Bernie Pope issues

Results 30 issues of


                                            Bernie Pope

How to safely close file handles with Fastx?

It is not clear how to safely close any file handles that are opened by Fastx (or any of the other classes provided by this library). It would be nice...

Consider using GitHub actions instead of Travis

Document generation for Sphinx

Consider adding example document generation for Sphinx.

GitHub API is deprecating password access. Use personal access token instead (PAT).

Currently the bionitio-boot.sh script uses curl to communicate with the GitHub API. Password authentication via this API is being deprecated and the recommendation from GitHub is to use a personal...

Consider mounting functional_tests directory in Docker, rather than including it in the containers

We could mount in the functional_tests directory, so that it doesn't have to be part of the Docker image itself (like it is now). However this would mean the users...

Test GitHub integration on Windows

A user has reported that GitHub integration failed on Windows under PowerShell. Running the bootstrap script: - a new/different command-line window was opened - this asked for the user's GitHub...

Make all implementations call their executable binitio (and remove any extensions in the name)

This will help homogenise our README.md All implementations should be called bionitio, and e.g. not bionitio-py or whatever.

Add paper citation to documentation

Python 3.x version and document 2.7 dependency

Support SLURM job scheduler

Add support for SLURM job scheduler.