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# -*- coding: utf-8 -*-
# This work is licensed under the GNU Public License (GPL).
# To view a copy of this license, visit http://www.gnu.org/copyleft/gpl.html
# Written by Abd Allah Diab (mpcabd)
# Email: mpcabd ^at^ gmail ^dot^ com
# Website: http://mpcabd.igeex.biz
# Ported and tweaked from Java to Python, from... | Edraak/circleci-edx-platform | lms/djangoapps/edraak_certificates/arabicreshaper.py | Python | agpl-3.0 | 15,374 | [
"VisIt"
] | d1b7cea32f2ef897e126196eb1b772112ef4bf2639b0920ec1f578e5198a1907 |
"""
Tests for django.utils.
"""
from unittest import TestCase
from django.utils import html, checksums
import timesince
import datastructures
import itercompat
from decorators import DecoratorFromMiddlewareTests
# We need this because "datastructures" uses sorted() and the tests are run in
# the scope of this modul... | weigj/django-multidb | tests/regressiontests/utils/tests.py | Python | bsd-3-clause | 5,639 | [
"ADF"
] | 6a5afc29da2e39b67800b9675e80b3a53bf089c195b32db753f9af48cac56ddc |
#import production
from asap3 import *
from asap3.md.verlet import VelocityVerlet
from cPickle import *
from numpy import *
#from Asap.Trajectories.NetCDFTrajectory import *
import sys, os, time
from asap3.testtools import *
from asap3.mpi import world
openkimmodel = "EMT_Asap_Standard_Jacobsen_Stoltze_Norskov_AlAgAu... | auag92/n2dm | Asap-3.8.4/Test/parallel/parallelOpenKIM_NeighMiopbc_F.py | Python | mit | 5,055 | [
"ASE",
"OpenKIM"
] | f22317e874505478260d0f5957bdecdceac23088f1dd2fe9615f73d8524ea7da |
"""Filter design.
"""
from __future__ import division, print_function, absolute_import
import warnings
import numpy
from numpy import atleast_1d, poly, polyval, roots, real, asarray, allclose, \
resize, pi, absolute, logspace, r_, sqrt, tan, log10, arctan, arcsinh, \
cos, exp, cosh, arccosh, ceil, co... | beiko-lab/gengis | bin/Lib/site-packages/scipy/signal/filter_design.py | Python | gpl-3.0 | 85,260 | [
"Gaussian"
] | bb20b09fb78529aec4fe04f104d615621810cc8e0faff2fecc14f384b4f5a2f5 |
# Copyright 2016 Google Inc. 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 applicable law or a... | deepakgupta1313/models | real_nvp/real_nvp_utils.py | Python | apache-2.0 | 16,422 | [
"Gaussian"
] | 784b335ba5ee6c66beda3b99c89cff414d29e1dc1370dbd884293011e596915b |
# Name: mapper_occci_online.py
# Purpose: Nansat mapping for OC CCI data, stored online in THREDDS
# Author: Anton Korosov
# Licence: This file is part of NANSAT. You can redistribute it or modify
# under the terms of GNU General Public License, v.3
# http://www.gnu.o... | nansencenter/nansat | nansat/mappers/mapper_opendap_globcurrent_thredds.py | Python | gpl-3.0 | 2,064 | [
"NetCDF"
] | 9de0a1aea3c20389ae00714e0827f3a8f5b331e7ee7dfed0a756b8a36c43c357 |
#!/usr/bin/env python
"""
Set the status of the replicas of given files at the provided SE
"""
from DIRAC.Core.Base.Script import Script
@Script()
def main():
# Registering arguments will automatically add their description to the help menu
Script.registerArgument(("LFN: LFN", "File: File name contai... | DIRACGrid/DIRAC | src/DIRAC/DataManagementSystem/scripts/dirac_dms_set_replica_status.py | Python | gpl-3.0 | 2,373 | [
"DIRAC"
] | 94d11052bd5adeab2074a599ba7a304fd5b1bee860238e58d7be87edab934235 |
#
# QAPI types generator
#
# Copyright IBM, Corp. 2011
#
# Authors:
# Anthony Liguori <aliguori@us.ibm.com>
#
# This work is licensed under the terms of the GNU GPLv2.
# See the COPYING.LIB file in the top-level directory.
from ordereddict import OrderedDict
from qapi import *
import sys
import os
import getopt
impor... | asias/qemu | scripts/qapi-types.py | Python | gpl-2.0 | 7,529 | [
"VisIt"
] | 7b64a97bdb90ac427ccc97516973988912af4cad4c18537ab636771848ead590 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | MOA-2011/enigma2-plugin-extensions-openwebif | plugin/controllers/views/web/getaudiotracks.py | Python | gpl-2.0 | 6,042 | [
"VisIt"
] | c42c8f9fc1a9662f918f026f2da3d51d2baa1bd7257352bc84d3c989df71e745 |
# ============================================================================
#
# Copyright (C) 2007-2012 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | jeroendierckx/Camelot | camelot/view/controls/delegates/codedelegate.py | Python | gpl-2.0 | 2,125 | [
"VisIt"
] | 97cebc8358bc603423c28e9020849f6f99cb8fc9d740497cc4a277c63dc3951d |
import math
import re
import cv2
import os
from opendm import dls
import numpy as np
from opendm import log
from opendm.concurrency import parallel_map
from opensfm.io import imread
from skimage import exposure
from skimage.morphology import disk
from skimage.filters import rank, gaussian
# Loosely based on https://g... | pierotofy/OpenDroneMap | opendm/multispectral.py | Python | gpl-3.0 | 20,483 | [
"Gaussian"
] | ba73c16e6de9e27ada5a5a17dd86771de21ad5baaca40f6589c4ee4c00b88f05 |
"""
.. class:: LineLuminosityFunctionFromSimulations
.. moduleauthor:: Johan Comparat <johan.comparat__at__gmail.com>
The class LineLuminosityFunctionFromSimulations is dedicated to measuring the line luminosity functions obtained from simulations.
"""
from os.path import join
import os
import astropy.cosmology as co... | JohanComparat/nbody-npt-functions | python/LineLuminosityFunctionFromSimulations.py | Python | cc0-1.0 | 7,700 | [
"Galaxy"
] | cbe68b49226d30d34c3a811221b35a93324a4849e23b00ccc3da9664a2333fcb |
"""
Module containing hdf file utility functions for the SD object
"""
import logging
from cis.utils import listify
# Optional HDF import, if the module isn't found we defer raising ImportError until it is actually needed.
try:
from pyhdf import SD
except ImportError:
SD = None
def get_hdf_SD_file_variables(f... | cedadev/jasmin_cis | cis/data_io/hdf_sd.py | Python | gpl-3.0 | 6,295 | [
"NetCDF"
] | be0fc69e0448f5c635f303128efe7c451037a375a99fa1a872b6756be6fb5380 |
# -*- coding: utf-8 -*-
"""Cut out parts. Kept for reference."""
# Part of py_pRF_mapping library
# Copyright (C) 2016 Ingo Marquardt
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either ... | ingo-m/py_pRF_mapping | pyprf/analysis/legacy/cutout.py | Python | gpl-3.0 | 4,193 | [
"Gaussian"
] | 137766fe7465a48fafbf98c92fe540f7105632b0b6b2e8b6fae204e18312609f |
import argparse
import os
from coalib.misc import Constants
from coalib.collecting.Collectors import get_all_bears_names
from coalib.parsing.filters import available_filters
class CustomFormatter(argparse.RawDescriptionHelpFormatter):
"""
A Custom Formatter that will keep the metavars in the usage but remove... | Nosferatul/coala | coalib/parsing/DefaultArgParser.py | Python | agpl-3.0 | 10,400 | [
"VisIt"
] | 581db65b2a487b8a1d22c1eb271f218ae8275c271d7b33555413901b7ac2a402 |
from Cython.Compiler import TypeSlots
from Cython.Compiler.ExprNodes import not_a_constant
import cython
cython.declare(UtilityCode=object, EncodedString=object, BytesLiteral=object,
Nodes=object, ExprNodes=object, PyrexTypes=object, Builtin=object,
UtilNodes=object, Naming=object)
import... | JulienMcJay/eclock | windows/Python27/Lib/site-packages/Cython/Compiler/Optimize.py | Python | gpl-2.0 | 143,143 | [
"VisIt"
] | 339eab3d8f56f61ecf2bcf4f2b4a773073b5d2840deeaa6d0870f6141736b03f |
""" Test class for Job Agent
"""
# imports
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import pytest
from mock import MagicMock
# DIRAC Components
from DIRAC.WorkloadManagementSystem.Agent.JobAgent import JobAgent
from DIRAC import gLogger
gLogger.setL... | yujikato/DIRAC | src/DIRAC/WorkloadManagementSystem/Agent/test/Test_Agent_JobAgent.py | Python | gpl-3.0 | 8,134 | [
"DIRAC"
] | 51619170a7332964ea125493fc387e5487d2596644f6e6fc113fd8a66f5f3ddd |
#!/usr/bin/env python
########################################################################
# File : dirac-dms-replicate-lfn
# Author : Stuart Paterson
########################################################################
"""
Replicate an existing LFN to another Storage Element
Usage:
dirac-dms-replicate-l... | yujikato/DIRAC | src/DIRAC/Interfaces/scripts/dirac_dms_replicate_lfn.py | Python | gpl-3.0 | 2,054 | [
"DIRAC"
] | e82e03b1b958da87bf19409e7549bd0462f550279f9d6d34725b2c37c4da16aa |
# Copyright 2014, Brian Coca <bcoca@ansible.com>
# Copyright 2017, Ken Celenza <ken@networktocode.com>
# Copyright 2017, Jason Edelman <jason@networktocode.com>
# Copyright 2017, Ansible Project
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of ... | caphrim007/ansible | lib/ansible/plugins/filter/mathstuff.py | Python | gpl-3.0 | 6,506 | [
"Brian"
] | 698d2c01e382e0f223afc3fcb544195f556dbb7012016c1ff78b0835cab3ad70 |
# Copyright 2008-2013 Nokia Siemens Networks Oyj
#
# 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... | ktan2020/legacy-automation | win/Lib/site-packages/robot/conf/gatherfailed.py | Python | mit | 1,434 | [
"VisIt"
] | 777bc712653892ee43555b61be24eb565a9a0a3f1ea344328cfb5794a9c124ab |
#!/usr/bin/env python
# -*- encoding: utf-8 -*-
# CREATED:2015-02-02 11:07:07 by Brian McFee <brian.mcfee@nyu.edu>
'''Pitch deformation algorithms'''
import librosa
import pyrubberband as pyrb
import re
import numpy as np
from ..base import BaseTransformer
__all__ = ['PitchShift', 'RandomPitchShift', 'LinearPitchShi... | silky/muda | muda/deformers/pitch.py | Python | apache-2.0 | 5,699 | [
"Brian"
] | 6237e8b43a01c19ecd70c418e9fa7a10a7b1e5e7a231117c56889f77229cedd3 |
import logging
import re
import os
import vcf
from sv_interval import SVInterval
logger = logging.getLogger(__name__)
mydir = os.path.dirname(os.path.realpath(__file__))
'''
From the CNVnator README
The output is as follows:
CNV_type coordinates CNV_size normalized_RD e-val1 e-val2 e-val3 e-val4 q0
normalized_RD... | msahraeian/metasv | metasv/cnvnator_reader.py | Python | bsd-2-clause | 4,105 | [
"Gaussian"
] | 30147abd6b51db05459226bc3b2ddea96a7be325a2e0e019092475d16c1a7187 |
import cv2
import numpy as np
from matplotlib import pyplot as plt
# cv2.getGaborKernel(ksize, sigma, theta, lambda, gamma, psi, ktype)
# ksize - size of gabor filter (n, n)
# sigma - standard deviation of the gaussian function
# theta - orientation of the normal to the parallel stripes
# lambda - wavelength of the si... | anooptoffy/Masters-Course-Work-Repository | Semester_2/Machine Perception/Assignment1/question_9.py | Python | mit | 993 | [
"Gaussian"
] | d6784ca42cd807e3b46974e608206c06feed03549307e628106d0b3aeee99057 |
import os, shutil
class calculate_stability(object):
def __init__(self):
self.new_sequences_list = []
self.split_new_seq_list = []
self.num_splits = 4
self.structure = "1HA0"
self.bash_file_name = "bash_file.sh"
if self.structure == "1HA0":
self.structur... | blab/stability | augur/mutator/mutate_everything_1HA0/mutator_stability.py | Python | agpl-3.0 | 5,914 | [
"FoldX"
] | 8c2f9c39011a54b00545d8eca5d28e32e2b444f42d9132d06b3ba09ea973da39 |
"""
Module for importing and exporting NeuroML
"""
from __future__ import print_function
from __future__ import division
from __future__ import absolute_import
from builtins import str
from builtins import range
try:
import neuroml
from pyneuroml import pynml
from pyneuroml import __version__ as pynml... | Neurosim-lab/netpyne | netpyne/conversion/neuromlFormat.py | Python | mit | 77,244 | [
"NEURON",
"VisIt"
] | f01481f9d3577967255c1aa785d3ebb6490ab8e361915bcb624a247f100f8eca |
from ase.dft import Wannier
from gpaw import restart
atoms, calc = restart('benzene.gpw', txt=None)
wan = Wannier(nwannier=18, calc=calc, fixedstates=15, file='wan18.pickle')
import pylab as pl
weight_n = pl.sum(abs(wan.V_knw[0])**2, 1)
N = len(weight_n)
F = wan.fixedstates_k[0]
pl.figure(1, figsize=(12, 4))
pl.bar(r... | misdoro/python-ase | doc/tutorials/wannier/plot_spectral_weight.py | Python | gpl-2.0 | 670 | [
"ASE",
"GPAW"
] | c3b1782fd07cd79709c8a7d688c3e2105598f57806785313c30ee24de1fed4f2 |
# -*- coding: utf-8 -*-
#
"""Solve the Ginzburg--Landau equation.
"""
import numpy as np
import meshplex
import krypy
import pynosh.numerical_methods as nm
import pynosh.modelevaluator_nls as gm
def _main():
args = _parse_input_arguments()
# read the mesh
print("Reading the mesh...")
mesh, _, _, _ ... | nschloe/pynosh | tools/find_beautiful_states.py | Python | mit | 8,204 | [
"ParaView"
] | 0e0791bdba51035e4c110a663a17cd58ed07dc6107ac57539dce0836a8778d4c |
"""
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... | davidgbe/scikit-learn | sklearn/datasets/samples_generator.py | Python | bsd-3-clause | 56,423 | [
"Gaussian"
] | 4579390d46116a6e4d08d1c839cb51d6dbebb10ed7120bd39aea12a63cd5fba3 |
'''
Constructors for the various cells.
( used for dmon config automation)
'''
import synapse.axon as s_axon
import synapse.neuron as s_neuron
import synapse.cryotank as s_cryotank
def cryo(dirn, conf=None):
return s_cryotank.CryoCell(dirn, conf=conf)
def axon(dirn, conf=None):
return s_axon.AxonCell(dirn, co... | vivisect/synapse | synapse/cells.py | Python | apache-2.0 | 475 | [
"NEURON"
] | a1fe9e59399577e2eff3c71b8de0559abbc9042c828a938682a78837994183a2 |
##############################################################################
# adaptiveMD: A Python Framework to Run Adaptive Molecular Dynamics (MD)
# Simulations on HPC Resources
# Copyright 2017 FU Berlin and the Authors
#
# Authors: Jan-Hendrik Prinz
# Contributors:
#
# `adaptiveMD` is free software: ... | thempel/adaptivemd | adaptivemd/mongodb/dictify.py | Python | lgpl-2.1 | 21,328 | [
"MDTraj",
"OpenMM"
] | be1df23822b824405c23846fe53822d775d6a12a6b0d112fb6ae6f6af955ee8e |
#
# Copyright (C) 2013,2014,2015,2016 The ESPResSo project
#
# 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 Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option)... | lahnerml/espresso | testsuite/python/particle.py | Python | gpl-3.0 | 6,182 | [
"ESPResSo"
] | 31a3431073464ce7836b17ddbb569d1b0da563a4f872d3b313e1cedc9a9549a2 |
#!/usr/bin/env python
# Copyright 2015 The Kubernetes Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appli... | abgworrall/test-infra | hack/verify_boilerplate.py | Python | apache-2.0 | 6,301 | [
"VisIt"
] | c113038d5fa8cb73175d134b9165c8e55874ea5b951dea5638a547f66e6b8721 |
from django.apps import apps
from django.contrib.postgres.fields import ArrayField
from django.core.exceptions import FieldDoesNotExist
from django.db import models
import numpy as np
from scipy.stats import f_oneway
class Experiment(models.Model):
"""Information about each experiment"""
slug = models.CharFi... | brookefitzgerald/neural-exploration | neural_exploration/visualize/models.py | Python | mit | 4,735 | [
"NEURON"
] | ea29bb1cd77fde59fb6bf49dced18cbd26f8be27f24298d7d42adb98fdde77da |
from aces.materials import Material
from aces.modify import get_unique_atoms
from ase import Atoms,Atom
from math import pi,sqrt
from ase.dft.kpoints import ibz_points
from aces import config
from ase.lattice import bulk
import numpy as np
from aces.tools import *
class structure(Material):
def set_parameters(self):
... | vanceeasleaf/aces | aces/materials/P_nacl.py | Python | gpl-2.0 | 1,993 | [
"ASE"
] | 8ef45e961dd0010daec8610ea82243340d394b266b5fd34506b128c2d579b4c1 |
# ===============================================================================
# Copyright (C) 2010 Diego Duclos
#
# This file is part of eos.
#
# eos is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, ... | pyfa-org/Pyfa | eos/saveddata/fit.py | Python | gpl-3.0 | 79,804 | [
"CRYSTAL"
] | f9ba5aff85fa851113801045aae1ce6e7f2458297efcefec65934bf691a143d9 |
#!/usr/bin/env python -i
# preceeding line should have path for Python on your machine
# simple.py
# Purpose: mimic operation of couple/simple/simple.cpp via Python
# Syntax: simple.py in.lammps
# in.lammps = LAMMPS input script
import sys
# parse command line
argv = sys.argv
if len(argv) != 2:
print "S... | slitvinov/lammps-swimmer | python/examples/simple.py | Python | gpl-2.0 | 1,214 | [
"LAMMPS"
] | ef40eb9bb97549bc331943b39a8fcbe5c63a1a0774c932dd62d87d34384cce9d |
import unittest
import ctree.c.nodes as C
from ctree.transforms import ConstantFold
class TestConstantFold(unittest.TestCase):
def test_add_zero(self):
tree = C.Add(C.SymbolRef("a"), C.Constant(0))
tree = ConstantFold().visit(tree)
self.assertEqual(tree, C.SymbolRef("a"))
tree = C... | ucb-sejits/ctree | test/test_transforms/test_constant_fold.py | Python | bsd-2-clause | 2,868 | [
"VisIt"
] | a5ff7fad999b29a4a2b4356a6fbfae9d19baced6f000d95d989ee29600b552d4 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
import unittest
import pymatgen
from pymatgen.analysis.cost import CostDBCSV, CostAnalyzer, CostDBElements
module_dir = os.path.join(os.path.dirname(pymatgen.__file__), '..', 'test_files')
class Co... | mbkumar/pymatgen | pymatgen/analysis/tests/test_cost.py | Python | mit | 1,557 | [
"pymatgen"
] | c099491d68a5aa0849ba1e60a1f025607e7e9281bc2cfb27ca312180afc01e4d |
"""
Adaptive thresholding
when image has different lighting conditions in different areas, simple thresholding no good
Adaptive: algorithm calculates threshold for small regions of image
- different thresholds for different regions of same image
- gives better results for images with varying illumination
"""
... | SSG-DRD-IOT/commercial-iot-security-system | opencv/tutorials/imageProcessing/thresholding/adaptive.py | Python | mit | 1,406 | [
"Gaussian"
] | fc3e0a9f301d6ac7e88a0ae6be5e5be856a1d329bb73a2639e55f9665f7902ce |
"""
Read all output flagstat files and store values in a text table.
Creates two tables in the output directory: readcounts.txt and readcounts_fractions.txt, which contains useful human-readable percentage statistics.
Each row will be a sample.
Values to store (columns) are:
Total reads from SAMPLE.bam.flagstat
... | vlsci/variant_calling_pipeline | count_flagstat_wgs.py | Python | mit | 3,621 | [
"BWA"
] | 4b6097f15aef6dccb4a642a604b55fe6f6d52bdeade788e28b3317724aa25c2c |
# encoding: utf-8
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding field 'GeoRecord.geo_id_segments'
db.add_column(u'profiles_georecord', 'geo_id_segments', self.gf... | ProvidencePlan/Profiles | communityprofiles/profiles/oldmigrations/0065_auto__add_field_georecord_geo_id_segments.py | Python | mit | 21,299 | [
"MOE"
] | b8331dd5ab111893bc412acb524adcf50ddd2baa8ea4babf9f7ac29fd262e4d4 |
# -*- coding: utf-8 -*-
#
# gif_cond_exp_multisynapse.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of t... | sdiazpier/nest-simulator | pynest/examples/gif_cond_exp_multisynapse.py | Python | gpl-2.0 | 1,466 | [
"NEURON"
] | c9a3980da7adb776eae1e88a10a360d6c6c14a9987097db05945163d3ee0af7b |
'''
Wifi Facade.
=============
The :class:`Wifi` is to provide access to the wifi of your mobile/ desktop
devices.
It currently supports `connecting`, `disconnecting`, `scanning`, `getting
available wifi network list` and `getting network information`.
Simple examples
---------------
To enable/ turn on wifi scannin... | bhaveshAn/crisscross | crisscross/facades/wifi.py | Python | mit | 2,974 | [
"VisIt"
] | bf54ed40d5d98be294dc4f1662c29c57aaac84ed06a4250f6f05c2f49241ea8f |
# a part of cropgui, a graphical front-end for lossless jpeg cropping
# Copyright (C) 2009 Jeff Epler <jepler@unpythonic.net>
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; eithe... | onno74/cropgui | cropgui_common.py | Python | gpl-2.0 | 12,672 | [
"FLEUR"
] | 7ed43a3534804bd403c1b9d50ed1a0db134106e0b3d124386639fc072071c4ed |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2018, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
"""
Basis Function Manipulation
################################
Functions for managing and manipulating basis set data.
Many of the ordering schemes used in computational codes can ... | avmarchenko/exatomic | exatomic/algorithms/basis.py | Python | apache-2.0 | 23,606 | [
"Gaussian",
"MOLCAS",
"NWChem"
] | f580a25597b43a859038ca190de4bc7fc40e77c8aac0a2f5857abee0a2f4ce5c |
"""
Atomic coordinate featurizer.
"""
import numpy as np
from deepchem.feat.base_classes import MolecularFeaturizer
from deepchem.utils.typing import RDKitMol
class AtomicCoordinates(MolecularFeaturizer):
"""Calculate atomic coordinates.
Notes
----
This class requires RDKit to be installed.
"""
def __i... | lilleswing/deepchem | deepchem/feat/molecule_featurizers/atomic_coordinates.py | Python | mit | 1,996 | [
"RDKit"
] | b62d47537a7fce1afa38f3b97a2a755a518f97d4f4b3a2e56e5bbbc9b623bd3a |
""" PublisherHandler
This service has been built to provide the RSS web views with all the information
they need. NO OTHER COMPONENT THAN Web controllers should make use of it.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = '$Id$'
# pyli... | yujikato/DIRAC | src/DIRAC/ResourceStatusSystem/Service/PublisherHandler.py | Python | gpl-3.0 | 11,914 | [
"DIRAC"
] | 24d457811bd56c5f64ee6b3aacf0b065d8024a3bf720a90d47f28f2b4cc480da |
import os
import subprocess
import luigi
# initialize parameters ---------------------------------------------------
OUT_PREFIX = "out/"
FILE_PREFIX = "test_" # a pefix to differentiate files
adapter_r1 = "ATGGTGAGCAAGGGCGAGGAGCTGTC"
adapter_r2 = "CTAGCTACCTA"
reference_transcriptome = "data/transcriptome/zfish"
#... | santiago1234/PipelinesBazziniLab | mapping_arielome/mapping.py | Python | mit | 6,513 | [
"Bowtie"
] | c194d27f844750b863074c505de5a03022115848e296443f92fa1271737df75c |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2009 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... | andrebellafronte/stoq | stoqlib/gui/wizards/renegotiationwizard.py | Python | gpl-2.0 | 6,772 | [
"VisIt"
] | dc74861d54bf0550397d518bd0eb9a3080a56f5b7e26460b282d939ef411f033 |
#!/usr/bin/env python
# Copyright 2015 The Kubernetes 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
#
# Unle... | nagarjung/kubernetes | hack/boilerplate/boilerplate.py | Python | apache-2.0 | 4,760 | [
"VisIt"
] | 9391d920592a821e32ec2d2d2c5f8f06f2273304e05ee2231261a963bd2614e4 |
#
#
# Trying to create V-I plot
#
# Author: Dan Ruedt
#
# This file has been developed as part of the neuroConstruct project
# This work has been funded by the Medical Research Council and the
# Wellcome Trust
#
#
from sys import *
from java.io import File
from GenerateV_ICurve import Voltage... | pgleeson/TestArea | models/GranCell_Dan_analysis/V_I_plot.py | Python | gpl-2.0 | 998 | [
"NEURON"
] | a99c1f82f3ebbb5ecd278b2644edeaada0a8133c766a92e469e850b8c1f1d5b9 |
import math
import unittest
from monty.serialization import MontyDecoder
from pymatgen.core.operations import SymmOp
from pymatgen.core.tensors import *
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from pymatgen.util.testing import PymatgenTest
class TensorTest(PymatgenTest):
_multiprocess_shared_ ... | gmatteo/pymatgen | pymatgen/core/tests/test_tensors.py | Python | mit | 25,048 | [
"pymatgen"
] | c09f5d683c7c81c7097087cfdc251ee20e53aa1255106594dd1d4baf8e2f2934 |
# -*- coding: utf-8 -*-
"""The check functions."""
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
#
# License: BSD (3-clause)
import operator
from distutils.version import LooseVersion
import os.path as op
import numpy as np
from ._logging import warn, logger
def _ensure_int(x, name='unknown', must_b... | adykstra/mne-python | mne/utils/check.py | Python | bsd-3-clause | 18,200 | [
"Mayavi"
] | 4f8925abd2e0816309e9e218a32b12225955257dbf04f3759509fc9ff1897752 |
from game_map import *
STARTING_MONEY = 30
class Player(object):
"""Player class contains a record of the money the player has."""
def __init__(self, money):
super(Player, self).__init__()
self.money = money
def pay(self, price):
self.money -= price
def receive(self, price):
self.money += price
class E... | huesitos/python-games | swf/engine.py | Python | gpl-2.0 | 3,388 | [
"VisIt"
] | c3d8e0e6d148c588fa977e9a3690cda5ab607532c775edce66892cc77b0a468a |
# 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/Spatial_Resolution/space_resolution_per_meter_percent.py | Python | mit | 3,500 | [
"Mayavi"
] | b47cd0deccbc362746113d349025c27df76040b6fdd2c55c98f29b0a3ae497d6 |
'''
Created on 28/09/2012
@author: Amr Hassan
'''
import os
import sys
import struct
import string
import math
import numpy
from random import randrange
import logging
import PGDBInterface
class SAGEDataReader:
#The Module handles the data reading from SAGE output to a memory data structure.
DebugToFile=F... | IntersectAustralia/asvo-tao | core/sageimport_mpi_BSP/SAGEReader.py | Python | gpl-3.0 | 11,167 | [
"Galaxy"
] | 9f435e81bde4ebe88e07c40aeeab1784f1237a3926847796f9ef797df2ec774b |
import sys, collections, itertools, os.path
if len( sys.argv ) != 3:
sys.stderr.write( "Script to prepare annotation for DEXSeq.\n\n" )
sys.stderr.write( "Usage: python %s <in.gtf> <out.gff>\n\n" % os.path.basename(sys.argv[0]) )
sys.stderr.write( "This script takes an annotation file in Ensembl GTF format\n"... | vipints/oqtans | oqtans_tools/DEXSeq/1.6/src/dexseq_prepare_annotation.py | Python | bsd-3-clause | 5,259 | [
"HTSeq"
] | af6a58805e2112644bd8a4f044419551119e882aeb2eb6baeeea5222d7d3bda7 |
#!/usr/bin/python
# Copyright: (c) 2020, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
ANSIBLE_METADATA = {
'metadata_version': '1.1',
'status': ['preview'],
... | azaghal/ansible | test/integration/targets/ansible-galaxy-collection/library/setup_collections.py | Python | gpl-3.0 | 5,506 | [
"Galaxy"
] | fd6c757597caed40d1b673a330fabb38ecc101a0be398037672db313fd3d93b0 |
#!/usr/bin/env python
"""
This file is part of RAPD
Copyright (C) 2009-2018, Cornell University
All rights reserved.
RAPD is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, version 3.
RAPD is distributed i... | RAPD/RAPD | src/sites/gatherers/necat_t.py | Python | agpl-3.0 | 29,403 | [
"CRYSTAL"
] | c37f4f41201dc9237e444e89ae7ef11dad1ed04be32304ea5266ba595994c39f |
""" Class that contains client access to the production DB handler. """
__RCSID__ = "$Id$"
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.Base.Client import Client
from DIRAC.ProductionSystem.Utilities.StateMachine import ProductionsStateMachine
class ProductionClient(Client):
""" Exposes the functiona... | petricm/DIRAC | ProductionSystem/Client/ProductionClient.py | Python | gpl-3.0 | 4,328 | [
"DIRAC"
] | f7dcaae9dec7744112f18bcf061a366e0f70c7525b80302b8674515456e10201 |
# Copyright Adam Cripps (2004, 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2013)
# Licensed under the GNU GPL v2.
# See https://www.gnu.org/licenses/gpl-2.0.html for more information.
from wxPython.lib.grids import wxGridSizer, wxFlexGridSizer
from wxPython.wx import *
from sndhdr import *
from wave import *
i... | kabads/jiletters | jiletters.py | Python | gpl-2.0 | 6,908 | [
"MOOSE",
"Octopus"
] | ba1ba4eba2a9fe4dfda313e080a57ae6e749d0cce8bb02ee2fcb279668c86a81 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# (c) 2012 Michal Kalewski <mkalewski at cs.put.poznan.pl>
#
# This file is a part of the Simple Network Simulator (sim2net) project.
# USE, MODIFICATION, COPYING AND DISTRIBUTION OF THIS SOFTWARE IS SUBJECT TO
# THE TERMS AND CONDITIONS OF THE MIT LICENSE. YOU SHOULD H... | mkalewski/sim2net | sim2net/mobility/nomadic_community.py | Python | mit | 15,334 | [
"VisIt"
] | 0c69fac05127573caf493889bc2117d4438e61d81ad6d3fe52bf68ec3c678cd3 |
import os
from vote_boat.models import Poll,IdeaTag,Idea,User,Vote
def add_poll(title,admin_user_id,description=""):
kws = dict(title=title,admin_user_id=admin_user_id,description=description)
return Poll.objects.get_or_create(**kws)[0]
def add_idea_tag (tag):
kws = dict(tag=tag)
return IdeaTag.object... | astrodsg/vote-boat-site | vote_boat_site/tests/populate_database.py | Python | bsd-3-clause | 2,118 | [
"Brian"
] | fe1514fa966f225a0d9a58f4e75436538a3c4b7367480f6da14df1ffac26f8bc |
# This file is not meant for public use and will be removed in SciPy v2.0.0.
# Use the `scipy.signal.windows` namespace for importing the functions
# included below.
import warnings
from . import _windows
__all__ = [ # noqa: F822
'boxcar', 'triang', 'parzen', 'bohman', 'blackman', 'nuttall',
'blackmanharris'... | ilayn/scipy | scipy/signal/windows/windows.py | Python | bsd-3-clause | 1,128 | [
"Gaussian"
] | 7a88f4c6200b4b2c4c912465b33f4ceee97a536fc849e467b1eb5b83f0ad11ff |
"""
A set of utilities for making velocity plots.
"""
from __future__ import (absolute_import, division, print_function,
unicode_literals)
from .general import Plot
from .utils import get_nrows_ncols
from ..data.atomic import AtomDat
from ..data.spectral import Absorber
from ..modeling.vpfit... | cwfinn/igmtools | igmtools/plot/velplot_utils.py | Python | bsd-3-clause | 26,932 | [
"Gaussian"
] | b5da145d9724ae07171435b36ffcba9985fc05066cdea491e03a5a75f92396d6 |
# -*- coding: utf-8 -*-
"""
Created on Thu Feb 18 08:49:01 2016
@author: Radu
"""
from neuron import h
class Motoneuron(object):
"""Two-section cell: A soma with active channels and
a dendrite with passive properties."""
def __init__(self):
self.x = self.y = self.z = 0
hoc_file =... | penguinscontrol/Spinal-Cord-Modeling | Python/motoneuron_template.py | Python | gpl-2.0 | 4,300 | [
"NEURON"
] | bf29ac41b5a72d1ee0473a1d3452b46f95a829821957179a3c57f5c56f48c1a9 |
# encoding: utf-8
from woo.dem import *
from woo.fem import *
import woo.core
import woo.dem
import woo.pyderived
import woo.models
import math
from minieigen import *
class FallingHorse(woo.core.Preprocessor,woo.pyderived.PyWooObject):
'''Preprocessor for the falling horse simulation. The falling horse is histor... | woodem/woo | py/pre/horse.py | Python | gpl-2.0 | 12,738 | [
"ParaView",
"VTK"
] | 127a5efd60f6c1d470fc4dd5b75cd448985512678ef79d44b3bfa2f51053d83e |
"""Print out the source text corresponding to AST nodes.
"""
import astroid
import colorama
from colorama import Fore, Back, Style
import python_ta.transforms.setendings as setendings
import os
colorama.init(strip=False, autoreset=True)
def _wrap_color(code_string):
"""Wrap key parts in styling and resets.
... | RyanDJLee/pyta | sample_usage/print_nodes.py | Python | gpl-3.0 | 3,026 | [
"VisIt"
] | 8e7edd657e7d2545b5d86241a9d62974514c0e64333bbcb7ec727fcb56eea559 |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publ... | thica/ORCA-Remote | src/ORCA/scripts/BaseScript.py | Python | gpl-3.0 | 4,707 | [
"ORCA"
] | 9fbdb6efdb4b3a4645645427c883c9f6d2aa8fb28ea49015cfbe33738415e38a |
"""
# Notes:
- This simulation seeks to emulate the COBAHH benchmark simulations of (Brette
et al. 2007) using the Brian2 simulator for speed benchmark comparison to
DynaSim. However, this simulation includes CLOCK-DRIVEN synapses, for direct
comparison to DynaSim's clock-driven architecture. The synaptic connec... | asoplata/dynasim-benchmark-brette-2007 | Brian2/brian2_benchmark_COBAHH_clocksyn_lodens_compiled_500.py | Python | gpl-3.0 | 3,912 | [
"Brian"
] | b1930a766a0212a7825168d97dfb71f10c440c710a618be7ec9169416ffa5e25 |
from app.models import Users
from app.service import UsersService
from app.service_tests.service_test_case import ServiceTestCase
class UsersServiceTests(ServiceTestCase):
# mark_user_as_authenticated tests #
def test_mark_user_as_authenticated(self):
email = 'phil@phil.phil'
user = Users(
... | pbraunstein/trackercise | app/service_tests/users_service_tests.py | Python | mit | 4,755 | [
"Brian"
] | 92bb4d2a93e5105eae1f5da0736d4d693908feda305ae24d8939f6145aa4f00e |
################################################################################
# #
# Copyright (C) 2010-2018 The ESPResSo project #
# ... | mkuron/espresso | doc/tutorials/06-active_matter/SOLUTIONS/enhanced_diffusion.py | Python | gpl-3.0 | 5,605 | [
"ESPResSo"
] | 5a0d86f4d04bba4bf8a3e58c0478f6d2102921a1abc524dbd01c1aee6ee022ef |
import os
from generic import obj
from simulation import Simulation,SimulationInput,SimulationAnalyzer
from vasp_input import VaspInput,generate_vasp_input
from vasp_analyzer import VaspAnalyzer
class Vasp(Simulation):
input_type = VaspInput
analyzer_type = VaspAnalyzer
generic_identifier ... | habanero-rice/hclib | test/performance-regression/full-apps/qmcpack/nexus/library/vasp.py | Python | bsd-3-clause | 6,365 | [
"VASP"
] | 39cb26593d4d0b3e64bee66cdf60452f6142badccbfda8fbe418b5d3730a53c1 |
import json
import os
import subprocess
import tempfile
import time
import splinter
import xvfbwrapper
class BaseTest(object):
def setup(self):
self.xvfb = xvfbwrapper.Xvfb()
self.xvfb.start()
self.browser = splinter.Browser('firefox')
def teardown(self):
self.browser.quit()
... | qsensei/dbpedia-tutorial | tests/test_scripts.py | Python | mit | 3,885 | [
"VisIt"
] | 3e8393aefc3fe5484a5af9abf3e902451701e56fe078b47acbd412f1d286ed15 |
# Copyright 2018 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... | theflofly/tensorflow | tensorflow/tools/compatibility/tf_upgrade_v2_test.py | Python | apache-2.0 | 60,327 | [
"Gaussian"
] | 585a8ed12ca4f518db82a08892137c813953de5225ab713aceb9d466125ad98e |
#
# Copyright (c) 2013, Novartis Institutes for BioMedical Research Inc.
# Copyright (c) 2021, Greg Landrum
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source... | bp-kelley/rdkit | rdkit/Chem/Draw/UnitTestSimilarityMaps.py | Python | bsd-3-clause | 8,913 | [
"RDKit"
] | 33e625fb51ca45363371291cbe1c68ea07c5557fd3dfcd6edef8011f47012b80 |
import copy
import gc
import pickle
import sys
import unittest
import warnings
import weakref
import inspect
import types
from test import support
class FinalizationTest(unittest.TestCase):
def test_frame_resurrect(self):
# A generator frame can be resurrected by a generator's finalization.
def ... | batermj/algorithm-challenger | code-analysis/programming_anguage/python/source_codes/Python3.5.9/Python-3.5.9/Lib/test/test_generators.py | Python | apache-2.0 | 59,594 | [
"VisIt"
] | 5535aa1f3b0aa6537192cce4fe999f162653344a487228023f176f90e3294600 |
########################################################################
# File : DownloadInputData.py
# Author : Stuart Paterson
########################################################################
""" The Download Input Data module wraps around the Replica Management
components to provide access to datas... | chaen/DIRAC | WorkloadManagementSystem/Client/DownloadInputData.py | Python | gpl-3.0 | 14,554 | [
"DIRAC"
] | 48dc78374bc53baebec57f527f6707bcfe8e42d93064156de796ea43a9ff3939 |
# -*- coding: utf-8 -*-
#
# test_step_rate_generator.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of th... | terhorstd/nest-simulator | pynest/nest/tests/test_step_rate_generator.py | Python | gpl-2.0 | 2,870 | [
"NEURON"
] | 3ba10f67f1f81f06be99b2b2bbd48c60cffe9f953ed8fd31d858c2ccbe02c48c |
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
gmm_N = int(sys.argv[1])
save_path = "/afs/slac.stanford.edu/u/ki/mwillia1/Thesis/Loca... | drphilmarshall/LocalGroupHaloProps | final_scripts/savegmm.py | Python | gpl-2.0 | 4,673 | [
"Gaussian"
] | 642394cf9eb49fd2c81a7dc33917b491554cc4317f14813a04fbdd0e711479e5 |
#
# Copyright 2019-2020 Johannes Hoermann (U. Freiburg)
# 2014-2016 Lars Pastewka (U. Freiburg)
# 2015-2016 Adrien Gola (KIT)
# 2014 James Kermode (Warwick U.)
#
# matscipy - Materials science with Python at the atomic-scale
# https://github.com/libAtoms/matscipy
#
# This program is free s... | libAtoms/matscipy | matscipy/electrochemistry/__init__.py | Python | lgpl-2.1 | 1,188 | [
"Matscipy"
] | 97a4a180455e5ae4a923deb342be1acb91730d48bb6f328f2445278e4bd643a0 |
#!/usr/bin/env python
#* 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... | harterj/moose | python/moosesqa/test/test_SQARequirementReport.py | Python | lgpl-2.1 | 1,711 | [
"MOOSE"
] | 588676772ab2840ffde536ac198382c90d91615e4be1ef5c4de61b171929a2b9 |
#
# Copyright (C) 2013-2019 The ESPResSo project
#
# 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 Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | psci2195/espresso-ffans | testsuite/python/cellsystem.py | Python | gpl-3.0 | 2,871 | [
"ESPResSo"
] | 7a43bf861abb4759477441eb748635a0fa0be1f03cb06f0c7362b6456571aa16 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Functions to calculate the electronic density of states (DOS).
TODO: Tetrahedra methods (linear and optimized).
"""
import numpy as np
from .constants import ev_to_ry
from .xmlfile import get_cell_data, get_calculation_data, get_band_strucure_data
from .pyqe import ... | QEF/postqe | postqe/dos_postqe.py | Python | lgpl-2.1 | 4,275 | [
"DIRAC",
"Gaussian"
] | 2d0ae3de6d498b7f1d437870c8cee706468ab23a674c71cfe6c9db7f58de2151 |
#!/usr/bin/env python
################################################################
# copyright (c) 2016 by William R. Pearson and The Rector &
# Visitors of the University of Virginia */
################################################################
# Licensed under the Apache License, Version 2.0 (the "License"... | uwbmrb/BMRB-API | server/wsgi/bmrbapi/submodules/fasta36/psisearch2/psisearch2_msa.py | Python | gpl-3.0 | 16,866 | [
"BLAST"
] | f7f2477bc15c7b3c3be22305bead145d2444af3c794685978d70be0e4917d26c |
"""
.. _glyph_table_example:
Table of Glyphs
~~~~~~~~~~~~~~~
``vtk`` supports tables of glyphs from which glyphs are looked
up. This example demonstrates this functionality.
"""
import pyvista as pv
import numpy as np
###############################################################################
#
# We can allow ... | akaszynski/vtkInterface | examples/01-filter/glyphs_table.py | Python | mit | 2,062 | [
"VTK"
] | b3815db2ad535b6f2b14a1a223dd42e842e8f1b4f9ed6cd13d37ae3458b94cf1 |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# 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... | googleapis/python-storage-transfer | tests/unit/gapic/storage_transfer_v1/test_storage_transfer_service.py | Python | apache-2.0 | 95,928 | [
"Octopus"
] | cd9288d0890a9b048e0c4b6f04e20dd3888c9d914a7b9fa41a3072ee0d93eb10 |
#!/usr/bin/python
# coding=utf-8
# NOTE: The reason the encoding of this file is specified as UTF-8 is that Tesseract
# sometimes returns UTF-8 characters as its guesses, and in those rare cases that
# we're actually interested in what Tesseract thinks, we may have string literals
# whose values are UTF-8. The only ... | avtobiff/virtualagc | Tools/ProoferComments/ProoferComments.py | Python | gpl-2.0 | 30,877 | [
"Octopus"
] | 0a78e42ebb57d2fbaf23248b538cfe6c9442f9e71444c1371d79c45e02fc69e6 |
#!/usr/bin/env python
""" Performs a DIPS ping on a given target and exit with the return code.
It uses the local host certificate
The target is specified as ""<port>/System/Service"
The script does not print anything, and just exists with 0 in case of success,
or 1 in case of error """
import sys
import os
import ti... | ic-hep/DIRAC | src/DIRAC/Interfaces/scripts/dirac_framework_self_ping.py | Python | gpl-3.0 | 1,043 | [
"DIRAC"
] | 554b4a361b2634185ba2e35ff1cbc694eb447b6e3bc833be44d868a826531390 |
# Copyright (C) 2016-2018 The ESPResSo project
# Copyright (C) 2014 Olaf Lenz
#
# 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 Public License as published by
# the Free Software Foundation, either version 3 of the License, or... | hmenke/espresso | src/python/espressomd/gen_pxiconfig.py | Python | gpl-3.0 | 1,873 | [
"ESPResSo"
] | d8f4808ffa7e07c77f6212cd720a0f3e285674f970257e295a77866c36692252 |
# -*- coding: utf-8 -*-
#
# intrinsic_currents_spiking.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of ... | hakonsbm/nest-simulator | pynest/examples/intrinsic_currents_spiking.py | Python | gpl-2.0 | 6,874 | [
"NEURON"
] | 2fbda6233701854dcb2c2365a30f87d16366963fccdcac2ca65b1e7db4fc5d76 |
import argparse
def ParseSg(p_sg):
sg_inp = p_sg.add_argument_group('Input options')
sg_inp.add_argument('-s', dest='sg', required=True, help='sgRNA Fastq File (required)', metavar='<sgRNA.fq>')
sg_otp = p_sg.add_argument_group('Output options')
sg_otp.add_argument('-o', dest='tdir', help='Output Direc... | bm2-lab/cage | src/ui/ui_sg.py | Python | mit | 816 | [
"BWA"
] | 09abd16457f0ce196a25acfdcb527778917cecd5abff5f97f424289256c435fd |
# Copyright (C) 2019 The ESPResSo project
#
# 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 Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later versio... | espressomd/espresso | testsuite/scripts/samples/test_grand_canonical.py | Python | gpl-3.0 | 1,479 | [
"ESPResSo"
] | 7a5d51b38abd0dff56055151dacabc4c181ecd86bf4fa198dd4bda161d341930 |
#
# This file is part of the CCP1 Graphical User Interface (ccp1gui)
#
# (C) 2002-2007 CCLRC Daresbury Laboratory
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 ... | alexei-matveev/ccp1gui | interfaces/mopac.py | Python | gpl-2.0 | 17,380 | [
"MOPAC"
] | ad392bad9e71070eccb7a71f116c49b2fe5862a871b7ddc417f47353952b26e2 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (C) 2014 The ProteinDF development team.
# see also AUTHORS and README if provided.
#
# This file is a part of the ProteinDF software package.
#
# The ProteinDF is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Publ... | ProteinDF/ProteinDF_bridge | proteindf_bridge/biopdb.py | Python | gpl-3.0 | 26,423 | [
"Amber"
] | 02a4839bc99b0f97809c1c581f740e12fe9468cbe73ca0160052d3ce612aad98 |
from functools import lru_cache
import math
from scipy import optimize, stats, integrate
import numpy as np
import quaternion # adds to numpy # noqa # pylint: disable=unused-import
import cv2
from scipy.optimize import leastsq
from visnav.settings import *
class ImageProc:
latest_opt = None
show_fit = No... | oknuutti/visnav-py | visnav/algo/image.py | Python | mit | 16,219 | [
"Gaussian"
] | f9d301e2325d2944e6ea18ba382dd11017b34be8cfefe2ad49d4caec6cd04b18 |
from django.test import TestCase
from django.test.client import Client
from reader.models import Feed, FeedEntry
from reader.forms import FeedForm
from reader.views import mark_read
from django.core.urlresolvers import reverse
import unittest, new, os, sys, glob, re, urllib, string, posixpath, time, codecs
import Sim... | ejesse/django-reader | src/reader/tests.py | Python | bsd-3-clause | 6,165 | [
"COLUMBUS"
] | 9c2aec5af752696e9f13a34a5b656ea71b07e9410de5520dcb16911091e76c87 |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publi... | thica/ORCA-Remote | src/ORCA/utils/Platform/generic/generic_GetMACAddress.py | Python | gpl-3.0 | 2,277 | [
"ORCA"
] | a7b6bcbd82850ce772fb412dfd08fe7d937e41781c442b282f5e3cb76c0187d1 |
"""
Views related to the Custom Courses feature.
"""
import csv
import datetime
import functools
import json
import logging
import pytz
from contextlib import contextmanager
from copy import deepcopy
from cStringIO import StringIO
from django.core.urlresolvers import reverse
from django.http import (
HttpResponse... | JCBarahona/edX | lms/djangoapps/ccx/views.py | Python | agpl-3.0 | 21,414 | [
"VisIt"
] | dae51bc8db2fd4ca1b7a77dbd5445552863b6c2b0d1d73c573b81a62777f45ff |
#!/usr/bin/env python
#-*- coding:utf-8 -*-
# vim:ai:sta:et:ts=4:sw=4:sts=4
"""kernelng 0.x
Tool for maintaining customized overlays of kernel-ng.eclass-based ebuilds
Copyright 2005-2014 Gentoo Foundation
Copyright (C) 2005 Colin Kingsley <tercel@gentoo.org>
Copyright (C) 2008 Zac Medico <zmedico@ge... | gmt/kernel-ng-util | kernelng/utils.py | Python | gpl-2.0 | 1,845 | [
"Brian"
] | 1a971b1438f76133c728e18a708725053b9f4766d71365a10ab978779bc2e2b2 |
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