Catherine Harvey Project Outline

[harveycas]

No description provided.

[leej3]

Looks like a nice project.

Does it have to be excel? Using non-proprietary formats like csv can be far more useful from the perspective of open science.

I strongly encourage you to fully explore the python package pandas before you do too much planning. Some of the datacamp courses teach its functionality. This will help you to get a sense of how the python community thinks about and works with this sort of tabular data.

[harveycas]

I was wondering if I could have my draft checked for the final project? I used JupyterLab to create my data and it comes out properly when I look at the file from my folder. However, when accessed here it doesn't look right

[harveycas]

I added a file defining my code and I was wondering if it's ok? In addition, I am still not sure regarding how to test my code and produce tests for them. I was wondering if I could have a bit of clarification? Thank you!

[leej3]

This is starting to look much better.

Some pointers:

• you have indentations of 1 and 5 spaces. They should all be multiples of 4.
• For my example the sample file path should have instead been: SAMPLE_XLSX = Path(__file__).parent / "data" / "python_test_list.xlsx"
• For your test of antibiotic_analysis you will need to call it and then read in the excel file and check that it matches a sample excel file. I would worry about this one though. That would be called an integration test. What I want to see is more along the line of unit tests. They are sanity checks to make sure as you change your code, it still maintains the same basic functionality.
• A similar situation for write_marker_dict_to_disk. You could give it a test path and a small dict of data frames to check that it writes output to disk but no need to do more in depth value comparisons.
• Focus your effort on clearly documenting what you expect sort_and_filter_by_col and combine_antibiotics to do. Given a specific input (that you can create from the sample xlsx file) you should have a clear output value you expect. Sub sampling the data like I have done in test_read_excel_file will likely be essential to make it manageable.
• you will need to add xlrd as a dependency to pass the tests

EDIT: I meant "would not worry about this one above"

[leej3]

I've suggested some fixes. Looks like you already made some. No worries. Reorganizing to functions and add tests all at the same was a bit much. I should have submitted smaller changes. Apologies

Overall well done. It's nice work. You grappled with tests which is what I wanted. You are not too far off passing them. Hopefully you got a feel for how they would make things easier and how they reveal bugs (unfortunately you had a lot to work through post merge).

[emilyyaklich]

Hi Catherine,

Your project is very well done, good work! I really appreciate the thorough documentation. Your unit tests are also nice as well.I think in the future, it might be helpful to update your .gitignore file with data/directories that you don't want in your final repository (the .ipynb_checkpoints or the miscellaneous-don't read). Overall, I think your project is good and it is clear to follow. Great job!

Cheers,

Emily