def train():
options = Options("train_commandline_args.txt")
with DescriptionLoader.context("genoml"):
if options.model_file:
error_on_exists(options.model_file)
elif options.model_dir:
error_on_exists(options.model_dir)
dependencies = check_dependencies()
tmp_dir = tempfile.mkdtemp()
options._options['--prune-prefix'] = os.path.join(tmp_dir, "model")
options._options['--best-model-name'] = "best_model"
if options.verbose > 0:
print(tmp_dir)
print(options._options)
processes = [DataPruneStep(), ModelTrainStep()]
if not options.no_tune:
processes += [ModelTuneStep()]
for process in processes:
process.set_environment(options, dependencies)
process.process()
model_name = os.path.join(tmp_dir, "model.genoml_model")
copy_originals(options, tmp_dir)
if options.model_file:
shutil.make_archive(model_name, 'bztar', os.path.dirname(options.prefix))
shutil.move(model_name + ".tar.bz2", options.model_file)
shutil.rmtree(tmp_dir, True)
elif options.model_dir:
shutil.move(tmp_dir, options.model_dir)
def inference():
options = Options("inference_commandline_args.txt")
with DescriptionLoader.context("genoml"):
error_on_exists(options.valid_dir)
dependencies = check_dependencies()
os.makedirs(options.valid_dir)
tmp_dir = tempfile.mkdtemp()
print(tmp_dir)
if options.model_file:
shutil.unpack_archive(options.model_file, tmp_dir, format="bztar")
elif options.model_dir:
shutil.rmtree(tmp_dir)
shutil.copytree(options.model_dir, tmp_dir)
load_originals(options, tmp_dir)
options._options['--prune-prefix'] = os.path.join(tmp_dir, "model")
if options.verbose > 0:
print(tmp_dir)
print(options._options)
for process in [ModelValidateStep()]:
process.set_environment(options, dependencies)
process.process()
for file in glob.glob(tmp_dir + "/model_validation*"):
shutil.copy(file, options.valid_dir)
shutil.rmtree(tmp_dir, True)
def cli():
options = Options("commandline_args.txt")
with DescriptionLoader.context("genoml"):
dependencies = check_dependencies()
if options.is_data_prune():
process = DataPruneStep()
elif options.is_model_train():
process = ModelTrainStep()
elif options.is_model_tune():
process = ModelTuneStep()
elif options.is_model_validate():
process = ModelValidateStep()
else:
raise Exception("ISSUE: received unrecognizable option.")
process.set_environment(options, dependencies)
process.process()