From 343b39345d85c657e869b01e5e16bdde308af30c Mon Sep 17 00:00:00 2001 From: JeanMainguy Date: Tue, 23 Jan 2024 01:19:41 +0100 Subject: [PATCH 1/5] add pypi badge --- README.md | 11 ++++++++--- docs/index.md | 11 ++++++++--- 2 files changed, 16 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index dfc390b..64b6dd9 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,11 @@ -[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/binette/README.html) [![Anaconda-Server Badge](https://anaconda.org/bioconda/binette/badges/downloads.svg)](https://anaconda.org/bioconda/binette) [![Anaconda-Server Badge](https://anaconda.org/bioconda/binette/badges/license.svg)](https://anaconda.org/bioconda/binette) [![Anaconda-Server Badge](https://anaconda.org/bioconda/binette/badges/version.svg)](https://anaconda.org/bioconda/binette) - -[![Test Coverage](https://genotoul-bioinfo.github.io/Binette/coverage-badge.svg)](https://genotoul-bioinfo.github.io/Binette/) [![CI Status](https://github.com/genotoul-bioinfo/Binette/actions/workflows/binette_ci.yml/badge.svg)](https://github.com/genotoul-bioinfo/Binette/actions/workflows) [![Documentation Status](https://readthedocs.org/projects/binette/badge/?version=latest)](https://binette.readthedocs.io/en/latest/?badge=latest) +[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/binette/README.html) [![Anaconda-Server Badge](https://anaconda.org/bioconda/binette/badges/downloads.svg)](https://anaconda.org/bioconda/binette) +[![Anaconda-Server Badge](https://anaconda.org/bioconda/binette/badges/license.svg)](https://anaconda.org/bioconda/binette) +[![Anaconda-Server Badge](https://anaconda.org/bioconda/binette/badges/version.svg)](https://anaconda.org/bioconda/binette) +[![PyPI version](https://badge.fury.io/py/Binette.svg)](https://badge.fury.io/py/Binette) + +[![Test Coverage](https://genotoul-bioinfo.github.io/Binette/coverage-badge.svg)](https://genotoul-bioinfo.github.io/Binette/) +[![CI Status](https://github.com/genotoul-bioinfo/Binette/actions/workflows/binette_ci.yml/badge.svg)](https://github.com/genotoul-bioinfo/Binette/actions/workflows) +[![Documentation Status](https://readthedocs.org/projects/binette/badge/?version=latest)](https://binette.readthedocs.io/en/latest/?badge=latest) # Binette diff --git a/docs/index.md b/docs/index.md index 0ecd6ae..7a1850c 100644 --- a/docs/index.md +++ b/docs/index.md @@ -4,9 +4,14 @@ % contain the root `toctree` directive. -[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/binette/README.html) [![Anaconda-Server Badge](https://anaconda.org/bioconda/binette/badges/downloads.svg)](https://anaconda.org/bioconda/binette) [![Anaconda-Server Badge](https://anaconda.org/bioconda/binette/badges/license.svg)](https://anaconda.org/bioconda/binette) [![Anaconda-Server Badge](https://anaconda.org/bioconda/binette/badges/version.svg)](https://anaconda.org/bioconda/binette) - -[![Test Coverage](https://genotoul-bioinfo.github.io/Binette/coverage-badge.svg)](https://genotoul-bioinfo.github.io/Binette/) [![CI Status](https://github.com/genotoul-bioinfo/Binette/actions/workflows/binette_ci.yml/badge.svg)](https://github.com/genotoul-bioinfo/Binette/actions/workflows) [![Documentation Status](https://readthedocs.org/projects/binette/badge/?version=latest)](https://binette.readthedocs.io/en/latest/?badge=latest) +[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/binette/README.html) [![Anaconda-Server Badge](https://anaconda.org/bioconda/binette/badges/downloads.svg)](https://anaconda.org/bioconda/binette) +[![Anaconda-Server Badge](https://anaconda.org/bioconda/binette/badges/license.svg)](https://anaconda.org/bioconda/binette) +[![Anaconda-Server Badge](https://anaconda.org/bioconda/binette/badges/version.svg)](https://anaconda.org/bioconda/binette) +[![PyPI version](https://badge.fury.io/py/Binette.svg)](https://badge.fury.io/py/Binette) + +[![Test Coverage](https://genotoul-bioinfo.github.io/Binette/coverage-badge.svg)](https://genotoul-bioinfo.github.io/Binette/) +[![CI Status](https://github.com/genotoul-bioinfo/Binette/actions/workflows/binette_ci.yml/badge.svg)](https://github.com/genotoul-bioinfo/Binette/actions/workflows) +[![Documentation Status](https://readthedocs.org/projects/binette/badge/?version=latest)](https://binette.readthedocs.io/en/latest/?badge=latest) # Binette From c5335ad611a84c55a3040ace6650593a20bde72b Mon Sep 17 00:00:00 2001 From: Jean Mainguy Date: Tue, 23 Jan 2024 01:01:48 +0100 Subject: [PATCH 2/5] Update version to 0.1.7 --- binette/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/binette/__init__.py b/binette/__init__.py index 63eb0cb..124e462 100644 --- a/binette/__init__.py +++ b/binette/__init__.py @@ -1 +1 @@ -__version__ = '0.1.6' \ No newline at end of file +__version__ = '0.1.7' From 0f5a0ff2e1983b288c76c4b7c03d4e26a9ed4ab5 Mon Sep 17 00:00:00 2001 From: JeanMainguy Date: Tue, 23 Jan 2024 23:28:08 +0100 Subject: [PATCH 3/5] update install doc with pip --- docs/installation.md | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/docs/installation.md b/docs/installation.md index e0743f0..fec4e02 100644 --- a/docs/installation.md +++ b/docs/installation.md @@ -58,7 +58,20 @@ binette -h ``` -## Downloading the CheckM2 database +## Installing with pip + +Binette is available on [PyPI](https://pypi.org/project/Binette/) and can be installed using pip as follows: + +```bash +pip install binette[main_deps] +``` + +Omitting the `[main_deps]` option will result in the installation of Binette without any Python dependencies. + +In addition to Python dependencies, Binette requires [Diamond](https://github.com/bbuchfink/diamond) to be installed and executable. + + +# Downloading the CheckM2 database Before using Binette, it is necessary to download the CheckM2 database: From 8d213eb7f3d88613d1047f0994258466f3ed08e6 Mon Sep 17 00:00:00 2001 From: JeanMainguy Date: Thu, 25 Jan 2024 08:32:18 +0100 Subject: [PATCH 4/5] add sections in paper --- paper/paper.bib | 27 +++++++++++++++++++++++++++ paper/paper.md | 9 +++++++++ 2 files changed, 36 insertions(+) diff --git a/paper/paper.bib b/paper/paper.bib index 33e696b..e88ad02 100644 --- a/paper/paper.bib +++ b/paper/paper.bib @@ -180,3 +180,30 @@ @article{metagWGS_inprep } +@article{gruning2018bioconda, + title={Bioconda: sustainable and comprehensive software distribution for the life sciences}, + author={Gr{\"u}ning, Bj{\"o}rn and Dale, Ryan and Sj{\"o}din, Andreas and Chapman, Brad A and Rowe, Jillian and Tomkins-Tinch, Christopher H and Valieris, Renan and K{\"o}ster, Johannes and Bioconda Team}, + journal={Nature methods}, + volume={15}, + number={7}, + pages={475--476}, + year={2018}, + publisher={Nature Publishing Group US New York}, + doi = {10.1038/s41592-018-0046-7}, +} + + +@article{Bioconda:2018, + title = {Bioconda: Sustainable and Comprehensive Software Distribution for the Life Sciences}, + shorttitle = {Bioconda}, + author = {Gr{\"u}ning, Bj{\"o}rn and Dale, Ryan and Sj{\"o}din, Andreas and Chapman, Brad A. and Rowe, Jillian and {Tomkins-Tinch}, Christopher H. and Valieris, Renan and K{\"o}ster, Johannes}, + year = {2018}, + month = jul, + journal = {Nature Methods}, + volume = {15}, + number = {7}, + pages = {475--476}, + publisher = {{Nature Publishing Group}}, + issn = {1548-7105}, +} + diff --git a/paper/paper.md b/paper/paper.md index 8b8bdf2..af49d6f 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -45,5 +45,14 @@ Bin completeness and contamination are assessed using CheckM2 [@chklovski2023che Binette serves as the bin refinement tool within the [metagWGS](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs) metagenomic analysis pipeline [@metagWGS_inprep], providing a robust and faster alternative to the bin refinement module of the metaWRAP pipeline as well as other similar bin refinement tools. +# Availability + +Binette is accessible through [PyPI](https://pypi.org/project/Binette/), and a Conda [package](https://anaconda.org/bioconda/binette) can be found in the Bioconda channel [gruning2018bioconda]. The source code for Binette is available on [GitHub](https://github.com/genotoul-bioinfo/binette) under the MIT license. The GitHub repository includes continuous integration tests, test coverage, and employs continuous deployment through GitHub actions. + + +# Acknowledgements + +We would like to thank Matthias Zytnicki for his valuable insights and support during the development of the binette algorithm. + # References From d4a5f323a05ab0830251b8ea0bef97077b543a22 Mon Sep 17 00:00:00 2001 From: JeanMainguy Date: Thu, 25 Jan 2024 09:00:03 +0100 Subject: [PATCH 5/5] fix ref --- paper/paper.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/paper/paper.md b/paper/paper.md index af49d6f..242bd51 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -47,7 +47,7 @@ Binette serves as the bin refinement tool within the [metagWGS](https://forgemia # Availability -Binette is accessible through [PyPI](https://pypi.org/project/Binette/), and a Conda [package](https://anaconda.org/bioconda/binette) can be found in the Bioconda channel [gruning2018bioconda]. The source code for Binette is available on [GitHub](https://github.com/genotoul-bioinfo/binette) under the MIT license. The GitHub repository includes continuous integration tests, test coverage, and employs continuous deployment through GitHub actions. +Binette is accessible through [PyPI](https://pypi.org/project/Binette/), and a Conda [package](https://anaconda.org/bioconda/binette) can be found in the Bioconda channel [@gruning2018bioconda]. The source code for Binette is available on [GitHub](https://github.com/genotoul-bioinfo/binette) under the MIT license. The GitHub repository includes continuous integration tests, test coverage, and employs continuous deployment through GitHub actions. # Acknowledgements