Make explicit cross-version support for Pydantic (#921)

As a follow-up to biopragmatics/curies#64 (and related
to #920 and #899),
this PR makes Bioregistry support both Pydantic v1 and v2

.github/workflows/tests.yml

@@ -60,6 +60,7 @@ jobs:
       matrix:
         os: [ ubuntu-latest, windows-latest ]
         python-version: [ "3.11", "3.8" ]
+        pydantic: [ "pydantic1", "pydantic2" ]
     steps:
       - uses: actions/checkout@v2
       - name: Set up Python ${{ matrix.python-version }}
@@ -72,7 +73,7 @@ jobs:
           pip install tox
       - name: Test with pytest
         run:
-          tox -e py
+          tox -e py-${{ matrix.pydantic }}
       - name: Doctests
         run:
           tox -e doctests

docs/source/conf.py

@@ -63,7 +63,6 @@
     "sphinx.ext.todo",
     # 'sphinx.ext.mathjax',
     "sphinx.ext.viewcode",
-    "sphinx_autodoc_typehints",
     "sphinx_click.ext",
     "sphinx_automodapi.automodapi",
     "sphinx_automodapi.smart_resolver",

setup.cfg

@@ -50,8 +50,8 @@ install_requires =
     pystow>=0.1.13
     click
     more_click>=0.1.2
-    pydantic<2.0
-    curies>=0.5.6
+    pydantic
+    curies>=0.6.0
 
 zip_safe = false
 include_package_data = True
@@ -75,7 +75,6 @@ docs =
     sphinx
     sphinx-rtd-theme
     sphinx-click
-    sphinx-autodoc-typehints==1.21.1
     sphinx_automodapi
     autodoc_pydantic
 gha =

src/bioregistry/app/impl.py

@@ -18,6 +18,7 @@
 from .api import api_router
 from .constants import BIOSCHEMAS
 from .ui import ui_blueprint
+from ..constants import PYDANTIC_1
 
 if TYPE_CHECKING:
     import bioregistry
@@ -192,6 +193,7 @@ def get_app(
         curie_to_str=curie_to_str,
         fastapi_url_for=fast_api.url_path_for,
         markdown=markdown,
+        is_pydantic_1=PYDANTIC_1,
     )
 
     if return_flask:

src/bioregistry/app/templates/meta/related.html

@@ -11,9 +11,15 @@
 {% endmacro %}
 
 {% macro registry_field_dl(cls, key) -%}
-    {% set field = cls.__fields__[key].field_info %}
-    <dt>{{ field.title or key.replace("_", " ").title() }}</dt>
-    <dd>{{ field.description }}</dd>
+    {% if is_pydantic_1 %}
+        {% set field = cls.__fields__[key].field_info %}
+        <dt>{{ field.title or key.replace("_", " ").title() }}</dt>
+        <dd>{{ field.description }}</dd>
+    {% else %}
+        {% set field = cls.__fields__[key] %}
+        <dt>{{ field.title or key.replace("_", " ").title() }}</dt>
+        <dd>{{ field.description }}</dd>
+    {% endif %}
 {% endmacro %}
 
 {% block styles %}

src/bioregistry/constants.py

@@ -2,6 +2,7 @@
 
 """Constants and utilities for registries."""
 
+import importlib.metadata
 import os
 import pathlib
 import re
@@ -19,6 +20,8 @@
     "BIOREGISTRY_MODULE",
 ]
 
+PYDANTIC_1 = importlib.metadata.version("pydantic").startswith("1.")
+
 HERE = pathlib.Path(os.path.abspath(os.path.dirname(__file__)))
 DATA_DIRECTORY = HERE / "data"
 EXTERNAL = DATA_DIRECTORY / "external"

src/bioregistry/schema/schema.json

@@ -832,6 +832,7 @@
         },
         "comments": {
           "title": "Comments",
+          "description": "Optional additional comments about the registry's governance model",
           "type": "string"
         },
         "accepts_external_contributions": {