Add SIST logo and refresh README ahead of release

README.md

@@ -1,21 +1,37 @@
-# SIST: Stress-Induced Structural Transitions in superhelical DNA 
+SIST: Stress-Induced Structural Transitions in superhelical DNA 
+==============================
+
+| Category       | Badges |
+|----------------|--------|
+| **Build**      | [![PR Checks](https://github.com/CCPBioSim/SIST/actions/workflows/pr.yaml/badge.svg)](https://github.com/CCPBioSim/SIST/actions/workflows/pr.yaml) |
+| **Documentation** | [![Docs - Status](https://app.readthedocs.org/projects/sist/badge/?version=latest)](https://sist.readthedocs.io/en/latest/?badge=latest) |
+| **Citation**      |  |
+| **Anaconda**       | [![Anaconda.org](https://anaconda.org/CCPBioSim/sist/badges/version.svg)](https://anaconda.org/CCPBioSim/sist/) [![Last Updated](https://anaconda.org/CCPBioSim/sist/badges/latest_release_date.svg)](https://anaconda.org/CCPBioSim/sist) [![Platforms](https://anaconda.org/CCPBioSim/sist/badges/platforms.svg)](https://anaconda.org/CCPBioSim/sist) [![License](https://anaconda.org/CCPBioSim/sist/badges/license.svg)](https://anaconda.org/CCPBioSim/sist) [![Downloads](https://anaconda.org/CCPBioSim/sist/badges/downloads.svg)](https://anaconda.org/CCPBioSim/sist)|
+| **Quality**    | [![Coverage Status](https://coveralls.io/repos/github/CCPBioSim/SIST/badge.svg?branch=main)](https://coveralls.io/github/CCPBioSim/SIST?branch=main) |
 
 ## Purpose of SIST
 
 The codes in this repository are for analyzing three types of structural transitions in superhelical DNA molecules of specified base sequences and kilobase lengths.  These are strand separation, BZ transitions and cruciform extrusion.  More types of transitions may be added as their energetics become known.  The statistical mechanical methods and algorithms used in these analyses are described in the papers cited below. 
 
-## Citations
+<p align="center">
+    <img src="docs/source/_static/logos/SIST-logo-white-text.svg#gh-dark-mode-only" alt="SIST logo" width="300"/>
+    <img src="docs/source/_static/logos/SIST-logo-black-text.svg#gh-light-mode-only" alt="SIST logo" width="300"/>
+</p>
 
-When using these algorithms you must cite the first paper below, and some or all of the others, depending on which types of analyses you perform:
+## Citations
 
-Zhabinskaya, D., Madden, S., & Benham, C. J. (2015). SIST: stress-induced structural transitions in superhelical DNA. Bioinformatics, 31(3), 421-422.
+If you use SIST, please cite the software itself (see [`CITATION.cff`](CITATION.cff)) along with the paper below, which is required for any use of these algorithms:
 
-Fye, R. M. and Benham, C. J. (1999), “Exact method for numerically analyzing a model of local denaturation in superhelically stressed DNA”, Phys Rev E, 59, 3408-3426.
+> Zhabinskaya, D., Madden, S., & Benham, C. J. (2015). SIST: stress-induced structural transitions in superhelical DNA. *Bioinformatics*, 31(3), 421-422.
 
-Zhabinskaya, D. and Benham, C. J. (2011), “Theoretical Analysis of the Stress Induced BZ Transition in Superhelical DNA”, PLoS Comput Biol, 7, 1-14.
+Additionally, cite whichever of the following apply to the type(s) of transition you analyze:
 
-Zhabinskaya, D. and Benham, C. J. (2013), “Competitive superhelical transitions involving cruciform extrusion”, Nucleic Acids Res, 41(21), 9610-9621.
+| Transition type | Reference |
+|---|---|
+| Strand separation | Fye, R. M. and Benham, C. J. (1999), "Exact method for numerically analyzing a model of local denaturation in superhelically stressed DNA", *Phys Rev E*, 59, 3408-3426. |
+| BZ transition | Zhabinskaya, D. and Benham, C. J. (2011), "Theoretical Analysis of the Stress Induced BZ Transition in Superhelical DNA", *PLoS Comput Biol*, 7, 1-14. |
+| Cruciform extrusion | Zhabinskaya, D. and Benham, C. J. (2013), "Competitive superhelical transitions involving cruciform extrusion", *Nucleic Acids Res*, 41(21), 9610-9621. |
 
 ## Contact Information
 
-For questions or problems, please contact either Dina Zhabinskaya (dzhabinskaya@ucdavis.edu), Craig Benham (cjbenham@ucdavis.edu), or Sally Madden (sallymadden@gmail.com).
+For questions or problems, please contact CCPBIOSIM@stfc.ac.uk.

docs/source/conf.py

@@ -38,4 +38,9 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
 html_theme = 'furo'
-# html_static_path = ['_static']
+html_theme_options = {
+    "dark_logo": "logos/SIST-logo-white-text.svg",
+    "light_logo": "logos/SIST-logo-black-text.svg",
+}
+
+html_static_path = ['_static']