Fixing test suite + no more warnings

Author: BESNIER AURELIEN

src/hydroshoot/energy.py

@@ -141,7 +141,7 @@ def set_local_wind_speed(g, meteo, leaf_lbl_prefix='L') -> dict:
 
     """
     leaves = get_leaves(g, leaf_lbl_prefix)
-    u = meteo.u[0]
+    u = meteo.u.iloc[0]
     return {vid: u for vid in leaves}
 
 
@@ -380,7 +380,7 @@ def force_soil_temperature(meteo):
         t_soil = meteo.Tsoil[0]
     else:
         dt_soil = [3, 3, 3, 3, 3, 3, 3, 3, 10, 15, 20, 20, 20, 20, 20, 15, 6, 5, 4, 3, 3, 3, 3, 3]
-        t_soil = meteo.Tac[0] + dt_soil[meteo.index.hour[0]]
+        t_soil = meteo.Tac.iloc[0] + dt_soil[meteo.index.hour[0]]
     return t_soil
 
 

src/hydroshoot/initialisation.py

@@ -26,7 +26,7 @@ def calc_nitrogen_distribution(g: MTG, gdd_since_budbreak: float, weather: DataF
             temperature_base=params.phenology.t_base)
 
     date_beg_sim = params.simulation.date_beg
-    date_range_last_10_days = date_range(date_beg_sim + timedelta(days=-10), date_beg_sim, freq='H')
+    date_range_last_10_days = date_range(date_beg_sim + timedelta(days=-10), date_beg_sim, freq='h')
     caribu_source, _ = irradiance_distribution(
         meteo=weather.loc[date_range_last_10_days, :],
         geo_location=params.simulation.geo_location,
@@ -70,7 +70,6 @@ def remove_stem_geometry(g: MTG):
     to_remove = [i for i in geom_prop if not g.node(i).label.startswith(('L', 'other', 'soil'))]
     [geom_prop.pop(x) for x in to_remove]
     g.properties()['geometry'] = geom_prop
-    pass
 
 
 def set_photosynthetic_capacity(g: MTG, photo_n_params: dict, deactivation_enthalopy: float, leaf_lbl_prefix: str):
@@ -82,7 +81,6 @@ def set_photosynthetic_capacity(g: MTG, photo_n_params: dict, deactivation_entha
         n.TPU25 = photo_n_params['TPU25_N'][0] * nitrogen_content + photo_n_params['TPU25_N'][1]
         n.Rd = photo_n_params['Rd_N'][0] * nitrogen_content + photo_n_params['Rd_N'][1]
         n.dHd = deactivation_enthalopy
-    pass
 
 
 def set_collar_water_potential_function(params: Params, **kwargs) -> Callable:

src/hydroshoot/params.py

@@ -91,8 +91,8 @@ def __init__(self, simulation_dict):
         self.is_negligible_shoot_resistance = simulation_dict['negligible_shoot_resistance']
         self.is_energy_budget = simulation_dict['energy_budget']
 
-        self.date_range = date_range(start=self.date_beg, end=self.date_end, freq='H')
-        self.conv_to_second = {'D': 86.4e3, 'H': 3600., 'T': 60., 'S': 1.}[self.date_range.freqstr]
+        self.date_range = date_range(start=self.date_beg, end=self.date_end, freq='h')
+        self.conv_to_second = {'D': 86.4e3, 'h': 3600., 'T': 60., 'S': 1.}[self.date_range.freqstr]
         self.conv_to_meter = {'mm': 1.e-3, 'cm': 1.e-2, 'm': 1.}[self.unit_scene_length]
         self.geo_location = (self._latitude, self._longitude, self._elevation)
 

src/hydroshoot/soil.py

@@ -1,4 +1,5 @@
 from math import pi, log
+import numpy as np
 
 from hydroshoot import constants as cst
 
@@ -174,7 +175,8 @@ def calc_root_soil_resistance(soil_conductivity: float, rhyzosphere_volume: floa
     root_length_density = root_length / rhyzosphere_volume  # [m m3]
     d = (pi * root_length_density) ** -0.5  # half distance between roots [m]
     k = soil_conductivity * 1.e-2 / 86400. * (2 * pi * d * root_length) * cst.water_density  # cm d-1 -> kg m-2 s-1
-    return log(d ** 2 / ((2 * root_radius) ** 2)) / (4 * pi * k)  # m2 s kg-1
+    with np.errstate(divide='ignore'):
+        return log(d ** 2 / ((2 * root_radius) ** 2)) / (4 * pi * k)  # m2 s kg-1
 
 
 def calc_collar_water_potential(transpiration: float, bulk_soil_water_potential: float, rhyzosphere_volume: float,

test/__init__.py

@@ -4,7 +4,7 @@
 import hydroshoot.energy as energy
 from hydroshoot.architecture import get_leaves
 from hydroshoot.energy import set_form_factors_simplified, calc_leaf_temperature, force_soil_temperature
-from test.non_regression_data import potted_syrah, meteo
+from non_regression_data import potted_syrah, meteo
 
 
 def test_pgl_scene():
@@ -47,7 +47,7 @@ def test_form_factors_simplified():
 def test_forced_soil_temperature():
     met = meteo().iloc[[12], :]
     tsoil = force_soil_temperature(met)
-    assert tsoil == met.Tac[0] + 20
+    assert tsoil == met.Tac.iloc[0] + 20
 
 
 def test_leaf_temperature():
@@ -73,4 +73,4 @@ def test_leaf_temperature():
     first = list(tleaf.keys())[0]
     for vid in tleaf:
         assert tleaf[vid] == tleaf[first]
-        assert tleaf[vid] != met.Tac[0]
+        assert tleaf[vid] != met.Tac.iloc[0]

test/test_energy.py

@@ -2,7 +2,7 @@
 from openalea.mtg import traversal
 
 from hydroshoot import hydraulic, architecture
-from test.non_regression_data import potted_syrah
+from non_regression_data import potted_syrah
 
 
 def test_conductivity_max_increases_as_segment_diameter_increases():

test/test_hydraulic.py

@@ -1,7 +1,7 @@
 from numpy.testing import assert_almost_equal
 
 from hydroshoot.irradiance import irradiance_distribution, hsCaribu, set_optical_properties, e_conv_PPFD
-from test.non_regression_data import potted_syrah, meteo
+from non_regression_data import potted_syrah, meteo
 
 
 def test_irradiance_distribution():

test/test_irradiance.py

@@ -4,7 +4,7 @@
 from numpy.testing import assert_array_almost_equal
 
 from hydroshoot import model
-from test import non_regression_data
+import non_regression_data
 
 
 def test_potted_grapevine():