Problem with ncbi-genome-download

[TullyMonster]

Environment:

$ conda info

       libmamba version : 1.5.1
     micromamba version : 1.5.1
           curl version : libcurl/7.88.1 OpenSSL/3.1.2 zlib/1.2.13 zstd/1.5.5 libssh2/1.11.0 nghttp2/1.52.0
     libarchive version : libarchive 3.6.2 zlib/1.2.13 bz2lib/1.0.8 libzstd/1.5.2
       envs directories : /home/tully/micromamba/envs
          package cache : /home/tully/micromamba/pkgs
                          /home/tully/.mamba/pkgs
            environment : bioinfo (active)
           env location : /home/tully/micromamba/envs/bioinfo
      user config files : /home/tully/.mambarc
 populated config files : /home/tully/.condarc
       virtual packages : __unix=0=0
                          __linux=5.15.133=0
                          __glibc=2.35=0
                          __archspec=1=x86_64
               channels : https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
                          https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
       base environment : /home/tully/micromamba
               platform : linux-64

$ conda list ncbi-genome-download

List of packages in environment: "/home/tully/micromamba/envs/bioinfo"

  Name                  Version  Build         Channel
─────────────────────────────────────────────────────────
  ncbi-genome-download  0.3.3    pyh7cba7a3_0  bioconda

Error:

$ ncbi-genome-download

Traceback (most recent call last):
  File "/home/tully/micromamba/envs/bioinfo/lib/python3.8/site-packages/requests/compat.py", line 11, in <module>
    import chardet
ModuleNotFoundError: No module named 'chardet'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/tully/micromamba/envs/bioinfo/bin/ncbi-genome-download", line 6, in <module>
    from ncbi_genome_download.__main__ import main
  File "/home/tully/micromamba/envs/bioinfo/lib/python3.8/site-packages/ncbi_genome_download/__init__.py", line 6, in <module>
    from .core import (
  File "/home/tully/micromamba/envs/bioinfo/lib/python3.8/site-packages/ncbi_genome_download/core.py", line 17, in <module>
    import requests
  File "/home/tully/micromamba/envs/bioinfo/lib/python3.8/site-packages/requests/__init__.py", line 45, in <module>
    from .exceptions import RequestsDependencyWarning
  File "/home/tully/micromamba/envs/bioinfo/lib/python3.8/site-packages/requests/exceptions.py", line 9, in <module>
    from .compat import JSONDecodeError as CompatJSONDecodeError
  File "/home/tully/micromamba/envs/bioinfo/lib/python3.8/site-packages/requests/compat.py", line 13, in <module>
    import charset_normalizer as chardet
  File "/home/tully/micromamba/envs/bioinfo/lib/python3.8/site-packages/charset_normalizer/__init__.py", line 24, in <module>
    from .api import from_bytes, from_fp, from_path, is_binary
  File "/home/tully/micromamba/envs/bioinfo/lib/python3.8/site-packages/charset_normalizer/api.py", line 5, in <module>
    from .cd import (
  File "/home/tully/micromamba/envs/bioinfo/lib/python3.8/site-packages/charset_normalizer/cd.py", line 14, in <module>
    from .md import is_suspiciously_successive_range
  File "charset_normalizer/md.py", line 10, in <module>
ImportError: cannot import name 'is_ascii' from 'charset_normalizer.utils' (/home/tully/micromamba/envs/bioinfo/lib/python3.8/site-packages/charset_normalizer/utils.py)

But when I initialized a brand new virtual environment and installed ncbi-genome-download, everything was fine:

$ conda info | grep environment && echo "ncbi-genome-download -V  # $(ncbi-genome-download -V)"

            environment : test (active)
       base environment : /home/tully/micromamba
ncbi-genome-download -V  # 0.3.3

Errors in virtual environment bioinfo, how to resolve, please?

[ialbert]

I have seen this one occur everyone once in a while, not sure why it started occurring

pip install chardet

see if that fixes it

[TullyMonster]

Thank U, Fixed by conda install chardet. ;)

[ialbert]

as you can see from the error, it comes from the charset_normalizer package that advertises itself as being a faster chardet

https://pypi.org/project/charset-normalizer/

but then it seems it imports chardet without declaring it, but only in some versions

[TullyMonster]

Thank you so much, you're my lifesaver!

[TullyMonster]

By the way, what is the meaning of the lib shown in blue?

[ialbert]

I never noticed it myself,

but now that I have investigated, I believe that to be a micromamba specific feature that shows which library is not the latest.

in some circumstances when installing multiple packages not all software can be the latest version

[TullyMonster]

But I checked the packages and some seemed to be in the latest version.

[TullyMonster]

It's okay. It doesn't matter