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# onetoonemsg.py ---
#
# Filename: onetoonemsg.py
# Description:
# Author:Subhasis Ray
# Maintainer:
# Created: Wed May 1 11:05:30 2013 (+0530)
# Version:
# Last-Updated: Wed May 1 11:12:07 2013 (+0530)
# By: subha
# Update #: 24
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#
# Change l... | BhallaLab/moose-examples | snippets/onetoonemsg.py | Python | gpl-2.0 | 1,912 | [
"MOOSE"
] | 9631af5460262dc82c9901c80c87087c6b2a25a2cbdd10f3a3872b04b9537b4f |
"""
Utility functionality (:mod:`skbio.util`)
=========================================
.. currentmodule:: skbio.util
This package provides general exception/warning definitions used throughout
scikit-bio, as well as various utility functionality, including I/O and
unit-testing convenience functions.
Testing functio... | wdwvt1/scikit-bio | skbio/util/__init__.py | Python | bsd-3-clause | 2,037 | [
"scikit-bio"
] | fd8de8a9fd8c78bea6a89e938665bc88ab101ea044b5cdcf917465684a1e7586 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011 Paul Franklin
#
# This program is free software; you can redistribute it and/or modify
# it under the terms o... | Fedik/gramps | gramps/plugins/tool/verify.py | Python | gpl-2.0 | 69,376 | [
"Brian"
] | 475521d96560d2fba3654cf7bd9d164e4adbc73753e062b6b8a3ff1200b6e59d |
from django.shortcuts import render, redirect
from django.contrib.auth.decorators import login_required
from django.views import generic
from django.views.generic.edit import DeleteView, UpdateView, CreateView
from django.core.urlresolvers import reverse_lazy
from django.contrib import messages
from .models import Vis... | dwagon/Scheduler | scheduler/visit/views.py | Python | gpl-2.0 | 3,225 | [
"VisIt"
] | 313f8984aeabf128b38b9da41e5d2ca2e678b2ea9d7621bb19ed3da67a0c2713 |
from simtk.openmm.app import *
from simtk.openmm import *
from simtk.unit import *
from sys import stdout
outfreq = 1e5
simlength = 1e9
pdb = PDBFile('input.pdb')
forcefield = ForceField('amber99sb.xml', 'amber99_obc.xml')
system = forcefield.createSystem(pdb.topology, nonbondedMethod=NoCutoff)
integrator = LangevinInt... | LCLS/Protein-Folding-Sims | hp24stab/sims/300K/91gamma/simulateUnfoldedPdb.py | Python | mit | 758 | [
"OpenMM"
] | ecd3821333d5000c56fbba08ec4a9f4d672225e13f9ad1728ac1eb30a67c4c66 |
# -*- coding: utf-8 -*-
"""
<DefineSource>
@Date : Fri Nov 14 13:20:38 2014 \n
@Author : Erwan Ledoux \n\n
</DefineSource>
A Leaker
"""
#<DefineAugmentation>
import ShareYourSystem as SYS
BaseModuleStr="ShareYourSystem.Standards.Recorders.Brianer"
DecorationModuleStr="ShareYourSystem.Standards.Classors.Classer"
S... | Ledoux/ShareYourSystem | Pythonlogy/ShareYourSystem/Standards/Recorders/Leaker/draft/__init__ copy 2.py | Python | mit | 20,212 | [
"Brian"
] | 4593dc3817c0eea90fdbe9fa758a249188b13b23c88b04a3b8c1e02b69c95731 |
# Copyright (C) 2007 CAMP
# Please see the accompanying LICENSE file for further information.
from ASE import Atom
from Asap import *
from Asap.Dynamics.VelocityVerlet import VelocityVerlet
from Asap.Utilities import BrennerImport
# read the coordinates and the types of atoms from a
# brenner dot d file:
brenner = B... | auag92/n2dm | Asap-3.8.4/Examples/BrennerExample.py | Python | mit | 1,104 | [
"ASE"
] | ab81407cd50f111f35405a06d6062f1f1694a5418d8e74a58920abcaf68ac668 |
"""Miscellaneous functions to analyze the simulation results.
Index
-----
.. currentmodule:: nanoqm.analysis.tools
.. autosummary::
API
---
"""
import os
from typing import List, Tuple
import numpy as np
import pyparsing as pa
from scipy.optimize import curve_fit
from ..common import fs_to_cm, h2ev, hbar, r2meV
... | SCM-NV/qmworks-namd | nanoqm/analysis/tools.py | Python | mit | 8,202 | [
"Gaussian",
"NAMD"
] | 71c7d9c93d5e7183a94a7425d0cb181d0bdcec5439ef552eaf7fc723a75dab1e |
#!/usr/bin/env python
# This example demonstrates the use and manipulation of lookup tables.
import vtk
from vtk.util.colors import *
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# First create pipeline a simple pipeline that reads a structure grid
# and then extracts a plane from the gr... | CMUSV-VisTrails/WorkflowRecommendation | examples/vtk_examples/Rendering/rainbow.py | Python | bsd-3-clause | 3,096 | [
"VTK"
] | a4c7fa3fc89fce7d03781e0235f599eb84b1a3bb47cc39e9a62e3a5a1d487cd6 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | alejob/mdanalysis | testsuite/MDAnalysisTests/plugins/capture_err.py | Python | gpl-2.0 | 4,445 | [
"MDAnalysis"
] | aca3b1d9f45036bb494e5e2a4e898670500ec760447f3540b8b17c043031bc01 |
# Copyright 2010-2017, The University of Melbourne
# Copyright 2010-2017, Brian May
#
# This file is part of Karaage.
#
# Karaage 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... | brianmay/karaage | karaage/plugins/kgapplications/signals.py | Python | gpl-3.0 | 969 | [
"Brian"
] | dcdf4ae0fb23a3e7f82b9a7e08e36b2a4bbd41c2f10614f788dd20dac6f9962a |
#!/usr/bin/env python
# Copyright (C) 2007--2016 the X-ray Polarimetry Explorer (XPE) team.
#
# For the license terms see the file LICENSE, distributed along with this
# software.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published... | lucabaldini/pyxpe | pyxpe/utils/logging_.py | Python | gpl-3.0 | 3,382 | [
"VisIt"
] | 68439f5b5310c333519c55827cd61da2c9ab07217efadf19f0c68aba2e13342e |
"""
Extended docstrings for functions.py
"""
pi = r"""
`\pi`, roughly equal to 3.141592654, represents the area of the unit
circle, the half-period of trigonometric functions, and many other
things in mathematics.
Mpmath can evaluate `\pi` to arbitrary precision::
>>> from mpmath import *
>>> mp.dps = 50; m... | ojengwa/sympy | sympy/mpmath/function_docs.py | Python | bsd-3-clause | 279,062 | [
"Gaussian"
] | 019afd4096b3b892c4168b6624b032e6d8961152720e481fbcdbf574b44736a3 |
#
# This file is part of the CCP1 Graphical User Interface (ccp1gui)
#
# (C) 2002-2005 CCLRC Daresbury Laboratory
#
# 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 ... | alexei-matveev/ccp1gui | interfaces/filemolden.py | Python | gpl-2.0 | 7,943 | [
"ChemPy"
] | d1ac39764e56f2d4aebe2f566800af25aba87a4c247183184ac78690409db4b2 |
import numpy as np
import pysal
import scipy.sparse as SP
import itertools as iter
from scipy.stats import f, chisqprob
import numpy.linalg as la
from utils import spbroadcast
"""
Tools for different regimes procedure estimations
"""
__author__ = "Luc Anselin luc.anselin@asu.edu, \
Daniel Arribas-Bel darribas... | spreg-git/pysal | pysal/spreg/regimes.py | Python | bsd-3-clause | 25,021 | [
"COLUMBUS"
] | af607f7f9399b60c58995774da2418a142fd6e3dffd2e6e7806ffe31baad0200 |
import numpy as np
import utool as ut
def get_toydata(rng):
if ut.get_argflag('--toy2'):
X_true, X, y = toydata2(rng)
else:
X_true, X, y = toydata1(rng)
return X_true, X, y
def toydata2(rng):
from sklearn.datasets import samples_generator
n_samples = 1000
n_features = 2
n... | Erotemic/ibeis | ibeis/algo/hots/toy_nan_rf.py | Python | apache-2.0 | 12,134 | [
"Gaussian"
] | d4d966b70b1402a0f5bafea90808aa50e75a9729d4ca79065704213052f84f8c |
# - Coding UTF8 -
#
# Networked Decision Making
# Development Sites (source code):
# http://code.google.com/p/global-decision-making-system/
# http://github.com/NewGlobalStrategy/NetDecisionMaking
#
# Demo Sites (Google App Engine)
# http://netdecisionmaking.appspot.com
# http://globaldecisionmaking.appspot.co... | NewGlobalStrategy/NetDecisionMaking | controllers/location.py | Python | mit | 4,889 | [
"VisIt"
] | 9ff6f7adefc59ec807815f185763404457d2637d755f70dba05d44463ce40d68 |
"""
Core module with functions to calculate Greens Functions and synthetics.
Also contains main classes for setup specific parameters.
"""
import os
import logging
import shutil
import copy
from time import time
from collections import OrderedDict
from beat import psgrn, pscmp, utility, qseis2d
from theano import co... | hvasbath/beat | beat/heart.py | Python | gpl-3.0 | 115,758 | [
"Gaussian"
] | c29fe0a964e28ab1d4a363039b46d3562940f93797047f1ff923e977fbf27561 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
An interface to the excellent spglib library by Atsushi Togo
(http://spglib.sourceforge.net/) for pymatgen.
v1.0 - Now works with both ordered and disordered structure.
v2.0 - Updated for spglib 1.6.
v3.0 ... | davidwaroquiers/pymatgen | pymatgen/symmetry/analyzer.py | Python | mit | 62,236 | [
"CRYSTAL",
"pymatgen"
] | 940cb863e63dc663b4a7feaea52c19236c1309dc8d6f86dafb39ea7f2d566f53 |
# Copyright 2018,2019,2020,2021 Sony Corporation.
# Copyright 2021 Sony Group Corporation.
#
# 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
#... | sony/nnabla | python/src/nnabla/utils/profiler.py | Python | apache-2.0 | 13,404 | [
"VisIt"
] | cbe10a9038d4e7e3ba4b4dfab615eab1c6722ef5cde7ed9acc78b8d884a13874 |
#!/usr/bin/env python
import random
import sys
import time
from hypertable.thriftclient import *
from hyperthrift.gen.ttypes import *
story = \
"""In 1815, M. Charles-Francois-Bienvenu Myriel was Bishop of D---- He was
an old man of about seventy-five years of age; he had occupied the see
of D---- since 1806.
Althou... | nkhuyu/hypertable | tests/integration/large-row/populate.py | Python | gpl-3.0 | 5,209 | [
"VisIt"
] | 18a0f4fa3c33ab322aba317e774c0fd3037c87bd487048c7c841c9d388a31bf2 |
########################################################################
# File : SSHComputingElement.py
# Author : Dumitru Laurentiu
########################################################################
""" SSH (Virtual) Computing Element: For a given list of ip/cores pair it will send jobs
directly through ... | fstagni/DIRAC | Resources/Computing/SSHBatchComputingElement.py | Python | gpl-3.0 | 7,235 | [
"DIRAC"
] | 81df2dfb3778f1f380f70536ae1e6d04675b45d70c0a58f68fdef68dfc42b554 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/item_title | openlp/plugins/songs/forms/editsongform.py | Python | gpl-2.0 | 43,752 | [
"Brian"
] | 8ef6e55e9d72fc9e54a549a0b9695f706917e97e2e6c846aa3e889c733d51b7c |
#!/usr/bin/env python
import vtk
from vtk.util.misc import vtkGetDataRoot
# create planes
# Create the RenderWindow, Renderer
#
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer( ren )
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# create pipeline
#
pl3d = vtk.vtkPLOT3... | naucoin/VTKSlicerWidgets | Graphics/Testing/Python/tubeComb.py | Python | bsd-3-clause | 1,865 | [
"VTK"
] | 928553c6131941e88a4b6954950228c4b85ec9bb6fd65edee9c87d7d549ae6d3 |
from sensordatainterface.base_views import *
from django.views.generic import DetailView
from sensordatainterface.forms import *
# Detail View Generic.
class GenericDetailView(DetailView):
@method_decorator(login_required(login_url=LOGIN_URL))
def dispatch(self, *args, **kwargs):
return super(GenericD... | UCHIC/ODM2Sensor | src/sensordatainterface/views/detail_views.py | Python | bsd-3-clause | 4,645 | [
"VisIt"
] | 621309c4740dff5d0fb07defb16030a472fac97652f871b77ee6cfc4c698db97 |
#!/usr/bin/env python
import pyemma
import numpy as np
import mdtraj
import time
import os
# Source directory
source_directory = '/cbio/jclab/projects/fah/fah-data/munged3/no-solvent/11406' # CK2
#source_directory = '11406' # CK2
################################################################################
# Load... | jchodera/MSMs | jchodera/CK2/pyemma-equitemporal/cluster.py | Python | gpl-2.0 | 3,345 | [
"MDTraj"
] | 2fc94b7f6972ba5b73b45348b4e1ce574cd7e0d8fd6d337609cbb4a3293cd3f7 |
"""
Provides the data structures for Gauss-Legendre quadrature on simplicial domains.
"""
# IMPORTS
import numpy as np
from .base import QuadRule
class GaussQuadSimp(QuadRule):
"""
Provides Gauss-Legendre quadrature points and weights
for standard simplicial domains in several spatial dimensions.
P... | pysofe/pysofe | pysofe/quadrature/gaussian.py | Python | bsd-3-clause | 10,911 | [
"Gaussian"
] | 804826525527125f80174bbec49d345c0bfc80f29d8812dc4408994cc7f0e0ce |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
chose m, c (parameters) for a straight line
from the line pick N points (N=3, 5, 50, 100, 1000)
pick sigma (size of the noise)
randomly deviate(offset) points in y direction by using
sigma*random number from normal distribution
sigma the same for all points
then defin... | lefthandedroo/Cosmo-models | History/Stats/emcee_ex_1.py | Python | mit | 4,686 | [
"Gaussian"
] | 9d37548113a99c2077a96d9df6225807c91d5ff9d2234cfa0c84e94f368c37a2 |
#!/usr/bin/env python
'''
MP2 at an individual k-point
'''
import numpy
from pyscf.pbc import gto, scf, mp
cell = gto.Cell()
cell.atom='''
C 0.000000000000 0.000000000000 0.000000000000
C 1.685068664391 1.685068664391 1.685068664391
'''
cell.basis = 'gth-szv'
cell.pseudo = 'gth-pade'
cell.a = '''
0.000000000... | gkc1000/pyscf | examples/pbc/22-k_points_mp2.py | Python | apache-2.0 | 3,492 | [
"PySCF"
] | 11ff4a75778e42230a4b5cdb52d6feb2068d0f648c6e306e53d579e7cb24e44a |
# Lint as: python3
# Copyright 2018 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 ... | tensorflow/lingvo | lingvo/tasks/asr/model_test.py | Python | apache-2.0 | 23,360 | [
"MOE"
] | 1012f9e62fbd44a2b46f5c0d5dfb0ed33c54d0a3fab5f4781c31bd998482c79e |
import ovito
from ovito import *
from ovito.data import *
from ovito.vis import *
import numpy as np
import math
import os
import multiprocessing
import itertools
def get_templates():
sqrt = np.sqrt
SC = [ [ 0. , 0. , 0. ],
[ 0. , 0. , -1. ... | pmla/polyhedral-template-matching | datagen/renderscript_diamond_structures.py | Python | mit | 11,517 | [
"OVITO"
] | 96317a5155e555d3dc58531edfe7604e54a9bfb277cc3c35ec8bcf8700b1b593 |
from django.db import models
import yaml
import os.path
import logging
import gzip
import numpy as np
import qmpy
import qmpy.db.custom as custom
from qmpy.utils import *
import bokeh.plotting as bkp
from bokeh.models import HoverTool, Span
logger = logging.getLogger(__name__)
# class Orbital(models.Model):
# n... | wolverton-research-group/qmpy | qmpy/analysis/vasp/dos.py | Python | mit | 15,063 | [
"VASP"
] | 039cbd9bf241af0e7ed81973b18cfbbb723113d30777b2ab19787bd8c72d7929 |
#!/usr/bin/env python
#
# Copyright (C) 2013-2017(H)
# 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, ei... | espressopp/espressopp | testsuite/LangevinThermostat/testLangevinThermostat.py | Python | gpl-3.0 | 6,345 | [
"ESPResSo"
] | 97eb58fa4e0b72462a1ac16862bb6b66f7a9ceea34b701f1d4460705a0606e26 |
from __future__ import print_function, division
import math
import numpy as np
# Import helper functions
from mlfromscratch.utils import train_test_split, to_categorical, normalize, accuracy_score
from mlfromscratch.deep_learning.activation_functions import Sigmoid, ReLU, SoftPlus, LeakyReLU, TanH, ELU
from mlfromscra... | eriklindernoren/ML-From-Scratch | mlfromscratch/supervised_learning/perceptron.py | Python | mit | 2,679 | [
"NEURON"
] | a4d31a98152218033f2d273951b16224a49530571f0377a90ff4db6af0a4aec4 |
"""
BenchExec is a framework for reliable benchmarking.
This file is part of BenchExec.
Copyright (C) 2007-2015 Dirk Beyer
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
... | michkot/benchexec | benchexec/tools/blast.py | Python | apache-2.0 | 2,590 | [
"BLAST"
] | 1b8ac945c442c9efc282ec26155f2136a1ba6c3eb8cc44a2f13012974a172151 |
# Copyright (C) 2017-2018 Michael Freitag, Shahin Amiriparian, Sergey Pugachevskiy, Nicholas Cummins, Björn Schuller
#
# This file is part of auDeep.
#
# auDeep 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, ... | auDeep/auDeep | audeep/cli/evaluate.py | Python | gpl-3.0 | 11,594 | [
"NetCDF"
] | b612067cc0e60f32681464bb0fffab2958f5d36279a3232a20ae5081a79ff9ca |
"""
Public and private exceptions
Copyright (c) 2009 John Markus Bjoerndalen <jmb@cs.uit.no>,
Brian Vinter <vinter@nbi.dk>, Rune M. Friborg <rune.m.friborg@gmail.com>.
See LICENSE.txt for licensing details (MIT License).
"""
# Public exceptions
class ChannelPoisonException(Exception):
""" ChannelPoisonExce... | runefriborg/pycsp | pycsp/parallel/exceptions.py | Python | mit | 6,387 | [
"Brian"
] | 26cb5aa9a288d267cac7cfd83df4a68333a3f641e8735fdc6db35a7554e1fb31 |
#!/usr/bin/env python
########################################################################
# File : dirac-admin-get-pilot-output
# Author : Ricardo Graciani
########################################################################
"""
Retrieve available info about the given pilot
"""
__RCSID__ = "$Id$"
# pyli... | andresailer/DIRAC | Interfaces/scripts/dirac-admin-get-pilot-info.py | Python | gpl-3.0 | 2,549 | [
"DIRAC"
] | 74c6a32ead0ad3911e98ba88a4488a17b2ac05627db91be68b4656084e8ddd7b |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | TheTimmy/spack | var/spack/repos/builtin/packages/r-biobase/package.py | Python | lgpl-2.1 | 1,680 | [
"Bioconductor"
] | daf9f8ef2dcc8ce54c1dc1f7f45ba6a04f5a8004e4f0e115cfb1d2dac0fd61a1 |
"""
===========================================
Sparse coding with a precomputed dictionary
===========================================
Transform a signal as a sparse combination of Ricker wavelets. This example
visually compares different sparse coding methods using the
:class:`sklearn.decomposition.SparseCoder` esti... | DailyActie/Surrogate-Model | 01-codes/scikit-learn-master/examples/decomposition/plot_sparse_coding.py | Python | mit | 4,054 | [
"Gaussian"
] | 2c4942c0746c566379dd6b370a73f43fcebecd7823c745c4dd166fad011b9207 |
# Copyright (c) 2014, the GREAT3 executive committee (http://www.great3challenge.info/?q=contacts)
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without modification, are permitted
# provided that the following conditions are met:
#
# 1. Redistributions of source code must retain... | barnabytprowe/great3-public | inputs/galdata/training_galaxy_props.py | Python | bsd-3-clause | 12,606 | [
"Galaxy"
] | 293112861d23130ff568e8c85cfa7066f4e2e043f6ba7aebb1e1dad61643be45 |
import logging
import logging.config
import sys
import threading
import traceback
import time
import os
from amberdriver.common.message_handler import MessageHandler
from amberdriver.dummy import dummy_pb2
from amberdriver.dummy.dummy import Dummy
from amberdriver.null.null import NullController
from amberdriver.tool... | project-capo/amber-python-drivers | src/amberdriver/dummy/dummy_controller.py | Python | mit | 5,099 | [
"Amber"
] | 85973c19aa38d4299dc0519d6e9385d931ee0b5acd56c2de89a96dd498d25549 |
import os, sys
import vtk, qt, ctk, slicer
from slicer.ScriptedLoadableModule import *
import collections
import itertools
import numpy as np
import time
import SimpleITK as sitk
import logging
from collections import OrderedDict
from CIP.logic.SlicerUtil import SlicerUtil
from CIP.logic import Util
from CIP.logic imp... | acil-bwh/SlicerCIP | Scripted/CIP_LesionModel/CIP_LesionModel.py | Python | bsd-3-clause | 130,907 | [
"VTK"
] | dcceaa910b0fd9f5f86fa7a25a011164d2e5a9cd2b7b3825aa68f1c1ded3ddb6 |
#!/usr/bin/python
#------------------------------------------------------------------------------
# askversion.py
#
# (C) 2001-2006 by Marco Paganini (paganini@paganini.net)
#
# This file is part of ASK - Active Spam Killer
#
# ASK is free software; you can redistribute it and/or modify
# it under the terms of th... | celer/ask | askversion.py | Python | gpl-2.0 | 1,430 | [
"VisIt"
] | f3d708a7877dde77f9439a1f9e790188d87e96fd8de50528239390bc234b45c0 |
# Copyright (C) 2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later versio... | KaiSzuttor/espresso | testsuite/python/unittest_decorators.py | Python | gpl-3.0 | 2,446 | [
"ESPResSo"
] | 804a817b3c24ba457dbada10a787037c710e84d6e0baf1593072e33af2a69675 |
import cv2
import Tool
from scipy import ndimage
class Denoise(Tool.Tool):
def on_init(self):
self.id = "denoise"
self.name = "Denoise"
self.icon_path = "ui/PF2_Icons/Denoise.png"
self.properties = [
# Detailer
Tool.Property("enabled", "Denoise", "Header", F... | Tilo15/PhotoFiddle2 | PF2/Tools/Denoise.py | Python | gpl-3.0 | 1,956 | [
"Gaussian"
] | 541ecf3938bd4dad7db8bb6194bc2fe51e86d3b8fc4c2e9bf76438e2598e5fb1 |
# -*- coding: utf-8 -*-
"""
End-to-end tests related to the cohort management on the LMS Instructor Dashboard
"""
from datetime import datetime
from pytz import UTC, utc
from bok_choy.promise import EmptyPromise
from nose.plugins.attrib import attr
from .helpers import CohortTestMixin
from ..helpers import UniqueCour... | solashirai/edx-platform | common/test/acceptance/tests/discussion/test_cohort_management.py | Python | agpl-3.0 | 54,443 | [
"VisIt"
] | 518b76bc114dabf2e3f9b20b34bf639d073c80d4d1abb61d2f35531d23430406 |
#!/usr/bin/env python
"""
Artificial Intelligence for Humans
Volume 1: Fundamental Algorithms
Python Version
http://www.aifh.org
http://www.jeffheaton.com
Code repository:
https://github.com/jeffheaton/aifh
Copyright 2013 by Jeff Heaton
Licensed under the Apache License, Version 2... | PeterLauris/aifh | vol1/python-examples/examples/example_ocr.py | Python | apache-2.0 | 8,445 | [
"VisIt"
] | 565282d41eb7015c8e6b090eb37108e0ef1e16fb1d2330fad719bc73e2c87435 |
from gpaw.xc.libxc import LibXC
from gpaw.xc.lda import LDA
from gpaw.xc.gga import GGA
from gpaw.xc.mgga import MGGA
def XC(kernel, parameters=None):
"""Create XCFunctional object.
kernel: XCKernel object or str
Kernel object or name of functional.
parameters: ndarray
Parameters for BEE ... | robwarm/gpaw-symm | gpaw/xc/__init__.py | Python | gpl-3.0 | 3,256 | [
"GPAW"
] | dda277c5167d25dd2daa5e1194feaa35b1fee20c184f4e323567f226fa44031a |
# Author: Brooke Husic <brookehusic@gmail.com>
# Contributors:
# Copyright (c) 2016, Stanford University and the Authors
# All rights reserved.
from __future__ import print_function, division, absolute_import
import warnings
import mdtraj as md
from mdtraj.utils import ensure_type
from mdtraj.utils.six import strin... | msultan/msmbuilder | msmbuilder/featurizer/multichain.py | Python | lgpl-2.1 | 23,224 | [
"MDTraj"
] | 9300dbfd4ec1cbcda295b72d41fee654347644c178def28e4b1c4aa920de746e |
"""Dynamically find and load plugins.
PyMT plugins are components that expose the CSDMS Basic
Model Interface and provide CSDMS Model Metadata. With
these two things, third-party components can be imported
into the PyMT modeling framework.
By default PyMT searches a package named `csdms`, if
it exists, for possible p... | csdms/coupling | deprecated/plugin.py | Python | mit | 5,749 | [
"VTK"
] | 28cf45d72c535aaff6b97b51ff0b15bdfc230c4de95702d030ecf23fdef6ca5b |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import warnings
from collections import defaultdict
from math import isnan
import numpy as np
from pymatgen.analysis.reaction_calculator import (
BalancedReaction,
ComputedReaction,
Reaction,
... | materialsproject/pymatgen | pymatgen/analysis/tests/test_reaction_calculator.py | Python | mit | 21,472 | [
"pymatgen"
] | 4e49438bf15e105ce525d7d6710a432b0d08035187c008625881ae3178ddb948 |
"""
==============================================
Use different base estimators for optimization
==============================================
Sigurd Carlen, September 2019.
Reformatted by Holger Nahrstaedt 2020
.. currentmodule:: skopt
To use different base_estimator or create a regressor with different paramete... | scikit-optimize/scikit-optimize | examples/optimizer-with-different-base-estimator.py | Python | bsd-3-clause | 4,857 | [
"Gaussian"
] | 5e38ed258686b6767016e37c6de9ff3bbe56dd047cb077523e5317f975b79d3f |
from __future__ import absolute_import, division, print_function
import ast
from jaspyx.ast_util import ast_call, ast_load
from jaspyx.context.function import FunctionContext
from jaspyx.visitor import BaseVisitor
from jaspyx.compat import get_arg_id
class Function(BaseVisitor):
def visit_FunctionDef(self, node):... | ztane/jaspyx | jaspyx/visitor/function.py | Python | mit | 2,365 | [
"VisIt"
] | 1cdb2e7ad404653ed346f7c9ef9a3b741cc14eb02a3c779f4c02c4edc58d24ec |
import numpy as np
import scipy.linalg as slg
from pyscf.lib import logger
def get_tdm_uhf(pymol, C0, C1, s1e=None, r_aos=None, orth=0, thr_zero=1.E-9):
""" C0 and C1 be a list of two numpy arrays, [Caocc, Cbocc]. For RHF, simply replicate the C matrix twice, i.e., np.asarray([Cocc, Cocc])
orth:
0 ... | hongzhouye/frankenstein | sgscf/tdm_utils.py | Python | bsd-3-clause | 9,603 | [
"PyMOL",
"PySCF"
] | 9b00d7b35e939fcfd7474be7edd6e31933b6d3cbbcbeff1973a0617b7ad2b60e |
#!/usr/bin/env python
#importo librerias
import netCDF4
import calendar
import numpy as np
from mpl_toolkits.basemap import Basemap
import matplotlib.pyplot as plt
from netCDF4 import Dataset
#creo objeto netcdf
#ACA NECESITO COMO INPUT FILENAME
f=Dataset("./ascat_20150805_010600_metopb_14937_eps_o_250_2201_ovw.l2... | carolinapepe/satelites | temp_files/ejemplo_lectura_nc.py | Python | gpl-3.0 | 2,242 | [
"NetCDF"
] | f29a44ec422f693e5407cb837717c0772661b9604ce3fd55b540eb31f3cd2bca |
# #
# Copyright 2009-2021 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (... | boegel/easybuild-framework | easybuild/tools/filetools.py | Python | gpl-2.0 | 118,067 | [
"NetCDF"
] | 28aced64e559fa60bb01dec36f0eee331c206b98552a492c307e22d27562ecb0 |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2011, 2013, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License... | zenoss/ZenPacks.zenoss.PostgreSQL | ZenPacks/zenoss/PostgreSQL/Database.py | Python | gpl-2.0 | 2,139 | [
"VisIt"
] | c4c4d9a0391cd848cf16714769a06eea2444d26a57ed7984fc6a5ffaaa38666d |
# -*- encoding: utf-8 -*-
import copy
class Graph:
def __init__(self):
self.vertex_map = dict()
def add(self, name, vertex):
self.vertex_map[name] = vertex
def find(self, name):
return self.vertex_map[name]
class Vertex:
def __init__(self, name):
self.name = name
... | morenice/learn-algorithms | acmicpc/1260/solve.py | Python | mit | 3,648 | [
"VisIt"
] | 08a5b4aecfd985c9937e3084082b16561bbdf9266dea707cd20f6a508fe76192 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import json
import zipfile
import os.path
import lxml.html
import time
import requests
import csv
import dryscrape
import random
import re
from unidecode import unidecode
json_dir = "./output"
cache_dir = "./cache"
tmp_dir = "./tmp"
inegi_base_url = 'http://buscador.in... | openaddresses/openaddresses | scripts/mx/process_inegi_census_files.py | Python | bsd-3-clause | 9,169 | [
"VisIt"
] | ed0798c9f200a7c07ecff1d7e3b12bed1fb8671927f2d7957f27263941d5c574 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2018 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
#... | amjames/psi4 | psi4/share/psi4/databases/HSG.py | Python | lgpl-3.0 | 46,405 | [
"Psi4"
] | 358b6d47ff737bf8907926227d407d63b515e73db854be78f2af9c032e87fa40 |
"""Crystal structure routines in direct and reciprocal spaces."""
# Copyright (C) 2021 Atsushi Togo
# All rights reserved.
#
# This file is part of phonopy.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# * Redist... | atztogo/phonopy | phonopy/structure/__init__.py | Python | bsd-3-clause | 1,647 | [
"CRYSTAL",
"phonopy"
] | 6ccac59c72cacbcec5cb43fe47119672bbf18439450fffe2c469e7a462dcb2b0 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module contains the definition of some objects used in the chemenv package.
"""
__author__ = "David Waroquiers"
__copyright__ = "Copyright 2012, The ... | xhqu1981/pymatgen | pymatgen/analysis/chemenv/utils/defs_utils.py | Python | mit | 3,527 | [
"pymatgen"
] | e06b6779d220a5a6970273decac1851dfe1d6efbc8e7fc71853b18b62900d33a |
"""Utility routines depending on the finder,
a combination of code by Jack Jansen and erik@letterror.com.
Most events have been captured from
Lasso Capture AE and than translated to python code.
IMPORTANT
Note that the processes() function returns different values
depending on the OS version it is running on. On MacO... | teeple/pns_server | work/install/Python-2.7.4/Lib/plat-mac/findertools.py | Python | gpl-2.0 | 30,176 | [
"BLAST"
] | acd3fc691c83a4e999cdf131eba1831abcc6085c4dc117183cdee8c9f9bad6d3 |
"""
This module provides sample kernels and inputs.
"""
import numpy as np
from .base import prepare_input
from . import models
##############################################################################
#
# Sample Kernels
#
def text_kernel():
kernel = np.zeros((16,16))
#con
con = [list(line) for li... | jahuth/convis | convis/samples.py | Python | gpl-3.0 | 16,394 | [
"Gaussian"
] | fead7288bd8465c073ef112e92eedc7f64e0c4c143a4a915a2881f3e3c49af98 |
###############################################################################
#
# ptsecstruct.py - object to represent secondary structure elements (SSEs) and
# their associated Hydrogen bonds and functions to parse
# these from external programs (DSSP, STRIDE, etc.)
#
# File: ptsecstruct.py
... | NirBenTalLab/proorigami-ptgraph | ptsecstruct.py | Python | mit | 47,718 | [
"PyMOL"
] | 0e44d6163ca08235dfcfa37cee7088d74ed30189d1e69f4c7bf375f2281d78e6 |
# Converts AMBER prmtop (and inpcrd) files to a MMTK database,
# which is basically a python script defining a molecule's
# atoms, bonds, and default coordinates
import os, sys, time, numpy
#################
### CONSTANTS ###
#################
# Map flag to variable names
varnames = ['POINTERS','TITLE','ATOM_NAME','... | CCBatIIT/AlGDock | Pipeline/prmtop2database.py | Python | mit | 5,960 | [
"Amber"
] | a9cb69f7ca08fa6fcea2231f170f57c1f1d99d6a907ce07dd85b3e3414ae5beb |
# eliteBonusGunshipExplosiveMissileDamage1
#
# Used by:
# Ship: Jaguar
type = "passive"
def handler(fit, src, context):
fit.modules.filteredChargeBoost(lambda mod: mod.charge.requiresSkill("Missile Launcher Operation"), "explosiveDamage",
src.getModifiedItemAttr("eliteBonusGuns... | bsmr-eve/Pyfa | eos/effects/elitebonusgunshipexplosivemissiledamage1.py | Python | gpl-3.0 | 354 | [
"Jaguar"
] | 340818296216d27870a5331adb2337f0c9eafa299060e1fbeadba50e986524ff |
"""
Connected components.
"""
import itertools
import logging
import networkx as nx
import numpy as np
from matplotlib.patches import Circle, FancyArrowPatch
from monty.json import MSONable, jsanitize
from networkx.algorithms.components import is_connected
from networkx.algorithms.traversal import bfs_tree
from pyma... | davidwaroquiers/pymatgen | pymatgen/analysis/chemenv/connectivity/connected_components.py | Python | mit | 42,543 | [
"pymatgen"
] | eb9e8873d4b5adddd6547225b438a2a0f655feb3d7608e44a253942d8e60c501 |
# ORANGE Domain Translation
# by Alex Jakulin (jakulin@acm.org)
#
# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
#
# CVS Status: $Id$
#
# Version 2.0 (20/11/2003)
# *DISABLED* - SVM no longer uses -1 for minimum value in categorical attributes
#
# Version 1.9 (17/11/2003)
# - Dumm... | yzl0083/orange | Orange/orng/orng2Array.py | Python | gpl-3.0 | 24,121 | [
"Gaussian"
] | c90b4d269c4505240e87fcc0ba7fbc6de12b1514e64d816edefdd02ee1e32d72 |
#!/usr/bin/env python
#
# MIMEHandler.py
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License version 2 as
# published by the Free Software Foundation.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANT... | tweemeterjop/thug | thug/DOM/MIMEHandler.py | Python | gpl-2.0 | 30,147 | [
"NetCDF"
] | 59659ca0591976063332fb91f83ec4dc0723dc5c8f2848eeb171691bbffc67de |
#
# Copyright 2016 The BigDL 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 agreed to in ... | intel-analytics/BigDL | python/orca/src/bigdl/orca/learn/openvino/estimator.py | Python | apache-2.0 | 12,432 | [
"ORCA"
] | 1128ec9b3d95c5cde8f05cd686de27e5688a28e5c1996406ca4a0f239895c4b3 |
"""
Recurrent layers.
TODO: write more documentation
"""
__docformat__ = 'restructedtext en'
__authors__ = ("Razvan Pascanu "
"KyungHyun Cho "
"Caglar Gulcehre ")
__contact__ = "Razvan Pascanu <r.pascanu@gmail>"
import numpy
import copy
import theano
import theano.tensor as TT
# Nicer i... | neozhangthe1/coverage_model | build/lib/groundhog/layers/rec_layers.py | Python | bsd-3-clause | 61,552 | [
"Gaussian"
] | 06882b79e4c5416b67794ca4603f7cd1d2bcf296a779621929c935c56c149693 |
from __future__ import annotations
import collections
import copy
import datetime
import gettext
import logging
import typing
import uuid
from nion.swift.model import Utility
if typing.TYPE_CHECKING:
from nion.swift.model import FileStorageSystem
PersistentDictType = typing.Dict[str, typing.Any]
_ = gettext.ge... | nion-software/nionswift | nion/swift/model/Migration.py | Python | gpl-3.0 | 54,620 | [
"Gaussian"
] | 5a2e7a8f5c7ffc105671eda30b451e49c76679d2502db3631971f53d46e7e331 |
########################################################################
# File : InstallTools.py
# Author : Ricardo Graciani
########################################################################
"""
Collection of Tools for installation of DIRAC components:
MySQL, DB's, Services's, Agents
It only makes use of ... | calancha/DIRAC | Core/Utilities/InstallTools.py | Python | gpl-3.0 | 88,612 | [
"DIRAC"
] | 45bd0ce5ff487ee6e14de28949d0cdffe30505526b7810e7fe3037260bd88c35 |
# -*- coding: utf-8 -*-
"""
Write initial ATP Profile for an ECs Mesh in legacy VTK format as .vtk.
"""
import os
import sys
# Run in current directory.
os.chdir(os.path.dirname(os.path.abspath(__file__)))
# Relative import path for the DumpATPMeshToLegacyFormat script.
importPath = os.path.abspath(os.path.join(os.p... | BlueFern/DBiharMesher | meshes/c216/Write216ATPMeshHdf5.py | Python | gpl-2.0 | 1,005 | [
"VTK"
] | df2dddc8a1f9886eccfdcdda6d9bf50f5699093cdd1685b02e6efd4e3615ae80 |
"""cdbgui.py
Developers: Christina Hammer, Noelle Todd
Last Updated: August 24, 2014
This file contains a class version of the interface, in an effort to
make a program with no global variables.
"""
from datetime import datetime, timedelta, date
from tkinter import *
from tkinter import ttk
from cdbifunc2 import *
im... | ChristinaHammer/Client_Database | cdbgui16.py | Python | mit | 64,173 | [
"VisIt"
] | 071e3941230aa59822e3efacbec900865e63c0221935202e726590d24be92915 |
""" PilotAgentsDB class is a front-end to the Pilot Agent Database.
This database keeps track of all the submitted grid pilot jobs.
It also registers the mapping of the DIRAC jobs to the pilot
agents.
Available methods are:
addPilotTQReference()
setPilotStatus()
deletePilot()
clearPilo... | vmendez/DIRAC | WorkloadManagementSystem/DB/PilotAgentsDB.py | Python | gpl-3.0 | 37,404 | [
"DIRAC"
] | eae53372905c24ffa2aebdb9ab5d40efa46de38462c8cc20b5aba70c0a965a0e |
""" DIRAC FileCatalog component representing a directory tree with enumerated paths
"""
# pylint: disable=protected-access
__RCSID__ = "$Id$"
import os
from DIRAC import S_OK, S_ERROR
from DIRAC.DataManagementSystem.DB.FileCatalogComponents.DirectoryTreeBase import DirectoryTreeBase
MAX_LEVELS = 15
class Directo... | andresailer/DIRAC | DataManagementSystem/DB/FileCatalogComponents/DirectoryLevelTree.py | Python | gpl-3.0 | 17,806 | [
"DIRAC"
] | 56e86754b7c28a471dfebd7058f3e5ba8f31af52df075f41f67d653b8f5c2362 |
import random
import unittest
from SDWLE.constants import MINION_TYPE
from testsSDW.agents.testing_agents import PlayAndAttackAgent, OneCardPlayingAgent, CardTestingAgent, \
HeroPowerAndCardPlayingAgent
from testsSDW.testing_utils import generate_game_for
from SDWLE.cards import *
from SDWLE.agents.basic_agents im... | jomyhuang/sdwle | testsSDW__copy/card_tests/rogue_tests.py | Python | mit | 32,792 | [
"TINKER"
] | 9d94c62b734050dbbcaffd049b3df97cf6efda49c397c16e9792b49679c65cf6 |
#!/usr/bin/env python
##
## @file create_sedml.py
## @brief cerates a SED-ML document.
## @author Frank T. Bergmann
##
## <!--------------------------------------------------------------------------
## This file is part of libSEDML. Please visit http://sed-ml.org for more
## information about SEDML, and the la... | 0u812/libSEDML | examples/python/create_sedml.py | Python | bsd-2-clause | 5,511 | [
"VisIt"
] | 81bdbdb5fe77669217268a90276f1661081dbeac5f09623e67edcc94d7a20fcb |
"""LAMMPS SimPhoNy Wrapper.
This module provides a wrapper for LAMMPS-md
"""
import os
import contextlib
import shutil
import tempfile
from simphony.api import CUDS, CUBA
from simphony.core.data_container import DataContainer
from simphony.cuds.abc_modeling_engine import ABCModelingEngine
from simphony.cuds.abc_parti... | simphony/simphony-lammps-md | simlammps/lammps_wrapper.py | Python | bsd-2-clause | 13,771 | [
"LAMMPS"
] | fd4b7ae78aabe98de84522ad1b603e65c54efc561a9d233538f58bcbff46e052 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright: (c) 2018, F5 Networks Inc.
# GNU General Public License v3.0 (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
DOCUMENTATION = r'''
---
module: bigip_asm_policy_server... | F5Networks/f5-ansible | ansible_collections/f5networks/f5_modules/plugins/modules/bigip_asm_policy_server_technology.py | Python | gpl-3.0 | 13,386 | [
"ASE",
"Galaxy"
] | 295e796a164642e7570d3c46a8a3feaad1fff4881c54cb000b1162806ad596c9 |
#! /usr/bin/env python
#
# Copyright (c) 2011 Brian House
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This... | brianhouse/wavefarm | housepy/drawing.py | Python | gpl-3.0 | 12,030 | [
"Brian"
] | 255ccd6313bea10785c71ea683f09d139cea1ab0028035d83db26c1c838b596e |
"""Quality control and summary metrics for next-gen alignments and analysis.
"""
import collections
import copy
import csv
import os
import yaml
from datetime import datetime
import pandas as pd
import glob
import toolz as tz
from bcbio import utils
from bcbio.cwl import cwlutils
from bcbio.log import logger
from bc... | a113n/bcbio-nextgen | bcbio/pipeline/qcsummary.py | Python | mit | 17,048 | [
"Galaxy"
] | a02447b762a36ad39981dccd3623d9eab85ec9c1d71387e650019392225d67b6 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | var/spack/repos/builtin/packages/py-pyvcf/package.py | Python | lgpl-2.1 | 1,730 | [
"pysam"
] | cfe846538a2aedc46f7f3dc67bcea9bbc5c37d46c9e9c8feee358fde8d4dd798 |
# Copyright 2014, Brian Coca <bcoca@ansible.com>
# Copyright 2017, Ken Celenza <ken@networktocode.com>
# Copyright 2017, Jason Edelman <jason@networktocode.com>
# Copyright 2017, Ansible Project
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of ... | pmarques/ansible | lib/ansible/plugins/filter/mathstuff.py | Python | gpl-3.0 | 9,327 | [
"Brian"
] | d809ba392ef4f93df7bfd8a86c8333c4e119e86c101860fd7dd7ae76134c3367 |
# encoding: utf-8
"""
Tools for the pan-M31 PHAT patch fitting exercise.
2015-05-28 - Created by Jonathan Sick
"""
import os
from collections import OrderedDict
import json
from pkg_resources import resource_stream, resource_exists
from matplotlib.path import Path
import numpy as np
from astropy.table import Table
... | jonathansick/androcmd | androcmd/phatpatchfit/pipeline.py | Python | mit | 16,446 | [
"Galaxy"
] | 249f3b12a245a0bcb3a6906c44e60a32e4b0d561451c954cbb2fbc5fb8811747 |
#
# Copyright (C) 2013-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | fweik/espresso | testsuite/python/virtual_sites_tracers_common.py | Python | gpl-3.0 | 7,053 | [
"ESPResSo"
] | 7bda7f97c5552b65ca24b49452298efd1674b4433a3aa6758ca2281c960f9210 |
#########################################################################
## This program is part of 'MOOSE', the
## Messaging Object Oriented Simulation Environment.
## Copyright (C) 2013 Upinder S. Bhalla. and NCBS
## It is made available under the terms of the
## GNU Lesser General Public License version 2... | BhallaLab/moose-examples | tutorials/ChemicalBistables/scaleVolumes.py | Python | gpl-2.0 | 6,001 | [
"MOOSE"
] | 53056f57be3ee63e6b326a84503951caccc9ec1adbda17138f870fbe440b6809 |
import numpy as np
import os
import mdtraj as md
import pdbfixer
from simtk.openmm import app
import simtk.openmm as mm
from simtk import unit as u
from .target import Target
from .simulation_parameters import *
import utils
class System(Target):
def __init__(self, temperature, padding=PADDING, cutoff=CUTOFF, k... | choderalab/TrustButVerify | trustbutverify/protein_system.py | Python | gpl-2.0 | 7,819 | [
"MDTraj",
"OpenMM"
] | 647d1b65dfeb16629dd6aacf3b2695202dce0bc8ad7fad4c7713f0ca1b86f9ed |
import re
from .smarty_grammar import SmartyLanguage, DollarSymbol, PrintStatement
# Stores the actual visitor methods
def make_visitor():
_methods = {}
# The actual @visitor decorator
def _visitor(arg_type):
"""Decorator that creates a visitor method."""
# Delegating visitor implementa... | Osso/smartytotwig | smartytotwig/tree_walker.py | Python | mit | 13,716 | [
"VisIt"
] | dd4c52b4cc68cc20dc5c5d14d7e0037734e32e18a579e34ff6688efd3279b1a5 |
#!/usr/bin/env python
import fnmatch
import os
from pathlib import Path
import re
import shlex
import shutil
import subprocess
import sys
import tempfile
import time
from concurrent.futures import ThreadPoolExecutor
from contextlib import contextmanager
from typing import Optional
import click
import git
import typer
... | ic-hep/DIRAC | integration_tests.py | Python | gpl-3.0 | 24,289 | [
"DIRAC"
] | 13ce07a46a927c29db5f35495168f1db5fc224594f53d30326db92d251f7cc3c |
#!/usr/bin/python
# coding=utf8
# author=zhtsh
import sys
import logging
from os import path
from optparse import OptionParser
sys.path.append(path.abspath(path.join(path.dirname(__file__), '../core')))
from context import SpamClassifierContext
from strategy import ClassifierStrategy
from strategy import SVMClassifie... | zhtsh/spam_email_classifier | script/train.py | Python | mit | 4,004 | [
"Gaussian"
] | ae97798260e1c0b123c7161193e921ed13b2bb9d2e776ea28062ec11c8bd3903 |
# -*- python -*-
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2001-2007 Donald N. Allingham, Martin Hawlisch
# Copyright (C) 2009 Yevgeny Zegzda <ezegjda@ya.ru>
# Copyright (C) 2010 Nick Hall
#
# This program is free software; you can redistribute it and/or mo... | Forage/Gramps | gramps/plugins/view/pedigreeview.py | Python | gpl-2.0 | 80,310 | [
"FLEUR"
] | 192c49ccf0c57151c787e866997e81d69b7d9af985043f8a266cc4329a7e2a62 |
"""
Simple frontend to the Laser Absorption Spectroscopy ANalysis package.
Makes use of the modules 'parse.py', and 'analyze.py'.
Submodules notwithstanding.
"""
# Standard
from os import path, makedirs
import math as m
# Part of package
from atoms import He
import gui
import lineshapes
import parse
import preproce... | l3enny/lasana | offset.py | Python | mit | 2,412 | [
"Gaussian"
] | 8413385313a04f85c41bad7543a534cd42d005346d3a1352dc98b5e6ddf91631 |
# commandBurstAoERoleBonus
#
# Used by:
# Ships from group: Carrier (4 of 4)
# Ships from group: Combat Battlecruiser (14 of 14)
# Ships from group: Command Ship (8 of 8)
# Ships from group: Force Auxiliary (6 of 6)
# Ships from group: Supercarrier (6 of 6)
# Ships from group: Titan (7 of 7)
# Subsystems named like: Of... | bsmr-eve/Pyfa | eos/effects/commandburstaoerolebonus.py | Python | gpl-3.0 | 623 | [
"ORCA"
] | 23ffcf7e9fa99ea09e1b817dd33716e9217840e9725bb45d535eb7c57abaebee |
# Copyright (c) 2015, Frappe Technologies Pvt. Ltd. and Contributors
# License: GNU General Public License v3. See license.txt
import frappe
from frappe.model.utils.rename_field import rename_field
from frappe.modules import scrub, get_doctype_module
rename_map = {
"Opportunity": [
["enquiry_details", "items"]
],... | anandpdoshi/erpnext | erpnext/patches/v5_0/rename_table_fieldnames.py | Python | agpl-3.0 | 6,567 | [
"VisIt"
] | 68c97ec83eab325abc2a0fa292069f268533f073c6a9b595141344261eed000b |
"""
==========================
metagenome simulation
bechmark pipeline
==========================
Usage
=====
See :ref:`PipelineSettingUp` and :ref:`PipelineRunning` on general information how to use CGAT pipelines.
Configuration
-------------
The pipeline requires a configured :file:`pipeline.ini` file.
The sphi... | CGATOxford/CGATPipelines | CGATPipelines/pipeline_docs/pipeline_metagenomebenchmark/pipeline_metagenomebenchmark.py | Python | mit | 27,582 | [
"pysam"
] | 7e53e03aa46431ee4b2f1332526569561415959b3d6bfc4ff8521d48d571b5be |
# Copyright (C) 2005-2012 Canonical Ltd
#
# 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 distribute... | stewartsmith/bzr | bzrlib/builtins.py | Python | gpl-2.0 | 273,180 | [
"VisIt"
] | 4b66a0dea87083e7fbc371e247008bac3e6b4a614fa0848e114b5d7f144d4b89 |
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