Open melonora opened 7 months ago
can we generate this with blobs().write()
at test time so we can keep it up to date with however spatialdata may update its format as well?
also what is the fate of this package anyway? should format tests go in the main test suite or here? on the one hand gathering all the array tests here would be nice, on the other hand if we're doing the work in the main repo (rather than importing from here) this could get desync'd
This would be possible at test time as far as I am aware.
@melonora do you want to modify the PR or make a new one?
I can modify the PR. Is it ok to add spatialdata as a dependency in order to create the files at test time?
Adding as a test dependency should be fine
On Sat, Feb 24, 2024 at 4:12 AM Wouter-Michiel Vierdag < @.***> wrote:
I can modify the PR. Is it ok to add spatialdata as a dependency in order to create the files at test time?
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I am trying to update the PR, just with poetry resolving the dependencies seems to take forever. This does not seem to be due to a conflict arising. I already adjusted the python dependency to >=3.9,<3.13
to comply with the xarray
requirements.
@cmungall I think this should be good to go now. I made it so that the data can be created on the fly by using a fixture. The demo test demonstrates this.
I like what im seeing here. Is the plan to use this repo for extended testing of the generators in the main linkml repo? Im mostly finished with the pure lists of lists implementation and am about to start the more advanced one that can hook into array libraries, and it would be cool to be testing on real data from a real format like this
I like what im seeing here. Is the plan to use this repo for extended testing of the generators in the main linkml repo? Im mostly finished with the pure lists of lists implementation and am about to start the more advanced one that can hook into array libraries, and it would be cool to be testing on real data from a real format like this
Would you like fixtures for the individual components as well? Because that can be added too.
Idk exactly what would be good yet, but will revisit when it's time to test the pydanticgen implementation of arrays
This PR allows the generation of a
SpatialData
object at test time. This is done by using apytest.fixture
. Here,tmp_path
is a fixture from_pytest.tmpdir
.It contains all the components currently present in
SpatialData
. More information here: github and scverseSpatialData
itself builds on top of OME-NGFF.