Merge branch 'Jacob-Stevens-Haas-diff-anyaxis'

.github/workflows/pull-docs.yml

@@ -7,7 +7,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ "3.7" ]
+        python-version: [ "3.9" ]
         poetry-version: [ "1.2.1" ]
     steps:
       # ======

.github/workflows/push-test.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.7"]
+        python-version: ["3.9"]
         poetry-version: ["1.2.1"]
 
     steps:

.github/workflows/release.yml

@@ -14,7 +14,7 @@ jobs:
       name: release
     strategy:
       matrix:
-        python-version: ["3.7"]
+        python-version: ["3.9"]
         poetry-version: ["1.2.1"]
     steps:
       # ======

derivative/__version__.py

@@ -1 +1 @@
-__version__: str = '0.6.0'
+__version__: str = '0.6.1'

derivative/differentiation.py

@@ -1,5 +1,6 @@
 import abc
 import numpy as np
+from numpy.typing import NDArray
 
 from .utils import _memoize_arrays
 
@@ -216,41 +217,38 @@ def x(self, X, t, axis=1):
         Returns:
             :obj:`ndarray` of float: Returns dX/dt along axis.
         """
-        X, flat = _align_axes(X, t, axis)
+        X, orig_shape = _align_axes(X, t, axis)
 
         if X.shape[1] == 1:
             dX = X
         else:
             dX = np.array([list(self.compute_x_for(t, x, np.arange(len(t)))) for x in X])
 
-        return _restore_axes(dX, axis, flat)
+        return _restore_axes(dX, axis, orig_shape)
 
 
-def _align_axes(X, t, axis):
-    # Cast
+def _align_axes(X, t, axis) -> tuple[NDArray, tuple[int, ...]]:
     X = np.array(X)
-    flat = False
-    # Check shape and axis
-    if len(X.shape) == 1:
+    orig_shape = X.shape
+    # By convention, differentiate axis 1
+    if len(orig_shape) == 1:
         X = X.reshape(1, -1)
-        flat = True
-    elif len(X.shape) == 2:
-        if axis == 0:
-            X = X.T
-        elif axis == 1:
-            pass
-        else:
-            raise ValueError("Invalid axis.")
     else:
-        raise ValueError("Invalid shape of X.")
-
+        ax_len = orig_shape[axis]
+        # order of operations coupled with _restore_axes.  Move differentiation axis to
+        # zero so reshape does not skew differentiation axis
+        X = np.moveaxis(X, axis, 0).reshape((ax_len, -1)).T
     if X.shape[1] != len(t):
         raise ValueError("Desired X axis size does not match t size.")
-    return X, flat
+    return X, orig_shape
 
 
-def _restore_axes(dX, axis, flat):
-    if flat:
+def _restore_axes(dX: NDArray, axis: int, orig_shape: tuple[int, ...]) -> NDArray:
+    if len(orig_shape) == 1:
         return dX.flatten()
     else:
-        return dX if axis == 1 else dX.T
+        # order of operations coupled with _align_axes
+        extra_dims = tuple(length for ax, length in enumerate(orig_shape) if ax != axis)
+        moved_shape = (orig_shape[axis],) + extra_dims
+        dX = np.moveaxis(dX.T.reshape((moved_shape)), 0, axis)
+        return dX

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "derivative"
-version = "0.6.0"
+version = "0.6.1"
 description = "Numerical differentiation in python."
 repository = "https://github.com/andgoldschmidt/derivative"
 documentation = "https://derivative.readthedocs.io/"
@@ -15,7 +15,7 @@ readme = "README.rst"
 
 
 [tool.poetry.dependencies]
-python = "^3.7"
+python = "^3.9"
 numpy = "^1.18.3"
 scipy = "^1.4.1"
 scikit-learn = "^1"
@@ -41,4 +41,4 @@ requires = ["poetry-core>=1.1.0"]
 build-backend = "poetry.core.masonry.api"
 
 [tool.poetry.plugins.'derivative.hyperparam_opt']
-"kalman.default" = "derivative.utils:_default_kalman"
+"kalman.default" = "derivative.utils:_default_kalman"

tests/test_interface.py

@@ -33,6 +33,10 @@ def test_axis():
     shape2 = ts.shape
     test3 = dxdt(ts, ts, axis=1).shape
     assert shape2 == test3
+    n = 4
+    x3d = np.tile(np.arange(n), (n, n, 1))
+    test_4 = dxdt(x3d, np.arange(n), axis=2)
+    np.testing.assert_array_equal(test_4, np.ones((n,n,n)))
 
 
 def test_empty():