Merge pull request #122 from openalea/namespace

pradal · web-flow · commit c56defbb7ddc · 2025-12-03T11:34:23.000+01:00
Add openalea namespace
diff --git a/conda/meta.yaml b/conda/meta.yaml
@@ -55,6 +55,6 @@ about:
 
 extra:
   recipe-maintainers:
-    - artzet-s
+    - RamiALBASHA
     - pradal
-    - fournier
+    - christian34
diff --git a/doc/usage.rst b/doc/usage.rst
@@ -62,7 +62,7 @@ Set the required files up
 
         .. code-block:: python
 
-            from hydroshoot import model
+            from openalea.hydroshoot import model
 
             model.run(g, working_directory, psi_soil=-0.5)
 
@@ -103,7 +103,7 @@ Let's build the mock-up using the digitalization data provided in "grapevine_pot
 
     from openalea.mtg import traversal
     from openalea.plantgl.all import Scene
-    from hydroshoot import architecture, display, model
+    from openalea.hydroshoot import architecture, display, model
 
     # Path for plant digitalization data.
     g = architecture.vine_mtg('grapevine_pot.csv')
diff --git a/example/figs/paper_figs.py b/example/figs/paper_figs.py
@@ -972,9 +972,9 @@ def estimate_energy_balance_contribution():
     from datetime import datetime, timedelta
     from matplotlib import dates, pyplot, patches, colors, colorbar, rcParams, ticker, gridspec
 
-    from hydroshoot.architecture import mtg_load
-    from hydroshoot.utilities import vapor_pressure_deficit as VPDa
-    from hydroshoot import display
+    from openalea.hydroshoot.architecture import mtg_load
+    from openalea.hydroshoot.utilities import vapor_pressure_deficit as VPDa
+    from openalea.hydroshoot import display
 
     rcParams.update({'font.size': 11})
     pyplot.style.use('seaborn-ticks')
diff --git a/example/gdc_can1_grapevine/sim.py b/example/gdc_can1_grapevine/sim.py
@@ -3,7 +3,7 @@
 from openalea.mtg import traversal
 from openalea.plantgl.all import Scene
 
-from hydroshoot import architecture, display, model
+from openalea.hydroshoot import architecture, display, model
 
 if __name__ == '__main__':
     path_project = Path(__file__).parent
diff --git a/example/gdc_can2_grapevine/sim.py b/example/gdc_can2_grapevine/sim.py
@@ -3,7 +3,7 @@
 from openalea.mtg import traversal
 from openalea.plantgl.all import Scene
 
-from hydroshoot import architecture, display, model
+from openalea.hydroshoot import architecture, display, model
 
 if __name__ == '__main__':
     path_project = Path(__file__).parent
diff --git a/example/gdc_can3_grapevine/sim.py b/example/gdc_can3_grapevine/sim.py
@@ -3,7 +3,7 @@
 from openalea.mtg import traversal
 from openalea.plantgl.all import Scene
 
-from hydroshoot import architecture, display, model
+from openalea.hydroshoot import architecture, display, model
 
 if __name__ == '__main__':
     path_project = Path(__file__).parent
diff --git a/example/misc/sim.py b/example/misc/sim.py
@@ -4,7 +4,7 @@
 from openalea.mtg import traversal
 from openalea.plantgl.all import Scene
 
-from hydroshoot import architecture, display, model
+from openalea.hydroshoot import architecture, display, model
 
 # =============================================================================
 # Construct the plant mock-up
diff --git a/example/modularity/ws/sim_1/sim.py b/example/modularity/ws/sim_1/sim.py
@@ -3,7 +3,7 @@
 from openalea.mtg import traversal
 from openalea.plantgl.all import Scene
 
-from hydroshoot import architecture, display, model
+from openalea.hydroshoot import architecture, display, model
 
 if __name__ == '__main__':
     path_project = Path(__file__).parent
diff --git a/example/modularity/ws/sim_2/sim.py b/example/modularity/ws/sim_2/sim.py
@@ -3,7 +3,7 @@
 from openalea.mtg import traversal
 from openalea.plantgl.all import Scene
 
-from hydroshoot import architecture, display, model
+from openalea.hydroshoot import architecture, display, model
 
 if __name__ == '__main__':
     path_project = Path(__file__).parent
diff --git a/example/modularity/ws/sim_3/sim.py b/example/modularity/ws/sim_3/sim.py
@@ -3,7 +3,7 @@
 from openalea.mtg import traversal
 from openalea.plantgl.all import Scene
 
-from hydroshoot import architecture, display, model
+from openalea.hydroshoot import architecture, display, model
 
 if __name__ == '__main__':
     path_project = Path(__file__).parent
diff --git a/example/modularity/ws/sim_4/sim.py b/example/modularity/ws/sim_4/sim.py
@@ -3,7 +3,7 @@
 from openalea.mtg import traversal
 from openalea.plantgl.all import Scene
 
-from hydroshoot import architecture, display, model
+from openalea.hydroshoot import architecture, display, model
 
 if __name__ == '__main__':
     path_project = Path(__file__).parent
diff --git a/example/modularity/ww/sim_1/sim.py b/example/modularity/ww/sim_1/sim.py
@@ -3,7 +3,7 @@
 from openalea.mtg import traversal
 from openalea.plantgl.all import Scene
 
-from hydroshoot import architecture, display, model
+from openalea.hydroshoot import architecture, display, model
 
 if __name__ == '__main__':
     path_project = Path(__file__).parent
diff --git a/example/modularity/ww/sim_2/sim.py b/example/modularity/ww/sim_2/sim.py
@@ -3,7 +3,7 @@
 from openalea.mtg import traversal
 from openalea.plantgl.all import Scene
 
-from hydroshoot import architecture, display, model
+from openalea.hydroshoot import architecture, display, model
 
 if __name__ == '__main__':
     path_project = Path(__file__).parent
diff --git a/example/modularity/ww/sim_3/sim.py b/example/modularity/ww/sim_3/sim.py
@@ -3,7 +3,7 @@
 from openalea.mtg import traversal
 from openalea.plantgl.all import Scene
 
-from hydroshoot import architecture, display, model
+from openalea.hydroshoot import architecture, display, model
 
 if __name__ == '__main__':
     path_project = Path(__file__).parent
diff --git a/example/modularity/ww/sim_4/sim.py b/example/modularity/ww/sim_4/sim.py
@@ -3,7 +3,7 @@
 from openalea.mtg import traversal
 from openalea.plantgl.all import Scene
 
-from hydroshoot import architecture, display, model
+from openalea.hydroshoot import architecture, display, model
 
 if __name__ == '__main__':
     path_project = Path(__file__).parent
diff --git a/example/potted_grapevine/sim.py b/example/potted_grapevine/sim.py
@@ -8,7 +8,7 @@
 from openalea.mtg import traversal, mtg
 from openalea.plantgl.all import Scene
 
-from hydroshoot import architecture, display, model
+from openalea.hydroshoot import architecture, display, model
 
 
 def build_mtg(path_file: Path, is_show_scene: bool = True) -> (mtg.MTG, Scene):
diff --git a/example/potted_grapevine/sim_with_preprocessed_inputs.py b/example/potted_grapevine/sim_with_preprocessed_inputs.py
@@ -9,7 +9,7 @@
 from openalea.plantgl.all import Scene
 
 from example.potted_grapevine.sim import build_mtg
-from hydroshoot import io, model, initialisation
+from openalea.hydroshoot import io, model, initialisation
 
 
 def preprocess_inputs(grapevine_mtg: MTG, path_project_dir: Path, psi_soil: float, gdd_since_budbreak: float,
diff --git a/example/virtual_canopies/gdc/sim.py b/example/virtual_canopies/gdc/sim.py
@@ -4,7 +4,7 @@
 from openalea.mtg import traversal
 from openalea.plantgl.all import Scene
 
-from hydroshoot import architecture, display, model
+from openalea.hydroshoot import architecture, display, model
 
 if __name__ == '__main__':
     path_project = Path(__file__).parent
diff --git a/example/virtual_canopies/lyre/sim.py b/example/virtual_canopies/lyre/sim.py
@@ -4,7 +4,7 @@
 from openalea.mtg import traversal
 from openalea.plantgl.all import Scene
 
-from hydroshoot import architecture, display, model
+from openalea.hydroshoot import architecture, display, model
 
 if __name__ == '__main__':
     path_project = Path(__file__).parent
diff --git a/example/virtual_canopies/vsp/sim.py b/example/virtual_canopies/vsp/sim.py
@@ -4,7 +4,7 @@
 from openalea.mtg import traversal
 from openalea.plantgl.all import Scene
 
-from hydroshoot import architecture, display, model
+from openalea.hydroshoot import architecture, display, model
 
 if __name__ == '__main__':
     path_project = Path(__file__).parent
diff --git a/example/vsp_ws_grapevine/sim.py b/example/vsp_ws_grapevine/sim.py
@@ -3,7 +3,7 @@
 from openalea.mtg import traversal
 from openalea.plantgl.all import Scene
 
-from hydroshoot import architecture, display, model
+from openalea.hydroshoot import architecture, display, model
 
 if __name__ == '__main__':
     path_project = Path(__file__).parent
diff --git a/example/vsp_ww_grapevine/sim.py b/example/vsp_ww_grapevine/sim.py
@@ -3,7 +3,7 @@
 from openalea.mtg import traversal
 from openalea.plantgl.all import Scene
 
-from hydroshoot import architecture, display, model
+from openalea.hydroshoot import architecture, display, model
 
 if __name__ == '__main__':
     path_project = Path(__file__).parent
diff --git a/pyproject.toml b/pyproject.toml
@@ -3,7 +3,7 @@ requires = ["setuptools", "setuptools-scm"]
 build-backend = "setuptools.build_meta"
 
 [project]
-name = "hydroshoot"
+name = "openalea.hydroshoot"
 authors = [
   { name = "Rami Albasha"},
   { name = "Christian Fournier"},
diff --git a/src/openalea/hydroshoot/__init__.py b/src/openalea/hydroshoot/__init__.py
diff --git a/src/openalea/hydroshoot/architecture.py b/src/openalea/hydroshoot/architecture.py
@@ -27,7 +27,7 @@
 from scipy.linalg import norm, svd
 from scipy.spatial import distance
 
-from hydroshoot.extern.roman import toRoman
+from openalea.hydroshoot.extern.roman import toRoman
 
 
 # ==============================================================================
diff --git a/src/openalea/hydroshoot/constants.py b/src/openalea/hydroshoot/constants.py
diff --git a/src/openalea/hydroshoot/display.py b/src/openalea/hydroshoot/display.py
@@ -14,7 +14,7 @@
 
 plt.style.use('ggplot')
 
-from hydroshoot.soil import SOIL_PROPS
+from openalea.hydroshoot.soil import SOIL_PROPS
 
 DEFAULT_LABELS = {
     'Eabs': r'$\mathregular{E_{abs}\/[\mu mol\/m^{-2}\/s^{-1}]}$',
diff --git a/src/openalea/hydroshoot/energy.py b/src/openalea/hydroshoot/energy.py
@@ -19,9 +19,9 @@
 from sympy import Symbol
 from sympy.solvers import nsolve
 
-import hydroshoot.constants as cst
-from hydroshoot import utilities as utils
-from hydroshoot.architecture import get_leaves
+import openalea.hydroshoot.constants as cst
+from openalea.hydroshoot import utilities as utils
+from openalea.hydroshoot.architecture import get_leaves
 
 
 def pgl_scene(g, flip=False):
diff --git a/src/openalea/hydroshoot/exchange.py b/src/openalea/hydroshoot/exchange.py
@@ -10,8 +10,8 @@
 from copy import deepcopy
 from math import exp, acos, sqrt, cos, log
 
-from hydroshoot import utilities as utils
-from hydroshoot.constants import oxygen_partial_pressure as o, ideal_gaz_cst as r
+from openalea.hydroshoot import utilities as utils
+from openalea.hydroshoot.constants import oxygen_partial_pressure as o, ideal_gaz_cst as r
 
 
 # ==============================================================================
diff --git a/src/openalea/hydroshoot/extern/__init__.py b/src/openalea/hydroshoot/extern/__init__.py
diff --git a/src/openalea/hydroshoot/extern/roman.py b/src/openalea/hydroshoot/extern/roman.py
diff --git a/src/openalea/hydroshoot/hydraulic.py b/src/openalea/hydroshoot/hydraulic.py
@@ -13,7 +13,7 @@
 import openalea.mtg.traversal as traversal
 from openalea.plantgl.all import surface as surf
 
-import hydroshoot.constants as cst
+import openalea.hydroshoot.constants as cst
 
 
 def conductivity_max(diameter, a=2.8, b=0.1, min_kmax=0.):
diff --git a/src/openalea/hydroshoot/initialisation.py b/src/openalea/hydroshoot/initialisation.py
@@ -6,15 +6,15 @@
 from pandas import DataFrame
 from pandas import date_range
 
-from hydroshoot import soil
-from hydroshoot.architecture import get_mtg_base, add_soil_surface_mesh, get_leaves
-from hydroshoot.energy import (set_form_factors_simplified, set_local_wind_speed, set_local_air_temperature,
+from openalea.hydroshoot import soil
+from openalea.hydroshoot.architecture import get_mtg_base, add_soil_surface_mesh, get_leaves
+from openalea.hydroshoot.energy import (set_form_factors_simplified, set_local_wind_speed, set_local_air_temperature,
                                set_local_vpd, set_leaf_temperature_to_air_temperature)
-from hydroshoot.exchange import leaf_Na
-from hydroshoot.io import HydroShootInputs, HydroShootHourlyInputs
-from hydroshoot.irradiance import irradiance_distribution, hsCaribu, set_optical_properties
-from hydroshoot.params import Params
-from hydroshoot.preprocess import calc_gdd_since_budbreak
+from openalea.hydroshoot.exchange import leaf_Na
+from openalea.hydroshoot.io import HydroShootInputs, HydroShootHourlyInputs
+from openalea.hydroshoot.irradiance import irradiance_distribution, hsCaribu, set_optical_properties
+from openalea.hydroshoot.params import Params
+from openalea.hydroshoot.preprocess import calc_gdd_since_budbreak
 
 
 def calc_nitrogen_distribution(g: MTG, gdd_since_budbreak: float, weather: DataFrame, params: Params) -> float:
diff --git a/src/openalea/hydroshoot/io.py b/src/openalea/hydroshoot/io.py
@@ -6,11 +6,11 @@
 from openalea.plantgl.all import Scene
 from pandas import DataFrame, read_csv, DatetimeIndex
 
-from hydroshoot.architecture import get_leaves
-from hydroshoot.display import visu
-from hydroshoot.energy import force_soil_temperature
-from hydroshoot.params import Params
-from hydroshoot.soil import update_soil_water_potential
+from openalea.hydroshoot.architecture import get_leaves
+from openalea.hydroshoot.display import visu
+from openalea.hydroshoot.energy import force_soil_temperature
+from openalea.hydroshoot.params import Params
+from openalea.hydroshoot.soil import update_soil_water_potential
 
 
 class HydroShootInputs(object):
diff --git a/src/openalea/hydroshoot/irradiance.py b/src/openalea/hydroshoot/irradiance.py
@@ -16,7 +16,7 @@
 from pvlib.solarposition import ephemeris
 from pytz import timezone
 
-from hydroshoot.architecture import vector_rotation
+from openalea.hydroshoot.architecture import vector_rotation
 
 
 def local2solar(local_time, latitude, longitude, time_zone, temperature=25.):
diff --git a/src/openalea/hydroshoot/model.py b/src/openalea/hydroshoot/model.py
@@ -11,9 +11,9 @@
 from openalea.plantgl.all import Scene, surface
 from pandas import DataFrame
 
-from hydroshoot import (architecture, solver, io, soil, constants)
-from hydroshoot.energy import calc_effective_sky_temperature
-from hydroshoot.initialisation import init_model, init_hourly, set_collar_water_potential_function
+from openalea.hydroshoot import (architecture, solver, io, soil, constants)
+from openalea.hydroshoot.energy import calc_effective_sky_temperature
+from openalea.hydroshoot.initialisation import init_model, init_hourly, set_collar_water_potential_function
 
 
 def run(g: MTG, wd: Path, path_weather: Path, params: dict = None, scene: Scene = None,
diff --git a/src/openalea/hydroshoot/params.py b/src/openalea/hydroshoot/params.py
diff --git a/src/openalea/hydroshoot/params_schema.json b/src/openalea/hydroshoot/params_schema.json
diff --git a/src/openalea/hydroshoot/preprocess.py b/src/openalea/hydroshoot/preprocess.py
@@ -2,7 +2,7 @@
 
 from pandas import date_range, DataFrame
 
-from hydroshoot.utilities import calc_effective_daily_temperature
+from openalea.hydroshoot.utilities import calc_effective_daily_temperature
 
 
 def calc_gdd_since_budbreak(weather: DataFrame, date_budbreak: datetime, date_beg_sim: datetime,
diff --git a/src/openalea/hydroshoot/primitive.py b/src/openalea/hydroshoot/primitive.py
diff --git a/src/openalea/hydroshoot/soil.py b/src/openalea/hydroshoot/soil.py
@@ -1,7 +1,7 @@
 from math import pi, log
 import numpy as np
 
-from hydroshoot import constants as cst
+from openalea.hydroshoot import constants as cst
 
 SOIL_PROPS = dict(
     Sand=(0.045, 0.430, 0.145, 2.68, 712.8),
diff --git a/src/openalea/hydroshoot/solver.py b/src/openalea/hydroshoot/solver.py
@@ -2,9 +2,9 @@
 
 import openalea.mtg.traversal as traversal
 
-from hydroshoot import hydraulic, exchange, energy
-from hydroshoot.architecture import get_leaves
-from hydroshoot.soil import update_soil_water_potential
+from openalea.hydroshoot import hydraulic, exchange, energy
+from openalea.hydroshoot.architecture import get_leaves
+from openalea.hydroshoot.soil import update_soil_water_potential
 
 
 def solve_interactions(g, meteo, psi_soil, t_soil, t_sky_eff, params, calc_collar_water_potential):
diff --git a/src/openalea/hydroshoot/utilities.py b/src/openalea/hydroshoot/utilities.py
diff --git a/test/non_regression_data.py b/test/non_regression_data.py
@@ -5,7 +5,7 @@
 from pandas import read_csv, DatetimeIndex
 
 from openalea.mtg import traversal
-from hydroshoot import architecture
+from openalea.hydroshoot import architecture
 
 sources_dir = join(dirname(__file__), 'data')
 
diff --git a/test/test_architecture.py b/test/test_architecture.py
@@ -1,6 +1,6 @@
 from os.path import dirname, join
 
-from hydroshoot import architecture
+from openalea.hydroshoot import architecture
 
 Source_Dir = join(dirname(__file__), 'data')
 
diff --git a/test/test_energy.py b/test/test_energy.py
@@ -1,9 +1,9 @@
 import openalea.plantgl.all as pgl
 from numpy.testing import assert_almost_equal
 
-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
+import openalea.hydroshoot.energy as energy
+from openalea.hydroshoot.architecture import get_leaves
+from openalea.hydroshoot.energy import set_form_factors_simplified, calc_leaf_temperature, force_soil_temperature
 from non_regression_data import potted_syrah, meteo
 
 
diff --git a/test/test_exchange.py b/test/test_exchange.py
diff --git a/test/test_hydraulic.py b/test/test_hydraulic.py
diff --git a/test/test_irradiance.py b/test/test_irradiance.py
diff --git a/test/test_model.py b/test/test_model.py
diff --git a/test/test_soil.py b/test/test_soil.py
diff --git a/test/test_utilities.py b/test/test_utilities.py
