Merge pull request #141 from Exabyte-io/chore/tmp-remove-rdkit

chore: tmp remove rdkit

Author: timurbazhirov

express/properties/material.py

@@ -3,7 +3,7 @@
 
 from express.parsers.apps.vasp.parser import VaspParser
 from express.parsers.crystal import CrystalParser
-from express.parsers.molecule import MoleculeParser
+# from express.parsers.molecule import MoleculeParser
 from express.parsers.utils import lattice_basis_to_poscar
 from express.properties import BaseProperty
 from express.properties.non_scalar.symmetry import Symmetry
@@ -48,7 +48,7 @@ def __init__(self, name, parser, *args, **kwargs):
                     structure_string = lattice_basis_to_poscar(lattice, basis)
 
         if self.is_non_periodic:
-            self.parser = MoleculeParser(
+            self.parser = CrystalParser(
                 structure_string=structure_string, structure_format=structure_format, cell_type=cell_type
             )
         else:

pyproject.toml

@@ -19,7 +19,8 @@ dependencies = [
     "pymatgen>=2023.8.10",
     "ase>=3.17.0",
     "mat3ra-esse>=2024.1.25.post7",
-    "rdkit-pypi>=2022.3.5",
+    # Temporarily disable rdkit to allow running in Jupyter Lite
+    # "rdkit-pypi>=2022.3.5",
     "jarvis-tools>=2023.12.12",
     # To avoid module 'numpy.linalg._umath_linalg' has no attribute '_ilp64' in Colab
     # "numpy==1.23.5",

tests/integration/parsers/test_molecule.py

@@ -74,22 +74,3 @@ def test_material_espresso_initial_structure(self):
     def test_material_espresso_final_structure(self):
         material = Material("material", self.espresso_parser, is_final_structure=True)
         self.assertPropertiesEqual(material)
-
-    def test_material_is_non_periodic(self):
-        material = Material("material", self.vasp_parser, is_initial_structure=True, is_non_periodic=True)
-        self.assertPropertiesEqual(material)
-
-    def test_material_from_structure(self):
-        material = Material(
-            "material",
-            parser=None,
-            cell_type="original",
-            structure_string=self.structure_string,
-            structure_format="espresso-in",
-            is_non_periodic=True,
-        )
-        self.assertPropertiesEqual(material)
-
-    def test_material_serialize_and_validate(self):
-        material = Material("material", self.vasp_parser, is_initial_structure=True, is_non_periodic=True)
-        self.assertJsonEqual(material)

tests/integration/properties/test_material.py

@@ -239,10 +239,6 @@ test_material_espresso_final_structure:
   workDir: fixtures/espresso/v5_4/test-001
   stdoutFile: fixtures/espresso/v5_4/test-001/pw-scf.out
 
-test_material_is_non_periodic:
-  workDir: fixtures/vasp/test-001
-  stdoutFile: fixtures/vasp/test-001/vasp.out
-
 test_material_from_structure:
   structurePath: fixtures/espresso/v5_4/test-001/pw-scf.in
   structureFormat: espresso-in