From 05b00e1297133bfaece68925e03ae59d1c5a16b9 Mon Sep 17 00:00:00 2001 From: betteridiot Date: Thu, 19 Jul 2018 10:53:13 -0400 Subject: [PATCH] Added community guideline information --- README.md | 5 +++++ README.rst | 10 ++++++++++ codemeta.json | 2 +- docs/paper/codemeta.json | 2 +- setup.py | 2 +- 5 files changed, 18 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index a77b350..1ccc6ce 100644 --- a/README.md +++ b/README.md @@ -194,3 +194,8 @@ A simple seek call against the BAM file will put the head at the start of your r The common practice within the field of genomics/genetics when analyzing BAM files is to use the program known as [samtools](http://samtools.sourceforge.net/). The maintainers of samtools have done a tremendous job of providing distributions that work on a multitude of operating systems. While samtools is powerful, as a command line interface, it is also limited in that it doesn't really afford the ability to perform real-time dynamic processing of reads (without requiring many system calls to samtools). Due to its general nature and inherent readability, a package was written in Python called [pysam](https://github.com/pysam-developers/pysam). This package allowed users a very comfortable means to doing such dynamic processing. However, the foundation of these tools is built on a C-API called [htslib](https://github.com/samtools/htslib) and htslib cannot be compiled in a Windows environment. By extension, neither can pysam.

In building a tool for genomic visualization, I wanted it to be platform agnostic. This is precisely when I found out that the tools I had planned to use as a backend did not work on Windows...the most prevalent operation system in the end-user world. So, I wrote **bamnostic**. As of this writing, bamnostic is OS-agnostic and written completely in Pure Python--requiring only the standard library (and `pytest` for the test suite). Special care was taken to ensure that it would run on all versions of CPython 2.7 or greater. Additionally, it runs in both stable versions of PyPy. While it may perform slower than its C counterparts, bamnostic opens up the science to a much greater end-user group. Lastly, it is lightweight enough to fit into any simple web server (e.g. [Flask](http://flask.pocoo.org/)), further expanding the science of genetics/genomics. + + +*** +## Community Guidelines: +Eagerly accepting PRs for improvements, optimizations, or features. For any questions or issues, please feel free to make a post to bamnostic's [Issue tracker](https://github.com/betteridiot/bamnostic/issues) on github. \ No newline at end of file diff --git a/README.rst b/README.rst index 1205b87..fdd110e 100644 --- a/README.rst +++ b/README.rst @@ -303,6 +303,16 @@ it is lightweight enough to fit into any simple web server (e.g. `Flask `__), further expanding the science of genetics/genomics. +-------------- + +Community Guidelines: +--------------------- + +Eagerly accepting PRs for improvements, optimizations, or features. For +any questions or issues, please feel free to make a post to bamnostic's +`Issue tracker `__ on +github. + .. |Build Status| image:: https://travis-ci.org/betteridiot/bamnostic.svg?branch=master :target: https://travis-ci.org/betteridiot/bamnostic .. |noarch| image:: https://img.shields.io/circleci/project/github/conda-forge/bamnostic-feedstock/master.svg?label=noarch diff --git a/codemeta.json b/codemeta.json index 68fa208..fe0c69f 100644 --- a/codemeta.json +++ b/codemeta.json @@ -37,7 +37,7 @@ "description": "BAMnostic is a Pure Python OS, version, and runtime agnostic BAM file parser", "keywords": "BAM, pysam, genomics, genetics, htslib, samtools", "license": "https://github.com/betteridiot/bamnostic/blob/master/LICENSE", - "softwareVersion": "v0.8.7b1", + "softwareVersion": "v0.8.7b2", "version": "v0.8.2", "readme": "https://github.com/betteridiot/bamnostic/blob/master/README.md", "buildInstructions": "https://github.com/betteridiot/bamnostic/blob/master/README.md", diff --git a/docs/paper/codemeta.json b/docs/paper/codemeta.json index 8f46e73..0a1ee0c 100644 --- a/docs/paper/codemeta.json +++ b/docs/paper/codemeta.json @@ -37,7 +37,7 @@ "description": "BAMnostic: an OS-agnostic toolkit for genomic sequence analysis", "keywords": "BAM, pysam, genomics, genetics, htslib, samtools", "license": "https://github.com/betteridiot/bamnostic/blob/master/LICENSE", - "softwareVersion": "v0.8.7b1", + "softwareVersion": "v0.8.7b2", "version": "v0.8.2", "readme": "https://github.com/betteridiot/bamnostic/blob/master/README.md", "buildInstructions": "https://github.com/betteridiot/bamnostic/blob/master/README.md", diff --git a/setup.py b/setup.py index 56a5c52..17af850 100644 --- a/setup.py +++ b/setup.py @@ -9,7 +9,7 @@ def readme(): setup( name='bamnostic', - version='0.8.7b1', + version='0.8.7b2', description='Pure Python, OS-agnostic Binary Alignment Map (BAM) random access and parsing tool', long_description=readme(), url='https://github.com/betteridiot/bamnostic/',