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from __future__ import print_function, division
import random
from sympy import Derivative
from sympy.core.basic import Basic
from sympy.core.compatibility import is_sequence, as_int, range
from sympy.core.function import count_ops
from sympy.core.decorators import call_highest_priority
from sympy.core.singleton impo... | drufat/sympy | sympy/matrices/dense.py | Python | bsd-3-clause | 44,527 | [
"DIRAC"
] | f5b00643b550af039b24bd8e8ffcaa3c1a7aa054f637e46f332eefff8d2c1f86 |
from __future__ import print_function
import os
import sys
from six import StringIO
import unittest2 as unittest
from nose.plugins.attrib import attr
from contextlib import contextmanager
from jnpr.junos import Device
from jnpr.junos.exception import RpcError, SwRollbackError, RpcTimeoutError
from jnpr.junos.utils.sw i... | spidercensus/py-junos-eznc | tests/unit/utils/test_sw.py | Python | apache-2.0 | 33,564 | [
"Firefly"
] | 17f2a0916d029af6003d34cd71c579ee3d1ba410038f283238227250c78e0000 |
# encoding: utf-8
from __future__ import unicode_literals
import re
from .common import InfoExtractor
from ..utils import (
int_or_none,
remove_end,
)
class MailRuIE(InfoExtractor):
IE_NAME = 'mailru'
IE_DESC = 'Видео@Mail.Ru'
_VALID_URL = r'http://(?:www\.)?my\.mail\.ru/(?:video/.*#video=/?(?P<... | AMOboxTV/AMOBox.LegoBuild | script.module.youtube.dl/lib/youtube_dl/extractor/mailru.py | Python | gpl-2.0 | 4,945 | [
"Galaxy"
] | 9aef30a28370e1eeb965b413b64a04a21999243f7a10fb63f3c60bfe6fdaf544 |
""" DIRAC Workload Management System Client class encapsulates all the
methods necessary to communicate with the Workload Management System
"""
from DIRAC.Core.DISET.RPCClient import RPCClient
from DIRAC.Core.Utilities.ClassAd.ClassAdLight import ClassAd
from DIRAC ... | avedaee/DIRAC | WorkloadManagementSystem/Client/WMSClient.py | Python | gpl-3.0 | 8,307 | [
"DIRAC"
] | 9a44592186d85a9f28f47c526459e46a318413349b7fee2e40f71d77314da067 |
import json
from random import gauss, uniform
class Capability(object):
def __init__(self, **kwargs):
if 'json' in kwargs or 'data' in kwargs:
data = {}
try:
data = json.loads(kwargs['json'])
except StandardError:
try:
... | asascience-open/paegan-transport | paegan/transport/models/behaviors/capability.py | Python | gpl-3.0 | 3,045 | [
"Gaussian"
] | 50b9f237c3799674813b5724c9cd515444bb3938ee5cc423510ce9a32843088d |
# 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... | snnn/tensorflow | tensorflow/python/data/experimental/kernel_tests/sql_dataset_test_base.py | Python | apache-2.0 | 4,409 | [
"MOE"
] | 8cab7598e98b912949290a6c4a0cbae32c7032edc9747c8ab2d36a5a71e2e52a |
from bottle import route, default_app
app = default_app()
data = {
"id": 78874,
"seriesName": "Firefly",
"aliases": [
"Serenity"
],
"banner": "graphical/78874-g3.jpg",
"seriesId": "7097",
"status": "Ended",
"firstAired": "2002-09-20",
"network": "FOX (US)",
"networkId": "... | romanvm/WsgiBoostServer | benchmarks/test_app.py | Python | mit | 1,229 | [
"Firefly"
] | 60570ebcb19cae1def27f8bb3c2c84b6c16ba7d84aef18c6918530bbfe6ad8de |
#!/usr/bin/env python
"""
Created on Wed May 7 11:30:31 2014
Author: Oren Freifeld
Email: freifeld@csail.mit.edu
"""
import numpy as np
#from cpa.cpa2d.calcs import PAT
from gpu.gaussian import calc_err_per_sample
from gpu.gaussian import calc_ll_per_sample
from gpu.gaussian import calc_err_by_der_per_sample
from ... | freifeld/cpabDiffeo | cpab/cpa1d/model/transformations/landmarks/_ScaleDependentLogLikelihoodGaussian.py | Python | mit | 3,919 | [
"Gaussian"
] | ce77cba911f425847541de17994a4b47eb8cf033298e4712adcea3d99fd0dbec |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
from PyQt5 ... | nuclear-wizard/moose | python/peacock/base/ViewerBase.py | Python | lgpl-2.1 | 3,111 | [
"MOOSE"
] | c54cdb441d327e4ed2651e54f1f54f77d8e854b796e8bb418c17aaac54ac1bbb |
"""
BufferedChannel implementation.
Automatically instantiated if buffer argument is used.
A = Channel(buffer=10)
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).
"""
from... | runefriborg/pycsp | pycsp/greenlets/buffer.py | Python | mit | 4,213 | [
"Brian"
] | 3f6a3ac50ad956ab98fc29468f64c7935a45596e647f27559349d70dfde6fb9e |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, subprocess, sys, glob, string
import zipfile
from datetime import date
cwd = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
os.chdir(cwd)
required_module_keys = ['name','version','moduleid','description','copyright','... | hieupham007/Titanium_Mobile | support/module/iphone/templates/build.py | Python | apache-2.0 | 6,808 | [
"VisIt"
] | 306ccccd06bae9bcee708e33306b13dcc569378c9b112973f9e1c1694f4176a6 |
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2003-2005 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2005-2012 Julio Sanchez
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Genera... | pmghalvorsen/gramps_branch | gramps/plugins/rel/rel_es.py | Python | gpl-2.0 | 36,181 | [
"Brian"
] | 0ee7e894c077431a4acd0f1b67e14b0a411f9d5689f74779262d944d8c2a06f2 |
#!/usr/bin/env python
""" Mission 7-Detect and Deliver
1. Random walk with gaussian at center of map until station position is acquired
2. loiter around until correct face seen
3. if symbol seen, move towards symbol perpendicularly
4. if close enough, do move_base aiming
task 7:
-----------------
Created by R... | ron1818/Singaboat_RobotX2016 | robotx_nav/nodes/task7_non_process.py | Python | gpl-3.0 | 8,010 | [
"Gaussian"
] | 97910ab69fec8a44c0f6daaabc97a8a8bbe562ee61bbebcf2c4df99c6f715a97 |
# Copyright (c) 2013, Joerg Raedler (Berlin, Germany)
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without modification,
# are permitted provided that the following conditions are met:
#
# Redistributions of source code must retain the above copyright notice, this list
# of cond... | jraedler/DyMat | DyMat/Export/netCDF4.py | Python | bsd-2-clause | 3,255 | [
"NetCDF"
] | b72f98ba02da33f480284b0ca3777eb16aefe819d1275332b06aa79140452884 |
#!/usr/bin/env python
"""Universal feed parser
Handles RSS 0.9x, RSS 1.0, RSS 2.0, CDF, Atom 0.3, and Atom 1.0 feeds
Visit http://feedparser.org/ for the latest version
Visit http://feedparser.org/docs/ for the latest documentation
Required: Python 2.1 or later
Recommended: Python 2.3 or later
Recommended: CJKCodecs... | onecore/rss2email-gui | feedparser.py | Python | mit | 157,546 | [
"NetCDF",
"VisIt"
] | e065ee99d68eec925e553ee45ee0c2dbfe73ea8dfddfe899c83c3e833cf6201e |
"""
Module for creating network connections
"""
from __future__ import print_function
from __future__ import division
from __future__ import unicode_literals
from __future__ import absolute_import
from builtins import dict
from builtins import range
from builtins import round
try:
basestring
except NameError:
... | Neurosim-lab/netpyne | netpyne/network/conn.py | Python | mit | 38,543 | [
"NEURON"
] | f251ed173beef99e3c98ee1408a091006f9778fdcb9359ef039a5907b22be16f |
"""
This class brings together a L{solve.Solver} to choose a set of implmentations, a
L{fetch.Fetcher} to download additional components, and the user's configuration
settings.
"""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import _
from logg... | timdiels/zeroinstall | zeroinstall/injector/policy.py | Python | lgpl-2.1 | 6,124 | [
"VisIt"
] | 7d6d5fd182cb32133ac211a6da620b248932b026f0adc57077eadd7a59f89432 |
r"""
Diametrically point loaded 2-D disk with postprocessing and probes. See
:ref:`sec-primer`.
Use it as follows (assumes running from the sfepy directory; on Windows, you
may need to prefix all the commands with "python " and remove "./"):
1. solve the problem::
./simple.py examples/linear_elasticity/its2D_4.py... | sfepy/sfepy | examples/linear_elasticity/its2D_4.py | Python | bsd-3-clause | 4,331 | [
"VTK"
] | 7edd63d58abc687e5b1daa13566b93d12dabbbb1fcfb95967dd8402b47ecf2a7 |
""" TopErrorMessagesReporter produces a list with the most common errors
injected in the SystemLoggingDB and sends a notification to a mailing
list and specific users.
"""
__RCSID__ = "$Id$"
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Base.AgentModule ... | hgiemza/DIRAC | FrameworkSystem/Agent/TopErrorMessagesReporter.py | Python | gpl-3.0 | 5,642 | [
"DIRAC"
] | 91b9d7590384f2e604428e5281b1af89fbc5d3c4c13f98319a380ac41c2ecb6e |
import numpy as np
import simtk.unit as u
from simtk.openmm import app
import simtk.openmm as mm
from repex.thermodynamics import ThermodynamicState
from repex.parallel_tempering import ParallelTempering
import repex.netcdf_io
from mpi4py import MPI # MPI wrapper
name = "1vii"
equil_filename = "./equil/%s.pdb" % name
... | kyleabeauchamp/RepexRuns | code/run_mpi.py | Python | gpl-2.0 | 1,145 | [
"OpenMM"
] | 08815bfc3acb9904fe1f874ce67f3a26fad2a78affee57e8b1a304a7277d5709 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
""" Module: observables
===================
"""
from pytim import utilities
from MDAnalysis.core.groups import Atom, AtomGroup, Residue, ResidueGroup
from .observable import Observable
fr... | balazsfabian/pytim | pytim/observables/__init__.py | Python | gpl-3.0 | 900 | [
"MDAnalysis"
] | a302784602f5a9e426b0d21ace6f40fedf6792d301beb6af9cea701588cf80f7 |
#!/usr/bin/env python
# Copyright 2014-2019 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/solvent/test/test_pol_embed.py | Python | apache-2.0 | 11,477 | [
"PySCF"
] | 1e48bed60cf4938fa7d4b694b0f618b921be015e4069fa9268f71ce7a7d9199a |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# License AGPLv3 (https://www.gnu.org/licenses/agpl-3.0-standalone.html)
"""
This script creates a migration issue for a new Odoo version
in all repositories. This issue lists all known addons in the previous version.
Installation
============
For using this utility, you... | acsone/maintainer-tools | tools/create_migration_issue.py | Python | agpl-3.0 | 7,723 | [
"VisIt"
] | a4c96a939b3609b08d554190ed84eacf13cee42e868e000949057471651e2f2d |
"""Execute a single step directly
"""
import logging
import os
import sys
from smif.controller.build import get_model_run_definition
from smif.data_layer import DataHandle
from smif.data_layer.model_loader import ModelLoader
from smif.decision.decision import DecisionManager
from smif.exception import SmifDataNotFound... | nismod/smif | src/smif/controller/execute_step.py | Python | mit | 4,961 | [
"CRYSTAL"
] | abdccda8cdef8d9ffe1a0b5f0f93b2cc5c35104f9eb1bddd7ba2227bcb36370d |
"""
============================================================
Sparse recovery: feature selection for sparse linear models
============================================================
Given a small number of observations, we want to recover which features
of X are relevant to explain y. For this :ref:`sparse linear ... | florian-f/sklearn | examples/linear_model/plot_sparse_recovery.py | Python | bsd-3-clause | 7,319 | [
"Gaussian"
] | 487e5f06d2f98334a8348917ed782ada9270083fb2663d581c39a8de3b75b3ed |
# ----------------------------------------------------------------------------
# Copyright 2014 Nervana Systems Inc. All rights reserved.
# ----------------------------------------------------------------------------
# ----------------------------------------------------------------------------
# Altered by Tim Dettme... | TimDettmers/dlearndb | cudanet/cudanet.py | Python | apache-2.0 | 68,737 | [
"Gaussian"
] | daddd7fd30b3c5b58d5193e4b7a75ee7e7eaa97682be371f5059af2e2cc2fba4 |
"""Perform validation of final calls against known reference materials.
Automates the process of checking pipeline results against known valid calls
to identify discordant variants. This provides a baseline for ensuring the
validity of pipeline updates and algorithm changes.
"""
import collections
import csv
import os... | elkingtonmcb/bcbio-nextgen | bcbio/variation/validate.py | Python | mit | 20,637 | [
"pysam"
] | 2b0b3bef1fe51a91f7de00dab7de456a70bc769b2682095acb7d4bb5bf7d9c24 |
#
# @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/driver/qcdb/psiutil.py | Python | lgpl-3.0 | 14,162 | [
"Psi4"
] | e2433aac62d19a95414dc421b994a0efe0ba5e80ba7e8bd2d6a2f8b145829fa8 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Entries are containers for calculated information, which is used in
many analyses. This module contains entry related tools and implements
the base Entry class, which is the basic entity that can be used ... | gVallverdu/pymatgen | pymatgen/entries/__init__.py | Python | mit | 3,283 | [
"pymatgen"
] | f4aa5191d73f9533183cf872ef645fd1a567bc62b689c44f5436d029b0172a72 |
#Input file for single transit fit
#Created by Barragan O., March 2021
#Input files
#fname_tr contains the transit data
fname_tr = ['lc_single.dat']
#MCMC controls
#the thin factor for the chains
thin_factor = 10
#The number of iterations to be taken into account
#The TOTAL number of iterations for the burn-in phase ... | oscaribv/pyaneti | inpy/example_single/input_fit.py | Python | gpl-3.0 | 2,840 | [
"Gaussian"
] | bf64cb1935482774b78b1508e14a1eb160122df0ec15706839ae2f8af5c8a28f |
# Copyright 2016-2018 Michael Peters
#
# 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 ag... | opiethehokie/march-madness-predictions | ratings/tests/test_markov.py | Python | apache-2.0 | 2,384 | [
"CRYSTAL"
] | 03ab3b80225039ca0fb4279ede8f2a08aeb0dc04013cb145994ce4547e98db0e |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses... | kustodian/ansible | lib/ansible/modules/network/avi/avi_networkprofile.py | Python | gpl-3.0 | 4,345 | [
"VisIt"
] | cf4f915539edc88e213142a91af43376ccd783b0791774c4e8c1bf7e770e3eed |
""" This module contain solvers for all kinds of equations:
- algebraic, use solve()
- recurrence, use rsolve()
- differential, use dsolve()
- transcendental, use tsolve()
- nonlinear (numerically), use nsolve()
(you will need a good starting point)
"""
from sympy.core.sympify import s... | jbaayen/sympy | sympy/solvers/solvers.py | Python | bsd-3-clause | 26,616 | [
"Gaussian"
] | 7a8a10a68e9197d3157d4b9342c7acc4fb0a73b8f8033aca9e15020493387bb2 |
#!/usr/bin/env python
# Copyright 2014-2020 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/cc/gccsd_lambda.py | Python | apache-2.0 | 8,214 | [
"PySCF"
] | 7c470684d9342f21daaedd5b7ae3074bf6416de99e857edaf424b3539be4a84d |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
# Authors: Christoph Klein
# Contributors:
#
# MDTraj is free software: yo... | kyleabeauchamp/mdtraj | mdtraj/tests/test_lammpstrj.py | Python | lgpl-2.1 | 3,450 | [
"MDTraj"
] | de7e99bcb33772f5b5f8f406a847742fafcb36d077e91a7d5ac77ef5def90a18 |
from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os
repository_name = 'filtering_0000'
repository_description = "Galaxy's filtering tool for test 0000"
repository_long_description = "Long description of Galaxy's filtering tool for test 0000"
import logging
log = logging.getLogger( __name__ )
class T... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/test/tool_shed/functional/test_0000_basic_repository_features.py | Python | gpl-3.0 | 25,205 | [
"Galaxy"
] | f0f63aa94e28fad78551ef61541ef11baa9eda7daefa7415037ca444f1a72111 |
#!/usr/bin/env python
import sys, os
import numpy
import numpy as np
import pylab
import time
sys.path.append('/home/aksenov/Simulation_wrapper/ase')
from ase.calculators.vasp import VaspChargeDensity
# sys.path.append('/home/aksenov/Simulation_wrapper/siman1')
# from header import runBash
def runBash(cmd, env = Non... | dimonaks/siman | chg_tools/aks_slice.py | Python | gpl-2.0 | 24,705 | [
"ASE",
"VASP"
] | ede4b2fccc14428a0783c1cb90ccd5d41384e42fbeff8229b93f264e195f9aff |
#
# Reflects the partial 3d grid for C2 c9h9+ as
# (x,y,z) -> (-x,-y,z)
# and prints GAUSSIAN cube data in x, y, z order
# (z changes fastest, followed by y and x)
#
# TODO(sean): Use a "*" here for string repetition.
# TODO(abel) Change this to use relations.
import csv
# set xyz lists and C2 opreating
x_loop = []
... | elekezem/3dGrid_Gen_for_Shielding_Surface | reflect.py | Python | mit | 3,988 | [
"Gaussian"
] | b77e11b689ad490ad849b741ee6903b8cdc1925439a45ecc54a3e641f6901056 |
import unittest
import os
import ruamel.yaml as yaml
from pymatgen import SETTINGS_FILE, _load_pmg_settings, get_structure_from_mp, \
SETTINGS
import warnings
class SettingsTestCase(unittest.TestCase):
def test_something(self):
SETTINGS = _load_pmg_settings()
if os.path.exists(SETTINGS_FILE):... | matk86/pymatgen | pymatgen/tests/test_init.py | Python | mit | 1,062 | [
"pymatgen"
] | e8aab99fd75824929074f89ee43c85713303b2f3dc0137576bb61852802a643f |
from __future__ import print_function, division
import unittest, numpy as np
from pyscf import gto, scf
from pyscf.nao import gw
class KnowValues(unittest.TestCase):
def test_gw_h2_ae_spin_rf0_spin_downgrade_consistence(self):
""" This is GW """
mol = gto.M( verbose = 1, atom = '''H 0 0 0; H 0.17 0.7 0.587... | gkc1000/pyscf | pyscf/nao/test/test_0063_gw_h2_ae_spin.py | Python | apache-2.0 | 935 | [
"PySCF"
] | 2a7f152d39d86d8786b25b4a99f120ecf38a1f5075002a13fe90be9430f06137 |
##############################################################################
# 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... | skosukhin/spack | var/spack/repos/builtin/packages/hdf/package.py | Python | lgpl-2.1 | 2,814 | [
"NetCDF"
] | b108cc9dd40f245343fb92dacc3e4ef109b79ed602fea881c22570c3d6d37505 |
#!/usr/bin/env python
#PBS -N testNPT
#PBS -m ae
#PBS -q verylong
#PBS -l nodes=1
from Numeric import *
from Scientific.Statistics import *
from Asap import *
from Asap.Dynamics.NPTdynamics import *
from Asap.Dynamics.Langevin import *
from Asap.Trajectories.NetCDFTrajectory import *
from Asap.Setup.Lattice.FCCOrtho ... | auag92/n2dm | Asap-3.8.4/Test/HooverNPTtraj.py | Python | mit | 3,992 | [
"ASE"
] | e4b6cc1466dc0db0b52b92efdd6869bf9b616a5ac775924ef8147a8b294b54ad |
from crystal_dashboard.dashboards.crystal.filters import tabs as filters_tabs
from django.utils.translation import ugettext_lazy as _
from horizon import tabs
class IndexView(tabs.TabbedTableView):
tab_group_class = filters_tabs.FiltersTabs
template_name = 'crystal/filters/index.html'
page_title = _("Filt... | Crystal-SDS/dashboard | crystal_dashboard/dashboards/crystal/filters/views.py | Python | gpl-3.0 | 451 | [
"CRYSTAL"
] | ac4cc54e6f257f6c86c2fbda26be59a20c0b61290c3ccc0f3f98b339b64ac503 |
#!/usr/bin/env python2.7
import logging
import sys
import os
import argparse
import numpy
import pysam
import json
import gzip
def is_unique(region, offset):
"""
Analyze region and return true if it represents a single,
contiguous region.
"""
if len(region) == 0:
return -1
else:
... | AlgoLab/PIntron-scripts | Postprocessing/cutfiller2.py | Python | agpl-3.0 | 14,833 | [
"pysam"
] | 614ecdd8f0d3d050936601c972796c569d0c72bae1abc5ab714bfa68eb493aad |
"""
#;+
#; NAME:
#; galaxy.core
#; Version 1.0
#;
#; PURPOSE:
#; Core routines for galaxy analysis
#; 29-Nov-2014 by JXP
#;-
#;------------------------------------------------------------------------------
"""
from __future__ import print_function, absolute_import, division, unicode_literals
import os, copy,... | profxj/xastropy | xastropy/galaxy/core.py | Python | bsd-3-clause | 1,700 | [
"Galaxy"
] | dc2dc6de06a84b74e33e1de61ac2833efb815c67752b24dd42b5f688b10ee93f |
from docutils import nodes
# Note: set_classes might have something to do with class=".." and css
# http://docutils.sourceforge.net/docs/howto/rst-roles.html
def make_site_linker(baseurl):
def role(role, rawtext, text, lineno, inliner, options={}, content=[]):
if text.endswith('>'):
startindex... | qsnake/gpaw | doc/sitelink.py | Python | gpl-3.0 | 818 | [
"ASE"
] | 16b01b4589643380c5e2b1f5fb68bd97cafc2fc5b54f649f65dfc7f9abe8a4f5 |
#! /usr/bin/env python3.6
# -*- coding: utf-8 -*-
from typing import Tuple, Callable as Function
from functools import wraps
from scipy.integrate import dblquad
from math import pi
import numpy as np
_either = any
def scale(f: Function) -> Function:
""" Decorator to conserve information """
@wraps(f)
d... | bjd2385/dist-fitting | psf.py | Python | mit | 3,226 | [
"Gaussian"
] | 6a2b7a4afca5b8cbd5f294faecbd66d794e833f81a3b7f560ff75bcfce6f6260 |
# 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 required by applica... | gunan/tensorflow | tensorflow/python/autograph/pyct/static_analysis/liveness.py | Python | apache-2.0 | 9,205 | [
"VisIt"
] | ee3de66886eac42c4fcde8925a1ac4128e56229638627db740aff79ccbdee18f |
# Natural Language Toolkit: Clusterers
#
# Copyright (C) 2004-2006 University of Melbourne
# Author: Trevor Cohn <tacohn@cs.mu.oz.au>
# Porting: Steven Bird <sb@csse.unimelb.edu.au>
# URL: <http://nltk.sf.net>
# For license information, see LICENSE.TXT
"""
This module contains a number of basic clustering algorithms. ... | rossgoodwin/musapaedia | musapaedia/en/parser/nltk_lite/cluster/__init__.py | Python | mit | 14,691 | [
"Gaussian"
] | d37aaa73ad2b88a9a0d5f5e89f76b20cfd7e9b79b4727b2ecabb46e46705ff5f |
#!/usr/bin/env python
""" update local cfg
"""
import os
from DIRAC.Core.Base.Script import Script
from DIRAC.ConfigurationSystem.Client.CSAPI import CSAPI
Script.setUsageMessage("\n".join([__doc__.split("\n")[1], "Usage:", " %s [options] " % Script.scriptName]))
Script.parseCommandLine()
args = Script.getPositiona... | DIRACGrid/DIRAC | tests/Jenkins/dirac-cfg-update-dbs.py | Python | gpl-3.0 | 2,857 | [
"DIRAC"
] | 03635032d174e22b0a2027d4f81cf14addf5367649c3a7ced2a60e65adcb12bf |
# -*- coding: utf-8 -*-
"""Tests for imfusion.insertions.aligners.tophat module."""
# pylint: disable=wildcard-import,redefined-builtin,unused-wildcard-import
from __future__ import absolute_import, division, print_function
from builtins import *
# pylint: enable=wildcard-import,redefined-builtin,unused-wildcard-impor... | jrderuiter/im-fusion | tests/imfusion/insertions/aligners/test_tophat.py | Python | mit | 6,740 | [
"Bowtie",
"pysam"
] | 438956dd948c1775d5d208b841c8f876f47149112eb83bba62a31d7c5b4118a0 |
#!/usr/bin/env python
# This file is part of the Printrun suite.
#
# Printrun 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.
#
# Prin... | ase1/421_521_final_project | GUI/toastGUI/printrun/pronsole.py | Python | gpl-2.0 | 68,671 | [
"Firefly"
] | 9dbbede14982db96d6e9ecfa1af196e60ae4de9bb565211fd95867c817a4d084 |
"""ase URL Configuration
The `urlpatterns` list routes URLs to views. For more information please see:
https://docs.djangoproject.com/en/1.11/topics/http/urls/
Examples:
Function views
1. Add an import: from my_app import views
2. Add a URL to urlpatterns: url(r'^$', views.home, name='home')
Class-based ... | alazo/ase | common/urls.py | Python | agpl-3.0 | 2,766 | [
"ASE"
] | 0869c051a8f588abe8f6832874f08ae7d7dc7f2e313dccd106818b12842dd08b |
# Copyright (c) 2012, Cloudscaling
# 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 applicable... | devendermishrajio/nova | nova/hacking/checks.py | Python | apache-2.0 | 21,636 | [
"VisIt"
] | 43d0403b3560f47ea7aeb7b86b5916d566b865aa8f2664ca6d3aa240b35149b8 |
#!/usr/bin/env python3
# Copyright 2018 The GraphicsFuzz Project Authors
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless requir... | google/graphicsfuzz | python/src/main/python/drivers/runspv.py | Python | apache-2.0 | 51,614 | [
"Amber"
] | 0c654461674cb27d5e39f10ad726c9aa88c2bb10adbfb201f739a90113224241 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
import unittest
import warnings
from pymatgen.analysis.structure_prediction.volume_predictor import (
DLSVolumePredictor,
RLSVolumePredictor,
)
from pymatgen.core import Structure
from pymatg... | gmatteo/pymatgen | pymatgen/analysis/structure_prediction/tests/test_volume_predictor.py | Python | mit | 5,293 | [
"pymatgen"
] | 01987c1b3ee3533c2c29f0b707a8c2cee3dac3d0e711994d2a301864feb40a01 |
"""
Sphinx plugins for Django documentation.
"""
import json
import os
import re
from docutils import nodes
from docutils.parsers.rst import Directive, directives
from sphinx import addnodes
from sphinx.builders.html import StandaloneHTMLBuilder
from sphinx.domains.std import Cmdoption
from sphinx.util.console import ... | ghedsouza/django | docs/_ext/djangodocs.py | Python | bsd-3-clause | 10,862 | [
"VisIt"
] | f8e71948a961ff5397fc9fece552c2608402a2ee3d6d14ca97b496b886747650 |
try:
from yt.mods import *
except:
import sys
sys.exit("yt not found or not in PYTHONPATH")
import numpy as np
import matplotlib.pyplot as plt
# List of constants in CGS units
pc = 3.08568025e18 # Parsec in cm
AU = 1.49598e13 # AU in cm
Msun = 1.98892e33 ... | mikhailklassen/flash-tools | flash_generic/toolbox.py | Python | bsd-3-clause | 11,243 | [
"Avogadro"
] | 7814deaf5074de892d2aa031ba1a7a3f585db3f9580bdc9c58008b6247b997f9 |
#!/usr/bin/env python
import sys
lines_gaff = sys.stdin.readlines()
#pair_style = 'lj/charmm/coul/long'
# NOTE: Long-range coulombic forces were disabled intentionally. (See below)
# If you want to use long-range electrostatics, uncomment these lines:
# Instead I use hybrid lj/charmm/coul/charmm b... | anshumang/lammps-analytics | tools/moltemplate/common/amber/amberparm_pair_to_lt.py | Python | gpl-2.0 | 1,036 | [
"CHARMM",
"LAMMPS"
] | 244a0880d3f19bb607293e19e0dfbb81e66f821fa7062288fbdb065bee4cc4b8 |
"""
API for initiating and tracking requests for credit from a provider.
"""
import datetime
import logging
import pytz
import uuid
from django.db import transaction
from lms.djangoapps.django_comment_client.utils import JsonResponse
from openedx.core.djangoapps.credit.exceptions import (
UserIsNotEligible,
... | vikas1885/test1 | openedx/core/djangoapps/credit/api/provider.py | Python | agpl-3.0 | 15,667 | [
"VisIt"
] | b6a985e9409cb3782ccf52cbdfeef38990d513e330dc69cb6143c8a111227eaf |
"""Function-like object creating hexagonal lattices.
The following lattice creators are defined:
* Hexagonal
* HexagonalClosedPacked
* Graphite
* Graphene
Example for using Graphene to create atoms object gra::
from ase.lattice.hexagonal import *
import ase.io as io
from ase import Atoms, Atom
... | grhawk/ASE | tools/ase/lattice/hexagonal.py | Python | gpl-2.0 | 3,971 | [
"ASE",
"CRYSTAL"
] | ffd65e8b590f02770df1531bd0c40081e532c8a694dedddfa769a4888b58934a |
ISO3166 = [
(_("Afghanistan"), "AF", "AFG"),
(_("Aland Islands"), "AX", "ALA"),
(_("Albania"), "AL", "ALB"),
(_("Algeria"), "DZ", "DZA"),
(_("American Samoa"), "AS", "ASM"),
(_("Andorra"), "AD", "AND"),
(_("Angola"), "AO", "AGO"),
(_("Anguilla"), "AI", "AIA"),
(_("Antarctica"), "AQ", "ATA"),
(_("Antigua and B... | openmips/stbgui | lib/python/Tools/CountryCodes.py | Python | gpl-2.0 | 8,534 | [
"BWA"
] | dc82ce822878f88b98ec8104b8ff13d4aa882d462b17232467e80379d1835a3d |
from __future__ import absolute_import
from typing import Any, Dict, List, Set, Tuple, TypeVar, Text, \
Union, Optional, Sequence, AbstractSet, Pattern, AnyStr
from typing.re import Match
from zerver.lib.str_utils import NonBinaryStr
from django.db import models
from django.db.models.query import QuerySet
from dja... | calvinleenyc/zulip | zerver/models.py | Python | apache-2.0 | 56,003 | [
"VisIt"
] | b11220f9798ab800a2e7ebf50864050799987a3a9d76aa62079a6c892e7e18fd |
#!/usr/bin/env python
"""Usage: check_test_times.py seconds inpath [outpath]
Reads test execution result from an output XML file and checks that no test
took longer than given amount of seconds to execute.
Optional `outpath` specifies where to write processed results. If not given,
results are written over the origi... | yahman72/robotframework | doc/api/code_examples/check_test_times.py | Python | apache-2.0 | 1,021 | [
"VisIt"
] | 594079db822fa49a39d7ee61a8c50fef14b7f45fcd8c2cf0820b08367b552c62 |
"""
Views for the verification flow
"""
import datetime
import decimal
import json
import logging
import urllib
from django.conf import settings
from django.contrib.auth.decorators import login_required
from django.contrib.staticfiles.storage import staticfiles_storage
from django.core.mail import send_mail
from djan... | philanthropy-u/edx-platform | lms/djangoapps/verify_student/views.py | Python | agpl-3.0 | 50,647 | [
"VisIt"
] | a00264180a101b5453394e5119ccb770c0d5f7d5b0e7c566112f3781a30db321 |
"""@package api
API views controllers.
@author 7Pros
@copyright
"""
from rest_framework import renderers, status
from rest_framework.authentication import SessionAuthentication, TokenAuthentication
from rest_framework import permissions, throttling, parsers
from rest_framework.views import APIView
from django.contrib... | 7Pros/circuit | api/views.py | Python | gpl-2.0 | 11,767 | [
"VisIt"
] | a8097a6378d55489de316c3f698c49fba645ab1a3373dc3d48bb19ec4bf69518 |
"""Random variable generators.
integers
--------
uniform within range
sequences
---------
pick random element
pick random sample
generate random permutation
distributions on the real line:
------------------------------
uniform
... | MalloyPower/parsing-python | front-end/testsuite-python-lib/Python-3.2/Lib/random.py | Python | mit | 25,303 | [
"Gaussian"
] | b428059e8a6f17f477d8294345184a35d49009d539b6c7fa29161a256e2374c0 |
##############################################################################
# Copyright (c) 2017, Los Alamos National Security, LLC
# Produced at the Los Alamos National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-647188
#
# For details, ... | EmreAtes/spack | var/spack/repos/builtin/packages/candle-benchmarks/package.py | Python | lgpl-2.1 | 2,482 | [
"MDAnalysis"
] | 65c8c4d09b9c3a21558e7bc0922821a695ad6bfa9517c156da3c94b4e5f8c412 |
# -*- coding: utf-8 -*-
#
# voltage_trace.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST 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, ... | alberto-antonietti/nest-simulator | pynest/nest/voltage_trace.py | Python | gpl-2.0 | 7,745 | [
"NEURON"
] | 5c6a75c1cbb7ec9de536e652431a11f579ed40eea6c6bf8c5d39bfd2d7ff646c |
'''
Created on Jul 5, 2015
@author: oleg
'''
from django import http
from let_me_app import models
from django.views.generic.list import ListView
from django.db.models.aggregates import Count, Max, Min, Sum
from let_me_auth.models import User
import itertools
from let_me_app.models import Visit
class CourtListView(L... | oleg-chubin/let_me_play | show_me_app/views.py | Python | apache-2.0 | 8,470 | [
"VisIt"
] | 1fb11fbcc459691db71078503a81e78f5b66f6a1cdad5cdb19f530ce94b2a800 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
from pymatgen.optimization.linear_assignment import LinearAssignment # type: ignore
import numpy as np
class LinearAssignmentTest(unittest.TestCase):
def test(self):
w0 = np.ar... | gVallverdu/pymatgen | pymatgen/optimization/tests/test_linear_assignment.py | Python | mit | 7,546 | [
"pymatgen"
] | 89bbd1adc7ed0cc4027b13c49e28e33fe47410259b401ba876b28147684fbcc7 |
'''TB Animation Tools is a toolset for animators
*******************************************************************************
License and Copyright
Copyright 2015-Tom Bailey
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public Licen... | tb-animator/tbtools | apps/tb_timeline.py | Python | mit | 4,440 | [
"VisIt"
] | 6e81c299c5204de499d541984e531b265ee7c5efed90218f34e7de52527b202f |
#!/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... | LucHermitte/ITK | Utilities/Maintenance/BuildHeaderTest.py | Python | apache-2.0 | 5,244 | [
"VTK"
] | 0e120840b1e96b83b5ea93782b5beccd21725629014f9210166ad295c49c81f9 |
from __future__ import print_function, division #, unicode_literals
import sys
import os
import imp
import platform
import re
# Handle py2, py3k differences.
py2 = sys.version_info[0] <= 2
if py2:
import cPickle as pickle
from cStringIO import StringIO
else:
from io import StringIO
import pickle
from... | SamKChang/abinit-7.10.5_multipole | tests/__init__.py | Python | gpl-3.0 | 30,394 | [
"ABINIT",
"VASP",
"Wannier90"
] | 3763a94ef1b6b4b062d0218597efe25ba9f2df5f9647466e2ae68f2e8d2e9190 |
from common import Modules, load_yara_rules, PEParseModule, ModuleMetadata
from pefile import PE, RESOURCE_TYPE
class Bozok(PEParseModule):
first_value_table = None
precomputed_list = None
def __init__(self):
md = ModuleMetadata(
module_name="bozok",
bot_name="Bozok",
... | bwall/bamfdetect | BAMF_Detect/modules/bozok.py | Python | mit | 3,290 | [
"Brian"
] | 32e904f401f4029baf0b49eb5496cb39d03a5014f28616e8d9a0d7252c3c7773 |
"""Element class."""
from __future__ import division
try:
range = xrange
except NameError:
pass
import math
from .utilities import is_near_zero, float_in_range, float_positive
from .material import Material
try:
str = basestring
except NameError:
pass
class Element(object):
"""Element object de... | chriswmackey/UWG_Python | uwg/element.py | Python | gpl-3.0 | 17,512 | [
"EPW"
] | e57a4beb92f553afb840c9df72b4bb49991bb2aad7e681647647b128f5a3fba7 |
import os as _os
import itertools as _itertools
from xml.etree import ElementTree as _ET
import scipy as _sp
import numpy as _np
import pandas as _pd
import yaml as _yaml
import OpenPNM
from OpenPNM.Utilities import misc as _misc
from OpenPNM.Base import logging
logger = logging.getLogger(__name__)
mgr = OpenPNM.Base.W... | stadelmanma/OpenPNM | OpenPNM/Utilities/IO.py | Python | mit | 53,384 | [
"ParaView",
"VTK"
] | 789a69b78c71a9db09e30f602b25fa8a4153265e2d43950a5317e7edcea76ed0 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""Tests for Bencode file parser."""
import unittest
# pylint: disable=unused-import
from plaso.formatters import bencode_parser as bencode_formatter
from plaso.lib import eventdata
from plaso.lib import timelib
from plaso.parsers import bencode_parser
from tests.parsers imp... | ostree/plaso | tests/parsers/bencode_parser.py | Python | apache-2.0 | 4,695 | [
"Brian"
] | 14762d538bd15002ac2a979c9bd0adabaf54a263cf3d7e716037771c64aa64bd |
# 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... | junghans/espressopp | src/integrator/BerendsenBarostatAnisotropic.py | Python | gpl-3.0 | 4,384 | [
"ESPResSo"
] | a42a5748de0b4e94d26fab4cb02c376a3ba19d101297d5d4bf50efe2e549908b |
"""
Python implementation of the original Bridge Cut algorithm.
Bridging Centrality: Graph Mining
from Element Level to Group Level
@see http://dl.acm.org/citation.cfm?id=1401934
The style guide follows the strict python PEP 8 guidelines.
@see http://www.python.org/dev/peps/pep-0008/
@author Aaron Zampaglione <azam... | azampagl/ai-ml-improved-bridgecut | dbc/src/main.py | Python | mit | 3,356 | [
"Bowtie"
] | 3c2e4a27995c993955c750cb2abbbdffb0a1b5d3f5eff4a58f6e318bbf44e069 |
import numpy
from amuse.units import constants, units
from amuse.support.literature import LiteratureReferencesMixIn
try:
from scipy.special import gammainc,gamma
scipy_imported = True
except:
scipy_imported = False
class NFW_profile(LiteratureReferencesMixIn):
"""
Gravitational potential of the ... | JPGlaser/Tycho | src/tycho/galactic_potentials.py | Python | mit | 9,705 | [
"Galaxy"
] | fd9dc67ba1e0033a29645ee49a66a3231f4add0ffd9286eb043d8ed8cc420c58 |
# Copyright (c) 2011 The Native Client Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
# Documentation on PRESUBMIT.py can be found at:
# http://www.chromium.org/developers/how-tos/depottools/presubmit-scripts
import os
import subproc... | Schibum/naclports | PRESUBMIT.py | Python | bsd-3-clause | 5,119 | [
"VisIt"
] | 7aaefe33a54ee2ee95a2a1471a97b6cd2fc26dff043dde48b78f15a441c8755d |
'''
Retrieve a PDB structure file from the web and parse it with Biopython.
-----------------------------------------------------------
(c) 2013 Allegra Via and Kristian Rother
Licensed under the conditions of the Python License
This code appears in section 21.2.2 of the book
"Managing Biological Data wi... | raymonwu/Managing_Your_Biological_Data_with_Python_3 | 21-pdb_structures/read_pdb_file.py | Python | mit | 780 | [
"Biopython"
] | fe5abad1ebf443891aaad34e4814d4dc903fb6fd5671f4122d8b017b782f5a12 |
# -*- coding: utf-8 -*-
{
'!langcode!': 'nl',
'!langname!': 'Nederlands',
'"update" is an optional expression like "field1=\'newvalue\'". You cannot update or delete the results of a JOIN': '"update" is an optional expression like "field1=\'newvalue\'". You cannot update or delete the results of a JOIN',
'%(nrows)... | twister077/OEECollectorAndOEEWeb | OEEWeb/languages/nl.py | Python | mit | 19,964 | [
"Elk"
] | faae6991ab3b9c606b6e56d12b175dc926cc5dd4ff645ce6ca47d344c6d9e807 |
"""API for Home Connect bound to HASS OAuth."""
from asyncio import run_coroutine_threadsafe
import logging
import homeconnect
from homeconnect.api import HomeConnectError
from homeassistant import config_entries, core
from homeassistant.components.sensor import SensorDeviceClass
from homeassistant.const import (
... | home-assistant/home-assistant | homeassistant/components/home_connect/api.py | Python | apache-2.0 | 18,787 | [
"ESPResSo"
] | 0fc15d32bef5b263e587f0c83634663dfea287a5666f9dcec5b812f43a3c19dc |
# Adapted for numpy/ma/cdms2 by convertcdms.py
"""---------------------------------------------------------------------------------------------
INTRODUCTION TO NGMATH
The ngmath library is a collection of interpolators and approximators for one-dimensional, two-dimensional
and three-dimensional da... | lofar-astron/PyBDSF | bdsf/nat/__init__.py | Python | gpl-3.0 | 88,775 | [
"ADF",
"NetCDF"
] | 9e92d86d847af188eb17ec75112677470824b2347124b3c247bc8a872a6992da |
#
# packages.py: package management - mainly package installation
#
# Copyright (C) 2001, 2002, 2003, 2004, 2005, 2006 Red Hat, Inc.
# All rights reserved.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software... | Rogentos/argent-anaconda | packages.py | Python | gpl-2.0 | 12,768 | [
"VisIt"
] | e111369100d5f2e14785222a5897aa94390ae2b97b921ae912ab047b0dfbda11 |
"""CNA (common neighbor analysis) Filter looking for FCC and HCP structure."""
__docformat__ = "restructuredtext en"
import ASE.ChemicalElements
import ASE.Utilities.Subject
import Numeric
import Asap
class RestrictedCNA(ASE.Utilities.Subject.Subject):
"""CNA (common neighbor analysis) Filter looking for FCC and... | auag92/n2dm | Asap-3.8.4/Python/asap3/Filters/RestrictedCNA.py | Python | mit | 6,836 | [
"ASE",
"CRYSTAL"
] | cb496db0ef3b3acca7fde7fa3bb57532b980f512eb5d5ca0a9c468bc35b07fc0 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This package implements modules for input and output to and from VASP. It
imports the key classes form both vasp_input and vasp_output to allow most
classes to be simply called as pymatgen.io.vasp.Incar fo... | dongsenfo/pymatgen | pymatgen/io/vasp/__init__.py | Python | mit | 416 | [
"VASP",
"pymatgen"
] | a874d4aeabdec42216eae7783458c928914d2fa05692d89089311347db00b284 |
'''
Created on Jan 30, 2011
@author: mkiyer
chimerascan: chimeric transcript discovery using RNA-seq
Copyright (C) 2011 Matthew Iyer
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 ... | genome-vendor/chimerascan | chimerascan/pipeline/nominate_spanning_reads.py | Python | gpl-3.0 | 12,633 | [
"pysam"
] | e455d3aa7bca80108d8c05368bd4e568b7d38229cb67f74c07ef6efcf2134d48 |
#!/usr/bin/env python
import glob
import os
import platform
import unittest
import numpy as np
from setuptools import Extension, setup
try:
import pybind11
except ImportError:
import pip
pip.main(['install', 'pybind11==2.1.1'])
import pybind11
# ======= S E T T I N G S ======= #
femzip_path_windows ... | qd-cae/qd | setup.py | Python | gpl-3.0 | 11,392 | [
"VTK"
] | 53c47c4bb7926cf0c7f17877c7ff5e538c8dcebaa238d1740666fe7055f8a86b |
# ##### BEGIN GPL LICENSE BLOCK #####
#
# 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 distrib... | PLyczkowski/Sticky-Keymap | 2.74/scripts/startup/bl_ui/space_sequencer.py | Python | gpl-2.0 | 39,171 | [
"Gaussian"
] | 12b8235b5c24e6bede5fa338942ceefe7ffa91202de4a9243636cda381ed1d2a |
import numpy
import sys
from mmdlab.datareader import readfile_tex_vic
from mmdlab.utils import make_mlab_scalar_field
from mmdlab.utils import show_scalar_planes
from mmdlab.utils import show_vector_planes
from mmdlab.utils import init_mlab_scene
from mmdlab.utils import showable
from mmdlab.utils import saveimg
fr... | detorto/mdvis | src/vic_viz.py | Python | mit | 1,290 | [
"Mayavi"
] | 72932c5201543732d5fd81c65ce9fa588b98792ec8d4e3a0ef05c95d38f19235 |
########################################################################
# This program is copyright (c) Upinder S. Bhalla, NCBS, 2015.
# It is licenced under the GPL 2.1 or higher.
# There is no warranty of any kind. You are welcome to make copies under
# the provisions of the GPL.
# This programme illustrates buildi... | BhallaLab/benchmarks | Solvers/HSolve/2000ComptModel/bigElec.py | Python | gpl-2.0 | 6,929 | [
"MOOSE",
"NEURON"
] | 6eea49b341225d5136e3c25e6cb9036fd76ad437a8f05b6001a7742f4fbfb991 |
"""
Multilayer Perceptron
"""
__authors__ = "Ian Goodfellow"
__copyright__ = "Copyright 2012-2013, Universite de Montreal"
__credits__ = ["Ian Goodfellow", "David Warde-Farley"]
__license__ = "3-clause BSD"
__maintainer__ = "LISA Lab"
import logging
import math
import operator
import sys
import warnings
import numpy ... | hyqneuron/pylearn2-maxsom | pylearn2/models/mlp.py | Python | bsd-3-clause | 164,858 | [
"Gaussian"
] | 7fed8f31ab8eaa40662e634b83f43af1f3085bbcf58b27e10691c4873c43691f |
import enum
import inspect
import pydoc
import sys
import unittest
import threading
from collections import OrderedDict
from enum import Enum, IntEnum, EnumMeta, Flag, IntFlag, unique, auto
from io import StringIO
from pickle import dumps, loads, PicklingError, HIGHEST_PROTOCOL
from test import support
from datetime im... | batermj/algorithm-challenger | code-analysis/programming_anguage/python/source_codes/Python3.8.0/Python-3.8.0/Lib/test/test_enum.py | Python | apache-2.0 | 108,504 | [
"MOE"
] | 8696e07918464839b14a20645cddcb5bdd4612b0a0901b0b5f4a1d3a30987c16 |
"""
TODO
"""
import numpy
from theano import function, shared
from theano import tensor as TT
import theano
import theano.sandbox.rng_mrg
sharedX = (lambda X, name:
shared(numpy.asarray(X, dtype=theano.config.floatX), name=name))
def kinetic_energy(vel):
"""Returns the kinetic energy associated with... | NoSRPKU/GradD | codes/hmc/hmc.py | Python | mit | 15,144 | [
"Gaussian"
] | accd15f4a918a9f3db5d7f0736be0d7afd9d8ada704e8e27d395ea83ebe2f58f |
import ocl
import camvtk
import time
import vtk
import datetime
import math
if __name__ == "__main__":
print(ocl.revision())
myscreen = camvtk.VTKScreen()
a = ocl.Point(0,1,0.3)
myscreen.addActor(camvtk.Point(center=(a.x,a.y,a.z), color=(1,0,1)))
b = ocl.Point(1,0.5,0.3)
myscreen.addActor... | aewallin/opencamlib | src/attic/waterline_4_weave.py | Python | lgpl-2.1 | 3,652 | [
"VTK"
] | 7041b75c0938d6366e082c24b6d6fd2ea09c066727e8e9ae89195d16ab49a147 |
#!/usr/bin/env python
# Created by: Lee Bergstrand
# Descript: A simple program that takes a RNA nucleotide stockholm file and returns a DNA FASTA file.
#
# Requirements: - This script requires the Biopython module: http://biopython.org/wiki/Download
#
# Usage: getGenbankSeqs.py <sequences.sto>
# Example: getGe... | LeeBergstrand/Phylogenetic-Tree-Building | HMMToFind16S/RNAStockholmToFASTA.py | Python | mit | 2,685 | [
"Biopython"
] | 28e5ef4c41b88c8282919e1f4f4e8d8a5a39900183b014f621155d7a3624037c |
# -*- coding: utf-8 -*-
"""
Generate centreline and write it out as .vtk legacy format.
"""
import os
import sys
# Run in current directory.
os.chdir(os.path.dirname(os.path.abspath(__file__)))
# Import path for the CentrelineGenerator script.
importPath = os.path.abspath(os.path.join(os.path.dirname(__file__), '../... | BlueFern/DBiharMesher | meshes/c4080Murrified/50/Generate4080Centreline.py | Python | gpl-2.0 | 1,055 | [
"VTK"
] | b1db773394768c2f24dbe41190cad081435a96995098f85da866f925f9e2a04a |
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