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navis-org / pymaid

Python library to interface with CATMAID servers. Fully interoperable with navis.
https://pymaid.readthedocs.io/en/latest/
GNU General Public License v3.0
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Deprecate get_annotation_graph for get_entity_graph #232

Closed clbarnes closed 1 year ago

clbarnes commented 1 year ago

The original implementation for fetching the annotation graph ignored volumes, and made some assumptions which fit a particular use case I've now outgrown :sweat_smile:

I've deprecated it in favour of the new get_entity_graph. It's more generic over semantic objects, but there's still an escape hatch for getting skeleton IDs rather than neuron IDs (the difference is documented). You can key entities in the graph on name or ID; the caveats of using name are documented and the errors should be informative. You can also cut down the result by annotations, which will hopefully speed it up.

Some last-minute additions still need some more testing.

clbarnes commented 1 year ago

Test failure seems unrelated.

clbarnes commented 1 year ago

At least some of the test failures are from the to_scipy_sparse_(matrix|array) fix in navis, which isn't released yet.

clbarnes commented 1 year ago

The remaining failure seems to be from the server used for unit tests returning a 500. Ideally these responses would be mocked rather than reaching out to a server (would save server load and also speed things up).

schlegelp commented 1 year ago

Hi Chris. Not sure if you were waiting for me to chip in here. In case you were: looks good to me.

Also thanks for the reminder to release a new navis version