Fix broken tests

.github/workflows/pytest.yaml

@@ -22,32 +22,18 @@ jobs:
 
     steps:
       - uses: "actions/checkout@v4"
+        # Whether to download Git-LFS files
+        with:
+          lfs: true
 
       - name: Setup python for test ${{ matrix.py }}
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.py }}
 
-      - name: Install system dependencies for PyTables (Linux/macOS)
-        run: |
-          python -m pip install --upgrade pip wheel
-          pip install numpy==1.26.4 
-          if [[ "$RUNNER_OS" == "Linux" ]]; then
-            sudo apt-get update
-            sudo apt-get install -y libhdf5-dev libblosc-dev
-          elif [[ "$RUNNER_OS" == "macOS" ]]; then
-            export HOMEBREW_NO_INSTALL_CLEANUP=1
-            brew update
-            brew install hdf5 c-blosc
-            export CPATH="$(brew --prefix hdf5)/include:$(brew --prefix c-blosc)/include:$CPATH"
-            export LIBRARY_PATH="$(brew --prefix hdf5)/lib:$(brew --prefix c-blosc)/lib:$LIBRARY_PATH"
-            export HDF5_DIR="$(brew --prefix hdf5)"
-          fi
-
-
       - name: Install development version
         run: |
-          pip install -v .
+          pip install -e .
 
       - name: Install extra test dependencies
         run: |
@@ -77,5 +63,3 @@ jobs:
           click-to-expand: true
           report-title: 'Dev Test Report'
           pytest-args: '-m dev'
-
-

atomdb/migration/periodic/elements_data.py

@@ -5,6 +5,7 @@
 import warnings
 from atomdb.utils import CONVERTOR_TYPES
 
+
 # Suppresses NaturalNameWarning warnings from PyTables.
 warnings.filterwarnings('ignore', category=pt.NaturalNameWarning)
 
@@ -25,7 +26,7 @@
 
     {
         'basic_property': 'symbol',
-        'table_name': 'symbol',
+        'table_name': 'elem',
         'description': 'Atom Symbol',
         'type': 'string',
     },

atomdb/species.py

@@ -38,18 +38,19 @@
 from numbers import Integral
 
 elements_hdf5_file = files("atomdb.data").joinpath("elements_data.h5")
-
-PROPERTY_NAME_MAP = {
-    "atmass": "atmass",
-    "cov_radius": "cov_radius",
-    "vdw_radius": "vdw_radius",
-    "at_radius": "at_radius",
-    "polarizability": "polarizability",
-    "dispersion_c6": "dispersion_c6",
-    "elem": "symbol",
-    "atnum": "atnum",
-    "name": "name",
-}
+ELEMENTS_H5FILE = pt.open_file(elements_hdf5_file, mode="r")
+
+PROPERTY_NAME_MAP = [
+    "atmass",
+    "cov_radius",
+    "vdw_radius",
+    "at_radius",
+    "polarizability",
+    "dispersion_c6",
+    "elem",
+    "atnum",
+    "name"
+]
 
 __all__ = [
     "Species",
@@ -116,6 +117,42 @@ def default_matrix():
 #     return wrapper
 
 
+# def scalar(method):
+#     r"""Expose a SpeciesData field."""
+#     name = method.__name__
+#
+#     @property
+#     def wrapper(self):
+#         print("hi")
+#
+#         # Map the name of the method in the SpeciesData class to the name in the Elements class
+#         # This dict can be removed if the Elements csv file uses the same names as the SpeciesData class.
+#         namemap = {
+#             "cov_radius": "cov_radius",
+#             "vdw_radius": "vdw_radius",
+#             "at_radius": "at_radius",
+#             "polarizability": "pold",
+#             "dispersion_c6": "c6",
+#             "atmass": "mass",
+#         }
+#
+#         if name == "atmass":
+#             print(f"inside atmass {getattr(Element(self._data.elem), namemap[name])}")
+#             return getattr(Element(self._data.elem), namemap[name])
+#         if name in namemap:
+#             # Only return Element property if neutral, otherwise None
+#             charge = self._data.atnum - self._data.nelec
+#             print(f"charge {charge}")
+#             print(f"inside the other {getattr(Element(self._data.elem), namemap[name])}")
+#             return getattr(Element(self._data.elem), namemap[name]) if charge == 0 else None
+#
+#         return getattr(self._data, name)
+#
+#     # conserve the docstring of the method
+#     wrapper.__doc__ = method.__doc__
+#     return wrapper
+
+
 def scalar(method):
     r"""Expose a SpeciesData field."""
     name = method.__name__
@@ -128,39 +165,37 @@ def wrapper(self):
 
         # calculate charge then if charge is not zero (ions) --> return none
         charge = self._data.atnum - self._data.nelec
-        if charge != 0:
+        if charge != 0 and name not in ["atmass", "elem", "atnum", "name"]:
             return None
 
-        # open the HDF5 file in read mode
-        with pt.open_file(elements_hdf5_file, mode="r") as h5file:
-            # get the element group
-            element_group = f"/Elements/{self._data.atnum:03d}"
-
-            table_name = PROPERTY_NAME_MAP[name]
-            table_path = f"{element_group}/{table_name}"
-
-            # get the table node from the HDF5 file
-            table = h5file.get_node(table_path)
-
-            # Handle basic properties (single row)
-            if table.nrows == 1:
-                value = table[0]["value"]
-                # if the value is an int, return it as an int
-                if isinstance(value, Integral):
-                    return int(value)
-                # if the value is a string, decode from bytes
-                elif isinstance(value, bytes):
-                    return value.decode("utf-8")
-            else:
-                # handle properties with multiple sources
-                result = {}
-                for row in table:
-                    source = row["source"].decode("utf-8")
-                    value = row["value"]
-                    # exclude none values
-                    if not np.isnan(value):
-                        result[source] = float(value)
-                return result if result else None
+        # get the element group
+        element_group = f"/Elements/{self._data.atnum:03d}"
+
+        table_name = name #PROPERTY_NAME_MAP[name]
+        table_path = f"{element_group}/{table_name}"
+
+        # get the table node from the HDF5 file
+        table = ELEMENTS_H5FILE.get_node(table_path)
+
+        # Handle basic properties (single column --> no sources)
+        if len(table.colnames) == 1 and table.colnames[0] == "value":
+            value = table[0]["value"]
+            # if the value is an int, return it as an int
+            if isinstance(value, Integral):
+                return int(value)
+            # if the value is a string, decode from bytes
+            elif isinstance(value, bytes):
+                return value.decode("utf-8")
+        else:
+            # handle properties with multiple sources
+            result = {}
+            for row in table:
+                source = row["source"].decode("utf-8")
+                value = row["value"]
+                # exclude none values
+                if not np.isnan(value):
+                    result[source] = float(value)
+            return result if result else None
 
     wrapper.__doc__ = method.__doc__
     return wrapper

atomdb/test/test_nist.py

@@ -11,6 +11,7 @@
 TEST_DATAPATH = files("atomdb.test.data")
 TEST_DATAPATH = os.fspath(TEST_DATAPATH._paths[0])
 
+ELEMENTS_HDF5_FILE = files("atomdb.data").joinpath("elements_data.h5")
 
 TEST_CASES_MAKE_PROMOLECULE = [
     pytest.param(
@@ -151,6 +152,9 @@ def test_nist_data(case):
     """
     Test getting the attributes of the atom for Hydrogen and Carbon.
     """
+    if not ELEMENTS_HDF5_FILE.exists():
+        pytest.skip(f"Required data file not found: {ELEMENTS_HDF5_FILE}")
+
     elem = case.get("elem")
     charge = case.get("atnum") - case.get("nelec")
     mult = case.get("nspin") + 1