Create mesh visualization - just for CI #185
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Actionable comments posted: 1
Out of diff range and nitpick comments (2)
structuretoolkit/build/__init__.py (1)
Line range hint
2-10: Many imports are flagged as unused. If these are intended for external use, consider adding them to__all__to clarify their purpose.+ __all__ = ['grainboundary', 'get_grainboundary_info', 'B2', 'C14', 'C15', 'C36', 'D03', 'pyxtal', 'sqs_structures', 'high_index_surface', 'get_high_index_surface_info', 'create_mesh']structuretoolkit/__init__.py (1)
Line range hint
5-54: Many imports are flagged as unused. If these are intended for external use, consider adding them to__all__to clarify their purpose.+ __all__ = ['find_mic', 'find_solids', 'get_adaptive_cna_descriptors', 'get_average_of_unique_labels', 'get_centro_symmetry_descriptors', 'get_cluster_positions', 'get_delaunay_neighbors', 'get_diamond_structure_descriptors', 'get_distances_array', 'get_equivalent_atoms', 'get_interstitials', 'get_layers', 'get_mean_positions', 'get_neighborhood', 'get_neighbors', 'get_steinhardt_parameters', 'get_strain', 'get_symmetry', 'get_voronoi_neighbors', 'get_voronoi_vertices', 'get_voronoi_volumes', 'B2', 'C14', 'C15', 'C36', 'D03', 'get_grainboundary_info', 'get_high_index_surface_info', 'grainboundary', 'high_index_surface', 'sqs_structures', 'create_mesh', 'SymmetryError', 'apply_strain', 'ase_to_pymatgen', 'ase_to_pyscal', 'center_coordinates_in_unit_cell', 'get_extended_positions', 'get_vertical_length', 'get_wrapped_coordinates', 'pymatgen_to_ase', 'select_index', 'plot3d', 'plot_isosurface']
Review Details
Configuration used: CodeRabbit UI
Review profile: CHILL
Files selected for processing (5)
- structuretoolkit/init.py (2 hunks)
- structuretoolkit/build/init.py (1 hunks)
- structuretoolkit/build/mesh.py (1 hunks)
- structuretoolkit/visualize.py (1 hunks)
- tests/test_mesh.py (1 hunks)
Additional Context Used
Ruff (69)
structuretoolkit/__init__.py (56)
5-5:
structuretoolkit.analyse.find_micimported but unused; consider removing, adding to__all__, or using a redundant alias
6-6:
structuretoolkit.analyse.find_solidsimported but unused; consider removing, adding to__all__, or using a redundant alias
7-7:
structuretoolkit.analyse.get_adaptive_cna_descriptorsimported but unused; consider removing, adding to__all__, or using a redundant alias
8-8:
structuretoolkit.analyse.get_average_of_unique_labelsimported but unused; consider removing, adding to__all__, or using a redundant alias
9-9:
structuretoolkit.analyse.get_centro_symmetry_descriptorsimported but unused; consider removing, adding to__all__, or using a redundant alias
10-10:
structuretoolkit.analyse.get_cluster_positionsimported but unused; consider removing, adding to__all__, or using a redundant alias
11-11:
structuretoolkit.analyse.get_delaunay_neighborsimported but unused; consider removing, adding to__all__, or using a redundant alias
12-12:
structuretoolkit.analyse.get_diamond_structure_descriptorsimported but unused; consider removing, adding to__all__, or using a redundant alias
13-13:
structuretoolkit.analyse.get_distances_arrayimported but unused; consider removing, adding to__all__, or using a redundant alias
14-14:
structuretoolkit.analyse.get_equivalent_atomsimported but unused; consider removing, adding to__all__, or using a redundant alias
15-15:
structuretoolkit.analyse.get_interstitialsimported but unused; consider removing, adding to__all__, or using a redundant alias
16-16:
structuretoolkit.analyse.get_layersimported but unused; consider removing, adding to__all__, or using a redundant alias
17-17:
structuretoolkit.analyse.get_mean_positionsimported but unused; consider removing, adding to__all__, or using a redundant alias
18-18:
structuretoolkit.analyse.get_neighborhoodimported but unused; consider removing, adding to__all__, or using a redundant alias
19-19:
structuretoolkit.analyse.get_neighborsimported but unused; consider removing, adding to__all__, or using a redundant alias
20-20:
structuretoolkit.analyse.get_steinhardt_parametersimported but unused; consider removing, adding to__all__, or using a redundant alias
21-21:
structuretoolkit.analyse.get_strainimported but unused; consider removing, adding to__all__, or using a redundant alias
22-22:
structuretoolkit.analyse.get_symmetryimported but unused; consider removing, adding to__all__, or using a redundant alias
23-23:
structuretoolkit.analyse.get_voronoi_neighborsimported but unused; consider removing, adding to__all__, or using a redundant alias
24-24:
structuretoolkit.analyse.get_voronoi_verticesimported but unused; consider removing, adding to__all__, or using a redundant alias
25-25:
structuretoolkit.analyse.get_voronoi_volumesimported but unused; consider removing, adding to__all__, or using a redundant alias
30-30:
structuretoolkit.build.B2imported but unused; consider removing, adding to__all__, or using a redundant alias
31-31:
structuretoolkit.build.C14imported but unused; consider removing, adding to__all__, or using a redundant alias
32-32:
structuretoolkit.build.C15imported but unused; consider removing, adding to__all__, or using a redundant alias
33-33:
structuretoolkit.build.C36imported but unused; consider removing, adding to__all__, or using a redundant alias
34-34:
structuretoolkit.build.D03imported but unused; consider removing, adding to__all__, or using a redundant alias
35-35:
structuretoolkit.build.get_grainboundary_infoimported but unused; consider removing, adding to__all__, or using a redundant alias
36-36:
structuretoolkit.build.get_high_index_surface_infoimported but unused; consider removing, adding to__all__, or using a redundant alias
37-37:
structuretoolkit.build.grainboundaryimported but unused; consider removing, adding to__all__, or using a redundant alias
38-38:
structuretoolkit.build.high_index_surfaceimported but unused; consider removing, adding to__all__, or using a redundant alias
39-39:
structuretoolkit.build.sqs_structuresimported but unused; consider removing, adding to__all__, or using a redundant alias
40-40:
structuretoolkit.build.create_meshimported but unused; consider removing, adding to__all__, or using a redundant alias
45-45:
structuretoolkit.common.SymmetryErrorimported but unused; consider removing, adding to__all__, or using a redundant alias
46-46:
structuretoolkit.common.apply_strainimported but unused; consider removing, adding to__all__, or using a redundant alias
47-47:
structuretoolkit.common.ase_to_pymatgenimported but unused; consider removing, adding to__all__, or using a redundant alias
48-48:
structuretoolkit.common.ase_to_pyscalimported but unused; consider removing, adding to__all__, or using a redundant alias
49-49:
structuretoolkit.common.center_coordinates_in_unit_cellimported but unused; consider removing, adding to__all__, or using a redundant alias
50-50:
structuretoolkit.common.get_extended_positionsimported but unused; consider removing, adding to__all__, or using a redundant alias
51-51:
structuretoolkit.common.get_vertical_lengthimported but unused; consider removing, adding to__all__, or using a redundant alias
52-52:
structuretoolkit.common.get_wrapped_coordinatesimported but unused; consider removing, adding to__all__, or using a redundant alias
53-53:
structuretoolkit.common.pymatgen_to_aseimported but unused; consider removing, adding to__all__, or using a redundant alias
54-54:
structuretoolkit.common.select_indeximported but unused; consider removing, adding to__all__, or using a redundant alias
58-58:
structuretoolkit.visualize.plot3dimported but unused; consider removing, adding to__all__, or using a redundant alias
58-58:
structuretoolkit.visualize.plot_isosurfaceimported but unused; consider removing, adding to__all__, or using a redundant alias
62-62:
structuretoolkit.analyse.find_solidsimported but unused; consider removing, adding to__all__, or using a redundant alias
63-63:
structuretoolkit.analyse.get_adaptive_cna_descriptorsimported but unused; consider removing, adding to__all__, or using a redundant alias
64-64:
structuretoolkit.analyse.get_centro_symmetry_descriptorsimported but unused; consider removing, adding to__all__, or using a redundant alias
65-65:
structuretoolkit.analyse.get_cluster_positionsimported but unused; consider removing, adding to__all__, or using a redundant alias
66-66:
structuretoolkit.analyse.get_diamond_structure_descriptorsimported but unused; consider removing, adding to__all__, or using a redundant alias
67-67:
structuretoolkit.analyse.get_equivalent_atomsimported but unused; consider removing, adding to__all__, or using a redundant alias
68-68:
structuretoolkit.analyse.get_steinhardt_parametersimported but unused; consider removing, adding to__all__, or using a redundant alias
69-69:
structuretoolkit.analyse.get_voronoi_volumesimported but unused; consider removing, adding to__all__, or using a redundant alias
74-74:
structuretoolkit.build.get_grainboundary_infoimported but unused; consider removing, adding to__all__, or using a redundant alias
75-75:
structuretoolkit.build.get_high_index_surface_infoimported but unused; consider removing, adding to__all__, or using a redundant alias
76-76:
structuretoolkit.build.grainboundaryimported but unused; consider removing, adding to__all__, or using a redundant alias
77-77:
structuretoolkit.build.sqs_structuresimported but unused; consider removing, adding to__all__, or using a redundant aliasstructuretoolkit/build/__init__.py (12)
2-2:
structuretoolkit.build.aimsgb.grainboundaryimported but unused; consider removing, adding to__all__, or using a redundant alias
3-3:
structuretoolkit.build.aimsgb.get_grainboundary_infoimported but unused; consider removing, adding to__all__, or using a redundant alias
5-5:
structuretoolkit.build.compound.B2imported but unused; consider removing, adding to__all__, or using a redundant alias
5-5:
structuretoolkit.build.compound.C14imported but unused; consider removing, adding to__all__, or using a redundant alias
5-5:
structuretoolkit.build.compound.C15imported but unused; consider removing, adding to__all__, or using a redundant alias
5-5:
structuretoolkit.build.compound.C36imported but unused; consider removing, adding to__all__, or using a redundant alias
5-5:
structuretoolkit.build.compound.D03imported but unused; consider removing, adding to__all__, or using a redundant alias
6-6:
structuretoolkit.build.random.pyxtalimported but unused; consider removing, adding to__all__, or using a redundant alias
7-7:
structuretoolkit.build.sqs.sqs_structuresimported but unused; consider removing, adding to__all__, or using a redundant alias
9-9:
structuretoolkit.build.surface.high_index_surfaceimported but unused; consider removing, adding to__all__, or using a redundant alias
10-10:
structuretoolkit.build.surface.get_high_index_surface_infoimported but unused; consider removing, adding to__all__, or using a redundant alias
12-12:
structuretoolkit.build.mesh.create_meshimported but unused; consider removing, adding to__all__, or using a redundant aliastests/test_mesh.py (1)
6-6:
numpyimported but unused
Additional comments not posted (5)
structuretoolkit/build/__init__.py (1)
12-12: The import ofcreate_meshis correctly added to enhance module capabilities.tests/test_mesh.py (1)
11-28: Comprehensive test cases forcreate_mesh. Ensure edge cases and error handling are thoroughly tested.structuretoolkit/build/mesh.py (1)
7-40: Well-implementedcreate_meshfunction with comprehensive documentation and error handling.structuretoolkit/__init__.py (1)
40-40: The import ofcreate_meshis correctly added to enhance module capabilities.structuretoolkit/visualize.py (1)
805-872: Well-implementedplot_isosurfacefunction with comprehensive documentation and error handling.
tests/test_mesh.py
Outdated
| # Distributed under the terms of "New BSD License", see the LICENSE file. | ||
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| import unittest | ||
| import numpy as np |
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Tip
Codebase Verification
The search results indicate that numpy is imported but not used in tests/test_mesh.py. Therefore, it is safe to remove the unused import.
tests/test_mesh.py: Remove the unusednumpyimport.
Analysis chain
Verify if numpy is actually unused. If it is, consider removing the import.
Scripts Executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check if `numpy` is used in `tests/test_mesh.py`.
# Test: Search for `numpy` usage. Expect: At least one occurrence.
rg --type python 'np' tests/test_mesh.py
Length of output: 71
Script:
#!/bin/bash
# Description: Check if `numpy` is used in `tests/test_mesh.py`.
# Test: Search for `numpy` usage. Expect: At least one occurrence.
rg --type py 'np' tests/test_mesh.py
Length of output: 55
…retoolkit into create_mesh_visualization
Co-authored-by: Liam Huber <liamhuber@greyhavensolutions.com>
Co-authored-by: Liam Huber <liamhuber@greyhavensolutions.com>
Summary by CodeRabbit
New Features
create_meshfunction for generating mesh grids based on atomic structures.plot_isosurfacefunction for creating customizable mesh plots using Plotly.Tests
create_meshfunction to ensure reliable mesh generation with various parameters.