nppoly / cyac Goto Github PK
View Code? Open in Web Editor NEWHigh performance Trie and Ahocorasick automata (AC automata) Keyword Match & Replace Tool for python
License: MIT License
High performance Trie and Ahocorasick automata (AC automata) Keyword Match & Replace Tool for python
License: MIT License
I'm getting the following error when trying to install cyac
% pip --version
pip 23.2.1 from /usr/local/lib/python3.9/site-packages/pip (python 3.9)
Don't even know if it's cyacs fault, but maybe you can help me?
% pip install cyac
Collecting cyac
Using cached cyac-1.9.tar.gz (47 kB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: cython>=0.29.0 in /usr/local/lib/python3.9/site-packages (from cyac) (3.0.2)
Building wheels for collected packages: cyac
Building wheel for cyac (pyproject.toml) ... error
error: subprocess-exited-with-error
× Building wheel for cyac (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [107 lines of output]
running bdist_wheel
running build
running build_py
creating build
creating build/lib.macosx-11-x86_64-cpython-39
creating build/lib.macosx-11-x86_64-cpython-39/cyac
copying lib/cyac/version.py -> build/lib.macosx-11-x86_64-cpython-39/cyac
copying lib/cyac/init.py -> build/lib.macosx-11-x86_64-cpython-39/cyac
running egg_info
writing cyac.egg-info/PKG-INFO
writing dependency_links to cyac.egg-info/dependency_links.txt
writing requirements to cyac.egg-info/requires.txt
writing top-level names to cyac.egg-info/top_level.txt
reading manifest file 'cyac.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no previously-included files matching 'pycache' found anywhere in distribution
adding license file 'LICENSE'
writing manifest file 'cyac.egg-info/SOURCES.txt'
copying lib/cyac/ac.pxd -> build/lib.macosx-11-x86_64-cpython-39/cyac
copying lib/cyac/ac.pyx -> build/lib.macosx-11-x86_64-cpython-39/cyac
copying lib/cyac/trie.pxd -> build/lib.macosx-11-x86_64-cpython-39/cyac
copying lib/cyac/trie.pyx -> build/lib.macosx-11-x86_64-cpython-39/cyac
copying lib/cyac/unicode_portability.c -> build/lib.macosx-11-x86_64-cpython-39/cyac
copying lib/cyac/utf8.pxd -> build/lib.macosx-11-x86_64-cpython-39/cyac
copying lib/cyac/utf8.pyx -> build/lib.macosx-11-x86_64-cpython-39/cyac
copying lib/cyac/util.c -> build/lib.macosx-11-x86_64-cpython-39/cyac
copying lib/cyac/util.pxd -> build/lib.macosx-11-x86_64-cpython-39/cyac
copying lib/cyac/util.pyx -> build/lib.macosx-11-x86_64-cpython-39/cyac
copying lib/cyac/xstring.pxd -> build/lib.macosx-11-x86_64-cpython-39/cyac
copying lib/cyac/xstring.pyx -> build/lib.macosx-11-x86_64-cpython-39/cyac
running build_ext
building 'cyac.util' extension
creating build/temp.macosx-11-x86_64-cpython-39
creating build/temp.macosx-11-x86_64-cpython-39/lib
creating build/temp.macosx-11-x86_64-cpython-39/lib/cyac
clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -I/usr/local/include -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -I/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c lib/cyac/util.c -o build/temp.macosx-11-x86_64-cpython-39/lib/cyac/util.o
Traceback (most recent call last):
File "/usr/local/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in
main()
File "/usr/local/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "/usr/local/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 251, in build_wheel
return _build_backend().build_wheel(wheel_directory, config_settings,
File "/private/var/folders/wk/xjxk9mdj7lz95cjvqc_nqxl80000gn/T/pip-build-env-tcws4eg3/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 434, in build_wheel
return self._build_with_temp_dir(
File "/private/var/folders/wk/xjxk9mdj7lz95cjvqc_nqxl80000gn/T/pip-build-env-tcws4eg3/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 419, in _build_with_temp_dir
self.run_setup()
File "/private/var/folders/wk/xjxk9mdj7lz95cjvqc_nqxl80000gn/T/pip-build-env-tcws4eg3/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 341, in run_setup
exec(code, locals())
File "", line 21, in
File "/private/var/folders/wk/xjxk9mdj7lz95cjvqc_nqxl80000gn/T/pip-build-env-tcws4eg3/overlay/lib/python3.9/site-packages/setuptools/init.py", line 103, in setup
return distutils.core.setup(**attrs)
File "/private/var/folders/wk/xjxk9mdj7lz95cjvqc_nqxl80000gn/T/pip-build-env-tcws4eg3/overlay/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 185, in setup
return run_commands(dist)
File "/private/var/folders/wk/xjxk9mdj7lz95cjvqc_nqxl80000gn/T/pip-build-env-tcws4eg3/overlay/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
dist.run_commands()
File "/private/var/folders/wk/xjxk9mdj7lz95cjvqc_nqxl80000gn/T/pip-build-env-tcws4eg3/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
self.run_command(cmd)
File "/private/var/folders/wk/xjxk9mdj7lz95cjvqc_nqxl80000gn/T/pip-build-env-tcws4eg3/overlay/lib/python3.9/site-packages/setuptools/dist.py", line 989, in run_command
super().run_command(command)
File "/private/var/folders/wk/xjxk9mdj7lz95cjvqc_nqxl80000gn/T/pip-build-env-tcws4eg3/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/private/var/folders/wk/xjxk9mdj7lz95cjvqc_nqxl80000gn/T/pip-build-env-tcws4eg3/overlay/lib/python3.9/site-packages/wheel/bdist_wheel.py", line 364, in run
self.run_command("build")
File "/private/var/folders/wk/xjxk9mdj7lz95cjvqc_nqxl80000gn/T/pip-build-env-tcws4eg3/overlay/lib/python3.9/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
self.distribution.run_command(command)
File "/private/var/folders/wk/xjxk9mdj7lz95cjvqc_nqxl80000gn/T/pip-build-env-tcws4eg3/overlay/lib/python3.9/site-packages/setuptools/dist.py", line 989, in run_command
super().run_command(command)
File "/private/var/folders/wk/xjxk9mdj7lz95cjvqc_nqxl80000gn/T/pip-build-env-tcws4eg3/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/private/var/folders/wk/xjxk9mdj7lz95cjvqc_nqxl80000gn/T/pip-build-env-tcws4eg3/overlay/lib/python3.9/site-packages/setuptools/_distutils/command/build.py", line 131, in run
self.run_command(cmd_name)
File "/private/var/folders/wk/xjxk9mdj7lz95cjvqc_nqxl80000gn/T/pip-build-env-tcws4eg3/overlay/lib/python3.9/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
self.distribution.run_command(command)
File "/private/var/folders/wk/xjxk9mdj7lz95cjvqc_nqxl80000gn/T/pip-build-env-tcws4eg3/overlay/lib/python3.9/site-packages/setuptools/dist.py", line 989, in run_command
super().run_command(command)
File "/private/var/folders/wk/xjxk9mdj7lz95cjvqc_nqxl80000gn/T/pip-build-env-tcws4eg3/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/private/var/folders/wk/xjxk9mdj7lz95cjvqc_nqxl80000gn/T/pip-build-env-tcws4eg3/overlay/lib/python3.9/site-packages/setuptools/command/build_ext.py", line 88, in run
_build_ext.run(self)
File "/private/var/folders/wk/xjxk9mdj7lz95cjvqc_nqxl80000gn/T/pip-build-env-tcws4eg3/overlay/lib/python3.9/site-packages/setuptools/_distutils/command/build_ext.py", line 345, in run
self.build_extensions()
File "/private/var/folders/wk/xjxk9mdj7lz95cjvqc_nqxl80000gn/T/pip-build-env-tcws4eg3/overlay/lib/python3.9/site-packages/setuptools/_distutils/command/build_ext.py", line 467, in build_extensions
self._build_extensions_serial()
File "/private/var/folders/wk/xjxk9mdj7lz95cjvqc_nqxl80000gn/T/pip-build-env-tcws4eg3/overlay/lib/python3.9/site-packages/setuptools/_distutils/command/build_ext.py", line 493, in _build_extensions_serial
self.build_extension(ext)
File "/private/var/folders/wk/xjxk9mdj7lz95cjvqc_nqxl80000gn/T/pip-build-env-tcws4eg3/overlay/lib/python3.9/site-packages/setuptools/command/build_ext.py", line 249, in build_extension
_build_ext.build_extension(self, ext)
File "/private/var/folders/wk/xjxk9mdj7lz95cjvqc_nqxl80000gn/T/pip-build-env-tcws4eg3/overlay/lib/python3.9/site-packages/Cython/Distutils/build_ext.py", line 127, in build_extension
super(build_ext, self).build_extension(ext)
File "/private/var/folders/wk/xjxk9mdj7lz95cjvqc_nqxl80000gn/T/pip-build-env-tcws4eg3/overlay/lib/python3.9/site-packages/setuptools/_distutils/command/build_ext.py", line 548, in build_extension
objects = self.compiler.compile(
File "/private/var/folders/wk/xjxk9mdj7lz95cjvqc_nqxl80000gn/T/pip-build-env-tcws4eg3/overlay/lib/python3.9/site-packages/setuptools/_distutils/ccompiler.py", line 600, in compile
self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)
File "/private/var/folders/wk/xjxk9mdj7lz95cjvqc_nqxl80000gn/T/pip-build-env-tcws4eg3/overlay/lib/python3.9/site-packages/setuptools/_distutils/unixccompiler.py", line 185, in _compile
self.spawn(compiler_so + cc_args + [src, '-o', obj] + extra_postargs)
File "/private/var/folders/wk/xjxk9mdj7lz95cjvqc_nqxl80000gn/T/pip-build-env-tcws4eg3/overlay/lib/python3.9/site-packages/setuptools/_distutils/ccompiler.py", line 1041, in spawn
spawn(cmd, dry_run=self.dry_run, **kwargs)
File "/private/var/folders/wk/xjxk9mdj7lz95cjvqc_nqxl80000gn/T/pip-build-env-tcws4eg3/overlay/lib/python3.9/site-packages/setuptools/_distutils/spawn.py", line 57, in spawn
proc = subprocess.Popen(cmd, env=env)
File "/usr/local/Cellar/[email protected]/3.9.1_3/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py", line 947, in init
self._execute_child(args, executable, preexec_fn, close_fds,
File "/usr/local/Cellar/[email protected]/3.9.1_3/Frameworks/Python.framework/Versions/3.9/lib/python3.9/subprocess.py", line 1739, in _execute_child
env_list.append(k + b'=' + os.fsencode(v))
File "/usr/local/Cellar/[email protected]/3.9.1_3/Frameworks/Python.framework/Versions/3.9/lib/python3.9/os.py", line 810, in fsencode
filename = fspath(filename) # Does type-checking offilename
.
TypeError: expected str, bytes or os.PathLike object, not int
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for cyac
Failed to build cyac
ERROR: Could not build wheels for cyac, which is required to install pyproject.toml-based projects
I am trying to use several AC, each one of them shared between several processes.
I cannot share the code, thus I will provide a pseudo code.
def target_function(ac_name):
with open(ac_name, "r+b") as bf:
buff_object = mmap.mmap(bf.fileno(), 0)
. automaton = AC.from_buff(buff_object, copy=False)
....
processes_per_AC = 3
total_ac = 0
for x in range(0, total_Ac):
x_patterns = [<some words here, different for every AC in the iteration>]
ac = AC.build(x_patterns)
ac.save("ac_{}".format(x))
for x in range(0, processes_per_AC):
p = Process(target_function, args=("ac_{}".format(x)))
p.start()
....
Basically what I am doing is create several AC, with different words in the main process, and then launching several child processes that share the AC created. In this case, 3 processes per AC.
The AC I am building contain the following type of information:
The exception:
...
File "lib/cyac/ac.pyx", line 413, in cyac.ac.AC.from_buff
File "lib/cyac/ac.pyx", line 465, in cyac.ac.ac_from_buff
Exception: invalid data, buf size is not correct
Occurs when I am trying to load from_buff in the target_function. It occurs randomly, and I have not been able to understand why. It does not matter if I have more or less words on the AC. The type of words (email, ip, domains, etc), does not seem to make a difference. I wish I could be more precise, but this is everything I can observe from the exception.
I can provide you the file I am using, it is just random generated emails, domains, ip, etc in json format.
Summary:
Previously saved case sensitive data loads without error into trie. However trie.get(val) fails get item, even though iterating through trie.items() show correct item.
Env: Archlinux using python 3.9, Ubuntu 20.0.4 using python 3.8.5
Cyac Version: 1.2
Cython Version:
Steps to reproduce:
The code below will should be run twice:
Script below:
from cyac import Trie
import os
import mmap
p=["M3 1AR", "M3 2AR", "M3 3AR"]
if os.path.isfile('./pinsens.bin'):
# Load into new tries
print("* * * Loaded from buffer * * * ")
with open('pinsens.bin', 'r+b') as fins:
bins = mmap.mmap(fins.fileno(), 0)
cins = Trie.from_buff(bins)
bins.flush()
with open('psens.bin', 'r+b') as fsens:
bsens = mmap.mmap(fsens.fileno(), 0)
csen = Trie.from_buff(bsens)
bsens.flush()
else:
print("* * * Clean data")
cins = Trie(ignore_case=True)
csen = Trie()
for x in p:
cins.insert(x)
csen.insert(x)
cins.save('pinsens.bin')
csen.save('psens.bin')
print("Case Insensitive")
print("{} is at {}".format(p[2], cins.get(p[2]))) # correctly returns 2
print("Case Sensitive")
print("{} is at {}".format(p[2], csen.get(p[2]))) # correctly returns 2 in first run, fails in second
for id in csen.items():
print(id)
I just want to point out that this library does not support overlap matches.
Consider the following:
import cyac
ac = cyac.AC.build([u"[email protected]", u"gmail.com"])
var1 = "[email protected]"
for id, start, end in ac.match(var1):
print(var1[start:end])
Outputs:
[email protected]
It should have output: [email protected] and gmail.com
This might also be one of the reasons why this lib is faster than pyahocorasick
ERROR: Failed building wheel for cyac
Failed to build cyac
my cython version is 3.0.0
python version is 3.9
gcc version is 10.2.1
system: debian:bullseye-slim
Thanks!
There is error during build of the latest 1.8 version when package downloaded from PyPI:
lib/cyac/xstring.cpp:1113:10: fatal error: 'unicode_portability.c' file not found
#include "unicode_portability.c"
^~~~~~~~~~~~~~~~~~~~~~~
1 error generated.
error: command '/usr/bin/clang' failed with exit code 1
When iterating over an AC trie, a segmentation fault occurs. For example:
import cyac
trie = cyac.AC.build(['hello', 'world'])
for w in trie:
print(w)
Output:
hello
world
Segmentation fault
However, AC.items()
is works as expected.
At https://github.com/nppoly/cyac/blob/master/lib/cyac/ac.pyx#L261,
The description is "return_all: by default, only return the longest. ..."
But when I run following code, I cannot understand the output.
ac = cyac.AC.build([u"py", u"python"])
text = 'python'
for idx,s,e in ac.match(text):
print(s, e, ac[idx])
-- output --
0 2 py <== ??
0 6 python
Is it a bug?
Is this library thread safe after calling the build function?
If the trie is built and several threads access it using the match function, would this be thread-safe?
The above two projects are currently excellent projects. Can people who have used them help evaluate their direct differences?
pip install cyac
Looking in indexes: https://pypi.tuna.tsinghua.edu.cn/simple
Collecting cyac
Downloading https://pypi.tuna.tsinghua.edu.cn/packages/db/2e/4a4916514b64694dd478ab085f01fb4ca599e3127c05704f98f3067e8fc7/cyac-1.3.tar.gz (38 kB) Preparing metadata (setup.py) ... error
error: subprocess-exited-with-error
× python setup.py egg_info did not run successfully.
│ exit code: 1
╰─> [6 lines of output]
Traceback (most recent call last):
File "<string>", line 2, in <module>
File "<pip-setuptools-caller>", line 34,
in <module>
File "C:\Users\admin\AppData\Local\Temp\pip-install-h1651_cj\cyac_4973446135a546ce84624d967d791583\setup.py", line 10, in <module>
long_description = open("README.md").read()
UnicodeDecodeError: 'gbk' codec can't decode byte 0x8c in position 3452: illegal multibyte sequence
[end of output]
note: This error originates from a subprocess,
and is likely not a problem with pip.
error: metadata-generation-failed
× Encountered error while generating package metadata.
╰─> See above for output.
note: This is an issue with the package mentioned above, not pip.
hint: See above for details.
python version: Python 3.10.1
pip version: pip 22.0.4
Hello,
I would like to run some memory analysis and tests using the new shared_buffer branch. I would post those memory analysis in an issue, so that you could put them in the README.md if you like.
How I am facing the following problem:
>>> import cyac
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/local/lib/python3.7/site-packages/cyac-1.0-py3.7-linux-x86_64.egg/cyac/__init__.py", line 2, in <module>
from .ac import AC
File "lib/cyac/ac.pyx", line 1, in init cyac.ac
#cython: language_level=3, boundscheck=False, overflowcheck=False
File "lib/cyac/trie.pyx", line 1, in init cyac.trie
#cython: language_level=3, boundscheck=False, overflowcheck=False
ModuleNotFoundError: No module named 'cyac.util'
What I did to install it:
Tried with python3.7 and 3.6.
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