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#!/usr/bin/env python
# Copyright 2016 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... | hyperhq/hypernetes | vendor/github.com/google/cadvisor/build/boilerplate/boilerplate.py | Python | apache-2.0 | 4,750 | [
"VisIt"
] | 0a054095f797425cc67b2aa969b904555605e399d11ed4f53671927d4469fd34 |
"""pepapot.
Usage:
pepapot.py webserver
pepapot.py steady util <name>...
pepapot.py timeseries <name> [--start-time=<t>][--stop-time=<t>]
[--output-interval=<t>]
pepapot.py -h | --help
pepapot.py --version
Options:
-h --help Show this screen.
--version Show version... | allanderek/pepapot | pepapot/pepapot.py | Python | bsd-3-clause | 99,850 | [
"VisIt"
] | 3f82f60c1c8c4ad887bf74ed3ad24a0675f98920feb9fea27a2bb96adb576766 |
#!/usr/bin/env python
#
#
# FreeType 2 glyph name builder
#
# Copyright 1996-2000, 2003 by
# David Turner, Robert Wilhelm, and Werner Lemberg.
#
# This file is part of the FreeType project, and may only be used, modified,
# and distributed under the terms of the FreeType project license,
# LICENSE.TXT. By continuin... | gestiweb/eneboo | src/qt/src/3rdparty/freetype/src/tools/glnames.py | Python | gpl-2.0 | 95,866 | [
"FEFF"
] | de8b043951da7b427ead47cba5af4046b6fdde6a2a2de776d2f1118078c36fd7 |
import numpy
import os
import pandas
import pysam
from grocsvs import datasets as svdatasets
from grocsvs import step
from grocsvs.stages import pair_evidence
class MatePairEvidenceStep(step.StepChunk):
"""
"""
@staticmethod
def get_steps(options):
for sample_name, sample in options.samples... | grocsvs/grocsvs | src/grocsvs/stages/mate_pair_evidence.py | Python | mit | 5,265 | [
"pysam"
] | bd2ba785fd573fc998e0aa0a3a904579a260cc1ca5b31072f3ba85c67a847d37 |
#!/usr/bin/env python2.7
# -*- coding: utf-8 -*-
"""
cpassdb - The Collaborative Password Database CLI Client.
Copyright (C) 2015 Brian Wiborg <baccenfutter@c-base.org>
This file is part of cpassdb.
cpassdb is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License a... | baccenfutter/cpassdb | cpassdb.py | Python | gpl-2.0 | 4,006 | [
"Brian"
] | 43a6c10c5e91434c9bcaaa7adc10f512d488b3fcfae8af7ccaec48a1af3b4891 |
# pyOCD debugger
# Copyright (c) 2020 NXP
# Copyright (c) 2006-2013,2018 Arm Limited
# Copyright (c) 2021 Chris Reed
# SPDX-License-Identifier: Apache-2.0
#
# 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... | pyocd/pyOCD | pyocd/target/builtin/target_MKL28Z512xxx7.py | Python | apache-2.0 | 11,380 | [
"CRYSTAL"
] | bfb9dbb30f55040ca2265565f494f6b26367d5910c5b65b3bbf1e2ec52524c2c |
# -*- coding: utf-8 -*-
# HORTON: Helpful Open-source Research TOol for N-fermion systems.
# Copyright (C) 2011-2015 The HORTON Development Team
#
# This file is part of HORTON.
#
# HORTON is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by th... | eustislab/horton | horton/io/test/test_molekel.py | Python | gpl-3.0 | 3,940 | [
"ORCA"
] | b6e59361ffe4be72fa309b3ff9b74b0369288518818a5b5f34649f3b682de362 |
"""Approximate bilateral rank filter for local (custom kernel) mean.
The local histogram is computed using a sliding window similar to the method
described in [1]_.
The pixel neighborhood is defined by:
* the given structuring element
* an interval [g-s0, g+s1] in greylevel around g the processed pixel greylevel
Th... | newville/scikit-image | skimage/filters/rank/bilateral.py | Python | bsd-3-clause | 7,652 | [
"Gaussian"
] | afab05d12935bce3892f1aa6c255c16f0b3c4dae73cf66e4fd218237b3146ec2 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes to perform analyses of
the local environments (e.g., finding near neighbors)
of single sites in molecules and structures.
"""
import json
import math
import os
import warnings
from bisect impo... | vorwerkc/pymatgen | pymatgen/analysis/local_env.py | Python | mit | 171,694 | [
"Gaussian",
"Jmol",
"VASP",
"pymatgen"
] | c87c097cd5108093593cd25db7fb87bb6cb0d18dc8d7f5b0d12910ff9384dc7b |
#!/usr/bin/env python
""" Which - locate a command
* adapted from proposal__ by Erik Demaine and patch__ by Brian Curtin, which adds this feature__ to shutil
__ http://bugs.python.org/file8185/find_in_path.py
__ http://bugs.python.org/file15381/shutil_which.patch
__ http://bugs.python.org/issue444582
... | liuyu81/mpreview | which.py | Python | bsd-3-clause | 11,034 | [
"Brian"
] | e6ffa0d535e1e08a9885284645b6c4006902b4124cab011504fe1ede7199dfbe |
#!/usr/bin/env python
"""A web application that retrieves other websites for you.
To start serving the application on port 8088, type
python webproxy.py
To start the server on some other interface/port, use
python -m gevent.wsgi -p 8000 -i 0.0.0.0 webproxy.py
"""
from __future__ import print_function
from geve... | hightemp/cappMiniWebServer | temporary/base_server.py | Python | mit | 4,972 | [
"VisIt"
] | 668f67e09cf6275aadde935e48e503e9403b4689340731162f4a26b522be6a0b |
#
# gPrime - A web-based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007-2012 Brian G. Matherly
# Copyright (C) 2009 Gary Burton
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011 Matt Keenan (matt.keenan@gmail.com)
# Copyright (C) 2013-2014 Paul Franklin
... | sam-m888/gprime | gprime/plugins/textreport/descendreport.py | Python | gpl-2.0 | 21,466 | [
"Brian"
] | fc3a1370c23bab18748349b64478a7f2805f785987871b6f7b3ece5b40511597 |
# 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
#
# Unless required by appl... | gkc1000/pyscf | examples/local_orb/nlocal.py | Python | apache-2.0 | 6,691 | [
"PySCF"
] | 18dffbe3a9491e08121e104e3c7406c26d76354bdc0e77f99a1afdd23ea10134 |
"""
Copyright (C) 2016 Hector Sanjuan
This file is part of "dccpi".
"dccpi" is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later... | hsanjuan/dccpi | setup.py | Python | gpl-3.0 | 2,524 | [
"VisIt"
] | f634bc5895e632f5b75391c7d32d34450639d3b61397cc8927c471a69790a9f3 |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publish... | thica/ORCA-Remote | src/ORCA/Queue.py | Python | gpl-3.0 | 14,728 | [
"ORCA"
] | 2369624f11240e83d7c33ca1053a68f68857fe7d956713d4dc012322fa53a3a9 |
#!/usr/bin/env python
# vim:fileencoding=UTF-8:ts=4:sw=4:sta:et:sts=4:ai
from __future__ import (unicode_literals, division, absolute_import,
print_function)
__license__ = 'GPL v3'
__copyright__ = '2011, Kovid Goyal <kovid@kovidgoyal.net>'
__docformat__ = 'restructuredtext en'
import re, thr... | alexston/calibre-webserver | src/calibre/ebooks/metadata/sources/base.py | Python | gpl-3.0 | 21,328 | [
"VisIt"
] | 0bde5778b5ba26c8f91edc49287507b422637f27a9e20dc3c13c45970784cca3 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Licensed to Cloudera, Inc. under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. Cloudera, Inc. licenses this file
# to you under the Apache License, Version 2.0 (... | yongshengwang/builthue | apps/useradmin/src/useradmin/tests.py | Python | apache-2.0 | 34,717 | [
"MOE"
] | bc6df758e39a5f70b0927fe8e43f4f7537b2991debf4d7584bb28158faf1f931 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors: Kyle A Beauchamp, Ravi Ramanat... | swails/mdtraj | mdtraj/geometry/dihedral.py | Python | lgpl-2.1 | 22,124 | [
"MDTraj"
] | 0fcb12d870e6fea30d1209ea566b2302f93be767d258f49a8fcf70633074e3e0 |
#
# Copyright (c) 2017 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yashdsaraf/scancode-toolkit | src/formattedcode/format_json.py | Python | apache-2.0 | 2,771 | [
"VisIt"
] | 8976f91a51284b9e43b786ba177d15a288a8d2e856e731e33bf759d7b5dc6662 |
# -*- coding: utf-8 -*-
import sys
sys.path.extend(['.', '../'])
from icalendar import Calendar as ICal
from Visitor.ToStringVisitor import *
from Visitor.ICS2ErebusVisitor import *
from Visitor.Erebus2ICSVisitor import *
from erebusconv import *
from CNode import *
if len(sys.argv) != 2:
print 'Usage: pyth... | orbekk/erebus | utils/icalconv.py | Python | gpl-2.0 | 831 | [
"VisIt"
] | 45a7a831f4c8a5151ac5bd7ea29e9092a93528ec34c87cff5ecbcb4a199a53be |
#!/usr/bin/env python2.5
#
# Copyright 2011 the Melange 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 applic... | adviti/melange | app/soc/modules/gsoc/views/student_evaluation.py | Python | apache-2.0 | 12,973 | [
"VisIt"
] | c3595e7a22382b6be7fdd6d28bcb459226547cbf2a9a3435d124ea6542b86219 |
#!/bin/python
"""
Program Polaron hop by Aksyonov Dmitry, Skoltech, Moscow
Multiset is not supported yet
Version naming
AR - atomic relaxation
SP - single point
1 - polaron and deformation at start position (AR)
2 - polaron and deformation at final position (AR)
21 - polaron and deformation at start positio... | dimonaks/siman | siman/polaron.py | Python | gpl-2.0 | 4,440 | [
"VASP"
] | 7a46d00fb117c391deab1f165bb366c4a0f283052a28c193aa1d821e9b77de9b |
#Configure file for PyMorph. Authors: Vinu Vikram, Yogesh Wadadekar and Ajit Kembhavi 2008
###----Specify the input images and Catalogues----###
imagefile = 'j8f643-1-1_drz_sci.fits'
whtfile = 'j8f643-1-1_drz_rms.fits'
sex_cata = 'sdss_sex.cat' #The sextractor catalogue which has
... | vvinuv/pymorph | examples/postage_stamps/results/config.py | Python | gpl-2.0 | 4,486 | [
"Galaxy"
] | 4a2340a8c41dd6416524170675e32d5acda3e19c64c998cb4c89aabcc158e82b |
#!/usr/bin/python3
"""
Preference Guide (CLI version) for onedrive-d
"""
import sys
import os
import subprocess
from . import od_glob
config = od_glob.get_config_instance(setup_mode=True)
from . import od_onedrive_api
def query_yes_no(question, default='yes'):
valid = {'yes': True, 'y': True, 'ye': True, 'no': Fals... | kevinwincott/onedrive-d | onedrive_d/od_pref_cli.py | Python | lgpl-3.0 | 5,653 | [
"VisIt"
] | 5d0bab2bf2c5bb61eea23d2c4d3a165f236d47ce5fa00a5cf2e74ab7c5a76ffa |
"""Cloud Messaging module."""
try:
from urllib.parse import urljoin # python 3
except ImportError:
from urlparse import urljoin # python 2
import requests
class CSRMessaging(object):
"""Cloud Services Router (CSR) class."""
def __init__(self, client):
"""Save a reference to the client."""
... | vicyap/python-hologram-api | python_hologram_api/cloud_messaging.py | Python | mit | 6,050 | [
"VisIt"
] | c213ed48a17310acbf5e45cc71f8580e5a23ab0dc33788acc1cf318a2e89e876 |
"""Interface with the tophat program"""
import command, tempfile, pysam, os.path, shutil
from Bio import SeqIO
from Bio.SeqRecord import SeqRecord
from Bio.Seq import Seq
verbose = True
class TopHat(command.Command):
"""Class to interface with tophat
See http://tophat.cbcb.umd.edu/manual.shtml
To set a parti... | haydnKing/waistcoat | waistcoat/tophat.py | Python | gpl-2.0 | 8,023 | [
"pysam"
] | 5738969c0d6a4dbf642c62df98c594b86b3902cd8a751f7adfa947f61e50caa6 |
'''
Source code for an attention based image caption generation system described
in:
Show, Attend and Tell: Neural Image Caption Generation with Visual Attention
International Conference for Machine Learning (2015)
http://arxiv.org/abs/1502.03044
Comments in square brackets [] indicate references to the equations/
mo... | elliottd/satyrid | model.py | Python | bsd-3-clause | 64,172 | [
"Gaussian"
] | c4438cd062b5cfefc99966019f13a2e7d7f425cd737fbece6e8ce8cb2ff5c55a |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/item_title | openlp/core/ui/formattingtagform.py | Python | gpl-2.0 | 9,627 | [
"Brian"
] | 99499a59910d050ed622dc0c8cb0bd3dc3964c9141f7103e285303d287ebb75c |
#!/usr/bin/env python
""" load mWGS Raw Seq Set into OSDF using info from data file """
import os
import re
from cutlass.Proteome import Proteome
import settings
from cutlass_utils import \
load_data, get_parent_node_id, list_tags, format_query, \
write_csv_headers, values_to_node_dict, write_out_csv... | TheJacksonLaboratory/osdf_submit | nodes/proteome.py | Python | gpl-3.0 | 5,373 | [
"VisIt"
] | e15487c8f409d6aaef633dea57328b9a6522716baeebdd3d5d10c4a985b5d674 |
import re
import collections
from enum import Enum
from ydk._core._dm_meta_info import _MetaInfoClassMember, _MetaInfoClass, _MetaInfoEnum
from ydk.types import Empty, YList, YLeafList, DELETE, Decimal64, FixedBitsDict
from ydk._core._dm_meta_info import ATTRIBUTE, REFERENCE_CLASS, REFERENCE_LIST, REFERENCE_LEAFLI... | 111pontes/ydk-py | cisco-ios-xe/ydk/models/cisco_ios_xe/_meta/_CISCO_NTP_MIB.py | Python | apache-2.0 | 34,180 | [
"CRYSTAL"
] | 6cffdbc040c20a33262fbab9ed68915866cf3a98d12ae34f30e3d07ed15fbac3 |
import sys
from datetime import datetime
from dateutil.parser import parse
import pytz
import csv
#Make a geochart
#https://developers.google.com/chart/interactive/docs/gallery/geochart
#from a csv file that has timestamps and addresses with the countries last
#takes one arg (the input file) and outputs the HTML to dr... | amac0/google-location-tools | make_country_chart.py | Python | apache-2.0 | 2,067 | [
"VisIt"
] | ffd57a1b431f6c6c21bf45bd60d32d179ae3ac78c1fcaa40b61fb77be2712dad |
""" Class for handling interaction with the PBS queuing system."""
from ase.io import write
import os
from ase.io.trajectory import PickleTrajectory
from subprocess import Popen, PIPE
import time
class PBSQueueRun(object):
""" Class for communicating with the commonly used PBS queing system
at a compute... | askhl/ase | ase/ga/pbs_queue_run.py | Python | gpl-2.0 | 4,508 | [
"ASE"
] | a227bfd9f34fd9a07090b246ade2558902a54d8972a3f208a29103f3045a1009 |
# -*- coding: utf-8 -*-
"""
Created on Thu Dec 19 09:00:25 2013
@author: clisle
"""
import pymongo
from bson import ObjectId
from pymongo import Connection
import json
import time
# needed to import R-based algorithms from Geiger and Picante
from ArborAlgorithmManagerAPI import ArborAlgorithmManager
class switch(ob... | arborworkflows/ProjectManager | tangelo/ArborWorksteps.py | Python | apache-2.0 | 30,922 | [
"VTK"
] | 9d2466fc0d7234e107e7b6b817b3c894f1eeee524190d5a4e56bbd718a3264a5 |
from django.db import models
from django.contrib.auth.models import User, UserManager
from django.contrib.contenttypes.models import ContentType
from django.contrib.contenttypes import generic
from apps.plus_groups.models import TgGroup
from django.core.mail import send_mail
from django.conf import settings
from d... | thehub/hubplus | apps/plus_contacts/models.py | Python | gpl-3.0 | 15,377 | [
"VisIt"
] | 8099d107ab3ce1e2bda412a67107abb8faac9f59a3a2f823b566f977759b4846 |
"""
Examples of loading all information about an object or set of objects from the
database.
"""
import PyOpenWorm as P
P.connect()
def pp_connection(conn):
print conn.pre_cell(), conn.post_cell(), conn.syntype(), conn.synclass(), conn.number()
try:
query_object = P.Connection(pre_cell='AVAL')
print 'ST... | hnunner/PyOpenWorm | examples/test_bgp.py | Python | mit | 1,501 | [
"NEURON"
] | 4518bebaae69ad4fd684b545e16234e4f5de39091af095bc090310ec01e008be |
# Copyright 2020 Google LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... | google/differential-privacy | python/dp_accounting/accountant.py | Python | apache-2.0 | 10,997 | [
"Gaussian"
] | aa2686a1a3ff89c1f4216309c706d2b6795d9a26a1d0afa459d52e3d78bc3249 |
"""
For testing how long generators take.
Will show the average time per batch a generator takes, as well as the average training time per batch of a model.
Shuffle test:
-------------
Generator shuffles the order in which data gets read out.
Tested on 5000 batches each of (64, 11, 13, 18, 60) xyzt data with the vgg ... | ViaFerrata/DL_pipeline_TauAppearance | scraps/stop_time.py | Python | agpl-3.0 | 8,926 | [
"ORCA"
] | 1a25eb8cbb508f01c16dfe67b9170a06af7e3c692b3d3554b3406623930ab9e6 |
## \file
## \ingroup tutorial_roofit
## \notebook
## Multidimensional models: projecting pdf and data slices in discrete observables
##
## \macro_code
##
## \date February 2018
## \authors Clemens Lange, Wouter Verkerke (C++ version)
import ROOT
# Create B decay pdf with mixing
# -------------------------------------... | root-mirror/root | tutorials/roofit/rf310_sliceplot.py | Python | lgpl-2.1 | 3,253 | [
"Gaussian"
] | 753635242c3f0e371b114b4a3f73ac84a89b7f5f7dc50234f29b43df938dccd0 |
#!/usr/bin/env python
# calcDelta.py determines the Delta values between two codes.
# Current version: 3.0
#
# Copyright (C) 2012 Kurt Lejaeghere <Kurt.Lejaeghere@UGent.be>, Center for
# Molecular Modeling (CMM), Ghent University, Ghent, Belgium
#
# calcDelta.py is free software; you can redistribute it and/or ... | molmod/DeltaCodesDFT | calcDelta.py | Python | lgpl-2.1 | 11,764 | [
"WIEN2k"
] | 88035c19db15e583e66fda084b3fa30c51de10c5462eb4e9fc9ecfeaee01ec71 |
#!/usr/bin/env python
# This example demonstrates how to use boolean combinations of implicit
# functions to create a model of an ice cream cone.
import vtk
from vtk.util.colors import chocolate, mint
# Create implicit function primitives. These have been carefully
# placed to give the effect that we want. ... | hlzz/dotfiles | graphics/VTK-7.0.0/Examples/Modelling/Python/iceCream.py | Python | bsd-3-clause | 3,304 | [
"VTK"
] | 138ac390f57b910dfc01f2c6c23caec374eed5d29f2a158014bdd0eafa7b804d |
"""
WAVESIM Test - Maria 2014
Testing program to obtain the dressed spectrum of Choppy waves,
in comparsion with the theoretical linear one.
Only 1 realization
"""
import numpy as np
from scipy import linalg
from trampa import utils
from oceansar import spec
from oceansar import spread
impor... | pakodekker/oceansar | misc/dressed_spectrum.py | Python | gpl-3.0 | 9,177 | [
"Gaussian"
] | 4a8862b2ef553a2ea1ee05408ae8e39cde4bd50048679f7e909178ab5875eea2 |
# -*- coding: utf-8 -*-
# Copyright 2014-2016 The HyperSpyUI developers
#
# This file is part of HyperSpyUI.
#
# HyperSpyUI 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
#... | hyperspy/hyperspyUI | hyperspyui/desktop_integration_windows.py | Python | gpl-3.0 | 7,144 | [
"NetCDF"
] | e48479331b54cfa9ac4f06ec29f6363f477c5575c574f56cfa2be2b7b8c307af |
import pytest
from pytest_bdd import (
scenarios,
then,
when,
)
from . import browsersteps
pytestmark = [
pytest.mark.bdd,
pytest.mark.usefixtures('workbook', 'admin_user'),
]
scenarios(
'title.feature',
'generics.feature',
'create_gene_disease.feature',
'curation_central.feature',... | philiptzou/clincoded | src/clincoded/tests/features/test_generics.py | Python | mit | 1,045 | [
"VisIt"
] | 2d24ef849ddb6ba45fbb0702c96ca2a345651a357e222fd1531440981ddd8b29 |
#!/usr/bin/env python2.7
import h5py, os, sys, argparse
import cStringIO as StringIO
from Bio import SeqIO
from fast5tools.f5class import *
from fast5tools.barcodeclass import *
from fast5tools.f5ops import *
from fast5tools.barcodeops import *
from fast5tools.helperops import *
from glob import glob
###############... | JohnUrban/fast5tools | bin/fast5_sw_alignment_viz.py | Python | mit | 18,037 | [
"BWA"
] | 3083c0ab1765eae7cb52665cfad4a6ce9d4a33c3610180ac4cd611ed7524bc0e |
# encoding: utf-8
"""
Global exception classes for IPython.core.
Authors:
* Brian Granger
* Fernando Perez
* Min Ragan-Kelley
Notes
-----
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2008 The IPython Development Team
#
# Distributed under the terms of the BSD ... | Vvucinic/Wander | venv_2_7/lib/python2.7/site-packages/IPython/core/error.py | Python | artistic-2.0 | 1,734 | [
"Brian"
] | 94be563f7134b063569014d02f4bbbf79c0b409092ac309fdf6f1fb7c4df0a39 |
from unittest import TestCase
import tempfile
import os
from wifi import Cell
from wifi.scheme import extract_schemes, Scheme
from wifi.exceptions import ConnectionError
NETWORK_INTERFACES_FILE = """
# This file describes the network interfaces available on your system
# and how to activate them. For more informatio... | luckydonald/wifi | tests/test_schemes.py | Python | bsd-2-clause | 6,051 | [
"VisIt"
] | 55c344428db2c2917ff0ab136a1056757409a56ba4e19a2920c86b40f2a77b79 |
# -*- coding: utf-8 -*-
"""Tests for the PyBEL processor."""
import os
from urllib import request
from pybel import BELGraph, constants as pc
from pybel.dsl import *
from pybel.language import Entity
from pybel.io import from_nodelink_file
from pybel.examples import egf_graph
from indra.statements import *
from indr... | johnbachman/belpy | indra/tests/test_pybel_api.py | Python | mit | 28,165 | [
"Pybel"
] | a4ccf0f2af840805a2e8f810fdc2413db9c3450c6a9ca811a7808c7d98827c3f |
#!/usr/bin/python
'''
this is why we can't have nice things. Also, where
we hide our functions.
'''
import gwdglobals
import pcapy
import ConfigParser
#import os.path
from netaddr import IPNetwork, IPAddress
from connected import Connected
from remote import Remote
from router import Router
def eth_addr(a):
b = ... | ashmastaflash/gwdetect | gwdfunctions.py | Python | mit | 12,984 | [
"VisIt"
] | 6dac236190340fb28f4fb0ef26405e00f963d9df1c4ec5c4b25e0eccd8b1aca0 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
########################################################################
# Solves problem 42 from projectEuler.net.
# Finds the number of words which have a triangular value.
# Copyright (C) 2010 Santiago Alessandri
#
# This program is free software: you can redi... | sanSS/programming-contests | project-euler/problem042.py | Python | gpl-3.0 | 1,478 | [
"VisIt"
] | 19c02be358d149a998c79bd7674fcd80cc30913e9cc4e994e7a990e7bd60f8e2 |
""" Introduction
--------------------
This package provides tools for estimating multidimensional
integrals numerically using an enhanced version of
the adaptive Monte Carlo |vegas| algorithm (G. P. Lepage,
J. Comput. Phys. 27(1978) 192, and J. Comput. Phys. 439(2021)
110386).
A |vegas| code generally involves two ob... | gplepage/vegas | src/vegas/__init__.py | Python | gpl-3.0 | 33,943 | [
"Gaussian"
] | 788e1f92f3209230d693a949a2c9aa045a5dc4f7b9f561aaa9cfb9b48b7acbf4 |
from __future__ import absolute_import, division, print_function
import ast
import os
from jaspyx.ast_util import ast_load, ast_store, ast_call
from jaspyx.visitor import BaseVisitor
class Import(BaseVisitor):
import_path = ['.']
def load_module(self, pieces):
module_name = '.'.join(pieces)
i... | ztane/jaspyx | jaspyx/visitor/import_.py | Python | mit | 4,248 | [
"VisIt"
] | e7c8972af5a279e9e727d76889385b91a782d8ac6320a5f43335365eb7d3215e |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class PyBayesianOptimization(PythonPackage):
"""Pure Python implementation of bayesian global
... | LLNL/spack | var/spack/repos/builtin/packages/py-bayesian-optimization/package.py | Python | lgpl-2.1 | 820 | [
"Gaussian"
] | dc47b3d7c35fd58383bce9d34bc469afe31395da97fc2dd1b8af43cb5bef9062 |
#!/usr/bin/env python
from __future__ import print_function
from pymatgen.core.periodic_table import PeriodicTable
pt = PeriodicTable()
atom_string = '/unitcell/atom-style-%s/.style={minimum size=%f\\@atom@scale},'
print('\\tikzset{')
for element in pt:
try:
radius = float(element.data['Atomic radius c... | ldamewood/figures | scripts/tikzlibraryatoms/tikzlibraryatoms.data.py | Python | mit | 423 | [
"pymatgen"
] | 933806560895590793933c48507149962519d33a73ede730db3d7e074e8e0b51 |
../../../../../../../share/pyshared/orca/scripts/apps/Banshee/formatting.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/scripts/apps/Banshee/formatting.py | Python | gpl-3.0 | 75 | [
"ORCA"
] | beb062910d0a12dcede3906d4b1c9a062307ef8eec94c9e2e1f52135b2ea14de |
# Copyright (c) 2001 Autonomous Zone Industries
# This file is licensed under the
# GNU Lesser General Public License v2.1.
# See the file COPYING or visit http://www.gnu.org/ for details.
__revision__ = "$Id: CommHints.py,v 1.2 2002/12/02 19:58:44 myers_carpenter Exp $"
### standard modules
import types
# T... | zooko/egtp_new | egtp/CommHints.py | Python | lgpl-2.1 | 2,565 | [
"VisIt"
] | 1f76bb36b70823b510711da196e1f7598c9ffd48c72dbbeec8728b25cffb97e0 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright: (c) 2014, Ruggero Marchei <ruggero.marchei@daemonzone.net>
# Copyright: (c) 2015, Brian Coca <bcoca@ansible.com>
# Copyright: (c) 2017, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ im... | jmighion/ansible | lib/ansible/modules/files/find.py | Python | gpl-3.0 | 12,570 | [
"Brian"
] | 0c595fef88eb7a60177f456905fb0020f299621810ae4660ad891c546d8ca64d |
#
# Author: Travis Oliphant 2002-2011 with contributions from
# SciPy Developers 2004-2011
#
from __future__ import division, print_function, absolute_import
from scipy._lib.six import string_types, exec_
from scipy._lib._util import getargspec_no_self as _getargspec
import sys
import keyword
import re
imp... | jlcarmic/producthunt_simulator | venv/lib/python2.7/site-packages/scipy/stats/_distn_infrastructure.py | Python | mit | 114,867 | [
"Gaussian"
] | acb3d99718d379b232a264ecde8b69055a04ca603fb2b5080cff60ef75824eba |
#This is a program that handles the actual image processing and
#answer detection. We are going to build mobile apps based on this
#program and hopefully we will be able to add more functionality to it.
import cv2
from android import Android
droid = Android()
import numpy as np
def rectify(h):
h = h.reshape((4,2))... | HuimingCheng/AutoGrading | learning/Android_app/test_code.py | Python | mit | 18,754 | [
"Gaussian"
] | 5a6a48c3348a0b4bac918412a7366d12cfc435363690c1005bd4332616a465f2 |
# coding=utf-8
# Copyright 2022 The Uncertainty Baselines Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by ap... | google/uncertainty-baselines | uncertainty_baselines/models/vit_batchensemble_gp_test.py | Python | apache-2.0 | 2,593 | [
"Gaussian"
] | 04d21f71cb04688d7a297e82200224f5e62c34fc87affc787b1dc94eac90c53e |
#########
# multiConfig.py
# This program is part of the online PS-Drone-API-tutorial on www.playsheep.de/drone.
# It shows how to set and read out multi-configuration of a Parrot AR.Drone 2.0 using the PS-Drone-API..
# The drone will stay on the ground.
# Dependencies: a POSIX OS, PS-Drone-API 2.0 beta or higher.
# (w... | reixd/ps-drone | tutorials/multiConfig.py | Python | artistic-2.0 | 2,059 | [
"VisIt"
] | 203de890c4015d3fd24b8a6654c0b2962f5e863b06bb67bd1da0487e4bea17cc |
# Copyright 2020 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | google-research/sound-separation | models/dcase2020_fuss_baseline/train/network.py | Python | apache-2.0 | 17,305 | [
"Brian"
] | dca9390ca573dd5441ebf66750869ce9f06f76a093f75b86ee730e87516aa6ae |
#!/usr/bin/env python
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2018 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistri... | amjames/psi4 | psi4/share/psi4/fsapt/copy_pymol.py | Python | lgpl-3.0 | 1,338 | [
"Psi4",
"PyMOL"
] | 99010b555ad502bbb417ab0c2b47651728dd263ab13d3171ac5984ea72a4ff58 |
# GromacsWrapper: test_example.py
# Copyright (c) 2009 Oliver Beckstein <orbeckst@gmail.com>
# Released under the GNU Public License 3 (or higher, your choice)
# See the file COPYING for details.
from __future__ import division, absolute_import, print_function
import pytest
from .datafiles import datafile
import gr... | Becksteinlab/GromacsWrapper | tests/test_run.py | Python | gpl-3.0 | 2,341 | [
"Gromacs"
] | c81aa73969cae880d550c5f9b26bb776581fce8dfee08cfc4f8f602d1ca7fc9d |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class PyPygps(PythonPackage):
"""pyGPs is a Python library for Gaussian Process (GP)
Regr... | iulian787/spack | var/spack/repos/builtin/packages/py-pygps/package.py | Python | lgpl-2.1 | 849 | [
"Gaussian"
] | a4eebd42d7635a4533abc3d53eb8e2d932fd28e79485467be43716f6e9c44439 |
#!/usr/bin/env python
# =============================================================================================
# MODULE DOCSTRING
# =============================================================================================
"""
Tools to build Yank experiments from a YAML configuration file.
"""
# =========... | pgrinaway/yank | Yank/yamlbuild.py | Python | lgpl-3.0 | 110,382 | [
"Amber",
"Gromacs",
"NetCDF",
"OpenMM"
] | e432e9a892ef8460575e2abc30b20df6153af9edfee040ef0110a8a3c16e3ece |
# -*- coding: utf-8 -*-
# compare_moose_nrn.py ---
#
# Filename: compare_moose_nrn.py
# Description:
# Author: subha
# Maintainer:
# Created: Sat Apr 30 02:43:29 2016 (-0400)
# Version:
# Last-Updated: Sat Apr 30 03:01:04 2016 (-0400)
# By: subha
# Update #: 19
# URL:
# Keywords:
# Compatibility:
#
#
# C... | dharmasam9/moose-core | tests/issues/hsolve/compare_moose_nrn.py | Python | gpl-3.0 | 1,679 | [
"MOOSE",
"NEURON"
] | 2d4db934d10c484163e0df3b29ba076b0482311be21653c338cef56ab3a3eb7f |
# Copyright (c) 2003-2013 LOGILAB S.A. (Paris, FRANCE).
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
#
# 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, o... | yorvic/.vim | bundle/python-mode/pylibs/pylama/checkers/pylint/lint.py | Python | gpl-3.0 | 45,200 | [
"VisIt"
] | f01606be08b947f7bdde29fafb8ece3d339724b26a37adc31ee4125c59afa776 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements more advanced transformations.
"""
import numpy as np
from fractions import Fraction
from math import gcd
from itertools import groupby, product
from string import ascii_lowercase
fr... | fraricci/pymatgen | pymatgen/transformations/advanced_transformations.py | Python | mit | 82,469 | [
"CRYSTAL",
"pymatgen"
] | eb975abfe27268a2f84db3dc0a17220afa673d8e74272cedf88956046696c24e |
# 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... | eric-haibin-lin/mxnet | example/distributed_training-horovod/resnet50_imagenet.py | Python | apache-2.0 | 17,929 | [
"Gaussian"
] | 1eaee80c3ca8d59f5cd9cc89abfc5606ba70c3881e2b7c1e93e8cfd8ca97debf |
from __future__ import print_function, division, unicode_literals
import operator
import os
import matplotlib as mpl
mpl.use('Agg')
import matplotlib.pyplot as plt
from pymatgen.core.structure import Structure
from pymatgen.entries.computed_entries import ComputedEntry
from pymatgen.io.vasp.outputs import Vasprun
#f... | henniggroup/MPInterfaces | mpinterfaces/mat2d/stability/analysis.py | Python | mit | 5,881 | [
"VASP",
"pymatgen"
] | 56236d33bf26e6cd1861e74f732aa005bcc66e5dfd610d8b6133281117033d3f |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | psci2195/espresso-ffans | src/python/espressomd/io/writer/h5md.py | Python | gpl-3.0 | 4,224 | [
"ESPResSo"
] | 0aa0e877e678fc2870aa3642a61c0937329c7255ff7c34fe63b72fb10d37eebf |
"""
====================================================
Imputing missing values before building an estimator
====================================================
Missing values can be replaced by the mean, the median or the most frequent
value using the basic ``SimpleImputer``.
The median is a more robust estimator f... | BiaDarkia/scikit-learn | examples/plot_missing_values.py | Python | bsd-3-clause | 5,117 | [
"Gaussian"
] | 9687f4d4e026fc3bff84ff12b707c6b517d36220fbf39e79daa6cdb5ce0ac814 |
# -*- coding: utf-8 -*-
#
# Copyright (C) 2004-2006 Edgewall Software
# Copyright (C) 2004 Daniel Lundin <daniel@edgewall.com>
# Copyright (C) 2004-2006 Christopher Lenz <cmlenz@gmx.de>
# Copyright (C) 2006 Jonas Borgström <jonas@edgewall.com>
# All rights reserved.
#
# This software is licensed as described in the fil... | cyphactor/lifecyclemanager | testenv/trac-0.10.4/trac/web/session.py | Python | gpl-3.0 | 9,025 | [
"VisIt"
] | d3f3af38febe695669244db5b85567319d391518175c147c5dd627004fe67365 |
"""Next-gen alignments with BWA (http://bio-bwa.sourceforge.net/)
"""
import os
import subprocess
import toolz as tz
from bcbio.pipeline import config_utils
from bcbio import bam, utils
from bcbio.distributed.transaction import file_transaction, tx_tmpdir
from bcbio.ngsalign import alignprep, novoalign, postalign
fro... | SciLifeLab/bcbio-nextgen | bcbio/ngsalign/bwa.py | Python | mit | 8,435 | [
"BWA"
] | 85d64fd50170ceffdd31738726e6488f0b2b0097115d6031f00336b6b8710745 |
#!/usr/bin/env python -i
# preceeding line should have path for Python on your machine
# demo.py
# Purpose: illustrate use of many library interface commands
# Syntax: demo.py
# uses in.demo as LAMMPS input script
from __future__ import print_function
import sys
# parse command line
argv = sys.argv
if len... | SGenheden/lammps | python/examples/demo.py | Python | gpl-2.0 | 1,303 | [
"LAMMPS"
] | 50742bed18cfef2feac72a2a51a0c3a520eb1903f9bfc06759ad9899a1ede21f |
"""
:mod: RSSCache
Extension of DictCache to be used within RSS
"""
__RCSID__ = '$Id$'
import datetime
import threading
import time
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Utilities.DictCache import DictCache
class RSSCache( object ):
'''
Cache with purgeThread integrated
'... | andresailer/DIRAC | ResourceStatusSystem/Utilities/RSSCache.py | Python | gpl-3.0 | 5,923 | [
"DIRAC"
] | 32ff0e1a01ca2538648d56076b37f0fc1acdad5083a37b8213b261096c092e41 |
import urllib
from urllib import parse
import urllib.request
from urllib import error
import time
import os
import sys
import datetime
from oi.IO import IO
import webbrowser
def launch_browser(url):
IO.put("Attempting to launch {} in a browser.".format(url))
try:
webbrowser.open(url)
except:
... | jadacyrus/searchgiant_cli | common/Common.py | Python | gpl-3.0 | 5,175 | [
"VisIt"
] | f123b0b91e9fd3f532ebd1e2d7718191db1870d3cb4f3689e9f128ea63af4fc8 |
""" PEP
PEP ( Policy Enforcement Point ) is the front-end of the whole Policy System.
Any interaction with it must go through the PEP to ensure a smooth flow.
Firstly, it loads the PDP ( Policy Decision Point ) which actually is the
module doing all dirty work ( finding policies, running them, merging their
... | fstagni/DIRAC | ResourceStatusSystem/PolicySystem/PEP.py | Python | gpl-3.0 | 8,339 | [
"DIRAC"
] | 6eb0d899588c0289c7a1105a39bea611cf4b31d490bf50cde156b9afd5e549e5 |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2020, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
"""
Interface to `cclib`_
#######################
.. _cclib: https://cclib.github.io/
"""
from ast import literal_eval
from exa.util.units import Length, Energy
from exatomic.algori... | exa-analytics/atomic | exatomic/interfaces/cclib.py | Python | apache-2.0 | 4,813 | [
"Gaussian",
"cclib"
] | 064db3730780253480bbbb6a2133d29f2f84115033392fa547233d5b12da575d |
# Hidden Markov Model Implementation
import pylab as pyl
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy as scp
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import rospy
#import hrl_lib.mayavi2_util as mu
import hrl_lib.viz ... | tapomayukh/projects_in_python | classification/Classification_with_HMM/Single_Contact_Classification/Final_Comparison_Variable_Length/Motion/hmm_crossvalidation_motion.py | Python | mit | 21,884 | [
"Gaussian",
"Mayavi"
] | bd5a4be691e86c82366b59a6df426383732aa01c57f9c7830d68e2cc4aff69f9 |
#!/usr/bin/python
# Copyright: Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version': '1.1',
'status': ['stableinterf... | veger/ansible | lib/ansible/modules/cloud/amazon/ec2_elb_lb.py | Python | gpl-3.0 | 53,509 | [
"Dalton"
] | b37fc33092aa0f28b24a90ec01fe5222c265569fe32638ac42bc2ae6529444bc |
# coding: utf-8
"""
vmd reader
"""
import io
import struct
from .. import common
from .. import vmd
class Reader(common.BinaryReader):
def read_text(self, size):
"""read cp932 text
"""
src=self.unpack("%ds" % size, size)
assert(type(src)==bytes)
pos = src.find(b"\x00")
... | GRGSIBERIA/mmd-transporter | mmd-transporter/pymeshio/vmd/reader.py | Python | gpl-2.0 | 2,940 | [
"VMD"
] | 01cc5c435cc61612df727f3619d09279ad822e8e626483e64148ae319fc4418a |
"""End-To-End Memory Networks.
The implementation is based on http://arxiv.org/abs/1503.08895 [1]
"""
from __future__ import absolute_import
from __future__ import division
import tensorflow as tf
import numpy as np
from six.moves import range
def position_encoding(sentence_size, embedding_size):
"""
Positio... | tianlongwang/memn2n | web-demo/server/memn2n.py | Python | mit | 13,203 | [
"Gaussian"
] | bd6f0bedaa2c6fd77f07ae3fe2749bdcfca1f8b4373046f1d724e4b3bd9b1fe1 |
#-------------------------------------------------------------------------------
# Copyright (c) 2012 Vincent Gauthier.
#
# 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,... | ComplexNetTSP/CooperativeNetworking | complex_systems/mobility/stabrnd.py | Python | mit | 9,090 | [
"Gaussian"
] | f511012aac260ecd36f473e8fcb9dc7593ea98f94287f72867042250a4248d3b |
import re
# Workaround for Windows ST2 not having disutils
try:
from distutils.version import LooseVersion
except:
# From distutils/version.py
class LooseVersion():
component_re = re.compile(r'(\d+ | [a-z]+ | \.)', re.VERBOSE)
def __init__ (self, vstring=None):
if vstring:
... | NicoSantangelo/sublime-gulp | gulp_version.py | Python | mit | 2,116 | [
"GULP"
] | 1d759c6affaa94857189ad5f02bb7d469a647b7cc3c14b8fccfcaecd5aac5f25 |
import os
import sys
import ast
from PyQt5.QtWidgets import QApplication, QMainWindow, QFileDialog
from GUI import Ui_MainWindow
import Header as Header
from pop_up_control.cpe_active import PopUpCPEActive
from pop_up_control.external_neuron_arrray import PopUpExternalNeuronArray
from pop_up_control.full_field_ifft imp... | andreashorn/lead_dbs | ext_libs/OSS-DBS/OSS_platform/GUI_tree_files/AppUI.py | Python | gpl-3.0 | 42,008 | [
"ParaView"
] | f4c4f9871991b6c09d023ed7d7f965d2d53193ad8642bec75775b553b4d0e9ed |
""" PieGraph represents a pie graph
The DIRAC Graphs package is derived from the GraphTool plotting package of the
CMS/Phedex Project by ... <to be added>
"""
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
import numpy
import math
import time
from... | yujikato/DIRAC | src/DIRAC/Core/Utilities/Graphs/PieGraph.py | Python | gpl-3.0 | 5,118 | [
"DIRAC"
] | 8018d3ef747a206fd5d056387a39f67570b0467e0feb0c326a1cb4aa09df02fd |
"""Generate artifical PIV images for par2vel"""
# Copyright Knud Erik Meyer 2017
# Open source software under the terms of the GNU General Public License ver 3
import numpy
import scipy
class ArtImage(object):
"""Generate an artificial PIV image"""
def __init__(self, camera, particle_image_size=2.0, ... | kemeyer/par2vel | par2vel/artimage.py | Python | gpl-3.0 | 9,087 | [
"Gaussian"
] | dbb3dac9d82f4acfea39869d7802323ec96cefc7a0f5118eae50e5e0ae464940 |
from __future__ import division
# iPython tricks:
# # automatically reload modified modules:
# %load_ext autoreload
# %autoreload 2
# Using Notebook:
# ipython notebook --pylab inline
# Using Qtconsole:
# ipython qtconsole --pylab=inline
__all__ = [ "Image",
"imread",
"imwrite",
... | trustswz/IRTK | wrapping/cython/irtk/image.py | Python | bsd-3-clause | 34,834 | [
"Gaussian"
] | 9a3e2e3cd64565e1ddf6a02e3324f886613b18fd07b64804e6e674f3192e20a4 |
'''
Computes the semantic similarity between two neuron mentions.
The main function is similarity()
Computation is delegated to similarity_inter and similarity_intra
'''
import similarity_inter, similarity_intra
from operator import itemgetter
from itertools import groupby
import re
from sherlok import Sherlok # pip ... | renaud/neuroNER | similarity/similarity.py | Python | lgpl-3.0 | 5,307 | [
"NEURON"
] | 2a149b76c7d118e5d88a283c6f2a37001a1feb27d066002a5c7a35c78afb335c |
"""
This class is used to define the plot using the plot attributes.
"""
from DIRAC import S_OK
from DIRAC.MonitoringSystem.Client.Types.WMSHistory import WMSHistory
from DIRAC.MonitoringSystem.private.Plotters.BasePlotter import BasePlotter
__RCSID__ = "$Id$"
class WMSHistoryPlotter( BasePlotter ):
"""
.. cl... | Andrew-McNab-UK/DIRAC | MonitoringSystem/private/Plotters/WMSHistoryPlotter.py | Python | gpl-3.0 | 6,416 | [
"DIRAC"
] | 7b4125fef5bc00b5160962001cc0ff665e4767ef744ff4b3896fdc3b65069257 |
import sys
import gzip
import os.path
import threading
from glob import glob
from io import BytesIO
from .. import backends, conventions
from .common import ArrayWriter
from ..core.combine import auto_combine
from ..core.utils import close_on_error, is_remote_uri
from ..core.pycompat import basestring
def _get_defau... | petercable/xray | xray/backends/api.py | Python | apache-2.0 | 17,670 | [
"NetCDF"
] | d2ba39be6ee2078a88e4cd1e35abed21c1c0f9d6595cb7178dd096d9342564b7 |
#!/usr/bin/python
import settings
from hardware.hardware import PortalHW
from flask import Flask
from flask import jsonify
import json
from flask import Response
from flask import render_template
app = Flask(__name__)
version = settings.constants['API_VERSION']
door_ids = settings.constants['DOOR_IDS']
api_endpoint = ... | hackernight/portal | service.py | Python | mit | 2,033 | [
"VisIt"
] | 546ccbff2a8679977074aab354181b4917fea5fb3a39baa1dd84f79c37f32b77 |
"""ParametricJobs Table."""
import os
import re
import time
import json
import logging
import calendar
from datetime import datetime
import cherrypy
from sqlalchemy import Column, SmallInteger, Integer, Boolean, String, PickleType, TIMESTAMP, ForeignKey, Enum, CheckConstraint
from sqlalchemy.ext.hybrid import hybrid_p... | alexanderrichards/LZProduction | lzproduction/sql/tables/ParametricJobs.py | Python | mit | 12,918 | [
"DIRAC"
] | e03397a29b07f2a1534aa8c81648b36491b72272219241fe13236c0562116ea7 |
#!/usr/bin/python
import csv
import os
import re
import sys
ign_keywords = [
"elemental",
"integer",
"logical",
"pure",
"recursive"]
with open("../abinit-orphans-7.9.1-raw.csv", "rb") as csvfile:
for row in csv.reader(csvfile):
my_dir, my_src, my_sub, my_typ, my_act, my_sta = row
if ( my_typ == "... | SamKChang/abinit-7.10.5_multipole | developers/maintainers/analyze-orphans.py | Python | gpl-3.0 | 1,705 | [
"ABINIT"
] | 3e88c7b3dc0b2470f47cc6e5e4271e056268b7d48b88bcc9eee25d8d165a457f |
# -*- coding: utf-8 -*-
# This file is part of Shoop.
#
# Copyright (c) 2012-2015, Shoop Ltd. All rights reserved.
#
# This source code is licensed under the AGPLv3 license found in the
# LICENSE file in the root directory of this source tree.
from __future__ import print_function
import sys
from ast import parse
imp... | taedori81/shoop | _misc/ensure_fk_style.py | Python | agpl-3.0 | 1,559 | [
"VisIt"
] | 3ecfc0934d5ab23c91a5025f944fd3c501cda2b800c41de6b4c31dd3090aad59 |
import pytest
from notifications_utils.countries import Country, CountryNotFoundError
def _country_not_found(*test_case):
return pytest.param(
*test_case,
marks=pytest.mark.xfail(raises=CountryNotFoundError),
)
@pytest.mark.parametrize('alpha_2, expected_name', (
('AF', 'Afghanistan'),
... | alphagov/notifications-utils | tests/test_countries_iso.py | Python | mit | 18,435 | [
"BWA"
] | c3d41f6b8cfae05119c9f76a1247fc6104931bdee552d189c9e3344a8f7422ef |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | kain88-de/mdanalysis | testsuite/MDAnalysisTests/coordinates/test_dcd.py | Python | gpl-2.0 | 23,615 | [
"CHARMM",
"MDAnalysis",
"NAMD",
"NetCDF"
] | 64f6c4cfab34ffde425fba082698b07e1e88bb36d8590b361f5488546253ff3c |
# Generated from /media/eddy/Erato/Zchool/Computer Science/4º/VIII Semestre/Simulación/Proyectos/2. Lógica difusa/fuzzy_logic/fuzzy/parsing/Fuzzy.g4 by ANTLR 4.7
from antlr4 import *
if __name__ is not None and "." in __name__:
from .FuzzyParser import FuzzyParser
else:
from FuzzyParser import FuzzyParser
# Th... | ealmuina/fuzzy-logic-evaluator | fuzzy/parsing/FuzzyVisitor.py | Python | mit | 2,495 | [
"VisIt"
] | 833b63e55ebf6d3eb05153a216a668ad1e07ce1aa3486a6caa49a429219a5eda |
"""
.. _ica:
==================================================
Background on Independent Component Analysis (ICA)
==================================================
.. contents:: Contents
:local:
:depth: 2
Many M/EEG signals including biological artifacts reflect non-Gaussian
processes. Therefore PCA-based ar... | Teekuningas/mne-python | tutorials/discussions/plot_background_ica.py | Python | bsd-3-clause | 3,282 | [
"Gaussian"
] | 5e59c58e6165c67575f7c18b71a6cc537f0414d5386e8f8d23980b260f44cc70 |
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