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# -*- coding: utf-8 -*-
# Copyright 2009 James Hensman and Michael Dewar
# Licensed under the Gnu General Public license, see COPYING
import numpy as np
import sys
sys.path.append('../src')
from pyvb import nodes,Network
def PCA_missing_data(plot=True):
#Principal Component Analysis, with randomly missing data
q = 2... | jameshensman/pyvb | examples/PCA_missing_data.py | Python | gpl-3.0 | 3,264 | [
"Gaussian"
] | 905b65c0c64a26bb697c65d26f7a0de86df1c75c0dcf8aa18a9de286ff01540e |
import chardet
import codecs
import os
import re
class Clippings(object):
def __init__(self, source, dest=None):
'''
Prepares the import and store it into the 'clippings' dict.
'''
self.source = source
self.dest = self._get_default_dest() if dest is None else dest
... | rejuvyesh/whoarder | whoarder/clippings.py | Python | mit | 5,790 | [
"FEFF"
] | ff2507a623511705aa53c775aadef2c2c218583d620aeaa50b9425e9a85ca30e |
#!/usr/bin/env vpython
# Copyright 2020 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.
"""Wrapper for running gpu integration tests on Fuchsia devices."""
import argparse
import logging
import os
import shutil
import subp... | endlessm/chromium-browser | content/test/gpu/run_gpu_integration_test_fuchsia.py | Python | bsd-3-clause | 3,076 | [
"Amber"
] | e6399bc79217941d183d3fefc0d9e3576b19e11c1bcbde2d0c13def9bf5cfcba |
"""
Synfirechain-like example
"""
#!/usr/bin/python
import os
import spynnaker.pyNN as p
import spynnaker_external_devices_plugin.pyNN as q
import numpy, pylab
p.setup(timestep=1.0, min_delay = 1.0, max_delay = 144.0)
nNeurons = 3 # number of neurons in each population
max_delay = 50
cell_params_lif = {'cm' ... | svadams/SpinnIOTest | examples/live_packet_output_synfire_chain.py | Python | gpl-3.0 | 2,220 | [
"NEURON"
] | 2b513f8091d5d7014bfa29656c846fe641dafa6056cc9a4324e6a63529c56809 |
# This file is part of the Minecraft Overviewer.
#
# Minecraft Overviewer is free software: you can redistribute it and/or
# modify it under the terms of the GNU General Public License as published
# by the Free Software Foundation, either version 3 of the License, or (at
# your option) any later version... | overviewer/Minecraft-Overviewer | overviewer_core/textures.py | Python | gpl-3.0 | 282,304 | [
"BLAST",
"CRYSTAL"
] | 59b726d7e0d802f50bee8286a96f691cf117a7f17d4ed073384db3c5a3b8fb87 |
from neuron import h,gui
from CPG_Network import ReflexNetwork
#h.load_file('stdgui.hoc')
rc = ReflexNetwork()
shape_window = h.PlotShape()
shape_window.exec_menu('Show Diam') | penguinscontrol/Spinal-Cord-Modeling | CPG/run_python.py | Python | gpl-2.0 | 176 | [
"NEURON"
] | 74aeb04c323d2c8f42df506544a3db439e458f053b3f1b5d63624ac6ac45a3b9 |
###
### This script can be run with pvpython rather than pvbatch, as it does not
### need mpi.
###
### Purpose:
###
### Generate a static image dataset of volume rendering on the ne cooling data
###
### Example usages (assumes you are in directory with this script):
###
### 1) To run on the coarse mesh with... | Kitware/cinema | scripts/data_generation/ne-cooling/volume-vel.py | Python | bsd-3-clause | 9,113 | [
"ParaView",
"VTK"
] | 772244f566ff0b693391583b9b3fd7810ed1acce3d3b74aba392bac12fd13618 |
#!/usr/bin/env python
# Copyright (C) 2012 Tianyang Li
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This progr... | tianyang-li/meta-transcriptome | trans-len/strip_dup_al_reads.py | Python | gpl-3.0 | 2,598 | [
"pysam"
] | fc244d004b46832d2b80d13bfff05a1a448217fb60bb3fadac43d9621446fc53 |
BISMARK_METH_CODE_TYPE_MAP = {
"H": "CHH",
"h": "CHH",
"X": "CHG",
"x": "CHG",
"Z": "CpG",
"z": "CpG",
}
def meth_call_for_read(read, overlap=True, min_qual=20):
''' Do methyltaion calling per read.
Parameters
----------
read : pysam.AlignedSegment
The read from fetch()... | Zymo-Research/mirror-seq | mirror_seq/hmc_calling.py | Python | apache-2.0 | 13,672 | [
"pysam"
] | 57b3e755a5b7b6c91c09dbe83e610a174b411cc91a5f01e26c5e315c0e21ffb5 |
import math
import random
from test import redis, flushdb
NUM_VALUES = 100000
def cdf(x, values):
n1 = 0
n2 = 0
for v in values:
n1 += 1 if v < x else 0
n2 += 1 if v <= x else 0
return (n1 + n2) / 2.0 / len(values)
def run_test_for_dist(redis, distfn):
key = distfn.__name__
keydest = key + '... | usmanm/redis-tdigest | test/test_integration.py | Python | mit | 4,392 | [
"Gaussian"
] | 2f0901df3c4d577d3bfac6ae43125d8be36e59f2857a9e1233d21127f2c68601 |
#! /usr/bin/env python
"""Unit tests for landlab.io.netcdf module."""
import os
import netCDF4 as nc
import numpy as np
import pytest
from numpy.testing import assert_array_equal
from landlab import RasterModelGrid
from landlab.io.netcdf import NotRasterGridError, write_netcdf
from landlab.io.netcdf.read import _get_... | landlab/landlab | tests/io/netcdf/test_write_netcdf.py | Python | mit | 10,251 | [
"NetCDF"
] | 39f09920e5f183547afc7993b736f5df529510e6461f59dc41e29263d01186c9 |
#!/usr/bin/env python
# Copyright 2015 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 idl_schema
import json_parse
from js_externs_generator import JsExternsGenerator
from datetime import datetime
import model
impo... | hujiajie/chromium-crosswalk | tools/json_schema_compiler/js_externs_generator_test.py | Python | bsd-3-clause | 8,543 | [
"exciting"
] | f30350432281ef0cebb247c043c484c86427cd69b6bc03070ed9eb305b93e6e0 |
import sys
import warnings
import numpy as np
from ase.io.trajectory import Trajectory
from ase.constraints import FixedLine, FixAtoms
from ase.optimize import QuasiNewton
from anh_base import BaseAnalysis
class TransAnalysis(BaseAnalysis):
"""Module for calculate the partition function of rotational modes!
... | keldLundgaard/ase-anharmonics | anh_trans.py | Python | lgpl-2.1 | 8,043 | [
"ASE"
] | d9b9a3d2272ff240b08c1a56c90f3fa93e3dd65b3ad57a5c977f28aca7d7aaec |
"""
[11/05/2014] Challenge #187 [Intermediate] Finding Time to Reddit
https://www.reddit.com/r/dailyprogrammer/comments/2ledaj/11052014_challenge_187_intermediate_finding_time/
#Description:
I cover the border of my monitor with post it notes with tasks I have to do during the week. I am very unorganized.
Each day I ... | DayGitH/Python-Challenges | DailyProgrammer/DP20141105B.py | Python | mit | 4,469 | [
"VisIt"
] | 367cdbc31cf721aa943108322dbb7c2e3e36a992aabfbba4903ba39e9c0ac2b0 |
import os
import unittest
import vtk, qt, ctk, slicer
from slicer.ScriptedLoadableModule import *
import logging
import glob
import sys
from subprocess import call
import numpy as np
import SimpleITK as sitk
import sitkUtils
#
# ImportSubject
#
class ImportSubject(ScriptedLoadableModule):
"""Uses ScriptedLoadableM... | andreashorn/lead_dbs | ext_libs/SlicerNetstim/ImportSubject/ImportSubject.py | Python | gpl-3.0 | 12,976 | [
"VTK"
] | 0663aaf5a7f0d37bcdd46ab11e01021eedbf71edac39999b90a6d04ac3c84cf7 |
#!/usr/bin/env python3
#
# vdbsetup.py - script for building Vdbench configurations
#
# Author: Ramon A. Lovato (ramonalovato.com)
# For: DeepStorage, LLC (deepstorage.net)
#
import argparse
import os.path
import os
import re
import statistics
import textwrap
import random
import numpy as np
import matplotlib as mpl
... | TheOtherOtherOperation/vdbsetup | vdbsetup.py | Python | mit | 34,423 | [
"Gaussian"
] | 505db2d22187e27df5a4e8e4182a8922634619316585fdc612642bad63250e4e |
from electrum_NMC.util import print_error
import httplib, urllib
import socket
import threading
import hashlib
import json
from urlparse import urlparse, parse_qs
try:
import PyQt4
except Exception:
sys.exit("Error: Could not import PyQt4 on Linux systems, you may try 'sudo apt-get install python-qt4'")
from ... | testalt/electrum-NMC | plugins/labels.py | Python | gpl-3.0 | 9,152 | [
"VisIt"
] | e52447b84b90895c317978c33750ff0f802d9d6a071acacc9061e0eec24b3bff |
#--------------------------------------------------------------------------
# Software: InVesalius - Software de Reconstrucao 3D de Imagens Medicas
# Copyright: (C) 2001 Centro de Pesquisas Renato Archer
# Homepage: http://www.softwarepublico.gov.br
# Contact: invesalius@cti.gov.br
# License: GNU ... | paulojamorim/invesalius3 | invesalius/constants.py | Python | gpl-2.0 | 28,589 | [
"VTK"
] | 9f3836ccf2098e7857dfc09f615d3a6f5118f722782e2314bc8f96cb1e7fa17e |
#!/usr/bin/env python3
#* 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/lgp... | nuclear-wizard/moose | python/peacock/Input/InputFileEditorPlugin.py | Python | lgpl-2.1 | 8,363 | [
"MOOSE"
] | 274f4c1e368d538d80811190421f68d66e4c51c51bc4c9de6362d3525fafe3a3 |
'''
Created on 23/11/2009
@author: brian
'''
import logging
from numpy import linspace
from scipysim.actors import Source, Event, LastEvent
class Constant(Source):
'''
This actor is a constant value source
'''
def __init__(self, out, value=1.0, resolution=10, simulation_time=120, endpoint=False):
... | hardbyte/scipy-sim | scipysim/actors/math/constant.py | Python | gpl-3.0 | 1,242 | [
"Brian"
] | c62b3eec572de70647b3dff704574dbb02526ad769e7da25774c7f72e0c24a07 |
# -*- coding: utf-8 -*-
try:
# Python 2.7
from collections import OrderedDict
except:
# Python 2.6
from gluon.contrib.simplejson.ordered_dict import OrderedDict
from gluon import current
from gluon.html import *
from gluon.storage import Storage
from gluon.validators import IS_NOT_EMPTY
from s3.s3fie... | devinbalkind/eden | private/templates/Philippines/config.py | Python | mit | 128,192 | [
"Amber"
] | b00c588d303175fa529f95d9d3a0edc02364f623aa1950b2976a900d74e0c062 |
"""
Integration with native distribution package managers.
@since: 0.28
"""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import _, logger
import os, platform, re, subprocess, sys
from zeroinstall.injector import namespaces, model
from zeroinsta... | afb/0install | zeroinstall/injector/distro.py | Python | lgpl-2.1 | 40,463 | [
"VisIt"
] | fd66d2125e00156fa4d5c1d3512ca08e59289869d9f74786131312c22b4116dc |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | var/spack/repos/builtin/packages/r-affyexpress/package.py | Python | lgpl-2.1 | 1,907 | [
"Bioconductor"
] | dbdcaef98499e222ccdbefedc591175b8614fde90905780ba88d9b45c34f5a36 |
#!/usr/bin/python
# marina von steinkirch @2014
# steinkirch at gmail
''' This program implements the EM algorithm for a two-class
Gaussian mixture model '''
import numpy as np
def load_data(datafile_name):
data = np.mat(np.loadtxt(datafile_name))
dataT = data.T
return dataT
def pe... | bt3gl/Advanced-Machine-Learning | expectation_maximization/em_main.py | Python | mit | 1,672 | [
"Gaussian"
] | ab1defa1e83226ff92ae2f91078f07bac5b96d1673f58698d79be30f939d7c9a |
# Copyright (c) 2012 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.
'''The 'grit build' tool.
'''
from __future__ import print_function
import collections
import codecs
import filecmp
import getopt
import gzip
import os... | chromium/chromium | tools/grit/grit/tool/build.py | Python | bsd-3-clause | 22,102 | [
"xTB"
] | be67c29e28b7479a538894c53597c0f60dfd46fe9b7a144b2b63fcc7b8640354 |
import webbrowser
import os
import socket
from urllib.parse import urlparse
from plugin import plugin, alias, require
FILE_PATH = os.path.abspath(os.path.dirname(__file__))
@require(network=True)
@alias("visit website")
@plugin("website")
class OpenWebsite:
"""
This plugin will visit a website using some par... | sukeesh/Jarvis | jarviscli/plugins/visit_website.py | Python | mit | 2,297 | [
"VisIt"
] | 9f60cc2e1b6046260cdcabc4b674cd31259d81a0f0a14e010549793c9bcf457b |
from __future__ import with_statement
import hashlib
import os
import posixpath
import stat
import re
from fnmatch import filter as fnfilter
from fabric.state import output, connections, env
from fabric.utils import warn
from fabric.context_managers import settings
def _format_local(local_path, local_is_path):
... | noslenfa/tdjangorest | uw/lib/python2.7/site-packages/fabric/sftp.py | Python | apache-2.0 | 11,344 | [
"VisIt"
] | ecbc99c2e1b94c678958bf8e73f6f0214eda04b4cac487fbccce8069b5571136 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Functional tests using WebTest."""
import datetime as dt
import httplib as http
import logging
import unittest
import markupsafe
import mock
import pytest
from nose.tools import * # noqa: F403
import re
from django.utils import timezone
from addons.wiki.utils import t... | mattclark/osf.io | tests/test_webtests.py | Python | apache-2.0 | 50,803 | [
"VisIt"
] | 7d155725e2c4794bd341eccca7d1c8b4fb0e9b35aab0e4578319745ea25509da |
# This file is part of Copernicus
# http://www.copernicus-computing.org/
#
# Copyright (C) 2011, Sander Pronk, Iman Pouya, Erik Lindahl, and others.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License version 2 as published
# by the Free Soft... | gromacs/copernicus | cpc/lib/plumed/mdrun.py | Python | gpl-2.0 | 18,804 | [
"Gromacs"
] | 34d28845c51b8a3d199f79621ba9c66c986e28a65ff7fab21621dd377f457251 |
# This file is part of RMANAGER.
#
# RMANAGER 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
# any later version.
#
# RMANAGER is distributed in the hope that it will be us... | raphaeldussin/RMANAGER | src/python/libdatetag4roms.py | Python | gpl-3.0 | 5,309 | [
"NetCDF"
] | 3ddd9cc6a4ce4bf5c0179eee00f6af1c48b4f01df39aba69f0f9b28415f7e546 |
"""
UI-level acceptance tests for OpenAssessment.
"""
from __future__ import absolute_import
from functools import wraps
import os
import time
import unittest
from bok_choy.promise import BrokenPromise, EmptyPromise
from bok_choy.web_app_test import WebAppTest
import ddt
from nose.plugins.attrib import attr
from pyin... | Stanford-Online/edx-ora2 | test/acceptance/tests.py | Python | agpl-3.0 | 52,571 | [
"VisIt"
] | 65db6cf122d7a9d24c5888db895da0e27af397fce1dfa6ddf1659a0ac9f46de0 |
#
# This Juno application runs my site (http://brianreily.com).
#
# It has been modified for added comments and improved readability.
# If you are interested in the full project for this site (i.e. with
# templates, static file setup, etc.), see my Github repository for it:
# http://github.com/breily/brianreily.com
#
... | breily/juno | doc/examples/basic_site.py | Python | mit | 3,013 | [
"Brian"
] | 6d5edf4aae28b00dde4c735705ed6edd01ba55bf65a67a92f25fbf31a5fda7d7 |
# convert -scale 30% /tmp/sim/*.png /tmp/balls6.gif
from random import random
from collections import defaultdict
import numpy as np, datetime
import sys, numpy.linalg as lin
from mayavi import mlab
G = np.array([0.0, 0.0, -0.8])
m = 0.1
B = 8 # top
EPS = 0.1
BOUND_DAMPING = -0.6
class Simulation:
def __init__... | burakbayramli/dersblog | compscieng/compscieng_bpp30sim/sim.py | Python | gpl-3.0 | 4,829 | [
"Mayavi"
] | 493cbb2003fb1b5763aedce62e2e937448c00a4aa07a3615d193126c2bc265de |
from graphql.core.language.ast import Field, Name, SelectionSet
from graphql.core.language.parser import parse
from graphql.core.language.visitor import visit, Visitor, REMOVE, BREAK
from fixtures import KITCHEN_SINK
def test_allows_for_editing_on_enter():
ast = parse('{ a, b, c { a, b, c } }', no_location=True)
... | gabriel-laet/graphql-py | tests/core_language/test_visitor.py | Python | mit | 16,608 | [
"VisIt"
] | 77c3c4785344e2a217864ca9aac60195a2c95046f60407280d421b3f716b3cf5 |
from datetime import datetime
from werkzeug.security import generate_password_hash, check_password_hash
from . import login_manager
from flask_sqlalchemy import SQLAlchemy
import enum
#TODO mixin created_at, modified_at
print('Initializing database')
db = SQLAlchemy()
# A registered user
class User(db.Model):
_... | alexd2580/evelyn | evelyn/models.py | Python | mit | 4,893 | [
"VisIt"
] | fac638299b80ede284d5a10a0e6c6213ca76b208b5b780bd02d3fa1a07f2e99c |
from ovito import *
from ovito.io import *
node = import_file("../../files/CFG/shear.void.120.cfg")
ptype_property = node.source.particle_type
assert(len(ptype_property.type_list) == 3)
assert(ptype_property.type_list[0].id == 1)
print(ptype_property.type_list[0].id)
print(ptype_property.type_list[0].color)
print(pt... | srinath-chakravarthy/ovito | tests/scripts/test_suite/particle_type.py | Python | gpl-3.0 | 423 | [
"OVITO"
] | 888745454aa8548fa01408444bbc8f2909db388875e40f7b5e6fd4f2506e08cd |
"""
################################################################################
# Copyright (c) 2003, Pfizer
# Copyright (c) 2001, Cayce Ullman.
# Copyright (c) 2001, Brian Matthews.
#
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provid... | audaciouscode/Books-Mac-OS-X | Export Plugins/WhatsOnMyBookShelf Exporter/SOAPpy/Types.py | Python | mit | 51,871 | [
"Brian"
] | 068dd60d06b64699e19ef4c5554e91eb2188d9dbf91492a6aee95e29cfa324e7 |
"""Analyze python import statements."""
from __future__ import absolute_import, print_function
import ast
import os
import uuid
from lib.util import (
display,
ApplicationError,
)
VIRTUAL_PACKAGES = set([
'ansible.module_utils.six',
])
def get_python_module_utils_imports(compile_targets):
"""Retur... | bjolivot/ansible | test/runner/lib/import_analysis.py | Python | gpl-3.0 | 8,577 | [
"VisIt"
] | c39ccdc30d64b0e8514a55371d798ce90c45852ec9cbb395ca73955605de1f68 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | skosukhin/spack | lib/spack/spack/url.py | Python | lgpl-2.1 | 29,938 | [
"HOOMD-blue",
"VTK"
] | aaae56526771c58d1659ab4042bd52cb6775715cf2593e4f186965fb04661b45 |
from __future__ import division, print_function
from CompyledFunc import CompyledFunc
from copy import deepcopy
from frozendict import frozendict
from HelpyFuncs.SymPy import is_non_atomic_sympy_expr, sympy_xreplace
from HelpyFuncs.Dicts import combine_dict_and_kwargs, merge_dicts_ignoring_dup_keys_and_none_values
from... | MBALearnsToCode/ProbabPy | ProbabPy/__init__.py | Python | mit | 26,081 | [
"Gaussian"
] | 16ce3701790d69aff34e339a9c33064cdd2524568599bb8eba0a9effe2f969dd |
# -*- coding: utf-8 -*-
#
#Created on Mon Apr 10 11:34:50 2017
#
#author: Elina Thibeau-Sutre
#
from .base import BaseMixture
from .base import _log_normal_matrix
from .base import _full_covariance_matrices
from .base import _spherical_covariance_matrices
from .initializations import initialize_log_assignements,initia... | 14thibea/megamix | megamix/batch/GMM.py | Python | apache-2.0 | 9,537 | [
"Gaussian"
] | cb0d5d3128b65483c95087aca27fb9732d09fe520a85d15165f68b9c0c31d67d |
# -*- coding: utf-8 -*-
# Copyright 2007-2020 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy 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... | dnjohnstone/hyperspy | hyperspy/tests/signal/test_remove_background.py | Python | gpl-3.0 | 11,665 | [
"Gaussian"
] | 3967bd158e6a833c6263b0aec293dbe1318eaabfd4d53eba418d618f31aae6ef |
from basesynapse import BaseSynapse
import numpy as np
import pycuda.gpuarray as garray
from pycuda.tools import dtype_to_ctype
import pycuda.driver as cuda
from pycuda.compiler import SourceModule
cuda_src = """
__global__ void alpha_synapse(
int num,
%(type)s dt,
int *spike,
int *Pre,
%(type)s ... | cerrno/neurokernel | neurokernel/LPU/synapses/AlphaSynapse.py | Python | bsd-3-clause | 3,696 | [
"NEURON"
] | 4156b595165fb7611a63949244068a182205ba37d45b39ed12f9471caf38957c |
## \file
## \ingroup tutorial_roofit
## \notebook
## Multidimensional models: complete example with use of conditional pdf with per-event errors
##
## \macro_code
##
## \date February 2018
## \authors Clemens Lange, Wouter Verkerke (C++ version)
import ROOT
# B-physics pdf with per-event Gaussian resolution
# -------... | root-mirror/root | tutorials/roofit/rf306_condpereventerrors.py | Python | lgpl-2.1 | 3,522 | [
"Gaussian"
] | ee1c2935a3336882d9f9a79c35e379e78541b85efe64df67c9070d75b84bd594 |
#
# Copyright (C) 2013-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | espressomd/espresso | testsuite/python/interactions_dihedral.py | Python | gpl-3.0 | 7,112 | [
"ESPResSo"
] | 13acd50dff9eb943ce122dc0d69c5d9c12ab840cd51373e4e3490dbd337b12de |
#
# @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/share/psi4/databases/NHTBH.py | Python | lgpl-3.0 | 36,605 | [
"Psi4"
] | 287a4fa46aa04a735eee98a06d12711cb09f256461c9d4adc5107cd32dc722d8 |
#!/usr/bin/env python
# Copyright (c) 2012 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.
"""Makes sure that all files contain proper licensing information."""
import optparse
import os.path
import subprocess
import sys... | zcbenz/cefode-chromium | tools/checklicenses/checklicenses.py | Python | bsd-3-clause | 15,813 | [
"Galaxy"
] | 811fed8698b6ab34ba1d0be5755a23d3e3dbce6a55d08992fd8ea559a0f56b54 |
"""
:copyright: (c) 2014 Building Energy Inc
:license: see LICENSE for more details.
"""
from salad.steps.everything import *
from lettuce import step
from django.core.urlresolvers import reverse
from landing.features.steps import *
@step(u'I visit the home page')
def i_visit_the_home_page(step):
world.browser.vi... | buildingenergy/buildingenergy-platform | seed/features/steps.py | Python | apache-2.0 | 2,282 | [
"VisIt"
] | 9d2ff3b7eb112457dc3596839bf56e38cec4975d8d493e5163db2de73ba758bf |
#!/usr/bin/env python3
################################################################
# copyright (c) 2017,2018 by William R. Pearson and The Rector &
# Visitors of the University of Virginia */
################################################################
# Licensed under the Apache License, Version 2.0 (the "Li... | uwbmrb/BMRB-API | server/wsgi/bmrbapi/submodules/fasta36/scripts/annot_blast_btop4.py | Python | gpl-3.0 | 27,071 | [
"BLAST"
] | 78e5d1991c2303bc1067fc5c896e76e3e50d6f19f5722097c4f8d1994a90cd5c |
#!/usr/bin/python
#This is a program for count Gene on Ensemble data "process subsection",
#Author: Maurizio Polano, mauriziopolano@blu.it
#Last revision: 03/06/2014
import subprocess
import os,os.path
import sys
import time
import re
from optparse import OptionParser
def main():
# select inupt
parser = OptionPa... | bioinfo-dirty-jobs/Scriptechunks | Count_ensemble.py | Python | mit | 2,237 | [
"HTSeq"
] | 53a17a38b4c244a1964cf5308fdb56e381cbb6091892b8b30febd06793a0cb97 |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
"""
Plot AMIGO style Gene Ontology graph using Graphviz.
"""
import os
import os.path as op
import sys
sys.path.insert(0, op.join(op.dirname(__file__), ".."))
from goatools.obo_parser import GODag, GraphEngines
if __name__ == "__main__":
import optparse
p = o... | tanghaibao/goatools | scripts/plot_go_term.py | Python | bsd-2-clause | 2,575 | [
"Cytoscape"
] | 4a413f38c420d16335ee5584ece7af38ea1e6457c184a4e6f2953c3991c44ff8 |
import numpy as np
from ase import Atom, Atoms
from ase.parallel import rank
from gpaw import GPAW
from gpaw.test import equal
try:
calc = GPAW('NaCl.gpw')
NaCl = calc.get_atoms()
e = NaCl.get_potential_energy()
niter = None
except IOError:
h = 0.21 # gridspacing
a = [6.5, 6.5, 7.7] # unit ce... | robwarm/gpaw-symm | gpaw/test/aedensity.py | Python | gpl-3.0 | 1,366 | [
"ASE",
"GPAW"
] | 9402e9c1722ae167d0960472214aa499984e76891187183abe38847e995e5c75 |
"""
Module for reading Gaussian cube files, which have become one of the standard file formats
for volumetric data in quantum chemistry and solid state physics software packages
(VASP being an exception).
Some basic info about cube files
(abridged info from http://paulbourke.net/dataformats/cube/ by Paul Bourke)
The ... | materialsproject/pymatgen | pymatgen/io/cube.py | Python | mit | 9,239 | [
"CPMD",
"Gaussian",
"VASP",
"pymatgen"
] | 0468a5c82210f75022f1e696375bf0593e512201413a994fca1223c658e81f8d |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 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
#... | jturney/psi4 | psi4/driver/procrouting/interface_cfour.py | Python | lgpl-3.0 | 19,085 | [
"CFOUR",
"Psi4"
] | 15974d2861457440bf4005d0cbda6e1c3732e5a9ddb491b9c54cd1612300ebe6 |
#
# gPrime - A web-based genealogy program
#
# Copyright (C) 2007-2012 Brian G. Matherly
# Copyright (C) 2009 Gary Burton
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2010 Nick Hall
# Copyright (C) 2013-2014 Paul Franklin
#
# This program is free software; you can redistribute it and/or modify
# it ... | sam-m888/gprime | gprime/plugins/textreport/tagreport.py | Python | gpl-2.0 | 34,619 | [
"Brian"
] | da6ef88e02fd8a369acfd26bde4625465c6b470e88eb1105f2a3abb7b804ae5b |
"""
simple, elegant templating
(part of web.py)
Template design:
Template string is split into tokens and the tokens are combined into nodes.
Parse tree is a nodelist. TextNode and ExpressionNode are simple nodes and
for-loop, if-loop etc are block nodes, which contain multiple child nodes.
Each node can emit som... | bobintetley/asm3 | src/web039/template.py | Python | gpl-3.0 | 50,611 | [
"VisIt"
] | 245c50fa610319ef405649cfd2fcf9defe0b2ebe2806e108064a4d688c38e64c |
from gpaw import GPAW
print('state LDA PBE')
for name in ['ferro', 'anti', 'non']:
calc = GPAW(name + '.gpw', txt=None)
atoms = calc.get_atoms()
eLDA = atoms.get_potential_energy()
deltaxc = calc.get_xc_difference('PBE')
ePBE = eLDA + deltaxc
if name == 'ferro':
eLDA0 =... | robwarm/gpaw-symm | doc/exercises/iron/PBE.py | Python | gpl-3.0 | 450 | [
"GPAW"
] | 2deb12f6327821b3d9e8f30d1ce0e1ff318449e1767362cc804e9944292f2ed3 |
#
# Copyright (C) 2010-2019 The ESPResSo project
# Copyright (C) 2002,2003,2004,2005,2006,2007,2008,2009,2010
# Max-Planck-Institute for Polymer Research, Theory Group
#
# 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... | psci2195/espresso-ffans | doc/tutorials/02-charged_system/scripts/nacl_units_confined.py | Python | gpl-3.0 | 6,242 | [
"ESPResSo"
] | 9ccba70f156505e0395c192c05a57905d15ea132e8c201819dcfa6cafce5f298 |
#
# @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 program is free software; you can redistribute it and/or modify
# it under the terms of ... | andysim/psi4 | psi4/driver/qcdb/periodictable.py | Python | gpl-2.0 | 78,238 | [
"CFOUR",
"Psi4"
] | 1e01e0d48fd3eea5fdde0ab748f30282a37bd18d7bb51d6ac5f9d136973e32ae |
import dryscrape
import sqlalchemy
import time
import re
import os
import numpy as np
import pandas as pd
project_dir = '/Users/mdelhey/rice-scrape/'
YEAR_SCRAPE = '2013'
TERM_SCRAPE = 'Spring'
dbuser = 'mdelhey'
dbname = 'ricedb'
dbhost = 'localhost'
tbl_out = 't_courses_raw2'
tbl_action = 'replace' # replace / a... | mdelhey/rice-scrape | scrape/scrape_courses.py | Python | mit | 3,405 | [
"VisIt"
] | 9fc31aeac8ea5981309fcaabbd09252ad2b069aed99333409e35468561bcc3cf |
"""A thorough test of polling PAIR sockets."""
#
# Copyright (c) 2010 Brian E. Granger
#
# This file is part of pyzmq.
#
# pyzmq is free software; you can redistribute it and/or modify it under
# the terms of the Lesser GNU General Public License as published by
# the Free Software Foundation; either ve... | takluyver/pyzmq | examples/poll/pair.py | Python | lgpl-3.0 | 1,813 | [
"Brian"
] | 4c84cb8f9311d8d12ad5a0eb332d9cca2fede899b612d5257653f5e5290d1821 |
# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
#
# Okinawa Institute of Science and Technology, Japan.
#
# This script runs on STEPS 2.x http://steps.sourceforge.net
#
# H Anwar, I Hepburn, H Nedelescu, W Chen and E De Schutter
# Stochastic calcium mechanisms cause dendritic calcium spike... | CNS-OIST/STEPS_Example | publication_models/API_1/Anwar_J Neurosci_2013/extra/constants_withampa.py | Python | gpl-2.0 | 9,093 | [
"Avogadro"
] | 10e500a725629751c1ea30f7c10f3fc08bbf81861821fd4c1b7a422f5310539f |
"""
A Galaxy wrapper script for corrector-1.0
Peter Li - GigaScience and BGI-HK
"""
import optparse
import os
import shutil
import subprocess
import sys
import tempfile
import fnmatch
def stop_err(msg):
sys.stderr.write(msg)
sys.exit()
def cleanup_before_exit(tmp_dir):
if tmp_dir and os.path.exists(tmp... | gigascience/galaxy-bgisoap | tools/corrector1/corrector1_wrapper.py | Python | gpl-3.0 | 5,068 | [
"Galaxy"
] | f431dcac8ba6e5dfc6685a3328e6cb2225df7196d40df8824b6ff5d0ece87ae3 |
# -*- coding: utf-8 -*-
import os
import logging
import unittest
from riboplot import config, ribocore
# use testing configuration
CFG = config.TestingConfig()
logging.disable(logging.CRITICAL)
# reference_orfs were obtained manually (UGENE, ORF finder)
REFERENCE_ORFS = [{'start': 45, 'stop': 203, 'sequence': 'ATGA... | vimalkumarvelayudhan/riboplot | tests/test_ribocore.py | Python | bsd-3-clause | 4,785 | [
"pysam"
] | b212199096329107709a7c2d3ca7ae84b2c681e1712fd6ff50cf6232a7e04cdc |
# 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/providers_geocode_response.py | Python | apache-2.0 | 12,870 | [
"VisIt"
] | 16c723949bf291aced74853c3b293ffac08968a0f65f18064045cdf73ac63b42 |
#### import the simple module from the paraview
from paraview.simple import *
#### disable automatic camera reset on 'Show'
paraview.simple._DisableFirstRenderCameraReset()
# create a new 'XML Unstructured Grid Reader'
xMLUnstructuredGridReader1 = XMLUnstructuredGridReader(FileName=['/raid/home/ksansom/caseFiles/mri/V... | kayarre/Tools | vtk/paraview_case4_2.py | Python | bsd-2-clause | 30,397 | [
"ParaView"
] | a5ee0baff2c1046596623d02cac06973464722fb1f4a9462ef4f6b7b255b2c40 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
#
#
# 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... | e-gob/plataforma-kioscos-autoatencion | scripts/ansible-play/.venv/lib/python2.7/site-packages/ansible/modules/network/avi/avi_scheduler.py | Python | bsd-3-clause | 5,098 | [
"VisIt"
] | 8658e992a6acccedc8e347e11e08fa1204a5ddde766878be5a83f6a9b64959c0 |
import os
from ase.test import NotAvailable
from ase.lattice import bulk
from ase.calculators.calculator import kpts2mp
from ase.calculators.elk import ELK
atoms = bulk('Al', 'bcc', a=4.0)
# save ELK_SPECIES_PATH
ELK_SPECIES_PATH = os.environ.get('ELK_SPECIES_PATH', None)
if ELK_SPECIES_PATH is None:
raise NotAv... | askhl/ase | ase/test/elk/Al_rmt.py | Python | gpl-2.0 | 2,300 | [
"ASE",
"Elk"
] | b00529d423dc59d7aca5514bea0292f89968c07501312eb3b51f675747337beb |
"""
This module contains code for generating toy examples
"""
# This software is distributed under BSD 3-clause license (see LICENSE file).
#
# Authors: Soeren Sonnenburg
import sys
import parse
import random
from numpy.random import randn
from numpy import ones, concatenate, array, transpose
from esvm.mldata import... | besser82/shogun | applications/easysvm/esvm/datafuncs.py | Python | bsd-3-clause | 4,836 | [
"Gaussian"
] | 99ad70e3863dfb6e73774ce2d6e679d5178ce4b91d73a9f511179e2595b2d26b |
"""
Author: Ang Ming Liang
Please run the following command before running the script
wget -q https://raw.githubusercontent.com/sayantanauddy/vae_lightning/main/data.py
or curl https://raw.githubusercontent.com/sayantanauddy/vae_lightning/main/data.py > data.py
Then, make sure to get your kaggle.json from kaggle.com... | probml/pyprobml | vae/standalone/vae_celeba_lightning.py | Python | mit | 7,878 | [
"Gaussian"
] | 2c5634aa58705e0a2db08f94108adc35fae311dee26ed3b711930ed0850a570a |
import time
import random
def cls():
for i in range(200):
print("")
def cool():
wn = random.randrange(0,27)
if wn == 1:
return "█ Now under New Management! █" #Avg line to line distance: 56
elif wn == 2:
return "█ ... | LTEGaming/PySOE | Main-Dev/pysoe_shell.py | Python | bsd-3-clause | 8,782 | [
"BLAST"
] | 3cac434f080151afadd41a425395cddf7b5745341b00d0c80347e526e5f11fa5 |
#!/usr/bin/python2
""" run bowtie with specified parameter file
"""
import subprocess
from logging import getLogger
import os
import shlex
import argparse
import csv
from glob import glob
from multiprocessing.pool import ThreadPool
logger = getLogger('pijp.bowtie_wrapper')
def build_bowtie_command(fastq_file, inde... | yanailab/CEL-Seq-pipeline | bowtie_wrapper.py | Python | gpl-3.0 | 3,008 | [
"Bowtie"
] | 6a849f9529c68686ea38660523fbabd6d0feb90a5b63935b473f4ebb011c29d3 |
# coding: utf-8
from __future__ import unicode_literals
import copy
import glob
import json
import os
from unittest import TestCase
import unittest
from pymatgen import Molecule
from pymatgen.io.qchemio import QcTask, QcInput, QcOutput
__author__ = 'xiaohuiqu'
test_dir = os.path.join(os.path.dirname(__file__), "... | Dioptas/pymatgen | pymatgen/io/tests/test_qchemio.py | Python | mit | 71,957 | [
"pymatgen"
] | a33bf0539f3e676063b9f278dc14c3d41d6e77e27e7462628afac1ae07085a3c |
import os
import numpy
from pyproj import Proj
from netCDF4 import Dataset
from trefoil.netcdf.variable import CoordinateVariable, BoundsCoordinateVariable
from trefoil.netcdf.variable import SpatialCoordinateVariable, SpatialCoordinateVariables
from trefoil.geometry.bbox import BBox
def test_coordinate_vari... | consbio/clover | trefoil/netcdf/tests/test_variable.py | Python | bsd-3-clause | 5,577 | [
"NetCDF"
] | 9bda6e7cfd9d046212d2c2991b9c9d4a916bb20fc9bf971f6d0ce0556118bb1f |
""" Test for StorageManagement clients
"""
# pylint: disable=protected-access,missing-docstring,invalid-name
import unittest
from mock import MagicMock, patch
from DIRAC import S_OK, S_ERROR
from DIRAC.StorageManagementSystem.Client.StorageManagerClient import getFilesToStage
from DIRAC.DataManagementSystem.Client.t... | andresailer/DIRAC | StorageManagementSystem/Client/test/Test_Client_StorageManagementSystem.py | Python | gpl-3.0 | 8,186 | [
"DIRAC"
] | 4baab3197a4c1fd4632401e3ea3926c040fdb05f87d7b527b4d35905839226f2 |
"""
@file bible/model.py
@author Brian Kim
@brief definition of bible objects
Language, Version, Chapter, Verse
"""
from flask.ext.sqlalchemy import SQLAlchemy
db = SQLAlchemy()
class Language(db.Model):
abbr = db.Column(db.String(5), primary_key=True)
name = db.Column(db.String(32))
def __init__... | briansan/bible | bible/model.py | Python | bsd-2-clause | 3,446 | [
"Brian"
] | 349910da542da8e2499d991122aacc19940b8352490d84d7ce1d478b99c02742 |
#modified to work with python3
##############################
import operator
import random
from collections import defaultdict
from functools import reduce
###Stats and math functions
def weighted_sampler(pop_dict):
"""randomly sample a dictionary's keys based on weights stored as values example:
m = {... | flag0010/python_common | old_versions/common3.py | Python | mit | 5,604 | [
"Biopython"
] | a65757b5ff5feda69ac7d6d513a87c7e8a94d8f641efacc326cd004f99c4a07b |
from __future__ import print_function
from builtins import range
import sys
sys.path.insert(1,"../../../")
import h2o
from tests import pyunit_utils
import random
from h2o.estimators.gbm import H2OGradientBoostingEstimator
def cv_cars_gbm():
# read in the dataset and construct training set (and validation set)
ca... | YzPaul3/h2o-3 | h2o-py/tests/testdir_algos/gbm/pyunit_cv_cars_gbm.py | Python | apache-2.0 | 7,071 | [
"Gaussian"
] | 34aa8d062d85b2fba451351db4f1711176d997aa280c448ad1bd6904c2c1cdd6 |
# ============================================================================
#
# Copyright (C) 2007-2010 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | kurtraschke/camelot | camelot/admin/validator/__init__.py | Python | gpl-2.0 | 1,346 | [
"VisIt"
] | afcbb20db1d318f71b9eff2e128e075dd3e69ce56ad163164f6f6a5ecf6a542d |
"""
Tests for the Piwik template tags and filters.
"""
from django.contrib.auth.models import User
from django.http import HttpRequest
from django.template import Context
from django.test.utils import override_settings
from analytical.templatetags.piwik import PiwikNode
from analytical.tests.utils import TagTestCase
... | pjdelport/django-analytical | analytical/tests/test_tag_piwik.py | Python | mit | 6,215 | [
"VisIt"
] | 87a64819cb5d3cf0f4e925132d7d136c29aacf81cbec05cfa0f1dc1efff34481 |
from behave import when
from django.core.management import execute_from_command_line
from selenium import webdriver
def before_all(context):
context.browser = webdriver.Firefox()
context.browser.implicitly_wait(1)
context.server_url = 'http://localhost:8081'
execute_from_command_line(['manage.py', 'loa... | evili/django-jenkins-plugin | src/test/resources/org/jenkinsci/plugins/django/simple_test_project/bdd_tests/features/environment.py | Python | apache-2.0 | 697 | [
"VisIt"
] | 6bd4324987fe2841ab49b0fb02e333571e24f0e801830050b4c04e8731bdd85b |
"""
Views for user API
"""
from django.shortcuts import redirect
from django.utils import dateparse
from rest_framework import generics, views
from rest_framework.decorators import api_view
from rest_framework.response import Response
from opaque_keys.edx.keys import UsageKey
from opaque_keys import InvalidKeyError
... | dkarakats/edx-platform | lms/djangoapps/mobile_api/users/views.py | Python | agpl-3.0 | 9,370 | [
"VisIt"
] | c3197a749acf29bafed67be21e7e279ab5939da697f28aea0bd11514896c938a |
########################################################################
# Author : Andrei Tsaregorodtsev
########################################################################
"""
Utilities for managing DIRAC configuration:
getCEsFromCS
getUnusedGridCEs
getUnusedGridSEs
getSiteUpdates
getSEUpdates
"""
... | andresailer/DIRAC | ConfigurationSystem/Client/Utilities.py | Python | gpl-3.0 | 22,730 | [
"DIRAC"
] | 10fa5dd1293a86c5aeffc22e3fd9593353b88f9c0c7839a87cbd4923ab179f3b |
import base64
import json
import os
from contextlib import closing
from urllib.parse import urlparse, parse_qs
from django.conf import settings
from django.core.exceptions import ImproperlyConfigured
from django.utils.timezone import datetime
from django.shortcuts import reverse
from django.test import override_setti... | concentricsky/badgr-server | apps/badgrsocialauth/tests/test_saml2.py | Python | agpl-3.0 | 31,708 | [
"MOE"
] | 023c2d700c70fdbcd27729b1200efd1d80b6372343e8acd67a306f87540976ef |
# coding=utf-8
# Copyright 2022 The Uncertainty Baselines 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 ap... | google/uncertainty-baselines | baselines/cifar/sngp_ensemble.py | Python | apache-2.0 | 14,238 | [
"Gaussian"
] | 3938496d5d92b8fa53271c234b2f68137be31b56760259652f9b4ef7cd1f1f00 |
# $HeadURL$
""" Queries BDII for unknown CE.
Queries BDII for CE information and puts it to CS.
"""
__RCSID__ = "$Id$"
from DIRAC import S_OK, S_ERROR, gConfig
from DIRAC.Core.Base.AgentModule import AgentModule
from DIRAC.Core.Utilities ... | sposs/DIRAC | ConfigurationSystem/Agent/CE2CSAgent.py | Python | gpl-3.0 | 21,176 | [
"DIRAC"
] | 7a70372462b087e24cda662162a4c50b5df8777bd83d61b980a77bf0a255f25e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# freeseer - vga/presentation capture software
#
# Copyright (C) 2011, 2013 Free and Open Source Software Learning Centre
# http://fosslc.org
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public Licens... | Freeseer/freeseer | src/freeseer/tests/framework/config/persist/test_jsonstorage.py | Python | gpl-3.0 | 1,605 | [
"VisIt"
] | cd9e2d388489a9d3617b797f64a94be2e051d6ca972286a2136731399d4f6545 |
#
#@BEGIN LICENSE
#
# PSI4: an ab initio quantum chemistry software package
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later ver... | spring01/libPSI | lib/databases/NCB31.py | Python | gpl-2.0 | 53,417 | [
"Psi4"
] | a06c8d4f46aa29d441f5641ef36f8a82a17c8e4b82cf77e1f4b103d051bfde34 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
Development script to test the algorithms of all the model coordination environments
"""
__author__ = "David Waroquiers"
__copyright__ = "Copyright 2012, ... | gmatteo/pymatgen | dev_scripts/chemenv/test_algos_all_geoms.py | Python | mit | 4,792 | [
"pymatgen"
] | 53f1bb00b57477e91cb0adda282c511759d7d317c1eb9eae9eb44faddd8a6ed4 |
"""
This file can be downloaded and used to create a .txt file containing only
the accession numbers from the ghost-tree.nwk that you plan to use for your
analyses.
You must have skbio installed. http://scikit-bio.org/
If you aren't familiar with skbio, make sure to check it out on its own, too!
You will then use "gh... | JTFouquier/ghost-tree | helper_files/get_otus_from_ghost_tree.py | Python | bsd-3-clause | 1,130 | [
"scikit-bio"
] | 477dc4e883bfcc13a062a596a4b65cd030081855fa3c1d8cb1bd3dace5b75671 |
"""
Fourier Aliasing
================
Here, we show that we can view the Fourier transform as an infinitely repeat
set of replicates (aliases, *s.t.*
:math:`Ш(\nu/t_{dw})*\tilde{f}(\nu)`) and view any of those aliases
(of width :math:`SW=1/t_{dw}`)
that we choose.
"""
# from JF noteobok sec:fourier_aliasing_test
from ... | jmfranck/pyspecdata | docs/_downloads/54c91e6b35ea86f52bd26d115eb9b78b/fourier_aliasing.py | Python | bsd-3-clause | 4,725 | [
"Gaussian"
] | b5308235206e214fa0da7211eae64104974d287ac41ffbe187dd0c9e560d16a1 |
# (C) British Crown Copyright 2010 - 2017, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | QuLogic/iris | lib/iris/tests/test_analysis.py | Python | gpl-3.0 | 50,394 | [
"NetCDF"
] | a0b0626648f826d3ec06d17fd3c9a994451243c319c6c35eb79d70d02a5bf272 |
# minimal.py ---
# Upi Bhalla, NCBS Bangalore 2013.
#
# Commentary:
#
# Testing system for loading in arbitrary multiscale models based on
# model definition files.
# This version has a minimal model with Ca in all 3 compartments,
# and CaM (just one step) in SPINE and PSD, with a nominal product Ca.CaM.
# In this d... | dilawar/moose-full | moose-examples/snippets/MULTI/diffusionOnly.py | Python | gpl-2.0 | 17,109 | [
"MOOSE",
"NEURON"
] | 690e53b178d491f852f16981cfdb5ff38f29530554c6dc391ff51271eeaffdad |
#!/usr/bin/env python
"""
Program to show the monte carlo error estimate of the polarization correction
operation, assuming a value and uncertainty for polarizer and flipper
efficiencies.
"""
n = 100000
err = 5
Ic = 100000
doplot = False
import numpy,math,pylab
import reflectometry.reduction as reflred
eff = reflre... | reflectometry/osrefl | osrefl/loaders/reduction/examples/polcorerr.py | Python | bsd-3-clause | 1,461 | [
"Gaussian"
] | 9f85f9e91a30514513f5e42b4b3f89bc2906b77368178855220e849236662c7c |
<<<<<<< HEAD
<<<<<<< HEAD
import base64
import re
import os
import sys
import urllib.request, urllib.parse, urllib.error
PY3 = sys.version_info[0] == 3
if PY3:
from io import StringIO
str = str
else:
from io import StringIO
try:
import json
except ImportError:
import simplejson as json
from .r... | ArcherSys/ArcherSys | archersys/Lib/site-packages/dropbox/client.py | Python | mit | 202,937 | [
"VisIt"
] | aebe852c6f83f4d8cde7897ea51ac9981062c9e87e201dd15cb453194559b606 |
import os.path as osp
from mastic.system import System, SystemType, AssociationType, Association
from rdkit import Chem
from mastic.interfaces.rdkit import RDKitMoleculeWrapper
trypsin_dir = osp.expanduser("~/Dropbox/lab/trypsin")
ben_pdb_path = osp.join(trypsin_dir, "BEN_Hs.pdb")
BEN_rdkit = Chem.MolFromPDBFile(be... | salotz/mast | prototypes/system_example.py | Python | mit | 1,341 | [
"RDKit"
] | 463992978c6a657d3ff22418442d911ed4e8443e021cdac08993a37db2912e84 |
#!/usr/bin/env python
import os, argparse, tempfile, operator, pickle
from collections import defaultdict
import pybedtools, pysam
def rev_comp(str):
"""
Given a DNA string, returns the reverse complement
>>> rev_comp("AATTGGCC")
'GGCCAATT'
"""
rev_dic = {'A':'T','G':'C','C':'G','T':'A'}
return ''.join([rev_d... | jpiper/pyDNase | pyDNase/scripts/dnase_bias_estimator.py | Python | mit | 4,662 | [
"pysam"
] | 77f7d12ff3332794c6170121914566e4a5de511f014019ed0bcf9080475f3f74 |
#(c) 2012 Massachusetts Institute of Technology. All Rights Reserved
# Code written by: Maksim Imakaev (imakaev@mit.edu)
#TODO:(MIU) Write tests for this module!
"""
Binned data - analysis of HiC, binned to resolution.
Concepts
--------
class Binned Data allows low-level manipulation of multiple HiC datasets,
bin... | bxlab/HiFive_Paper | Scripts/HiCLib/mirnylab-hiclib-460c3fbc0f72/src/hiclib/binnedData.py | Python | bsd-3-clause | 64,389 | [
"Gaussian"
] | 6c2c5e49ca350894a58e66149f788b5ccba90d78183be202d092d5c8c02fff74 |
#
# Copyright 2016 The BigDL 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 applicable law or agreed to in ... | intel-analytics/BigDL | python/orca/src/bigdl/orca/data/pandas/__init__.py | Python | apache-2.0 | 766 | [
"ORCA"
] | 01726e1cb8f70987a116d40dc8c8ae9a67b305156b835c0e957e2c31d06a7d60 |
"""Forest of trees-based ensemble methods
Those methods include random forests and extremely randomized trees.
The module structure is the following:
- The ``BaseForest`` base class implements a common ``fit`` method for all
the estimators in the module. The ``fit`` method of the base ``Forest``
class calls the ... | kashif/scikit-learn | sklearn/ensemble/forest.py | Python | bsd-3-clause | 64,796 | [
"Brian"
] | fb80c4c7414f1f4034854b3abdf695ef25b0193f44fb08a230602df33f3b7de9 |
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