Code cleanup and refactoring

[agitter]

Work in progress pull request for #76. I'll edit this to add details when it's ready for review.

[agitter]

The scope of this pull request is large enough so I'm going to stop here. This closes #76 even though it does not add pre-commit hooks. Reviewing the commit messages is the best way to get an overview of the changes made. To summarize:

• Closes proposed change to src code organization #7 by moving all *.py files out of the top level of the repository into appropriate subdirectories and removing an unnecessary level of analysis subdirectories
• Following Python file naming conventions for *.py files and refactoring code accordingly
• Closes candidate files to remove #6 by deleting the old prototype files. They are interesting relics of old design ideas, but they will confuse new contributors and clutter the repository. Also removes the docker-demo for the same reason and should also close Clean up non-functional components #29.
• Closes Switch pathway output format to tab-separated text #75 by switching the universal output pathway file format to tab-separated and adding an example of nodes with spaces in the names for the ML analysis testing.
• Other code factoring to address Python linting issues.

@ntalluri can you please review these changes? Some affect your ML code, and you also have a good sense of how all of the SPRAS components work together.

@annaritz you don't need to do a full review but could quickly browse the summary above and commit messages to make sure you don't object to any changes.

[ntalluri]

I had to update the test files to work with the version 2 code so directory names are different to make it work with the updated ml code

[ntalluri]

I can manually tab separate these files once these changes are added

[ntalluri]

can keep this, I can just update the names to work with the new code that is used in version 2

[ntalluri]

I can update the tab seperated part on my end since I had to change names that are in this file for version2

[annaritz]

This all looks great to me! Thanks @agitter and @ntalluri for tying up these loose ends.

[agitter]

@ntalluri and I discussed her review comments during our meeting today. These changes will create conflicts with her work in #80. Our plan is to merge this during our next meeting and clean up the merge conflicts together.