def cli_pull(command, raw_args):
"""Pull the repository
"""
assert command == "pull"
parser = argparse.ArgumentParser('kipoi {}'.format(command),
description="Downloads the directory" +
" associated with the model.")
parser.add_argument(
'model',
help='Model name. '
'<model> can also refer to a model-group - e.g. if you '
'specify MaxEntScan then the dependencies\n'
'for MaxEntScan/5prime and MaxEntScan/3prime will be installed')
add_source(parser)
args = parser.parse_args(raw_args)
src = kipoi.config.get_source(args.source)
sub_models = list_subcomponents(args.model, args.source, which='model')
if len(sub_models) == 0:
logger.error("Model {0} not found in source {1}".format(
args.model, args.source))
sys.exit(1)
if len(sub_models) > 1:
logger.info(
"Found {0} models under the model name: {1}. Pulling all of them".
format(len(sub_models), args.model))
for sub_model in sub_models:
src.pull_model(sub_model)
def cli_ls(command, raw_args):
"""List all kipoi models
"""
assert command == "ls"
parser = argparse.ArgumentParser('kipoi {}'.format(command),
description="Lists available models")
parser.add_argument("group_filter", nargs='?', default='',
help="A relative path to the model group used to subset the model list. Use 'all' to show all models")
parser.add_argument("--tsv", action='store_true',
help="Print the output in the tsv format.")
add_source(parser)
args = parser.parse_args(raw_args)
grp = kipoi.get_source(args.source)
df = grp.list_models()
ls_helper(df, args.group_filter, args.tsv)
def cli_pull(command, raw_args):
"""Pull the repository
"""
assert command == "pull"
parser = argparse.ArgumentParser('kipoi {}'.format(command),
description="Downloads the directory" +
" associated with the model.")
parser.add_argument('model', help='Model name.')
add_source(parser)
parser.add_argument(
'-e',
'--env_file',
default=None,
help='If set, export the conda environment to a file.' +
'Example: kipoi pull mymodel -e mymodel.yaml')
args = parser.parse_args(raw_args)
kipoi.config.get_source(args.source).pull_model(args.model)
if args.env_file is not None:
env = kipoi.cli.env.export_env(args.env_file, args.model, args.source)
print("Activate the environment with:")
print("source activate {0}".format(env))