Installation & Setup

Installation & Setup#

Install UV#

To begin, configure your environment with uv, a fast and versatile Python package manager written in Rust. Please follow the installation instructions on the official uv website.

On Linux or macOS, you can install uv with a single command (requires an internet connection):

curl -LsSf https://astral.sh/uv/install.sh | sh

It is highly recommended that configuring high-performance mirrors based on your IP location. For example, for users in China, you cloud using the mirror provided by TUNA

# Add the following lines into ~/.config/uv/uv.toml
[[index]]
url = "https://mirrors.tuna.tsinghua.edu.cn/pypi/web/simple/"
default = true

Create deeph python virtual environment#

Create python 3.13 environments with uv:

mkdir ~/.uvenv
cd ~/.uvenv
uv venv deeph --python=3.13 # Create `deeph` venv in current dir

Then, the uv virtual environment can be activate with command,

source ~/.uvenv/deeph/bin/activate

Conveniently, all files installed into the deeph venv will be located in the ~/.uvenv/deeph directory.

Quick Install (for Common Users)#

Ensure you’ve activated the uv environment as described in the previous section, and that you’re currently in the deeph environment you created.

Execute the following commands to automatically install DeepH-dock and all its dependencies:

For publish version:

uv pip install deepx-dock

For development version:

uv pip install git+https://github.com/kYangLi/DeepH-dock

Note: During the installation process, an internet connection is required. DeepH-dock and DeepH-pack can be installed under the same python venv.

Install from Source (for Developers)#

Ensure you’ve activated the uv environment as described in the previous section, and that you’re currently in the deeph environment you created.

Execute the following commands to establish the development environment.

git clone https://github.com/kYangLi/DeepH-dock.git
# or, git clone https://github.com/<YourAccount>/DeepH-dock.git
# after fork the repository

cd DeepH-dock
uv pip install -e .[docs]

Commandline Auto-Completion#

Set up intelligent tab completion to save time and reduce errors when using the dock command. After configuration, press Tab to auto-complete subcommands, options, and file paths while in the deeph environment.

Setup Instructions#

Add to Shell Configuration#

Paste the appropriate alias into your shell’s config file:

  • Bash (~/.bashrc):

    alias act-deeph='source ${HOME}/.uvenv/deeph/bin/activate ; eval "$(_DOCK_COMPLETE=bash_source dock)"'

  • Zsh (~/.zshrc):

    alias act-deeph='source ${HOME}/.uvenv/deeph/bin/activate ; eval "$(_DOCK_COMPLETE=zsh_source dock)"'

  • Fish (~/.config/fish/completions/dock.fish):

    alias act-deeph='source ${HOME}/.uvenv/deeph/bin/activate ; _DOCK_COMPLETE=fish_source dock | source'

Restart your terminal session to reload the shell settings.

Activate the Completion#

Execute this command in your terminal:

act-deeph

This will:

  • Activate the deeph Python virtual environment

  • Enable tab completion for dock in your current session

Using Auto-Completion#

  1. Type dock followed by a space

  2. Press Tab to:

    • View available subcommands/options

    • Auto-complete partially typed arguments

    • Suggest file paths when relevant

Note: Auto-completion persists only for the terminal session where act-deeph was executed. Re-run act-deeph in new sessions.

Contents