1483 memilio.simulation incompatible with pandas 3

docs/source/python/m-epidata.rst

@@ -31,7 +31,6 @@ After installation the following functions are available:
 * ``get_divi_data``: Downloads ICU data from German DIVI Intensivregister (DIVI).
 * ``get_hospitalization_data``: Downloads data about COVID-19 hospitalizations data from Robert Koch-Institut (RKI-H).
 * ``get_jh_data``: Downloads COVID-19 case data from Johns Hopkins University (JH).
-* ``get_npi_data``: Loads a certain resolution of recorded NPI data from the Corona Datenplattform and extracts the counties asked for and activates the NPIs if they are incidence dependent.
 * ``get_population_data``: Downloads population data for German federal states and counties from various public sources (P).
 * ``get_simulation_data``: Downloads all data required for a simulation with the graph-metapopulation model which are SARS-CoV-2 case data(RKI-C), population data (P), ICU data (DIVI) and COVID-19 vaccination data from Robert Koch-Institut (RKI-V).
 * ``get_testing_data``: Downloads data about SARS-CoV-2 PCR tests from Robert Koch-Institut (RKI-T).
@@ -41,14 +40,14 @@ After installation the following functions are available:
 * ``transformWeatherData``: Transforms weather data.
 
 For a detailed description of the run options and the resulting data files written
-see the `epidata subfolder <memilio/epidata/README.rst>`_.
+see the `epidata subfolder <https://github.com/SciCompMod/memilio/blob/main/pycode/memilio-epidata/README.rst>`_.
 
 The downloaded data is written either to HDF5 or json files.
 
 Additional Tools
 ----------------
 
-Some additional tools for processing or analysing data can be found in `tools directory <tools/README.md>`_.
+Some additional tools for processing or analysing data can be found in `tools directory <https://github.com/SciCompMod/memilio/tree/main/tools>`_.
 
 Notes for developers
 --------------------

pycode/memilio-epidata/memilio/epidata/README.rst

@@ -214,7 +214,7 @@ BAA            Germany     mobility_bfa_2020_dim400           number of commuter
 ============== ==========  =================================== =================
 
 More detailed information can be found in the
-`documentation <https://scicompmod.github.io/memilio/documentation/index.html>`_  of the different functions.
+`documentation <https://memilio.readthedocs.io/en/latest/python/m-epidata.html>`_  of the different functions.
 
 Notes for developers
 --------------------

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

@@ -373,7 +373,7 @@ def get_nuts3_county_id_map():
     county_table = get_official_county_table()
     # delete rows with nuts3 = 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
@@ -84,8 +84,6 @@ def __init__(self, out_folder, **kwargs):
         path = os.path.join(os.path.dirname(
             os.path.abspath(__file__)), 'download_config.conf')
 
-        # activate CoW for more predictable behaviour of pandas DataFrames
-        pd.options.mode.copy_on_write = True
         # read in config file
         # if no config file is given, use default values
         if os.path.exists(path):
@@ -196,9 +194,12 @@ 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 +439,7 @@ 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 +455,10 @@ 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'],
@@ -504,7 +506,8 @@ def cli(what):
     if '--interactive' in sys.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):
         parser.add_argument(