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

@@ -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):

pycode/memilio-epidata/tests/test_epidata_getDataIntoPandasDataFrame.py

@@ -518,8 +518,7 @@ def test_get_file_read(self):
         df = gd.get_file(filepath, url, read_data, param_dict)
 
         # check if non-empty dataframe is returned (Error is raised if dataframe is empty)
-        self.assertEqual(
-            str(type(df)), "<class 'pandas.core.frame.DataFrame'>")
+        self.assertIs(df.empty, False)
 
     @patch('pandas.read_json')
     def test_get_file_empty_df(self, mock_json):

pycode/memilio-simulation/tests/test_osecir.py

@@ -146,7 +146,7 @@ def test_compare_with_cpp(self):
 
             for index_compartment in range(0, 10):
                 self.assertAlmostEqual(
-                    timestep[index_compartment + 1],
+                    timestep.iloc[index_compartment + 1],
                     result[index_timestep][index_compartment], delta=1e-9)
 
     def test_study(self):

pycode/memilio-simulation/tests/test_osecir_ageres.py

@@ -146,7 +146,7 @@ def test_compare_with_cpp(self):
                         index_compartment + self.nb_comp * index_agegroup]
 
                 self.assertAlmostEqual(
-                    timestep[index_compartment + 1],
+                    timestep.iloc[index_compartment + 1],
                     dummy, delta=1e-10)
 
 

pycode/memilio-simulation/tests/test_osecirvvs.py

@@ -192,7 +192,7 @@ def test_compare_with_cpp(self):
             # compare compartments
             for index_compartment in range(0, 27):
                 self.assertAlmostEqual(
-                    timestep[index_compartment+1],
+                    timestep.iloc[index_compartment+1],
                     result[index_timestep][index_compartment], delta=1e-10)
 
     def test_check_constraints_parameters(self):

pycode/memilio-simulation/tests/test_oseir.py

@@ -107,7 +107,7 @@ def test_compare_with_cpp(self):
                 delta=1e-10)
 
             for index_compartment in range(0, 4):
-                ref = timestep[index_compartment+1]
+                ref = timestep.iloc[index_compartment+1]
                 actual = result[index_timestep][index_compartment]
 
                 tol = rel_tol * ref