Register subparsers recursively

Keeps consistent with Nextstrain CLI.
nextstrain · Sep 24, 2024 · 21160bc · 21160bc
1 parent bf05db8
commit 21160bc
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Showing 16 changed files with 27 additions and 52 deletions.
diff --git a/augur/__init__.py b/augur/__init__.py
@@ -14,7 +14,7 @@
 from .debug import DEBUGGING
 from .errors import AugurError
 from .io.print import print_err
-from .argparse_ import add_command_subparsers, add_default_command
+from .argparse_ import register_commands, add_default_command
 
 DEFAULT_AUGUR_RECURSION_LIMIT = 10000
 sys.setrecursionlimit(int(os.environ.get("AUGUR_RECURSION_LIMIT") or DEFAULT_AUGUR_RECURSION_LIMIT))
@@ -58,8 +58,7 @@ def make_parser():
     add_default_command(parser)
     add_version_alias(parser)
 
-    subparsers = parser.add_subparsers()
-    add_command_subparsers(subparsers, COMMANDS)
+    register_commands(parser, COMMANDS)
 
     return parser
 

diff --git a/augur/argparse_.py b/augur/argparse_.py
@@ -1,6 +1,7 @@
 """
 Custom helpers for the argparse standard library.
 """
+import argparse
 from argparse import Action, ArgumentDefaultsHelpFormatter
 
 
@@ -30,16 +31,14 @@ def run(args):
     parser.set_defaults(__command__ = default_command)
 
 
-def add_command_subparsers(subparsers, commands, command_attribute='__command__'):
+def register_commands(parser: argparse.ArgumentParser, commands, command_attribute='__command__'):
     """
     Add subparsers for each command module.
 
     Parameters
     ----------
-    subparsers: argparse._SubParsersAction
-        The special subparsers action object created by the parent parser
-        via `parser.add_subparsers()`.
-
+    parser
+        ArgumentParser object.
     commands: list[types.ModuleType]
         A list of modules that are commands that require their own subparser.
         Each module is required to have a `register_parser` function to add its own
@@ -49,6 +48,8 @@ def add_command_subparsers(subparsers, commands, command_attribute='__command__'
         Optional attribute name for the commands. The default is `__command__`,
         which allows top level augur to run commands directly via `args.__command__.run()`.
     """
+    subparsers = parser.add_subparsers()
+
     for command in commands:
         # Allow each command to register its own subparser
         subparser = command.register_parser(subparsers)
@@ -68,6 +69,10 @@ def add_command_subparsers(subparsers, commands, command_attribute='__command__'
         if not getattr(command, "run", None):
             add_default_command(subparser)
 
+        # Recursively register any subcommands
+        if getattr(subparser, "subcommands", None):
+            register_commands(subparser, subparser.subcommands)
+
 
 class HideAsFalseAction(Action):
     """

diff --git a/augur/curate/__init__.py b/augur/curate/__init__.py
@@ -7,7 +7,7 @@
 from textwrap import dedent
 from typing import Iterable, Set
 
-from augur.argparse_ import ExtendOverwriteDefault, add_command_subparsers
+from augur.argparse_ import ExtendOverwriteDefault
 from augur.errors import AugurError
 from augur.io.json import dump_ndjson, load_ndjson
 from augur.io.metadata import DEFAULT_DELIMITERS, InvalidDelimiter, read_table_to_dict, read_metadata_with_sequences, write_records_to_tsv
@@ -103,21 +103,9 @@ def create_shared_parser():
 
 
 def register_parser(parent_subparsers):
-    shared_parser = create_shared_parser()
     parser = parent_subparsers.add_parser("curate", help=__doc__)
 
-    # Add print_help so we can run it when no subcommands are called
-    parser.set_defaults(print_help = parser.print_help)
-
-    # Add subparsers for subcommands
-    subparsers = parser.add_subparsers(dest="subcommand", required=False)
-    # Add the shared_parser to make it available for subcommands
-    # to include in their own parser
-    subparsers.shared_parser = shared_parser
-    # Using a subcommand attribute so subcommands are not directly
-    # run by top level Augur. Process I/O in `curate`` so individual
-    # subcommands do not have to worry about it.
-    add_command_subparsers(subparsers, SUBCOMMANDS, SUBCOMMAND_ATTRIBUTE)
+    parser.subcommands = SUBCOMMANDS
 
     return parser
 

diff --git a/augur/curate/abbreviate_authors.py b/augur/curate/abbreviate_authors.py
@@ -52,7 +52,6 @@ def register_parser(
 ) -> argparse._SubParsersAction:
     parser = parent_subparsers.add_parser(
         "abbreviate-authors",
-        parents=[parent_subparsers.shared_parser],  # type: ignore
         help=first_line(__doc__),
     )
 

diff --git a/augur/curate/apply_geolocation_rules.py b/augur/curate/apply_geolocation_rules.py
@@ -188,7 +188,6 @@ def transform_geolocations(geolocation_rules, geolocation):
 
 def register_parser(parent_subparsers):
     parser = parent_subparsers.add_parser("apply-geolocation-rules",
-        parents=[parent_subparsers.shared_parser],
         help=first_line(__doc__))
 
     parser.add_argument("--region-field", default="region",

diff --git a/augur/curate/apply_record_annotations.py b/augur/curate/apply_record_annotations.py
@@ -11,7 +11,6 @@
 
 def register_parser(parent_subparsers):
     parser = parent_subparsers.add_parser("apply-record-annotations",
-        parents=[parent_subparsers.shared_parser],
         help=first_line(__doc__))
 
     parser.add_argument("--annotations", metavar="TSV", required=True,

diff --git a/augur/curate/format_dates.py b/augur/curate/format_dates.py
@@ -24,7 +24,6 @@
 
 def register_parser(parent_subparsers):
     parser = parent_subparsers.add_parser("format-dates",
-        parents=[parent_subparsers.shared_parser],
         help=__doc__)
 
     required = parser.add_argument_group(title="REQUIRED")

diff --git a/augur/curate/normalize_strings.py b/augur/curate/normalize_strings.py
@@ -11,7 +11,6 @@
 
 def register_parser(parent_subparsers):
     parser = parent_subparsers.add_parser("normalize-strings",
-        parents=[parent_subparsers.shared_parser],
         help=first_line(__doc__))
 
     optional = parser.add_argument_group(title="OPTIONAL")

diff --git a/augur/curate/parse_genbank_location.py b/augur/curate/parse_genbank_location.py
@@ -50,7 +50,6 @@ def register_parser(
 ) -> argparse._SubParsersAction:
     parser = parent_subparsers.add_parser(
         "parse-genbank-location",
-        parents=[parent_subparsers.shared_parser],  # type: ignore
         help=first_line(__doc__),
     )
 

diff --git a/augur/curate/passthru.py b/augur/curate/passthru.py
@@ -6,7 +6,6 @@
 
 def register_parser(parent_subparsers):
     return parent_subparsers.add_parser("passthru",
-        parents=[parent_subparsers.shared_parser],
         help=__doc__)
 
 

diff --git a/augur/curate/rename.py b/augur/curate/rename.py
@@ -9,7 +9,6 @@
 
 def register_parser(parent_subparsers):
     parser = parent_subparsers.add_parser("rename",
-    parents = [parent_subparsers.shared_parser],
     help = __doc__)
 
     required = parser.add_argument_group(title="REQUIRED")

diff --git a/augur/curate/titlecase.py b/augur/curate/titlecase.py
@@ -10,7 +10,6 @@
 
 def register_parser(parent_subparsers):
     parser = parent_subparsers.add_parser("titlecase",
-    parents = [parent_subparsers.shared_parser],
     help = __doc__)
 
     required = parser.add_argument_group(title="REQUIRED")

diff --git a/augur/curate/transform_strain_name.py b/augur/curate/transform_strain_name.py
@@ -42,7 +42,6 @@ def register_parser(
 ) -> argparse._SubParsersAction:
     parser = parent_subparsers.add_parser(
         "transform-strain-name",
-        parents=[parent_subparsers.shared_parser],  # type: ignore
         help=first_line(__doc__),
     )
 

diff --git a/augur/export.py b/augur/export.py
@@ -1,7 +1,8 @@
 """
 Export JSON files suitable for visualization with auspice.
+
+Augur export now needs you to define the JSON version you want, e.g. `augur export v2`.
 """
-from .argparse_ import add_command_subparsers
 from . import export_v1, export_v2
 
 SUBCOMMANDS = [
@@ -12,10 +13,7 @@
 
 def register_parser(parent_subparsers):
     parser = parent_subparsers.add_parser("export", help=__doc__)
-    # Add subparsers for subcommands
-    metavar_msg ="Augur export now needs you to define the JSON version " + \
-                 "you want, e.g. `augur export v2`."
-    subparsers = parser.add_subparsers(title="JSON SCHEMA",
-                                       metavar=metavar_msg)
-    add_command_subparsers(subparsers, SUBCOMMANDS)
+
+    parser.subcommands = SUBCOMMANDS
+
     return parser
diff --git a/augur/import_/__init__.py b/augur/import_/__init__.py
@@ -1,18 +1,15 @@
 """
 Import analyses into augur pipeline from other systems
 """
-from augur.argparse_ import add_command_subparsers
-from augur.utils import first_line
 from . import beast
 
 SUBCOMMANDS = [
     beast,
 ]
 
 def register_parser(parent_subparsers):
-    parser = parent_subparsers.add_parser("import", help=first_line(__doc__))
-    metavar_msg = "Import analyses into augur pipeline from other systems"
-    subparsers = parser.add_subparsers(title="TYPE",
-                                       metavar=metavar_msg)
-    add_command_subparsers(subparsers, SUBCOMMANDS)
+    parser = parent_subparsers.add_parser("import", help=__doc__)
+
+    parser.subcommands = SUBCOMMANDS
+
     return parser
diff --git a/augur/measurements/__init__.py b/augur/measurements/__init__.py
@@ -1,8 +1,6 @@
 """
 Create JSON files suitable for visualization within the measurements panel of Auspice.
 """
-from augur.argparse_ import add_command_subparsers
-from augur.utils import first_line
 from . import export, concat
 
 SUBCOMMANDS = [
@@ -12,8 +10,8 @@
 
 
 def register_parser(parent_subparsers):
-    parser = parent_subparsers.add_parser("measurements", help=first_line(__doc__))
-    # Add subparsers for subcommands
-    subparsers = parser.add_subparsers(dest='subcommand')
-    add_command_subparsers(subparsers, SUBCOMMANDS)
+    parser = parent_subparsers.add_parser("measurements", help=__doc__)
+
+    parser.subcommands = SUBCOMMANDS
+
     return parser