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.
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:
Clone and build the SAMMY Repository:
Use git to clone the SAMMY repository from GitLab:
git clone https://code.ornl.gov/RNSD/SAMMY.git
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
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.
Clone the PLEIADES Repository:
Use git to clone the pleiades repository from GitHub:
git clone https://github.com/along4/Pleiades
Navigate to the Directory:
Change directories to the cloned pleiades repository:
cd Pleiades
Install the Package:
Use pip to install the pleiades package:
pip install -e .
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.
This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.