From 1298061466357d7f8ef7546df90928a4547728cd Mon Sep 17 00:00:00 2001
From: Peter Van Dyken <pvandyk2@uwo.ca>
Date: Mon, 29 Apr 2024 15:46:28 -0400
Subject: [PATCH] Add hook to update and read argv before parsing

---
 snakebids/bidsapp/hookspecs.py  |  5 ++++
 snakebids/bidsapp/run.py        |  8 +++++-
 snakebids/tests/test_bidsapp.py | 51 +++++++++++++++++++++++++--------
 3 files changed, 51 insertions(+), 13 deletions(-)

diff --git a/snakebids/bidsapp/hookspecs.py b/snakebids/bidsapp/hookspecs.py
index b1b289ed..6b83242a 100644
--- a/snakebids/bidsapp/hookspecs.py
+++ b/snakebids/bidsapp/hookspecs.py
@@ -46,6 +46,11 @@ def add_cli_arguments(
     """
 
 
+@hookspec(firstresult=True)
+def get_argv(argv: list[str], config: dict[str, Any]) -> list[str]:  # type: ignore
+    """Set or modify the CLI parameters that will be parsed by the parser."""
+
+
 @hookspec
 def handle_unknown_args(args: list[str], config: dict[str, Any]):
     """If ``parse_known_args`` enabled, handle unknown arguments.
diff --git a/snakebids/bidsapp/run.py b/snakebids/bidsapp/run.py
index 894da89f..44841ad6 100644
--- a/snakebids/bidsapp/run.py
+++ b/snakebids/bidsapp/run.py
@@ -182,7 +182,13 @@ def parse_args(self, args: list[str] | None = None):
         """Run all plugins and parse arguments."""
         if not self._processed:
             self.build_parser()
-            namespace, unknown = self.parser.parse_known_args(args=args)
+            args = sys.argv[1:] if args is None else args
+            argv: list[str] | None = self.pm.hook.get_argv(
+                argv=args, config=self.config
+            )
+            namespace, unknown = self.parser.parse_known_args(
+                args=args if argv is None else argv
+            )
             self.pm.hook.handle_unknown_args(args=unknown, config=self.config)
             self.pm.hook.update_cli_namespace(
                 namespace=namespace.__dict__, config=self.config
diff --git a/snakebids/tests/test_bidsapp.py b/snakebids/tests/test_bidsapp.py
index 6e2d0e1c..321ead2c 100644
--- a/snakebids/tests/test_bidsapp.py
+++ b/snakebids/tests/test_bidsapp.py
@@ -5,6 +5,7 @@
 from typing import Any
 
 import pytest
+from pytest_mock import MockerFixture
 
 from snakebids import bidsapp, plugins
 from snakebids.bidsapp.args import ArgumentGroups
@@ -36,19 +37,28 @@ def add_cli_arguments(
         parser.add_argument("arg_one")
         parser.add_argument("--arg-two")
 
+    @bidsapp.hookimpl
+    def get_argv(self, argv: list[str], config: dict[str, Any]):
+        self.hooks_run += 1
+        assert config["added_args"]
+        config["provided_args"] = argv
+        assert argv == ["default"]
+        return ["known", "--arg-two", "known", "unknown"]
+
     @bidsapp.hookimpl
     def handle_unknown_args(self, args: list[str], config: dict[str, Any]):
         self.hooks_run += 1
         assert args == ["unknown"]
-        assert len(config) == 2
+        assert len(config) == 3
         assert config["initialized"]
         assert config["added_args"]
+        assert config["provided_args"] == ["default"]
         config["unknown_args"] = args
 
     @bidsapp.hookimpl
     def update_cli_namespace(self, namespace: dict[str, Any], config: dict[str, Any]):
         self.hooks_run += 1
-        assert len(config) == 3
+        assert len(config) == 4
         assert config["initialized"]
         assert config["added_args"]
         assert config["unknown_args"] == ["unknown"]
@@ -60,7 +70,7 @@ def update_cli_namespace(self, namespace: dict[str, Any], config: dict[str, Any]
     @bidsapp.hookimpl
     def finalize_config(self, config: dict[str, Any]):
         self.hooks_run += 1
-        assert len(config) == 5
+        assert len(config) == 6
         assert config["initialized"]
         assert config["added_args"]
         assert config["unknown_args"] == ["unknown"]
@@ -71,7 +81,7 @@ def finalize_config(self, config: dict[str, Any]):
     @bidsapp.hookimpl
     def run(self, config: dict[str, Any]):
         self.hooks_run += 1
-        assert len(config) == 6
+        assert len(config) == 7
         assert config["initialized"]
         assert config["added_args"]
         assert config["unknown_args"] == ["unknown"]
@@ -89,17 +99,34 @@ def test_build_parser(self):
 
     def test_parse_args(self):
         app = bidsapp.app(plugins=[self])
-        app.parse_args(args=["known", "--arg-two", "known", "unknown"])
-        assert self.hooks_run == 5
-        app.parse_args(args=["known", "--arg-two", "known", "unknown"])
-        assert self.hooks_run == 5
+        app.parse_args(args=["default"])
+        assert self.hooks_run == 6
+        app.parse_args(args=["default"])
+        assert self.hooks_run == 6
 
     def test_run(self):
         app = bidsapp.app(plugins=[self])
-        app.run(args=["known", "--arg-two", "known", "unknown"])
-        assert self.hooks_run == 6
-        app.run(args=["known", "--arg-two", "known", "unknown"])
-        assert self.hooks_run == 6
+        app.run(args=["default"])
+        assert self.hooks_run == 7
+        app.run(args=["default"])
+        assert self.hooks_run == 7
+
+
+class TestNoArgvHook:
+    @bidsapp.hookimpl
+    def handle_unknown_args(self, args: list[str]):
+        assert args == ["mocked", "args"]
+
+    def test_with_mocked_args(self, mocker: MockerFixture):
+        from snakebids.bidsapp.run import sys
+
+        mocker.patch.object(sys, "argv", ["program", "mocked", "args"])
+        app = bidsapp.app(plugins=[self])
+        app.parse_args()
+
+    def test_with_provided_args(self):
+        app = bidsapp.app(plugins=[self])
+        app.parse_args(args=["mocked", "args"])
 
 
 class TestDependencies: