python-neo
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NeuralEnsemble
Extract events from spike glx
Thanks @manimoh
This is great! Could you add a test for it? We have several SpikeGLX test files in the GIN epy_testing_data repo, and I'm sure (hope) at least one of them has digital events!
Hi @alejoe91 Sorry for the late reply! I actually did end up looking at the SpikeGLX test files in the repo you mentioned, but none of them have digital events. I had shared a couple of files in a separate spikeinterface issue, if you could add one or both of those two the test files repo, I could write some tests using that.
@alejoe91 I pushed a test for it. Won't work right now, since there's no testing data. Should we submit a PR for that on the gin repo directly?
DigitalChannelTest_g0.zip @TheChymera This archive are the required files that will work for the tests that we wrote
@alejoe91 I submitted a PR here → https://gin.g-node.org/NeuralEnsemble/ephy_testing_data/pulls/125
Will fix the reference as soon as that's merged.
Thanks! Can you add a line to the README (on the GIN PR) with the provenance of the file?
@alejoe91 done in https://gin.g-node.org/TheChymera/ephy_testing_data/commit/19f7708a8393b34821584922d1dc0ae499242c16
@alejoe91 done in https://gin.g-node.org/TheChymera/ephy_testing_data/commit/19f7708a8393b34821584922d1dc0ae499242c16
Merged ;)
@alejoe91 good? https://github.com/NeuralEnsemble/python-neo/pull/1383/commits/5c1d2d975d2192d8a1c264a10dd2c930c0e7eb0e
Also, why is the entities_to_test variable defined but never used? 🤔
@TheChymera acually, there seem to be somthing wrong with the files you uploaded to GIN, see https://gin.g-node.org/NeuralEnsemble/ephy_testing_data/src/master/spikeglx/DigitalChannelTest_g0/DigitalChannelTest_g0_t0.nidq.bin
This seems to arise from a missing sync command: https://gin.g-node.org/G-Node/Info/wiki/Annexed+Content
Can you make another PR with the fix?
@TheChymera acually, there seem to be somthing wrong with the files you uploaded to GIN, see https://gin.g-node.org/NeuralEnsemble/ephy_testing_data/src/master/spikeglx/DigitalChannelTest_g0/DigitalChannelTest_g0_t0.nidq.bin
This seems to arise from a missing
synccommand: https://gin.g-node.org/G-Node/Info/wiki/Annexed+ContentCan you make another PR with the fix?
@TheChymera acually, there seem to be somthing wrong with the files you uploaded to GIN, see https://gin.g-node.org/NeuralEnsemble/ephy_testing_data/src/master/spikeglx/DigitalChannelTest_g0/DigitalChannelTest_g0_t0.nidq.bin
This seems to arise from a missing
synccommand: https://gin.g-node.org/G-Node/Info/wiki/Annexed+ContentCan you make another PR with the fix?
Actually tried one here: https://gin.g-node.org/NeuralEnsemble/ephy_testing_data/pulls/127
@TheChymera the new test files were tested! But triggered some errors. Have you seen this before?
Ok should be fixed now :)
@TheChymera entities_to_test is indeed used by the base testing class, and that was one source of failures because "standard" tests expect some analog signals too
I wonder why other CI workflows didn't run., e.g.
- https://github.com/NeuralEnsemble/python-neo/blob/master/.github/workflows/core-test.yml
@yarikoptic that workflow only runs if changes in core/project.toml/workflows ;)
@yarikoptic that workflow only runs if changes in core/project.toml/workflows ;)
makes sense.. but why not to sweep python versions for call-iotests which are the only ones triggered here?
makes sense.. but why not to sweep python versions for call-iotests which are the only ones triggered here?
@yarikoptic, our iotests are currently being run from a cached conda environment to make them faster when dependencies don't change. This requires a fixed python version. If we got rid of the caching the env we could sweep versions, but then creating the new envs would take time. We actually just ran into an issue with testing where it autoupdated to python 3.12 which broke a lot of code during one of our PRs, so that would be a bit more work to improve the CI.
