Cg particle support

pyproject.toml

@@ -28,6 +28,11 @@ maintainers = [
     { name = "Joseph F. Rudzinski", email = "[email protected]" }
 ]
 license = { file = "LICENSE" }
+# dependencies = [
+#     "nomad-lab>=1.3.0",
+#     "matid>=2.0.0.dev2",
+#     "nomad-simulations@file:///home/bmohr/software/nomad-simulations",
+# ]
 dependencies = [
     "nomad-lab>=1.3.0",
     "matid>=2.0.0.dev2",
@@ -40,12 +45,13 @@ dependencies = [
 
 [project.optional-dependencies]
 dev = [
-    "mypy==1.0.1",
-    "ruff",
-    "pytest",
-    "pytest-timeout",
-    "pytest-cov",
-    "structlog",
+    'mypy==1.0.1',
+    'pytest>= 5.3.0, <8',
+    'pytest-timeout>=1.4.2',
+    'pytest-cov>=2.7.1',
+    'ruff>=0.6',
+    'structlog>=1.0',
+    'typing-extensions>=4.12',
 ]
 
 [tool.uv]

src/nomad_simulations/schema_packages/__init__.py

@@ -31,8 +31,8 @@ class NOMADSimulationsEntryPoint(SchemaPackageEntryPoint):
         description='Limite of the number of atoms in the unit cell to be treated for the system type classification from MatID to work. This is done to avoid overhead of the package.',
     )
     equal_cell_positions_tolerance: float = Field(
-        1e-12,
-        description='Tolerance (in meters) for the cell positions to be considered equal.',
+        12,
+        description='Decimal order or tolerance (in meters) for comparing cell positions.',
     )
 
     def load(self):

src/nomad_simulations/schema_packages/general.py

@@ -217,6 +217,7 @@ def _set_system_branch_depth(
                 system_parent=system_child, branch_depth=branch_depth + 1
             )
 
+    #! Generalize from checks for atomic systems, error with CG input
     def resolve_composition_formula(self, system_parent: ModelSystem) -> None:
         """Determine and set the composition formula for `system_parent` and all of its
         descendants.
@@ -275,6 +276,7 @@ def get_composition_recurs(system: ModelSystem, atom_labels: list[str]) -> None:
                 for subsystem in subsystems:
                     get_composition_recurs(system=subsystem, atom_labels=atom_labels)
 
+        # ! CG: system_parent.cell[0].particles_state instead of atoms_state!
         atoms_state = (
             system_parent.cell[0].atoms_state if system_parent.cell is not None else []
         )