pydivsufsort 0.0.8

String algorithms

pydivsufsort: bindings to libdivsufsort

pydivsufsort prebuilds libdivsufsort as a shared library and includes it in a Python package with bindings.

Features:

• bindings to divsufsort that return numpy arrays
• handle almost any integer data type (e.g. int64) and not only char
• additional string algorithms

Installation

On Linux, macOS and Windows:

python -m pip install pydivsufsort

We provide precompiled wheels for common systems using cibuildwheel, and a source distribution for Unix systems. Manual compilation on Windows might require some tweaking, please create an issue.

Usage

Using String Inputs

import numpy as np
from pydivsufsort import divsufsort, kasai

string_inp = "banana$"
string_suffix_array = divsufsort(string_inp)
string_lcp_array = kasai(string_inp, string_suffix_array)
print(string_suffix_array, string_lcp_array)
# [6 5 3 1 0 4 2] [0 1 3 0 0 2 0]

Using Integer Inputs

import numpy as np
from pydivsufsort import divsufsort, kasai

string_inp = "banana$"

# Convert the string input to integers first
int_inp = np.unique(np.array(list(string_inp)), return_inverse=True)[1]
int_suffix_array = divsufsort(int_inp)
int_lcp_array = kasai(int_inp, int_suffix_array)
print(int_suffix_array, int_lcp_array)
# [6 5 3 1 0 4 2] [0 1 3 0 0 2 0]

Using Multiple Sentinel Characters Witin A String

import numpy as np
from pydivsufsort import divsufsort, kasai

sentinel_inp = "a$banana#and@a*bandana+"
sentinel_suffix_array = divsufsort(sentinel_inp)
sentinel_lcp_array = kasai(sentinel_inp, sentinel_suffix_array)
print(sentinel_suffix_array, sentinel_lcp_array)
# [ 8  1 14 22 12  7  0 13 21  5 19  3  9 16  2 15 11 18  6 20  4 10 17] [0 0 0 0 0 1 1 1 1 3 3 2 3 0 3 0 1 0 2 2 1 2 0]

Development

You can install locally with

pip install -e .

A useful command to iterate quickly when changing Cython code is

python setup.py build_ext --inplace && pytest -s

Profiling

Profiling can be activated with the environment variable PROFILE:

PROFILE=1 python setup.py build_ext --inplace && pytest -s

Here is an example with line_profiler (requires pip install "line_profiler<4"):

import line_profiler
from pydivsufsort import common_substrings
from pydivsufsort.stringalg import (
    _common_substrings,
    repeated_substrings,
)

s1 = "banana" * 10000
s2 = "ananas" * 10000

func = common_substrings
profile = line_profiler.LineProfiler(func)
profile.add_function(_common_substrings)
profile.add_function(repeated_substrings)
profile.runcall(func, s1, s2, limit=15)
profile.print_stats()

Testing

pytest

Technical details (for performance tweaks)

libdivsufsort is compiled in both 32 and 64 bits, as the 32 bits version is faster. pydivsufsort automatically chooses to use the 32 bits version when possible (aka when the input size is less than 2**31-1).

For best performance, use contiguous arrays. If you have a sliced array, pydivsufsort converts it automatically with numpy.ascontiguousarray.

The precompiled libraries use OpenMP. You can disable it by setting the env variable OMP_NUM_THREADS=1, and it will yield the same performance as the version compiled without OpenMP

The original libdivsufsort only supports char as the base type. pydivsufsort can handle arrays of any integer type (even signed), by encoding each element as multiple chars, which makes the computation slower. If your values use an integer type that is bigger than required, but they span over a small contiguous range, pydivsufsort will automatically change their type (see #6).

Acknowledgements

• Yuta Mori for writing libdivsufsort
• Sean Law for initiating this project and contributing

Citing

If you have used this software in a scientific publication, please cite it using the following BibLaTeX code:

@software{pydivsufsort,
  author       = {Louis Abraham},
  title        = {pydivsufsort},
  year         = 2023,
  publisher    = {Zenodo},
  doi          = {10.5281/zenodo.7932458},
  url          = {https://github.com/louisabraham/pydivsufsort}
}