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Issue Description

I am attempting to install and use AlphaPulldown (APD) on Google Colab. According to the installation manual, a Conda-based virtual environment is required to ensure smooth operations. Considering Colab's characteristic of resetting the environment every time a session reconnects, I decided to create a custom kernel using the virtual environment to avoid repeatedly setting up and installing large dependencies.

Here’s what I did:

  1. Installed Conda and created a virtual environment specifically for AlphaPulldown.
  2. Installed all necessary dependencies for AlphaPulldown in the environment.
  3. Registered the virtual environment as a custom kernel in Colab.
  4. Attempted to switch to the custom kernel in Colab to start using AlphaPulldown.

However, when switching to the custom kernel, Colab fails to connect to the backend, while the default Colab kernel works perfectly. I suspect there might be a conflict between the custom kernel and Colab's backend, but as a new user, I’m unsure how to debug or resolve the issue.

I have created and shared my Colab notebook here, which contains the full code and setup steps. I would greatly appreciate it if someone could review it and help identify what might be going wrong.

Here’s what I’ve tried so far to debug and resolve the issue:

  • Verified the custom kernel uses a compatible Python version (3.8, as required by AlphaPulldown).
  • Ensured the virtual environment includes essential dependencies like jupyter and ipykernel.
  • Reduced the environment complexity by installing only the minimum required packages.
  • Changed the Colab runtime hardware (CPU-only mode, GPU, TPU) to rule out hardware-related issues.
  • Re-registered the custom kernel multiple times.

Unfortunately, none of these steps have resolved the issue.

Expecting help：

  • Suggestions on debugging kernel connection issues in Colab.
  • Insights into potential compatibility problems between Colab’s backend and Conda-based virtual environments.
  • Recommendations for setting up AlphaPulldown in Colab without encountering these issues.
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