data converted to atomic units / change value type in scalar

Author: enjyashraf18

.github/workflows/pytest.yaml

@@ -18,7 +18,7 @@ jobs:
         # windows-latest is not supported because pyscf is not supported on windows
         # https://pyscf.org/user/install.html
         os: ["ubuntu-latest", "macos-latest"]
-        py: ["3.9", "3.10", "3.11", "3.12"]
+        py: ["3.10", "3.11", "3.12"]
 
     steps:
       - uses: "actions/checkout@v4"
@@ -28,6 +28,23 @@ jobs:
         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 .
@@ -37,6 +54,7 @@ jobs:
           pip install --upgrade pip
           pip install .[test_extra]
 
+
       - name: Run pytest default tests
         uses: pavelzw/pytest-action@v2
         with:
@@ -59,3 +77,5 @@ jobs:
           click-to-expand: true
           report-title: 'Dev Test Report'
           pytest-args: '-m dev'
+
+

atomdb/data/elements_data.h5

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:16446a533b7bf82ff72277579d8c99e8e1a1f6eb6c55b1641b635f9f1b0538e0
+oid sha256:fde2a5f5db8c0adb8418016ea8b85d5f12af4e2e40a7f07bef7bcfe474ae3e81
 size 105117616

atomdb/datasets/slater/db/H_000_002_000.msg

@@ -3,6 +3,7 @@
 import numpy as np
 from importlib_resources import files
 import warnings
+from atomdb.utils import CONVERTOR_TYPES
 
 # Suppresses NaturalNameWarning warnings from PyTables.
 warnings.filterwarnings('ignore', category=pt.NaturalNameWarning)
@@ -91,7 +92,7 @@
     },
     {
         'property': 'eneg',
-        'table_name': 'Energy',
+        'table_name': 'eneg',
         'description': 'Electronegativity'
     }
 ]
@@ -150,6 +151,7 @@ def create_properties_tables(hdf5_file, parent_folder, table_name, table_descrip
         if col in row_data and row_data[col].strip():
             try:
                 value = float(row_data[col])
+                value = CONVERTOR_TYPES[unit](value)
             except (ValueError, TypeError):
                 value = np.nan
 

atomdb/migration/periodic/elements_data.py

@@ -35,6 +35,7 @@
 from importlib_resources import \
 files
 import tables as pt
+from numbers import Integral
 
 elements_hdf5_file = files("atomdb.data").joinpath("elements_data.h5")
 
@@ -140,19 +141,16 @@ def wrapper(self):
 
             # get the table node from the HDF5 file
             table = h5file.get_node(table_path)
-            # get the data type of the 'value' col in the table
-            value_col = table.coltypes.get("value")
 
             # 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_col, pt.Int32Col):
+                if isinstance(value, Integral):
                     return int(value)
                 # if the value is a string, decode from bytes
-                elif isinstance(value_col, pt.StringCol):
+                elif isinstance(value, bytes):
                     return value.decode("utf-8")
-
             else:
                 # handle properties with multiple sources
                 result = {}

atomdb/species.py

@@ -25,7 +25,7 @@ authors = [
 description = "AtomDB is a database of atomic and ionic properties."
 readme = "README.md"
 license = {text = "GPL-3.0-or-later"}
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 classifiers = [
     'Development Status :: 5 - Production/Stable',
     'Environment :: Console',
@@ -36,13 +36,12 @@ classifiers = [
     'Intended Audience :: Science/Research',
     "Intended Audience :: Education",
     "Natural Language :: English",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
 ]
 dependencies = [
-    "numpy>=1.23.0",
+    "numpy>=1.26.4",
     "scipy>=1.4",
     "msgpack>=1.0.0",
     "msgpack-numpy>=0.4.8",
@@ -93,6 +92,9 @@ doc = [
 
 [tool.setuptools]
 packages = ["atomdb"]
+# Adding the package data
+package-data = { "atomdb" = ["data/*.h5", "data/*.msg"] }
+include-package-data = true
 
 [tool.black]
 line-length = 100