Jupyter notebooks don’t work with git by default. With nbdev2, the Jupyter+git problem has been totally solved. It provides a set of hooks which provide clean git diffs, solve most git conflicts automatically, and ensure that any remaining conflicts can be resolved entirely within the standard Jupyter notebook environment. To get started, follow the directions on Git-friendly Jupyter. Contents The Jupyter+git problem The solution The nbdev2 git merge driver The nbdev2 Jupyter save hook Background The result Postscript: other Jupyter+git tools ReviewNB An alternative solution: Jupytext n ..read more

Contents Our new secret weapon for productivity nbdev in industry What’s nbdev? What we learned after three years of using nbdev Enter Quarto: A pandoc super-processor A blazing fast notebook kernel: execnb Towards a dialect of python that embraces its dynamic nature The future of nbdev How you can get started with nbdev Thank You A conversation with JJ Allaire Our new secret weapon for productivity Today we’re excited to announce that we’ve teamed up with Quarto to give nbdev superpowers. nbdev offers Python programmers a common set of tools for using Jupyter notebooks to: Write & dist ..read more

My colleague Dr Uri Manor was a senior author on a study in March this year which has become the most discussed paper in the history of Circulation Research and is in the top 0.005% of discussed papers across all topics. That’s because it got widely picked up by anti-vaxx groups that totally misunderstood what it says. Uri and I decided to set the record straight, and we wrote a paper that explains that “SARS-CoV-2 Spike Protein Impairment of Endothelial Function Does Not Impact Vaccine Safety”. Unfortunately peer review has taken months, so it’s still not published. Therefore, we’ve decided ..read more

Summary: Statistical tests need to be paired with proper data and study design to yield valid results. A recent review paper on Long Covid in children provides a useful example of how researchers can get this wrong. We use causal diagrams to decompose the problem and illustrate where errors were made. Contents Background Control groups and RCTs Control groups and observational studies Structure of the Long Covid review The problem of p-values Conclusion and next steps Acknowledgements Background A recent review paper by Australian and Swiss doctors, How Common Is Long COVID in Children and ..read more

Experts warn that we are not prepared for the surge in disability due to long covid, an illness that afflicts between one-fourth and one-third of people who get covid, including mild cases, for months afterwards. Some early covid cases have been sick for 18 months, with no end in sight. The physiological damage that covid causes can include cognitive dysfunction and deficits, brain activity scans similar to those seen in Alzheimer’s patients, GI immune system damage, cornea damage, immune dysfunction, increased risk of kidney outcomes, dysfunction in T cell memory generation, pancreas damage ..read more

If you haven’t already read the terrible New Yorker long covid article, I don’t recommend doing so. Here is the letter I sent to the editor. Feel free to reuse or modify as you like. The below are just a subset of the many issues with the article. If you are looking for a good overview of long covid and patient advocacy, please instead read Ed Yong’s Long-Haulers Are Fighting for their Future. Dear New Yorker editors, I was disturbed by the irresponsible description of a suicide (in violation of journalism guidelines), undisclosed conflicts of interest, and omission of relevant medical resea ..read more

Summary: today we’re announcing fastchan, a new conda mini-distribution with a focus on the PyTorch ecosystem. Using fastchan, installation and updates of libraries such as PyTorch and RAPIDS is faster, easier, and more reliable. This detailed blog post by the brilliant Aman Arora of Weights and Biases provides a great overview of what fastchan is for, how it relates to other parts of the ecosystem, and how it makes life easier in practice. What you need to know If you use Anaconda, you can now install Python software like fastai, RAPIDS, timm, OpenCV, and Hugging Face Transformers with a si ..read more

I’ve just returned to Australia to live, after a decade as an entrepreneur in San Francisco. For my first in-person talk in Australia, I shared my thoughts on how to build a successful tech startup nearly anywhere in the world. I spent nearly three months researching and preparing for this talk, interviewing dozens of entrepreneurs, investors, and academics. I also drew from my 20+ years of experience as an entrepreneur — ten years in Australia, and ten years in the US. Creating a tech startup in the San Francisco Bay Area (i.e. San Francisco, Silicon Valley, and Oakland) is easier than most o ..read more

Update Oct 30, 2020: NumFOCUS has apologized to me. I accept their apology. I do not accept their assertion that “At the time of the interview, the committee had not determined that there was a violation of the code of conduct, only that there were two complaints filed and being examined.” The email to set up the call said “We would like to schedule a meeting so that we can discuss the results of our investigation with you” - nothing further. During the call, the committee stated the list of violations, and said “that is what the reporters stated, and what we found”. I asked why they didn’t t ..read more

If you’re in western USA (like us) at the moment, you might be finding it hard to breath. Breathing air that contains the fallout from fires can make you feel pretty awful, and it can be bad for long-term health as well. Wildfire smoke contains fine particulate matter, known as “PM2.5”, which can be inhaled deep into the lungs. The “2.5” here refers to the size of the particles — they are 2.5 microns or smaller. To see the air quality in your area, check out this AirNow map. Once it’s orange, you might find you start feeling the effects. If it’s red or purple, you almost certainly will. (Somet ..read more