Final submission

[JessvLS]

Hi John, sorry there are several branches, but it started to get messy as we worked on the final product. The latest, most complete version of a package we have is under the "final" branch. As far as testing, many of these dependencies in the environment were more complex than we were familiar with, and some were not written in python. We did make an effort to include the tests and modify the examples of tests for each dependency we could find. As per our original plan, we just wanted to manipulate preexisting code to make it display what we wanted. We outline in the README what we wanted to change, which involved a lot of manipulation of the csv and json files and less of the python code itself. Nevertheless, minor changes were made to a couple .py files in an effort to get the amplicons mapping to references better. Hopefully that demonstrates at least a tiny bit of the coding we learned, which may have been easier to show had we made our own code from the start. Even still, the class and datacamp made reading this code and understanding what needed to be changed a lot easier than before we delved into it. That sort of knowledge may not be entirely apparent in this project, so we demonstrated it to the best of our ability. Thanks for teaching the class!

[leej3]

No worries. I'll look through and give feedback on this branch.

[leej3]

And I wouldn't worry about the lack of python code you wrote. I appreciate that using git and thinking about tests and packaging is hard.

By the way you can add multiple changes to a single commit. That would drop the number of commits you had to make.

git add filea fileb filec
git commit -m 'add files a b and c'

[leej3]

General note, do not add lots of large files to git. Ideally you would store this somewhere else. It quickly becomes unmanageable to work with git if you have such a large size on disk. Solutions include:

• Make the data much smaller (often impractical)
• storing the images separately on a webserver
• storing the data in a git submodule
• using git-annex or datalad

Thanks for documenting your progress clearly and the comment describing your efforts. It made it a lot easier to grade you for this work. It is far from the typical attempt and you did not fulfil various aspects of the rubric. With that said, in attempting to solve your problem you have made the correct choice in struggling through someone else's code and adapting it for your needs rather than re-inventing the wheel and wasting time rewriting a similar project yourself. The latter would indeed have been an easier project to do, scoring more marks but outside of that it would have been largely pointless. I encourage you to use such a strategy for solving your scientific problems in the future too. Studying the code of others is often a superior way to learn how to code than writing and debugging your own code with the limited skills of a beginner.

Seeing the edits you made, you have clearly demonstrated knowledge of the codebase you co-opted for your purposes (and by association the python programming language). Additionally you have very clearly demonstrated significant effort in achieving your stated goal, along with proficiency in many of the skills we covered (including the foundational skills like bash and git, github, and markdown). So overall, well done.