def cli_create(cmd, raw_args):
"""Create a conda environment for a model
"""
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>]")
args = parser.parse_args(raw_args)
# create the tmp dir
tmpdir = "/tmp/kipoi/envfiles/" + str(uuid.uuid4())[:8]
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)
# 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)
logger.info("Done!")
print("\nActivate the environment via:")
print("source activate {0}".format(env))
def cli_remove(cmd, raw_args):
"""Remove a conda environment for a model
"""
parser = argparse.ArgumentParser(
'kipoi env {}'.format(cmd),
description=
'Remove environment compatible with this model. If `--all` is not set then only remove the most '
'recently generated environment compatible with this model.')
add_env_args(parser)
parser.add_argument(
'-a',
'--all',
action='store_true',
help=
"Remove all environments every created that are compatible with this model"
)
parser.add_argument(
'-y',
'--yes',
action='store_true',
help="If set then do NOT ask before deleting environments.")
args = parser.parse_args(raw_args)
to_delete = get_envs_by_model(args.model,
args.source,
only_most_recent=not args.all)
if len(to_delete) != 0:
ask_and_delete_envs(to_delete, args)
else:
logger.info("Nothing to remove!")
logger.info("Done!")
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 cli_name(cmd, raw_args):
"""Show the name of the environment
"""
parser = argparse.ArgumentParser(
'kipoi env {}'.format(cmd),
description='Show the name of the environment.')
add_env_args(parser)
args = parser.parse_args(raw_args)
env = get_env_name(args.model, args.dataloader, args.source, gpu=args.gpu)
print("\nEnvironment name: {0}".format(env))
def cli_get_cli(cmd, raw_args):
"""Print a kipoi cli path for a model
"""
parser = argparse.ArgumentParser(
'kipoi env {}'.format(cmd),
description='Print kipoi cli path for specific model.'
)
add_env_args(parser)
parser.add_argument('-a', '--all', action='store_true',
help="If set all environments compatible with this model will be printed!")
args = parser.parse_args(raw_args)
entries = get_envs_by_model(args.model, args.source, only_most_recent=not args.all, only_valid=True)
print_env_cli_paths(entries)
def cli_install(cmd, raw_args):
"""Install the required packages for the model
"""
parser = argparse.ArgumentParser(
'kipoi env {}'.format(cmd),
description='Install all the dependencies for a model into the current conda environment.'
)
add_env_args(parser)
args = parser.parse_args(raw_args)
deps = merge_deps(models=args.model,
dataloaders=args.dataloader,
source=args.source,
vep=args.vep,
gpu=args.gpu)
deps.install()
logger.info("Done!")
def cli_export(cmd, raw_args):
parser = argparse.ArgumentParser(
'kipoi env {}'.format(cmd),
description='Export the environment.yaml file for a specific model.')
add_env_args(parser)
parser.add_argument('-o',
'--output',
default='environment.yaml',
required=True,
help="Output file name")
parser.add_argument('-e', '--env', default=None, help="Environment name")
args = parser.parse_args(raw_args)
env, env_file = export_env(args.model,
args.dataloader,
args.source,
env_file=args.output,
env=args.env,
vep=args.vep,
gpu=args.gpu)
print("Create the environment with:")
print("conda env create --file {0}".format(env_file))
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>/"))
parser.add_argument('-v',
'--verbose',
action='store_true',
help="Increase output verbosity. Show conda stdout.")
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.safe_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, use_stdout=args.verbose)
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("conda activate {0}".format(env))
else:
print("Dry run. Conda file path: {}".format(env_file))