jgcri / divittorio_et_albiodiversity

metarepo

Template repository for a single point of access meta-repository to reproduce an experiment

Purpose

A meta-repository creates a single point of access for someone to find all of the components that were used to create a published work for the purpose of reproducibility. This repository should contain references to all minted data and software as well as house any ancillary code used to transform the source data, create figures for your publication, conduct the experiment, and / or execute the contributing software.

Using the template

Simply click Use this template on the main repository page (shows up to the left of Clone or download) and fill in your Repository name, the Description, select whether you want the repository to be Public or Private, and leave Include all branches unchecked.

Naming your meta-repository

The following naming conventions should be used when naming your repository:

• Single author: lastname_year_journal
• Multi author: lastname-etal_year_journal
• Multiple publications in the same journal: lastname-etal_year-letter_journal (e.g., human-etal_2020-b_nature)

Customize your .gitignore file

A general .gitignore for use with Python or R development is included. However, you may wish to customize this to the needs of your project. The .gitignore file lets Git know what to push to the remote repository and what needs to be ignored and stay local.

Suggestions

• Don't bog down your repository with a bunch of raw data. Instead archive and mint a DOI for your data and provide the reference in this repository with instructions for use.
• Create complete and tested documentation for how to use what is in this repository to reproduce your experiment.

Creating a minted release for your meta-repository

It is important to version and release your meta-repository as well due to changes that may occur during the publication review process. If you do not know how to conduct a release on GitHub when linked with Zenodo, please contact [email protected] to get set up.

The meta-repository markdown template

A sample meta-repository template is provided in this repository in the file metarepo_template.md.

To use it, do the following:

1. Create the template repository as mentioned above in Using the template
2. Clone your new repository to you local machine
3. Change directories into your new meta-repository directory you just cloned
4. Run git rm README.md to delete this file (README.md) and commit it using git commit -m 'remove instructions'
5. Rename metarepo_template.md as README.md
6. Run git add README.md to stage the new file that will show up on load in your remote GitHub repository
7. Run git rm metarepo_template.md to remove the original template
8. Run git commit -m 'set up new template as readme' to set the changes
9. Run git push to send the changes to your remote GitHub repository
10. Modify the README.md file to represent your experiement and use the add, commit, push workflow to update your remote repository