lab-notes

A simple, easy lab notebook website

• Note: Consider integrating your HackMD or Obsidian with your GitHub account. This could make formatting each of your markdown files a simpler task. Check out Issue #1 for more detailed information.

Intended usage

To automatically update a simple website with your markdown documents!

That's it.... Thanks?

Set up

To create your own website!

1. Fork this repo as lab-notes

   When forking you have the option of renaming the fork. Rename your fork to remove _templates from its name for a simpler URL.

2. Click Settings > Pages
3. In the Source dropdown, select Deploy from a branch
4. In the Branch dropdown, select main then click Save
5. There is now a Your site is live at followed by a URL!

   Note: You may need to refresh the page.

6. Head back to <> Code, in the upper right hand corner there is an About section
   1. Click the Settings (Actually looks like this -> ⚙️)
   2. Toggle the checkbox under Website that says Use your GitHub Pages website
7. Update the title yaml header in the index.md file with your name i. Something like <YourName>'s Lab Notebook (e.g. Brenda's Lab Notebook)

How to use

The idea was a straight-forward one when I thought this up. Each markdown document added to the docs directory will become a link on your website. Each link will take you to the rendered markdown document on a new nested website. The trick was to automate this! (For those interested in Github Actions as an automation tool, check out the .github/workflows/update_index.yaml file!)

1. Consider removing the notes-template.md file in the docs directory... or don't and just keep it and update it in to a template that works for you.
2. Add any number of your own markdown documents to the docs directory
   • The document file name must not contain any whitespaces and must end in .md
     • Whitespaces in filename will not work! (eg. whitespaces in file names.md)
     • Filename must contain .md at the end! (eg. must-contain-.-md-at-the-end)
     • Name the files similar to this -> 2024-week-1.md.
3. The contents of the document will be rendered as markdown.
4. If you want to have unique titles for each document, include a yaml header with title:. See the template below.

A basic document template for you (specifically)

---
title: Year Week number
---

# Goals
In this section I will list the weekly, quarterly, and yearly goals I hope to achieve or have completed this week.

**Weekly:**
- [x]  Create a lab notebook repo
- [ ]  Read the docs

**Quarterly:**
- [ ] Present my work to the lab
- [ ] Write some python code
- [ ] Write some snakemake files

**Yearly:**
- [ ] Have a well documented project in github that is functional (if not perfect)

# Results
In this section write the verbatim results (eg. copy the code chunks, error reports, plots) that relate to the goals you have achieved this week.

example:
This week I created a lab notebook repo using this method (include the cli arguments and the process below)

# Discussion
In this section explain your results and how they relate to you goals

example:
I am applying for credit this quarter. Therefore, I chose to create a lab notebook repo in github to continue practicing git and github as it is an important tool for biotech/bioinformatics.

# Journal
In this section add anything else you may wish to include.

example:
Nothing additional to comment this week. Work has been taken allot of my time this week. It's finals, I was not able to complete the goals I thought I would. I got a new hamster and it is very fluffy.

Resources (ie. The things I looked at to avoid other work and how I figured out how to do this!)

1. github actions commit bot
2. github markdown syntax
3. github jekyll themes
4. github theme title fix
5. easy markdown to github pages