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# Copyright (c) 2015 James Hensman
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
from ..core import GP
from . import GPLVM
from .. import mappings
class BCGPLVM(GPLVM):
"""
Back constrained Gaussian Process Latent Variable Model
:param Y: observed data
:type Y: np.n... | SheffieldML/GPy | GPy/models/bcgplvm.py | Python | bsd-3-clause | 1,475 | [
"Gaussian"
] | 35a0932fbb41ded2bbfb71ee578b00cb78455ba132b6ca022a73a3f02721f3ae |
"""
WhatsUP: astronomical object suggestions for Las Cumbres Observatory Global Telescope Network
Copyright (C) 2014-2015 LCOGT
models.py - Database schemas
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 Found... | LCOGT/whatsup | whatsup/models.py | Python | gpl-3.0 | 3,519 | [
"Galaxy"
] | 4a56054b099592100f24ce0d63fbc4176535f27a9205d92f0d909fbb0ff52438 |
"""Reproduce by simulation of PCA estimation using wheelerdata"""
import sys, os
import numpy as np
from numpy.random import RandomState
import argparse
import json
from sklearn.decomposition import PCA
from simfMRI.noise import white
from wheelerdata.load.meta import get_data
from fmrilearn.analysis import fir
fro... | parenthetical-e/wheelerexp | meta/reproduce_pca.py | Python | bsd-2-clause | 5,081 | [
"Gaussian"
] | 41b3a71409acfe2ed956dbbf23e547452149f5aad611360790f27dca20209cb5 |
# -*- coding: utf-8 -*-
#
# Magic-Wormhole documentation build configuration file, created by
# sphinx-quickstart on Sun Nov 12 10:24:09 2017.
#
# 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... | warner/magic-wormhole | docs/conf.py | Python | mit | 5,669 | [
"Brian"
] | a4b0055054bb275f2823d52a681cc742992f71ac7a7500f5fa125d83545586fc |
# This file is part of PyEMMA.
#
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
#
# PyEMMA 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 vers... | markovmodel/PyEMMA | pyemma/coordinates/tests/test_api_source.py | Python | lgpl-3.0 | 9,871 | [
"NetCDF"
] | e16f2a078e7bf531f87363e4070b4872383754ad6d8404bbddc27424e48cb355 |
# $Id$
#
# Copyright (C) 2003-2006 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.
#
"""unit testing code ... | rdkit/rdkit-orig | rdkit/Chem/Suppliers/UnitTestSmilesMolSupplier.py | Python | bsd-3-clause | 3,020 | [
"RDKit"
] | 8c72f964cf8c2b0e8e180438e0de9d466dc1229cbf7438df92a5f0cfad33b9d1 |
from enum import Enum
from itertools import product
from psi4 import core
from psi4.driver import psifiles as psif
import numpy as np
from qcelemental.util import which_import
class RemovalPolicy(Enum):
LargestError = 1
OldestAdded = 2
class StoragePolicy(Enum):
InCore = 1
OnDisk = 2
def axpy(y, al... | psi4/psi4 | psi4/driver/procrouting/diis.py | Python | lgpl-3.0 | 17,437 | [
"Psi4"
] | 4385c948926ae906a49cbb0cc504c2d430e0b72ab51ba64133afe6f2a5104c5b |
##############################################################################
# Copyright (c) 2013-2017, 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... | lgarren/spack | var/spack/repos/builtin/packages/r-affycomp/package.py | Python | lgpl-2.1 | 1,773 | [
"Bioconductor"
] | 518fd0dbb7be874494140a72ac5914d412a51d120b415f543e9468b9a4f6dfaa |
"""
vtk - surface and countours
"""
import enaml
from enaml.qt.qt_application import QtApplication
def run():
with enaml.imports():
from vtk_canvas_views import Main
app = QtApplication()
view = Main(custom_title='VTK Demo Example')
view.show()
# Start the application event loop
ap... | viz4biz/PyDataNYC2015 | tutorial/vtk_canvas_views_run.py | Python | apache-2.0 | 338 | [
"VTK"
] | 56c326f936789e77a8964e6ba9cd01e425a63de55f428391db7e08d10560ad9e |
################################################################
# SQUAD - superconducting quantum dot #
# Copyright (C) 2012-2019 Vladislav Pokorny; pokornyv@fzu.cz #
# homepage: github.com/pokornyv/SQUAD #
# config_squad.py - config and global variables ... | pokornyv/josephson | config_squad.py | Python | mit | 5,659 | [
"DIRAC"
] | c4f88335aef495d5d6adef6c975feaa743dcf95d709d3b1429972ac049ea82af |
# $HeadURL$
__RCSID__ = "$Id$"
from DIRAC.AccountingSystem.Client.Types.BaseAccountingType import BaseAccountingType
import DIRAC
class Job( BaseAccountingType ):
def __init__( self ):
BaseAccountingType.__init__( self )
self.definitionKeyFields = [ ( 'User', 'VARCHAR(32)' ),
... | Sbalbp/DIRAC | AccountingSystem/Client/Types/Job.py | Python | gpl-3.0 | 2,736 | [
"DIRAC"
] | 4030219ebfa0c287fddafc08461f27d8b778ed345b4cc73bb8e5956db57db449 |
from dataclasses import dataclass
from typing import Iterator, TypeVar, Union
from blib2to3.pytree import Node, Leaf, type_repr
from blib2to3.pgen2 import token
from black.nodes import Visitor
from black.output import out
from black.parsing import lib2to3_parse
LN = Union[Leaf, Node]
T = TypeVar("T")
@dataclass
cl... | psf/black | src/black/debug.py | Python | mit | 1,595 | [
"VisIt"
] | 05b945f4bf3c84d19bb95a3e107e92cc7a398e005b160587c8b2f5e338653b76 |
#!/usr/bin/python
import getopt
import sys
from Bio import SeqIO
from Bio.SeqUtils import GC
import time# import time, gmtime, strftime
import os
import shutil
import pandas
from Bio.SeqRecord import SeqRecord
from Bio.Seq import Seq
import csv
#from datetime import datetime
import numpy as np
from scipy import stats
... | nyirock/mg_blast_wrapper | mg_xwrapser_latest.py | Python | mit | 26,958 | [
"BLAST"
] | 0a51ab19dcb4ec9412f0833dea526a616c7ec895ecfdfc565214595a1c6c8097 |
from rest_framework.authentication import SessionAuthentication, BasicAuthentication
from rest_framework_jwt.authentication import JSONWebTokenAuthentication
from rest_framework.permissions import IsAuthenticated
from rest_framework import viewsets
from .models import Vault, Recent
from .serializers import VaultSeriali... | pyprism/Hiren-Vault | password/views.py | Python | mit | 6,310 | [
"VisIt"
] | 9b9fcb377c4a64f8648e46c12ea1bde03294d49ff1341f934d00ba66d6373c6b |
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2006,2007,2012,2014,2015, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public v... | jchodera/cclib | test/data/testSPun.py | Python | lgpl-2.1 | 5,462 | [
"Jaguar",
"Molpro",
"ORCA",
"cclib"
] | e8ecff0add3828c5b4e26083aefee2d1fb1d13f475fa13935edaceb534a9e2d5 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
from pymatgen.util.testing import PymatgenTest
from pymatgen.transformations.defect_transformations import \
DefectTransformation
from pymatgen.analysis.defects.core import Vacancy
class ... | mbkumar/pymatgen | pymatgen/transformations/tests/test_defect_transformations.py | Python | mit | 1,327 | [
"pymatgen"
] | cd2f7c5eee5c909086a75bbf04560b48b4ce85dd6cefa202d5629b912863d3d1 |
# This module provides classes that represent VRML objects for use
# in data visualization applications.
#
# Written by: Konrad Hinsen <hinsen@cnrs-orleans.fr>
# With contributions from Frank Horowitz <frank@ned.dem.csiro.au>
# Last revision: 2004-7-19
#
"""This module provides definitions of simple 3D graphics object... | OS2World/DEV-PYTHON-UTIL-ScientificPython | src/Lib/site-packages/Scientific/Visualization/VRML2.py | Python | isc | 21,701 | [
"VMD"
] | 8875a10ee8c5010f26b9903d4599c70fc64b76400e41eb8372f200783b351a19 |
#
# Test the multipole transformation rules
#
import sys
from math import exp, sqrt, sin, cos, pi
from cmath import exp as cexp
import random
import numpy as np
import ase
from hotbit.coulomb.multipole import zero_moments, get_moments
from _hotbit import multipole_to_multipole, multipole_to_local, local_to_local,... | pekkosk/hotbit | hotbit/test/multipole_operations.py | Python | gpl-2.0 | 5,584 | [
"ASE"
] | cc30ba3117e6ae3b27758082b17185f36adeeb96cbb4187ea1823889fd103de6 |
"""
This module contains unit tests for the theano autocorrelation function
"""
import unittest
import numpy as np
from mjhmc.misc.autocor import autocorrelation, slow_autocorrelation, sample_to_df
from mjhmc.misc.distributions import Gaussian, MultimodalGaussian
from mjhmc.samplers.markov_jump_hmc import MarkovJump... | rueberger/MJHMC | mjhmc/tests/test_fast_ac.py | Python | gpl-2.0 | 2,761 | [
"Gaussian"
] | 0dbfa86f2ba0c024c84d6023167a0867383450179db851fec163e3044c3a4ec5 |
# -*- coding: utf-8 -*-
# @Author: Zachary Priddy
# @Date: 2016-12-24 12:39:45
# @Last Modified by: Zachary Priddy
# @Last Modified time: 2016-12-24 20:34:28
import difflib
import json
import logging
import requests
from core import ffCommand
from core.database.device_db import getDeviceList
from core.database.ro... | zpriddy/Firefly | Firefly/core/api/ha_bridge.py | Python | apache-2.0 | 3,051 | [
"Firefly"
] | 98ff8307f665dea81cd1c2cd781c56a41064a761aacbd742c5ce76d5d25c626e |
#!/usr/bin/python
#
# Copyright 2015 John Kendrick
#
# This file is part of PDielec
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the MIT License
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied wa... | JohnKendrick/PDielec | PDielec/Utilities.py | Python | mit | 9,784 | [
"ABINIT",
"CASTEP",
"CRYSTAL",
"GULP",
"VASP",
"phonopy"
] | bddbd34967f95d01bd334c3cbdea539f54d0df913ecf573f4712c63863c6e171 |
WORDS = (
'Smith',
'Johnson',
'Williams',
'Brown',
'Jones',
'Miller',
'Davis',
'Garcia',
'Rodriguez',
'Wilson',
'Martinez',
'Anderson',
'Taylor',
'Thomas',
'Hernandez',
'Moore',
'Martin',
'Jackson',
'Thompson',
'White',
'Lopez',
'Lee',
'Gonzalez',
'Harris',
'Clark',
'Lewis',
'Robinson',
'Wal... | geradcoles/random-name | randomname/lists/surnames_american.py | Python | apache-2.0 | 44,764 | [
"Dalton",
"MOE"
] | 2540284e7c1128eabb3b5ebb267b25c1649fc56aa80d2b90f9a6ecaa4e7b9890 |
# Copyright 2010-2017, The University of Melbourne
# Copyright 2010-2017, Brian May
#
# This file is part of Karaage.
#
# Karaage 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... | brianmay/karaage | karaage/common/models.py | Python | gpl-3.0 | 4,374 | [
"Brian"
] | e7594792239fbbcbf381acbbc7631088964b5c21a1046d0bcaccf4748fc64cb0 |
import numpy as np
from .base import classifier
from .base import regressor
from numpy import asarray as arr
from numpy import asmatrix as mat
################################################################################
## KNNCLASSIFY #################################################################
############... | sameersingh/ml-discussions | week9/mltools/knn.py | Python | apache-2.0 | 9,133 | [
"Gaussian"
] | 2847c6a96b44c36ec0026ef843966ada9dd42b65593ce0296cc4684e6ff8d6db |
'''
Author information. This is an extension to the Utils class from Allen Brain API.
The parallel wiring related functions are written by Russell Jarvis rjjarvis@asu.edu
'''
import logging
import glob
from mpi4py import MPI
import numpy as np
import logging
from copy import deepcopy
logger = logging.getLogger()
log... | russelljjarvis/neurogateway | utils.py | Python | gpl-3.0 | 40,897 | [
"NEURON"
] | 12f6575df386aeec2472b32899bdd03a7eff85837638ce513d5abd4881988b32 |
# coding: utf-8
# Distributed under the terms of the MIT License.
from .model import AppModel
from ababe.stru.scaffold import ModifiedCell
from ababe.stru.element import Specie
from ababe.io.io import GeneralIO
import os
import numpy as np
class App(AppModel):
def __init__(self, infile, radius):
gcell = ... | unkcpz/ababe | ababe/cmdline/apps/atomperturb.py | Python | mit | 854 | [
"MCell",
"VASP"
] | fc6f52b653bdf2c35ab7de7c1f9e064bbd448797dcd802c0c0448631d63c2cd0 |
from __future__ import absolute_import
# #START_LICENSE###########################################################
#
#
# This file is part of the Environment for Tree Exploration program
# (ETE). http://etetoolkit.org
#
# ETE is free software: you can redistribute it and/or modify it
# under the terms of the GNU Gener... | karrtikr/ete | ete3/phylo/reconciliation.py | Python | gpl-3.0 | 8,169 | [
"VisIt"
] | 4ee78de4848634c0d3da590a5a0a2fde973182ce2199e827132c3fd5f79afca4 |
W, B = 1, 0
def fill_enclosed(grid):
reached = set()
for r, row in enumerate(grid):
for c, col in enumerate(row):
if r in (0, len(grid) - 1) or c in (0, len(grid[0]) - 1) and col == W and (r, c) not in reached:
visit(grid, r, c, reached)
# go through the matrix, for all... | misscindy/Interview | Graph/19_03_enclosed_region.py | Python | cc0-1.0 | 1,326 | [
"VisIt"
] | b0c0f2aeac3c31be3c3818e19da6ba83488d1b0c1a828d3b8f3f2158fb5dd684 |
"""Galaxy (ansible-galaxy) plugin for integration tests."""
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import os
import tempfile
from . import (
CloudProvider,
CloudEnvironment,
CloudEnvironmentConfig,
)
from ..util import (
find_executable,
display,
)... | agaffney/ansible | test/lib/ansible_test/_internal/cloud/galaxy.py | Python | gpl-3.0 | 9,011 | [
"Galaxy"
] | e56e64cf71408e05665f1db2fbcb2322f539416690ae94093b9e3d846c802def |
"""
Tests GeoTsRepositoryCollection
"""
from __future__ import print_function
from __future__ import absolute_import
from os import path
# import random
import unittest
# import numpy as np
from shyft import api
from shyft import shyftdata_dir
from shyft.repository.geo_ts_repository_collection import GeoTsRepositoryC... | felixmatt/shyft | shyft/tests/test_geo_ts_repository_collection.py | Python | lgpl-3.0 | 5,798 | [
"NetCDF"
] | 29f44b47dfe48ea1d26d155fae00aa5d65268b22e9513fc77a901b23f886e7f5 |
# -*- coding: utf-8 -*-
#
# Author: Sam Rushing <rushing@nightmare.com>
#
# Copyright (C) 2013 Alexander Shorin
# All rights reserved.
#
# This software is licensed as described in the file COPYING, which
# you should have received as part of this distribution.
#
"""
.. module:: astm.asynclib
:synopsis: Forked vers... | eddiep1101/python-astm | build/lib/astm/asynclib.py | Python | bsd-3-clause | 32,188 | [
"Amber"
] | 9d66837527c5dd05f3b22bd0fd7152f99005b0e4806fe1ddc94484715b47d3f5 |
# Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# http://www.sphinx-doc.org/en/master/config
# -- Path setup --------------------------------------------------------------
# If extensions (or module... | PaloAltoNetworks-BD/ansible-pan | docs/conf.py | Python | isc | 2,088 | [
"Galaxy"
] | 216e44a1be2501ec67a2339b6c5eed98aa6cb0d1f226959923893ae445d98765 |
'''
Script to mosaic TopoWx tiles into single CONUS-wide netCDF files
'''
from twx.interp import TileMosaic
from twx.utils import TwxConfig, mkdir_p
import fnmatch
import numpy as np
import os
if __name__ == '__main__':
np.seterr(all='raise')
np.seterr(under='ignore')
twx_cfg = TwxConfig(os.getenv(... | jaredwo/topowx | scripts/step26_mosaic_tiles.py | Python | gpl-3.0 | 1,767 | [
"NetCDF"
] | f91c9f2a6206474e0e977a03462b43599f38dd032c74952b8a22c4dd404a54ec |
"""setuptools.command.bdist_egg
Build .egg distributions"""
# This module should be kept compatible with Python 2.3
import sys, os, marshal
from setuptools import Command
from distutils.dir_util import remove_tree, mkpath
try:
from distutils.sysconfig import get_python_version, get_python_lib
except Imp... | diego-d5000/MisValesMd | env/lib/python2.7/site-packages/distribute-0.6.24-py2.7.egg/setuptools/command/bdist_egg.py | Python | mit | 18,884 | [
"VisIt"
] | d60c7b14414aba0bb640c889a45d6e0b208b751fd64b3bb1bcf8bb5d809f93c3 |
# -*- coding: utf-8 -*-
"""
jinja2.meta
~~~~~~~~~~~
This module implements various functions that exposes information about
templates that might be interesting for various kinds of applications.
:copyright: (c) 2010 by the Jinja Team, see AUTHORS for more details.
:license: BSD, see L... | fancasy/final | lib/jinja2/meta.py | Python | apache-2.0 | 4,301 | [
"VisIt"
] | 451412f982c4da29e088a58dac0733016b6f6c205f0bd23fcd9a178c59f48825 |
#!/usr/bin/python
import pylab
import sys
import argparse
import numpy as np
import matplotlib.pyplot as plt
import readpng as rpng
import tikhonov as tik
import scipy.sparse.linalg
import time
def create_data_and_designmatrix(img,N=500,width=10,p=1.0,deltaa=None,ixrand=None,iyrand=None,Mx=None,My=None):
if Mx is ... | HajimeKawahara/pinvprob | pinvprob/random_light.py | Python | gpl-2.0 | 7,271 | [
"Gaussian"
] | 4c43d7ba17f93f624b3d408479ab806a288f9fc56128f90967199e1b150f42d3 |
# -*- coding: utf-8 -*-
#!/usr/bin/env python
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007 Johan Gonqvist <johan.gronqvist@gmail.com>
# Copyright (C) 2007-2009 Gary Burton <gary.burton@zen.co.uk>
# Copyright (C) 2007-2009 Stephane Charet... | Nick-Hall/gramps | gramps/plugins/webreport/narrativeweb.py | Python | gpl-2.0 | 129,918 | [
"Brian"
] | d95cdd3c228857437be314ef69d53704b32b4c0285964ae9f214788e393f6ec0 |
# Copyright (C) 2016 Collin Capano, Christopher M. Biwer, Alex Nitz
# 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.
#
#... | cdcapano/pycbc | pycbc/distributions/__init__.py | Python | gpl-3.0 | 8,988 | [
"Gaussian"
] | e64199c1b32b7a592e604ed01ad0bdd69d97d475b6672b9bd9ee991b0e741896 |
# -*- coding: utf-8 -*-
from __future__ import print_function
import random
import time
from numpy import random as nprand
import moose
def make_network():
size = 1024
timestep = 0.2
runtime = 100.0
delayMin = timestep
delayMax = 4
weightMax = 0.02
Vmax = 1.0
thresh = 0.2
tau = 1 # Range of tau
tau0 = 0.5... | upibhalla/moose-core | tests/python/mpi/recurrentIntFire.py | Python | gpl-3.0 | 2,839 | [
"MOOSE",
"NEURON"
] | 2bca83131ffe565ceb6da18f5a7bca7dd640e813f03649b06789c2fcf064c731 |
"""
Support for managing apps (as created with "0install add").
@since: 1.9
"""
# Copyright (C) 2012, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import _, SafeException, logger
from zeroinstall.support import basedir, portable_rename
from zeroinstall.injector impo... | dabrahams/0install | zeroinstall/apps.py | Python | lgpl-2.1 | 13,519 | [
"VisIt"
] | 98ab00a9ba97cd523970f0b7463d276f248cd2efdec73277c13dc5195bcdb4e6 |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
"""A visitor that pauses the print at a layer
"""
from gcodeutils.visit.visitor import GCodeVisitor
__author__ = "wireddown"
PAUSE_COMMAND = "M226"
class PauseAtLayer(GCodeVisitor):
"""This class inserts a pause command at the start of each layer specified
"""... | zeograd/gcodeutils | gcodeutils/visit/pause_at_layer.py | Python | gpl-2.0 | 1,005 | [
"VisIt"
] | b6311dac738616605e64a073a553c0281c529045c3f168af9d105cb5dd9b04d1 |
from django.db import connection
from django.db.models import Sum, Q
from datetime import date, timedelta
from . import TemplateFileReport, register_report
REPORT_TYPE = 'clinic'
TEMPLATE_DIR = 'tracking/reports/clinic'
class ClinicReport(TemplateFileReport):
''' Base class for Email Reports'''
def __init__... | Heteroskedastic/Dr-referral-tracker | tracking/reports/clinic_reports.py | Python | mit | 8,655 | [
"VisIt"
] | 91d6a641ad39a13fe1cd4560497d581f2ec5487f33a7f723254c33380a725b3a |
#!/usr/bin/env python
#=============================================================================
#
# Gradient Noise Generation
#
# TODO:
#
# Add a more intelligent noise filter that is aware of the number of samples
# needed between the gradient positions, and expands the filter envelope to
# more evenly (Gau... | zhester/hzpy | development/gradnoise.py | Python | bsd-2-clause | 8,891 | [
"Gaussian"
] | 9d53781c1116910f6788fc59d48268c90fa2f4beba5ee9fc7d65a4f73304d8d6 |
# -*- coding: utf-8 -*-
"""
Enrich BEL graphs
=================
In the current build it is possible to enrich BEL graphs containing metabolites with associated
disease or protein information and to enrich BEL graphs containing disease or protein information with associated metabolites.
This can be done with the functi... | bio2bel/hmdb | src/bio2bel_hmdb/enrich.py | Python | mit | 9,194 | [
"Pybel"
] | 2d1e184f9f8a20d840edfb5244d7faeebe831757b0a8b495f81539619315a28f |
#!/usr/bin/env python
"""
Simple little script that allows one to automatically update DNS records through Fastmail's GUI.
I could not find an official API, so this relies on beautiful soup to naviagate through fastmail's
HTML pages.
"""
import requests, re, os, sys
import json
from bs4 import BeautifulSoup
FASTMAIL... | ZachAnders/ddfastmail | ddfastmail.py | Python | bsd-3-clause | 8,377 | [
"ASE"
] | 467455bc8671cf6d7a5176dca82334caadb066eb7339e2e66ab690964d76d0a9 |
import re
from collections import defaultdict, namedtuple
from datetime import datetime, timedelta
from dateutil.parser import parse as dt_parse
from hashlib import md5
from optparse import make_option
from user_agents import parse
from django.conf import settings
from django.core.management.base import BaseCommand
... | analytehealth/django-analytics | djanalytics/management/commands/collect_reporting_stats.py | Python | bsd-2-clause | 15,156 | [
"VisIt"
] | 74e96b383a680243c6272913845209f74cd654e3932eda50b651f4fe4bedcdbf |
#!/usr/bin/python
from scipy.stats import cauchy
import random
import math
import csv
import numpy as np
#import netCDF4 as nc
import argparse
#import matplotlib.pyplot as plt
#from mpl_toolkits.mplot3d import Axes3D
#import plotly.plotly as py
#import plotly.graph_objs as go
########################################... | WillArmentrout/galSims | simulate/old/Simulate_Draft_ChangeArmPositions_6.5.18.py | Python | gpl-2.0 | 22,890 | [
"Galaxy",
"Gaussian"
] | 0ecbd341466ff0c57fe0d38dd653c134c875f2e1068a7ac86c1c45d10bb4741f |
#
# 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/ibm.py | Python | gpl-3.0 | 9,741 | [
"ESPResSo"
] | dee9bee47fb42885ab3bca7f83d74a2f5889734344f13e5ce92bec51a9c0d720 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import os
from django.db import models, migrations
from django.contrib.staticfiles.finders import find
from django.core.files import File
DEFAULT_ICON = ('default.jpg', 'Default')
ICON_CHOICES = (
DEFAULT_ICON,
('blake.jpg', 'Blake'),
('joh... | simpleenergy/bughouse-ranking | bughouse/migrations/0003_auto_20150207_1846.py | Python | mit | 1,458 | [
"Brian"
] | 2830706a18fa9d081278e6a9b7c04861dee71e38933483ef6af137883bce559e |
# -*- coding: utf-8 -*-
# Frozen Gaussian and quantum trajectories
# The GWPs is used to approximate the amplitude instead of the wavefunction
# Quantum force is computed from the approximated amplitude
# A problem is that the quantum force obtained from the approximate amplitude is not accurate at the tail
#i... | binghongcha08/pyQMD | GWP/QTGB/Amplitude_GWP/gwp.py | Python | gpl-3.0 | 16,058 | [
"Gaussian"
] | e49dcdd167a38294214907475ccc4441a4f9b479bf0056627e97149c866b8fe5 |
from __future__ import unicode_literals
import io
import re
import ast
from .exceptions import MoultScannerError
from .compat import str_
from . import utils, log
_fallback_re = re.compile(r'''
^[\ \t]*(
from[\ \t]+[\w\.]+[\ \t]+import\s+\([\s\w,]+\)|
from[\ \t]+[\w\.]+[\ \t]+import[\ \t\w,]+|
... | tweekmonster/moult | moult/ast_scanner.py | Python | mit | 11,216 | [
"VisIt"
] | c4947cb82b2cabdcc88ebce1e25a55d23f32677dd8c47b55575dd0ce3121c0d7 |
"""
Common 2D and 3D plot, quiver, text functions
2013 (BSD-3) California Institute of Technology
"""
from __future__ import division
from warnings import warn
#import numpy as np
from matplotlib import pyplot as plt
from vectorized_meshgrid import vec2meshgrid
def dimension(ndarray):
"""dimension of ndarray
... | johnyf/pyvectorized | pyvectorized/multidim_plot.py | Python | bsd-3-clause | 5,949 | [
"Mayavi"
] | 569691bc33e6ee229dd5987cf70e288e1b7c0017a4e5bf74e0b44b283e89de54 |
#!/usr/bin/env python
#
# This file is part of Buildbot. Buildbot is free software: you can
# redistribute it and/or modify it under the terms of the GNU General Public
# License as published by the Free Software Foundation, version 2.
#
# This program is distributed in the hope that it will be useful, but WITHOUT
# A... | grembo/buildbot | master/setup.py | Python | gpl-2.0 | 20,409 | [
"Brian"
] | 229800312cc1257ec48933fc16f5a072c923304158cdabb86df2110f73178910 |
from __future__ import print_function
import random
import time
import threading
import thread
from hashlib import md5
from DIRAC.Core.Utilities.ReturnValues import S_ERROR, S_OK
from DIRAC.Core.Utilities.DIRACSingleton import DIRACSingleton
class LockRing( object ):
__metaclass__ = DIRACSingleton
def __init__(... | fstagni/DIRAC | Core/Utilities/LockRing.py | Python | gpl-3.0 | 2,987 | [
"DIRAC"
] | 72eb085d053732ff87377ed750c87b6ec2da8eef0e020f043031146dce1d7219 |
"""
Base classes used by studio tests.
"""
from bok_choy.page_object import XSS_INJECTION
from common.test.acceptance.fixtures.course import CourseFixture
from common.test.acceptance.fixtures.library import LibraryFixture
from common.test.acceptance.pages.common.auto_auth import AutoAuthPage
from common.test.accepta... | stvstnfrd/edx-platform | common/test/acceptance/tests/studio/base_studio_test.py | Python | agpl-3.0 | 6,561 | [
"VisIt"
] | f03dd54a245aa485f5a0f3ecf61262402fc295bb374f4dea864e7e1e1be28a33 |
##-------------------------------------------------------------------------
## Author: Owen Arnold @ ISIS/Tessella
## Date: 24/03/2011
## Purpose: Show signal cell data as surface plot. Sets color range between 0 and 3 for signal value.
##
##-------------------------------------------------------------------------
try... | dymkowsk/mantid | qt/paraview_ext/PVPlugins/Macros/ShowSignal.py | Python | gpl-3.0 | 1,010 | [
"ParaView"
] | 238dac2707de088bfc73c9650cda5ea61644a6f5855b1e60a3c80d06d7950a0c |
# this file does statistic analysis for the results
# from collections import Counter
from Bio.Blast import NCBIXML
from Bio import SeqIO
import os
from combine_files import *
#============analyse the output sam file : notchok1_virus.final.sort.sam==========
#============================================================... | shl198/Pipeline | DetectVirus/reads_stat.py | Python | mit | 12,645 | [
"BLAST"
] | 1cc938183561e416a6a9161f7bf17a24075ff071d79c2061edfc1f5f478046ef |
# !/usr/bin/env python
# -*- mode: python; coding: utf-8; -*-
# ---------------------------------------------------------------------------
#
# Copyright (C) 1998-2003 Markus Franz Xaver Johannes Oberhumer
# Copyright (C) 2003 Mt. Hood Playing Card Co.
# Copyright (C) 2005-2009 Skomoroh
#
# This program is free softwar... | shlomif/PySolFC | pysollib/game/__init__.py | Python | gpl-3.0 | 123,237 | [
"CASINO"
] | 79fb2dd4f9b4d568735c71954cb07968fdacafbc8e5b6ac64bd262aa03ec7550 |
"""Factor Analysis.
A latent linear variable model.
FactorAnalysis is similar to probabilistic PCA implemented by PCA.score
While PCA assumes Gaussian noise with the same variance for each
feature, the FactorAnalysis model assumes different variances for
each of them.
This implementation is based on David Barber's B... | soulmachine/scikit-learn | sklearn/decomposition/factor_analysis.py | Python | bsd-3-clause | 12,046 | [
"Gaussian"
] | 653d5c96c05806fe581c433639474468c576cc2b8f58e142f9bb60ecbc34c22c |
"""
pyparticleprobe.io.read_p3_2dimage_probe
=========================
A grouping of scripts designed to read in various file formats containing data
from 2-D precipitation and cloud imaging probes (PIP and CIP) aboard
the NOAA WP-3D aircraft.
Created by Nick Guy.
"""
# HISTORY::
# 8 Jan 2014 - Nick Guy. NRC,... | nguy/pyparticleprobe | pyparticleprobe/io/read_p3_2dimage_probe.py | Python | lgpl-2.1 | 23,133 | [
"NetCDF"
] | b1048f549b173286e037af05cf74ed1eaac7c1ff932f9d0f806a3c843ced8044 |
# -*- coding: utf-8 -*-
from south.utils import datetime_utils as datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding field 'Subscription.is_active'
db.add_column(u'visits_subscripti... | clincher/phuketstash | visits/migrations/0005_auto__add_field_subscription_is_active.py | Python | bsd-3-clause | 9,061 | [
"VisIt"
] | 17a35705d28dae5085424c7c2f55ac5fca220ccc707d8609bd3baba6901524ec |
"""
Alpha diversity measures (:mod:`skbio.diversity.alpha`)
=======================================================
.. currentmodule:: skbio.diversity.alpha
This package provides implementations of various alpha diversity measures,
including measures of richness, dominance, and evenness. Some functions
generate confi... | jensreeder/scikit-bio | skbio/diversity/alpha/__init__.py | Python | bsd-3-clause | 5,395 | [
"scikit-bio"
] | dbe62e49f8533cb5fc80ed0cec2610431480ae661460a1c73153abbe1f6efe00 |
# This test calculates derivatives of lcao overlap matrices such as
#
# a ~a
# P = < p | Phi >
# i mu i mu
#
# and compares to finite difference results.
from ase.data.molecules import molecule
from ase.units import Bohr
from gpaw import GPAW
from gpaw.atom.basis import BasisMaker
o... | qsnake/gpaw | oldtest/tci_derivative.py | Python | gpl-3.0 | 2,468 | [
"ASE",
"GPAW"
] | 1837f0c05cdac672ebf4b9c8f9d8523f73b0fd903ba9501aa2b82b1f502f77bd |
# Orca
#
# Copyright (C) 2010 Joanmarie Diggs
# Copyright (C) 2011-2012 Igalia, S.L.
#
# Author: Joanmarie Diggs <jdiggs@igalia.com>
#
# 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; eith... | h4ck3rm1k3/orca-sonar | src/orca/scripts/toolkits/WebKitGtk/speech_generator.py | Python | lgpl-2.1 | 7,888 | [
"ORCA"
] | daa19852ed2cc93ed54448dcc001651eeb1ae2179a78b9a96955aa19565d89d5 |
import unicodedata
import numpy as np
from .. import coding
from ..core.variable import Variable
# Special characters that are permitted in netCDF names except in the
# 0th position of the string
_specialchars = '_.@+- !"#$%&\\()*,:;<=>?[]^`{|}~'
# The following are reserved names in CDL and may not be used as name... | xray/xray | xarray/backends/netcdf3.py | Python | apache-2.0 | 4,174 | [
"NetCDF"
] | 5b702aebd7eed41a09ea653d1537727c9665a90971f7fb2d55c12188ba9800af |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Created on Jan 22, 2013
@author: Bharat Medasani
"""
import unittest
import os
from pymatgen.analysis.bond_valence import BVAnalyzer
from pymatgen.command_line.gulp_caller import GulpIO, GulpCaller, \
... | mbkumar/pymatgen | pymatgen/command_line/tests/test_gulp_caller.py | Python | mit | 12,876 | [
"GULP",
"VASP",
"pymatgen"
] | da0ffb0645d084d9e857dc9a2affe01f42e73f33551107406db425e718a14f80 |
# -*- coding: utf-8 -*-
"""Factories for the OSF models, including an abstract ModularOdmFactory.
Example usage: ::
>>> from tests.factories import UserFactory
>>> user1 = UserFactory()
>>> user1.username
fred0@example.com
>>> user2 = UserFactory()
fred1@example.com
Factory boy docs: http://f... | caneruguz/osf.io | tests/factories.py | Python | apache-2.0 | 29,464 | [
"Brian"
] | 0ba5b610cd2a7a8c7584fd8227fc51f90e9d1c96e08f9a757947d790a7ce04df |
from netCDF4 import *
from numpy import ndarray
from sys import getsizeof
class NetcdfCopier(object):
"""create a copy of the netcdf, can exclude certain variables and/or dimensions"""
# vbl : variables black list
# dbl : dimensions black list
# f : format
def copy(self,src,dst,dbl=[],vbl=[],f="NETCDF4")... | RDCEP/hybrid-dile-server | lib/utils/netcdfcopier.py | Python | apache-2.0 | 1,230 | [
"NetCDF"
] | 01cbea2812de8ceb02625ba6026bf191b1b377aff8cb9a2d2057f12e30730258 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# oidping - Check OpenID server availability
# 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 L... | heromod/migrid | mig/cgi-bin/oidping.py | Python | gpl-2.0 | 1,170 | [
"Brian"
] | f2dbeedaa72dcfc3c07e1aa2b4dcce693a4b9d45f08d7ae762af945653cd1cdd |
#!/usr/bin/python
#Audio Tools, a module and set of tools for manipulating audio data
#Copyright (C) 2007-2012 Brian Langenberger
#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... | R-a-dio/python-audio-tools | test/test.py | Python | gpl-2.0 | 17,878 | [
"Brian"
] | a0e008efbb8859d044588f33f56b477cd9155e2d9a6c84ece7b01ff50d461fa9 |
import cv2
import numpy as np
#from skimage.measure import compare_ssim
'''
MOG2
virtual int getHistory() const { return history; }
virtual void setHistory(int _nframes) { history = _nframes; }
virtual int getNMixtures() const { return nmixtures; }
virtual void setNMixtures(int nmix) { nmixtures ... | barney-NG/pyCAMTracker | src/tracker/Background.py | Python | mit | 10,695 | [
"Gaussian"
] | b32256dc7c09768ebdc95e9a773d5d6f9c706c4bf98976ebd19d42e100d6c28a |
"""
## Automatically adapted for numpy.oldnumeric Jun 27, 2008 by -c
Replaced numpy.oldnumeric with numpy methods - Jan 2015, PGedeck
"""
#pylint: disable=E1101,C0111,R0904
import rdkit.Numerics.rdAlignment as rdAlg
from rdkit import Geometry
import unittest
import numpy as np
import math
import copy
def lstFeq(l1,... | bp-kelley/rdkit | Code/Numerics/Alignment/Wrap/testAlignment.py | Python | bsd-3-clause | 5,911 | [
"RDKit"
] | a7ec4c744156ec5ca70483f61c098713fe09bdf1d871bf7cfa5e885cbbb15981 |
# -*- coding: utf-8 -*-
"""SQLite parser plugin for Mozilla Firefox history database files."""
from dfdatetime import posix_time as dfdatetime_posix_time
from plaso.containers import events
from plaso.containers import time_events
from plaso.lib import definitions
from plaso.parsers import sqlite
from plaso.parsers.s... | joachimmetz/plaso | plaso/parsers/sqlite_plugins/firefox_history.py | Python | apache-2.0 | 19,252 | [
"VisIt"
] | 0e7619e7e4f6f4ca452be38fcb36f8194633c4893b3a3921e4e282bf0494d64c |
########################################################################
# $Id$
########################################################################
""" The BQS TimeLeft utility interrogates the BQS batch system for the
current CPU consumed and CPU limit.
"""
from DIRAC import gLogger, gConfig, S_OK, S_ERROR
... | avedaee/DIRAC | Core/Utilities/TimeLeft/BQSTimeLeft.py | Python | gpl-3.0 | 3,025 | [
"DIRAC"
] | 7a7d3954c0a81d575bdc7beab36e6bb56dc4d6d996cbd52119004da83aed5cdd |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module provides classes that operate on points or vectors in 3D space.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2011, The Materi... | migueldiascosta/pymatgen | pymatgen/core/operations.py | Python | mit | 14,998 | [
"pymatgen"
] | d4fae7c6cb5796496f41c1cb42c208e041843802b175b45daa359835918d716a |
from __future__ import absolute_import
import re
from collections import namedtuple, defaultdict
from copy import deepcopy
from datetime import datetime
import six
from django.utils.functional import cached_property
from parsimonious.expressions import Optional
from parsimonious.exceptions import IncompleteParseError... | mvaled/sentry | src/sentry/api/event_search.py | Python | bsd-3-clause | 32,277 | [
"VisIt"
] | ec618d8443d799d6d387145cb36989e0cf20359898205afc82dcb0fbfd3fc558 |
# Copyright (c) 2018, Henrique Miranda
# All rights reserved.
#
# This file is part of the yambopy project
#
from yambopy import *
from netCDF4 import Dataset
from math import sqrt
import numpy as np
from cmath import exp
from yambopy.units import ha2ev, ev2cm1, I
class YamboElectronPhononDB():
"""
Python clas... | henriquemiranda/yambo-py | yambopy/dbs/elphondb.py | Python | bsd-3-clause | 8,789 | [
"Yambo"
] | f32bd5c08c918a542354a780f017c942a382162303070d7f2acdfb1bf27394fe |
#
# Copyright (C) 2007, Mark Lee
#
#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 required... | mguzdial3/MineCode | python-codec/src/rlglue/agent/AgentLoader.py | Python | apache-2.0 | 1,942 | [
"Brian"
] | d931cc42493ae6af05ac4d8e4eab1cdbaa6318c64a8bd90b175f4313c65372f7 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# resedit - Front end to resource editor
# Copyright (C) 2003-2009 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 Licen... | heromod/migrid | mig/cgi-bin/resedit.py | Python | gpl-2.0 | 1,075 | [
"Brian"
] | 60f61735b52293a86c8632a4f5f6baddec1af026180f10d5ba5d02e6041c5104 |
#!/usr/local/bin/python
# -*- coding: utf8
"""
this is a Library for SOM.
CopyLight Masato MASUDA. 2017.23.AUG.
"""
import SOM.Map as Map
import SOM.Coefficients as coef
import SOM.logger as logger
import SOM.SOM_config as SOM_config
from SOM.Topology import hexagonal_tbl
import numpy as np
from numpy.random import ... | kinect110/RPSOM | src/SOM/Model.py | Python | mit | 16,178 | [
"Gaussian"
] | 5702a7d1a78df01a16c0364b6313cb631b65b782d82b671f45955438e1e50e63 |
from galaxy.util import xml_text
DEFAULT_REQUIREMENT_TYPE = "package"
DEFAULT_REQUIREMENT_VERSION = None
class ToolRequirement( object ):
"""
Represents an external requirement that must be available for the tool to
run (for example, a program, package, or library). Requirements can
optionally asser... | jmchilton/lwr | galaxy/tools/deps/requirements.py | Python | apache-2.0 | 3,157 | [
"BWA",
"Galaxy"
] | ada523eaaeedc2026d629d9cc44a9335d42982251c630de7cb564c447d15184c |
#!/usr/bin/python3
#Author: Brian Raaen
#Original code: https://www.brianraaen.com/2016/11/04/superputty-to-pac-manager/
#
#This script can convert a SuperPutty Sessions.xml file to an Asbru-cm yaml file. The
#resulting yaml file can then be imported into Asbru-cm.
#This script does require tweaking for your personal s... | asbru-cm/asbru-cm | utils/asbru_from_superputty.py | Python | gpl-3.0 | 8,343 | [
"Brian"
] | 452087d2c4c04af9bc4d67a9d97c5dd216913d155e00b81b54417060355ac020 |
# -*- coding: utf-8 -*-
# <nbformat>2</nbformat>
# <codecell>
# Demo python notebook for sklearn elm and random_hidden_layer modules
#
# Author: David C. Lambert [dcl -at- panix -dot- com]
# Copyright(c) 2013
# License: Simple BSD
# <codecell>
from time import time
from sklearn.cluster import k_means
from dl_elm i... | alexsavio/elm-test | elm_notebook.py | Python | bsd-3-clause | 6,787 | [
"Gaussian"
] | e96b11a719ac0af15e099deee73d924434d52640b7387d705d64e8ff50f21b23 |
import mdtraj as md
from simtk.openmm import app
import simtk.openmm as mm
from simtk import unit as u
from fah_parameters import *
deviceid = 2
ff_name = "amber99sbildn"
water_name = 'tip3p'
which_forcefield = "%s.xml" % ff_name
which_water = '%s.xml' % water_name
pdb_filename = "./OLDRUN0/system.pdb"
out_pdb_fil... | kyleabeauchamp/fah-projects | code/equilibrate_npt.py | Python | gpl-2.0 | 2,006 | [
"MDTraj",
"OpenMM"
] | 4fbe4dd7d716b8090352f091d30a4aaf46f9df0a404aa389bbd233d4445afed9 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
"""
This example shows how to use pytim classes online during
a simulation performed with openmm (http://mdtraj.org/)
(see also the mdtraj interoperability)
"""
# openmm imports
f... | balazsfabian/pytim | pytim/examples/example_openmm.py | Python | gpl-3.0 | 1,160 | [
"MDTraj",
"OpenMM"
] | d26e92f628c78d66a3290775bfbc637cd15a83463ecb85e119bade83d2d08854 |
import unittest
import fun_bd
class TestStringMethods(unittest.TestCase):
def test_devuelve_clasificacion(self):
clasi=fun_bd.selectClasificacion()
self.assertEquals(clasi, fun_bd.selectClasificacion())
def test_devuelve_marcador(self):
marc=fun_bd.selectMarcador()
self.assertEquals(marc, fun_bd.selectMar... | manuelalonsobraojos/proyectoIV | bot_LaLiga/test.py | Python | gpl-3.0 | 616 | [
"VisIt"
] | 6141b218e6066a943723e8fc9b7990593e0ec196df161ac30179b1e01c23f235 |
# Copyright 2009 by Osvaldo Zagordi. All rights reserved.
# Revisions copyright 2010 by Peter Cock.
# 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.
"""Command line wrapper for the short read aligner ... | bryback/quickseq | genescript/Bio/Sequencing/Applications/_Novoalign.py | Python | mit | 8,639 | [
"Biopython"
] | c79d2cc707a593da49767e6d6fff02a9d05c62a8506589ff044338b85f3a47e5 |
"""
EMBL format (:mod:`skbio.io.format.embl`)
=========================================
.. currentmodule:: skbio.io.format.embl
EMBL format stores sequence and its annotation together. The start of the
annotation section is marked by a line beginning with the word "ID". The start
of sequence section is marked by a li... | gregcaporaso/scikit-bio | skbio/io/format/embl.py | Python | bsd-3-clause | 53,962 | [
"scikit-bio"
] | ec9f5ec4bc56603f6e3c49800c86aa58cd8f3217c14d9ee3284c4d64206146f1 |
# coding: utf-8
from __future__ import unicode_literals
from textwrap import dedent
from kinko.i18n import Extractor, Translator
from kinko.nodes import Tuple, Symbol, String, List
from kinko.compat import PY3
from kinko.parser import parser
from kinko.tokenizer import tokenize
from .base import TestCase, NODE_EQ_PA... | vmagamedov/kinko | tests/test_i18n.py | Python | bsd-3-clause | 1,747 | [
"VisIt"
] | 2c44107cc145b39721ad1d4bcbb72b879f1acf1fa070cbb3893a619cd2f1ad72 |
import json
import logging
import requests
from urllib import urlencode
from django.conf import settings
from django.contrib.auth.views import logout as auth_logout
from django.contrib import messages
from django.contrib.auth.decorators import login_required
from django.contrib.auth.models import User
from django.http... | mozilla/mozillians | mozillians/phonebook/views.py | Python | bsd-3-clause | 31,909 | [
"VisIt"
] | b324afb710dec866cb038ff865b87cdfa6dc7a127203a9b57b89415fb3314f26 |
import py, re, os, signal, time, commands
from subprocess import Popen, PIPE
mod_re = (r"\bmodule\s+(", r")\s*\(\s*")
func_re = (r"\bfunction\s+(", r")\s*\(")
def extract_definitions(fpath, name_re=r"\w+", def_re=""):
regex = name_re.join(def_re)
matcher = re.compile(regex)
return (m.group(1) for m in mat... | 1up3d/Stallman | src/MCAD/openscad_utils.py | Python | gpl-3.0 | 1,933 | [
"VisIt"
] | 174f02033620f96196f05363845c1b71a971f6fc36b44484b6c3c76c0019bc2f |
###############################################################################
##
## Copyright (C) 2014-2015, New York University.
## Copyright (C) 2011-2014, NYU-Poly.
## Copyright (C) 2006-2011, University of Utah.
## All rights reserved.
## Contact: contact@vistrails.org
##
## This file is part of VisTrails.
##
## ... | hjanime/VisTrails | vistrails/packages/vtk/vtk_wrapper/specs.py | Python | bsd-3-clause | 26,973 | [
"VTK"
] | 9de40f7126379a77b03e5bcd8376cf9702d42ef7b085b6e430a91a6797431fbf |
from django.conf import settings
import urllib, subprocess, os, sys, datetime, mwclient
'''
Handles linking PDB structure images to ProteinBox templates.
'''
description_skeleton = '''== {{{{int:filedesc}} ==
{{{{Information
| Description={{{{en | 1=Structure of protein {symbol}.
Based on [[w:PyMol | PyMol]] rende... | SuLab/genewiki | genewiki/bio/images.py | Python | mit | 7,651 | [
"PyMOL"
] | 6087a3593423be3baef6d05618244b2f3aeeff42ad51e68156b8ea817e161bc8 |
# 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.
#
"""Tests the basic functionality of the GEO parsers.
"""
from __future__ import print_function
import os
import sys
import Bio.Geo
testfiles = ['... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_geo.py | Python | gpl-2.0 | 1,239 | [
"Biopython"
] | 635f9e48c74a0d4095ef2ab17712cc212409e765d2c99417611d61d8bbfc9a34 |
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under ... | zzhao0/presto | presto-docs/src/main/sphinx/conf.py | Python | apache-2.0 | 5,695 | [
"Amber"
] | dd0ef9f1d2fa45e7141998878fbb89da0d9576d18e4f31fe68206b57531177a7 |
from __future__ import (absolute_import, division, print_function)
import re
from six import string_types
parNamePattern = re.compile(r'([a-zA-Z][\w.]+)')
class FunctionParameters(object):
"""
A helper class that simplifies access to parameters of nested composite fitting functions.
"""
def __init__(... | ScreamingUdder/mantid | scripts/Inelastic/CrystalField/function.py | Python | gpl-3.0 | 26,175 | [
"Gaussian"
] | 59038c91957f71233609e6747c4a318b63c656a86c6d4a9ca73342bd8406625e |
#!/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/gto/ecp.py | Python | apache-2.0 | 5,175 | [
"PySCF"
] | 2ceb3de52c64c535ec43c7c37993dba10a5b9dd0cd105d61bff849ea4c375a92 |
# Copyright 2008 by Bartek Wilczynski.
# Adapted from Bio.MEME.Parser by Jason A. Hackney. 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.
from Bio.Alphabet import IUPAC
from Bi... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/Motif/Parsers/MAST.py | Python | gpl-2.0 | 4,534 | [
"Biopython"
] | bd281be86b480dc59635564a11bda0e399b5c958510f9b2a9289a328b8069446 |
"""
cclib (http://cclib.sf.net) is (c) 2006, the cclib development team
and licensed under the LGPL (http://www.gnu.org/copyleft/lgpl.html).
"""
__revision__ = "$Revision: 620 $"
import sys
if 'qt' in sys.modules.keys():
from qtprogress import QtProgress
if 'PyQt4' in sys.modules.keys():
from qt4progress im... | connie/RMG-Java | source/cclib/progress/__init__.py | Python | mit | 376 | [
"cclib"
] | 49ae66bd37e50f67a00423fadcb7d2e3286003c79b749c416eed5791898c2813 |
#!/usr/bin/env python
"""
wxBlender
=========
wxPython in Blender Addon
wxPython toolkit widgets running in Blender.
Menus, Frames, Dialogs, Custom Buttons, Thumbnails, etc...
Requirements
------------
* Blender 2.65+(built w... | Metallicow/wxBlender | wx_blender/wxblender.py | Python | gpl-2.0 | 24,689 | [
"VisIt"
] | 7d703eb5e5a6e842a01381f4dad0af3f16a55def58075be93d9ea7f3dbc7d1bc |
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