chore: tmp remove rdkit

express/parsers/molecule.py

@@ -1,5 +1,5 @@
 import ase.io
-import rdkit.Chem
+# import rdkit.Chem
 from io import StringIO
 from typing import Dict, Tuple
 
@@ -19,7 +19,8 @@ class MoleculeParser(StructureParser):
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
         self.ase_format = ASE_FORMATS[self.structure_format]
-        self.inchi_long, self.inchi = self.get_inchi()
+        self.inchi_long, self.inchi = "", ""
+        # self.inchi_long, self.inchi = self.get_inchi()
 
     def get_rdkit_mol(self) -> rdkit.Chem.Mol:
         """

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:

tests/integration/properties/test_material.py

@@ -1,4 +1,5 @@
 import os
+import unittest
 from copy import deepcopy
 from typing import Dict, List
 
@@ -75,6 +76,7 @@ def test_material_espresso_final_structure(self):
         material = Material("material", self.espresso_parser, is_final_structure=True)
         self.assertPropertiesEqual(material)
 
+    @unittest.skip("to avoid using rdkit tmp")
     def test_material_is_non_periodic(self):
         material = Material("material", self.vasp_parser, is_initial_structure=True, is_non_periodic=True)
         self.assertPropertiesEqual(material)
@@ -90,6 +92,7 @@ def test_material_from_structure(self):
         )
         self.assertPropertiesEqual(material)
 
+    @unittest.skip("to avoid using rdkit tmp")
     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/manifest.yaml

@@ -220,8 +220,8 @@ test_structure_jarvis_db_entry_lattice_bravais:
   structurePath: fixtures/structural/test-002/JVASP-677.json
   structureFormat: jarvis-db-entry
 
-test_molecule_inchi:
-  structurePath: fixtures/structural/test-001/POSCAR
+# test_molecule_inchi:
+#  structurePath: fixtures/structural/test-001/POSCAR
 
 test_material_vasp_initial_structure:
   workDir: fixtures/vasp/test-001
@@ -239,17 +239,17 @@ 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_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
 
-test_material_serialize_and_validate:
-  workDir: fixtures/vasp/test-001
-  stdoutFile: fixtures/vasp/test-001/vasp.out
+# test_material_serialize_and_validate:
+#  workDir: fixtures/vasp/test-001
+#  stdoutFile: fixtures/vasp/test-001/vasp.out
 
 test_espresso_hubbard_u:
   workDir: fixtures/espresso/v7_2/test-007