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Move to Pandas 1.x #1266

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Aug 11, 2020
Merged

Move to Pandas 1.x #1266

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618a44e
Pin pandas to v1.1
epassaro Aug 5, 2020
e35a30f
Replace `codes` with `labels`
epassaro Aug 5, 2020
56cc45d
Empty data exception moved to `errors` module
epassaro Aug 5, 2020
3224952
`ix` method is deprecated
epassaro Aug 5, 2020
6ee0fb4
Pin pandas to v1.0
epassaro Aug 5, 2020
abf4b6c
[skip-ci] Remove `ix` method from documentation scripts
epassaro Aug 5, 2020
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8 changes: 4 additions & 4 deletions docs/physics/plasma/plasma_plots/lte_ionization_balance.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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)

Expand All @@ -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,
Expand Down
18 changes: 9 additions & 9 deletions docs/physics/plasma/plasma_plots/nebular_ionization_balance.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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)

Expand All @@ -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,
Expand Down Expand Up @@ -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,
Expand Down
2 changes: 1 addition & 1 deletion tardis/io/parsers/csvy.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
4 changes: 2 additions & 2 deletions tardis/plasma/properties/atomic.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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()))
Expand Down
2 changes: 1 addition & 1 deletion tardis/plasma/properties/partition_function.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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]
Expand Down
2 changes: 1 addition & 1 deletion tardis_env3.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ dependencies:
- pip
- numpy=1.16
- scipy=1.5
- pandas=0.24
- pandas=1.0
- astropy=3
- numba=0.50
- numexpr
Expand Down