text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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|---|---|---|---|---|---|---|---|
import random
def setup():
if hsb == 0:
NUMSTR = random.randrange(1, 100)
elif hsb == 1:
NUMSTR = random.randrange(100, 1000)
elif hsb == 2:
NUMSTR = random.randrange(1000, 100000)
elif hsb == 3:
NUMSTR = random.randrange(100000, 1000000)
elif hsb == 4:
NUMS... | Joshwoo70/Horizons-2 | src/UniverseGen/Globals.py | Python | gpl-3.0 | 471 | [
"Galaxy"
] | 8d78f04802c84afb496c35a839503fa009a1060a17c66b96ce709009f481b877 |
# -*- coding: utf-8 -*-
#
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as pu... | thica/ORCA-Remote | src/scripts/tools/tool_repositorymanager/script.py | Python | gpl-3.0 | 15,498 | [
"ORCA"
] | d397c468f3fdb82d02a75e5915cbfd6e27a85032a18da63f32de0370abb33c08 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | mattwthompson/mdtraj | mdtraj/geometry/hbond.py | Python | lgpl-2.1 | 18,033 | [
"MDTraj"
] | c589b748300e891a773f011955d1f92baebc81f40932a5ad02ede1b9c27b8341 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007 Zsolt Foldvari
# Copyright (C) 2008-2009 Brian G. Matherly
#
# 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; eithe... | arunkgupta/gramps | gramps/plugins/docgen/gtkprint.py | Python | gpl-2.0 | 21,417 | [
"Brian"
] | e980ebae9a6dfe96879287214c5129e5194d0e72630ce557b565985b3e064aa0 |
import logging, threading, sys, os, time, subprocess, string, tempfile, re, traceback, shutil
from galaxy import util, model
from galaxy.model.orm import lazyload
from galaxy.datatypes.tabular import *
from galaxy.datatypes.interval import *
from galaxy.datatypes import metadata
from galaxy.util.json import from_json_... | volpino/Yeps-EURAC | lib/galaxy/jobs/__init__.py | Python | mit | 44,538 | [
"Galaxy"
] | 9a4fb44d9accb20f116726b5b967875e8a7fe8f90af924f5e7c73b2bc758a24b |
import numpy as np
from tensorflow.python.keras.layers import Conv2D
from tensorflow.python.keras.layers import Dense, Flatten, GlobalMaxPooling2D, Input, Reshape
from tensorflow.python.keras import Model
from tensorflow.python.keras.optimizers import Adam
from tensorflow.python.keras.layers import LeakyReLU, BatchNorm... | 5agado/data-science-learning | deep learning/autoencoders/VAE.py | Python | apache-2.0 | 6,523 | [
"Gaussian"
] | cb6da22e04115eca96502229bc1c3fcd1015b81eb04b52079362c1164a980e72 |
######################################################################
# Alchemical Analysis: An open tool implementing some recommended practices for analyzing alchemical free energy calculations
# Copyright 2011-2015 UC Irvine and the Authors
#
# Authors: Pavel Klimovich, Michael Shirts and David Mobley
#
#This libra... | FEPanalysis/alchemical-analysis-OLD | alchemical_analysis/parser_gromacs.py | Python | lgpl-2.1 | 15,822 | [
"Gromacs"
] | 6d81c6fed01c39633603104b36d4bb999e21bcaf04b8efa4e584538b282e7e2a |
# 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... | nburn42/tensorflow | tensorflow/python/ops/linalg/linear_operator_test_util.py | Python | apache-2.0 | 28,767 | [
"Gaussian"
] | 5f236266c5a2499d679d8f35217afe6767a3044e4f38771a9626f21bb57ffd19 |
import numpy as np
def isophotes(img, n, limits, scale, smoothing_fun='gaussian'):
"""Generate soft isophote images.
Generate n soft isophote images with equally spaced isophote lines between
limits[0] and limits[1]. The isophote images are soft because the
contributions to each isophote line are smo... | andersbll/ipcv | ipcv/misc/isophotes.py | Python | mit | 1,700 | [
"Gaussian"
] | 0fcab6f12fad61492a8b79ca1057da26554fff1ef419e210eab18d5a6ea6e947 |
# !usr/bin/env python2
# -*- coding: utf-8 -*-
#
# Licensed under a 3-clause BSD license.
#
# @Author: Brian Cherinka
# @Date: 2017-05-19 17:47:12
# @Last modified by: Brian Cherinka
# @Last Modified time: 2017-07-29 20:11:29
from __future__ import print_function, division, absolute_import
from tests.api.conftest ... | sdss/marvin | tests/api/test_rss.py | Python | bsd-3-clause | 2,999 | [
"Brian",
"Galaxy"
] | b0e40060908c09bcbff02e3863f1830e413d76160c7b907c691acbf68830c91c |
########################################################################
# $HeadURL$
########################################################################
""" ProxyManager is the implementation of the ProxyManagement service
in the DISET framework
"""
__RCSID__ = "$Id$"
import types
from DIRAC.Core.DISET.Requ... | avedaee/DIRAC | FrameworkSystem/Service/ProxyManagerHandler.py | Python | gpl-3.0 | 17,054 | [
"DIRAC"
] | ab7c265adc55b164498dd385c1f08bf012f9689c702d59fbe96371147a5cc2ff |
"""
desispec.resolution
===================
Standardized handling of sparse wavelength resolution matrices.
Use ``python -m desispec.resolution`` to run unit tests.
"""
from __future__ import division, absolute_import
import numpy as np
import scipy.sparse
import scipy.special
# The total number of diagonals that ... | gdhungana/desispec | py/desispec/resolution.py | Python | bsd-3-clause | 5,412 | [
"Gaussian"
] | 81a66232a2d7fd991a9f2d3fa665090472a8e80beed6d1b6a15eb6acdb537777 |
"""
Test helper functions and base classes.
"""
import functools
import inspect
import io
import json
import operator
import os
import pprint
import sys
from contextlib import contextmanager
from datetime import datetime
from unittest import SkipTest, TestCase
import requests
import six
from bok_choy.javascript impo... | edx-solutions/edx-platform | common/test/acceptance/tests/helpers.py | Python | agpl-3.0 | 37,454 | [
"VisIt"
] | 64fc4369eda664c559b7140e00957d2bfc62a5690df748d3763c1d91ade5aa2e |
# -*- coding: utf-8 -*-
from __future__ import absolute_import
import pytest
import responses
import six
from libsourcemap import Token
from mock import patch
from requests.exceptions import RequestException
from sentry.interfaces.stacktrace import Stacktrace
from sentry.lang.javascript.processor import (
BadSo... | alexm92/sentry | tests/sentry/lang/javascript/test_processor.py | Python | bsd-3-clause | 21,838 | [
"VisIt"
] | eddd8b91471b43784f3c889688350dad200a88005bbadf7b8ceb5bfa67def413 |
'''
Created on 07/31/2014
@Ronak Shah
'''
import argparse
import sys
import time
import os.path
import stat
from subprocess import Popen
import shlex
import shutil
from datetime import date
def main():
parser = argparse.ArgumentParser(prog='Run_Pindel.py', description='Run Pindel for Long Indels & MNPS (32bp-350b... | rhshah/IMPACT-Pipeline | bin/Run_Pindel.py | Python | apache-2.0 | 8,144 | [
"BWA"
] | f9240c862b78f2fdc961931cf7504963384614eb433782255713a97557b20244 |
#
# Author: Henrique Pereira Coutada Miranda
# Run a BSE calculation using yambo
# one job per q-point for the dielectric function
#
from __future__ import print_function
from yambopy import *
from qepy import *
import multiprocessing
import argparse
import sys
yambo = "yambo"
folder = "bse_par"
def databases():
... | henriquemiranda/yambopy | tutorial/bn/bse_par_bn.py | Python | bsd-3-clause | 4,425 | [
"Yambo"
] | 619f7942a189e8d3b4f9b7601b4cb01db9d977eba34fac3884bd47534dae485d |
#!/usr/bin/env python
####################################################################################################
# @file wsappframework.py
# @package
# @author Arnaud Chassagne, Jean-Baptiste Spieser
# @date 2008/12/01
# @version 0.1
#
# @mainpage
#
############################################################... | mikrosimage/OpenRenderManagement | src/octopus/core/framework/wsappframework.py | Python | bsd-3-clause | 3,738 | [
"Octopus"
] | c47276990f7317617627c7f5a6e814badfe514e9dbc41b44ff491df760310773 |
# coding: utf-8
"""
Vericred API
Vericred's API allows you to search for Health Plans that a specific doctor
accepts.
## Getting Started
Visit our [Developer Portal](https://developers.vericred.com) to
create an account.
Once you have created an account, you can create one Application for
Production and an... | vericred/vericred-python | vericred_client/models/county_bulk.py | Python | apache-2.0 | 14,829 | [
"VisIt"
] | 1dc0eb7059e04b8aec25c86b805a9bd8a5d00b4f613c35336de65a21ade83075 |
# Copyright 2019 The Oppia 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 applicable ... | brianrodri/oppia | scripts/setup.py | Python | apache-2.0 | 10,366 | [
"VisIt"
] | c889b7b8f560cef5d4af2c89df8477371eceb37390be13f13f14a04763c53067 |
import logging
import numpy
from paraview import vtk
from paraview.numpy_support import get_vtk_array_type, create_vtk_array
from simphony.core.cuba import CUBA
from .cuba_utils import supported_cuba, default_cuba_value
from .constants import cuba_value_types
logger = logging.getLogger(__name__)
class CUBADataAc... | simphony/simphony-paraview | simphony_paraview/core/cuba_data_accumulator.py | Python | bsd-2-clause | 6,411 | [
"ParaView",
"VTK"
] | 909db06b577e159b539518cefe0408ffbb70950832adbc8c84469f948127a47e |
########################################################################
# $HeadURL$
# File : Occi09.py
# Author : Victor Mendez ( vmendez.tic@gmail.com )
########################################################################
# subset occi API based in the OpenNebula client command line implemention
import os
impo... | myco/VMDIRAC | WorkloadManagementSystem/Client/Occi09.py | Python | gpl-3.0 | 15,545 | [
"DIRAC"
] | eebfa2f34bba5a82dec4de6b4d74a57038734982446bc58ca6a0b498bce76de4 |
from matplotlib import pyplot as plt, cm
import photutils
import numpy as np
from astropy import wcs
from astropy.io import fits
from astropy.table import Table
from os import path
from photutils.psf import DAOGroup
from photutils.psf import BasicPSFPhotometry
from photutils.background import MMMBackground
from photuti... | srodney/hstphot | hstphot/astropyphot.py | Python | bsd-3-clause | 25,473 | [
"Gaussian"
] | efebc27edcce10e1fe0a08c654e4a606ca5730d2b9a9bfca04a2563c405c7327 |
import datetime
import matplotlib.pyplot as plt
import netCDF4
import numpy
import os
import pytz
import scipy
import sys
# check the scripts directory is present
if not os.path.exists("../scripts/"):
print "erai2nc: the scripts directory is missing"
sys.exit()
# since the scripts directory is there, try import... | OzFlux/OzFluxQC | utilities/evi2nc.py | Python | gpl-3.0 | 9,696 | [
"NetCDF"
] | 88fd2e00787a221c8fc0c1b3c7a492e13e992aeb240c4ccbb2d906ea668262fe |
__author__ = 'sulantha'
import os
defaultT1config = "{'n3Dist':'75', 'headHeight':'150'}"
defaultAV45config = "{'blur':'8'}"
defaultAV1451config = "{'blur':'8'}"
defaultFDGconfig = "{'blur':'8'}"
defaultFMRIconfig = "{'nu_correct':'-75', 'fwhm_smoothing':'6'}"
# For Fmri
niak_location = '/data/data01/wang/references/... | sulantha2006/Processing_Pipeline | Config/PipelineConfig.py | Python | apache-2.0 | 5,681 | [
"VisIt"
] | 65dac6e95184f9084e44e8eafe503f77ed96395310b8143072d4d9b1785eaded |
#
# This module is for reading and writing the simple BADC text file format.
# This file format is based on the comma seperated value (CSV) format
# that is commonly produced by spreadsheet applications. It also checks
# to see if certain metadata is available.
#
# SJP 2008-09-22
# BNL 2013-08 Some updates
#... | cedadev/badctext | BADCtf.py | Python | bsd-3-clause | 31,892 | [
"NetCDF"
] | ca41aecd553c468b40b322e36477f2011c14dc89722f871c2b65359db7eaaca0 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2017, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Test the Electrons method in cclib"""
from __future__ import print_function
import sys
import os
import re
import log... | gaursagar/cclib | test/method/testelectrons.py | Python | bsd-3-clause | 1,475 | [
"Gaussian",
"cclib"
] | c41a098617087d65081d991b84e4c39fce2e92abe3e31e9a2aa38c92734d26ed |
import os
import sys
# setting the absolute path of the previous directory
# getting the this py module path by __file__ variable
# pass that __file__ to the os.path.dirname, returns the path of this module
__curDir__ = os.path.dirname(__file__)
diagDir = os.path.abspath(os.path.join(__curDir__, '../../..'))
# adding t... | arulalant/mmDiagnosis | diagnosis1/mjo/level1/variance/make_model_anomaly.py | Python | gpl-3.0 | 3,204 | [
"NetCDF"
] | b9fb938cea5b13937f84ad279dd65fb8e30c55660916c71c5720462c592f87db |
# (c) 2017, Brian Coca
# (c) 2017 Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
# Make coding more python3-ish
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
DOCUMENTATION = '''
cache: yaml
short_descriptio... | e-gob/plataforma-kioscos-autoatencion | scripts/ansible-play/.venv/lib/python2.7/site-packages/ansible/plugins/cache/yaml.py | Python | bsd-3-clause | 1,924 | [
"Brian"
] | 4df783f7bacf243a89db683deec779ce082bdc7db7e6fcc445346700c13697f7 |
# 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 License as published by
# the Free Software Foundati... | Freeseer/freeseer | src/freeseer/plugins/audioinput/autoaudiosrc/__init__.py | Python | gpl-3.0 | 1,679 | [
"VisIt"
] | 4fd0b8cd025f9c9bd2df7571aecce9c28c338b800eb8f3cce8a91ca28931eed1 |
"""Shared functionality useful across multiple structural variant callers.
Handles exclusion regions and preparing discordant regions.
"""
import collections
import os
import numpy
import pybedtools
import pysam
import toolz as tz
import yaml
from bcbio import bam, utils
from bcbio.distributed.transaction import fil... | vladsaveliev/bcbio-nextgen | bcbio/structural/shared.py | Python | mit | 14,360 | [
"pysam"
] | af5cae042e6ba21399c9dc14ca72ca3547a0d3cf7d1869fdd28c9fac3c2a1a79 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 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
#... | rmcgibbo/psi4public | psi4/driver/qcdb/subsetgenerator.py | Python | lgpl-3.0 | 4,294 | [
"Psi4"
] | 7f58aa1ec1acb5782e2be761fcfd7f4dbcbc87e0f1a0a53cfe0ae38436a9883a |
#
# This source file is part of the EdgeDB open source project.
#
# Copyright 2008-present MagicStack Inc. and the EdgeDB 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... | edgedb/edgedb | edb/pgsql/compiler/expr.py | Python | apache-2.0 | 24,540 | [
"VisIt"
] | 80f9762832f20fa8a477e648650093c4723622f827512ebdc570a5e50016e1ec |
#!/usr/bin/env python
# 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
"""
nc2csv.py
=========
Converts a NetCDF file into one or m... | eufarn7sp/egads | egads/thirdparty/nappy/script/nc2csv.py | Python | gpl-3.0 | 2,206 | [
"NetCDF"
] | 1663e664ac0e5a5e8d31905a63c8d1ab5f65da5b864f3949beffff69aaf5cd48 |
###############################################################################
# #
# 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 #
... | dparks1134/RefineM | refinem/ssu.py | Python | gpl-3.0 | 22,285 | [
"BLAST"
] | 4bf101ff86e3e7103a92a41ee371eb6f5363fbc25f4b0a35e837ab7d9630f349 |
#!/usr/bin/env python
import os, sys
from forcebalance.molecule import Molecule
from collections import defaultdict
# Atom classes belonging to the backbone or termini.
exc_mid = [1, 2, 3, 7, 40]
# Atom classes belonging to methyl hydrogens.
exc_end = []#6, 9]
# Atom class names from TINKER.
acnames = ["", "Backbon... | hainm/open-forcefield-group | forcebalance/amber-intra/forcefield/highlight-amoeba.py | Python | gpl-2.0 | 4,006 | [
"TINKER"
] | 4a9720c0fd263d80cdb50fed906618ed23e9b57e7d828434c2f1bd2d7f1a0b6f |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Makes sure files have the right permissions.
Some developers have broken SCM configurations that flip the svn:executable
permis... | AndroidOpenDevelopment/android_external_chromium_org | tools/checkperms/checkperms.py | Python | bsd-3-clause | 15,392 | [
"Galaxy",
"xTB"
] | 78f0f77cbd4dd34058588180cfb22e4853eebbd0c181807e746adce5c6b16e74 |
# -*- coding: utf-8 -*-
""" Tests for student account views. """
import re
from unittest import skipUnless
from urllib import urlencode
import json
import mock
import ddt
from django.conf import settings
from django.core.urlresolvers import reverse
from django.core import mail
from django.contrib import messages
from... | hamzehd/edx-platform | lms/djangoapps/student_account/test/test_views.py | Python | agpl-3.0 | 20,663 | [
"VisIt"
] | 52d672744d06ca282c2c6619ac8bf61e50bc806ab39999c2a766804de8e500a9 |
# -*- coding: utf-8 -*-
"""
***************************************************************************
OTBUtils.py
---------------------
Date : 11-12-13
Copyright : (C) 2013 by CS Systemes d'information (CS SI)
Email : otb at c-s dot fr (CS SI)
Contrib... | adwiputra/LUMENS-repo | processing/otb/maintenance/OTBSpecific_XMLcreation.py | Python | gpl-2.0 | 26,959 | [
"Gaussian"
] | c9859f424b987f60caa3608ad76f99f54d57087e7172d88baf335280fc57a41b |
#!/usr/bin/env python
# ----------------------------------------------------------------------------
# Copyright 2015-2017 Nervana Systems Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#... | mas-dse-greina/neon | luna16/old_code/LUNA16_VGG_no_batch.py | Python | apache-2.0 | 8,084 | [
"Gaussian"
] | 65ab39d34f9d8c5a7e97993967dcea99878ef4d774d54ac7e3995099258ddb09 |
# This code was modified from the tss plot code, that it can plot any other ChIP-seq signal
# at other genomic positions. In this case, it is the ERE. ERa ChIP-seq data
# GSM594602
# is available, peaks were called by MACS, generated a bed file. the middle point
# of each peak is used as the center of the plot
# 04/18... | crazyhottommy/some-unorganized-old-scripts | python_scripts/metaPlot_at_HBS.py | Python | mit | 3,907 | [
"HTSeq"
] | 03fb63f704e45c6ebf242d0ef40e4bd8d7c6c78ff7775423b7cafe0d6434329e |
#!/usr/bin/env python
# generate Python Manifest for the OpenEmbedded build system
# (C) 2002-2010 Michael 'Mickey' Lauer <mlauer@vanille-media.de>
# (C) 2007 Jeremy Laine
# licensed under MIT, see COPYING.MIT
#
# June 22, 2011 -- Mark Hatle <mark.hatle@windriver.com>
# * Updated to no longer generate special -dbg pa... | Rookdroid/mie443_ws | poky/scripts/contrib/python/generate-manifest-2.7.py | Python | gpl-2.0 | 16,645 | [
"VisIt"
] | 39360e9cc0ae9335fe69dd3f8e28f520490c39daed39c2163549698c77dd6d7f |
#!/usr/bin/env python3
# -*-coding:UTF-8 -*
'''
Flask functions and routes for the trending modules page
'''
##################################
# Import External packages
##################################
import re
import os
import sys
import json
import string
import datetime
import redis
import unicodedata
impo... | CIRCL/AIL-framework | var/www/modules/PasteSubmit/Flask_PasteSubmit.py | Python | agpl-3.0 | 22,191 | [
"Galaxy"
] | 44ca4255811f989dfa38549c76d39b8b40fbb6eb2a352965f3a2386928304c3d |
'''
Created on 19.08.2011
@author: Sergey Khayrulin
'''
from __future__ import absolute_import
from Entity.Helper import HelpPoint
from Entity.Vertex import Vertex
import pprint
class Slice(list):
'''
Definition for Slice
'''
def __init__(self, coll, faces, use_method2 = False, vertices = None):... | openworm/Blender2NeuroML | src/Entity/Slice.py | Python | mit | 15,739 | [
"NEURON"
] | 6432ea3d0ab5f8638de526b7ab7b198bf3bb449610309c1b5c3475dfb5f12362 |
# Copyright (c) 2020 PaddlePaddle Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appli... | PaddlePaddle/Paddle | python/paddle/fluid/dygraph/dygraph_to_static/utils.py | Python | apache-2.0 | 54,722 | [
"VisIt"
] | c48b0dbdc974ff07fc9e62ec46e64ff43d2a941a23ad309a7d17daf224ebf81a |
from PyQt5.QtGui import QIcon
from PeacockMainWindow import PeacockMainWindow
import argparse, os
from peacock.utils import qtutils
class PeacockApp(object):
"""
Main Peacock application.
Builds the Qt main window and processes any command line arguments.
"""
def __init__(self, args, qapp, **kwds):... | backmari/moose | python/peacock/PeacockApp.py | Python | lgpl-2.1 | 3,407 | [
"MOOSE"
] | 8f8827f291f35a817f4e3d14d6b83dd22e252bd5e6d0013fb58ed806d998a7a0 |
import numpy as np
from dipy.align import floating
from numpy.testing import (assert_array_equal,
assert_array_almost_equal,
assert_raises)
from scipy import ndimage
from dipy.align.metrics import SSDMetric, CCMetric, EMMetric
def test_exceptions():
for invalid... | oesteban/dipy | dipy/align/tests/test_metrics.py | Python | bsd-3-clause | 9,088 | [
"Gaussian"
] | d1af080d7cbc625b0c26fa569180e01ae8480b416e7890f7ef68d19cea20db73 |
from mlxtend.preprocessing import DenseTransformer
from pandas import DataFrame
from sklearn.cluster import KMeans
from sklearn.compose import ColumnTransformer
from sklearn.discriminant_analysis import LinearDiscriminantAnalysis
from sklearn.ensemble import IsolationForest, RandomForestRegressor
from sklearn.linear_mo... | jpmml/jpmml-sklearn | pmml-sklearn-extension/src/test/resources/extensions/sklego.py | Python | agpl-3.0 | 7,510 | [
"VisIt"
] | 7b032033d2c3931adb3273ea2bafe18260a72089a03581f1e214c2f3f6f954fa |
########################################################################
# $HeadURL$
# File: Operation.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2012/07/24 12:12:05
########################################################################
"""
:mod: Operation
.. module: Operation
:synopsis: Operation implem... | sposs/DIRAC | RequestManagementSystem/Client/Operation.py | Python | gpl-3.0 | 14,190 | [
"DIRAC"
] | 4b04ea549b90d34af9be80ab1ff0cdb42a23180008585a5ec904a195e70020ef |
import os, sys
import argparse
import types
import numpy as np
import pickle
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
from matplotlib.backends.backend_pdf import PdfPages
import tensorflow as tf
import data
import model
from util import *
from learning import LearnerCls, LearnerDACls,... | googleinterns/intern2020_cocal | uncertainty/plots/plot_prec_cov_twoparams.py | Python | apache-2.0 | 17,554 | [
"Gaussian"
] | 264e113d66ad115d654ea92e65841635c5cb34dbae521608a3ceda8b18768f24 |
print "Initializing..."
import cPickle
from SimpleXMLRPCServer import SimpleXMLRPCServer
from threading import Thread, Lock
from time import sleep
import wx
from numpy import zeros
from enthought.mayavi import mlab
from enthought.pyface.api import GUI
gui_lock = Lock()
iter = 0
s = None
def plot(vert, triangles):
... | certik/mhd-hermes | plot_server.py | Python | bsd-3-clause | 2,466 | [
"Mayavi",
"VTK"
] | 2497b12008adb00f8974743869e3b27d547f0c33b21380fd627887c92a9bd99a |
import random
import numpy as np
import matplotlib.pyplot as plt
from sklearn import datasets
from mla.kmeans import KMeans
from mla.gaussian_mixture import GaussianMixture
random.seed(1)
np.random.seed(6)
def make_clusters(skew=True, *arg, **kwargs):
X, y = datasets.make_blobs(*arg, **kwargs)
if skew:
... | zhuhuifeng/PyML | examples/gaussian_mixture.py | Python | apache-2.0 | 1,117 | [
"Gaussian"
] | 20bf6df856603b0456ecff4eee6351a25b519ccc3dba52ca58d510198d32bd2a |
#
# Copyright 2001 - 2006 Ludek Smid [http://www.ospace.net/]
#
# This file is part of IGE - Outer Space.
#
# IGE - Outer Space 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 Lice... | OuterDeepSpace/OuterDeepSpace | libs/server/ige/ospace/IUniverse.py | Python | gpl-2.0 | 20,112 | [
"Galaxy"
] | 4d41eb7df77fc5d0f4154d87ae9294b4d6cb443f82fc86cb02237c611f7505d6 |
"""
Rotate a fasta sequence so that the start is just before the terminase.
We need a blast hit to the terminase large subunit, but we don't necessarily need
a hit to the terminase small subunit. These two are usually adjacent and on the same
strand (in 2,127 out of 2,165 times!), and so we look upstream of the
large ... | linsalrob/EdwardsLab | manipulate_genomes/rotate_phage.py | Python | mit | 8,295 | [
"BLAST"
] | f908721f4c8a6fc281e55c1dc7e8f294e9db4b10f8aeb50533a9e8fbebbced83 |
"""Computation of Kullback-Leibler divergence"""
from math import log, sqrt
eps = 1e-15
def klBern(x, y):
"""Kullback-Leibler divergence for Bernoulli distributions."""
x = min(max(x, eps), 1 - eps)
y = min(max(y, eps), 1 - eps)
return x * log(x / y) + (1 - x) * log((1 - x) / (1 - y))
def klPoisso... | chengsoonong/digbeta | python/digbeta/kullback.py | Python | gpl-3.0 | 1,686 | [
"Gaussian"
] | 9a66d1a7587a2c2bfbbe3bc270aa7ca975354ea105481bf701f4bc44ae7e78e3 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | mfherbst/spack | var/spack/repos/builtin/packages/adios/package.py | Python | lgpl-2.1 | 7,312 | [
"NetCDF"
] | e19fd484a78b8538b9ba385fac992b88876d7dc56f0bfdc74687c6f1de25e217 |
import Sofa
import RigidScale.API
import SofaPython.sml
import Compliant.StructuralAPI
import Compliant.sml
import Flexible
from Compliant.Tools import cat as concat
printLog = True
def insertRigidScale(parentNode, rigidModel, param):
"""
Create a RigidScale.API.ShearlessAffineBody from the so... | hdeling/sofa | applications/plugins/RigidScale/python/RigidScale/sml.py | Python | lgpl-2.1 | 10,675 | [
"VTK"
] | 53d703c701648e5c08263871718560e6d942ac8c18c7005047484466d6c7693f |
import unittest
import numpy as np
import pysal
from pysal.spreg.twosls_sp import BaseGM_Lag, GM_Lag
import pysal.spreg.diagnostics as D
from scipy import sparse as SP
class TestBaseGMLag(unittest.TestCase):
def setUp(self):
self.w = pysal.rook_from_shapefile(pysal.examples.get_path("columbus.shp"))
... | spreg-git/pysal | pysal/spreg/tests/test_twosls_sp_sparse.py | Python | bsd-3-clause | 22,375 | [
"COLUMBUS"
] | c5246a8b2dc1226037c0d9f89cf4f78ba70552048fdcf152099f142befc3eda3 |
import unittest
import logging
import sys
import mock
from kalliope import parse_args, configure_logging, main
class TestInit(unittest.TestCase):
def test_parse_args(self):
# start option
parser = parse_args(['value'])
self.assertEqual(parser.action, "value")
# no option
... | kalliope-project/kalliope | Tests/test_init.py | Python | gpl-3.0 | 3,507 | [
"NEURON"
] | 1500cc2a3cfbfc41f9752e0f116b470f3366b90c88c46a36ad1ee1a6e496c410 |
"""
Copyright (c) 2015 Andreea Georgescu
Created on Fri Nov 21 02:49:53 2014
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.
... | Andreea-G/Codds_DarkMatter | src/globalfnc.py | Python | gpl-2.0 | 18,872 | [
"Gaussian"
] | c529e00f6ddc6540145b4db18bc80fc4686d816ea8ed9299d71da137afcf8a2e |
# Generated from SpecificationGrammar.g4 by ANTLR 4.7.2
from antlr4 import *
if __name__ is not None and "." in __name__:
from .SpecificationGrammarParser import SpecificationGrammarParser
else:
from SpecificationGrammarParser import SpecificationGrammarParser
# This class defines a complete generic visitor fo... | HyVar/hyvar-rec | SpecificationGrammar/SpecificationGrammarVisitor.py | Python | isc | 3,665 | [
"VisIt"
] | d1cb477ff7dad0a54d82af187ad88d7f4668fd542431f4c041addf3130e07803 |
#!/usr/bin/env python
#
# Copyright 2008 Jose Fonseca
#
# 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 3 of the License, or
# (at your option) any later version.
#
# This ... | mruse/openxenmanager | src/OXM/xdot.py | Python | gpl-2.0 | 88,463 | [
"FLEUR"
] | 9e22c5cc3390b994902377cf4ee558b6295c316d31eb61396c6cef1635959f9c |
# $HeadURL$
"""
DIRAC.Core.Utils package
"""
__RCSID__ = "$Id$"
from DIRAC.Core.Utilities.File import makeGuid, checkGuid, getSize, getGlobbedTotalSize, getGlobbedFiles, getCommonPath, getMD5ForFiles
from DIRAC.Core.Utilities.List import uniqueElements, appendUnique, fromChar, randomize, ... | vmendez/DIRAC | Core/Utilities/__init__.py | Python | gpl-3.0 | 1,633 | [
"DIRAC"
] | 15368e91528467a8fe71c2fdf5170e60436e4011819238c82417c52334dd3032 |
"""
Tests for VASP DFT calculations.
"""
# pylint: disable=redefined-outer-name
import os
import shutil
import tempfile
import pytest
import z2pack
@pytest.fixture
def vasp_system(sample):
"""
Create a VASP system.
"""
def inner(build_dir):
samples_dir = sample('vasp')
input_files = ... | Z2PackDev/Z2Pack | tests/fp/test_vasp.py | Python | gpl-3.0 | 2,357 | [
"VASP",
"Wannier90"
] | 9f5ec10248bc96cdf33b1faf0eb5942b50858e2e6c7234908cdacc970943f77d |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2016, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Tools for skipping data tests in cclib."""
def skipForParser(parser, msg):
"""Return a decorator that skips the t... | Schamnad/cclib | test/data/skip.py | Python | bsd-3-clause | 1,034 | [
"cclib"
] | 0805bfbf6fb152d37078c58c007f91a942c81c265a28669ac04e8621506da767 |
#!/usr/bin/env python3
import os
import sys
import atexit
import inspect
import tempfile
from pprint import pformat
from pathlib import Path, PurePath as PPath
from importlib import import_module
from collections import defaultdict
from urllib.error import HTTPError
import git
import rdflib
import requests
import ontqu... | tgbugs/pyontutils | neurondm/neurondm/core.py | Python | mit | 144,063 | [
"NEURON"
] | 78e2fda4113ff8d556920db58818380c8f81142c861b14f55712ed0d17a9dbf6 |
##
# Copyright 2013-2018 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | bartoldeman/easybuild-easyblocks | easybuild/easyblocks/c/cblas.py | Python | gpl-2.0 | 3,544 | [
"GPAW"
] | 110b2713e4409ddb55d7568d7308f2fa8672674606ed8a1dbe7e6defd86c2cff |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
import unittest
from pymatgen.util.testing import PymatgenTest
from pymatgen.analysis.cost import CostAnalyzer, CostDBCSV, CostDBElements
class CostAnalyzerTest(unittest.TestCase):
def setUp(se... | gmatteo/pymatgen | pymatgen/analysis/tests/test_cost.py | Python | mit | 1,538 | [
"pymatgen"
] | 9e4453a555e878b12f82a13550f51a9b81ee9ff0359a4d4a96118599ebfca20d |
model = """
# PySCeS test input file
# Stochastic Simulation Algorithm input format
# BurstModel
R1:
ONstate > OFFstate
koff*ONstate
R2:
OFFstate > ONstate
kon*OFFstate
R3:
ONstate > mRNA + ONstate
ksyn*ONstate
R4:
mRNA > $pool
kdeg*mRNA
# InitPar
kon = 0.05
koff = 0.05
kdeg = 2.5... | SystemsBioinformatics/stochpy | stochpy/pscmodels/Burstmodel.py | Python | gpl-3.0 | 381 | [
"PySCeS"
] | be6b3383a8edac47cee8a92c60d6d505433fecb96d671bec2e7e621e54e58887 |
from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os
datatypes_repository_name = 'emboss_datatypes_0020'
datatypes_repository_description = "Galaxy applicable data formats used by Emboss tools."
datatypes_repository_long_description = "Galaxy applicable data formats used by Emboss tools. This reposit... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py | Python | gpl-3.0 | 10,675 | [
"Galaxy"
] | 419a6834490bb67b2492280b990d3bc3a4092d413a4e21cc68c031cb73bc7938 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, print_function, unicode_literals
"""
Code derived from asteval library.
"""
import ast
import logging
from sys import version_info
from .errors import ScriptSyntaxError
supported_nodes = ('arg', 'assert', 'assign', 'attribute', 'augassign',
... | eavatar/eavatar-me | src/ava/job/validator.py | Python | apache-2.0 | 7,616 | [
"VisIt"
] | 37e4d3e9b70a8b41c2f0071fb5b2df9f65169e02b7cb288e08e4312e8ecd9a00 |
# -*- coding: utf-8 -*-
#
# test_current_recording_generators.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 versio... | sdiazpier/nest-simulator | testsuite/pytests/test_current_recording_generators.py | Python | gpl-2.0 | 9,206 | [
"NEURON"
] | 7ed986d2ccbee3cbff03dfc563ffd7dec0517c600e6478b998fb78d33ffb6895 |
from __vmd_assist__ import *
ofs = open('config.tcl', 'w')
vmd = SystemVMD()
vmd.AddMol('confout.gro')
vmd.AddRep(modselect='fragment 0', modstyle='cpk')
vmd.ToTCL(ofs)
ofs.close()
| 12AngryMen/votca-scripts | lib/Carlstuff/vmd.py | Python | apache-2.0 | 189 | [
"VMD"
] | 140d18158987b09c815382b8181577ed2cac18fda7d496060f666484934c7c5f |
#-*- coding: utf-8 -*-
#! /usr/bin/env python
'''
#------------------------------------------------------------
filename: lab6_runTFMultiANN_clusterinclusterdata.py
A Multi-Hidden Layers Fully Connected Neural Network implementation with TensorFlow.
This example is using two class cluster in cluster data
... | jwkanggist/EveryBodyTensorFlow | lab6_runTFMultiANN_clusterinclusterdata.py | Python | unlicense | 7,733 | [
"NEURON"
] | 941c405e7d3c13f383415a7ae3043a1ead00cb29b732421eb0234d587f31471e |
# -*- coding: utf-8 -*-
# -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.#
#* File Name : som_nn.py
#
#* Purpose :
#
#* Creation Date : 17-10-2018
#
#* Last Modified : Wed 17 Oct 2018 12:52:28 AM IST
#
#* Created By :
#_._._._._._._._._._._._._._._._._._._._._.#
# SOM implementation in tensorflow taken from
# here.(https:/... | softwaremechanic/Miscellaneous | nnmodels/keras_models/som_nn.py | Python | gpl-2.0 | 8,487 | [
"Gaussian",
"NEURON"
] | e385d75f2c5fb2b57b201652c6c2c2b4570094270471ee8416ed4866bd94f7b8 |
# -*-python-*-
#
# Copyright (C) 1999-2013 The ViewCVS Group. All Rights Reserved.
#
# By using this file, you agree to the terms and conditions set forth in
# the LICENSE.html file which can be found at the top level of the ViewVC
# distribution or at http://viewvc.org/license-1.html.
#
# For more information, visit h... | marcellodesales/svnedge-console | svn-server/lib/viewvc/sapi.py | Python | agpl-3.0 | 13,024 | [
"VisIt"
] | d25f0d59ecd720d4c793b63314a4f5219f875004db92499627fc037cc94f8d19 |
from Bio.PDB import Selection, PDBParser
from Bio.PDB.NeighborSearch import NeighborSearch
from contactnetwork.interaction import *
from contactnetwork.pdb import *
from contactnetwork.models import *
from io import StringIO
from protein.models import ProteinConformation
from structure.models import Structure
from ... | protwis/protwis | contactnetwork/cube.py | Python | apache-2.0 | 13,068 | [
"Biopython"
] | 8483c65731166df55b9637c5303755b76c53fb453598e8751c7d85e799a113cb |
"""
@name: Modules/House/Family/insteon/insteon_security.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2016-2020 by D. Brian Kimmel
@note: Created on Nov 2, 2016
@license: MIT License
@summary:
"""
__updated__ = '2020-02-18'
# Import system type stuff
# Import PyMh... | DBrianKimmel/PyHouse | Project/src/Modules/House/Family/Insteon/insteon_security.py | Python | mit | 4,917 | [
"Brian"
] | 5eb3449637943070a9714c39b70bf5b71c76925f6aa8a120178f8be1a15cd3db |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2017, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""A reader for XYZ (Cartesian coordinate) files."""
from cclib.io import filereader
from cclib.parser.data import ccData... | langner/cclib | cclib/io/xyzreader.py | Python | bsd-3-clause | 2,454 | [
"cclib"
] | 660a6866339981bfd6fb1d4c3980193079e3900bbb4ef4b6656f70c845b163e7 |
# ----------------------------------------------------------------------------
# pyglet
# Copyright (c) 2006-2008 Alex Holkner
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# * Redistribu... | mpasternak/michaldtz-fix-552 | pyglet/graphics/__init__.py | Python | bsd-3-clause | 25,528 | [
"VisIt"
] | d69c28e2ab6357686087672ccdfcba340100b1653a4d720990862dc671b03af1 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Copyright (C) 2020 Computational Neuroscience Group, NMBU.
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 you... | LFPy/LFPy | LFPy/test/test_morphology_import.py | Python | gpl-3.0 | 1,705 | [
"NEURON"
] | b56f4160a07415dff5a0e27248af8f3d776fc5059b109e26033e46f0ecdcc289 |
#!/usr/bin/env python2
#-*-coding: utf-8 -*-
from __future__ import print_function
import argparse, sys, os.path
pkg_dir = os.path.dirname(os.path.realpath(__file__)) + '/../'
sys.path.append(pkg_dir)
from CRPGaussianSamplers import *
import numpy as np
import pyopencl as cl
from time import time
from datetime import... | tqian86/MPBNP | benchmarking/CRPGaussianTimeTest.py | Python | mit | 4,557 | [
"Gaussian"
] | 06931a274be58b5594f990905c9509e053a963530df83aed6cbe4947a47a5952 |
#!/usr/bin/env python
# Perform psuedo volume rendering in a structured grid by compositing
# translucent cut planes. This same trick can be used for unstructured
# grids. Note that for better results, more planes can be created. Also,
# if your data is vtkImageData, there are much faster methods for volume
# re... | hlzz/dotfiles | graphics/VTK-7.0.0/Examples/VolumeRendering/Python/PseudoVolumeRendering.py | Python | bsd-3-clause | 3,914 | [
"VTK"
] | 07bd428699d7bc1c1e1710176c68887c35d8f9ff8d0bcfb51fb5c9cae95cbdd6 |
"""
Test the about xblock
"""
import datetime
from unittest import mock
from unittest.mock import patch
import ddt
import pytz
from ccx_keys.locator import CCXLocator
from django.conf import settings
from django.test.utils import override_settings
from django.urls import reverse
from milestones.tests.utils import Mi... | eduNEXT/edunext-platform | lms/djangoapps/courseware/tests/test_about.py | Python | agpl-3.0 | 19,966 | [
"VisIt"
] | a2b455c489636a4174aba0987de3008a42d51f17e57dc3ffad068bfac9500f7b |
# Paperwork - Using OCR to grep dead trees the easy way
# Copyright (C) 2012-2014 Jerome Flesch
#
# Paperwork 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
... | kschwank/paperwork | src/paperwork/frontend/settingswindow/__init__.py | Python | gpl-3.0 | 35,970 | [
"ADF"
] | 9d238b897786949b29b4f6a50b0fe5f0bf8deb04b5d71179abc01fbfd181fce6 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# CREATED:2015-02-01 19:25:59 by Brian McFee <brian.mcfee@nyu.edu>
"""Core functionality for muda"""
import jams
import librosa
import soundfile as psf
import jsonpickle
import six
from .version import version
from . import deformers
__all__ = ["load_jam_audio", "save",... | bmcfee/muda | muda/core.py | Python | isc | 7,739 | [
"Brian"
] | eefa9dd5453eb7c9dc4ca4ce477a797b0c8ab7454f6520bb369a61719980c858 |
# -*- coding: utf-8 -*-
# Copyright: (c) 2018, Red Hat | Ansible
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
# Options for authenticating with the API.
class ModuleDocFragment(object):
DOCUMENTATION = r'''
options:
host:
description:
- Provide a URL f... | Dhivyap/ansible | lib/ansible/plugins/doc_fragments/k8s_auth_options.py | Python | gpl-3.0 | 3,530 | [
"VisIt"
] | 565527b0e055ddf8ddcd24892f20f206d876c045a24e006e3b3f88a242ca7319 |
import matplotlib.pyplot as plt
import numpy as np
# Import the library.
import intprim
# Set a seed for reproducibility
np.random.seed(213413414)
# Define some parameters used when generating synthetic data.
num_train_trajectories = 100
train_translation_mean = 0.0
train_translation_std = 5.0
train_noise_std = 0.01... | ir-lab/intprim | intprim/examples/minimal.py | Python | mit | 2,558 | [
"Gaussian"
] | 780908fd2c187b02601c3fbceb1b74c571c2baf88bb6c70655b8b55dc2ebb09e |
# -*- coding: utf-8 -*-
"""
Some dictionaries and data_types for SW4 output files.
.. module:: headers
:author:
Shahar Shani-Kadmiel (s.shanikadmiel@tudelft.nl)
Omry Volk (omryv@post.bgu.ac.il)
Tobias Megies (megies@geophysik.uni-muenchen.de)
:copyright:
Shahar Shani-Kadmiel (s.shanikadmiel@tudelft... | shaharkadmiel/seispy | pySW4/headers.py | Python | gpl-3.0 | 12,849 | [
"DIRAC",
"Gaussian"
] | 5e008891c07bed00cb8720fcdae0f8c57ad341f6e9f7e347366d536045f6dc01 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2016 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kannon92/psi4 | psi4/driver/qcdb/molpro_basissets.py | Python | gpl-2.0 | 196,869 | [
"Psi4"
] | a12daa30f09db4cf4456a3b93fdc37ebdfba1515aa58f974acdb3e5e55b475f2 |
# This file is part of xrayutilities.
#
# xrayutilities 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 distributed... | dkriegner/xrayutilities | examples/xrayutilities_export_data2vtk.py | Python | gpl-2.0 | 2,898 | [
"VTK"
] | 217d5c678ac90f08ae26fa90f5a00a60a53f7820a77139b9eaa07bfc015d3ddb |
'''
stash.py
sta.sh specific uploader
'''
from __future__ import print_function
import json
import urllib
import urlparse
from sqlite3 import IntegrityError
import httplib2
import requests
import mercury.log
log = mercury.log.getLogger()
redirect_url = 'http://localhost/oauth2'
def authenticate(config):
log.d... | tdreyer1/mercury | mercury/services/stash.py | Python | mit | 9,008 | [
"VisIt"
] | 22b33841e958732c84cbe8bf9a2675a43b243fe5aa982fa7367960b448d360f8 |
#!/usr/bin/python3
#
# Copyright (C) 2015 by Red Hat, Inc. All rights reserved.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any late... | wgwoods/anaconda | dracut/driver_updates.py | Python | gpl-2.0 | 21,945 | [
"Brian"
] | 5ad595eaf2f3e0286d0845eb2b638a80432b8304ef6fa440779d0a3ca196f6e7 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides utility classes for io operations.
"""
import codecs
import errno
import os
import re
import tempfile
from monty.io import zopen
__author__ = "Shyue Ping Ong, Rickard Armiento, Anub... | gmatteo/pymatgen | pymatgen/util/io_utils.py | Python | mit | 6,283 | [
"pymatgen"
] | 7be196647809206629193fdf50f087b46ecacfa97462f7815052d94a5eb7b2af |
#!env/python3
# coding: utf-8
import os
import sys
import datetime
import sqlalchemy
import subprocess
import reprlib
import time
from progress.bar import Bar
from sqlalchemy import Table, Column, Integer, String, Boolean, ForeignKey, Sequence, UniqueConstraint, Index, func, distinct
from sqlalchemy.orm import rela... | REGOVAR/Sandbox | benchs/db/sandbox/poc_006.py | Python | agpl-3.0 | 6,639 | [
"pysam"
] | 56975de63d39daaf3d00c1dfac917455ea86770d3153b8a833bfac8396b2f6b0 |
"""
CBMPy: setup.py
===============
PySCeS Constraint Based Modelling (http://cbmpy.sourceforge.net)
Copyright (C) 2010-2022 Brett G. Olivier, VU University Amsterdam, Amsterdam, The Netherlands
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as... | SystemsBioinformatics/cbmpy | setup.py | Python | gpl-3.0 | 9,112 | [
"Biopython",
"PySCeS"
] | 0d940a41c57cecadd4627dadbfc69a354dbf59cedb0bf143e4e463213ee73ed5 |
import os
import sys
import shutil
import itertools
from distutils.spawn import find_executable
import tempfile
import mdtraj as md
import numpy as np
from mdtraj.utils import enter_temp_directory
from mdtraj.testing import get_fn, eq, SkipTest
from mdtraj.geometry.dihedral import (compute_chi1, compute_chi2, compute_... | kyleabeauchamp/mdtraj | mdtraj/geometry/tests/test_dihedral.py | Python | lgpl-2.1 | 6,838 | [
"MDTraj",
"PyMOL"
] | 84f684976444b1303ebb637ae0ac9eb1c02830e29a6cb692eed5c65082fd5c88 |
from distutils.core import setup
setup(
name = "nip",
version = "0.1a1",
py_modules = [
"nip",
],
scripts = [
"bin/nip",
],
author = "Brian Rosner",
author_email = "brosner@gmail.com",
description = "nip is environment isolation and installation for Node.js",
lo... | brosner/nip | setup.py | Python | mit | 461 | [
"Brian"
] | 4a34a818ba7f93049b686cfbfb446a2fe6cb94b9bd56302b1675de5b53190345 |
# -*- coding: utf-8 -*-
#########################################################################
## This program is part of 'MOOSE', the
## Messaging Object Oriented Simulation Environment.
## Copyright (C) 2014 Upinder S. Bhalla. and NCBS
## It is made available under the terms of the
## GNU Lesser General ... | upibhalla/moose-core | tests/python/test_Xreacs5.py | Python | gpl-3.0 | 3,655 | [
"MOOSE"
] | e6a03ad9b5d0b31e8243f3603cea028d841e45f90a9766833b981a525cdd9925 |
"""
Command line interface for Daruma
"""
from providers.TestProvider import TestProvider, TestProviderState
from providers.BaseProvider import ProviderStatus
from managers.ProviderManager import ProviderManager
from driver.Daruma import Daruma
from custom_exceptions import exceptions
from contextlib import contextmana... | sudssm/daruma | driver/daruma_cli.py | Python | gpl-3.0 | 11,988 | [
"VisIt"
] | 5eb668b4e93ab46b0f397661d0829af054fd96ab6991684ec3d885705e9a5afb |
class Room(object):
def __init__(self, name, description):
self.name = name
self.description = description
self.paths = {}
def go(self, direction):
return self.paths.get(direction, None)
def add_paths(self, paths):
self.paths.update(paths)
central_corridor = Room... | githubfun/lphw | gothonweb/gothonweb/map.py | Python | mit | 4,707 | [
"BLAST"
] | 49f0cfad10b07d8764facb24938efc0443fa40fd4af6f547e6f91799e75dee2a |
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