requirements.txt

# ProtDomRetriever requirements
# Python 3.8+ is required

# Required packages:
# HTTP library for making API requests
# ProtDomRetriever.py was tested with requests 2.31.0,
# but should work with 2.25.1 or newer
requests>=2.25.1

# GUI library for file dialog (usually comes pre-installed with Python)
# tkinter is usually included with Python installations and is not installed via pip.
# If it's missing, follow the OS-specific instructions below
# Recommended tkinter version: 8.6 or newer

# Note for macOS users:
# You might see a message like:
# "Python[XXXXX:XXXXX] +[IMKInputSession subclass]: chose IMKInputSession_Legacy"
# This is a harmless macOS-specific diagnostic message related to the input method system
# when using tkinter. It does not affect the program's functionality and can be safely ignored.


# Note: The following are used from Python's standard library (no installation needed):
# - logging: for error and info logging
# - threading: for parallel processing
# - queue: for managing concurrent tasks

# Installation and Virtual Environment Setup Instructions
# (These instructions are comments and will not affect package installation)

# Note: For most users, these detailed instructions are not necessary for simply installing the packages.
# They are provided for educational purposes, troubleshooting, and for users who want to set up a specific Python environment.
# If you're familiar with pip and virtual environments, you can simply run 'pip install -r requirements.txt' in your preferred environment.

# 1. Check your Python versions:
#    a. For macOS users:
#       - Find all paths to your Python 3 installations:
#         where python3
#       - This will show you all executable paths, e.g.:
#         /opt/homebrew/bin/python3 (if using Apple Silicon Mac)
#         /usr/local/bin/python3 (if using Intel Mac)
#         /usr/bin/python3
#       - Check the version of a specific Python installation:
#         /path/to/python3 --version
#         Replace '/path/to/' with the actual path shown by the 'where' command
#
#    b. For Linux users:
#       - Find the path to your Python 3 installation:
#         which python3
#       - This will show you the full path, e.g., /usr/bin/python3
#       - For more detailed information, you can also use:
#         whereis python3
#       - Check the Python version:
#         python3 --version
#       - If you have multiple Python installations, you might want to use the full path:
#         /path/to/python3 --version
#       - Replace '/path/to/' with the actual path shown by the 'which' command
#
#    c. Default Python version (for all systems):
#       python3 --version
#
#    d. For Homebrew users on macOS:
#       - List all Homebrew-installed Python versions:
#         brew list --versions | grep python
#       - Check Python symlinks in Homebrew:
#         ls -l $(brew --prefix)/bin/python*
#
#    Note: You might see multiple versions. Decide which one you want to use for this project.

# 2. Create a virtual environment:
#    a. For Homebrew users on macOS:
#       - Identify the most recent Python version installed:
#         brew list --versions | grep python | sort -V | tail -n 1
#       - Create the virtual environment with the most recent version:
#         "$(brew --prefix)/bin/python3" -m venv .venv
#
#    b. For other systems:
#       python3 -m venv .venv
#
#    Note: It's recommended to use the most recent stable Python version
#    for optimal performance and security.
#
#    If you need to use a specific version for compatibility reasons:
#    /path/to/python3.X -m venv .venv
#    Replace 'X' with the specific version number (e.g., 3.9, 3.10, etc.)

# 3. Activate the environment:
#    On macOS and Linux:
#    source .venv/bin/activate
#    On Windows:
#    .venv\Scripts\activate
#    Your prompt should change to indicate the active environment

# 4. Verify the Python version in your virtual environment:
#    python --version
#    This should match the version you used to create the environment

# 5. Install the requirements:
#    pip install -r requirements.txt

# 6. When done, deactivate the environment:
#    deactivate

# 7. For future use, reactivate the environment:
#    On macOS and Linux:
#    source .venv/bin/activate
#    On Windows:
#    .venv\Scripts\activate

# Note on virtual environments:
# - The name '.venv' is a common convention for project-specific virtual environments.
# - You can create multiple environments for different projects, each with a unique name.
# - The 'venv' in the creation command is the Python module, not the environment name.

# IDE Integration:
# Note: If you're using an IDE like PyCharm or VS Code, you can often create and manage
# virtual environments directly through the IDE's interface.

# For other operating systems:
# The process is similar, but the paths and commands might differ.
# Ensure you're using the correct Python version for your needs.

# If tkinter is missing:
# - macOS (Homebrew): brew install python-tk@X.Y  # Replace X.Y with your Python version
# - Ubuntu/Debian: sudo apt-get install python3-tk
# - Fedora: sudo dnf install python3-tkinter

# Troubleshooting:
# - If you encounter SSL certificate errors, ensure your Python installation has SSL support.
# - For any other issues, check the project's GitHub issues page or pull a request.

# End of requirements and instructions