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tyjo / coptr

Accurate and robust inference of microbial growth dynamics from metagenomic sequencing
GNU General Public License v3.0
16 stars 5 forks source link

Package up coptr #4

Closed Midnighter closed 3 years ago

Midnighter commented 3 years ago

Hi,

First of all thank you for creating this cool. I'm testing it at the moment but it looks promising already!

I was a bit annoyed that coptr is not installable but has to be run from the script so I went ahead and fixed that. So in principle, with these changes, you can distribute coptr on PyPI and create a conda-forge feedstock. When the package is installed it creates a command line tool simply called coptr.

I see a number of things that can still be improved but this was the minimal workable thing for me. If you look at the individual commits, I hope you can follow what I did without being overwhelmed by all changes.

Please let me know if this is of interest to you.

tyjo commented 3 years ago

Thanks for the pull request! I am interested in merging this into the main branch.

I think it might be better to distribute CoPTR on bioconda or conda-forge rather than PyPI. PyPI doesn't appear to support dependencies that are not themselves Python packages---like bowtie2. Is there a reason you prefer conda-forge over bioconda?

Midnighter commented 3 years ago

I think it might be better to distribute CoPTR on bioconda or conda-forge rather than PyPI. PyPI doesn't appear to support dependencies that are not themselves Python packages---like bowtie2.

While that is true, there are many Python packages that have other system dependencies. It is still very convenient to be able to pip install the package when one doesn't want to use conda and simply require that bowtie2 is installed on the system separately.

Is there a reason you prefer conda-forge over bioconda?

In this case not really. Conda-forge builds packages for Linux, Mac, and Windows so that's an advantage when there are compiled components. Since that is not the case 🤷🏼‍♂️

tyjo commented 3 years ago

I merged this into the main branch and updated the documentation. I still need to look into distribution on PyPI / conda.

Midnighter commented 3 years ago

Let me know if you want some help with that. I maintain a number of packages both on PyPI and conda-forge so I'm quite familiar with the process.

tyjo commented 3 years ago

CoPTR is up on PyPI and installable via pip: https://pypi.org/project/coptr/