Command Line/Git & Version Control/Markdown/

Linda Wang

The Plan

Time August 22, 2025
8:00 Breakfast
9:00 Introduction
10:00 Reproducible practices, A template README
10:50 Coffee break
11:00 Data provenance, data citations
12:00 Lunch Break

Full Plan

Basic Toolkit

LDI Lab Toolkit

  • Command line
  • Git
  • Markdown

Command Line/Git & Version Control/Markdown/

Command Line

This slide is based on the Carpentries tutorial on the Unix shell (which you might want to do on your own).

  • What is a command line and why use it?
    • Graphical user interfaces are the most common way to give instruction to our computers. They are not good when we need to scale things up, do repetitive tasks, or have people reproduce instructions across systems.
    • Command-line interfaces are another way to pass instructions to computers.
    • “Shell” instructions can be scripted, allowing repetitive tasks to be done automatically and fast.

Commands in the Unix Shell

  • list files
$ ls
  • moving around
    • where are we (pwd = present working directory)
$ pwd

Commands in the Unix Shell

  • Create directories
$ mkdir somepath

Commands in the Unix Shell

  • change to where we want to be
$ cd somepath 
$ pwd
$ cd ..
$ cd ./somepath
$ pwd

Commands in the Unix Shell

  • Move or rename files
$ mv somepath otherpath
  • Copy (cp) files
$ cp test.do otherpath/

Commands in the Unix Shell

  • Remove (rm) files
$ rm filename.do

Git

Version Control system. Track the progress in a project: what changes?, who made changes? Again see the Carpentries tutorial

Git and the command line

  • Clone a repository
git clone https://github.com/labordynamicsinstitute/prettygood-example

(don’t forget to change directory)

  • Check where my local repository is vs. remote repository
git status

Git and the command line

  • Get the current version of an existing repository
git pull

Git and the command line

  • after making changes, how to reflect them in the external repository.
git add otherpath/fileimodified.do
git add otherpath/fileicreated.do
git commit -m "you write here a commit message"
git push

Markdown

We use Markdown to write reports. why?

  • It’s easy, fast, multi-platform, and it works great.

Basic Syntax (https://www.markdownguide.org/basic-syntax/)

Headings

# Heading level 1
## Heading level 2
### Heading level 3
#### Heading level 4
##### Heading level 5

Lists

Ordered lists

1. First item
2. Second item
3. Third item
    1. Indented item
    2. Indented item
4. Fourth item

Lists

Unordered lists

- First item
- Second item
- Third item
    - Indented item
    - Indented item
- Fourth item

Blockquotes and Code Blocks

  • Blockquotes

This is a block quote, and it is created like this

> This is a block quote, and it is created like this

Blockquotes and Code Blocks

  • Code Block

Code embedded in the document:

 ```
 gen var1= var2/var3
 
 ```

Spacing

  • Be sure to leave an empty line after a header.
### Bad example
#### U.S.Census Population Division
- Retrieved from https://www.census.gov/geographies/reference-files/2017/demo/popest/2017-fips.html

Spacing

### Good example

#### U.S.Census Population Division

- Retrieved from https://www.census.gov/geographies/reference-files/2017/demo/popest/2017-fips.html

Spacing

  • Leave an empty line if you want to start a new paragraph.
Bad example:
Thank you for your replication archive.Blablabla.
**Conditional on making the requested changes to the manuscript and the openICPSR deposit prior to publication, the replication package is accepted.**
Good example:

Thank you for your replication archive. Blablabla.

**Conditional on making the requested changes to the manuscript and the openICPSR deposit prior to publication, the replication package is accepted.**

The Plan

Time August 22, 2025
8:00 Breakfast
9:00 Introduction
10:00 Reproducible practices, A template README
10:50 Coffee break
11:00 Data provenance, data citations
12:00 Lunch Break

Full Plan