Refactor AtomDB: Migrate Elements Data from CSV to HDF5

.gitattributes

@@ -0,0 +1 @@
+*.h5 filter=lfs diff=lfs merge=lfs -text

.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'
+
+