Notes

Getting helps

Consult git-scm command reference,

man git
man git-add
...

The latter will give more specific command-line options available.

Git Bash for Windows

It is helpful to note that c:/ and u:/ can be used as well as /c and /u, respectively.

Windows subsystem for Linux (WSL)

It may be necessary to map network drives, as is noted here, https://jinghuazhao.github.io/Computational-Statistics/SYSTEMS/#wsl.

sudo mkdir /mnt/u
sudo mount -t drvfs U: /mnt/u
sudo umount /mnt/u

or

sudo mkdir /mnt/u
sudo mount -t drvfs '\\me-filer1.medschl.cam.ac.uk\home$\jhz22' /mnt/u
sudo mount -t drvfs U: /mnt/u

Markitdown

Available from https://github.com/microsoft/markitdown, it is a Python utility for converting various files to Markdown.

It now supports the following file types,

• PDF
• PowerPoint
• Word
• Excel
• Images (EXIF metadata and OCR)
• Audio (EXIF metadata and speech transcription)
• HTML
• Text-based formats (CSV, JSON, XML)
• ZIP files (iterates over contents)
• Youtube URLs
• EPubs

MarkDown code extraction

To extract bash code from GitHub markdown, the following is helpful,

sudo apt install npm
sudo npm install -g codedown
cat README.md | \
codedown bash

This also works when the keyword is wrapped in braces, e.g., {r}. In fact, we it is a rather short implementation:

#!/usr/bin/env node

var marked   = require('marked');
var readline = require('readline');
var codedown = require('./lib/codedown.js');

if (process.argv.length >= 3) {

  var source = [];

  readline.createInterface({
    terminal: false,
    input: process.stdin,
  }).on('line', function (line) {
    source.push(line);
  }).on('close', function () {
    var lang = process.argv[2];
    var separator = process.argv[3];
    output = codedown(source.join('\n'), lang, separator);
    console.log(output);
  });

} else {
  console.log('usage: codedown <lang> [<separator>]');
  console.log('ex: codedown haskell');
}

Additional information on npm (Node Package Manager) is available from https://www.w3schools.com/whatis/whatis_npm.asp.

Node.js® is a JavaScript runtime built on Chrome's V8 JavaScript engine, available from https://nodejs.org/en/download/.

Markdown to ipynb

pip install notedown
pip install ipython
pip install nbconvert
notedown DeepSeek.md > DeepSeek.ipynb
jupyter nbconvert --to html --execute DeepSeek.ipynb
jupyter nbconvert DeepSeek.ipynb --to script

where the Markdown document is converted to Jupyter notebook, which is executed before converted to .html. The Python script is also obtained later on.

MarkDown editor

One may prefer Typora, available from https://typora.io/. In particular, it supports mermaid, e.g., https://mermaid-js.github.io/mermaid-live-editor/. The following is an example generated from the link to SVG,

The following code sets up remarkable.

wget https://remarkableapp.github.io/files/remarkable_1.87_all.deb
sudo apt-get update
sudo apt-get install gir1.2-webkit-3.0
sudo dpkg -i remarkable_1.87_all.deb
sudo apt-get install -f
git clone https://github.com/mathjax/MathJax.git MathJax

The last step enables mathtype formatting in the html format (e.g., via pandoc) with

<script type="text/javascript" src="MathJax/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
<script type="text/javascript" src="MathJax/MathJax.js"></script>

MathJax and mermaid

On-the-fly examples for html are initially here from the SCALLOP-Seq projects,

• MathJax, https://jinghuazhao.github.io/SCALLOP-Seq/tests/mathjax.html
• mermaid, https://jinghuazhao.github.io/SCALLOP-Seq/tests/mermaid.html

and found their new home here,

• MathJax, https://jinghuazhao.github.io/physalia/tests/mathjax.html
• mermaid, https://jinghuazhao.github.io/physalia/tests/mermaid.html

It is somewhat unwieldy to create a mermaid diagram in PDF via pandoc. Suppose our diagram is in gaawr2.mmd,

module load ceuadmin/node
npm install -g @mermaid-js/mermaid-cli
which mmdc
mmdc -p puppeteer-config.json -i gaawr2.mmd -o gawwr2.png

where our puppeteer-config.json is as follows,

{
  "executablePath": "/usr/local/Cluster-Apps/ceuadmin/chrome/132.0.6834.110/chrome",
  "args": ["--no-sandbox", "--disable-setuid-sandbox"]
}

When gaawr2.mmd contains mermaid directives as in Markdown, many image files can be generated.

Octotree

Employ this add-on for a drop-down menu within your browser for GitHub repositories.

Pop-up windows

A window may pop up for password, which could cause problems with command-line interface but this can be disabled with

 unset SSH_ASKPASS

or unset GIT_ASKPASS which could be part of .bashrc. Alternatively, this could be achieved with disabling DISPLAY, i.e.,

DISPLAY=
git push

Additional tips

# https://stackoverflow.com/questions/953481/find-and-restore-a-deleted-file-in-a-git-repository
# recover directory R-packages that has been deleted

git checkout $(git rev-list -n 1 HEAD -- "R-packages")^ -- "R-packages"

# or zsh with the EXTENDED_GLOB option enabled for $file
git checkout $(git rev-list -n 1 HEAD -- "$file")~1 -- "$file"

# Recursive clone

git clone --recursive https://github.com/ekg/vcflib/

# add

git add README.md

# config

git config --global --unset-all core.editor
git config --unset-all core.editor
git config --global core.editor "pico -w"

# commit

git commit -m "README"

# diff

git diff README.md

# mv

git mv -f README.md NOTES.md

# pull

git pull

# push

git push

# rebase

git rebase

# reset

git reset --hard

# revert

git revert

# rm

git rm README.md

# clean

git clean -d -f -x

As with many repositories here, a collection of the commands can be built into a batch file to save typing.

Token

Login at https://github.com/settings/tokens and regenerate; make sure to make a copy afterwards.

Utilities

• git recall.
• git-extras.