biosimspace
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An interoperable Python framework for biomolecular simulation.
BioSimSpace <https://biosimspace.openbiosim.org>
__
.. image:: https://github.com/openbiosim/biosimspace/workflows/Build/badge.svg :target: https://github.com/openbiosim/biosimspace/actions?query=workflow%3ABuild) :alt: Build status
.. image:: https://anaconda.org/openbiosim/biosimspace/badges/downloads.svg :target: https://anaconda.org/openbiosim/biosimspace :alt: Conda Downloads
.. image:: https://img.shields.io/badge/License-GPL%20v3-blue.svg :target: https://www.gnu.org/licenses/gpl-3.0.html :alt: License
.. image:: https://joss.theoj.org/papers/4ba84ad443693b5dded90e35bf5f8225/status.svg :target: https://joss.theoj.org/papers/4ba84ad443693b5dded90e35bf5f8225 :alt: Paper
About
BioSimSpace <https://biosimspace.openbiosim.org>
__ is an interoperable Python framework
for biomolecular simulation. With it you can:
- Write robust and portable biomolecular workflow components that work on
different hardware, with different software packages, and that can be
run in different ways, e.g. command-line,
Jupyter <https://jupyter.org>
__. - Start, stop, and monitor molecular simulation processes within interactive Python environments.
Citation |DOI for Citing BioSimSpace|
If you use BioSimSpace in any scientific software, please cite the following paper: ::
@article{Hedges2019,
doi = {10.21105/joss.01831},
url = {https://doi.org/10.21105/joss.01831},
year = {2019},
publisher = {The Open Journal},
volume = {4},
number = {43},
pages = {1831},
author = {Lester Hedges and Antonia Mey and Charles Laughton and Francesco Gervasio and Adrian Mulholland and Christopher Woods and Julien Michel},
title = {BioSimSpace: An interoperable Python framework for biomolecular simulation},
journal = {Journal of Open Source Software}
}
.. |DOI for Citing BioSimSpace| image:: https://joss.theoj.org/papers/4ba84ad443693b5dded90e35bf5f8225/status.svg :target: https://joss.theoj.org/papers/4ba84ad443693b5dded90e35bf5f8225
Documentation
Full documentation can be found here <https://biosimspace.openbiosim.org>
__.
Installation
Conda package ^^^^^^^^^^^^^
The easiest way to install BioSimSpace is using our conda channel <https://anaconda.org/openbiosim/repo>
.
BioSimSpace is built using dependencies from conda-forge <https://conda-forge.org/>
,
so please ensure that the channel takes strict priority. We recommend using
Miniforge <https://github.com/conda-forge/miniforge>
__.
To create a new environment:
.. code-block:: bash
conda create -n openbiosim -c conda-forge -c openbiosim biosimspace
conda activate openbiosim
To install the latest development version you can use:
.. code-block:: bash
conda create -n openbiosim-dev -c conda-forge -c openbiosim/label/dev biosimspace
conda activate openbiosim-dev
When updating the development version it is generally advised to update Sire <https://github.com/openbiosim/sire>
_
at the same time:
.. code-block:: bash
conda update -c conda-forge -c openbiosim/label/dev biosimspace sire
Unless you add the required channels to your Conda configuration, then you'll need to add them when updating, e.g., for the development package:
.. code-block:: bash
conda update -c conda-forge -c openbiosim/label/dev biosimspace
Installing from source ^^^^^^^^^^^^^^^^^^^^^^
Alternatively, to install BioSimSpace from source:
(Before starting, you'll need a working Git <https://git-scm.com>
__ installation.)
BioSimSpace is built on top of the Sire <https://github.com/openbiosim/sire>
__
molecular simulation framework. To download and install Sire, follow the
instructions here <https://github.com/openbiosim/sire#installation>
__, making
sure that BioSimSpace's dependencies are installed into the Sire conda
environment at the point at which Sire is installed.
Next you will need to download BioSimSpace and install it into your Sire Conda environment.
.. code-block:: bash
git clone https://github.com/openbiosim/biosimspace cd biosimspace/python python setup.py install
If you plan to develop and want an editable install, use:
.. code-block:: bash
python setup.py develop
If you want to skip the installation of BioSimSpace dependencies, e.g. if they are already installed, then you can use:
.. code-block:: bash
BSS_SKIP_DEPENDENCIES=1 python setup.py develop
Once finished, you can test the installation by running:
.. code-block:: bash
python
Then try importing the BioSimSpace package:
.. code-block:: python
import BioSimSpace as BSS
If you don't want to install Sire from source, an alternative is to create a conda environment containing only the dependencies of BioSimSpace, then install the latest development code into that.
.. code-block:: bash
conda create -n openbiosim-dev -c conda-forge -c openbiosim/label/dev biosimspace --only-deps conda activate openbiosim-dev git clone https://github.com/openbiosim/biosimspace cd biosimspace/python BSS_SKIP_DEPENDENCIES=1 python setup.py develop
(You may also want to install optional dependencies, such as ambertools
and
gromacs
into your environment.)
Developers
Please follow the developer's guide <https://biosimspace.openbiosim.org/contributing>
__.
Issues
Please report bugs and other issues using the GitHub issue tracker <https://github.com/openbiosim/biosimspace/issues>
__.
When reporting issues please try to include a minimal code snippet that reproduces
the problem. Additional files can be also be uploaded as an archive, e.g. a zip
file. Please also report the branch on which you are experiencing the issue,
along with the BioSimSpace version number. This can be found by running:
.. code-block:: python
import BioSimSpace as BSS print(BSS.version)