pySBOL2 is a pure Python implementation of the SBOL standard Synthetic Biology Open Language (SBOL) - an open standard for the representation of in silico biological designs. It draws from libSBOL and pySBOL.
We recommend installing with a virtual environment.
Please note that this project uses
git submodules,
so please use the --recurse-submodules option when cloning.
# Create and activate the virtual environment
python3 -m venv sbol2env
source sbol2env/bin/activate
pip install -U pip
# Clone and install pySBOL2
git clone --recurse-submodules https://github.com/SynBioDex/pySBOL2.git
cd pySBOL2
pip install -e .You should now be able to run the unit tests in the test directory:
python3 -m unittestNOTE: files required to run the tests are in a git submodule test/SBOLTestSuite. These get downloaded if you clone the repo with --recurse-submodules https://github.com/SynBioDex/pySBOL2.git. If you have not, you can download them with git submodule update --init from the project root directory.
We use pycodestyle for our coding guidelines. pycodestyle
follows PEP8. Please ensure that any contributions pass pycodestyle
with a max line width of 90 characters.
If you are a developer, please run ./dev/bootstrap.sh to set up the pre-commit hooks.
This will ensure that unit tests and style checking is performed before each commit.
