From 6bf9c260deaa014ce9cf5327c5c8e521ce9883a2 Mon Sep 17 00:00:00 2001
From: Joris Snellenburg <jsnel@users.noreply.github.com>
Date: Fri, 28 Jul 2023 20:49:32 +0200
Subject: [PATCH] =?UTF-8?q?=E2=9C=A8=20Update=20README.md=20with=20setup?=
 =?UTF-8?q?=20instructions=20(#3)?=
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Update the README.md to include basic instructions on setting up pyglotaran and using this repository.
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 ## Energy transfer and trapping in photosystem I with and without chlorophyll-f
 
-Ivo H.M. van Stokkum<sup>1,3\*</sup>, Marc G. Müller<sup>2</sup>, Jörn Weißenborn<sup>1</sup>, Sebastian Weigand<sup>1</sup>, Joris J. Snellenburg<sup>1</sup>, Alfred R. Holzwarth<sup>1,2</sup>
+Ivo H.M. van Stokkum<sup>1,\*</sup>, Marc G. Müller<sup>2</sup>, Jörn Weißenborn<sup>1</sup>, Sebastian Weigand<sup>1</sup>, Joris J. Snellenburg<sup>1</sup>, Alfred R. Holzwarth<sup>1,2</sup>
 
 <sub><sup>1</sup> Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands</sub><br>
 <sub><sup>2</sup> Max-Planck-Institut für chemische Energiekonversion, D-45470 Mülheim a.d. Ruhr, Germany</sub><br>
-<sub><sup>3</sup> Lead contact</sub>
 
 <sub>\*Correspondence: i.h.m.van.stokkum@vu.nl</sub>
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7958154.svg)](https://doi.org/10.5281/zenodo.7958154)
 
+## Getting started with this pyglotaran and this repository
+
+For more detailed instructions on setting up pyglotaran, and usage instructions, refer to the [pyglotaran user manual](https://pyglotaran.readthedocs.io/) online.
+
+### Repository Quick-Start
+
+Ensure you have a working Python 3.10 (or later) installation, and use your preferred python package manager to install the following Python packages:
+
+- `pyglotaran` ([pip](https://pypi.org/project/pyglotaran/), [conda](https://anaconda.org/conda-forge/pyglotaran))
+- `pyglotaran-extras` ([pip](https://pypi.org/project/pyglotaran-extras/), [conda](https://anaconda.org/conda-forge/pyglotaran-extras))
+
+<sub>At a minimum version 0.7.1 of both packages is required</sub>
+
+When using VS Code, additionally the `ipykernel` package is needed (but VS Code will prompt for this).
+
+When using Jupyter Notebook in the browser, also install: `jupyterlab` ([pip](https://pypi.org/project/jupyterlab/), [conda](https://anaconda.org/conda-forge/jupyterlab)) and then run `jupyter lab` to start a jupyter server.
+
+Then use VS Code or Jupyter to open one of the .ipynb notebooks from one of the subfolders in this project.
+
 ## License
 
 Except where otherwise noted, the work in this repository is dual-licensed under `GNU Lesser General Public License v3.0 or later` ([LGPL-3.0-or-later](https://spdx.org/licenses/LGPL-3.0-or-later.html)) or `Creative Commons Attribution 4.0 International` [(CC-BY-4.0)](https://spdx.org/licenses/CC-BY-4.0.html).