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from behave import given, when, then
import json
import os
from django.contrib.auth.models import User, Group
from pybel import readfile
@given('I have valid salted compound')
def step(context):
context.inchi = "InChI=1S/2CHF3O3S.Cu/c2*2-1(3,4)8(5,6)7;/h2*(H,5,6,7);/q;;+2/p-2"
context.post_data["ctab"] = """
... | strets123/cbh_chembl_ws_extension | cbh_chembl_ws_extension/features/steps/salts.py | Python | mit | 3,160 | [
"Pybel",
"RDKit"
] | 1663aae05a10a49641f1a4f02832b2b7c5ee1b69b3a9c65e2d1c8ccc3f81def2 |
#!/usr/bin/python
# -*- coding: UTF-8 -*-
# This file is part of pyAlienFX.
#
# pyAlienFX is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any... | jrobeson/pyalienfx | pyAlienFX.py | Python | gpl-3.0 | 59,796 | [
"VisIt"
] | 1fc37231d12adea6e2ad7d6187fa4567de70f58cee5c603a56879029d4d9bb5c |
from __future__ import print_function
import pkg_resources
import string
import random
import os
import sys
from biomaj.bank import Bank
from biomaj.mongo_connector import MongoConnector
from biomaj_core.config import BiomajConfig
from biomaj_core.utils import Utils
import logging
class SchemaVersion(object):
"... | genouest/biomaj | biomaj/schema_version.py | Python | agpl-3.0 | 9,035 | [
"BLAST"
] | 7656f5e90e1dc0a5d29a50420b1c59ffe227386d8d382287eb96610d7488e5fc |
#!/usr/local/sci/bin/python
#*****************************
#
# Detect outliers from station and neighbour
#
#
#************************************************************************
# SVN Info
#$Rev:: 116 $: Revision of last commit
#$Author:: rdunn ... | rjhd2/HadISD_v2 | neighbour_utils.py | Python | bsd-3-clause | 28,477 | [
"Gaussian"
] | ba95ed90cf9179ae8746d2c72f485906bc77943a0561bd3fd400643e14b2a477 |
#!/usr/bin/env python3
import numpy as np
np.set_printoptions(suppress=True, precision=4)
from pyscf.geomopt.berny_solver import optimize
from pyscf import gto, scf
def opt_h2o():
mol = gto.M(atom="""
O -0.00000000 -0.11081188 0.00000000
H 0.78397589 0.4432475... | eljost/pysisyphus | tests_staging/test_internal_coordinates/berny_pyscf.py | Python | gpl-3.0 | 2,599 | [
"PySCF"
] | a34718356d4ffd51ea3b75e438e606eefc98cf404436af2fd35abae6f379103f |
'''
synbiochem (c) University of Manchester 2015
synbiochem is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
__CHEMICAL_NAMESPACE = {
# value (namespace) corresponds to identifiers.org:
'bigg': 'bigg.metabolite',
'... | synbiochem/biochem4j | sbcdb/namespace_utils.py | Python | mit | 1,781 | [
"VisIt"
] | 4a00880bee6691504e44673143da5804016a3d1732df234269a21d2e3b5b0910 |
#!/usr/bin/python
#
# Copyright 2012 Google Inc.
#
# 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 applicable law or a... | NealJMD/Grinbox-server | oauth2.py | Python | gpl-3.0 | 12,394 | [
"VisIt"
] | 64b26d156c0ae3597cf61b52765a113626e3dd4607b81a9281441c1b365f202f |
import subprocess
import re
import json
from collections import namedtuple
def is_valid(author):
if 'fail@studentrobotics.org' in author.email:
return False
if 'BRIAN' in author.name:
return False
return True
DATA_REGEX = re.compile('^\s*(\d+)\t(.*) <(.*)>$')
Author = namedtuple('Author', ... | prophile/srweb-jekyll | utils/authors.py | Python | mit | 946 | [
"Brian"
] | ef31a5a35d3e61150c6291e235932fc93e95a3500734c708b22e7aabc49ee803 |
import copy
import csv
import datetime
import json
import mock
import re
import urllib
import pyquery
from cStringIO import StringIO
from nose.tools import eq_, ok_, assert_raises
from nose.plugins.skip import SkipTest
from django.test.client import RequestFactory
from django.test.utils import override_settings
from ... | twobraids/socorro | webapp-django/crashstats/crashstats/tests/test_views.py | Python | mpl-2.0 | 187,898 | [
"VisIt"
] | de553ee77dbbbf7d62703ef23391a4ca1a91a618aa934fc50df958cdf7de21c5 |
# Author: Travis Oliphant
# 2003
#
# Feb. 2010: Updated by Warren Weckesser:
# Rewrote much of chirp()
# Added sweep_poly()
from __future__ import division, print_function, absolute_import
import numpy as np
from numpy import asarray, zeros, place, nan, mod, pi, extract, log, sqrt, \
exp, cos, sin, polyval, po... | valexandersaulys/airbnb_kaggle_contest | venv/lib/python3.4/site-packages/scipy/signal/waveforms.py | Python | gpl-2.0 | 14,814 | [
"Gaussian"
] | 756e8e483cb76bf31627f6c82fb29bb9e6a78e3c579d9e217b9695fd520ae8aa |
from django.views.generic import ListView, DetailView, TemplateView
# from django.views.generic import TemplateView, RedirectView, CreateView
# from django.views.generic import UpdateView, DeleteView
from django.shortcuts import render
from django.shortcuts import get_object_or_404
from django.shortcuts import get_list... | robjordan/unesco_project | unesco/whsites/views.py | Python | apache-2.0 | 3,453 | [
"VisIt"
] | e57d189b5677a9f9a7b0866cf7dc5142bc754e9e181fbcb1a7adc05cf495340d |
#! /usr/bin/env python
# Copyright 2019 John Hanley.
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the "Software"),
# to deal in the Software without restriction, including without limitation
# the rights to use, copy, modify, me... | jhanley634/testing-tools | problem/code_explode/exploder.py | Python | mit | 7,690 | [
"VisIt"
] | 90113e646a5e98ca401dd3131a1e50ed560765139ff3ded847e9cab24a804f6d |
# Copyright (c) 2015-2017 Cisco Systems, Inc.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to
# deal in the Software without restriction, including without limitation the
# rights to use, copy, modify, merge... | retr0h/molecule | test/unit/command/test_init.py | Python | mit | 4,998 | [
"Galaxy"
] | 0fb2f4302d80b6fe4dc67a3f50ba8f1a12af91d8e2c2ac21347ed0bdb1f8634d |
"""
Multivariate Conditional and Unconditional Kernel Density Estimation
with Mixed Data Types.
References
----------
[1] Racine, J., Li, Q. Nonparametric econometrics: theory and practice.
Princeton University Press. (2007)
[2] Racine, Jeff. "Nonparametric Econometrics: A Primer," Foundation
and Trends in Eco... | yarikoptic/pystatsmodels | statsmodels/nonparametric/kernel_density.py | Python | bsd-3-clause | 24,750 | [
"Gaussian"
] | 6d2f28aafa8f3332b6792b373d297ea4c8b629d3d548430cd3c4fe17a499cf8d |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
***************************************************************************
qgis.v.kernel.rast.py
---------------------
Date : February 2010
Copyright : (C) 2010 by Radim Blazek
Email : radim dot blazek at g... | mhugent/Quantum-GIS | src/plugins/grass/scripts/qgis.v.kernel.rast.py | Python | gpl-2.0 | 2,584 | [
"Gaussian"
] | 0d5e3b601ef74fd2c73e4768db7e6b04acb044b72ce3c88278fa42f68f946326 |
import pzgram
from datetime import datetime, timedelta
import SQL_function
import apiKey
import useful_function
bot = pzgram.Bot(apiKey.apiBot)
# IDEA
# TODO: MORE EMOJI!!!!!
# Subjects Emoji
def start_command(chat, message):
chat.send('Hi, *'+message.sender.first_name+'*\n'
'Welcome to schoolDia... | infopz/pzGram_schoolDiary | main.py | Python | gpl-3.0 | 29,506 | [
"VisIt"
] | de162552b3c3e8fe023576040a25ddbf72c3c9c47c4a1fc294ecbbd6632b348f |
import re
from django.utils.translation import ugettext as _
from eulxml.xpath import parse as parse_xpath
from eulxml.xpath.ast import FunctionCall, Step, UnaryExpression, serialize
from corehq.apps.case_search.xpath_functions import (
XPATH_FUNCTIONS,
XPathFunctionException,
)
from corehq.apps.es import fi... | dimagi/commcare-hq | corehq/apps/case_search/filter_dsl.py | Python | bsd-3-clause | 9,832 | [
"VisIt"
] | 5489efb9c416b22c251408c8ad3eb604fa1be88521ed9d9c5ae10a188cdb61af |
"""PyDock scoring function parameters"""
default_hydrogen_extension = '.H'
default_amber_extension = '.amber'
# Energetic terms
scoring_vdw_weight = 0.1
vdw_input_file = 'vdw.in'
default_max_electrostatics_cutoff = 1
default_min_electrostatics_cutoff = -1
default_vdw_cutoff = 1.0
# AMBER
amber_elec_constant = 18.2223... | brianjimenez/lightdock | lightdock/scoring/cpydock/energy/parameters.py | Python | gpl-3.0 | 321 | [
"Amber"
] | fffb4425ee0b85c2f18d28547c16f86c4fc9c576df101aa30e425e6ba4f4a364 |
#!/usr/bin/env python
"""
Definitions for the ectyper project
"""
import os
ROOT_DIR = os.path.dirname(os.path.abspath(__file__))
DATA_DIR = os.path.join(ROOT_DIR, 'Data')
WORKPLACE_DIR = os.getcwd()
SEROTYPE_ALLELE_JSON = os.path.join(DATA_DIR, 'ectyper_alleles_db.json')
#ECOLI_MARKERS = os.path.join(DATA_DIR,... | phac-nml/ecoli_serotyping | ectyper/definitions.py | Python | apache-2.0 | 2,126 | [
"BLAST"
] | d77a9ea8542107d821ae45ee7f0363fe8ac7feaffc47a5dd6bb1ee60ec27d830 |
# -*- coding: utf-8 -*-
'''
Support for the Git SCM
'''
from __future__ import absolute_import
# Import python libs
import copy
import logging
import os
import re
import shlex
from distutils.version import LooseVersion as _LooseVersion
# Import salt libs
import salt.utils
import salt.utils.files
import salt.utils.ite... | smallyear/linuxLearn | salt/salt/modules/git.py | Python | apache-2.0 | 123,499 | [
"Octopus"
] | 317c053af79038bb7ff750ac16d5b6649444dd3612fd16a8d9175cb58d109a1b |
# -*- coding: utf-8 -*-
"""Strongly connected components.
"""
# Copyright (C) 2004-2013 by
# Aric Hagberg <hagberg@lanl.gov>
# Dan Schult <dschult@colgate.edu>
# Pieter Swart <swart@lanl.gov>
# All rights reserved.
# BSD license.
import networkx as nx
from networkx.utils.decorators import not_implemen... | jni/networkx | networkx/algorithms/components/strongly_connected.py | Python | bsd-3-clause | 9,636 | [
"VisIt"
] | ab71f78d6be354e66d75fbb48ec9d53d837447732439e609cc34a547d9184323 |
#!/usr/bin/python
#
# PyIRCBot
# Copyright (C) Pierre Jaury 2011 <pierre@jaury.eu>
#
# PyIRCBot is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | kaiyou/pyircbot | src/pyircbot/basics.py | Python | gpl-3.0 | 3,971 | [
"VisIt"
] | c30e9dfc8d51c91fe69341569bc0637ab860c28f5a2b52d586e7c1d7a108b909 |
#!/usr/bin/env python3
import logging
import numpy as num
import utm
import os.path as op
import copy
import hashlib
import time
from datetime import datetime as dt
from scipy import interpolate
from pyrocko.guts import Object, Float, StringChoice, String, Timestamp, \
Dict, load
from pyrocko.dataset.topo import s... | pyrocko/kite | src/scene.py | Python | gpl-3.0 | 38,821 | [
"Gaussian"
] | 2f26fc99c3137e2a5cff857e15b364eeec7d973ba215a14d01487fd744014c59 |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
#
ANSIB... | hryamzik/ansible | lib/ansible/modules/network/avi/avi_l4policyset.py | Python | gpl-3.0 | 4,121 | [
"VisIt"
] | a06d072f83395f723beec7eb8d344d40a1327f23f3f1179af01434d6e4930094 |
import ocl
import camvtk
import time
import vtk
import datetime
import math
def drawFiber(myscreen, f, fibercolor=camvtk.red):
inter = f.getInts()
for i in inter:
if not i.empty():
ip1 = f.point( i.lower )
ip2 = f.point( i.upper )
myscreen.addActor( camvtk.Line(p1=(ip... | tectronics/opencamlib | scripts/fiber_09_ballcutter.py | Python | gpl-3.0 | 3,565 | [
"VTK"
] | 1a6909740f02cd8b38b3252178fe4de6482c8d645748b96235e0c155aeda6fc2 |
# -*- coding: utf-8 -*-
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Mathieu Blondel <mathieu@mblondel.org>
# Robert Layton <robertlayton@gmail.com>
# Andreas Mueller <amueller@ais.uni-bonn.de>
# Philippe Gervais <philippe.gervais@inria.fr>
# Lars Buitinck
... | Titan-C/scikit-learn | sklearn/metrics/pairwise.py | Python | bsd-3-clause | 46,720 | [
"Gaussian"
] | c85d20a5dd442dbc529f364e4407b9e2f294035ac974e26216649ad538ed8541 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | kain88-de/mdanalysis | testsuite/MDAnalysisTests/test_imports.py | Python | gpl-2.0 | 2,512 | [
"MDAnalysis"
] | d5d52bcdf9d9678f4baa49fc7a84c314e3d65cbee822b4b84dfeb48ea4718e9a |
#!/usr/bin/env python
########################################################################
# $HeadURL: svn+ssh://svn.cern.ch/reps/dirac/DIRAC/trunk/DIRAC/Core/scripts/dirac-create-svn-tag.py $
# File : dirac-create-svn-tag
# Author : Adria Casajus
################################################################... | avedaee/DIRAC | Core/scripts/dirac-create-svn-branch.py | Python | gpl-3.0 | 6,912 | [
"DIRAC"
] | e0571dd4403a036206c36d080cb1c130858dd755bd31911a4a445ebd429814bb |
#!/usr/bin/env python
# coding: utf-8
from datetime import datetime
from HTMLParser import HTMLParser
import argparse
import json
import os
import sys
import urllib2
###############################################################################
# Options
#############################################################... | wodore/wodore-gae | magic.py | Python | mit | 6,241 | [
"VisIt"
] | 9fcbc397e81eee47f3aded2e8367ea1ee1e15c7cc7b76d607afe40a0324e5ecb |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# 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 applica... | drpngx/tensorflow | tensorflow/contrib/autograph/converters/call_trees.py | Python | apache-2.0 | 12,348 | [
"VisIt"
] | cf11d84ddf1aae9cd1eb1a000f5d4d27206eeeebe888b04911b03511016f7709 |
from typing import Union, Collection, Optional, Any, Sequence, Tuple, List
import numpy as np
import pandas as pd
from anndata import AnnData
from ..._settings import settings
from ..._compat import Literal
def mnn_correct(
*datas: Union[AnnData, np.ndarray],
var_index: Optional[Collection[str]] = None,
... | theislab/scanpy | scanpy/external/pp/_mnn_correct.py | Python | bsd-3-clause | 5,829 | [
"Gaussian"
] | bc9f0d03b115eb533d774af46cfb200c8e54b3add31ebda844f667636d97f18d |
#-------------------------------------------------------------------------------
# Copyright (c) 2012 Gael Honorez.
# All rights reserved. This program and the accompanying materials
# are made available under the terms of the GNU Public License v3.0
# which accompanies this distribution, and is available at
# htt... | IDragonfire/modular-client | src/galacticWar/defenseitem.py | Python | gpl-3.0 | 2,059 | [
"Galaxy"
] | 62de45405b0db6ade7b298d6835df662e8ff06b32b4cacccf8f26434959fd61e |
# This file is part of PyEMMA.
#
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
#
# PyEMMA is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either vers... | marscher/PyEMMA | pyemma/coordinates/tests/test_stride.py | Python | lgpl-3.0 | 4,463 | [
"MDTraj"
] | d3699d41353c1edaebb8eba2adef898e1678c4c2dcd85b98b227b64fae6f19ad |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkImageHSIToRGB(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.... | nagyistoce/devide | modules/vtk_basic/vtkImageHSIToRGB.py | Python | bsd-3-clause | 489 | [
"VTK"
] | 362c2f07dbbd8018f8a4d6fd47fafaeb56bf1048d6bcaca64ac8879ab17e1e01 |
"""
unidesign.spatial.generator
---------------------------
(Statistical) generators of spatial geometry derived from small sets of parameters
* e.g. L-Neuron
* NETMORPH http://www.ncbi.nlm.nih.gov/pubmed/19672726 http://netmorph.org/
* Hermann Cuntz http://transcurve.net/profiles/blogs/blueprint-for-the-brain
* http:... | unidesigner/unidesign | unidesign/spatial/generator/tree.py | Python | bsd-3-clause | 436 | [
"NEURON"
] | d305f63e664e6b03d4dd92a1ec6984e7486ee1723ef30d5aa2f835b35e52323b |
# -*- coding: utf-8 -*-
#
# MCell Quick Reference Guide documentation build configuration file, created by
# sphinx-quickstart on Mon Aug 11 08:51:36 2014.
#
# 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
# autogen... | mcellteam/mcell_qrg | conf.py | Python | lgpl-2.1 | 8,697 | [
"MCell"
] | 863c39b615af6ee0e8c4c717ca6a2fd91d345ee072ba4984bc579b0098fab871 |
#!/usr/bin/env python3
"""Render a tree from a predicate root pair.
Normally run as a web service.
Usage:
ontree server [options]
ontree [options] <predicate-curie> <root-curie>
ontree --test
Options:
-a --api=API Full url to SciGraph api endpoint
-k --key=APIKEY apikey for SciG... | tgbugs/pyontutils | nifstd/nifstd_tools/ontree.py | Python | mit | 43,210 | [
"NEURON"
] | 06363e7cb1cdec8fee9b5dff1baa382d88dff0331aeb24539b272ebea1c0b9df |
from __future__ import absolute_import
from Qpyl.core.qparameter import QPrm
from Qpyl.core.qlibrary import QLib
from Qpyl.core.qstructure import QStruct
from Qpyl.core.qtopology import QTopology
def is_close(a, b, rel_tol=1e-09, abs_tol=0.0):
return abs(a-b) <= max(rel_tol * max(abs(a), abs(b)), abs_tol)
def te... | mpurg/qtools | tests/Qpyl/core/qtopology_test.py | Python | mit | 2,952 | [
"Amber"
] | 0a9bc6fd8d7d2b6e7b05c5305bbab78189911794ded029849cee157ab809f4b2 |
"""nodes: An easy-to-use graph-oriented programming model for Python.
"""
import collections
import copy
import types
Settable = 0x1
Serializable = 0x2
Saved = Settable | Serializable
Overlayable = 0x4
class Graph(object):
"""A directed, acyclic graph of nodes.
"""
def __init__(self):
... | adamdonahue/nodes | nodes/nodes.py | Python | bsd-2-clause | 37,912 | [
"VisIt"
] | 3be8b0ae26d7630037593b56b712ac97703abaeb5f32e0cbbeed63c4fb06609e |
import numpy as np # from numpy import mgrid, empty, sin, pi
import pandas as pd
from scipy import special
import meshio
import pooch
import os
import optimesh
import sys
import pyacvd
import pyvista as pv
np.set_printoptions(threshold=sys.maxsize)
def Cart_to_Spherical_np(xyz):
# physics notation
# print(x... | kayarre/Tools | mesh/gen_sphere.py | Python | bsd-2-clause | 28,938 | [
"VTK"
] | a8402eebd5568ce85eb155c9482accffbfcb76dc69a21351fc13d16abb0993e8 |
'''
Utilities for dealing with galaxy catalogs, projecting catalogs into pixelated maps, etc.
'''
import numpy as np
from pixell import enmap,utils
import healpy as hp
from astropy.io import fits
from orphics import maps
class Pow2Cat(object):
def __init__(self,ells,clgg,clkg=None,clkk=None,depth_map=None,lmax=N... | msyriac/orphics | orphics/catalogs.py | Python | bsd-2-clause | 26,273 | [
"Galaxy"
] | e43bf6e5249bbe3a33be7bf41963918b474e5ce353908ffd32d7922a2fb024c4 |
# Copyright (c) 2017 ARM Limited
# All rights reserved.
#
# The license below extends only to copyright in the software and shall
# not be construed as granting a license to any other intellectual
# property including but not limited to intellectual property relating
# to a hardware implementation of the functionality ... | powerjg/gem5-ci-test | src/python/m5/SimObject.py | Python | bsd-3-clause | 57,936 | [
"VisIt"
] | 4208e109605201e343f0c999cd34db7013962fb3eb10bb5b83da1f1eef8877f2 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2014 - 2019 Adam.Dybbroe
# Author(s):
# Adam.Dybbroe <adam.dybbroe@smhi.se>
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, ei... | adybbroe/mesan_compositer | mesan_compositer/netcdf_io.py | Python | gpl-3.0 | 22,923 | [
"NetCDF"
] | 1e87fe1e6c3abd153370664b007be331c86dc564726c7b0d086a1db6f2a7e441 |
"""
================================
Gaussian Mixture Model Selection
================================
This example shows that model selection can be performed with
Gaussian Mixture Models using information-theoretic criteria (BIC).
Model selection concerns both the covariance type
and the number of components in the ... | RPGOne/Skynet | scikit-learn-0.18.1/examples/mixture/plot_gmm_selection.py | Python | bsd-3-clause | 3,310 | [
"Gaussian"
] | e6472319e9d482b226e4f5991f64baac6f4d5232b3c9f57d34c712d1e6ff3882 |
from common import HTTPBruteModule, ModuleMetadata, WebRequests, Modules
class madnesspro_v114(HTTPBruteModule):
def __init__(self):
md = ModuleMetadata(
module_name="madnesspro_v114",
bot_name="Madness Pro v114",
description="Distributed Denial of Service botnet capabl... | bwall/BAMF | bamfbrute/modules/madnesspro_v114.py | Python | mit | 1,339 | [
"Brian"
] | f59f95ab419e3a40cf5eee46987075aa9e8edd7dc034cadedb7923f3bf3f4179 |
""" Test functions for stats module
WRITTEN BY LOUIS LUANGKESORN <lluang@yahoo.com> FOR THE STATS MODULE
BASED ON WILKINSON'S STATISTICS QUIZ
https://www.stanford.edu/~clint/bench/wilk.txt
Additional tests by a host of SciPy developers.
"""
from __future__ import division, print_function, absolute_imp... | Eric89GXL/scipy | scipy/stats/tests/test_stats.py | Python | bsd-3-clause | 185,775 | [
"Gaussian"
] | bd71358e16bf1512871e4195f9516d32573f413ed2d49b4061331dd2531cf870 |
##################################################################
# Copyright 2018 Open Source Geospatial Foundation and others #
# licensed under MIT, Please consult LICENSE.txt for details #
##################################################################
"""Unit tests for complex validator
"""
import uni... | bird-house/PyWPS | tests/validator/test_complexvalidators.py | Python | mit | 6,759 | [
"NetCDF"
] | fc1630b3bb3192aefb47efc8acbf9e767686b66b438a4bd9c451581b8f8a4190 |
# -*- coding: utf-8 -*-
from glob import glob
import numpy as np
#from scipy import interpolate
#from ext_func.occultquad import occultquad
#from ext_func.rsky import rsky
import matplotlib.pyplot as plt
import os.path
import time
from collections import OrderedDict
try:
from helper_funcs import poly_lc_cwrapper,... | savvytruffle/cauldron | keblat.py | Python | mit | 144,830 | [
"Gaussian"
] | 2c1591eec6016b432f7018bbb689b17740affda035c40c43d7a977700cf8de56 |
"""
run_pcaproj
Main file for running the projection algorithm
1) import statistical model
2) project statistical model to 2D
3) align statistical model with 2D airway
4) optimise the fit of the statistical components
Benjamin Irving
2013 / 08 / 25
"""
print __doc__
#Python modules
import numpy as np
import time, co... | benjaminirving/Mesh-Silhouette-Projection | Example2_pca_mesh.py | Python | bsd-3-clause | 3,017 | [
"Mayavi"
] | 5fe5594fbaad964125232fba0c2bbc68a057041f575578d978094ae8c866b9e3 |
import os.path as op
from sfepy.base.base import *
import sfepy.base.ioutils as io
from sfepy.fem import ProblemDefinition
from sfepy.solvers.generic import solve_direct
from application import Application
def assign_standard_hooks(obj, get, mod):
"""
Set standard hook function attributes from `mod` to `obj` ... | olivierverdier/sfepy | sfepy/applications/simple_app.py | Python | bsd-3-clause | 4,220 | [
"VTK"
] | 7731e22d930ea6706b08335374544b17a6e76410dfa638dfc3cbe67812b70c12 |
#!/usr/bin/env python
from Bio import SeqIO
from collections import OrderedDict
import Psl
import truthtable as tt
import numpy as np
import argparse
import sys
import re
# CIGAR matcher for aligning regions
matcher = re.compile(r'([0-9]+)M')
def count_aligned(cigar):
"""
Sum the length of aligned regions... | koadman/proxigenomics | simulation/pipeline/bin/alignmentToTruth.py | Python | gpl-2.0 | 14,719 | [
"BWA"
] | 1e2827de3b2c2f39d995210fefb0f404f26fbab4c63fdc3e50d887906cc99ae8 |
#
# Copyright (c) 2010 Brian E. Granger
#
# This file is part of pyzmq.
#
# pyzmq is free software; you can redistribute it and/or modify it under
# the terms of the Lesser GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option)... | takluyver/pyzmq | zmq/tests/test_log.py | Python | lgpl-3.0 | 4,187 | [
"Brian"
] | b99c42f2485a7921e319bb7201f04aab8bde31ef48eb52667c478edadf742bd5 |
import json
from urllib.parse import quote
from django.conf import settings
from django.contrib.auth.models import AnonymousUser, User
from django.contrib.contenttypes.models import ContentType
from django.http import Http404
from django.test import RequestFactory, TestCase
from django.urls import reverse
import mock... | pinax/pinax-likes | pinax/likes/tests/test_views.py | Python | mit | 10,460 | [
"Brian"
] | 9c6da9b894cdd5de177f566771757ebe6f5d4b30291d29358ec541a08a8279c7 |
# -*- coding: utf-8 -*-
import json
import itertools
from hashlib import md5
from math import isnan
from datetime import datetime
from flask import current_app
from importlib import import_module
from fastnumbers import isfloat
from flask_mongoengine import DynamicDocument
from mongoengine import CASCADE, signals
from... | materialsproject/MPContribs | mpcontribs-api/mpcontribs/api/contributions/document.py | Python | mit | 9,673 | [
"VisIt"
] | a0982df88d6c76697bb00d8439403e7699cd026f4c818dd2f0e29af35d6edc97 |
from __future__ import with_statement
from fabric.api import local
from fabric.colors import green, yellow, red
from db import cache
import config
import os
def vpsql():
"""Connect to the acousticbrainz database running on vagrant."""
local("psql -h localhost -p 15432 -U postgres acousticbrainz")
def vssh(... | abhinavjain241/acousticbrainz-server | fabfile.py | Python | gpl-2.0 | 1,424 | [
"GULP"
] | e7a723ea67187b24fa16afddd91eef56bc3a0a64e9f4a8e6e64a3325a93dceba |
import matplotlib.pyplot as plt
import matplotlib as mpl
import numpy as np
"""
This module contains function for predicting fracture times in signals.
"""
# apply a fracture predictor to a whole dataset
def applyFracturePredictor(dataSet, fracturePredictor, **kwargs):
"""
This function takes a datas... | thonstad/acoustical_monitoring | pythonCode/fracture_prediction.py | Python | bsd-3-clause | 4,800 | [
"Gaussian"
] | aa5c3ccc02538f995a0467d9be51d66a124d2bca467462f4f26f0ea0e3700f01 |
# This file is part of the Fluggo Media Library for high-quality
# video and audio processing.
#
# Copyright 2010-1 Brian J. Crowell <brian@fluggo.com>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foun... | fluggo/Canvas | fluggo/logging.py | Python | gpl-3.0 | 2,619 | [
"Brian"
] | 5d1b375f6afc1a0cdac8845c66336c442e523a071acb749ec167d4b1154cdca2 |
import abc
import datetime
import enum
import typing
import jsii
import jsii.compat
import publication
from jsii.python import classproperty
import aws_cdk.aws_iam
import aws_cdk.aws_lambda
import aws_cdk.aws_sns
import aws_cdk.aws_sqs
import aws_cdk.core
__jsii_assembly__ = jsii.JSIIAssembly.load("@aws-cdk/aws-sns-... | randyzingle/tools | kub/services/archive/cdk/python/sample-app/.env/lib/python3.6/site-packages/aws_cdk/aws_sns_subscriptions/__init__.py | Python | apache-2.0 | 13,735 | [
"CDK"
] | 3c2e9dd5cc0a37b97a209ecc6a6c86774d298f52d53a8cc427ff145f8d93cc31 |
""" Page Object for Log In Page """
from . import common
from ..page_locators import common as locators
class LoginPageObject(common.CommonPageObject):
""" Page Object for Log In Page """
def visit(self):
""" Go to the login page """
return self.go_to_page('login')
def fill_out_login_for... | Gimpneek/jobseek | jobseekr/cv/features/steps/page_objects/login.py | Python | agpl-3.0 | 805 | [
"VisIt"
] | 7ac2cca66df246dc029b9d860b413ece214c646d6b5fcf11d880c5f09ae1a835 |
# -*- coding: utf-8 -*-
# Generated by the protocol buffer compiler. DO NOT EDIT!
# source: google/cloud/websecurityscanner_v1alpha/proto/crawled_url.proto
import sys
_b = sys.version_info[0] < 3 and (lambda x: x) or (lambda x: x.encode("latin1"))
from google.protobuf import descriptor as _descriptor
from google.pro... | tseaver/google-cloud-python | websecurityscanner/google/cloud/websecurityscanner_v1alpha/proto/crawled_url_pb2.py | Python | apache-2.0 | 4,689 | [
"VisIt"
] | 8aed6e276f7139f8ecc71c6149bb03e12bad238308e1fbe92c22f20e39933885 |
# coding=utf8
#
# Copyright 2013 Dreamlab Onet.pl
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation;
# version 3.0.
# This library is distributed in the hope that it will be useful,
# bu... | tikan/rmock | src/rmock/runners/http/proxy/choosers.py | Python | lgpl-3.0 | 1,082 | [
"VisIt"
] | 5f0b7b4c87b60a528d9a67b0d133f711c234a3107d43210151eade1dc4beea69 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS Instructor Dashboard.
"""
import ddt
from common.test.acceptance.fixtures.certificates import CertificateConfigFixture
from common.test.acceptance.fixtures.course import CourseFixture
from common.test.acceptance.pages.common.auto_auth import AutoAuthPage
from ... | stvstnfrd/edx-platform | common/test/acceptance/tests/lms/test_lms_instructor_dashboard.py | Python | agpl-3.0 | 8,857 | [
"VisIt"
] | 52ceea62dbce7557b843725316f65300f8b7b7f4dcbd0b8473feaf71b3c1f947 |
import re
import numpy
import sys
import os
try:
import __builtin__ # for Python 2
except ImportError:
import builtins as __builtin__ # for Python 3
col_types = {'^di': 3,
'^ext_f': 3,
'^ext_t': 3,
'^f': 3,
'^fix': 3,
'^i': 1,
'^ma': 1,
'^mo': 1,
'^omega': 3,
'^omega_b': 3,
'^omega_l': 3,
'^p': 3,
... | gizeminci/espresso | tools/blockfile.py | Python | gpl-3.0 | 5,472 | [
"ESPResSo"
] | 69b5956e3295994973ff9eb69687c0a6d5d4731f9170610a0abefecc820fd06c |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module defines the events signaled by abinit during the execution. It also
provides a parser to extract these events form the main output file and the log file.
"""
from __future__ import unicode_litera... | xhqu1981/pymatgen | pymatgen/io/abinit/events.py | Python | mit | 28,225 | [
"ABINIT",
"NetCDF",
"pymatgen"
] | 6a3cea1ed37e67a3cdf9d235c3256e53cdcb34b7dc74bb4ec02adf621fdde275 |
""" Class that collects utilities used in Accounting and Monitoring systems
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from DIRAC.Core.Utilities import Time
class DBUtils(object):
def __init__(self, db, setup):
self._acDB = db
self._set... | yujikato/DIRAC | src/DIRAC/AccountingSystem/private/DBUtils.py | Python | gpl-3.0 | 11,834 | [
"DIRAC"
] | 065bec284da79d25f3549a603be0b0cd7a00fa48b7c9e478e8186135bc893bb6 |
"""
# Notes:
- This simulation seeks to emulate the COBAHH benchmark simulations of (Brette
et al. 2007) using the Brian2 simulator for speed benchmark comparison to
DynaSim. However, this simulation includes CLOCK-DRIVEN synapses, for direct
comparison to DynaSim's clock-driven architecture. The synaptic connec... | asoplata/dynasim-benchmark-brette-2007 | Brian2/brian2_benchmark_COBAHH_clocksyn_lodens_compiled_0002.py | Python | gpl-3.0 | 3,912 | [
"Brian"
] | 7a13309d8437d9e8974f9fa47346a40ed81d0db021651e97ebf3951120c06e82 |
'''
MPI script for infilling missing values in incomplete Tmin/Tmax station time series.
Must be run using mpiexec or mpirun.
'''
from mpi4py import MPI
from netCDF4 import Dataset
from twx.db import StationDataDb, STN_ID, NNRNghData, create_quick_db
from twx.db.station_data import get_mean_varname, get_variance_varna... | jaredwo/topowx | scripts/step16_mpi_infill_stn_daily.py | Python | gpl-3.0 | 15,262 | [
"NetCDF"
] | e4f07a0cef9a9e9cff1f5c7f435bb4738df0863c221d48cb4fdab606fdb6f2be |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RApe(RPackage):
"""Analyses of Phylogenetics and Evolution
Functions for reading, wri... | LLNL/spack | var/spack/repos/builtin/packages/r-ape/package.py | Python | lgpl-2.1 | 2,332 | [
"Bioconductor"
] | f4ddb1282ce2ef8aa68ddfdc4aa82e4b2c60eca73e651e96756511d3959a82e7 |
from core.datacontainer import DataContainer
from bio.brainregion import BrainRegion
from PyQt5 import QtGui, QtWidgets, QtCore
class BrainRegionGUI(QtWidgets.QGroupBox):
"""This is the dock widget for the properties of a selected data item(s)"""
def __init__(self, data_container):
if not isinstance(data_conta... | zibneuro/brainvispy | gui/brainregiongui.py | Python | bsd-3-clause | 7,799 | [
"VTK"
] | 738a933fd377a4d6fefd557cf54b9756cddb0db4bdac2d693c3afcc6d8feb863 |
## \package Aspects A collection of global (enum) constants
# \author Brian Muller <mullerb@musc.edu>
ALLSPACENAMES = ["biological_process", "molecular_function", "cellular_component"]
BP = "biological_process"
MF = "molecular_function"
CC = "cellular_component"
ROOTS = { BP : "GO:0008150",
MF : "GO:00036... | aswarren/GOGranny | GOGranny/Aspects.py | Python | gpl-2.0 | 356 | [
"Brian"
] | fcb8bdde609f6584a10aa82bd93a7a9901aa8958ca2dce0dd833f49d555e5b08 |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# 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 applica... | shayben/procrustes-net | TF/cifar10.py | Python | apache-2.0 | 20,408 | [
"Gaussian"
] | d36381ee2415263d8a4e988465d97709fbba515551aaaa8acd2935d3f3c2559d |
from builtins import object
import numpy as np
from cs231n.layers import *
from cs231n.fast_layers import *
from cs231n.layer_utils import *
class ThreeLayerConvNet(object):
"""
A three-layer convolutional network with the following architecture:
conv - relu - 2x2 max pool - affine - relu - affine - sof... | d-li14/CS231n-Assignments | assignment2/cs231n/classifiers/cnn.py | Python | gpl-3.0 | 5,939 | [
"Gaussian"
] | ee53b83365b1c7acc6808ad58f90f1324ce9f3e46574ed0570acadb436ac9a6f |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
class Migration(migrations.Migration):
dependencies = [
('visit', '0047_auto_20150809_2313'),
]
operations = [
migrations.AddField(
model_name='location',
nam... | koebbe/homeworks | visit/migrations/0048_auto_20150809_2319.py | Python | mit | 685 | [
"VisIt"
] | 1d89305ef6ff52d432c3333161707c39527f2655bc8810b60975be360a2bd058 |
import sygma
from rdkit import Chem, Geometry
from rdkit.Chem import AllChem
def test_treenode_init():
"""Test init of TreeNode class"""
# generate phenol molecule
mol = Chem.MolFromSmiles('c1ccccc1O')
node = sygma.TreeNode(mol)
# test if inchikey is generated correctly
assert node.ikey == "... | 3D-e-Chem/sygma | sygma/test/test_units.py | Python | gpl-3.0 | 1,151 | [
"RDKit"
] | c1b8834d181288572cc4cebae178b63d550aebc4eef103a7f8e414754111220c |
from __future__ import division, print_function, absolute_import
import sys
import subprocess
MODULES = [
"scipy.cluster",
"scipy.cluster.vq",
"scipy.cluster.hierarchy",
"scipy.constants",
"scipy.fftpack",
"scipy.integrate",
"scipy.interpolate",
"scipy.io",
"scipy.io.arff",
"s... | Eric89GXL/scipy | scipy/_lib/tests/test_import_cycles.py | Python | bsd-3-clause | 1,284 | [
"NetCDF"
] | fd565abc4652ffe59f8fe2725fb71592c8c5c6aaaabfc184afa96eb41746f1a5 |
import json
import os
from shutil import copytree
from subprocess import CalledProcessError, check_call, check_output
import pytest
import pkgpanda.build
import pkgpanda.build.cli
from pkgpanda.util import expect_fs
def get_tar_contents(filename):
return set(check_output(["tar", "-tf", filename]).decode().split... | movicha/dcos | pkgpanda/build/tests/test_build.py | Python | apache-2.0 | 6,392 | [
"VisIt"
] | 70413465652d8a15c5c3a9610fa22b8c9efeca1114cd54b0696cf89d637873f9 |
# The original enum test suite, applied to enum_native.
import enum_native as enum
import inspect
import pydoc
import unittest
from collections import OrderedDict
from enum_native import Enum, IntEnum, EnumMeta, unique
from io import StringIO
from pickle import dumps, loads, PicklingError, HIGHEST_PROTOCOL
# for pick... | ze-phyr-us/fastenum | test_enum_native.py | Python | mit | 56,820 | [
"MOE"
] | db84956bdddca819a40b531d61994804049afa03c0badeebb56643bf2adfb0b4 |
#!/usr/bin/env python
import re
import sys
import time
from Bio import SeqIO
from StringIO import StringIO
from Bio import AlignIO
import os
import argparse
"""
Transcriptome Annotation by Modular Algorithms (TAMA)
TAMA Variant Caller
Author: Richard I. Kuo
This script cvalls variants from a ba... | GenomeRIK/tama | tama_go/call_variants/tama_variant_caller.py | Python | gpl-3.0 | 234,754 | [
"pysam"
] | 88d1947db7fab21f10f8fcaf7ff7057c081404711500dab0ab0b52810bde5e4f |
#!/usr/bin/env python
# Copyright 2015 The Kubernetes 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 appli... | gambol99/kubernetes | cluster/juju/layers/kubernetes-master/reactive/kubernetes_master.py | Python | apache-2.0 | 62,093 | [
"CDK"
] | 2d37156365472d91b9fa12b6766c8fc52ee27e1a388eda92e3a8c25fab664a4e |
# -*- coding: UTF-8 -*-
"""
``RSEM_prep``
-----------------------------------------------------------------
:Authors: Menachem Sklarz
:Affiliation: Bioinformatics core facility
:Organization: National Institute of Biotechnology in the Negev, Ben Gurion University.
A module for running ``rsem-prepare-reference``:
Re... | bioinfo-core-BGU/neatseq-flow_modules | neatseq_flow_modules/mapping/RSEM_prep.py | Python | gpl-3.0 | 7,176 | [
"Bowtie"
] | 91ea9fa7ca67e989480ec4fec7b43eb2a8f59831d3a7ff5b7c1baa4c7415fe7f |
#!/usr/bin/env python
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import os
import sys
import glob
import shutil
import subprocess
from monty.serialization import loadfn, dumpfn
from pymatgen import SETT... | johnson1228/pymatgen | pymatgen/cli/pmg_config.py | Python | mit | 6,791 | [
"VASP",
"pymatgen"
] | 3cf469dce759f8402a7f039fcf85c69a99b94e99a1acccbb81cd57fa482ac7dc |
# Ricky Harding, Caden Bringhurst, Josh Jimenez, Brian
def abs(x):
"""This function finds the distance X is from 0."""
if x < 0:
return x * -1
else:
return x
def fact(x):
""" This function calculates the factorial of the number x """
if x == 0:
return 1
elif x < 0:
return "Not a real number"
else:
r... | alveyworld-dev/calculator7 | team2.py | Python | apache-2.0 | 339 | [
"Brian"
] | 4576f9dd5872f76580b25427965c9696530a938cd561b167258db6dc78d5c4ab |
import os
from src.core import prep
from sgprocessor import *
def ProcessSg(p, opts):
if opts.anno == True:
if 'BEDDB' not in os.environ:
p.error('$BEDDB Not Exist. See README')
str_path_sgfq = opts.sg
str_nm = os.path.basename(os.path.splitext(opts.sg)[0])
str_proj = 'aux'
str_... | bm2-lab/cage | src/core/sg/interface_sg.py | Python | mit | 2,004 | [
"BWA"
] | 6e10d13b11ebc4689e66839656b3eeaf9605d00173bd23eebf42f6749aa69130 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Moodle Development Kit
Copyright (c) 2012 Frédéric Massart - FMCorz.net
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the Lic... | mudrd8mz/mdk | mdk/jira.py | Python | gpl-3.0 | 13,497 | [
"VisIt"
] | 9d4d6be40214903443f8051a1fce86798af011c810d6d021b17952ff85ab9267 |
"""
https://leetcode.com/explore/featured/card/june-leetcoding-challenge-2021/603/week-1-june-1st-june-7th/3764/
"""
from typing import List
"""
taken from:
https://leetcode.com/discuss/explore/june-leetcoding-challenge-2021/1244554/Max-Area-of-Island-or-JS-Python-Java-C%2B%2B-or-Simple-DFS-Recursion-Solution-w-Expla... | kalyons11/kevin | kevin/leet/max_area_of_island.py | Python | mit | 956 | [
"VisIt"
] | 0323634403dfd6505e0d38181ce1f5ddae05118ac1fa1cd7481ecbfa41aadfa5 |
# -*- coding: utf-8 -*-
# Part of Odoo. See LICENSE file for full copyright and licensing details.
import base64
import datetime
import random
import re
import string
import requests
from lxml import html
from werkzeug import urls, utils
from odoo import models, fields, api, _
from odoo.tools import ustr
URL_REGEX ... | Aravinthu/odoo | addons/link_tracker/models/link_tracker.py | Python | agpl-3.0 | 10,059 | [
"VisIt"
] | 254e1af933da3805ad7f6a18ceed50f31096b475f9bc099b9d587c04357f3510 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# .. _poisson-topology-example:
#
# .. py:currentmodule:: dolfin_adjoint
#
# Topology optimisation of heat conduction problems governed by the Poisson equation
# ==================================================================================
#
# .. sectionauthor:: Patri... | pf4d/dolfin-adjoint | examples/poisson-topology/poisson-topology-optizelle.py | Python | lgpl-3.0 | 12,634 | [
"ParaView",
"VTK"
] | b36df8b1fa9b450995e6198a03c9f8d445e5e33f535a7dbc5930b921354602c5 |
########################################################################
# $HeadURL $
# File: CleanFTSDBAgent.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/05/17 07:46:34
########################################################################
""" :mod: CleanFTSDBAgent
=====================
.. modul... | Sbalbp/DIRAC | DataManagementSystem/Agent/CleanFTSDBAgent.py | Python | gpl-3.0 | 4,740 | [
"DIRAC"
] | bccc58064a823cfedda2ca2fa39906acf9906f7bd02c27c6067e7110bbe9d24f |
# -*- coding: utf-8 -*-
#
# brunel_alpha_nest.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the Licen... | jhnnsnk/nest-simulator | pynest/examples/brunel_alpha_nest.py | Python | gpl-2.0 | 13,272 | [
"NEURON"
] | ea97f6ce4ecc742d13b0ab67c4ade853d1217a3be9258d075c38251fa1d8335f |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | CDSherrill/psi4 | psi4/share/psi4/databases/BAKERJCC96.py | Python | lgpl-3.0 | 16,142 | [
"Psi4"
] | 57eea1c14fa51674520fddd586a0e14c24ca715346905d675eab8914ec9c14ae |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkInterpolateDataSetAttributes(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | nagyistoce/devide | modules/vtk_basic/vtkInterpolateDataSetAttributes.py | Python | bsd-3-clause | 515 | [
"VTK"
] | 527aaa16138509db240d10d6360d04019581c70da420a46afc96d120a88f7c1f |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Nick Hall
# Copyright (C) 2011 Tim G L Lyons
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of t... | Forage/Gramps | gramps/gui/displaystate.py | Python | gpl-2.0 | 20,352 | [
"Brian"
] | 11a7546d30e65366cd32adc47f9914d69e92a9a4e1a67d58b80dc01a367b0711 |
#! /usr/bin/env python
""" This script convolutes the calculated oscillator strengts for different snapshots in a MD trajectory and plot the average spectrum.
Usage:
convolution.py -sigma 0.05 -n 2 -nm True -write True
Use the sigma flag to change the sigma parameter of the gaussian functions
used in the convolution. ... | SCM-NV/qmworks-namd | scripts/qmflows/convolution.py | Python | mit | 3,694 | [
"Gaussian"
] | 8d00dcda450345234255b0d4f687945787dba24ede641359a4b3efefd62b0725 |
"""
Photovoltaic thermal panels
"""
import os
import time
from itertools import repeat
from math import *
import geopandas as gpd
import numpy as np
import pandas as pd
from geopandas import GeoDataFrame as gdf
from numba import jit
import cea.inputlocator
import cea.utilities.parallel
import cea.utilities.worke... | architecture-building-systems/CEAforArcGIS | cea/technologies/solar/photovoltaic_thermal.py | Python | mit | 42,510 | [
"EPW"
] | 6b0f8569ebcf3fd0b86747f9ef88f5d3e98528f1b7d278865d0483562ca7122e |
"""
===============================================================
Inverted pendulum balancing (:mod:`raam.examples.pendulum`)
===============================================================
An inverted pendulum (http://en.wikipedia.org/wiki/Inverted_pendulum)
is a pendulum which has its center of mass above its... | marekpetrik/RAAM | raam/examples/pendulum.py | Python | mit | 3,737 | [
"Gaussian"
] | 1c2556c0eb99483388612fead3d09802513938d8be3f89a51da373a8bf4ee3d7 |
#!/usr/bin/env python
################################################################################
# Copyright (C) 2014, 2015 GenAP, McGill University and Genome Quebec Innovation Centre
#
# This file is part of MUGQIC Pipelines.
#
# MUGQIC Pipelines is free software: you can redistribute it and/or modify
# it und... | ccmbioinfo/mugqic_pipelines | bfx/trinity.py | Python | lgpl-3.0 | 10,211 | [
"BLAST",
"Bowtie"
] | c1249c95aa1a64b498be627483f2be756e0385ce054fe9c5dc34ee935c2ceb58 |
import argparse
import multiprocessing
import warnings
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Alphabet import generic_protein
from sklearn.externals import joblib
from sklearn.preprocessing import normalize
from lib.hmmer import hmmstats
from lib.hmmer import hmmscan
def ... | trappedInARibosome/go-model | go_predict_blast.py | Python | mit | 3,616 | [
"BLAST"
] | 46e9281e010e3000238ecf6a765659fbb278355b318878004a7fbdd87264a0c8 |
import _modeller
import physical
class restraint_form(object):
"""Base class for all restraint forms"""
_builtin_index = None
_user_index = None
_use_array = False
ndim = None
def __init__(self, group, features, modality, parameters):
if '_builtin_index' not in self.__class__.__dict__... | bjornwallner/proq2-server | apps/modeller9v8/modlib/modeller/forms.py | Python | gpl-3.0 | 9,807 | [
"Gaussian"
] | 4146271bc6b6a3bf8f993935f603b32bc8ac06e1d90de78f4682665b35c45561 |
#-*- coding:utf-8 -*-
"""
Implementation of some image ditortion teniques
Author: Chienli Ma
Date: 2015.01.08
Incentive:
These distortion techniques were first designed for MNIST and grayscale.
I modified them so that it can deal with RGB images.
However, the performance is not very good the when dealing ... | ChienliMa/Distortions | distortions.py | Python | gpl-2.0 | 12,341 | [
"Gaussian"
] | 9e7f450726819bcc628389fb055453b2fef6a3225a4a769714e691d638f2c5f4 |
from BAMF_Detect.preprocessors.common import Preprocessor, Preprocessors
from pefile import PE
from tempfile import mkstemp
from os import write, close, remove
from subprocess import Popen, PIPE
def is_upx_compressed(data):
pe = PE(data=data)
for entry in pe.sections:
if entry.Name.startswith("UPX0") ... | bwall/bamfdetect | BAMF_Detect/preprocessors/UPXPreprocessor.py | Python | mit | 1,706 | [
"Brian"
] | 0dc76ccda53dd5164bd32124f25ee0f518d9e646e46d5aedd514a2237b766d26 |
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