ICES provides the following GitHub areas to facilitate scientific collaboration in marine research:
-
Transparent Assessment Framework
https://github.com/ices-taf -
Expert Groups
https://github.com/ices-eg -
Tools under development
https://github.com/ices-tools-dev -
Tools maintained by ICES
https://github.com/ices-tools-prod -
ICES Publications
https://github.com/ices-publications
The code in these repositories can be browsed and downloaded. To apply for write access to specific repositories, please send an email to [email protected].
The distinction between tools-prod and tools-dev is that github.com/ices-tools-prod contains software that is operational and maintained by the ICES Secretariat, while github.com/ices-tools-dev contains everything else (operational software maintained by scientists outside the Secretariat, experimental projects, etc.)
github.com/ices-publications contains the text and source files necessary to generate some ICES publications.
The main guidelines for working in the ICES GitHub areas are:
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Users should register their GitHub username at https://taf.ices.dk/github. This allows you to be added as a member of your ICES Working Groups on GitHub and get write access to repositories.
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Repositories should be kept under 1 GB and should mainly contain code and configuration files. Please contact [email protected] if you are working with large datasets.
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Expert Group chairs are free to recommend a certain workflow for that group.
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It is suggested that users provide their full name in their GitHub profile (https://github.com/settings/profile), so that others can see who is doing what, but this is not a strict rule.
Most ICES scientists connect to their GitHub repositories inside RStudio. The very first steps for beginning users are then to install the required software (R, RStudio, Git), create a username on https://github.com, and register their username on https://taf.ices.dk/github.
To work on a repository in RStudio, select File - New Project - Version Control - Git, then paste the URL (e.g. https://github.com/ices-eg/wg_HAWG) and
create the project. This action is called to clone a repository, creating a
special directory on the hard drive that is linked to the GitHub repository.
A Git tab will now appear in the upper-right window, containing the following commands:
| Command | Purpose |
|---|---|
Commit |
Write a log message about changes in files |
Pull |
Get the newest updates from GitHub repository |
Push |
Submit committed changes to GitHub repository |
It is always recommended to pull the newest updates before editing files, committing, and pushing them to GitHub. Right-clicking a file in the Git window will show useful commands to diff and revert changes.
The main GitHub help page can be found at:
https://help.github.com
A hello world tutorial can be found at:
https://guides.github.com/activities/hello-world/
A very useful guide on how to get yourself out of a fix and many other helpful
Git commands can be found here:
https://github.com/k88hudson/git-flight-rules
Happy Git provides opinionated instructions on how to install Git and link RStudio with Git and Github: https://happygitwithr.com/rstudio-git-github.html
Other help resources, including the Git book, are listed in the ICES R development
guidelines:
https://github.com/ices-tools-prod/doc#62-development-tools