add unit test and update pytest settings

pyproject.toml

@@ -44,3 +44,14 @@ pre-commit = "^4.0.1"
 # --------------------------------------------- #
 # The rest all 3rd party plugins configurations #
 # --------------------------------------------- #
+[tool.pytest.ini_options]
+pythonpath = [
+  ".", "src", "scripts"
+]
+testpaths = ["tests"]
+python_files = ["test*.py"]
+norecursedirs = [".git", "tmp*", "_tmp*", "__pycache__", "*dataset*", "*data_set*"]
+
+[tool.ruff]
+line-length = 120
+select = ["A", "ARG","ASYNC","BLE","C90", "E", "F", "I", "N", "UP032", "W"]

src/pleiades/core/data_manager.py

@@ -65,11 +65,11 @@ def _initialize_cache(self) -> None:
         for category in DataCategory:
             try:
                 category_path = self._get_category_path(category)
-                with resources.files('pleiades.data').joinpath(category_path).iterdir() as path:
-                    self._cached_files[category] = {
-                        item for item in path
-                        if item.suffix in self._VALID_EXTENSIONS[category]
-                    }
+                data_path = resources.files('pleiades.data').joinpath(category_path)
+                self._cached_files[category] = {
+                    item.name for item in data_path.iterdir()
+                    if item.suffix in self._VALID_EXTENSIONS[category]
+                }
             except Exception as e:
                 logger.error(f"Failed to initialize cache for {category}: {str(e)}")
                 self._cached_files[category] = set()
@@ -136,10 +136,10 @@ def list_files(self, category: Optional[DataCategory] = None) -> Dict[DataCatego
         if category is not None:
             if not isinstance(category, DataCategory):
                 raise ValueError(f"Invalid category: {category}")
-            return {category: [p.name for p in sorted(self._cached_files[category])]}
+            return {category: sorted(self._cached_files[category])}
 
         return {
-            cat: [p.name for p in sorted(self._cached_files[cat])]
+            cat: sorted(self._cached_files[cat])
             for cat in DataCategory
         }
 
@@ -227,6 +227,11 @@ def get_mass_data(self, element: str, mass_number: int) -> Optional[IsotopeMassD
                         atomic_mass_fine = line[110:124].replace("*", "nan").replace("#", ".0")
 
                         if "nan" not in [atomic_mass_coarse, atomic_mass_fine]:
+                            # use string concatenation to combine the two parts
+                            # e.g. "238" + "050786.936" 
+                            # -> "238050786.936"
+                            # -> 238050786.936/1e6
+                            # = 238.050786936
                             atomic_mass = float(atomic_mass_coarse + atomic_mass_fine) / 1e6
                         else:
                             atomic_mass = float("nan")
@@ -310,6 +315,17 @@ def get_mat_number(self, isotope: str) -> Optional[int]:
             element, nucleon = isotope.split('-')
 
             with self.get_file_path(DataCategory.ISOTOPES, "neutrons.list").open() as f:
+                # Line matching breakdown:
+                # "496)  92-U -238 IAEA       EVAL-DEC14 IAEA Consortium                  9237"
+                # When line matches pattern
+                # We get groups:
+                #   match.group(1) = "92"  
+                #   match.group(2) = "U"
+                #   match.group(3) = "238"
+                # Check if constructed string matches input:
+                #   match.expand(r"\2-\3") = "U-238"
+                # If match found, get MAT number:
+                # Take last 5 characters of line "  9237" -> 9237
                 pattern = r"\b\s*(\d+)\s*-\s*([A-Za-z]+)\s*-\s*(\d+)([A-Za-z]*)\b"
 
                 for line in f:

tests/unit/pleiades/core/test_data_manager.py

@@ -0,0 +1,71 @@
+#!/usr/bin/env python
+"""Unit tests for the NuclearDataManager class."""
+# tests/unit/pleiades/core/test_data_manager.py
+import pytest
+from pleiades.core.data_manager import (
+    NuclearDataManager, 
+    DataCategory,
+    IsotopeInfo,
+    IsotopeMassData,
+    CrossSectionPoint
+)
+
+@pytest.fixture
+def data_manager():
+    """Create a NuclearDataManager instance using actual package data."""
+    return NuclearDataManager()
+
+def test_list_files(data_manager):
+    """Test listing available files."""
+    files = data_manager.list_files()
+    assert DataCategory.ISOTOPES in files
+    # Test for known files that should exist
+    isotope_files = files[DataCategory.ISOTOPES]
+    assert 'isotopes.info' in isotope_files
+    assert 'mass.mas20' in isotope_files
+    assert 'neutrons.list' in isotope_files
+
+def test_get_isotope_info_u238(data_manager):
+    """Test U-238 isotope information retrieval."""
+    info = data_manager.get_isotope_info('U-238')
+    assert isinstance(info, IsotopeInfo)
+    # Test against known U-238 values
+    assert info.spin == 0.0
+    assert abs(info.abundance - 0.992745*100) < 1e-6
+
+def test_get_mass_data_u238(data_manager):
+    """Test U-238 mass data retrieval."""
+    mass_data = data_manager.get_mass_data('U', 238)
+    assert isinstance(mass_data, IsotopeMassData)
+    # Test against known U-238 values from mass.mas20
+    expected_mass = 238.050786936
+    assert abs(mass_data.atomic_mass - expected_mass) < 1e-6
+
+def test_read_cross_section_data_u238(data_manager):
+    """Test U-238 cross-section data reading."""
+    xs_data = data_manager.read_cross_section_data('u-n.tot', 'U-238')
+    assert len(xs_data) > 0
+    assert all(isinstance(point, CrossSectionPoint) for point in xs_data)
+
+def test_get_mat_number_u238(data_manager):
+    """Test U-238 MAT number retrieval."""
+    mat = data_manager.get_mat_number('U-238')
+    assert mat == 9237  # Verify this is the correct MAT number
+
+# Error cases
+def test_get_isotope_info_nonexistent(data_manager):
+    """Test handling of nonexistent isotope."""
+    assert data_manager.get_isotope_info('Xx-999') is None
+
+def test_get_isotope_info_invalid_format(data_manager):
+    """Test handling of invalid isotope format."""
+    with pytest.raises(ValueError, match="Invalid isotope format"):
+        data_manager.get_isotope_info('U238')
+
+def test_file_not_found(data_manager):
+    """Test handling of nonexistent file."""
+    with pytest.raises(FileNotFoundError):
+        data_manager.get_file_path(DataCategory.ISOTOPES, "nonexistent.info")
+
+if __name__ == '__main__':
+    pytest.main(['-v', __file__])