aiagents4pharma 1.22.1__py3-none-any.whl → 1.22.2__py3-none-any.whl

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/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-1.22.1.dist-info → aiagents4pharma-1.22.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: aiagents4pharma
-Version: 1.22.1
+Version: 1.22.2
 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.dist-info → aiagents4pharma-1.22.2.dist-info}/RECORD

@@ -19,14 +19,14 @@ aiagents4pharma/talk2biomodels/configs/tools/custom_plotter/default.yaml,sha256=
 aiagents4pharma/talk2biomodels/configs/tools/get_annotation/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
 aiagents4pharma/talk2biomodels/configs/tools/get_annotation/default.yaml,sha256=o5kqLJ5QGJsLMUhAqotudIMhxxNfPUVcDVH1tdRIutU,304
 aiagents4pharma/talk2biomodels/models/__init__.py,sha256=5fTHHm3PVloYPNKXbgNlcPgv3-u28ZquxGydFYDfhJA,122
-aiagents4pharma/talk2biomodels/models/basico_model.py,sha256=0vHS-wPZ3kHTMf1KLrcMTgqz67tgK9sswffSQjAs6vw,4851
+aiagents4pharma/talk2biomodels/models/basico_model.py,sha256=4LjeHKGcXsdm1gFxs9SGVNDerajZ7REvCeNch0s2pDg,5242
 aiagents4pharma/talk2biomodels/models/sys_bio_model.py,sha256=JeoiGQAvQABHnG0wKR2XBmmxqQdtgO6kxaLDUTUmr1s,2001
 aiagents4pharma/talk2biomodels/states/__init__.py,sha256=YLg1-N0D9qyRRLRqwqfLCLAqZYDtMVZTfI8Y0b_4tbA,139
 aiagents4pharma/talk2biomodels/states/state_talk2biomodels.py,sha256=S1UtXvocWR8Y9OVUp6pIDFnmaCcjbwmUbW8u79TuGcg,1508
 aiagents4pharma/talk2biomodels/tests/__init__.py,sha256=Jbw5tJxSrjGoaK5IX3pJWDCNzhrVQ10lkYq2oQ_KQD8,45
 aiagents4pharma/talk2biomodels/tests/test_api.py,sha256=7Kz2r5F5tjmn3F0LoM33oP-21W633936YHiyf5toGg0,1716
 aiagents4pharma/talk2biomodels/tests/test_ask_question.py,sha256=rdForKfj2zj2IXl6ntK9_I0AbgsCv8MXOZ2khBnaPms,1620
-aiagents4pharma/talk2biomodels/tests/test_basico_model.py,sha256=y82fpTJMPHwtXxlle1cGQ_2Bewwpxi0aJSVrVAYLhN0,2060
+aiagents4pharma/talk2biomodels/tests/test_basico_model.py,sha256=-2g7HGHXsJeaE06FUI380Br3uh1Wb-JV51mgqcb3GJw,2423
 aiagents4pharma/talk2biomodels/tests/test_get_annotation.py,sha256=GbobfjtCAOV0HddM4pb2o3c49Q05fKIM0Ubnf8BRxHM,8273
 aiagents4pharma/talk2biomodels/tests/test_getmodelinfo.py,sha256=CIKeIm5FGTCyW-FR2nIo3Tr5AyAdxBelNngkdUd5-kk,3206
 aiagents4pharma/talk2biomodels/tests/test_integration.py,sha256=9nYRqpJ_OtmUypuHm4URzoHhcpKEldCEwKxLzh8jcZU,5193
@@ -162,8 +162,8 @@ aiagents4pharma/talk2scholars/tools/s2/query_results.py,sha256=EUfzRh5Qc_tMl5fDI
 aiagents4pharma/talk2scholars/tools/s2/retrieve_semantic_scholar_paper_id.py,sha256=Lg1L4HQCN2LaQEyWtLD73O67PMoXkPHi-Y8rCzHS0A4,2499
 aiagents4pharma/talk2scholars/tools/s2/search.py,sha256=mnBQWDuQ50UVw6B-bRuL8Ek1av-pEtdgzVMxpEA2BpI,4296
 aiagents4pharma/talk2scholars/tools/s2/single_paper_rec.py,sha256=xgnUj9W9JkeTvB2VJBJUAnia789GGNGqdqgJ_G16v2s,5120
-aiagents4pharma-1.22.1.dist-info/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
-aiagents4pharma-1.22.1.dist-info/METADATA,sha256=5mWYXohM-eUXLQ8w_3ZpIEWE4jmr3YBKEJWj9bzbgxg,7789
-aiagents4pharma-1.22.1.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-aiagents4pharma-1.22.1.dist-info/top_level.txt,sha256=-AH8rMmrSnJtq7HaAObS78UU-cTCwvX660dSxeM7a0A,16
-aiagents4pharma-1.22.1.dist-info/RECORD,,
+aiagents4pharma-1.22.2.dist-info/LICENSE,sha256=IcIbyB1Hyk5ZDah03VNQvJkbNk2hkBCDqQ8qtnCvB4Q,1077
+aiagents4pharma-1.22.2.dist-info/METADATA,sha256=OMtzAMhrSQiB7SpK7-waB0SLh8Je5i5HSHE5J9lY7xQ,7789
+aiagents4pharma-1.22.2.dist-info/WHEEL,sha256=nn6H5-ilmfVryoAQl3ZQ2l8SH5imPWFpm1A5FgEuFV4,91
+aiagents4pharma-1.22.2.dist-info/top_level.txt,sha256=-AH8rMmrSnJtq7HaAObS78UU-cTCwvX660dSxeM7a0A,16
+aiagents4pharma-1.22.2.dist-info/RECORD,,

{aiagents4pharma-1.22.1.dist-info → aiagents4pharma-1.22.2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.8.0)
+Generator: setuptools (75.8.1)
 Root-Is-Purelib: true
 Tag: py3-none-any