From c0cc4a748b84d618670989b545638135bba7991c Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Fri, 27 Jan 2023 16:39:06 -0800
Subject: [PATCH 1/2] Consolidate date code to one directory

Instead of having most functions in dates.py, an exception class in
errors.py, and a helper class in util_support/date_disambiguator.py,
this puts everything under one directory.

No functional changes, just moving things around.
---
 augur/{dates.py => dates/__init__.py}              |  5 +++--
 .../{util_support => dates}/date_disambiguator.py  |  2 +-
 augur/dates/errors.py                              | 11 +++++++++++
 augur/errors.py                                    | 14 --------------
 ...ator.rst => augur.dates.date_disambiguator.rst} |  4 ++--
 docs/api/developer/augur.dates.errors.rst          |  7 +++++++
 docs/api/developer/augur.dates.rst                 |  5 +++++
 docs/api/developer/augur.util_support.rst          |  1 -
 .../test_date_disambiguator.py                     |  6 +++---
 tests/{ => dates}/test_dates.py                    |  0
 10 files changed, 32 insertions(+), 23 deletions(-)
 rename augur/{dates.py => dates/__init__.py} (97%)
 rename augur/{util_support => dates}/date_disambiguator.py (99%)
 create mode 100644 augur/dates/errors.py
 rename docs/api/developer/{augur.util_support.date_disambiguator.rst => augur.dates.date_disambiguator.rst} (50%)
 create mode 100644 docs/api/developer/augur.dates.errors.rst
 rename tests/{util_support => dates}/test_date_disambiguator.py (94%)
 rename tests/{ => dates}/test_dates.py (100%)

diff --git a/augur/dates.py b/augur/dates/__init__.py
similarity index 97%
rename from augur/dates.py
rename to augur/dates/__init__.py
index 382336537..b83e760ce 100644
--- a/augur/dates.py
+++ b/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 .date_disambiguator import DateDisambiguator
 
 SUPPORTED_DATE_HELP_TEXT = dedent("""\
     1. an Augur-style numeric date with the year as the integer part (e.g. 2020.42) or
diff --git a/augur/util_support/date_disambiguator.py b/augur/dates/date_disambiguator.py
similarity index 99%
rename from augur/util_support/date_disambiguator.py
rename to augur/dates/date_disambiguator.py
index 81ccfe9dc..0b5b8c5eb 100644
--- a/augur/util_support/date_disambiguator.py
+++ b/augur/dates/date_disambiguator.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):
diff --git a/augur/dates/errors.py b/augur/dates/errors.py
new file mode 100644
index 000000000..d7619f604
--- /dev/null
+++ b/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}"
diff --git a/augur/errors.py b/augur/errors.py
index d353f0014..3d0ae8a18 100644
--- a/augur/errors.py
+++ b/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}"
diff --git a/docs/api/developer/augur.util_support.date_disambiguator.rst b/docs/api/developer/augur.dates.date_disambiguator.rst
similarity index 50%
rename from docs/api/developer/augur.util_support.date_disambiguator.rst
rename to docs/api/developer/augur.dates.date_disambiguator.rst
index ebae8164e..54422268e 100644
--- a/docs/api/developer/augur.util_support.date_disambiguator.rst
+++ b/docs/api/developer/augur.dates.date_disambiguator.rst
@@ -1,7 +1,7 @@
-augur.util\_support.date\_disambiguator
+augur.dates.date\_disambiguator
 =======================================
 
-.. automodule:: augur.util_support.date_disambiguator
+.. automodule:: augur.dates.date_disambiguator
    :members:
    :undoc-members:
    :show-inheritance:
diff --git a/docs/api/developer/augur.dates.errors.rst b/docs/api/developer/augur.dates.errors.rst
new file mode 100644
index 000000000..d4da219fc
--- /dev/null
+++ b/docs/api/developer/augur.dates.errors.rst
@@ -0,0 +1,7 @@
+augur.dates.errors
+==================
+
+.. automodule:: augur.dates.errors
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/api/developer/augur.dates.rst b/docs/api/developer/augur.dates.rst
index 1e2684513..6a21a1d45 100644
--- a/docs/api/developer/augur.dates.rst
+++ b/docs/api/developer/augur.dates.rst
@@ -5,3 +5,8 @@ augur.dates
    :members:
    :undoc-members:
    :show-inheritance:
+
+.. toctree::
+
+   augur.dates.date_disambiguator
+   augur.dates.errors
diff --git a/docs/api/developer/augur.util_support.rst b/docs/api/developer/augur.util_support.rst
index e9fdae55b..0c20d9f1e 100644
--- a/docs/api/developer/augur.util_support.rst
+++ b/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
diff --git a/tests/util_support/test_date_disambiguator.py b/tests/dates/test_date_disambiguator.py
similarity index 94%
rename from tests/util_support/test_date_disambiguator.py
rename to tests/dates/test_date_disambiguator.py
index 5a4d7bb51..fb2768acf 100644
--- a/tests/util_support/test_date_disambiguator.py
+++ b/tests/dates/test_date_disambiguator.py
@@ -1,8 +1,8 @@
 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 date_disambiguator
+from augur.dates.date_disambiguator import DateDisambiguator
+from augur.dates.errors import InvalidDate
 
 from freezegun import freeze_time
 import pytest
diff --git a/tests/test_dates.py b/tests/dates/test_dates.py
similarity index 100%
rename from tests/test_dates.py
rename to tests/dates/test_dates.py

From 82a91fa583371afb2bc38cfd3e4e7b57d04e0000 Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Mon, 30 Jan 2023 16:41:58 -0800
Subject: [PATCH 2/2] =?UTF-8?q?Rename=20DateDisambiguator=20=E2=86=92=20Am?=
 =?UTF-8?q?biguousDate?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

"DateDisambiguator" is a mouthful, and also uses a verb in a class name
which is a bad pattern. Use a noun instead.
---
 augur/dates/__init__.py                        |  4 ++--
 ...date_disambiguator.py => ambiguous_date.py} |  2 +-
 ...ator.rst => augur.dates.ambiguous_date.rst} |  4 ++--
 docs/api/developer/augur.dates.rst             |  2 +-
 ...disambiguator.py => test_ambiguous_date.py} | 18 +++++++++---------
 5 files changed, 15 insertions(+), 15 deletions(-)
 rename augur/dates/{date_disambiguator.py => ambiguous_date.py} (99%)
 rename docs/api/developer/{augur.dates.date_disambiguator.rst => augur.dates.ambiguous_date.rst} (54%)
 rename tests/dates/{test_date_disambiguator.py => test_ambiguous_date.py} (80%)

diff --git a/augur/dates/__init__.py b/augur/dates/__init__.py
index b83e760ce..c8969ba19 100644
--- a/augur/dates/__init__.py
+++ b/augur/dates/__init__.py
@@ -8,7 +8,7 @@
 from augur.errors import AugurError
 from .errors import InvalidDate
 
-from .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
@@ -115,7 +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:
diff --git a/augur/dates/date_disambiguator.py b/augur/dates/ambiguous_date.py
similarity index 99%
rename from augur/dates/date_disambiguator.py
rename to augur/dates/ambiguous_date.py
index 0b5b8c5eb..525dad257 100644
--- a/augur/dates/date_disambiguator.py
+++ b/augur/dates/ambiguous_date.py
@@ -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):
diff --git a/docs/api/developer/augur.dates.date_disambiguator.rst b/docs/api/developer/augur.dates.ambiguous_date.rst
similarity index 54%
rename from docs/api/developer/augur.dates.date_disambiguator.rst
rename to docs/api/developer/augur.dates.ambiguous_date.rst
index 54422268e..2471f3e8f 100644
--- a/docs/api/developer/augur.dates.date_disambiguator.rst
+++ b/docs/api/developer/augur.dates.ambiguous_date.rst
@@ -1,7 +1,7 @@
-augur.dates.date\_disambiguator
+augur.dates.ambiguous\_date
 =======================================
 
-.. automodule:: augur.dates.date_disambiguator
+.. automodule:: augur.dates.ambiguous_date
    :members:
    :undoc-members:
    :show-inheritance:
diff --git a/docs/api/developer/augur.dates.rst b/docs/api/developer/augur.dates.rst
index 6a21a1d45..5f314f3ce 100644
--- a/docs/api/developer/augur.dates.rst
+++ b/docs/api/developer/augur.dates.rst
@@ -8,5 +8,5 @@ augur.dates
 
 .. toctree::
 
-   augur.dates.date_disambiguator
+   augur.dates.ambiguous_date
    augur.dates.errors
diff --git a/tests/dates/test_date_disambiguator.py b/tests/dates/test_ambiguous_date.py
similarity index 80%
rename from tests/dates/test_date_disambiguator.py
rename to tests/dates/test_ambiguous_date.py
index fb2768acf..ce8f90370 100644
--- a/tests/dates/test_date_disambiguator.py
+++ b/tests/dates/test_ambiguous_date.py
@@ -1,14 +1,14 @@
 import datetime
 
-from augur.dates import date_disambiguator
-from augur.dates.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)