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# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | anderspitman/scikit-bio | skbio/diversity/beta/tests/test_unifrac.py | Python | bsd-3-clause | 29,880 | [
"scikit-bio"
] | 97991952c4296e9e29d64dcbd2a7b2b201497f1399ca65b6b1d796a4f389334a |
# This file is part of the myhdl library, a Python package for using
# Python as a Hardware Description Language.
#
# Copyright (C) 2003-2013 Jan Decaluwe
#
# The myhdl library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public License as
# published by t... | palashahuja/myhdl | myhdl/conversion/_analyze.py | Python | lgpl-2.1 | 47,160 | [
"VisIt"
] | 1802508105e12920e70d3b472341347cf14b329507c8180c597933ad9aecb418 |
"""
Tests for posting/ingetsting dflow and ripcas data to each respective model
to/from the virtual watershed.
"""
import glob
import numpy
import os
import shutil
import traceback
import unittest
import numpy as np
from click.testing import CliRunner
from netCDF4 import Dataset
from cord import (
ESRIAsc, Pol, r... | VirtualWatershed/CoRD | test/test_cord.py | Python | bsd-3-clause | 15,625 | [
"NetCDF"
] | 5b2d50114c18eef90ed3d0bf4878568686ec8bd4fde21fce3ee9415dc8912095 |
import util as ut, glob, os, dset, box, img as ig, experiments, numpy as np, scipy.io, camo, copy, rotation, mvg, imtable, iputil as ip, pylab, planefit, glob, tour
# Code for generating the figures/videos in the paper and the talk
RESDIR_LOO = '/data/scratch/aho/camo-results/camera-ready-loo/loo'
RESDIR_NOLOO = '/da... | andrewowens/camo | src/figures.py | Python | mit | 45,088 | [
"Octopus"
] | f2e1ab100fda67d0a627dd190386f081372a59a8cafee0de6621a7229e2d9c26 |
from vtk import *
csv_source = vtkDelimitedTextReader()
csv_source.SetFieldDelimiterCharacters(",")
csv_source.SetHaveHeaders(True)
csv_source.SetDetectNumericColumns(True)
csv_source.SetFileName("authors.csv")
csv_source.Update()
T = csv_source.GetOutput()
print "Table loaded from CSV file:"
T.Dump(10)
| collects/VTK | Examples/Infovis/Python/delimited_text_reader1.py | Python | bsd-3-clause | 308 | [
"VTK"
] | 95df2c643efab7bb314fb0e9168cb8623dd3adfdca58fe8723c11cc3bde7a796 |
# coding=utf-8
from __future__ import unicode_literals
from .. import Provider as PersonProvider
class Provider(PersonProvider):
formats = (
'{{first_name}} {{last_name}}',
'{{first_name}} {{last_name}}',
'{{first_name}} {{last_name}}',
'{{first_name}} {{last_name}}',
'{{fi... | deanishe/alfred-fakeum | src/libs/faker/providers/person/no_NO/__init__.py | Python | mit | 7,121 | [
"MOE"
] | 9e73afef7581fb7d95a939b13671059c19a93671ac54a222d9a96ca41164f2d1 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | BackupTheBerlios/espressopp | src/FixedPairList.py | Python | gpl-3.0 | 3,127 | [
"ESPResSo"
] | 2688d69e0052db1156c73fa91bd15cc57ca5bd709ef50cff22e6f80064f40769 |
# -*- coding: utf-8 -*-
"""
Regression tests for the Test Client, especially the customized assertions.
"""
from __future__ import unicode_literals
import os
from django.conf import settings
from django.core.exceptions import SuspiciousOperation
from django.core.urlresolvers import reverse
from django.template import... | lz1988/django-web2015 | tests/regressiontests/test_client_regress/tests.py | Python | bsd-2-clause | 48,345 | [
"VisIt"
] | 2bf0ac8d6feb80bffdef2e90d769afd2636f30f2d1b451e98a0c152d724cc5db |
#!/usr/bin/env python
from optparse import OptionParser
import os
import numpy as np
import pysam
import pyBigWig
import tensorflow as tf
from basenji.dna_io import hot1_dna
from basenji.tfrecord_batcher import order_tfrecords
'''
tfr_bw.py
Generate BigWig tracks from TFRecords.
Experimental!
'''
#################... | calico/basenji | bin/tfr_bw.py | Python | apache-2.0 | 5,364 | [
"pysam"
] | 9dc8da3f9e09cced2a721f3dfe787632cc33fda7d86eb81520faba8c78bec27c |
#
# Copyright (C) 2016-2020 University of Oxford
#
# This file is part of msprime.
#
# msprime 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... | jeromekelleher/msprime | tests/test_models.py | Python | gpl-3.0 | 37,566 | [
"DIRAC"
] | 9e22d1dda4b23e34272d29da947ab9c1013efb008b89f133a83c1c885ab7eb9a |
# Copyright 2013 OpenStack Foundation
# 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 requ... | klmitch/glance | glance/api/v2/image_members.py | Python | apache-2.0 | 14,585 | [
"Brian"
] | 0736e10776bef78275e14bb8fbc95d13b64b5eac1350a17819905544c7202700 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
def test_ccsdtq():
"""Test CCSDTQ on H4 using RHF/DZ orbitals"""
import pytest
import forte.proc.scc as scc
import forte
import psi4
ref_energy = -2.225370535177 # from psi4
geom = """
H 0.0 0.0 0.0
H 0.0 0.0 1.0
H 0.0 0.0 2.... | evangelistalab/forte | tests/pytest/sparse_ci/srcc/test_ccsdtq.py | Python | lgpl-3.0 | 951 | [
"Psi4"
] | dc9373e20b40ba5f1146acdf30b7ad778bff2c38bf2bb2a88fd4bb76df74168d |
"""
This is a procedural interface to the matplotlib object-oriented
plotting library.
The following plotting commands are provided; the majority have
MATLAB |reg| [*]_ analogs and similar arguments.
.. |reg| unicode:: 0xAE
_Plotting commands
acorr - plot the autocorrelation function
annotate - annotate som... | jonyroda97/redbot-amigosprovaveis | lib/matplotlib/pylab.py | Python | gpl-3.0 | 10,766 | [
"Gaussian"
] | 0afc9439707aebd60b6bf0e8dd56899e8532eff0a0b583689aef2693c4a62e7d |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Kyle A. Beauchamp
# Contributors: Robert McGibbon, John D. Cho... | gph82/mdtraj | mdtraj/formats/mol2.py | Python | lgpl-2.1 | 9,925 | [
"MDTraj",
"OpenMM"
] | b495bbc5b5bfe38387b75c143a7fa8cd815cc8d2bd617b9c1b0a7ed8aab9f9e6 |
import os
from setuptools import setup, find_packages, Extension
def read(fname):
return open(os.path.join(os.path.dirname(__file__), fname)).read()
preprocess = Extension('waistcoat.preprocess',
sources=['waistcoat/preprocess.c',])
setup(
name = "waistcoat",
version = "0.01",
packages = find_package... | haydnKing/waistcoat | setup.py | Python | gpl-2.0 | 724 | [
"pysam"
] | 63fe47541817560c4ed0ed70e2b447bb141761cc58a072b06fa4d5ddf7f79441 |
#!/usr/bin/python
import httplib2
import os
import random
import sys
import time
from apiclient.discovery import build
from apiclient.errors import HttpError
from oauth2client.file import Storage
from oauth2client.client import flow_from_clientsecrets
from oauth2client.tools import run
from optparse import OptionPars... | lhongskie/yt-samples-python | create_broadcast.py | Python | apache-2.0 | 4,566 | [
"VisIt"
] | 503b46f1f1b08d1cee0915ac00eaa4d7ba282dfd01c5dac013e2cd29d7d7806d |
""" Models for the shopping cart and assorted purchase types """
from collections import namedtuple
from datetime import datetime
from decimal import Decimal
import analytics
import pytz
import logging
import smtplib
import StringIO
import csv
from courseware.courses import get_course_by_id
from boto.exception import ... | peterm-itr/edx-platform | lms/djangoapps/shoppingcart/models.py | Python | agpl-3.0 | 65,637 | [
"VisIt"
] | fc4eefa7ccdc300ad69e7c8f6351cac5445573249c136935bfe63f3dd71a01b2 |
"""
Dragonchess for Python
http://en.wikipedia.org/wiki/Dragonchess
Dragonchess is a three-dimensional fantasy chess variant created by Gary Gygax,
co-creator of the famed role-playing game Dungeons & Dragons. The game was introduced
in 1985 in issue No. 100 of Dragon Magazine.[1][2][3]
The Dragonchess gamebo... | shaolinmike/dragonchess | core.py | Python | gpl-3.0 | 8,876 | [
"Amber"
] | d026e95f166605757552d2756384061ff0ce2af7ca123caa9298b6a4fe8b8346 |
# -*- coding: utf-8 -*-
import sys
import os
from setuptools import setup, Command
PKG_PATH = os.path.abspath(os.path.dirname(__file__))
SRC_PATH = os.path.join(PKG_PATH, 'src')
VER_PATH = os.path.join(PKG_PATH, 'src', 'anima', '__init__.py')
REQ_PATH = os.path.join(PKG_PATH, 'requirements.txt')
sys.path.append(SRC_P... | damianignacio/anima | setup.py | Python | mit | 2,167 | [
"GULP"
] | 13d056891e301160c0b7092bca6fa0e043100438ec27993d560ccf5618af37df |
"""Test class for Repository CLI
:Requirement: Repository
:CaseAutomation: Automated
:CaseLevel: Component
:CaseComponent: Repositories
:Assignee: chiggins
:TestType: Functional
:CaseImportance: High
:Upstream: No
"""
from random import choice
from string import punctuation
import pytest
import requests
from f... | JacobCallahan/robottelo | tests/foreman/cli/test_repository.py | Python | gpl-3.0 | 110,296 | [
"Galaxy"
] | 4eba4960d891dec378fee8b86e83a0f12259e58c88cfc23ef59a2a2db3d6b9fe |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#alfie.py
#05/2015
__author__ = 'Igor Rodrigues da Costa'
__contact__ = 'igor.bioinfo@gmail.com'
''' This program will wrap all ALs predictor scripts in a user-friendly interface.'''
import os
import argparse
import al_finder
import al_formatdb
import al_blast
import al_... | igorrcosta/alfie | alfie.py | Python | gpl-2.0 | 9,171 | [
"BLAST"
] | 760f6e589bbd60ab6e7e58197bd4405f8737dbf52357dd8791373c8db2566008 |
# 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... | mlperf/training_results_v0.7 | Fujitsu/benchmarks/resnet/implementations/implementation_open/mlperf_implementations/train_imagenet.py | Python | apache-2.0 | 7,846 | [
"Gaussian"
] | f48cccc828a54e42b20414d030d169e6e94a6d9cc02aa2fe09d1281c2471c6fb |
from six import ensure_str, ensure_text
from .node import NodeVisitor, ValueNode, ListNode, BinaryExpressionNode
from .parser import atoms, precedence
atom_names = {v:"@%s" % k for (k,v) in atoms.items()}
named_escapes = {"\a", "\b", "\f", "\n", "\r", "\t", "\v"}
def escape(string, extras=""):
# Assumes input b... | UK992/servo | tests/wpt/web-platform-tests/tools/wptrunner/wptrunner/wptmanifest/serializer.py | Python | mpl-2.0 | 4,444 | [
"VisIt"
] | c42bb800e09a9ec3fcf4e9c4bdf511d9945fe057ec9ade8136a08654e498cbaf |
import os, sys, string
from collections import OrderedDict
import unittest
import vtk, qt, ctk, slicer
import numpy as np
import SimpleITK as sitk
import sitkUtils
from slicer.ScriptedLoadableModule import *
from CIP.ui import CaseReportsWidget
from CIP.ui import PreProcessingWidget
from CIP.ui import PdfReporter
fr... | acil-bwh/SlicerCIP | Scripted/CIP_CalciumScoring/CIP_CalciumScoring.py | Python | bsd-3-clause | 25,296 | [
"VTK"
] | 73b0ed67b8d1173d28f965d8d3f15c1164d2fdebf74721eaee1708a8bc8f1c48 |
#!/usr/bin/python
"""This script applies parsed BLAST results from a CSV file (produced by
parseblast.pl) to a series of GenBank files.
Oct 26, 2009 by Simon Eng
Changed the method of outputting statistics.
"""
try:
import optparse, csv, re, sys
from os import path
import logging.handlers
from... | wholebiome/MetaPathways_Python_Koonkie.3.0 | libs/python_scripts/MetaPathways_create_amino_sequences.py | Python | mit | 16,149 | [
"BLAST"
] | 99b01f9d231249fbfd5c235e2013e6a711fd093076b83e83fe588656eb0794b0 |
#!/bin/env python
# -*- coding: utf-8 -*-
"""
| This file is part of the web2py Web Framework
| Copyrighted by Massimo Di Pierro <mdipierro@cs.depaul.edu>
| License: LGPLv3 (http://www.gnu.org/licenses/lgpl.html)
| Thanks to ga2arch for help with IS_IN_DB and IS_NOT_IN_DB on GAE
Validators
-----------
"""
import os
i... | xiang12835/python_web | py2_web2py/web2py/gluon/validators.py | Python | apache-2.0 | 139,260 | [
"CASINO",
"MOE"
] | f0b7fa041affa219cf3410d114f318e45e2377a24f2949031b1d6ead6677121d |
#
# This source file is part of appleseed.
# Visit https://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2016-2019 Esteban Tovagliari, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaini... | appleseedhq/appleseed-maya2 | scripts/appleseedMaya/renderGlobals.py | Python | mit | 80,143 | [
"VisIt"
] | 8aebc47da635e93db6a44aa6c45a9248e42ec910b1461f16bae55de1b9445ef5 |
#!/usr/bin/env pythonw
"""
Runs Demag GUI PmagPy's main analysis GUI for demagnetization data. This
can be used for PCA of both AF and Thermal demag data, and calculation
of VGP's. It allows export of figures and analysis results for upload to
the MagIC database and/or publication. For more information on how to interp... | Caoimhinmg/PmagPy | programs/demag_gui.py | Python | bsd-3-clause | 356,391 | [
"ADF"
] | 6a323dfdbda97e8b819be9c2bde91ac068d38915620cfbaf6ae543f0e0557582 |
#===============================================================================
# load_ERAinterim.py
#-------------------------------------------------------------------------------
# @author D. T. Milodowski, September 2017
# This is a set of functions to load in ERAInterim meteorological data into
# numpy arrays. Th... | DTMilodowski/EO_data_processing | src/meteorology/load_ERAinterim.py | Python | gpl-3.0 | 20,948 | [
"NetCDF"
] | 7dacab3bc526ad491ba9b0300695c253cab8b3a8056c7bdc07f5cfe1818d2d5e |
from pyaxiom.netcdf.dataset import EnhancedDataset, EnhancedMFDataset
from pyaxiom.netcdf.cf import CFDataset
| axiom-data-science/pyaxiom | pyaxiom/netcdf/__init__.py | Python | mit | 110 | [
"NetCDF"
] | c10f3e64db9626767b07f2f4c960bb6200543151529a4c0bbe035abbb6807a05 |
"""
Utility functions for transcripts.
++++++++++++++++++++++++++++++++++
"""
import os
import copy
import json
import requests
import logging
from pysrt import SubRipTime, SubRipItem, SubRipFile
from lxml import etree
from HTMLParser import HTMLParser
from xmodule.exceptions import NotFoundError
from xmodule.contents... | romain-li/edx-platform | common/lib/xmodule/xmodule/video_module/transcripts_utils.py | Python | agpl-3.0 | 24,875 | [
"FEFF"
] | b737676e2243de08a809332e9b1335674c93b5ac48a14fd073158e4f88c18d0b |
# This code is part of Ansible, but is an independent component.
# This particular file snippet, and this file snippet only, is BSD licensed.
# Modules you write using this snippet, which is embedded dynamically by Ansible
# still belong to the author of the module, and may assign their own license
# to the complete wo... | camradal/ansible | lib/ansible/module_utils/basic.py | Python | gpl-3.0 | 97,269 | [
"VisIt"
] | 123c22d41db28be73c6cda3f42fa67c534a07dba01bf9df65020cd513964c8fd |
rule map_bwa_index:
"""Index with bwa"""
input:
fa = RAW + "genome.fa"
output:
mock = touch(MAP_INDEX + "genome"),
buckets = expand(
MAP_INDEX + "genome.{suffix}",
suffix="amb ann bwt pac sa".split()
)
log:
MAP_INDEX + "bwa_index.log"
b... | jlanga/smsk_popoolation | src/snakefiles/map.py | Python | mit | 5,050 | [
"BWA"
] | 2ac0fff648147557e9e9669abc742fc0090d7119fb138cdccc1e7d501aa40abd |
#!/usr/bin/env python
########################################################################
""" System Administrator Client Command Line Interface """
import sys
import pprint
import os
import atexit
import readline
import datetime
import time
from DIRAC import gConfig, gLogger
from DIRAC.Core.Base.CLI import CLI,... | arrabito/DIRAC | FrameworkSystem/Client/SystemAdministratorClientCLI.py | Python | gpl-3.0 | 47,795 | [
"ASE",
"DIRAC"
] | 433e50a0bc0612191f68d96525cce6d2aea52bd1a5a4e1e1d6fa1bdaa8452d3b |
#!/usr/bin/env python
import sys
import argparse
import numpy as np
import netCDF4 as nc
import mayavi.mlab as mlab
"""
Use MayaVi to visualise the bathymetry at a certain point.
Example:
./visualise_bathymetry 100 100 topog.nc --halo 100
"""
def main():
parser = argparse.ArgumentParser()
parser.add_argu... | CWSL/access-cm-tools | visualise/visualise_bathymetry.py | Python | apache-2.0 | 1,556 | [
"Mayavi"
] | 85ba5c3aec32b19727f67bdf7f2a0eaa85ef08a9ce5afd1fee804fc2f267006a |
# -*- coding: utf-8 -*-
#############################################################################
#
# expr.py
#
# description: types and expressions in Boole, all constructors inherit from
# the Expr class, except Tele, which inherits from BaseExpr
#
#
# Authors:
# Jeremy Avigad
# Cody Roux
#
#
###################... | avigad/boole | boole/core/expr.py | Python | apache-2.0 | 45,815 | [
"VisIt"
] | 19574e0fe746ece25587cffab972d26ab44245ef24f9429f7f1efd93a566439c |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS.
"""
from ..helpers import UniqueCourseTest
from ...pages.studio.auto_auth import AutoAuthPage
from ...pages.lms.courseware import CoursewarePage
from ...pages.lms.staff_view import StaffPage
from ...fixtures.course import CourseFixture, XBlockFixtureDesc
from t... | dsajkl/reqiop | common/test/acceptance/tests/lms/test_lms_staff_view.py | Python | agpl-3.0 | 7,357 | [
"VisIt"
] | fc848ad09d6cc9fc46a9c833c99166f48b2f15e5ee4cc1e6297fd2c302d805e6 |
"""
Acceptance tests for the teams feature.
"""
import json
import random
import time
from dateutil.parser import parse
import ddt
from nose.plugins.attrib import attr
from selenium.common.exceptions import TimeoutException
from uuid import uuid4
from common.test.acceptance.tests.helpers import get_modal_alert, Event... | itsjeyd/edx-platform | common/test/acceptance/tests/lms/test_teams.py | Python | agpl-3.0 | 84,795 | [
"VisIt"
] | 56664bbb313ea7188148614b69445229f3c9c56fd12b9aeef957dfd11e64ce26 |
# Copyright 2007 by Tiago Antao <tiagoantao@gmail.com>. 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 module allows to control fdist.
This will allow to call fdist... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/PopGen/FDist/Controller.py | Python | apache-2.0 | 8,622 | [
"Biopython"
] | de35118dd2ff17b3b96c6bd8fd59916bc3d4f143add48d990182bd7c581068a9 |
"""
Copyright (C) 2014-2016 Jakub Krajniak <jkrajniak@gmail.com>
This file is part of Backmapper.
Backmapper 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) a... | MrTheodor/bakery | src/files_io.py | Python | gpl-3.0 | 53,980 | [
"Gromacs",
"LAMMPS"
] | f2494f01b0fd7662bbd13da8bb265cbbdc6047107b031e3a7c9a0b4f2da6f8fc |
# -*- coding: utf-8 -*-
# script for computing the spectrum and associated quantities of the
# Fokker-Planck operator for the exponential integrate-and-fire neuron model
# on a rectangle of input mean and standard deviation (mu, sigma)
#
# the SpectralSolver class (written by Moritz Augustin in 2016-2017) is used he... | methods-for-neuronal-network-dynamics/fokker-planck-based-spike-rate-models | adex_comparison/calculate_quantities_spectral.py | Python | gpl-3.0 | 46,317 | [
"NEURON"
] | 2330fd81dc029fe2a0d4cf54f78fa529e5202211a06d0d882732f698ec8f307c |
"""
Programa de Segmentacion
Contiene Binarizacion, promedios de polarizacion, corte mediante contornos
"""
import cv2 #Opencv 3.000 a 32bits
import numpy as np
from skimage.filters import threshold_otsu
from scipy.ndimage import gaussian_filter
from skimage import measure
from skimage import filters
def avgPol(matrix... | xteeven/multispectral | Bin/Segment.py | Python | apache-2.0 | 2,509 | [
"Gaussian"
] | bc0bcc390a505cae0f4bfaa62af87bbdb2763fafcdf8bd654a8d8e3994eda13d |
'''
Created on Jan 18, 2013
@author: brian
'''
import openid
from openid.fetchers import HTTPFetcher, HTTPResponse
from urlparse import parse_qs
from django.conf import settings
from django.test import TestCase, LiveServerTestCase
from django.test.utils import override_settings
# from django.contrib.auth.models impor... | kalebhartje/schoolboost | common/djangoapps/external_auth/tests/test_openid_provider.py | Python | agpl-3.0 | 12,120 | [
"Brian"
] | e9f7352a6ff52cc3ba1ac8a2a9fdf6c2239eb2f899490f9484e2099acff1b6de |
#!/usr/bin/env python
"""
runtests.py [OPTIONS] [-- ARGS]
Run tests, building the project first.
Examples::
$ python runtests.py
$ python runtests.py -t {SAMPLE_TEST_FILE}
$ python runtests.py -t {SAMPLE_TEST}
Run a debugger:
$ gdb --args python runtests.py [...other args...]
"""
from __future__ i... | tcmoore3/mdtraj | runtests.py | Python | lgpl-2.1 | 7,784 | [
"MDTraj"
] | 781dc73e67437e6e18e2a221fca4d39b7c913c69cfbb42f233c6b46b18b91761 |
# $HeadURL$
""" The CountryMapping module performs the necessary CS gymnastics to resolve country codes """
__RCSID__ = "$Id$"
from DIRAC import S_OK, S_ERROR
from DIRAC.ConfigurationSystem.Client.Helpers.Operations import Operations
def getCountryMapping( country ):
""" Determines the associated country from the... | avedaee/DIRAC | Core/Utilities/CountryMapping.py | Python | gpl-3.0 | 1,175 | [
"DIRAC"
] | ccae46648a664e584d9275c8593c6b6ea326f492772f63c3c0e529cf1391e98e |
import random as rand
import numpy as np
import vtk
import os
import sys
import molar,molar.pdb
import vtk
PATH = os.environ['MOLECULES']
class Box():
def __init__(self,x=753,y=753,z=300):
#self.vertices=np.array(np.empty([8,3],dtype=float))
x=0.5*x
y=0.5*y
z=0.5*z
sel... | alinar/Molar | molar/mask_box.py | Python | gpl-2.0 | 6,274 | [
"VTK"
] | 7d6a3a13b4bf460b190ba273f9b01807f637734155e2a925098786fa3437f673 |
"""
################################################################################
# Copyright (c) 2003, Pfizer
# Copyright (c) 2001, Cayce Ullman.
# Copyright (c) 2001, Brian Matthews.
#
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provid... | xyproto/turbine | djl/libs/SOAPpy/Utilities.py | Python | gpl-3.0 | 4,973 | [
"Brian"
] | 999869c9f9aa3c744e87d090888d4d2d50191eb303d4f401b7154ce45ba05153 |
#!/usr/bin/env python
# ============================================================================
# RS 2013/01/24: Rewriting SN Ia Monte Carlo Markov Chain Reconstruction
# ----------------------------------------------------------------------------
# Now rewriting stuff I wrote in C++ some time ago, in the hope ... | rscalzo/pyBoloSN | run_S12_mcmc.py | Python | mit | 5,817 | [
"Galaxy"
] | 6b39ede9402a4fa3875c287eaa7a604aeb625632fd7c95a6f8657a2bb0e931a6 |
from django.shortcuts import render
from django.http import HttpResponse
from rest_framework import viewsets
from .serializers import StrainSerializer, CrisprArraySerializer, CrisprEntrySerializer
from .models import Strain, CrisprEntry, CrisprArray
from crispr.tasks import blastn, crt
import os
BASE_DIR = os.path.d... | Milt0n/CRISPR-Exposed | webapp/crispr_exposed/crispr/views.py | Python | lgpl-3.0 | 6,186 | [
"BLAST"
] | e5e6d608a846abab5ca0cc8441253c3bf37e8509d5ec3ce1857e15c2602b3379 |
# PyVision License
#
# Copyright (c) 2006-2008 David S. Bolme
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistributions of source code must retain the above copyright
# notice, thi... | wolfram2012/nimo | perception/ros_track_ssd/scripts/pyvision/features/v1like.py | Python | gpl-3.0 | 23,459 | [
"Gaussian"
] | e8027e68a1d7539ba52e6abd2f7e722a86aa35e3d5b6693531f758f1d03533c8 |
# Copyright 2007-2021 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 your option) any later ve... | erh3cq/hyperspy | hyperspy/tests/component/test_component_set_parameters.py | Python | gpl-3.0 | 1,914 | [
"Gaussian"
] | 754b6527859a04ad3d1ab4c021c045f9ab14c155faff16d877a7ddc09e16b7b8 |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-aiplatform | tests/unit/gapic/aiplatform_v1/test_tensorboard_service.py | Python | apache-2.0 | 360,461 | [
"Octopus"
] | e64f296b12d818c14f8d99ffbce50f6d6d673b71db92d645107eafff711d5c86 |
import sys
from os import path, devnull
from numpy.ma import log10
from numpy import array, errstate, nanmin, nanmax, nonzero, float64,\
bool_, string_, ones
from pysces.PyscesModel import PysMod
from IPython.display import HTML
from sympy import sympify
from functools import wraps
from ..config import ConfigRead... | exe0cdc/PyscesToolbox | psctb/utils/misc/_misc.py | Python | bsd-3-clause | 33,617 | [
"PySCeS"
] | c4b165a47fefbeb888b3529295de11276ce8c6942539a86a7fb35e471aa2ade0 |
#!/usr/bin/env python3
#* 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/lgp... | harterj/moose | modules/stochastic_tools/examples/batch/plot.py | Python | lgpl-2.1 | 2,833 | [
"MOOSE"
] | 7113c4017b8e5668170d88dbe350bdbb6d6d369fb30ddec30ff45141907eef89 |
#!/usr/bin/env python2
from __future__ import division
import sys
import os
from math import floor, ceil, sqrt, sin, cos
from collections import namedtuple
import numpy as np
import h5py
from optparse import OptionParser
from PIL import Image, ImageFont, ImageDraw
# Print pretty pictures from the wave functions comput... | luosaiyu/itp2d | scripts/itp_draw_art.py | Python | gpl-3.0 | 17,442 | [
"Gaussian"
] | fb3261086aeb5d037d48ebee79ffc646e250fd18ee6400c6b13366e3e9a8904b |
# =============================================================================
#
# CopyProjection.py
#
# This file is part of ANNarchy.
#
# Copyright (C) 2019 Julien Vitay <julien.vitay@gmail.com>,
# Helge Uelo Dinkelbach <helge.dinkelbach@gmail.com>
#
# This program is free software: you can redi... | vitay/ANNarchy | ANNarchy/extensions/convolution/Copy.py | Python | gpl-2.0 | 9,367 | [
"NEURON"
] | 959ffd17ce4df2bb495421d8427347fe40737271f1669be00d2c8391a147fbb6 |
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Provides an interface to communicate with the device via the adb command.
Assumes adb binary is currently on system path.
"""
import collections
imp... | cvsuser-chromium/chromium | build/android/pylib/android_commands.py | Python | bsd-3-clause | 61,574 | [
"Galaxy"
] | a2d9a3e12e5b3162e00a48b07adcaa50b08be3eeb00700862f2245f5dfe92ac0 |
import sys
import antlr
version = sys.version.split()[0]
if version < '2.2.1':
False = 0
if version < '2.3':
True = not False
class Stack:
def __init__(self):
self.data = []
def push(self,item):
self.data.append(item)
def pop(self):
self.data.pop()
def peek(self):
return se... | sirbrialliance/boo | lib/antlr-2.7.5/examples/python/tinybasic/basic.py | Python | bsd-3-clause | 21,563 | [
"VisIt"
] | b4f98eb018f9ba30c336c937b336e671c82fd123a54f4493a4366d8fb45ba951 |
""" Test class for JobWrapper
"""
# imports
import unittest
import importlib
import os
from mock import MagicMock
from DIRAC import gLogger, S_OK
from DIRAC.WorkloadManagementSystem.JobWrapper.JobWrapper import JobWrapper
from DIRAC.WorkloadManagementSystem.JobWrapper.WatchdogLinux import WatchdogLinux
class JobWra... | vmendez/DIRAC | WorkloadManagementSystem/JobWrapper/test/Test_JobWrapper.py | Python | gpl-3.0 | 2,741 | [
"DIRAC"
] | 920fc36c2dafaf13cb48bbc976cf2c8036833b9dd51e2989a3f0f9394e9d862b |
from pytest_bdd import given, when, then, parsers
from urllib.parse import urljoin
from django.contrib.auth.models import User
from model_mommy import mommy
from time import sleep
import pytest
import random
pytestmark = pytest.mark.django_d... | bronycub/sugarcub | utils/bdd.py | Python | gpl-3.0 | 2,311 | [
"VisIt"
] | 770ba6cbed639b5e83b9ada13c3a6faa35580cf7069f903715ce0a3f963d64b3 |
from os import sys, path
sys.path.append(path.dirname(path.dirname(path.abspath(__file__))))
import requests
from datetime import datetime
from geotrigger import GeotriggerClient
CLIENT_ID = 'YOUR_CLIENT_ID'
def device_example():
# Create the GeotriggerClient using only a client_id, a device will be
# regi... | Esri/geotrigger-python | examples/device_example.py | Python | apache-2.0 | 2,598 | [
"VisIt"
] | 99c09e34ed5fd83f928188afa5a72ffd584aa38c7a7d83fcb2e73dd20af887da |
## PRODUCE MEAN PLOTS
from __future__ import print_function
path = '/home/mkloewer/python/swm/'
path = '/home/kloewer/swm_scripts/back/'
import os; os.chdir(path) # change working directory
import numpy as np
from scipy import sparse
from scipy.integrate import cumtrapz
import matplotlib.pyplot as plt
import time as ti... | milankl/swm | calc/misc/final_plots.py | Python | gpl-3.0 | 7,295 | [
"NetCDF"
] | ab6eeb428f7f219543243159e9b89947e963c59efbbbef877a0403df39adcf10 |
from __future__ import division, absolute_import, print_function
import warnings
import sys
import collections
import operator
import numpy as np
import numpy.core.numeric as _nx
from numpy.core import linspace, atleast_1d, atleast_2d
from numpy.core.numeric import (
ones, zeros, arange, concatenate, array, asarr... | nbeaver/numpy | numpy/lib/function_base.py | Python | bsd-3-clause | 144,151 | [
"Gaussian"
] | 1eb5561bf983d3c5777910fcae1697ab2c24ffda17ced3de90f1138a3808233a |
# -*- coding: utf-8 -*-
# <nbformat>3.0</nbformat>
# <markdowncell>
# # netCDF File Visualization Case Study
#
# I was asked by a colleague to visualize data contained within this [netCDF file](https://motherlode.ucar.edu/repository/entry/show/RAMADDA/Unidata/Staff/Julien+Chastang/netcdf-explore?entryid=c7239224-d3f... | rsignell-usgs/notebook | Siphon/casestudy.py | Python | mit | 10,318 | [
"NetCDF"
] | 0b67dadb29f1c0a137be7b7c3b276900c8b76d295bb723ebc7ce1fa1a68ab7c2 |
import pandas as pd
import numpy as np
import scipy.io as sio
import ipdb, sys, traceback
import pickle
store_path = 'tmp/kohn.h5'
store = pd.HDFStore(store_path)
FILES = ['02', '10', '08', '05']
for f in FILES:
fp = 'data/timeseries/'+f+'_timeseries.mat'
print('loading file...'+fp)
matfile = sio.loadma... | elijahc/ml_v1 | hdf5_load_data.py | Python | mit | 1,696 | [
"NEURON"
] | 6f0b039e0ff43f59b0c6c9c603c42459d750fa5fc0fbb190da2948e838c84656 |
"""
NH3 fitter wrapper
==================
Wrapper to fit ammonia spectra. Generates a reasonable guess at the position
and velocity using a gaussian fit
Example use:
.. code:: python
import pyspeckit
sp11 = pyspeckit.Spectrum('spec.nh3_11.dat', errorcol=999)
sp22 = pyspeckit.Spectrum('spec.nh3_22.dat',... | vlas-sokolov/pyspeckit | pyspeckit/wrappers/fitnh3.py | Python | mit | 14,315 | [
"Gaussian"
] | 9efde82581c206cc6a927a1cf4887b88281d84732ce078fd2487c179f690c9b5 |
from datetime import timedelta
from dateutil.relativedelta import relativedelta
from datetime import datetime
from model_mommy import mommy
from django.test import TestCase, tag
from edc_constants.constants import YES, NO, NEG, IND
from edc_map.site_mappers import site_mappers
from bcpp_community import is_intervent... | botswana-harvard/bcpp-subject | bcpp_subject/tests/test_referral.py | Python | gpl-3.0 | 12,562 | [
"VisIt"
] | 5e802006e24f31e6d81b04a6a939cd74d50ea2a7953f91d52ecf9cdacd048813 |
"""Test the FixAtoms constraint and the Subset filter."""
from asap3 import *
from ase.lattice.cubic import FaceCenteredCubic
from asap3.md.velocitydistribution import MaxwellBoltzmannDistribution
from asap3.md.verlet import VelocityVerlet
from asap3.io.trajectory import PickleTrajectory
from asap3.constraints import ... | auag92/n2dm | Asap-3.8.4/Test/parallel/parallelConstraints.py | Python | mit | 2,899 | [
"ASE"
] | dbf77350932b3016a613ea416676a147b1f507c0a6270c83c1d43d2156b0c75c |
#!/usr/bin/env python
# Copyright 2015(c) The Ontario Institute for Cancer Research. All rights reserved.
#
# This program and the accompanying materials are made available under the
# terms of the GNU Public License v3.0.
#
# You should have received a copy of the GNU General Public License along with
# this program.... | oicr-ibc/cssscl | cssscl/build_dbs.py | Python | gpl-3.0 | 20,509 | [
"BLAST"
] | f4f256c9dd704157a681c93577b6a0d16b05f7adaf7cf5d1da13d6d1390a1c63 |
"""Helper functions for creating the most common surfaces and related tasks.
The helper functions can create the most common low-index surfaces,
add vacuum layers and add adsorbates.
"""
from math import sqrt
import numpy as np
from ase.atom import Atom
from ase.atoms import Atoms
from ase.data import reference_st... | grhawk/ASE | tools/ase/lattice/surface.py | Python | gpl-2.0 | 12,604 | [
"ASE"
] | e14475f25da92d7a166bd6f346b18f929cdc28206f28bacb00bb3c8092ed9aed |
"""Test the Transformationinfo."""
from collections import OrderedDict
from contextlib import contextmanager
import pytest
from mock import MagicMock as Mock, patch
from DIRAC import S_OK, S_ERROR
import DIRAC
import DIRAC.TransformationSystem.Client.TransformationClient
import DIRAC.Resources.Catalog.FileCatalogCli... | andresailer/DIRAC | TransformationSystem/test/Test_TransformationInfo.py | Python | gpl-3.0 | 15,069 | [
"DIRAC"
] | 75272f9e1514b97898ac2c3889264c69f07e724471e8c58babb7ab63d3309373 |
#!/bin/env python2.7
'''
chromachron clone in python2.7
and pygame1.9
inspired by awesome german design and pixies
@author brian morrow
'''
import pygame, sys, random, time, math, pygame.gfxdraw
from pygame.locals import *
from datetime import datetime
fps = 1
winwidth = 500
winheight = 500
def main():
pygam... | killerbat00/pyChromachron | clock.py | Python | mit | 2,143 | [
"Brian"
] | b7f3aedb98beb5cd8225edae55a166ee8126be2ce63cde2e42273051aff11c3d |
# -*- coding: utf-8 -*-
# @Author: YangZhou
# @Date: 2017-06-18 22:24:41
# @Last Modified by: YangZhou
# @Last Modified time: 2017-06-26 22:28:03
from aces.tools import mkdir, cd, mkcd, shell_exec,\
write, pwd, ls, to_txt
import aces.config as config
from ase import io, Atoms
from aces.io.vasp import writevas... | vanceeasleaf/aces | aces/runners/negf/__init__.py | Python | gpl-2.0 | 24,666 | [
"ASE",
"LAMMPS",
"VASP",
"phonopy"
] | f7f5dd54295a9aa14127be9ba633fbb585526fd4f42ea86e54cc002a3d3dc4ce |
import numpy as np
def spatial_rate_map(x, y, t, spike_train, binsize=0.01, box_xlen=1,
box_ylen=1, mask_unvisited=True, convolve=True,
return_bins=False, smoothing=0.02):
"""Divide a 2D space in bins of size binsize**2, count the number of spikes
in each bin and divi... | CINPLA/exana | exana/tracking/fields.py | Python | gpl-3.0 | 32,391 | [
"Gaussian"
] | ba9f9d89ff4f62ba5cee16e9ba15e5ecddcc18a2e8d341c707d203a20196d69a |
# import ocl
import openvoronoi as ovd
import ovdvtk
# import time
import vtk
# import datetime
import math
import random
"""
This script does not use OpenVoronoi, it is used merely for drawing and
verifying solutions etc.
There are functions for:
- voronoi-bisectors and verifying the parametric equations for bisector... | aewallin/openvoronoi | python_examples/arc/arc_predicates.py | Python | lgpl-2.1 | 6,658 | [
"VTK"
] | 908f2eb6a4cf9f3383d1d6c5b46b0f505c2c5c606151d856cb7c332908a12b6c |
import sublime
import threading
import json
import sys
import time
import urllib.request
from .threads import ThreadTracker
from .threads import ThreadProgress
from .threads import PanelThreadProgress
from .printer import PanelPrinter
import MavensMate.lib.command_helper as command_helper
from MavensMate.lib.response_h... | frontendloader/MavensMate-SublimeText | lib/cli.py | Python | gpl-3.0 | 8,762 | [
"VisIt"
] | 320e7757d079e07f525c4f97f4e9f4f700b313f25b8e3061888f3fb7046e07dc |
"""
The :mod:`sklearn.covariance` module includes methods and algorithms to
robustly estimate the covariance of features given a set of points. The
precision matrix defined as the inverse of the covariance is also estimated.
Covariance estimation is closely related to the theory of Gaussian Graphical
Models.
"""
from ... | B3AU/waveTree | sklearn/covariance/__init__.py | Python | bsd-3-clause | 1,204 | [
"Gaussian"
] | 259434c1ecc107663d211fc768a1af69b703ad24c9c0fc5fff9b25607a99897d |
#!/usr/bin/env python
from __future__ import division
# ----------------------------------------------------------------------------
# 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 s... | Jorge-C/bipy | skbio/core/tests/test_distance.py | Python | bsd-3-clause | 23,043 | [
"scikit-bio"
] | 8fe1db5fbc22a7895d4b242cca3f6a34b7dfd4d28fd76a7163ebd2555ecea293 |
import numpy as np
import autograd.numpy as npa
import matplotlib.pylab as plt
import argparse
import os
import json
import sys
sys.path.append('../ceviche')
from ceviche import fdfd_ez as fdfd
from ceviche import fdtd, jacobian
from ceviche.constants import *
from ceviche.utils import imarr, aniplot, my_fft
# note,... | fancompute/ceviche | examples/forwardmode_grating_coupler.py | Python | mit | 17,404 | [
"Gaussian"
] | c140421268ef20df6190436d87e76634945a9ff0738a9c5967114b1b42a1325c |
import numpy as np
import cPickle
import pdb, sys, os, time
import matplotlib.pyplot as plt
from bayes.pyhm_dev import pyhm
from bayes.gps_dev.gps import gp_class, gp_routines, spgp_routines
import irac_kernels
from planetc import transit
import utils
def get_chain_from_walkers( walker_chains, acor_integs, ncorr_bu... | tomevans/pyirac | pyirac/misc/fitting.py | Python | gpl-2.0 | 51,017 | [
"Gaussian"
] | 326e58174a54e93bdf1063c1ac863c4d1dd88f41bd51cf2876494ee796623eae |
# -*- coding: utf-8 -*-
from south.utils import datetime_utils as datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Deleting field 'SurveyQuestion.for_display'
db.delete_column(u'survey_s... | myvoice-nigeria/myvoice | myvoice/survey/migrations/0006_auto__del_field_surveyquestion_for_display__del_field_surveyquestion_d.py | Python | bsd-2-clause | 12,977 | [
"VisIt"
] | c843c438071aa1ec996c3db846a2cb53f6acf70f094ce1df4f93684dc2264dc1 |
#!/usr/bin/env python
"""
Calculate core duration, minimum core base, maximum core height, mean core mass,
formation time, dissipation time, maximum depth, depth evolution and
corresponding times for tracked clouds.
Output is saved in a pkl file as a list of dictionaries, with one dictionary per
core id. Dictionary ... | vladpopa/ent_analysis | id_stats/core_id_stats.py | Python | mit | 3,715 | [
"NetCDF"
] | d2b2ad2c3715002a4871aacbc166448146685ad9a4dca3f76cdf73b65698b76a |
#!/usr/bin/env python
import sys
def convert(filename):
lines = open(filename).readlines()
t1 = ''.join(lines)
first = True
for i in range(len(lines)):
line = lines[i]
if line.startswith('from ASE'):
if first:
lines[i] = 'from ase.all import *\n'
... | slabanja/ase | tools/ASE2ase.py | Python | gpl-2.0 | 2,847 | [
"ASE"
] | 4f0a34dbcff1ec132629715650ad3b18336b080ee9d793860493e3b6a21ce5b0 |
# Copyright 2018 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | mlperf/training_results_v0.5 | v0.5.0/intel/intel_minigo_submission_public_tensorflow/code/minigo/tensorflow/minigo/gtp_extensions.py | Python | apache-2.0 | 6,425 | [
"VisIt"
] | f425a9a63f5a4329d38a4ef8a7134be2f448c325a06665ebbdfb5dd5ed438853 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# PCR-GLOBWB (PCRaster Global Water Balance) Global Hydrological Model
#
# Copyright (C) 2016, Ludovicus P. H. (Rens) van Beek, Edwin H. Sutanudjaja, Yoshihide Wada,
# Joyce H. C. Bosmans, Niels Drost, Inge E. M. de Graaf, Kor de Jong, Patricia Lopez Lopez,
# Stefanie Pes... | UU-Hydro/PCR-GLOBWB_model | modflow/scripts/configuration.py | Python | gpl-3.0 | 29,314 | [
"NetCDF"
] | d5348d7a149e8244b0bb93408e9ca7221fe48917697ec2862e522c6a06ebce3d |
# Copyright 2015 CERN. This software is distributed under the
# terms of the GNU General Public Licence version 3 (GPL Version 3),
# copied verbatim in the file LICENCE.md.
# In applying this licence, CERN does not waive the privileges and immunities
# granted to it by virtue of its status as an Intergovernment... | kiliakis/BLonD | __TEST_CASES/main_files/TC4_Stationary_multistation.py | Python | gpl-3.0 | 4,516 | [
"Gaussian"
] | 32f643ad9494145d035326c658cc5d911c6cac731caafd347773ef93454b05a9 |
__all__ = [
'BadRequestException',
'BadStateException',
'CsrfException',
'DropboxOAuth2Flow',
'DropboxOAuth2FlowNoRedirect',
'NotApprovedException',
'ProviderException',
]
import base64
import os
import six
import sys
import urllib
from .dropbox import Dropbox
from .session import pinned_s... | smarx/dropbox-sdk-python | dropbox/oauth.py | Python | mit | 16,430 | [
"VisIt"
] | c02fbe4a98e8ec4ae43e76561b9de45433dd33091c4973ef4bb0c666f400b50c |
from selenium.webdriver.common.keys import Keys
from xvfbwrapper import Xvfb
from torutils import TorBrowserDriver
from log import wl_log
import os
import common as cm
from dumputils import Sniffer
import time
import utils as ut
BAREBONE_HOME_PAGE = "file://%s/barebones.html" % cm.ETC_DIR
VBOX_GATEWAY_IP = "10.0.2.2... | pankajb64/webfp-crawler-phantomjs | tor-browser-crawler-webfp-paper/datacollection/visit.py | Python | gpl-2.0 | 7,196 | [
"VisIt"
] | 6e7b215796d0a2d38d8ffc8fa223938882fb35bbdab0ccfb8abbe29445c57bf2 |
#!/usr/bin/env python
# encoding: utf-8
#| Copyright Inria May 2015
#| This project has received funding from the European Research Council (ERC) under
#| the European Union's Horizon 2020 research and innovation programme (grant
#| agreement No 637972) - see http://www.resibots.eu
#|
#| Contributor(s):
#| - Jean-Bap... | jbmouret/limbo | waf_tools/mkl.py | Python | gpl-3.0 | 4,827 | [
"Gaussian"
] | b87bd966f06eb5997531900119cc94f9fc6019b0143e9130e3e8b97d8718361f |
# This file is part of PyImgur.
# PyImgur 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.
# PyImgur is distributed in the hope... | ronnienv/antTrails | libs/pyimgur/__init__.py | Python | apache-2.0 | 63,507 | [
"VisIt"
] | 0667277a100e900d06dc959914a8ce5a15643fb3f747cfe1989b0eb3ef595a9c |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# thumbor imaging service
# https://github.com/thumbor/thumbor/wiki
# Licensed under the MIT license:
# http://www.opensource.org/licenses/mit-license
# Copyright (c) 2011 globo.com thumbor@googlegroups.com
# pylint: disable=no-member
import argparse
import sys
from importl... | scorphus/thumbor | thumbor/doctor.py | Python | mit | 5,480 | [
"VisIt"
] | 7edf92e30e70114b9760f0b484d9f045c2c758fd03ddcf7d023c8c9f5adbe9ac |
"""
Utility methods for testing.
"""
import fileinput
import os
import vcf
from django.contrib.auth.models import User
from main.models import AlignmentGroup
from main.models import Chromosome
from main.models import Dataset
from main.models import ExperimentSample
from main.models import Project
from main.models i... | woodymit/millstone_accidental_source | genome_designer/main/testing_util.py | Python | mit | 4,495 | [
"BWA"
] | a3aa3c854043b1db369bc30c21ee2d753d7b67006235a63025bb5f248d7a3399 |
#!/usr/bin/python
# dr14_t.meter: compute the DR14 value of the given audiofiles
# Copyright (C) 2011 Simone Riva
#
# 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 Lic... | magicgoose/dr14_t.meter | dr14tmeter/dr14_tmeter.py | Python | gpl-3.0 | 6,395 | [
"VisIt"
] | 1301f6f43f2816fba026587bfdff7165074cdca999ee969cc9dd7846de62bde1 |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
# Copyright (C) 2008 Evan Martin <martine@danga.com>
"""A git-command for integrating reviews on Rietveld."""
from distutils.vers... | fanjunwei/depot_tools | git_cl.py | Python | bsd-3-clause | 109,253 | [
"VisIt"
] | 1e2c240ea8639fa1ebd329be36810ce51e6b49c1affba75225004d3ea1467e37 |
from __future__ import (absolute_import, division, print_function)
from reduction_gui.instruments.interface import InstrumentInterface
from reduction_gui.widgets.inelastic.dgs_sample_setup import SampleSetupWidget
from reduction_gui.widgets.inelastic.dgs_data_corrections import DataCorrectionsWidget
from reduction_gui.... | dymkowsk/mantid | scripts/Interface/reduction_gui/instruments/dgs_interface_dev.py | Python | gpl-3.0 | 2,316 | [
"CRYSTAL"
] | d18a3f798b02658881e9f3e0ea28ec64d37120f2f44c32df243fd9b352c4b673 |
'''
imgur.py
imgur.com specific uploader
'''
from sqlite3 import IntegrityError
import pyimgur
import mercury.log
log = mercury.log.getLogger()
def authenticate(config):
log.debug('[imgur] Starting authentication setup.')
if not config['services']['imgur']['client_id'] and not config['services']['imgur']['... | tdreyer1/mercury | mercury/services/imgur.py | Python | mit | 4,928 | [
"VisIt"
] | fd9c89341377210a0f9019d997583194410ce13bea9d9009825c8b47c2efe739 |
# Libraries
import pandas as pd
import editdist
import mmap
import os
import sys
import time
import itertools
import gzip
import numpy as np
from collections import Counter
import random
# ALIGNER BLAST
def rasl_probe_blast(read_file_path, blastn_path, db_path):
"""
This function returns blast results ... | SuLab/RASLseqAligner | src/RASLseqAnalysis_NAR.py | Python | mit | 21,108 | [
"BLAST"
] | 87dfb0de5db21d19343b13857e22b6526bf04d513641ef0f0e3ec0e874931cc1 |
# Test run of VTK-logger by MW - Adapted from Tomek Sokolowski
# ### INSTRUCTIONS ###
"""
1. Set the directories with which the script should work:
"""
# Root directory of the eGFRD algorithm files:
# Use the full path (e.g. NOT a tilde)
egfrd_directory ='/storage1/wehrens/sep2011_eGFRD'
# Output directory of the VTK... | gfrd/egfrd | visualization/run_pipeline.py | Python | gpl-2.0 | 1,444 | [
"ParaView",
"VTK"
] | f10fa36bcafb779d3f5ccc5428135ac2955dda9298afda7c9c70382ded78e727 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Mapsplice2(MakefilePackage):
"""MapSplice is a software for mapping RNA-seq data to refer... | LLNL/spack | var/spack/repos/builtin/packages/mapsplice2/package.py | Python | lgpl-2.1 | 1,770 | [
"Bowtie"
] | b38c46ab0642b9cca99e82e09314e8254e6bc0593bf13f1977bb44c54adc44a3 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright 2013 The Plaso Project Authors.
# Please see the AUTHORS file for details on individual authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the Li... | cvandeplas/plaso | plaso/parsers/sqlite_plugins/firefox_test.py | Python | apache-2.0 | 10,548 | [
"VisIt"
] | 9ec40fcd70d91a0559ea17b27a6f96e5bcc60e900a0d9d90bb28bdc979155ad5 |
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