update namespace oawidgets and rsml

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:

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

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"
    ]
   },
   {

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"
    ]
   },
   {

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"
    ]
   },
   {

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"
    ]
   },
   {

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"
    ]
   },
   {

example/example_rsml_io.py

@@ -26,7 +26,7 @@
 """
 
 import glob
-import rsml
+import openalea.rsml as rsml
 import argparse
 import sys
 

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"
    ]

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
 ]
 

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
 

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()
 

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