Merge branch 'main' into main

biopragmatics · Aug 13, 2023 · 060244d · 060244d
2 parents 33f5384 + fc1cda6
commit 060244d
Show file tree

Hide file tree

Showing 7 changed files with 20 additions and 16 deletions.
diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.9.3-dev
+current_version = 0.10.1-dev
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(?:-(?P<release>[0-9A-Za-z-]+(?:\.[0-9A-Za-z-]+)*))?(?:\+(?P<build>[0-9A-Za-z-]+(?:\.[0-9A-Za-z-]+)*))?

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -60,6 +60,7 @@ jobs:
       matrix:
         os: [ ubuntu-latest ]
         python-version: [ "3.8", "3.11" ]
+        pydantic: [ "pydantic1", "pydantic2" ]
         exclude:
           - os: windows-latest
             python-version: 3.8
@@ -77,4 +78,4 @@ jobs:
           pip install tox
       - name: Test with pytest
         run:
-          tox -e py
+          tox -e py-${{ matrix.pydantic }}
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -26,11 +26,9 @@
     "sphinx.ext.todo",
     # 'sphinx.ext.mathjax',
     "sphinx.ext.viewcode",
-    "sphinx_autodoc_typehints",
     "sphinx_click.ext",
     "sphinx_automodapi.automodapi",
     "sphinx_automodapi.smart_resolver",
-    # 'texext',
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -60,7 +58,7 @@
 #
 
 # The full version, including alpha/beta/rc tags.
-release = "0.9.3-dev"
+release = "0.10.1-dev"
 
 # The short X.Y version.
 parsed_version = re.match(

diff --git a/setup.cfg b/setup.cfg
@@ -3,7 +3,7 @@
 ##########################
 [metadata]
 name = pyobo
-version = 0.9.3-dev
+version = 0.10.1-dev
 description = Handling and writing OBO
 long_description = file: README.rst
 
@@ -59,9 +59,9 @@ install_requires =
     tabulate
     cachier
     pystow>=0.2.7
-    bioversions>=0.5.181
-    bioregistry>=0.9.62
-    bioontologies>=0.3.0
+    bioversions>=0.5.202
+    bioregistry>=0.10.0
+    bioontologies>=0.4.0
     zenodo-client>=0.0.5
     class_resolver
     psycopg2-binary
@@ -85,11 +85,13 @@ package_dir =
 where = src
 
 [options.extras_require]
+tests =
+    coverage
+    pytest
 docs =
-    sphinx<7.0
+    sphinx
     sphinx-rtd-theme
     sphinx-click
-    sphinx-autodoc-typehints
     sphinx_automodapi
 web =
     flask

diff --git a/src/pyobo/struct/reference.py b/src/pyobo/struct/reference.py
@@ -20,7 +20,7 @@
 class Reference(curies.Reference):
     """A namespace, identifier, and label."""
 
-    name: Optional[str] = Field(description="the name of the reference")
+    name: Optional[str] = Field(default=None, description="the name of the reference")
 
     @validator("prefix")
     def validate_prefix(cls, v):  # noqa

diff --git a/src/pyobo/version.py b/src/pyobo/version.py
@@ -14,7 +14,7 @@
     "get_git_hash",
 ]
 
-VERSION = "0.9.3-dev"
+VERSION = "0.10.1-dev"
 
 
 def get_git_hash() -> str:

diff --git a/tox.ini b/tox.ini
@@ -19,15 +19,18 @@ envlist =
     readme
     docs
     # the actual tests
-    py
+    py-pydantic1
+    py-pydantic2
     # always keep coverage-report last
     # coverage-report
 
 [testenv]
 commands = coverage run -p -m pytest --durations=20 {posargs:tests}
 deps =
-    coverage
-    pytest
+    pydantic1: pydantic<2.0
+    pydantic2: pydantic>=2.0
+extras =
+    tests
 
 [testenv:coverage-clean]
 deps = coverage