Issues with installation?

[vkulaganathan]

Is there an issue with installation?
After the successfull installation using the "pip install bio"; it seems not called upon.

$ bio fetch MN996532 NC_045512 > genomes.gb
No command 'bio' found, did you mean:
Command 'bro' from package 'bro' (universe)
Command 'bip' from package 'bip' (universe)
Command 'biom' from package 'biom-format-tools' (universe)
Command 'fio' from package 'fio' (universe)
Command 'bino' from package 'bino' (universe)
Command 'rio' from package 'rio' (universe)
bio: command not found

[ialbert]

There has been no new version pushed out recently.

That is super weird error frankly, make sure to activate the right environment, then also try a new env just to make sure

conda create -n test -y python=3.8
conda activate test
pip install bio --upgrade
bio

I just tried this and for me it worked as expected.

[vkulaganathan]

I have older version of python, perhaps that is the issue.
--version
Python 3.6.5

I will check and post the comment if that fixes the issue.

[ialbert]

Unexpectedly indeed when I create a python 3.6 distribution I get the following error upon installation

ERROR: Cannot uninstall 'certifi'. It is a distutils installed project and thus 
we cannot accurately determine which files belong to it which would lead to only a partial uninstall.

[ialbert]

After googling some I found the following recommendation to solve the error:

ERROR: Cannot uninstall 'certifi'. It is a distutils installed project and thus 
we cannot accurately determine which files belong to it which would lead to only a partial uninstall.

add the --ignore-installed flag to pip:

pip install bio  --ignore-installed

it did work and the tests seem to pass:

 bio test

[vkulaganathan]

Thank you very much for promptly replying and helping with solving the problems.
The issue is resolved by upgrading the python3.6.5 to python3.8.

[ialbert]

thanks for the note, I was not aware that Python 3.6 would not work, but it makes sense, some of the dependencies seem to require that (even if tacitly so)

I will make the change in the installer to indicate Python 3.8 as a requirement