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# Copyright 2020 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | GoogleCloudPlatform/functions-framework-python | tests/test_cloud_event_functions.py | Python | apache-2.0 | 6,917 | [
"Galaxy"
] | e71584641d989d2629385b605948fdb3042e59d6ad712d36faebaa3f626d162d |
#-------------------------------------------------------------------------------
# Name: utils
# Purpose: Helper functions for unit tests
#
# Author: Brian Skinn
# bskinn@alum.mit.edu
#
# Created: 12 Mar 2016
# Copyright: (c) Brian Skinn 2016
# License: The MIT License; see "lic... | bskinn/opan | opan/test/utils.py | Python | mit | 4,217 | [
"Brian"
] | c8a5f8ec48deb3ca8733b92004e4ec4b335085f49aaf40d3f989485bd1e3a8af |
""" Models for the shopping cart and assorted purchase types """
from collections import namedtuple
from datetime import datetime
from datetime import timedelta
from decimal import Decimal
import json
import analytics
from io import BytesIO
from django.db.models import Q
import pytz
import logging
import smtplib
impor... | adoosii/edx-platform | lms/djangoapps/shoppingcart/models.py | Python | agpl-3.0 | 89,116 | [
"VisIt"
] | ac8ad8f7f39b4fe96f3190fce12b2356c63d0d6748d82f9a27e7124c70f193bb |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | skosukhin/spack | var/spack/repos/builtin/packages/r-mzid/package.py | Python | lgpl-2.1 | 2,260 | [
"Bioconductor"
] | 787bd08e8d1d346671cf7f4f242d045a2e70f5d810399094cfcfdccc54c4ca91 |
# Copyright (C) 2015, Carlo de Franchis <carlo.de-franchis@ens-cachan.fr>
# Copyright (C) 2015, Gabriele Facciolo <facciolo@cmla.ens-cachan.fr>
# Copyright (C) 2015, Enric Meinhardt <enric.meinhardt@cmla.ens-cachan.fr>
# Copyright (C) 2015, Julien Michel <julien.michel@cnes.fr>
import os
import numpy as np
from s2pli... | dyoussef/s2p | s2plib/block_matching.py | Python | agpl-3.0 | 12,358 | [
"Gaussian"
] | 1681b330d49e8d3df77d2397225927f9029564fc5c293b64df3852a0f87c45ec |
__author__ = 'bptripp'
from os import listdir
from os.path import isfile, join
import time
import numpy as np
import matplotlib.pyplot as plt
import cPickle
from PIL import Image
from scipy.optimize import bisect
from quaternion import angle_between_quaterions, to_quaternion
def get_random_points(n, radius, surface=... | bptripp/grasp-convnet | py/perspective.py | Python | mit | 30,382 | [
"NEURON"
] | 6ec0c97e0ac0dd0c323f847c8d0601fdb13550231748c4a1d878544bc3b99b63 |
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
from findyour3d.contact.views import contact
urlpatterns = [
... | hqpr/findyour3d | config/urls.py | Python | mit | 2,600 | [
"VisIt"
] | 13bba454297a5f3daff33d500c9edb7dae7193388898942c8060c7906b375d0f |
from __future__ import annotations
import math
import pickle
import random
from scitbx import matrix
from dials.model.data import Shoebox
def random_shoeboxes(num, mask=False):
for i in range(num):
x0 = random.randint(0, 100)
y0 = random.randint(0, 100)
z0 = random.randint(0, 100)
... | dials/dials | tests/model/data/test_shoebox.py | Python | bsd-3-clause | 9,971 | [
"Gaussian"
] | 438b5147b5c86c35ceef42893341f3a0bba87eec90cc2d44f91a3bce93352859 |
from validate_app import validateApp
import os
from distutils import spawn
import sys
from parse_files import parseOut, bringTogether
from bashSub import bashSub
def checkPreprocessApplications():
applications = ["super_deduper", "sickle", "flash2", "bowtie2"]
source = ["https://github.com/dstreett/Sup... | msettles/expHTS | expHTS/preprocessCMD.py | Python | apache-2.0 | 7,647 | [
"Bowtie"
] | c948ca01dd5e567792280beed205525c0515533700d4551305aa0030dbaec87c |
# Copyright (c) 2017 ARM Limited
# All rights reserved.
#
# The license below extends only to copyright in the software and shall
# not be construed as granting a license to any other intellectual
# property including but not limited to intellectual property relating
# to a hardware implementation of the functionality ... | HwisooSo/gemV-update | src/python/m5/stats/__init__.py | Python | bsd-3-clause | 7,711 | [
"VisIt"
] | da34aa352b1383cb9dae36af5c8ac2cdf08c1192f48bd45aa5990a51243a6a15 |
#!/usr/bin/env python
import sys
import os
import vtk
import numpy
from siconos.io.mechanics_hdf5 import MechanicsHdf5
## the best way to dump all data
# $ h5dump toto.hdf5 > toto.txt
import h5py
import getopt
def usage():
"""
{0} <hdf5 file>
""".format(sys.argv[0])
print '{0}: Usage'.format(sys.a... | radarsat1/siconos | io/swig/io/filter_output_frequency.py | Python | apache-2.0 | 6,832 | [
"VTK"
] | b2f51bfc03c1b421ece1a35c12479a438c53d51e6df745735a08b4836eec0ba5 |
#!/usr/bin/python
# -*- encoding: utf-8; py-indent-offset: 4 -*-
# +------------------------------------------------------------------+
# | ____ _ _ __ __ _ __ |
# | / ___| |__ ___ ___| | __ | \/ | |/ / |
# | | | | '_ \ / _ \/ __| |/ /... | ypid-bot/check_mk | web/htdocs/userdb.py | Python | gpl-2.0 | 51,514 | [
"VisIt"
] | 213eeffa017a6fe59fc929750d95511ae609e43bc47b1d1ae21a9fa4d269a268 |
"""
Seismic wavelets.
:copyright: 2021 Agile Geoscience
:license: Apache 2.0
"""
import warnings
from collections import namedtuple
import numpy as np
import scipy.signal
import matplotlib.pyplot as plt
from bruges.util import deprecated
def _get_time(duration, dt, sym=True):
"""
Make a time vector.
If... | agile-geoscience/bruges | bruges/filters/wavelets.py | Python | apache-2.0 | 26,725 | [
"Gaussian"
] | 86c684bd23d4d0ca0e6d4c7a48d93575dbe8818d694bbdd05899a31ba32718be |
#!/usr/bin/env python
__author__ = 'waroquiers'
import unittest
from pymatgen.util.testing import PymatgenTest
from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import DistanceCutoffFloat
from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import AngleCutoffFloat
fr... | Bismarrck/pymatgen | pymatgen/analysis/chemenv/coordination_environments/tests/test_chemenv_strategies.py | Python | mit | 4,858 | [
"pymatgen"
] | 0dcc599097c3873eafcb1143aaf6c9c4819346d2942991d1d66669f7682c7c8e |
# Copyright 2014 NeuroData (http://neurodata.io)
#
# 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 ag... | neurodata/ndstore | test/test_neuron.py | Python | apache-2.0 | 2,722 | [
"NEURON"
] | 2d7832d68eb7f87fe2f7dff2db7aa025b048d0d17c46e6c3fa9cb2689cc11ab0 |
# -*- coding: utf-8 -*-
import os
import tempfile
import types
import json
from mock import patch
from nose.tools import eq_
from helper import TestCase
import appvalidator.constants
from appvalidator.errorbundle import ErrorBundle
from appvalidator.specs.webapps import WebappSpec
import appvalidator.webapp
class T... | stasm/app-validator | tests/test_webapp.py | Python | bsd-3-clause | 48,765 | [
"exciting"
] | 3652827949f41bc33a16855c4d3bc2f5fe3c7c4b394dfafbdf72e6b775143070 |
"""
Functions to spot hemy regions
"""
import os.path as op
import datetime
from collections import defaultdict, Counter
from tabulate import tabulate
from scipy import stats
import numpy as np
import pybedtools
import pysam
import vcf
from bcbio.distributed.transaction import file_transaction
from bcbio.provenance ... | lpantano/ASMfinder | asm/select.py | Python | mit | 16,220 | [
"pysam"
] | 459cb20dc4d3f339c7c46798b41e4438678d43cda5de3f3be063d27dd7f890dc |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import textwrap
"""
This module implements input and output processing from QChem.
"""
import copy
import re
import os
import numpy as np
from string import Template
i... | matk86/pymatgen | pymatgen/io/qchem.py | Python | mit | 87,768 | [
"Gaussian",
"Q-Chem",
"pymatgen"
] | 045274848fee1c3edc603bfc0f3a673ebbe1aabd6b9863ae44cb283649808fb7 |
#! /usr/bin/env python
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 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 redistr... | psi-rking/psi4 | psi4/versioner.py | Python | lgpl-3.0 | 14,574 | [
"Psi4"
] | 7a7a630cf8f6e74392a4afc0b09f571449ffdad32ba146695dc65321159f04a0 |
from __future__ import absolute_import, division, print_function
import sys
import os.path
import warnings
import datetime, time
import numpy as np
import astropy.table
# See pixsim.py
import astropy.time
from astropy.io import fits
import fitsio
import desitarget
import desitarget.targetmask
from desitarget.target... | desihub/desisim | py/desisim/simexp.py | Python | bsd-3-clause | 38,406 | [
"Galaxy"
] | 4b409860f9c115021d249f74441ba05dbda68773cb8924b68ad3ecbf843a741c |
""" Models for the shopping cart and assorted purchase types """
from collections import namedtuple
from datetime import datetime
from decimal import Decimal
import pytz
import logging
import smtplib
from boto.exception import BotoServerError # this is a super-class of SESError and catches connection errors
from dja... | adlnet-archive/edx-platform | lms/djangoapps/shoppingcart/models.py | Python | agpl-3.0 | 42,752 | [
"VisIt"
] | 2f2a6866c8129f1b381404b34d2c287591282896db7c70ccf27e49ea645b9093 |
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import _
from zeroinstall.support import tasks
from zeroinstall.injector import handler, download
gobject = tasks.get_loop().gobject
glib = tasks.get_loop().glib
version = '2.5-post'
class GUIHandl... | afb/0install | zeroinstall/gui/gui.py | Python | lgpl-2.1 | 3,020 | [
"VisIt"
] | 668a475b78054b4eb18377dfc6b6dea57004784aa6c23e664a99f14388f00c62 |
# Copyright (C) 2004 CCLRC & NERC( Natural Environment Research Council ).
# This software may be distributed under the terms of the
# Q Public License, version 1.0 or later. http://ndg.nerc.ac.uk/public_docs/QPublic_license.txt
"""
na_to_cdms.py
=============
Container module for class NADictToCdmsObjects that... | eufarn7sp/egads | egads/thirdparty/nappy/nc_interface/na_to_cdms.py | Python | gpl-3.0 | 15,829 | [
"NetCDF"
] | be46f6f722f9dd037f0168e4f70ca7936c22a5acbfed0797a295f81700bacdac |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# king_phisher/server/database/models.py
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# n... | hdemeyer/king-phisher | king_phisher/server/database/models.py | Python | bsd-3-clause | 17,588 | [
"VisIt"
] | f0764e1ab5b6eca95af71aa3b9d108a00134f01013f0d32301db79954a24ac59 |
"""
This module defines most special functions and mathematical constants
provided by mpmath. [Exception: elliptic functions are currently
in elliptic.py]
Most of the actual computational code is located in the lib* modules
(libelefun, libhyper, ...); this module simply wraps this code to
handle precision management i... | gnulinooks/sympy | sympy/mpmath/functions.py | Python | bsd-3-clause | 166,515 | [
"Gaussian"
] | 9da3d36483a990e4b6ee2708f6c9fdf093965c3d22f8c44db8faa152945f5093 |
################################################################################
#
# Copyright (c) 2012 The MadGraph Development team and Contributors
#
# This file is a part of the MadGraph 5 project, an application which
# automatically generates Feynman diagrams and matrix elements for arbitrary
# high-energy proce... | cms-externals/sherpa | Examples/UFO_MSSM/MSSM/build_restrict.py | Python | gpl-3.0 | 3,624 | [
"VisIt"
] | 3f3e74a186d66137fb903453705c6ace4ccb5430600ba7c1c63869fb973a0429 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Analysis classes for batteries
"""
import math
from collections import defaultdict
import scipy.constants as const
from pymatgen.core.periodic_table import Element, Species
from pymatgen.core.structure import Compositio... | vorwerkc/pymatgen | pymatgen/apps/battery/analyzer.py | Python | mit | 8,942 | [
"pymatgen"
] | c771ce5efde01c889efe773aa67c750e4c34e8bfb006acce36c3986613ad2376 |
# Copyright 2018 The TensorFlow Probability 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 applicable law o... | tensorflow/probability | tensorflow_probability/python/sts/components/seasonal.py | Python | apache-2.0 | 40,275 | [
"Gaussian"
] | 276e3113b9347e8216305fe68abcc8a685fc5166a173e8c745100fdc84f0d9fc |
# $Id$
#
# Copyright (C) 2007,2008 Greg Landrum
#
# @@ All Rights Reserved @@
#
import os,sys
import io
import unittest
from rdkit.six.moves import cPickle
from rdkit import RDConfig
from rdkit import DataStructs as ds
def feq(v1,v2,tol=1e-4):
return abs(v1-v2)<tol
class TestCase(unittest.TestCase):
def setUp(sel... | soerendip42/rdkit | Code/DataStructs/Wrap/testSparseIntVect.py | Python | bsd-3-clause | 4,950 | [
"RDKit"
] | 63cb78c8bd2cdf90fb2c4cb5519011a6d477da100c05f1090a592b4bbd38875b |
from __future__ import absolute_import
import numpy as nm
from sfepy.base.base import output, OneTypeList, Struct
from sfepy.discrete.fem.mesh import Mesh
from sfepy.discrete.fem.meshio import MeshIO
from sfepy.solvers.ts import TimeStepper
from sfepy.base.ioutils import get_trunk, write_dict_hdf5
import six
from six.... | vlukes/sfepy | sfepy/postprocess/time_history.py | Python | bsd-3-clause | 7,716 | [
"VTK"
] | 1d8cfda61776faccdb6ff12237cc6cb0d850521cfdbccda1048fd56966141924 |
# -*- coding: utf-8 -*-
# Copyright (C) 2012, Almar Klein, Ant1, Marius van Voorden
#
# This code is subject to the (new) BSD license:
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of s... | wangtai/py_gif_processor | images2gif.py | Python | apache-2.0 | 37,041 | [
"NEURON"
] | ca51e40e66ce11c34ec9064a87fd98d694c56cd3601a928578ceaef75c786917 |
"""Classes to handle SAXS (Small Angle X-ray Scattering) data"""
import _modeller
from modeller.util.modobject import modobject
from modeller.util import modlist, array
__docformat__ = "epytext en"
class SAXSList(modlist.LinkList):
"""A list of L{saxsdata} objects"""
def __init__(self, edat):
self.__... | bjornwallner/proq2-server | apps/modeller9v8/modlib/modeller/saxsdata.py | Python | gpl-3.0 | 17,392 | [
"Gaussian"
] | f7aae6f3c28974ed705f1be51d0481101774518836586faa953aae10ece1eb55 |
"""Gaussian normalization to normalize standalone modality."""
import numpy as np
from joblib import Parallel, delayed
from scipy.linalg import norm
from .mrsi_normalization import MRSINormalization
KNOWN_KIND = ('l2', 'l1')
class LNormNormalization(MRSINormalization):
"""Normalization of MRSI data using l-... | glemaitre/protoclass | protoclass/preprocessing/l_norm_normalization.py | Python | gpl-2.0 | 5,323 | [
"Gaussian"
] | a28b254d72b3e8443616cf65d782fbb7708bc6c9c3b5da9217eb3f708cd5cd8a |
import numpy as np
from matplotlib import pyplot
import rft1d
eps = np.finfo(float).eps
def here_anova1(Y, X, X0, Xi, X0i, df):
Y = np.matrix(Y)
### estimate parameters:
b = Xi*Y
eij = Y - X*b
R = eij.T*eij
### reduced design:
b0 = X0i*Y
eij0 = Y - X0*b0
... | 0todd0000/rft1d | rft1d/examples/val_conj_2_F.py | Python | gpl-3.0 | 2,258 | [
"Gaussian"
] | b84a17b6d0a804166d0b1924fc5f35aa387e752327ab0177a69ec3a656df6950 |
"""Tests for dials.report.analysis module"""
from __future__ import annotations
from unittest import mock
import pytest
from cctbx import miller
from dxtbx.model import Crystal
from dxtbx.serialize import load
from dials.algorithms.scaling.scaling_library import (
merging_stats_from_scaled_array,
scaled_da... | dials/dials | tests/report/test_analysis.py | Python | bsd-3-clause | 8,850 | [
"CRYSTAL"
] | dbae99c6dc89739aeee56ccb6bd61cf3ce5accc779bdf466e747d6974b9ccb9b |
#!/usr/bin/python
import os
import sys
import argparse
from argparse import RawTextHelpFormatter
import subprocess
import fileinput
CWD = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))
ESPRESSO_TEMAPLTE_ZIP = 'EspressoProjectTestTemplate.zip'
PROJECT_NAME_TEMPLATE_TEXT = 'PROJECT_NAME_TEMPLATE'
PKG_NAME... | neoranga55/espresso-cucumber | espresso-test-lib/espresso.py | Python | apache-2.0 | 9,644 | [
"ESPResSo",
"VisIt"
] | aadd0e7e334b2989409ed016b3c0b71123d181f1e8913d3d34149013d35eb8dc |
# Copyright (C) 2016-2018 The ESPResSo project
# Copyright (C) 2014 Olaf Lenz
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or... | mkuron/espresso | src/python/espressomd/gen_pxiconfig.py | Python | gpl-3.0 | 1,845 | [
"ESPResSo"
] | 12ffb1c7a776a768accfbf7b19684225db3f24298fd050908e353f8242f1effe |
# 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 RBiocneighbors(RPackage):
"""Nearest Neighbor Detection for Bioconductor Packages.
... | rspavel/spack | var/spack/repos/builtin/packages/r-biocneighbors/package.py | Python | lgpl-2.1 | 1,650 | [
"Bioconductor"
] | 336cb261278ec65b2bda5c3700e26e9dce74539dd38f87cb6487dcb61ce48ba8 |
"""Helper functions for formating and rendering units."""
from typing import Optional, Union
import libsbml
import numpy as np
import pint
from sbmlutils.console import console
ureg = pint.UnitRegistry()
ureg.define("item = dimensionless")
ureg.define("avogadro = 6.02214179E23 dimensionless")
Q_ = ureg.Quantity
sh... | matthiaskoenig/sbmlutils | src/sbmlutils/report/units.py | Python | lgpl-3.0 | 4,366 | [
"Avogadro"
] | 7fc8654312fd756a6dae31ce90122ac86a48c9e9832fc4b9cc450678f24f7b5c |
#! /usr/bin/env python
#coding=utf-8
""" DESCRIPTION
"""
import glob, sys, csv
from tabulate import tabulate
from Bio.Blast.Applications import NcbiblastnCommandline
"""--- FUNCTIONS ---"""
def carga_csv(file_name):
""" creates a list of lists with a csv file """
tabla = list()
archivo = open(file_name+... | fernan9/LANGEBIO-Internship | BLAST_tricho_run.py | Python | gpl-2.0 | 4,183 | [
"BLAST"
] | ce21af6f5587d29898369174fc8c457771be50acd35dbead0da4afdef121e508 |
# -*- coding: iso-8859-1 -*-
############################################################
#Example 1: Simple basin hopping
############################################################
import numpy as np
import pygmin.potentials.lj as lj
import pygmin.basinhopping as bh
from pygmin.takestep import displace
natoms = 12... | js850/PyGMIN | examples/basinhopping_no_system_class/1_basic.py | Python | gpl-3.0 | 721 | [
"PyMOL"
] | bb86eaad84c4a7582c7ba95a4ec7b7c8d5cf2cc867312a9b87cc46dbc1845cec |
"""
Tests for discussion pages
"""
import datetime
from pytz import UTC
from uuid import uuid4
from nose.plugins.attrib import attr
from .helpers import BaseDiscussionTestCase
from ..helpers import UniqueCourseTest
from ...pages.lms.auto_auth import AutoAuthPage
from ...pages.lms.courseware import CoursewarePage
from... | beni55/edx-platform | common/test/acceptance/tests/discussion/test_discussion.py | Python | agpl-3.0 | 34,315 | [
"VisIt"
] | fd2e3d6373965d5a71ddfbad54f5aa7301ead216f3ea2a580efaf54541ca32c0 |
#####################################################################
# File: ReqManagerHandler.py
########################################################################
"""
:mod: ReqManagerHandler
.. module: ReqManagerHandler
:synopsis: Implementation of the RequestDB service in the DISET framework
"""
__RCSID__... | marcelovilaca/DIRAC | RequestManagementSystem/Service/ReqManagerHandler.py | Python | gpl-3.0 | 12,159 | [
"DIRAC"
] | 49dc6feb433cce415840ea15c347c19ddda484ddc574e2658f4cb12ed84a7329 |
import glob
import os
import shutil
from pathlib import Path
from django.conf import settings
from django.core.management import BaseCommand, CommandError
from django.db import transaction
from ncdjango.models import Service, Variable
from netCDF4 import Dataset
from pyproj import Proj
from trefoil.netcdf.describe imp... | consbio/seedsource-core | seedsource_core/django/seedsource/management/commands/publish_netcdf.py | Python | bsd-3-clause | 4,185 | [
"NetCDF"
] | d8933d7145d1e4f7f69ae6c139d83f9695daa5f447bc826198ca568d440a25a1 |
"""
Migration script to add a 'tool_version' column to the hda/ldda tables.
"""
from sqlalchemy import *
from sqlalchemy.orm import *
from migrate import *
from migrate.changeset import *
from galaxy.model.custom_types import *
metadata = MetaData()
def upgrade(migrate_engine):
metadata.bind = migrate_engine
... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/model/migrate/versions/0081_add_tool_version_to_hda_ldda.py | Python | gpl-3.0 | 1,370 | [
"Galaxy"
] | 32aa62d285e5b2d8d5d704339e3b9a1079e500f56ae9d7d28d8edd18d37e5d03 |
import functools
def resolve_internal(tree):
""" Given a tree, replace any nodes with an 'href' attribute
with the node with a corresponding 'id'. """
# get all the nodes with an id attribute
id_map = {}
id_visitor = functools.partial(get_id_nodes, id_map)
tree.visit(id_visitor)
# get a... | annegentle/wadl2rst | wadl2rst/transformations/resolve_internal.py | Python | apache-2.0 | 1,553 | [
"VisIt"
] | d874f4640a4f8e4a2021ab87e656b15910491f07b96528d5745adf50dc0855b5 |
# coding: utf-8
from __future__ import unicode_literals
import hmac
import hashlib
import base64
from .common import InfoExtractor
from ..utils import (
determine_ext,
float_or_none,
int_or_none,
js_to_json,
mimetype2ext,
parse_iso8601,
remove_start,
)
class NYTimesBaseIE(InfoExtractor):... | Tithen-Firion/youtube-dl | youtube_dl/extractor/nytimes.py | Python | unlicense | 8,836 | [
"Octopus"
] | 00a78c6338c0ba0b12a4edb587e05f264492b47e1f0248aafe42796efd78e603 |
from builtins import range
import sys
sys.path.insert(1,"../../../")
import h2o
from tests import pyunit_utils
from h2o.estimators.glm import H2OGeneralizedLinearEstimator
# in this test, I compare the results obtained from R run with H2O-3 runs using a much larger datasets to test
# multiple chunks operation.
def t... | h2oai/h2o-3 | h2o-py/tests/testdir_algos/glm/pyunit_PUBDEV_6876_HGLM_compare_R_large.py | Python | apache-2.0 | 1,607 | [
"Gaussian"
] | b9a1549ca17327c7775f097018165f180c9591a8d2cefa2dbd745616b420197f |
import numpy as np
import cv2
def readFile(file, dx, dy):
rdata = np.fromfile(file, dtype='float32')
#rdata[rdata > 280] = 330
# For global tracking
#rdata[rdata > 220] = 330
#rdata[rdata <= 221] = 100
rdata -= 75
rdata.shape = (dy,dx)
data = rdata.astype(np.uint8)
return data
def read... | harishd10/cloud-track | python/fileutils.py | Python | apache-2.0 | 2,322 | [
"VTK"
] | 66a111097646a91ce63ebf28d20cc6a298414fa048ebfdcc479501f72581dd39 |
# GromacsWrapper: utilities.py
# Copyright (c) 2009 Oliver Beckstein <orbeckst@gmail.com>
# Released under the GNU Public License 3 (or higher, your choice)
# See the file COPYING for details.
"""
:mod:`gromacs.utilities` -- Helper functions and classes
========================================================
The mod... | PicoCentauri/GromacsWrapper | gromacs/utilities.py | Python | gpl-3.0 | 22,926 | [
"Gromacs"
] | 3be933cecee02ebc870dfb2b936305182909ae710d1395ef3c15c8f50fd67f4e |
"""mBuild conversion utilities."""
import numpy as np
def RB_to_OPLS(c0, c1, c2, c3, c4, c5):
"""Convert Ryckaert-Bellemans type dihedrals to OPLS type.
Parameters
----------
c0, c1, c2, c3, c4, c5 : Ryckaert-Belleman coefficients (in kcal/mol)
Returns
-------
opls_coeffs : np.array, sha... | iModels/mbuild | mbuild/utils/conversion.py | Python | mit | 6,621 | [
"CHARMM"
] | 0635a4694bd9189a9ff29cd9ab7ced13a6b38490e51d3376ef662b67cbcf684c |
# -*- coding: utf-8 -*-
# This script creates a transparent red dice to explore further the capabilities
# of mayavi.
#
# To run (in a Python shell):
# run red_dice.py
#
# Created January 2015 by F.P.A.Vogt for the ANITA astroinformatics summer
# school 2015.
# Published as supplementary material in Vogt, Owen et al... | fpavogt/x3d-pathway | fits_to_x3d/red_dice/red_dice.py | Python | gpl-3.0 | 3,293 | [
"Mayavi"
] | d7d01dfc8d773536cca7bd5fd2724fc7d77f9b2abc27b77d9ca818ab58cbfb3b |
"""
The ``sdm`` module contains functions to fit single diode models.
Function names should follow the pattern "fit_" + name of model + "_" +
fitting method.
"""
import numpy as np
import scipy.constants
from scipy import optimize
from scipy.special import lambertw
from scipy.misc import derivative
from pvlib.pvs... | pvlib/pvlib-python | pvlib/ivtools/sdm.py | Python | bsd-3-clause | 50,560 | [
"pysam"
] | ab361b5ea5c4234e62276e500c834817db9ab465cae7b5092c201a9aaad5779b |
# see https://github.com/pypa/sampleproject
"""Installation script for ProPhyle.
To include binaries into the package, run make and set the system variable
PROPHYLE_PACKBIN to a non-zero value, e.g.,
PROPHYLE_PACKBIN=1 python3 setup.py install
"""
import glob
import os
import setuptools
import sys
if sys.version_inf... | karel-brinda/prophyle | setup.py | Python | mit | 3,999 | [
"BWA",
"pysam"
] | 72bc35b03ac3441ff5717ca677122e7cd588b09864ea18068c1cf1e05bbc0d4c |
#!/usr/bin/env python
#
# Copyright (C) 2017 - Massachusetts Institute of Technology (MIT)
#
# 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... | azariven/BioSig_SEAS | SEAS_Main/simulation/observed_spectra_simulator.py | Python | gpl-3.0 | 3,855 | [
"Gaussian"
] | d2e911dabb0f9ecb3486f230d31a0adbe8efae6b009f66f07f51c4e9df9dcaed |
"""
Nonnegative CP decomposition by Hierarchical alternating least squares (HALS).
Author: N. Benjamin Erichson <erichson@uw.edu>
"""
import numpy as np
import numba
from tensortools.operations import unfold, khatri_rao
from tensortools.tensors import KTensor
from tensortools.optimize import FitResult, optim_utils
... | ahwillia/tensortools | tensortools/optimize/ncp_hals.py | Python | mit | 6,382 | [
"Gaussian"
] | 9bbfde57a299480707642cab6473549b274a0a1401a574a10b916d24ef2f5ae6 |
# Orca
#
# Copyright 2005-2008 Sun Microsystems Inc.
#
# 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 License, or (at your option) any later version.
#
# This... | ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/scripts/apps/gnome-mud/__init__.py | Python | gpl-3.0 | 846 | [
"ORCA"
] | 3d558ec7af108531bca3aa2f773c59c039b61bb0303ef854b9de5a6dc19e2e37 |
# Copyright (C) 2004-2008 Paul Cochrane
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.
#
# This program is distribut... | paultcochrane/pyvisi | pyvisi/renderers/vtk/tests/test_renderer.py | Python | gpl-2.0 | 2,108 | [
"VTK"
] | baae460217037150dd2786ead635bf01309772dfe26918f6abb0782cd116ce66 |
#!/usr/bin/env python
# \author: Bruno Combal, IOC/UNESCO, EC/FP7 GEOWOW
# \date: July 2013
# to run the script with the correct version of uvcdat:
# source /usr/local/uvcdat/1.2.0/bin/setup_cdat.sh
# version 1: regrid lat/lon, for all t and z
# version 2: add z interpolation, for all t, lat, lon
import cdms2
import ... | IOC-CODE/esgf_ensemble_mean | regrid_thetao/bin/regrid_thetao.py | Python | gpl-2.0 | 6,151 | [
"NetCDF"
] | 7c896766b45628ffb765999a2bd94f837ed72504e935c654a95ae9b63a8f4f69 |
import pyparsing as pp
LPAR = pp.Suppress('(')
RPAR = pp.Suppress(')')
LBRACK = pp.Suppress('[')
RBRACK = pp.Suppress(']')
LBRACE = pp.Suppress('{')
RBRACE = pp.Suppress('}')
COMMA = pp.Suppress(',')
LT = pp.Suppress('<')
GT = pp.Suppress('>')
TITLE = pp.Keyword('TITLE')
UNITS = pp.Keyword('UNITS')
PARAMETER = pp.Ke... | borismarin/nmodl-parse | nmodl/terminals.py | Python | gpl-3.0 | 922 | [
"NEURON"
] | c729a260a94d45ab2d1ce18e6501d9e79afb3924bcf5617de1cadc2bd7aa2adf |
#!/usr/bin/env python
#
#
# computes analytical solution for a double-couple source
# according to Aki & Richards, eq. 4.32 and 4.33
#
#
from __future__ import print_function
import sys
from numpy import sqrt,fabs,sin,cos,arccos,arctan2,pi,zeros
from math import erf
##################################################... | geodynamics/specfem3d | EXAMPLES/small_elastic_analytic_solution/analytical_solution_Aki.py | Python | gpl-3.0 | 10,970 | [
"Gaussian"
] | e7c268453971ba678c342d12b71e643b900ec7010669dcb7df27dd92d813f97e |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-wms-job-status
# Author : Stuart Paterson
########################################################################
"""
Retrieve status of the given DIRAC job
"""
__RCSID__ = "$Id$"
import os
... | andresailer/DIRAC | Interfaces/scripts/dirac-wms-job-status.py | Python | gpl-3.0 | 2,067 | [
"DIRAC"
] | ddc90a618da8e615a23bd1a498ed665a5124abb5e163fdb8e308a666ec77cbf1 |
# 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 Spglib(CMakePackage):
"""C library for finding and handling crystal symmetries."""
ho... | LLNL/spack | var/spack/repos/builtin/packages/spglib/package.py | Python | lgpl-2.1 | 2,706 | [
"CRYSTAL"
] | c396c32f9d286bbffa592da817518005db3960374ec59e28c4c8047d0df92afd |
# Copyright 2003-2008 by Leighton Pritchard. 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.
#
# Contact: Leighton Pritchard, Scottish Crop Research Institute,
# ... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/Graphics/GenomeDiagram/_Colors.py | Python | gpl-2.0 | 9,061 | [
"Biopython"
] | 46f802e4be66746286db853c4bbe827808b15dda48d1b08148ad3606520a36b1 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals, division, print_function
import yaml
import unittest
import sys
from pymatgen.util.testing import PymatgenTest
from pymatgen.io.abinit.tasks import ParalConf
from pymat... | xhqu1981/pymatgen | pymatgen/io/abinit/tests/test_qadapters.py | Python | mit | 15,154 | [
"ABINIT",
"pymatgen"
] | 6d0c17a2391ff3e1175ab5e025d8b6f6cc12d62baca4da8b7bb87d79d78b3283 |
'''This example shows how to use importance sampling and how to
adapt the proposal density using the pmc algorithm.
'''
import numpy as np
import pypmc
# define the target; i.e., the function you want to sample from.
# In this case, it is a bimodal Gaussian
#
# Note that the target function "log_target" returns the... | fredRos/pypmc | examples/pmc.py | Python | gpl-2.0 | 4,459 | [
"Gaussian"
] | 147bea1a87fcf67b4b65c13e30c95516ba59d17d94471c009d8833c058517e13 |
#==============================================================================
#
# Program: ParaView
# Module: numeric.py
#
# Copyright (c) Kitware, Inc.
# All rights reserved.
# See Copyright.txt or http://www.paraview.org/HTML/Copyright.html for details.
#
# This software is distributed WITHOUT ANY WAR... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/Wrapping/Python/paraview/numeric.py | Python | gpl-3.0 | 2,496 | [
"ParaView",
"VTK"
] | 3665cd08ce9b00db63f05300ddc21e83b8c890282d77b1f22cc8789e473cc1f0 |
# Copyright 2018 The TensorFlow Probability 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 applicable law o... | tensorflow/probability | tensorflow_probability/python/distributions/distribution.py | Python | apache-2.0 | 86,727 | [
"Gaussian"
] | 9884f926c507ebc9ad0349aaa70470ae6ad640d3d187cd05f01a3d9714ac749b |
#!/usr/bin/python3
''' XYZ2VTK.py - Takes in an XYZ file containing coordinates
and vectors then converts them into VTK structured grids
(snapshots) for use in ParaView.
'''
import argparse
import os
from os import path
parser = argparse.ArgumentParser()
parser.add_argument(
"-n",
help="Number of frames to d... | hsidky/MolSimScripts | XYZ2VTK.py | Python | mit | 4,111 | [
"ParaView",
"VTK"
] | e73f396f6cdd41817b5a956977f264e5dcf50f1b03fb3d06158b7bcf33c6fd76 |
import time
from itertools import chain
import pysam
import numpy as np
from mitty.lib.bedfile import read_bed
from mitty.lib.sanitizeseq import sanitize
import logging
logger = logging.getLogger(__name__)
SEED_MAX = (1 << 32) - 1 # Used for seeding rng
def main(fp_out, fasta_fname, sample_name, bed_fname, see... | sbg/Mitty | mitty/simulation/genome/simulatevariants.py | Python | apache-2.0 | 6,543 | [
"pysam"
] | 3c1ee038f2ce6be77909985bd682ec317c69ce3f092eb9b715559e789a1c822f |
#
# Copyright (c) 2017 Brian J. Kidney
# Copyright (c) 2017 Jonathan Anderson
# All rights reserved.
#
# This software was developed by BAE Systems, the University of Cambridge
# Computer Laboratory, and Memorial University under DARPA/AFRL contract
# FA8650-15-C-7558 ("CADETS"), as part of the DARPA Transparent Comput... | musec/py-cdg | cdg/filters.py | Python | apache-2.0 | 3,585 | [
"Brian"
] | 0ca7f5e117430c625a5350c9e8a5bb3b4ef3d984ad8a63b21f28214617a6e706 |
import sys
import os
import gzip
import argparse
import numpy as np
from itertools import product, groupby
import pysam
import util
import snptable
import tables
MAX_SEQS_DEFAULT = 64
MAX_SNPS_DEFAULT = 6
class DataFiles(object):
"""Object to hold names and filehandles for all input / output
datafiles"""... | bmvdgeijn/WASP | mapping/find_intersecting_snps.py | Python | apache-2.0 | 42,682 | [
"pysam"
] | 566d8bad54d9f0a85bbadc21c1edbe27026061500f9512f341657aced8ec7edb |
# -*- coding: utf-8 -*-
from __future__ import print_function
import ast
import json
import logging
from collections import OrderedDict
from time import time
from lxml import html
from lxml import etree
from werkzeug import urls
from odoo.tools import pycompat
from odoo import api, models, tools
from odoo.tools.safe... | Aravinthu/odoo | odoo/addons/base/ir/ir_qweb/ir_qweb.py | Python | agpl-3.0 | 14,416 | [
"VisIt"
] | db24df4a85d98fd3836dc85f1b2c3c57cb3fe217d952d8d143818468d06108c4 |
#!/usr/bin/env python
__author__ = 'waroquiers'
import unittest
from pymatgen.analysis.chemenv.utils.func_utils import CSMFiniteRatioFunction
from pymatgen.analysis.chemenv.utils.func_utils import CSMInfiniteRatioFunction
from pymatgen.analysis.chemenv.utils.func_utils import DeltaCSMRatioFunction
import numpy as np... | mbkumar/pymatgen | pymatgen/analysis/chemenv/utils/tests/test_func_utils.py | Python | mit | 6,455 | [
"pymatgen"
] | 985f5ed6502fe12f4a80ac9fea117afe54e4bc8d7c677b679212b50e4a4f8651 |
# Copyright (C) 2017,2018(1H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++ -> Powered by HeSpaDDA algorithm developed by horacio.v.g@gmail.com
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publ... | MrTheodor/espressopp | src/tools/loadbal.py | Python | gpl-3.0 | 32,052 | [
"ESPResSo"
] | f55a52af8e0df9af7bbdf78a76c1cdd8b569e9d18252303a81493df07e50f5c9 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | harterj/moose | python/MooseDocs/test/extensions/test_devel.py | Python | lgpl-2.1 | 4,858 | [
"MOOSE"
] | 430c5300e613b3c03936a2b4f3cd79a4bc31b855a0544de50d787b0a5156c6e8 |
#!/usr/bin/env python
# encoding: utf-8
import os
import sys
import time
import pprint
import pytest
import signal
import threading
import Queue
import traceback
from urlparse import urlsplit, parse_qsl, urlunsplit, urljoin
from urllib import urlencode
from bs4 import BeautifulSoup
from testlib import web, var_dir
fr... | huiyiqun/check_mk | tests/integration/web/test_crawl.py | Python | gpl-2.0 | 15,021 | [
"VisIt"
] | 88ef05ab00919d801d3b996b19e9a2a8f028c5e4faf8f3764b4e9945d9cb200c |
# -*- coding: utf-8 -*-
from collections import OrderedDict, Counter
import csv
from datetime import datetime, timedelta
import hashlib
import json
import os
import platform
import plistlib
import re
import shutil
import sqlite3
from subprocess import call
import sys
import time
import urllib
import u... | grwllrnc/BrowsingHistoryEditor | main.py | Python | mit | 44,796 | [
"VisIt"
] | 688800071c8bb99be8bbeb30931cea2f2d2f71e4a069f6b525a64d73c699f507 |
import os, sys, re, inspect, types, errno, pprint, subprocess, io, shutil, time, copy
import path_tool
path_tool.activate_module('FactorySystem')
path_tool.activate_module('argparse')
from ParseGetPot import ParseGetPot
from socket import gethostname
#from options import *
from util import *
from RunParallel import R... | giopastor/moose | python/TestHarness/TestHarness.py | Python | lgpl-2.1 | 43,648 | [
"MOOSE",
"VTK"
] | 9e927497387b03dcd8a74da6b3d72a63dbc470df04edf88070f34ce1f3d562ed |
#!/usr/bin/env python
###############################################################################
#
# __template__.py - Description!
#
###############################################################################
# #
# This program is free software: you can redistribute it and/or modify #
# it under the terms of ... | JoshDaly/scriptShed | parse_blast_vectors.trackm.py | Python | gpl-2.0 | 4,899 | [
"Biopython"
] | 364fb867e91e74750c7b770896e649be285f0ce62778578ca7ec96100bb6b6dd |
# 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... | gVallverdu/pymatgen | pymatgen/command_line/gulp_caller.py | Python | mit | 26,619 | [
"GULP",
"pymatgen"
] | 4c73ae2ab8d53f59079effd37c0ba04fbc6a8e794075e50dc9490fd1a0045be0 |
"""Support for Ecobee Thermostats."""
import collections
from typing import Optional
import voluptuous as vol
from homeassistant.components.climate import ClimateDevice
from homeassistant.components.climate.const import (
ATTR_TARGET_TEMP_HIGH,
ATTR_TARGET_TEMP_LOW,
CURRENT_HVAC_COOL,
CURRENT_HVAC_DRY... | Teagan42/home-assistant | homeassistant/components/ecobee/climate.py | Python | apache-2.0 | 23,976 | [
"VisIt"
] | b093ce9505bc0378c5d0f65b88c2067744a782e9c88e63f309bc499b0c2bb284 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007 Zsolt Foldvari
# Copyright (C) 2009 Benny Malengier
# Copyright (C) 2009 Brian Matherly
# Copyright (C) 2010 Peter Landgren
# Copyright (C) 2010 Jakim Friant
# Copyright ... | gramps-project/gramps | gramps/plugins/lib/libcairodoc.py | Python | gpl-2.0 | 62,883 | [
"Brian"
] | 6990571cb14bc9c7cbf85f7e5c17d49f9fcfbaee272ebeb1dabf420b904ba8d1 |
#!/usr/bin/env python
from math import sqrt
import gtk
from ase.gui.languages import translate as _
from ase.gui.widgets import pack, help
class Graphs(gtk.Window):
def __init__(self, gui):
gtk.Window.__init__(self)
#self.window.set_position(gtk.WIN_POS_CENTER)
#self.window.connect("dest... | freephys/python_ase | ase/gui/graphs.py | Python | gpl-3.0 | 2,816 | [
"ASE"
] | 6ae2a91afc801c1c45f83f5f440a0f2d6fbebc62a06d6a47bd665bb3e157d571 |
import GalaxyCommunication_data_manager
import ProtonCommunication_data_manager
from bioblend.galaxy import GalaxyInstance
import logging
def grou():
return ("this is the init.py script")
| CARPEM/GalaxyDocker | data-manager-hegp/datamanagerpkg/datamanagerpkg/__init__.py | Python | mit | 193 | [
"Galaxy"
] | 76a0632f9abcd9839dca792ac18c75cb910a803c9e32f33cb1596d3e1fa5aa91 |
'''
=================================================================================================
R Cipher Suite
Includes all variants of the R cipher
=================================================================================================
Developed by: ProgramRandom, a division of RandomCorporations
A Pa... | lakewood999/Ciphers | rcipherx.py | Python | mit | 5,693 | [
"VisIt"
] | 4fecddce30c1e6ce7319517db521dde1fde99790573597847154bc1fe85e064f |
# -*- coding: utf-8 -*-
#
# Buildbot documentation build configuration file, created by
# sphinx-quickstart on Tue Aug 10 15:13:31 2010.
#
# This file is exec()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... | anish/buildbot | master/docs/conf.py | Python | gpl-2.0 | 12,154 | [
"Brian"
] | 5a4379da1a0dbe5f4b85b6543c310c7886764d1630f776eda354cb77c6cf8ca4 |
from django.db import IntegrityError
from experiments.models import Enrollment
from experiments.manager import experiment_manager
from experiments.dateutils import now, fix_awareness, datetime_from_timestamp, timestamp_from_datetime
from experiments.signals import user_enrolled
from experiments.experiment_counters imp... | bjarnoldus/django-experiments | experiments/utils.py | Python | mit | 20,243 | [
"VisIt"
] | 5f07cddd33ca3d8ea99c62b7bc8e41be9a7a1601cb2d7286543a1ee6a558523a |
#! /usr/bin/env python3
# Copyright (c) 2014, HashFast Technologies LLC
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# 1. Redistributions of source code must retain the above copyright
# ... | HashFast/hashfast-tools | hftool.py | Python | bsd-3-clause | 3,207 | [
"EPW"
] | b636c93029689978dc06451922848ae82b631ca4170f5fdaa2ed440fee0a3139 |
"""
################################################################################
#
# SOAPpy - Cayce Ullman (cayce@actzero.com)
# Brian Matthews (blm@actzero.com)
# Gregory Warnes (Gregory.R.Warnes@Pfizer.com)
# Christopher Blunck (blunck@gst.com)
#
##########################... | krux/adspygoogle | adspygoogle/SOAPpy/Server.py | Python | apache-2.0 | 27,092 | [
"Brian"
] | dec22cfa49f0c3aa969ea623a179653b452cf9bd3bb408fcc33c60f8efa4efaf |
#!/usr/bin/env python
"""
The APIRUS API as an Abstract Base Class
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
from abc import ABCMeta, abstractmethod
class APIRUS:
"""
ABC for the API for Regular,... | ioos/APIRUS | apirus_abc.py | Python | cc0-1.0 | 3,009 | [
"NetCDF"
] | 1f95c629338da0e2ec54a7a12fed900ba2a72153e369a733847b6e65bcddd14f |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This package implements various grain boundary analyses
"""
| gVallverdu/pymatgen | pymatgen/analysis/gb/__init__.py | Python | mit | 174 | [
"pymatgen"
] | 31d92203566360a61f2612416f2f176d13a1796db50a9215ba649d4bc65f0b4a |
"""
Test the Hartree-Fock Objective function
1. Hamiltonian expectation
2. The gradient values (local)
3. The Hessian values (local)
The local gradient is the gradient assuming $kappa = 0$. This is the case
in most electronic structure codes because the Hamiltonian (or orbitals)
are always rotated to the $kappa=0$ p... | quantumlib/OpenFermion-Cirq | openfermioncirq/experiments/hfvqe/objective_test.py | Python | apache-2.0 | 6,832 | [
"Psi4"
] | 6bc43f2cb8df2e47980318bc5e2fafb85723833e493ea684795eb51f0671c34b |
# -*- coding: utf-8 -*-
# This file is part of beets.
# Copyright 2016, Adrian Sampson.
#
# Permission is hereby granted, free of charge, to any person obtaining
# a copy of this software and associated documentation files (the
# "Software"), to deal in the Software without restriction, including
# without limitation t... | jetskijoe/headphones | lib/beetsplug/beatport.py | Python | gpl-3.0 | 18,360 | [
"VisIt"
] | 6eef24014f58b83340ce93ca00139e0acab082505b7dcbf1fae5941472c894ba |
# This code is part of Ansible, but is an independent component.
# This particular file snippet, and this file snippet only, is BSD licensed.
# Modules you write using this snippet, which is embedded dynamically by Ansible
# still belong to the author of the module, and may assign their own license
# to the complete wo... | emersonsoftware/ansiblefork | lib/ansible/module_utils/basic.py | Python | gpl-3.0 | 98,105 | [
"VisIt"
] | fa23e4b59b4bc33c9051499a217e8f0080ba249274df128b288f019ac6d0a957 |
# -*- coding: utf-8 -*-
# Copyright 2007-2016 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy 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... | CodeMonkeyJan/hyperspy | hyperspy/drawing/utils.py | Python | gpl-3.0 | 47,617 | [
"ADF"
] | def92fb30484063d82f37011b97be8798820476e8ef25e8752a3bd54efbdf669 |
# $Id$
#
# Copyright (C) 2003-2006 Greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" class definitions f... | rvianello/rdkit | rdkit/Chem/Fingerprints/SimilarityScreener.py | Python | bsd-3-clause | 4,634 | [
"RDKit"
] | 4525d318ceef042af50170b5f170ac9bdb2da0f74f00bd44d16769a194f1b9fb |
"""
blast module
Requirements:
- getSequence uses BLAST's fastacmd
"""
import os, sys, copy, re
from mungoCore import *
import fasta, sequence
from useful import smartopen
def sign_to_strand(x):
if x<0:
return '-'
else:
return '+'
def test_to_strand(test):
if test:
return '+... | PapenfussLab/Mungo | mungo/blast.py | Python | artistic-2.0 | 9,823 | [
"BLAST"
] | 12eb3ad45f5f17ff71ee7bdc76f72f79e510481b506ee3552fc1cd56ea467ab8 |
from galaxy import web, util
from galaxy.web.base.controller import BaseAPIController
from galaxy.web.framework.helpers import is_true
def get_id( base, format ):
if format:
return "%s.%s" % ( base, format )
else:
return base
class GenomesController( BaseAPIController ):
"""
RESTful co... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/webapps/galaxy/api/genomes.py | Python | gpl-3.0 | 1,289 | [
"Galaxy"
] | 9ddb07cbf0d55b4d07bdae7be9a463b041590bc49abba2674cb37f2761f42ba6 |
"""
Displays Agg images in the browser, with interactivity
"""
from __future__ import (absolute_import, division, print_function,
unicode_literals)
# The WebAgg backend is divided into two modules:
#
# - `backend_webagg_core.py` contains code necessary to embed a WebAgg
# plot inside of a web... | yavalvas/yav_com | build/matplotlib/lib/matplotlib/backends/backend_webagg.py | Python | mit | 12,895 | [
"VisIt"
] | 75c30758425d37ca29ff51d25670bd31b6aeb564066dcbca84c419b8c22b562f |
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