def test_kipoi_env_create_all_dry_run():
from kipoi.cli.env import cli_create
args = [
"python",
os.path.abspath("./kipoi/__main__.py"), "env", "create", "all",
"--dry-run"
]
# pretend to run the CLI
cli_create(*process_args(args))
def test_kipoi_env_create_all(tmpdir, monkeypatch):
from kipoi.cli.env import cli_create
conda = PseudoConda(tmpdir)
monkeypatch.setattr(kipoi.conda, 'create_env_from_file', conda.add_env)
monkeypatch.setattr(kipoi.conda, 'remove_env', conda.delete_env)
monkeypatch.setattr(kipoi.conda, 'get_kipoi_bin', conda.get_cli)
args = [
"python",
os.path.abspath("./kipoi/__main__.py"), "env", "create", "all"
]
# pretend to run the CLI
cli_create(*process_args(args))
def test_kipoi_env_create_cleanup_remove(tmpdir, monkeypatch):
from kipoi.cli.env import cli_create, cli_cleanup, cli_remove, cli_get, cli_get_cli, cli_list
tempfile = os.path.join(str(tmpdir), "envs.json")
# Define things necessary for monkeypatching
def get_assert_env(equals):
def assert_to(val):
assert len(val) == len(equals)
assert all([v.create_args.env == e for v, e in zip(val, equals)])
return assert_to
def get_assert_env_cli(equals):
def assert_to(val):
assert len(val) == len(equals)
assert all([v.cli_path == e for v, e in zip(val, equals)])
return assert_to
# pseudo kipoi CLI executable
conda = PseudoConda(tmpdir)
if os.path.exists(tempfile):
os.unlink(tempfile)
test_model = "example/models/pyt"
test_env_name = "kipoi-testenv"
source_path = kipoi.get_source("dir").local_path
# monkeypatch:
old_env_db_path = kipoi.config._env_db_path
monkeypatch.setattr(kipoi.config, '_env_db_path', tempfile)
monkeypatch.setattr(kipoi.conda, 'create_env_from_file', conda.add_env)
monkeypatch.setattr(kipoi.conda, 'remove_env', conda.delete_env)
monkeypatch.setattr(kipoi.conda, 'get_kipoi_bin', conda.get_cli)
monkeypatch.setattr(kipoi.cli.env, 'print_env_names',
get_assert_env([test_env_name]))
# load the db from the new path
kipoi.conda.env_db.reload_model_env_db()
args = [
"python",
os.path.abspath("./kipoi/__main__.py"), "env", "create", "--source",
"dir", "--env", test_env_name, test_model
]
# pretend to run the CLI
cli_create(*process_args(args))
# make sure the successful flag is set and the kipoi-cli exists
kipoi.conda.env_db.reload_model_env_db()
db = kipoi.conda.env_db.get_model_env_db()
entry = db.get_entry_by_model(os.path.join(source_path, test_model))
assert entry.successful
assert os.path.exists(entry.cli_path)
# add a new entry that does not exist:
cfg = entry.get_config()
cfg["create_args"]["env"] += "____AAAAAA_____"
cfg["cli_path"] += "____AAAAAA_____"
db.append(EnvDbEntry.from_config(cfg))
# now test the get environment name and the get_kipoi_bin
args = [
"python",
os.path.abspath("./kipoi/__main__.py"), "env", "get", "--source",
"dir", test_model
]
cli_get(*process_args(args))
monkeypatch.setattr(kipoi.cli.env, 'print_env_cli_paths',
get_assert_env_cli([conda.get_cli(test_env_name)]))
args = [
"python",
os.path.abspath("./kipoi/__main__.py"), "env", "get_bin", "--source",
"dir", test_model
]
cli_get_cli(*process_args(args))
# list environments:
monkeypatch.setattr(kipoi.cli.env, 'print_valid_env_names',
get_assert_env([test_env_name]))
monkeypatch.setattr(kipoi.cli.env, 'print_invalid_env_names',
get_assert_env([test_env_name + "____AAAAAA_____"]))
monkeypatch.setattr(subprocess, 'call', lambda *args, **kwargs: None)
args = ["python", os.path.abspath("./kipoi/__main__.py"), "env", "list"]
cli_list(*process_args(args))
# pretend also the first installation didn't work
entry.successful = False
first_config = entry.get_config()
db.save()
args = [
"python",
os.path.abspath("./kipoi/__main__.py"), "env", "cleanup", "--all",
'--yes'
]
print(conda.existing_envs)
print(db.entries)
# pretend to run the CLI
cli_cleanup(*process_args(args))
# now
kipoi.conda.env_db.reload_model_env_db()
db = kipoi.conda.env_db.get_model_env_db()
assert len(db.entries) == 1
assert_rec(db.entries[0].get_config(), cfg)
args = [
"python",
os.path.abspath("./kipoi/__main__.py"), "env", "cleanup", "--all",
"--db", '--yes'
]
# pretend to run the CLI
cli_cleanup(*process_args(args))
kipoi.conda.env_db.reload_model_env_db()
db = kipoi.conda.env_db.get_model_env_db()
assert len(db.entries) == 0
assert len(conda.existing_envs) == 0
# now final test of creating and removing an environment:
args = [
"python",
os.path.abspath("./kipoi/__main__.py"), "env", "create", "--source",
"dir", "--env", test_env_name, test_model
]
# pretend to run the CLI
cli_create(*process_args(args))
args = [
"python",
os.path.abspath("./kipoi/__main__.py"), "env", "remove", "--source",
"dir", test_model, '--yes'
]
cli_remove(*process_args(args))
kipoi.conda.env_db.reload_model_env_db()
db = kipoi.conda.env_db.get_model_env_db()
assert len(db.entries) == 0
assert len(conda.existing_envs) == 0
# just make sure this resets after the test.
kipoi.config._env_db_path = old_env_db_path
kipoi.conda.env_db.reload_model_env_db()