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#!/usr/bin/env python -i
# preceeding line should have path for Python on your machine
# viz_pymol.py
# Purpose: viz running LAMMPS simulation via PyMol
# Syntax: viz_pymol.py in.lammps Nfreq Nsteps
# in.lammps = LAMMPS input script
# Nfreq = dump and viz shapshot every this many steps
# Ns... | slitvinov/lammps-sph-multiphase | python/examples/viz_pymol.py | Python | gpl-2.0 | 1,874 | [
"LAMMPS",
"PyMOL"
] | 9f41969562cda3ceda62589cefc8a68af4030eb552290073d1ab6a508884f5a0 |
#
# Author: Travis Oliphant 2002-2011 with contributions from
# SciPy Developers 2004-2011
#
from __future__ import division, print_function, absolute_import
import warnings
from scipy.special import comb
from scipy.misc.doccer import inherit_docstring_from
from scipy import special
from scipy import optim... | felipebetancur/scipy | scipy/stats/_continuous_distns.py | Python | bsd-3-clause | 119,828 | [
"Gaussian"
] | bdcd2fb237df0904845c90e816dc8c7ee9f2131dd3ededc05dea8b6d5f6d52a9 |
import unittest
import os
import warnings
import json
from sympy import Number, Symbol
from pymatgen.analysis.surface_analysis import SlabEntry, SurfaceEnergyPlotter, \
NanoscaleStability, WorkFunctionAnalyzer
from pymatgen.util.testing import PymatgenTest
from pymatgen.entries.computed_entries import ComputedStr... | dongsenfo/pymatgen | pymatgen/analysis/tests/test_surface_analysis.py | Python | mit | 23,554 | [
"pymatgen"
] | 465a0bf0cc1795ab552a517d08fe8618f39d4107adb7f43a963cad569b79d22b |
#! /usr/bin/python
"""versioneer.py
(like a rocketeer, but for versions)
* https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Version: 0.7+
This file helps distutils-based projects manage their version number by just
creating version-control tags.
For developers who work from a V... | htygithub/bokeh | versioneer.py | Python | bsd-3-clause | 25,745 | [
"Brian"
] | 4dbcd0d1a24b9ce40a18a281d096f086557192eb160aafddae0805b581d9b2f2 |
import glob
import pandas as pd
import numpy as np
pd.set_option('display.max_columns', 50) # print all rows
import os
os.chdir("/gpfs/commons/home/biederstedte-934/evan_projects/correct_phylo_files")
normalB = glob.glob("binary_position_RRBS_normal_B_cell*")
mcell = glob.glob("binary_position_RRBS_NormalBCD19pCD27... | evanbiederstedt/RRBSfun | trees/chrom_scripts/normal_chr05.py | Python | mit | 25,843 | [
"MCell"
] | 9f5cbdb6b6871cf850a2bc563197f96c545addb5d44cf9f6cf553085080b0845 |
__author__ = "Sunil Kumar (kumar.sunil.p@gmail.com)"
__copyright__ = "Copyright 2014, Washington University in St. Louis"
__credits__ = ["Sunil Kumar", "Steve Pieper", "Dan Marcus"]
__license__ = "XNAT Software License Agreement " + \
"(see: http://xnat.org/about/license.php)"
__version__ = "2.1.1"
__main... | MokaCreativeLLC/XNATSlicer | XNATSlicer/XnatSlicerLib/utils/Timer.py | Python | bsd-3-clause | 4,718 | [
"VTK"
] | ad2652286b06195f42d717ba5c5f90780131a8e0ea1be0fe018aac6a0c8caf48 |
from .generic import ObsIO
import numpy as np
import pandas as pd
import xarray as xr
class NcObsIO(ObsIO):
"""ObsIO to read observations from a local NetCDF store created by ObsIO.to_netcdf
"""
def __init__(self, fpath, elems):
"""
Parameters
----------
fpath : str
... | jaredwo/obsio | obsio/providers/netcdf.py | Python | gpl-3.0 | 2,227 | [
"NetCDF"
] | 421ee90bc798ae0764d930d9859aa79b09bc81763b4c8e5d81fe074eb39004b8 |
# -*- Mode: Python; coding: utf-8; indent-tabs-mode: nil; tab-width: 4 -*-
### BEGIN LICENSE
# Copyright (C) 2013 Brian Douglass bhdouglass@gmail.com
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License version 3, as published
# by the Free Soft... | bhdouglass/remindor-common | remindor_common/dbus_service.py | Python | gpl-3.0 | 2,729 | [
"Brian"
] | 563c183139a7187dbbcb74cd810d85fbc3f8870b97c48b9c422a7f41c616e0cd |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2002-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2011 Tim G L Lyons
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publ... | beernarrd/gramps | gramps/gen/filters/rules/citation/__init__.py | Python | gpl-2.0 | 2,223 | [
"Brian"
] | ee9248ce75ea925fe6731afa1f403ffde13ef8862ab9991d5bc7be166600442b |
import sys, shutil
sys.path.insert(1, "../../../")
import h2o
import random
def milsong_checkpoint(ip,port):
milsong_train = h2o.upload_file(h2o.locate("bigdata/laptop/milsongs/milsongs-train.csv.gz"))
milsong_valid = h2o.upload_file(h2o.locate("bigdata/laptop/milsongs/milsongs-test.csv.gz"))
distribution... | weaver-viii/h2o-3 | h2o-py/tests/testdir_algos/gbm/pyunit_milsongs_largeGBM.py | Python | apache-2.0 | 1,982 | [
"Gaussian"
] | e6700394557860e8132f756632881a2119ab541c1184394baf7dcbb9b449ac75 |
# Copyright (c) 2015, Frappe Technologies Pvt. Ltd. and Contributors
# MIT License. See license.txt
from __future__ import unicode_literals
import frappe
import unittest
from bs4 import BeautifulSoup
import re
from frappe.utils import set_request
from frappe.website.render import render
from frappe.utils import random... | adityahase/frappe | frappe/website/doctype/blog_post/test_blog_post.py | Python | mit | 3,774 | [
"VisIt"
] | bd92984b2bc19e3725910ea0c3269dc34883899565cbe4c37cf6e25978bd7c99 |
import os
import unittest
from custodian.vasp.validators import VasprunXMLValidator, VaspFilesValidator, \
VaspNpTMDValidator
test_dir = os.path.join(os.path.dirname(__file__), "..", "..", "..",
'test_files')
cwd = os.getcwd()
class VasprunXMLValidatorTest(unittest.TestCase):
def tes... | xhqu1981/custodian | custodian/vasp/tests/test_validators.py | Python | mit | 2,302 | [
"VASP"
] | 2d69c5a9042c73ce4865f1c107e311f9bbc6a3d4bc9add6f6989a4d70d8dc7ca |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
import subp... | nuclear-wizard/moose | python/TestHarness/tests/test_Recover.py | Python | lgpl-2.1 | 1,329 | [
"MOOSE"
] | 8e1875258afb7ad9f6c3bc7ef1e8263dc363287e93a415b5a4ff604b2fbf0fca |
#-----------------------------------------------------
# Author: Yaqiang Wang
# Date: 2014-12-27
# Purpose: MeteoInfo Dataset module
# Note: Jython
#-----------------------------------------------------
from org.meteoinfo.data.meteodata import MeteoDataType
from ucar.ma2 import DataType
from ucar.nc2 import Att... | meteoinfo/meteoinfolab | pylib/mipylib/dataset/dimdatafile.py | Python | lgpl-3.0 | 24,253 | [
"NetCDF"
] | d6c2a0d6d1903c2612901cdadce04af274bfb8b28da5808e445fd2255ceee08a |
#!/usr/bin/env python
# Convert DES_BCC Galaxy catalogs (Risa Wechler et al.) to a Root tree
import os
import argparse
import numpy as np
from astropy.io import fits
from root_numpy import array2root
parser= argparse.ArgumentParser(description="Convert a DES_BCC Galay Catalog (fits) into a Root tree")
parser.add_ar... | boutigny/GPU4Cosmo | util/readCat.py | Python | gpl-2.0 | 1,897 | [
"Galaxy"
] | d0e85151c53dbfcd5cf4a3b0f793f577147d105dde7adf59b0143625d92a7422 |
# Copyright (C) 2016 The BET Development Team
# -*- coding: utf-8 -*-
import numpy as np
from dolfin import *
from meshDS import meshDS
from projectKL import projectKL
from poissonRandField import solvePoissonRandomField
import scipy.io as sio
import sys
def computeSaveKL(numKL):
'''
++++++++++++++++ Steps i... | smattis/BET-1 | examples/FEniCS/Compute_Save_KL.py | Python | gpl-3.0 | 2,350 | [
"Gaussian"
] | 000781159459b815d5687737d4d70af64be7ee1028842cdfdda10a633a148e0e |
"""
Pydwolla is a client library for Dwolla's API version 2. By using Pydwolla, you can
do Dwolla things like register new user, add bank account, or transfer funds.
For more information, visit https://github.com/roycehaynes/pydwolla
Author: Royce, royce.haynes@gmail.com
Publish Date: 01 Jul 2013
Reference(s):
... | roycehaynes/pydwolla | dwolla/__init__.py | Python | bsd-3-clause | 12,175 | [
"VisIt"
] | 70d656c5d6a8a2bc4a611117940bc9963e2487971a37020edebe2f2c1584cf1f |
# TODO
# * default settings for color and rep
# * make the final viewing step a function
# * setup_map(name,levels=,colors=,reps=)
import pymol
from pymol import headering
import Pmw
import Tkinter as TK
import os
import string
class PyMOLMapLoad:
def __init__(self,parent,app,f):
self._parent = paren... | gratefulfrog/lib | python/pmg_tk/PyMOLMapLoad.py | Python | gpl-2.0 | 15,967 | [
"PyMOL"
] | 30ec8d0005a8c3852108d18cdeb9a4ab2ae265fa222ca54c58266be625e9781f |
# Licensed under an MIT open source license - see LICENSE
"""
Utility functions for fil-finder package
"""
import itertools
import numpy as np
from scipy import optimize as op
import thread
import threading
import time
import os
def removearray(l, arr):
'''
Removes an array from a list. Code from
http... | keflavich/fil_finder | fil_finder/utilities.py | Python | mit | 5,115 | [
"Gaussian"
] | e5927f1c17b40e8b0b6a1c0fd607daa1e55c5a015ba00289afdcdd42d07070b7 |
# -*- coding: utf-8 -*-
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
This package defines the astrophysics-specific units. They are also
available in the `astropy.units` namespace.
"""
from . import si
from astropy.constants import si as _si
from .core import (UnitBase, def_unit, si_prefixes,... | stargaser/astropy | astropy/units/astrophys.py | Python | bsd-3-clause | 7,750 | [
"Dalton"
] | df0d564a9a79b30f97724c0935e4f4c87d1c0f0898a8a271b9ed6f8bb500b298 |
"""
This class builds the structure of k-knights and chessboard
"""
from libs.graph.Graph import GraphAdjacenceList
class Knight:
def __init__(self, x, y, k):
"""
This class builds up the knight whit its attributes and methods.
@param x: int, the row position in chessboard
@param y... | IA-MP/KnightTour | libs/structure.py | Python | mit | 20,687 | [
"VisIt"
] | dac81dee13135fc75ed9a4ad12e72d1b4b5b2392e44c62eaf4980727c4101e04 |
#!/usr/bin/python
import os, sys, string, anydbm
from low import *
from orthomcl import OrthoMCLCluster
# =============================================================================
def usage():
print >> sys.stderr, "add significant BLAST hits (e.g. in-paralogs) to an existing orthomcl cluster.\n"
print >> sys.... | lotharwissler/bioinformatics | python/orthomcl/add-blasthits-to-cluster.py | Python | mit | 2,938 | [
"BLAST"
] | c53dd5a392f196dff3dd772814c9bb7142190148d8051ec7791ecf9724d9c168 |
from toee import *
from utilities import *
from batch import *
from itt import *
from math import sqrt, atan2
import _include
from co8Util.PersistentData import *
## Contained in this script
TS_CRITTER_KILLED_FIRST_TIME = 504 # KOS monster on Temple Level 1
TS_EARTH_CRITTER_KILLED_FIRST_TIME = 505 # Ro... | GrognardsFromHell/TemplePlus | tpdatasrc/co8fixes/scr/py00439script_daemon.py | Python | mit | 95,140 | [
"CRYSTAL"
] | ecf650f2a991aef93f8db5ceea1854ae81ae5c0ca7dbfd1fba73169e44cdf484 |
import glob
import MDAnalysis as MDA
import numpy
#targets = glob.glob('../CSAR_FULL_RELEASE_29NOVEMBER2012/*/SETUP_DOCKING_FILES/PROTEIN_ALONE/*pdb')
targets = glob.glob('../CSAR_FULL_RELEASE_29NOVEMBER2012/*/SETUP_DOCKING_FILES/COMPLEX/*pdb')
for target in targets:
print target
for rotation in range(5):
... | j-wags/POVME | POVME/tests/surf_area/rotateProteins.py | Python | gpl-3.0 | 706 | [
"MDAnalysis"
] | 248d6d8abafe83cd9ff13570f079d6bdce81024d2965063bd5126230b1057966 |
# Copyright (C) 2003-2005 Peter J. Verveer
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following d... | ygenc/onlineLDA | onlineldavb_new/build/scipy/scipy/ndimage/filters.py | Python | gpl-3.0 | 40,022 | [
"Gaussian"
] | 213975213fff1dc4539db294aa976777fc87a5355388a7cc1ba3e1a447d385cc |
from __future__ import division
from builtins import range
import os
import numpy as np
import numpy.random as npr
from matplotlib import pyplot as plt
plt.ion()
npr.seed(0)
import pyhsmm
###############
# load data #
###############
data = np.loadtxt(os.path.join(os.path.dirname(__file__),'example-data.txt'))[:12... | mattjj/pyhsmm | examples/animation.py | Python | mit | 1,424 | [
"Gaussian"
] | 47eef1e81b52394d7b72443acfbe05984b3284457ad31bef090492ff09a67721 |
#
# Copyright (c) 2015, Daniel Guterding <guterding@itp.uni-frankfurt.de>
#
# This file is part of dhva.
#
# dhva 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 ... | danielguterding/dhva | scripts/fs3d.py | Python | gpl-3.0 | 2,660 | [
"Mayavi"
] | 6a2f9c41c0a63adce80918c203f801ce3b74cf26690d62a7bd98385b663c793f |
# Computes the gaussian gradients on a boxm_alpha_scene
import bvpl_octree_batch;
import os;
import optparse;
bvpl_octree_batch.register_processes();
bvpl_octree_batch.register_datatypes();
class dbvalue:
def __init__(self, index, type):
self.id = index # unsigned integer
self.type = type # string
p... | mirestrepo/voxels-at-lems | bvpl/bvpl_octree/gauss_gradient_to_binary.py | Python | bsd-2-clause | 1,608 | [
"Gaussian"
] | e07582b93a692833caf8383a931dc059df75543e015588cd992a050845a601a6 |
#Translates DNA sequences in all 6 reading frames, ignoring start / stop codons.
from Bio import SeqIO
from Bio.Seq import Seq
from Bio import AlignIO
import sys
import tempfile
import subprocess
from collections import Counter
from scipy.spatial import distance
import numpy as np
import os
def translate_6frames(inpu... | alexcritschristoph/VICA | marker_genes/meta_marker.py | Python | gpl-2.0 | 5,461 | [
"BLAST"
] | 36ef5f3b0dbeb67e1c3c7100980bc5a71df8cf637b6b48b5f42be78910b88120 |
#! /usr/bin/env python
# Hi There!
# You may be wondering what this giant blob of binary data here is, you might
# even be worried that we're up to something nefarious (good for you for being
# paranoid!). This is a base64 encoding of a zip file, this zip file contains
# a fully functional basic pytest script.
#
# Pyt... | bonzanini/luigi-slack | runtests.py | Python | mit | 237,463 | [
"ASE"
] | 34a36f79008b10ef9f08cbf1e9efdd4df3285989c543cd4727eae3c30ebd4b55 |
##
# Copyright 2013 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
# the Hercules foundation (http://w... | hajgato/easybuild-easyblocks | easybuild/easyblocks/d/dl_poly_classic.py | Python | gpl-2.0 | 2,190 | [
"DL_POLY"
] | a636f4fd1ab5508bda7748d45171ad984463199f411684d44413148df44afe53 |
from math import pi, sqrt
import numpy as np
from ase.atoms import Atoms
from gpaw.aseinterface import GPAW
from gpaw.wavefunctions.base import WaveFunctions
from gpaw.atom.radialgd import EquidistantRadialGridDescriptor
from gpaw.utilities import unpack
from gpaw.utilities.lapack import general_diagonalize
from gpaw... | robwarm/gpaw-symm | gpaw/atom/atompaw.py | Python | gpl-3.0 | 10,523 | [
"ASE",
"GPAW"
] | bb5a0f48640dffd17c28f2acf01de35ffe2fae4d0505c87406c03f9dd9f398f7 |
import numpy as np
import tensorflow as tf
from backend.networks import Model
#import backend.visualizations as V
from backend.simulation_tools import Simulator
import matplotlib.pyplot as plt
# Builds a dictionary of parameters that specifies the information
# about an instance of this specific task
def set_params... | davidbrandfonbrener/Project-Sisyphus | tasks/n_fixed_points.py | Python | mit | 9,304 | [
"NEURON"
] | 7f00954b655d1d1fba029fcaedf8732264c8b2eacfe5ce6d01b789a5ea307fd5 |
#!/usr/bin/env python
# tests the support to pass generic vertex attributes to be used in Cg shaders.
xmlMaterial = '<?xml version="1.0" encoding="UTF-8"?> \
<Material name="GenericAttributes1"> \
<Shader \
scope="Vertex" \
name="VertexShader" \
location="Inline" \
language="Cg" \
entry="main"> \... | collects/VTK | Rendering/Core/Testing/Python/TestGenericVertexAttributesCg.py | Python | bsd-3-clause | 2,663 | [
"VTK"
] | d2ee702c4bd9d98f823448156daeeec989f1cc7421584d061dd86fe921dc4141 |
# Principal Component Analysis Code :
from numpy import mean,cov,double,cumsum,dot,linalg,array,rank,size,flipud
from pylab import *
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import ro... | tapomayukh/projects_in_python | sandbox_tapo/src/skin_related/BMED_8813_HAP/Features/multiple_features/results/cross_validate_objects_BMED_8813_HAP_scaled_method_II_area_shape.py | Python | mit | 3,997 | [
"Mayavi"
] | 53f8bc6c0eda35b0f7deb49ce75ad665585432fb6568b929f04f1f60c66907fd |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#... | MDAnalysis/mdanalysis | testsuite/MDAnalysisTests/lib/test_distances.py | Python | gpl-2.0 | 62,939 | [
"MDAnalysis"
] | eb5e922bec38e5fe33cbc5d3b74ccb310e007a14d0d855c27e11f47d12e7b0ed |
"""Simple XML-RPC Server.
This module can be used to create simple XML-RPC servers
by creating a server and either installing functions, a
class instance, or by extending the SimpleXMLRPCServer
class.
It can also be used to handle XML-RPC requests in a CGI
environment using CGIXMLRPCRequestHandler.
A list ... | alanjw/GreenOpenERP-Win-X86 | python/Lib/SimpleXMLRPCServer.py | Python | agpl-3.0 | 26,475 | [
"Brian"
] | 2790f1e0a63974e4d777596e3cc0f5ac06a2bad3d35436ee640e5249c39e3938 |
# Copyright (c) 2015, Frappe Technologies Pvt. Ltd. and Contributors
# License: GNU General Public License v3. See license.txt
from __future__ import unicode_literals
import frappe
import json
import frappe.utils
from frappe.utils import cstr, flt, getdate, comma_and, cint
from frappe import _
from frappe.model.mapper... | gangadharkadam/saloon_erp_install | erpnext/selling/doctype/sales_order/sales_order.py | Python | agpl-3.0 | 16,677 | [
"VisIt"
] | 9f2b6f7dade695e31476ca129762fef1947ce1e9aac217a3254e55090a3715a7 |
# -*- coding: utf-8 -*-
"""
***************************************************************************
GrassAlgorithm.py
---------------------
Date : August 2012
Copyright : (C) 2012 by Victor Olaya
Email : volayaf at gmail dot com
************************... | AsgerPetersen/QGIS | python/plugins/processing/algs/grass/GrassAlgorithm.py | Python | gpl-2.0 | 22,802 | [
"NetCDF"
] | 3c01b62e53977f5b5f90a87b07e2cb580847713bfd3541b2b59a1f2a74f2d620 |
"""
@package medpy.filter.image
Filters for multi-dimensional images.
These filter rely heavily on and are modelled after the scipy.ndimage package.
@author Oskar Maier
@version d0.2.0
@since 2013-11-29
@status Development
"""
# build-in module
import itertools
# third-party modules
import numpy
from scipy.ndimage.... | kleinfeld/medpy | medpy/filter/image.py | Python | gpl-3.0 | 14,384 | [
"Gaussian"
] | fbfd48c8d7bdb4b1c7a2a000cde82ddd57749fffc34219fcca411547d8e494f3 |
from django.test import TestCase
from django.contrib.auth.models import User
from txtalert.apps.googledoc.models import SpreadSheet, GoogleAccount
from txtalert.apps.googledoc.importer import Importer
from txtalert.apps.googledoc.reader.spreadsheetReader import SimpleCRUD
from txtalert.core.models import Patient, MSISD... | praekelt/txtalert | txtalert/apps/googledoc/_tests/importer.py | Python | gpl-3.0 | 20,734 | [
"VisIt"
] | e5c3b2f5fc9bb68ba285e5e996a4dc1841ce01dac438799341477951aab379e9 |
#!/usr/bin/env python
description = """
This produces a bam file corresponding to junctional regions in a given gtf file
"""
import sys
import pysam
from pythomics.genomics.parsers import GFFReader
from pythomics.templates import CustomParser
parser = CustomParser(description = description)
parser.add_bam()
parser.a... | pandeylab/pythomics | scripts/junctionalReads.py | Python | gpl-3.0 | 2,928 | [
"pysam"
] | c793193147a5e1bff7cf29782de379f98797e92cab3a49fc38ce6236c0b4a2f1 |
# Version: 0.11
"""
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, and pypy
[]... | ibest/grcScriptsPy | versioneer.py | Python | apache-2.0 | 35,320 | [
"Brian"
] | 3750378e1371ae9f66e0c2393f462a6061e8351ed5ad145aed577fcb4740d862 |
# Copyright (c) Twisted Matrix Laboratories.
# See LICENSE for details.
from __future__ import division, absolute_import
import sys
import traceback
from zope.interface import implementer
from twisted.python.compat import _PY3
from twisted.python.failure import Failure
from twisted.trial import util
from twisted.tr... | geodrinx/gearthview | ext-libs/twisted/trial/test/test_pyunitcompat.py | Python | gpl-3.0 | 9,130 | [
"VisIt"
] | 3121efdffa76f41059f39029fd0f807343f0bef2d271715abc2497acafee55c0 |
import datetime
import unittest
from decimal import Decimal
from pheme.longitudinal.tables import create_tables
from pheme.longitudinal.tables import AdmissionSource, AssignedLocation
from pheme.longitudinal.tables import AdmissionTemp, AdmissionO2sat
from pheme.longitudinal.tables import ChiefComplaint, FluVaccine, H... | pbugni/pheme.longitudinal | pheme/longitudinal/tests/test_tables.py | Python | bsd-3-clause | 12,281 | [
"VisIt"
] | f007fcaa0d2536f9b3bad7f9de47ced8ad6cd79da31c85e5d0175c2fadd8450b |
from neuron import h
from nrn import *
load_hoc_obj=h
#self.hoc_obj.execute('load_file("'+str(self.model)+'")')
#self.hoc_obj.execute('load_file("stdrun.hoc")')
load_hoc_obj.load_file(str("hh_pas.hoc"))
load_hoc_obj.load_file("stdrun.hoc")
#self.vec=h.Vector
load_vec=load_hoc_ob... | KaliLab/optimizer | optimizer/new_test_files/hh_pas_surrogate/hoc_load.py | Python | lgpl-2.1 | 331 | [
"NEURON"
] | f907b49322b6bd02a2e4c3da5351dab8fbbd3c128cad48caafad2d6405818c55 |
#!/usr/bin/env python
import argparse
import json
import logging
import os
import eutils
logging.basicConfig(level=logging.INFO)
if __name__ == '__main__':
parser = argparse.ArgumentParser(description='EFetch', epilog='')
parser.add_argument('db', help='Database to use, sometimes "none" (e.g. *check)')
... | galaxyproject/tools-iuc | tools/ncbi_entrez_eutils/elink.py | Python | mit | 5,682 | [
"Biopython"
] | fd642e451798238ec51bc1032dbd009ee6dceabfd0d6fd35dbed97f1974c4ef2 |
###############################################################################
##
## Copyright (C) 2014-2016, New York University.
## Copyright (C) 2011-2014, NYU-Poly.
## Copyright (C) 2006-2011, University of Utah.
## All rights reserved.
## Contact: contact@vistrails.org
##
## This file is part of VisTrails.
##
## ... | minesense/VisTrails | vistrails/core/system/__init__.py | Python | bsd-3-clause | 14,635 | [
"VTK"
] | f8047cdfa55a7575fffe8b7d090b30223d18a40fc7b3d51ad61a188214ecd6f1 |
"""Unit tests for the VTK io library"""
# Copyright (C) 2011 Garth N. Wells
#
# This file is part of DOLFIN.
#
# DOLFIN is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either version 3 of the License, ... | akshmakov/Dolfin-Fijee-Fork | test/unit/io/python/vtk.py | Python | lgpl-3.0 | 6,797 | [
"VTK"
] | 5be5135dcf328b11ed04894c3c4e48f6e817aff35724f5d18ad88ed72316dea3 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes to identify optimal substrates for film growth
"""
import warnings
from pymatgen.analysis.interfaces import SubstrateAnalyzer, ZSLGenerator # noqa
__author__ = "Shyam Dwaraknath"
__copyrigh... | materialsproject/pymatgen | pymatgen/analysis/substrate_analyzer.py | Python | mit | 707 | [
"pymatgen"
] | 2f1daf6029c67a1cae685976d2e04bd52f23885ed9790af11ea06e3915dfbc60 |
from __future__ import print_function
import logging
from datetime import datetime
import barotropic
import interpolation as interp
import numpy as np
from netCDF4 import Dataset, date2num
import IOinitial
import IOsubset
import IOwrite
import datetimeFunctions
import forcingFilenames as fc
import interp2D
try:
... | trondkr/model2roms | model2roms.py | Python | mit | 23,882 | [
"NetCDF"
] | a4995442fc60bfb77e7fd60de771fdfd3d8539c80c1a4d2f1d7b54d445297fd9 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2005,2006 Async Open Source
##
## 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 Foundation; either version 2
## of the Licens... | andrebellafronte/stoq | stoqlib/database/exceptions.py | Python | gpl-2.0 | 1,470 | [
"VisIt"
] | cd7526f2ffd89c44d752ce28c2aaedc3e0d5c3ee6ec2619dcf449ae6556abb75 |
"""Reading raw data
This file holds all functions necessary to read in information
and data to run the energy demand model.
"""
import os
import csv
import math
import logging
from collections import defaultdict
import fiona
import pandas as pd
from shapely.geometry import shape, mapping
import numpy as np
from ruamel... | nismod/energy_demand | energy_demand/read_write/read_data.py | Python | mit | 44,047 | [
"BLAST"
] | ff12ea2af6d8b2d8b42ab4cd38e6288e7fae2218335317e350bb5061d9476396 |
# 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... | junghans/espressopp | src/analysis/PressureTensorMultiLayer.py | Python | gpl-3.0 | 3,826 | [
"ESPResSo"
] | 39d88df03615d31f290c6866108a5d1f449b98214e26406b83be5962182a8b30 |
# This file is part of Androguard.
#
# Copyright (c) 2012 Geoffroy Gueguen <geoffroy.gueguen@gmail.com>
# 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://... | 0x0mar/androguard | androguard/decompiler/dad/writer.py | Python | apache-2.0 | 25,568 | [
"VisIt"
] | 498fa6ced781605fc751daac5457c3a06f96b3c1bf3f18551631712c66cc66a0 |
from compiler import *
####################################################################################################################
# Each quest record contains the following fields:
# 1) Quest id: used for referencing quests in other files. The prefix qst_ is automatically added before each quest-id.
# 2) ... | Ikaguia/LWBR-WarForge | module_quests.py | Python | unlicense | 16,618 | [
"VisIt"
] | 604308b2a3231f4defc550600762fef6292c6a7911f154621c2a18281417d7bb |
# -*- coding: utf-8 -*-
#
# gPodder - A media aggregator and podcast client
# Copyright (c) 2005-2011 Thomas Perl and the gPodder Team
#
# gPodder 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... | elelay/gPodderAsRSSReader | src/gpodder/gui.py | Python | gpl-3.0 | 207,780 | [
"VisIt"
] | 573b6f37bf03de8af9ea222ef53f42884904ccf8011d5b353145c6a5ba8e9323 |
##############################################################################
# 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... | msultan/mdtraj | mdtraj/geometry/tests/test_distance.py | Python | lgpl-2.1 | 7,022 | [
"MDTraj"
] | 6a981dc3b747cc3d8b0588f69c71a943f492cb6b70fc302c990e528641668593 |
#!/usr/bin/env python
# file exclude_seqs_by_blast.py
from __future__ import division
"""
A lightweight script for BLASTing one or more sequences against a number of BLAST databases, and returning FASTA files a) of the results that did match b) of the results that didn't match c) raw blast results and also d) ret... | wasade/qiime | qiime/exclude_seqs_by_blast.py | Python | gpl-2.0 | 11,970 | [
"BLAST"
] | 93f49b030712d14251a9919cf86b1b070dfb5cd5b23626e163705473f4e997bd |
# Copyright 2017 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... | xodus7/tensorflow | tensorflow/python/autograph/converters/return_statements.py | Python | apache-2.0 | 11,029 | [
"VisIt"
] | e8ea2abdafcade9ffff580f2dd9f20746c3f297bf161c390be0f1ac3b103a1d0 |
import pytest
from numpy.testing import assert_array_equal
from landlab import RasterModelGrid
from landlab.io.netcdf import from_netcdf, to_netcdf
@pytest.mark.parametrize("include", ((), [], set(), None))
def test_include_keyword_is_empty(tmpdir, format, include):
grid = RasterModelGrid((4, 3), xy_spacing=(2, ... | cmshobe/landlab | tests/io/netcdf/test_from_netcdf.py | Python | mit | 2,314 | [
"NetCDF"
] | 29f1beeb0292b9fc4d13cde88f857719b88b4fba64909aa9ac0e43ada819c472 |
r"""
File I/O (:mod:`skbio.io`)
==========================
.. currentmodule:: skbio.io
This package provides I/O functionality for skbio.
Supported file formats
----------------------
For details on what objects are supported by each format,
see the associated documentation.
.. currentmodule:: skbio.io.format
.. au... | demis001/scikit-bio | skbio/io/__init__.py | Python | bsd-3-clause | 7,513 | [
"scikit-bio"
] | fd8f6a5d14513c92bd631845700f4ceb1e1d140302332528b5c287425537e6c6 |
# ----------------------------------------------------------------------------------------------------
#
# Copyright (c) 2007, 2012, Oracle and/or its affiliates. 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... | md-5/jdk10 | src/jdk.internal.vm.compiler/.mx.graal/sanitycheck.py | Python | gpl-2.0 | 21,104 | [
"VisIt"
] | 9ed7cbeeb8dc23ab1420e0f160c790f247ce9fa360fb934b016c54436663e56c |
#!/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/fci/direct_spin0.py | Python | apache-2.0 | 17,952 | [
"PySCF"
] | fc29905e8145713cb701089a7bfc56c3934c58ecafb12dc4e606cfa52ac42d5b |
import lxml.objectify
import httplib
import urlparse
from utils.dates import *
from feeds import InvalidFeed
__all__ = ('ParseError', 'InvalidFeed', 'from_string', 'from_url', 'from_file', 'parse_date')
# TODO: change the feeds to a registration model
from feeds.atom10 import Atom10Feed
from feeds.rss20 import RSS20... | dcramer/feedreader | feedreader/parser.py | Python | bsd-2-clause | 2,172 | [
"NetCDF"
] | 07357ed5c4a9f115ed5474cf5395f31254568c344556e465e102eb96938e9262 |
from django.conf import settings
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.PDB import *
from Bio.PDB.PDBIO import Select
from common.definitions import *
from protein.models import Protein, ProteinSegment
from residue.models import Residue
from structure.functions import BlastSearch... | cmunk/protwis | structure/assign_generic_numbers_gpcr.py | Python | apache-2.0 | 11,967 | [
"BLAST"
] | 2739927a73889126f66d77f73d66f192834ada318ba50acf26714ca2cc5ff1f5 |
"""
This file implements a brew resolver for Galaxy requirements. In order for Galaxy
to pick up on recursively defined and versioned brew dependencies recipes should
be installed using the experimental `brew-vinstall` external command.
More information here:
https://github.com/jmchilton/brew-tests
https://github.com... | ssorgatem/pulsar | galaxy/tools/deps/resolvers/homebrew.py | Python | apache-2.0 | 1,947 | [
"Galaxy"
] | f5edfdedb55f01c32131dd9339ac363a62afe21cad23b2f0fdcf87b66edfffcc |
'''
Created on 2012-11-10
@author: Andre R. Erler
'''
## imports
from numpy import array, arange, zeros, diff
import os
import re
# netcdf stuff
from netcdf import Dataset, add_coord, copy_dims, copy_ncatts, copy_vars
# data root folder
from socket import gethostname
hostname = gethostname()
if hostname=='komputer':... | aerler/WRF-Tools | Python/archive/avgWRF_1979-1981.py | Python | gpl-3.0 | 8,576 | [
"NetCDF"
] | 7d154a2bacd0dcc112fe9ec8be8615391c300203db857f1ce74f3a460188fd89 |
"""
DIRAC Logger client
"""
import sys
import traceback
import inspect
import DIRAC
from DIRAC.FrameworkSystem.private.logging.LogLevels import LogLevels
from DIRAC.FrameworkSystem.private.logging.Message import Message
from DIRAC.Core.Utilities import Time, List
from DIRAC.Core.Utilities.ReturnValues import isRet... | Andrew-McNab-UK/DIRAC | FrameworkSystem/private/logging/Logger.py | Python | gpl-3.0 | 12,267 | [
"DIRAC"
] | 72475ca84d2ba0ee05790e6fbad0855f5f5feb6c1431be67f874788cde38f94b |
from setuptools import setup
pypi_classifiers = [
'Programming Language :: Python :: 3',
"Development Status :: 4 - Beta",
"Environment :: Console",
"Operating System :: OS Independent",
'Intended Audience :: Science/Research',
'Natural Language :: English',
'Topic :: Scientific/Engineering... | Adamtaranto/mimeo | setup.py | Python | mit | 1,464 | [
"Biopython"
] | 8bca96f31dff1742edef4fdd436aef5b016e7f6a180d4a597102ef16c3466801 |
# coding=utf-8
# Copyright 2022 The Google Research Authors.
#
# 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 applicab... | google-research/google-research | jaxnerf/nerf/utils.py | Python | apache-2.0 | 15,504 | [
"Gaussian"
] | 83fd35577594eb0e49e0d167ac82ee1cc5500314cb3c6784c5188b28a495100e |
#!/usr/bin python3.5
"""
Provide code and solution for Application 4
"""
import math
import random
import matplotlib.pyplot as plt
# import alg_project4_solution as student
import matrix_and_alignment_func as student
# URLs for data files
PAM50 = "alg_PAM50.txt"
HUMAN_EYELESS = "alg_HumanEyelessProtein.txt"
FRUITFLY... | MohamedAbdultawab/FOC_RiceUniv | algorithmic-thinking-2/module-4-project-and-application/02_application-4-applications-to-genomics-and-beyond/alg_application4_provided.py | Python | gpl-3.0 | 6,270 | [
"Firefly"
] | 9f33510bb5b6c3456fdf4c53cc8b49c8a017851975962ff67ec2098a1a7b2ade |
#!/usr/bin/env python
import os
import sys
import numpy as np
import argparse as arg
from datetime import datetime
from collections import OrderedDict
import QM_parser.parser as parser
def checkfile(filename):
if not os.path.isfile(filename):
# print(banner(text='ERROR', ch='#', length=80))
prin... | dpadula85/ExSPy | dev/Opts.py | Python | gpl-3.0 | 14,029 | [
"Gaussian"
] | 34b53b96712030b701ed4de3b9b813470fc32bf1a07b83f52252b947b856cc05 |
#!/usr/bin/env python
"""
refguide_check.py [OPTIONS] [-- ARGS]
Check for a Scipy submodule whether the objects in its __all__ dict
correspond to the objects included in the reference guide.
Example of usage::
$ python refguide_check.py optimize
Note that this is a helper script to be able to check if things ar... | e-q/scipy | tools/refguide_check.py | Python | bsd-3-clause | 32,497 | [
"Gaussian"
] | 2dff2f49a0e300881713380beb79ef2ce784f610ace56f43fd6b1ccd5b30dd1c |
# -*- coding: utf-8 -*-
#
# CampbellSiegert.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License... | INM-6/nest-git-migration | pynest/examples/CampbellSiegert.py | Python | gpl-2.0 | 5,481 | [
"NEURON"
] | 07bdb7c828eea20746dd2c925711ea7fc3edda2f316cbbfc343247a91f524df0 |
import numpy as np, os, glob
from astropy.table import Table, vstack, join
from astropy.coordinates import SkyCoord
from astropy import units as u
from astropy.stats import sigma_clipped_stats
from scipy.interpolate import interp1d, interp2d, RegularGridInterpolator
from scipy.sparse import lil_matrix, save_npz
from... | FRBs/FRB | frb/halos/photoz.py | Python | bsd-3-clause | 26,428 | [
"Galaxy"
] | 74f083d90c5200688a09f87bbc3906ee2f3e32cada60ad97c073fc6e83b5f2b2 |
import numpy as np
from ase.io import read as aseread
import networkx as nx
import itertools
import pandas as pd
from bokeh import palettes
import matplotlib.pyplot as plt
from fundef import atoms_to_nxgraph, minimal_cycles, cycle_dual_graph
########################################################################
###... | marcocaccin/Glass_Cycle_Network | src/at_cycles.py | Python | gpl-2.0 | 4,063 | [
"ASE"
] | b8931d772b881aee108eb74b87aa91bfe4df6717220686a5c099e45dff61b8c1 |
#! /usr/bin/python
# -*- coding: utf-8 -*-
"""
Module is used for visualization of segmentation stored in pkl file.
"""
from loguru import logger
# logger = logging.getLogger()
# from PyQt4.QtCore import Qt
import argparse
import numpy as np
from dicom2fem import seg2fem
import io3d
import dicom2fem
from imtools.imag... | mjirik/lisa | lisa/convert.py | Python | bsd-3-clause | 3,272 | [
"VTK"
] | 6dde82f6ae482a7519eed65140440cc5afdc825b0a1aba69e8ec318ee98a47ed |
"""
Two-dimensional pattern generators drawing from various random distributions.
$Id$
"""
__version__='$Revision$'
import numpy
from numpy.oldnumeric import zeros,floor,where,choose,less,greater,Int,random_array
import param
from param.parameterized import ParamOverrides
from patterngenerator import PatternGener... | ioam/svn-history | imagen/random.py | Python | bsd-3-clause | 8,904 | [
"Gaussian"
] | 9d38a6d2f465729f0d51ea95a4b26d6e458522f93876402ba846bfb4e018f9d1 |
# $Id: test_MurckoScaffold.py 3672 2010-06-14 17:10:00Z landrgr1 $
#
# Created by Peter Gedeck, June 2008
#
from rdkit.Chem.Scaffolds.MurckoScaffold import *
import unittest
import random
from rdkit import Chem
class TestCase(unittest.TestCase):
testMolecules = [
("CC1CCC1", "C1CCC1"),
("NCNCC2CC2C1CC1O", "... | adalke/rdkit | rdkit/Chem/Scaffolds/test_MurckoScaffold.py | Python | bsd-3-clause | 27,412 | [
"RDKit"
] | 670a4b621447c891faf1b23403e4b0f5a202fcebaf259f0481c58452c06d65f8 |
import math
import sys
def validate_image_equality(image_1_path, image_2_path, max_delta):
import pyrap.images as pim
# get the difference between the two images
print("comparing images from paths:")
print(image_1_path)
print(image_2_path)
im = pim.image('"{0}" - "{1}"'.format(image_1_path, im... | kernsuite-debian/lofar | CEP/Pipeline/test/regression_tests/selfcal_imager_pipeline_test.py | Python | gpl-3.0 | 19,176 | [
"Gaussian"
] | 487a143301d6f451c8044c5ffa0885ef06edcb3e96382e8e733f6ace67889d2e |
#! usr/bin/sh
# -*- coding:utf8 -*-
# randomQuizGenerator.py - Create quizzes with questions and answers in
# random order , along with thw answer key
import random
# The quiz data. Keys are states and values are their capitals.
capitals = {'Alabama': 'Montgomery', 'Alaska': 'Juneau', 'Arizona': 'Phoenix',
'Arkansas':... | liuyepiaoxiang/es6-learning | 032-python/chap2/project-8.0/randomQuizGenerator.py | Python | mit | 2,905 | [
"COLUMBUS"
] | ed97e1080eb0abe63d06782fe03a68beb6acb2e0599068a5933dbd1dd2b51396 |
"""A component that allows one to place colored and scaled glyphs at
input point data.
"""
# Author: Prabhu Ramachandran <prabhu_r@users.sf.net>
# KK Rai (kk.rai [at] iitb.ac.in)
# R. Ambareesha (ambareesha [at] iitb.ac.in)
# Copyright (c) 2005-2007, Enthought, Inc.
# License: BSD Style.
# Enthought li... | dmsurti/mayavi | mayavi/components/glyph.py | Python | bsd-3-clause | 11,129 | [
"Mayavi",
"VTK"
] | 91108bc1ed9b9dc223065926d2bc9e806c2f7952e6bb396ac7900693f255c25f |
# Import our awesome modules.
import numpy as np
import matplotlib.pyplot as plt
import seaborn
import glob
# Image processing modules.
import skimage.io
import skimage.filters
import skimage.measure
import skimage.segmentation
# Here's what we've done so far.
im = skimage.io.imread('data/lacI_titration/O2_delta_phas... | RPGroup-PBoC/gist_pboc_2017 | code/inclass/project_part3_in_class.py | Python | mit | 4,078 | [
"Gaussian"
] | d7189efbe1207d6fe1a8523ec91fd0cfe5de5136423668500ed514884eea1a36 |
""" core implementation of testing process: init, session, runtest loop. """
import re
import py
import pytest, _pytest
import os, sys, imp
try:
from collections import MutableMapping as MappingMixin
except ImportError:
from UserDict import DictMixin as MappingMixin
from _pytest.runner import collect_one_node... | jessekl/flixr | venv/lib/python2.7/site-packages/_pytest/main.py | Python | mit | 25,584 | [
"VisIt"
] | adb076fa259e8f6a56c7f6321638655ed90c0ed918a2971392a53cca9210d0c8 |
#
# Copyright (C) 2013-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | mkuron/espresso | testsuite/python/widom_insertion.py | Python | gpl-3.0 | 4,391 | [
"ESPResSo"
] | a41482d3fcdc418a38f1cfc6617fb7e2ce16d3da404bc625493f4580e213bc1a |
""" Accounting reporter
"""
import hashlib
import re
from DIRAC import S_OK, S_ERROR, gConfig
from DIRAC.Core.Utilities.ObjectLoader import loadObjects
from DIRAC.ConfigurationSystem.Client.PathFinder import getServiceSection
from DIRAC.AccountingSystem.private.Policies import gPoliciesList
from DIRAC.AccountingSystem... | DIRACGrid/DIRAC | src/DIRAC/AccountingSystem/private/MainReporter.py | Python | gpl-3.0 | 2,673 | [
"DIRAC"
] | 7a7a2373b871054514b3f73f714946324694b8d04e5b7ad32ce755fa29a5f760 |
# -*- coding: UTF-8 -*-
from __future__ import division
import numpy as np
import pandas as pd
import sys
import math
import re
from scipy import stats
class ConfidenceInterval(object):
def getPercentageForConfidenceInterval(self, # three things we can measure
N_sample=... | pligor/predicting-future-product-prices | 00_skroutz_import/confidence_interval.py | Python | agpl-3.0 | 3,044 | [
"Gaussian"
] | a9eccbec0c44014b1c2cdc9bee21d3c84d149f17c346bf998611790f60e37cb1 |
#!/usr/bin/env python
"""
Time decoding algorithms that make use of the integrate-and-fire
neuron model and the trigonometric polynomial approximation.
- iaf_decode - IAF time decoding machine.
- iaf_decode_pop - MISO IAF time decoding machine.
"""
# Copyright (c) 2009-2015, Lev Givon
# All rights ... | bionet/ted.python | bionet/ted/iaf_trig.py | Python | bsd-3-clause | 6,764 | [
"NEURON"
] | 27784c72d90ef73466ff63c71784c0ed9e1fe117bae6d9c7278e0e7a0e4a6cd0 |
# Author: Robert McGibbon <rmcgibbo@gmail.com>
# Contributors:
# Copyright (c) 2014, Stanford University and the Authors
# All rights reserved.
# -----------------------------------------------------------------------------
# Imports
# -----------------------------------------------------------------------------
from ... | msultan/msmbuilder | msmbuilder/example_datasets/met_enkephalin.py | Python | lgpl-2.1 | 2,514 | [
"MDTraj",
"OpenMM"
] | e9f793a2c1b597039ea11811f6b31c05a6ea8b85e96410f38a5be7dcaee920dd |
import nest
import nest.raster_plot
import numpy as np
import pylab as pl
nest.ResetKernel()
nest.SetKernelStatus({"overwrite_files": True})
sim_time = 0.
weight = []
if (not 'bcpnn_dopamine_synapse' in nest.Models()):
#nest.Install('ml_module')
nest.Install('/media/backup/temp_milner/save/17.10.14/modu... | pierreberthet/local-scripts | reduce_dopa.py | Python | gpl-2.0 | 4,102 | [
"NEURON"
] | eff669daa805400b7b992294a65cd8bf9fe9db9d3b96dee806103f12bb115322 |
#!/usr/bin/env python
#pylint: disable=missing-docstring
#################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment #
# #... | Chuban/moose | python/chigger/tests/exodus/blocks/none.py | Python | lgpl-2.1 | 1,177 | [
"MOOSE"
] | 6a3c9ab2eccba905e693492c47560fc066a5e8d3d23181ea2366cabc84fb6ad1 |
# Copyright 2007 Google Inc.
# Licensed to PSF under a Contributor Agreement.
"""Unittest for ipaddress module."""
import unittest
import re
import contextlib
import operator
import ipaddress
class BaseTestCase(unittest.TestCase):
# One big change in ipaddress over the original ipaddr module is
# error rep... | PennartLoettring/Poettrix | rootfs/usr/lib/python3.4/test/test_ipaddress.py | Python | gpl-2.0 | 74,848 | [
"FEFF"
] | d778f3e7b798c7a8349e9bb8d2bc4466158d3d2943eae852b86ce3f441c1a1c1 |
"""Code for converting notebooks to and from the v2 format.
Authors:
* Brian Granger
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2008-2011 The IPython Development Team
#
# Distributed under the terms of the BSD License. The full license is in
# the file COP... | noslenfa/tdjangorest | uw/lib/python2.7/site-packages/IPython/nbformat/v3/convert.py | Python | apache-2.0 | 1,966 | [
"Brian"
] | c92c616d309b814bb46ff4b8d9fc7fd5168d1c0ee37b4013511f4de52c61335d |
#-*- coding: iso-8859-15 -*-
# SADR METEOLLSKY
# http://www.sadr.fr
# SEBASTIEN LECLERC 2017
# Inspired by :
# NACHO MAS 2013
# http://induino.wordpress.com
# Config file
##### INDI RELATED #####
#To start indiserver use 'localhost'
#otherwise not start and connect remote
#indiserver
#INDISERVER="localhost"
INDISERVE... | broadcastyourseb/SADR | raspberry/allskySCRIPT/dev/meteollskyconfig.py | Python | apache-2.0 | 1,549 | [
"VisIt"
] | 6db2a662bec179d318d8b914d3f50490cce89aa15d895c3236993a385808ed4e |
# Copyright (c) 2001 Autonomous Zone Industries
# This file is licensed under the
# GNU Lesser General Public License v2.1.
# See the file COPYING or visit http://www.gnu.org/ for details.
__revision__ = "$Id: __init__.py,v 1.2 2002/12/02 19:58:54 myers_carpenter Exp $"
| zooko/egtp_new | egtp/crypto/__init__.py | Python | lgpl-2.1 | 280 | [
"VisIt"
] | 8363443d689a0d249f8cc0e69fa4fac53a1b3c6512583356698b7500536b3613 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | e-gob/plataforma-kioscos-autoatencion | scripts/ansible-play/.venv/lib/python2.7/site-packages/ansible/modules/network/avi/avi_gslbapplicationpersistenceprofile.py | Python | bsd-3-clause | 3,659 | [
"VisIt"
] | 7489335b8957769e7e2b5c0b159a09a5686d3024de695fe45cd4773e76f81607 |
import tornado.ioloop, tornado.web
from tornado.httpserver import HTTPServer
from drenaj.client.config.config import *
from drenaj.client.frontend.routes_config import routes_config
from jinja2 import Environment, FileSystemLoader
import drenaj.utils.drnj_time as drnj_time
application = tornado.web.Application(route... | boun-cmpe-soslab/drenaj | drenaj/client_startup.py | Python | mit | 6,386 | [
"VisIt"
] | 2f9587cd96a5d015e010a215ccd4c5005c153eb6e1adaf5939d67116e2e24ff3 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 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/lib/test/test_formatters.py | Python | gpl-2.0 | 3,551 | [
"VisIt"
] | aae6e8708e562a9f938fbb196ffaefd866bf6f5f2dc7154ce6a864a5a0729abc |
# -*- coding: utf-8 -*-
"""Test sequences for graphiness.
"""
# Copyright (C) 2004-2013 by
# Aric Hagberg <hagberg@lanl.gov>
# Dan Schult <dschult@colgate.edu>
# Pieter Swart <swart@lanl.gov>
# All rights reserved.
# BSD license.
from collections import defaultdict
import heapq
import networkx as nx
_... | KNMI/VERCE | verce-hpc-pe/src/networkx/algorithms/graphical.py | Python | mit | 12,990 | [
"Brian"
] | 95ac421862d267ac17d54abed2216a7b85aad7248fa9dfb8fac300a3aad26b26 |
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