Fixing Nightly Docker Builds For Neurobagel

Hey guys, have you ever run into a snag while building your Docker images? I recently hit a pretty annoying one with the neurobagel project, specifically with the bagel-cli tool. The nightly builds were failing, and the culprit turned out to be a missing piece of the puzzle related to how Git and Docker interact. Let's dive into what happened, how we fixed it, and what you can learn from it.

The Problem: Missing Git Context in Nightly Docker Builds

So, the main issue revolved around the nightly Docker builds failing. If you've ever worked with Docker, you know that the .dockerignore file is your best friend when it comes to keeping your builds lean and efficient. This file tells Docker which files and directories to ignore when building the image. In this case, the .git directory was being excluded. That's usually a good thing, because it keeps your image size down. However, when we tried to install bagel-cli from source in our nightly builds, things went sideways.

Basically, the pip package manager, which is used to install Python packages, couldn't find the necessary Git metadata inside the working directory. This metadata is crucial for determining the package version information when you're installing from a Git repository. Because the .git directory was excluded, pip couldn't access the version details, leading to an error. The error message clearly stated the problem, "LookupError: Error getting the version from source 'vcs': setuptools-scm was unable to detect version for /app". This made it so the nightly build will not work as it could not get the package version info.

Let's be real, debugging Docker builds can sometimes feel like a treasure hunt. You're sifting through logs, trying to piece together what went wrong. In this case, the error message pointed us directly to the source of the problem. It told us that setuptools-scm (a tool used to manage package versions based on Git tags) couldn't find the version information. The error message also provided a clear hint. It said, "Make sure you're either building from a fully intact git repository or PyPI tarballs." This pointed towards the fact that building from a Git repository required that the .git directory is not excluded from the build context. The issue came to light because of the way we were building nightly builds, which is a common practice in software development to create automated builds for the latest code. This ensures that the code that is deployed is always working and up to date, however, the Docker file was configured in a way that the .git directory was excluded.

The Root Cause

• .dockerignore Exclusion: The .git directory was excluded, which is common practice for production builds to reduce image size. However, it caused an issue when installing from source during the nightly builds.
• Version Information Dependency: The bagel-cli package relied on Git metadata to determine its version during installation.

Understanding the Impact of Missing Git Context

Okay, so why is this such a big deal? Well, in the world of software development, especially when you're working with CI/CD pipelines, consistent and reliable builds are absolutely critical. If your nightly builds are failing, that means you're not getting automated testing, integration, and deployment of your latest code. The nightly builds are important because they should be the most up-to-date and have the latest code changes. Nightly builds allow you to catch bugs early, integrate new features, and ensure the latest changes are ready for production. When these builds fail, it creates a bottleneck in your development process. It slows down the feedback loop, and it can delay the release of new features and fixes.

Without a functioning nightly build, you lose the benefits of continuous integration and continuous delivery. This can lead to increased development time and decreased stability. Think about it: if you're not automatically testing and deploying your code, you're more likely to run into integration issues. You might have to spend more time manually testing and deploying your application, which can be a real pain. So, ensuring your nightly builds are working correctly is not just a good practice – it's essential for maintaining a healthy and efficient development workflow. The missing git context directly impacted the ability to install the bagel-cli package, which is a core component of the neurobagel project. This meant that the nightly builds couldn't complete successfully, halting the progress of the project. This can cause frustration and delays, and it can affect the overall project timeline.

The Solution: Modifying the Dockerfile and Installation Process

The solution involved a few tweaks to the Dockerfile.nightly to ensure the Git context was available during the build. We had to rethink how we were building the image to include the necessary Git metadata. Here's a breakdown of the steps we took:

• Removing .git from .dockerignore (or modifying the build context): The most straightforward solution is to ensure that the .git directory is not excluded in the build context. This can be achieved by removing the .git line from the .dockerignore file, or by adjusting the build context to include the .git directory. This is essential for the setuptools-scm to function correctly and determine the package version.
• Installing from Source (and making sure Git is available): By installing from source, we need to ensure that the Git repository is available in the build context. This allows pip to find the necessary metadata and determine the correct package version. Ensure the necessary build dependencies like Git are installed in the Dockerfile.

Code Snippets and Explanations

Here's how you might modify your Dockerfile to include the .git directory or include git installation:

# Example Dockerfile snippet (adjust based on your needs)
FROM python:3.9

# Install Git (if not already installed)
RUN apt-get update && apt-get install -y git

# Copy the application code. Make sure that the `.git` folder is copied too.
COPY . /app
WORKDIR /app

# Install the package from source
RUN pip install -e .

# Your application entrypoint or commands
CMD [