Add linting test to ensure use of ExtendOverwriteDefault for nargs=*/+

LICENSE.nextstrain-cli

@@ -1,8 +1,11 @@
-This license applies to the original copy of resource functions from the
-Nextstrain CLI project into this project, incorporated in
-"augur/data/__init__.py". Any subsequent modifications to this project's copy of
-those functions are licensed under the license of this project, not of
-Nextstrain CLI.
+This license applies to the original copy of functions from the Nextstrain CLI
+project into this project, namely
+
+- resource functions incorporated as "augur/data/__init__.py"
+- walk_commands() function incorporated into "augur/argparse_.py"
+
+Any subsequent modifications to this project's copy of these functions are
+licensed under the license of this project, not of Nextstrain CLI.
 
 MIT License
 

augur/argparse_.py

@@ -1,8 +1,9 @@
 """
 Custom helpers for the argparse standard library.
 """
-from argparse import Action, ArgumentParser, _ArgumentGroup, HelpFormatter, SUPPRESS, OPTIONAL, ZERO_OR_MORE, _ExtendAction
-from typing import Union
+from argparse import Action, ArgumentParser, _ArgumentGroup, HelpFormatter, SUPPRESS, OPTIONAL, ZERO_OR_MORE, _ExtendAction, _SubParsersAction
+from itertools import chain
+from typing import Iterable, Optional, Tuple, Union
 from .types import ValidationMode
 
 
@@ -148,3 +149,28 @@ def add_validation_arguments(parser: Union[ArgumentParser, _ArgumentGroup]):
         action="store_const",
         const=ValidationMode.SKIP,
         help="Skip validation of input/output files, equivalent to --validation-mode=skip. Use at your own risk!")
+
+
+# Originally copied from nextstrain/cli/argparse.py in the Nextstrain CLI project¹.
+#
+# ¹ <https://github.com/nextstrain/cli/blob/4a00d7100eff811eab6df34db73c7f6d4196e22b/nextstrain/cli/argparse.py#L252-L271>
+def walk_commands(parser: ArgumentParser, command: Optional[Tuple[str, ...]] = None) -> Iterable[Tuple[Tuple[str, ...], ArgumentParser]]:
+    if command is None:
+        command = (parser.prog,)
+
+    yield command, parser
+
+    subparsers = chain.from_iterable(
+        action.choices.items()
+            for action in parser._actions
+             if isinstance(action, _SubParsersAction))
+
+    visited = set()
+
+    for subname, subparser in subparsers:
+        if subparser in visited:
+            continue
+
+        visited.add(subparser)
+
+        yield from walk_commands(subparser, (*command, subname))

tests/test_argparse_linting.py

@@ -0,0 +1,26 @@
+# Originally based on tests/help.py from the Nextstrain CLI project.¹
+#
+# ¹ <https://github.com/nextstrain/cli/blob/4a00d7100eff811eab6df34db73c7f6d4196e22b/tests/help.py>
+import pytest
+from argparse import ArgumentParser
+from typing import List, Tuple
+
+from augur import make_parser
+from augur.argparse_ import walk_commands, ExtendOverwriteDefault
+
+
+# Walking commands is slow, so do it only once and use it for all tests in this
+# file (though currently n=1).
+commands = list(walk_commands(make_parser()))
+
+
+# Ensure we always use ExtendOverwriteDefault for options that take a variable
+# number of arguments.  See <https://github.com/nextstrain/augur/pull/1709>.
+@pytest.mark.parametrize("action", [
+    pytest.param(action, id = " ".join(command) + " " + "/".join(action.option_strings))
+        for command, parser in commands
+        for action in parser._actions
+         if action.nargs in {"+", "*"}
+])
+def test_ExtendOverwriteDefault(action):
+    assert isinstance(action, ExtendOverwriteDefault)