Merge branch 'main' into py313

.github/workflows/test.yml

@@ -59,7 +59,7 @@ jobs:
           pip uninstall -y lxml xmlschema
           pytest --cov --cov-report=xml --cov-append
 
-      - uses: codecov/codecov-action@v4
+      - uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
 
@@ -75,7 +75,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.11", "3.13"]
+        python-version: ["3.9", "3.10", "3.12"]
 
   test-widget:
     name: test-widget
@@ -133,7 +133,7 @@ jobs:
           python -m pip install 'pydantic>=2'
           pytest --cov --cov-report=xml --cov-append
 
-      - uses: codecov/codecov-action@v4
+      - uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
 
@@ -153,7 +153,7 @@ jobs:
         run: pytest --cov --cov-report=xml --cov-append -k test_autogen
         env:
           TEST_AUTOGEN: "1"
-      - uses: codecov/codecov-action@v4
+      - uses: codecov/codecov-action@v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
 

.github/workflows/test_dependents.yml

@@ -58,42 +58,6 @@ jobs:
             aicsimageio/tests/readers/extra_readers/test_bioformats_reader.py \
             aicsimageio/tests/readers/extra_readers/test_ome_zarr_reader.py 
 
-  test-paquo:
-    name: test paquo
-    runs-on: ubuntu-latest
-    env:
-      QUPATH_VERSION: 0.4.3
-    steps:
-      - uses: actions/checkout@v4
-      - name: Set up Python
-        uses: actions/setup-python@v5
-        with:
-          python-version: "3.10"
-      - name: Install dependencies
-        run: |
-          python -m pip install -U pip
-          python -m pip install .[test]
-          python -m pip install paquo
-
-      - name: Restore qupath cache
-        uses: actions/cache@v4
-        env:
-          CACHE_NUMBER: 0
-        with:
-          path: ./qupath/download
-          key: ${{ runner.os }}-qupath-v${{ env.CACHE_NUMBER }}
-
-      - name: Install qupath and set PAQUO_QUPATH_DIR
-        shell: bash
-        run: |
-          python -c "import os; os.makedirs('qupath/download', exist_ok=True)"
-          python -c "import os; os.makedirs('qupath/apps', exist_ok=True)"
-          python -m paquo get_qupath --install-path ./qupath/apps --download-path ./qupath/download ${{ env.QUPATH_VERSION }} \
-              | grep -v "^#" | sed "s/^/PAQUO_QUPATH_DIR=/" >> $GITHUB_ENV
-
-      - name: Test with pytest
-        run: pytest tests/test_paquo.py
-
   test-nd2:
     name: test nd2
     runs-on: ubuntu-latest
@@ -144,7 +108,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.9"
+          python-version: "3.10"
       - name: Install dependencies
         run: |
           python -m pip install -U pip

.pre-commit-config.yaml

@@ -5,30 +5,30 @@ ci:
 
 repos:
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.19
+    rev: v0.23
     hooks:
       - id: validate-pyproject
 
   - repo: https://github.com/crate-ci/typos
-    rev: v1.24.5
+    rev: typos-dict-v0.11.35
     hooks:
       - id: typos
         args: [--force-exclude]  # omit --write-changes
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.4
+    rev: v0.7.4
     hooks:
       - id: ruff
         args: [--fix, --unsafe-fixes]
       - id: ruff-format
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.11.2
+    rev: v1.13.0
     hooks:
       - id: mypy
         exclude: ^tests|^docs|_napari_plugin|widgets
         additional_dependencies:
-          - pydantic>=2
+          - pydantic>=2.10
           - pydantic-compat
           - xsdata==24.2.1
           - Pint

CHANGELOG.md

@@ -1,5 +1,18 @@
 # Changelog
 
+## [v0.5.3](https://github.com/tlambert03/ome-types/tree/v0.5.3) (2024-11-21)
+
+[Full Changelog](https://github.com/tlambert03/ome-types/compare/v0.5.2...v0.5.3)
+
+**Fixed bugs:**
+
+- fix: fix pydantic 2.10 [\#267](https://github.com/tlambert03/ome-types/pull/267) ([tlambert03](https://github.com/tlambert03))
+
+**Merged pull requests:**
+
+- ci\(dependabot\): bump codecov/codecov-action from 4 to 5 [\#264](https://github.com/tlambert03/ome-types/pull/264) ([dependabot[bot]](https://github.com/apps/dependabot))
+- ci\(pre-commit.ci\): autoupdate [\#263](https://github.com/tlambert03/ome-types/pull/263) ([pre-commit-ci[bot]](https://github.com/apps/pre-commit-ci))
+
 ## [v0.5.2](https://github.com/tlambert03/ome-types/tree/v0.5.2) (2024-09-23)
 
 [Full Changelog](https://github.com/tlambert03/ome-types/compare/v0.5.1.post1...v0.5.2)

pyproject.toml

@@ -28,7 +28,11 @@ classifiers = [
   "Programming Language :: Python :: 3.13",
 ]
 dynamic = ["version"]
-dependencies = ["pydantic >=1.10.0", "pydantic-compat >=0.1.0", "xsdata >=23.6,<24.4"]
+dependencies = [
+  "pydantic >=1.10.16, !=2.0, !=2.1, !=2.2, !=2.3",
+  "pydantic-compat >=0.1.0",
+  "xsdata >=23.6,<24.4",
+]
 
 [project.urls]
 Source = "https://github.com/tlambert03/ome-types"
@@ -57,6 +61,7 @@ test = [
   "xmlschema <2.5",                 # FIXME: determine why
   "xsdata[cli]",
   "types-lxml",
+  "pdbpp; sys_platform != 'win32'",      # for debugging
 ]
 test-qt = ["qtpy", "pytest-qt"]
 # pin ruff for builds because it changes often

src/ome_autogen/main.py

@@ -142,7 +142,8 @@ def _fix_formatting(package_dir: str, ruff_ignore: list[str] = RUFF_IGNORE) -> N
 def _check_mypy(package_dir: str) -> None:
     _print_gray("Running mypy ...")
 
-    mypy = ["mypy", package_dir, "--strict"]
+    # FIXME: the call-overload disable is due to Field() in pydantic/pydantic-compat.
+    mypy = ["mypy", package_dir, "--strict", "--disable-error-code", "call-overload"]
     try:
         subprocess.check_output(mypy, stderr=subprocess.STDOUT)  # noqa S
     except subprocess.CalledProcessError as e:  # pragma: no cover
@@ -221,7 +222,9 @@ def _disp_type(obj: Any) -> str:
         else:
             _fields = [
                 f"{k}: {_disp_type(v.annotation)}"
-                for k, v in sorted(m.model_fields.items())
+                # this type ignore indicates something that may break in pydantic 3
+                # but for now, it's confusing and I think it's an error
+                for k, v in sorted(m.model_fields.items())  # type: ignore
             ]
             if _fields:
                 module += CLASS.format(

src/ome_types/_conversion.py

@@ -4,7 +4,7 @@
 import operator
 import os
 import warnings
-from contextlib import AbstractContextManager, nullcontext, suppress
+from contextlib import nullcontext, suppress
 from functools import cache
 from pathlib import Path
 from struct import Struct
@@ -27,6 +27,7 @@
 
 if TYPE_CHECKING:
     from collections.abc import Iterable
+    from contextlib import AbstractContextManager
     from typing import Any, BinaryIO, Literal, TypedDict
     from xml.etree import ElementTree
 
@@ -175,7 +176,7 @@ def _unpack(fh: BinaryIO, strct: Struct) -> int:
 def tiff2xml(path: Path | str | BinaryIO) -> bytes:
     """Extract the OME-XML from a TIFF file."""
     if hasattr(path, "read"):
-        ctx: AbstractContextManager = nullcontext(path)
+        ctx: AbstractContextManager[BinaryIO] = nullcontext(path)  # type: ignore[arg-type]
     else:
         ctx = Path(path).open(mode="rb")
 
@@ -562,7 +563,7 @@ def _get_ns_elem(elem: ET._Element | AnyElementTree) -> str:
     """Get namespace from an element or element tree."""
     root = elem.getroot() if hasattr(elem, "getroot") else elem
     # return root.nsmap[root.prefix]  this only works for lxml
-    return root.tag.split("}", 1)[0].lstrip("{")
+    return str(root.tag).split("}", 1)[0].lstrip("{")
 
 
 def _get_ns_file(source: FileLike) -> str:
@@ -583,7 +584,7 @@ def _get_root_ome_type(xml: FileLike | AnyElementTree) -> type[OMEType]:
         if hasattr(xml, "seek"):
             xml.seek(0)
         _, root = next(ET.iterparse(xml, events=("start",)))
-    localname = cast("ET._Element", root).tag.rsplit("}", 1)[-1]
+    localname = str(root.tag).rsplit("}", 1)[-1]
 
     if hasattr(xml, "seek"):
         xml.seek(0)

src/ome_types/_pydantic_compat.py

@@ -9,8 +9,12 @@
 if TYPE_CHECKING:
     from pydantic.fields import FieldInfo
 
+pydantic_version: tuple[int, ...] = tuple(
+    int(x) for x in pydantic.version.VERSION.split(".")[:2]
+)
 
-if pydantic.version.VERSION.startswith("2"):
+
+if pydantic_version >= (2,):
     try:
         from pydantic_extra_types.color import Color as Color
     except ImportError:
@@ -20,7 +24,8 @@ def field_type(field: FieldInfo) -> Any:
         return field.annotation
 
     def field_regex(obj: type[BaseModel], field_name: str) -> str | None:
-        field_info = obj.model_fields[field_name]
+        # typing is incorrect at the moment, but may indicate breakage in pydantic 3
+        field_info = obj.model_fields[field_name]  # type: ignore [index]
         meta = field_info.json_schema_extra or {}
         # if a "metadata" key exists... use it.
         # After pydantic-compat 0.2, this is where it will be.
@@ -30,9 +35,10 @@ def field_regex(obj: type[BaseModel], field_name: str) -> str | None:
             return meta.get("pattern")  # type: ignore
         return None
 
-    def get_default(f: FieldInfo) -> Any:
-        return f.get_default(call_default_factory=True)
+    kw: dict = {"validated_data": {}} if pydantic_version >= (2, 10) else {}
 
+    def get_default(f: FieldInfo) -> Any:
+        return f.get_default(call_default_factory=True, **kw)
 else:
     from pydantic.color import Color as Color  # type: ignore [no-redef]
 

src/xsdata_pydantic_basemodel/compat.py

@@ -45,11 +45,11 @@ class AnyElement(PydanticCompatMixin, BaseModel):
     tail: Optional[str] = Field(default=None)
     children: list["AnyElement"] = Field(
         default_factory=list,
-        metadata={"type": XmlType.WILDCARD},  # type: ignore [call-arg]
+        metadata={"type": XmlType.WILDCARD},  # type: ignore [call-arg,call-overload]
     )
     attributes: dict[str, str] = Field(
         default_factory=dict,
-        metadata={"type": XmlType.ATTRIBUTES},  # type: ignore [call-arg]
+        metadata={"type": XmlType.ATTRIBUTES},  # type: ignore [call-arg,call-overload]
     )
 
     model_config: ClassVar["ConfigDict"] = {"arbitrary_types_allowed": True}

src/xsdata_pydantic_basemodel/pydantic_compat.py

@@ -105,5 +105,5 @@ def dataclass_fields(obj: type[M]) -> tuple[dc.Field, ...]:
     """Return a tuple of dataclass fields for the given pydantic model class."""
     return tuple(
         _pydantic_field_to_dataclass_field(name, f)
-        for name, f in obj.model_fields.items()
+        for name, f in obj.model_fields.items()  # type: ignore
     )

tests/test_validation.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 import contextlib
-from contextlib import nullcontext
+from contextlib import AbstractContextManager, nullcontext
 from typing import TYPE_CHECKING, Callable
 
 import pytest
@@ -29,10 +29,10 @@
 @pytest.mark.filterwarnings("ignore:unclosed file")
 @pytest.mark.parametrize("backend", VALIDATORS)
 def test_validation_good(valid_xml: Path, backend: str) -> None:
-    if valid_xml.name not in REQUIRES_TRANSFORM:
-        ctx = nullcontext()
+    if valid_xml.name in REQUIRES_TRANSFORM:
+        ctx: AbstractContextManager = pytest.warns(match="Transformed source from")
     else:
-        ctx = pytest.warns(match="Transformed source from")
+        ctx = nullcontext()
     with ctx:
         VALIDATORS[backend](valid_xml)