This may be extremely niche, but if you need to run a Jupyter kernel in a SLURM job, e.g., to reserve a GPU, and connect it to a notebook in VS Code, here's a solution: docs.calkit.org/tutorials/vs... #opensource #jupyter #hpc #cuda

The best time to automate your project is 10 months ago when you started. The second best time is now.

One of the limitations of DVC is that it's relatively slow/inefficient working with large folders consisting of many small files. Here's a solution: docs.calkit.org/version-cont... #dataversioncontrol #datascience #python

Is there a parallel to Conway's Law for cognitive load, i.e., that software complexity will increase to hit the cognitive load limit of the team that owns it regardless of the inherent complexity of the problem? #softwareengineering

In support of #OpenScience, we routinely ask authors to openly share their #research #code before publication. We are now formalizing this practice with a mandatory #CodeSharing policy and clarifying what we mean by code sharing.

Quick demo of something I've been working on: Execute some Python, R, Julia, MATLAB, and LaTeX scripts/notebooks/docs and they automatically become a DVC pipeline (DAG). #opensource #reproducibility #datascience

A demo of the new calkit xr ("execute-and-record") feature that will automatically turn a sequence of Python, R, Julia, or MATLAB scripts, notebooks, or LaTeX docs into a pipeline by simply running them. No need to learn Make, Snakemake, DVC, et al. Environment management included!

Why #openscience? Whether or not the input data and processes are described accurately in prose/mathematics doesn't matter if the code and data are included--those become the actual source of truth. A paper is almost never sufficient to describe what actually happened in the research.

If you're stuck with Conda (can't switch to uv or Pixi for whatever reason), here's a way to get a similar experience (no need to create/activate/update environments): github.com/calkit/calki...

What do you do if you're reviewing a paper and the journal policy clearly states all code and data must be supplied, but the authors only share the source code--no input data, no configs, no run scripts, no plotting scripts? #openscience #opendata #reproducibility

This article focuses more on the positive potential of doing open science, but I find it very frustrating how common it is to see openness done in a half-baked, almost performative way. doi.org/10.1073/pnas... #openscience #opensource

Being able to reproduce a computational environment is not the same thing as being able to reproduce the science, but it is an important step

Stop numbering your Jupyter Notebooks and running them one-by-one to deliver "final" results. Turn them into a reproducible pipeline instead: youtu.be/8q-nFxqfP-k #openscience #reproducibility #datascience #jupyter

New JupyterLab extension just dropped! Manage environments and assemble your notebooks into a pipeline all in the UI. Give it a try with: uv tool install --upgrade calkit-python or pip install --upgrade calkit-python docs.calkit.org/jupyterlab/ #openscience #reproducibility #jupyter

What if we had an open-source, decentralized "GitHub for science?" Instead of all the code needed to build the binary of an app or library, researchers would share all of the code, data, etc., necessary to build their papers. #openscience #opensource

Should you put your front end and back end in separate repos? Probably not. You should have at lease one product per repo, and if the front end can't provide value on its own, it's not a product.

Before moving code away from other code, e.g., into a different module, package, repo, etc., make sure it's loosely coupled. If you can't loosely couple it, keep it close together. #swe #softwareengineering #softwaredesign

Check out this cool CFD simulation I did with my "in house code." Just kidding. I faked this in 5 seconds using AI. Are journals requiring source code and reproducibility checks for all submissions yet? #openscience #cfd #aislop

True or false: If your paper can't be reproduced by everyone on your team it's an indication that it could have been done much more quickly. #openscience #reproducibility

NASA's free course "Open Science 101" recently reopened for registration: science.nasa.gov/open-science... #openscience

When I was in grad school and started learning software engineering, I got midway between these. I had multiple instead of one pipeline to run to build each paper but there was no environment management or "staleness detection" for intermediate outputs. Working on making those easy/obvious.

I'm still angry they renamed NREL. Stupid political nonsense.

Has "open science" even been attempted yet? About 10% of articles share code, and of those, maybe 10% share code and data in a way that actually runs. Virtually none are single-button reproducible. We have a long way to go. #openscience #reproducibility

Next year, instead of filing a tax return, I will file a "tax return availability statement": Available upon reasonable request. #openscience #opendata

Couldn't find any extensions for research/analytics project management in JupyterLab, so I started building one. Here's the PR if you want to chime in with your wish list: github.com/calkit/calki... Happy holidays! ⛄ 🎅 #opensource #jupyter #openscience

TIL about ipyflow, which adds a reactive IPython kernel for Jupyter (basically the marimo value prop): github.com/ipyflow/ipyf...

When is closed-source commercial software okay to use for science? As long as it's interoperable with an open file format/protocol? GitHub, for example. #openscience #opensource

Thanks @insidehighered.com for publishing our OpEd w Annie K. Lamar #publicvoices of The Oped Project @ucsantabarbara.bsky.social ! 🤖Open source software & infra accelerates scientific discoveries by removing financial & technical barriers. It's about time we start treating it as a public good👇

For those who think we can solve the reproducibility crisis with policy and education alone, consider the pedestrian and cyclist injury/fatality rate from drivers in the US versus somewhere like the Netherlands. Infrastructure matters. #openscience #reproducibility

Overleaf to VS Code in the browser in under 2 minutes: youtu.be/GjyMxwYbdXk #phdstudents #academia #openscience

What uv has done for Python project management is what I hope Calkit can do for research/analytics projects. #openscience #datascience #reproducibility

Small improvement to the declarative Conda environment handling in Calkit: Now you can put editable install paths in the pip section. No more "create, mutate, export" cycles--just use the environment for something like `calkit nb execute`, and it just works. #python github.com/calkit/calki...

Jupyter notebooks are fine to use in production as long as their outputs aren't considered "official" unless they are run in batch mode, e.g., with nbconvert or papermill. That is, you should never deliver any result from a notebook you ran interactively. #reproducibility #openscience

Tired of manually uploading figures to Overleaf? Over the past few weeks I tried to make it as easy as possible to sync an Overleaf project with a Calkit project so updating the data or analysis can automatically be reflected in a LaTeX document: youtu.be/BuzLFO0JYxU #openscience #reproducibility

Separation of concerns is great but we also need minimization of concerns. In other words, "the main thing is to keep the main thing the main thing." #softwareengineering #swe #developer

The Calkit Run GitHub Action now authenticates with OIDC tokens, so no secrets are required to push artifacts, e.g., the latest PDF of your paper, up to the cloud: github.com/calkit/run-a... #automation #openscience #reproducibility

💥 First "real world" Calkit repro pack just dropped! In this paper we did a bunch of benchmarking for a brand new astronomical alert brokering system designed to interface with the Rubin Observatory. Check out the repo here: github.com/boom-astro/b... #openscience #reproducibility #opensource

Really love this kind of reality-check meta-research 👉“The struggle to make transparency mainstream: initial evidence for a slow uptake of open science practices in PhD theses” royalsocietypublishing.org/doi/full/10....

"8% of authors shared code and software openly..." insights.taylorandfrancis.com/research-imp... #openscience #opendata #reproducibility

If you publish a "repro pack" with your paper, you're awesome, but there's about a 10% chance it will actually run on someone else's computer. In this post I explain why that isn't your fault, why it matters, and what we should do about it: petebachant.me/single-button #openscience #reproducibility

Calkit projects can now incorporate Julia Jupyter notebooks into their pipelines: calkit.io/calkit/examp... #julialang #reproducibility #openscience

Why number your notebooks/scripts and execute them manually when you could simply put them into a pipeline that automatically manages their environments and caches their outputs? docs.calkit.org/pipeline/ #datascience #automation

1. Generate evidence to support some claims 2. Don't automate the creation of said evidence Congratulations, you've just contributed to the reproducibility crisis! #reproducibility #openscience

So much brilliant work never makes it into a paper. The code, the data, the long nights helping others debug. At pyOpenSci, we believe that code, data, and community are the pulse. Research advances quickly when we build together & openly. Join us. 💛 bit.ly/pyos-volunteer #openscience #opensource

Don't be ashamed of "messy" code. If it works, it's good. Share it. #openscience #reproducibility

Reading through some slides from 2013 titled "how to succeed in reproducible research without really trying". It's true we have all the tools needed for researchers to build their own reproducible workflows, but still many do not. Maybe the tools are still too hard to learn and use!

Programming tip: Name classes after the data they encapsulate, not the actions they perform on that data. For example, instead of SchemaProcessor, just call it Schema: processed_schema = Schema().process() #programming #oop #softwareengineering

Hot take: Notebooks are fine in production as long as they're part of a reproducible pipeline docs.calkit.org/notebooks/ #reproducibility #datascience #openscience

Please don't number your scripts. Refer back to (2) and use a pipeline (like Calkit's of course)! www.nature.com/articles/d41... #reproducibility #automation #openscience

In a newly released arXiv preprint, we explore how open science practice like sharing data, code and preprints relate to citation impact in French-authored research over a 3-year period. Thanks to @ouvrirlascience.bsky.social for highlighting its national importance. 🔗 Read more: plos.io/3Vmykrj