run_resfinder.py missing version information

[Peter Cock]

There is no obvious way to check what version of resfinder is installed (and the user may not be the person who installed it).

It is common practice to offer a -v or --version switch at the command line to report (just) the tool version.

Another convention is to include the version number near the start of the -h or --help text.

I am using version 4.1.6 but I only know this because I installed from git and examined the tags and picked this (the current latest tag) explicitly with “git checkout 4.1.6” during installation.

[CGE Helpdesk]

Dear Peter,

We appreciate your feedback and suggestions.
The ResFinder version can now be extracted from the git tag when using -v or --version.

Help information can be displayed with

python3 run_resfinder.py -h

Best,
Karen, CGE Helpdesk

[Peter Cock]

I’m not convinced that 5cc9412f0502d9bdbc69dc59d5e6631b8bd7063f is enough, that change will report any version information from the git history - so it can only work if the user’s copy of run_resfinder.py is in a clone of the git repository.

It will not work if ResFinder was installed from a tar-ball or other copy of the source code. This would be a problem for example if ResFinder is packaged for installation by Conda, a Linux distribution, or similar.

[CGE Helpdesk]

Dear Peter,

Although it is a fair point, due to our limited resources we can only cover the functionality of ResFinder for the installation that we recommend (clone the repository). However, as you might already know, a conda versions are in the making. We will make sure create tags and update to these as well. We hope you understand.

Best,
Karen, CGE Helpdesk

[Peter Cock]

Having ResFinder on conda will cover a lot of potential users, so as long as you keep this in mind during the packaging work, it should be fine. Thank you.

[RolfKaas]

Resolved in version 4.2.1. ResFinder is now available through pip (and docker hub) and verion can be obtained through "-v" or "--version".

[Peter Cock]

Excellent - having releases on PyPI https://pypi.org/project/resfinder/ ought to make it possible to add ResFinder to BioConda as well. Thank you.