Update readme with beta notice

README.md

@@ -1,4 +1,4 @@
-<img src="https://github.com/compomics/ms2rescore/raw/master/img/ms2rescore_logo.png" width="150" height="150" />
+<img src="https://github.com/compomics/ms2rescore/raw/master/img/ms2rescore_logo.png" width="150" height="150" alt="MS²Rescore"/>
 <br/><br/>
 
 [![GitHub release](https://img.shields.io/github/release-pre/compomics/ms2rescore.svg?style=flat-square)](https://github.com/compomics/ms2rescore/releases)
@@ -10,6 +10,10 @@
 
 Modular and user-friendly platform for AI-assisted rescoring of peptide identifications
 
+> ⚠️ Note: This is the documentation for the fully redeveloped version 3.0 of MS²Rescore, which is
+> now in the beta stage. While MS²Rescore 3.0 has been drastically improved over the previous
+> version, you might run into some unforeseen issues. Please report any issues you encounter on the
+> [issue tracker][issues] or post your questions on the [GitHub Discussions][discussions] forum.
 
 ## About MS²Rescore
 
@@ -23,56 +27,53 @@ such as proteogenomics, metaproteomics, or immunopeptidomics.
 
 MS²Rescore can read peptide identifications in any format supported by [psm_utils][psm_utils]
 (see [Supported file formats][file-formats]) and has been tested with various search engines output
-files (
-[PeptideShaker](https://compomics.github.io/projects/peptide-shaker.html) `.mzid`,
-[MaxQuant](https://www.maxquant.org/) `msms.txt`,
-[MSGFPlus](https://omics.pnl.gov/software/ms-gf) `.mzid`,
-[X!Tandem](https://www.thegpm.org/tandem/) X!Tandem `.xml`, and
-[PEAKS](https://www.bioinfor.com/peaksdb/) `.mzid`).
+files:
+
+- [MS Amanda](http://ms.imp.ac.at/?goto=msamanda) `.csv`
+- [PeptideShaker](https://compomics.github.io/projects/peptide-shaker.html) `.mzid`
+- [MSGFPlus](https://omics.pnl.gov/software/ms-gf) `.mzid`
+- [MaxQuant](https://www.maxquant.org/) `msms.txt`
+- [X!Tandem](https://www.thegpm.org/tandem/) X!Tandem `.xml`
+- [PEAKS](https://www.bioinfor.com/peaksdb/) `.mzid`
 
 MS²Rescore is available as a [desktop application][desktop], a [command line tool][cli], and a
 [modular Python API][python-package].
 
-
 ## Citing
 
 **Latest MS²Rescore publication:**
 
 > **MS2Rescore: Data-driven rescoring dramatically boosts immunopeptide identification rates.**
 > Arthur Declercq, Robbin Bouwmeester, Aurélie Hirschler, Christine Carapito, Sven Degroeve, Lennart Martens, and Ralf Gabriels.
 > _Molecular & Cellular Proteomics_ (2021) [doi:10.1016/j.mcpro.2022.100266](https://doi.org/10.1016/j.mcpro.2022.100266)
-> <span class="__dimensions_badge_embed__" data-doi="10.1016/j.mcpro.2022.100266" data-hide-zero-citations="true" data-style="small_rectangle"></span><script async src="https://badge.dimensions.ai/badge.js" charset="utf-8"></script>
+> <span class="__dimensions_badge_embed__" data-doi="10.1016/j.mcpro.2022.100266" data-hide-zero-citations="true" data-style="small_rectangle"></span>
 
 **Original publication describing the concept of rescoring with predicted spectra:**
 
 > **Accurate peptide fragmentation predictions allow data driven approaches to replace and improve upon proteomics search engine scoring functions.**
 > Ana S C Silva, Robbin Bouwmeester, Lennart Martens, and Sven Degroeve.
 > _Bioinformatics_ (2019) [doi:10.1093/bioinformatics/btz383](https://doi.org/10.1093/bioinformatics/btz383)
-> <span class="__dimensions_badge_embed__" data-doi="10.1093/bioinformatics/btz383" data-hide-zero-citations="true" data-style="small_rectangle"></span><script async src="https://badge.dimensions.ai/badge.js" charset="utf-8"></script>
+> <span class="__dimensions_badge_embed__" data-doi="10.1093/bioinformatics/btz383" data-hide-zero-citations="true" data-style="small_rectangle"></span>
 
 To replicate the experiments described in this article, check out the
 [publication branch][publication-branch] of the repository.
 
-
 ## Getting started
 
 The desktop application can be installed on Windows with a [one-click installer][desktop-installer].
 The Python package and command line interface can be installed with `pip`, `conda`, or `docker`.
 Check out the [full documentation][docs] to get started.
 
-
 ## Questions or issues?
 
 Have questions on how to apply MS²Rescore on your data? Or ran into issues while using MS²Rescore?
 Post your questions on the [GitHub Discussions][discussions] forum and we are happy to help!
 
-
 ## How to contribute
 
 Bugs, questions or suggestions? Feel free to post an issue in the [issue tracker][issues] or to
 make a [pull request][pr]!
 
-
 [docs]: https://ms2rescore.readthedocs.io/
 [issues]: https://github.com/compomics/ms2rescore/issues/
 [discussions]: https://github.com/compomics/ms2rescore/discussions/

docs/source/conf.py

@@ -34,6 +34,7 @@
 html_theme = "sphinx_rtd_theme"
 html_static_path = ["_static"]
 html_css_files = ["css/custom.css"]
+html_js_files = ["js/badge.min.js"]
 
 # Autodoc options
 autodoc_default_options = {"members": True, "show-inheritance": True}