1489 Fix Epidata ci

pycode/memilio-epidata/memilio/epidata/geoModificationGermany.py

@@ -371,9 +371,9 @@ def get_nuts3_county_id_map():
     """
     # download county list
     county_table = get_official_county_table()
-    # delete rows with nuts3 = NaN
+    # delete rows with nuts3 or idCounty = NaN
     # take just columns with name dd.EngEng['idCounty'] and dd.EngEng['nuts3']
-    key_nuts3 = county_table.dropna(subset=[dd.EngEng['nuts3']])[
+    key_nuts3 = county_table.dropna(subset=[dd.EngEng['nuts3'], dd.EngEng['idCounty']])[
         [dd.EngEng['idCounty'], dd.EngEng['nuts3']]]
     # convert ID data types
     key_nuts3 = key_nuts3.astype({dd.EngEng['idCounty']: int})

pycode/memilio-epidata/memilio/epidata/getDataIntoPandasDataFrame.py

@@ -42,7 +42,7 @@
 from io import BytesIO
 from zipfile import ZipFile
 from enum import Enum
-from pkg_resources import parse_version
+from packaging.version import parse
 
 import pandas as pd
 
@@ -66,7 +66,7 @@ class Conf:
 
     v_level = 'Info'
     show_progr = False
-    if parse_version(pd.__version__) < parse_version('2.2'):
+    if parse(pd.__version__) < parse('2.2'):
         excel_engine = 'openpyxl'
     else:
         # calamine is faster, but cannot be used for pandas < 2.2
@@ -196,9 +196,12 @@ def download_file(
 
     """
     if verify not in [True, False, "interactive"]:
-        warnings.warn('Invalid input for argument verify. Expected True, False, or'
-                      ' "interactive", got ' + str(verify) + '.'
-                      ' Proceeding with "verify=True".', category=RuntimeWarning)
+        warnings.warn(
+            'Invalid input for argument verify. Expected True, False, or'
+            ' "interactive", got ' + str(verify) +
+            '.'
+            ' Proceeding with "verify=True".',
+            category=RuntimeWarning)
         verify = True
     # send GET request as stream so the content is not downloaded at once
     try:
@@ -438,8 +441,7 @@ def cli(what):
         parser.add_argument(
             '-s', '--start-date', default=start_date_default,
             help='Defines start date for data download. Should have form: YYYY-mm-dd.'
-            'Default is ' +
-            str(dd.defaultDict['start_date']) +
+            'Default is ' + str(dd.defaultDict['start_date']) +
             ' (2020-04-24 for divi and 2020-01-22 for jh)',
             type=lambda s: datetime.datetime.strptime(s, '%Y-%m-%d').date())
     if 'end_date' in what_list:
@@ -455,8 +457,10 @@ def cli(what):
             ' omitting dates where no data was reported', action='store_true')
     if 'moving_average' in what_list:
         parser.add_argument(
-            '-m', '--moving-average', type=int, default=dd.defaultDict['moving_average'],
-            help='Compute a moving average of N days over the time series. Default is ' + str(dd.defaultDict['moving_average']))
+            '-m', '--moving-average', type=int, default=dd.defaultDict
+            ['moving_average'],
+            help='Compute a moving average of N days over the time series. Default is '
+            + str(dd.defaultDict['moving_average']))
     if 'split_berlin' in what_list:
         parser.add_argument(
             '-b', '--split-berlin', default=dd.defaultDict['split_berlin'],
@@ -485,46 +489,56 @@ def cli(what):
         )
 
     # add optional download options
-    if '--no-progress-indicators' in sys.argv:
+    argv = sys.argv[1:]
+    if '--no-progress-indicators' in argv:
         parser.add_argument(
             '--no-progress-indicators', dest='show_progress',
             help='Disables all progress indicators (used for downloads etc.).',
             action='store_false')
 
-    if not {'--no-raw', '-n'}.isdisjoint(sys.argv):
+    if not {'--no-raw', '-n'}.isdisjoint(argv):
         parser.add_argument(
             '-n', '--no-raw',
             help='Defines if raw data will be stored for further use.',
             action='store_true')
 
-    if not {'--make_plot', '-p'}.isdisjoint(sys.argv):
+    if not {'--make_plot', '-p'}.isdisjoint(argv):
         parser.add_argument('-p', '--make-plot',
                             help='Plots the data.', action='store_true')
 
-    if '--interactive' in sys.argv:
+    if '--interactive' in argv:
         parser.add_argument(
             '--interactive',
-            help='Interactive download (Handle warnings, passwords etc.).', action='store_true')
+            help='Interactive download (Handle warnings, passwords etc.).',
+            action='store_true')
 
-    if not {'--verbose', '-v', '-vv', '-vvv', '-vvvv', '-vvvvv', '-vvvvvv'}.isdisjoint(sys.argv):
+    if not {'--verbose', '-v', '-vv', '-vvv', '-vvvv', '-vvvvv', '-vvvvvv'}.isdisjoint(argv):
         parser.add_argument(
             '-v', '--verbose', dest='verbosity_level',
             help='Increases verbosity level (Trace, Debug, Info, Warning, Error, Critical, Off).',
             action='count', default=0)
 
-    if '--skip-checks' in sys.argv:
+    if '--skip-checks' in argv:
         parser.add_argument(
             '--skip-checks', dest='run_checks', action='store_false',
             help='Skips sanity checks etc.')
 
-    if '--to-dataset' in sys.argv:
+    if '--to-dataset' in argv:
         parser.add_argument(
             '--to-dataset', dest='to_dataset',
             help="To return saved dataframes as objects.",
             action='store_true'
         )
 
-    args = vars(parser.parse_args())
+    args, unknown = parser.parse_known_args()
+    if unknown:
+        # if unknown arguments are present, check if they are from
+        # a test runner (unittest, pytest). If not, we want to fail.
+        if not any(x in sys.argv[0] for x in
+                   ['unittest', 'pytest']):
+            parser.parse_args()
+
+    args = vars(args)
 
     return args
 

pycode/memilio-epidata/pyproject.toml

@@ -14,7 +14,7 @@ maintainers = [
   { email = "martin.kuehn@dlr.de" }
 ]
 dependencies = [
-  "setuptools>=68",
+  "packaging",
   "pandas>=2.0.0",
   "pyarrow",
   "matplotlib",