Amin1.0

[tristanpwdennis]

Hi guys

I've refactored the old amin1 API to include (I think) all the functionality of malariagen_data for unphased data - just like Adir1.0. This has involved:

• Reorganising the release bucket (under sample sets, updating metadata, re-org of filters, reference files, etc).
• Updating the amin1 class file - basically a copy of the Adir1 class file.
• Updating the docs.

Relates to PR #795

[tristanpwdennis]

I think this is running into the same issues as on Adir1 - GH actions can't access the bucket - but @ahernank suggests we need to move the bucket to us-central anyway.

[ahernank]

Just created vo_amin_release_master_us_central1 and added the permissions for GH actions, hth.

[tristanpwdennis]

updated now

[tristanpwdennis]

Hi guys, making some progress on coverage tests for Amin1.0 now.

The sticking points I am running into are the same as for Adir1.x (see #795 for discussion) and I think I will deal with them the same way. Mainly no phasing data, no sex_call data. I have put 'UKN' for the sex_calls.

I can deal with these mostly by using tags to exclude amin1 from tests that require specific data that these releases don't have. Because Amin1 is one sample set from one country, I am running into my main problem with tests that require multiple sample sets or samples.

Specifically, test_fst.py , test_pca.py, test_snp_frqs.py and test_sample_metadata.py

I have either tagged amin1 out of tests that specifically test multiple sample sets (this is fine), or removed amin1 from tests where multiple sample sets are used. Attempting to modify the number of sample sets used breaks things, as sometimes insufficient samples are returned (e.g. in PCA) to run the tests in ag3/adir/af1.

UD:integration and notebooks tests are failing because of github actions access issues with GCP

UD 2: Linting is failing on GH, but passes locally?

[ahernank]

@tristanpwdennis are you happy to close this PR in favour of #839?

[tristanpwdennis]

Closing (see #839)