Testing Fatiando installation: Failed

Shib Ganguli

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May 17, 2019, 12:53:40 AM5/17/19

to Fatiando a Terra

Hi There!

I an new to Fatiando and installed it last day. While testing the installation I got the following message:

-- Docs: https://docs.pytest.org/en/latest/warnings.html

============ 31 failed, 184 passed, 263 warnings in 169.18 seconds ============

Can anybody help me to fix this issue? Thanking you in anticipation.

My OS: Windows 10

Version of Python: Python 2.7.16

Best regards,

Shib S Ganguli

Leonardo Uieda

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May 17, 2019, 9:11:06 PM5/17/19

to fati...@googlegroups.com

Hi Shib,

Could you please post the entire log of the tests? The screen you posted is only the end of it and I can't see what the actual errors are.

--
Leonardo Uieda

Visiting Research Scholar

Department of Earth Sciences - SOEST

University of Hawai'i at Mānoa

ORCID: 0000-0001-6123-9515

www.leouieda.com

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Shib Sankar Ganguli

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May 18, 2019, 2:56:57 AM5/18/19

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Hi Uieda!

Many thanks for your quick response. As you suggested, I am providing the entire log of test, given below

Last login: Sat May 18 11:34:07 on ttys000

/Users/ganguli/.anaconda/navigator/a.tool ; exit;

(base) Shibs-MacBook-Pro:~ ganguli$ /Users/ganguli/.anaconda/navigator/a.tool ; exit;

Python 2.7.16 |Anaconda, Inc.| (default, Mar 14 2019, 16:24:02)

Type "copyright", "credits" or "license" for more information.

IPython 5.8.0 -- An enhanced Interactive Python.

? -> Introduction and overview of IPython's features.

%quickref -> Quick reference.

help -> Python's own help system.

object? -> Details about 'object', use 'object??' for extra details.

In [1]: import fatiando

...: fatiando.test()

...:

============================= test session starts ==============================

platform darwin -- Python 2.7.16, pytest-4.3.1, py-1.8.0, pluggy-0.9.0

rootdir: /Users/ganguli12, inifile:

collected 215 items

gridder.py F.FF.F [ 2%]

mesher.py FF.FF.F.F......F....... [ 13%]

utils.py .FF...FFF. [ 18%]

geothermal/climsig.py . [ 18%]

gravmag/_tesseroid_numba.py F [ 19%]

gravmag/basin2d.py F..FF [ 21%]

gravmag/eqlayer.py F. [ 22%]

gravmag/harvester.py . [ 22%]

gravmag/magdir.py . [ 23%]

gravmag/normal_gravity.py . [ 23%]

gravmag/tensor.py .F [ 24%]

gravmag/tesseroid.py . [ 25%]

gravmag/tests/test_eqlayer.py ...... [ 27%]

gravmag/tests/test_euler.py ... [ 29%]

gravmag/tests/test_normal_gravity.py .... [ 31%]

gravmag/tests/test_polyprism.py .................................. [ 46%]

gravmag/tests/test_prism.py ...F. [ 49%]

gravmag/tests/test_sphere.py ................. [ 57%]

gravmag/tests/test_tesseroid.py ............ [ 62%]

gravmag/tests/test_transform.py ............... [ 69%]

inversion/__init__.py F [ 70%]

inversion/base.py ... [ 71%]

inversion/hyper_param.py F [ 72%]

inversion/regularization.py F..... [ 74%]

seismic/epic2d.py . [ 75%]

seismic/profile.py FF [ 76%]

seismic/srtomo.py F [ 76%]

seismic/ttime2d.py F [ 77%]

seismic/wavefd.py .. [ 78%]

seismic/tests/test_seismic_conv.py FF... [ 80%]

seismic/tests/test_seismic_srtomo.py ... [ 81%]

tests/test_random.py .............. [ 88%]

tests/gridder/test_gridder_padarray.py ....... [ 91%]

tests/mesher/test_geometric_element.py . [ 92%]

tests/mesher/test_pointgrid.py ........ [ 95%]

tests/mesher/test_polygon.py . [ 96%]

tests/mesher/test_polygonal_prism.py . [ 96%]

tests/mesher/test_prism.py . [ 97%]

tests/mesher/test_prism_mesh.py . [ 97%]

tests/mesher/test_sphere.py . [ 98%]

tests/mesher/test_square.py . [ 98%]

tests/mesher/test_square_mesh.py . [ 99%]

tests/mesher/test_tesseroid.py . [ 99%]

tests/mesher/test_tesseroid_mesh.py . [100%]

================================================================================================= FAILURES =================================================================================================

___________________________________________________________________________________ [doctest] fatiando.gridder.pad_array ___________________________________________________________________________________

555 Padded array. The array core is a deep copy of the original array

556 * nps : list

557 List of tuples containing the number of elements padded onto each

558 dimension.

559

560 Examples:

561

562 >>> z = numpy.array([3, 4, 4, 5, 6])

563 >>> zpad, nps = pad_array(z)

564 >>> zpad

Expected:

array([ 4.4, 3.2, 3. , 4. , 4. , 5. , 6. , 4.4])

Got:

array([4.4, 3.2, 3. , 4. , 4. , 5. , 6. , 4.4])

/anaconda2/lib/python2.7/site-packages/fatiando/gridder.py:564: DocTestFailure

____________________________________________________________________________________ [doctest] fatiando.gridder.regular ____________________________________________________________________________________

144 * ``[x, y]``

145 Numpy arrays with the x and y coordinates of the grid points

146 * ``[x, y, z]``

147 If *z* given. Numpy arrays with the x, y, and z coordinates of the grid

148 points

149

150 Examples::

151

152 >>> x, y = regular((0, 10, 0, 5), (5, 3))

153 >>> x

Expected:

array([ 0. , 0. , 0. , 2.5, 2.5, 2.5, 5. , 5. , 5. ,

7.5, 7.5, 7.5, 10. , 10. , 10. ])

Got:

array([ 0. , 0. , 0. , 2.5, 2.5, 2.5, 5. , 5. , 5. , 7.5, 7.5,

7.5, 10. , 10. , 10. ])

/anaconda2/lib/python2.7/site-packages/fatiando/gridder.py:153: DocTestFailure

____________________________________________________________________________________ [doctest] fatiando.gridder.scatter ____________________________________________________________________________________

218

219 * ``[x, y]``

220 Numpy arrays with the x and y coordinates of the points

221 * ``[x, y, z]``

222 If *z* given. Arrays with the x, y, and z coordinates of the points

223

224 Examples::

225

226 >>> x, y = scatter((0, 10, 0, 2), 4, seed=0)

227 >>> x

Expected:

array([ 5.48813504, 7.15189366, 6.02763376, 5.44883183])

Got:

array([5.48813504, 7.15189366, 6.02763376, 5.44883183])

/anaconda2/lib/python2.7/site-packages/fatiando/gridder.py:227: DocTestFailure

__________________________________________________________________________________ [doctest] fatiando.gridder.unpad_array __________________________________________________________________________________

694 Returns:

695

696 * b : array

697 Array of same dimension as a, with padding removed

698

699 Examples:

700

701 >>> z = numpy.array([3, 4, 4, 5, 6])

702 >>> zpad, nps = pad_array(z)

703 >>> zpad

Expected:

array([ 4.4, 3.2, 3. , 4. , 4. , 5. , 6. , 4.4])

Got:

array([4.4, 3.2, 3. , 4. , 4. , 5. , 6. , 4.4])

/anaconda2/lib/python2.7/site-packages/fatiando/gridder.py:703: DocTestFailure

___________________________________________________________________________________ [doctest] fatiando.mesher.PointGrid ____________________________________________________________________________________

831 each point in the grid.

832

833 Examples::

834

835 >>> g = PointGrid([0, 10, 2, 6], 200, (2, 3))

836 >>> g.shape

837 (2, 3)

838 >>> g.size

839 6

840 >>> g[0].center

Expected:

array([ 0., 2., 200.])

Got:

array([ 0., 2., 200.])

/anaconda2/lib/python2.7/site-packages/fatiando/mesher.py:840: DocTestFailure

________________________________________________________________________________ [doctest] fatiando.mesher.PointGrid.split _________________________________________________________________________________

949 >>> grids = g.split((2, 3))

950 >>> for s in grids:

951 ... s.props['bla']

952 array([1, 4])

953 array([2, 5])

954 array([3, 6])

955 array([ 7, 10])

956 array([ 8, 11])

957 array([ 9, 12])

958 >>> for s in grids:

Differences (unified diff with -expected +actual):

@@ -1,6 +1,6 @@

-array([ 0., 1.])

-array([ 2., 3.])

+array([0., 1.])

+array([2., 3.])

/anaconda2/lib/python2.7/site-packages/fatiando/mesher.py:958: DocTestFailure

_________________________________________________________________________________ [doctest] fatiando.mesher.PolygonalPrism _________________________________________________________________________________

755 Physical properties assigned to the prism.

756 Ex: ``props={'density':10, 'magnetization':10000}``

757

758 Examples:

759

760 >>> verts = [[1, 1], [1, 2], [2, 2], [2, 1]]

761 >>> p = PolygonalPrism(verts, 0, 3, props={'temperature':25})

762 >>> p.props['temperature']

763 25

764 >>> print p.x

Expected:

[ 1. 1. 2. 2.]

Got:

[1. 1. 2. 2.]

/anaconda2/lib/python2.7/site-packages/fatiando/mesher.py:764: DocTestFailure

____________________________________________________________________________ [doctest] fatiando.mesher.PolygonalPrism.topolygon ____________________________________________________________________________

789

790 * polygon : :func:`fatiando.mesher.Polygon`

791 The polygon

792

793 Example:

794

795 >>> verts = [[1, 1], [1, 2], [2, 2], [2, 1]]

796 >>> p = PolygonalPrism(verts, 0, 100)

797 >>> poly = p.topolygon()

798 >>> print poly.x

Expected:

[ 1. 1. 2. 2.]

Got:

[1. 1. 2. 2.]

/anaconda2/lib/python2.7/site-packages/fatiando/mesher.py:798: DocTestFailure

__________________________________________________________________________________ [doctest] fatiando.mesher.Prism.center __________________________________________________________________________________

479

480 Returns:

481

482 * coords : list = [xc, yc, zc]

483 Coordinates of the center

484

485 Example:

486

487 >>> prism = Prism(1, 2, 1, 3, 0, 2)

488 >>> print prism.center()

Expected:

[ 1.5 2. 1. ]

Got:

[1.5 2. 1. ]

/anaconda2/lib/python2.7/site-packages/fatiando/mesher.py:488: DocTestFailure

___________________________________________________________________________________ [doctest] fatiando.mesher.PrismMesh ____________________________________________________________________________________

1184 >>> for p in mesh:

1185 ... print p

1186 x1:0 | x2:1 | y1:0 | y2:4 | z1:0 | z2:3 | density:200

1187 x1:1 | x2:2 | y1:0 | y2:4 | z1:0 | z2:3 | density:-1000

1188

1189 You can use :meth:`~fatiando.mesher.PrismMesh.get_xs` (and similar

1190 methods for y and z) to get the x coordinates of the prisms in the mesh::

1191

1192 >>> mesh = PrismMesh((0, 2, 0, 4, 0, 3), (1, 1, 2))

1193 >>> print mesh.get_xs()

Expected:

[ 0. 1. 2.]

Got:

[0. 1. 2.]

/anaconda2/lib/python2.7/site-packages/fatiando/mesher.py:1193: DocTestFailure

_________________________________________________________________________________ [doctest] fatiando.mesher.TesseroidMesh __________________________________________________________________________________

1581 ... print p

1582 w:0 | e:1 | s:0 | n:4 | top:3 | bottom:0 | density:200

1583 w:1 | e:2 | s:0 | n:4 | top:3 | bottom:0 | density:-1000

1584

1585 You can use :meth:`~fatiando.mesher.PrismMesh.get_xs` (and similar

1586 methods for y and z) to get the x coordinates of the tesseroidss in the

1587 mesh::

1588

1589 >>> mesh = TesseroidMesh((0, 2, 0, 4, 3, 0), (1, 1, 2))

1590 >>> print mesh.get_xs()

Expected:

[ 0. 1. 2.]

Got:

[0. 1. 2.]

/anaconda2/lib/python2.7/site-packages/fatiando/mesher.py:1590: DocTestFailure

_____________________________________________________________________________________ [doctest] fatiando.utils.ang2vec _____________________________________________________________________________________

411

412 Returns:

413

414 * vec : array = [x, y, z]

415 The vector

416

417 Examples::

418

419 >>> import numpy

420 >>> print ang2vec(3, 45, 45)

Expected:

[ 1.5 1.5 2.12132034]

Got:

[1.5 1.5 2.12132034]

/anaconda2/lib/python2.7/site-packages/fatiando/utils.py:420: DocTestFailure

___________________________________________________________________________________ [doctest] fatiando.utils.contaminate ___________________________________________________________________________________

690 * results : list = [contam, stddev]

691 The contaminated data array and the standard deviation used to

692 contaminate it.

693

694 Examples:

695

696 >>> import numpy as np

697 >>> data = np.ones(5)

698 >>> noisy = contaminate(data, 0.1, seed=0)

699 >>> print noisy

Expected:

[ 1.03137726 0.89498775 0.95284582 1.07906135 1.04172782]

Got:

[1.03137726 0.89498775 0.95284582 1.07906135 1.04172782]

/anaconda2/lib/python2.7/site-packages/fatiando/utils.py:699: DocTestFailure

_____________________________________________________________________________________ [doctest] fatiando.utils.vecmean _____________________________________________________________________________________

468 List of arrays

469

470 Returns:

471

472 * mean : array

473 The mean of each element in the arrays

474

475 Example::

476

477 >>> print vecmean([[1, 1, 2], [2, 3, 5]])

Expected:

[ 1.5 2. 3.5]

Got:

[1.5 2. 3.5]

/anaconda2/lib/python2.7/site-packages/fatiando/utils.py:477: DocTestFailure

_____________________________________________________________________________________ [doctest] fatiando.utils.vecnorm _____________________________________________________________________________________

213

214 Returns:

215

216 * norms : list

217 The norms of the vectors

218

219 Examples::

220

221 >>> v = [[1, 1, 1], [2, 2, 2], [3, 3, 3]]

222 >>> print vecnorm(v)

Expected:

[ 1.73205081 3.46410162 5.19615242]

Got:

[1.73205081 3.46410162 5.19615242]

/anaconda2/lib/python2.7/site-packages/fatiando/utils.py:222: DocTestFailure

_____________________________________________________________________________________ [doctest] fatiando.utils.vecstd ______________________________________________________________________________________

491 List of arrays

492

493 Returns:

494

495 * std : array

496 Standard deviation of each element in the arrays

497

498 Example::

499

500 >>> print vecstd([[1, 1, 2], [2, 3, 5]])

Expected:

[ 0.5 1. 1.5]

Got:

[0.5 1. 1.5]

/anaconda2/lib/python2.7/site-packages/fatiando/utils.py:500: DocTestFailure

_______________________________________________________________________________ [doctest] fatiando.gravmag._tesseroid_numba ________________________________________________________________________________

006

007 A few doctests for the numba code::

008

009 >>> import numpy as np

010 >>> stack = np.empty((6, 6))

011 >>> stktop = -1

012 >>> stktop = split(0, 4, 3, 6, 11, 5, 2, 1, 3, stack, stktop)

013 >>> stktop

014 5

015 >>> stack

Differences (unified diff with -expected +actual):

@@ -1,6 +1,6 @@

-array([[ 0., 2., 3., 6., 7., 5.],

- [ 0., 2., 3., 6., 9., 7.],

- [ 0., 2., 3., 6., 11., 9.],

- [ 2., 4., 3., 6., 7., 5.],

- [ 2., 4., 3., 6., 9., 7.],

- [ 2., 4., 3., 6., 11., 9.]])

+array([[ 0., 2., 3., 6., 7., 5.],

+ [ 0., 2., 3., 6., 9., 7.],

+ [ 0., 2., 3., 6., 11., 9.],

+ [ 2., 4., 3., 6., 7., 5.],

+ [ 2., 4., 3., 6., 9., 7.],

+ [ 2., 4., 3., 6., 11., 9.]])

/anaconda2/lib/python2.7/site-packages/fatiando/gravmag/_tesseroid_numba.py:15: DocTestFailure

_________________________________________________________________________ [doctest] fatiando.gravmag.basin2d.PolygonalBasinGravity _________________________________________________________________________

093 ... props)]

094 >>> x = np.linspace(0, 3000, 50)

095 >>> z = -np.ones_like(x) # Put data at 1m height

096 >>> data = talwani.gz(x, z, model)

097 >>> # Make the solver, configure, and invert.

098 >>> # Will use only 2 points because the two in the corners are

099 >>> # considered fixed in the inversion (at 'top').

100 >>> misfit = PolygonalBasinGravity(x, z, data, 2, props, top=0)

101 >>> _ = misfit.config('levmarq', initial=100*np.ones(misfit.nparams)).fit()

102 >>> misfit.p_

Expected:

array([ 800., 500.])

Got:

array([800., 500.])

/anaconda2/lib/python2.7/site-packages/fatiando/gravmag/basin2d.py:102: DocTestFailure

______________________________________________________________________________ [doctest] fatiando.gravmag.basin2d.Trapezoidal ______________________________________________________________________________

426 >>> solver = Trapezoidal(x, z, gz, verts[0:2], 500).config(

427 ... 'levmarq', initial=[1000, 500]).fit()

428 >>> # p_ is the estimated parameter vector (z1 and z2 in this case)

429 >>> z1, z2 = solver.p_

430 >>> print('{:.1f}, {:.1f}'.format(z1, z2))

431 5000.0, 3000.0

432 >>> # The parameter vector is not that useful so use estimate_ to get a

433 >>> # Polygon object

434 >>> poly = solver.estimate_

435 >>> poly.vertices

Differences (unified diff with -expected +actual):

@@ -1,4 +1,4 @@

-array([[ 1.00000000e+04, 1.00000000e+00],

- [ 9.00000000e+04, 1.00000000e+00],

- [ 9.00000000e+04, 5.00000000e+03],

- [ 1.00000000e+04, 3.00000000e+03]])

+array([[1.e+04, 1.e+00],

+ [9.e+04, 1.e+00],

+ [9.e+04, 5.e+03],

+ [1.e+04, 3.e+03]])

/anaconda2/lib/python2.7/site-packages/fatiando/gravmag/basin2d.py:435: DocTestFailure

______________________________________________________________________________ [doctest] fatiando.gravmag.basin2d.Triangular _______________________________________________________________________________

292 >>> solver = Triangular(x, z, gz, [left, middle], 500).config(

293 ... 'levmarq', initial=[10000, 1000]).fit()

294 >>> # p_ is the estimated parameter vector (x and z in this case)

295 >>> x, z = solver.p_

296 >>> print('{:.1f}, {:.1f}'.format(x, z))

297 50000.0, 5000.0

298 >>> # The parameter vector is not that useful so use estimate_ to get a

299 >>> # Polygon object

300 >>> poly = solver.estimate_

301 >>> poly.vertices

Differences (unified diff with -expected +actual):

@@ -1,3 +1,3 @@

-array([[ 1.00000000e+04, 1.00000000e+00],

- [ 9.00000000e+04, 1.00000000e+00],

- [ 5.00000000e+04, 5.00000000e+03]])

+array([[1.e+04, 1.e+00],

+ [9.e+04, 1.e+00],

+ [5.e+04, 5.e+03]])

/anaconda2/lib/python2.7/site-packages/fatiando/gravmag/basin2d.py:301: DocTestFailure

_______________________________________________________________________________ [doctest] fatiando.gravmag.eqlayer._bkmatrix _______________________________________________________________________________

231

232 * bk : 2d-array

233 The matrix

234

235

236 Examples:

237

238 >>> from fatiando.mesher import PointGrid

239 >>> grid = PointGrid((0, 1, 0, 2), 10, (2, 2))

240 >>> print _bkmatrix(grid, 2)

Differences (unified diff with -expected +actual):

@@ -1,4 +1,4 @@

-[[ 1. 0. 0. 0. 0. 0.]

- [ 1. 2. 0. 4. 0. 0.]

- [ 1. 0. 1. 0. 0. 1.]

- [ 1. 2. 1. 4. 2. 1.]]

+[[1. 0. 0. 0. 0. 0.]

+ [1. 2. 0. 4. 0. 0.]

+ [1. 0. 1. 0. 0. 1.]

+ [1. 2. 1. 4. 2. 1.]]

/anaconda2/lib/python2.7/site-packages/fatiando/gravmag/eqlayer.py:240: DocTestFailure

_________________________________________________________________________________ [doctest] fatiando.gravmag.tensor.eigen __________________________________________________________________________________

102 * eigval1,2,3 : array

103 The first, second, and third eigenvalues

104 * eigvec1,2,3 : array (shape = (N, 3) where N is the number of points)

105 The first, second, and third eigenvectors

106

107 Example:

108

109 >>> tensor = [[2], [0], [0], [3], [0], [1]]

110 >>> eigenvals, eigenvecs = eigen(tensor)

111 >>> print eigenvals[0], eigenvecs[0]

Expected:

[ 3.] [[ 0. 1. 0.]]

Got:

[3.] [[0. 1. 0.]]

/anaconda2/lib/python2.7/site-packages/fatiando/gravmag/tensor.py:111: DocTestFailure

_________________________________________________________________________________________ test_cython_agains_numpy _________________________________________________________________________________________

def test_cython_agains_numpy():

"gravmag.prism numpy and cython implementations give same result"

inc, dec = -30, 50

model = [

Prism(100, 300, -100, 100, 0, 400,

{'density': -1000,

'magnetization': utils.ang2vec(-2, inc, dec)}),

Prism(-300, -100, -100, 100, 0, 200,

{'density': 2000, 'magnetization': utils.ang2vec(5, 25, -10)})]

tmp = np.linspace(-500, 500, 101)

xp, yp = [i.ravel() for i in np.meshgrid(tmp, tmp)]

zp = -1 * np.ones_like(xp)

kernels = ['xx', 'xy', 'xz', 'yy', 'yz', 'zz']

for comp in kernels:

for p in model:

py = getattr(_prism_numpy, 'kernel' + comp)(xp, yp, zp, p)

cy = getattr(prism, 'kernel' + comp)(xp, yp, zp, p)

assert_almost(py, cy, 10,

'Kernel = %s, max field %.15g max diff %.15g'

% (comp, np.abs(cy).max(), np.abs(py - cy).max()))

funcs = ['potential', 'gx', 'gy', 'gz',

'gxx', 'gxy', 'gxz', 'gyy', 'gyz', 'gzz',

'bx', 'by', 'bz', 'tf']

for f in funcs:

if f == 'tf':

py = getattr(_prism_numpy, f)(xp, yp, zp, model, inc, dec)

cy = getattr(prism, f)(xp, yp, zp, model, inc, dec)

else:

py = getattr(_prism_numpy, f)(xp, yp, zp, model)

cy = getattr(prism, f)(xp, yp, zp, model)

if f in ['bx', 'by', 'bz', 'tf']:

precision = 8

else:

precision = 10

assert_almost(py, cy, precision,

'Field = %s, max field %.15g max diff %.15g'

> % (f, np.abs(cy).max(), np.abs(py - cy).max()))

E AssertionError:

E Arrays are not almost equal to 10 decimals

E Field = gxz, max field 1275.32059263158 max diff 1.63866044344818e-08

E Mismatch: 0.0392%

E Max absolute difference: 1.63866044e-08

E Max relative difference: 6.76092762e-08

E x: array([0.5628180735, 0.5510096309, 0.5360277294, ..., 1.3668270773,

E 1.3800995844, 1.3893268537])

E y: array([0.5628180735, 0.5510096309, 0.5360277294, ..., 1.3668270773,

E 1.3800995844, 1.3893268537])

/anaconda2/lib/python2.7/site-packages/fatiando/gravmag/tests/test_prism.py:233: AssertionError

_______________________________________________________________________________________ [doctest] fatiando.inversion _______________________________________________________________________________________

107 ... jac = np.empty((self.ndata, self.nparams))

108 ... jac[:, 0] = self.x

109 ... jac[:, 1] = 1

110 ... return jac

111

112 To test our regression, let's generate some data based on known values of a and

113 b.

114

115 >>> x = np.linspace(0, 5, 6)

116 >>> x

Expected:

array([ 0., 1., 2., 3., 4., 5.])

Got:

array([0., 1., 2., 3., 4., 5.])

/anaconda2/lib/python2.7/site-packages/fatiando/inversion/__init__.py:116: DocTestFailure

_____________________________________________________________________________ [doctest] fatiando.inversion.hyper_param.LCurve ______________________________________________________________________________

072 >>> from fatiando.mesher import SquareMesh

073 >>> from fatiando.seismic import ttime2d, srtomo

074 >>> from fatiando.inversion import Smoothness2D, LCurve

075 >>> from fatiando import utils, gridder

076 >>> area = (0, 2, 0, 2)

077 >>> shape = (10, 10)

078 >>> model = SquareMesh(area, shape)

079 >>> vp = 4*numpy.ones(shape)

080 >>> vp[3:7,3:7] = 10

081 >>> vp

Differences (unified diff with -expected +actual):

@@ -1,10 +1,10 @@

-array([[ 4., 4., 4., 4., 4., 4., 4., 4., 4., 4.],

- [ 4., 4., 4., 4., 4., 4., 4., 4., 4., 4.],

- [ 4., 4., 4., 10., 10., 10., 10., 4., 4., 4.],

- [ 4., 4., 4., 4., 4., 4., 4., 4., 4., 4.],

- [ 4., 4., 4., 4., 4., 4., 4., 4., 4., 4.]])

+array([[ 4., 4., 4., 4., 4., 4., 4., 4., 4., 4.],

+ [ 4., 4., 4., 4., 4., 4., 4., 4., 4., 4.],

+ [ 4., 4., 4., 10., 10., 10., 10., 4., 4., 4.],

+ [ 4., 4., 4., 4., 4., 4., 4., 4., 4., 4.],

+ [ 4., 4., 4., 4., 4., 4., 4., 4., 4., 4.]])

/anaconda2/lib/python2.7/site-packages/fatiando/inversion/hyper_param.py:81: DocTestFailure

___________________________________________________________________________ [doctest] fatiando.inversion.regularization.Damping ____________________________________________________________________________

103 The number of parameter

104

105 Examples:

106

107 >>> import numpy

108 >>> damp = Damping(3)

109 >>> p = numpy.array([0, 0, 0])

110 >>> damp.value(p)

111 0.0

112 >>> damp.hessian(p).todense()

Differences (unified diff with -expected +actual):

@@ -1,3 +1,3 @@

-matrix([[ 2., 0., 0.],

- [ 0., 2., 0.],

- [ 0., 0., 2.]])

+matrix([[2., 0., 0.],

+ [0., 2., 0.],

+ [0., 0., 2.]])

/anaconda2/lib/python2.7/site-packages/fatiando/inversion/regularization.py:112: DocTestFailure

____________________________________________________________________________ [doctest] fatiando.seismic.profile.LayeredStraight ____________________________________________________________________________

155 >>> zp = range(1, sum(thicks), 5)

156 >>> # Calculate the travel-times

157 >>> tts = layered_straight_ray(thicks, vels, zp)

158 >>> # Solve for the slowness assuming known thicknesses

159 >>> solver = LayeredStraight(tts, zp, thicks).fit()

160 >>> # The estimated velocities

161 >>> solver.estimate_

162 array([ 2., 4., 10., 8.])

163 >>> # and the corresponding slownesses

164 >>> solver.p_

Expected:

array([ 0.5 , 0.25 , 0.1 , 0.125])

Got:

array([0.5 , 0.25 , 0.1 , 0.125])

/anaconda2/lib/python2.7/site-packages/fatiando/seismic/profile.py:164: DocTestFailure

_________________________________________________________________________ [doctest] fatiando.seismic.profile.layered_straight_ray __________________________________________________________________________

055

056 >>> import numpy as np

057 >>> # Make a 4 layer model

058 >>> thicks = [10, 20, 10, 30]

059 >>> vels = [2, 4, 10, 5]

060 >>> # Set the recording depths

061 >>> zs = [10, 30, 40, 70]

062 >>> # Calculate the travel-times from a surface source

063 >>> tt = layered_straight_ray(thicks, vels, zs)

064 >>> tt

Expected:

array([ 5., 10., 11., 17.])

Got:

array([ 5., 10., 11., 17.])

/anaconda2/lib/python2.7/site-packages/fatiando/seismic/profile.py:64: DocTestFailure

______________________________________________________________________________ [doctest] fatiando.seismic.srtomo.slowness2vel ______________________________________________________________________________

129 Returns:

130

131 * velocity : array

132 The converted velocities

133

134 Examples:

135

136 >>> import numpy as np

137 >>> slow = np.array([1, 2, 0.000001, 4])

138 >>> slowness2vel(slow, tol=0.00001)

Expected:

array([ 1. , 0.5 , 0. , 0.25])

Got:

array([1. , 0.5 , 0. , 0.25])

/anaconda2/lib/python2.7/site-packages/fatiando/seismic/srtomo.py:138: DocTestFailure

_______________________________________________________________________________ [doctest] fatiando.seismic.ttime2d.straight ________________________________________________________________________________

056

057 >>> # One source was recorded at 3 receivers.

058 >>> # The medium is homogeneous and can be

059 >>> # represented by a single Square

060 >>> from fatiando.mesher import Square

061 >>> cells = [Square([0, 10, 0, 10], {'vp':2})]

062 >>> src = (5, 0)

063 >>> srcs = [src, src, src]

064 >>> recs = [(0, 0), (5, 10), (10, 0)]

065 >>> print straight(cells, 'vp', srcs, recs)

Expected:

[ 2.5 5. 2.5]

Got:

[2.5 5. 2.5]

/anaconda2/lib/python2.7/site-packages/fatiando/seismic/ttime2d.py:65: DocTestFailure

__________________________________________________________________________________________ test_impulse_response ___________________________________________________________________________________________

def test_impulse_response():

"""

conv.convolutional_model raises the source wavelet as result when the model

is a centred spike, considering the dimension of the model equal to the

source wavelet

"""

> w = conv.rickerwave(30., 2.e-3)

/anaconda2/lib/python2.7/site-packages/fatiando/seismic/tests/test_seismic_conv.py:14:

_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

f = 30.0, dt = 0.002

def rickerwave(f, dt):

r"""

Given a frequency and time sampling rate, outputs ricker function. The

length of the function varies according to f and dt, in order for the

ricker function starts and ends as zero. It is also considered that the

functions is causal, what means it starts at time zero. To satisfy sampling

and stability:

.. math::

f << \frac{1}{2 dt}.

Here, we consider this as:

.. math::

f < 0.2 \frac{1}{2 dt}.

Parameters:

* f : float

dominant frequency value in Hz

* dt : float

time sampling rate in seconds (usually it is in the order of ms)

Returns:

* ricker : float

Ricker function for the given parameters.

"""

assert f < 0.2*(1./(2.*dt)), "Frequency too high for the dt chosen."

nw = 2.2/f/dt

nw = 2*np.floor(nw/2)+1

nc = np.floor(nw/2)

> ricker = np.zeros(nw)

E TypeError: 'numpy.float64' object cannot be interpreted as an index

/anaconda2/lib/python2.7/site-packages/fatiando/seismic/conv.py:214: TypeError

_______________________________________________________________________________________ test_rc_shorter_than_wavelet _______________________________________________________________________________________

def test_rc_shorter_than_wavelet():

"""

When the reflectivity series is shorter than the wavelength, the spike

response is observed like in the opposite case. The difference is that the

the ricker wavelet (or other symmetric wavelet) is shorter in the result.

"""

> w = conv.rickerwave(30., 2.e-3)

/anaconda2/lib/python2.7/site-packages/fatiando/seismic/tests/test_seismic_conv.py:28:

_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

f = 30.0, dt = 0.002

def rickerwave(f, dt):

r"""

Given a frequency and time sampling rate, outputs ricker function. The

length of the function varies according to f and dt, in order for the

ricker function starts and ends as zero. It is also considered that the

functions is causal, what means it starts at time zero. To satisfy sampling

and stability:

.. math::

f << \frac{1}{2 dt}.

Here, we consider this as:

.. math::

f < 0.2 \frac{1}{2 dt}.

Parameters:

* f : float

dominant frequency value in Hz

* dt : float

time sampling rate in seconds (usually it is in the order of ms)

Returns:

* ricker : float

Ricker function for the given parameters.

"""

assert f < 0.2*(1./(2.*dt)), "Frequency too high for the dt chosen."

nw = 2.2/f/dt

nw = 2*np.floor(nw/2)+1

nc = np.floor(nw/2)

> ricker = np.zeros(nw)

E TypeError: 'numpy.float64' object cannot be interpreted as an index

/anaconda2/lib/python2.7/site-packages/fatiando/seismic/conv.py:214: TypeError

============================================================================================= warnings summary =============================================================================================

/anaconda2/lib/python2.7/site-packages/fatiando/vis/mpl.py:76

/anaconda2/lib/python2.7/site-packages/fatiando/vis/mpl.py:76: UserWarning: This module will be removed in v0.6. We recommend the use of matplotlib.pyplot module directly. Some of the fatiando specific functions will remain.

"specific functions will remain.")

/anaconda2/lib/python2.7/site-packages/fatiando/seismic/wavefd.py:162

/anaconda2/lib/python2.7/site-packages/fatiando/seismic/wavefd.py:162: UserWarning: This code is experimental and poorly tested! We cannot guarantee that the results are accurate and strongly discourage use of this code for research purposes.

"strongly discourage use of this code for research purposes.")

/anaconda2/lib/python2.7/site-packages/fatiando/vis/myv.py:51

/anaconda2/lib/python2.7/site-packages/fatiando/vis/myv.py:51: UserWarning: This module will be removed in v0.7.

warnings.warn("This module will be removed in v0.7.")

mesher.py::fatiando.mesher.PointGrid.split

/anaconda2/lib/python2.7/site-packages/fatiando/gridder.py:319: RuntimeWarning: invalid value encountered in double_scalars

dy = (y2 - y1)/(ny - 1)

geothermal/climsig.py::fatiando.geothermal.climsig.SingleChange

gravmag/basin2d.py::fatiando.gravmag.basin2d.PolygonalBasinGravity

gravmag/basin2d.py::fatiando.gravmag.basin2d.Trapezoidal

gravmag/basin2d.py::fatiando.gravmag.basin2d.Triangular

gravmag/tests/test_eqlayer.py::test_eqlgrav_prism_interp

gravmag/tests/test_eqlayer.py::test_eqlayer_polereduce

seismic/epic2d.py::fatiando.seismic.epic2d.Homogeneous

/anaconda2/lib/python2.7/site-packages/scipy/sparse/compressed.py:347: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.

return np.matrix(result, copy=False)

geothermal/climsig.py::fatiando.geothermal.climsig.SingleChange

/anaconda2/lib/python2.7/site-packages/fatiando/inversion/optimization.py:282: RuntimeWarning: Exited because couldn't take a step without increasing the objective function. Might not have achieved convergence. Try inscreasing the max number of step attempts allowed.

RuntimeWarning)

gravmag/tests/test_eqlayer.py::test_eqlgrav_prism_interp

gravmag/tests/test_eqlayer.py::test_eqlayer_polereduce

inversion/regularization.py::fatiando.inversion.regularization.Damping

inversion/regularization.py::fatiando.inversion.regularization.Smoothness1D

inversion/regularization.py::fatiando.inversion.regularization.Smoothness2D

inversion/regularization.py::fatiando.inversion.regularization.fd1d

inversion/regularization.py::fatiando.inversion.regularization.fd2d

seismic/tests/test_seismic_srtomo.py::test_jacobian

/anaconda2/lib/python2.7/site-packages/numpy/matrixlib/defmatrix.py:71: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray.

return matrix(data, dtype=dtype, copy=False)

seismic/tests/test_seismic_srtomo.py::test_general

/anaconda2/lib/python2.7/site-packages/scipy/sparse/linalg/isolve/iterative.py:2: DeprecationWarning: scipy.sparse.linalg.cgs called without specifying `atol`. The default value will be changed in a future release. For compatibility, specify a value for `atol` explicitly, e.g., ``cgs(..., atol=0)``, or to retain the old behavior ``cgs(..., atol='legacy')``

tests/gridder/test_gridder_padarray.py::test_pad_and_unpad_equal_2d

/anaconda2/lib/python2.7/site-packages/fatiando/gridder.py:713: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result.

b = a[o]

-- Docs: https://docs.pytest.org/en/latest/warnings.html

=========================================================================== 32 failed, 183 passed, 266 warnings in 44.44 seconds ===========================================================================

Out[1]: 1

I believe now you can help me. I am very much interested to learn your moho inversion program and would like to implement it on some major parts of Indian subcontinent. So, initially I would like to follow your paper on Moho inversion for South America to build up some confidence.

Look forward to hear from you!

Best regards,

Shib Sankar Ganguli, Ph.D.

Research Scientist | Deep Seismics Research Group

CSIR-National Geophysical Research Institute (http://www.ngri.org.in/index.php)

Office: Room No. 114 | First Floor | Gas Hydrate & CSS Building | CSIR-NGRI

Uppal Road | Hyderabad-500007 | Telangana State | India

Phone: +91-40-27012736 | Mobile: +91 7306343464

Web: https://shibganguli.wixsite.com/shib

My Research: https://scholar.google.com/citations?user=XCeaUN4AAAAJ

+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Young Scientist Awardee, National Geoscience Awards 2017, Ministry of Mines (Govt. of India)

Former DST Inspire Faculty | Indian Institute of Technology (IIT) Kanpur (http://iitk.ac.in)

Ph.D., Academy of Scientific and Innovative Research (AcSIR) (http://acsir.res.in/) | Hyderabad | India

Former Senior Research Fellow & Project Associate| CSIR-NGRI

+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

"Research is what I'm doing when I don't know what I'm doing"--Wernher von Braun

Please don't print this email unless it is absolutely necessary. Save pages, Save tree

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Shib Ganguli

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Jun 13, 2019, 5:34:07 AM6/13/19

to Fatiando a Terra

Hi !

I'm still waiting for kind help regarding installation error that I discussed few weeks ago (plz refer to trailing email). I would appreciate much if someone help me to fix this.

Best,

Shib

Leonardo Miquelutti

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Jun 14, 2019, 10:57:01 AM6/14/19

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Dear Shib,

I am not a domain expert, but once I had this or a similar problem, and it seems that Fatiando has rounding issues. Below there is an example from your own email from May, 18th.

As you can see, the Expected and Got results are the same even though the unit test accused an error. This repeats for other examples you show. It probably arises from comparing numbers with too many decimal places. IMHO, I wouldn't mind much about this and would follow with the work.

Cheers,

Leonardo (not Uieda)

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Shib Sankar Ganguli

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Jun 14, 2019, 11:56:00 AM6/14/19

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Hi Leonardo!

Many thanks for the clarification. Much appreciated. My bad that I assumed it is not installed properly. According to your email, I should now start with the program and learn step by step as per your instructions provided in the paper.

Thanks again for your help. Oh yes, from now, I will not address you as Uieda which I did as got confused seeing your profile in gitter.fatiando.

Also, I believe you won't mind if I contact you further while getting stuck with fatiando.

Best,

Shib

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Leonardo Miquelutti

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Jun 14, 2019, 1:13:36 PM6/14/19

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Hi Shib,

first of all, there are two (maybe more) Leonardos. Uieda is the main developer of the package. I only use it. I signed that way to make it clear I am not the developer thus my opinion should be regarded as a user's opinion. :)

Secondly, feel free to contact me whenever you want. There is a fair possibility that I cannot help you depending on the issue, but feel free! :) If it is in my reach, I can help!

Cheers,

Leonardo (the Miquelutti one)

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Shib Sankar Ganguli

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Jun 15, 2019, 1:03:12 AM6/15/19

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Hi Leo!

My bad again. However, my sincere thanks to you for the help that you provided. Now it's crystal clear to me about all the Leonardos due to you.

To view this discussion on the web visit https://groups.google.com/d/msgid/fatiando/CACVk%3D4YtMies4cRf3zsvd%2BWX5U_%3DuCkBC9K_%2BMVTN7gf6CwaJA%40mail.gmail.com.

Shib Ganguli

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Jun 18, 2019, 9:10:56 AM6/18/19

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Hi Leo!

I was trying to run the code by Leonardo Uieda using Jupiter to invert the synthetic data based on a simple model (https://github.com/pinga-lab/paper-moho-inversion-tesseroids#running-things-on-your-machine), and ended up with some error (attached herewith). It seems it couldn't import the module. As you said you are an user of Fatiando, I thought of sharing this with you. I will appreciate if you could help.

Best,

Shib

Hi Leo!

Shib

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Leonardo Miquelutti

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Jun 18, 2019, 1:28:19 PM6/18/19

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Hi Shib,

I've never dealt with this, but my guess is that something went amiss while setting up your environment as detailed in the link you sent.

Best

Hi Leo!

Shib

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Shib Sankar Ganguli

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Jun 19, 2019, 2:23:58 AM6/19/19

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Hi Leo!

Thanks for pointing this. What I could see is Fatiando version is mismatched, the environment required v0.4 and I have isntalled V0.5. Any idea how to downgrade from 0.5 to 0.4 then I might be helpful?