Coding · Python

A Twitter bot to find the most interesting bioRxiv preprints

TLDR: I wrote a Twitter bot to tweet the most interesting bioRxiv preprints. Follow it to stay up to date about the most recent preprints which received a lot of attention. https://t.co/r7PjEfCzUGDeepATAC: A deep-learning method to predict regulatory factor binding activity from ATAC-seq signals — PromisingPreprints (@PromPreprint) August 8, 2017 The past few months have… Continue reading A Twitter bot to find the most interesting bioRxiv preprints

development

Convenient uploading of a project to PyPI using a bash alias

Earlier I thought that using pypandoc in your setup.py was a great idea to solve the long_description and the README.rst, when you write your README in Markdown. Spoiler: it’s a pretty terrible idea… So: I have my README files in Markdown I would like to have them also in reStructuredText for PyPI submission I don’t want to copy paste… Continue reading Convenient uploading of a project to PyPI using a bash alias

development · Python

Committing the new version file to GitHub

As part of committing recently made changes to GitHub you also have to commit the changed version.py file. Perhaps this is overly lazy, but I wrote a small Python script called bumpversion.py to save myself just a few keystrokes per commit. When I prepared the setup.py to submit this script to PyPI I discovered someone… Continue reading Committing the new version file to GitHub

Coding · development

How to avoid duplicating your package version number using a version.py file

I thought it was rather annoying to specify the version of your package both in the tool itself and in your setup.py, so I searched the internet for solutions and below I’ll explain how I set it up. I have a version.py file in my project folder and this is the only spot where I… Continue reading How to avoid duplicating your package version number using a version.py file

Coding · development

Getting the setup.py long_description in reStructuredText from your Markdown README

I write my README files for Python/GitHub projects in Markdown, which is quite easy and convenient. But the PyPi guidelines for projects require a README.rst file in “reStructuredText”. The setup.py file also has a field for a “long description”, which will get inserted on the Pypi project page,  see for example this one for NanoPlot. UPDATE: TURNS… Continue reading Getting the setup.py long_description in reStructuredText from your Markdown README