Tutorial "The Effects of Interlaced Painting" is broken, should use resampler method

[hsgg]

The tutorial on The Effects of Interlaced Painting does not work. The function mesh.CompensateCIC no longer exists in the same place.

To reproduce, I installed nbodykit with pip3 install --user nbodykit on Debian. Then, copied the non-Jupyter code in the aforementioned tutorial into a text file, and run it on the command line with python-3.7.3.

This results in the following output:

$ ./interlaced.py 
./interlaced.py:24: DeprecationWarning: The window argument is deprecated. Use `resampler=` instead
  mesh = cat.to_mesh(window='tsc', Nmesh=512, compensated=True)
./interlaced.py:33: DeprecationWarning: The window argument is deprecated. Use `resampler=` instead
  mesh = cat.to_mesh(Nmesh=256, window=window, compensated=False, interlaced=interlaced)
Traceback (most recent call last):
  File "./interlaced.py", line 34, in <module>
    compensation = mesh.CompensateCIC if window == 'CIC' else mesh.CompensateTSC
AttributeError: 'CatalogMesh' object has no attribute 'CompensateCIC'

Expected behavior: Reproduce the example plot shown in the tutorial. Ideally, without the deprecation warnings.

nbodykit version:

<module 'nbodykit' from '/home/gebhardt/.local/lib/python3.7/site-packages/nbodykit/__init__.py'> 0.3.13

[rainwoodman]

The methods are moved to module methods under nbodykit/nbodykit/source/mesh/catalog.py.

Freshing the notebooks is not as streamlines as we'd like (I think they are hosted on a different repository but I need to revisit the maintenance doc). It will probably take a while for me to get to fix it -- unless you'd like to file a PR for the fix.

[wms10086]

I checked nbodykit/nbodykit/source/mesh/catalog.py, and I found CompensateCIC is not in the CatalogMesh class.I put a series of functions into this class by indentation.This results in the following output:

 `---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-4-fabc16e8388b> in <module>
      3 
      4 # compute the 1D power of this mesh
----> 5 r = FFTPower(mesh, mode='1d')
      6 
      7 # create a smooth interpolation

~/anaconda3/envs/nbk/lib/python3.6/site-packages/nbodykit/algorithms/fftpower.py in __init__(self, first, mode, Nmesh, BoxSize, second, los, Nmu, dk, kmin, kmax, poles)
    222         self.attrs['kmax'] = kmax
    223 
--> 224         self.power, self.poles = self.run()
    225 
    226         # for compatibility, copy power's attrs into self.

~/anaconda3/envs/nbk/lib/python3.6/site-packages/nbodykit/algorithms/fftpower.py in run(self)
    279 
    280         # measure the 3D power (y3d is a ComplexField)
--> 281         y3d, attrs = self._compute_3d_power(self.first, self.second)
    282 
    283         # binning in k out to the minimum nyquist frequency

~/anaconda3/envs/nbk/lib/python3.6/site-packages/nbodykit/algorithms/fftpower.py in _compute_3d_power(self, first, second)
    103         attrs.update(self.attrs)
    104 
--> 105         c1 = first.compute(mode='complex', Nmesh=self.attrs['Nmesh'])
    106 
    107         # compute the auto power of single supplied field

~/anaconda3/envs/nbk/lib/python3.6/site-packages/nbodykit/base/mesh.py in compute(self, mode, Nmesh)
    248             Compute / Fetch the mesh object into memory as a RealField or ComplexField object.
    249         """
--> 250         return self._paint_XXX(mode=mode, Nmesh=Nmesh)
    251 
    252     def paint(self, mode="real", Nmesh=None):

~/anaconda3/envs/nbk/lib/python3.6/site-packages/nbodykit/base/mesh.py in _paint_XXX(self, mode, Nmesh)
    284 
    285         # add a dummy action to ensure the right mode of return value
--> 286         actions = self.actions + [(mode, )]
    287 
    288         # if we expect complex, be smart and use complex directly.

~/anaconda3/envs/nbk/lib/python3.6/site-packages/nbodykit/source/mesh/catalog.py in actions(self)
    411         actions = MeshSource.actions.fget(self)
    412         if self.compensated:
--> 413             actions = self._get_compensation() + actions
    414         return actions
    415 

~/anaconda3/envs/nbk/lib/python3.6/site-packages/nbodykit/source/mesh/catalog.py in _get_compensation(self)
    415 
    416     def _get_compensation(self):
--> 417         return get_compensation(self.interlaced, self.resampler)
    418     def CompensateTSC(w, v):
    419         """

NameError: name 'get_compensation' is not defined`

Then, I'm going to copy and paste the function that I just moved behind the class, but it's not in this class.This results in the following output:

`---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-5-9af93b1333ff> in <module>
      9         mesh = mesh.apply(compensation, kind='circular', mode='complex')
     10         # compute the 1D power P(k)
---> 11         r = FFTPower(mesh, mode='1d')
     12         Pk = r.power
     13         # compare P(k) to the hi-resolution mesh P(k)

~/anaconda3/envs/nbk/lib/python3.6/site-packages/nbodykit/algorithms/fftpower.py in __init__(self, first, mode, Nmesh, BoxSize, second, los, Nmu, dk, kmin, kmax, poles)
    222         self.attrs['kmax'] = kmax
    223 
--> 224         self.power, self.poles = self.run()
    225 
    226         # for compatibility, copy power's attrs into self.

~/anaconda3/envs/nbk/lib/python3.6/site-packages/nbodykit/algorithms/fftpower.py in run(self)
    279 
    280         # measure the 3D power (y3d is a ComplexField)
--> 281         y3d, attrs = self._compute_3d_power(self.first, self.second)
    282 
    283         # binning in k out to the minimum nyquist frequency

~/anaconda3/envs/nbk/lib/python3.6/site-packages/nbodykit/algorithms/fftpower.py in _compute_3d_power(self, first, second)
    103         attrs.update(self.attrs)
    104 
--> 105         c1 = first.compute(mode='complex', Nmesh=self.attrs['Nmesh'])
    106 
    107         # compute the auto power of single supplied field

~/anaconda3/envs/nbk/lib/python3.6/site-packages/nbodykit/base/mesh.py in compute(self, mode, Nmesh)
    248             Compute / Fetch the mesh object into memory as a RealField or ComplexField object.
    249         """
--> 250         return self._paint_XXX(mode=mode, Nmesh=Nmesh)
    251 
    252     def paint(self, mode="real", Nmesh=None):

~/anaconda3/envs/nbk/lib/python3.6/site-packages/nbodykit/base/mesh.py in _paint_XXX(self, mode, Nmesh)
    311                     kwargs['kind'] = action[2]
    312                 kwargs['out'] = Ellipsis
--> 313                 var.apply(**kwargs)
    314 
    315         # FIXME: get rid of this after pmesh 0.1.45+

~/anaconda3/envs/nbk/lib/python3.6/site-packages/pmesh/pm.py in apply(self, func, kind, out)
   1068         """
   1069         assert kind in ['wavenumber', 'circular', 'index']
-> 1070         return Field.apply(self, func, kind, out)
   1071 
   1072 class UntransposedComplexField(BaseComplexField):

~/anaconda3/envs/nbk/lib/python3.6/site-packages/pmesh/pm.py in apply(self, func, kind, out)
    643             elif kind == 'circular':
    644                 w = [ ki * L / N for ki, L, N in zip(x, self.BoxSize, self.Nmesh)]
--> 645                 oslab[...] = func(w, islab)
    646             else:
    647                 raise ValueError("unknown kind of apply function.")

TypeError: CompensateCIC() takes 2 positional arguments but 3 were given`. 

I hope I described what I did clearly. How to fix this issue? @rainwoodman