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Contributing |
The µbinfie blog is a peer-reviewed collection of thing we microbial bioinformaticians have thought worth writing down for posterity.
🎉 First off, thanks for taking the time to contribute! 🎉
The following is a set of guidelines for contributing to this training material on GitHub.
- What should I know before I get started?
- How can I contribute?
- How do I add new content?
- How is the training material maintained?
By contributing, you agree that we may redistribute your work under this repository's license.
We will address your issues and/or assess your change proposal as promptly as we can, and help you become a member of our community.
If you have any questions, you can reach us using GitHub issues, or another manner.
You can report mistakes or errors, create more contents, etc. Whatever is your background, there is probably a way to do it: via the GitHub website, via command-line. If you feel it is too much, you can even write it with any text editor and contact us: we will work together to integrate it.
- In the
_posts
folder - Click "Add a new file" in the top right
- Add your contents
- Commit those changes to a new branch (or a fork if you don't have access.)
- Open a pull request. We will review and merge it.
A good methoded of writing a new post with multiple authors simultaneously is the online editor HackMD.io, where authors can edit the same document in real-time. Optionally, it is possible to log-in using your GitHub or Google account, which allows for adding comments to the document. Once the text is written, just copy and paste it to the new post as described above.
- We recommend using
rvm
to setup a Ruby installation - Install a recent Ruby (e.g. 3.2.0) via
rvm install ruby-3.2.0
- Run
gem install bundler
bundle install
will install this repository's dependenciesbundle exec jekyll serve --livereload
will run the website and dynamically reload it upon changes.
- Install Docker if you have not already done so.
- Run the
./serve.sh
script in the top level of the repository. This will download the Ruby 3.2 Docker image and use it to serve the website onhttps://localhost:4000
.
Each post should have a metadata block at the top of the file. This is used to generate the post's page and should look like:
---
title: Welcome to the µbinfie blog
tags: news blog meta
contributors:
- hexylena
---
The tags can be provided as space separated, or as a proper yaml list. Contributors should be referenced in CONTRIBUTORS.yaml
.
If you wish to link to an external blog post, please format it like this:
---
title: An external blog post
external: https://example.org
---
This uses standard markdown so all of your favourite constructs are available like bold and italic and struck text.
Simply write their username @ username
(without the space) and it'll be rendered: @happykhan
Code syntax highlighting is available when you tag the language you're using:
```perl
$a = 0;
```
will produce:
$a = 0;
Citations are possible with {% raw %}{% cite Bankevich2012 %}{% endraw %}
, which render like: {% cite Bankevich2012 %}. They will appear at the bottom of the page and be appropriately hyperlinked.
The BibTeX formatted citation should be placed in references.bib
, we suggest using doi2bib to convert your publication into the appropriate format.