Add common data structures #134
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Will this satisfy #60? |
Codecov Report
@@ Coverage Diff @@
## dev #134 +/- ##
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+ Coverage 69.2% 69.73% +0.53%
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Files 24 29 +5
Lines 4981 5726 +745
Branches 1143 1351 +208
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+ Hits 3447 3993 +546
- Misses 1168 1306 +138
- Partials 366 427 +61
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src/hdmf/build/map.py
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| for subspec, value in subspecs.items(): | ||
| # FOR SOME REASON, no specs are getting mapped to the 'data' constructor argument |
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can this comment be removed now?
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more remnants of debugging
| ret = ret['namespaces'] | ||
| if self.__cache is None: | ||
| self.__cache = self.__read(ns_path) | ||
| ret = self.__cache['namespaces'] |
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Note to self: caching of the spec by the H5SpecReader should be mentioned in the release notes
src/hdmf/validate/validator.py
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| @@ -152,6 +152,7 @@ class ValidatorMap(object): | |||
| def __init__(self, **kwargs): | |||
| ns = getargs('namespace', kwargs) | |||
| self.__ns = ns | |||
| self._ns = ns | |||
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remnants of debugging... I'll remove that
| {'name': 'colnames', 'type': 'array_data', 'doc': 'the names of the columns in this table', | ||
| 'default': None}) | ||
| def __init__(self, **kwargs): | ||
| id, columns, desc, colnames = popargs('id', 'columns', 'description', 'colnames', kwargs) |
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The init for DynamicTable is quite complex. It would be nice to add some documentation to indicate what happens where.
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| @staticmethod | ||
| def __build_columns(columns, df=None): | ||
| tmp = list() |
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Add docstring to describe what __build_columns does
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| @classmethod | ||
| def _getter(cls, field): | ||
| doc = field.get('doc') |
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| @staticmethod | ||
| def _transform_arg(field): | ||
| tmp = field |
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Add docstring for _transform_arg
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This looks good to me. Great job in porting all this functionality over. I added few comments to fix some documentation issues. In addition, it would be useful to also updated the developer docs to mention the submodules in this repo and also describe how to checkout and updated the submodules
Motivation
HDMF is used to build PyNWB. There are some useful data structures in PyNWB that have been moved into HDMF-common for use in other HDMF applications. The class/types that have been moved are DynamicTable and its dependencies. Additionally, a data type for storing compressed row sparse matrices.
These types will be introduced into the HDMF-common schema by hdmf-dev/hdmf-common-schema#1
Fix #60. This also moves some useful functionality from NWBContainer over to the general Container class.
Notable changes:
isinstance(..., Container)were changed toisinstance(..., AbstractContainer).