Publishing

Zenodo

Create drafts, edit metadata, upload files, publish and create new versions (sandbox supported).

TIP

Link a GitHub repo in Zenodo's GitHub settings and every GitHub release from Codeome gets a DOI.

Packages

Open Packages with ⌘6. It has stacked sections, like Files: Python (pip) and, in R projects, R libraries. Each works on the Mac or the HPC.

• Python: list, install, upgrade and remove packages; build your package and upload it to TestPyPI or PyPI (Publish).
• R: every library in .libPaths() (project renv, user, site, system) as its own group, with each package's version and where it came from (CRAN, Bioconductor, GitHub). Install from CRAN, Bioconductor or GitHub (user/repo), update, remove, or load one into the R console. Check for updates (⋯) marks outdated packages, and you can update them all at once. R runs in the project folder, so renv projects install into their own library.
• A project counts as an R project if it has an .Rproj, DESCRIPTION, renv.lock, .Rprofile or R / R Markdown files at the top. Right-click a section header to show or hide R libraries anywhere.
• Not an R project yet? Right-click the active project (in the project list or on its tag) and choose Set up as R project…. A dialog offers a .Rproj file (on), renv (renv::init(), on for This Mac and off for the HPC), .gitignore entries for .Rproj.user, .Rhistory, .RData and renv/library (on), and a starter analysis.Rmd (off). It works in the project folder on the Mac or the HPC, following the R selector, and never overwrites existing files: skipped ones are named in a message. renv runs in a terminal task, and the R libraries section appears afterwards.

Packages has a Python section and an R libraries section, each on This Mac or the HPC, with an install box and a filter.

Tokens for Zenodo and PyPI are set in Settings and stored as described under Secrets.