dates: Remove unused is_date_ambiguous()

The re-implementation of augur filter accounts for this directly in
filter_by_ambiguous_date().

Remove old tests and add equivalent tests. Note that some date strings
have been changed since the previous values would fail date format
validation.

augur/dates/__init__.py

@@ -76,37 +76,6 @@ def numeric_date_type(date):
     except InvalidDate as error:
         raise argparse.ArgumentTypeError(str(error)) from error
 
-def is_date_ambiguous(date, ambiguous_by):
-    """
-    Returns whether a given date string in the format of YYYY-MM-DD is ambiguous by a given part of the date (e.g., day, month, year, or any parts).
-
-    Parameters
-    ----------
-    date : str
-        Date string in the format of YYYY-MM-DD
-    ambiguous_by : str
-        Field of the date string to test for ambiguity ("day", "month", "year", "any")
-    """
-    date_components = date.split('-', 2)
-
-    if len(date_components) == 3:
-        year, month, day = date_components
-    elif len(date_components) == 2:
-        year, month = date_components
-        day = "XX"
-    else:
-        year = date_components[0] if date_components[0] else 'X'
-        month = "XX"
-        day = "XX"
-
-    # Determine ambiguity hierarchically such that, for example, an ambiguous
-    # month implicates an ambiguous day even when day information is available.
-    return any((
-        "X" in year,
-        "X" in month and ambiguous_by in ("any", "month", "day"),
-        "X" in day and ambiguous_by in ("any", "day")
-    ))
-
 def get_numerical_date_from_value(value, fmt=None, min_max_year=None, ambiguity_resolver='both'):
     value = str(value)
     if re.match(r'^-*\d+\.\d+$', value):

tests/dates/test_dates.py

@@ -60,35 +60,6 @@ def test_get_numerical_date_from_value_current_day_limit(self):
             == pytest.approx(2000.138, abs=1e-3)
         )
 
-    def test_is_date_ambiguous(self):
-        """is_date_ambiguous should return true for ambiguous dates and false for valid dates."""
-        # Test complete date strings with ambiguous values.
-        assert dates.is_date_ambiguous("2019-0X-0X", "any")
-        assert dates.is_date_ambiguous("2019-XX-09", "month")
-        assert dates.is_date_ambiguous("2019-03-XX", "day")
-        assert dates.is_date_ambiguous("201X-03-09", "year")
-        assert dates.is_date_ambiguous("20XX-01-09", "month")
-        assert dates.is_date_ambiguous("2019-XX-03", "day")
-        assert dates.is_date_ambiguous("20XX-01-03", "day")
-
-        # Test incomplete date strings with ambiguous values.
-        assert dates.is_date_ambiguous("2019", "any")
-        assert dates.is_date_ambiguous("201X", "year")
-        assert dates.is_date_ambiguous("2019-XX", "month")
-        assert dates.is_date_ambiguous("2019-10", "day")
-        assert dates.is_date_ambiguous("2019-XX", "any")
-        assert dates.is_date_ambiguous("2019-XX", "day")
-
-        # Test complete date strings without ambiguous dates for the requested field.
-        assert not dates.is_date_ambiguous("2019-09-03", "any")
-        assert not dates.is_date_ambiguous("2019-03-XX", "month")
-        assert not dates.is_date_ambiguous("2019-09-03", "day")
-        assert not dates.is_date_ambiguous("2019-XX-XX", "year")
-
-        # Test incomplete date strings without ambiguous dates for the requested fields.
-        assert not dates.is_date_ambiguous("2019", "year")
-        assert not dates.is_date_ambiguous("2019-10", "month")
-
     def test_get_numerical_dates_dict_error(self):
         """Using get_numerical_dates with metadata represented as a dict should raise an error."""
         metadata = {

tests/filter/__init__.py

@@ -0,0 +1,16 @@
+import argparse
+import shlex
+from augur.filter import register_arguments
+
+
+def parse_args(args: str):
+    parser = argparse.ArgumentParser()
+    register_arguments(parser)
+    return parser.parse_args(shlex.split(args))
+
+
+def write_metadata(tmpdir, metadata):
+    fn = str(tmpdir / "metadata.tsv")
+    with open(fn, "w") as fh:
+        fh.write("\n".join(("\t".join(md) for md in metadata)))
+    return fn

tests/filter/test_exclude_ambiguous_dates_by.py

@@ -0,0 +1,60 @@
+# This file contains functional tests that would normally be written as
+# Cram-style tests. However, pytest is nice here since it is easy to use with
+# parameterized inputs/outputs (not straightforward to set up for Cram tests¹).
+# ¹ https://github.com/nextstrain/augur/pull/1183#discussion_r1142687476
+
+import pytest
+
+from augur.errors import AugurError
+from augur.filter._run import run
+
+from . import parse_args, write_metadata
+
+
+@pytest.mark.parametrize(
+    "date, ambiguity",
+    [
+        # Test complete date strings with ambiguous values.
+        ("2019-0X-0X", "any"),
+        ("2019-XX-XX", "month"),
+        ("2019-XX-XX", "day"),
+        ("2019-03-XX", "day"),
+        ("201X-XX-XX", "year"),
+        ("201X-XX-XX", "month"),
+        ("201X-XX-XX", "day"),
+
+        # Test incomplete date strings with ambiguous values.
+        ("2019", "month"),
+        ("2019", "day"),
+        ("2019", "any"),
+        ("201X", "year"),
+        ("201X", "month"),
+        ("201X", "day"),
+        ("201X", "any"),
+    ],
+)
+def test_date_is_dropped(tmpdir, date, ambiguity):
+    metadata = write_metadata(tmpdir, (("strain","date"),
+                                       ("SEQ1"  , date)))
+    args = parse_args(f'--metadata {metadata} --exclude-ambiguous-dates-by {ambiguity}')
+    with pytest.raises(AugurError, match="All samples have been dropped"):
+        run(args)
+
+@pytest.mark.parametrize(
+    "date, ambiguity",
+    [
+        # Test complete date strings without the specified level of ambiguity.
+        ("2019-09-03", "any"),
+        ("2019-03-XX", "month"),
+        ("2019-09-03", "day"),
+        ("2019-XX-XX", "year"),
+
+        # Test incomplete date strings without the specified level of ambiguity.
+        ("2019", "year"),
+    ],
+)
+def test_date_is_not_dropped(tmpdir, date, ambiguity):
+    metadata = write_metadata(tmpdir, (("strain","date"),
+                                       ("SEQ1"  , date)))
+    args = parse_args(f'--metadata {metadata} --exclude-ambiguous-dates-by {ambiguity}')
+    run(args)

tests/filter/test_relative_dates.py

@@ -4,26 +4,12 @@
 # straightforward to set up for Cram tests¹).
 # ¹ https://github.com/nextstrain/augur/pull/1183#discussion_r1142687476
 
-import argparse
 from freezegun import freeze_time
 import pytest
-import shlex
 
-from augur.filter import register_arguments
 from augur.filter._run import run
 
-
-def parse_args(args):
-    parser = argparse.ArgumentParser()
-    register_arguments(parser)
-    return parser.parse_args(shlex.split(args))
-
-
-def write_metadata(tmpdir, metadata):
-    fn = str(tmpdir / "metadata.tsv")
-    with open(fn, "w") as fh:
-        fh.write("\n".join(("\t".join(md) for md in metadata)))
-    return fn
+from . import parse_args, write_metadata
 
 
 @freeze_time("2020-03-25")