Welcome to the SEAMM Util documentation!
This is documentation for developers! There is nothing here for users, since this is part of the underlying framework of SEAMM. Anything a users sees is documented either in the main SEAMM documentation or in the plug-in documentation.
Contents:
SEAMM Util
Utility classes and functions that support other SEAMM tools
Free software: BSD license
Documentation: https://seamm-util.readthedocs.io.
Features
TODO
Credits
This package was created with Cookiecutter and the molssi-seamm/cookiecutter-seamm-plugin project template.
Developed by the Molecular Sciences Software Institute (MolSSI), which receives funding from the National Science Foundation under awards OAC-1547580 and CHE-2136142
Installation
Stable release
Some of the requirements to run the SEAMM framework cannot be automatically installed using e.g. pip but can be using Conda Forge. Please use the SEAMM installer to install this module and the other core modules that comprise SEAMM.
From sources
The sources for SEAMM Util can be downloaded from the Github repo.
You can either clone the public repository:
$ git clone git://github.com/molssi-seamm/seamm_util
Or download the tarball:
$ curl -OL https://github.com/molssi-seamm/seamm_util/tarball/master
Once you have a copy of the source, you can install it with:
$ python setup.py install
or more simply:
$ make install
make or make help will provide a list of all the targets.:
$ make
make
clean remove all build, test, coverage and Python artifacts
clean-build remove build artifacts
clean-pyc remove Python file artifacts
clean-test remove test and coverage artifacts
lint check style with black and flake8
format reformat with with yapf and isort
typing check typing
test run tests quickly with the default Python
test-all run tests on every Python version with tox
coverage check code coverage quickly with the default Python
docs generate Sphinx HTML documentation, including API docs
servedocs compile the docs watching for changes
release package and upload a release
dist builds source and wheel package
install install the package to the active Python's site-packages
uninstall uninstall the package
$
Typically it is a good idea to check the formatting of your changes using black and flake8 which is what the lint target does, e.g.:
$ make lint install
Usage
To use SEAMM Util in a project:
import seamm_util
Contributing
Contributions are welcome, and they are greatly appreciated! Every little bit helps, and credit will always be given.
You can contribute in many ways:
Types of Contributions
Report Bugs
Report bugs at https://github.com/molssi-seamm/seamm_util/issues.
If you are reporting a bug, please include:
Your operating system name and version.
Any details about your local setup that might be helpful in troubleshooting.
Detailed steps to reproduce the bug.
Fix Bugs
Look through the GitHub issues for bugs. Anything tagged with “bug” and “help wanted” is open to whoever wants to implement it.
Implement Features
Look through the GitHub issues for features. Anything tagged with “enhancement” and “help wanted” is open to whoever wants to implement it.
Write Documentation
SEAMM Util could always use more documentation, whether as part of the official SEAMM Util docs, in docstrings, or even on the web in blog posts, articles, and such.
Submit Feedback
The best way to send feedback is to file an issue at https://github.com/molssi-seamm/seamm_util/issues.
If you are proposing a feature:
Explain in detail how it would work.
Keep the scope as narrow as possible, to make it easier to implement.
Remember that this is a volunteer-driven project, and that contributions are welcome :)
Get Started!
Ready to contribute? Here’s how to set up seamm_util for local development.
Fork the seamm_util repo on GitHub.
Clone your fork locally:
$ git clone git@github.com:your_name_here/seamm_util.git
Install your local copy into a virtualenv. Assuming you have virtualenvwrapper installed, this is how you set up your fork for local development:
$ mkvirtualenv seamm_util $ cd seamm_util/ $ python setup.py developCreate a branch for local development:
$ git checkout -b name-of-your-bugfix-or-feature
Now you can make your changes locally.
When you’re done making changes, check that your changes pass flake8 and the tests, including testing other Python versions with tox:
$ flake8 seamm_util tests $ python setup.py test or py.test $ toxTo get flake8 and tox, just pip install them into your virtualenv.
Commit your changes and push your branch to GitHub:
$ git add . $ git commit -m "Your detailed description of your changes." $ git push origin name-of-your-bugfix-or-featureSubmit a pull request through the GitHub website.
Pull Request Guidelines
Before you submit a pull request, check that it meets these guidelines:
The pull request should include tests.
If the pull request adds functionality, the docs should be updated. Put your new functionality into a function with a docstring, and add the feature to the list in README.rst.
The pull request should work for Python 2.6, 2.7, 3.3, 3.4 and 3.5, and for PyPy. Check https://travis-ci.org/molssi-seamm/seamm_util/pull_requests and make sure that the tests pass for all supported Python versions.
Tips
To run a subset of tests:
$ py.test tests.test_seamm_util
Credits
Development Lead
Paul Saxe <psaxe@molssi.org>
Contributors
None yet. Why not be the first?
History
- 2023.6.4 – Added more unit conversions to support thermochemistry
added E_h/K –> kJ/mol/K
- 2023.4.6 – Added more unit conversions to support Buckingham potentials
added e.g. eV*Å^6 to kcal/mol*Å^6 to support Buckingham pontetials
- 2023.2.28 – Added a compact JSON encoder
To make the schema-type JSON more human-readable.
- 2022.11.3 – More conversions involving substance (mol) to number
Added energy/mol/Å^2 –> energy/Å^2 for force constants
Added energy/mol/Å^3 –> energy/Å^3 for stress/pressure/elastic constants
- 0.1.0 (2017-12-07)
First release on PyPI.