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#
# Copyright 2010, Kay Hayen, mailto:kayhayen@gmx.de
#
# Part of "Nuitka", an attempt of building an optimizing Python compiler
# that is compatible and integrates with CPython, but also works on its
# own.
#
# If you submit Kay Hayen patches to this software in either form, you
# automatically... | pombredanne/nuitka-old-no-longer-maintained | src/templates/CodeTemplatesCompiledGenexprType.py | Python | gpl-3.0 | 10,550 | [
"VisIt"
] | 01cd17e286bc4a320f2dc193fe27a469a364b7ede17757e59c8e3c2187a402a9 |
# -*- coding: utf-8 -*-
"""
Display Yahoo! Weather forecast.
See http://developer.yahoo.com/weather for more information.
Visit http://woeid.rosselliot.co.nz for WOEID, Where On Earth IDentifier.
Configuration parameters:
cache_timeout: refresh interval for this module (default 7200)
forecast_days: specifiy n... | vvoland/py3status | py3status/modules/weather_yahoo.py | Python | bsd-3-clause | 12,117 | [
"VisIt"
] | e296ebefde291cd445626029818f9cf0803c3af488b5f6d8837c1cf2e04e5da8 |
from simtk.openmm import app
import simtk.openmm as mm
from simtk import unit as u
code = "2LCB_GLY-112-ALA"
#code = "3DMV_GLY-112-ALA"
#code = "3DMV"
#code = "2LCB"
padding = 1.0 * u.nanometers
cutoff = 0.95 * u.nanometers
ff = app.ForceField('amber99sbnmr.xml', 'tip3p-fb.xml')
temperature = 300.
pressure = 1.0 *... | kyleabeauchamp/fah-projects | old/equilibrate.py | Python | gpl-2.0 | 1,488 | [
"OpenMM"
] | 4a7c050b8b6a1ceb9019b132f9ab40bf0ff3803d0ca03b35a7755628eb9e20ac |
# Copyright (C) 2003 CAMP
# Please see the accompanying LICENSE file for further information.
from os import path
import sys
ON_POSIX = 'posix' in sys.builtin_module_names
try:
from subprocess import Popen
except ImportError:
from os import popen3
else:
def popen3(cmd):
from subprocess import PI... | askhl/ase | ase/svnversion_io.py | Python | gpl-2.0 | 1,375 | [
"ASE"
] | 958941658a90a410759dcdf34341a28bbe4ad346ae9bf9fdaca8c5a784fd4ebe |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Gary Burton
#
# 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 v... | SNoiraud/gramps | gramps/gen/plug/menu/_menu.py | Python | gpl-2.0 | 4,229 | [
"Brian"
] | c7c68bd9beb8471eb0de3785d0705d175acf63326eef9ea116c89e800389f8e9 |
class Ellipse:
def Ellipse(self,r):
#Creates a blank 2d Array galaxy of radius 'r'
galaxy = [[0 for i in range((r+1)*2)] for i in range((r+1)*2)]
sectors = 0
#Checks whether or not sectors are contained in galaxy
for x in range (2*r+2):
for y in range (2*r+2):
... | ctrom/trek | Galaxy.py | Python | gpl-3.0 | 1,586 | [
"Galaxy"
] | 16e98160aab3ec10a615d0e486f2ba25cce41e72c7dc9f256cb04b1bf3319a86 |
"""
##########################################################################
#
# QGIS-meshing plugins.
#
# Copyright (C) 2012-2013 Imperial College London and others.
#
# Please see the AUTHORS file in the main source directory for a
# full list of copyright holders.
#
# Dr Adam S. Candy, adam.candy@imp... | adamcandy/qgis-plugins-meshing-initial | release/rasterise_polygons/rasterisepolygons.py | Python | lgpl-2.1 | 18,104 | [
"NetCDF"
] | 2c15e8c350fcaa7eeb88c1877d661ae713a062bea7b8950ac75896fd48df0f6f |
# Sample module in the public domain. Feel free to use this as a template
# for your modules (and you can remove this header and take complete credit
# and liability)
#
# Contact: Brian Carrier [carrier <at> sleuthkit [dot] org]
#
# This is free and unencumbered software released into the public domain.
#
# Anyone is f... | rcordovano/autopsy | pythonExamples/Registry_Example.py | Python | apache-2.0 | 13,356 | [
"Brian"
] | 56b81481cc1f6deaff85fb1442dd9e1dde2b9458a91d5a0c672c925f1b6c8fe5 |
# Copyright 2021 DeepMind Technologies Limited.
#
# 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 ag... | deepmind/deepmind-research | fusion_tcv/noise.py | Python | apache-2.0 | 4,535 | [
"Gaussian"
] | 510109dc462401ae4b47a4d7a2733e3af7f2cba5c7c894ca969a0399624da07b |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | gregcaporaso/scikit-bio | skbio/stats/ordination/_correspondence_analysis.py | Python | bsd-3-clause | 7,748 | [
"scikit-bio"
] | ecd13c997347ed3344b50ff2755335b6580ea7a9e27356864f7c5fab23bc6496 |
#
# This file is a part of Siesta Help Scripts
#
# (c) Andrey Sobolev, 2013
#
from abc import ABCMeta, abstractmethod
import shs.errors
import plotdata
class ClassProperty(object):
def __init__(self, getter):
self.getter = getter
def __get__(self, instance, owner):
return self.getter(owner)... | ansobolev/shs | shs/data/abstract.py | Python | mit | 4,745 | [
"SIESTA"
] | 9dae0290a599fa979d72e20a674c26fea8d5461e42028bd062dfedb2d199f499 |
#Last-modified: 08 Dec 2013 01:13:36
# generic packages
import numpy as np
#np.seterr(all='raise')
from numpy.random import normal, multivariate_normal
from scipy.optimize import fmin
import matplotlib.pyplot as plt
# internal packages
from cholesky_utils import cholesky, trisolve, chosolve, chodet, chosolve_from_tri... | askielboe/JAVELIN | javelin/lcmodel.py | Python | gpl-2.0 | 100,414 | [
"Gaussian"
] | b33d07ca80198adb5a783da5825f0989c833dd2af575eb1b3d93e870936e81a5 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# #########################################################################
# Copyright (c) 2020, UChicago Argonne, LLC. All rights reserved. #
# #
# Copyright 2020. UChicago Argonne, LLC. This ... | lucarebuffi/OASYS1 | oasys/widgets/abstract/error_profile/abstract_multiple_height_profile_simulator_S.py | Python | gpl-3.0 | 38,247 | [
"Gaussian"
] | 01ff01017f6c1f1ab9f0babdbe02a9c308695c126a4803fb013a17cb482973bb |
#
# This source file is part of appleseed.
# Visit https://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2016-2019 Esteban Tovagliari, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaini... | appleseedhq/appleseed-maya | scripts/appleseedMaya/renderer.py | Python | mit | 4,028 | [
"VisIt"
] | 49335e41821793fae5e53e8a7ceb157c54dd92289ba9ad43b64104f48668a3eb |
# -*- coding: utf-8 -*-
##
## This file is part of Invenio.
## Copyright (C) 2010, 2011, 2013 CERN.
##
## Invenio 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 (at yo... | inspirehep/invenio | modules/docextract/lib/refextract_regression_tests.py | Python | gpl-2.0 | 135,093 | [
"DIRAC"
] | 1c1795028b0cf02495a44ee22c84c849aa826ac53478db82d130d672f2b18f59 |
#Copyright ReportLab Europe Ltd. 2000-2016
#see license.txt for license details
#history http://www.reportlab.co.uk/cgi-bin/viewcvs.cgi/public/reportlab/trunk/reportlab/pdfbase/cidfonts.py
#$Header $
__version__='3.3.0'
__doc__="""CID (Asian multi-byte) font support.
This defines classes to represent CID fonts.... | EduPepperPDTesting/pepper2013-testing | lms/djangoapps/reportlab/pdfbase/cidfonts.py | Python | agpl-3.0 | 19,371 | [
"Brian"
] | add221b7e4f27c0c433889355078d5f590e7e7aa8f76c5088d1d37a100ecfec8 |
#!/usr/bin/env python2.7
# tool_versions.py v1.1 Creates "SW" versions json string for a particular DX applet.
# Write request to stdout and verbose info to stderr. This
# allows easy use in dx app scripts.
import sys, os, argparse, json, commands
# APP_TOOLS is a dict ... | ENCODE-DCC/dna-me-pipeline | dnanexus/tools/tool_versions.py | Python | mit | 8,751 | [
"Bowtie"
] | 5f450bdf330203e583875e15ee71079f7c1bb01bdba62f71f782ed00b4f2d5c9 |
#
# Copyright (C) 2008, Brian Tanner
#
#http://rl-glue-ext.googlecode.com/
#
# 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 requ... | okkhoy/mo-rlglue-python-codec | tests/test_empty_environment.py | Python | mit | 2,002 | [
"Brian"
] | 9655bffd6f0d37431ffbddf678e148900ec1790593ad195a1e8b5a5734d11a5b |
#!/usr/bin/python
# script find clusters of small RNA reads in the genome
# version 2 - 22-11-2013 evolution to use a subinstance extraction approach
# Usage clustering.py <bowtie input> <output> <bowtie index> <clustering_distance> <minimum read number per cluster to be outputed> <collapse option> <extention value> <a... | mvdbeek/tools-artbio | unstable/local_tools/clustering.py | Python | mit | 4,996 | [
"Bowtie"
] | 7609faad22dbdf6d6936df3d504f100926f9ffb448365f6e41f343076bc2b7a4 |
""" DIRAC.ResourceStatusSystem.PolicySystem package
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = '$Id$'
| yujikato/DIRAC | src/DIRAC/ResourceStatusSystem/PolicySystem/__init__.py | Python | gpl-3.0 | 185 | [
"DIRAC"
] | 8f1f922d9d5b716dc237f553700fa83a1bd46d6775d991f1b95fcfb6769ea670 |
# -*- coding: utf-8 -*-
"""
Parse pykit IR in the form of C.
"""
from __future__ import print_function, division, absolute_import
from io import StringIO
from os.path import dirname, abspath, join
import tempfile
import json
import tokenize
from functools import partial
from collections import defaultdict, namedtupl... | ContinuumIO/pykit | pykit/parsing/cirparser.py | Python | bsd-3-clause | 14,105 | [
"VisIt"
] | e3627352d709824ca9cda54715030ac2faa433f67124e9e73ca5b76a2385b31d |
#!/usr/bin/env python
disk = vtk.vtkDiskSource()
disk.SetRadialResolution(2)
disk.SetCircumferentialResolution(9)
clean = vtk.vtkCleanPolyData()
clean.SetInputConnection(disk.GetOutputPort())
clean.SetTolerance(0.01)
piece = vtk.vtkExtractPolyDataPiece()
piece.SetInputConnection(clean.GetOutputPort())
... | hlzz/dotfiles | graphics/VTK-7.0.0/Filters/Parallel/Testing/Python/TestExtrudePiece.py | Python | bsd-3-clause | 1,395 | [
"VTK"
] | 67110ab5374aded1ce73eab680fb439eaa6a16c3efd9c7127478754f9df9a952 |
from setuptools import setup, Extension
from setuptools.command.build_py import build_py as _build_py
from setuptools.command.build_ext import build_ext
from distutils.errors import CCompilerError, DistutilsExecError, DistutilsPlatformError
import subprocess
import os
import itertools
import warnings
import logging
lo... | ViennaRNA/forgi | setup.py | Python | gpl-3.0 | 5,831 | [
"Biopython"
] | 91afbe201e4f1ea19fcaf761d8a6a9ba4e26d20f1912d03641a3fb41ed846886 |
"""
This script can be used to generate simple plots.
"""
import matplotlib
matplotlib.rc('text', usetex=True)
matplotlib.rcParams['font.size'] = 17
matplotlib.rc('xtick', labelsize=14)
matplotlib.rc('axes', linewidth=1.1)
matplotlib.rcParams['legend.fontsize'] = 11
matplotlib.rcParams['legend.handlelength'] = 3
matplo... | sniemi/EuclidVisibleInstrument | plotting/plotSNRsForStars.py | Python | bsd-2-clause | 7,919 | [
"Gaussian"
] | b86e10c35a4c16b14df1afc3bec450f77d891b45631cd27bff09faef9c39a4dc |
"""
# Notes:
- This simulation seeks to emulate the COBAHH benchmark simulations of (Brette
et al. 2007) using the Brian2 simulator for speed benchmark comparison to
DynaSim. However, this simulation does NOT include synapses, for better
comparison to Figure 5 of (Goodman and Brette, 2008) - although it uses the... | asoplata/dynasim-benchmark-brette-2007 | Brian2/brian2_benchmark_COBAHH_nosyn_compiled_0008.py | Python | gpl-3.0 | 3,481 | [
"Brian"
] | 9ef1a7513603bdd191800762d08e77549f97e274507dcf44614d9147721036c8 |
from ase.structure import molecule
from ase.optimize import BFGS
from gpaw import GPAW
for name in ['H2', 'N2', 'O2', 'NO']:
mol = molecule(name)
mol.center(vacuum=5.0)
if name == 'NO':
mol.translate((0, 0.1, 0))
calc = GPAW(xc='PBE',
h=0.2,
txt=name + '.txt')
... | ajylee/gpaw-rtxs | gpaw/test/big/Ru001/molecules.py | Python | gpl-3.0 | 464 | [
"ASE",
"GPAW"
] | 9d21e3943afc2a30be0b9891991d9419985ebaa343bf0dca12ae111548254b43 |
import logging
import os
import stat
from galaxy.util import asbool
from pulsar.managers.base import BaseManager
from pulsar.managers import PULSAR_UNKNOWN_RETURN_CODE
from ..util.job_script import job_script
from ..util.env import env_to_statement
log = logging.getLogger(__name__)
# TODO: Rename these to abstract o... | galaxyproject/pulsar | pulsar/managers/base/directory.py | Python | apache-2.0 | 7,264 | [
"Galaxy"
] | dc6a816399f84448a001c02a656a585c0b1bca258b6523f5a1e6e107bceb4edf |
from netCDF4 import Dataset
import datetime as dt
import unittest
import numpy as np
from cis.cis_main import aggregate_cmd
from cis.test.integration.base_integration_test import BaseIntegrationTest
from cis.test.integration_test_data import *
from cis.test.utils_for_testing import *
from cis.parse import parse_args
... | cedadev/cis | cis/test/integration/test_aggregate.py | Python | lgpl-3.0 | 32,878 | [
"NetCDF"
] | 1a9b1480f0d9be2445aee4f2ad6f34bf357f982679d30ceae0fc441443f65121 |
# Licensed under GPL version 3 - see LICENSE.rst
import numpy as np
import pytest
from scipy.stats import normaltest
from astropy.table import Table
from astropy.coordinates import SkyCoord
import astropy.units as u
from ...source import (SymbolFSource, Source, poisson_process,
PointSource,
... | hamogu/marxs | marxs/source/tests/test_source.py | Python | gpl-3.0 | 8,619 | [
"Gaussian"
] | a7d123d7c2d3b38e6ce089b9b7cb51f19eca47cf8b82d42b322a4944b26e3576 |
"""Contains the implementation of the Wikipedia list of colors."""
__all__ = (
'Wiki',
)
import enum
from colors import base
class Wiki(base.ColorGroup):
"""
The Wiki color group.
The following is a list of colors. A number of the color swatches below are
taken from domain-specific naming schem... | xlorepdarkhelm/colors | colors/wiki.py | Python | mit | 85,887 | [
"Amber"
] | 53897c4e7a297843378614b756c2bd53f1dfc9a1cc3fc95f8f96c9d112330965 |
from django.core.exceptions import ValidationError
from django.contrib.gis.geos import Point
from django.contrib.gis.measure import D
from site_config.site_config import SiteConfig
class SomervilleConfig(SiteConfig):
group_name = "somervillema"
hostnames = ["somerville.cornerwise.org", "cornerwise.somervill... | codeforboston/cornerwise | server/site_config/somervillema.py | Python | mit | 2,930 | [
"VisIt"
] | 4e7d19ffe65cf4b7c1e9860c546c26b1d68a603d83958d91e8a26240b949695b |
#!/usr/bin/env python
import askap.analysis.data
from numpy import *
import MySQLdb
from optparse import OptionParser
import os
import askap.parset as parset
import math
SKADS_host = "delphinus.atnf.csiro.au"
SKADS_user = "skads"
SKADS_pass = "skads"
#SKADS_db = "S3SEX"
SuperBrightSource = 67005861 # component numb... | ATNF/askapsdp | Code/Components/Analysis/data/current/scripts/createSKADSspectralline.py | Python | gpl-2.0 | 15,121 | [
"Galaxy"
] | 6c43e64d212eb9d69197fc5eaddf499f25440886a7332b7ef538b5f860d97fbc |
# -*- coding: utf-8 -*-
# Author: Vincent Dubourg <vincent.dubourg@gmail.com>
# (mostly translation, see implementation details)
# Licence: BSD 3 clause
from __future__ import print_function
import numpy as np
from scipy import linalg, optimize
from ..base import BaseEstimator, RegressorMixin
from ..metrics... | Djabbz/scikit-learn | sklearn/gaussian_process/gaussian_process.py | Python | bsd-3-clause | 34,913 | [
"Gaussian"
] | aca580e0b2935e41beb621721d48a938e5744049b9f908a0aee2de1ab885bca4 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
from pymatgen.core.molecular_orbitals import MolecularOrbitals
from pymatgen.util.testing import PymatgenTest
test_case = MolecularOrbitals("NaCl")
class MolecularOrbitalTestCase(PymatgenTe... | gmatteo/pymatgen | pymatgen/core/tests/test_molecular_orbitals.py | Python | mit | 1,469 | [
"pymatgen"
] | e1f860cd93882944194b176dd01bf29502fa16e5519512f41e1652164f7d9092 |
#!/usr/bin/env python
"""compare.py: Compare data generated by MOOSE and NEURON.
Last modified: Wed May 28, 2014 02:48PM
"""
__author__ = "Dilawar Singh"
__copyright__ = "Copyright 2013, NCBS Bangalore"
__credits__ = ["NCBS Bangalore", "Bhalla Lab"]
__license__ = "GPL"
__vers... | BhallaLab/moose-full | moose-core/tests/python/Rallpacks/moose_vs_neuron/rallpack3/compare.py | Python | gpl-2.0 | 4,113 | [
"MOOSE",
"NEURON"
] | 847cdb30b2ec7a35fc5a5ebe2a6d64ac3a237a9951e3385fd6d168b00ed28655 |
#!/usr/bin/env python
########################################################################
#
# (C) 2013, James Cammarata <jcammarata@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published ... | benjixx/ansible | lib/ansible/galaxy/api.py | Python | gpl-3.0 | 9,703 | [
"Galaxy"
] | 766ef8c7deb4595adb1b47ac56a954c9ff5bf12e77d436e6a30bde6bf6259a06 |
"""The official API for working with notebooks in the current format version.
Authors:
* Brian Granger
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2008-2011 The IPython Development Team
#
# Distributed under the terms of the BSD License. The full license is ... | Carreau/gistpynb | nbformat/current.py | Python | apache-2.0 | 6,217 | [
"Brian"
] | f1e2299be5fe7fea30774bdac344da0fd900a88b622110d2c565605102613600 |
#!/usrbin/env python
# -*- coding: utf-8 -*-
# Copyright (C) 2015 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 Publi... | ProteinDF/QCLObot | scripts/relax_protein.py | Python | gpl-3.0 | 35,346 | [
"Amber"
] | 38b304d0fcb284b688806028f94a73b2cf39612545f2845fc87dde078d6413b5 |
#!/usr/bin/python
# this file parses a trace from (a modified) simulavr, and prints
# execution times of all functions that were called, as well as
# execution counts for a user-defined list of instructions (if given).
#
# TODO: include alias symbols
#
# (C) 2015-2018 Martin Becker <becker@rcs.ei.tum.de>
import os
im... | TRDDC-TUM/wcet-benchmarks | scripts/simulavr2times.py | Python | mit | 16,597 | [
"VisIt"
] | 6fdd2507e1f8aac49524d4ef277a3210790669661e6ff3c2aaa4d179e94d5769 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkImageCast(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkI... | nagyistoce/devide | modules/vtk_basic/vtkImageCast.py | Python | bsd-3-clause | 481 | [
"VTK"
] | cac6828d1dde55b5622efb76d01fc4cba1a92bb2110e26a545d230e3bfaad761 |
# -*- coding: utf-8 -*-
"""
codegen
~~~~~~~
Extension to ast that allow ast -> python code generation.
:copyright: Copyright 2008 by Armin Ronacher.
:license: BSD.
fixed 2010 by Stefan Koegl
"""
from ast import *
__all__ = ["to_source", "BINOP_SYMBOLS",]
BOOLOP_SYMBOLS = {
And: ... | tastyproject/tasty | tasty/tastyc/codegen.py | Python | gpl-3.0 | 16,631 | [
"VisIt"
] | af5f1660ba74321ccf67183083a1fa0189d9cdead8090b4d304c5cb7bcab92fe |
# Copyright 2003-2008 by Leighton Pritchard. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
# Contact: Leighton Pritchard, Scottish Crop Research Institute,
# ... | LyonsLab/coge | bin/last_wrapper/Bio/Graphics/GenomeDiagram/_Track.py | Python | bsd-2-clause | 15,956 | [
"Biopython"
] | 05190eddd5eabd5a977a19628b1e47aa19ef1ca900ca9177503c89d0016e44ca |
#!/usr/bin/env python2
# vim:fileencoding=utf-8
from __future__ import (unicode_literals, division, absolute_import,
print_function)
__license__ = 'GPL v3'
__copyright__ = '2013, Kovid Goyal <kovid at kovidgoyal.net>'
import inspect, time
from io import BytesIO
from repr import repr
from funct... | jelly/calibre | src/calibre/db/tests/legacy.py | Python | gpl-3.0 | 39,096 | [
"MOOSE"
] | 790343a2ff9e79031219684a78641e076444a2f77dd3d35444dd31402d313146 |
from sys import exit
from random import randint
class Scene(object):
def enter(self):
print "This scene is not yet configured. Subclass it and implement enter()."
exit(1)
class Engine(object):
def __init__(self,scene_map):
self.scene_map=scene_map
def play(self):
current_scene=self.scene_map.opening_sc... | JeffreyCA/illacceptanything | code/Gothons_from_Planet_Percal/classes.py | Python | mit | 7,438 | [
"BLAST"
] | 08fa0e3ed37c7c4b7dd6c464ddeb20e8e5588539c51de7231c1468c0edae8e80 |
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Top-level presubmit script for Chromium.
See http://dev.chromium.org/developers/how-tos/depottools/presubmit-scripts
for more details about the presu... | timopulkkinen/BubbleFish | PRESUBMIT.py | Python | bsd-3-clause | 31,990 | [
"VisIt"
] | 7ec400e4e1f30f35a084af1a100ab799e86d3452d701102db8c67feeec718696 |
from __future__ import division, unicode_literals
import matplotlib
matplotlib.use('pdf')
import unittest as unittest
import numpy as np
from pymatgen import Composition
from pymatgen.entries.computed_entries import ComputedEntry
from pymatgen.analysis.phase_diagram import PhaseDiagram, \
GrandPotentialPhaseDia... | matk86/pymatgen | pymatgen/analysis/tests/test_interface_reactions.py | Python | mit | 11,082 | [
"pymatgen"
] | 955a54314bb1e8f7cd66d2f70284dee415725ebe6eaf60f329b2b7659faf770d |
#
# 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... | espressomd/espresso | samples/minimal-diamond.py | Python | gpl-3.0 | 4,135 | [
"ESPResSo"
] | 83597b98657746c7c0b0e535d119803ad94851eedccd72d092b514512b64d9bd |
from sys import exit
from random import randint
class Scene(object):
def enter(self):
print "This scene is not yet configured. Subclass it and implement enter()."
exit(1)
class Engine(object):
def __init__(self, scene_map):
self.scene_map = scene_map
def play(self):
... | chrisortman/CIS-121 | k0458928/midtermex.py | Python | mit | 8,940 | [
"BLAST"
] | df9924178d1d0048cbe905ae95bac8a6f643286fe4a8ae8794d855cd9d05199c |
from __future__ import print_function
try:
input = raw_input
except NameError:
pass
import random
HANGMANPICS = ['''
+---+
| |
|
|
|
|
=========''', '''
+---+
| |
O |
|
|
|
=========''', '''
+---+
| |
O |
| |
... | Shashwat986/WTM-IITKanpur | hangman.py | Python | mit | 4,232 | [
"MOOSE"
] | bd4e5b725036e0cc98d6201e61bbcd28a901ac174c515156c03638e048a5b381 |
# -*- coding: utf-8 -*-
#
# Copyright (C) 2014 Google Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicabl... | GoogleCloudPlatform/gce-oreilly | ch3-1.py | Python | apache-2.0 | 6,291 | [
"VisIt"
] | 281a8cf5692bfa5db537926ebaf8cc8a0aef29ccf0478142e5698ed7281d7507 |
# coding=utf-8
# Distributed under the MIT software license, see the accompanying
# file LICENSE or http://www.opensource.org/licenses/mit-license.php.
from unittest import TestCase
from mock import Mock
from pyqrllib.pyqrllib import bin2hstr, hstr2bin
from qrl.daemon.walletd import WalletD
from qrl.generated import ... | randomshinichi/QRL | tests/daemon/test_walletd.py | Python | mit | 50,295 | [
"Jaguar"
] | a344ddc043863fcb4b2abc80c5e423250b5a1f15810f92820af9ec783a0e5811 |
# Copyright (c) 2013-2014 by California Institute of Technology
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistributions of source code must retain the above copyright
# notice,... | necozay/tulip-control | tulip/graphics.py | Python | bsd-3-clause | 7,509 | [
"Mayavi"
] | f0dc0c05163a845c6500807c5b76c4b4b6a63c5132151096d825477e692a902d |
"""
this file does variant calling for RNAseq
"""
import pdb
#============= import required packages =================
import os
import sys
import subprocess
sys.path.append('/home/shangzhong/Codes/Projects')
sys.stdout = os.fdopen(sys.stdout.fileno(), 'w', 0) # disable buffer
from Modules.f00_Message import Message
... | shl198/Pipeline | VariantCall/02_GATK_RNA_vari_call.py | Python | mit | 8,493 | [
"BWA"
] | b46c7969d2cebc2aaac0729e4882bf49d50fb65e156fae2fc81f3ffa0ef5790e |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# signup - general sign up entry point backend
# Copyright (C) 2003-2015 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public... | heromod/migrid | mig/shared/functionality/signup.py | Python | gpl-2.0 | 7,764 | [
"Brian"
] | 17a0b120ed264ae95aca33436521f7fc4e26cbae70ca5c285a76a2f8fb5f1c81 |
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# License: Simplified BSD
import numpy as np
from ..forward import is_fixed_orient
from ..minimum_norm.inverse import _check_reference, _log_exp_var
from ..utils import logger, verbose, warn
from .mxne_i... | bloyl/mne-python | mne/inverse_sparse/_gamma_map.py | Python | bsd-3-clause | 10,205 | [
"Gaussian"
] | f32efeeae2eca14521491bf898006b6c9d4140d56aee4c7dc22d117a764602a6 |
#!/usr/bin/env python
"""Test for speedup in using the alignment function in this folder.
This file is to visualise the speedup in using the alignment provided in
this folder w.r.t. Bio.pairwise2, also with the non-documented parameters
force_generic=True and one_alignment_only=True.
Author: Federico Tomasi
Copyright... | slipguru/ignet | icing/align/test_speedup_c_alignment.py | Python | bsd-2-clause | 1,369 | [
"Biopython"
] | 12a82ef80d0e53bf6e5e6037a4b4f244d809b46fb88bdd7376c02eef40fc223b |
import os
import sys
import glob
import re
import mkdocs
import livereload
import logging
import shutil
import MooseDocs
import build
log = logging.getLogger(__name__)
def serve_options(parser, subparser):
"""
Command-line options for serve command.
"""
serve_parser = subparser.add_parser('serve', help='Gene... | vityurkiv/Ox | python/MooseDocs/commands/serve.py | Python | lgpl-2.1 | 2,473 | [
"MOOSE"
] | e536bd1399f0cb34f97a6b86018b2380f22b7f41eda61bb7a710748518964b3c |
# coding: utf-8
""" Wavelength calibration using arc lamps """
from __future__ import division, print_function
__author__ = "adrn <adrn@astro.columbia.edu>"
# Standard library
import os, sys
import glob
import logging
import json
# Third-party
from astropy.io import fits
import astropy.units as u
import matplotlib... | adrn/MDM | mdm/arc.py | Python | mit | 11,804 | [
"Gaussian"
] | 6c88387e154c82ee26c19509e3b03ae25f02ab128458d9d70293020792177da7 |
import hyperspy.api as hs
import _spectrum
import matplotlib.pyplot as plt
from ase import Atoms
import spglib as spg
import numpy as np
class Atom(object):
"""Atom so define in unit Cell"""
def __init__(self, number, position):
self.number = number
self.position = position
class Cell(object):
"""Cell object ... | sindrerb/VecDiSCS | eels/pyeels/eels_old.py | Python | gpl-3.0 | 9,063 | [
"ASE"
] | fdc3e16c24446684205a1868e27369710b9eb3737f07f5b15a28290c68a25195 |
from os import remove, environ
import logging
from emmail.objects.blast import BLAST
from emmail.objects.clusterer import Clusterer
from emmail.utilities import *
logging.basicConfig(level=environ.get("LOGLEVEL", "INFO"))
logger = logging.getLogger(__name__)
def buildSubparser(parser):
"""
Add ... | Andre-Tan/EmMAIL | emmail/utilities/runBLAST.py | Python | gpl-3.0 | 2,951 | [
"BLAST"
] | c5772cfd11785820d28ec0e38aa9698750d251ec4fc2f19617eddb4129347f3d |
"""Dynamic Imaging of Coherent Sources (DICS)."""
# Authors: Marijn van Vliet <w.m.vanvliet@gmail.com>
# Britta Westner <britta.wstnr@gmail.com>
# Susanna Aro <susanna.aro@aalto.fi>
# Roman Goj <roman.goj@gmail.com>
#
# License: BSD (3-clause)
import numpy as np
from ..utils import logger, ... | teonlamont/mne-python | mne/beamformer/_dics.py | Python | bsd-3-clause | 37,262 | [
"NEURON"
] | 91a97a3af53d207c36b9104e97110b80b6c225fbb5a36957a8e6bb9c104831e3 |
# Copyright (C) 2012-2016
# 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 terms of t... | kkreis/espressopp | src/interaction/FENE.py | Python | gpl-3.0 | 5,474 | [
"ESPResSo"
] | e201bdb98acb9b46eefa48a73331e0f74ae193d28b19c6f35c5413183540d1be |
# Copyright (c) 2012 ARM Limited
# All rights reserved.
#
# The license below extends only to copyright in the software and shall
# not be construed as granting a license to any other intellectual
# property including but not limited to intellectual property relating
# to a hardware implementation of the functionality ... | andrewfu0325/gem5-aladdin | src/python/m5/SimObject.py | Python | bsd-3-clause | 57,426 | [
"VisIt"
] | 4e02a6cd9a91a56a0aae378d079e3e5bc2dcc6ecea94e7045e2eb30c36b96a85 |
'''
Generates the reward spikes!
'''
import argparse
from brian_multiprocess_udp import BrianConnectUDP
def reward_generator(spikes_pipe_in, spikes_pipe_out):
"""
This function substitutes the run_brian_simulation and converts the received spikes into Baxter joint angles.
"""
import numpy
im... | ricardodeazambuja/BrianConnectUDP | examples/Baxter_reward_node.py | Python | cc0-1.0 | 4,507 | [
"NEURON"
] | 1d32ac1f31beb3744b05b001e8ce2ea136c87dfc70616da81805f9b8e8e18dda |
""" Contains the ModeController class."""
# mode_controller.py
# Mission Pinball Framework
# Written by Brian Madden & Gabe Knuth
# Released under the MIT License. (See license info at the end of this file.)
# Documentation and more info at http://missionpinball.com/mpf
import logging
import os
from collections impo... | spierepf/mpf | mpf/system/mode_controller.py | Python | mit | 13,556 | [
"Brian"
] | 60e2c22b56de0b9f00dddc1d090c32db41fa8f1caefe022d2e810852d0e49fb4 |
# $Id$
#
# Copyright (C) 2002-2008 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# 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 RDKit source tree.
#
""" Atom-based calculat... | soerendip42/rdkit | rdkit/Chem/Crippen.py | Python | bsd-3-clause | 6,129 | [
"RDKit"
] | d40cb81fd8fdeb2f4b32ffc2c4be67d21573f6852bd7a331915813f60f9ac9d1 |
#! /usr/bin/env python
act2_spice = """\
* Lab 1, Act 2, BJT {bjt}, Part {part}, Plot Num {qn}
Vs Vi1 0 {wave}
Vcc Vi2 0 DC 5
RC1 Vi2 Vo1 {rc}
RB1 Vi1 Vb {rb}
Q1 Vo1 Vb 0 {bjt}
{extra}
* Model for 2N3904 NPN BJT (from Eval library in Pspice)
.model 2N3904 NPN(Is=6.734f Xti=3 Eg=1.11 Vaf=74.03 Bf=416.4 Ne... | jmesmon/trifles | 2011s_lab2/gen_spice2.py | Python | gpl-3.0 | 4,333 | [
"xTB"
] | 4ead843283b288d5d7c428043c223213d7250c918039fc9d15f2b49852aa8f4a |
#! /usr/bin/python3
#
# This source code is part of icgc, an ICGC processing pipeline.
#
# Icgc 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... | ivanamihalek/tcga | icgc/50_production/60_clustering_on_the_structure.py | Python | gpl-3.0 | 4,814 | [
"PyMOL"
] | e4232d44c18922c595cbae79658e255ae3e0d4d17ab388ac8d8f2a6d5de06f8f |
#!/usr/bin/env python
########################################
#Globale Karte fuer tests
# from Rabea Amther
########################################
# http://gfesuite.noaa.gov/developer/netCDFPythonInterface.html
import math
import numpy as np
import pylab as pl
import Scientific.IO.NetCDF as IO
import matplotlib as... | CopyChat/Plotting | Python/climate_change/swio_changes_tas_rcp85.py | Python | gpl-3.0 | 8,298 | [
"NetCDF"
] | 7a841f8ebfa51a6394b03204437f7522cbace039a498ae0dd472fe13e5b76078 |
##############################################################################
# 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... | mfherbst/spack | var/spack/repos/builtin/packages/r-annotationhub/package.py | Python | lgpl-2.1 | 2,489 | [
"Bioconductor"
] | f272f0b206916b6e6d8da83d73ee1e75d88acf989d2c14e21b7053ad1b330bdf |
#!/usr/bin/env python
import argparse, os, string, json
import xml.etree.ElementTree as ET
from bioblend import galaxy
def main(master_api_key, api_url, galaxy_admin_user, galaxy_admin_pass, workflows_dir):
gi = galaxy.GalaxyInstance(url=api_url, key=master_api_key)
#adding new user
admin_key = create_use... | phac-nml/snvphyl-galaxy | packer/python/install-workflow-tools.py | Python | apache-2.0 | 3,036 | [
"Galaxy"
] | 6a33b3a2026aa1141175b826ae9e3bcb4c6411c27ba0c257faf471b42b1cdb33 |
# Translated from vib.tcl
import vtk
def main():
file_name = get_program_parameters()
colors = vtk.vtkNamedColors()
# Set the colors.
colors.SetColor("PlateColor", [255, 160, 140, 255])
colors.SetColor("BkgColor", [65, 99, 149, 255])
# Read a vtk file
#
plate = vtk.vtkPolyDataReade... | lorensen/VTKExamples | src/Python/VisualizationAlgorithms/PlateVibration.py | Python | apache-2.0 | 2,575 | [
"VTK"
] | 68330884ce3cba75091f7a05f436fb9f71a3078ea995961c53e49f76cd8c3448 |
r"""
Contact of two elastic bodies with a penalty function for enforcing the contact
constraints.
Find :math:`\ul{u}` such that:
.. math::
\int_{\Omega} D_{ijkl}\ e_{ij}(\ul{v}) e_{kl}(\ul{u})
+ \int_{\Gamma_{c}} \varepsilon_N \langle g_N(\ul{u}) \rangle \ul{n} \ul{v}
= 0
\;, \quad \forall \ul{v} \;,
... | lokik/sfepy | examples/linear_elasticity/two_bodies_contact.py | Python | bsd-3-clause | 5,231 | [
"VTK"
] | 49cecab73c7c5f4be664d64c5f9eae11c418bfad48c0c19109cb67c589621399 |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses... | alexlo03/ansible | lib/ansible/modules/network/avi/avi_gslb.py | Python | gpl-3.0 | 6,716 | [
"VisIt"
] | 63553a948f24779e6d7592c82d7a93fbc7e87f5870a872f8e756e516e70ae463 |
from django.test import TestCase
import mock
from webfaction.models import User
from .models import Application, Database, APPTYPES, ENGINES
class ApplicationTests(TestCase):
def setUp(self):
with mock.patch('webfaction.tasks.create_user.delay'):
owner = User.objects.create(email=u'brian... | gfavre/beyondthehost | beyondthehost/applications/tests.py | Python | mit | 1,483 | [
"Brian"
] | 57d0a44a98b69584ec117b656a5dab727986f33ee69a7e6a0a171e2e03f12c47 |
#!/usr/bin/env python
"""
Artificial Intelligence for Humans
Volume 1: Fundamental Algorithms
Python Version
http://www.aifh.org
http://www.jeffheaton.com
Code repository:
https://github.com/jeffheaton/aifh
Copyright 2013 by Jeff Heaton
Licensed under the Apache License, Version 2... | PeterLauris/aifh | vol1/python-examples/examples/example_normalize.py | Python | apache-2.0 | 17,086 | [
"VisIt"
] | 9b4c5b28d32b97056f49c2708d2afb287c5d6223840fd49d852ad16ee89739b4 |
#!/usr/bin/env python
import numpy as np
import pylab
import os
import Infer
import MyFuncs as MF
#create transit parameters (pars, errors, guess)
tpar = np.array([0.0,1.0,10.,0.1,0.1,0.2,0.2,1.0,0.0,0.0003])
epar = np.array([0.0001,0.0,0.02,0.01,0.02,0.0,0.0,0.0001,0.00001,0.0000])
gpar = np.array([0.001,1.0,12.,0.... | nealegibson/Infer | examples/LevenbergMarquardt_eg.py | Python | gpl-3.0 | 1,815 | [
"Gaussian"
] | ae8577b31ffdb196710ab875ba8de4ff7341dc1574112b038ee6454d4b0532d5 |
# -*- coding: utf-8 -*-
#
# hl_api_types.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, o... | Silmathoron/nest-simulator | pynest/nest/lib/hl_api_types.py | Python | gpl-2.0 | 32,816 | [
"Gaussian"
] | 53e0a9cda078b24685f53da1f56c8b59b95e764ddbc595d37e918c2fe61823eb |
#
# Copyright (C) 2008, Brian Tanner
#
#http://rl-glue-ext.googlecode.com/
#
# 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 requ... | okkhoy/mo-rlglue-python-codec | tests/glue_test.py | Python | mit | 1,465 | [
"Brian"
] | f90ccfd6f14f237dc53b3b518f52465d25372620eb9b14f0258f9a6c65e5722c |
# Copyright (c) 2012, Cloudscaling
# 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... | alaski/nova | nova/hacking/checks.py | Python | apache-2.0 | 30,206 | [
"VisIt"
] | 6044d6eb69131f1262f9b565a1d58f6799251af1144876d33be94907451c81ab |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | harterj/moose | modules/stochastic_tools/examples/surrogates/pod_rb/2d_multireg/rbpod_study.py | Python | lgpl-2.1 | 3,180 | [
"MOOSE"
] | 10f4e616ec83205837136717b2e4fceaa68d2d4c83ea070b0578446337dd89b4 |
"""
MRS.analysis
------------
Analysis functions for analysis of MRS data. These include a variety of
functions that can be called independently, or through the interface provided
in :mod:`MRS.api`.
"""
import os
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.mlab as mlab
import nitime as nt
i... | rhancockn/MRS | MRS/analysis.py | Python | mit | 27,891 | [
"Gaussian"
] | 2e0620343c92bdc74c216681012142e3be5dd10d54e7d1ac0520fdc78de6ce52 |
# Copyright (C) 2013 Oskar Maier
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in ... | lfrdm/medpy | medpy/filter/noise.py | Python | gpl-3.0 | 7,591 | [
"Gaussian"
] | dabe86ffb0bf96b68bfae20563f36bb4fcbffa03e382a667196cf654ed883db1 |
#
# 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... | espressomd/espresso | testsuite/python/cluster_analysis.py | Python | gpl-3.0 | 11,031 | [
"ESPResSo"
] | b8a7dba2683fa3f251c2f0ab851dac91598a96c0760b4f3bf9f3dfc4dd30b5e6 |
# encoding: utf-8
"""
An application for IPython.
All top-level applications should use the classes in this module for
handling configuration and creating componenets.
The job of an :class:`Application` is to create the master configuration
object and then create the configurable objects, passing the config to them.
... | cloud9ers/gurumate | environment/lib/python2.7/site-packages/IPython/core/application.py | Python | lgpl-3.0 | 13,356 | [
"Brian"
] | 297af91acf8e9b17080f6ab1942fea4fb76f35a286819fa39b1bc013c031aee6 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | harterj/moose | modules/geochemistry/test/tests/solubilities_and_activities/gypsum_solubility.py | Python | lgpl-2.1 | 1,232 | [
"MOOSE"
] | 330becb76be27b4fa98fab2c69e2b285d33d5a1661e322510e6af4cb8a1e94d2 |
'''
Created on Jan 22, 2011
@author: mkiyer
chimerascan: chimeric transcript discovery using RNA-seq
Copyright (C) 2011 Matthew Iyer
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 ... | madhavsuresh/chimerascan | chimerascan/deprecated/align_full.py | Python | gpl-3.0 | 7,240 | [
"Bowtie",
"pysam"
] | 20a7bb22c132268fd326b4ff710eaf5faa29108c99d6fa0ee6b6756bfa2f529e |
#!/usr/bin/env python
"""
Creates an intersection vcf file from two vcf files.
usage: %prog [options]
-p, --input1=p: vcf file
-q, --input2=q: vcf file
-f, --priority=f: file #
-i, --intersect=i: Intersect or unique
-o, --output1=o: Output vcf
"""
import os, shutil, subprocess, sys, tempfile
from gala... | maxplanck-ie/Megamapper | NewIntersect.py | Python | bsd-3-clause | 4,062 | [
"Galaxy"
] | 402dc87f3fc3d4a56a7afed18da203e9bf8a8629f579bbf122b0595dae97298a |
import vtk
# create a rendering window and renderer
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
# create a renderwindowinteractor
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# create source
source = vtk.vtkCylinderSource()
source.SetCenter(0,0,0)
source.SetR... | tjssmy/CuviewerPy | vtkTests/cyl.py | Python | mit | 662 | [
"VTK"
] | 6699a03b080c9a4e2562e9030c1fab808678ad4c28d3ff87e4ac5a017cec650d |
import math
import numpy
import numpy.linalg
import MDAnalysis
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt
class KabschAlign(object):
def __init__(self):
"""
Constructor
"""
def kabsch(self, toXYZ, fromXYZ):
"""
Input is a 3 x N array of coordinates.
"""
len1 = numpy.... | acadev/pyACA | src/KabschAlign.py | Python | gpl-2.0 | 4,592 | [
"MDAnalysis"
] | 4c2987416a0d31b46fd3fb215d31cb0a24c068c3d7680413258d52e570fa0704 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# publicscriptgen - Basic script generator functions
# Copyright (C) 2003-2015 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU General ... | heromod/migrid | mig/shared/publicscriptgen.py | Python | gpl-2.0 | 19,194 | [
"Brian"
] | c1697d8a7522cdc0b5a3ea6ab81c4121f542ac8108fee8281dd728c739331350 |
# -*- coding: utf-8 -*-
# This file is part of MyPaint.
# Copyright (C) 2007-2015 by Martin Renold <martinxyz@gmx.ch>
# Copyright (C) 2015-2016 by the MyPaint Development Team
#
# 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
... | dothiko/mypaint | gui/meta.py | Python | gpl-2.0 | 6,999 | [
"Brian"
] | e7434f5beeb0178f063b6dd5780e968dab84bc5d1b1d67fc83caee59fa28ce0a |
from dominate import tags
from dominate.util import raw
from flask import current_app
from markupsafe import Markup
from visitor import Visitor
def render_form(form, **kwargs):
r = WTFormsRenderer(**kwargs)
return Markup(r.visit(form))
class WTFormsRenderer(Visitor):
def __init__(self,
... | moha24/flask-bootstrap | flask_bootstrap/forms.py | Python | apache-2.0 | 4,514 | [
"VisIt"
] | 4ec7516f6b27ab2712b8ef215180db1bf29ea62ed62b12982e1d770fb31d59c3 |
import abc
import copy
import logging
import pathlib
from collections import ChainMap
from . import chembridge, constants
_logger = logging.getLogger(__name__)
class BaseCalculator(abc.ABC):
"""Base class for quantum calculators
This class should not be used directly, use a class appropriate for your
q... | ppqm/ppqm | ppqm/calculator.py | Python | mit | 3,617 | [
"RDKit"
] | 99c0fdc780c52593ead3b52baf9bbdd97ca136a5d0bee79a0308ac0a7d9e82bd |
# Copyright 2008 Brian Boyer, Ryan Mark, Angela Nitzke, Joshua Pollock,
# Stuart Tiffen, Kayla Webley and the Medill School of Journalism, Northwestern
# University.
#
# This file is part of Crunchberry Pie.
#
# Crunchberry Pie is free software: you can redistribute it and/or modify
# it under the terms of the GNU Gene... | brianboyer/newsmixer | social/letters/admin.py | Python | gpl-3.0 | 1,285 | [
"Brian"
] | 7876c876aafa7e513747102cb9ab44150abd186ec9fc6d394341d23f7a914862 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2018 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | amjames/psi4 | psi4/share/psi4/databases/BBI.py | Python | lgpl-3.0 | 150,764 | [
"Psi4"
] | 0ef405bba8ee8b8187b7a7f431e9e0ab89ae1608fcb890ce3c652b50f0dc02de |
"""
align.py
"""
import numpy as np
from scipy import ndimage
from matplotlib import pyplot as plt
_WARN = False
def blob_align(images, init_peak_loc=None):
"""
Align a series of images on the strongest peak.
Pad your image beforehand if you want to retain information at the
very edges of the im... | tjlane/electrolysis | electrolysis/align.py | Python | mit | 7,236 | [
"Gaussian"
] | 04817719b81ef607c523213b6d61c99ed2912bf3e2462891b1ad4f1dd2369c52 |
import os
import sys
import tempfile
from icqsol.shapes.icqShapeManager import ShapeManager
from icqsol.bem.icqLaplaceSolver import LaplaceSolver
PLY = 'ply'
POLYDATA = 'POLYDATA'
VTK = 'vtk'
def asbool(val):
return str(val).lower() in ['yes', 'true']
def get_format_and_type(galaxy_ext):
# Define the outp... | gregvonkuster/galaxy-csg | tools/icqsol_utils.py | Python | mit | 2,199 | [
"Galaxy",
"VTK"
] | 405f4de12f2c33d7890c4600c9bd0b7607b1b8375e0579751d2fd89e63a2f882 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import unittest
import os
import warnings
import random
from pymatgen import SETTINGS
from pymatgen.ext.matproj import MPRester, MPRestError
from pymatgen.core... | gpetretto/pymatgen | pymatgen/ext/tests/test_matproj.py | Python | mit | 15,874 | [
"pymatgen"
] | 4a816a603f00a1505ac6bd34a17bb03bc21bf100c5897b8ef674f5cee1ec7b83 |
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | gkc1000/pyscf | pyscf/pbc/df/test/test_aft_jk.py | Python | apache-2.0 | 6,054 | [
"PySCF"
] | a678de64ef5b8df5ddf8baca3d38f271214b109c40c0db4f669b2f4bca4630e4 |
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