publish latest version on PyPi

[dlaehnemann]

Thanks for developing this software!

I would like to package it on bioconda to be able to reliably and reproducibly install it in a snakemake analysis workflow. For packaging on bioconda, the easiest path for a Python package is usually if it is consistently published on PyPi, as this will also facilitate automated updates of the package upon the release of newer versions. I can see that you previously published a version on PyPi and was wondering why you turned it off in this commit:
0dc3b6d

I have started work on the packaging with the existing version from PyPi here:
bioconda/bioconda-recipes#61008

But this is currently stalled, because it also requires adding multiprocessingpandas to conda-forge:
conda-forge/staged-recipes#31592

At the same time, later versions don't seem to use multiprocessingpandas any more. So if you could package the latest version 0.13.0 on PyPi, that would speed this bit up.

separate requirements for setup

This was something that the auto-generation of the bioconda recipe via grayskull didn't pick up, so it seems to be rather non-standard to have a separate requirements-setup.txt. But I'm not expert on Python packaging, and the Python packaging ecosystem can be very confusing.

However, should you be interested in a well-documented modern Python packaging setup, I have recently found the pyOpenSci documentation and it provides very thorough walkthroughs and linkouts:
https://www.pyopensci.org/python-package-guide/package-structure-code/intro.html

[dlaehnemann]

Just a quick update regarding getting the upstream dependency multiprocessingpandas into conda-forge. This package has not been maintained for three years now, and its pinning of multiprocess leads to conflicts on conda-forge. So I decided not to pursue getting this package into conda-forge any more:
conda-forge/staged-recipes#31592 (comment)

So I also closed the pull request to add howard to bioconda. But if you publish your latest version of howard to PyPi (which doesn't depend on multiprocessingpandas any more), feel free to ping me. I'd be glad to start a new bioconda pull request to get howard in there with this newer version.

[antonylebechec]

Hi @dlaehnemann,

Thank you very much for opening this issue and for your thoughtful comments. We really appreciate the time and effort you’re putting into improving HOWARD and helping with its distribution!

We completely agree with your points regarding consistent availability of the package. Making HOWARD easy to install and integrate in workflows (e.g., via Bioconda and PyPI) is something we want to support, and your feedback and work toward that goal are truly valuable to us. We’re also learning and improving our practices around packaging and distribution. Feedback like yours helps us do better with each release.

The version currently available on GitHub will be published on PyPi soon (actually on testPyPi), which should help with packaging and automated updates. In parallel, a new version of HOWARD is actively in development with various improvements and fixes; we’re working to align the release process so that updates on PyPI follow smoothly after new releases.

Thanks again for your support and for helping move HOWARD forward. Please don’t hesitate to share any further suggestions or questions!

[antonylebechec]

The last release 0.13.0 of HOWARD is available on PyPi now (as pyhoward package):
https://pypi.org/project/pyhoward/
We will take into account your suggestions as much as possible for further releases.

[dlaehnemann]

Nice. I reopened the pull request in bioconda:
bioconda/bioconda-recipes#61008 (comment)

And I realized that the bgzip python package is indeed used, I must have previously overlooked the import bgzip statement. So I'll edit my initial post accordingly.

[dlaehnemann]

Also, the main initial point of this issue is now addressed. So feel free to close this issue, or rename it to also reflect the planned updates to the packaging. Or just open another tracking issue for this. Whatever works best for you.

[antonylebechec]

Great!
I'll keep this issue, as it can be a thread for future releases and packaging issues.
Concerning bgzip, I'll take a look at the devel version.
Thanks again for your interest and your help on packaging!
Best,