def test_Dependencies_merge():
dep1 = Dependencies(conda=["conda_pkg1", "conda_pkg2"],
pip=["pip_pkg1>=1.1", "pip_pkg2"])
dep2 = Dependencies(conda=["conda_pkg1", "conda_pkg3>=1.1"],
pip=["pip_pkg1>=1.0", "pip_pkg2==3.3"])
dep_merged = dep1.merge(dep2)
assert dep_merged.conda == ['conda_pkg1', 'conda_pkg2', 'conda_pkg3>=1.1']
assert dep_merged.pip == ['pip_pkg1>=1.1,>=1.0', 'pip_pkg2==3.3']
assert dep_merged.conda_channels == ["defaults"]
def merge_deps(models,
dataloaders=None,
source="kipoi",
vep=False,
interpret=False,
gpu=False):
"""Setup the dependencies
"""
special_envs, only_models = split_models_special_envs(models)
deps = Dependencies()
# Treat the handcrafted environments differently
for special_env in special_envs:
from related import from_yaml
logger.info("Loading environment definition: {0}".format(special_env))
# Load and merge the handcrafted deps.
yaml_path = os.path.join(
kipoi.get_source(source).local_path, special_env + ".yaml")
if not os.path.exists(yaml_path):
raise ValueError(
"Environment definition file {0} not found in source {1}".
format(yaml_path, source))
with open(yaml_path, "r", encoding="utf-8") as fh:
special_env_deps = Dependencies.from_env_dict(from_yaml(fh))
deps = deps.merge(special_env_deps)
for model in only_models:
logger.info("Loading model: {0} description".format(model))
parsed_source, parsed_model = parse_source_name(source, model)
sub_models = list_subcomponents(parsed_model, parsed_source, "model")
if len(sub_models) == 0:
raise ValueError("Model {0} not found in source {1}".format(
parsed_model, parsed_source))
if len(sub_models) > 1:
logger.info(
"Found {0} models under the model name: {1}. Merging dependencies for all"
.format(len(sub_models), parsed_model))
for sub_model in sub_models:
model_descr = kipoi.get_model_descr(sub_model, parsed_source)
model_dir = kipoi.get_source(parsed_source).get_model_dir(
sub_model)
deps = deps.merge(model_descr.dependencies)
# handle the dataloader=None case
if dataloaders is None or not dataloaders:
if isinstance(model_descr.default_dataloader,
DataLoaderImport):
# dataloader specified by the import
deps = deps.merge(
model_descr.default_dataloader.dependencies)
if model_descr.default_dataloader.parse_dependencies:
# add dependencies specified in the yaml file
# load from the dataloader description if you can
try:
with cd(model_dir):
dataloader_descr = model_descr.default_dataloader.get(
)
deps = deps.merge(dataloader_descr.dependencies)
except ImportError as e:
# package providing the dataloader is not installed yet
if model_descr.default_dataloader.defined_as.startswith(
"kipoiseq."):
logger.info(
"kipoiseq not installed. Using default kipoiseq dependencies for the dataloader: {}"
.format(model_descr.default_dataloader.
defined_as))
deps = deps.merge(KIPOISEQ_DEPS)
else:
logger.warning(
"Unable to extract dataloader description. "
"Make sure the package containing the dataloader `{}` is installed"
.format(model_descr.default_dataloader.
defined_as))
else:
dataloader = os.path.normpath(
os.path.join(sub_model,
str(model_descr.default_dataloader)))
logger.info("Inferred dataloader name: {0} from".format(
dataloader) + " the model.")
dataloader_descr = kipoi.get_dataloader_descr(
dataloader, parsed_source)
deps = deps.merge(dataloader_descr.dependencies)
if dataloaders is not None or dataloaders:
for dataloader in dataloaders:
parsed_source, parsed_dataloader = parse_source_name(
source, dataloader)
sub_dataloaders = list_subcomponents(parsed_dataloader,
parsed_source, "dataloader")
if len(sub_dataloaders) == 0:
raise ValueError(
"Dataloader: {0} not found in source {1}".format(
parsed_dataloader, parsed_source))
if len(sub_dataloaders) > 1:
logger.info(
"Found {0} dataloaders under the dataloader name: {1}. Merging dependencies for all"
.format(len(sub_dataloaders), parsed_dataloader))
for sub_dataloader in sub_dataloaders:
dataloader_descr = kipoi.get_dataloader_descr(
sub_dataloader, parsed_source)
deps = deps.merge(dataloader_descr.dependencies)
# add Kipoi to the dependencies
deps = KIPOI_DEPS.merge(deps)
if vep:
# add vep dependencies
logger.info("Adding the vep dependencies")
deps = VEP_DEPS.merge(deps)
if interpret:
# add vep dependencies
logger.info("Adding the interpret dependencies")
deps = INTERPRET_DEPS.merge(deps)
if gpu:
logger.info("Using gpu-compatible dependencies")
deps = deps.gpu()
if platform == "darwin":
logger.info("Using osx-type dependencies")
deps = deps.osx()
return deps
def merge_deps(models, dataloaders=None, source="kipoi", vep=False, gpu=False):
"""Setup the dependencies
"""
deps = Dependencies()
for model in models:
logger.info("Loading model: {0} description".format(model))
parsed_source, parsed_model = parse_source_name(source, model)
sub_models = list_subcomponents(parsed_model, parsed_source, "model")
if len(sub_models) == 0:
raise ValueError("Model {0} not found in source {1}".format(
parsed_model, parsed_source))
if len(sub_models) > 1:
logger.info(
"Found {0} models under the model name: {1}. Merging dependencies for all"
.format(len(sub_models), parsed_model))
for sub_model in sub_models:
model_descr = kipoi.get_model_descr(sub_model, parsed_source)
model_dir = kipoi.get_source(parsed_source).get_model_dir(
sub_model)
deps = deps.merge(model_descr.dependencies)
# handle the dataloader=None case
if dataloaders is None or not dataloaders:
if isinstance(model_descr.default_dataloader,
DataLoaderImport):
# dataloader specified by the import
deps = deps.merge(
model_descr.default_dataloader.dependencies)
if model_descr.default_dataloader.parse_dependencies:
# add dependencies specified in the yaml file
# load from the dataloader description if you can
try:
with cd(model_dir):
dataloader_descr = model_descr.default_dataloader.get(
)
deps = deps.merge(dataloader_descr.dependencies)
except ImportError as e:
# package providing the dataloader is not installed yet
if model_descr.default_dataloader.defined_as.startswith(
"kipoiseq."):
logger.info(
"kipoiseq not installed. Using default kipoiseq dependencies for the dataloader: {}"
.format(model_descr.default_dataloader.
defined_as))
deps = deps.merge(KIPOISEQ_DEPS)
else:
logger.warn(
"Unable to extract dataloader description. "
"Make sure the package containing the dataloader `{}` is installed"
.format(model_descr.default_dataloader.
defined_as))
else:
dataloader = os.path.normpath(
os.path.join(sub_model,
str(model_descr.default_dataloader)))
logger.info("Inferred dataloader name: {0} from".format(
dataloader) + " the model.")
dataloader_descr = kipoi.get_dataloader_descr(
dataloader, parsed_source)
deps = deps.merge(dataloader_descr.dependencies)
if dataloaders is not None or dataloaders:
for dataloader in dataloaders:
parsed_source, parsed_dataloader = parse_source_name(
source, dataloader)
sub_dataloaders = list_subcomponents(parsed_dataloader,
parsed_source, "dataloader")
if len(sub_dataloaders) == 0:
raise ValueError(
"Dataloader: {0} not found in source {1}".format(
parsed_dataloader, parsed_source))
if len(sub_dataloaders) > 1:
logger.info(
"Found {0} dataloaders under the dataloader name: {1}. Merging dependencies for all"
.format(len(sub_dataloaders), parsed_dataloader))
for sub_dataloader in sub_dataloaders:
dataloader_descr = kipoi.get_dataloader_descr(
sub_dataloader, parsed_source)
deps = deps.merge(dataloader_descr.dependencies)
# add Kipoi to the dependencies
deps = KIPOI_DEPS.merge(deps)
if vep:
# add vep dependencies
logger.info("Adding the vep dependencies")
deps = VEP_DEPS.merge(deps)
if gpu:
logger.info("Using gpu-compatible dependencies")
deps = deps.gpu()
if platform == "darwin":
logger.info("Using osx-type dependencies")
deps = deps.osx()
return deps
def merge_deps(models, dataloaders=None, source="kipoi", vep=False, gpu=False):
"""Setup the dependencies
"""
deps = Dependencies()
for model in models:
logger.info("Loading model: {0} description".format(model))
parsed_source, parsed_model = parse_source_name(source, model)
sub_models = list_subcomponents(parsed_model, parsed_source, "model")
if len(sub_models) == 0:
raise ValueError("Model {0} not found in source {1}".format(
parsed_model, parsed_source))
if len(sub_models) > 1:
logger.info(
"Found {0} models under the model name: {1}. Merging dependencies for all"
.format(len(sub_models), parsed_model))
for sub_model in sub_models:
model_descr = kipoi.get_model_descr(sub_model, parsed_source)
deps = deps.merge(model_descr.dependencies)
# handle the dataloader=None case
if dataloaders is None or not dataloaders:
dataloader = os.path.normpath(
os.path.join(sub_model, model_descr.default_dataloader))
logger.info(
"Inferred dataloader name: {0} from".format(dataloader) +
" the model.")
dataloader_descr = kipoi.get_dataloader_descr(
dataloader, parsed_source)
deps = deps.merge(dataloader_descr.dependencies)
if dataloaders is not None or dataloaders:
for dataloader in dataloaders:
parsed_source, parsed_dataloader = parse_source_name(
source, dataloader)
sub_dataloaders = list_subcomponents(parsed_dataloader,
parsed_source, "dataloader")
if len(sub_dataloaders) == 0:
raise ValueError(
"Dataloader: {0} not found in source {1}".format(
parsed_dataloader, parsed_source))
if len(sub_dataloaders) > 1:
logger.info(
"Found {0} dataloaders under the dataloader name: {1}. Merging dependencies for all"
.format(len(sub_dataloaders), parsed_dataloader))
for sub_dataloader in sub_dataloaders:
dataloader_descr = kipoi.get_dataloader_descr(
sub_dataloader, parsed_source)
deps = deps.merge(dataloader_descr.dependencies)
# add Kipoi to the dependencies
deps = KIPOI_DEPS.merge(deps)
if vep:
# add vep dependencies
logger.info("Adding the vep dependencies")
deps = VEP_DEPS.merge(deps)
if gpu:
logger.info("Using gpu-compatible dependencies")
deps = deps.gpu()
if platform == "darwin":
logger.info("Using osx-type dependencies")
deps = deps.osx()
return deps