Coordinate quality of life improvements (#235)

* Add `__repr__` methods to `CoordinateTransform` methods
* Add `from_axis_names` creation method to `CoordinateSpace`

python-spec/src/somacore/coordinates.py

@@ -2,11 +2,13 @@
 
 import abc
 import collections.abc
-from typing import Optional, Sequence, Tuple, Union
+import itertools
+from typing import Iterable, Optional, Sequence, Tuple, Union
 
 import attrs
 import numpy as np
 import numpy.typing as npt
+from typing_extensions import Self
 
 from .types import str_or_seq_length
 from .types import to_string_tuple
@@ -37,6 +39,10 @@ class CoordinateSpace(collections.abc.Sequence[Axis]):
 
     axes: Tuple[Axis, ...] = attrs.field(converter=tuple)
 
+    @classmethod
+    def from_axis_names(cls, axis_names: Sequence[str,]) -> Self:
+        return cls(tuple(Axis(name) for name in axis_names))  # type: ignore[misc]
+
     @axes.validator
     def _validate(self, _, axes: Tuple[Axis, ...]) -> None:
         if not axes:
@@ -95,6 +101,25 @@ def _check_rmatmul_inner_axes(self, other: "CoordinateTransform"):
                 f"{type(self).__name__}."
             )
 
+    @abc.abstractmethod
+    def _contents_lines(self) -> Iterable[str]:
+        return
+        yield
+
+    def _my_repr(self) -> Iterable[str]:
+        yield f"{type(self).__name__}"
+        yield f"  input axes: {self._input_axes}"
+        yield f"  output axes: {self._output_axes}"
+
+    def __repr__(self) -> str:
+        content = self._contents_lines
+        lines = (
+            self._my_repr()
+            if content is None
+            else itertools.chain(self._my_repr(), self._contents_lines())
+        )
+        return "<" + "\n".join(lines) + ">"
+
     @abc.abstractmethod
     def __matmul__(self, other: object) -> "CoordinateTransform":
         raise NotImplementedError()
@@ -185,6 +210,10 @@ def __init__(
                 f"Unexpected shape {self._matrix.shape} for the input affine matrix."
             )
 
+    def _contents_lines(self) -> Iterable[str]:
+        yield "  augmented matrix:"
+        yield "    " + str(self._matrix).replace("\n", "\n    ")
+
     def __matmul__(self, other: object) -> CoordinateTransform:
         if not isinstance(other, CoordinateTransform):
             raise NotImplementedError(
@@ -259,6 +288,9 @@ def __init__(
 
         super().__init__(input_axes, output_axes, np.diag(self._scale_factors))
 
+    def _contents_lines(self) -> Iterable[str]:
+        yield f"  scales: {self._scale_factors}"
+
     def __matmul__(self, other: object) -> CoordinateTransform:
         if not isinstance(other, CoordinateTransform):
             raise NotImplementedError(
@@ -312,6 +344,9 @@ def __init__(
         rank = str_or_seq_length(input_axes)
         super().__init__(input_axes, output_axes, rank * [self._scale])
 
+    def _contents_lines(self) -> Iterable[str]:
+        yield f"  scale: {self._scale}"
+
     def __matmul__(self, other: object) -> CoordinateTransform:
         if not isinstance(other, CoordinateTransform):
             raise NotImplementedError(
@@ -361,6 +396,10 @@ def __init__(
     ):
         super().__init__(input_axes, output_axes, 1)
 
+    def _contents_lines(self) -> Iterable[str]:
+        return
+        yield
+
     def __matmul__(self, other: object) -> CoordinateTransform:
         if not isinstance(other, CoordinateTransform):
             raise NotImplementedError(

python-spec/testing/test_coordinates.py

@@ -39,6 +39,14 @@ def test_coordinate_space():
     assert coord_space[0] == Axis("x", unit="nanometer")
 
 
+def test_coordiante_space_from_axis_names():
+    coord_space = CoordinateSpace.from_axis_names(["alpha", "beta"])
+    assert len(coord_space) == 2
+    assert coord_space.axis_names == ("alpha", "beta")
+    assert coord_space[0] == Axis("alpha", unit=None)
+    assert coord_space[1] == Axis("beta", unit=None)
+
+
 @pytest.mark.parametrize(
     ("input", "expected"),
     [