[WIP] Introduce more intuitive method names in Data classes and reduce required input parameter for TrajectoryData.set_trajectory() method #2310
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Change tests for dataclasses (StructureData, TrajectoryData) to call the renamed functions .get_structures() (former ._get_aiida_structures()) and .get_cif() (former ._get_cif())
Change TrajectoryData to make passing stepids and cells optional. While nothing will be stored for cells if not given a consecutive sequence will be automatically assigned to stepids if missing from the inputs.
As proposed in issue aiidateam#201 symbols are now stored in a TrajectoryData attribute rather than an array to simplify the query for these symbols
Move set of pylint options inside CifData class. Disable check for too-many-public-methods complaining about 21/20 public methods after renaming _get_aiida_structure -> get_structure making get_structure() method public
Make class methods .is_alloy() and .has_vacancies() for StrutureData and Kind classes accessible as class properties .is_alloy and .has_vacancies
giovannipizzi
requested changes
Dec 7, 2018
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Beside the comments above:
- rename
is_hiddento hidden - we would need a data migration before merging, for the symbols going from an array to a attribute.
If you do all other changes, we can then fork off your branch and implement the migration ourselves. Thanks!
giovannipizzi
changed the title
In function _internal_validate the 'symbols' list containing atomic names is checked for being 1D using the shape of the array. However, each entry of this list is ensured to be of type six.string_types somewhere upstream in this function which would already have triggered if the list is not purely 1D (contains one or more lists as entry somewhere)
Had to reformat the warning.warn() function arguments to get pylint invoke the set 'disable=no-member' option.
giovannipizzi
changed the base branch from
provenance_redesign
to
fix_201_method_names_for_data
|
Squash-merged into a working branch to keep attribution to @astamminger and we'll continue working from there |
elsapassaro
pushed a commit
to elsapassaro/aiida-core
that referenced
this pull request
Jan 25, 2019
…ired input parameter for TrajectoryData.set_trajectory() method (aiidateam#2310) * Rename ArrayData.iterarrays() to ArrayData.get_iterarrays() * [TrajectoryData] Rename _get_aiida_structure() -> get_structure() * [TrajectoryData] Rename _get_cif() -> get_cif() * Rename _get_cif() -> get_cit() in tcod.py * [StructureData] Rename _get_cif() -> get_cif() * Make stepid and cells parameter optional Change TrajectoryData to make passing stepids and cells optional. While nothing will be stored for cells if not given a consecutive sequence will be automatically assigned to stepids if missing from the inputs. * Store symbols in TrajectoryData attribute instead of array As proposed in issue aiidateam#201 symbols are now stored in a TrajectoryData attribute rather than an array to simplify the query for these symbols * Change passed symbols from numpy.ndarray to list in set_structurelist * Change TrajectoryData tests to use symbols attribute rather than symbols array * Make Code.is_hidden() available as class property * Rename Code.full_text_info() method to .get_full_text_info() * Change RemoteData.is_empty() method to class property .is_empty * Change is_alloy() and has_vacancies() methods to properties Make class methods .is_alloy() and .has_vacancies() for StrutureData and Kind classes accessible as class properties .is_alloy and .has_vacancies * Change symbols type from numpy.array to list * Add deprecation warning to renamed methods * Rename code attribute is_hidden to hidden. * Set allowed symbols type to be Iterable rather than list * Ensure symbols are stored as list * Adjust argument ordering in set_trajectory() docstring. * Document introduced changes in concepts/workflows
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The changes in this pull request address issue #201 providing more intuitive method names. I clustered the changes into three major topics and would be glad to hear your opinion
1. Renamed functions
ArrayData.iterarrays()->.get_iterarrays()TrajectoryData._get_cif()->.get_cif()._get_aiida_structure->.get_structure()StructureData._get_cif()->.get_cif()Code.full_text_info()->.get_full_text_info()Functions have been renamed and the tests have been adopted accordingly. (Deprecation warnings have been added to all "old" functions)
2. Methods changed to properties
Code.is_hidden()->.hiddenRemoteData.is_empty()->.is_emptyStructureData,Kind.is_alloy()->.is_alloy.has_vacancies()->.has_vacanciesIdea was that these values are rather "attributes" of these classes and it is more intuitive to treat them as properties rather than actual methods. Question here is: Is this OK and how to exactly deal with this since we cannot simply add deprecation warnings.
3. Changes in
TrajectoryData.set_trajectory():Input parameters
stepidandcellsare now optional and the implemented behavior is as follows:cellsparameter is missing: Nothing will be stored for cells.stepidsparameter is missing:stepidsdefaults to the consecutive sequence [0,1,...,len(positions)-1]Element symbols passed to the
set_trajectory()method are now passed as a list (instead of a numpy.ndarray) and are stored in theTrajectoryData.symbolsattribute (as requested in #201 to simplify querying)