scalems 0.0.1

Reference implementation of the SCALE-MS data flow scripting and graph execution API for molecular science computational research protocols.

SCALE-MS

[DockerHub]

NSF Awards

• 1835449 Matteo Turilli, Rutgers University New Brunswick
• 1835607 Kristen Fichthorn, Pennsylvania State University
• 1835720 Michael Shirts, University of Colorado at Boulder
• 1835780 Peter Kasson, University of Virginia

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Git

This project is managed with a git repository hosted at https://github.com/SCALE-MS/scale-ms

Test data submodule

Data for some examples and tests is stored in a separate testdata repository, but the external repository is embedded as a git submodule for convenience. (testdata/) This fact should be uninteresting to most readers, but if you need the extra files, you will appreciate the convenience of a couple of extra arguments available to git commands.

• When cloning this repository, use the --recursive argument to git clone.
• When updating a local copy of this repository, use the --recurse-submodules argument to git pull or git checkout.

Documentation

Refer to https://scale-ms.readthedocs.io/en/latest/ for the most up-to-date documentation.

To build the documentation locally, clone this repository and go to the root directory of the local repository, then

1. Install Sphinx and additional requirements: pip install -r docs/requirements.txt
2. Install the scalems package so that Sphinx can import it when run: pip install .
3. Optionally, install plantuml for rendering diagrams. (e.g. on Ubuntu, do sudo apt-get install plantuml)

Build with Sphinx using the docs/conf.py file in this repository.

Example

From the root of a local copy of the repository, build HTML documentation for the scalems package into a new ./web directory (or some directory of your choosing). ./docs is the input directory.

python3 -m sphinx docs web -b html

Then open ./web/index.html

Note: Depending on your Sphinx installation, you may have a sphinx-build executable or you may access the sphinx module with the -m Python interpreter option (python -m sphinx ...).