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# (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... | Jozhogg/iris | lib/iris/io/__init__.py | Python | lgpl-3.0 | 13,488 | [
"NetCDF"
] | 19155faa67564129e9ebe6499ab205c61ae24b44a73e751e26c157632ecf4bf3 |
#!/usr/bin/env python
# This example shows how to use decimation to reduce a polygonal
# mesh. We also use mesh smoothing and generate surface normals to
# give a pleasing result.
import vtk
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# We start by reading some data that was originally ... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Examples/VisualizationAlgorithms/Python/deciFran.py | Python | gpl-3.0 | 1,662 | [
"VTK"
] | be1f561a934c8b1a93cea4872f969f93391facb87f6596a3e074fc25e74c1dce |
import urllib
import bleach
import ssl
import socket
import re
import datetime, time
from OpenSSL import SSL
from django.conf import settings
####################################################
##### URL CHECK ####################################
# returns True if url is checked to be non-malicious, else... | haoqili/MozSecWorld | apps/msw/utils.py | Python | bsd-3-clause | 10,383 | [
"VisIt"
] | 7137ce24ec96153bad6da016e89ec0e1cca66738d4fc5341bd0a42dd80861f33 |
"""Module to read and write atoms in cif file format.
See http://www.iucr.org/resources/cif/spec/version1.1/cifsyntax for a
description of the file format. STAR extensions as save frames,
global blocks, nested loops and multi-data values are not supported.
"""
import shlex
import re
import numpy as np
from ase.par... | slabanja/ase | ase/io/cif.py | Python | gpl-2.0 | 9,777 | [
"ASE",
"CRYSTAL"
] | 47fe31e17597e4852bf77c689dfb9382dff41ef2f5480e1bf35182b40bd77abe |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# create pipeline
#
pl3d = vtk.vtkMultiBlockPLOT3DReader()
pl3d.SetXYZFileName(VTK_DATA_ROOT + "/Data/combxyz.bin")
pl3d.SetQFileName(VTK_DATA_ROOT + "/Data/combq.bin")
pl3... | hlzz/dotfiles | graphics/VTK-7.0.0/Filters/General/Testing/Python/clipComb.py | Python | bsd-3-clause | 2,190 | [
"VTK"
] | ea851088c16ca64d0346da236f6f9aff75a7a54c0a784ee39f44e095258899d9 |
##!/usr/bin/env python
#! -*- coding: utf-8 -*-
### Copyright Paul Brian 2013
# This program is licensed, without under the terms of the
# GNU General Public License version 2 (or later). Please see
# LICENSE.txt for details
###
import os
import datetime
import math # wow!
import json
class SaffLibError(Except... | lifeisstillgood/saffrondigital | safflib.py | Python | gpl-2.0 | 4,892 | [
"Brian"
] | 1943d0db5ea65354c2f7f2eaa5e973cbc7a1143726c7ca4f44630bd8c6508467 |
from DIRAC.TransformationSystem.Client.TransformationClient import TransformationClient
from WebAppDIRAC.Lib.WebHandler import WebHandler, WErr, asyncGen
from DIRAC import gConfig, gLogger
from DIRAC.Core.Utilities import Time
import json
class TransformationMonitorHandler( WebHandler ):
AUTH_PROPS = "authenticated... | zmathe/WebAppDIRAC | WebApp/handler/TransformationMonitorHandler.py | Python | gpl-3.0 | 21,480 | [
"DIRAC"
] | 1ddd4d745c084ca2fba685b4db40a49bc5ba8ce0c235bf85bddb898e7618892d |
import pycalphad
dbf = pycalphad.Database('steel_database_fix.tdb')
| richardotis/pycalphad-sandbox | db-perf.py | Python | mit | 70 | [
"pycalphad"
] | 9269412087bf6c3088b2a0cc88a7c35d5d137270f53e9d4766f45c60b08b6ddc |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Gary Burton
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either v... | sam-m888/gramps | gramps/gen/plug/menu/_person.py | Python | gpl-2.0 | 1,787 | [
"Brian"
] | 4535d7621086e1ee9cfd436f89f21919feb86cb6c253b5b7155485b7fe0e82d2 |
import pytest
from tests.common.common import ADMIN_PASSWORD
# TODO: Find a way to test the sudo mode behaviour
@pytest.mark.xfail
def test_sudo_mode_required(admin_browser_once):
b = admin_browser_once
b.visit('/sys/useradmin/')
assert b.path == '/sys/sudo/', (
'when viewing sysadmin-only pages f... | saukrIppl/seahub | tests/ui/test_sudo_mode.py | Python | apache-2.0 | 1,420 | [
"VisIt"
] | 40a8fbb08f45d5f4635edeef12bacd054d9773efe410ac6bc5fc7966fbf8abff |
# -*- coding: utf-8 -*-
"""
sphinx.quickstart
~~~~~~~~~~~~~~~~~
Quickly setup documentation source to work with Sphinx.
:copyright: Copyright 2007-2015 by the Sphinx team, see AUTHORS.
:license: BSD, see LICENSE for details.
"""
from __future__ import print_function
import re
import os
import sys... | lucywyman/slides-ii | v/lib/python2.7/site-packages/sphinx/quickstart.py | Python | apache-2.0 | 51,733 | [
"VisIt"
] | e566c86fe755f4f8c782e6b7b3017f57e040ac768b82836e10d10fb257f56b8b |
# Copyright 2020 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 agreed to in writing,... | google/differential-privacy | python/dp_accounting/privacy_loss_distribution_test.py | Python | apache-2.0 | 72,571 | [
"Gaussian"
] | 9a1649c2c8f3053b5405887353ee2f3ebc5fd3cd301583c43d3fe34bacd52e38 |
"""
BenchExec is a framework for reliable benchmarking.
This file is part of BenchExec.
Copyright (C) 2007-2015 Dirk Beyer
All rights reserved.
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
... | ahealy19/F-IDE-2016 | benchexec/tools/blast.py | Python | apache-2.0 | 2,640 | [
"BLAST"
] | 123d7315af13ba42e994826f6996ab8600a71890f5286bf2a76697fb08078d84 |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2007, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | zenoss/Community-Zenpacks | ZenPacks.AndreaConsadori.Colubris/ZenPacks/AndreaConsadori/Colubris/modeler/plugins/ColubrisDeviceMap.py | Python | gpl-2.0 | 1,365 | [
"VisIt"
] | 2b8b764439a0c8cf3a5bc5256f91fab15f106c3780edb8e241cd4da692fb571c |
"""
Contains functionality needed in every web interface
"""
import os, time, logging
# Pieces of Galaxy to make global in every controller
from galaxy import config, tools, web, model, util
from galaxy.web import error, form, url_for
from galaxy.model.orm import *
from Cheetah.Template import Template
log = loggin... | volpino/Yeps-EURAC | lib/galaxy/web/base/controller.py | Python | mit | 1,501 | [
"Galaxy"
] | 7029db5d9aa370b3adfa87687c54f1eaea07acfc55d26127afea16c871777f7c |
from django.apps import apps as django_apps
class MetadataGetter:
"""A class that gets a filtered queryset of metadata --
`metadata_objects`.
"""
metadata_model = None
def __init__(self, appointment=None, subject_identifier=None, visit_code=None,
visit_code_sequence=None):
... | botswana-harvard/edc-entry | edc_metadata/metadata/metadata_getter.py | Python | gpl-2.0 | 1,618 | [
"VisIt"
] | 95d599f6da6d25da90a562a2cc7ea939bd169de519489736d8237293374f51dd |
from __future__ import print_function, division, unicode_literals
import os
import matplotlib as mpl
mpl.use('Agg')
import matplotlib.pyplot as plt
from matplotlib.font_manager import FontProperties
import numpy as np
from scipy.spatial.distance import euclidean
from pymatgen.core.structure import Structure
from p... | joshgabriel/MPInterfaces | mpinterfaces/mat2d/electronic_structure/analysis.py | Python | mit | 32,250 | [
"DIRAC",
"VASP",
"pymatgen"
] | 80fa4fc00632da87ba8848abf0af7820539ee2b3395f67d47ef024ca7543cb3a |
import sys
import re
cell_params = []
with open(sys.argv[1]) as f:
lines = f.readlines()
Bohr2Ang = 0.52917721092
read = False
atompos = []
for l in lines:
if re.search("bravais-lattice index\s+=\s+(\d+)", l):
ibrav = int(l.split("=")[-1])
if re.search("celldm\(1\)=\s+([\d\.]+)\s", l):
m ... | adengz/nano266 | labs/lab4/convert_to_cif.py | Python | bsd-3-clause | 1,828 | [
"CRYSTAL"
] | 497f600d2fd90711f9bcd20fac8239a9e01e71b488fcf61d5b1489f66485448e |
from math import sqrt,log
import numpy as np
from matplotlib import pyplot
from spm1d import rft1d
eps = np.finfo(float).eps
def here_cca_single_node(y, x):
N = y.shape[0]
X,Y = np.matrix(x.T).T, np.matrix(y)
Z = np.matrix(np.ones(N)).T
Rz = np.eye(N) - Z*np.linalg.in... | 0todd0000/spm1d | spm1d/rft1d/examples/val_broken_4_X2.py | Python | gpl-3.0 | 2,813 | [
"Gaussian"
] | a0c6e59dcf775483b495fcc51ae0f347eefcb36a83d3c3031f3a2cf536c85d57 |
# -*- coding: utf-8 -*-
#
# Moonstone is platform for processing of medical images (DICOM).
# Copyright (C) 2009-2011 by Neppo Tecnologia da Informação LTDA
# and Aevum Softwares LTDA
#
# This file is part of Moonstone.
#
# Moonstone is free software: you can redistribute it and/or modify
# it under the terms of the GN... | aevum/moonstone | src/moonstone/ilsa/plugins/angle/protractor.py | Python | lgpl-3.0 | 4,651 | [
"VTK"
] | cb2ff2960da674b530ff230bf3c2d096badca02396a5059cac0e41a3db5d0985 |
import ocl
import camvtk
import time
import vtk
import datetime
import math
def DrawLoops(myscreen, loops):
# draw the loops
nloop=0
for lop in loops:
n = 0
N = len(lop)
first_point=ocl.Point(-1,-1,5)
previous=ocl.Point(-1,-1,5)
for p in lop:
if n==0: # d... | AlanZatarain/opencamlib | scripts/zigzag_1.py | Python | gpl-3.0 | 3,358 | [
"VTK"
] | 0ed4b2a285d46f2d4cb777d9835b7f7602ecf4788122833755684f232812cf65 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/pbc/scf/__init__.py | Python | apache-2.0 | 2,623 | [
"PySCF"
] | ca46d40628ab248ab677f312d2183c38a37b2d4d6f4763add316b4e35c196619 |
# Copyright (C) 2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later versio... | espressomd/espresso | testsuite/scripts/samples/test_lj_liquid.py | Python | gpl-3.0 | 982 | [
"ESPResSo"
] | dcc56f2599f91abee94c8ceb83b55f6b125a39044e2fdf07bfcd9158461a9b1a |
"""ropemacs, an emacs mode for using rope refactoring library"""
import sys
from os.path import join
import ropemode.decorators
import ropemode.environment
import ropemode.interface
from Pymacs import lisp
from rope.base import utils
class LispUtils(ropemode.environment.Environment):
def ask(self, prompt, defau... | python-rope/ropemacs | ropemacs/__init__.py | Python | gpl-2.0 | 24,889 | [
"VisIt"
] | 2cd7565c7297537e6ebae1e79de36ed3def190f1389aa9541a0373c62ea909a8 |
# This is the code for experiments performed on the Toy dataset for DeLiGAN model. Minor adjustments
# in the code as suggested in the comments can be done to test GAN and other baseline models such as
# GAN++, Nx-GAN, MoE-GAN, Ensemble-GAN. Corresponding details about these experiments can be found
# in section 5.2... | val-iisc/deligan | src/Toy/dg_toy.py | Python | mit | 7,387 | [
"MOE"
] | 03cea5f0f9fad66de62307c2ee7457f3d877ccc693ab6e6ee2ec617ac51adae3 |
#!/usr/bin/env python
"""
Michael Hirsch
Procedure:
0) ingest simulation parameters from XLS file, sanity check, load data
1) Make an auroral phantom (if not real data, a Simulation, and optionally for a first guess for reconstruction)
2) create projection matrix
3) fit differential number flux to reconstructed ... | scienceopen/histfeas | histfeas/main_hist.py | Python | gpl-3.0 | 4,816 | [
"Gaussian"
] | fb8029f2bb9e35be5aac5579d2ac85c3528b9fec53b6d65b5c0d795f8eb4026e |
#!/usr/bin/env python
# -*- encoding: utf-8 -*-
# CREATED:2015-02-16 13:10:05 by Brian McFee <brian.mcfee@nyu.edu>
'''Regression tests on metlab features'''
from __future__ import print_function
import warnings
# Disable cache
import os
try:
os.environ.pop('LIBROSA_CACHE_DIR')
except:
pass
import numpy as np
... | carlthome/librosa | tests/test_met_features.py | Python | isc | 4,589 | [
"Brian"
] | 1f631e78a4a2a40d0e57e902752d5e612755940bae88da2b798a21efde70b4b2 |
#!/usr/bin/env python
# File created on 20 Feb 2013
from __future__ import division
__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["Greg Caporaso", "Kyle Bittinger", "Justin Kuczynski",
"Jai Ram Rideout"]
__license__ = "GPL"
__version__ = "1.9.1-dev"
__ma... | adamrp/qiime | qiime/workflow/upstream.py | Python | gpl-2.0 | 19,937 | [
"BLAST"
] | 6fd6ab84a1560cd370cbd6dcb63b3b53b2de18a5496331572e79a2ab12128936 |
#!/usr/bin/python
# checker
# Make sure the critical EcoSpec components keep running
import datetime
import ecospec
import pifacedigitalio
import piface
import subprocess
import sys
import time
import traceback
def log(message):
logfile = open('/var/log/checker/checker.log' ,'a', 0)
logfile.write(str(datetime.dat... | donaldbales/ecospec | checker.py | Python | gpl-3.0 | 4,917 | [
"xTB"
] | 1e46cd3cd42cf1739b71c0aa54966ed812401be1745feac897c186778afce662 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
sphere = vtk.vtkSphereSource()
# make two copies of the shape and distort them a little
transform1 = vtk.vtkTransform()
transform1.Translate(0.2, 0.1, 0.3)
transform1.Scale(1.3, 1.1,... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Filters/Hybrid/Testing/Python/TestProcrustes.py | Python | gpl-3.0 | 4,422 | [
"VTK"
] | c06a74b996720816c86fe42fa8d2cf12473ccb26314ae968390f82a060b3702c |
"""
==========================================================
Comparison of kernel ridge and Gaussian process regression
==========================================================
Both kernel ridge regression (KRR) and Gaussian process regression (GPR) learn
a target function by employing internally the "kernel trick... | jmschrei/scikit-learn | examples/gaussian_process/plot_compare_gpr_krr.py | Python | bsd-3-clause | 5,187 | [
"Gaussian"
] | 578b7b4cfc7a09d4b7f6dbd13c3bc0318c5b506235c032c9311898ead85ee318 |
#!/usr/bin/env python
# Copyright 2015 The Kubernetes Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appli... | hartsock/kubernetes | cluster/juju/layers/kubernetes-worker/reactive/kubernetes_worker.py | Python | apache-2.0 | 37,936 | [
"CDK"
] | 16cbd481a1973873838f22d4e28d99db1eef951a1bb1b471c6a89fb47d64da47 |
#
# Copyright (C) 2021 Carmen Esposito
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
from rdkit import Chem
from rdkit.Chem import rdFMCS
impor... | bp-kelley/rdkit | Contrib/CalcLigRMSD/CalcLigRMSD.py | Python | bsd-3-clause | 3,483 | [
"CRYSTAL",
"RDKit"
] | e6cf48fc41da6425aa4d6167112881eb8b4d972fe4101ee3fcc08af7b80f8c09 |
#!/usr/bin/env python
"""
Delete a given production
Usage:
dirac-prod-delete prodID
Arguments:
prodID: Production ID (mandatory)
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import DIRAC
from DIRAC.Core.Base import Script
fr... | yujikato/DIRAC | src/DIRAC/ProductionSystem/scripts/dirac_prod_delete.py | Python | gpl-3.0 | 927 | [
"DIRAC"
] | 5f564ec36ced42b898692a065ca94a9dedf7cf017526c95181ffa05510e44234 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | Stargrazer82301/CAAPR | CAAPR/CAAPR_AstroMagic/PTS/pts/magic/sources/extractor.py | Python | mit | 18,243 | [
"Galaxy"
] | 96a7d15230e18a4a95d2ba57fb24baa76b987bb7955cf423c0894de9312f4aeb |
import utils,os,zf_grid
import numpy as np
# more modules are loaded in astro_filter.__init__()
# they are split up this way so that astro_filter_light doesn't have to import those modules
__ver__ = '2.0'
class astro_filter(object):
""" filter = ezgal.astro_filter( filename, units='a', cosmology=None )
Loads a filt... | drdangersimon/EZgal | ezgal/src/astro_filter.py | Python | gpl-2.0 | 23,114 | [
"Gaussian"
] | 0b5ef94e1c3504ebefde0ffc7e57a85facc3d42751ea48a479540e6468b7c1d0 |
# Copyright 2014, Brian Coca <bcoca@ansible.com>
# Copyright 2017, Ken Celenza <ken@networktocode.com>
# Copyright 2017, Jason Edelman <jason@networktocode.com>
# Copyright 2017, Ansible Project
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of ... | le9i0nx/ansible | lib/ansible/plugins/filter/mathstuff.py | Python | gpl-3.0 | 6,492 | [
"Brian"
] | 183d9fae9fee56e99a2d85de36f1cce356697ca61ca69a6d14670f1a23f3b560 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2005 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundati... | tiagocardosos/stoq | stoqlib/domain/test/test_domain.py | Python | gpl-2.0 | 10,274 | [
"VisIt"
] | bd91ffb7f75ad8c763f6387555f554df3a31430db17c767a7e22cdade84f5d86 |
""" Base Storage Class provides the base interface for all storage plug-ins
exists()
These are the methods for manipulating files:
isFile()
getFile()
putFile()
removeFile()
getFileMetadata()
getFileSize()
prestageFile()
getTransportURL()
These are the methods for... | ic-hep/DIRAC | src/DIRAC/Resources/Storage/StorageBase.py | Python | gpl-3.0 | 16,613 | [
"DIRAC"
] | 012b084a27cabf96e7981a9730908d0d63503faa506e9b7eddf176b8a3a9ec6b |
# Copyright (C) 2008-2011 Canonical Ltd
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distribute... | levibostian/launchpad-2-github | bzr-fastimport/build/lib.linux-x86_64-2.7/bzrlib/plugins/fastimport/__init__.py | Python | mit | 3,156 | [
"VisIt"
] | 654a9b10e6bbfa7cb12fedc329bf5ba1e7baf373987f495157c4760aa81022f4 |
import numpy as np
from mushroom_rl.algorithms.value.td import TD
from mushroom_rl.utils.table import Table
class WeightedQLearning(TD):
"""
Weighted Q-Learning algorithm.
"Estimating the Maximum Expected Value through Gaussian Approximation".
D'Eramo C. et. al.. 2016.
"""
def _... | carloderamo/mushroom | mushroom_rl/algorithms/value/td/weighted_q_learning.py | Python | mit | 3,521 | [
"Gaussian"
] | 45ec5a282bb38be0b154d1f8882089cf1bbf90fc283b0ccd5752b2ccdd2cd79a |
from __future__ import print_function, division
#
# Author: Henrique Pereira Coutada Miranda
# Check the convergence of the coulomb cutoff for a BSE calculation using yambo
#
from yambopy import *
from qepy import *
from schedulerpy import *
from functools import partial
import multiprocessing
import argparse
import sy... | henriquemiranda/yambo-py | tutorial/bn/bse_cutoff.py | Python | bsd-3-clause | 7,455 | [
"Quantum ESPRESSO",
"Yambo"
] | e2b57e55dc11d0f7af0c1addc5ea93ec59773a9cdba90b01ad3d326f44793e7b |
import os
from lutris.runners.runner import Runner
from lutris.util.libretro import RetroConfig
from lutris.util import system
from lutris.util.log import logger
from lutris import settings
# List of supported libretro cores
# First element is the human readable name for the core with the platform's short name
# Secon... | daniel-j/lutris | lutris/runners/libretro.py | Python | gpl-3.0 | 13,972 | [
"Jaguar"
] | 8685d899c2c0816bebb92b65e9f74ee10886576f223c7ef4eda495fee7eb2c27 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | krafczyk/spack | var/spack/repos/builtin/packages/r-quantro/package.py | Python | lgpl-2.1 | 2,304 | [
"Bioconductor"
] | 9c194342f462464781ba10b1bccecdfed4266ecb718e8b96b360ec104773e77a |
# -*- 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-compute | tests/unit/gapic/compute_v1/test_region_instance_group_managers.py | Python | apache-2.0 | 293,453 | [
"Octopus"
] | 7bebe0b3f5dd7ce41690d826a2c701fd3afb6a43fef20b5e98ed78215fdbbe59 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | skosukhin/spack | var/spack/repos/builtin/packages/macsio/package.py | Python | lgpl-2.1 | 5,041 | [
"NetCDF"
] | 3f36431aa97dccd4f8df0d58e90f7802c58bc4504da03dd4df9ec2bcc9680b3e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright 2014-2018 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/li... | sunqm/pyscf | pyscf/dft/xcfun.py | Python | apache-2.0 | 35,884 | [
"Gaussian",
"PySCF"
] | 3945713f862be4a88bd13f5d4402b019f42e4cc0e76af65a5dbcff079d246b2c |
"""
Updated by Lin Xiong Jul-21, 2017
Modified by Lin Xiong Oct-30, 2017 (add SE building block)
Thanks to Cher Keng Heng
"""
import argparse,logging,os
import mxnet as mx
from symbol_se_inception_v4 import get_symbol
logger = logging.getLogger()
logger.setLevel(logging.INFO)
formatter = logging.Formatt... | bruinxiong/SENet.mxnet | train_se_inception_v4.py | Python | apache-2.0 | 9,167 | [
"Gaussian"
] | 95900387a521118d0291114bf1c5d295996f04841109b396d88274355f8b6fac |
########################################################################
# File: StorageElementHandler.py
########################################################################
"""
:mod: StorageElementHandler
.. module: StorageElementHandler
:synopsis: StorageElementHandler is the implementation of a simple Storag... | fstagni/DIRAC | DataManagementSystem/Service/StorageElementHandler.py | Python | gpl-3.0 | 17,902 | [
"DIRAC"
] | d2ac765abe481438b8ecddf9802e61bf30ae9d59fcbda1fc6f67e7df905549da |
#
# Copyright (C) 2013,2014 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... | Smiljanic/espresso | samples/python/lbf.py | Python | gpl-3.0 | 2,020 | [
"ESPResSo"
] | fdcbb4132dec110d74147309ab6bb06097c66418a64a2d24126cc8d5ddeaad30 |
from ..libtcod import libtcod
black = libtcod.black
darkest_grey = libtcod.darkest_grey
darker_grey = libtcod.darker_grey
dark_grey = libtcod.dark_grey
grey = libtcod.grey
light_grey = libtcod.light_grey
lighter_grey = libtcod.lighter_grey
lightest_grey = libtcod.lightest_grey
darkest_gray = libtcod.darkest_gray
darke... | v4nz666/7drl2017 | RoguePy/UI/Colors.py | Python | gpl-3.0 | 7,033 | [
"Amber"
] | 216c4ee3a217e12d6ae7422c7be9135c1610a6ddb71a374120a13ded8aa8015e |
from datetime import datetime
from app.data import CRUDMixin, db
class Experiment(CRUDMixin, db.Model):
id = db.Column(db.Integer, primary_key=True)
hardware = db.Column(db.Text)
t_stamp = db.Column(db.DateTime)
label = db.Column(db.Text)
sensors = db.relationship('Sensor', backref='experiment',... | ChristopherGS/sensor_readings | app/sensors/models.py | Python | bsd-3-clause | 3,951 | [
"VisIt"
] | e6c5e22a8b7de608a6fbdc6e26d38944121ad1d896c83f42f94b0a0787d9e6d8 |
"""
Randomizes a subhalo galaxy position (RA and DEC)
:Author: Sami-Matias Niemi
:contact: sammy@sammyniemi.com
"""
import matplotlib
matplotlib.use('PDF')
matplotlib.rc('text', usetex=True)
matplotlib.rcParams['font.size'] = 11
matplotlib.rc('xtick', labelsize=12)
matplotlib.rc('axes', linewidth=1.1)
matplotlib.rcPar... | sniemi/SamPy | bolshoi/randomizeSubhaloPosition.py | Python | bsd-2-clause | 9,414 | [
"Galaxy"
] | 7165ab190aa29a63fa04f6d7d158e8d333e8044aee4cd8ccad3f3de7600b15b4 |
# Copyright (c) 2003-2013 LOGILAB S.A. (Paris, FRANCE).
#
# This program is free software; you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
# Foundation; either version 2 of the License, or (at your option) any later
# version.
#
# This progr... | lukaszpiotr/pylama_with_gjslint | pylama/checkers/pylint/checkers/format.py | Python | lgpl-3.0 | 16,279 | [
"VisIt"
] | 924796e9d7b465b16d4ab15c09edba3186c2ebb91a2bc3ce5e7274b7ca822dbf |
"""
Distributions
-------------
A widget for plotting attribute distributions.
"""
from math import sqrt
import sys
import collections
from xml.sax.saxutils import escape
from PyQt4 import QtGui, QtCore
from PyQt4.QtCore import Qt
import numpy
import pyqtgraph as pg
import Orange.data
from Orange.statistics import ... | hugobuddel/orange3 | Orange/widgets/visualize/owdistributions.py | Python | gpl-3.0 | 24,607 | [
"Gaussian"
] | e4f793196f80abe9e792e1c3cb49492726333aa17b73fa501470c000295a3afb |
# This file is part of EAP.
#
# EAP 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 later version.
#
# EAP is distributed in ... | vhavlena/appreal | netbench/pattern_match/bin/library/eap/gp.py | Python | gpl-2.0 | 12,769 | [
"ADF"
] | caf520bba63a5bb0bd62fa997d209334ce243867b097aa2369eee2ad640054e9 |
##############################################################################
# adaptiveMD: A Python Framework to Run Adaptive Molecular Dynamics (MD)
# Simulations on HPC Resources
# Copyright 2017 FU Berlin and the Authors
#
# Authors: Jan-Hendrik Prinz
# Contributors:
#
# `adaptiveMD` is free software: ... | thempel/adaptivemd | adaptivemd/misc/archive.py | Python | lgpl-2.1 | 2,560 | [
"MDTraj"
] | 4540ec76fafee5a20f141ecb06c0a095646a5b5e7e9696f63dbbdf0c32b66516 |
#
# 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 us... | rangadi/beam | sdks/python/apache_beam/pipeline_test.py | Python | apache-2.0 | 22,449 | [
"VisIt"
] | 4e1917c3304127431b30f7d6e7addb1f17a31676df34884a52707cabcfdef2f5 |
#!/usr/bin/env python
from setuptools import setup, find_packages
setup(name="bipy",
version="0.1.0",
author="Rory Kirchner",
author_email="rory.kirchner@gmail.com",
description="Simple analysis pipelines",
url="https://github.com/roryk/bipy",
license="MIT",
namespace_packages... | roryk/bipy | setup.py | Python | mit | 898 | [
"Biopython",
"HTSeq",
"pysam"
] | 6ff122e2ad8cc88a1888a8a2d4ba59a93064e345a31d91443927af6219a4cf8b |
"""Conventinal and generalized regular grid routines."""
# Copyright (C) 2014 Atsushi Togo
# All rights reserved.
#
# This file is part of phonopy.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# * Redistribution... | atztogo/phonopy | phonopy/structure/grid_points.py | Python | bsd-3-clause | 24,272 | [
"VASP",
"phonopy"
] | 329fb735711989c81f5fd697b3e221674fc5fd5628034c717738b620e4f985eb |
# -*- coding: utf-8 -*-
import random
INSTANCE_NAME_ADJECTIVES = [
'autumn', 'hidden', 'bitter', 'misty', 'silent', 'empty', 'dry', 'dark',
'summer', 'icy', 'delicate', 'quiet', 'white', 'cool', 'spring', 'winter',
'patient', 'twilight', 'dawn', 'crimson', 'wispy', 'weathered', 'blue',
'billowing', 'br... | Syncano/syncano-cli | syncano_cli/init/helpers.py | Python | mit | 1,601 | [
"Firefly"
] | faafcd1ce476d98dab9ebb703efcf9fade4eee3e9acb89646e3148845e913b70 |
"""Create genome index for BWA-MEM2 aligner."""
import shutil
from pathlib import Path
from plumbum import TEE
from resolwe.process import Cmd, DataField, DirField, FileField, Process, StringField
class BWAMEM2Index(Process):
"""Create BWA-MEM2 genome index."""
slug = "bwamem2-index"
process_type = "da... | genialis/resolwe-bio | resolwe_bio/processes/alignment/bwamem2_index.py | Python | apache-2.0 | 2,382 | [
"BWA"
] | 8574f765823294b40b1bee702cdca38fb3e279f976a732c0a3f3cd873b640b11 |
from numpy.testing import (assert_equal, assert_raises, assert_almost_equal,
assert_array_equal, raises)
import numpy as np
import os
import MDAnalysis as mda
from MDAnalysisTests.datafiles import AUX_XVG, XVG_BAD_NCOL, XVG_BZ2
from MDAnalysisTests.auxiliary.base import (BaseAuxReaderTest,... | alejob/mdanalysis | testsuite/MDAnalysisTests/auxiliary/test_xvg.py | Python | gpl-2.0 | 3,264 | [
"MDAnalysis"
] | 12e67ed0043b2c63ca9f0736ef6eaf19e52e20ce14138b2251f01fae14d57a8f |
'''
Created on Feb 6, 2014
@author: marko
'''
import os
import sys
import time
import unittest
import ConfigParser
test = os.path.dirname(os.path.realpath(__file__))
sys.path.append(os.path.join(test, '..', 'plugin'))
MOVIE_PATH = os.path.join(test, 'moviefiles')
from seekers import SubtitlesDownloadError, Subtitle... | mx3L/subssupport | test/test_xbmc_subtitle.py | Python | gpl-2.0 | 15,506 | [
"VisIt"
] | ac89d6c2cf00d67ffcdff6cde533ccedfcbeb16eba4e67445bab467fe3629ec4 |
import datetime
import re
import smtplib
import time
import urllib
from typing import Any, List, Optional, Sequence
from unittest.mock import MagicMock, patch
from urllib.parse import urlencode
import orjson
from django.conf import settings
from django.contrib.auth.views import INTERNAL_RESET_URL_TOKEN
from django.con... | kou/zulip | zerver/tests/test_signup.py | Python | apache-2.0 | 204,294 | [
"VisIt"
] | 62402b1db1ab0346d95714602ee9f2c9d39f0168030359afd795b1c40d5961dc |
"""Simplify adding markup to a piece of text."""
import warnings
warnings.warn("""\
Bio.MarkupEditor is deprecated.
If you use the code in Bio.MarkupEditor, Please get in touch on
the Biopython mailing lists to prevent permanent removal of this
module.""",
DeprecationWarning)
from xml.sax import saxu... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/MarkupEditor.py | Python | apache-2.0 | 3,500 | [
"Biopython"
] | 28b6cbeb3d8b81d526e27f38f8c70c873150203cccba1cde89e5cbc8da53c6da |
# FIXME: send fsgs as parameter to ValueConfigLoader instead
import json
import os
from typing import Dict, List, Mapping, Optional, Set, Tuple
from typing_extensions import TypedDict
from fsbc.paths import Paths
from fsgamesys.amiga import whdload
from fsgamesys.amiga.amiga import Amiga
from fsgamesys.context import... | FrodeSolheim/fs-uae-launcher | fsgamesys/amiga/valueconfigloader.py | Python | gpl-2.0 | 21,279 | [
"ADF"
] | 2e36bbb1f222bbc2626fe44adba00d8634c880b84ac2a7b17f11256dcb5ff989 |
# encoding: utf-8
"""
Tests for IPython.config.loader
Authors:
* Brian Granger
* Fernando Perez (design help)
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2008-2011 The IPython Development Team
#
# Distributed under the terms of the BSD License. The full lice... | noslenfa/tdjangorest | uw/lib/python2.7/site-packages/IPython/config/tests/test_loader.py | Python | apache-2.0 | 9,015 | [
"Brian"
] | 2ddaea5e279ec46e9cbe6f7f6eed5196ea2d3b5e7afd2dc51a7822e191799488 |
import math
from itertools import chain
from rdkit import Chem
from ._base import Descriptor
__all__ = ("PathCount",)
class PathCountBase(Descriptor):
__slots__ = ()
explicit_hydrogens = False
class PathCountCache(PathCountBase):
__slots__ = ("_order", "_bonds")
def parameters(self):
ret... | mordred-descriptor/mordred | mordred/PathCount.py | Python | bsd-3-clause | 4,030 | [
"RDKit"
] | 614cc003441a3db36a1029f021c55a2c3407da4153f3ada7f616305f3e6d5efd |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
"""Wrapper ... | harterj/moose | python/pyhit/pyhit.py | Python | lgpl-2.1 | 12,760 | [
"MOOSE"
] | 6d29c0a5fc65711787237180579650b2ab3e9afb83acac356778baa90b003436 |
# Copyright 2018 Amazon.com, Inc. or its affiliates. All Rights Reserved.
# SPDX-License-Identifier: Apache-2.0
"""
Contains code for non-linear model multi-fidelity model.
It is based on this paper:
Nonlinear information fusion algorithms for data-efficient multi-fidelity modelling.
P. Perdikaris, M. Raissi, A. Da... | EmuKit/emukit | emukit/multi_fidelity/models/non_linear_multi_fidelity_model.py | Python | apache-2.0 | 16,604 | [
"Gaussian"
] | f5fdd131a2ef8f9f29ccc505b70b45ab8cfee8ca99effbd8c3189199e23747e4 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | johnchase/scikit-bio | skbio/io/tests/test_qseq.py | Python | bsd-3-clause | 11,452 | [
"scikit-bio"
] | 87ab194a73ad7f8f7ae9dc060d412e7acb414e2e164b52c98ba608d7ca5d8112 |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2020, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
"""
Input Generator and Parser
###############################
"""
from .editor import Editor
_template = """\
{seward}
{calc}
{postcalc}
"""
_seward = """\
&SEWARD &END
Title
... | exa-analytics/atomic | exatomic/molcas/inputs.py | Python | apache-2.0 | 6,379 | [
"MOLCAS"
] | 26ca3ab01fbe38929e042341027e30ed0ffb0d5fe8a933782497ce7d437908a0 |
# encoding: utf-8
from woo.dem import *
from woo.fem import *
import woo.core
import woo.dem
import woo.pyderived
import woo.pack
import woo
import math
from minieigen import *
import numpy
class CylTriaxTest(woo.core.Preprocessor,woo.pyderived.PyWooObject):
r'''
Preprocessor for cylindrical triaxial test wit... | woodem/woo | py/pre/cylTriax.py | Python | gpl-2.0 | 29,326 | [
"VTK"
] | 4e45b36417ac225a4dba80104fe88e3948cacbf4fae2e0912a3e96d9b483e0f6 |
import argparse
import logging
import os
import zipfile
import time
import mxnet as mx
import horovod.mxnet as hvd
from mxnet import autograd, gluon, nd
from mxnet.test_utils import download
# Training settings
parser = argparse.ArgumentParser(description='Apache MXNet MNIST Example')
parser.add_argument('--batch-si... | kubeflow/mpi-operator | examples/v1/mxnet/mxnet_mnist.py | Python | apache-2.0 | 5,687 | [
"Gaussian"
] | 173134ec7c23b6bf76cd8f4c0bc392aea2150c6189566a98f4f6a6bc488752b2 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, print_function
from .utils.visibility import getLogger
logger = getLogger(__name__)
import logging
plainLogger = logging.getLogger(__name__)
import getpass
import gzip
import hashlib
import io
import os
import re
import ruamel
import shutil
import sys
i... | chouseknecht/ansible-container | container/core.py | Python | lgpl-3.0 | 47,848 | [
"Galaxy"
] | 38b249d17a27c5fd01bce48d47287820033a55c214eb4b4b55bb84c080a8a6fb |
#
# AtHomePowerlineServer - networked server for CM11/CM11A/XTB-232 X10 controllers
# Copyright (C) 2014 Dave Hocker
#
# 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, version 3 of the Lic... | dhocker/athomepowerlineserver | SocketServerThread.py | Python | gpl-3.0 | 1,562 | [
"xTB"
] | dbc5bf570114acea38ca1ca111d26c314895dd88cec8352293125af6c04c5150 |
''' FreeDiskSpaceCommand
The Command gets the free space that is left in a Storage Element
Note: there are, still, many references to "space tokens",
for example ResourceManagementClient().selectSpaceTokenOccupancyCache(token=elementName)
This is for historical reasons, and shoud be fixed one day.
... | yujikato/DIRAC | src/DIRAC/ResourceStatusSystem/Command/FreeDiskSpaceCommand.py | Python | gpl-3.0 | 8,426 | [
"DIRAC"
] | e7a963217f06ab29dfc9061b18598dcaeb034dbb601c19b89a9f7e50c21e757e |
# creates: pt_h2.png
from ase import Atoms
from ase.io import write
a = 2.41 # Pt binding lenght
b = 0.90 # H2 binding lenght
c = 1.70 # Pt-H binding lenght
L = 7.00 # width of unit cell
# Setup the Atoms for the scattering region.
atoms = Atoms('Pt5H2Pt5',
cell=[3 * a + b + 2 * c, L, L],
... | qsnake/gpaw | doc/exercises/transport/pt_h2.py | Python | gpl-3.0 | 658 | [
"ASE"
] | 6ad482a25e88e0b19e1fc42014f8a3115e9338e583273da1e72822143030c94e |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import numpy as np
import collections
from numbers import Number
import numbers
from functools import partial
import scipy.constants as const
"""
This module implements a FloatWithUnit, which is a subclass o... | montoyjh/pymatgen | pymatgen/core/units.py | Python | mit | 28,041 | [
"pymatgen"
] | aac0a1783e316257b4ec45b4ef66743c06e8f0e64dab145acb555f89b4835efe |
"""
Project
FPGA-Imaging-Library
Design
RowsGenerator
Function
Generate rows cache.
Module
Software simulation.
Version
1.0
Modified
2015-05-17
Copyright (C) 2015 Tianyu Dai (dtysky) <dtysky@outlook.com>
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser G... | wamgoo/FPGA-Imaging-Library | LocalFilter/ThresholdLocal/SoftwareSim/RowsGenerator.py | Python | lgpl-2.1 | 2,111 | [
"MOE"
] | 46c1c8d61288d4f231f598e88b9121bb690ba44eb4022b21ca66bfce2ebd7964 |
import numpy as np
import pandas as pd
import mdtraj as md
import itertools
trj0 = md.load("./system.subset.pdb")
atom_indices = np.array([i for i, atom in enumerate(trj0.top.atoms) if ((atom.element.symbol != "H")|(atom.name == "H"))])
pair_indices = np.array(list(itertools.combinations(atom_indices, 2)))
n_choose ... | hainm/MSMs | attic/src/code/hmsm/save_heavy_atom_indices.py | Python | gpl-2.0 | 496 | [
"MDTraj"
] | 30ee1a801f67aced8d9818464d4c336e0f17568c231b455131b67a8e31ef3397 |
from galaxy.jobs import JobDestination
import os
import multiprocessing
# This rules file determines the number of local cpus and then sets the
# Slurm --ntasks parameter appropriately. The maximum and minimum cpus
# to use per job is listed below. These values can be altered to suit the
# current system. So for a 1 -... | gvlproject/gvl.ansible.filesystem | files/galaxy-app/lib/galaxy/jobs/rules/dyndests.py | Python | mit | 1,906 | [
"Galaxy"
] | f78e0eb837b7c400c4c81795d8764bec3ebf73707241c1ebb61e8039473b2185 |
# -*- coding: utf-8 -*-
"""
Created on Wed Jul 15 08:28:46 2015
@author: Chris Simpson
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import numpy as np
def plane_strain(e_xx, e_yy, E, v):
""" Stress calcul... | Simclass/EDXD_Analysis | pyxe/fitting_functions.py | Python | mit | 3,690 | [
"Gaussian"
] | 99a5f32079e8dd73a5458c857929dab9d205f097d9bf64e0de68491125f2497e |
# $Id$
#
# Copyright (C) 2005-2006 Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
from __future__ import print_function
... | jandom/rdkit | rdkit/Chem/FeatFinderCLI.py | Python | bsd-3-clause | 3,262 | [
"RDKit"
] | a55a5a3e38387c044f48502d40f7db959c09fe07a23bd868927ea0debd2dce96 |
# Copyright 2013 by Christian Brueffer. 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.
"""Command line wrapper for the multiple sequence alignment program MSAProbs.
"""
from _... | zjuchenyuan/BioWeb | Lib/Bio/Align/Applications/_MSAProbs.py | Python | mit | 3,292 | [
"Biopython"
] | 9b156ee31c09ccc50cbfb003440ee2557c5ce676cbb69cadd6968cc6d905d7ab |
'''
PathwayGenie (c) University of Manchester 2017
PathwayGenie is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
# pylint: disable=too-many-arguments
import sys
from assembly_genie.assembly import AssemblyThread, _AMPLIGASE, ... | synbiochem/PathwayGenie | assembly_genie/phospho_lcr.py | Python | mit | 6,434 | [
"VisIt"
] | f7a5aa4d20df5d9e89f733c7e80a746ed6851eaf0291a38ee92aa8b57e4c4255 |
from __future__ import division, print_function
import random
import unittest
from rdkit import DataStructs
from rdkit.ML.Data import DataUtils
from rdkit.ML.InfoTheory import rdInfoTheory
try:
from rdkit.ML.InfoTheory import BitClusterer
except ImportError:
BitClusterer = None
def getValLTM(i, j, mat):
if i... | rvianello/rdkit | rdkit/ML/InfoTheory/UnitTestCorrMatGen.py | Python | bsd-3-clause | 3,979 | [
"RDKit"
] | 7c2951fd5ea1667218f3b8f908636bed64019a0b2f31c921c08e0266d11da60a |
from __future__ import division
#
# following the initial file creation with the full Twitter data
# this program
# 1. consolidates the resulting three output files
# 2. adds lat and lon to the tweet['geo'] field
#
# Usage: nohup python update_geo_data.py &
def process_output_file(output_list, output_json_filenam... | grfiv/healthcare_twitter_analysis | code/update_geo_data.py | Python | mit | 13,602 | [
"COLUMBUS"
] | 8b3eb91b80e142168bfe44eb7064f9e22ada40d79812423bbe84b099888555e3 |
# -*- coding: utf-8 -*-
"""
Output Plugin for FLAC
Copyright (c) 2006-2008 by Nyaochi
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) an... | rinrinne/cueproc-alternative | src/ce_flac.py | Python | gpl-2.0 | 2,836 | [
"VisIt"
] | c9178ec693c061789a411b7092b62c56b007ac94a8c6643d7e631822ed626a9e |
from flyingpigeon.timeAggregation import aggregatTime
from pywps.Process import WPSProcess
import logging
class TimeAggregationProcess(WPSProcess):
def __init__(self):
WPSProcess.__init__(self,
identifier = "time_aggregation",
title="aggregate the time frequency",
ver... | sradanov/flyingpigeon | flyingpigeon/processes/wps_time_aggregation.py | Python | apache-2.0 | 2,395 | [
"NetCDF"
] | 4c2a6ba5242198055cbd521876e2bc2a98329cd6d77f627cd6764aa7a4accb34 |
"""
[2015-09-03] Challenge #230 [Hard] Logo De-compactification
https://www.reddit.com/r/dailyprogrammer/comments/3jn6te/20150903_challenge_230_hard_logo/
# [](#HardIcon) _(Hard)_: Logo De-compactification
After Wednesday's meeting, the board of executives drew up a list of several thousand logos for their company. C... | DayGitH/Python-Challenges | DailyProgrammer/DP20150903C.py | Python | mit | 2,916 | [
"VisIt"
] | 0e048a9e0f33ed1538ff1a45573057ab0cf166e24ffeaceac1f1a882dfb184f6 |
"""Test the wrapping of vtkCommand
The following vtkCommmand functionality must be tested
- Event enum constants
- Event names
- Adding/removing observers
Created on Mar 22, 2012 by David Gobbi
"""
import sys
import exceptions
import gc
import vtk
from vtk.test import Testing
class callback:
def __init__(self):... | collects/VTK | Common/Core/Testing/Python/TestCommand.py | Python | bsd-3-clause | 3,300 | [
"VTK"
] | bad5be071c36e9833c889ea258cd420bb7379f1b558c37e50d591d3e99033feb |
# coding=utf-8
"""Signup in the application feature tests."""
import pytest
from django.contrib.auth.models import User
from pytest_bdd import (
given,
scenario,
then,
when,
)
@pytest.mark.django_db
@scenario('features/signup.feature', 'Can\'t signup with blank e-mail')
def test_cant_signup_with_blank... | jesuejunior/golingo | quiz/tests/functional/test_signup.py | Python | bsd-3-clause | 8,403 | [
"VisIt"
] | 529a758a6120d7d0ce27b229bbfd830078edaeb00f48f13e5128684bbee8d1a7 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# relevant imports
import sys
import time
import espresso
import mpi4py.MPI as MPI
import Tetracryst # Preparation of tetrahedral crystal and constuctions of bonds in tetrahedral liquid
from espresso import Real3D, Int3D
from espresso.tools import decomp
from espresso.to... | BackupTheBerlios/espressopp | examples/hadress/hadressFEC/hadressPressureFEC.py | Python | gpl-3.0 | 8,446 | [
"CRYSTAL",
"ESPResSo"
] | cc8858c05226d490a4b2ddd642e7726dfc1b9386784388b3a6a4b22aa341a0ca |
"""
Visualization of Anthracene
"""
import os
import time
import pychemia
import pychemia.external.pymatgen
path = 'tests/data'
def test_anthracene():
"""
Visualization of anthracene :
"""
print(os.getcwd())
assert (os.path.isdir(path))
filename = path + '/xyz/anthracene.xyz'
ass... | MaterialsDiscovery/PyChemia | tests/notest_visual.py | Python | mit | 1,386 | [
"pymatgen"
] | 214c53e200f772b9d4f34f294ecd66167394fd5fa6eeabe9c36ff840a17b4906 |
import matplotlib
matplotlib.use('Agg')
import sys
sys.path.append('../../')
import numpy as np
import scipy.stats
import matplotlib.pylab as plt
import os, sys
import geepee.aep_models as aep
import geepee.vfe_models as vfe
import geepee.ep_models as ep
from geepee.config import PROP_MC, PROP_MM
import pdb
np.random.... | thangbui/geepee | exps/gpssm/kink_exp.py | Python | mit | 8,749 | [
"Gaussian"
] | e3e9d3bc7ce0561f05c4e11f02a9e1ae8c966ed82b758f680caae5a0a2c4f7a5 |
import yt
import numpy as np
import matplotlib as mpl
mpl.use('Agg')
import matplotlib.pyplot as plt
from matplotlib import rc, cm
from collections import Iterable, OrderedDict
COMPUTE_ACF = False # global disable for now - not working and time consuming
fsize = 17
rc('text', usetex=False)
rc('font', size=fsize)#, ft... | aemerick/galaxy_analysis | particle_analysis/abundances.py | Python | mit | 32,577 | [
"Galaxy"
] | 60c83b2037e6283c10ce03e218cb559d74e52f0192fa9c8150080c084c5324a6 |
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2015 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier (bgoli@users.sourceforge.net)
Triple-J Group for Molecular Cell Physiology
Stellenbosch University, South Africa.
Permiss... | asttra/pysces | pysces/PyscesLink.py | Python | bsd-3-clause | 52,634 | [
"ORCA",
"PySCeS"
] | 52c3e7b9c2acc418ed2bb0df2351f73b3bb5160d0a9da227f70fedb5398642d4 |
import copy
import exchange
import lan
from lan import ast_buildingblock as ast_bb
from processing import collect_array as ca
from processing import collect_device as cd
from processing import collect_gen as cg
from processing import collect_id as ci
from processing import collect_loop as cl
class PlaceInLocal(objec... | dikujepsen/OpenTran | v3.0/framework/transformation/place_in_local.py | Python | mit | 9,352 | [
"VisIt"
] | 2684808fcf3b1cdbfec97b5279d17a965fe0940a87e0a4e0d28d74a0911c734a |
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