README
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Introduction Following application is a Django web page that helps the user to generate valid SBML short. The main motivation for its development is the difficulty to produce valid SBML when its write in a text editor. The program has two main parts a Django application in the package SBMLsite and a sbml class in the SBMLshort package, which defines classes that could be used to store and represent a SML short model. Django website provides a set of forms on different subpages that could be used to create, store and edit instances of classes defined in SBMLshort. SBMLshort classes are store in a file based session using pickling.
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Development and Version control During the development, git was used for version control in a local repository and a remote repository on github (https://github.com/alex-steinke/sbml). I was using the branching model described in the following article http://nvie.com/posts/a-successful-git-branching-model/ with main master branch for release, development branch and multiple feature branches, which were merged back into development after completion of the feature. The program was developed in a Docker container and could be deployed using the provided Dockerfile. To run the application following command could be used: docker run -d -p 127.0.0.1:8000:8000 sbml bash -c "python /opt/sbml/manage.py runserver 0.0.0.0:8000" If the application is installed without Docker some additional python pakages have to be installed according to the pip install line in the Dockerfile.
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Testing For testing, I was using nose testing suite and flake8. Because the program could be deployed using Docker I was able to run the tests using travis-ci service after commits. So far only SBMLshort classes were tested.
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Use After the installation, the user can access the website and define a new SBML model, add and change parameters and generate a valid SBML short.
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To do Because I run out of time, I had to make a simplified version of Species and Reactions that could be extended. For example, the user should be able to pick from existing species and parameter when defining Reactions and from existing compartments when defining Species. Also testing could be improved adding Django form tests. Validation could be extended and Views should be changed so that each view deals just with one type of request, like creation or update.
(References: For design, I was using Bootstrap)
Sry, run out of time, so most of comments are missing.