From bcbdacd2158260adf6991882b34919841c916a35 Mon Sep 17 00:00:00 2001 From: JeanMainguy Date: Mon, 29 Jan 2024 18:46:48 +0100 Subject: [PATCH] adjust install and tests doc --- docs/installation.md | 10 ++++++---- docs/tests.md | 8 +++++--- 2 files changed, 11 insertions(+), 7 deletions(-) diff --git a/docs/installation.md b/docs/installation.md index fec4e02..f5964df 100644 --- a/docs/installation.md +++ b/docs/installation.md @@ -1,7 +1,9 @@ # Installation -## With Bioconda +## Installation of Binette + +### With Bioconda Binette can be esailly installed with conda @@ -23,7 +25,7 @@ For quicker installation and potential resolution of conflicting dependencies, c ``` -## Installing from Source Code within a conda environnement +### From the source code within a conda environnement A straightforward method to install Binette from the source code is by utilizing a conda environment that includes all the necessary dependencies. @@ -58,7 +60,7 @@ binette -h ``` -## Installing with pip +### With PyPI Binette is available on [PyPI](https://pypi.org/project/Binette/) and can be installed using pip as follows: @@ -71,7 +73,7 @@ Omitting the `[main_deps]` option will result in the installation of Binette wit In addition to Python dependencies, Binette requires [Diamond](https://github.com/bbuchfink/diamond) to be installed and executable. -# Downloading the CheckM2 database +## Downloading the CheckM2 database Before using Binette, it is necessary to download the CheckM2 database: diff --git a/docs/tests.md b/docs/tests.md index ce91038..b6c0e60 100644 --- a/docs/tests.md +++ b/docs/tests.md @@ -30,8 +30,10 @@ pytest --cov=binette ``` -```note +```{note} + Test coverage is updated by a github workflow in the Action Tab. The test coverage report is then deployed on the github-pages and avaible [here](https://genotoul-bioinfo.github.io/Binette/). + ``` @@ -40,7 +42,7 @@ Test coverage is updated by a github workflow in the Action Tab. The test covera A functional test has been implemented in the CI github workflow. It performs an execution of binette on a toy dataset consisting of 4 small genomes. The test uses a checkm2 database that has been shrunk to the minimum to make diamond run faster. Finally, the results are compared with the expected results. -The test dataset is stored in this github repository: https://github.com/genotoul-bioinfo/Binette_TestData +The test dataset is stored in this github repository: [Binette TestData](https://github.com/genotoul-bioinfo/Binette_TestData). You can replicate this test locally by following the next steps: @@ -94,7 +96,7 @@ python scripts/compare_results.py expected_results/final_bins_quality_reports.ts ``` -```warning +```{warning} The CheckM2 database used for the test dataset is very small and is only valid for the 4 genomes included in the test datasets. It should not be used elsewhere. ``` \ No newline at end of file