Fast and lightweight set for unsigned 32 bits integers.
Project description
An efficient and light-weight ordered set of 32 bits integers. This is a Python wrapper for the C library CRoaring.
The wrapping used to be done with Ctypes. We recently switched to Cython for the following reasons:
Much better performances for short function calls (e.g. addition/deletion of a single element).
Easier installation, no need to install manually the C library, it is now distributed with PyRoaring.
Extensibility, it will be easier to write efficient codes with Cython (e.g. some data structures based on roaring bitmaps).
If for some reason you wish to keep using the old version, based on Ctypes, use PyRoaring 0.0.7.
Requirements
Environment like Linux and MacOS
Python 2.7, or Python 3.4 or better
A recent C compiler like GCC
The package manager pip
The Python package hypothesis (optional, for testing)
The Python package Cython (optional, for compiling pyroaring from the sources)
The Python package wheel (optional, to build a wheel for the library)
Installation
To install pyroaring on your local account, use the following command:
pip install pyroaring --user # installs PyRoaringBitMap
For a system-wide installation, use the following command:
pip install pyroaring
Naturally, the latter may require superuser rights (consider prefixing the commands by sudo).
If you want to use Python 3 and your system defaults on Python 2.7, you may need to adjust the above commands, e.g., replace pip by pip3.
Manual compilation / installation
If you want to compile (and install) pyroaring by yourself, for instance to modify the Cython sources or because you do not have pip, follow these steps. Note that the Python package Cython is required.
Clone this repository.
git clone https://github.com/Ezibenroc/PyRoaringBitMap.git
cd PyRoaringBitMap
git submodule init && git submodule update
Build pyroaring locally, e.g. to test a new feature you made.
python setup.py build_ext -i
python test.py # run the tests, optionnal but recommended
Install pyroaring (use this if you do not have pip).
python setup.py install # may require superuser rights, add option --user if you wish to install it on your local account
Package pyroaring.
python setup.py sdist
pip install dist/pyroaring-0.1.?.tar.gz # optionnal, to install the package
Build a wheel.
python setup.py bdist_wheel
For all the above commands, two environment variables can be used to control the compilation.
DEBUG=1 to build pyroaring in debug mode.
ARCHI=<cpu-type> to build pyroaring for the given platform. The platform may be any keyword given to the -march option of gcc (see the documentation). Note that cross-compiling for a 32-bit architecture from a 64-bit architecture is not supported.
Example of use:
DEBUG=1 ARCHI=x86-64 python setup.py build_ext
Utilization
First, you can run the tests to make sure everything is ok:
pip install hypothesis --user
python test.py
Note: you can define the environment variable HYPOTHESIS_PROFILE to debug to print every values, or ci to perform more tests (warning: very long). For instance:
HYPOTHESIS_PROFILE=debug ./test.py
You can use a bitmap nearly as the classical Python set in your code:
from pyroaring import BitMap
bm1 = BitMap()
bm1.add(3)
bm1.add(18)
bm2 = BitMap([3, 27, 42])
print("bm1 = %s" % bm1)
print("bm2 = %s" % bm2)
print("bm1 & bm2 = %s" % (bm1&bm2))
print("bm1 | bm2 = %s" % (bm1|bm2))
Output:
bm1 = BitMap([3, 18]) bm2 = BitMap([3, 27, 42]) bm1 & bm2 = BitMap([3]) bm1 | bm2 = BitMap([3, 18, 27, 42])
Benchmark
Pyroaring is compared with the built-in set and other implementations:
A Python wrapper of CRoaring called python-croaring
A Cython implementation of Roaring bitmaps called roaringbitmap
A Python implemenntation of ordered sets called sortedcontainers
The script quick_bench.py measures the time of different set operations. It uses randomly generated sets of size 1e6 and density 0.125. For each operation, the average time (in seconds) of 30 tests is reported.
The results have been obtained with:
CPU Intel Xeon CPU E5-2630 v3
CPython version 3.5.3
gcc version 6.3.0
Cython version 0.28.3
pyroaring commit dcf448a
python-croaring commit 3aa61dd
roaringbitmap commit 502d78d
sortedcontainers commit 7d6a28c
operation |
pyroaring |
python-croaring |
roaringbitmap |
set |
sortedcontainers |
---|---|---|---|---|---|
range constructor |
3.09e-04 |
1.48e-04 |
8.72e-05 |
7.29e-02 |
2.08e-01 |
ordered list constructor |
3.45e-02 |
6.93e-02 |
1.45e-01 |
1.86e-01 |
5.74e-01 |
list constructor |
1.23e-01 |
1.33e-01 |
1.55e-01 |
1.12e-01 |
5.12e-01 |
ordered array constructor |
5.06e-03 |
6.42e-03 |
2.89e-01 |
9.82e-02 |
3.01e-01 |
array constructor |
1.13e-01 |
1.18e-01 |
4.63e-01 |
1.45e-01 |
5.08e-01 |
element addition |
3.08e-07 |
8.26e-07 |
2.21e-07 |
1.50e-07 |
1.18e-06 |
element removal |
3.44e-07 |
8.17e-07 |
2.61e-07 |
1.78e-07 |
4.26e-07 |
membership test |
1.24e-07 |
1.00e-06 |
1.50e-07 |
1.00e-07 |
5.72e-07 |
union |
1.61e-04 |
1.96e-04 |
1.44e-04 |
2.15e-01 |
1.11e+00 |
intersection |
9.08e-04 |
9.48e-04 |
9.26e-04 |
5.22e-02 |
1.65e-01 |
difference |
1.57e-04 |
1.97e-04 |
1.43e-04 |
1.56e-01 |
4.84e-01 |
symmetric diference |
1.62e-04 |
2.01e-04 |
1.44e-04 |
2.62e-01 |
9.13e-01 |
equality test |
7.80e-05 |
7.82e-05 |
5.89e-05 |
1.81e-02 |
1.81e-02 |
subset test |
7.92e-05 |
8.12e-05 |
8.22e-05 |
1.81e-02 |
1.81e-02 |
conversion to list |
4.71e-02 |
2.78e-01 |
4.35e-02 |
5.77e-02 |
5.32e-02 |
pickle dump & load |
4.02e-04 |
6.27e-04 |
5.08e-04 |
2.41e-01 |
5.75e-01 |
“naive” conversion to array |
5.12e-02 |
2.92e-01 |
4.75e-02 |
1.20e-01 |
1.18e-01 |
“optimized” conversion to array |
1.27e-03 |
3.40e-02 |
nan |
nan |
nan |
selection |
1.77e-06 |
5.33e-05 |
1.14e-06 |
nan |
1.64e-05 |
contiguous slice |
9.38e-05 |
9.51e-05 |
6.99e-05 |
nan |
2.04e-02 |
slice |
2.88e-03 |
3.04e-01 |
1.00e-01 |
nan |
4.74e-01 |
small slice |
8.93e-05 |
3.00e-01 |
3.60e-03 |
nan |
1.79e-02 |
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