text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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"""Tests for the Glyph module.
"""
# Author: Prabhu Ramachandran <prabhu_r@users.sf.net>
# Copyright (c) 2005, Enthought, Inc.
# License: BSD Style.
# Standard library imports.
from os.path import abspath
from StringIO import StringIO
import copy
import numpy
# Enthought library imports.
from traits.api import Trait... | liulion/mayavi | integrationtests/mayavi/test_glyph.py | Python | bsd-3-clause | 5,668 | [
"Mayavi"
] | 85de912ef0a182c3675630d882df043ccc2af4792ec7d77009ad8419f62a0c13 |
import sys
sys.path.insert(0, "../../build/examples/callback")
import c
def visitor(value):
print value
c.visit(visitor)
| neweagle/ns-3_multisim | pybindgen/examples/callback/c_test.py | Python | gpl-2.0 | 128 | [
"VisIt"
] | fb6958082f732d370eb9d78a91dab0dbc86b900ed96c362d82b1057c24577d51 |
import matplotlib.pyplot as p
from pandas import read_csv
from spectral_cube import SpectralCube, Projection
import numpy as np
import astropy.units as u
from astropy.coordinates import Angle
from astropy.io import fits
import os
from os.path import join as osjoin
from cube_analysis.profiles import radial_profile
fro... | e-koch/VLA_Lband | 14B-088/HI/analysis/HI_veldisp_profile.py | Python | mit | 12,397 | [
"Gaussian"
] | cf0e595e3ed37ecacd37dc411ab08e45563b33396e6086495c046b8a2234ff7c |
# -*- coding: utf-8 -*-
r"""
Tools for downloading and converting NOAA/NWS weather station data.
Data is downloaded from the NOAA ftp server:
ftp://ftp.ncdc.noaa.gov/pub/data/ish/
Example
--------
>>> from datetime import datetime
>>> import getNOAAWeatherStation as noaa
>>>
>>> latlon = [... | UT-CWE/Hyospy | Hyospy_ensemble/lib/SUNTANS/DataDownload/getNOAAWeatherStation.py | Python | mit | 27,500 | [
"NetCDF"
] | 3e1fac05b9f40f7b142da8250a7f740887a5b3e0bca17bd51078b6b05cf3b29e |
from ase.units import Bohr
import gpaw.mpi as mpi
from gpaw.lrtddft.spectrum import Writer
ds_prefactor = {
'Ang' : Bohr**2,
'a.u.': 1.0,
'Mb' : Bohr**2 * 100,
}
class PESpectrum(Writer):
def __init__(self,
enlist,
folding='Gauss',
width=0.08 ... | qsnake/gpaw | gpaw/pes/__init__.py | Python | gpl-3.0 | 1,450 | [
"ASE",
"GPAW"
] | 2de16734e15b39e808db5e03562a08d51788983effe1c7f731265f71a3eb5ed4 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# kate: word-wrap off; remove-trailing-spaces all;
#
# Copyright (c) 2010-2015 Marcel Martin <marcel.martin@scilifelab.se>
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software")... | Chris7/cutadapt | cutadapt/scripts/cutadapt.py | Python | mit | 32,305 | [
"BWA"
] | 47ea2fa949127d4b22c92710b314414cd70053e6a49e0d434b0a976b07147684 |
###############################################################################
##
## Copyright (C) 2011-2014, NYU-Poly.
## Copyright (C) 2006-2011, University of Utah.
## All rights reserved.
## Contact: contact@vistrails.org
##
## This file is part of VisTrails.
##
## "Redistribution and use in source and binary for... | Nikea/VisTrails | scripts/gen_vtk_examples/convert_to_vt.py | Python | bsd-3-clause | 4,349 | [
"VTK"
] | 753a320eb0b91c73524369ffe4cc3a279b6cf4d9e074f57ef06628aba817c207 |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-admin-list-users
# Author : Adrian Casajus
########################################################################
__RCSID__ = "$Id$"
from DIRAC.Core.Base import Script
Script.registerSwitch(... | sposs/DIRAC | Interfaces/scripts/dirac-admin-list-hosts.py | Python | gpl-3.0 | 1,043 | [
"DIRAC"
] | 006d911f47543adf24150ad2d07de3f87c6b3b65807f8e476160400317b32346 |
# Copyright 2011-2015, Damian Johnson and The Tor Project
# See LICENSE for licensing information
"""
Basic enumeration, providing ordered types for collections. These can be
constructed as simple type listings...
::
>>> from stem.util import enum
>>> insects = enum.Enum('ANT', 'WASP', 'LADYBUG', 'FIREFLY')
>>... | FedericoCeratto/stem | stem/util/enum.py | Python | lgpl-3.0 | 4,385 | [
"Firefly"
] | a517bd175a53bb4ee69c50aae50242913e7d1d28212312ec0936f59deafb9294 |
"""Class to predict memory usage for runs at various nsides.
"""
import os
import numpy as np
import healpy as hp
import esutil
import fitsio
from ..configuration import Configuration
from ..catalog import Entry
class MemPredict(object):
def __init__(self, configfile):
"""Instantiate a MemPredict.
... | erykoff/redmapper | redmapper/pipeline/mempredict.py | Python | apache-2.0 | 3,672 | [
"Galaxy"
] | ba56ec7a67805a641b778bcbb8aa3f0a99f7f7331d253922310c72ebcc192222 |
__author__ = 'noe'
import numpy as np
import unittest
import time
from bhmm.output_models.gaussian import GaussianOutputModel
print_speedup = False
class TestOutputGaussian(unittest.TestCase):
def setUp(self):
nstates = 3
means = np.array([-0.5, 0.0, 0.5])
sigmas = np.array([0.2, 0.2,... | bhmm/legacy-bhmm-force-spectroscopy-manuscript | bhmm/tests/test_output_gaussian.py | Python | lgpl-3.0 | 1,156 | [
"Gaussian"
] | 9630a49e011733441c4ead3c8b1b5ec0ac2fbab95aef1bdeb4109703cd61359e |
#!/usr/bin/python
#
# pyLirc, lirc (remote control) module for python
# Copyright (C) 2003 Linus McCabe <pylirc.linus@mccabe.nu>
#
# This library 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 Found... | offlinehacker-playground/pylirc2 | pylirc_testUnExtended.py | Python | lgpl-2.1 | 2,554 | [
"Brian"
] | 8e2fc857f41d65106e86ad8c2261a3ab7722186cdcb02a28a4c6e7489bade3e1 |
# Copyright (C) 2011-2012 CRS4.
#
# This file is part of Seal.
#
# Seal 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.
#
# Seal is dis... | ilveroluca/seal | seal/seqal/seqal_config.py | Python | gpl-3.0 | 5,628 | [
"BWA"
] | 2d677f78fcd599b73be1e0f7b30107287ee0663addc27d72a5ae35ee248165e1 |
#!/usr/bin/python
# Filename: example_flat.py
#
# Code by Martin Jucker, distributed under an MIT License
# Any publication benefitting from this piece of code should cite
# Jucker, M 2014. Scientific Visualisation of Atmospheric Data with ParaView.
# Journal of Open Research Software 2(1):e4, DOI: http://dx.doi.org/10... | mjucker/pv_atmos | examples/example_flat.py | Python | mit | 5,005 | [
"ParaView"
] | 1b1d59165cfafe6a69dddd713dba335d966a977e83b3e74b453436ff43af71eb |
import numpy as np
from ase.io import Trajectory
from ase.build import bulk
from ase.calculators.emt import EMT
from ase.io import read
# we do the 9 calculations (three values for a and three for c):
a0 = 3.52 / np.sqrt(2)
c0 = np.sqrt(8 / 3.0) * a0
traj = Trajectory('Ni.traj', 'w')
eps = 0.01
for a in a0 * np.li... | miroi/open-collection | theoretical_chemistry/software_runs/ase/runs/lattice_constant/find_a_c_latt_con.py | Python | mit | 455 | [
"ASE"
] | 42055656a18f20f021a2144cbcf3c1fff24971001ee13f0cdbe7b71e7f9ee244 |
import time
import numpy as np
import xarray as xr
from . import dc_utilities
import datacube
import rasterio
## Export ##
def export_xarray_to_netcdf(data, path):
"""
Exports an xarray object as a single NetCDF file.
Parameters
----------
data: xarray.Dataset or xarray.DataArray
The Dat... | ceos-seo/data_cube_utilities | data_cube_utilities/import_export.py | Python | apache-2.0 | 6,273 | [
"NetCDF"
] | 20097610bb089ba8fa495d1e5118ab14a2718c310d04e89ae19d96ace155cbaf |
import os
import sys
import time
from math import sin, cos, radians, atan2, degrees
from contextlib import contextmanager
import numpy as np
from ase.data import chemical_symbols
# Python 2+3 compatibility stuff:
if sys.version_info[0] == 3:
import builtins
exec_ = getattr(builtins, 'exec')
basestring =... | suttond/MODOI | ase/utils/__init__.py | Python | lgpl-3.0 | 7,206 | [
"ASE"
] | f38f4e0e50832b5def98f0777a86e0bdc1551ac2de447f03b0d2ccb5d736f750 |
"""
Tests for the Course Outline view and supporting views.
"""
import datetime
import json
import re
import ddt
import six
from completion import waffle
from completion.models import BlockCompletion
from completion.test_utils import CompletionWaffleTestMixin
from django.contrib.sites.models import Site
from django.... | edx-solutions/edx-platform | openedx/features/course_experience/tests/views/test_course_outline.py | Python | agpl-3.0 | 34,510 | [
"VisIt"
] | 7c6bf9197b6f7226b1412773cf085f641d06e514a291a02256e3c1ce7e20398f |
# pylint: disable=C
# coverage: ignore
"""
Construct MolecularData objects for various molecules
"""
from typing import Optional
import openfermion as of
NO_PSI4 = False
try:
import psi4 # type: ignore
except ImportError:
NO_PSI4 = True
import numpy as np
import scipy as sp
NO_OFPSI4 = False
try:
from... | quantumlib/OpenFermion-Cirq | openfermioncirq/experiments/hfvqe/molecular_data/molecular_data_construction.py | Python | apache-2.0 | 4,918 | [
"Psi4"
] | 7c89cf1daffd6309933a3829ff94b2c3730dc0d0054226ab0aaf7d52dc921bf1 |
#!/usr/bin/env python
'''unit testing code for pysam.'''
import pysam
import unittest
import os
import itertools
import subprocess
import shutil
class TestExceptions(unittest.TestCase):
def setUp(self):
self.samfile=pysam.Samfile( "ex1.bam","rb" )
def testOutOfRangeNegativeNewFormat(self):
s... | pkaleta/pysam | tests/segfault_tests.py | Python | mit | 1,213 | [
"pysam"
] | 0f3589bc2cde3a9f6f75c67c0c55799a182360b0cc802d0194bdcaac6fd7b96c |
# -*- coding: utf-8 -*-
__license__ = 'GPL v3'
__copyright__ = '2009, John Schember <john at nachtimwald.com>'
__docformat__ = 'restructuredtext en'
'''
Generic USB Mass storage device driver. This is not a complete stand alone
driver. It is intended to be subclassed with the relevant parts implemented
for a partic... | songfj/calibre | src/calibre/devices/usbms/driver.py | Python | gpl-3.0 | 23,329 | [
"VisIt"
] | b04c6f487d3ebc7932ede2212256fee478cc84f2b73d820534039170fca89dad |
""" Tests for the garbage collection of objects in mayavi package.
"""
# Authors: Deepak Surti, Ioannis Tziakos
# Copyright (c) 2015, Enthought, Inc.
# License: BSD Style.
from numpy import sqrt, sin, mgrid
from traits.api import Instance, HasTraits
from traitsui.api import View, Item
from traits.etsconfig.api import ... | dmsurti/mayavi | mayavi/tests/test_garbage_collection.py | Python | bsd-3-clause | 3,557 | [
"Mayavi"
] | 7541019196bea2b8b1244328f78c3f9a5e8db3ed8a54ad0ca54d6070452c346e |
#!/usr/bin/env python
from __future__ import division
__author__ = "Jai Ram Rideout"
__copyright__ = "Copyright 2012, The QIIME project"
__credits__ = ["Jai Ram Rideout"]
__license__ = "GPL"
__version__ = "1.9.1-dev"
__maintainer__ = "Jai Ram Rideout"
__email__ = "jai.rideout@gmail.com"
from os.path import split
from... | ssorgatem/qiime | qiime/parallel/identify_chimeric_seqs.py | Python | gpl-2.0 | 9,174 | [
"BLAST"
] | 1c8c69d27937c6a4b93c9f80dccd34cf8af37b638babae7a186bfa2401578930 |
# $Id$
#
# Copyright (C) 2007,2008 Greg Landrum
#
# @@ All Rights Reserved @@
#
import os, sys
import io
import unittest
import pickle
from rdkit import RDConfig
from rdkit import DataStructs as ds
import random
def feq(v1, v2, tol=1e-4):
return abs(v1 - v2) < tol
class TestCase(unittest.TestCase):
def setUp(s... | bp-kelley/rdkit | Code/DataStructs/Wrap/testSparseIntVect.py | Python | bsd-3-clause | 5,355 | [
"RDKit"
] | 439f9b9845cc67cfb0e51f73da4243855dc69370d96fa8fe8f24653e34121429 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
'''
freeseer - vga/presentation capture software
Copyright (C) 2013 Free and Open Source Software Learning Centre
http://fosslc.org
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the ... | Freeseer/freeseer | src/freeseer/frontend/talkeditor/CommandButtons.py | Python | gpl-3.0 | 2,950 | [
"VisIt"
] | cacd3d0c317d7ac87f9c0c845a1f872f971809265306cdaa922156bcf96aa045 |
import subprocess
import sys
import numpy as np
from functools import partial
from glob import glob
from importlib import import_module
from os.path import basename, join
from seisflows.config import ParameterError, custom_import
from seisflows.plugins import solver_io
from seisflows.tools import msg, unix
from seisf... | luan-th-nguyen/seisflows_ndt | seisflows/solver/base.py | Python | bsd-2-clause | 19,096 | [
"Gaussian"
] | de2dc9f9a86fbd0baa49c0a8937e58b881347eccb8c49df11a1afc035af15c6b |
#!/usr/bin/python
import sys
import string
import pylab
import numpy as np
import monetdb.sql as db
db_host = "localhost"
db_dbase = "barts"
db_user = "barts"
db_passwd = "barts"
db_port = 50000
db_autocommit = True
def alpha(theta, decl):
"""
"""
if abs(decl) + theta > 89.9:
return 180.0
else... | jjdmol/LOFAR | CEP/GSM/src/lsm_upgrade/new_lsm.py | Python | gpl-3.0 | 3,604 | [
"Gaussian"
] | 82d513506adf2c3ddd33f567769937b1933c47d69d520403ade0071a4d18cda4 |
r"""
Two Laplace equations with multiple linear combination constraints.
The two equations are coupled by a periodic-like boundary condition constraint
with a shift, given as a non-homogeneous linear combination boundary condition.
Find :math:`u` such that:
.. math::
\int_{\Omega_1} \nabla v_1 \cdot \nabla u_1
... | RexFuzzle/sfepy | examples/diffusion/laplace_coupling_lcbcs.py | Python | bsd-3-clause | 4,023 | [
"VTK"
] | 6b28285722f6516f850223aa5fc5f2cd66ba15db1ff067eaec024e1230315b37 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Create the RenderWindow, Renderer and both Actors
#
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
iren = vtk.vtkRenderWindowInteractor(... | hlzz/dotfiles | graphics/VTK-7.0.0/Filters/Texture/Testing/Python/socbal.py | Python | bsd-3-clause | 13,848 | [
"VTK"
] | ad62ccf6c49bde6c060b53e3053d1a210d4ec2d131f388482f759497da8a8a59 |
import media
import fresh_tomatoes
# Create instances of class media.Movie(title, poster, trailer)
rock_n_rolla = media.Movie("RocknRolla",
"https://miguelvaca.files.wordpress.com/2009/11/rocknrolla.jpg", # NOQA
"https://youtu.be/WEIykbkkq6I")
the_martian = media.Mov... | MariiaSurmenok/Movie-Trailer-Website | entertainment_center.py | Python | mit | 1,530 | [
"Galaxy"
] | b80a7048309f952b608c35c25086ce05c601e23a353d717198183e472e4623aa |
#!/usr/bin/env python3
'''
description: Utilities used in wrfpy
license: APACHE 2.0
author: Ronald van Haren, NLeSC (r.vanharen@esciencecenter.nl)
'''
import logging
import sys
import os
# define global LOG variables
DEFAULT_LOG_LEVEL = 'debug'
LOG_LEVELS = {'debug': logging.DEBUG,
'i... | rvanharen/wrfpy | wrfpy/utils.py | Python | apache-2.0 | 7,819 | [
"NetCDF"
] | 9ef9b17a0c258855edccc1a6e11bac1b16b7f60fdefd2179554ede9d1174b3d1 |
"""
=============================================
Whitening evoked data with a noise covariance
=============================================
Evoked data are loaded and then whitened using a given noise covariance
matrix. It's an excellent quality check to see if baseline signals match
the assumption of Gaussian white... | teonlamont/mne-python | examples/visualization/plot_evoked_whitening.py | Python | bsd-3-clause | 3,040 | [
"Gaussian"
] | a526030ae8cc020164173da547716b138f13bbc85e5742173e2c20f1da5613a5 |
# -*- coding: utf-8 -*-
#
# hl_api_connections.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 Lice... | uahic/nest-simulator | pynest/nest/lib/hl_api_connections.py | Python | gpl-2.0 | 34,718 | [
"NEURON"
] | 390b7e53e5059d51639dc1daf587c4ff68a6c2f491429341013c3803d2f14a70 |
# Copyright 1999 by Jeffrey Chang. All rights reserved.
# 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.
"""Code to parse the keywlist.txt file from SwissProt/UniProt
See:
http://www.expasy.ch/sprot... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/SwissProt/KeyWList.py | Python | gpl-2.0 | 3,171 | [
"Biopython"
] | 1d9bfbf6b2f95af23b179fba772067e78cb21cb67b82ae8625711617ab5e479e |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 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
#... | psi4/psi4 | psi4/driver/dependency_check.py | Python | lgpl-3.0 | 1,568 | [
"Psi4"
] | 0ac8e14d731412b944625617f92b3bbf3b9dab60cc86fd4dce25ed350a3122cb |
import heapq
from random import random
from warnings import warn
# --- PRIORITY QUEUE ----------------------------------------------------------------------------------
# Currently not in use.
INFINITY = 1e20
class priorityqueue(dict):
def push(self, e, w):
self[e] = w
def pop(self):
p, w =... | mediafactory/yats | modules/graph/proximity.py | Python | mit | 8,658 | [
"VisIt"
] | 826f21e6d4dfb011f0f3aab844168b47e2ad79461e845196a1e89a89f795e747 |
# Copyright (C) 2014,2016
# Jakub Krajniak
# 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 redistribut... | espressopp/espressopp | src/interaction/DihedralHarmonicNCos.py | Python | gpl-3.0 | 5,589 | [
"ESPResSo"
] | 1fa42742414fd9ede3d17710d1a00fba2d54f292850427c14c00e5d73e9391a6 |
""" This contains unit tests to make sure that the migration between PyGSI and M2Crypto is as smooth as possible
The test covers only the method exposed by the PyGSI version for the time being.
We are not testing:
-> setChain: simple setter
-> setPKey: simple setter
* generateProxyRequest
* ge... | DIRACGrid/DIRAC | src/DIRAC/Core/Security/test/Test_X509Chain.py | Python | gpl-3.0 | 19,955 | [
"DIRAC"
] | 11c8b2434e981fbf1d6f7a317ce96ab348d2402f329d29941cc2c45f5bf2dc99 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | Kleptobismol/scikit-bio | skbio/stats/distance/tests/test_mantel.py | Python | bsd-3-clause | 21,073 | [
"scikit-bio"
] | ef6b65c21259519ba26258519792b442f757968f23f57ffedcacaa7e8771c154 |
#!/usr/bin/python
from multiprocessing import Pool
import time
import os
import sys
import simplejson as json
import argparse
from Bio import SeqIO
from Bio.SeqUtils import GC
from Bio.SeqRecord import SeqRecord
from Bio.Seq import Seq
# Copyright(C) 2014 David Ream
# Released under Biopython license. http://www.biop... | reamdc1/gene_block_evolution_old | make_operon_query.py | Python | gpl-3.0 | 33,874 | [
"BLAST",
"Biopython"
] | 71149bfa73d1276762cded3fea5577ed1c5e2d5ea8db15361a9760a35478f5f0 |
import glob
import pandas as pd
import numpy as np
pd.set_option('display.max_columns', 50) # print all rows
import os
os.chdir("/gpfs/commons/home/biederstedte-934/evan_projects/correct_phylo_files")
normalB = glob.glob("binary_position_RRBS_normal_B_cell*")
mcell = glob.glob("binary_position_RRBS_NormalBCD19pCD27... | evanbiederstedt/RRBSfun | trees/chrom_scripts/normal_chrY.py | Python | mit | 25,843 | [
"MCell"
] | 337374cca181ba85f5eb43938e50cd1b88b643e9d84981cf31cc557e36e67b80 |
import pysam
import csv
def get_new_row(orig_bam, new_bam, row):
# assert '1/1' in row['DGRP-362'] or '1/1' in row['DGRP-765']
# Check that we actually have a SNP here - i.e. the fastas will have
# different bases at this position
# if '1/1' in row['DGRP-362'] and '1/1' in row['DGRP-765']:
#... | d-quinn/bio_quinn2013 | multiple_reference/phased/combining_snps_with_vcf.py | Python | mit | 4,431 | [
"pysam"
] | e7b52ea384f0d5fad8bd64d62e1b42769ea9c4211851d63260a36f260fce1a7d |
# Copyright 2014 Diamond Light Source Ltd.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed t... | FedeMPouzols/Savu | savu/plugins/filters/dials_find_spots.py | Python | gpl-3.0 | 3,298 | [
"CRYSTAL"
] | be5413859cb662ba9990d77dc33555e09126af7ed560165412228f1cd0dfc92a |
# -*- coding: utf-8 -*-
import ast
import base64
import csv
import glob
import itertools
import logging
import operator
import datetime
import hashlib
import os
import re
import simplejson
import time
import urllib
import urllib2
import urlparse
import xmlrpclib
import zlib
from xml.etree import ElementTree
from cStri... | 3dfxmadscientist/cbss-server | addons/web/controllers/main.py | Python | agpl-3.0 | 68,561 | [
"VisIt"
] | c8a3705f2fa0e910df852f7603ab1e9c4d07cc7eadce8b86e71d99d825d55157 |
import director.vtkAll as vtk
import director.thirdparty.numpyjsoncoder as nje
from collections import OrderedDict
from director import fieldcontainer
from director import transformUtils
import json
class ConstraintEncoder(nje.NumpyConvertEncoder):
def default(self, obj):
if isinstance(obj, vtk.vtkTransfo... | patmarion/director | src/python/director/ikconstraintencoder.py | Python | bsd-3-clause | 1,410 | [
"VTK"
] | a6ef08817ca94c709ce5bc2914380298a9be5f50468700faa8c8ef9bafd6c9e6 |
# encoding: utf-8
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding field 'FlatValue.numerator_moe'
db.add_column(u'profiles_flatvalue', 'numerator_moe', self.gf('dj... | ProvidencePlan/Profiles | communityprofiles/profiles/oldmigrations/0082_auto__add_field_flatvalue_numerator_moe.py | Python | mit | 25,224 | [
"MOE"
] | 44d942dae6aad1c5273ecfabcdd747023b6bed8772e35d8a967588e4f0c068c8 |
# -*- coding: utf-8 -*-
"""Provide base checkers metaclass"""
class BaseCheckerMeta(type):
"""Base checker type
This will automatically register an instance of any checker subclass
into self._checks. This will be used by OpenERPConventionsChecker
to run all checkers. A checker must have a visit(root_n... | nbessi/openerp-conventions | common_checker/base_checker.py | Python | mit | 885 | [
"VisIt"
] | 6b8ebacc14693520ab73f9811cb6bd891483a42504fe4dca4498ba416c10022e |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2016, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Löwdin population analysis."""
import random
import numpy
from .population import Population
class... | Schamnad/cclib | src/cclib/method/lpa.py | Python | bsd-3-clause | 5,089 | [
"cclib"
] | efbcff6cf277a7d56018da32fef74ab6e71d500f2f2cdaf86eb9b3beace72f20 |
#!/usr/bin/python
'''
GARNET primary script executes 5 sub scripts according to provided configuration file. We provide vertebrate motif data and gene/xref data for hg19 and mm9.
--------------------------------------------------------------------
Config file:
---------------------------------------------------------... | jpgulliver/OmicsIntegrator | scripts/garnet.py | Python | bsd-2-clause | 11,299 | [
"Galaxy"
] | eb896ed9f993f1c05b09b05c7c1f7b282c143029f5e4a6edabeba61cefb89292 |
#!/usr/bin/python
# -*- coding: UTF-8 -*-
#Copyright (C) 2007 Adam Spencer - Free Veterinary Management Suite
#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 ... | cyncyncyn/evette | language.py | Python | gpl-2.0 | 71,852 | [
"VisIt"
] | 2b80686ed1f83ad89618a7d33653cccc9c480e2cacc09685dd20541f2332d082 |
# overrides for the webapp deployment
DEBUG = True
PORT = 5017
SSL = False
THREADED = True
MAIL_FROM_ADDRESS = "sysadmin@cottagelabs.com"
# important overrides for the ES module
# elasticsearch back-end connection settings
ELASTIC_SEARCH_HOST = "http://localhost:9200"
ELASTIC_SEARCH_INDEX = "wellcome"
# FIXME: shor... | CottageLabs/oacwellcome | config/service.py | Python | apache-2.0 | 2,172 | [
"Octopus"
] | b953219ca34fe9462ad0b0359af98185db1fb686a55a69512fadf2da4afca8e7 |
import cl
import primitives as p
import ast
import more_ast
import builtins
import collections
import inspect
import imp
import operator
import sys
import threading
import types
from cl import error, list_, list__, gensym, gensymname, intern, append, identity, reduce, gethash, progv as _progv, defun
from cl import fi... | deepfire/partus | py.py | Python | gpl-3.0 | 104,072 | [
"VisIt"
] | 65c0ee4510f343f17a64f1bc46316a63996c0284a935f51caa379713570f3eed |
"""
An example script utilising the Config class to read in a configuration
and output in .xyz format
USAGE:
$ python2.7 dump_read_xyz.py -f <path-to-lammps-output-file>
-tse <start-timestep> <end-timestep>
-re <read-every-n-timeste... | JMuscatello/python-lammps-tools | dump_read_xyz.py | Python | gpl-3.0 | 1,956 | [
"LAMMPS"
] | 3e3d5c7a71cacac7a2f90386263e52200ee63e4d9a9c163870ced881c3cf3ebc |
import itertools
import math
from math import gcd
from math import cos, sin, sqrt
import numpy as np
import pprint
class FormatPrinter(pprint.PrettyPrinter):
def __init__(self, formats):
super(FormatPrinter, self).__init__()
self.formats = formats
def format(self, obj, ctx, maxlvl, lvl):
... | MaterialsDiscovery/PyChemia | pychemia/utils/mathematics.py | Python | mit | 28,950 | [
"Gaussian"
] | 77e2489a5722ad760c54adfc2042822186a1485567c63d17c1d2772aca62534e |
##
# Copyright 2009-2017 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... | ULHPC/easybuild-easyblocks | easybuild/easyblocks/n/netcdf_fortran.py | Python | gpl-2.0 | 2,768 | [
"NetCDF"
] | 5c4a2177f705d978ba617d52651ce501c81af9898714010f97dae915acb086cd |
# Copyright (C) 2012,2013,2015,2016
# 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 term... | espressopp/espressopp | src/FixedPairListAdress.py | Python | gpl-3.0 | 3,687 | [
"ESPResSo"
] | 76d63b91b7a5f9c54d81e11b941d513e2e438ba31930d4d0884284f8660178b6 |
import praw
import evernote.edam.userstore.constants as UserStoreConstants
import evernote.edam.type.ttypes as Types
from evernote.api.client import EvernoteClient
auth_token = "EVERNOTE_TOKEN"
if auth_token == "EVERNOTE_TOKEN":
print("Please fill in your developer token")
print("To get a developer token, vis... | Sapping/reddit-evernote-saver | reddit-evernote-saver.py | Python | mit | 2,247 | [
"VisIt"
] | e5e8cadbc5a5bf49e2b7347fb101cb5bf6cd44ff2940ca0fb827b457557a217c |
# Copyright 2005-2008 by Frank Kauff & Cymon J. Cox. All rights reserved.
# 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.
"""Tree class to handle phylogenetic trees.
Provides a set of methods to read... | go-bears/Final-Project | weblogo-3.4_rd/corebio/seq_io/_nexus/Trees.py | Python | mit | 37,615 | [
"Biopython"
] | c0093c4e05e0e440d93e4e64e481b2450980b0d36d9ba00c2cc01532855bdda1 |
# /usr/bin/python
# To run this test you need python nose tools installed
# Run test just use:
# nosetest tests.py
#
# *Note: If you add additional test, please prefix the function name
# to the type of operation being performed. For instance modifying an
# image, test_image_erode(). If you are looking for lines, t... | beni55/SimpleCV | SimpleCV/tests/tests.py | Python | bsd-3-clause | 107,405 | [
"Gaussian"
] | 6b1e13a68718ecbf7584e918722a46fa03adda30ebbfdd4ae67978a708a11971 |
# Copyright (c) 2014-2017, NVIDIA CORPORATION. All rights reserved.
from __future__ import absolute_import
from wtforms import validators
from ..forms import ModelForm
from digits import utils
class ImageModelForm(ModelForm):
"""
Defines the form used to create a new ImageModelJob
"""
crop_size = ... | Deepomatic/DIGITS | digits/model/images/forms.py | Python | bsd-3-clause | 3,851 | [
"Gaussian"
] | 2b7ad01c3998433d24f15127d46d43e4168063dccf59b49dd5cf8c1ea22675d5 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2017, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Run method unit tests for cclib."""
import sys
import unittest
sys.path.append("method")
from testcda import *
from t... | gaursagar/cclib | test/test_method.py | Python | bsd-3-clause | 467 | [
"cclib"
] | 5f8eb28fda51852368675035614dc99b2eac9e973136056a55f54f2e4909daf7 |
"""
generate methylation data given a reference genome and a set of bisulfite
treated reads. usage:
methylcoder [options] reads.fastq (or fasta)
or for pair-end reads:
methylcoder [options] reads1.fastq reads2.fastq
extra arguments to the aligner (bowtie or gmap/gsnap) should be sent as a string via
... | brentp/methylcode | methylcoder/__init__.py | Python | bsd-3-clause | 30,376 | [
"Bowtie"
] | 3fc8d891053118fc5ca763b2a0aa416cc836e3e8068c09a3dec68d2c3146d424 |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
# -*- coding: utf-8 -*-
"""
Change directory to provide relative paths for doctests
>>> import os
>>> filepath = os.path.dirname(os.path.realpath(__file__ ))
>>> datadir = os.path.realpath(... | carolFrohlich/nipype | nipype/interfaces/mrtrix3/utils.py | Python | bsd-3-clause | 15,216 | [
"Gaussian",
"VTK"
] | d7feabaf5048a48bd7dfdfb51a2a8167773da3a3290b96cc30b7d03e0b97bc39 |
# -*- coding: utf-8 -*-
import numpy as np
u"""Collection of bulk systems.
From this paper:
Kevin F. Garrity , Joseph W. Bennett, Karin M. Rabe, David Vanderbilt
Pseudopotentials for high-throughput DFT calculations
Computational Materials Science 81 (2014) 446-452
http://dx.doi.org/10.1016/j.commatsci.20... | suttond/MODOI | ase/test/tasks/gbrv.py | Python | lgpl-3.0 | 20,153 | [
"ASE",
"CRYSTAL",
"DIRAC",
"FHI-aims"
] | 807b28304ac88f29f2bb7413fd5250533a42fd33673c5d5d8d207b2abf0d765c |
"""
Extreme deconvolution solver
This follows Bovy et al.
http://arxiv.org/pdf/0905.2979v2.pdf
Arbitrary mixing matrices R are not yet implemented: currently, this only
works with R = I.
"""
from time import time
import numpy as np
from scipy import linalg
try: # SciPy >= 0.19
from scipy.special import logsumex... | astroML/astroML | astroML/density_estimation/xdeconv.py | Python | bsd-2-clause | 7,199 | [
"Gaussian"
] | 06a533b339065967294929e19c4e1359981642fee39f5f5ad81eda1a62f3d315 |
########################################################################
# File : ProxyGeneration.py
# Author : Adrian Casajus
########################################################################
import sys
from prompt_toolkit import prompt
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.Base.Script impo... | DIRACGrid/DIRAC | src/DIRAC/FrameworkSystem/Client/ProxyGeneration.py | Python | gpl-3.0 | 11,616 | [
"DIRAC"
] | 519c9cbf13dc71b46a44217b1517971626527535bbca58a185bc682c2bdbebcd |
#!/usr/bin/env python
'''
Description
If using files, (call by command line or from python):
all the inputs are raw float32 vectors files that are reshaped by the number
of f0 values in ff0.
There are three safe patches that were not described in the publication[1]:
(These are not critical, they might re... | etosha/pulsemodel | synthesis.py | Python | apache-2.0 | 13,347 | [
"DIRAC",
"Gaussian"
] | dcd40da25e259eb65a0d5503e2e6994178c8342006daf7f5968dc6e4d065d2f7 |
"""Implementation of the WebSocket protocol.
`WebSockets <http://dev.w3.org/html5/websockets/>`_ allow for bidirectional
communication between the browser and server.
WebSockets are supported in the current versions of all major browsers,
although older versions that do not support WebSockets are still in use
(refer ... | SickGear/SickGear | lib/tornado_py3/websocket.py | Python | gpl-3.0 | 61,544 | [
"VisIt"
] | 23d917af3a9b7478d4d974d20a328b6f6eb89297cd0691bc2b9e26ae7dc6154d |
#!python
# Copyright (C) 2010, 2011 by Eric Brochu
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, mer... | misterwindupbird/IBO | ego/gaussianprocess/kernel.py | Python | mit | 9,132 | [
"Gaussian"
] | 0edfb50953d2f3a351142b07a3142c544f9a0bd5216b9c439cb7b714e2056c45 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | alejob/mdanalysis | testsuite/MDAnalysisTests/topology/test_guessers.py | Python | gpl-2.0 | 3,593 | [
"MDAnalysis"
] | 4405f5d5151380751525f89c78cc154c8989295813dbf9fb8fcf50ecc13ecc54 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
This file is part of the web2py Web Framework
Copyrighted by Massimo Di Pierro <mdipierro@cs.depaul.edu>
License: LGPLv3 (http://www.gnu.org/licenses/lgpl.html)
The widget is called from web2py.
"""
import sys
import cStringIO
import time
import thread
import re
impo... | trosa/forca | gluon/widget.py | Python | gpl-2.0 | 30,257 | [
"VisIt"
] | accb307b1bcb5cb23be98cb3f8ca70b8ff6f4b5cc1a93b604d1ba13c754f1cc8 |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import functools
from collections import Mapping, defaultdict
from distutils.version import LooseVersion
from numbers import Number
import sys
import numpy as np
import pandas as pd
from . import ops
from . i... | jhamman/xray | xarray/core/dataset.py | Python | apache-2.0 | 115,414 | [
"NetCDF"
] | 9ba6f3b4383cf27aae87cc060d96d28394530e07f09b336aeb818d61e4ead47f |
# Copyright 2009 Brian Quinlan. All Rights Reserved.
# Licensed to PSF under a Contributor Agreement.
"""Implements ThreadPoolExecutor."""
__author__ = 'Brian Quinlan (brian@sweetapp.com)'
from concurrent.futures.multithreaded import Future
from concurrent.futures.old.executor import Executor
import atexit
import qu... | mikhtonyuk/rxpython | concurrent/executors/thread.py | Python | mit | 4,780 | [
"Brian"
] | f5e2836dbb804ff8c31416228a3e2b957143679498dd70c0addc4afab5540744 |
#!/usr/bin/env python
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import numpy as np
import argparse
import random
import ray
from ray.tune import Trainable, run
from ray.tune.schedulers import PopulationBasedTraining
class PBTBenchmarkExample(Traina... | ujvl/ray-ng | python/ray/tune/examples/pbt_example.py | Python | apache-2.0 | 3,975 | [
"Gaussian"
] | d6d9e775cc7f7d0cbfa1543d0469f78a341c89c8c3644fc8a1b7473e6f71bcc0 |
# Copyright (c) 2012 Google Inc. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
from __future__ import print_function
from compiler.ast import Const
from compiler.ast import Dict
from compiler.ast import Discard
from compiler.ast import List
... | TooTallNate/node-gyp | gyp/pylib/gyp/input.py | Python | mit | 116,306 | [
"VisIt"
] | 2478fa51f970cf05f21c1e6a5c3b3ba8ce452f7bcafb9dd44f516020d8776300 |
../../../../../../../share/pyshared/orca/scripts/toolkits/WebKitGtk/script_utilities.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/scripts/toolkits/WebKitGtk/script_utilities.py | Python | gpl-3.0 | 87 | [
"ORCA"
] | a9bbb797f72f7828fb7ea59ac06bb161678b226aa076298460cedd962a710292 |
"""
MZ - 2021 - Mar - 18
Basic plotting script for Chronostar results. Make a quick plot for
the final or partial results of the fit to see what's going on.
Plot CMD, gx plot and XU and XY plots.
python quickplot.py path/to/final/folder/ path/to/the/input/fits/file/with/stellar/data.fits
"""
import numpy as np
from ... | mikeireland/chronostar | scripts/quickplot.py | Python | mit | 9,117 | [
"Galaxy"
] | 6982b48127e623b63ab5e59f5a67e9bf1c80b90eefa6849e525916ba6fbeb7aa |
#!/usr/bin/python
# -*- coding: utf-8 -*-
dimensions = 1
size1d = 500
GRIDSIZE = [512]
halfSize = [size1d,0.1,0.1]# must be three components, because yade is inherently 3D and uses Vector3r. Remaining components will be used for AABB
dampMarginBandMin = 5
dampMarginBandMax = 100
dampFormulaSmooth = True # ... | cosurgi/trunk | examples/qm/1d-free-propagation-small.py | Python | gpl-2.0 | 5,945 | [
"Gaussian"
] | 8695896d52cef0dbb3a40b4e05507a0121868b8ef66b592fc7ca0701e490d266 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2013 Radim Rehurek <me@radimrehurek.com>
# Licensed under the GNU LGPL v2.1 - http://www.gnu.org/licenses/lgpl.html
"""
Warnings
--------
.. deprecated:: 3.3.0
Use :mod:`gensim.models.word2vec` instead.
Produce word vectors with deep learning via wo... | mattilyra/gensim | gensim/models/deprecated/word2vec.py | Python | lgpl-2.1 | 87,836 | [
"VisIt"
] | 7c829a7b3e16a4931a616f9c6d114024da253cd81b4fc80c4dc5a193bc8a131e |
import numpy
from orbkit import grid
from .tools import meshgrid2
def view_with_mayavi(x,y,z,data,is_vectorfield=False,geo_spec=None,datalabels=None,
iso_min=1e-4,iso_val=0.01,iso_max=10.0,**kwargs):
''' Creates an interactive mayavi dialog showing isosurface plots of the input
data.
Co... | orbkit/orbkit | orbkit/output/mayavi_interface.py | Python | lgpl-3.0 | 6,840 | [
"Mayavi"
] | efc3ae7e204fbc3d6b02cd0b2244068f52c62bc51d19381496eb023983db4dc6 |
#!/usr/bin/env python
#
# controllers/base.py
# TurboHvZ
#
# Copyright (C) 2008 Ross Light
#
# 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
# (... | zombiezen/turbohvz | hvz/controllers/base.py | Python | gpl-3.0 | 8,636 | [
"VisIt"
] | 05693050d61e3c7fb47012c03e14dab41c217ff6d247c8e80f6237c5884bc413 |
# -*- 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) 2010 Andrew I Baznikin
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Ge... | beernarrd/gramps | gramps/plugins/rel/rel_is.py | Python | gpl-2.0 | 9,904 | [
"Brian"
] | fbe7af09da7ae698e36b7e31ddf71c2263491e5fb44b827a2645aec5b3c43461 |
import sys
import os
import os.path
import logging
import argparse
import pysam
import subprocess
from os import path
DEBUG = True
if DEBUG:
inputFile="/scratch/cqs/maureen_gannon_projects/20200131_rnaseq_joseph_mmul10_byTiger_old/star_featurecount/result/GLDPH.bam"
#inputFile="/scratch/cqs/maureen_g... | shengqh/ngsperl | lib/Samtools/getConsensusSequenceSegment.py | Python | apache-2.0 | 3,245 | [
"pysam"
] | 118fba5fa83678a03e8082ebe570c461c5e3af6a31e6041de522e572194592ca |
import sys
import paraview
import paraview.vtk as vtk
import paraview.simple as pvsimple
import math
import time
import os
fEnsemble=open("wavelet.evtp", "w")
fEnsemble.write("YMag,ZMag,\n")
numSteps = 10
currentDir = os.getcwd()
for yMag in (18, 36, 72):
for zMag in (5, 10, 20):
fileNameTime = currentDir ... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/Testing/Scripts/generate-ensemble.py | Python | gpl-3.0 | 1,645 | [
"ParaView",
"VTK"
] | ecfa878f465e5a20137542af1e6d2838974ea1b84ecf00af80a2d43ad847a482 |
# Encoding: utf-8
import os
import sys
import matplotlib.pyplot as plt
import numpy as np
import pymatgen as pmg
import pymatgen.io.nwchem as nwchem
import cage.utils as utils
from cage.core import Cage
"""
Script to extract all the necessary information from a facet energy landscape
analysis.
"""
OUTPUT_FILENAME ... | mbercx/cage | cage/scripts/facetLandscape.py | Python | mit | 3,464 | [
"NWChem",
"pymatgen"
] | 6f3781e8f363e0ca6de95c983bab6b7050cfb52be013ac9e553e30a2757a302e |
from django.conf import settings
from django.contrib.auth import BACKEND_SESSION_KEY, SESSION_KEY, get_user_model
from django.contrib.sessions.backends.db import SessionStore
from .base import FunctionalTest
User = get_user_model()
class MyListsTest(FunctionalTest):
def create_pre_authenticated_session(self,... | fantasycheung/django_learning | functional_tests/test_my_lists.py | Python | mit | 1,177 | [
"VisIt"
] | 034449cb529421ed9eaef586418ad430a66408cd86cb7e676402e8e08b35e4b7 |
# !/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Filename: MPL8.py
# Project: dap
# Author: Brian Cherinka
# Created: Friday, 8th February 2019 2:10:30 pm
# License: BSD 3-clause "New" or "Revised" License
# Copyright (c) 2019 Brian Cherinka
# Last Modified: Friday, 17th May 2019 2:42:07 pm
# Modified By: Brian Cheri... | sdss/marvin | python/marvin/utils/datamodel/dap/MPL8.py | Python | bsd-3-clause | 12,968 | [
"Brian",
"Gaussian"
] | 79634af4ee19f4268b5488958983dbd2b547a34501434092c0de93cec9947b98 |
# -*- coding:utf-8 -*-
from __future__ import (
absolute_import, division, print_function, unicode_literals
)
import imp
import os
import time
from decimal import Decimal
from unittest import skipUnless
import django
import pytest
from django.core.cache import CacheKeyWarning, cache, caches
from django.core.manag... | nickmeharry/django-mysql | tests/testapp/test_cache.py | Python | bsd-3-clause | 49,590 | [
"Brian"
] | 135a60c03ca43b9e3548f7f95157759cc81bd95ba8c54e21456a7b6903630c65 |
import mdtraj as md
import mdtraj.geometry.alignment
import numpy as np
import pytest
import tensorflow as tf
import tftraj.rmsd_op
def test_load():
rmsd = tftraj.rmsd_op.load()
assert rmsd is not None
def test_rank_error():
rmsd = tftraj.rmsd_op.load()
with pytest.raises(ValueError):
rmsd.... | mdtraj/tftraj | tests/test_rmsd_op.py | Python | mit | 1,996 | [
"MDTraj"
] | 511afea9e1eb0d18ebb7b6d80e6fb2108a5763594635e1641cf22e2bebd67cff |
#
# Copyright (C) 2013-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | psci2195/espresso-ffans | testsuite/python/coulomb_cloud_wall_duplicated.py | Python | gpl-3.0 | 3,890 | [
"ESPResSo"
] | c7a6f3984ff0bae646e796d6dbe97b05a7503f66a94fc148f1f75edbea06a0d1 |
import unittest
import numpy.testing as np_test
import pandas as pd
import numpy as np
from pgmpy.factors.continuous import LinearGaussianCPD
class TestLGCPD(unittest.TestCase):
# @unittest.skip("TODO")
def test_class_init(self):
mu = np.array([7, 13])
sigma = np.array([[4, 3], [3, 6]])
... | pgmpy/pgmpy | pgmpy/tests/test_factors/test_continuous/test_Linear_Gaussian_CPD.py | Python | mit | 3,420 | [
"Gaussian"
] | 208f3eb0494ff3105cd21592c6262ae0605a9162cc040a866455cc227e2944bb |
__author__ = 'Xiang-Guo Li'
__copyright__ = 'Copyright 2018, The Materials Virtual Lab'
__email__ = 'xil110@eng.ucsd.edu'
__date__ = '07/30/18'
from pymatgen.util.testing import PymatgenTest
import os
import unittest
import numpy as np
import warnings
from pymatgen import Structure
from pymatgen.analysis.gb.grain impo... | gVallverdu/pymatgen | pymatgen/analysis/gb/tests/test_grain.py | Python | mit | 19,404 | [
"pymatgen"
] | 961614b00d15f38bd1617b1b809e6a2450a8f6c52c2721adf1f631e3ef9e09f7 |
from blaze.expr.graph import IntNode, FloatNode
from blaze.expr.visitor import BasicGraphVisitor, MroVisitor, GraphVisitor
from blaze.expr import visitor
#------------------------------------------------------------------------
# Sample Graph
#------------------------------------------------------------------------
a... | davidcoallier/blaze | blaze/tests/test_visitor.py | Python | bsd-2-clause | 2,931 | [
"VisIt"
] | 8c315616fe915cc65345c2e07ff3c657f98a6e8efa1856a4f8691de12a9d9200 |
#!/usr/bin/python
#
# 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) 2015-2018 Hans Hoogenboom, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any... | est77/appleseed | scripts/oslextractmeta.py | Python | mit | 17,079 | [
"VisIt"
] | fdfa6b3cc8d4cec184936af6f036fe664dadaaf264e53155e885bb9766dc0aad |
import os
from uuid import uuid4
from pulsar import __version__ as pulsar_version
from .util import filter_destination_params
REMOTE_SYSTEM_PROPERTY_PREFIX = "remote_property_"
def build(client, destination_args):
""" Build a SetupHandler object for client from destination parameters.
"""
# Have define... | galaxyproject/pulsar | pulsar/client/setup_handler.py | Python | apache-2.0 | 4,388 | [
"Galaxy"
] | 57c849a6cb3498d564d6b231e1b5870bb7ba3c26d513449cccbd5690deb2729a |
import re
from datetime import datetime
import hashlib
import time
import stat
from urllib.parse import urlencode
from io import BytesIO
import pycurl
import ftputil
import humanfriendly
from biomaj_core.utils import Utils
from biomaj_core.config import BiomajConfig
from biomaj_download.download.interface import Do... | genouest/biomaj-download | biomaj_download/download/curl.py | Python | agpl-3.0 | 22,458 | [
"BLAST"
] | 28a864983502d66f0bcb1f8964c005a1b7a176653058f75685ea065215250fa6 |
#! /usr/bin/env python3
# -*- coding: utf-8 -*-
# demo.py --- Demonstration program and cheap test suite for pythondialog
#
# Copyright (C) 2002-2010, 2013-2016 Florent Rougon
# Copyright (C) 2000 Robb Shecter, Sultanbek Tezadov
#
# This program is in the public domain.
"""Demonstration program for pythondialog.
T... | Morphux/installer | pythondialog/examples/with-autowidgetsize/demo.py | Python | apache-2.0 | 72,389 | [
"Galaxy"
] | 8958838993151b21f685fa029cde323abc533f51426942431e75410efd63a4c9 |
#!/usr/bin/python2.7
# encoding: utf-8
#Libs import
from __future__ import division
import numpy as np
import sys
from utide import ut_solv, ut_reconstr
#TR comment: 2 alternatives
#import netCDF4 as nc
from scipy.io import netcdf
from scipy.io import savemat
from scipy.io import loadmat
from pydap.client import open_... | pwcazenave/PySeidon | pyseidon/fvcomClass/fvcomClass.py | Python | agpl-3.0 | 15,046 | [
"NetCDF"
] | 8afccab4c7a7a41ea3a9f2cf88859d883eebb34de59ad4eadd63beb8282ad6e5 |
#!/usr/bin/env python3
"""
A script that correctly accounts for nondefault values of AMBER's SCEE and
SCNB. Originally, this is needed do to account for GLYCAM06's usage of
SCEE=SCNB=1.0. As of ~Amber11 (ca. 2010), SCEE and SCNB can be defined in the
comments section of the dihedral parameters within AMBER force-field... | austenb28/acpype_fix | patch_acpype_14scale.py | Python | gpl-3.0 | 7,536 | [
"Amber",
"Gromacs"
] | 0019e38835e4456b4c406118869dc8f3f3133f991a3a91b51534b45e0d4ed969 |
# Autodetecting setup.py script for building the Python extensions
import argparse
import importlib._bootstrap
import importlib.machinery
import importlib.util
import os
import re
import sys
import sysconfig
from glob import glob
from distutils import log
from distutils.command.build_ext import build_ext
from distuti... | batermj/algorithm-challenger | code-analysis/programming_anguage/python/source_codes/Python3.8.0/Python-3.8.0/setup.py | Python | apache-2.0 | 104,153 | [
"VisIt"
] | 00956d3f625b6e0a80c0f6c268be7257df07cde98c9a738aa238f8720b4d11eb |
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