Installation

Before installing MISPR, you need to follow the steps below in order:

  1. (Optional) Create a Conda environment

  2. Make sure you have access to the computational chemistry software dependencies needed to run the DFT and MD simulations

  3. Install python package dependencies

  4. Set up MongoDB database

  5. Install MISPR

  6. Prepare the configuration files

  7. Run a test workflow

Note

Throughout the installation instructions, it is assumed that you are familiar with Python and with basic Linux shell commands. If not, Linux Journey and Python For Beginners are some recommended starting points.

Installing MISPR

MISPR can be installed either from the python package index (good for most users) or directly from its GitHub repository (good for developers).

Installation Method 1: Using pip

For most users, install directly from PyPI:

pip install mispr

Installation Method 2: Development mode

For developers or users who need to modify the source code, install MISPR in development mode.

Note

If you had already installed MISPR via pip or conda, you should uninstall that first before starting the installation in development mode. This ensures that you will not have any conflicts resulting from two different code installations.

The steps for installing the package in development mode are below.

  1. Activate your conda environment or virtual environment

  2. Create a codes directory in |CODES_DIR|

  3. cd to your newly created |CODES_DIR|/codes directory

  4. Clone the package you want to install in development mode using git:

    git clone https://github.com/molmd/mispr.git

    Now you should have mispr directory in your codes directory.

  5. cd into the mispr directory and run pip install -e . or use the conda equivalent. Once installed, if you make changes to the code, the changes will take effect immediately without having to reinstall the package.

Post-installation

  1. Before you go any further, confirm your package installations are correct. First start IPython by typing ipython in your terminal, then confirm that the command import mispr executes without any errors

  2. To update the mispr code later on, execute git pull followed by pip install -e . or the conda equivalent in the mispr directory. If you installed via pip, you can simply execute pip install --upgrade mispr.