diff --git a/conda/environment.yml b/conda/environment.yml index 0a92ea8..0988965 100644 --- a/conda/environment.yml +++ b/conda/environment.yml @@ -10,9 +10,9 @@ dependencies: - pip - openalea.mtg - openalea.plantgl - - oawidgets + - openalea.oawidgets - yaml - - rsml + - openalea.rsml - matplotlib-base # let pip install the rest using pyproject.toml (if you are okay with conda/pip mix) - pip: diff --git a/doc/usage.rst b/doc/usage.rst index 3aca8b7..eb39a18 100644 --- a/doc/usage.rst +++ b/doc/usage.rst @@ -125,7 +125,7 @@ arabidopsis-simple example http://rootsystemml.github.io/images/examples/arabido .. code-block:: python - import rsml + import openalea.rsml as rsml from openalea.hydroroot import radius from openalea.hydroroot.main import hydroroot_flow from openalea.hydroroot.display import plot diff --git a/example/example_archi_from_file.ipynb b/example/example_archi_from_file.ipynb index 4b45ee8..0a04268 100644 --- a/example/example_archi_from_file.ipynb +++ b/example/example_archi_from_file.ipynb @@ -64,7 +64,7 @@ "metadata": {}, "outputs": [], "source": [ - "from oawidgets.plantgl import PlantGL # notebook viewer 3D\n", + "from openalea.oawidgets.plantgl import PlantGL # notebook viewer 3D\n", "from openalea.plantgl.algo.view import view # 2D view\n", "from openalea.hydroroot.display import mtg_scene\n", "from openalea.hydroroot.read_file import read_archi_data\n", @@ -204,7 +204,7 @@ "source": [ "You may change the property to display to the hydrostatic pressure inside the xylem vessels for instance\n", "\n", - "to reduce notebook size we use here a 2D view but you can use the oawidgets `PlantGL(s)` to display an interactive 3D view" + "to reduce notebook size we use here a 2D view but you can use the openalea.oawidgets `PlantGL(s)` to display an interactive 3D view" ] }, { diff --git a/example/example_archi_from_rsml.ipynb b/example/example_archi_from_rsml.ipynb index 51d599b..da28cd5 100644 --- a/example/example_archi_from_rsml.ipynb +++ b/example/example_archi_from_rsml.ipynb @@ -27,10 +27,10 @@ "metadata": {}, "outputs": [], "source": [ - "import rsml\n", + "import openalea.rsml as rsml\n", "from openalea.hydroroot import radius\n", "from openalea.hydroroot.main import hydroroot_flow\n", - "from oawidgets.plantgl import PlantGL # notebook viewer 3D\n", + "from openalea.oawidgets.plantgl import PlantGL # notebook viewer 3D\n", "from openalea.plantgl.algo.view import view # 2D view\n", "from openalea.hydroroot.display import mtg_scene\n", "from openalea.hydroroot.hydro_io import import_rsml_to_discrete_mtg, export_mtg_to_rsml" @@ -191,7 +191,7 @@ "source": [ "Display the local water uptake heatmap\n", "\n", - "to reduce notebook size we use here a 2D view but you can use the oawidgets `PlantGL(s)` to display an interactive 3D view" + "to reduce notebook size we use here a 2D view but you can use the openalea.oawidgets `PlantGL(s)` to display an interactive 3D view" ] }, { diff --git a/example/example_generated_archi.ipynb b/example/example_generated_archi.ipynb index 6826d0b..1f41fe8 100644 --- a/example/example_generated_archi.ipynb +++ b/example/example_generated_archi.ipynb @@ -27,7 +27,7 @@ "source": [ "import pandas \n", "from openalea.hydroroot.main import root_builder, hydroroot_flow\n", - "from oawidgets.plantgl import PlantGL # notebook viewer 3D\n", + "from openalea.oawidgets.plantgl import PlantGL # notebook viewer 3D\n", "from openalea.plantgl.algo.view import view # 2D view\n", "from openalea.hydroroot.display import mtg_scene" ] @@ -141,7 +141,7 @@ "source": [ "Display the local water uptake heatmap\n", "\n", - "to reduce notebook size we use here a 2D view but you can use the oawidgets `PlantGL(s)` to display an interactive 3D view" + "to reduce notebook size we use here a 2D view but you can use the openalea.oawidgets `PlantGL(s)` to display an interactive 3D view" ] }, { diff --git a/example/example_k_adjustment.ipynb b/example/example_k_adjustment.ipynb index 00d83e4..fcdab20 100644 --- a/example/example_k_adjustment.ipynb +++ b/example/example_k_adjustment.ipynb @@ -31,7 +31,7 @@ "from openalea.hydroroot.main import hydroroot_flow, root_builder\n", "from openalea.hydroroot.init_parameter import Parameters\n", "from openalea.hydroroot.read_file import read_archi_data\n", - "from oawidgets.plantgl import PlantGL # notebook viewer 3D\n", + "from openalea.oawidgets.plantgl import PlantGL # notebook viewer 3D\n", "from openalea.plantgl.algo.view import view # 2D view\n", "from openalea.hydroroot.display import mtg_scene" ] @@ -174,7 +174,7 @@ "source": [ "Display the local water uptake heatmap\n", "\n", - "to reduce notebook size we use here a 2D view but you can use the oawidgets `PlantGL(s)` to display an interactive 3D view" + "to reduce notebook size we use here a 2D view but you can use the openalea.oawidgets `PlantGL(s)` to display an interactive 3D view" ] }, { diff --git a/example/example_parameter_class.ipynb b/example/example_parameter_class.ipynb index c9bb82e..eb5ed9f 100644 --- a/example/example_parameter_class.ipynb +++ b/example/example_parameter_class.ipynb @@ -192,7 +192,7 @@ "from openalea.hydroroot.main import hydroroot_flow, root_builder\n", "from openalea.hydroroot.init_parameter import Parameters\n", "from openalea.hydroroot.read_file import read_archi_data\n", - "from oawidgets.plantgl import PlantGL # notebook viewer 3D\n", + "from openalea.oawidgets.plantgl import PlantGL # notebook viewer 3D\n", "from openalea.plantgl.algo.view import view # 2D view\n", "from openalea.hydroroot.display import mtg_scene" ] @@ -344,7 +344,7 @@ "source": [ "Display the local water uptake heatmap\n", "\n", - "to reduce notebook size we use here a 2D view but you can use the oawidgets `PlantGL(s)` to display an interactive 3D view" + "to reduce notebook size we use here a 2D view but you can use the openalea.oawidgets `PlantGL(s)` to display an interactive 3D view" ] }, { diff --git a/example/example_rsml_io.py b/example/example_rsml_io.py index 5170832..0677e80 100644 --- a/example/example_rsml_io.py +++ b/example/example_rsml_io.py @@ -26,7 +26,7 @@ """ import glob -import rsml +import openalea.rsml as rsml import argparse import sys diff --git a/example/example_solute_water_transport.ipynb b/example/example_solute_water_transport.ipynb index 4e7d777..330af48 100644 --- a/example/example_solute_water_transport.ipynb +++ b/example/example_solute_water_transport.ipynb @@ -32,7 +32,7 @@ "from openalea.hydroroot.read_file import read_archi_data\n", "from openalea.hydroroot.conductance import set_conductances\n", "from openalea.hydroroot.water_solute_transport import pressure_calculation_no_non_permeating_solutes, init_some_MTG_properties\n", - "from oawidgets.plantgl import PlantGL # notebook viewer 3D\n", + "from openalea.oawidgets.plantgl import PlantGL # notebook viewer 3D\n", "from openalea.plantgl.algo.view import view # 2D view\n", "from openalea.hydroroot.display import mtg_scene" ] diff --git a/pyproject.toml b/pyproject.toml index c0d735c..063a093 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -60,9 +60,9 @@ channels = [ dependencies = [ "openalea.mtg", "openalea.plantgl", - "oawidgets", + "openalea.oawidgets", "yaml", - "rsml", + "openalea.rsml", "matplotlib-base" # does not exist in pip ] diff --git a/src/openalea/hydroroot/hydro_io.py b/src/openalea/hydroroot/hydro_io.py index 21a3e4a..fb48940 100644 --- a/src/openalea/hydroroot/hydro_io.py +++ b/src/openalea/hydroroot/hydro_io.py @@ -5,7 +5,7 @@ from openalea.mtg.algo import axis from openalea.mtg.traversal import * -from rsml import continuous, io +from openalea.rsml import continuous, io from openalea.hydroroot import display diff --git a/test/21-06-11-test_rsml.py b/test/21-06-11-test_rsml.py index 87cbd65..7caba93 100644 --- a/test/21-06-11-test_rsml.py +++ b/test/21-06-11-test_rsml.py @@ -3,7 +3,7 @@ from openalea.mtg import * from openalea.hydroroot import display from path import Path -from rsml.continuous import toporder +from openalea.rsml.continuous import toporder data = Path('./data/200703-YBFB-Col-2.mtg') # gini = MTG(data) @@ -30,7 +30,7 @@ def quotient_axis(v): g = g.insert_scale(inf_scale=1, partition=lambda v: v==root_id, default_label='P') #3 Transform to rsml -from rsml import continuous, io, plot +from openalea.rsml import continuous, io, plot gcopy = g.copy() diff --git a/test/test_rsml_yaml.py b/test/test_rsml_yaml.py index 41eaf32..949f64b 100644 --- a/test/test_rsml_yaml.py +++ b/test/test_rsml_yaml.py @@ -1,5 +1,5 @@ -import rsml +import openalea.rsml as rsml from openalea.mtg import MTG, traversal from openalea.hydroroot.hydro_io import export_mtg_to_rsml, import_rsml_to_discrete_mtg