Test failing with TreeTime 0.11.2 release

[victorlin]

translate-with-gff-and-locus-tag.t is failing:

--- tests/functional/translate/cram/translate-with-gff-and-locus-tag.t
+++ tests/functional/translate/cram/translate-with-gff-and-locus-tag.t.err
@@ -15,[12](https://github.com/nextstrain/augur/actions/runs/7615222099/job/20739237313#step:9:13) +[15](https://github.com/nextstrain/augur/actions/runs/7615222099/job/20739237313#step:9:16),21 @@
   >   --output-node-data aa_muts.json \
   >   --alignment-output translations.vcf \
   >   --vcf-reference-output translations_reference.fasta
-  Gene length of 'rrs' is not a multiple of 3. will pad with N
+  ERROR: The VCF file '/home/runner/work/augur/augur/tests/functional/translate/cram/../data/tb/nt_muts.vcf' had genotype calls of ploidy 2 but sample 'NODE_0000001' has a genotype of ploidy 1
+  
+  
+  ERROR from TreeTime: This error is most likely due to a problem with your input data.
+  Please check your input data and try again. If you continue to have problems, please open a new issue including
+  the original command and the error above:  <https://github.com/nextstrain/augur/issues/new/choose>
+  
   Read in 187 specified genes to translate.
   Read in 188 features from reference sequence file
-  [16](https://github.com/nextstrain/augur/actions/runs/7615222099/job/20739237313#step:9:17)2 genes had no mutations and so have been be excluded.
-  amino acid mutations written to .* (re)
+  [2]

@jameshadfield can you check if the test file is bad and needs to be updated?

[jameshadfield]

Yes. It was changed in 2c9db82 (PR #1355). Do you want to help coordinate release of that PR with me?

P.S. I expected us to tightly pin treetime, given it's aversion to major releases -- any particular reason we aren't?

[victorlin]

TreeTime is pinned to the minor version which seems to be aiming for the same thing as pinning on major version on other dependencies. But just like any other dependency, breaking changes can happen on any version regardless of major/minor/patch.

augur/setup.py

Line 65 in 9cd915a

"phylo-treetime >=0.10.0, <0.12",

I think fine to keep the version pinning semi-flexible as-is, and deal with unexpected breaking changes occasionally.

[victorlin]

Also, we're coordinating Augur release 24.0.0 on Slack.

[victorlin]

Addressed in #1355.