Updated multiqc from 1.9 to 1.10 and no longer works.

[rebeelouise]

Description of bug:

MultiQC Error log:

File "/home/hlrpenri/miniconda2/envs/mypython3/bin/multiqc", line 6, in <module>
    from multiqc.__main__ import multiqc
  File "/home/hlrpenri/miniconda2/envs/mypython3/lib/python3.6/site-packages/multiqc/__main__.py", line 53, in <module>
    multiqc.run_cli(prog_name="multiqc")
  File "/home/hlrpenri/miniconda2/envs/mypython3/lib/python3.6/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "/home/hlrpenri/miniconda2/envs/mypython3/lib/python3.6/site-packages/click/core.py", line 782, in main
    rv = self.invoke(ctx)
  File "/home/hlrpenri/miniconda2/envs/mypython3/lib/python3.6/site-packages/click/core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/hlrpenri/miniconda2/envs/mypython3/lib/python3.6/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/home/hlrpenri/miniconda2/envs/mypython3/lib/python3.6/site-packages/multiqc/multiqc.py", line 248, in run_cli
    kwargs=kwargs,
  File "/home/hlrpenri/miniconda2/envs/mypython3/lib/python3.6/site-packages/multiqc/multiqc.py", line 565, in run
    report.get_filelist(run_module_names)
  File "/home/hlrpenri/miniconda2/envs/mypython3/lib/python3.6/site-packages/multiqc/utils/report.py", line 256, in get_filelist
    rich.progress.SpinnerColumn(),
AttributeError: module 'rich.progress' has no attribute 'SpinnerColumn'

File that triggers the error:

MultiQC run details (please complete the following):

• Command used to run MultiQC: multiqc .
• MultiQC Version: 1.10
• Operating System: linux
• Python Version: python 3.6.1
• Method of MultiQC installation: conda

Additional context

[ewels]

Hi @rebeelouise ,

When did you try to install MultiQC from conda? This issue happens when you already have the Python rich library installed (a new dependency for MultiQC v1.10) but it is too old. We fixed the conda recipe to solve this soon after the release here: bioconda/bioconda-recipes#27287

I would hope that installing now with the second build (conda version 1.10-1) would solve this.

Anyway, either way, the fix is simple:

conda update rich

If you have rich version 9.4.0 or higher installed then you should have no problem.

Phil

[ewels]

Just bumped this requirement in the main MultiQC code base, so will also be applied on PyPI in the next release.