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Fix numpy 1.25 issues #930

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merged 7 commits into from
Jun 26, 2023
Merged

Fix numpy 1.25 issues #930

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c4ccf54
Replace deprecated `numpy.alltrue()` with `numpy.all()`
guyer Jun 22, 2023
f417247
Replace deprecated `numpy.round_()` with `numpy.round()`
guyer Jun 22, 2023
ca2d651
Replace deprecated `numpy.sometrue()` with `numpy.any()`
guyer Jun 22, 2023
3327e7c
Use builtin `max()`
guyer Jun 22, 2023
94fa8ce
Consistently dilate grids as a vector multiply
guyer Jun 23, 2023
23930bb
Extract single values from array
guyer Jun 23, 2023
0744827
Alias `round()`
guyer Jun 23, 2023
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6 changes: 3 additions & 3 deletions examples/phase/symmetry.py
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Original file line number Diff line number Diff line change
Expand Up @@ -69,9 +69,9 @@
... x = dx * (i + 0.5)
... y = dx * (j + 0.5)
... testResult[i, j] = x * y
... bottomRight[i, j] = var(((L - x,), (y,)))
... topLeft[i, j] = var(((x,), (L - y,)))
... topRight[i, j] = var(((L - x,), (L - y,)))
... bottomRight[i, j] = var(((L - x,), (y,)))[0]
... topLeft[i, j] = var(((x,), (L - y,)))[0]
... topRight[i, j] = var(((L - x,), (L - y,)))[0]
>>> numerix.allclose(testResult, bottomRight, atol = 1e-10)
1
>>> numerix.allclose(testResult, topLeft, atol = 1e-10)
Expand Down
63 changes: 61 additions & 2 deletions fipy/meshes/mesh.py
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Expand Up @@ -386,14 +386,13 @@ def __mul__(self, factor):
[[ 1.5 4.5 1.5 4.5]
[ 1. 1. 3. 3. ]]


but the vector must have the same dimensionality as the `Mesh`

>>> dilatedMesh = baseMesh * ((3,), (2,), (1,)) #doctest: +IGNORE_EXCEPTION_DETAIL
Traceback (most recent call last):
...
ValueError: shape mismatch: objects cannot be broadcast to a single shape
"""
"""
newCoords = self.vertexCoords * factor
newmesh = Mesh(vertexCoords=newCoords,
faceVertexIDs=numerix.array(self.faceVertexIDs),
Expand Down Expand Up @@ -786,6 +785,66 @@ def _test(self):
... # doctest: +SERIAL
True



Check dilation of 1D meshes

>>> from fipy.meshes import Grid1D
>>> baseMesh = Grid1D(dx = 1.0, nx = 2)
>>> print(baseMesh.cellCenters)
[[ 0.5 1.5]]

The `factor` can be a scalar

>>> dilatedMesh = baseMesh * 3
>>> print(dilatedMesh.cellCenters)
[[ 1.5 4.5]]

or a vector

>>> dilatedMesh = baseMesh * ((3,),)
>>> print(dilatedMesh.cellCenters)
[[ 1.5 4.5]]

but the vector must have the same dimensionality as the `Mesh`

>>> dilatedMesh = baseMesh * ((3,), (2,), (1,)) #doctest: +IGNORE_EXCEPTION_DETAIL
Traceback (most recent call last):
...
ValueError: shape mismatch: objects cannot be broadcast to a single shape


Check dilation of 3D meshes

>>> from fipy.meshes import Grid3D
>>> baseMesh = Grid3D(dx = 1.0, dy = 1.0, dz = 1.0, nx = 2, ny = 2, nz = 2)
>>> print(baseMesh.cellCenters)
[[ 0.5 1.5 0.5 1.5 0.5 1.5 0.5 1.5]
[ 0.5 0.5 1.5 1.5 0.5 0.5 1.5 1.5]
[ 0.5 0.5 0.5 0.5 1.5 1.5 1.5 1.5]]

The `factor` can be a scalar

>>> dilatedMesh = baseMesh * 3
>>> print(dilatedMesh.cellCenters)
[[ 1.5 4.5 1.5 4.5 1.5 4.5 1.5 4.5]
[ 1.5 1.5 4.5 4.5 1.5 1.5 4.5 4.5]
[ 1.5 1.5 1.5 1.5 4.5 4.5 4.5 4.5]]

or a vector

>>> dilatedMesh = baseMesh * ((3,), (2,), (1,))
>>> print(dilatedMesh.cellCenters)
[[ 1.5 4.5 1.5 4.5 1.5 4.5 1.5 4.5]
[ 1. 1. 3. 3. 1. 1. 3. 3. ]
[ 0.5 0.5 0.5 0.5 1.5 1.5 1.5 1.5]]

but the vector must have the same dimensionality as the `Mesh`

>>> dilatedMesh = baseMesh * ((3,), (2,)) #doctest: +IGNORE_EXCEPTION_DETAIL
Traceback (most recent call last):
...
ValueError: shape mismatch: objects cannot be broadcast to a single shape
"""

def _test():
Expand Down
5 changes: 4 additions & 1 deletion fipy/meshes/uniformGrid1D.py
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Expand Up @@ -249,7 +249,10 @@ def _translate(self, vector):
overlap=self.args['overlap'])

def __mul__(self, factor):
return UniformGrid1D(dx=self.dx * factor,
dx = numerix.array([[self.args['dx']]])
dx *= factor

return UniformGrid1D(dx=dx[0,0],
nx=self.args['nx'],
origin=self.args['origin'] * factor,
overlap=self.args['overlap'])
Expand Down
9 changes: 5 additions & 4 deletions fipy/meshes/uniformGrid2D.py
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Expand Up @@ -425,11 +425,12 @@ def _translate(self, vector):
origin = numerix.array(self.args['origin']) + vector, overlap=self.args['overlap'])

def __mul__(self, factor):
if numerix.shape(factor) is ():
factor = numerix.resize(factor, (2, 1))
dxdy = numerix.array([[self.args['dx']],
[self.args['dy']]])
dxdy *= factor

return UniformGrid2D(dx=self.args['dx'] * numerix.array(factor[0]), nx=self.args['nx'],
dy=self.args['dy'] * numerix.array(factor[1]), ny=self.args['ny'],
return UniformGrid2D(dx=dxdy[0,0], nx=self.args['nx'],
dy=dxdy[1,0], ny=self.args['ny'],
origin=numerix.array(self.args['origin']) * factor, overlap=self.args['overlap'])

@property
Expand Down
13 changes: 9 additions & 4 deletions fipy/meshes/uniformGrid3D.py
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Original file line number Diff line number Diff line change
Expand Up @@ -382,10 +382,15 @@ def _translate(self, vector):
origin = numerix.array(self.args['origin']) + vector, overlap=self.args['overlap'])

def __mul__(self, factor):
return UniformGrid3D(dx = self.dx * factor, nx = self.nx,
dy = self.dy * factor, ny = self.ny,
dz = self.dz * factor, nz = self.nz,
origin = self.origin * factor)
dxdydz = numerix.array([[self.args['dx']],
[self.args['dy']],
[self.args['dz']]])
dxdydz *= factor

return UniformGrid3D(dx=dxdydz[0,0], nx=self.nx,
dy=dxdydz[1,0], ny=self.ny,
dz=dxdydz[2,0], nz=self.nz,
origin=self.origin * factor)

@property
def _concatenableMesh(self):
Expand Down
58 changes: 29 additions & 29 deletions fipy/tools/dimensions/physicalField.py
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Original file line number Diff line number Diff line change
Expand Up @@ -257,7 +257,7 @@ def _sum(self, other, sign1 = lambda a: a, sign2 = lambda b: b):
other = PhysicalField(value = other)

if not isinstance(other, PhysicalField):
if numerix.alltrue(other == 0):
if numerix.all(other == 0):
new_value = sign1(selfValue)
elif self.unit.isDimensionlessOrAngle() or self.unit.isInverseAngle():
new_value = sign1(selfValue) + sign2(other)
Expand Down Expand Up @@ -484,7 +484,7 @@ def _inMyUnits(self, other):
if not isinstance(other, PhysicalField):
if isinstance(other, string_types):
other = PhysicalField(other)
elif numerix.alltrue(other == 0) or self.unit.isDimensionlessOrAngle():
elif numerix.all(other == 0) or self.unit.isDimensionlessOrAngle():
other = PhysicalField(value = other, unit = self.unit)
else:
raise TypeError('Incompatible units')
Expand Down Expand Up @@ -654,7 +654,7 @@ def __float__(self):
As a special case, quantities with angular units are converted to
base units (radians) and then assumed dimensionless.

>>> print(numerix.round_(float(PhysicalField("2. deg")), 6))
>>> print(numerix.round(float(PhysicalField("2. deg")), 6))
0.034907

If the quantity is not dimensionless, the conversion fails.
Expand Down Expand Up @@ -908,7 +908,7 @@ def numericValue(self):
"""
Return the `PhysicalField` without units, after conversion to base SI units.

>>> print(numerix.round_(PhysicalField("1 inch").numericValue, 6))
>>> print(numerix.round(PhysicalField("1 inch").numericValue, 6))
0.0254
"""
return self.inSIUnits().value
Expand Down Expand Up @@ -971,7 +971,7 @@ def arccos(self):

The input `PhysicalField` must be dimensionless

>>> print(numerix.round_(PhysicalField("1 m").arccos(), 6))
>>> print(numerix.round(PhysicalField("1 m").arccos(), 6))
Traceback (most recent call last):
...
TypeError: Incompatible units
Expand All @@ -988,7 +988,7 @@ def arccosh(self):

The input `PhysicalField` must be dimensionless

>>> print(numerix.round_(PhysicalField("1. m").arccosh(), 6))
>>> print(numerix.round(PhysicalField("1. m").arccosh(), 6))
Traceback (most recent call last):
...
TypeError: Incompatible units
Expand All @@ -1004,7 +1004,7 @@ def arcsin(self):

The input `PhysicalField` must be dimensionless

>>> print(numerix.round_(PhysicalField("1 m").arcsin(), 6))
>>> print(numerix.round(PhysicalField("1 m").arcsin(), 6))
Traceback (most recent call last):
...
TypeError: Incompatible units
Expand Down Expand Up @@ -1065,9 +1065,9 @@ def cos(self):
"""
Return the cosine of the `PhysicalField`

>>> print(numerix.round_(PhysicalField(2*numerix.pi/6, "rad").cos(), 6))
>>> print(numerix.round(PhysicalField(2*numerix.pi/6, "rad").cos(), 6))
0.5
>>> print(numerix.round_(PhysicalField(60., "deg").cos(), 6))
>>> print(numerix.round(PhysicalField(60., "deg").cos(), 6))
0.5

The units of the `PhysicalField` must be an angle
Expand Down Expand Up @@ -1099,9 +1099,9 @@ def tan(self):
"""
Return the tangent of the `PhysicalField`

>>> numerix.round_(PhysicalField(numerix.pi/4, "rad").tan(), 6)
>>> numerix.round(PhysicalField(numerix.pi/4, "rad").tan(), 6)
1.0
>>> numerix.round_(PhysicalField(45, "deg").tan(), 6)
>>> numerix.round(PhysicalField(45, "deg").tan(), 6)
1.0

The units of the `PhysicalField` must be an angle
Expand Down Expand Up @@ -1133,15 +1133,15 @@ def arctan2(self, other):
"""
Return the arctangent of `self` divided by `other` in radians

>>> print(numerix.round_(PhysicalField(2.).arctan2(PhysicalField(5.)), 6))
>>> print(numerix.round(PhysicalField(2.).arctan2(PhysicalField(5.)), 6))
0.380506

The input `PhysicalField` objects must be in the same dimensions

>>> print(numerix.round_(PhysicalField(2.54, "cm").arctan2(PhysicalField(1., "inch")), 6))
>>> print(numerix.round(PhysicalField(2.54, "cm").arctan2(PhysicalField(1., "inch")), 6))
0.785398

>>> print(numerix.round_(PhysicalField(2.).arctan2(PhysicalField("5. m")), 6))
>>> print(numerix.round(PhysicalField(2.).arctan2(PhysicalField("5. m")), 6))
Traceback (most recent call last):
...
TypeError: Incompatible units
Expand All @@ -1153,12 +1153,12 @@ def arctan(self):
"""
Return the arctangent of the `PhysicalField` in radians

>>> print(numerix.round_(PhysicalField(1).arctan(), 6))
>>> print(numerix.round(PhysicalField(1).arctan(), 6))
0.785398

The input `PhysicalField` must be dimensionless

>>> print(numerix.round_(PhysicalField("1 m").arctan(), 6))
>>> print(numerix.round(PhysicalField("1 m").arctan(), 6))
Traceback (most recent call last):
...
TypeError: Incompatible units
Expand All @@ -1174,7 +1174,7 @@ def arctanh(self):

The input `PhysicalField` must be dimensionless

>>> print(numerix.round_(PhysicalField("1 m").arctanh(), 6))
>>> print(numerix.round(PhysicalField("1 m").arctanh(), 6))
Traceback (most recent call last):
...
TypeError: Incompatible units
Expand All @@ -1186,12 +1186,12 @@ def log(self):
"""
Return the natural logarithm of the `PhysicalField`

>>> print(numerix.round_(PhysicalField(10).log(), 6))
>>> print(numerix.round(PhysicalField(10).log(), 6))
2.302585

The input `PhysicalField` must be dimensionless

>>> print(numerix.round_(PhysicalField("1. m").log(), 6))
>>> print(numerix.round(PhysicalField("1. m").log(), 6))
Traceback (most recent call last):
...
TypeError: Incompatible units
Expand All @@ -1202,12 +1202,12 @@ def log10(self):
"""
Return the base-10 logarithm of the `PhysicalField`

>>> print(numerix.round_(PhysicalField(10.).log10(), 6))
>>> print(numerix.round(PhysicalField(10.).log10(), 6))
1.0

The input `PhysicalField` must be dimensionless

>>> print(numerix.round_(PhysicalField("1. m").log10(), 6))
>>> print(numerix.round(PhysicalField("1. m").log10(), 6))
Traceback (most recent call last):
...
TypeError: Incompatible units
Expand Down Expand Up @@ -1415,7 +1415,7 @@ def _checkSame(self, other):
return self.isDimensionless()
else:
raise TypeError('PhysicalUnits can only be compared with other PhysicalUnits')
if not numerix.alltrue(self.powers == other.powers):
if not numerix.all(self.powers == other.powers):
raise TypeError('Incompatible units')

def __eq__(self, other):
Expand Down Expand Up @@ -1651,7 +1651,7 @@ def conversionFactorTo(self, other):

>>> a = PhysicalField("1. mm")
>>> b = PhysicalField("1. inch")
>>> print(numerix.round_(b.unit.conversionFactorTo(a.unit), 6))
>>> print(numerix.round(b.unit.conversionFactorTo(a.unit), 6))
25.4

Units must have the same fundamental SI units
Expand All @@ -1673,7 +1673,7 @@ def conversionFactorTo(self, other):
...
TypeError: Unit conversion (K to degF) cannot be expressed as a simple multiplicative factor
"""
if not numerix.alltrue(self.powers == other.powers):
if not numerix.all(self.powers == other.powers):
if self.isDimensionlessOrAngle() and other.isDimensionlessOrAngle():
return self.factor / other.factor
else:
Expand All @@ -1691,10 +1691,10 @@ def conversionTupleTo(self, other): # added 1998/09/29 GPW
>>> a = PhysicalField("1. K").unit
>>> b = PhysicalField("1. degF").unit
>>> from builtins import str
>>> [str(numerix.round_(element, 6)) for element in b.conversionTupleTo(a)]
>>> [str(numerix.round(element, 6)) for element in b.conversionTupleTo(a)]
['0.555556', '459.67']
"""
if not numerix.alltrue(self.powers == other.powers):
if not numerix.all(self.powers == other.powers):
raise TypeError('Incompatible units')

# let (s1,d1) be the conversion tuple from 'self' to base units
Expand Down Expand Up @@ -1886,17 +1886,17 @@ def _Scale(quantity, scaling):

`quantity` can be a `PhysicalField`

>>> print(numerix.round_(_Scale(PhysicalField("1. inch"), PhysicalField("1. mm")), 6))
>>> print(numerix.round(_Scale(PhysicalField("1. inch"), PhysicalField("1. mm")), 6))
25.4

or a value-unit string convertible to a `PhysicalField`

>>> print(numerix.round_(_Scale("1. inch", PhysicalField("1. mm")), 6))
>>> print(numerix.round(_Scale("1. inch", PhysicalField("1. mm")), 6))
25.4

or a dimensionless number. A dimensionless number is left alone.

>>> print(numerix.round_(_Scale(PhysicalField(2.), PhysicalField("1. mm")), 6))
>>> print(numerix.round(_Scale(PhysicalField(2.), PhysicalField("1. mm")), 6))
2.0

It is an error for the result to have dimensions.
Expand Down