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Bugfixes in StructurePlot and error handling for Atoms.get_symmetry #812

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merged 7 commits into from
Nov 7, 2022

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pmrv
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@pmrv pmrv commented Oct 11, 2022

There were some small typos in StructurePlots. Additionally I found that for "weird" structures spglib can run into internal errors when calling get_symmetry. This then produced unrelated errors in the Symmetry class, because we're not expecting spglib to fail. So I've added a simple error class and None checks.

@pmrv pmrv added the bug Something isn't working label Oct 11, 2022
@pmrv pmrv requested a review from samwaseda October 11, 2022 14:10
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coveralls commented Oct 11, 2022

Pull Request Test Coverage Report for Build 3408972172

  • 18 of 26 (69.23%) changed or added relevant lines in 2 files are covered.
  • 328 unchanged lines in 8 files lost coverage.
  • Overall coverage increased (+0.03%) to 68.667%

Changes Missing Coverage Covered Lines Changed/Added Lines %
pyiron_atomistics/atomistics/structure/structurestorage.py 1 5 20.0%
pyiron_atomistics/atomistics/structure/symmetry.py 17 21 80.95%
Files with Coverage Reduction New Missed Lines %
pyiron_atomistics/atomistics/structure/structurestorage.py 1 43.22%
pyiron_atomistics/interactive/scipy_minimizer.py 2 87.39%
pyiron_atomistics/atomistics/structure/factories/materialsproject.py 21 41.86%
pyiron_atomistics/atomistics/structure/has_structure.py 21 68.18%
pyiron_atomistics/lammps/base.py 36 81.06%
pyiron_atomistics/atomistics/job/atomistic.py 61 75.6%
pyiron_atomistics/vasp/base.py 73 65.51%
pyiron_atomistics/sphinx/base.py 113 81.71%
Totals Coverage Status
Change from base Build 3228348380: 0.03%
Covered Lines: 12108
Relevant Lines: 17633

💛 - Coveralls

@samwaseda
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samwaseda commented Oct 12, 2022

It looks good to me. Can you maybe add a test? The symmetry search typically fails when there are two atoms on top of each other, so if you create a structure by:

structure = pr.create.structure.bulk('Al', cubic=True)
structure += structure[-1]
structure.get_symmetry()

it should fail.

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stale bot commented Oct 29, 2022

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

@stale stale bot added the stale label Oct 29, 2022
@stale stale bot removed the stale label Nov 3, 2022
@pmrv pmrv added the format_black reformat the code using the black standard label Nov 7, 2022
@pmrv pmrv merged commit 0257817 into master Nov 7, 2022
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4 participants