Streamline Your Workflows with SAMSON’s Python Package Manager

One of the common challenges for molecular modelers and researchers is efficiently managing Python packages for their computational workflows. Whether you’re integrating tools for bioinformatics, deep learning, or data analysis, a seamless handling of Python packages can make or break your productivity. Fortunately, SAMSON’s integrated Python Package Manager provides a straightforward solution to manage Python packages directly within the platform.

Why Python Package Management is Crucial

Modelers often require a dynamic environment where various Python packages can work hand-in-hand with their molecular modeling workflows. Standard tools like pip are effective but managing packages within a separate terminal, switching between environments, and troubleshooting dependencies can become cumbersome. The Python Package Manager in SAMSON is designed to simplify this process by providing an easy-to-use interface embedded in the platform itself.

Getting Started with the Python Package Manager

To manage your Python packages, follow these steps:

  • In the SAMSON Python Console, navigate to Edit > Manage packages… to open the Python Package Manager window.

Manage packages...

From this window, you can:

  • View all installed packages and their versions.
  • Install new packages from PyPI or local directories.
  • Uninstall packages you no longer need.

Installing Python Packages

Installing a package is as simple as typing its name in the provided input field and clicking Install. Additionally, you can specify package versions or add flags like --upgrade. For example:

  • numpy==1.21.2 installs version 1.21.2 of NumPy.
  • pandas --upgrade updates Pandas to the latest version.

Package Manager: install a Python package

Installing Local Python Packages

If you have a local Python package you’d like to install—such as one you’re actively developing—you can specify its path and install it. You also have the option to install it in editable mode, equivalent to using pip install -e. This makes it easy to test and modify the package’s code without needing to reinstall it.

Package Manager: install a local Python package

Do note that on macOS, editable installations may not always persist between launches. If you encounter issues, you may need to reinstall the package or use non-editable mode and register package paths in sys.path.

Uninstalling Python Packages

Uninstalling packages is just as straightforward. Enter the package name in the input field and click Uninstall. This works for both PyPI and local packages.

Enhance Your Molecular Modeling Experience

SAMSON’s Python Package Manager ensures that you can effortlessly manage dependencies directly within the platform, enabling smoother workflows and faster iterations. By consolidating scripting, package management, and molecular modeling into one interface, this feature removes the need to juggle multiple tools.

For a deeper dive, refer to the official documentation page on Python Scripting in SAMSON.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. To get SAMSON, visit SAMSON Connect.

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