What is the maximum one can be doing with someone else and still be hanging out?

Austin Kleon talks about the 13-month International Fixed Calendar. It reminds of the ISO week numbers that the Danes love so much. It always weirded me out when they ask something like “Are you free week 14?” But thinking back, they might have been onto something.

Despite all the damage done by the ice in Texas, it still created quite a bit of beauty (or at least novelty).

Icicle agave during the Texas winter storm.

Lessons Learned During My PhD

I shared these notes with my friends and colleagues at the Technical University of Denmark (DTU) when I finished my PhD in December 2015.

Here are things that I either learned during my PhD, or that helped me get through it. I in no way have all the answers, but there are a few things that helped me that I think would be helpful to other people as well.

I split the content in six different sections, meta-things, writing, reading, speaking, programming, and mind and body. I included links to articles, books, and tools that are related to each section.


The main recommendation here is to have a system to deal with all the things you have to do and the things you want to do. I personally used the GTD method, which stands for Getting Things Done. I highly recommend getting the latest book. You can find it delivered at your desk for 100 kr. The main ideas of the system are: everything goes in an inbox (physical and/or on a computer). Periodically, process the inbox and decide if you’ll do the thing, trash it, or store it in your reference system. “Tasks” that require more than two action are considered projects, and a project consist of a list of physical, actionable actions. The other important thing about GTD is that it includes a weekly review of all the projects in your system, as well as your calendar and other active things in your life. I learned about this almost 10 years ago now1 and I would go as far as to say that it changed my life.

There are many applications designed to implement the GTD system. On the Mac, there’s OmniFocus, Things, and TaskPaper (really worth checking). Todoist is multi-platform.

I also recommend reading Getting Results the Agile Way, by J.D. Meier, which proposes a different take on selecting what you should work in. The basic idea is to pick 3 things to focus on every day, three per week, three per month, and three per year. The things you do every day should go towards you weekly goals, etc. The Asian Efficiency blog (weird name, I know), is a good noise-free resource about that kind of material (check the “specialty topics” in the sidebar).

Make checklists

Keep checklists for processes and things you do often but with lots of time in between, like how to log on to remote computers, adding printers to your computer, etc. It will save you a lot of time in the long run. Similarly, save info about things you never remember how to do, such as the behavior of the FFT implementation in MATLAB, check if a file exists using bash, undo a Git merge, etc.

I keep all my notes in individual text files. I have about 800. They live on Dropbox, which means I can edit them and view them anywhere. On my Mac I use nvAlt to search and write them. ResophNotes does the same thing on Windows. Evernote is a web-based service that can be used for a similar purpose. I write all my notes in Markdown (I even wrote a paper in it!), which also allows me to easily export my notes or view in nice previews. Both nvAlt and ResophNotes are “markdown-aware”.

Keep a Logbook

I kept a daily or weekly text file in which I wrote almost everything I did within the day. I would write down either thing that I wanted to do, notes to clarify my thoughts, or the things I just did. For example, I would save the Git commit for a particular simulation and my comments about the results. It helped me when I wanted to look back at why I did certain things or to find the source of certain ideas.

Sometimes Paper Is the Best Tool for the Job

I tried doing everything on the computer, but sometime paper really is the best tool for the job. The final product doesn’t have to be on paper but paper is often really helpful to develop ideas because of the freedom you have to place things wherever you want!

If It’s Broken, Fix It

If you see something that is broken, or that could be better, just fix it. Especially if other people have noticed the same problem. I mean to fix both immaterial things (BitBucket, for example) but also physical things. Did you know you can report broken things to CAS and they’ll come repair it within a day or so? Blocked toilet, dead light, water leek? Report it at https://fejlmeld.cas.dtu.dk or use their iOS or Android apps (can’t find the link, but look for DTU Fejlrapportering).


Build an Outline When Writing a Paper

At first, I did not have a method for writing but then I read this article by Timothée Poisot, which really helped me. The main idea is to start building an outline as soon as you’re working on the new project. As you read papers, or have ideas, you add quotes, citations, and snippets to your outline. You can start writing sentences and whole paragraphs whenever you want. The big advantage is that all the relevant things you find for a given project are all together; no need to go hunting for where you read that thing, six months ago.

On the Mac, I use Tree2, which I love. OmniOutliner is the most famous alternative, but it much more expensive. I don’t know about Windows or Linux. I know Microsoft Word has an outlining mode that could work. You could also outline in a normal Word document, or a text file, but good outliners give you many shortcuts to move things around and to insert new ideas. The new Manuscripts application for Mac looks amazing. Scrivener is an amazing writing tool for both Mac and Windows. It is particularly good for large projects.

Other good resources include:

Get Good Early and Write More

Do not despair, you will get better at writing! I don’t really know how to do it, but the earlier you get good the easier your life will be. :-) A possible way to get better is certainly to write more. Maybe having a writing club would help. There are many good books about writing. I read How to write a lot, by Paul J. Silvia and really liked it.

Here are a few articles about writing:


Make Time

You never find time, you’ll have to make some. Personally I found out that I could read an article on the bus and while walking. When I needed to read many article, I would take the bus mornings and nights for a week. That way I could read about 10 articles in week. It helped me to keep a stack of papers that I wanted to read on my desk; I could grab one whenever had a moment.

Read With a Goal

I find that it’s much easier to understand and remember papers if I read with a purpose, as a way of answering a question. Also, if that question is related to what you’re currently working on, you can add your discoveries in the outline of your paper.

Give Faces to Names

I found that being able to associate a face with an author name helped me remember who was talking about what and made it easier to remember different papers and ideas.

Take Notes and Highlights

That one is pretty obvious, but writing down notes and ideas while reading papers really helps. It helps while reading the paper but also later when coming back to it. I designed a highlight system for myself based on the idea of Walton Jones. I used specific colors to code different things, for example paper-specific results were yellow, new references in green, and paper summaries in red. This way could look back at a paper and have a general overview of what was important without reading the whole paper again.

On the Mac, Skim allows you to export notes including their color. It also works well with DEVONthink (see below).

Have a Good “Personal Search Engine”

I recommend having a good search system for your notes and papers. On the Mac I use an application called DEVONthink which can show you documents related to the one you’re currently reading. It also does non-exact searches, e.g., it can search for the meaning of your query, not just the exact words you typed. It really is magic. I am not aware of anything exactly the same on Windows or Linux, but The Brain (Windows) and Recoll might be good places to start.

Give Your Articles Unique Identifiers

I gave all my articles the same file name structure, authorYEARfirstword, e.g. chabotleclerc2014predicting. I picked this format because it has no space and it’s also very short and compact. It’s essentially a unique identifier. I used the identifier everywhere: in handwritten notes, computer notes, outlines, marginalia. This way, I knew exactly which paper I was talking about.

Remembering Things

I tried to use spaced repetition (also see this link) for a while but it didn’t stick for really long. Anki is probably the best tool for the job.

Things That Didn’t Work

Having a Wiki

Based on the idea of this crazy guy, Stian Håklev, I tried setting up a wiki using either DokuWiki or TiddlyWiki. I managed to keep it updated for about a month and then abandoned it. It required a lot of maintenance and a lot of diligence to keep up with the linking between subjects.

2021 update: These days, I would strongly recommend looking into Zettelkasten as an alternative.

A Single Giant Outline, Mind Map or Concept Map

I tried building a gigantic outline or mind map or concept map of all the things I learned, but it became unmanageable. I still find these methods really useful when fleshing out an idea for a project or paper, but they were not really good tools for me to manage such a large amount of knowledge. If you want to try these tools, on the Mac I recommend MindNode (simple and cheap), and iThoughtsX (more powerful, more expensive). MindMeister is online and very popular. Docear mixes an outliner, a reference manager (JabRef) and an outliner. It’s power and complex. If you want to know everything about mind mapping and the best tools, check out Brett Terpstra’s blog.

For concept maps, I love Scapple, which works on Mac and Windows. Cmap is also multi-platform, but heavier. I use them when I want to find structure in a mess of ideas floating in my head.


This series of articles by David L Stern really influenced me: How to Give a Talk. He suggests 5 rules3:

  1. Don’t put words on slides
  2. Use black slides
  3. Show your data
  4. Don’t tell jokes
  5. Don’t take a data dump on your audience
  6. Practice, practice, practice.

Of course, some rules are meant to be broken, but it’s worth a read. I also liked the book Presentation Zen: Simple Ideas on Presentation Design and Delivery by Garr Reynolds.


When Modeling, Optimize for a Metric

When working on a new model, first decide what you’re optimizing for, is it a correlation, the mean square error, or some other metric. Make sure this metric is computed automatically with each simulation, so you have immediate feedback about how good your model is. Just eyeballing the results is a really bad idea.


Don’t. Repeat. Yourself. When you see that you have the same code in multiple places, it’s a good hint that you need to refactor it into a function, and to call that function. Also, if your function is hundred lines long it’s probably a sign that he should be chopped into smaller functions that have clear names.

If you’re interested in becoming a better programmer, I recommend The Pragmatic Programmer, by Andrew Hunt and David Thomas, Clean Code and Code Complete.

Write Tests

You should write tests for your functions to make sure that they are actually doing what you think they are doing. They help make sure that code is correct, they help detecting regressions (when you break things that used to work), they act as a specification, design and documentation, and they make refactoring easier.

I cannot tell you how many times I found small and huge bugs because of the tests I wrote. All decent programming languages, including Matlab include a framework to automatically run tests. The words you want to look for are “unit testing”. You should run tests every time you make changes. You can even set Git to run the tests before every commit. This way you can make sure you never commit broken code.

The advantage of working with a free language (Python!) and in the open is that you can use “continuous integration” system to have them run tests every time you push new changes to GitHub (or BitBucket). Travis CI is one of those services.

These articles or sites are worth reading for info about testing.

Don’t Overuse Code Comments

Code comments are useful to explain why you’re doing something, but they should not explain every single line of code. Otherwise one day you will change the comment or the code and then one of them will be lying and you won’t be able to know which one.

Instead, use explicit names for variables and functions. Write function help files. Write documentation. Write README files. And break up long and complicated lines of code into smaller ones where you can name concepts and variables.

Use Version Control

Version control is a communication tool and a collaboration tool. It’s invaluable even if you don’t work with someone else, I can assure you that your future self will be really happy to know what your past self was thinking when he/she wrote that code/text. I heard your future self can get really upset. :-)

Track Where Stuff Comes From

Track where experiment results and figures come from. You can do it by hand, by keeping your log book and tracking output folders and inputs commits, but you can also use automated solutions. I used Sumatra, which is written in Python but can be used with Matlab. Every time you run a simulation it saves to a database: the experimental parameter used, the input files, and the command line outputs. It also allows you to comment and tag results. You can look back and see where things are from, what worked and what didn’t, and rerun experiments with exactly the same parameters. A provenance-tracking tool like Sumatra paired with version control is a good step towards making reproducible research. Recipy is a new Python-only solution that looks interesting.

Follow “Best practices”

Some very bright people have written “Best practices” for scientific computing. It’s worth reading the two or three articles below and applying their recommendations. I also recommend looking at this shablona project, which proposes a standard folder structure for a given project, I found it to work really well. It’s written with Python in mind but it could easily be adapted for Matlab.

Learn about literate programming, a useful concept where the code and the text (of, e.g., an article) live together. This can be done in Matlab using the publish command. In Python, the Jupyter notebook is the way to go. Actually, you can use the Jupyter notebook with Matlab.

If you want to do more than just read things, you should try to organizing a Software Carpentry workshop. It’s pretty much free and would probably help a lot of people.

Your Computer Should Work for You

If you find out you’re doing the same thing over and over again it might be worth automating it. On the Mac, Keyboard Maestro can do magic (like activating menu items for you, clicking places, moving windows, etc.) On Windows, AutoHotkey can do similar things, and on Linux, I found AutoKey to be the best.

Use a shortcut expander application. For example, I never type “intelligibility”, I just type inty and it expands to the full word. Same thing with my name, my bank account, my phone number, etc. On the Mac, Keyboard Maestro and TextExpander are the best. On Windows, PhraseExpress is compatible with TextExpander; you can sync your snippets via Dropbox. On Linux, Autokey can also do snippet expansions.

Mind and body

Take Care of Your Body

Seriously, take care of your body. If you start having wrist, forearm, or shoulder pain, don’t just live with it. Seek help and get proper a keyboard, mouse and chair. Learn some basic ergonomic practices about keyboard, mouse and screen placement. See the articles below for more info and recommendations.

If you are in pain, really look for help: find a massage therapist, a doctor, and stretch often. Here are a few good ressources.

Spend Money Where Your Time Is

It’s worth paying for things that make your life better, more comfortable, and easier, especially if you use those things all day long. Buy a nice keyboard, you probably write eight or nine hours a day. Buy nice headphones, good software, a mattress, a bike, etc.

Ask for Help

Ask for help when you’re stuck. Ask for a meeting if you need one. Everyone is super busy, but everyone is super generous. People rarely say no, but they might say “later”. In a perfect world, everyone would be proactive, everyone would have their slot in the calendar, but sometimes the world is not perfect. Also talking to people if often waaaay faster than googling for an answer.

Make Every Day a Non-Zero Day

This idea is not from me, it is from ryans01 on Reddit (and it’s also in the PhD Starter Kit, below). His idea is to make sure that every day you do at least one small thing towards your goal. No day should be completely wasted, even if the thing you do is really small. Keeping a log or journal helps realizing all the things you’ve done in a day and keeping your mood up.

Other people have written really good and more in-depth guides than this. The PhD Starter Kit is simply amazing. Philip Guo’s Advice for first year PhD students is a must-read/must-watch (as well as many of his other articles. He also wrote: The Ph.D. Grind, a 115-page e-book, is the first known detailed account of an entire Ph.D. experience.” That guy is amazing.

  1. Make it 13 years in 2021. [return]
  2. Not available anymore, 2021-01-23. [return]
  3. Yes, that 6 rules. And it 2021, it grew to 8 rules. ¯\(ツ)[return]

They could have used additional time during the bulk fermentation to account for the cold, but it’s still a good rise.

Great Resident Advisor podcast episode. Noisy, glitchy, grimy, dark. RA.760 Hyph11E ⟋ RA Podcast🎵

Installing air filters in classrooms has surprisingly large educational benefits

[…] Math scores went up by 0.20 standard deviations and English scores by 0.18 standard deviations […] this is comparable in scale to […] the potential benefits of smaller class sizes.”

ferd.ca – Home Alone: A Post Incident Review

It’s so many things in one: a movie review, an intro to “post incident reviews,” a lesson into which kinds of precautions work and which don’t, and a reminder that things can still go wrong even when well prepped.

Ad Fontes Media rates media outlets according to their bias and reliability. 1) factual reporting has very slight left-leaning bias (see also “Facts Have a Well-Known Liberal Bias”) and consequently 2) it doesn’t seem to be possible to be reliable and biased at the same time.

In Hard to discover tips and apps for making macOS pleasant Tristan Hume says:

Chrome and Firefox have much better sounding audio resampling for watching videos on 1.5x or 2x speed. This is the only reason I don’t use Safari.

I just tried it and oh my is this true!

2020 Holiday Newsletter

For the past 4 years, just before the holidays, I’ve sent a newsletter to my colleagues about all the things I’ve read, watched, listened to, cooked, or ate in the last year. This is the 2020 edition.

The Christopher Alexander idea patch

Where I’m from, there are so many blueberries that people from that region are called bleuets. (The tourist info phone number is 1-877-BLEUETS (253-8387). You should go and visit.) When you go out to pick them (the blueberries, not the people) and you hit a patch with tons of them, we say “I found une talle!” That’s how it felt getting into Christopher Alexander’s ideas.

You might know of Alexander without realizing it. He’s considered as the father of the idea of design patterns, which were heavily inspired by his book architecture book A Pattern Language. Patterns are part of a larger process to solve design problems, from problem definitions, to solutions, to the evaluation of how good the solution is. It’s that larger process that I found interesting. He named the parts of the process context, form, and fit. In brief, the context is the problem to be solved together with its constraints. It’s totally independent of the solution. The form is the solution. It has a shape that fits the context more of less well. Once I had these words in my mind, I started seeing them everywhere.

Clay Christiensen’s Jobs-to-be-Done framework (from Competing Against Luck) is a way of defining product opportunities (jobs) as a context that can be fulfilled in many different ways. To get an idea of what that means, watch him telling the story of the job of a milkshake and how milkshakes compete with bananas, donuts, and bagels, and not with ice cream.

In Demand-Side Sales, Bob Moesta (who did the milkshake research) talks about selling from the buyer’s perspective, from their struggles, from their context. In contrast to selling from the supply-side, which talks about features and form words. I highly recommend this book.

On the programming side, unit testing has morphed into form testing, whereas the original intent was context testing. Behavior-driven development tried to get that spirit back. What I heard Ian Cooper say in his TDD, Where Did It All Go Wrong talk was “Write context tests.”

Basecamp’s Shape Up is basically Alexander’s ideas applied to product development and management. It makes a clear distinction between shaping (defining the problem and the context) and doing the work (creating a form). Which in turns allows a new dimension of diagnosis when a project fails: was the project badly shaped or is it that the execution failed and form was a bad fit?

Ryan Singer, head of strategy at Basecamp, did a great intro to Alexander’s work this summer.

The Best Writing

Losing the War by Lee Sandlin is the best writing I read this year (and I read it on January 1, 2020). It’s an incredible essay on war (the Second World One), and memories. I found the “flow” to be exemplary with plenty of historical context and commentary. Well worth the time.

programming == cooking

I used to tell students that I was “teaching them how to fish.” But after reading Robin Sloan’s Home Cooked App, I’ve started telling people I’m teaching them how to cook. It’s a much richer analogy.

If you don’t know how to cook, you eat pre-packaged meals or you eat out (or you live with your mom forever). But there are tons of reasons to want to learn how to cook and tons of things to do once you’ve learned how. You can cook for health reasons, to please friends, to create the perfect version of something, as a creative output, because you’re picky, to make food you want to eat, because it’s fun. You can specialize and become a baker, or open a taco truck, or start a family restaurant, or run a fine-dining restaurant. You can teach others how to cook. In the end, you can still go out and eat if you want, you have a choice. There are so many reasons to learn to cook.

If you don’t know how to program (or how to reason about programming) you use apps you bought and hire consultants. But there are tons of reasons to want to learn how to program and tons of things to do once you’ve learned how. You can create little scripts to rename files, write notebooks to make custom analyzes, write an app to enable friends and colleagues to explore data like you can, write your own text editor (!) because vim is holding you back, because it’s fun. You can specialize and build deep learning models, or design data management systems, or build custom web apps, or start a scientific software development consultancy. You can teach others how to program. In the end, you can still hire consultants if you want, you have a choice. There are so many reasons to learn to program.


The Glamorous Toolkit is an impressive “moldable development environment”. I’d describe it as a strange hybrid between a notebook editor and an IDE. Any objects can have a rich and interactive representations, which is not new (to us), but the cool part is that it’s easy to dynamically add new rich representations to the development environment. Watch this talk by Tudor Gîrba to get a taste of what’s possible.

Simon Willison’s (co-creator of Django) Datasette is an impressive project to “explore and publish data”. It relies heavily on sqlite. I look forward to playing with it some more over the holidays. He’s done super cool things with it, including finding the best photo of a pelican according to Apple Photos, and building a regex search engine across a collection of Github repos using ripgrep.


I started many books this year, but didn’t finish that many:

  • Thinking in Systems by Donella Meadows is a short introduction to “systems thinking,” their components (stocks, flows, feedback loops), common system configurations, common pitfalls/opportunities of those configurations, and leverage points to intervene in those systems. I had so many “Ah ha!” moments. Many about things I “knew” but hadn’t realized the consequences of. Like how “systems with similar feedback structures produce similar dynamic behaviors, even if the outward appearance of these systems is completely dissimilar.” For example, a population system (controlled by births and deaths) has a similar configuration as an economic capital system (controlled by investment and depreciation). Reading this book, it was so easy to think “Here’s a silver bullet!” but then she totally called me out on it:

    People who are raised in the industrial world and who get enthused about systems thinking are likely to make a terrible mistake. They are likely to assume that here, in systems analysis, in interconnection and complication, in the power of the computer, here at last, is the key to prediction and control. This mistake is likely because the mind-set of the industrial world assumes that there is a key to prediction and control.

  • Elements of Typographic Style by Robert Bringhurst. Yes it’s a typography book, but it may also be the funniest thing I read all year. Bonus: the book itself is a beautiful object.

  • Lab Girl by Hope Jahren is a wonderful memoir of a “life in science.” She’s a good storyteller, telling a good story, about how the path to success in academia can be wild.

But I read a lot of good articles:

TYIL (This Year I Learned)

The Ouarzazate Solar Power Station melts salt by concentrating the power of 7400 parabolic mirrors towards a central tower. The molten salt is then used to superheat water and power steam-powered generators.

It’s possible to tell one’s position in the sea based on wave patterns. The 2016 NYT piece by Kim Tingley, The Secrets of the Wave Pilots, is an impressive testament of what our brains can perceive using our full bodies as sensors. See also these beautiful Marshall Islands navigation charts, and the Eagle Eyes Radiolab story about the vest David Eagleman is building to help deaf people hear.

Some Nice Pandemic things


I started making pizza just after the pandemic started. I can’t wait for it to be over to organize pizza parties. My source of knowledge is Ken Forkish’s Elements of Pizza. Using tipo 00 flour is worth it. So is a baking steel/stone.

Kenji Alt Lopez’s Serious Eats episode on emulsions has a really compelling demonstration of why you should put a surfactant in your emulsions. Now I put a little dollop of mustard in all my vinaigrettes.


My friend Matt shared some bardcore videos by Hildegard von Blingin’ earlier this year. Here’s Somebody That I Used To Know (Bardcore/Medieval Style Cover with Vocals). Bardcore is medieval renditions of pop songs. Obviously. So… the name Hildegard von Blingin’, is a reference to Hildegard von Bingen, an 11th century badass abbess, composer, and scientist (among others). In the early 2000, my mom gave me a CD by Garmarna, a Swedish band that does… electro-folk renditions of her 11th-century music. Hildegard von Blingin' = 1/Garmarna! Here’s one song and here’s the whole Garmarna album.

According to Spotify and Last.fm, I’ve listened to 1,700+ different artists this year, 600 of which were new to me. I won’t give you the whole list, don’t worry. Although I do have a playlist of every album I liked in 2020 and one of only the best songs I listened to in 2020.

Here are my favorite albums released in 2020, in no particular order.

Here’s more great music I discovered this year but that wasn’t made this year.

I somehow ended up listening to a lot of Japanese indie music (for a lack of better term).


  • The Newsroom by Aaon Sorkin is the best series I watched this year. Great characters, surprisingly funny, great storylines and overall arc.
  • Ted Lasso is a close second.
  • Crictor makes wonderful short, really short, videos. Do watch Popcorn (15 sec) and Hanabi (fireworks in Japanese, a big 45 sec).
  • The Last Dance (Netflix), on Michael Jordan’s career was a riveting watch. I vividly remember the 1997 Utah game where Jordan “had the flu” and still scored 38 points. At the time, my English wasn’t so great and I remembered being puzzled by the fact that the announcer said Jordan had “the flu” (which in québécois basically means diarrhea). Well, I learned that he probably did have the runs! He didn’t have the flu, he had food poisoning from a bad pizza probably given to him by disgruntled Jazz fans. Take that, Jazz!
  • The Good Place (Netflix) is an unlikely great show about… philosophy. My favorite character is Jason Mendoza. I’d watch it again.
  • The West Wing: got me into Sorkin. I shed a tear during 5 of the first 5 episodes.
  • I was going to say that The Magicians was funny, smart, emotional, with a great cast, and a fantastic ending. But as I write this, I learned there’s a 5th season I didn’t know existed. So take my “great ending” comment with a grain of salt.

I just finished reading Thinking in Systems: A Primer by Donella H. Meadows. I believe sometimes one was to be “ready” to read a book. I must have been ready for this one because I had more “Holy sh!t” moments than any other book I’ve read in years.📚

Austin, TX, 8:15. Morning walk around the neighborhood. There are many good Halloween decorations, but this one is particularly entertaining. #adayinthelife

Given what happened to the other saguaro, it makes me fear that this one will fall too.

I took this photo of a saguaro a month ago. It had been partially burnt during the fires that happened north of Phoenix earlier this summer. This weekend I realized it had fallen. According to Wikipedia, saguaros grow their first arm around 75–100 years of age. 👋🌵😔

Custom URL Handler for Files With Unique IDs

Yesterday I read a series of posts on custom URL scheme handlers on the Zettelkasten forums. The handler registers itself to open links like zettel://202006061337, where the number is the unique ID of a zettel (here it’s a timestamp). I’m not sure everyone realized the magnitude of what that means.

Combining a custom URL with a unique ID means notes and links can become entirely independent from your apps. Only the handler needs to know about the apps you’re using.

That alone is very nice, but then I thought: URLs can have query parameters… That means I can have URLs like zettel://202006061337&edit that open in my text editor of choice: TextMate, BBEdit, WriteRoom, FoldingText, etc. Or zettel://202006061337&preview to open in Marked. Or I could even pick the app interactively with zettel://202006061337&pick.

Handling the ID alone is pretty easy since the common Zettelkasten-like apps respond to a URL scheme to search and open files. The Archive uses thearchive://match/ID, nvUltra uses x-nvultra://find/ID, and nvAlt uses nvalt://find/ID.

But how to open in a text editor or in Marked given only the ID? With Spotlight. I used mdfind -name ID to find the file. This could be further refined with the -onlyin FOLDER option but I didn’t need it. Then it’s a matter of calling open -a Marked FILEPATH.

There’s also a zettel://create special case that will create a new zettel with the current time stamp (YYYYMMDDHHMM). It’s always done with the default Zettelkasten app because the script doesn’t know where to write the file but the app does.

I wrote the handler in Applecript because it’s the easiest way I know to create something that macOS considers an “app” and that can therefore handle URLs.

The full script is below. To use it:

  1. Open Script Editor and paste the code below in a new file.
  2. [Optional] Modify values in the Configuration section to pick a different URL prefix, default Zettelkasten app URL, editor, and previewer. You can add as many apps as you’d like in the appChoices array.
  3. Save as “Application”. You can save it anywhere. Make sure none of the boxes are checked.
  4. Register the app as a URL handler. You can do it with the SwiftDefaultApps Preference pane, or using the instructions provided by Christian Tietze in the forums:
    • Locate the application file you just created
    • Right-click the app, select “Show Package Contents”
    • Inside, open Contents/Info.plist with a text editor
    • Paste the following in a blank line right below the <dict> line. Replace zettel with the URL prefix you’ve chosen:
        <string>Zettel Link Opener</string>

Here’s the full script:

-- Zettel Link Opener
-- Created by Alexandre Chabot-Leclerc
-- Source: https://alexchabot.net/2020/06/06/custom-url-handler-for-zettels/
-- URL Handler for zettelkasten unique IDs, e.g., zettel://202006061017
-- Handles options after the ID to open different apps:
--    zettel://202006061017&edit to open is a text editor like TextMate
--    zettel://202006061017&preview to open in a preview app like Marked
--    zettel://202006061017&pick to open a menu of apps to pick from

-- URL prefix for your custom URL, e.g. zettel://ZETTEL_ID
property urlPrefix : "zettel"

-- Default URL to call to open a note with a given ID. The ID will be appended
property defaultZkAppUrl : "thearchive://match/"
--property defaultZkAppUrl : "nvalt://find/"
--property defaultZkAppUrl : "x-nvultra://find/"

-- URL to use to create a new zettle with the current timestamp YYYYMMDDHHMM
property urlForCreation : "thearchive://matchOrCreate/"
--property urlForCreation : "nvalt://make?txt="
--property urlForCreation : "x-nvultra://make?txt="

-- Apps to use for the different query parameters
property editApp : "FoldingText" -- App to used with "&edit" query parameter
property previewApp : "Marked" -- App to used with "&preview" query parameter 

-- List of app to display in the menu with with &pick query option
-- The apps will appear in the order defined here
property appChoices : {defaultZkAppUrl, editApp, previewApp, "TextMate"}
property defaultApp : {defaultZkAppUrl})

on splitText(theText, theDelimiter)
	set AppleScript's text item delimiters to theDelimiter
	set theTextItems to every text item of theText
	set AppleScript's text item delimiters to ""
	return theTextItems
end splitText

on removeUrlPrefix(original)
	-- Remove URL prefix so we're left with only the ID and the optional query parameter
	return do shell script "echo " & quoted form of original & " | sed 's;" & urlPrefix & "://;;'"
end removeUrlPrefix

on getIdAndOption(resouceAndQuery)
	-- Split the zettel ID and the optional parameter
	-- For example 202006061012&edit or 202006061012&preview
	set theItems to splitText(resouceAndQuery, "&")
	if length of theItems is 1 then
		-- Append an empty string if there's no option so this
		-- function always returns an array of 2 elements
		copy "" to the end of theItems
	end if
	return theItems
end getIdAndOption

on findFilepath(zk_id)
	-- Finds the filepath using Spotlight.
	-- It's easier than finding the proper filename given only the zettel ID
	return do shell script "mdfind -name " & zk_id
end findFilepath

on createZettel()
	set newZkId to do shell script "date +'%Y%m%d%H%M'"
	do shell script "open " & urlForCreation & newZkId
end createZettel

on openInChoosenApp(zkId, zkFilepath)
	--	From Simple List Handler by Patrick Welker <http://rocketink.net>
	-- Promp the use for the app to use
	set selectedApp to item 1 of (choose from list the appChoices with title "Available App" with prompt "Which app do you want to use?" default items defaultApp)
	if selectedApp is false then
		-- Exit prematurly if the user clicked Cancel
		error number -128
	end if
	-- Open the URL directly, or open by app name
	if selectedApp contains "://" then
		do shell script "open " & selectedApp & zkId
		do shell script "open -a " & selectedApp & " " & quoted form of zkFilepath
	end if
end openInChoosenApp

on open location thisURL
	set resouceAndQuery to removeUrlPrefix(thisURL)
	set idAndOption to getIdAndOption(resouceAndQuery)
	set zkId to item 1 of idAndOption
	if zkId is "create" then
	end if
	set zkFilepath to findFilepath(zkId)
	if item 2 of idAndOption is "edit" then
		do shell script "open -a " & editApp & " " & quoted form of zkFilepath
		-- Exit the script immediately so we don't also open in the default app
	else if item 2 of idAndOption is "preview" then
		do shell script "open -a " & previewApp & " " & quoted form of zkFilepath
		-- Exit the script immediately so we don't also open in the default app(
	else if item 2 of idAndOption is "pick" then
		openInChoosenApp(zkId, zkFilepath)
	end if
	-- Fall back to the default handler if there was no option
	-- or the option was invalid
	do shell script "open " & defaultZkAppUrl & zkId
end open location

What does %matplotlib do in IPython?

TLDR; Use %matplotlib if you want interactive plotting with matplotlib. If you’re only interested in the GUI’s event loop, %gui <backend> is sufficient.

I never really understood the difference between %gui and %matplotlib in IPython. One of my colleagues at Enthought once told me that at some point in his career, he more or less stopped reading documentation and instead went straight to the code. That’s what I did here. But let’s do a bit of history first.

In the “beginning”, there was pylab. It (still) is a module of matplotlib and was a flag to IPython designed to facilitate the adoption of Python as a numerical computing language by providing a MATLAB-like syntax.1 The reference was so explicit that before being renamed to pylab on Dec 9, 2004, the module was called matplotlib.matlab. IPython adopted the rename on the same day.2 With the ‑‑pylab flag or the %pylab magic function, IPython would set up matplotlib for interactive plotting and executed a number of imports from IPython, NumPy and matplotlib. Even thought it helped a few people transition to Python (including myself), it turned out to be a pretty bad idea from a usability point of view. Matthias Bussonnier wrote up a good list of the many things that are wrong with it in “No Pylab Thanks.”

For the 1.0.0 release of IPython in August 2013, all mentions of %pylab were removed from the examples (in a July 18, 2013 commit) and were replaced by calls to the %matplotlib magic function, which only enables interactive plotting but does not perform any imports. The %matplotlib function had already been introduced in a 2013 refactoring to separate the interatice plotting from the imports. The %gui magic command had already been introduced in 2009 by Brian Granger to “manage the events loops” (hint hint).

Now we know that the (my) confusion with %gui and %matplotlib started in 2013.

This analysis refers to IPython 7.8.0 and ipykernel 5.1.2.

Our entry point will be the %matplotlib magic command. Its source code is in the IPython.core.pylab.py file. The essential call is to shell.enable_matplotlib(gui), which is itself implemented in IPython.core.interactiveshell.InteractiveShell, and does five things:

  1. Select the “backend” given the choice of GUI event loop. This is done by calling IPython.core.pylabtools.find_gui_and_backend(gui). It encapsulates the logic to go from a GUI name, like "qt5" or "tk", to a backend name, like "Qt5Agg" and "TkAgg".
  2. Activate matplotlib for interactive use by calling IPython.core.pylabtools.activate_matplotlib(backend), which:
    1. Activates the interactive mode with matplotlib.interactive(True);
    2. Switches to the new backend with matplotlib.pyplot.switch_backend(backend);
    3. Replaces the matplotlib.pyplot.draw_if_interactive method with the same method, but wrapped by a flag_calls decorator, which adds a called flag to the method. That flag will be used by the new %run runner that’s introduced below at point #5;
  3. Configure inline figure support by calling IPython.core.pylabtools.configure_inline_support(shell, backend). This is where some very interesting stuff happens. It first checks that InlineBackend is actually importable from ipykernel.pylab.backend_inline, otherwise it returns immediately. But if it’s importable and the backend is "inline", it:
    1. Imports the ipykernel.pylab.backend_inline.flush_figures function, and register it as a callback for the "post_execute" event of the shell. As we’ll see later, callbacks for "post_execute" are called after executing every cell;
    2. If the backend was not "inline", it’ll unregister the flush_figures callback;
  4. Enable the GUI by calling shell.enable_gui(gui). This method is not implemented in the IPython.core.interactiveshell.InteractiveShell base class, but rather in IPython.terminal.interactiveshell.TerminalInteractiveShell. If a gui as specified, it gets the name of the active_eventloop and its corresponding inputhook function using IPython.terminal.pt_intputhooks.get_inputhook_name_and_func(gui). The active_eventloop is just a string, such as 'qt', but the inputhook is more interesting. It’s the function to call to start that GUI toolkit’s event loop. Let’s dig further into get_inputhook_name_and_func(gui). That function checks a few things, but it essentially:
    1. Imports the correct inputhook function for the chosen GUI by importing it from IPython.terminal.pt_intputhooks.<gui_mod>. For example, the Qt inputhook is imported from IPython.terminal.pt_intputhooks.qt. Later on, when inputhook is executed for Qt, it will:
      1. Create a QCoreApplication;
      2. Create a QEventLoop for that application;
      3. Execute the event loop and register the right events to make sure the loop is shut down properly. The exact operations to start and stop the loop are slightly different for other GUI toolkits, like tk, wx, or osx, but they all essentially do the same thing. At this point we’re ready to go back up the stack to enable_matplotlib in %matplotlib;
  5. Replace IPython’s default_runner with the one defined in IPython.core.pylabtools.mpl_runner. The default_runner is the function that executes code when using the %run magic. The mpl_runner:
    1. Saves the matplotlib.interactive state, and disables it;
    2. Executes the file;
    3. Restores the interactive state;
    4. Makes the rendering call, if the user asked for it, by checking the plt.draw_if_interactive.called flag that was introduced at point #1.3 above.

As for the other magic, %gui, it only executes a subset of what %matplotlib does. It only calls shell.enable_gui(gui), which is point #4 above. This means that if your application requires interaction with a GUI’s event loop, but doesn’t require matplotlib, then it’s sufficient to use %gui. For example, if you’re writing applications using TraitsUI or PyQt.

The Effect of Calling %gui and %matplotlib

Let’s start with the “simplest” one, %gui. If you execute it in a fresh IPython session, it’ll only start the event loop. On macOS, the obvious effect of this is to start the Rocket icon.

Animation of the Python rocket icon starting because of a call to `%gui`.

At that point, if you import matplotlib and call plt.plot(), no figure will appear unless you either call plt.show() afterwards, or manually enable interactive mode with plt.interactive(True).

On the other hand, if you start your session by calling %matplotlib, it’ll start the Rocket and activate matplotlib’s interactive mode. This way, if you call plt.plot(), your figure will show up immediately and your session will not be blocked.

Using %run

If you call %run my_script.py after calling %matplotlib, my_script.py will be executed with the mpl_runner introduced above at point #5.

Executing a Jupyter Notebok Cell When Using the "inline" Backend

In the terminal the IPython.terminal.interactiveshell.TerminalInteractiveShell.interact() method is where all the fun stuff happens. It prompts you for code, checks if you want to exit, and then executes the cell with InteractiveShell.run_cell(code) and then trigger the "post_execute" event for which we’ve registered the ipykernel.pylab.backend_inline.flush_figures callback. As you might have noticed, the flush_figures function comes from ipykernel, and not from IPython. It tries to return all the figures produced by the cell as PNG of SVG, displays them on screen using IPython’s display function, and then closes all the figures, so matplotlib doesn’t end up littered will all the figures we’ve ever plotted.


To sum it up, use %matplotlib if you want interactive plotting with matplotlib. If you’re only interested in the GUI’s event loop, %gui <backend> is sufficient._ Although as far as I understand, there’s nothing very wrong with using %matplotlib all the time.

  1. Basically, no namespaces, and direct access to functions like plot, figure, subplot, etc. [return]
  2. The earliest commit I found for the IPyhon project was on July 6, 2005 by Fernando Perez, 7 months after the name change. Its Git hash is 6f629fcc23ba63342548f61cc7307eeef4f55799. But the earliest mention is an August 2004 entry in the ChangeLog: “ipythonrc-pylab: Add matplotlib support,” which is before the offical rename in matplotlib. [return]

2019 Holiday Newsletter

Every year since 2017 I send my colleague a long email about ideas and media I’ve come across during that year. This is the 2019 edition. You can read the 2017 and [2018]() editions.

Hi all,

Time for installment #3 of my Holiday Newsletter! For once, I started a bit earlier collecting links and summarizing why things are interesting. Let me know if you’d be interested in receiving something like this more than once a year. It’s something I’m considering doing in 2020.

I hope you find some time to read/listen/watch something good over the break, even if it’s not from this list. :) Happy Holidays!


If You Read Just One Thing

The End of Bureaucracy by Gary Hamel and Michele Zanini at HBR is the most mind-blowing thing I’ve read this year. It features a Chinese company named Haier, which is the worlds largest appliance maker with $35 billon/year in revenue. The business is structured around 4,000 independent microentreprises (MEs) made of 10 to 15 employees. Each ME provides different of services to other MEs: marketing, R&D, design, manufacturing, HR, etc. Each ME is free to contract with any other ME, or go to an external provider if they don’t think they’d be well served internally. It’s a setup that flies in the face of pretty much any other large company. Definitely worth a read.

Good Reads

Dan Barber (chef and co-owner of Blue Hill at Stone Barns) writes Save Our Food. Free the Seed. at the NYT. It’s an inspiring, and also infuriating, article about seeds and how they’re at the root of our entire food supply chain. I didn’t realize that seed “designers” make their seeds work hand in hand with insecticides, which are often made by the same companies (e.g., Monsanto). That wouldn’t matter too much if we weren’t down to just two mega seed producers, and if the seeds weren’t patented.

I still haven’t read any of Michael Lewis’ books (somehow), but every time I read one of his articles I’m completely sucked in. Here are two good ones I read this year. In Jonathan Lebed’s Extracurricular Activities, Lewis tells the story of a 15-year old “stock manipulator.” In Portrait of an Inessential Government Worker talks about Art Allen, the only oceanographer inside the U.S. Coast Guard’s Search and Rescue division, and the person who’s basically single-handedly responsible for mankind’s ability to find things lost a sea. Lewis also started a podcast this year called Against the Grain. Recommended.

In Stab a Book, the Book Won’t Die Craig Mod (real name) speaks of different forms of content and their respective “contracts” with their consumers. Books have edges, a clear “I buy you, I read you or I don’t” contract. Online publications, like Netflix, Twitter, and Instagram don’t have such clear contracts. They’re infinity pools. I really liked his observation that with print newspapers, only the front page (often just above the fold) needs sensational headlines to get people to buy it. Internal headlines can afford to be factual. Online, all headlines are on the front page.

Cormac McCarthy, in his “free time”, does editing for faculty and post docs at the Santa Fe Institute. Van Savage and Pamela Yeh publish McCarthy’s advice on writing scientific papers at Nature. It’s equally good advice for writing documentations and reports.

The Japanese addressing system is strange and wonderful. When written in Japanese, the addresses start with the largest geographical entity and proceed to the most specific one.

Someone who’s name I can’t figure out writes Becoming a magician, with an interesting approach to “personal growth”: surround yourself with people who feel to you like they’re magicians.

Technology & Software

Julia Evans’ What does debugging a program look like? is a great read about the multiple ways to approach debugging. Julia started writing zines full-time this year. If you’re interested in having a look, I have one on my desk. And on the topic of debugging, Greg Wilson recommends Why Programs Fail: A Guide to Systematic Debugging by Andreas Zeller.

In Open Source is not about you, Rich Hickey, creator of Clojure, writes a wonderful article about expectations one should have about open source software (I still find strange people who “blog” using Github repos and Gists…)

As a user of something open source you are not thereby entitled to anything at all. You are not entitled to contribute. You are not entitled to features. You are not entitled to the attention of others. You are not entitled to having value attached to your complaints. You are not entitled to this explanation.

If you have expectations (of others) that aren’t being met, those expectations are your own responsibility. You are responsible for your own needs. If you want things, make them.

And on a related topic, License Zero has a thoughtful look at funding models for open source.

I award “Data Structure of the Year” to Conflict-free Replicated Data Types (CRDTs). I learned about them through Ink and Switch’s article Local-first software: You own your data, in spite of the cloud, where they use them to write a real-time syncing engine that doesn’t require a central server. But then, in pure Baader–Meinhof, it seemed like everyone was talking about them, e.g., the Xi editor, and Figma.

Basecamp published Shape Up, the “manual” for their software development process. It’s a 1-hour read that I highly recommend. It’s a variation on Agile, with thoughtful additions, structures, and rationales for why the do things in certain ways.

Lowtech Magazine hosts their website on a solar-powered Raspberry Pi. Warning, their site might be down when you visit if it’s been cloudy for a while in Barcelona. Roel Roscam Abbing wrote about the technical details.

Jakob Nielsen explains Why You Only Need to Test with 5 Users.

Here are some people I discovered this year. They are so inspiring, and also so frustrating, because they make you wonder “And what have I done today?”


My “Podcast of the Year” is the The Amelia Project, a fiction podcast about Amelia, an organization that helps clients fake their death and then reappear as whatever they want. It’s original, beautifully produced, endearing, and funny. Do start with the 1st episode, and go get yourself a hot cocoa. And if you’re new to fiction podcasts, check out Limetown, and Passenger List.

Michael Lopp (author of Managing Humans, which was in last year’s email) has a podcast called The Important Thing. If you’re interested in management and leadership, I recommend the The One About Management (Pt. 1) and The One About Management (Pt. 2) for a good discussion of what it means and what it’s like to be a manager.

The Nevermore, Amazon episode of Rework (by Basecamp), talks about about the economics of bookstores, and how selling new hardcovers for $15 (like Amazon does) would put them out of business. Independent bookstores are the best. If you prefer the convenience of shopping online but want to support independent bookstores, use Biblio. Cool fact: they offset the carbon emissions of their shipping.

Food, Drinks & Restaurants

For the Austinites, and people visiting Austin, go eat at:

  • Nixta Taqueria: yes, they’re hipster tacos, but they’re also delicious.
  • Launderette is still our favorite restaurant in Austin. Laura Sawicki is the best pastry chef in town.
  • Get ice cream at Manoli’s. Just do it.
  • Everything I drank from Vista Brewing this year was delicious.
  • Get some pastries at Le Politique’s Patisserie. I recommend scheduling your afternoon coffee break for the 3–4PM window, when pastries are half price.
  • I finally went to a Home Slice and it’s really that good.
  • Bombay Express makes delicious india food. Get the pani puri, and the chole puri, and the carrot halwa, and a dosa, and… get all the things. It’s worth going on the weekend just for the Thali.

Make bread at home. It’s easy and it’s better than anything you can get in Austin (except maybe from Sour Duck, and from the late Miche Bread). Just buy Flour Water Salt Yeast by Ken Forkish, and make the Saturday Overnight White bread. Bring the extra loaf to the office, please.


It was a good year. It’s always a good year. Here’s a playlist of every song I “liked” in 2019, and one of every album. The music on those playlists wasn’t necessarily released in 2019 though. Just to name a few albums that were release in 2019:

  • Charlie Hunter and Lucy Woodward - Music!Music!Music! (Spotify)
  • MADMADMAD - Proper Music (Spotify)
  • Dan Tepfer - Natural Machines (Spotify)
  • Rhye - Spirit (Spotify)
  • voljum - Cyberglove (Spotify)
  • Bibio - Ribbons (Spotify)
  • Archive - 25 (Spotify)
  • Lite - Multiple (Spotify)
  • Canine - Dune (Deluxe) (Spotify)
  • Lambert - True (Spotify)
  • Himura Yoshiteru - View from Bottom (Spotify)
  • Janus Rasmussen - Vin (Spotify)
  • The Comet Is Coming - Trust in the Lifeforce of the Deep Mystery (Spotify)
  • Battles - Juice B Crypts (Spotify)
  • Anna Meredith - FIBS (Spotify)
  • Trentemøller - Obverse (Spotify)
  • And So I Watch You from Afar - ASIWYFA Live 10 Year Anniversary (Spotify)
  • Eprom - AIKON (Spotify)
  • Floating Points - Crush (Spotify)
  • Bon Iver - i,i (Spotify)
  • Jacob Collier - Djesse Vol.2 (Spotify)
  • And many more…

Movies, TVs, and Videos

  • Woman at War tells the story of a choir conductor and eco-activist who plans to disrupt the operations of an aluminum plant in Iceland, but whose plans are temporarily interrupted by the opportunity to finally adopt a child from Ukraine. It’s funny, beautiful, and strange.

  • The Marvelous Mrs. Maisel and Killing Eve were the two best series we watched this year. One great quality of Killing Eve is that it ends, in only two seasons.

  • Simple Made Easy by Rich Hickey. Simple is the not the same as easy.

  • In his 2019 State of Mozilla talk, Mike Hoye makes this wonderful point about caring about making it possible to care. Paraphrasing from his talk: There’s no Keurig machine in the Toronto office because there’s no amount of care that will make it produce good coffee. I like that a lot (coffee, but also this statement).

2018 Holiday Newsletter

This is the 2nd installment of an email I sent to my Enthought colleagues just before the Christmas holidays. The other installment is 2017.

Hi everyone,

This is installment #2 of Alex’s annual Holidays newsletter. I decided to send it company-wide this year. It’s a collection of interesting reads/listens/watchs I “consumed” this year.

Programming & Technology

Getting better at it:

I found out what people meant by level up about three and a half years into my programming career when I played my first game of Dungeons and Dragons. […] It sounds like most folks picture leveling up as a little avatar of themselves advancing up a ladder of 20 levels, moving up to the next rung incrementally as they gain experience. This creates this visual of our skills improving linearly with our time spent in tech. I’ll henceforth call this the ladder interpretation.

I pictured, instead, what I will call the derivative interpretation. It comprises a series of maybe three levels.

  • Level One: Getting better, adding skills
  • Level Two: Improving at getting better/adding skills
  • Level Three: Getting better techniques for improving at getting better/adding skills

I think if there’s one technology we should be “concerned” or excited about, as Python users, it’s Javascript (there are many reasons to be afraid, I know). This year, Michael Droettboom compiled NumPy to WebAssembly. The project is called pyodide


As a newly minted manager, I read quite a few management books this year. Here are my favorites. I highly recommend reading Managing Humans, even if you’re not a manager.

  • First Time Manager: A high-level overview of what the new responsibilities are.
  • Managing Humans by Michael Lopp aka Rands. Now at Slack, previously at Palantir and Apple, he is an amazing storyteller. The story form also makes the lessons stick better.
  • High Output Management by Andy Grove, Intel CEO. Ian Tien wrote a good summary. It’s often quoted as the source of much of modern management in tech companies.
  • The Five Dysfunctions of a Team by Patrick Lencioni. It’s a fable about management and leading a team. It’s a bit corny, and yet it was a page-turner.
  • It’s Your Ship: Management Techniques from the Best Damn Ship in the Navy by D. Michael Abrashoff. Don’t let the title (and the cover) fool you, it’s great. Not all lessons apply to the Enthought, but it’s amazing what he managed to do in the Navy.



You know, there has to be a section about podcasts!

  • This American Life - NUMMI: It’s from a few years back but it’s relevant to us, to what Enthought is doing with JSR/TEL/AK/Exxon. It’s the story of the NUMMI plant, a joint venture between GM and Toyota, of the transformative experience of the immersion process, and about what do to with the people who did not go through the immersion process.
  • New York Times - The Caliphate a fascinating story by Brokmini, who’s been following ISIS for years. It should be more widely known. It’s leaps and bounds better than Serial.
  • 99% Invisible - 330 - Raccoon Resistance on the design of Toronto’s raccoons-resistant compost bins. 99pi at its best. Funny and informative.
  • The Dollop - 342 - The John Paul Getty’s: a hysterical account of the Getty family (yes, the museum Getty’s).
  • The knowledge project - The Kids are Worth It with Barbara Coloroso. I’m not a parent, but if I were I’d probably re-listen to this once a week until my kids are 18.
  • Limetown, season 2, and 1! The best “radio-drama” I’ve listened to. Season 2 started on Halloween this year and it’s now over. You can binge listen to it while walking on dark Albuquerque streets at night and freak out!
  • Reply All - 131 - Surefire Investigations, a Yes-Yes-No that showcases Gritty, the new Philly Flyers’ mascot.
  • Reply All - 114 - Apocalypse Soon: 2018 started strong.


Things I learned

Don’t use sed to replace spaces with new lines, use tr instead. (tr ‘ ‘ ‘ ’ < input_file), and join newlines with paste (paste -s -d ‘ ‘ < input_file)

On macOS, increase your keyboard repeat speed with defaults write -g KeyRepeat -int 1 # normal minimum is 2 (30 ms)


  • Kakoune, code editor
  • Kitty, a terminal emulator
  • Feedbin, an RSS read that gives you a customer email to subscribe to newsletters. Game changer.


Highlight from Trainer reports

[…] led us to discover a bug in IE. The crux of the issue is that cowsay uses angle brackets in its speech bubble, leading to text that looks like:

< moo >
        \   ^__^
         \  (oo)\_______
            (__)\       )\/
                ||----w |
                ||     ||

Internet Explorer interprets the “< moo >” as an unclosed html element, which breaks its rendering of the page. Both Firefox and Chrome ignore moo tags.

Both Firefox and Chrome ignore <moo> tags.

Happy Holidays!


Manually Merging Day One Journals

My first Day One entry is from January 24, 2012. I used it often to take note about what I was doing during my PhD with the #wwid tag (what was I doing, an idea from Brett Terpstra, I think), and sometimes to clarify some thoughts.

When Day One went The Way of the Subscription, I didn’t bother too much because Dropbox sync still worked. Until it didn’t. I somehow didn’t realized it and kept adding entries to both the iOS and the macOS versions. Not good. It’s been on my to do list for a while to find a way to merge the two journals. I could probably subscribe to the Day One sync service and have it figure out the merging but I didn’t want to subscribe just for that.

I learned somewhere that Day One 2 could export journals as a folder of photos and a JSON file. I figure I could probably write a script to do the merging. So I downloaded Day One 2 on my iPhone and Mac, imported my Day One Classic journals, exported them as JSON to a folder on my Mac, and unzipped them. I also created a merged/ folder where to put the merged journal. The hierarchy looks like this:

$ tree -L 2
├── Journal-JSON-ios/
│   ├── Journal.json
│   └── photos/
├── Journal-JSON-ios.zip
├── Journal-JSON-mac/
│   ├── Journal.json
│   └── photos/
├── Journal-JSON-mac.zip
├── merge_journals.py
└── merged/

I first copied the photo folder from Journal-JSON-ios/ to merged/ and the photos from Journal-JSON-mac/photos/. I was pretty confident that I would end up with the union of all the photos because Day One uses UUIDs to identify each photo. The -n option to cp prevents overwriting files.

$ cp -r Journal-JSON-ios/photos merged/
$ cp -n Journal-JSON-mac/photos merged/photos/

I then ran the merge_journals.py script (below) to do a similar merge of the entries, based on the UUIDs. The merging happens by building a dictionary with UUID of each entry as the key and the entry itself as the value. It’s two loops over the iOS and the macOS entries. Entries with the same UUID should have the same contents, unless I’ve edited some metadata on one platform but not the other. I’m not too worried about that.

The output dictionary will be written to the Journal.json file. The entries are sorted chronologically because that’s how it was in the exported journal files, but I doubt it matters.

The output dictionary is written to disk without enforcing the conversion to ASCII since the exported journals are encoded using UTF-8. The indent is there to make the output more readable and diff-able with the exported journals.

import json

with open('./Journal-JSON-ios/Journal.json') as f:
    ios = json.load(f)
with open('./Journal-JSON-mac/Journal.json') as f:
    mac = json.load(f)

# Extract and merge UUIDs
uniques = {entry['uuid']: entry for entry in ios['entries']}
for entry in mac['entries']:
    uniques[entry['uuid']] = entry

# Create the output JSON data structure
output = {}
output['metadata'] = mac['metadata']
output['entries'] = list(uniques.values())
# I'm not sure it matters, but Day One usually exports the entries
# in chronological order
output['entries'].sort(key=lambda e: e['creationDate'])

# ensure_ascii print unicode characters as-is.
with open('merged/Journal.json', 'w', encoding='utf-8') as f:
    json.dump(output, f, indent=True, ensure_ascii=False)

The last step is to zip the journal and photos together, which tripped me up a few times. The Journal.json and the photos/ folder must be at the top level of the archive, so I zip the file from within the merged/ folder and then move it back up one level.

$ cd merged
$ zip -r merged.zip *
$ mv merged.zip ..

I could then import merged.zip in Day One, which created a new Journal, and delete the old one.

I guess I could somewhat automate this to roll my own, DIY, sync between versions of Day One, but I’d rather pay them money once I decide to use Day One frequently again. Still, I really appreciate that the Day One developers picked formats that could be manipulated so easily.

2017 Holiday Newsletter

This is the first installment of what became a yearly email I sent to my colleagues at Enthought.

Hi everyone,
I’ve been collecting these things for a while with the intent of sharing with some of you, but I decided why not share them with more people. I thought now’s a good time because you will maybe have some time during the holidays. It’s a grab bag of interesting things. Some of them are tangentially related to what we do here, some others not at all. I hope you find one or two good ones.

Happy Holidays,


Some great podcasts episodes:
- This episode of The Knowledge Project with Naval Ravikant, CEO and co-founder of AngelList.
- This two-part series from Reply All. A a telephone scammer makes a terrible mistake. He calls Alex Goldman. Seriously, listen to part 1. And then there will be part 2.
- The Dollop talks about Uber. You probably know how terrible they are, but they’re terribler than that.
- And an “old” one, one of my favorite 99% Invisible episodes. It’s about high heels.

Blogs and particular posts

Loren Shure is probably the most well known public face of The MathWorks. She’s been blogging forever about “cool things one can do with MATLAB”, or nice features of MATLAB. It runs every two weeks. I think it’s a great example of content marketing.

A nice application of the Heath brothers’ “SUCCESS” approach from “Made to Stick” (Simple, Unexpected, Concrete, Credible, Emotion, Story) and how it applies to teaching: How to break the first rule of systems thinking | thinkpurpose.

Some articles about leadership, from the great Michael Lopp, aka Rands, who was a manager at Apple, Palantir, Pinterest, and now Slack. Also the author of “Managing Humans” and the “The Nerd Handbook”. Here are some recent good posts. His Don’t Skip This is also a good place to start.

Laurel Norris wrote a great post on “Working-Learning Research” called Robust Responses to Open-Ended Questions. It’s a bit of a sales pitch for SmileSheets.com, but it’s convincing. It’s about picking good questions for post-presentation and post-class surveys.

This article by Marc Cranney from Andreesen-Horowitz provides an interesting framework for doing enterprise sales. I particularly liked how the language changes when one targets executives vs VP/directors vs group leads/regular employees.

Joey H is the developer of git-annex, was a core contributor to Debian, writes a really interesting blog, and lives off-grid in the North East (he used to live in a yurt). He wrote this really nice post about finding old bitcoins, and receiving positive user feedback. Here’s what he added at the end of his bug report template: “Have you had any luck using git-annex before? (Sometimes we get tired of reading bug reports all day and a lil’ positive end note does wonders)”. He shares some of the replies.


New Directions in Open Education is the transcript of a Keynote Mike Caulfield gave at Metropolitan State’s TLTS conference in Denver, CO. Here are my notes from the talk:

  1. The student’s sense of belonging is extremely important. Belonging increases engagement and enhances learning. Belonging is affected by how the class is taught, but also by the class content. The material should be targeted to the audience. A drawing class to kids who like manga should be about manga, not renaissance painters. The students should be able to relate to the materials.
  2. Students should be able to share the result of their work. It gives them an audience, and then their output can itself be used as teaching materials. He mentions a class where students had to do an assignment (do something that makes you uncomfortable and then write about your experience and why you were uncomfortable) and post the results in a bank of assignment outcomes. The next batch of students could see those assignments and either “replicate them” (do the same thing that makes them uncomfortable) or simply get inspired. If they choose to replicate an assignment, then we get two “solutions” to the same assignment. If they choose to do something else, the assignment bank just got bigger. That’s genius!

Again, this is what I think about, when I think of this human core of open:

  1. We are encouraged to modify materials to create a sense of local belonging
  2. We use the power of the open internet to create work that is relevant and impactful, with a real audience
  3. We see the diversity of our students not as challenge to be solved, but as potential to be tapped

By far the best thing I’ve seen at Disney World so far.

Bread #2.