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'''
SASSIE: Copyright (C) 2011 Joseph E. Curtis, Ph.D.
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.
... | madscatt/zazzie | src_2.7/sassie/test_sassie/interface/energy_minimization/test_smaller1.py | Python | gpl-3.0 | 5,535 | [
"CHARMM"
] | 1f602c2834bae4821baf3c72a01fe5661e5a35b123f7e6b6556a821e15a388f0 |
# coding: utf8
{
'': '',
' Module is the main communications hub of the Sahana system. It is used to send alerts and/or messages using SMS & Email to various groups and individuals before, during and after a disaster.': ' Module is the main communications hub of the Sahana system. It is used to send alerts and/or me... | ksetyadi/Sahana-Eden | languages/en-gb.py | Python | mit | 220,276 | [
"VisIt"
] | 36c29fca14c9a1702959865df7d3b08f364ab8e352b521eae3be01c4f22b2354 |
# Copyright 2019 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, s... | google/pyctr | analysis/cfg_test.py | Python | apache-2.0 | 24,542 | [
"VisIt"
] | 3ec2dd8f9de1a812082d39c1f58c9d79b92996e1a061ff15aa845507f77f633e |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/pbc/scf/kghf.py | Python | apache-2.0 | 7,388 | [
"PySCF"
] | bb57224640e7f5ae0f8c08e7b47df4d3141ae35098b34d94991f4d95636d3b6e |
# =============================================================================
# Copyright (C) 2010 Diego Duclos
#
# This file is part of pyfa.
#
# pyfa 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 ... | pyfa-org/Pyfa | gui/builtinViewColumns/misc.py | Python | gpl-3.0 | 42,823 | [
"CRYSTAL"
] | 5526780bad57906329d55900001e3b5a0d0c29a431a0bfa6159062245fd712a8 |
"""
Shared code for builders.
For developers implementing a new builder,
you should inherit from :class:`Builder`.
"""
__author__ = "Dan Gunter <dkgunter@lbl.gov>"
__date__ = "5/29/13"
## Imports
# system
from abc import ABCMeta, abstractmethod
import copy
import logging
import multiprocessing
import queue as Queue... | materialsproject/pymatgen-db | pymatgen/db/builders/core.py | Python | mit | 17,314 | [
"pymatgen"
] | 4be6dc6b783132078e03fae58759238f7b12b1e243902c10d4d4c5c088f7094a |
# regression tests with mosaicing gridders doing single field
# imaging (essentially just primary beam correction, hence the name)
# some fixed parameters are given in pbcorrtest_template.in
from synthprogrunner import *
import math
def analyseResult(spr, expected_rms):
'''
spr - synthesis program runner (to... | ATNF/askapsdp | Code/Components/Synthesis/testdata/current/simulation/synthregression/noisetest.py | Python | gpl-2.0 | 3,417 | [
"Gaussian"
] | dc0076301bf53c44e26026a656a39f471dd4ebc1c1bb68d4dccc066dbfb8aa39 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | Stargrazer82301/CAAPR | CAAPR/CAAPR_AstroMagic/PTS/pts/do/fitskirt/rotate.py | Python | mit | 2,909 | [
"Galaxy"
] | 9fd94c70d7812e34bb36e25fbfa0f17e25f45347fffefb9401c0da008da2b2e1 |
# Author: Samuel Genheden samuel.genheden@gmail.com
"""
Program to setup a ComQum-ELBA run
Part of ComQum-ELBA
"""
import argparse
import numpy as np
from sgenlib import lammps
control_str = \
"""$point_charges file=pointcharges
$operating system unix
$path
$symmetry c1
$coord file=coord
$scfintunit
unit=30 ... | SGenheden/Scripts | Lammps/lmp_comqum.py | Python | mit | 2,693 | [
"LAMMPS"
] | 7942feecda3deb29c7be60981a2ca39c24aa4dce2fa8f663c69764321453407d |
import numpy as np
from astropy import units as u
class EjectionModel:
'''
Ejection model class
'''
_name = 'Unknown'
def __init__(self, name):
self._name = name
def g(self, r):
'''
Survival function of HVS as a function of flight time expressed as lifetime ... | contigiani/hvs | ejection.py | Python | gpl-3.0 | 17,326 | [
"Gaussian"
] | f779d0b0a050efbf4d5c34e7645e415d68c03a324d82438cb4faca558075525c |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-error-reporting | tests/unit/gapic/errorreporting_v1beta1/test_report_errors_service.py | Python | apache-2.0 | 57,358 | [
"Octopus"
] | 59e412d1216c35778da31960e720e44106e137984294a9419f7909ec2114a97f |
from django.contrib.auth import logout, login, authenticate
from django.contrib.auth.decorators import login_required
from django.http import HttpResponse, HttpResponseRedirect, Http404
from django.shortcuts import get_object_or_404, render, redirect
from django.template import RequestContext
from django.core.exception... | illegal-llamas/djangazon | website/views.py | Python | mit | 21,021 | [
"VisIt"
] | b5c54bb950d8d86091ca3119a3bc38ee87c85877fbd00b8d69e33d1fd744ea83 |
"""
Tools for the instructor dashboard
"""
import json
import dateutil
from django.contrib.auth.models import User
from django.http import HttpResponseBadRequest
from pytz import UTC
from django.utils.translation import ugettext as _
from opaque_keys.edx.keys import UsageKey
from six import text_type
from courseware.... | hastexo/edx-platform | lms/djangoapps/instructor/views/tools.py | Python | agpl-3.0 | 7,739 | [
"VisIt"
] | 545328fe20727ff53d8308b3f40207df0cee3bb2e5c0f62352748b2bceb0d5d5 |
# -*- coding: utf-8 -*-
# Copyright (C) 2019 - 2020 by Pedro Mendes, Rector and Visitors of the
# University of Virginia, University of Heidelberg, and University
# of Connecticut School of Medicine.
# All rights reserved.
# Copyright (C) 2017 - 2018 by Pedro Mendes, Virginia Tech Intellectual
# Properties, Inc.,... | copasi/COPASI | copasi/bindings/python/unittests/Test_CReportDefinition.py | Python | artistic-2.0 | 4,068 | [
"COPASI"
] | 437bb56e416524c26c4f90c56e4e7b03b1bfc0612d90aae841ce553cd10dd192 |
# Hidden Markov Model Implementation
import pylab as pyl
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy as scp
import scipy.ndimage as ni
import scipy.io
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import rospy
#import hrl_lib.mayavi2_util as mu
imp... | tapomayukh/projects_in_python | classification/Classification_with_HMM/Single_Contact_Classification/simulation_results/Combined/hmm_crossvalidation_force_20_states.py | Python | mit | 14,357 | [
"Gaussian",
"Mayavi"
] | 4fbebf8150018545ceb4d0748c46c010ff473547be90fee3d2a34112395eecbd |
from setuptools import setup
from setuptools.command.develop import develop
from setuptools.command.install import install
from setuptools.command.bdist_egg import bdist_egg
from setuptools.command.easy_install import easy_install
import subprocess
import os
SETUP_DIR = os.path.dirname(os.path.abspath(__file__))
def ... | JohnAbel/gillespy | setup.py | Python | gpl-3.0 | 3,350 | [
"Brian"
] | bfec276e7b9b0aaf371d1c6da42ec68b8c7eea7de7c1243cc5ad067093ed1f47 |
import os
from os.path import join
import numpy as n
def writeScript(rootName, plate):
f=open(rootName+".sh",'w')
f.write("#!/bin/bash \n")
f.write("#PBS -l walltime=260:00:00 \n")
f.write("#PBS -o "+plate+".o.$PBS_JOBID \n")
f.write("#PBS -e "+plate+".e$PBS_JOBID \n")
f.write("#PBS -M comparat@mpe.mpg.de \n")
f... | JohanComparat/pySU | spm/bin/write_run_scripts_dr7_kroupa-ND.py | Python | cc0-1.0 | 967 | [
"Galaxy"
] | 3d34bbe9dec26cc6a96eefd2eb174acf11457101e9faacf615f2516d2582e034 |
#!/usr/bin/env python
# encoding:utf-8
# author:dbr/Ben
# project:tvdb_api
# repository:http://github.com/dbr/tvdb_api
# license:unlicense (http://unlicense.org/)
"""Unittests for tvdb_api
"""
import os
import sys
import types
import datetime
import pytest
# Force parent directory onto path
sys.path.insert(0, os.pa... | dbr/tvdb_api | tests/test_tvdb_api.py | Python | unlicense | 18,071 | [
"Firefly"
] | 748168a0203a72d63b5c101279b57c6dedf39be6ce2af5ea11b3eb8f6bbf4d1f |
"""HTTPS module based on the GFAL2_StorageBase class."""
# from DIRAC
from DIRAC.Resources.Storage.GFAL2_StorageBase import GFAL2_StorageBase
from DIRAC import gLogger
class GFAL2_HTTPSStorage( GFAL2_StorageBase ):
""" .. class:: GFAL2_HTTPSStorage
HTTP interface to StorageElement using gfal2
"""
# davs i... | fstagni/DIRAC | Resources/Storage/GFAL2_HTTPSStorage.py | Python | gpl-3.0 | 882 | [
"DIRAC"
] | 68e02c7ddbec36550d9d2dc7882f44ffd113317954803dbe5e365d35255105d1 |
# MonkeyRunner tool to input generated coordinate list
from com.android.monkeyrunner import MonkeyRunner, MonkeyDevice
import time
import os
OK_BUTTON = (675, 275)
RESUME_BUTTON = (395, 715)
cwd = os.getcwd()
datadir = cwd + "/solutiondata"
os.chdir(datadir)
sfile = open('solution.txt', 'r')
sfile.seek(0, 2)
endfi... | thaReal/scramble-solver | src/tournament_monkey.py | Python | mit | 1,719 | [
"BLAST"
] | 8a78d5f374cfa452543303edb1d24bcd3db76a3b300f26fc63672b7b91ea44b0 |
# -*- coding: utf-8 -*-
def main():
startApplication("sasview")
mouseClick(waitForObject(":groupBox_6.cbCategory_QComboBox_2"), 68, 16, 0, Qt.LeftButton)
mouseClick(waitForObjectItem(":groupBox_6.cbCategory_QComboBox_2", "Cylinder"), 66, 7, 0, Qt.LeftButton)
clickButton(waitForObject(":groupBox_7.chkPo... | SasView/sasview | src/sas/qtgui/UnitTesting/SquishTestSuites/suite_sasview_qt/tst_PolydispTable/test.py | Python | bsd-3-clause | 4,899 | [
"Gaussian"
] | 31a15a2b23a70d64ad5ccdb7a58bce126d90854ef4701dcd1b40baac0a2bf767 |
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | gkc1000/pyscf | pyscf/pbc/ci/cisd.py | Python | apache-2.0 | 4,715 | [
"PySCF"
] | b648db58d754c71f659d31799cfeba1c018be109959cc5390e52e47d66773171 |
# $Id$
#
# Copyright (c) 2003-2006 Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" utility functionality for molecular... | rdkit/rdkit-orig | rdkit/Chem/Fingerprints/MolSimilarity.py | Python | bsd-3-clause | 10,684 | [
"RDKit"
] | 1df18335e5beb627b89cdd1b73ade96bff54cb9b38559ed3acc3b08310ac5b39 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | skosukhin/spack | var/spack/repos/builtin/packages/exodusii/package.py | Python | lgpl-2.1 | 3,575 | [
"NetCDF"
] | 17eb32b3aaa7d795cdf4efdd0425af787b4e37b5d1374af1f0b9aaed7750dd63 |
#!/usr/bin/env python
# vim:fileencoding=UTF-8:ts=4:sw=4:sta:et:sts=4:fdm=marker:ai
from __future__ import (unicode_literals, division, absolute_import,
print_function)
__license__ = 'GPL v3'
__copyright__ = '2013, Kovid Goyal <kovid at kovidgoyal.net>'
__docformat__ = 'restructuredtext en'
... | sharad/calibre | src/calibre/db/tests/writing.py | Python | gpl-3.0 | 32,831 | [
"MOOSE"
] | 8ab21ba228f93a3beccad63f419f97bac3467f7c3d2057070076533295c57e05 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | espressomd/espresso | doc/tutorials/electrokinetics/scripts/eof_analytical.py | Python | gpl-3.0 | 4,709 | [
"ESPResSo"
] | e3e8efaed6108c445e7a66b357125ce961eac2da50e58893f3f704ed4e92d221 |
#! /usr/bin/python
# This script reads through the Bstricta_278_v1.2.annotation_info.txt
# (obtained from the JGI Boechera stricta assembly files) and creates
# a file that contains the GO associations for each gene as well as
# the best TAIR10 hit symbols and defline. Note that one single column
# for GO associatio... | schimar/hts_tools | RNAseq/get_GO_associations.py | Python | gpl-2.0 | 7,598 | [
"Bioconductor"
] | cadc35997391e895442e04b41af600bde08ded1f87b91b59cfa5546f4048c4b9 |
""" This module allows the user to place text in 3D at a location on the
scene.
Unlike the 'Text' module, this module positions text in 3D in the scene,
and in 2D on the screen. As a result the text resizes with the figure,
and can be masked by objects in the foreground.
"""
# Author: Gael Varoquaux <gael dot varoquau... | dmsurti/mayavi | mayavi/modules/text3d.py | Python | bsd-3-clause | 6,288 | [
"Mayavi"
] | 7fe6fefd2547f04d9521ecacb3c043d4e423569adce36a159a4f2a4aff565674 |
# Copyright 2020, The TensorFlow Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed t... | tensorflow/privacy | tutorials/mnist_dpsgd_tutorial_tpu.py | Python | apache-2.0 | 6,302 | [
"Gaussian"
] | 1c6c7f317964dd8dcd75406d1f54bac66d20ed0cc022e0e70adc398fc64a0ebd |
'''
Calculates the maximum wind velocity based on hourly wind vector data.
A netcdf file with hourly data from 07:00 to 06:00 UTC serves as data source.
The amplitude of the hourly wind vectors is calculated for each cell.
The amplitudes are then averaged over 24h. The result is interpolated from the
4 km UM g... | kmunve/pysenorge | pysenorge/themes/max_wind_speed_daily.py | Python | gpl-3.0 | 5,267 | [
"NetCDF"
] | 626e37b725f93d7cc08a280cd32d0a01ca56f55ae9b52fe3b06acf89881f6d81 |
from deepmonster.machinery.architecture import Architecture
from deepmonster.nnet.activations import Rectifier, Softmax
from deepmonster.nnet.blocks import ConvBlock, FullyConnectedBlock
from deepmonster.nnet.initializations import Initialization, Gaussian
from deepmonster.nnet.extras import Reshape
from deepmonster.nn... | olimastro/DeepMonster | deepmonster/testing/mnist-test/mnist-arch.py | Python | mit | 1,472 | [
"Gaussian"
] | a01873d3dc30281352830b38f8fdd4f3796e69ae8c8b438e3495fe1e4253464f |
# -*- coding: utf-8 -*-
import datetime
from south.db import db
from south.v2 import DataMigration
from django.db import models
class Migration(DataMigration):
EMAILS = [
('approve.html',
'Hello {{ title }} {{ first_name }} {{ last_name }}.\n'
'\n'
'Welcome to ASVO ... | IntersectAustralia/asvo-tao | web/tao/migrations/0036_add_email_templates.py | Python | gpl-3.0 | 13,784 | [
"VisIt"
] | 55d1c65ef2b6ad4c0b4b49fa35ccc644f7d61f7c8edbcd4dfc4dd16671357f28 |
"""Fortran/C symbolic expressions
References:
- J3/21-007: Draft Fortran 202x. https://j3-fortran.org/doc/year/21/21-007.pdf
"""
# To analyze Fortran expressions to solve dimensions specifications,
# for instances, we implement a minimal symbolic engine for parsing
# expressions into a tree of expression instances. A... | numpy/numpy | numpy/f2py/symbolic.py | Python | bsd-3-clause | 53,004 | [
"VisIt"
] | dc4472482de660ef3e35f01f4c398c39dd327cfb98b3c91c7aac535ca15ba590 |
""" This is the StorageElement class.
"""
# # custom duty
import copy
import datetime
import errno
import os
import re
import sys
import threading
import time
from functools import reduce
# # from DIRAC
from DIRAC import gLogger, gConfig, siteName
from DIRAC.Core.Utilities import DErrno
from DIRAC.Core.Utilities.F... | arrabito/DIRAC | Resources/Storage/StorageElement.py | Python | gpl-3.0 | 48,638 | [
"DIRAC"
] | 7164aafe6b8b4f6534d18e5f8623edb85acea04f9440e685f0b2b37b8c7f9ce9 |
# coding: utf-8
from __future__ import unicode_literals
"""
This module provides classes to comparsion the structures of the two
molecule. As long as the two molecule have the same bond connection tables,
the molecules are deemed to be same. The atom in the two molecule must be
paired accordingly.
This module is supp... | yanikou19/pymatgen | pymatgen/analysis/molecule_structure_comparator.py | Python | mit | 6,625 | [
"Dalton",
"pymatgen"
] | da7473d3f645b2685d2714ab2376c196259c63ee0c365d43be436b861523673c |
"""Example of inference with the stochastic Lotka-Volterra predator prey model.
Treatment roughly follows:
Owen, J., Wilkinson, D. and Gillespie, C. (2015) Likelihood free inference for
Markov processes: a comparison. Statistical Applications in Genetics and
Molecular Biology, 14(2).
"""
import logging
from fun... | HIIT/elfi | elfi/examples/lotka_volterra.py | Python | bsd-3-clause | 8,407 | [
"Gaussian"
] | 29eb0f9959bb68cf7fc3f9fc69a231b7e452425c927c61f838369ddb018a2769 |
#-------------------------------------------------------------------------------
# rbtlib: test_rbt.py
#
# Tests for rbt.py.
#-------------------------------------------------------------------------------
# The MIT License (MIT)
# Copyright (c) 2016 Brian Minard
#
# Permission is hereby granted, free of charge, to an... | bminard/rbtlib | rbtlib/test_rbt.py | Python | mit | 4,092 | [
"Brian"
] | 2e786fb769b953b7e3ba7a872c04695a3626183ddda2ed0d420788dffb0e9aa3 |
import numpy as np
from .. import backend as K
try:
import librosa
except ImportError:
librosa = None
TAGS = ['rock', 'pop', 'alternative', 'indie', 'electronic',
'female vocalists', 'dance', '00s', 'alternative rock', 'jazz',
'beautiful', 'metal', 'chillout', 'male vocalists',
'class... | surgebiswas/poker | PokerBots_2017/Johnny/keras/applications/audio_conv_utils.py | Python | mit | 2,978 | [
"VisIt"
] | 124ba2c368349ac0cc7e5d2499de3fb17d6ce586171f22bad15351dec4a80695 |
"""
################################################################################
#
# SOAPpy - Cayce Ullman (cayce@actzero.com)
# Brian Matthews (blm@actzero.com)
# Gregory Warnes (Gregory.R.Warnes@Pfizer.com)
# Christopher Blunck (blunck@gst.com)
#
##########################... | nagyistoce/devide.johannes | extra/soappy-cvp/SOAPpy/Server.py | Python | bsd-3-clause | 27,136 | [
"Brian"
] | 2f7324c195ecbe76d7921fd4de730060493a1f1abf00c47f33105176b2d2bd1c |
import copy
import errno
import glob
import inspect
import os
import time
import uuid
import sys
import GangaCore.Core.FileWorkspace
from GangaCore.GPIDev.MonitoringServices import getMonitoringObject
from GangaCore.Core.exceptions import GangaException, IncompleteJobSubmissionError, JobManagerError, TypeMismatchErro... | ganga-devs/ganga | ganga/GangaCore/GPIDev/Lib/Job/Job.py | Python | gpl-3.0 | 118,272 | [
"DIRAC"
] | 0b7557fddac077c2f1f9ba70aaf5dfa1eb978f26a1fdabf1e165a0163b651f87 |
"""Core functions of Iphigen package."""
from __future__ import division
import time
import numpy as np
import compoda.core as coda
from scipy.ndimage import gaussian_filter
from iphigen.utils import truncate_range, set_range
np.seterr(divide='ignore', invalid='ignore')
def multi_scale_retinex(image, scales=None, ve... | ofgulban/retinex_for_mri | iphigen/core.py | Python | bsd-3-clause | 6,307 | [
"Gaussian"
] | d34152aba7db82ed8316e490a1703f9a2adf26146edf55af987de29db0a1150e |
"""Support for Konnected devices."""
import asyncio
import hmac
import json
import logging
import voluptuous as vol
from aiohttp.hdrs import AUTHORIZATION
from aiohttp.web import Request, Response
from homeassistant.components.binary_sensor import DEVICE_CLASSES_SCHEMA
from homeassistant.components.discovery import ... | molobrakos/home-assistant | homeassistant/components/konnected/__init__.py | Python | apache-2.0 | 18,709 | [
"VisIt"
] | c07959568a7ddfe61b15b200903fc830639abd19d5deeb487bd9c16d823d4072 |
#!/usr/bin/env python
# """make coverage stats for bam files in directory"""
import sys
import pysam
import os
input_dir = sys.argv[1]
watson_bam = pysam.AlignmentFile(os.path.join(input_dir,'watson.dedup.bam'),'rb')
crick_bam = pysam.AlignmentFile(os.path.join(input_dir,'crick.dedup.bam'),'rb')
coverage_dict = {'s... | thomasvangurp/epiGBS | mapping_varcall/statistics/coverage_stats.py | Python | mit | 3,670 | [
"pysam"
] | 39d85891a29c71fffa37b1417c50766e607aab42206c17177af734af8371ab4a |
#!/usr/bin/env python
#-*- coding:utf-8 -*-
#
# This file is part of the NNGT project to generate and analyze
# neuronal networks and their activity.
# Copyright (C) 2015-2019 Tanguy Fardet
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License a... | Silmathoron/NNGT | doc/examples/random_balanced.py | Python | gpl-3.0 | 6,728 | [
"NEURON"
] | 574af740c9e743b08cc0586c49642a2235d0177ab2882459caff400db961136b |
# Copyright 2013 Amazon.com, Inc. or its affiliates. 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. A copy of
# the License is located at
#
# http://aws.amazon.com/apache2.0/
#
# or in the "license" file acc... | mnahm5/django-estore | Lib/site-packages/awscli/argprocess.py | Python | mit | 20,751 | [
"VisIt"
] | 2345af74f28abc42e0b19086f7ba34a447d26b303dd5a93d73224d48ae9f416b |
"""
@created_at 2014-07-15
@author Exequiel Fuentes <efulet@gmail.com>
@author Brian Keith <briankeithn@gmail.com>
"""
# Se recomienda seguir los siguientes estandares:
# 1. Para codificacion: PEP 8 - Style Guide for Python Code (http://legacy.python.org/dev/peps/pep-0008/)
# 2. Para documentacion: PEP 257 - Docst... | efulet/pca | pca/lib/opciones.py | Python | mit | 883 | [
"Brian"
] | c7b9067344f0f5cc6eb8e61652de56999b1565d3c7067aeaf5132b917a49cc97 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# ---------------------------------------------------------------------
# Copyright (c) 2012 Michael Hull.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are m... | mikehulluk/morphforge | src/morphforgecontrib/simulation/synapse_templates/neurounit/__init__.py | Python | bsd-2-clause | 7,445 | [
"NEURON"
] | d706258616bf0c20a3390f28aa8f0d75158d50713636267b996ac2c66498785c |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# This example demonstrates how to permute an image with vtkImageReslice.
# The advantage of using vtkImageReslice for this (rather than
# vtkImagePermute) is that you can specify neg... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Imaging/Core/Testing/Python/ReslicePermuteResample.py | Python | gpl-3.0 | 1,159 | [
"VTK"
] | 3dba512fdd659beb6bb2d39b4ded4174fbb9f34c310787ec382ea5c3c88b1f87 |
"""
Useful pickle-type stuff
@license: GPL-3+
@author: Paul Tagliamonte <paultag@gmail.com>
@date: August 6th, 2011, 01:50 -0000
Uses a JsonBfile to store package info
"""
import Syn.Log as l
import Syn.JsonBfile as flatfile
import Syn.Policy.PackageRegistry as R
import Syn.Policy.Universal as U
fro... | digitalvectorz/syn | Syn/PackageRegistry.py | Python | gpl-3.0 | 4,458 | [
"BLAST"
] | 253e8af7b3324660223c9ac721863fc7719673c2bf206af545f9b7a04810442a |
#!/usr/bin/python3
# -*- coding: utf-8 -*-
from MuParser import MuParser
from LibGraphes import Graph
import sys
import networkx as nx
import graphviz as gz
import copy
# API for LEIA 3-address instructions
# + CFG construction + Dataflow Analysis.
# Utilitary function: pretty-prints a set of locations.
def regset... | lauregonnord/cap-labs | TP06/MuSmartCodeGen/APICodeLEIA.py | Python | gpl-3.0 | 21,386 | [
"VisIt"
] | 0750ba3ba706a47b24b2d75abad6825efda1281b19629cb508c60cbbfbf9bb2d |
# MARTINIZE
# A simple, versatile tool for coarse-graining molecular systems
# Copyright (C) 2017 Tsjerk A. Wassenaar and contributors
#
# 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 v... | Tsjerk/Martinize | martinize/core.py | Python | gpl-2.0 | 23,149 | [
"Gromacs",
"PyMOL"
] | 8ff2338d529c356efa34b735d4d7d1afd253a8676930eae5b6efb5d4684c5ce9 |
from __future__ import print_function
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Author: Vincent Dubourg <vincent.dubourg@gmail.com>
# (mostly translation, see implementation details)
# Licence: BSD 3 clause
import numpy as np
from scipy import linalg, optimize, rand
from ..base import BaseEstimator, Regres... | depet/scikit-learn | sklearn/gaussian_process/gaussian_process.py | Python | bsd-3-clause | 33,784 | [
"Gaussian"
] | 564e6466aca78658bcf717163ab3d5fc2b32d3b01efe0d6653333bcc4c2d9092 |
##############################################################################
##
## game.py - Flask wrapper application, for interacting with various messenger
## apps.
##
## Copyright (C) 2016 Brent.Englehart@gmail.com
##
## This program is free software; you can redistribute it and/or
## modify it under ... | brentje/turbo-potato | bot.py | Python | gpl-3.0 | 1,717 | [
"VisIt"
] | 076733db440f815d3c2e1418d2d61ed3617a28a984e510c6208d1bc4f3366aa4 |
import numpy as np
import numpy.random as npr
import theano
import theano.tensor as T
#from theano.tensor.shared_randomstreams import RandomStreams as RandStream
from theano.sandbox.cuda.rng_curand import CURAND_RandomStreams as RandStream
#from pylearn2.sandbox.cuda_convnet.filter_acts import FilterActs
#from pylearn... | capybaralet/Sequential-Generation | NetLayers.py | Python | mit | 24,067 | [
"Gaussian"
] | 2e0796511bb50a896262ba13e5b5ed1c9618cef3ccc64addb1f6b9c9ed73833f |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""Tests for the Popularity Contest (popcontest) parser."""
import unittest
from plaso.formatters import popcontest as _ # pylint: disable=unused-import
from plaso.lib import timelib
from plaso.parsers import popcontest
from tests.parsers import test_lib
__author__ = 'Fra... | jorik041/plaso | tests/parsers/popcontest.py | Python | apache-2.0 | 5,304 | [
"ORCA"
] | 647533c3bb0e75a8d6ebe585f528f9d8073dfcf2931d3205818bb2c5ce1e77db |
#!/usr/bin/env python2
"""List available machines on all clouds, using mist.io API
This will show all machines on all clouds, no matter if they are
enabled or disabled from the mist.io dashboard
"""
import json
import sys
import time
import json
import multiprocessing.pool
try:
import requests
except ImportError... | mistio/mist.io-api-examples | list_machines.py | Python | agpl-3.0 | 4,265 | [
"VisIt"
] | dd69792a660aaf957e69fb51825a2b68d5f765ece9dd091bbd6c9ff94d912537 |
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Daniel Strohmeier <daniel.strohmeier@tu-ilmenau.de>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
#
# License: BSD (3-clause)
import copy
import numpy as np
from ..io.pick import pick_channels_cov
from ..forward import apply_f... | dimkal/mne-python | mne/simulation/evoked.py | Python | bsd-3-clause | 4,355 | [
"Gaussian"
] | ffe0465d16445cd26aa02b31d29f30c4ca738dd57d4d3028b55c125a73619e06 |
#!/usr/bin/env python
"""Writing for HTML pages."""
import distutils.dir_util
import json
import os
import os.path
import shutil
import sys
import xml.sax.saxutils
import urllib
import jinja2
import proc_doc
import raw_doc
def escapeForXml(s):
"""Return escaped XML of s."""
return xml.sax.saxutils.escape(s)... | h-2/seqan | util/py_lib/seqan/dox/write_html.py | Python | bsd-3-clause | 22,285 | [
"VisIt"
] | 59fde1e6ce911d3f1b0c2d8b0fa27aa3c598bbef3fd67fe94d6f4dcd73f8b2b3 |
#!/usr/bin/env python
"""A translation of a Scheme interpreter in Python, modeling the
metacircular evaluator in Ch. 4 of The Structure and Interpretation of
Computer Programs. (http://www-mitpress.mit.edu/sicp/)
AUTHOR:
Danny Yoo (dyoo@hkn.eecs.berkeley.edu)
SYNOPSIS:
It's Scheme. *grin* At least, quit... | thousandparsec/libtpclient-py | tp/client/pyscheme/scheme.py | Python | gpl-2.0 | 12,155 | [
"VisIt"
] | db5cc804afc7b418d65118d6073fc2e073e25c0d17f94a5e328c0bf672a05448 |
import numpy as np
import matplotlib.pyplot as plt
from scipy.integrate import simps
def rejection_sampling(pdf, x_min, x_max, pdf_max):
while True:
x = np.random.uniform(x_min, x_max)
y = np.random.uniform(0, pdf_max)
if y < pdf(x):
return x
def gaussian(x, mean, std):
ret... | orion-42/numerics-physics-stuff | rejection_sampling.py | Python | mit | 1,035 | [
"Gaussian"
] | d0640b95515a15fdae79c56c3cb8e2c120713cb551e54a1f2a2bff35cf72d00b |
#
# 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 us... | RyanSkraba/beam | sdks/python/apache_beam/pipeline.py | Python | apache-2.0 | 44,467 | [
"VisIt"
] | db4737ea4393a2bbb0d194af5dd5e9c54268be27621c159026d1bf8c8a8cd708 |
# 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... | mkuron/espresso | samples/constraints.py | Python | gpl-3.0 | 4,512 | [
"ESPResSo"
] | fb6dce73b29c7af9e1a664ce7443ad846d1d8d7f85143532ac3df2b5649c0a2f |
#-----------------------------------------------------------------------------
# Copyright (c) 2012 - 2019, Anaconda, Inc., and Bokeh Contributors.
# All rights reserved.
#
# The full license is in the file LICENSE.txt, distributed with this software.
#-------------------------------------------------------------------... | timsnyder/bokeh | bokeh/model.py | Python | bsd-3-clause | 30,091 | [
"VisIt"
] | 2a82e093f9f041259df64028d75d6f350a29b98128e6884c1ab8852c0e483dc8 |
######################################################
#
# SCFpy: A Simple restricted Hartree-Fock code
# written by Pu Du (pudugg@gmail.com)
#
######################################################
from __future__ import print_function, division
import os
import re
import subprocess
import numpy as np
class parser(... | pudu1991/SCFpy | SCFpy/parser.py | Python | mit | 4,216 | [
"NWChem"
] | f7c8d11adf51e27a9d36e9808b7afea89775242e972fae9993187f133a46572e |
#!/usr/bin/env python3
"""
# dl_poly_parse
# If ran as script, takes a DL_POLY OUTPUT file and returns the physical properties
# as a parsed file of simple columns, for easy readability by plotting software.
# It can also be imported as a module with functions to return lists of properties or averages.
"""
OUTPUT = "O... | keirwl/dl_poly_parse | dl_poly_parse.py | Python | mit | 6,185 | [
"DL_POLY"
] | 05ac4685030ffaea35295b48a3d59f16dde6f593bf027259d123e97861360f47 |
##
## This file is part of the libsigrokdecode project.
##
## Copyright (C) 2014 Sławek Piotrowski <sentinel@atteo.org>
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundation; either version 2 of ... | hufsm/tu_gen2_libsigrokdecode | decoders/rfm12/pd.py | Python | gpl-3.0 | 18,366 | [
"CRYSTAL"
] | c2ccdb8c8bb7b5a3457782cbf80713ea330319d2dd47480df23861a73f3e3269 |
# -*- coding: utf-8 -*-
'''
Support for the Git SCM
'''
from __future__ import absolute_import
# Import python libs
import copy
import logging
import os
import re
from distutils.version import LooseVersion as _LooseVersion
# Import salt libs
import salt.utils
import salt.utils.files
import salt.utils.itertools
import... | stephane-martin/salt-debian-packaging | salt-2016.3.3/salt/modules/git.py | Python | apache-2.0 | 131,301 | [
"Octopus"
] | c768440deda2ea0ac71f919b01399c47b4ff24e1caa403c52a57e1b69a38f72f |
""" DIRAC FileCatalog utilities
"""
import six
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Utilities.List import intListToString
def getIDSelectString(ids):
"""
:param ids: input IDs - can be single int, list or tuple or a SELECT string
:return: Select string
"""
if isinstance(ids, six.string_... | DIRACGrid/DIRAC | src/DIRAC/DataManagementSystem/DB/FileCatalogComponents/Utilities.py | Python | gpl-3.0 | 622 | [
"DIRAC"
] | 5bce3943c292ae80295e3f792f6d744d2302c7fd92a5f3bdb237f49919d4221f |
"""Detect all Python scripts in HTML pages in current folder and subfolders.
Generate brython_modules.js, a bundle with all the modules and packages used
by an application.
Generate a Python package ready for installation and upload on PyPI.
"""
import os
import shutil
import html.parser
import ast
import json
import ... | jonathanverner/brython | setup/list_modules.py | Python | bsd-3-clause | 18,067 | [
"VisIt"
] | d7508e129c96a9e518f629e7aeed81108df71783d1cf7332bdc0444871fc8007 |
"""
Convolutional Restricted Boltzmann Machine using chainer
"""
from __future__ import print_function
import os, sys
import argparse
import timeit
import numpy as np
try:
import PIL.Image as Image
except ImportError:
import Image
import chainer
from chainer import computational_graph
from chainer import cu... | corochann/SeRanet | src/arch/convolution_rbm.py | Python | mit | 17,573 | [
"Gaussian"
] | 5561ba99c360d5a9ff38a49b0657a5fc994193bc1b685ceba43d7f728c9e04a9 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | ashutoshvt/psi4 | psi4/driver/p4util/util.py | Python | lgpl-3.0 | 9,241 | [
"Psi4"
] | 12e2db144bdbc92af152967fccccd53773704092e8f77f6a330008325729cdae |
##
# Copyright 2016-2018 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | bartoldeman/easybuild-easyblocks | easybuild/easyblocks/a/adf.py | Python | gpl-2.0 | 3,997 | [
"ADF"
] | 9a79f05f2d235fdaa388957208d3208364871dd4b87193587ff0670d20e5e557 |
#! /bin/env python
from __future__ import print_function
import sys
import argparse
import os
import os.path
#import tabix
import pysam
from pysam import VCF
import csv
import cPickle as pickle
# python data tables!
#import pandas
from collections import defaultdict
import pymongo
#from bson import Binary, Code
#from b... | pontikos/uclex_browser | load_vcfs/vcf_to_json.py | Python | mit | 6,805 | [
"pysam"
] | 239c112bd41a435b7c76ad323cf7d5079b8f6c392ec66063e7eaac2d933f9f53 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Count and export redundancy of sequences found in a fasta file.
Warning: may crash by using the whole memory.
Usage:
%program <input_file> <output_file> [data_column]"""
import sys
import re
from collections import defaultdict
try:
from Bio import SeqIO
exce... | wkh124/wkh124 | fasta_distribution.py | Python | gpl-3.0 | 920 | [
"Biopython"
] | 040be0e995ec22bcbc9f3331804070b7b52e99207af2b242aa855139374700f7 |
# interpol.py ---
#
# Filename: interpol.py
# Description:
# Author: Subhasis Ray
# Maintainer:
# Created: Wed Jun 25 16:13:26 2014 (+0530)
# Version:
# Last-Updated:
# By:
# Update #: 0
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#
# Change log:
#
#
#
#
# This progr... | dilawar/moose-full | moose-examples/snippets/interpol.py | Python | gpl-2.0 | 2,154 | [
"MOOSE"
] | 4df050ed460295bc278e346064b996676acd7488008118c38ff88cabaa11a878 |
import numpy as np
from mayavi import mlab
from tvtk.api import tvtk
# 3-----4-----5 y=1
# | \ 1 \ 3 |
# | 0 \ | 2 \ |
# 0-----1-----2 y=0
# x=0 x=1 x=2
def generate_points(z):
return np.array([(0,0,z), (1,0,z), (2,0,z),
(0,1,z), (1,1,z), (2,1,z)], 'd')
@mlab.show
@mlab... | dfroger/quickstart | mayavi/poly_data_anim.py | Python | gpl-3.0 | 930 | [
"Mayavi"
] | bbaafe880918008c39d3835c87bd403c0eb91969222fd7043882f10e8b3b76b9 |
# coding: utf-8
# In[15]:
import numpy
import matplotlib # TODO bug in ipython? (sometime can't call the module directly)
from matplotlib import pyplot
import scipy
from scipy import stats
from scipy import optimize
# %matplotlib tk
# %matplotlib notebook ???
get_ipython().magic(u'matplotlib inline')
# define ... | FedericoMuciaccia/SistemiComplessi | src/histograms and fitting.py | Python | mit | 3,619 | [
"Gaussian"
] | 7a2c20e9f5f5f4cb9bdad8c35bccf7224c5005697b195f0b9f2f50d9eecba1e4 |
#ImportModules
import ShareYourSystem as SYS
from ShareYourSystem.Specials.Simulaters import Populater,Brianer
#Definition of a brian structure
MyBrianer=Brianer.BrianerClass(
).push(
[
(
'First',
Populater.PopulaterClass().update(
[
('PopulatingUnitsInt',3),
(
'PopulatingEquationStr',
... | Ledoux/ShareYourSystem | Pythonlogy/draft/Simulaters/Brianer/draft/01_ExampleCell copy 2.py | Python | mit | 1,268 | [
"Brian"
] | 849116e4df0ae8cd03878141065591ecdc3dfee77a8c6659608dc53989500e84 |
import os
import sys
import argparse
import json
import signal
import numpy as np
import mockgallib as mock
import emcee
signal.signal(signal.SIGINT, signal.SIG_DFL) # stop with ctrl-c
def print0(*a):
if mock.comm.rank == 0:
print(*a)
#
# Command-line options
#
parser = argparse.ArgumentParser()
parser.a... | junkoda/mockgallib | script/mcmc_hod_mpi.py | Python | gpl-3.0 | 12,732 | [
"Galaxy"
] | 23ac15bc6b9c194e438033a53ec1a09a6821e9c6c1855f84f9e9c6c128b0b29f |
# -*- coding: utf-8 -*-
import logging
import os
import re
import bpy
import math
import mathutils
from collections import OrderedDict
from mmd_tools.core import vmd
from mmd_tools.core.camera import MMDCamera
from mmd_tools.core.lamp import MMDLamp
class _FCurve:
def __init__(self, default_value):
se... | lordscales91/blender_mmd_tools | mmd_tools/core/vmd/exporter.py | Python | mit | 14,792 | [
"VMD"
] | bd1c2d734747a295e5b35ef061b916ec1aafddcf78d6735745d27a7c422d3428 |
# -*- coding: utf-8 -*-
#!/usr/bin/python
"""Test of Orca's interaction with the Microsoft ARIA tree example. In
It's current format, it's rather wacky. See bug 570571."""
from macaroon.playback import *
import utils
sequence = MacroSequence()
########################################################################... | h4ck3rm1k3/orca-sonar | test/keystrokes/firefox/ms_tree_bug_570571.py | Python | lgpl-2.1 | 7,205 | [
"ORCA"
] | d9ae374ef1b659b210e16c1bf32fd851258906a542172eb268ca5043e6ee7f2f |
# coding: utf-8
from __future__ import unicode_literals
import itertools
import json
import os.path
import random
import re
import time
import traceback
from .common import InfoExtractor, SearchInfoExtractor
from ..jsinterp import JSInterpreter
from ..swfinterp import SWFInterpreter
from ..compat import (
compa... | remitamine/youtube-dl | youtube_dl/extractor/youtube.py | Python | unlicense | 150,015 | [
"ADF"
] | 7ff116405a2b9b7eb6cedc947ce772c85fd431a6a31d15f1705ebd2ce9f8290f |
# -*- coding: utf-8 -*-
#
# BrodyHopfield.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, ... | SepehrMN/nest-simulator | pynest/examples/BrodyHopfield.py | Python | gpl-2.0 | 4,218 | [
"Gaussian",
"NEURON"
] | 8f12de8be522c431969e0911a0dd22d82107676b81ade3717484244b14697ddc |
import json
import sys
import networkx as nx
from networkx.algorithms import weakly_connected_component_subgraphs
from collections import defaultdict
from itertools import chain, ifilter
from functools import partial
from synapseclustering import tree_max_density
from numpy import subtract
from numpy.linalg import no... | AdaEne/CATMAID | django/applications/catmaid/control/graph.py | Python | gpl-3.0 | 19,644 | [
"NEURON"
] | 8d7d0c227ec46a599cce4e0fd1c3ded42e532c544183884b0c6ba47a06b8899a |
"""
.. _statsrefmanual:
==========================================
Statistical functions (:mod:`scipy.stats`)
==========================================
.. currentmodule:: scipy.stats
This module contains a large number of probability distributions as
well as a growing library of statistical functions.
Each univari... | pizzathief/scipy | scipy/stats/__init__.py | Python | bsd-3-clause | 10,256 | [
"Gaussian"
] | 9af165efbc7e79d147634cd9fc3a11a8a99271b2441e8536028ca5ada5438182 |
import base64
import importlib
import numpy as np
from openpathsampling.integration_tools import is_simtk_quantity, unit
import math
import abc
from uuid import UUID
import ujson
import marshal
import types
import opcode
from .base import StorableObject
from openpathsampling.tools import word_wrap
from .cache im... | choderalab/openpathsampling | openpathsampling/netcdfplus/dictify.py | Python | lgpl-2.1 | 26,770 | [
"MDTraj",
"OpenMM"
] | 049b7831448f9287ee2b5f3c9d46c9df20303384e9618b2dfbf45f9d4c00db21 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2016 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kannon92/psi4 | psi4/driver/qcdb/interface_dftd3.py | Python | gpl-2.0 | 10,325 | [
"Psi4"
] | 286acbee719087947b3cb19821cd75a5c92a7f4e44a4a90ff2935c2baa1a324f |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkGraphReader(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vt... | chrisidefix/devide | modules/vtk_basic/vtkGraphReader.py | Python | bsd-3-clause | 472 | [
"VTK"
] | 0066ba05ad4d0a58ed59cff10ff8ed5791ceab34d9862cfd94293a533f81d7e2 |
import os, ConfigParser, errno
class SafeSetup:
user_config_file = os.path.expanduser("~/.safecfg")
project_config_file = "./.safe/project.cfg"
def make_sure_path_exists(self, path):
try:
os.makedirs(path)
except OSError as exception:
if exception.errno != errno.EEX... | BenElgar/SafeSync | safesetup.py | Python | gpl-2.0 | 2,361 | [
"NEURON"
] | 63a92ec5b08f5e51008fa48e89de1ea1fe644b1bf06049c03dcb169e07e210d2 |
import os
import re
from pypers.core.step import Step
class SamPe(Step):
spec = {
'version': '0.6.1',
'descr': [
'Generate alignments in the SAM format given paired-end reads.',
'Repetitive read pairs will be placed randomly.',
'If sample id is provided, includes... | frankosan/pypers | pypers/steps/bwa/sampe.py | Python | gpl-3.0 | 2,399 | [
"BWA"
] | 9610ece52f3802464768aeeb5f3fb168f82fe2aa4ef05e46840a4dc58572fa6f |
#!/usr/bin/env python
# Copyright (C) 2011-2012, 2014 The PISM Authors
# script to generate figure: results from SeaRISE experiments
# usage: if UAFX_G_D3_C?_??.nc are result NetCDF files then do
# $ slr_show.py -m UAFX
# try different netCDF modules
try:
from netCDF4 import Dataset as CDF
except:
print "ne... | talbrecht/pism_pik07 | util/slr_show.py | Python | gpl-3.0 | 3,817 | [
"NetCDF"
] | f1af94af1d0e52f46905ff1ebdeb4ebb91747f99531c3fa92f19701dbb2e4f2f |
"""
DIRAC.StorageManagementSystem.Client package
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
| yujikato/DIRAC | src/DIRAC/StorageManagementSystem/Client/__init__.py | Python | gpl-3.0 | 165 | [
"DIRAC"
] | b537e6281fd215035904778f29fb8e4044de749bf9f547205895486b2bbe151a |
# -----------------------------------------------------------------------------
# Milky Way - Turn based strategy game from Milky Way galaxy
#
# URL: https://github.com/FedericoRessi/milkyway/
# License: GPL3
# -----------------------------------------------------------------------------
'''
Module for UI ba... | FedericoRessi/milkyway | milkyway/ui/base.py | Python | gpl-3.0 | 4,170 | [
"Galaxy"
] | 25f97c0c5dd30b7dd3010ba6cfc51622249538f2878b52f40f8bedf7d427907a |
########################################################################
# $Id$
########################################################################
""" DIRAC DirectoryTree base class """
__RCSID__ = "$Id$"
from DIRAC.DataManagementSystem.DB.FileCatalogComponents.Utilities import getIDSelectString
from DIRAC impo... | andresailer/DIRAC | DataManagementSystem/DB/FileCatalogComponents/DirectoryTreeBase.py | Python | gpl-3.0 | 40,645 | [
"DIRAC"
] | 452f92f1fc21797015c7d774a40cf8e28ecb89210b562949b2c191e76fc495fc |
import math
import numpy as np
from scipy import ndimage
from ..transform import resize
from ..util import img_as_float
def _smooth(image, sigma, mode, cval):
"""Return image with each channel smoothed by the Gaussian filter."""
smoothed = np.empty(image.shape, dtype=np.double)
# apply Gaussian filter t... | bennlich/scikit-image | skimage/transform/pyramids.py | Python | bsd-3-clause | 9,910 | [
"Gaussian"
] | 22c0fa4b5b2c569267504c40f9d939551ef92e27ab23b75985927ea945afdb53 |
#!/usr/bin/env python3
#
# Copyright (c) 2012 Brian Yi ZHANG <brianlions at gmail dot com>
#
# This file is part of pynebula.
#
# pynebula 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 th... | brianlions/python-nebula | tests/histogram_ut.py | Python | gpl-3.0 | 3,654 | [
"Brian"
] | bf931293e767523d7933ac95f8db6d049646ca30c04583da9b9676af118b314f |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publi... | thica/ORCA-Remote | src/ORCA/widgets/TextField.py | Python | gpl-3.0 | 5,736 | [
"ORCA"
] | c3fd3c5b52fa35478873100682f638676188cae19bc8afe06e31c930055ce680 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Create the RenderWindow, Renderer and both Actors
#
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
iren = vtk.vtkRenderWindowInteractor()
iren.SetR... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Filters/Sources/Testing/Python/Disk.py | Python | gpl-3.0 | 938 | [
"VTK"
] | 7ede0519f6b9431302eaeb3d3c14b511a8d99922d72c41f301d32ff32a62c8f9 |
# Copyright (c) 2015, Frappe Technologies Pvt. Ltd. and Contributors
# License: GNU General Public License v3. See license.txt
from __future__ import unicode_literals
import frappe
import json
import frappe.utils
from frappe.utils import cstr, flt, getdate, comma_and, cint
from frappe import _
from frappe.model.mapper... | mahabuber/erpnext | erpnext/selling/doctype/sales_order/sales_order.py | Python | agpl-3.0 | 22,175 | [
"VisIt"
] | 8f9ace00066ce0c3e11b3c4fa53e1b4da6811e514dd9499606971b88a244a1a2 |
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are ... | eleftherioszisis/NeuroM | neurom/view/view.py | Python | bsd-3-clause | 15,032 | [
"NEURON"
] | 2e3593948a9d08f59a6674afb2164620610c4149368a222a1ec4f6884181c06d |
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