I wanted to share some stuff I’ve built and lessons learned regarding the use of Jupyter notebooks as part of a larger research project. Namely, how to keep things reproducible (with a single command) while retaining the benefits of interactivity notebooks provide. You can read the docs here: https…

Hi @petebachant , that’s a nice project! I like the way you integrate the code, data, and setup into the workflow specification! You have specifically pinned down the ML-setups very flexible and user-specific using Docker and/or Conda/venv. Only few have realized that the “open setup” is (besides co…

Hi @csc , GPU-Jupyter looks super interesting. Workflows that use both notebooks and GPUs are becoming more prevalent, and the complexity will certainly make reproducibility more difficult. I definitely think a combination of Calkit and GPU-Jupyter would be interesting to explore. Pre-processing st…

@petebachant , Allowing also non-sequential preprocessing brings very important flexibility and is an advantage over many existing solutions. Yes, this example project is good to try GPU-Jupyter for reproducibility (the README will be shortened soon). I would be very glad for a demo for using GPU-J…

Just opened a PR here: Add Calkit compatibility by petebachant · Pull Request #1 · iot-salzburg/reproducible-research-with-gpu-jupyter · GitHub Let me know what you think if you get a chance to try it out.

Thanks @petebachant , I’ll check it out later this week. What makes me wonder is, that (some of) the resulting errors are different, even though only the package notebook was changed. Do you know why this is the case? Additionally, there seems to be a lot of redundant files within the .calkit direc…

[image] csc: What makes me wonder is, that (some of) the resulting errors are different, even though only the package notebook was changed. Do you know why this is the case? I assume this is non-reproducibility coming from PyTorch, but I’m not sure. Maybe it’s worth running on different machi…

Hi @petebachant , eventually I had time to dive into calkit. That’s an impressive and comprehensive software project you created! It took quite a time to get into it, but I guess it would be quite fast for subsequent projects. I guess that some hands-on video tutorial could help a lot of users. Ove…

Some tips and tools for maintaining reproducibility in scientific workflows that use Jupyter notebooks

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csc July 14, 2025, 12:30pm 3

Btw, I stick to the Jupyter’s docker stacks in GPU-Jupyter to allow a similar UI. I have already posted a question regarding the GPU-support here: Proposal: GPU-Support.

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Some tips and tools for maintaining reproducibility in scientific workflows that use Jupyter notebooks

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