Step 1: The SNAPPY Python Templates uses cookiecutter to generate a project from a templates. Start by checking you have cookiecutter installed
pip install cookiecutter
Step 2: Use the Python Template to create your new project. This tutorial uses a sphere fitting algorithm as an example case, as it strikes a nice balance between simplicity and usefulness. Fitting models to data is a key part of medical image computing, so hopefully the user can see how their own algorithms could be inserted into the software template.
If that doesn’t work try,
python -m cookiecutter https://weisslab.cs.ucl.ac.uk/WEISS/SoftwareRepositories/PythonTemplate.git
Follow the prompts, we should call our project something descriptive, so if you’re doing sphere fitting:
project_name [My New Project]: scikit-surgery-sphere-fitting project_slug [scikit-surgery-sphere-fitting]: sksurgeryspherefitting project_description [scikit-surgery-sphere-fitting is a Python package]: scikit-surgery-sphere-fitting implements a least squares sphere fitting algorithm, to read a vtk poly data file, a config file, and outputs the fitted sphere pkg_name [sksurgeryspherefitting]: Select repository_server: 1 - https://weisslab.cs.ucl.ac.uk 2 - https://cmiclab.cs.ucl.ac.uk 3 - https://github.com 4 - https://gitlab.com Choose from 1, 2, 3, 4 (1, 2, 3, 4) : full_name [Your Name]: Stephen Thompson repository_profile_name [StephenThompson]: Select repository_path: 1 - StephenThompson/sksurgeryspherefitting 2 - WEISS/SoftwareRepositories/sksurgeryspherefitting 3 - WEISS/SoftwareRepositories/SNAPPY/sksurgeryspherefitting Choose from 1, 2, 3 (1, 2, 3) : project_url [https://weisslab.cs.ucl.ac.uk/StephenThompson/sksurgeryspherefitting]: Select open_source_license: 1 - BSD-3 license 2 - Apache Software License 2.0 3 - MIT License Choose from 1, 2, 3 (1, 2, 3) :
Enter the source directory and initialise git repository.
cd sksurgeryspherefitting/ git init git add . git commit -m "Initial commit of my sphere fitter"
Create a new project on WeissLab (or GitLab, GitHub or your preferred git host), making sure the URL matches what you set in step 3.
Add the remote to git and push your first commit
git remote add origin https://weisslab.cs.ucl.ac.uk/StephenThompson/scikit-surgery-sphere-fitting.git git push origin master
Visit the web interface to WEISSLab and checkout out your first commit
You may notice that it says that your commit failed. This refers to the continuous integration test having failed, not that your project was lost. By the end this tutorial you will have a green tick where now there is a red cross, for know though, don’t worry.