freshen cwltool/software_requirements.py

Author: mr-c

cwltool/software_requirements.py

@@ -12,7 +12,10 @@
 import string
 from typing import Dict, List, MutableMapping, MutableSequence, Optional, Union, cast
 
-from .builder import Builder, HasReqsHints
+from typing_extensions import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from .builder import Builder, HasReqsHints
 
 try:
     from galaxy.tool_util.deps.requirements import ToolRequirement, ToolRequirements
@@ -34,8 +37,7 @@
 
 
 class DependenciesConfiguration(object):
-    def __init__(self, args):
-        # type: (argparse.Namespace) -> None
+    def __init__(self, args: argparse.Namespace) -> None:
         """Initialize."""
         conf_file = getattr(args, "beta_dependency_resolvers_configuration", None)
         tool_dependency_dir = getattr(args, "beta_dependencies_directory", None)
@@ -55,8 +57,7 @@ def __init__(self, args):
         else:
             self.use_tool_dependencies = False
 
-    def build_job_script(self, builder, command):
-        # type: (Builder, List[str]) -> str
+    def build_job_script(self, builder: "Builder", command: List[str]) -> str:
         ensure_galaxy_lib_available()
         resolution_config_dict = {
             "use": self.use_tool_dependencies,
@@ -87,7 +88,7 @@ def build_job_script(self, builder, command):
         return job_script
 
 
-def get_dependencies(builder: HasReqsHints) -> ToolRequirements:
+def get_dependencies(builder: "HasReqsHints") -> ToolRequirements:
     (software_requirement, _) = builder.get_requirement("SoftwareRequirement")
     dependencies = []  # type: List[ToolRequirement]
     if software_requirement and software_requirement.get("packages"):
@@ -117,8 +118,9 @@ def get_dependencies(builder: HasReqsHints) -> ToolRequirements:
     return ToolRequirements.from_list(dependencies)
 
 
-def get_container_from_software_requirements(use_biocontainers, builder):
-    # type: (bool, HasReqsHints) -> Optional[str]
+def get_container_from_software_requirements(
+    use_biocontainers: bool, builder: "HasReqsHints"
+) -> Optional[str]:
     if use_biocontainers:
         ensure_galaxy_lib_available()
         from galaxy.tool_util.deps.dependencies import AppInfo, ToolInfo
@@ -144,8 +146,7 @@ def get_container_from_software_requirements(use_biocontainers, builder):
     return None
 
 
-def ensure_galaxy_lib_available():
-    # type: () -> None
+def ensure_galaxy_lib_available() -> None:
     if not SOFTWARE_REQUIREMENTS_ENABLED:
         raise Exception(
             "Optional Python library galaxy-lib not available, it is required for this configuration."