Dan Foreman-Mackey

That would be a start, but the current implementation actually assumes GitHub throughout, so actually fixing this sensibly would require a more thorough overhaul. I'm going to label this with...

@palumbom — Awesome! Thanks for sharing. I'm not familiar enough with Julia to be too sure what the best approach is for managing dependencies wrt Snakemake. Adding an example either...

I wouldn't want to add it during a `showyourwork build`, but adding it to the `cookiecutter` template so that it gets added during `showyourwork setup` could be fine if sensible...

@jacob-hjortlund — Thanks for checking in and sorry that you've hit this! I haven't had too much experience combining showyourwork with cluster execution, and I'm currently on leave so I...

Thanks for the report! We [pin the version of `snakemake`](https://github.com/showyourwork/showyourwork/blob/f75a063e2f4a81c899924d6d9121a465e9bfd9ec/setup.py#L29) since we use some pretty brittle patches to get all the behavior we want so even if `snakemake` is compatible...

Yeah - this issue is still open because the currently released SYW still isn't compatible with Python 3.11. Working on it! :D > Related to this, I noticed that this...

> It's not really on-topic, but I think the docs lack an explanation of how the internal conda environment works. I don't understand if it gets created at every build...

Great question! Would you like both documents to be showyourwork'ed? For example, are there figure scripts in both and do you want the margin icons in both? I don't think...

Got it - our journals normally don't have a "supplementary information" document separately, so it's not something we typically support. I'll think a little more about how that would fit...

I've come up with a scheme for supporting this post refactor in #285, but I think it's probably infeasible in the existing infrastructure. The idea that there is a single...