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# coding: utf-8
# (c) 2015-12-30 Teruhisa Okada
import visit_writer, math
NX = 10
NY = 20
NZ = 30
# Create a zonal variable
zonal = []
index = 0
for k in range(NZ-1):
for j in range(NY-1):
for i in range(NX-1):
zonal = zonal + [index]
index = index + 1
# Create a noda... | okadate/romspy | romspy/visit.py | Python | mit | 672 | [
"VTK"
] | 0a94ac671a8fc4faf66ace99d3b7eaaaafd2c5c0b9ea418e3fb5d11168f0896d |
# $Id$
#
# Copyright (C) 2007 Greg Landrum
# All Rights Reserved
#
import copy
class pySparseIntVect(object):
""" this class is pretty much obsolete (it's in C++ now) """
size=0
container={}
def __init__(self,size):
self.size=size
self.container={}
def UpdateFromSequence(self,seq):
"""
>>... | rdkit/rdkit-orig | rdkit/DataStructs/SparseIntVect.py | Python | bsd-3-clause | 9,456 | [
"RDKit"
] | 3222e316c4a9de194da6fbd53c4d61cad0676c05a128b27af6b75b07e7d58365 |
"""
libChEBIpy (c) University of Manchester 2015-2020
libChEBIpy is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
"""
import os.path
import tempfile
import shutil
import six.moves.urllib.parse as urlparse
from google.cloud impo... | libChEBI/libChEBIpy | libchebipy/_parsers/googlestorage.py | Python | mit | 3,287 | [
"VisIt"
] | c47e01c64a9cdfb57023f91e84504bb6db5e982911a2f7b250def65293bd2c51 |
##############################################################################
# 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... | EmreAtes/spack | var/spack/repos/builtin/packages/py-htseq/package.py | Python | lgpl-2.1 | 1,930 | [
"HTSeq",
"pysam"
] | 99aad6ed4e87937be3e25db706ffaef659018af7dee042e3d045c83f12dffa28 |
import os.path
import cPickle as pickle
import functools
import numpy as np
from ml import mnist, utils, optimize, rbm, grbm, data, meta
from ml import regularization as reg
DATA_PATH = os.path.expanduser("~/Development/ml/datasets")
def load_inputs():
# This data set is sampled from Bruno Olshausen's unwhitene... | phorsfall/ml | ex/grbm/patches.py | Python | mit | 5,475 | [
"Gaussian"
] | 45011d60e153aa5b4ff4c33355a0f39472753a3ae6dea6af73967b05f06f6a8b |
# -*- coding: utf-8 -*-
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
from time import time
import os.path
from os import listdir
import re
from math import exp, log
import sys
import numpy as np
from scipy.specia... | stggh/PyAbel | abel/basex.py | Python | mit | 22,115 | [
"Gaussian"
] | 733142321b8b0772078b4806b231d40c5b173dc7d2adc9e1c73e8b47ada3b231 |
#!/usr/local/sci/bin/python
#***************************************
#11 Jun 2015 KMW - v1
# Takes any gridded field of mnnthly mean sea level pressure
# Can have long/lat/time manually or read in
# Pulls out gridbox closest to Darwin and Tahiti
# Calculates SOI for series
# Saves SOI time series to file
#***********... | Kate-Willett/Climate_Explorer | PYTHON/PullSOIfromGrids_JUN2015.py | Python | cc0-1.0 | 15,236 | [
"NetCDF"
] | 8054224e4becdf6bb603c804b62e29fffde24454364606ad9840ec9fe32c2ab1 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2018 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | amjames/psi4 | psi4/driver/qcdb/modelchems.py | Python | lgpl-3.0 | 30,590 | [
"CHARMM",
"Psi4"
] | bcc07bf417f83a5f12a383e9532ea003f35d39a8074b407ddd36a83dc21c42cc |
import functools
import logging
from pip._vendor import six
from pip._vendor.packaging.utils import canonicalize_name
from pip._vendor.resolvelib import BaseReporter, ResolutionImpossible
from pip._vendor.resolvelib import Resolver as RLResolver
from pip._internal.exceptions import InstallationError
from pip._interna... | sserrot/champion_relationships | venv/Lib/site-packages/pip/_internal/resolution/resolvelib/resolver.py | Python | mit | 10,149 | [
"VisIt"
] | 908f20d0d565608b03311983a65590768c7a58efb41fb088db037ed62c6769ec |
# -*- encoding: utf-8 -*-
"""Test class for Remote Execution Management UI
:Requirement: Remoteexecution
:CaseAutomation: Automated
:CaseLevel: Acceptance
:CaseComponent: RemoteExecution
:TestType: Functional
:CaseImportance: High
:Upstream: No
"""
from datetime import datetime, timedelta
from fauxfactory impor... | ldjebran/robottelo | tests/foreman/cli/test_remoteexecution.py | Python | gpl-3.0 | 28,883 | [
"Galaxy"
] | 6576c85d69e201835f36e941681d6ded85cc8d7f58fb2c76aa650b091ea89893 |
import ast
import pytest
from pre_commit_hooks.debug_statement_hook import debug_statement_hook
from pre_commit_hooks.debug_statement_hook import DebugStatement
from pre_commit_hooks.debug_statement_hook import ImportStatementParser
from testing.util import get_resource_path
@pytest.fixture
def ast_with_no_debug_im... | arahayrabedian/pre-commit-hooks | tests/debug_statement_hook_test.py | Python | mit | 1,705 | [
"VisIt"
] | 2cf43ea8a35c2cbe490401ff52f2a689df15772d780805f1f82e494a00a61fef |
from __future__ import print_function
def square(val):
return val*val
def bool_to_val(txt):
if txt.upper() in ["TRUE", "YES"]:
return 1.0
return 0.0
def val_to_bool(val):
if val != 0:
return "True"
return "False"
def printnum():
print("2.25")
def printtxt():
print("some... | akohlmey/lammps | unittest/python/func.py | Python | gpl-2.0 | 565 | [
"LAMMPS"
] | 9e613ce9528be013cfc6bfe492010b11aa351e0e065e7918bef3445b3aea2aff |
#!/usr/bin/env python3
# Ian Czekala
# Harvard University Astronomy Grad Student
# Routines for interpreting astronomical spectra of expanding objects.
# All units cgs, angstroms.
# docstrings can be called on any of the functions by doing Python's
# "help(function)"
import matplotlib
matplotlib.use("Qt4Agg")
import... | iancze/Pysplotter | spectrum.py | Python | mit | 18,908 | [
"Galaxy",
"Gaussian"
] | bef762e8fd3d471d7b88ae12c4b8eccf73417050006d1d756edc78cd28f8540d |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements various equation of states.
Note: Most of the code were initially adapted from ASE and deltafactor by
@gmatteo but has since undergone major refactoring.
"""
from copy import deepc... | dongsenfo/pymatgen | pymatgen/analysis/eos.py | Python | mit | 19,152 | [
"ASE",
"pymatgen"
] | ebfcb100dadf0ee10fbdc8f36354b5d80ac74290f94ab24bc5bb22195d5478da |
##############################################################################
# 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... | tmerrick1/spack | var/spack/repos/builtin/packages/fast-gbs/package.py | Python | lgpl-2.1 | 2,356 | [
"BWA"
] | ce25e17a07b50a8bcbf149067f09fe9bc6b44cdb13567991dfe5b191dad430f5 |
from sympy.physics.matrices import msigma, mgamma, minkowski_tensor
from sympy import zeros, eye, I
def test_Pauli():
#this and the following test are testing both Pauli and Dirac matrices
#and also that the general Matrix class works correctly in a real world
#situation
sigma1=msigma(1)
sigma2=m... | devs1991/test_edx_docmode | venv/lib/python2.7/site-packages/sympy/physics/tests/test_physics_matrices.py | Python | agpl-3.0 | 1,312 | [
"DIRAC"
] | 922abae3ccd55052d8e056650d452c09872877fb985862e2c4d8188a207d7d71 |
"""
Tests for geography support in PostGIS
"""
import os
from unittest import skipIf, skipUnless
from django.contrib.gis.db import models
from django.contrib.gis.db.models.functions import Area, Distance
from django.contrib.gis.measure import D
from django.db import connection
from django.db.models.functions import Ca... | mitya57/django | tests/gis_tests/geogapp/tests.py | Python | bsd-3-clause | 6,952 | [
"VisIt"
] | e7a33ee43c0da04ed9743c8b845fdead4c1bcb2425c6aeb536d3c0146232ef4e |
#
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2006 Donald N. Allingham
# Copyright (C) 2007-2009 Brian G. Matherly
# Copyright (C) 2008 Raphael Ackermann
# 2002-2003 Donald A. Peterson
# 2003 Alex Roitman
# 200... | pmghalvorsen/gramps_branch | gramps/plugins/docgen/latexdoc.py | Python | gpl-2.0 | 48,547 | [
"Brian"
] | 9b14cb038ae2b8a81cc1a2c9179c231e54a08b151e883e35ce4dce2e7ef47c11 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# This file is part of pyunicorn.
# Copyright (C) 2008--2015 Jonathan F. Donges and pyunicorn authors
# URL: <http://www.pik-potsdam.de/members/donges/software>
# License: BSD (3-clause)
"""
Provides classes for generating and analyzing complex climate networks.
"""
#
# Im... | leftaroundabout/pyunicorn | pyunicorn/climate/rainfall.py | Python | bsd-3-clause | 12,122 | [
"Gaussian"
] | 63106d03cfc077b3c91e03ee4713baa226eb4f62813dcbc466df05d600a3f36c |
"""
https://github.com/kudkudak
"""
import os
import pybel
import tempfile
import subprocess
import numpy as np
# from openbabel import OBSpectrophore # uncomment after Segmentation fault fix
# from pybel import Molecule
def molprint2d_fingerprint(mpd, d=50):
"""
mpd: str molprint2D repr of mol
D - size... | DentonJC/virtual_screening | moloi/descriptors/spectrophore_descriptor.py | Python | gpl-3.0 | 3,817 | [
"Pybel"
] | bba3ff838be8f2d09caec17687866c3b2f4c15c47cf4fff8e3671ad9ee62f7d4 |
# ============================================================================
#
# Copyright (C) 2007-2010 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | kurtraschke/camelot | camelot/view/plugins/__init__.py | Python | gpl-2.0 | 2,018 | [
"VisIt"
] | a6e144a5a5bd5e140a47893fa3d1a5d65f95261a2361e2a9119861ab21e2644b |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright 2010 British Broadcasting Corporation and Kamaelia Contributors(1)
#
# (1) Kamaelia Contributors are listed in the AUTHORS file and at
# http://www.kamaelia.org/AUTHORS - please extend this file,
# not this notice.
#
# Licensed under the Apache License, Ve... | sparkslabs/kamaelia_ | Sketches/MH/exceptions/Axon/util.py | Python | apache-2.0 | 3,208 | [
"MOE"
] | 1a472ed22c0787c84f89df17239c1b99d3ea13b064d707431328ab0036890deb |
"""Python wrapper for Google web APIs
This module allows you to access Google's web APIs through SOAP,
to do things like search Google and get the results programmatically.
Described here:
http://www.google.com/apis/
You need a Google-provided license key to use these services.
Follow the link above to get one. ... | XtremeTeam/Talisman-xmpp-bot | modules/google.py | Python | gpl-2.0 | 16,801 | [
"VisIt"
] | 65eb36adda597b1116e79588005ccf021cb6cb9311a49bf8282c85ff515ef9e3 |
# -*- coding: utf-8 -*-
# Copyright (C) 2010-2015 Bastian Kleineidam
#
# 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.
#... | wummel/patool | tests/archives/test_unadf.py | Python | gpl-3.0 | 1,355 | [
"ADF"
] | 89044671f22138cd678befc707e41376645445db1ca26d8e9a8f0b243db99ee7 |
from __future__ import print_function, division
import imgaug as ia
from imgaug import augmenters as iaa
from imgaug import parameters as iap
import numpy as np
from scipy import ndimage, misc
from skimage import data
import matplotlib.pyplot as plt
from matplotlib import gridspec
import six
import six.moves as sm
impo... | nektor211/imgaug | generate_example_images.py | Python | mit | 21,547 | [
"Gaussian"
] | f60696cf92cc784b50c5ab1c50670df3772c23fb4f6eb0b146d17f9922ab5dc9 |
#Written by Amanda Daigle
#Ernest Fraenkel's lab
#MIT Biological Engineering
#2013-2014
import sys, argparse, random, copy, os
import subprocess, tempfile
import networkx as nx
from operator import itemgetter
import multiprocessing as mp
def score(value, mu, musquared):
"""
Helper function for use in assig... | agitter/OmicsIntegrator | scripts/forest.py | Python | bsd-2-clause | 75,288 | [
"Cytoscape",
"Gaussian"
] | ea4c5a95c9964214b9dc370c9e2424b6dd175bb98f1a015988e4f95eb93dab68 |
import grace
import grace.times
import grace.ols
import numpy as np
import matplotlib.pyplot as plt
import cPickle as pickle
import sklearn.mixture as skm
import sklearn.decomposition as skd
import time
import mpl_toolkits.basemap as maps
import matplotlib as mpl
import grace
import grace.times
days=grace.ols.time_ve... | AndreasMadsen/grace | Code/clustering_ica_10.py | Python | mit | 2,833 | [
"Gaussian"
] | 5d04e9cf42654d91ed4334f5beaadfbc17ea6b5b0bfbcd7e225c47c25f8bc9d8 |
#This code packages manually calibrated and imaged datasets
# --------------------------------------------------------------------------------------------------
def ReadDataFromWeb(mousid):
# --------------------------------------------------------------------------------------------------
"""
This function... | bmarshallk/NAASC | packaging_scripts/PackageManualDataset.py | Python | gpl-3.0 | 14,173 | [
"VisIt"
] | c4c0cc28ae0ad53474358c37978931119b32bd26260bc08240aba5da8a2e7d35 |
"""
PyEarthScience: Cartopy contour plot example
- filled contour over map plot
- rectilinear grid (lat/lon)
- colorbar
10.11.15 kmf
"""
import netCDF4 as nc
import matplotlib.pyplot as plt
import numpy as np
import cartopy.crs as ccrs
def read_netCDF_file():
"""Read netcdf file and return ar... | KMFleischer/PyEarthScience | Visualization/Cartopy/contour_rectilinear_cartopy.py | Python | mit | 983 | [
"NetCDF"
] | 6320d26ffed5e1855001b89715841f415b27657effd7e4709ca173fe0a6703a2 |
import os
import lan
debug = False
class CGenerator(object):
""" Uses the same visitor pattern as the NodeVisitor, but modified to
return a value from each visit method, using string accumulation in
generic_visit.
"""
def __init__(self):
self.output = ''
self.quotes = '\... | dikujepsen/OpenTran | v3.0/framework/codegen/cgen.py | Python | mit | 9,632 | [
"VisIt"
] | 8a0ccc8e5b364b83352cc037b63d9b178c343843b00e5ffd6998cf109fb310cf |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements an interface to enumlib, Gus Hart"s excellent Fortran
code for enumerating derivative structures.
This module depends on a compiled enumlib with the executables enum.x and
makestr.x available in the... | vorwerkc/pymatgen | pymatgen/command_line/enumlib_caller.py | Python | mit | 17,447 | [
"VASP",
"pymatgen"
] | cfef6fab2021cd4f410615990aeeefe4b96998fed29456f8c5940982e7c181c3 |
from setuptools import setup, find_packages
setup(
name='bayesian-optimization',
version='1.2.0',
url='https://github.com/fmfn/BayesianOptimization',
packages=find_packages(),
author='Fernando Nogueira',
author_email="fmfnogueira@gmail.com",
description='Bayesian Optimization package',
... | fmfn/BayesianOptimization | setup.py | Python | mit | 682 | [
"Gaussian"
] | fa0f3e8b9fc9f7972d3b395e4ac6a74b0d6331881603d253a26e8e70471daf5c |
# -*- coding: utf-8 -*-
"""
Python module to help specify the source parameters.
.. module:: source
:author:
Shahar Shani-Kadmiel (s.shanikadmiel@tudelft.nl)
:copyright:
Shahar Shani-Kadmiel
:license:
This code is distributed under the terms of the
GNU Lesser General Public License, Version 3
(h... | shaharkadmiel/seispy | pySW4/prep/source.py | Python | gpl-3.0 | 3,289 | [
"DIRAC",
"Gaussian"
] | 6996ad7076b0cd61775ee11ab2d96d1d9e243bb1d7cfc55e38eb7d904b994a94 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/transitions | openlp/plugins/custom/lib/mediaitem.py | Python | gpl-2.0 | 13,924 | [
"Brian"
] | 6a203da33034f72cc86cdbde8ea0b95c3c0adcb5aa87e96c4a351855b6157656 |
#!/usr/bin/env python
from __future__ import division
import unittest
import numpy as np
from pymatgen.symmetry.maggroups import *
from pymatgen.symmetry.groups import SpaceGroup
__author__ = "Matthew Horton"
__copyright__ = "Copyright 2017, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Matthew Horton... | matk86/pymatgen | pymatgen/symmetry/tests/test_maggroups.py | Python | mit | 7,084 | [
"pymatgen"
] | a694479ece6430572a67b382e56026986b4fcc546c4e928216e2d7f209049bef |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | MOA-2011/enigma2-plugin-extensions-openwebif | plugin/controllers/views/web/timerlistwrite.py | Python | gpl-2.0 | 5,262 | [
"VisIt"
] | 70e0ebd2441a082c26cfdb7498cdb92ec608c85fdb5429483a7e26cceaea5cf9 |
#!/usr/bin/env python
##############################################################################################
#
#
# regrid_emissions_N96e.py
#
#
# Requirements:
# Iris 1.10, time, cf_units, numpy
#
#
# This Python script has been written by N.L. Abraham as part of the UKCA Tutorials:
# http://www.ukca.ac.u... | acsis-project/emissions | emissions/python/timeseries_1950-2020/regrid_C5H8_emissions_n96e_360d.py | Python | gpl-3.0 | 19,187 | [
"NetCDF"
] | 30cd096771d90414b289a3f0219f4fad39260b552d939064ae14f5deaf8ba686 |
import os
import lan
import lan.ast_buildingblock as ast_bb
debug = False
class SSGenerator(object):
""" Uses the same visitor pattern as the NodeVisitor, but modified to
return a stringstream from each visit method, using string accumulation in
generic_visit.
"""
def __init__(self):
... | dikujepsen/OpenTran | src/framework/codegen/stringstream.py | Python | mit | 10,809 | [
"VisIt"
] | 09c29cabf7cb168c2c2dbfbd6d38c19bce2167108b3648341121ed5eeebab0aa |
from aces.materials import Material
from .atomic import get_unique_atoms
from ase import Atoms,Atom
from math import pi,sqrt
from ase.dft.kpoints import ibz_points
from aces import config
class structure(Material):
def set_parameters(self):
self.gnrtype='armchair'
self.ax=4.6059999466
self.ay=3.3002998829
sel... | vanceeasleaf/aces | aces/materials/BP.py | Python | gpl-2.0 | 1,542 | [
"ASE"
] | 5e58742026f19df0d83b853fb58da0f5864fcfcd3c9e2b3627fae4722b5b9dde |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
try:
from setuptools import setup
except ImportError:
from distutils.core import setup
from distutils.extension import Extension
from setuptools import *
from glob import glob
try:
from Cython.Distutils import build_ext
except ImportError:
use_cython =... | everestial/g2gtools | setup.py | Python | gpl-3.0 | 3,009 | [
"Biopython",
"pysam"
] | cd6a76478306f8f2c5e0434d31340f47f5b95729b3a9b1d4db2f7be791652d62 |
import py
from rpython.rlib.parsing.parsing import PackratParser, Rule
from rpython.rlib.parsing.tree import Nonterminal
from rpython.rlib.parsing.regex import StringExpression, RangeExpression
from rpython.rlib.parsing.lexer import Lexer, DummyLexer
from rpython.rlib.parsing.deterministic import compress_char_set, DFA... | oblique-labs/pyVM | rpython/rlib/parsing/regexparse.py | Python | mit | 76,335 | [
"VisIt"
] | f3cec810b356abdeed54ad7af2ddbd3b79e4c08211e3920515ea95e23c6038f1 |
# Optimize MGH suite with sufficient descent Nelder-Mead optimizer.
from pyopus.optimizer.sdnm import SDNelderMead
from pyopus.optimizer.base import Reporter
from pyopus.problems.mgh import *
from numpy import array, sqrt
from platform import system
if system()=='Windows':
# clock() is the most precise timer in Wind... | blorgon9000/pyopus | demo/optimizer/sdnm.py | Python | gpl-3.0 | 4,148 | [
"Gaussian"
] | 596aef8fe1640c550f173c56494c7c9665473b8b70ee49341b6b62769cbdb2f6 |
# ============================================================================
#
# Copyright (C) 2007-2012 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | jeroendierckx/Camelot | camelot/core/orm/__init__.py | Python | gpl-2.0 | 5,300 | [
"VisIt"
] | 53642445f0b1fa9f37b6d2a945fd91763aa1255b8e8c1d81b78e289c56e1e1fa |
# Copyright (c) 2006-2007, 2009-2014 LOGILAB S.A. (Paris, FRANCE) <contact@logilab.fr>
# Copyright (c) 2012 FELD Boris <lothiraldan@gmail.com>
# Copyright (c) 2013-2021 Claudiu Popa <pcmanticore@gmail.com>
# Copyright (c) 2014 Google, Inc.
# Copyright (c) 2014 Eevee (Alex Munroe) <amunroe@yelp.com>
# Copyright (c) 2015... | PyCQA/astroid | tests/unittest_nodes.py | Python | lgpl-2.1 | 64,148 | [
"VisIt"
] | c06487a524192328b02f99f7472d7534a9356c6e257057be097ace4c8d3b246b |
import os.path
from parser.leftLexer import *
from parser.leftVisitor import *
from parser.leftParser import *
from CodeGen.variables import *
from CodeGen.functions import *
from CodeGen.visitor import *
from CodeGen.irgenerator import IRGenerator
from CodeGen.compiler import IRCompiler
from llvmlite import ir
varn... | LFUnion/left | compiler/CodeGen/visitor.py | Python | mit | 14,758 | [
"VisIt"
] | 7d2dfeafdc0ec704d889c3162e4f15e61a2cc5fa68fb13d8b8c61d8f04b0630b |
# Copyright 2010-2017, The University of Melbourne
# Copyright 2010-2017, Brian May
#
# This file is part of Karaage.
#
# Karaage 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... | brianmay/karaage | karaage/plugins/kgsoftware/tests/test_software.py | Python | gpl-3.0 | 1,561 | [
"Brian"
] | a02ba54082e6903932fc47c7a0e3d820d08c827ba0f3989d7ecf0ed04c7a83cc |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS.
"""
from datetime import datetime
from flaky import flaky
from textwrap import dedent
from unittest import skip
from nose.plugins.attrib import attr
from bok_choy.promise import EmptyPromise
from ..helpers import (
UniqueCourseTest,
EventsTestMixin,
... | IndonesiaX/edx-platform | common/test/acceptance/tests/lms/test_lms.py | Python | agpl-3.0 | 44,694 | [
"VisIt"
] | 24489eb258c5575eb5b062d62b927717cb52df7ae5ac742f8570adb4ae38f006 |
#!/usr/bin/env python
# This file is part of MSMBuilder.
#
# Copyright 2011 Stanford University
#
# MSMBuilder 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 opt... | mpharrigan/msmbuilder | scripts/ConvertDataToHDF.py | Python | gpl-2.0 | 7,660 | [
"MDTraj"
] | 4d6014b96c751e00011de1decb50e0edb5650c1ecef8e808d811bb59d19cbc3c |
# Copyright 2016 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... | shakamunyi/tensorflow | tensorflow/contrib/distributions/python/ops/distribution.py | Python | apache-2.0 | 38,481 | [
"Gaussian"
] | 98d6a0fe9d18340a2e1eec80b71fceb418b18b3da16bfc5edfc7716a9c71e373 |
""" LineGraph represents line graphs both simple and stacked. It includes
also cumulative graph functionality.
The DIRAC Graphs package is derived from the GraphTool plotting package of the
CMS/Phedex Project by ... <to be added>
"""
from DIRAC.Core.Utilities.Graphs.PlotBase import PlotBase
from DIRAC.Core... | DIRACGrid/DIRAC | src/DIRAC/Core/Utilities/Graphs/LineGraph.py | Python | gpl-3.0 | 4,756 | [
"DIRAC"
] | 6326f8683c8d577acd356f1c63e751fbb4a82442aeec12979c38d1983499ec2f |
# coding: utf-8
"""
Vericred API
Vericred's API allows you to search for Health Plans that a specific doctor
accepts.
## Getting Started
Visit our [Developer Portal](https://developers.vericred.com) to
create an account.
Once you have created an account, you can create one Application for
Production and an... | vericred/vericred-python | test/test_network_details.py | Python | apache-2.0 | 10,021 | [
"VisIt"
] | 9decdc288e1ab6314909b763df20f412a979357294ba3449bdb362c0b9346994 |
# -*- coding: utf-8 -*-
from . import cif
from . import poscar
import ase
import ase.io
class StructureFormatError(Exception):
"""Problem reading an input file"""
class FormatNotSupportedError(Exception):
"""The provided input format is not supported"""
def read(source_file, *args, **kwargs):
"""
... | wolverton-research-group/qmpy | qmpy/io/__init__.py | Python | mit | 3,220 | [
"ASE"
] | 4828a61ed3d88d89b0a396a6a3095a3f5974b7f1ed5ae68c69d50d1e34faa1a5 |
# ============================================================================
#
# Copyright (C) 2007-2010 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | kurtraschke/camelot | camelot/view/controls/editors/languageeditor.py | Python | gpl-2.0 | 2,920 | [
"VisIt"
] | fa8f7e02d7b0fbee53686a8b4091b6933bf2023f62802c81f0d8b99c349aa925 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
##
## (C) 2015 Muthiah Annamalai
## Licensed under GPL Version 3
##
## Interpreter for Ezhil language
from __future__ import print_function
import sys
PYTHON3 = (sys.version[0] == '3')
if PYTHON3:
unicode = str
## Tx
from transform import Visitor, TransformVisitor
from ... | kracekumar/Ezhil-Lang | ezhil/ezhil_transforms.py | Python | gpl-3.0 | 5,817 | [
"VisIt"
] | 73b5fd5375dfb32add3ca88d167498249b7feadd640288bc572a0978f7b4fb3a |
'''
# This script is an example of calculation of long range interactions
# (Coulomb interaction) using the Ewald summation and the P3M methods.
#
# Initially, the simple cubic structure is generated in order to represent the
# NaCl crystal. Then the energy and forces are calculated and compared using both
# the... | capoe/espressopp.soap | examples/electrostatics/electrostatics_example.py | Python | gpl-3.0 | 8,984 | [
"CRYSTAL",
"VMD"
] | ee2ffe87455526aa06994354327eab2cfa42018eed7df5be344855c20393e802 |
'''The script converts Bowtie format to CisGenome format.
Author: Likit Preeyanon, preeyano@msu.edu.
'''
import sys, csv
def convert(filename):
reader = csv.reader(open(filename), dialect='excel-tab')
writer = csv.writer(sys.stdout, dialect='excel-tab')
for row in reader:
strand = 'F' if row[1]=... | likit/BioUtils | map2CisGenome.py | Python | bsd-2-clause | 480 | [
"Bowtie"
] | f12f3f9095cfc13f3db75446b27dffa88fd7536bd946bc86f19581639eb73f2e |
# iCraft is Copyright 2010 both
#
# The Archives team:
# <Adam Guy> adam@adam-guy.com AKA "Adam01"
# <Andrew Godwin> andrew@aeracode.org AKA "Aera"
# <Dylan Lukes> lukes.dylan@gmail.com AKA "revenant"
# <Gareth Coles> colesgareth2@hotmail.com... | TheArchives/Nexus | core/entities/jello.py | Python | bsd-2-clause | 6,606 | [
"VisIt"
] | 10c6287aa117415a731f1b3571d6d7feb7cb0f799d33464ff076a4b328a8060a |
# Copyright (c) 2005 Gavin E. Crooks <gec@threeplusone.com>
#
# This software is distributed under the MIT Open Source License.
# <http://www.opensource.org/licenses/mit-license.html>
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentatio... | NarlikarLab/DIVERSITY | weblogoMod/corebio/utils/__init__.py | Python | gpl-3.0 | 16,777 | [
"BioPerl",
"Biopython"
] | 22f7f437bda230dfd98ba65f780d2c72505ca0c33c09f7c2cd42d282ff860ff8 |
# -*- coding: utf-8 -*-
"""
Module to generate surrogates of a spike train by randomising its spike times
in different ways (see [2]_ and [3]_). Different methods destroy different
features of the original data:
* randomise_spikes:
randomly reposition all spikes inside the time interval (t_start, t_stop).
Keep... | JuliaSprenger/elephant | elephant/spike_train_surrogates.py | Python | bsd-3-clause | 55,993 | [
"Gaussian",
"NEURON"
] | 9277b553ec249a9cbbb3ffb23121029d76a24a87c64092f8bc72500f07624522 |
# $Id: dbexts.py 4185 2008-02-28 16:55:33Z cgroves $
"""
This script provides platform independence by wrapping Python
Database API 2.0 compatible drivers to allow seamless database
usage across implementations.
In order to use the C version, you need mxODBC and mxDateTime.
In order to use the Java version, you need ... | babble/babble | include/jython/Lib/dbexts.py | Python | apache-2.0 | 31,053 | [
"Brian"
] | 500a502f7424a8039a2c44136ccf8a4c2c4386e62964d0bca5b0d04410099e46 |
# -*- coding: utf-8 -*-
# __init__.py ---
#
# Filename: __init__.py
# Description:
# Author: subha
# Maintainer:
# Created: Sun Apr 17 13:55:30 2016 (-0400)
# Version:
# Last-Updated: Sun Apr 17 14:59:06 2016 (-0400)
# By: subha
# Update #: 20
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#... | dilawar/moose-core | python/moose/neuroml2/__init__.py | Python | gpl-3.0 | 1,662 | [
"MOOSE"
] | 73df00406559755b449fac2354c69f928ea9315b6ed5cebd0cc9ea8995e09d2a |
# -*- coding: utf-8 -*-
#
# PERI documentation build configuration file, created by
# sphinx-quickstart on Fri Jun 17 12:12:07 2016.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All co... | peri-source/peri | docs/conf.py | Python | mit | 9,852 | [
"Brian"
] | 661008f3b53c3b5661be7e448b2a20c86f9adb2b9114be7eed69347aee4f917e |
# Copyright 2013-2021 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 Fms(CMakePackage):
"""GFDL's Flexible Modeling System (FMS) is a software environment
... | LLNL/spack | var/spack/repos/builtin/packages/fms/package.py | Python | lgpl-2.1 | 1,500 | [
"NetCDF"
] | 556d09570a3e51539a07b9a07df5036d3ed8553a57a19684452b0f85eb011e96 |
# Copyright 2017 Battelle Energy Alliance, 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 t... | joshua-cogliati-inl/raven | framework/CodeInterfaces/Rattlesnake/RattlesnakeInterface.py | Python | apache-2.0 | 8,342 | [
"MOOSE"
] | 9a601bc5c23124454034943f5969acc905f17a61d53278c762c1ad66d50d7092 |
"""
module to test the NetCDF module
"""
import unittest
from netCDF4 import Variable
from hamcrest import *
from nose.tools import istest, raises, eq_
from cis.test.integration_test_data import *
from cis.data_io.netcdf import *
class TestNetCDF(unittest.TestCase):
@raises(IOError)
def should_raise_io_erro... | cedadev/cis | cis/test/integration/test_io/test_netcdf.py | Python | lgpl-3.0 | 5,585 | [
"NetCDF"
] | af4450907b88c8612b81ef9f530e1d2c1e1818f246c5f86b72b9795b520cfeff |
import astropy.units as u
from galaxies import Galaxy
from astropy.coordinates import Angle, SkyCoord
def update_galaxy_params(gal, param_table):
'''
Use the fit values rather than the hard-coded values in galaxies.
'''
assert isinstance(gal, Galaxy)
gal.inclination = Angle(param_table["inc"][0... | e-koch/CubeAnalysis | cube_analysis/rotation_curves/update_galaxy_params.py | Python | mit | 630 | [
"Galaxy"
] | bddd07aa8f6fce3f5630892e56e12aab8176a4b158a69f702c89ad5d1fd419c9 |
"""
A buffered iterator for big arrays.
This module solves the problem of iterating over a big file-based array
without having to read it into memory. The `Arrayterator` class wraps
an array object, and when iterated it will return sub-arrays with at most
a user-specified number of elements.
"""
from __future__ impor... | ViralLeadership/numpy | numpy/lib/arrayterator.py | Python | bsd-3-clause | 7,201 | [
"NetCDF"
] | a837e3c26da51851372f96e072ef6d4a2edfeacbb288c246c0a630da44053b64 |
#!/usr/bin/python3
# -*- Mode:Python; indent-tabs-mode:nil; tab-width:4 -*-
#
# Copyright (C) 2015, 2016 Canonical Ltd
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License version 3 as
# published by the Free Software Foundation.
#
# This progra... | dpniel/snapcraft | snapcraft/main.py | Python | gpl-3.0 | 14,174 | [
"VisIt"
] | b1cba4466387de0c82584c32bcc6d2ca690425478336cf823bbd4d4e61b539d9 |
# Authors: Lukas Breuer <l.breuer@fz-juelich.de>
"""
----------------------------------------------------------------------
--- jumeg.decompose.fourier_ica_plot ---------------------------------
----------------------------------------------------------------------
autor : Lukas Breuer
email : l.breuer@fz-... | fboers/jumegX | decompose/fourier_ica_plot.py | Python | bsd-3-clause | 71,111 | [
"Mayavi"
] | 3ec3e00af57c2893be9670f9ef887b254cf919689dab8a6c61a3c66f3a99bcd3 |
# -*- coding: utf-8 -*-
#
# glif_psc_neuron.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... | SepehrMN/nest-simulator | pynest/examples/glif_psc_neuron.py | Python | gpl-2.0 | 9,617 | [
"NEURON"
] | c654909127575b1e8636d04be3841aee0b3d12496fbe47976b1b5018ad1e4680 |
#coding:utf8
'''
Created on 2013-8-8
@author: lan (www.9miao.com)
'''
from firefly.management import commands
import sys
class CommandError(Exception):
"""
"""
def __str__(self):
return "command error"
class Command:
def __init__(self,subcommond,*args):
'''工具类指令
'''
... | yangdw/PyRepo | src/annotation/Firefly/firefly/management/__init__.py | Python | mit | 750 | [
"Firefly"
] | a96d4b35261c5dd5e791e44eac2ab15892e1835fc157cd9365d55e5698f5a411 |
##
# Django module h5p.
##
from django.conf import settings
from django.contrib.auth.models import User
from h5pp.models import *
from h5pp.h5p.h5pclasses import H5PDjango
import collections
import hashlib
import shutil
import uuid
import time
import math
import json
import os
import re
STYLES = [
... | DrClockwork/H5PP | h5pp/h5p/h5pmodule.py | Python | gpl-2.0 | 24,571 | [
"VisIt"
] | db036637d98059ca3a406401faf93f77f9d40ef409133a487011b6aa61e3f492 |
"""
Conditional Restricted Boltzmann Machines (CRBM) Implementation in Tensorflow
"""
import tensorflow as tf
import numpy as np
import scipy.io as sio
from xrbm.utils import tfutils
class CRBM():
'Conditional Restricted Boltzmann Machines (CRBM)'
def __init__(self, num_vis, num_cond, num_hid, vis_type='bina... | omimo/xRBM | xrbm/models/crbm.py | Python | mit | 12,873 | [
"Gaussian"
] | de30a2d1253ab39f6d2d8287ad7ca256237b5fcaf75dff5849f4a6467e69caeb |
r"""
Alignments and Sequence collections (:mod:`skbio.alignment`)
============================================================
.. currentmodule:: skbio.alignment
This module provides functionality for working with biological sequence
collections and alignments. These can be composed of generic sequences,
nucelotide s... | wdwvt1/scikit-bio | skbio/alignment/__init__.py | Python | bsd-3-clause | 7,240 | [
"scikit-bio"
] | ec3392aaefbc8b63be461380ae66bf99aaa521ca69f5ab721143e9145c047de3 |
'''
Copyright 2014, Jared Oyler.
This file is part of TopoWx.
TopoWx 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.
TopoWx is distributed... | jaredwo/topowx | twx/interp/optimize.py | Python | gpl-3.0 | 20,508 | [
"NetCDF"
] | 84d5d37656a7c0557c3ac627664fa2bd090a89fa4efc2c983987bb0305fffc2f |
# -*- coding: utf-8 -*-
"""Tests for Hipathia."""
import os
import unittest
from pybel.dsl import ComplexAbundance, Protein
from pybel.io.hipathia import from_hipathia_paths, group_delimited_list
HERE = os.path.abspath(os.path.dirname(__file__))
TEST_1_ATT_PATH = os.path.join(HERE, "test_1.att")
TEST_1_SIF_PATH = ... | pybel/pybel | tests/test_io/test_hipathia/test_hipathia.py | Python | mit | 1,666 | [
"Pybel"
] | 22f2580412b2f7fc16fbaf27e922b977bd390dbe55fb1091766428372a53c85e |
# Copyright 2013 by Zheng Ruan (zruan1991@gmail.com).
# All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Code for dealing with Codon Alignment.
"""
from __future__ import print... | updownlife/multipleK | dependencies/biopython-1.65/build/lib.linux-x86_64-2.7/Bio/codonalign/__init__.py | Python | gpl-2.0 | 32,881 | [
"Biopython"
] | 850f59b202558cce504ca0c6663732e90d15a3f776d428acc1692d2a74e10eff |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2021, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Test NMR logfiles in cclib."""
import os
import unittest
from skip import skipForParser
__filedir__ = os.path.realpa... | cclib/cclib | test/data/testNMR.py | Python | bsd-3-clause | 919 | [
"cclib"
] | 88cdf7414e23b036e21ea0f360690404888980a2812831cf538d0be0fed91efe |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
class Migration(migrations.Migration):
dependencies = [
('contacts', '0012_data_action_time'),
]
operations = [
migrations.AddField(
model_name='visit',
name=... | I-TECH-UW/mwachx | contacts/migrations_old/0013_visit_sms.py | Python | apache-2.0 | 593 | [
"VisIt"
] | b05c33d92d056dbd135d5d7f0a6bde4d7ae82cdc420a1c426096d388490fcdc9 |
# Version: 0.15
"""
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, and pypy
* [![Latest Version]
(https://pypip.in/version/versioneer/badge.svg?style=flat)
](ht... | louispotok/pandas | versioneer.py | Python | bsd-3-clause | 62,522 | [
"Brian"
] | 601eab22a71dcb3f3a979afb1f8ed7229c54a2cd9c7adbc28c4de70d6fc55e69 |
import lateral_inhibitions
from itertools import product
def visualize(kohonen, points, lines_col):
if kohonen.lateral_inhibition == lateral_inhibitions.gauss_limited:
return visualize_square(kohonen, points, lines_col)
if kohonen.lateral_inhibition == lateral_inhibitions.gauss_hex:
return vis... | gyfis/kohonen-nn-implementation-II | visualizer.py | Python | mit | 3,042 | [
"NEURON"
] | 859b560ef3327b4a210082c83b5665eeb1afb802620068218e47ef226ea48064 |
# Copied from GPAW (https://trac.fysik.dtu.dk/projects/gpaw/)
import time
import math
import sys
from ase.parallel import world
def function_timer(func, *args, **kwargs):
out = kwargs.pop('timeout', sys.stdout)
t1 = time.time()
r = func(*args, **kwargs)
t2 = time.time()
print >> out, t2 - t1
... | auag92/n2dm | Asap-3.8.4/Python/asap3/Tools/Timing.py | Python | mit | 4,795 | [
"ASE",
"GPAW"
] | 1962a96c836dae82bfb7cad8a504f0eb116498f221989fbbdc6ec39402eb7af5 |
# -*- coding: utf-8 -*-
#
# Copyright (C) 2004-2009 Edgewall Software
# Copyright (C) 2004 Daniel Lundin <daniel@edgewall.com>
# Copyright (C) 2004-2006 Christopher Lenz <cmlenz@gmx.de>
# Copyright (C) 2006 Jonas Borgström <jonas@edgewall.com>
# Copyright (C) 2008 Matt Good <matt@matt-good.net>
# All rights reserved.
#... | dafrito/trac-mirror | trac/web/session.py | Python | bsd-3-clause | 20,519 | [
"VisIt"
] | cefa3e3ab94879518b288015bdcdccda5a675b8b9feea6b11cac5e632446d730 |
#!/usr/bin/env python
from subprocess import call
import os
import random
from random import randint
import time
import math
# Set the global properties below:
NUM_OF_IMAGES = 50 # The number of images to generate
PERCENTAGE_OF_IMAGES_WITH_TUMOR = 100
IMAGE_BASE_NAME = "breast_" # The base name for the images.
IMAGE... | jnarhan/Breast_Cancer | src/img_simulation/simulate_images_01.py | Python | mit | 10,904 | [
"Gaussian"
] | 19cd526aec5fc367059353de1244fd25f030369a858345faf83d56e33c293210 |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-admin-modify-user
# Author : Adrian Casajus
########################################################################
"""
Modify a user in the CS.
"""
from __future__ import print_function
__RC... | fstagni/DIRAC | Interfaces/scripts/dirac-admin-modify-user.py | Python | gpl-3.0 | 2,345 | [
"DIRAC"
] | 499223c441c80fc1133153d0cd6090f2c022a311269792d0bd1f1507f932b972 |
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2006-2014, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version 2.1 or l... | Clyde-fare/cclib | test/testScan.py | Python | lgpl-2.1 | 2,211 | [
"cclib"
] | 5817c00c940fc8b5ce046dba5b431393d9435c7c5025f93fa5c97a26f0e8c93c |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides some useful functions for dealing with magnetic Structures
(e.g. Structures with associated magmom tags).
"""
import logging
import os
import warnings
from collections import namedtuple
from enum impo... | vorwerkc/pymatgen | pymatgen/analysis/magnetism/analyzer.py | Python | mit | 46,777 | [
"VASP",
"pymatgen"
] | 2cb3098413238e904b26a5f60ec9c0f5851e776fa40996fbfed8eaeb039a6fb7 |
import base64
import hmac
import json
import requests
import time
import datetime
import urllib
import os
from hashlib import sha1
from hashlib import md5
def parse_time(timestr):
format = "%Y-%m-%d %H:%M:%S"
return datetime.datetime.fromtimestamp(
time.mktime(time.strptime(timestr, format))
).str... | congrieb/yikBot | pyak.py | Python | mit | 14,574 | [
"Galaxy"
] | a9ad9ca51465e0addfe689e352e33e0073b45b241c8d8fefbc29cf503e975b38 |
"""Random variable generators.
integers
--------
uniform within range
sequences
---------
pick random element
pick random sample
generate random permutation
distributions on the real line:
------------------------------
uniform
... | firmlyjin/brython | www/src/Lib/random.py | Python | bsd-3-clause | 26,080 | [
"Gaussian"
] | 383042b2d3272a701854ec3117bc94b1f2636d2e383196cdf357d0059f983762 |
"""
Companion code for the Roam blog post on hyperparameter optimization.
"""
import itertools as it
import matplotlib
import matplotlib.pyplot as plt
import numpy as np
from operator import itemgetter
import pandas as pd
import random
from scipy import stats
from time import time
from hyperopt import fmin, tpe, hp, S... | roaminsight/roamresearch | BlogPosts/Hyperparameter_tuning_comparison/hyperparameter_tuning_comparison_code.py | Python | apache-2.0 | 31,340 | [
"Gaussian"
] | b2c9b4d7c1b0bf1199101a7295c7888a638659652e5be3ccfbe56a1aeea0f8e0 |
##############################################################################
# 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... | wscullin/spack | var/spack/repos/builtin/packages/mfem/package.py | Python | lgpl-2.1 | 11,965 | [
"NetCDF"
] | b6e08049071497d1302e6065719889317044008a81631cf850cd6c8e8f3abdb0 |
'''
Awesome people who have directly contributed to the project:
Jon Palmer - Bug finder & advice on project direction
Mahmut Uludag - Bug finder
Help: print pybam.wat
Github: http://github.com/JohnLonginotto/pybam
This code was written by John Longinotto, a PhD student of the Pospisilik Lab at the Max Plan... | nextgenusfs/ufits | amptk/pybam.py | Python | bsd-2-clause | 53,405 | [
"Biopython",
"VisIt"
] | 7b075656fc281eb139906ddacc559a76314ad4a72ebe1a625d68d53d29ff3761 |
from __future__ import absolute_import, division, print_function, unicode_literals
import numpy
import keras
from keras import backend as K
from keras.layers.merge import Concatenate
from keras.layers import Lambda
from keras.layers.core import Reshape
def split(start, stop):
return Lambda(lambda x: x[:, start:s... | jhartford/DeepIV | deepiv/densities.py | Python | mit | 2,227 | [
"Gaussian"
] | f9d44c32e0e927c6a7c20d90d30a5a968e00b36168528c1b6fa655d7ae561b06 |
# (c) 2015, Brian Coca <briancoca+dev@gmail.com>
#
# This file is part of Ansible
#
# Ansible 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 v... | brokenjacobs/ansible | lib/ansible/plugins/action/patch.py | Python | gpl-3.0 | 2,503 | [
"Brian"
] | adfbd294b9348356ec11f61e6f19a5c8cb90c0eb044e98c189d2d64b8320ff29 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""Tests for the Google Chrome cookie database plugin."""
import unittest
# pylint: disable=unused-import
from plaso.formatters import chrome_cookies as chrome_cookies_formatter
from plaso.lib import eventdata
from plaso.lib import timelib
from plaso.parsers.sqlite_plugins im... | ostree/plaso | tests/parsers/sqlite_plugins/chrome_cookies.py | Python | apache-2.0 | 4,631 | [
"VisIt"
] | a8738285c20fcec082d99791b9954732ee1df44dc0f5ceab3e45a20b78077088 |
import os
import sys
import types
import re
from numpy.core.numerictypes import issubclass_, issubsctype, issubdtype
from numpy.core import product, ndarray
__all__ = ['issubclass_', 'get_numpy_include', 'issubsctype',
'issubdtype', 'deprecate', 'deprecate_with_doc',
'get_numarray_include',
... | illume/numpy3k | numpy/lib/utils.py | Python | bsd-3-clause | 29,067 | [
"VisIt"
] | 876502a367aa7ce05eb4d85912d9f2046491d6e3cb05ee04474e93ee324b0a12 |
# Copyright (c) 2014-2018 Matteo Degiacomi and Valentina Erastova
#
# Assemble 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.
# Assemb... | degiacom/assemble | Database.py | Python | gpl-3.0 | 5,195 | [
"Gromacs"
] | 0402429a44a252d5b94e3437527461f2ed1d3a286a2baf4f227a75660a6e611f |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright 2009 Benoit Chesneau <benoitc@e-engura.org>
#
# This software is licensed as described in the file LICENSE, which
# you should have received as part of this distribution.
#
import httplib
import os
import re
import shutil
import socket
import sys
import time
... | perplexes/couchapp | python/couchapp/file_manager.py | Python | apache-2.0 | 24,692 | [
"VisIt"
] | abacc014d0b35514635af71a626f0ef48f2040470da34db619fbee720574a15e |
#!/usr/bin/env python
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Implementation for `pmg structure` CLI.
"""
import sys
from tabulate import tabulate
from pymatgen.analysis.structure_matcher import ElementComparator, StructureMatcher
from pymatgen.core.structure... | materialsproject/pymatgen | pymatgen/cli/pmg_structure.py | Python | mit | 3,774 | [
"pymatgen"
] | 724fc4c84d1bd0af3c4b238c35d79e4a708e657b5f72a69b585553e98002e766 |
from time import time
from StringIO import StringIO
from tests.web2unittest import Web2UnitTest
from gluon import current
try:
from twill import get_browser
from twill import set_output
from twill.browser import *
except ImportError:
raise NameError("Twill not installed")
try:
from mechanize import... | anubhav929/eden | modules/tests/smoke/broken_links.py | Python | mit | 7,597 | [
"VisIt"
] | fd7b2930892f62c06f8eb2abf51c17027a9e9979d4572951eee76f85bb583877 |
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