Refactor database

.gitattributes

@@ -0,0 +1,2 @@
+*.h5 filter=lfs diff=lfs merge=lfs -text
+atomdb/datasets/datasets_data-v000.h5 filter=lfs diff=lfs merge=lfs -text

.github/workflows/pytest.yaml

@@ -18,10 +18,13 @@ 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"
+        # Whether to download Git-LFS files
+        with:
+          lfs: true
 
       - name: Setup python for test ${{ matrix.py }}
         uses: actions/setup-python@v5
@@ -30,12 +33,8 @@ jobs:
 
       - name: Install development version
         run: |
-          pip install -v .
+          pip install -e '.[dev,test_extra]'
 
-      - name: Install extra test dependencies
-        run: |
-          pip install --upgrade pip
-          pip install .[test_extra]
 
       - name: Run pytest default tests
         uses: pavelzw/pytest-action@v2
@@ -46,10 +45,6 @@ jobs:
           click-to-expand: true
           report-title: 'Test Report'
 
-      - name: Install Dev Dependencies
-        run: |
-          pip install .[dev]
-
       - name: Run pytest Dev Tests
         uses: pavelzw/pytest-action@v2
         with:
@@ -59,3 +54,4 @@ jobs:
           click-to-expand: true
           report-title: 'Dev Test Report'
           pytest-args: '-m dev'
+

.gitignore

@@ -150,6 +150,8 @@ cython_debug/
 #*.msg
 repo_data.txt
 atomdb/datasets/*/raw/
+atomdb/datasets/*/db/
+
 
 # Generated documentation
 docs/source/api/

atomdb/__init__.py

@@ -30,7 +30,6 @@
 
 from atomdb.promolecule import make_promolecule
 
-
 __all__ = [
     "Element",
     "Species",

atomdb/__main__.py

@@ -30,7 +30,10 @@
 command_group = command.add_mutually_exclusive_group(required=True)
 
 command_group.add_argument(
-    "-c", "--compile_species", action="store_true", help="compile_species a species into the database"
+    "-c",
+    "--compile_species",
+    action="store_true",
+    help="compile_species a species into the database",
 )
 
 command_group.add_argument(