utils.write_json: Serialize Pandas Series #1213
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This isn't strictly used for numpy.
There is a possibility that data to be written by this function contains a pandas Series which was un-serializable prior to this change.
Codecov ReportPatch coverage:
Additional details and impacted files@@ Coverage Diff @@
## master #1213 +/- ##
=======================================
Coverage 68.81% 68.82%
=======================================
Files 64 64
Lines 6936 6938 +2
Branches 1692 1693 +1
=======================================
+ Hits 4773 4775 +2
Misses 1856 1856
Partials 307 307
☔ View full report in Codecov by Sentry. |
huddlej
approved these changes
May 17, 2023
There was a problem hiding this comment.
Thank you for figuring this out and fixing it, @victorlin! This looks like a useful enhancement and bug fix, even if we aren't sure whether the existence of pandas Series instances in TreeTime output is intended or not.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Description of proposed changes
There is a possibility that data to be written by this function contains a pandas Series which was un-serializable prior to this change.
Note: I did some digging to see what other possible data types could be in
node_dataand when they would be used, but didn't get too far. It has to do with modifications on the tree from TreeTime. This investigation should be continued to ensure all possible data types are serialized, so we can avoid similar bugs in the future.Related issue(s)
Fixes #1209
Similar to #1119
Testing
Checklist