text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
"""
SDoc
Copyright 2016 Set Based IT Consultancy
Licence MIT
"""
# ----------------------------------------------------------------------------------------------------------------------
import os
import antlr4
from sdoc.antlr.sdoc1Lexer import sdoc1Lexer
from sdoc.antlr.sdoc1Parser import sdoc1Parser
from sdoc.sdoc... | OlegKlimenko/py-sdoc | sdoc/sdoc1/SDoc1Interpreter.py | Python | mit | 1,796 | [
"VisIt"
] | 34c88ec9f5d19d2b6c027151bf58c16dd5677e1cdaa183d4cbeea6b26fc24751 |
# Copyright 2006-2009 by Peter Cock. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
#Nice link:
# http://www.ebi.ac.uk/help/formats_frame.html
"""Sequence input/output as Seq... | NirBenTalLab/proorigami-cde-package | cde-root/usr/lib64/python2.4/site-packages/Bio/SeqIO/__init__.py | Python | mit | 36,262 | [
"BioPerl",
"Biopython"
] | 33a0ccadb72518825bdf33c0b4da013026240bd3c4bb7dee5ce7a7d3ed041ad5 |
# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
import re
import warnings
from Bio.PDB.PDBIO import PDBIO
_hydrogen=re.compile("[123 ]*... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/PDB/Dice.py | Python | gpl-2.0 | 1,986 | [
"Biopython"
] | a8047b6c2e4656c1bc888b04b8c35792c0f12d91251665afadcd65979b489c4b |
import os
from django.conf import settings
FRONTEND_DIRS = getattr(settings, 'FRONTEND_DIRS', {
'svg': os.path.join(settings.BASE_DIR, 'frontend', 'svg'),
})
FRONTEND_BUILDER = {
'COMMAND': 'gulp',
'ARGS': '',
'WATCH_TASK': 'watch',
'BUILD_TAKS': 'default',
}
| redisca/django-redisca | redisca/frontend/settings.py | Python | mit | 283 | [
"GULP"
] | 0db8b8ecd98370d731abbe97a97f3d68195e500fe2b05bcf09121f67f1bd779d |
#!/usr/bin/env python
"""This preprocessing script is part of the CLAM pipeline.
This subcommand (new v1.1) will prepare the input files for CLAM pipeline. As of the current version (v1.1), it looks for
reads passing QC, splits the input bam file by sorting them into `unique.sorted.bam` and `multi.sorted.bam`, ... | Xinglab/CLAM | CLAM/preprocessor.py | Python | gpl-3.0 | 9,955 | [
"pysam"
] | 106a32f425d343be8410a54d7cd649f2063a3bc51b94f6e90176e3ea47a2f597 |
#!/usr/bin/env python
#
# texttable - module for creating simple ASCII tables
# Copyright (C) 2003-2011 Gerome Fournier <jef(at)foutaise.org>
#
# This 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 the Free Software Foundat... | thasso/pyjip | jip/vendor/texttable.py | Python | bsd-3-clause | 20,869 | [
"Brian"
] | b23db19eb6cd38e198fd2a77d52551efd9bb3de67a486d5af443a32ade629389 |
# Author: Samuel Genheden samuel.genheden@gmail.com
"""
Classes to help with the processing of MD trajectories
"""
import argparse
import sys
import MDAnalysis as md
class TrajectoryProcessor(object):
"""
Class to process an MD trajectory
The program that uses this initialises an instance that setups u... | SGenheden/Scripts | sgenlib/moldyn.py | Python | mit | 5,176 | [
"MDAnalysis"
] | 2cd668c6bc502b2bd9b4e15958ae6ca0583e0481497de1bf052b78c5b6fc8ea7 |
import unittest
from fluggo.media import process, formats
from fluggo.media.basetypes import *
from fluggo.editor import model, plugins
from PyQt4.QtGui import *
vidformat = plugins.VideoFormat(
pixel_aspect_ratio = fractions.Fraction(40, 33),
frame_rate = fractions.Fraction(24000, 1001),
full_frame = box2... | fluggo/Canvas | tests/canvas/ItemManipulator.py | Python | gpl-3.0 | 66,509 | [
"exciting"
] | c03261a2b7b644ebddb5e5727dd27cb26ede7fe1a9c6afe918389b5454861a82 |
from __future__ import (absolute_import, division,
print_function, unicode_literals)
from builtins import *
import logging
import re
import sys
import tempfile
from datetime import datetime
import pytz
import psycopg2
import numpy
from netCDF4._netCDF4 import Dataset, chartostring
from windb2.i... | sailorsenergy/windb2 | windb2/model/wrf/insert.py | Python | gpl-3.0 | 15,067 | [
"NetCDF"
] | b97de939b3bb9f45334e8f9f68022e740d6cf2acb2632ed13a0eb47a206d1ddc |
from __future__ import division
import numpy as np
import sys, time
from megaman.geometry.rmetric import riemann_metric_lazy
from megaman.geometry.affinity import compute_affinity_matrix
from megaman.geometry.laplacian import compute_laplacian_matrix
import multiprocessing as mp
from multiprocessing.pool import ThreadP... | mmp2/megaman | megaman/utils/estimate_radius.py | Python | bsd-2-clause | 6,736 | [
"Gaussian"
] | 1ef54ca9b45e783741f1e77655a5a14f8cd5cfcfb714ca238ff969ce4c99f561 |
# AudioDB - routines for audio database I/O, searching, and manipulation
# Bregman - python toolkit for music information retrieval
__version__ = '1.0'
__author__ = 'Michael A. Casey'
__copyright__ = "Copyright (C) 2010 Michael Casey, Dartmouth College, All Rights Reserved"
__license__ = "New BSD License"
__email__ =... | daleloogn/singerID-Theano-DBN | use_dbn_on_bigset/audiodb.py | Python | gpl-2.0 | 14,021 | [
"Gaussian"
] | 51d600baddc81be206679a31b25a771a5fc9c33634920c6ddaf213630db9ed68 |
"""Example creating random network."""
import random
from pathlib import Path
from sbmlutils import EXAMPLES_DIR
from sbmlutils.cytoscape import visualize_sbml
from sbmlutils.factory import *
random.seed(1234)
n_species = 20
n_links = 30
# ----------------------------------------------------------------------------... | matthiaskoenig/sbmlutils | src/sbmlutils/examples/random_network.py | Python | lgpl-3.0 | 1,369 | [
"Cytoscape"
] | cebebbdca3d4a0e7a80df145d196703da049887497d0f648425b58a25f62d28d |
__author__ = 'Justin McClure'
from django.test import TestCase, Client
from django.core.urlresolvers import reverse
from random import choice
from MyInfo.models import MaintenanceNotice, Department
from MyInfo.forms import ChangeOdinPasswordForm, SetOdinPasswordForm
from datetime import datetime, timedelta
class MyI... | hhauer/myinfo | MyInfo/tests/test_views.py | Python | mit | 14,356 | [
"VisIt"
] | 04452fc76d05f29c61e25c1fd6a22a06c783103a1b9512b228e0fd4629884667 |
# encoding: utf-8
"""Classes used in scattering and gathering sequences.
Scattering consists of partitioning a sequence and sending the various
pieces to individual nodes in a cluster.
Authors:
* Brian Granger
* MinRK
"""
#-------------------------------------------------------------------------------
# Copyrig... | noslenfa/tdjangorest | uw/lib/python2.7/site-packages/IPython/parallel/client/map.py | Python | apache-2.0 | 5,263 | [
"Brian"
] | 517500cc2d88e998c02a430ca1cc45fc357c912101691c5232a1ecdba6a048b1 |
import scipy.constants
"""
molar gas constant (R) in J mol^-1 K^-1
"""
gas_constant = scipy.constants.gas_constant
"""
Avogadro constant (N_A) in mol ^ -1
"""
Avogadro = scipy.constants.Avogadro
"""
Boltzmann constant (k_B) in J K^-1.
Note that we are not using scipy.constants.Boltzmann because it is not
availabl... | QuLogic/burnman | burnman/constants.py | Python | gpl-2.0 | 372 | [
"Avogadro"
] | 0fb170c839a14a3131788c92f00544401f53d864f60eca479b36830eab641a51 |
# -*- coding: utf-8 -*-
"""
weppy.validators.helpers
------------------------
Provides utilities for validators.
Ported from the original validators of web2py (http://www.web2py.com)
:copyright: (c) by Massimo Di Pierro <mdipierro@cs.depaul.edu>
:license: LGPLv3 (http://www.gnu.org/licenses/l... | daxslab/web2py-model-class-declaration | modules/plugin_model_class_declaration/validators/helpers.py | Python | mit | 18,997 | [
"CASINO",
"MOE"
] | 9a81af552069ba8b947a94bde3fa0edc8f2102a06fd21ed85495808285d8b29b |
##
# Copyright 2009-2018 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/l/libsmm.py | Python | gpl-2.0 | 8,352 | [
"CP2K"
] | 50ff67a36ae5bcba17583619a8f93b62811ebe893e5ea24664942fa6b3f7f87c |
"""
Author: Remi Lafage <remi.lafage@onera.fr>
This package is distributed under New BSD license.
Mixture of Experts
"""
# TODO : support for best number of clusters
# TODO : implement verbosity 'print_global'
# TODO : documentation
import numpy as np
import warnings
OLD_SKLEARN = False
try: # scikit-learn < 0.20.... | SMTorg/smt | smt/applications/moe.py | Python | bsd-3-clause | 25,286 | [
"MOE"
] | 7c7b8b54b88886adde625e9d8f7d0352241304ca5b9be4c95cfb9b6abfd32834 |
'''
Created on 2 Aug 2013
@author: danielfisher
'''
import matplotlib.pyplot as plt
import numpy as np
import os
import scipy.ndimage as ndimage
import netCDF4 as nc
from mpl_toolkits.basemap import Basemap
import pyresample as pr
import cv2
import NPT.NonParametricTransform
import NPT.NonParametricMatcher
import mss... | dabillox/opticalflowwinds | opticalFlowWinds.py | Python | mit | 9,653 | [
"NetCDF"
] | f507fc027eb56030ae72ccf6efbb364fb3ab0e27b0ba48d2636b6ab9293598fe |
# BLASTN 2.0a19MP-WashU [05-Feb-1998] [Build decunix3.2 01:53:29 05-Feb-1998]
# BLASTP 2.0.4 [Feb-24-1998]
class Algorithm:
def __init__(self, name, version, description = ""):
self.name = name # 'blastx', 'blastn', etc.
self.version = version # '2.1.2' or '2.0a19MP-WashU'
... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/Search.py | Python | apache-2.0 | 5,580 | [
"BioPerl"
] | 6830a7b6969632129c9dfa6a429a14ec5b2837575e8815c40045e40dc3f23c42 |
# -*- coding: utf-8 -*-
# Copyright 2007-2016 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at... | sem-geologist/hyperspy | hyperspy/_components/expression.py | Python | gpl-3.0 | 12,968 | [
"Gaussian"
] | fdb2f466840872bf0764d648f1056748048fdf0119c64acff133e70330f7369d |
# -*- coding: utf-8 -*-
__version__ = '0.7.0'
__author__ = 'Tomasz Czyż <tomaszczyz@gmail.com>'
__license__ = "Apache 2"
import os
import re
import sys
import json
import copy
import uuid
import hashlib
import argparse
import functools
import posixpath
import pkg_resources
import sphinx
from sphinx.locale import _
f... | flytbase/flytdocs | source/_extensions/sphinxcontrib/images.py | Python | mit | 12,401 | [
"VisIt"
] | 27050aad19a8ea182a4aab6b3b2ebd058afe4489c127ff88147110840cae7cdd |
# -*- coding: utf-8 -*-
"""
A Cell
A cell is a single input/output block. Worksheets are built out of
a list of cells.
"""
###########################################################################
# Copyright (C) 2006 William Stein <wstein@gmail.com>
#
# Distributed under the terms of the GNU General Public ... | damahou/sagewui | sagewui/gui/cell.py | Python | gpl-3.0 | 60,347 | [
"Jmol"
] | 526e4fd0e63c1951c5b632aa54196d2f1a69b28677623ecf698a03e1e303010d |
"""
Instructor Dashboard Views
"""
import logging
import datetime
from opaque_keys import InvalidKeyError
from opaque_keys.edx.keys import CourseKey
import uuid
import pytz
from django.contrib.auth.decorators import login_required
from django.views.decorators.http import require_POST
from django.utils.translation imp... | ampax/edx-platform | lms/djangoapps/instructor/views/instructor_dashboard.py | Python | agpl-3.0 | 30,932 | [
"VisIt"
] | fb0f7037902b039d9b2fe6c7889495149041b4453dc75fc3a5fdf39b3497aace |
""" JobManagerHandler is the implementation of the JobManager service
in the DISET framework
The following methods are available in the Service interface
submitJob()
rescheduleJob()
deleteJob()
killJob()
"""
from DIRAC import S_OK, S_ERROR
from DIRAC.ConfigurationSystem.Client.Helpers.Operati... | DIRACGrid/DIRAC | src/DIRAC/WorkloadManagementSystem/Service/JobManagerHandler.py | Python | gpl-3.0 | 26,204 | [
"DIRAC"
] | 83feecc491262c22052cc9cdc152769c9a661f25fe1a39f77c1de6215d4c5eeb |
import characterquests
from characterutil import *
def charquest_z_98_legion_intro(count,datatree,openfile):
characterquests.charquestheader(count,"98: Legion Invasion",openfile)
characterquests.charquestprintfaction(count,datatree,openfile,40519,"The Legion Returns","alliance")
characterquests.charquestprintfactio... | DreamsofPeace/WoW-Quests | characterquests7legion.py | Python | mit | 98,766 | [
"CRYSTAL",
"MOOSE"
] | 5f0045a64b594c434ebd1177259cc448287168fdfb8f24f3afdc4a8c2bc77311 |
import numpy as np
def circular_distance(p1, p2, dimension):
"""
Euclidean distance with periodic boundary conditions
In particular this measures the distance in a a grid
with dimension as the number of squres
"""
total = 0
for (x, y) in zip(p1, p2):
delta = abs(x - y)
... | h-mayorquin/Neural_Pattern_Doursat | distance_functions.py | Python | gpl-2.0 | 3,048 | [
"NEURON"
] | a72022d21589d21c0f8ddaa58abbf060c39069eb71f237e8bf908bb3b4fb4732 |
# Copyright 2014-2020 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | sunqm/pyscf | pyscf/tdscf/__init__.py | Python | apache-2.0 | 2,434 | [
"PySCF"
] | 47545802498db62db0cb2bb45a6b68fc55911a39e99b979850b7c3db68803168 |
#### import the simple module from the paraview
from paraview.simple import *
import glob, re, os, numpy, csv
def CreatePointSelection(ids):
source = IDSelectionSource()
source.FieldType = "POINT"
sids = []
for i in ids:
sids.append(0) #proc-id
sids.append(i) #cell-id
source.IDs = sids
... | jhaase1/zapdos | problems/Schottky_emission/transient/no_ballast/parametric/base/OldUnAveragedSystemData.py | Python | lgpl-2.1 | 5,514 | [
"ParaView"
] | 19320d92018fec7b8d9e1570a6e51a7b1b1eb49908d631603ef6d5498ce7c207 |
import contextlib
import itertools
import math
import os.path
import pickle
import shutil
import sys
import tempfile
import warnings
from contextlib import ExitStack
from io import BytesIO
from pathlib import Path
from typing import Optional
import numpy as np
import pandas as pd
import pytest
from pandas.errors impor... | jhamman/xarray | xarray/tests/test_backends.py | Python | apache-2.0 | 172,910 | [
"NetCDF"
] | 07d5b47074a7a9f6725047c978cf0354e67ca19779b3d82ed4501cadd985b272 |
# This file is part of Merlin/Arthur.
# Merlin/Arthur is the Copyright (C)2009,2010 of Elliot Rosemarine.
# Individual portions may be copyright by individual contributors, and
# are included in this collective work with permission of the copyright
# owners.
# This program is free software; you can redistribute it an... | d7415/merlin | Arthur/views/exiles/exiles.py | Python | gpl-2.0 | 3,390 | [
"Galaxy"
] | 1499a76da667bc542c6ceef42bf26328cce04f19b3a455e11116ff803b746677 |
#!/usr/local/python-2.7.1/bin/python2.7 -W ignore::DeprecationWarning
"""
FILE
prestackspec_v2.15.py
DESCRIPTION
Remove duplicates.
Remove AGN using BPT diagram and emission line cuts as described in Tremonti
et al. (2004) and using the separation criteria from Kauffmann et
al. (2003). These ga... | bretthandrews/stacking | stacking/prestackspec_v2.15.py | Python | bsd-3-clause | 10,305 | [
"Galaxy"
] | 4188736c9f1b566b5057c8081eb3e740aca8f472e2973083fabdb951d564da67 |
# -*- 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-managed-identities | tests/unit/gapic/managedidentities_v1/test_managed_identities_service.py | Python | apache-2.0 | 145,565 | [
"Octopus"
] | 6a16acae3b5225769739a3bace43c899b25735fc2717174cd15e88a20e60b9bb |
# Copyright (C) 2012,2013,2015
# 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... | kkreis/espressopp | src/FixedQuadrupleAngleList.py | Python | gpl-3.0 | 3,945 | [
"ESPResSo"
] | 546614cce540c2ad7cf829bea20a59d94973aa02e864542ec985ce87bad06066 |
import numpy as np
from numpy.linalg import cholesky, inv
def poisson_log_posterior(y, f, cK_inv, f0=0.0,
grad=False, hess=False,
hessp=False, p=None):
""" Poisson regression log likelihood with correlated gaussian prior
Computes the log likelihood (techn... | andymiller/flecks | likelihoods/poisson.py | Python | mit | 3,428 | [
"Gaussian"
] | e2d319e0a4e7cd2ace6ca8893c5b693e594613c3090687364f7d671e9c90bf4a |
# Copyright (c) 2015-2017 Cisco Systems, Inc.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to
# deal in the Software without restriction, including without limitation the
# rights to use, copy, modify, merge... | retr0h/maquina | test/unit/conftest.py | Python | mit | 5,333 | [
"Galaxy"
] | 3d1170aa2c51d9cb57a7ca8e40723ad12c93058119b98edaae37d35b605765f6 |
#!/usr/bin/env python
# Copyright 2014-2020 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/scf/hf.py | Python | apache-2.0 | 74,001 | [
"PySCF"
] | 1cb0a601bd7e2390c277d17ad539b0281b3d9570aafceaea64b15c309dd7b91a |
"""
Implements the Lamson command line tool's commands, which are run
by the lamson.args module dynamically. Each command has it's
actual user displayed command line documentation as the __doc__
string.
You will notice that all of the command functions in this module
end in _command. This is not required by the lams... | pitch-sands/i-MPI | flask/Lib/site-packages/lamson/commands.py | Python | bsd-3-clause | 13,288 | [
"BLAST"
] | 55b2261b33f2a3025a342abe06e255c9aebabf48e783b01de124cbbd78475e03 |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# -----------------------------------------------------------------------------
# Copyright (c) 2014, Nicolas P. Rougier. All Rights Reserved.
# Distributed under the (new) BSD License.
# -----------------------------------------------------------------------------
""" Thi... | duyuan11/glumpy | examples/interpolations.py | Python | bsd-3-clause | 4,303 | [
"Gaussian"
] | 762e0428363b5474259ea43de568e142bc3073689b0fadbfdc01b608d641c8d5 |
"""
Tools for working with raw SFF files
"""
import itertools
# Complement of sequence in which nucleotides are flowed.
# THe standard bases read would be ATGC
FLOW_ORDER = 'TACG'
# Sequence at the beginning of reads
READ_BEGIN = 'TCAG'
def cumsum(iterable):
"""
Generates a cumulative sum from iterable
... | fhcrc/ampliconnoise | anoisetools/sff.py | Python | gpl-3.0 | 1,984 | [
"Biopython"
] | b38aca6b5204939542e1d755c0ed738e84598a51ec47399a5d0d2643d7c90aa9 |
import pathlib
import attr
_LICENSES = {
"Glide": {
"name": "3dfx Glide License",
"url": "http://www.users.on.net/~triforce/glidexp/COPYING.txt",
},
"Abstyles": {
"name": "Abstyles License",
"url": "https://fedoraproject.org/wiki/Licensing/Abstyles",
},
"AFL-1.1": {... | clld/clldutils | src/clldutils/licenses.py | Python | apache-2.0 | 38,642 | [
"NetCDF"
] | 8e436b64e02ed3e62938b829934c9a0b58944e8327ce103681b92c32f825a5b5 |
from Module import AbstractModule
class Module(AbstractModule):
def __init__(self):
AbstractModule.__init__(self)
def run(
self, network, antecedents, out_attributes, user_options, num_cores,
out_path):
import os
from genomicode import filelib
from genomicode im... | jefftc/changlab | Betsy/Betsy/modules/call_variants_mutect.py | Python | mit | 6,188 | [
"VisIt"
] | efce7f87d5072102649cb4223be083e7874c8bd6b05dfe743ab213a4a0e124b9 |
# Copyright (C) 2014 Olaf Lenz
#
# 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 version.
#
# ESPR... | olenz/espresso | src/python/espressomd/gen_pxiconfig.py | Python | gpl-3.0 | 1,825 | [
"ESPResSo"
] | 1dadccc336d50c6499da9ce3150b81ca3015672d035feb35e0ea5e5cf7582be1 |
# Copyright 1999 by Jeffrey Chang. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Index.py
This module provides a way to create indexes to text files.
Classes:
Index D... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/Index.py | Python | apache-2.0 | 4,947 | [
"Biopython"
] | d60b6675f66ae2608a4bf2172acca9abe0f958be8325417b0855189f56e9e939 |
from __future__ import print_function
from six.moves import map
"""
Description:
Input: event / site data previously analyzed by photostim
Output:
- per-event probability of being direct / evoked / spont
- per-site probability of having evoked / direct input
- per-cell measurements of direct and presy... | acq4/acq4 | acq4/analysis/tools/poissonScore/poissonScore.py | Python | mit | 53,772 | [
"Gaussian"
] | 4a4fcea7729a1fffbcd65b430e27ba93a710a5f9af09d22c07894a33620010c4 |
import logging
import os
import time
import math
from cpc.dataflow import IntValue, FloatValue, StringValue
import cpc.command
from cpc.lib.gromacs import iterate
log=logging.getLogger(__name__)
def sleep(inp):
if (inp.testing()):
return
pers = cpc.dataflow.Persistence(os.path.join(inp.getPersistentD... | soellman/copernicus | cpc/lib/benchmark/sleep.py | Python | gpl-2.0 | 2,542 | [
"Gromacs"
] | be6c00d2f232a7ec48fa68f5ec2225064a7d88fcf4107bf8e6494abda98e3877 |
'''
fs.contrib.tahoelafs
====================
This modules provides a PyFilesystem interface to the Tahoe Least Authority
File System. Tahoe-LAFS is a distributed, encrypted, fault-tolerant storage
system:
http://tahoe-lafs.org/
You will need access to a Tahoe-LAFS "web api" service.
Example (it wil... | revolunet/pyfilesystem | fs/contrib/tahoelafs/__init__.py | Python | bsd-3-clause | 15,428 | [
"VisIt"
] | f2f68fd4214b85aa9755cfee6e05ea7e2b849e20ffeb552c2b34025b1e539f89 |
import numpy as np
import simtk.openmm as mm
import simtk.openmm.app as app
import simtk.unit as u
eu = u.kilocalories_per_mole
temperature = 300 * u.kelvin
friction = 1.0 / u.picosecond
pdb = app.PDBFile('pdb/resi-1-15.pdb')
forcefield = app.ForceField('amber99sb.xml',"tip3p.xml")
m = app.modeller.Modeller(pdb.to... | kyleabeauchamp/AlphaSynuclein | python/solvate.py | Python | apache-2.0 | 830 | [
"OpenMM"
] | 2d4d6458866dd1963306953bb43c190d5665229100a0653835d38aa3b03ee5e4 |
"""
=============================
Generic SpectralModel wrapper
=============================
.. moduleauthor:: Adam Ginsburg <adam.g.ginsburg@gmail.com>
"""
import numpy as np
from pyspeckit.mpfit import mpfit,mpfitException
from pyspeckit.spectrum.parinfo import ParinfoList,Parinfo
import copy
from astropy import lo... | dinossimpson/pyspeckit | pyspeckit/spectrum/models/model.py | Python | mit | 40,407 | [
"Gaussian"
] | 6361fb0faa3c0f9333b9cb59a469b83ed566928d2d7ae70dc1234c99b20e54a6 |
import deepchem as dc
import numpy as np
import tensorflow as tf
import unittest
import tempfile
from tensorflow.keras.layers import Input, Concatenate, Dense
from flaky import flaky
def generate_batch(batch_size):
"""Draw training data from a Gaussian distribution, where the mean is a conditional input."""
mean... | lilleswing/deepchem | deepchem/models/tests/test_gan.py | Python | mit | 8,376 | [
"Gaussian"
] | c022a38d9bf01620fb4417c37b86cc70168b6373e3cc918b2bb1789d4b187a03 |
'''This module contains the ComplexityVisitor class which is where all the
analysis concerning Cyclomatic Complexity is done. There is also the class
HalsteadVisitor, that counts Halstead metrics.'''
import ast
import operator
import collections
# Helper functions to use in combination with map()
GET_COMPLEXITY = op... | AtomLinter/linter-pylama | bin/deps/radon/visitors.py | Python | mit | 13,949 | [
"VisIt"
] | 051d12ea61245b82f6f219363e20c3c8c894b1db57ca68fba19831bcf172b99c |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
from FileTe... | nuclear-wizard/moose | python/TestHarness/testers/CSVValidationTester.py | Python | lgpl-2.1 | 6,150 | [
"MOOSE"
] | 91a91c0c584d8b8236b9b00c0dc3661c64ec9b3501299ac17a36d04416ace03e |
""" Encapsulate here the logic for limiting the matching of jobs
Utilities and classes here are used by the Matcher
"""
__RCSID__ = "$Id"
from DIRAC import S_OK, S_ERROR
from DIRAC import gLogger
from DIRAC.Core.Utilities.DictCache import DictCache
from DIRAC.ConfigurationSystem.Client.Helpers.Operations import... | andresailer/DIRAC | WorkloadManagementSystem/Client/Limiter.py | Python | gpl-3.0 | 8,216 | [
"DIRAC"
] | 7c7220852e600280b513e633042618d51a00a6a8685ff69f677f2ebc5b2aa94f |
# -*- coding: utf-8 -*-
# $Id: manpage.py 6110 2009-08-31 14:40:33Z grubert $
# Author: Engelbert Gruber <grubert@users.sourceforge.net>
# Copyright: This module is put into the public domain.
"""
Simple man page writer for reStructuredText.
Man pages (short for "manual pages") contain system documentation on unix-li... | dscho/hg | doc/hgmanpage.py | Python | gpl-2.0 | 34,084 | [
"VisIt"
] | b5a684062f5788354948a80a90f70b035c9c7f73e5545eae1771fd2d65399786 |
# (c) 2012-2014, 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) an... | atsaki/ansible | lib/ansible/constants.py | Python | gpl-3.0 | 19,080 | [
"Galaxy",
"MOOSE"
] | 6af0764a0e8875f0adbb6d5521159b95723b5ea73253ad185cb9e1564e676a45 |
# GUI Application automation and testing library
# Copyright (C) 2006 Mark Mc Mahon
#
# This 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 the Free Software Foundation; either version 2.1
# of the License, or (at your o... | pywinauto/pywinauto-sandbox | sandbox/playing_RepeatedHotkeyFixing.py | Python | lgpl-2.1 | 7,438 | [
"Galaxy"
] | a63e70deb1b36e6251d6e58bbc5e707a080088ecc7d7a9ffdd6d8665110ff0ed |
from unittest import TestCase
from abyes.ab_exp import AbExp
from scipy.stats import norm
import numpy as np
import logging
import sys
class TestFunctions(TestCase):
def test_hpd(self):
"""
Test that the hpd functions returns the correct interval
for a normal standard distribution,
... | cbellei/abyes | abyes/test/test_abExp.py | Python | apache-2.0 | 5,968 | [
"Gaussian"
] | 34e77cfb06a205467997ea8b3566081234e8d0c4eb2586c62e5e794f2b1e9f1c |
"""
.. module:: assembler3
:synopsis: assemble genes from RNASeq data (reads and junction coverages (bigwig) and junction paths)
jGEM version 3 assembler
.. moduleauthor:: Ken Sugino <ken.sugino@gmail.com>
"""
# system imports
import subprocess
import multiprocessing
import gzip
import os
import copy
import... | kensugino/jGEM | jgem/assembler3.py | Python | mit | 162,434 | [
"VisIt"
] | 5ff93418328d032a83f5bece7b0142e417f4d1838b15d4bac3dae5053d960d6e |
# -*- coding: utf-8 -*-
#
# test_connect_array_fixed_indegree.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 versio... | tobikausk/nest-simulator | pynest/nest/tests/test_connect_array_fixed_indegree.py | Python | gpl-2.0 | 3,315 | [
"NEURON"
] | 6380a69492751749e179a1bc7e51d4ec38e6445181580d69dcfd3e845f681fc8 |
# -*- coding: utf-8 -*-
from scipy import spatial
import numpy as np
class MegKDE(object):
""" Matched Elliptical Gaussian Kernel Density Estimator
Adapted from the algorithm specified in the BAMBIS's model specified Wolf 2017
to support weighted samples.
"""
def __init__(self, train, weight... | Samreay/ChainConsumer | chainconsumer/kde.py | Python | mit | 3,332 | [
"Gaussian"
] | dcce42e1643a99d125ba9f1e0d6a8b106e6eba3a1ae873550c7e1d8e1db49e1a |
'''It tests the representation of the results from programs like blast,
ssaha2, etc. that align one sequence against a database.'''
# Copyright 2012 Jose Blanca, Peio Ziarsolo, COMAV-Univ. Politecnica Valencia
# This file is part of seq_crumbs.
# seq_crumbs is free software: you can redistribute it and/or modify
# it ... | JoseBlanca/seq_crumbs | test/seq/test_alignment_result.py | Python | gpl-3.0 | 50,239 | [
"BLAST"
] | 156259b113aee00e6ea8a9563c1b53948c3ac4d28ab24229d6a99712665a80dd |
"""
Events related to the Motion process.
"""
from dropbox import client, session
from multiprocessing import Process, Queue
from os.path import basename
from watchdog.events import FileSystemEventHandler
import os
import webbrowser
TOKEN_FILE = '/tmp/dropbox_token_file'
class SnapshotEventHandler(FileSystemEventHa... | platzhirsch/security-cam | server/securitas/events.py | Python | mit | 4,354 | [
"VisIt"
] | 9845c43718a7ac10d00c669e8558b429453cd33972d127d67ee4d18faa8ad2cb |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#===============================================================================
# Copyright (c) 2012 - 2014, GPy authors (see AUTHORS.txt).
# Copyright (c) 2014, James Hensman, Max Zwiessele
# Copyright (c) 2015, Max Zwiessele
#
# All rights reserved.
#
# Redistribution a... | esiivola/GPYgradients | setup.py | Python | bsd-3-clause | 9,631 | [
"Gaussian"
] | 09b8ce59018c119778714bbe948605b4eb13519c27935d82480ad1845510a4ad |
""" RocciEndpoint class is the implementation of the rocci interface to
a cloud endpoint via rOCCI-cli
"""
from __future__ import print_function
from __future__ import division
from __future__ import absolute_import
import os
import json
import subprocess
import tempfile
from DIRAC import gLogger, S_OK, S_ERROR
... | DIRACGrid/VMDIRAC | VMDIRAC/Resources/Cloud/RocciEndpoint.py | Python | gpl-3.0 | 7,198 | [
"DIRAC"
] | 364a8d66089dea16da9890c628b1e14ab667c48f78b58437c0803573de5e49ea |
# Copyright 2002 by Andrew Dalke. All rights reserved.
# Revisions 2007-2009 copyright by Peter Cock. All rights reserved.
# Revisions 2008-2009 copyright by Cymon J. Cox. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should ha... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/BioSQL/BioSeq.py | Python | gpl-2.0 | 22,741 | [
"Biopython"
] | 47f5a02e8e9651bb880b6af8c13b3917ca8e583a915b16674848de6e7478f624 |
# ----------------------------------------------------------------------
# Numenta Platform for Intelligent Computing (NuPIC)
# Copyright (C) 2013, Numenta, Inc. Unless you have an agreement
# with Numenta, Inc., for a separate license for this software code, the
# following terms and conditions apply:
#
# This progra... | syl20bnr/nupic | nupic/research/FDRCSpatial2.py | Python | gpl-3.0 | 109,579 | [
"Gaussian",
"VisIt"
] | 376e24845be1c84f5ebaf6081e06d0244d7bd5277a1737c3ec1719c32c851f29 |
from ase.lattice.spacegroup import Spacegroup
sg = Spacegroup(225)
print('Space group:', sg.no, sg.symbol)
print('Primitive cell:\n', sg.scaled_primitive_cell)
print('Reciprocal cell:\n', sg.scaled_reciprocal_cell)
print('Lattice type:', sg.lattice)
print('Lattice sub-translations', sg.subtrans)
print('Centerosymmetr... | misdoro/python-ase | doc/tutorials/spacegroup/spacegroup-sg.py | Python | gpl-2.0 | 491 | [
"ASE"
] | c3cb500f4b811f2d14db2bc31fcf45ac7f02cd398809cb8d74d0be20b51c2e23 |
# proxy module
from __future__ import absolute_import
from mayavi.sources.vrml_importer import *
| enthought/etsproxy | enthought/mayavi/sources/vrml_importer.py | Python | bsd-3-clause | 97 | [
"Mayavi"
] | 24380959816b14de8d52be8e1273dff0ee4eef7c6576fff66552a981e3307cbb |
# 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/nao/test/test_0165_bse_h2b_spin1_uhf_rpa.py | Python | apache-2.0 | 2,104 | [
"PySCF"
] | 69fca1d20f85c7c699b7fde8b25f69c94e3e85d5a7056cf271dc57580f3d3ce3 |
# Copyright (C) 2000 Greg Landrum
#
# This 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 the Free Software Foundation; either
# version 2 of the License, or (at your option) any later version.
#
# This library is distribu... | greglandrum/rdkit | rdkit/sping/SVG/pidSVG.py | Python | bsd-3-clause | 23,751 | [
"RDKit"
] | bb3f74e6882b30cfbd3f074902c49b81c1eb5ec27988ee64348287172fb09a0b |
#anilkumarravuru
from splinter.browser import Browser
b=Browser()
database_url="http://gepir.gs1.org/v32/xx/gtin.aspx?Lang=en-US"
b.visit(database_url)
b.fill('TabContainerGTIN:TabPanelGTIN:txtRequestGTIN','k.ravuru')
b.find_by_type('submit').click()
f=open("barcode.txt","r+")
line=f.read()
while(not l==""):
b.fill('T... | muraliraghubabu1994/Bar-code-Scanner | barcode_program/search.py | Python | gpl-2.0 | 416 | [
"VisIt"
] | a8577bdd14f1feaebab529a1e70097737b6e43f47d8eebdf196bd62ef7422c56 |
# (C) 2013, James Cammarata <jcammarata@ansible.com>
# Copyright: (c) 2019, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import hashlib
import json
import os
import t... | 2ndQuadrant/ansible | lib/ansible/galaxy/api.py | Python | gpl-3.0 | 25,745 | [
"Galaxy"
] | 1d0355f75d853465de0c6997920f52928d02c1a7650a7480345db3db7d969363 |
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
import sys
import time
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Utilities.DIRACScript import DIRACScript as Script
from DIRAC.Core.DISET.MessageClient import MessageClient
Script.parseCommandLine()
def... | ic-hep/DIRAC | docs/source/DeveloperGuide/Systems/Framework/stableconns/client.py | Python | gpl-3.0 | 1,632 | [
"DIRAC"
] | 6cd935b836e658440c7c60edf201fc6783ea2e095f7f66fe9c2c0c56220df5a1 |
import sys, os
import re
import networkx as nx
import pyparsing
import cPickle as pickle
import matplotlib.pyplot as plt
nodes = []
relations = []
amr_nx_graph = None
def add_edge(node_A, node_B):
global relations
global amr_nx_graph
if amr_nx_graph.has_node(node_A) and amr_nx_graph.has_node(node_B) and relations... | raosudha89/vowpal_wabbit | demo/amrparsing/count_proj.py | Python | bsd-3-clause | 8,318 | [
"VisIt"
] | c908ed4c720a23b254f9300768d01cedd41ecf32a40c5b9944c021b6b6e93fce |
#!/usr/bin/env python
# Install.py tool to download, unpack, build, and link to the LATTE library
# used to automate the steps described in the README file in this dir
from __future__ import print_function
import sys,os,re,subprocess
# help message
help = """
Syntax from src dir: make lib-latte args="-b"
... | junghans/lammps | lib/latte/Install.py | Python | gpl-2.0 | 5,265 | [
"LAMMPS"
] | 730e3c471673cc8da38bba4c644e8e18537d49c0ef8acc20d8d955d91ca108a0 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, print_function, unicode_literals, absolute_import
"""
This module implements classes for processing Lammps output files:
1. log file: contains the thermodynamic data with ... | nisse3000/pymatgen | pymatgen/io/lammps/output.py | Python | mit | 22,027 | [
"LAMMPS",
"MDAnalysis",
"pymatgen"
] | eab53f8219b807651a0740682cf2524f315aeb01facce11a8bcd0a20f5cdc12a |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import random
import sys
import openpyxl
import base64
# Source: http://www.svb.nl/int/nl/kindernamen/
FIRSTNAMES = [
'Lars', 'Lotte', 'Lynn', 'Fenna', 'Sara', 'Saar', 'Fleur', 'Tim',
'Daan', 'Sophie', 'Anna', 'Tess', 'Max', 'Ruben', 'Noa', 'Levi', 'Mees',
'Sarah', ... | jonge-democraten/testdata | generate_testdata.py | Python | mit | 41,057 | [
"FLEUR"
] | 93285439c111e8576ccb154e1200fafda64b7eea85121c5f3db10697d7bf6503 |
# TODO: GI deprecation.
# # -*- coding: utf-8 -*-
# """This script is designed to create a gi list based on the refseq_rna database
# for each taxonomy id on the MCSR. It will also convert the gi list into a
# binary file which is more efficient to use with NCBI's Standalone Blast tools.
# """
# import os
# from datet... | datasnakes/Datasnakes-Scripts | examples/gi-list-multiprocessing/get_gi_lists.py | Python | mit | 2,805 | [
"BLAST"
] | f6db75dd9ae75547388390159d9aa57b31aec788daac4d2e7b421931916ed846 |
import threading
#Because eval(valenc) might require it
import datetime
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.Utilities import DEncode, List
from DIRAC.Core.Base.ExecutorModule import ExecutorModule
from DIRAC.WorkloadManagementSystem.Client.JobState.CachedJobState import CachedJobState
class Optimi... | calancha/DIRAC | WorkloadManagementSystem/Executor/Base/OptimizerExecutor.py | Python | gpl-3.0 | 6,366 | [
"DIRAC"
] | c4a65102296b88d36b7e48f30eb97267f0f12240a3d1659e084c4a4ee640df73 |
"""
Add Cell Connectivity To Points
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Example for :class:`PVGeo.filters.AddCellConnToPoints`
This filter will add **linear** cell connectivity between scattered points.
You have the option to add ``VTK_LINE`` or ``VTK_POLYLINE`` connectivity.
``VTK_LINE`` connectivity makes a straight li... | banesullivan/ParaViewGeophysics | examples/filters-general/add-cell-connectivity-to-points.py | Python | bsd-3-clause | 2,665 | [
"VTK"
] | b1716a873cf066659c9328fa69d6621618552dbcf20826a1b4156eacce07de06 |
import click
from parsec.cli import pass_context, json_loads
from parsec.decorators import custom_exception, json_output
@click.command('upload_from_galaxy_filesystem')
@click.argument("library_id", type=str)
@click.argument("filesystem_paths", type=str)
@click.option(
"--folder_id",
help="id of the folder wh... | galaxy-iuc/parsec | parsec/commands/libraries/upload_from_galaxy_filesystem.py | Python | apache-2.0 | 1,950 | [
"Galaxy"
] | be45fe6c94c07a01725971110aecf4aa59c25954de9e419734689a022d44b9be |
from OpenGL import GL
from cocos.director import director
from .node import GUINode
def _anchor_to_position_a(anchor, window_size, self_size):
abs_anchor = abs(anchor)
if isinstance(abs_anchor, int):
result = abs_anchor
elif isinstance(abs_anchor, float):
result = int(window_size * abs_anchor)
# TODO ... | Saluev/cocos2d-gui | cocosgui/windows.py | Python | mit | 3,030 | [
"VisIt"
] | d28d455419a603ddb16b1203fcccb0a5ccb0b7105b88e3933a1a213c72b7fc3c |
from __future__ import absolute_import
input_name = '../examples/linear_elasticity/its2D_2.py'
output_name = 'test_its2D_2.vtk'
from tests_basic import TestInput
class Test(TestInput):
pass
| vlukes/sfepy | tests/test_input_its2D_2.py | Python | bsd-3-clause | 195 | [
"VTK"
] | 1d3f6c8979e37e3249c7e582982804071a0b53a80cf1d2fb4a8c573667c9885a |
#!/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/General/Testing/Python/contoursToSurface.py | Python | gpl-3.0 | 4,169 | [
"VTK"
] | 0c63e80199df7ec5f33bd42609068d67d04ead88082782850c88e12bae132a99 |
#!/usr/bin/env python
"""
Easy Install
------------
A tool for doing automatic download/extract/build of distutils-based Python
packages. For detailed documentation, see the accompanying EasyInstall.txt
file, or visit the `EasyInstall home page`__.
__ https://pythonhosted.org/setuptools/easy_install.html
"""
from... | DanteOnline/free-art | venv/lib/python3.4/site-packages/setuptools/command/easy_install.py | Python | gpl-3.0 | 85,920 | [
"VisIt"
] | 63beea8195369ae321abebd29672a3875ddacf52803b561febc33fe988b17238 |
'''
The only working example in bowtie so far. ¯\(°_o)/¯
python 2.7
bowtie==0.3.2
'''
from bowtie.visual import Plotly
from bowtie.control import Nouislider
import numpy as np
import plotlywrapper as pw
sine_plot = Plotly()
freq_slider = Nouislider(caption='frequency', minimum=1, maximum=10, start=5)
def listener(fre... | karlafej/WebAppEx | bowtie/simple_sine.py | Python | mit | 705 | [
"Bowtie"
] | b04124a543c715dbb502df49289ba36e76279018ca954b3823bf4c85ea9e4ea0 |
"""
Course Outline page in Studio.
"""
import datetime
from bok_choy.page_object import PageObject
from bok_choy.promise import EmptyPromise
from selenium.webdriver.support.ui import Select
from selenium.webdriver.common.keys import Keys
from selenium.webdriver.common.action_chains import ActionChains
from .course_p... | epam-mooc/edx-platform | common/test/acceptance/pages/studio/overview.py | Python | agpl-3.0 | 23,006 | [
"VisIt"
] | 6c74e97f7d7e94b848b397a8834a9cd8dca535777adec3876d174dbb557ed805 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | tmerrick1/spack | var/spack/repos/builtin/packages/gromacs/package.py | Python | lgpl-2.1 | 4,113 | [
"Gromacs"
] | 403eca5baac881842fb18d9c3f44ec1e74c737e074eff1673f00ec29d1630ab3 |
# -*- coding: utf-8 -*-
"""Testing functions."""
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
#
# License: BSD-3-Clause
from contextlib import contextmanager
from distutils.version import LooseVersion
from functools import partial, wraps
import os
import inspect
from io import StringIO
from shutil impor... | pravsripad/mne-python | mne/utils/_testing.py | Python | bsd-3-clause | 17,568 | [
"Mayavi",
"VTK"
] | 0a662a1756889c6b162fd56d252dbf1111ebc771fed2c5a85c06dbef465b9af0 |
#!/usr/bin/env python
'''
setup board.h for chibios
'''
import argparse, sys, fnmatch, os, dma_resolver, shlex, pickle, re
import shutil
parser = argparse.ArgumentParser("chibios_pins.py")
parser.add_argument(
'-D', '--outdir', type=str, default=None, help='Output directory')
parser.add_argument(
'--bootloade... | bithollow/ardupilot | libraries/AP_HAL_ChibiOS/hwdef/scripts/chibios_hwdef.py | Python | gpl-3.0 | 44,184 | [
"CRYSTAL"
] | 332f659223db475c06624d7322ab8ebb1740d5592c155fac4dcb6b2d02204fb7 |
version = '0.1.0'
required_versions = {
'toil': '>=3.6.0',
'tsv': '>=1.1',
'biopython': '==1.68',
'pyvcf': '==0.6.8',
'pysam': '==0.10.0',
'intervaltree': '==2.1.0',
'toil-vg': '>=1.1.0a1',
'more_itertools': '==3.0.0'
}
dependency_links = []
| adamnovak/hgvm-builder | src/hgvmbuilder/version.py | Python | apache-2.0 | 276 | [
"Biopython",
"pysam"
] | 69e61a64563b2519c76f80cb5c46c4117a5542771ea2fa22966b3315d3566267 |
# -*- coding: utf-8 -*-
"""
CPP函数定义,用于生成函数.
"""
from cppvisitattr import CppVisit
class CppFun(object):
VISIT_NONE = 0
VISIT_PUBLIC = 1
VISIT_PROTECTED = 2
VISIT_PRIVATE = 3
def __init__(self, name, rtn='void', args=(), visit=CppVisit(CppVisit.NONE)):
self.__name = name
self.__r... | lailongwei/llbc | tools/building_script/cpputils/cppfun.py | Python | mit | 1,739 | [
"VisIt"
] | 4a9d6b2ec3a7d645811ed7379641255214f2070f8b3a782ec7fb0d6f01aaa4aa |
#
# Copyright (C) 2017-2019 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... | pkreissl/espresso | testsuite/python/accumulator_mean_variance.py | Python | gpl-3.0 | 2,619 | [
"ESPResSo"
] | 6a025e5e5dde00391fb2423c68ed48c89338735f4f0519c4d4712076d8392a5b |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2018 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
#... | amjames/psi4 | psi4/driver/qcdb/pdict.py | Python | lgpl-3.0 | 4,533 | [
"Psi4"
] | 9505ee0c257e78ab86a206219221c470c629909509aed6c86ad5308b2d7ca520 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
import subp... | harterj/moose | python/TestHarness/tests/test_UnknownPrereq.py | Python | lgpl-2.1 | 770 | [
"MOOSE"
] | 9ff96696429bcde6f00f4caf7891ea01b8a47c8665ec61b4fbd53642275af5d5 |
import ez_setup
import sys
ez_setup.use_setuptools()
from setuptools import setup
# from mpld3
def get_version(path):
"""Get the version info from the mpld3 package without importing it"""
import ast
with open(path) as init_file:
module = ast.parse(init_file.read())
version = (ast.literal_eva... | dariober/bwa-meth | setup.py | Python | mit | 1,250 | [
"BWA"
] | 835528b2f7b8f392168db6b5829cc08b9c48d055ff0b5ef3d52cbb63c4ac3270 |
#!/usr/bin/env python
#
# $File: trackRec.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can redistribute i... | BoPeng/simuPOP | docs/trackRec.py | Python | gpl-2.0 | 1,518 | [
"VisIt"
] | 7db162d849b6f9852b03e2c4a97ae80948d4f74744e73c1968326d55906ab3ff |
# Copyright 2008-2015 Nokia Networks
# Copyright 2016- Robot Framework Foundation
#
# 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
... | alexandrul-ci/robotframework | src/robot/reporting/resultwriter.py | Python | apache-2.0 | 5,968 | [
"VisIt"
] | de2b43d66dd32bfc7bb8c620a9253d71d0ecbe8cb249be61551c978688e00d75 |
"""
The Job Agent class instantiates a CE that acts as a client to a
compute resource and also to the WMS.
The Job Agent constructs a classAd based on the local resource description in the CS
and the current resource status that is used for matching.
"""
# ## This agent might potentially still need to be run i... | DIRACGrid/DIRAC | src/DIRAC/WorkloadManagementSystem/Agent/JobAgent.py | Python | gpl-3.0 | 37,346 | [
"DIRAC"
] | a02714da7209d52d0728a2786ad263856515cae541106ef5dd56d0ead6588c18 |
"""
LMS Course Home page object
"""
from collections import OrderedDict
from bok_choy.page_object import PageObject
from .bookmarks import BookmarksPage
from .course_page import CoursePage
from .courseware import CoursewarePage
from .staff_view import StaffPreviewPage
class CourseHomePage(CoursePage):
"""
... | angelapper/edx-platform | common/test/acceptance/pages/lms/course_home.py | Python | agpl-3.0 | 9,167 | [
"VisIt"
] | 57904768b59724d27becfddba209f7a353034f04af6787d5164ffd95d0723ccb |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.