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"""
Simple prism model
------------------
Create a simple geologic model using rectangular prisms
(:class:`fatiando.mesher.Prism`) and plot it in 3D with
:mod:`fatiando.vis.myv`.
"""
from fatiando.mesher import Prism
from fatiando.vis import myv
# Models in Fatiando are basically sequences of geometric elements from... | mtb-za/fatiando | gallery/3-mesh/prism_model.py | Python | bsd-3-clause | 1,037 | [
"Mayavi"
] | 03752ece38005a9285586a52a76319defcc14ae8fd8e59e57611a08760f2ed7c |
#!/usr/bin/python
# -*- coding: utf-8 -*-
'''
An example of a Wikidata page
'''
from collections import OrderedDict
from pywikibot import (Claim)
from pywikibot.site import DataSite
itempage = {
u'claims': {u'P535': [Claim.fromJSON(DataSite("wikidata", "wikidata"),
{u'typ... | weblyzard/ewrt | src/eWRT/ws/wikidata/sample_itempage.py | Python | gpl-3.0 | 367,647 | [
"Galaxy",
"VisIt"
] | 7c4c68add73d71fcc0b7b579cde07b83bf0f653a7faffae0adc680116d026950 |
#
# This file is part of Bakefile (http://www.bakefile.org)
#
# Copyright (C) 2003-2008 Vaclav Slavik
#
# 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 wit... | Distrotech/bakefile | src/reader.py | Python | mit | 39,248 | [
"VisIt"
] | d3d059efadf6c5dddb0b8d90b46d28eded7db2c391c947ccbc1923cd178a3ea2 |
""" Tools for using spherical harmonic models to fit diffusion data
References
----------
Aganj, I., et al. 2009. ODF Reconstruction in Q-Ball Imaging With Solid
Angle Consideration.
Descoteaux, M., et al. 2007. Regularized, fast, and robust analytical
Q-ball imaging.
Tristan-Vega, A., et al. 2010. A new metho... | nilgoyyou/dipy | dipy/reconst/shm.py | Python | bsd-3-clause | 34,589 | [
"DIRAC"
] | 026458cb7cc3b1913daa979147ee6ea07a45efaaecfe7fc59ac7e2535d6dc74b |
# -*- coding: utf-8 -*-
from __future__ import division
import numpy as np
import pandas as pd
from scipy.stats import multivariate_normal
from pgmpy.factors.base import BaseFactor
class LinearGaussianCPD(BaseFactor):
"""
For, X -> Y the Linear Gaussian model assumes that the mean
of Y is a linear func... | khalibartan/pgmpy | pgmpy/factors/continuous/LinearGaussianCPD.py | Python | mit | 8,361 | [
"Gaussian"
] | 979146fb93e5b3fa4be2623421a2063e237708e90c9f6b18046e0da49a4a7fe1 |
#!/usr/bin/env python
##################################################################
#
# This module is the class of Navarro-Frenk-White Model.
#
##################################################################
import numpy as np
from math import *
import cosmolopy.distance as cosdist
import cosmolopy.density a... | inonchiu/NavarroFrenkWhite | NFW.py | Python | mit | 52,804 | [
"Galaxy"
] | 4a42fc58908317cac5f35a761286c76120888419ee6f961c3e530f5c2ad31bb2 |
#!/usr/bin/python
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Ansible is distributed... | mkrupcale/ansible | lib/ansible/modules/cloud/amazon/elasticache.py | Python | gpl-3.0 | 21,698 | [
"Dalton"
] | 87f955bdb28f18bb00e41ff66bee446e0396e10cb806731b8f30930a013ef813 |
"""
This test verifies that vtk's Xdmf reader will read a sampling of small
to moderate size data files that cover a spectrum of file format features.
"""
import sys
import vtk
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
smallFiles = [
#from XDMF
"2DCoRectMesh.xmf",
"2DRectMesh.xmf",
"2D... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/IO/Xdmf3/Testing/Python/ManyFiles.py | Python | gpl-3.0 | 1,694 | [
"ParaView",
"VTK"
] | dc539261ddbabb9cc4bb21ac8a7b172d760d72589bd990574e1c208d95db043d |
#!/usr/bin/env python
__author__ = "waroquiers"
import os
import random
import unittest
import numpy as np
from monty.tempfile import ScratchDir
from pymatgen.analysis.chemenv.coordination_environments.voronoi import (
DetailedVoronoiContainer,
)
from pymatgen.core.lattice import Lattice
from pymatgen.core.str... | materialsproject/pymatgen | pymatgen/analysis/chemenv/coordination_environments/tests/test_voronoi.py | Python | mit | 9,769 | [
"pymatgen"
] | cccecef986d5b68d7eb3c470a2e5420fa66ac3e0d38da74bc5ec6a2dca3c9982 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
# ... | SKIRT/PTS | core/config/create_model.py | Python | agpl-3.0 | 3,190 | [
"Galaxy"
] | f38b8b9f7c72bbb900f7d1133628bca62c986280494e747f4bac73e3bc2c595d |
# -*- coding: utf-8 -*-
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import matplotlib.pyplot as plt
from time import time
import sys
from abel.direct import direct_transform
from abel.tools.analytical import Gaus... | DhrubajyotiDas/PyAbel | examples/example_direct_gaussian.py | Python | mit | 1,467 | [
"Gaussian"
] | d9ed46e0a22ac70554805110ef4e5daee75eb41ade1c7fa46ae474804ece572b |
# (c) 2014 Michael DeHaan, <michael@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later ve... | azaghal/ansible | lib/ansible/playbook/role/requirement.py | Python | gpl-3.0 | 4,308 | [
"Galaxy"
] | 14c3d08e30b0481ad99100c7b8cfd25f4ef3a21202df199c57224aaffe98d246 |
#!/usr/bin/env python
"""Lower-level functionality for parsing CMA (.cma) files.
This handles .chn (CHAIN) files as a collection of CMA blocks, i.e. alignments.
"""
import itertools
import logging
import re
from . import sugar
def parse(infile):
with sugar.maybe_open(infile) as instream:
for block in ... | etal/biocma | biocma/cma.py | Python | bsd-2-clause | 21,928 | [
"Biopython"
] | 6604ca98f32079b0aaa192e7ae68740a6825e455a220db261ecd419dbb7ab8fd |
# (C) British Crown Copyright 2014 - 2015, 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... | Jozhogg/iris | lib/iris/tests/integration/test_grib2.py | Python | lgpl-3.0 | 10,470 | [
"Gaussian"
] | a09baaccbe2be223de420db3f1c67b7a48f2af1c5035d8e1215d5788d4dbeaa0 |
# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Use the DSSP program to calculate secondary structure and accessibility.
You need to h... | foxtrotmike/pairpred | DSSP.py | Python | gpl-3.0 | 11,467 | [
"Biopython"
] | 8283adc0062332a85513846593eff077770be185c5f9dea8ab503b274e036f36 |
from django.db import models
from django.contrib.auth.models import User
class ParamDict(models.Model):
name = models.CharField(max_length=50)
def __unicode__(self):
return self.name
class KeyVal(models.Model):
container = models.ForeignKey(ParamDict, db_index=True, on_delete=models.CASCADE)
... | openworm/ChannelWorm | channelworm/ion_channel/models.py | Python | mit | 14,559 | [
"NEURON"
] | a482d1be04937ff45561042ae2ac8bf77101f775b4480851e9d600e9aff31b06 |
# (C) British Crown Copyright 2014 - 2017, 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... | duncanwp/iris | lib/iris/tests/integration/test_pickle.py | Python | lgpl-3.0 | 2,925 | [
"NetCDF"
] | 8c422357fc76c0af89bdc245272f623f5b9d984e8b27901457e82a81c653a378 |
#
# Copyright 2001 - 2016 Ludek Smid [http://www.ospace.net/]
#
# This file is part of Outer Space.
#
# Outer Space 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
# (... | ospaceteam/outerspace | server/lib/ige/BookingMngr.py | Python | gpl-2.0 | 12,077 | [
"Galaxy"
] | 6b7247f77fb171cf69ccced38e8f98b078a982ea88f2d85027e1d87116fe6a16 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
########################################################################
# Solves problem 33 from projectEuler.net.
# Finds the denominator of the product of 4 fractions with a property
# Copyright (C) 2010 Santiago Alessandri
#
# This program is free software: y... | sanSS/programming-contests | project-euler/problem033.py | Python | gpl-3.0 | 2,051 | [
"VisIt"
] | 897acf8b447d17f7d45e53020e0f8c42375b90f1c7daca4aae102d9deecddf4a |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# create a rendering window
renWin = vtk.vtkRenderWindow()
renWin.SetMultiSamples(0)
renWin.SetSize(200,200)
wavelet = vtk.vtkRTAnalyticSource()
wavelet.SetWholeExtent(-100... | hlzz/dotfiles | graphics/VTK-7.0.0/Rendering/Core/Testing/Python/TransformImageData.py | Python | bsd-3-clause | 1,110 | [
"VTK"
] | d95ca547edbce306b237e3ce6a9c8b7b870708a60954d70c3326629625c63e0a |
# Copyright (C) 2008 Max Hofheinz
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in ... | McDermott-Group/LabRAD | LabRAD/TestScripts/fpgaTest/pyle/pyle/registry.py | Python | gpl-2.0 | 7,284 | [
"VisIt"
] | a4da4a13deec2fc0088ff0361c0c2fe4ca1982f0dc80a316db7213b7f930eb10 |
#!/usr/bin/env python
# -*- coding: iso-8859-1 -*-
#################################
# #
# ESPResSo++ Python script #
# #
#############... | junghans/espressopp | examples/stillinger_weber_Si/stillinger_weber_silicon.py | Python | gpl-3.0 | 8,183 | [
"ESPResSo"
] | ba8aeb084ee4d0bdb9c9dd568d13beb91b6c56287109e95b51daaa0f058af564 |
import os
#import pysam
import subprocess
import sys
import tempfile
import errno
import glob
import pandas
import numpy
import collections
#import train
import pysam
import yaml
vcf_required_fields = ['CHROM', 'POS', 'ID', 'REF', 'ALT',
'QUAL', 'FILTER']
def mergeFieldsForVariant(x):... | asalomatov/variants | variants/func.py | Python | mit | 27,565 | [
"pysam"
] | 6e7eb89111a4422679d2d3cc8c6c25cc7b730df76d1eb02939ba6fb5e9a8c0e4 |
"""
"""
import os
import imp
import unittest
utility = imp.load_source( 'utility', os.path.join( os.path.dirname( __file__ ), '../../util/utility.py' ) )
log = utility.set_up_filelogger( __name__ + '.log' )
relative_test_path = '/test/unit/visualizations/registry'
utility.add_galaxy_lib_to_path( relative_test_path )
... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/test/unit/visualizations/registry/test_VisualizationsRegistry.py | Python | gpl-3.0 | 6,321 | [
"Galaxy"
] | 7140d1f3ee238f01d6282374fdde0476a3eae5c21ac58736647901ebd6c5547c |
from PIL import Image
from PIL import ImageDraw
from pyimage import PyImage
from gausspyramid import GaussPyramid
import threading
import numpy as np
# ------------------------------------------------------------------------
# Helper Matrix functions
# -----------------------------------------------------------------... | Thurler/imgprocess | klttracker.py | Python | gpl-3.0 | 21,266 | [
"Gaussian"
] | a6264fb4e21f51617d7e260fd67ba56b2eb31e6d2298479f0637b7591ef17fcd |
import inspect
import subprocess
import os
from PyQt5 import QtCore, QtWidgets
from ExodusPlugin import ExodusPlugin
from VTKWindowPlugin import VTKWindowPlugin
import mooseutils
import chigger
class ExternalVTKWindowPlugin(VTKWindowPlugin):
"""
VTK window for external gold/diff use.
"""
def __init__(... | backmari/moose | python/peacock/ExodusViewer/plugins/GoldDiffPlugin.py | Python | lgpl-2.1 | 9,771 | [
"MOOSE",
"VTK"
] | b87d914f1bec594fbb48ea47d89517e67a0dcec7c7041195f6be327c46f8d971 |
"""Compute the sound field generated by a sound source.
The Green's function describes the spatial sound propagation over time.
.. include:: math-definitions.rst
.. plot::
:context: reset
import matplotlib.pyplot as plt
import numpy as np
from scipy.signal import unit_impulse
import sfs
xs ... | sfstoolbox/sfs-python | sfs/td/source.py | Python | mit | 4,598 | [
"DIRAC"
] | d9832bb14edf2f0f8478a99808d3039c40eba3e434459474c4c2b61288c0adfa |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Generated from FHIR 3.0.0.11832 on 2017-03-22.
# 2017, SMART Health IT.
import io
import json
import os
import unittest
from . import appointmentresponse
from .fhirdate import FHIRDate
class AppointmentResponseTests(unittest.TestCase):
def instantiate_from(se... | all-of-us/raw-data-repository | rdr_service/lib_fhir/fhirclient_3_0_0/models/appointmentresponse_tests.py | Python | bsd-3-clause | 2,992 | [
"Brian"
] | 8f01cddc9c4686641ddca89683d47da732570e7c7533581e42ae7e6395d0c7b8 |
import sys
import os
import vtk
from obj import OBJReader
# Make sure we have enough arguments passed by the user
if len(sys.argv) < 3:
print("usage:\npython main.py <input folder> <output folder>")
exit()
input_folder_name = sys.argv[1]
output_folder_name = sys.argv[2]
# Check if the input directory exists
if n... | zibneuro/convert | obj2ply/main.py | Python | bsd-3-clause | 2,609 | [
"VTK"
] | c2dcaa47ba009ebe90be3db8191b43bd10afefbcc66c1baf08f98b4d319e807e |
#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* Copyright (c) Schrodinger, LLC.
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove this copyright notice.
#F* -------... | gratefulfrog/lib | python/pymol/m4x.py | Python | gpl-2.0 | 14,813 | [
"ChemPy",
"PyMOL"
] | a0aadcb16e95adb9b41b93d40d524eff3e499cb1e3e59b287457995cd5e3f918 |
from echam_ham_pascals import ECHAM_HAM_Pascals
from cis.utils import demote_warnings
class ECHAM_HAM(ECHAM_HAM_Pascals):
"""
Plugin for reading ECHAM-HAM NetCDF output files. **Air pressure is converted to hPa**
"""
priority = 100
def _add_available_aux_coords(self, cube, filenames):
... | duncanwp/cis_plugins | echam_ham.py | Python | lgpl-3.0 | 2,005 | [
"NetCDF"
] | a996f4b609c24f7e923ec352e4d74e12db2c3ea0d5bdd83a1e389be6748e6e0b |
#!/usr/bin/env python
"""
Just a demo script to test out the DIMACS reader/writer function
"""
import time
from vtk import *
# generate a random graph
source = vtkRandomGraphSource()
source.SetNumberOfVertices(100)
source.SetAllowSelfLoops(False)
source.SetEdgeProbability(0.1)
source.SetUseEdgeProbability(True)
source... | biddisco/VTK | Examples/Infovis/Python/dimacs.py | Python | bsd-3-clause | 1,452 | [
"VTK"
] | 495e5085ec62a026d24de6cb5ca7026e77dfd5ef8211c2be2de08ac7cbc44b88 |
# -*- coding: utf-8 -*-
"""Tools for identifying common HGVS mistakes in BEL graphs."""
from typing import Iterable, Mapping, Optional, TextIO, Tuple
from pybel import BELGraph
from pybel.dsl import CentralDogma, Hgvs
from pybel.language import amino_acid_dict, dna_nucleotide_labels
from pybel.struct import has_hgvs... | pybel/pybel-tools | src/pybel_tools/validators/hgvs_validator.py | Python | mit | 4,750 | [
"Pybel"
] | 54e855bc5d71a01d8508c9f1a5867f0c5021666526359241054a1d250388dcd0 |
# encoding: utf-8
"""
System command aliases.
Authors:
* Fernando Perez
* 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... | boompieman/iim_project | project_python2/lib/python2.7/site-packages/IPython/core/alias.py | Python | gpl-3.0 | 9,984 | [
"Brian"
] | 625323fc8742cab674a18d2f7557d9143f3c107793ea4368af796de333741b32 |
# -*- coding: utf-8 -*-
#
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2007-2014, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Pub... | ghutchis/cclib | src/cclib/parser/orcaparser.py | Python | lgpl-2.1 | 37,840 | [
"Gaussian",
"ORCA",
"cclib"
] | 51b6d2148025d0a3f525301a2ba441b16c7fa1a44c03ad8c90d397f7ddfcb17d |
# Copyright (c) Twisted Matrix Laboratories.
# See LICENSE for details.
"""
This is a Twisted Web Server with Named-Based Virtual Host Support.
Usage:
$ sudo twistd -ny rootscript.py
Note: You need to edit your hosts file for this example
to work. Need to add the following entry:
127.0.0.1 example.com
Th... | EricMuller/mynotes-backend | requirements/twisted/Twisted-17.1.0/docs/web/examples/rootscript.py | Python | mit | 1,364 | [
"VisIt"
] | 6bae88ccb91ea46ef30198b573f8adad08397b815c5f7405c5f2b91874041baa |
''' Provide a base class for all objects (called Bokeh Models) that can go in
a Bokeh |Document|.
'''
from __future__ import absolute_import, print_function
import logging
logger = logging.getLogger(__name__)
from json import loads
from operator import itemgetter
from six import iteritems
from .core.json_encoder i... | Karel-van-de-Plassche/bokeh | bokeh/model.py | Python | bsd-3-clause | 25,004 | [
"VisIt"
] | 526b3a80154134326e6f0c06451c6102525c8c442fec378ff1aae2ffade83261 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class PerlBioSearchioHmmer(PerlPackage):
"""BioPerl parser to HMMER output."""
homepage = "... | LLNL/spack | var/spack/repos/builtin/packages/perl-bio-searchio-hmmer/package.py | Python | lgpl-2.1 | 675 | [
"BioPerl"
] | 310c25bfece1d6bff7b8c2e4c4736c8bc504b8d281420e4c99e0eb633d13bd26 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright @ 2014 Mitchell Chu
from __future__ import absolute_import, division, print_function, with_statement
from torndsession.driver import SessionDriver
from torndsession.session import SessionConfigurationError
import os
from os.path import join, exists, isdir
im... | controlzee/torndsession | torndsession/filesession.py | Python | mit | 3,101 | [
"VisIt"
] | 85b5b0c3e2fb735fdee688cb963dcf5bbf27134a1716e57052afa0fc9dcac7ca |
# -*- coding: utf-8 -*-
import datetime
from django.conf import settings
from django.contrib.auth.models import User
from django.utils import timezone
from celery.task.base import periodic_task
from civmail.messages import LastLoginNotifyEmail
from .models import Visitor
import logging
logger = logging.getLogger('... | CivilHub/CivilHub | user_tracker/tasks.py | Python | gpl-3.0 | 1,444 | [
"VisIt"
] | f0cea26ce2d0088c6f0be43475be67d8375340f1aad4e04364fb3f9321e7490d |
#!/usr/bin/env python
"""
ColorScalars
"""
"""
Copyright 2001 Pearu Peterson all rights reserved,
Pearu Peterson <pearu@ioc.ee>
Permission to use, modify, and distribute this software is given under the
terms of the LGPL. See http://www.fsf.org
NO WARRANTY IS EXPRESSED OR IMPLIED. USE AT YOUR O... | ddempsey/PyFEHM | pyvtk/ColorScalars.py | Python | lgpl-2.1 | 2,079 | [
"VTK"
] | cbbb33c3574192aa62b675a0358631904d5b8cc69a4a6b69dcb0c1e32a5dbf25 |
"""20.07.2015 PyOSE: Stacked exomoons with the Orbital Sampling Effect."""
# Stacked exomoons with the Orbital Sampling Effect (OSE, Heller 2014, ApJ 787)
#
# _.--"~~ __"-. Copyright 2015 Michael Hippke and contributors
# ,-" .-~ ~"-\ OSE-Sampler is free software
# .^ / ... | hippke/PyOSE | PyOSE.py | Python | mit | 15,868 | [
"Gaussian",
"VisIt"
] | 8eacb6e05f5f43e494a30e159e66df49f87b8529044ea6f2b1faaa990c768132 |
import os
import pkg_resources
import numpy as np
import pysam
import pytest
from ngs_tk.io import tabix
@pytest.fixture
def gtf_path():
rel_path = os.path.join('tests', 'data', 'mm10.test.gtf.gz')
gtf_path = pkg_resources.resource_filename(tabix.__name__, rel_path)
return gtf_path
@pytest.fixture
def... | jrderuiter/ngs-tk | ngs_tk/io/tests/test_tabix.py | Python | gpl-2.0 | 4,918 | [
"pysam"
] | 6796d49c1f0047a1c3c50b13a3d9778327526e02401fabc05155668912266ce1 |
from setuptools import setup
from setuptools.command.test import test as TestCommand
import sys
import os
if float(sys.version[:3])<2.7 or float(sys.version[:3])>=2.8:
sys.stderr.write("CRITICAL: Python version must be 2.7!\n")
sys.exit(1)
class NoTestCommand(TestCommand):
def run(self):
... | GreenleafLab/NucleoATAC | setup.py | Python | mit | 1,322 | [
"pysam"
] | e4055dcf5a55d79b2a7bdf5e56b8aa1a2bffdd02137580813eadfa589b5f21f2 |
#!/usr/bin/env python
#
# Wrapper script for starting the biopet-validatevcf JAR package
#
# This script is written for use with the Conda package manager and is copied
# from the peptide-shaker wrapper. Only the parameters are changed.
# (https://github.com/bioconda/bioconda-recipes/blob/master/recipes/peptide-shaker/... | joachimwolff/bioconda-recipes | recipes/biopet-validatevcf/biopet-validatevcf.py | Python | mit | 3,373 | [
"Bioconda"
] | 26e11df7e26dd28fa233b106d603957eedf80e9189d66704f4a6975abc18d632 |
"""
Univariate Kernel Density Estimators
References
----------
Racine, Jeff. (2008) "Nonparametric Econometrics: A Primer," Foundation and
Trends in Econometrics: Vol 3: No 1, pp1-88.
http://dx.doi.org/10.1561/0800000009
http://en.wikipedia.org/wiki/Kernel_%28statistics%29
Silverman, B.W. Density Estimation... | matthew-brett/draft-statsmodels | scikits/statsmodels/sandbox/kde.py | Python | bsd-3-clause | 7,892 | [
"Gaussian"
] | cb253fb9812f5ca151503b542d2e0659447370f27f21b04b0b3ed8542c914b26 |
#!/usr/bin/env python
"H2O using Gaussians to test the DFT module"
import unittest, sciunittest
from PyQuante.dft import *
from PyQuante.Molecule import Molecule
# Getting -75.857635 with the old style grid patching
# Getting -75.905545 with the Becke projection operator.
# Getting -75.896366 with Becke projection a... | berquist/PyQuante | Tests/h2o_dft.py | Python | bsd-3-clause | 1,001 | [
"Jaguar",
"NWChem"
] | f313fc73119acb428f95255c734bd304f56968296ef52ffe43379efdf748cf3a |
import multiprocessing as mp
from timeit import default_timer
from datetime import datetime, timedelta
from itertools import repeat, islice
import ctypes
import sys
import traceback
from textwrap import dedent
from functools import partial
from pathlib import Path
import shutil
import pandas as pd
import numpy as np
... | TUW-GEO/rt1 | rt1/rtprocess.py | Python | apache-2.0 | 72,127 | [
"NetCDF"
] | 6b7f871f0ef66a57d9b8c8be40e6e6044a0bfc13f20a05215b24c7b13f0a364f |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
from fractions import Fraction
import numpy as np
import re
import warnings
from pymatgen.core import Lattice
from pymatgen.util.string import transformation_t... | matk86/pymatgen | pymatgen/symmetry/settings.py | Python | mit | 7,169 | [
"pymatgen"
] | f2fbe19e4f5e06927033d0bf8a2edc7c57fa6b8435e671a2f6d34d4df4d8882d |
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant#
# Copyright (C) 2010 Craig J. Anderson
#
# This program is free software; you can redistribute it and/or modify
# it under the t... | arunkgupta/gramps | gramps/plugins/drawreport/ancestortree.py | Python | gpl-2.0 | 44,379 | [
"Brian"
] | 5148d3a8ac97cc82dc5c4c5ccb4cdbf27742afc5fc29138d8d97f5a8bc7188e7 |
# -*- coding: utf-8 -*-
"""
Acceptance tests for Video.
"""
import os
from mock import patch
from nose.plugins.attrib import attr
from unittest import skipIf, skip
from ..helpers import UniqueCourseTest, is_youtube_available, YouTubeStubConfig
from ...pages.lms.video.video import VideoPage
from ...pages.lms.tab_nav i... | franosincic/edx-platform | common/test/acceptance/tests/video/test_video_module.py | Python | agpl-3.0 | 48,661 | [
"VisIt"
] | e57b2474caa3ab5115af8fed8d2c130c6ad366e53ed7e8c24ae0ed6ccf9b1aa0 |
"""
Classes and functions for easier management of the InstalledComponents database
"""
__RCSID__ = "$Id$"
import datetime
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.ConfigurationSystem.Client.Utilities import getDBParameters
from sqlalchemy import MetaData, \
Column, \
... | marcelovilaca/DIRAC | FrameworkSystem/DB/InstalledComponentsDB.py | Python | gpl-3.0 | 32,890 | [
"DIRAC"
] | 4324986c9d1b86504f8b7752bd7d38748897ab849b21dea663176dbdb4653212 |
import sys, os
sys.path.insert(0, os.path.abspath('..'))
import numpy as np
import math
import scipy.linalg
from pypsmove.transformations import quaternion_matrix, quaternion_conjugate, quaternion_multiply
from filterpy.common import Q_discrete_white_noise, dot3
from filterpy.kalman import MerweScaledSigmaPoints
from ... | zelmon64/PSMoveService | misc/python/examples/filter_datafiles.py | Python | apache-2.0 | 15,501 | [
"Gaussian"
] | a2bd40096c27542c436b0ad6c3512da38e2d34a92385c5be2322b92faf997bd4 |
#!/usr/bin/env python3
"""
Copyright 2020 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester 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 Software Foundation, either version 3 ... | pwillworth/galaxyharvester | html/message.py | Python | gpl-3.0 | 4,154 | [
"Galaxy",
"VisIt"
] | fb861654d7c9c407d2f2cfc9d13bb3d01fb74d25d347f378154daf230c184e4f |
__author__ = 'sebastians'
# PyMOL Animation Tutorials -- 05 - Camera Movements
# This tutorial will show you how to add more camera movements to your animation
# Import all necessary modules
import pymol
from pymol import cmd
# The custom viewpoint
closeup = '''
-0.775189936, 0.267432511, -0.572329581,\
... | ssalentin/pymol-animations | tutorials/basics/05-camera-movements.py | Python | mit | 3,349 | [
"PyMOL"
] | 41996c45077a3e7eef2b2c2021c5273c8110114f675723480e743dcdbb82f992 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
import sys
class Gdal(AutotoolsPackage):
"""GDAL (Geospatial Data Abstraction Library) is a tran... | rspavel/spack | var/spack/repos/builtin/packages/gdal/package.py | Python | lgpl-2.1 | 20,971 | [
"NetCDF"
] | 9378b7f38ff226de61f1b4e2e3189594ec1d72d13fd282c7f139811fc8693d77 |
# -*- coding: utf-8 -*-
# this file is released under public domain and you can use without limitations
#########################################################################
## This is a samples controller
## - index is the default action of any application
## - user is required for authentication and authorizatio... | dmnfarrell/epitopemap | controllers/default.py | Python | apache-2.0 | 49,804 | [
"BLAST"
] | 24123a1ba500ff9d7233d0d69ad980dd6ff1acb83edfb6b20d726455dbae5947 |
# 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... | tensorflow/tensorflow | tensorflow/python/autograph/pyct/templates_test.py | Python | apache-2.0 | 10,320 | [
"VisIt"
] | b65c0b335c56684c4e171f61a2c9832bbbce97d9b1ffcfed0bdc48973c2064ba |
#!/usr/bin/env python
import sys
import importlib
import math
Unit = object()
World = object()
class IdrisError(Exception):
pass
def _idris_error(msg):
raise IdrisError(msg)
def _idris_pymodule(name):
return importlib.import_module(name)
def _idris_call(f, args):
return f(*list(args))
def _idris_foreach(... | ziman/idris-py | examples/example.py | Python | bsd-3-clause | 89,106 | [
"exciting"
] | fb13b3b9a88f1441858a4e650617cd8aef3872968637e0a5b60993226f3e39a5 |
#
#@BEGIN LICENSE
#
# v2rdm_casscf by Psi4 Developer, a plugin to:
#
# Psi4: an open-source quantum chemistry software package
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 ... | edeprince3/v2rdm_casscf | pymodule.py | Python | gpl-2.0 | 16,599 | [
"Psi4"
] | 4037db68a0d7dc343e48d116aff55a020826271946b507cfcb59aad9725c6c5f |
#
# @file TestReadFromFile7.py
# @brief Reads test-data/l2v3-all.xml into memory and tests it.
#
# @author Akiya Jouraku (Python conversion)
# @author Sarah Keating
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatic... | TheCoSMoCompany/biopredyn | Prototype/src/libsbml-5.10.0/src/bindings/python/test/sbml/TestReadFromFile7.py | Python | bsd-3-clause | 9,504 | [
"VisIt"
] | d55e1351bad98c443104b78c550a84b46a00c84d58b7c5953df01a2e59190734 |
import Cython.Compiler.Errors as Errors
from Cython.CodeWriter import CodeWriter
from Cython.Compiler.TreeFragment import TreeFragment, strip_common_indent
from Cython.Compiler.Visitor import TreeVisitor, VisitorTransform
from Cython.Compiler import TreePath
import unittest
import os, sys
import tempfile
class NodeT... | bdh1011/wau | venv/lib/python2.7/site-packages/Cython/TestUtils.py | Python | mit | 7,698 | [
"VisIt"
] | c6f3973e4cd63b201b1e05f0613eece7f75275f4d7a6b38a4a74d824f1727eec |
# Copyright (C) 2009 by Eric Talevich (eric.talevich@gmail.com)
# 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.
"""Unit tests for Bio.Phylo functions with external dependencies."""
# Check for any mi... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_Phylo_depend.py | Python | gpl-2.0 | 2,836 | [
"Biopython"
] | f8ae658bc4f8c8d53481015793cfab1a87b0713f23e6d8afae6473a59e579532 |
"""
To know more or get code samples, please visit my website:
https://morvanzhou.github.io/tutorials/
Or search: 莫烦Python
Thank you for supporting!
"""
# please note, all tutorial code are running under python3.5.
# If you use the version like python2.7, please modify the code accordingly
# 6 - CNN example
# to try... | MediffRobotics/DeepRobotics | DeepLearnMaterials/tutorials/kerasTUT/6-CNN_example.py | Python | gpl-3.0 | 2,812 | [
"VisIt"
] | 69b47ec0516c36b66da885c196d8c18ad6165d334d5e8b8bc6d2df1da48c0046 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | fevangelista/psi4 | psi4/driver/p4util/python_helpers.py | Python | lgpl-3.0 | 44,094 | [
"Psi4"
] | d61918eb51858428b5649ec95e4b4c1234e355c835499e0136f0c6668d926c89 |
__author__ = 'Rohin Kumar Y'
# Calculate anisotropic 2pCF
from tpcf import *
import scipy as sp
# antpcf(dat,datR,bins,parmetric,permetric) returns numpy 2d array DD, RR, DR correl
# poserr(xi,DD) returns (1.0+xi)/np.sqrt(DD)
def atpcf(datfile, binspar, binsper, **kwargs):
"""Main function to calculate anisotro... | rohinkumar/correlcalc | correlcalc/antpcf.py | Python | mit | 33,232 | [
"Galaxy"
] | 122db8e10569b8729d7f26604c21e89d5c3d1ea5d4ca9e8add5304316b1fab10 |
import argparse
import traceback
import sys
from biokbase.probabilistic_annotation.Helpers import get_url
from biokbase.probabilistic_annotation.Client import ProbabilisticAnnotation
from biokbase.workspace.ScriptHelpers import user_workspace
desc1 = '''
NAME
pa-annotate -- generate probabilistic annotation for ... | kbase/probabilistic_annotation | scripts/pa-annotate.py | Python | mit | 4,085 | [
"BLAST"
] | fc219c0306d0ceb0660cde796f60d0c55141fa6b8ffc65cd18e0de3b806465c2 |
import numpy as np
import constants as c
import asciidata as AD
import dust
import scipy.special as special # Needed for WD01 equations
MW_caseA_file = 'Table1.WD.dat'
LMC_avg_file = 'Table3_LMCavg.WD.dat'
LMC_2_file = 'Table3_LMC2.WD.dat'
SMC_file = 'T... | Doctorhoenikker/dust | WD01.py | Python | bsd-2-clause | 6,636 | [
"Galaxy"
] | d3adc9105365498f67d18a4e5f6ff7de09639f6bcfb9289964ba05f649ea5a34 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import re
import collections
import itertools
import math
import logging
from monty.json import MSONable, MontyDecoder
from functools import lru_cache
import numpy as np
from scipy.spatial import ConvexHull
... | montoyjh/pymatgen | pymatgen/analysis/phase_diagram.py | Python | mit | 83,286 | [
"pymatgen"
] | e6f69a4a220aa0bf2c13e9993e8cfa70d3e7acdfc5001231fe2cc67049b1efe0 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# freeseer - vga/presentation capture software
#
# Copyright (C) 2012, 2013 Free and Open Source Software Learning Centre
# http://fosslc.org
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publ... | Freeseer/freeseer | src/freeseer/tests/frontend/record/test_record.py | Python | gpl-3.0 | 5,587 | [
"VisIt"
] | 1624187d201c2c55f0372788a7e66d714d35f327bcb1aef441fdaa268464daa7 |
"""Machinery for interspersing lines of text with linked and colored regions
The typical entrypoints are es_lines() and html_line().
Within this file, "tag" means a tuple of (file-wide offset, is_start, payload).
"""
import cgi
from itertools import chain
try:
from itertools import compress
except ImportError:
... | jbradberry/dxr | dxr/lines.py | Python | mit | 19,289 | [
"VisIt"
] | 56add91ca651cc1752e629db208337255198961e7fb5b9002ff102baede10f2b |
#!/usr/bin/env python
import sys
import time
import enum
import threading
import traceback
import numpy
from mpi4py import MPI
from . import mpi_pool
from .mpi_pool import MPIPool
from pyscf import lib
_registry = {}
if 'pool' not in _registry:
import atexit
pool = MPIPool(debug=False)
_registry['pool'] ... | sunqm/mpi4pyscf | mpi4pyscf/tools/mpi.py | Python | gpl-3.0 | 27,145 | [
"PySCF"
] | a92418b0789d4f44a0e6ebab4b03a107557ef97f8150165aa9e0279a15bfa9fe |
"""
Given a binary tree, return all root-to-leaf paths.
For example, given the following binary tree:
1
/ \
2 3
\
5
All root-to-leaf paths are:
["1->2->5", "1->3"]
"""
# Definition for a binary tree node.
class TreeNode(object):
def __init__(self, x):
self.val = x
self.left = None
self.right =... | Ahmed--Mohsen/leetcode | binary_tree_paths.py | Python | mit | 991 | [
"VisIt"
] | e4d712abbb4bcc4b382aa9bb3f8b7c6efac0e1f4c26a265587a5cabe58bea0c2 |
import textwrap
from . import piquant_options as po
from . import options as opt
COMMANDS = {}
_INDENT = " "
class _PiquantCommand(object):
INDEX = 0
def __init__(self, name, description, option_list):
self.name = name
self.description = description
self.option_list = option_lis... | lweasel/piquant | piquant/piquant_commands.py | Python | mit | 9,170 | [
"Bowtie"
] | 209b4376f93c505e073d3554a4e2afff9700ad645702bf1fd0a0ca428b39c2b7 |
""" Class defining a production step """
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import json
from DIRAC import S_OK, S_ERROR
class ProductionStep(object):
"""Define the Production Step object"""
def __init__(self, **k... | ic-hep/DIRAC | src/DIRAC/ProductionSystem/Client/ProductionStep.py | Python | gpl-3.0 | 2,408 | [
"DIRAC"
] | 35b4ec651449e2ae730ace8dbb2cec59eed03c55d74816567f484eb9fc33ac8d |
#!/usr/bin/python
import numpy as np
import matplotlib.pyplot as plt
from numpy.random import rand, randn, permutation, multivariate_normal
from modshogun import BinaryLabels, RealFeatures, IndexBlock, IndexBlockGroup, FeatureBlockLogisticRegression
def generate_synthetic_logistic_data(n, p, L, blk_nnz, gcov, nstd)... | c4goldsw/shogun | examples/undocumented/python_modular/graphical/group_lasso.py | Python | gpl-3.0 | 7,792 | [
"Gaussian"
] | 1d6512730cafcb6877abeac8f8fc3485470029510482c8e70df34438732dc5eb |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Peter Eastman, Robert McGibbon
# Contributors: Carlos Hernande... | leeping/mdtraj | mdtraj/formats/pdb/pdbfile.py | Python | lgpl-2.1 | 29,794 | [
"MDTraj",
"OpenMM"
] | a31b12529e8c63a17cb879e0da022e9e785f5d14423914eab7dcfcc91eec1fe8 |
# pylint: disable=missing-docstring
import json
import platform
import re
import time
from textwrap import dedent
from urllib import quote_plus
# django_url is assigned late in the process of loading lettuce,
# so we import this as a module, and then read django_url from
# it to get the correct value
import lettuce.d... | procangroup/edx-platform | common/djangoapps/terrain/ui_helpers.py | Python | agpl-3.0 | 21,557 | [
"VisIt"
] | 0ab61e4be514bc0508c0ee4083211cf6d08464b71e41e44dbabc4cfaf34950fa |
from Sire.MM import *
from Sire.FF import *
from Sire.System import *
from Sire.Move import *
from Sire.IO import *
from Sire.Mol import *
from Sire.Maths import *
from Sire.Vol import *
from Sire.Base import *
from Sire.Units import *
from Sire.Qt import *
from nose.tools import assert_almost_equal
(mols, space) = ... | chryswoods/SireTests | unittests/SireMM/test_interff.py | Python | gpl-2.0 | 17,332 | [
"Amber"
] | 045ddb8bd0db40ff062573f29bcf6842f07ccf96562982cc78f5dad0619f35c9 |
"""
# Notes:
- This simulation seeks to emulate the COBAHH benchmark simulations of (Brette
et al. 2007) using the Brian2 simulator for speed benchmark comparison to
DynaSim. However, this simulation includes CLOCK-DRIVEN synapses, for direct
comparison to DynaSim's clock-driven architecture. The synaptic connec... | asoplata/dynasim-benchmark-brette-2007 | Brian2/brian2_benchmark_COBAHH_clocksyn_lodens_compiled_0016.py | Python | gpl-3.0 | 3,913 | [
"Brian"
] | 414e4ead023da31936e857f5d570bdd3c4cdd1b2815bc08008866f73ee3240b0 |
#!/usr/bin/env python3
import os
import argparse
import sys
from time import sleep
import subprocess
parser = argparse.ArgumentParser(
description="The goal of this python3 code is to automatically create \
the project template as fast as possible. Written by Wei Lu."
)
parser.add_argument("protein", help="The ... | luwei0917/awsemmd_script | archive/casp_create_project.py | Python | mit | 11,222 | [
"CRYSTAL",
"PyMOL"
] | ad23af7adfb66fb7e4a86408f2ed1cf3c85e74e8b2f1a088666ab50b6816cb49 |
#!/usr/local/sci/bin/python
#***************************************
# 28th April 2015
# This version reads in from /data/local/hadkw/HADCRUH2
# Reads in station file for CRUTEM4 (downloaded APR 2015) and for HadISDH.landT
# Plots a map for each with gridboxes coloured by number of stations contributing
# Plots a thr... | SurfaceTemp/ISTI_Clean_Worlds | PlotStationDensityGrids_JUN2015.py | Python | cc0-1.0 | 24,241 | [
"NetCDF"
] | 7b7a3ff571f08c036621ef8eecffaa7217b6df2ccbb93b8cff162a98bd8887b7 |
# coding=utf-8
# Copyright 2022 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... | google-research/google-research | graph_compression/compression_lib/kmeans_quantize_test.py | Python | apache-2.0 | 2,989 | [
"Gaussian"
] | 226bd2334237c30f3c7846d6b73def1077182b3c3aed98e22aff36ce44f32075 |
#
# Copyright (C) 2001-2006 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.
#
""" Functionality for SATIS t... | rvianello/rdkit | rdkit/Chem/SATIS.py | Python | bsd-3-clause | 2,844 | [
"RDKit"
] | eee876130a7b51bd9e7d610adb20b564288473457f36c92c9c64fb8335e66bd7 |
# Load dependencies
import ovito
import ovito.vis
# Load the native modules.
import PyScriptGUI
# Inject selected classes into parent module.
ovito.vis.OpenGLRenderer = PyScriptGUI.OpenGLRenderer | srinath-chakravarthy/ovito | src/plugins/pyscript/gui/python/ovito/vis/gui/__init__.py | Python | gpl-3.0 | 197 | [
"OVITO"
] | 3cc80fdc64abac12474da1e37a116886b7ef3243a039b7605914dd4e030affb1 |
import datetime
import difflib
from flask import redirect, render_template, render_template_string, Blueprint, flash
from flask import request, url_for, jsonify
from flask_user import current_user, login_required, roles_accepted
from flask_login.mixins import AnonymousUserMixin
from flask_mail import Mail, Message
fro... | ignotus-peverell/nash | app/views.py | Python | bsd-2-clause | 13,953 | [
"VisIt"
] | 3ff31874f5db918c3a395ddd376c6b1b5646d99f9e61ee1800fc8db10ecc0e0c |
# Copyright 2015 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... | unnikrishnankgs/va | venv/lib/python3.5/site-packages/tensorflow/python/ops/template.py | Python | bsd-2-clause | 13,029 | [
"VisIt"
] | 5ede986f35f71b7f219e9bf7b8935f3f23f6f52ebcba579ac9a4ee9bba28770e |
from frappe import _
def get_data():
return [
{
"label": _("Sales Pipeline"),
"icon": "fa fa-star",
"items": [
{
"type": "doctype",
"name": "Lead",
"description": _("Database of potential customers."),
},
{
"type": "doctype",
"name": "Opportunity",
"description": _... | elba7r/system | erpnext/config/crm.py | Python | gpl-3.0 | 2,853 | [
"VisIt"
] | b57ee26f78536e39db980369a7ade19337132171ce72b609b3cec3e131903092 |
#!/usr/bin/env python
### this is galaxy code
### https://bitbucket.org/peterjc/galaxy-central/src/5cefd5d5536e/tools/ncbi_blast_plus/blast.py
import sys
xmlfiles = sys.argv[2:]
xmlout = sys.argv[1]
def merge(split_files, output_file):
"""Merging multiple XML files is non-trivial and must be done in subclas... | IGB-UIUC/webblast | bin/BlastXMLmerge.py | Python | gpl-3.0 | 3,532 | [
"BLAST",
"Galaxy"
] | 65eb7cbe7c7c142f19a04dffd2f5fbf2aa699b6e4fd09395a9a8242d39c8e13f |
""" The Script class provides a simple way for users to specify an executable
or file to run (and is also a simple example of a workflow module).
"""
# FIXME: Remove me after v6r10
# just a copy of Wokflow.Modules.Script, for backward compatibility with jobs already in the system.
import os, sys, re
from DIRAC.C... | avedaee/DIRAC | Workflow/Modules/Script.py | Python | gpl-3.0 | 4,302 | [
"DIRAC"
] | a567729bec882688328d6c0cc3ef59d82e18daba31a61f980a3e3698087fb73e |
#for more info and material (source codes )about lr please visit: https:https://github.com/PhenixI/machine-learning/tree/master/15-SVM
#load dataset
from sklearn import datasets
import numpy as np
iris = datasets.load_iris()
X= iris.data[:,[2,3]]
y = iris.target
#split the dataset into separate training and test da... | PhenixI/machine-learning | 1_supervised_classification/15-SVM/svm/svm.py | Python | gpl-2.0 | 1,315 | [
"VisIt"
] | 38995d9886592c02f63e30fa2ef4199b1ea5c61c5e79c231043bc0ddcf7cbf4c |
import re
REGEXES = map(re.compile, (' (?P<name>[A-Z]{6,7} [A-Z0-9]{3,9}) ',
'\((?P<name>[A-Z0-9\-]{4,8}[lpsu]{,4})\)',
'^(J-PHONE|Vodafone|SoftBank)/\d.\d/V?(?P<name>[A-Z0-9\-f]{3,})(/|_?[a-c]|$)',
' (Sony)?(Ericsson)?(?P<name>[A-Z\-]{,... | ikegami-yukino/kpy | kpy/kpy.py | Python | mit | 1,802 | [
"Galaxy"
] | eef0b22cf2df4189e4c77dc69a7089f878a8ea9da0762e5e2fbe961c1480b6e4 |
#
# This file is part of Healpy.
#
# Healpy is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# Healpy is distributed in the hope... | healpy/healpy | healpy/sphtfunc.py | Python | gpl-2.0 | 43,322 | [
"Gaussian"
] | e5c6680132f30140626dd719f00ad51cb7e488e7832a3ef544906d48572fa7cc |
from django.shortcuts import render, redirect
from .models import UsersRedirect, SettingsUser, AnalyticsTwo, AnalyticsOne
from django.contrib.auth.models import User
from django.contrib.auth import authenticate, login, logout
# Create your views here.
percentage = 50
siteTwo = 'page1.html'
siteOne = 'page2.html'
if... | vigzmv/AB-Split-Tester | testerhack/views.py | Python | mit | 5,675 | [
"VisIt"
] | c2078f6724ac7da74c96534be94921cb6314ceb92ef03b5ebe27df8714ec1160 |
import numpy as np
import sys, os, math
import datetime as dt
import scipy, scipy.signal
import parmap
from scipy.interpolate import splrep, splev, make_interp_spline, splder, sproot
from tqdm import tqdm
# doing imports inside module until travis is fixed
# Cat: TODO: move these to the top once Peter's workstation wo... | paninski-lab/yass | src/yass/deconvolve/match_pursuit_gpu_OLD.py | Python | apache-2.0 | 65,891 | [
"NEURON"
] | 3c402156deba134b13e1bc92f555982b9db5e5570e8c4f8c0897f5ff10c4fbc7 |
"""API description for managing plotting theme parameters in pyvista.
Examples
--------
Apply a built-in theme
>>> import pyvista
>>> pyvista.set_plot_theme('default')
>>> pyvista.set_plot_theme('document')
>>> pyvista.set_plot_theme('dark')
>>> pyvista.set_plot_theme('paraview')
Load a theme into pyvista
>>> theme... | akaszynski/vtkInterface | pyvista/themes.py | Python | mit | 62,256 | [
"ParaView",
"VTK"
] | 7aeb0dfe01564805471d28fc4e996bcc6e21b1542d0f0fc8c6db4297df683622 |
#!/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/geomopt/test/test_geometric_solver.py | Python | apache-2.0 | 2,489 | [
"PySCF"
] | 583964a45b86d3031272ad24dcb52a19f02de6a427e2013bf0f8d197e0af8226 |
import sys
if sys.version_info >= (3, 5, 0):
# Add async functions
from .async_ import Route
else:
from .sync_ import Route
imgtypes = [
"cry", "cuddle", "hug", "kiss", "lewd",
"lick", "nom", "nyan", "owo", "pat",
"pout", "rem", "slap", "smug", "stare",
"tickle", "triggered", "nsfw-gtn",
... | martmists/ram-api-wrapper | ram/v1.py | Python | mit | 556 | [
"MOE"
] | b9b5661efab5e3a4fa7bb0465f1210da30e7121037b45da27af50dbc5b6e10c4 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
#
#
# 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... | e-gob/plataforma-kioscos-autoatencion | scripts/ansible-play/.venv/lib/python2.7/site-packages/ansible/modules/network/avi/avi_prioritylabels.py | Python | bsd-3-clause | 3,614 | [
"VisIt"
] | 9f6241233cb933428949bbc9224f1a41eea42755abf382a5d3362b1e39f2606a |
import collections
import multiprocessing
import pysam
import os
import pandas as pd
def bedgraph_coverage(intervals, zero=False, lengths=None):
''' Function creates coverage from a supplied interval list.
Function takes 1 argument:
1) intervals - Either a pair of 'multiprocessing.connection' objects... | adam-rabinowitz/ngs_python | bed/bedgraph.py | Python | gpl-2.0 | 9,388 | [
"pysam"
] | d14132fe232e7fa6a8e05b19d1a0bee901cf69e1519f6a6d0ca1f385c84582fc |
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