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import unittest
import pysal
import numpy as np
from pysal.spreg import error_sp_het as HET
from pysal.common import RTOL
class TestBaseGMErrorHet(unittest.TestCase):
def setUp(self):
db=pysal.open(pysal.examples.get_path("columbus.dbf"),"r")
y = np.array(db.by_col("HOVAL"))
self.y = np.res... | ljwolf/pysal | pysal/spreg/tests/test_error_sp_het.py | Python | bsd-3-clause | 19,417 | [
"COLUMBUS"
] | 3698f97b2a027c219dea952fe0d32867712721566086fabbf8c0dc5d1df35510 |
"""
Extreme deconvolution solver
This follows Bovy et al.
http://arxiv.org/pdf/0905.2979v2.pdf
Arbitrary mixing matrices R are not yet implemented: currently, this only
works with R = I.
"""
from __future__ import print_function, division
from time import time
import numpy as np
from scipy import linalg
from sklea... | nhuntwalker/astroML | astroML/density_estimation/xdeconv.py | Python | bsd-2-clause | 6,911 | [
"Gaussian"
] | 5f6005a10ba155c7d114b12d2c5b68e25fd7ce06b3dda26df1f18951d0256399 |
import pandas as pd
from sklearn.ensemble import RandomForestRegressor
from sklearn.ensemble import BaggingRegressor
from sklearn.ensemble import ExtraTreesRegressor
from sklearn.ensemble import AdaBoostRegressor
from sklearn.ensemble import GradientBoostingRegressor
from sklearn.ensemble import RandomTreesEmbedding
fr... | rupakc/Kaggle-Compendium | Corporacion Favorita Grocery Sales Prediction/corporacion-baseline.py | Python | mit | 4,838 | [
"Gaussian"
] | e5fe3c38ebe77a02d5e71e425f10aab1fa199d1030dfbd749f0c456494d3f1f0 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/transitions | openlp/core/lib/imagemanager.py | Python | gpl-2.0 | 13,973 | [
"Brian"
] | a91a35bad1b3690934fcf13cc6ae16e8a4eaeaed05acaf3e7803770e3f2a0c11 |
legendary_items = [ "Death Note", "Future Diary", "The Treasured Tools of the Sage of the Six Paths", "Soshuga", "Yoru", "Poke Ball", "soul gem", "Wolfwood's Punisher","Sech's Titan Blade",
"Zabuza's Kubikiri Hocho","Gyro's steel balls", "Hisoka's cards", "Feitan's Umbrella", "Berserker Armor", "Behelit", "senzu bean... | St00pid/TheAnimus | mainlist.py | Python | mit | 4,842 | [
"VisIt"
] | d83e0f0e44b685506df0f5668493c5f6c7cae86ff833b19fa887b4ad897bc6bf |
import os
import unittest
import pysal
import numpy as np
class TestDistanceWeights(unittest.TestCase):
def setUp(self):
np.random.seed(1234)
self.polyShp = pysal.examples.get_path('columbus.shp')
self.arcShp = pysal.examples.get_path('stl_hom.shp')
self.points = [(
10,... | volaya/processing_pysal | ext-libs/pysal/weights/tests/test_Distance.py | Python | gpl-2.0 | 7,025 | [
"COLUMBUS",
"Gaussian"
] | 9b63e3192cee8909a579a3dd128dd9aecb55896ac8994e1517c0ba53135eaa77 |
import pysam
import ws_server
MAX_REGION = 100000
class BamServ:
def __init__(self, f):
self.bam = pysam.Samfile(f, "rb")
def serv(self, data):
if data == 'refs':
return 'refs||' + str([[self.bam.references[r], int(self.bam.lengths[r])] for r in xrange(self.bam.nreferences)])
... | txje/web-pileup-viewer | wgv.py | Python | mit | 3,478 | [
"pysam"
] | 6e43cfa226b776a6a38c49896d1b001b20723d979eafd82cd17aeb6956192a0a |
"""
Holds information about what the user asked for (which program, version constraints, etc).
"""
# Copyright (C) 2011, Thomas Leonard
# See the README file for details, or visit http://0install.net.
class Requirements(object):
"""
Holds information about what the user asked for (which program, version constraints... | timdiels/0install | zeroinstall/injector/requirements.py | Python | lgpl-2.1 | 2,476 | [
"VisIt"
] | eb26c4f9c46c271f10c0a027e19129f23a23134a852933d43149a3f3ab7c047e |
# (c) 2012-2018, Ansible by Red Hat
#
# This file is part of Ansible Galaxy
#
# Ansible Galaxy is free software: you can redistribute it and/or modify
# it under the terms of the Apache License as published by
# the Apache Software Foundation, either version 2 of the License, or
# (at your option) any later version.
#
... | chouseknecht/galaxy | galaxy/tests/__init__.py | Python | apache-2.0 | 679 | [
"Galaxy"
] | 106dff1a46fd27e0a314b7268f6bf9a95375396a3f9ab2ade8e8e74d56e09c10 |
#!/usr/bin/env python3
import itertools as it
import os
from pathlib import Path
from pysisyphus.helpers import geom_from_library, highlight_text
from pysisyphus.calculators.Turbomole import Turbomole
from pysisyphus.optimizers.RFOptimizer import RFOptimizer
THIS_DIR = Path(os.path.dirname(os.path.realpath(__file__... | eljost/pysisyphus | tests_staging/test_cytosin_tracking/test_cytosin_tracking.py | Python | gpl-3.0 | 1,695 | [
"TURBOMOLE"
] | 04cd21aa66ea6c13485ff10a204df64e5179664da3988ec40dece2c3b3814fe3 |
''' Header reading / writing functions for nifti1 image format
Author: Matthew Brett
'''
import numpy as np
import numpy.linalg as npl
from nipy.io.imageformats.volumeutils import Recoder, make_dt_codes, \
HeaderDataError, HeaderTypeError, allopen
from nipy.io.imageformats.batteryrunners import Report
from nipy... | yarikoptic/NiPy-OLD | nipy/io/imageformats/nifti1.py | Python | bsd-3-clause | 52,993 | [
"Gaussian"
] | acb873b72391554e31bedd7b86e8e546d6baac9397ba4bc0d969d935b092c566 |
import lightcurve
import supernova
class SupernovaFit():
ccMjdMaxFlux = 0
def __init__(self, supernova, GPkern=''):
# check on supernova type HAS TO BE ADDED
self.g = LightCurve("g")
self.r = LightCurve("r")
self.i = LightCurve("i")
self.z = LightCurve("z")
self.... | mdepasca/miniature-adventure | classes_dir/supernova_fit.py | Python | unlicense | 11,776 | [
"Gaussian"
] | ad731f82c3385819ec91adaff9e5a966f0fd2768e44372c68be2f52c2b25974a |
import struct, time, array, os
from Sire.Mol import *
from Sire.IO import *
#
# Adapted from Peter Eastman's code in OpenMM python API to write a DCD file
#
class DCDFile(object):
"""DCDFile provides methods for creating DCD files.
DCD is a file format for storing simulation trajectories. It is suppor... | chryswoods/Sire | wrapper/Tools/DCDFile.py | Python | gpl-2.0 | 9,516 | [
"CHARMM",
"NAMD",
"OpenMM"
] | 96c97d06203e62a6c55465a5d2b23d3a6ed61b9b8bb42468a2215a646a366488 |
# encoding: utf8
#
# Engineering Calculator Actions
#
# An RPN calculator that supports numbers with SI scale factors and units.
# Imports {{{1
from .calculator import (
BinaryIoOp,
BinaryOp,
Calculator,
Category,
Command,
Constant,
Convert,
Dup,
Help,
Number,
Print,
Qua... | KenKundert/ec | engineering_calculator/actions.py | Python | gpl-3.0 | 94,229 | [
"Avogadro"
] | 05ef360baa6dae3964121fbe00f3293f726f01a6ebabcb0ebc356d40d9d0a074 |
#!/usr/bin/env python
#********************************************************************
# Filename: FINally.py
# Authors: Daniel Sisco
# Date Created: 4-20-2007
#
# Abstract: This is the primary file for the FINally expense analysis tool. It is responsible for
# handling read/write access to the... | tectronics/fin-ally | FINally.py | Python | gpl-3.0 | 9,765 | [
"VisIt"
] | 15b683bfdff784232a373e60e33e89513c77f27ca4306c666ec412d936955dac |
#!/usr/local/bin/env python
#=============================================================================================
# MODULE DOCSTRING
#=============================================================================================
"""
Set up YANK calculations.
"""
#============================================... | sonyahanson/yank | Yank/commands/prepare.py | Python | lgpl-3.0 | 20,505 | [
"Amber",
"Gromacs",
"MDTraj",
"OpenMM"
] | 74516db8dc3bd1895bcc4a21a1c215df06e9e1060d4642f701cc8f21a8e8bafe |
# coding: utf-8
"""Some useful Django template context processors.
"""
from __future__ import absolute_import, print_function, unicode_literals
from django.conf import settings
def track_visit(request):
"""Whether the current visit should be tracked by analytics software/services.
.. warning:
The se... | lookup/lu-dj-utils | lu_dj_utils/context_processors.py | Python | bsd-3-clause | 809 | [
"VisIt"
] | 60779110680017a126ad910e7cb5f4124c14b6c613860846ea04a1d9cf2bafe4 |
#!/usr/local/bin/python
# Script: dump2xyz.py
# Purpose: convert a LAMMPS dump file to XYZ format
# Syntax: dump2xyz.py dumpfile Nid Ntype Nx Ny Nz xyzfile
# dumpfile = LAMMPS dump file in native LAMMPS format
# Nid,Ntype,Nx,Ny,Nz = columns #s for ID,type,x,y,z
# (usua... | val-github/lammps-dev | tools/python/dump2xyz.py | Python | gpl-2.0 | 908 | [
"LAMMPS"
] | 9c74828b0b063f6f3b50991cfee4b52c04a0ec835bec80023cd5287c4a2aa620 |
""" Contains the Switch parent class. """
# switch.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
from mpf.system.device import Device
from mpf.system.tim... | spierepf/mpf | mpf/devices/switch.py | Python | mit | 3,000 | [
"Brian"
] | b93d78d37f1a603a67218d2c993b3627355acca279b6e0a348546239ab89deae |
# Copyright (c) 2012 OpenStack Foundation.
#
# 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... | neoareslinux/neutron | neutron/tests/unit/test_policy.py | Python | apache-2.0 | 25,826 | [
"BLAST"
] | 0999cc16dae963516242b6ee9f5e38c05cb060e3a3994d938c2e170c0b241760 |
import sys
import time
import atexit
import pickle
import numpy as np
def paropen(name, mode='r', buffering=0):
"""MPI-safe version of open function.
In read mode, the file is opened on all nodes. In write and
append mode, the file is opened on the master only, and /dev/null
is opened on all other ... | grhawk/ASE | tools/ase/parallel.py | Python | gpl-2.0 | 4,256 | [
"ASE",
"GPAW"
] | 2179d8d12af184a5b3aee1044dec88ec9565583352bccf5ab0637078ce1862b9 |
from pyneuroml.neuron import export_to_neuroml2
export_to_neuroml2(
"test.hoc", "test.morphonly.cell.nml", includeBiophysicalProperties=False
)
export_to_neuroml2(
"test.hoc", "test.biophys.cell.nml", includeBiophysicalProperties=True
)
| NeuroML/pyNeuroML | examples/export_neuroml2.py | Python | lgpl-3.0 | 246 | [
"NEURON"
] | 819084c49c1ed27fc59cf006dfacc949b1b4208a7b291c6c403688d656f7c7fb |
#!/usr/bin/env python
"""
Script to apply update to all or some dirac servers and restart them
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
from io import open
import DIRAC
from DIRAC.Core.Utilities.DIRACScript import DIRACScript ... | ic-hep/DIRAC | src/DIRAC/FrameworkSystem/scripts/dirac_admin_update_instance.py | Python | gpl-3.0 | 9,679 | [
"DIRAC"
] | ac3fd11a66b3621a366d491eef39781baa3f7885bb672a01c5c7c0ab65fee584 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
This code is copied from https://github.com/vsvinayak/mnist-helper.
It requires Scipy to perform convolve2d.
Default parameters are modified.
"""
import numpy as np
import math
from scipy.signal import convolve2d
from deepy.core import env
def create_2d_gaussian(di... | zomux/deepy | deepy/preprocessing/elastic_distortion.py | Python | mit | 3,673 | [
"Gaussian"
] | 666a749f08f20eb3be612dd9e000f4a9a5031c8193a6383729aba52522eb9b5c |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | krafczyk/spack | var/spack/repos/builtin/packages/fast-gbs/package.py | Python | lgpl-2.1 | 2,309 | [
"BWA"
] | 1e127238544440e69cc4136b486d9471ed1f1a5b22a4ee76669932fb96db820e |
""" TransformationAgent processes transformations found in the transformation database.
"""
import time, re, random, Queue, os, datetime, pickle
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Base.AgentModule import AgentModu... | avedaee/DIRAC | TransformationSystem/Agent/TransformationAgent.py | Python | gpl-3.0 | 25,624 | [
"DIRAC"
] | 25f62f28fbce6f07cdfe7a447b7c88305be3b96f4e941eef9acb691e328e6ae6 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#-------------------------------------------------------------------------------
'''
This software has been developed by:
GI Genética, Fisiología e Historia Forestal
Dpto. Sistemas y Recursos Naturales
ETSI Montes, Forestal y del Medio Natural
Universida... | GGFHF/NGScloud | Package/xdetonate.py | Python | gpl-3.0 | 59,926 | [
"Bowtie"
] | 0e8bbeec9b8bfa81e3c16c60d618e4d31010a85f2b3fb55d945cbd488fa730b5 |
# 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.
"""Additional protein alphabets used in the SCOP database and PDB files.
See Bio.SCOP for more information about SCOP and Biopython"s SCOP module.
"""... | zjuchenyuan/BioWeb | Lib/Bio/Data/SCOPData.py | Python | mit | 17,075 | [
"Biopython"
] | a63d95c3402d2d62547b17d11a4556a0dd39b68d4e535da7848670a340321f00 |
# -*- coding: utf-8 -*-
""" Sahana Eden Common Alerting Protocol (CAP) Model
@copyright: 2009-2012 (c) Sahana Software Foundation
@license: MIT
Permission is hereby granted, free of charge, to any person
obtaining a copy of this software and associated documentation
files (the "Software"), to dea... | madhurauti/Map-Polygon | modules/eden/cap.py | Python | mit | 44,476 | [
"VisIt"
] | 0d657812ce2d36873a52e75452a15b86923beaf9b6e9c5438dabf04d82f35eb7 |
# RABDAM
# Copyright (C) 2020 Garman Group, University of Oxford
# This file is part of RABDAM.
# RABDAM is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your... | GarmanGroup/RABDAM | rabdam/Subroutines/CalculateBDamage.py | Python | lgpl-3.0 | 35,945 | [
"CRYSTAL"
] | 456b008e56c61ccdb17ba7d569c2ce9739f54772a0b6b7b07560000d1caa6911 |
# Copyright (c) Anand Patil, 2007
__docformat__='reStructuredText'
__all__ = ['Realization', 'StandardRealization', 'BasisRealization']
from numpy import *
from numpy.random import normal
from numpy.linalg import cholesky, eigh, solve
from Covariance import Covariance
from BasisCovariance import BasisCovariance
from... | askielboe/JAVELIN | javelin/gp/Realization.py | Python | gpl-2.0 | 7,422 | [
"Gaussian"
] | a7abe742f686c6313bfdd7ab3e494c902438ed3620957cc9e5a7b4b95e907b33 |
# -*- coding: utf-8 -*-
"""
pyroon.main
~~~~~~~~~~~~~~~
This module performs recursively explores roos
"""
import praw
import re
import json
import time
from .config import getRedditAuth
from .helpers import getRooText, recoverDeletedComment
from bs4 import BeautifulSoup
COMMENT_ID_RE = re.compile('reddit\.com/r/[0-... | kittsville/Pyroon | pyroon/main.py | Python | mit | 6,349 | [
"Cytoscape"
] | 98a97b2b840a8fddc95a5de0cba938bb310cf3fda435248b75cb9dec5e5564f8 |
from datetime import date
from . import GenericCalendarTest
from ..core import MON
from ..america.canada import (
Canada, Ontario, Quebec, BritishColumbia, Alberta, Saskatchewan, Manitoba,
NewBrunswick, NovaScotia, PrinceEdwardIsland, Newfoundland, Yukon,
NorthwestTerritories, Nunavut
)
class CanadaTest(G... | jaraco/calendra | calendra/tests/test_canada.py | Python | mit | 17,371 | [
"Desmond"
] | 1a3184253429fc7b9bf715b48cd30d91bc98236fb4096b7f1ac1bd4e5df3ad22 |
# Keg sizes from here:
# http://en.wikipedia.org/wiki/Keg
KEG_SIZE_CHOICES = (
(18.9, 'Sixth Barrel 18.9L'),
(29.33, 'Quarter Barrel 29.3L'),
(58.66, 'Half Barrel 58.66L'),
)
# Beer sizes from here:
# @TODO: Get reference
BEER_TYPE_CHOICES = (
('def', 'DEFAULT'),
('alt', 'Altbier'),
('amb', 'A... | philips/tapkick | web/webapp/beer/beer_types.py | Python | bsd-2-clause | 1,534 | [
"Amber"
] | 13155eec7166a829643a310cdf4f09b3c05e67793a4ac05db4db3771c9297072 |
#!/usr/bin/env python
import pysam
import sys
import os
import argparse
import logging
from collections import Counter
logger = logging.getLogger(__name__)
def rmtag(read):
''' remove non-essential tags '''
oldtags = read.tags
newtags = []
for tag in oldtags:
if tag[0] in ('NM', 'MC', 'MD'... | adamewing/tebreak | scripts/reduce_bam.py | Python | mit | 3,213 | [
"pysam"
] | afe167a162d3a2c3eff53b26dc182359c3d8e5a1b6c60207df0c84440dd5de45 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# (c) 2015, Brian Coca <bcoca@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 by
# the Free Software Foundation, either version 3 of the Licen... | bjolivot/ansible | lib/ansible/modules/notification/jabber.py | Python | gpl-3.0 | 4,800 | [
"Brian"
] | 778232e6c5d27727b46246bd450cb740f19f31cad9ca6f72400d7d7bae952ab4 |
from jaspyx.context.block import BlockContext
from jaspyx.visitor import BaseVisitor
class While(BaseVisitor):
def visit_While(self, node):
self.indent()
self.output('while(')
self.visit(node.test)
self.output(') ')
self.block(node.body, context=BlockContext(self.stack[-1])... | iksteen/jaspyx | jaspyx/visitor/while_.py | Python | mit | 348 | [
"VisIt"
] | aef5f0a217e7e139e44c80eab2591e0df8989d3cf282079232a9d8b0a3c694a6 |
'''
Greymind Sequencer for Maya
Version: 1.8.0
(c) 2009 - 2015 Greymind Inc.
Balakrishnan (Balki) Ranganathan (balki_live_com)
All Rights Reserved.
'''
# from Common import *
from functools import partial as Partial
SequencerVersion = "1.8.0"
class Animation:
Id = -1
Name = ""
StartFrame = -1
... | greymind/Sequencer | Scripts/Sequencer.py | Python | mit | 33,575 | [
"BLAST"
] | b7f40f4e6a0ca5ccd4aa6d87effdda8bd4b651bc6330057bb6032f66e165bf27 |
from numpy import zeros
from os import fstat
from re import compile
from ase.io.fortranfile import FortranFile
def read_rho(fname):
"Read unformatted Siesta charge density file"
# TODO:
#
# Handle formatted and NetCDF files.
#
# Siesta source code (at least 2.0.2) can possibly also
# s... | grhawk/ASE | tools/ase/io/siesta.py | Python | gpl-2.0 | 8,034 | [
"ASE",
"NetCDF",
"SIESTA"
] | 73f3e7e5018373314dbcdc7d7093315fb6e1eeedc7e7281becc2943822c330af |
# This file is part of wger Workout Manager.
#
# wger Workout Manager is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# wger W... | wger-project/wger | wger/manager/tests/test_weight_log.py | Python | agpl-3.0 | 18,204 | [
"VisIt"
] | 4c27b867efefe1478180cbcbcf3d0e2047d560541819f3dbd3db94d19be0a4c6 |
#!/usr/bin/python
"""Main project file, contains everything to generate stereograms."""
import argparse
import json
import os
import re
import codecs
import time
from random import choice, random
# This "PIL" refers to Pillow, the PIL fork. Check https://pillow.readthedocs.io/en/
from PIL import Image as im
from PIL ... | mexomagno/stereogramaxo | main.py | Python | gpl-2.0 | 20,666 | [
"Gaussian"
] | 70e482ba1fb23ed4c8d132ae0e0934cd98ad9c237a6503cf4a07b7ee576abc01 |
__title__ = 'silverlining'
__version__ = '0.1'
__author__ = 'John Miller'
__license__ = 'MIT'
__copyright__ = 'Copyright 2014 ' + __author__
import atexit
import os
import simplejson
import sys
# Get settings
DOT_FILES = os.path.expanduser('~/.silverlining')
CONFIG_FILE = os.path.expanduser('~/.silverlining/config.js... | iterati/silverlining | silverlining/__init__.py | Python | mit | 3,621 | [
"VisIt"
] | 00ff14bce617bc07e59d12fc32aeb828e6fb01db7e173fcf654a65efa2be4f88 |
# This file is part of Korman.
#
# Korman 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.
#
# Korman is distributed i... | Deledrius/korman | korman/exporter/mesh.py | Python | gpl-3.0 | 31,732 | [
"GULP"
] | 3a9bb3394655e77d3d3137c3c99f1762ad1e1e49f35f7d208dd7146003b55b98 |
#This script is for doing the leading edge fit on SP2 scattering signals
#If run on non-incandescent particles, it can be used to check the performance of the LEO procedure (by plotting actual or FF scat amp vs LF scat amp)
#When run on incandescent particle it is used to recover the unperturbed peak scattering signal... | annahs/atmos_research | LEO_calibration_LF.py | Python | mit | 14,699 | [
"Gaussian"
] | 9a760c1e5122028d88da4956eb1de2bea19247e1227b7be43ce355062b1ba612 |
"""
======================================
Decision Tree Regression with AdaBoost
======================================
A decision tree is boosted using the AdaBoost.R2 [1] algorithm on a 1D
sinusoidal dataset with a small amount of Gaussian noise.
299 boosts (300 decision trees) is compared with a single decision tr... | RPGOne/Skynet | scikit-learn-0.18.1/examples/ensemble/plot_adaboost_regression.py | Python | bsd-3-clause | 1,529 | [
"Gaussian"
] | 83229f0741729868bed6ee34886691839ef964db72327d77868981e2764dc52a |
#
# Copyright (C) 2003-2008 Greg Landrum and Rational Discovery LLC
# All Rights Reserved
#
from __future__ import print_function
import random
from rdkit import RDRandom
SeqTypes = (list, tuple)
def SplitIndices(nPts, frac, silent=1, legacy=0, replacement=0):
""" splits a set of indices into a data set into... | rvianello/rdkit | rdkit/ML/Data/SplitData.py | Python | bsd-3-clause | 8,850 | [
"RDKit"
] | 170c86ac5622e12afcee107f66c76f10841d51ba5d02c0a522e067820c1f5217 |
import numpy as np
import pandas as pd
# from matplotlib.pyplot import plot,show,draw
import scipy.io
import sys
sys.path.append("../")
from functions import *
from pylab import *
from sklearn.decomposition import PCA
import _pickle as cPickle
import matplotlib.cm as cm
import os
#####################################... | gviejo/ThalamusPhysio | python/figure_article_v4/main_article_v4_fig_7.py | Python | gpl-3.0 | 9,139 | [
"Gaussian"
] | 2af10b4a005021323fbc6214ed57661b0c9ffd1175808501b35ec72a2b066e9a |
import os
from ase import Atom, Atoms
from gpaw import GPAW
from gpaw.test import equal
from gpaw.lrtddft import LrTDDFT
from gpaw.mpi import world
txt='-'
txt='/dev/null'
io_only=False
#io_only=True
load=False
#load=True
if not io_only:
R=0.7 # approx. experimental bond length
a = 3.0
c = 4.0
H2 = At... | qsnake/gpaw | gpaw/test/lrtddft.py | Python | gpl-3.0 | 2,571 | [
"ASE",
"GPAW"
] | e5ee37df24bfadfcafbf0ea306c782f2fbf6afd5b0114a56376ad6b7c90ca7d9 |
# Copyright 2012 Hewlett-Packard Development Company, L.P.
#
# 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... | hanlind/nova | nova/tests/unit/policy_fixture.py | Python | apache-2.0 | 4,970 | [
"TINKER"
] | 3fabb4f3174271d5a7fbdaaae23bef31a881ae98e059b2f4fc3900b6e9e99996 |
from classylss.binding import *
import pytest
@pytest.mark.parametrize("a_max", [1.0, 2.0])
def test_ba(a_max):
cosmo = ClassEngine({'a_max':a_max, 'N_ncdm': 1, 'm_ncdm':[0.06]})
ba = Background(cosmo)
assert ba.hubble_function(0.1).shape == ()
assert ba.hubble_function([0.1]).shape == (1,)
assert ... | nickhand/classylss | classylss/tests/test_binding.py | Python | gpl-3.0 | 2,445 | [
"VTK"
] | ffe70fe8a951ea2c9e9a281de9246dfc49e53bf640197e20c462f55f1d7a4f43 |
#pylint: disable=missing-docstring
####################################################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment ... | yipenggao/moose | python/MooseDocs/commands/latex.py | Python | lgpl-2.1 | 9,073 | [
"MOOSE"
] | f5e987c5d28894dcabd3f97e55ca0eddb07cd66ecaea328ef8a1a432ed893f9f |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | apache/incubator-airflow | airflow/providers/microsoft/azure/hooks/data_factory.py | Python | apache-2.0 | 31,220 | [
"ADF"
] | 3c546fdfa323f2cddbc585e11a03d2d24026bf5bcc2f47dc2705353680a5e743 |
""" Basic unit tests for AuthManager
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import unittest
from diraccfg import CFG
from DIRAC import gConfig
from DIRAC.Core.DISET.AuthManager import AuthManager
__RCSID__ = "$Id$"
testSystemsCFG = """
System... | yujikato/DIRAC | src/DIRAC/Core/DISET/test/Test_AuthManager.py | Python | gpl-3.0 | 11,586 | [
"DIRAC"
] | efdbfe4fe84aee39cebd93ec3646239684a7cae6da4d052b1c643fc5569616f7 |
"""
Collection of DIRAC useful operating system related modules
by default on Error they return None
"""
import os
import multiprocessing
import distutils.spawn #pylint: disable=no-name-in-module,import-error
import DIRAC
from DIRAC.Core.Utilities.Subprocess import shellCall, systemCall
from DIRAC.Core.Utilitie... | Andrew-McNab-UK/DIRAC | Core/Utilities/Os.py | Python | gpl-3.0 | 4,415 | [
"DIRAC"
] | 3b52d930d64fad28220d9a521caa5a67b50e5efa2aef4e5125c1ae5ebb97a0eb |
import aeropy.CST_3D as cst
import aeropy.CST_3D.mesh_tools as meshtools
from aeropy.filehandling.vtk import generate_surface
from aeropy.geometry.fitting import fitting
import time
import pickle
import numpy as np
from scipy.optimize import minimize
import matplotlib.pyplot as plt
from multiprocessing import Pool
d... | leal26/pyXFOIL | examples/3D_fitting/fitting_shape.py | Python | mit | 2,669 | [
"VTK"
] | ea92c00573d13fd708c5410f56cb0d27d99cbf5dbefbb2e67bc1898e2dc572b2 |
#! /usr/bin/env python
"""Generate C code from an ASDL description."""
# TO DO
# handle fields that have a type but no name
import os, sys
import asdl
TABSIZE = 8
MAX_COL = 80
def get_c_type(name):
"""Return a string for the C name of the type.
This function special cases the default types provided by asd... | teeple/pns_server | work/install/Python-2.7.4/Parser/asdl_c.py | Python | gpl-2.0 | 41,412 | [
"VisIt"
] | cc685870febce618fbd8e6d4202365142b6a34f8afcf7fc2d26b45c9d5a7fbe5 |
#!/usr/bin/env python
# Copyright 2015 The Kubernetes Authors All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unle... | timstclair/kube-contrib | hack/boilerplate/boilerplate.py | Python | apache-2.0 | 4,743 | [
"VisIt"
] | 9a6dbb68ab355a6ea872d87cd30e43e69ee44f2d5ee0b0785383067908aa7225 |
import subprocess
from pybuilder.core import Author, init, use_plugin, task, before, after
use_plugin("filter_resources")
use_plugin("python.core")
use_plugin("python.install_dependencies")
use_plugin("python.distutils")
use_plugin("python.pycharm")
name = "fuct"
url = "https://github.com/MrOnion/fuct"
description = ... | fredcooke/fuct | build.py | Python | mit | 1,200 | [
"VisIt"
] | f7bf83501c58883ed187381ccae40ebe5350c509d61058de4b8d3cfa4a1745df |
try:
from django.urls import reverse
except ImportError:
from django.core.urlresolvers import reverse
from tastypie import authorization
from tastypie.authentication import MultiAuthentication
from tastypie.exceptions import BadRequest
from crits.core.api import CRITsApiKeyAuthentication, CRITsSessionAuthentic... | Magicked/crits | crits/screenshots/api.py | Python | mit | 4,342 | [
"Amber"
] | 3ec9ff85e3034d666f7f5ac392bf7da11e73964471333fd797e024c9783d207a |
from __future__ import absolute_import
import os
import locale
from gi.repository import Gtk
try:
from configparser import ConfigParser
except:
from ConfigParser import ConfigParser
from sunflower.widgets.settings_page import SettingsPage
class Column:
ACTIVE = 0
LOCATION = 1
NAME = 2
AUTHOR = 3
VERSION = 4
... | MeanEYE/Sunflower | sunflower/gui/preferences/plugins.py | Python | gpl-3.0 | 9,145 | [
"VisIt"
] | be1296c7f47ca1f44f001fb1056e8e2f47cf2bd748ab2c0b8c2f0d39ce88af00 |
#!/usr/bin/env python
from DIRAC.Core.Base import Script
from DIRAC.Core.Utilities.DIRACScript import DIRACScript
@DIRACScript()
def main():
Script.parseCommandLine(ignoreErrors=False)
from DIRAC.WorkloadManagementSystem.Client.VirtualMachineCLI import VirtualMachineCLI
cli = VirtualMachineCLI(vo="enmr.e... | ic-hep/DIRAC | src/DIRAC/WorkloadManagementSystem/scripts/dirac_vm_cli.py | Python | gpl-3.0 | 382 | [
"DIRAC"
] | fce0fafa5c1aad8e7683ec8793f38c53e4d8177085b753fc5141e4a19f416ef9 |
#
# gPrime - A web-based genealogy program
#
# Copyright (C) 2007 Brian G. Matherly
# Copyright (C) 2010 Nick Hall
# Copyright (C) 2011 Tim G L Lyons
#
# 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 Fr... | sam-m888/gprime | gprime/proxy/private.py | Python | gpl-2.0 | 45,418 | [
"Brian"
] | 1fcd6402d7012d9ba8d82df8b71f6cc0f3e7fa9af9dba210ccbc987ccc1fa70e |
#!/usr/bin/python3.5
# -*- coding: utf-8 -*-
# @package mappingOnRef.py
# @author Sebastien Ravel
"""
The mappingOnRef script
=========================
:author: Sebastien Ravel
:contact: sebastien.ravel@cirad.fr
:date: 08/11/2016
:version: 0.1
Script description
------------------
This Programme map fasta w... | sravel/scripts | local/mappingOnRef.py | Python | gpl-3.0 | 7,184 | [
"BWA"
] | f78f1929c09889762e94eb6b63781c2953b514472cd2f5167f3475392b92581d |
# Copyright 2020 Google LLC
#
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... | google/qkeras | experimental/args.py | Python | apache-2.0 | 4,297 | [
"ESPResSo"
] | c1e085e748ecf83439904882aa5c5a17751efc3381ad227bfe3ef46d200444eb |
from __future__ import print_function
import six
import bz2
from json import dumps, loads
from operator import itemgetter
from collections import Counter
from Bio.File import as_handle
from dark.hsp import HSP, LSP
from dark.score import HigherIsBetterScore
from dark.alignments import Alignment, ReadAlignments
from ... | terrycojones/dark-matter | dark/diamond/conversion.py | Python | mit | 18,385 | [
"BWA"
] | 987e5a650802fdbdfea8e28f6c62ccfbb1d37ce25126754580e45c6b163fbeb6 |
from setuptools import setup
setup( name='gruppy',
version='0.1.1',
description='Provides smart logstash flows optimized for use with S3',
url='https://github.com/wutufubapoobah/gruppy',
author='WutuFuBaPooBah',
author_email='wutufubapoobah@gmail.com',
license='MIT',
platforms=['CentOS7'],
packages=['g... | wutufubapoobah/gruppy | setup.py | Python | mit | 955 | [
"Elk"
] | c5431a9d655372a7e3f2c3ce0174ee87d2e9dba49bcb18b9f7c3faa7a56a0a5f |
#!/usr/bin/env python3
# hamt_py/test_root.py
""" Test properties of the HAMT Root. """
# import hashlib
# import os
import time
import unittest
from rnglib import SimpleRNG
from hamt import HamtNotFound, Root, Leaf, uhash # , countem
class TestRoot(unittest.TestCase):
""" Test properties of the HAMT Root. ""... | jddixon/hamt_py | tests/test_root.py | Python | mit | 5,148 | [
"VisIt"
] | 48f3a05e5ec78333672f14cde7752859316bd381fbe6780c397e79ff3c37ee94 |
import asyncio
import concurrent.futures
import logging
import multiprocessing
import os
import tempfile
import traceback
from collections import defaultdict
from functools import reduce, wraps
from inspect import isawaitable
from pathlib import Path
from http import HTTPStatus
from typing import (
Any,
Callabl... | RasaHQ/rasa_nlu | rasa/server.py | Python | apache-2.0 | 52,939 | [
"VisIt"
] | e31f6501f1de57dc67a3ab944919112c3d613822eb4fd26ce452fd2171d0d27b |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/item_title | openlp/plugins/presentations/lib/__init__.py | Python | gpl-2.0 | 2,301 | [
"Brian"
] | 14e907131b056623607db29f68a2a3f196d7e65a8afc39bd56f320cd50d10af2 |
# -*- coding: utf-8 -*-
import sys
import pickle
import traceback
import os.path as path
from ase.data.g2_1 import data
from ase.structure import molecule
from ase.data.molecules import latex
from ase.atoms import string2symbols
from ase.parallel import paropen
from ase.parallel import rank, barrier
from ase.io.trajec... | ajylee/gpaw-rtxs | gpaw/testing/old_molecule_test.py | Python | gpl-3.0 | 6,841 | [
"ASE",
"GPAW"
] | 36a74542bc229c9ab481d895fdad39fb587640e32491b23bdbfebd6f66d770dc |
#post processing, add sequence and additional annoation info if available
from urllib import urlencode
from galaxy.datatypes.images import create_applet_tag_peek
def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
primary_data = out_data.items()[0][1]
#default params for LAJ ty... | lappsgrid-incubator/GalaxyMods | tools/visualization/LAJ_code.py | Python | apache-2.0 | 2,183 | [
"Galaxy"
] | 34c60133498d0a449bf7de69d5398eef3889ab387acdf413d80f93ff7092780a |
# MIT License
#
# Copyright (c) 2017, Stefan Webb. All Rights Reserved.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to us... | stefanwebb/tensorflow-models | tensorflow_models/models/vae_concrete_made_fixed.py | Python | mit | 11,410 | [
"Gaussian"
] | d42b50c4136d5b1720ccd22a8899a2e426f10155e76cd8f038b0d2d508fa6580 |
import numpy as np
import pylab as plt
from gpaw import GPAW
# Read in the 5-layer slab:
calc = GPAW('slab-5.gpw', txt=None)
slab = calc.get_atoms()
# Get the height of the unit cell:
L = slab.get_cell()[2, 2]
# Get the effective potential on a 3D grid:
v = calc.get_effective_potential()
nx, ny, nz = v.shape
z = n... | robwarm/gpaw-symm | doc/exercises/surface/work_function.py | Python | gpl-3.0 | 759 | [
"GPAW"
] | 87ec7522dd41161281afd4cbd55851bc35643560678953bcf8c5b44174f8cc25 |
# Created by John Travers, Robert Hetland, 2007
""" Test functions for rbf module """
import numpy as np
from numpy.testing import (assert_, assert_array_almost_equal,
assert_almost_equal)
from numpy import linspace, sin, cos, random, exp, allclose
from scipy.interpolate._rbf import Rbf
FUN... | anntzer/scipy | scipy/interpolate/tests/test_rbf.py | Python | bsd-3-clause | 6,547 | [
"Gaussian"
] | 77446836a4828658b3a29bf2e71eaf4318621a473e2de90d6e709814837f6758 |
"""
Object Store plugin for the Amazon Simple Storage Service (S3)
"""
import logging
import multiprocessing
import os
import shutil
import subprocess
import threading
import time
from datetime import datetime
from galaxy.exceptions import ObjectNotFound
from galaxy.util import string_as_bool, umask_fix_perms
from g... | ssorgatem/pulsar | galaxy/objectstore/s3.py | Python | apache-2.0 | 27,569 | [
"Galaxy"
] | 0bc76a4121332e3e73805383607e2a05839e257380f2c8982daa9c56eaccdf92 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import numpy as np
import pandas as pd
#TODO: Move global means into regional dicts
PARAMS = {
'BCC_CSM': pd.DataFrame({
'ARL': np.array([0.832341, 257.031747, 7.760533, 7.760533, 0.16191]),
'ARO': np.array([0.813758, 258.029818, 9.335264, 9.335264, 0... | RDCEP/climate_emulator | emulator/params/geophysical.py | Python | gpl-3.0 | 43,461 | [
"EPW"
] | 6baf285f90ba0b408c6bddf5331e0a02ff7de778dc458253ed31199ee5a3a578 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/e2-openwbif | plugin/controllers/views/web/getpid.py | Python | gpl-2.0 | 4,882 | [
"VisIt"
] | 3c4c03a03a72d26a7aea117100695768145f18ceb851c4471dedd4b6f4aab449 |
import glob
import mixtape.featurizer, mixtape.tica, mixtape.cluster, mixtape.markovstatemodel
import numpy as np
import mdtraj as md
from mixtape import ghmm, feature_selection, subset_featurizer
import sklearn.pipeline, sklearn.externals.joblib
import mixtape.utils
n_iter = 1000
n_choose = 50
stride = 1
lag_time = 1... | kyleabeauchamp/PMTStuff | code/score.py | Python | gpl-2.0 | 1,103 | [
"MDTraj"
] | df5cd518a9730585654ffdffa6f148bf686aa13bb6c300589483590fe2b03c71 |
'''
Created on Aug 5, 2014
@author: gearsad
'''
# To allow the project to be run from outside Eclipse PyDev
import sys
sys.path.append('../')
import vtk
from math import cos, sin
from scene import Terrain
from scene import Bot
from scene import Axes
from scene import LIDAR
if __name__ == '__main__':
# A re... | GearsAD/semisorted_arnerve | sandbox/bot_vis_platform_post3b/bot_vis_platform/bot_vis_main.py | Python | mit | 1,914 | [
"VTK"
] | 3777f70e42fa0491674897efdcf3d3d808e76bfe154fef112901dc4185a62fa6 |
###########################################################################
#
# Copyright 2020 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/l... | google/starthinker | dags/dataset_dag.py | Python | apache-2.0 | 4,468 | [
"VisIt"
] | 1d3621bf7d2234ab627922a2f650a44cd20a67f02ac450d42ec12bd24c3f3853 |
# -*- coding: utf-8 -*-
"""
===============================================================================
Defect generator base classes (:mod:`sknano.generators._defect_generators`)
===============================================================================
.. currentmodule:: sknano.generators._defect_generators... | scikit-nano/scikit-nano | sknano/generators/_defect_generators.py | Python | bsd-2-clause | 10,181 | [
"VMD"
] | ac363b7ef685242f8643e5efa0b606b234aa235dfb73df01c859ab4fd35d0fae |
#######################################################################
#
#
# Next Event Renderer for Dreambox/Enigma-2
# Coded by Vali (c)2010
# Support: www.dreambox-tools.info
#
#
# This plugin is licensed under the Creative Commons
# Attribution-NonCommercial-ShareAlike 3.0 Unported License.
# To view a... | openatv/enigma2 | lib/python/Components/Renderer/NextEvent.py | Python | gpl-2.0 | 1,942 | [
"VisIt"
] | f4574950505123ce1a089ef80f18842163640a865100995392ec98788528fbbc |
#! /usr/bin/python
# Version info: $Id: NeuralNetwork2D.py 314 2011-07-11 08:50:50Z zunzun.com $
'''
# the pythonequations base is located up one directory from the top-level examples
# directory, go up one directory in the path from there for the import to work properly
import sys, os
if os.path.join(sys.path[0][:s... | JMoravec/unkRadnet | zunzunCode/pythonequations/Examples/SimpleExamples/NeuralNetwork2D.py | Python | bsd-3-clause | 2,765 | [
"NEURON"
] | 4059c3939511a0e08c5f57e689c47f99371594f17e1d082e9fae36c31062552e |
#
# Copyright 2016-2017 Andreas Klemenz (Fraunhofer IWM)
#
# matscipy - Materials science with Python at the atomic-scale
# https://github.com/libAtoms/matscipy
#
# 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 Soft... | libAtoms/matscipy | matscipy/opls.py | Python | lgpl-2.1 | 17,112 | [
"ASE",
"Matscipy"
] | 959f4b0dbe951a6c1648b36330619028843d46208e9cf73f13e9673e8a438853 |
#!/usr/bin/env python
from optparse import OptionParser
code_choices = ['gpaw', 'dacapo', 'abinit', 'elk']
xc_choices = ['PW91', 'LDA', 'PBE']
parser = OptionParser(usage='%prog [options] package.\nExample of call:\n'+
'Report adsorption on Ru001 system'
'python %prog --co... | qsnake/gpaw | gpaw/test/big/Ru001/adsRu001_results.py | Python | gpl-3.0 | 2,165 | [
"ABINIT",
"ASE",
"Elk",
"GPAW",
"VASP"
] | 13d69d93309928c49899b82a7db15bcf6adca844d95668c9c5047820986d21fa |
from __future__ import division, absolute_import, print_function
import os
import sys
import types
import re
import warnings
from numpy.core.numerictypes import issubclass_, issubsctype, issubdtype
from numpy.core.overrides import set_module
from numpy.core import ndarray, ufunc, asarray
import numpy as np
# getargs... | shoyer/numpy | numpy/lib/utils.py | Python | bsd-3-clause | 36,736 | [
"VisIt"
] | bd4ce40eda11a31d92506acfdd1430b8f2ff9aab82b1850cdff690fb4dbd9b98 |
from random import choice
import string
def parse_and_fill_mad_lib(mad_lib):
tokens = mad_lib.split(" ")
for idx, token in enumerate(tokens):
exclude = set(string.punctuation)
naked_token = ''.join(ch for ch in token[1:] if ch not in exclude)
if len(token) == 0:
... | joshuag/speakerbot | speakerbot/util/words.py | Python | mit | 18,183 | [
"VisIt",
"exciting"
] | bd1f88586816c373ae759b1133d5fdc48e650a17b9823052675e1701b1c915c0 |
# -*- coding: utf-8 -*-
#
# This file is part of INSPIRE.
# Copyright (C) 2014, 2015 CERN.
#
# INSPIRE 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... | jalavik/inspire-next | inspire/modules/authors/views.py | Python | gpl-2.0 | 12,285 | [
"VisIt"
] | 4a6384076f53fd0085055f170eb54042b1591006ba469e6b4150b09903727497 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
from numpy import diff
from scipy.misc import central_diff_weights
from scipy import signal, interpolate
from scipy.ndimage import filters
def D1(x, y, axis=-1):
""" Simplest numerical derivative of order 1
returns x', dy/dx(x')
"""
dx = diff(x... | MaximeLapointeMajor/QuantumDot-AutomatedTuning | derivative.py | Python | mit | 4,166 | [
"Gaussian"
] | 2fa50dcb905bd25e44569372a34a6a06fb73092877a6556f2757349f41d23f54 |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2022, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
import pandas as pd
import numpy as np
#from exatomic.exa.util.utility import mkp
from exatomic.exa.util.units import Length, Energy, Mass
from exatomic.core import Atom
from exatomi... | exa-analytics/exatomic | exatomic/va/inputs.py | Python | apache-2.0 | 14,710 | [
"Gaussian",
"NWChem"
] | 3a4a113d8e57d44ab67f07113d596494b952b0903f3e3e323b08ce9c9e84828f |
#!/usr/bin/env python
# This version is created at Mon Mar 17 12:54:44 CET 2014
# Author: Asli I. Ozen (asli@cbs.dtu.dk)
# License: GPL 3.0 (http://www.gnu.org/licenses/gpl-3.0.txt)
import sys, gzip
#import re, string
#import argparse
import os
#from Bio.Blast import NCBIStandalone
#from Bio import SeqIO
from operator ... | MG-group-tools/MGFunc | mgfunc_v2/Utils.py | Python | gpl-3.0 | 25,237 | [
"BLAST"
] | a93dbffd01d183382e2ee74d330fa8eeb778d1e6ce580e3b0d12ee87ec6da856 |
########################################################################
# $HeadURL$
# File : InstallTools.py
# Author : Ricardo Graciani
########################################################################
"""
Collection of Tools for installation of DIRAC components:
MySQL, DB's, Services's, Agents
It only ... | rajanandakumar/DIRAC | Core/Utilities/InstallTools.py | Python | gpl-3.0 | 88,014 | [
"DIRAC"
] | 29afc8bf9b887dd5cb4007744ab54317e9d201808419ce6f5b402e565e09daad |
# -*- 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... | SNoiraud/gramps | gramps/plugins/webreport/addressbook.py | Python | gpl-2.0 | 4,744 | [
"Brian"
] | db33f7025fc4e995a3192bd179e3baee1fb57ffb67234cbe2a782d0f721f2bb7 |
########################################################################
#
# (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 by
# the Free Software ... | pheanex/ansible | lib/ansible/cli/galaxy.py | Python | gpl-3.0 | 24,544 | [
"Galaxy"
] | e57d18341b2e2a2a9d6f2242a2706868d54fc5a9290bb5cb674df71adc5ad12b |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2017 Lenovo, Inc.
#
# 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 by
# the Free Software Foundation, either version 3 of the License, or
# ... | e-gob/plataforma-kioscos-autoatencion | scripts/ansible-play/.venv/lib/python2.7/site-packages/ansible/modules/network/lenovo/cnos_interface.py | Python | bsd-3-clause | 26,957 | [
"VisIt"
] | 05794fff148c18b761440364e0e2191f5226869efc1d25c0247d8c02d3f2a49d |
import numpy as np
from matplotlib.figure import Figure
from .c_bilayer import F2FiveGaussSymmetricHeadBilayer
from ..core import FitFunction
class FiveGaussianSymmetricHeadBilayer(FitFunction):
name = 'Bilayer with guests'
description = 'Symmetric head bilayer with inner and outer bilayers'
arguments ... | awacha/saxsfittool | src/saxsfittool/fitfunction/bilayer/bilayer.py | Python | bsd-3-clause | 8,596 | [
"Gaussian"
] | 15c6557270af77d25927865d3d80558f470d32e04182d76a66c0a4a9b3b48a42 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Jason Swails
# Contributors:
#
# MDTraj is free software: you ... | daviddesancho/mdtraj | mdtraj/tests/test_restart.py | Python | lgpl-2.1 | 4,483 | [
"Amber",
"MDTraj",
"NetCDF"
] | f7890c4aecd564d15ab7bb3b31e1c1495bf16b952a0590f2d34d6fa987bd89be |
# Copyright (c) 2009-2014 LOGILAB S.A. (Paris, FRANCE) <contact@logilab.fr>
# Copyright (c) 2013-2020 Claudiu Popa <pcmanticore@gmail.com>
# Copyright (c) 2013-2014 Google, Inc.
# Copyright (c) 2014 Alexander Presnyakov <flagist0@gmail.com>
# Copyright (c) 2014 Eevee (Alex Munroe) <amunroe@yelp.com>
# Copyright (c) 201... | ruchee/vimrc | vimfiles/bundle/vim-python/submodules/astroid/astroid/rebuilder.py | Python | mit | 39,526 | [
"VisIt"
] | bf15296a8cf13b62204724797d96e730a5fa8d8508e8ae424cd51e88abd7351d |
# coding: utf-8
#
# Copyright 2012 NAMD-EMAP-FGV
#
# This file is part of PyPLN. You can get more information at: http://pypln.org/.
#
# PyPLN 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 o... | NAMD/pypln.backend | pypln/backend/workers/bigrams.py | Python | gpl-3.0 | 1,748 | [
"NAMD"
] | a48b6a2873ac30fa68b7779b0ba3a7375ff16295914c37757b231a9f9ab04637 |
from django.db import models
from edc_base.model.fields import OtherCharField
from edc_constants.choices import YES_NO_UNKNOWN
from edc_base.model.models import BaseUuidModel
from edc_base.model.validators import date_not_future
from edc_visit_tracking.models import CrfInlineModelMixin
from edc_sync.models import Sync... | botswana-harvard/tshilo-dikotla | td_infant/models/infant_fu_immunizations.py | Python | gpl-2.0 | 3,574 | [
"VisIt"
] | e46f73607e08d533fecb4df0dbdbcf81c1044e1f6394da2b723f965e84c39e67 |
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