir,
env=args.env,
vep=args.vep,
interpret=args.interpret,
gpu=args.gpu)
if not args.dry_run:
env_db_entry = generate_env_db_entry(args, args_env_overload=env)
envdb = get_model_env_db()
envdb.append(env_db_entry)
envdb.save()
# setup the conda env from file
logger.info("Creating conda env from file: {0}".format(env_file))
kipoi.conda.create_env_from_file(env_file)
env_db_entry.successful = True
# env is environment name
env_db_entry.cli_path = get_kipoi_bin(env)
get_model_env_db().save()
logger.info("Done!")
print("\nActivate the environment via:")
print("source activate {0}".format(env))
else:
print("Dry run. Conda file path: {}".format(env_file))
