Move to Pandas 1.x (#1266)

* Pin pandas to v1.1

* Replace `codes` with `labels`

* Empty data exception moved to `errors` module

* `ix` method is deprecated

* Pin pandas to v1.0

* [skip-ci] Remove `ix` method from documentation scripts

docs/physics/plasma/plasma_plots/lte_ionization_balance.py

@@ -40,7 +40,7 @@
 # Initializing a dataframe to store the ion populations  and level populations for the different temperatures
 ion_number_densities = pd.DataFrame(index=lte_plasma.ion_populations.index)
 level_populations = pd.DataFrame(
-    index=lte_plasma.level_populations.ix[14, 1].index
+    index=lte_plasma.level_populations.loc[14, 1].index
 )
 t_rads = np.linspace(2000, 20000, 100)
 
@@ -54,19 +54,19 @@
     ion_number_densities[t_rad] = ion_density
 
     # normalizing the level_populations for Si II
-    current_level_population = lte_plasma.level_populations[0].ix[
+    current_level_population = lte_plasma.level_populations[0].loc[
         14, 1
     ] / lte_plasma.ion_populations.get_value((14, 1), 0)
 
     # normalizing with statistical weight
-    current_level_population /= atom_data.levels.ix[14, 1].g
+    current_level_population /= atom_data.levels.loc[14, 1].g
 
     level_populations[t_rad] = current_level_population
 
 ion_colors = ["b", "g", "r", "k"]
 
 for ion_number in [0, 1, 2, 3]:
-    current_ion_density = ion_number_densities.ix[14, ion_number]
+    current_ion_density = ion_number_densities.loc[14, ion_number]
     ax1.plot(
         current_ion_density.index,
         current_ion_density.values,

docs/physics/plasma/plasma_plots/nebular_ionization_balance.py

@@ -38,7 +38,7 @@
 # Initializing a dataframe to store the ion populations  and level populations for the different temperatures
 ion_number_densities = pd.DataFrame(index=nebular_plasma.ion_populations.index)
 level_populations = pd.DataFrame(
-    index=nebular_plasma.level_populations.ix[14, 1].index
+    index=nebular_plasma.level_populations.loc[14, 1].index
 )
 t_rads = np.linspace(2000, 20000, 100)
 
@@ -53,18 +53,18 @@
 
     # normalizing the level_populations for Si II
     current_level_population = (
-        nebular_plasma.level_populations.ix[14, 1]
-        / nebular_plasma.ion_populations.ix[14, 1]
+        nebular_plasma.level_populations.loc[14, 1]
+        / nebular_plasma.ion_populations.loc[14, 1]
     )
     # normalizing with statistical weight
-    current_level_population /= atom_data.levels.ix[14, 1].g
+    current_level_population /= atom_data.levels.loc[14, 1].g
 
     level_populations[t_rad] = current_level_population
 
 ion_colors = ["b", "g", "r", "k"]
 
 for ion_number in [0, 1, 2, 3]:
-    current_ion_density = ion_number_densities.ix[14, ion_number]
+    current_ion_density = ion_number_densities.loc[14, ion_number]
     ax1.plot(
         current_ion_density.index,
         current_ion_density.values,
@@ -98,19 +98,19 @@
 
     # normalizing the level_populations for Si II
     current_level_population = (
-        nebular_plasma.level_populations.ix[14, 1]
-        / nebular_plasma.ion_populations.ix[14, 1]
+        nebular_plasma.level_populations.loc[14, 1]
+        / nebular_plasma.ion_populations.loc[14, 1]
     )
     # normalizing with statistical weight
-    current_level_population /= atom_data.levels.ix[14, 1].g
+    current_level_population /= atom_data.levels.loc[14, 1].g
 
     level_populations[t_rad] = current_level_population
 
 # Plotting the ion fractions
 
 for ion_number in [0, 1, 2, 3]:
     print("w=0.5")
-    current_ion_density = ion_number_densities.ix[14, ion_number]
+    current_ion_density = ion_number_densities.loc[14, ion_number]
     ax1.plot(
         current_ion_density.index,
         current_ion_density.values,

tardis/io/parsers/csvy.py

@@ -38,7 +38,7 @@ def load_csvy(fname):
         yaml_dict = yaml.load("".join(yaml_lines[1:-1]), YAMLLoader)
         try:
             data = pd.read_csv(fname, skiprows=yaml_end_ind + 1)
-        except pd.io.common.EmptyDataError as e:
+        except pd.errors.EmptyDataError as e:
             data = None
 
     return yaml_dict, data

tardis/plasma/properties/atomic.py

@@ -226,8 +226,8 @@ class ZetaData(BaseAtomicDataProperty):
     outputs = ("zeta_data",)
 
     def _filter_atomic_property(self, zeta_data, selected_atoms):
-        zeta_data["atomic_number"] = zeta_data.index.labels[0] + 1
-        zeta_data["ion_number"] = zeta_data.index.labels[1] + 1
+        zeta_data["atomic_number"] = zeta_data.index.codes[0] + 1
+        zeta_data["ion_number"] = zeta_data.index.codes[1] + 1
         zeta_data = zeta_data[zeta_data.atomic_number.isin(selected_atoms)]
         zeta_data_check = counter(zeta_data.atomic_number.values)
         keys = np.array(list(zeta_data_check.keys()))

tardis/plasma/properties/partition_function.py

@@ -248,7 +248,7 @@ def _main_nlte_calculation(
                         )
                     else:
                         raise e
-                general_level_boltzmann_factor[i].ix[species] = (
+                general_level_boltzmann_factor[i].loc[species] = (
                     level_boltzmann_factor
                     * g.loc[species][0]
                     / level_boltzmann_factor[0]

tardis_env3.yml

@@ -8,7 +8,7 @@ dependencies:
   - pip
   - numpy=1.16
   - scipy=1.5
-  - pandas=0.24
+  - pandas=1.0
   - astropy=3
   - numba=0.50
   - numexpr