Comments from Pierre

[markziemann]

To be truly honest, your manuscript is very well advanced and carries many valuable advises. I don't know if I could improve much what you wrote so far.

In any case, here are the subjects I may help you with:

• I'm a Python guy meaning I know quite well the Python ecosystem. Regarding Streamlit for instance, I don't think it should be compare to notebooks. To me it is more similar to what could be done in R with Shiny. However, the newcomer in Python is MyST (https://aus01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmyst-parser.readthedocs.io%2Fen%2Flatest%2F&data=05%7C01%7Cm.ziemann%40deakin.edu.au%7Cfa29ebc3a7ca4056fffe08db5d402a37%7Cd02378ec168846d585401c28b5f470f6%7C0%7C0%7C638206302395941888%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=bwPE8OfBc37OB2Rl7Jg%2BWlnCKzLehgfYXtyUEfsFuwk%3D&reserved=0) that could really improve the way we wrote documentation.

• Regarding the archival of source code, this is indeed essential as a repository may at some point disappear. I wouldn't recommend to archive source code in Figshare nor Zenodo since these data repositories have been designed for data. Source code should be archived in Software Heritage (https://aus01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.softwareheritage.org%2F&data=05%7C01%7Cm.ziemann%40deakin.edu.au%7Cfa29ebc3a7ca4056fffe08db5d402a37%7Cd02378ec168846d585401c28b5f470f6%7C0%7C0%7C638206302395941888%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=%2Bd%2BRH1O4d%2FY6BFGWhhomFhoOZuNrtGOcyq2PPwW55QE%3D&reserved=0), that is the universal archive for source code (disclaimer: I'm a Software Heritage ambassador).

• Finally, I guess the GUIX project could get more emphasized since the aim of the project is to offer fully reproducible results (similar to what you could get with a VM) but without using any VM. It's conda on steroids.

These sound like great suggestions. I will work on incorporating them into the MS

[markziemann]

@pierrepo thanks for the comments.

1. Yes I agree that streamlit is more for building websites rather than a tool for reproducible research - I might remove it in favour of MyST notebook for this purpose.
2. Agree with your overall sentiment. While Zenodo has github integration figshare does not. I will include Software Heritage.
3. I am new to Guix but it looks very powerful. Based on your comment and correspondence with Altuna, I will dive deeper into Guix an expand on its capabilities in the MS. Do you have any quick start guides I can try for R or python environments with packages?

[markziemann]

I have addressed no.1 and 2 in this list and Guix is mentioned in another issue. I am in the process of learning it. I will make an example Guix workflow to reproduce this manuscript.