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Molmed / checkQC

CheckQC inspects the content of an Illumina runfolder and determines if it passes a set of quality criteria
http://checkqc.readthedocs.io/
GNU General Public License v3.0
25 stars 16 forks source link

Develop 2548 add nova seq x support #106

Closed Aratz closed 1 year ago

Aratz commented 1 year ago

This PR updates CheckQC's dependencies, and specifically interop, which is needed to process the new runfolder.

It also makes instrument detection case insensitive and adds tests for that.

matrulda commented 1 year ago

Looks good! I do however get this error when trying to build the docs: 

$ sphinx-autobuild . _build/html
Running Sphinx v7.0.0

Configuration error:
There is a programmable error in your configuration file:

Traceback (most recent call last):
  File "/home/matilda/.pyenv/versions/checkqc/lib/python3.8/site-packages/sphinx/config.py", line 354, in eval_config_file
    exec(code, namespace)  # NoQA: S102
  File "/home/matilda/workspace/checkQC/docs/conf.py", line 25, in <module>
    from recommonmark.parser import CommonMarkParser
ModuleNotFoundError: No module named 'recommonmark'

Command exited with exit code: 2

It seems like looks like it solved by installing recommonmark with pip. So perhaps we need to add that to the requirements, weird that it's not included with Sphinx thoug :thinking: Maybe you can see if you can reproduce this so it's not only a thing in my environment.

I've tried it in a virtual env with py3.8.13.

Aratz commented 1 year ago

Looks like recommonmark is not maintained anymore (https://github.com/readthedocs/recommonmark) and Sphynx recommends myst-parser instead (https://www.sphinx-doc.org/en/master/usage/markdown.html) so I'm gonna adapt the configuration for that.