pyglotaran-release-paper-supplementary-information

Supplementary Information (SI) to the pyglotaran release paper (details below).

Publication details

pyglotaran: a lego-like Python framework for global and target analysis of time resolved spectra

Ivo H.M. van Stokkum^a, Jörn Weißenborn^a, Sebastian Weiganda^a,b, Joris J. Snellenburg^a

_{^a Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands
^b Fakultät II Institut für Festkörperphysik, Technische Universität Berlin}

_{DOI: 10.1007/s43630-023-00460-y}

Getting started with this repository

This readme describes the steps needed to run the jupyter notebooks provided as supplementary information to the publication pyglotaran: a lego-like Python framework for global and target analysis of time resolved spectra.

If you already have a Python 3.10 (virtual environment) on your computer, or you know how to setup one, skip to step 3.

1. Setting up Python with Anaconda

Download Anaconda from its official website.

Pick the installer that's appropriate for your operating system. It is assumed you install with default settings.

2. Setting up a Python virtual environment

Start an Anaconda Prompt or shell.

You should see a terminal windows open in the (base) environment.

Type the following command to create a new standalone environment for pyglotaran.

conda create -c conda-forge -y --name pyglotaran python=3.10

Following the instructions in step 3 to activate the environment and install dependencies.

3. Installing dependencies to run the notebooks

Activate the pyglotaran environment (created in step 2), e.g. by executing in your Anaconda Prompt or shell:

conda activate pyglotaran

Your prompt should now reflect that you are in the pyglotaran environment.

Now you can install the necessary packages, by executing the following command.

conda install -c conda-forge -y pyglotaran pyglotaran-extras jupyterlab

Alternatively (if you are more familiar with it) you can install using pip as well (but don't do both):

pip install pyglotaran pyglotaran-extras jupyterlab

Look at the installation output to verify that you installed pyglotaran version 0.7.1 or later, and pyglotaran-extras version 0.7.1 or later.

_{Note: the main package is pyglotaran, pyglotaran-extras provides additional plotting functionality, whereas jupyterlab provides a way to work with notebooks.}

4. Start Jupyter notebook within Supplementary Information folder

From within your Anaconda Prompt or shell, navigate (using the command cd for 'change directory') to the location where you downloaded and extracted the archive pyglotaran-release-paper-supplementary-information.zip (or .7z).

For example under Windows, assuming you downloaded and extracted the archive into your Downloads folder, type:

cd %USERPROFILE%\Downloads\pyglotaran-release-paper-supplementary-information-main

On Mac OS X or Linux

cd ~/Downloads/pyglotaran-release-paper-supplementary-information-main

Where pyglotaran-release-paper-supplementary-information-main is the name of the folder you extract from the (.zip|.7z) archive.

Then start Jupyter Lab by executing the command:

jupyter lab

5. Notes on order of notebook evaluation

The first case study Broadband absorption case study of intersystem crossing in 4-thiothymidine is covered by the notebook:

• 4TT/sequential_doas_4TT.ipynb

The second case study Transient absorption case study of the chromophoric systems rc and rcg is covered by the notebooks inside the rc folder.

For this case study, it is important to execute the notebooks in order:

1. rc/target_rc_part1.ipynb
2. rc/target_rcg_compare_part2.ipynb
3. rc/target_rcg_gcrcg_rcgcr_refine_part3.ipynb

The third case study Time-resolved emission case study of whole photosynthetic cells is covered by the notebook:

• dPSI/ex_four_datasets_two_guidance_with_area_irf-with_sum_plot_minimal.ipynb

6. Future updates

Future updates on the usage of the current version of pyglotaran or these case studies will be uploaded to the github repository located here:

• https://github.com/glotaran/pyglotaran-release-paper-supplementary-information

For each (new) release of pyglotaran, there will be a corresponding release of the updated notebooks reflecting the usage with that version of pyglotaran.

More information on the most recent version of pyglotaran and pyglotaran-extras can be found via their respective github repository pages:

• https://github.com/glotaran/pyglotaran
• https://github.com/glotaran/pyglotaran-extras

License

Except where otherwise noted, the work in this repository is dual-licensed:

• The source code is available under the (MIT License)
• Documentation, text, figures, etc, are licenses under Creative Commons Attribution 4.0 International (CC-BY-4.0). You can attribute them by citing the pyglotaran publication accompanying this supplementary information.

These licenses are provided in plain text as a convenience to the user as LICENSE and LICENSE-CC-BY respectively.