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