text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
#Copyright ReportLab Europe Ltd. 2000-2012
#see license.txt for license details
#history http://www.reportlab.co.uk/cgi-bin/viewcvs.cgi/public/reportlab/trunk/reportlab/pdfbase/cidfonts.py
#$Header $
__version__=''' $Id$ '''
__doc__="""CID (Asian multi-byte) font support.
This defines classes to represent CID fonts. ... | Microvellum/Fluid-Designer | win64-vc/2.78/python/lib/reportlab/pdfbase/cidfonts.py | Python | gpl-3.0 | 18,856 | [
"Brian"
] | 48c50c1e1c0cf536f582710f57f6f610bfca7f880c21330385770a2c7fb920a0 |
# runs after the job (and after the default post-filter)
from galaxy import datatypes, jobs
def validate(incoming):
"""Validator"""
#raise Exception, 'not quite right'
pass
def exec_before_job( trans, inp_data, out_data, param_dict, tool=None):
"""Sets the name of the data"""
outputType = param_di... | jmchilton/galaxy-central | tools/data_source/ucsc_filter.py | Python | mit | 2,608 | [
"Galaxy"
] | 3220bec99d1f27e37beb728a29dbf2760192b2ab39fe777f2ca2ed60c2571340 |
""" NOTA BENE: This agent should NOT be run alone. Instead, it serves as a base class for extensions.
The TaskManagerAgentBase is the base class to submit tasks to external systems,
monitor and update the tasks and file status in the transformation DB.
This agent is extended in WorkflowTaskAgent and Reque... | sposs/DIRAC | TransformationSystem/Agent/TaskManagerAgentBase.py | Python | gpl-3.0 | 24,781 | [
"DIRAC"
] | 93ea660fab2b2bc74a30c758f78cf6a4f304e89895e2535712fd84d18704cf48 |
#!/usr/bin/env python
"""moose_methods.py: Some helper function related with moose to do multiscale
modelling.
Last modified: Thu Jun 05, 2014 01:20AM
"""
__author__ = "Dilawar Singh"
__copyright__ = "Copyright 2013, NCBS Bangalore"
__credits__ = ["NCBS Bangalore", "Bhalla Lab"]
__li... | rahulgayatri23/moose-core | python/libmumbl/helper/moose_methods.py | Python | gpl-3.0 | 5,570 | [
"MOOSE"
] | bb551f126def14add249fface72d112d6e138489f9e877c93a0b5f2184c149f8 |
import asyncio
import logging
from copy import deepcopy
import discord
from redbot.core import Config, bank
from collections import namedtuple
from .cache import OldMessageTypeManager
from .utils import is_input_unsupported, min_int, max_int
user_defaults = {
"Pending_Credits": 0,
"Membership": {"Name": "Bas... | ARG-TLQ/Red-DiscordBot | cogs/casino/data.py | Python | gpl-3.0 | 14,355 | [
"CASINO"
] | 715da2eb04c5fab2375cfe45e27d5dbfd6da5ab012b2667fe4868580135f120b |
# -*- coding: utf-8 -*-
"""
Created on Mon Jan 19 16:53:16 2015
@author: rongen
"""
# -*- coding: utf-8 -*-
"""
Created on Mon Jan 12 16:51:34 2015
@author: rongen
"""
import mayavi.mlab as mlab
from tvtk.api import tvtk
from mayavi.modules.glyph import Glyph
from mayavi.tools.sources import MGlyphSource
import time... | grongen/point-cloud-visualization | filter_out_sea.py | Python | gpl-3.0 | 1,906 | [
"Mayavi"
] | 138565562258a0ba09b86252e80d688cc6208e8bbad81ca47ada6763b2c8136e |
"""
CBMPy: CBSolver2 module
=======================
PySCeS Constraint Based Modelling (http://cbmpy.sourceforge.net)
Copyright (C) 2009-2022 Brett G. Olivier, VU University Amsterdam, Amsterdam, The Netherlands
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General P... | SystemsBioinformatics/cbmpy | cbmpy/CBSolverX.py | Python | gpl-3.0 | 4,014 | [
"PySCeS"
] | 366d4eea826f4ec303e89ee0e1f855c4d74be942dc953adb7b4594a51e670e8c |
# -*- coding:Utf-8 -*-
"""
Body Class
===========
This class implements the body model
.. autoclass:: Body
:members:
Cylinder Class
==============
.. autoclass:: Cylinder
:members:
"""
#import mayavi.mlab as mlab
import os
import sys
import copy
import numpy as np
import scipy.stats as sp
if sys.version... | pylayers/pylayers | pylayers/mobility/ban/body.py | Python | mit | 97,549 | [
"Mayavi"
] | 356bc34b02fbb66be62075d426da88dcd9558c660febe7c9f9f58eb77781c0db |
from django.core.management.base import BaseCommand, AppCommand
from optparse import make_option
import os
class Command(BaseCommand):
option_list = AppCommand.option_list + (
make_option('--ext', action='store', dest='ext', default=None,
help="Extension to be used for rasters in folder."),
... | Alwnikrotikz/marinemap | lingcod/raster_stats/management/commands/update_rasterdatasets.py | Python | bsd-3-clause | 6,719 | [
"ADF"
] | fbee74ebff1783912af16f4d64cb47125544e3d9cf89deb6b61fbda81cdb65d3 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
## all SI units
########################################################################################
## Plot the firing rate vs current injection curve for a leaky integrate and fire neuron
## Author: Aditya Gilra
## Creation Date: 2012-06-08
## Modification Date: 2012-06-0... | h-mayorquin/camp_india_2016 | tutorials/chemical switches/moose/neuroml/LIF/FvsI_LIF.py | Python | mit | 2,004 | [
"MOOSE",
"NEURON"
] | 6c7e1626909b8de745c9786c2bfbdc66f2d62299a1ccff3353b273389db58091 |
# Copyright 2000 by Jeffrey Chang. 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.
"""This provides code for a general Naive Bayes learner.
Naive Bayes is a supervised classifi... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/NaiveBayes.py | Python | gpl-2.0 | 8,748 | [
"Biopython"
] | 1148e5c620724e95b93f746ee79c431d4bc581f29cf81488cc845a5837326d6f |
import csv
import numpy as np
import random
## Create a numpy array from the connectome csv file
## Delimiter and usecols params may have to be changed to match csv if using outside csv source
print 'Reading connectome file...'
with open('connectome.csv', 'rb') as connectomefile:
namesreadfile = np.genfromtxt(conne... | cmeresearch/epilepsymodeling | csvreader.py | Python | mit | 1,192 | [
"NEURON"
] | c4cb714ca9a5ab129e7f731fe4c83429c3b77c0ba4468c25366dcf2c47a7c191 |
# This file is part of Androguard.
#
# Copyright (C) 2012, Geoffroy Gueguen <geoffroy.gueguen@gmail.com>
# 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:/... | CZ-NIC/thug | src/Analysis/androguard/decompiler/dad/instruction.py | Python | gpl-2.0 | 38,507 | [
"VisIt"
] | 9e1fc4fb03310adde44ee133223947c816d05f9e171d9849acb0cf335ab80654 |
#
# QAPI parser test harness
#
# Copyright (c) 2013 Red Hat Inc.
#
# Authors:
# Markus Armbruster <armbru@redhat.com>
#
# This work is licensed under the terms of the GNU GPL, version 2 or later.
# See the COPYING file in the top-level directory.
#
from __future__ import print_function
import sys
from qapi.common imp... | marioli/qemu | tests/qapi-schema/test-qapi.py | Python | gpl-2.0 | 3,082 | [
"VisIt"
] | 00c5d22476c31657277eb9c667a70f7bae3eafabeb9a55a9ff1e738037960637 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# pyRunner.py
#
# Copyright 2010 dhatch387 (David Hatch) <dhatch387@gmail.com>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the... | dhatch/PyRunner | pyRunner.py | Python | gpl-2.0 | 52,273 | [
"Brian"
] | d9f08784b8e2aea57dcf3ddb1c3cd0e7d4b81988d0a5a25e0c805b07f250daa5 |
from astropy.table import Table
import matplotlib.pyplot as plt
import os
# read in data files
degas = Table.read(os.path.join(os.environ['SCRIPTDIR'],'degas_base.fits'))
stack = Table.read('/users/akepley/cv_lustre/degas/stack_test/test_mom1.fits')
dr1 = degas[degas['DR1'] == 1]
mymarkers = ['o','o','o','o','o','o'... | low-sky/degas | scripts/plot_LTIR_LHCN.py | Python | gpl-3.0 | 864 | [
"Galaxy"
] | 1340eac9e9676347d4cd641a063f2d57fa2d87300fbca0c884d164212cf0d1aa |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, division, print_function, unicode_literals
import os
import sys
from datetime import timedelta
import sentry_sdk
from sentry_sdk.integrations.celery import CeleryIntegration
from sentry_sdk.integrations.django import DjangoIntegration
from sentry_sdk.int... | Ilhasoft/ureport | ureport/settings_common.py | Python | agpl-3.0 | 54,471 | [
"BWA"
] | 1db3d00b753ed2a2a4e1fdbb36a8fad8e7d60736a93a5411247b4d59f5afc208 |
# Copyright 2008-2009 Brian Boyer, Ryan Mark, Angela Nitzke, Joshua Pollock,
# Stuart Tiffen, Kayla Webley and the Medill School of Journalism, Northwestern
# University.
#
# This file is part of django-facebookconnect.
#
# django-facebookconnect is free software: you can redistribute it and/or modify
# it under the te... | mapmyfitness/django-facebookconnect | facebookconnect/middleware.py | Python | gpl-3.0 | 4,679 | [
"Brian"
] | c4cef9699f978c17cc7efa42a3663a6c879c6d8885725bb36411a53cc8f34ed4 |
import os, sys
import numpy as np
import pandas as pd
from pytrack_analysis import Node
from pytrack_analysis.array import rle
from pytrack_analysis.cli import colorprint, flprint, prn
"""
Classifier class: loads kinematics data and metadata >> processes and returns classification data
"""
class Classifier(Node):
... | degoldschmidt/pytrack-analysis | pytrack_analysis/classifier.py | Python | gpl-3.0 | 7,563 | [
"Gaussian",
"VisIt"
] | dab2bc08a155c7dd81a44fa166d31051ca3226aadaf5a56cd76418b95cd1192b |
""" Pilot logger module for the remote logging system.
"""
import os
import logging
import argparse
from PilotLoggerTools import generateDict, encodeMessage
from PilotLoggerTools import generateTimeStamp
from PilotLoggerTools import isMessageFormatCorrect
from PilotLoggerTools import readPilotJSONConfigFile
from Pilot... | wkrzemien/Pilot | Pilot/PilotLogger.py | Python | gpl-3.0 | 7,766 | [
"DIRAC"
] | c671970acf1ec394fb12da714eb9bc8c45ed078e9cd3ee901722558c3fe4c84c |
#!/usr/bin/env python
# Copyright 2020 Informatics Matters Ltd.
#
# 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 applicab... | InformaticsMatters/pipelines | src/python/pipelines/xchem/xcos.py | Python | apache-2.0 | 11,705 | [
"RDKit"
] | 96215c2b904f97434a27c558f0d97ce6d81a8088b7b9e4f6ef121e41087f0612 |
#! /usr/bin/env python3
"""Analyze results of ProPhyle's classification
Authors: Karel Brinda <kbrinda@hsph.harvard.edu>, Simone Pignotti <pignottisimone@gmail.com>
Licence: MIT
"""
import argparse
import os
import sys
import pysam
from ete3 import Tree
from ete3.coretype.tree import TreeError
from collections impo... | karel-brinda/prophyle | prophyle/prophyle_analyze.py | Python | mit | 21,074 | [
"pysam"
] | b9a490378d574a58dd29a09c1606fab799235160e3384e5448321e10ac4ae0d7 |
#!/usr/bin/env python
#
# $Id: daemon.py 7274 2008-03-05 01:00:09Z bmc $
# NOTE: Documentation is intended to be processed by epydoc and contains
# epydoc markup.
"""
Overview
========
Convert the calling process to a daemon. To make the current Python process
into a daemon process, you need two lines of code::
... | mattcaldwell/django-denorm | denorm/daemon.py | Python | bsd-3-clause | 7,308 | [
"Brian"
] | cb2adb28344cdcd5b8b511a706290f122961dd84dba31e38e25ccd24a57dc3ef |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, division, print_function, unicode_literals
from nose.tools import * # noqa PEP8 asserts
from osf_tests import factories
from tests.base import OsfTestCase
from website.util import api_url_for
from website.views import find_bookmark_collection
class Te... | hmoco/osf.io | osf_tests/test_search_views.py | Python | apache-2.0 | 9,999 | [
"Brian"
] | 34fe86bd35677daee3a9eb92a1163bdff3eac8a6b2e642d5d7bc43ca9dc7abc5 |
"""
Demonstrates a incremental search for finding the weights of a neural net.
Set the random_search = True for a random search
random_search=False will use incremental improvement using a mutation determined by amount
"""
import brain
import math
import copy
import random
random_search=Fa... | pauljohnleonard/pod-world | CI_2015/CI_examples/NNSearchForTruthTable/03_incremental_search.py | Python | gpl-2.0 | 4,142 | [
"NEURON"
] | d0c621a22f9ab8599e92520111ebfe1cb7c78c7065c76f6bbcf1c45417fe2a8d |
# -*- test-case-name: buildbot.test.test_svnpoller -*-
# Based on the work of Dave Peticolas for the P4poll
# Changed to svn (using xml.dom.minidom) by Niklaus Giger
# Hacked beyond recognition by Brian Warner
from twisted.python import log
from twisted.internet import defer, reactor, utils
from twisted.internet.task... | CauldronDevelopmentLLC/buildbot | buildbot/changes/svnpoller.py | Python | gpl-2.0 | 20,308 | [
"Brian"
] | 578889a956861dd139d636765dd4d77e2ea3c4687d9f44d49a1436ddc155dcb9 |
from fitstools import manage_dtype, mask_fits, display, row_avg, col_avg
from astropy.io import fits
from scipy.optimize import minimize
import numpy as np
from math import floor, ceil
from scipy.optimize import curve_fit
#Helper function to get the number of fibers in a fits object using
# information from the fit... | richardseifert/Hydra_pipeline | libs/flat.py | Python | mit | 10,742 | [
"Gaussian"
] | 6d61c92ff184baa6ce725775d31b485db8d88bced4216ef58996d058c8620a60 |
# coding: utf-8
# # Convert OOI Parsed pwrsys JSON to NetCDF file
# using CF-1.6, Discrete Sampling Geometry (DSG) conventions, **`featureType=timeSeries`**
# In[1]:
get_ipython().magic('matplotlib inline')
import json
import pandas as pd
import numpy as np
from pyaxiom.netcdf.sensors import TimeSeries
# In[2]:
... | rsignell-usgs/notebook | OOI/from_ooi_json-pwrsys.py | Python | mit | 2,768 | [
"NetCDF"
] | 37c6de40ff521ce5011a6efa95dc56fe513bc61557d928fa6051bd365d81063a |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | mfherbst/spack | var/spack/repos/builtin/packages/biopieces/package.py | Python | lgpl-2.1 | 3,764 | [
"BLAST",
"BWA",
"Bowtie"
] | 755853f2bccb4810cbcf6958bbf4a7b47f35561f51039db4ae1f15d3d0df60c7 |
#!/usr/bin/env python
# Copyright (C) 2011-2012 CRS4.
#
# This file is part of Seal.
#
# Seal 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 ve... | ilveroluca/seal | tests/tseal/lib/aligner/bwa/test_bwa_aligner.py | Python | gpl-3.0 | 3,688 | [
"BWA"
] | 8fffd7c71d40b07147ea8b1b0eb76cb5f060f6ef3380b953eed837d9df52ca41 |
import os
import numpy as np
from netCDF4 import Dataset
from compliance_checker.acdd import ACDD1_1Check, ACDD1_3Check
from compliance_checker.tests import BaseTestCase
from compliance_checker.tests.helpers import MockTimeSeries, MockVariable
from compliance_checker.tests.resources import STATIC_FILES
def to_sing... | aodn/compliance-checker | compliance_checker/tests/test_acdd.py | Python | apache-2.0 | 21,174 | [
"NetCDF"
] | d8883f992fd301d9eb0b9792b7d4d0c312b5771f85e1993dbda6eb7ff872692f |
#!/usr/bin/env python3
class Character:
def __init__(self, favouriteWeapon):
self.__fv = favouriteWeapon
def favouriteWeapon(self):
return self.__fv
def accept(self, visitor):
visitor.visit(self)
class Elf(Character):
def __init__(self):
super().__init__("bow")
... | SPbAU-ProgrammingParadigms/materials | python_4/blizzard_another.py | Python | unlicense | 2,561 | [
"VisIt"
] | 9c699de0b7850d322b528c7dfae1398abca6145ec0e6d33f8d4fbe4c2d52238b |
import datetime
from custom.bihar import getters, BIHAR_DOMAINS
from custom.bihar.calculations.homevisit import DateRangeFilter
from custom.bihar.calculations.utils import filters
from fluff.filters import Filter
from pillowtop.listener import BasicPillow
from casexml.apps.case.models import CommCareCase
from couchform... | puttarajubr/commcare-hq | custom/bihar/models.py | Python | bsd-3-clause | 6,063 | [
"VisIt"
] | 711471269c426814667a0be17df31218ff77ea21b6d10c3ee24ff16207c1f10d |
r"""
Elastic contact planes simulating an indentation test.
Four contact planes bounded by polygons (triangles in this case) form a very
rigid pyramid shape simulating an indentor.
Find :math:`\ul{u}` such that:
.. math::
\int_{\Omega} D_{ijkl}\ e_{ij}(\ul{v}) e_{kl}(\ul{u})
+ \sum_{i=1}^4 \int_{\Gamma_i} \u... | rc/sfepy | examples/linear_elasticity/elastic_contact_planes.py | Python | bsd-3-clause | 4,756 | [
"VTK"
] | c41a5ba78214953c498484e5c37d58b3e68c19067823f30d7f37aa98984e4ec3 |
from __future__ import absolute_import
import theano
import theano.tensor as T
import numpy as np
from six.moves import range
if theano.config.floatX == 'float64':
epsilon = 1.0e-9
else:
epsilon = 1.0e-7
def mean_squared_error(y_true, y_pred):
return T.sqr(y_pred - y_true).mean(axis=-1)
def mean_absolu... | MingyuanXie/CopyNet | emolga/basic/objectives.py | Python | mit | 3,130 | [
"Gaussian"
] | 7847b7db6fc3b6bb4c692beebb372ecb76c07e82f8f0b1635b0e72ab61380505 |
#!/usr/bin/env python
#-*- coding: utf-8 -*-
#python imports
from cgi import escape
from urlparse import urljoin
from re import findall
from sys import exit
from urllib import urlencode
import cgi
#project imports
from session import Session
from dbconnection import dbConnection
from general import General, DefDict
f... | cria/microSICol | py/modules/getdata.py | Python | gpl-2.0 | 254,713 | [
"VisIt"
] | c72e11d5e38f744ddb6fc73254cef7362a29200b7c68b4b2e396c49df9f81195 |
#!/usr/bin/env python
"""
# Created: Tue, 10 Jan 2012 11:57:35 +1000
Formats homologs for phylogenetic analysis
TODO: Detailed description
"""
import sys
import os
import traceback
import optparse
import time
import re
from Bio.Blast.Applications import NcbiblastxCommandline
from Bio.Blast.Applications import Ncbibla... | happykhan/igor | igor/Dryad.py | Python | gpl-3.0 | 20,290 | [
"BLAST"
] | 1892a0cfe8283523e9a21d3a7cd5e3fdedbb4733dabf0b95fe68b49b553c30ca |
import math
import numpy
from chainer.functions.connection import deconvolution_2d
from chainer import link
class Deconvolution2D(link.Link):
"""Two dimensional deconvolution function.
This link wraps the :func:`~chainer.functions.deconvolution_2d` function
and holds the filter weight and bias vector ... | AlpacaDB/chainer | chainer/links/connection/deconvolution_2d.py | Python | mit | 3,966 | [
"Gaussian"
] | dbebeab35a856a4cb01456296a1d3dc7cdb7acb0765e4cafe88385515e30208c |
import numpy as np
import scipy.stats as ss
class Posterior(object):
"""Class representing the correlated 2D Gaussian posterior on masses
and proxies described in arXiv:XXXX.XXXX. Objects of this class
can be used to
* Compute the likelihood and prior for a set of parameters given
the observati... | farr/galmassproxy | posterior.py | Python | mit | 7,474 | [
"Gaussian"
] | 9ac49e84d79772d4d2ba12c2c0fe92bdc04a7477d0bc5d3fd7388fd47e56c367 |
__author__ = 'Tom Schaul, tom@idsia.ch'
from pybrain.utilities import blockCombine
from scipy import mat, dot, outer
from scipy.linalg import inv, cholesky
def calcFisherInformation(sigma, invSigma=None, factorSigma=None):
""" Compute the exact Fisher Information Matrix of a Gaussian distribution,
given its... | pybrain/pybrain | pybrain/tools/fisher.py | Python | bsd-3-clause | 1,662 | [
"Gaussian"
] | fcaf34104c3911bf251ead4a5a561988c4b775f4760b6aeeacbf23a99c8594fe |
import yt
#yt.funcs.mylog.setLevel(40)
#
# Nov 2017: Units bug in Enzo domain mass flux that needs to be corrected
# by root grid dx^2. However, to avoid confusion, for now,
# just make this a global post-process correction. Leaving as bug
# in Enzo.
#
APPLY_CORRECTION_TO_BOUNDARY_MASS_... | aemerick/galaxy_analysis | analysis/_galaxy_analysis.py | Python | mit | 59,804 | [
"Galaxy"
] | dc2faf1c4229dcca1616236e6338e0c6e87982bbe47d25263ebe9cfac5942085 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
"""Auto pyth... | nuclear-wizard/moose | python/mooseutils/AutoPropertyMixin.py | Python | lgpl-2.1 | 10,162 | [
"MOOSE"
] | 312f543e5725980abd0277eec72aa5160d61ee284c301834b5a41992eb109349 |
"""
A collection of functions for fast MLE fits to light curves.
MLE: Maximum Likelihood Estimation
The 'fit' is to an array of intensities (y[]: float) that comprise the light
curve.
"""
import numpy as np
import sys
from math import log, pi, sqrt, exp
from typing import Tuple
from pyoteapp.solverUtils import calcN... | bob-anderson-ok/py-ote | src/pyoteapp/iterative_logl_functions.py | Python | mit | 23,172 | [
"Gaussian"
] | c0135591235256cdf4bd2adc7d5a6c358fed1f97b8701400c9208f537a305f18 |
#!/usr/bin/env python
"""
Easy Install
------------
A tool for doing automatic download/extract/build of distutils-based Python
packages. For detailed documentation, see the accompanying EasyInstall.txt
file, or visit the `EasyInstall home page`__.
__ https://pythonhosted.org/setuptools/easy_install.html
"""
from... | xpavlus/parabaramba | venv/lib/python2.7/site-packages/setuptools/command/easy_install.py | Python | gpl-3.0 | 85,008 | [
"VisIt"
] | 403822be9bc17a6d98d3dd8c3305e8f61a5ccadb8c3c3521a4b2de7bca36dfd3 |
# codegen.py
# Copyright (C) 2006, 2007 Michael Bayer mike_mp@zzzcomputing.com
#
# This module is part of Mako and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""provides functionality for rendering a parsetree constructing into module source code."""
import time
import re
... | tebeka/pythonwise | tagcloud/mako/codegen.py | Python | bsd-3-clause | 31,288 | [
"VisIt"
] | 1976ce452a0aee88c0c0b07158a03ddfd05f5beb0ac67de5f9fab720bc0eb911 |
"""
Image classes
"""
import data
import logging
from galaxy.datatypes.sniff import *
from urllib import urlencode, quote_plus
import zipfile
log = logging.getLogger(__name__)
class Ab1( data.Data ):
"""Class describing an ab1 binary sequence file"""
file_ext = "ab1"
def set_peek( self, dataset ):
... | dbcls/dbcls-galaxy | lib/galaxy/datatypes/images.py | Python | mit | 9,636 | [
"Galaxy"
] | 6236dc66a5018fefd14608482625d8312a590f60904a7df79e565d91ecf1c13d |
#
# ----------------------------------------------------------------------------------------------------
#
# Copyright (c) 2015, Oracle and/or its affiliates. All rights reserved.
# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
#
# This code is free software; you can redistribute it and/or modify it
# u... | smarr/mxtool | mx_compat.py | Python | gpl-2.0 | 5,030 | [
"VisIt"
] | d1debed9d36f606917dc90c58a7fdc633e8d02bd812d807b2a2b59ddcc484999 |
import os
import time
import argparse
import traceback
from ase.asec.command import Command
from ase.calculators.calculator import get_calculator
from ase.utils import Lock, OpenLock
from ase.tasks.io import read_json, write_json
def str2dict(s, namespace={}, sep='='):
"""Convert comma-separated key=value string... | alexei-matveev/ase-local | ase/asec/run.py | Python | gpl-2.0 | 5,545 | [
"ASE"
] | df49c647279be84a8d7b66036144857d58076653984c065717bbbafc5f7e564b |
# Version: 0.15
"""
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, and pypy
* [![Latest Version]
(https://pypip.in/version/versioneer/badge.svg?style=flat)
](ht... | Connexions/cnx-publishing | versioneer.py | Python | agpl-3.0 | 62,495 | [
"Brian"
] | 2d9b46a95e5c1976f73d5265d26d13c2b7b38db542cf66b11c0079537267ab1c |
import vtk
import glob
import sys
import os
import scipy.stats
import pylab
import math
import numpy
from fluidity_tools import stat_parser
import le_tools
################################################
#--------------- FROUDE NUMBER ----------------#
################################################
def Froudenum... | FluidityStokes/fluidity | examples/lock_exchange/plot_data.py | Python | lgpl-2.1 | 10,329 | [
"VTK"
] | 54e6a7fe92759a45ab92a02cffa8354d8c8cdbf86f9a0cc9143d91f29194b3e5 |
#
# Copyright (C) 2013-2019 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... | fweik/espresso | testsuite/python/lj.py | Python | gpl-3.0 | 2,361 | [
"ESPResSo"
] | d630d5385b736bb42859322f80403ff544d88f9afb4277e5eb2741fdff42ab10 |
# 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/tests_common.py | Python | gpl-3.0 | 17,903 | [
"ESPResSo",
"Gaussian",
"VTK"
] | efe11f3c4fc0d60245175ed231b9d76a451fe39741ceb6b70fcfd0b9471e731b |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | xguse/scikit-bio | skbio/tree/tests/test_tree.py | Python | bsd-3-clause | 41,651 | [
"scikit-bio"
] | bd1b0889dec00895e1fd5d6eea780f046172ce17f717f13ad5708fe8edf91a28 |
# -*- coding: utf-8 -*-
"""
@authors: R. Sanchez-Martin / C. Zambaldi / D. Mercier
"""
from tools import Tools
from .indenter import Indenter
import logging
logger = logging.getLogger('root')
logger.info('logger says : proc.indent')
class Indentation(Indenter, Tools):
""" Generates an Abaqus Python file for inde... | stabix/stabix | third_party_code/python/abaqus/proc/indentation.py | Python | agpl-3.0 | 66,197 | [
"CRYSTAL"
] | 861f46e266b5dbb5e706069a2f855d4794d57e37a8d48617de4c87d34795b04b |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | gregcaporaso/scikit-bio | skbio/stats/distance/_anosim.py | Python | bsd-3-clause | 8,598 | [
"scikit-bio"
] | 3c0167a9b2926038849b3f51b257e62d8711d50cf6db90cc455c4fce713625e7 |
"""Helper functions to handle AMI creation with packer"""
import os
from os.path import dirname
import shutil
import subprocess
import logging
from cfn.utils.cfn import get_recent_ami
from cfn.utils.constants import CANONICAL_ACCOUNT_ID
LOGGER = logging.getLogger(__file__)
LOGGER.addHandler(logging.StreamHandler())... | WikiWatershed/model-my-watershed | deployment/packer/driver.py | Python | apache-2.0 | 4,157 | [
"Galaxy"
] | 72df7f600a3ab1b4455d9abcf28950ce30618883eddcbe87400c53a13b6bfb25 |
# -*- coding: utf-8 -*-
"""
Created on Thu Dec 19 09:14:34 2013
@author: Shreejoy
"""
queryStr = "input resistance resting membrane potential neuron"
def get_full_text_links(queryStr):
NUMHITS = 200
maxURLTries = 5
waitTime = 60
queryStrQuoted = re.sub(' ', '+', queryStr)
testYe... | neuroelectro/neuroelectro_org | neurotree/scopus_test.py | Python | gpl-2.0 | 2,234 | [
"NEURON"
] | 7f24c96af61d7836afe6c7803838577a18d82827bd5f0f77633ef96e7148c0c7 |
"""Utility functions for plotting M/EEG data
"""
from __future__ import print_function
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Denis Engemann <denis.engemann@gmail.com>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Eric Larson <larson.eric.d@gmail.com>
# ... | rajegannathan/grasp-lift-eeg-cat-dog-solution-updated | python-packages/mne-python-0.10/mne/viz/utils.py | Python | bsd-3-clause | 30,185 | [
"Mayavi"
] | 07dd168b4ad135260415f9cbc35bdbf95c1d83f4fb47f0cb5dbea69c74da13a7 |
"""Utilities used in the Kadenze Academy Course on Deep Learning w/ Tensorflow.
Creative Applications of Deep Learning w/ Tensorflow.
Kadenze, Inc.
Parag K. Mital
Copyright Parag K. Mital, June 2016.
"""
import matplotlib.pyplot as plt
import tensorflow as tf
import urllib
import numpy as np
import zipfile
import os
... | srippa/nn_deep | tf/libs_3/utils.py | Python | mit | 19,400 | [
"Gaussian"
] | 1f5ab485f13e538e67413596a772d4a27061d1725c552fbd872dfe7c59e79592 |
#!/usr/bin/env python
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 3
# of the License, or (at your option) any later version.
#
# This program is distributed in the hope that ... | dmnfarrell/smallrnaseq | smallrnaseq/novel.py | Python | gpl-3.0 | 31,911 | [
"BLAST"
] | ab5504c4aecfd2b1d9fa4fb113d16681db301a5c5731361d185db81a494ebb86 |
# -*- coding: utf-8 -*-
"""
Created on Fri Mar 14 01:34:41 2014
@author: deokwoo
"""
from __future__ import division # To forace float point division
import numpy as np
from numpy.linalg import norm
from scipy.interpolate import interp1d
from shared_constants import *
from data_tools import *
from scipy.stats import s... | TinyOS-Camp/DDEA-DEV | Archive/[14_09_12] DDEA_example_code/data_preprocess (Deokwoo Jung's conflicted copy 2014-07-01).py | Python | gpl-2.0 | 35,926 | [
"Gaussian"
] | e966b97b1759db1f2b0d31c3d2204942ae1c2dcb714da43c970e70cac3b99121 |
#
# CCLib_proxy Interface Library for High-Level operations
# Copyright (c) 2014 Ioannis Charalampidis
#
# 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... | wavesoft/CCLib | Python/cclib/__init__.py | Python | gpl-3.0 | 3,858 | [
"cclib"
] | 7b5a2b1e8818c5e55c8136a92912545d8a563e5a2b872ab6101593f6857ff658 |
>>> import vtk
>>> r = vtkDataSetReader()
Traceback (most recent call last):
File "<console>", line 1, in <module>
NameError: name 'vtkDataSetReader' is not defined
>>> r = vtk.vtkDataSetReader()
>>> r.SetFileName('/Users/sunilkumar/Downloads/Skin.vtk')
>>> w = vtk.vtkDataSetWriter()
>>> w.SetInput(r.GetOGetOutput())
T... | MokaCreativeLLC/XNATImageViewer | utility-scripts/python/vtkBinaryToVtkAscii.py | Python | bsd-3-clause | 525 | [
"VTK"
] | adf82de13710616070b3ed3ed44f5e5ddc117fced65b5209b5584faadb8c35ca |
#===============================================================================
#
# CSR_T.py
#
# This file is part of ANNarchy.
#
# Copyright (C) 2020 Helge Uelo Dinkelbach <helge.dinkelbach@gmail.com>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of... | ANNarchy/ANNarchy | ANNarchy/generator/Projection/SingleThread/CSR_T.py | Python | gpl-2.0 | 7,272 | [
"NEURON"
] | 57649168203bf47249a1c6d7afd9fe5460d7b66ada13171b7cb1eaa90c96dff7 |
# run with: python manage.py test hs_core.tests.serialization.test_resourcemeta_sax_parsing
import unittest
import xml.sax
from hs_core.serialization import GenericResourceSAXHandler
from hs_geo_raster_resource.serialization import RasterResourceSAXHandler
from hs_app_netCDF.serialization import NetcdfResourceSAXHandl... | FescueFungiShare/hydroshare | hs_core/tests/serialization/test_resourcemeta_sax_parsing.py | Python | bsd-3-clause | 11,026 | [
"Brian"
] | 8b042d6e22f21ce2d9791a3c7010618973900d6b94dbfcf34b3172aa49fcf749 |
'''
Created on Aug 3, 2011
@author: sean
'''
import _ast
from ...asttools.visitors import Visitor
class Replacer(Visitor):
'''
Visitor to replace nodes.
'''
def __init__(self, old, new):
self.old = old
self.new = new
def visitDefault(self, node):
for field in node._fiel... | jasonyaw/SFrame | oss_src/unity/python/sframe/meta/asttools/mutators/replace_mutator.py | Python | bsd-3-clause | 2,056 | [
"VisIt"
] | ccfc38960828b4ad5aaaed547c4012db2d3895ce77c03c9b5e88894c676f2252 |
"""
Classes for the analysis of fluorescence assay data.
"""
#=============================================================================================
# IMPORTS
#=============================================================================================
import numpy as np
import pymc
from scipy.misc import lo... | MehtapIsik/assaytools | AssayTools/analysis.py | Python | lgpl-2.1 | 47,867 | [
"Avogadro",
"Gaussian"
] | 4b8470236cfd35e4fe7413d52a5c928d9cf7b15ef010e8fb0453bc010119850f |
import os
import re
import MooseDocs
from MooseDocs.testing import MarkdownTestCase
class TestDiagramExtension(MarkdownTestCase):
"""
Test that the MooseDiagram extension for using dot-language is working.
"""
REGEX = r'<img class="moose-diagram" src="media/tmp_(.*?)\.moose\.svg" style="background:tra... | backmari/moose | docs/tests/diagram/test_diagram.py | Python | lgpl-2.1 | 760 | [
"MOOSE"
] | ae6cb619112ea87204c28c57180ecb071b7ec274f105191466d6596869fc1655 |
#
# Copyright (c) 2009-2015, Jack Poulson
# All rights reserved.
#
# This file is part of Elemental and is under the BSD 2-Clause License,
# which can be found in the LICENSE file in the root directory, or at
# http://opensource.org/licenses/BSD-2-Clause
#
import El
import time
m = 2000
n = 4000
k = 3000
testMe... | justusc/Elemental | examples/interface/LPAffine.py | Python | bsd-3-clause | 4,124 | [
"Gaussian"
] | 92f9c7f17ac4fb40cf318ff62cfc04ddf848ef621483d63155001eaf6fda5d20 |
import os
from uwg import UWG
import math
import logging
TEST_DIR = os.path.dirname(__file__)
DEFAULT_EPW_PATH = os.path.join(
TEST_DIR, 'epw', 'SGP_Singapore.486980_IWEC.epw')
DEFAULT_PARAM_PATH = os.path.join(
TEST_DIR, 'parameters', 'initialize_singapore.uwg')
NEW_DIR = os.path.join(TEST_DIR, 'epw_uwg')
MAT... | chriswmackey/UWG_Python | tests/test_base.py | Python | gpl-3.0 | 4,777 | [
"EPW"
] | 4e018323d0bafb556db6a6dda3dd23aaa087c5512fab1335551dbb2adfa0a15e |
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2003-2005 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2009-2010 Andrew I Baznikin
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Ge... | sam-m888/gramps | gramps/plugins/rel/rel_sl.py | Python | gpl-2.0 | 15,244 | [
"Brian"
] | 80d2cd1b4c48d421b3ecea2a76cddd1b01d999841dc67dd99fe963f46adf0904 |
#!/usr/bin/python
"""
Tracking of rotating point.
Rotation speed is constant.
Both state and measurements vectors are 1D (a point angle),
Measurement is the real point angle + gaussian noise.
The real and the estimated points are connected with yellow line segment,
the real and the measured points ar... | glo/ee384b | opencv/samples/python/kalman.py | Python | lgpl-2.1 | 3,867 | [
"Gaussian"
] | 2eb50c06042c633ca0024dd379448107b94c19e43417bd6c7180eb9db91f801e |
"""
Parsing methods for multiple core functions
"""
__license__ = """
This file is part of RAPD
Copyright (C) 2011, Cornell University
All rights reserved.
RAPD is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Founda... | RAPD/RAPD | src/plugins/subcontractors/parse.py | Python | agpl-3.0 | 133,248 | [
"ADF"
] | dfdef053b384a0b09eb5ffe268212ea1b46da1f7a23fbcf72789862d9540ffa9 |
"Module for creating clusters."
from ase.cluster.cluster import Cluster
from ase.cluster.wulff import wulff_construction
from ase.cluster.cubic import SimpleCubic, BodyCenteredCubic,\
FaceCenteredCubic
from ase.cluster.octahedron import Octahedron
from ase.cluster.hexagonal import Hexago... | grhawk/ASE | tools/ase/cluster/__init__.py | Python | gpl-2.0 | 442 | [
"ASE"
] | a2bd9ffb3f7e17c0e08f9f6a13a55bc4575f2e03739ec7685ee8ff52131ae18e |
#
# @file TestXMLNode.py
# @brief XMLNode unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Michael Hucka <mhucka@caltech.edu>
#
# $Id: TestXMLNode.py 11441 2010-07-09 02:22:23Z mhucka $
# $HeadURL: https://sbml.svn.sourceforge.net/svnroot/sbml/trunk/libsbml/src/bindings/python/test/xml/TestXML... | alexholehouse/SBMLIntegrator | libsbml-5.0.0/src/bindings/python/test/xml/TestXMLNode.py | Python | gpl-3.0 | 44,507 | [
"VisIt"
] | fc31d123dcf435dc7f1d02438e479cc13644b6d978249fe550882051482350e5 |
from disco.test import TestCase, TestPipe
from disco.worker.pipeline.worker import Stage
from disco.compat import str_to_bytes
def map(interface, state, label, inp):
out = interface.output(0)
for e in inp:
out.add(e, '')
class RawJob(TestPipe):
pipeline = [("split", Stage("map", process=map))]
cl... | oldmantaiter/disco | tests/test_raw_pipeline.py | Python | bsd-3-clause | 695 | [
"MOE"
] | ee0c62125dc0ff13e641969ddcf4d5b7ebddf14c5fc7502b6d1233655a514e20 |
# Copyright (C) 2013 by Zheng Ruan (zruan1991@gmail.com)
# 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.
"""Unit tests for the Bio.codonalign modules.
"""
import sys
import warnings
import tempfile
im... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_codonalign.py | Python | gpl-2.0 | 10,771 | [
"Biopython"
] | d6cf20e9b4eca9f610e12ed3e01a420e972d5da5687d64ab81a5837315742b7a |
# -*- coding: utf-8 -*-
# Copyright (c) 2015, Mayo Clinic
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without modification,
# are permitted provided that the following conditions are met:
#
# Redistributions of source code must retain the above copyright notice, this
# list of ... | hsolbrig/shexypy | scripts/shex_parser.py | Python | mit | 6,026 | [
"VisIt"
] | 846aad9330d3583a4883566db204cd9598eecc8a84dd59c7427f67b262aad63e |
# -*- coding: utf-8 -*-
#
# Matroska support in direct Python.
#
# This file is part of the Fluggo Media Library for high-quality
# video and audio processing.
#
# Copyright 2012 Brian J. Crowell <brian@fluggo.com>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU ... | fluggo/Canvas | fluggo/media/matroska.py | Python | gpl-3.0 | 31,245 | [
"Brian"
] | 96e70cfeb4eb96a16e70caa92c7836b0d4e5157aa40119a94ed0de9a3f77f00f |
"""
Browser set up for acceptance tests.
"""
#pylint: disable=E1101
#pylint: disable=W0613
#pylint: disable=W0611
from lettuce import before, after, world
from splinter.browser import Browser
from logging import getLogger
from django.core.management import call_command
from django.conf import settings
from selenium.c... | elimence/edx-platform | common/djangoapps/terrain/browser.py | Python | agpl-3.0 | 3,050 | [
"VisIt"
] | 0036720e63327108516afaeca3dcb8cc0c23317d31417b4138db4a86417a0726 |
#!/usr/bin/env python
# coding=utf-8
"""Node definitions for intermediary node tree."""
from __future__ import absolute_import
import re
import types
from base64 import standard_b64decode, standard_b64encode
from functools import partial
from math import isnan
from future.utils import implements_iterator, binary_type... | bionikspoon/pureyaml | pureyaml/nodes.py | Python | mit | 9,985 | [
"VisIt"
] | a315834fca7477349f4695feedbe407fc3581547db49da858f4ae392824cb53b |
"""MedleyDB melody Dataset Loader
.. admonition:: Dataset Info
:class: dropdown
MedleyDB melody is a subset of the MedleyDB dataset containing only
the mixtures and melody annotations.
MedleyDB is a dataset of annotated, royalty-free multitrack recordings.
MedleyDB was curated primarily to suppor... | mir-dataset-loaders/mirdata | mirdata/datasets/medleydb_melody.py | Python | bsd-3-clause | 8,346 | [
"VisIt"
] | 94c8b34f4d0ff5223466994696f52622176d15ed2a4800a472ff54a9b5ad3f1d |
import datetime
committees = [
{
u'_all_ids': [u'EXC000001'],
u'_id': u'EXC000001',
u'_type': u'committee',
u'chamber': u'lower',
u'committee': u'Standing Committee on Phony',
u'country': u'us',
u'level': u'state',
u'members': [
{u'+chamb... | mileswwatkins/billy | billy/tests/fixtures/ex/committees.py | Python | bsd-3-clause | 1,368 | [
"MOE"
] | 29cad34ee9161a9f8ea65e5701bc6f0f6276a59f6614ffa5bbc9ed8317fd6ea8 |
# ######################################################################
# Copyright (c) 2014, Brookhaven Science Associates, Brookhaven #
# National Laboratory. All rights reserved. #
# #
# @author: Li Li (lili@bnl.g... | giltis/scikit-xray | skxray/core/cdi.py | Python | bsd-3-clause | 12,998 | [
"Gaussian"
] | 958c3af2e75640bcd79a1e23f3ac023d679cee0397c2022083232f2d6810a672 |
#!/usr/bin/python
from math import cos, pi, log, exp
import sys
min=4
max=64
def dnorm(x, m, s):
return exp(-0.5 * log(2*pi) - log(s) - 0.5*((x-m)*1.0/s)**2)
# Old cosine based distribution
#def dvmax(v,min,max):
# return (max-min) / 2 * (cos(2*pi/255*v) + 1) + min
# New gaussian distribution
def dvmax(v,min... | illinoistechrobotics/ITR-Gumstix-Controller | robot/mklut.py | Python | gpl-2.0 | 743 | [
"Gaussian"
] | 84fcb9cd154719a6458d54fb07ae0569be7d3137fe03eeb9ab62c602ca93d1bd |
# -*- coding: utf-8 -*-
# Copyright 2007-2022 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy 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 y... | jat255/hyperspy | hyperspy/tests/model/test_set_parameter_value.py | Python | gpl-3.0 | 3,805 | [
"Gaussian"
] | 1d951b08a0518f7cb33f88323cbc17a39fcda812378aa1180226c6dfeab204b6 |
from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os
class TestToolMigrationStages( ShedTwillTestCase ):
'''Verify that the migration stages display correctly.'''
def test_0000_initiate_users( self ):
"""Create necessary user accounts and login as an admin user."""
self.logo... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/test/tool_shed/functional/test_1400_review_migration_stages.py | Python | gpl-3.0 | 3,266 | [
"BLAST",
"BWA",
"Bowtie"
] | dcd3b20126ff117e5720002749c82caa00e5199a4a606f64c436560aeecc937f |
# -*- coding: utf-8 -*-
import json
from django.utils.decorators import method_decorator
from django.shortcuts import get_object_or_404
from django.views.decorators.cache import never_cache
from typing import Optional
from guardian.utils import get_anonymous_user
from rest_framework.exceptions import PermissionDen... | tomka/CATMAID | django/applications/catmaid/control/client.py | Python | gpl-3.0 | 15,033 | [
"NEURON"
] | d84548f2b202303f0b909de265b44cd0d650a7d59ac568fc60d6e8b5c3c76f55 |
#
# This file is part of the Connection-Set Algebra (CSA).
# Copyright (C) 2010,2011,2012 Mikael Djurfeldt
#
# CSA 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
# (a... | INCF/csa | csa/misc.py | Python | gpl-3.0 | 1,308 | [
"Gaussian"
] | ddbe3f19c1254e8aee793f9e01604fa9a111ce1ee914ae2c4ad6bf09bb4c9d38 |
#!/usr/bin/env python
########################################################################
# File : dirac-admin-add-site
# Author : Federico Stagni
########################################################################
"""
Add a new DIRAC SiteName to DIRAC Configuration, including one or more CEs.
If site is al... | yujikato/DIRAC | src/DIRAC/ConfigurationSystem/scripts/dirac_admin_add_site.py | Python | gpl-3.0 | 3,641 | [
"DIRAC"
] | 89fff970e16d321fc3a80a93a54fbe18ba32f54dd579f59d8c6a3490a8a00aa5 |
#!/usr/bin/env python
###
### This file is managed by Ansible. ALL CHANGES WILL BE OVERWRITTEN.
###
import re
import sys
import datetime
import smtplib
from email.mime.text import MIMEText
yesterday = datetime.date.today() - datetime.timedelta(days=1)
md = '%s ' % yesterday.strftime('%b %d')
recmp = re.compile(' ([\... | galaxyproject/infrastructure-playbook | roles/mailman/files/mm_discard_report.py | Python | mit | 1,720 | [
"Galaxy"
] | a9949f7c887848fc89c9d6b13cb453d647bca5ba63e5880bba9b808861778571 |
"""
Image classes
"""
import data
import logging
from galaxy.datatypes.metadata import MetadataElement
from galaxy.datatypes import metadata
from galaxy.datatypes.sniff import *
from urllib import urlencode, quote_plus
import zipfile
import os, subprocess, tempfile
log = logging.getLogger(__name__)
class Image( data... | volpino/Yeps-EURAC | lib/galaxy/datatypes/images.py | Python | mit | 6,536 | [
"Galaxy"
] | 5ae6d7dbd3f44a8fcc1bacc56af2a46d4d97d00cd36251b8517bca5ea29f061e |
# cs.po
val = {"" : "Project-Id-Version: sheltermanager\nReport-Msgid-Bugs-To: FULL NAME <EMAIL@ADDRESS>\nPOT-Creation-Date: 2013-01-24 10:55+0000\nPO-Revision-Date: 2012-04-15 16:53+0000\nLast-Translator: Martina K <martk123@seznam.cz>\nLanguage-Team: Czech <cs@li.org>\nMIME-Version: 1.0\nContent-Type: text/plain; ch... | aubzen/sheltermanager | src/locale/locale_cs.py | Python | gpl-3.0 | 112,906 | [
"Amber",
"VisIt"
] | 039ecf0f0bdba65b844ec3782cb1f2b58a1d1d1ba359f82f01cf7180f5ced71a |
"""
Cell_builder.py
Authors:
Claudia Espinoza, claumespinoza@gmail.com
Jose Guzman, sjm.guzman@gmail.com
Last change: Wed Oct 12 16:11:56 CEST 2016
File that contains detailed morphologies of principal cells (PC)
and basquet cells (BC) in the prefrontal cortex
To use it:
>>> from Cell_builder import PC
>>> m... | JoseGuzman/NeuralNetworks | PFCNetwork/Cell_builder.py | Python | gpl-2.0 | 6,629 | [
"NEURON"
] | 8a3e986acfa758a60341f881049aa9a4fd34d5b6b495db4135056953c752b7d3 |
# 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/stress.py | Python | gpl-3.0 | 14,208 | [
"ESPResSo"
] | b6e7ecaa1500b06dbc72e132594709d6d0da5ca0e14cff54a3c2caf92ee29410 |
#!/usr/bin/env python
#
# This code was copied from the data generation program of Tencent Alchemy
# project (https://github.com/tencent-alchemy).
#
#
# Copyright 2019 Tencent America LLC. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in com... | sunqm/pyscf | pyscf/df/grad/uhf.py | Python | apache-2.0 | 3,087 | [
"PySCF"
] | 6e7c2e1b407e8888b29543c607a68f9d0c3f72bbc33f499d5804fb8d41dad432 |
import sys,os,time,re
from PyQt4 import QtGui, QtCore
from Logging import Logger
from FileUploader import FileUploader
from BasicWidgets import Tooltip
from QColorWidget import QColorWidget
from Logging import defaultLog
class Preferences(QtGui.QWidget):
"""
Main preferences user interface.
The main purpo... | lpedit-devs/lpedit | lpedit/Preferences.py | Python | bsd-3-clause | 17,566 | [
"VisIt"
] | 5623372732b7460846230366da0c3de6ccebf406fb159ccfad0ff8fe2c91c653 |
"""
Octave (and Matlab) code printer
The `OctaveCodePrinter` converts SymPy expressions into Octave expressions.
It uses a subset of the Octave language for Matlab compatibility.
A complete code generator, which uses `octave_code` extensively, can be found
in `sympy.utilities.codegen`. The `codegen` module can be us... | sahilshekhawat/sympy | sympy/printing/octave.py | Python | bsd-3-clause | 21,270 | [
"DIRAC"
] | 8d5568a029d86cd6da295e1a54c25237f1c1ae241c108d9ac846f0181fad2622 |
"""
"""
__RCSID__ = "$Id$"
import os
import hashlib
import time
import threading
from DIRAC import S_OK, gLogger
from DIRAC.Core.Utilities.ThreadSafe import Synchronizer
from DIRAC.FrameworkSystem.private.monitoring.RRDManager import RRDManager
from DIRAC.FrameworkSystem.Client.MonitoringClient import gMonitor
gSy... | vmendez/DIRAC | FrameworkSystem/private/monitoring/PlotCache.py | Python | gpl-3.0 | 3,307 | [
"DIRAC"
] | b5febd9dd203de86fddeaa25807a8c492b5edcb94abb944c1bec0371068f3d40 |
from mako import runtime, filters, cache
UNDEFINED = runtime.UNDEFINED
__M_dict_builtin = dict
__M_locals_builtin = locals
_magic_number = 5
_modified_time = 1262381927.6520419
_template_filename='templates/dataset/errors.mako'
_template_uri='dataset/errors.mako'
_template_cache=cache.Cache(__name__, _modified_time)
_s... | volpino/Yeps-EURAC | database/compiled_templates/dataset/errors.mako.py | Python | mit | 5,823 | [
"Galaxy"
] | cb041e6c661251660edc61b8824747dd8853833424c54c38dc109ddb8ed8de63 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.