WIP solver wrappers

conda/environment.yml

@@ -1,8 +1,8 @@
 name: hydroroot_dev
 channels:
-  - openalea3/label/dev
-  - openalea3/label/rc
   - openalea3
+  - openalea3/label/rc
+  - openalea3/label/dev
   - conda-forge
 dependencies:
   # list here manually conda-only deps (listed in [tool.conda.environment] section of pyproject)

src/openalea/hydroroot/init_parameter.py

@@ -69,15 +69,15 @@ def __init__(self):
             'read_architecture': False,
             'input_dir': '',
             'input_file': [],
-            'seed': None,
+            'seed': [None],
             'length_file': ['data/length*order2*.csv', 'data/length*order2*.csv'],
             'length_data': [],
-            'primary_length': 0.13,
-            'branching_delay': 2e-3,
+            'primary_length': [0.13],
+            'branching_delay': [2e-3],
             'branching_variability': 0.25,
             'order_max': 4,
             'segment_length': 1.e-4,
-            'nude_length': 0.021,
+            'nude_length': [0.021],
             'ref_radius': 7.0e-5,
             'order_decrease_factor': 0.7}
 
@@ -97,8 +97,8 @@ def __init__(self):
             'psi_base': 0.101325}
 
         self.output = {
-            'radfold': 1.0,
-            'axfold': 1.0,
+            'radfold': [1.0],
+            'axfold': [1.0],
             'intercepts': [0.01, 0.02, 0.03, 0.045, 0.06, 0.08],
             'run_nb': 1}
 
@@ -154,7 +154,7 @@ def init_calculation(self):
         # set the data used to calculate the length laws
         # column names in the length law files
         col_names = ('LR_length_mm', 'relative_distance_to_tip')
-
+        self.archi['length_data'] = []
         for f in self.archi['length_file']:
             d_path = glob.glob(f)[0]
             pd = pandas.read_csv(d_path, sep = ';', header = 1, names = col_names)

src/openalea/hydroroot/solver_wrapper.py

@@ -526,18 +526,19 @@ def Jv_cnf_calculation(g, sigma, Js, Ps):
     #     archi_f = archi_f[0]
     #     df_archi = read_archi_data(archi_f) if parameter.archi['read_architecture'] else None
     #     index = archi_f.replace(glob.glob(parameter.archi['input_dir'])[0], "")
-    
+
     if parameter.archi['read_architecture']:
         # architecture with filename in aqua team format
         # archi_f = glob.glob(parameter.archi['input_dir'] + parameter.archi['input_file'][0])
         # archi_f = archi_f[0]
         fname = str(Path(parameter.archi['input_dir']) / parameter.archi['input_file'][0]) # deals with path in windows
         archi_f = glob.glob(fname) # deals with wildcards ? deprecated ???
         archi_f = archi_f[0]
-        
+
         if df_archi is None: df_archi = read_archi_data(archi_f)
         index = archi_f.replace(glob.glob(parameter.archi['input_dir'])[0], "")
-    index = parameter.archi['input_file'][0]
+    if len(parameter.archi['input_file']) > 0:
+        index = parameter.archi['input_file'][0]
 
     # length law data: override if necessary
     if df_law is not None:
@@ -1254,16 +1255,18 @@ def fun3(x):
 
 
     # architecture with filename in aqua team format
-    if df_archi is None:
-        # archi_f = glob.glob(parameter.archi['input_dir'] + parameter.archi['input_file'][0])
-        # archi_f = archi_f[0]
-        fname = str(Path(parameter.archi['input_dir']) / parameter.archi['input_file'][0]) # deals with path in windows
-        archi_f = glob.glob(fname) # deals with wildcards ? deprecated ???
-        archi_f = archi_f[0]
-
-        df_archi = read_archi_data(archi_f) if parameter.archi['read_architecture'] else None
-    index = archi_f.replace(glob.glob(parameter.archi['input_dir'])[0],"")
-
+    if len(parameter.archi['input_file']) > 0:
+        if df_archi is None:
+            # archi_f = glob.glob(parameter.archi['input_dir'] + parameter.archi['input_file'][0])
+            # archi_f = archi_f[0]
+            fname = str(Path(parameter.archi['input_dir']) / parameter.archi['input_file'][0]) # deals with path in windows
+            archi_f = glob.glob(fname) # deals with wildcards ? deprecated ???
+            archi_f = archi_f[0]
+
+            df_archi = read_archi_data(archi_f) if parameter.archi['read_architecture'] else None
+        index = archi_f.replace(glob.glob(parameter.archi['input_dir'])[0],"")
+    else:
+        index = ''
     # length law data: override if necessary
     if df_law is not None:
         parameter.archi['length_data'] = df_law