Sire

Note

Sire is now supported and maintained by OpenBioSim and is available through their GitHub organisation. This repository will only be maintained for legacy development work, with bug-fixes back-ported periodically. Developers can update their remote to point to the new location.

About

Sire is a molecular modelling framework that provides extensive functionality to manipulate representations of biomolecular systems.

It is used as a key component of BioSimSpace, and is distributed and supported as an open source community project by OpenBioSim.

For more information about how to use Sire, and about application built with Sire, please visit the Sire website.

Installation

The easiest way to install Sire is using our conda channel. Sire is built using dependencies from conda-forge, so please ensure that the channel takes strict priority. We recommend using mambaforge.

To create a new environment:

mamba create -n openbiosim python==3.9
mamba activate openbiosim
mamba install -c openbiosim sire

To install the latest development version you can use:

mamba create -n openbiosim-dev python==3.9
mamba activate openbiosim-dev
mamba install -c openbiosim/label/dev sire

However, as you are here, it is likely you want to download the latest, greatest version of the code, which you will need to compile. To compile sire, you need a git client to download the source, and a working internet connection (needed by the sire compilation scripts to download additional dependencies).

First, you need to create and activate a conda environment, e.g.

mamba create -n openbiosim-dev python==3.9
mamba activate openbiosim-dev

Next, you need to install the Sire build dependencies.

mamba install cmake pip-requirements-parser

You will also need to install compilers, e.g. on Linux use

mamba install gcc gxx

on MacOS use

mamba install clang clangxx

and on Windows use

mamba install conda-build

Next, you can clone the Sire source code and compile and install Sire:

git clone https://github.com/OpenBioSim/sire
cd sire
python setup.py install

A small word of warning, the compilation can easily take over an hour!

The above will compile sire in your existing conda environment.

If you plan to build BioSimSpace on top of sire, then you will need to resolve BioSimSpace's dependencies at the time sire is installed to ensure that it is built in a self-consistent way. This can be achieved as follows:

python setup.py --install-bss-deps install

Support and Development

Bugs, Comments, Questions

For bug reports/sugguestions/complains please file an issue on GitHub.

Developers guide

Please visit the website for information on how to develop applications using sire.

GitHub actions

Since sire is quite large, a build can take quite long and might not be neccessary if a commit is only fixing a couple of typos. Simply add ci skip to your commit message and GitHub actions will not invoke an autobuild.

Note that every time you commit to devel, it will trigger a build of sire, full testing, construction of a Conda package and upload to our Anaconda channel. Please think twice before committing directly to devel. You should ideally be working in a _feature_ branch, and only commit to devel once you are happy the code works on your branch. Use ci skip until you are happy that you want to trigger a full build, test and deployment. This full pipeline will take several hours to complete.

Have fun :-)