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"""
Module to set up run time parameters for Clawpack -- classic code.
The values set in the function setrun are then written out to data files
that will be read in by the Fortran code.
"""
import os
import numpy as np
#------------------------------
def setrun(claw_pkg='classic'):
#--------------------------... | ForestClaw/forestclaw | applications/cudaclaw/acoustics/2d/radial/1drad/setrun.py | Python | bsd-2-clause | 7,145 | [
"NetCDF"
] | ff74001451092c9c0b0f86a69ae3b4c4420acc74d5ac459e4c1ae86ee66ded66 |
#!/usr/bin/env python
# MIDAS: Metagenomic Intra-species Diversity Analysis System
# Copyright (C) 2015 Stephen Nayfach
# Freely distributed under the GNU General Public License (GPLv3)
import argparse, sys, os, platform
from midas import utility
def get_program():
""" Get program specified by user (species, genes,... | snayfach/PhyloCNV | scripts/run_midas.py | Python | gpl-3.0 | 35,400 | [
"BLAST"
] | f3eb47780cffd53652f696f9501b257a2f34784fbb13dd01a796423a5ef7a879 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
#
# Copyright (C) 2020 Stoq Tecnologia <http://www.stoq.com.br>
# All rights reserved
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public License
# as published by the Free Software Foundation;... | stoq/stoq-server | stoqserver/lib/duplicitybackup.py | Python | gpl-2.0 | 1,657 | [
"VisIt"
] | c082cbb84dcf41b04393428a1a70b2f4447ba454f132020202ea3aa6f0b3aeb4 |
#!/usr/bin/env python2
#
# Copyright (C) 2013-2018
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, eith... | govarguz/espressopp | testsuite/AdResS/HAdResS/test_HAdResS.py | Python | gpl-3.0 | 12,808 | [
"ESPResSo"
] | 7560bf3caa00402256f4c5db257402dd56779fbc264af01e99ac1772ffc7c0dc |
"""Tests for module utils for timing and parallel computation """
# Author: Remi Flamary <remi.flamary@unice.fr>
#
# License: MIT License
import ot
import numpy as np
import sys
def test_parmap():
n = 100
def f(i):
return 1.0 * i * i
a = np.arange(n)
l1 = list(map(f, a))
l2 = list(... | aje/POT | test/test_utils.py | Python | mit | 3,832 | [
"Gaussian"
] | f51e8c61f0c8a312491ca6dcbe96ab4d3f5db42cb77c9993813ab22f0eab5305 |
from degas.analysis_setup import calc_LTIR
from astropy.table import Table, Column
from astropy.io import fits
import numpy as np
import os
import glob
multiDir = os.path.join(os.environ['ANALYSISDIR'],'ancillary_data','multiwavelength')
TIRDir = os.path.join(multiDir,'data','TIR','convolved15arc')
z0mgsDir = os.path.... | low-sky/degas | scripts/calc_LIR.py | Python | gpl-3.0 | 4,989 | [
"Galaxy"
] | d190131fdc3128beabe38ac072357ef463b26d32af8515e83a09de09017da883 |
import pytest
import qcelemental as qcel
import psi4
from .utils import compare_values
perturbation_strength = 0.001
@pytest.mark.slow
# TODO: That "true" needs to be a string is silly. Convert it to a boolean when you can do that without incurring a NaN energy.
@pytest.mark.parametrize("inp", [
pytest.param({'... | jgonthier/psi4 | tests/pytests/test_dipoles.py | Python | lgpl-3.0 | 2,311 | [
"Psi4"
] | 7de73dff121c3856271044d7f4460ed70b22c64a9b61ab94913f10c712d3c7fd |
# Generate UV-Vis spectra from electronic structure TDHF/TDDFT output files.
# Copyright (C) 2014 Li Research Group (University of Washington)
#
# 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... | liresearchgroup/uvspecgen | uvspec/logfile.py | Python | gpl-3.0 | 3,403 | [
"ADF",
"GAMESS",
"Jaguar",
"cclib"
] | d926976a5554e10398f280c70e5985f5cc3a30d6f0ab4902cebab59e25ef0294 |
import unittest
from shyft import api
from shyft.repository.netcdf.time_conversion import convert_netcdf_time
from netcdftime import utime
import numpy as np
class NetCdfTimeTestCase(unittest.TestCase):
def test_extract_conversion_factors_from_string(self):
u = utime('hours since 1970-01-01 00:00:00')
... | felixmatt/shyft | shyft/tests/test_netcdftime.py | Python | lgpl-3.0 | 1,214 | [
"NetCDF"
] | c1b0a1897a4a5562fc310c6329ad20e41ff874d444091bc6a8ceb13432ac9edf |
#!/usr/bin/env python2.7
from __future__ import print_function
import pdb
import atexit
#atexit.register(pdb.set_trace)
import SocketServer
import argparse
import array
import collections
import json
import socket
import struct
import threading
import time
import usb.core
import lcm
from Forseti import Flags
from For... | pioneers/forseti | GoalReader.py | Python | apache-2.0 | 18,977 | [
"Octopus"
] | 335a6f59d4fcd1ba97d0bea923ec1f5b478e4f440e141e36642b8ff64cc375c3 |
# vim: ft=python fileencoding=utf-8 sts=4 sw=4 et:
# Copyright 2014-2017 Florian Bruhin (The Compiler) <mail@qutebrowser.org>
#
# This file is part of qutebrowser.
#
# qutebrowser 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 S... | NoctuaNivalis/qutebrowser | scripts/dev/pylint_checkers/qute_pylint/config.py | Python | gpl-3.0 | 2,838 | [
"VisIt"
] | f28801ad5bc7634f22ad422e99d36ebc7d4b9bbd6cc99c617b41ab4176d6eee3 |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
"""
Process Hi-C output into AGP for chromosomal-scale scaffolding.
"""
import array
import json
import logging
import math
import os
import os.path as op
import sys
from collections import defaultdict
from functools import partial
from multiprocessing import Pool
import ... | tanghaibao/jcvi | jcvi/assembly/hic.py | Python | bsd-2-clause | 57,613 | [
"BLAST",
"pysam"
] | 406c7189f7b97817e9e7aeba42e88744cb6dc7a793ff199f370229e524187958 |
# -*- coding: utf-8 -*-
"""Converts .pyfr[m, s] files to a Paraview VTK UnstructuredGrid File"""
from collections import defaultdict
import os
import numpy as np
from pyfr.shapes import BaseShape
from pyfr.util import subclass_where
from pyfr.writers import BaseWriter
class ParaviewWriter(BaseWriter):
# Suppo... | tjcorona/PyFR | pyfr/writers/paraview.py | Python | bsd-3-clause | 14,232 | [
"ParaView",
"VTK"
] | aa5344e82ba8bcaf3aae593e666dc761ddd16952fefe728f0047001d645fdd95 |
from __future__ import division
from iotbx.pdb.multimer_reconstruction import multimer
from iotbx.ncs.ncs_preprocess import ncs_only
import mmtbx.monomer_library.server
import iotbx.reflection_file_utils
from libtbx.utils import null_out
from iotbx.pdb import fetch
from libtbx import easy_run
import cPickle as pickle
... | youdar/work | work/NCS/ncs_paper/collect_ncs_files.py | Python | mit | 35,737 | [
"CRYSTAL"
] | 5822840d6a0e60d1460ed5ba25b024db4bc26747013ae037674f7150de9c4a80 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | BackupTheBerlios/espressopp | src/bc/__init__.py | Python | gpl-3.0 | 1,005 | [
"ESPResSo"
] | 9fd06557c89838763cc0b6b88bf445201e7b378aa6b2381d95288cde9a452301 |
import PyOpenWorm as P
from PyOpenWorm import *
__all__ = ['Connection']
class SynapseType:
Chemical = "send"
GapJunction = "gapJunction"
class Connection(Relationship):
"""Connection between neurons
Parameters
----------
pre_cell : string or Neuron, optional
The pre-synaptic cell
... | hnunner/PyOpenWorm | PyOpenWorm/connection.py | Python | mit | 3,348 | [
"NEURON"
] | c240505f9ba31fc2a65b5047b2f153d558b2b36b5abc21adcb59a7b2a32be93b |
"""
Represents a diffraction setup.
Except for energy all units are in SI.
"""
from collections import OrderedDict
from copy import deepcopy
import xraylib
import numpy
from crystalpy.util.Vector import Vector
class DiffractionSetup(object):
def __init__(self, geometry_type, crystal_name, thickness,
... | edocappelli/crystalpy | crystalpy/diffraction/DiffractionSetup.py | Python | mit | 13,055 | [
"CRYSTAL"
] | c7e994a4055f4a7cc33da175939b67c1533a9404a39ac9e3c15215f2f8792f9d |
import sys
tests=[
("python", "testReactionWrapper.py",{}),
("python", "testEnumerations.py",{}),
]
longTests=[
]
if __name__=='__main__':
import sys
from rdkit import TestRunner
failed,tests = TestRunner.RunScript('test_list.py',0,1)
sys.exit(len(failed))
| rvianello/rdkit | Code/GraphMol/ChemReactions/Wrap/test_list.py | Python | bsd-3-clause | 276 | [
"RDKit"
] | 44df6b38909d04f68e1b8158a229f76416376e2bddcf476f641016fed37c9ad8 |
import numpy as np
from mmap import mmap
import os
def dict_nparr_to_list(some_dict):
for key,val in some_dict.iteritems():
if isinstance(val,dict):
dict_nparr_to_list(val)
elif isinstance(val,np.ndarray):
some_dict[key] = val.tolist()
# end if
# end for
# end de... | Paul-St-Young/QMC | nexus_addon.py | Python | mit | 16,482 | [
"QMCPACK",
"Quantum ESPRESSO"
] | 5055de2a05e4ec072bb86d54c854434dd4fd0bf96ee80c0244d5f221bfd410a3 |
# -*- coding: UTF-8 -*-
# From GitHub
__all__ = ['EMO_UNICODE', 'UNICODE_EMO', 'EMOTICONS', 'EMOTICONS_EMO', 'chat_words_str']
EMOTICONS = {
u":‑\)":"Happy face or smiley",
u":\)":"Happy face or smiley",
u":-\]":"Happy face or smiley",
u":\]":"Happy face or smiley",
u":-3":"Happy face smiley",
... | AdityaSoni19031997/Machine-Learning | kaggle/simple_sentiment_baseline/emojis.py | Python | mit | 161,146 | [
"FLEUR",
"Octopus"
] | 54a63756f9045787a4e20bb094361c902968df2e7360709f98f8844d8732b894 |
"""Logging for molecular dynamics."""
import weakref
import sys
import ase.units as units
# ase.parallel imported in __init__
class MDLogger:
"""Class for logging molecular dynamics simulations.
Parameters:
dyn: The dynamics. Only a weak reference is kept.
atoms: The atoms.
l... | grhawk/ASE | tools/ase/md/logger.py | Python | gpl-2.0 | 3,264 | [
"ASE"
] | e5c873ec4eab3933f257ed731e92b014690f0034f10df7604f24c17057d01eec |
# -*- coding: utf-8 -*-
#
# twoneurons.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, or
... | weidel-p/nest-simulator | pynest/examples/twoneurons.py | Python | gpl-2.0 | 1,260 | [
"NEURON"
] | 6caca9c5c9c2a489db032b9717030bbd6df83f7dc74262df3865946fd69d1842 |
##############################################################################
# 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/ncview/package.py | Python | lgpl-2.1 | 1,852 | [
"NetCDF"
] | 5c71754f7ff6ac3364af557f553bb2812198d52ed134b12f1950601518b440ed |
""" PlottingClient is a client of the Plotting Service
"""
import tempfile
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Tornado.Client.ClientSelector import TransferClientSelector as TransferClient
from DIRAC.Core.Base.Client import Client
class PlottingClient(object):
def __init__(self, rpcClient=None, transf... | DIRACGrid/DIRAC | src/DIRAC/FrameworkSystem/Client/PlottingClient.py | Python | gpl-3.0 | 4,195 | [
"DIRAC"
] | b9763492ee1531b34ab0c0449a6802e5cf08f9d53796783563cdb5a597c0baaa |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-wms-job-kil
# Author : Stuart Paterson
########################################################################
"""
Issue a kill signal to a running DIRAC job
"""
__RCSID__ = "$Id$"
import DIR... | Sbalbp/DIRAC | Interfaces/scripts/dirac-wms-job-kill.py | Python | gpl-3.0 | 1,186 | [
"DIRAC"
] | f4c6bfaffb66fd8933b22f7f0f4b46432fbe020f668b19ec3df0576d5bbf2ff8 |
"""Compare ECFP4 and E3FP runtimes.
Author: Seth Axen
E-mail: seth.axen@gmail.com
"""
import time
import sys
import os
from rdkit import Chem
from rdkit.Chem import AllChem
from python_utilities.parallel import Parallelizer
from e3fp.conformer.util import smiles_to_dict, mol_from_sdf
from e3fp.pipeline import params_... | keiserlab/e3fp-paper | project/benchmark/run_benchmark.py | Python | lgpl-3.0 | 2,169 | [
"RDKit"
] | 4fde7b70bae941be0c9c97cd4fea00b2ead18f319fe38c883aabe723c7bb6d8e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
import time
import numpy as np
real_str = r'[+-]?(?:\d+\.\d*|\d*\.\d+)(?:[Ee][+-]?\d+)?' # Regex for floats
# =======================================================================
# MESH LOADERS
# =============================================================... | LHEEA/meshmagick | meshmagick/mmio.py | Python | gpl-3.0 | 49,282 | [
"ParaView",
"VTK",
"VisIt"
] | 8f1f06b5f66106cce911908eb4e876a9d47cf4e2720499fcc7865b990df806fe |
"""
Unit tests for the vector renderer
"""
from __future__ import absolute_import
from __future__ import unicode_literals
import unittest
import numpy as np
import vtk
from vtk.util import numpy_support
from .. import vectorRenderer
from ... import utils
from six.moves import range
###############################... | chrisdjscott/Atoman | atoman/rendering/renderers/tests/test_vectorRenderer.py | Python | mit | 3,182 | [
"VTK"
] | c58dea34d74ef2ae441b6984d7119a60b3f83f7bac36f16a80b6b2a034b4e81b |
# _external_paths in AlGDock directory
import os, inspect
dir_external_paths = os.path.dirname(os.path.abspath(\
inspect.getfile(inspect.currentframe())))
### Google drive downloader from
# http://stackoverflow.com/questions/25010369/wget-curl-large-file-from-google-drive
try:
import requests # for downloading ad... | CCBatIIT/AlGDock | AlGDock/path_tools.py | Python | mit | 7,676 | [
"Amber",
"NAMD",
"NetCDF",
"VMD"
] | e080d9b6faaf9420e15e7e569ba87e943a583c448075717453a39d102212546f |
from labutil.plugins.lammps import lammps_run, get_lammps_energy
from labutil.objects import Struc, Dir, ClassicalPotential, ase2struc
from ase.spacegroup import crystal
from ase.build import make_supercell
import numpy, os
import matplotlib.pyplot as plt
input_template = """
# ---------- 1. Initialize simulation ---... | bkoz37/labutil | samples/lab1_samples/Al_lat_eam.py | Python | mit | 2,409 | [
"ASE",
"CRYSTAL",
"LAMMPS"
] | d92a13ba186cafdf6457c35891fff3cde45f73f6eb9226760e9822f48978e0b2 |
"""
============================================================================
Comparing anomaly detection algorithms for outlier detection on toy datasets
============================================================================
This example shows characteristics of different anomaly detection algorithms
on 2D d... | vortex-ape/scikit-learn | examples/plot_anomaly_comparison.py | Python | bsd-3-clause | 6,348 | [
"Gaussian"
] | a7a2f0dc6503b93255111ee9432d3127cdaf7bd4daf62b32b4f3c443d0bae92a |
#!/usr/bin/env python
import sys
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Prevent .pyc files being created.
# Stops the vtk source being polluted
# by .pyc files.
sys.dont_write_bytecode = True
import backdrop
# Contour every qu... | timkrentz/SunTracker | IMU/VTK-6.2.0/Common/DataModel/Testing/Python/LineIntersectQuadraticCells.py | Python | mit | 16,947 | [
"VTK"
] | f40cb9f272a96ea3dca3dd8647980dc9b23646fb7244d7f0061ee5952942e05a |
from string import Template
from outsourcer import CodeBuilder, Code, Val
from . import expressions as ex
from .expressions import (
TEXT, POS, Choice, Class, Ref, Right, Rule, Skip, visit
)
def generate_source_code(docstring, nodes):
out = CodeBuilder()
out.add_docstring(docstring)
out += Code(_pro... | jvs/sourcer | sourcer/translator.py | Python | mit | 15,827 | [
"VisIt"
] | 7e50c8c420f308bed26469ce9f95d2bd9bf84e55c50a5e46727c5213849bc2f9 |
"""
cclib (http://cclib.sf.net) is (c) 2006, the cclib development team
and licensed under the LGPL (http://www.gnu.org/copyleft/lgpl.html).
gmagoon 4/5/10-4/6/10 (this notice added 4/29/10): Gregory Magoon modified this file from cclib 1.0
"""
__revision__ = "$Revision: 863 $"
# These import statements are a... | faribas/RMG-Java | source/cclib/parser/__init__.py | Python | mit | 905 | [
"ADF",
"GAMESS",
"Gaussian",
"Jaguar",
"MOPAC",
"Molpro",
"ORCA",
"cclib"
] | 7045ce6bf3b37f36b46154240df7588765536973c281cb3b2cbf5db6e8e1c967 |
# coding: utf8
{
' Quotas: %(quotas)s x%(quota_amount).2f': ' Quotas: %(quotas)s x%(quota_amount).2f',
' Transaction number: %s': ' Transaction number: %s',
'"update" is an optional expression like "field1=\'newvalue\'". You cannot update or delete the results of a JOIN': '"更新" 是選擇性的條件式, 格式就像 "欄位1=\'值\'". 但是 JOIN 的資料不可... | reingart/gestionlibre | languages/zh-tw.py | Python | agpl-3.0 | 19,642 | [
"VisIt"
] | ad4867ad9f5cc6780c68634840fc34ad4bf282d92f25d39b1811ae135c607a46 |
#!/usr/bin/env python
import sys
if sys.version_info < (2, 7, 0):
print('error: python version >= 2.7 required')
sys.exit(27)
import argparse, csv
epilog = "Please read the ncDataReader2 manual for additional information."
arg = argparse.ArgumentParser(description='Generate a ncDataReader2-compatible netCDF ... | modelica-3rdparty/netCDF-DataReader | NcDataReader2/Resources/tools/ncdr2Import.py | Python | lgpl-2.1 | 4,148 | [
"NetCDF"
] | 43128d31157e2bf84a662e3338703bf28ce1386c3d5816bc1ae93c6f536490d4 |
"""\
PyQuante2 contains a more structured interface to all of the functions
in PyQuante.
solver = SCF(molecule,**options)
Create a solver that can perform a HF calculation on *molecule*.
General options
Option Value Description
-------- ----- -----------
method HF Use the HF method for t... | gabrielelanaro/pyquante | PyQuante/PyQuante2.py | Python | bsd-3-clause | 31,825 | [
"Gaussian"
] | 5f252a6e23f9ce0f7efc834db9ddf666d20a8b78d5f8c463c301757a88c5dff3 |
# This file is adapted from https://github.com/ray-project/ray/blob
# /master/examples/parameter_server/async_parameter_server.py
#
# 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 ... | intel-analytics/BigDL | python/orca/example/ray_on_spark/parameter_server/async_parameter_server.py | Python | apache-2.0 | 6,622 | [
"ORCA"
] | 539407df95855f6cb58577ce6be0d336b5f266806123845a06b3aaab2754fd54 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
__author__ = "Jifu Zhao"
__email__ = "jzhao59@illinois.edu"
__date__ = "04/07/2017"
__modify__ = "05/15/2017"
"""
# -------------------------------------------------------------------------
# Currently there are two problems
# 1. for semivariogram, when... | JifuZhao/Poisson-Kriging | old/05272017/kriging.py | Python | mit | 15,382 | [
"Gaussian"
] | 28d43efceddb9d8d0eec83aa98da1556d5f9e2d02b012edcb969476164f6ab40 |
"""
this pipeline annotation variant calling results in vcf file and then
use provean to predict the effect
"""
import sys,subprocess,os
sys.path.append('/home/shangzhong/Codes/Projects')
sys.stdout = os.fdopen(sys.stdout.fileno(), 'w', 0) # disable buffer
from Modules.f11_snpEff_provean import *
from Modules.p01_File... | shl198/Pipeline | VariantCall/05_snpEff_Provean_Vari_annotation.py | Python | mit | 8,356 | [
"BLAST"
] | 2a21af45c40b73ff2c4073b443632011f8ab7c5ca991b7d9d5f0165cd5c1b1a5 |
# $HeadURL$
"""
DIRAC - Distributed Infrastructure with Remote Agent Control
The LHCb distributed data production and analysis system.
DIRAC is a software framework for distributed computing which
allows to integrate various computing resources in a single
system. At the same time it integrates all kin... | avedaee/DIRAC | __init__.py | Python | gpl-3.0 | 4,985 | [
"DIRAC"
] | dbf9588755ba421b76f2d2cea4f3ef8034573a8d2f9e6458305994b159275bba |
# -*- coding: utf-8 -*-
#
# PyZMQ documentation build configuration file, created by
# sphinx-quickstart on Sat Feb 20 23:31:19 2010.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All c... | IsCoolEntertainment/debpkg_python-pyzmq | docs/source/conf.py | Python | lgpl-3.0 | 7,275 | [
"Brian"
] | 805e34d3035861a3f62383fa525992f6b56d1880ab27a976b76de7ec3eb2e183 |
# coding: utf-8
from __future__ import unicode_literals
"""
This module provides various representations of transformed structures. A
TransformedStructure is a structure that has been modified by undergoing a
series of transformations.
"""
__author__ = "Shyue Ping Ong, Will Richards"
__copyright__ = "Copyright 2012... | Dioptas/pymatgen | pymatgen/alchemy/materials.py | Python | mit | 14,370 | [
"VASP",
"pymatgen"
] | d1a8841e23af2990e6c5e0dc24c1cfd59b0cc6e7a0c4c5f02b69b4d83373f073 |
########################################################################
# This example demonstrates random (Poisson) synaptic input to a cell.
# Copyright (C) Upinder S. Bhalla NCBS 2018
# Released under the terms of the GNU Public License V3. No warranty.
##############################################################... | BhallaLab/moose-examples | tutorials/Rdesigneur/ex5.0_random_syn_input.py | Python | gpl-2.0 | 806 | [
"MOOSE"
] | 26af24e667451fcdd07374086772a7581289e8d768a403422dad4cdc4dc6f9b8 |
"""
Script to generate the standardised primitive cell structure
Some notes:
- The "standard" is based on: https://doi.org/10.1016/j.commatsci.2016.10.015
- Pymatgen is used for loading files and calculating the symmetry info
- Seekpath is used to generate the standard primitive cell as the pymatgen
"standar... | utf/materials-toolbox | matools/prim.py | Python | mit | 2,452 | [
"VASP",
"pymatgen"
] | 73a421740c0e21c53cfe27484ee2b8a13e2e16fc9bd6c413dcecd5f88071f4f5 |
##
# Copyright 2009-2020 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 (F... | pescobar/easybuild-easyblocks | easybuild/easyblocks/w/wrf_fire.py | Python | gpl-2.0 | 10,206 | [
"NetCDF"
] | 32cbb6508e6f84f6c46d3e996b81a69865bd017012e8039e8401e24a8aa44b81 |
from __future__ import print_function
__author__ = """Alex "O." Holcombe, Charles Ludowici, """ ## double-quotes will be silently removed, single quotes will be left, eg, O'Connor
import time, sys, platform, os
from math import atan, atan2, pi, cos, sin, sqrt, ceil, radians, degrees
import numpy as np
import psychopy, ... | alexholcombe/dot-jump | dataRaw/Fixed Cue/test_dot-jump21Nov2016_13-55.py | Python | gpl-3.0 | 26,149 | [
"Gaussian"
] | b71bc40ed5e8263febc9a78d68de6f8d234d823993f5cef791db4de90aaa9f29 |
from coalib.bearlib.abstractions.Linter import linter
from dependency_management.requirements.DistributionRequirement import (
DistributionRequirement)
@linter(executable='verilator',
output_format='regex',
use_stderr=True,
output_regex=r'\%(?:(?P<severity>Error|Warning.*?).*?):'
... | IPMITMO/statan | coala-bears/bears/verilog/VerilogLintBear.py | Python | mit | 1,660 | [
"VisIt"
] | a7557f43fa4ff197814e167dc30721a2d21341adf47fd5c0aaf67e62a37517cc |
# Converting Olivier's fundi into VTK format.
# Two inputs: tex-format fundi, VTK file of original mesh
# Output: one VTK file where fundi is labeled as non -1
# Gifti to tex conversion done by using AimsFileConvert in BrainVISA
# for i in *; do AimsFileConvert -i $i/$i\_Lwhite_sulcalines.gii -o $i/L.tex -e 1 ; done... | binarybottle/mindboggle_sidelined | code_fundi_evaluation/tex2vtk.py | Python | apache-2.0 | 2,977 | [
"VTK"
] | c801f20a4d48330b50958c5e6ab2f3294e1327b3aa785737ba9851a1cada9652 |
# -*- coding: utf-8 -*-
"""
pbm_ImageAnalysis is an analysis module for ACQ4.
This module provides:
1. Bleaching correction of image stacks
2. Normalization of image stacks
3. ROI's on Z-stacks (or T-stacks), including saving and retrieving the ROI files
(the format is the same as in PyImageAnalysis... | hiuwo/acq4 | acq4/analysis/modules/pbm_ImageAnalysis/pbm_ImageAnalysis.py | Python | mit | 135,736 | [
"Gaussian"
] | ad631ca2c2889d006f363c50902c9a818cc25dd886adb9f49e490672b67988d0 |
"""Rewrite assertion AST to produce nice error messages"""
import ast
import errno
import functools
import importlib.abc
import importlib.machinery
import importlib.util
import io
import itertools
import marshal
import os
import struct
import sys
import tokenize
import types
from typing import Callable
from typing impo... | JoelMarcey/buck | third-party/py/pytest/src/_pytest/assertion/rewrite.py | Python | apache-2.0 | 42,695 | [
"VisIt"
] | 96053594d76694b6a028455b9862d60d7886aebefd8651749de8ae341d66a3b2 |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, 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','license','co... | ClinicalSoftwareSolutions/UDID | build.py | Python | gpl-2.0 | 5,947 | [
"VisIt"
] | 5ed5f35aa8ebcddcf772f924ab83f1b53458306656d8a20f77d599ca60002de1 |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-videointelligence | tests/unit/gapic/videointelligence_v1p3beta1/test_streaming_video_intelligence_service.py | Python | apache-2.0 | 53,368 | [
"Octopus"
] | 20b70bf338b9e50ccbaa32db8e955b38dfa663136adc0c8a449ed9762d843ef3 |
# Natural Language Toolkit: Feature Structures
#
# Copyright (C) 2001-2007 University of Pennsylvania
# Author: Edward Loper <edloper@gradient.cis.upenn.edu>,
# Rob Speer,
# Steven Bird <sb@csse.unimelb.edu.au>
# URL: <http://nltk.sourceforge.net>
# For license information, see LICENSE.TXT
#
# $Id$
"""... | LowResourceLanguages/hltdi-l3 | disambiguatr/l3/morpho/featstruct.py | Python | gpl-3.0 | 102,263 | [
"VisIt"
] | c294652dc78f41154c766b2f74f10c0d9b431752e3c47e98e4e75f43130aadbd |
# -*- coding: utf-8 -*-
# (c) University of Strathclyde 2020
# Author: Leighton Pritchard
#
# Contact:
# leighton.pritchard@strath.ac.uk
#
# Leighton Pritchard,
# Strathclyde Institute for Pharmacy and Biomedical Sciences,
# Cathedral Street,
# Glasgow,
# G1 1XQ
# Scotland,
# UK
#
# The MIT License
#
# Copyright (c) 20... | widdowquinn/pyani | pyani/dependencies.py | Python | mit | 3,603 | [
"BLAST",
"Biopython"
] | 1dcfa35bc5d32854dac3c0fcfa6610d6eb8611a27fd3b120d6cd851c30f849e5 |
# lintory - keep track of computers and licenses
# Copyright (C) 2008-2009 Brian May
#
# 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 ... | VPAC/lintory | lintory/fields.py | Python | gpl-3.0 | 7,577 | [
"Brian"
] | 0629540de4cd5a0bde3c258501b131838d1e30120086632839c529d0c29ce00c |
# Docstrings for generated ufuncs
#
# The syntax is designed to look like the function add_newdoc is being
# called from numpy.lib, but in this file add_newdoc puts the
# docstrings in a dictionary. This dictionary is used in
# _generate_pyx.py to generate the docstrings for the ufuncs in
# scipy.special at the C level... | gertingold/scipy | scipy/special/add_newdocs.py | Python | bsd-3-clause | 197,889 | [
"Gaussian"
] | 30edd007b9cd2225e17ac17679f79a05534f54f48bb0e24a155d0ed22a882d7e |
"""
Module containing functions and classes to produce posterior predictive
distribution.
"""
from math import pi
# import warnings
import numpy as np
class Predictor(object):
"""
Global class implementing predictors.
Predictors using different distribution functions should be subclassed
from this on... | exord/pyboas | pyboas/predictor.py | Python | mit | 9,569 | [
"Gaussian"
] | 2142bdeb4c1829a631e808758605d2692debd4041e2b6b67c4bc55b3149363da |
from kivy.app import App
from time import time
from kivy.uix.button import Button
from kivy.uix.scrollview import ScrollView
from kivy.uix.boxlayout import BoxLayout
from kivy.uix.behaviors import ButtonBehavior
from kivy.uix.label import Label
from random import randrange
from kivy.metrics import cm
from kivy.lang imp... | Bakterija/log_fruit | src/app_modules/widgets/databox/recycle_databox_example.py | Python | unlicense | 6,119 | [
"VisIt"
] | 2259d6f440ac8de8401b44059e0e6f28ec99255a026e514a8399260ff0afb5ad |
import numpy as np
from mayavi import mlab
from mesh import vismesh
from ..geodesic import GeodesicDistanceComputation
from ..util import veclen
def compute_fake_weights(verts, tris, ci, expo=7):
geo = GeodesicDistanceComputation(verts, tris)
H = np.column_stack([geo(i) for i in ci])
H = H.max(axis=0) - ... | tneumann/cmm | cmmlib/vis/correspondence.py | Python | gpl-2.0 | 3,443 | [
"Mayavi"
] | 169645dcfb299249b344be8d088051ef41808f442929ef12a76000fbddc09474 |
# -*- coding: utf-8 -*-
#
# This file is part of Invenio.
# Copyright (C) 2011, 2012, 2015 CERN.
#
# Invenio 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 optio... | CERNDocumentServer/invenio | modules/bibauthorid/lib/bibauthorid_webinterface.py | Python | gpl-2.0 | 148,885 | [
"VisIt"
] | 62abeebeb61090676276f317e063ee524950834b9cc1e2ea6075697e71679ac9 |
import numpy as np
import vtk
from math import pi,cos,sin
def threedtorusvtk(eps):
"""
Output a vtk torus mesh given eps.
Just a demonstration at the moment.
"""
R = 1.
Z = 0.
npoints = 21
## create the points in XYZPoints
xyz=np.array([1.,1.,1.],dtype=float)
XYZPoints=vtk.vtkPoints()
XYZPoints... | tectronics/gkw | python/gkw/vtk/vtktorus.py | Python | gpl-3.0 | 1,553 | [
"VTK"
] | 86541700176378ad50bdac61fac32d32ae8a60f18f28dd3f28caacb434c7aab6 |
import wx
import os
import os.path
import platform
import sys
from wx.lib.embeddedimage import PyEmbeddedImage
sys.path.append("/home/balto/VirtualBox VMs/shared/InteractiveROSETTA/dist/InteractiveROSETTA/eggs")
import poster
#from poster.encode import multipart_encode
#from poster.streaminghttp import register_openers... | schenc3/InteractiveROSETTA | InteractiveROSETTA/scripts/tools.py | Python | gpl-2.0 | 129,028 | [
"Biopython",
"PyMOL"
] | d1d63b08508f8d8e2876aab4d0fc45590834c64aa6cd026909610eb4228cddfe |
#!/usr/bin/env python3
import numpy as np
from pysisyphus.calculators.ORCA import ORCA
from pysisyphus.helpers import geom_from_xyz_file, do_final_hessian
def test_do_final_hessian(data_dir):
fn = data_dir / "final_geometry.xyz"
geom = geom_from_xyz_file(fn, coord_type="redund")
calc = ORCA("")
gra... | eljost/pysisyphus | tests_staging/test_do_hess/test_do_hess.py | Python | gpl-3.0 | 631 | [
"ORCA"
] | 33545683bbfa1d857910b07d1025efa4ebd96375841e2b3c589c856872d2b0fa |
import unittest
import os
import filecmp
import pysam
from iva import graph, assembly, edge
from pyfastaq import intervals
modules_dir = os.path.dirname(os.path.abspath(graph.__file__))
data_dir = os.path.join(modules_dir, 'tests', 'data')
class TestGraph(unittest.TestCase):
def setUp(self):
self.asm = a... | satta/iva | iva/tests/graph_test.py | Python | gpl-3.0 | 11,141 | [
"pysam"
] | 24171e2d726135edc86cdc52df6a437164713877222f691247d4d74fee5e19dc |
""" :mod: RegisterReplica
==================
.. module: RegisterReplica
:synopsis: register replica handler
RegisterReplica operation handler
"""
from DIRAC import S_OK, S_ERROR
from DIRAC.FrameworkSystem.Client.MonitoringClient import gMonitor
from DIRAC.DataManagementSystem.Agent.RequestOperations... | DIRACGrid/DIRAC | src/DIRAC/DataManagementSystem/Agent/RequestOperations/RegisterReplica.py | Python | gpl-3.0 | 7,792 | [
"DIRAC"
] | f2e8223fe736d04fc349079ae1c18766118753d406c829958cab8bac359fd42f |
#!/usr/bin/env python
"""Fetch GenBank entries for given accessions.
Adapted from https://www.biostars.org/p/66921/
DEPENDENCIES:
Biopython
"""
import argparse
import sys
import textwrap
from Bio import Entrez
def main():
parser = argparse.ArgumentParser(
usage='cat INPUT | python acc2gb.py EMAIL DB ... | mbonsma/phageParser | parserscripts/acc2gb.py | Python | mit | 2,546 | [
"BLAST",
"Biopython"
] | ae601546bc4e3f1158d846adf4a9d80162ded0669145885c836ec174a951489c |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, print_function, unicode_literals
from django.conf import settings
DEFAULT_THEMES = (
('a11y-dark', 'A 11 Y Dark'),
('a11y-light', 'A 11 Y Light'),
('agate', 'Agate'),
('androidstudio', 'An Old Hope'),
('an-old-hope', 'Androidstudio'),... | nephila/djangocms-highlightjs | djangocms_highlightjs/settings.py | Python | bsd-3-clause | 7,428 | [
"CRYSTAL"
] | f1d4bec35198a236b8d4eb1591c8855b09c47e2e8cd91dc790ca631a5ae24a6e |
import dataclasses
import functools
from multiprocessing import Pool
import numpy
import scipy.optimize
from logging import getLogger, DEBUG
_log = getLogger(__name__)
__all__ = ["blob_detection", "spot_detection"]
def blob_detection(data, min_sigma=1, max_sigma=50, num_sigma=10, threshold=0.2, overlap=0.5):
"... | ecell/bioimaging | scopyon/analysis/spot_detection.py | Python | bsd-3-clause | 6,271 | [
"Gaussian"
] | 6229eae822f6a4d898987021c1d2d4ce70ea55b304c08e375e8c3aa14ab9dabe |
# Copyright (C) 2004, Thomas Hamelryck (thamelry@binf.ku.dk)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Vector class, including rotation-related functions."""
from __future__ import print_fu... | zjuchenyuan/BioWeb | Lib/Bio/PDB/Vector.py | Python | mit | 9,547 | [
"Biopython"
] | 22d84e857e9c4180037fdd230615273dae6a95d3fdc2e436e43f809b7ea41380 |
# -*- coding: utf8 -*-
__author__ = 'Clemens Prescher'
import unittest
import tempfile
import numpy as np
from scipy.interpolate import PchipInterpolator
from ..widget.qt import QTest, QtCore, QtGui, QtWidgets
from ..controller.MainController import MainController
from ..model.PickModels import PickGaussianModel
fr... | Luindil/PeakThis | peakthis/test/test_FunctionalTest.py | Python | gpl-3.0 | 11,926 | [
"Gaussian"
] | 9c7a53789b389cf2e5bbb31fb1c5610ebc7623ad98ad138ef6febaad97583695 |
import numpy as np
from ase.calculators.calculator import Calculator, all_properties
class SinglePointCalculator(Calculator):
"""Special calculator for a single configuration.
Used to remember the energy, force and stress for a given
configuration. If the positions, atomic numbers, unit cell, or
bo... | askhl/ase | ase/calculators/singlepoint.py | Python | gpl-2.0 | 4,559 | [
"ASE"
] | f521ac38648e2f76df8323734fcf7ffd4827d1db5797fd679fd068c8c10b4899 |
#!/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... | gkc1000/pyscf | pyscf/grad/tdrks.py | Python | apache-2.0 | 16,052 | [
"PySCF"
] | 1eeb22b7b688fc1ecf4fdb12a6641d1795bdc647680efc20a9b487d59b5f2ac9 |
import discord
import json
from discord.ext import commands
from bs4 import BeautifulSoup
from urllib.parse import quote_plus
from urllib.parse import urlparse
from urllib.parse import parse_qs
class Google:
def __init__(self, bot):
self.bot = bot
self.aiohttp_session = bot.aiohttp_session
... | PrestigeDox/Watashi-SelfBot | cogs/google.py | Python | mit | 6,136 | [
"VisIt"
] | 4fc5fcb2174bea23ff754bf50d5515c2b7802f18b3febae9ca3a2d3e13dbddf6 |
#
# This source file is part of appleseed.
# Visit https://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2016-2019 Esteban Tovagliari, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaini... | luisbarrancos/appleseed-maya2 | scripts/appleseedMaya/xgenseedutil.py | Python | mit | 1,639 | [
"VisIt"
] | 93489b989ba3d7042d5acb5c3d12d42de735c807ac81f5e9332a16f0bf5cda8d |
from sys import exit
from random import randint
class Scene(object):
def enter(self):
print "Now you are in the room, Here's ..."
exit(1)
class Engine(object):
def __init__(self, scene_map):
self.scene_map = scene_map
def play(self):
current_scene = self.scene_map.opening_scene()
last_scene = self... | chidaobanjiu/works-on-LPTHW | Gothons#25.py | Python | cc0-1.0 | 7,744 | [
"BLAST"
] | 9efc31a28fc347f28b2ba5fd465f6fe2d19349cb0024974e3b10d3632e3da2ca |
#!/usr/bin/env python3
"""
This module applies global filters to the image sets
Author: Joshua Stuckner
Date: 2017/06/21
"""
import warnings
import sys
import time
import math
import warnings
from scipy.ndimage import filters
from scipy.misc import imresize, imsave
import scipy.ndimage as ndim
fro... | JStuckner/smart_tem | dmreader/operations.py | Python | mit | 17,879 | [
"Gaussian"
] | aded23e8d3a6f8cacebd045e8055c8dc0a1eebea214e674776bf592f147822b4 |
# pylint: disable-msg=C0301
# pylint: disable-msg=C0103
import os
import re
import shutil
import subprocess
import sys
import tempfile
import types
import warnings
import uuid
import numpy
import scipy.io
import scipy.sparse
from model import *
import inspect
try:
# This is only needed if we are running in an... | Aratz/pyurdme | pyurdme/pyurdme.py | Python | gpl-3.0 | 100,595 | [
"Jmol",
"ParaView",
"VMD",
"VTK"
] | f223e371d13990bf695f9a5bb3e6b43565e4682b8d4dbb576f75f6943aeaaf1d |
"""Django app for persisting prov.model.ProvBundle
Save and load provenance bundles from databases
References:
PROV-DM: http://www.w3.org/TR/prov-dm/
@author: Trung Dong Huynh <trungdong@donggiang.com>
@copyright: University of Southampton 2014
"""
from collections import defaultdict, OrderedDict
import uuid
impor... | pymonger/prov-0.5.4 | prov/persistence/models.py | Python | mit | 13,371 | [
"VisIt"
] | e74d61610f09df409732b474ca52bcdd1df692678fa7bc03058821bc84530789 |
# 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 objects that are used to describe the environments in a structure. The most detailed object
(StructureEnvironments) contains a very th... | gpetretto/pymatgen | pymatgen/analysis/chemenv/coordination_environments/structure_environments.py | Python | mit | 89,796 | [
"pymatgen"
] | 74cda3a6c630a23dd465bbefb0d5a83e727825f19a8af13d0ea1a27e219e942d |
# (C) British Crown Copyright 2010 - 2015, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | andrewcbennett/iris | lib/iris/fileformats/netcdf.py | Python | gpl-3.0 | 69,448 | [
"NetCDF"
] | 2ee2536fd63902ac7973a463aafe0f035fe4674bfe7e0d85d687d6a2f154252c |
"""
This module contains functionality for reading an ASE
Atoms object in ABINIT input format.
"""
def read_abinit(filename='abinit.in'):
"""Import ABINIT input file.
Reads cell, atom positions, etc. from abinit input file
"""
from ase import Atoms, units
if isinstance(filename, str):
f... | suttond/MODOI | ase/io/abinit.py | Python | lgpl-3.0 | 5,874 | [
"ABINIT",
"ASE"
] | 83715b0567d206eef0d521c82a0c3f00d1f5033fafdc647e0b1586fc1ee01e18 |
import modshogun as sg
import data
import numpy as np
# load data
feature_matrix = data.swissroll()
# create features instance
features = sg.RealFeatures(feature_matrix)
# create Kernel Locally Linear Embedding converter instance
converter = sg.KernelLocallyLinearEmbedding()
# set target dimensionality
converter.set... | abhiatgithub/shogun-toolbox | applications/tapkee/samples/klle.py | Python | gpl-3.0 | 1,046 | [
"Gaussian"
] | 2dc986d7ae7a1c2a90757b78e820ad2e2051b1b58c648e8f509ecf950a35c5e8 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views import defaults as default_views
from django.views.generic import TemplateView
# from ... | watchdogpolska/watchdog-id | config/urls.py | Python | mit | 2,082 | [
"VisIt"
] | c79630483a6c5c9b97f538a3f2398abd3215e4049e2124d2877977b0efc6dec2 |
import ckan.plugins as p
class Mopac(p.SingletonPlugin):
p.implements(p.IConfigurer)
def update_config(self, config):
p.toolkit.add_template_directory(config, 'templates')
| whythawk/ckanext-client-mopac | ckanext/mopac/plugin.py | Python | agpl-3.0 | 192 | [
"MOPAC"
] | ed47c6e3b4f8f9a20435eaab67fd5cdaba08f5177ec48f4b0291d31721021762 |
import sys
import pysam
from deeptools.mapReduce import mapReduce
def countReadsInInterval(args):
chrom, start, end, fname, toEOF = args
bam = openBam(fname)
mapped = 0
unmapped = 0
for b in bam.fetch(chrom, start, end):
if chrom == "*":
unmapped += 1
continue
... | fidelram/deepTools | deeptools/bamHandler.py | Python | gpl-3.0 | 3,346 | [
"pysam"
] | 54018e8cc33a7a1a77b7e0974c6478c0dba2f07fc5dbf1e92a3e07cdbdb30981 |
from pyatompaw import AtompawMaster
# Atom definition
atom = AtompawMaster('34-Se')
atom.Atom_name = 'Se'
atom.Z = 34
# Keywords
atom.XC_functional = 'LDA-PW'
atom.rel_keyword = 'scalarrelativistic'
atom.grid_keyword = 'loggrid', 2001, 80.0, 2.4
atom.logderivrange = 'logderivrange', -10, 35, 201
atom.projector_keywor... | GkAntonius/pyatompaw | examples/Se.py | Python | gpl-3.0 | 1,240 | [
"ABINIT"
] | 73d98c9159be0dd9fbc25e2a19d3b34141a0d5fca020283f650f501d02c7eb5c |
from distutils.core import setup
setup(
name='bam2fpkc',
version='0.1.0',
author='Michael Imelfort',
author_email='mike@mikeimelfort.com',
packages=['bam2fpkc', 'bam2fpkc.test'],
scripts=['bin/bam2fpkc'],
url='http://pypi.python.org/pypi/bam2fpkc/',
license='LICENSE.txt',
descriptio... | minillinim/bam2fpkc | setup.py | Python | gpl-3.0 | 464 | [
"pysam"
] | f7f48dec427078a8449852c526ab0c5ccd4b053243e99e531a031fd4190da6f9 |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | kwhitehall/climate | ocw/tests/test_utils.py | Python | apache-2.0 | 8,348 | [
"NetCDF"
] | 6b54d4df1ca1947117c3f66a6f202997245931ddb59846e8cebccf5da07da5d2 |
#!/usr/local/bin/env python
"""
A module for extracting uncorrelated samples from correlated timeseries data.
This module provides various tools that allow one to examine the correlation functions and
integrated autocorrelation times in correlated timeseries data, compute statistical inefficiencies,
and automatically... | shirtsgroup/checkensemble | checkensemble/timeseries.py | Python | gpl-2.0 | 26,906 | [
"Gaussian"
] | b2c7069e7ae80aee02d1e4bd56587418a07a8a4bf6a3cd4c82f99c79a6ff3241 |
import numpy as np
import matplotlib.pyplot as plt
from numpy import mean,pi,cos,sin,sqrt,tan,arctan2,exp,dot,array,log,inf, eye, zeros, ones, arange,reshape,concatenate,diag
from matplotlib.pyplot import *
from numpy.random import uniform as rand
from numpy.random import randn as randn
from numpy.linalg import i... | laranjma/robmooc | py_scripts/roblib.py | Python | bsd-2-clause | 7,471 | [
"Gaussian"
] | 51fbfb387f85b0f42f9e3bae1eab0003f4afec1bc7041b42729ff654763fec36 |
try: paraview.simple
except: from paraview.simple import *
def RequestDataDescription(datadescription):
"Callback to populate the request for current timestep"
if datadescription.GetForceOutput() == True:
for i in range(datadescription.GetNumberOfInputDescriptions()):
datadescription.GetIn... | openmichigan/PSNM | CubicNonlinearSchrodinger/Programs/NLS3dFortranMPIParaView/pipeline_vtis.py | Python | bsd-2-clause | 6,758 | [
"ParaView"
] | 2568f7a9b1f4974d7745dded0f0de8a70b7c6a11400bfa7a58e8e0c35b0e830a |
"""
This is basically just an exploration of how Betamax works
"""
from unittest import TestCase
from mock import Mock
from auth0plus.management.rest import RestClient
from auth0plus.settings import TIMEOUT
HTTP = 'http://httpbin.org/'
class TestRestClient(TestCase):
def setUp(self):
self.client = Res... | bretth/auth0plus | tests/test_management/test_rest.py | Python | isc | 2,510 | [
"Brian"
] | f83fe99a36ec4e423e88772850f3572e7fe891630425cf5ac049aa5fc3495376 |
# from model_mommy import mommy
# def test_simple(timbrowser):
# timbrowser.visit(timbrowser.url)
# assert timbrowser.is_text_present('Timtec')
#
#
# def test_login(timbrowser, user):
# timbrowser.visit(timbrowser.url)
# timbrowser.find_by_xpath('//a[normalize-space(text())="Entrar"]').click()
# t... | hacklabr/timtec | tests/test_fullstack.py | Python | agpl-3.0 | 816 | [
"VisIt"
] | bedede90553e4b72912c00a567910d87bc00229af2179dd4607cf648611c3a25 |
import HTMLParser
import flickrapi
import json
import logging
import os
import re
import urllib
"""
1. To use this script, you must apply for your own private Flickr API keys
2. Visit URL
https://www.flickr.com/services/api/misc.api_keys.html
3. Apply for your key online
4. Apply for a non-comme... | inspector2211/flickrsmartsync_oauth | flickrsmartsync_oauth/remote.py | Python | mit | 12,062 | [
"VisIt"
] | cb8a1b923e91dc46556d9af05e0b1beafdbca3b069962590f529c80c990e3d96 |
#!/usr/bin/env python
"""
Python wrapper around jnml command.
Also a number of helper functions for
handling/generating/running LEMS/NeuroML2 files
Thanks to Werner van Geit for an initial version of a python wrapper for jnml.
"""
from __future__ import absolute_import
import os
import sys
import subprocess
impor... | 34383c/pyNeuroML | pyneuroml/pynml.py | Python | lgpl-3.0 | 25,765 | [
"Brian",
"NEURON"
] | 7f33196b99603607acd7a3f48da4da6a5e4a9aaf7d65a5cc15977afbb73e211b |
"""
submtr.gaussian
~~~~~~~~~~~~~~~
Implements the GaussianJob class for processing Gaussian jobs.
:copyright: (c) 2014 by Li Research Group.
:license: MIT, see LICENSE for more details.
"""
import os.path
from submtr.config import settings
from submtr.job import Job
from submtr.ui import error,... | liresearchgroup/submtr | submtr/jobs/gaussian.py | Python | mit | 6,300 | [
"Gaussian"
] | 8be41aea2ec5019d63f7856851739a5342665845951639952bf44c1d094b8e4b |
#! /usr/bin/env python
'''
Read in stellar catalogs from simulations with Absolute AB mags and
background galaxy catlogs. Using the WingsTips lib, produce mixed list
of objects including stars and appropriate sampling of background
galaxies in STIPS input format
'''
from wingtips import WingTips as stips
from wingtips... | swc2124/starcat | starcat/make_mix.py | Python | mit | 3,658 | [
"Galaxy"
] | cb12391c3dd2c2f37be026fa7213c5cf39a66b5a18eed9a0ac474488d8f6abc6 |
#!/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.vtkMulti... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Filters/Core/Testing/Python/streamComb.py | Python | gpl-3.0 | 1,702 | [
"VTK"
] | 85b085dda583a32856cfba20dc4f1c7990646e078e3acb6a538a0e7f73e376f0 |
import pytest
import platform
import uuid
from datetime import datetime
from time import sleep
"""
1] Retrieve a model description by its model_id or alias.
"""
#1.1) Without model_id or alias
def test_getModel_none(modelCatalog):
model_catalog = modelCatalog
with pytest.raises(Exception) as excinfo:
... | apdavison/hbp-validation-client | tests/test_models.py | Python | bsd-3-clause | 19,994 | [
"NEURON"
] | c9606e79f903b9d49726666a4492ed50de415a7a700959b16b01d8a2fe1b3e7f |
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