#24 from achalbajpai/week-4

week 4 : implementing proper testing for our application

Author: achalbajpai

src/peptide_calculator.py

@@ -0,0 +1,164 @@
+import pytest
+import sys
+import os
+from unittest.mock import MagicMock, patch
+
+# Add project root to path for imports
+PROJECT_ROOT = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
+sys.path.insert(0, PROJECT_ROOT)
+
+
+def pytest_configure(config):
+    """
+    Configure pytest with custom markers for test categorization.
+    These markers help categorize and run specific sets of tests.
+    """
+    config.addinivalue_line("markers", "unit: Unit tests for individual functions")
+    config.addinivalue_line("markers", "integration: Integration tests")
+    config.addinivalue_line("markers", "validation: Validation function tests")
+    config.addinivalue_line("markers", "parsing: Parsing function tests")
+    config.addinivalue_line("markers", "modification: Modification handling tests")
+    config.addinivalue_line("markers", "calculation: M/Z calculation tests")
+    config.addinivalue_line("markers", "edge_case: Edge case tests")
+
+
+@pytest.fixture
+def mock_pyopenms():
+    """
+    Mocks the pyOpenMS library to enable testing of
+    peptide m/z calculation logic without requiring
+    the actual pyOpenMS dependency to be installed.
+    This fixture provides mock objects for AASequence and ModificationsDB
+    with predefined return values for common methods, simulating
+    the behavior of pyOpenMS for testing purposes.
+    """
+    mock_poms = MagicMock()
+    mock_poms.__version__ = "2.9.1"
+
+    mock_aa_seq = MagicMock()
+    mock_aa_seq.getMZ.return_value = 500.25
+    mock_aa_seq.getMonoWeight.return_value = 999.49
+    mock_aa_seq.getFormula.return_value.toString.return_value = "C43H66N12O12"
+    mock_poms.AASequence.fromString.return_value = mock_aa_seq
+
+    mods = {
+        "Oxidation": {
+            "id": "Oxidation",
+            "full_name": "Oxidation",
+            "mass": 15.994915,
+            "specificity": 0,
+            "origin": "M",
+        },
+        "Carbamidomethyl": {
+            "id": "Carbamidomethyl",
+            "full_name": "Carbamidomethyl",
+            "mass": 57.021464,
+            "specificity": 0,
+            "origin": "C",
+        },
+        "Phospho": {
+            "id": "Phospho",
+            "full_name": "Phosphorylation",
+            "mass": 79.966331,
+            "specificity": 0,
+            "origin": "STY",
+        },
+        "Acetyl": {
+            "id": "Acetyl",
+            "full_name": "Acetylation",
+            "mass": 42.010565,
+            "specificity": 1,
+            "origin": "",
+        },
+        "Methyl": {
+            "id": "Methyl",
+            "full_name": "Methylation",
+            "mass": 14.015650,
+            "specificity": 0,
+            "origin": "KR",
+        },
+        "Deamidated": {
+            "id": "Deamidated",
+            "full_name": "Deamidation",
+            "mass": 0.984016,
+            "specificity": 0,
+            "origin": "NQ",
+        },
+        "Amidated": {
+            "id": "Amidated",
+            "full_name": "Amidation",
+            "mass": -0.984016,
+            "specificity": 2,
+            "origin": "",
+        },
+    }
+
+    def get_mod_side_effect(mod_id):
+        if mod_id in mods:
+            mod_data = mods[mod_id]
+            mock_mod = MagicMock()
+            mock_mod.getId.return_value = mod_data["id"]
+            mock_mod.getFullName.return_value = mod_data["full_name"]
+            mock_mod.getDiffMonoMass.return_value = mod_data["mass"]
+            mock_mod.getTermSpecificity.return_value = mod_data["specificity"]
+            mock_mod.getOrigin.return_value = mod_data["origin"]
+            return mock_mod
+        raise ValueError(f"Mock modification not found: {mod_id}")
+
+    mock_mod_db = MagicMock()
+    mock_mod_db.getModification.side_effect = get_mod_side_effect
+    mock_poms.ModificationsDB.return_value = mock_mod_db
+
+    mock_poms.ResidueModification.ANYWHERE = 0
+    mock_poms.ResidueModification.N_TERM = 1
+    mock_poms.ResidueModification.C_TERM = 2
+
+    with patch.dict(sys.modules, {"pyopenms": mock_poms}):
+        yield mock_poms
+
+
+@pytest.fixture
+def sample_peptides():
+    """
+    Provides a dictionary of sample peptide sequences categorized
+    by their characteristics (e.g., basic, with modifications, with charge, invalid).
+    Useful for testing various peptide parsing and calculation scenarios.
+    """
+    return {
+        "basic": ["PEPTIDE", "SEQUENCE", "PROTEIN", "ANALYSIS"],
+        "with_modifications": [
+            "M[Oxidation]PEPTIDE",
+            "C[Carbamidomethyl]PEPTIDE",
+            "[Acetyl]PEPTIDE",
+            "PEPTIDE[Amidated]",
+        ],
+        "with_charge": ["PEPTIDE/2", "SEQUENCE/3", "PEPTIDE2", "SEQUENCE3"],
+        "mass_deltas": [
+            "M[+15.9949]PEPTIDE",
+            "C[+57.021464]PEPTIDE",
+            "PEPTIDE[+42.0106]",
+        ],
+        "complex": [
+            ".[Acetyl]M[Oxidation]PEPTIDEC[Carbamidomethyl]/2",
+            "EM[+15.9949]EVEES[-79.9663]PEK",
+            "ALSSC[UNIMOD:4]VVDEEQDVER/2",
+        ],
+        "invalid": ["PEPTIDEZ", "PEPTIDE123", "", "   "],
+    }
+
+
+@pytest.fixture
+def expected_modifications():
+    """
+    Provides a dictionary of common peptide modifications and their
+    expected monoisotopic mass deltas.
+    Useful for validating modification parsing and mass calculations.
+    """
+    return {
+        "Oxidation (M)": 15.994915,
+        "Carbamidomethyl (C)": 57.021464,
+        "Phosphorylation (S/T/Y)": 79.966331,
+        "Acetylation (N-term)": 42.010565,
+        "Methylation (K/R)": 14.015650,
+        "Deamidation (N/Q)": 0.984016,
+    }