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changed the generic cells property #1379

Merged
merged 5 commits into from
Apr 17, 2024
Merged

changed the generic cells property #1379

merged 5 commits into from
Apr 17, 2024

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skatnagallu
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Changed the cells property to repeat based on number of steps to fix issue #1378

@skatnagallu skatnagallu linked an issue Apr 12, 2024 that may be closed by this pull request
get_structure() for sphinx jobs gives error #1378
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@skatnagallu skatnagallu requested a review from samwaseda April 12, 2024 09:45
@skatnagallu
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Unittest fails with AttributeError: energy_free. I am not sure why

@freyso
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freyso commented Apr 16, 2024

I think this approach is suboptimal.

The relaxHist.sx output replicates the cell, so it should be parsable (and it actually seems to be parsed into "output.cell" rather than ...".cells" (with s), see sphinx/output_parsers.py lines 192-196. I'd rather rename the parsing target in the parser, because then we would be ready for future implementations of automatic cell optimization.

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Based on @freyso's comment, I suggest to copy generic.cell, which will probably also solve the problem with CI

@skatnagallu @samwaseda
Update pyiron_atomistics/sphinx/base.py
e518927 
using self.generic.cell

Co-authored-by: Sam Dareska <[email protected]>
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coveralls commented Apr 17, 2024 •
edited
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Pull Request Test Coverage Report for Build 8720068328

Warning: This coverage report may be inaccurate.

This pull request's base commit is no longer the HEAD commit of its target branch. This means it includes changes from outside the original pull request, including, potentially, unrelated coverage changes.

Details

  • 4 of 4 (100.0%) changed or added relevant lines in 1 file are covered.
  • 1 unchanged line in 1 file lost coverage.
  • Overall coverage increased (+0.01%) to 93.209%
Files with Coverage Reduction New Missed Lines %
pyiron_atomistics/init.py 1 97.92%
Totals Coverage Status
Change from base Build 8572185654: 0.01%
Covered Lines: 14275
Relevant Lines: 15315
💛 - Coveralls

@skatnagallu
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Shouldn't we change the key to 'cells' here ?

@samwaseda
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Shouldn't we change the key to 'cells' here ?

I guess we should discuss it at the pyiron meeting. For now if the tests pass we can live with what we get here.

@skatnagallu
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can be merged now

@samwaseda samwaseda added the format_black reformat the code using the black standard label Apr 17, 2024
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samwaseda approved these changes Apr 17, 2024
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As soon as Black runs I'm fine with merging it

@samwaseda samwaseda merged commit 2df0ae1 into main Apr 17, 2024
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@samwaseda samwaseda deleted the 1378-fix_get_structure-for-sphinx branch April 17, 2024 16:02
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@samwaseda samwaseda samwaseda approved these changes

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get_structure() for sphinx jobs gives error
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@skatnagallu @freyso @samwaseda @coveralls @pmrv @pyiron-runner