build: drop support for pydantic 1 (#167)

* build: drop pydantic 1

* remove timedelta junk

* use typing extensions

* fix cov

* fix source

* cov

.github/workflows/ci.yml

@@ -6,10 +6,8 @@ concurrency:
 
 on:
   push:
-    branches:
-      - main
-    tags:
-      - "v*"
+    branches: [main]
+    tags: ["v*"]
   pull_request: {}
   workflow_dispatch:
 
@@ -22,25 +20,25 @@ jobs:
       - run: pip3 install check-manifest && check-manifest
 
   test:
-    uses: pyapp-kit/workflows/.github/workflows/test-pyrepo.yml@main
+    uses: pyapp-kit/workflows/.github/workflows/test-pyrepo.yml@v2
     with:
       os: ${{ matrix.os }}
       python-version: ${{ matrix.python-version }}
-      pip-post-installs: ${{ matrix.pydantic }}
-    secrets:
-      codecov-token: ${{ secrets.CODECOV_TOKEN }}
+      coverage-upload: artifact
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
         include:
-          - python-version: "3.11"
-            platform: ubuntu-latest
-            pydantic: "'pydantic<2'"
-          - python-version: "3.8"
-            platform: ubuntu-latest
-            pydantic: "'pydantic<2'"
+          - os: ubuntu-latest
+            python-version: "3.8"
+
+  upload_coverage:
+    if: always()
+    needs: [test]
+    uses: pyapp-kit/workflows/.github/workflows/upload-coverage.yml@v2
+    secrets: inherit
 
   test-dependents:
     uses: pyapp-kit/workflows/.github/workflows/test-dependents.yml@v2
@@ -85,4 +83,4 @@ jobs:
       - uses: softprops/action-gh-release@v2
         with:
           generate_release_notes: true
-          files: './dist/*'
+          files: "./dist/*"

.pre-commit-config.yaml

@@ -26,4 +26,3 @@ repos:
         additional_dependencies:
           - types-PyYAML
           - pydantic >=2
-          - pydantic-compat >=0.0.4

README.md

@@ -54,7 +54,7 @@ for more details.
 
 > **Note:** `useq-schema` uses [`pydantic`](https://pydantic-docs.helpmanual.io/) to
 > define models, so you can retrieve the [json schema](https://json-schema.org/)
-> for the `MDAEvent` object with `MDAEvent.schema_json()`
+> for the `MDAEvent` object with `MDAEvent.model_json_schema()`
 
 ## `MDASequence`
 
@@ -80,7 +80,7 @@ Time Plan, a Z Plan, a list of channels and positions, etc.).  A
 See [`useq.MDASequence` documentation](https://pymmcore-plus.github.io/useq-schema/schema/sequence/)
 for more details.
 
-### example `MDASequence` usage:
+### example `MDASequence` usage
 
 ```python
 from useq import MDASequence
@@ -149,6 +149,7 @@ z_plan:
   range: 4.0
   step: 0.5
 ```
+
 ## Executing useq-schema experiments with pymmcore-plus
 
 [pymmcore-plus](https://github.com/pymmcore-plus/pymmcore-plus) implements an

pyproject.toml

@@ -32,7 +32,7 @@ classifiers = [
     "Typing :: Typed",
 ]
 dynamic = ["version"]
-dependencies = ["pydantic >=1.7,!=2.4.1", "numpy", "pydantic-compat >=0.0.4"]
+dependencies = ["pydantic >=2,!=2.4.1", "numpy", "typing-extensions"]
 
 # extras
 # https://peps.python.org/pep-0621/#dependencies-optional-dependencies
@@ -91,7 +91,7 @@ select = [
     "SLF",  # private access
 ]
 ignore = [
-    "D100",  # Missing docstring in public module
+    "D100", # Missing docstring in public module
     "D401", # First line should be in imperative mood (remove to opt in)
 ]
 
@@ -122,6 +122,9 @@ pretty = true
 plugins = ["pydantic.mypy"]
 
 # https://coverage.readthedocs.io/en/6.4/config.html
+[tool.coverage.run]
+source = ["useq"]
+
 [tool.coverage.report]
 exclude_lines = [
     "pragma: no cover",

src/useq/__init__.py

@@ -63,9 +63,8 @@
 ]
 
 
-# type ignores because pydantic-compat consumes the kwargs
-MDAEvent.model_rebuild(MDASequence=MDASequence)  # type: ignore  [call-arg]
-Position.model_rebuild(MDASequence=MDASequence)  # type: ignore  [call-arg]
+MDAEvent.model_rebuild()
+Position.model_rebuild()
 
 
 def __getattr__(name: str) -> Any:

src/useq/_base_model.py

@@ -14,7 +14,7 @@
 )
 
 import numpy as np
-from pydantic_compat import BaseModel
+from pydantic import BaseModel
 
 if TYPE_CHECKING:
     from pydantic import ConfigDict

src/useq/_grid.py

@@ -20,7 +20,7 @@
 )
 
 import numpy as np
-from pydantic_compat import Field, field_validator
+from pydantic import Field, field_validator
 
 from useq._base_model import FrozenModel
 

src/useq/_mda_event.py

@@ -14,7 +14,7 @@
     Tuple,
 )
 
-from pydantic_compat import Field, field_validator
+from pydantic import Field, field_validator
 
 from useq._actions import AcquireImage, AnyAction
 from useq._base_model import UseqModel

src/useq/_mda_sequence.py

@@ -15,8 +15,7 @@
 from warnings import warn
 
 import numpy as np
-from pydantic import Field, PrivateAttr
-from pydantic_compat import field_validator, model_validator
+from pydantic import Field, PrivateAttr, field_validator, model_validator
 
 from useq._base_model import UseqModel
 from useq._channel import Channel
@@ -378,10 +377,10 @@ def _check_order(
         if Axis.Z in order and z_plan and not z_plan.is_relative:
             err = "Absolute Z positions cannot be used with autofocus plan."
             if isinstance(autofocus_plan, AxesBasedAF):
-                raise ValueError(err)
+                raise ValueError(err)  # pragma: no cover
             for p in stage_positions:
                 if p.sequence is not None and p.sequence.autofocus_plan:
-                    raise ValueError(err)
+                    raise ValueError(err)  # pragma: no cover
 
     @property
     def shape(self) -> Tuple[int, ...]:

src/useq/_time.py

@@ -1,59 +1,18 @@
-import datetime
-from typing import (
-    TYPE_CHECKING,
-    Any,
-    Callable,
-    Dict,
-    Generator,
-    Iterator,
-    Sequence,
-    Union,
-)
-
-from pydantic import Field
+from datetime import timedelta
+from typing import Iterator, Sequence, Union
 
-from useq._base_model import FrozenModel
-from useq._utils import parse_duration
-
-if TYPE_CHECKING:
-    from pydantic_core import CoreSchema, core_schema
-
-
-# FIXME: please!!
-# This is a gross amalgamation of fixes that tries to work with both pydantic1 and 2
-class timedelta(datetime.timedelta):
-    @classmethod
-    def __get_validators__(cls) -> Generator[Callable[..., Any], None, None]:
-        yield cls.validate
-
-    @classmethod
-    def validate(cls, v: Any) -> datetime.timedelta:
-        return datetime.timedelta(**v) if isinstance(v, dict) else parse_duration(v)
+from pydantic import BeforeValidator, Field, PlainSerializer
+from typing_extensions import Annotated
 
-    @classmethod
-    def __get_pydantic_core_schema__(
-        cls, source_type: Any, handler: Any
-    ) -> "CoreSchema":
-        from pydantic_core.core_schema import (
-            no_info_plain_validator_function,
-            plain_serializer_function_ser_schema,
-        )
-
-        serializer = plain_serializer_function_ser_schema(
-            cls._serialize, when_used="json"
-        )
-
-        return no_info_plain_validator_function(cls.validate, serialization=serializer)
-
-    @classmethod
-    def _serialize(cls, v: datetime.timedelta) -> float:
-        return v.total_seconds()
+from useq._base_model import FrozenModel
 
-    @classmethod
-    def __get_pydantic_json_schema__(
-        cls, core_schema: "core_schema.CoreSchema", handler: Any
-    ) -> Dict[str, Any]:
-        return {"type": "number", "format": "float"}
+# slightly modified so that we can accept dict objects as input
+# and serialize to total_seconds
+TimeDelta = Annotated[
+    timedelta,
+    BeforeValidator(lambda v: timedelta(**v) if isinstance(v, dict) else v),
+    PlainSerializer(lambda td: td.total_seconds()),
+]
 
 
 class TimePlan(FrozenModel):
@@ -67,7 +26,7 @@ def __iter__(self) -> Iterator[float]:  # type: ignore
     def num_timepoints(self) -> int:
         return self.loops  # type: ignore  # TODO
 
-    def deltas(self) -> Iterator[datetime.timedelta]:
+    def deltas(self) -> Iterator[timedelta]:
         current = timedelta(0)
         for _ in range(self.loops):  # type: ignore  # TODO
             yield current
@@ -89,11 +48,11 @@ class TIntervalLoops(TimePlan):
         of conflict. By default, `False`.
     """
 
-    interval: timedelta
+    interval: TimeDelta
     loops: int = Field(..., gt=0)
 
     @property
-    def duration(self) -> datetime.timedelta:
+    def duration(self) -> timedelta:
         return self.interval * (self.loops - 1)
 
 
@@ -112,11 +71,11 @@ class TDurationLoops(TimePlan):
         of conflict. By default, `False`.
     """
 
-    duration: timedelta
+    duration: TimeDelta
     loops: int = Field(..., gt=0)
 
     @property
-    def interval(self) -> datetime.timedelta:
+    def interval(self) -> timedelta:
         # -1 makes it so that the last loop will *occur* at duration, not *finish*
         return self.duration / (self.loops - 1)
 
@@ -136,8 +95,8 @@ class TIntervalDuration(TimePlan):
         of conflict. By default, `True`.
     """
 
-    interval: timedelta
-    duration: timedelta
+    interval: TimeDelta
+    duration: TimeDelta
     prioritize_duration: bool = True
 
     @property
@@ -159,13 +118,13 @@ class MultiPhaseTimePlan(TimePlan):
 
     phases: Sequence[SinglePhaseTimePlan]
 
-    def deltas(self) -> Iterator[datetime.timedelta]:
-        accum = datetime.timedelta(0)
+    def deltas(self) -> Iterator[timedelta]:
+        accum = timedelta(0)
         yield accum
         for phase in self.phases:
             for i, td in enumerate(phase.deltas()):
                 # skip the first timepoint of later phases
-                if i == 0 and td == datetime.timedelta(0):
+                if i == 0 and td == timedelta(0):
                     continue
                 yield td + accum
             accum += td

src/useq/_utils.py

@@ -59,7 +59,7 @@ class TimeEstimate(NamedTuple):
     def __add__(self, other: object) -> TimeEstimate:
         """Add two TimeEstimates."""
         if not isinstance(other, TimeEstimate):
-            return NotImplemented
+            return NotImplemented  # pragma: no cover
         return TimeEstimate(
             self.total_duration + other.total_duration,
             self.per_t_duration + other.per_t_duration,

src/useq/_z.py

@@ -4,7 +4,7 @@
 from typing import Callable, Iterator, List, Sequence, Union
 
 import numpy as np
-from pydantic_compat import field_validator
+from pydantic import field_validator
 
 from useq._base_model import FrozenModel
 

src/useq/pycromanager.py

@@ -63,7 +63,9 @@ def to_pycromanager(
         return _event_to_pycromanager(obj)
     elif isinstance(obj, MDASequence):
         return [_event_to_pycromanager(event) for event in obj]
-    raise TypeError(f"invalid argument: {obj!r}. Must be MDAEvent or MDASequence.")
+    raise TypeError(  # pragma: no cover
+        f"invalid argument: {obj!r}. Must be MDAEvent or MDASequence."
+    )
 
 
 _USEQ_AXIS_TO_PYCRO: dict[str, PycroAxis] = {

tests/fixtures/mda.yaml

@@ -46,10 +46,10 @@ stage_positions:
   z: 50.0
 time_plan:
   phases:
-  - interval: 0:00:03
+  - interval: 3.0
     loops: 3
-  - duration: 0:40:00
-    interval: 0:00:10
+  - duration: 2400.0
+    interval: 10.0
 z_plan:
   range: 1.0
   step: 0.5

tests/test_misc.py

@@ -141,12 +141,3 @@ def test_time_estimation_with_position_seqs(seq: useq.MDASequence) -> None:
     if not isinstance(expect, tuple):
         expect = (expect, False)
     assert _duration_exceeded(seq) == expect
-
-
-def test_pydantic_compat(mda1: useq.MDASequence) -> None:
-    # testing names of deprecated methods and cross-compatible API
-    assert mda1.json()
-    assert mda1.model_dump_json()
-
-    assert mda1.model_dump()
-    assert mda1.dict()

tests/test_serialization.py

@@ -13,13 +13,13 @@ def test_serialization(mda1: MDASequence, ext: str) -> None:
     mda = MDASequence.from_file(str(FILE))
     assert mda == mda1
     if ext == "json":
-        assert json.loads(mda.json(exclude={"uid"})) == json.loads(text)
+        assert json.loads(mda.model_dump_json(exclude={"uid"})) == json.loads(text)
     else:
         assert mda.yaml() == text
 
     it = iter(mda)
     for _ in range(20):
         if ext == "json":
-            assert next(it).json()
+            assert next(it).model_dump_json()
         else:
             assert next(it).yaml()