MAINT: update SPAdes to 4.0.0

[misialq]

In response to the issue reported on the QIIME 2 forum: https://forum.qiime2.org/t/q2-assembly-assemble-spades-failing/32165/3.

[lizgehret]

Hey @misialq - I fixed the merge conflicts here bc I wanted to check and see if spades 4.0.0 would work (since we'll also need to include this in our environment file updates). if it doesn't, we should be able to try 3.15.5 (there's a confirmed report of someone having success with that version for python 3.10).

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 98.32%. Comparing base (8926cb0) to head (e02e2ac).
Report is 1 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #108   +/-   ##
=======================================
  Coverage   98.32%   98.32%           
=======================================
  Files          38       38           
  Lines        2745     2745           
=======================================
  Hits         2699     2699           
  Misses         46       46           

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[misialq]

Hey @lizgehret, thanks! I still need to test that everything works ok with that new version - maybe we can just merge this for now (I guess you need that to happen today, right?) and I test afterwards?

[lizgehret]

Hey @lizgehret, thanks! I still need to test that everything works ok with that new version - maybe we can just merge this for now (I guess you need that to happen today, right?) and I test afterwards?

Hey @misialq - what you could actually do is remove the version pin entirely from assembly's recipe file (this would actually make my changes in distributions easier as well). Then I'd just add the version pin into distributions, and you could test out the updated environment that contains that newer version - and if you run into any problems, you can just update the requisite code in assembly, and the next round of prepare PRs will include those changes. LMK if that makes sense or if you have any questions!

[misialq]

Oh, that would make it easier... However, that means that information about pinned versions (wrt to q2-assembly) would now be in two places: here and in distributions? The only problem I see with this approach is that if someone wants to install q2-assembly on its own they would not know that there is an actual pin required for the plugin, right?

[lizgehret]

Oh, that would make it easier... However, that means that information about pinned versions (wrt to q2-assembly) would now be in two places: here and in distributions?

So technically it would just be in one place (if you remove the version pin here). For some background, we are hoping to slowly move all version pinning into distributions, so that there's just one location (or source of truth) for all of our package requirements.

Once we get a working distro build with spades 4.0.0, what you can do is update the spades instance in assembly's recipe file to be templated out- which will then just pull the version required from the environment file:

spades {{ spades }}

The only problem I see with this approach is that if someone wants to install q2-assembly on its own they would not know that there is an actual pin required for the plugin, right?

Hey good question - if folks were installing it on top of the tiny distribution (as an example), then they would need to specify the version of SPAdes. You could add a line into the install instructions (if installing separately from metagenome/pathogenome) that includes the following:

conda install -c bioconda spades=4.0.0

I'd say that's probably the easiest way of handling a separate install- is that something you think will be a common occurrence (vs a distro install)?

[misialq]

Alright, thanks for the explanation! I think that all makes sense - I'm going to drop the pin in the next commit then. I don't think non-distro installs would be super common - just trying to keep such use cases in mind :) Thanks!

[lizgehret]

Thanks @misialq, this lgtm! Would you mind merging this as soon as you're able? I've got this distro PR open that won't pass until this is merged: qiime2/distributions#558

[lizgehret]

Awesome, thanks @misialq! 🙏