iiinova — where your digital self keeps evolving

Pete Bachant @petebachant.me · 30/09/2026

Calkit 0.47.11 greatly improves math handling in LaTeX --> Word --> LaTeX round-tripping, including support for LibreOffice. github.com/calkit/calki... #opensource #openscience #reproducibility

A screenshot showing Calkit's LaTeX to Word to LaTeX conversion results.

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Pete Bachant @petebachant.me · 29/09/2026

Writing code, like manufacturing parts for machines, is technician work, not engineering. Engineering is simply predicting if something is going to work. Both can be done by the same person, but we shouldn't confuse the two.

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Pete Bachant @petebachant.me · 24/09/2026

How to prevent this problem? Instrumentation stamping artifacts with cryptographically signed attestation for provenance? That could be useful for more than just fraud detection. #metascience

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Pete Bachant @petebachant.me · 10/09/2026

Maybe problems solved with AI should be attributed to every author whose work is present in the training data, not the company that trained the model.

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Pete Bachant @petebachant.me · 09/09/2026

Emailing Word documents back and forth, despite its many drawbacks, is still one path of least resistance for collaborative writing.

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Pete Bachant @petebachant.me · 05/09/2026

How do you force an AI agent to work reproducibly? Trying to figure that out myself as I have Claude experiment with CUDA kernel optimization. Not perfect, but having it work with a pipeline with definitive staleness detection is helping: calkit.io/petebachant/... #agenticai #reproducibility

calkit.io

Calkit

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Pete Bachant @petebachant.me · 29/08/2026

Many scientific papers are tightly-coupled to the code, data, and environments that produced them, and therefore the paper itself fails to provide much standalone value. Failure to reproduce or replicate is a direct consequence of this coupling. #openscience #replicationcrisis #metascience

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Pete Bachant @petebachant.me · 28/08/2026

Calkit now has online figure and notebook editors that run in the browser with WASM/Pyodide, but produce code and environments integrated into a local-first reproducible pipeline. #opensource #openscience #reproducibility

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Pete Bachant @petebachant.me · 18/08/2026

Thinking of revamping the Calkit onboarding a bit. What use case is more valuable to you: 1. You have a research project in progress that's a bit of a disaster and you'd like to get it under control 2. You're starting a new project and want to follow best practices from day one #reproducibility

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Pete Bachant @petebachant.me · 13/08/2026

We are definitely going to need some social norms around asking people to read things generated with AI. It at least needs to be explicit, and it probably should be okay to respond with: can you explain in your own words?

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Pete Bachant @petebachant.me · 11/08/2026

Calkit Chrome extension just dropped. Collect references and notes directly into a BibTeX file in a GitHub repo from journal websites and arXiv, sync figures and results into Overleaf, and review DVC-tracked files and LaTeX diffs directly on GitHub. #opensource #openscience #reproducibility

Calkit Chrome extension showing a LaTeX diff on GitHub.

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Pete Bachant @petebachant.me · 04/08/2026

Doing open science gets you more citations (arxiv.org/pdf/2607.00546) However, does it also result in less individualistic innovation (less notoriety, more scooping, worse tenure outcomes)? #openscience #publishorperish

arxiv.org

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Pete Bachant @petebachant.me · 04/08/2026

Leaders are responsible for vision and strategy, i.e., prioritizing problems and giving insights into avenues for solutions. If you're handing off fully-baked solution specs to your engineers you're wasting their talent and holding them back from growing.

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Pete Bachant @petebachant.me · 03/08/2026

There's an interesting distinction between "this can run again" and "I can prove that I ran this and here's the output" and the latter is becoming more important with increasing AI usage #agenticai #aiforscience #reproducibility

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Pete Bachant @petebachant.me · 01/08/2026

How many more times can I hear "agentic AI" this week before I quit using computers for the rest of my life challenge

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Pete Bachant @petebachant.me · 29/07/2026

AI agents, like humans, should be creating pipelines. They should not be parts of pipelines.

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Pete Bachant @petebachant.me · 28/07/2026

Moving steadily towards a free, open-source, vertically-integrated research platform, calkit.io now has a project-based reference manager that can sync bidirectionally with Zotero. #openscience #opensource #reproducibility

A screenshot of the Calkit reference manager.

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Pete Bachant @petebachant.me · 27/07/2026

New feature on calkit.io: attach evidence to answers to research questions and quickly verify that they're still up-to-date given their provenance. Example project: calkit.io/calkit/examp... #reproducibility #openscience #opensource

A screenshot of Calkit's questions section.

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Pete Bachant @petebachant.me · 26/07/2026

Unifying development and operations in the same team/repository was a boon for software. Would science see similar gains from moving its various stages/functions closer together? #devops #openscience #opendata

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Pete Bachant @petebachant.me · 18/07/2026

"utils" modules are bad because they show you value DRY (don't repeat yourself) more than modularity, and you end up with tight coupling and low cohesion #softwareengineering #swe #softwarearchitecture

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Pete Bachant @petebachant.me · 17/07/2026

There are lots of great computational tools out there for doing different stages of research, but they're poorly integrated with each other, which is a source of errors and inefficiency.

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Pete Bachant @petebachant.me · 14/07/2026

How well does failure to reproduce correlate with failure to replicate? #metascience #reproducibility

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Pete Bachant @petebachant.me · 11/07/2026

If your collaborators don't want to learn Git/GitHub but you don't want to silo paper writing away from your code and data, calkit.io now has a LaTeX editor and WASM compiler :) #opensource #openscience #reproducibility

A screenshot of Calkit's in-browser LaTeX editor.

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Pete Bachant @petebachant.me · 08/07/2026

If you're building a writing tool for scientists, it's pretty important to make it easy to connect to visualization/analysis tools. That is, if you make users manually upload their data or figures, that's bad.

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Reposted by Pete Bachant

Konrad Hinsen @khinsen.net · 06/07/2026

New blog post: "Conviviality in computational science" blog.khinsen.net/posts/2026/0... "Conviviality matters for science ... if you want to derive knowledge from your work, you need to know exactly what you are doing, and that includes a detailed understanding of your tools." 🧪 #metascience

blog.khinsen.net

Konrad Hinsen's blog

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Pete Bachant @petebachant.me · 02/07/2026

Instead of compiling a replication package or repro pack at journal article submission time, imagine if you worked inside of a repro pack the whole project... #reproducibility #openscience

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Pete Bachant @petebachant.me · 01/07/2026

@plos.org's concept of the "knowledge stack" in science is interesting from an architectural perspective. Is any layer truly valuable on its own? I'd argue the full stack is the most valuable unit, which means you should be shipping the whole thing with every study. #openscience #opensource

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Pete Bachant @petebachant.me · 29/06/2026

If you know what individual to ask for help in a separate team, you are probably tightly-coupled, and maybe should be part of the same team

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Pete Bachant @petebachant.me · 28/06/2026

The Calkit VS Code extension now allows viewing interactive @plotly.com figures, and includes a gallery view.

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Pete Bachant @petebachant.me · 24/06/2026

If a human is supposed to read it, it shouldn't be written by AI

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Pete Bachant @petebachant.me · 23/06/2026

For those who manage research groups: Do you tend to be more individual-focused, with each member getting their own independent project, or team-focused, where individuals need to find their niche to contribute to a larger collective goal?

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Pete Bachant @petebachant.me · 15/06/2026

Been spending some time on the Calkit VS Code extension. Here's a screenshot using it with Claude to profile CUDA kernels in SLURM jobs and keep track of Nsight reports for each code change: #aiagents #cuda #gpu #claude

A screenshot of the Calkit VS Code extension.

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Pete Bachant @petebachant.me · 07/06/2026

AI agents will happily create figures for you. They'll even export some source code. But can you trust that they did what they said they did? Here's a tutorial on how to get your AI agents to work reproducibly: docs.calkit.org/tutorials/ai...

docs.calkit.org

Declarative, structured prompting to make AI agents work reproducibly - Calkit

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Pete Bachant @petebachant.me · 02/06/2026

I'm not a fan of splitting up code into a bunch of tiny functions as a default practice. It's like creating a bunch of minor characters in a story. It should only be done if those characters really add something, because each one will take away some attention. #swe #softwareengineering #dev

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Pete Bachant @petebachant.me · 26/05/2026

The golden rule of architecture: Avoid moving horizontal slices away from each other, either into different repos or different teams

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Pete Bachant @petebachant.me · 05/05/2026

Maybe we can build more human interfaces for our computing tools without making them nondeterministic and extremely computationally expensive

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Pete Bachant @petebachant.me · 02/05/2026

On one side, you have literate programming, which views code and prose as belonging to a monolithic artifact. On the other, you have total fragmentation with code in one silo, data in another, writing in another, and no real interface between them. I think we need modularity with real interfaces.

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Pete Bachant @petebachant.me · 01/05/2026

Tightly coupled code should not be split across multiple repos #softwareengineering #swe #softwaredesign

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Pete Bachant @petebachant.me · 30/04/2026

IMO, the most important rule for using AI agents to do scientific research: Don't allow them to create artifacts like figures or numerical results on their own. Have them create, save, and run pipelines that create artifacts so provenance is preserved and traceable. #openscience #agentic

docs.calkit.org

Use with AI tools - Calkit

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Pete Bachant @petebachant.me · 29/04/2026

Success boils down to properly defining how to measure it then doing as many iterations as possible.

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Pete Bachant @petebachant.me · 20/04/2026

New feature on calkit.io: Comment on publication PDFs and create GitHub issues from them. This was inspired by the process I used to get my PhD thesis done on time. Every comment from my advisor became a GitHub issue and I calculated the necessary daily "velocity" working backward from the deadline.

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Pete Bachant @petebachant.me · 08/04/2026

Super helpful, Google. Thanks. #nodejs

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Pete Bachant @petebachant.me · 06/04/2026

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

docs.calkit.org

Connect a Jupyter Notebook to a kernel in a SLURM environment in VS Code - Calkit

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Pete Bachant @petebachant.me · 31/03/2026

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

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Pete Bachant @petebachant.me · 30/03/2026

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

docs.calkit.org

Version control - Calkit

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Pete Bachant @petebachant.me · 18/03/2026

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

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Pete Bachant @petebachant.me · 27/02/2026

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

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