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class: MW 1-2:15 in 133 SMI
office hours: M 10-11 & T 3-4, 1208 Medical Sciences Center


Mon 11/19

final project (due R 12/6): group work in class

Wed 11/14

  • final project: group work in class
  • homework for M 11/19: peer-review of hw 2

Mon 11/12

  • python classes and methods
  • description of final project
  • homework for M 11/19: peer-review of hw 2

Wed 11/7

  • python list comprehension, running external programs, classes and methods
  • homework
    • for Sunday 11/11: homework 2. hard deadline! peer review assignments will be made M 11/12
    • for M 11/19: peer-review of hw 2 due
    • week of 11/19: the final project will be assigned

Mon 11/5

  • more with python: working with files and directories, break and continue loops, dictionaries
  • homework for W 11/7: homework 2 (link on Canvas) individually or in groups of 2

Wed 10/31

  • python functions & scripts continued: we will finish our script / module and make it use arguments
  • homework
    • for M 11/5: submit your “binomial” python code on your github course note repo; if this is group work, submit to one of your repositories and indicate all student names in the github issue
    • for W 11/7: do homework 2, in groups of 1 or 2: see link on Canvas.

Mon 10/29

Wed 10/24

Mon 10/22

Wed 10/17

  • intro to python
  • homework for M 10/22:
    • python scw: finish section 1 analyzing patient data and do section 2 repeating actions with loops
    • git branch exercise:
      • pair up with one other student in the class
      • decide which git repository to work on: class notes repo from one or the other student, say student A
      • student A goes to her/his own repository, clicks on “Settings” then “Collaborator” (github might ask for your password) then enters the gihub user name for student B, then click “Add collaborator”: to give push access to student B
      • student A: start a new branch “A”, add something to it, push the branch to github
      • student B: clone the repo on her/his laptop, start new branch “B”, add changes or new file to it, push the branch to github
      • student A: pull branch B, add changes to it, push to github
      • student B: pull branch A, add changes to it, push to github
      • student A and B: each checkout master branch, merge his/her own branch into master, push to github. The second student doing this will need to pull first.
      • both students: check the branches and merge on the repo’s network: click on “Insights” then “Network”; there should be at least 1 merge commit and labels for at least 3 branches: master, A and B.
      • open a github issue with a link to the url with the “network” view; tag the instructor & TA on this issue, give both student names.

Mon 10/15

Wed 10/10

  • awk, curl & wget
  • homework for M 10/15: peer reviews. Both reviewers will be given access and will be tagged on the github issue Check your issues here and click on the “Mentioned” tab to see the list of issues where you were tagged (provided that you have read access to the repo).

Mon 10/8

Wed 10/3

  • shell scripts: if, arguments
  • homework:
    • for Wed 10/10 8pm: exercise 3 of homework assignment 1, including submission via github issue
    • for M 10/15: peer reviews

Mon 10/1

  • back to shell tools: e.g. sed
  • homework for W 10/3:
    • get these data and do the exercise
    • open an issue in your “course note” GitHub repository to give your solution: either within the issue itself; or within your repository and with a link from the issue to where the solution is in your repository.
      Tag the instructor & TA in your issue.

Wed 9/26

  • git and github for collaboration
  • homework for M 10/1:
    • finish to create your own github repo for your course notes, and to push your local repo there, if not done in class already
    • open an issue on your github course note repo, where you tag the instructor + TA, with a comment on one particular thing that you learned in the course so far; use at least 1 markdown syntax feature when you write this github issue.
    • do shell scripts from the software carpentry: how to pass arguments to a script
    • do “tracking a species” from the software carpentry: combines grep, cut, pipes and script arguments usage.

Mon 9/24

  • reflexions on hw 1.1: one solution, and video on Unix by Gary Bernhardt
  • git for version control
  • homework for W 9/26:
    do the exercise in this recap section
    include as many markdown syntax features as you can within your local repo

Wed 9/19

  • more practice with grep
  • project management & markdown format
  • homework for M 9/24: exercise 2 of homework assignment 1

Mon 9/17

  • less and man
  • search with regular expressions, grep and find
  • homework
    • for W 9/19: finish finding things except for “tracking a species”
    • for M 9/24: exercise 2 of homework assignment 1

Wed 9/12

  • pipes, shell loops, and more on redirection, processes, controls.
  • homework for M 9/17:
    • finish loops
    • do exercise 1 in homework assignment 1: see link on canvas
      to get homework data & submit assignments, see instructions
    • for help with git: offices hours; and help session to “commit” and “push” your work, after class M 9/17 2:15-3:15 in 133 SMI

Mon 9/10

  • auditors: email me to be added to the course mailing list (canvas)
  • everyone: turn on your canvas notifications
  • shell basics
  • homework for W 9/12:

Wed 9/5

  • course intro: why should we learn these things? expectations? logistics?
  • best practices
  • intro to the Unix shell
  • homework for M 9/10:
    • create a github account, pick a “professional” name (like your real name)
    • install a good text editor
    • software carpentry introduction: do “Setup” to download the data and open a terminal, and do “Navigating Files and Directories”. note all your questions.