Clean Amin1.0 branch from master

[tristanpwdennis]

See #825

[leehart]

Hi @tristanpwdennis , @ahernank , @jonbrenas

Noting linting check failures here:

malariagen_data/anoph/pca.py:354: error: Unsupported operand types for + ("Series[Any]" and "str")  [operator]
malariagen_data/anoph/pca.py:458: error: Unsupported operand types for + ("Series[Any]" and "str")  [operator]

Noting that anoph/pca.py has not changed in this PR.

Looking at the existing code for pca.py in the master branch, line 354:

        # Convenience variables.
        data["country_location"] = data["country"] + " - " + data["location"]

....and line 458 is similar:

        # Convenience variables.
        data["country_location"] = data["country"] + " - " + data["location"]

I recognise this problem, which has already been addressed in the pending PR #833

The solution appears to be to ensure that the country and location values are strings. For example, in the pending PR mentioned:

        # Convenience variables.
        # Prevent lint error (mypy): Unsupported operand types for + ("Series[Any]" and "str")
        data["country_location"] = (
            data["country"].astype(str) + " - " + data["location"].astype(str)
        )

[tristanpwdennis]

Thanks @leehart, should I wait until #833 is merged before requesting a review?

[leehart]

Hi @tristanpwdennis , #833 has been merged now.

[tristanpwdennis]

Tests are passing locally but failing here?

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 92.01%. Comparing base (6168f4c) to head (90da5cc).
⚠️ Report is 23 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #839      +/-   ##
==========================================
+ Coverage   90.68%   92.01%   +1.33%     
==========================================
  Files          49       49              
  Lines        5175     5175              
==========================================
+ Hits         4693     4762      +69     
+ Misses        482      413      -69     

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[tristanpwdennis]

hi guys - I am struggling to find the source of this. @ahernank suggested it may be due to threading issues that were fixed in #833, but the branch has incorporated these changes.

[ahernank]

Thanks so much @tristanpwdennis, super exciting! I've left some minor notes after a light review.

[ahernank]

I don't think the data-side of these has been sorted. I am conscious part of this is because we are missing accessions for some of the vobs-asia samples. What do you think about commenting these out to avoid confusion around this functionality and we can open an issue separately to fix these for Adir/Amin later on?

[ahernank]

I don't think we need this file here, as this is up in curation.

[ahernank]

It seems there is an extra metadata/metadata dir here, including an extra copy of this file & the ones below.

[ahernank]

Thanks @tristanpwdennis, looks good to me, I've added an issue on vobs-asia to address the surveillance flags/accessions separately. Happy to merge and we can do any other fixes post.