text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
"""
Copyright 2009 Zepheira
Provides basic functions for interacting with Yammer via the Yammer API v1:
https://www.yammer.com/api_doc.html
Depends on the installation of a Python OAuth library:
http://code.google.com/p/oauth/
http://oauth.googlecode.com/svn/code/python/
This will behave like a bot. To that... | dpla/zen | lib/yammer.py | Python | apache-2.0 | 6,366 | [
"VisIt"
] | 48742901871b2909543e4c1579abbde0e0d389bde01d77394371bc598be33955 |
# -*- coding: utf-8 -*-
#
# twoneurons.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
... | suku248/nest-simulator | pynest/examples/twoneurons.py | Python | gpl-2.0 | 2,663 | [
"NEURON"
] | 2f0c71d1f6733c14507f8dea2a3e2683f08c8ab27224ac107f05e7765a3f5c6d |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# adminfreeze - front end to freezing files into write-once archive
# Copyright (C) 2003-2014 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of t... | heromod/migrid | mig/cgi-bin/adminfreeze.py | Python | gpl-2.0 | 1,106 | [
"Brian"
] | 360b50abec33ac56ef019e3ea9dbee572095685bc269b575d14b16c24e639c1d |
#
# The MIT License (MIT)
#
# Copyright (c) 2016 Robert Hammelrath
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, cop... | robert-hh/SSD1963-TFT-Library-for-PyBoard | pyboard/tft.py | Python | mit | 34,687 | [
"CRYSTAL"
] | 9e804a48ad27ad56d0cd1b63d6539d08923e8456924246d42f1b4dc6aaddada3 |
from examples.stencil_grid.stencil_kernel import *
from examples.stencil_grid.stencil_grid import StencilGrid
from ctree.util import Timer
import sys
import numpy
import math
width = int(sys.argv[2])
height = int(sys.argv[3])
image_in = open(sys.argv[1], 'rb')
stdev_d = 3
stdev_s = 70
radius = stdev_d * 3
class Kern... | ucb-sejits/ctree | examples/stencil_grid/bilateral_filter.py | Python | bsd-2-clause | 3,304 | [
"Gaussian"
] | 2aa941f3877491ddc08cff77815b27c20c1f47a073558638964c5f950d631ffe |
# -*- coding: utf-8 -*-
""" *==LICENSE==*
CyanWorlds.com Engine - MMOG client, server and tools
Copyright (C) 2011 Cyan Worlds, Inc.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3... | zrax/moul-scripts | Python/plasma/Plasma.py | Python | gpl-3.0 | 263,368 | [
"VisIt"
] | e8b01fb607b31d22313aca18eb6c951c5ef9cbc8e4cdc46a2d6847cf1a42628f |
import numpy as np
import mdtraj as md
from simtk.openmm import app
import simtk.openmm as mm
from simtk import unit as u
from repex import rest
code = "benzene"
ff_name = "amber99sbildn"
water_name = 'tip3p'
which_forcefield = "%s.xml" % ff_name
which_water = '%s.xml' % water_name
ligand_filename = "./benzene2.pdb... | kyleabeauchamp/T4Binding | code/benzene_box.py | Python | gpl-2.0 | 2,030 | [
"MDTraj",
"OpenMM"
] | a32fa37a836b560fce72f78495f5d7e4b01d3c86b367fb880042bc329d6a2a1b |
# -*- coding: utf-8 -*-
# Copyright (c) 2006-2011, 2013-2014 LOGILAB S.A. (Paris, FRANCE) <contact@logilab.fr>
# Copyright (c) 2011-2014 Google, Inc.
# Copyright (c) 2012 Tim Hatch <tim@timhatch.com>
# Copyright (c) 2013-2018 Claudiu Popa <pcmanticore@gmail.com>
# Copyright (c) 2014 Brett Cannon <brett@python.org>
# Co... | ekwoodrich/python-dvrip | env/lib/python3.5/site-packages/pylint/checkers/exceptions.py | Python | mit | 21,418 | [
"VisIt"
] | 5e752bf3d2619e1ffb492fdf6aa31cce14031a7547d01348421bfe2e4ad53c81 |
# Generated by Django 1.11.2 on 2017-06-22 10:22
import bitfield.models
import django.contrib.auth.models
import django.core.validators
import django.db.models.deletion
import django.utils.timezone
from django.conf import settings
from django.db import migrations, models
from django.db.backends.postgresql.schema import... | brainwane/zulip | zerver/migrations/0001_initial.py | Python | apache-2.0 | 29,467 | [
"VisIt"
] | e801b4fb19acf48c97a7e5c31c2c5872a1572b9c81472446dbbb3e77fbc3a6b6 |
#!/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... | nuclear-wizard/moose | test/tests/variables/fe_hermite_convergence/plot.py | Python | lgpl-2.1 | 1,471 | [
"MOOSE"
] | bd888078b8f0aee70c3baf8b5589fd46d1660ac0837bac36a9c2586c6531869c |
import sys
import pylink
from time import sleep
from threading import Thread, Event, Condition
import logging
import re
if sys.version_info < (3, 0):
import Queue as queue
# __class__ = instance.__class__
else:
import queue
from avatar2.archs.arm import ARM
from avatar2.targets import TargetStates
from av... | avatartwo/avatar2 | avatar2/protocols/jlink.py | Python | apache-2.0 | 8,768 | [
"MOE"
] | 7e3ce4c7ed9927d80a3ec45a342d46472a3c7a052ba3bf9a1d549faa5aac4543 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2005-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2009 Benny Malengier
# Copyright (C) 2010 Nick Hall
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2012 Gary Burton
# Copyright (C) 2... | prculley/gramps | gramps/gui/viewmanager.py | Python | gpl-2.0 | 76,169 | [
"Brian"
] | ac37dcfdcd5aed5d69f78e8b56fb1dc40514713a1e87d3a9806da16717a48183 |
import tensorflow as tf # neural network for function approximation
import gym # environment
import numpy as np # matrix operation and math functions
from gym import wrappers
import gym_morph # customized environment for cart-pole
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import time
star... | GitYiheng/reinforcement_learning_test | test03_monte_carlo/t41_rlvps03.py | Python | mit | 7,665 | [
"NEURON"
] | b54e596fd106a0ae2c513343867dd94ce0ed46bf610bdcebf4b71f750574f26a |
# -*- coding: utf-8 -*-
"""
tests.datastructures
~~~~~~~~~~~~~~~~~~~~
Tests the functionality of the provided Werkzeug
datastructures.
Classes prefixed with an underscore are mixins and are not discovered by
the test runner.
TODO:
- FileMultiDict
- Immutable types undertested... | magne4000/werkzeug | tests/test_datastructures.py | Python | bsd-3-clause | 30,907 | [
"TINKER"
] | e2e2f697434be1c9e1cbe760100c6341758216d3201ba2eb6acfe48488c89911 |
#!/usr/bin/env python
"""
test.py
Author: Tony Papenfuss
Date: Mon Jun 23 22:35:08 EST 2008
"""
import os, sys
from sqlalchemy import MetaData, Table, Column, Integer, Float, Text
from sqlalchemy import create_engine
from sqlalchemy.orm import mapper, sessionmaker, relation
from sqlalchemy.sql.expression import joi... | PapenfussLab/Mungo | mungo/alchemy/tests/query.py | Python | artistic-2.0 | 1,096 | [
"BLAST"
] | 4d816658c66429671893fa02260604e9492f84e781e65d7341953636c3d0fd59 |
########################################################################
# $HeadURL$
########################################################################
""" DIRAC FileCatalog mix-in class to manage users and groups
"""
__RCSID__ = "$Id$"
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.Sec... | miloszz/DIRAC | DataManagementSystem/DB/FileCatalogComponents/UserAndGroupManager.py | Python | gpl-3.0 | 11,944 | [
"DIRAC"
] | 5da4bd76b600ced0df50a103574f9f02096c17e4d9418f71e19fc7acca1a27f6 |
# -*- coding: utf-8 -*-
from collections import defaultdict
import numpy as np
from chemreac import ReactionDiffusion
from chempy import ReactionSystem
from chempy.units import to_unitless, SI_base_registry, get_derived_unit, allclose, default_units as u
analytic = [
lambda y0, k, t: (
y0[0] * np.exp(-k[0]... | bjodah/chemreac | chemreac/tests/test_odesys.py | Python | bsd-2-clause | 6,214 | [
"ChemPy"
] | 6e4557c996c0482ca60cff8d1587fa823559b270ac8a483e862dd01598b794b2 |
import os
import time
import json
import numpy as np
from ..dftb import DFTBplus, read_detailed_out
from pychemia.crystal import KPoints
from pychemia import pcm_log, Structure
class KPointConvergence:
def __init__(self, structure, workdir='.', slater_path='.', waiting=False, energy_tolerance=1E-3,
... | MaterialsDiscovery/PyChemia | pychemia/code/dftb/task/kpconv.py | Python | mit | 3,982 | [
"CRYSTAL"
] | f0a7cedbfa76246be45b6b7445ffe564393c140b47689ed59c1271f5b35ca198 |
## \file
## \ingroup tutorial_pyroot
## \notebook
## Example of function called when a mouse event occurs in a pad.
## When moving the mouse in the canvas, a second canvas shows the
## projection along X of the bin corresponding to the Y position
## of the mouse. The resulting histogram is fitted with a gaussian.
## A ... | root-mirror/root | tutorials/pyroot/DynamicSlice.py | Python | lgpl-2.1 | 3,997 | [
"Gaussian"
] | c3e4398f3ab4260ad8ed853a069bcfb06ac648d446e2c5af6dfbb582112e823b |
# Lint as: python2, python3
# Copyright 2015 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 req... | ddexnet/dsrf | setup.py | Python | apache-2.0 | 4,199 | [
"VisIt"
] | 70d9c5a48832a28996bd3b50c384584212bf93e794e4f9053a33bf26b6dedb87 |
# Copyright (c) 2014, the GREAT3 executive committee (http://www.great3challenge.info/?q=contacts)
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without modification, are permitted
# provided that the following conditions are met:
#
# 1. Redistributions of source code must retain... | barnabytprowe/great3-public | inputs/galdata/training_galaxy_props_real.py | Python | bsd-3-clause | 7,274 | [
"Galaxy",
"Gaussian"
] | 54e12b540dcb242e8bf91851a2909f992d7256bd2e841b808b6fe68ad9a6552b |
"""Module for evaluating (PATH|MANNER|COMPOUND) classifier."""
__author__ = "Zachary Yocum"
__email__ = "zyocum@brandeis.edu"
import os, warnings
from corpus import *
import numpy as np
from collections import Counter
from scipy.stats.stats import pearsonr
from sklearn import svm, metrics, cross_validation
from sk... | zyocum/motion-type-classifier | eval.py | Python | mit | 12,561 | [
"VisIt"
] | 14a74d0bca5348a027cf83997876aa5ef7aded36774a6f36bd7c3718ed7695f3 |
# -*- coding: utf-8 -*-
""" Tests for student account views. """
import logging
import re
from unittest import skipUnless
from urllib import urlencode
import mock
import ddt
from django.conf import settings
from django.core import mail
from django.core.files.uploadedfile import SimpleUploadedFile
from django.core.url... | fintech-circle/edx-platform | lms/djangoapps/student_account/test/test_views.py | Python | agpl-3.0 | 35,614 | [
"VisIt"
] | 349ef73e28a09cc74b203e33b4d1d8fd82237a59cf4c79fc2a18096e764340cf |
#!/usr/bin/env python
# ** The MIT License **
#
# Copyright (c) 2015 The Brookhaven Group, LLC
# Author: Marc Schwarzschild
#
# 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 restricti... | Schwarzschild/gback | gback/gback.py | Python | mit | 11,964 | [
"VisIt"
] | 1ae81f63391b4ad11de3728fe8a2af47a0d6366942df4c6714bf0958a2d37572 |
"""Copy number detection using read counts, with cn.mops.
http://www.bioconductor.org/packages/release/bioc/html/cn.mops.html
"""
import os
import re
import shutil
import subprocess
import pysam
import toolz as tz
from bcbio import bam, install, utils
from bcbio.distributed.multi import run_multicore, zeromq_aware_l... | brainstorm/bcbio-nextgen | bcbio/structural/cn_mops.py | Python | mit | 11,115 | [
"Bioconductor",
"pysam"
] | 71301c5bae2e3a7499c89ad307937da6ce045c5ab28adebae62005eaaf482daf |
#!/usr/bin/env python
"""
CsPython Tutorial Example 3
By Mark Gossage (mark@gossage.cjb.net)
A pure-Python script to show the use of Crystal Space.
To use this, ensure that your PYTHONPATH, CRYSTAL, and LD_LIBRARY_PATH
(or DYLD_LIBRARY_PATH for MacOS/X; or PATH for Windows) variables are set
approrpriately, and then ... | baoboa/Crystal-Space | scripts/python/tutorial3.py | Python | lgpl-2.1 | 7,068 | [
"CRYSTAL"
] | 931db963f8d83c109dd146b316de202d128bb1bdd28042fb6e0101d730bfdc04 |
# -*- coding: utf-8 -*-
# Copyright 2014-2016 The HyperSpyUI developers
#
# This file is part of HyperSpyUI.
#
# HyperSpyUI 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
#... | hyperspy/hyperspyUI | hyperspyui/plugins/align.py | Python | gpl-3.0 | 14,382 | [
"Gaussian"
] | a2a7d80eefd4dc9cdfb659171b1781ddd7c681630d15c1d909931683a650b1c8 |
# Copyright (C) 2012,2013,2015,2016
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# 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 ... | fedepad/espressopp | src/interaction/CoulombTruncatedUniqueCharge.py | Python | gpl-3.0 | 7,179 | [
"ESPResSo"
] | 3c592b5950f7e9777963ded160c941dc2ce56e34a05c352e237109f2516e50a5 |
import abc
import array
import math
import os
import pickle
import re
import signal
import subprocess as sub
from datetime import datetime
from shutil import copy2, rmtree, which
from acpype import __version__ as version
from acpype.logger import set_logging_conf as logger
from acpype.mol import Angle, Atom, AtomType,... | alanwilter/acpype | acpype/topol.py | Python | gpl-3.0 | 125,476 | [
"Amber",
"CHARMM",
"GAMESS",
"Gaussian",
"Gromacs",
"Jaguar",
"MOPAC",
"NAMD",
"ORCA",
"Pybel",
"VMD"
] | e963ce2df0d238234c6d8ec945607d1b9babdb19c35aea7d6ab67bae74e85612 |
# -*- coding: utf-8 -*-
""" Tests for student account views. """
import re
from unittest import skipUnless
from urllib import urlencode
import json
import mock
import ddt
import markupsafe
from django.conf import settings
from django.core.urlresolvers import reverse
from django.core import mail
from django.contrib im... | kamalx/edx-platform | lms/djangoapps/student_account/test/test_views.py | Python | agpl-3.0 | 17,533 | [
"VisIt"
] | 42f71b0a464f369666215dd196139f162d48d0442516d110c59c8d5594bbaec0 |
import ocl
import camvtk
import time
import vtk
import datetime
import math
import random
import numpy as np
import gc
def drawVertex(myscreen, p, vertexColor, rad=1):
myscreen.addActor( camvtk.Sphere( center=(p.x,p.y,p.z), radius=rad, color=vertexColor ) )
def drawEdge(myscreen, e, edgeColor=camvtk.yellow):
... | AlanZatarain/opencamlib | scripts/voronoi/voronoi_8_scale-test.py | Python | gpl-3.0 | 6,627 | [
"VTK"
] | 4ffde84519768c8a0898058ed3e061c521d8bf8ed4254ee5de59e8df3067a1bf |
# rdesignerProtos.py ---
#
# Filename: rdesignerProtos.py
# Description:
# Author: Subhasis Ray, Upi Bhalla
# Maintainer:
# Created: Tue May 7 12:11:22 2013 (+0530)
# Version:
# Last-Updated: Wed Dec 30 13:01:00 2015 (+0530)
# By: Upi
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#
# Change l... | rahulgayatri23/moose-core | python/rdesigneur/rdesigneurProtos.py | Python | gpl-3.0 | 13,405 | [
"MOOSE",
"NEURON"
] | b38cbcd0e83adf804fbb801219fe4afacd0e9916a67ac9996df677a3e29ad973 |
import numpy as np
import scipy.ndimage as ndi
from .._shared.utils import warn
from . import _marching_cubes_cy
def marching_cubes(volume, level, spacing=(1., 1., 1.),
gradient_direction='descent'):
"""
Marching cubes algorithm to find iso-valued surfaces in 3d volumetric data
Paramet... | pratapvardhan/scikit-image | skimage/measure/_marching_cubes.py | Python | bsd-3-clause | 14,778 | [
"Mayavi"
] | 9004c626daa3202f5b350d4de7da969d970ff91ec0aea944366548b8555e3303 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module contains an algorithm to solve the Linear Assignment Problem.
It has the same functionality as linear_assignment.pyx, but is much slower
as it ... | xhqu1981/pymatgen | pymatgen/optimization/linear_assignment_numpy.py | Python | mit | 8,228 | [
"pymatgen"
] | 6f91df2f7619cb1162b099704f6d2473f99ca8e8a480dd4de679ad7d096c5afa |
# -*- coding: utf-8 -*-
from .. Error import RINGError
class Reader(object):
"""
Reader reads the parsed RING input, and returns the RDkit wrapper objects
in pgradd.RDkitWrapper.
Attributes
----------
ast : abstract syntax tree obtrained from parser
"""
def __init__(self, ast):
... | VlachosGroup/VlachosGroupAdditivity | pgradd/RINGParser/Reader.py | Python | mit | 2,491 | [
"RDKit"
] | 2824fea4260dfd31243c41928a6c2f6ec310679f8b11aa06feea3b334b0c3883 |
#! /usr/bin/env python
#PBS -N Timing
#PBS -l nodes=1:ppn=4:opteron285
#PBS -q small
from numpy import *
from asap3 import *
from asap3.md.verlet import VelocityVerlet
from asap3.md.langevin import Langevin
from ase.lattice.cubic import FaceCenteredCubic
from asap3.Timing import report_timing
import sys, cPickle, tim... | auag92/n2dm | Asap-3.8.4/Test/Timing/TimingLangevin.py | Python | mit | 3,432 | [
"ASE"
] | 783ba638d1b9650a9e386883d9323026421ba37253ed76e85180ea252995c6db |
from __future__ import division
import os.path
from subprocess import Popen, PIPE
from operator import itemgetter
from itertools import izip
from array import array
from numpy import histogram, zeros, median, sum as np_sum
import pysam
try:
from pysam.csamtools import Samfile
except ImportError:
from pysam im... | pziarsolo/bam_crumbs | bam_crumbs/statistics.py | Python | gpl-3.0 | 12,923 | [
"pysam"
] | 9f610f6a58dcf4b6f66168a04a1bcb6c14e34ffe38e71b76926065d2260903e8 |
import io
import os
import sys
from configparser import ConfigParser
import fsbc.application
from fsgamesys.application import ApplicationMixin
from fsgamesys.context import fsgs
from fsgamesys.Database import Database
from fsgamesys.util.gamenameutil import GameNameUtil
class Application(ApplicationMixin, fsbc.appl... | FrodeSolheim/fs-uae-launcher | fsgamesys/main.py | Python | gpl-2.0 | 3,786 | [
"ADF"
] | 79ee3194ac2b6ccb52b3c4193919576e1ed99a8d98c1629936ff60ac82f5416d |
# -*- Mode: Python; coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2013 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 General Public License as published by
## the Free Sof... | andrebellafronte/stoq | stoq/gui/shell/statusbar.py | Python | gpl-2.0 | 3,793 | [
"VisIt"
] | 61491a658c6419d53c698d2a3254c43d19e71e5b538b0548f68e7e7a6da9c1db |
"""Classes of random variables."""
import numpy as np
import numpy.random as rnd
from numpy import sqrt
from struct_tools import NicePrint
from dapper.tools.matrices import CovMat
class RV(NicePrint):
"""Class to represent random variables."""
printopts = NicePrint.printopts.copy()
printopts["ordering"... | nansencenter/DAPPER | dapper/tools/randvars.py | Python | mit | 7,783 | [
"Gaussian"
] | 0f243550c4659986f674e5adeb80b1ae80d531df34b79a322a73f1884d2d39a7 |
#############################################################################
## Pipeline is now on github: https://github.com/pminguez/geneticaPipeline ##
#############################################################################
import sys
from glob import glob
from subprocess import call
import argparse
import ... | pminguez/geneticaPipeline | pipeline_v4.py | Python | gpl-3.0 | 15,242 | [
"BWA"
] | 50a4582647df6ce00d1c47e91ee2a62493f24faba950baa6c9a873f7de989ac4 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import os
from datetime import datetime
from unittest import TestCase
from django.test import ignore_warnings
from django.utils import html, safestring
from django.utils._os import upath
from django.utils.deprecation import RemovedInDjango20Warning
from ... | maxsocl/django | tests/utils_tests/test_html.py | Python | bsd-3-clause | 8,173 | [
"ADF"
] | bc8c147f1a27b5ea43a1a462d641561f75d9fefafb96c28b3affa9837b4d928a |
#!/usr/bin/python
# Copyright 2012, SIL International
# All rights reserved.
#
# This library is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published
# by the Free Software Foundation; either version 2.1 of License, or
# (at y... | silnrsi/graide | lib/graide/runview.py | Python | lgpl-2.1 | 16,301 | [
"VisIt"
] | 69692404a664b53b2d4fe02b2917b61e8751d56a879f51fce828d05303172abb |
import json
from CommonServerPython import *
from FindSimilarIncidentsByText import main
import random
nouns = ['people', 'history', 'way', 'art', 'world', 'information', 'map', 'two', 'family', 'government', 'health',
'system', 'computer', 'meat', 'year', 'thanks', 'music', 'person', 'reading', 'method', 'd... | demisto/content | Packs/Base/Scripts/FindSimilarIncidentsByText/FindSimilarIncidentsByText_test.py | Python | mit | 19,458 | [
"VisIt"
] | 6e7ef50a5259df7fb20e0bae98e24ae68252fe141e05ec180d0885049e1a4a4a |
#
# This file is part of the CCP1 Graphical User Interface (ccp1gui)
#
# (C) 2002-2006 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/smeagol.py | Python | gpl-2.0 | 11,038 | [
"GAMESS"
] | b72f22b427ec6d1eab822c2dfb341ba6bd757d3da722ce2ea66835baa2fe938e |
# vim: set expandtab ts=4 sw=4 filetype=python fileencoding=utf8:
import copy
import logging
import textwrap
import psycopg2.extras
from profiles.pg import RelationWrapper
log = logging.getLogger(__name__)
class IndicatorsFactory(psycopg2.extras.CompositeCaster):
def make(self, values):
d = dict(zip(s... | 216software/Profiles | profiles/profiles/pg/indicators.py | Python | mit | 25,205 | [
"MOE"
] | ae1f20a43a6b044adbc5458d74cf915e7543cb41ac8597d689356b051e393021 |
COLORS = [
{
"x": 93,
"y": 138,
"z": 168,
"label": "Air Force blue"
},
{
"x": 240,
"y": 248,
"z": 255,
"label": "Alice blue"
},
{
"x": 227,
"y": 38,
"z": 54,
"label": "Alizarin crimson"
},
{
"x": 239,
"y": 222,
"z": 205,
"label": "Almond"
}... | adregan/pnger | colors/colors.py | Python | mit | 59,169 | [
"Amber"
] | 98055cc4d72545d8c8ae733eaf891f001cedf2ec69341d6fbd65e1a445985aad |
from ase.dft import get_distribution_moment
import numpy as np
precision = 1E-8
x = np.linspace(-50., 50., 1000)
y = np.exp(-x**2 / 2.)
area, center, mom2 = get_distribution_moment(x, y, (0, 1, 2))
assert sum((abs(area - np.sqrt(2. * np.pi)), abs(center), abs(mom2 - 1.))) < precision
x = np.linspace(-1., 1., 100000)... | grhawk/ASE | tools/ase/test/distmom.py | Python | gpl-2.0 | 661 | [
"ASE"
] | 7267918a5170f0deb2220dc0d29cf6a1f5cbb6481efee28c94fb5d9b61d8d529 |
# materials.py is a subroutine of NumBAT that defines Material objects,
# these represent dispersive lossy refractive indices and possess
# methods to interpolate n from tabulated data.
# Copyright (C) 2017 Bjorn Sturmberg, Kokou Dossou.
# NumBAT is free software: you can redistribute it and/or modify
# it un... | bjornsturmberg/NumBAT | backend/materials.py | Python | gpl-3.0 | 18,724 | [
"CRYSTAL"
] | 09fbef764f105529ae1c28be380d42a2d9f19a127bf8fbb4edc3248a264ccb23 |
'''
Given a TableDataSet and an output file name write a netCDF file.
Created on Feb 28, 2017
@author: cyoung
'''
class NetCDFWriter :
def __init__(self,tableDataSet,outputFile) :
self.tableDataSet=tableDataSet
self.outputFile=outputFile
def write (self):
pass | charles-g-young/Table2NetCDF | gov/noaa/gmd/table_2_netcdf/NetCDFWriter.py | Python | apache-2.0 | 306 | [
"NetCDF"
] | 03115d283b8962aa72cdec6590a69317a270a0fced101375050cf05f56074fe0 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import unittest
import tempfile
from monty.json import MontyDecoder
from monty.serialization import loadfn
from pymatgen.io.vasp.sets import *
from pymatgen.io.vasp.inp... | johnson1228/pymatgen | pymatgen/io/vasp/tests/test_sets.py | Python | mit | 32,924 | [
"VASP",
"pymatgen"
] | f97fcfa23476659282c1b683d00d068eedc168263b918ed7c13df35a7b2750a4 |
import gp_controller as gpc
import iCubInterface
import numpy as np
import yarp
import time
import math
import matplotlib.pylab
import random
import os
import sys
#import as find_lines
def exitModule(resetProbability):
randomNum = random.random()
if randomNum < resetProbability:
return True
return... | tacman-fp7/tactile-control | python/iCubControllerOld.py | Python | gpl-2.0 | 13,070 | [
"Gaussian"
] | 77c56d5bda89b893b73c01bb0727fcd20ed8c335a62a80abf72d9c7805201dd5 |
# noqa
import pytest
from pathlib import Path
from birdy import utils
from .common import resource_file
def test_is_url(): # noqa: D103
assert utils.is_url("http://localhost:5000/wps")
assert utils.is_url("file:///path/to/my/file.txt")
assert not utils.is_url("myfile.txt")
def test_is_file(): # noq... | bird-house/birdy | tests/test_utils.py | Python | apache-2.0 | 4,521 | [
"NetCDF"
] | 4d9656c6593e146e35babf7fe976f04d9d685e8f64574265a054b41f0f3e3491 |
# -*- coding: utf-8 -*-
#
# MNE documentation build configuration file, created by
# sphinx-quickstart on Fri Jun 11 10:45:48 2010.
#
# This file is execfile()d with the current directory set to its containing
# dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All c... | antiface/mne-python | doc/conf.py | Python | bsd-3-clause | 9,345 | [
"Mayavi"
] | 654433d8eaa180bde2cf00a1c0d7a5b08de60c11a869e0e68e48dcc4f3b045d2 |
#! /usr/bin/env python
#
# Copyright 2000-2001, GMD, Sankt Augustin
# -- German National Research Center for Information Technology
#
# Copyright 2010, LIFIA - Facultad de Informatica - Univ. Nacional de La Plata
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GN... | 0xalen/opencaster_isdb-tb | tools/oc2sec/file2mod.py | Python | gpl-2.0 | 15,593 | [
"VisIt"
] | 64b96f23a189b134f2f7762b23c8b918454db00a2ca97a54b2a996046df3ddee |
"""
DIRAC.StorageManagementSystem package
"""
| DIRACGrid/DIRAC | src/DIRAC/StorageManagementSystem/__init__.py | Python | gpl-3.0 | 49 | [
"DIRAC"
] | d08d8d7218f0b1ca98e276017c1745e35271d7728c027544227891ab57911175 |
from unittest import TestCase
from dark.blast.score import bitScoreToEValue, eValueToBitScore
class TestBitScoreToEValue(TestCase):
"""
Tests for the bitScoreToEValue function.
"""
def testTrivial(self):
"""
For a bit score of 1.0 on a database of size 1 with a query length
1,... | terrycojones/dark-matter | test/blast/test_score.py | Python | mit | 12,605 | [
"BLAST"
] | 697a5c41b86c16767476a3f7975db18fe09d89137444d6736ebba7d7a78b14ab |
# coding=utf-8
# Copyright 2022 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... | google-research/google-research | smurf/smurf_flags.py | Python | apache-2.0 | 8,532 | [
"Gaussian"
] | 2fae5e8eb701cace514a05d15e8dcb288f85b9bc3b3fec5462e8ca9626b8e6a3 |
""" DIRAC FileCatalog Security Manager mix-in class
"""
__RCSID__ = "$Id$"
import os
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Security.Properties import FC_MANAGEMENT
_readMethods = ['exists', 'isFile', 'getFileSize', 'getFileMetadata',
'getReplicas', 'getReplicaStatus', 'getFileAncestors',
... | fstagni/DIRAC | DataManagementSystem/DB/FileCatalogComponents/SecurityManager.py | Python | gpl-3.0 | 12,375 | [
"DIRAC"
] | 2f6204f9fe6acf78d78f2055be322209f97eb97fa4df3ffc75dc76ff2d3e75c9 |
#!/usr/bin/env python
"""
ADS to BibDesk -- frictionless import of ADS publications into BibDesk
Copyright (C) 2013 Rui Pereira <rui.pereira@gmail.com> and
Jonathan Sick <jonathansick@mac.com>
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Genera... | wschoenell/ads_bibdesk | adsbibdesk.py | Python | gpl-3.0 | 55,654 | [
"VisIt"
] | 88bc38ec33448ee862009b14f0d4616a4b1bf0813e88a1f58b80737e5942290f |
import unittest
from mock import MagicMock, patch
from ncclient.transport.ssh import SSHSession
from ncclient.transport import AuthenticationError, SessionCloseError
import paramiko
from ncclient.devices.junos import JunosDeviceHandler
import sys
try:
import selectors
except ImportError:
import selectors2 as s... | einarnn/ncclient | test/unit/transport/test_ssh.py | Python | apache-2.0 | 13,804 | [
"Firefly"
] | eb31fdf38d5102d40212b634f7fce51852b70e809d1b39c22732ac425b975950 |
"""Acceptance tests for LMS-hosted Programs pages"""
from nose.plugins.attrib import attr
from ...fixtures.programs import FakeProgram, ProgramsFixture, ProgramsConfigMixin
from ...fixtures.course import CourseFixture
from ..helpers import UniqueCourseTest
from ...pages.lms.auto_auth import AutoAuthPage
from ...pages.... | devs1991/test_edx_docmode | common/test/acceptance/tests/lms/test_programs.py | Python | agpl-3.0 | 3,590 | [
"VisIt"
] | d07811190a59865c5e8608106dbc6ce19a4c15d4e5b28c97aee1d2a4d82666c5 |
"""
Utilities for handling the Graphic Unit Interface.
.. todo::
- Switch to Ttk instead of Tk for a better look of the GUI.
- Insert a button to decide if plot or not the singular values.
- Insert a button to decide the path where to save the structures at the end of the procedure.
- Use grid instead of pack
"... | fsalmoir/EZyRB | ezyrb/gui.py | Python | mit | 13,946 | [
"VTK"
] | c7a599edc3f919f8095c77b8c33d7e56b138b72319eefe6a4b8579c81f10f03c |
#!/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/pbc/df/mdf.py | Python | apache-2.0 | 17,797 | [
"Gaussian",
"PySCF"
] | ba6c6a9a9e534045b3c3f1dc0a4f22f115215ef119f232869a526d0f00037df2 |
#!/usr/bin/python
########################################################################
# 15 May 2014
# Patrick Lombard, Centre for Stem Stem Research
# Core Bioinformatics Group
# University of Cambridge
# All right reserved.
########################################################################
import subproce... | pdl30/rnaseq_misc | rna_track_norm.py | Python | gpl-2.0 | 3,947 | [
"HTSeq",
"pysam"
] | e53c9eff3cdd62ee7e91eee3285423a88fb4363e5e98e449bd5d045991679dc5 |
from .. import node
import pytest
from ..util.dispatch import method_store, multimethod
from .. import special
class DummyNode(node.Node):
def __init__(self, a, b, c):
node.Node.__init__(self)
self.a = a
self.b = b
self.c = c
def test_node_shared_methods():
dummy = DummyN... | dacjames/mara-lang | bootstrap/mara/test/test_node.py | Python | mit | 4,741 | [
"VisIt"
] | 66be9b7ff73b11be75c663372a9b2eaddb9adbd11d25ce9980af499fb1879a29 |
#!/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 | scripts/are_queued_jobs_finished.py | Python | lgpl-2.1 | 2,058 | [
"MOOSE"
] | d6cd718b80b04bcb54418450137950ba5c99b5a1df2ed993d3e1e22560a07ee2 |
import numpy as np
import os
import pickle
import pytest
import re
import time
import shutil
from copy import deepcopy
from numpy import allclose, isclose
from flare import struc, env, gp
from flare.parameters import Parameters
from flare.mgp import MappedGaussianProcess
from flare.lammps import lammps_calculator
fro... | mir-group/flare | tests/test_mgp.py | Python | mit | 12,643 | [
"ASE",
"LAMMPS"
] | d7dd81604769e8b6207537b6eb13a1285839a6b08058106129df2d7e290cccc6 |
# -*- 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-talent | tests/unit/gapic/talent_v4beta1/test_event_service.py | Python | apache-2.0 | 56,292 | [
"Octopus"
] | d3dbdabc0ea9bc8c78f228c19b20898e30ff487b35f4e193d3d6d38037d86585 |
# coding=utf-8
# Copyright 2022 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... | google-research/google-research | representation_batch_rl/batch_rl/policies.py | Python | apache-2.0 | 12,631 | [
"Gaussian"
] | bfe75b22e2d8833b6762f00467605265a439ac96180ff668674029cfc9074746 |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
"""
%prog blast_file --qbed query.bed --sbed subject.bed
accepts .bed format: <http://genome.ucsc.edu/FAQ/FAQformat.html#format1>
and a blast file.
local dup filter:
if the input is query.bed and subject.bed, the script files query.localdups and subject.localdups are cre... | asherkhb/coge | bin/quota-alignment/scripts/blast_to_raw.py | Python | bsd-2-clause | 12,941 | [
"BLAST"
] | d2345bac6d7a51afb74bdf23ff8760f80e7fa3d27671f554562d74ae1821b956 |
#!/usr/bin/env python
'''
CREATED:2014-01-24 12:42:43 by Brian McFee <brm2132@columbia.edu>
Compute beat evaluation metrics
Usage:
./beat_eval.py REFERENCE.TXT ESTIMATED.TXT
'''
from __future__ import print_function
import argparse
import sys
import os
import eval_utilities
import mir_eval
def process_arguments... | bmcfee/mir_eval | evaluators/beat_eval.py | Python | mit | 1,856 | [
"Brian"
] | fc5e631a18207a2a01fb8dcf4f055c374bbed1469935412d5ee86e2f2c2ba463 |
WAXY_VERSION = "0.0.1"
WAXY_VERSION_TUPLE = tuple(map(int, WAXY_VERSION.split(".")))
__version__ = WAXY_VERSION
__license__ = "BSD"
__author__ = "Brian Blais (bblais@bryant.edu)"
import sys
import core # builtin functions and such
import wx
from wx import Yield
from aboutbox import AboutBox
from application import ... | bblais/plasticity | plasticity/dialogs/waxy/__init__.py | Python | mit | 2,837 | [
"Brian"
] | c68ad578f1d7343e4a345cc8bbff2b78ec0da25697bfef3d0f33603f81261d24 |
# Mantid Repository : https://github.com/mantidproject/mantid
#
# Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
# NScD Oak Ridge National Laboratory, European Spallation Source
# & Institut Laue - Langevin
# SPDX - License - Identifier: GPL - 3.0 +
from __future__ import (absolute_import, divi... | mganeva/mantid | Framework/PythonInterface/test/python/mantid/api/FunctionPropertyTest.py | Python | gpl-3.0 | 2,329 | [
"Gaussian"
] | bfad823cb46e543d7250e7cae53b2f96a3506495cea6a9d941623fd58088ab82 |
from setuptools import setup
setup(
name='gautools',
packages=['gautools'],
scripts=[
'gautools/aml.py',
'gautools/create_runs.py',
'gautools/geomRegex.py',
'gautools/out_to_list.py',
'gautools/out_to_list_sf.py',
'gautools/submit_gaussian.py',
'gauto... | thompcinnamon/QM-calc-scripts | setup.py | Python | apache-2.0 | 1,048 | [
"MDAnalysis"
] | f734c71bfccbb22aaec5771167c0b1f14573fb49b6aaf928ab61005ea46452c2 |
#!/usr/bin/env python
# -*- encoding: utf-8 -*-
'''
Helper to generate OVH API consumer key. In a nutshell, the consumer key
identifies a specific user in an application while application key and
application secret identifies the application itself. In the case of ovh-cli
each instance of the CLI must hav its own, dedi... | yadutaf/ovh-cli | create-consumer-key.py | Python | bsd-3-clause | 2,679 | [
"VisIt"
] | 29b2981978627b73d64152e89cf8fae320701be76b7d8b5dbff05e6f93cef59f |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | krafczyk/spack | var/spack/repos/builtin/packages/lammps/package.py | Python | lgpl-2.1 | 5,249 | [
"LAMMPS",
"NetCDF"
] | cf623e6fbbb575c8eff1a3a35bb25e7d20d266036265c254b6c5f2135473c1aa |
import pytest
from labkey.api_wrapper import APIWrapper
from labkey.exceptions import ServerContextError
pytestmark = pytest.mark.integration # Mark all tests in this module as integration tests
STUDY_NAME = "TestStudy"
SCHEMA_NAME = "study"
QUERY_NAME = "KrankenLevel"
DATASET_DOMAIN = {
"kind": "StudyDatasetVis... | LabKey/labkey-api-python | test/integration/test_query.py | Python | apache-2.0 | 5,294 | [
"VisIt"
] | 6674e05c05b641ad94d8e1b25ae1cc35397de134c5bbeabc29485bbdc4345795 |
#!/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/scf/test/test_bz.py | Python | apache-2.0 | 1,828 | [
"PySCF"
] | abf5ee26ea927358ad5af15711f6e4371ed0268a5599d48ed7bdb684d710fc35 |
## NIFTY (Numerical Information Field Theory) has been developed at the
## Max-Planck-Institute for Astrophysics.
##
## Copyright (C) 2015 Max-Planck-Society
##
## Author: Marco Selig
## Project homepage: <http://www.mpa-garching.mpg.de/ift/nifty/>
##
## This program is free software: you can redistribute it and/or mod... | ultimanet/nifty | rg/nifty_rg.py | Python | gpl-3.0 | 57,120 | [
"Gaussian"
] | e9c44ee1cc2723e2e07c080bca300e40406be2ef855dc84bd51d7cc345fb8f0f |
# $Id$
#
from __future__ import print_function
from rdkit import Chem
from rdkit.Chem import rdMolDescriptors as rdMD, Descriptors
from rdkit.Chem import AllChem
from rdkit import DataStructs
from rdkit import RDConfig
from rdkit.Geometry import rdGeometry as rdG
import unittest
def feq(v1, v2, tol=1.e-4):
return a... | rvianello/rdkit | Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py | Python | bsd-3-clause | 21,553 | [
"RDKit"
] | a90d638fcca5da13ddbc5cf8917d73606f793da5c3de797ff8a2982490a7ae32 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright 2008-2009 Zuza Software Foundation
#
# This file is part of Pootle.
#
# 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... | lehmannro/pootle | local_apps/pootle_misc/dbinit.py | Python | gpl-2.0 | 4,588 | [
"VisIt"
] | e590e223e379634033220fe68264e0665187fd7d2734e180fffa48db353ae49c |
# -*- coding: utf-8 -*-
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import numpy as np
import abel
import bz2
import matplotlib.pylab as plt
# Demonstration of two techniques to determine the anisotropy parameter
# (a) directly, using `linbasex`
# (b)... | stggh/PyAbel | examples/example_anisotropy_parameter.py | Python | mit | 4,917 | [
"Gaussian"
] | f9f509de9b4bf09f6f1e1aa29bc26c568423eda277485281258194e81e6a595c |
##############################################################################
#
# Copyright (C) 2018 Compassion CH (http://www.compassion.ch)
# Releasing children from poverty in Jesus' name
# @author: Emanuel Cino
#
# The licence is in the file __manifest__.py
#
###########################################... | CompassionCH/compassion-switzerland | website_event_compassion/controllers/events_controller.py | Python | agpl-3.0 | 14,186 | [
"VisIt"
] | d682fb07d2682fcbd2321cf75a52d4a51c679c2c0fe266b0655150579e956bc3 |
#!/usr/bin/python
from datetime import datetime, timedelta
import httplib2
import os
import sys
import pandas as pd
from pprint import pprint as pp
from apiclient.discovery import build
from apiclient.errors import HttpError
from oauth2client.client import flow_from_clientsecrets
from oauth2client.file import Storage... | facemelters/data-science | Atlas/test-youtube2.py | Python | gpl-2.0 | 5,639 | [
"VisIt"
] | 60e76aab617219fab6838eda2f145adaa8e195496ae9c04f227318e063700b2f |
from JMol import JMol
from JSMol import JSMol
| mtthwflst/terse | Engine3D/__init__.py | Python | mit | 46 | [
"Jmol"
] | e976ec79bf02d2c9783ae7e7cd5ea9a346cc086c4c8f555db351ccb800577e66 |
import os
import re
import sys
import wx
import IO
import shutil
import oscaar
import urllib2
import zipfile
import datetime
import subprocess
import webbrowser
import numpy as np
import systematics
import timeConversions
from glob import glob
from matplotlib import pyplot
from mathMethods import medianBin
from oscaar... | bluegod/OSCAAR | oscaar/oscaarGUI.py | Python | mit | 238,923 | [
"VisIt"
] | f5dc0137c3972f63a32374f8c3e4fa60b51ad3fa8b5b3824a4b0b42d3b758ccf |
# -*- coding: utf-8 -*-
# Copyright (c) 2016-2017, Zhijiang Yao, Jie Dong and Dongsheng Cao
# All rights reserved.
# This file is part of the PyBioMed.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the PyBioMed source tree.
"""
This ... | gadsbyfly/PyBioMed | PyBioMed/PyPretreat/PyPreTools.py | Python | bsd-3-clause | 3,932 | [
"RDKit"
] | 221c33ad305197e5d369b7bee1298971a9ea9e8354ef49498d7536fc4ff3b697 |
# coding: utf-8
from __future__ import unicode_literals
"""
Defines an abstract base class contract for Transformation object.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2011, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep@gmail.com"
__date__ = "Sep... | Dioptas/pymatgen | pymatgen/transformations/transformation_abc.py | Python | mit | 2,653 | [
"pymatgen"
] | d1cc4d105ef45d9b179ba566d9ffb25d5d38208def61466faa0a39e1f9c5d7a8 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | CDSherrill/psi4 | psi4/driver/qcdb/exceptions.py | Python | lgpl-3.0 | 5,158 | [
"Psi4"
] | 9428d486ac1ba07ff9f0a89015a693d57e481593eff5b725b303155090b79677 |
__RCSID__ = "$Id$"
from DIRAC import gLogger, S_OK, S_ERROR, siteName
from DIRAC.Core.Base.AgentModule import AgentModule
from DIRAC.StorageManagementSystem.Client.StorageManagerClient import StorageManagerClient
from DIRAC.Resources.Storage.StorageElement imp... | Andrew-McNab-UK/DIRAC | StorageManagementSystem/Agent/StageMonitorAgent.py | Python | gpl-3.0 | 8,412 | [
"DIRAC"
] | 3ece9de34428850018bd5bd0225d4859e9ca8c87b61f33ed5757ffa656a6255f |
#!/usr/bin/env python
import re
import math as m
import numpy as np
def read_frequences(filename):
"""Return data from <seedname>.phonon
The CASTEP and related PHONON codes both
generate a file containing phonon frequences and
related information. This function returns a
list of frequencies fro... | andreww/isofrac | calc_beta.py | Python | bsd-3-clause | 3,616 | [
"CASTEP"
] | e6e4a227071c4e0f3d58add1da34462ef15a0f9ea268a75d305caa55d3714c09 |
import numpy as np
import pylab
import pyfits
import sys
import glob
import os
from pyraf import iraf
import glob
import time
from astropy.io import fits as fits
print " -----------------------------------------------------------------"
print " . * . . + . . . "
print... | emsnyder/geminiDRpipeline | gemreductionpipeline.py | Python | mit | 35,479 | [
"Galaxy"
] | 760551e098d93d802384651a309d5b6c8281e1d9edbdffd6562dccce9a9c7098 |
"""
Acceptance tests for Studio related to the textbooks.
"""
from nose.plugins.attrib import attr
from common.test.acceptance.pages.lms.textbook_view import TextbookViewPage
from common.test.acceptance.pages.studio.textbook_upload import TextbookUploadPage
from common.test.acceptance.tests.helpers import disable_anim... | Stanford-Online/edx-platform | common/test/acceptance/tests/studio/test_studio_textbooks.py | Python | agpl-3.0 | 3,412 | [
"VisIt"
] | 54904931347d5fe26bb0fdb3ee863fd764524e115bd0044b6b69bd84a8d9b10a |
# Copyright 2015 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 ... | GirlsCodePy/girlscode-coursebuilder | modules/data_removal/data_removal_tests.py | Python | gpl-3.0 | 37,916 | [
"VisIt"
] | bdfd260e977200055642c848df0f3337519232993034071d9bbaea61915c9ce0 |
"""
ExampleRawIO is a class of a fake example.
This is to be used when coding a new RawIO.
Rules for creating a new class:
1. Step 1: Create the main class
* Create a file in **neo/rawio/** that endith with "rawio.py"
* Create the class that inherits from BaseRawIO
* copy/paste all methods that need to... | INM-6/python-neo | neo/rawio/examplerawio.py | Python | bsd-3-clause | 18,423 | [
"NEURON"
] | 8b7c2f0857c4453b2be82dcaf536f8ab6eee948eaa3a79549a3a32072ac60ce6 |
#!/usr/bin/env python
# $Id: Compiler.py,v 1.148 2006/06/22 00:18:22 tavis_rudd Exp $
"""Compiler classes for Cheetah:
ModuleCompiler aka 'Compiler'
ClassCompiler
MethodCompiler
If you are trying to grok this code start with ModuleCompiler.__init__,
ModuleCompiler.compile, and ModuleCompiler.__getattr__.
Meta-Data
==... | CymaticLabs/Unity3D.Amqp | lib/rabbitmq-dotnet-client-rabbitmq_v3_4_4/docs/pyle2-fcfcf7e/Cheetah/Compiler.py | Python | mit | 78,232 | [
"VisIt"
] | 395f77f98eb5f853f96bd312ee2eccd44e5f8b36c848f0e7d4c428f519c19ad1 |
# system modules
import os
from unittest import TestCase
# custom module
from iago import Reader
BASE_DIR = os.path.join(os.path.dirname(os.path.abspath(__file__)), '..')
class TestReader(TestCase):
def test_emtpy_universe(self):
e = Reader.EmptyUniverse()
self.assertEqual(len(e), 0)
self.assertEqual(len(e.t... | ferchault/iago | tests/unit/test_reader.py | Python | mit | 1,679 | [
"CP2K",
"NAMD"
] | fd3ae18e52e1b647136d98ea914605752f7dd3a44f8c6f99ea37a5f124d0415a |
from __future__ import absolute_import
import os
import os.path as op
from copy import copy
import numpy as nm
from sfepy.base.base import (
dict_from_keys_init, select_by_names, is_string, is_integer, is_sequence,
output, get_default, Struct, IndexedStruct)
import sfepy.base.ioutils as io
from sfepy.base.con... | vlukes/sfepy | sfepy/discrete/problem.py | Python | bsd-3-clause | 75,579 | [
"VTK"
] | 622fecedd560fb415f7442f0160ebf437e48f19b7c7065ef83824339c857e65f |
""" An app to draw glacier geometry on top of a background image (local plotly)
"""
from outletglacierapp import app
import os
import warnings
import itertools
import json
import numpy as np
from flask import Flask, redirect, url_for, render_template, request, jsonify, flash, session, abort, make_response, send_from_d... | perrette/webglacier1d | outletglacierapp/views.py | Python | mit | 16,362 | [
"NetCDF"
] | ddf8441ee379c2ac23a7ebb254857d879890d149e686453f76e5951743b3e6ff |
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