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# cx_Freeze setup file
import sys
from cx_Freeze import setup, Executable
# Dependencies are automatically detected, but it might need fine tuning.
build_exe_options = {"packages": ["pysam"]}
# GUI applications require a different base on Windows (the default is for a
# console application).
base = None
if sys.platf... | mjsull/HapFlow | setup.py | Python | gpl-3.0 | 592 | [
"pysam"
] | 983e4f224120726e3442d9d8da4281a9e569aedb79e76451b00aff2876ebf54a |
import math
import sys
# http://www.wwpdb.org/documentation/format33/sect9.html#ATOM
# get more from http://www.rasmol.org/software/RasMol_2.7.4/src/abstree.h
radii = {
' H': 1.100,
' C': 1.548,
' N': 1.400,
' O': 1.348,
' P': 1.880,
' S': 1.808,
'CA': 1.948,
'FE': 1.948,
'ZN': 1.1... | bradgrantham/fragment-shader-rt | pdb_to_ray.py | Python | apache-2.0 | 2,823 | [
"Jmol",
"RasMol"
] | 8739585bad9b7b8f6f13e4bf9b6204c8ca8dec5c82477e853cb0c4a22d9f6eeb |
"""Astronomical and physics constants.
This module complements constants defined in `astropy.constants`,
with gravitational paremeters and radii.
Note that `GM_jupiter` and `GM_neptune` are both referred to the whole planetary system gravitational parameter.
Unless otherwise specified, gravitational and mass paramet... | Juanlu001/poliastro | src/poliastro/constants/general.py | Python | mit | 14,923 | [
"Brian"
] | bcebd1ad7c970f7f6b46cb58ba5e2d7607621681d2b07956af04ad9fa721dd4e |
# $HeadURL$
__RCSID__ = "$Id$"
import os
import types
import time
from DIRAC.Core.DISET.private.FileHelper import FileHelper
from DIRAC.Core.Utilities.ReturnValues import S_OK, S_ERROR, isReturnStructure
from DIRAC.FrameworkSystem.Client.Logger import gLogger
from DIRAC.ConfigurationSystem.Client.Config import gConfig... | avedaee/DIRAC | Core/DISET/RequestHandler.py | Python | gpl-3.0 | 19,908 | [
"DIRAC"
] | d7eb057290892490c8b9353f9d316f75894ac9b80638565ec9b0ea52bf68de4b |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Makes sure that all files contain proper licensing information."""
import json
import optparse
import os.path
import subproces... | was4444/chromium.src | tools/checklicenses/checklicenses.py | Python | bsd-3-clause | 23,516 | [
"Galaxy"
] | b6252cc7cd8721df72978ec5a6f60f3e4b11d40c4192a06f4628f4fe28d9f755 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | MOA-2011/enigma2-plugin-extensions-openwebif | plugin/controllers/views/web/getservices.py | Python | gpl-2.0 | 5,530 | [
"VisIt"
] | 668e7b9e25e813e13f9ebb583963aa11270d0178aa67c00302b32c99ff7c3d1b |
"""
Sheets for simulating a moving eye.
This module provides two classes, ShiftingGeneratorSheet, and
SaccadeController, that can be used to simulate a moving eye,
controlled by topographic neural activity from structures like the
superior colliculus.
ShiftingGeneratorSheet is a subclass of GeneratorSheet that accept... | Tasignotas/topographica_mirror | topo/sheet/saccade.py | Python | bsd-3-clause | 13,040 | [
"Gaussian"
] | 5c011952e4335d1eac39de3999ffe8f776fac0719ffb3201c667d2ca5095563e |
#
# Copyright (c) 2015 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... | vinodpanicker/scancode-toolkit | tests/cluecode/test_finder.py | Python | apache-2.0 | 19,903 | [
"VisIt"
] | 9ec90133d4a0a10345ff90d66a1568469ab65c47c74f6de4132683851ab5f127 |
import math
import re
import numpy as np
from .utilities import unittest
import cantera as ct
from . import utilities
class TestReactor(utilities.CanteraTest):
reactorClass = ct.Reactor
def make_reactors(self, independent=True, n_reactors=2,
T1=300, P1=101325, X1='O2:1.0',
... | imitrichev/cantera | interfaces/cython/cantera/test/test_reactor.py | Python | bsd-3-clause | 45,181 | [
"Gaussian"
] | eaff1ff6dee408f4fcfefb4624c2c572e8a25fb9a20d8857a7109b764bdf38f1 |
#!/usr/bin/python
"""SPF (Sender Policy Framework) implementation.
Copyright (c) 2003 Terence Way <terry@wayforward.net>
Portions Copyright(c) 2004,2005,2006,2007,2008,2011,2012 Stuart Gathman <stuart@bmsi.com>
Portions Copyright(c) 2005,2006,2007,2008,2011,2012,2013 Scott Kitterman <scott@kitterman.com>
Portions Copy... | abpai/mailin-test | python/spf.py | Python | mit | 78,209 | [
"VisIt"
] | dadc927f24b827ef5dc774586b2c2eb9b8c3f6f2bc922517a4378f9f63cf4478 |
# This module provides classes that represent VRML objects for use
# in data visualization applications.
#
# Written by: Konrad Hinsen <hinsen@cnrs-orleans.fr>
# Last revision: 2004-7-19
#
"""This module provides definitions of simple 3D graphics objects and
VRML scenes containing them. The objects are appropriate for... | OS2World/DEV-PYTHON-UTIL-ScientificPython | src/Lib/site-packages/Scientific/Visualization/VRML.py | Python | isc | 19,517 | [
"VMD"
] | 1ee6dd40a59aa0367061f1972f1ebda9468d6737465178af1347c6e4093262ee |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
.. py:currentmodule:: sample_viewer
:synopsis: Script to view the mcxray sample in 3D.
.. moduleauthor:: Hendrix Demers <hendrix.demers@mail.mcgill.ca>
Script to view the mcxray sample in 3D.
"""
#######################################################... | drix00/pymcxray | pymcxray/gui/sample_viewer.py | Python | apache-2.0 | 5,618 | [
"VTK"
] | 6e4e4427d14373bc9944f4eb39d235c8a103bb69d291ea8997a057b8e1fe8bf2 |
import os, sys
from pprint import pprint
import importlib
import logging.handlers
from utils.processes import local_subprocess, mp_pool
import utils.xutils as xutils
import utils.log
import sites.necat as site
from utils.modules import load_module
def run_analysis(work_dir, logfile=False):
""" RUN Analysis """
... | RAPD/RAPD | src/test/test_plugin.py | Python | agpl-3.0 | 8,427 | [
"ADF"
] | ba02549e70e00581842bdc4cd1675f070ff64cc0cc521555aeb3690053546f09 |
from django.http import HttpResponseForbidden
from django.shortcuts import get_object_or_404
from django.http import HttpResponseRedirect, HttpResponse
from django.utils.translation import ugettext_lazy as _
from organizations.models import Organization, OrganizationUser
class OrganizationMixin(object):
"""Mixin... | meletakis/collato | esn/organizations/mixins.py | Python | gpl-2.0 | 4,111 | [
"VisIt"
] | 21fa539552dbf272dff7a13790325cbd6f65e5afb523630f94cf2b6395d03ebf |
#!/usr/bin/env python
"""
Simple script that uses Biopython SeqIO to convert
between various file formats for sequence data.
See documentation online at:
http://biopython.org/wiki/SeqIO
"""
# This program is free software: you can redistribute it and/or
# modify it under the terms of the GNU General Public License ... | jrjhealey/bioinfo-tools | x2y.py | Python | gpl-3.0 | 4,332 | [
"Biopython"
] | ce516ba50f00a27916b62d17b1c2ced50f0144b1e7b0b2798091781f78981bba |
"""
Implementation of WebApplication that logs memory usage before and after
calling each controller method.
"""
import pkg_resources
pkg_resources.require( "PSI" )
import psi.process
import os
import logging
from galaxy.web.framework import WebApplication
log = logging.getLogger( __name__ )
pid = os.getpid()
clas... | volpino/Yeps-EURAC | lib/galaxy/web/framework/memdebug.py | Python | mit | 897 | [
"Galaxy"
] | 50dc2a96210b8b49b3bcf226bbb81183008dd10f871c0f9d9d16560ac6b9953a |
import numpy as np
import regreg.api as rr
from selection.randomized.glm import pairs_bootstrap_glm, bootstrap_cov
from selection.randomized.query import query
from selection.randomized.randomization import split
import functools
def pairs_bootstrap_glm(glm_loss,
active,
... | selective-inference/selective-inference | selectinf/sandbox/bayesian/estimator.py | Python | bsd-3-clause | 29,896 | [
"Gaussian"
] | 6b0330afe4186269312884948e252830312f52a11d48779d2250f86f0d0da655 |
#Copyright ReportLab Europe Ltd. 2000-2012
#see license.txt for license details
#history http://www.reportlab.co.uk/cgi-bin/viewcvs.cgi/public/reportlab/trunk/reportlab/platypus/paraparser.py
__version__=''' $Id$ '''
__doc__='''The parser used to process markup within paragraphs'''
import string
import re
import sys
im... | agramian/PythonExternalProgramTestFramework | reportlab/platypus/paraparser.py | Python | mit | 45,455 | [
"VisIt"
] | 35d39491e16eb51860a2acafa26b41eb1a147d168cd12def4918e81d76f1e0b5 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2011 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Software F... | tiagocardosos/stoq | stoqlib/gui/search/callsearch.py | Python | gpl-2.0 | 6,419 | [
"VisIt"
] | 38243817b5777adba62b73a0980e88208379d903711f1c2db83fa6625267fcc5 |
import unittest
import os
import json
from io import open
from pymatgen.phonon.bandstructure import PhononBandStructure, PhononBandStructureSymmLine
from pymatgen.util.testing import PymatgenTest
test_dir = os.path.join(os.path.dirname(__file__), "..", "..", "..",
'test_files')
class Phono... | dongsenfo/pymatgen | pymatgen/phonon/tests/test_bandstructure.py | Python | mit | 3,599 | [
"pymatgen"
] | cae294ad22b64636890abd6cde85ef66c44e135f056de93d5e3279288a06e8b3 |
##
## Biskit, a toolkit for the manipulation of macromolecular structures
## Copyright (C) 2004-2009 Raik Gruenberg & Johan Leckner
##
## 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 v... | graik/biskit | archive_biskit2/Biskit/Mod/SequenceSearcher.py | Python | gpl-3.0 | 34,486 | [
"BLAST",
"Biopython"
] | a137d826177d0738c78cda1fc94d607e9114c6f1b98802e5cc02e52682576210 |
from boto import connect_s3, connect_ec2
from boto.s3.key import Key
from datetime import datetime
from django.conf import settings
from django.contrib import admin
from django.db import models
from django.forms import TextInput, Textarea
from kombu import Exchange
from models import InstanceRequest, AmazonMachineImage... | opentripplanner/OTPSetup | otpsetup/client/admin.py | Python | gpl-3.0 | 12,559 | [
"VisIt"
] | 8b0ed9f1c5dc7d18c3706d5596c4730245e8417ad08086d8d41fafdea206bb5c |
from pele.amber.amberSystem import AMBERSystem
from pele.gui import run as gr
sysAmb = AMBERSystem('coords.prmtop', 'coords.inpcrd')
gr.run_gui(sysAmb, db="optimdb.sqlite")
| kjs73/pele | playground/amber/aladipep/optim2pele/run_gui.py | Python | gpl-3.0 | 182 | [
"Amber"
] | bd8c5dfb6ec7dab29b1b55b27153f53e0266901968a55ef1c82135590e997a34 |
from random import choice
import pysam
import os
import sys
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('input_bam', help="input BAM or SAM file (must be sorted!)")
parser.add_argument("output_bam", help="output BAM or SAM file")
options = parser.parse_args()
if options.input_bam.endswith(... | TheFraserLab/Hornet | mapping/rmdup.py | Python | apache-2.0 | 1,396 | [
"pysam"
] | 01253d98cfa6c061d22750ad5b920c80ad53e8d1d8c7c1f2da55e2cfbfca5ece |
#!/usr/bin/env python
import gtk
from math import sqrt
from gettext import gettext as _
import numpy as np
from ase.gui.widgets import pack, Help
class Repeat(gtk.Window):
def __init__(self, gui):
gtk.Window.__init__(self)
self.set_title(_('Repeat'))
vbox = gtk.VBox()
pack(vbox, ... | JConwayAWT/PGSS14CC | lib/python/multimetallics/ase/gui/repeat.py | Python | gpl-2.0 | 1,331 | [
"ASE"
] | 0682c41925e080e2b99d151b5a62f2f15b2db76b1bb9d74e067f00c823f7a91e |
"""Testing simple density estimation baselines for IRL."""
from typing import Sequence
import numpy as np
import pytest
from imitation.algorithms.density_baselines import (
STATE_ACTION_DENSITY,
STATE_DENSITY,
STATE_STATE_DENSITY,
DensityReward,
DensityTrainer,
)
from imitation.data import rollou... | humancompatibleai/imitation | tests/test_density_baselines.py | Python | mit | 3,376 | [
"Gaussian"
] | f35887041475f9715edc17eac984796861615de49187589d20b867564f7b550f |
""" Snob, 'because it arbitrarily puts things in classes' -- C.S. Wallace. """
import logging
from . import (estimator, gaussian, slf)
__version__ = "0.0.1"
logger = logging.getLogger(__name__)
logger.setLevel(logging.DEBUG)
handler = logging.StreamHandler()
handler.setFormatter(logging.Formatter(
"%(asctime)... | andycasey/snob | snob/__init__.py | Python | mit | 411 | [
"Gaussian"
] | 0b3cb9819437faeada75777aabfc9c139561c915e3c8e26027d98977e299f520 |
import requests
from difflib import SequenceMatcher
from bears.general.URLHeadBear import URLHeadBear
from coalib.results.Diff import Diff
from coalib.bears.LocalBear import LocalBear
from dependency_management.requirements.PipRequirement import PipRequirement
from coalib.results.RESULT_SEVERITY import RESULT_SEVERIT... | coala-analyzer/coala-bears | bears/general/InvalidLinkBear.py | Python | agpl-3.0 | 4,387 | [
"VisIt"
] | 595fabf55fadb55decb5afb7c74bf973c6035fe7b0a02bf7ea5e91f7baf68de4 |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
"""
%prog rice.sorghum.last --qbed=rice.bed --sbed=sorghum.bed
Given a blast, we find the syntenic regions for every single gene. The
algorithm works by expanding the query gene to a window centered on the gene. A
single linkage algorithm follows that outputs the synteny ... | sgordon007/jcvi_062915 | compara/synfind.py | Python | bsd-2-clause | 8,974 | [
"BLAST"
] | 51e2d060d9ce0b3d5d798687e4619bdfd79ba1a53f85737a2cd0c833920aab2f |
#
# This file is a part of Siesta Help Scripts
#
# (c) Andrey Sobolev, 2013
#
import numpy as np
from abstract import PerStepData
class CoordinationNumbers(PerStepData):
''' Data for plotting stepwise evolution of partial coordination
numbers of the system
'''
_shortDoc = "Coordination numbers"
... | ansobolev/shs | shs/data/per_step.py | Python | mit | 1,129 | [
"SIESTA"
] | b9f9e6bb468332222c67df19df6f560c3e73be408ae4622fbc3ba5c2d9b77ace |
#!/usr/bin/env python3
# PYTHON_ARGCOMPLETE_OK
# ======================================================================
# matscipy - Python materials science tools
# https://github.com/libAtoms/matscipy
#
# Copyright (2019) Johannes Hoermann, University of Freiburg
#
# This program is free software: you can redistribut... | libAtoms/matscipy | matscipy/cli/electrochemistry/c2d.py | Python | lgpl-2.1 | 12,367 | [
"ASE",
"Avogadro",
"LAMMPS",
"Matscipy"
] | 3e2f13424bb3041bf7d2d9dc7b8e459077d9434234ea8ca4a8fe725be62c6505 |
import numpy as np
import matplotlib.pyplot as plt
import uncertainties
from scipy.signal import find_peaks
from scipy.optimize import curve_fit
import scipy.constants as sc
import scipy.integrate as integrate
from uncertainties import ufloat
from uncertainties import unumpy as unp
from uncertainties.unumpy import nomi... | smjhnits/Praktikum_TU_D_16-17 | Fortgeschrittenenpraktikum/Protokolle/V18_Germaniumdetektor/Python/unbekannt2.py | Python | mit | 4,968 | [
"Gaussian"
] | d1015e8c9b2b7e7e396797ef4210c517837b822d51e6c9e901b45fdf3969b10f |
import sys
import os
import paraview
import paraview.simple as pvsimple
paraview.servermanager.misc.GlobalMapperProperties.GlobalImmediateModeRendering = 1
# trying to import the library where I can specify the global and subcontrollers
import vtkParallelCorePython
paraview.options.batch = True # this may not be nec... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/Wrapping/Python/paraview/spatiotemporalparallelism.py | Python | gpl-3.0 | 4,861 | [
"ParaView"
] | 29528879e6d780e81de2e2ed053554593279e3c032e53e50d005479e67de7980 |
import pysam
import argparse
import sys
import logging
import os
import subprocess
DEBUG=False
NOT_DEBUG=not DEBUG
parser = argparse.ArgumentParser(description="Comet Peptide Spectrum Match Distiller.",
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('-i',... | shengqh/ngsperl | lib/Proteomics/Distiller/CometDistiller.py | Python | apache-2.0 | 2,700 | [
"pysam"
] | b5b0f4784079fa007508abc2ecb64d474ff779763e0c322409b2cad008b728b3 |
# Copyright (C) 2018
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, o... | niktre/espressopp | src/interaction/TabulatedSubEnsDihedral.py | Python | gpl-3.0 | 6,664 | [
"ESPResSo"
] | 8e78d5974ecfb5203b495c94889b584b73dc15a740a04fc3b1eafc2836b9003f |
"""Tools to create photometric catalogues from VPHAS data.
Classes
-------
VphasFrame
VphasOffsetCatalogue
Example command-line use
------------------------
Create a photometric catalogue of VPHAS pointing 0149a from the command-line:
```
$ vphas-offset-catalogue 0149a
```
Build an index table of catalogues created:
... | barentsen/surveytools | surveytools/catalogue.py | Python | mit | 62,470 | [
"Gaussian"
] | b4c3a1054fbe4a73cb085e8ac07c13234977aeb15fb2bba78a488acdb8c1a848 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2005-2012 Async Open Source
##
## This program is free software; you can redistribute it and/or
## modify it under the terms of the GNU Lesser General Public License
## as published by the Free Software Foundation; either version 2
## of the Licens... | andrebellafronte/stoq | stoqlib/lib/defaults.py | Python | gpl-2.0 | 4,296 | [
"VisIt"
] | f8885112a399c583b3f96b0877775aaeead282243d72088f7fe42a27a2fc60b7 |
# coding=utf-8
# Copyright 2017 The DLT2T 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 applicable law or ... | renqianluo/DLT2T | DLT2T/data_generators/algorithmic.py | Python | apache-2.0 | 14,442 | [
"Gaussian"
] | cb257b444f9800720782f9823576ca533b005e1d2d3e50e863f150e76cac5315 |
from __future__ import print_function
from orphics import maps,io,cosmology,stats
from enlib import enmap
import numpy as np
import os,sys
"""
What I've learned from this script.
There's no difference between PS calculated on
sims that have been kspace convolved with a gaussian beam
and real-space convolved with a ga... | msyriac/orphics | tests/legacy/convolve.py | Python | bsd-2-clause | 4,145 | [
"Gaussian"
] | 6faa1b81b2ffff355de6471ee53e55b8b0e1e353f03cd2109d81d46380066e6b |
# /usr/local/bin/python3
# --*-- coding: utf-8 --*--
# __author__ = 'Jieer'
import sys
import random
import collections
print("System.args",sys.argv)
print(sys.path)
possibilities = ['rain','snow','sleet','frog','sun','who knows']
print(random.choice(possibilities))
peridoic_talbe = {'Hydrogen':1,'Helium':2}
carbon... | lmee/exercise1 | basic_function.py | Python | apache-2.0 | 1,408 | [
"MOE"
] | 00cc680fa4a7bcffbceb8c0227b6813f650ed99c5381623d061f86f0652b8f5a |
# 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... | allenlavoie/tensorflow | tensorflow/contrib/autograph/converters/single_return.py | Python | apache-2.0 | 11,039 | [
"VisIt"
] | 3021d3191d169b789061e4420de508b0a7cf782b099518532637f5a566159653 |
#!/usr/bin/env python
#
# $File: PySelector.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can redistribute... | BoPeng/simuPOP | docs/PySelector.py | Python | gpl-2.0 | 2,188 | [
"VisIt"
] | 41a66798838c6857db7add0478a256162ad8e6ab1070e5c2c95ebfbe48bfa2a3 |
# -*- coding: utf-8 -*-
# Generated by Django 1.11.3 on 2017-10-12 22:15
from __future__ import unicode_literals
from django.db import migrations
def add_sector_teams(apps, schema_editor):
SectorTeam = apps.get_model('fdi', 'SectorTeam')
sector_teams = {'Aero': 'Aerospace',
'AESC': 'Advan... | UKTradeInvestment/export-wins-data | fdi/migrations/0020_auto_20171012_2215.py | Python | gpl-3.0 | 21,669 | [
"CASINO"
] | f86ae133907b00fe255477a2e68be5ca5cd2e65d62469bb0d297241d66a5f95c |
'''
Created on Jul 14, 2011
@author: mkiyer
'''
import os
import subprocess
import chimerascan.lib.config as config
from chimerascan.lib.feature import GeneFeature
from chimerascan.lib.seq import DNA_reverse_complement
from chimerascan import pysam
BASES_PER_LINE = 50
def split_seq(seq, chars_per_line):
pos = 0... | tectronics/chimerascan | chimerascan/deprecated/generate_transcript_reads.py | Python | gpl-3.0 | 3,842 | [
"pysam"
] | f9b3571eb6d820b3295b5dd53fadaa3b34c652e96955ffe759fcb8025e8580ba |
########################################################################
#
# (C) 2015, Brian Coca <bcoca@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... | amenonsen/ansible | lib/ansible/galaxy/__init__.py | Python | gpl-3.0 | 2,391 | [
"Brian",
"Galaxy"
] | 65a8b509147f41cfd4a1cb38457765b9433f296a88e0b291d33c58b4441f0bad |
from astropy.coordinates import Distance, Angle, SkyCoord
from astropy import units as u
import numpy as np
def rho_phi(coord, glx_ctr):
'''
Eqs 1, 2 & 3 from van der Marel & Cioni (2001).
Parameters
----------
coord : :class:`astropy.coordinates.ICRS`
Coordinate of points to compute gal... | Gabriel-p/mcs_rot_angles | aux_modules/deproj_dist.py | Python | gpl-3.0 | 10,366 | [
"Galaxy"
] | 768fb57997b56b4238407ad75d863e56fa45b34b25269209ef339db8700baaed |
######################################################################
# Copyright (C) 2011,2012 Jaakko Luttinen
#
# This file is licensed under Version 3.0 of the GNU General Public
# License. See LICENSE for a text of the license.
######################################################################
###############... | nipunreddevil/bayespy | bayespy/inference/vmp/nodes/__init__.py | Python | gpl-3.0 | 1,782 | [
"Gaussian"
] | 818731bdbdbb592a050555beb13777343951f35287cedc010f49b193e5d39dfe |
#!/usr/bin/env python3
import optparse
import re
def parse_options():
"""
Parse the options guiven to the script
"""
parser = optparse.OptionParser(description='Get unmatched blast queries')
parser.add_option('-f', '--fasta', dest='fasta_file',
help='Query fasta file used du... | drosofff/tools-artbio | tools/blast_unmatched/blast_unmatched.py | Python | mit | 2,033 | [
"BLAST"
] | a8e0cd86911fb69e9cea310d828fa4852b6a9c0d6293e50188e6f26f2ff24712 |
# Copyright Anne M. Archibald 2008
# Released under the scipy license
import os
from numpy.testing import (assert_equal, assert_array_equal, assert_,
assert_almost_equal, assert_array_almost_equal,
assert_allclose)
from pytest import raises as assert_raises
import ... | anntzer/scipy | scipy/spatial/tests/test_kdtree.py | Python | bsd-3-clause | 48,898 | [
"VisIt"
] | a83678dbcaacb0a7fe74681545f2b7af64f695da8614714c0e1611c212659dff |
#
# Copyright (C) 2001 greg Landrum
#
""" unit testing code for MLData sets
"""
import contextlib
import random
import unittest
from rdkit import RDConfig
from rdkit.ML.Data import MLData, DataUtils
from rdkit.six import StringIO
from rdkit.six.moves import cPickle
class TestCase(unittest.TestCase):
def setUpQ... | rvianello/rdkit | rdkit/ML/Data/UnitTestMLData.py | Python | bsd-3-clause | 7,115 | [
"RDKit"
] | 5b8b520f4e8a61b8495dcd2efabc4c549bd16860a9425848ab27bdecb69ce187 |
# coding: utf-8
#!/usr/bin/env python
from __future__ import division, unicode_literals
"""
#TODO: Write module doc.
"""
__author__ = 'Shyue Ping Ong'
__copyright__ = 'Copyright 2013, The Materials Virtual Lab'
__version__ = '0.1'
__maintainer__ = 'Shyue Ping Ong'
__email__ = 'ongsp@ucsd.edu'
__date__ = '8/1/15'
i... | rousseab/pymatgen | pymatgen/io/nwchemio.py | Python | mit | 490 | [
"NWChem",
"pymatgen"
] | 2abc6b7c04f15d7f6b224e0f85eb3d779e65e29105cb87febb21e099cc6902ce |
from ovito import *
from ovito.io import *
from ovito.modifiers import *
import numpy as np
node = import_file("../../files/CFG/shear.void.120.cfg")
modifier = AffineTransformationModifier()
node.modifiers.append(modifier)
print(modifier.relative_mode)
modifier.relative_mode = True
print(modifier.transform_particle... | srinath-chakravarthy/ovito | tests/scripts/test_suite/affine_transformation_modifier.py | Python | gpl-3.0 | 811 | [
"OVITO"
] | 66bf626a911d9c4e3cf4e57e0dca418cc3ba52df12155e067db1586089521abc |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
This example shows how to control DIIS parameters and how to use different
DIIS schemes (CDIIS, ADIIS, EDIIS) in SCF calculations.
Note the calculations in this example is served as a demonstration for the use
of DIIS. Without other convergenc... | gkc1000/pyscf | examples/scf/24-tune_diis.py | Python | apache-2.0 | 1,705 | [
"PySCF"
] | e7f85481d4b7078b650422a093127278f07626cc0cd58ff226f034fa24f7261e |
# coding=utf-8
"""
The XFSCollector collects XFS metrics using /proc/fs/xfs/stat.
#### Dependencies
* /proc/fs/xfs/stat
"""
import diamond.collector
import sys
class XFSCollector(diamond.collector.Collector):
PROC = '/proc/fs/xfs/stat'
def get_default_config_help(self):
config_help = super(XFS... | acquia/Diamond | src/collectors/xfs/xfs.py | Python | mit | 6,543 | [
"VisIt"
] | 62cf1e6bd392f75f94c21d6d3cc61c979f9aceb2549a4edcb77a613722e7d064 |
"""Functional tests for cross country app
"""
from selenium import webdriver
import unittest
class NewVisitorTest(unittest.TestCase):
""" Test new visitor flow
"""
def setUp(self):
self.browser = webdriver.Firefox()
self.browser.implicitly_wait(3)
def tearDown(self):
self.browser.quit()
def te... | ColCarroll/cross_tracker | functional_tests.py | Python | mit | 553 | [
"VisIt"
] | 2292743265144e3fdced499635cbccdc2fa3f9a097bf58d15760ddfbd3280ad5 |
from PyQt5 import QtCore, QtWidgets, QtGui
import util
class gameSettingsWizard(QtWidgets.QWizard):
def __init__(self, client, *args, **kwargs):
QtWidgets.QWizard.__init__(self, *args, **kwargs)
self.client = client
self.settings = GameSettings()
self.settings.gamePortSpi... | GrotheFAF/client | src/client/loginwizards.py | Python | gpl-3.0 | 2,789 | [
"VisIt"
] | 3bafb2373fb68c27b1dd57bf8fcdc4d9dc59b85dc59b8155c2f428bcd72f02e5 |
""" The WorkflowTaskAgent takes workflow tasks created in the TransformationDB and submits them to the WMS.
The following options can be set for the WorkflowTaskAgent.
.. literalinclude:: ../ConfigTemplate.cfg
:start-after: ##BEGIN WorkflowTaskAgent
:end-before: ##END
:dedent: 2
:caption: WorkflowTaskAgent op... | andresailer/DIRAC | TransformationSystem/Agent/WorkflowTaskAgent.py | Python | gpl-3.0 | 1,743 | [
"DIRAC"
] | c9269501182b1d732b446fd4252c131f353c2084c3ac27418b9ba246af01102c |
"""
Acceptance tests for Studio.
"""
from bok_choy.web_app_test import WebAppTest
from ..pages.studio.asset_index import AssetIndexPage
from ..pages.studio.auto_auth import AutoAuthPage
from ..pages.studio.checklists import ChecklistsPage
from ..pages.studio.course_import import ImportPage
from ..pages.studio.course_i... | nanolearning/edx-platform | common/test/acceptance/tests/test_studio_general.py | Python | agpl-3.0 | 5,023 | [
"VisIt"
] | f3c06a126e39e64070fb41db4d4ef49920201e5df9fbb468cd0cacc5a65e34e1 |
'''
Created on 25 Jan. 2018
@author: Alex Ip
Quick-and-dirty point fetching demo
'''
import os
import sys
import csv
import netCDF4
import argparse
import logging
import re
from datetime import datetime
from pprint import pformat
import numpy as np
from geophys_utils import NetCDFPointUtils
# Setup logging handlers... | alex-ip/geophys_utils | examples/geophys_point_fetcher.py | Python | apache-2.0 | 13,150 | [
"NetCDF"
] | d7fecdac62fe9a29eeed0ca2f01e1a73d54d803c67f62cb45a9945e545477cb4 |
#! /usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requi... | googleapis/python-redis | scripts/fixup_redis_v1beta1_keywords.py | Python | apache-2.0 | 6,526 | [
"VisIt"
] | 6ddf453aad85d8f159b2c4b54a9c7cd7948790239f30cff8698388f22cb21465 |
# -*- coding: utf-8 -*-
#
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as pu... | thica/ORCA-Remote | src/scripts/tools/tool_importexport/script.py | Python | gpl-3.0 | 8,006 | [
"ORCA"
] | 0c1c29da309ca9718035d6899cbff27c93cc9b76f5c88b7fc3027827575bc115 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2003-2007 Donald N. Allingham
# Copyright (C) 2007-2012 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2012-2016 Paul Franklin
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of th... | Fedik/gramps | gramps/plugins/drawreport/timeline.py | Python | gpl-2.0 | 21,963 | [
"Brian"
] | 89c328af2da4deb7cdd9401532b85490f3c5919fc889f4303e0e45ba116d80b8 |
#!/usr/bin/env python
#
# Copyright (c) 2002, 2003 Bryce "Zooko" Wilcox-O'Hearn
# portions Copyright (c) 2001 Autonomous Zone Industries
# This file is licensed under the
# GNU Lesser General Public License v2.1.
# See the file COPYING or visit http://www.gnu.org/ for details.
__revision__ = "$Id: test_system... | zooko/egtp_new | egtp/test/test_system.py | Python | lgpl-2.1 | 10,903 | [
"VisIt"
] | 2c0d7a7a5db955bfe250740c10848e2294ac97a66d5936fe55b261f2ec1bfc41 |
from pycket.ast_visitor import ASTVisitor
from pycket.env import SymList
from pycket.interpreter import (
App,
Begin,
Begin0,
BeginForSyntax,
CaseLambda,
Cell,
CellRef,
DefineValues,
If,
Lambda,
Let,
Letrec,
LexicalVar,
Module,
ModuleVar,
LinkletV... | pycket/pycket | pycket/assign_convert.py | Python | mit | 12,937 | [
"VisIt"
] | 34db442bfc09ea4122867ae65605ac46d198c143db5d4d27446ce91cb7fba086 |
"""Test if VTK-Python objects support weak referencing.
Run this test like so:
$ vtkpython TestWeakref.py
or
$ python TestWeakref.py
Created on July, 8 2005
Prabhu Ramachandran <prabhu_r at users dot sf dot net>
"""
import sys
import vtk
from vtk.test import Testing
try:
import weakref
except... | timkrentz/SunTracker | IMU/VTK-6.2.0/Common/Core/Testing/Python/TestWeakref.py | Python | mit | 1,058 | [
"VTK"
] | 5d264ce86c681d317b02d2413db55122c82c414db3372df0d6d3d1e427d43a68 |
# Copyright 2016 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Descriptive metrics for Clovis.
When executed as a script, prints the amount of data attributed to Ads, and
shows a graph of the amount of data to downlo... | axinging/chromium-crosswalk | tools/android/loading/metrics.py | Python | bsd-3-clause | 5,221 | [
"VisIt"
] | d2c1030202873da879540aa539f4845e8ed9fea275f419ecbc920616ccc38fc6 |
"""
circleseq.py as the wrapper for CIRCLE-seq analysis
"""
from alignReads import alignReads
from visualization import visualizeOfftargets
from mergeReads import mergeReads
import argparse
import os
import sys
import subprocess
import traceback
import log
import yaml
import validation
import findCleavageSites
import ... | tsailabSJ/circleseq | circleseq/circleseq.py | Python | agpl-3.0 | 14,736 | [
"BWA"
] | fcdec1791b24f8a37cd43413f9d0479435aaa824d8aa517137240b52cc265d07 |
#!/usr/bin/env python
# Copyright (C) 2008-2012 Kai Blin <kai.blin@biotech.uni-tuebingen.de>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your opti... | kblin/spire | ire/__init__.py | Python | gpl-3.0 | 25,301 | [
"BLAST"
] | dc533b2b043693f6aa61198ec3383f53ba86a10ce92fa3f0ac5a81a0dbee002e |
from selenium.webdriver.common.keys import Keys
from selenium.webdriver.support.ui import WebDriverWait
from selenium.webdriver.support import expected_conditions as EC
from selenium.common.exceptions import MoveTargetOutOfBoundsException
from selenium.common.exceptions import TimeoutException
from selenium.webdriver.c... | lightnarcissus/PlayfulMesh | OpenWPM/automation/Commands/browser_commands.py | Python | gpl-3.0 | 7,964 | [
"VisIt"
] | df3a59e288379b3d80660c39985b2c89a57217aa51ad08a114b3820210c1d782 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2014 Stanford University and the Authors
#
# Authors: Peter Eastman, Robert McGibbon
# Contributors: Kyle A. Beaucha... | swails/mdtraj | mdtraj/core/topology.py | Python | lgpl-2.1 | 48,729 | [
"MDTraj",
"OpenMM",
"VMD"
] | 464440ca4aab2a4af4b833f0f316efa0871093e7301c84360d5486b043501ca8 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import warnings
import copy
from pymatgen.core.structure import Molecule
from pymatgen.analysis.graphs import MoleculeGraph
from monty.dev import requires
try:
import openbabel as ob
import pybel as p... | fraricci/pymatgen | pymatgen/io/babel.py | Python | mit | 13,450 | [
"Open Babel",
"Pybel",
"pymatgen"
] | 0426dd4ba1b0799cdb73f7e7d98885edec1e3d8fb51b21872c2d0a0272482904 |
#/*
# *
# * TuneIn Radio for XBMC.
# *
# * Copyright (C) 2013 Brian Hornsby
# *
# * This program is free software: you can redistribute it and/or modify
# * it under the terms of the GNU General Public License as published by
# * the Free Software Foundation, either version 3 of the License, or
# * (at your option) any... | SMALLplayer/smallplayer-image-creator | storage/.xbmc/addons/plugin.audio.tuneinradio.smallplayer/resources/lib/tunein.py | Python | gpl-2.0 | 37,835 | [
"Brian"
] | 55e8e15189d6dba2165d12538f4c89e875370c43a52a4f13e598fd0e48454772 |
# Copyright 2010 http://www.collabq.com
# Copyright 2009 Google 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 ... | CollabQ/CollabQ | common/templatetags/format.py | Python | apache-2.0 | 15,390 | [
"Elk",
"MOOSE",
"Octopus"
] | 0e5a28241b8d63bf9d22afa37396e87f5a72a20031e43a63ff21e03596673457 |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publish... | thica/ORCA-Remote | src/ORCA/utils/FTP.py | Python | gpl-3.0 | 8,913 | [
"ORCA"
] | bcfe51c66466ad9868ae68322696ade4389e0a2b7ba7d88721b2ec951ca3ad7d |
from PyOpenWorm import *
from string import Template
import neuroml
__all__ = [ "Cell" ]
# XXX: Should we specify somewhere whether we have NetworkX or something else?
ns = {'ns1': 'http://www.neuroml.org/schema/neuroml2/'}
segment_query = Template("""
SELECT ?seg_id ?seg_name ?x ?y ?z ?d ?par_id ?x_prox ?y_prox ?z_p... | hnunner/PyOpenWorm | PyOpenWorm/cell.py | Python | mit | 7,222 | [
"BLAST",
"NEURON"
] | 64ce9482ade9812ac6de58c97c2669dee547308a1a85c13909eedee35e70e58d |
########################################################################
# $HeadURL$
########################################################################
""" The SystemAdministratorClient is a class representing the client of the DIRAC
SystemAdministrator service. It has also methods to update the Configuratio... | sposs/DIRAC | FrameworkSystem/Client/SystemAdministratorClient.py | Python | gpl-3.0 | 793 | [
"DIRAC"
] | 4173eca4c7462d361bbf0f42335cdd99173989362eb235375a135df702d17f63 |
from simtk.openmm import app
import simtk.openmm as mm
from simtk import unit
pdb = app.PDBFile("./liquid.pdb")
forcefield = app.ForceField('tip3p.xml')
system = forcefield.createSystem(pdb.topology, nonbondedMethod=app.PME, nonbondedCutoff=0.9*unit.nanometers)
integrator = mm.LangevinIntegrator(300 * unit.kelvin, 1.... | kyleabeauchamp/DBayes | dbayes/simulate/simulate_water.py | Python | gpl-2.0 | 1,047 | [
"OpenMM"
] | dcf50e4f4275b2090817b6e888c1480fb43505f6a251c3bef2e81398ec71ded2 |
##
## Biskit, a toolkit for the manipulation of macromolecular structures
## Copyright (C) 2004-2012 Raik Gruenberg
##
## This program is free software; you can redistribute it and/or
## modify it under the terms of the GNU General Public License as
## published by the Free Software Foundation; either version 3 of the
... | ostrokach/biskit | Biskit/delphi.py | Python | gpl-3.0 | 26,819 | [
"Amber"
] | 4bf59f0565b1910fd7774b8435909423d23a38ffeb4f5c3bd6c70d81e4e8d6c3 |
# -*- coding: utf-8 -*-:
# Copyright 2012 splinter authors. All rights reserved.
# Use of this source code is governed by a BSD-style
# license that can be found in the LICENSE file.
"""
This module contains the basic API for splinter drivers and elements.
"""
from splinter.meta import InheritedDocs
class DriverAP... | cobrateam/splinter | splinter/driver/__init__.py | Python | bsd-3-clause | 28,490 | [
"VisIt"
] | d4e857a55a48562899720a91609fef029146163ea11809a40e73d522f8a23d20 |
#!/usr/bin/env python
"""
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the te... | rbberger/lammps | examples/USER/cgdna/examples/oxDNA2/unique_bp/generate_unique.py | Python | gpl-2.0 | 26,821 | [
"LAMMPS"
] | 61d9c1e95d3487d9ee208351a93f218b7a2f05b818cef296b042650462264dc5 |
import numpy as np
from ase.calculators.emt import EMT
from ase import Atoms
a = 3.60
b = a / 2
cu = Atoms('Cu',
positions=[(0, 0, 0)],
cell=[(0, b, b),
(b, 0, b),
(b, b, 0)],
pbc=1,
calculator=EMT())
e0 = cu.get_potential_energy()
print(e0)... | suttond/MODOI | ase/test/emt.py | Python | lgpl-3.0 | 1,586 | [
"ASE"
] | 00599de0b825af3e24dc0f734db73b4e9fef59104e774fa124d644d2a35750c3 |
import numpy as np
import tensorflow as tf
import h5py
from sklearn.preprocessing import OneHotEncoder
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import time
import scipy.io
# Functions for initializing neural nets parameters
def weight_variable(shape):
initial = tf.truncat... | Haunter17/MIR_SU17 | exp8/exp8a_relu.py | Python | mit | 7,887 | [
"NEURON"
] | 9e3658ad5d1f28906e7e16fcf65a3f3e6a2e457069434d6056944985b40520e2 |
import socket
import sys
from random import randint
import re
import time
import random
#----------------------------------- Settings --------------------------------------#
network = 'irc.goat.chat'
port = 6667
homechan = '#nascar'
irc = socket.socket ( socket.AF_INET, socket.SOCK_STREAM )
irc.connect ( ( network, por... | pembo210/voat-stylesheets | NASCAR/nascarBot.py | Python | gpl-2.0 | 6,910 | [
"Brian"
] | 36186e6bc72d7d36e9455049184c743629eb75c6fde43773acfe64d24ea7971e |
# Copyright (c) 2012, 2013, 2014 James Hensman
# Licensed under the GPL v3 (see LICENSE.txt)
import numpy as np
from collapsed_mixture import CollapsedMixture
import GPy
from GPy.util.linalg import mdot, pdinv, backsub_both_sides, dpotrs, jitchol, dtrtrs, tdot
from utilities import multiple_mahalanobis
from sc... | mzwiessele/GPclust | GPclust/OMGP.py | Python | gpl-3.0 | 7,710 | [
"Gaussian"
] | 69ca664cb88f806ea1b1b93779d84263597ab287e78a688e2ff6fdd3b07bcb98 |
# This code was taken and modified from Alex Martelli's
# "determine the name of the calling function" recipe (Thanks, Alex!)
#
# This code also benefits from a useful enhancement from Gary Robinson, allowing
# only the arguments to __init__ to be copied, if that is desired.
#
# use sys._getframe() -- it returns a fra... | ActiveState/code | recipes/Python/286185_Automatically_initializing_instance_variables/recipe-286185.py | Python | mit | 1,435 | [
"Octopus"
] | f06ee5d31a4e4ff6cf82156c530ff675ac9437e2fd44e920580a0479613ed0b7 |
#! /usr/bin/python2.7
# -*- coding: utf-8 -*-
import numpy as np
from errval import *
from errvallist import *
'''
Convenience functions in order to get standard errors.
The standard error (ste; here designated as \Delta)
\Delta = \frac{1}{\sqrt{n}} \sqrt{\frac{1}{n-1} \sum\limits_{i=0}^{n-1} (x_i - \bar{x})^2}
is... | stefantkeller/errorvalues | stderrval.py | Python | mit | 3,221 | [
"Gaussian"
] | 3f5c144c75599e93b33f57ff6e2b1d026182b492831906271c869555e8bd932e |
import sys
import numpy as np
import pywcs
from astrodata.adutils import gemLog
from gempy import gemini_tools as gt
from astrodata import Errors
from gempy import managers as man
# correct_wcs_to_reference_image and align_to_reference_image functions
# will go into gempy/science/registration
def correct_wcs_to_ref... | pyrrho314/recipesystem | trunk/devel/imcoadd/registration_functions.py | Python | mpl-2.0 | 61,932 | [
"Gaussian"
] | 6a3a661d147e47db97804b27ca5a6e829e52573cc8f5e0716169649d66f50903 |
# - Coding UTF8 -
#
# Networked Decision Making
# Site: http://code.google.com/p/global-decision-making-system/
#
# License Code: GPL, General Public License v. 2.0
# License Content: Creative Commons Attribution 3.0
#
# Also visit: www.web2py.com
# or Groups: http://groups.google.com/group/web2py
# For details on the... | NewGlobalStrategy/NetDecisionMaking | models/utils.py | Python | mit | 1,852 | [
"VisIt"
] | 4a1abc122f298f1afe8f9ced3c8a4fa4564b01aebc4c3da2905dee3324dc503e |
import distance
import numpy as np
import copy
import sugarbee.distance as distance
def assign_undirected_weight(M, i, j, v):
M[i,j] = M[j,i] = v
def get_degree_matrix(A):
n = len(A)
D = np.zeros((n,n))
for i in range(n):
D[i,i] = np.sum(A[i,:])
return D
def get_affinity_matrix(proj, metr... | zedoul/AnomalyDetection | sugarbee/affinity.py | Python | mit | 1,157 | [
"Gaussian"
] | 689d08c1f6a205e2e4b5f299102c6a7cfdd94b0921070116018ad9097a3d67a3 |
# 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... | BackupTheBerlios/espressopp | src/standard_system/__init__.py | Python | gpl-3.0 | 1,115 | [
"ESPResSo"
] | 9c6c86d8ce15336f28864bc177dcb4b6700c2eea0095d66dfba4b320d0913439 |
import sys
from numpy import *
from PyQt4 import QtGui
from matplotlib.figure import Figure
from matplotlib.backends.backend_qt4agg \
import FigureCanvasQTAgg as FigureCanvas
import src.quadrature as quad
from gui.main_window import Ui_main_window
from src.utils import MethodNames, parse_function
class QuadMeth... | Cheeser12/quadrature_tool | quad_program.py | Python | mit | 18,080 | [
"Gaussian"
] | db5beaf65feaac3bb5af5efc6fc26d3ee636c30d5644bd306a41d44f2d0dc6e5 |
"""
This module contains the a list of supporting classes and functions for the
SPARC smoothness analysis notebook.
"""
import numpy as np
import sys
from scipy import signal
# from smoothness import spectral_arclength
# from smoothness import log_dimensionless_jerk
from movements import gaussian_discrete_movement a... | siva82kb/SPARC | scripts/support.py | Python | isc | 13,355 | [
"Gaussian"
] | a0fa83911309429b9518dee4b622013a2fc69c33f4fe24bfd19807bf61466fd0 |
#!/usr/bin/env/ python3
"""
Generate a netCDF file with a vortex field.
"""
import sys
import argparse
import numpy as np
import matplotlib.pyplot as plt
import netCDF4
import fitting
args = []
if __name__ == '__main__':
parser = argparse.ArgumentParser(description='generate a vortex field in a netCDF file',
... | guilindner/VortexFitting | vortexfitting/generateNetCDF.py | Python | mit | 2,589 | [
"NetCDF"
] | 428df0077752d76399999c2cc199b003caa44b326cfb4f82e421703764f72032 |
#!/usr/bin/env python
#==========================================================================
#
# Copyright Insight Software Consortium
#
# 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 Licen... | clangguth/statismo | scripts/BuildHeaderTest.py | Python | bsd-3-clause | 5,424 | [
"VTK"
] | 53abf837e50b188d3393b2dd8618019c24c2fdd76916bf2825f805ad92efd02e |
# -*- coding: utf-8 -*-
"""Readability Exporter
A tiny tool that helps you export your Readability bookmarks through the Readability Reader API.
See `the GitHub project page <https://github.com/goetzb/readability-exporter>`_ for more information.
"""
# TODO: Make the script compatible with Python 2.7
# TODO: Add /docs... | goetzb/readability-exporter | readability-exporter.py | Python | mit | 17,987 | [
"VisIt"
] | 187342af2fb440a62ab0e9ea500e93a46d9fa678eb523a83702ade9a0738c330 |
# vim: fdm=indent
'''
author: Fabio Zanini
date: 22/08/12
content: Test script for the python bindings (haploid_highd)
'''
# Import module
import sys
sys.path.insert(0, '../pkg/python')
import numpy as np
import matplotlib.pyplot as plt
import FFPopSim as h
from Bio import Phylo
# Globals
L = 1000 # ... | wrshoemaker/ffpopsim | tests/python_highd.py | Python | gpl-3.0 | 1,710 | [
"Biopython"
] | cc1d236f8d883bd6382125297a03684f84048d5a256244aaa34c013a68c7c87b |
#!/usr/bin/env python -W ignore
# This code is licensed under the New BSD License
# 2009, Alexander Artemenko <svetlyak.40wt@gmail.com>
# For other contacts, visit http://aartemenko.com
import sys
import os
import locale
import shutil
import gtdzen
from ConfigParser import ConfigParser
from datetime import date
from ... | svetlyak40wt/gtdzen | gtdzen/client.py | Python | bsd-3-clause | 9,019 | [
"VisIt"
] | a7ceb76852c2b0a569100269af54aec68b604d6c673a7a26bff953a8e42c23ea |
# -*- coding: utf-8 -*-
# Zeobuilder is an extensible GUI-toolkit for molecular model construction.
# Copyright (C) 2007 - 2012 Toon Verstraelen <Toon.Verstraelen@UGent.be>, Center
# for Molecular Modeling (CMM), Ghent University, Ghent, Belgium; all rights
# reserved unless otherwise stated.
#
# This file is part of Z... | molmod/zeobuilder | share/plugins/molecular/geometry.py | Python | gpl-3.0 | 9,677 | [
"MOPAC"
] | 05a7cdba515fac313a329174ab6f8bac1a3d1daac854378b0c35b9216424a423 |
import random
from splinter import Browser
# BELOW: ALL FUNC DEFINITIONS
def main():
print "********************************************************"
print "Hello and welcome to my Twitter account generator"
print "author: gh054"
print ""
print ""
print "Features:"
print "1. Generate Usernames"
print "2. Gene... | gh054/TwitterCreate | twitter-bot.py | Python | gpl-2.0 | 5,688 | [
"VisIt"
] | 8ab080de8ccac589e721fc67b5e558cbf73bcb75dfedbbda1c4ec59cc8b19c72 |
"""
module assign_targeting_score
"""
from itertools import chain
import numexpr as ne
import numpy as np
from easyquery import Query, QueryMaker
from .. import utils
from ..objects import cuts as C
from ..utils import (fill_values_by_query, get_all_colors, get_sdss_bands,
get_sdss_colors)
from .... | sagasurvey/saga | SAGA/targets/assign_targeting_score.py | Python | mit | 34,805 | [
"Galaxy"
] | 7590326db141b4121c539dd800aaf579176c6082f8a629f9bb335431626cdfc9 |
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