code standards and unit testing

[celalp]

It would be great if we can implement some sort of code standard and some basic linting and other checks and balances.

Unit testing is also important as this thing grows bigger.

[celalp]

There are couple of modules that are ready for writing unit tests. @aarthi-mohan you can look at this repo for some examples on how to use pytest for writing tests.

The modules we can start right away are:

ranges
genome
variant
literature

For sequence and structure there may be additional features that will get added later and we will need to write tests for that as well.

under the tests folder please create another folder called data and use that for data and other variables that you will need for testing. For the time being do not worry about interoperability, we will need to come up with way to integrate all of this w/o an LLM.

For genome please do not use a whole genome but select a small chrom from hg38.
For variant, especially to_hgvs function there might be some errors, I have not fully tested that on non-snvs but write the tests anyway. You will need to find genome hgvs representations of a lot of different variants.

For literature, please pick a paper with both wetlab experiments and computational experiments. And a long paper would be a good choice too. Journals like Cell do not have page or word limits on articles so those tend to be quite long and dense and interesting formatting. We will need to come up with a way to compare images, I am thinking about simple embedding distances using ColPali but ignore that for now.

For ranges, I think it's quite straightforward but please create a (Genomic)RangesList and (Genomic)RangesDict as well and test all the dunder (__) methods.

Thanks.