test: improve tests structure with test cases in test_position_sequence (#233)

* update test patterns

* add pyright

* more typing

* make pyright manual

* update lock

* add comprehensive test cases for MDASequence functionality

* update AF

* rename file

* more reorg

Author: tlambert03

.pre-commit-config.yaml

@@ -27,3 +27,14 @@ repos:
           - types-PyYAML
           - pydantic >=2
           - numpy >=2
+
+  - repo: local
+    hooks:
+      - id: pyright
+        stages: [manual]
+        name: pyright
+        language: system
+        types_or: [python, pyi]
+        require_serial: true
+        files: "src"
+        entry: uv run pyright

pyproject.toml

@@ -62,6 +62,7 @@ dev = [
     "rich>=14.0.0",
     "ruff>=0.11.9",
     "types-pyyaml>=6.0.12.20250402",
+    "pyright>=1.1.401",
 ]
 docs = [
     "mkdocs >=1.4",
@@ -89,6 +90,8 @@ packages = ["src/useq"]
 line-length = 88
 target-version = "py39"
 src = ["src", "tests"]
+fix = true
+unsafe-fixes = true
 
 [tool.ruff.lint]
 pydocstyle = { convention = "numpy" }

src/useq/__init__.py

@@ -1,7 +1,7 @@
 """Implementation agnostic schema for multi-dimensional microscopy experiments."""
 
 import warnings
-from typing import Any
+from typing import TYPE_CHECKING, Any
 
 from useq._actions import AcquireImage, Action, CustomAction, HardwareAutofocus
 from useq._channel import Channel
@@ -39,6 +39,10 @@
     ZTopBottom,
 )
 
+if TYPE_CHECKING:
+    from useq._grid import GridRelative
+
+
 __all__ = [
     "AbsolutePosition",
     "AcquireImage",

src/useq/_actions.py

@@ -38,7 +38,7 @@ class AcquireImage(Action):
         This action can be used to acquire an image.
     """
 
-    type: Literal["acquire_image"] = "acquire_image"
+    type: Literal["acquire_image"] = "acquire_image"  # pyright: ignore[reportIncompatibleVariableOverride]
 
 
 class HardwareAutofocus(Action):
@@ -62,7 +62,7 @@ class HardwareAutofocus(Action):
         The number of retries if autofocus fails. By default, 3.
     """
 
-    type: Literal["hardware_autofocus"] = "hardware_autofocus"
+    type: Literal["hardware_autofocus"] = "hardware_autofocus"  # pyright: ignore[reportIncompatibleVariableOverride]
     autofocus_device_name: Optional[str] = None
     autofocus_motor_offset: Optional[float] = None
     max_retries: int = 3
@@ -89,7 +89,7 @@ class CustomAction(Action):
         Custom data associated with the action.
     """
 
-    type: Literal["custom"] = "custom"
+    type: Literal["custom"] = "custom"  # pyright: ignore[reportIncompatibleVariableOverride]
     name: str = ""
     data: dict = Field(default_factory=dict)
 

src/useq/_channel.py

@@ -1,6 +1,6 @@
-from typing import Optional
+from typing import Any, Optional
 
-from pydantic import Field
+from pydantic import Field, model_validator
 
 from useq._base_model import FrozenModel
 
@@ -38,3 +38,10 @@ class Channel(FrozenModel):
     z_offset: float = 0.0
     acquire_every: int = Field(default=1, gt=0)  # acquire every n frames
     camera: Optional[str] = None
+
+    @model_validator(mode="before")
+    @classmethod
+    def _cast(cls, value: Any) -> Any:
+        if isinstance(value, str):
+            value = {"config": value}
+        return value

src/useq/_grid.py

@@ -76,15 +76,15 @@ class _GridPlan(_MultiPointPlan[PositionT]):
         Engines MAY override this even if provided.
     """
 
-    overlap: tuple[float, float] = Field((0.0, 0.0), frozen=True)
-    mode: OrderMode = Field(OrderMode.row_wise_snake, frozen=True)
+    overlap: tuple[float, float] = Field(default=(0.0, 0.0), frozen=True)
+    mode: OrderMode = Field(default=OrderMode.row_wise_snake, frozen=True)
 
     @field_validator("overlap", mode="before")
     def _validate_overlap(cls, v: Any) -> tuple[float, float]:
         with contextlib.suppress(TypeError, ValueError):
             v = float(v)
         if isinstance(v, float):
-            return (v,) * 2
+            return (v, v)
         if isinstance(v, Sequence) and len(v) == 2:
             return float(v[0]), float(v[1])
         raise ValueError(  # pragma: no cover
@@ -288,7 +288,7 @@ class GridRowsColumns(_GridPlan[RelativePosition]):
     # everything but fov_width and fov_height is immutable
     rows: int = Field(..., frozen=True, ge=1)
     columns: int = Field(..., frozen=True, ge=1)
-    relative_to: RelativeTo = Field(RelativeTo.center, frozen=True)
+    relative_to: RelativeTo = Field(default=RelativeTo.center, frozen=True)
 
     def _nrows(self, dy: float) -> int:
         return self.rows
@@ -346,7 +346,7 @@ class GridWidthHeight(_GridPlan[RelativePosition]):
 
     width: float = Field(..., frozen=True, gt=0)
     height: float = Field(..., frozen=True, gt=0)
-    relative_to: RelativeTo = Field(RelativeTo.center, frozen=True)
+    relative_to: RelativeTo = Field(default=RelativeTo.center, frozen=True)
 
     def _nrows(self, dy: float) -> int:
         return math.ceil(self.height / dy)

src/useq/_iter_sequence.py

@@ -197,7 +197,7 @@ def _iter_sequence(
                 # determine any relative position shifts or global overrides
                 _pos, _offsets = _position_offsets(position, event_kwargs)
                 # build overrides for this position
-                pos_overrides = MDAEventDict(sequence=sequence, **_pos)
+                pos_overrides = MDAEventDict(sequence=sequence, **_pos)  # pyright: ignore[reportCallIssue]
                 pos_overrides["reset_event_timer"] = False
                 if position.name:
                     pos_overrides["pos_name"] = position.name

src/useq/_plot.py

@@ -181,7 +181,7 @@ def plot_plate(
     for well in plate_plan.selected_well_positions:
         x, y = float(well.x), float(well.y)  # type: ignore[arg-type]
         # draw name next to spot
-        ax.text(x + offset_x, y - offset_y, well.name, fontsize=7)
+        ax.text(x + offset_x, y - offset_y, well.name or "", fontsize=7)
 
     ax.axis("equal")
     if show:

src/useq/_position.py

@@ -1,7 +1,8 @@
 from collections.abc import Iterator
-from typing import TYPE_CHECKING, Generic, Optional, SupportsIndex, TypeVar
+from typing import TYPE_CHECKING, Any, Generic, Optional, SupportsIndex, TypeVar
 
-from pydantic import Field
+import numpy as np
+from pydantic import Field, model_validator
 
 from useq._base_model import FrozenModel, MutableModel
 
@@ -73,6 +74,20 @@ def __round__(self, ndigits: "SupportsIndex | None" = None) -> "Self":
         # not sure why these Self types are not working
         return type(self).model_construct(**kwargs)  # type: ignore [return-value]
 
+    @model_validator(mode="before")
+    @classmethod
+    def _cast(cls, value: Any) -> Any:
+        if isinstance(value, (np.ndarray, tuple)):
+            x = y = z = None
+            if len(value) > 0:
+                x = value[0]
+            if len(value) > 1:
+                y = value[1]
+            if len(value) > 2:
+                z = value[2]
+            value = {"x": x, "y": y, "z": z}
+        return value
+
 
 class AbsolutePosition(PositionBase, FrozenModel):
     """An absolute position in 3D space."""
@@ -120,9 +135,9 @@ class RelativePosition(PositionBase, _MultiPointPlan["RelativePosition"]):
     be used to define a single field of view for a "multi-point" plan.
     """
 
-    x: float = 0
-    y: float = 0
-    z: float = 0
+    x: float = 0  # pyright: ignore[reportIncompatibleVariableOverride]
+    y: float = 0  # pyright: ignore[reportIncompatibleVariableOverride]
+    z: float = 0  # pyright: ignore[reportIncompatibleVariableOverride]
 
     def __iter__(self) -> Iterator["RelativePosition"]:  # type: ignore [override]
         yield self

src/useq/_time.py

@@ -1,8 +1,8 @@
 from collections.abc import Iterator, Sequence
 from datetime import timedelta
-from typing import Annotated, Union
+from typing import Annotated, Any, Union
 
-from pydantic import BeforeValidator, Field, PlainSerializer
+from pydantic import BeforeValidator, Field, PlainSerializer, model_validator
 
 from useq._base_model import FrozenModel
 
@@ -122,16 +122,25 @@ def deltas(self) -> Iterator[timedelta]:
         accum = timedelta(0)
         yield accum
         for phase in self.phases:
+            td = None
             for i, td in enumerate(phase.deltas()):
                 # skip the first timepoint of later phases
                 if i == 0 and td == timedelta(0):
                     continue
                 yield td + accum
-            accum += td
+            if td is not None:
+                accum += td
 
     def num_timepoints(self) -> int:
         # TODO: is this correct?
         return sum(phase.loops for phase in self.phases) - 1
 
+    @model_validator(mode="before")
+    @classmethod
+    def _cast(cls, value: Any) -> Any:
+        if isinstance(value, Sequence) and not isinstance(value, str):
+            value = {"phases": value}
+        return value
+
 
 AnyTimePlan = Union[MultiPhaseTimePlan, SinglePhaseTimePlan]