Merge pull request #1143: Consolidate date code to one directory

augur/dates.py → augur/dates/__init__.py

@@ -5,9 +5,10 @@
 import pandas as pd
 import re
 import treetime.utils
-from .errors import AugurError, InvalidDate
+from augur.errors import AugurError
+from .errors import InvalidDate
 
-from augur.util_support.date_disambiguator import DateDisambiguator
+from .ambiguous_date import AmbiguousDate
 
 SUPPORTED_DATE_HELP_TEXT = dedent("""\
     1. an Augur-style numeric date with the year as the integer part (e.g. 2020.42) or
@@ -114,7 +115,7 @@ def get_numerical_date_from_value(value, fmt=None, min_max_year=None):
         value = fmt.replace('%Y', value).replace('%m', 'XX').replace('%d', 'XX')
     if 'XX' in value:
         try:
-            ambig_date = DateDisambiguator(value, fmt=fmt, min_max_year=min_max_year).range()
+            ambig_date = AmbiguousDate(value, fmt=fmt, min_max_year=min_max_year).range()
         except InvalidDate as error:
             raise AugurError(str(error)) from error
         if ambig_date is None or None in ambig_date:

augur/util_support/date_disambiguator.py → augur/dates/ambiguous_date.py

@@ -3,7 +3,7 @@
 import functools
 import re
 
-from augur.errors import InvalidDate
+from .errors import InvalidDate
 
 
 def tuple_to_date(year, month, day):
@@ -38,7 +38,7 @@ def resolve_uncertain_int(uncertain_string, min_or_max):
 
 
 # This was originally from treetime.utils.ambiguous_date_to_date_range.
-class DateDisambiguator:
+class AmbiguousDate:
     """Transforms a date string with uncertainty into the range of possible dates."""
 
     def __init__(self, uncertain_date, fmt="%Y-%m-%d", min_max_year=None):

augur/dates/errors.py

@@ -0,0 +1,11 @@
+class InvalidDate(Exception):
+    """Custom exception class to handle dates in unsupported formats."""
+
+    def __init__(self, date, message):
+        """Initialize the error with the culprit date string and a meaningful message."""
+        self.date = date
+        self.message = message
+
+    def __str__(self):
+        """Return a human-readable summary of the error."""
+        return f"Invalid date '{self.date}': {self.message}"

augur/errors.py

@@ -1,16 +1,2 @@
 class AugurError(Exception):
     pass
-
-
-# TODO: Move this to something like dates/errors.py
-class InvalidDate(Exception):
-    """Custom exception class to handle dates in unsupported formats."""
-
-    def __init__(self, date, message):
-        """Initialize the error with the culprit date string and a meaningful message."""
-        self.date = date
-        self.message = message
-
-    def __str__(self):
-        """Return a human-readable summary of the error."""
-        return f"Invalid date '{self.date}': {self.message}"

docs/api/developer/augur.util_support.date_disambiguator.rst → docs/api/developer/augur.dates.ambiguous_date.rst

@@ -1,7 +1,7 @@
-augur.util\_support.date\_disambiguator
+augur.dates.ambiguous\_date
 =======================================
 
-.. automodule:: augur.util_support.date_disambiguator
+.. automodule:: augur.dates.ambiguous_date
    :members:
    :undoc-members:
    :show-inheritance:

docs/api/developer/augur.dates.errors.rst

@@ -0,0 +1,7 @@
+augur.dates.errors
+==================
+
+.. automodule:: augur.dates.errors
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/api/developer/augur.dates.rst

@@ -5,3 +5,8 @@ augur.dates
    :members:
    :undoc-members:
    :show-inheritance:
+
+.. toctree::
+
+   augur.dates.ambiguous_date
+   augur.dates.errors

docs/api/developer/augur.util_support.rst

@@ -10,7 +10,6 @@ augur.util\_support
 
    augur.util_support.color_parser
    augur.util_support.color_parser_line
-   augur.util_support.date_disambiguator
    augur.util_support.node_data
    augur.util_support.node_data_file
    augur.util_support.node_data_reader

tests/util_support/test_date_disambiguator.py → tests/dates/test_ambiguous_date.py

@@ -1,14 +1,14 @@
 import datetime
-from augur.errors import InvalidDate
 
-from augur.util_support import date_disambiguator
-from augur.util_support.date_disambiguator import DateDisambiguator
+from augur.dates import ambiguous_date
+from augur.dates.ambiguous_date import AmbiguousDate
+from augur.dates.errors import InvalidDate
 
 from freezegun import freeze_time
 import pytest
 
 
-class TestDateDisambiguator:
+class TestAmbiguousDate:
     @freeze_time("2111-05-05")
     @pytest.mark.parametrize(
         "date_str, expected_range",
@@ -19,7 +19,7 @@ class TestDateDisambiguator:
         ],
     )
     def test_range(self, date_str, expected_range):
-        assert DateDisambiguator(date_str).range() == expected_range
+        assert AmbiguousDate(date_str).range() == expected_range
 
     @pytest.mark.parametrize(
         "date_str, fmt",
@@ -31,7 +31,7 @@ def test_range(self, date_str, expected_range):
         ],
     )
     def test_range_separators(self, date_str, fmt):
-        assert DateDisambiguator(date_str, fmt=fmt).range() == (
+        assert AmbiguousDate(date_str, fmt=fmt).range() == (
             datetime.date(2005, 2, 1),
             datetime.date(2005, 2, 28),
         )
@@ -46,12 +46,12 @@ def test_range_separators(self, date_str, fmt):
     )
     def test_uncertain_date_components(self, date_str, expected_components):
         assert (
-            DateDisambiguator(date_str).uncertain_date_components == expected_components
+            AmbiguousDate(date_str).uncertain_date_components == expected_components
         )
 
     def test_uncertain_date_components_error(self):
         with pytest.raises(InvalidDate, match="Date does not match format"):
-            DateDisambiguator("5-5-5-5-5").uncertain_date_components
+            AmbiguousDate("5-5-5-5-5").uncertain_date_components
 
     @pytest.mark.parametrize(
         "date_str, min_or_max, expected",
@@ -68,7 +68,7 @@ def test_uncertain_date_components_error(self):
     )
     def test_resolve_uncertain_int(self, date_str, min_or_max, expected):
         assert (
-            date_disambiguator.resolve_uncertain_int(date_str, min_or_max) == expected
+            ambiguous_date.resolve_uncertain_int(date_str, min_or_max) == expected
         )
 
     @pytest.mark.parametrize(
@@ -80,4 +80,4 @@ def test_resolve_uncertain_int(self, date_str, min_or_max, expected):
     )
     def test_assert_only_less_significant_uncertainty(self, date_str, expected_error):
         with pytest.raises(InvalidDate, match=expected_error):
-            DateDisambiguator(date_str)
+            AmbiguousDate(date_str)