Development Environment Setup Guide#

This repository provides a bootstrap script to simplify the setup of the MolSysMT development environment.
The script automatically creates or updates the conda/mamba/micromamba environment, installs MolSysMT in editable mode, and optionally registers a Jupyter kernel.

The script is located at:

devtools/start_dev_env.sh

🚀 Basic Usage#

1. Setup without activation#

bash devtools/start_dev_env.sh --mode print

This will:

Create or update the environment.
Install MolSysMT in editable mode.
Print clear instructions on how to activate the environment manually.

2. Setup and persist activation#

source devtools/start_dev_env.sh --mode persist

This will:

Create or update the environment.
Install MolSysMT in editable mode.
Activate the environment in your current shell and keep it active.
⚠️ You must use source for persistence to work.

🐍 Choosing Python Version#

By default, the environment uses the Python version specified in development_env.yaml.
You can override this with the --python option:

bash devtools/start_dev_env.sh --mode print --python 3.12

📂 Flexible Execution Paths#

You can run the script from different locations:

Parent directory of the repository
Repository root
Inside molsysmt/
Inside devtools/

The script automatically detects the correct path to:

molsysmt/devtools/conda-envs/development_env.yaml

⚙️ Options#

--mode {print|persist}
    print   : Do not activate, only print activation instructions (default).
    persist : Activate and keep the environment active (requires 'source').

--python <version>
    Override Python version (e.g. 3.11, 3.12).

--env-name <name>
    Set environment name (default: molsysmt).

--env-yaml <path>
    Provide a custom path to a YAML file.

--no-kernel
    Skip Jupyter kernel registration.

-h, --help
    Show usage help and exit.

Environment variables:

REGISTER_KERNEL=0|1 → disable/enable Jupyter kernel registration (default: 1).
USER_ENV_YAML=<path> → provide YAML path via environment variable.

📊 Diagnostics#

At the end of the run, the script prints:

Python version inside the environment.
Installed versions of numpy and pandas.
Available OpenMM platforms (if OpenMM is installed).

✅ Summary#

Use --mode print for setup only (manual activation).
Use source ... --mode persist for setup + activation.
Override Python version with --python <version>.
Script auto-detects YAML path regardless of where it is called from.

This script ensures a consistent, reproducible, and editable development environment for MolSysMT.