enables highly_variable_genes_seurat_v3 to accept pseudocounts

[giovp]

fixes #1642 .

I'll reply to the comments here @adamgayoso

shouldn't both not be Optional?

I removed optional type from both span and check_values

On another note, in this current state check_nonnegative_integers is an unused import. Do you guys check for this with flake8?

we don't have pre-commit in place, we are discussing it here #1563 . I do check flake8 but clearly didn't do it this time.

I think a bug has been introduced @ivirshup @giovp. Namely, the call to check_nonnegative_integers(X) was removed (should be here on line 61) if returns False, raise the warning

this should be fixed now

Sorry again for very sloppy handling of this, should be ready to review

[adamgayoso]

LGTM

[adamgayoso]

we don't have pre-commit in place, we are discussing it here #1563 . I do check flake8 but clearly didn't do it this time.

I thought at one point you guys were checking flake8 with CI.

[ivirshup]

I thought at one point you guys were checking flake8 with CI.

We were, sorta. The CI tool we were using had pretty stochastic reporting (which isn't really what we want in a CI tool). Hopefully it'll be back in a more reliable form soon: #1563 (comment)

[ivirshup]

Some minor style comments (up to you on making the changes), but looks good overall.

[ivirshup]

@meeseeksdev backport to 1.7.x

[lumberbot-app]

Owee, I'm MrMeeseeks, Look at me.

There seem to be a conflict, please backport manually. Here are approximate instructions:

1. Checkout backport branch and update it.

$ git checkout 1.7.x
$ git pull

2. Cherry pick the first parent branch of the this PR on top of the older branch:

$ git cherry-pick -m1 f7279f6342f1e4a340bae2a8d345c1c43b2097bb

3. You will likely have some merge/cherry-pick conflict here, fix them and commit:

$ git commit -am 'Backport PR #1679: enables highly_variable_genes_seurat_v3 to accept pseudocounts'

4. Push to a named branch :

git push YOURFORK 1.7.x:auto-backport-of-pr-1679-on-1.7.x

5. Create a PR against branch 1.7.x, I would have named this PR:

"Backport PR #1679 on branch 1.7.x"

And apply the correct labels and milestones.

Congratulation you did some good work ! Hopefully your backport PR will be tested by the continuous integration and merged soon!

If these instruction are inaccurate, feel free to suggest an improvement.