adjust install and tests doc

genotoul-bioinfo · Jan 29, 2024 · bcbdacd · bcbdacd
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diff --git 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
@@ -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.
 
 ```