Université Laval

7-8 mars 2017

8 h 30 - 17 h 00

Instructors: Maxime Boissonneault, Félix-Antoine Fortin

Helpers: Julie Faure-Lacroix

Informations génériques

La mission de Software Carpentry est d'aider les scientifiques et ingénieurs à accélérer et faciliter le travail de recherche en leur enseignant des compétences de base en calcul scientifique. Cet atelier pratique couvre des concepts et outils de base, incluant le design de programmes, la gestion de révisions, la gestion de données, et l'automatisation de tâches. Les participants seront encouragés à s'entraider et à appliquer ce qu'ils ont appris à leur propre problématique de recherche.

Pour davantage d'information sur la façon dont nous enseignons et le raisonnement derrière, voir l'article (en anglais) "Best Practices for Scientific Computing".

Qui: L'atelier s'adresse principalement aux étudiants aux cycles supérieures et autres chercheurs.

Où: Pavillon Adrien-Pouliot, PLT-3928, 1065, avenue de la Médecine, Québec. Obtenez les informations pour vous rendre à l'événement OpenStreetMap ou Google Maps.

Quand: 7-8 mars 2017. Add to your Google Calendar.

Prérequis: Les participants doivent apporter leur propre ordinateur de préférence. Il est aussi recommandé d'installer les logiciels suivants. Des accès à un serveur de calcul de Calcul Québec seront fournis lorsque nécessaire. Les participants doivent aussi adhérer au code de conduite de Software Carpentry (en anglais).

Contact: Veuillez contacter support@calculquebec.ca pour avoir davantage d'informations.

Horaire

Jour 1

08:30 Automatiser des tâches avec la ligne de commande Unix
10:30 Pause
12:00 Dîner
13:30 Premiers pas sur les serveurs de calcul
15:00 Pause
17:00 Conclusion

Jour 2

08:30 Gestion des révisions avec Git
10:30 Pause
12:00 Dîner
13:30 Introduction à la programmation avec Python
15:00 Pause
17:00 Conclusion

Etherpad: http://pad.software-carpentry.org/2017-03-07-Universite-Laval.
Nous utiliserons cet Etherpad pour discuter, prendre des notes, et partager des adresses et extraits de code.

Plan de cours

Ligne de commande Unix

  • Introduction à la ligne de commande
  • Arborescence de fichiers et répertoires
  • Création, suppression et gestion de fichiers et répertoires
  • Combinaisons de commandes, redirections et filtres
  • Boucles
  • Scripts bash
  • Recherche de fichiers
  • Reference...

Premiers pas sur les serveurs de calcul

  • Introduction au calcul informatique de pointe
  • Vocabulaire, composantes d’un ordinateur et structure d’une grappe de calcul
  • Transfert de fichiers à partir de/vers la grappe de calcul avec Globus
  • Utilisation de modules
  • Utilisation de l’ordonnanceur et soumission de tâches

Gestion de révisions avec Git

  • Introduction à la gestion des révisions
  • Configuration de Git
  • Créer un dépôt
  • Suivre les révisions
  • Explorer l’historique
  • Ignorer certains fichiers
  • Dépôts distants
  • Collaborer
  • Gestion des conflits
  • Science ouverte, licences et hébergement
  • Reference...

Introduction à la programmation avec Python

  • Analyser des données avec des bibliothèques externes
  • Répéter des actions avec des boucles
  • Stocker des données dans des listes
  • Analyser des données issues de plusieurs fichiers
  • Faire des choix
  • Créer des fonctions
  • Tester son code, prévoir les erreurs et déboguer
  • Reference...

Setup

To participate in a Software Carpentry workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.

Windows

Video Tutorial
  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps bellow:
    1. Click on "Next".
    2. Click on "Next".
    3. Keep "Use Git from the Windows Command Prompt" selected and click on "Next". If you forgot to do this programs that you need for the workshop will not work properly. If this happens rerun the installer and select the appropriate option.
    4. Click on "Next".
    5. Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
    6. Keep "Use Windows' default console window" selected and click on "Next".
    7. Click on "Install".
    8. Click on "Finish".
  3. If your "HOME" environment variable is not set (or you don't know what this is):
    1. Open command prompt (Open Start Menu then type cmd and press [Enter])
    2. Type the following line into the command prompt window exactly as shown:

      setx HOME "%USERPROFILE%"

    3. Press [Enter], you should see SUCCESS: Specified value was saved.
    4. Quit command prompt by typing exit then pressing [Enter]

This will provide you with both Git and Bash in the Git Bash program.

Mac OS X

The default shell in all versions of Mac OS X is Bash, so no need to install anything. You access Bash from the Terminal (found in /Applications/Utilities). See the Git installation video tutorial for an example on how to open the Terminal. You may want to keep Terminal in your dock for this workshop.

Linux

The default shell is usually Bash, but if your machine is set up differently you can run it by opening a terminal and typing bash. There is no need to install anything.

Git

Git is a version control system that lets you track who made changes to what when and has options for easily updating a shared or public version of your code on github.com. You will need a supported web browser (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above).

You will need an account at github.com for parts of the Git lesson. Basic GitHub accounts are free. We encourage you to create a GitHub account if you don't have one already. Please consider what personal information you'd like to reveal. For example, you may want to review these instructions for keeping your email address private provided at GitHub.

Windows

Git should be installed on your computer as part of your Bash install (described above).

Mac OS X

Video Tutorial

For OS X 10.9 and higher, install Git for Mac by downloading and running the most recent "mavericks" installer from this list. After installing Git, there will not be anything in your /Applications folder, as Git is a command line program. For older versions of OS X (10.5-10.8) use the most recent available installer labelled "snow-leopard" available here.

Linux

If Git is not already available on your machine you can try to install it via your distro's package manager. For Debian/Ubuntu run sudo apt-get install git and for Fedora run sudo yum install git.

Text Editor

When you're writing code, it's nice to have a text editor that is optimized for writing code, with features like automatic color-coding of key words. The default text editor on Mac OS X and Linux is usually set to Vim, which is not famous for being intuitive. if you accidentally find yourself stuck in it, try typing the escape key, followed by :q! (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.

Windows

Video Tutorial

nano is a basic editor and the default that instructors use in the workshop. To install it, download the Software Carpentry Windows installer and double click on the file to run it. This installer requires an active internet connection.

Others editors that you can use are Notepad++ or Sublime Text. Be aware that you must add its installation directory to your system path. Please ask your instructor to help you do this.

Mac OS X

nano is a basic editor and the default that instructors use in the workshop. See the Git installation video tutorial for an example on how to open nano. It should be pre-installed.

Others editors that you can use are Text Wrangler or Sublime Text.

Linux

nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

Others editors that you can use are Gedit, Kate or Sublime Text.

Python

Python is a popular language for research computing, and great for general-purpose programming as well. Installing all of its research packages individually can be a bit difficult, so we recommend Anaconda, an all-in-one installer.

Regardless of how you choose to install it, please make sure you install Python version 3.x (e.g., 3.4 is fine).

We will teach Python using the IPython notebook, a programming environment that runs in a web browser. For this to work you will need a reasonably up-to-date browser. The current versions of the Chrome, Safari and Firefox browsers are all supported (some older browsers, including Internet Explorer version 9 and below, are not).

Windows

Video Tutorial
  1. Open http://continuum.io/downloads with your web browser.
  2. Download the Python 3 installer for Windows.
  3. Install Python 3 using all of the defaults for installation except make sure to check Make Anaconda the default Python.

Mac OS X

Video Tutorial
  1. Open http://continuum.io/downloads with your web browser.
  2. Download the Python 3 installer for OS X.
  3. Install Python 3 using all of the defaults for installation.

Linux

  1. Open http://continuum.io/downloads with your web browser.
  2. Download the Python 3 installer for Linux.
    (Installation requires using the shell. If you aren't comfortable doing the installation yourself stop here and request help at the workshop.)
  3. Open a terminal window.
  4. Type 
    bash Anaconda3-
    and then press tab. The name of the file you just downloaded should appear. If it does not, navigate to the folder where you downloaded the file, for example with: 
    cd Downloads
    Then, try again.
  5. Press enter. You will follow the text-only prompts. To move through the text, press the space key. Type yes and press enter to approve the license. Press enter to approve the default location for the files. Type yes and press enter to prepend Anaconda to your PATH (this makes the Anaconda distribution the default Python).
  6. Close the terminal window.