Daniel Himmelstein
Daniel Himmelstein
I recently switched a workflow that includes `peaceiris/actions-gh-pages` to use a self-hosted runner. When using `peaceiris/actions-gh-pages@v3` and when the output branch doesn't already exist, the deploy step succeeded but placed...
Is it possible for a notebook cell to detect whether it is being executed by papermill (either by the command line interface or by `pm.execute_notebook`? I'm interested in the following...
`add_argument` from `argparse` has a `type` [option](https://docs.python.org/3/library/argparse.html#type) that "allows any necessary type-checking and type conversions to be performed". The ability to ensure the CLI args are converted to certain types...
refs #32 work in progress
[Athenapdf](https://github.com/arachnys/athenapdf) has worked well but has two problems: 1. it appears to no longer be maintained 2. it requires docker and has started to hit docker hub rate limits on...
Oftentimes, it's important (and required in scholarly publishing) to show the changes between two versions of a manuscript. It would be ideal if Manubot users could "track changes" between two...
https://github.com/manubot/rootstock/commit/defe787b0ad8a21a745cc82c3117770896caaf8b updated Pandoc which caused the HTML bibliography styling to change. We also updated our plugins. Notice the layout of the reference numbers before: https://greenelab.github.io/connectivity-search-manuscript/v/650112ab029fbe6ce1f8acdf65d7d60da03fa49f/#references  And now after (currently):...
Very preliminary proof of concept. The idea is to have CI create a Docker image for the environment. This would have two potential benefits: 1. improve build times for subsequent...
Supersedes https://github.com/greenelab/manubot-rootstock/pull/51. - [ ] Update pandoc to 2.0.1 to resolve https://github.com/jgm/pandoc/issues/4020.
Helps with https://github.com/manubot/rootstock/issues/381. Runs common filters and produces markdown output that should be portable to other Pandoc systems like Rmarkdown.