describer.py line 247 en.join(orientations): ValidationError Input should be a valid string

[ViktoriiaBaib]

Hi,

When calling:

from pymatgen.core import Structure
from robocrys import StructureCondenser
from robocrys import StructureDescriber

structure = Structure.from_file("C.cif")
sc = StructureCondenser()
describer = StructureDescriber()
condensed_structure = sc.condense_structure(structure)
description = describer.describe(condensed_structure)

I was having this error:

File ".../robocrys/describe/describer.py", line 247, in get_component_makeup_summary
en.join(orientations), s_direction
File ".../pydantic/_internal/_validate_call.py", line 100, in __call__
res = self.__pydantic_validator__.validate_python(pydantic_core.ArgsKwargs(args, kwargs))
pydantic_core._pydantic_core.ValidationError: 1 validation error for join
0.0
Input should be a valid string [type=string_type, input_value=(0, 0, 1), input_type=tuple]
For further information visit https://errors.pydantic.dev/2.4/v/string_type

Fix that helped in describer.py lines 241-249 is adding orientations_str:

               if component_group.dimensionality in [1, 2]:
                    orientations = list(
                        {c.orientation for c in component_group.components}
                    )
                    orientations_str = [str(o) for o in orientations]
                    s_direction = en.plural("direction", len(orientations))
                    comp_desc += " oriented in the {} {}".format(
                        en.join(orientations_str), s_direction
                    )

I am using Python 3.10.13 and the following package versions:
matminer 0.9.1.dev5
monty 2023.11.3
pydantic 2.4.2
pydantic_core 2.10.1
pydantic-settings 2.1.0
pymatgen 2023.3.23
robocrys 0.2.8
ruamel.yaml 0.17.40
ruamel.yaml.clib 0.2.7

And that is my "C.cif" file:

# generated using pymatgen
data_C
_symmetry_space_group_name_H-M   P6/mmm
_cell_length_a   2.46803014
_cell_length_b   2.46803014
_cell_length_c   19.99829300
_cell_angle_alpha   90.00000000
_cell_angle_beta   90.00000000
_cell_angle_gamma   120.00000000
_symmetry_Int_Tables_number   191
_chemical_formula_structural   C
_chemical_formula_sum   C2
_cell_volume   105.49320255
_cell_formula_units_Z   2
loop_
 _symmetry_equiv_pos_site_id
 _symmetry_equiv_pos_as_xyz
  1  'x, y, z'
  2  '-x, -y, -z'
  3  'x-y, x, z'
  4  '-x+y, -x, -z'
  5  '-y, x-y, z'
  6  'y, -x+y, -z'
  7  '-x, -y, z'
  8  'x, y, -z'
  9  '-x+y, -x, z'
  10  'x-y, x, -z'
  11  'y, -x+y, z'
  12  '-y, x-y, -z'
  13  '-y, -x, -z'
  14  'y, x, z'
  15  '-x, -x+y, -z'
  16  'x, x-y, z'
  17  '-x+y, y, -z'
  18  'x-y, -y, z'
  19  'y, x, -z'
  20  '-y, -x, z'
  21  'x, x-y, -z'
  22  '-x, -x+y, z'
  23  'x-y, -y, -z'
  24  '-x+y, y, z'
loop_
 _atom_site_type_symbol
 _atom_site_label
 _atom_site_symmetry_multiplicity
 _atom_site_fract_x
 _atom_site_fract_y
 _atom_site_fract_z
 _atom_site_occupancy
  C  C0  2  0.33333333  0.66666667  0.00000000  1

Could you look into this please?

[zakidotai]

This error also occurs in
pydantic==2.6.1 pydantic-settings==2.1.0

all other versions are the same as above.

[rookiexiong7]

hello! I encountered the same problem, how did you solve it?

[Grenzlinie]

This is because variable "orientations_str" is None and the en module need the "orientations_str" has a value.
For example,
condenser = StructureCondenser().
describer = StructureDescriber()
structure = Structure.from_file("DyBi2IO4.cif")
condensed_structure = condenser.condense_structure(structure)
for k,v in condensed_structure.items():
print(k, v)
You will get:
components {0: {'formula': 'Dy(BiO2)2', 'dimensionality': 2, 'orientation': (0, 0, 1), 'molecule_name': None, 'sites': [0, 1, 1, 4, 4, 4, 4]}, 1: {'formula': 'I', 'dimensionality': 0, 'orientation': None, 'molecule_name': 'hydriodic acid', 'sites': [3]}}.

Notice: orientation of I is None. And if you use description = describer.describe(condensed_structure), you will get this error.

To avoid it, a simple method is
describer = StructureDescriber(describe_component_makeup=False)

Or you can dive into the source code describer.py, and change the code from line 240 to 249:
if component_group.dimensionality in [1, 2]:
orientations = list(
{c.orientation for c in component_group.components}
)
s_direction = en.plural("direction", len(orientations))
# comp_desc += " oriented in the {} {}".format(
# en.join(orientations), s_direction
# )
comp_desc += f" oriented in the {orientations} {s_direction}"

[utf]

Thanks for raising this. It has been fixed in the most recent version.