snp test

[davek44]

Description of your changes

This is an example integration test. It takes a few minutes to run and depends on local files. How should we handle these?

[lruizcalico]

Hi Dave, do you want to have this test integrated to the external facing package or only for the internal one?

[nalien-calico]

Hi Dave,

How large are the files required to run the integration tests? We can approach this in a few ways. See below.

1. Commit test dataset into the repo, copy them into the dockerfile and run with gihub actions
2. Upload the test dataset onto a GCS bucket. Build a dockerfile, download test data from GCS bucket and run with github actions.
3. Dynamically create a test dataset as a fixture in memory. Build a dockerfile and run with github actions.

[davek44]

In this case, one data file is pretty small. I added it into the github. The other data file is a human genome sequence in FASTA format. It's 3 GB unzipped. How should we handle that?

[nalien-calico]

In this case, one data file is pretty small. I added it into the github. The other data file is a human genome sequence in FASTA format. It's 3 GB unzipped. How should we handle that?

Since one of the data files is that large, I think it makes sense to have all the data stored in a GCS bucket. That way, we can just download all the data together from GCS bucket when we run the integration tests, rather than trying to pull multiple data files from different sources.

Is the test example in this PR the actual test you want to run? If not, can you provide the integration tests and test files so I can start putting a github action workflow together?

[davek44]

Yes, this is the actual test. Once we have a framework, I'll begin adding more.