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:
- Make sure you have a GitHub account.
- Fork a repository.
- Create a new branch on which to make your change, e.g.
git checkout -b my_code_contribution
- 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.
- 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:
- Navigate to https://github.com/cambridge-ceu/TwoSampleMR.
- Click
Compare & pull request
, which will redirect you to https://github.com/MRCIEU/TwoSampleMR/pulls, with the following parameters: - Base repository: MRCIEU/TwoSampleMR
- Base branch: main (or the target branch, e.g., master)
- Head repository: cambridge-ceu/TwoSampleMR
- Head branch: jhz
5. View the artist's impression:
- Visit https://cambridge-ceu.github.io/TwoSampleMR/ (with a logo) and compare it to https://mrcieu.github.io/TwoSampleMR/.