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from __future__ import absolute_import
import numpy as np
from scipy.stats import pearsonr
from scipy import signal
from scipy import interpolate
from sklearn.model_selection import train_test_split
from sklearn.metrics import mean_squared_error, mean_absolute_error, r2_score
import warnings
def generate_index_distr... | ECP-CANDLE/Benchmarks | common/uq_utils.py | Python | mit | 33,264 | [
"Gaussian"
] | eabbdecff5d5c09c51235459ecd43fc8d4ca505d8e837c8239fecbf98d482dec |
#!/usr/bin/python
"""Simple shallow test of the CASTEP interface"""
import os
import shutil
import tempfile
import traceback
from ase.test.castep import installed
assert installed()
# check if we can import everything
ase_castep_dir = "ase"
try:
castep_calc = __import__(ase_castep_dir + ".calculators.castep", ... | conwayje/ase-python | ase/test/castep/castep_interface.py | Python | gpl-2.0 | 3,044 | [
"ASE",
"CASTEP"
] | 7b4af872c94b5c55b37bc9897a33f4474576542ad964ef7d50bf26391719c255 |
# $HeadURL$
"""
DISETSubRequest Class encapsulates a request definition to accomplish a DISET
RPC call
:deprecated:
"""
__RCSID__ = "$Id$"
import commands
from DIRAC.Core.Utilities import DEncode
from DIRAC import Time
from DIRAC.Core.Utilities.File import makeGuid
class DISETSubRequest:
##############... | calancha/DIRAC | RequestManagementSystem/Client/DISETSubRequest.py | Python | gpl-3.0 | 1,516 | [
"DIRAC"
] | bcd5a99ef4954d164029065ddef979f92e57bf1a4d408d712fa7a637ba35b111 |
# Copyright (c) 2003-2013 LOGILAB S.A. (Paris, FRANCE).
#
# 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
# version.
#
# This progr... | hkupty/python-mode | pymode/libs/pylama/lint/pylama_pylint/pylint/checkers/format.py | Python | lgpl-3.0 | 38,105 | [
"VisIt"
] | 416cbb27ee5d136b32fee6fc52b6890b1e5d15c0d7c474fd503153b048c78e9f |
#!/usr/bin/env python
"""
Copyright (c) 2006-2016 sqlmap developers (http://sqlmap.org/)
See the file 'doc/COPYING' for copying permission
"""
class PRIORITY:
LOWEST = -100
LOWER = -50
LOW = -10
NORMAL = 0
HIGH = 10
HIGHER = 50
HIGHEST = 100
class SORT_ORDER:
FIRST = 0
SECOND = 1
... | undefinedv/Jingubang | sqlmap/lib/core/enums.py | Python | gpl-3.0 | 9,868 | [
"Galaxy"
] | e0466b33ff2ed434ef67f94afcc19191f1f85b91bd96e6d602663f38e84e84f4 |
from .cdk import CDApproximator
| omimo/xRBM | xrbm/train/__init__.py | Python | mit | 32 | [
"CDK"
] | 132a44e5f921bcd03847631b68b6b33e212a314fc629df4c829f9eb8f49607f7 |
import AlGDock.BindingPMF_plots
from AlGDock.BindingPMF import *
self = AlGDock.BindingPMF_plots.BPMF_plots()
#import numpy as np
#
#for k in range(self._cool_cycle):
# confs = self.confs['cool']['samples'][-1][k]
# for c in range(len(confs)):
# self.universe.setConfiguration(Configuration(self.universe,confs[c]... | luizcieslak/AlGDock | notebook/2015-03-30-Cluster.py | Python | mit | 3,566 | [
"MDTraj"
] | 54927c150fcdad4bfda313ad17227e671790fc51f28829cf8f5373fe417334fc |
# Licensed under an MIT open source license - see LICENSE
'''
Data Reduction Routines for PPV data cubes
'''
import numpy as np
from scipy import ndimage as nd
from operator import itemgetter
from itertools import groupby
from astropy.io import fits
import copy
from scipy.optimize import curve_fit
... | keflavich/TurbuStat | turbustat/data_reduction/data_reduc.py | Python | mit | 14,244 | [
"Gaussian"
] | 0b9cc0404555de80e5eb186abba824e06740fd2dd4e23544885026a79d30a685 |
# -*- coding: utf-8 -*-
# Generated by Django 1.11.12 on 2018-06-05 05:20
from __future__ import unicode_literals
import core.models.custom_fields
from django.db import migrations, models
import django.db.models.deletion
class Migration(migrations.Migration):
dependencies = [
('pmm', '0002_auto_20180522... | sauli6692/ibc-server | pmm/migrations/0003_auto_20180605_0520.py | Python | mit | 8,709 | [
"VisIt"
] | 8cdb40455292d0fe28ffa3a04382c1d8638d798de9431f5a64166bc7d4caad84 |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publi... | thica/ORCA-Remote | src/ORCA/utils/Platform/generic/generic_GetSubnetV6.py | Python | gpl-3.0 | 986 | [
"ORCA"
] | fce486c20d9416cb0aa9d953464fcc7b7ef33fca3844e0536173db6dcfac3da7 |
import numpy
#from numpy import exp,pi
#from scipy.special import gamma
#import copy
#import matplotlib,pylab as plt
#from scipy import interpolate
#=========================================================================
"""
NAME
scalingrelations
PURPOSE
Scaling relations between various ga... | drphilmarshall/Pangloss | pangloss/scalingrelations.py | Python | gpl-2.0 | 8,506 | [
"Galaxy"
] | a5b1e01113c695260c7fb3797dde05f8ecd0fe6117c3220e77f779b2f7c9a0c6 |
#* 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 os
im... | harterj/moose | python/MooseDocs/tree/pages.py | Python | lgpl-2.1 | 4,188 | [
"MOOSE"
] | bbf9067ec46f2efd72b25f6df1bbcff06d963a53ebe0151afdc99540dbeaa847 |
import cPickle
import gzip
import os, sys, errno
import time
import math
import subprocess
import socket # only for socket.getfqdn()
# numpy & theano imports need to be done in this order (only for some numpy installations, not sure why)
import numpy
#import gnumpy as gnp
# we need to explicitly import this in some... | ligz07/merlin | src/run_merlin.py | Python | apache-2.0 | 56,913 | [
"NEURON"
] | 170f63e2fe0424862d7578ba005315f5d51c81a11c7cb1ec0129ac688a22d0b0 |
# -*- Mode: Python; coding: utf-8; indent-tabs-mode: nil; tab-width: 4 -*-
### BEGIN LICENSE
# Copyright (C) 2012 Andrew Starr-Bochicchio <a.starr.b@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... | andrewsomething/typecatcher | typecatcher/html_preview.py | Python | gpl-3.0 | 5,739 | [
"Galaxy"
] | 664b05a65a0957e5642e7c6499bd535f99edf656e9d6cab6b519d3fb4fc84d2e |
from gpaw.mpi import world
from gpaw.blacs import BlacsGrid, Redistributor
if world.size < 2:
raise ValueError('Runs on two or more processors')
grid = BlacsGrid(world, 2, world.size // 2)
desc = grid.new_descriptor(12, 8, 2, 3)
a = desc.zeros()
a[:] = world.rank
subdesc = grid.new_descriptor(7, 7, 2, 2)
b = s... | qsnake/gpaw | gpaw/test/parallel/submatrix_redist.py | Python | gpl-3.0 | 688 | [
"GPAW"
] | 7efa3e71529e13845e1c5f4609d5ebb9446e9dd622d80195e5638ed4ea328fd0 |
# Copyright (c) 2011, Alex Krizhevsky (akrizhevsky@gmail.com)
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without modification,
# are permitted provided that the following conditions are met:
#
# - Redistributions of source code must retain the above copyright notice,
# this ... | zygmuntz/kaggle-cifar | dropconnect/shownet.py | Python | bsd-2-clause | 24,244 | [
"NEURON"
] | e423384050167d55c77de407a5f456875d2d899b4229021cbae6a6f8b44b03f1 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# (c) 2013, Jeroen Hoekx <jeroen.hoekx@dsquare.be>, Alexander Bulimov <lazywolf0@gmail.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free So... | CenturylinkTechnology/ansible-modules-extras | system/lvol.py | Python | gpl-3.0 | 16,600 | [
"Firefly"
] | 8f9c346c65c3637f94da7107de8a20c567d120b75606546db05ca30a6242e94b |
from ..helpers import UniqueCourseTest
from ...fixtures.course import CourseFixture
from ...pages.lms.auto_auth import AutoAuthPage
from ...pages.lms.create_mode import ModeCreationPage
from lms.envs.bok_choy import EMAIL_FILE_PATH
from ..ga_helpers import GaccoTestMixin
from ...pages.lms.ga_pay_and_verify import Cou... | nttks/edx-platform | common/test/acceptance/tests/lms/test_ga_paid_course.py | Python | agpl-3.0 | 3,226 | [
"VisIt"
] | 910ccdd4b0578f2232ae914339321c354ba3967d9c2415067d573944cfb073fc |
#!/usr/bin/env python
# This example demonstrates the use of vtkAssembly. In an assembly,
# the motion of one actor affects the position of other actors.
import vtk
# Create four parts: a top level assembly (in this case, a
# vtkCylinder) and three primitives (using vtkSphereSource,
# vtkCubeSource, and vt... | hlzz/dotfiles | graphics/VTK-7.0.0/Examples/Rendering/Python/assembly.py | Python | bsd-3-clause | 2,777 | [
"VTK"
] | cf34aeee57fa61f5a63c0ae34030bc7fe6a92051b0fe1cad69467207691e5075 |
# ##### BEGIN GPL LICENSE BLOCK #####
#
# 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 version.
#
# This program is distrib... | floaltvater/molblend | mb_datastructure.py | Python | gpl-2.0 | 31,708 | [
"Quantum ESPRESSO"
] | bd950f8534b8572758751e6af0f28c04111dea35febc95ef8b640ee9f7bc97bf |
#!/usr/bin/env python
# encoding: utf-8
try:
from urllib import urlencode
except ImportError:
from urllib.parse import urlencode
from pyshorteners import Shortener, Shorteners
from pyshorteners.exceptions import ShorteningErrorException
import responses
import pytest
s = Shortener(Shorteners.ADFLY, uid='TEST... | Oire/pyshorteners | tests/test_adfly.py | Python | gpl-3.0 | 1,581 | [
"ADF"
] | 69423a1e707fd026ecee94a6ce3d5a2cefcbf14e99d715e22b4a0dd9fce25d87 |
#!/usr/bin/env python
import os
import sys
import numpy as np
import galsim
from .psfmaker import PSFMaker
from ..observation import Observation
class DESPSFMaker(PSFMaker):
"""
make a DES-like PSF
from esheldon's fork of the great3 code
blessed by Mike and Aaron to roughly match DES
M. R... | kstory8/egret | egret/psfmakers/despsfmaker.py | Python | bsd-3-clause | 7,218 | [
"Gaussian"
] | 7190a4d3cf0b47a4c93713bc7b4e56ff5c17b6772e09b6c8b22a951ed51bc311 |
#
# 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/chronos/test/bigdl/chronos/data/utils/test_impute.py | Python | apache-2.0 | 3,359 | [
"ORCA"
] | dfb2adb39d4faafe2c0df82f0794ac22228cf41bed3640257050fe077da4a09a |
# Orca
#
# Copyright 2008-2009 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | chrys87/orca-beep | src/orca/tutorialgenerator.py | Python | lgpl-2.1 | 30,663 | [
"ORCA"
] | a94e338b4aff32a28abbd854535b8aa63362a7dbb0a641126df7a843dacb2a8b |
#!/usr/bin/python2.5
#
# Copyright 2009 Google Inc. 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 require... | marcosdiez/pytracker | tracker2gcal.py | Python | apache-2.0 | 8,815 | [
"VisIt"
] | 6b8c181a0fd394c0a43aea0fd87ce0518b333383c3c87d74658e0e628a98a8f3 |
# Copyright 2015 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... | chemelnucfin/tensorflow | tensorflow/python/ops/image_grad_test.py | Python | apache-2.0 | 21,897 | [
"Gaussian"
] | 923d9819957a01f2bc12f7e163e760822bfa9b77d677347319cf76c3b182175f |
# Copyright 2012 by Wibowo Arindrarto. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Tests for SearchIO exonerate-text indexing."""
import os
import unittest
from search_... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_SearchIO_exonerate_text_index.py | Python | gpl-2.0 | 954 | [
"Biopython"
] | 0b85279bcc6c0f1e43520761c1969cf48bc628bc0d3054d50f4b69f5d894f49d |
import os
from setuptools import setup, find_packages
import multiprocessing
template_files = os.listdir(os.path.join(os.path.dirname(__file__), 'citation_reporter', 'templates'))
templates = [os.path.join('templates', template) for template in template_files]
example_files = os.listdir(os.path.join(os.path.dirname(_... | sanger-pathogens/citation_reporter | setup.py | Python | gpl-3.0 | 1,057 | [
"Biopython"
] | 05f5797e5adac2352594365067d014844809bb954c3dbbeb355ec2400d559750 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
import uuid
class Migration(migrations.Migration):
dependencies = [
('visit', '0039_auto_20150723_0019'),
]
operations = [
migrations.AlterField(
model_name='staff',
... | koebbe/homeworks | visit/migrations/0040_auto_20150723_0020.py | Python | mit | 442 | [
"VisIt"
] | ded38b14e06456b4eed2af476d1ce87680bc91135885c3e721a09035a43a2773 |
"""
Copyright (C) 2014, Jaguar Land Rover
This program is licensed under the terms and conditions of the
Mozilla Public License, version 2.0. The full text of the
Mozilla Public License is at https://www.mozilla.org/MPL/2.0/
Maintainer: Rudolf Streif (rstreif@jaguarlandrover.com)
"""
| dvthiriez/rvi_backend | config/__init__.py | Python | mpl-2.0 | 288 | [
"Jaguar"
] | f675540eee93df6ff2f7af4b0fd5d11cfe6eb4197fe3cb39c14d3527218e5408 |
#!/usr/bin/env python2
#
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# 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,... | govarguz/espressopp | bench/polymer_melt/espressopp/espressopp_polymer_melt_tabulated.py | Python | gpl-3.0 | 6,896 | [
"ESPResSo",
"Gromacs",
"LAMMPS"
] | 0fce6120917ed4a85405a0710458d53d70654fd484f4d8423435c3f00e03877e |
"""Example creating minimal model.
This demonstrates just the very core SBML functionality.
"""
from pathlib import Path
import libsbml
from sbmlutils import EXAMPLES_DIR
from sbmlutils.cytoscape import visualize_sbml
from sbmlutils.examples import templates
from sbmlutils.factory import *
from sbmlutils.metadata im... | matthiaskoenig/sbmlutils | src/sbmlutils/examples/complete_model.py | Python | lgpl-3.0 | 4,944 | [
"Cytoscape"
] | ed69b9a1c4b4fcac4340c3f62ff286d9e0c61985419257e0e39fae41f8720e32 |
#!/usr/bin/env python
"""Find the functions in a module missing type annotations.
To use it run
./functions_missing_types.py <module>
and it will print out a list of functions in the module that don't
have types.
"""
import argparse
import ast
import importlib
import os
NUMPY_ROOT = os.path.dirname(os.path.join(
... | simongibbons/numpy | tools/functions_missing_types.py | Python | bsd-3-clause | 3,211 | [
"VisIt"
] | 9b8428ffb8f0539def9937a36e3d50528cc626eb01bb8b37b867e778193b7705 |
import logging
import os
import pysam
import subprocess
class AnnotationError(Exception):
pass
def ensureIndexed(bedPath, preset="bed", trySorting=True):
if not bedPath.endswith(".gz"):
if not os.path.exists(bedPath+".gz"):
logging.info("bgzf compressing {}".format(bedPath))
p... | gatoravi/svviz | src/svviz/tabix.py | Python | mit | 2,083 | [
"pysam"
] | bea6b69d391e49e08f17fc4871aa84ee8e89c7ff96052feede00874fa1a1d1d4 |
import simtk.openmm as mm
import simtk.unit as u
import numpy as np
class Unpacker(object):
def __init__(self, state):
positions, velocities, forces, time, kinetic_energy, potential_energy, boxes, parameters = self.state_to_tuple(state)
self.kinetic_energy_unit = kinetic_energy.unit
... | kyleabeauchamp/DBayes | dbayes/unpacking.py | Python | gpl-2.0 | 4,727 | [
"OpenMM"
] | 69c4945f1bf0c61e750cdf11c1d45478751dc9369608d572b3c83cac24bf79a5 |
from django.conf import settings
from django.core.management.base import BaseCommand, CommandError
from optparse import make_option
import os
import sys
try:
from django.contrib.staticfiles.handlers import StaticFilesHandler
USE_STATICFILES = 'django.contrib.staticfiles' in settings.INSTALLED_APPS
except Impor... | rtucker-mozilla/inventory | vendor-local/src/django-extensions/django_extensions/management/commands/runserver_plus.py | Python | bsd-3-clause | 4,895 | [
"VisIt"
] | 016578c3721273f5021a1fcd543efc40d19455668e23ecad228a6af2b19062ae |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# king_phisher/client/export.py
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, th... | guitarmanj/king-phisher | king_phisher/client/export.py | Python | bsd-3-clause | 20,188 | [
"VisIt"
] | 022ab9e955332fab9997ba20c387e6a961b94d9d50c8d977817ff4cdb2960b92 |
import logging
import time
import functools
import urllib
import random
try:
import simplejson as json
except ImportError:
import json # pyflakes.ignore
import tornado.ioloop
import tornado.httpclient
from backoff_timer import BackoffTimer
from client import Client
import nsq
import async
class Reader(Cli... | pombredanne/pynsq | nsq/reader.py | Python | mit | 26,239 | [
"BLAST"
] | fd26db185b4cf2a522630d2bb7d3b0b049193191652ef6c78b8e9039e55e5976 |
import h5py
import sys
import numpy as np
"""
sl files use an lz4 compression filter for which a plugin needs to be installed
Mac:
sudo port install hdf5-lz4-plugin
Ubuntu: (http://gisaxs.com/index.php/HDF5)
sudo add-apt-repository ppa:eugenwintersberger/pni
sudo apt-get update
sudo apt-get install hdf5-plugin-lz4
... | andy-d-palmer/pyIMS | pyImagingMSpec/convert/sl.py | Python | apache-2.0 | 8,335 | [
"VisIt"
] | 88afb3c628ba60e6360fd2315cf3ed0a462dbe7ecddb5ee7bc01d55127bc809f |
#
# Parse tree nodes for expressions
#
import cython
cython.declare(error=object, warning=object, warn_once=object, InternalError=object,
CompileError=object, UtilityCode=object, TempitaUtilityCode=object,
StringEncoding=object, operator=object,
Naming=object, Nodes=objec... | JulienMcJay/eclock | windows/Python27/Lib/site-packages/Cython/Compiler/ExprNodes.py | Python | gpl-2.0 | 420,289 | [
"VisIt"
] | ef8e378f69a16b2f09789fdf625f85b3a12eb41659c1e485c1572349f2dc1e34 |
"""
mlab: a simple scripting interface to Mayavi2 for 3D plotting.
Can be used inside Mayavi2 itself, in "ipython -wthread", or in any
application with the WxWidget mainloop running.
"""
# Author: Prabhu Ramachandran <prabhu_r@users.sf.net>
# Gael Varoquaux <gael dot varoquaux at normalesup dot org>
# Copyrig... | liulion/mayavi | mayavi/mlab.py | Python | bsd-3-clause | 3,018 | [
"Mayavi"
] | 762bd5a1bc96f9dd56a51e2996d0cacc198be964e2be9efb6f359f754b21c79c |
import re
import copy
from numpy import array,floor,sqrt,zeros,prod,dot,ones,empty,min,max
from numpy import pi,sin,cos,arccos as acos,arctan2 as atan2
from numpy.linalg import inv,det
from extended_numpy import simplestats,ndgrid,ogrid,arange,simstats
from hdfreader import HDFgroup
from qaobject import QAobject
#simp... | habanero-rice/hcpp | test/performance-regression/full-apps/qmcpack/nexus/library/spacegrid.py | Python | bsd-3-clause | 45,391 | [
"QMCPACK"
] | 0696880867ab09ba75ea54697525e9161fd2bca003d1f3e590cedff7bad0014c |
#! /usr/bin/env python3
#
# SCANIT - Control A spectrometer and collect data
#
# LICENSE:
# This work is licensed under the Creative Commons Zero License
# Creative Commons CC0.
# To view a copy of this license, visit
# http://directory.fsf.org/wiki/License:CC0
# or send a letter to:
# Creative Commons, PO Box 1866, M... | jluscher/SCANIT | scanit_v032.py | Python | cc0-1.0 | 81,068 | [
"VisIt"
] | 1ffccdb492845519d02ce1dcd41eb9ce527a78f321cde46ea2fd97bffd7ca613 |
#!/usr/bin/env python
from __future__ import print_function
from operator import itemgetter
import math
import numpy
import vtk
import math
class CoarsenSurface:
EPS = 1.23456789e-10
TWOPI = 2.0 * math.pi
def __init__(self, pdata):
"""
Constructor
@param pdata vtkPolyData instanc... | gregvonkuster/icqsol | shapes/icqCoarsenSurface.py | Python | mit | 12,617 | [
"VTK"
] | 98b6b9fc86d6873e18e8a59d22efc006a20e6781674278de6be46ac43c588181 |
"""
Script for an easy installation/compilation of aRMSD from command line
License: MIT
(c) 2016 by Arne Wagner
*Recent changes:
- Installer writes PyInstaller .spec file on-the-fly
- Added support for openbabel (writes hook if none exists)
- PyInstaller imports/excludes can be modified in the functions
- Add... | armsd/aRMSD | compile_aRMSD.py | Python | mit | 20,550 | [
"Pybel",
"VTK"
] | df3fc877cee394075c3b7bbeaad0e8bda950372f492e60dab10afd712ed9e72d |
# test_corrector.py
from malaprop.correction.corrector import *
from recluse.nltk_based_segmenter_tokeniser import *
from malaprop.correction.HMM import *
from DamerauLevenshteinDerivor.cderivor import Derivor
from BackOffTrigramModel.BackOffTrigramModelPipe import BackOffTMPipe
import unittest, StringIO, subprocess
... | ambimorph/malaprop | malaprop/test/test_corrector.py | Python | agpl-3.0 | 3,109 | [
"ORCA"
] | 9a8ca44bb8ac0c78cfc1a15b5af7e8a971f5e3cfd3aab2a41374a19350d9bd9a |
from noaaclass import noaaclass
import itertools
import sys
import os
from urllib import urlretrieve
import threading
from Queue import Queue
from datetime import datetime
from goescalibration import instrument as calibrator
from netcdf import netcdf as nc
import logging
import logging.handlers
logger = logging.getLo... | gersolar/goesdownloader | goesdownloader/instrument.py | Python | mit | 4,027 | [
"NetCDF"
] | 76db1255355205ad58466e6f31ca7037c0a5168b00821a9eed2d8e627e2733cb |
import unittest
import time
import os, sys, numpy, pysam
from margin.marginCallerLib import vcfRead
from margin.utils import ReadAlignmentStats, pathToBaseNanoporeDir, getFastaDictionary
from cPecan.cPecanEm import Hmm
from sonLib.bioio import system, parseSuiteTestOptions, logger, getBasicOptionParser
import vcf
impor... | isovic/marginAlign | tests/tests.py | Python | mit | 12,560 | [
"BWA",
"pysam"
] | 70fc20fe85a7e55887cc4530d281768f58e136f28b82f69c7bb119ae90857925 |
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at https://mozilla.org/MPL/2.0/.
"""
Tests specific functionality of the bands plot.
Different inputs are tested (siesta .bands and sisl Hamiltonian).
... | zerothi/sisl | sisl/viz/plots/tests/test_geometry.py | Python | mpl-2.0 | 9,456 | [
"SIESTA"
] | 9ac31046f9fd8fb1b33f84cbd1e8266c9d96989a71cf129efa30a53ebbda2851 |
##############################################################################
# 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/pexsi/package.py | Python | lgpl-2.1 | 4,943 | [
"DIRAC"
] | b0370b087c8d29683d5d1bb43a4b589bd19421a620c49d6aeab49c177a179dc1 |
#
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not... | apache/airflow | airflow/www/utils.py | Python | apache-2.0 | 26,115 | [
"VisIt"
] | ef66c5d948f8bb7df5f40e0812ee761879507f9d67a206acea66b1f3a9b0e536 |
"""
KeepNote
Classic three-paned viewer for KeepNote.
"""
#
# KeepNote
# Copyright (c) 2008-2009 Matt Rasmussen
# Author: Matt Rasmussen <rasmus@mit.edu>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Fr... | reshadh/Keepnote-LaTeX | keepnote/gui/three_pane_viewer.py | Python | gpl-2.0 | 36,245 | [
"VisIt"
] | 4f857ab012976eb6cd7fc3b6bad04b532d9837aa88d53c6c015801910694db78 |
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Mathieu Blondel <mathieu@mblondel.org>
# Olivier Grisel <olivier.grisel@ensta.org>
# Andreas Mueller <amueller@ais.uni-bonn.de>
# Eric Martin <eric@ericmart.in>
# Giorgio Patrini <giorgio.patrini@anu.edu.au>
# ... | glemaitre/scikit-learn | sklearn/preprocessing/_data.py | Python | bsd-3-clause | 115,697 | [
"Gaussian"
] | 5a2f5dfb8f2e10dfc2cd39c7c90d1ce6ab87f0211472deb3bad66127ef9f4c26 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 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
#... | CDSherrill/psi4 | psi4/driver/qcdb/qcprog_psi4.py | Python | lgpl-3.0 | 12,630 | [
"CFOUR",
"Psi4"
] | ee9b698de4043ff6ac95c8cd6eb021e9fc20c8cef125ff69d4a1f6d0aea4a210 |
#!/home-1/asierak1@jhu.edu/ParaView-4.2.0-Linux-64bit/bin/pvpython
# README
#
# Dependencies (I have tested it with these; others may also work):
# - ParaView-4.2.0
# - ffmpeg release/2.8 (git://source.ffmpeg.org/ffmpeg.git)
#
# Usage:
# - Change the path given in Line 1 to point to pvpython inside your Paraview
# ... | teethfish/bluebottle | tools/animate-cgns.py | Python | apache-2.0 | 3,991 | [
"ParaView"
] | 8390189abb3e73a1de1fc6a3bc075b5945cd1a4b3365fe502c025d694df5d69d |
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
"""Code to interact with the ever-so-useful EMBOSS programs.
"""
| Ambuj-UF/ConCat-1.0 | src/Utils/Bio/Emboss/__init__.py | Python | gpl-2.0 | 236 | [
"Biopython"
] | f006b6ed087cbc5d3578c0d8ceaf830cbbd838301eff9be9e6aaa13e17b6c1ef |
# -*- coding:utf-8 -*-
import test_core
import demjson
import datetime
test_core.title("登录测试")
f = open("testconfig.json", 'r')
lines = f.read()
f.close()
jsonfiledata = demjson.decode(lines)
if jsonfiledata["url"] == "":
test_core.terr("错误： 'testconfig.json' 配置不完全。")
exit()
uurl = jsonfiledata["url"]+"nyalogin... | cxchope/YashiLogin | tests/test_login.py | Python | mit | 712 | [
"MOE"
] | 04d888187c48d6d7c5b981d5fbeaf772bbc16e22b30a44a2277816a0ad92cf8f |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | reminisce/mxnet | python/mxnet/ndarray/numpy/random.py | Python | apache-2.0 | 9,554 | [
"Gaussian"
] | f1460b452400ca080bb0c50d00cd14628fdc226e502494af13b8b1f029872a32 |
# archan.py ---
#
# Filename: archan.py
# Description:
# Author: subhasis ray
# Maintainer:
# Created: Mon Apr 27 15:34:07 2009 (+0530)
# Version:
# Last-Updated: Fri Oct 21 16:04:17 2011 (+0530)
# By: Subhasis Ray
# Update #: 10
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#... | BhallaLab/moose-thalamocortical | DEMOS/pymoose/traub2005/py/archan.py | Python | lgpl-2.1 | 966 | [
"MOOSE"
] | a2cde406b0695f896ec1d721a71590b087df4b0d28966ceefbb7426917b2ec67 |
from gpaw import GPAW
from ase import *
from gpaw.utilities import equal
a = 7.0
Be_solid = Atoms([Atom('Be', (0.0, 0.0, 0.0), magmom=0)],
cell=(a, a, a), pbc=True)
Be_alone = Atoms([Atom('Be', (a/2., a/2., a/2.), magmom=0)],
cell=(a, a, a), pbc=False)
Be_solidC = Atoms([Atom('Be'... | qsnake/gpaw | oldtest/Be_charged.py | Python | gpl-3.0 | 2,014 | [
"ASE",
"GPAW"
] | 5a04ab10649c40ecbd5a9af0047cd5c8464cf62ffe72d5302fcd034a96df755a |
"""DIRAC Administrator API Class
All administrative functionality is exposed through the DIRAC Admin API. Examples include
site banning and unbanning, WMS proxy uploading etc.
"""
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
__RCSID__ = "$Id$"
import... | yujikato/DIRAC | src/DIRAC/Interfaces/API/DiracAdmin.py | Python | gpl-3.0 | 29,759 | [
"DIRAC"
] | 7d0ce51b2bfef9fe21fa95db571cd550aa958e06f6196219bc04eb6513416940 |
"""Random variable generators.
integers
--------
uniform within range
sequences
---------
pick random element
pick random sample
generate random permutation
distributions on the real line:
------------------------------
uniform
... | google/grumpy | third_party/stdlib/random.py | Python | apache-2.0 | 22,864 | [
"Gaussian"
] | d1f29fd27da70591b1ba3054551d81b271dc4d1986bee32a1fd818e4134b02a7 |
#!/usr/bin/env python
# Copyright (c) 2015, Matt Johansen
# All rights reserved.
# 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
# l... | mattjay/WebLogStats | webStats.py | Python | mit | 3,876 | [
"VisIt"
] | b0b30a6febd0a50fe33840f02635abe1ee98ddeb04be51c32bb0d917450c2c17 |
"""Cliches are cliché."""
from proselint.tools import existence_check, memoize
@memoize
def check_cliches_garner(text):
"""Check the text.
source: Garner's Modern American Usage
source_url: http://bit.ly/1T4alrY
"""
err = "cliches.garner"
msg = "'{}' is cliché."
cliches = [
... | amperser/proselint | proselint/checks/cliches/misc.py | Python | bsd-3-clause | 25,334 | [
"BLAST",
"CRYSTAL"
] | 6ff7d19e6f185104cfe49411ec4f2b0f593e00a61d807a73b3721033a594f9ee |
#!/usr/bin/env python
#
# Copyright 2005, 2006, 2007 Free Software Foundation, Inc.
#
# This file is part of GNU Radio
#
# GNU Radio 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, or (at y... | trnewman/VT-USRP-daughterboard-drivers_python | gnuradio-examples/python/digital/benchmark_loopback.py | Python | gpl-3.0 | 7,150 | [
"Gaussian"
] | c6024c0e2c819dc7d9e4e860bec75b1b175aa4a2ab17fcbeaa3ec02f9300c2c8 |
import textwrap
def print_intro():
# Level - 1
# TODO print an introduction to the game, with some helpful hints
pprint("intro")
def print_help():
# Level - 2
# TODO print help text
pprint("help")
def print_goodbye():
# Level - 2
global g_score
# TODO print goodbye text, alo... | kkrugler/bitney-adventure | adventure-skeleton.py | Python | apache-2.0 | 29,758 | [
"exciting"
] | 19b65cbd13bc4eeb92f4e8352f797dd12b0581491f80b4f2e25a5e3c17b582d7 |
# axes.py
from pymol.cgo import *
from pymol import cmd
from pymol.vfont import plain
# create the axes object, draw axes with cylinders coloured red, green,
#blue for X, Y and Z
obj = [
CYLINDER, 0., 0., 0., 10., 0., 0., 0.2, 1.0, 1.0, 1.0, 1.0, 0.0, 0.,
CYLINDER, 0., 0., 0., 0., 10., 0., 0.2, 1.0, 1.0, 1.0,... | demharters/git_scripts | pymol_axes2.py | Python | apache-2.0 | 845 | [
"PyMOL"
] | 4334a1701742de7618cf347658a81f6d617882aff701bf10515153345aa2c0dc |
"""
Test for the various mlab source functions.
These tests are higher level than the tests testing directly the
MlabSource subclasses. They are meant to capture errors in the formatting
of the input arguments.
"""
# Author: Gael Varoquaux <gael dot varoquaux at normalesup dot org>
# Copyright (c) 2008, Enthought, Inc... | liulion/mayavi | mayavi/tests/test_mlab_source_integration.py | Python | bsd-3-clause | 16,642 | [
"Mayavi"
] | 3dc1d26ae3b94c15f4c0c5d702d38e6290c037a00c93d847bb29de770bf59379 |
#
# @file TestReadSBML.py
# @brief Read SBML unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Ben Bornstein
#
# $Id$
# $HeadURL$
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatically by converting ... | alexholehouse/SBMLIntegrator | libsbml-5.0.0/src/bindings/python/test/sbml/TestReadSBML.py | Python | gpl-3.0 | 55,343 | [
"VisIt"
] | 2afea172e5a7226cc0a396267f03ff6cd6ac20d0c0e1a8d694189c76a8375f60 |
#!/ysr/bin/env python
from __future__ import division
import utils as utils
import numpy as np
import numpy.random as npr
import theano
import theano.tensor as T
import time
from HelperFuncs import to_fX
def my_batched_dot(A, B):
"""
Compute: [np.dot(A[i,:,:], B[i,:,:]) for i in range(A.shape[0])]
"""
... | Philip-Bachman/Sequential-Generation | MotionRenderers.py | Python | mit | 14,522 | [
"Gaussian"
] | acc46b05920952088209602197b702c365980d873c8d7d4380b70a62db8ac8e3 |
import numpy as np
import scipy as sp
from scipy import fftpack as fft
import cv2
import math
import os
import os.path
from scipy.ndimage.filters import gaussian_filter
import cvUtils
import principalColorSpace as pcs
import saliency
def colorSRS(image, weights = None, avgHalfsize = 8, gaussianSigma = 32, maxDim = 500... | alexisVallet/anime-bgrm | spectralResidualSaliency.py | Python | gpl-2.0 | 3,853 | [
"Gaussian"
] | 38cabc1318c9863a815ec413a8e4414d47582ddcc75b745b4a907cb9be134dea |
from test import test_support
import unittest
import codecs
import locale
import sys, StringIO
def coding_checker(self, coder):
def check(input, expect):
self.assertEqual(coder(input), (expect, len(input)))
return check
class Queue(object):
"""
queue: write bytes at one end, read bytes from th... | HiSPARC/station-software | user/python/Lib/test/test_codecs.py | Python | gpl-3.0 | 81,185 | [
"FEFF"
] | aba645de64c417b14f50dff964cf5ae21f8bee0e7346df71cbb8a7f96fa31c5e |
import pandas as pd
from sklearn.ensemble import RandomForestClassifier
from sklearn.ensemble import GradientBoostingClassifier
from sklearn.ensemble import BaggingClassifier
from sklearn.ensemble import AdaBoostClassifier
from sklearn.ensemble import ExtraTreesClassifier
from sklearn.neural_network import MLPClassifie... | rupakc/Kaggle-Compendium | can-you-predict-product-backorders/backorder-baseline.py | Python | mit | 3,036 | [
"Gaussian"
] | b115e68ab3e401cf516ba523e6748ef8e1ebeb045c76c42c246aaab8d473158b |
# Import of the relevant tools
import time
import numpy as np
import theano
import theano.tensor as T
from theano import pp, config
from plotly.tools import FigureFactory as FF
import plotly.graph_objs as go
from ..io.read_vtk import ReadVTK
from ..data_attachment.measures import Measures
from ..data_attachment.v... | jeanfeydy/lddmm-ot | LDDMM_Python/lddmm_python/modules/manifolds/theano_shapescarrier.py | Python | mit | 3,957 | [
"Gaussian"
] | 687b1970b1a0e53a4d1ad91ecd67ac458996a480d8bbe99f1af8ae309ada2c89 |
import cv2
import scipy
from scipy import signal
import pylab
import math
import numpy as np
from dynamicThreshold import OtsuThresholdMethod
class SimpleEdgeDetect:
def smooth_image(self, im):
gaussian = [2, 4, 5, 4, 2,
4, 9, 12, 9, 4,
5, 12, 15, 12, 5,
... | lancekindle/canny-edge | Cartoonizer.py | Python | gpl-3.0 | 10,855 | [
"Gaussian"
] | bde17a94ed06dafac86befd1e29584357d7f82350f1f18c9134c37cae1b701ae |
#!/bin/env python
""" create and put 'ReplicateAndRegister' request """
__RCSID__ = "$Id: $"
import os
from DIRAC.Core.Base import Script
Script.setUsageMessage( '\n'.join( [ __doc__,
'Usage:',
' %s [option|cfgfile] requestName LFNs targetSE1 [ta... | vmendez/DIRAC | DataManagementSystem/scripts/dirac-dms-replicate-and-register-request.py | Python | gpl-3.0 | 4,138 | [
"DIRAC"
] | 943f6b3322be9cb46d739ebbc7b2724bbaa5196e7238f515be6ffc04a609d7fe |
#!/usr/bin/env python
__author__ = 'waroquiers'
import unittest
import os
import json
import numpy as np
import shutil
from monty.tempfile import ScratchDir
from pymatgen.util.testing import PymatgenTest
from pymatgen.analysis.chemenv.coordination_environments.structure_environments import StructureEnvironments
fr... | dongsenfo/pymatgen | pymatgen/analysis/chemenv/coordination_environments/tests/test_structure_environments.py | Python | mit | 12,696 | [
"pymatgen"
] | dbbfff4d8e02273d26a10f3a2b30f6347db19defcff3dab0ebb2c4004d442dd1 |
# encoding: utf-8
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding field 'Indicator.last_generated_at'
db.add_column('profiles_indicator', 'last_generated_at', self... | 216software/Profiles | communityprofiles/profiles/oldmigrations/0046_auto__add_field_indicator_last_generated_at.py | Python | mit | 15,298 | [
"MOE"
] | 95b001b74823db562ec58ccc60c2cad84bc9e900bc9f5252f9dc093e67086205 |
"""All models (or business logic) for the web app should be here.
This including wrappers around talking with the database.
"""
from .customerfamily import CustomerFamily # noqa
from .dependent import Dependent # noqa
from .shopping_category import ShoppingCategory # noqa
from .shopping_item import ShoppingItem ... | jlutz777/FreeStore | models/__init__.py | Python | mit | 458 | [
"VisIt"
] | b69132ea3363b97452a101591df3ae1b34494296e3ce3c911bcebdf1293e271d |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""SPM wrappers for preprocessing data
Change directory to provide relative paths for doctests
>>> import os
>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
>>> datadir = os.path... | sgiavasis/nipype | nipype/interfaces/spm/preprocess.py | Python | bsd-3-clause | 77,455 | [
"Gaussian"
] | 50e6f1c119c36c272ac9fb13263280b2a7a7bbbb81f212e0cf485eb25ca260c2 |
import os,sys
import numpy as np
import pandas as pd
from tqdm import tqdm
from rdkit import Chem
from rdkit.Chem import MACCSkeys
from utils import (ohe_label,
PAD_ID,
remove_salts)
max_char_len = 100
min_char_len = 20
data_dir = 'data/compounds'
out_file = 'data/features_fp166.npz'
sdf_list = [os.pa... | kdmarshall/FingerprintDecoder | scripts/featurize_maccs.py | Python | mit | 1,424 | [
"RDKit"
] | e044bdbec1a8a32e833809f1918cbe690208f08119e8455efc63fa538b2774c5 |
#!/usr/bin/env python
"""
Kill or delete DIRAC job
"""
__RCSID__ = "$Id$"
import DIRAC
from DIRAC.Core.Base import Script
from COMDIRAC.Interfaces import DSession
class Params:
def __init__ ( self ):
self.delete = False
self.selectAll = False
self.verbose = False
def setDelete( self, arg = None ):
... | pigay/COMDIRAC | Interfaces/scripts/dkill.py | Python | gpl-3.0 | 2,337 | [
"DIRAC"
] | ddf53f9c01b5db1f76257af25f6ee1dcbd7c1e78e8edb488ee10f3eaa998e764 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# (c) 2012 Michal Kalewski <mkalewski at cs.put.poznan.pl>
#
# This file is a part of the Simple Network Simulator (sim2net) project.
# USE, MODIFICATION, COPYING AND DISTRIBUTION OF THIS SOFTWARE IS SUBJECT TO
# THE TERMS AND CONDITIONS OF THE MIT LICENSE. YOU SHOULD H... | mkalewski/sim2net | sim2net/speed/constant.py | Python | mit | 2,039 | [
"VisIt"
] | dabcc65dc555604ea1863a79363efd917878b1128758ba4502b44d3a49a2f20d |
"""
Testing for Gaussian Process module (sklearn.gaussian_process)
"""
# Author: Vincent Dubourg <vincent.dubourg@gmail.com>
# License: BSD 3 clause
import numpy as np
from sklearn.gaussian_process import GaussianProcess
from sklearn.gaussian_process import regression_models as regression
from sklearn.gaussian_proce... | herilalaina/scikit-learn | sklearn/gaussian_process/tests/test_gaussian_process.py | Python | bsd-3-clause | 7,049 | [
"Gaussian"
] | a2031c5b08d5d24395c548a957b053e6e50dea5a914192464a5b5d3bf65359f0 |
# Copyright 2013 by Michiel de Hoon. All rights reserved.
# Copyright 2016 modified by Kevin Ha
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
from Bio.motifs import matrix
from Bio.Alphabet imp... | morrislab/rnascan | rnascan/BioAddons/motifs/matrix.py | Python | agpl-3.0 | 2,895 | [
"Biopython"
] | 21c81620a95e71c59b70bd656b4143b95a72d6dea4153cf6b9abba6e7788dfdd |
#!/usr/bin/env python
r"""
Example of solving Laplace's equation on a block domain refined with level 1
hanging nodes.
The domain is progressively refined towards the edge/face of the block, where
Dirichlet boundary conditions are prescribed by an oscillating function.
Find :math:`u` such that:
.. math::
\int_{\... | sfepy/sfepy | examples/diffusion/laplace_refine_interactive.py | Python | bsd-3-clause | 8,056 | [
"VTK"
] | 802f9adb21cfcbeb2727bfff8618aae651d9cbf393ad6a2b9a663b63a10a0080 |
# Python test set -- part 1, grammar.
# This just tests whether the parser accepts them all.
# NOTE: When you run this test as a script from the command line, you
# get warnings about certain hex/oct constants. Since those are
# issued by the parser, you can't suppress them by adding a
# filterwarnings() call to this... | zephyrplugins/zephyr | zephyr.plugin.jython/jython2.5.2rc3/Lib/test/test_grammar.py | Python | epl-1.0 | 21,632 | [
"GULP"
] | 1aea9c77c161a1e4bafc069df2679fc95036f34eb31dbb7003f97d9e9b5bcc66 |
from ase import Atoms
from gpaw import GPAW, ConvergenceError
from gpaw.mixer import Mixer, MixerSum
# C2 singlet from http://toc.uni-muenster.de/GMTKN/GMTKN30/W4-08.html
m = Atoms(symbols='C2',
positions=[
[ 0. , 0. , -0.62000006],
[ 0. , 0. , 0.62000006]],
)... | robwarm/gpaw-symm | gpaw/test/big/scf/C2/C2.py | Python | gpl-3.0 | 1,670 | [
"ASE",
"GPAW"
] | 8f0cead4a6ecfaa607f9b90a7801521ec8e4d86c7031c6c684fa55e1686e5c7b |
#!/usr/bin/env python
"""
Demos of MIMO time encoding and decoding algorithms that use IAF
neurons with delays.
"""
# Copyright (c) 2009-2015, Lev Givon
# All rights reserved.
# Distributed under the terms of the BSD license:
# http://www.opensource.org/licenses/bsd-license
import numpy as np
# Set matplotlib backe... | bionet/ted.python | demos/iaf_delay_demo.py | Python | bsd-3-clause | 3,443 | [
"NEURON"
] | 7ea3fc6eb6950c5ba79c3e97182b446fd880d01d2571e65f7a4ab0fc95e1e4ca |
#!/usr/bin/env python
"""Module cma implements the CMA-ES, Covariance Matrix Adaptation Evolution
Strategy, a stochastic optimizer for robust non-linear non-convex
derivative-free function minimization for Python versions 2.6, 2.7, 3.x
(for Python 2.5 class SolutionDict would need to be re-implemented, because
it ... | CG-F16-24-Rutgers/steersuite-rutgers | steerstats/tools/cma/cma.py | Python | gpl-3.0 | 315,091 | [
"exciting"
] | 6d03ce069db3e5f888b2167c38869ca9bf0cdb0a9aec209cc27f6b233a16da86 |
import mdtraj as md
import numpy as np
from mdtraj.testing import get_fn, eq
from msmbuilder.featurizer import SASAFeaturizer
def _test_sasa_featurizer(t, value):
sasa = md.shrake_rupley(t)
rids = np.array([a.residue.index for a in t.top.atoms])
for i, rid in enumerate(np.unique(rids)):
mask = (... | msultan/msmbuilder | msmbuilder/tests/test_sasa_featurizer.py | Python | lgpl-2.1 | 1,041 | [
"MDTraj"
] | 0b97f566ad394a3c89ea1e5a29f871ec7df574248ebed03e5a9b7e206590bfda |
import urllib.request as ul
import re
from bs4 import BeautifulSoup
import time
import random
class HotBlog(object):
url_pattern = "http://www.baidu.com/s?ie=utf-8&pn={pn}&wd={wd}"
headers = {
'User-Agent': 'Mozilla/5.0 (Windows; U; Windows NT 6.1; en-US; rv:1.9.1.6) Gecko/20091201 Firefox/3.5.6'}
... | gavinfish/Awesome-Python | HotBlog/HotBlog.py | Python | apache-2.0 | 2,166 | [
"VisIt"
] | 82d0a129ddb1a7980cc81b07772a4458aa1f084feaa9cee42662062f1c479fe5 |
from setuptools import setup, Extension
from setuptools.command.build_ext import build_ext as _build_ext
from setuptools.command.sdist import sdist as _sdist
from distutils.errors import CompileError
from warnings import warn
import os.path
from glob import glob
try:
from Cython.Distutils import build_ext as _buil... | mackelab/pyRRHDLDS | setup.py | Python | bsd-3-clause | 2,633 | [
"Gaussian"
] | 0bd9c05a5f86499b718aca597139324687238f45ee4909673c1297ac8c538616 |
#! /usr/bin/env python
"""
##############################################################################
##
##
## @name : WeeklyGraphicsWebPageGenerator.py
##
##
## @author: Nicholas Lemay
##
## @license : MetPX Copyright (C) 2004-2006 Environment Canada
## MetPX comes with ABSOLUTELY NO WARRANTY; For ... | khosrow/metpx | pxStats/lib/WeeklyGraphicsWebPageGenerator.py | Python | gpl-2.0 | 39,530 | [
"VisIt"
] | 897ff2c36d3a18bf582652afbf623cd1d1edf7333b61e84a04ffa40ea63a36a3 |
# -*- coding: utf-8 -*-
"""Collection of physical constants and conversion factors.
The magnitudes of the defined constants are taken from
:mod:`typhon.constants`.
This module adds units defined with pint's UnitRegistry..
Physical constants
==================
============================ =========================... | atmtools/typhon | typhon/physics/units/constants.py | Python | mit | 4,058 | [
"Avogadro"
] | 3842ebff2759fe43d6785b26f14b02dce42dea21abbcecd10b6f75686329eed0 |
"""Store configuration options as a singleton."""
import os
import re
import subprocess
import sys
from argparse import Namespace
from functools import lru_cache
from typing import Any, Dict, List, Optional, Tuple
from packaging.version import Version
from ansiblelint.constants import ANSIBLE_MISSING_RC
DEFAULT_KIND... | ansible/ansible-lint | src/ansiblelint/config.py | Python | mit | 6,042 | [
"Galaxy"
] | 92dbab92fe56e5b4e0969cff0af7a116a6c97e1214cc6d9da1c43fb7b3ff7cb1 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for Student's Profile Page.
"""
from datetime import datetime
from bok_choy.web_app_test import WebAppTest
from ...pages.common.logout import LogoutPage
from ...pages.lms.account_settings import AccountSettingsPage
from ...pages.lms.auto_auth import AutoAuthPage
from ...pag... | DefyVentures/edx-platform | common/test/acceptance/tests/lms/test_learner_profile.py | Python | agpl-3.0 | 30,799 | [
"VisIt"
] | 844b1425866bc0365917af1ff362cca1dfa53ba1e2acf0e5730bb261768837c8 |
# -*- coding: utf-8 -*-
__author__ = "Andres Giordano"
__version__ = "1.0"
__maintainer__ = "Andres Giordano"
__email__ = "andresgiordano.unlu@gmail.com"
__status__ = "Produccion"
import matplotlib as mpl
import matplotlib.pyplot as plt
import setuptools
import os.path
from pyart.graph import RadarDisplay, common, ... | INTA-Radar/radar-cmd | Procesador/RainbowRadarProcessor.py | Python | gpl-3.0 | 18,237 | [
"NetCDF"
] | a7e71f67defd0e63ba7bb9a574d663eddaac0a2fef2b82a1f2971ec3e4464c24 |
# Copyright (c) 2012, GPy authors (see AUTHORS.txt).
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
from .stationary import Stationary
from .psi_comp import PSICOMP_RBF, PSICOMP_RBF_GPU
from ...core import Param
from paramz.caching import Cache_this
from paramz.transformations import L... | esiivola/GPYgradients | GPy/kern/src/rbf.py | Python | bsd-3-clause | 9,472 | [
"Gaussian"
] | 5711df051c87baacf8ae6e2f211e8b497e992da11d6fd4dd924514b9cd37a10f |
# (c) 2012-2014, Michael DeHaan <michael.dehaan@gmail.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) an... | majidaldo/ansible | v2/ansible/utils/color.py | Python | gpl-3.0 | 3,134 | [
"Brian"
] | 4b458630f3d0d824aaa53f9508fca0e7ad4b098d5d6fad5e821afba7e997e606 |
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