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

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

where the Markdown document is converted to Jupyter notebook, which is executed before converted to .html.

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.