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#!/usr/bin/env python
# Copyright 2014-2021 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/pbc/gw/kugw_ac.py | Python | apache-2.0 | 31,525 | [
"Gaussian",
"PySCF"
] | b0ce7ca8f0a4b88c78c3153895a833966a98b21170fe9fb004b9176f4019e420 |
import pytest
from ..cube import SyntheticCube
from hyperion.model.image import Image
from hyperion.util.constants import c, pc, au
import numpy as np
import os
class TestSyntheticCube(object):
def setup_method(self, method):
np.random.seed(3)
nu = c / (np.logspace(-1,3,30) * 1e-4)
... | koepferl/FluxCompensator | fluxcompensator/tests/test_cube.py | Python | bsd-2-clause | 8,838 | [
"Gaussian"
] | cc3b6e3fc57e0f8aaeaf36aee6d3bfe3fc0a86ba159772d74dfd5610157ad982 |
########################################################################
# File : Watchdog.py
# Author: Stuart Paterson
########################################################################
""" The Watchdog class is used by the Job Wrapper to resolve and monitor
the system resource consumption. The Watchdog... | arrabito/DIRAC | WorkloadManagementSystem/JobWrapper/Watchdog.py | Python | gpl-3.0 | 38,280 | [
"DIRAC"
] | 86125802f16c23953435e3e592fe07ff2caafb7ac3671ecf93f3575811f0a5ca |
"""
seqdb contains a set of classes for interacting with sequence databases.
Primary sequence database classes:
- SequenceDB - base class for sequence databases
- SequenceFileDB - file-based sequence database
- PrefixUnionDict - container to combine multiple sequence databases
- XMLRPCSequenceD... | cjlee112/pygr | pygr/seqdb.py | Python | bsd-3-clause | 42,330 | [
"BLAST"
] | a344c61d81aee538ac3ddd2fd00beb99cf621d2a6c01aea01f292385ffb85f89 |
#!/usr/bin/env python
"""
Start DIRAC component using runsvctrl utility
"""
from __future__ import print_function
__RCSID__ = "$Id$"
from DIRAC.Core.Base import Script
Script.disableCS()
Script.setUsageMessage('\n'.join([__doc__.split('\n')[1],
'Usage:',
... | fstagni/DIRAC | FrameworkSystem/scripts/dirac-start-component.py | Python | gpl-3.0 | 1,222 | [
"DIRAC"
] | 140b3fe12f7cc6b08f74dfed51977cccecd5ebaed38b1e77e216c858bcbbf9e8 |
import sys
import io
from itertools import islice
import codecs
"""
@var file_path: path to input csv file (UTF-8 encoded). Given file would be used for training.
Input file should be `#` separated and should have following columns in order
=> domainID # review # terms from # terms to # polarity # terms
@return: aspe... | pnisarg/ABSA | src/ate_crf_learn.py | Python | mit | 2,651 | [
"ADF"
] | aebafd4edd0e84f0f8bff734bee7dc346ddf0324bb6f112869a2b1936f42d804 |
#
# This source file is part of appleseed.
# Visit http://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2017 Petra Gospodnetic, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaining a co... | Aakash1312/appleseed | sandbox/tests/test scenes/many light sampling/generators/grid_emt.py | Python | mit | 10,724 | [
"VisIt"
] | a1643c653b0213d4dd166f3798c3326b1e2c0480f68d716f708e5a5380b6246a |
r"""Extended Topochemical Atom(ETA) descriptor.
References
* :doi:`10.1021/ci0342066`
* :doi:`10.1016/j.jhazmat.2013.03.023`
"""
from __future__ import division
import numpy as np
from rdkit import Chem
from . import _atomic_property as ap
from ._base import Descriptor
from ._util import atoms_to_numpy
from... | mordred-descriptor/mordred | mordred/ExtendedTopochemicalAtom.py | Python | bsd-3-clause | 20,747 | [
"RDKit"
] | cdcce5361d3d8369b88b1184b9d6d37e130cde2822a1a9fceae9aaaa1fff7178 |
from paraview.simple import *
import glob
import re
#liste = glob.glob('/home/bruno/CFDEM/bruno-PUBLIC-2.2.1/runv2-6/particle_only/loadingSquare/post/cylinder*.vtk')
liste = glob.glob('./post/VTK/mixer_*.vtk')
listeImpl = glob.glob('./post/VTK/impeller_*.stl')
listeTank=glob.glob('/home/bruno/doctorat/mesh/PBT_Manon/t... | blaisb/cfdemUtilities | paraview/mixerParticles.py | Python | lgpl-3.0 | 5,155 | [
"ParaView",
"VTK"
] | 2542f464ba13613b910fd3b50be6d696334730c63496175d799832060464df9e |
#!/usr/bin/python
# Author: Sari Sabban
# Email: sari.sabban@gmail.com
# URL: https://github.com/sarisabban
#
# Created By: Sari Sabban
# Created Date: 13 January 2017
#
# Modified By: Sari Sabban
# Modified Date: 3 February 2017
import re
import itertools
import sys
from Bio.PDB import *
print 'File mus... | sarisabban/RefineAssist | RefineAssist.py | Python | mit | 7,270 | [
"Biopython",
"PyMOL"
] | 8d29178fbc08c45494e838c050a9d4388fefa6b53f48dc7e8958d4cdcf5ab38e |
"""This module defines the Atom object."""
import numpy as np
from ase.data import atomic_numbers, chemical_symbols, atomic_masses
# Singular, plural, default value:
names = {'position': ('positions', np.zeros(3)),
'number': ('numbers', 0),
'tag': ('tags', 0),
'momentum': ('momenta', np.z... | askhl/ase | ase/atom.py | Python | gpl-2.0 | 5,702 | [
"ASE"
] | d96124750a85ccc01b5dfcae8327619dbb52061bef7853190990ecfebac8c95d |
#!/usr/bin/python2
# ----------------------------------------------------------------------
# Copyright (2010) Aram Davtyan and Garegin Papoian
# Papoian's Group, University of Maryland at Collage Park
# http://papoian.chem.umd.edu/
# Last Update: 03/04/2011
# -----------------------------------------------... | luwei0917/awsemmd_script | archive/casp_create_project_helper.py | Python | mit | 9,761 | [
"LAMMPS"
] | 2cf1364d7e69b6833b4aeafe961c6fbe1b009f2d33d6e3bcc3c46922ef0d9d9a |
"""Prevent unwanted files from being added to the source tree."""
from __future__ import annotations
import os
import sys
def main():
"""Main entry point."""
paths = sys.argv[1:] or sys.stdin.read().splitlines()
allowed_extensions = (
'.cs',
'.ps1',
'.psm1',
'.py',
)
... | mattclay/ansible | test/sanity/code-smell/no-unwanted-files.py | Python | gpl-3.0 | 1,157 | [
"Galaxy"
] | a777b73317a7e93a1fbb8654c2fa61f27599af0080ce7345722ece3ff1a1bd29 |
from setuptools import setup
setup(name="pyurdme",
version="1.1.1",
packages=['pyurdme'],
#include_package_data = True,
package_data={'pyurdme':['data/*.c','data/three.js_templates/js/*','data/three.js_templates/*.html','urdme/AUTHORS','urdme/LICENCE','urdme/bin/*','urdme/build/*','urdme... | pyurdme/pyurdme | setup.py | Python | gpl-3.0 | 850 | [
"Brian"
] | dc85751e793df926fd27ababcb0ed04309bf35ac8265d133a1251e5ff847eaca |
# -*- coding: utf-8 -*-
"""
jinja2.visitor
~~~~~~~~~~~~~~
This module implements a visitor for the nodes.
:copyright: Copyright 2008 by Armin Ronacher.
:license: BSD.
"""
from jinja2.nodes import Node
class NodeVisitor(object):
"""Walks the abstract syntax tree and call visitor functions for... | scyclops/Readable-Feeds | jinja2/visitor.py | Python | gpl-3.0 | 3,322 | [
"VisIt"
] | c5b15bc6c70f87cd25cb8025cda1c55b4a0348f732ad4681f15d6c5385cd985d |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# LAMMPS documentation build configuration file, created by
# sphinx-quickstart on Sat Sep 6 14:20:08 2014.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# aut... | PabloPiaggi/lammps | doc/utils/sphinx-config/conf.py | Python | gpl-2.0 | 10,214 | [
"LAMMPS"
] | 2c2535cdcbf3d5184f9adc708d61782c4e6a169da4b706a2047064fa46ec3da0 |
import unittest
import pysal.lib
import numpy as np
from pysal.model.spreg import error_sp_hom_regimes as SP
from pysal.model.spreg.error_sp_hom import GM_Error_Hom, GM_Endog_Error_Hom, GM_Combo_Hom
from pysal.lib.common import RTOL
class TestGM_Error_Hom_Regimes(unittest.TestCase):
def setUp(self):
db=pys... | lixun910/pysal | pysal/model/spreg/tests/test_error_sp_hom_regimes.py | Python | bsd-3-clause | 14,732 | [
"COLUMBUS"
] | 4c1d311182c9b1126096ebc6e7668bcf13561ab9aba2a133e34994d6d161b0f9 |
__author__ = 'robert'
from pypet import Environment, Trajectory,progressbar, Parameter
from pypet.brian import BrianParameter
from pypet.tests.testutils.ioutils import make_temp_dir, get_log_config
import os
from brian import ms
import time
import matplotlib.pyplot as plt
import cProfile as profile
def job(traj):
... | nigroup/pypet | pypet/tests/profiling/speed_analysis/many_runs_profiling.py | Python | bsd-3-clause | 1,247 | [
"Brian"
] | cc1d2660638b68205d2b87a70447899b238d867b0c6e215c4783eaba8f6ce176 |
#DOI: 10.5281/zenodo.58767
from __future__ import print_function
__author__='Yuqian Liu yl1260@nyu.edu '
# -*- coding: utf-8 -*-
##############################################################################
'''
Fits a template SN spectrum to an observed SN spectrum.
Measures broadening and blue-shift of the SN featur... | nyusngroup/SESNspectraLib | Ic_conv_Icbl_MCMC.py | Python | mit | 21,815 | [
"Gaussian"
] | e840f8b5ee7636cbffa96cb49ab817b408d6c07ee7b7d39b2625861b9fa8fc88 |
# Zulip Settings intended to be set by a system administrator.
#
# See http://zulip.readthedocs.io/en/latest/settings.html for
# detailed technical documentation on the Zulip settings system.
#
### MANDATORY SETTINGS
#
# These settings MUST be set in production. In a development environment,
# sensible default values w... | dawran6/zulip | zproject/prod_settings_template.py | Python | apache-2.0 | 17,533 | [
"VisIt"
] | 5f06aed5d9cd34f844f47cf0d3d1be82d06af63cb993b5c11310b610b58b9403 |
from __future__ import with_statement
__license__ = 'GPL v3'
__copyright__ = '2008, Kovid Goyal <kovid at kovidgoyal.net>'
'''
Defines various abstract base classes that can be subclassed to create powerful news fetching recipes.
'''
__docformat__ = "restructuredtext en"
import os, time, traceback, re, urlparse, sy... | pra85/calibre | src/calibre/web/feeds/news.py | Python | gpl-3.0 | 73,308 | [
"VisIt"
] | 07efcfa19f10f07637dcb3b1052d0418ee480bf87c283fd7d64d7bfe5ab807de |
def regionalize(infile, basedir, variable, aggregate, scenario ):
"""generates a file structure for polygons and fieldmeans
:param infile: netCDF infile with DRS name convention
:param basedir: path to base directory
:param variable: variable name
:param aggregate: time aggregation
:param scenario: scenario na... | KatiRG/flyingpigeon | flyingpigeon/shapefiles/extremoscope.py | Python | apache-2.0 | 725 | [
"NetCDF"
] | c1536c03df8e873b5a3315b7ca6afd6cd330d80c25064c60e080f06d13eeb178 |
import numpy as np
from scipy import special, integrate, stats
from ._utils import move_axis_to_end, argsort_indices, suppress_warnings
# The normalization constant for the univariate standard Gaussian pdf
_normconst = 1.0 / np.sqrt(2.0 * np.pi)
def _normpdf(x):
"""Probability density function of a univariate... | TheClimateCorporation/properscoring | properscoring/_crps.py | Python | apache-2.0 | 13,369 | [
"Gaussian"
] | a04ee1ead857a0e8af4f0fe3a675b13a1d7872fdce00c5f7e42370221ca529a8 |
import threading
import oauth2 as oauth
import urlparse
import urllib2
import json
import BaseHTTPServer
API_SECRET_FILE='.flickr.api-key.json'
ACCESS_TOKEN_SECRET_FILE='.flickr.access-token.json'
class ValidationHTTPRequestHandler(BaseHTTPServer.BaseHTTPRequestHandler):
def do_HEAD(self):
self.send_resp... | e-tothe-ipi/flickr-download-originals | authorize_flickr.py | Python | bsd-2-clause | 2,796 | [
"VisIt"
] | 25db36ea82101b89681c1ddab65fa01ae8d2b752cde590d3e0bfa3886942a705 |
#
#
# A file which opens a neuroConstruct project and generates it, then generates a series
# of slightly different NEURON simulations, using the same network, but different stimulations.
# An input current vs firing frequency plot is generated afterwards.
# The simulations can also be viewed and analysed ... | rgerkin/neuroConstruct | pythonnC/Ex5_MultiSimGenerate.py | Python | gpl-2.0 | 7,929 | [
"NEURON"
] | 05b4241074122601da44cdff229ad4ada9d22b0f232bcafcf4fc9a8ecaa5438b |
#!/usr/bin/python
##################################################################
#
# Title: Poltype
# Description: Atomic typer for the polarizable AMOEBA force field
#
# Copyright: Copyright (c) Johnny C. Wu,
# Gaurav Chattree, & Pengyu Ren 2010-2011
#
# Poltype is free software; you ... | pren/poltype | poltype.py | Python | gpl-2.0 | 143,482 | [
"Gaussian",
"TINKER"
] | aca7b27b90ba0b5a9d92539a78f8f8cea212c6b12ceb8edef9dc3833e63bd692 |
# -*- coding: utf-8 -*-
# Author: Vincent Dubourg <vincent.dubourg@gmail.com>
# (mostly translation, see implementation details)
# License: BSD 3 clause
from __future__ import print_function
import numpy as np
from scipy import linalg, optimize
from ..base import BaseEstimator, RegressorMixin
from ..metrics... | potash/scikit-learn | sklearn/gaussian_process/gaussian_process.py | Python | bsd-3-clause | 35,041 | [
"Gaussian"
] | 61a0e852f6ef583fc376a5abbd08b6f371709d76f9ceae0fd7c29200e75a422b |
# encoding: utf-8
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Deleting field 'Author.intials'
db.delete_column('neuroelectro_author', 'intials')
... | lessc0de/neuroelectro_org | neuroelectro/south_migrations/0028_auto__del_field_author_intials__add_field_author_initials.py | Python | gpl-2.0 | 17,206 | [
"NEURON"
] | 37d2ec8fd9fea7cb923c2c2fb161860472e113430f4260abb31c1bfeb237758a |
# -*- coding: utf-8 -*-
#
# test_connect_helpers.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the Li... | mschmidt87/nest-simulator | pynest/nest/tests/test_connect_helpers.py | Python | gpl-2.0 | 17,143 | [
"NEURON"
] | 1d73df2fcf89d2412094011a7579ded0c47aeb6d17a957f84fd36073f4350b91 |
# coding=utf-8
#
# ROSREPO
# Manage ROS workspaces with multiple Gitlab repositories
#
# Author: Timo Röhling
#
# Copyright 2016 Fraunhofer FKIE
#
# 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 a... | fkie/rosrepo | src/rosrepo/gitlab.py | Python | apache-2.0 | 14,005 | [
"VisIt"
] | eea458260de35c3182414bd407b7caf343e2f06536627064aa761603abe40dd5 |
#!/usr/bin/env python
#
# Electrum - Lightweight Bitcoin Client
# Copyright (C) 2015 Thomas Voegtlin
#
# 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... | dashpay/electrum-dash | plugins/trustedcoin/qt.py | Python | mit | 10,153 | [
"VisIt"
] | c11b89a22dcf7e1e9ce9868cee811565b341dd088bafdc46b8e6a7cfaa030b00 |
"""
============================================
K-fold cross-validation for model comparison
============================================
Different models of diffusion MRI can be compared based on their accuracy in
fitting the diffusion signal. Here, we demonstrate this by comparing two
models: the diffusion tensor ... | FrancoisRheaultUS/dipy | doc/examples/kfold_xval.py | Python | bsd-3-clause | 6,195 | [
"Gaussian"
] | 06e5b078cd52e8639c5403c0488de8ee3c611327e466ca1c26d5289e7016f67c |
from __future__ import unicode_literals
import base64
import datetime
import hashlib
import json
import netrc
import os
import re
import socket
import sys
import time
import xml.etree.ElementTree
from ..compat import (
compat_cookiejar,
compat_cookies,
compat_getpass,
compat_HTTPError,
compat_http... | ZacariasBendeck/youtube-dl | youtube_dl/extractor/common.py | Python | unlicense | 57,374 | [
"VisIt"
] | 0d4415a7506278433ef63dd102235603af453e2fc9ee7fc039fcc0d9c268a8a1 |
# -*- coding: utf-8 -*-
"""
Models used to implement SAML SSO support in third_party_auth
(inlcuding Shibboleth support)
"""
from __future__ import absolute_import
import json
import logging
import re
from config_models.models import ConfigurationModel, cache
from django.conf import settings
from django.contrib.sites... | hastexo/edx-platform | common/djangoapps/third_party_auth/models.py | Python | agpl-3.0 | 32,720 | [
"VisIt"
] | 3e00bc909900b22dde219d1e76c84cbf373e36effac688596115555776e7523f |
# Script control setup area
# script info
__script__.title = 'KKB Plot and Reduction 25.1.2016'
__script__.version = '2.0'
# 15.6.2017 Allow to reduce the detector range
# 15.6. Throw out points below resolution
# 16.6. Tidy up run time to display in the reduction; tidy up display properties
# 11.7.2018 S... | Gumtree/Kookaburra_scripts | Internal/KKB-Plot and Reduction_Tube11_insteadof_9_back_to_11.py | Python | epl-1.0 | 59,190 | [
"CRYSTAL"
] | fd30de4a56c269824c403ecad75ddb7b91388574f7540ef305e97597c041b8c3 |
##
# Copyright 2015-2017 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... | ULHPC/easybuild-easyblocks | easybuild/easyblocks/n/nemo.py | Python | gpl-2.0 | 4,557 | [
"NetCDF"
] | 5e46d1ec352d49ef937980b6d999e3c1f77e837eb85683b0a762f7b4bfcef38c |
# ######################################################################
# Copyright (c) 2014, Brookhaven Science Associates, Brookhaven #
# National Laboratory. All rights reserved. #
# #
# @author: Li Li (lili@bnl.g... | scikit-xray/scikit-xray | skbeam/core/fitting/xrf_model.py | Python | bsd-3-clause | 61,286 | [
"Gaussian"
] | 10a7646288c264d4121d213dc3dafd3712e716ed26e284da78ae4eb8d7087395 |
import math
import random
from typing import Optional
import scipy.stats
import elo
def sign(x: float) -> float:
"""Returns +1.0 for positive `x` and -1.0 for negative `x`"""
return math.copysign(1., x)
def inv_erf(x: float) -> float:
"""Function implementing the inverse error function via approximati... | lbianch/nfl_elo | inv_erf.py | Python | mit | 3,998 | [
"Gaussian"
] | 8ea6d7bf09621dfcde95d3098af9c5000af60781e6ff2227f5f1da7a3dc9875f |
#!/usr/bin/env python
# Copyright 2014-2021 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/pbc/tdscf/krhf.py | Python | apache-2.0 | 12,504 | [
"PySCF"
] | 49e26ad3c4609f5d9e05002e36ae85ab3d98449f4b31e905d60acbe5a4a5429b |
"""
===================
Canny edge detector
===================
The Canny filter is a multi-stage edge detector. It uses a filter based on the
derivative of a Gaussian in order to compute the intensity of the gradients.The
Gaussian reduces the effect of noise present in the image. Then, potential
edges are thinned dow... | SamHames/scikit-image | doc/examples/plot_canny.py | Python | bsd-3-clause | 1,631 | [
"Gaussian"
] | 0a54f70b8876648b88273d667ac73df6a7e918c45e9a7353f634261d6ad224f4 |
"""Sphinx extension that embeds Disqus comments in documents.
https://sphinx-disqus.readthedocs.io
https://github.com/Robpol86/sphinx-disqus
https://pypi.org/project/sphinx-disqus
"""
import os
import re
from typing import Dict, List
from docutils import nodes
from docutils.nodes import document
from docutils.parsers... | Robpol86/sphinxcontrib-disqus | sphinx_disqus/disqus.py | Python | mit | 4,830 | [
"VisIt"
] | b52a5b8d741ca133eeee8493d3beb48e9d22ba20121035a4953da068744de60a |
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Mathieu Blondel <mathieu@mblondel.org>
# Olivier Grisel <olivier.grisel@ensta.org>
# Andreas Mueller <amueller@ais.uni-bonn.de>
# License: BSD 3 clause
from itertools import chain, combinations
import numbers
import numpy as np
f... | soulmachine/scikit-learn | sklearn/preprocessing/data.py | Python | bsd-3-clause | 38,539 | [
"Gaussian"
] | 7203bfc98dc45d906c3a04b22243929c33b0e38ed6d943e4502a99a6037ef8bb |
from galaxy_analysis.plot.plot_styles import *
import yt
from galaxy_analysis.analysis import Galaxy
import numpy as np
import matplotlib.pyplot as plt
from collections import OrderedDict
from yt.visualization.base_plot_types import get_multi_plot
import matplotlib.colorbar as cb
from matplotlib.colors import LogNorm
i... | aemerick/galaxy_analysis | plot/plot_radiation_comparison.py | Python | mit | 4,557 | [
"Galaxy"
] | ffbb71557dc7df61f60a04eada01cb663de33625015adec2394bf70749d210bc |
#!/usr/bin/env python
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "Li... | TiVo/kafka | release.py | Python | apache-2.0 | 35,383 | [
"VisIt"
] | 01aaf554d05a0c1e5992893c1221a22d1ffcf96608be8a2e9233a70436fd3993 |
# Copyright 2019 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | google-research/computation-thru-dynamics | lfads_tutorial/distributions.py | Python | apache-2.0 | 7,030 | [
"Gaussian"
] | 0c617783d016cd5bdac076a949b30f95ab8607e2d1bf9469ac6e577fb7005f32 |
from __future__ import print_function, division
import json
from glob import glob
import fitsio
import numpy as np
import matplotlib as mpl
mpl.use('Agg')
from matplotlib import pyplot as plt
from matplotlib import gridspec
from matplotlib.ticker import NullLocator
from .extern import ADR, Hyper_PSF3D_PL
from .main ... | snfactory/cubefit | cubefit/plotting.py | Python | mit | 16,621 | [
"Galaxy"
] | b61cf3d766f2dfdee171bdc142cdd13c58c52830c6e5ccf1aa8606145f1d6a68 |
# -*- coding: utf-8 -*-
"""
Pytest plugin entry point
"""
import logging
import logging.config
import os
import re
import testinfra
import pytest
# Use testinfra to get a handy function to run commands locally
local_command = testinfra.get_backend('local://').get_module('Command')
def pytest_addoption(parser):
... | infOpen/pytest-ansible-docker | pytest_ansible_docker.py | Python | mit | 10,220 | [
"Galaxy"
] | 75b20ab56507524330454df4e22e0f7898fe5510d74a9760f16c7ac48bf3bf84 |
# $HeadURL$
__RCSID__ = "$Id$"
import os
import DIRAC
from DIRAC import gConfig
g_SecurityConfPath = "/DIRAC/Security"
def getProxyLocation():
""" Get the path of the currently active grid proxy file
"""
for envVar in [ 'GRID_PROXY_FILE', 'X509_USER_PROXY' ]:
if os.environ.has_key( envVar ):
proxyPat... | Sbalbp/DIRAC | Core/Security/Locations.py | Python | gpl-3.0 | 4,275 | [
"DIRAC"
] | cdf5365727794766824dfc694eabe912a62d2105bd976ed84cea41935d9b4aa0 |
#
# Copyright (C) 2013 Uninett AS
#
# This file is part of Network Administration Visualized (NAV).
#
# NAV is free software: you can redistribute it and/or modify it under
# the terms of the GNU General Public License version 3 as published by
# the Free Software Foundation.
#
# This program is distributed in the hope... | hmpf/nav | tests/unittests/netmap/metadata_json_test.py | Python | gpl-3.0 | 9,186 | [
"Galaxy"
] | 15c1d148ad99af98e1a580d217f4721feff325319d791c67c058d3b7ee609b9f |
# This file is part of Radler.
#
# Radler 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.
#
# Radler is distributed in the hope that it... | SRI-CSL/radler | radler/radlr/rast.py | Python | gpl-3.0 | 7,144 | [
"VisIt"
] | 0e61d9fc517d1abacc870edd92f0e1a165263897751d51d8fbe19c255762ef51 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
import os
import re
from HTMLParser import HTMLParseError
from time import time
from urlparse import urlparse
import requests
from bs4 import BeautifulSoup
from bs4 import UnicodeDammit
from lxml import etree
from app import logger
from http_cache import http_get
from http_c... | Impactstory/sherlockoa | webpage.py | Python | mit | 62,074 | [
"ORCA"
] | ef4579b6ae83de77df4dd6cf8f516a4cda0720f1cd2cb1db34929c9f69a82959 |
#!/usr/bin/env python
# encoding: utf-8
# Thomas Nagy, 2005-2018 (ita)
"""
Runner.py: Task scheduling and execution
"""
import heapq, traceback
try:
from queue import Queue, PriorityQueue
except ImportError:
from Queue import Queue
try:
from Queue import PriorityQueue
except ImportError:
class PriorityQueue(Q... | drobilla/pugl | waflib/Runner.py | Python | isc | 16,330 | [
"VisIt"
] | 72b3dfee011336d068df8dce53ba553c5be9f381fa2184e3b06b4b8bb05f1fff |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS Instructor Dashboard.
"""
from nose.plugins.attrib import attr
from ..helpers import UniqueCourseTest, get_modal_alert
from ...pages.common.logout import LogoutPage
from ...pages.lms.auto_auth import AutoAuthPage
from ...pages.lms.instructor_dashboard import In... | dkarakats/edx-platform | common/test/acceptance/tests/lms/test_lms_instructor_dashboard.py | Python | agpl-3.0 | 16,349 | [
"VisIt"
] | 2dd459598bdcf0e0d86ee16959ed3c2f2afca3c8fc4972d525d7d92e1265f272 |
#!/usr/bin/env python
# for tgi cluster:
#/gapp/x64linux/opt/pythonbrew/venvs/Python-2.7.6/gemini/bin/python
# for uva cluster:
import pysam
import json
import sys
import argparse
from argparse import RawTextHelpFormatter
import string
from string import *
__author__ = "Colby Chiang (colbychiang@wustl.edu)"
__versio... | cc2qe/bamkit | bamfixflags.py | Python | mit | 9,297 | [
"pysam"
] | b14fc4272c2b7ef5540d79da04f69e1266832748295440cf99da8b10b81053ed |
# -*- coding: utf-8 -*-
from south.utils import datetime_utils as datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding field 'Visit.wrhi_orig_date'
db.add_column(u'core_visit', 'wrhi_... | praekelt/txtalert | txtalert/core/migrations/0022_auto__add_field_visit_wrhi_orig_date__add_field_historicalvisit_wrhi_o.py | Python | gpl-3.0 | 17,124 | [
"VisIt"
] | 026af8641137b90bed6672a873745951bd8fda334ed8642f7090151a90cfa8ec |
# Copyright 2005 by Frank Kauff & 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 have been included
# as part of this package.
#
# Nodes.py
#
# Provides functionality of a linked list.
# Each node has one (or n... | NarlikarLab/DIVERSITY | weblogoMod/corebio/seq_io/_nexus/Nodes.py | Python | gpl-3.0 | 5,743 | [
"Biopython"
] | 7264c7da97251687f46aaf07ad8b7430d4b0df2d10397f6a7be4c5fd98206cea |
# -*- coding: utf-8 -*-
#!/usr/bin/env python
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2002 Gary Shao
# Copyright (C) 2007 Brian G. Matherly
# Copyright (C) 2009 Benny Malengier
# Copyright (C) 2009 Gary Burton
#
# This pr... | arunkgupta/gramps | gramps/gen/plug/docgen/graphdoc.py | Python | gpl-2.0 | 39,112 | [
"Brian"
] | 78fe1c8a5d744239cc11002395dad87eff7b89409222ef97510d398733acb211 |
# 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... | seanli9jan/tensorflow | tensorflow/python/autograph/core/converter.py | Python | apache-2.0 | 16,329 | [
"VisIt"
] | 534cb50230c7abf2dbb146dc325c92edd280c3876b9aa1ae52ba533f4cadf6bb |
# Copyright 2009 Brian Quinlan. All Rights Reserved.
# Licensed to PSF under a Contributor Agreement.
"""Implements ProcessPoolExecutor.
The follow diagram and text describe the data-flow through the system:
|======================= In-process =====================|== Out-of-process ==|
+----------+ +----------... | maxrothman/aws-alfred-workflow | venv/lib/python2.7/site-packages/concurrent/futures/process.py | Python | mit | 14,894 | [
"Brian"
] | 3940e89853e8fc99d3ea1d4a7e22068f808dd99f4a834c052d34278a86b87f2d |
# -*- coding: cp949 -*-
# Author: Ivan Cao-Berg, Baek Cho and Jennifer Bakal
# Created: December, 2011
#
# Copyright (C) 2011-2018 Murphy Lab
# Lane Center for Computational Biology
# School of Computer Science
# Carnegie Mellon University
#
# This program is free software; you can redistribute it and/or modify
# it u... | icaoberg/ricerca | ricerca/content.py | Python | gpl-3.0 | 13,964 | [
"VisIt"
] | 202be326fd4684b743401665f4e91e6d345acf6a4ba3a7cc39db76eb3d622abf |
from openzwave.network import ZWaveNode
from openzwave.value import ZWaveValue
from Firefly import logging
from Firefly.components.zwave.device_types.switch import ZwaveSwitch
from Firefly.const import ACTION_OFF, ACTION_ON, SWITCH, LEVEL
TITLE = 'Leviton DZMX1 Dimmer'
BATTERY = 'battery'
ALARM = 'alarm'
COMMANDS =... | Firefly-Automation/Firefly | Firefly/components/zwave/leviton/dzmx1.py | Python | apache-2.0 | 1,662 | [
"Firefly"
] | cdfdcf4083fc522a11ffe5501556477c01338709cf06a785a380429835dbdbc0 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# gpload - load file(s) into Greenplum Database
# Copyright Greenplum 2008
'''gpload [options] -f configuration file
Options:
-h hostname: host to connect to
-p port: port to connect to
-U username: user to connect as
-d database: database to connect to
... | lintzc/gpdb | gpMgmt/bin/gpload.py | Python | apache-2.0 | 99,744 | [
"ADF"
] | f3ca1876a54ef4fe41fea453b185508e25d2a0779d181cfd2c1fc6f7e248caef |
# coding: utf-8
from __future__ import unicode_literals
from pymatgen.util.testing import PymatgenTest
from pymatgen.core.operations import SymmOp
import numpy as np
class SymmOpTestCase(PymatgenTest):
def setUp(self):
self.op = SymmOp.from_axis_angle_and_translation([0, 0, 1], 30, False,
... | rousseab/pymatgen | pymatgen/core/tests/test_operations.py | Python | mit | 4,573 | [
"pymatgen"
] | 1e27fd5962100975b793d9b9beb423a801019d5e505d954a17e7a6fa13c58f87 |
# Copyright 2017 Google Inc. 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 applicable law or a... | tombstone/models | research/lfads/run_lfads.py | Python | apache-2.0 | 34,738 | [
"Gaussian"
] | 8b2bc1cdb9ec489fe9f0e18f33e871ded980da98f7a592deac9c255940977c59 |
# Copyright (C) 2011-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | KaiSzuttor/espresso | testsuite/python/ek_eof_one_species_z.py | Python | gpl-3.0 | 1,384 | [
"ESPResSo"
] | c2e7b9225d04bea1c50629fc67fee67c7a7df5622b00a4366e164a0c801598a9 |
from setuptools import setup, find_packages
setup(
name='debacl',
version='1.1',
description='DEnsity-BAsed CLustering',
url='https://github.com/CoAxLab/DeBaCl',
author='Brian Kent',
author_email='bpkent@gmail.com',
license='BSD',
classifiers=[
'License :: OSI Approved :: BSD Li... | CoAxLab/DeBaCl | setup.py | Python | bsd-3-clause | 731 | [
"Brian"
] | 0027133f5b70f9ce1cda813ff2d7736f73ad43770b6ff4cc86a813c4c3c7a006 |
"""RabbitMQAdmin module serves for the management of the internal RabbitMQ
users database. It uses rabbitmqctl command. Only the user with the right
permissions can execute those commands.
"""
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
import re
fr... | yujikato/DIRAC | src/DIRAC/Core/Utilities/RabbitMQAdmin.py | Python | gpl-3.0 | 4,681 | [
"DIRAC"
] | 63bf1302fbefd025474602b921476347627d8ea37ae362e7a731073922d64218 |
import re
import glob
import os
import time
from datetime import datetime
import utm
import scipy.io
import numpy as num
from kite import util
__all__ = ['Gamma', 'Matlab', 'ISCE', 'GMTSAR', 'ROI_PAC', 'SARscape', 'SNAP_Gamma']
try:
from osgeo import gdal
__all__.append('LiCSAR')
__all__.append('ARIA')
... | pyrocko/kite | src/scene_io.py | Python | gpl-3.0 | 45,708 | [
"NetCDF"
] | 91718624b15751d7c1f1accb7f4222a6d638731e767f75ffd951f89c860101d4 |
#! /usr/bin/env python3
# -*- 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 requi... | googleapis/python-security-private-ca | scripts/fixup_privateca_v1_keywords.py | Python | apache-2.0 | 8,262 | [
"VisIt"
] | 75771356f23da40b719e2ccc3d3664c54cceae1204a23ee92208ab71e3945d41 |
# Copyright (c) 2017 MetPy Developers.
# Distributed under the terms of the BSD 3-Clause License.
# SPDX-License-Identifier: BSD-3-Clause
"""
Four Panel Map
===============
By reading model output data from a netCDF file, we can create a four panel plot showing:
* 300 hPa heights and winds
* 500 hPa heights and absol... | metpy/MetPy | v0.7/_downloads/Four_Panel_Map.py | Python | bsd-3-clause | 5,657 | [
"NetCDF"
] | 9607a834bd6da710afcd4ffe282c265362012ee92d14b467553f5e0f29c632ae |
# Copyright 2014 Roberto Brian Sarrionandia
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed t... | sarrionandia/tournatrack | resetrooms.py | Python | apache-2.0 | 1,361 | [
"Brian"
] | b305c8f16d52d2d1201119763323faff4d921909885d755136bdf8398334c8ef |
#!/usr/bin/env python
"""Create netCDF files for use as GCM input data."""
import datetime
import os
import netCDF4
import numpy as np
import scipy.interpolate
from aospy_user import regions, variables
def pivot_index(longitudes):
"""Get index where longitudes change sign."""
return np.where(np.diff(np.sign(... | spencerahill/aospy-obj-lib | aospy_user/create_nc.py | Python | apache-2.0 | 9,215 | [
"NetCDF"
] | 2187dbb1d98679c29057d75d07a5aa4ef4b2026f2d42098bf0376a422a6cc319 |
# Predicted Mean Vote Comfort Calculator
#
# Ladybug: A Plugin for Environmental Analysis (GPL) started by Mostapha Sadeghipour Roudsari
#
# This file is part of Ladybug.
#
# Copyright (c) 2013-2015, Chris Mackey <Chris@MackeyArchitecture.com>
# Ladybug is free software; you can redistribute it and/or modify
# it u... | boris-p/ladybug | src/Ladybug_PMV Comfort Calculator.py | Python | gpl-3.0 | 39,930 | [
"EPW"
] | a680efc5404b18abb727e86422813f3800796ab1f81a37d60d1ae03a88c8e7e7 |
#!/usr/bin/python
# PD license by Beherith
# You like pasghetti code? No problem, you get pasghetti code.
import sys
from sys import exit
import struct
from PIL import Image
import png
import random
import argparse
import os
import math
import gc
pymapconv_version = "3.8"
def print_flushed(message, args=""):
print ... | Beherith/springrts_smf_compiler | pymapconv.py | Python | cc0-1.0 | 56,349 | [
"Gaussian"
] | 3b996b911d9749cab177f4c73e585b65600aff440d3b81bc049d32983b2ced8a |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
from pymatgen.analysis.xas.spectrum import XANES
import unittest
from pymatgen.util.testing import PymatgenTest
import json
from monty.json import MontyDecoder
import numpy as np
test_dir = os.path.j... | setten/pymatgen | pymatgen/analysis/xas/tests/test_spectrum.py | Python | mit | 1,663 | [
"pymatgen"
] | 684c0db8a32a41e3f305136e715c6e90ac8dfc311577b1f71780a726f450d51e |
# ----------------------------------------------------------------------------
# Copyright 2015 Nervana Systems Inc.
# 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.o... | misko/neon | tests/test_gru.py | Python | apache-2.0 | 13,765 | [
"Gaussian"
] | 0b305414f87518f82e08c1109dd8a10428585e52d0f0f996b07694fc5f6c7ae1 |
#!/usr/bin/env python
########################################################################
# $HeadURL$
########################################################################
__RCSID__ = "$Id$"
import DIRAC
from DIRAC.Core.Base import Script
userName = None
userDN = None
userMail... | Sbalbp/DIRAC | Interfaces/scripts/dirac-admin-add-user.py | Python | gpl-3.0 | 2,988 | [
"DIRAC"
] | 13196e4cb371f79c25954948df5c28fd9ececad3ac16ea662c283b2a8c1a6076 |
"""
Actions to be run at job completion. Currently only used in workflows.
"""
import datetime
import logging
from galaxy.util import send_mail
from galaxy.util.json import dumps
log = logging.getLogger( __name__ )
def get_form_template(action_type, title, content, help, on_output=True ):
if on_output:
... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/jobs/actions/post.py | Python | gpl-3.0 | 24,575 | [
"Galaxy"
] | 95e78be314d32fa2bcadc5e7e03e710259a6899cba9a769d91a93c8906fc548b |
#
# Author: Travis Oliphant 2002-2011 with contributions from
# SciPy Developers 2004-2011
#
from __future__ import division, print_function, absolute_import
import warnings
from scipy.special import comb
from scipy.misc.doccer import inherit_docstring_from
from scipy import special
from scipy import optim... | niknow/scipy | scipy/stats/_continuous_distns.py | Python | bsd-3-clause | 124,080 | [
"Gaussian"
] | 5aef7eafa3f55aca5f7f933dc5f8cfe09bec686a3bbcf5c9812a65b2780a4d56 |
import os
import sys
import numpy as np
import scipy.io
from synth_dataset import mkdir_p, eval_gp
from real_dataset import test_predict
from sigvisa.models.spatial_regression.SparseGP import SparseGP, sparsegp_nll_ngrad
from sigvisa.models.spatial_regression.SparseGP_CSFIC import SparseGP_CSFIC
from sigvisa.models.d... | davmre/treegp | experiments/old/eval_product_tree_on_matlab_hyperparams.py | Python | gpl-3.0 | 6,140 | [
"Gaussian"
] | f3f59a10928c82dea1c7247bb0ea41abedc208c2110d42f81036b4ebbe1445d0 |
#
# Copyright (C) 2011, 2015, 2016, 2019, 2020, 2021
# Smithsonian Astrophysical Observatory
#
#
# 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... | anetasie/sherpa | sherpa/sim/sample.py | Python | gpl-3.0 | 29,984 | [
"Gaussian"
] | 3df72fa4e9f2f4c76d326e35b2d0fd36050a02c9a7ce3d62a315a64585006d62 |
from distutils.core import setup
setup(
name="vlgp",
version="2019.3.19",
packages=["vlgp"],
url="https://github.com/catniplab/vlgp",
license="MIT",
author="yuan",
author_email="yuanz271@gmail.com",
description="variational Latent Gaussian Process",
python_requires=">=3.5.0",
i... | catniplab/vLGP | setup.py | Python | mit | 701 | [
"Gaussian"
] | 80650b44fb56214062f00f41d28a085f2e16e159acd875fb1721af04f5d0c4ae |
'''
First pass at some active learners
'''
import random
class ActiveLearner():
'''
Base class for all active learners.
'''
def __init__(base_learner, unlabeled_data=None):
'''
base_learner should be a subclass of BaseLearner
unlabeled_data should be an array of tuples (int i... | gvanhorn38/active_neurofinder | activelearner.py | Python | mit | 1,897 | [
"NEURON"
] | c68494a7ab56bd744b65d2039e164af5fa02181ad1c7a849160b60ad6f98bdf4 |
import multiprocess as mp
import pandas as pd
from itertools import combinations
import cooler
import bioframe
from .. import api
from ..lib.common import make_cooler_view
from ..lib.io import read_viewframe_from_file
import click
from . import cli
@cli.command()
@click.argument("cool_path", metavar="COOL_PATH", typ... | open2c/cooltools | cooltools/cli/expected_cis.py | Python | mit | 3,812 | [
"Gaussian"
] | f0350b8479b2f6580fbe2673fc68a3d8be6555044b1297c988f84fc936cad99d |
""" Test_RSS_Command_GOCDBStatusCommand
"""
import mock
import unittest
import importlib
from datetime import datetime, timedelta
from DIRAC.ResourceStatusSystem.Command.DowntimeCommand import DowntimeCommand
from DIRAC import gLogger
__RCSID__ = '$Id: $'
#########################################################... | calancha/DIRAC | ResourceStatusSystem/Command/test/Test_RSS_Command_GOCDBStatusCommand.py | Python | gpl-3.0 | 17,700 | [
"DIRAC"
] | de02ee12506530ec669a1a34060e0480fa4a27117fe28004ad657c405cc1fded |
from __future__ import print_function, absolute_import
import os
import sys
import json
import shutil
import subprocess
import tempfile
import warnings
from setuptools import Extension
from distutils.dep_util import newer_group
from distutils.errors import DistutilsExecError, DistutilsSetupError
from distutils.ccompil... | mattwthompson/mdtraj | basesetup.py | Python | lgpl-2.1 | 15,301 | [
"MDTraj"
] | 43d3795c33cd8251c62dc971553ad1ab30b599df790df76c4676cfc542ed7cd7 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, division, print_function, unicode_literals
import time
import unittest
import logging
import functools
from nose.tools import * # flake8: noqa (PEP8 asserts)
import mock
from framework.auth.core import Auth
from website import settings
import website.... | chennan47/osf.io | osf_tests/test_elastic_search.py | Python | apache-2.0 | 39,152 | [
"Brian"
] | 7da5a19e8f083b12bab34dae9d96d384ade6d1481a02a83654f10b189f46a868 |
# -*- coding: utf-8 -*-
#
# test_quantal_stp_synapse.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of th... | synergetics/nest | pynest/nest/tests/test_quantal_stp_synapse.py | Python | gpl-2.0 | 4,117 | [
"NEURON"
] | 57cc72c8adc16f9afaef117c0e6d05dc75b556e5297045807d1d333cdca94b48 |
#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific.
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove ... | gratefulfrog/lib | python/chempy/water_residues.py | Python | gpl-2.0 | 1,454 | [
"PyMOL"
] | d6c80aa67962140615f2f77e29686ebe94d5357df30b76db4d299fff3e1d10e1 |
"""
Open ugrid-ish subdomains and approximate a global domain
Currently this is pretty slow, due to the add_grid() step.
The ghost-cell handling is also very basic, and does not
properly distinguish ghost cells along land boundaries.
TODO: handling isel for partitioned dimensions
handling DFM output with FlowLink ... | rustychris/stompy | stompy/grid/multi_ugrid.py | Python | mit | 21,931 | [
"NetCDF"
] | 72f6c17fda413c338196f5895894190f529416c7f03af5a7fcef71191de76925 |
"""
bowtie
"""
from mungoCore import AbstractDataReader
from useful import smartopen
class Feature(object):
def __init__(self, tokens):
self.tokens = tokens
self.name = tokens[0]
self.strand = tokens[1]
self.chrom = tokens[2]
self.start = int(tokens[3]) # 1-indexed
... | PapenfussLab/Mungo | mungo/bowtie.py | Python | artistic-2.0 | 2,865 | [
"Bowtie"
] | b47c0e8e92476a9bd08ccab79b0b9918b44c4952cea2555610b6bd7d9bf066b2 |
# coding: utf-8
#
# This file is part of Sequana software
#
# Copyright (c) 2016 - Sequana Development Team
#
# File author(s):
# Thomas Cokelaer <thomas.cokelaer@pasteur.fr>
# Dimitri Desvillechabrol <dimitri.desvillechabrol@pasteur.fr>,
# <d.desvillechabrol@gmail.com>
#
# Distributed under the ... | sequana/sequana | sequana/modules_report/bwa_bam_to_fastq.py | Python | bsd-3-clause | 3,254 | [
"BWA"
] | f41f2e1e1ea4ea9676514357de9f6202ee5217113dc3b6cb4c0d15bdd13872be |
import os, sys, socket, random
from urllib import quote_plus
from pandac.PandaModules import HTTPClient
from pandac.PandaModules import HTTPCookie
from pandac.PandaModules import URLSpec
from pandac.PandaModules import Ramfile
from pandac.PandaModules import Ostream
from pandac.PandaModules import HTTPDate
from pandac.... | ksmit799/Toontown-Source | toontown/toonbase/UserFunnel.py | Python | mit | 26,155 | [
"Jaguar"
] | e7bb8ebe3549965aad229abe69be5f4eb778a3f3a0780bb2257cea9856c8b3d2 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
import unittest
import numpy as np
from pymatgen.core import Structure
from pymatgen.core.sites import PeriodicSite
from pymatgen.analysis.defects.core import Vacancy, Interstitial, Substitution, \
... | dongsenfo/pymatgen | pymatgen/analysis/defects/tests/test_core.py | Python | mit | 15,067 | [
"pymatgen"
] | 14a3d82fc51b52dee85a8f74b9c0e25f04e2a2c3ee5684037b05dbcf9e8c0d6a |
import os
from director.componentgraph import ComponentFactory
from director import consoleapp
import director.objectmodel as om
import director.visualization as vis
from director.fieldcontainer import FieldContainer
from director import applogic
from director import appsettings
from director import drcargs
import fun... | mitdrc/director | src/python/director/mainwindowapp.py | Python | bsd-3-clause | 15,527 | [
"VTK"
] | 6462866e2809c877faa886357e002315f208284bc762ec86c06a4aab0b025cab |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (C) 2005, Pierre Legrand
#
# 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 lat... | RAPD/RAPD | src/old_agents/subcontractors/xdsme/XOconv.py | Python | agpl-3.0 | 39,804 | [
"CRYSTAL"
] | 01e58d484ad455290551b15dfdc0c53c4a78a86bebb3c2a32e80354696d21353 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | kdmurray91/scikit-bio | skbio/tree/tests/test_nj.py | Python | bsd-3-clause | 8,925 | [
"scikit-bio"
] | f4f99fc730869739bede0f5b96a82f510ed8fe8ee6508ab30dd884a5293c8d1c |
from galaxy import exceptions
from abc import ABCMeta
from abc import abstractmethod
from galaxy import model
import logging
log = logging.getLogger( __name__ )
class DatasetCollectionType(object):
__metaclass__ = ABCMeta
@abstractmethod
def build_collection( self, dataset_instances ):
"""
... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/dataset_collections/types/__init__.py | Python | gpl-3.0 | 1,063 | [
"Galaxy"
] | 250e00193d9ac63a25deed27204340e77715a09e5ce74ab9d7330597e8f22bad |
# Copyright 2014 Cloudera Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, so... | wesm/ibis | ibis/sql/compiler.py | Python | apache-2.0 | 44,856 | [
"VisIt"
] | 0cb93c8a1a8b502d981d22417205fbc03ca0bdeb2182eef2c020818ec63f4f45 |
from __future__ import print_function, division, absolute_import
# Std. lib imports
from sys import stdout
from math import pi
# Non-std. lib imports
from numpy import array, loadtxt
from input_reader import InputReader, SUPPRESS, ReaderError, \
range_check, abs_file_path
HZ2WAVENUM = 1 / ( ... | jensengrouppsu/rapid | rapid/common/read_input.py | Python | mit | 5,734 | [
"Gaussian"
] | 3ea93cdf4688a5aab5c435794c4826711a1c881141fe22d2705d8a7f463cde98 |
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