From e073415109b71d205d0f36d0c4c32f4feca3ccea Mon Sep 17 00:00:00 2001
From: Wout Bittremieux <bittremieux@users.noreply.github.com>
Date: Mon, 11 Dec 2023 11:54:07 +0100
Subject: [PATCH] Check for invalid/missin config entries (#268)

* Refactor config checking

- More efficient checking for unknown and missing config entries (no needless conversions/creations of sets and lists).
- Avoid creating temporary files in root directories during unit testing.
- Update outdated test.

* Add unit test fix
---
 casanovo/config.py              | 25 ++++++++++---------
 tests/unit_tests/test_config.py | 44 ++++++++++++++++-----------------
 2 files changed, 35 insertions(+), 34 deletions(-)

diff --git a/casanovo/config.py b/casanovo/config.py
index c07073d6..c175eef1 100644
--- a/casanovo/config.py
+++ b/casanovo/config.py
@@ -83,17 +83,20 @@ def __init__(self, config_file: Optional[str] = None):
         else:
             with Path(config_file).open() as f_in:
                 self._user_config = yaml.safe_load(f_in)
-                # check for missing entries in config file
-                if len(self._user_config.keys()) < len(self._params.keys()):
-                    keys_set = set(self._params.keys())
-                    users_set = set(self._user_config.keys())
-                    missing = list(keys_set - users_set)
-                    raise KeyError(f"Missing expected entry {missing}")
-                # detect unrecognized config file entries
-                keys = list(self._params.keys())
-                for key, val in self._user_config.items():
-                    if key not in keys:
-                        raise KeyError(f"Unrecognized config file entry {key}")
+                # Check for missing entries in config file.
+                config_missing = self._params.keys() - self._user_config.keys()
+                if len(config_missing) > 0:
+                    raise KeyError(
+                        "Missing expected config option(s): "
+                        f"{', '.join(config_missing)}"
+                    )
+                # Check for unrecognized config file entries.
+                config_unknown = self._user_config.keys() - self._params.keys()
+                if len(config_unknown) > 0:
+                    raise KeyError(
+                        "Unrecognized config option(s): "
+                        f"{', '.join(config_unknown)}"
+                    )
         # Validate:
         for key, val in self._config_types.items():
             self.validate_param(key, val)
diff --git a/tests/unit_tests/test_config.py b/tests/unit_tests/test_config.py
index fd8ed22e..7a0d7a26 100644
--- a/tests/unit_tests/test_config.py
+++ b/tests/unit_tests/test_config.py
@@ -1,8 +1,9 @@
 """Test configuration loading"""
-from casanovo.config import Config
 import pytest
 import yaml
 
+from casanovo.config import Config
+
 
 def test_default():
     """Test that loading the default works"""
@@ -14,27 +15,24 @@ def test_default():
 
 
 def test_override(tmp_path, tiny_config):
-    """Test overriding the default"""
-    yml = tmp_path / "test.yml"
-    with yml.open("w+") as f_out:
-        f_out.write(
-            """random_seed: 42
-top_match: 3
-residues:
-  W: 1
-  O: 2
-  U: 3
-  T: 4
-"""
-        )
-
-    with open(tiny_config, "r") as read_file:
-        contents = yaml.safe_load(read_file)
-        contents["random_seed_"] = 354
-
-    with open("output.yml", "w") as write_file:
-        yaml.safe_dump(contents, write_file)
+    # Test expected config option is missing.
+    filename = str(tmp_path / "config_missing.yml")
+    with open(tiny_config, "r") as f_in, open(filename, "w") as f_out:
+        cfg = yaml.safe_load(f_in)
+        # Remove config option.
+        del cfg["random_seed"]
+        yaml.safe_dump(cfg, f_out)
+
     with pytest.raises(KeyError):
-        config = Config("output.yml")
+        Config(filename)
+
+    # Test invalid config option is present.
+    filename = str(tmp_path / "config_invalid.yml")
+    with open(tiny_config, "r") as f_in, open(filename, "w") as f_out:
+        cfg = yaml.safe_load(f_in)
+        # Insert invalid config option.
+        cfg["random_seed_"] = 354
+        yaml.safe_dump(cfg, f_out)
+
     with pytest.raises(KeyError):
-        config = Config(yml)
+        Config(filename)