Add type annotation

planemo/commands/cmd_lint.py

@@ -3,7 +3,10 @@
 import click
 
 from planemo import options
-from planemo.cli import command_function
+from planemo.cli import (
+    command_function,
+    PlanemoCliContext,
+)
 from planemo.tool_lint import (
     build_tool_lint_args,
     lint_tools_on_path,
@@ -43,7 +46,7 @@
 # default=False,
 # )
 @command_function
-def cli(ctx, uris, **kwds):
+def cli(ctx: PlanemoCliContext, uris, **kwds):
     """Check for common errors and best practices."""
     lint_args = build_tool_lint_args(ctx, **kwds)
     exit_code = lint_tools_on_path(ctx, uris, lint_args, recursive=kwds["recursive"])

planemo/commands/cmd_shed_lint.py

@@ -7,7 +7,10 @@
     shed,
     shed_lint,
 )
-from planemo.cli import command_function
+from planemo.cli import (
+    command_function,
+    PlanemoCliContext,
+)
 
 
 @click.command("shed_lint")
@@ -41,7 +44,7 @@
 #     default=False,
 # )
 @command_function
-def cli(ctx, paths, **kwds):
+def cli(ctx: PlanemoCliContext, paths, **kwds):
     """Check Tool Shed repository for common issues.
 
     With the ``--tools`` flag, this command lints actual Galaxy tools

planemo/commands/cmd_workflow_lint.py

@@ -3,7 +3,10 @@
 import click
 
 from planemo import options
-from planemo.cli import command_function
+from planemo.cli import (
+    command_function,
+    PlanemoCliContext,
+)
 from planemo.workflow_lint import (
     build_wf_lint_args,
     lint_workflow_artifacts_on_paths,
@@ -23,7 +26,7 @@
     help="Check workflows directory with the standards of iwc",
 )
 @command_function
-def cli(ctx, paths, **kwds):
+def cli(ctx: PlanemoCliContext, paths, **kwds):
     """Check workflows for syntax errors and best practices."""
     # Unlike tools, lets just make this recursive by default.
     lint_args = build_wf_lint_args(ctx, **kwds)

planemo/lint.py

@@ -1,6 +1,11 @@
 """Utilities to help linting various targets."""
 
 import os
+from typing import (
+    Any,
+    Dict,
+    TYPE_CHECKING,
+)
 from urllib.request import urlopen
 
 import requests
@@ -13,8 +18,11 @@
 from planemo.shed import find_urls_for_xml
 from planemo.xml import validation
 
+if TYPE_CHECKING:
+    from planemo.cli import PlanemoCliContext
+
 
-def build_lint_args(ctx, **kwds):
+def build_lint_args(ctx: "PlanemoCliContext", **kwds) -> Dict[str, Any]:
     """Handle common report, error, and skip linting arguments."""
     report_level = kwds.get("report_level", "all")
     fail_level = kwds.get("fail_level", "warn")
@@ -39,7 +47,7 @@ def build_lint_args(ctx, **kwds):
     if len(invalid_skip_types):
         error(f"Unknown linter type(s) {invalid_skip_types} in list of linters to be skipped. Known linters {linters}")
 
-    lint_args = dict(
+    lint_args: Dict[str, Any] = dict(
         level=report_level,
         fail_level=fail_level,
         skip_types=skip_types,

planemo/shed_lint.py

@@ -2,6 +2,7 @@
 
 import os
 import xml.etree.ElementTree as ET
+from typing import TYPE_CHECKING
 
 import yaml
 from galaxy.tool_util.lint import lint_tool_source_with
@@ -31,6 +32,9 @@
 from planemo.tools import yield_tool_sources
 from planemo.xml import XSDS_PATH
 
+if TYPE_CHECKING:
+    from planemo.cli import PlanemoCliContext
+
 TOOL_DEPENDENCIES_XSD = os.path.join(XSDS_PATH, "tool_dependencies.xsd")
 REPO_DEPENDENCIES_XSD = os.path.join(XSDS_PATH, "repository_dependencies.xsd")
 
@@ -50,7 +54,7 @@
 ]
 
 
-def lint_repository(ctx, realized_repository, **kwds):
+def lint_repository(ctx: "PlanemoCliContext", realized_repository, **kwds):
     """Lint a realized shed repository.
 
     See :mod:`planemo.shed` for details on constructing a realized

planemo/tool_lint.py

@@ -1,4 +1,5 @@
 from os.path import basename
+from typing import TYPE_CHECKING
 
 from galaxy.tool_util.lint import lint_tool_source
 
@@ -22,10 +23,13 @@
     yield_tool_sources_on_paths,
 )
 
+if TYPE_CHECKING:
+    from planemo.cli import PlanemoCliContext
+
 LINTING_TOOL_MESSAGE = "Linting tool %s"
 
 
-def build_tool_lint_args(ctx, **kwds):
+def build_tool_lint_args(ctx: "PlanemoCliContext", **kwds):
     lint_args = build_lint_args(ctx, **kwds)
     extra_modules = _lint_extra_modules(**kwds)
     lint_args["extra_modules"] = extra_modules

planemo/workflow_lint.py

@@ -60,9 +60,9 @@ class WorkflowLintContext(LintContext):
     training_topic = None
 
 
-def build_wf_lint_args(ctx, **kwds):
+def build_wf_lint_args(ctx: "PlanemoCliContext", **kwds) -> Dict[str, Any]:
     lint_args = build_lint_args(ctx, **kwds)
-    lint_args["iwc_grade"] = str(kwds.get("iwc", False))
+    lint_args["iwc_grade"] = kwds.get("iwc", False)
     return lint_args