physalia

The purpose for this repository, named after the Physalia GWAS-course, https://github.com/jinghuazhao/GWAS-course when in preparation, was to record basic uses of GitHub as well as call for contributions to GitHub repositories.

A summary of files

File Description
api.md Command-line repository creation
IDE.md GUI for GitHub repository maintenance
Notes.md Important notes
slides.md A showcase of Markdown slides
tests.md Tests of MathJax and mermaid
README.md this file
csd3.sh A package-building example
setup.sh setup for a standard repository
ssh.sh setup for SSH
docs.sh batch file for add/commit/push operations

See also GitHub-matters, https://cambridge-ceu.github.io/GitHub-matters/.

How to contribute

(Adapted from Apress)

Efforts are highly welcome as a long-term project, via the following steps:

  1. Make sure you have a GitHub account.
  2. Fork a repository.
  3. Create a new branch on which to make your change, e.g. git checkout -b my_code_contribution
  4. Commit your change. Include a commit message describing the correction. Please note that if your commit message is not clear, the correction will not be accepted.
  5. Submit a pull request.

See also instructions to GDAL. Additional information is given in Notes.md.

TwoSampleMR/jhz

It appears you're seeking assistance with the formatting of section numbers in your document. Here's a revised version with corrected section numbering:

Several steps are necessary:

1. Fork TwoSampleMR from https://github.com/MRCIEU/TwoSampleMR.

2. Clone the package locally, add a fork, add a branch, modify files, and build the web files:

git clone https://github.com/MRCIEU/TwoSampleMR
cd TwoSampleMR
git remote -v
git remote add myfork https://github.com/cambridge-ceu/TwoSampleMR.git
git remote -v
git checkout -b jhz
git branch
git status
cp -r ../tests/man/figures man
cp -r ../tests/pkgdown/favicon pkgdown
mv index.md pkgdown
cp ../tests/README.Rmd .
Rscript -e 'knitr::knit("README.Rmd");library(pkgdown);build_site()'

Note: In this step, we copy/replace files from the tests/ directory created locally.

3. Add files:

for f in .github .gitignore .Rbuildignore $(ls)# .Rinstignore
do
  echo adding ${f}
  git add ${f}
  git commit -m "${f}"
done
git add --force docs
git commit -m "docs"
git push myfork jhz
du -h --exclude .git --exclude docs
git log --oneline

4. Create a pull request:

5. View the artist's impression: