AmberPrep / SETUP_STEPS.md
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Sync with development: Dockerfile (meeko, vina, openbabel, PYTHONPATH), amberflow package, .gitignore. Exclude Test/ (binary .ncrst not allowed on HF Hub).
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AmberFlow_development Repository Setup Steps

This document outlines all the steps taken to create the AmberFlow_development repository and sync files from the original AmberFlow repository.

Steps Performed

1. Create New Folder

mkdir -p AmberFlow_development

Created a new directory called AmberFlow_development in the home directory (/home/hn533621/).

2. Copy All Files from AmberFlow

cp -r AmberFlow/* AmberFlow_development/
cp -r AmberFlow/.[!.]* AmberFlow_development/

Copied all files and hidden files (except . and ..) from the AmberFlow directory to the new AmberFlow_development directory.

Files copied:

  • add_caps.py
  • css/ directory
  • Dockerfile
  • .gitattributes
  • html/ directory
  • js/ directory
  • obsolete/ directory
  • output/ directory
  • python/ directory
  • README.md
  • start_web_server.py

3. Remove Old Git Repository

rm -rf .git

Removed the existing .git directory from the copied files to start fresh with a new git repository.

4. Create .gitignore File

Created a .gitignore file to exclude unnecessary files from version control:

Contents:

  • Python cache files (__pycache__/, *.pyc, etc.)
  • Output files (output/, *.pdb, *.cif, *.log)
  • IDE files (.vscode/, .idea/, etc.)
  • OS files (.DS_Store, Thumbs.db)
  • Environment files (.env, venv/, etc.)

5. Initialize Git Repository

git init

Initialized a new empty git repository in the AmberFlow_development directory.

6. Rename Branch to main

git branch -m main

Renamed the default branch from master to main to follow modern git conventions.

7. Stage All Files

git add .

Staged all files in the repository for the initial commit.

8. Create Initial Commit

git commit -m "Initial commit: Copy from AmberFlow"

Created the initial commit with all copied files.

Commit details:

  • 11 files changed
  • 6,567 insertions
  • Files included: .gitattributes, .gitignore, Dockerfile, README.md, add_caps.py, CSS, HTML, JS files, Python application files, and start_web_server.py

9. Create Private GitHub Repository

gh repo create AmberFlow_development --private --source=. --remote=origin --push

Created a private GitHub repository named AmberFlow_development and pushed all files.

Repository details:

10. Verify Setup

git remote -v
git status

Verified that:

  • Remote origin is correctly configured to point to the GitHub repository
  • All files are committed and pushed
  • Working tree is clean

Summary

The AmberFlow_development repository has been successfully created as a private GitHub repository with all files from the original AmberFlow directory. The repository is now ready for development work and version control.

Future Git Operations

To make changes and push them to GitHub:

  1. Stage changes:

    git add .
    
  2. Commit changes:

    git commit -m "Your commit message"
    
  3. Push to GitHub:

    git push
    

Notes

  • The original AmberFlow repository remains unchanged and still points to the Hugging Face Space
  • The new AmberFlow_development repository is completely independent
  • A .gitignore file has been added to exclude unnecessary files from version control