Merge pull request #1948 from cmu-delphi/release/indicators_v0.3.53_utils_v0.3.23

Release covidcast-indicators 0.3.53

Author: melange396

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.3.52
+current_version = 0.3.53
 commit = True
 message = chore: bump covidcast-indicators to {new_version}
 tag = False

_delphi_utils_python/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.3.22
+current_version = 0.3.23
 commit = True
 message = chore: bump delphi_utils to {new_version}
 tag = False

_delphi_utils_python/delphi_utils/__init__.py

@@ -15,4 +15,4 @@
 from .nancodes import Nans
 from .weekday import Weekday
 
-__version__ = "0.3.22"
+__version__ = "0.3.23"

_delphi_utils_python/setup.py

@@ -12,7 +12,7 @@
     "freezegun",
     "gitpython",
     "mock",
-    "moto",
+    "moto~=4.2.14",
     "numpy",
     "pandas>=1.1.0",
     "pydocstyle",
@@ -27,7 +27,7 @@
 
 setup(
     name="delphi_utils",
-    version="0.3.22",
+    version="0.3.23",
     description="Shared Utility Functions for Indicators",
     long_description=long_description,
     long_description_content_type="text/markdown",

changehc/setup.py

@@ -12,7 +12,7 @@
     "delphi-utils",
     "covidcast",
     "boto3",
-    "moto",
+    "moto~=4.2.14",
     "paramiko"
 ]
 

changehc/version.cfg

@@ -1 +1 @@
-current_version = 0.3.52
+current_version = 0.3.53

claims_hosp/delphi_claims_hosp/backfill.py

@@ -44,7 +44,10 @@ def store_backfill_file(claims_filepath, _end_date, backfill_dir):
     backfilldata = gmpr.add_geocode(backfilldata, from_code="fips", new_code="state_id",
                            from_col="fips", new_col="state_id")
     #Store one year's backfill data
-    _start_date = _end_date.replace(year=_end_date.year-1)
+    if _end_date.day == 29 and _end_date.month == 2:
+        _start_date = datetime(_end_date.year-1, 2, 28)
+    else:
+        _start_date = _end_date.replace(year=_end_date.year-1)
     selected_columns = ['time_value', 'fips', 'state_id',
                         'den', 'num']
     backfilldata = backfilldata.loc[(backfilldata["time_value"] >= _start_date)

claims_hosp/version.cfg

@@ -1 +1 @@
-current_version = 0.3.52
+current_version = 0.3.53

doctor_visits/version.cfg

@@ -1 +1 @@
-current_version = 0.3.52
+current_version = 0.3.53

google_symptoms/version.cfg

@@ -1 +1 @@
-current_version = 0.3.52
+current_version = 0.3.53

hhs_hosp/version.cfg

@@ -1 +1 @@
-current_version = 0.3.52
+current_version = 0.3.53

nchs_mortality/tests/test_run.py

@@ -69,3 +69,26 @@ def test_output_file_format(self, run_as_module, date):
                     "missing_val", "missing_se", "missing_sample_size"
                 ]
                 assert (df.columns.values == expected_columns).all()
+
+    # the 14th was a Monday
+    @pytest.mark.parametrize("date", ["2020-09-14", "2020-09-17", "2020-09-18"])
+    def test_national_prop(self, run_as_module, date):
+        is_mon_or_thurs = dt.datetime.strptime(date, "%Y-%m-%d").weekday() == (0 or 3)
+
+        folders = ["daily_cache"]
+        if is_mon_or_thurs:
+            folders.append("receiving")
+
+        for output_folder in folders:
+            num = pd.read_csv(
+                join(output_folder, f"weekly_202026_nation_deaths_covid_incidence_num.csv")
+            )
+            prop = pd.read_csv(
+                join(output_folder, f"weekly_202026_nation_deaths_covid_incidence_prop.csv")
+            )
+            # hardcoded value from the geomapper CSV
+            US_POPULATION = 334103109
+            INCIDENCE_BASE = 100000
+            numeric_value = num.iloc[0]["val"] / US_POPULATION * INCIDENCE_BASE
+            assert(numeric_value > 0)
+            assert(prop.iloc[0]["val"] == round(numeric_value, 7))

nchs_mortality/version.cfg

@@ -1 +1 @@
-current_version = 0.3.52
+current_version = 0.3.53

quidel_covidtest/delphi_quidel_covidtest/backfill.py

@@ -45,7 +45,10 @@ def store_backfill_file(df, _end_date, backfill_dir):
                         "totalTest_age_0_17": "den_age_0_17"},
                         axis=1, inplace=True)
     #Store one year's backfill data
-    _start_date = _end_date.replace(year=_end_date.year-1)
+    if _end_date.day == 29 and _end_date.month == 2:
+        _start_date = datetime(_end_date.year-1, 2, 28)
+    else:
+        _start_date = _end_date.replace(year=_end_date.year-1)
     selected_columns = ['time_value', 'fips', 'state_id',
                         'den_total', 'num_total',
                         'num_age_0_4', 'den_age_0_4',

quidel_covidtest/version.cfg

@@ -1 +1 @@
-current_version = 0.3.52
+current_version = 0.3.53

sir_complainsalot/version.cfg

@@ -1 +1 @@
-current_version = 0.3.52
+current_version = 0.3.53