[WIP] openalea configuration

conda/meta.yaml

@@ -25,12 +25,14 @@ build:
 requirements:
   host:
     - python
+    - pyyaml
     {% for dep in build_deps %}
     - {{ dep }}
     {% endfor  %}
 
   run:
     - python
+    - pyyaml
     {% for dep in deps + conda_deps %}
     - {{ dep }}
     {% endfor %}

pyproject.toml

@@ -45,6 +45,7 @@ dependencies = [
     "configobj",
     "six",
     "setuptools",
+    "pyyaml",
 ]
 
 [tool.setuptools.dynamic]

src/openalea/core/config.py

@@ -0,0 +1,184 @@
+# -*- python -*-
+#
+#       OpenAlea.Core
+#
+#       Copyright 2006-2026 CIRAD - INRAE - inria
+#
+#       File author(s): Leticia Napolitano
+#                       Christophe Pradal <christophe.prada@cirad.fr>
+#                       Fabrice Bauget <fabrice.bauget@cirad.fr>
+#
+#       Distributed under the Cecill-C License.
+#       See accompanying file LICENSE.txt or copy at
+#           http://www.cecill.info/licences/Licence_CeCILL-C_V1-en.html
+#
+#       OpenAlea WebSite : http://openalea.gforge.inria.fr
+#
+##############################################################################
+"""Configuration of OpenAlea models"""
+
+__license__ = "Cecill-C"
+
+import yaml
+import json
+from openalea.core.singleton import Singleton
+from openalea.core.observer import Observed
+from pathlib import Path
+
+def _load_json(filename: str):
+    """Load configuration from a JSON file."""
+
+    file = Path(filename)
+    with file.open() as f:
+        data = json.load(f)
+    return data
+
+def _load_yml(filename: str):
+    """Load configuration from a YAML file."""
+
+    file = Path(filename)
+    with file.open() as f:
+        data = yaml.load(f, Loader=yaml.SafeLoader)
+    return data
+
+def _dump_yml(data, filename: str, sort_keys=False):
+    """Dump configuration to a YAML file."""
+
+    file = Path(filename)
+    with file.open("w") as f:
+        yaml.dump(data, f, sort_keys=sort_keys)
+
+def _dump_json(data, filename: str):
+    """Dump configuration to a JSON file."""
+
+    file = Path(filename)
+    with file.open("w") as f:
+        json.dump(data, f, indent=4)
+
+
+class Parameter:
+    def __init__(self, name, value=None, unit=None, param_type=None, description="", uid=None, uri=None):
+        self.name =  name
+        self.value = value
+        self.unit = unit
+        self.param_type = param_type
+        self.description = description
+        self.uid = uid
+        self.uri = uri
+
+    def to_dict(self):
+        return {
+            self.name: {
+            "value": self.value,
+            "unit": self.unit,
+            "description": self.description,
+            "type": self.param_type,
+            "uid": self.uid,
+            "uri": self.uri
+            }
+        }
+
+    def __str__(self):
+        return f"name={self.name}, value={self.value}, unit={self.unit}, param_type={self.param_type}, description={self.description}, uid={self.uid}, uri={self.uri}"
+
+class MyModelUnit:
+    def __init__(self, name, parameters: list):
+        self.name = name
+        self.parameters=parameters
+
+    def to_dict(self):
+        params = {k : v  for param in self.parameters for k, v in param.to_dict().items()}
+        return {
+            self.name : params
+        }
+
+    def __str__(self):
+        return f"name={self.name}, parameters={self.to_dict()}"
+
+
+class Config:
+    """Configuration of OpenAlea models
+
+    TODO : Documentation to write
+    """
+    def __init__(self, model_unit_configs: list):
+        """Initialize the configuration with a list of unit configurations."""
+        self.model_unit_configs = model_unit_configs
+
+    def to_dict(self):
+        dict = {}
+        for unit in self.model_unit_configs:
+            dict.update(unit.to_dict())
+        return dict
+
+    def __len__(self):
+        return len(self.model_unit_configs)
+
+    def __getitem__(self, key):
+        return self.to_dict()[key]
+
+    def __str__(self):
+        return f"{self.model_unit_configs}"
+
+
+    def add_section(self, unit):
+        self.model_unit_configs.append(unit)
+
+    #@staticmethod
+    def load(self, filename: str):
+        """Load configuration from a file.
+
+        Dispatch method based on file extension (YAML, JSON, etc.).
+        """
+
+        extension = filename.split(".")[-1]
+
+        if extension in ("yml", "yaml"):
+            data = _load_yml(filename)
+
+        elif extension == "json":
+            data = _load_json(filename)
+
+        units = []
+
+        '''
+        for unit_name, params in data.items():
+            parameters = [Parameter(name=k, value=v) for k, v in params.items()]
+            unit = MyModelUnit(unit_name, parameters)
+            units.append(unit)
+        '''
+        for unit_name, params in data.items():
+            parameters = [
+            Parameter(
+            name=name,
+            value=params[name]["value"],
+            unit=params[name].get("unit"),
+            description=params[name].get("description"),
+            param_type=params[name].get("type"),
+            uid=params[name].get("uid"),
+            uri=params[name].get("uri")
+        )
+            for name in params
+    ]
+
+            unit = MyModelUnit(unit_name, parameters)
+            units.append(unit)
+
+
+        #print(data)
+
+        return Config(units)
+
+    def dump(self, filename: str):
+        """Dump configuration to a file."""
+
+        extension = filename.split(".")[-1]
+        data = self.to_dict()
+
+        if extension in ("yml", "yaml"):
+            _dump_yml(data, filename)
+
+        elif extension == "json":
+            _dump_json(data, filename)
+
+