Start skeleton of convert tutorial and try fixing logo rendering on r…

…eadme/install page for RTD
SPAAM-community · Mar 28, 2024 · 81edcf3 · 81edcf3
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 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4003825.svg)](https://doi.org/10.5281/zenodo.4003825) [![PyPI version](https://badge.fury.io/py/AMDirT.svg)](https://pypi.org/project/AMDirT) [![Documentation Status](https://readthedocs.org/projects/amdirt/badge/?version=dev)](https://amdirt.readthedocs.io/en/dev/?badge=dev) [![AMDirT-CI](https://github.com/SPAAM-community/AMDirT/actions/workflows/ci_test.yml/badge.svg)](https://github.com/SPAAM-community/AMDirT/actions/workflows/ci_test.yml)
 
-<div align="center">
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-![AMDirT](https://raw.githubusercontent.com/SPAAM-community/AMDirT/master/assets/logo_rectangular.png#gh-light-mode-only) 
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-</div>
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-<div align="center">
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-![AMDirT](https://raw.githubusercontent.com/SPAAM-community/AMDirT/master/assets/logo_rectangular_dark.png#gh-dark-mode-only)
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+  <picture>
+    <source media="(prefers-color-scheme: light)" srcset="https://raw.githubusercontent.com/SPAAM-community/AMDirT/master/assets/logo_rectangular_dark.png">
+    <img alt="AMDirT Logo" src="https://raw.githubusercontent.com/SPAAM-community/AMDirT/master/assets/logo_rectangular.png">
+  </picture>
 
 **AMDirT**: [**A**ncient**M**etagenome**Dir**](https://github.com/SPAAM-community/ancientmetagenomedir) **T**oolkit
 
-AMDirT is a toolkit for interacting with the AncientMetagenomeDir metadata repository of ancient metagenomic samples and ancient microbial genomes. This tool provides ways to validate AncientMetagenomeDir submissions, explore and download sequencing data for ancient microbial and environmental (meta)genomes, and automatically prepare input samplesheets for a range of bioinformatic processing pipelines.
+AMDirT is a toolkit for interacting with the AncientMetagenomeDir metadata repository of ancient metagenomic samples and ancient microbial genomes.
+
+This tool provides ways to explore and download sequencing data for ancient microbial and environmental (meta)genomes, automatically prepare input samplesheets for a range of bioinformatic processing pipelines, and to validate AncientMetagenomeDir submissions.
 
 For documentation on using the tool, please see [How Tos](https://amdirt.readthedocs.io/en/latest/how_to/index.html), [Tutorials](https://amdirt.readthedocs.io/en/latest/tutorials/index.html) and/or [Quick Reference](https://amdirt.readthedocs.io/en/latest/reference.html).
 

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diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -11,7 +11,9 @@ Welcome to AMDirT's documentation!
 
 🛠️ **AMDirT**: `AncientMetagenomeDir <https://github.com/SPAAM-community/ancientmetagenomedir>`_ Toolkit  🛠️
 
-AMDirT is a toolkit for interacting with the AncientMetagenomeDir metadata repository of ancient metagenomic samples and ancient microbial genomes. This tool provides ways to validate AncientMetagenomeDir submissions, explore and download sequencing data for ancient microbial and environmental (meta)genomes, and automatically prepare input samplesheets for a range of bioinformatic processing pipelines.
+AMDirT is a toolkit for interacting with the AncientMetagenomeDir metadata repository of ancient metagenomic samples and ancient microbial genomes.
+
+This tool provides ways to explore and download sequencing data for ancient microbial and environmental (meta)genomes, automatically prepare input samplesheets for a range of bioinformatic processing pipelines, and to validate AncientMetagenomeDir submissions.
 
 For more information on installation see: :doc:`README`. For how to use the toolkit (tutorials, how-toes, references) please see the table of contents.
 

diff --git a/docs/source/tutorials/convert.md b/docs/source/tutorials/convert.md
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+# convert
diff --git a/docs/source/tutorials/index.rst b/docs/source/tutorials/index.rst
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     :maxdepth: 1
     :caption: Tutorials:
 
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+    convert
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         :maxdepth: 1
         :caption: Tutorials:
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+        convert