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

Reproducibility tip: Any figure, dataset, ML model, etc., should not be shared until it is produced with an automated, version-controlled pipeline. #reproducibility #openscience

While profiling some CUDA code on a SLURM cluster I realized I was not working in a very reproducible way, which could become a problem down the road if I ever needed to know how a certain result was generated, so Calkit now has SLURM integration: docs.calkit.org/pipeline/slu...

Julia should have an option that automatically does the same thing as: export JULIA_LOAD_PATH=@:@stdlib julia --project=. -e 'using Pkg; Pkg.instantiate()' before running any command. Maybe an enhanced reproducibility mode option, like --repro? #julialang #reproducibility

I don't know why, but I always found it hard to remember the process for adding an SSH key to GitHub, so I made a wizard for it: calkit config github-ssh (might be buggy, but still an improvement over manually running commands from the docs)

Moving pieces of code farther apart from each other (into different packages, modules, repos) doesn't guarantee you've decoupled them. In fact, if you haven't, you probably just made your life a whole lot harder. #softwareengineering

If you're a leader of knowledge workers you should be giving teams fewer, vaguer goals. Handing out well-defined projects and tasks to individuals is a waste of their abilities.

How much "waste" do you have in your scientific workflow? For example, do you manually rerun plotting scripts/notebooks after updating processing logic? Do you then manually re-upload these figures to Overleaf? Want to automate this stuff away? Reach out and I will help!

Code, data, config files, etc. all must be shared in order to describe computational methods with sufficient detail. #reproducibility #openscience

Anyone have any good references that examine the relationship between computational reproducibility and time to publication? I'd assume more automated, reproducible workflows will help studies get through peer review more quickly. #openscience #reproducibility

Calkit now has its own GitHub Action to run your project's pipeline and optionally commit and push results: docs.calkit.org/tutorials/gi...

In software engineering, it's well established that it's worth the effort to automate testing and deployment, but in research, it's not. That is, research computations are almost never fully automated. There's almost always some list of manual steps like data transfer or interactive work involved.

Hot take: YAML is fine.

Graphic design is not my passion. Anyone want to collaborate on an infographic to explain the value of fully automating and version controlling research projects? docs.google.com/drawings/d/1... #openscience #reproducibility #automation

📢 Calkit now supports Julia environments and pipeline stages. Here's an example project: github.com/calkit/examp... #julialang #openscience #reproducibility

Interactive workflows are great for doing things once, not so great for doing things twice. #reproducibility

Naming files like 01_do-something.sh, 02_do-something-else.sh is a bit of a code smell. The order of execution in a project should be automated, not left to the user to follow a sequence of file names.

Calkit 0.27 introduces parameterization for notebooks run in pipeline stages, and these can even be iterated over: github.com/calkit/calki...

Getting started with Julia. First impression is that there is a lot done interactively from the REPL, which feels weird and antithetical to reproducibility. It's also strange that Julia will load packages from both project-level and system-level environments simultaneously.

To prevent being scooped: Instead of working in a closed, non-transparent way, why not make it easier to collaborate? #openscience

Too few researchers work reproducibly because it costs too much for too little benefit. We need to make it easier in such a way that helps researchers get papers out the door faster.

Put succinctly, Calkit's goal is to make "repro pack" READMEs unnecessary #openscience #reproducibility

Classes should be named after the data they encapsulate, not the actions they perform #softwarenengineering

When you describe the computational methods in your paper without sharing the code and data: #openscience #reproducibility

One major cause of the reproducibility crisis is that the way we describe computational methods in research articles has not kept pace with the increase in complexity of the methods themselves. Human language and mathematical formulas are not adequate in many cases.