README: new GECKO logo, GECKO 4 and geckopy

README.md

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-<img src="./GECKO.png" width="200px">
+<picture>
+  <source media="(prefers-color-scheme: dark)" srcset="img/gecko-logo-white.png">
+  <img src="img/gecko-logo.png" alt="GECKO" width="400px">
+</picture>
 
-[![Current release](https://img.shields.io/github/release/CompMetEng/GECKO/all.svg)](https://github.com/CompMetEng/GECKO/releases/)
+[![Documentation](https://readthedocs.org/projects/gecko-docs/badge/?version=latest)](https://gecko-docs.readthedocs.io/en/latest/)
 [![GitHub Discussions](https://img.shields.io/github/discussions-search?query=repo%3ACompMetEng%2FGECKO&label=GitHub%20Discussions)](https://github.com/CompMetEng/GECKO/discussions)
-[![Zenodo](https://zenodo.org/badge/DOI/10.5281/zenodo.7699818.svg)](https://doi.org/10.5281/zenodo.7699818)
-[![MATLAB File Exchange](https://www.mathworks.com/matlabcentral/images/matlab-file-exchange.svg)](https://se.mathworks.com/matlabcentral/fileexchange/125960-gecko-toolbox)
 
+**[Documentation](https://gecko-docs.readthedocs.io/en/latest/)** · [Installation](https://gecko-docs.readthedocs.io/en/latest/installation/) · [Guide](https://gecko-docs.readthedocs.io/en/latest/guide/) · [API reference](https://gecko-docs.readthedocs.io/en/latest/api/) · [Migrate](https://gecko-docs.readthedocs.io/en/latest/migrate.html) · [Citations](https://gecko-docs.readthedocs.io/en/latest/references.html)
 
-## About GECKO 3
+## About GECKO
 
 The **GECKO** toolbox enhances a **G**enome-scale model to account for **E**nzyme **C**onstraints, using **K**inetics and **O**mics. The resulting enzyme-constrained model (**ecModel**) can be used to perform simulations where enzyme allocation is either drawn from a total protein pool, or constrained by measured protein levels from proteomics data.
 
-💡 In the [`GECKO/tutorials`](https://github.com/CompMetEng/GECKO/tree/develop/tutorials) folder there are examples of how GECKO can be applied to GEMs, in either of its _full_ or _light_ forms. Each `protocol.m` contains instructions on how to reconstruct and analyze an ecModel, demonstrating how different fuctions in GECKO can be used. These two scripts complement the [Nature Protocols](https://doi.org/10.1038/s41596-023-00931-7) paper ([**PDF**](https://drive.google.com/file/d/1_AGz6GmQPOyshfUZ6K-L2myzU43rQ6tu/view)).
+GECKO is written in MATLAB. Its Python port, [geckopy](https://github.com/CompMetEng/geckopy), reads and writes the same ecModel YAML files, and the two toolboxes are kept in step by a [parity ledger](https://github.com/CompMetEng/raven-gecko-parity). The documentation covers both.
 
-### Significant changes since protocol publication
-- GECKO **3.2.0**: all protein usage reactions draw from the protein pool, even if they are constrained by proteomics data. This affects **Step 58** in the protocol, changing behaviour of `constrainEnzConcs` and making `updateProtPool` obsolete, `tutorials/full_ecModel/protocol.m` is updated to reflect this change. See [#357](https://github.com/SysBioChalmers/GECKO/issues/375) for more details.  
-
-_**Note:** Regarding code and model compatibility with earlier GECKO versions, see [Previous versions: GECKO 1 and 2](https://github.com/SysBioChalmers/GECKO/wiki/Previous-versions:-GECKO-1-and-2)_.
+This is GECKO **4.0.0b1**. For the changes from GECKO 3, see [GECKO 3 → GECKO 4](https://gecko-docs.readthedocs.io/en/latest/gecko3-to-gecko4.html); for the differences between GECKO and geckopy, see [GECKO vs. geckopy](https://gecko-docs.readthedocs.io/en/latest/gecko-to-geckopy.html).
+
+## Get started
+
+1. Install GECKO as described in the [installation instructions](https://gecko-docs.readthedocs.io/en/latest/installation/).
+2. Follow [Getting started](https://gecko-docs.readthedocs.io/en/latest/guide/getting-started.html) and [Building an ecModel](https://gecko-docs.readthedocs.io/en/latest/guide/building-ec-model.html) in the guide, or open `tutorials/full_ecModel/protocol.m` or `tutorials/light_ecModel/protocol.m` in MATLAB. Each script reconstructs and analyses an ecModel step by step, in its _full_ or _light_ form ([GECKO light](https://gecko-docs.readthedocs.io/en/latest/guide/gecko-light.html)), and complements the [Nature Protocols](https://doi.org/10.1038/s41596-023-00931-7) paper.
+
+## Documentation and support
+
+The installation instructions, the protocol and the API reference for MATLAB and Python are at [gecko-docs](https://gecko-docs.readthedocs.io/en/latest/). Use [GitHub Discussions](https://github.com/CompMetEng/GECKO/discussions) for questions and comments.
 
 ## Cite us
 
 If you have used GECKO in your work, please cite:
 
 > Chen Y, Gustafsson J, Tafur Rangel A, Anton M, Domenzain I, Kittikunapong C, Li F, Yuan L, Nielsen J & Kerkhoven EJ. Reconstruction, simulation and analysis of enzyme-constrained metabolic models using GECKO Toolbox 3.0. *Nature Protocols* **19**, 629-667 (2024). doi:[10.1038/s41596-023-00931-7](https://doi.org/10.1038/s41596-023-00931-7).
 
-## Documentation
-**Installation instructions**, the protocol and the API reference are published at **[gecko-docs](https://gecko-docs.readthedocs.io/en/latest/)**. Use [GitHub Discussions](https://github.com/CompMetEng/GECKO/discussions) for support, to ask questions or leave comments.
-
 ## Contributing
 
-Contributions are always welcome! Please read the [contributing guidelines](https://github.com/CompMetEng/GECKO/blob/develop/.github/CONTRIBUTING.md) to get started.
+Contributions are welcome. Read the [contributing guidelines](https://github.com/CompMetEng/GECKO/blob/develop/.github/CONTRIBUTING.md) first. A change to a function that geckopy also has needs the matching change there; the [parity ledger](https://github.com/CompMetEng/raven-gecko-parity) lists the pairs.

_config.yml

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+logo: img/gecko-logo.png
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