text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
import sys
sys.path.insert(1,"../../../")
import h2o
from tests import pyunit_utils
from h2o.estimators.glm import H2OGeneralizedLinearEstimator
import random
def getLambdaModel():
print("Read data")
prostate = h2o.import_file(path=pyunit_utils.locate("smalldata/logreg/prostate.csv"))
myX = ["AGE","RACE","... | madmax983/h2o-3 | h2o-py/tests/testdir_algos/glm/pyunit_NOFEATURE_getLambdaModel_mediumGLM.py | Python | apache-2.0 | 1,845 | [
"Gaussian"
] | e55ef276d9d5c4d548408e66cb1630cb1b7cf0fdba0c0cd7cc7aedfe77ba5207 |
'''
just some basic image operations
'''
import numpy as np
import skimage as sk
import scipy.ndimage as nd
class LinearOperations(object):
def __init__(self, fname):
'''
an image object. Loads in some image from jpg and converts it to useful
'''
self.image = nd.imread(fname,flatt... | aaron-parsons/repoNoData | repoNoData/image_operations.py | Python | apache-2.0 | 1,279 | [
"Gaussian"
] | 3f92f6095612349dbfb1c9affb81617bff32d25e7c20ca554f35051e61d0d567 |
"""Contains the Credit (coin play) mode code"""
# credits.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 math import floor
from mpf.system.data_manag... | qcapen/mpf | mpf/modes/credits/code/credits.py | Python | mit | 17,280 | [
"Brian"
] | 75931db004971d44b832c087ec56a42ed20b8abff4a6e33fa684ac00e5e7e6dc |
# vi: ts=4 sw=4
import random
import numpy
import math
def compute_kinetic_energies(vx, vy, vz, m):
"""Compute the kinetic energies of a set of particles."""
return 0.5 * m * (vx**2 + vy**2 + vz**2)
def compute_temperature(vx, vy, vz, m):
"""Compute temperature of neutral particles in free space.
... | Tech-XCorp/ultracold-ions | uci/Ptcls.py | Python | mit | 3,129 | [
"Gaussian"
] | 40079ecf2ee71b51c8833a032072226fc87b6a07a5dd681eeffe5a13ab24e962 |
from __future__ import absolute_import
import sys, os, yaml, glob
import subprocess
import argparse
import re
from sciLifeLab_utils import submit_job
def main(args):
projectFolder = os.getcwd()
assemblies_dir = args.assembly_dir
lineage = args.lineage
for sample_dir_name in [dir for dir in os.listdi... | senthil10/NouGAT | sciLifeLab_utils/run_validation.py | Python | mit | 6,370 | [
"BWA"
] | b879cc13583361429d67a06e8722c8456e9dbd86f6cb9b8e0379d766d3e5868b |
# This file is part of victims-web.
#
# Copyright (C) 2013 The Victims Project
#
# This program 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... | jasinner/victims-web | test/__init__.py | Python | agpl-3.0 | 3,181 | [
"VisIt"
] | dc0021e7d2d2a94fc2645d6a40c7fc54c52b5aeb35be24eda65e796ea2849ff3 |
"""Known matrices related to physics"""
from sympy import Matrix, I
def msigma(i):
"""Returns a Pauli matrix sigma_i. i=1,2,3
See also:
http://en.wikipedia.org/wiki/Pauli_matrices
"""
if i==1:
mat=( (
(0, 1),
(1, 0)
) )
elif i==2:
mat=( (
... | certik/sympy-oldcore | sympy/physics/matrices.py | Python | bsd-3-clause | 2,063 | [
"DIRAC"
] | 8150b2d84142805bdfc6a684792249680fd7bc0f801ef28a3fba8702b648f32b |
#
# File:
# TRANS_read_multiple_netCDF.py
#
# Synopsis:
# Illustrates how to read multiple netCDF files
#
# Categories:
# I/O
#
# Author:
# Karin Meier-Fleischer, based on NCL example
#
# Date of initial publication:
# September 2018
#
# Description:
# This example shows how to read multiple n... | KMFleischer/PyEarthScience | Transition_examples_NCL_to_PyNGL/read_data/TRANS_read_multiple_netCDF.py | Python | mit | 1,123 | [
"NetCDF"
] | 9c982b6268a372689c40fbc593e8b269a272f17bec334d2aff500dae08bbfd04 |
#!/usr/bin/env python
# =====================================================================
# MODULE DOCSTRING
# =====================================================================
"""
Tests for custom collections classes.
"""
# =====================================================================
# GLOBAL IMPO... | open-forcefield-group/openforcefield | openff/toolkit/tests/test_utils_collections.py | Python | mit | 8,990 | [
"MOE"
] | f074e3265c84518831de35a9265c88f3959640bc7a6f7f41a35aacbd552ad00e |
# -*- coding: utf-8 -*-
r'''This module contains classes for different types of network layers.
.. image:: _static/feedforward_neuron.svg
In a standard feedforward neural network layer, each node :math:`i` in layer
:math:`k` receives inputs from all nodes in layer :math:`k-1`, then transforms
the weighted sum of the... | devdoer/theanets | theanets/layers/base.py | Python | mit | 15,976 | [
"Gaussian"
] | 5ac2433dc7b811ac358bcabbcd092419516ec46ea19624e6face342ea15c1c94 |
"""
FASTA/QUAL format (:mod:`skbio.io.format.fasta`)
================================================
.. currentmodule:: skbio.io.format.fasta
The FASTA file format (``fasta``) stores biological (i.e., nucleotide or
protein) sequences in a simple plain text format that is both human-readable
and easy to parse. The fi... | SamStudio8/scikit-bio | skbio/io/format/fasta.py | Python | bsd-3-clause | 37,721 | [
"BLAST",
"scikit-bio"
] | 348202bf0c948306ed28cf18c42ea7efc8fcc2f8f9265f399b3ec8fcee042889 |
from __future__ import print_function
from __future__ import absolute_import
import unittest
import csv
from owmeta_core.context import Context
from owmeta_core.command import OWM
from owmeta_core.bundle import Bundle
from owmeta.worm import Worm
from owmeta.cell import Cell
from owmeta.neuron import Neuron
from owme... | openworm/PyOpenWorm | tests/DataIntegrityTest.py | Python | mit | 10,284 | [
"NEURON"
] | 1c4856ab884a92de75f8cddcc0be4020b72218b650abfd00b598d5532742c4aa |
from __future__ import unicode_literals
import re
from .common import InfoExtractor
from .theplatform import ThePlatformIE
from ..utils import (
find_xpath_attr,
lowercase_escape,
smuggle_url,
unescapeHTML,
update_url_query,
int_or_none,
HEADRequest,
parse_iso8601,
)
class NBCIE(Info... | wndias/bc.repository | script.module.youtube.dl/lib/youtube_dl/extractor/nbc.py | Python | gpl-2.0 | 13,096 | [
"Brian"
] | ad01c4343ea66d82dc7ad9c897ae49fb81d7c01ff74ce2a696aec914431cd8b9 |
"""
FCKeditor - The text editor for internet
Copyright (C) 2003-2005 Frederico Caldeira Knabben
Licensed under the terms of the GNU Lesser General Public License:
http://www.opensource.org/licenses/lgpl-license.php
For further information visit:
http://www.fckeditor.net/
"Support Open Source software. ... | dapfru/gladiators | parsek/cls/editor/fckeditor.py | Python | gpl-2.0 | 3,897 | [
"VisIt"
] | cfba5fbf012f8bd66c8605aa215eb4440d767c0f29f89f88de9681c09bfb467b |
"""Crossover classes, that cross the elements in the supplied
atoms objects.
"""
import random
import numpy as np
from ase.ga.offspring_creator import OffspringCreator
class ElementCrossover(OffspringCreator):
"""Base class for all operators where the elements of
the atoms objects cross.
"""
def __... | askhl/ase | ase/ga/element_crossovers.py | Python | gpl-2.0 | 5,476 | [
"ASE"
] | 635ceed3ada4cf33c77fb7f58876ef9d73bf757bcb812cb18dd7ef17e69f6f08 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import sys
import itertools
import json
import re
import warnings
from monty.json import MontyDecoder, MontyEncoder
from six import string_types
from pymatge... | matk86/pymatgen | pymatgen/ext/matproj.py | Python | mit | 39,785 | [
"VASP",
"pymatgen"
] | caf37e6b51b96e8445ca41972cf0351c7d7662e6bc20d8f980c99c172bcfe415 |
import sys
from rpython.rlib.objectmodel import specialize, we_are_translated, enforceargs
from rpython.rlib.rstring import StringBuilder, UnicodeBuilder
from rpython.rlib.rarithmetic import r_uint, intmask, widen
from rpython.rlib.unicodedata import unicodedb
from rpython.tool.sourcetools import func_with_new_name
fro... | oblique-labs/pyVM | rpython/rlib/runicode.py | Python | mit | 71,177 | [
"FEFF"
] | 729ab459136b6a2cb0195dbf678397fa90a82554d3c6644d0d66105fae61a2a6 |
import tkinter
tk = tkinter.Tk()
canvas = tkinter.Canvas(tk, width = 500, height = 500)
canvas.pack()
canvas.create_text(150, 100, text = 'There once was a man from Toulouse,')
canvas.create_text(130, 120, text = 'Who rode around on a moose.', fill = 'red')
canvas.create_text(150, 150, text = 'He said, "It\'s my cur... | amosnier/python_for_kids | course_code/12_033_tkinter_text.py | Python | gpl-3.0 | 610 | [
"MOOSE"
] | dcec05fbf288bd372df09392154779d1a0f90936f9e238fc8921765e786b665f |
#!/usr/bin/env python3
"""
File Integrity monitoring and logging daemon
Copyright (C) 2011,2016 Glen Pitt-Pladdy
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 ... | glenpp/integrityd | integrityd-file.py | Python | gpl-3.0 | 24,849 | [
"VisIt"
] | 3dda5d55b9842c7940c8760d6d75b8cf2a037308ccd3a3163419fdb8aa0b55da |
# Orca
#
# Copyright 2005-2008 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/scripts/apps/gnome-mud/script.py | Python | gpl-3.0 | 6,038 | [
"ORCA"
] | d93926d301c7f84deedbef7762eaab97e9f1f6299a60589d7ed124b8e572c7b9 |
#!/usr/bin/python
# -*- coding: ISO-8859-1 -*-
"""
Mara.ANN.Arch (v. 0.1):
Neural network architectures.
Author: Martti Louhivuori (martti.louhivuori@helsinki.fi)
Date: 14.2.2006
"""
from random import Random
class Neuron:
"A single artificial neuron."
def __init__(self, id=None, activation='lin... | navjeet0211/Mara | ANN/Arch.py | Python | gpl-2.0 | 10,881 | [
"NEURON"
] | 5a099995573975c27b042002f704593270e599662d8b6413a3f9fee43df2bfb6 |
""" VirtualMachineManager Service Integration Tests
"""
import uuid
import unittest
from DIRAC.Core.Base.Script import parseCommandLine
parseCommandLine()
from DIRAC.Core.Base.Client import Client
class VirtualMachineManagerTests(unittest.TestCase):
"""These tests check the VirtualMachineManager functions."""... | ic-hep/DIRAC | tests/Integration/WorkloadManagementSystem/Test_VirtualMachineManagerClient.py | Python | gpl-3.0 | 4,221 | [
"DIRAC"
] | 516b46c1404df7a1e15bf8845e647d0353e09097553d0c189e71626f302f58bc |
from __future__ import division, print_function, absolute_import
from scipy import stats
import numpy as np
from numpy.testing import assert_almost_equal, assert_, assert_raises, \
assert_array_almost_equal, assert_array_almost_equal_nulp
def test_kde_1d():
#some basic tests comparing to normal distribution
... | sargas/scipy | scipy/stats/tests/test_kdeoth.py | Python | bsd-3-clause | 5,947 | [
"Gaussian"
] | 80d5f6482109bc8580c75a5f0dc8377186cb5cecf12664c9066902443c3e4044 |
from ovito import *
from ovito.io import import_file
node = import_file("../../files/LAMMPS/animation.dump.gz")
cell = node.source.cell
print(" input pbc flags: {}".format(cell.pbc))
cell.pbc = (False, True, True)
print(" input cell: {}".format(cell.matrix))
cell.matrix = [[10,0,0,0],[0,2,0,0],[0,0,1,0]]
node.com... | srinath-chakravarthy/ovito | tests/scripts/test_suite/simulation_cell.py | Python | gpl-3.0 | 404 | [
"LAMMPS",
"OVITO"
] | ee41c933af1abb52fd9ba1c0ac66ae8924536e875799451ea6772ae8a2e218be |
# FRETBursts - A single-molecule FRET burst analysis toolkit.
#
# Copyright (C) 2014-2016 The Regents of the University of California,
# Antonino Ingargiola <tritemio@gmail.com>
#
"""
This module provides functions to compute photon rates from timestamps
arrays. Different methods to compute rates are imp... | chungjjang80/FRETBursts | fretbursts/phtools/phrates.py | Python | gpl-2.0 | 8,325 | [
"Gaussian"
] | c7f4f7aed18cc07280258c70ae61c35772fb50288bba1c2c2c0770d964ea1c43 |
# This plugin is adapted from the Python Console plugin and the IPython
# cookbook at:
# http://ipython.scipy.org/moin/Cookbook/EmbeddingInGTK
# Copyright (C) 2009-2010 Brian Parma
# Updated 2012 Brian Parma
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU... | strahlc/exaile | plugins/ipconsole/__init__.py | Python | gpl-2.0 | 7,788 | [
"Brian"
] | 486a5e0db89b72a8d9ccedb61fe83ec184b548a624d4b35ba306ce193f22df94 |
"""A collection of utilities for dealing with Molecular Fragments"""
import itertools
import numpy as np
from typing import List, Optional, Sequence, Set, Tuple, Union
import logging
from deepchem.utils.typing import RDKitAtom, RDKitMol
from deepchem.utils.geometry_utils import compute_pairwise_distances
logger = log... | deepchem/deepchem | deepchem/utils/fragment_utils.py | Python | mit | 12,339 | [
"RDKit"
] | b305a24979c2a0597c2127622296ca8cd030a589f331723fb5d64a498724bab0 |
#
# Copyright 2011-2013 Blender 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 in... | Gamebasis/3DGamebasisServer | GameData/blender-2.71-windows64/2.71/scripts/addons/cycles/properties.py | Python | gpl-3.0 | 35,668 | [
"Gaussian"
] | c5cc6c5b932c1d4dbb723f5a65e15545bacf3ca72f6c09504349d712ca705961 |
"""
Kernel Density Estimation
-------------------------
"""
# Author: Jake Vanderplas <jakevdp@cs.washington.edu>
import numpy as np
from scipy.special import gammainc
from .ball_tree import BallTree, DTYPE
from .kd_tree import KDTree
from ..base import BaseEstimator
from ..utils import check_array, check_random_stat... | DailyActie/Surrogate-Model | 01-codes/scikit-learn-master/sklearn/neighbors/kde.py | Python | mit | 7,984 | [
"Gaussian"
] | 86dec849fc530ee1e0f4616b545451703a4eb0dd6b5649fb16d49627fdaed0d2 |
import operator
import numpy as np
import sys
if sys.argv[0] != "gen_py.py":
from api_autogen import *
import cgt
from . import core, utils
# Every non-underscored function in this file should have a docstring, and it should enforce that the input data is valid
# ==================================================... | RichardWarfield/cgt | cgt/api.py | Python | mit | 23,221 | [
"Gaussian"
] | 907e5c13fae5c137bd7fe3cab189a139e03d4b40754891e9e24c38b427698cc3 |
# -*- coding: utf-8 -*-
"""
Promote and demote values of differing types in a minivect AST. This is run
before code generation. In LLVM types need to be equivalent for binary
operations.
"""
from __future__ import print_function, division, absolute_import
import sys
import copy
from . import minivisitor
from . import... | shiquanwang/numba | numba/minivect/type_promoter.py | Python | bsd-2-clause | 1,821 | [
"VisIt"
] | 657ad64eb3d31e795bfa4a22bab243fa15b655a069b3926392e0a56b0bd2353b |
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.cm as cm
def rhodelta(dist, xxdist, ND, N, percent = 2.0):
'''
Input file format: 3 columns ,seperated by ' '
Return (rho,delta,ordrho)
'''
print('Caculating rho and delta...')
print('average percentage of neighbours (hard cod... | GuipengLi/Dcluster | Dcluster/rhodelta.py | Python | gpl-3.0 | 1,427 | [
"Gaussian"
] | 91acbcb95885442bc22a22b7a0e885673d1e735d2e1007a9ce21afba8a52edec |
from __future__ import print_function, division
from sympy.core.basic import C
from sympy.core.singleton import S
from sympy.core.function import Function
from sympy.core import Add
from sympy.core.evalf import get_integer_part, PrecisionExhausted
######################################################################... | dennisss/sympy | sympy/functions/elementary/integers.py | Python | bsd-3-clause | 5,303 | [
"VisIt"
] | f5473f8d45ca239cdb40644503c09c7a4a55c287f7cb1c7284404a5fbef1273b |
# Copyright 2018 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | lukeiwanski/tensorflow | tensorflow/contrib/distributions/python/kernel_tests/util/correlation_matrix_volumes_lib.py | Python | apache-2.0 | 13,554 | [
"Gaussian"
] | b4e34b4e7319007e70563215030ac11db3fc14534b50a3e37627521aa40a7cfd |
"""
@name: Modules/Core/Drivers/_test/test_Usb.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2015-2019 by D. Brian Kimmel
@license: MIT License
@note: Created on Jul 30, 2015
@Summary:
Passed all tests - DBK - 2019-01-10
"""
__updated__ = '2020-01-21'
# Import system... | DBrianKimmel/PyHouse | Project/src/Modules/Core/Drivers/_test/test_USB.py | Python | mit | 845 | [
"Brian"
] | 750651c3bdf37bf09b436eed8ce1b8f639936d92d72be26dcedff2f49e0c1382 |
# Make me coffee!
# maybe someday we'll actually make this order coffee using a phone-connection service :D
from espresso.main import robot
@robot.respond(r'(?i)make (me )?(a )?coffee')
def make_coffee(res):
res.reply(res.msg.user, "http://dreamatico.com/data_images/coffee/coffee-3.jpg")
| ratchetrobotics/espresso | plugins/brew.py | Python | bsd-3-clause | 295 | [
"ESPResSo"
] | 5839571a690a7c5b40a5c80fb076429a06ee7fa3198d2a1a9d145ec05bd385f9 |
import os
from uuid import uuid4
from datetime import datetime
from unittest import skipUnless
from ..helpers import UniqueCourseTest
from ...fixtures.course import CourseFixture, XBlockFixtureDesc
from ...pages.lms.auto_auth import AutoAuthPage
from ...pages.lms.course_nav import CourseNavPage
from ...pages.lms.course... | beni55/edx-platform | common/test/acceptance/tests/lms/test_lms_edxnotes.py | Python | agpl-3.0 | 29,664 | [
"VisIt"
] | 3632def628309386c8846ca50b708a3117835877856a346b38299be5b6f5f761 |
from __future__ import division
from functools import reduce
import numpy as np
from math import log,sqrt,fabs,exp
from abc import ABCMeta,abstractmethod
import random
from random import sample,gauss,randrange,uniform
from scipy.interpolate import LSQUnivariateSpline
from scipy.signal import savgol_filter
from scipy.st... | johnveitch/cpnest | cpnest/proposal.py | Python | mit | 28,372 | [
"Gaussian"
] | 10d346cb78d259020412161092d7f4655cdbb527db2451235b641f6293e15ebb |
# coding=utf-8
EMAILS = [
'0-mail.com',
'0box.eu',
'0clickemail.com',
'0hdear.com',
'0mixmail.info',
'0u.ro',
'0v.ro',
'0w.ro',
'0wnd.net',
'0wnd.org',
'0x00.name',
'0x207.info',
'001.igg.biz',
'027168.com',
'0815.ru',
'0815.ry',
'0815.su',
'084... | WCF/burner-email-providers | burner_email_providers/__init__.py | Python | mit | 78,227 | [
"Galaxy"
] | 2935ea6698d8df4f6562d34cd54ade0939ba77053d27535a0a21ef0a38bb771a |
#
# Copyright (C) 2013,2014,2015,2016 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option)... | Marcello-Sega/espresso | samples/python/debye_hueckel.py | Python | gpl-3.0 | 7,867 | [
"ESPResSo"
] | a259eb1ba1e0d3cc82e5f3b443f2c9fc9af448cbeb3d4f4b16c6fb31ee15df5c |
'''TB Animation Tools is a toolset for animators
*******************************************************************************
License and Copyright
Copyright 2015-Tom Bailey
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public Licen... | tb-animator/tbtools | apps/tb_manipulators.py | Python | mit | 6,708 | [
"VisIt"
] | fdc98845b1ef0413ae76c10c29394f7ec3fc39dd08a55a844e62beaa9b32bbdc |
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Daniel Strohmeier <daniel.strohmeier@tu-ilmenau.de>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
#
# License: BSD (3-clause)
import copy
import numpy as np
from ..io.pick import pick_channels_cov
from ..forward import apply_f... | trachelr/mne-python | mne/simulation/evoked.py | Python | bsd-3-clause | 3,964 | [
"Gaussian"
] | 680310894e3d6150b1a9f7a9fefb52d4d4f67d16471702566a4ac409a34c56a4 |
import numpy as np
import sys
import time
from math import sqrt
from ase import Atoms, Atom, view
from ase.units import Bohr
from ase.parallel import paropen
from gpaw import GPAW
from gpaw.response.grid_chi import CHI
from gpaw.mpi import serial_comm, rank, size
from gpaw.utilities import devnull
if rank != 0:
sy... | qsnake/gpaw | gpaw/test/big/response/graphene.py | Python | gpl-3.0 | 2,773 | [
"ASE",
"GPAW"
] | f3d0cae63fd67e38026c715d447d5bef2bbaabf66a6294d153ad06b41a99fd8a |
#!/usr/bin/env python3
import os
import ast
import stat
import subprocess
fouts = {x.decode('utf-8') for x in subprocess.check_output(['git', 'ls-files']).strip().split()}
pyf = []
for d in ["cereal", "common", "scripts", "selfdrive", "tools"]:
for root, dirs, files in os.walk(d):
for f in files:
if f.end... | commaai/openpilot | scripts/code_stats.py | Python | mit | 1,365 | [
"VisIt"
] | a02ec3f0e9c2c8c65ff91280da1de1e9116a8de07dba23ce26787db89e3e562c |
import os
import vtkAll as vtk
import math
import time
import numpy as np
from director import callbacks
from director import transformUtils
from director import lcmUtils
from director import objectmodel as om
from director.utime import getUtime
from director import robotstate
import drc as lcmdrc
class Manipulati... | RobotLocomotion/director | src/python/director/robotplanlistener.py | Python | bsd-3-clause | 9,714 | [
"VTK"
] | 9887473e36269ae065e9076f7f58a94fd669cbfe390211d7c8805cc647e231d7 |
#!/usr/local/bioinfo/python/3.4.3_build2/bin/python
# -*- coding: utf-8 -*-
# @package buildJobArray.py
# @author Sebastien Ravel
"""
The buildJobArray script
=========================
:author: Sebastien Ravel
:contact: sebastien.ravel@cirad.fr
:date: 08/06/2017
:version: 0.1
Script description
--------------... | sravel/scripts | local/buildJobArray.py | Python | gpl-3.0 | 7,869 | [
"BLAST"
] | 294584af5c7ae8a0c1731e73c01fc73400b04c3c03dfe204f3688aa1c630c9a5 |
index = {
"ID0": "Vanilla",
"ID2": "Groundwater",
"ID3": "Candy Apple",
"ID5": "Forest DDPAT",
"ID6": "Arctic Camo",
"ID8": "Desert Storm",
"ID9": "Bengal Tiger",
"ID10": "Copperhead",
"ID11": "Skulls",
"ID12": "Crimson Web",
"ID13": "Blue Streak",
"ID14": "Red Laminate",... | adamb70/CSGO-Market-Float-Finder | itemIndex.py | Python | mit | 17,947 | [
"Amber",
"Galaxy",
"Jaguar"
] | 8323bdc31a5a20a78f6eea26fc6daf78ef6fcffd556f5b92756808e70f0515c8 |
#!/usr/bin/env python
"""
Script that dumps the DB information for the elements into the standard output.
If returns information concerning the StatusType and Status attributes.
"""
from DIRAC import gLogger, exit as DIRACExit, version
from DIRAC.Core.Base.Script import Script
from DIRAC.ResourceStatusSystem.Client imp... | DIRACGrid/DIRAC | src/DIRAC/ResourceStatusSystem/scripts/dirac_rss_list_status.py | Python | gpl-3.0 | 4,945 | [
"DIRAC"
] | a8a97ede28aedd32ab4129ca7d4e93dc55bdd6e467e682dd3bef397d2270a6c4 |
#
# 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 require... | evenmarbles/rlglued | rlglued/rlglue.py | Python | bsd-3-clause | 8,951 | [
"Brian"
] | 2a1f34b34b96017fae1636d2d71856a65882bb4e601649d4f6fa34c91f549493 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | MOA-2011/e2openplugin-OpenWebif | plugin/controllers/views/web/getservices.py | Python | gpl-2.0 | 5,495 | [
"VisIt"
] | d14bc4e5e4a1e8b99e7367709946ae997996e1e667b2663fb8212a3f70062dc6 |
from ply import *
import MonkeyLex
tokens = MonkeyLex.tokens
def p_program(p):
'''program : program compound_action actions
| compound_action actions
| program actions
| actions
'''
if len(p) == 4:
p[0] = p[1]
if not p[0]: p[0] = []
... | ideaworld/FHIR_Tester | FHIR_Tester_backend/services/monkey/MonkeyParser.py | Python | mit | 5,662 | [
"VisIt"
] | cd68ad510695c44dab4fa7775aad89e73b6d8a5102a448d9f95bb937cfe8b83d |
from __future__ import absolute_import
import base64
import re
import os
import sys
import urllib
PY3 = sys.version_info[0] == 3
if PY3:
from io import StringIO
basestring = str
else:
from StringIO import StringIO
try:
import json
except ImportError:
import simplejson as json
from .rest import ... | GhostAlgorithm/sugar-dropbox | extensions/webservice/dropbox/client.py | Python | gpl-2.0 | 59,182 | [
"VisIt"
] | a1247082049dcce7cb8680ef7f4d50350d1aadf1744e09b25fbccc671435f488 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/pbc/cc/kuccsd_rdm.py | Python | apache-2.0 | 8,134 | [
"PySCF"
] | 73786d794ff9d35d12e70e040db671c03b1240e5d75f47160357413967992191 |
# This is the instrument-specific file for the PS6000 series of instruments.
#
# pico-python is Copyright (c) 2013-2014 By:
# Colin O'Flynn <coflynn@newae.com>
# Mark Harfouche <mark.harfouche@gmail.com>
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are pe... | arunpersaud/pico-python | picoscope/ps6000.py | Python | bsd-2-clause | 24,613 | [
"Gaussian"
] | 40f06cceed384dae0aa7342a7b17528fe062f678fd3b3a289997ff977c1b0f28 |
from __future__ import print_function
from __future__ import division
from builtins import str
from builtins import range
from past.utils import old_div
# Routines for manipulating restart files
try:
from boututils import DataFile
except ImportError:
print("ERROR: restart module needs DataFile")
raise
imp... | kevinpetersavage/BOUT-dev | tools/pylib/boutdata/restart.py | Python | gpl-3.0 | 14,822 | [
"Gaussian"
] | 6ec65e86c7cafd9fdb255e1b630835c4d2853c7f4cf8198244a67a15e2de4dca |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Abinit Post Process Application
author: Martin Alexandre
last edited: May 2013
"""
import sys,os
import string, math
#gui
import gui.graph as Graph
#Utility
import utility.analysis as Analysis
try:
from PyQt4 import Qt,QtGui,QtCore
except:
pass
from numpy im... | SamKChang/abinit-7.10.5_multipole | scripts/post_processing/appa/gui/vdos.py | Python | gpl-3.0 | 3,540 | [
"ABINIT",
"Gaussian"
] | 7d0462ffb1611b399ea57f638742b3d83059e6844cc9353ef70f399c1b0bbe8b |
'''
version 5.7
Created on Aug 1, 2013
@author: Ozgur Yapar
'''
import os
import re
import shutil
from numpy import *
import xml.etree.ElementTree as ET
import json
import math
def makeFolder(directory):
if not os.path.exists(directory):
os.makedirs(directory)
#define necessary v... | pombredanne/metamorphosys-desktop | metamorphosys/META/analysis_tools/CFD/PreProcessing/CFDPreprocess.py | Python | mit | 255,731 | [
"ParaView",
"VTK"
] | ae7ed63455bc67a8abc7cba2653e571964042dec4c7e60f3e1ceb2f4a4458bd7 |
#!/usr/bin/env python
#----------------------------------------------------------------------------------------------#
#Android Framework for Exploitation v-1 #
# (C)opyright 2010 - XYS3C #
#---Imp... | appknox/AFE | modules/get_content_provider/content.py | Python | gpl-3.0 | 3,361 | [
"VisIt"
] | bf8457749d5a9d697942368d798e2683c9b62e68e5e452f4ff5e30512ad5e32d |
##############################################################################
# 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-affyrnadegradation/package.py | Python | lgpl-2.1 | 2,025 | [
"Bioconductor"
] | 2ea12ca0d78454f9d519f70622d04a914d0e73eab0ef8596e350b64950cb1ba3 |
import random
import math
import copy
import Class
import csv
with open('classroomData.csv', 'r') as csvfile:
spamreader = csv.reader(csvfile)
for row in spamreader:
print(row);
random.seed(0) # repeatable random for problem generation
'''
numMajors = 10
classesPerMajor = 15
minClassSize = 10
maxC... | tupl/classOpt | ICS169Proj.py | Python | mit | 12,046 | [
"VisIt"
] | c47dc4659ad4462d3480e9e6ac10c9ff8023fdee22787337d22436fd4fdb491b |
import pytest
from capybara.exceptions import ModalNotFound
@pytest.mark.requires("modals")
class TestDismissPrompt:
@pytest.fixture(autouse=True)
def setup_session(self, session):
session.visit("/with_js")
def test_dismisses_the_prompt(self, session):
with session.dismiss_prompt():
... | elliterate/capybara.py | capybara/tests/session/test_dismiss_prompt.py | Python | mit | 1,103 | [
"VisIt"
] | ee0ce6a7c4c9acbe60125af316824325c9e48d6e9c0e90cd42a6542046c99d61 |
#coding:utf8
'''
Created on 2013-5-22
@author: lan (www.9miao.com)
'''
from firefly.utils.singleton import Singleton
class MAdminManager:
__metaclass__ = Singleton
def __init__(self):
"""
"""
self.admins = {}
def registe(self,admin):
"""
"""
se... | yangdw/PyRepo | src/annotation/Firefly/firefly/dbentrust/madminanager.py | Python | mit | 757 | [
"Firefly"
] | 4a95846896a1686c8e0c0c52a5139264d7e636bfd05d42dca0621d39b7e3c8f0 |
__author__ = 'ddeconti'
import FileObjects
import re
import sys
from rdkit.Chem import AllChem, MolFromSmiles
from rdkit.Chem.rdSLNParse import MolFromSLN
from rdkit.Chem import SDMolSupplier
class WikiScrapedDB():
'''
Custom wrapper around drug name - side effect counts - gene count - SMILES
Produce a ... | dkdeconti/PAINS-train | training_methods/clustering/FileHandler.py | Python | mit | 7,819 | [
"RDKit"
] | 6552705196c2b721ffe5bc94bab214867e8b158045f2b342ec3bb1680a1981eb |
# -*- coding:utf-8 -*-
# Copyright (c) 2015, Galaxy Authors. All Rights Reserved
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
import datetime
import logging
from sofa.pbrpc import client
import query_pb2
LOG = logging.getLogger('ftrace')
class FtraceSDK(object)... | bdtbd/mdt | python/ftrace/sdk.py | Python | bsd-3-clause | 1,435 | [
"Galaxy"
] | 982b4aaf263f844c1979a74e4134f28b2cbd9e09a209ffc691b994b73e8d6736 |
#!/usr/bin/env python3
"""
Converts the tabular output of NCBI's tblastn output when using the -m 9
or -m 9 options to GFF3 with match and match_part features.
This script assumes you're using the protein file as the query and the
DNA one as the subject.
Note, this is NOT for 'btab' output, which is the tabular outp... | jorvis/biocode | sandbox/jorvis/convert_tblastn_tab_to_gff3.py | Python | mit | 8,042 | [
"BLAST"
] | 3272c9c87df289be749e278a4f54b47029fdaef12aa85f8581ceec969df49e22 |
#!/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... | sunqm/pyscf | pyscf/gto/moleintor.py | Python | apache-2.0 | 38,006 | [
"PySCF"
] | e64d623c95d21ae55204bea2560db947eedc03965b1f4f0d241661a189bb4518 |
# ----------------------------------------------------------------------------
# Copyright 2015 Nervana Systems Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.o... | chetan51/neon | tests/test_optimizer.py | Python | apache-2.0 | 5,939 | [
"Gaussian"
] | 3365e64544e114ed85d4bb4074d5a30d9817c7c621e6c9230ff2d0ec00be3f54 |
import pdb, sys, os, glob, pickle, time, re
import numpy as np
import scipy.ndimage
#import batman
from bayes.pyhm_dev import pyhm
import numexpr
def DERamp( t, torb, pars ):
"""
Implementation of the double-exponential ramp model for WFC3 systematics.
Taken from Eq 1-3 of de Wit et al (2018).
"""
... | tomevans/wfc3 | UtilityRoutines.BACKUP.py | Python | mit | 18,951 | [
"Gaussian"
] | 48f328bc910232dcbfdebf227f5c7f0ca0491ec91f71f72baa41e49e7d410cb1 |
"""
tests.test_all_forms.py
---------------------------
Flask-User automated tests:
Tests posting a sequence of valid forms for all possible config combinations
:copyright: (c) 2013 by Ling Thio
:author: Ling Thio (ling.thio@gmail.com)
:license: Simplified BSD License, see LICENSE.txt for m... | jamescarignan/Flask-User | flask_user/tests/test_multiple_emails.py | Python | bsd-2-clause | 3,721 | [
"VisIt"
] | 127ae24f89a019eec5eb887c35dbd23d0320b1bce392f46dd72dd6850a31bda8 |
"""Universal feed parser
Handles RSS 0.9x, RSS 1.0, RSS 2.0, CDF, Atom 0.3, and Atom 1.0 feeds
Visit https://code.google.com/p/feedparser/ for the latest version
Visit http://packages.python.org/feedparser/ for the latest documentation
Required: Python 2.4 or later
Recommended: iconv_codec <http://cjkpython.i18n.org... | slava-sh/NewsBlur | utils/feedparser.py | Python | mit | 155,455 | [
"NetCDF",
"VisIt"
] | 7e6d3caf5dc49316d643f31f7e768a6953da3e32e08f95e6157dc3850d17cb76 |
""" This is a test of the chain
ReqClient -> ReqManagerHandler -> ReqDB
It supposes that the DB is present, and that the service is running
"""
from DIRAC.Core.Base.Script import parseCommandLine
parseCommandLine()
import unittest
from DIRAC import gLogger
from DIRAC.RequestManagementSystem.Client.Request ... | Andrew-McNab-UK/DIRAC | tests/Integration/RequestManagementSystem/Test_Client_Req.py | Python | gpl-3.0 | 11,413 | [
"DIRAC"
] | 6144bb6fc8c2e3874c60ae2ef7df610022141bbe8e1c3b31e0fba88c3e8c2ef2 |
# Copyright 2014 Google Inc. All Rights Reserved.
"""The 'gcloud test android run' command."""
import os
import types
from googlecloudapis.storage import v1 as storage_v1
from googlecloudsdk.calliope import base
from googlecloudsdk.core import config
from googlecloudsdk.core import log
from googlecloudsdk.core.conso... | wemanuel/smry | smry/server-auth/ls/google-cloud-sdk/lib/googlecloudsdk/test/commands/android/run.py | Python | apache-2.0 | 9,591 | [
"ESPResSo"
] | b50f4a7b1cc027d1ab1958bac041e14b386533cd7ea0c332e09955b1e7b4bf26 |
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yasharmaster/scancode-toolkit | tests/licensedcode/test_match.py | Python | apache-2.0 | 32,780 | [
"VisIt"
] | 669d1c23f7b6290aff8a02cd4b286adf3d51fcab30b61e046df89505bbf842aa |
"""
Compare cross-validation performance of Gaussian mixture model (GMM) and
hidden Markov model with Gaussian mixture emissions (GMM-HMM), using principal components
as features. Parameters are number of principal components and number of Gaussians to use
in mixtures. The CV-scores for both models are calculated for a... | phihes/sds-models | examples/gmm_vs_gmmhmm__mix_vs_pc__scatter.py | Python | mit | 1,849 | [
"Gaussian"
] | 0486b70a949e750218ee76499a75b6c0dab60b39183c66c88b10f296ec78ae9c |
##############################################################################
# adaptiveMD: A Python Framework to Run Adaptive Molecular Dynamics (MD)
# Simulations on HPC Resources
# Copyright 2017 FU Berlin and the Authors
#
# Authors: Jan-Hendrik Prinz
# Contributors:
#
# `adaptiveMD` is free software: ... | markovmodel/adaptivemd | adaptivemd/engine/__init__.py | Python | lgpl-2.1 | 1,176 | [
"MDTraj"
] | c3a4729ac2f7c1864fe85b9340d88582946eb1043d888494e676722c7986ce1a |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | kyleabeauchamp/mdtraj | mdtraj/tests/test_binpos.py | Python | lgpl-2.1 | 5,327 | [
"MDTraj",
"VMD"
] | 7ba491be17613b98c98089976531ba8407ee06f8c0e6fbe982f89a7d0b142108 |
######
# Copyright 2007-2009 Sun Microsystems, Inc. All Rights Reserved.
# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER
#
# This code is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License version 2
# only, as published by the Free Software... | SunLabsAST/AURA | Bridge/pyaura/tagclustering/docclassifier/location.py | Python | gpl-2.0 | 1,060 | [
"VisIt"
] | 15e3848a4ff6c4b53e946a4fc75eb4263e22dbb2f0414a3a84450e772910c9ea |
from collections import deque
import time
import requests
# Constants
BRAZIL = 'br'
EUROPE_NORDIC_EAST = 'eune'
EUROPE_WEST = 'euw'
KOREA = 'kr'
LATIN_AMERICA_NORTH = 'lan'
LATIN_AMERICA_SOUTH = 'las'
NORTH_AMERICA = 'na'
OCEANIA = 'oce'
RUSSIA = 'ru'
TURKEY = 'tr'
# Platforms
platforms = {
BRAZIL: 'BR1',
EUR... | gnozell/Yar-Ha-Har | lib/riotwatcher/riotwatcher.py | Python | mit | 22,700 | [
"CRYSTAL"
] | f091252e3fa2b9f1ea3dac88b7641b0b00e6f867a862544ebb32afdcb9fad776 |
# Copyright (c), Michael DeHaan <michael.dehaan@gmail.com>, 2012-2013
# Copyright (c), Toshio Kuratomi <tkuratomi@ansible.com> 2016
# Simplified BSD License (see licenses/simplified_bsd.txt or https://opensource.org/licenses/BSD-2-Clause)
from __future__ import absolute_import, division, print_function
SIZE_RANGES = ... | fxfitz/ansible | lib/ansible/module_utils/basic.py | Python | gpl-3.0 | 117,157 | [
"VisIt"
] | 83da09b53c253b5734992ba726bfebb41273d8fab9865381465a014c2a40395b |
import sys
sys.path.insert(1, "../../../")
import h2o, tests
def link_correct_default():
print("Reading in original prostate data.")
h2o_data = h2o.upload_file(path=tests.locate("smalldata/prostate/prostate.csv.zip"))
print("Compare models with link unspecified and canonical link specified.")
print("GAUSSIAN... | kyoren/https-github.com-h2oai-h2o-3 | h2o-py/tests/testdir_algos/glm/pyunit_link_correct_default_largeGLM.py | Python | apache-2.0 | 1,990 | [
"Gaussian"
] | d05e04bd4a39ea7d851806f727ff5b128d4ebb60d973c7a74e10940ba89c31a6 |
#!/usr/bin/env python
"""
Command line tool to extract obsHistIDs (visit numbers) from an OpSim db
file given a fieldID.
"""
from __future__ import absolute_import, print_function
import os
import argparse
import pandas as pd
#from desc.twinkles import get_twinkles_visits
from desc.twinkles import OpSimOrdering
from ls... | LSSTDESC/Twinkles | bin/get_twinkles_visits.py | Python | mit | 3,505 | [
"VisIt"
] | 8c38854efcd1d232ae26ffe054f7ef5ea05f5bed100d338609bf2140a63ef833 |
__author__ = 'xiaoxiaoliu'
import pandas as pd
import numpy as np
import os
from os import sys, path
import seaborn as sb
import matplotlib.pyplot as plt
WORK_PATH = "/Users/xiaoxiaoliu/work"
p = WORK_PATH + '/src/morphology_analysis'
sys.path.append(p)
sb.set_context("poster")
data_DIR = WORK_PATH+"/data/201510... | XiaoxiaoLiu/morphology_analysis | bigneuron/comparison_and_plots.py | Python | gpl-3.0 | 4,676 | [
"NEURON"
] | 1b89799a95c7362f2c1347102d44f2ff8d4f74f8b8c59cbefe77af34f34698d5 |
#!/usr/bin/env python
from collections import namedtuple
from ase.data import covalent_radii, atomic_numbers, vdw_radii
from ase import Atoms
#from tsase.optimize import SDLBFGS
from ase.optimize import FIRE
import numpy
numpy.seterr(all='raise')
import os
class VSEPR:
def __init__(self, atoms, bonds, angles='aut... | SamChill/ligandizer | ligandizer/vsepr.py | Python | bsd-2-clause | 14,275 | [
"ASE"
] | 2af6f14e49fddcbdb52b7b846e0ce9bcfd7483790401a6ceeda45b543e20ea5a |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2013 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Software F... | andrebellafronte/stoq | stoqlib/gui/utils/filters.py | Python | gpl-2.0 | 2,012 | [
"VisIt"
] | 61ec6a7c3aa5516ca9196874fd890060508d0236eac0b4f8dd1df14d6a623864 |
from __future__ import absolute_import
input_name = '../examples/linear_elasticity/elastic_contact_planes.py'
output_name = 'test_elastic_contact_planes.vtk'
from tests_basic import TestInput
class Test(TestInput):
pass
| rc/sfepy | tests/test_input_elastic_contact_planes.py | Python | bsd-3-clause | 225 | [
"VTK"
] | 5071d948d82e62c4469e43ab14b625f4314470cbea5a94edf0a7adf5ae70b0df |
# -*- coding: utf-8 -*-
{
'# selected': '# được lựa chọn',
"'Cancel' will indicate an asset log entry did not occur": "'Hủy' sẽ chỉ dẫn một lệnh nhập không thực hiện được",
"A location that specifies the geographic area for this region. This can be a location from the location hierarchy, or a 'group location', or a... | ahaym/eden | languages/vi.py | Python | mit | 374,007 | [
"VisIt"
] | 47ebf658fe66072a3a92f8cc36630142f8c5161da439a2461278abd5c09a7b70 |
# ============================================================================
#
# Copyright (C) 2007-2012 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | jeroendierckx/Camelot | camelot/view/controls/editors/dateeditor.py | Python | gpl-2.0 | 7,177 | [
"VisIt"
] | 87809b65b86c599f24e407d5c610d1b03bd5d56d2ca7fd4f93ca0566ff732a57 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | jH0ward/psi4 | psi4/driver/procrouting/dft_funcs/superfuncs.py | Python | lgpl-3.0 | 12,041 | [
"Psi4"
] | f4e863611a45d58139705f212a7879dc127abdabdf2412b99c6c3508b4026d8c |
# Setup customisation for gpaw/cuda
import os
# compiler and linker
compiler = 'gcc'
mpicompiler = 'mpicc'
mpilinker = 'mpicc'
extra_compile_args = ['-std=c99', '-mcpu=power8']
# libraries
libraries = ['z']
# cuda
library_dirs += [os.environ['CUDA_LIB'], './c/cuda']
include_dirs += [os.environ['CUDA_HOME'] + '/inclu... | mlouhivu/build-recipes | gpaw/examples/davide-1.1.0-cuda/setup/customize-cuda.py | Python | mit | 1,052 | [
"GPAW"
] | 669779be03a016001d1bf7650b4525f3c4401184952f52c7d5289027b16357dd |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
What it does
============
B{This is the third step of ZIBgridfree.}
After a set of initial nodes has been created by L{zgf_create_nodes}, this tool will, for each node, setup all the files that are necessary for Gromacs to run the sampling. This includes writing the... | CMD-at-ZIB/ZIBMolPy | tools/zgf_setup_nodes.py | Python | lgpl-3.0 | 7,646 | [
"Gromacs"
] | f4248cdf884224731e4a8090f586b0793be7271afa9f282383123b9d3f780201 |
""" This integration test runs the RMS test scenari using
the MySQL DB
"""
# pylint: disable=invalid-name,wrong-import-position
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
from DIRAC.Core.Base.Script import parseCommandLine
parseCommandLine()
from p... | ic-hep/DIRAC | tests/Integration/RequestManagementSystem/Test_ReqDB.py | Python | gpl-3.0 | 675 | [
"DIRAC"
] | 13051418428ffc7247c335e69f672e3b49869baea7bc2471fd2b79cbdc1314f9 |
from MuVisitor import MuVisitor
from MuParser import MuParser
from APICodeLEIA import (
LEIAProg,
Condition, Immediate,
R7
)
from antlr4.tree.Trees import Trees
class MyMuCodeGen3AVisitor(MuVisitor):
def __init__(self, d, s, parser):
super().__init__()
self._outputname = s
... | lauregonnord/cap-labs | TP06/MuSmartCodeGen/MyMuCodeGen3AVisitor.py | Python | gpl-3.0 | 8,007 | [
"VisIt"
] | 2492286b0a46f81198bfba344cabf346dcb70ce5f09d11f9fb5652c5ce884330 |
# $HeadURL$
#
""" SystemLoggingDB class is a front-end to the Message Logging Database.
The following methods are provided
insertMessage()
getMessagesByDate()
getMessagesByFixedText()
getMessages()
"""
__RCSID__ = "$Id$"
import re
import os
import sys
from types import ListType, StringTypes
fro... | avedaee/DIRAC | FrameworkSystem/DB/SystemLoggingDB.py | Python | gpl-3.0 | 27,062 | [
"DIRAC"
] | b711b61dc34a9569a72125233cd851074214cf68e096746f86e43f8e3c90c4c6 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | Kleptobismol/scikit-bio | skbio/parse/record.py | Python | bsd-3-clause | 18,897 | [
"scikit-bio"
] | 0880050cecf00f75fa4686b31219ea844d1f0198640ccd7e856649664653f83e |
# encoding:utf-8
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2009 Benny Malengier
#
# 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 of the License, or
# ... | jralls/gramps | gramps/plugins/lib/libplugins.gpr.py | Python | gpl-2.0 | 9,038 | [
"Brian"
] | 497aebba30af70d9bb646ca3329b5e01e274fce3654482c67c4e5c8adddc6aa3 |
'''plotChromVariantFrequency.py
Usage:
plotChromVariantFrequency.py <snpfile> <mincov> <bamfile> <outfile>
'''
import collections
import os
import re
import pysam
import matplotlib as mpl
mpl.use('Agg')
import matplotlib.pyplot as plt
from general_python import docopt
# Extract and process arguments
args = do... | adam-rabinowitz/ngs_python | scripts/Variants/plotChromVariantFrequency.py | Python | gpl-2.0 | 4,545 | [
"pysam"
] | 17ca1606e4ecfafae0c8d7b275cc4456f4514319e4821d6b35b1caa1a2a8120c |
from math import log
import numpy
from scipy import linalg
from scipy.stats import chi2, norm
from countermap import CounterMap
from lib import mvncdf
from future_math import gaussian_cdf
class Gaussian(object):
"""multivariate gaussian with independent components
"""
@classmethod
def prob(cls, point, mean, prec... | nuance/python-nlp | nlp/distributions.py | Python | gpl-2.0 | 2,836 | [
"Gaussian"
] | 1853a42f59db7e0cf72f50c9bd2ac08ed2464ad0fabc93154eef1646d1f78dd0 |
# sql/util.py
# Copyright (C) 2005-2015 the SQLAlchemy authors and contributors
# <see AUTHORS file>
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""High level utilities which build upon other modules here.
"""
from .. import exc, u... | rosudrag/Freemium-winner | VirtualEnvironment/Lib/site-packages/sqlalchemy/sql/util.py | Python | mit | 20,382 | [
"VisIt"
] | 51e5bfc6097abd92ce07efbd2c8ca7379b3519e7045e049d06725859a3ee83cf |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under t... | alejob/mdanalysis | package/MDAnalysis/tests/datafiles.py | Python | gpl-2.0 | 2,056 | [
"MDAnalysis"
] | b56f07e1444395d48fa885b4b755d78709bdf2454e1e045be6cff1d068c06589 |
#
# Copyright (C) 2002-2009 greg Landrum and Rational Discovery LLC
#
""" module with functionality for 2D pharmacophores
"""
def DefaultSigFactory(fdefFile=None,
minPointCount=2,maxPointCount=3,
bins=[(2,3),(3,4),(4,5),(5,6),(6,7),(7,8),(8,100)]):
from rdkit.Chem.Pharm... | adalke/rdkit | rdkit/Chem/Pharm2D/__init__.py | Python | bsd-3-clause | 996 | [
"RDKit"
] | acd0c123d4bde0937df36243535b5440faf0be53684d4dd7ea05c347ca90c678 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.