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nanoporetech / medaka

Sequence correction provided by ONT Research
https://nanoporetech.com
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Tensorflow and Python version upgrade request: Tensorflow >=2.8.0 for Python 3.10 support #396

Closed StephDC closed 1 year ago

StephDC commented 1 year ago

Medaka is a Research Release.

Research releases are provided as technology demonstrators to provide early access to features or stimulate Community development of tools. Support for this software will be minimal and is only provided directly by the developers. Feature requests, improvements, and discussions are welcome and can be implemented by forking and pull requests. However much as we would like to rectify every issue and piece of feedback users may have, the developers may have limited resource for support of this software. Research releases may be unstable and subject to rapid iteration by Oxford Nanopore Technologies.

We provide no guarantees that feature requests will be implemented. They may be implemented if sufficient interest is generated or if the request aligns with research objectives.

Is your feature request related to a problem? Please describe. medaka does not support python version >=3.10

With some investigation it seems that the root cause of such is that the specified version of tensorflow (v.2.7.0) do not support python version >=3.10

Describe the solution you'd like

Describe alternatives you've considered State the required python version on README so we know which version of medaka require which version of python.

Additional context I am attempting to run this software on Gentoo, and Gentoo has upgraded python to python3.10 a little while ago. When I try to install it with pip, I was greeted with the error message of all versions of medaka requires a different python version.

When attempting to compile medaka from scratch against python 3.10, I figured out that the tensorflow 2.7.0 is not available on python 3.10. After changing tensorflow to 2.8.0 and allowing python 3.10, it seems that make install can complete successfully, although further testing is not done yet.

asan-emirsaleh commented 1 year ago

Was the upgrade successful? Did medaka proceed with both python and TF being upgraded?

cjw85 commented 1 year ago

The Tensorflow dependency has been upgraded to to 2.8 in v1.7.3 of medaka.