Prep for V1.0.2 (#431)

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "ontogpt"
-version = "1.0.1"
+version = "1.0.2"
 description = "OntoGPT"
 authors = ["Chris Mungall <cjmungall@lbl.gov>", "J. Harry Caufield <jhc@lbl.gov>"]
 license = "BSD-3"

src/ontogpt/engines/pheno_engine.py

@@ -142,7 +142,7 @@ def evaluate(self, phenopackets: List[PHENOPACKET]) -> List[DiagnosisPrediction]
                     dp.rank = i
                     dp.matching_disease_ids = list(matches)
                     break
-            print(dump_minimal_yaml(dp.dict()))
+            print(dump_minimal_yaml(dp.model_dump()))
             results.append(dp)
         return results
 

src/ontogpt/io/html_exporter.py

@@ -38,7 +38,7 @@ def export(
         self.export_metadata(extraction_output)
         self.export_results(extraction_output.extracted_object, extraction_output)
         self.h2("YAML Object")
-        self.details(yaml.dump(extraction_output.dict()), output, code="yaml")
+        self.details(yaml.dump(extraction_output.model_dump()), output, code="yaml")
         self.h2("Prompt")
         self.details(extraction_output.prompt, output)
         self.h2("Completion")

src/ontogpt/io/owl_exporter.py

@@ -54,7 +54,7 @@ def export(
     def _as_dataclass_object(self, element: pydantic.BaseModel, schemaview: SchemaView):
         cls_name = type(element).__name__
         schemaview.merge_imports()
-        element_dict = element.dict()
+        element_dict = element.model_dump()
         dataclasses_module = PythonGenerator(schemaview.schema).compile_module()
         target_class_py = dataclasses_module.__dict__[cls_name]
         element_as_dataclass = target_class_py(**element_dict)

tests/__init__.py

@@ -1,4 +1,5 @@
 """Tests for ontogpt."""
+
 import logging
 import os
 from pathlib import Path

tests/integration/test_evaluation/test_eval_drugmechdb.py

@@ -106,7 +106,7 @@ def test_transform(self):
         obj = _fix_source_mechanism(objs[0])
         src_mechanism = Mechanism(**obj)
         r = self.engine.transform_mechanism(src_mechanism)
-        print(yaml.dump(r.dict()))
+        print(yaml.dump(r.model_dump()))
 
     def test_load_and_transform_source_database(self):
         """

tests/output/task-classes.tsv

@@ -0,0 +1,9 @@
+code	task	description
+default='sat'	OntologyCoherencyTask	A task to determine if an ontology is coherent.      There should be a single answer, which is a boolean.
+default='indirect'	EntailedIndirectSuperClassTask	A task to determine the indirect superclasses of a class.
+default='superc'	EntailedTransitiveSuperClassTask	A task to determine the all transitive superclasses of a class.
+default='expr'	EntailedSubClassOfExpressionTask	A task to determine the subclasses of a class expression.
+default='dir-sup'	EntailedDirectSuperClassTask	A task to determine the direct superclasses of a class.      Includes those entailed by other axioms, e.g. equivalence axioms.      Context: a standard pattern in bio-ontologies is to infer the structure     of one ontology from another - e.g. the metabolic process branch in GO     may be entailed by GO equivalence axioms plus the IS_A links in CHEBI.
+default='mrca'	MostRecentCommonSubsumerTask	A task to determine the most specific common ancestors.
+default='tc'	TaxonConstraintTask	A task to determine inapplicable classes by taxon.
+default='abox'	ABoxTask	A task to infer assertions over property chains and transitvity in aboxes.

tests/unit/__init__.py

@@ -1,4 +1,3 @@
 from tests import OUTPUT_DIR
 
 UNIT_CACHE_DB = str(OUTPUT_DIR / "unit_test_cache.db")
-GENE_REQUESTS_CACHE_DB = str(OUTPUT_DIR / "gene_requests_cache.db")

tests/unit/test_exporters/test_html_exporter.py

@@ -1,4 +1,5 @@
 """Core tests."""
+
 import pickle
 import unittest
 

tests/unit/test_exporters/test_markdown_exporter.py

@@ -1,4 +1,5 @@
 """Core tests."""
+
 import pickle
 import unittest
 

tests/unit/test_exporters/test_owl_exporter.py

@@ -1,4 +1,5 @@
 """Core tests."""
+
 import pickle
 import unittest
 

tests/unit/test_exporters/test_rdf_exporter.py

@@ -1,4 +1,5 @@
 """Core tests."""
+
 import pickle
 import unittest
 

tests/unit/test_unit_cli.py

@@ -1,4 +1,5 @@
 """CLI test."""
+
 import unittest
 
 from click.testing import CliRunner