pleiades-neutron 2.1.5

PLEIADES - Python Libraries Extensions for Isotopic Analysis via Detailed Examination of SAMMY

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

For Users:

Install from PyPI:

pip install pleiades-neutron

Or from conda-forge:

conda install -c conda-forge pleiades-neutron

For Developers:

Prerequisites:

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

• pixi: A package installer for Python that manages environments and dependencies. You can install it following the instructions at Pixi Installation.

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/lanl/PLEIADES.git

5. Navigate to the Directory:

   Change directories to the cloned PLEIADES repository:

   cd PLEIADES

6. Install Using Pixi:

   Use pixi to create and activate the development environment:

   pixi install

   This will install all required dependencies in an isolated environment and activate it.

   You can run the post-installation check after SAMMY is installed:

   pixi run post_install_check

   Pixi manages all dependencies and environments for you, making it easy to work with PLEIADES alongside other Python projects.

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

8. Development Tasks (Optional):

   PLEIADES provides several convenient development tasks through Pixi:

   # Run tests
   pixi run test
   
   # Build documentation
   pixi run build-docs
   
   # Format code
   pixi run format
   
   # Run linting checks
   pixi run lint
   
   # Install pre-commit hooks
   pixi run pre-commit-install

Troubleshooting:

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

• For Pixi-related issues, check the Pixi documentation.

Additional Notes:

• Two environments available: default (development) and jupyter (notebook work). Use pixi shell -e jupyter to activate jupyter environment.

• See available tasks: pixi task list

License

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