Export ambiguous date strings for tips #1760
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This is only exported when using `--timetree` and is intended to be used by `augur export` to inform Auspice whether a date is inferred or not. An alternative approach would be for `augur export` to parse the already exported `raw_date` and decide whether that includes ambiguity but with the proposed changes in <#1304> this approach is cleaner and less error-prone. Note that `raw_date_constraint` is None on internal nodes and a list (of len 2) on terminal nodes with ambiguous dates.
These provide two important pieces of information for Auspice: 1. A way to unambiguously know if a tip date was inferred or not. 2. When a tip date was inferred we can now display the raw (ambiguous) date string. Note that the new output would validate on the old schema as additional properties are allowed (by default).
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## master #1760 +/- ##
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- Coverage 73.23% 73.21% -0.03%
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Failing docs are due to this issue which arises on Sphinx v8.2.0. I'm not sure of the best course of action w.r.t fixing the docs, but their failure is unrelated to the work in this PR and thus shouldn't be blocking. |
| node["node_attrs"]["num_date"]["inferred"] = raw_data['date_inferred'] | ||
| if raw_data['date_inferred'] and raw_data.get('raw_date', False): |
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Why the check for raw_data['date_inferred'] in L866 after it's already been used in L865?
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It can be false (not inferred, i.e. known) and if so then date==raw_date so we don't export the raw date string.
See commit messages for details.
This is the
num_datecase of the more general #386Auspice PR nextstrain/auspice#1943 will read these exported values, and that PR has a visual summary of what it enables.