Fix type annotations

Author: nsoranzo

planemo/config.py

@@ -21,7 +21,7 @@
     from planemo.cli import PlanemoCliContext
 
 PLANEMO_CONFIG_ENV_PROP = "PLANEMO_GLOBAL_CONFIG_PATH"
-DEFAULT_CONFIG = {}  # type: Dict[str, Any]
+DEFAULT_CONFIG: Dict[str, Any] = {}
 
 VALUE_UNSET = object()
 
@@ -30,10 +30,10 @@
 
 
 def _default_callback(
-    default: Optional[Union[bool, int, str]],
+    default: Any,
     use_global_config: bool = False,
-    resolve_path: Optional[bool] = False,
-    extra_global_config_vars: List[Union[Any, str]] = [],
+    resolve_path: bool = False,
+    extra_global_config_vars: List[str] = [],
 ) -> Callable:
     def callback(ctx, param, value):
         planemo_ctx = ctx.obj
@@ -66,11 +66,11 @@ def callback(ctx, param, value):
 
 
 def _find_default(
-    ctx: "PlanemoCliContext", param: Option, use_global_config: bool, extra_global_config_vars: List[Union[Any, str]]
-) -> Tuple[object, None]:
+    ctx: "PlanemoCliContext", param: Option, use_global_config: bool, extra_global_config_vars: List[str]
+) -> Union[Tuple[Any, OptionSource], Tuple[object, None]]:
     if use_global_config:
         global_config = ctx.global_config
-        global_config_keys = ["default_%s" % param.name] + extra_global_config_vars
+        global_config_keys = [f"default_{param.name}"] + extra_global_config_vars
         for global_config_key in global_config_keys:
             if global_config_key in global_config:
                 default_value = global_config[global_config_key]
@@ -87,7 +87,7 @@ def planemo_option(*args, **kwargs) -> Callable:
     defaults from ~/.planemo.yml, and tracks how parameters are specified
     using the Planemo Context object.
     """
-    option_type = kwargs.get("type", None)
+    option_type = kwargs.get("type")
     use_global_config = kwargs.pop("use_global_config", False)
     use_env_var = kwargs.pop("use_env_var", False)
     extra_global_config_vars = kwargs.pop("extra_global_config_vars", [])
@@ -101,7 +101,7 @@ def planemo_option(*args, **kwargs) -> Callable:
         outer_callback = kwargs.pop("callback", None)
 
         def callback(ctx, param, value):
-            resolve_path = option_type and getattr(option_type, "resolve_path", False)
+            resolve_path = bool(option_type and getattr(option_type, "resolve_path", False))
             result = _default_callback(
                 default,
                 use_global_config=use_global_config,
@@ -125,7 +125,7 @@ def callback(ctx, param, value):
             if arg.startswith("--"):
                 name = arg[len("--") :]
         assert name
-        kwargs["envvar"] = "PLANEMO_%s" % name.upper()
+        kwargs["envvar"] = f"PLANEMO_{name.upper()}"
 
     option = click.option(*args, **kwargs)
     return option
@@ -138,7 +138,7 @@ def global_config_path(config_path: Optional[str] = None) -> str:
     return config_path
 
 
-def read_global_config(config_path: str) -> Dict[Any, Any]:
+def read_global_config(config_path: Optional[str]) -> Dict[str, Any]:
     config_path = global_config_path(config_path)
     if not os.path.exists(config_path):
         return DEFAULT_CONFIG

planemo/context.py

@@ -10,10 +10,13 @@
 import sys
 import traceback
 from typing import (
+    Any,
     Dict,
+    Optional,
     TYPE_CHECKING,
 )
 from urllib.request import urlopen
+
 from planemo.config import read_global_config
 
 if TYPE_CHECKING:
@@ -62,26 +65,26 @@ class PlanemoContext(PlanemoContextInterface):
     def __init__(self) -> None:
         """Construct a Context object using execution environment."""
         self.home = os.getcwd()
-        self._global_config = None
+        self._global_config: Optional[Dict] = None
         # Will be set by planemo CLI driver
         self.verbose = False
-        self.planemo_config = None
+        self.planemo_config: Optional[str] = None
         self.planemo_directory = None
-        self.option_source = {}
+        self.option_source: Dict[str, "OptionSource"] = {}
 
     def set_option_source(self, param_name: str, option_source: "OptionSource", force: bool = False) -> None:
         """Specify how an option was set."""
         if not force:
-            assert param_name not in self.option_source, "No option source for [%s]" % param_name
+            assert param_name not in self.option_source, f"Option source for [{param_name}] already set"
         self.option_source[param_name] = option_source
 
     def get_option_source(self, param_name: str) -> "OptionSource":
         """Return OptionSource value indicating how the option was set."""
-        assert param_name in self.option_source, "No option source for [%s]" % param_name
+        assert param_name in self.option_source, f"No option source for [{param_name}]"
         return self.option_source[param_name]
 
     @property
-    def global_config(self) -> Dict[str, Dict[str, str]]:
+    def global_config(self) -> Dict[str, Any]:
         """Read Planemo's global configuration.
 
         As defined most simply by ~/.planemo.yml.
@@ -131,7 +134,7 @@ def cache_download(self, url, destination):
             with urlopen(url) as fh:
                 content = fh.read()
             if len(content) == 0:
-                raise Exception("Failed to download [%s]." % url)
+                raise Exception(f"Failed to download [{url}].")
             with open(cache_destination, "wb") as f:
                 f.write(content)
 
@@ -141,9 +144,7 @@ def _ensure_directory(self, path: str, name: str) -> str:
         if not os.path.exists(path):
             os.makedirs(path)
         if not os.path.isdir(path):
-            template = "Planemo %s directory [%s] unavailable."
-            message = template % (name, path)
-            raise Exception(message)
+            raise Exception(f"Planemo {name} directory [{path}] unavailable.")
         return path
 
     def _log_message(self, message):

planemo/database/factory.py

@@ -1,6 +1,7 @@
 """Create a DatabaseSource from supplied planemo configuration."""
 from galaxy.util.commands import which
 
+from .interface import DatabaseSource
 from .postgres import LocalPostgresDatabaseSource
 from .postgres_docker import DockerPostgresDatabaseSource