From b5142d9ebac74109696cc42462f2488350c05e72 Mon Sep 17 00:00:00 2001
From: Timothy Willard <9395586+TimothyWillard@users.noreply.github.com>
Date: Wed, 11 Dec 2024 11:45:20 -0500
Subject: [PATCH] Upgrade TL key collision from warning to error

---
 .../gempyor_pkg/src/gempyor/shared_cli.py     |  4 +++-
 .../tests/cli/test_flepimop_patch_cli.py      | 23 +++++++------------
 .../shared_cli/test_parse_config_files.py     |  2 +-
 3 files changed, 12 insertions(+), 17 deletions(-)

diff --git a/flepimop/gempyor_pkg/src/gempyor/shared_cli.py b/flepimop/gempyor_pkg/src/gempyor/shared_cli.py
index 4c446d643..f98449e61 100644
--- a/flepimop/gempyor_pkg/src/gempyor/shared_cli.py
+++ b/flepimop/gempyor_pkg/src/gempyor/shared_cli.py
@@ -242,7 +242,9 @@ def _parse_option(param: click.Parameter, value: Any) -> Any:
             tmp = confuse.Configuration("tmp")
             tmp.set_file(config_file)
             if intersect := set(tmp.keys()) & set(cfg_data.keys()):
-                warnings.warn(f"Configuration files contain overlapping keys: {intersect}.")
+                raise ValueError(
+                    f"Configuration files contain overlapping keys: {intersect}."
+                )
             for k in tmp.keys():
                 cfg_data[k] = tmp[k].get()
         cfg.set(cfg_data)
diff --git a/flepimop/gempyor_pkg/tests/cli/test_flepimop_patch_cli.py b/flepimop/gempyor_pkg/tests/cli/test_flepimop_patch_cli.py
index 72d0134b9..053aed7f0 100644
--- a/flepimop/gempyor_pkg/tests/cli/test_flepimop_patch_cli.py
+++ b/flepimop/gempyor_pkg/tests/cli/test_flepimop_patch_cli.py
@@ -9,7 +9,7 @@
 
 
 @pytest.mark.parametrize(
-    ("data_one", "data_two", "expected_parameters"),
+    ("data_one", "data_two"),
     (
         (
             {
@@ -26,7 +26,6 @@
                     }
                 }
             },
-            {"gamma": {"value": 3.4}},
         ),
         (
             {
@@ -44,16 +43,14 @@
                     }
                 }
             },
-            {"gamma": {"value": 3.4}},
         ),
     ),
 )
-def test_patch_seir_parameters_behavior(
+def test_overlapping_sections_value_error(
     tmp_path: Path,
     monkeypatch: pytest.MonkeyPatch,
     data_one: dict[str, Any],
     data_two: dict[str, Any],
-    expected_parameters: dict[str, Any],
 ) -> None:
     # Setup the test
     monkeypatch.chdir(tmp_path)
@@ -64,13 +61,9 @@ def test_patch_seir_parameters_behavior(
 
     # Invoke the command
     runner = CliRunner()
-    with pytest.warns(
-        UserWarning, match="^Configuration files contain overlapping keys: {'seir'}.$"
-    ):
-        result = runner.invoke(patch, [config_one.name, config_two.name])
-    assert result.exit_code == 0
-
-    # Check the output
-    patched_config = yaml.safe_load(result.output)
-    assert "seir" in patched_config
-    assert patched_config["seir"]["parameters"] == expected_parameters
+    result = runner.invoke(patch, [config_one.name, config_two.name])
+    assert result.exit_code == 1
+    assert isinstance(result.exception, ValueError)
+    assert (
+        str(result.exception) == "Configuration files contain overlapping keys: {'seir'}."
+    )
diff --git a/flepimop/gempyor_pkg/tests/shared_cli/test_parse_config_files.py b/flepimop/gempyor_pkg/tests/shared_cli/test_parse_config_files.py
index a64fc38f6..a2aa55c47 100644
--- a/flepimop/gempyor_pkg/tests/shared_cli/test_parse_config_files.py
+++ b/flepimop/gempyor_pkg/tests/shared_cli/test_parse_config_files.py
@@ -158,7 +158,7 @@ def test_multifile_config_collision(
         tmpconfigfile1 = config_file(tmp_path, testdict1, "config1.yaml")
         tmpconfigfile2 = config_file(tmp_path, testdict2, "config2.yaml")
         mockconfig = mock_empty_config()
-        with pytest.warns(UserWarning, match=r"foo"):
+        with pytest.raises(ValueError, match=r"foo"):
             parse_config_files(mockconfig, config_files=[tmpconfigfile1, tmpconfigfile2])
         for k, v in (testdict1 | testdict2).items():
             assert mockconfig[k].get(v) == v