4. Code and Documentation Update

4.1. Code Update

1. Push Code Changes from Server to GitHub
   After modifying the code on your server, push the code to GitHub:

   git add .
   git commit -m "your comment"
   git push -u origin <your-branch>:<github-branch>
   # if it fails, try
   git push -u origin <your-branch>:<github-branch> --force
   

2. Add Submodule
   If you want to make contributions to the PaleoDA, try to add it as a submodule

   cd PaleoDA
   git submodule add https://github.com/<your-repository> <submodule-name>
   

3. Pull Updated Code from GitHub to Server
   Once the code on GitHub is updated (by you or others), update the code on your server:

   cd PaleoDA
   git submodule update --remote <submodule-name>
   git add <submodule-name>
   git commit -m "your comment"
   git push -u origin <your-branch>:<github-branch>
   

4.2. Documentation Update

1. Preview HTML Documentation Locally
   Open the HTML documentation locally using a live server to review your changes:

    cd PaleoDA_docs/build/html
    live-server
   

2. Edit Documentation Source Files
   To add or modify documentation content, change to the source directory, edit the relevant .rst files, then return to the main documentation directory to rebuild the HTML:

    cd PaleoDA_docs/source/pages
    # Make edits to the .rst files
    cd ../../
    make clean
    make html
   

3. Deploy Updated Documentation to GitHub
   Copy the newly generated HTML files from build/html to docs and push the updated files to GitHub:

   cp -r PaleoDA_docs/build/html/* PaleoDA_docs/docs/
   git add *
   git commit -m "your comment"
   git push -u origin <your-branch>:<github-branch>