text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
"""
Robust location and covariance estimators.
Here are implemented estimators that are resistant to outliers.
"""
# Author: Virgile Fritsch <virgile.fritsch@inria.fr>
#
# License: BSD 3 clause
import warnings
import numbers
import numpy as np
from scipy import linalg
from scipy.stats import chi2
from . import empi... | kevin-intel/scikit-learn | sklearn/covariance/_robust_covariance.py | Python | bsd-3-clause | 32,366 | [
"Gaussian"
] | 8b53654689ac541ab6f1ff78896ed3474eab046f3fabcad86026bd389f9a7220 |
# Copyright 2016-2020 The GPflow Contributors. 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 appli... | GPflow/GPflow | gpflow/models/sgpr.py | Python | apache-2.0 | 20,495 | [
"Gaussian"
] | 645221fbaa798179413ab447bc8ee9c82e7c805653c83dbbe87e97c888bef0f4 |
import os
import unittest
import warnings
from pymatgen.analysis.solar.slme import optics, slme
from pymatgen.util.testing import PymatgenTest
class SolarTest(PymatgenTest):
_multiprocess_shared_ = True
def setUp(self):
warnings.simplefilter("ignore")
def tearDown(self):
warnings.simple... | vorwerkc/pymatgen | pymatgen/analysis/solar/tests/test_slme.py | Python | mit | 713 | [
"pymatgen"
] | 1f0124a7518986bfcc8c190b67671114a8d16de2b67ab3b2a5e75844bec21ae4 |
"""
This app is intended to provide the core functionality for tracking user
engagement with content and Kolibri in general. As such, it is intended
to store details of user interactions with content, a summary of those
interactions, interactions with the software in general, as well as user
feedback on the content and... | DXCanas/kolibri | kolibri/core/logger/models.py | Python | mit | 11,759 | [
"VisIt"
] | ae85f38e33102bf30f632ce2992a05cc3b80daa82174f772aa65569fbe156683 |
# Import modules from standard Python library
import os, sys, re, datetime, shutil, types, UserDict, glob
# Import additional third party modules
import numpy
# Import our custom modules
import xmlplot.common, xmlstore.util
def openNetCDF(path,mode='r'):
# Test if the path contains wildcard, and resolves to mult... | BoldingBruggeman/gotm | gui.py/xmlplot/data/netcdf.py | Python | gpl-2.0 | 87,431 | [
"NetCDF"
] | 60b840e869077281b5d23c326a37e92d1aedb6feb4f8722d153e79c0fb2f3a2b |
#
# @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
#... | lothian/psi4 | psi4/driver/driver_cbs.py | Python | lgpl-3.0 | 83,107 | [
"CFOUR",
"Psi4"
] | b8b84f1d4784e82177e8e9bb40a67be1e7671b38d73d91026ec94b9841e7379d |
#! /usr/bin/env python
#import math, pdb, sys
#from numpy import *
#from numpy.linalg import *
#import random
#from copy import copy
from random import choice
from numpy import array, random, ones, zeros, sin, vstack, hstack, argmax, diag, linalg, dot, exp
#from sg import sg # Import shogun
import string, ... | booi/aracna | RobotPi/SVMStrategy.py | Python | gpl-3.0 | 12,810 | [
"Gaussian"
] | 6ce5c3025e514e6dd186addae7ad1d02b0230819101e0e5d7bc3da3791f21c5c |
#!/bin/env python
#----------------------------------------------------------------------------
# Name: Main.py
# Purpose: Testing lots of stuff, controls, window types, etc.
#
# Author: Robin Dunn
#
# Created: A long time ago, in a galaxy far, far away...
# Copyright: (c) 1999-2017 by Total ... | dnxbjyj/python-basic | gui/wxpython/wxPython-demo-4.0.1/demo/Main.py | Python | mit | 94,659 | [
"Galaxy"
] | 616c4e274497dc1e8adc06e136364174122fe13df74089ff87051c9f117bd20b |
# Copyright (c) 2013, Web Notes Technologies Pvt. Ltd. and Contributors
# License: GNU General Public License v3. See license.txt
from __future__ import unicode_literals
import frappe
import frappe.utils
from frappe.utils import cstr, flt, getdate, comma_and,cint
from frappe import _
from frappe.model.mapper import g... | indictranstech/focal-erpnext | selling/doctype/sales_order/sales_order.py | Python | agpl-3.0 | 20,315 | [
"VisIt"
] | 7b3ef017ee92f0865b76a7ab44cacc523f5da7e5c85c5109c8f73429911f7a6a |
#!/usr/bin/env python
import functools
import getpass
import sys
import subprocess
import urllib2
import json
import os
import re
import webbrowser
import zipfile
import threading
import time
from contextlib import contextmanager
HEADER = '\033[95m'
OKBLUE = '\033[94m'
OKGREEN = '\033[92m'
WARNING = '\033[93m'
FAIL =... | rfw/socorromatic | installer.py | Python | mpl-2.0 | 11,431 | [
"VisIt"
] | 4767f50a65c110589356d37162a32ebb89c9ed3b398fe16c048bda14bb775051 |
from typing import Optional
from backend.common.run_after_response import run_after_response
class GoogleAnalytics:
"""
Class that manages sending information to Google Analytics
For more information about GAnalytics Protocol Parameters, visit
https://developers.google.com/analytics/devguides/collec... | the-blue-alliance/the-blue-alliance | src/backend/common/google_analytics.py | Python | mit | 1,848 | [
"VisIt"
] | c099e68b2fc25acbcef668ac008e768f380b97cd557103f0a225a330a5a03eea |
##############################################################################
# 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/r-spem/package.py | Python | lgpl-2.1 | 1,722 | [
"Bioconductor"
] | 409ea052fd0be0a581c2f530f462629d63be0ea9014331e9cf3278b7e985fccd |
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2009 Brian G. Matherly
#
# 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 op... | SNoiraud/gramps | gramps/plugins/lib/libgrampsxml.py | Python | gpl-2.0 | 1,447 | [
"Brian"
] | 7551143b5d685c57d9839c3ff81193ed92060fce2aa9816db7b0076abab9cccd |
# -*- coding: utf-8 -*-
"""
For information and usage see README, or http://pypi.python.org/pypi/numericalunits
"""
#Copyright (C) 2012 Steven Byrnes
#
#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 Softw... | schoolie/numericalunits | numericalunits.py | Python | mit | 10,760 | [
"Avogadro",
"Dalton"
] | 0c122dcadd2ce10630a4c94329a6f124aea195f385a20d5be37ce04d67adc73e |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
Integrals for spin-orbit coupling
See also functions make_h1_soc, direct_spin_spin in pyscf/prop/zfs/uhf.py
'''
import numpy
from pyscf import gto
from pyscf import lib
mol = gto.M(
verbose = 0,
atom = 'C 0 0 0; O 0 0 1.5',
basi... | gkc1000/pyscf | examples/gto/20-soc_ao_integrals.py | Python | apache-2.0 | 1,462 | [
"PySCF"
] | b29a2ef02094a1836725ad4c3c3f399f544c80c50894a657dc83048bef9fb05d |
##############################################################################
# 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... | krafczyk/spack | var/spack/repos/builtin/packages/py-phonopy/package.py | Python | lgpl-2.1 | 1,833 | [
"phonopy"
] | 33a189cf07ca08589f53fda5208b006d7b48d004073fb560e9c4d71c6d26d8a0 |
# $HeadURL: $
''' SpaceTokenOccupancyCommand
The Command gets information of the SpaceTokenOccupancy from the lcg_utils
'''
import lcg_util
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.Utilities.Subprocess import py... | Sbalbp/DIRAC | ResourceStatusSystem/Command/SpaceTokenOccupancyCommand.py | Python | gpl-3.0 | 6,129 | [
"DIRAC"
] | 8d19b79a8846971db9b9860e216e9a1253e23a662051a956e127d2a577ada740 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/pbc/gto/basis/parse_cp2k.py | Python | apache-2.0 | 2,822 | [
"CP2K",
"PySCF"
] | df676e6e398d00f170f8bd9b48f296645b207a9073a06108a90bdaba026dec3a |
#!/usr/bin/env python
# This script requires all matrices to be in PETSc binary format in the petsc subdir
import sys, os, glob, random
import datetime,time
from solvers import *
petsc = False
if petsc:
tmdir = 'timing-aciss'
matrixsubdir = 'petsc'
petsc_matrix_suffix='.petsc'
donefile = 'DONE'
jobname = 'p... | LighthouseHPC/lighthouse | sandbox/petsc/new/solverscript-aciss.py | Python | mit | 3,666 | [
"MOOSE"
] | cbb318b2ae9a64c6fa0391405f975d7d4d6be026e240ecb1075ef040477fc334 |
"""
created on Feb 3, 2014
@author: Nikola Jajcay, jajcay(at)cs.cas.cz
inspired by A Practical Guide to Wavelet Analysis by Ch. Torrence and G. Compo
-- http://paos.colorado.edu/research/wavelets/ --
"""
import numpy as np
from scipy.fftpack import fft, ifft
from scipy.special import gamma
def morlet(k, scale, k0 =... | jajcayn/pyclits | pyclits/wavelet_analysis.py | Python | mit | 5,336 | [
"Gaussian"
] | ca054f6b0aa39b328c6a451074e2d601b7552102007a12f620d717f7e781db6a |
"""
The ``model`` module
======================
Contains the class Model which implements the core model for CG detection,
training, testing and visualization functions.
"""
import os
import time
import random
from . import image_loader as il
import tensorflow as tf
import matplotlib.pyplot as plt
... | NicoRahm/CGvsPhoto | CGvsPhoto/model.py | Python | mit | 57,552 | [
"Gaussian"
] | 5b36eeb2f1d560d32900c7533d1257625f20971760c2c8cda10fdbfbe1d2ac66 |
import mayavi
import vtk
import pyvtk
import numpy as N
try:
from vtk.util import vtkConstants
except ImportError:
class vtkConstants:
pass
vtkConstants.VTK_CHAR=2
vtkConstants.VTK_UNSIGNED_CHAR = 3
vtkConstants.VTK_SHORT = 4
vtkConstants.VTK_UNSIGNED_SHORT = 5
vtkConstant... | martindurant/misc | mayatools.py | Python | mit | 6,427 | [
"Mayavi",
"VTK"
] | 6a04fc446c400a4003a8bb746962470a83db8bb8a5d6804c35d4cc3ef596cb98 |
# -*- coding: utf-8 -*-
# QuickFF is a code to quickly derive accurate force fields from ab initio input.
# Copyright (C) 2012 - 2019 Louis Vanduyfhuys <Louis.Vanduyfhuys@UGent.be>
# Steven Vandenbrande <Steven.Vandenbrande@UGent.be>,
# Jelle Wieme <Jelle.Wieme@UGent.be>,
# Toon Verstraelen <Toon.Verstraelen@UGent.be>,... | molmod/QuickFF | quickff/tests/test_valence.py | Python | gpl-3.0 | 14,711 | [
"Gaussian"
] | 4ab92d5381efcbaf779e8618a52cc426943c98c1833e8531b095126e738c4cea |
import sys
import json
from os.path import expanduser, isfile
import locale
import ap2en
import click
import requests
from collections import OrderedDict
import zipfile
import os
import time
import xml.etree.ElementTree as ET
import re
# Workaround to support the correct input for both Python 2 and 3. Always use
# in... | therzka/runner | transcriptic.py | Python | bsd-3-clause | 25,847 | [
"VisIt"
] | 4c5692012271afd3bf035e5a19d6b2eafc0f3b84fcf477bcdb717c14d8380d38 |
"""
Custom nodes for a Tree Editor that provide views for adding various nodes
to the tree.
"""
# Authors: Judah De Paula <judah@enthought.com>
# Prabhu Ramachandran <prabhu_r@users.sf.net>
# Copyright (c) 2008, Enthought, Inc.
# License: BSD Style.
# Enthought library imports.
from traits.api import (HasTrai... | dmsurti/mayavi | mayavi/core/adder_node.py | Python | bsd-3-clause | 13,361 | [
"Mayavi"
] | cbe6ddb9edc3db4f2421570ba4d0bf8d065a775c7bec67cbba1cc54592d82a69 |
# -*- coding: utf-8 -*-
# File: deform.py
from .base import ImageAugmentor
from ...utils import logger
import numpy as np
__all__ = []
# Code was temporarily kept here for a future reference in case someone needs it
# But it was already deprecated,
# because this augmentation is not a general one that people will o... | eyaler/tensorpack | tensorpack/dataflow/imgaug/deform.py | Python | apache-2.0 | 3,718 | [
"Gaussian"
] | b0aeda6dd9d36cf53cdc168386bd109dca80677ef63e97d955a479253a501692 |
#!/usr/bin/env python
# Copyright 2015 The Kubernetes 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 appli... | hodovska/cluster-capacity | verify/boilerplate/boilerplate.py | Python | apache-2.0 | 6,314 | [
"VisIt"
] | 70b61e53977c7cf756f769d0c7dd9c140b3270b260bd338cdfbefc1fbf5cdc22 |
# -*- coding: utf-8 -*-
import os
import swc2vtk
import swcfilelist
# input_dir = '/home/nebula/git/LAL-VPCmapping/converted_swc'
input_dir = './swc'
output_dir = '/home/nebula/work/paraview/standardbrain20170131/'
if not os.path.isdir(output_dir):
os.mkdir(output_dir)
filelist = swcfilelist.filelist_lalvpc
vt... | DaisukeMiyamoto/swc2vtk | examples/append_allswc.py | Python | apache-2.0 | 639 | [
"ParaView",
"VTK"
] | bacc18099410147c56346216fddaba36a98d91c1b2744e210393b547f18fb5da |
"""
Migration script to create the tool_version and tool_version_association tables and drop the tool_id_guid_map table.
"""
from sqlalchemy import *
from sqlalchemy.orm import *
from migrate import *
from migrate.changeset import *
import datetime
now = datetime.datetime.utcnow
# Need our custom types, but don't imp... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/model/migrate/versions/0091_add_tool_version_tables.py | Python | gpl-3.0 | 5,125 | [
"Galaxy"
] | 99e9ad15c6dc830ec3bba8964bf554de1faf2b2fff3432dba6a496ae50a5294b |
#! /usr/bin/env python
# Hi There!
# You may be wondering what this giant blob of binary data here is, you might
# even be worried that we're up to something nefarious (good for you for being
# paranoid!). This is a base64 encoding of a zip file, this zip file contains
# a fully functional basic pytest script.
#
# Pyt... | dmargala/tpcorr | runtests.py | Python | mit | 236,863 | [
"Elk"
] | b1dde6cfd35b8be1183cf1cf35efaa310e6f4ce3ed33dfb881c3fba1f0ab7d04 |
# Orca
#
# Copyright 2005-2009 Sun Microsystems Inc.
# Copyright 2010 Orca Team.
#
# 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)... | h4ck3rm1k3/orca-sonar | src/orca/scripts/toolkits/Gecko/script.py | Python | lgpl-2.1 | 179,946 | [
"ORCA"
] | cde85454020b8b5315d6c148cf3a042744c1138973c509d2bcf2e7cb728f80fe |
# -*- coding: utf-8 -*-
# SyConn - Synaptic connectivity inference toolkit
#
# Copyright (c) 2016 - now
# Max-Planck-Institute of Neurobiology, Munich, Germany
# Authors: Philipp Schubert, Joergen Kornfeld
import os
import glob
import shutil
import sys
import argparse
import numpy as np
from syconn import global_param... | StructuralNeurobiologyLab/SyConn | examples/start.py | Python | gpl-2.0 | 13,097 | [
"NEURON"
] | dc155c310ad810c4c19f89dac4897e757abaec5a7d3ef0d97abaf97708975ccb |
# $Id$
#
# Copyright (C) 2001-2008 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
"""unit testing code ... | ptosco/rdkit | rdkit/ML/Cluster/UnitTestCluster.py | Python | bsd-3-clause | 6,718 | [
"RDKit"
] | 2c01812618917c5121340971b0dcbca300b7b9d7b32d5ab99f4e8b605ef30897 |
from __future__ import division
import os
import os.path as osp
import inspect
from threading import Thread
from functools import partial
from glob import glob
from importlib import import_module
import re
import six
from collections import defaultdict
from itertools import chain, product, repeat, starmap, count, cycle... | Chilipp/psyplot | psyplot/data.py | Python | gpl-2.0 | 191,460 | [
"NetCDF"
] | 32debfed6101e650ae0fab04e49c27c5046cd71d833e0137c5acee30cd3cebc7 |
"""
Choropleth mapping using PySAL
ToDo:
* map_line_shp, map_point_shp should take a shp object not a shp_link
* Same for map_poly_shp(_lonlat)
"""
__author__ = "Sergio Rey <sjsrey@gmail.com>", "Dani Arribas-Bel <daniel.arribas.bel@gmail.com"
from warnings import warn
import pandas as pd
import pysal as ps... | TaylorOshan/pysal | pysal/contrib/viz/mapping.py | Python | bsd-3-clause | 42,037 | [
"COLUMBUS"
] | 605b3727f664df5bdc4d7f2465e513c7918b38099f34cac91d7b5d507865bc99 |
""" JobMonitoringHandler is the implementation of the JobMonitoring service
in the DISET framework
The following methods are available in the Service interface
"""
__RCSID__ = "$Id$"
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.DISET.RequestHandler import RequestHandler
import DIRAC.Core.Utilities.Time as... | andresailer/DIRAC | WorkloadManagementSystem/Service/JobMonitoringHandler.py | Python | gpl-3.0 | 19,283 | [
"DIRAC"
] | 4ccf006f1ce159462313222d0bd09734dc1d5262d47a9d9c2ce16f24f98aec04 |
# List Splunk Hosts by Sourcetype
# For use with Munk - Maltego for Splunk
# Author: Brian Warehime @nulltr0n
# 9/6/2014
# Importing various modules
from MaltegoTransform import *
import subprocess
import sys
import re
import ConfigParser
import os
# Configuration Parser to grab necessary options.
def getLocalConfP... | brianwarehime/munk | transforms/listhostsourcetype.py | Python | gpl-2.0 | 3,584 | [
"Brian"
] | febe9ee4159e7a4825b0330a0106a2380374241b50cb636fc9d6fd1579da4da0 |
"""
A set of useful functions for working with OAI-PMH data
"""
from datetime import datetime
import base64, json
from octopus.core import app
class DateFormat(object):
"""
Class which helps us manage the date formats allowed by the standard
"""
@classmethod
def granularity(self):
"""
... | JiscPER/jper-oaipmh | service/oaitools.py | Python | apache-2.0 | 5,812 | [
"Octopus"
] | aac08dd22613fdd3c4fb090060fd40892b34763724bfb2754c0850969259a033 |
# Transformer/Framework/BatchIO.py
# -------
# Imports
# -------
import os;
import warnings;
from Transformer.IO import StructureSetIO;
# -----------------------------
# Batch Import/Export Functions
# -----------------------------
def ExportResultSet(resultSet, fileFormat = 'vasp', prefix = None, archiveDirecto... | JMSkelton/Transformer | Transformer/Framework/BatchIO.py | Python | gpl-3.0 | 7,480 | [
"VASP"
] | a748d2a7c90c842df09297e72fc8fb40d1fca2dfd2d98392fe3435cfc684f8ac |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | capoe/espressopp.soap | src/interaction/DihedralHarmonicUniqueCos.py | Python | gpl-3.0 | 3,722 | [
"ESPResSo"
] | 017f475499e2b435bb01d3c34e93eaa9e6dc7ce79c9989eaa7350b1b613bb347 |
import astroid
import inspect
from pylint.interfaces import IAstroidChecker
from pylint.checkers import BaseChecker
from pylint.checkers.utils import check_messages
class ForbiddenImportChecker(BaseChecker):
__implements__ = IAstroidChecker
name = 'forbidden_import'
msgs = {'E9999':
('Yo... | RyanDJLee/pyta | python_ta/checkers/forbidden_import_checker.py | Python | gpl-3.0 | 2,792 | [
"VisIt"
] | b6c31168ba0fd299f2d954df27c718bd0375029e3e9fb2ad3313e6d9abbaf483 |
#!/usr/bin/env python
"""Prevent unwanted files from being added to the source tree."""
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import os
import sys
def main():
"""Main entry point."""
paths = sys.argv[1:] or sys.stdin.read().splitlines()
allowed_extension... | maxamillion/ansible | test/sanity/code-smell/no-unwanted-files.py | Python | gpl-3.0 | 1,232 | [
"Galaxy"
] | 590d5aa0f80bddccecd0f73624023354462a3457966e29f8c9eafaf383a83ddf |
#!/usr/bin/python
#FILE DESCRIPTION=======================================================
#~ Python script used for post-processing automatization of flow on an
#~ inclined (?textured?) plate (minimal postprocessing to test the results)
#~
#~ NOTES:
#~ - still unfinished BUT improvement
#~ USAGE:
#~ paraF... | MartinIsoz/CFD_oF | 05_freibergExpSetUp/00_Scripts/postProcMinimalV2.py | Python | gpl-2.0 | 6,562 | [
"ParaView"
] | 7a8ac627cc964966254a0962c1ccca54243f69b6d8837db1ec03f09ccc553f49 |
# -*- coding: utf-8 -*-
#
# test_parrot_neuron.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the Lice... | SepehrMN/nest-simulator | pynest/nest/tests/test_parrot_neuron.py | Python | gpl-2.0 | 10,016 | [
"NEURON"
] | 7151170dd330dd22ac7c7d392aafa80da8465d425221a5edec1d557f178b79e4 |
from __future__ import absolute_import
# coding=utf-8
from flask import request
from flask.views import MethodView
from flask.blueprints import Blueprint
from firefly.models.consts import KEYBOARD_URL_MAPS
from firefly.libs.template import render_template
bp = Blueprint('keyboard', __name__, url_prefix='/keyboard')
... | matrixorz/firefly | firefly/views/keyboard.py | Python | mit | 817 | [
"Firefly"
] | 7eac1f20fdaf37603e4546bebd5585aa02fd8162ef9faa792b25d83c738143a2 |
#!/usr/bin/env python
"""
Testing k-means clustering
for purely random and normally distributed data
"""
import os
import math
import random
from numpy import array, random as numpy_random
from ase.data import chemical_symbols
from kmeans import Point, kmeans, k_from_n
from element_groups import get_element_group
from... | ansobolev/tilde | tutorials/simple_data_mining/sample_kmeans.py | Python | mit | 2,670 | [
"ASE",
"Gaussian"
] | e274284b7253052758de0741c2b76de2458feb0bc544e79666673cc5b934cc53 |
import os
import re
from datetime import datetime
from flask import current_app as app, render_template, request, redirect, abort, jsonify, url_for, session, Blueprint, Response, send_file
from jinja2.exceptions import TemplateNotFound
from passlib.hash import bcrypt_sha256
from sqlalchemy import union_all
from CTFd.... | jaboyles/CFTD_Senior_Project | CTFd/views.py | Python | apache-2.0 | 12,054 | [
"Brian"
] | f911a8e1046ed35399aab23c6c39c306a23ddf30a41b453a18107cda2c8b85da |
#!/usr/bin/env python
""" File Catalog Client Command Line Interface. """
__RCSID__ = "$Id$"
import stat
import cmd
import commands
import os.path
import time
import sys
from types import DictType, ListType
from DIRAC import gConfig
from DIRAC.Core.Security import CS
from DIRAC.Core.Security.ProxyInfo import getPro... | Sbalbp/DIRAC | DataManagementSystem/Client/FileCatalogClientCLI.py | Python | gpl-3.0 | 76,823 | [
"DIRAC"
] | c80329ccf449dc6e8f664535bfef3c6f289319610112597ecbf4e73e227b422c |
# -*- coding: utf-8 -*-
import document
import interface
import package
import rulegenerator
import testgenerator
class ArgumentVisitorBase(interface.ArgumentVisitor):
def visitReturnValue(self, retValue):
self.visitAllocation(retValue)
class SingleArgumentVisitor(ArgumentVisitorBase):
"""
V... | uboot/stromx-opencv | opencv/methodgenerator.py | Python | apache-2.0 | 62,812 | [
"VisIt"
] | 50161b6438dfe7282357aaf833b623146d3651871ae0083b74be15c1df46eeeb |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# html_writer - [insert a few words of module description on this line]
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms ... | heromod/migrid | mig/reST/html_writer.py | Python | gpl-2.0 | 1,966 | [
"Brian"
] | 965e3ce4dfc91bc837b1e2ed01fcface72579c98654231af7420171e395df2de |
# -*- coding: utf-8 -*-
"""readers module of the nc2map python module
This script contains the basic data danagement utilities in the nc2map
module.
It contains the following reader classes
- The ReaderBase class defines the main methods for all readers,
such as data extraction, the merging method and the a... | Chilipp/nc2map | readers.py | Python | gpl-2.0 | 129,034 | [
"NetCDF"
] | 9f005a857e866b94a6a15a58fdd5ba0f92d555db673851a7937547bb5547552f |
# coding: utf-8
"""
Unicode Emojis for Python-Markdown
==================================
Converts defined emoticon symbols to Unicode emojis, supported on a
variety of devices [1].
[1]: http://apps.timwhitlock.info/emoji/tables/unicode#block-1-emoticons
Usage:
>>> from __future__ import print_function
>>> ... | Naereen/cuisine | plugins/mdx_unimoji/mdx_unimoji.py | Python | mit | 47,452 | [
"Bowtie",
"CASINO",
"CRYSTAL",
"ESPResSo",
"Octopus"
] | 4cc7ae572137d38c54165eb282487b7d5548594a760d9da395de4dc28d1e7170 |
# -*- coding: utf-8 -*-
#
# This file is part of EventGhost.
# Copyright © 2005-2016 EventGhost Project <http://www.eventghost.net/>
#
# EventGhost 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... | WoLpH/EventGhost | _build/Build.py | Python | gpl-2.0 | 5,391 | [
"VTK"
] | 31a15048105129e69d38a292bb52670361c4f10f0a06130fe1e168f748e336a3 |
import requests
import os
class attack:
session = requests.Session()
# the login page
url1 = 'http://127.0.0.1:8080/WebGoat/login.mvc'
# where login credentials are posted to
url2 = 'http://127.0.0.1:8080/WebGoat/j_spring_security_check'
# login payload
payload = {'username':'guest','password':'guest'}
# tak... | mtesauro/gauntlt-demo | examples/webgoat/vuln-26/attack.py | Python | mit | 1,189 | [
"VisIt"
] | 5671274f77308bcf9a6a3ba6a987feafbc67b1489d9e1b31e3600f6b60226da2 |
import sys
sys.path.append('../../')
import amber_run_tests as ar
def test_get_tests_from_test_name():
assert ar.get_tests_from_test_name('test.serial', 'Makefile.amber') == \
['test.serial.MM', 'test.serial.QMMM',
'test.serial.sander.SEBOMD',
'test.serial.emil', 'test.seria... | Amber-MD/ambertools-conda-build | conda_tools/test/test_amber_run_tests/test_amber_run_tests.py | Python | mit | 432 | [
"Amber"
] | b757fb5f092fdf6eee3b96547116e43cf7d63b85109f3a5c86d8ecd06f52228c |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
JahnTeller distortion analysis.
"""
import os
import warnings
from typing import Any, Dict, Optional, Tuple, Union
import numpy as np
from pymatgen.analysis.bond_valence import BVAnalyzer
from pymatgen.... | gmatteo/pymatgen | pymatgen/analysis/magnetism/jahnteller.py | Python | mit | 20,445 | [
"CRYSTAL",
"pymatgen"
] | 5a76833640aec69d63e1a8eb59ece7281c0eb73facdb7f80f82e4e70c7b20579 |
"""Gaussian processes classification."""
# Authors: Jan Hendrik Metzen <jhm@informatik.uni-bremen.de>
#
# License: BSD 3 clause
from operator import itemgetter
import numpy as np
from scipy.linalg import cholesky, cho_solve, solve
import scipy.optimize
from scipy.special import erf, expit
from ..base import BaseEst... | shyamalschandra/scikit-learn | sklearn/gaussian_process/_gpc.py | Python | bsd-3-clause | 35,129 | [
"Gaussian"
] | 7b21ec5046d4f0d483c242e6f9db84f001a9c710c7f33502b697e2990ad1ece0 |
#!/usr/bin/env python
# Copyright 2013 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""The frontend for the Mojo bindings system."""
import argparse
import imp
import os
import pprint
import sys
script_dir = os.path.... | anirudhSK/chromium | mojo/public/bindings/mojom_bindings_generator.py | Python | bsd-3-clause | 4,091 | [
"VisIt"
] | 22451d564fca7ab3d0ac36305095b234eaf345299fc379c801c5e58905572bb0 |
"""Oral Argument Audio Scraper for Eighth Circuit Court of Appeals
CourtID: ca8
Court Short Name: 8th Cir.
Author: Brian W. Carver
Date created: 2014-06-21
History:
- 2014-07-22: download_url fixed by mlr
"""
from datetime import datetime
from juriscraper.OralArgumentSite import OralArgumentSite
class Site(OralArg... | Andr3iC/juriscraper | oral_args/united_states/federal_appellate/ca8.py | Python | bsd-2-clause | 2,115 | [
"Brian"
] | f586af308ededdbdae13ed25fb26cb629be5b107192ce45c7033086d4a833a4a |
#!/usr/bin/env
"""
HROISST_Station.py
Retrieve NCEP HighRes OI SST for defined station:
Save in EPIC NetCDF standard
Modified 2016-12-06: Use sbell unified package subroutines for netcdf/time - cleanup code
"""
#System Stack
import datetime
import sys
import argparse
#Science Stack
import numpy as np
from n... | shaunwbell/FOCI_Analysis | NCEP_WindsSFCtemp_Station.py | Python | mit | 9,719 | [
"NetCDF"
] | 3cf9a8a82c81b86847b9445a78b247ca14367720d0b49ead7683eee4e2b859b5 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import unittest
import tempfile
import numpy.testing.utils as nptu
from six.moves import zip
from io import open
import os
import json
from monty.json import MontyDecode... | xhqu1981/pymatgen | pymatgen/util/testing.py | Python | mit | 6,039 | [
"pymatgen"
] | 5978bd4d39eb24576b9d6c4c573d10908c2677e2ffb758bed0e72c222fe8faa7 |
# coding=utf-8
import os
import platform
import sys
from typing import Optional, Dict, Any, List
from dbt.logger import GLOBAL_LOGGER as logger
import dbt.clients.system
import dbt.config
import dbt.utils
import dbt.exceptions
from dbt.links import ProfileConfigDocs
from dbt.adapters.factory import get_adapter, regist... | fishtown-analytics/dbt | core/dbt/task/debug.py | Python | apache-2.0 | 13,454 | [
"VisIt"
] | 7e41cb858ae5701931a0d58e107395eebe2841911ee75f6803b5082f8583491d |
# Checks for Ticket #11
from asap3 import *
from ase.lattice.cubic import FaceCenteredCubic
from asap3.testtools import ReportTest
print "Test for Ticket #11: https://trac.fysik.dtu.dk/projects/Asap/ticket/11"
atoms = FaceCenteredCubic(directions=[[1,0,0],[0,1,0],[0,0,1]], size=(6,6,6),
sym... | auag92/n2dm | Asap-3.8.4/Test/ChangeUnitCell.py | Python | mit | 928 | [
"ASE"
] | 0947e0e963651d954137b9169afb870bda0f5318f585965230522569026e83ff |
#!/usr/bin/env python3
"""
INPUT
Expected input file format (pileup):
Each line consists of 5 (or optionally 6) tab-separated columns:
1. Sequence identifier
2. Position in sequence (starting from 1)
3. Reference nucleotide at that position
4. Number of aligned reads covering that position (depth of co... | jorvis/biocode | sandbox/jorvis/generate_read_coverage_figure.py | Python | mit | 4,414 | [
"Bowtie"
] | 95e424674eab37f5ca1dd49e526c7816cd890ebbf338725436376c53ffa7e39f |
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Provides an interface to start and stop Android emulator.
Emulator: The class provides the methods to launch/shutdown the emulator with
... | appknox/xysec_adb | xysec_adb/pylib/utils/emulator.py | Python | apache-2.0 | 14,436 | [
"Galaxy"
] | fa68ed57b49f44ec70012b818c0dd1eb4a5f390e6b651259ddba0a293d8c5eec |
# MIT License
#
# Copyright (c) 2016 Daily Actie
#
# 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 without restriction, including without limitation the rights
# to use, copy, modify, merge, ... | DailyActie/Surrogate-Model | surrogate/sampling/samRandom.py | Python | mit | 56,444 | [
"Gaussian"
] | ffc816185b298a568d71c1cde06ca3414e01ed8c01c9f82ae3e10aca14fc9c0c |
"""
Filename: lss.py
Reference: http://quant-econ.net/py/linear_models.html
Computes quantities associated with the Gaussian linear state space model.
"""
from textwrap import dedent
import numpy as np
from numpy.random import multivariate_normal
from scipy.linalg import solve
import warnings
#-Check if Numba is Ava... | dingliumath/quant-econ | quantecon/lss.py | Python | bsd-3-clause | 10,481 | [
"Gaussian"
] | e923c035361c63ae10c015aeae3248355765a940f8c91675f087d94ffba8f108 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | capoe/espressopp.soap | src/analysis/NPart.py | Python | gpl-3.0 | 1,624 | [
"ESPResSo"
] | c022a59e5387f84e29fdc6cc73b28a569e2383031bc5895460814b5620f36fd2 |
#
# gPrime - A web-based genealogy program
#
# Copyright (C) 2002-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
#
# 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 ... | sam-m888/gprime | gprime/filters/rules/person/_hasnameof.py | Python | gpl-2.0 | 3,872 | [
"Brian"
] | 0ba59e7f70a0af9b3b8c071a27d7ac091894c3733b30935c15127fb644c33a57 |
import os
import numpy
from PyML.classifiers import svm,multi,ridgeRegression,knn,composite,modelSelection,platt
from PyML.feature_selection import featsel
from PyML.containers import ker,labels
from PyML.containers import vectorDatasets
from PyML.containers.aggregate import Aggregate
from PyML.containers.kernelData i... | cathywu/Sentiment-Analysis | PyML-0.7.9/PyML/demo/test.py | Python | gpl-2.0 | 7,168 | [
"Gaussian"
] | 7a590baef54d86443e699f326a8e3e857658e9833f86d01585baae452f1ff277 |
import pylab
from matplotlib.font_manager import FontProperties
import matplotlib.cm
def graph_pop_heatmap_raw(pop, identify, minimize=False, colormap="jet", filesave=None):
pylab.imshow(pop, aspect="auto", interpolation="gaussian", cmap=matplotlib.cm.__dict__[colormap])
pylab.title("Plot of pop. raw scores alon... | ecervera/ga-nb | pyevolve_plot.py | Python | mit | 10,489 | [
"Gaussian"
] | cdb768308a55a58869a97b8ca187b0ad8e087ee2d9d41aa048c85923a097d750 |
# -*- coding: utf-8 -*-
from south.utils import datetime_utils as datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding index on 'Visit', fields ['wrhi_orig_date']
db.create_index(u'co... | praekelt/txtalert | txtalert/core/migrations/0023_auto__add_index_visit_wrhi_orig_date__add_index_visit_date__add_index_.py | Python | gpl-3.0 | 17,476 | [
"VisIt"
] | 60fa4402a27da64aa25be51eca01089438c72000750df7255fa2476d3f039c64 |
#
# Copyright (C) 2005 John Ashley Burgoyne and Ichiro Fujinaga
# 2012 Andrew Hankinson
# 2011-2012 Christoph Dalitz
#
# 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 F... | hsnr-gamera/gamera | gamera/plugins/binarization.py | Python | gpl-2.0 | 15,930 | [
"Brian"
] | aaafd2da41c685f82230f9aebaf979351730b4fb908c0fe73b08723564d21786 |
import bge
class Ressource(bge.types.KX_GameObject):
def __init__(self, parent):
self.material = 10000
class Mine(Ressource):
def __init__(self, parent):
super(Mine, self).__init__(parent)
self.material = 10000
class Tree(Ressource):
def __init__(self, parent):
super... | folkrav/rts-b51 | src/projectX/ressource.py | Python | gpl-3.0 | 519 | [
"CRYSTAL"
] | aafd27a6f9b1ec82498e179176767ec6203030f78643723694074d6193dcde48 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
#
# Copyright (C) 2017 Lenovo, Inc.
#
# 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 Licens... | hryamzik/ansible | lib/ansible/modules/network/cnos/cnos_factory.py | Python | gpl-3.0 | 5,299 | [
"VisIt"
] | a0ef776eb2c2ef0ac85d6475230556d46b754003bb70381427cd20be198a1389 |
#!/usr/bin/env python
########################################################################
# File : dirac-wms-cpu-normalization
# Author : Ricardo Graciani
########################################################################
"""
Determine Normalization for current CPU
"""
__RCSID__ = "$Id$"
import DIRAC
f... | sposs/DIRAC | WorkloadManagementSystem/scripts/dirac-wms-cpu-normalization.py | Python | gpl-3.0 | 2,118 | [
"DIRAC"
] | 59ebb5d9fa3d99f3d94d00d899f390faa830c60292ff9277eaaee3d131b3bc09 |
# -*- coding: utf-8 -*-
"""
.. _tut-artifact-ica:
Repairing artifacts with ICA
============================
This tutorial covers the basics of independent components analysis (ICA) and
shows how ICA can be used for artifact repair; an extended example illustrates
repair of ocular and heartbeat artifacts. For conceptu... | bloyl/mne-python | tutorials/preprocessing/40_artifact_correction_ica.py | Python | bsd-3-clause | 29,351 | [
"Gaussian"
] | b0c26ec8fe42b2d8880eaa7c64a2cfb7decfee5b8148b231257ba94e61dfaedd |
#
# 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/src/bigdl/chronos/forecaster/tfpark_forecaster.py | Python | apache-2.0 | 1,366 | [
"ORCA"
] | 9fc21a0c0eadaf2c49bf1d0954cb2610e14c82117afedea2b09e47b4a12807d5 |
import numpy as np
import numpy.matlib
import math
import random
import os
import xml.etree.ElementTree as ET
import tensorflow as tf
from utils import *
class Model():
def __init__(self, args, logger):
self.logger = logger
# ----- transfer some of the args params over to the model
# model params
self.rnn_... | Charleo85/ml_project | resource/scribe/model.py | Python | mit | 10,496 | [
"Gaussian"
] | 4a6ac518c568bac94dcca650aec0fa95b9b37e0a6eb35686ab925be3fb3fec61 |
"""
omniCLIP is a CLIP-Seq peak caller
Copyright (C) 2017 Philipp Boss
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) an... | philippdre/omniCLIP | omniCLIP/data_parsing/GetCoverageFromBam.py | Python | gpl-3.0 | 10,108 | [
"pysam"
] | c9721cec0c86c23e16579c0709f26c60afb1f2669f3c9624c6f9c669e8a3cb02 |
#
# 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 us... | charlesccychen/beam | sdks/python/apache_beam/runners/portability/fn_api_runner.py | Python | apache-2.0 | 70,063 | [
"VisIt"
] | b9df03e3f65ede93640782f9baa9e91cf48e6a3eedb17d4b723b2d1d1ff07216 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import warnings
warnings.warn("pymatgen.analysis.elasticity.tensors has been moved to "
"pymatgen.core.tensors, please update dependencies accordingly. "
"Links will removed in v201... | dongsenfo/pymatgen | pymatgen/analysis/elasticity/tensors.py | Python | mit | 366 | [
"pymatgen"
] | 13fdfc2e47628b663aad41c8e94eb40c192f527bf4d5e388984803dc8bc01f74 |
from ..error import GraphQLError
from ..language.ast import FragmentDefinition, FragmentSpread
from ..language.visitor import Visitor, visit
from ..utils import TypeInfo
from ..type import GraphQLSchema
from . import rules as Rules
specified_rules = [
Rules.UniqueOperationNames,
Rules.LoneAnonymousOperation,
... | jhgg/graphqllib | graphql/core/validation/__init__.py | Python | mit | 4,372 | [
"VisIt"
] | 34628bf452bc97a7bf428b5a0673b9b6fb82735fa6665778352ec476d2edc8ba |
"""annotate fusion outputs from STAR and Tophat
Supported:
oncofuse: http://www.unav.es/genetica/oncofuse.html
github: https://github.com/mikessh/oncofuse
"""
from __future__ import print_function
import os
import pysam
from bcbio.utils import file_exists
from bcbio.distributed.transaction import file_transaction... | mjafin/bcbio-nextgen | bcbio/rnaseq/oncofuse.py | Python | mit | 7,469 | [
"pysam"
] | d2843315735610fc1a3b1cb58f574804f967acbdd66779cd5904ea3c273d70c9 |
# Orca
#
# Copyright 2005-2008 Google Inc.
# Portions Copyright 2007-2008, 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... | GNOME/orca | src/orca/acss.py | Python | lgpl-2.1 | 3,569 | [
"ORCA"
] | aeed5e5ea790645c5a055e1b70282bd6983bddbd136802c34ad7b76b8de077d8 |
#!/usr/bin/env python
##
## Biskit, a toolkit for the manipulation of macromolecular structures
## Copyright (C) 2004-2018 Raik Gruenberg & Johan Leckner
##
## 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 Softwar... | graik/biskit | archive_biskit2/scripts/Mod/analyse.py | Python | gpl-3.0 | 3,127 | [
"PyMOL"
] | fa9f5eda6a1b7d5b331f0cb303e4f8b3454bf373be6a3034f54120783bd0c4aa |
import os
import math
import numpy as np
import pickle as pickle
from ase import Atoms
from ase.data import chemical_symbols
from ase.cluster.base import ClusterBase
class Cluster(Atoms, ClusterBase):
symmetry = None
surfaces = None
lattice_basis = None
resiproc_basis = None
atomic_basis = None
... | suttond/MODOI | ase/cluster/cluster.py | Python | lgpl-3.0 | 4,164 | [
"ASE"
] | ca8c27e8c24c2296035aa73c02b4b99f68bf0af7f1e01782927444abbba45aa9 |
# Line too long - pylint: disable=C0301
# Copyright (c) Greenplum Inc 2011. All Rights Reserved.
from contextlib import closing
import os
import platform
import shutil
import sys
import tarfile
try:
from gppylib import gplog
from gppylib.commands import gp
from gppylib.commands.base import Command, REMOTE... | lpetrov-pivotal/gpdb | gpMgmt/bin/gppylib/operations/package.py | Python | apache-2.0 | 53,027 | [
"ORCA"
] | 6e64536d248d25e8db8b17d528a1885c1ad23dd0151853a0f83f8889f0944c41 |
__author__ = 'chris hamm'
#NetworkServer_r9E
#Created: 1/17/2015
#THINGS ADDED/CHANGED FROM THIS REVISION
#Now able to receive a chunk object from the controller class
#Extract information from a chunk object (THESE FUNCTIONS ARE NO LONGER NEEDED)
#(In progress)Send extracted information over the network to the client... | COCS4950G7/COSC4950 | Source/Network/Obsolete/NetworkServer_r9E.py | Python | gpl-3.0 | 90,551 | [
"ADF"
] | 8d6e131289202630223e045070d5867df2ed8ceafa7054fb7012c6fe98f65303 |
# coding=utf-8
# !/usr/bin/env python
import sys
try:
from setuptools import setup
except ImportError:
sys.stderr.write('using distutils\n')
from distutils.core import setup
with open('requirements.txt') as f:
required = f.read().splitlines()
required = [ req.split('#egg=')[1] if '#' in req else r... | project-capo/amber-python-drivers | setup.py | Python | mit | 2,925 | [
"Amber"
] | 9e92427f76d9d504beccc6b60836c17759792aa08f6cb44fe462b8c212bf3f6c |
import tempfile
from mayavi import mlab
import Image
import numpy as np
import geoprobe
import scipy.ndimage
import matplotlib.colors as mcolors
import matplotlib.cm as cm
import utils
def main():
vol, top = load_data()
downsample = 3
fig = mlab.figure(bgcolor=(1,1,1))
x, y, z = hor2xyz(top, vol, d... | joferkington/scipy2015-3d_printing | make_base.py | Python | mit | 3,380 | [
"Mayavi"
] | 49aa995f949fb04eddf7a84e8fe8454e40a7296a62b441692cb4a879fc6e75f1 |
# __ File: ATOM3.py __________________________________________________________________________________________________
#
# Implements : class ATOM3
# Author : Juan de Lara and Denis Du... | Balannen/LSMASOMM | atom3/Kernel/ATOM3.py | Python | gpl-3.0 | 249,434 | [
"OpenMM",
"VisIt"
] | 11bc8b3da76dcfd80ecb3c37bb3bfb9a2dc454f2f5eaaa9a4f8b574da3ed22ba |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module defines classes to represent the density of states, etc.
"""
import functools
import warnings
from typing import Dict
import numpy as np
from monty.json import MSONable
from scipy.constants.co... | richardtran415/pymatgen | pymatgen/electronic_structure/dos.py | Python | mit | 39,371 | [
"DIRAC",
"Gaussian",
"VASP",
"pymatgen"
] | effed105ee490215690fa8e71c387eb6c9fca34eb821876444089f6cda5950f9 |
"""This contains classes modelling optical elements such as lenses.
Each optical element has a focal length and width and implements the method
"apply", which enables it to modify an incident wave
Authors:
Adam Rains
"""
from __future__ import division, print_function
import numpy as np
import opticstools as optics_... | mikeireland/astro-optics | optics.py | Python | mit | 15,640 | [
"Gaussian"
] | 714a3e7f1b2d61c308b2ddc6b4261947f3f4eada72798a0fcb202e2e30d73614 |
# $Id$
#
# Copyright (C) 2007-2010 Greg Landrum
# All Rights Reserved
#
from rdkit import Chem
class PropertyMol(Chem.Mol):
""" allows rdkit molecules to be pickled with their properties saved.
>>> import cPickle
>>> m = Chem.MolFromMolFile('test_data/benzene.mol')
>>> m.GetProp('_Name')
'benzene.mol'
... | rdkit/rdkit-orig | rdkit/Chem/PropertyMol.py | Python | bsd-3-clause | 2,973 | [
"RDKit"
] | fb0e754af5d720da2a522804601c9ec62100c9edf9a4eacf29596204bbbf67a4 |
#!/usr/bin/env python
"""
Install.py tool to do a generic build of a library
soft linked to by many of the lib/Install.py files
used to automate the steps described in the corresponding lib/README
"""
from __future__ import print_function
import sys, os, subprocess
from argparse import ArgumentParser
sys.path.append... | Pakketeretet2/lammps | lib/Install.py | Python | gpl-2.0 | 2,989 | [
"LAMMPS"
] | e656cbc92acf1f9f8c72696fe2c9672132bdfc9335f759eb8dfa4339f1b75032 |
#
# Copyright (C) 2007, Mark Lee
#
#http://rl-glue-ext.googlecode.com/
#
# 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... | okkhoy/mo-rlglue-python-codec | rlglue/agent/Agent.py | Python | mit | 1,727 | [
"Brian"
] | 73d8c1785a771b47ac650af7350e99fb7741e555fb88b4a1aafdfc8505f1be5e |
#!/usr/bin/env python3
"""
Copyright 2020 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 ... | pwillworth/galaxyharvester | html/getResourceGroupList.py | Python | gpl-3.0 | 3,121 | [
"Galaxy"
] | ebcccff6b47a27935b8f9a43edd0f21869effc7dc4c79024d2dd429d6f38629a |
"""Guess the MIME type of a file.
This module defines two useful functions:
guess_type(url, strict=True) -- guess the MIME type and encoding of a URL.
guess_extension(type, strict=True) -- guess the extension for a given MIME type.
It also contains the following, for tuning the behavior:
Data:
knownfi... | edmundgentle/schoolscript | SchoolScript/bin/Debug/pythonlib/Lib/mimetypes.py | Python | gpl-2.0 | 20,950 | [
"NetCDF"
] | 6143f6ff33c58e059fbee4a1cd03c43f9887551a011ffed109b8db61fa47babd |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright 2014-17 Neil Freeman contact@fakeisthenewreal.org
# 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
# ... | fitnr/twitter_bot_utils | src/twitter_bot_utils/cli.py | Python | gpl-3.0 | 8,641 | [
"VisIt"
] | 1d39b425d8a04465dd9191ea59d872ebcb711d4c3b6cfd73f101fbbd85b83137 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.