Installation

Independently of how you install asyncmd you will need a working installation of GROMACS and, if you want to submit jobs via the queuing system, SLURM on the machine you install asyncmd.

pip install from PyPi

asyncmd is published on PyPi (since v0.3.2), installing is as easy as:

pip install asyncmd

pip install directly from the repository

In case you you intend to run the tests or example notebooks yourself or if want to install the latest and greatest development version of asyncmd (see the changelog for whats new) you will need to install asyncmd from the git repository.

This will clone the repository to the current working directory and install asyncmd into the current python environment:

git clone https://github.com/bio-phys/asyncmd.git
cd asyncmd
pip install .

Tests

Tests use pytest. To run them you can install asyncmd with the tests requirements. All tests should either pass or be skipped.

This will clone the repository to the current working directory and install asyncmd with the tests requirement into the current python environment:

git clone https://github.com/bio-phys/asyncmd.git
cd asyncmd
pip install .\[tests\]
# or use
pip install .\[tests-all\]
# to also install optional dependencies needed to run all tests

you can then run the tests (against the installed version) as

pytest
# or use
pytest -v
# to get a more detailed report

Note

Previously some of the files needed to run the tests were stored with git-lfs. This means that if you want to checkout an old commit of asyncmd and run the tests against it, you will need to have git-lfs installed.

Documentation

Note

Use pip install .\[docs\] to install the requirements needed to build the documentation.

The documentation can be build with sphinx, use e.g. the following to build it in html format:

cd asyncmd  # Need to be at the top folder of the repository for the next line to work
sphinx-build -b html docs/source docs/build/html

The documentation is located in the docs/source/ folder and (mostly) written in MyST markdown. MyST-NB and the sphinx-book-theme are needed to build the documentation and include the example notebooks into it.

Developer installation

If you intend to contribute to asyncmd, it is recommended to use the dev extra and use an editable install to enable you to directly test your changes:

git clone https://github.com/bio-phys/asyncmd.git
cd asyncmd
pip install -e .\[dev\]

This will, in addition to the requirements to run the tests and to build the documentation, install jupyterlab such that you can easily contribute to the example notebooks. It will also install coverage and its pytest-cov plugin such that you have an idea of the test coverage for your newly added code. To get a nice html coverage report you can run the tests as

pytest --cov=asyncmd --cov-report=html