Issue error for unrecognized/missing config file entry (#257)

* added unit tests to raise exceptions when unrecognized/missing file entry * fixed lint issue * fix lint issue * fixed failing unit test * lint issue * lint * lint issue --------- Co-authored-by: Isha Gokhale <[email protected]>
Noble-Lab · Nov 9, 2023 · 235420f · 235420f
1 parent 7721962
commit 235420f
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Showing 3 changed files with 81 additions and 12 deletions.
diff --git a/casanovo/config.py b/casanovo/config.py
@@ -83,7 +83,17 @@ 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}")
         # Validate:
         for key, val in self._config_types.items():
             self.validate_param(key, val)

diff --git a/tests/conftest.py b/tests/conftest.py
@@ -188,14 +188,70 @@ def tiny_config(tmp_path):
     """A config file for a tiny model."""
     cfg = {
         "n_head": 2,
-        "dim_feedfoward": 10,
+        "dim_feedforward": 10,
         "n_layers": 1,
         "warmup_iters": 1,
         "max_iters": 1,
         "max_epochs": 20,
         "val_check_interval": 1,
         "model_save_folder_path": str(tmp_path),
         "accelerator": "cpu",
+        "precursor_mass_tol": 5,
+        "isotope_error_range": [0, 1],
+        "min_peptide_len": 6,
+        "predict_batch_size": 1024,
+        "n_beams": 1,
+        "top_match": 1,
+        "devices": None,
+        "random_seed": 454,
+        "n_log": 1,
+        "tb_summarywriter": None,
+        "save_top_k": 5,
+        "n_peaks": 150,
+        "min_mz": 50.0,
+        "max_mz": 2500.0,
+        "min_intensity": 0.01,
+        "remove_precursor_tol": 2.0,
+        "max_charge": 10,
+        "dim_model": 512,
+        "dropout": 0.0,
+        "dim_intensity": None,
+        "max_length": 100,
+        "learning_rate": 5e-4,
+        "weight_decay": 1e-5,
+        "train_batch_size": 32,
+        "num_sanity_val_steps": 0,
+        "train_from_scratch": True,
+        "calculate_precision": False,
+        "residues": {
+            "G": 57.021464,
+            "A": 71.037114,
+            "S": 87.032028,
+            "P": 97.052764,
+            "V": 99.068414,
+            "T": 101.047670,
+            "C+57.021": 160.030649,
+            "L": 113.084064,
+            "I": 113.084064,
+            "N": 114.042927,
+            "D": 115.026943,
+            "Q": 128.058578,
+            "K": 128.094963,
+            "E": 129.042593,
+            "M": 131.040485,
+            "H": 137.058912,
+            "F": 147.068414,
+            "R": 156.101111,
+            "Y": 163.063329,
+            "W": 186.079313,
+            "M+15.995": 147.035400,
+            "N+0.984": 115.026943,
+            "Q+0.984": 129.042594,
+            "+42.011": 42.010565,
+            "+43.006": 43.005814,
+            "-17.027": -17.026549,
+            "+43.006-17.027": 25.980265,
+        },
     }
 
     cfg_file = tmp_path / "config.yml"

diff --git a/tests/unit_tests/test_config.py b/tests/unit_tests/test_config.py
@@ -1,5 +1,7 @@
 """Test configuration loading"""
 from casanovo.config import Config
+import pytest
+import yaml
 
 
 def test_default():
@@ -11,7 +13,7 @@ def test_default():
     assert config.file == "default"
 
 
-def test_override(tmp_path):
+def test_override(tmp_path, tiny_config):
     """Test overriding the default"""
     yml = tmp_path / "test.yml"
     with yml.open("w+") as f_out:
@@ -26,12 +28,13 @@ def test_override(tmp_path):
 """
         )
 
-    config = Config(yml)
-    assert config.random_seed == 42
-    assert config["random_seed"] == 42
-    assert config.accelerator == "auto"
-    assert config.top_match == 3
-    assert len(config.residues) == 4
-    for i, residue in enumerate("WOUT", 1):
-        assert config["residues"][residue] == i
-    assert config.file == str(yml)
+    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)
+    with pytest.raises(KeyError):
+        config = Config("output.yml")
+    with pytest.raises(KeyError):
+        config = Config(yml)