Introducing git to scientists who code

Šimon Podhajský9 Comments

Many scientists treat coding -- tasks, analysis, you name it -- as a necessary evil we have to do in order to get to the science. You might know the result from your own scientific practice: subtle changes to the code strewn across many folders, days spent getting into the mind of the postdoc author five years gone, and a general unwillingness to touch the code unless it's time to re-use it.

Before joining a research lab, I was lucky to have spent several years as a back-end programmer with the Yale Student Developers. (Best work-study job ever.) Consequently, working without proper version control and thorough documentation of each step now just feels icky.

(This isn't my personal quirk, by the way. "Use version control" is the fifth recommendation of both Aruliah et al.'s Best Practices for Scientific Computing (2012) and Wilson et al.'s Good Enough Practices for Scientific Computing (2016). So, at the very least, I can say that I share a squick with a number of published researchers.)

Since joining Yale Decision Neuroscience Lab, I've been inducing colleagues to use git. The presentation that I gave yesterday is a very high-level overview of what git is good for:

(It doesn't hold a candle to Alice Bartlett's excellent Git for humans, which I heartily recommend, but it does use our lab's problems as illustrations.)

Where do we from here?

Giving a tech presentation is only the first step in tech adoption. I lack a detailed roll-out plan, but here's what I'm doing now:

  • Since jumping straight to the command line might be too scary, I've been recommending GitKraken and GitHub Desktop.
  • Any code I touch lands in a remote repository rather than the lab file-share. If someone wants to use it, that's where they'll get it. If I'm asked to with anyone's code, it will need to be on that remote. This is on the theory that necessity is the best incentive.
  • And, of course, I've made it clear that anyone who struggles with anything git-related can contact me at any time and I'll do my best to help.

We'll see how it goes.

Introducing git to scientists who code

The Hidden Curriculum

Šimon Podhajský15 Comments

This winter was longer than it had any right to be.

It started with the cold that froze my face, the snow that covered the campus, and the hope that every new semester brings. But the cold grew colder, and coldest still on the January day when Luchang Wang took her life.

I wasn't close to Luchang, but I knew her: we worked together in a small group, aiming to make the world as good as it can get. I regret not being closer to her, because by all accounts, she was a brilliant, amazing friend. I got just a glimpse of it on a ride to Boston, when we ran through our friend Aaron's Goodreads account. We talked Ayn Rand, and how Atlas Shrugged is my secret crack, and how rapey the Fountainhead is; the ride went by too quickly. The last time I saw her, she came late to our group meeting, but still she came, visibly tired and not entirely there. She jumped to her death from the Golden Gate Bridge four days later.

It wasn't until her wake in Battell Chapel that I realized how many friends we had in common, how many of my frequented groups she belonged in, how much of who she was I aspired to. The reverberations of her passing went deep: the shockwaves it sent through our community took weeks to calm. They made this winter a winter of discontent.

*

Our anger didn't replace sadness.

We raged at Yale for not making Luchang's life just a little easier, in the hope that greater ease would ward off the void and the hopelessness and the pain. We saw incompetence and we were quick to label it systematic, because there was a system and it hurt some of our friends and one of our friends was gone, forever gone, and this was the only thing we could do. Maybe making it a little better for others could quench our rage and heal our hearts.

Maybe.

*

People talk about the hidden curriculum at Ivy League schools.

The theory goes that classes don't matter as much as the skills you pick up from the elite environment, skills that the state-school riffraff can't pick up because state schools are not the elite tower of pretentious assholes. They don’t wine and dine with the members of the elite, so they’ll never join their ranks.

That might well be true. But perhaps there is another set of lessons I would not have picked up at a Czech university. Namely: How to cope with the suicide of a friend you admired. How to handle the fear that your friends and loved ones might follow suit. How to survive battles with yourself that you only stand to lose.

How to face the void and stare it down.

It helps to realize that elsewhere is fine, too; that even if our lives will never be as good as they are now, they will still be good enough. It helps to realize that even if the top of Yale's totem pole is hopelessly far, our goals do not require us to reach it. It helps to realize that we have friends, and we can make new ones, and we can fight battles together.

*

Luchang still lingers around the edges of my mind.

Just two days into Spring Break, I was passing through Berkeley's deserted halls - and as I swiped into the computer cluster, I remembered when Yale Security told us Luchang's last Yale ID swipe happened days ago, she was not on campus, our search was useless and her fate out of our hands. This will happen less and less, but I doubt it will stop completely.

This wasn't helped by the fact that I chose to spend my spring break in San Francisco.

Call me stupid, but I honestly hadn't realized until that moment that that was where the Golden Gate Bridge is. To attend a Harvard-Yale dodgeball trampoline game, I walked two miles with the bridge dominating the skyline as the sun was setting; I almost turned around and skipped the game.

It took me a week to muster the courage to actually go. It felt like I had to; if nothing else, as a form of exposure therapy. Plus, I'd be rewarded by an unprecedented view of the skyline! Except that on the day of, the entire bridge was enveloped in impenetrable fog. I should have known; it has its own Twitter account.

I walked the entire length of the bridge there and back. The fog itself never dissipated; it just made the next "THERE IS HOPE, MAKE THE CALL" crisis counseling sign on every other pylon pop out of nowhere.

In the end, I emerged out of the fog into the sunny San Francisco. I'm not sure if the trip was worth it.

*

It is the end of March, two months later now. Spring has come to campus, wavering, uncertain, frail. The snow melts into puddles and the puddles seep into the ground and soon, we'll put the coats and scarves away. Spring has come.

But this winter still marches on.

The Hidden Curriculum

How To Write About France: A Guide For a Rising Junior English Major from Kentucky

Šimon Podhajský

This essay was a creative-writing assignment in the first week of ENGL S247: Travel Writing.

Start your piece in the middle of a quarrel with the chef cuisiner at a high-class Parisian restaurant. The chef, of course, wears a toque and a white double-breasted jacket; he must have a thin curly moustache and thick black eyebrows, but no beard, and must call you "monsieur". The quarrel concerns the choice of vin blanc to go with the saumon you ordered; he strongly suggests Sauvignon Blanc for you, but you insist on Beaujolais, which he snortles at for no good reason. (You attempted to order the poisson d'avril that your last one-night-stand suggested to you during pillow talk, but the waiter's raised eyebrow made you reconsider.)

Conclude the argument by ordering un caffé Américano as dessert triumphantly. In your mind, make psychoanalytic conjectures that use the Second World War and inherent French défaitisme to explain the chef’s rudeness as an artifact of being beholden to and ashamed by valiant foreigners like you.

In your writing, use French mots in abundance.

Let your memory wander to the last night at le bar. Since all French people are sex-crazed, they all wanted you, men and women alike; since you're tolerant, you did not discriminate and made love to them all. Do not describe the love-making; refer to your partners as numbers and make sure the only vivid detail of the sex scene is the discussion of their nipple hair. Write:

"Numéro deux slowly pushed me down on my hotel lit. As she took her brassière off, I saw that, much like the roots of her hair, the pubes on her medium-large round nipples had started to gray."

Rapidly progress to the current night, when you have sex with the chef from earlier. Make sure the curls on his nipple hairs match his mustache. When the night turns to whips and chains, make sure to meditate on Foucault's Surveiller et punir.

Use this moment to describe the French people in more detail. Make sure that you describe all French men as dark and tall or plump and stodgy; and all French women as seductive, especially in their middle age, but also surprisingly long past it. Say that all men resemble either Jean-Paul Belmondo in their rugged handsomeness, or Louis de Funès in everything else. Say that most women are thin and dress fashionably; all have Sophia Loren's fundamental charm, if not her looks. Make an exception for French feminists, who are hairy, smell bad and refuse to have sex with you.

Never actually go to France.

How To Write About France: A Guide For a Rising Junior English Major from Kentucky