From b5c4f1bae557757d6a73e0bb5f9ee7da075f7761 Mon Sep 17 00:00:00 2001 From: "C. Titus Brown" Date: Mon, 22 Jan 2024 11:26:33 -0800 Subject: [PATCH] MRG: update README with repostatus and pyver badges, and Windows support (#2928) Direct link to updated README: [link](https://github.com/sourmash-bio/sourmash/blob/update_readme/README.md) Adds repostatus badge as well as list of python versions supported. Switches to recommending conda-forge and sourmash-minimal, since that supports Windows ref #1923. Also adds direct mention of operating systems supported, including Windows (ref https://github.com/sourmash-bio/sourmash/issues/1923). Fixes https://github.com/sourmash-bio/sourmash/issues/2909 Fixes https://github.com/sourmash-bio/sourmash/issues/2910 --- README.md | 50 +++++++++++++++++++++----------------------------- 1 file changed, 21 insertions(+), 29 deletions(-) diff --git a/README.md b/README.md index b05d8f517e..085c07309e 100644 --- a/README.md +++ b/README.md @@ -2,14 +2,21 @@ Quickly search, compare, and analyze genomic and metagenomic data sets. +[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) +License: 3-Clause BSD [![Documentation](https://readthedocs.org/projects/sourmash/badge/?version=latest)](http://sourmash.readthedocs.io/en/latest/) [![Gitter](https://badges.gitter.im/sourmash-bio/community.svg)](https://gitter.im/sourmash-bio/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge) -[![Build Status](https://github.com/sourmash-bio/sourmash/workflows/Python%20tests/badge.svg)](https://github.com/sourmash-bio/sourmash/actions/) +[![DOI](http://joss.theoj.org/papers/10.21105/joss.00027/status.svg)](http://joss.theoj.org/papers/10.21105/joss.00027) + [![Bioconda install](https://img.shields.io/conda/dn/bioconda/sourmash.svg?style=flag&label=Bioconda)](https://anaconda.org/bioconda/sourmash) PyPI +[![Conda Platforms](https://img.shields.io/conda/pn/conda-forge/sourmash-minimal.svg)](https://anaconda.org/conda-forge/sourmash-minimal) + +![Python 3.10](https://img.shields.io/badge/python-3.10-blue.svg) +![Python 3.11](https://img.shields.io/badge/python-3.11-blue.svg) +![Python 3.12](https://img.shields.io/badge/python-3.12-blue.svg) +[![Build Status](https://github.com/sourmash-bio/sourmash/workflows/Python%20tests/badge.svg)](https://github.com/sourmash-bio/sourmash/actions/) [![codecov](https://codecov.io/gh/sourmash-bio/sourmash/branch/latest/graph/badge.svg)](https://codecov.io/gh/sourmash-bio/sourmash) -[![DOI](http://joss.theoj.org/papers/10.21105/joss.00027/status.svg)](http://joss.theoj.org/papers/10.21105/joss.00027) -License: 3-Clause BSD

@@ -44,10 +51,10 @@ community. ## Installation -We recommend using bioconda to install sourmash: +We recommend using conda-forge to install sourmash: ``` -conda install -c conda-forge -c bioconda sourmash +conda install -c conda-forge sourmash-minimal ``` This will install the latest stable version of sourmash 4. @@ -61,22 +68,21 @@ A quickstart tutorial [is available](https://sourmash.readthedocs.io/en/latest/t ### Requirements -sourmash runs under Python 3.10 and later. The base -requirements are screed, cffi, numpy, matplotlib, and scipy. Conda -(see below) will install everything necessary, and is our recommended -installation method. +sourmash runs under Python 3.10 and later on Windows, Mac OS X, and +Linux. The base requirements are screed, cffi, numpy, matplotlib, and +scipy. Conda will install everything necessary, and is +our recommended installation method (see below). ### Installation with conda -Bioconda is a channel for the -[conda](http://conda.pydata.org/docs/intro.html) package manager with -a focus on bioinformatics software. After +conda-forge is a community maintained channel for the +[conda](http://conda.pydata.org/docs/intro.html) package manager. [installing conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/), you can install sourmash by running: ```bash -$ conda create -n sourmash_env -c conda-forge -c bioconda sourmash -$ source activate sourmash_env +$ conda create -n sourmash_env -c conda-forge sourmash-minimal +$ conda activate sourmash_env $ sourmash --help ``` @@ -110,19 +116,5 @@ Tests require py.test and can be run with `make test`. Please see [the developer notes](doc/developer.md) for more information on getting set up with a development environment. -## Research notice - -Please note that this repository is participating in a study into sustainability - of open source projects. Data will be gathered about this repository for - approximately the next 12 months, starting from 2021-06-11. - -Data collected will include number of contributors, number of PRs, time taken to - close/merge these PRs, and issues closed. - -For more information, please visit -[our informational page](https://sustainable-open-science-and-software.github.io/) or download our [participant information sheet](https://sustainable-open-science-and-software.github.io/assets/PIS_sustainable_software.pdf). - ----- - CTB -Feb 2021 +Jan 2024