repo stringlengths 7 90 | file_url stringlengths 81 315 | file_path stringlengths 4 228 | content stringlengths 0 32.8k | language stringclasses 1
value | license stringclasses 7
values | commit_sha stringlengths 40 40 | retrieved_at stringdate 2026-01-04 14:38:15 2026-01-05 02:33:18 | truncated bool 2
classes |
|---|---|---|---|---|---|---|---|---|
pnnl/safekit | https://github.com/pnnl/safekit/blob/92c004bc72f1480a4f9b26d304a900cbc8dea48d/safekit/models/lstm_agg.py | safekit/models/lstm_agg.py | """
"""
import json
import os
import sys
# TODO: Comment for usage.
# TODO: Test this on DS data
# TODO: skipheader error message that is informative
# TODO: Make consistent output printing and writing to file for aggregate and baseline models.
# TODO: Comment crazy transform functions
# So we can run this code on a... | python | MIT | 92c004bc72f1480a4f9b26d304a900cbc8dea48d | 2026-01-05T07:13:08.019988Z | false |
pnnl/safekit | https://github.com/pnnl/safekit/blob/92c004bc72f1480a4f9b26d304a900cbc8dea48d/safekit/models/__init__.py | safekit/models/__init__.py | python | MIT | 92c004bc72f1480a4f9b26d304a900cbc8dea48d | 2026-01-05T07:13:08.019988Z | false | |
pnnl/safekit | https://github.com/pnnl/safekit/blob/92c004bc72f1480a4f9b26d304a900cbc8dea48d/safekit/models/iso_forest.py | safekit/models/iso_forest.py | """
Isolation Forest baseline.
"""
import sys
import os
cyberpath = '/'.join(os.path.realpath(__file__).split('/')[:-3])
sys.path.insert(0, cyberpath)
import argparse
from sklearn.ensemble import IsolationForest
from safekit.batch import DayBatcher
from safekit.util import apr
import time
import math
def sample_hyps... | python | MIT | 92c004bc72f1480a4f9b26d304a900cbc8dea48d | 2026-01-05T07:13:08.019988Z | false |
pnnl/safekit | https://github.com/pnnl/safekit/blob/92c004bc72f1480a4f9b26d304a900cbc8dea48d/safekit/models/dnn_agg.py | safekit/models/dnn_agg.py | #!/usr/bin/env python
"""
Multivariate Deep Neural Network Autoencoder network anomaly detection. Anomaly detection is performed on model output
by ranking of loss scores within a time window from output of model. An output file is created with a timestamp prepended,
and values of hyper-parameters in name.
**Abbreviat... | python | MIT | 92c004bc72f1480a4f9b26d304a900cbc8dea48d | 2026-01-05T07:13:08.019988Z | false |
pnnl/safekit | https://github.com/pnnl/safekit/blob/92c004bc72f1480a4f9b26d304a900cbc8dea48d/safekit/features/merge_streams.py | safekit/features/merge_streams.py | from datetime import datetime
class Merge:
"""
Live merging of csv files. The call of this object is a generator function
which interleaves lines from a collection of files, ordered by a sort_column
parameter.
Assumes:
(i) Individual files are ordered by ascending sort column values.
... | python | MIT | 92c004bc72f1480a4f9b26d304a900cbc8dea48d | 2026-01-05T07:13:08.019988Z | false |
pnnl/safekit | https://github.com/pnnl/safekit/blob/92c004bc72f1480a4f9b26d304a900cbc8dea48d/safekit/features/__init__.py | safekit/features/__init__.py | python | MIT | 92c004bc72f1480a4f9b26d304a900cbc8dea48d | 2026-01-05T07:13:08.019988Z | false | |
pnnl/safekit | https://github.com/pnnl/safekit/blob/92c004bc72f1480a4f9b26d304a900cbc8dea48d/safekit/features/lanl/char_feats.py | safekit/features/lanl/char_feats.py | """
SOS = 0, EOS = 1, all other chars are ASCII values - 30
,, Note:: Line numbers in raw_char are off by one from original raw data in auth_h.txt. However, no data is changed.
.. Note:: The first field time stamp is not transliterated here, just used for meta data
"""
import argparse
from word_feats import second_to... | python | MIT | 92c004bc72f1480a4f9b26d304a900cbc8dea48d | 2026-01-05T07:13:08.019988Z | false |
pnnl/safekit | https://github.com/pnnl/safekit/blob/92c004bc72f1480a4f9b26d304a900cbc8dea48d/safekit/features/lanl/__init__.py | safekit/features/lanl/__init__.py | python | MIT | 92c004bc72f1480a4f9b26d304a900cbc8dea48d | 2026-01-05T07:13:08.019988Z | false | |
pnnl/safekit | https://github.com/pnnl/safekit/blob/92c004bc72f1480a4f9b26d304a900cbc8dea48d/safekit/features/lanl/word_feats.py | safekit/features/lanl/word_feats.py | """
@authors: Ryan Baerwolf, Aaron Tuor (rdbaerwolf@gmail.com, baerwor@wwu.edu, aaron.tuor@pnnl.gov)
Derives word-level features for LANL using auth_h.txt. Weekend days are filtered out of data set.
"""
import argparse
import operator
import json
weekend_days = [3, 4, 10, 11, 17, 18, 24, 25, 31, 32, 38, 39, 45, 46, ... | python | MIT | 92c004bc72f1480a4f9b26d304a900cbc8dea48d | 2026-01-05T07:13:08.019988Z | false |
pnnl/safekit | https://github.com/pnnl/safekit/blob/92c004bc72f1480a4f9b26d304a900cbc8dea48d/safekit/features/lanl/lanl_agg_features.py | safekit/features/lanl/lanl_agg_features.py | """
New method for determining general notion of common/uncommon: >< mean.
Also this script doesn't print weekend events.
"""
import os
import sys
# So we can run this code on arbitrary environment which has tensorflow but not safekit installed
cyberpath = '/'.join(os.path.realpath(__file__).split('/')[:-4])
sys.path.i... | python | MIT | 92c004bc72f1480a4f9b26d304a900cbc8dea48d | 2026-01-05T07:13:08.019988Z | false |
pnnl/safekit | https://github.com/pnnl/safekit/blob/92c004bc72f1480a4f9b26d304a900cbc8dea48d/test/agg_tests.py | test/agg_tests.py | """
"""
import os
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('lanl_datapath', type=str, help="path to lanl parent directory of aggregate model features.")
parser.add_argument('cert_datapath', type=str, help="path to cert parent directory of aggregate model features.")
parser.add_argument('... | python | MIT | 92c004bc72f1480a4f9b26d304a900cbc8dea48d | 2026-01-05T07:13:08.019988Z | false |
pnnl/safekit | https://github.com/pnnl/safekit/blob/92c004bc72f1480a4f9b26d304a900cbc8dea48d/test/lanl_lm_tests.py | test/lanl_lm_tests.py | """
"""
# TODO: Change test calls to reflect good hyper-parameters for reference
# TODO: Add more tests for different model configurations
# TODO: Make new test script for running all tests on full data set
import os
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('datapath', type=str, help... | python | MIT | 92c004bc72f1480a4f9b26d304a900cbc8dea48d | 2026-01-05T07:13:08.019988Z | false |
pnnl/safekit | https://github.com/pnnl/safekit/blob/92c004bc72f1480a4f9b26d304a900cbc8dea48d/docs/conf.py | docs/conf.py | # -*- coding: utf-8 -*-
#
# safekit documentation build configuration file, created by
# sphinx-quickstart on Thu Jan 5 17:42:22 2017.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# A... | python | MIT | 92c004bc72f1480a4f9b26d304a900cbc8dea48d | 2026-01-05T07:13:08.019988Z | false |
pnnl/safekit | https://github.com/pnnl/safekit/blob/92c004bc72f1480a4f9b26d304a900cbc8dea48d/docs/sphinxext/sphinxtogithub.py | docs/sphinxext/sphinxtogithub.py | #! /usr/bin/env python
from optparse import OptionParser
import os
import sys
import shutil
import codecs
class DirHelper(object):
def __init__(self, is_dir, list_dir, walk, rmtree):
self.is_dir = is_dir
self.list_dir = list_dir
self.walk = walk
self.rmtree = rmtree
class Fil... | python | MIT | 92c004bc72f1480a4f9b26d304a900cbc8dea48d | 2026-01-05T07:13:08.019988Z | false |
pnnl/safekit | https://github.com/pnnl/safekit/blob/92c004bc72f1480a4f9b26d304a900cbc8dea48d/docs/sphinxext/sphinxarg/parser.py | docs/sphinxext/sphinxarg/parser.py | from argparse import _HelpAction, _SubParsersAction
import re
class NavigationException(Exception):
pass
def parser_navigate(parser_result, path, current_path=None):
if isinstance(path, str):
if path == '':
return parser_result
path = re.split('\s+', path)
current_path = curr... | python | MIT | 92c004bc72f1480a4f9b26d304a900cbc8dea48d | 2026-01-05T07:13:08.019988Z | false |
pnnl/safekit | https://github.com/pnnl/safekit/blob/92c004bc72f1480a4f9b26d304a900cbc8dea48d/docs/sphinxext/sphinxarg/ext.py | docs/sphinxext/sphinxarg/ext.py | from argparse import ArgumentParser
import os
from docutils import nodes
from docutils.statemachine import StringList
from docutils.parsers.rst.directives import flag, unchanged
from sphinx.util.compat import Directive
from sphinx.util.nodes import nested_parse_with_titles
from sphinxarg.parser import parse_parser, p... | python | MIT | 92c004bc72f1480a4f9b26d304a900cbc8dea48d | 2026-01-05T07:13:08.019988Z | false |
pnnl/safekit | https://github.com/pnnl/safekit/blob/92c004bc72f1480a4f9b26d304a900cbc8dea48d/docs/sphinxext/sphinxarg/__init__.py | docs/sphinxext/sphinxarg/__init__.py | python | MIT | 92c004bc72f1480a4f9b26d304a900cbc8dea48d | 2026-01-05T07:13:08.019988Z | false | |
pnnl/safekit | https://github.com/pnnl/safekit/blob/92c004bc72f1480a4f9b26d304a900cbc8dea48d/docs/sphinxext/sphinx-argparse-0.1.15/setup.py | docs/sphinxext/sphinx-argparse-0.1.15/setup.py | import sys
from setuptools import setup
# from tests import PyTest
deps = ["sphinx"]
if sys.version_info[:2] == (2, 6):
deps.append('argparse')
setup(
name='sphinx-argparse',
version='0.1.15',
packages=[
'sphinxarg',
],
url='',
license='MIT',
author='Aleksandr Rudakov',
a... | python | MIT | 92c004bc72f1480a4f9b26d304a900cbc8dea48d | 2026-01-05T07:13:08.019988Z | false |
pnnl/safekit | https://github.com/pnnl/safekit/blob/92c004bc72f1480a4f9b26d304a900cbc8dea48d/docs/sphinxext/sphinx-argparse-0.1.15/sphinxarg/parser.py | docs/sphinxext/sphinx-argparse-0.1.15/sphinxarg/parser.py | from argparse import _HelpAction, _SubParsersAction
import re
class NavigationException(Exception):
pass
def parser_navigate(parser_result, path, current_path=None):
if isinstance(path, str):
if path == '':
return parser_result
path = re.split('\s+', path)
current_path = curr... | python | MIT | 92c004bc72f1480a4f9b26d304a900cbc8dea48d | 2026-01-05T07:13:08.019988Z | false |
pnnl/safekit | https://github.com/pnnl/safekit/blob/92c004bc72f1480a4f9b26d304a900cbc8dea48d/docs/sphinxext/sphinx-argparse-0.1.15/sphinxarg/ext.py | docs/sphinxext/sphinx-argparse-0.1.15/sphinxarg/ext.py | from argparse import ArgumentParser
import os
from docutils import nodes
from docutils.statemachine import StringList
from docutils.parsers.rst.directives import flag, unchanged
from sphinx.util.compat import Directive
from sphinx.util.nodes import nested_parse_with_titles
from sphinxarg.parser import parse_parser, p... | python | MIT | 92c004bc72f1480a4f9b26d304a900cbc8dea48d | 2026-01-05T07:13:08.019988Z | false |
pnnl/safekit | https://github.com/pnnl/safekit/blob/92c004bc72f1480a4f9b26d304a900cbc8dea48d/docs/sphinxext/sphinx-argparse-0.1.15/sphinxarg/__init__.py | docs/sphinxext/sphinx-argparse-0.1.15/sphinxarg/__init__.py | python | MIT | 92c004bc72f1480a4f9b26d304a900cbc8dea48d | 2026-01-05T07:13:08.019988Z | false | |
pnnl/safekit | https://github.com/pnnl/safekit/blob/92c004bc72f1480a4f9b26d304a900cbc8dea48d/docs/sphinxext/sphinx-argparse-0.1.15/test/test_parser.py | docs/sphinxext/sphinx-argparse-0.1.15/test/test_parser.py | import argparse
import json
from pprint import pprint
from sphinxarg.parser import parse_parser, parser_navigate
def test_parse_options():
parser = argparse.ArgumentParser()
parser.add_argument('--foo', action='store_true', default=False, help='foo help')
parser.add_argument('--bar', action='store_true', ... | python | MIT | 92c004bc72f1480a4f9b26d304a900cbc8dea48d | 2026-01-05T07:13:08.019988Z | false |
pnnl/safekit | https://github.com/pnnl/safekit/blob/92c004bc72f1480a4f9b26d304a900cbc8dea48d/docs/sphinxext/sphinxtogithub-1.1.0/setup.py | docs/sphinxext/sphinxtogithub-1.1.0/setup.py | #!/usr/bin/env python
# -*- coding: utf-8 -*-
import codecs
import os
import unittest
try:
from setuptools import setup, find_packages, Command
except ImportError:
from ez_setup import use_setuptools
use_setuptools()
from setuptools import setup, find_packages, Command
import sphinxtogithub
from sphi... | python | MIT | 92c004bc72f1480a4f9b26d304a900cbc8dea48d | 2026-01-05T07:13:08.019988Z | false |
pnnl/safekit | https://github.com/pnnl/safekit/blob/92c004bc72f1480a4f9b26d304a900cbc8dea48d/docs/sphinxext/sphinxtogithub-1.1.0/tests/__init__.py | docs/sphinxext/sphinxtogithub-1.1.0/tests/__init__.py | python | MIT | 92c004bc72f1480a4f9b26d304a900cbc8dea48d | 2026-01-05T07:13:08.019988Z | false | |
pnnl/safekit | https://github.com/pnnl/safekit/blob/92c004bc72f1480a4f9b26d304a900cbc8dea48d/docs/sphinxext/sphinxtogithub-1.1.0/tests/testreplace.py | docs/sphinxext/sphinxtogithub-1.1.0/tests/testreplace.py | # -*- coding: utf-8 -*-
from unittest import TestCase
import sphinxtogithub
class TestReplace(TestCase):
def setUp(self):
pass
def tearDown(self):
pass
def test_unicode_replace(self):
print u"this is a test ✓".replace( "this", "that" )
| python | MIT | 92c004bc72f1480a4f9b26d304a900cbc8dea48d | 2026-01-05T07:13:08.019988Z | false |
pnnl/safekit | https://github.com/pnnl/safekit/blob/92c004bc72f1480a4f9b26d304a900cbc8dea48d/docs/sphinxext/sphinxtogithub-1.1.0/sphinxtogithub/sphinxtogithub.py | docs/sphinxext/sphinxtogithub-1.1.0/sphinxtogithub/sphinxtogithub.py | #! /usr/bin/env python
from optparse import OptionParser
import os
import sys
import shutil
import codecs
class DirHelper(object):
def __init__(self, is_dir, list_dir, walk, rmtree):
self.is_dir = is_dir
self.list_dir = list_dir
self.walk = walk
self.rmtree = rmtree
class Fil... | python | MIT | 92c004bc72f1480a4f9b26d304a900cbc8dea48d | 2026-01-05T07:13:08.019988Z | false |
pnnl/safekit | https://github.com/pnnl/safekit/blob/92c004bc72f1480a4f9b26d304a900cbc8dea48d/docs/sphinxext/sphinxtogithub-1.1.0/sphinxtogithub/__init__.py | docs/sphinxext/sphinxtogithub-1.1.0/sphinxtogithub/__init__.py | """Script for preparing the html output of the Sphinx documentation system for
github pages. """
VERSION = (1, 1, 0, 'dev')
__version__ = ".".join(map(str, VERSION[:-1]))
__release__ = ".".join(map(str, VERSION))
__author__ = "Michael Jones"
__contact__ = "http://github.com/michaeljones"
__homepage__ = "http://github... | python | MIT | 92c004bc72f1480a4f9b26d304a900cbc8dea48d | 2026-01-05T07:13:08.019988Z | false |
pnnl/safekit | https://github.com/pnnl/safekit/blob/92c004bc72f1480a4f9b26d304a900cbc8dea48d/docs/sphinxext/sphinxtogithub-1.1.0/sphinxtogithub/tests/renamer.py | docs/sphinxext/sphinxtogithub-1.1.0/sphinxtogithub/tests/renamer.py |
from sphinxtogithub.tests import MockExists, MockRemove, MockStream
import sphinxtogithub
import unittest
import os
class MockRename(object):
def __call__(self, from_, to):
self.from_ = from_
self.to = to
class TestForceRename(unittest.TestCase):
def testCall(self):
rename = Moc... | python | MIT | 92c004bc72f1480a4f9b26d304a900cbc8dea48d | 2026-01-05T07:13:08.019988Z | false |
pnnl/safekit | https://github.com/pnnl/safekit/blob/92c004bc72f1480a4f9b26d304a900cbc8dea48d/docs/sphinxext/sphinxtogithub-1.1.0/sphinxtogithub/tests/filehandler.py | docs/sphinxext/sphinxtogithub-1.1.0/sphinxtogithub/tests/filehandler.py |
import unittest
import sphinxtogithub
class MockFileObject(object):
before = """
<title>Breathe's documentation — BreatheExample v0.0.1 documentation</title>
<link rel="stylesheet" href="_static/default.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" ... | python | MIT | 92c004bc72f1480a4f9b26d304a900cbc8dea48d | 2026-01-05T07:13:08.019988Z | false |
pnnl/safekit | https://github.com/pnnl/safekit/blob/92c004bc72f1480a4f9b26d304a900cbc8dea48d/docs/sphinxext/sphinxtogithub-1.1.0/sphinxtogithub/tests/setup.py | docs/sphinxext/sphinxtogithub-1.1.0/sphinxtogithub/tests/setup.py |
import sphinxtogithub
import unittest
class MockApp(object):
def __init__(self):
self.config_values = {}
self.connections = {}
def add_config_value(self, name, default, rebuild):
self.config_values[name] = (default, rebuild)
def connect(self, stage, function):
self.con... | python | MIT | 92c004bc72f1480a4f9b26d304a900cbc8dea48d | 2026-01-05T07:13:08.019988Z | false |
pnnl/safekit | https://github.com/pnnl/safekit/blob/92c004bc72f1480a4f9b26d304a900cbc8dea48d/docs/sphinxext/sphinxtogithub-1.1.0/sphinxtogithub/tests/layoutfactory.py | docs/sphinxext/sphinxtogithub-1.1.0/sphinxtogithub/tests/layoutfactory.py |
from sphinxtogithub.tests import MockStream
import sphinxtogithub
import unittest
import os
import shutil
root = "test_path"
dirs = ["dir1", "dir2", "dir_", "d_ir", "_static", "_source"]
files = ["file1.html", "nothtml.txt", "file2.html", "javascript.js"]
def mock_is_dir(path):
directories = [ os.path.join(roo... | python | MIT | 92c004bc72f1480a4f9b26d304a900cbc8dea48d | 2026-01-05T07:13:08.019988Z | false |
pnnl/safekit | https://github.com/pnnl/safekit/blob/92c004bc72f1480a4f9b26d304a900cbc8dea48d/docs/sphinxext/sphinxtogithub-1.1.0/sphinxtogithub/tests/__init__.py | docs/sphinxext/sphinxtogithub-1.1.0/sphinxtogithub/tests/__init__.py |
class MockExists(object):
def __call__(self, name):
self.name = name
return True
class MockRemove(MockExists):
pass
class MockStream(object):
def __init__(self):
self.msgs = []
def write(self, msg):
self.msgs.append(msg)
| python | MIT | 92c004bc72f1480a4f9b26d304a900cbc8dea48d | 2026-01-05T07:13:08.019988Z | false |
pnnl/safekit | https://github.com/pnnl/safekit/blob/92c004bc72f1480a4f9b26d304a900cbc8dea48d/docs/sphinxext/sphinxtogithub-1.1.0/sphinxtogithub/tests/remover.py | docs/sphinxext/sphinxtogithub-1.1.0/sphinxtogithub/tests/remover.py |
from sphinxtogithub.tests import MockExists, MockRemove
import sphinxtogithub
import unittest
class TestRemover(unittest.TestCase):
def testCall(self):
exists = MockExists()
remove = MockRemove()
remover = sphinxtogithub.Remover(exists, remove)
filepath = "filepath"
rem... | python | MIT | 92c004bc72f1480a4f9b26d304a900cbc8dea48d | 2026-01-05T07:13:08.019988Z | false |
pnnl/safekit | https://github.com/pnnl/safekit/blob/92c004bc72f1480a4f9b26d304a900cbc8dea48d/docs/sphinxext/sphinxtogithub-1.1.0/sphinxtogithub/tests/directoryhandler.py | docs/sphinxext/sphinxtogithub-1.1.0/sphinxtogithub/tests/directoryhandler.py |
import unittest
import os
import sphinxtogithub
class MockRenamer(object):
def __call__(self, from_, to):
self.from_ = from_
self.to = to
class TestDirectoryHandler(unittest.TestCase):
def setUp(self):
self.directory = "_static"
self.new_directory = "static"
self... | python | MIT | 92c004bc72f1480a4f9b26d304a900cbc8dea48d | 2026-01-05T07:13:08.019988Z | false |
pnnl/safekit | https://github.com/pnnl/safekit/blob/92c004bc72f1480a4f9b26d304a900cbc8dea48d/docs/sphinxext/sphinxtogithub-1.1.0/sphinxtogithub/tests/replacer.py | docs/sphinxext/sphinxtogithub-1.1.0/sphinxtogithub/tests/replacer.py |
import unittest
import sphinxtogithub
class TestReplacer(unittest.TestCase):
before = """
<title>Breathe's documentation — BreatheExample v0.0.1 documentation</title>
<link rel="stylesheet" href="_static/default.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="t... | python | MIT | 92c004bc72f1480a4f9b26d304a900cbc8dea48d | 2026-01-05T07:13:08.019988Z | false |
pnnl/safekit | https://github.com/pnnl/safekit/blob/92c004bc72f1480a4f9b26d304a900cbc8dea48d/docs/sphinxext/sphinxtogithub-1.1.0/sphinxtogithub/tests/layout.py | docs/sphinxext/sphinxtogithub-1.1.0/sphinxtogithub/tests/layout.py |
from sphinxtogithub.tests import MockExists, MockRemove
import sphinxtogithub
import unittest
class MockHandler(object):
def __init__(self):
self.processed = False
def process(self):
self.processed = True
class TestLayout(unittest.TestCase):
def testProcess(self):
directo... | python | MIT | 92c004bc72f1480a4f9b26d304a900cbc8dea48d | 2026-01-05T07:13:08.019988Z | false |
google/bi-tempered-loss | https://github.com/google/bi-tempered-loss/blob/1c65c7770a3aa76a9515c67f15cfdbaad0e8cf88/jax/loss.py | jax/loss.py | # coding=utf-8
# Copyright 2019 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... | python | Apache-2.0 | 1c65c7770a3aa76a9515c67f15cfdbaad0e8cf88 | 2026-01-05T07:13:09.810991Z | false |
google/bi-tempered-loss | https://github.com/google/bi-tempered-loss/blob/1c65c7770a3aa76a9515c67f15cfdbaad0e8cf88/jax/loss_test.py | jax/loss_test.py | # coding=utf-8
# Copyright 2019 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... | python | Apache-2.0 | 1c65c7770a3aa76a9515c67f15cfdbaad0e8cf88 | 2026-01-05T07:13:09.810991Z | false |
google/bi-tempered-loss | https://github.com/google/bi-tempered-loss/blob/1c65c7770a3aa76a9515c67f15cfdbaad0e8cf88/tensorflow/loss.py | tensorflow/loss.py | # coding=utf-8
# Copyright 2019 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... | python | Apache-2.0 | 1c65c7770a3aa76a9515c67f15cfdbaad0e8cf88 | 2026-01-05T07:13:09.810991Z | false |
google/bi-tempered-loss | https://github.com/google/bi-tempered-loss/blob/1c65c7770a3aa76a9515c67f15cfdbaad0e8cf88/tensorflow/loss_test.py | tensorflow/loss_test.py | # coding=utf-8
# Copyright 2019 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... | python | Apache-2.0 | 1c65c7770a3aa76a9515c67f15cfdbaad0e8cf88 | 2026-01-05T07:13:09.810991Z | false |
SparkSharly/DL_for_xss | https://github.com/SparkSharly/DL_for_xss/blob/aaf555a4f53bf136cf5fadbe35ac294894f3bbe1/SVM.py | SVM.py | import time
from keras.preprocessing.sequence import pad_sequences
from sklearn.metrics import precision_score,recall_score
from sklearn.model_selection import train_test_split
from sklearn.svm import LinearSVC
from utils import GeneSeg
import csv,random,pickle
batch_size=50
maxlen=200
vec_dir="file\\word2vec.pickle"... | python | MIT | aaf555a4f53bf136cf5fadbe35ac294894f3bbe1 | 2026-01-05T07:13:06.526795Z | false |
SparkSharly/DL_for_xss | https://github.com/SparkSharly/DL_for_xss/blob/aaf555a4f53bf136cf5fadbe35ac294894f3bbe1/word2vec.py | word2vec.py | import nltk,re,csv,random,math,pickle,time
from urllib.parse import unquote
from collections import Counter,deque
import numpy as np
import tensorflow as tf
import matplotlib.pyplot as plt
from sklearn.manifold import TSNE
from utils import GeneSeg
learning_rate=0.1
vocabulary_size=3000
batch_size=128
embedding_size=12... | python | MIT | aaf555a4f53bf136cf5fadbe35ac294894f3bbe1 | 2026-01-05T07:13:06.526795Z | false |
SparkSharly/DL_for_xss | https://github.com/SparkSharly/DL_for_xss/blob/aaf555a4f53bf136cf5fadbe35ac294894f3bbe1/MLP.py | MLP.py | import time
from keras.models import Sequential
from keras.layers import Dense,InputLayer,Dropout,Flatten
from keras.callbacks import TensorBoard
from keras.optimizers import Adam
from keras.models import load_model
from processing import build_dataset
import numpy as np
from utils import init_session
from sklearn.metr... | python | MIT | aaf555a4f53bf136cf5fadbe35ac294894f3bbe1 | 2026-01-05T07:13:06.526795Z | false |
SparkSharly/DL_for_xss | https://github.com/SparkSharly/DL_for_xss/blob/aaf555a4f53bf136cf5fadbe35ac294894f3bbe1/LSTM.py | LSTM.py | import time
from keras.models import Sequential
from keras.layers import Dense,InputLayer,Dropout,LSTM
from keras.callbacks import TensorBoard
from keras.optimizers import Adam
from processing import build_dataset
from utils import init_session
from MLP import test
init_session()
batch_size=350
epochs_num=1
process_dat... | python | MIT | aaf555a4f53bf136cf5fadbe35ac294894f3bbe1 | 2026-01-05T07:13:06.526795Z | false |
SparkSharly/DL_for_xss | https://github.com/SparkSharly/DL_for_xss/blob/aaf555a4f53bf136cf5fadbe35ac294894f3bbe1/utils.py | utils.py | import nltk
import re
from urllib.parse import unquote
import tensorflow as tf
import keras.backend.tensorflow_backend as ktf
def GeneSeg(payload):
#数字泛化为"0"
payload=payload.lower()
payload=unquote(unquote(payload))
payload,num=re.subn(r'\d+',"0",payload)
#替换url为”http://u
payload,num=re.subn(r'(... | python | MIT | aaf555a4f53bf136cf5fadbe35ac294894f3bbe1 | 2026-01-05T07:13:06.526795Z | false |
SparkSharly/DL_for_xss | https://github.com/SparkSharly/DL_for_xss/blob/aaf555a4f53bf136cf5fadbe35ac294894f3bbe1/processing.py | processing.py | from utils import GeneSeg
import csv,pickle,random,json
import numpy as np
from keras.preprocessing.sequence import pad_sequences
from keras.utils import to_categorical
from sklearn.model_selection import train_test_split
import tensorflow as tf
vec_dir="file\\word2vec.pickle"
pre_datas_train="file\\pre_datas_train.cs... | python | MIT | aaf555a4f53bf136cf5fadbe35ac294894f3bbe1 | 2026-01-05T07:13:06.526795Z | false |
SparkSharly/DL_for_xss | https://github.com/SparkSharly/DL_for_xss/blob/aaf555a4f53bf136cf5fadbe35ac294894f3bbe1/Conv.py | Conv.py | import time
from keras.models import Sequential
from keras.layers import Dense,InputLayer,Dropout,LSTM,Conv1D,Flatten,GlobalAveragePooling1D,MaxPool1D
from keras.callbacks import TensorBoard
from keras.optimizers import Adam
from processing import build_dataset
from utils import init_session
from MLP import test
init_s... | python | MIT | aaf555a4f53bf136cf5fadbe35ac294894f3bbe1 | 2026-01-05T07:13:06.526795Z | false |
SparkSharly/DL_for_xss | https://github.com/SparkSharly/DL_for_xss/blob/aaf555a4f53bf136cf5fadbe35ac294894f3bbe1/word2vec_gensim.py | word2vec_gensim.py | import csv,pickle,time
from collections import Counter
import matplotlib.pyplot as plt
from sklearn.manifold import TSNE
from utils import GeneSeg
from gensim.models.word2vec import Word2Vec
learning_rate=0.1
vocabulary_size=3000
batch_size=128
embedding_size=128
num_skips=4
skip_window=5
num_sampled=64
num_iter=5
plot... | python | MIT | aaf555a4f53bf136cf5fadbe35ac294894f3bbe1 | 2026-01-05T07:13:06.526795Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/tests/test_ms2.py | tests/test_ms2.py | import os
import numpy as np
import pyteomics
pyteomics.__path__ = [os.path.abspath(os.path.join(os.path.dirname(__file__), os.path.pardir, 'pyteomics'))]
import unittest
import copy
import pickle
from pyteomics.ms2 import read, read_header, MS2, IndexedMS2, chain
import data
class MS2Test(unittest.TestCase):
maxD... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/tests/test_idxml.py | tests/test_idxml.py | from os import path
import pyteomics
pyteomics.__path__ = [path.abspath(path.join(path.dirname(__file__), path.pardir, 'pyteomics'))]
import unittest
from pyteomics.openms.idxml import IDXML, read, chain
from data import idxml_data
from itertools import product
class IdxmlTest(unittest.TestCase):
maxDiff = None
... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/tests/test_featurexml.py | tests/test_featurexml.py | from os import path
import pyteomics
pyteomics.__path__ = [path.abspath(path.join(path.dirname(__file__), path.pardir, 'pyteomics'))]
import unittest
import operator as op
from itertools import product
from data import features
from pyteomics.openms.featurexml import FeatureXML, read, chain
class FeatureXMLTest(unit... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/tests/test_fasta.py | tests/test_fasta.py | from os import path
import tempfile
import unittest
import random
import string
import pickle
import re
from collections import Counter
import pyteomics
pyteomics.__path__ = [path.abspath(path.join(path.dirname(__file__), path.pardir, 'pyteomics'))]
from pyteomics import fasta
class ReadWriteTest(unittest.TestCase):
... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/tests/test_mzmlb.py | tests/test_mzmlb.py | import unittest
from urllib.request import urlopen
import os
import shutil
import pickle
import pyteomics
from io import BytesIO
pyteomics.__path__ = [os.path.abspath(os.path.join(os.path.dirname(__file__), os.path.pardir, 'pyteomics'))]
from data import mzmlb_spectra
try:
from pyteomics.mzmlb import MzMLb, read, c... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/tests/test_auxiliary.py | tests/test_auxiliary.py | import warnings
import unittest
import string
from itertools import count
import operator as op
import numpy as np
import pandas as pd
import tempfile
import os
import pyteomics
pyteomics.__path__ = [os.path.abspath(os.path.join(os.path.dirname(__file__), os.path.pardir, 'pyteomics'))]
from pyteomics import auxiliary a... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | true |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/tests/test_peff.py | tests/test_peff.py | from os import path
import unittest
import pyteomics
pyteomics.__path__ = [path.abspath(path.join(path.dirname(__file__), path.pardir, 'pyteomics'))]
from pyteomics import peff
class PEFFTest(unittest.TestCase):
maxDiff = None
def setUp(self):
self.peff_file = 'test.peff'
def test_parse(self, re... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/tests/test_util.py | tests/test_util.py | import unittest
import platform
import os
import pyteomics
import multiprocessing as mp
pyteomics.__path__ = [os.path.abspath(os.path.join(os.path.dirname(__file__), os.path.pardir, 'pyteomics'))]
from pyteomics import auxiliary as aux
class UtilTest(unittest.TestCase):
def test_ensure_prefix(self):
pairs... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/tests/test_mztab.py | tests/test_mztab.py | from os import path
import unittest
import warnings
import pyteomics
pyteomics.__path__ = [path.abspath(path.join(path.dirname(__file__), path.pardir, 'pyteomics'))]
from pyteomics import mztab
class MzTabTest(unittest.TestCase):
path_mztab1 = 'test.mztab'
path_mztab2 = 'test_mztab2.mztab'
def test_meta... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/tests/test_mgf.py | tests/test_mgf.py | import os
import numpy as np
import pyteomics
pyteomics.__path__ = [os.path.abspath(os.path.join(os.path.dirname(__file__), os.path.pardir, 'pyteomics'))]
import tempfile
import unittest
import pickle
import shutil
import json
from collections import OrderedDict
import warnings
from pyteomics import mgf, auxiliary as... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/tests/test_ms1.py | tests/test_ms1.py | import os
import numpy as np
import pyteomics
pyteomics.__path__ = [os.path.abspath(os.path.join(os.path.dirname(__file__), os.path.pardir, 'pyteomics'))]
import unittest
import pickle
from pyteomics.ms1 import read, read_header, MS1, IndexedMS1, chain
import data
class MS1Test(unittest.TestCase):
maxDiff = None
... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/tests/test_parser.py | tests/test_parser.py | from os import path
import pyteomics
pyteomics.__path__ = [path.abspath(path.join(path.dirname(__file__), path.pardir, 'pyteomics'))]
import unittest
from pyteomics import parser
from string import ascii_uppercase as uppercase
import random
class ParserTest(unittest.TestCase):
def setUp(self):
self.simple... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/tests/test_tandem.py | tests/test_tandem.py | from os import path
import pyteomics
pyteomics.__path__ = [path.abspath(path.join(path.dirname(__file__), path.pardir, 'pyteomics'))]
import unittest
from pyteomics import tandem
from data import tandem_spectra
class TandemTest(unittest.TestCase):
def setUp(self):
self.maxDiff = None
self.path = '... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/tests/test_traml.py | tests/test_traml.py | from os import path
import pyteomics
pyteomics.__path__ = [path.abspath(path.join(path.dirname(__file__), path.pardir, 'pyteomics'))]
import unittest
from itertools import product
import operator as op
from data import transitions
from pyteomics.traml import TraML, read, chain
from psims.controlled_vocabulary.control... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/tests/test_mzid.py | tests/test_mzid.py | from os import path
import pyteomics
pyteomics.__path__ = [path.abspath(path.join(path.dirname(__file__), path.pardir, 'pyteomics'))]
import unittest
from pyteomics.mzid import MzIdentML, read, chain
from pyteomics import auxiliary as aux
from data import mzid_spectra
from itertools import product
from psims.controlled... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/tests/test_mzml.py | tests/test_mzml.py | import os
import shutil
import tempfile
import pyteomics
from io import BytesIO
from lxml import etree
pyteomics.__path__ = [os.path.abspath(os.path.join(os.path.dirname(__file__), os.path.pardir, 'pyteomics'))]
from itertools import product
import unittest
from pyteomics.mzml import MzML, PreIndexedMzML, read, chain
f... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/tests/test_mass.py | tests/test_mass.py | from os import path
import pyteomics
pyteomics.__path__ = [path.abspath(path.join(path.dirname(__file__), path.pardir, 'pyteomics'))]
import unittest
import random
import pickle
from pyteomics import mass, auxiliary, parser
import gzip
class MassTest(unittest.TestCase):
def setUp(self):
self.mass_data = {
... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/tests/test_pepxml.py | tests/test_pepxml.py | from os import path
import pyteomics
pyteomics.__path__ = [path.abspath(path.join(path.dirname(__file__), path.pardir, 'pyteomics'))]
from itertools import product
import unittest
from pyteomics.pepxml import PepXML, read, chain, filter
from data import pepxml_results
class PepxmlTest(unittest.TestCase):
maxDiff ... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/tests/test_achrom.py | tests/test_achrom.py | from os import path
import doctest
import unittest
import pyteomics
pyteomics.__path__ = [path.abspath(path.join(path.dirname(__file__), path.pardir, 'pyteomics'))]
from pyteomics import achrom
# doctest.testmod(achrom, verbose=True)
def load_tests(loader, tests, ignore):
tests.addTests(doctest.DocTestSuite(achro... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/tests/test_proforma.py | tests/test_proforma.py | from os import path
import unittest
import pickle
import pyteomics
pyteomics.__path__ = [path.abspath(
path.join(path.dirname(__file__), path.pardir, 'pyteomics'))]
from pyteomics.proforma import (
PSIModModification, ProForma, TaggedInterval, parse, MassModification, ProFormaError, TagTypeEnum,
Modificatio... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/tests/test_protxml.py | tests/test_protxml.py | from os import path
import pyteomics
pyteomics.__path__ = [path.abspath(path.join(path.dirname(__file__), path.pardir, 'pyteomics'))]
from itertools import product
import unittest
from pyteomics import protxml
from data import protxml_results
import operator as op
class ProtXMLTest(unittest.TestCase):
maxDiff = No... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/tests/test_usi.py | tests/test_usi.py | from data import usi_proxi_data
from os import path
import pyteomics
pyteomics.__path__ = [path.abspath(path.join(path.dirname(__file__), path.pardir, 'pyteomics'))]
import unittest
from pyteomics.usi import USI, proxi, AGGREGATOR_KEY
from pyteomics.auxiliary import PyteomicsError
class USITest(unittest.TestCase):
... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/tests/test_trafoxml.py | tests/test_trafoxml.py | from os import path
import pyteomics
pyteomics.__path__ = [path.abspath(path.join(path.dirname(__file__), path.pardir, 'pyteomics'))]
import unittest
from itertools import product
from data import pairs
from pyteomics.openms.trafoxml import *
class TrafoXMLTest(unittest.TestCase):
maxDiff = None
def testRead(... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/tests/test_mzxml.py | tests/test_mzxml.py | import os
import pyteomics
pyteomics.__path__ = [os.path.abspath(os.path.join(os.path.dirname(__file__), os.path.pardir, 'pyteomics'))]
from itertools import product
import unittest
from pyteomics.mzxml import MzXML, read, chain
from pyteomics import xml
from data import mzxml_spectra
import tempfile
import shutil
impo... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/tests/test_electrochem.py | tests/test_electrochem.py | from os import path
import pyteomics
pyteomics.__path__ = [path.abspath(path.join(path.dirname(__file__), path.pardir, 'pyteomics'))]
import unittest
from pyteomics.electrochem import charge, pI
from pyteomics.auxiliary import PyteomicsError
class ElectrochemTest(unittest.TestCase):
def setUp(self):
pass
... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/tests/data.py | tests/data.py | """
Bulky data structures for assertion in pyteomics test suites.
"""
import numpy as np
from copy import copy
import sys
# http://stackoverflow.com/q/14246983/1258041
# updated to avoid calling np.allclose: since numpy 2.0 this results in a RecursionError
class ComparableArray(np.ndarray):
def __new__(cls, *arg... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | true |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/tests/test_unimod.py | tests/test_unimod.py | import unittest
from os import path
import pyteomics
pyteomics.__path__ = [path.abspath(path.join(path.dirname(__file__), path.pardir, 'pyteomics'))]
from pyteomics.mass import unimod
class UnimodTests(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.handle = unimod.Unimod()
def test_mo... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/pyteomics/protxml.py | pyteomics/protxml.py | """
protxml - parsing of ProteinProphet output files
================================================
Summary
-------
**protXML** is the output format of the `ProteinProphet software <http://proteinprophet.sourceforge.net/>`_.
It contains information about identified proteins and their statistical significance.
This... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/pyteomics/pylab_aux.py | pyteomics/pylab_aux.py | """
pylab_aux - auxiliary functions for plotting with pylab
=======================================================
This module serves as a collection of useful routines for data plotting with
matplotlib.
Generic plotting
----------------
:py:func:`plot_line` - plot a line.
:py:func:`scatter_trend` - plot a sca... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | true |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/pyteomics/fasta.py | pyteomics/fasta.py | """
fasta - manipulations with FASTA databases
==========================================
FASTA is a simple file format for protein sequence databases. Please refer to
`the NCBI website <http://www.ncbi.nlm.nih.gov/blast/fasta.shtml>`_
for the most detailed information on the format.
Data manipulation
---------------... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | true |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/pyteomics/pepxml.py | pyteomics/pepxml.py | """
pepxml - pepXML file reader
===========================
Summary
-------
`pepXML <http://tools.proteomecenter.org/wiki/index.php?title=Formats:pepXML>`_
was the first widely accepted format for proteomics search engines' output.
Even though it is to be replaced by a community standard
`mzIdentML <http://www.psidev... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/pyteomics/tandem.py | pyteomics/tandem.py | """
tandem - X!Tandem output file reader
====================================
Summary
-------
`X!Tandem <http://thegpm.org/tandem/>`_ is an open-source proteomic search
engine with a very simple, sophisticated application programming interface
(API): it simply takes an XML file of instructions on its command line,
a... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/pyteomics/mzmlb.py | pyteomics/mzmlb.py | # -*- coding: utf8 -*-
"""
mzmlb - reader for mass spectrometry data in mzMLb format
=========================================================
.. warning::
This is a **Provisional Implementation**. The mzMLb format has been published
but is not yet broadly available.
Summary
-------
mzMLb is an HDF5 container... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/pyteomics/mztab.py | pyteomics/mztab.py | """
mztab - mzTab file reader
=========================
Summary
-------
`mzTab <https://github.com/HUPO-PSI/mzTab>`_ is one of the standards
developed by the Proteomics Informatics working group of the HUPO Proteomics
Standard Initiative.
This module provides a way to read mzTab files into a collection of
:py:class... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/pyteomics/parser.py | pyteomics/parser.py | """
parser - operations on modX peptide sequences
=============================================
modX is a simple extension of the `IUPAC one-letter peptide sequence
representation <http://www.chem.qmul.ac.uk/iupac/AminoAcid/A2021.html>`_.
The labels (or codes) for the 20 standard amino acids in modX are the same as
i... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | true |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/pyteomics/proforma.py | pyteomics/proforma.py | '''
proforma - Proteoform and Peptidoform Notation
==============================================
ProForma is a notation for defining modified amino acid sequences using
a set of controlled vocabularies, as well as encoding uncertain or partial
information about localization. See `ProForma specification <https://www.p... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | true |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/pyteomics/mzxml.py | pyteomics/mzxml.py | """
mzxml - reader for mass spectrometry data in mzXML format
=========================================================
Summary
-------
**mzXML** is a (formerly) standard XML-format for raw mass spectrometry data storage,
intended to be replaced with **mzML**.
This module provides a minimalistic way to extract infor... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/pyteomics/ms2.py | pyteomics/ms2.py | """
ms2 - read and write MS/MS data in MS2 format
=============================================
Summary
-------
`MS2 <http://dx.doi.org/10.1002/rcm.1603>`_ is a simple
human-readable format for MS2 data. It allows storing MS2 peak lists and
exprimental parameters.
This module provides minimalistic infrastructure for... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/pyteomics/version.py | pyteomics/version.py | """
version - Pyteomics version information
=======================================
This module is provided for convenience and captures information about the current version number of Pyteomics.
Classes
-------
:py:class:`VersionInfo` - a namedtuple for version numbers that supports comparisons and can be initial... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/pyteomics/xml.py | pyteomics/xml.py | """
xml - utilities for XML parsing
===============================
This module is not intended for end users. It implements the abstract classes
for all XML parsers, :py:class:`XML` and :py:class:`IndexedXML`, and some utility functions.
Dependencies
------------
This module requres :py:mod:`lxml` and :py:mod:`nump... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | true |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/pyteomics/mzid.py | pyteomics/mzid.py | """
mzid - mzIdentML file reader
============================
Summary
-------
`mzIdentML <http://www.psidev.info/mzidentml>`_ is one of the standards
developed by the Proteomics Informatics working group of the HUPO Proteomics
Standard Initiative.
This module provides a minimalistic way to extract information from ... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/pyteomics/_schema_defaults.py | pyteomics/_schema_defaults.py | _protxml_schema_defaults = {'bools': set(),
'charlists': set(),
'floatlists': set(),
'floats': {('ASAPRatio', 'heavy2light_ratio_mean'),
('ASAPRatio', 'heavy2light_ratio_standard_dev'),
('ASAPRatio', 'ratio_mean'),
('ASAPRatio', 'ratio_standard_dev'),
('ASAPRatio_pvalue', 'adj_ratio_mean'),
('ASAPRatio_pva... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/pyteomics/peff.py | pyteomics/peff.py | """
peff - PSI Extended FASTA Format
================================
PEFF is a forth-coming standard from PSI-HUPO formalizing and extending the
encoding of protein features and annotations for building search spaces for
proteomics. See `The PEFF specification <http://www.psidev.info/peff>`_ for
more up-to-date infor... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/pyteomics/mgf.py | pyteomics/mgf.py | """
mgf - read and write MS/MS data in Mascot Generic Format
========================================================
Summary
-------
`MGF <http://www.matrixscience.com/help/data_file_help.html>`_ is a simple
human-readable format for MS/MS data. It allows storing MS/MS peak lists and
exprimental parameters.
This mo... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | true |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/pyteomics/mzml.py | pyteomics/mzml.py | """
mzml - reader for mass spectrometry data in mzML format
=======================================================
Summary
-------
mzML is a standard rich XML-format for raw mass spectrometry data storage.
Please refer to `psidev.info <http://www.psidev.info/index.php?q=node/257>`_
for the detailed specification of ... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/pyteomics/ms1.py | pyteomics/ms1.py | """
ms1 - read and write MS/MS data in MS1 format
=============================================
Summary
-------
`MS1 <http://dx.doi.org/10.1002/rcm.1603>`_ is a simple
human-readable format for MS1 data. It allows storing MS1 peak lists and exprimental parameters.
This module provides minimalistic infrastructure for... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/pyteomics/achrom.py | pyteomics/achrom.py | """
achrom - additive model of polypeptide chromatography
=====================================================
Summary
-------
The additive model of polypeptide chromatography, or achrom, is the most basic
model for peptide retention time prediction. The main equation behind
achrom has the following form:
.. math::... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | true |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/pyteomics/traml.py | pyteomics/traml.py | """
traml - targeted MS transition data in TraML format
===================================================
Summary
-------
TraML is a standard rich XML-format for targeted mass spectrometry method definitions.
Please refer to `psidev.info <http://www.psidev.info/traml>`_
for the detailed specification of the format ... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/pyteomics/electrochem.py | pyteomics/electrochem.py | """
electrochem - electrochemical properties of polypeptides
========================================================
Summary
-------
This module is used to calculate the
electrochemical properties of polypeptide molecules.
The theory behind most of this module is based on the Henderson-Hasselbalch
equation and was ... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/pyteomics/usi.py | pyteomics/usi.py | """
usi - Universal Spectrum Identifier (USI) parser and minimal PROXI client
=========================================================================
Summary
-------
`USI <http://www.psidev.info/usi>`_ is a standardized method of referencing a specific
spectrum in a dataset, possibly attached to an interpretation. T... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/pyteomics/openms/idxml.py | pyteomics/openms/idxml.py | """
idxml - idXML file reader
=========================
Summary
-------
**idXML** is a format specified in the
`OpenMS <http://open-ms.sourceforge.net/about/>`_ project.
It defines a list of peptide identifications.
This module provides a minimalistic way to extract information from idXML
files. You can use the old ... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
levitsky/pyteomics | https://github.com/levitsky/pyteomics/blob/17e7f6bad7d273846de0a398a3870afe10c74be6/pyteomics/openms/featurexml.py | pyteomics/openms/featurexml.py | """
featurexml - reader for featureXML files
========================================
Summary
-------
**featureXML** is a format specified in the
`OpenMS <http://open-ms.sourceforge.net/about/>`_ project.
It defines a list of LC-MS features observed in an experiment.
This module provides a minimalistic way to extrac... | python | Apache-2.0 | 17e7f6bad7d273846de0a398a3870afe10c74be6 | 2026-01-05T07:13:10.794267Z | false |
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