Installation

pySBOL2 is a pure Python package and is available on any platform that supports Python. pySBOL2 requires Python 3.6 or higher, and can be installusing using pip

Note

Python 2 is not supported.

Install the current release

To install the latest release of pySBOL2 using pip, execute the following line in a console or terminal:

pip install sbol2

If you encounter permission errors, you may want to install pySBOL2 to your user site-packages directory as follows:

pip install sbol2 --user

Or alternatively, you may install as a super-user (on Unix-like platforms):

sudo pip install sbol2

To update pySBOL2 using pip, run:

pip install -U sbol2

Install the latest from GitHub

You can also install the latest version from GitHub. This might be appropriate for you if you need a specific feature or bug fix that has been fixed in git and not yet been incorporated into a release. Please exercise caution though, the latest version might also contain new bugs.

python3 -m pip install git+https://github.com/synbiodex/pysbol2

For developers

  1. Clone the repository using git:

$ git clone --recurse-submodules https://github.com/SynBioDex/sbol2.git

  1. Install pySBOL2 using the setup.py file:

$ cd sbol2
$ python setup.py install

  1. Test the installation by importing it in a Python interpreter:

$ python3
Python 3.8.0 (v3.8.0:fa919fdf25, Oct 14 2019, 10:23:27)
[Clang 6.0 (clang-600.0.57)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import sbol2
RDFLib Version: 5.0.0
>>> sbol2.__version__
'1.0'

Note

Your version number may be different than the version number displayed above.

  1. Optionally run the unit test suite:

$ python3 -m unittest discover -s test

Note

The unit tests take several minutes to run. You may see some deprecation warnings which can be ignored.

Installing on macOS

Macs do not ship with Python 3 so it is necessary to download and install Python 3 before installing pySBOL2. You can download the latest Python 3 release from python.org. After Python 3 is installed please follow the instructions above to install pySBOL2.

Using PyPy

PyPy is “a fast, compliant alternative implementation of Python.” PyPy uses a just-in-time compiler (JIT), which can make certain programs faster.

pySBOL2 uses RDFlib which can be slow for reading and writing SBOL files when compared to a C implementation like Raptor .

Programs that might benefit from PyPy’s JIT are programs that have longer runtimes and repeat tasks. A program that iterates over a directory reading each SBOL file, modifying the contents, and then writing the file is a good example of a program that might benefit from PyPy’s JIT. On the other hand a program that reads or writes a single file is an example of a program that would probably not benefit from PyPy because the JIT complier doesn’t have a chance to optimize the code.

pySBOL2 is compatible with PyPy. The installation and use of PyPy is out of scope for this document. Please see the PyPy documentation if you want to try using PyPy with pySBOL2.