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Allow readonly arrays in numba jit signature #23

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merged 3 commits into from Feb 12, 2023

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jvdd
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@jvdd jvdd commented Jan 29, 2023

This PR is a continuation of the work contributed in PR #13

Contributions of this PR:

  • allow readonly arrays in the numba jit signature
    -> this was an issue for sample_entropy and detrended_fluctuation
  • minor refactoring of the tests - moving duplicate code to a utils.py file
  • adding 2 additional tests that test whether non-writable (i.e., readonly) arrays can be used as input for a range of datatypes

Other contribution:

  • set nopython to True for the _higuchi_fd function - this was the only @jit decorated function for which this flag was not set.

Illustration of the issue that this PR tackles:

In [1]: import antropy as ant; import numpy as np

In [2]: ant.__version__
Out[2]: '0.1.5'

In [3]: x = np.random.randn(3_000).astype("float32")
   ...: x.flags.writeable = False
   ...: ant.detrended_fluctuation(x)
Out[3]: 0.5552594723035992

In [4]: x = np.random.randn(3_000).astype("float64")
   ...: x.flags.writeable = False
   ...: ant.detrended_fluctuation(x)
---------------------------------------------------------------------------
TypeError
    ...
TypeError: No matching definition for argument type(s) readonly array(float64, 1d, C)

In [5]: x = np.random.rand(3_000).astype("float32")
   ...: x.flags.writeable = False
   ...: ant.sample_entropy(x)
Out[5]: 2.17591547251706

In [6]: x = np.random.rand(3_000).astype("float64")
   ...: x.flags.writeable = False
   ...: ant.sample_entropy(x)
---------------------------------------------------------------------------
TypeError
    ...
TypeError: No matching definition for argument type(s) readonly array(float64, 1d, C), int64, float64

@jvdd
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jvdd commented Jan 29, 2023

Should be ready for review! @raphaelvallat :)

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@raphaelvallat raphaelvallat left a comment

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Beautiful work 🚀 Merging now! Thanks again :)

@raphaelvallat raphaelvallat merged commit e76a8c7 into raphaelvallat:master Feb 12, 2023
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2 participants