text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
from paraview.simple import *
from tonic.paraview.dataset_builder import *
dataset_destination_path = '/tmp/cylinder_v2'
# Initial ParaView scene setup
Cylinder(Resolution = 30, Height = 10.0, Center = (1,2,3))
rep = Show()
view = Render()
view.UseGradientBackground = 1
view.Background = [0.6818646524757763, 0.72323... | Kitware/tonic-data-generator | scripts/paraview/samples/camera-cylindrical_v2.py | Python | bsd-3-clause | 910 | [
"ParaView"
] | a70e942f16c57f0538bea9d2d71f191c44d5c29363f762626c6482b63506adca |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | modeling/decomposition/s4g.py | Python | agpl-3.0 | 3,789 | [
"Galaxy"
] | a88d1569f72680567eee7890c1149f4311d21a8eee1903a9e448cfbc5fb26013 |
"""
End-to-end tests for the LMS.
"""
import ddt
from ..ga_helpers import GaccoTestMixin, SUPER_USER_INFO
from ..helpers import UniqueCourseTest
from ...fixtures.course import CourseFixture, XBlockFixtureDesc
from ...pages.lms.auto_auth import AutoAuthPage
from ...pages.lms.course_nav import CourseNavPage
from ...page... | nttks/edx-platform | common/test/acceptance/tests/lms/test_ga_courseware.py | Python | agpl-3.0 | 12,702 | [
"VisIt"
] | 12dd87c1e04b13ce4c6a5c5803a7f1509b424b8dd41446563bd9db73ea59caf3 |
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | googlefonts/nanoemoji | src/nanoemoji/pngquant.py | Python | apache-2.0 | 2,064 | [
"VisIt"
] | b6416af2fd768bbb2078d01d534132772a27aee3cabeec2446cb7d414ddcb121 |
# Copyright 2016 Hewlett Packard Enterprise Development LP
#
# 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... | opveclib/opveclib | opveclib/operator.py | Python | apache-2.0 | 105,584 | [
"VisIt"
] | d3079b1f4c161c5295b70fff8bb4a43eef342ff60b58e9b5cdebf488e332e842 |
'''
Created on 08.04.2012
@author: bluesbreaker
'''
from logilab.common.configuration import ConfigurationMixIn
from pylint.pyreverse.main import OPTIONS
from CSUStAn.astng.simple import NamesCheckLinker
from CSUStAn.reflexion.rm_tools import ReflexionModelVisitor,HighLevelModelDotGenerator,SourceModelXMLGenerator
fr... | exbluesbreaker/csu-code-analysis | logilab-astng XML Generator/src/CSUStAn/runners.py | Python | gpl-2.0 | 17,681 | [
"VisIt"
] | 4143f9523d6aa43aa8a9f082208f1a7365474a3fdcb6e124e30563732e3df652 |
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at https://mozilla.org/MPL/2.0/.
""" pytest test configures """
import pytest
import os.path as osp
import sisl
pytestmark = [pytest.mark.io, pytest.m... | zerothi/sisl | sisl/io/siesta/tests/test_bands.py | Python | mpl-2.0 | 1,365 | [
"SIESTA"
] | 57e0f59846020578f3e414a6168e200eeabbede96aae8b30ce15f58854797df9 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# cgiscriptstub - cgi wrapper functions for functionality backends
# Copyright (C) 2003-2014 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of th... | heromod/migrid | mig/shared/cgiscriptstub.py | Python | gpl-2.0 | 4,800 | [
"Brian"
] | 10c59a571adc20f4b6870220fa6283c8914eb979702bbc9161e611c9de66c9f7 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
r"""
K2 Pixel Photometry (K2P\ :sup:`2`)
Create pixel masks and extract light curves from Kepler and K2 pixel data
using clustering algorithms.
To read more about the methods used, please see the following papers:
* Lund et al. (2015): K2P\ :sup:`2` - A photometric pipe... | tasoc/photometry | photometry/AperturePhotometry/k2p2v2.py | Python | gpl-3.0 | 27,217 | [
"Gaussian"
] | 5cb6e9300bd7abd77dc1eed925cbd6945bfc5c5e8967788902c284723b80dbe5 |
# Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import math
import torch
from torch.distributions.utils import lazy_property
from torch.nn.functional import pad
from pyro.distributions.multivariate_studentt import MultivariateStudentT
from pyro.distributions.torch import Multi... | uber/pyro | pyro/ops/gamma_gaussian.py | Python | apache-2.0 | 17,954 | [
"Gaussian"
] | 48df1d2277a3692efa347e20cefa19faa91d8fa5b33fcf924e1594d37f25a84f |
# mako/pyparser.py
# Copyright (C) 2006-2011 the Mako authors and contributors <see AUTHORS file>
#
# This module is part of Mako and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Handles parsing of Python code.
Parsing to AST is done via _ast on Python > 2.5, otherwise th... | casanovainformationservices/LazyLibrarian | mako/pyparser.py | Python | gpl-3.0 | 17,990 | [
"VisIt"
] | 3f9a4b00628f4cba70501dd42da68c05a08ce22854994a95193dc8e0a4717693 |
#!/usr/bin/env python
#
# Copyright 2008,2009,2011 Free Software Foundation, Inc.
#
# This file is part of GNU Radio
#
# GNU Radio 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, or (at you... | gnychis/gnuradio-3.5.0-dmr | gr-uhd/apps/uhd_siggen.py | Python | gpl-3.0 | 14,999 | [
"Gaussian"
] | d6909a3aa30e2475f03e974a7eeb492bb34a611a319a91d8e90d890568f29b10 |
# Copyright 2010 Torbjorn Bjorkman
# This file is part of cif2cell
#
# cif2cell 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.
#
# cif... | stuartcampbell/vision | cif2cell-1.2.7/uctools.py | Python | apache-2.0 | 82,654 | [
"CRYSTAL",
"Gaussian"
] | bb29da827a9a499db40ae6040af9d7595034ad0381eced815fd80a984e0040cc |
#!/usr/bin/env python
import numpy as np
import pandas as pd
# from matplotlib.pyplot import plot,show,draw
import scipy.io
import sys
sys.path.append("../")
from functions import *
from pylab import *
from sklearn.decomposition import PCA
import _pickle as cPickle
import neuroseries as nts
import os
import hsluv
da... | gviejo/ThalamusPhysio | python/figure_article_v4/main_article_v4_fig_1.py | Python | gpl-3.0 | 16,035 | [
"Gaussian"
] | 15271d28586e7527604684086a222b08a880a92db95ff748337ba8d3152e3a64 |
"""Support for package tracking sensors from 17track.net."""
from datetime import timedelta
import logging
from py17track import Client as SeventeenTrackClient
from py17track.errors import SeventeenTrackError
import voluptuous as vol
from homeassistant.components.sensor import PLATFORM_SCHEMA, SensorEntity
from homea... | lukas-hetzenecker/home-assistant | homeassistant/components/seventeentrack/sensor.py | Python | apache-2.0 | 10,764 | [
"VisIt"
] | 47980e8150c6fa9d8f7200918c5015022ec35908f947e283fdbcc09e7d373a5e |
import re
import logging
from datetime import datetime
from django.contrib.gis.db import models
from django.contrib.auth.models import User
from django.db.models.signals import pre_save, post_save, pre_delete
from django.dispatch import receiver
from django.core.urlresolvers import reverse
from sorl.thumbnail import Im... | ProvidencePlan/Profiles | communityprofiles/profiles/models.py | Python | mit | 60,698 | [
"MOE"
] | 3f2186bfdeb0543f992abdffb9607a4773693159beb9c699e2188bb9c480a814 |
""" Collection of utilities for locating certs, proxy, CAs
"""
import os
import DIRAC
from DIRAC import gConfig
g_SecurityConfPath = "/DIRAC/Security"
def getProxyLocation():
"""Get the path of the currently active grid proxy file"""
for envVar in ["GRID_PROXY_FILE", "X509_USER_PROXY"]:
if envVar in... | DIRACGrid/DIRAC | src/DIRAC/Core/Security/Locations.py | Python | gpl-3.0 | 5,896 | [
"DIRAC"
] | fead79b0c0c24ea1a07da61ce20f1b12f7f6d15bd3f3e4c32bbe39f72aa60440 |
# !usr/bin/env python
# -*- coding: utf-8 -*-
#
# Licensed under a 3-clause BSD license.
#
# @Author: Brian Cherinka
# @Date: 2018-08-01 17:50:48
# @Last modified by: Brian Cherinka
# @Last Modified time: 2018-08-08 14:01:33
from __future__ import print_function, division, absolute_import
import numpy as np
impor... | sdss/marvin | tests/tools/test_image.py | Python | bsd-3-clause | 4,596 | [
"Brian"
] | dd4a36c38031c4c1a77d2893fe01b5ae82b115ce84f27eb83946adb630bedab5 |
"""
Utility functions for transcripts.
++++++++++++++++++++++++++++++++++
"""
import os
import copy
import json
import requests
import logging
from pysrt import SubRipTime, SubRipItem, SubRipFile
from lxml import etree
from HTMLParser import HTMLParser
from xmodule.exceptions import NotFoundError
from xmodule.contents... | prarthitm/edxplatform | common/lib/xmodule/xmodule/video_module/transcripts_utils.py | Python | agpl-3.0 | 24,691 | [
"FEFF"
] | 30e0b54663ffcbfefcda1ae4076ccf689552d5c69a99a17fcb379bfda82a7d0e |
# Import and make available things that are convenient to have around in
# iPythonNotebook following 'from dark.ipynb import *'.
from .fasta import FastaReads
from .blast.alignments import BlastReadsAlignments
from .titles import titleCounts, TitlesAlignments
from .html import (
summarizeTitlesByLength, summarizeT... | terrycojones/dark-matter | dark/ipynb.py | Python | mit | 1,108 | [
"BLAST"
] | f3f7b4a2cf02a676c17a353b8e6d39c4e7dc278ed51b5c9b599d70cd94c630e1 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2018 Piero Dalle Pezze
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the ... | pdp10/sbpipe | sbpipe/simul/simul.py | Python | mit | 23,085 | [
"COPASI"
] | e940edfa1928fff8af780685002d319f86d377dd9d4207616723d1175ef19802 |
import networkx
from claripy.utils.orderedset import OrderedSet
# errors
from ..errors import AngrForwardAnalysisError
# notices
from ..errors import AngrSkipJobNotice, AngrDelayJobNotice, AngrJobMergingFailureNotice, \
AngrJobWideningFailureNotice
from .cfg.cfg_utils import CFGUtils
#
# Graph traversal
#
clas... | Ruide/angr-dev | angr/angr/analyses/forward_analysis.py | Python | bsd-2-clause | 22,372 | [
"VisIt"
] | 428f55c8f428b8b75c04873e7253e1f1767de7c253e482ccdccc446d4ed9f455 |
# coding: utf-8
from __future__ import division, unicode_literals, print_function
"""
This module implements plotter for DOS and band structure.
"""
__author__ = "Shyue Ping Ong, Geoffroy Hautier"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ ... | rousseab/pymatgen | pymatgen/electronic_structure/plotter.py | Python | mit | 42,354 | [
"Gaussian",
"pymatgen"
] | 39da5e0cd9a7177a671c3c36fa97eebf83344576440b666fa00ad738d528756f |
#!/usr/bin/env python
"""
Get parameters assigned to the CE
"""
from __future__ import print_function
from __future__ import division
from __future__ import absolute_import
__RCSID__ = "$Id$"
import json
from DIRAC.Core.Base import Script
from DIRAC import gLogger, exit as DIRACExit
Script.setUsageMessage('\n'.jo... | DIRACGrid/VMDIRAC | VMDIRAC/Resources/scripts/dirac-resource-get-parameters.py | Python | gpl-3.0 | 1,596 | [
"DIRAC"
] | 746f39821268c37d01ef2530d979e74ef51a2031a382b8fea4d090e29407317f |
class Neuron(object):
def __init__(self, config, finder, manager):
self.config = config
self.finder = finder
self.manager = manager
def load_all(self):
path = self.config.get_neurons_path()
neuron_modules = self.finder(path)
for neuron in neuron_modules:
... | Le-Bot/cerebro | cerebro/neuron/neuron.py | Python | mit | 533 | [
"NEURON"
] | 165e48d1f1e5635c794fc596b2211b3149701042d93dc50e4dcb40db2e764f19 |
# coding=utf-8
import collections as coll
import numpy as np
from scipy import ndimage as ndi
from .._shared.utils import warn
from ..util import img_as_float, regular_grid
from ..segmentation._slic import (_slic_cython,
_enforce_label_connectivity_cython)
from ..color import rgb2lab... | endolith/scikit-image | skimage/segmentation/slic_superpixels.py | Python | bsd-3-clause | 7,874 | [
"Gaussian"
] | 999854e55071c4a0ba761e581af6ef056f5a58caee9c57dae86a9b0adc4fa0e3 |
import sys
sys.path.insert(1,"../../../")
import h2o
from tests import pyunit_utils
from h2o.estimators.glm import H2OGeneralizedLinearEstimator
def link_correct_default():
print("Reading in original prostate data.")
h2o_data = h2o.upload_file(path=pyunit_utils.locate("smalldata/prostate/prostate.csv.zip"))
pr... | madmax983/h2o-3 | h2o-py/tests/testdir_algos/glm/pyunit_link_correct_default_glm_large.py | Python | apache-2.0 | 2,657 | [
"Gaussian"
] | 3c61ab1e23aec3d303091dca993a32c06d26a24e78084fb270b8df44910f1df8 |
# -*- coding: utf-8 -*-
# Copyright (C) 2017-2018 CIRCL Computer Incident Response Center Luxembourg (smile gie)
# Copyright (C) 2017-2018 Christian Studer
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published... | FIRSTdotorg/MISP | app/files/scripts/stix2misp.py | Python | agpl-3.0 | 73,227 | [
"Galaxy"
] | c6c1dcc84fcfbc190a1babf4617aefd1ddc66e56aeca37b0e7e53bd823da821a |
# 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/mvn_linear_operator.py | Python | apache-2.0 | 14,891 | [
"Gaussian"
] | 50d46eb0fe5d3e1ac22fc4fb6d0c7eb8a1eba4ae4023ee8d2113fd8e4a5803e4 |
#!/usr/bin/env python3
#
# gw2wannier90 interface
#
# This file is distributed as part of the Wannier90 code and
# under the terms of the GNU General Public License. See the
# file `LICENSE' in the root directory of the Wannier90
# distribution, or http://www.gnu.org/copyleft/gpl.txt
#
# The webpage of the Wannier90 co... | jryates/wannier90 | utility/gw2wannier90.py | Python | gpl-2.0 | 19,414 | [
"Quantum ESPRESSO",
"Wannier90",
"Yambo"
] | ee5e0112912a6816d6c4ce192de8709f696e2e876e83268c349026ad9e47b874 |
import argparse
import os
from common import FileSizeDistr, FileAccessDistr
from common import BYTES_PER_KiB
TypeExc = argparse.ArgumentTypeError
# if we throw exceptions, do it with this
# so caller can specifically catch them
class FsDriftParseException(Exception):
pass
# the next few routines implement data ... | parallel-fs-utils/fs-drift | parser_data_types.py | Python | apache-2.0 | 4,434 | [
"Gaussian"
] | e8f8c31f3708c080cc5c8c949754282f03ce4c53a97566b8f653454b7dbb225b |
# -*- Mode:Python; indent-tabs-mode:nil; tab-width:4 -*-
#
# Copyright (C) 2016-2018 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 program is distributed in ... | sergiusens/snapcraft | tests/unit/plugins/test_gulp.py | Python | gpl-3.0 | 7,447 | [
"GULP"
] | 55311ce578e86666f47f26f5bc8c99c9857d911d7e917e6ff0f7cd90c49ed349 |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2011, 2013, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License... | zenoss/ZenPacks.zenoss.PostgreSQL | ZenPacks/zenoss/PostgreSQL/modeler/plugins/zenoss/PostgreSQL.py | Python | gpl-2.0 | 3,822 | [
"VisIt"
] | 769018d549f93b4386708432ff91a6c14a38be7ed10baa90577d5d3078e2ecc9 |
# -*- coding: utf-8 -*-
##
## This file is part of Invenio.
## Copyright (C) 2013, 2014 CERN.
##
## Invenio 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... | lnielsen/invenio | invenio/modules/workflows/testsuite/test_workflows.py | Python | gpl-2.0 | 30,731 | [
"Galaxy"
] | a5eb354119d7d298c183f9a2c10e25f4df1508218bf5199fb3e55f91ba597631 |
import numpy as np
import pandas as pd
import inspect
from .parameters import Parameters
from numba import jit, vectorize, guvectorize
from functools import wraps
from six import StringIO
import ast
import toolz
class GetReturnNode(ast.NodeVisitor):
"""
A Visitor to get the return tuple names from a calc-styl... | mcdeaton13/Tax-Calculator | taxcalc/decorators.py | Python | mit | 11,728 | [
"VisIt"
] | fb509fa577d8bfb3376a72f79c6aeb94cfeefa39fa54740eb0d8241782cda11b |
#!/usr/bin/env python3
"""Script to create a source/binary RPM.
"""
# $Id: make_rpm.py 496041 2016-03-23 14:47:36Z camacho $
from __future__ import print_function
import sys, os, shutil
from optparse import OptionParser
import subprocess
import tarfile
SCRIPT_DIR = os.path.dirname(os.path.abspath(sys.argv[0]))
sys.pat... | kyungtaekLIM/PSI-BLASTexB | src/ncbi-blast-2.5.0+/c++/scripts/projects/blast/post_build/rpm/make_rpm.py | Python | lgpl-3.0 | 5,741 | [
"BLAST"
] | 0aaa70fcb416a171911c2cd4d4c75b2f616148679a75654762c64205094aebce |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2014 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors: Kyle A Beauchamp
#
# MDTraj is... | ctk3b/mdtraj | mdtraj/tests/test_trajectory.py | Python | lgpl-2.1 | 27,502 | [
"MDTraj"
] | 8c5b2d4abe86d8ea76fbac20a04bc566408e01236f330ffec6b6a95b4cd6ee7b |
#This file does classification using scikit for reduced features: Gaussian,Bernolli NaiveBayes,
#Decision Tree, RF,knn,svm
from sklearn.naive_bayes import GaussianNB
from sklearn.ensemble import RandomForestClassifier
from sklearn import metrics, preprocessing
from sklearn import svm, naive_bayes, neighbors, tree
fr... | LighthouseHPC/lighthouse | sandbox/petsc/solvers/scripts/ScikitClassifiersRS2.py | Python | mit | 13,950 | [
"Gaussian"
] | ceff1cf48d3486878321564fa6f56c146fa1488011b52da980fa098e1f57c845 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/ao2mo/test/test_incore.py | Python | apache-2.0 | 3,403 | [
"PySCF"
] | 4f795d12629f6bbaa1d706fe0b5a9d9f740254a280b6a57905ba6faad0eca1d8 |
"""
Extended math utilities.
"""
# Authors: Gael Varoquaux
# Alexandre Gramfort
# Alexandre T. Passos
# Olivier Grisel
# Lars Buitinck
# Stefan van der Walt
# Kyle Kastner
# License: BSD 3 clause
from __future__ import division
from functools import partial
import ... | Garrett-R/scikit-learn | sklearn/utils/extmath.py | Python | bsd-3-clause | 20,521 | [
"Gaussian"
] | 9d1b3e308eb13d568c24ebdf9e22f4a4376ecad67ba0a3afd0614514f5625dea |
# 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... | renyi533/tensorflow | tensorflow/python/ops/linalg/linear_operator_test_util.py | Python | apache-2.0 | 37,872 | [
"Gaussian"
] | 95e4ca496951e3c24cbec8e8720453d77ccde029fb37958b07349b743564f2a1 |
#!/usr/bin/env python
# This example demonstrates the use of VTK data arrays as attribute
# data as well as field data. It creates geometry (vtkPolyData) as
# well as attribute data explicitly.
import vtk
# Create a float array which represents the points.
pcoords = vtk.vtkFloatArray()
# Note that by defau... | hlzz/dotfiles | graphics/VTK-7.0.0/Examples/DataManipulation/Python/Arrays.py | Python | bsd-3-clause | 2,749 | [
"VTK"
] | 3597b0a0a4e6a8604811ca042763040703ef18bd7e7877446c669cc8778875ee |
from setuptools import setup
import glob,os,sys
# To use a consistent encoding
from codecs import open
from os import path
here = path.abspath(path.dirname(__file__))
scriptlist =glob.glob(os.path.join('bin', '*.py'))
scriptlist+=glob.glob(os.path.join('sbin', '*.py'))
from PyFoam import versionString
# with open(... | Unofficial-Extend-Project-Mirror/openfoam-extend-Breeder-other-scripting-PyFoam | setup.py | Python | gpl-2.0 | 2,106 | [
"ParaView"
] | 9f4e07eae1c1d232f80b5322cc24a1e6143057c9fa94183336de58ba8fbdcc10 |
import luigi
from path import Path
import sh
import shlex
download_pth = Path('download').abspath()
class FilePath(luigi.Parameter):
def parse(self, value):
return Path(value)
class Reads(luigi.Task):
r1 = luigi.Parameter()
r2 = luigi.Parameter(default=False)
def output(self):
o = []... | necrolyte2/luigi-test | tasks.py | Python | apache-2.0 | 1,797 | [
"Bowtie"
] | 6a592be9a2d512f5c2295838e2573c7abbc2a06cd3fbe2b8842048fed41a2607 |
import os
print('setenv...', end=' ')
print(os.environ['USER']) # show current shell variable value
os.environ['USER'] = 'Brian' # runs os.putenv behind the scenes
os.system('python echoenv.py')
os.environ['USER'] = 'Arthur' # changes passed to spawned programs
os.system(... | simontakite/sysadmin | pythonscripts/programmingpython/System/Environment/setenv.py | Python | gpl-2.0 | 466 | [
"Brian"
] | 31e514f4ba8efb6142df79bbcb6d47fa854ca17bb3cb61b6f015e9d19ce3492f |
########################################################################
# $Id$
# File : PoolComputingElement.py
# Author : A.T.
########################################################################
""" The Computing Element to run several jobs simultaneously in separate processes
managed by a ProcessPool
"""... | andresailer/DIRAC | Resources/Computing/PoolComputingElement.py | Python | gpl-3.0 | 8,523 | [
"DIRAC"
] | ff9f35ab002225f1ab1bfeda0328b491181f1eb9b948cad185a3c227c802da99 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import numpy as np
import unittest
import os
from pymatgen.analysis.local_env import ValenceIonicRadiusEvaluator, \
VoronoiNN, VoronoiNN_modified, JMolNN, \
... | czhengsci/pymatgen | pymatgen/analysis/tests/test_local_env.py | Python | mit | 33,674 | [
"Jmol",
"pymatgen"
] | bf69721913c3a008b5f143ba2b1a271cb592198b9be323266a3071fede0454b5 |
# Copyright (c) 2019, NVIDIA CORPORATION. All rights reserved.
#
# This work is licensed under the Creative Commons Attribution-NonCommercial
# 4.0 International License. To view a copy of this license, visit
# http://creativecommons.org/licenses/by-nc/4.0/ or send a letter to
# Creative Commons, PO Box 1866, Mountain ... | microsoft/DiscoFaceGAN | dataset_tool.py | Python | mit | 30,421 | [
"VisIt"
] | 5400ea95214e258c336ab37e8817711987029809fba223891f9743d10dda9447 |
# Copyright (C) 2010-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | mkuron/espresso | src/python/object_in_fluid/oif_classes.py | Python | gpl-3.0 | 67,723 | [
"ESPResSo",
"VTK"
] | 02907e28e90b4c272a10b83a130c4962739eb8c38b1a2f9e507e5df95424db3c |
import pylab
import numpy
#import pymc
import matplotlib as mpl
import matplotlib.patches
import matplotlib.colors as mcolors
from mpl_toolkits.axes_grid1 import make_axes_locatable
import scipy.stats
def frac_inside_poly(x,y,polyxy):
"""Calculate the fraction of points x,y inside polygon polyxy.
... | NumCosmo/NumCosmo | scripts/plot2Ddist.py | Python | gpl-3.0 | 10,518 | [
"Gaussian"
] | d02d53a35897a77f1f9c8bdddf8e5052ad524004abd2246502b56264eb71af61 |
# -*- mode: python; -*-
# Copyright 2011 Google Inc. 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 require... | adambyram/bite-project-mod | builddefs/soy_rule.py | Python | apache-2.0 | 2,323 | [
"xTB"
] | c29e39ddadf251518fba37f22c27d6c841f8e6c8faedcd451a435e76e1d381ab |
#-------------------------------------------------------------------------------
# ______ _ ____ __ __
# | ____| _| |_ / __ \ /\ | \/ |
# | |__ _ __ ___ ___ / \| | | | / \ | \ / |
# | __| '__/ _ \/ _ ( (| |) ... | themiwi/freefoam-debian | data/python/FreeFOAM/util.py | Python | gpl-3.0 | 14,700 | [
"ParaView",
"VTK"
] | f28f58dec6467a3990fc607dafb19372ea9408f09b4046889e82569788a5c269 |
# coding: utf-8
from __future__ import division, unicode_literals
"""
This module defines classes for point defects
"""
import os
import abc
import json
from bisect import bisect_left
from pymatgen.core.periodic_table import Specie, Element
from pymatgen.core.sites import PeriodicSite
from pymatgen.symmetry.analyze... | ctoher/pymatgen | pymatgen/analysis/defects/point_defects.py | Python | mit | 52,773 | [
"GULP",
"pymatgen"
] | d024a9f07161410f0d76d6aa524cc545f71456999b0a0e1ec85aa4985e9869d7 |
# Copyright 2021 Google LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | google-research/vmoe | vmoe/nn/routing.py | Python | apache-2.0 | 7,081 | [
"Gaussian",
"MOE"
] | 833dee0ffcfc4ae689469cdd176e8b48527238dca369f8e7db33daf3841334fb |
#
# FRETBursts - A single-molecule FRET burst analysis toolkit.
#
# Copyright (C) 2014 Antonino Ingargiola <tritemio@gmail.com>
#
"""
Module containing automated unit tests for FRETBursts.
Running the tests requires `py.test`.
"""
from __future__ import division
from builtins import range, zip
from collections impor... | tritemio/FRETBursts | fretbursts/tests/test_burstlib.py | Python | gpl-2.0 | 41,583 | [
"Gaussian"
] | 0278359d7e7b5caa82517497bc62acafb8fe38b0a42031a14eda8454a28d639c |
# 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 RTximport(RPackage):
"""Import and summarize transcript-level estimates for transcript- an... | LLNL/spack | var/spack/repos/builtin/packages/r-tximport/package.py | Python | lgpl-2.1 | 1,310 | [
"Bioconductor"
] | 1d687424f1f00d5af16edc3453e6f5de0a542ce1b8d5e83a6dee02db88b77203 |
# HF XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
# HF X
# HF X f90wrap: F90 to Python interface generator with derived type support
# HF X
# HF X Copyright James Kermode 2011
# HF X
# HF X These portions of the source code are released under the GNU General
# HF X Public License, ve... | citibob/f90wrap | f90wrap/f90wrapgen.py | Python | gpl-2.0 | 30,567 | [
"VisIt"
] | 72c305adfd98e97eee6ca6dad27ee55253fe72544db1baafb1c5fb445fd1cf44 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals, absolute_import
import os
import unittest
import mock
import nikola
import nikola.plugins.command.import_wordpress
from .base import BaseTestCase
class BasicCommandImportWordpress(BaseTestCase):
def setUp(self):
self.module = nikola.plugi... | schettino72/nikola | tests/test_command_import_wordpress.py | Python | mit | 22,421 | [
"VisIt"
] | dff397a773dd8daa61f763a88f7ab180257a5ee38b44759e28fbc6eb65e7343a |
import numpy
from syned.syned_object import SynedObject
class DistributionGeneric(SynedObject):
def __init__(self):
SynedObject.__init__(self)
def get_dimension(self):
raise Exception("To be implemented in the subclasses")
def get_sampled_points(self):
raise Exception("To be imp... | srio/minishadow | shadow4/sources/source_geometrical/probability_distributions.py | Python | mit | 11,878 | [
"Gaussian"
] | f7c688710c20d033c5ff880ac584bc2a5a96f73e546befaf6ebf8364cd8d80ff |
# -*- coding: utf-8 -*-
eng_lengthened = {
"againn": "again",
"aghh": "agh",
"aah": "ah",
"aahh": "ah",
"ahh": "ah",
"ahaa": "aha",
"ahha": "aha",
"al": "all",
"alonee": "alone",
"alreadyy": "already",
"allways": "always",
"alwayss": "always",
"amm": "am",
"amazi... | ikegami-yukino/pytypo | pytypo/_conv_table.py | Python | mit | 331,306 | [
"BLAST",
"Brian",
"ESPResSo",
"Galaxy",
"VisIt",
"exciting"
] | e716530273bec8bcbeea830ee4a3f24e325cb9b2cfb3984c5146789f5d4faa9a |
#!/usr/bin/env python
"""
Show details of currently active Task Queues
Example:
$ dirac-admin-show-task-queues
Getting TQs..
* TQ 401
CPUTime: 360
Jobs: 3
OwnerDN: /O=GRID-FR/C=FR/O=CNRS/OU=CPPM/CN=Vanessa Hamar
OwnerGroup: dirac_user
Priority: 1.0
Set... | ic-hep/DIRAC | src/DIRAC/WorkloadManagementSystem/scripts/dirac_admin_show_task_queues.py | Python | gpl-3.0 | 3,338 | [
"DIRAC"
] | 55e2e40750f7df8629f8dae6a2aadcc6b8b202f1612a20fac0e2bddb0cf6c3b3 |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, subprocess, sys, glob, string, optparse, subprocess
import zipfile
from datetime import date
cwd = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
os.chdir(cwd)
required_module_keys = ['name','version','moduleid','desc... | ryugoo/TiImageManipulator | build.py | Python | mit | 8,804 | [
"VisIt"
] | c1c48df581a86377de3209e1f4efedef3845f12444125bae213991cbec00bdc1 |
# -*- coding: utf-8 -*-
#
# hl_api_simulation.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 Licen... | janhahne/nest-simulator | pynest/nest/lib/hl_api_simulation.py | Python | gpl-2.0 | 6,987 | [
"NEURON"
] | b96447c0f25f2c129e4994d65c3d5560b77986c994e7b54398ed621251b0edff |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Functional tests using WebTest."""
import datetime as dt
import httplib as http
import logging
import unittest
import httpretty
import markupsafe
import mock
from nose.tools import * # flake8: noqa (PEP8 asserts)
import re
from framework.mongo.utils import to_mongo_ke... | hmoco/osf.io | tests/test_webtests.py | Python | apache-2.0 | 46,417 | [
"VisIt"
] | b4d2722bc01ee312313cdf47984b3881c4edd42e8b306798e7b8fd336bace445 |
import numpy as np
import pytest
from pandas.errors import UnsupportedFunctionCall
import pandas.util._test_decorators as td
from pandas import (
DataFrame,
Series,
Timedelta,
concat,
date_range,
)
import pandas._testing as tm
from pandas.api.indexers import BaseIndexer
@td.skip_if_no_scipy
def ... | jorisvandenbossche/pandas | pandas/tests/window/test_win_type.py | Python | bsd-3-clause | 16,165 | [
"Gaussian"
] | 74a4981040b452e988c2c3a8764dff18554cd17aac55666f47834d689b0b6973 |
# * fb.py main module for pythons fbpy package. Draws stuff in the
# * Linux framebuffer.
# * Copyright (C) 2014 Marcell Marosvolgyi aka noisegate
# *
# * 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 Softwar... | noisegate/fbpy | build/lib.linux-armv6l-2.7/fbpy/fb.py | Python | gpl-2.0 | 33,714 | [
"VisIt"
] | 3be27e43a0d2b89325040d00be37d47cdc17d42f743818ada1a5af7b41df5043 |
import numpy as np
from scipy import ndimage as nd
import matplotlib.pyplot as plt
from Kuwahara import Kuwahara
from KuwaharaFourier import KuwaharaFourier
import time
from scipy.misc import face
I=face(gray=True)
Id=face(gray=True).astype(np.double)/255
t = time.time();
I2 = nd.gaussian_filter(I, [5.0, 5.0], ... | elhuhdron/emdrp | emdrp/emdrp/utils/test_filters.py | Python | mit | 1,342 | [
"Gaussian"
] | 0c73734b572a30d178c70fb5f3900ebfc31b3ce0585b65bbb0b9f9f50df61375 |
#!/usr/bin/env python
from __future__ import print_function
from collections import OrderedDict
import re
regexes = {
"ASCAT": ["v_ascat.txt", r"Version: (\S+)"],
"AlleleCount": ["v_allelecount.txt", r"(\S+)"],
"BWA": ["v_bwa.txt", r"Version: (\S+)"],
"CNVkit": ["v_cnvkit.txt", r"(\S+)"],
"Co... | MaxUlysse/CAW | bin/scrape_software_versions.py | Python | mit | 3,902 | [
"BWA"
] | 8856031e63c3804052f250f0c4ad4708291f0a68fd38455a5ca96d8e5e5d184c |
#!/usr/bin/env python
# Copyright (C) 2013, 2014, 2016, 2017 the PISM Authors
# This script creates a graph of the modeled margin radius time series
# by using the ice_area_glacierized variable. Compare Figure 4(a) in Sayag & Worster (2012).
# Try something like:
# ./showradius.py -o foo.png ts_lab51.nc
import n... | talbrecht/pism_pik | examples/labgum/showradius.py | Python | gpl-3.0 | 1,943 | [
"NetCDF"
] | 20155e1393fbd013c01eec8d61f87eefd5a6bac61d66c4aba94a7f8ab5d26b80 |
#!/usr/bin/env python
#
# BrainBrowser: Web-based Neurological Visualization Tools
# (https://brainbrowser.cbrain.mcgill.ca)
#
# Copyright (C) 2011 McGill University
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by t... | rdvincent/brainbrowser | scripts/minc2volume-viewer.py | Python | agpl-3.0 | 5,294 | [
"VisIt"
] | 3ad5704db33a2c137d59c65fee182de260a15c40588a8e91e9344be67c04a5e2 |
# coding: utf-8
# Copyright (c) Materials Virtual Lab
# Distributed under the terms of the BSD License.
from __future__ import division, print_function, unicode_literals, \
absolute_import
import itertools
import subprocess
import io
import re
import numpy as np
import pandas as pd
from monty.io import zopen
from... | materialsvirtuallab/veidt | veidt/describer/atomic_describer.py | Python | bsd-3-clause | 15,865 | [
"Gaussian",
"LAMMPS",
"pymatgen"
] | 401d5f7688b5a9134146955a34712821ff683d37300d0c0cf3b0c18980609fbe |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import division
import numpy as np
from scipy.optimize import fmin_bfgs
class NeuralNetwork:
"""A simple neural network."""
def __init__(self, hidden_layers=(25,), reg_lambda=0, num_labels=2):
"""Instantiates the class."""
self.__h... | pqn/neural | neural/neural.py | Python | bsd-3-clause | 6,404 | [
"NEURON"
] | 36b4227eb9a8e336c6ae5f474f4d4370be071714fe5c19227f449c26f3a50e99 |
import re
import urlparse
import requests
from BeautifulSoup import BeautifulSoup
from ..common import clean_title, random_agent
from ..scraper import Scraper
import xbmc
from nanscrapers.modules import cfscrape
class Mfree(Scraper):
domains = ['m4ufree.info']
name = "M4U"
def __init__(self):
sel... | mrquim/repository.mrquim | script.module.nanscrapers/lib/nanscrapers/scraperplugins/mfree.py | Python | gpl-2.0 | 9,984 | [
"VisIt"
] | ac844e318cfbd06a46592d34ee54ac9f5931b7c962cba78fbd785fa914042a67 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 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
#... | jgonthier/psi4 | psi4/driver/qcdb/molecule.py | Python | lgpl-3.0 | 79,322 | [
"CFOUR",
"Molpro",
"ORCA",
"Psi4",
"Q-Chem"
] | becc8466175fef33cdad55fe11ad89ff949ca37008a70a0b0bf78317acd4493e |
""" A set of common tools to be used in pilot commands
"""
__RCSID__ = '$Id$'
import sys
import time
import os
import pickle
import getopt
import imp
import urllib2
import signal
def printVersion( log ):
log.info( "Running %s" % " ".join( sys.argv ) )
try:
with open( "%s.run" % sys.argv[0], "w" ) as fd:
... | arrabito/DIRAC | WorkloadManagementSystem/PilotAgent/pilotTools.py | Python | gpl-3.0 | 18,484 | [
"DIRAC"
] | 63d68228dbd5f4f3ac82cb07bb1ccd30e2d8a59f718a86c87f1f7b2ba351f231 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# freeseer - vga/presentation capture software
#
# Copyright (C) 2011, 2013 Free and Open Source Software Learning Centre
# http://fosslc.org
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public Licens... | Freeseer/freeseer | src/freeseer/framework/config/persist/jsonstorage.py | Python | gpl-3.0 | 2,419 | [
"VisIt"
] | e3905e2927e0507156e779cc84770221f98496344cdc14caf068d6aee565f652 |
# Copyright (C) 2014-2015 DNAnexus, Inc.
#
# This file is part of dx-toolkit (DNAnexus platform client libraries).
#
# 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.a... | andyshinn/dx-toolkit | src/python/dxpy/utils/file_load_utils.py | Python | apache-2.0 | 15,770 | [
"BWA"
] | 1c3c9fbf30a5c148bac41a57b956f683b8c6bd1f71d0523edb5a77577ae9a62e |
set#! /usr/env/python
"""
A class used to create and manage regular square raster
grids for 2D numerical models in Landlab.
Getting Information about a Grid
--------------------------------
The following attributes, properties, and methods provide data about a
RasterModelGrid, its geometry, and the connectivity among ... | laijingtao/landlab | landlab/grid/raster.py | Python | mit | 229,053 | [
"NetCDF"
] | 8a3273ff2f9952a48fcf0df13b71679e7c2730750eb807dfb2017c2e41df6326 |
import os
from django.http import Http404
from django.shortcuts import render, redirect
from django.views.generic.edit import CreateView
from django.views.generic.edit import UpdateView
from django.views.generic.edit import DeleteView
from django.views.generic.detail import SingleObjectMixin
from django.views.generic ... | internship2016/sovolo | app/event/views.py | Python | mit | 24,507 | [
"MOE"
] | dfbd2217092a38c111e615a75aa1f8cdb131f8cd5b988d04a103a8936bd42fb1 |
from nanopore.analyses.abstractAnalysis import AbstractAnalysis
from nanopore.analyses.utils import AlignedPair, getFastaDictionary, getFastqDictionary, getExonerateCigarFormatString, samIterator, pathToBaseNanoporeDir
import os
import pysam
import numpy
import math
import random
import xml.etree.cElementTree as ET
fro... | mitenjain/nanopore | nanopore/analyses/marginAlignSnpCaller.py | Python | mit | 20,859 | [
"pysam"
] | afc87e6b17c04d9bcce3f5c75f76fe5847a40b54df000c91f00f82756408f12a |
# -*- coding: utf-8 -*-
__license__ = "GNU Affero General Public License, Ver.3"
__author__ = "Pablo Alvarez de Sotomayor Posadillo"
# This file is part of Kirinki.
#
# Kirinki is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by the ... | i02sopop/Kirinki | kirinki/user.py | Python | agpl-3.0 | 13,135 | [
"VisIt"
] | 2a3e84f5e155fe1500f4fcdf7b50f31b49b3d77edb107ddc3af41ec49a57be56 |
# This file is part of wger Workout Manager.
#
# wger Workout Manager is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# wger W... | kjagoo/wger_stark | wger/core/tests/test_temporary_users.py | Python | agpl-3.0 | 7,496 | [
"VisIt"
] | f0c377d0a9acb04b6cf05ad39110949efca5ed642d74954f7b5f20b3e235344a |
#!/usr/bin/env python
"""
Pegasus DAX generator for the Montage toolkit. The generated
workflow will support multiple bands and colors to produce
a color image.
# Copyright 2016 University Of Southern California
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except ... | pegasus-isi/montage-workflow-v2 | montage-workflow.py | Python | apache-2.0 | 17,151 | [
"Gaussian"
] | 93687ac5da3611e03aea06330d422352866a964463e465c035bb7e46946367db |
import logging
import warnings
from typing import List, Dict, Union, Callable
from inspect import signature
from copy import deepcopy
import functools as ft
import numpy as np
log = logging.getLogger(__name__)
class PulseAtoms:
"""
A class full of static methods.
The basic pulse shapes.
Any pulse ... | WilliamHPNielsen/broadbean | broadbean/broadbean.py | Python | mit | 5,260 | [
"Gaussian"
] | 4c10b8adba85864e7d912d874de705451fb8a5070a95e91e4f778fe937994f6e |
#!/usr/bin/env python
#########################################################################################
#
# Extract metrics within spinal labels as defined by the white matter atlas and the
# template
# The folder atlas should have a .txt file that lists all tract files with labels.
#
# ------------------------... | 3324fr/spinalcordtoolbox | scripts/sct_extract_metric.py | Python | mit | 69,329 | [
"Gaussian"
] | 38fea73f18ebd361ad30bb59f0a864aceeb61f0bfa85ecebe20b69b4089d0c6b |
import os
import inspect
import ase.db
import tmd.bilayer.cell
from tmd.bilayer.bilayer_util import _base_dir, global_config
def _base_dir():
frame = inspect.getfile(inspect.currentframe())
this_dir = os.path.dirname(os.path.abspath(frame))
base_dir = os.path.join(this_dir, "..", "..")
return os.path.n... | tflovorn/tmd | tmd/bilayer/material.py | Python | mit | 5,629 | [
"ASE"
] | e8b1e8e370b7a590dcd0576a83213c054379d5a8448304303de2d5b3839004b7 |
from .. import Provider as CompanyProvider
class Provider(CompanyProvider):
formats = (
"{{last_name}} {{company_suffix}}",
"{{last_name}} & {{last_name}}",
"{{company_prefix}} {{last_name}}",
"{{large_company}}",
)
company_prefixes = (
"Stichting",
"Konin... | joke2k/faker | faker/providers/company/nl_NL/__init__.py | Python | mit | 11,854 | [
"CASINO"
] | d40edf7db43970c63c4937ad0486894ec7252f18602cb32c2e1ec4d1ff819494 |
# Copyright 2014-2020 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | sunqm/pyscf | pyscf/agf2/test/test_dfuagf2_beh.py | Python | apache-2.0 | 2,972 | [
"PySCF"
] | 17ade7969a98453131ed9aa3bc14faf920692e45434106feaa5bd7bb47982d75 |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-monitoring | tests/unit/gapic/monitoring_v3/test_group_service.py | Python | apache-2.0 | 108,267 | [
"Octopus"
] | e6a43587e8f184ba5277fb7f7cee6057e21e5c19f8fa0dd01c1846654a491b9c |
from aces.materials.POSCAR import structure as Material
class structure(Material):
def getPOSCAR(self):
return self.getMinimized()
def csetup(self):
from ase.dft.kpoints import ibz_points
#self.bandpoints=ibz_points['hexagonal']
import numpy as np
x=0.5*np.cos(np.arange(8)/8.0*2.0*np.pi)
y=0.5*np... | vanceeasleaf/aces | aces/materials/MoN2_alpha_rect.py | Python | gpl-2.0 | 1,320 | [
"ASE"
] | 2f1f657cd7483432f04544714eb98cda5b8730b351560c851ec77aaaaf4a3f73 |
description = """
proteinswap is a method developed and implemented using Sire that allows relative binding free energies of a ligand to two different proteins to be calculated from first-principles, condensed-phase simulations. The method is currently under development and is not yet published (so use at your own risk... | chryswoods/Sire | wrapper/python/scripts/proteinswap.py | Python | gpl-2.0 | 11,435 | [
"Amber",
"VisIt"
] | 862cf3d62feefebe6319b217d50deaab77ba89f3a46b73b7de1c5e68eb03c3b5 |
import os
import unittest
import csv
import numpy
from __main__ import vtk, qt, ctk, slicer
from slicer.ScriptedLoadableModule import *
#
# NeedleGuideTemplate
#
class NeedleGuideTemplate(ScriptedLoadableModule):
"""Uses ScriptedLoadableModule base class, available at:
https://github.com/Slicer/Slicer/blob/master... | ProstateBRP/NeedleGuideTemplate | NeedleGuideTemplate/NeedleGuideTemplate.py | Python | bsd-3-clause | 22,912 | [
"VTK"
] | c1a4b930f158c863897689fc1b8032daca2c7eee22fc1875611afdacce02de5a |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from chempy.kinetics.integrated import (
pseudo_irrev,
pseudo_rev,
binary_irrev,
binary_rev,
)
import sympy
funcs = (pseudo_irrev, pseudo_rev, binary_irrev, binary_rev)
def main():
"""
This example demonstrates how to generate pretty equations ... | bjodah/aqchem | examples/demo_kinetics.py | Python | bsd-2-clause | 1,292 | [
"ChemPy"
] | 8efef131168b20fe0c04086056e7d734769159195fe1de279e63a97164ca2a32 |
""" AlwaysProbingPolicy module """
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from DIRAC import S_OK
from DIRAC.ResourceStatusSystem.PolicySystem.PolicyBase import PolicyBase
__RCSID__ = '$Id$'
class AlwaysProbingPolicy(PolicyBase):
"""
The Alw... | yujikato/DIRAC | src/DIRAC/ResourceStatusSystem/Policy/AlwaysProbingPolicy.py | Python | gpl-3.0 | 721 | [
"DIRAC"
] | 120134495ce862e038e54edcf8c6cd5b1efdbd245311a8b65a6291a6961203e0 |
import tempfile
import numpy as np
def load_pyassimp(file_obj, file_type=None):
'''
Use the pyassimp library to load a mesh, from a file object and type,
or filename (if file_obj is a string)
Arguments
---------
file_obj: file object, or str of file path
file_type: str, file extension (ak... | mwmuni/LIGGGHTS_GUI | trimesh/io/assimp.py | Python | gpl-3.0 | 3,025 | [
"ASE"
] | 2aef5c353ec553a52151a3041bbc6fd94b35fd144a46092afcc04a8b42a3b356 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2007 Async Open Source
##
## This program is free software; you can redistribute it and/or
## modify it under the terms of the GNU Lesser General Public License
## as published by the Free Software Foundation; either version 2
## of the License, or... | andrebellafronte/stoq | stoqlib/lib/sintegra.py | Python | gpl-2.0 | 21,260 | [
"VisIt"
] | 7afa56ddbb18f2be27f60001e4f162fecf7398c273a9dfccf711852792a61caf |
import theano
import theano.tensor as T
from lasagne import init
from lasagne.layers import Conv2DLayer, TransposedConv2DLayer, ConcatLayer, SliceLayer, DropoutLayer
from base import Model
from ..lasagne_extensions.layers import (SampleLayer, MultinomialLogDensityLayer,
GaussianLo... | JohnReid/auxiliary-deep-generative-models | adgm/models/conv_sdgmssl.py | Python | mit | 26,737 | [
"Gaussian"
] | 083fe1557f121122e984759f7d6c13b4ccf9b64848959b46017299d92cf8bdc1 |
"""Galaxy background classes for redmapper.
This file contains classes to describe the b(x) background terms for computing
richness and other redmapper likelihoods.
"""
import fitsio
import numpy as np
import healpy as hp
import time
import copy
import os
import esutil
import multiprocessing
import types
try:
im... | erykoff/redmapper | redmapper/background.py | Python | apache-2.0 | 28,461 | [
"Galaxy"
] | 0ea6b4cc0f37674c0702f9c247b22b648924dddcb7d398e63587580fbd397170 |
# -*- coding: utf-8 -*-
"""
.. _tut-artifact-ica:
Repairing artifacts with ICA
============================
This tutorial covers the basics of independent components analysis (ICA) and
shows how ICA can be used for artifact repair; an extended example illustrates
repair of ocular and heartbeat artifacts.
.. contents... | mne-tools/mne-tools.github.io | 0.19/_downloads/7e29f93bd4df8429aa43c25d9f1ede6c/plot_40_artifact_correction_ica.py | Python | bsd-3-clause | 29,529 | [
"Gaussian"
] | f76d73e582b165eb37102369f5ea2c46f74d884879658b86798b2871a0417abc |
'''
Created on Aug 3, 2011
@author: sean
'''
from graphlab.meta.asttools.visitors import Visitor
import ast
class SymbolVisitor(Visitor):
def __init__(self, ctx_types=(ast.Load, ast.Store)):
if not isinstance(ctx_types, (list, tuple)):
ctx_types = (ctx_types,)
self.ctx_types = tuple(... | ypkang/Dato-Core | src/unity/python/graphlab/meta/asttools/visitors/symbol_visitor.py | Python | agpl-3.0 | 1,536 | [
"VisIt"
] | 4ac6756369ee2c985c5754d1cbfe005f4463bfbd82ae0b80d9fd2daf973abaa7 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.