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Merged
merged 8 commits into from
Nov 15, 2018
Merged

[nixio] New library version 1.5 #576

merged 8 commits into from
Nov 15, 2018

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achilleas-k
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The NIX library is being updated to v1.5. This brings changes to the metadata format and the IO needs to be updated to work with the new version.

List of changes in this PR:

  • New metadata handling: Property values are no longer of the type nix.Value. Values are simply created and returned as native Python types.
  • HDF5 backend option removed from Python nixpy library (only h5py supported now), so the selection argument is removed.
  • The neo-nixio loads metadata from linked nix.Sections into a Neo object's annotations now. NIX metadata sections can be linked to other sections and inherit their properties. If a user does this kind of linking in the NIX file, the linked metadata properties are loaded along with the metadata properties of the primary data object's metadata section.
  • Updated the filename for the NIXRawIO test (associated data repository PR: https://web.gin.g-node.org/NeuralEnsemble/ephy_testing_data/pulls/5)

@pep8speaks
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Hello @achilleas-k! Thanks for submitting the PR.

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coveralls commented Sep 23, 2018 •
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Coverage Status

Coverage decreased (-0.01%) to 48.647% when pulling 4f39a64 on G-Node:nixio-new-metadata into ce01ce2 on NeuralEnsemble:master.

@achilleas-k
[nixio] Remove deprecated file backend argument
9b00815
@achilleas-k
[nixio] nix.Value removal: New metadata compatibility
7032d68 
NIX no longer uses Value class for managing the value of metadata
properties. Values are added and retrieved directly.

Empty property values are now supported, but require a type to be
specified. The IO uses string as a default.

NIX returns collections of property values as tuples. The IO returns
lists explicitly for consistency with older behaviour.
@achilleas-k
[nixio] Inherit properties from linked sections
ce09164 
When reading the metadata from NIX objects, add the inherited properties
to the object as well, allowing users to link the primary metadata of
the object to extended metadata properties that are added later.
@achilleas-k
[nixio] Change filename for NIXRawIO tests
92e7164
@achilleas-k
[setup] Update nixio minimum version
1087151
@achilleas-k
[doc] Update min version for nixio in install docs
9d8906a
@achilleas-k
[testing] Update circleci config for newer nixio version
4f39a64
@samuelgarcia samuelgarcia added the IO label Oct 2, 2018
@samuelgarcia samuelgarcia added this to the 0.7.0 milestone Oct 2, 2018
@JuliaSprenger JuliaSprenger merged commit 937946b into NeuralEnsemble:master Nov 15, 2018
@achilleas-k achilleas-k deleted the nixio-new-metadata branch November 19, 2018 10:22
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