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import os
import subprocess
import unittest
class Calculation:
def __init__(self, **settings):
self.structure = os.path.join(os.path.dirname(os.path.realpath(__file__)), settings['structure'])
self.method = settings['method']
self.molecular_charge = settings['molecular_charge']
sel... | qcscine/sparrow | src/Sparrow/Tests/AppTests/test_sparrow.py | Python | bsd-3-clause | 25,445 | [
"MOPAC"
] | e1e44733b314622063dced864ecaa96fe096ecda5ce1035fffbf8b6c72a43c2a |
#!/usr/bin/env python2.5
from Bio import AlignIO
import Bio.PDB
from optparse import OptionParser
import sys
import array
from rosettautil.protein import util
from rosettautil.protein import alignment
from rosettautil.protein import pdbStat
from rosettautil.util import fileutil
def list_to_generator(list):
for x ... | decarboxy/py_protein_utils | scripts/thread_pdb_from_alignment.py | Python | mit | 7,756 | [
"Biopython"
] | d2e81f296b95eae0478e25e77dd4772b2228d0f962a0963e9dbd0dfd0669e6d4 |
#!/usr/bin/env python
# -*- coding: iso-8859-1 -*-
#
# Impressive, a fancy presentation tool
# Copyright (C) 2005-2010 Martin J. Fiedler <martin.fiedler@gmx.net>
# portions Copyright (C) 2005 Rob Reid <rreid@drao.nrc.ca>
# portions Copyright (C) 2006 Ronan Le Hy <rlehy@free.fr>
# portions Copyright (C) 2007 Luke Campag... | leeper/Impressive | impressive.py | Python | gpl-2.0 | 166,549 | [
"VisIt"
] | bf17cf4f7fd9da01c2a37229e4c0d6dd22707f970a8432792ac7e381cb954208 |
import numpy as np
try:
import Numeric as num
except ImportError:
pass
else:
def npy2num(a, typecode=num.Float):
return num.array(a, typecode)
if num.__version__ <= '23.8':
#def npy2num(a, typecode=num.Float):
# return num.array(a.tolist(), typecode)
def npy2num(a, typ... | grhawk/ASE | tools/ase/old.py | Python | gpl-2.0 | 6,716 | [
"ASE"
] | c0bd88cb59d315009468d154bd000430d4a3609dfff81c9f6264970e8e19cecf |
# Copyright (C) 2003-2005 Peter J. Verveer
#
# 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 above copyright
# notice, this list of conditions and the following d... | jrversteegh/softsailor | deps/scipy-0.10.0b2/scipy/ndimage/tests/test_ndimage.py | Python | gpl-3.0 | 204,064 | [
"Gaussian"
] | fe70054cb0b9fbfe58eb9caa587a1c3484c1138281e32507a5243792659ee344 |
# -*- coding: utf-8 -*-
"""
This script reproduces the results for Figure 7, analyzing 1p microendoscopic
data using the CaImAn implementation of the CNMF-E algorithm. The algorithm
using both a patch-based and a non patch-based approach and compares them with
the results obtained from the MATLAB implementation.
More ... | agiovann/Constrained_NMF | use_cases/eLife_scripts/Figure_7-1p_striatum.py | Python | gpl-2.0 | 7,274 | [
"Gaussian",
"NEURON"
] | 7d21aa2eff376979379a2fbf94f4b4e6c7c595777c39102c4b67305d2f4e0666 |
"""Test module for Dashboard UI
:Requirement: Dashboard
:CaseAutomation: Automated
:CaseLevel: Acceptance
:CaseComponent: UI
:TestType: Functional
:CaseImportance: High
:Upstream: No
"""
from nailgun import entities
from nailgun.entity_mixins import TaskFailedError
from pytest import raises
from requests.excepti... | sghai/robottelo | tests/foreman/ui_airgun/test_dashboard.py | Python | gpl-3.0 | 12,773 | [
"VisIt"
] | 72df51051e067e4ea90ba045d554366994101f966ee48d259685cb80f3f5fbc2 |
"""
Script for multi channel classifications.
see also:
multichannel_classifier - business logic for multichannel classifiers
"""
import argparse
import logging
import os
import pickle
import datetime
import numpy as np
from config import BED_GRAPH_RESULTS_DIR, MEAN_DNASE_DIR, MODELS_DIR
from data_provider impor... | eranroz/dnase | src/multichannel_classify.py | Python | mit | 7,126 | [
"Gaussian"
] | da9c7920329a67fcda66437910fac3fd0d3cb4bb1e1a4c4ff4a3264883b0a7aa |
from taj.exception import IllegalCondition
from taj.operator.join import BinaryJoin
from taj.operator.table import RelationProxy
from taj.operator.window import TimedWindowOperator, AmountWindowOperator
from taj.parser.visitor import LogicVisitor, ExpressionVisitor, QueryVisitor
class JoinBuilder(QueryVisitor):
''... | david-furminieux/movingForest | src/taj/operator/visit.py | Python | lgpl-3.0 | 3,420 | [
"VisIt"
] | a07f48aaf66e82667ec575423d11e2577456769174dbee9f93cb72761233e32a |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 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
#... | rmcgibbo/psi4public | psi4/driver/inputparser.py | Python | lgpl-3.0 | 31,243 | [
"CFOUR",
"Psi4"
] | 83971cd16e7cfe5a14182880dd154db0bb87f22057154be012e6b0e585a342ee |
"""
Views for user API
"""
from django.shortcuts import redirect
from django.utils import dateparse
from rest_framework import generics, views
from rest_framework.decorators import api_view
from rest_framework.response import Response
from opaque_keys.edx.keys import UsageKey
from opaque_keys import InvalidKeyError
... | jswope00/griffinx | lms/djangoapps/mobile_api/users/views.py | Python | agpl-3.0 | 9,137 | [
"VisIt"
] | f7b9c999adedb516e4543f50490419d3a5601331ff496068c43143ff4c0c1c62 |
import os
import numpy as np
from time import time
from ase import molecule
from gpaw import GPAW
from gpaw.lcao.projected_wannier import ProjectedWannierFunctions, get_phs
if not os.path.isfile('C6H6.gpw'):
atoms = molecule('C6H6')
atoms.center(vacuum=2.5)
calc = GPAW(h=0.2, basis='szp', width=0.05, con... | qsnake/gpaw | oldtest/pwftest_C6H6.py | Python | gpl-3.0 | 1,689 | [
"ASE",
"GPAW"
] | 6581885c6e5f57adc8174031990b29bf16ea014ef1a91a1ad173ce5644a931eb |
import numpy as np
from ase import Atoms
from vtk import vtkOutlineSource, vtkAxesActor, vtkProperty2D, vtkTextProperty
from ase.visualize.vtk.module import vtkModule, vtkPolyDataModule
# -------------------------------------------------------------------
class vtkUnitCellModule(vtkPolyDataModule):
def __init_... | suttond/MODOI | ase/visualize/vtk/cell.py | Python | lgpl-3.0 | 4,067 | [
"ASE",
"VTK"
] | 7760f0920476d7e0108f783704e18a6cffd5380a39fa9070c5d4284f6443267a |
from __future__ import print_function
import MDAnalysis.analysis.psa
from MDAnalysis import SelectionError, SelectionWarning, FinishTimeException
from numpy.testing import *
import numpy as np
import nose
from nose.plugins.attrib import attr
import os
import shutil
import errno
import tempfile
import itertools
import... | sseyler/PSAnalysis | tests/test_psa.py | Python | gpl-3.0 | 2,620 | [
"MDAnalysis"
] | b94e294aab30d64b40d0045d096f192bc828ce87b24ab8429959565291d7284e |
#!/usr/bin/env python
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
#einit
#Essential Pathways v1.0.1
#Author:realasking
#Email:realasking@gmail.com,tomwangsim@163.com
#Aug-23,2017,in USTB
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
import sys
import os
import r... | realasking/essential-pathway | build/lib/epw/einit.py | Python | lgpl-3.0 | 1,502 | [
"EPW"
] | 46e7e3127cca89e93f945b11ebe64246956009a273700b0a316c6a7abb947dca |
""" Utilities to process parametric job definitions and generate
bunches of parametric jobs. It exposes the following functions:
getParameterVectorLength() - to get the total size of the bunch of parametric jobs
generateParametricJobs() - to get a list of expanded descriptions of all the jobs
"""
__RCSID_... | hgiemza/DIRAC | WorkloadManagementSystem/Utilities/ParametricJob.py | Python | gpl-3.0 | 6,881 | [
"DIRAC"
] | 47390a18506febd0f03157ab6330afb7e9e43a69006e255c49e2c5261c736c93 |
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.ticker as ticker
x = np.arange(1,100.)/50.
def weib(x,u,a,y):
# http://www.itl.nist.gov/div898/handbook/eda/section3/eda3668.htm
# x >= u, x is vector
# y,a > 0
# y: shape parameter
# u: location parameter
# a: scale paramete... | paztronomer/kepler_tools | weibull_v01.py | Python | mit | 2,461 | [
"Gaussian"
] | 703ee8b75a7b83210d306e5a3a9577b99fc463549298992ac2af9d3d79a11f14 |
from __future__ import division
from scipy import *
from scipy import stats
import pylab
p_o = 0.5
q_o = 1 - p_o
z_alpha = 1.96
As = [1,1.25,2,5,10,100]
legend_val = ""
for A in As:
p_a = A/(A + 1)
q_a = 1 - p_a
betas = []
ns = xrange(1,500,1)
for n in ns:
z_beta = (p_o + z_alpha*sqrt(p_o*q_o/n) - p_a)/sqrt(p... | polarise/RP-python | allelic_power.py | Python | gpl-2.0 | 831 | [
"ASE"
] | 2caeb5f8867d46c18a3c216e321ce4447d44810ea8346f32171f0bc00a704ec3 |
import json
import socket
from .url_config import URLS
from .util import kbase_env
"""
A simple ELK stack logger for a few Narrative events.
"""
# TODO:
# * add more log events (or generalize further. don't much like using magic strings, tho)
# * TESTS
# * local log testing mode, for when we point this to the prod lo... | pranjan77/narrative | src/biokbase/narrative/common/narrative_logger.py | Python | mit | 1,878 | [
"Elk"
] | 8ae7992773cc910ccea1b57010e198574bdaf24257224c271c3fb71631308d2c |
# -*- coding: utf-8 -*-
"""
Tutorials / radar cross section of a metal sphere
Tested with
- python 3.4
- openEMS v0.0.34+
(C) 2016 Thorsten Liebig <thorsten.liebig@gmx.de>
"""
### Import Libraries
import os, tempfile
from pylab import *
from CSXCAD import ContinuousStructure
from openEMS import openEMS
from... | thliebig/openEMS | python/Tutorials/RCS_Sphere.py | Python | gpl-3.0 | 3,415 | [
"Gaussian"
] | d3066216909429533ac4d7eecf2555860c34ff36851363b3daa2b44ce04cc415 |
#!/usr/bin/env python
"""
sa.py
Parse and possibly sanity-check a .sa file output by bowtie2-build in --sa
mode. These files have a very simple format: first is a uint32_t containing
the length of the suffix array, the rest is an array of that many uint32_ts
containing the suffix array.
"""
import sys
import struct... | roryk/hisat2 | scripts/sa.py | Python | gpl-3.0 | 2,156 | [
"Bowtie"
] | 586f1480099df861c04c90377bda39351ec047703ee6f66cb669d4b83cec1bac |
"""
Generate StyledLayerDescriptor objecs for django querysets.
This generator uses the python-sld and pysal libraries to generate classes
for map classification, and returns a StyledLayerDescriptor class object. This
class object may be serialized to an SLD XML file, which is useful for many
GIS and mapping software ... | azavea/django-sld | djsld/generator.py | Python | apache-2.0 | 16,053 | [
"VisIt"
] | d5eda32711f33346eac07f47298408182bf6bf17171c5a3e152a09ec03e8c0a8 |
"""
Generate samples of synthetic data sets.
"""
# Authors: B. Thirion, G. Varoquaux, A. Gramfort, V. Michel, O. Grisel,
# G. Louppe, J. Nothman
# License: BSD 3 clause
import numbers
import array
import numpy as np
from scipy import linalg
import scipy.sparse as sp
from ..preprocessing import MultiLabelBin... | vortex-ape/scikit-learn | sklearn/datasets/samples_generator.py | Python | bsd-3-clause | 58,736 | [
"Gaussian"
] | 561170a867b3681ac7e18a4c99b8df27f8be8134184e91385dd9309466dd7649 |
import numpy as np
from scipy.optimize import curve_fit
from .functions import gaussian
class Analyzer:
def __init__(self, data):
self.data = data
def determine_energy_window(self, sigma_window=(7, 7)):
good_detectors = self.data.adc[16:]
central_det, index = self._find_best_detect... | mmoran0032/pyne | sap/analyze.py | Python | mit | 1,953 | [
"Gaussian"
] | 92d58b54335510bdae1e9b1c653d703e6ad3ed2c89c64d3c8a9e493da6350f68 |
# Copyright (c) 2015, Frappe Technologies Pvt. Ltd. and Contributors
# License: GNU General Public License v3. See license.txt
from __future__ import unicode_literals
import frappe
from frappe.utils import add_days, getdate, cint
from frappe import throw, _
from erpnext.utilities.transaction_base import TransactionB... | gangadhar-kadam/verve_test_erp | erpnext/support/doctype/maintenance_schedule/maintenance_schedule.py | Python | agpl-3.0 | 9,561 | [
"VisIt"
] | 69fca4ac0a60cc7972f2a764c1964a44e90aa74d62cd01ae1902ab797746c34e |
"""
this simple program describes the basic concept of DFS. it takes input of nodes & edges and prints the traversal routes.
"""
graph = [] # list to store 2D graph
parent = [] # list to store parent
visit = [] # list to check if visited or not
def dfs(u):
global parent # global access to edit
gl... | ahmadalsajid/PythonNotes | DFSImplementation.py | Python | mit | 1,308 | [
"VisIt"
] | fce0fc23f9e8af364f362b0a76969e12f889b9646e2ce7280c491cdb87d74671 |
# coding=utf-8
from __future__ import unicode_literals
from ..person import Provider as PersonProvider
class Provider(PersonProvider):
formats = (
'{{first_name}} {{last_name}}',
'{{first_name}} {{last_name}}',
'{{first_name}} {{last_name}}',
'{{first_name}} {{last_name}}',
... | DonHilborn/DataGenerator | faker/providers/no_NO/person.py | Python | mit | 7,706 | [
"MOE"
] | 62cb338d951d5e01e3854938e7c25a4b1bc16480f29adc55d85e55d829af1788 |
#* 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/lgpl-2.1.html
import sys
i... | harterj/moose | python/MooseDocs/extensions/bibtex.py | Python | lgpl-2.1 | 11,614 | [
"MOOSE"
] | c2a5a275653d629f67b09d561e681b374f0c089586f1f3c81409c18e8404fa53 |
# -*- coding: utf-8 -*-
"""
Created on Thu Jul 6 17:25:02 2017
@author: yamada
"""
import numpy as np
from scipy.special import wofz
from scipy.constants import c, k, R
# =============================================================================
# h =6.62607004*10**-34 # Js or mmkg/s
# k = 1.38064852*10**-23 # m... | atmtools/typhon | typhon/nonlte/spectra/lineshape.py | Python | mit | 5,161 | [
"Avogadro"
] | aab8d97233a4586a70ecea7c9342a9f43f52d5080165d01d7a60d5c53a1bf1a0 |
import numpy as np
from BDSpace.Coordinates import Cartesian
from BDSpace import Space
from BDSpace.Curve.Parametric import Helix
from BDSpace.Field import HyperbolicPotentialCurveConservativeField
import BDSpaceVis as Visual
from mayavi import mlab
space = Space('Charged helix Space')
coordinate_system = Cartesian... | bond-anton/Space_visualization | demo/05_curve_field_demo.py | Python | apache-2.0 | 1,632 | [
"Mayavi"
] | c41b9e4310cee98f5ae6d78dbaff8ebd44824af3169ec3eaa8d9cbcc1be9944e |
#!/usr/bin/env python
# Copyright (c) 2004-2006 ActiveState Software Inc.
#
# Contributors:
# Trent Mick (TrentM@ActiveState.com)
"""
pythoncile - a Code Intelligence Language Engine for the Python language
Module Usage:
from pythoncile import scan
mtime = os.stat("foo.py")[stat.ST_MTIME]
... | archifix/settings | sublime/Packages/SublimeCodeIntel/libs/codeintel2/pythoncile1.py | Python | mit | 73,315 | [
"VisIt"
] | 1c55b5509bcf0990202688403da7ef5150a6d0aeb671ab87b3a3c3021e105554 |
import os
import time
import miasm2.expression.expression as m2_expr
from miasm2.arch.x86.arch import mn_x86, deref_mem_ad, parse_ast, ast_int2expr, \
base_expr, rmarg, print_size
from miasm2.arch.x86.sem import ir_x86_16, ir_x86_32, ir_x86_64
from miasm2.core.bin_stream import bin_stream_str
filename = os.environ... | rom1sqr/miasm | test/arch/x86/arch.py | Python | gpl-2.0 | 87,644 | [
"VisIt"
] | 751b38a4df22302af4b7d0905d7826f144b80e9ed51d236d5fed628b4aa4fb1b |
# Copyright 2012 Nebula, 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 agree... | froyobin/horizon | horizon/base.py | Python | apache-2.0 | 36,939 | [
"VisIt"
] | dcc8f2c1d872c1e3c22428ba88b2ddfd0a6098775586936a3d3cbb87f1a0e872 |
# Copyright (c) 2017 kamyu. All rights reserved.
#
# Google Code Jam 2017 Qualification Round - Problem C. Bathroom Stalls
# https://code.google.com/codejam/contest/3264486/dashboard#s=p2
#
# Time: O(logK)
# Space: O(1)
#
# 1. by intuition, after the first person chooses the mid stall of the single row,
# the rema... | kamyu104/GoogleCodeJam-2017 | Qualification Round/bathroom-stalls.py | Python | mit | 2,831 | [
"VisIt"
] | 4815b565cbdbe0f55533260aa9adbfcc2170ad3ca4c5cfaff779c1e032841a9e |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module contains objects that are used to describe the environments in a structure. The most detailed object
(StructureEnvironments) contains a very thorough analysis of the environments of a given ato... | gVallverdu/pymatgen | pymatgen/analysis/chemenv/coordination_environments/structure_environments.py | Python | mit | 103,729 | [
"pymatgen"
] | 8ee32fb14d3763a66bed27caa4689bea1e89b0b150ba092c91bdfe5cf3e39dbf |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (t... | apache/incubator-allura | Allura/allura/model/auth.py | Python | apache-2.0 | 32,533 | [
"VisIt"
] | 36cefce0ed0a0baf83c5403418bf9d246883ff8ad264b8ee51aa091f7749a749 |
# -*- coding: utf-8 -*-
__date__ = "2011/02/21"
#__doc__ = """ texte doc """
import os, sys
import datetime
import itertools
#now = datetime.datetime.now()
try:
import pysam
except ImportError:
print "\tError: Pysam is not installed. \n\
Please see: https://github.com/pysam-developers/pysam\n\... | gillet/ulysses | inversions.py | Python | gpl-3.0 | 37,195 | [
"pysam"
] | b7d1bcb7ec3a53d5bd698a455368d423deb76dff3f035902eb2dc661de76eb70 |
"""
This module gathers tree-based methods, including decision, regression and
randomized trees. Single and multi-output problems are both handled.
"""
# Authors: Gilles Louppe <g.louppe@gmail.com>
# Peter Prettenhofer <peter.prettenhofer@gmail.com>
# Brian Holt <bdholt1@gmail.com>
# Noel Da... | schets/scikit-learn | sklearn/tree/tree.py | Python | bsd-3-clause | 34,304 | [
"Brian"
] | fa46bd6fe679dd5b7022dece48dd5f8353d52eb3c6d1144bf62b5c741de5dcaf |
# This file is part of cldoc. cldoc 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, version 2.
#
# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the ... | jessevdk/cldoc | cldoc/nodes/node.py | Python | gpl-2.0 | 7,646 | [
"VisIt"
] | 46f99d8709436115159c6a0c0e885d8bf9f0158ecbcb6f4cf498e4ad3147ce64 |
# Copyright (c) Roman Lutz. All rights reserved.
# The use and distribution terms for this software are covered by the
# Eclipse Public License 1.0 (http://opensource.org/licenses/eclipse-1.0.php)
# which can be found in the file LICENSE.md at the root of this distribution.
# By using this software in any fashion, you ... | romanlutz/fantasy-football-prediction | get_data.py | Python | epl-1.0 | 6,500 | [
"Brian",
"Dalton"
] | 1da088c4bc26234d706ed5d802d79cb302a69bfd67181dcffa4f488f6b6b4ada |
# BEGIN_COPYRIGHT
#
# Copyright (C) 2013-2014 CRS4.
#
# This file is part of vispa.
#
# vispa 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
#... | crs4/vispa | bl/tiget/mr/blast/mapper.py | Python | gpl-3.0 | 9,138 | [
"BLAST"
] | 20db5cb73610cd8bb68b7ef33c3a8f536b6452cddeb748272ed1772922f7c96f |
""" TopErrorMessagesReporter produces a list with the most common errors
injected in the SystemLoggingDB and sends a notification to a mailing
list and specific users.
"""
__RCSID__ = "$Id$"
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Base.AgentModule ... | vmendez/DIRAC | FrameworkSystem/Agent/TopErrorMessagesReporter.py | Python | gpl-3.0 | 5,376 | [
"DIRAC"
] | f93c9918ad2b610eb784be43dde556dd8df8821c76c11f63d646ade88356ff96 |
import functools
import operator
from chainer.functions.connection import linear
from chainer import initializers
from chainer import link
from chainer import variable
class Linear(link.Link):
"""Linear layer (a.k.a.\\ fully-connected layer).
This is a link that wraps the :func:`~chainer.functions.linear`... | aonotas/chainer | chainer/links/connection/linear.py | Python | mit | 4,390 | [
"Gaussian"
] | 3011110308f88a7d40c298e0767a1a2d41347373dce1438b05948163d7d02f32 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 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
#... | psi4/psi4 | psi4/share/psi4/databases/A24.py | Python | lgpl-3.0 | 29,690 | [
"Psi4"
] | 74065cc01d8feadc4e73a8abe32a4d7ecb0751096f6b75a731e523558a3648ea |
# Code Taken from Cytoscape App Store
from django.core.files import File
from PIL import Image
from io import StringIO
def scale_img(f, name, max_px, dim):
try:
img = Image.open(f, 'r')
except IOError:
raise ValueError('invalid image file')
(w, h) = img.size
if dim == 'h':
if... | abhijithanilkumar/ns-3-AppStore | src/util/img_util.py | Python | mit | 938 | [
"Cytoscape"
] | f13acc2546f445ffe68310c302cb48e2b61da6b4b91dd654dae769eb1f201f2c |
"""Module containing class `ClassifyCommand`."""
import logging
import time
from vesper.command.command import Command
from vesper.django.app.models import AnnotationInfo, Job, Processor
from vesper.singleton.extension_manager import extension_manager
import vesper.command.command_utils as command_utils
import vespe... | HaroldMills/Vesper | vesper/command/classify_command.py | Python | mit | 7,103 | [
"VisIt"
] | e776c625d740bc54fa79dd9a0c957134ef773acf834e1e13a0f611e43d672cb7 |
########################################################################
# $Id$
########################################################################
""" DIRAC FileCatalog Storage Element Manager mix-in class """
__RCSID__ = "$Id$"
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.Utilities.Pfn import pfnun... | sposs/DIRAC | DataManagementSystem/DB/FileCatalogComponents/SEManager.py | Python | gpl-3.0 | 8,953 | [
"DIRAC"
] | eb2ce0aa244df0ceb684ff69696ddc9c14f436651fd60dcd0c9a6d67720b28ee |
#!/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... | sunqm/pyscf | pyscf/gto/test/test_ecp.py | Python | apache-2.0 | 12,368 | [
"PySCF"
] | 709e1ecbae0a494052878d17864fac7f9bd78337d92f901341a7dabf93a1ad55 |
#! /usr/bin/env python3.5
# -*- coding: utf-8 -*-
""" A simple implementation of OaA convolution """
from PIL import Image
from typing import Union, Tuple, Callable as Function
from functools import wraps
from glob import iglob
from scipy.integrate import dblquad
from math import pi
from numpy.fft import fft2 as FFT,... | bjd2385/fftconvolve | oaconvolution.py | Python | mit | 9,557 | [
"Gaussian"
] | 72244871ad139c021d2a2706090b2666a81ca8e729bcdc65cc126c4a964d6d32 |
from itertools import product
import pytest
import warnings
from warnings import catch_warnings
from datetime import datetime, timedelta
from numpy.random import randn
import numpy as np
from pandas import _np_version_under1p12
import pandas as pd
from pandas import (Series, DataFrame, bdate_range,
... | louispotok/pandas | pandas/tests/test_window.py | Python | bsd-3-clause | 149,640 | [
"Gaussian"
] | f5515f4c5b4cdcef00f3e4333965214720f83bc169989f5e8cfc145e46953e17 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2011 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program 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 F... | tiagocardosos/stoq | stoqlib/gui/search/sellableunitsearch.py | Python | gpl-2.0 | 2,718 | [
"VisIt"
] | 978ab43bb8d9412838e04890095d70c093b920be95416d94e43d6223e935c56c |
#!/usr/bin/python
import numpy as np
import scipy as sp
import matplotlib.pyplot as plt
import scipy.integrate as spint
import scipy.linalg as spal
import time
import matplotlib as mpl
from mpl_toolkits.mplot3d import Axes3D
import itertools
def hash(x):
return '%f_%f_%f_%f'%(x[0],x[-1],x[1]-x[0],x[-1]-x[-2])
de... | StochasticNumerics/mimclib | tests/HJM/HJM.py | Python | gpl-2.0 | 32,203 | [
"Gaussian"
] | 63451f820b968a9eda3bb5ef74d9fd5a6c374aa61df11179cb5781ffa23a4430 |
# Copyright (C) 2012-2016
# Max Planck Institute for Polymer Research
# Copyright (C) 2008-2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General... | espressopp/espressopp | src/integrator/LBInitPopWave.py | Python | gpl-3.0 | 2,410 | [
"ESPResSo"
] | 9b59db236fcdac7a5aef986d9acf8e162ddebd418424f6a760484f641b7aecfc |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
################################################################################
#
# qooxdoo - the new era of web development
#
# http://qooxdoo.org
#
# Copyright:
# 2006-2010 1&1 Internet AG, Germany, http://www.1und1.de
#
# License:
# LGPL: http://www.gnu.org/li... | sebastienhupin/qxrad | qooxdoo/tool/pylib/ecmascript/frontend/treeutil.py | Python | lgpl-3.0 | 27,723 | [
"VisIt"
] | d2fb9b94a35d76d1c5dc7af12cd458f78f7940f09f367bb5d02c2bb75672f8b7 |
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Matti Hamalainen <msh@nmr.mgh.harvard.edu>
# Denis Engemann <denis.engemann@gmail.com>
# Andrew Dykstra <andrew.r.dykstra@gmail.com>
# Mads Jensen <mje.mads@gmail.com>
#
# License: BSD (3-clause)
from copy imp... | matthew-tucker/mne-python | mne/evoked.py | Python | bsd-3-clause | 48,018 | [
"Mayavi"
] | 758b7188991a2760bb0901632134047f40fb103dac5b77015710d36969598520 |
import pylab
import sys
import gkcLinear
################## gs2 Data Analysis #############
import Scientific.IO.NetCDF as NetCDF
# Open File
gs2_file = NetCDF.NetCDFFile(sys.argv[1],'r')
# Get time evolution of
phi2 = gs2_file.variables['phi2_by_ky'][:]
T = gs2_file.variables['t'][:]
ky = gs2_file.variab... | philscher/gkc | Benchmarks/gs2/ShearlessSlab/Analyze.py | Python | gpl-3.0 | 804 | [
"NetCDF"
] | 320cdf302cdbd6890ac8c5e69b1dfa42627fe69a3a332d8f509eaeed6712ba42 |
"""
Provide a generic structure to support window functions,
similar to how we have a Groupby object.
"""
from collections import defaultdict
from datetime import timedelta
from textwrap import dedent
from typing import List, Optional, Set
import warnings
import numpy as np
import pandas._libs.window as libwindow
fro... | kushalbhola/MyStuff | Practice/PythonApplication/env/Lib/site-packages/pandas/core/window.py | Python | apache-2.0 | 85,115 | [
"Gaussian"
] | 504c6c365569ecc3548e51493bf4de798680546ebccc9e5c199067acfe0f06f3 |
#!/usr/bin/env python
#
# Electrum - Lightweight Bitcoin Client
# Copyright (C) 2015 Thomas Voegtlin
#
# 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... | GroestlCoin/electrum-grs | electrum_grs/plugins/trustedcoin/qt.py | Python | gpl-3.0 | 13,381 | [
"VisIt"
] | 8bba4a990bb4b156821d1b0f232f537c245ef2093ee41dfa89c3522a222d3141 |
# -*- coding: utf-8 -*-
"""
Tests the "preview" selector in the LMS that allows changing between Staff, Student, and Content Groups.
"""
from ..helpers import UniqueCourseTest, create_user_partition_json
from ...pages.studio.auto_auth import AutoAuthPage
from ...pages.lms.courseware import CoursewarePage
from ...pages... | Shrhawk/edx-platform | common/test/acceptance/tests/lms/test_lms_user_preview.py | Python | agpl-3.0 | 13,747 | [
"VisIt"
] | 7b1ad0cb4965c3bf4f7298bb685aae0d78f3f1bdcc6b54e6e4c94a82c19cd925 |
# -*- coding: utf-8 -*-
from __future__ import generators
import rdflib
from rdflib.graph import ConjunctiveGraph
from rdflib import plugin
from rdflib.store import Store, NO_STORE, VALID_STORE
from rdflib.namespace import Namespace
from rdflib.term import Literal, URIRef
from types import TupleType
import time
from ... | alcides/rdflib | rdflib/sparql/sql/QueryCostEstimator.py | Python | bsd-3-clause | 44,459 | [
"VisIt"
] | 6f7e21535f8eca550a9115365f1ce4b5700538fef8fe976e7b96db7007db4469 |
#
# Copyright 2018 Analytics Zoo 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... | intel-analytics/analytics-zoo | pyzoo/test/zoo/orca/learn/spark/test_estimator_keras_for_spark.py | Python | apache-2.0 | 24,793 | [
"ORCA"
] | c6f3afe4691a9d22a4ca7a5a2a692062f6295d4008d5bc84dd75c9d2a9781221 |
from __future__ import absolute_import
import tensorflow as tf
import numpy as np
from gpflow import settings,autoflow
from gpflow import densities
from gpflow.densities import multivariate_normal
from gpflow import transforms
from gpflow.decors import (params_as_tensors, name_scope)
from gpflow.params import (Parame... | Joshuaalbert/IonoTomo | src/ionotomo/bayes/gpflow_contrib.py | Python | apache-2.0 | 11,117 | [
"Gaussian"
] | d5e95077ceab1c4f6145ce389d14f2bb74389ecb5c650a4c2b9fe5c9242875ad |
#!/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 | modules/porous_flow/test/tests/dirackernels/dirackernels.py | Python | lgpl-2.1 | 7,569 | [
"MOOSE"
] | 37d579a9fb539b2862aa22a5f7ec7e63753a966d58c8667d05b68f4696e60434 |
"""
Generic implementation of precise permissive field of view. This is Aaron
MacDonald's python implemention, as published on Roguebasin. The original
copyright notice follows.::
Author: Aaron MacDonald
Date: June 14, 2007
Description: An implementation of the precise permissive fiel... | gdos/parole | src/parole/fov.py | Python | gpl-2.0 | 12,352 | [
"VisIt"
] | 8429fb2999ab9cdaae4cc393da9fe1c5578c6578b78a8a22a42ddfe30ad42aed |
"""A package for submitting and managing PBS jobs"""
from job import *
from jobdb import *
from misc import *
from templates import *
from custom import *
__all__ = dir()
__version__ = '1.1.0'
__release__ = __version__ + '-dev'
__authors__ = 'Brian Puchala, Tyghe Vallard, Michael panciera'
__authoremails__ = 'bpuchala@... | demis001/pbs | pbs/__init__.py | Python | lgpl-2.1 | 511 | [
"Brian"
] | ac641b27a167a622263a476a3271831a78430a780618c3bcee12aeccfdd1bfc5 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publi... | arunkgupta/gramps | gramps/plugins/tool/desbrowser.py | Python | gpl-2.0 | 5,491 | [
"Brian"
] | 8f2292aff543af88a9267610c5a7aad286e29e8a195a50297ced15405cf89582 |
from ase.test import cli, require
# warning! parameters are not converged - only an illustration!
require('elk')
cli("""ase-build -x fcc -a 4.04 Al | \
ase-run elk -p \
"tasks=0,kpts=1.5,rgkmax=5.0,tforce=True,smearing=(fermi-dirac,0.05)" """)
| grhawk/ASE | tools/ase/test/elk/elk_cmdline.py | Python | gpl-2.0 | 245 | [
"ASE",
"DIRAC",
"Elk"
] | 3a531c96b05fc07001298ca1f7c961cfb0938953e0ac8baca31dd0c9efc4e328 |
from string import maketrans
import operator
import random
from collections import defaultdict
###Stats and math functions
def weighted_sampler(pop_dict):
"""randomly sample a dictionary's keys based on weights stored as values
example:
m = {'a':3, 'b':2, 'c':5}
samps = [weighted_sampl... | flag0010/pop_gen_cnn | tajimas_D/common.py | Python | gpl-3.0 | 7,301 | [
"Biopython"
] | 846e1f333bebf39734b5db94422504b95c1be118cfa757b2ffb6c24a10a7665a |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2006 Donald N. Allingham
# Copyright (C) 2007-2009 Brian G. Matherly
# Copyright (C) 2009-2010 Benny Malengier <benny.malengier@gramps-project.org>
# Copyright (C) 2010 Peter Landgren
# Copyright (C) 2011 Adam Stein <adam@csh.rit.ed... | pmghalvorsen/gramps_branch | gramps/plugins/docgen/asciidoc.py | Python | gpl-2.0 | 17,021 | [
"Brian"
] | e3d5ca50414246770db01f06046905bd5cb979a16379e9fd283706ebf1f07639 |
# Exploit Title: Nagios XI 5.5.6 Remote Code Execution and Privilege Escalation
# Date: 2019-08-24
# Exploit Author: elbae
# Vendor Homepage: https://www.nagios.com/
# Product: Nagios XI
# Software Link: https://assets.nagios.com/downloads/nagiosxi/5/xi-5.5.6.tar.gz
# Version: From 2012r1.0 to 5.5.6
# Tested on:
# - U... | elbae/misc | nagios-xi-5.5.6-rce-root-reverse.py | Python | gpl-3.0 | 10,146 | [
"VisIt"
] | 0516a231798696bc1eb5635b588e5d8717f479dd8c442a8db9eabf9dee8a332d |
# Copyright 2017 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... | npuichigo/ttsflow | third_party/tensorflow/tensorflow/contrib/timeseries/python/timeseries/state_space_models/varma.py | Python | apache-2.0 | 8,860 | [
"Gaussian"
] | babec8fa02aa7ea334baafe98d0be3fef4df78662d467afefdb35e5b57d38436 |
#!/usr/bin/env python
# -*- mode: python; coding: utf-8; -*-
# ---------------------------------------------------------------------------##
#
# Copyright (C) 1998-2003 Markus Franz Xaver Johannes Oberhumer
# Copyright (C) 2003 Mt. Hood Playing Card Co.
# Copyright (C) 2005-2009 Skomoroh
#
# This program is free softwa... | shlomif/PySolFC | pysollib/options.py | Python | gpl-3.0 | 27,460 | [
"CRYSTAL"
] | f4fa9d6b80fc34ba1043e7ce73f8958fc9b80493aa7f54f4710472b9b2b86519 |
import pysam, sys, os, random
from jobTree.src.bioio import fastaRead, fastqRead, \
cigarReadFromString,PairwiseAlignment, fastaWrite, fastqWrite, logger, absSymPath, reverseComplementChar
def pathToBaseNanoporeDir():
"""Returns path to base directory "marginAlign"
"""
import marginAlign
i = absSymPath... | isovic/marginAlign | src/margin/utils.py | Python | mit | 18,995 | [
"BWA",
"pysam"
] | 325a2ebdf08b7606cec85e1dfa2e2f8b6b7c3daa7e6d529c08249e5563ab398f |
#!/usr/bin/env python
"""
Crystal Module for Grabber v0.1
Copyright (C) 2006 - Romain Gaucher - http://rgaucher.info
"""
import sys,os,re, string, shutil
from xml.sax import * # Need PyXML [http://pyxml.sourceforge.net/]
from grabber import getContent_POST, getContentDirectURL_POST
from grabber import getCo... | goofwear/raspberry_pwn | src/pentest/grabber/crystal.py | Python | gpl-3.0 | 16,280 | [
"CRYSTAL"
] | 83503b4489accf7fcb2425f7de3cafa8397e1a13b36d46adc99d1509709a04b1 |
"""
Tests for IPython.config.application.Application
Authors:
* Brian Granger
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2008-2011 The IPython Development Team
#
# Distributed under the terms of the BSD License. The full license is in
# the file COPYING, d... | cloud9ers/gurumate | environment/lib/python2.7/site-packages/IPython/config/tests/test_application.py | Python | lgpl-3.0 | 6,003 | [
"Brian"
] | f80e262c3d7883911810979e45bbe5bbd264c8032d8d467534624e3b4e54bf47 |
# Principal Component Analysis Code :
from numpy import mean,cov,double,cumsum,dot,linalg,array,rank,size,flipud
from pylab import *
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import ro... | tapomayukh/projects_in_python | classification/Classification_with_kNN/Single_Contact_Classification/Feature_Comparison/multiple_features/best_kNN_PCA/test11_cross_validate_categories_1200ms_scaled_method_v_area_motion.py | Python | mit | 5,090 | [
"Mayavi"
] | a5e814aaaa1a418bad55fd5f5a8b4581f2562a4c783c6f1c142cf156e18ab6fd |
from __future__ import print_function
import espressomd
from espressomd import thermostat
from espressomd import integrate
import numpy as np
from threading import Thread
from math import *
from espressomd.visualization_opengl import *
# Minimal interactive OpenGL visualization for ESPResSo
print("Press u/j to change... | KonradBreitsprecher/espresso | samples/visualization_interactive.py | Python | gpl-3.0 | 1,920 | [
"ESPResSo"
] | 49fa05a39ae604003e72e4de8083adccebed98002bfaf047858eb2d26c22e0a4 |
import sys
from distutils.core import setup
if (sys.version_info.major, sys.version_info.minor) < (3, 4):
sys.exit("Python < 3.4 not supported.")
setup(
name='octopus-tools',
version='0.1',
license='LGPLv3',
packages=['octopus', 'octopus.server', 'octopus.server.orientdb', 'octopus.plugins', 'octo... | fabsx00/bjoern | python/octopus-tools/setup.py | Python | gpl-3.0 | 511 | [
"Octopus"
] | 3186fe9f7736bbaa744f08b41595ffbe0895df67ae18cc6b255d7ffb0edd7dc6 |
# Copyright 2012-2014 Brian May
#
# This file is part of python-tldap.
#
# python-tldap 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 version.... | Karaage-Cluster/python-tldap | tldap/modlist.py | Python | gpl-3.0 | 5,474 | [
"Brian"
] | 1d056d5880a2c1947384184e93ad8e85a5aec5c00843d7d49a0d966da07b7778 |
import sys
import petsc4py
petsc4py.init(sys.argv)
from petsc4py import PETSc
from src.objComposite import createEcoliComp_tunnel
from codeStore.ecoli_common import *
# @profile
def main_fun(**main_kwargs):
OptDB = PETSc.Options()
fileHandle = OptDB.getString('f', 'singleEcoliPro')
OptDB.setValue('f', f... | pcmagic/stokes_flow | ecoli_in_pipe/single_ecoli_plot.py | Python | mit | 784 | [
"VTK"
] | 503a5aed06558af7af78452032dd36fc9961b6be424e4b60e59b2340bbb1aa75 |
"""
Testing for Gaussian Process module (sklearn.gaussian_process)
"""
# Author: Vincent Dubourg <vincent.dubourg@gmail.com>
# Licence: BSD 3 clause
from nose.tools import raises
from nose.tools import assert_true
import numpy as np
from sklearn.gaussian_process import GaussianProcess
from sklearn.gaussian_process ... | shikhardb/scikit-learn | sklearn/gaussian_process/tests/test_gaussian_process.py | Python | bsd-3-clause | 6,761 | [
"Gaussian"
] | 3e85f6a3068359bbaffbe9ddfbefc8f22c13c6eaadb10b875c054406f72ff1b8 |
import functools
import warnings
from collections import Mapping
from numbers import Number
import numpy as np
import pandas as pd
from . import ops
from . import utils
from . import common
from . import groupby
from . import indexing
from . import alignment
from . import formatting
from .. import conventions
from .a... | NicWayand/xray | xarray/core/dataset.py | Python | apache-2.0 | 89,861 | [
"NetCDF"
] | a8608efc50f40fd55413bbca5ff4fb18f9b96d4f379c30b5915a462358ede892 |
__author__ = 'Tom Schaul, tom@idsia.ch'
from scipy import zeros, randn
from random import random, sample, gauss
from topology import TopologyEvolvable
class MaskedParameters(TopologyEvolvable):
""" A module with a binary mask that can disable (=zero) parameters.
If no maximum is set, the mask can ... | iut-ibk/Calimero | site-packages/pybrain/structure/evolvables/maskedparameters.py | Python | gpl-2.0 | 4,226 | [
"Gaussian"
] | c53d802ff840156e51dc0b17af200df556b0d2c72aede128621080500309b800 |
"""
Views for the verification flow
"""
import json
import logging
import decimal
import datetime
from collections import namedtuple
from pytz import UTC
from ipware.ip import get_ip
from django.conf import settings
from django.core.urlresolvers import reverse
from django.http import (
HttpResponse, HttpResponseB... | beni55/edx-platform | lms/djangoapps/verify_student/views.py | Python | agpl-3.0 | 47,604 | [
"VisIt"
] | c12b61f80736baa0c4457955af47b431e74814972f12069a465ec415d2b9759b |
# -*- coding: utf-8 -*-
"""
Created on Wed Jan 13 09:41:53 2016
@author: Radu
"""
# -*- coding: utf-8 -*-
"""
Created on Tue Jan 12 10:34:07 2016
@author: Radu
"""
from interneuron import Interneuron
from neuron import h
class Renshaw(Interneuron): #### Inherits from Cell
"""Two-section cell: A soma with acti... | penguinscontrol/Spinal-Cord-Modeling | CPG/rc_in.py | Python | gpl-2.0 | 379 | [
"NEURON"
] | 04ee735ab5df544d0fea71aa3351e322651710942af76029b2908dc1356417bf |
#!/usr/bin/env python
'''
K-means clusterization sample.
Usage:
kmeans.py
Keyboard shortcuts:
ESC - exit
space - generate new distribution
'''
# Python 2/3 compatibility
from __future__ import print_function
import numpy as np
import cv2
from gaussian_mix import make_gaussians
if __name__ == '__main__'... | makelove/OpenCV-Python-Tutorial | 官方samples/kmeans.py | Python | mit | 1,211 | [
"Gaussian"
] | acbc7ed536246c93d5ae8e57e503f354eb075a0a5e7e98ee01e2452c120ffb16 |
# ICE Revision: $Id:$
"""Working with a directory of surface samples
Should be able to generalize this with SampleDirectory, but not right now"""
from os import path,listdir
from glob import glob
from PyFoam.Error import error
import math
class SurfaceDirectory(object):
"""A directory of sampled times"""
d... | takaakiaoki/PyFoam | PyFoam/RunDictionary/SurfaceDirectory.py | Python | gpl-2.0 | 4,298 | [
"VTK"
] | d8e1b483fe7eedb36c5b80e511a1c6582a197bd19da0ec1be7a1e0e974276258 |
########################################################################
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2012/12/11 18:04:25
########################################################################
""" :mod: SubprocessTests
=======================
.. module: SubprocessTests
:synopsis: uni... | ic-hep/DIRAC | src/DIRAC/Core/Utilities/test/Test_Subprocess.py | Python | gpl-3.0 | 2,095 | [
"DIRAC"
] | 6460c0775dc30346f16ce019c7309d4ae4c1c4ab7ae2e1dfbf21d63241053292 |
import random
from templates.text import TextTemplate
def process(input, entities=None):
greetings = [
'Welcome home, sir...',
'All wrapped up here, sir. Will there be anything else?',
'I seem to do quite well for a stretch, and then at the end of the sentence I say the wrong cranberry.',... | swapagarwal/JARVIS-on-Messenger | modules/src/hello.py | Python | mit | 886 | [
"VisIt"
] | 0e4972218f554940aeadfccbc4bed5870a5ee19eac3698f6f5971f7ef17d16e4 |
import getpass
import argparse
from os import path
from string import Template
dirname = path.relpath(".", "..")
username = getpass.getuser()
parser = argparse.ArgumentParser("Initialize a boilerplate package.json")
parser.add_argument('-n', '--project_name', nargs="?", const=dirname, default=dirname)
parser.add_argu... | imdaveho/boilerplates | js-boilerplate/project_init.py | Python | gpl-2.0 | 1,423 | [
"GULP"
] | 3e4aa231e72dbce53b2028d084357c10c6a6228cd36fecf348c4a74100be1f1a |
import os
import sched
import time
from datetime import date
from datetime import datetime
from os.path import join, dirname
from pymongo import MongoClient
import sys
import base64
import cdsapi
from sendgrid import SendGridAPIClient
from sendgrid.helpers.mail import Mail
import sendgrid
from sendgrid.helpers.mail imp... | ajijohn/ebm | index1.py | Python | apache-2.0 | 8,943 | [
"NetCDF"
] | 98a2d92e7a42d7cf92a9e25e3bba05c95cf104cd464b217735f526d42e9a1441 |
# -*- coding: utf-8 -*-
# Copyright: (c) 2020-2021, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
"""Requirement provider interfaces."""
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import functools
import typing... | mattclay/ansible | lib/ansible/galaxy/dependency_resolution/providers.py | Python | gpl-3.0 | 19,439 | [
"Galaxy"
] | cb2a4ceb4575f85acd83e8ad56ca98461b0718c7ac5e9cbb6f69208630d2da89 |
from . import css
WaveSkin = {}
WaveSkin['default'] = ["svg", {"id": "svg", "xmlns": "http://www.w3.org/2000/svg", "xmlns:xlink": "http://www.w3.org/1999/xlink", "height": "0"},
["style", {"type": "text/css"}, css.css.default],
["defs",
["g", {"id":... | BreizhGeek/wavedrompy | wavedrom/waveskin.py | Python | mit | 67,433 | [
"VMD"
] | c2a2f444d5dd1d53deadebb904386827b775204e3e580040cd6f815be90421d7 |
#!/usr/bin/env python
'''
Given HLA-A and HLA-B genes annotated with BLAST IMGT/HLA database
genotypes, determine associated serotypes
DQA1 | DQB1 | type
--------------------
02:01| 02:02| DQ2.2
03:03| 02:02| DQ2.3
05:01| 02:01| DQ2.3
03:01| 03:02| DQ8
03:02| 03:02| DQ8
03:03| 03:02| DQ8
Annotations are of form DQ[A... | ErasmusMC-Bioinformatics/galaxytools-emc | tools/hla_dq/hla_dq.py | Python | mit | 2,849 | [
"BLAST"
] | 43bbbc64fd1f0e4f4966621da56d3ad59a7529d70c7e09a1d0071839eb73f0cf |
# This file is part of cldoc. cldoc 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, version 2.
#
# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the ... | kostyll/cldoc | cldoc/nodes/cclass.py | Python | gpl-2.0 | 3,157 | [
"VisIt"
] | 66074cb3f0cc92d4f90bbe031e71c3205ac82843a795441ff4a3688daed39d12 |
# -*- coding: utf-8 -*-
'''
*GSASIIstrMath - structure math routines*
-----------------------------------------
'''
########### SVN repository information ###################
# $Date: 2018-06-13 20:58:28 +0300 (Wed, 13 Jun 2018) $
# $Author: vondreele $
# $Revision: 3433 $
# $URL: https://subversion.xray.aps.a... | AntonGagin/GSAS_USE | patchSystErrors/originalOld/GSASIIstrMath.py | Python | gpl-3.0 | 233,633 | [
"CRYSTAL",
"Gaussian"
] | 29bc6c404385650b4068733fa99f31e9e3d02a053c5dbb45fe8b94e7653349c5 |
"""
This module implements an interface to the critic2 Bader analysis code.
For most Bader analysis purposes, users are referred to
pymatgen.command_line.bader_caller instead, this module is for advanced
usage requiring identification of critical points in the charge density.
This module depends on a compiled critic2... | mbkumar/pymatgen | pymatgen/command_line/critic2_caller.py | Python | mit | 34,948 | [
"CRYSTAL",
"VASP",
"pymatgen"
] | 48419c98b1570dbf7ac8f5f33b3ee112411392c391c239024f235a4b8b44a8ad |
import pysam
import sys
def snp_sort_key(snp):
return int(snp.contig) << 32 | snp.pos
class SNPInfo:
def __init__(self, contig, pos, nuc, name=None, ref="C"):
self.contig = contig
self.pos = int(pos)
self.nuc = nuc
self.ref = ref
self.name = name if name else "%s:%i:... | ARUP-NGS/BMFtools | scripts/variant_table.py | Python | mit | 6,812 | [
"pysam"
] | 56fb6c1c01f1dfa5860d0e441913b2eb1679b47d1814542d87ba693ca7b331fa |
#!/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/grad/test/test_tdrhf_grad.py | Python | apache-2.0 | 6,704 | [
"PySCF"
] | f12a0809d76792f420762c4ec2dc893a285bc9ab64c038a4ebb41177f6442027 |
import pygtk
pygtk.require20()
import gtk, gobject, cairo
from gtk import gdk
import time
class CairoDrawingArea(gtk.DrawingArea, object):
__gsignals__ = {
"expose-event" : "override",
"motion-notify-event" : "override",
"button-press-event" : "override",
"button-release-event" : "... | antoinevg/survival | core/cairodrawingarea.py | Python | gpl-2.0 | 7,350 | [
"BLAST"
] | 973e963fede0b08ae717410c4473c3691ae166d016b511f660f33eeb591ec23f |
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