def load_oml_benchmark(
benchmark: str) -> Tuple[str, Optional[str], List[Namespace]]:
""" Loads benchmark defined by openml suite or task, from openml/s/X or openml/t/Y. """
domain, oml_type, oml_id = benchmark.split('/')
path = None # benchmark file does not exist on disk
name = benchmark # name is later passed as cli input again for containers, it needs to remain parsable
if oml_type == 't':
log.info("Loading openml task %s.", oml_id)
# We first have the retrieve the task because we don't know the dataset id
t = openml.tasks.get_task(oml_id, download_data=False)
data = openml.datasets.get_dataset(t.dataset_id, download_data=False)
tasks = [
Namespace(name=str_sanitize(data.name),
description=data.description,
openml_task_id=t.id)
]
elif oml_type == 's':
log.info("Loading openml suite %s.", oml_id)
suite = openml.study.get_suite(oml_id)
# Here we know the (task, dataset) pairs so only download dataset meta-data is sufficient
tasks = []
for tid, did in zip(suite.tasks, suite.data):
data = openml.datasets.get_dataset(did, download_data=False)
tasks.append(
Namespace(name=str_sanitize(data.name),
description=data.description,
openml_task_id=tid))
else:
raise ValueError(f"The oml_type is {oml_type} but must be 's' or 't'")
return name, path, tasks
def test_framework_definition_lookup_is_case_insensitive(
frameworks, lookup, expected):
res = NS(_frameworks=frameworks)
# binding `framework_definition` method to our resource mock: use pytest-mock instead?
res.framework_definition = Resources.framework_definition.__get__(res)
assert res.framework_definition(lookup) == (frameworks[expected],
frameworks[expected].name)
def test_find_all_parents_returns_empty_list_if_framework_has_no_parent():
frameworks = Namespace(
gama=Namespace(name="gama", version="latest", description="flexible automl"),
h2o_automl=Namespace(name="h2o", version="1.3"),
)
parents = _find_all_parents(frameworks.gama, frameworks)
assert parents == []
def test_update_frameworks_with_parent_definitions_does_not_overwrite_child(field, p_value, c_value):
frameworks = Namespace(
gama=Namespace(name="gama", **{field: p_value}),
gama_old=Namespace(name="gama_20.1", **{field: c_value}, extends="gama"),
)
_update_frameworks_with_parent_definitions(frameworks)
assert frameworks.gama_old[field] == c_value
def test_sanitize_and_add_defaults_child_inherits_module(simple_resource):
frameworks = Namespace(
auto_sklearn=Namespace(),
auto_sklearn_old=Namespace(extends="auto_sklearn")
)
_sanitize_and_add_defaults(frameworks, simple_resource.config)
assert frameworks.auto_sklearn_old.module == "frameworks.auto_sklearn"
def test_update_frameworks_with_parent_definitions_add_missing_field_from_parent(field, value):
frameworks = Namespace(
gama=Namespace(name="gama", **{field: value}),
gama_old=Namespace(name="gama_20.1.0", extends="gama"),
)
_update_frameworks_with_parent_definitions(frameworks)
assert frameworks.gama_old[field] == value
def call_run(run_fn):
import numpy as np
params = NS.from_dict(json.loads(sys.stdin.read()))
def load_data(name, path, **ignored):
if isinstance(path, str) and data_keys.match(name):
return name, np.load(path, allow_pickle=True)
return name, path
print(params.dataset)
ds = NS.walk(params.dataset, load_data)
config = params.config
config.framework_params = NS.dict(config.framework_params)
try:
result = run_fn(ds, config)
res = dict(result)
for name in ['predictions', 'truth', 'probabilities']:
arr = result[name]
if arr is not None:
res[name] = os.path.join(config.result_dir, '.'.join([name, 'npy']))
np.save(res[name], arr, allow_pickle=True)
except Exception as e:
log.exception(e)
res = dict(
error_message=str(e),
models_count=0
)
print(config.result_token)
print(json.dumps(res, separators=(',', ':')))
def test_update_frameworks_with_parent_definitions_parent_overwrites_grandparent_yaml(field, g_value, p_value):
frameworks = Namespace(
gama=Namespace(name="gama", **{field: g_value}),
gama_old=Namespace(name="gama_2", **{field: p_value}, extends="gama"),
gama_oldest=Namespace(name="gama_1", extends="gama_old"),
)
_update_frameworks_with_parent_definitions(frameworks)
assert frameworks.gama_oldest[field] == p_value
def test_remove_frameworks_with_unknown_parent_keeps_children_with_known_parents():
f = Namespace(
dummy=Namespace(name="dummy", extends="does_exist"),
does_exist=Namespace(name="does_exist"),
)
_remove_frameworks_with_unknown_parent(f)
assert "dummy" in f
assert "does_exist" in f
def test_framework_definition_raises_error_if_no_matching_framework():
res = NS(config=NS(frameworks=NS(definition_file="none")),
_frameworks=NS(present=NS(name="present")))
# binding `framework_definition` method to our resource mock: use pytest-mock instead?
res.framework_definition = Resources.framework_definition.__get__(res)
assert res.framework_definition("present")
with pytest.raises(ValueError, match=r"Incorrect framework `missing`"):
res.framework_definition("missing")
def test_find_all_parents_returns_parent_of_framework_with_single_parent(framework):
frameworks = Namespace(
gama=Namespace(name="gama", version="latest", description="flexible automl"),
gama_old=Namespace(name="gama_20.1.0", version="20.1.0", extends="gama"),
h2o_automl=Namespace(name="h2o", version="latest"),
h2o_automl_old=Namespace(name="h2o_1.2", version="1.2", extends="h2o_automl"),
)
parents = _find_all_parents(frameworks[f"{framework}_old"], frameworks)
assert parents == [frameworks[framework]]
def test_setup_args_set_to_version_if_undefined():
f_my_version = Namespace(version="my_version")
f_my_other_version = Namespace(version="my_other_version")
_add_default_setup_args(f_my_version)
_add_default_setup_args(f_my_other_version)
assert f_my_version.setup_args == ["my_version"]
assert f_my_other_version.setup_args == ["my_other_version"]
def simple_resource():
return Resources(
Namespace(input_dir="my_input",
output_dir="my_output",
user_dir="my_user_dir",
root_dir="my_root_dir",
docker=Namespace(image_defaults=Namespace(
author="author",
image=None,
tag=None,
)),
frameworks=Namespace(root_module="frameworks",
definition_file=[])))
def _add_default_image(framework: Namespace, config: Namespace, props: Optional[List[str]] = None):
if "image" not in framework:
framework.image = copy.deepcopy(config.docker.image_defaults)
else:
framework.image = Namespace.merge(config.docker.image_defaults, framework.image)
if framework.image.tag is None and (not props or 'tag' in props):
framework.image.tag = framework.version.lower()
if framework.image.image is None and (not props or 'image' in props):
framework.image.image = framework.name.lower()
if framework.image.author is None and (not props or 'author' in props):
framework.image.author = ""
def _add_default_image(framework: Namespace, config: Namespace):
if "image" not in framework:
framework.image = copy.deepcopy(config.docker.image_defaults)
else:
framework.image = Namespace.merge(config.docker.image_defaults, framework.image)
if framework.image.tag is None:
framework.image.tag = framework.version.lower()
if framework.image.image is None:
framework.image.image = framework.name.lower()
if framework.image.author is None:
framework.image.author = ""
def _load_and_merge_framework_definitions(frameworks_file: Union[str, List[str]], config) -> Namespace:
""" Load and merge the framework file(s), does not allow duplicate definitions. """
log.info("Loading frameworks definitions from %s.", frameworks_file)
if not isinstance(frameworks_file, list):
frameworks_file = [frameworks_file]
definitions_by_tag = Namespace()
for tag in [default_tag]+config.frameworks.tags:
definitions_by_file = [config_load(_definition_file(file, tag)) for file in frameworks_file]
if not config.frameworks.allow_duplicates:
for d1, d2 in itertools.combinations([set(dir(d)) for d in definitions_by_file], 2):
if d1.intersection(d2) != set():
raise ValueError(f"Duplicate entry '{d1.intersection(d2).pop()}' found.")
definitions_by_tag[tag] = Namespace.merge(*definitions_by_file)
return definitions_by_tag
def load_oml_benchmark(
benchmark: str) -> Tuple[str, Optional[str], List[Namespace]]:
""" Loads benchmark defined by openml suite or task, from openml/s/X or openml/t/Y. """
domain, oml_type, oml_id = benchmark.split('/')
path = None # benchmark file does not exist on disk
name = benchmark # name is later passed as cli input again for containers, it needs to remain parsable
if openml.config.retry_policy != "robot":
log.debug("Setting openml retry_policy from '%s' to 'robot'." %
openml.config.retry_policy)
openml.config.set_retry_policy("robot")
if oml_type == 't':
log.info("Loading openml task %s.", oml_id)
# We first have the retrieve the task because we don't know the dataset id
t = openml.tasks.get_task(oml_id,
download_data=False,
download_qualities=False)
data = openml.datasets.get_dataset(t.dataset_id,
download_data=False,
download_qualities=False)
tasks = [
Namespace(name=str_sanitize(data.name),
description=data.description,
openml_task_id=t.id)
]
elif oml_type == 's':
log.info("Loading openml suite %s.", oml_id)
suite = openml.study.get_suite(oml_id)
# Here we know the (task, dataset) pairs so only download dataset meta-data is sufficient
tasks = []
datasets = openml.datasets.list_datasets(data_id=suite.data,
output_format='dataframe')
datasets.set_index('did', inplace=True)
for tid, did in zip(suite.tasks, suite.data):
tasks.append(
Namespace(
name=str_sanitize(datasets.loc[did]['name']),
description=
f"{openml.config.server.replace('/api/v1/xml', '')}/d/{did}",
openml_task_id=tid))
else:
raise ValueError(f"The oml_type is {oml_type} but must be 's' or 't'")
return name, path, tasks
def test_find_all_parents_returns_frameworks_closest_first_if_two_parents(framework):
frameworks = Namespace(
gama=Namespace(name="gama", version="latest", description="flexible automl"),
gama_old=Namespace(name="gama_20.1.0", version="20.1.0", extends="gama"),
gama_older=Namespace(name="gama_20.0.0", version="20.0.0", extends="gama_old"),
h2o_automl=Namespace(name="h2o", version="latest"),
h2o_automl_old=Namespace(name="h2o_1.2", version="1.2", extends="h2o_automl"),
h2o_automl_older=Namespace(name="h2o_1.1", version="1.1", extends="h2o_automl_old"),
)
parents = _find_all_parents(frameworks[f"{framework}_older"], frameworks)
assert parents == [frameworks[f"{framework}_old"], frameworks[framework]]
def _add_default_params(framework):
if "params" not in framework:
framework.params = dict()
else:
framework.params = Namespace.dict(framework.params)
'--extra',
default=[],
action='append',
help=argparse.SUPPRESS)
args = parser.parse_args()
extras = {
t[0]: t[1] if len(t) > 1 else True
for t in [x.split('=', 1) for x in args.extra]
}
# script_name = os.path.splitext(os.path.basename(__file__))[0]
# log_dir = os.path.join(args.outdir if args.outdir else '.', 'logs')
# os.makedirs(log_dir, exist_ok=True)
# now_str = datetime_iso(date_sep='', time_sep='')
amlb.logger.setup(root_level='DEBUG', console_level='INFO')
root_dir = os.path.dirname(__file__)
config = config_load(os.path.join(root_dir, "resources", "config.yaml"))
config_args = ns.parse(
root_dir=root_dir,
script=os.path.basename(__file__),
run_mode='script',
) + ns.parse(extras)
config_args = ns({k: v for k, v in config_args if v is not None})
amlb.resources.from_configs(config, config_args)
if args.reconnect:
amlb.AWSBenchmark.reconnect(args.instances)
else:
amlb.AWSBenchmark.fetch_results(args.instances)
def run_in_venv(caller_file,
script_file: str,
*args,
input_data: Union[dict, ns],
dataset: Dataset,
config: TaskConfig,
process_results=None,
python_exec=None):
here = dir_of(caller_file)
venv_bin_path = os.path.join(here, 'venv', 'bin')
if python_exec is None: # use local virtual env by default
python_exec = os.path.join(venv_bin_path, 'python -W ignore')
script_path = os.path.join(here, script_file)
cmd = f"{python_exec} {script_path}"
input_data = ns.from_dict(input_data)
with TemporaryDirectory() as tmpdir:
def make_path(k, v, parents=None):
if isinstance(v, np.ndarray):
path = os.path.join(tmpdir, '.'.join(parents + [k, 'npy']))
if vector_keys.match(k):
v = v.reshape(-1, 1)
np.save(path, v, allow_pickle=True)
return k, path
return k, v
ds = ns.walk(input_data, make_path)
dataset.release()
config.result_dir = tmpdir
config.result_file = mktemp(dir=tmpdir)
params = json_dumps(dict(dataset=ds, config=config), style='compact')
with Timer() as proc_timer:
output, err = run_cmd(
cmd,
*args,
_input_str_=params,
_live_output_=True,
_error_level_=logging.DEBUG,
_env_=dict(PATH=os.pathsep.join(
[venv_bin_path, os.environ['PATH']]),
PYTHONPATH=os.pathsep.join([
rconfig().root_dir,
]),
AMLB_PATH=os.path.join(rconfig().root_dir, "amlb")),
)
res = ns(lambda: None)
if os.path.exists(config.result_file):
res = json_load(config.result_file, as_namespace=True)
log.debug("Result from subprocess:\n%s", res)
if not res:
raise NoResultError(f"Process crashed:\n{err}")
if res.error_message is not None:
raise NoResultError(res.error_message)
for name in ['predictions', 'truth', 'probabilities']:
res[name] = np.load(
res[name],
allow_pickle=True) if res[name] is not None else None
if callable(process_results):
res = process_results(res)
if res.output_file:
save_predictions(
dataset=dataset,
output_file=res.output_file,
predictions=res.predictions.reshape(-1)
if res.predictions is not None else None,
truth=res.truth.reshape(-1) if res.truth is not None else None,
probabilities=res.probabilities,
probabilities_labels=res.probabilities_labels,
target_is_encoded=res.target_is_encoded)
return dict(models_count=res.models_count
if res.models_count is not None else 1,
training_duration=res.training_duration if
res.training_duration is not None else proc_timer.duration,
predict_duration=res.predict_duration,
**res.others.__dict__)
def test_version_is_set_to_stable_if_undefined():
framework = Namespace()
_add_default_version(framework)
assert "version" in framework
assert framework.version == "stable"
def test_setup_script_kept_if_defined(simple_resource):
framework = Namespace(module="my_module", setup_script="t.sh")
_add_default_setup_script(framework, simple_resource.config)
assert framework.setup_script == "t.sh"
def test_setup_script_set_to_none_if_undefined(simple_resource):
framework = Namespace()
_add_default_setup_script(framework, simple_resource.config)
assert framework.setup_script is None
def test_setup_args_kept_if_defined():
f_with_extra = Namespace(setup_args="w_extra", version="my_version", repo="my_repo")
_add_default_setup_args(f_with_extra)
assert f_with_extra.setup_args == ["w_extra"]
def test_params_set_to_empty_dict_if_undefined():
framework = Namespace()
_add_default_params(framework)
assert framework.params == dict()
def test_setup_args_also_includes_repo_if_repo_is_defined(version, repo):
f_my_version = Namespace(version=version, repo=repo)
_add_default_setup_args(f_my_version)
assert f_my_version.setup_args == [version, repo]
def test_version_is_kept_if_defined():
framework = Namespace(version="v1.0")
_add_default_version(framework)
assert "version" in framework
assert framework.version == "v1.0"
root_file=os.path.join(log_dir, '{script}.{now}.full.log'.format(script=script_name, now=now_str)),
root_level='INFO', app_level='DEBUG', console_level='INFO', print_to_log=True)
log.info("Running `%s` on `%s` benchmarks in `%s` mode.", args.framework, args.benchmark, args.mode)
log.debug("Script args: %s.", args)
config = config_load(os.path.join(root_dir, "resources", "config.yaml"))
# allowing config override from user_dir: useful to define custom benchmarks and frameworks for example.
config_user = config_load(os.path.join(args.userdir if args.userdir is not None else config.user_dir, "config.yaml"))
# config listing properties set by command line
config_args = ns.parse(
{'results.save': args.keep_scores},
input_dir=args.indir,
output_dir=args.outdir,
user_dir=args.userdir,
root_dir=root_dir,
script=os.path.basename(__file__),
run_mode=args.mode,
parallel_jobs=args.parallel,
sid=sid,
) + ns.parse(extras)
if args.mode != 'local':
config_args + ns.parse({'monitoring.frequency_seconds': 0})
config_args = ns({k: v for k, v in config_args if v is not None})
log.debug("Config args: %s.", config_args)
# merging all configuration files
amlb.resources.from_configs(config, config_user, config_args)
try:
if args.mode == 'local':
bench = amlb.Benchmark(args.framework, args.benchmark, args.constraint)
def test_setup_script_interpolates_module(simple_resource):
framework = Namespace(module="my_module", setup_script="{module}/t.sh")
_add_default_setup_script(framework, simple_resource.config)
assert framework.setup_script == "my_module/t.sh"
