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Deprecate CifParser.get_structures() in favor of new parse_structures in which primitive defaults to False #3419

Merged
merged 10 commits into from
Nov 8, 2023
Merged

Deprecate CifParser.get_structures() in favor of new parse_structures in which primitive defaults to False #3419

merged 10 commits into from
Nov 8, 2023

Commits on Oct 24, 2023

  1. breaking: change default primitive=True to False in CifParser.get_str… 

    …uctures()
    @janosh
    janosh committed Oct 24, 2023
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  2. fix CifParser tests

    @janosh
    janosh committed Oct 24, 2023
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  3. add test to ensure CIfParser.get_structures() and Structure.from_file… 

    …() remain consistent in the future
    @janosh
    janosh committed Oct 24, 2023
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  4. Structure.from_file add type hints and fix doc str claiming primitive… 

    … keyword only passed to CIF
    @janosh
    janosh committed Oct 24, 2023
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  5. add UserWarning for change of default primitive=True to False made on… 

    … 2023-10-24
    @janosh
    janosh committed Oct 24, 2023
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Commits on Nov 2, 2023

  1. deprecate get_structures() and change primitive default to False in n… 

    …ew parse_structures() method
    @janosh
    janosh committed Nov 2, 2023
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  2. use parse_structures in tests

    @janosh
    janosh committed Nov 2, 2023
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  3. fix TestCifTransmuter.test_init 

    return self.parse_structures(*args, **kwargs)
E       TypeError: CifParser.parse_structures() got multiple values for argument 'primitive'
    @janosh
    janosh committed Nov 2, 2023
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  4. add comment suggested by @JaGeo

    @janosh
    janosh committed Nov 2, 2023
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Commits on Nov 8, 2023

  1. remove all internal use of deprecated CifParser.get_structures()

    @janosh
    janosh committed Nov 8, 2023
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