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#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Extracts coordinates from CP2K input format into XYZ files.
Supports scaled CP2K coordinates and scaled XYZ output.
Command Line Interface
----------------------
.. program:: es_cp2k2xyz.py
.. option:: input
CP2K input filename.
.. option:: output
XYZ outpu... | ferchault/euston | src/tools/es_cp2k2xyz.py | Python | lgpl-3.0 | 2,425 | [
"CP2K"
] | cc1bedf4281c5e8e79ce1a12f584a1ed95bbe9c606e15291dfed0be6cb3c335d |
# This file is part of the myhdl library, a Python package for using
# Python as a Hardware Description Language.
#
# Copyright (C) 2003-2012 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... | juhasch/myhdl | myhdl/conversion/_toVerilog.py | Python | lgpl-2.1 | 52,023 | [
"VisIt"
] | d3ff28dce5fb1b6d4e26cc128e80c0f4a3d86f1edb6f7ecc0179fd2ac3a4b6dc |
import numpy as np
import pytest
from pysisyphus.calculators import Gaussian16, ORCA5, Turbomole
from pysisyphus.calculators.PySCF import PySCF
from pysisyphus.helpers import geom_loader
from pysisyphus.testing import using
np.set_printoptions(suppress=True, precision=8)
@pytest.mark.parametrize(
"XY", ["X", "... | eljost/pysisyphus | tests/test_overlap_calculator/test_canonical.py | Python | gpl-3.0 | 2,859 | [
"ORCA",
"PySCF",
"TURBOMOLE"
] | a12e2b72b17ed6f7d4aa3a43bf5acc1b87454869ea19cc8625ee8a43777a9e99 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2017 Lenovo, Inc.
#
# This file is part of Ansible
#
# Ansible 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
# ... | faust64/ansible | lib/ansible/modules/network/lenovo/cnos_bgp.py | Python | gpl-3.0 | 19,389 | [
"VisIt"
] | 0fe4b2c851184b07cf374348f76df2e30094ca3ede31b9cde468cdcf51b9ed52 |
#
# ----------------------------------------------------------------------------------------------------
#
# Copyright (c) 2007, 2016, Oracle and/or its affiliates. All rights reserved.
# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
#
# This code is free software; you can redistribute it and/or modify ... | mcberg2016/graal-core | mx.graal-core/mx_graal_tools.py | Python | gpl-2.0 | 7,954 | [
"VisIt"
] | db8fa011af0fc1f0bebdd76432a2b734bc9e57f8649b1236d3e06aadfe0d4a25 |
#!/usr/bin/env python
import datetime
import itertools
import json
import re
from bisect import bisect_left, bisect_right
from typing import List, Union
import cftime
import numpy as np
import pytz
def find_le(a, x):
"""
Find right-most value in `a` that is <= x.
`a` MUST be sorted in ascending order f... | DFO-Ocean-Navigator/Ocean-Data-Map-Project | data/utils.py | Python | gpl-3.0 | 3,457 | [
"NetCDF"
] | 5c8d28a6d2f6838c38445a8812af781fbd31d09f525a04391b12740c8f7fb207 |
#!/usr/bin/env python
__author__ = "Mike McCann"
__copyright__ = "Copyright 2012, MBARI"
__license__ = "GPL"
__maintainer__ = "Mike McCann"
__email__ = "mccann at mbari.org"
__doc__ = '''
Base classes for writing NetCDF files for CANON campaigns. Reuse
Use the conventions for Trajectory feature type and write as m... | josephmfaulkner/stoqs | stoqs/loaders/CANON/toNetCDF/__init__.py | Python | gpl-3.0 | 7,152 | [
"NetCDF"
] | 44e6ed7532c76016b21289c6f665925b4e4560302c9d3c8fd9629c63642d235d |
#! /usr/bin/env python
"""
manipulate metadata in the FileCatalog
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import DIRAC
from DIRAC import S_OK, S_ERROR
from COMDIRAC.Interfaces import critical
from COMDIRAC.Interfaces import DSession
from COMDIR... | DIRACGrid/COMDIRAC | src/COMDIRAC/Interfaces/scripts/dmeta.py | Python | gpl-3.0 | 6,204 | [
"DIRAC"
] | 741de78dba57b8de97ce24d1fba691675531df05e924df0ad346c04c0617badb |
#
# Copyright 2020-2021 Lars Pastewka (U. Freiburg)
# 2021 Jan Griesser (U. Freiburg)
# 2020-2021 Jonas Oldenstaedt (U. Freiburg)
#
# matscipy - Materials science with Python at the atomic-scale
# https://github.com/libAtoms/matscipy
#
# This program is free software: you can redistribute it and/or ... | libAtoms/matscipy | tests/test_bop.py | Python | lgpl-2.1 | 15,254 | [
"ASE",
"CRYSTAL",
"Matscipy"
] | e40bed48f78ebc76faa61f31266527fcd0130ee630851d0123e84d689cf94f97 |
# -*- coding: utf-8 -*-
countries=(
(u"DE", u"DEU", u"276", u"Deutschland", u"Federal Republic of Germany"),
(u"AT", u"AUT", u"040", u"Österreich", u"Republic of Austria"),
(u"CH", u"CHE", u"756", u"Schweiz", u"Swiss Confederation"),
(u"AF", u"AFG", u"004", u"Afghanistan", u"Islamic Republic of Afghanistan"),
(... | nive-cms/nive | nive/utils/country_data.py | Python | gpl-3.0 | 15,635 | [
"BWA"
] | 2f893cf7814f60e30d8591000e9b6d1c99da749c4d3912a91fd10f2dc7677b25 |
# This file is part of TxtAlert.
#
# TxtALert 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.
#
# TxtAlert is distributed in the ... | praekelt/txtalert | txtalert/apps/therapyedge/reminders.py | Python | gpl-3.0 | 8,538 | [
"VisIt"
] | 962431135f5b2c6abcc3110be2a84b16a62728220e2f74a473c7a3c4f196d2be |
# -*- 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-speech | tests/unit/gapic/speech_v1p1beta1/test_speech.py | Python | apache-2.0 | 64,655 | [
"Octopus"
] | c996848af94a74bd18cb2a0c33bcaf7b3eeb65dc5dea9dfe5b7e7a2bf2c3ecdb |
import json
import logging
import hashlib
import uuid
import requests
from collections import namedtuple
import docker
from remoteappmanager.docker.docker_labels import (
SIMPHONY_NS,
SIMPHONY_NS_ENV,
SIMPHONY_NS_RUNINFO)
log = logging.getLogger(__name__)
# internal, convenience classes. Do not export (... | simphony/simphony-remote | remoteappmanager/tests/mocking/virtual/docker_client.py | Python | bsd-3-clause | 13,846 | [
"Mayavi",
"ParaView"
] | 4a90b9a5a8817460716435811fea06825e2ace035cdac4bf3eb33ea3229eb1ed |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2008 Jerome Rapinat
# Copyright (C) 2008 Benny Malengier
#
# 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 Fre... | beernarrd/gramps | gramps/gen/filters/rules/source/_hasgallery.py | Python | gpl-2.0 | 1,828 | [
"Brian"
] | 312bc4941f28c9d1ee7973160162d396b5dd3bdc65f42884abba32e75e22170c |
../../../../../../../share/pyshared/orca/scripts/apps/Thunderbird/__init__.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/scripts/apps/Thunderbird/__init__.py | Python | gpl-3.0 | 77 | [
"ORCA"
] | 5a04c7452893bb051ae524718fed4927589ca34e09663f002ec73f0d32e7086e |
from os.path import dirname, join
from rabix.common.ref_resolver import from_url
from rabix.main import TEMPLATE_JOB, dot_update_dict, init_context, fix_types
def test_remap_job():
job = TEMPLATE_JOB
tool = from_url(join(dirname(__file__), 'bwa-mem.json#tool'))
context = init_context()
fix_types(tool... | RitwikGupta/rabix | rabix/tests/test-mount/test.py | Python | agpl-3.0 | 583 | [
"BWA"
] | 3808fe88e292d724a4c57fd72ac6054aacfa575cd6ddc6ea997c970953b2df91 |
# (c) 2012, Michael DeHaan <michael.dehaan@gmail.com>
#
# This file is part of Ansible
#
# Ansible 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 lat... | indrajitr/ansible | lib/ansible/template/safe_eval.py | Python | gpl-3.0 | 5,664 | [
"VisIt"
] | efe6d370083d44a004b60c8cf00e6b334654432796e7373333213a23fbf0fa73 |
# -*- coding: utf-8 -*-
"""
Bok choy acceptance tests for problems in the LMS
See also old lettuce tests in lms/djangoapps/courseware/features/problems.feature
"""
from nose.plugins.attrib import attr
from textwrap import dedent
from common.test.acceptance.tests.helpers import UniqueCourseTest
from common.test.accept... | itsjeyd/edx-platform | common/test/acceptance/tests/lms/test_lms_problems.py | Python | agpl-3.0 | 33,546 | [
"VisIt"
] | ad165ef5bf11c1a7fcfb3f3b69842dc8126968b595b745e6b4a40f28b13c8e14 |
from django.shortcuts import render
from django.views.decorators.cache import cache_page
from main.contact import contact as send_message
from django.http import HttpResponse
import json
def home(request):
return render(request, 'home.html', {'footer': False})
@cache_page(60 * 15)
def exhibits(request):
return r... | bobbyluig/IDP | main/views.py | Python | mit | 1,209 | [
"VisIt"
] | 6d58b3b8cb34794d200df3d429e00ee743f883b295d1bda88bbf4ba87dbf47ba |
"""
Performance test created using multi-mechnize to analyze time
for query processing with MySQL.
"""
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
import random
import time
from DIRAC.WorkloadManagementSystem.DB.JobDB import JobDB
class Transaction(ob... | yujikato/DIRAC | tests/Performance/MySQLJobMonitoring/test_scripts/query.py | Python | gpl-3.0 | 775 | [
"DIRAC"
] | bfd3f27d7926567d7d8b37a8e3627b6da13d71a8797476845d4ac198c94d8406 |
from setuptools import setup, find_packages
import codecs
import os
here = os.path.abspath(os.path.dirname(__file__))
version_file = open(os.path.join(here, 'pypkg', 'VERSION'))
version = version_file.read().strip()
# Get the long description from the relevant file
with codecs.open(os.path.join(here, 'DESCRIPTION.rs... | dghubble/pypkg | setup.py | Python | mit | 2,940 | [
"Dalton"
] | bde6be1c18ecc8324bcbfbf0364b45660d0a69098d2619fa5cc5d3f791afbbfb |
"""
rplot.py is a stand-alone Python program which makes
two-dimensional plots easier.
It allows the user to create a map with colorbar and
a contour within one line of program.
You have to load mymap module from this file into your python program
and use it as shown in the following examples.
It works both for P... | reza35/rplot | rplot.py | Python | mit | 8,871 | [
"Gaussian"
] | 63d94143aa7fe368125fc4113e9b11fca8b2aedc9f9aff4d35db58c114e30505 |
__author__ = 'Robert Meyer'
from pypet.tests.testutils.ioutils import make_temp_dir, run_suite, \
get_root_logger, parse_args, get_log_config
from pypet.tests.testutils.ioutils import unittest
try:
import brian
from brian import *
from pypet.brian.parameter import BrianParameter, BrianMonitorResult
e... | nigroup/pypet | pypet/tests/integration/briantests/another_network_test.py | Python | bsd-3-clause | 7,769 | [
"Brian",
"NEURON"
] | bf8ebcd25604b7a916567dfec3c94f2571b0e7d959216fe5270ab6585faeaa3e |
# -*- coding: utf-8 -*-
# vispy: testskip
# -----------------------------------------------------------------------------
# A Galaxy Simulator based on the density wave theory
# (c) 2012 Ingo Berg
#
# Simulating a Galaxy with the density wave theory
# http://beltoforion.de/galaxy/galaxy_en.html
#
# Python version... | Eric89GXL/vispy | examples/demo/gloo/galaxy/galaxy_simulation.py | Python | bsd-3-clause | 7,726 | [
"Galaxy"
] | 59914e7924bc404f7530e21e45840783fc1da22cbdcc6c06e05c88e1f5a9de2f |
#!/usr/bin/env python
# Author: Andrew Jewett (jewett.aij at g mail)
# License: MIT License (See LICENSE.md)
# Copyright (c) 2013
# All rights reserved.
"""
lttree_postprocess.py
This is a stand-alone python script which checks the files created by
lttree.py to insure that the standard instance-variables... | jewettaij/moltemplate | moltemplate/lttree_postprocess.py | Python | mit | 20,953 | [
"LAMMPS"
] | 24e82367b4de8d1c560690e13daa7cd88cbb6568ba700130e2db15fccdc8c809 |
#!/usr/bin/env python
#
# Electrum - lightweight Bitcoin client
# Copyright (C) 2015 Thomas Voegtlin
#
# 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 y... | edb1rd/BTC | plugins/__init__.py | Python | gpl-3.0 | 4,656 | [
"VisIt"
] | 17cba1fa29932c4c656c2e6edf6a352ba90c3a70dd6a10b4bd10bd8bc64ac068 |
#!/usr/bin/env python
import pysam
import re
import matplotlib
import matplotlib.pyplot as plt
import numpy
from pbcore.io import CmpH5Reader
from pbcore.io import CmpH5Alignment
def IdentityFromCIGAR(cigar):
nMatch = 0
nIns = 0
nDel = 0
for cig in cigar:
if (cig[0] == 0):
nMat... | EichlerLab/chm1_scripts | GC_content_explore.py | Python | mit | 8,819 | [
"pysam"
] | 12f8d414cbe07b7da8f67ef02984618b9a3b8a85f06f53740c36748b2d1a915d |
import math
import random
import firefly
class Population:
population = []
leader = []
def __init__(self, member_count):
for i in range(member_count):
temp_firefly = firefly.Firefly()
self.population.append(temp_firefly)
self.leader = self.identify_leader()
def display(self):
for membe... | SeniorMorales/metaheuristics | firefly_o.py | Python | mit | 965 | [
"Firefly"
] | 9b4f5c7060010db6705ca973f3b96eee32cdb7d2b0722acc483199314d36e466 |
#PYTHON IMPORTS
#ASE imports
import ase
from ase.build import molecule
from ase import Atoms
from dscribe.descriptors import CoulombMatrix
#Other
import pandas as pd
import os
from dscribe.descriptors import SOAP
from sklearn.manifold import MDS
import matplotlib
import matplotlib.pyplot as plt
import numpy as np
imp... | CondensedOtters/PHYSIX_Utils | Projects/Aertgeerts_2019/Zundel-KRR/3_model_exploration/model_explorator.py | Python | gpl-3.0 | 17,202 | [
"ASE"
] | d6cf4a4c294a9a841c5c957c0d1ce4c7c8269bf7046da1617e2f6a55be046728 |
"""
.. See the NOTICE file distributed with this work for additional information
regarding copyright ownership.
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.... | Multiscale-Genomics/mg-process-fastq | tests/test_pipeline_chipseq.py | Python | apache-2.0 | 7,060 | [
"BWA"
] | 39c0590fab3f4a4c7f9741ea28189480c5f395d073f9b3abcd1f33096af21b07 |
#/usr/bin/env python
"""
Molecular graph and structure io methods.
"""
from datetime import date
import numpy as np
from scipy.spatial import distance
import math
import shlex
import re
from .CIFIO import CIF, get_time
from .atomic import METALS, MASS, COVALENT_RADII
from copy import copy
from .mof_sbus import Inorgani... | peteboyd/lammps_interface | lammps_interface/structure_data.py | Python | mit | 103,433 | [
"ASE",
"CRYSTAL",
"LAMMPS",
"RASPA"
] | 61ca1468423041dd7872d05753199e44418c3d38e4be34fa591dda28eec76ef6 |
# (C) British Crown Copyright 2010 - 2016, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | jswanljung/iris | lib/iris/tests/test_grib_save.py | Python | lgpl-3.0 | 10,963 | [
"NetCDF"
] | 85efd5de13a6000978839fcb4b4e0603093cfc0fc05c702995a26a2826d29538 |
#!/usr/bin/env python
# flake8: noqa
# pylint: disable=C0103,C0301,R0903
#
# A library that provides a Python interface to the Telegram Bot API
# Copyright (C) 2015 Leandro Toledo de Souza <devs@python-telegram-bot.org>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the... | tormich/pybot | libs/telegram/emoji.py | Python | gpl-2.0 | 39,882 | [
"Octopus"
] | a621170db484ee61b7c5ff19814114d6b8b107c91ea6804752fbbdfa2de2022f |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
from pymatgen.util.testing import PymatgenTest
from pymatgen.io.atat import Mcsqs
from pymatgen.core.structure import Structure
test_dir = os.path.join(
os.path.dirname(__file__), "..", "..", "..... | mbkumar/pymatgen | pymatgen/io/tests/test_atat.py | Python | mit | 3,220 | [
"pymatgen"
] | 604b38ba2c4f3faa10449e6af563c2b1d2f78866aff6adc92c6ff3ec61f1610e |
import lan
import copy
opencl_builtins = ['CLK_LOCAL_MEM_FENCE']
class Ids(lan.NodeVisitor):
""" Finds all unique IDs, excluding function IDs"""
def __init__(self):
self.ids = set()
def visit_FuncDecl(self, node):
if node.compound.statements:
self.visit(node.arglist)
de... | dikujepsen/OpenTran | v3.0/framework/processing/collect_id.py | Python | mit | 3,786 | [
"VisIt"
] | 59416597091a5519b5ddf0f445e4dce5a53723855cb67efdf6c0c539a254c850 |
##############################################################################
# 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/r-biostrings/package.py | Python | lgpl-2.1 | 2,013 | [
"Bioconductor"
] | af116982b826542d5ef5606b2c9fe17cb9718e0c7c75ff94651d4deb8666fcfb |
# -*- coding: utf-8 -*-
'''
This file is part of beam-cam, a camera project to monitor and characterise laser beams.
Copyright (C) 2015 Christian Gross <christian.gross@mpq.mpg.de>, Timon Hilker <timon.hilker@mpq.mpg.de>, Michael Hoese <michael.hoese@physik.lmu.de> and Konrad Viebahn <kv291@cam.ac.uk>
This program is... | kviebahn/beam-cam | ImageViewerTemplate.py | Python | gpl-3.0 | 20,252 | [
"Gaussian"
] | 92a848d9165dfba2f07cd2f5905e08446852c560f8adfaf78b4e1c35ebc835ed |
import astropy.io.fits as pyfits
import astropy.wcs as pywcs
import os
import numpy as np
from pdb import set_trace
import montage_wrapper as montage
import shutil
import sys
import gal_data
import config
import glob
#_TOP_DIR = '/data/tycho/0/leroy.42/allsky/'
#_INDEX_DIR = os.path.join(_TOP_DIR, 'code/')
_HOME_DIR ... | arlewis/arl_galbase | test_known_files.py | Python | mit | 14,048 | [
"Galaxy"
] | efda959552fae793fd41c823dc42f079f646ddce2f77659676e934b1bf41392e |
# coding=utf-8
# Copyright 2022 The TensorFlow Datasets 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 appl... | tensorflow/datasets | tensorflow_datasets/image_classification/siscore/siscore_labels.py | Python | apache-2.0 | 33,145 | [
"Bowtie",
"ESPResSo",
"Jaguar",
"ORCA"
] | bd488bd3079bbd54352035ccc1cad74525eed6a128a1ba0b1bb2b96f7072dd00 |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, subprocess, sys, glob, string
import zipfile
from datetime import date
cwd = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
os.chdir(cwd)
required_module_keys = ['architectures', 'name','version','moduleid','descripti... | chreck/movento-webview | iphone/build.py | Python | mit | 8,631 | [
"VisIt"
] | 5e2ca2f759fe9cea501d936d02adce6ba1037e52cbcc6e2b7a11830c47a6f551 |
# -*- coding: utf-8 -*-
#
# Copyright (C) 2013 Dirk Stöcker
# All rights reserved.
#
# This software is licensed as described in the file COPYING, which
# you should have received as part of this distribution. The terms
# are also available at http://trac.edgewall.com/license.html.
#
# This software consists of volunta... | Puppet-Finland/trac | files/spam-filter/tracspamfilter/users.py | Python | bsd-2-clause | 17,130 | [
"VisIt"
] | edc683817eeb3eb6a2205c9402aca812b8982bd201a0d5e2b46866f8b776cba1 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
#
# Copyright (C) 2017 Lenovo, Inc.
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public Licens... | Nitaco/ansible | lib/ansible/modules/network/cnos/cnos_reload.py | Python | gpl-3.0 | 5,200 | [
"VisIt"
] | 44a1066ce58a75b18f085b36c204b23095c01c8aa84bf78e70df831b2af0c337 |
# -------------------------------------------------------------------------
# Name: INITCONDITION
# Purpose: Read/write initial condtions for warm start
#
# Author: PB
#
# Created: 19/08/2016
# Copyright: (c) PB 2016
# -------------------------------------------------------------------------
from ... | CWatM/CWatM | cwatm/hydrological_modules/initcondition.py | Python | gpl-3.0 | 6,705 | [
"NetCDF"
] | bff7ef0e643a314f23f10427c04d2292cac2c6db599daae8e39919ffb3623764 |
# encoding: utf-8
from __future__ import unicode_literals
import json
import mock
import datetime
import pytest
import responses
from nose.tools import * # noqa
from dateutil.parser import parse as parse_datetime
from website import settings
from addons.osfstorage.models import OsfStorageFileNode, OsfStorageFolder
... | caseyrollins/osf.io | addons/osfstorage/tests/test_views.py | Python | apache-2.0 | 42,334 | [
"Galaxy"
] | 390ddabbd3630e4eb3c7c02e5b4e23566bc8e95fe87ed8001f1c5b295542fb2b |
# Copyright (C) 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 versio... | KaiSzuttor/espresso | testsuite/scripts/tutorials/test_07-electrokinetics.py | Python | gpl-3.0 | 2,558 | [
"ESPResSo"
] | 2b76f7e9a9399d062c762dae90577bd76645c6519afbc2d00a1f498430bebf1c |
from __future__ import division
import numpy as np
def add_exp2(h,seg,spktimes,e=0,tau1=0.5,tau2=20,weight=0.001):
"""
Adds a double-exponential synapse at seg, with spikes
specified by the list/np.array spktimes. Optional arguments
specify parameters for the synapse. Returns a list of
hocObjects t... | ahwillia/PyNeuron-Toolbox | PyNeuronToolbox/synapses.py | Python | mit | 1,222 | [
"NEURON"
] | 3eb1016372faf3bdd35772556be850683ad814c565bebf4cc9d281e4bed93c8e |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-wms-select-jobs
# Author : Stuart Paterson
########################################################################
"""
Select DIRAC jobs matching the given conditions
"""
__RCSID__ = "$Id$"
i... | Sbalbp/DIRAC | Interfaces/scripts/dirac-wms-select-jobs.py | Python | gpl-3.0 | 3,118 | [
"DIRAC"
] | 93ffa0939dbf145e244fc9e2eecf188e0d8f9766025eac51a083835408aeac76 |
#
# Honeybee: A Plugin for Environmental Analysis (GPL) started by Mostapha Sadeghipour Roudsari
#
# This file is part of Honeybee.
#
# Copyright (c) 2013-2020, Anton Szilasi <ajszilas@gmail.com>
# Honeybee is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public Licens... | mostaphaRoudsari/Honeybee | src/Honeybee_AddEarthtube.py | Python | gpl-3.0 | 32,325 | [
"EPW"
] | 89bd3d8dcbd0421cf99835731e5490326c40cc1954484d95b3efc22444783efe |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
This is an example scripts using LFPy with an active cell model adapted from
Mainen and Sejnowski, Nature 1996, for the original files, see
http://senselab.med.yale.edu/modeldb/ShowModel.asp?model=2488
This scripts is set up to use the model, where the active conductanc... | csdori/skCSD | sejnowski.py | Python | bsd-3-clause | 5,493 | [
"NEURON"
] | 55e4bc8da692e999ce0ed745853172012c7f06b790fca25db297676ebcd2a94a |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | rabipanda/tensorflow | tensorflow/contrib/py2tf/converters/side_effect_guards.py | Python | apache-2.0 | 5,060 | [
"VisIt"
] | 128b0abc3bc0ca541164e853820a02483e2711dafce47ece96f2736ff15552a9 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import os
from pathlib import Path
import json
import gzip
import numpy as np
import warnings
from shutil import copyfile, copyfileobj
from monty.tempfile import ScratchDir
import xml.etree.c... | mbkumar/pymatgen | pymatgen/io/vasp/tests/test_outputs.py | Python | mit | 83,669 | [
"VASP",
"Wannier90",
"pymatgen"
] | 3eee6c95ce7f39286d2340fd5062c3fe5962222b128dec99b59ddf1008c9bcf4 |
#!/usr/bin/python
#
# 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) 2010-2013 Francois Beaune, Jupiter Jazz Limited
# Copyright (c) 2014-2018 Francois Beaune, The appleseedhq Organ... | Biart95/appleseed | scripts/convertmany.py | Python | mit | 5,686 | [
"VisIt"
] | 310bd5f4689d6d9cc3d0bf9630703a34609144274eca159d4627a03f3bfd5f7a |
from flask import flash
from flask.ext.login import current_user
from octopus.models import User, Task
def create_query(args, q):
valid = True
user_id = args.get('user_id')
type = args.get('type')
if user_id:
if user_id == "me":
user = User.get_by_id(current_user.id)
else:
try:
u... | quaintm/octopus | octopus/task/utils.py | Python | bsd-3-clause | 799 | [
"Octopus"
] | 169d050062210445ec8c7c0124ac4a265168662f8a7db35b4dfd767140212e4c |
'''
Created on Jan 17, 2014
@author: oliwa
'''
import sys as sys
import numpy as np
from prody.dynamics.anm import calcANM, ANM
from prody.dynamics.editing import extendModel, sliceModel
from prody.dynamics.functions import saveModel, loadModel, writeArray
from prody.proteins.pdbfile import writePDB, parsePDB
from pro... | Shen-Lab/cNMA | Software/ANMs.py | Python | mit | 131,770 | [
"PyMOL"
] | 1e9397e4d6f89d5c317786fd8b5c9c622151256c0169209dcd2e4203d0166352 |
"""
Ionosphere space weather
========================
This space weather example plots a filled contour of rotated pole point
data with a shaded relief image underlay. The plot shows aggregated
vertical electron content in the ionosphere.
The plot exhibits an interesting outline effect due to excluding data
values be... | SusanJL/iris | docs/iris/example_code/Meteorology/TEC.py | Python | gpl-3.0 | 1,207 | [
"NetCDF"
] | c5d593c0b67239900f666c6758a86719a7ec00bbea17dd41710cc9a5ebaae057 |
#!/usr/bin/env python
# =========================================================================
#
# Copyright NumFOCUS
#
# 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:/... | richardbeare/SimpleITK | Examples/DemonsRegistration1/DemonsRegistration1.py | Python | apache-2.0 | 2,723 | [
"Gaussian"
] | ae261e92f24522b4975491a56674d0ad1c3618a37795f5da1614c12f910aa030 |
# prep cmip5 data downloaded using SYNDA for EPSCoR SE project
# author: Michael Lindgren -- June 09, 2016
import pandas as pd
import os
class Files( object ):
def __init__( self, base_dir, *args, **kwargs ):
'''
list the files from the nested directory structure
generated by SYNDA application and access of th... | ua-snap/downscale | snap_scripts/epscor_sc/older_epscor_sc_scripts_archive/prep_raw_epscor_se.py | Python | mit | 3,136 | [
"NetCDF"
] | 8a003d24cae17318d951a01d3e3bb45e1e308c7ea00b63909f265c0569e4b82d |
"""This file contains code used in "Think Stats",
by Allen B. Downey, available from greenteapress.com
Copyright 2012 Allen B. Downey
License: GNU GPLv3 http://www.gnu.org/licenses/gpl.html
"""
import matplotlib.pyplot as pyplot
import thinkplot
import csv
import math
import numpy
import random
import thinkstats2
i... | AllenDowney/HeriReligion | archive/heri15.py | Python | mit | 13,254 | [
"Gaussian"
] | 6143f6d63dee8c65f881dabd008db6c7c7629ebe49fe5ab381c0ee3c1af0b361 |
# -*- coding: utf-8 -*-
"""
Acceptance tests for CMS Video Module.
"""
import os
from mock import patch
from nose.plugins.attrib import attr
from unittest import skipIf
from ...pages.studio.auto_auth import AutoAuthPage
from ...pages.studio.overview import CourseOutlinePage
from ...pages.studio.video.video import Vid... | 10clouds/edx-platform | common/test/acceptance/tests/video/test_studio_video_module.py | Python | agpl-3.0 | 12,196 | [
"VisIt"
] | d215f6bcd36764f4cc3c35c57670d5c9d2512fef8f50f260bd220807b31a5f27 |
#!/usr/bin/env python
#
#
# Mike Dvorak
# Sail Tactics
# mike@sailtactics.com
#
# Created: 2014-11-05
# Modified: 2014-12-20
#
#
# Description: Inserts a SUNTANS tide forecast netCDF file into a WindDB at the 0-m height. This script assumes that
# the winds are being inserted into a WRF forecast with the same XLONG and... | sailorsenergy/windb2 | bin/insert-suntans-into-windb2.py | Python | gpl-3.0 | 1,989 | [
"NetCDF"
] | 874496f4f12db411dd8b27f872a1c018a22dd12f92d9d7be45f8b5bc0473442d |
#!/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/exponential_form/expsyn/__init__.py | Python | bsd-2-clause | 1,566 | [
"NEURON"
] | dfc2b330cb159a47cb30d7a53ac256580d2ffd78229c6d250243e1f46bc2671d |
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2007-2014, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version 2.1 or later. ... | Clyde-fare/cclib | test/testCore.py | Python | lgpl-2.1 | 1,605 | [
"ADF",
"cclib"
] | 816785c83080b6bf53c0798ad4e010cb40a47783caf0b41b2e2d2d5bef46abd9 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | nburn42/tensorflow | tensorflow/contrib/autograph/converters/break_statements.py | Python | apache-2.0 | 4,651 | [
"VisIt"
] | 9526122486e599fbee2a88b1f1f33c2e18892a4de3967a8ce4ba9d04ccd8accb |
# Copyright (C) 2009-2012 Paul Cochrane, Matthias Zach and Marco Reps
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.
... | paultcochrane/pbsclusterviz | pbsclusterviz/node_grid_display.py | Python | gpl-2.0 | 9,302 | [
"VTK"
] | 95c001b423e1551f77b35a1ea596ea9de83cec1cfad475d58b99d9df6f35efb2 |
# coding: utf-8
from __future__ import division, unicode_literals
"""
This class implements definitions for various kinds of bonds. Typically used in
Molecule analysis.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__e... | rousseab/pymatgen | pymatgen/core/bonds.py | Python | mit | 3,782 | [
"pymatgen"
] | e707639cb16aeae1238456430e64a7fd8ce9d4391367315b12dc6eb94f97dd60 |
"""
Module to calculate radial profiles.
The **settings** dict used for the evaluation has the following entries:
* lmax_r (int): Radius used for local maximum detection in [px].
* lmax_thresh (int): Threshold for local maximum detection in [intensity].
* lmax_cinit (int, int): Initial guess for ... | ercius/openNCEM | ncempy/algo/radial_profile.py | Python | gpl-3.0 | 13,313 | [
"Gaussian"
] | b3bad692bde7f336600725823527000c2f08ea8fb8381784a5840511221e6fdc |
import json
from typing import Callable
from uuid import uuid4
from Firefly import aliases, logging
from Firefly.const import ACTION_OFF, ACTION_ON, CONTACT, CONTACT_CLOSED, CONTACT_OPEN, EVENT_TYPE_BROADCAST, GROUPS_CONFIG_FILE, LEVEL, MOTION, MOTION_ACTIVE, MOTION_INACTIVE, STATE, SWITCH, TYPE_DEVICE
from Firefly.he... | Firefly-Automation/Firefly | Firefly/helpers/groups/groups.py | Python | apache-2.0 | 12,585 | [
"Firefly"
] | b5a11cb45c9c1d71b1239780c95c0704a1f623a2b49b75f5c3009c2e0dfc5046 |
"""Deal with an Organism in a Genetic Algorithm population.
"""
# standard modules
import random
import array
# Sequence objects from Biopython
from Bio.Seq import MutableSeq
def function_population(new_genome, num_organisms, fitness_calculator):
"""Generate a population given a function to create genomes
Ar... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/GA/Organism.py | Python | apache-2.0 | 4,884 | [
"Biopython"
] | 40dc8fd472d341702074ed7e8661d1ea63561e87f60c8e368eacb379077c376d |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2020, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
"""
Gaussian Output Editor
#########################
Editor classes for various types of Gaussian output files
"""
from __future__ import absolute_import
from __future__ import print... | exa-analytics/atomic | exatomic/gaussian/output.py | Python | apache-2.0 | 49,890 | [
"Gaussian"
] | 54a5466b788f649fb8b90aa7b1d2cb901e8593c03f61c6b2e600e59dd511390a |
"""
How to use the documentation
----------------------------
MOOSE documentation is split into Python documentation and builtin
documentation. The functions and classes that are only part of the
Python interface can be viewed via Python's builtin ``help``
function::
>>> help(moose.connect)
The documentation built i... | rahulgayatri23/moose-core | python/moose/__init__.py | Python | gpl-3.0 | 769 | [
"MOOSE"
] | c7467bf7f6efe4188fbe0b116d0ee65e6ef4e900271c748b6b95788ed85527b4 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | jdrudolph/scikit-bio | skbio/stats/distance/_base.py | Python | bsd-3-clause | 32,415 | [
"scikit-bio"
] | afe176de185f6e98f56a1865c5a55ff4470e03a82d77a2011f216b80a3903cc1 |
'''
Created on Mar 28, 2012
@author: jan
'''
import random
import numpy as np
from scipy.stats import norm, expon, gamma
from scipy.spatial.distance import squareform
def gaussian_influence(mu, width):
''' creates a 2D-function for gaussian influence sphere'''
return lambda x, y: np.exp(-width * ((x - mu[0])... | jansoe/FUImaging | regnmf/datamaker.py | Python | mit | 6,868 | [
"Gaussian"
] | 35782b91fb2fde31287ef7b26743776e47663cf707240ce5e5aee65f48c83e22 |
#pylint: disable=missing-docstring
#################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment #
# #
# (c) 2010... | backmari/moose | python/chigger/exodus/ExodusSourceLineSampler.py | Python | lgpl-2.1 | 3,716 | [
"MOOSE",
"VTK"
] | 391fea5efa978cb4ffc537985bd7e04ac8b3acce9cd06b59a6b7a7c646f81611 |
# Authors: Matti Hämäläinen <msh@nmr.mgh.harvard.edu>
# Alexandre Gramfort <alexandre.gramfort@inria.fr>
#
# License: BSD (3-clause)
# Many of the computations in this code were derived from Matti Hämäläinen's
# C code.
from copy import deepcopy
from functools import partial
from gzip import GzipFile
import ... | rkmaddox/mne-python | mne/source_space.py | Python | bsd-3-clause | 127,361 | [
"Mayavi"
] | ba24a1b38bc160460b672f21db0c29116420605b274be3846235ae08b224d991 |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import unittest
import time
import logging
import sys
import os
import mock
from DIRAC.Resources.MessageQueue.MQCommunication import createProducer
import DIRAC.Resources.MessageQueue.MQCommunication as MQComm
f... | yujikato/DIRAC | tests/Integration/Resources/MessageQueue/Test_ActiveClose.py | Python | gpl-3.0 | 9,754 | [
"DIRAC"
] | c54519f845d78424dbb3ff697227371dbc2f2ec4f41b1ebc23903bd6b109a3ce |
#!/usr/bin/env python
# -*-coding:utf-8-*-
import sys
import warnings
import requests
from requests.packages.urllib3.exceptions import InsecureRequestWarning
import logging
import os
from PIL import Image
import io
import configparser
import win32serviceutil, win32api, win32con, win32gui
TILE_WALLPAPER = ... | eloyrgz/APOD-Windows-Wallpaper | apod_wallpaper.py | Python | apache-2.0 | 5,667 | [
"VisIt"
] | aa4b260a4529dd6bbd07096f547d14504a6634b5baf78bbaa9b939e79885f1d3 |
# File generated from python blocks in "doc/async-ops.tex"
>>> import sys
>>> HOST = sys.argv[2]
>>> PORT = int(sys.argv[3])
>>> import hyperdex.admin
>>> a = hyperdex.admin.Admin(HOST, PORT)
>>> a.add_space('''
... space friendlists
... key username
... attributes
... string first,
... string last,
... set(st... | hyc/HyperDex | test/doc.async-ops.py | Python | bsd-3-clause | 2,051 | [
"Brian"
] | 66e84b7392d046ee0f94e5608eb390fb3825acb0b1209d21a60a1ba4089666c9 |
# ===========================================================================
import pangloss
import cPickle
import numpy
import pylab as plt
from math import pi
# ======================================================================
class Lightcone(object):
"""
NAME
Lightcone
PURPOSE
... | drphilmarshall/Pangloss | pangloss/lightcone.py | Python | gpl-2.0 | 27,232 | [
"Galaxy",
"Gaussian"
] | 0c6d97f0e77cef598103eb58e756a78ea6b232bef3fed31e8382c82cc8a7a0b6 |
import unittest, re, sys, random
sys.path.extend(['.','..','../..','py'])
import h2o2 as h2o
import h2o_cmd, h2o_import as h2i, h2o_args
from h2o_test import verboseprint
DO_RF = False
DO_SUMMARY = False
DO_INTERMEDIATE_RESULTS = False
class Basic(unittest.TestCase):
def tearDown(self):
h2o.check_sandbox_... | YzPaul3/h2o-3 | py2/testdir_single_jvm/test_parse_many_cases.py | Python | apache-2.0 | 9,104 | [
"Dalton"
] | 1418413daa7847ab95568dae290cf2d3818d5e86655a9eecfad14297a147d17e |
# (c) 2014, Brian Coca, Josh Drake, et al
#
# This file is part of Ansible
#
# Ansible 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.
... | dvarrazzo/ansible | lib/ansible/cache/memcached.py | Python | gpl-3.0 | 5,814 | [
"Brian"
] | 1c92de458d6e05debd28c1a3ce4c0482915a967347928ded95c1244c039bd9e6 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import cv2
import tensorflow as tf
import os
import sys
import glob
import argparse
import numpy as np
#TF-slim
#from nets import inception_utils
#from nets import inception_v4
#from preprocessing import inception_preprocessing
#import tensorflow.cont... | velastin/UAndes | KCF/BgsubTrack_KCF.py | Python | gpl-3.0 | 23,607 | [
"Gaussian"
] | 1b92a4007251ec1cee57a980e1ef59375d775a1be0459bd7d0de2dfbfa02a2f9 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2014 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Software F... | andrebellafronte/stoq | plugins/bikeshop/bikeshopreport.py | Python | gpl-2.0 | 1,146 | [
"VisIt"
] | d0b7cc0e3443256a542a178d7340bf458be0cbaa8a249d2b6f2bb3446160097b |
# $Id$
#
# Copyright (C) 2004 Rational Discovery LLC
# All Rights Reserved
#
from rdkit import RDConfig
import os, sys
import unittest
from rdkit import Chem
from rdkit import Geometry
from rdkit.Geometry import Point3D
def feq(v1, v2, tol2=1e-4):
return abs(v1 - v2) <= tol2
def ptEq(pt1, pt2, tol=1e-4)... | rvianello/rdkit | Code/GraphMol/Wrap/testConformer.py | Python | bsd-3-clause | 3,871 | [
"RDKit"
] | e9334147a9c2394d1382c67e97d284e362be9dd86ceb37235c13633c9f5472c3 |
#!/usr/bin/python
"""
Python source code - Developed to
send email or SMS to a list of recipients after a fresh reboot as a
component of the TorilMUD bot Katumi
"""
import smtplib
import tokens
from email.mime.text import MIMEText
def boot_notify():
msg = MIMEText('Katumi detected a new TorilMUD boot.')
pass... | grokh/torilbot | notify.py | Python | mit | 843 | [
"EPW"
] | 7abfda856e978e9a1b26dadd26fe250cf98db8d37ee6fa3ffa0762965dd47198 |
"""Read and write notebooks in JSON format.
Authors:
* Brian Granger
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2008-2011 The IPython Development Team
#
# Distributed under the terms of the BSD License. The full license is in
# the file COPYING, distribute... | maximsch2/SublimeIPythonNotebook | external/nbformat3/nbjson.py | Python | gpl-3.0 | 2,038 | [
"Brian"
] | 1e74e898b392a20285fa43f09515ce0309d7328d647f786e5a71cb58e88ec2a9 |
"""
.. currentmodule:: lino.utils.mti
Warning: This document is **deprecated**.
See :mod:`lino.test_apps.nomti`
.. contents::
:local:
:depth: 2
.. The following lines are here for running doctest
on this document. Sphinx removes them because they are a
comment, but doctest executes them.
>>> fr... | MaxTyutyunnikov/lino | lino/test_apps/mti/tests.py | Python | gpl-3.0 | 10,281 | [
"VisIt"
] | 343c6f95faea6587a90e9bf8696ef2c4701a432e64610e5cf407291b8940e647 |
import sys
sys.path.insert(1,"../../")
import h2o
from tests import pyunit_utils
def offset_1388():
print "Loading datasets..."
pros_hex = h2o.import_file(pyunit_utils.locate("smalldata/prostate/prostate.csv"))
pros_hex[1] = pros_hex[1].asfactor()
pros_hex[3] = pros_hex[3].asfactor()
pros_... | madmax983/h2o-3 | h2o-py/tests/testdir_jira/pyunit_NOPASS_pubdev_1388_offset_comparisons.py | Python | apache-2.0 | 3,073 | [
"Gaussian"
] | 1a265e73a5e23ea35b546e7d2476ee408ef23c10264ad5f4efce2ca0d524a704 |
########################################################################
# File: FTSJob.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/04/02 13:41:20
########################################################################
"""
:mod: FTSJob
.. module: FTSJob
:synopsis: class representing FTS job
.. moduleau... | coberger/DIRAC | DataManagementSystem/Client/FTSJob.py | Python | gpl-3.0 | 25,221 | [
"DIRAC"
] | f0a8bc9ff8a4ae81f4807c27cb419f3755c071a0ae1f1b7575fa640291c0654b |
import numpy as np
from nose.tools import (
assert_true,)
from hyperspy import signals
from hyperspy import components
class TestRemoveBackground1D:
def setUp(self):
gaussian = components.Gaussian()
gaussian.A.value = 10
gaussian.centre.value = 10
gaussian.sigma.value = 1
... | pburdet/hyperspy | hyperspy/tests/signal/test_remove_background.py | Python | gpl-3.0 | 749 | [
"Gaussian"
] | 7ea6d8377da353f92739234928ee47b697a3220915289b39ce8cafc12e4310d1 |
#!/usr/bin/env python
import sys
import numpy as np
import argparse
import matplotlib.pyplot as plt
from plotTools import addContourf
from analysisTools import sensibleIds, groundOffset, continuousWaveletAnalysis
from netcdfTools import read3dDataFromNetCDF, netcdfOutputDataset, \
createNetcdfVariable, netcdfWriteAnd... | saskartt/P4UL | pyNetCDF/waveletAnalysisProfile.py | Python | mit | 5,556 | [
"NetCDF"
] | bfe3b22d08e8dfdc15600e4d42523f9dea734461bf25f4ef4fdaa681dcf234b0 |
#!/usr/bin/python
# Audio Tools, a module and set of tools for manipulating audio data
# Copyright (C) 2007-2016 Brian Langenberger
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either vers... | tuffy/python-audio-tools | test/test_utils.py | Python | gpl-2.0 | 255,218 | [
"Brian"
] | 0e2989fbad677d700c33c70fac65070c74ee87f0745b8a371a2dd397df4d171f |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Gary Burton
#
# 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... | arunkgupta/gramps | gramps/gen/plug/menu/_personlist.py | Python | gpl-2.0 | 1,820 | [
"Brian"
] | 256527b5a274999e871db0d5c87fed66257dc55821251a1f988a770ed4db9b9a |
###############################################################################
#
# coverage.py - calculate coverage of all sequences
#
###############################################################################
# #
# This program is fre... | fw1121/CheckM | checkm/coverage.py | Python | gpl-3.0 | 14,394 | [
"pysam"
] | d8f99abab1f9cb511a4a69a359a3724e9a4748e853e479df075a365c9e18dd62 |
#!/usr/bin/python
# Copyright (C) 2012 W. Trevor King <wking@drexel.edu>
# Copyright (C) 2012 Sebastian Pipping <sebastian@pipping.org>
# Copyright (C) 2013 Brian dolbec <dolsen@gentoo.org>
# Licensed under GPL v2 or later
# This script should be run from the root of the catalyst source.
# source the testpath file the... | benkohler/catalyst | doc/make_target_table.py | Python | gpl-2.0 | 1,266 | [
"Brian"
] | e9d4e57b366a4248a8ef3a93e2080ef315d3148d3097c512edc04f2d3e45e21b |
import os, re
import numpy as np
import scipy
from scipy.misc import logsumexp
from scipy.special import gammaln, beta
from scipy.integrate import simps
from numpy import newaxis as na
import scipy.sparse
from scipy.sparse import csr_matrix, csc_matrix, lil_matrix
import pypolyagamma as ppg
from pgmult.internals.d... | HIPS/pgmult | pgmult/utils.py | Python | mit | 17,648 | [
"Gaussian"
] | 788f733811cb777624f64912dc7d8abb3d3076e4537890a5e1dd7d3bd1a2c258 |
# c: 14.04.2008, r: 14.04.2008
import numpy as nm
from sfepy import data_dir
filename_mesh = data_dir + '/meshes/2d/square_unit_tri.mesh'
def get_pars(ts, coors, mode=None, extra_arg=None,
equations=None, term=None, problem=None, **kwargs):
if mode == 'special':
if extra_arg == 'hello!':
... | RexFuzzle/sfepy | tests/test_functions.py | Python | bsd-3-clause | 4,879 | [
"VTK"
] | fee7dd4f22b391f509413a8e9f5fc3417ce438a19a0a361663763af43821e03c |
# 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/integrator/VelocityVerlet.py | Python | gpl-3.0 | 1,750 | [
"ESPResSo"
] | 81f9f20c3dfcb1e59129ea26e5653fa08a57343deb9cf072e0ac67dc481bbc64 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | kyleabeauchamp/mdtraj | mdtraj/tests/test_hdf5.py | Python | lgpl-2.1 | 10,468 | [
"MDTraj",
"OpenMM"
] | ddf9e362fc0a707389695fb5a77fd4755c2d42ba78a3fce04fa72739825d775f |
"""
test views
"""
import datetime
import json
import re
import pytz
import ddt
import urlparse
from mock import patch, MagicMock
from nose.plugins.attrib import attr
from capa.tests.response_xml_factory import StringResponseXMLFactory
from courseware.courses import get_course_by_id
from courseware.tests.factories imp... | ahmadiga/min_edx | lms/djangoapps/ccx/tests/test_views.py | Python | agpl-3.0 | 34,247 | [
"VisIt"
] | bfcecdf6f090c28681777b321270eba6a69a181dae65587b7072f36cbb2f407f |
#!/usr/bin/env/python
# =============================================================================
# MODULE DOCSTRING
# =============================================================================
"""
Module which houses all the handling instructions for reading and writing to netCDF files for a given type.
This... | choderalab/openmmtools | openmmtools/storage/iodrivers.py | Python | mit | 61,896 | [
"NetCDF",
"OpenMM"
] | cd9fbca9fa5a588d8cfaa2613915fc4beb7dada298ba5e15bcaeb8a1954b7025 |
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