GitHub Primer

The science blog archive Rogue Scholar depends heavily on GitHub Actions. They are used to trigger content and metadata extraction of new blog posts and to register DOIs for these posts with Crossref. More recently they have also been used to push this content and metadata to the new InvenioRDM-based Rogue Scholar platform. GitHub Actions are workflows that typically operate on the command line.

Following on from Annotating and cleaning GBIF data: Darwin Core Archive, GitHub, ORCID, and DataCite here's a quick and dirty example of using GitHub to help clean up a Darwin Core Archive. The dataset 3i - Cicadellinae Database has 2,152 species and 4,749 taxa, but GBIF says it has no georeferenced data.

Today I managed to publish some data from a GitHub repository directly to GBIF. Within a few minutes (and with Tim Robertson on hand via Skype to debug a few glitches) the data was automatically indexed by GBIF and its maps updated. You can see the data I uploaded here.The data I uploaded came from this paper:This is the data I used to build the geophylogeny for Banza using Google Earth.

Some time ago, the brilliant GitHub people gave me the following tip. Rajarshi is lazy, and might find it interesting. By appending .patch to the commit URL, a commit can easily be downloaded as patch. That way, developers can easily download it with wget or curl and apply it locally with git am, without having the fetch the full repository.

There is an excellent post on open science, prestige economies, and the social web over at Marciovm's posterous*. For those of you who aren't insanely nerdy** GitHub is… well… let's just call it a very impressive collaborative tool for developing and sharing software***. But don't worry, you don't need to spend your days tied to a computer […]