madvn / infotheory Goto Github PK

I have clone the repository.
When I run pip install infotheory I get the following errors:

Collecting infotheory
Using cached infotheory-1.0.01.tar.gz (19 kB)
Preparing metadata (setup.py) ... done
Building wheels for collected packages: infotheory
Building wheel for infotheory (setup.py) ... error
error: subprocess-exited-with-error

× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [23 lines of output]
C:\Users\a-v-d\anaconda3\envs\MasterThesis\lib\site-packages\setuptools\dist.py:314: InformationOnly: Normalizing '1.0.01' to '1.0.1'
self.metadata.version = self._normalize_version(self.metadata.version)
PyLinker.cpp
C:\Users\a-v-d\AppData\Local\Temp\pip-install-__062f80\infotheory_d9c2c9609954478b9b95cf02d1db283a\infotheory\InfoTools.h(71): warning C4244: 'argument': conversion from 'double' to 'EltType', possible loss of data
with
[
EltType=int
]
C:\Users\a-v-d\AppData\Local\Temp\pip-install-__062f80\infotheory_d9c2c9609954478b9b95cf02d1db283a\infotheory\InfoTools.h(79): warning C4244: 'argument': conversion from 'double' to 'EltType', possible loss of data
with
[
EltType=int
]
C:\Users\a-v-d\AppData\Local\Temp\pip-install-__062f80\infotheory_d9c2c9609954478b9b95cf02d1db283a\infotheory\InfoTools.h(1333): warning C4244: 'argument': conversion from 'double' to 'EltType', possible loss of data
with
[
EltType=int
]
./infotheory\PyLinker.cpp(25): warning C4244: 'initializing': conversion from 'Py_ssize_t' to 'int', possible loss of data
./infotheory\PyLinker.cpp(33): warning C4244: 'initializing': conversion from 'Py_ssize_t' to 'int', possible loss of data
LINK : error LNK2001: unresolved external symbol PyInit_infotheoryClass
build\temp.win-amd64-cpython-39\Release./infotheory\infotheoryClass.cp39-win_amd64.lib : fatal error LNK1120: 1 unresolved externals
error: command 'C:\Program Files (x86)\Microsoft Visual Studio\2022\BuildTools\VC\Tools\MSVC\14.39.33519\bin\HostX86\x64\link.exe' failed with exit code 1120
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for infotheory
Running setup.py clean for infotheory
Failed to build infotheory
ERROR: Could not build wheels for infotheory, which is required to install pyproject.toml-based projects

I do have BuildTools downloaded on my computer.
Is there anythin I am missing?

Can this toolbox be used to calculate conditional mutual information and transfer entropy?

If you wouldn't mind, please add a link in the readme to the corresponding preprint which is https://arxiv.org/abs/1907.02339 . Thanks.

This is the STDERR from pip install --upgrade infotheory, in a conda 4.7.5 environment in an up to date archlinux. Let me know if you need any further info.

Thanks!
Manolo
pip.log

Hi, you're probably not even maintaining this anymore, but in case you do, I've found that NaNs in the input data are not handled correctly, I think. In case you want to add something about this in the docs...

I'm not sure exactly what happens, but if I have a matrix with 3 columns, and I make some values in the third column NaNs, that will affect calculations of MI between the first two:

import infotheory
import numpy as np

it = infotheory.InfoTools(dims=3, nreps=0)
it.set_equal_interval_binning(nbins=[10, 10, 10], mins=[0, 0, 0], maxs=[1, 1, 1])

mat = np.random.default_rng(42).random((100, 3))
# mat[40:50, 2] = np.nan

it.add_data(mat)
it.mutual_info([0, 1, -1])

Without NaNs in the third variable the resulting MI between the first two variables is 0.6699268749439261. With NaNs, the result is 0.7039212101565637. So the strange thing is that data in an unrelated variable affects the MI between the first two.

After a quick Iook only, one thing that may be happening is that PyFloat_AsDouble may silently convert NaNs to -1 (https://docs.python.org/3/c-api/float.html#c.PyFloat_AsDouble) perhaps? Which would then mean that the minima passed in are not correct anymore. Though I don't know how this would then affect unrelated variables.

Let me know if you want me to help out addressing this, if you're still aiming to support this package.

Btw, I'm an old friend of Eduardo Izquierdo's ;)