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Add classes for coordinate spaces and transforms #218

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merged 25 commits into from
Sep 18, 2024
Merged

Add classes for coordinate spaces and transforms #218

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b02dd45
Add classes for coordinate spaces and transforms
jp-dark Sep 12, 2024
ff532b6
Add coordinate space/transform classes to `__all__`
jp-dark Sep 13, 2024
cbaa95f
Update docstrings, add tests, handle init edge cases better
jp-dark Sep 13, 2024
a2b3c1f
Fix linting/test in test_coordinates.py
jp-dark Sep 13, 2024
75e77d6
Respond to PR feedback (docstring clarity + operator ambiguity)
jp-dark Sep 13, 2024
36ae037
Add lifecycle to docstrings
jp-dark Sep 13, 2024
e4ec1f6
Remove redundant rank methods
jp-dark Sep 13, 2024
fa4918e
Change RuntimeError -> ValueError
jp-dark Sep 13, 2024
40cbe3a
Add UniformScaleTransform class
jp-dark Sep 13, 2024
8148c1a
Clean-up coordinate transform matrix multiply methods
jp-dark Sep 13, 2024
afe2e54
Adjust names and docstrings
jp-dark Sep 13, 2024
9c514cd
Update coordinate class based on feedback
jp-dark Sep 16, 2024
0b63287
Run linters
jp-dark Sep 17, 2024
99d5df2
Update attrs usage based on PR feedback
jp-dark Sep 17, 2024
79de67f
Improve __matmul__, __rmatmul__ types/errors based on PR feedback
jp-dark Sep 17, 2024
893b34e
Improve CoordinateSpace inheritance based on PR feedback
jp-dark Sep 17, 2024
7350d2a
Fix typo python-spec/src/somacore/types.py
jp-dark Sep 17, 2024
7deb1e6
Add helper methods for checking axes for `@` based on PR feedback
jp-dark Sep 17, 2024
d63117f
Fix error messages
jp-dark Sep 18, 2024
509a462
Specify sequence type for CoordinateSpace abc
jp-dark Sep 18, 2024
64b1362
Remove stray duplicate value check
jp-dark Sep 18, 2024
7365f37
Add matmul coordinate transform tests and fix matmul bug
jp-dark Sep 18, 2024
6bcec59
For CoordinateTransform drop __rmatmul__ and depend only on __matmul__
jp-dark Sep 18, 2024
b896712
Narrow type for inverse transforms
jp-dark Sep 18, 2024
ff235d0
Fix 3.8 type error
jp-dark Sep 18, 2024
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12 changes: 12 additions & 0 deletions python-spec/src/somacore/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,12 @@

from .base import SOMAObject
from .collection import Collection
from .coordinates import AffineTransform
from .coordinates import Axis
from .coordinates import CoordinateSpace
from .coordinates import CoordinateTransform
from .coordinates import IdentityTransform
from .coordinates import ScaleTransform
from .data import DataFrame
from .data import DenseNDArray
from .data import NDArray
Expand Down Expand Up @@ -61,4 +67,10 @@
"AxisQuery",
"ExperimentAxisQuery",
"ContextBase",
"Axis",
"CoordinateSpace",
"CoordinateTransform",
"AffineTransform",
"ScaleTransform",
"IdentityTransform",
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