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nextstrain / augur

Pipeline components for real-time phylodynamic analysis
https://docs.nextstrain.org/projects/augur/
GNU Affero General Public License v3.0
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CI failing on JSON diff #1605

Closed victorlin closed 1 month ago

victorlin commented 1 month ago

CI failing on master as of this run:

Run cram tests/
!
--- tests/functional/clades.t
+++ tests/functional/clades.t.err
@@ -41,7 +41,7 @@

   $ python3 "$TESTDIR/../../scripts/diff_jsons.py" clades/clades.json "$TMP/clades_no-labels.json" \
   >   --exclude-paths "root['generated_by']"
-  {'dictionary_item_removed': [root['branches']]}
+  {'dictionary_item_removed': ["root['branches']"]}

The timing makes me suspect this is caused by release of deepdiff 8.0.0 which happened 1 hour ago and has this in changelog:

With the introduction of threshold_to_diff_deeper, the values returned are different than in previous versions of DeepDiff. You can still get the older values by setting threshold_to_diff_deeper=0. However to signify that enough has changed in this release that the users need to update the parameters passed to DeepDiff, we will be doing a major version update.

Possible solutions

  1. https://github.com/nextstrain/augur/pull/1606
  2. Pin deepdiff >=8.0.0 and update output checks