text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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#-------------------------------------------------------------------------------
# Copyright (c) 2012 Gael Honorez.
# All rights reserved. This program and the accompanying materials
# are made available under the terms of the GNU Public License v3.0
# which accompanies this distribution, and is available at
# htt... | IDragonfire/modular-client | src/trueSkill/FactorGraphs/Schedule.py | Python | gpl-3.0 | 2,765 | [
"VisIt"
] | 1cec2553b96ee81a93d1642655b8e62e3a8b4af5c3a2dcc8e250eb89558fd6f0 |
# Copyright (c) 2012-2014, James Hensman
# Licensed under the BSD 3-clause license (see LICENSE.txt)
from .posterior import Posterior
from ...util.linalg import jitchol, tdot, dtrtrs, dpotri, pdinv
import numpy as np
from . import LatentFunctionInference
log_2_pi = np.log(2*np.pi)
class DTC(LatentFunctionInference):
... | befelix/GPy | GPy/inference/latent_function_inference/dtc.py | Python | bsd-3-clause | 5,766 | [
"Gaussian"
] | 9974cbc02a03f6b902c7419cf06f198b63d3e9607cfc97eddb4012a111c349b2 |
# -*- coding: utf-8 -*-
#
# test_stdp_dopa.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License,... | kristoforcarlson/nest-simulator-fork | testsuite/manualtests/test_stdp_dopa.py | Python | gpl-2.0 | 3,451 | [
"NEURON"
] | bb958e099754ee901e9905f27d1b6c3a3ecf5979100fcd8abb885fdd050d7a03 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | anderspitman/scikit-bio | skbio/diversity/tests/test_util.py | Python | bsd-3-clause | 9,899 | [
"scikit-bio"
] | 9bc52961e05e30a7011d5ecc4cae1456699ea13324808f6dd3c2988f9f962145 |
#########################################################
#
# DO NOT EDIT THIS FILE. IT IS GENERATED AUTOMATICALLY. #
# PLEASE LOOK INTO THE README FOR MORE INFORMATION. #
#
#########################################################
# coding: utf-8
# # Multi-GPU Training with Caffe2
#
# ![caffe2 imagenet logo](... | Yangqing/caffe2 | caffe2/python/tutorials/py_gen/Multi-GPU_Training.py | Python | apache-2.0 | 50,348 | [
"TINKER"
] | e26c790b3b1dc301b004072d3cbaca471007dc185d8db173e2686753b045d5ef |
from __future__ import (absolute_import, division, print_function,
unicode_literals)
from matplotlib.externals import six
from matplotlib.externals.six.moves import xrange
import warnings
import numpy as np
from matplotlib.testing.decorators import image_comparison, knownfailureif
from matplot... | yuanagain/seniorthesis | venv/lib/python2.7/site-packages/matplotlib/tests/test_delaunay.py | Python | mit | 7,137 | [
"Gaussian"
] | 2b3728890a640e1b5504c33808286744e72f9af790b5b26fea4a4c1ca5cef85f |
"""
Module containing wrappers to create, load, simulate, analyze networks
"""
from __future__ import unicode_literals
from __future__ import print_function
from __future__ import division
from __future__ import absolute_import
from future import standard_library
standard_library.install_aliases()
#----------------... | Neurosim-lab/netpyne | netpyne/sim/wrappers.py | Python | mit | 19,548 | [
"NEURON"
] | e7b0d1772803249d54c3483b77552be7ead4ea86c9a11c7ed5af90871a2ba7a6 |
# coding: utf8
from __future__ import unicode_literals, print_function, division
from unittest import TestCase
from cdk.scripts.util import Headword, yield_variants, yield_examples
class HeadwordTests(TestCase):
def test_Headword(self):
w = Headword('ambel <rus.>')
self.assertEqual(w.donor, 'rus'... | clld/cdk | cdk/tests/test_import.py | Python | apache-2.0 | 26,718 | [
"CDK"
] | c2773d1087157f3faa1a429b56be423f84448e149c4ac83a3d4c4fde2a357987 |
#!/usr/bin/env python
#
# Electrum - lightweight Bitcoin client
# Copyright (C) 2011 thomasv@gitorious
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at... | undeath/joinmarket-clientserver | jmclient/jmclient/old_mnemonic.py | Python | gpl-3.0 | 17,930 | [
"CRYSTAL",
"VisIt"
] | 8cae77962905fede3cd71b040bf8102a9f633e5eb44cdacf494b5f0d55f4a0ba |
import sys
import os
import re
# pycalphad must be importable to build API documentation and for version retreival
sys.path.insert(0, os.path.abspath('../pycalphad'))
from pycalphad import __version__ as pycalphad_version
pycalphad_version = re.sub('\.d[0-9]{8}', '', pycalphad_version) # remove .d<date>
# -- General... | tkphd/pycalphad | docs/conf.py | Python | mit | 9,435 | [
"pycalphad"
] | 3ab81573d13520de2163246811dd9622fb0e15ba06f6ce6057757342fc69624e |
# Copyright (c) 2014, James Hensman, Alan Saul
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
from ..core import Model
from paramz import ObsAr
from .. import likelihoods
class GPKroneckerGaussianRegression(Model):
"""
Kronecker GP regression
Take two kernels computed on s... | SheffieldML/GPy | GPy/models/gp_kronecker_gaussian_regression.py | Python | bsd-3-clause | 4,296 | [
"Gaussian"
] | d71f88181445c1fa386bea973979b4c75c7eb3041f22b10841c7dae4336db1c5 |
#!/usr/bin/env python
# coding: utf-8
#
# Copyright 2007 Google Inc.
#
# 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 ... | ClockworkNet/cw-code-review-upload | upload.py | Python | mit | 103,273 | [
"VisIt"
] | 1ed210cf0e3ec1ee4c02fb73d75f0f3d8f55e473b27d646e3d88de5bb64d8349 |
"""initial migration
Revision ID: 995d0aeda211
Revises:
Create Date: 2018-11-24 00:44:55.926212
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = '995d0aeda211'
down_revision = None
branch_labels = None
depends_on = None
def upgrade():
op.create_table('dro... | der-michik/c3bottles | migrations/versions/995d0aeda211_.py | Python | mit | 2,792 | [
"VisIt"
] | 922b4751418a606a3518856a377f056a9faa8190a38b5c35377dfa1c8c3dd5db |
#!/usr/bin/env python
# use_express.py
# October 2012 Matthew MacManes (macmanes@gmail.com)
#
# This wrapper is free software: you can redistribute it and/or modify
#
# v.0.3.1 Changes: Do not remake index if already made, added -k30 option to Bowtie2 mapping step
import sys
import subprocess
import optpar... | macmanes/trinityrnaseq | util/eXpress_util/use_express.py | Python | bsd-3-clause | 6,192 | [
"Bowtie"
] | 2de6bccbba1f2d1a9bfb20a17ecef2e383a5db0d050e6bf1e780240d5c573f15 |
# -*- coding: utf-8 -*-
"""
Tests for bandwidth selection and calculation.
Author: Padarn Wilson
"""
import numpy as np
from scipy import stats
from statsmodels.sandbox.nonparametric import kernels
from statsmodels.distributions.mixture_rvs import mixture_rvs
from statsmodels.nonparametric.kde import KDEUnivariate ... | huongttlan/statsmodels | statsmodels/nonparametric/tests/test_bandwidths.py | Python | bsd-3-clause | 1,860 | [
"Gaussian"
] | b45fbe539ce2b03fbb0dfc7ddfa6205256026b3707ce14cc586a86a558b66f3d |
#!/usr/bin/python
import numpy as np
import healpy as hp
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import sys
infile = sys.argv[1]
outfile = infile[:-5] + ".png"
print outfile
DPI=300
m = hp.read_map(infile)
hp.mollview(m, title="Mollview image RING")
if sys.argv[2]=='1':
#galact... | bencebecsy/galaxy-priors | plot_skymap.py | Python | mit | 1,865 | [
"Galaxy"
] | d4955cd0cf8e289fae3674a31a55e25a26a80bcf42737d050510635547107a40 |
#!/usr/bin/env python
# coding=utf-8
## @package biopredyn
## Copyright: [2012-2019] Cosmo Tech, All Rights Reserved
## License: BSD 3-Clause
import copy
import libsbml
import libsedml
import libsbmlsim
import algorithm, result, statistics
import numpy as np
from cobra.io.sbml import create_cobra_model_from_sbml_doc
... | TheCoSMoCompany/biopredyn | Prototype/python/biopredyn/simulation.py | Python | bsd-3-clause | 26,014 | [
"COPASI"
] | f5e15895ee7167c604661bc5a9381f48c8a2fa0a109d09ef2a0a343da3af4cfb |
# MIT License
#
# Copyright (c) 2016 Anders Steen Christensen, Felix A. Faber, Lars A. Bratholm
#
# 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 limita... | qmlcode/qml | qml/kernels.py | Python | mit | 10,752 | [
"Gaussian"
] | fd32dbaa217ed20608dd763ac9953a20c50ff57fa817bbda20b703446d14f23a |
"""
General utility module.
"""
# Copyright (c) 2017 Ben Zimmer. All rights reserved.
import pickle
import dill
import numpy as np
from sklearn.neighbors import KernelDensity
dill.settings["recurse"] = True
def load(input_filename):
"""unpickle an object from a file"""
with open(input_filename, "rb") a... | bdzimmer/handwriting | handwriting/util.py | Python | bsd-3-clause | 2,953 | [
"Gaussian"
] | 2a0699f67f7533555181c8fe6fca73aba36459dfca4edd1535581eeb5915b1b0 |
# Copyright 2008-2014 Jaap Karssenberg <jaap.karssenberg@gmail.com>
'''This module defines the ExportTemplateContext, which is a dictionary
used to set the template parameters when exporting.
Export template parameters supported::
generator
.name -- "Zim x.xx"
.user
title
navigation - links to other ex... | jaap-karssenberg/zim-desktop-wiki | zim/export/template.py | Python | gpl-2.0 | 15,774 | [
"VisIt"
] | 73f515117689e5a747c9780cafbd1d271506ad9b810d0ba104366660cf7b28c0 |
#!/usr/bin/env python
# Script to rename atoms in PDB based on 'original' MOE fit conformation,
# with coordinates substituted for 'new' conformation
# Uses Parmed to print PDB in Amber compatible format
# Usage: rename_pdb.py old_file new_file
import parmed as pmd
import sys
old = pmd.load_file(sys.argv[1])
new = ... | rtb1c13/scripts | General/rename_pdb.py | Python | gpl-2.0 | 413 | [
"Amber",
"MOE"
] | bb788f0ea37a98c5e5dd12330ae9609af11231f0978838b4b603fa8df234d300 |
# Lint as: python3
# Copyright 2019 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless ... | tensorflow/lingvo | lingvo/tasks/car/waymo/waymo_decoder.py | Python | apache-2.0 | 13,038 | [
"VisIt"
] | d10ba2d0db4d78daa2bc077d39ce96bfdb10b5d767ac150663b63ce1a9e718ff |
# -*-python-*-
#
# Copyright (C) 1999-2006 The ViewCVS Group. All Rights Reserved.
#
# By using this file, you agree to the terms and conditions set forth in
# the LICENSE.html file which can be found at the top level of the ViewVC
# distribution or at http://viewvc.org/license-1.html.
#
# For more information, visit h... | foresthz/fusion5.1 | www/scm/viewvc/bin/mod_python/query.py | Python | gpl-2.0 | 1,502 | [
"VisIt"
] | df96896b82c7a9c5226b373e2ef1eac337d7f4acfc79c3de1df3df0ab4e23d02 |
# Monte Carlo policy evaluation
# Every-visit
# Uncertain state transition
import numpy as np
from grid_world import standard_grid, negative_grid
from dp_ipe_dst_dp import print_values, print_policy
SMALL_ENOUGH = 1e-4
GAMMA = 0.9
P_ACTION = 0.6
def affected_action(grid, s, a):
p = np.random.random()
if p < P_ACTI... | GitYiheng/reinforcement_learning_test | test00_previous_files/mc_pe_ust_ev.py | Python | mit | 2,099 | [
"VisIt"
] | bd28a4fe51c3019637d0d50b0a1dfdcbcdd04365f1e3f981dad9cd0c66e5ccff |
from optparse import OptionParser
import argparse
import numpy as np
import pandas as pd
import csv
import pysam
import pdb
from bx.intervals.intersection import Interval, IntervalTree
import cluster
import genotyper as gt
from GC_data import GC_data
if __name__=="__main__":
parser = argparse.ArgumentParser()
... | EichlerLab/read_depth_genotyper | scripts/combine_genotypes.py | Python | mit | 4,355 | [
"Gaussian",
"pysam"
] | 356c165c1880b495ec472905e713db082129dbd0c818280eb0670ada972e93f8 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RFdbInfiniummethylationHg19(RPackage):
"""Compiled HumanMethylation27 and HumanMethylation... | iulian787/spack | var/spack/repos/builtin/packages/r-fdb-infiniummethylation-hg19/package.py | Python | lgpl-2.1 | 1,076 | [
"Bioconductor"
] | 2131e790c6afc88d9588a63f92ec71afcf6b500e7b0c9618679b62460d2f44b2 |
#!/usr/bin/python
#
# Copyright 2012 Google Inc.
#
# 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 a... | tripleee/gmail-oauth2-tools | python/oauth2.py | Python | apache-2.0 | 12,198 | [
"VisIt"
] | 4b65d694ddc28f786d334c0950cafec02f699877e0f549d93092a3bfe7619b1f |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | core/misc/images.py | Python | agpl-3.0 | 83,531 | [
"Gaussian"
] | 13dd408c714e0dc8f7b75accd81d1da1c5841871162fd4f6978f7557a01a3ea8 |
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yasharmaster/scancode-toolkit | tests/licensedcode/test_detect.py | Python | apache-2.0 | 47,823 | [
"VisIt"
] | 860cdeac874f037774638adf1376c3c510d0e22fd341d9a85e3e44143d6e249d |
import os
import re
import sys
import numpy
try:
from setuptools import setup, Extension
except ImportError:
from distutils.core import setup, Extension
from Cython.Build import cythonize
libraries = []
if os.name == "posix":
libraries.append("m")
include_dirs = [
"../C",
numpy.get_include(),
]
... | ericagol/TTVFaster | Python/setup.py | Python | mit | 1,132 | [
"Gaussian"
] | 292106538d0ba2fd692df98cc4712368d70753145122b1f135c4fce0f106fa8c |
from __future__ import division
from sklearn.model_selection import KFold
from sklearn.pipeline import Pipeline
from sklearn.grid_search import GridSearchCV
#from sklearn.metrics import classification_report
import sklearn.metrics as mtrx
from sklearn.neighbors import KNeighborsClassifier as KNC
from sklearn.ensemble... | melaniebeck/GZExpress | analysis/MachineClassifier.py | Python | mit | 22,084 | [
"Galaxy"
] | 3f4c8ca4a11d1754f89db7fd3403b70c15e75c022d97ea5b167c3d07e718a28b |
#
# Copyright (C) 2018 Susan H. Leung
# All Rights Reserved
#
from rdkit import RDConfig
import os
import sys
import math
from datetime import datetime, timedelta
import unittest
from rdkit import DataStructs
from rdkit import Chem
from rdkit.Geometry import rdGeometry as geom
from rdkit.Chem.rdchem import Atom... | bp-kelley/rdkit | Code/GraphMol/MolStandardize/Wrap/testMolStandardize.py | Python | bsd-3-clause | 42,057 | [
"RDKit"
] | d1fddc5079ae6391b983b9f9096a050cfa36d802b10f86fdf6b6e8274878e1a5 |
#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific.
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove ... | SBRG/ssbio | ssbio/biopython/Bio/Struct/cpv.py | Python | mit | 14,035 | [
"PyMOL"
] | b6d58e3df9db7f9d0c4fdadc50cd6967ae81472d7b274ff145a2d4c9ec895c3f |
# coding: utf8
# Copyright 2014-2017 CERN. This software is distributed under the
# terms of the GNU General Public Licence version 3 (GPL Version 3),
# copied verbatim in the file LICENCE.md.
# In applying this licence, CERN does not waive the privileges and immunities
# granted to it by virtue of its status as an I... | blond-admin/BLonD | __EXAMPLES/main_files/EX_04_Stationary_multistation.py | Python | gpl-3.0 | 5,450 | [
"Gaussian"
] | c3845388a5adbef015e48b8c4a3fbed904804929e2b5a3d0eef3ae3863031fdb |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2011 Async Open Source
##
## This program is free software; you can redistribute it and/or
## modify it under the terms of the GNU Lesser General Public License
## as published by the Free Software Foundation; either version 2
## of the License, or... | tiagocardosos/stoq | stoqlib/gui/editors/accounttransactioneditor.py | Python | gpl-2.0 | 6,369 | [
"VisIt"
] | c6595d54e7295fcb1c90db6dbaf2d9cb0bdf779db3dfaef778279dcaebc3942a |
import os
import sys
import urllib
import urllib2
import tarfile
import zipfile
import csv
import numpy as np
from ase.test import NotAvailable
from ase import units
from ase.test.tasks.dcdft import DeltaCodesDFTTask as Task
dir = 'Delta'
if len(sys.argv) == 1:
tag = None
reffile = os.path.join(dir, '... | robwarm/gpaw-symm | gpaw/test/big/dcdft/analyse.py | Python | gpl-3.0 | 4,143 | [
"ASE",
"WIEN2k"
] | 93ca74cea47cda1a6a00c50f58c270799441406640bb22c73f1a53ec63410e1f |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
### This program plots a channel's state variables / hinf, htau etc. as a function of voltage.
mechanisms = {
'H_STG': ['minf','mtau'],
'CaS_STG': ['minf','mtau','hinf','htau'],
'CaT_STG': ['minf','mtau','hinf','htau'],
'KA_STG': ['minf','mtau','hinf','htau'],
'Kd_STG': [... | h-mayorquin/camp_india_2016 | tutorials/chemical switches/moose/neuroml/lobster_pyloric/channels/ChannelTest.py | Python | mit | 2,394 | [
"MOOSE"
] | eade9d172f5c5d10ee18d2d7bfe320b38310b5d598b74375d00ebb66ca174df7 |
# coding=utf-8
# Copyright 2022 The Google Research 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 applicab... | google-research/google-research | mol_dqn/experimental/optimize_800_mols.py | Python | apache-2.0 | 54,010 | [
"RDKit"
] | f81a4421d3414ac46c52be2fc1c963f748f16efce740b88d3ef606794055c32b |
#
# Copyright (C) 2001 greg Landrum
#
""" unit testing code for variable quantization
"""
import unittest
from rdkit.ML.Data import Quantize
from rdkit.six.moves import map
class TestCase(unittest.TestCase):
def testOneSplit1(self):
# """ simple case (clear division) """
d = [(1., 0), (1.1, 0), (1.2, 0... | rvianello/rdkit | rdkit/ML/Data/UnitTestQuantize.py | Python | bsd-3-clause | 10,913 | [
"RDKit"
] | c26a131ba442d42bfd2b4f29795da7c4267f647ee6dac360c4cb349431e6d442 |
"""Utilities that can be used by tests."""
import difflib
import re
import sys
import gi
gi.require_version("Gdk", "3.0")
gi.require_version("Gtk", "3.0")
from gi.repository import Gio
from gi.repository import Gdk
from gi.repository import Gtk
from macaroon.playback import *
testLogger = Gio.DBusProxy.new_for_bus_... | GNOME/orca | test/harness/utils.py | Python | lgpl-2.1 | 7,648 | [
"ORCA"
] | 4b4f125f8e437f58db0206641de214d950b6540e900d804fd288f3cc2123e49d |
import json
import os
import os.path
import re
import datetime
from os.path import exists, isdir, realpath, isfile, islink
from os import pathsep, listdir, environ, fdopen
import subprocess
import GangaCore.Utility.logging
import GangaCore.Utility.Config
from optparse import OptionParser, OptionValueError
from GangaCo... | ganga-devs/ganga | ganga/GangaLHCb/__init__.py | Python | gpl-3.0 | 8,963 | [
"DIRAC"
] | b9a0407905ed4156a2d239f532912e7f396e1c0b3740f9964b50938999344ed5 |
import datetime
import pytest
import pytz
from events.models import (
Location, Time,
CustomEvent, KeynoteEvent, ProposedTalkEvent,
)
from proposals.models import AdditionalSpeaker
cst = pytz.timezone('Asia/Taipei')
class RendererTestUtils:
@staticmethod
def is_safe(s):
"""Check whether a ... | pycontw/pycontw2016 | src/events/tests/renderers/conftest.py | Python | mit | 8,032 | [
"Amber"
] | 49ac2af6f3aefd0c160b09f177bf357af48b734df75391b8ff4505ce37191f46 |
#########################################################################
#
# detectors.py - This file is part of the Spectral Python (SPy)
# package.
#
# Copyright (C) 2012-2013 Thomas Boggs
#
# Spectral Python is free software; you can redistribute it and/
# or modify it under the terms of the GNU General P... | ohspite/spectral | spectral/algorithms/detectors.py | Python | gpl-2.0 | 28,119 | [
"Gaussian"
] | 574c3f225b5b3728cc1b315f4019b2b9b8b85d48e831fc2d6a671446f90b4b91 |
#!/usr/bin/env python3
# Tool to discover 'smells' in the Discogs data via the API. It downloads
# release data and flags releases that need to be fixed.
#
# The checks are (nearly) identical to cleanup-discogs.py
#
# The results that are printed by this script are by no means complete
# or accurate.
#
# Licensed unde... | armijnhemel/cleanup-for-discogs | cleanup-discogs-continuous.py | Python | gpl-3.0 | 63,272 | [
"CASINO",
"exciting"
] | 5c55787fb12194df5fa585a39d9b61bf87fa78fe0b48ba4251b762ec99509959 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, division, print_function, unicode_literals
import mock
import time
import unittest
import logging
import functools
from nose.tools import * # noqa: F403
import pytest
from framework.auth.core import Auth
from website import settings
import website.sea... | saradbowman/osf.io | osf_tests/test_elastic_search.py | Python | apache-2.0 | 61,608 | [
"Brian"
] | 6176d9588d7c7a3ab7ad45fa83c58fbe179a1aa465689cd8540684ccb0e122bf |
"""
Lemur
=====
Is a TLS management and orchestration tool.
:copyright: (c) 2015 by Netflix, see AUTHORS for more
:license: Apache, see LICENSE for more details.
"""
from __future__ import absolute_import
import json
import os.path
import datetime
from distutils import log
from distutils.core import Command
from se... | rhoml/lemur | setup.py | Python | apache-2.0 | 4,716 | [
"GULP"
] | 19b3305531ed6d1b0dea4e22b7ef243360fea306179291a806ba3f7360a911c5 |
import numpy as np
class ModelParameters(object):
'''
In this class the model parameters are specified. It contains a lot of information which is (not always) necessary to run Chempy.
The individual definitions are given as comments.
'''
# Which zero point of abundances shall be used. Asplund 2005 is corrected... | jan-rybizki/Chempy | Chempy/parameter.py | Python | mit | 14,117 | [
"ChemPy",
"Gaussian"
] | 1f419baea665b86e2ba6d7681a542931717601a2e539eea412903735a241a878 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Interface with command line GULP.
http://projects.ivec.org
WARNING: you need to have GULP installed on your system.
"""
__author__ = "Bharat Medasani, Wenhao Sun"
__copyright__ = "Copyright 2013, The Mate... | montoyjh/pymatgen | pymatgen/command_line/gulp_caller.py | Python | mit | 26,921 | [
"GULP",
"pymatgen"
] | 5d090d36fd263ff3a6667df1938b9c168035800f371572d7ff21222b72e61548 |
#!/usr/bin/env python2.7
# Copyright 2015 Cisco Systems, Inc.
#
# 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 applicabl... | tbarrongh/cosc-learning-labs | src/learning_lab/02_capability_matrix.py | Python | apache-2.0 | 4,027 | [
"VisIt"
] | a984c4c95ffbb30e43cdc4e4e441106001c0186d3f19c7e8bab209c21338e1bd |
# -*- coding: utf-8 -*-
"""
Created on Mon Jun 23 10:17:53 2014
@author: ibackus
"""
# External modules
import numpy as np
import pynbody
SimArray = pynbody.array.SimArray
# diskpy modules
from diskpy.pdmath import smoothstep
from diskpy.utils import match_units
def make_profile(ICobj):
"""
A wrapper for g... | ibackus/diskpy | diskpy/ICgen/sigma_profile.py | Python | mit | 9,111 | [
"Gaussian"
] | 6c863b17f9b541ad0f391a0cab45d5c212e4e713cbe3c1ff0192b057f10bb242 |
# Copyright (c) 2018 PaddlePaddle Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by app... | luotao1/Paddle | python/paddle/fluid/initializer.py | Python | apache-2.0 | 42,276 | [
"Gaussian"
] | 2bc34e7fe4094e7b6235747a687ef2bd76cff3ea967108cc1e4c9a454a6c6436 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import print_function
__version__ = '0.1.3'
from pipes import quote
from subprocess import Popen, PIPE
from datetime import date, timedelta
def count_git_log(range='', paths=None, options=None):
if options is None:
options = {}
options['... | moskytw/git-count | gitcount.py | Python | mit | 4,092 | [
"VisIt"
] | 3b6c0b6e6d67a975b1f5c0e1f1dc2d8dc419133adcb2f2ad7557b8dacdcbc424 |
"""
TornadoREST is the base class for your RESTful API handlers.
It directly inherits from :py:class:`tornado.web.RequestHandler`
"""
import os
import inspect
from tornado.escape import json_decode
from tornado.web import url as TornadoURL
from urllib.parse import unquote
from functools import partial
from DIRAC impo... | DIRACGrid/DIRAC | src/DIRAC/Core/Tornado/Server/TornadoREST.py | Python | gpl-3.0 | 16,420 | [
"DIRAC"
] | bdf44a56829893de55497f7eaed1c1e1f93fe4b95f008d0ad6a9a08f030b2b06 |
"""Environment file for PyFEHM. Set default attribute values."""
"""
Copyright 2013.
Los Alamos National Security, LLC.
This material was produced under U.S. Government contract DE-AC52-06NA25396 for
Los Alamos National Laboratory (LANL), which is operated by Los Alamos National
Security, LLC for the U.S. De... | ddempsey/PyFEHM | fdflt.py | Python | lgpl-2.1 | 14,730 | [
"ParaView",
"VisIt"
] | 434a1583875051054da87240ff28ff7b340d772aab97b881e54dccf2d1fb0b2d |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
urlpat... | gwhigs/tweeter | config/urls.py | Python | mit | 1,666 | [
"VisIt"
] | 6d086c9744d1e5962832643981958d69f078874b059440085567624c657179b7 |
# -*- coding: utf-8 -*-
from south.utils import datetime_utils as datetime
from south.db import db
from south.v2 import DataMigration
from django.db import models
class Migration(DataMigration):
def forwards(self, orm):
"Write your forwards methods here."
# Note: Don't use "from appname.models imp... | myvoice-nigeria/myvoice | myvoice/survey/migrations/0014_positive_response.py | Python | bsd-2-clause | 13,404 | [
"VisIt"
] | afe5993cea71c98b4e4ceaa19a2305a1dd9ab6b55054d167a578439a6dae8197 |
import numpy as np
from ase import Atoms
from gpaw import GPAW, FermiDirac
from gpaw.response.df import DielectricFunction
from gpaw.test import equal, findpeak
GS = 1
ABS = 1
if GS:
cluster = Atoms('Au2', [(0, 0, 0), (0, 0, 2.564)])
cluster.set_cell((6, 6, 6), scale_atoms=False)
cluster.center()
calc ... | robwarm/gpaw-symm | gpaw/test/au02_absorption.py | Python | gpl-3.0 | 2,114 | [
"ASE",
"GPAW"
] | 6f3138757b0b46fa9e9e3176d2d384ca93041a22f83b16a2f7cbe4be745e517e |
# $HeadURL$
__RCSID__ = "$Id$"
from socket import socket, AF_INET, SOCK_DGRAM
import struct
import time as time
import datetime
from DIRAC import S_OK, S_ERROR
TIME1970 = 2208988800
gDefaultNTPServers = [ "pool.ntp.org" ]
def getNTPUTCTime( serverList = None, retries = 2 ):
data = '\x1b' + 47 * '\0'
if not serve... | fstagni/DIRAC | Core/Utilities/NTP.py | Python | gpl-3.0 | 1,161 | [
"DIRAC"
] | 173db7b04fc0f039c7d813479d8ad8b71e8b2ca6368e8cebcbf040a44f4dc2a1 |
'''
Arthur Glowacki
APS ANL
10/17/2014
'''
import sys
import vtk
import math
from PyQt4 import QtCore, QtGui
from vtk.qt4.QVTKRenderWindowInteractor import QVTKRenderWindowInteractor
from Scanner import Scanner
from Volumizer import Volumizer
import h5py
from Generator import GenerateWithCubesAndSphereThread
import r... | aglowacki/ScanSimulator | MainWindow.py | Python | gpl-2.0 | 17,635 | [
"VTK"
] | 5bf2d02bad8db54def53ce370d722d5e04e74657861f18cd61af5222e5ef7075 |
from math import floor
from world import World
import queue
import socketserver
import datetime
import random
import re
import requests
import sqlite3
import sys
import threading
import time
import traceback
DEFAULT_HOST = '0.0.0.0'
DEFAULT_PORT = 4080
DB_PATH = 'craft.db'
LOG_PATH = 'log.txt'
CHUNK_SIZE = 32
BUFFER... | a101010/Craft | server.py | Python | mit | 24,788 | [
"VisIt"
] | b6fd7fb78399ecbda1f0b2b88346c92acdda84299d63ff321a00b596715607a9 |
"""
A simple implementation of the Kalman Filter, Kalman Smoother, and EM
algorithm for Linear-Gaussian state space models.
Primarily adapted from Daniel Duckworth's pykalman library.
"""
import warnings
import numpy as np
import numpy.random
from numpy import shape, zeros, outer, dot, array, all, asarray
from scipy ... | rbharath/switch | Switch/simple_kalman.py | Python | bsd-2-clause | 17,759 | [
"Gaussian"
] | 1588cf544ddba034d0252ec0698d1cc8a38ff2a393b01f9d5715181730bab379 |
# Copyright 2010-2011 by Peter Cock. 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.
"""Provides code to access the TogoWS integrated websevices of DBCLS, Japan.
This module ai... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/TogoWS/__init__.py | Python | gpl-2.0 | 13,691 | [
"BLAST",
"Biopython"
] | 592a1b9b9c1bb913442c84b5857c087e4666ddef89a449c07cdd1170a0f0173f |
"""
test views
"""
import datetime
import json
import re
import pytz
import ddt
import urlparse
from mock import patch, MagicMock
from nose.plugins.attrib import attr
from capa.tests.response_xml_factory import StringResponseXMLFactory
from courseware.courses import get_course_by_id
from courseware.tests.factories imp... | ZLLab-Mooc/edx-platform | lms/djangoapps/ccx/tests/test_views.py | Python | agpl-3.0 | 40,635 | [
"VisIt"
] | 46a01b32f373d6f190b2b39d8171d2152b0ca46b798a4f03853d6eac35279ee6 |
# -*- coding: utf-8 -*-
"""
@namespace Desenho
Pixmap manipulation
Copyright 2007, NATE-LSI-EPUSP
Oficina is developed in Brazil at Escola Politécnica of
Universidade de São Paulo. NATE is part of LSI (Integrable
Systems Laboratory) and stands for Learning, Work and Entertainment
Research Group. Visit our web p... | samdroid-apps/paint-activity | Desenho.py | Python | gpl-2.0 | 32,007 | [
"VisIt"
] | 7f04d5b6bfd9ff4b9d170d7b66358233074a62f252d6bbf1538875d94c90ee23 |
# coding=utf-8
# Copyright 2022 The Uncertainty Baselines 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 ap... | google/uncertainty-baselines | baselines/jft/experiments/imagenet21k_vit_base16_sngp_finetune_cifar.py | Python | apache-2.0 | 5,192 | [
"Gaussian"
] | b5bccf94c6e08e198a5440438c39a1779811823e73dae4f7c60b60f015b70ae9 |
#!/usr/bin/env python
#
# This example reads a volume dataset and displays it via volume rendering.
#
import vtk
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Create the renderer, the render window, and the interactor. The renderer
# draws into the render window, the interact... | hlzz/dotfiles | graphics/VTK-7.0.0/Examples/Medical/Python/Medical4.py | Python | bsd-3-clause | 4,778 | [
"VTK"
] | a051f5d56b0c931bb8f48e861abd46078daa480f39a0f6d2bcae36c79a9f6e5f |
# Copyright (c) 2001-2014, Canal TP and/or its affiliates. All rights reserved.
#
# This file is part of Navitia,
# the software to build cool stuff with public transport.
#
# Hope you'll enjoy and contribute to this project,
# powered by Canal TP (www.canaltp.fr).
# Help us simplify mobility and open public tr... | Tisseo/navitia | source/jormungandr/jormungandr/utils.py | Python | agpl-3.0 | 19,960 | [
"VisIt"
] | 264eb9ad853c0291078c959178ecc49e484142cfca2f3760fe186fe470f7192c |
"""
Tests for miscellaneous utilities.
"""
import cPickle
import gzip
import numpy as np
import shutil
import tempfile
import unittest
from rdkit import Chem
from rdkit.Chem import AllChem
from vs_utils.utils import (DatasetSharder, pad_array, read_pickle,
ScaffoldGenerator, SmilesGenerato... | rbharath/vs-utils | vs_utils/utils/tests/test_utils.py | Python | gpl-3.0 | 12,316 | [
"RDKit"
] | cd9122a53d4b36a3e523f4c653f9a52567f55f32cc4ea366ee329fda9383fb67 |
#!/usr/bin/env python
# vim:fileencoding=utf-8
from __future__ import (unicode_literals, division, absolute_import,
print_function)
__license__ = 'GPL v3'
__copyright__ = '2013, Kovid Goyal <kovid at kovidgoyal.net>'
import sys
from functools import partial
from PyQt4.Qt import (
QMainWin... | palerdot/calibre | src/calibre/gui2/tweak_book/editor/image.py | Python | gpl-3.0 | 10,092 | [
"Gaussian"
] | e00ca7965efaa50ec3797f0dd70a42e8306aa1eed67b1f4d9d5bef72ee624c60 |
"""Print out the source text corresponding to AST nodes.
"""
import os
import astroid
import colorama
import inflection
from colorama import Back, Fore, Style
import python_ta.transforms.setendings as setendings
colorama.init(strip=False, autoreset=True)
def _wrap_color(code_string):
"""Wrap key parts in styli... | pyta-uoft/pyta | sample_usage/print_nodes.py | Python | gpl-3.0 | 3,092 | [
"VisIt"
] | b55d4dce3ff79e6918b0e8eee251519fc5a12ce27c200c0bc20aeafb47b67cb3 |
import numpy
from .network import generate_full_rank_matrix
def unscaled_control_coefficients(stoichiometry, elasticity):
_, n = stoichiometry.shape
# do Gaussian elimination,
# and get reduced stoichiometry, kernel and link matrix
link_matrix, kernel_matrix, independent_list = generate_full_rank_ma... | ecell/ecell4 | ecell4/mca/cc.py | Python | gpl-3.0 | 2,045 | [
"Gaussian"
] | 25f943a51dc69c14c40ea2a5ba2fa3e5977d1777f549bf518396cfcf527951e6 |
# Writing Functions That Accept Any Number of Arguments
def avg(first, *rest):
return (first + sum(rest)) / (1 + len(rest))
# Sample use
print(avg(1, 2)) # 1.5
print(avg(1, 2, 3, 4)) # 2.5
# Writing Functions That Only Accept Keyword Arguments
def mininum(*values, clip=None):
m = min(values)
if clip is not... | rmzoni/python3-training | study/functions.py | Python | apache-2.0 | 1,877 | [
"Brian"
] | bd9cc8f9c723bf28881857f6d9af735dc6475d0f1f5b0d5855785667d748277d |
# -*- coding: utf-8 -*-
# coding: utf-8
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Generic interfaces to manipulate registration parameters files, including
transform files (to configure warpings)
"""
from __future__ import print_function, div... | carolFrohlich/nipype | nipype/interfaces/elastix/utils.py | Python | bsd-3-clause | 5,816 | [
"VTK"
] | 1acec2477f38e738762c85aad6ae6a35a4e13896bca8b618e92665612561c29e |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | sugartom/tensorflow-alien | tensorflow/contrib/layers/python/layers/feature_column_test.py | Python | apache-2.0 | 38,569 | [
"MOOSE",
"Octopus"
] | c36c2a64d5b77c9e725f820e1606820c3e9bfb1e12e6ac2773ab06caef8da3dc |
import click
from parsec.cli import pass_context, json_loads
from parsec.decorators import custom_exception, json_output
@click.command('show_data_table')
@click.argument("data_table_id", type=str)
@pass_context
@custom_exception
@json_output
def cli(ctx, data_table_id):
"""Get details of a given data table.
Out... | galaxy-iuc/parsec | parsec/commands/tool_data/show_data_table.py | Python | apache-2.0 | 807 | [
"Galaxy"
] | 2532fe21f8911301706f8732e7ab402828912b26fa720e6e4263ca97dd4c3bbf |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
@brief: Import netcdf temperature data in GRASS GIS
This program is free software under the GNU General Public License
(>=v2). Read the file COPYING that comes with GRASS for details.
@author: Brendan Harmon (brendanharmon@gmail.com)
"""
import os
import sys
import ... | baharmon/panama_hydrological_modeling | utilities/temperature_stats.py | Python | gpl-2.0 | 2,943 | [
"NetCDF"
] | 82bd00712a2ac3b5c43f56e35854391acd61878fd904a789fa6c82ac54379ab2 |
#!/usr/bin/env python
__author__ = "Mike McCann"
__copyright__ = "Copyright 2011, MBARI"
__credits__ = ["Chander Ganesan, Open Technology Group"]
__license__ = "GPL"
__version__ = "$Revision: 1.1 $".split()[1]
__maintainer__ = "Mike McCann"
__email__ = "mccann at mbari.org"
__status__ = "Development"
'''
The DAPloader... | stoqs/stoqs | stoqs/loaders/DAPloaders.py | Python | gpl-3.0 | 144,075 | [
"NetCDF"
] | 0143ccf3804a3af19bbbf35907354ff7469fcf685916bf76bc406c49cb02051c |
# coding: utf-8
from django.shortcuts import render
def hello(request):
# request.GET, request.POST and request.COOKIES are dictionary-like
# objects, meaning you can access them like you can access a dictionary.
# So you can make request.GET['name'] or request.POST['name'] or
# request.COOKIES['na... | sametmax/Django--an-app-at-a-time | apps/app5_get_post_and_cookies/views.py | Python | mit | 2,209 | [
"VisIt"
] | 25d1193b2ef5dedf1d60b93d4da2c506c8f1e03cc6177ce34e2b1a5ceefa29b0 |
import jinja2 as j
import os, errno
import visitors.visitor as v
import state_machinery.state_mach as sm
class Template(v.Visitor):
def __init__(self,filename):
self.filename = filename
loader = j.PackageLoader('statemach', 'visitors/templates')
self.environment = j.Environment(loader=loader)
... | bwtaylor/statemach | visitors/template.py | Python | apache-2.0 | 1,512 | [
"VisIt"
] | e55db31158025b9be0203b6cb4e4bab16f91bce3371a271c7f3c54d69d1ab7bf |
import os
import MooseDocs
import utils
import logging
log = logging.getLogger(__name__)
def generate_options(parser, subparser):
"""
Command-line options for generate command.
"""
generate_parser = subparser.add_parser('generate', help="Check that documentation exists for your application and generate the ma... | vityurkiv/Ox | python/MooseDocs/commands/generate.py | Python | lgpl-2.1 | 2,000 | [
"MOOSE"
] | e115a29a95bacab98f42d961957d6fc9ca096b65d2df29bcd2a55e52719cccc3 |
from __future__ import (absolute_import, division, print_function)
import numpy as np
import time
from mantid import mtd
from mantid.kernel import StringListValidator, Direction, FloatBoundedValidator
from mantid.api import PythonAlgorithm, MultipleFileProperty, FileProperty, FileAction, WorkspaceGroupProperty, Progre... | wdzhou/mantid | Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/IndirectILLReductionFWS.py | Python | gpl-3.0 | 26,218 | [
"CRYSTAL"
] | e383b390b954402e937269f6ab4900f1dc78ddbd7c4acc16cd6280ee6b19cc89 |
# Basic imports
import os
import sys
import inspect
import debug
from lxml import etree
import collections
def parseAndValidateWithSchema(modelName, modelPath) :
prefixPath = ''
if modelName == 'xml' :
schemaPath = os.path.join(prefixPath, 'schema/moose/moose.xsd')
if not os.path.isfile(schem... | rahulgayatri23/moose-core | python/libmumbl/utility/xml_parser.py | Python | gpl-3.0 | 2,282 | [
"MOOSE"
] | d2a22f3902e3f231ea54a6443f437efb3a35373dd19b88ea879171724fa4097a |
# -*- coding: utf-8 -*-
"""
End-to-end tests related to the cohort management on the LMS Instructor Dashboard
"""
import os
import uuid
from datetime import datetime
import unicodecsv
from bok_choy.promise import EmptyPromise
from pytz import UTC, utc
from common.test.acceptance.fixtures.course import CourseFixture
... | jolyonb/edx-platform | common/test/acceptance/tests/discussion/test_cohort_management.py | Python | agpl-3.0 | 42,473 | [
"VisIt"
] | d46c2d349d7dd823ffc1c1f519c82a5e83751dcdb4cdf6f4fd7cc84c3e21cb62 |
from __future__ import print_function
from builtins import range
import sys
sys.path.insert(1,"../../../")
import h2o
from tests import pyunit_utils
import random
from h2o.estimators.gbm import H2OGradientBoostingEstimator
def cv_cars_gbm():
# read in the dataset and construct training set (and validation set)
ca... | h2oai/h2o-3 | h2o-py/tests/testdir_algos/gbm/pyunit_cv_cars_gbm.py | Python | apache-2.0 | 7,143 | [
"Gaussian"
] | fbb607408cb7f80195976a7d498026f73f7b1542d2e50021a9652534eaaa6aaf |
"""This is the main file you run to start a pinball machine."""
# mpf.py
# Mission Pinball Framework
# Written by Brian Madden & Gabe Knuth
# Released under the MIT License. (See license info at the end of this file.)
# Documentation and more info at http://missionpinball.com/mpf
import logging
from datetime import da... | jabdoa2/mpf | mpf.py | Python | mit | 5,347 | [
"Brian"
] | 0bc37921bab5c90011e0185a17cb0ed8b779f3747ed49aae5379ee62a60fcd7d |
from setuptools import setup
setup(
name = "GPclust",
version = "0.1.0",
author = "James Hensman",
author_email = "james.hensman@sheffield.ac.uk",
url = "http://staffwww.dcs.sheffield.ac.uk/people/J.Hensman/gpclust.html",
description = ("Clustering of time series using Gaussian processes and va... | jameshensman/GPclust | setup.py | Python | gpl-3.0 | 583 | [
"Gaussian"
] | 3be3cf22c2897160cdb4e12642992a3625d51263c3ead1013440eb69163d53bc |
import numpy as np
import os
from os.path import join as pjoin
from numpy.testing import assert_raises, assert_array_equal
from tempfile import mktemp
import nibabel as nib
from surfer import Brain
from surfer import io, utils
from surfer.utils import requires_fsaverage
from mayavi import mlab
subj_dir = utils._get_s... | aestrivex/PySurfer | surfer/tests/test_viz.py | Python | bsd-3-clause | 9,130 | [
"Mayavi"
] | 263ef0d56edc819183684bcb33b0123a30907de9c613a8439e50a44078b987e4 |
# Copyright 2021 Open Source Robotics Foundation, Inc.
#
# 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... | ros2/launch | launch_yaml/test/launch_yaml/test_reset.py | Python | apache-2.0 | 2,408 | [
"VisIt"
] | 5de241c108962f30f059988f898ec9159c4983cf909578e0f5140317ddfc5f6b |
from __future__ import division, print_function
from __future__ import absolute_import
from __future__ import unicode_literals
from os import path
from re import match, findall, sub
import pysces
from sympy import Symbol, sympify
from datetime import datetime
# File reading/validation functions
def get_term_types_... | PySCeS/PyscesToolbox | psctb/analyse/_thermokin_file_tools.py | Python | bsd-3-clause | 36,903 | [
"PySCeS"
] | c2862f4cae32939526b05e67067a70a0314dab395b5ac98a2717be7c2b844de6 |
#!/usr/bin/env python
# this script checks if any piRNA sequences BLAST to the TE sequences with varying percent identities
# first 8 bases of piRNA must match
# USE: piBLAST.py
import re
import sys
import os
from subprocess import Popen, PIPE
from collections import defaultdict
from collections import Counter
import... | klaricch/Transposons2 | scripts/piBLAST.py | Python | mit | 4,911 | [
"BLAST"
] | b8c92789a48fefafc59303fd11104cea5059e01fa8b567f50a612ddb76fd30b0 |
import math
import numpy
import numpy.ma
import datetime
from scipy.interpolate import RegularGridInterpolator
import matplotlib.pyplot as plt
from antpat.io.feko_ffe import FEKOffe, FEKOffeRequest
from .pntsonsphere import sph2crtISO
class TVecFields(object):
"""Provides a tangetial vector function on a spherica... | 2baOrNot2ba/AntPat | antpat/reps/sphgridfun/tvecfun.py | Python | isc | 21,293 | [
"Mayavi"
] | 86cfc63df249fd9c15fc2fc59239879cce7cd6f05662707efcae186f302e1fc4 |
#!/usr/bin/python
#
# Open SoundControl for Python
# Copyright (C) 2002 Daniel Holth, Clinton McChesney
#
# 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 Foundation; either
# version 2.1 of the Licen... | shouldmakemusic/yaas | LiveOSC/OSCMessage.py | Python | gpl-2.0 | 2,574 | [
"VisIt"
] | 77bcd241ae2e9f30e4d2d946b94873a16c7f94b8d2fe269a733cd2eb96a31deb |
"""
Module containing analysis functions for raster datasets.
"""
import itertools, operator
from .data import *
from . import manager
from .. import vector
import PIL.Image, PIL.ImageMath, PIL.ImageStat, PIL.ImageMorph
import math
# Zonal aggregation
def zonal_statistics(zonaldata, valuedata, zonalband=0, valueb... | karimbahgat/PythonGis | pythongis/raster/analyzer.py | Python | mit | 25,155 | [
"Gaussian"
] | b4324153bf174d79c32b3ee5048e959583c5fd42fa784423578083274f56d745 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2008 Jerome Rapinat
# Copyright (C) 2008 Benny Malengier
#
# 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 Fre... | Forage/Gramps | gramps/gen/filters/rules/person/_haslds.py | Python | gpl-2.0 | 1,770 | [
"Brian"
] | 24bdb44e3e65211b42b49481c702f2fc5215761696810d4f1855e31a4eff85c6 |
from openpnm.network import GenericNetwork, Cubic
from openpnm import topotools
from openpnm.utils import logging, Workspace
import numpy as np
logger = logging.getLogger(__name__)
ws = Workspace()
class Bravais(GenericNetwork):
r"""
Crystal lattice types including fcc, bcc, sc, and hcp
These arrangement... | TomTranter/OpenPNM | openpnm/network/Bravais.py | Python | mit | 9,623 | [
"CRYSTAL",
"ParaView"
] | e8ff1d61d09dbfa7356a2d9019df7aeeceeb8adaae8090b59a1e48cd6243246a |
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import json
import os
import os.path
import re
import sys
import warnings
from collections import defaultdict
try:
from setuptools import setup, find_packages
from setuptools.command.build_py import build_py as BuildPy
... | Fale/ansible | setup.py | Python | gpl-3.0 | 15,580 | [
"Galaxy"
] | d5abb02396368d644a242e65dfa64224a163f33e2392b2711a5bf62c129b011a |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
import tempfile
import numpy as np
from pymatgen.core.structure import Structure
from pymatgen.io.abinit.inputs import (
BasicAbinitInput,
BasicMultiDataset,
ShiftMode,
calc_shiftk,
ebands_input... | materialsproject/pymatgen | pymatgen/io/abinit/tests/test_inputs.py | Python | mit | 10,855 | [
"ABINIT",
"pymatgen"
] | 747285d6d0354463ef17b21d6d7f4d12be5e8be1b292711c803a33ae86c0d271 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import sys
from os import system
try:
import pygimli as pg
except ImportError:
sys.stderr.write('ERROR: cannot import the library pygimli.' +
'Ensure that pygimli is in your PYTHONPATH')
sys.exit(1)
def createCoarsePoly(coarseData):
... | florian-wagner/gimli | python/apps/pycreatesurface.py | Python | gpl-3.0 | 4,685 | [
"VTK"
] | e7698abfc341632630b5d0ea8f0e7e7ba8c505780193f3466129b0d7efe6ad00 |
import pynet,netext,percolator
import random
import numpy as np
def mst(net,maximum=False):
"""Find a minimum/maximum spanning tree
"""
return mst_kruskal(net,True,maximum)
def mst_kruskal(net,randomize=True,maximum=False):
"""Find a minimum/maximum spanning tree using Kruskal's algorithm
If ran... | jsaramak/ants | transforms.py | Python | gpl-2.0 | 16,559 | [
"VisIt"
] | cd0405199267f96a1a25e9ee7d2b1ad6db9d5d1d81d70b535f186ef16f4c2dea |
# Copyright (C) 2012 Alex Nitz
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 3 of the License, or (at your
# option) any later version.
#
# This program is distributed in the... | pannarale/pycbc | pycbc/waveform/waveform.py | Python | gpl-3.0 | 43,562 | [
"Gaussian"
] | 16e36a92a946b4c5b436a12b06b40008ebd088122d1a11c47e6e7c7cf297f8bb |
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