Confusion over name - PHEnix or Phoenix ?

[tseemann]

The repo is called PHEnix but the docs call it Phoenix.

And the repo doesn't have a runnable command called either of those? eg. phenix

[alexjironkin]

We do not have a runnable phenix.py command in favour of more appropriately named scripts in the scripts directory.

If used in python to import modules we felt its also more appropriate and readable to have statement like import phe.mapping instead of import phe.phenix.mapping.

Thanks for the notice on the docs not correctly reflecting the name in the repo. @ALL can we correct the docs.

[tseemann]

I would rename your two main scripts to phenix-prepare_reference and phenix-run_blah etc, or have a single phenix script with sub-commands (like samtools and sga etc).

You want to avoid name clashes, and it provides a single place to get a --version option.

As per https://gigascience.biomedcentral.com/articles/10.1186/2047-217X-2-15 ;-)

[antunderwood]

I think that could work nicely. We'll look into it and maybe use the nesting parsers feature of argparse (https://pymotw.com/2/argparse/#nesting-parsers).

[alexjironkin]

Just added phenix.py with the command subparsers.

Have not implemented --version option yet, as there is an ongoing discussion on how to make in universal from git/pip. I have used versioneer in the past and like it. But I am not certain yet if this is the most appropriate way of doing it yet. It's coming though.

[antunderwood]

It would be good to transfer the updated instructions reflected in readthedocs to the README.md

[alexjironkin]

No need, it's automatically done via the docs build system:

http://phenix.readthedocs.org/en/latest/scripts/modules.html

[antunderwood]

The README.md on the front page still reflects the old way of calling the scripts

[alexjironkin]

Oh yeah, totally forgot about that. :)

[alexjironkin]

--version is there now. It is also in the VCF headers for future reference. I had to ditch cool git version string in favour of more simplistic approach. Mostly due to difficulties in getting it done decently in different places.