Cheat Sheet

Most important bash commands for managing processes, Git, Python, R, SQL/SQLite and LaTeX for researchers and data scientists. This cheat sheet only focusses on bash commands run from the terminal.

Table of Contents

• Managing processes
  - First-aid procedure for killing a running process
  • Cronjobs and Crontab
  • Tmux sessions
  • Bash profiles
• Git
  - Clone repository from GitHub to local machine
  • Commit file from terminal
  • Managing branches
  • global .gitignore file
  • local .gitignore file
  • How to prevent conflicts in a collaborative Github project
  • Solve conflict using VIM editor
  • Push commits from terminal with two-factor authentification
• Python
  - Virtual environments
  • Check which python packages are installed
  • Start scrapy project
• R
  - Open new window
  • Add R project to Github
  • Markdown and R
  • Options settings
• SQL and SQLite
  - Repair corrupt database
  • Merge two SQLite databases
  • Open new SQLiteBrowser window from terminal
• Text editing and LaTeX
  - Calculate the number of words in a Latex file

Managing processes

First-aid procedure for killing a running process

• open new terminal window
• type ps + enter
• identify PID (processid) of the process
• type kill -9 <PID>

OR:

• control + C (twice if needed)

Cronjobs and Crontab

Schedule crontab task

• If you want to run the cronjob on a server: enter the server
• enter crontab -e in the terminal
• enter <minutes> <hours> <day of month> <month> <day of week>
• for example 6 0 * * 1-6 cd /home/annerose/Python/continuousscraper/ && python processcontrol.py
• this signifies that the process will start to run Monday through Saturday at 6 minutes past midnight.

For more information, see

• http://www.everydaylinuxuser.com/2014/10/an-everyday-linux-user-guide-to.html and
• http://stackoverflow.com/questions/12409101/scrapy-crawl-on-crontab-under-virtual-environment

Kill an existing cronjob

• enter ps -e in the terminal to see all existing processes.
• determine which processid your process has.
• enter kill -9 <processid>

Tmux sessions

Tmux allows to keep processes running after ending an ssh session. For more detailed explanation, see here.

• ssh into the remote machine
• start tmux by typing tmux into the shell
• start the process you want inside the started tmux session
• leave/detach the tmux session by typing Ctrl+B and then D

You can now safely logoff from the remote machine, your process will keep running inside tmux. When you come back again and want to check the status of your process you can use tmux attach to attach to your tmux session.

If you want to have multiple session running side-by-side you should name each session using Ctrl-B and $. You can get a list of the currently running sessions using tmux list-sessions.

Some more useful tmux commands (see also this video):

Bash profiles

Create bash profile

touch ~/.bash_profile; open ~/.bash_profile

touch creates the file, so no need to run this command when the file already exists. Alternative:

open ~/.bashrc

For editing the .bash_profile. opens in a text editor. See here

Git

Clone repository from GitHub to local machine

• create new repository on GitHub
• go to the directory on your local machine where the cloned repository should be saved.
• type git clone https://github.com/your-name/repository-name.git
• the repository should now appear in the local folder on your machine.

Commit file from terminal

• go to the directory of your repository inside the terminal
• type git add . This recurses into sub-directories. Alternative: git add or git commit -a
• git commit -m “your commit message”. Commit the changes.
• git push. Push the changes.

To see the status of your repository: git status.

See this useful blog.

Managing branches

Branches are very important when you collaboratively work on Github.

This github page contains useful information on how to create a new branch and how to manage branches on github.

• go to the directory of your repository inside the terminal
• before creating a new branch, make sure all changes are pulled to your local repository
• Create new branch by typing git checkout -b [name_of_your_new_branch]
• Push the new branch to github by typing git push origin [name_of_your_new_branch]
• Check out which branches exist for this repository: git branch. (If there is only the master branch, it will return * master.)
• Add a new remote for your branch: git remote add [name_of_your_remote]. A remote (URL) is Git’s fancy way of saying “the place where your code is stored.” (see here)
• Push changes from your commit into your branch (= into your remote): git push [name_of_your_new_remote] [name_of_your_branch]
• Update your branch from the original (master) branch: git fetch [name_of_your_remote]
• To merge changes between your branch and the original (master) branch, you should first switch to master branch in your terminal: git checkout master. Then simply type git merge [name_of_your_branch].

global .gitignore file

See here

Create a global .gitignore file (file types to be excluded from every git project):

git config --global core.excludesfile ~/.gitignore_global

The file is found under Documents/Username (as a hidden file). Open it in a text editor to edit it and add files you don’t want to sync with git/GitHub.

local .gitignore file

In the terminal, go to the working directory of the project you want to commit to github.

touch .gitignore

The file is found locally in the working environment of the project. Open it in a text editor to edit it and add files.

How to prevent conflicts in a collaborative Github project

The following procedure should help you considerably to prevent conflicts in collaborative Github and Git project.

Before you start working: pull

Once you’ve made any changes to the project:

1. Commit
2. Pull
3. If you get an error message, clean the file, solve conflicts
4. Push

To summarize: pull, commit, pull, clean, push

Solve conflict using VIM editor

See this Stackoverflow post: http://stackoverflow.com/questions/5599122/problems-with-entering-git-commit-message-with-vim

If there is a conflict between your local version of the project and the version on Github, a window of the VIM editor will open after you’ve tried to commit your local changes. In this case, you should proceed as follows:

• type i into the VIM editor, which opens the editing (insert”) mode
• type your merge message
• press Esc to be sure to have left insert mode
• then type :wq followed by Enter, which writes the current file and then closes it.
• your merge should now have been accepted.

Push commits from terminal with two-factor authentification

See this helpful page on how to push commits from the terminal when using two-factor authentification on Github:
https://gist.github.com/wikimatze/9790374

Important: You need to use your personal access token, not your Github password to push commits from the terminal.

Python

Virtual environments

Change virtual environment:

workon <name of virtual environment>
workon annerose2015-11  # python 2 environment
workon annerose_python3_2016-07 # python 3 environment

How to set up and manage virtual environments in Ubuntu: http://askubuntu.com/questions/244641/how-to-set-up-and-use-a-virtual-python-environment-in-ubuntu

Configure Pycharm to use a virtual environment

touch ~/.pycharmrc; open ~/.pycharmrc

See here.

Then set the shell Preferences->Tools->Terminal->Shell path to
/bin/bash --rcfile ~/.pycharmrc

Check which python packages are installed

pip freeze

Start scrapy project

Start scrapy project for webscraping: enter the following command in the terminal (in the directory where you want to start your project).

scrapy startproject name_of_project

R

Open new window

• Open new RStudio window from terminal (e.g. when one RStudio needs to run for an extended period of time):
• enter open -n -a "rstudio" in terminal
• How to add an RStudio project to Github: https://www.r-bloggers.com/rstudio-and-github/

Add R project to Github

Add the following commands in shell after having created the project in Github:

git remote add origin https://github.com/your-name/repository-name.git    
git config remote.origin.url git@github.com:your-name/repository-name.git     
git pull origin master    
git push origin master    

Markdown and R

Render/compile an R Markdown file from Terminal:

render("yourfile.Rmd")

This resource on R Markdown is helpful.

An R Markdown cheatsheet is available from RStudio here.

Options settings

Set options, even options that aren’t defined by default. This can be useful for example for setting your consumer key, consumer secret etc. of your Twitter app:

> options(<name of new option> = "")    
> options(consumer_key = "xyz")    
> getOption("consumer_key")    
[1] "xyz"

SQL and SQLite

Repair corrupt database

How to repair db database: see stackoverflow

echo '.dump'|sqlite3 corrupt.db|sqlite3 corrupt_fixed.db    
cat <( sqlite3 corrupt.db .dump | grep "^ROLLBACK" -v ) <( echo "COMMIT;" ) | sqlite3 corrupt_fixed.db    

Merge two SQLite databases

• http://stackoverflow.com/questions/3689694/merge-sqlite-files-into-one-db-file-and-begin-commit-question
• http://stackoverflow.com/questions/80801/how-can-i-merge-many-sqlite-databases

Leaving out duplicates:

• http://sqlite.1065341.n5.nabble.com/Merging-two-SQLites-leaving-out-duplicates-td46337.html

Open new SQLiteBrowser window from terminal

SQLiteBrowser is well suited for viewing and editing database files compatible with SQLite.

If you want to view several databases side by side, you have to open a new SQLiteBrowser window from terminal (it doesn’t seem to be possible to open a new window from within SQLiteBrowser). To this end, go to the directory where your applications are stored (in Mac). Normally, this should be:

cd			# go to home directory
cd ../../..		# go three levels up
cd Applications		# go to Applications

Thereafter, type the command to open a new SQLiteBrowser window:

open -n sqlitebrowser.app

Text editing and LaTeX

Calculate the number of words in a Latex file

• Change the working directory of your terminal to where the LaTeX TeX file is located.
• I use one of the two options: (1) detex or (2) texcount
  • detex:
    Enter detex <document_name>.tex | wc -w -c -l or just detex <document_name>.tex | wc
    To calculate word count in pdf document: pdftotext <document_name>.pdf - | wc -w
  • texcount:
    Enter texcount -1 <document_name>.tex
    There are thousands of options for texcount
    For example, for including the bibliography in the word count, use texcount -1 -incbib <document_name>.tex
    To include several documents in the word count (e.g. main paper and appendix), just add the different documents behind one another: texcount -1 -incbib <main_document>.tex <appendix>.tex
    For more information on texcount, see this website