scikit-surgery

https://github.com/UCL/scikit-surgery/raw/master/project-icon.png Travis CI test status Test coverage Documentation Status

SciKit-Surgery is part of the SciKit-Surgery image guided surgery software project, developed at the Wellcome EPSRC Centre for Interventional and Surgical Sciences, part of University College London (UCL).

scikit-surgery is a meta-package that will install several other packages:

Installing

You can install the latest version from PyPI:

pip install scikit-surgery

Developing

Cloning

You can clone the repository using the following command:

git clone https://github.com/UCL/scikit-surgery

Running the tests

You can run the unit tests by installing and running tox:

pip install tox
tox

Encountering Problems?

Please check list of common issues.

Contributing

Please see the contributing guidelines.

Acknowledgements

Supported by Wellcome and EPSRC.

Requirements for scikit-surgery

This is the software requirements file for scikit-surgery, part of the SNAPPY project. The requirements listed below should define what scikit-surgery does. Each requirement can be matched to a unit test that checks whether the requirement is met.

Requirements

ID Description Unit test
0000 Module has a help page  
0001 Functions are documented  
0002 Package has a version number  

Get started with PyCharm

PyCharm is a popular python editor. This is a quickstart guide setting up PyCharm for developing sksurgery. This assumes you have PyCharm installed and configured to support virtual environments.

  1. Start PyCharm
  2. Select File > Open
  3. Select the project’s folder
  4. Open in a new window
  5. Open Preferences
  6. Click on Project: [YourProject] and select Project Interpreter
  7. At the right of the Project Interpreterm, click the cog
  8. Select Add Local…
  9. Select Virtual Environment
  10. Choose a location for your virtual environment (for example, [YourHomeFolder]/VirtualEnvs/[YourProjectName])
  11. Select a base interpreter (usually the latest version of Python 3).
  12. Recommended settings: Do not inherit global site-packages, and do not make available to all projects.
  13. Click OK
  14. Click on Terminal
  15. pip install tox
  16. tox
  17. Expand the project
  18. Right-click on the Tests folder and choose “Run Unittests in tests”. This will create a new configuration for running tests
  19. Right-click on sksurgery and select Run sksurgery. This will create a new configuration for running the project.
  20. Switch between the program and test configurations using the drop-down at the top of the screen, and the green arrow to run or the green bug to debug.