text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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"""Identify program versions used for analysis, reporting in structured table.
Catalogs the full list of programs used in analysis, enabling reproduction of
results and tracking of provenance in output files.
"""
import os
import contextlib
import subprocess
import sys
import yaml
import toolz as tz
from bcbio import... | Cyberbio-Lab/bcbio-nextgen | bcbio/provenance/programs.py | Python | mit | 11,503 | [
"BWA",
"Bioconductor",
"Galaxy",
"HTSeq"
] | 8c981e51adb526adc6cfa3b624f4a7d40d464367f88e0ac77d7fd2e824393554 |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""The fsl module provides classes for interfacing with the `FSL
<http://www.fmrib.ox.ac.uk/fsl/index.html>`_ command line tools. This
was written to work with FSL version 4.1.4.
Change directory to p... | mick-d/nipype_source | nipype/interfaces/fsl/preprocess.py | Python | bsd-3-clause | 71,199 | [
"Gaussian",
"VTK"
] | 3f593c847210e09129d5648c7bdb24634e564e3e640ae5b5e2baa49696b65bc2 |
"""
A module primarily defining the :class:`~DFFit` class, which brings together :class:`~Data`, :class:`~._Grid`,
:class:`~.selection.Selection` and :class:`~.model.Model` to perform a parameter fit, using the MML method of Obreschkow et al., (2017).
"""
import attr
import numpy as np
from cached_property import cach... | steven-murray/pydftools | pydftools/dffit.py | Python | mit | 39,280 | [
"Galaxy",
"Gaussian"
] | 5af3c8f2eb5791c79026b46a2aaf9af3a05cfbef8b3701d1b99bf10eb87e9947 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | fedepad/espressopp | src/interaction/CoulombKSpaceEwald.py | Python | gpl-3.0 | 5,786 | [
"ESPResSo"
] | bbf5909d48dd0a288b4c5ec627e56238885ee654d31864efabc0b33502daed80 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2016 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kannon92/psi4 | psi4/driver/procedures/mcscf/mcscf_solver.py | Python | gpl-2.0 | 14,357 | [
"Psi4"
] | efa88ea149605512639e79526f45fe246d547e74595dd284ce568dedf20fa6ae |
# -*- coding: utf-8 -*-
"""Infrared intensities"""
import pickle
from math import sin, pi, sqrt, exp, log
from sys import stdout
import numpy as np
import ase.units as units
from ase.io.trajectory import PickleTrajectory
from ase.parallel import rank, barrier, parprint, paropen
from ase.vibrations import Vibration... | askhl/ase | ase/vibrations/infrared.py | Python | gpl-2.0 | 13,001 | [
"ASE",
"Gaussian",
"SIESTA",
"VASP"
] | 14a66d029cedde44bfc0a2c4f8d26117a356300a5cb4ce6d3c2ab2a60759b206 |
#### import the simple module from the paraview
from paraview.simple import *
#### disable automatic camera reset on 'Show'
paraview.simple._DisableFirstRenderCameraReset()
# find source
clip = FindSource('Clip')
# set active source
SetActiveSource(clip)
# find source
contour = FindSource('Contour')
# set active so... | tjcorona/PyFR | pyfr-catalyst/Macros/Preset2.py | Python | bsd-3-clause | 1,197 | [
"ParaView"
] | 2c9954dcbdf01c57149955caacc79d8e92cd41845cb3cebcee79a685b04207eb |
"""
Tests i18n in courseware
"""
import re
from nose.plugins.attrib import attr
from django.conf import settings
from django.contrib.auth.models import User
from django.core.urlresolvers import reverse, NoReverseMatch
from django.test import TestCase
from django.test.client import Client
from dark_lang.models import ... | solashirai/edx-platform | lms/djangoapps/courseware/tests/test_i18n.py | Python | agpl-3.0 | 7,965 | [
"VisIt"
] | 2ef3b18ceffa186458dc844812887ecaf50abe8a49650126a3fee1178ded6587 |
# -*- coding: utf-8 -*-
#Copyright Aksyonov D.A
from __future__ import division, unicode_literals, absolute_import
from operator import itemgetter
import copy, traceback, datetime, sys, os, glob, shutil, re, io, json
from itertools import product
import numpy as np
try:
# pmg config --add VASP_PSP_DIR $VASP_PSP... | dimonaks/siman | siman/calc_manage.py | Python | gpl-2.0 | 141,354 | [
"ABINIT",
"CRYSTAL",
"Jmol",
"LAMMPS",
"VASP",
"phonopy",
"pymatgen"
] | bbb4bfbd4f9932e6af2972b8fc1695a199f1fc3515041144aefeb28eece82730 |
import pysam
import os
import sys
def qi_nr_index (index_info_pair1, index_info_pair2, output):
################################
#declear dictionary to count number of reads for each ref genome in each index file
ref_nr_d = dict()
################################
with open(index_info_pair1,"r") as ... | NIASC/VirusMeta | SAM_BAM/qi_by_index.py | Python | gpl-3.0 | 1,459 | [
"pysam"
] | 7167268e98649dfae6feb824fa6c63194496ce9b806bcd4a280ef412958f1707 |
""" Collection of utilities for finding paths in the CS
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
from urllib import parse
from DIRAC.Core.Utilities import List
from DIRAC.ConfigurationSystem.Client.ConfigurationData import gCo... | ic-hep/DIRAC | src/DIRAC/ConfigurationSystem/Client/PathFinder.py | Python | gpl-3.0 | 10,966 | [
"DIRAC"
] | 60902a8418d9696ec8b306e65a6727157134c0734cf5b3bc1ead026ef51cf7b5 |
# Copyright (C) 2003 CAMP
# Please see the accompanying LICENSE file for further information.
import os
import xml.sax
import re
from cStringIO import StringIO
from math import sqrt, pi
import numpy as np
from ase.data import atomic_names
from ase.units import Bohr, Hartree
from gpaw import setup_paths
from gpaw.spl... | ajylee/gpaw-rtxs | gpaw/setup_data.py | Python | gpl-3.0 | 20,734 | [
"ASE",
"GPAW"
] | 86325910c9ebafa755083117bf50947519bbf6754f96fe9036298fca072d688e |
"""Utilities to assist with commerce tasks."""
from __future__ import absolute_import
import json
import logging
import requests
import six
import waffle
from django.conf import settings
from django.contrib.auth import get_user_model
from django.urls import reverse
from django.utils.translation import ugettext as _
f... | ESOedX/edx-platform | lms/djangoapps/commerce/utils.py | Python | agpl-3.0 | 15,709 | [
"VisIt"
] | 8ba33e9b46cd0348623dd4556a777ffea4141054434a98a7a8680b9583bf155c |
import json
from datetime import datetime
from sqlalchemy import desc
from flask_babel import lazy_gettext
from c3bottles import app, db
from c3bottles.model.category import Category, all_categories
from c3bottles.model.location import Location
from c3bottles.model.report import Report
from c3bottles.model.visit impo... | der-michik/c3bottles | c3bottles/model/drop_point.py | Python | mit | 14,568 | [
"VisIt"
] | d03b3c215e9ffb734c7c05a6d40400e7d8e9fb16b95e8cc726ff82e50f4f4a6d |
"""
Test Help links in LMS
"""
import json
from common.test.acceptance.tests.lms.test_lms_instructor_dashboard import BaseInstructorDashboardTest
from common.test.acceptance.pages.lms.instructor_dashboard import InstructorDashboardPage
from common.test.acceptance.tests.studio.base_studio_test import ContainerBase
fro... | pabloborrego93/edx-platform | common/test/acceptance/tests/lms/test_lms_help.py | Python | agpl-3.0 | 5,325 | [
"VisIt"
] | 05f47c95cce8edf8a6ac60af7bfeddf75e11a305ed18c02a27448947d9cb6f17 |
# -*- coding: utf-8 -*-
# ----------------------------------------------------------------------------
# GPS Tagger.py
#
# Created on: 2017-08-08
# Stephan Garland
# stephan.marc.garland@gmail.com
#
# Captures NMEA outputs from GPS card and allows user comments to be added
# Records Long/Lat and comments in a ... | stephanGarland/gps-point-tagger | GPS Tagger.py | Python | mpl-2.0 | 19,367 | [
"Brian",
"VisIt"
] | 9c79150f803260b3c2f85ad4303f105c31ae2b86bebff319a3cd07b3991ea013 |
import glob
import os
import re
import unittest
import cMarkdown
md = cMarkdown.markdown
class TestMarkdown(unittest.TestCase):
def test_basic_html_rendering(self):
self.assertEqual(md('# Hello, world!\n\nNow is the time for all good men to come to the aid of their party.'),
'<h1>... | paulsmith/cMarkdown | tests/test.py | Python | isc | 4,362 | [
"VisIt"
] | 9a30e4da8483f345f4b084cd9b5d17d424440f6a3deb2d562246f50d479fd789 |
# reinforcementTestClasses.py
# ---------------------------
# Licensing Information: You are free to use or extend these projects for
# educational purposes provided that (1) you do not distribute or publish
# solutions, (2) you retain this notice, and (3) you provide clear
# attribution to UC Berkeley, including a li... | some-un/RLcourse5 | reinforcementTestClasses.py | Python | gpl-3.0 | 43,930 | [
"VisIt"
] | 0ac03fa216706f6461b2fa1c5b4c27ca9fa0158e91d58048490ec01cd712bbae |
#!/usr/bin/env python
# -*- coding: utf8 -*-
"""
This script check that only whitelisted headers are included (transitivly) by
including chemfiles.h or chemfiles.hpp.
"""
from __future__ import print_function
import os
import sys
import re
import codecs
ROOT = os.path.join(os.path.dirname(__file__), "..", "..")
GENERA... | Luthaf/Chemharp | tests/lints/check-public-headers.py | Python | mpl-2.0 | 3,005 | [
"Chemfiles"
] | 0b81698b673d900827ebdebf10a2ad285925ffb2e2ecdd36e8dbd9e112af2e72 |
# -*- coding: utf-8 -*-
#
# Copyright 2012 - 2013 Brian R. D'Urso
#
# This file is part of Python Instrument Control System, also known as Pythics.
#
# Pythics 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 Foundati... | LunarLanding/Pythics | pythics/examples/ODE_solver.py | Python | gpl-3.0 | 6,740 | [
"Brian"
] | f250643b286b85fdf8658b0fb4c0b5cadb461ae5fc9b610bd665d0376d79b5fd |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/bug_1117098 | openlp/core/ui/media/__init__.py | Python | gpl-2.0 | 4,361 | [
"Brian"
] | 77225ebeb0e2e7d0ff6ce86f00b73fcf112fc28a90d2c193a44e8d989e405571 |
'''
jackknife.py
Author: Amanda Buyan
Written: March2013-October2013
Runs an interative jackknife analysis for crossing angle and contacts on a set of TM helix dimer
simulations - see full description below in the main method for a more detailed explanation
'''
import os,sys,MDAnalysis,numpy,shutil,math,multiprocess... | acbuyan/jackknife | jackknife.py | Python | mit | 123,682 | [
"Gromacs",
"MDAnalysis"
] | c5bb1c652fd961020a4a5c33200ce785a814ab75dbb1e5158a6c9a218535a9ae |
''' Controller Code '''
# Python imports
import logging
# AppEngine imports
from google.appengine.runtime import DeadlineExceededError
from google.appengine.runtime.apiproxy_errors import CapabilityDisabledError
# Django imports
from django.http import HttpResponse, HttpResponseRedirect, Http404
from django.contrib... | avastjohn/maventy_new | healthdb/views.py | Python | bsd-3-clause | 29,753 | [
"VisIt"
] | e532773ad9134ff9bc1dddc887acd55071ea3e3423735bbceecebe7c1a10b129 |
#!/usr/bin/env python
"""
The program manual!
"""
import os
import re
import time
from common import *
from compat import ts_to_iso
MAN_NAME = ("""\
pagekite.py - Make localhost servers publicly visible
""")
MAN_SYNOPSIS = ("""\
<b>pagekite.py</b> [<a>--options</a>] [<a>service</a>] <a>kite-name</a> [<a>+flag... | SunilMohanAdapa/pagekite | pagekite/manual.py | Python | agpl-3.0 | 21,926 | [
"VisIt"
] | a91cfade63353689d6191f3b4b31c3af70c337637d7da5a5cc7388d0422946b5 |
class ExampleCtrl2(object):
"""Mealy transducer.
Internal states are integers, the current state
is stored in the attribute "state".
To take a transition, call method "move".
The names of input variables are stored in the
attribute "input_vars".
Automatically generated by tulip.dumpsmach ... | GaloisInc/planning-synthesis | examples/sitl_client/democontroller2new.py | Python | bsd-2-clause | 127,282 | [
"VisIt"
] | 23f07ab762fb78c2645df37d0a985b0dc03d44c2899e4dc56dc680ae7decff52 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module contains classes to wrap Python VTK to make nice molecular plots.
"""
import itertools
import math
import os
import subprocess
import time
import numpy as np
try:
import vtk
from vtk... | davidwaroquiers/pymatgen | pymatgen/vis/structure_vtk.py | Python | mit | 49,468 | [
"Jmol",
"VTK",
"pymatgen"
] | 51ae6d2d8132f03c424cf925df86ebb31f733fd518bf34bf7fef267f7f2a2d69 |
#!/usr/bin/env python
# -*- coding: utf-8 *-*
"""
Module to handle symbols.
"""
import ast
import sys
class SymbolFinder(ast.NodeVisitor):
"""
Utility class that helps find a particular symbol by position (line and
column).
"""
def __init__(self, source):
"""
Initializes the S... | fryntiz/preparar_entorno | conf/home/.ninja_ide/addins/plugins/debugger_plugin/core/symbols.py | Python | gpl-3.0 | 4,009 | [
"VisIt"
] | d2f26762deb1a7da8eea000550e396ff933749b3a122707881cff1a06ddb1beb |
#! /usr/bin/env python
# ==========================================================================
# Shows one or several CTA response functions.
#
# Copyright (C) 2014-2020 Juergen Knoedlseder
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public Licen... | ctools/ctools | examples/show_response.py | Python | gpl-3.0 | 12,103 | [
"Gaussian"
] | 2f3807908adcfe68e9f635ce816df0c4c3809b745f919200d93f1f9a94962c5b |
#
# (c) 2015 Brian Ccoa, <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 License, or
# (at your option) any later versio... | Tatsh-ansible/ansible | lib/ansible/module_utils/api.py | Python | gpl-3.0 | 3,629 | [
"Brian"
] | 7304176748ebf1df3414fee89e74110990dc3909a0c7765ba235c0d00aa4af95 |
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at https://mozilla.org/MPL/2.0/.
import pytest
from functools import partial
import warnings
import numpy as np
from scipy.linalg import block_diag
from... | zerothi/sisl | sisl/physics/tests/test_hamiltonian.py | Python | mpl-2.0 | 68,089 | [
"Gaussian"
] | bdbbd5b5879e9363d6e3ec387818464f6174180e30b1c1b5e865ed99ad826762 |
import unittest
import pysam
from .. import samutil
OPNAMES = "MIDNSH"
OP_LOOKUP = {c: i for i, c in enumerate(OPNAMES)}
S = OP_LOOKUP['S']
M = OP_LOOKUP['M']
I = OP_LOOKUP['I']
D = OP_LOOKUP['D']
class AllPairsIterTestCase(unittest.TestCase):
def test_simple(self):
a = pysam.AlignedRead()
a.se... | fhcrc/prepdrm | python/prep_drm/test/test_samutil.py | Python | gpl-3.0 | 1,954 | [
"pysam"
] | 0db3560aa0fcf95777e4a776d59a77eec56ef7506d2bf679070867760d4f8464 |
import contextlib
import functools
import warnings
import numpy as np
import pandas as pd
from ..plot.plot import _PlotMethods
from . import indexing
from . import groupby
from . import ops
from . import utils
from .alignment import align
from .common import AbstractArray, BaseDataObject, squeeze
from .coordinates i... | drewokane/xray | xarray/core/dataarray.py | Python | apache-2.0 | 48,145 | [
"NetCDF"
] | 3ed36d12e75ae771c1b7826e9572f64fb0821ac6f5eb25abe08800e9cc1f8df2 |
#! /usr/bin/env python
# coding:utf-8
####################################################################
# covconv.py
# covconv for ATOK
# Copyright (c) 2014 mohemohe
#
# this code licensed under the MIT/X11 License .
# please visit ' http://opensource.org/licenses/mit-license.php '.
################################... | mohemohe/covconv-for-ATOK | covconv.py | Python | mit | 3,382 | [
"VisIt"
] | f4bd1df59e34a9c8d715c169655c03a8ea24fd18e845d9c1a18687bd6666a95e |
# -*- coding: utf-8 -*-
############################ Copyrights and license ############################
# #
# Copyright 2012 Christopher Gilbert <christopher.john.gilbert@gmail.com> #
# Copyright 2012 Steve English <steve.english@naveta... | Vagab0nd/SiCKRAGE | lib3/github/Repository.py | Python | gpl-3.0 | 144,275 | [
"Brian"
] | 2326937429af8e12c701604424e2995bc156c04c9c3c4bba021ce1b9f58ab64c |
#!/usr/bin/python
import zmq
import sys
import urllib
import urllib2
import optparse
from multiprocessing import Process
AGENTS = ["MSIE", "Chrome", "Firefox", "Safari", "Opera"]
# The "worker" functions listen on a zeromq PULL connection for "work"
# (URLs to be warmed) from the ventilator, warm those urls for all... | viable-hartman/varnish_cache_warmer | cache_worker.py | Python | mit | 4,468 | [
"VisIt"
] | 57615b51df629d1e0cc5e0ea97617ba0cb06861b74fc01c4a5acc0248c7712d1 |
# 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... | MJJoyce/climate | ocw-cli/cli_app.py | Python | apache-2.0 | 67,674 | [
"NetCDF"
] | 3c228699cc00a8f9815ca4f058105b55ea9528de82e1a79b88d208318a776a8d |
#!/usr/bin/python
# Copyright (c) 2010 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
import glob
import logging
import os
import pyauto_functional # Must be imported before pyauto
import pyauto
class ThemesTest(pyaut... | meego-tablet-ux/meego-app-browser | chrome/test/functional/themes.py | Python | bsd-3-clause | 3,933 | [
"VisIt"
] | f678449e9d83179b8c55c2789f434bd7638a9de67c1084afdf85c4d19abb8cfe |
import datetime
import time
import urlparse
from bs4 import BeautifulSoup
from django.test import TestCase
from django.contrib.auth.models import User, Group
from group_messaging.models import Message
from group_messaging.models import MessageMemo
from group_messaging.models import SenderList
from group_messaging.model... | PearsonIOKI/compose-forum | askbot/deps/group_messaging/tests.py | Python | gpl-3.0 | 16,547 | [
"VisIt"
] | 64043381b31155a6704cbd9be29be90546fd71b690e25f2f4868e29830e077b0 |
import vtkwithexceptions as vtk
def execute(inputs):
tree1 = inputs["tree1"]
tree2 = inputs["tree2"]
filter = vtk.vtkTreeDifferenceFilter()
filter.SetInputDataObject(0, tree1)
filter.SetInputDataObject(1, tree2)
filter.SetIdArrayName("node name")
filter.SetComparisonArrayIsVertexData(True)
filter.Set... | Visomics/Visomics | scripts/CompareTrees.py | Python | apache-2.0 | 567 | [
"VTK"
] | 5e7c885576c44d0b009cc7f6b9ed9717359e98cf6d23907057835e110b04c230 |
# -*- coding=utf-8 -*-
from __future__ import absolute_import, print_function, unicode_literals
from ctypes import c_uint64
import numpy as np
from .utils import CxxPointer, _call_with_growing_buffer
from .ffi import chfl_match
class Selection(CxxPointer):
"""
Select atoms in a :py:class:`Frame` with a sele... | Luthaf/Chemharp-python | chemfiles/selection.py | Python | mpl-2.0 | 2,992 | [
"Chemfiles"
] | da322c334307c34b869b5190ed2b179bfb71fde712e7f76ac5d84c3d3a7241e8 |
try: paraview.simple
except: from paraview.simple import *
paraview.simple._DisableFirstRenderCameraReset()
import os,sys
sys.path.append(os.getcwd())
import ImageGaussianSource
import ImageEllipsoidSource
import PlatonicSolidSource
| jeromevelut/Peavip | Testing/TestSources.py | Python | gpl-3.0 | 235 | [
"ParaView"
] | f6aaafae3413dc097b49136bcc04852f79ff0a0baf1b165e76081644c5ac11d5 |
#!/usr/bin/python
import pytz
import re, sys, os, shutil
from geoip import geolite2
from dateutil import parser
from datetime import datetime
import ConfigParser
from weblog.models import db, Visit, Setting
import gzip
from weblog import app
# From https://github.com/lethain/apache-log-parser/blob/master/apache_pars... | Tethik/apache-web-log | weblog/parser.py | Python | gpl-3.0 | 2,387 | [
"VisIt"
] | 40ca6b7788de905e9d3da77361db41cf3b7c851e99685d10ebbe8b395a3e52e9 |
# -*- coding: utf-8 -*-
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding field 'brands.meta_dias_estoque'
db.add_column(u'salesReport_brands', 'meta_dias_estoque',
... | akiokio/centralfitestoque | src/salesReport/migrations/0032_auto__add_field_brands_meta_dias_estoque__chg_field_item_cmm__chg_fiel.py | Python | bsd-2-clause | 8,916 | [
"VMD"
] | b4595d273fe5055071a599a5d19ea5b85074f1d86122459c3e32690d6286f7e2 |
#
# Copyright 2016, 2020-2021 Lars Pastewka (U. Freiburg)
# 2016 Richard Jana (KIT & U. Freiburg)
#
# 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 Gen... | libAtoms/matscipy | tests/test_spatial_correlation_function.py | Python | lgpl-2.1 | 5,889 | [
"ASE",
"Matscipy"
] | 43af806f2e32551f158d4451297756411cba818e54b87584773e0424b6d16d13 |
import nrrd
import json
import numpy as np
import pickle
import os
from pyemd import emd
from itertools import cycle
import pandas as pd
import scipy.stats as stats
#from scipy.optimize import fsolve
#from scipy.special import iv
#from scipy.special import factorial2, factorial
#from scipy.special import hyp1f1
from ... | kayarre/Tools | process_Distance.py | Python | bsd-2-clause | 24,901 | [
"Gaussian"
] | 488163f6add89290623c8b6c7be1a3f9f061a0f9686eaba301ac2a902dd14958 |
#!/usr/bin/env python2.7
# -*- coding: utf-8 -*-
####################################################################################
### Copyright (C) 2015-2019 by ABLIFE
####################################################################################
########################################################... | ablifedev/ABLIRC | ABLIRC/bin/Clip-Seq/MC/reads_region_cluster.py | Python | mit | 12,394 | [
"HTSeq"
] | d09204557fa80c6b88b3a693a3d845f1b32366dd3f1ad5e9ec4e90a0d9bd0752 |
#!/usr/bin/env python
# ----------------------------------------------------------------------------
# Copyright (c) 2015--, 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.
# ---------------------... | johnchase/q2d2 | setup.py | Python | bsd-3-clause | 2,372 | [
"scikit-bio"
] | 2b650405d91d07591d97a531e368ea4add4955b34dd9035f31c09e603e83c204 |
# Apache HTTP requests manipulation module
import requests
import json
import os
# The REST server url
#REST_URL = 'https://ccdirac06.in2p3.fr:9178'
REST_URL = 'https://dirac.ba.infn.it:9910'
###########################################
# Get the access token first
# GET request parameters
params = {'response_type':'... | SuperDIRAC/TESTDIRAC | sample-script/rest/list_setups.py | Python | gpl-3.0 | 895 | [
"DIRAC"
] | 3121c44ef9a83be368b7315495ce0b5dde4dab0e2c7e6d7868d3d40b049bf1af |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | gregcaporaso/scikit-bio | skbio/diversity/tests/test_util.py | Python | bsd-3-clause | 10,265 | [
"scikit-bio"
] | 71a650ac8b0603f4a393bb0c1b84802c0b57674e0c1b2bb9a7fecec910d64483 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
=================================================================
Iso-probability lines for Gaussian Processes classification (GPC)
=================================================================
A two-dimensional classification example showing iso-probability lines for... | vortex-ape/scikit-learn | examples/gaussian_process/plot_gpc_isoprobability.py | Python | bsd-3-clause | 3,044 | [
"Gaussian"
] | 96f5fcb8c0c8d652621c44caf1eca14c5a5c44b541d1bff9a147183597b3596e |
# -*- coding: utf-8 -*-
import os
import re
import zipfile
from django import forms
from django.conf import settings
from django.core.cache import cache
from django.core.files.storage import default_storage as storage
from django.core.urlresolvers import reverse
from mock import Mock, patch
from nose.tools import eq_... | kumar303/zamboni | mkt/files/tests/test_helpers.py | Python | bsd-3-clause | 10,653 | [
"exciting"
] | f25294851c0cd0d4868aeab859c75dc6b53ee26210dbc1e6c5c0238ff1208571 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""Tests for the Opera browser history parsers."""
from __future__ import unicode_literals
import unittest
from plaso.parsers import opera
from tests.parsers import test_lib
class OperaTypedParserTest(test_lib.ParserTestCase):
"""Tests for the Opera Typed History p... | rgayon/plaso | tests/parsers/opera.py | Python | apache-2.0 | 3,099 | [
"VisIt"
] | e37861f75e8f5aa074000ce8fa73974f88d7e0e7180011f2802e477cfa1cab2d |
''' Step. Steps are included in the workflows, and include modules
'''
import os
import time
import types
import traceback
import sys
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Workflow.Parameter import Parameter, AttributeCollection, ParameterCollection, indent
from DIRAC.Core.Workflow.Module import InstancesP... | Sbalbp/DIRAC | Core/Workflow/Step.py | Python | gpl-3.0 | 17,136 | [
"DIRAC"
] | f6e527d58e16266151795f8f8e2f3955d349ee043bd8aee55a929c79d995485c |
# -*- coding: utf-8 -*-
import numpy as np
import matplotlib.pyplot as plt
# ==========================================
P = 1
w = 0.5
lap = 0.25
N = 50
# ==========================================
def gaussian(dx,dy):
x = np.linspace(-3,3,N)
[X,Y] = np.meshgrid(x+dx,x+dy)
R = np.sqrt(X**2+Y**2)
... | HarrisonKramer/optiland | temp.py | Python | gpl-3.0 | 577 | [
"Gaussian"
] | d0c0dca0f451c4476591115881bd5b3f1ee6ea535bad263d547fbd214f6b2aff |
from django.conf import settings
from django.core import mail
from django.test import RequestFactory
import httpretty
import mock
from oscar.test import factories
from oscar.test.newfactories import BasketFactory
from threadlocals.threadlocals import get_current_request
from ecommerce.core.tests import toggle_switch
f... | mferenca/HMS-ecommerce | ecommerce/extensions/checkout/tests/test_signals.py | Python | agpl-3.0 | 3,857 | [
"VisIt"
] | 03afbec8c6d61130bbfb1c61f814483d8347a8a24baac123f68211e1e9a30c27 |
from __future__ import with_statement
import optparse
import functools
import re
import os
import os.path
import posixpath
try:
from com.xhaus.jyson import JysonCodec as json # jython embedded in buck
except ImportError:
import json # python test case
# TODO(user): upgrade to a jython including os.relpath
def r... | azatoth/buck | src/com/facebook/buck/parser/buck.py | Python | apache-2.0 | 17,946 | [
"ORCA"
] | e38dd8edea6974d859f0199ca8f29233cca7582e7885ffd4dac24576f630e2f8 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | kkreis/espressopp | src/integrator/LangevinBarostat.py | Python | gpl-3.0 | 6,779 | [
"ESPResSo",
"Gaussian"
] | 7d75971ef43a82c88d8d4346ed6e5038b4cb5f34dabcecdcabae15913e7b5c64 |
import os, sys
VERBOSE=False
class Diagram(object):
"""
This class represents a parsed diagram, the methods of this class are used
to extract information of the electronic configuration stored in the class.
It needs to be given upon initializazion a file to read the electronic
structure from. At... | alejandrogallo/show-me-your-electrons | smye/smye.py | Python | mit | 15,214 | [
"VASP"
] | 88c648df8e632b7577f5f079722710acc586c67931ca928a6a9d14e05bff349a |
#!/usr/bin/python
import httplib2
import os
import sys
from apiclient.discovery import build
from oauth2client.file import Storage
from oauth2client.client import flow_from_clientsecrets
from oauth2client.tools import run
from optparse import OptionParser
parser = OptionParser()
parser.add_option("--src", dest="src"... | fearofcode/plcat | plcat.py | Python | mit | 3,773 | [
"VisIt"
] | 18341ab0d54e22741e3fd9fcf7eb273286e095e64243f8b1cba31f8981b25dc6 |
import logging
import numpy as np
import scipy.stats
logger=logging.getLogger(__file__)
def poisson_point_process_2D(lam, bounds):
"""
lam is the intensity.
bounds are (xlow, xhigh, ylow, yhigh).
Used this article.
http://connor-johnson.com/2014/02/25/spatial-point-processes/
"""
N=scipy.s... | adolgert/PyGSPN | gspn/point_process.py | Python | bsd-3-clause | 1,401 | [
"Gaussian"
] | 9f7eeeb375ba95246fe8a60a3565fedeb188772ddcb7db548eea2e63ae9a06f6 |
"""testCount3.py.
Written by: Brian O'Dell, October 2017
A program to run each program a 500 times per thread count.
Then uses the data collected to make graphs and tables that
are useful to evaluate the programs running time.
"""
from subprocess import *
import subprocess
# from numba import jit
# import numpy as n... | brian-o/CS-CourseWork | CS491/PlatformEvaluation/testCount3java.py | Python | gpl-3.0 | 2,887 | [
"Brian"
] | 03e6170bcceb2ae03be988e1309f2c4bdb132226973b3868a9c3dcc087376605 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module provides classes for calculating the ewald sum of a structure.
"""
__author__ = "Shyue Ping Ong, William Davidson Richard"
__copyright__ = "Co... | aykol/pymatgen | pymatgen/analysis/ewald.py | Python | mit | 24,011 | [
"GULP",
"pymatgen"
] | 00232b8ff659cf0b3093408069fd7c80b65f7e4b37f0376ac18dc2305c1e4a19 |
# TODO check num_threads before testing / 8 for Cisco Server
# TODO ATTTENTION! Maybe there are some mistakes in neuron parameters! Write to alexey.panzer@gmail.com.
from func import *
logger = logging.getLogger('neuromodulation')
startbuild = datetime.datetime.now()
nest.ResetKernel()
nest.SetKernelStatus({'overwri... | research-team/NEUCOGAR | NEST/cube/noradrenaline/scripts-2/neuromodulation.py | Python | gpl-2.0 | 16,395 | [
"NEURON"
] | 8f3fbbe0fed45bae1db724cac46b670a3a437671d70ec1bf93aa7c42df0d25df |
from math import sqrt, pi
import numpy as np
from gpaw.setup import create_setup
from gpaw.grid_descriptor import GridDescriptor
from gpaw.localized_functions import create_localized_functions
from gpaw.xc import XC
n = 60#40 /8 * 10
a = 10.0
gd = GridDescriptor((n, n, n), (a, a, a))
c_LL = np.identity(9, float)
a_Lg ... | qsnake/gpaw | gpaw/test/multipoletest.py | Python | gpl-3.0 | 1,278 | [
"GPAW"
] | 6e63bd53af5ce3048e213a9e606a6a2f4a27460718b960a33b731593e8d7a389 |
from common import Modules, load_yara_rules, PEParseModule, ModuleMetadata
from string import printable
from struct import unpack
class PoisonIvy(PEParseModule):
first_value_table = None
precomputed_list = None
def __init__(self):
md = ModuleMetadata(
module_name="poisonivy",
... | bwall/bamfdetect | BAMF_Detect/modules/poisonivy.py | Python | mit | 6,655 | [
"Brian"
] | ee0dfa5ccdd41f7cf91a4d77ad6d2f43c788dd7d08432fded7fc23658b4ea832 |
"""
This module gathers tree-based methods, including decision, regression and
randomized trees. Single and multi-output problems are both handled.
"""
# Authors: Gilles Louppe <g.louppe@gmail.com>
# Peter Prettenhofer <peter.prettenhofer@gmail.com>
# Brian Holt <bdholt1@gmail.com>
# Noel Da... | 0asa/scikit-learn | sklearn/tree/tree.py | Python | bsd-3-clause | 31,479 | [
"Brian"
] | ab89ef7a9d5fcc4c58fd6684dd8e8d55659c80f5e48f5fb76f48f94909d6bde4 |
# Copyright 2008, 2009 CAMd
# (see accompanying license files for details).
"""Definition of the Atoms class.
This module defines the central object in the ASE package: the Atoms
object.
"""
import numbers
import warnings
from math import cos, sin
import copy
import numpy as np
import ase.units as units
from ase.a... | andrew031191/pyneb | atoms.py | Python | lgpl-3.0 | 60,427 | [
"ASE"
] | bd3b210a9bef604999d44ed4b5dd695ad63fa454b0570c14145b90a2e70f2f03 |
def load_parameters():
"""
Loads the defined hyperparameters
:return parameters: Dictionary of loaded parameters
"""
# Input data params
TASK_NAME = 'my_task' # Task name
DATASET_NAME = TASK_NAME # Dataset name
SRC_LAN = 'fr' ... | lvapeab/nmt-keras | examples/configs/config_rnn.py | Python | mit | 22,888 | [
"Gaussian"
] | 427ff36da35005c0058bbb261de120f6241d703d03affb8b24229aa7a43468fb |
"""
Statistical tools for time series analysis
"""
from statsmodels.compat.python import (iteritems, range, lrange, string_types, lzip,
zip, map)
import numpy as np
from numpy.linalg import LinAlgError
from scipy import stats
from statsmodels.regression.linear_model import OLS, yule_walk... | hlin117/statsmodels | statsmodels/tsa/stattools.py | Python | bsd-3-clause | 37,127 | [
"ADF"
] | 675ded71bdfa52fa4343c07a47ea254e521e4d0fd0210fca2cb8bb27a299809d |
""" MPF plugin for a score controller which handles all scoring and bonus
tracking."""
# scoring.py
# Mission Pinball Framework
# Written by Brian Madden & Gabe Knuth
# Released under the MIT License. (See license info at the end of this file.)
# Documentation and more info at http://missionpinball.com/mpf
import log... | spierepf/mpf | mpf/system/scoring.py | Python | mit | 4,646 | [
"Brian"
] | 51fb104a8d3c7b25f259e263d99758482684a6b6bab9cad2f054bb8bd5c490b0 |
# Copyright 2012 Nebula, Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agree... | zouyapeng/horizon-newtouch | horizon/base.py | Python | apache-2.0 | 36,170 | [
"VisIt"
] | 88c69f92e4ee295909a8bf1757415c5b3face91955b0edf0b3b2cc49925c2223 |
#! /usr/bin/env python
import rospy, math
import sys, termios, tty, select, os
from geometry_msgs.msg import Twist
from std_msgs.msg import UInt16
import sys
from geometry_msgs.msg import Point, Pose, Quaternion, Twist, Vector3
import signal
from GestureModel import*
from Creator import*
from Classifier import*
from nu... | enriquecoronadozu/HMPy | src/ros_modificar/test_demo.py | Python | gpl-3.0 | 4,078 | [
"Gaussian"
] | aa37499e14745419dbbaad9b07fe6564b0dd326629efe512141b25d49824558a |
from clisn import loads, loads_file
ALL_TYPES = set([
"trailer", "name", "literal",
"binop", "unop", "assign",
"suite", "xexpr"
])
def _check_lisn_validity(lisn):
if not isinstance(lisn, dict):
raise ValueError("LISN object should be a dict object")
_type = lisn['type']
if 'type' not ... | Algy/tempy | lisn/utils.py | Python | apache-2.0 | 3,792 | [
"VisIt"
] | 70c9724e01330f18aa13431287f4c1b2b4e0893739cdb14c509a429ffd3662e1 |
""" The POOL XML File module provides a means to extract the GUID of a file or list
of files by searching for an appropriate POOL XML Catalog in the specified directory.
"""
import os
import glob
import tarfile
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Resources.Catalog.PoolXMLCatalog import PoolXMLCatal... | DIRACGrid/DIRAC | src/DIRAC/Resources/Catalog/PoolXMLFile.py | Python | gpl-3.0 | 4,872 | [
"DIRAC"
] | d0b7d1c04074321a8a1b23bd30fb3c057d7eb85c693a92b1c59798b9a8e14cbd |
# Copyright (c) 2005 Gavin E. Crooks <gec@compbio.berkeley.edu>
#
# This software is distributed under the MIT Open Source License.
# <http://www.opensource.org/licenses/mit-license.html>
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentat... | JohnReid/bioinf-utilities | python/corebio/seq.py | Python | mit | 22,295 | [
"Biopython"
] | fa136c00af3f6db63014dc33b973f9037a173bfda72de72c66d57710c80bc9fb |
## @package mumax2_cmp
# This file contains function to set initial field given a array (with grid-size and cell-size already set up)
import os
import json
import png
import re
import sys
import math
from mumax2 import *
regionNameDictionary = {'empty':0.}
regionDefinition = [[]]
regionInitialised = False
## Sets ... | mumax/2 | src/python/mumax2_cmp.py | Python | gpl-3.0 | 22,057 | [
"Gaussian"
] | d9229c051ede82600c76f2425b9b5785af6fdcaa22b4d5e45df12472a9fb6032 |
from __future__ import print_function, division, absolute_import
import numpy as np
import mdtraj as md
__all__ = ['map_drawn_samples']
def map_drawn_samples(selected_pairs_by_state, trajectories, top=None):
"""Lookup trajectory frames using pairs of (trajectory, frame) indices.
Parameters
----------
... | rmcgibbo/msmbuilder | msmbuilder/utils/draw_samples.py | Python | lgpl-2.1 | 2,656 | [
"MDTraj"
] | 655c422cdf7939ca09421da786c2322bfd103efed60d515d6bbf1e2174e4ac2c |
#
# @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
#... | rmcgibbo/psi4public | psi4/driver/procrouting/dft_funcs/libxc_xc_funcs.py | Python | lgpl-3.0 | 11,911 | [
"Psi4"
] | 2160e2f17787e823287d1c414b9e60fa75055ea9e69ddec3b231e11b69c6f999 |
# ICanHasCheezBurger Random Lol XBMC Plugin
# Based on Dan Dare's Comics.com plugin
#
# Modified from the original Comics.com plugin
# by Brian Millham <brian@millham.net>
#
# Imports
#
import sys
import xbmcgui
import xbmcplugin
import urllib
import xbmcaddon
__settings__ = xbmcaddon.Addon(id='plugin.pictures.ican... | bmillham/plugin.pictures.icanhascheezburger.com | resources/lib/current_cheez_selection.py | Python | gpl-3.0 | 2,444 | [
"Brian"
] | 80b56732e9b06e146f11b4c8b799458eac1bc107b8b99c01f3e1270b62a2d817 |
import pyspeckit
import numpy as np
from pyspeckit.spectrum.models import inherited_voigtfitter
# technically, the voigt fitter works as a singlefitter (i.e., you can fit the
# background level and the peak simultaneously)
# in practice, however, you need to fit the background independently except for
# gaussians. I... | vlas-sokolov/pyspeckit | examples/multivoigt.py | Python | mit | 2,418 | [
"Gaussian"
] | 998e935ae3b38945fb6385289642747fbf4c32a2afd26fc031f10ecba0aa6951 |
from neuron import *
from nrn import *
def clear_neuron():
print(' - Clearing NEURON contents...')
h('forall delete_section()')
print(' - Cleared NEURON contents...')
h('topology()')
def replace_brackets(ref):
return ref.replace('[', '_').replace(']', '')
def get_cell_name(nrn_section_name, c... | rgerkin/pyNeuroML | pyneuroml/neuron/nrn_export_utils.py | Python | lgpl-3.0 | 1,514 | [
"NEURON"
] | 1f46b133bbf501d214fce9081a1ac13682fd0eed1abe3af513e9b952b3309781 |
#!/usr/bin/env python
import numpy as np
"""
Bayesian Block implementation
=============================
Dynamic programming algorithm for finding the optimal adaptive-width histogram.
Based on Scargle et al 2012 [1]_
References
----------
.. [1] http://adsabs.harvard.edu/abs/2012arXiv1207.5578S
"""
class Fitness... | KeltyAllen/Amazon-Reviews-Project | BayesianBlocks.py | Python | mit | 11,813 | [
"Gaussian"
] | 95a5ceec6ee8dd41ab7e64dc6eba1b1dd33cc2b9eb7a465adc43c83139d5aa65 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
import sys
import argparse
def read_fasta_file_handle(fasta_file_handle):
"""
Parse a fasta file and return a generator
"""
# Variables initialization
header = ''
seqlines = list()
sequence_nb = 0
# Reading input file
for line in fast... | ppericard/matamog | scripts/compute_assembly_stats.py | Python | agpl-3.0 | 9,759 | [
"BLAST"
] | 3907748151c257332c228051aad7da3864cf242f87476b55ee7b953e6efa9180 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2016 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kannon92/psi4 | psi4/driver/qcdb/dbproc.py | Python | gpl-2.0 | 3,968 | [
"Psi4"
] | 485d571c5b7040bb8d6499096e9c1e3c94659fa1d42ffe54f891575d0b4d2ab8 |
""" Affine image registration module consisting of the following classes:
AffineMap: encapsulates the necessary information to perform affine
transforms between two domains, defined by a `static` and a `moving`
image. The `domain` of the transform is the set of points in the
`static` image'... | nilgoyyou/dipy | dipy/align/imaffine.py | Python | bsd-3-clause | 57,192 | [
"Gaussian"
] | 4d91afffff3d957ca30c5511845d82e74b32db8908cb37c38fa227cf7df2a76e |
import theano.tensor as TT
import numpy as np
from rllab.distributions.base import Distribution
class DiagonalGaussian(Distribution):
def __init__(self, dim):
self._dim = dim
@property
def dim(self):
return self._dim
def kl_sym(self, old_dist_info_vars, new_dist_info_vars):
o... | brain-research/mirage-rl-qprop | rllab/distributions/diagonal_gaussian.py | Python | mit | 3,610 | [
"Gaussian"
] | dc87a1a7ac886cc6c665e4dc58362ef621f91b64be0a56899ca64f495e02c412 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Christian Schwantes
# Contributors: Robert McGibbon
#
# MDTraj... | mattwthompson/mdtraj | mdtraj/geometry/contact.py | Python | lgpl-2.1 | 13,200 | [
"MDTraj"
] | f3e66f5649c7324342ce2e2954bcd24145eac51c3f127fe4166de058ae4d8c9a |
# -*- coding: utf-8 -*-
#
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publ... | thica/ORCA-Remote | src/scripts/tools/tool_wikidocgit/script.py | Python | gpl-3.0 | 7,602 | [
"ORCA"
] | 7005cb5797515f32e37dbf54fd7524231a759b73eed679b96ae2e3a06784adfc |
# tasks.py (contains classes for various playfield devices)
# Mission Pinball Framework
# Written by Brian Madden & Gabe Knuth
# Released under the MIT License. (See license info at the end of this file.)
# Documentation and more info at http://missionpinball.com/mpf
import logging
from copy import copy
import time
i... | spierepf/mpf | mpf/system/tasks.py | Python | mit | 9,550 | [
"Brian"
] | 9c1ee9cc2dbd014ae1ba45a50c20ee79ca24936eba65dca3c5113135fc1ad2ef |
import os.path
import unittest
from unittest import mock
import vcr
import mopidy_soundcloud
from mopidy.models import Track
from mopidy_soundcloud import Extension
from mopidy_soundcloud.soundcloud import SoundCloudClient, readable_url
local_path = os.path.abspath(os.path.dirname(__file__))
my_vcr = vcr.VCR(
se... | mopidy/mopidy-soundcloud | tests/test_api.py | Python | mit | 10,194 | [
"BLAST"
] | 26da51834cc9008179eff006f1af708c4022f88a7e315b7f2cbfb0f5dc7608d5 |
import numpy as np
from ase import Atoms
from ase.io import write, read
from ase.test import NotAvailable
a = 5.0
d = 1.9
c = a / 2
atoms = Atoms('AuH',
positions=[(c, c, 0), (c, c, d)],
cell=(a, a, 2 * d),
pbc=(0, 0, 1))
extra = np.array([ 2.3, 4.2 ])
atoms.set_array("extra",... | slabanja/ase | ase/test/io.py | Python | gpl-2.0 | 2,042 | [
"ASE",
"NetCDF"
] | 3141c91ba40a0456ae7e26cb4f402e2cc58597feb3121dcbbd3128f9995a8250 |
#!/usr/bin/env python
"""Utility functions that can be used in multiple scripts."""
# Core Library modules
import csv
import logging
import os
import shutil
import tarfile
import tempfile
from typing import Any, Dict, List, Optional, Tuple
# Third party modules
import h5py
import numpy as np
import yaml
# First par... | MartinThoma/nntoolkit | nntoolkit/utils.py | Python | mit | 7,505 | [
"NEURON"
] | d3501452039278753c57b7f9525f841b074e5d3d1c8adf812877e44c8495db7a |
'''
Created on Jun 2, 2011
@author: mkiyer
chimerascan: chimeric transcript discovery using RNA-seq
Copyright (C) 2011 Matthew Iyer
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3... | madhavsuresh/chimerascan | chimerascan/deprecated/sam_v1.py | Python | gpl-3.0 | 8,725 | [
"pysam"
] | 7daa1970d23f3dda5f3e07d1ef0f46121aec1e32cd38ce0d1db34d4ad813ab8a |
########################################################################
#
# (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 ... | romain-dartigues/ansible | lib/ansible/cli/galaxy.py | Python | gpl-3.0 | 33,051 | [
"Galaxy"
] | 5072897f42ff65edc413b192e65aa28e7dcafd3372dda1fc1476464376478c01 |
########################################################################
# File : ModuleFactory.py
# Author : Stuart Paterson
########################################################################
""" The Module Factory instantiates a given Module based on a given input
string and set of arguments to be pas... | DIRACGrid/DIRAC | src/DIRAC/Core/Utilities/ModuleFactory.py | Python | gpl-3.0 | 1,860 | [
"DIRAC"
] | b468d2f27c21e6c66b581fb18a7cba92df384fe76fd0327998ff89eb2425367e |
from paraview import servermanager
from paraview import simple as smp
from paraview import smtesting
# Make sure the test driver know that process has properly started
print "Process started"
def getHost(url):
return url.split(':')[1][2:]
def getPort(url):
return int(url.split(':')[2])
def runTest():
opti... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/Applications/ParaView/Testing/Python/TestCompositedGeometryCulling.py | Python | gpl-3.0 | 976 | [
"ParaView"
] | 3aa761ebc871f12e787f0a5358c916402d871f4e17fb828848d98d055ed45a01 |
# -*- coding: utf-8 -*-
#
# test_multiple_synapses.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the ... | lekshmideepu/nest-simulator | testsuite/pytests/test_multiple_synapses.py | Python | gpl-2.0 | 19,022 | [
"Gaussian"
] | 0a099c9d6b955567037ec4cb72ed3bf14177b009454fc8edd6bec6139c30261d |
import numpy as np
import scipy
from collections import Counter
from . import process_objects
from . import misc
class QuadraticBMAOptimizer(process_objects.EnrichedQuadraticBMAProcess):
def __init__(self,
ndim,
kernel_type='Gaussian',
kernel_prior_type='Gamma',
... | altaetran/bayesianoracle | build/lib/bayesianoracle/optimizer.py | Python | apache-2.0 | 19,248 | [
"Gaussian"
] | f31e7d4fa0328e5ca5cb01724d2605baf3882df13cefa8b4f6ae6c9720c3eeb5 |
# coding: utf-8
"""
Vericred API
Vericred's API allows you to search for Health Plans that a specific doctor
accepts.
## Getting Started
Visit our [Developer Portal](https://developers.vericred.com) to
create an account.
Once you have created an account, you can create one Application for
Production and an... | vericred/vericred-python | vericred_client/models/rating_area.py | Python | apache-2.0 | 12,602 | [
"VisIt"
] | b272229f5aa816397098ba62da1b7072ecea4f521e49ceaac25c9a6aacb7f077 |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
from pyscf import gto
from pyscf import scf, dft
'''
As a Python script, you can use any Python trick to create your calculation.
In this example, we read the molecule geometry from another file.
'''
mol = gto.Mole()
mol.verbose = 5
mol.atom = ope... | gkc1000/pyscf | examples/scf/10-glycine.py | Python | apache-2.0 | 439 | [
"PySCF"
] | 02ca007730a63a3ead41584541dd4ce1c6c98b19570f65e043f6e21d6cb4c9cd |
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