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Tab2 Example#

R Markdown TIps#

the keyboard shortcut Ctrl + Alt + I (OS X: Cmd + Option + I)

This runs command lines here in the file, below the chunk, and runs all commands at once.

{sh, eval=FALSE}

pwd
brew --version

You can run commands line by line (Cmd+Enter) in .R file only. It requires the system2(command = "command_name") code line, result will be display in console and below the code chunk all commands at once (no line by line option).

{r, eval=FALSE} 

system2(command = "ls")
system2(command = "pwd")

r 

system2(command = "ls")
system2(command = "pwd")

sh 

ls 
pwd 
git commit -m "message"

{yml}

site_name: LabNotes
site_url: https://example.com_or_my.github

yml

site_name: LabNotes
site_url: https://example.com_or_my.github

Plan 220826#

  • Create all the files in .Rmd as normal (in Box sync service) as bs4_book
    Use Rstudio::New Project.
    mkdocs new LabNotes....
  • Build site in bs4 -> Converts .Rmd to .m -> Creates a folder with all converted .md files (all files in Box Sync, do NOT connect with git or GitHub)
  • Create Mkdocs repositories in /documents/GitHub/
  • Confect them to a GitHub repo
  • Use symlinks for the .md files stored in doc/github/ folders
  • Make GitHub commits as normal?
  • Build and deploy site as normal?

Create Mkdocs site#

:::{.note} Installed required (>_) brew --version
python --version
brew list || brew install
brew install python3
brew install python@3.10
pip --version
pip3 install --upgrade pip
pip3 install mkdoc
brew install mkdocs (error)
pip3 install mkdocs-material
Other Plugins:
pip install mkdocs-static-i18n
pip install mkdocs-material

Create a site with Terminal (>_)
mkdocs -h (help)
mkdocs new {dir-name}
cd {dir-name}
ls
tree
mkdocs serve
Cnt+C
+ code .
+ rstudio . ?
+ open -na Rstudio
+ open myproject.Rproj
- Modify yml (simple, just to check if render)
- Theme, nav, plugs
- Create Tab2.md, Tab3.md, Tab4.md for trial 

site_name: LabNotes
site_url: https://example.com_or_my.github
repo_url: https://github.com/squidfunk/mkdocs-material # url link of ripo in navbar
repo_name: squidfunk/mkdocs-material # name of ripo to be displayed in navbar


nav:
  - Home:
    -  Hi: "index.md"
  - Tab2: "01-Tab2.md"
  - Tab3: "02-Tab3.md"
  - Tab4: 
    - sub1:
      - sub2: 
        - sub3: 
          - sub4: "03-Tab4.md"


theme: # https://squidfunk.github.io/mkdocs-material/setup/changing-the-colors/#accent-color 
  name: material
  favicon: assets/NiigataUicon.png #small icon in the "browser`s" tap.Save @ /dir  
  features:
    #- navigation.instant
    - navigation.tabs #Nav tabs on top
    - navigation.tabs.sticky # Keeps top nav menu from hiding.
    #- header.autohide # Hides all top menu.
    #- navigation.sections  #uncollapse all tab sections.
    - navigation.top

  palette:
    #primary: green # Color of the Header
    #accent: red # Colors change on hover. 
    # Palette toggle for light mode
    - primary: Default  # The original was scheme: Default 
      accent: red # Colors change on hover. 
      toggle:
        icon: material/brightness-7 
        name: Switch to dark mode
    # Palette toggle for dark mode
    - scheme: slate
      accent: light green # Colors change on hover. 
      toggle:
        icon: material/brightness-4
        name: Switch to light mode
        accent: red # Colors change on hover. 
  logo: # assets/logo.png
        assets/NiigataUicon.png
  icon:
    repo: fontawesome/brands/git-alt # repo icon


extra:
  homepage: https://www.niigata-u.ac.jp/ # url for the logo icon




#include_sidebar: true

#===================================================================================
# Mkdocs Markdown Extentions, Plugins & extras
#===================================================================================
markdown_extensions:
  - admonition
  - abbr
  - attr_list
  - def_list
  - footnotes
  - meta
  - md_in_html
  - codehilite
  - pymdownx.critic
  - pymdownx.caret
  - pymdownx.keys
  - pymdownx.mark
  - pymdownx.tilde
  - pymdownx.tabbed
  - pymdownx.details
  - pymdownx.inlinehilite
  - pymdownx.smartsymbols
  - pymdownx.tasklist:
      custom_checkbox: true
  - pymdownx.superfences
  - pymdownx.tabbed:
      alternate_style: true
  - toc:
      # insert a blank space before the character
      permalink: "#"

plugins:
  - glightbox # istall requied: images/lightbox
  - search # add search box.
  - i18n: # language plugin. 
      default_language: en
      languages:
        en: English
        ja: 日本語
        es: Español

    - Add content files: **Copy/paste Tabs.md files**

mkdocs serve Cnt+C

mkdocs build mkdocs gh-deploy

In github.com:
create git repo in github.com (follow recommendation of Hernandez?)
1. Github > create new repo > name: {x: demo_docmaker } > description {dockmaker demo} > ©Public > <© Add readme file > <© Add .gitignore: ˇ{R} > © Create repository

mkdocs build

  1. Repo settings > Pages > Source: Deploy form a branch > ˇBranch: © main > /(root) > ©save (new page is created)
  2. Got to // Code > code > clone > htpps (copy github page address)
    https://github.com/MarceloRosales/mkd_LabNotes.git

Connect Mkdocs to Git >_:
git init
git add .
git status

Connect Mkdocs to Github repository >_:
git remote add origin {git_url}

Sometime requires: git config --global user.name “MyGitAccount”
git config --global user.email “myemail.com”
git config credential.helper store
gedit gitignore (edit gitignore to don’t track files…??)

git commit -m “Initial Commit”
git status (empty) git push origin master

Sometime requires: type github username: type github Password: (push from local master branch to remote master branch)

Mkdocs site build and deploy in >_:
mkdocs build
mkdocs gh-deploy

In github.com:
Make sure deploy branch is gh-pages.
1. Repo settings > Pages > Source: Deploy form a branch > ˇBranch: © gh-paages > /(root) > ©save (new page is created)

===================================
After first commit:
Modify code. (and save files)
mkdocs build
mkdocs gh-deploy
git add .
git status
git commit -m “commit message”
git push origin master

Other git commands:
git reflog (past git logs)
git checkout -b other-branch (Switch to a new branch)
git branch -a (lists of branches)
rm -fr .git (remove git files)
git config --global user.name "MarceloRosales"
git config --global user.email "...@hotmail.com"
git config credential.helper store
git commit -m "1st commit"
git log # If want to revert to a preview’s version, Copy hash click Q to quit.
git checkout {hash copied from log}
git checkout -b {new branch name} # Create a new branch.
git branch {new branch name} {hash} # Create new branch, if revert to previous, add hash
git checkout {branch name} # To change branches
git merge {branch name} # merge branch to main
:::

Create bs4_book in Rstudio#

//Rstudio > New Project >
Book project using bookdown > …[]… >
Select book format: bs4_book >
© Open in new session.
Add 08-Preparation.Rmd
[Build] > Build Book >
bs4_book (wil convert .Rmd -> .md in /_book)

To make symlink: 

ln -s /path/of/original/file /path/to/taget/dir/{filename}

Box Sync/../.md -> ~/Documents/gitrepo/.md

Ex.
From: “/Users/marcelorosales/Box Sync/Github/mkdocs/bs4_LabNotes/_book/08-Preparation.md”
To: “/Users/marcelorosales/Documents/GitHub/Mkdocs_books/mkd_LabNotebooks/mkd_LabNotes/docs”

Samples "/Users/marcelorosales/Box Sync/Github/mkdocs/mkdocs_dumpAll/Samples/08-Preparation.Rmd"

 ln -s "/Users/marcelorosales/Box Sync/Github/mkdocs/bs4_LabNotes/_book/08-Preparation.md" "/Users/marcelorosales/Documents/GitHub/Mkdocs_books/mkd_LabNotebooks/mkd_LabNotes/docs"

 ln -s "/Users/marcelorosales/Box Sync/Github/mkdocs/bs4_LabNotes/_book/08-Preparation.md" "/Users/marcelorosales/Box Sync/Github/mkdocs/mkdocs_dumpAll/Samples/08-Preparation.Rmd"

Fail

Partial address do NOT work.
“~/Box Sync/Github/mkdocs/bs4_LabNotes/_book/08-Preparation.md”
“~/Documents/GitHub/Mkdocs_books/mkd_LabNotebooks/mkd_LabNotes/docs”
ln -s "~/Box Sync/Github/mkdocs/bs4_LabNotes/_book/08-Preparation.md"

Allways work the in bs4_book .Rmd