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 |
|---|---|---|---|---|---|---|---|
""" Nodes are elemental signal processing steps
They are arranged in mostly :mod:`serial node chains<pySPACE.environments.chains.node_chain>`.
Between the nodes in one chain several :mod:`signal types <pySPACE.resources.data_types>` can be sent:
* :class:`~pySPACE.resources.data_types.time_series.TimeSeries` or
... | Crespo911/pyspace | pySPACE/missions/nodes/__init__.py | Python | gpl-3.0 | 9,544 | [
"VisIt"
] | 0810aa4403586dfcdd53e5acc6593026649a90ada761a8d4baee7d39afc0be1f |
# -*- coding: utf-8 -*-
# Copyright (c) 2010-2016, MIT Probabilistic Computing Project
#
# 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/LICENS... | probcomp/bayeslite | src/backends/iid_gaussian.py | Python | apache-2.0 | 3,299 | [
"Gaussian"
] | bacf91364472629149f8d61a944872a0b3fc66941ebaa20bf6ee42ca96e3e02c |
"""
Student Views
"""
import datetime
import logging
import uuid
import json
import warnings
from collections import defaultdict
from urlparse import urljoin
from pytz import UTC
from requests import HTTPError
from ipware.ip import get_ip
from django.conf import settings
from django.contrib.auth import logout, authen... | simbs/edx-platform | common/djangoapps/student/views.py | Python | agpl-3.0 | 96,840 | [
"VisIt"
] | b4fa04c1700a146aacef7801cb691556539b556af9f74e4ad74d445d5bdd22c0 |
""" Create ERA-Interim daily anomalies.
The file is filled in by generate_obs_ts_anom.ksh.
"""
import os
import pandas as pd
# Sections of code to run
download_data = 0 # 1, 0. conda acivate ECMWF
create_anom = 1 # 1, 0. conda activate SubX
create_mme_anom = 0 # 1, 0. conda activate SubX
# Inputs
moPath = 'moddir'
... | kpegion/SubX | Python/create_obs_anomalies/ERA-Interim/createobsanom_ts_template.py | Python | mit | 6,808 | [
"NetCDF"
] | 2df860619ec70dc7a407214d79e497a3f316d45800f08413ab4e52a8f087a47d |
# FreeCAD TemplatePyMod module
# (c) 2010 Werner Mayer LGPL
"""
The module can be executed with:
FreeCAD -P <path_to_file> Automation.py
FreeCADCmd -P <path_to_file> Automation.py
"""
import FreeCAD, Part
import os
import tempfile
def makeSnapshotWithGui():
from PySide import QtGui
import FreeCADG... | Fat-Zer/FreeCAD_sf_master | src/Mod/TemplatePyMod/Automation.py | Python | lgpl-2.1 | 2,523 | [
"CRYSTAL"
] | d925f379b3257444e385c8ac3bb33bfdc3dec5b1e63e5cc2c01422f221e42187 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | nburn42/tensorflow | tensorflow/contrib/timeseries/python/timeseries/state_space_models/state_space_model.py | Python | apache-2.0 | 57,267 | [
"Gaussian"
] | bca8f5190939f743afab9e4a50e69a238a7fc595b8e5e894c950499653825c20 |
# $Id$
#
# Copyright (C) 2005-2006 greg landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
from __future__ import... | rvianello/rdkit | rdkit/DataStructs/VectCollection.py | Python | bsd-3-clause | 6,307 | [
"RDKit"
] | b9fa162c0e582944455d8ae1e396115a2615cffc026b6fb6fb8e3c9a12d34465 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Example script, part of MDAnalysis
"""
Example: Comparing a trajectories from different methods
========================================================
Example implementation of Path Similarity Analysis that shows how to read in a
set of trajectories, compute (discrete)... | sseyler/PSAnalysisTutorial | psa_short.py | Python | gpl-3.0 | 4,839 | [
"CRYSTAL",
"MDAnalysis"
] | f5049e45ad4c088e2ede9abddffa82c457e8090c3dc64e082861ac30104d3e0d |
# coding=utf-8
import random
import numpy as np
from scipy.stats import multivariate_normal
import matplotlib.pyplot as plt
from mla.base import BaseEstimator
from mla.kmeans import KMeans
class GaussianMixture(BaseEstimator):
"""Gaussian Mixture Model: clusters with Gaussian prior.
Finds clusters by repeate... | zhuhuifeng/PyML | mla/gaussian_mixture.py | Python | apache-2.0 | 6,713 | [
"Gaussian"
] | 5c04d9d5109eaad783d9bd2695142df7c4ac78f771ea1be159288b3c6f74f367 |
import numpy as np
import tensorflow as tf
from tensorflow.python.framework import ops
from tensorflow.python.ops import nn_ops, math_ops
def get_seq_length(sequence):
used = tf.sign(tf.reduce_max(tf.abs(sequence), reduction_indices=2))
length = tf.reduce_sum(used, reduction_indices=1)
length = tf.cast(le... | ethancaballero/neural-engineers-first-attempt | utils.py | Python | mit | 5,075 | [
"Gaussian"
] | c1ad08153fa12daebbddad64f661f890a99f3d8ccb14452593be4c9aba4582f6 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors: Kyle A. Beauchamp
#
# MDTraj i... | leeping/mdtraj | mdtraj/geometry/__init__.py | Python | lgpl-2.1 | 2,220 | [
"MDTraj"
] | 7cbcbdb931ce3b415627b0e79dda76ceb31fa0f78adedd7b37944b2f4459bb46 |
"""
Example of plotting lines with pyvisi
This is the original code used to develop the vtk renderer module
"""
# set up some data to plot
from numpy import *
x = arange(10, dtype=floating)
y = x**2
import vtk
# do a quick check to make sure x and y are same length
if len(x) != len(y):
raise ValueError, "x an... | paultcochrane/pyvisi | examples/renderers/vtk/simpleLinePlot.py | Python | gpl-2.0 | 2,489 | [
"VTK"
] | 9d62477cafd2adab21911862a6cc84b556ece1272d046c975ff6519bf15aff1b |
from kol.database import ItemDatabase
from kol.manager import PatternManager
from kol.request.GenericRequest import GenericRequest
class BountyHunterRequest(GenericRequest):
"""Interacts with the Bounty Hunter Hunter in the Forest Village."""
VISIT = None
ACCEPT_BOUNTY = 'takebounty'
ABANDON_BOUNT... | ijzer/cwbot-ndy | kol/request/BountyHunterRequest.py | Python | bsd-3-clause | 3,005 | [
"VisIt"
] | 5b073360dc450cdbc9d8e3231842dd4c5ef8cb5e3143222782532c3421e3c41f |
# (C) British Crown Copyright 2010 - 2014, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | bblay/iris | lib/iris/tests/test_plot.py | Python | gpl-3.0 | 32,144 | [
"NetCDF"
] | eea710e6c1b9e852d66ceacd18316ea9030de98943f2c177ef5a32969c199986 |
# -*- coding: utf-8 -*-
#
# This file is part of INSPIRE.
# Copyright (C) 2016 CERN.
#
# INSPIRE is free software; you can redistribute it
# and/or modify it under the terms of the GNU General Public License as
# published by the Free Software Foundation; either version 2 of the
# License, or (at your option) any later... | nikpap/inspire-next | inspirehep/modules/literaturesuggest/views.py | Python | gpl-2.0 | 3,641 | [
"VisIt"
] | f8fd4569b88aa1dff66091714ca54015cc2cf6f823c1113cfc0b29a73867cf2b |
"""Kernels for Gaussian process regression and classification.
The kernels in this module allow kernel-engineering, i.e., they can be
combined via the "+" and "*" operators or be exponentiated with a scalar
via "**". These sum and product expressions can also contain scalar values,
which are automatically converted to... | dwettstein/pattern-recognition-2016 | mlp/model_selection/kernels.py | Python | mit | 66,352 | [
"Gaussian"
] | c2b3546991eac441dadb31ef51e754055ebc8268249ba5cff678ca82ce665872 |
import numpy as np
from cs231n.layers import *
from cs231n.fast_layers import *
from cs231n.layer_utils import *
class ConvNet(object):
"""
A convolutional network with the following architecture:
conv - relu - 2x2 max pool - affine - relu - affine - softmax
The network operates on minibatches of d... | YeEmrick/learning | cs231/assignment/assignment2/cs231n/classifiers/convnet.py | Python | apache-2.0 | 7,683 | [
"Gaussian"
] | 44ee5e72d6abec571fc9494690094fe68c064824d98b133cafb8931903286cc3 |
# Author: Brian M. Clapper, G. Varoquaux, Lars Buitinck
# License: BSD
import numpy as np
from numpy.testing import assert_array_equal, assert_raises
from clustering_metrics.hungarian import linear_sum_assignment
from clustering_metrics.entropy import assignment_cost
from nose.tools import assert_equal, assert_almost_... | escherba/clustering-metrics | tests/test_hungarian.py | Python | bsd-3-clause | 3,103 | [
"Brian"
] | c026a32d67f4180e660df3484010884309d66b73d9035ea1547ce23f12a78644 |
import os, sys
import numpy as np
import matplotlib.pyplot as plt
from PIL import Image
from getIQU import IQU
from scipy import ndimage
from astropy import units as u
from astropy.coordinates import Angle
from astropy.visualization.wcsaxes import WCSAxes
from astropy.visualization.wcsaxes import SphericalCircle
from a... | sbg2133/miscellaneous_projects | carina/overplots.py | Python | gpl-3.0 | 3,822 | [
"BLAST"
] | 12f31ca6d9880c00cbae3b6a98bedabccd385b27d4a36a38c9a10858f1c03227 |
def extractShizunMoe(item):
'''
Parser for 'shizun.moe'
'''
vol, chp, frag, postfix = extractVolChapterFragmentPostfix(item['title'])
if not (chp or vol) or "preview" in item['title'].lower():
return None
tagmap = [
('stains of filth', 'stains of filth', 'translated'),
('PRC', ... | fake-name/ReadableWebProxy | WebMirror/management/rss_parser_funcs/feed_parse_extractShizunMoe.py | Python | bsd-3-clause | 613 | [
"MOE"
] | e8da712eed3c15c5b39b9d2cf0a661d0fc2deb10e72efcd3e407a39bac316c51 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, division, print_function, unicode_literals
from nose.tools import * # noqa PEP8 asserts
from osf_tests import factories
from tests.base import OsfTestCase
from website.util import api_url_for
from website.views import find_bookmark_collection
class Te... | laurenrevere/osf.io | osf_tests/test_search_views.py | Python | apache-2.0 | 15,111 | [
"Brian"
] | f050f608022250dbbbdda1d40e47945b3458a34ac46fbee70500ca3cb425919b |
# -*- coding: utf-8 -*-
import os
mpl.rcParams['text.usetex'] = False
import moose
import numpy as np
import moose.fixXreacs as fixXreacs
def countCrossings( plot, thresh ):
vec = moose.element( plot ).vector
#print (vec[:-1] < thresh)
return sum( (vec[:-1] < thresh) * (vec[1:] >= thresh ) )
def main( sta... | upibhalla/moose-core | tests/python/testXreacs2.py | Python | gpl-3.0 | 2,103 | [
"MOOSE"
] | d985c692707693e0f3412ccf18ddfa4e0d4614507244da5658fdf9e8d745abef |
# -*- coding: utf-8 -*-
import forms.form_models.bfsql as bfsql
import forms.form_models.bform as bforms
from forms.form_models.bfbdb import *
bf = bforms.BerkeleyForm()
bf.theme='nain'
bf.doctype='html'
bf.name='nain'
qdb = [
{'type':'Section','label':'I. Your Organization','style':'section'},
{'type':'Section... | cbears/octoform | test/forms/nain.py | Python | gpl-3.0 | 12,099 | [
"COLUMBUS",
"VisIt"
] | cb04d17562192bfcdd34012faaaf792eb1f4469740d3487c3e129bc3650bc320 |
# ==================================================================================================
#
# Copyright (c) 2016, Chen Kian Wee (chenkianwee@gmail.com)
#
# This file is part of py4design
#
# py4design is free software: you can redistribute it and/or modify
# it under the terms of the GNU General ... | chenkianwee/pyliburo | py4design/citygml2eval.py | Python | gpl-3.0 | 38,302 | [
"EPW"
] | 5bc9ffe2c9e76bf2bb9188be5144dd66adb010b9fbed3ab45dea6eb368853286 |
# Author: Travis Oliphant, 2002
#
# Further updates and enhancements by many SciPy developers.
#
from __future__ import division, print_function, absolute_import
import math
import warnings
import numpy as np
from numpy import (isscalar, r_, log, sum, around, unique, asarray,
zeros, arange, sort, amin, amax, an... | ogrisel/scipy | scipy/stats/morestats.py | Python | bsd-3-clause | 70,237 | [
"Gaussian"
] | 8434598bdb861451ea7ddb11d56a1a49f4aeae7b13d0fe96f3722cec3708c488 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Takes *.mae structure files and generates *.com files for
conformational searches.
The *.mae files must contain several properties on the atoms and bonds. These
properties can be manually entered into the *.mae. They can also be
accessed using Schrödinger's structure m... | ericchansen/q2mm | screen/setup_com_from_mae.py | Python | mit | 19,927 | [
"MacroModel"
] | c67741f6a00f58bacd0eb4f2da6a59b9d9acf68c5940de6c6072753b8b0539f3 |
# BEGIN_COPYRIGHT
#
# Copyright (C) 2014 CRS4.
#
# This file is part of blast-python.
#
# blast-python 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)
# ... | crs4/blast-python | test/test_streams.py | Python | gpl-3.0 | 8,218 | [
"BLAST"
] | bb94d41a245037c1805b1f4ef71a06d24867bfe3f8ec2b3c028405935589dc79 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2002-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
#
# 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; ... | arunkgupta/gramps | gramps/gen/filters/rules/person/_hasnameof.py | Python | gpl-2.0 | 7,576 | [
"Brian"
] | 32eedb010cffa5c68811e1fd1222f6e627b2a36e6a4aff877abc9e908e6a5f87 |
# 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/model/modifier.py | Python | apache-2.0 | 2,090 | [
"VisIt"
] | ac9b71bcfb7a1f028806c5c417de278d0787848b0fcaeddb9b3e10a801a88006 |
'''
Created on 2013-05-28
@author: brian
'''
from pygame.color import THECOLORS
from projectiles import Arrow
from random import randint
from src.util import Vector2
class BowShot(object):
range = 7
damage = 2, 5
heal = False
name = "Shoot"
icon = "arrow"
cooldown = 0
def __init__(self, caster, location,... | Greymerk/python-rpg | src/abilities/bowshot.py | Python | gpl-3.0 | 1,783 | [
"Brian"
] | a8e01bdca3b8a39a80915554460061fc2b3fbedb6d24113469dd8bc4fe6bd629 |
# coding: utf8
{
' (leave empty to detach account)': ' (leave empty to detach account)',
' Module is the main communications hub of the Sahana system. It is used to send alerts and/or messages using SMS & Email to various groups and individuals before, during and after a disaster.': 'モジュールでは、Sahanaに登録された様々な組織がお互いに連絡... | ptressel/sahana-eden-madpub | languages/ja.py | Python | mit | 289,411 | [
"VisIt"
] | 5e60005d99337fb5c05aa0d6eff488446453d5ada466e2a2ba41fc063da295dd |
"""
Test SBML capabilities of PyMOOSE
"""
__author__ = "Dilawar Singh"
__copyright__ = "Copyright 2015, Dilawar Singh and NCBS Bangalore"
__credits__ = ["NCBS Bangalore"]
__license__ = "GNU GPL"
__version__ = "1.0.0"
__maintainer__ = "Dilawar Singh"
__email__ ... | dilawar/moose-full | moose-core/tests/python/test_sbml.py | Python | gpl-2.0 | 1,194 | [
"MOOSE"
] | 4b02f5df2a81d99e9a5cde75cd975e4a6228954e88440e217a99d77ddc1c5048 |
# Copyright (c) 2018 MetPy Developers.
# Distributed under the terms of the BSD 3-Clause License.
# SPDX-License-Identifier: BSD-3-Clause
"""Interpolate data valid at one set of points to another in multiple dimensions."""
import logging
import numpy as np
from scipy.interpolate import griddata, Rbf
from scipy.spatia... | ShawnMurd/MetPy | src/metpy/interpolate/points.py | Python | bsd-3-clause | 12,988 | [
"Gaussian"
] | ae9cd4757721864feb43a52dafa745d550ac7687fc7981401f884c84091fae60 |
from socket import *
import subprocess
from pkg_resources import resource_filename as res
from PyQt5.QtWidgets import QWidget, QGridLayout, QLabel, QPushButton, QLineEdit
from PyQt5 import QtCore
from .Dialogues import TopoTrajLoaderDialog
from ..core.Biochemistry import *
# from ..cy_modules import wrap_vmd as vmd
... | maxscheurer/pycontact | PyContact/gui/VMDControlPanel.py | Python | gpl-3.0 | 11,968 | [
"VMD"
] | 4c11cc7af383fc760eba7768e8c87de3778171d7a7b34f532732b38a38882a9d |
import argparse
import logging
import shelve
from rdkit.Chem.rdmolfiles import SDMolSupplier, MolToMolBlock
from ..db import FragmentsDb
from ..hdf5 import SimilarityMatrix
from ..pdb import PdbReport
def make_fragments_parser(subparsers):
"""Creates a parser for fragments sub commands
Args:
subpar... | 3D-e-Chem/python-modified-tanimoto | kripodb/script/fragments.py | Python | apache-2.0 | 6,891 | [
"RDKit"
] | 4161e20d127f9d90c101c83b4106c86d5cea7fd04b5784d4a188057d5b08e264 |
__author__ = 'swebb'
"""
This is a test to determine whether the two-body Coulomb attraction between
an electron and a positron is correct.
"""
from opal.fields import discrete_fourier_electrostatic as dfe
from opal.interpolaters_depositers import tent_dfes as depinterp
from opal.particles import non_rel_ptcl as ptcls... | radiasoft/opal | tests/integration_tests/coulomb_interaction.py | Python | apache-2.0 | 3,488 | [
"Gaussian"
] | d4bb8fab83868c136d4e90f3046a64a51c2dc58af3bb269120439cc309f0a65d |
'''
SASSIE: Copyright (C) 2011 Joseph E. Curtis, Ph.D.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
... | madscatt/zazzie | src_2.7/sassie/analyze/density_plot/density_plot_1.0.py | Python | gpl-3.0 | 28,936 | [
"Gaussian"
] | 2bb5bb441616e859c7923df1562e012dfa32d8b70a70731e40f19272899d7cb5 |
#!/usr/bin/env python3
import csv
import json
import numpy as np
def get_quantization(g, gMin, gMax):
return {'type': "DoubleColumnQuantization",
'granularity': g,
'globalMin': gMin,
'globalMax': gMax}
def main():
mean = 0.0
stdev = 25.0
nsamples = 100000
value... | mbudiu-vmw/hiero | data/synthetic/gen_synthetic_gaussian.py | Python | apache-2.0 | 944 | [
"Gaussian"
] | 08b62c56f3cce40909d6efbeec7e32eb1689452446dd7e8bf97f3593e302c9c7 |
#!/usr/bin/env python
# -*- encoding: utf-8 -*-
# CREATED:2015-03-03 21:29:49 by Brian McFee <brian.mcfee@nyu.edu>
"""Additive background noise"""
import soundfile as psf
import librosa
import numpy as np
import os
import six
from ..base import BaseTransformer, _get_rng
def sample_clip_indices(filename, n_samples, ... | bmcfee/muda | muda/deformers/background.py | Python | isc | 5,892 | [
"Brian"
] | 2909cf2b013a88fa2d3cb2cb4b79ab8fb10efa63c9fb0d58e920ccc526483338 |
# -*- coding: utf-8 -*-
"""ANTS Apply Transforms interface
Change directory to provide relative paths for doctests
>>> import os
>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
>>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
>>> os.chdir(datadir)
"""
from __fu... | carolFrohlich/nipype | nipype/interfaces/ants/resampling.py | Python | bsd-3-clause | 22,112 | [
"Gaussian"
] | 4834a3a875aa91b8622508cded34eaf9e7f4912dffb10a6a538b8b9a22b69baa |
#
# Copyright (C) 2013-2019 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... | psci2195/espresso-ffans | testsuite/python/collision_detection.py | Python | gpl-3.0 | 30,574 | [
"ESPResSo"
] | 73c5b4fe3233c5edaa036ac4c3005b1ba9a7b49c94b7dbcbd110bc5b5aba1756 |
"""
The InputData Optimizer Executor queries the file catalog for specified job input data and adds the
relevant information to the job optimizer parameters to be used during the scheduling decision.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__... | yujikato/DIRAC | src/DIRAC/WorkloadManagementSystem/Executor/InputData.py | Python | gpl-3.0 | 16,556 | [
"DIRAC"
] | 9957a56613a71a7118c65aab538ccdc0c48c280eacfb935004ec63ae174cb176 |
import sys
from coolections import subdict
from magic import magic
class SafeSub(dict):
"""Use with str.format_map to leave missing keys untouched.
>>> '{key} {missing key}'.format_map(SafeSub({'key': 'value'}))
'value {missing key}'
"""
def __missing__(self, key):
return '{' + key + '}'... | doctaphred/phredutils | strfmt.py | Python | gpl-3.0 | 7,748 | [
"Octopus"
] | 237412dd09007dca65479bc5207d72dd1672a57dbb9ce1a233aff0fbdf8abd0f |
"""
.. _tut-viz-stcs:
Visualize source time courses (stcs)
====================================
This tutorial focuses on visualization of :term:`source estimates <STC>`.
Surface Source Estimates
------------------------
First, we get the paths for the evoked data and the time courses (stcs).
"""
# %%
import os.pat... | bloyl/mne-python | tutorials/inverse/60_visualize_stc.py | Python | bsd-3-clause | 7,901 | [
"Mayavi"
] | 0f6cd170ddd2bcab7ab2ed76af578dd0439b745fe5801fdb124546dc36e28ce8 |
# -*- coding: utf-8
# pylint: disable=line-too-long
"""Lots of under-the-rug, operational garbage in here. Run. Run away."""
import os
import sys
import json
import copy
import platform
from tabulate import tabulate
# yes, this library is imported but never used, but don't remove it
# unless you want to explode `bo... | meren/anvio | anvio/__init__.py | Python | gpl-3.0 | 202,415 | [
"BLAST",
"Bowtie"
] | 812695108dc50a95bee7b40d7aedc8ecb35fec2fb3b45521878c331d3df4879b |
#!/usr/bin/env python
"""
This script takes an alignment file in SAM/BAM format and a
feature file in GFF format and calculates for each feature
the number of reads mapping to it.
This is a modified version of htseq-count
Copyright:
count_features.py Counts coverage of GFF file from SAM/BAM file
Copyright (C... | Brazelton-Lab/lab_scripts | count_features.py | Python | gpl-2.0 | 13,565 | [
"HTSeq"
] | 97f6b5f912a591e7c4090f93c52243a61e26201d5e7ef304e6c1f3c92c11bba7 |
"""The sourceLoader is used to handle the import capabilities for
hash-identified loaded sources.
Sources are loaded via the ActorSystem().loadSource(...) operation,
verified by the SourceAuthority, then made available for creating
actors in them via createActor("actorname", sourceHash=H).
1. The Actor generated from... | kquick/Thespian | thespian/system/sourceLoader.py | Python | mit | 18,835 | [
"VisIt"
] | 08d22844079a1a258853c8a78d1284b1e1f7d859d373b522fca3a2757dcd8726 |
import numpy as np
from mdtraj import io
from msmbuilder import arglib
from msmbuilder import msm_analysis
from msmbuilder import Project
import scipy.io
import logging
logger = logging.getLogger('msmbuilder.scripts.SampleTrajectory')
DEBUG = True
parser = arglib.ArgumentParser(description="""
Create an MSM movie by s... | mpharrigan/msmbuilder | scripts/SampleTrajectory.py | Python | gpl-2.0 | 1,673 | [
"MDTraj"
] | ca2ecc1f3a1638a575e0f8f149529cedf773fcd76026a13e1f3847b4dcb04189 |
#!/usr/bin/env python
""" File Catalog Client Command Line Interface. """
from __future__ import print_function
__RCSID__ = "$Id$"
import commands
import os.path
import time
import sys
import getopt
from DIRAC.Core.Utilities.ReturnValues import returnSingleResult
from DIRAC.Core.Base.CLI import CLI
from DIRAC.Core.S... | petricm/DIRAC | DataManagementSystem/Client/FileCatalogClientCLI.py | Python | gpl-3.0 | 68,854 | [
"DIRAC"
] | 3eb2fdf574e5025a03be762b7cccde6e306cd5067d70c97690ba2454636ac78d |
# 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... | sunqm/pyscf | pyscf/pbc/mpitools/mpi_helper.py | Python | apache-2.0 | 3,158 | [
"PySCF"
] | e2286d96834a7b5526007c61bc011781d31629ed2382686084e93c4929a39e3e |
########################################################################
# $HeadURL$
########################################################################
""" ProxyRepository class is a front-end to the proxy repository Database
"""
__RCSID__ = "$Id$"
import time
import random
import types
try:
import hashlib
... | avedaee/DIRAC | FrameworkSystem/DB/ProxyDB.py | Python | gpl-3.0 | 43,574 | [
"DIRAC"
] | 8be9727ae48a9086e44232bd356370c3123077f66c33d4a59e35bd9934f0b78a |
# -*- coding: utf-8 -*-
"""
3D PSF-based point-source extractor. The PSF is a constrained
Gaussian+Moffat with elliptical distortion.
Todo:
* one could use Aitchison (or 'additive log-ratio') transform to
enforce the normalization constraint on alphas (see
http://thread.gmane.org/gmane.comp.python.scientific.use... | snfactory/extract-star | extract_star/main.py | Python | mit | 86,928 | [
"Gaussian"
] | 6da411e559923246e27a85c9ded801f66d9940cf666620357712d47374bf1320 |
__author__ = 'Henri Bunting'
try:
import brian2
from brian2 import pF, mV, defaultclock, ms, NeuronGroup, linspace, SpikeMonitor, \
PopulationRateMonitor, StateMonitor, run, msecond, nS, nA
except ImportError:
brian2 = None
def run_network():
monitor_dict={}
defaultclock.dt= 0.01*ms
... | SmokinCaterpillar/pypet | pypet/tests/unittests/brian2tests/run_a_brian2_network.py | Python | bsd-3-clause | 1,382 | [
"NEURON"
] | 9628bd24abcf305db1b2558feef412d57822a195dc97af9899cd81c47790c105 |
#!/usr/bin/env
"""
GOA_Winds_NARR_6hr.py
Compare NARR Winds with NCEP V2 (with Mooring Winds) for 6hr intervals. Uses 3hr NARR and 6hr NCEP
Using Anaconda packaged Python
"""
#System Stack
import datetime
#Science Stack
import numpy as np
from scipy import stats
# User Stack
import general_utilities.haversin... | shaunwbell/FOCI_Analysis | ReanalysisRetreival_orig/GOA_Winds/GOA_Winds_NARR_hr.py | Python | mit | 22,263 | [
"NetCDF"
] | f79bd9635e1f3ba74b97584c9fdeb42bbfba61b3a2b8d5021485116b67aaf858 |
##
# Copyright 2009-2020 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... | pescobar/easybuild-easyblocks | easybuild/easyblocks/l/libsmm.py | Python | gpl-2.0 | 8,174 | [
"CP2K"
] | 72726ccd6bc7ce2693e363f1f1c9026fe296f1cbc2c15c8c20554cfefe4fb49e |
# -*- Mode: Python; indent-tabs-mode: nil; tab-width: 4; coding: utf-8 -*-
'''apport package hook for update-manager
(c) 2011 Canonical Ltd.
Author: Brian Murray <brian@ubuntu.com>
'''
import re
from apport.hookutils import (
attach_gsettings_package, attach_root_command_outputs,
attach_file_if_exists, recen... | Snowlinux/snowupdate | debian/source_update-manager.py | Python | gpl-2.0 | 879 | [
"Brian"
] | 2fb51ce47f49a593e5ed2b32d93195f1e0a9be7718d60090caf5e19ef047ae5d |
import sys
from collections import OrderedDict
# Verbosity level
verbosity = 1
# Indentation string in messages
INDENT_STR = " " * 2
def write_crystal(geometry, atoms_coords, atoms_idx, axis, resultfilename,
append, gen, latvecsfilename):
"""Write out the resulting crystaline structure.
... | aradi/nanocut | src/nanocut/output.py | Python | bsd-2-clause | 4,543 | [
"CRYSTAL"
] | d2ccf41941cf5bc5a7847719075c09570683faf81575b5ca9ee353f35e551fda |
import sys
sys.path.append('./summary')
sys.path.append('./test')
from distutils.core import setup
from setuptools import setup
description = """\
Extractor to get main content from the web page.
- guessed title of main content
- guessed main content
- guessed summarization
- candidate of main image
Install
sudo... | after12am/summary | setup.py | Python | mit | 1,378 | [
"VisIt"
] | 257b164520135aa76453314370e15349b7afb39a7021552eaf42b391f12a66fe |
#!/usr/bin/python
#
# Copyright 2014 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 b... | dietrichc/streamline-ppc-reports | examples/adwords/v201406/campaign_management/validate_text_ad.py | Python | apache-2.0 | 2,828 | [
"VisIt"
] | 4026d11e631d3d9ae635bb2663257d13ce43b585fc39edbccd16b909ac74fc5e |
from yargy.visitor import Visitor
from yargy.dot import (
style,
DotTransformator,
BLUE,
GREEN
)
from yargy.pipelines import PipelineProduction
from yargy.interpretation.interpretator import InterpretatorInput
from .constructors import (
Tree,
Node,
Leaf
)
class InplaceTreeTransformator... | bureaucratic-labs/yargy | yargy/tree/transformators.py | Python | mit | 4,463 | [
"VisIt"
] | 1c8d94c8a576988646ff68ef4bdcae3fdcf39c39c83face59c916edbf26f153f |
# proxy module
from __future__ import absolute_import
from mayavi.core.module_manager import *
| enthought/etsproxy | enthought/mayavi/core/module_manager.py | Python | bsd-3-clause | 95 | [
"Mayavi"
] | 6f1023fc11b176884e0253ddaf93fb172b46566562d5ca8ed160a0377fd18965 |
# -*- coding: utf-8 -*-
"""
Created on Sat Dec 14 17:23:25 2013
Author: Josef Perktold
"""
import os
import numpy as np
from numpy.testing import assert_allclose, assert_array_less
import pytest
from statsmodels.sandbox.nonparametric import kernels
DEBUG = 0
curdir = os.path.dirname(os.path.abspath(__file__))
fna... | jseabold/statsmodels | statsmodels/nonparametric/tests/test_kernels.py | Python | bsd-3-clause | 4,411 | [
"Gaussian"
] | 8bc8d9ec7baca0bd08f4a9b1a7aee4bc8a45f10e90c59bdd643bef5e6766b457 |
#!/usr/bin/env python
#
# Merge bams using pysam
#
# @author James Boocock
#
import argparse
def main():
"""
Merges reads using the readgroup
"""
parser = argparse.ArgumentParser(description='Merge reads')
args = parser.parse_args()
if __name__ == "__main__":
main()
| smilefreak/ancient_dna_pipeline | python_scripts/merge_reads.py | Python | mit | 303 | [
"pysam"
] | abd1a936a80539efd0af7e8e6b88112a2a43754067717cb239ff460e08abe71b |
import sys
import argparse
import numpy as np
import pysam
import util
import snptable
import tables
import os
def write_results(out_f, chrom_name, snp_tab, ref_matches,
alt_matches, oth_matches, geno_sample):
haps = None
has_haps = False
if geno_sample:
# get index for t... | smozaffari/WASP | mapping/get_as_counts.py | Python | apache-2.0 | 12,826 | [
"pysam"
] | e5eadade305b7e92be3d68617c0c40cf80fb5285cbaa6d88ea12aa898ef7e8ed |
"""
An estimator to model data using a fixed number of multivariate Gaussian
distributions with a single multivariate latent factor, using minimum message
length as the objective function.
"""
__all__ = ["MMLMixtureModel"]
import logging
import numpy as np
import scipy
from sklearn import cluster
from .base import... | andycasey/snob | snob/slf_mixture/mml.py | Python | mit | 9,889 | [
"Gaussian"
] | 74e267ed164de91f26e5549a74182600152b486faa791d4c0e0d7148168fb7ac |
# -*- coding: utf-8 -*-
#
# Lara Schneider
# 2010-05-20
#
# TODO: description
# for use in BALLView
#
import sys
from BALL import *
system = getSystems()[0]
#open a fragment database
print "reading fragment DB..."
db = FragmentDB("")
# and normalize the atom names, i.e. we convert different
# naming standards to t... | tkemmer/ball | doc/examples/PYTHON/BALLView/amberEnergy_BV.py | Python | lgpl-2.1 | 1,508 | [
"Amber"
] | fe285217fbcff3234971a4b8023f544dda162e07dff3b58d005604eb45482a05 |
# mxdatareduction.py
#
# Copyright (C) 2017 Diamond Light Source, Karl Levik
#
# 2017-08-31
#
# Methods to store data from MX processing
#
import copy
import json
import ispyb.interface.processing
from ispyb.strictordereddict import StrictOrderedDict
class MXProcessing(ispyb.interface.processing.IF):
"""MXPr... | DiamondLightSource/ispyb-api | src/ispyb/sp/mxprocessing.py | Python | apache-2.0 | 13,646 | [
"CRYSTAL"
] | 56df3f8d6220dd814b8da462542f6afea02422d16a2da8d1951703836bea4ebc |
# encoding: utf-8
"""
Emcee: seriously kick-ass sampling. Modified by Rutger van Haasteren
full working implementation. Just include as:
"import mcmchammer as emcee"
"""
from __future__ import division
from __future__ import print_function
import numpy as np
import numpy as np
import multiprocessing
t... | vhaasteren/piccard | piccard/mcmchammer.py | Python | gpl-3.0 | 24,477 | [
"Gaussian"
] | 692e0c58459a298e75aae2167c58f80467694dac3f678887a066b60b4e0bb1ef |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module defines the Cp2k output parser along with a few other functions for parsing cp2k-related
outputs.
"""
import glob
import logging
import os
import re
import warnings
import numpy as np
import pandas as pd
from... | materialsproject/pymatgen | pymatgen/io/cp2k/outputs.py | Python | mit | 55,491 | [
"CP2K",
"Gaussian",
"VASP",
"pymatgen"
] | 09f85c38470e47b056972dbdd70535756e265d33c611782d5a104039ddbd6ea4 |
#!/usr/bin/env python
# Copyright 2012 Google Inc. All Rights Reserved.
"""Bigquery Client library for Python."""
import abc
import collections
import datetime
import hashlib
import itertools
import json
import logging
import os
import pkgutil
import random
import re
import string
import sys
import textwrap
import ... | wemanuel/smry | smry/server-auth/ls/google-cloud-sdk/platform/bq/bigquery_client.py | Python | apache-2.0 | 91,406 | [
"VisIt"
] | 9998db8e761360e3fd8e9bebe2297331a87d6fa2c58246a7015155eba7f34422 |
"""van der Waals correction schemes for DFT"""
import numpy as np
from ase.units import Bohr, Hartree
from gpaw.mpi import rank
# dipole polarizabilities and C6 values from
# X. Chu and A. Dalgarno, J. Chem. Phys. 129 (2004) 4083
# atomic units, a_0^3
vdWDB_Chu04jcp = {
# Element: [alpha, C6]; units [Bohr^3, Har... | JConwayAWT/PGSS14CC | lib/python/multimetallics/ase/calculators/vdwcorrection.py | Python | gpl-2.0 | 7,766 | [
"ASE",
"GPAW"
] | c319fa977b2d4e3f06f93b4cb54c77c289a4e0950a1b6fbd29f020c50a95c930 |
"""
Message Queue wrapper
"""
import time
from pythonjsonlogger.jsonlogger import JsonFormatter
from DIRAC.FrameworkSystem.private.standardLogging.Handler.MessageQueueHandler import MessageQueueHandler
from DIRAC.FrameworkSystem.private.standardLogging.LogLevels import LogLevels
from DIRAC.Resources.LogBackends.Abstra... | DIRACGrid/DIRAC | src/DIRAC/Resources/LogBackends/MessageQueueBackend.py | Python | gpl-3.0 | 2,872 | [
"DIRAC"
] | 54a77b8f54cde65382beed42ce2716fab190e611f9022bd8283e46e77eb935a9 |
from numpy import *
from asap3 import *
from ase.lattice.cubic import FaceCenteredCubic
from ase.constraints import Filter
from asap3.testtools import *
atoms = FaceCenteredCubic(size=(5, 5, 5), symbol="Cu")
#p = RasMol(atoms)
ReportTest("Total number of atoms", len(atoms), 500, 0)
ss = Filter(atoms, indices=[2,5,7,... | auag92/n2dm | Asap-3.8.4/Test/Subset.py | Python | mit | 1,680 | [
"ASE",
"RasMol"
] | 4758df97f1daa65d2f878eeaa465e05503533d9153a221cfbb1fc32339958d84 |
from __future__ import division, absolute_import, print_function
import warnings
import numpy as np
from numpy.testing import (
run_module_suite, assert_, assert_raises, assert_equal, assert_warns,
assert_no_warnings, assert_array_equal, assert_array_almost_equal,
suppress_warnings
)
fr... | solarjoe/numpy | numpy/random/tests/test_random.py | Python | bsd-3-clause | 64,352 | [
"Gaussian"
] | 0c8f68e94007ac03a6f56423c6c528318f70887890a16e0f4fc62ca9fa256cb7 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# =============================================================================
## @file ostap/fitting/signals.py
#
# Set of useful PDFs for various ``signal'' 1D and 2D fits
# It includes
# - soeme empricial PDFs to describe narrow peaks: Gauss, CrystalBall, ....
# - s... | OstapHEP/ostap | ostap/fitting/signals.py | Python | bsd-3-clause | 181,711 | [
"CRYSTAL",
"Gaussian"
] | 1806c09c86f2f13531bb31553cc195fd3291d9c3de74875c2baecd2d6324d3ca |
###BAMtoJunctionBED
#Author Nathan Salomonis - nsalomonis@gmail.com
#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... | wuxue/altanalyze | BAMtoJunctionBED.py | Python | apache-2.0 | 12,661 | [
"pysam"
] | 7d94fc8bd772ee1b45810d3864b6236f40db2be19fe0be42454fe9bcfb91990a |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2010 Radim Rehurek <radimrehurek@seznam.cz>
# Licensed under the GNU LGPL v2.1 - http://www.gnu.org/licenses/lgpl.html
"""
Module for Latent Semantic Analysis (aka Latent Semantic Indexing) in Python.
Implements fast truncated SVD (Singular Value Decomp... | duyet-website/api.duyet.net | lib/gensim/models/lsimodel.py | Python | mit | 34,466 | [
"Gaussian"
] | c83e2ae37f49b205b2d7fbc127378c3dab2fbd3b8ff3fb119d5d78a419718f84 |
from __future__ import print_function
import re
from collections import OrderedDict
import clang.cindex
from .constants import (
UNARY_OPERATOR_MAP,
BINARY_OPERATOR_MAP,
OTHER_OPERATOR_MAP,
NOT_DEFAULT_ARG_KINDS,
)
from .abstract import NodeVisitor
from .parser import AstNode
from . import utils
FU... | mugwort-rc/pypp | pypp/generator.py | Python | gpl-3.0 | 23,465 | [
"VisIt"
] | c3302b35e85a3ed1cf2736eff06295256971efca5835032ff3f5654112591328 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundati... | tiagocardosos/stoq | stoqlib/gui/test/test_receivingsearch.py | Python | gpl-2.0 | 4,031 | [
"VisIt"
] | f9ca29bfb93609a75cd13525bc6ec0af5be7d66a0622ffceca0adadbff0b5d1f |
###
# Copyright (c) 2002-2004, Jeremiah Fincher
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright notice,
# this list of co... | tecan/xchat-rt | plugins/scripts/encryption/supybot-code-6361b1e856ebbc8e14d399019e2c53a35f4e0063/plugins/URL/test.py | Python | gpl-2.0 | 4,066 | [
"COLUMBUS"
] | b05dbd63be5c0dd65d33fbb89329d44b1f62a6a99c71e8d173fe09ebaf2fd39b |
#
# Project: MXCuBE
# https://github.com/mxcube
#
# This file is part of MXCuBE software.
#
# MXCuBE is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your... | IvarsKarpics/mxcube | gui/widgets/vertical_crystal_dimension_widget_layout.py | Python | lgpl-3.0 | 7,702 | [
"CRYSTAL"
] | f8aa7436985fb99a0dcd5193f7af7e92a4a4c233f674066aef217b86c317b036 |
from copy import deepcopy
from warnings import warn
from itertools import chain
from ast import NodeTransformer
from six import iteritems
from .. import Reaction
from .delete import get_compiled_gene_reaction_rules
from ..core.Gene import ast2str
from ..io.sbml3 import _renames
def _escape_str_id(id_str):
"""ma... | jerkos/cobrapy | cobra/manipulation/modify.py | Python | lgpl-2.1 | 9,166 | [
"VisIt"
] | 383cc19c0077c32449bcce645dded8fc748de7ff3801d0be2d7c44e302ffde5f |
#!/usr/bin/env python2.7
import os, sys
from numpy import *
##################
### For RESTMD ###
##################
#
# Take walker enthalpies/energies from multiple, identical
# length trajectories, concatenate, and follow exchanges
# to get replica enthalpies/energies. Start and stop are
# file handles for each re... | dstelter92/RESTMD | tools/get-hist-enthalpies.py | Python | gpl-2.0 | 2,915 | [
"LAMMPS"
] | 813a2093ce9185dcc92cdbfcf85b0f9b2135e8562f038207a0f9df77205a9272 |
from django.core.checks import Error
from django.core.checks.translation import (
check_language_settings_consistent, check_setting_language_code,
check_setting_languages, check_setting_languages_bidi,
)
from django.test import SimpleTestCase
class TranslationCheckTests(SimpleTestCase):
def setUp(self):
... | georgemarshall/django | tests/check_framework/test_translation.py | Python | bsd-3-clause | 3,854 | [
"ASE"
] | 372bf8c47e7e74ca69a8a9340abbb17c5c20d18347b4aac7b8f717aafd190bb6 |
# Copyright (c) 2015, Frappe Technologies Pvt. Ltd. and Contributors
# License: GNU General Public License v3. See license.txt
import frappe
from frappe.model import rename_field
from frappe.modules import scrub, get_doctype_module
rename_map = {
"Opportunity": [
["enquiry_details", "items"]
],
"Quotation": [
... | netfirms/erpnext | erpnext/patches/v5_0/rename_table_fieldnames.py | Python | agpl-3.0 | 6,610 | [
"VisIt"
] | 212a81ead13a2c8bfdc1d9324cd0cd16aa32943a36f3f340b0cededa644b10ab |
import functools
import time
import inspect
import collections
import types
import itertools
import more_itertools
from typing import Callable, TypeVar
CallableT = TypeVar("CallableT", bound=Callable[..., object])
def compose(*funcs):
"""
Compose any number of unary functions into a single unary function.... | rembo10/headphones | lib/jaraco/functools.py | Python | gpl-3.0 | 13,494 | [
"CRYSTAL"
] | 3ed1076d766cb60549af08dee06bc93accf9a446e0b2539c8049f6109369af67 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/Openwebif | plugin/controllers/views/web/parentcontrollist.py | Python | gpl-2.0 | 5,579 | [
"VisIt"
] | 396f121d15f3674f90d6b9b0584117dcf89a8e0b328bdb58f1b27b951fc7bd05 |
#!/usr/bin/env python
# Copyright(c)2012-2013 Internet Archive. Software license AGPL version 3.
#
# This file is part of the `surt` python package.
#
# surt is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published by
# the Free Soft... | ysangkok/surt | surt/surt.py | Python | agpl-3.0 | 3,712 | [
"VisIt"
] | 8b04453762abb01865d8015cb0db41b25dd854a550545f8382fd746657bd8430 |
#!/usr/bin/env python
# Copyright (c) Twisted Matrix Laboratories.
# See LICENSE for details.
from __future__ import absolute_import
from django.core.management.base import BaseCommand, CommandError
import sys
import re
from twisted.internet.protocol import DatagramProtocol
from twisted.internet import reactor
impor... | kiwiheretic/logos-v2 | symbolics/management/commands/symbolics_server.py | Python | apache-2.0 | 2,921 | [
"VisIt"
] | f4698bb4a444b01e5f535a39078661988147b350339e2dde61cdccc497a07d5f |
# -*- coding: utf-8 -*-
# Orca
#
# Copyright 2006-2008 Sun Microsystems Inc.
# Copyright 2011 The Orca Team.
#
# 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 ... | ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/brlmon.py | Python | gpl-3.0 | 7,154 | [
"ORCA"
] | 826c5eb6588a3ed8915a54d94524bb3600eb116bd59577f37b9c3d155e81bb86 |
'''
Determine optimum aperture and use Source Extractor to get photometry
'''
import sys
import os
from subprocess import call, Popen, PIPE
import glob
import math
import numpy as np
import Sources
import Quadtree
import createSexConfig
import createSexParam
import findBestAperture
import calcZeropoint
import makeRegi... | SAGES-UCSC/Photometry | Examples/Matched_Catalog.py | Python | mit | 5,724 | [
"Galaxy"
] | 4c7d16013fa5e1dba109bc98e2397acb9a890faf120e238dc9c7cd96acd27eef |
"""Creates a small axes on the side that indicates the position of the
co-ordinate axes and thereby marks the orientation of the scene. It
uses the OrientationMarkerWidget which requires VTK-4.5 and above.
"""
# Author: Prabhu Ramachandran <prabhu_r@users.sf.net>
# Copyright (c) 2005, Prabhu Ramachandran, Enthought, ... | liulion/mayavi | mayavi/modules/orientation_axes.py | Python | bsd-3-clause | 7,978 | [
"Mayavi",
"VTK"
] | b5609121c0bdbfdf360d3c5e6503bd226f0737ebaa08e2cd7d7ea6b1375aa5a0 |
""" CStoJSONSynchronizer
Module that keeps the pilot parameters file synchronized with the information
in the Operations/Pilot section of the CS. If there are additions in the CS,
these are incorporated to the file.
The module uploads to a web server the latest version of the pilot scripts.
"""
from __future__... | yujikato/DIRAC | src/DIRAC/WorkloadManagementSystem/Utilities/PilotCStoJSONSynchronizer.py | Python | gpl-3.0 | 14,410 | [
"DIRAC"
] | b7bfc484520a63cd7c9cfb50f77132a5c568dda42130bee1b55f0d975ef9311d |
#!/usr/bin/env python
__author__ = "Vivek Balasubramanian"
__email__ = "vivek.balasubramanian@rutgers.edu"
__copyright__ = "Copyright 2017, The RADICAL Project at Rutgers"
__license__ = "MIT"
""" Setup script. Used by easy_install and pip. """
import os
import sys
import subprocess
from setuptools imp... | vivek-bala/radical.entk | setup.py | Python | mit | 7,121 | [
"VisIt"
] | 0f49af7726a885137c6f09163a7592746b508055979a9262e57ea1be28415239 |
# Copyright 2016 Jochen Kursawe. See the LICENSE file at the top-level directory
# of this distribution and at https://github.com/kursawe/MCSTracker/blob/master/LICENSE.
"""In this file the main mesh classes 'Mesh', 'Element', and 'Node' are defined.
"""
import numpy as np
import networkx as nx
import itertools
impo... | kursawe/MCSTracker | src/mesh/core.py | Python | bsd-3-clause | 82,782 | [
"VTK"
] | 4bae062b3717069340bc77f6748c331a3ca32e19df0789aa80d264544ccbb8d9 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/dmrgscf/test/test_chemps2_n2.py | Python | apache-2.0 | 1,508 | [
"PySCF"
] | 5e33bedd50b79bddbb62305b3d20659eaaf9d1b30545ca4a047770f073f1404d |
# -*- coding: utf-8 -*-
import unittest
try:
from unittest.mock import MagicMock, patch # Python 3.4 and later
except ImportError:
from mock import MagicMock, patch
from ncclient.transport.ssh import SSHSession
from ncclient.transport import AuthenticationError, SessionCloseError, NetconfBase
import paramiko
f... | earies/ncclient | test/unit/transport/test_ssh.py | Python | apache-2.0 | 15,452 | [
"Firefly"
] | ba2327b31070897adac4a0f0ac6030c31eaefe8977bc63b4b6c6b248a8e862b0 |
#!/usr/bin/env python3
"""galactic_orientation
Uses cumulative distribution functions (CDF) for portions of a galaxy to
determine the orientation of the galaxy.
"""
from sys import stdin
from argparse import ArgumentError, ArgumentParser, FileType
import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as ... | astroswego/cepheid-scripts | python/galactic_orientation.py | Python | mit | 3,345 | [
"Galaxy"
] | fe9642ba639a93fd22e4ccdb9e3d01aa96302c6b6cc5f965d8d08a206c1405ba |
# Copyright (c) 2012, James Hensman
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
from ..core.sparse_gp_mpi import SparseGP_MPI
from .. import likelihoods
from .. import kern
from ..inference.latent_function_inference import VarDTC
from GPy.core.parameterization.variational import Nor... | SheffieldML/GPy | GPy/models/sparse_gp_regression.py | Python | bsd-3-clause | 2,677 | [
"Gaussian"
] | 32e52a37d8007506bdc76f0eefb6226e9cadb4323f97a54116751e9a1c752a92 |
############################################################################
# $HeadURL$
# GE class representing SGE batch system
# 10.11.2014
# Author: A.T.
############################################################################
""" Torque.py is a DIRAC independent class representing Torque batch system.
... | miloszz/DIRAC | Resources/Computing/BatchSystems/GE.py | Python | gpl-3.0 | 7,114 | [
"DIRAC"
] | bd9a5ff85fadef222564921c1b8038ace94bd54975db768150475b35088e36a2 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.