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feat: support treetime ambiguous date format #1305

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feat: support treetime ambiguous date format #1305

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6 changes: 6 additions & 0 deletions augur/dates/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -121,6 +121,12 @@ def get_numerical_date_from_value(value, fmt=None, min_max_year=None):
except InvalidDate as error:
raise AugurError(str(error)) from error
return [treetime.utils.numeric_date(d) for d in ambig_date]
if value.startswith('[') and value.endswith(']') and len(value[1:-1].split(':'))==2:
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For added context, this is the corresponding logic in TreeTime: treetime/utils.py#L305-L312

# Treetime ambiguous date format, e.g. [2019.5:2020.5]
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I'm curious how you get the numerical dates in metadata. Is this a standard format outside of TreeTime, or do you run ISO dates through something like treetime.utils.numeric_date to get the float representation?

Asking because I think a good next step after this gets merged is to generalize for any [A:B] date pair where A and B can be anything that's currently supported as an exact scalar date (e.g. [2023-07-31:2023-08-06]). I did some prototyping of this a while back but never got back to creating a proper PR for it.

try:
return [float(x) for x in value[1:-1].split(':')]
except ValueError as error:
raise AugurError(str(error)) from error
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Suggestion: customize the error message.

When given something like [2023-07-31:2023-08-06], the ValueError message looks something like:

could not convert string to float: '2023-07-31'

It's obvious what this means to us as developers, but maybe not so obvious to users. Something like this might be more clear:

The date range format must be `[A:B]` where both `A` and `B` are numerical dates.

try:
return treetime.utils.numeric_date(datetime.datetime.strptime(value, fmt))
except:
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4 changes: 4 additions & 0 deletions tests/dates/test_dates.py
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Expand Up @@ -99,3 +99,7 @@ def test_get_numerical_dates_dict_error(self):
}
with pytest.raises(AugurError):
dates.get_numerical_dates(metadata)

def test_get_numerical_date_from_value_treetime_ambiguous_date_format(self):
assert dates.get_numerical_date_from_value("[2019.5:2020.5]") == [2019.5, 2020.5]
assert dates.get_numerical_date_from_value("[2013.543:2013.544]") == [2013.543, 2013.544]
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