text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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from bs4 import BeautifulSoup
import requests
import hashlib
import shutil
import os
import re
import sys
import unshortenit
if sys.version_info[0] == 3:
from urllib.parse import quote
else:
from urllib import quote
class Download():
item = None
repo = None
def __init__(self, repo, item):
... | MCProHosting/at-helper | at_helper/download.py | Python | mit | 3,492 | [
"ADF"
] | 427148c4368263a48660dfb2bfc829836f62f69081d3addb7a2d358576dbf1ea |
# -*- coding: utf-8 -*-
"""
A serial module for accessing data from a vehicles OBD-II port
For more documentation, visit:
http://python-obd.readthedocs.org/en/latest/
"""
########################################################################
# ... | brendan-w/python-OBD | obd/__init__.py | Python | gpl-2.0 | 2,856 | [
"VisIt"
] | dceb5f0c5bcb4520ea0e505cef3a6e05d9323b5ce2de2ca427b779c7457fe161 |
# This component assembles an analysis recipe for the annual adaptive comfort component
#
# Honeybee: A Plugin for Environmental Analysis (GPL) started by Mostapha Sadeghipour Roudsari
#
# This file is part of Honeybee.
#
# Copyright (c) 2013-2020, Chris Mackey <Chris@MackeyArchitecture.com>
# Honeybee is free softw... | mostaphaRoudsari/Honeybee | src/Honeybee_Outdoor Comfort Analysis Recipe.py | Python | gpl-3.0 | 41,063 | [
"EPW"
] | 0bf1ab7baa2a09b7629f1db262cc8b432adabe28e1e6a54b7555502d875a1d08 |
import locale
import re
import json
from StringIO import StringIO
from django.template.defaultfilters import slugify
from django.contrib.humanize.templatetags.humanize import intcomma
from django.core.exceptions import ValidationError
from huey.api import Huey
from huey.backends.base import BaseEventEmitter
from huey.b... | 216software/Profiles | communityprofiles/profiles/utils.py | Python | mit | 11,855 | [
"MOE"
] | 1b84d9ff1d6981113e95ba4d8c8af9aadc9c0347f885d257c52cd0be217e2780 |
#! /usr/bin/env python
# coding=utf8
# ECDSA BTC lib
# Copyright (C) 2014 Antoine FERRON
# Some portions based on :
# "python-ecdsa" Copyright (C) 2010 Brian Warner (MIT Licence)
# "Simple Python elliptic curves and ECDSA" Copyright (C) 2005 Peter Pearson (public domain)
# "Electrum" Copyright (C) 2011 thom... | antonio-fr/SGenAdr | lib/ECDSA_BTC.py | Python | gpl-3.0 | 12,587 | [
"Brian"
] | 719a00099d20681838d394138187554a4ed59f4d586add846df1f68fe382e14c |
#!/bin/env python
""" display information about FTSJobs for a given requestID """
__RCSID__ = "$Id: $"
from DIRAC.Core.Base import Script
Script.setUsageMessage( '\n'.join( [ __doc__,
'Usage:',
' %s [option|cfgfile] requestID' % Script.scriptNa... | Sbalbp/DIRAC | DataManagementSystem/scripts/dirac-dms-show-ftsjobs.py | Python | gpl-3.0 | 2,085 | [
"DIRAC"
] | 45f668519065960b210362eba69ab0adb1b9dad56ef316ad4b3b930a048bf1ed |
import sys
import os
import subprocess
import bpy
from bpy.types import AddonPreferences
from bpy.props import BoolProperty, FloatVectorProperty, EnumProperty, IntProperty, FloatProperty, StringProperty
from sverchok.dependencies import sv_dependencies, pip, ensurepip, draw_message, get_icon
from sverchok import data_... | DolphinDream/sverchok | settings.py | Python | gpl-3.0 | 23,850 | [
"VisIt"
] | 8f31f05e726bf4ea789305e76982a4b26c173520a2d0a2fba65a39b041715254 |
#! /usr/bin/env python
# ECDSA BTC of SimpleBitID
# Copyright (C) 2014 Antoine FERRON
# Some portions based on :
# "python-ecdsa" Copyright (C) 2010 Brian Warner (MIT Licence)
# "Simple Python elliptic curves and ECDSA" Copyright (C) 2005 Peter Pearson (public domain)
# This program is free software: you can redistr... | antonio-fr/SimpleBitID | ECDSA_BTC.py | Python | gpl-3.0 | 6,006 | [
"Brian"
] | 1cd759584b0e0bd1b0112ca65e9fc36269a4804392306c276943f6c528bff5b2 |
from django.forms.models import formset_factory
from django.forms import BaseFormSet
from django.contrib import messages
from mezzanine.pages.page_processors import processor_for
from crispy_forms.layout import Layout, HTML
from functools import partial, wraps
from hs_core import page_processors
from hs_core.forms im... | ResearchSoftwareInstitute/MyHPOM | hs_app_netCDF/page_processors.py | Python | bsd-3-clause | 7,300 | [
"NetCDF"
] | 04302733950b26a0c1cc2da2d7f0133b14d963458a97087bb2280c83a6b971c1 |
# -*- coding: utf-8 -*-
#
# 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 "L... | rikima/spark | python/pyspark/ml/tests.py | Python | apache-2.0 | 118,275 | [
"Gaussian"
] | d390263e20f7d7c2634767414d9499aae3c4cc249bd929259d5ebd7870973b67 |
import os
import sys
import time
import flask_restless
import jinja2
from celery import Celery
from flask import (Flask, Response, jsonify, redirect, render_template,
request, url_for)
from flask_cors import CORS
from flask_jwt import jwt_required
from json_tricks import dumps
from raspapreco.model... | IvanBrasilico/raspa-preco | raspapreco/restless.py | Python | gpl-3.0 | 6,870 | [
"RASPA"
] | 8c8576e53e23d23c462d083b9e979bb039b3b71a8fb46bed3f32f192c9db0b0d |
#!/usr/bin/env python3
# vim: set fileencoding=utf-8 :
#
# Copyright 2011,2013 Communications Engineering Lab, KIT
#
# This 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 your option)... | kit-cel/gr-specest | python/fam_matplotlib.py | Python | gpl-3.0 | 3,914 | [
"Gaussian"
] | d09dfe3b9b968372745907b88839932e5ac3d550598d63447bdde5970e59a852 |
# -*- coding: utf8
"""Random Projection transformers
Random Projections are a simple and computationally efficient way to
reduce the dimensionality of the data by trading a controlled amount
of accuracy (as additional variance) for faster processing times and
smaller model sizes.
The dimensions and distribution of Ra... | florian-f/sklearn | sklearn/random_projection.py | Python | bsd-3-clause | 21,689 | [
"Gaussian"
] | 1859b6dcf4b2c5f687967bb140119cb8f566cf864462add193e972fa0a4aadc0 |
from pymol import cmd
def ligandNeighbors(prot, chain, ligand):
print ligand
# set some string names for temporary objects/selections
tmpObj = cmd.get_unused_name("_tmp")
tmpObj2 = cmd.get_unused_name("_bla")
# operate on a new object & turn off the original
sel = "{} and chain {}".format(prot... | smoitra87/mrfs | data/multicols/ligand.py | Python | apache-2.0 | 592 | [
"PyMOL"
] | aa4a8ad6b72227bd05b8e92ebe0397e04b739864025f6dbf9ad04e35515ed9e6 |
# -*- coding: utf-8 -*-
# Load configuration file before pyplot
import os, sys
config_path = os.path.abspath('../matplotlib/')
sys.path.append(config_path)
import configuration as config
# Library path
import os, sys
print("CWD: " + os.getcwd() )
lib_path = os.path.abspath('../../lib')
sys.path.append(lib_path)
impo... | peter-kiechle/tactile-sensors | python/filtering_temporal_and_derivatives/temporal_filtering_visualization.py | Python | gpl-3.0 | 26,278 | [
"Gaussian"
] | dde52b17cf1515f5bbf66afe9f297e417694668e858907a6645d6a680d238d5e |
"""
SAS distributions for polydispersity.
"""
# TODO: include dispersion docs with the disperser models
from __future__ import division, print_function
from math import sqrt # type: ignore
from collections import OrderedDict
import numpy as np # type: ignore
from scipy.special import gammaln # type: ignore
# pyli... | SasView/sasmodels | sasmodels/weights.py | Python | bsd-3-clause | 10,247 | [
"Gaussian"
] | 5130f349527928cbeec3d99a4c8aaa6f0b16c1ede0495abce10a39d16db34487 |
# test_nachans.py ---
#
# Filename: test_nachans.py
# Description:
# Author:
# Maintainer:
# Created: Sat May 26 10:29:41 2012 (+0530)
# Version:
# Last-Updated: Wed May 30 21:47:11 2012 (+0530)
# By: subha
# Update #: 349
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
# Unit tests ... | dilawar/moose-full | moose-examples/traub_2005/py/test_nachans.py | Python | gpl-2.0 | 11,787 | [
"MOOSE",
"NEURON"
] | e7abe188927ebd83818e44da84a8f6ba83ae4c508f4de2d0a1219342ae16c86c |
# ///////////////////////////////////\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\
# // BioDigital Content API OAuth using Python 3
# //
# // Author: BioDigital Inc.
# // Email: developers@biodigital.com
# //
# // This example uses the Flask and requests libraries for Python 3
# // found here: http://flask.pocoo.org/
# // ... | biodigital-inc/bdhuman-contentapi | python/client.py | Python | mit | 5,797 | [
"VisIt"
] | fd043230ddb5a9e52d768203b4059d69a4dea3eb044e4779c1b8389b9642cc24 |
'''
synbiochem (c) University of Manchester 2016
synbiochem is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
# pylint: disable=invalid-name
import csv
import re
import sys
import tempfile
import urllib
from Bio.PDB import par... | neilswainston/development-py | synbiochemdev/dali/dali.py | Python | mit | 2,517 | [
"VisIt"
] | ae6803ed84939dd859b8d487974e268f1bf0e20150216a34abea0ef1a8af5ea4 |
# from the Python Standard Library
import os, re, socket, sys, subprocess
# from Twisted
from twisted.internet import defer, threads, reactor
from twisted.internet.protocol import DatagramProtocol
from twisted.python.procutils import which
from twisted.python import log
try:
import resource
def increase_rlimi... | heathseals/CouchPotatoServer | libs/pyutil/iputil.py | Python | gpl-3.0 | 9,752 | [
"Brian"
] | 3f080118789aa78825d6d7724d968caa139b15bb4ac4ea6c108d5e336a55e3a5 |
"""Test generation helpers
Intended to functionalize common tasks when working with the pytest_generate_tests hook.
When running a test, it is quite often the case that multiple parameters need to be passed
to a single test. An example of this would be the need to run a Provider Add test against
multiple providers. W... | lehinevych/cfme_tests | utils/testgen.py | Python | gpl-2.0 | 20,153 | [
"VisIt"
] | 2179008cd54d12a0f1b632a9ba48e103f5b2cc070cbfb7e5c909ef2aa4af0b7c |
# Config Wizard By: Blazetamer 2013-2014
# Thanks to Blazetamer, TheHighway, and the rest of the crew at TVADDONS.ag (XBMCHUB.com).
import urllib,urllib2,re,xbmcplugin,xbmcgui,xbmc,xbmcaddon,os,sys,downloader,extract,time,shutil
import wizardmain as main
AddonTitle='Config Wizard'; wizardUrl='http://tribeca.tvaddons.ag... | azumimuo/family-xbmc-addon | plugin.video.hubwizard/default.py | Python | gpl-2.0 | 9,465 | [
"VisIt"
] | 8f3300d4bc4cb4a5bed2dc0af149ab05e029d707a71de271a568a29cdc61216c |
"""Omega matrix for functionals with Hartree-Fock exchange.
"""
from math import sqrt
import numpy as np
from numpy.linalg import inv
from ase.units import Hartree
import gpaw.mpi as mpi
from gpaw.lrtddft.omega_matrix import OmegaMatrix
from gpaw.pair_density import PairDensity
from gpaw.utilities import pack
from ... | robwarm/gpaw-symm | gpaw/lrtddft/apmb.py | Python | gpl-3.0 | 10,936 | [
"ASE",
"GPAW"
] | 050368446e5b9a0ba1fccea40969c79291cb3509f7ed94785f9607691fc73070 |
#!/usr/bin/env python
import numpy
import random
import glob
import time
import colored_traceback.always
import argparse
import subprocess
import sys
import os
# sys.path.insert(1, './python')
# if you move this script, you'll need to change this method of getting the imports
partis_dir = os.path.dirname(os.path.realp... | psathyrella/partis | test/mobille-igblast-run.py | Python | gpl-3.0 | 11,923 | [
"scikit-bio"
] | 7b283ee47a8f69dd7f7acf3e3bcbb9d48fdbe01656aa6e12383d5b9914292594 |
from builtins import range
# -*- coding: utf-8 -*-
from datetime import timedelta
import re
from qgis._core import QgsSingleBandPseudoColorRenderer
from timemanager.utils import time_util
from timemanager.layers.timerasterlayer import TimeRasterLayer
from timemanager.layers.timelayer import TimeLayer, NotATimeAttri... | anitagraser/TimeManager | raster/cdflayer.py | Python | gpl-2.0 | 5,778 | [
"NetCDF"
] | 489c54b3d25b2753a2168f1150fb0b95673e956443d736dca9ec28d4ff8d8637 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2018 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
#... | amjames/psi4 | psi4/driver/p4util/procutil.py | Python | lgpl-3.0 | 16,645 | [
"CFOUR",
"Psi4"
] | 33ee1910f72b617d7c648444cf85fc86d1d00aaa80e6470c39053208095ae181 |
"""Analyze python import statements."""
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import ast
import os
import re
from .. import types as t
from ..io import (
read_binary_file,
)
from ..util import (
display,
ApplicationError,
is_subdir,
)
from ..data im... | pmarques/ansible | test/lib/ansible_test/_internal/classification/python.py | Python | gpl-3.0 | 14,070 | [
"VisIt"
] | 687e990745b48fd3e866c7f81a7b633bd499ecbe44b40ad5f8dd63662894aaa4 |
"""
Potentials in ultracold atom experiments are typically constructed using
Gaussian laser beams, here we provide some definitions that will make it easy
to assemble a generic optical dipole potential.
"""
import numpy as np
import matplotlib.pyplot as plt
import matplotlib
from vec3 import vec3, cross
import sc... | PedroMDuarte/thesis-hubbard-lda_evap | udipole.py | Python | mit | 18,892 | [
"Gaussian"
] | 81dec170cfb7ec13ef623eeb45bc76964c9437b5f7937ca34377c0546b3b1ea0 |
# Copyright 2009 Brian Quinlan. All Rights Reserved.
# Licensed to PSF under a Contributor Agreement.
__author__ = 'Brian Quinlan (brian@sweetapp.com)'
import collections
import logging
import threading
import time
FIRST_COMPLETED = 'FIRST_COMPLETED'
FIRST_EXCEPTION = 'FIRST_EXCEPTION'
ALL_COMPLETED = 'ALL_COMPLETED... | timm/timmnix | pypy3-v5.5.0-linux64/lib-python/3/concurrent/futures/_base.py | Python | mit | 19,601 | [
"Brian"
] | 43f037135aafa8ff6a5153c3a622f1d9e32455f757a1ad5682ab6b0d5666c507 |
""" tests for the JobDB module """
#pylint: disable=protected-access, missing-docstring
import unittest
from mock import MagicMock, patch
from DIRAC import S_OK
MODULE_NAME = "DIRAC.WorkloadManagementSystem.DB.JobDB"
class JobDBTest( unittest.TestCase ):
def setUp( self ):
def mockInit(self ):
self.l... | Andrew-McNab-UK/DIRAC | WorkloadManagementSystem/DB/tests/Test_JobDB.py | Python | gpl-3.0 | 1,000 | [
"DIRAC"
] | 2599d8e1c94bd54ec3c52caff894917aa33c798371e6bbccc436a529236983b9 |
"""After analysis with WiFeS, this suite of routines can extract a star optimally
and calculate its radial velocity.
WARNING - this code is still not properly documented or complete. Any contributions
welcome!
example lines of code...
Executing from the code directory, e.g. with Margaret's output directory:
rv_proce... | PyWiFeS/tools | process_stellar.py | Python | mit | 40,839 | [
"Gaussian"
] | 06bf1d84b574ce91d121f4c2f6ccbfea80a77d6ddfaa4ef56e22d255ec0953c4 |
#
# Copyright (c) 2017 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yasharmaster/scancode-toolkit | src/commoncode/paths.py | Python | apache-2.0 | 9,708 | [
"VisIt"
] | 350987270c0bd74b8393608ddfc2475f53e72b35abda918f9b6d9febc48bfa3f |
# NeHe Tutorial Lesson: 43 - FreeType fonts in OpenGL
#
# Ported to PyOpenGL 2.0 by Brian Leair 18 Jan 2004
#
# This code was created by Jeff Molofee 2000
#
# The port was based on the PyOpenGL tutorials and from
# PyOpenGLContext (tests/glprint.py)
#
# If you've found this code useful, feel free to let me know
# at ... | mgood7123/UPM | Sources/PyOpenGL-Demo-3.0.1b1/PyOpenGL-Demo/NeHe/lesson43/lesson43.py | Python | gpl-3.0 | 6,133 | [
"Brian"
] | 7d8d96b0b87723da72bb0e89b27bc44d57dfb6148608d810795f6b888f7baeed |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides objects for extracting timing data from the ABINIT output files
It also provides tools to analye and to visualize the parallel efficiency.
"""
import collections
import logging
import os
import sys
im... | vorwerkc/pymatgen | pymatgen/io/abinit/abitimer.py | Python | mit | 31,345 | [
"ABINIT",
"pymatgen"
] | 53311b893ab3614848ac91bba8936ab304ebfb3ea4c527753acc2e01d379c939 |
# -*- coding: utf-8 -*-
SKIP_PROTOCOLS = ("javascript",
"ftp",
)
class edentest_smoke(object):
""" Smoke Test, visit every link it can find and report on the outcome """
def __init__(self, base_url, do_not_follow, ext_links):
self.base_url = base_url
self.d... | flavour/eden | tests/implementation/testsuites/smoke_tests/edentest_smoke.py | Python | mit | 1,520 | [
"VisIt"
] | 12c70ba9738c54ab7ab2ea44351e131a66d92b2cbca4815ac4c8481ea14ea785 |
import datetime
import os
import json
import ctypes # An included library with Python install.
import re
import psycopg2 as dbapi2
from flask import Flask
from flask import redirect
from flask import request
from flask import render_template
from flask import jsonify
from flask.helpers import url_for
from initializ... | itucsdb1612/itucsdb1612 | server.py | Python | gpl-3.0 | 60,554 | [
"VisIt"
] | b650ebb422014bfb41b05aa79b71fbe317ab13cbaafb8ac6fc9bd8cdcd877082 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Gary Burton
# Copyright (C) 2008 Robert Cheramy <robert@cheramy.net>
# Copyright (C) 2011 Tim G L Lyons
#
# This program is free software; you can redistribute it and/or... | ennoborg/gramps | gramps/gen/proxy/filter.py | Python | gpl-2.0 | 21,094 | [
"Brian"
] | 1a37908ae30d2aca87362ffe46ae71a959066c6d55b907ee3d0f75d1c37cb9e3 |
#
# GFSK modulation and demodulation.
#
#
# Copyright 2005-2007,2012 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 v... | courtarro/gnuradio | gr-digital/python/digital/gfsk.py | Python | gpl-3.0 | 11,172 | [
"Gaussian"
] | 50f340652b42b048da3dc7e566e7d75527fc2bf9196916c0316004d4a6a65d86 |
import numpy as np
from mpl_toolkits.basemap import pyproj
from datetime import datetime
try:
import netCDF4 as netCDF
except:
import netCDF3 as netCDF
import pyroms
class BGrid_GFDL(object):
"""
Arakawa B-Grid for GFDL CM2.1
"""
def __init__(self, lon_t, lat_t, lon_uv, lat_uv, \
... | dcherian/pyroms | pyroms_toolbox/pyroms_toolbox/BGrid_GFDL/BGrid_GFDL.py | Python | bsd-3-clause | 1,958 | [
"NetCDF"
] | cc0b307f12e5d9a402d8fbd11d8fdd25c79164fd60e8967d2bbda5e22a30ce92 |
# -*- coding: utf-8 -*-
#
# Snowbird documentation build configuration file, created by
# sphinx-quickstart on Mon Oct 4 21:45:04 2010.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# Al... | unbracketed/snowbird | docs/conf.py | Python | mit | 7,162 | [
"Brian"
] | 83d904e6a82e334f05b058405677f620b7d53bbadf2e588522f8c814e7e6d931 |
# encoding: utf-8
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2006 Martin Hawlisch, Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011 Tim G L Lyons
#
# This program is free software; you can redistribute it a... | arunkgupta/gramps | gramps/plugins/tool/testcasegenerator.py | Python | gpl-2.0 | 82,564 | [
"Brian"
] | 2132fa7a729edb0af3d4bbcfce046db6c668390e5f53b5f021ec1bf0bfd56a88 |
from __future__ import print_function, division, unicode_literals
import os
import twod_materials.utils as utl
from pymatgen.matproj.rest import MPRester
from pymatgen.core.structure import Structure
from pymatgen.core.periodic_table import Element
from pymatgen.io.vasp.inputs import Kpoints, Incar
from monty.seria... | ashtonmv/twod_materials | twod_materials/stability/startup.py | Python | gpl-3.0 | 3,859 | [
"VASP",
"pymatgen"
] | 259d6dafb59c345cc7f89f3d81373f7ef1e70f5a7a1eae60321a89fa457454c4 |
import datetime
import hashlib
import itertools
import logging
import os
import time
from collections import defaultdict
from dataclasses import asdict, dataclass, field
from operator import itemgetter
from typing import (
AbstractSet,
Any,
Callable,
Collection,
Dict,
Iterable,
List,
Map... | punchagan/zulip | zerver/lib/actions.py | Python | apache-2.0 | 288,277 | [
"Octopus"
] | dbc8dcc2e6c44007016fe18121d34f5a537ab448f48ef79c2d1c5bff6645078d |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Yambo(AutotoolsPackage):
"""Yambo is a FORTRAN/C code for Many-Body calculations in solid
... | LLNL/spack | var/spack/repos/builtin/packages/yambo/package.py | Python | lgpl-2.1 | 5,358 | [
"ABINIT",
"NetCDF",
"Yambo"
] | eff4fe06110c00d2e3fbc863727092f3e8f8c56bcdcc5764ab96134e8b041376 |
#!/usr/bin/env python
"""
Artificial Intelligence for Humans
Volume 2: Nature-Inspired Algorithms
Python Version
http://www.aifh.org
http://www.jeffheaton.com
Code repository:
https://github.com/jeffheaton/aifh
Copyright 2014 by Jeff Heaton
Licensed under the Apache License, Versi... | PeterLauris/aifh | vol2/vol2-python-examples/examples/capstone_alife/alife_milestone2.py | Python | apache-2.0 | 11,519 | [
"VisIt"
] | 2155ee2e18b5801bf277d4b457280c791e921b47547bfdf45551c9f161c6ea37 |
from ase.cluster import Icosahedron
from ase.ga.particle_crossovers import CutSpliceCrossover
from random import shuffle
ico1 = Icosahedron('Cu', 5)
ico1.info['confid'] = 1
ico2 = Icosahedron('Ni', 5)
ico2.info['confid'] = 2
op = CutSpliceCrossover({(28, 29): 2.0, (28, 28): 2.0, (29, 29): 2.0},
... | askhl/ase | ase/test/ga/particle_operators.py | Python | gpl-2.0 | 1,435 | [
"ASE"
] | a2b98b1e2dfaf2182066384743ad6eb115f35a4af438250a4ceba90f0e4aed7b |
#
# @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/diatomic.py | Python | lgpl-3.0 | 11,347 | [
"Psi4"
] | f1b7837ab691eadd6749e720ea529bf80a6786b8b983efb6b516335691eae227 |
import time
import datetime
from django.db import models
from django.conf import settings
import django.contrib.localflavor.us.models as us
from django.core.files.uploadedfile import SimpleUploadedFile
from django.core.urlresolvers import reverse
from face_client import face_client
from sorl.thumbnail import get_thum... | pizzapanther/Church-Source | churchsource/people/models.py | Python | gpl-3.0 | 10,654 | [
"VisIt"
] | 1950cfb235ebcda56bbe129706770feef38263ee57be2a924c479721dbd37f29 |
#
# Copyright 2001 - 2006 Ludek Smid [http://www.ospace.net/]
#
# This file is part of IGE - Outer Space.
#
# IGE - Outer Space 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 t... | mozts2005/OuterSpace | client-pygame/lib/osci/messages.py | Python | gpl-2.0 | 11,738 | [
"Galaxy"
] | 7a12b6f31b4edf8232ade72952975e8f6a9a6f40ea8b9aaf9b62a52b50f5215d |
# -*- coding: utf-8 -*-
'''
Exodus Add-on
Copyright (C) 2016 lambda
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 l... | KodiColdkeys/coldkeys-addons | repository/plugin.video.white.devil/resources/lib/sources/torba_mv.py | Python | gpl-2.0 | 6,332 | [
"VisIt"
] | c9672a2430894ea29c22db2e73fde828dd500f587c806d067607d0143dbb8ac3 |
#
# Copyright (C) 2011, 2012 Pablo Barenbaum <foones@gmail.com>
#
# 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.
#
# Th... | mateoqac/unqTip | language/vgbs/lang/gbs_lint.py | Python | gpl-3.0 | 24,397 | [
"VisIt"
] | 60526756d8781475dbef457840eb37178c68fcc4c70aaa0a7db5d022c9cc607f |
#-*- coding:utf-8 -*-
"""
This file is part of openexp.
openexp 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.
openexp is distributed in ... | SCgeeker/OpenSesame | libopensesame/sketchpad_elements/_noise.py | Python | gpl-3.0 | 1,619 | [
"Gaussian"
] | 6f73da1090fbb856d7555630fbdc182fa7899c3a81c55f14967b9671443b182a |
# -*- coding: utf-8 -*-
"""
coq_install_buckeye.py is part of Coquery.
Copyright (c) 2016–2021 Gero Kunter (gero.kunter@coquery.org)
Coquery is released under the terms of the GNU General Public License (v3).
For details, see the file LICENSE that you should have received along
with Coquery. If not, see <http://www.... | gkunter/coquery | coquery/installer/coq_install_buckeye.py | Python | gpl-3.0 | 29,028 | [
"COLUMBUS"
] | 07d8cedb0b59f90c4c8225d89e68c8f748deb0a2d830c89b0be9fe2e36c1dcf4 |
"""Contains PyVista mappings from vtkmodules.vtkCommonDataModel."""
from typing import Sequence
from pyvista import _vtk
def perlin_noise(amplitude, freq: Sequence[float], phase: Sequence[float]):
"""Return the implicit function that implements Perlin noise.
Uses ``vtk.vtkPerlinNoise`` and computes a Perlin... | akaszynski/vtkInterface | pyvista/core/common_data.py | Python | mit | 2,075 | [
"VTK"
] | 8b1b2dbd30743480054887d0b8f2a3e01db525f01fd47a274c31f8aadc6ab6dc |
from __future__ import print_function
import sys
print("\nexecuting test file", __file__, file=sys.stderr)
exec(compile(open('set_paths.py', "rb").read(), 'set_paths.py', 'exec'))
import fastfilters as ff
import numpy as np
import vigra
def test_vigra_compare3d():
a = np.random.randn(1000000).reshape(100,100,100)... | svenpeter42/fastfilters | tests/test_vigra_compare3d.py | Python | mit | 2,974 | [
"Gaussian"
] | e98a3eff911640c022fb38845ddb067af53073db6808035438ce8ef4ea146d74 |
from _plotly_utils.importers import relative_import
import sys
if sys.version_info < (3, 7):
from ._orca import to_image, write_image
from . import orca
from ._json import to_json, from_json, read_json, write_json
from ._templates import templates, to_templated
from ._html import to_html, write_htm... | plotly/python-api | packages/python/plotly/plotly/io/__init__.py | Python | mit | 1,401 | [
"ORCA"
] | 8d46189087fb03e1dc8778b78e15cdd94e065d49047bad27896f24bec0dd0221 |
import json
import os
import unittest
import numpy as np
import tensorflow as tf
from pymatgen.core import Molecule
from megnet.data.graph import DummyConverter
from megnet.data.molecule import (MolecularGraph, MolecularGraphBatchGenerator,
SimpleMolGraph, mol_from_smiles, pybel,
... | materialsvirtuallab/megnet | megnet/data/tests/test_molecule.py | Python | bsd-3-clause | 10,890 | [
"Pybel",
"pymatgen"
] | 5ee3f28606a971c43f567305a2254cea65b4641d5714d27f16de78587d3bfb3e |
# -*- coding: utf-8 -*-
from __future__ import absolute_import
import datetime
from django.conf import settings
from django.contrib.contenttypes.models import ContentType
from django.contrib.sites.models import Site
from django.http import HttpResponse
from django.test import TestCase
from django.utils.timezone import ... | jphilipsen05/zulip | zerver/tests/test_signup.py | Python | apache-2.0 | 80,514 | [
"VisIt"
] | 4faf56c1919d86d9094be1e065913fdddeb131df6fabd587c3b2a2f4115829a4 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | mdtraj/mdtraj | mdtraj/formats/hdf5.py | Python | lgpl-2.1 | 40,764 | [
"MDTraj",
"OpenMM"
] | 4938e8b913c334211899b055716fb1b63073b7307af90eea4fd7eaa63d983d14 |
from .base import *
class command(object):
"""
cytoscape command as shown in CyREST's swagger documentation for 'Command'.
:param url: an url of the type 'http://' + host + ':' + str(port) + '/' + version + '/'.
"""
def __init__(self, url):
self.__url = url + 'commands/command'
def e... | idekerlab/py2cytoscape | py2cytoscape/cyrest/command.py | Python | mit | 3,120 | [
"Cytoscape"
] | cb007570fe2fd12a7fabeb0f9779c67b32da3598771f6061289305bd06c1d6d5 |
"""
Utility functions of matrix and vector transformations.
NOTE: convention for quaternions is (x, y, z, w)
"""
import math
import numpy as np
from robosuite.utils.numba import jit_decorator
PI = np.pi
EPS = np.finfo(float).eps * 4.0
# axis sequences for Euler angles
_NEXT_AXIS = [1, 2, 0, 1]
# map axes strings... | ARISE-Initiative/robosuite | robosuite/utils/transform_utils.py | Python | mit | 26,577 | [
"Gaussian"
] | f2580092ef324104d3757a5c4b9ddec7d69601a86e1f7725a167ea36aa76fc7b |
"""
Tests absolute box size with ignored selection
"""
import os
import pytest
dir = os.path.dirname(__file__) + "/"
#==============================================================================
@pytest.mark.skip(reason="Missing input file")
def test_absolute_box(tmpdir):
"""
Tests the absolute box size for... | Eigenstate/dabble | dabble/test/dor_abssel/test_dor_absolute_sel.py | Python | gpl-2.0 | 1,915 | [
"VMD"
] | faa7b95066a0e5ae07b798fc03c4f2c78e70be79fc0ea885fe8e62d790f93f41 |
##############################################################################
# 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... | mfherbst/spack | var/spack/repos/builtin/packages/hic-pro/package.py | Python | lgpl-2.1 | 3,450 | [
"pysam"
] | e8a7b0292ad526101bf1ed142e1a668712a17e0dc9717eaae629434e6e06a47c |
#: c11:FlowerVisitors.py
# Demonstration of "visitor" pattern.
from __future__ import generators
import random
# The Flower hierarchy cannot be changed:
class Flower(object):
def accept(self, visitor):
visitor.visit(self)
def pollinate(self, pollinator):
print self, "pollinated by", pollinator
def eat(... | tapomayukh/projects_in_python | sandbox_tapo/src/refs/TIPython/code/c11/FlowerVisitors.py | Python | mit | 2,257 | [
"VisIt"
] | 7c16b8fb0fc4f627a11d4302a1042f80bdf2aefba925e5415d094c3caa369a43 |
#!/usr/bin/env python
"""Run signal-to-reference alignments
"""
from __future__ import print_function
from signalAlignLib import *
from variantCallingLib import scan_for_proposals, update_reference_with_marginal_probs
from serviceCourse.file_handlers import FolderHandler
from argparse import ArgumentParser
from random ... | ArtRand/signalAlign | scripts/jamison.py | Python | mit | 8,325 | [
"BWA"
] | dc10a4d1506db581cda5b128892a524d4df2a6e05d9ee9d7f72b6fc100805d51 |
import numpy as np
from astropy.coordinates import Angle, Distance
from astropy import units as u
from .angles2Plane import gal_theta
def vdm_2001_dep_dist_kpc(rho, phi, glx_theta, glx_incl, D_0):
"""
Deprojected angular distance from vdM & Cioni (2001).
D is the distance associated to a point defined ... | Gabriel-p/mcs_rot_angles | modules/i_PA_DeprjDist.py | Python | gpl-3.0 | 4,382 | [
"Galaxy"
] | bfbf9f34396a66215d334f54c9f40b9cca292f3525e39fb29149859b4158343c |
#!/usr/bin/env python
# Run this test like so:
# vtkpython TestLinePlot.py -D $VTK_DATA_ROOT \
# -B $VTK_DATA_ROOT/Baseline/Charts/
import os
import vtk
import vtk.test.Testing
import math
class TestLinePlot(vtk.test.Testing.vtkTest):
def testLinePlot(self):
"Test if line plots can be built with python"... | Wuteyan/VTK | Charts/Testing/Python/TestLinePlot.py | Python | bsd-3-clause | 2,165 | [
"VTK"
] | c9bc8b33c4bde848aa7ecb87d7eddf2fe4898cb1afa426a85f08230a4945eaea |
# -*- coding: utf-8 -*-
# Generated by Django 1.9 on 2016-05-04 14:45
from __future__ import unicode_literals
from django.db import migrations, models
import django.db.models.deletion
import django_hstore.fields
import picklefield.fields
class Migration(migrations.Migration):
dependencies = [
('cbh_chem... | thesgc/cbh_chembl_model_extension | cbh_chembl_model_extension/migrations/0035_auto_20160504_0945.py | Python | mit | 7,369 | [
"Pybel"
] | be265ca9bd692bd7123c290bb03612f2e5b3ab45d704e94bb2910315e262f312 |
"""
sphinx.application
~~~~~~~~~~~~~~~~~~
Sphinx application class and extensibility interface.
Gracefully adapted from the TextPress system by Armin.
:copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS.
:license: BSD, see LICENSE for details.
"""
import os
import pickle
import s... | lmregus/Portfolio | python/design_patterns/env/lib/python3.7/site-packages/sphinx/application.py | Python | mit | 50,133 | [
"VisIt"
] | c00ac349a3c461cdf08ce95acaa1f56559a576f4337a0c0a3703e523dab86148 |
"""
The calculate module contains a routine for calculating the
property surface of a system.
"""
import itertools
from collections import OrderedDict
from collections.abc import Mapping
import numpy as np
from numpy import broadcast_to
import pycalphad.variables as v
from pycalphad import ConditionError
from pycalpha... | tkphd/pycalphad | pycalphad/core/calculate.py | Python | mit | 21,066 | [
"pycalphad"
] | a385a1f53d2f42398f8b81ae37d158651ddcfeb5c92bea17f474e347d775943f |
# Copyright 2017 Google LLC
#
# 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 writing, ... | google/decoupled_gaussian_process | decoupled_gaussian_process_example.py | Python | apache-2.0 | 12,353 | [
"Gaussian"
] | fa5d73c0e4dbcb38ea37755bd10428d1ca5e6b41d1ef0ba33413d1537d28dc15 |
from selenium import webdriver
from selenium.webdriver.common.keys import Keys
from selenium.webdriver.support.ui import Select
from selenium.webdriver.common.by import By
from selenium.webdriver.support.ui import WebDriverWait
from selenium.webdriver.support import expected_conditions as EC
from selenium.webdriver.rem... | ansab/Big-Data-Project | Acquisition/Weather/WaterScrapper.py | Python | mit | 6,422 | [
"VisIt"
] | 6bc13ffc99b3e9eeafb5464c036dc0ffc75a6f867ef0691df8f3aa3814c48c79 |
try:
paraview.simple
except:
from paraview.simple import *
XDMF_temporalFields_xmf = GetActiveSource()
ProgrammableFilter1 = ProgrammableFilter()
ProgrammableFilter1.RequestUpdateExtentScript = ''
ProgrammableFilter1.PythonPath = ''
ProgrammableFilter1.RequestInformationScript = ''
ProgrammableFilter1.Scrip... | OlympusMonds/lithospheric_modelling_recipe | scripts/paraview_macros/classify_regime_3D.py | Python | gpl-3.0 | 1,468 | [
"ParaView"
] | 22887a7c3c2a418e479c989cdd8db113a5f3285681b3f2c7cb46faab8aa1df1f |
"""
Tools for the instructor dashboard
"""
import dateutil
import json
from django.conf import settings
from django.contrib.auth.models import User
from django.http import HttpResponseBadRequest
from django.utils.timezone import utc
from django.utils.translation import ugettext as _
from courseware.models import Stud... | Semi-global/edx-platform | lms/djangoapps/instructor/views/tools.py | Python | agpl-3.0 | 8,635 | [
"VisIt"
] | d757aff9041838ac73d206a3b9910d74152958f995d5c1f7fe4dfb45f9f0afc1 |
#!/usr/bin/env python
"""
Uses pysam to bgzip a vcf file as-is.
Headers, which are important, are kept.
Original ordering, which may be specifically needed by tools or external display applications, is also maintained.
usage: %prog in_file out_file
"""
import optparse
from pysam import ctabix
def main():
# Re... | icaoberg/cellorganizer-galaxy-tools | datatypes/converters/vcf_to_vcf_bgzip.py | Python | gpl-3.0 | 559 | [
"pysam"
] | 71ba56b8dc09aa64a59348de8be5951ed94c4b3844287e005e029414fb7467b5 |
from __future__ import division
from __future__ import print_function
import ninemlcatalog
from nineml.abstraction import Parameter, TimeDerivative, StateVariable
import nineml.units as un
from pype9.simulate.nest import CellMetaClass
from pype9.simulate.common.cells.with_synapses import WithSynapses
from pype9.excepti... | tclose/PyPe9 | test/unittests/test_build.py | Python | mit | 1,069 | [
"NEURON"
] | d82fa3486d86d2ab153fb20498cdfe49614c4b14962c160bf625f08114d6f8b3 |
from pytest_bdd import scenario, given, when, then
from pytest_bdd import parsers
from urllib.parse import urljoin
import pytest
import sys
# pytestmark means it this mark will apply to all tests in the module
pytestmark = pytest.mark.skipif(sys.platform in ('win32', 'cygwin', 'darwin'),
... | pfctdayelise/allseasons | tests/bdd/steps/test_calculate_season.py | Python | bsd-3-clause | 2,619 | [
"VisIt"
] | 44bb375287e8124bc087d67d7cc4c06dac9a46d73888d7160c2c4fe41f62ffe0 |
##########################################################################
#
# Copyright 2008-2010 VMware, Inc.
# All Rights Reserved.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software withou... | PeterLValve/apitrace | wrappers/trace.py | Python | mit | 32,944 | [
"VisIt"
] | 0dbf624fc0cd5795e81a09c9039c453b9d3d60b7be9b73f30968f700a715f5a2 |
# -*- coding: utf-8 -*-
"""
Created on Tue Aug 30 08:57:31 2016
@author: nicholas
"""
import sys
import logging
import shutil
# import subprocess
import os
import unittest
# import multiprocessing
from Bio import SeqIO
from Bio.SeqRecord import SeqRecord
from argparse import Namespace
from unittest.mock import MagicM... | nickp60/riboSeed | tests/test_riboSwap.py | Python | mit | 5,786 | [
"BWA"
] | 2bc82eb97d4a4648ec58682bc190a26947d6d27df44e2a8303309ffee79b2d13 |
from Firefly import logging
from Firefly.components.hue.hue_device import HueDevice
from Firefly.components.virtual_devices import AUTHOR
from Firefly.const import (ACTION_LEVEL, ACTION_OFF, ACTION_ON, ACTION_TOGGLE, DEVICE_TYPE_SWITCH, EVENT_ACTION_OFF, LEVEL, STATE, SWITCH)
TITLE = 'Firefly Hue Group'
DEVICE_TYPE = ... | Firefly-Automation/Firefly | Firefly/components/hue/hue_group.py | Python | apache-2.0 | 1,182 | [
"Firefly"
] | 39267e2cd2e7c960753249c11ef4770e830c59a392729a332d9281d06738f612 |
'''
@brief
utility functions can be used for model gen
(mostly just some analytical geometry)
@author:
Henry Zhou, April 1st, 2018
'''
import pdb
import numpy as np
import math
import random
def gaussian_noise(mu, std, discrete, step_size=None,):
'''
'''
if discrete and (st... | WilsonWangTHU/neural_graph_evolution | util/model_gen_util.py | Python | mit | 5,393 | [
"Gaussian"
] | 252b0af9ae77ba3acc267180b8f674488c590a00a263aaf5ecdc7ca52d4bf156 |
from __future__ import division
import numpy as np
from scipy.ndimage import gaussian_filter, gaussian_laplace
import math
from math import sqrt, log
from scipy import spatial
from skimage.util import img_as_float
from skimage.feature.peak import peak_local_max
# code from
# https://github.com/emmanuelle/scikit-image... | xiedidan/luna-data-pre-processing | blobs_detection.py | Python | gpl-3.0 | 14,955 | [
"Gaussian"
] | f898d603dc3bea8715209c8b0e91b46ae98758c7cf0fefbf3eb7de7f9f4afc6f |
#!/usr/bin/env python3
"""
Reads files from an EggNOG release and stores them as an indexed SQLite3 file for
rapid lookups by protein ID. The use case for development here is our functional
annotation pipeline.
INPUT
COG.members.txt
---------------
COG1110 579137.Metvu_1264 1 865
COG1110 573064.Mefer_00... | zctea/biocode | blast/eggnog_to_sqlite3.py | Python | gpl-3.0 | 5,890 | [
"BLAST"
] | f5af06752a62bc73cdeac1f74b3d8f46d31c195135832f0a9b9308a34f6a63c3 |
# -*- coding: utf-8 -*-
#------------------------------------------------------------
# streamondemand - XBMC Plugin
# Conector para longurl (acortador de url)
# http://www.mimediacenter.info/foro/viewforum.php?f=36
#------------------------------------------------------------
import urlparse
from lib import unshort... | costadorione/purestream | servers/expurl.py | Python | gpl-3.0 | 725 | [
"ADF"
] | a567f9d799c0fae518be64525873d8c95d16447e5c3340cd700f4f76868f4603 |
# Authors: John Dennis <jdennis@redhat.com>
#
# Copyright (C) 2011 Red Hat
# see file 'COPYING' for use and warranty information
#
# 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... | msimacek/freeipa | ipapython/log_manager.py | Python | gpl-3.0 | 62,629 | [
"VisIt"
] | 720bd475fa9965ccc4d8b7b22068811a6a10594d4072d427ff98bb07bd1cbc00 |
from __future__ import print_function, division
import os,unittest,numpy as np
from pyscf.nao.m_fermi_dirac import fermi_dirac_occupations
from pyscf.nao.m_fermi_energy import fermi_energy as get_fermi_energy
class KnowValues(unittest.TestCase):
def test_fermi_energy_spin_saturated(self):
""" This is to test ... | gkc1000/pyscf | pyscf/nao/test/test_0018_fermi_energy.py | Python | apache-2.0 | 3,980 | [
"PySCF"
] | 793611596673cf758b6a0a606437db7627b7b2c37b79472e5fedc07358f1aadb |
import numpy as np
import matplotlib.pyplot as plt
import sys
# Add the PyRsw tools to the path
# At the moment it is given explicitely.
# In the future, it could also be added to the
# pythonpath environment variable
sys.path.append('../src')
import Steppers as Step
import Fluxes as Flux
from PyRsw import Simulation... | PyRsw/PyRsw | testing/test_does_2d_run/test_walls_periodic.py | Python | mit | 1,488 | [
"Gaussian"
] | 001260f035fcb97dde2d25fc03704be17d16b80150bba2ea32428d9a9fe7cf46 |
import GSI
requiredGSIVersion = "0.6.3"
if GSI.version.__version__ < requiredGSIVersion:
raise Exception("pyGSI is not the latest version (installed %s required %s)" %
(GSI.version.__version__, requiredGSIVersion))
GSI.SSL.set_thread_safe()
nid = GSI.crypto.create_oid("1.2.42.42", "diracGroup", "... | fstagni/DIRAC | Core/Security/pygsi/__init__.py | Python | gpl-3.0 | 810 | [
"DIRAC"
] | 750a478d638264152bab73ef5154ad9b62fb68645b81372fc44e04f0a217b338 |
#!/usr/bin/env python3
#
# Copyright (c) 2017-2019 Aaron LI
# MIT License
#
# Create image from OSKAR simulated visibility data using `WSClean`.
# WSClean: https://sourceforge.net/p/wsclean/
#
# 2017-09-01
#
import os
import sys
import re
import argparse
import subprocess
import time
import tempfile
WSCLEAN_BIN = o... | liweitianux/atoolbox | astro/oskar/wsclean.py | Python | mit | 10,662 | [
"Gaussian"
] | 75a3116ae46730cf563af7d5a0e4a624f7be727237236972104ce1ca093c7077 |
from __future__ import absolute_import, print_function
from pony.py23compat import izip
import imp
import os
import marshal
import struct
import sys
from . import ast, parse, walk, syntax
from . import pyassem, misc, future, symbols
from .consts import SC_LOCAL, SC_GLOBAL_IMPLICIT, SC_GLOBAL_EXPLICIT, \
SC_FREE,... | gwecho/pony | pony/thirdparty/compiler/pycodegen.py | Python | agpl-3.0 | 47,787 | [
"VisIt"
] | 223b6932cb0d8555c3e5ee1059f8850c93280fdb12438cfc858f81461076fbfe |
#!/usr/bin/env python
from __future__ import (absolute_import, division,
print_function, unicode_literals)
import sys
import os
import re
import argparse
import subprocess
import csv
import shutil
from Bio import SeqIO
from natsort import natsorted
import amptk.amptklib as lib
class MyFormatt... | nextgenusfs/amptk | amptk/assign_taxonomy.py | Python | bsd-2-clause | 30,295 | [
"BLAST"
] | c2cdb2aad402e2091d0787c7933788c3fdf66f455d58f6936cc69495fd194e0c |
#! /usr/bin/env python
from hermes2d import Mesh, MeshView, H1Shapeset, PrecalcShapeset, H1Space, \
WeakForm, Solution, ScalarView, LinSystem, DummySolver
from hermes2d.forms import set_forms
from hermes2d.examples import get_example_mesh
mesh = Mesh()
mesh.load(get_example_mesh())
mesh.refine_element(0)
shap... | davidquantum/hermes2dold | python/examples/03.py | Python | gpl-2.0 | 1,045 | [
"Mayavi"
] | dd8f11f81e5f1612d15a13e386104d6c153b7f28b260b3614dca728a4c62cd0d |
##############################################################################
# adaptiveMD: A Python Framework to Run Adaptive Molecular Dynamics (MD)
# Simulations on HPC Resources
# Copyright 2017 FU Berlin and the Authors
#
# Authors: Jan-Hendrik Prinz
# Contributors:
#
# `adaptiveMD` is free software: ... | markovmodel/adaptivemd | adaptivemd/mongodb/proxy.py | Python | lgpl-2.1 | 5,024 | [
"MDTraj"
] | 64000974b4bc7877eaf3254068a08129ffa35146a084aae33198266bdc85101d |
# -*- coding: utf-8 -*-
#########################################################################
#
# Copyright (C) 2012 OpenPlans
#
# 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 versio... | pcecconi/mapground | layers/enumerations.py | Python | mit | 14,226 | [
"BWA"
] | caa436b31a4cba63aa83c1806acf003bfc4950abe55e95417f78b58d07f31b05 |
from kernel_hmc.densities.gaussian import sample_gaussian
import numpy as np
def leapfrog(q, dlogq, p, dlogp, step_size=0.3, num_steps=1):
# for storing trajectory
Ps = np.zeros((num_steps + 1, len(p)))
Qs = np.zeros(Ps.shape)
# create copy of state
p = np.array(p.copy())
q = np.array(q.c... | karlnapf/kernel_hmc | kernel_hmc/hamiltonian/leapfrog.py | Python | bsd-3-clause | 2,833 | [
"Gaussian"
] | 782f9f48cd8e1952808d5a1f83318676f2f0975c2e0f73fa6c448a75d9c200c6 |
'''
Created on 29.04.2017
@author: Mr. Jones
'''
from jimplify.visitors.replacementvisitor import ReplacementVisitor
def check_node_type(node,varName):
return type(node).__name__ == varName
class FoldingVisitor():
def __init__(self):
self.optimization = 0
self.replaceme... | mrj0n3s/jimplify | Jimplify/jimplify/visitors/foldingvisitor.py | Python | mit | 3,056 | [
"VisIt"
] | 3c1d4bbb4ac5b07795179f53e1670b0e7b7013c9a2f753814193397d90f7575a |
#!/usr/bin/python
import os, sys, math, random, getopt
import filecmp
"""
ConfBuster-Rotamer-Search.py
Copyright (C) 2017 Xavier Barbeau, Antony T. Vincent and Patrick Lague
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as p... | patricklague/ConfBuster | ConfBuster-Rotamer-Search.py | Python | gpl-3.0 | 7,964 | [
"PyMOL"
] | daed21a4763484cce1dc2fc7d5ca93b59cca1e9920966b87a658f75cfa6c333a |
# -*- coding: utf-8 -*-
# YAFF is yet another force-field code.
# Copyright (C) 2011 Toon Verstraelen <Toon.Verstraelen@UGent.be>,
# Louis Vanduyfhuys <Louis.Vanduyfhuys@UGent.be>, Center for Molecular Modeling
# (CMM), Ghent University, Ghent, Belgium; all rights reserved unless otherwise
# stated.
#
# This file is pa... | molmod/yaff | yaff/examples/007_monte_carlo/co2_in_mil53/gcmc.py | Python | gpl-3.0 | 3,170 | [
"Avogadro"
] | 3de93c92674162df14ff271638bb818e2a791caf1c1958b33f3214a8ec39ea47 |
import os
import deepchem as dc
import numpy as np
def load_gaussian_cdf_data():
"""Load example with numbers sampled from Gaussian normal distribution.
Each feature and task is a column of values that is sampled
from a normal distribution of mean 0, stdev 1."""
current_dir = os.path.dirname(os.path.abs... | lilleswing/deepchem | deepchem/trans/tests/test_power.py | Python | mit | 3,354 | [
"Gaussian"
] | 34e7d7b787a98c716021f5394009001c5e55a9afb5cbd6b160939519171ed5bd |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import os
import shutil
import tempfile
import zipfile
from django.test import TransactionTestCase
from django.test.utils import override_settings
from ..models import Artist, Album, Song, CustomStorage
from .. import update
from ..utils import (
d... | rafikdraoui/vortex | library/tests/test_utils.py | Python | mit | 6,268 | [
"Brian"
] | 18604862f80dc1138493c68a204830c8be87eed50da416beb000299347e3e1e2 |
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