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# -*- coding: utf-8 -*-
"""
Subraph centrality and communicability betweenness.
"""
# Copyright (C) 2011 by
# Aric Hagberg <hagberg@lanl.gov>
# Dan Schult <dschult@colgate.edu>
# Pieter Swart <swart@lanl.gov>
# All rights reserved.
# BSD license.
import networkx as nx
from networkx.utils import *
__au... | jfinkels/networkx | networkx/algorithms/centrality/subgraph_alg.py | Python | bsd-3-clause | 9,498 | [
"Desmond"
] | 6d87dd9391ddec42898c62320798b81753a5312c2752ef49c14219bbcb2f295f |
"""Test suite for the crystal field calculations in the Inelastic/CrystalField package
"""
from __future__ import (absolute_import, division, print_function)
import unittest
import numpy as np
from scipy.constants import physical_constants
# Import mantid to setup the python paths to the bundled scripts
import mantid
... | wdzhou/mantid | scripts/test/CrystalFieldTest.py | Python | gpl-3.0 | 89,180 | [
"CRYSTAL",
"Gaussian"
] | 265af31a56ede0704c0a24453af024871d1320d2bc3fa81a2680089f29d017e7 |
#!/usr/bin/env python
# ----------------------------------------------------------------------
# Numenta Platform for Intelligent Computing (NuPIC)
# Copyright (C) 2013, Numenta, Inc. Unless you have an agreement
# with Numenta, Inc., for a separate license for this software code, the
# following terms and conditions... | Lyleo/nupic | nupic/regions/extra/GaborNode2.py | Python | gpl-3.0 | 136,577 | [
"Gaussian"
] | f8f7df9a8a7a2ac766426c77e3fad4ca084c6f30dd9056178a55981339ae5574 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes to perform fitting of structures.
"""
import numpy as np
import itertools
import abc
from monty.json import MSONable
from pymatgen.core import PeriodicSite
from pymatgen.core.... | gVallverdu/pymatgen | pymatgen/analysis/structure_matcher.py | Python | mit | 48,921 | [
"pymatgen"
] | 9eef03206ac0e254db5af52d86315024554131fc473e3d83e67b80b8f7dc9569 |
# Constants to describe the start, end, and actual due date of a
# visit window in a scheduler module.
VISIT_WINDOW_START = 'WINDOW_START'
VISIT_WINDOW_END = 'WINDOW_END'
VISIT_WINDOW_DUE_DATE = 'WINDOW_DUE_DATE'
| dimagi/commcare-hq | corehq/messaging/scheduling/const.py | Python | bsd-3-clause | 215 | [
"VisIt"
] | 0ae09f225bb8e63c9c75bbb2172a1ea04660a20b1b56b96dbe2dff2f8f73ff86 |
# -*- coding: utf-8 -*-
# Copyright 2022 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... | googleapis/python-error-reporting | tests/unit/gapic/errorreporting_v1beta1/test_error_stats_service.py | Python | apache-2.0 | 87,049 | [
"Octopus"
] | 625a3f562e61cae0bd08a739b7ee7f03a5fe88714e57a99b9fad2fcb2c9093f5 |
#!/usr/bin/env python
# Copyright 2014-2020 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... | sunqm/pyscf | pyscf/pbc/scf/cphf.py | Python | apache-2.0 | 5,923 | [
"PySCF"
] | 0c8f49d75705758197141aa4492ea4349d0c42a55e7ac03f4031e6b27e93fdfa |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Module containing class to create an ion
"""
__author__ = "Sai Jayaraman"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.0"
__maintainer__ = "Sai Jayaraman"
__email__ = "sjayaram... | dongsenfo/pymatgen | pymatgen/core/ion.py | Python | mit | 6,398 | [
"pymatgen"
] | 0a8ccffbe8f1b78ed46f8fc5e96da38f31a127f3bd4e81e9b3c0f1cd9ad06cd1 |
''' -- imports from python libraries -- '''
# from datetime import datetime
import datetime
import json
''' -- imports from installed packages -- '''
from django.http import HttpResponseRedirect # , HttpResponse uncomment when to use
from django.http import HttpResponse
from django.http import Http404
from django.sho... | AvadootNachankar/gstudio | gnowsys-ndf/gnowsys_ndf/ndf/views/gcourse.py | Python | agpl-3.0 | 112,451 | [
"VisIt"
] | b30b7692262821f4dc70b285f90bf36acc5700309c8fe5a788d5bce9e6e5e348 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | MOA-2011/enigma2-plugin-extensions-openwebif | plugin/controllers/views/web/movierename.py | Python | gpl-2.0 | 5,238 | [
"VisIt"
] | 80096917249d362b59d2fd32571fe44a5057791be036d7d838f7f6f8eb161515 |
import numpy as np
from sklearn import cluster, mixture
def extract_pix_from_marks(im, marks):
"""
Extract pixels at marked locations.
Take
im: image in skimage ndarray format
Give
fg_pix, bg_pix: tuple of N x 3 ndarrays,
for foreground and background pixels
"""
fg_color = (2... | shelhamer/coop-cut | pycoop/potentials/potentials.py | Python | bsd-2-clause | 2,697 | [
"Gaussian"
] | d1aa06e11172ef58117fe2284c0b542b19c840f7adb72a8f09b7d2731b5d109a |
from math import sqrt, pi
import numpy as np
from ase.units import Bohr
from gpaw.utilities import pack, pack2
from gpaw.analyse.hirshfeld import HirshfeldDensity
from gpaw.utilities.tools import coordinates
from gpaw.mpi import MASTER
def wignerseitz(gd, atoms, scale=None):
"""Determine which atom is closest to... | robwarm/gpaw-symm | gpaw/analyse/wignerseitz.py | Python | gpl-3.0 | 5,665 | [
"ASE",
"GPAW"
] | d75c3740eee5ae9008f43b613ea6091fabf6ddeb578a4330798908cb5beb12ca |
#/**********************************************************************
#** This program is part of 'MOOSE', the
#** Messaging Object Oriented Simulation Environment.
#** Copyright (C) 2003-2014 Upinder S. Bhalla. and NCBS
#** It is made available under the terms of the
#** GNU Lesser General Public License... | BhallaLab/moose-examples | snippets/STDP.py | Python | gpl-2.0 | 8,585 | [
"MOOSE",
"NEURON"
] | 69ba5de73ee48b22463809e4eb539acfd9cbc8026766b49756d071e6d6a846ba |
#!/usr/bin/env python
#---------------- EDIT JOB NAME -------------------
#$ -N NAME
#--------------------------------------------------
#$ -S /usr/bin/python
# Importing the whole environment is important for setting up Charmm:
#$ -V
#$ -v PYTHONPATH=/home/oliver/Library/python-lib
#$ -v LD_LIBRARY_PATH=/opt/intel/cmk... | iwelland/hop | doc/examples/recenter_orient_LAMPPS.py | Python | lgpl-3.0 | 4,521 | [
"CHARMM",
"LAMMPS"
] | bdb21dd83144311af48c0f53c64f9913df4d20d08706ab426efdb2ea1b9bfb5a |
#!/usr/bin/env python
# Author: Andrew Jewett (jewett.aij at g mail)
# http://www.chem.ucsb.edu/~sheagroup
# License: 3-clause BSD License (See LICENSE.TXT)
# Copyright (c) 2011, Regents of the University of California
# All rights reserved.
"""
lttree_check.py
The original template file format supports any... | ramisetti/lammps | tools/moltemplate/moltemplate/lttree_check.py | Python | gpl-2.0 | 139,819 | [
"LAMMPS"
] | ba0dc51abb3453348c987bbd3b0dbbb3be4fd9e75c07a2406c93a3068e671fdb |
"""Bayesian Gaussian Mixture Models and
Dirichlet Process Gaussian Mixture Models"""
from __future__ import print_function
# Author: Alexandre Passos (alexandre.tp@gmail.com)
# Bertrand Thirion <bertrand.thirion@inria.fr>
#
# Based on mixture.py by:
# Ron Weiss <ronweiss@gmail.com>
# Fabian Ped... | depet/scikit-learn | sklearn/mixture/dpgmm.py | Python | bsd-3-clause | 31,018 | [
"Gaussian"
] | d147d949a4396902660babdd819c27d894aa02bed3c8e52dff9292d2a9c7aa41 |
#!/usr/bin/env python
import sys
from time import sleep
import os
from os import path
from Bio import Entrez
from Bio import SeqIO
from urllib.error import HTTPError
import argparse
from helperFunctions import awk_files, is_dir
#Entrez.email = "curtisross@tamu.edu"
class CPTEfetch:
""" Object that has built in... | TAMU-CPT/galaxy-tools | tools/efetch/cpt_efetch.py | Python | gpl-3.0 | 6,658 | [
"Galaxy"
] | 3790d0e299139b268400a5e577673fc9181fafce50b197f07a126aa987235176 |
# coding: utf-8
# Copyright 2013 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by ap... | ram8647/gcb-mobilecsp | tests/functional/test_classes.py | Python | apache-2.0 | 258,550 | [
"VisIt"
] | 029d0e2c4fc71f1b4328a1ec4715d475a0ccd6539f07f4371fa3f9b4a2f1191a |
from Sire.MM import *
from Sire.FF import *
from Sire.System import *
from Sire.Move import *
from Sire.IO import *
from Sire.Mol import *
from Sire.Maths import *
from Sire.Vol import *
from Sire.Base import *
from Sire.Units import *
from Sire.Qt import *
from nose.tools import assert_almost_equal
(mols, space) = ... | michellab/SireUnitTests | unittests/SireMM/test_interff.py | Python | gpl-3.0 | 17,338 | [
"Amber"
] | bdb1938d5ba143ed3c8ed58d128fb5c23e6f193c04f78ced59500df016538204 |
"""Helpful utilities for performing Blastn."""
# Standard Library
import csv
import itertools
import os
import shutil
import sqlite3
import subprocess as sp
import sys
import pkg_resources
from threading import Timer
from datetime import datetime
from importlib import import_module
from pathlib import Path
from subproc... | datasnakes/Datasnakes-Scripts | OrthoEvol/utilities.py | Python | mit | 45,355 | [
"BLAST",
"Biopython"
] | db520205ad013999dfced776751721782be3c7cc3a72391a68df7ff5c1af2e95 |
import numpy as np
from ase.units import Bohr
"""This module defines different external potentials to be used in
time-independent and time-dependent calculations."""
class ExternalPotential:
""" External potential
"""
def __init__(self, vext_g=None, gd=None):
"""Initialize with a grid and the c... | robwarm/gpaw-symm | gpaw/external_potential.py | Python | gpl-3.0 | 9,057 | [
"ASE"
] | 6de65b24accaee2010f48005604825c5cc440b9fc14b7ce155a49f847a50174c |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under t... | MDAnalysis/mdanalysis | package/MDAnalysis/coordinates/DCD.py | Python | gpl-2.0 | 16,909 | [
"CHARMM",
"LAMMPS",
"MDAnalysis",
"NAMD",
"VMD"
] | e7b1add2bbe23faa51d924c734ad153e537692851428a1d899f0b365f1fce366 |
# Copyright (c) 2016 Ansible, Inc.
# All Rights Reserved.
# Python
import logging
import threading
import contextlib
import re
# Django
from django.db import models, transaction, connection
from django.contrib.contenttypes.models import ContentType
from django.contrib.contenttypes.fields import GenericForeignKey
from... | snahelou/awx | awx/main/models/rbac.py | Python | apache-2.0 | 21,451 | [
"VisIt"
] | ea144d2d76328ab558ab1f734bbfa170b66f3a3d333a8d889aa530c4d77a9c09 |
import os
import warnings
import numpy as np
import fitsio
from astrometry.util.fits import fits_table, merge_tables
import logging
logger = logging.getLogger('legacypipe.reference')
def info(*args):
from legacypipe.utils import log_info
log_info(logger, args)
def debug(*args):
from legacypipe.utils import... | legacysurvey/pipeline | py/legacypipe/reference.py | Python | gpl-2.0 | 31,480 | [
"Galaxy"
] | de09d3554cb7174583894d5bd0fb1ae4eb40c54a90f9f5e13c43791737053ac1 |
# TO-DO: to be moved to TestDIRAC
########################################################################
# File: DataLoggingClientTests.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2012/07/12 12:28:30
########################################################################
""" :mod: DataLoggingClientTests
... | sposs/DIRAC | DataManagementSystem/Client/test/DataLoggingClientTests.py | Python | gpl-3.0 | 1,733 | [
"DIRAC"
] | 557472f55fb2919cdce020dcbb3a62648d27e67eb5c51abc27bf2842ce27e704 |
# -*- Mode: Python; coding: utf-8; indent-tabs-mode: nil; tab-width: 4 -*-
### BEGIN LICENSE
# Copyright (C) 2014 Brian Douglass bhdouglass@gmail.com
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License version 3, as published
# by the Free Softwa... | bhdouglass/agui | agui/backends/pyside/widgets/label.py | Python | gpl-3.0 | 1,218 | [
"Brian"
] | a66faf9f64d11efc7ed5dc8dbe03402d7dea208cda2010a37f80807d0cff3be7 |
import sys
def dft(dihedrals):
"""Writes dft calculations for nwchem. This is wrong. Uses dihedrals. Runs
Keyword Arguments:
dihedrals - The list of dihedrals to generate a nwchem output from. If the dihedral is marked as dft it will run
"""
dftfile = open('outputs/dft.nw','w')
sys.stdou... | sipjca/cmlparser_py | write_nwchem.py | Python | apache-2.0 | 1,749 | [
"NWChem"
] | 90dd9643d535cf47257d631d1de9fa642da459d6762ad44cc1d539dbb8569229 |
from tools.load import LoadMatrix
from sg import sg
from numpy import *
num=100
labelstrain=concatenate((-ones([1,num]), ones([1,num])),1)[0]
featuretrain=concatenate((random.normal(size=(2,num))-1,random.normal(size=(2,num))+1),1)
parameter_list=[[1.,labelstrain,featuretrain],
[1.,labelstrain,featuretrain]]
def m... | AzamYahya/shogun | examples/undocumented/python_static/mkl_twoclass.py | Python | gpl-3.0 | 992 | [
"Gaussian"
] | 517000b1a4abc7b1164a6fa6911c6d714b1cb70ac4094edd4de55e465b88c7b5 |
#!/usr/bin/env python
"""
Populates blank uuid fields in datasets with randomly generated values
Going forward, these ids will be generated for all new datasets. This
script fixes datasets that were generated before the change.
"""
import sys, os, ConfigParser
import galaxy.app
from galaxy.util.bunch import Bunch
im... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/scripts/cleanup_datasets/populate_uuid.py | Python | gpl-3.0 | 1,193 | [
"Galaxy"
] | ecbdfde9712568a2abe6f882d015d3ff57a6a54f1b6d9ccd9b4aa64816964e35 |
"""Handles genomes (individuals in the population)."""
from __future__ import division, print_function
from itertools import count
from random import choice, random, shuffle
import sys
from neat.activations import ActivationFunctionSet
from neat.aggregations import AggregationFunctionSet
from neat.config import Con... | drallensmith/neat-python | neat/genome.py | Python | bsd-3-clause | 24,213 | [
"NEURON"
] | ed19b3e89ee1ecbf64926c3f1beb22ad4f17c01f5c90976729cef9f01d990b47 |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | Laurawly/tvm-1 | python/tvm/relay/transform/transform.py | Python | apache-2.0 | 38,367 | [
"VisIt"
] | d07b2eba59df257628a8d2e0aed0ff0b90e7f404d8c32b96fbe89d6027f94cad |
# -*- coding: UTF-8 -*-
import math
import random
import sys
from invesalius.pubsub import pub as Publisher
import numpy as np
import vtk
import invesalius.constants as const
import invesalius.project as prj
import invesalius.session as ses
import invesalius.utils as utils
from invesalius import math_utils
from in... | paulojamorim/invesalius3 | invesalius/data/measures.py | Python | gpl-2.0 | 53,521 | [
"VTK"
] | a5ba4d0eb651a5b5e543cb970385035905dfcac5d9fc0a2c7143777af0523f76 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/Openwebif | plugin/controllers/views/web/vol.py | Python | gpl-2.0 | 5,574 | [
"VisIt"
] | 757af2ca5540c26d7079dfb4098eecf90e6f5d29f5170d128b5d5547aec58b77 |
# Copyright 2015 Canonical, Ltd.
#
# This program 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 of the
# License, or (at your option) any later version.
#
# This program is distribute... | CanonicalLtd/subiquity | console_conf/ui/views/identity.py | Python | agpl-3.0 | 1,976 | [
"VisIt"
] | 305c0cd2e71779dda76d16db9ea48a6621663df081794a67b2042a569ac4ff50 |
"""
Written By:
Chris Humphreys
Email: < chris (--AT--) habitualcoder [--DOT--] com >
Jan Weiß
Email: < jan (--AT--) geheimwerk [--DOT--] de >
Copyright 2010 Chris Humphreys
Copyright 2012-2013 Jan Weiß
This program ... | chrishumphreys/p2j | translator/parser.py | Python | gpl-3.0 | 6,923 | [
"VisIt"
] | 28133616e3752c5174406e80aa5c22c333c10bb0d3465ca0a7231def72425576 |
# -*- coding: utf-8 -*-
"""
Created on Mon Apr 25 15:50:57 2016
@author: Gaspar Pandy
"""
from build.management.commands.base_build import Command as BaseBuild
from protein.models import Protein, ProteinConformation, ProteinSequenceType, ProteinSource, ProteinState
from residue.models import Residue
from structure.mo... | fosfataza/protwis | structure/management/commands/new_xtals.py | Python | apache-2.0 | 20,686 | [
"CRYSTAL"
] | f8f0de2cfb7390feb8e4b0db19b8ee0a968eecaaff45a06de87f86e8097e4af8 |
import os
import orca
import pandas as pd
from activitysim import activitysim as asim
from .util.misc import add_dependent_columns
"""
The school location model predicts the zones in which various people will
go to school.
"""
@orca.table()
def school_location_spec(configs_dir):
f = os.path.join(configs_dir, ... | bhargavasana/activitysim | activitysim/defaults/models/school_location.py | Python | agpl-3.0 | 2,377 | [
"ORCA"
] | 2c072dafafcd7e3b525557cb9580ca55ca37b828e655ca77f1fa004f85158c66 |
import os
import warnings
# silence matplotlib.use() warning
warnings.filterwarnings('ignore', '.*This call to matplotlib\.use.*',)
import csv
import numpy as np
import heapq
import matplotlib.pyplot as plt
from ase.data.molecules import latex
ann_fontsize = 'small'
label_fontsize = 12
from ase.data import atomi... | robwarm/gpaw-symm | gpaw/test/big/g2_1/pbe_gpaw_nrel_plot.py | Python | gpl-3.0 | 7,442 | [
"ASE",
"GPAW"
] | 5ff269a9d2bf6f16f1c58a8b71ecd8a3ef00049318d051f37a45309fe7efcb41 |
import numpy as np
from .._shared.utils import warn
from ._felzenszwalb_cy import _felzenszwalb_grey
def felzenszwalb(image, scale=1, sigma=0.8, min_size=20):
"""Computes Felsenszwalb's efficient graph based image segmentation.
Produces an oversegmentation of a multichannel (i.e. RGB) image
using a fast... | pratapvardhan/scikit-image | skimage/segmentation/_felzenszwalb.py | Python | bsd-3-clause | 3,049 | [
"Gaussian"
] | 303de708352b15e964b3ae389f1420fa747f64847ca482a32fc37c5d1e05964e |
#!/bin/env python3
import sys
from VASP import readVasp
from VASP import writeGjf
if len(sys.argv) == 1:
print('')
print('Usage: %s vasp_file1 vasp_file2 ...' % sys.argv[0].split('/')[-1])
print('')
exit(1)
print('')
print('############### This script converts vasp file into gview file ##############... | Mabinogiysk/VASP-script | vas2gjf.py | Python | gpl-2.0 | 896 | [
"VASP"
] | 2f91ca03e6373cc1d1dafeaf2b236fc2d38a3e11342f618531fb2dce561c7b48 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module defines the BorgQueen class, which manages drones to assimilate
data using Python's multiprocessing.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
... | gVallverdu/pymatgen | pymatgen/apps/borg/queen.py | Python | mit | 5,015 | [
"pymatgen"
] | 4efe45e09e9f643e93e60d3913f749b506a28aa90a85f593d64dcff87d74e487 |
from distutils.core import setup
DESCRIPTION = "Branching Gaussian process."
LONG_DESCRIPTION = DESCRIPTION
NAME = "BranchedGP"
AUTHOR = "Alexis Boukouvalas"
AUTHOR_EMAIL = "alexis.boukouvalas@gmail.com"
MAINTAINER = "Alexis Boukouvalas"
MAINTAINER_EMAIL = "alexis.boukouvalas@gmail.com"
DOWNLOAD_URL = 'https://github.... | ManchesterBioinference/BranchedGP | setup.py | Python | apache-2.0 | 881 | [
"Gaussian"
] | 8fcd4abd981a1e68eb4657dae612fb6720dd4a48c7012b7ef120df14709e9cba |
import os
import shutil
import glob
import numpy as np
import astropy.io.ascii as ascii
import time
import medianstats_bootstrap as msbs
import matplotlib
#matplotlib.use('PDF')
import matplotlib.pyplot as pyplot
import matplotlib.colors as pycolors
import matplotlib.cm as cm
from matplotlib.ticker import FormatStrForm... | gsnyder206/synthetic-image-morph | panstarrs/old/check_mock_efficiency.py | Python | gpl-2.0 | 6,835 | [
"Galaxy"
] | e813a2082d2ebcde9f2be88695239c376e8e7eb213983d220a1461c46fa93f1a |
""" DIRAC FileCatalog Storage Element Manager base class for mix-in classes """
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import threading
from DIRAC import S_ERROR
class SEManagerBase(object):
def _refreshSEs(self, connectio... | ic-hep/DIRAC | src/DIRAC/DataManagementSystem/DB/FileCatalogComponents/SEManager/SEManagerBase.py | Python | gpl-3.0 | 980 | [
"DIRAC"
] | ce806ae14c3e5ad574225a1a44e9f2281e3031c59ecc8b93e065ec0e7a4316c3 |
#
#
# pow server
# khz / 2016
#
import tornado.httpserver
import os
import os.path
import sys
from {{appname}}.config import server_settings as app_settings
from {{appname}}.config import myapp
from {{appname}}.config import database as db_settings
from {{appname}}.powlib import merge_two_dicts
from {{appname}}.appl... | pythononwheels/pow_clean | start/server.py | Python | mit | 2,484 | [
"VisIt"
] | f2bb77ebf03e8dd4aebec84185cc495837d11011a0337aa08dab60467ef566b3 |
from unittest import TestCase
import unittest
from equadratures import *
import numpy as np
from scipy.stats import skew, linregress, multivariate_normal
def fun(x):
return 5.0 * x[0] ** 3 - x[0] * x[1] + 3.0 * x[1] * x[2] ** 3 + 32.0
class TestF(TestCase):
def test_nataf(self):
np.random.seed(1)
... | Effective-Quadratures/Effective-Quadratures | tests/test_correlated_sampling.py | Python | lgpl-2.1 | 3,877 | [
"Gaussian"
] | 8f57d58e596052561891c2a690a0b55a8cbba4944bebcf6012a93dbcbfdf4bcb |
from ovito.io import import_file
from ovito.modifiers import ColorCodingModifier
# This creates a new node with an empty modification pipeline:
node = import_file('first_file.dump')
# Populate the pipeline with a modifier:
node.modifiers.append(ColorCodingModifier(particle_property='Potential Energy'))
# Call FileSo... | srinath-chakravarthy/ovito | doc/python/example_snippets/file_source_load_method.py | Python | gpl-3.0 | 469 | [
"OVITO"
] | cc19a7c8ca7982cab4cf7a9295809073a0bbf5dcbb2b91f4d191912aebb54b40 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright 2014 Lucas Lin
#
# 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... | AzurNova/Neuron-Simulation | Theta Neuron/neuron_simulation_bivariate_bimodal_uncorrelated.py | Python | apache-2.0 | 8,687 | [
"NEURON"
] | eca29ed8a15adea031cdec3e7365e8512fec7bd1e04c3de289c2c21794726af3 |
# -*- coding: utf-8 -*-
#
# This file is part of Invenio.
# Copyright (C) 2015-2018 CERN.
#
# Invenio is free software; you can redistribute it and/or modify it
# under the terms of the MIT License; see LICENSE file for more details.
"""Invenio module that implements OAuth 2 server.
Protecting your REST API with auth... | inveniosoftware/invenio-oauth2server | invenio_oauth2server/__init__.py | Python | mit | 4,219 | [
"VisIt"
] | 8a83b291f6647dfb26c45fcff3a0754f989f30d218d6bf829e87cd4114b3ca02 |
#!/usr/bin/env python3
## INFO ########################################################################
## ##
## cutils ##
## ====== ... | petervaro/cutils | dev/proj.py | Python | gpl-3.0 | 3,718 | [
"VisIt"
] | 6aa13740bba35667fe8f3ae568f6227f702f566c243c3d0c0a763481ded79708 |
from octopus.core import app
import esprit
import json
from flask import Blueprint, request, abort, make_response
from octopus.lib import webapp, plugin
blueprint = Blueprint('autocomplete', __name__)
@blueprint.route("/term/<config_name>")
@webapp.jsonp
def term(config_name):
# get the configuration
acc =... | JiscPER/magnificent-octopus | octopus/modules/es/autocomplete.py | Python | apache-2.0 | 5,180 | [
"Octopus"
] | 2c4d5f9d9e993dd2c33d9ad7b4acf44ea218a4542d1c7224ae2b2b69041a81b4 |
"""
This module gathers tree-based methods, including decision, regression and
randomized trees. Single and multi-output problems are both handled.
"""
# Authors: Gilles Louppe <g.louppe@gmail.com>
# Peter Prettenhofer <peter.prettenhofer@gmail.com>
# Brian Holt <bdholt1@gmail.com>
# Noel Da... | mjudsp/Tsallis | sklearn/tree/tree.py | Python | bsd-3-clause | 40,469 | [
"Brian"
] | 41f42d43ac313186228897a8a15541709efe920964130945a735d227097e53d6 |
#
# This source file is part of appleseed.
# Visit https://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2019 Jonathan Dent, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
#... | dictoon/blenderseed | utils/path_util.py | Python | mit | 3,832 | [
"VisIt"
] | 3a496d50fda6f49ccce98e8e98c6ba7d7e639fa56a9eca7fdd474e3b23fbc096 |
""" Test class for EmailAction / EmailAgent
"""
# imports
import unittest
import importlib
from mock import MagicMock
from DIRAC import gLogger
from DIRAC.ResourceStatusSystem.Agent.EmailAgent import EmailAgent
from DIRAC.ResourceStatusSystem.PolicySystem.Actions.EmailAction import EmailAction
gLogger.setLevel( 'DE... | hgiemza/DIRAC | ResourceStatusSystem/Agent/test/Test_EmailActionAgent.py | Python | gpl-3.0 | 3,314 | [
"DIRAC"
] | 26ff7f7245e38937a829e3960624173ce50649e1dd316d10acf49bfb589c7276 |
# ----------------------------------------------------------------------------
# cocos2d
# Copyright (c) 2008-2012 Daniel Moisset, Ricardo Quesada, Rayentray Tappa,
# Lucio Torre
# Copyright (c) 2009-2015 Richard Jones, Claudio Canepa
# All rights reserved.
#
# Redistribution and use in source and binary forms, with o... | twenty0ne/CocosBuilder-wxPython | cocos/cocos/layer/scrolling.py | Python | mit | 16,146 | [
"VisIt"
] | 0370620e9f5ca8e53b878da207c850a97fbe8463901a6494bdcc61f814ebdc1b |
"""
Extract Edges
~~~~~~~~~~~~~
Extracts edges from a surface.
"""
# sphinx_gallery_thumbnail_number = 2
import pyvista as pv
from pyvista import examples
###############################################################################
# From vtk documentation, the edges of a mesh are one of the following:
#
# 1. bou... | akaszynski/vtkInterface | examples/01-filter/extract-edges.py | Python | mit | 2,718 | [
"VTK"
] | e50c61626ca3f9f9fc4f3cd1e270f487259290075a2bf2a06113c0e9580e42a6 |
# Copyright 2008 Brian Boyer, Ryan Mark, Angela Nitzke, Joshua Pollock,
# Stuart Tiffen, Kayla Webley and the Medill School of Journalism, Northwestern
# University.
#
# This file is part of Crunchberry Pie.
#
# Crunchberry Pie is free software: you can redistribute it and/or modify
# it under the terms of the GNU Gene... | brianboyer/newsmixer | pie/profiles/models.py | Python | gpl-3.0 | 8,911 | [
"Brian"
] | a909224bf6c950abc0b49e6fa1edfd5630691f09025cc966ce96f2d8b274b5f0 |
# -*- coding: utf-8 -*-
# Copyright 2022 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... | googleapis/python-documentai | tests/unit/gapic/documentai_v1/test_document_processor_service.py | Python | apache-2.0 | 77,392 | [
"Octopus"
] | c754490494a9ff1d8f48e59673e9d1e2ac64b05d3948521a435de9f5cf747b0c |
"""Tools for simulation of transients."""
import sys
import math
import copy
from collections import OrderedDict
import numpy as np
from numpy import random
from scipy.interpolate import InterpolatedUnivariateSpline as Spline1d
from astropy.table import Table
from astropy.cosmology import FlatLambdaCDM
from .utils i... | dannygoldstein/sncosmo | sncosmo/simulation.py | Python | bsd-3-clause | 8,543 | [
"Gaussian"
] | a49d029d56fddb43f42a2736110f60de16162609cf867b41a7d1201806c7074b |
# -*- coding: utf-8 -*-
import shutil
import os
import re
import requests
import urllib2
from pprint import pprint
from bs4 import BeautifulSoup
import html2text
import time
import argparse
import concurrent.futures
cookies = dict()
cookies['tcsso'] = '40451530|b0be8a6e3acae9d8743c91ada7294a5b65a698b0dfa82cda539d54a7d... | ethancaballero/neural-engineers-first-attempt | scrapers/topcoder/topcoder_scraper_clean.py | Python | mit | 11,576 | [
"ESPResSo"
] | 4f01c4f63897ef331dba898b4558eec4fe2ff621a4effe95b1b182216ee8241c |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | wangyum/tensorflow | tensorflow/python/ops/gradients_impl.py | Python | apache-2.0 | 37,963 | [
"VisIt"
] | 5bddff15665a4765497320b5eab9b59b63122c13c9a9ad4514ed4af87afab9e2 |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Base.Client import Client
from DIRAC.Core.Utilities import DEncode
class UserProfileClient(object):
def __init__(self, profile, rpcClientFunctor=Client):
... | ic-hep/DIRAC | src/DIRAC/FrameworkSystem/Client/UserProfileClient.py | Python | gpl-3.0 | 3,258 | [
"DIRAC"
] | 1a81c3c899f3dc8ee943fb8a1a839b1922c7254009696bb237535b8245e41b10 |
########################################################################
# $HeadURL$
# File : CPUNormalization.py
# Author : Ricardo Graciani
########################################################################
""" DIRAC Workload Management System Client module that encapsulates all the
methods necessary t... | miloszz/DIRAC | WorkloadManagementSystem/Client/CPUNormalization.py | Python | gpl-3.0 | 6,215 | [
"DIRAC"
] | 89ae94ecd1d9d2468f1f63fee2a5b3e7c04749cc9977a399090e2f47030a54a6 |
# demonstrate 3d postprocessing with yade
#
# 1. qt.SnapshotEngine saves images of the 3d view as it appears on the screen periodically
# utils.makeVideo is then used to make real movie from those images
# 2. VTKRecorder saves data in files which can be opened with Paraview
# see the User's manual for an intro to... | gladk/trunk | doc/sphinx/tutorial/05-3d-postprocessing.py | Python | gpl-2.0 | 1,765 | [
"ParaView",
"VTK"
] | 3705a48d9e745b4618b35f7e09140480c23c0e92b1b436525383298a98515005 |
# -*- coding: utf-8 -*-
###############################################################################
#
# PyLint tests that will never be applied by Trump.
#
# ... is not callable, ignored because a property that returns a callable
# becomes callable.
# pylint: disable-msg=E1102
# miss... | Equitable/trump | trump/orm.py | Python | bsd-3-clause | 82,666 | [
"ADF"
] | cc22e1559e1ccd785b03f0752b27cfe8e8677f5aee03eaff631dd50af55a674a |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2009 Brian G. Matherly
# Copyright (C) 2009 Gary Burton
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publis... | sam-m888/gramps | gramps/gui/dbman.py | Python | gpl-2.0 | 45,605 | [
"Brian"
] | 2742959cf38ccd85ba5e5e1a26ea0bce21ca539ec6f315c132c3fe6b529ef052 |
# -*- Mode: Python; coding: utf-8; indent-tabs-mode: nil; tab-width: 4 -*-
### BEGIN LICENSE
# Copyright (C) 2014 Brian Douglass bhdouglass@gmail.com
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License version 3, as published
# by the Free Softwa... | bhdouglass/agui | agui/signal.py | Python | gpl-3.0 | 1,110 | [
"Brian"
] | 6fc99413d051b53eeb9046999c88f81a8460b0ced00423c1049f228b2e7e0825 |
"""
cclib (http://cclib.sf.net) is (c) 2006, the cclib development team
and licensed under the LGPL (http://www.gnu.org/copyleft/lgpl.html).
"""
__revision__ = "$Revision: 839 $"
try:
import openbabel
except Exception:
pass
else:
from cclib2openbabel import makeopenbabel
try:
import PyQuante
except I... | faribas/RMG-Java | source/cclib/bridge/__init__.py | Python | mit | 476 | [
"cclib"
] | fda010972ed64a32a459bfe0fa3e5326cbd9e292680cb9c6bed97efaf83eef9a |
# -*- coding: utf-8 -*-
"""
ClearMap default parameter module.
This module defines default parameter used by various sub-packages.
See Also:
:mod:`~ClearMap.Settings`
"""
#:copyright: Copyright 2015 by Christoph Kirst, The Rockefeller University, New York City
#:license: GNU, see LICENSE.txt for details.
import ... | ChristophKirst/ClearMapUnstable | ClearMap/Parameter.py | Python | gpl-3.0 | 8,831 | [
"Gaussian"
] | 3b17384986c100973fb41a6c8e08ead6d67ae34c3bd7e60469d6c23569abf1a3 |
"""
Detects brightest region in image and finds angles needed to rotate
to center it based on GoPro 4 FOV
Algorithms: Gaussian Blur and Min/Max Loc
Python Version: 2.7.12
See trello for a comprehensive description of the communication protocol
Dependencies: PySerial, Numpy, time, gopro_wifi_api_hero4, log, ui, and Open... | AdlerFarHorizons/eclipse-tracking | software/Pi/process.py | Python | mit | 2,824 | [
"Gaussian"
] | 014189e0d0bf22d58d4c46313853d08174a2108ae8a5d75d34cbbd6eac2619ab |
# MicroPython SSD1306 OLED driver, I2C and SPI interfaces
import time
import framebuf
# register definitions
SET_CONTRAST = const(0x81)
SET_ENTIRE_ON = const(0xa4)
SET_NORM_INV = const(0xa6)
SET_DISP = const(0xae)
SET_MEM_ADDR = const(0x20)
SET_COL_ADDR = const(0x21)
SET_... | muqiuq/pyp | lib/ssd1306.py | Python | mit | 5,569 | [
"BLAST"
] | 72d5e0bbdcd2a12f03144267860017d4515f91491ef871b2055801a97fe98484 |
#!/usr/bin/env python
""" Drop DBs from the MySQL server
"""
from __future__ import print_function
from DIRAC.Core.Base import Script
Script.setUsageMessage('\n'.join([__doc__.split('\n')[1],
'Usage:',
' %s [option|cfgFile] ... DB ...' % Script.scrip... | fstagni/DIRAC | tests/Jenkins/dirac-drop-db.py | Python | gpl-3.0 | 774 | [
"DIRAC"
] | ab24583db925adc0c687980ec64e634350ef898a8f82de6f5246c9c00d49a924 |
import re
wires = {}
for i in open('day7.txt'):
set = re.match(r'([a-z0-9]+) -> ([a-z]+)',i)
if set:
wires[set.group(2)] = set.group(1)
op1 = re.match(r'(NOT) ([a-z0-9]+) -> ([a-z]+)',i)
if op1:
wires[op1.group(3)] = [op1.group(1), op1.group(2)]
op2 = re.match(r'([a-z0-9]+) (AND|OR|LSHIFT|RSHIFT) ([a-z0-9]+) ... | jsvennevid/adventofcode | 2015/07/puzzle1.py | Python | mit | 1,038 | [
"VisIt"
] | 5bd271e57495ab5e5bb7fbf5594d510b30528a4805a8d4c09aff7ddff8d1f379 |
import logging
from time import time, gmtime, strftime
from DIRAC.Core.Utilities import Time
from dirac.lib.base import *
from dirac.lib.diset import getRPCClient
from dirac.lib.credentials import authorizeAction
#from dirac.lib.sessionManager import *
from DIRAC import gConfig, gLogger
import dirac.lib.credentials a... | DIRACGrid/DIRACWeb | dirac/controllers/jobs/PilotSummary.py | Python | gpl-3.0 | 7,439 | [
"DIRAC"
] | 340f74d470194c35771fe2be43593533accd6912c6de4947e9488e00558dc697 |
#!/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/cc/ccsd_rdm_slow.py | Python | apache-2.0 | 9,110 | [
"PySCF"
] | f4861768259086f3a20242d0674880f67438788b24ad62543e594949b4f4fdea |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes to identify optimal substrates for film growth
"""
from dataclasses import dataclass
from typing import Tuple
from pymatgen.analysis.elasticity.strain import Deformation, Strain
from pymatgen... | vorwerkc/pymatgen | pymatgen/analysis/interfaces/substrate_analyzer.py | Python | mit | 7,382 | [
"pymatgen"
] | 1f51c30f97bb997aec5edda8164ae9a3e6070348395f5386b05aca14659396d9 |
"""
IO functions for geoerefernecer. A to-do list:
:py:class:readRiegl A class for handling Riegl SDC/2DD/3DD files
:py:class:readNCOM A class for handling OXTS NCOM format trajectory files
:py:class:outputLAS Uses LASpy or PDAL to handle LAS writing
:py:class:outputPGPC outputs data as postgres-pointcloud table (r... | adamsteer/LiDAR_georeference | georeference/georeferencerIO.py | Python | apache-2.0 | 837 | [
"NetCDF"
] | fd9e62f35f14b70d80d36da4757594c130af7c0ee0f7b08bde2a63d0453f5c9e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Author:Renato Arnellas Coelho renatoac at gmail dot com
#
# Script to create Sicol's new version zip file
#
# Obs: This script must be run on Sicol's root directory
import zipfile
import os
import sys
try:
sys_version = str(int(raw_input("System Version number = ")))
... | cria/microSICol | zipversion.py | Python | gpl-2.0 | 1,767 | [
"VisIt"
] | 919e3a85b75a7b73a2da2ca24e8a3239e2f8469df983b8e818ff92892d380ce6 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# md_format_converter.convert.py
#
# Copyright (C) 2012-2016 Karl T Debiec
# All rights reserved.
#
# This software may be modified and distributed under the terms of the
# BSD license. See the LICENSE file for details.
"""
Converts Molecular Dynamics (MD) simulation ... | KarlTDebiec/MDFormatConverter | convert.py | Python | bsd-3-clause | 3,691 | [
"Amber",
"Gromacs",
"VMD"
] | 99fbecc7da4ecb9aef3d226176e045648f95f459dad7c54ea069237713ecb02c |
import ocl
import camvtk
import time
import vtk
import datetime
import math
import gzip
# Travelling Salesman Problem
# a.k.a. drill-path optimization
#
# we have multiple points in the 2D plane to visit.
# the task is to optimize the distance travelled by the tool while
# visiting all points
#
# uses data from TSPLIB... | aewallin/opencamlib | examples/python/tsp/tsp_01.py | Python | lgpl-2.1 | 6,600 | [
"VTK",
"VisIt"
] | f0c7b28a732572f259e8512a89f6036b67e761cab09377e082716dd362e0d9e6 |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | yufengg/tensorflow | tensorflow/python/ops/gradients_impl.py | Python | apache-2.0 | 36,585 | [
"VisIt"
] | 42da365ca95c3a7d8ad57eee725acf694b1648b9b806a66b4ed62a199dba5f92 |
# -*- coding: utf-8 -*-
#
# This file is part of NINJA-IDE (http://ninja-ide.org).
#
# NINJA-IDE is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# any later version.
#
# NIN... | open-motivation/motivation-ide | ninja_ide/gui/misc/find_in_files.py | Python | gpl-3.0 | 19,937 | [
"ASE"
] | fdd320c04143ea2d16f7c6d5122535601cd4c5f9a0175cb55b4d47b980233fbb |
# ######################################################################
# Copyright (c) 2014, Brookhaven Science Associates, Brookhaven #
# National Laboratory. All rights reserved. #
# #
# @author: Li Li (lili@bnl.g... | hainm/scikit-xray | skxray/core/fitting/tests/test_background.py | Python | bsd-3-clause | 4,017 | [
"Gaussian"
] | 0dfd6371a132f525ed1d331c0aa4478f4504c5473f481aede09a0b764015085b |
#!/usr/bin/env python
import matplotlib.pyplot as plt
import numba
import numpy as np
from mayavi import mlab
from sklearn.datasets import load_digits
from sklearn.model_selection import train_test_split
import umap
digits = load_digits()
X_train, X_test, y_train, y_test = train_test_split(
digits.data, digits.t... | lmcinnes/umap | examples/mnist_torus_sphere_example.py | Python | bsd-3-clause | 3,478 | [
"Mayavi"
] | 14995f0740852919acc997b15bc19e3d6c6a85eb6c2734e54e5964f1a0670084 |
#!/usr/bin/env python
#
# parse_pdb_header.py
# parses header of PDB files into a python dictionary.
# emerged from the Columba database project www.columba-db.de.
#
# author: Kristian Rother
#
# license: same as BioPython, read LICENSE.TXT from current BioPython release.
#
# last modified: 9.2.2004
#
# Added some smal... | zjuchenyuan/BioWeb | Lib/Bio/PDB/parse_pdb_header.py | Python | mit | 9,123 | [
"Biopython"
] | e28cd50b03f474288812bb96598fd0b7e18de8cf2799f5fb16d775fc245e6a3f |
from copy import deepcopy
from functools import reduce
from core.expressions import Expression, UnaryBooleanOperation, BinaryBooleanOperation, BinaryComparisonOperation, \
BinaryArithmeticOperation, Literal, UnaryArithmeticOperation
from core.special_expressions import VariadicArithmeticOperation
def iter_fields... | gitsimon/spadup-lyra | core/expressions_tools.py | Python | mpl-2.0 | 18,820 | [
"VisIt"
] | 5b6be0c223ec5383d5661d0cce9c6185fb23e3c55c101b0d73369518eafe503e |
"""Command line options, ini-file and conftest.py processing."""
import argparse
import collections.abc
import contextlib
import copy
import enum
import inspect
import os
import re
import shlex
import sys
import types
import warnings
from functools import lru_cache
from pathlib import Path
from types import TracebackTy... | nicoddemus/pytest | src/_pytest/config/__init__.py | Python | mit | 57,464 | [
"VisIt"
] | 5ded2dbcbc56021696014d0ffd95e3f70c592e4542d09ddd1a3a2486e7123215 |
"""Country names to ISO3166_alpha2 codes mapping
Roughly generated by the following bash script on GNU/Linux:
while read cc name; do
[ ! "$cc" ] &&
continue
out=$(isoquery $cc | cut -f3 --complement);
[ ! "$out" ] &&
out="$cc"
[ "$(echo $out | cut -f3)" = "$... | david-novak/orange3-text | orangecontrib/text/country_codes.py | Python | bsd-2-clause | 20,814 | [
"BWA",
"COLUMBUS",
"Elk"
] | c7eef811769f66e9c98eceb0bf4261b2f0471f881a9f5a0ecf5be34f88ce263a |
"""
Test for weights in GLM, Poisson and OLS/WLS, continuous test_glm.py
Below is a table outlining the test coverage.
================================= ====================== ====== ===================== === ======= ======== ============== ============= ============== ============= ============== ==== =========
Tes... | jseabold/statsmodels | statsmodels/genmod/tests/test_glm_weights.py | Python | bsd-3-clause | 40,201 | [
"Gaussian"
] | b8ef8fe393af825e5c6dee93014d20e4a16cc397e25aaf1f7c97595255821e52 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
##
## See COPYING file distributed along with the ncanda-data-integration package
## for the copyright and license terms
##
"""
Transform Redcap Youth/Parent Report data into an ASEBA ADM-compatible format.
`--demographics-file` is used for both subject exclusion and NCA... | sibis-platform/ncanda-datacore | scripts/reporting/aseba_prep.py | Python | bsd-3-clause | 10,733 | [
"VisIt"
] | 2ba2c37da1f119d22f2cd58c8515fb14bc72712ce36de3aa45b792b8074c164f |
""" Container for TaskManager plug-ins, to handle the destination of the tasks
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import six
from DIRAC import gLogger
from DIRAC.Core.Utilities.List import fromChar
from DIRAC.Core.Utilities.SiteSEMapping im... | yujikato/DIRAC | src/DIRAC/TransformationSystem/Client/TaskManagerPlugin.py | Python | gpl-3.0 | 5,486 | [
"DIRAC"
] | 85ec7a24c4966c8680f8ccd1c9df94a83acc9845e22079132e10c77b62865cd3 |
########################################################################
# $HeadURL $
# File: RemoveFile.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/03/25 07:44:19
########################################################################
""" :mod: RemoveFile
================
.. module: RemoveFile
... | rajanandakumar/DIRAC | DataManagementSystem/Agent/RequestOperations/RemoveFile.py | Python | gpl-3.0 | 6,562 | [
"DIRAC"
] | 7ef55cdc912064caf4ae605e089221be424532bacda95a595ba2834a3ffd67a7 |
from ase.test import NotAvailable
import warnings
# cmr calls all available methods in ase.atoms detected by the module inspect.
# Therefore also deprecated methods are called - and we choose to silence those warnings.
warnings.filterwarnings('ignore', 'ase.atoms.*deprecated',)
try:
import cmr
except ImportError:
... | JConwayAWT/PGSS14CC | lib/python/multimetallics/ase/test/cmr/reactions_run.py | Python | gpl-2.0 | 1,360 | [
"ASE"
] | 798acd1feb03aad768834166ec2575040bb9033ad8f11fff37a6d564f4720b1b |
# Script control setup area
# script info
__script__.title = 'KKB Plot and Reduction 29.12.2021'
__script__.version = '2.0'
# 15.6.2017 Allow to reduce the detector range
# 15.6. Throw out points below resolution
# 16.6. Tidy up run time to display in the reduction; tidy up display properties
# 11.7... | Gumtree/Kookaburra_scripts | Internal/KKB-Plot and Reduction_Dec2021b.py | Python | epl-1.0 | 82,352 | [
"CRYSTAL"
] | a83dd028b56e20283134749d6717ce1581586b202b2cba11a3d2790aab4864f2 |
""" @package antlr3.tree
@brief ANTLR3 runtime package, treewizard module
A utility module to create ASTs at runtime.
See <http://www.antlr.org/wiki/display/~admin/2007/07/02/Exploring+Concept+of+TreeWizard> for an overview. Note that the API of the Python implementation is slightly different.
"""
# begin[licence]
#... | ekcs/congress | thirdparty/antlr3-antlr-3.5/runtime/Python3/antlr3/treewizard.py | Python | apache-2.0 | 18,114 | [
"VisIt"
] | d716527306b589e0342d95d7fb6f18640a0a2d3a6a590d13862338117d93faa0 |
""" Module to looks for a specified pattern in a given AST. """
from gast import AST, iter_fields, NodeVisitor, Dict, Set
from itertools import permutations
from math import isnan
MAX_UNORDERED_LENGTH = 10
class DamnTooLongPattern(Exception):
""" Exception for long dict/set comparison to reduce compile time. "... | serge-sans-paille/pythran | pythran/analyses/ast_matcher.py | Python | bsd-3-clause | 7,363 | [
"VisIt"
] | fa10d82ffa3b7df1325c148ba6ca255e9f8e496cb7476afeed9da1b3c14d5c8e |
"""
Courseware views functions
"""
import logging
import urllib
import json
import cgi
from collections import OrderedDict
from datetime import datetime
from django.utils import translation
from django.utils.translation import ugettext as _
from django.utils.translation import ungettext
from django.conf import setti... | edcast-inc/edx-platform-edcast | lms/djangoapps/courseware/views.py | Python | agpl-3.0 | 60,161 | [
"VisIt"
] | bd47a69a245fb41f5556cf1b04f83cb2065cdab3fb851d8504cb1d5bb5cbc687 |
# -------------------------------------------------------------------------
# Copyright (C) 2005-2013 Martin Strohalm <www.mmass.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 Foundat... | sauliusl/mMass-fork | gui/main_frame.py | Python | gpl-3.0 | 168,402 | [
"BLAST"
] | a799dfbf7837c076edac5503e7c1253ec8d69217ec9852e654cac62bfad21aab |
"""Minimal Python 2 & 3 shim around all Qt bindings
DOCUMENTATION
Qt.py was born in the film and visual effects industry to address
the growing need for the development of software capable of running
with more than one flavour of the Qt bindings for Python - PySide,
PySide2, PyQt4 and PyQt5.
1. Bu... | mottosso/pyblish-qml | pyblish_qml/vendor/Qt.py | Python | lgpl-3.0 | 51,627 | [
"VisIt"
] | 8d1c8fc0ca46d1b3c9f77c5b2d9447551a37f26bd9e90ba0186cd81fa3ce9ab5 |
#!/usr/bin/env python
"""
OpenMM Restraint Forces shared between modules
.2019. joaor@stanford.edu
"""
from __future__ import print_function, division
import logging
import os
import sys
import simtk.openmm as mm
import simtk.openmm.app as app
import simtk.unit as units
# Setup logger
logging.basicConfig(stream=s... | csblab/md_scripts | openmm/amberff/_restraints.py | Python | mit | 8,760 | [
"OpenMM"
] | ed0e886ce1b14e224789b58f41762f292c7bb50b2b1c2e3de4aecd0b58685f5f |
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