GitHub landing page

The profile/README.md file in this repository is the landing page for the saezlab GitHub organization. Do not edit that file directly. Instead, read the guide below how to edit the landing page.

How to edit

1. Install poetry if you don't have it already installed:

   curl -sSL https://install.python-poetry.org | python3 -
   

2. Navigate into the directory of the public landing page repo (.github). If does not exist yet, create the poetry environment required to run the Python script generating the markdown for the landing page:

   poetry install
   

3. Do your edits:

   • The main text can be edited in profile/src/README.main.md

   • The resources are defined in profile/src/resources.yaml. To add a new resource, include the logo in the profile/logos directory by the name of the resource all lowercase, in svg or png format. For example, for OmniPath we have omnipath.svg. Then add the name, title and URLs of the resource in resources.yaml. And also include the name of the resource in the list at the top of the file. By removing a name from the list, a resource can be hidden while still keeping its information in the yaml. Each link has a type, see the possible types below. For links to packages, add a suffix to the URL type, such as package:PYPI or package:BIOC, for PyPI and Bioconductor respectively.

     Link type	For links to...
     home	Homepage
     python	Python repository
     r	R repository
     package	Package
     docs-py	Python documentation
     docs-r	R documentation
     article	Publication
     main	Link for the logo (to override the default)

   • The footer of the landing page (anything after the table) can be edited in profile/src/README.foot.md

4. Run the profile/src/update_md.py script to generate the landing page, i.e. the profile/README.md file:

   poetry run python profile/src/update_md.py
   

5. Check by grip, the GitHub-identical markdown renderer, whether your updates are correct. If you added a new image, it won't be visible yet, because the images are referenced by their absolute URLs under github.com.

   poetry run grip profile/README.md
   

   Copy the address to your browser to open the test server and see the rendered page.
6. Commit and push your changes.

   git add -u
   git commit -m "describe the changes"
   git push
   

   Check if the updates are shown correctly. Don't forget, you see a different page depending on whether you are logged in with an account in the saezlab GitHub organization.
7. Finally, cross-merge your changes between the .github and .github-private, by adding the one you edited to the other one as a new remote, then pulling from it, it, and pushing to the other. Edit the public version first, push it to GitHub, then navigate to the directory of the private version:

   # adding the new remote required only once:
   git remote add public git@github.com:saezlab/.github.git
   git config pull.rebase false
   
   # after finishing your edits:
   git pull public main
   git push origin main