Day 2 / Morning: Python scripts, and git, and github

Etherpad: http://openetherpad.org/KTUX7IJJTx

Miscellaneous notes

To upgrade packages, you can do:

pip install -U <package>

e.g.

pip install -U ipython

will upgrade your IPython installation.

Scripting

We’re going to be combining the code in two notebooks,

99-generate-lots-of-birds

and

10-introducing-bird-counting

into scripts that we can run at the command line and place under version control.

Notes and tips on scripts in Python

See the scripts here:

make-bigbirdlist.py make-birdcounts.py plot-birdcounts.py

• ‘sys.argv’ is a list of the command-line arguments. For example, if

  you run:

  python script.py foo bar baz

  then sys.argv will contain [‘script.py’, ‘foo’, ‘bar’, ‘baz’]

• You don’t need to name Python scripts with ‘.py’; that’s just a convention.

• ‘#! /usr/bin/env python’ is known as the she-bang line, and it tells

  the UNIX operating system to use ‘python’ to run the text file.

• If you add the she-bang above, and the do ‘chmod +x <filename>’, you will be able to run the script without specifying Python.

• ‘nano’ is a good, simple text editor that will get you 40% of the way there. Learn emacs or vim or one of the many text editors on the install page. Do not, under any circumstances, use Word.

Ways to improve these scripts:

• put everything in a function main(args), and then put:

  if __name__ == '__main__':
     main(sys.argv)
  

  at the bottom. This lets the scripts be imported and tested without running them.

• write tests for them :)

• put shebangs and chmod +x them.

• put usage instructions in.

Git

Setting up:

Possible workflow:

• Tell git who you are:

  git config –global user.name “YOUR NAME”

  git config –global user.email “YOUR EMAIL”

• Initiate a local repository in the folder you are currently working in:

  git init

• Add files to be tracked under version control. If you want to track file.txt :

  git add file.txt

• Check git status to see if you have properly added the file to version control:

  git status

• Commit file (or files). Use descriptive commit messages:

  git commit -m “Changed introductory paragraph on the manuscript to reflect new publications.”

• Check git status to make sure that your commit was successful:

  git status

• To see changes between 2 files:

  git diff file1 file2

• To check the git log of commits:

  git log

• To remove a file from staging area (ignores changes):

  git reset filename

• To remove a file from the git repository (not tracking file anymore):

  git rm filename

Undoing things in git:

• If you made a commit and decide that it should not have been done then use git revert. Find the commit hash using the git log command:

  git revert 4717a5c

• If you want to take a project back in time to a certain commit and discard the history of commits that came after it use reset with that commit’s hash. You can also use this to remove a commit that you have not pushed to a repository:

  git reset 4717a5c

• If you want to make a new branch based on the repository at a certain commit use:

  git checkout 4717a5c

Branching:

• Use branches to create parallel copies of your repository that can be changed and commited in parallel to the original

• To see which branch you are currently working on:

  git branch

• To add a new branch:

  git branch March2013Experiment

• To switch to another branch:

  git checkout March2013Experiment

• To swithc back to your original branch:

  git checkout master

• If you have been working on one branch (let’s say March2013Experiment) and want to merge the contents into another branch (let’s say master) use merge.

• Make sure you are on the branch you want it to be merged into:

  git branch #checks to see what branch you are on

  git checkout master

  git merge March2013Experiment

Using a remote repository:

• Set up your github account see here: http://github.com

• Create new repository on github. Give it a useful name.

• Copy the address for your repository. Should be something like: https://github.com/username/Descriptive_Repository_Name_Here.git

• In your local git repository:

  git remote add origin https://github.com/username/Descriptive_Repository_Name_Here.git

• To check that your remote has been added properly:

  git remote -v

• To send your local repository commits to your remote repository:

  git push origin master

• To get commits from the remote repository (updates local repository):

  git pull origin master

• If you want to get the changes from the remote without changing your local repository use fetch:

  git branch newbranch

  git checkout newbranch

  git fetch origin

• If you want to integrate these changes into your local copy then you need to merge (pull is like doing fetch+merge):

  git checkout master

  git merge newbranch

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