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#!/usr/bin/python
#Copyright (C) 2020- The University of Notre Dame
#This software is distributed under the GNU General Public License.
#See the file COPYING for details.
import os
import sys
import json
from work_queue_server import WorkQueueServer
from time import time
from create_splits import create_splits
tasks... | nkremerh/cctools | apps/wq_bwa_json/wq_bwa_json.py | Python | gpl-2.0 | 2,791 | [
"BWA"
] | a602e3708cf86b43bbf2061a9b272113587c9d701ca8b489bad5b225d904f4d8 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS.
"""
from datetime import datetime, timedelta
from flaky import flaky
from textwrap import dedent
from unittest import skip
from nose.plugins.attrib import attr
import pytz
import urllib
from bok_choy.promise import EmptyPromise
from common.test.acceptance.tests... | louyihua/edx-platform | common/test/acceptance/tests/lms/test_lms.py | Python | agpl-3.0 | 53,429 | [
"VisIt"
] | 0f6f1387cf64ee82428aa61d04f3c9dcf1ddd17f3314f144d16d5200a144ec92 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/bug_1117098 | openlp/plugins/custom/forms/__init__.py | Python | gpl-2.0 | 2,106 | [
"Brian"
] | 45003622b1fbe54a5e2b898389f4fcb7af8443d4f1697a178a78b93dd7920526 |
from fem import DofHandler, Basis, QuadFE
from gmrf import GaussianField, Covariance
from assembler import Form, Assembler
from mesh import Mesh1D, QuadMesh
from plot import Plot
from function import Nodal
import numpy as np
from scipy import sparse as sp
import matplotlib.pyplot as plt
"""
Goal:
Investigate opt... | hvanwyk/quadmesh | experiments/multiscale_gmrf/ex04/ex04.py | Python | mit | 13,614 | [
"Gaussian"
] | f50515a4eec68ce14b0c58fce2d1e42a69745d7629792e47fe9d03a70d9a6a21 |
"""The Mayavi Envisage application.
"""
# Author: Prabhu Ramachandran <prabhu_r@users.sf.net>
# Copyright (c) 2008, Enthought, Inc.
# License: BSD Style.
# Standard library imports.
import sys
import os.path
import logging
# Enthought library imports.
from apptools.logger.api import LogFileHandler, FORMATTER
from tra... | liulion/mayavi | mayavi/plugins/app.py | Python | bsd-3-clause | 8,773 | [
"Mayavi"
] | 86f2e98412d6f51150a089df7d836302512bbcd82e2381a1411bff3166ceb794 |
""" Diffusion 2: jump diffusion, stochastic volatility, stochastic time
Created on Tue Dec 08 15:03:49 2009
Author: josef-pktd following Meucci
License: BSD
contains:
CIRSubordinatedBrownian
Heston
IG
JumpDiffusionKou
JumpDiffusionMerton
NIG
VG
References
----------
Attilio Meucci, Review of Discrete and Contin... | bashtage/statsmodels | statsmodels/sandbox/tsa/diffusion2.py | Python | bsd-3-clause | 13,371 | [
"Gaussian"
] | f1a9643fd7c409ad17ae3ccaff9019fdb69e1d70f75701bf316dfa08a996038d |
#!/usr/bin/env python
########################################################################
# File : dirac-dms-pfn-accessURL
# Author : Stuart Paterson
########################################################################
"""
Retrieve an access URL for a PFN given a valid DIRAC SE
"""
import DIRAC
from DIRAC.... | ic-hep/DIRAC | src/DIRAC/Interfaces/scripts/dirac_dms_pfn_accessURL.py | Python | gpl-3.0 | 1,287 | [
"DIRAC"
] | 66d6ea27258fd8b06077e8416ab42f312e501729338136ed35f7c1aef066895f |
""" Failover Transfer
The failover transfer client exposes the following methods:
- transferAndRegisterFile()
- transferAndRegisterFileFailover()
Initially these methods were developed inside workflow modules but
have evolved to a generic 'transfer file with failover' client.
The transferAndR... | fstagni/DIRAC | DataManagementSystem/Client/FailoverTransfer.py | Python | gpl-3.0 | 11,111 | [
"DIRAC"
] | dcd50d74113edc25d59505947aa8d1a8be28ef959e37b7f59e773ec0a581dba6 |
# This file is part of PyEMMA.
#
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
#
# PyEMMA 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 versi... | gph82/PyEMMA | pyemma/coordinates/tests/test_fragmented_trajectory.py | Python | lgpl-3.0 | 8,281 | [
"MDTraj"
] | 6ca4717746f958cff6106b9acd9c65bb61305b3603921320cc96d8c9f209e184 |
#
# Copyright (c) 2017 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yashdsaraf/scancode-toolkit | src/licensedcode/match.py | Python | apache-2.0 | 52,884 | [
"VisIt"
] | 30848972af59b1764bfee9d8f79d9d5437f5779e15808078ef25dfbf61cdab51 |
# Copyright (C) 2010 CAMd
# Please see the accompanying LICENSE file for further information.
"""This module provides all the classes and functions associated with the
evaluation of exact exchange with k-point sampling."""
from math import pi, sqrt
import sys
import numpy as np
from ase import Atoms
from ase.units i... | ajylee/gpaw-rtxs | gpaw/xc/hybridq.py | Python | gpl-3.0 | 16,477 | [
"ASE",
"GPAW"
] | 34fa95107507bc33c75c1e84b5128a57b6ee2209fbcbfa6ff1aea831a7022629 |
# -*- coding: utf-8
from yade import ymport, utils,pack,export,qt
import gts,os
from yade import geom
#import matplotlib
from yade import plot
#from pylab import *
#import os.path, locale
#################################
##### FUNCTIONS ####
#################################
def limitfinder():
for ... | anna-effeindzourou/trunk | examples/anna_scripts/triax/triaxial_test.py | Python | gpl-2.0 | 13,308 | [
"ParaView"
] | 826687be038b8a1d9aefd663623a65242fc2a61c8de30bf8417c01c51d865c71 |
""" Plotting Service generates graphs according to the client specifications
and data
"""
__RCSID__ = "$Id$"
import os
import hashlib
from types import DictType, ListType
from DIRAC import S_OK, S_ERROR, rootPath, gConfig, gLogger, gMonitor
from DIRAC.ConfigurationSystem.Client import PathFinder
from DIRAC.Core.... | coberger/DIRAC | FrameworkSystem/Service/PlottingHandler.py | Python | gpl-3.0 | 2,415 | [
"DIRAC"
] | 3faf0de094668bfcaf6df8bfde47a069c63e556b1e0ab9b05a585516e880eb06 |
"""Read and write notebooks in JSON format.
Authors:
* Brian Granger
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2008-2011 The IPython Development Team
#
# Distributed under the terms of the BSD License. The full license is in
# the file COPYING, distribute... | mattvonrocketstein/smash | smashlib/ipy3x/nbformat/v1/nbjson.py | Python | mit | 1,503 | [
"Brian"
] | b300ab603aaba5e8087e1cd024f75b6aaee430c8258b77122180451da529993d |
# -*- coding: utf-8 -*-
#
# DAX documentation build configuration file, created by
# sphinx-quickstart on Tue Jan 12 14:43:53 2016.
#
# 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
# autogenerated file.
#
# All c... | VUIIS/dax_spiders | docs/conf.py | Python | mit | 9,546 | [
"Brian"
] | 3deb0d71736dc963349606d769281dadee69dfb3c950331f400a09b74a9b9ecd |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
class Migration(migrations.Migration):
dependencies = [
('api', '0128_auto_20160419_1708'),
]
operations = [
migrations.AlterField(
model_name='usicalvote',
n... | dburr/SchoolIdolAPI | api/migrations/0129_auto_20160511_1442.py | Python | apache-2.0 | 956 | [
"CRYSTAL"
] | c951415ab309cfa3bce7f896125b5817f7e384bf6b8fcffa9ae9d769ca594b1a |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright 2013 The Plaso Project Authors.
# Please see the AUTHORS file for details on individual authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the L... | iwm911/plaso | plaso/parsers/cookie_plugins/ganalytics.py | Python | apache-2.0 | 5,883 | [
"VisIt"
] | dbf23d6d150ca01a405f8a265c2cf69a7ec4ed7856406dd84e7fb8226a306b3c |
# -*- coding: utf-8 -*-
"""
Created on Sat Dec 10 16:26:15 2016
@author: Rachid & Chaima
"""
import numpy as np
import matplotlib.pyplot as plt
from scipy import ndimage, misc
import image
import utils
import pdb
#
#def div0( a, b ):
# """ ignore / 0, div0( [-1, 0, 1], 0 ) -> [0, 0, 0] """
# with np.errstate(d... | Rachine/ExposureFusion | laplacianfusion.py | Python | mit | 4,883 | [
"Gaussian"
] | 05dc594411b1cdabd2399638caac38a57de0d11d6b55029bbe4bf8efb5867083 |
import os
import datetime
import numpy as np
import xarray as xr
import requests
import logging
log=logging.getLogger('noaa_coops')
from ... import utils
from .common import periods
all_products=dict(
water_level="water_level",
air_temperature="air_temperature",
water_temperature="water_temperature",
... | rustychris/stompy | stompy/io/local/noaa_coops.py | Python | mit | 11,330 | [
"NetCDF"
] | e8f929cef0ba04738270749b2b1d10389c9d057ef3e6e7c2570a57d4732c761b |
#!/usr/bin/python
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute... | susilehtola/psi4 | doc/sphinxman/document_cfour.py | Python | lgpl-3.0 | 2,632 | [
"CFOUR",
"Psi4"
] | 07c4fb85a15fc8cb43ea62b6aab88b353af162ae95511a72ebe37a72021838c9 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# read data
#
reader = vtk.vtkGene... | collects/VTK | IO/EnSight/Testing/Python/EnSight6OfficeBin.py | Python | bsd-3-clause | 2,072 | [
"VTK"
] | 81a0d2ce603bc3006bdb439847e1c094011f2f69910c5dfdb4941a4985c3dc21 |
import unittest, time, sys, random
sys.path.extend(['.','..','../..','py'])
import h2o2 as h2o
import h2o_cmd, h2o_import as h2i, h2o_jobs, h2o_glm
from h2o_test import verboseprint, dump_json, OutputObj
from tabulate import tabulate
class Basic(unittest.TestCase):
def tearDown(self):
h2o.check_sandbox_fo... | bikash/h2o-dev | py2/testdir_single_jvm/test_GLM_basic_1.py | Python | apache-2.0 | 4,180 | [
"Gaussian"
] | 4a80d6d6e8dc3a0dd2de4030a1a5cecbd6d5f2076d0f3535882dd445ebaf1228 |
import logging
from django.contrib.auth.decorators import login_required
from django.shortcuts import render
from django.http import HttpResponseRedirect
from core.utils import get_context
from .utils import BLASTNew
from .forms import BLASTNewForm
log = logging.getLogger(__name__)
@login_required
def index(reque... | carlosp420/VoSeq | blast_new/views.py | Python | bsd-3-clause | 1,590 | [
"BLAST"
] | 6868e3b58d08cec3b69841210dcc4d723377271a89ef3f0e187bdf611551d33c |
from distutils.core import setup
setup(
name='ss2csv',
version='0.0.1',
author='Brian Downs',
author_email='brian.downs@gmail.com',
maintainer='Brian Downs',
maintainer_email='brian.downs@gmail.com',
scripts=['ss2csv.py'],
packages=['ss2csv'],
package_data={
'': ['*.txt'],
... | briandowns/ss2csv | setup.py | Python | apache-2.0 | 513 | [
"Brian"
] | 6d5ef635e04afced635a95b88ffa7c2742fe1691bc7eea681958e7a80a6ecda8 |
import pickle
import numpy as np
from numpy.testing import assert_array_almost_equal
from sklearn.neighbors.ball_tree import (BallTree, NeighborsHeap,
simultaneous_sort, kernel_norm,
nodeheap_sort, DTYPE, ITYPE)
from sklearn.neighbors.dis... | theoryno3/scikit-learn | sklearn/neighbors/tests/test_ball_tree.py | Python | bsd-3-clause | 10,258 | [
"Gaussian"
] | f0573e79ab0489180937032f5ebdc21739f228a07e7f0c8f67a60cf39e88e23e |
#!/usr/bin/env python
# Copyright 2014-2020 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/dft/gen_grid.py | Python | apache-2.0 | 23,326 | [
"NWChem",
"PySCF"
] | 5ebe08aa099445f23040f371db4cd7b76603d5565f8037ad674645623c656232 |
"""
String multi-replace for all appropriate files in directory
Requires manual use
"""
import os, sys
directory = "../src/org/mhag/model/data/mh3g/"
pretend = False # If True, don't actually write
# IMPORTANT - removes all temporary files created by bakaneko tools,
# to prevent cross contamination
directory = ".... | PrincessTeruko/MHAGr | tools_(bakaneko)/dir_replace.py | Python | gpl-3.0 | 4,136 | [
"BLAST"
] | 00a473981eba7c502d3917556a61b5f2708ab4c4ed8d14809289ed71abcc5a51 |
#!/usr/bin/env python3
# -*- coding=utf-8 -*-
"""
cry2cif\n\n
Read the last geometry corresponding to the CRYSTALLOGRAPHIC CELL on a
CRYSTAL09 output file and print it in a cif format. If geometry
optimization did not converge, input geometry is printed instead.
"""
# TODO:
# * returns coordinates instead of write ... | gVallverdu/myScripts | CRYSTAL/cry2cif_old.py | Python | gpl-2.0 | 16,643 | [
"CRYSTAL",
"VASP"
] | 7cc338cb136a0317a5dec2f23dc03ed6650e04b16f4c255133ae2113d3a05175 |
from __future__ import print_function
#!/usr/bin/env python
'''
isotropy
http://stokes.byu.edu/isolinux.html
http://stokes.byu.edu/iso.tar.gz
You will need to create a directory to unzip the above tarfile in,
cd
mkdir iso
cd iso
wget http://stokes.byu.edu/iso.tar.gz
tar xvzf iso.tar.gz
#put this in your .cshrc
se... | suttond/MODOI | ase/calculators/jacapo/utils/findsym.py | Python | lgpl-3.0 | 3,108 | [
"ASE"
] | 296fb2a20d135476881ef543f11e48d3036a80c670761f5efb006874d482feca |
#!python
# coding=utf-8
import os
from datetime import datetime
from .utils import all_subclasses
from .dataset import EnhancedDataset
from . import logger
class CFDataset(EnhancedDataset):
default_fill_value = -9999.9
default_time_unit = 'seconds since 1990-01-01 00:00:00'
@classmethod
def load(cl... | joefutrelle/pocean-core | pocean/cf.py | Python | mit | 5,636 | [
"NetCDF"
] | bf1a443a758764001a70bbea31356b66db3ded5179fc91355e3755416159ee82 |
# Set up a basic scene for rendering.
from paraview.simple import *
import sys
script = """
import numpy
import paraview.numpy_support
def setup_data(view):
# Don't actually need any data
pass
def render(view, width, height):
cb = numpy.zeros((height, width, 4), dtype=numpy.uint8)
for i in xrange(width):
... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/Applications/ParaView/Testing/Python/TestPythonViewNumpyScript.py | Python | gpl-3.0 | 974 | [
"ParaView",
"VTK"
] | 80a99973b3115222caf69ea3d2697b548d0fad6415ad5c3016a7b7edf3bae883 |
# coding=utf-8
"""**Utilities for storage module**
"""
import os
import re
import copy
import numpy
import math
from ast import literal_eval
from osgeo import ogr
from collections import OrderedDict
from geometry import Polygon
from safe.gis.numerics import ensure_numeric
from safe.common.utilities import verify
from... | wonder-sk/inasafe | safe/storage/utilities.py | Python | gpl-3.0 | 37,736 | [
"NetCDF"
] | 219aa9f2cf2881972a39e44850fba949ac5edfde5cf6648dd0439fb2318c7a6d |
###########################################################################
# (C) Vrije Universiteit, Amsterdam (the Netherlands) #
# #
# This file is part of AmCAT - The Amsterdam Content Analysis Toolkit #
# ... | amcat/amcat | amcat/tools/amcattest.py | Python | agpl-3.0 | 15,168 | [
"VisIt"
] | acf02bfd812025fac44cebdce04a8a265e7c4b407b6537469693ce746737a9ff |
#!/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/scf/test/test_diis.py | Python | apache-2.0 | 3,064 | [
"PySCF"
] | cbb99000ca02f759127576fb396115d8a4cd9f625c1a82f050ccac521c49e4e0 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2017 Lenovo, Inc.
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# ... | dmitry-sobolev/ansible | lib/ansible/modules/network/lenovo/cnos_interface.py | Python | gpl-3.0 | 27,026 | [
"VisIt"
] | c0456ef3e1a944c51ae96133c08b62cc64e30eb5d324bfa7058782241e2054cd |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | andreaso/ansible | lib/ansible/modules/network/avi/avi_cloud.py | Python | gpl-3.0 | 9,205 | [
"VisIt"
] | 184def41458fd123e358112153a741e0ab9f23cf972ad6f3b4b0060f53ea6200 |
# Authors: Nicolas Goix <nicolas.goix@telecom-paristech.fr>
# Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# License: BSD 3 clause
import numbers
import numpy as np
from scipy.sparse import issparse
from warnings import warn
from ..tree import ExtraTreeRegressor
from ..utils import (
chec... | xuewei4d/scikit-learn | sklearn/ensemble/_iforest.py | Python | bsd-3-clause | 18,579 | [
"Gaussian"
] | 35f9a977d0bb84873c32ac480413f0de89f209e279736706be91e5cf67625394 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
class Migration(migrations.Migration):
dependencies = [
('visit', '0018_auto_20150505_0322'),
]
operations = [
migrations.AlterField(
model_name='staff',
name... | koebbe/homeworks | visit/migrations/0019_auto_20150505_0324.py | Python | mit | 413 | [
"VisIt"
] | 693dfdf15cddc102ae1d9b9648a36c718d4eb56feb8efb2e1169adcee8cfb496 |
# This file is part of PyEMMA.
#
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
#
# PyEMMA 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 vers... | gph82/PyEMMA | pyemma/coordinates/tests/test_cluster.py | Python | lgpl-3.0 | 5,596 | [
"Gaussian"
] | dab7011098c9cbce75143b4ec43bbb2cc515a25d7de9cd5888d10eae56b855f0 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements a core class LammpsData for generating/parsing
LAMMPS data file, and other bridging classes to build LammpsData from
molecules. This module also implements a subclass CombinedData for
merging LammpsD... | materialsproject/pymatgen | pymatgen/io/lammps/data.py | Python | mit | 60,452 | [
"LAMMPS",
"pymatgen"
] | 968cb54512883f047a11560a867ee8de46e255a74c8a40e928428c2b3850795d |
# Copyright 2015-2016 The James Hutton Institute
# Author: Leighton Pritchard
#
# blast.py
#
# This code is part of the pyrbbh package, and is governed by its licence.
# Please see the LICENSE file that should have been included as part of this
# package.
"""Module to produce BLAST command-line jobs for RBH analysis.... | widdowquinn/pyrbbh | pyrbbh/blast.py | Python | mit | 7,943 | [
"BLAST"
] | 4d40b5e552073283053af7038e15b94f658de80d44677e9fcd05e763d9670333 |
# -*- test-case-name: buildbot.test.test_web -*-
from zope.interface import implements
from twisted.python import log, components
import urllib
import time, locale
import operator
from buildbot import interfaces, util
from buildbot.status import builder
from buildbot.status.web.base import Box, HtmlResource, IBox, ... | centrumholdings/buildbot | buildbot/status/web/waterfall.py | Python | gpl-2.0 | 29,662 | [
"VisIt"
] | 6581e2c147db1e55f1e4954a1b0421b98cbaf3522756ca703ee7e9451213b407 |
from cloudbio.galaxy.tools import _install_application
def install_tool(options):
version = options.get("galaxy_tool_version")
name = options.get("galaxy_tool_name")
install_dir = options.get("galaxy_tool_dir", None)
_install_application(name, version, tool_install_dir=install_dir)
configure_actions... | heuermh/cloudbiolinux | cloudbio/deploy/plugins/galaxy.py | Python | mit | 368 | [
"Galaxy"
] | ae9a0ac69a2f6a7f84838c342d40e7453ad6812f92708b8e7bf70a0c284a5a71 |
"""
Records who we trust to sign feeds.
Trust is divided up into domains, so that it is possible to trust a key
in some cases and not others.
@var trust_db: Singleton trust database instance.
"""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall i... | timdiels/0install | zeroinstall/injector/trust.py | Python | lgpl-2.1 | 8,547 | [
"VisIt"
] | b964cf3b94b0f311ffc499b1c731ab9facb0e972e00caf8bcc6b0bf3ad81bbc5 |
# ----------------------------------------------------------------------------
# cocos2d
# Copyright (c) 2008-2012 Daniel Moisset, Ricardo Quesada, Rayentray Tappa,
# Lucio Torre
# Copyright (c) 2009-2014 Richard Jones, Claudio Canepa
# All rights reserved.
#
# Redistribution and use in source and binary forms, with o... | google-code-export/los-cocos | cocos/batch.py | Python | bsd-3-clause | 4,493 | [
"VisIt"
] | a03b01e2b9b59574cd9edb9c27ca16eccc76fc66ef0a435c8d410b9a1f76a05f |
"""
Definition of the direction class
"""
import os
import logging
from astropy.coordinates import Angle
import numpy as np
import lsmtool
from lsmtool.operations_lib import radec2xy
import matplotlib.path as mplPath
from scipy.ndimage import gaussian_filter
from scipy.special import erf
import sys
import glob
class ... | revoltek/factor | factor/lib/direction.py | Python | gpl-2.0 | 54,010 | [
"Gaussian"
] | d30c90e2b07a781739a66560680ca8621b40b5dd4321be3fe0e585a380284271 |
#!/usr/bin/env python -i
# preceding line should have path for Python on your machine
# vizplotgui_vmd.py
# Purpose: viz running LAMMPS simulation via VMD with plot and GUI
# Syntax: vizplotgui_vmd.py in.lammps Nfreq compute-ID
# in.lammps = LAMMPS input script
# Nfreq = plot data point and viz shap... | akohlmey/lammps | python/examples/vizplotgui_vmd.py | Python | gpl-2.0 | 4,114 | [
"LAMMPS",
"VMD"
] | db8e103443a5bd804975c6c0c5269f6fc908ab8163644162285b627a991afd0a |
from __future__ import division, print_function
# Multicut Pipeline implemented with luigi
# Blockwise solver tasks
import luigi
from .pipelineParameter import PipelineParameter
from .dataTasks import ExternalSegmentation
from .customTargets import HDF5DataTarget
from .multicutProblemTasks import MulticutProblem
fro... | constantinpape/mc_luigi | mc_luigi/blockwiseMulticutTasks.py | Python | mit | 28,304 | [
"VisIt"
] | cd764d442511f063e1340667daf813c97ac8cec86aa47beb72d463fbece64c04 |
# This module implements classes for peptide chains and proteins.
#
# Written by Konrad Hinsen
# last revision: 2001-4-2
#
import Biopolymers, Bonds, ChemicalObjects, Collection, ConfigIO, Database
import Units, Universe, Utility
from Scientific.Geometry import Vector
import operator, string, umath
from Biopolymers i... | fxia22/ASM_xf | PythonD/site_python/MMTK/Proteins.py | Python | gpl-2.0 | 24,134 | [
"CHARMM"
] | d5b0e406e070974e9c911ca40f56fdcbfb2a3d8f9ac6c5e606f9c6b8a775ea3c |
#!/usr/bin/env Python
##########################################################################
#
# Copyright (C) 2015-2016 Sam Westreich
#
# 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;
#
# T... | transcript/samsa_v2 | python_scripts/DIAMOND_subsystems_analysis_counter.py | Python | gpl-3.0 | 6,159 | [
"BLAST"
] | 77a5cb808ee37c2b026b964ca3883e157b2b3783aa94daca028ddd7e8a4358ec |
class User(object):
def __init__(self):
pass
def schema():
_schema = {
"title" : "User",
"type" : "object",
"properties" : {
"id" : {"type": "string"},
"apikey" : {
"description" : "User apikey for webservic... | materials-commons/materialscommons-clients | python/materialscommons/dm.py | Python | gpl-2.0 | 25,238 | [
"VASP"
] | 798bf5d3760a623603e5ad0a799bec21ed2c1395fb85cb422f466d44069c1bc0 |
#!/bin/env python3
import sys
import argparse
import math
import re
import traceback
from directives import DirectiveProcessor, D_Pragma
from tokens import Tokenizer
from renderers import *
from sdscp_errors import *
import statements
import getpass
VERSION = '1.5.0'
# ==================== Command Line Arguments pr... | naro/sdscp | sdscp.py | Python | gpl-2.0 | 7,989 | [
"VisIt"
] | 77857521bc1548a979afadf757f3c28c9a97525eb57373fab1d7d8f32f2e2f7a |
# $Id$
#
# Copyright (c) 2010, Novartis Institutes for BioMedical Research Inc.
# 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... | jandom/rdkit | rdkit/Chem/FunctionalGroups.py | Python | bsd-3-clause | 5,073 | [
"RDKit"
] | 06d2d98598fc35bbe02e3787eae51764430f61c33eb431840ac99b8e1cc864a4 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
def to_string(x):
if x.__class__.__name__ == 'bytes':
return x.decode('utf-8')
return x
import unittest, regex, os
from __init__ import oprex, OprexSyntaxError
class TestErrorHandling(unittest.TestCase):
def given(self, oprex_sourc... | rooney/oprex | tests.py | Python | lgpl-3.0 | 249,199 | [
"ESPResSo"
] | 7109831d33cf9aa7ad59454a62135a391d69fd433656939318dd9bbd503b86bb |
# Read in soil temperature data (assumes this is always there)
# ref: http://bigladdersoftware.com/epx/docs/8-2/auxiliary-programs/epw-csv-format-inout.html
soilData = self.header[3]
self.nSoil = int(soilData[1]) # Number of ground temperature depths
self.Tsoil = utilities.zeros(self.nSoil,12) # nSoil x 1... | saeranv/UWG_Python | UWG/roadscratch.py | Python | gpl-3.0 | 2,019 | [
"EPW"
] | df7ff9dbc2df9cb0559f29fe88a2aa57e11083d6ffc3390f1f6f3f97eea2e1c7 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | tmerrick1/spack | var/spack/repos/builtin/packages/mirdeep2/package.py | Python | lgpl-2.1 | 2,851 | [
"Bowtie"
] | 65563f24aa7c3c94eeee6b7b79e020ce70043b959d2920157566eab2e48a7ab4 |
import individual
import copy
import numpy as np
class Simulated_Annealing(object):
''''
Simulated Annealing
It is a probabilistic technique for approximating the global optimum of a given function.
Specifically, it is a metaheuristic to approximate global optimization in a large
s... | Alfo5123/PolyPic | docs/sim_annealing.py | Python | mit | 3,207 | [
"VisIt"
] | a01a196f77f06895dd695b3bb46937e6a78ecddc28aeb0798c2142f1f004f451 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011 Paul Franklin
#
# This program is free software; you can redistribute it and/or modify
# it under the terms o... | jralls/gramps | gramps/plugins/tool/verify.py | Python | gpl-2.0 | 69,208 | [
"Brian"
] | 73a7eece57660ca472b908368baf9261c3e527fa993df6d602724e2251176995 |
#!/usr/bin/env python
'''
useage: LCSiellipse.py fileprefix
run from OffCenter subdirectory
the program:
- grabs all files with CLUSTER*.fits
- makes sure that masked image mCLUSTER*.fits exists
- will run imedit if mask is not found
- runs ellipse interactively
- saves result in ../Final subdirectory
'''
i... | rfinn/LCS | paper1code/LCSiellipse.py | Python | gpl-3.0 | 12,042 | [
"Galaxy"
] | b914c510074cdc9c7ff276c95ebbd17b2cdad4ce40652b60e5a7fba8313b71ec |
__author__ = 'Luqman'
import cv2
import numpy as np
import PostProcessing
from BackgroundSubtraction import BackgroundSubtraction
from BackgroundSubtraction import BackgroundSubtractionColor
"""
Author: Luqman A. M.
BackgroundSubtractionImpl.py
Background Subtraction Algorithms Implementation for Object Detection in ... | umanium/trafficmon | BackgroundSubtractionImpl.py | Python | mit | 14,858 | [
"Gaussian"
] | b0787f99dd0b1047048f7fc489e2f9d141e451239fc73628e08397fe7acf810c |
# Copyright 2013 Nebula 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... | openstack/python-openstackclient | openstackclient/tests/unit/identity/v3/fakes.py | Python | apache-2.0 | 34,955 | [
"exciting"
] | bb1739d63252aebd3c97b733af499b5e6641fd024e6fc8cd2964da5aac4baf22 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | govarguz/espressopp | src/standard_system/__init__.py | Python | gpl-3.0 | 1,125 | [
"ESPResSo"
] | 729318ddb15bb17cbdf13188bdefb0b9aa2f99fabf688ea507f860c0e329115a |
# coding=utf-8
# Copyright 2020 The TF-Agents Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable la... | tensorflow/agents | tf_agents/policies/samplers/cem_actions_sampler_continuous_and_one_hot.py | Python | apache-2.0 | 21,624 | [
"Gaussian"
] | 5743f3d0ccb1d2b8356c1e30373418857f7ff85a811860f01b41cfbc9deef5d1 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import datetime
import os
from django.contrib.auth.models import Permission
from django.conf import settings
from django.core import mail
from django.core.cache import cache
from django.core.urlresolvers import reverse
from django.core.exceptions import V... | skolsuper/pybbm | pybb/tests.py | Python | bsd-2-clause | 104,993 | [
"VisIt"
] | 0e47a1977f2734e2270c506975dbad3dfc0693addafc0c5fc7a4dfb6cf27610a |
#!/usr/bin/env python
"""moose_sim.py:
A cable with 1000 compartments with HH-type channels in it.
Last modified: Wed May 21, 2014 09:51AM
"""
__author__ = "Dilawar Singh"
__copyright__ = "Copyright 2013, NCBS Bangalore"
__credits__ = ["NCBS Bangalore", "Bhalla Lab"]
__license__... | subhacom/moose-core | tests/python/Rallpacks/moose_vs_neuron/rallpack3/moose_sim.py | Python | gpl-3.0 | 10,110 | [
"MOOSE"
] | 452f996e5620911943fd76be51787de935832379cce55bd44ad697831ba67648 |
#!/usr/bin/env python
'''
Quantile regression model
Model parameters are estimated using iterated reweighted least squares. The
asymptotic covariance matrix estimated using kernel density estimation.
Author: Vincent Arel-Bundock
License: BSD-3
Created: 2013-03-19
The original IRLS function was written for Matlab by... | statsmodels/statsmodels | statsmodels/regression/quantile_regression.py | Python | bsd-3-clause | 14,115 | [
"Gaussian"
] | 9c442d418bad7f23de3d12a4c89022519d0f34b3a4790b974245001382cb11f3 |
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
from edi.content import views as content_views
urlpatterns = [
url(... | CT-Data-Collaborative/edi-v2 | config/urls.py | Python | mit | 1,773 | [
"VisIt"
] | e7aef10c0419f3e5012c0dd0bd41a94217aadaa699b296a1ac62b226b90e7a26 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes to define everything related to band structures.
"""
import numpy as np
import re
import math
import itertools
import collections
import warnings
from monty.json import MSONab... | tschaume/pymatgen | pymatgen/electronic_structure/bandstructure.py | Python | mit | 52,834 | [
"CRYSTAL",
"pymatgen"
] | 5d7a60652d48de0ea98da5c234d48d3ad817485a0b1281fe078a28a2ebe4d4c8 |
from __future__ import print_function
import os
import pytest
from os.path import join
import sys
import unittest
import subprocess
if sys.platform == "win32":
GULP = "gulp.cmd"
else:
GULP = "gulp"
@pytest.mark.js
class TestBokehJS(unittest.TestCase):
def test_bokehjs(self):
os.chdir('bokehjs')
... | phobson/bokeh | tests/test_bokehjs.py | Python | bsd-3-clause | 669 | [
"GULP"
] | 24efdbe3655256c8a0ff721edf0471a73f2ce3863ea0a8985fd065dfa164eca7 |
#
# @file TestXMLNode.py
# @brief XMLNode unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Michael Hucka <mhucka@caltech.edu>
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatically by converting th... | TheCoSMoCompany/biopredyn | Prototype/src/libsbml-5.10.0/src/bindings/python/test/xml/TestXMLNode.py | Python | bsd-3-clause | 44,331 | [
"VisIt"
] | d97be3e2bf2005fb33985443bc0968020788ebe0c74bbbdaa2ce101b8ff4ae3b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# beads.py
"""
Calculate bead densities.
Copyright (c) 2016, David Hoffman
"""
import click
from scipy.constants import Avogadro, pi
def good_N(ci, M, Nf=5e10):
"""
This function is for converting a dye solution into desired number of particles.
Paramet... | david-hoffman/scripts | beads.py | Python | apache-2.0 | 3,050 | [
"Avogadro"
] | e6b91df1c90389406ad9ac16aaf5b9dcad95c961d9119d5440f9c8774a295e94 |
# for LEGO Movie Module
LEGO_QUOTES = [
"He is coming... cover your butt.",
"You've hidden the Kragle well old man. Robots! Destroy him.",
"Your robots are no match for a Master Builder, for I see everything!",
"Ahh Haa Haa! Now my evil power will be unlimited. Can you feel me?!",
"One day a talent... | idooo/pancake-hipchat-bot | plugins/lego/lego_quotes.py | Python | mit | 14,822 | [
"Galaxy"
] | 661e12a64729f13bea3539320de55650d376c32e0a65fcfbfbca280d530727f1 |
# coding: utf-8
# Copyright (c) Materials Virtual Lab.
# Distributed under the terms of the BSD License.
"""
Implementation for `pmg query` CLI.
"""
from pymatgen.ext.matproj import MPRester
import json
from monty.serialization import dumpfn
import re
from tabulate import tabulate
def do_query(args):
"""
P... | gVallverdu/pymatgen | pymatgen/cli/pmg_query.py | Python | mit | 1,959 | [
"pymatgen"
] | 563e0fe941749d0e5057fce910ec24b04f3040996177b3114df7eaea532976e7 |
"""
A python wrapper for SkyNet neural network that
can de downloaded here :
http://ccpforge.cse.rl.ac.uk/gf/project/skynet/
SkyNet is an efficient and robust neural network
training code for machine learning. It is able to
train large and deep feed-forward neural networks,
including autoencoders, for use in a wide ra... | cbonnett/SkyNet_wrapper | src/SkyNet.py | Python | gpl-3.0 | 28,963 | [
"exciting"
] | b55ac763ec9d3ee498d51c6209b2adbaec9937965c909403b9c3131baa6d1a5f |
#!/usr/bin/env python
"""
LAMMPS Replica Exchange Molecular Dynamics (REMD) trajectories are arranged by
replica, i.e., each trajectory is a continuous replica that records all the
ups and downs in temperature. However, often the requirement is trajectories
that are continuous in temperature, which is achieved by this... | Pakketeretet2/lammps | tools/replica/reorder_remd_traj.py | Python | gpl-2.0 | 20,165 | [
"LAMMPS"
] | 3de368d200a0a239160d86c0bf94d117e3bd860a66764523c2435d6f7ee4efcb |
# -*- coding: utf-8 -*-
import subprocess
import random
from splinter import Browser
from splinter import exceptions
import time
import threading
from selenium.common.exceptions import ElementNotVisibleException
from splinter.exceptions import ElementDoesNotExist
from urllib2 import URLError
import string
import const... | mmulazzani/alibiFramework | simulator/scheduler/surfThread.py | Python | gpl-3.0 | 17,461 | [
"VisIt"
] | 1a6998dd2125b192a35f7ed778c114d0a758f626bfd47de438bd51d11a439a04 |
# Copyright 2001 by Gavin E. Crooks. 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.
# Gavin E. Crooks 2001-10-10
"""ASTRAL RAF (Rapid Access Format) Sequence Maps.
The ASTRAL... | bryback/quickseq | genescript/Bio/SCOP/Raf.py | Python | mit | 10,101 | [
"Biopython"
] | fd30570ba9e120927286b8c5c1dafc93a02a2af4587c7a4324ceed9b5f49d314 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | lib/spack/spack/test/url_parse.py | Python | lgpl-2.1 | 20,084 | [
"BLAST",
"Gromacs",
"HOOMD-blue",
"Jmol",
"Octopus",
"VisIt"
] | 42d280b6d11bfff6f557db4c21a95259aeadb28b9291284cc4d8b7edd6cb6cfa |
import os
import sys
from math import sin, cos, radians, atan2, degrees
import numpy as np
from ase.parallel import world
class DevNull:
def write(self, string):
pass
def flush(self):
pass
def seek(self, offset, whence=0):
return 0
def tell(self):
return 0
def... | conwayje/ase-python | ase/utils/__init__.py | Python | gpl-2.0 | 5,632 | [
"ASE"
] | e0dc82394e2fb516d99438be6439538e92abd4225541d2194eb9b0409adfc11c |
"""
Extended math utilities.
"""
# Authors: Gael Varoquaux
# Alexandre Gramfort
# Alexandre T. Passos
# Olivier Grisel
# Lars Buitinck
# Stefan van der Walt
# Kyle Kastner
# Giorgio Patrini
# License: BSD 3 clause
from __future__ import division
from funct... | Djabbz/scikit-learn | sklearn/utils/extmath.py | Python | bsd-3-clause | 23,268 | [
"Gaussian"
] | 42ac3b70321f1c83a314ebe7ac7171d60dac3f2758db60fc3034bba7bf11f298 |
# -*- coding: utf-8 -*-
# Copyright 2007-2016 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at... | sem-geologist/hyperspy | hyperspy/io.py | Python | gpl-3.0 | 23,941 | [
"NetCDF"
] | 941b412166dd548329f08505badc908e803591148b83a9b7b7e14bd2a83b9aab |
# -*- coding:utf-8; python-indent:2; indent-tabs-mode:nil -*-
# Copyright 2013 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/l... | pombredanne/pytype | pytype/pytd/parse/parser_test.py | Python | apache-2.0 | 3,604 | [
"VisIt"
] | 1218f5f7ab02f40353fb87c03d90561add99c20aae87260e69db7cfb21abeee7 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements a Composition class to represent compositions,
and a ChemicalPotential class to represent potentials.
"""
import collections
import numbers
import os
import re
import string
import warnings
from fun... | vorwerkc/pymatgen | pymatgen/core/composition.py | Python | mit | 50,992 | [
"pymatgen"
] | b81b0e8806c6bc74f924c7d5104968f0b49fbafef8bca0bae631070de046e55c |
from setuptools import setup, find_packages
setup(
name = 'octopus',
version = '1.0.0',
packages = find_packages(),
install_requires = [
"werkzeug==0.8.3",
"Flask==0.9",
"Flask-Login==0.1.3",
"requests",
"esprit",
"simplejson",
"lxml==3.4.4",
... | JiscPER/magnificent-octopus | setup.py | Python | apache-2.0 | 966 | [
"Octopus"
] | 5eab7892b032c43b6fec385a968729d232e11d2917ce63ce4a6231fc1f76df5f |
# -----------------------------------------------------------------------------------------------------
# CONDOR
# Simulator for diffractive single-particle imaging experiments with X-ray lasers
# http://xfel.icm.uu.se/condor/
# -------------------------------------------------------------------------------------------... | mhantke/condor | condor/particle/particle_spheroid.py | Python | bsd-2-clause | 10,607 | [
"Gaussian"
] | 279b6ae68d7b6e5fa83d0ef04e5eab69fca99984ea9048aa86cb9c8c975fcc35 |
from django.core.management.base import BaseCommand
from schools.models import School, BoundaryType
from stories.models import Question, Questiongroup, QuestionType, QuestiongroupQuestions, Source
class Command(BaseCommand):
args = ""
help = """Populate DB with GKA IVRS questions
./manage.py populategka... | klpdotorg/dubdubdub | apps/ivrs/management/commands/archived_commands/populategkaivrsdata.py | Python | mit | 5,178 | [
"VisIt"
] | 4396fb34b2a4a468daaf1ae3878fdeb19f942eb674a92306dc7aa437e6ec0875 |
# Copyright 2009, Mark Fassler
# 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, version 2 of the License.
import vtk
class create2dRectangle:
def __init__ (self, xmin, ymin, xmax, ymax):
... | mfassler/jaivis | jv/primitives.py | Python | gpl-2.0 | 1,181 | [
"VTK"
] | d48002630a39c8cc1796ab4a6e5bd2135c966d2a530511cff1253ce73490cb3a |
# Date: September 2017
# Author: Kutay B. Sezginel
"""
Initialize Lammps simulation using lammps_interface
"""
import os
import glob
from lammps_interface.lammps_main import LammpsSimulation
from lammps_interface.structure_data import from_CIF
from . import read_lines, write_lines
from thermof.sample import lammps_inpu... | kbsezginel/tee_mof | thermof/initialize/lammps.py | Python | mit | 9,487 | [
"LAMMPS"
] | 8639766def96a6a2ed51abff11050e591b736c9e2b59509878d6a64cdd8f0889 |
################################################################################
# Copyright (C) 2013-2014 Jaakko Luttinen
#
# This file is licensed under the MIT License.
################################################################################
import numpy as np
import matplotlib.pyplot as plt
import functoo... | jluttine/bayespy | bayespy/inference/vmp/nodes/node.py | Python | mit | 47,354 | [
"Gaussian"
] | ccea97391589ca39fb6a7f997ebc9d2a25ae2f02b9a5070909c1f0be80b04d81 |
# -*- coding: utf-8 -*-
#------------------------------------------------------------
# pelisalacarta - XBMC Plugin
# Conector para longurl (acortador de url)
# http://blog.tvalacarta.info/plugin-xbmc/pelisalacarta/
#------------------------------------------------------------
import urlparse
from lib import unshort... | ChopChopKodi/pelisalacarta | python/main-classic/servers/expurl.py | Python | gpl-3.0 | 725 | [
"ADF"
] | 5e5d2e02ada13f6ab110d0dd55526acbd8ef89844a953d46516c5fc138e2cf87 |
#****************************************************************************
# This file has been modified from its original version. It has been
# formatted to fit your irc bot.
#
# The original version is a nifty PyQt application written by Douglas Bell,
# available at http://convertall.bellz.org/
#
# Below is the ... | tecan/xchat-rt | plugins/scripts/encryption/supybot-code-6361b1e856ebbc8e14d399019e2c53a35f4e0063/plugins/Math/local/convertcore.py | Python | gpl-2.0 | 42,339 | [
"Avogadro"
] | dbc286ee4777a1c89968675c515235b031089e12451356e07f89b5dd3a792ea3 |
#!/usr/bin/env python
# File created on 17 Feb 2010
from __future__ import division
from setuptools import setup
from stat import S_IEXEC
from os import (chdir, getcwd, listdir, chmod, walk, rename, remove, chmod,
stat, devnull)
from os.path import join, abspath
from sys import platform, argv
from subpr... | wasade/qiime | setup.py | Python | gpl-2.0 | 9,528 | [
"Brian",
"scikit-bio"
] | e708c4043a8982cc1161fff78b1a52ee445b24fd8c0885a76a80abbcaa4a15e4 |
""" Test class for Stalled Job Agent
"""
# imports
from __future__ import absolute_import
from mock import MagicMock
# DIRAC Components
from DIRAC.WorkloadManagementSystem.Agent.StalledJobAgent import StalledJobAgent
from DIRAC import gLogger
# Mock Objects
mockAM = MagicMock()
mockNone = MagicMock()
mockNone.return... | fstagni/DIRAC | WorkloadManagementSystem/Agent/test/Test_Agent_StalledJobAgent.py | Python | gpl-3.0 | 4,552 | [
"DIRAC"
] | 5544f48a394849de8161ac24a22c676dd3d76fac65eb97ab18a9e8d9e7484aff |
"""
Pandas dataframes for Census tables.
"""
from ambry.pands import AmbryDataFrame, AmbrySeries
import numpy as np
from six import string_types
def melt(df):
"""Melt a census dataframe into two value columns, for the estimate and margin"""
import pandas as pd
# Intial melt
melted = pd.melt(df, id_... | CivicKnowledge/censuslib | censuslib/dataframe.py | Python | mit | 8,628 | [
"MOE"
] | b0bd155bba7bb90c9e1a35a9cd8495bc58c33aa5082f7560db654b3fd5bbb809 |
# Copyright 1999 by Jeffrey Chang. All rights reserved.
# Copyright 2009 by Michiel de Hoon. 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.
"""
This module provides code to wo... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/ExPASy/Enzyme.py | Python | gpl-2.0 | 4,440 | [
"Biopython"
] | 96cd5f3e224edc427479e47e127d24ae8c9af3565254b96438aed6ec00e8fc89 |
#! /usr/bin/env python
"""
usage:
vk <command> [<args>...]
vk setup
vk -h | --help
vk --version
commands:
calc
call
filter
geno
genome
hmm
phylo
primer
rename
tajima
vcf2tsv
"""
from vcfkit import __version__
from .utils import lev, message
from docopt import docopt
from subprocess impo... | AndersenLab/vcf-toolbox | vcfkit/vk.py | Python | mit | 3,184 | [
"BLAST",
"BWA"
] | c9d94e658c3e1ae0e4df174a16afe5905ab32f3f47a94230b824dc481769a162 |
from datetime import datetime
from flask_babel import lazy_gettext
from c3bottles import db
from c3bottles.model import drop_point
class Report(db.Model):
"""
The report of a visitor that a drop point needs maintenance.
When visitors find a drop point needing maintenance, they may report
the drop p... | der-michik/c3bottles | c3bottles/model/report.py | Python | mit | 3,885 | [
"VisIt"
] | df3014fe594304f17dab6a1728733433ea1f5f1d5c5bb1610f209f1f7473e01c |
from ase.data import atomic_numbers, chemical_symbols, reference_states
from ase.units import *
import fcc
import au
lattice = {'fcc': fcc.data,
}
element = {79: au.data, #Au
}
| auag92/n2dm | Asap-3.8.4/Python/asap3/nanoparticle_mc/data/__init__.py | Python | mit | 200 | [
"ASE"
] | 95a1d2fb8fccb07695416eb5810cd4b58943b7a94262fddb5170c913f6e56bce |
from numpy import *
from asap3 import *
from ase.lattice.compounds import B2
from asap3.testtools import ReportTest
atoms = B2(size=(332,166,5), symbol=('Cu', 'Zr'), latticeconstant=2.7)
lj = LennardJones((29,40), 0.2*array([0.5, 1.0, 1.0, 0.5]),
array([1.236, 2.0, 2.0, 2.352]),
rCu... | auag92/n2dm | Asap-3.8.4/Test/LJ_Stress.py | Python | mit | 722 | [
"ASE"
] | 1c771a3aed3f36811a31bf3d375a48f4301c6960dcabc74e2f006805ee9b14b5 |
# Copyright (C) 2015 Henrique Pereira Coutada Miranda, Alejandro Molina-Sanchez
# All rights reserved.
#
# This file is part of yambopy
#
import xml.etree.ElementTree as ET
from qepy.auxiliary import *
from numpy import array
from lattice import *
HatoeV = 27.2107
class PwXML():
""" Class to read data from ... | henriquemiranda/yambopy | qepy/pwxml.py | Python | bsd-3-clause | 7,356 | [
"Quantum ESPRESSO"
] | 7f352e991453c8ad57a1c4bcd137194371fdd5ca43efa4f94b6bcc09e36b8e27 |
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