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# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Eric Larson <larson.eric.d@gmail.com>
# Oleh Kozynets <ok7mailbox@gmail.com>
# Guillaume Favelier <guillaume.favelier@gmail.com>
# jona-sassenhagen <jona.sassenhagen@gmail.com>
# Joan Massich <mailsik@gmail.com>
#... | bloyl/mne-python | mne/viz/_brain/_brain.py | Python | bsd-3-clause | 152,554 | [
"Mayavi",
"VTK"
] | 6e9127dcdaf01fd6798c6be9a9c7c72a14e3e9abdf10886ad76e91eb056f4350 |
import os, sys
import vtk, ctk, slicer
import logging
#
# MRMLUtility
#
'''
This class harbors all the utility functions to load, add, save and remove mrml nodes
'''
class MRMLUtility(object):
@staticmethod
def loadMRMLNode(node_name, file_dir, file_name, file_type):
node = slicer.mrmlScene.GetFirstNodeByNam... | bpaniagua/SPHARM-PDM | Modules/Scripted/ShapeAnalysisModule/CommonUtilities/utility.py | Python | apache-2.0 | 4,575 | [
"VTK"
] | a194be7b51560ae8f494d10371c00b51cb9f40b0bc83d9ef64e0a006b99d77f4 |
import numpy as np
import pickle
import cv2
from skimage.feature import hog
from skimage.transform import pyramid_gaussian
print(cv2.__version__)
windowSize = [120,120]
stepSize = 60
def sliding_window(image, stepSize, windowSize):
# slide a window across the image
for x in range(0, image.shape[0], stepSize):... | Rawash/parking-car-counter | skimage-Hog-CLFfromVideos.py | Python | mit | 1,866 | [
"Gaussian"
] | 791e8c5648bceb5d8dcda8747b30ea62a61c8d81ac725648e99c5e4620b61993 |
"""
# Notes:
- This simulation seeks to emulate the COBAHH benchmark simulations of (Brette
et al. 2007) using the Brian2 simulator for speed benchmark comparison to
DynaSim. However, this simulation does NOT include synapses, for better
comparison to Figure 5 of (Goodman and Brette, 2008) - although it uses the... | asoplata/dynasim-benchmark-brette-2007 | output/Brian2/brian2_benchmark_COBAHH_nosyn_0016/brian2_benchmark_COBAHH_nosyn_0016.py | Python | gpl-3.0 | 3,344 | [
"Brian"
] | 2e2126c3534bb42e521d717b4a4335b5863d13d3951715be1ff975cd60cbb9f1 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# rangefileaccess - [insert a few words of module description on this line]
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the te... | heromod/migrid | mig/cgi-bin/rangefileaccess.py | Python | gpl-2.0 | 10,395 | [
"Brian"
] | 8acaf3cc84f0a9ece570bf0d5cfc2f158041c2870c75dc3a08ec53f7168bc6fe |
#-------------------------------------------------------------------------------
# Parser for ASDL [1] definition files. Reads in an ASDL description and parses
# it into an AST that describes it.
#
# The EBNF we're parsing here: Figure 1 of the paper [1]. Extended to support
# modules and attributes after a product. W... | FFMG/myoddweb.piger | monitor/api/python/Python-3.7.2/Parser/asdl.py | Python | gpl-2.0 | 12,881 | [
"VisIt"
] | 6b9d6d23991268bc16af70adbab4e3a5c8be3c15bcf5af6359baeddebca736c5 |
#!/usr/bin/env python
from splinter import Browser
from bs4 import BeautifulSoup
from time import sleep
import sys
separator = ''.join( [ '-' * 175 ] )
if( len( sys.argv ) > 1 ):
query = sys.argv[1]
else:
exit( 'No query specified' )
print( 'Searching...\n%s' % separator )
with Browser( 'phantomjs' ... | Dashius/terminal-google | googleScraper.py | Python | gpl-3.0 | 1,334 | [
"VisIt"
] | 912ec18e806c3291fa17c101cc4280bb82a18cda4212b1e5d1c295c692bbf3b4 |
"""Some functions to generate simulated data"""
try:
from os import link
except ImportError:
# Hack for windows
from shutil import copy2
def link(src, dst):
copy2(src, dst)
from numpy.random import randn, rand, permutation, randint, seed
from numpy import where, nonzero, sqrt, real
from numpy ... | chengsoonong/didbits | DataWrangling/simdata.py | Python | apache-2.0 | 18,355 | [
"Gaussian"
] | 72631724061b5df9659883fe0fb65792001e89f63c0a30c308330bc79eb3b0a6 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Vrrtep CLI is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public Licence as published by
# the Free Software Foundation, either version 3 of the Licence, or
# (at your option) any later version.
#
# Vrrtep CLI is... | tirea/vrrtepcli | src/root.py | Python | gpl-3.0 | 9,200 | [
"MOE"
] | fefd94d996c61690a9e88bee4141a73c97371ff316d158e8cf500ddaa812a43f |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import time
# !! This is the configuration of Nikola. !! #
# !! You should edit it to your liking. !! #
# ! Some settings can be different in different languages.
# ! A comment stating (translatable) is used to denote those.
# ! There are two ways to... | disconsented/website | conf.py | Python | mit | 54,721 | [
"VisIt"
] | ae211ac3a2ed6879837180d12f5aff9225b35a198c806d8ab5112851b8e752fe |
"""
@name: PyHouse/src/Modules/Families/_test/test_X10.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2015-2018 by D. Brian Kimmel
@license: MIT License
@note: Created on Jul 29, 2015
@Summary:
Passed all tests - DBK - 2018-02-13
"""
__updated__ = '2018-02-13'
# Impor... | DBrianKimmel/PyHouse | Project/src/Modules/House/Family/_test/test_X10.py | Python | mit | 815 | [
"Brian"
] | 750ec115435bb4b24224ab47303cd77f84d4df638e75060c27462bd12bdc42ac |
# 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
#
# Unless required by appl... | sunqm/pyscf | pyscf/pbc/dft/__init__.py | Python | apache-2.0 | 1,793 | [
"PySCF"
] | 74775cfdd0b00849f0d9db9f62fc6d34f9181a65697f715830d5e29fd0972dd1 |
# taken from http://www.piware.de/2011/01/creating-an-https-server-in-python/
# generate server.xml with the following command:
# openssl req -new -x509 -keyout server.pem -out server.pem -days 365 -nodes
# run as follows:
# python simple-https-server.py
# then in your browser, visit:
# https://localhost:4443
... | k-yang/techcrunchDoppler | httpServer.py | Python | mit | 580 | [
"VisIt"
] | 8633647e250b901fa86b12c671a930b22785cc0f842bb5676115aa518e5b8b91 |
#
# 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 n... | agoodm/climate | ocw/dataset_processor.py | Python | apache-2.0 | 61,239 | [
"NetCDF"
] | fed73bc04ef65f3f43fd8b3a38776081e3b2675205730e6c73a4770abce4a977 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Generated from FHIR 1.0.2.7202 on 2016-06-23.
# 2016, SMART Health IT.
import io
import json
import os
import unittest
from . import appointmentresponse
from .fhirdate import FHIRDate
class AppointmentResponseTests(unittest.TestCase):
def instantiate_from(sel... | all-of-us/raw-data-repository | rdr_service/lib_fhir/fhirclient_1_0_6/models/appointmentresponse_tests.py | Python | bsd-3-clause | 2,839 | [
"Brian"
] | 05a6f8114dcb54b5beda4219611fde4eab7fab129f57725aaa632d34cb18ad2f |
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2015, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version 2.1 or later. You s... | ghutchis/cclib | test/test_bridge.py | Python | lgpl-2.1 | 650 | [
"cclib"
] | 90991ea7e36678325b12944735cfe540891c83a551af0b79f7fe870fadb12c36 |
"""Integration with Python standard library module urllib2: Request class.
Copyright 2004-2006 John J Lee <jjl@pobox.com>
This code is free software; you can redistribute it and/or modify it
under the terms of the BSD or ZPL 2.1 licenses (see the file
COPYING.txt included with the distribution).
"""
from __future__... | Masood-M/yalih | mechanize/_request.py | Python | apache-2.0 | 3,172 | [
"VisIt"
] | 44c48b42a12e96a1f538e17db05105938905beb6a1b938871dc8ebfa7b3376ef |
"""
This module provides classes and functions for pass management.
There are two kinds of passes: transformations and analysis.
* ModuleAnalysis, FunctionAnalysis and NodeAnalysis are to be
subclassed by any pass that collects information about the AST.
* gather is used to gather (!) the result of an an... | serge-sans-paille/pythran | pythran/passmanager.py | Python | bsd-3-clause | 8,177 | [
"VisIt"
] | 1aaefe9bf6a1b8a34283da5f4e43e73eaf157a84912704e074537e160c6c6fc6 |
# Copyright (C) 2010-2018 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... | hmenke/espresso | testsuite/python/analyze_distance.py | Python | gpl-3.0 | 4,504 | [
"ESPResSo"
] | ed54589eb739f57fb1707327f789f8b528d6a5a36bc51edd0e334f7bdc6222fe |
"""
Service handler for FTS3DB using DISET
.. literalinclude:: ../ConfigTemplate.cfg
:start-after: ##BEGIN FTS3Manager
:end-before: ##END
:dedent: 2
:caption: FTS3Manager options
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$... | yujikato/DIRAC | src/DIRAC/DataManagementSystem/Service/FTS3ManagerHandler.py | Python | gpl-3.0 | 6,531 | [
"DIRAC"
] | 05546a0cdb2e53e72e166189f2567220fe88ac98508ab728d39e5d5a2ddeb5e7 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, division, print_function
import os
import py.path
import pytest
import sys
import time
import _pytest.pytester as pytester
from _pytest.pytester import HookRecorder
from _pytest.pytester import CwdSnapshot, SysModulesSnapshot, SysPathsSnapshot
from _pytest... | ddboline/pytest | testing/test_pytester.py | Python | mit | 13,571 | [
"Brian"
] | 085206fe6fa2a1aa80f79e59d49f7575860e79e5a66b900e65d0b032a459a4ed |
# Copyright 2018 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | chemelnucfin/tensorflow | tensorflow/tools/compatibility/tf_upgrade_v2_test.py | Python | apache-2.0 | 94,696 | [
"Gaussian"
] | 90da89996b8fb807c87973ffd90bb8370976cc01cd4e51138c79cf179a7e8539 |
# Copyright 2001-2004 Brad Chapman.
# Revisions copyright 2009-2010 by Peter Cock.
# All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""General mechanisms to access applications i... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/Application/__init__.py | Python | gpl-2.0 | 30,273 | [
"BLAST",
"Biopython"
] | a629ec70f06eeff188d4652ed70690be327433d7708ff2bb35b7be3b0363f2ca |
#!/usr/bin/env python
# encoding: utf-8
#Created by on 2008-05-07.
# Copyright (C) 2008 Graham I Cummins
# This program is free software; you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
# Foundation; either version 2 of the License, or (at... | gic888/MIEN | dsp/old_style_PF_needs_update.py | Python | gpl-2.0 | 24,699 | [
"Gaussian"
] | b6a788377626e488ae5c51fe76aa4fe3140f33fbeb54a593a275578ac26f5e84 |
#!/usr/bin/env python
"""
--- Day 1: No Time for a Taxicab ---
Santa's sleigh uses a very high-precision clock to guide its movements, and the clock's oscillator is regulated by stars. Unfortunately, the stars have been stolen... by the Easter Bunny. To save Christmas, Santa needs you to retrieve all fifty stars by De... | Hwesta/advent-of-code | aoc2016/day1.py | Python | mit | 3,056 | [
"VisIt"
] | d3f869b79f26e9aa27f6a9cb10b508818a30efb4a856502491cd854c0e743ea4 |
../../../../../../../share/pyshared/orca/scripts/apps/ubiquity/script.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/scripts/apps/ubiquity/script.py | Python | gpl-3.0 | 72 | [
"ORCA"
] | 764dcdca931b0322dbaa58b6f5b2480c08a5bccd59ee3eb74a02fb1c400f4a8d |
# Principal Component Analysis Code :
from numpy import mean,cov,double,cumsum,dot,linalg,array,rank,size,flipud
from pylab import *
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import ro... | tapomayukh/projects_in_python | sandbox_tapo/src/skin_related/BMED_8813_HAP/Scaling/results/cross_validate_objects_BMED_8813_HAP_scaled_method_II.py | Python | mit | 3,949 | [
"Mayavi"
] | 9fda05c8da19c678ea4ab039ac4898ecd6cdd5bb205a78d864eff4a149b8f1da |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2008, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | anksp21/Community-Zenpacks | ZenPacks.Nagios.CheckPing/setup.py | Python | gpl-2.0 | 3,268 | [
"VisIt"
] | 2a9b23fccf421368c54534428afded5c9192c851b99b1f35074f4b78513346c9 |
import sys
import argparse
import time
import Bio
from Bio.SeqFeature import FeatureLocation
from Bio.SeqFeature import SeqFeature
class MySeqFeature(SeqFeature):
def __str__(self):
out = "type: %s\n" % self.type
if self.strand == 1:
out += "location: [%s:%s](%s)\n" % (self.location.st... | nikolaichik/SigmoID | Python/_HmmGen.py | Python | gpl-3.0 | 37,178 | [
"Biopython"
] | c8a3e659c5385716509526d91dbe781750498f45909e6c142d659bb9358360e9 |
#!/usr/bin/env python
"""
Get computing resources capable to execute a job with the given description.
Note that only statically defined computing resource parameters are considered although sites
can fail matching due to their dynamic state, e.g. occupancy by other jobs. Also input data
proximity is not taken into ac... | yujikato/DIRAC | src/DIRAC/WorkloadManagementSystem/scripts/dirac_wms_match.py | Python | gpl-3.0 | 3,660 | [
"DIRAC"
] | adec821dbab2e20f7ab4953dcd9cb9c218501b7f9dd60d39c91db7b67436dc6b |
# coding=utf-8
from __future__ import division
from __future__ import print_function
import pylab as plt
from imgProcessor.measure.FitHistogramPeaks import FitHistogramPeaks
from fancytools.os.PathStr import PathStr
# move into iomgProc.scripts
def plotFitResult(fit, show_legend=True, show_plots=True, save... | radjkarl/imgProcessor | imgProcessor/scripts/_FitHistogramPeaks.py | Python | gpl-3.0 | 3,840 | [
"Gaussian"
] | dd6100a67b139132a0c05a969160e1a14de7e32f18968701f8ba0f4ebbce6274 |
# coding: utf-8
import json
import os
import unittest
from pymatgen.analysis.wulff import WulffShape
from pymatgen.core.lattice import Lattice
from pymatgen.core.structure import Structure
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from pymatgen.util.coord import in_coord_list
from pymatgen.util.testin... | gmatteo/pymatgen | pymatgen/analysis/tests/test_wulff.py | Python | mit | 7,525 | [
"pymatgen"
] | fcda1a7fe5b00ef0e9c61e1493c30a0978b0ac19ac9dae4d54f98b66b9ee4229 |
# Copyright 2017-2020 The GPflow Contributors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appli... | GPflow/GPflow | gpflow/kernels/periodic.py | Python | apache-2.0 | 3,848 | [
"Gaussian"
] | d2479a776f794f552f4f246dea4072889a20327a0960ea50b8cd987ac48a32cb |
# This file is part of Buildbot. Buildbot 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, version 2.
#
# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without eve... | seankelly/buildbot | master/buildbot/test/unit/test_steps_shell.py | Python | gpl-2.0 | 43,221 | [
"exciting"
] | db667302d3e597484020c92c662c8b5bc3dff0383aa86c1cdbace256e4c18b06 |
#!/usr/bin/env python3
import argparse
import glob
import os
import time
import random
COLOURS = (b'\xFF\x00\x00', b'\x00\xFF\x00', b'\x00\x00\xFF', b'\xFF\xFF\x00', b'\xFF\x00\xFF', b'\x00\xFF\xFF')
def write_binary(driver_path, device_file, payload):
with open(os.path.join(driver_path, device_file), 'wb') as ... | z3ntu/razer-drivers | scripts/driver/firefly/test.py | Python | gpl-2.0 | 5,522 | [
"Firefly"
] | 6cb3e81b7895b23bfe2fcc90d4a18b49f293e5791c168f9c33c41810363fa2c0 |
#!/usr/bin/env python
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
A convenience script engine to read Gaussian output in a directory tree.
"""
import argparse
import logging
import multiprocessing
import os
import re
from tabulate import tabulate... | davidwaroquiers/pymatgen | pymatgen/cli/gaussian_analyzer.py | Python | mit | 3,013 | [
"Gaussian",
"pymatgen"
] | 19e011f0d62179ff08c06eb595b0118d4c683c4e23a1ac4dd19f517a7b18fa19 |
"""
Test course discovery.
"""
import datetime
import json
import uuid
from common.test.acceptance.tests.helpers import AcceptanceTest, remove_file
from common.test.acceptance.pages.common.logout import LogoutPage
from common.test.acceptance.pages.studio.auto_auth import AutoAuthPage
from common.test.acceptance.pages.... | caesar2164/edx-platform | common/test/acceptance/tests/lms/test_lms_course_discovery.py | Python | agpl-3.0 | 2,206 | [
"VisIt"
] | 67de0e8ffd225a8b1a502e42e09fc8f517c84180690e0865be231243d41e0405 |
#!/usr/bin/env python
"""Cross-validation test main
Script for running cross-valiation performance test
Examples:
To run subtyping routine on Stx1 genes:
$ python main.py subtype ../phylotyper_example.ini ecoli_stx1 test/ecoli_stx1.ffn output/test/
"""
import argparse
import csv
import inspect
import... | superphy/insilico-subtyping | phylotyper/performance/cv.py | Python | apache-2.0 | 16,044 | [
"BLAST"
] | 7985e7003dc9964cea51e630b5fa020af12b39791b46e9df6bc5b3aff5fda15a |
"""This module handles resolution of SoftwareRequirement hints.
This is accomplished mainly by adapting cwltool internals to galaxy-lib's
concept of "dependencies". Despite the name, galaxy-lib is a light weight
library that can be used to map SoftwareRequirements in all sorts of ways -
Homebrew, Conda, custom scripts... | dleehr/cwltool | cwltool/software_requirements.py | Python | apache-2.0 | 5,316 | [
"Galaxy"
] | e1aadf438e3080934b53b2ac53e372be6b1f1c7165e85bda1ea562895087e736 |
# Licensed GNU Affero GPL v3 or later: http://www.gnu.org/licenses/agpl.html
import Config, Statistics, collections
import HtmlStmt # tidy_html, with_tags for DIV, PRE, A, etc
class TopVisits (Statistics.GaugeIface):
def __init__ (self, statistics):
super (self.__class__, self).__init__ (statistics)
self.NN ... | tim-janik/tobin | TopVisits.py | Python | agpl-3.0 | 3,073 | [
"VisIt"
] | 47c02fc79043daa13da0451bf52031e6b590beb697540b38f9194a0b213e2503 |
# coding: utf-8
# Copyright (c) Henniggroup.
# Distributed under the terms of the MIT License.
from __future__ import division, print_function, unicode_literals, \
absolute_import
"""
Put data into mongo database
"""
from six.moves import range
import sys
import os
import json
import logging
import socket
impor... | henniggroup/MPInterfaces | mpinterfaces/database.py | Python | mit | 9,981 | [
"CRYSTAL",
"VASP",
"pymatgen"
] | 9fdd400ad1a6c3701716e3199c40a9327b59160ce99808151f7a71221fe919fb |
"""
JSON serialization and deserialization utilities.
"""
from __future__ import absolute_import, unicode_literals
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2014, The Materials Virtual Lab"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "ongsp@ucsd.edu"
__date__ = "1/24/14"
import j... | gpetretto/monty | monty/json.py | Python | mit | 8,247 | [
"pymatgen"
] | e8b7c327154c35dca6cd061c23072a36b858d83e0ec996673c57f48b799e839e |
# coding: utf-8
# #Statistical Inference for Everyone: Technical Supplement
#
#
#
# This document is the technical supplement, for instructors, for [Statistical Inference for Everyone], the introductory statistical inference textbook from the perspective of "probability theory as logic".
#
# <img src="http://web... | bblais/Tech-SIE | Estimating_Difference_Between_Means/Estimating_Difference_Between_Means.py | Python | mit | 7,551 | [
"Gaussian"
] | a36a24edab3217ef68d70989d0a07ad083d1ac4ffef656c8a5f7d4df425c646b |
""" DIRAC FileCatalog mix-in class to manage users and groups from the CS Registry
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import time
import threading
from DIRAC import S_OK, S_ERROR, gConfig, gLogger
from DIRAC.DataManageme... | yujikato/DIRAC | src/DIRAC/DataManagementSystem/DB/FileCatalogComponents/UserGroupManager/UserAndGroupManagerCS.py | Python | gpl-3.0 | 1,877 | [
"DIRAC"
] | 52725d3e66b2d9e8ec8b505dbb632dae549f318a6c3895f1eaee0a66c6d98706 |
#!/usr/bin/python
from django.core.management.base import BaseCommand, CommandError
import contacts.models as cont
import backend.models as back
import transports.africas_talking.api as at
import datetime as dt
from django.db import models
from django.db.models import Count
import code, os
def count_field(qs,field):
... | tperrier/mwachx | utils/management/commands/qshell.py | Python | apache-2.0 | 2,687 | [
"VisIt"
] | 81b3a080aac6fe8f0d4a2b06bedb3414fea994256e437228460e6a8de19b8359 |
#!/usr/bin/env python
# ============================================================================
# Project Name : iTrade
# Module Name : itrade_wxabout.py
#
# Description: wxPython About box
#
# The Original Code is iTrade code (http://itrade.sourceforge.net).
#
# The Initial Developer of the Original Cod... | eternallyBaffled/itrade | itrade_wxabout.py | Python | gpl-3.0 | 8,786 | [
"ASE"
] | 53e01f013b68e0bbbf8a108f8bfb256a170e9c38ecbf8250901defe7f2b7ea9e |
# Copyright Yair Benita Y.Benita@pharm.uu.nl
# Biopython (http://biopython.org) license applies
"""Calculate isoelectric points of polypeptides using methods of Bjellqvist.
pK values and the methos are taken from:
* Bjellqvist, B.,Hughes, G.J., Pasquali, Ch., Paquet, N., Ravier, F., Sanchez,
J.-Ch., Frutiger, S. & H... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/SeqUtils/IsoelectricPoint.py | Python | gpl-2.0 | 4,300 | [
"Biopython"
] | 8323fba986433f6764d1a5f972338adc9869f7f8ff1743cf71b10a198cf99613 |
from django.contrib.auth.models import User
from django.db import models
class WebPage(models.Model):
user = models.ForeignKey(User)
main_domain = models.CharField(max_length=20)
page_id = models.CharField(max_length=20)
selected = models.BooleanField(default=False)
def __unicode__(self):
... | sasasaftic/owatam | analysis/models.py | Python | mit | 3,610 | [
"VisIt"
] | cf5d304b3adf17b6c9fb38dddfcd741f696a3c5b04fdb10ddb404cd34a8e9525 |
#! /usr/bin/python
from setuptools import setup
def readme() :
with open('README.md') as f:
return f.read()
setup(name='BreaKmer',
version='0.0.7',
description='Structural variation detection tool, designed for targeted sequencing data.',
long_description=readme(),
url='https://github.c... | a-bioinformatician/BreaKmer | setup.py | Python | mit | 570 | [
"Biopython",
"pysam"
] | 80ce3cb8961963ef12c5314fbc96082d08cc217e9f8b2bd91c387e667d0d09d4 |
#!/usr/bin/env python
# moosegui.py ---
#
# Filename: moosegui.py
# Description:
# Author: subhasis ray
# Maintainer:
# Created: Wed Jan 20 15:24:05 2010 (+0530)
# Version:
# Last-Updated: Wed Nov 2 16:54:31 2011 (+0530)
# By: Subhasis Ray
# Update #: 2674
# URL:
# Keywords:
# Compatibility:
#
#... | BhallaLab/moose-thalamocortical | pymoose/gui/qt/moosegui.py | Python | lgpl-2.1 | 82,895 | [
"MOOSE"
] | 18b2b45685d011b64ca7567973689ff65e1172abc6c78f41abbc6d7dd5534692 |
# -*- coding: utf-8 -*-
"""
--------------------------------------------------------------------------
glmnet.py:
Fit a GLM with lasso or elastic-net regularization.
glmnet.py provides a wrapper to the glmnet fortran routines. All
variables in the arguments are keyword-only. (see examples below).
--------... | hanfang/glmnet_python | glmnet_python/glmnet.py | Python | gpl-2.0 | 19,010 | [
"Gaussian"
] | 0150475e4dd7d8fc2b3a6382a33a15781040a0eff1d7036c49689ba3e253909c |
# -*- coding: utf-8 -*-
#!/usr/bin/python
"""Test of line navigation output of Firefox on bugzilla's advanced
search page.
"""
from macaroon.playback import *
import utils
sequence = MacroSequence()
########################################################################
# We wait for the focus to be on a blank Fir... | h4ck3rm1k3/orca-sonar | test/keystrokes/firefox/label_guess_bugzilla_search.py | Python | lgpl-2.1 | 24,546 | [
"ORCA"
] | 08fa7b3ba9779f026fac888cff837b3f434123d3f5f80a3bfc01787a723ff433 |
"""
Portable Executable (PE) 32 bit, little endian
Used on MSWindows systems (including DOS) for EXEs and DLLs
1999 paper:
http://download.microsoft.com/download/1/6/1/161ba512-40e2-4cc9-843a-923143f3456c/pecoff.doc
2006 with updates relevant for .NET:
http://download.microsoft.com/download/9/c/5/9c5b2167-8017-4bae-9... | gkonstantyno/construct | construct/formats/executable/pe32.py | Python | mit | 11,713 | [
"MOE"
] | e4f0785d5a6f17fe119beb739c33f4df07a103bd8cdb5398a065b5b567907273 |
# Copyright 2012 by Wibowo Arindrarto. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Bio.SearchIO objects to model similarity search program outputs.
The SearchIO object m... | zjuchenyuan/BioWeb | Lib/Bio/SearchIO/_model/__init__.py | Python | mit | 2,396 | [
"Biopython"
] | 05bfb06b9dfc6c2adefd64164d0c16c7e146b191f5968df3b3cc32082c5f9069 |
import os
import sys
import types
import re
from numpy.core.numerictypes import issubclass_, issubsctype, issubdtype
from numpy.core import product, ndarray
__all__ = ['issubclass_', 'get_numpy_include', 'issubsctype', 'issubdtype',
'deprecate', 'deprecate_with_doc', 'get_numarray_include',
'get_inclu... | Ademan/NumPy-GSoC | numpy/lib/utils.py | Python | bsd-3-clause | 36,140 | [
"VisIt"
] | 66306672da027cc5cb5bdb801545f8aadc0ce14e9ce6c1f8c4c8c7787919555b |
# This script is part of pymaid (http://www.github.com/schlegelp/pymaid).
# Copyright (C) 2017 Philipp Schlegel
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of ... | schlegelp/pymaid | pymaid/cytoscape.py | Python | gpl-3.0 | 14,485 | [
"Cytoscape",
"NEURON"
] | d59c98a174d7d201d55bd4785d1d658aec74038856a99adf69491cbac3ce2d08 |
from __future__ import absolute_import, division, print_function
from trakt.core.helpers import popitems
from trakt.interfaces.base import Interface, authenticated, application
class ScrobbleInterface(Interface):
path = 'scrobble'
@application
@authenticated
def action(self, action, movie=None, show... | gborri/SickRage | sickrage/libs/trakt/interfaces/scrobble.py | Python | gpl-3.0 | 11,824 | [
"Galaxy"
] | b44d136c8eb0cc86deede0327150edd887a730d84ca2e7a802526409c4fc7e19 |
# Copyright 2009 by Peter Cock. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Runs a few EMBOSS tools to check our wrappers and parsers."""
import os
import sys
import unit... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_Emboss.py | Python | gpl-2.0 | 41,766 | [
"Biopython"
] | d5a0151f422b218f116d4e98276249faee49fe8ade376495874154f966586235 |
"""
Tests for materialized_variant_filter.py.
"""
import os
from django.db import connection
from django.contrib.auth.models import User
from django.test import TestCase
from sympy.core.function import sympify
from main.models import AlignmentGroup
from main.models import Chromosome
from main.models import Dataset
f... | woodymit/millstone_accidental_source | genome_designer/variants/tests/test_materialized_variant_filter.py | Python | mit | 25,546 | [
"BWA"
] | 6c936eff9d827ee0f940338b2f03f5fbaa527dad20a5b970fdfb5ce6ebe72c95 |
#! /usr/bin/env python
"""Simple test script for imgfile.c
Roger E. Masse
"""
from test_support import verbose, unlink, findfile
import imgfile, uu, os
def main():
uu.decode(findfile('testrgb.uue'), 'test.rgb')
uu.decode(findfile('greyrgb.uue'), 'greytest.rgb')
# Test a 3 byte colo... | DarioGT/OMS-PluginXML | org.modelsphere.sms/lib/jython-2.2.1/Lib/test/test_imgfile.py | Python | gpl-3.0 | 4,325 | [
"Gaussian"
] | 6f4125d3b5d84e3a0f1fbe6e3e8b11b676589dea721372f5ac1d68d80a99d208 |
import numpy as np
from scipy.stats import norm as normal
from sklearn.neighbors import NearestNeighbors
import matplotlib.pyplot as pl
from matplotlib import rcParams
from scvelo.tools.utils import groups_to_bool
from scvelo.tools.velocity_embedding import quiver_autoscale, velocity_embedding
from .docs import doc_p... | theislab/scvelo | scvelo/plotting/velocity_embedding_grid.py | Python | bsd-3-clause | 10,757 | [
"Gaussian"
] | eec26f55b025bd6aac4d0c3540db978ba9024032775498f9206d1dc13be42b49 |
#!/usr/bin/env python
# spud - keep track of photos
# Copyright (C) 2008-2013 Brian May
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) ... | brianmay/spud | setup.py | Python | gpl-3.0 | 3,634 | [
"Brian"
] | ef67fcd763890755f612ad8e784dcab4bf8e329e307baa9f4ab6e9e3bc3587b4 |
class County():
def county_finder(code):
dict = {
'01000': 'Alabama', '01001': 'Autauga County', '01003': 'Baldwin County', '01005': 'Barbour County',
'01007': 'Bibb County', '01009': 'Blount County', '01011': 'Bullock County', '01013': 'Butler County',
'01015': 'Calhoun County', '01017': 'Chambers County',... | toms3t/Propalyzer | propalyzer_site/propalyzer_app/county.py | Python | mit | 89,257 | [
"COLUMBUS",
"Elk"
] | 43c904e088aeee5277c922d7fbb63f4fab87ff18430a1002f19ae7e3879b0253 |
"""
BIANA: Biologic Interactions and Network Analysis
Copyright (C) 2009 Javier Garcia-Garcia, Emre Guney, Baldo Oliva
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 vers... | emreg00/biana | biana/BianaObjects/sequenceUtilities.py | Python | gpl-3.0 | 48,971 | [
"BLAST"
] | bcbf8114f57ff47482d3e1c585eee8c79b8366d3fa97ada3615d072da5d00770 |
from asap3 import *
from numpy import *
from asap3.testtools import ReportTest
from ase.lattice.cubic import *
from OpenKIM_modelname import openkimmodel
element = 'Au'
sizes = arange(10,0,-1)
energy = None
force = None
for s in sizes:
atoms = FaceCenteredCubic(symbol=element, size=(s,s,s), pbc=True)
uc = a... | auag92/n2dm | Asap-3.8.4/Test/SizeConsist_LeftHand.py | Python | mit | 1,320 | [
"ASE"
] | 519b82799726bc174e8f218aa10cc69b53da9933a0d04ba76b5498b057a21b07 |
# 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... | indhub/mxnet | python/mxnet/symbol/random.py | Python | apache-2.0 | 12,198 | [
"Gaussian"
] | 94686025e3df661a84939206ad61280a7bb62157342986db2f1ace23816e2efe |
#pylint: disable=no-init,invalid-name
"""
System test that loads TOPAZ single-crystal data,
converts to Q space, finds peaks and indexes
them.
"""
from __future__ import (absolute_import, division, print_function)
import stresstesting
import numpy
from mantid.simpleapi import *
class TOPAZPeakFinding(stresstesting.Ma... | ScreamingUdder/mantid | Testing/SystemTests/tests/analysis/TOPAZPeakFinding.py | Python | gpl-3.0 | 5,516 | [
"CRYSTAL"
] | 8c80b46dcfa8f41139322d517051f9b0d33565b6b4b0609a5e40db30382f22b6 |
#===============================================================================
# LICENSE XOT-Framework - CC BY-NC-ND
#===============================================================================
# This work is licenced under the Creative Commons
# Attribution-Non-Commercial-No Derivative Works 3.0 Unported Li... | SMALLplayer/smallplayer-image-creator | storage/.xbmc/addons/net.rieter.xot.smallplayer/resources/libs/helpers/taghelperbase.py | Python | gpl-2.0 | 3,175 | [
"VisIt"
] | 676b09436fe9499cd27d6b93b0df372c6ff62bcf723d3c6d48f4dcfadfe32ca3 |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
A simple example of using solvent model in the mean-field calculations.
'''
from pyscf import gto
from pyscf import scf
from pyscf import dftd3
mol = gto.Mole()
mol.atom = ''' O 0.00000000 0.00000000 -0.11081188
H -0.0... | gkc1000/pyscf | examples/dftd3/00-hf_with_dftd3.py | Python | apache-2.0 | 526 | [
"PySCF"
] | ecd38a346583d5ea804a30694c8293d2e1cae526f413a9d0f75904814ac9f404 |
# 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.
# Ian Kenney's pytest-gmx plugin
# https://github.com/ianmkenney/pytest-gmx/
import pytest
def pytest_addoption(parser):
... | PicoCentauri/GromacsWrapper | gromacs/tests/conftest.py | Python | gpl-3.0 | 750 | [
"Gromacs"
] | 6c139f117a11ab511016edfde2ee957a89ec710dfcd18b0875a6152473e16e93 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kratman/psi4public | psi4/src/psi4/libfunctional/matlab/mfiles/assemble.py | Python | gpl-2.0 | 2,877 | [
"Psi4"
] | 7792d6a3512fe463536a3aa16df68c8df9f651a3dc5f0fbb9cc6805feb3527de |
# -*-python-*-
#
# Copyright (C) 1999-2013 The ViewCVS Group. All Rights Reserved.
#
# By using this file, you agree to the terms and conditions set forth in
# the LICENSE.html file which can be found at the top level of the ViewVC
# distribution or at http://viewvc.org/license-1.html.
#
# For more information, visit h... | marcellodesales/svnedge-console | svn-server/lib/viewvc/vclib/ccvs/rcsparse/__init__.py | Python | agpl-3.0 | 704 | [
"VisIt"
] | 68ee77e66fcc9f1ead5ccc37585c1a7f4b83ce23b79b0ca809250b0070017b9c |
import re
# taken from Python 3 html module
"""HTML character entity references."""
# maps the HTML5 named character references to the equivalent Unicode character(s)
_html5 = {
'Aacute': '\xc1',
'aacute': '\xe1',
'Aacute;': '\xc1',
'aacute;': '\xe1',
'Abreve;': '\u0102',
'abreve;': '\u0103',
... | atodorov/django-phpbb-static-html | html.py | Python | mit | 58,739 | [
"Bowtie"
] | 7ca52141f754849f0235c2e9d723dffe92424bcccb80f9d2a187f81e12cb2f19 |
# -*- coding: utf-8 -*-
# -----------------------------------------------------------------------
# Copyright (c) 2009 Jendrik Seipp
#
# RedNotebook 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 vers... | tomka/rednotebook | rednotebook/gui/menu.py | Python | gpl-2.0 | 12,086 | [
"VisIt"
] | 57b634118037117c50e85636040a340b02de263c5cb2558ee6c1d6e4ee18ac39 |
#! /usr/bin/env python
#
# Copyright (C) 2008 Lorenzo Pallara, l.pallara@avalpa.com
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any... | aventuri/opencaster | tutorials/mhp-streamevents/mhpconfig2.py | Python | gpl-2.0 | 14,727 | [
"Yambo"
] | 2d0c4ed0d28d3220074c419a1dcf9c5160fa786358fcab7a4a2c79d1a62bcf6d |
"""White Matter Tract Segmentation as Multiple Linear Assignment Problems
"""
import numpy as np
from dissimilarity import compute_dissimilarity, dissimilarity
from dipy.tracking.distances import bundles_distances_mam
from sklearn.neighbors import KDTree
from nibabel import trackvis
from dipy.tracking.utils import len... | nusratsharmin/Tract_segmentation_as_Multiple_LAP | segmentation_as_NN_and_lap.py | Python | mit | 13,236 | [
"VTK"
] | 04b14e4d6e45f9ef90a32b16edef930e6902cead286eca7ae4cd876ebc28889c |
#!/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... | sunqm/pyscf | pyscf/hessian/test/test_uhf.py | Python | apache-2.0 | 1,735 | [
"PySCF"
] | d70402566179ea51a03a9027ad1d4cecbc72afe5d99288044bf8d6ce2bfae63c |
import sys
import os
import re
import codecs
from setuptools import setup, find_packages
from setuptools.command.test import test as TestCommand
class Tox(TestCommand):
def finalize_options(self):
TestCommand.finalize_options(self)
self.test_args = []
self.test_suite = True
def run_t... | jthi3rry/django-pods | setup.py | Python | mit | 1,957 | [
"VisIt"
] | 9b4cdfaf39654dba55aa2b7dab46ffafbdc9f08b666398ea641d1ceef0ff5c73 |
# Copyright (c) 2002 Autonomous Zone Industries
# Copyright (c) 2003 Bryce "Zooko" Wilcox-O'Hearn
# 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.
"""
@see ListenerManager class
"""
__version__ = "$Revision: 1.11 $"
#... | zooko/egtp_new | egtp/ListenerManager.py | Python | lgpl-2.1 | 6,624 | [
"VisIt"
] | 38514ba53972aa5dc6cc473b8902ffb4ff1c729124c909c62e44768633a42004 |
from WebAppDIRAC.Lib.WebHandler import WebHandler, WErr, WOK, asyncGen
from DIRAC import gConfig, S_OK, S_ERROR, gLogger
from DIRAC.Core.Utilities import Time
import json
class ApplicationWizardHandler(WebHandler):
AUTH_PROPS = "authenticated"
| atsareg/WebAppDIRAC | WebApp/handler/ApplicationWizardHandler.py | Python | gpl-3.0 | 254 | [
"DIRAC"
] | ae96bdf37e5627fbe5d7080f479ac7e47cffccd4b71f011de3f43bab20d19792 |
#!/usr/bin/env python
import pyfits
import numpy as np
import matplotlib.pyplot as pl
from astro.io import saveobj
from astro.utilities import between, adict
from astro.convolve import convolve_psf
from astro.spec import find_cont
import astro.sed as sed
from VIMOS_util import \
get_object_IDs, get_1st_order_reg... | nhmc/findz_VIMOS | findz_VIMOS.py | Python | bsd-3-clause | 8,989 | [
"Gaussian"
] | 4370e1cc0d562ba10360afd6d90a488286d496192dfcaff69af92d1a8d2eafa3 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | kyleabeauchamp/mdtraj | mdtraj/testing/docstrings.py | Python | lgpl-2.1 | 8,819 | [
"MDTraj"
] | 918bca2ea7fc001a838f3811689cbd71a1ea5f19a3cd0e0f005e062f4a281730 |
# ICE Revision: $Id$
"""Reads configuration-files that define defaults for various PyFoam-Settings
Also hardcodes defaults for the settings"""
from PyFoam.ThirdParty.six.moves import configparser
from PyFoam.ThirdParty.six import iteritems,PY3
from PyFoam.Infrastructure.Hardcoded import globalConfigFile,userConfigF... | takaakiaoki/PyFoam | PyFoam/Infrastructure/Configuration.py | Python | gpl-2.0 | 12,856 | [
"ParaView"
] | 71aba07c229ff0bf87e5104a7992b448bc4c9828ea5b340cdc1c33a9dee3f20d |
# Python Imports
import datetime
# Rest Framework Imports
from rest_framework import serializers
from rest_framework import viewsets
from rest_framework.decorators import detail_route, list_route
from rest_framework.response import Response
#Local Imports
import contacts.models as cont
from messages import Participan... | I-TECH-UW/mwachx | contacts/serializers/visits.py | Python | apache-2.0 | 4,325 | [
"VisIt"
] | 3339221f813b2e2804f437c3b80dfe2e078b9db13afa34188e079bf2741cdc2a |
import re
import warnings
from datetime import datetime
from distutils.version import LooseVersion
from functools import partial
import numpy as np
import pandas as pd
from pandas.errors import OutOfBoundsDatetime
from ..core import indexing
from ..core.common import contains_cftime_datetimes
from ..core.formatting i... | jhamman/xarray | xarray/coding/times.py | Python | apache-2.0 | 17,150 | [
"NetCDF"
] | 87e49e6ed55a008bdc39a4fc5c593ab2673783afd0980759ce5ba6899ce72f67 |
"""
********************************************************************************
* Name: workspace.py
* Author: tbayer
* Created On: February 5, 2019
* Copyright: (c) Aquaveo 2018
********************************************************************************
"""
from django.contrib.auth.models import User
from te... | tethysplatform/tethys | tethys_quotas/handlers/workspace.py | Python | bsd-2-clause | 2,023 | [
"VisIt"
] | d7a1c7ce2e0a920c5618658888333f287ef8c07c9ae3b1e3174671f056e7b683 |
from __future__ import print_function
""" class Wannier provides the function get_wannier_localization_matrix and initial_wannier.
"""
import numpy as np
from Scientific.IO.NetCDF import NetCDFFile as netCDF
def dagger(matrix,copy=1):
# First change the axis: (Does not allocate a new array)
matrix_con... | suttond/MODOI | ase/calculators/jacapo/utils/wannier.py | Python | lgpl-3.0 | 24,405 | [
"ASE",
"NetCDF"
] | 23f27ce67bc2b2675ef579086440b5ff731eb07bb6b3976da55c6b2410b3c28e |
import random
import numpy as np
import matplotlib.pyplot as pp
import recog.dict.facedicts as facedicts
import recog.opt.shrinkers as shrinkers
import recog.opt.salsa as salsa
import recog.faces.classify as classify
import recog.dct2_xforms as dct
import recog.faces.distortions as fd
N = 1200
## N = 50
shape = (192,1... | miketrumpis/machine_learning_project | scripts/sparse_error_classify.py | Python | bsd-2-clause | 3,685 | [
"Gaussian"
] | 4a82a4a7a2db1cec5c555915c915784a6b0b67f49c5360de4531640ddd6831d7 |
""" Implements ThreadActor """
from concurrent.futures import _base
from concurrent.futures import thread
from ibeis.web.futures_utils import _base_actor
import queue
import threading
import weakref
# Most of this code is duplicated from the concurrent.futures.thread and
# concurrent.futures.process modules, writen by... | Erotemic/ibeis | ibeis/web/futures_utils/thread_actor.py | Python | apache-2.0 | 4,873 | [
"Brian"
] | 705230dcdbea81886bd7c0afb0fcc557b0e85de65f7545c77d20b5d4e484bd95 |
from math import pi
import numpy as np
from ase import Atoms
from ase.units import Hartree, Bohr
from gpaw import GPAW
from gpaw.xc import XC
from gpaw.test import equal
from gpaw.xc.kernel import XCNull
from gpaw.poisson import NoInteractionPoissonSolver
a = 4.0
x = Atoms(cell=(a, a, a)) # no atoms
class Harmoni... | robwarm/gpaw-symm | gpaw/test/harmonic.py | Python | gpl-3.0 | 1,021 | [
"ASE",
"GPAW"
] | 1d6d54ed9c9ccb5fcb53069b4886e5475871609592fa7b10cd5b9f7cab6fea74 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | lgarren/spack | var/spack/repos/builtin/packages/adios/package.py | Python | lgpl-2.1 | 6,439 | [
"NetCDF"
] | b25d695ace36751f2caa922a39724078d31cae5da5f3907e03cc98806fbb9890 |
__all__ = ['fixed_quad','quadrature','romberg','trapz','simps','romb',
'cumtrapz','newton_cotes','composite']
from scipy.special.orthogonal import p_roots
from scipy.special import gammaln
from numpy import sum, ones, add, diff, isinf, isscalar, \
asarray, real, trapz, arange, empty
import numpy as np... | jasonmccampbell/scipy-refactor | scipy/integrate/quadrature.py | Python | bsd-3-clause | 25,374 | [
"Gaussian"
] | caf0fb0aaea87da8defcf7c7d8580e773384f4cf7b031f68a9f8bb54c79442a9 |
# coding=utf-8
"""Building and simulating spiking neural networks using Neuron.
All the work is done in pyNN, so we simply redirect :py:mod:`neuron_target_sim`
to :py:mod:`pyNN_target_sim` here.
@author: rbodo
"""
# noinspection PyUnresolvedReferences
from snntoolbox.simulation.target_simulators.pyNN_target_sim impo... | NeuromorphicProcessorProject/snn_toolbox | snntoolbox/simulation/target_simulators/neuron_target_sim.py | Python | mit | 327 | [
"NEURON"
] | 5fde1372b6e4f474e19b1c941da2d4a70db1057ec8aa2f0f675ea16f14b27c34 |
from edc_visit_schedule import FormsCollection, Crf, Requisition
from edc_visit_schedule import VisitSchedule, Schedule, Visit
from dateutil.relativedelta import relativedelta
app_label = 'edc_offstudy'
crfs = FormsCollection(
Crf(show_order=1, model=f'{app_label}.crfone', required=True),
)
visit0 = Visit(
... | botswana-harvard/edc-offstudy | edc_offstudy/tests/visit_schedule.py | Python | gpl-2.0 | 1,874 | [
"VisIt"
] | 4e8bdc7aad35cabb3c610b7e1ef668c85eef3fc8b0a7a90476563bc97c8f7e8a |
from pysimm import system, lmps, forcefield
def run(test=False):
# use a smiles string to query the pubchem search database and read the mol file returned from the http request
try:
s = system.read_pubchem_smiles('CO')
except:
import os
s = system.read_mol(os.path.join(os.path.dirna... | polysimtools/pysimm | Examples/02_methanol/dreiding/create.py | Python | mit | 898 | [
"LAMMPS"
] | fbfed320f44a61f8e5848f5014d1b8c07c6ae927489827295b1a8b528e7a9232 |
# force floating point division. Can still use integer with //
from __future__ import division
# other good compatibility recquirements for python3
from __future__ import absolute_import
from __future__ import print_function
from __future__ import unicode_literals
# This file is used for importing the common utilities ... | prheenan/Research | Perkins/Projects/DNA/protein-interactions/prc2/bulk_analysis/main_bulk_analysis.py | Python | gpl-3.0 | 16,301 | [
"Gaussian"
] | 282798ea98b05d15dc7275400cc4109f65ae940ae65ca3154f7f5187ad44befc |
# 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)
import glob
from os import chmod
from spack import *
class Mirdeep2(Package):
"""miRDeep2 is a completely overhaule... | LLNL/spack | var/spack/repos/builtin/packages/mirdeep2/package.py | Python | lgpl-2.1 | 1,910 | [
"Bowtie"
] | 6d689504ff7a4f00b1bc33d275c5542e731027b2dd6e9579e8224cfbdefa405f |
"""
Instructor Dashboard Views
"""
import logging
import datetime
from opaque_keys import InvalidKeyError
from opaque_keys.edx.keys import CourseKey
import uuid
import pytz
from django.contrib.auth.decorators import login_required
from django.views.decorators.http import require_POST
from django.utils.translation imp... | B-MOOC/edx-platform | lms/djangoapps/instructor/views/instructor_dashboard.py | Python | agpl-3.0 | 26,360 | [
"VisIt"
] | 403a566325f9ebfc1f5b4dd6a126ed60d56f4ad27bc9e64afdae77dac427f053 |
import sys
from getch import getch
commands = '><+-.,[]'
class BrainfuckInterpreter:
def __init__(self):
self.i = 0
self.p = 0
self.cells = [0]
@staticmethod
def find_matching_paren(source, c):
paren = 0
d = {'[':']', ']':'['}
for k in range(len(source)):
... | handrake/brainfuck | brainfuck.py | Python | bsd-3-clause | 2,763 | [
"VisIt"
] | c1530a22887153438fe5f87d5781f340067e5e92123abd190024665f73a2ac15 |
#!/usr/bin/env python
'''
File name: main_make_map.py
Author: Guillaume Viejo
Date created: 28/09/2017
Python Version: 3.5.2
To make shank mapping
'''
import numpy as np
import pandas as pd
# from matplotlib.pyplot import plot,show,draw
import scipy.io
from functions import *
from pylab import *
from sklear... | gviejo/ThalamusPhysio | python/main_make_map_from_clustering.py | Python | gpl-3.0 | 10,594 | [
"NEURON"
] | 730b212849b5330e30c1758fa620f432069e5a95c5ad3afd04ab5547954f1134 |
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