core-bioimage-io-python

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ideally we would bump this with every spec release... we could auto generate a PR for this purpose... but maybe I've just looked too much at github workflows lately to...

FynnBe

Support out-of-core prediction_with_tiling (with dask?)

1

Maybe relevant https://xarray.pydata.org/en/stable/user-guide/dask.html

constantinpape

Why does `load_resource_description` download the `git_repo`? I assume that this is only metadata and there should be no reason to download it. This leads to issues when trying to run...

constantinpape

Add the option to disable insecure weight types

3

For serving models with the core library from a public server, we need to have an option to disable all the model weight types that uses source code (e.g. pytorch...

oeway

Is license checked in the validation?

3

We have a model with incorrect license name ("BSD-3") and rdf version 0.3.2. The validator says that the specs are correct but test-model complains about the licensing: ```python marshmallow.exceptions.ValidationError: {'license':...

esgomezm

ImplicitShape is supported for input tensors now, see https://github.com/bioimage-io/spec-bioimage-io/issues/234. We should add a test case for this.

constantinpape

Cache handling needs improvement

2

caching everyting to `~/bioimageio_cache` with the current pattern of only analysing the url fails for updates to the remote resource, e.g. a 'master' branch on github, etc...

FynnBe

How to reliably free GPU memory after tensorflow/keras inference?

2

> Atm, only pytorch_state_dict and pytorch_script models actually unload, TF and keras model adapters give a warning and skip unloading. -- https://github.com/bioimage-io/core-bioimage-io-python/pull/155#issue-1060594661 @constantinpape @esgomezm @tomburke-rse @oeway let's gather some snippets...

FynnBe

Add example images for the test notebook

3

Hi @constantinpape Could you provide some examples for the example notebook so we can reproduce it easily? Either download it from somewhere (e.g. github release) or in the repo directory.

oeway

Add tests to compare all pre-and-postprocessing implementations

5

We should add tests to check that the pre/post-processing operations are implemented consistently across all different bioimage.io libraries / consumers. cc @FynnBe @esgomezm @tomburke-rse

constantinpape