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cfe-lab / MiCall

Pipeline for processing FASTQ data from an Illumina MiSeq to genotype human RNA viruses like HIV and hepatitis C
https://cfe-lab.github.io/MiCall
GNU Affero General Public License v3.0
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Multiple python interpreters in dev container cause issues #1033

Closed Donaim closed 1 month ago

Donaim commented 1 year ago

Our docker image is based on python:3.8, which includes two versions of python. One comes from the underlying distribution, and another one from the image maintainers.

As a result, when python packages are install during docker build, they are not immediately visible to vscode.

Donaim commented 1 year ago

Simply removing the "incorrect" python binary fixes the problem.

Donaim commented 1 year ago

Removing the whole incorrect python3.9 package does not work because apt remove fails with a dependency related error.

Donaim commented 1 year ago

We hope that the cleaner solution will be available after we switch to a more recent python version, like python 3.12.

However, an outstanding issue with minimap is currently preventing us from upgrading.

Donaim commented 1 year ago

Another alternative is to configure virtualenv for MiCall as it seems that editors default to the python version set in the .venv/pyvenv.cfg.

This requires more investigation.

Donaim commented 1 month ago

Solved by upgrading to a new python version (https://github.com/cfe-lab/MiCall/pull/1167)

However this may come up again, as the python versions deviate inside the container.

Maybe we should base the container on generic "Debian" or "Ubuntu" instead of "python:whatever"