LANG: python 3.10 update (amplicon)

[lizgehret]

local install of all external dependencies was successful, so now it's time to see what breaks!

[lizgehret]

Okay so current issue here is from q2-fragment-insertion's pin of dendropy. This pin is because sepp depends on an old version of dendropy (because it imports a private function that no longer exists in the current versions) which is (of course) not compatible with python 3.10. We'll need to figure out what to do about this because this blocks q2-fragment-insertion from being included in the 3.10 update.

[lizgehret]

Okay so it looks like the latest version of sepp resolved this issue (less than two weeks ago!) and builds are now up on bioconda. Paired PR in fragment-insertion that removes this pin - we'll see if this works!

[lizgehret]

Another paired PR in alignment - this punts the mafft pin back to alignment's recipe, using the min pin previously present

[ebolyen]

Wow, it looks like it practically worked!

Now that you have a solve, I would recommend putting mafft back into the seed env with the new pin (whatever that ended up being), and also maybe we should do the same for dendropy? That way we can control all of these in one place.

(I realize that you needed the >= operator to try and solve for mafft, which wouldn't have worked in the seed env... probably?)

[lizgehret]

PR to address test failures in vsearch (very minor): qiime2/q2-vsearch#99

I'll try adding mafft as a min pin in the seed env @ebolyen - conda's docs do state that pin ranges are supported, and that might be better for this situation. I'm debating between pinning sepp and dendropy, since sepp is the root offender. Now that I've written that out, I think I'm leaning towards a min pin for sepp - that way we're just ensuring we have at least the build that's fixed that old dendropy dependency.

EDIT: so even though conda supports pin ranges, it doesn't seem to be easily compatible with the jinja templating for package versions (within each individual package) - so i've just set the pins for mafft and sepp, and we'll just fuss with them if/when they stop working.

[lizgehret]

We've got a working build! 🥳