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Post Release #101

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6838703
WIP wrapper to work without input file
baugetfa Jan 23, 2026
b65951b
correction on example
baugetfa Jan 30, 2026
7b0e8ca
removed dev and rc channel in environment.yml
baugetfa Jan 30, 2026
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2 changes: 0 additions & 2 deletions conda/environment.yml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,5 @@
name: hydroroot_dev
channels:
- openalea3/label/dev
- openalea3/label/rc
- openalea3
- conda-forge
dependencies:
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46 changes: 23 additions & 23 deletions example/example_generated_archi.ipynb
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10 changes: 5 additions & 5 deletions example/parameters.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -27,13 +27,13 @@ archi:
#file format: "LR_length_mm" ; "relative_distance_to_tip"
#laws used to generate lateral roots of the 1st order (1_order_law), and lateral roots of order above 1 (2_order_law)
length_file:
- data/length*order1*.csv
- data/length*order2*.csv
- data/length*order1_16*.csv
- data/length*order2_16*.csv

#length of the primary root
#float or list of float
#unit: m
primary_length: 0.16
primary_length: 0.13

#branching delay
#float or list of float
Expand All @@ -49,12 +49,12 @@ archi:

#vertices length
#unit: m
segment_length: 1.0e-3
segment_length: 1.0e-4

#part of roots without any lateral root, distance from tip
#float or list of float
#unit: m
nude_length: 0.2
nude_length: 0.02

#reference radius of the primary root
#float
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14 changes: 7 additions & 7 deletions src/openalea/hydroroot/init_parameter.py
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Expand Up @@ -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}

Expand All @@ -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}

Expand Down Expand Up @@ -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)
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29 changes: 16 additions & 13 deletions src/openalea/hydroroot/solver_wrapper.py
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Expand Up @@ -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:
Expand Down Expand Up @@ -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
Expand Down
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