Daniel Herrera-Esposito

Daniel Herrera-Esposito

Computational Neuroscientist. Interested in the brain, math, computers, and sometimes epidemiology

GitHub releases to keep your old projects from breaking

3 minute read

Published:

If you are a scientist who uses code in your research, you might have experienced the following scenario. You wrote some code, let’s say in directory my_code/, or GitHub repository https://github.com/my_user/my_code. You use this code in a certain project and analyses are currently working. Then, you have the idea of modifying my_code, for example, to add a new feature required by a new project. However, the new modified code might (and probably will) break the old project.

Of course, you don’t want your old project to now become unreplicable because of these changes. But you also don’t want to make the old project work with the new code, which can involve a lot of work. One way to avoid this situation is to use GitHub releases.

What are GitHub releases?

Here we’ll assume that you are familiar with the very basics of GitHub, and that you know how to create a repository, commit and push code. If not, consider reading this guide for scientists in PLoS Comp Bio to start incorporating this amazing tool into your workflow.

The basic GitHub workflow of committing and pushing does not protect you from the situation described above, however. If you push changes to the repository, the old project will use the new code and might break.

GitHub releases basically allow you to “freeze” a version of your code that you want to be able to access later (e.g. the version that works with the old project), while still letting you work on the code and make changes. You have probably seen this in many software projects, where you can download a specific version of the software, like useful_package_v1.0.0, useful_package_v1.0.1, etc. GitHub releases allow you to do the same thing with your code, so that for different projects you can specify which version of the code you and your users should use.

How to use GitHub releases

Using GitHub releases is quite simple, and the GitHub documentation is clear and helpful.

Once you have the desired working version of your code in your repository, all you need to do is go to your repository, click on the “Releases” tab on the right. Then a page to create the new release will open up. You can give the release a tag (e.g. v1.0.0), a title (e.g. First release), and a description (e.g. Project X works with this release).

After you create the release, you can go back to the “Releases” tab and see all the releases you have created. You can download the code for a specific release using the command line

git clone https://github.com/my_user/my_packave --branch v1.0.0

In the repository of your older project, you can now direct users to download the code from the release that works with the project by using this command. If you already have a environment.yml file that you use to set up the environment for the project, you can specify the version of the code that should be used by adding the version tag to the URL, like this:

- git+https://github.com/my_user/my_package.git@v1.0.0

You can also just download the code by clicking on the release and then on the “Source code” link.

You May Also Enjoy

Covariance shrinkage for begginers with Python implementation

8 minute read

Published:

Covariance matrices are one of the most important objects in statistics and machine learning, essential to many algorithms. But estimating covariance matrices can be difficult, especially in high-dimensional settings. In this post we introduce covariance shrinkage, a technique to improve covariance matrix estimation. We also provide a PyTorch implementation of a popular shrinkage technique, the Oracle Approximating Shrinkage (OAS) estimator.

Is the world as we see it?

36 minute read

Published:

Author translation of the chapter “Es el mundo como lo vemos?” (link to pdf in Spanish) for the book “Hitos y Mitos del Cerebro”, edited for the homonymous first year course at Universidad de la República, Uruguay. The chapter aims to introduce several ideas of perception and neuroscience to first year students through the guiding question of whether the world is as we see it. In particular, the chapter discusses the question from three perspectives: an evolutionary perspective, a resource optimization perspective, and the perspective of ambiguity of sensory information.