text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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|---|---|---|---|---|---|---|---|
import ast
import inspect
import copy
import six
import random
import sys
import textwrap
if sys.version_info[0] == 3 and sys.version_info[1] > 2:
_TryNode = ast.Try
else:
_TryNode = ast.TryExcept
if six.PY3:
def getFunctionArgumentIdentifiers(node):
return set(arg.arg for arg in node.args.args)
... | KholdStare/generators-to-coroutines | generators_to_coroutines/ast_transformers.py | Python | bsd-2-clause | 11,280 | [
"VisIt"
] | d89aed4a308a1d885126f7f5742a1356f235c13c63eaaae6a3d284eba18bc9f6 |
# -*- coding: utf-8 -*-
"""
ga_analyze.py
=============
.. moduleauthor:: Geoff Hutchison <geoffh@pitt.edu>
"""
import sys
import argparse
from collections import deque
from multiprocessing import Pool
from scipy import ndimage, misc
from skimage import morphology
import numpy as np
from PIL import Image
import itert... | LangmuirSim/langmuir | LangmuirPython/ga2d/ga_analyze.py | Python | gpl-2.0 | 16,957 | [
"VisIt"
] | 6705e8b539a8fd434e6ea27b1b79f0f316a5040555436dd2bfb5569124bb7b53 |
import os
import glob
import tarfile
import shutil
import logging
from optparse import OptionParser
from Pegasus.db import connection
from Pegasus.tools import utils
from Pegasus.command import LoggingCommand, CompoundCommand
from Pegasus.db.schema import *
log = logging.getLogger(__name__)
class SubmitDirException... | elainenaomi/sciwonc-dataflow-examples | sbbd2016/experiments/1-postgres/3_workflow_full_10files_primary_nosh_nors_annot_with_proj_3s/pegasus.bDkvI/pegasus-4.6.0/lib/python2.7/dist-packages/Pegasus/submitdir.py | Python | gpl-3.0 | 18,513 | [
"VisIt"
] | a043c92a391b911ac2f9464d02bac270fe11abc056953caa43b05acfe2c58525 |
"""
========================
Decimating scalp surface
========================
This can be useful to reduce computation time when
using a cloud of digitization points for coordinate alignment
instead of e.g. EEG-cap positions.
"""
# Authors: Denis Engemann <denis.engemann@gmail.com>
# Alexandre Gramfort <ale... | rajegannathan/grasp-lift-eeg-cat-dog-solution-updated | python-packages/mne-python-0.10/examples/forward/plot_decimate_head_surface.py | Python | bsd-3-clause | 1,082 | [
"Mayavi"
] | 0f1e13b3212384c04241a2d3418e9604553924bfd39a07787227e08f019f9716 |
import numpy as np
import scipy
import re
import os
import hashlib
import csb
from csb.bio.io.wwpdb import StructureParser
def chunks(l, n):
""" Yield successive n-sized chunks from l.
"""
for i in xrange(0, len(l), n):
yield l[i:i+n]
class ScatteringFactor(object):
"""
Cacluates the ... | mmechelke/bayesian_xfel | bxfel/core/structure_factor.py | Python | mit | 18,608 | [
"Gaussian",
"Mayavi"
] | a6186ec87c1161a6a885c77a69d3eed37a8d5834c086a0edef61f970b9d969a6 |
# -*- coding: utf-8 -*-
"""
Some tools for measuring line profiles of emission lines.
Author: R. Lombaert
"""
import os
import numpy as np
from scipy import mean,sqrt,log, std,median
from scipy import argmin,argmax,array
from scipy.integrate import trapz
from matplotlib import pyplot as plt
from astropy import unit... | IvS-KULeuven/ComboCode | cc/data/LPTools.py | Python | gpl-3.0 | 33,638 | [
"Gaussian"
] | ecd2942aab7b248c0b7b3431566de3b5dae1bf900863a81af9d99ef0eeb36aa5 |
# proxy module
from __future__ import absolute_import
from mayavi.tools.sources import *
| enthought/etsproxy | enthought/mayavi/tools/sources.py | Python | bsd-3-clause | 89 | [
"Mayavi"
] | 22598be9ff0ea014fd89dbd5494b66a641c31cb0d05887d0afbcadf0f1bef28e |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
import math
import numpy as np
from .core import Kernel1D, Kernel2D, Kernel
from .utils import KernelSizeError
from ..modeling import models
from ..modeling.core import Fittable1DModel, Fittable2DModel
from ..utils.decorators import deprecated_renamed_a... | funbaker/astropy | astropy/convolution/kernels.py | Python | bsd-3-clause | 32,546 | [
"Gaussian"
] | 9c45a19c8e74da0c26d242cf6c8ef504f1ad856a775983d550ebfcd84cc38210 |
from ase import *
a = Atoms('H2', positions=[(0, 0, 0), (0, 0, 1.1)])
a.pbc[0] = 1
assert a.pbc.any()
assert not a.pbc.all()
a.pbc = 1
assert a.pbc.all()
a.cell = (1, 2, 3)
a.cell *= 2
a.cell[0, 0] = 3
assert not (a.cell.diagonal() - (3, 4, 6)).any()
| freephys/python_ase | ase/test/properties.py | Python | gpl-3.0 | 253 | [
"ASE"
] | 4d48cc351d3c8c4e54ea907e83ade2d853d1dcb71b447c028e1936d25c39fd63 |
#!/usr/bin/env python
# Copyright (c) 2011-2021, wradlib developers.
# Distributed under the MIT License. See LICENSE.txt for more info.
# flake8: noqa
"""
Raw Data I/O
============
Please have a look at the tutorial :ref:`/notebooks/fileio/wradlib_radar_formats.ipynb`
for an introduction on how to deal with different ... | wradlib/wradlib | wradlib/io/__init__.py | Python | mit | 1,036 | [
"NetCDF"
] | 19f7478c95f0640b20881b75469229029d77d27c7117f97e362d217fa542ab20 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under ... | MDAnalysis/mdanalysis | package/MDAnalysis/topology/GMSParser.py | Python | gpl-2.0 | 3,947 | [
"GAMESS",
"MDAnalysis"
] | 47081610add331da0ac52175b0ec9a2fec3da693e8665130c6d7e235a690d762 |
########################################################################
# File : StalledJobAgent.py
########################################################################
""" The StalledJobAgent hunts for stalled jobs in the Job database. Jobs in "running"
state not receiving a heart beat signal for more than stalle... | petricm/DIRAC | WorkloadManagementSystem/Agent/StalledJobAgent.py | Python | gpl-3.0 | 22,527 | [
"DIRAC"
] | f48d4424b18cd6b3cf8fd99cf246f36648f8dfda4636dc1abbe13b35a23c8cfc |
# coding=utf-8
# Copyright 2020 The TF-Agents 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable la... | tensorflow/agents | tf_agents/bandits/environments/wheel_py_environment.py | Python | apache-2.0 | 6,966 | [
"Gaussian"
] | 20b625d83df961c2aaa566ae958c6f0c87ad6adce5d5af852be7981f5d2a1694 |
# Copyright (C) 2009 by Eric Talevich (eric.talevich@gmail.com)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Base classes for Bio.Phylo objects.
All object representations for phylogenetic tree... | asherkhb/coge | bin/last_wrapper/Bio/Phylo/BaseTree.py | Python | bsd-2-clause | 36,414 | [
"Biopython",
"Octopus"
] | 6f738951c0d8d5ac0a1818757c0f32d0205ff01c4aa622bddeff784c789a7ea0 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
urlpat... | sethmenghi/mixify_django | config/urls.py | Python | bsd-3-clause | 1,458 | [
"VisIt"
] | 169f1d19ed60dec08fe01caf3050341896b0705a8e5773c20ce468810b6ef50d |
import matplotlib
matplotlib.use('Agg')
from matplotlib.pyplot import *
import localgroup
import triangle
import sklearn
from sklearn import mixture
import numpy as np
import pickle
import matplotlib.patches as mpatches
import sys
exist = int(sys.argv[1])
if exist:
save_path = '/afs/slac.stanford.edu/u/ki/mwillia... | drphilmarshall/LocalGroupHaloProps | final_scripts/gmm_prior_pair.py | Python | gpl-2.0 | 10,310 | [
"Gaussian"
] | 53536742679c74f57b1ddf374d717d30c5a96c052fe2525bc82ae04a899f9b92 |
""" This module handles everything related to log parsing """
import re # For parsing the log file (regular expressions)
import os # For working with files on the operating system
import logging # For logging
from game_objects.item import Item
from game_objects.floor import Floor, Curse
from game_objects.... | Hyphen-ated/RebirthItemTracker | src/log_parser.py | Python | bsd-2-clause | 12,176 | [
"GULP"
] | 221367f2720beadaa8a2e8c6bd01eb667bf5a77364dc69a31dbfae7abad6e5f5 |
import numpy as np
import numpy.linalg as la
from ase.units import Hartree
from gpaw.wavefunctions.lcao import add_paw_correction_to_overlap
from gpaw.lcao.overlap import NewTwoCenterIntegrals as TwoCenterIntegrals
from gpaw.lfc import BasisFunctions
from gpaw.utilities import unpack
from gpaw.utilities.tools import d... | robwarm/gpaw-symm | gpaw/lcao/projected_wannier.py | Python | gpl-3.0 | 14,480 | [
"ASE",
"GPAW"
] | fd150ad8a613518a81dca9fd0a8bc0d38e2cc5ca821f2967ba935198277ea1ce |
import os
import pprint
# thanks https://stackoverflow.com/a/36693250
def package_files(directory, extensions):
"""
Walk package directory to make sure we include all relevant files in
package.
"""
paths = []
for (path, directories, filenames) in os.walk(directory):
for filename in fil... | vorwerkc/pymatgen | test.py | Python | mit | 621 | [
"pymatgen"
] | e800be143292725c20a6bfd9e7b18e58dd667bdd5e9218200eef88cd1dd2491f |
#!/usr/bin/env python
"""
Artificial Intelligence for Humans
Volume 1: Fundamental Algorithms
Python Version
http://www.aifh.org
http://www.jeffheaton.com
Code repository:
https://github.com/jeffheaton/aifh
Copyright 2013 by Jeff Heaton
Licensed under the Apache License, Version 2... | trenton3983/Artificial_Intelligence_for_Humans | vol1/python-examples/examples/example_logit.py | Python | apache-2.0 | 4,421 | [
"VisIt"
] | 1c37b136ad6dba055fff233bfef0534cedec212fa276fa38d83c34bfe87e9ada |
"""
Basic function objects.
TransferFns: accept and modify a 2d array
ResponseFns: accept two 2d arrays and return a scalar
LearningFns: accept two 2d arrays and a scalar, return one of the arrays modified
"""
# CEBALERT: Documentation is just draft.
import numpy
import param
from imagen.transferfn import Transfer... | Tasignotas/topographica_mirror | topo/base/functionfamily.py | Python | bsd-3-clause | 3,061 | [
"NEURON"
] | e60d5b3f5499592fffb6945fa3d7339d03e8d0164281c2745171d2fb1c32ac26 |
#! /usr/bin/env python
from __future__ import absolute_import
from __future__ import print_function
import sys
import os
import ez_setup
import hashlib
import time, random
import re
try:
from urllib2 import quote
from urllib2 import urlopen
from urllib2 import HTTPError
except ImportError:
from urllib.p... | fmaguire/ete | setup.py | Python | gpl-3.0 | 5,987 | [
"VisIt"
] | 82f51186c3755d1d12ca1fa75d16b93acf9d705b5564698df0ade35c9e670804 |
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2003-2005 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 lcc & Robert Jerome
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU ... | arunkgupta/gramps | gramps/plugins/rel/rel_pt.py | Python | gpl-2.0 | 18,927 | [
"Brian"
] | 5be614bc635e0b9af5210ed58b49e7e5a2754758014bea5746d84fd4b38e24e7 |
# Copyright 2008 by Michiel de Hoon. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Parser for XML results returned by NCBI's Entrez Utilities. This
parser is used by the re... | bryback/quickseq | genescript/Bio/Entrez/Parser.py | Python | mit | 21,386 | [
"Biopython"
] | 53c5bb90100fb07ee0ef95926d830594ad4b5e43f5a7355a14612f645bf0fac5 |
#!/usr/local/bin/python3
# This work is licensed under the Creative Commons Attribution 3.0 United
# States License. To view a copy of this license, visit
# http://creativecommons.org/licenses/by/3.0/us/ or send a letter to Creative
# Commons, 171 Second Street, Suite 300, San Francisco, California, 94105, USA.
# f... | ohnorobo/pokemon | transparent.py | Python | mit | 1,475 | [
"VisIt"
] | 42971a35cf57c24ed3f2fc7cf099902480702b86688246f31309805b4f8fb053 |
# -*- coding: utf-8 -*-
import ast
import base64
import csv
import glob
import itertools
import logging
import operator
import datetime
import hashlib
import os
import re
import simplejson
import time
import urllib
import urllib2
import urlparse
import xmlrpclib
import zlib
from xml.etree import ElementTree
from cStri... | quanvm009/codev7 | openerp/addons/web/controllers/main.py | Python | agpl-3.0 | 68,922 | [
"VisIt"
] | 27c2deae111fc31bcf085915ecbeb3e136ecae69d1d4de31fed615ad825287cf |
#!/usr/bin/env python
# coding=utf8
#
# Copyright (c) Jakub Olczyk
# Published under GNU General Public License version 2 or above
# For full text of the license visit www.gnu.org/licenses/gpl.html
""" Main module with the abstraction for getting input from user """
from src.Utils import Singleton
from src.Screen imp... | jakub-olczyk/miniVim | src/Input.py | Python | gpl-3.0 | 2,984 | [
"VisIt"
] | 71e699a6e4cc7d1fcb6333dc18631e06018d8fbd3cbb4065b190c6de1ad8c55d |
########################################################################
# $HeadURL $
# File: RequestValidatorTests.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2012/09/25 13:49:20
########################################################################
""" :mod: RequestValidatorTests
=====================... | sposs/DIRAC | RequestManagementSystem/test/RequestValidatorTests.py | Python | gpl-3.0 | 5,106 | [
"DIRAC"
] | 161390dd61ae81b293fa1a9b0986055f2d1a46aee7164dfb7bdb757bd067a1ea |
########################################################################
#
# (C) 2015, Chris Houseknecht <chouse@ansible.com>
#
# This file is part of Ansible
#
# Ansible 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 Fo... | thaim/ansible | lib/ansible/galaxy/token.py | Python | mit | 5,634 | [
"Galaxy"
] | 083f0b0dbd4cad9d8e564b0e3afaa8b3198d5c38a046c2a8eea058e8ba99d86f |
"""
A vtkTkImageViewerWidget for python, which is based on the
vtkTkImageWindowWidget.
Specify double=1 to get a double-buffered window.
Created by David Gobbi, Nov 1999
"""
from __future__ import absolute_import
import math, os, sys
import vtk
if sys.hexversion < 0x03000000:
# for Python2
import Tkinter as... | mspark93/VTK | Wrapping/Python/vtk/tk/vtkTkImageViewerWidget.py | Python | bsd-3-clause | 11,101 | [
"VTK"
] | 794187766551c47b812211b541357dc65be91541e3c9ffff8acdb33e3cc4f870 |
# -*- coding: utf-8 -*-
"""
Build the scaffold PDB to be used as the basis of the final parameterized
model. Also need to store data about regions to be completed.
SASSIE: Copyright (C) 2011 Joseph E. Curtis, Ph.D.
This program is free software: you can redistribute it and/or modify
it under the terms of ... | madscatt/zazzie | src_2.7/sassie/build/pdbrx/pdbrx/scaffold_builder.py | Python | gpl-3.0 | 23,423 | [
"CHARMM"
] | f3d036d3131422173e47b83822417811a30d24b125f6821703abe251c16ca57e |
"""
# 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 does NOT include synapses, for better
comparison to Figure 5 of (Goodman and Brette, 2008) - although it uses the... | asoplata/dynasim-benchmark-brette-2007 | output/Brian2/brian2_benchmark_COBAHH_nosyn_0064/brian2_benchmark_COBAHH_nosyn_0064.py | Python | gpl-3.0 | 3,344 | [
"Brian"
] | 4f8f38af7bc259af61bea4510de47658803feb726bde13a5c4cf608a28144209 |
__all__ = ["pdb2permList"]
def pdb2permList(pdbfname):
"""
Create permutation groups from an Amber pdb file
Adapted from svn/SCRIPTS/make_perm.allow/perm-py.pdb
Input:
pdb file name
- with terminal residues start with 'N' or 'C'
e.g. ALA -> 'NALA... | kjs73/pele | pele/amber/obsolete/pdb2permlist.py | Python | gpl-3.0 | 44,564 | [
"Amber",
"CHARMM",
"OpenMM"
] | 43be38ffb38176718aa7cebe1d32554b32514818a12fff2b24ac0d40bbacc3a9 |
"""Concatenate conformers from each SDF file in directory into one SDF file.
Author: Seth Axen
E-mail: seth.axen@gmail.com
"""
import sys
import os
import glob
import rdkit
import rdkit.Chem
from python_utilities.io_tools import smart_open
from e3fp.conformer.util import mol_from_sdf
FIRST = 3
def mol_conf_id_fro... | keiserlab/e3fp-paper | project/fingerprint_comparison/sdf_files_to_file.py | Python | lgpl-3.0 | 1,686 | [
"RDKit"
] | d408828d14ac656439f84231cfbe588722e05409773c699748f24fc0768acb82 |
# -*- coding: utf-8 -*-
"""Deletion functions to supplement :mod:`pybel.struct.mutation.deletion`."""
from typing import Iterable, Tuple
from pybel import BELGraph
from pybel.dsl import BaseEntity
from pybel.struct.pipeline import in_place_transformation
from ..summary.edge_summary import pair_is_consistent
__all__... | pybel/pybel-tools | src/pybel_tools/mutation/deletion.py | Python | mit | 1,029 | [
"Pybel"
] | 31d1887166d0444b857d568f1a866aaab6de1577aa86392cf1d1435e0a5550df |
#!/usr/bin/env python
"""
Verify all subtests contain required minimum sections, ini's doc all options
"""
import os
import re
import sys
import docutils.nodes
from dockertest.documentation import SubtestDoc
from dockertest.documentation import PretestDoc
from dockertest.documentation import IntratestDoc
from dockertes... | luwensu/autotest-docker | run_checkdocs.py | Python | gpl-2.0 | 9,931 | [
"VisIt"
] | de246a9a6d101e42c5a98d6afd23e9442161656f61879713bc42b371d1206d85 |
import json
import os
import unittest
import datetime
import time
from botocore.exceptions import ClientError
from envs import env
from kev import (Document,CharProperty,DateTimeProperty,
DateProperty,BooleanProperty,IntegerProperty,
FloatProperty)
from kev.exceptions import QueryErr... | kevproject/kev | kev/tests/documents.py | Python | gpl-3.0 | 15,007 | [
"Brian"
] | 1c14ea963de6893a1fe07d10c129f57640949504b35f3446a65c1072a467a769 |
try: paraview.simple
except: from paraview.simple import *
from paraview import coprocessing
#--------------------------------------------------------------
# Code generated from cpstate.py to create the CoProcessor.
# ----------------------- CoProcessor definition -----------------------
def CreateCoProcessor():... | acbauer/miniFE-2.0_ref_Catalyst | src/gridwriter.py | Python | lgpl-3.0 | 3,963 | [
"ParaView"
] | b567856414c5b74cdf42fe38b99f5da24a9df562d8e12e9929b289d22e7e4fa9 |
"""
Functions to visualize an Experiment.
"""
from __future__ import print_function
import math
import sys
from past.builtins import xrange
from hyperopt.mongoexp import MongoJobs
try:
unicode = unicode
except NameError:
basestring = (str, bytes)
else:
basestring = basestring
# -- don't import this here be... | denik/vwoptimize | vwoptimizelib/third_party/hyperopt/plotting.py | Python | mit | 20,590 | [
"Gaussian"
] | 51e77a8b526609db45d437c0be6452b3b430bbaf80a885611de7cf1db23883db |
"""Bravais.py - class for generating Bravais lattices etc.
This is a base class for numerous classes setting up pieces of crystal.
"""
import math
import numpy as np
from ase.atoms import Atoms
import ase.data
class Bravais:
"""Bravais lattice factory.
This is a base class for the objects producing various ... | freephys/python_ase | ase/lattice/bravais.py | Python | gpl-3.0 | 18,212 | [
"ASE",
"CRYSTAL"
] | 013edfaedf1cf1259900ff9a6f1f94dc12b362aaf11957da0e8a0faa1effb0cb |
#!/usr/bin/env python
# for tgi cluster:
#/gapp/x64linux/opt/pythonbrew/venvs/Python-2.7.6/gemini/bin/python
# for uva cluster:
import pysam
import sys
import argparse
from argparse import RawTextHelpFormatter
import string
from string import *
__author__ = "Ira Hall (ihall@genome.wustl.edu) and Colby Chiang (cc2qe@... | cc2qe/bamkit | bamtofastq.py | Python | mit | 6,859 | [
"BWA",
"pysam"
] | f85ee14022477d1fd21fc8d17b19e890160e6f32ebb287a3e55cb34c64c4ff46 |
# context.py - changeset and file context objects for mercurial
#
# Copyright 2006, 2007 Matt Mackall <mpm@selenic.com>
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 or any later version.
from node import nullid, nullrev, short, hex, bin
from i18n im... | iaddict/mercurial.rb | vendor/mercurial/mercurial/context.py | Python | mit | 45,249 | [
"VisIt"
] | aa62df4bd5177dc8a8e5eda2a0b6ba97f6b55fa99d9e814327d1def85162371d |
from Bio.Blast.Applications import NcbiblastnCommandline
from Bio import SeqIO
import StringIO
import os.path
import glob
import re
fasta_in_dir = '' # directory of fasta files to check
fasta_out_dir = '' # directory to save hits fasta too
blast_db = '' # repbase local blast db
file_hits_file = 'te_file_hits.csv' # ... | lcoghill/transeeker | transeeker.py | Python | bsd-3-clause | 3,382 | [
"BLAST"
] | ad90117a45fb506659c577176a0cc2af1aa65982f2bc54b6e12f214d8af51b59 |
"""Structural variation detection for split and paired reads using lumpy.
Uses lumpyexpress for lumpy integration and samblaster for read preparation:
https://github.com/GregoryFaust/samblaster
https://github.com/arq5x/lumpy-sv
"""
import contextlib
import os
import sys
import shutil
import vcf
from bcbio import uti... | biocyberman/bcbio-nextgen | bcbio/structural/lumpy.py | Python | mit | 13,358 | [
"BWA"
] | 97459da8be230dc6f724795fa8317eb788a11d2783ee4c645398043c488773b9 |
branding = {
"toolsName" : "Citrix XenServer Tools",
"installerProductName" : "Citrix XenServer Tools Installer",
"manufacturer" : "Citrix",
"installerKeyWords" : "Citrix XenServer Windows Installer",
"shortTools" : "XenTools",
"installerServiceName" : "Citrix Xen... | xenserver/win-xenguestagent | src/branding/branding.py | Python | bsd-2-clause | 7,258 | [
"VMD"
] | 8f576a6a50c7ba76044f19581f9ac8c513e5fcb2ffc13972d9f558e03497a193 |
"""
ex20170225_Model_REG.py
Build Model REG from Godley & Lavoie (Chapter 6)
Uses the model builder from the sfc_models.gl_book sub-package.
Copyright 2017 Brian Romanchuk
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 ... | brianr747/SFC_models | sfc_models/examples/scripts/ex20170225_Model_REG.py | Python | apache-2.0 | 1,795 | [
"Brian"
] | 2cf44cb1c64b72ecb6737b51b844707b15d51a51e5869d2911a1e80cef88df8c |
"""
Tools for spike train analysis
Includes an object class, SpikingEvent, that is useful for detecting and
analyzing firing events within a spike raster. Also provides functions for
binning spike times into a histogram (`binspikes`) and a function
for smoothing a histogram into a firing rate (`estfr`)
"""
import sys
... | baccuslab/pyret | pyret/spiketools.py | Python | mit | 10,135 | [
"Gaussian"
] | cb830d637a8eb462d296afb8078a1e40c61d4714431edde31808674df51ab564 |
"""Test the JobInfo"""
import unittest
import sys
from StringIO import StringIO
from mock import MagicMock as Mock
from parameterized import parameterized, param
from DIRAC import S_OK, S_ERROR, gLogger
import DIRAC
from DIRAC.TransformationSystem.Utilities.JobInfo import TaskInfoException, JobInfo
import DIRAC.In... | andresailer/DIRAC | TransformationSystem/test/Test_JobInfo.py | Python | gpl-3.0 | 26,303 | [
"DIRAC"
] | 556cbee3336e2eed5b3f511a00035e404aca35f1410c1ccd0c873cc8d8c798ce |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkGenericDataSetTessellator(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | nagyistoce/devide | modules/vtk_basic/vtkGenericDataSetTessellator.py | Python | bsd-3-clause | 525 | [
"VTK"
] | 05757b4d75aa1f2fb8d4b0131afeb520e66f1243f6e10143493ebf72ce7ad76e |
# Copyright (C) 2014 Bernd Feige
# This file is part of avg_q and released under the GPL v3 (see avg_q/COPYING).
'''DC-Correct a continuous file by sampling and subtracting a low-frequency representation.
DC_Correct_Script must be set up complete with Epochsource etc, possibly transform
methods, but without coll... | berndf/avg_q | python/avg_q/DC_Correct.py | Python | gpl-3.0 | 4,274 | [
"Gaussian"
] | 000bc28d66d2d4dec2f3b6e5d7e346d2be4abf20c1b78915f925b98378b09ff4 |
"""
Aravind Veerappan
BNFO 601 - Exam 2
Question 2. Protein BLAST
"""
import math
from PAM import PAM
class BLAST(object):
FORWARD = 1 # These are class variables shared by all instances of the BLAST class
BACKWARD = -1
ROW = (0, 1)
COLUMN = (1, 0)
def __init__(self, query=None,... | aravindvrm/bnfo | Veerappan_bnfo601_exam2/Veerappan_BLAST_prot.py | Python | mit | 19,404 | [
"BLAST"
] | 0909d215565db6748e50e99559262432ef041c82d4bd3be1da203287bb9b3832 |
import json
import logging
import random
import geometry3d as g3d
from math import exp, pi, sqrt, sin, cos
logger = logging.getLogger()
logger.setLevel(logging.INFO)
logger.info('Loading function')
# extract position from a particle set
def get_position(p):
x = 0.0
y = 0.0
z = 0.0
orientation = 0.... | andreynech/robobrain | pyparticle/montecarlo.py | Python | mit | 5,110 | [
"Gaussian"
] | 5755c0baf9bf603e24a6f65dae4b4581194aa4f9ee2b1ddef842b4041b3427d5 |
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
'''Collections of messages and their translations, called cliques. Also
collections of cliques (uber-cliques).
'''
from __future__ import print_functio... | ric2b/Vivaldi-browser | chromium/tools/grit/grit/clique.py | Python | bsd-3-clause | 18,821 | [
"xTB"
] | ac57a1f6e2117700439d6f44de70e0ef60abb2b81f9f5b537896c6fb7f4153b7 |
# retroviralMapping.py
# 1/8/14
# Retroviral_mapping.ipynb, in script form
import sys, os, re, cmath, math, glob, subprocess, csv, matplotlib, argparse
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.backends.backend_pdf import PdfPages
import pandas as pd
matplotlib.rcParams['savefig.dp... | enguy/FAST-iCLIP | retroviralMapping.py | Python | gpl-2.0 | 9,133 | [
"Bowtie"
] | a77a7acd2f40952a20b3ef5bfe1cefea1cb9ac00ada9444b999fe5e62d85d9da |
"""
Created on 01.06.2015
@author: Andreea Plocon andreea.plocon@geo.tuwien.ac.at
"""
import os
import netCDF4
from datetime import datetime
def netcdf_results_manager(results, save_path):
"""
Function for writing the results of the validation process as NetCDF file.
Parameters
----------
resul... | christophreimer/pytesmo | pytesmo/validation_framework/results_manager.py | Python | bsd-3-clause | 1,472 | [
"NetCDF"
] | adf5f383272c8739da4021b8c7d8686400efef957d950cd30a8d5159a69f6ee0 |
import wx
import wx.grid
import wx.lib.scrolledpanel
import os
import os.path
import platform
from tools import *
import webbrowser
from threading import Thread
class SuperimpositionPanel(wx.lib.scrolledpanel.ScrolledPanel):
def __init__(self, parent, W, H):
#if (platform.system() == "Windows"):
wx... | schenc3/InteractiveROSETTA | InteractiveROSETTA/scripts/superimposition.py | Python | gpl-2.0 | 19,855 | [
"PyMOL"
] | f023687db3f75b818dbc293a4302f1359be3536c3a016cd951788605609c064e |
from QC import *
from Numeric import *
from IPAF import IPAF
from Upset import *
from Visualization.Avatars.RasMol import *
from Setup.Dislocation.Screw import Screw
pot = EMTPotential()
a = pot.GetLatticeConstant()
b = a / sqrt(2)
h = b * sqrt(3) / 2
h3 = a / sqrt(3)
D = array((0.0, 0.0, 0.0))
A = array((h / 3, h3, b... | auag92/n2dm | Asap-3.8.4/Examples/qcscrew.py | Python | mit | 1,202 | [
"RasMol"
] | 31331521eb95e310600bedb50d217b0e416dc80433fdf834822cf158cde7b41f |
from pycket.util import snake_case
from rpython.rlib import jit, objectmodel
class Visitable(type):
def __new__(cls, name, bases, dct):
visit_method_name = "visit_" + snake_case(name)
@objectmodel.specialize.argtype(1)
def dispatch_visitor(self, visitor, *args):
return getattr(... | magnusmorton/pycket | pycket/AST.py | Python | mit | 4,629 | [
"VisIt"
] | b096fb149c087796a4f47d9d8c9ff52b73b6596eede470552e9c8804d6ca1301 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under t... | MDAnalysis/mdanalysis | package/MDAnalysis/coordinates/TRR.py | Python | gpl-2.0 | 6,721 | [
"Gromacs",
"MDAnalysis"
] | d314d46e55d5a968f469e2276b94dfe08646bd49b074f8dfe243b1ac2f62ca93 |
#!/usr/bin/env python
"""
Get relative energy of the system of DIR w.r.t. the energies ERG.
There must be erg.ref and POSCAR in the DIR.
Relative energy of the system and that per atom will be printed.
Usage:
get_relative_energy.py [options] DIR
Options:
-h, --help Show this message and exit.
--specorder=SPECO... | ryokbys/nap | nappy/fitpot/get_relative_energy.py | Python | mit | 1,463 | [
"ASE",
"VASP"
] | bc8f99bf36b28a7de5717bced7e2de035bc226150619c128fb8cb8030f17d1bb |
# -*- coding: utf-8 -*-
"""This module tests various ways how to set up the provisioning using the provisioning dialog."""
from datetime import datetime, timedelta
import fauxfactory
import pytest
import re
from widgetastic.utils import partial_match
from widgetastic_patternfly import CheckableBootstrapTreeview as CbT... | lkhomenk/integration_tests | cfme/tests/infrastructure/test_provisioning_dialog.py | Python | gpl-2.0 | 11,543 | [
"VisIt"
] | 8f459e51a86a843e0f9bd147145c540bc49016878a6780fdb32426f731fadc97 |
"""Translation of the BioNetGen example "egfr_simple" from the BNG wiki.
added delete_molecules=True to egfr_dimer_degrade to conserve adapter proteins
http://bionetgen.org/index.php/Egfr_simple
"""
from __future__ import print_function
from pysb import *
Model()
Parameter('NA', 6.02e23) # Avogadro's number (mol... | AMICI-developer/AMICI | python/tests/pysb_test_models/bngwiki_egfr_simple_deletemolecules.py | Python | bsd-2-clause | 3,398 | [
"Avogadro"
] | b8504ec07bd3989b1d78ce0bb653aeccc16a336be297571e7d2077627445547a |
import os
import time
import DIRAC
import threading
from DIRAC import gConfig, gLogger, S_OK, S_ERROR, gMonitor
from DIRAC.Core.Utilities import List, Time, MemStat
from DIRAC.Core.DISET.private.LockManager import LockManager
from DIRAC.FrameworkSystem.Client.MonitoringClient import MonitoringClient
from DIRAC.Core.DI... | miloszz/DIRAC | Core/DISET/private/Service.py | Python | gpl-3.0 | 23,470 | [
"DIRAC"
] | 7effa33db795ebdadc4a4a1a2cbf815b6584495115fd4d84ae375768b088ee17 |
# Copyright 2014-2018 The PySCF Developers. 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 appl... | gkc1000/pyscf | pyscf/nao/test/test_0029_lil_vs_coo_nao.py | Python | apache-2.0 | 1,081 | [
"PySCF"
] | 0c76ad75bfe4fb676bc440078f5376b10b6b8e89a43a1efcdaaea16c2b7aad48 |
import os
import urllib.parse
import requests
import splinter
from selenium.webdriver.common.by import By
from selenium.webdriver.support.wait import WebDriverWait
from selenium.webdriver.support import expected_conditions as EC
from tests.common.utils import urljoin
class Browser(object):
'''Drives the browser in... | miurahr/seahub | tests/ui/driver.py | Python | apache-2.0 | 2,791 | [
"VisIt"
] | 32e6463fc42983f06965e61a6d134dec1fdd623119031eff6911243ac088291c |
import sys
from ase.build import molecule, fcc111, add_adsorbate
from ase.optimize import QuasiNewton
from ase.constraints import FixAtoms
from ase.calculators.emt import EMT
from ase.vibrations import Vibrations
sys.path.append("..")
from __init__ import AnharmonicModes
slab = fcc111('Au', size=(2, 2, 2), vacuum=4... | keldLundgaard/ase-anharmonics | tests/test_vib_and_trans.py | Python | lgpl-2.1 | 1,016 | [
"ASE"
] | fecb61c2c1bdee5b62f00b645146434a26425907beb2a84dd59f959f12ac9355 |
#!/usr/bin/env python
"""
Map2KO
Genome library
Handle a KO search on a local machine (Blast-BBH) or online (KAAS)
"""
from Bio import SeqIO
from ductape.common.commonmultiprocess import CommonMultiProcess
from ductape.common.utils import slice_it
from ductape.genome.blast import Blaster, RunBBH
import sys
if sys.ver... | combogenomics/DuctApe | ductape/genome/map2KO.py | Python | bsd-2-clause | 12,228 | [
"BLAST"
] | d8b55943bdeeea533c7c2f86f44982583acfaae9723c1b27e62bc6c6159a484e |
#!/usr/bin/env python
from gpaw.atom.configurations import configurations
import os
import numpy as np
import matplotlib.pyplot as plt
econf_strs={
'He':'1s',
'Ne':'1s2s2p',
'Ar':'1s2s2p3s3p',
'Kr':'1s2s2p3s3p3d4s4p',
'Xe':'1s2s2p3s3p3d4s4p4d5s5p',
'Rn':'1s2s2p3s3p3d4s4p4d4f5s5p5d6s6p'
}
def ... | mailhexu/pyDFTutils | pyDFTutils/pseudopotential/gen_pp.py | Python | lgpl-3.0 | 7,507 | [
"GPAW"
] | a1515eb66f23c278510f9d5527e9b00c20b5f53f0400102ecfa622784a8bc7d1 |
from discord.ext import commands
import time
class Information():
def __init__(self, hermes):
self.hermes = hermes
@commands.command()
async def website(self):
await self.hermes.say("You can find our official website @ https://hermes.apticode.co.uk")
@commands.command()
... | Apticode/hermes.py | cogs/information.py | Python | gpl-3.0 | 1,136 | [
"VisIt"
] | 80472ab18b10669a3fce51ba65e0b151aa84cd72b05d7b93831a8902dcb13cf7 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. 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
#
# U... | gkc1000/pyscf | pyscf/x2c/sfx2c1e_grad.py | Python | apache-2.0 | 10,160 | [
"PySCF"
] | ff040f6557a8927ec6f4d8878f29ae786433be0363c6e7c1989459cf7dfd280f |
# coding=utf-8
from __future__ import unicode_literals
try:
from json import JSONDecodeError as MyJSONDecodeError
except ImportError:
MyJSONDecodeError = Exception
"""
在 Py3 下是 json.JSONDecodeError。
在 Py2 下是 BaseException，因为 Py2 的 json 模块没有提供解析异常。
"""
__all__ = [
# warnings
'ZhihuWar... | lbc001/zhihu-oauth | zhihu_oauth/exception.py | Python | mit | 5,519 | [
"VisIt"
] | ee946122039d0d003df4c32cc4a6d64857adb628c0daabdece19751b558c6529 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | harterj/moose | test/tests/multiapps/picard_multilevel/multilevel_dt_rejection/test_multilevel.py | Python | lgpl-2.1 | 1,313 | [
"MOOSE"
] | 26dca41d4d7f045d4fc77b699b377397dd4abc447f6e70255084c82e1dab7a37 |
# c: 07.05.2007, r: 25.06.2008
from sfepy import data_dir
filename_mesh = data_dir + '/meshes/2d/special/circle_in_square.mesh'
dim = 2
field_1 = {
'name' : 'a_harmonic_field',
'dtype' : 'real',
'shape' : 'scalar',
'region' : 'Omega',
'approx_order' : 1,
}
variables = {
't': ('unknown field'... | RexFuzzle/sfepy | tests/test_msm_laplace.py | Python | bsd-3-clause | 4,418 | [
"VTK"
] | c4bc9f8911da60fcbd9696fa19da2460f0f77c70bbd8e58ce61a2bb094eca19b |
"""Class to access NCBI's ftp server and easily download databases."""
# Standard Library
import os
import re
import shutil
import gzip
import tarfile
from time import time
from pathlib import Path
from datetime import datetime
from multiprocessing.pool import ThreadPool
from ftplib import error_perm, all_errors
# Orth... | datasnakes/Datasnakes-Scripts | OrthoEvol/Tools/ftp/ncbiftp.py | Python | mit | 17,903 | [
"BLAST"
] | 4d28e0a63485b2dfdba2d424f38af0353e6f3f1fbda0e788f3baa4db4197985b |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
# Copyright (C) 2008 Evan Martin <martine@danga.com>
"""A git-command for integrating reviews on Rietveld."""
import datetime
fro... | cybertk/depot_tools | git_cl.py | Python | bsd-3-clause | 92,483 | [
"VisIt"
] | b9061f75e0830b824d0c7b70afca5277a9aeeb31f98519dcab073068b167480f |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2016, Shogun Toolbox Foundation
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# 1. Redistributions of source code must retain the... | cfjhallgren/shogun | setup.py | Python | gpl-3.0 | 10,571 | [
"Gaussian"
] | 5223ef5b165b467a538aefbce619bc2d036dd02b224ae7cb2299b31cfa19a0d7 |
''' TransferCommand module
'''
__RCSID__ = '$Id$'
from datetime import datetime, timedelta
from DIRAC import S_OK, S_ERROR
from DIRAC.AccountingSystem.Client.ReportsClient import ReportsClient
from DIRAC.Core.DISET.RPCClient import RPCClient
from DIRAC.ResourceStatusSystem.Client.ResourceManagementClient import Res... | arrabito/DIRAC | ResourceStatusSystem/Command/TransferCommand.py | Python | gpl-3.0 | 7,245 | [
"DIRAC"
] | 3a94197df607dc2e5d30cbad33f620b13ec73e90ce46131ffe7671b99aee716b |
import sys
import time
import signal
import numpy as np
from asap3.Tools.ParameterOptimization.ScipyFmin import fmin, fmin_bfgs
from asap3.Tools.ElasticConstants import ElasticConstants, minimize_unit_cell
from asap3.Tools.SurfaceEnergies import SurfaceEnergy
from asap3.Tools.AtomicEnergies import CohesiveEnergy, Vaca... | auag92/n2dm | Asap-3.8.4/Python/asap3/Tools/ParameterOptimization/Quantities.py | Python | mit | 33,900 | [
"ASE"
] | 320a8c3b6b64dcb88bfbddec7913a0f9b167b38e2721c7e41f2f4387cd46c0f1 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2018 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
#... | amjames/psi4 | psi4/driver/util/tty/color.py | Python | lgpl-3.0 | 7,149 | [
"Psi4"
] | 05a42fbbdaf53ee980c447ff2401303172f3bb48e6b9aeff59d427ec10933f94 |
"""
Bok choy acceptance and a11y tests for problem types in the LMS
"""
import random
import textwrap
from abc import ABCMeta, abstractmethod
import ddt
import six
from bok_choy.promise import BrokenPromise
from capa.tests.response_xml_factory import (
AnnotationResponseXMLFactory,
ChoiceResponseXMLFactory,... | stvstnfrd/edx-platform | common/test/acceptance/tests/lms/test_problem_types.py | Python | agpl-3.0 | 34,846 | [
"VisIt"
] | f66795eef9c861bc4e8489b5859b9faa37c9ed18319dd59a938c9e031aef313d |
#!/usr/bin/env python
#Original script from /home/james/work/encode/feature_partitions/split_by_partitions.py
#Usage: python(2.4) split_by_partitions.py partition_index in_file out_file chrCol startCol endCol strandCol
from __future__ import division
import sys
from galaxy import eggs
import pkg_resources; pkg_resou... | dbcls/dbcls-galaxy | tools/encode/split_by_partitions.py | Python | mit | 4,509 | [
"Galaxy"
] | 881d6cdcfbd44b90f7221253aca7968a052bad7f3c4f43772e8882a76c985e68 |
########################################################################
# $HeadURL$
# File : SSHComputingElement.py
# Author : Dumitru Laurentiu, A.T.
########################################################################
""" SSH (Virtual) Computing Element: For a given IP/host it will send jobs directly through ... | avedaee/DIRAC | Resources/Computing/SSHComputingElement.py | Python | gpl-3.0 | 24,289 | [
"DIRAC"
] | c834d9ee746531213891aef96107d78ce55ea36f52af4a6586347b641c4bacee |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# #########################################################################
# Copyright (c) 2020, UChicago Argonne, LLC. All rights reserved. #
# #
# Copyright 2020. UChicago Argonne, LLC. This ... | lucarebuffi/OASYS1 | oasys/widgets/abstract/error_profile/abstract_multiple_height_profile_simulator_T.py | Python | gpl-3.0 | 38,252 | [
"Gaussian"
] | 151272cd5fc79958d3d85b99f1f70bc1c7a15b6f51c60532e06b0c16bbbea289 |
# Copyright 2011 the Melange 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 applicable law or agreed to in wr... | rhyolight/nupic.son | app/soc/views/helper/access_checker.py | Python | apache-2.0 | 25,400 | [
"VisIt"
] | 40cf29502e454866432d2046117371bed7eb64e1873aa389bc33a89ce700a24b |
""" Accounting class to stores network metrics gathered by perfSONARs.
Filled by "Accounting/Network" agent
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
from DIRAC.AccountingSystem.Client.Types.BaseAccountingType import BaseA... | yujikato/DIRAC | src/DIRAC/AccountingSystem/Client/Types/Network.py | Python | gpl-3.0 | 1,211 | [
"DIRAC"
] | 8943076b1e097237669c5c2c4bc850202c0d2fd60577df4e9c5348973138e1fa |
# -*- coding:utf8 -*-
# File : __init__.py
# Author : Jiayuan Mao
# Email : maojiayuan@gmail.com
# Date : 2/23/17
#
# This file is part of TensorArtist.
# This file is part of NeuArtist2
from ..core.utils.nd import isndarray
from .rng import *
import random as _random
import functools
__all__ = ['get_rng', 're... | vacancy/TensorArtist | tartist/random/__init__.py | Python | mit | 3,956 | [
"Gaussian"
] | b122a8d57ed1a84c2c27d02fe34b7d332897b5626f312b1bb9450483e89cb1c3 |
#!/usr/bin/env python
# qm.py -- A Quine McCluskey Python implementation
#
# Copyright (c) 2006-2013 Thomas Pircher <tehpeh@gmx.net>
#
# 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 ... | jtanx/ImplicationTable | sequential-analysis/qm.py | Python | mit | 20,952 | [
"ESPResSo"
] | a659d96ebefbe623db7dbbf32c96d3df008a4112d9bd92fd7f225c9b4b2b14a1 |
#!/usr/bin/env python
"""
The Requester module is in charge of simplifying HTTP requests and
automatically log HTTP transactions by calling the DB module.
"""
import sys
import cgi
import httplib
import logging
import urllib
import urllib2
from framework.dependency_management.dependency_resolver import BaseComponent
f... | DePierre/owtf | framework/http/requester.py | Python | bsd-3-clause | 13,163 | [
"VisIt"
] | d1a6fa090582b55c78046915350ee37c6cbfb98b34696571908297fde4e6d80e |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
# Copyright (C) 2008 Evan Martin <martine@danga.com>
"""A git-command for integrating reviews on Rietveld."""
from distutils.vers... | coreos/depot_tools | git_cl.py | Python | bsd-3-clause | 82,832 | [
"VisIt"
] | 3b8a6f9266f5b07cde7f1d44a6357d477789fa1123488a9fe39c9609071f6326 |
import numpy as np
from numpy import linalg as LA
from numpy.linalg import norm, inv
import shutil, copy
from sklearn.decomposition import PCA
from scipy import spatial
import matplotlib.path as mplPath
import transforms3d
from scipy.optimize import minimize
import cPickle
import os
from ast import literal_eval as make... | mfxox/ILCC | ILCC/pcd_corners_est.py | Python | bsd-2-clause | 35,494 | [
"VTK"
] | 0e379d4cefa42409d4f05f701d1d31e435e94853d48d0cac8658bc861074a717 |
# import openvoronoi as ovd
# import ovdvtk
# import time
# import vtk
# import datetime
import math
# import random
# import os
import gzip
import pickle
import numpy as np
from numpy import numarray as na
import pylab as P
def sortedDict(adict):
keys = adict.keys()
keys.sort()
l = []
for key in key... | aewallin/openvoronoi | python_examples/poisson/poisson_analyse.py | Python | lgpl-2.1 | 4,428 | [
"VTK"
] | 92829211539ef472898dcd04a82047bb04c31c71517d0b651b2e106a43b57281 |
"""Test fixtures."""
import copy
import lxml
import yaml
import pytest
from napalm.base.test import conftest as parent_conftest
from napalm.base.test.double import BaseTestDouble
from napalm.junos import junos
from ncclient.devices.junos import JunosDeviceHandler
@pytest.fixture(scope="class")
def set_device_para... | spotify/napalm | test/junos/conftest.py | Python | apache-2.0 | 6,041 | [
"Firefly"
] | dba697410f733944b33dbc3ad0782d279f8464ea334fde54fe509e4a1fa72514 |
# Mantid Repository : https://github.com/mantidproject/mantid
#
# Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
# NScD Oak Ridge National Laboratory, European Spallation Source
# & Institut Laue - Langevin
# SPDX - License - Identifier: GPL - 3.0 +
#pylint: disable=no-init
from __future__ impo... | mganeva/mantid | Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/TOSCABankCorrection.py | Python | gpl-3.0 | 9,207 | [
"Gaussian"
] | 882c1d756590e05d351b20e843ef390fd41978b1e7e5ec75c661f029241e94d9 |
#!/usr/bin/env python
# Copyright 2014-2019 The PySCF Developers. 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
#
# U... | gkc1000/pyscf | pyscf/cc/eom_rccsd.py | Python | apache-2.0 | 84,201 | [
"PySCF"
] | 1310777f19c11397511d0b80769b05d468e8243ec6c5a9e65857a6415b19591d |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2002 Gary Shao
# Copyright (C) 2007 Brian G. Matherly
# Copyright (C) 2009 Benny Malengier
# Copyright (C) 2009 Gary Burton
#
# This program is free software; you can redistribute i... | pmghalvorsen/gramps_branch | gramps/gen/plug/docgen/fontstyle.py | Python | gpl-2.0 | 5,397 | [
"Brian"
] | 694b7a64a3781890db25b02d9ea3b1f2c0268f8a5ef69e8dadf3dc70028e373d |
#!/usr/bin/env python3
# Version 1.1
# Author Alexis Blanchet-Cohen
# Date: 09/06/2014
import argparse
import glob
import os
import pandas
import subprocess
import util
# Read the command line arguments.
parser = argparse.ArgumentParser(description="Generates Picard tools MarkDuplicates scripts.")
parser.add_argumen... | blancha/abcngspipelines | utils/markduplicates.py | Python | gpl-3.0 | 3,518 | [
"BWA"
] | 3fcf0f993cef2af897312abf52e0588c279d53cab94d4a6592f9902b5de79e7a |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
GPLv3 license (ASTRA toolbox)
Note that the TomoPhantom package is released under Apache License, Version 2.0
* Script to generate 3D analytical phantoms and their projection data using TomoPhantom
* Projection data using OBJECT function is also generated numerically ... | dkazanc/TomoPhantom | Demos/Python/3D/ReconASTRA_object3D.py | Python | apache-2.0 | 3,964 | [
"Gaussian"
] | 54f6b72ac750d7fdd08d6f0d84986e7439b4a3f948245d03b8c70b2098ba67da |
import pandas as pd
import numpy as np
def readElkOutput(filename):
with open(filename) as fp:
lines = fp.readlines()
d = {}
species = -1
atom = -1
nu = -1
l1 = -1
l2 = -1
k = -1
p = -1
r = -1
t = -1
for line in lines:
words = line.split()
if lin... | fthoele/tensormoments | tensormoments/io.py | Python | mit | 2,750 | [
"Elk",
"VASP"
] | a55830554138955eceb20acc209555b82a47a1e7c74d5c06fb7563c9e130bb79 |
##
## \file addingEvidenceCodes_1.py
## \brief adds controlled vocabulary terms to a reaction in a model
## \author Sarah Keating
##
## This file is part of libSBML. Please visit http://sbml.org for more
## information about SBML, and the latest version of libSBML.
##
import sys
import os.path
from libsbml ... | dilawar/moose-full | dependencies/libsbml-5.9.0/examples/python/addingEvidenceCodes_1.py | Python | gpl-2.0 | 1,661 | [
"VisIt"
] | 06026e8c4f94340983779b930c51aa516d7c7d9b56c2eb6b5d7dd2b8f4e6474b |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# migsftpbench - sample paramiko-based sftp client benchmark
# Copyright (C) 2003-2015 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU ... | heromod/migrid | mig/user/migsftpbench.py | Python | gpl-2.0 | 10,782 | [
"Brian"
] | 0b1ac98d9c6d9a3b54bb74a9e67dceb0383a4c77b1c87e9250301ed1ff955df6 |
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