Add openalea namespace

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')

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')

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

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

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

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

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

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

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

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

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

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

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

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

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):

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,

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

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

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

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

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

setup.py

@@ -8,7 +8,7 @@
 from os.path import abspath, normpath
 from os.path import join as pj
 
-from setuptools import setup, find_packages
+from setuptools import setup, find_namespace_packages
 
 
 short_descr = "HydroShoot is an FSPM model to simulate gas-exchange on vine"
@@ -17,14 +17,15 @@
 
 
 # find version number in src/hydroshoot/version.py
-version = {}
-with open("src/hydroshoot/version.py") as fp:
-    exec(fp.read(), version)
+_version = {}
+with open("src/openalea/hydroshoot/version.py") as fp:
+    exec(fp.read(), _version)
 
+version = _version["__version__"]
 
 data_files = []
 
-nb = len(normpath(abspath("src/hydroshoot_data"))) + 1
+nb = len(normpath(abspath("src/openalea/hydroshoot_data"))) + 1
 
 
 def data_rel_pth(pth):
@@ -34,25 +35,26 @@ def data_rel_pth(pth):
     return abs_pth[nb:]
 
 
-for root, dnames, fnames in walk("src/hydroshoot_data"):
+for root, dnames, fnames in walk("src/openalea/hydroshoot_data"):
     for name in fnames:
         data_files.append(data_rel_pth(pj(root, name)))
 
 
 setup_kwds = dict(
     name='hydroshoot',
-    version=version["__version__"],
+    version=version,
     description=short_descr,
     long_description=readme + '\n\n' + history,
     author="Rami Albasha, Christian Fournier, Christophe Pradal, Eric Lebon, ",
     author_email="rami albasha at inra dot fr, @fournier-ch, @pradal, eric dot lebon at inra dot fr, ",
     url='https://github.com/openalea/hydroshoot',
-    license='cecill-c',
+    license='CeCILL-C',
     zip_safe=False,
 
-    packages=find_packages('src'),
+    packages=find_namespace_packages(where='src', include=['openalea', 'openalea.*']),
     package_dir={'': 'src'},
-
+    namespace_packages=['openalea'],
+
     include_package_data=True,
     package_data={'hydroshoot_data': data_files},
     install_requires=[
@@ -61,7 +63,7 @@ def data_rel_pth(pth):
         "pytest",
         ],
     entry_points={},
-    keywords='',
+    keywords=['FSPM', 'openalea', 'plant', 'MTG', 'Hydraulic Structure', 'gas-exchange', 'energy balance'],
     test_suite='nose.collector',
 )
 # #}

src/hydroshoot/architecture.py → 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
 
 
 # ==============================================================================

src/hydroshoot/display.py → 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'$\mathregular{E_{abs}\/[\mu mol\/m^{-2}\/s^{-1}]}$',

src/hydroshoot/energy.py → 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):

src/hydroshoot/exchange.py → 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
 
 
 # ==============================================================================

src/hydroshoot/hydraulic.py → 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.):

src/hydroshoot/initialisation.py → 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:

src/hydroshoot/io.py → 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):

src/hydroshoot/irradiance.py → 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.):

src/hydroshoot/model.py → 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,

src/hydroshoot/preprocess.py → 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,