Gregor Sturm

Installation with `install_github` fails with ``` ERROR: dependencies ‘Biobase’, ‘xbioc’ are not available for package ‘SCDC’ ``` Adding the `biocViews` keyword to the DESCRIPTION should fix that, since it tells...

RMarkdown/RNotebook support

2

I created [RMarkdown](http://rmarkdown.rstudio.com/r_notebooks.html) support for ipymd. With my extension, Rmd files edited in rstudio can be directly opened with jupyter. Notably, this format two output-files: * `.Rmd`, the rmarkdown source...

Bump version

3

## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested,...

Switch to scverse cookiecutter template

1

Mudata should adopt the cookiecutter template for all its benefits. Since there are few PRs open, the disruption should be minimal.

Come up with a recommended way to render/store tutorials

15

I think that wherever it is computationally feasible, tutorials should be run as a CI check and the tutorial use the version rendered by the CI to avoid failing or...

Create actual merge conflicts on template sync

2

Currently, if there are merge conflicts, `cruft` either creates `.rej` files or some inline merge markers (`>>>>>>>`). Both are hard to overlook, in particular if pre-commit CI is not activated...

images in tutorials are rendered too large if not constrained by page width

2


consider adding gitpod or codespaces

5

Setting up github codespaces or gitpod is a nice way of getting contributors started more quickly. It essentially starts a virtual machine somewhere with a containerized workspace with all dev...

Unified logging and settings

5

Should we propose a default mechanism for logging and settings? Benefits IMO would be consistent behaviour for all ecosystem packages. Ideally there would be a way to set the logging...

Feedback on concatenate()

5

While I in the end was able to concatenate the data the way I like, the user experience wasn't as great as I had hoped, so wanted to drop some...