merenlab / anvio

An analysis and visualization platform for 'omics data
http://merenlab.org/software/anvio
GNU General Public License v3.0
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[BUG] anvi-help not working anymore #2146

Closed FlorianTrigodet closed 9 months ago

FlorianTrigodet commented 9 months ago

Short description of the problem

With v8 or dev version, anvi-help is not working anymore.

anvi'o version

v8 and dev version.

Detailed description of the issue

Example command:

anvi-help gene

Here is the first error:

Traceback (most recent call last):
  File "/gss/work/nand5072/SOFTWARE/anvio/bin/anvi-help", line 35, in <module>
    TABLE_BG = back.GREY_11
AttributeError: 'function' object has no attribute 'GREY_11'

This is an error I can fix. The package colored has changed a little bit and all 'back', 'fore' and 'style' need to be replaced with a capital letter: 'Back', 'Fore', 'Style'.

But even when I fix this issue, I have a new error and I don't know what's happening:

Traceback (most recent call last):
  File "/Users/fltrig002/github/anvio/bin/anvi-help", line 5, in <module>
    from anvio.argparse import ArgumentParser
  File "/Users/fltrig002/github/anvio/anvio/argparse.py", line 7, in <module>
    import argparse
  File "/Users/fltrig002/github/anvio/anvio/argparse.py", line 11, in <module>
    from rich_argparse import RichHelpFormatter
  File "/Users/fltrig002/miniconda3/envs/anvio-dev/lib/python3.10/site-packages/rich_argparse/__init__.py", line 25, in <module>
    class RichHelpFormatter(argparse.HelpFormatter):
AttributeError: partially initialized module 'argparse' has no attribute 'HelpFormatter' (most likely due to a circular import)
FlorianTrigodet commented 9 months ago

I made a mistake with the above error. Forget about the second issue: it is because I ran the anvi'o command from the anvio directory 🤦

fixed with #2147