Make pydantic 1/2 compatible

.github/workflows/tests.yml

@@ -14,6 +14,7 @@ jobs:
       matrix:
         os: [ ubuntu-latest ]
         python-version: [ "3.11" ]
+        pydantic: [ "pydantic1", "pydantic2" ]
     steps:
       - uses: actions/checkout@v2
       - name: Set up Python ${{ matrix.python-version }}
@@ -22,7 +23,7 @@ jobs:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
         run: |
-          pip install hatch
+          pip install tox
       - name: Test with pytest
         run:
-          hatch run test
+          tox -e py-${{ matrix.pydantic }}

pyproject.toml

@@ -34,6 +34,12 @@ dependencies = [
   "uvicorn",
 ]
 
+[project.optional-dependencies]
+tests = [
+    "pytest",
+    "coverage",
+]
+
 [project.urls]
 Documentation = "https://github.com/biopragmatics/semra#readme"
 Issues = "https://github.com/biopragmatics/semra/issues"

src/semra/pipeline.py

@@ -58,7 +58,7 @@ class Input(BaseModel):
 class Mutation(BaseModel):
     """Represents a mutation operation on a mapping set."""
 
-    source: str = Field()
+    source: str = Field(..., description="The source type")
     confidence: float = 1.0
     old: Reference = Field(default=DB_XREF)
     new: Reference = Field(default=EXACT_MATCH)
@@ -69,7 +69,7 @@ class Configuration(BaseModel):
 
     inputs: list[Input]
     negative_inputs: list[Input] = Field(default=[Input(source="biomappings", prefix="negative")])
-    priority: list[str] = Field(description="If no priority is given, is inferred from the order of inputs")
+    priority: list[str] = Field(..., description="If no priority is given, is inferred from the order of inputs")
     mutations: list[Mutation] = Field(default_factory=list)
     exclude_pairs: list[tuple[str, str]] = Field(
         default_factory=list,
@@ -91,7 +91,7 @@ class Configuration(BaseModel):
 
     sssom_add_labels: bool = False
 
-    @root_validator
+    @root_validator(skip_on_failure=True)
     def infer_priority(cls, values):  # noqa:N805
         """Infer the priority from the input list of not given."""
         priority = values["priority"]

src/semra/struct.py

@@ -14,6 +14,7 @@
 from curies import Reference
 from more_itertools import triplewise
 from pydantic import Field
+from pydantic.types import UUID, UUID4
 
 __all__ = [
     "Reference",
@@ -63,10 +64,10 @@ def curie(self) -> str:
 
 
 class MappingSet(pydantic.BaseModel):
-    name: str
-    version: str | None = Field(description="The version of the dataset from which the mapping comes")
-    license: str | None = Field(description="License name or URL for mapping set")
-    confidence: float | None = Field(description="Mapping set level confidence")
+    name: str = Field(..., description="Name of the mapping set")
+    version: str | None = Field(default=None, description="The version of the dataset from which the mapping comes")
+    license: str | None = Field(default=None,description="License name or URL for mapping set")
+    confidence: float | None = Field(default=None,description="Mapping set level confidence")
 
     def key(self):
         return self.name, self.version or "", self.license or "", 1.0 if self.confidence is None else self.confidence
@@ -98,12 +99,13 @@ class Config:
         default=Reference(prefix="semapv", identifier="UnspecifiedMapping"),
         description="A SSSOM-compliant justification",
     )
-    mapping_set: MappingSet = Field(description="The name of the dataset from which the mapping comes")
+    mapping_set: MappingSet = Field(..., description="The name of the dataset from which the mapping comes")
     author: Reference | None = Field(
+        default=None,
         description="A reference to the author of the mapping (e.g. with ORCID)",
         example=Reference(prefix="orcid", identifier="0000-0003-4423-4370"),
     )
-    uuid: uuid.UUID = Field(default_factory=uuid.uuid4)
+    uuid: UUID4 = Field(default_factory=uuid.uuid4)
 
     def key(self):
         """Get a key suitable for hashing the evidence.
@@ -136,7 +138,7 @@ class Config:
         frozen = True
 
     evidence_type: Literal["reasoned"] = Field(default="reasoned")
-    justification: Reference = Field(description="A SSSOM-compliant justification")
+    justification: Reference = Field(..., description="A SSSOM-compliant justification")
     mappings: list[Mapping] = Field(
         ..., description="A list of mappings and their evidences consumed to create this evidence"
     )

tox.ini

@@ -0,0 +1,19 @@
+# Tox (http://tox.testrun.org/) is a tool for running tests
+# in multiple virtualenvs. This configuration file will run the
+# test suite on all supported python versions. To use it, "pip install tox"
+# and then run "tox" from this directory.
+
+[tox]
+isolated_build = true
+envlist =
+    # the actual tests
+    py-pydantic1
+    py-pydantic2
+
+[testenv]
+commands = python -m coverage run -p -m pytest --durations=20 {posargs:tests}
+deps =
+    pydantic1: pydantic<2.0
+    pydantic2: pydantic>=2.0
+extras =
+    tests