PLEIADES

PLEIADES' user documentation

PLEIADES: Python Libraries Extensions for Isotopic Analysis via Detailed Examination of SAMMY. This is a Python package that sets up, executes, and analyzes, SAMMY runs. If you are unfamiliar with SAMMY, please see the SAMMY website.

The user documentation can be found at Read the Docs.

Installation

Prerequisites:

• git: A version control system used to clone the SAMMY repository. You can usually install it using your system's package manager.
• pip: A package installer for Python. You can usually install it using your system's package manager.

Steps:

1. Clone and build the SAMMY Repository:

   Use git to clone the SAMMY repository from GitLab:

   git clone https://code.ornl.gov/RNSD/SAMMY.git

2. Build and Install SAMMY:

   Navigate to the cloned SAMMY directory (SAMMY/sammy) and follow the SAMMY installation instructions to build and install it. Refer to the SAMMY documentation for specific instructions.

   cd SAMMY/sammy
   mkdir myscript
   cp script/configure_sammy_gcc.sh myscript/
   mkdir build
   cd build
   ../myscript/configure_sammy_gcc.sh ../
   make -j4
   make install

3. Verification (Optional):

   Open a new terminal window and check if the SAMMY executables are accessible. You can try running a SAMMY command, such as sammy. If successful, the command should execute.

4. Clone the PLEIADES Repository:

   Use git to clone the pleiades repository from GitHub:

   git clone https://github.com/along4/Pleiades

5. Navigate to the Directory:

   Change directories to the cloned pleiades repository:

   cd Pleiades

6. Install the Package:

   Use pip to install the pleiades package:

   pip install -e .

   Alternatively, you can use poetry to install the package. First, install poetry using the following command:

   pip install poetry

   Use poetry to install the pleiades package:

   poetry install

   Then run the following command to perform the post-installation check after sammy is installed:

   poetry run post_install_check

   Using Poetry is recommended for managing dependencies and virtual environments, especially if you are working with multiple Python projects sharing the same base Python installation.

7. Add SAMMY's bin Directory to PATH:

   You'll need to add the bin directory of the installed SAMMY package to your system's PATH environment variable. This allows pleiades to locate the necessary SAMMY executables.

   • Open your terminal and edit your shell configuration file (e.g., .bashrc for Bash).

   • Add the following line (replace <SAMMY_INSTALL_DIR> with the actual installation directory of SAMMY):

     export PATH=$PATH:<SAMMY_INSTALL_DIR>/bin

   • Save the changes and source the configuration file to apply the changes immediately:

     source ~/.bashrc  # Replace with your shell configuration file name

Troubleshooting:

• If you encounter issues during the SAMMY installation or path configuration, refer to the SAMMY documentation for specific guidance.

Additional Notes:

• You can uninstall pleiades using pip uninstall pleiades.

License

This project is licensed under the MIT License - see the LICENSE file for details.