aiagents4pharma 1.22.1__tar.gz → 1.22.3__tar.gz

{aiagents4pharma-1.22.1 → aiagents4pharma-1.22.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: aiagents4pharma
-Version: 1.22.1
+Version: 1.22.3
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License

{aiagents4pharma-1.22.1 → aiagents4pharma-1.22.3}/aiagents4pharma/talk2biomodels/models/basico_model.py

@@ -58,19 +58,24 @@ class BasicoModel(SysBioModel):
             # check if the param_name is not None
             if param_name is None:
                 continue
-            # if param is a kinetic parameter
+            # Extract all parameters and species from the model
             df_all_params = basico.model_info.get_parameters(model=self.copasi_model)
+            df_all_species = basico.model_info.get_species(model=self.copasi_model)
+            # if param is a kinetic parameter
             if param_name in df_all_params.index.tolist():
                 basico.model_info.set_parameters(name=param_name,
                                             exact=True,
                                             initial_value=param_value,
                                             model=self.copasi_model)
             # if param is a species
-            else:
+            elif param_name in df_all_species.index.tolist():
                 basico.model_info.set_species(name=param_name,
                                             exact=True,
                                             initial_concentration=param_value,
                                             model=self.copasi_model)
+            else:
+                logger.error("Parameter/Species %s not found in the model.", param_name)
+                raise ValueError(f"Parameter/Species {param_name} not found in the model.")
 
     def simulate(self, duration: Union[int, float] = 10, interval: int = 10) -> pd.DataFrame:
         """

{aiagents4pharma-1.22.1 → aiagents4pharma-1.22.3}/aiagents4pharma/talk2biomodels/tests/test_basico_model.py

@@ -26,8 +26,15 @@ def test_with_biomodel_id(model):
     assert df_parameters.loc['KmPFKF6P', 'initial_value'] == 1.5
     # check if the simulation results are a pandas DataFrame object
     assert isinstance(model.simulate(duration=2, interval=2), pd.DataFrame)
+    # Pass a None value to the update_parameters method
+    # and it should not raise an error
     model.update_parameters(parameters={None: None})
+    # check if the model description is updated
     assert model.description == basico.biomodels.get_model_info(model.biomodel_id)["description"]
+    # check if an error is raised if an invalid species/parameter (`Pyruv`)
+    # is passed and it should raise a ValueError
+    with pytest.raises(ValueError):
+        model.update_parameters(parameters={'Pyruv': 0.5})
 
 def test_with_sbml_file():
     """

aiagents4pharma-1.22.3/aiagents4pharma/talk2scholars/configs/tools/retrieve_semantic_scholar_paper_id/default.yaml

@@ -0,0 +1,12 @@
+api_endpoint: "https://api.semanticscholar.org/graph/v1/paper/search"
+request_timeout: 10
+api_fields:
+  - "paperId"
+  - "title"
+  - "abstract"
+  - "year"
+  - "authors"
+  - "citationCount"
+  - "url"
+# Commented fields that could be added later if needed
+# - "externalIds"

{aiagents4pharma-1.22.1 → aiagents4pharma-1.22.3}/aiagents4pharma.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: aiagents4pharma
-Version: 1.22.1
+Version: 1.22.3
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License

{aiagents4pharma-1.22.1 → aiagents4pharma-1.22.3}/aiagents4pharma.egg-info/SOURCES.txt

@@ -151,6 +151,7 @@ aiagents4pharma/talk2scholars/configs/tools/__init__.py
 aiagents4pharma/talk2scholars/configs/tools/multi_paper_recommendation/__init__.py
 aiagents4pharma/talk2scholars/configs/tools/multi_paper_recommendation/default.yaml
 aiagents4pharma/talk2scholars/configs/tools/retrieve_semantic_scholar_paper_id/__init__.py
+aiagents4pharma/talk2scholars/configs/tools/retrieve_semantic_scholar_paper_id/default.yaml
 aiagents4pharma/talk2scholars/configs/tools/search/__init__.py
 aiagents4pharma/talk2scholars/configs/tools/search/default.yaml
 aiagents4pharma/talk2scholars/configs/tools/single_paper_recommendation/__init__.py

{aiagents4pharma-1.22.1 → aiagents4pharma-1.22.3}/pyproject.toml

@@ -89,6 +89,7 @@ aiagents4pharma = [
   "talk2scholars/configs/tools/multi_paper_recommendation/*",
   "talk2scholars/configs/tools/search/*",
   "talk2scholars/configs/tools/single_paper_recommendation/*",
+  "talk2scholars/configs/tools/retrieve_semantic_scholar_paper_id/*"
 
 ]
 

aiagents4pharma-1.22.3/release_version.txt

@@ -0,0 +1 @@
+v1.22.3

aiagents4pharma-1.22.1/release_version.txt

@@ -1 +0,0 @@
-v1.22.1