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# module for loading parameters.
import os
#### Base parameters
# These are parameters which users are not likely to need to change.
# We store them in a string of the same format as a parameters file.
baseParamStr = """
#### Genbank ####
# output from parsing genbank files
# gene order
geneOrderFN = 'geneOrder.tx... | ecbush/xenoGI | xenoGI/parameters.py | Python | gpl-3.0 | 11,689 | [
"BLAST"
] | 00eb39dddc3fd6f17cc5e62d2b24fc5f7e142c6726552cd5a2e0956c0c451c6d |
# -*- coding: utf-8 -*-
from south.utils import datetime_utils as datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding field 'DataDomain.publish'
db.add_column(u'profiles_datadomain',... | 216software/Profiles | communityprofiles/profiles/migrations/0004_auto__add_field_datadomain_publish.py | Python | mit | 27,632 | [
"MOE"
] | 21b2dd6c9f6cefa66d762b9035bfdf973681b641b2ebb09a75808095b6559b6b |
#!/usr/bin/env python2.4
"""
Script that Creates a zip file for use by GMAJ
"""
import os, sys, zipfile
import pkg_resources; pkg_resources.require( "bx-python" )
from bx.align import maf
out_file = sys.argv[1]
maf_file = sys.argv[2]
dbkey = sys.argv[3]
if dbkey == "?": dbkey="unspecified"
exons_file = sys.argv[4]
hi... | jmchilton/galaxy-central | tools/visualization/GMAJ.py | Python | mit | 2,746 | [
"Galaxy"
] | 14a60dee9540e09a0f73857fb46c048fd98f39156d4c17f5ce8b2187d20ef176 |
##
## Draw gene structure from a GFF file
##
import os, sys, operator, subprocess
import math
import pysam
import glob
from pylab import *
from matplotlib.patches import PathPatch
from matplotlib.path import Path
import misopy
import misopy.gff_utils as gff_utils
import misopy.sam_utils as sam_utils
from misopy.sash... | wuxue/altanalyze | misopy/sashimi_plot/plot_utils/plot_gene.py | Python | apache-2.0 | 31,107 | [
"pysam"
] | 146a81bb17a1cc18d74d30ff6844e4584d5fb28f93059b03c62c49f50b1db24e |
# Copyright 2006-2011 by Peter Cock. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""
AlignIO support for the "phylip" format used in Joe Felsenstein's PHYLIP tools.
You are ... | asherkhb/coge | bin/last_wrapper/Bio/AlignIO/PhylipIO.py | Python | bsd-2-clause | 19,457 | [
"Biopython"
] | fbd44faede1b686f77a9cfd3a5112abcad5694c544798b94dd5021b18b16a06a |
from __future__ import absolute_import
import copy
import cython
cython.declare(PyrexTypes=object, Naming=object, ExprNodes=object, Nodes=object,
Options=object, UtilNodes=object, LetNode=object,
LetRefNode=object, TreeFragment=object, EncodedString=object,
error=object, w... | hickford/cython | Cython/Compiler/ParseTreeTransforms.py | Python | apache-2.0 | 117,668 | [
"VisIt"
] | 0ab248f40a1d4305e5b4f9186035a4630a440d58dbfd7ab29b15df31b2a1048d |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# createfreeze - back end for freezing archives
# Copyright (C) 2003-2015 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 the GNU General Publi... | heromod/migrid | mig/shared/functionality/createfreeze.py | Python | gpl-2.0 | 11,411 | [
"Brian"
] | 273d735c5422cd84a20add22acbc42791b737d0fe2b5fcec4b218134aa06be52 |
#!/usr/bin/env python
'''
Selects parameters from force fields.
ASSUMES THERE IS NO OVERLAP BETWEEN THE PARAMETERS SELECTED BY THE PARAMETER
FILE AND BY PTYPES!
'''
from __future__ import print_function
import argparse
import logging
import logging.config
import numpy as np
import sys
import constants as co
import da... | arosale4/q2mm | q2mm/parameters.py | Python | mit | 12,461 | [
"MacroModel"
] | 27dc9f2e4019a2dfe4d575d22b2a67b95cd5e1bd7ced352869bb0b42d156d2a3 |
#!/usr/bin/env python2
# * **************************************************************** **
# File: TranStrings.py
# Requires: Python 2.7+ (but not Python 3.0+)
# Note: For history, changes and dates for this file, consult git.
# Author: Brian Danilko, Likeable Software (brian@likeablesoftware.com)
# Copyright 2015-... | Bdanilko/EdPy | src/TranStrings.py | Python | gpl-2.0 | 7,668 | [
"Brian"
] | 5b16160f90acc965bd3b6b0207d0b6dc32e6f0c3fa4a347457b071c125d8495d |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/bug_1117098 | openlp/plugins/alerts/lib/alertstab.py | Python | gpl-2.0 | 10,418 | [
"Brian"
] | 9570760af9d4f741240ef2ba5dc85a423ae40bdc2a02814e252f868ef76b5a3c |
# Copyright 2019 The TensorNetwork 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 or agreed ... | google/TensorNetwork | tensornetwork/block_sparse/utils.py | Python | apache-2.0 | 15,216 | [
"Gaussian"
] | 4ea049a91bf6756e61b16e258fbd2784402ecf6254de1082d4b6ba27d7ef71e8 |
#!/usr/bin/env python
'''
setup board.h for chibios
'''
import argparse
import sys
import fnmatch
import os
import dma_resolver
import shlex
import pickle
import re
import shutil
parser = argparse.ArgumentParser("chibios_pins.py")
parser.add_argument(
'-D', '--outdir', type=str, default=None, help='Output directo... | jmachuca77/ardupilot | libraries/AP_HAL_ChibiOS/hwdef/scripts/chibios_hwdef.py | Python | gpl-3.0 | 73,841 | [
"CRYSTAL"
] | cf9be7e66f5c2098e72cc5499f50ab215ba281cde557dfa9c8518c0bde892cd3 |
"""A setuptools based setup module.
See:
https://packaging.python.org/en/latest/distributing.html
https://github.com/pypa/sampleproject
"""
# Always prefer setuptools over distutils
from setuptools import setup, find_packages
# To use a consistent encoding
from codecs import open
from os import path
here = path.abspa... | cwaldbieser/txsshadmin | setup.py | Python | gpl-3.0 | 7,280 | [
"VisIt"
] | cc41d58f16e9677b2f495dabc75304efb50e7852f0ec5c4e86e9fead5f9b69ef |
#
# Copyright (C) 2003 Greg Landrum and Rational Discovery LLC
#
"""unit testing code for the SimilarityScreeners
"""
import unittest
from rdkit import Chem
from rdkit.Chem.Fingerprints import SimilarityScreener
from rdkit import DataStructs
def feq(v1, v2, tol=1e-4):
return abs(v1 - v2) <= tol
class TestCase(... | jandom/rdkit | rdkit/Chem/Fingerprints/UnitTestSimScreener.py | Python | bsd-3-clause | 3,073 | [
"RDKit"
] | 52fbe71afba73f7fc636c551dbba403288d6e26451097c75151bf38da207340f |
#!/usr/bin/python
"""Test to verify bug #364086 is still fixed.
Orca reports "paragraph 0 paragraph" <char> when you begin typing
in a Calc cell.
"""
from macaroon.playback import *
import utils
sequence = MacroSequence()
######################################################################
# 1. Start oocal... | h4ck3rm1k3/orca-sonar | test/keystrokes/oocalc/bug_364086.py | Python | lgpl-2.1 | 3,986 | [
"ORCA"
] | 462f0682ee1e61b6c9450ac743d4fdc48204ecf334b84ea82e327477ead8eced |
""" Class that contains client access to the StorageManagerDB handler.
"""
__RCSID__ = "$Id$"
import random
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Base.Client import Client
from DIRAC.Core.Utilities.Proxy import executeWithUserProxy
from DIRAC.DataManagementSystem... | marcelovilaca/DIRAC | StorageManagementSystem/Client/StorageManagerClient.py | Python | gpl-3.0 | 2,353 | [
"DIRAC"
] | 72a37f5d5318c53886baa0d3b72dddad8c687ff4f18ae46dd3c0b361e698aa6b |
#!/usr/bin/python
#
# @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 ... | kannon92/psi4 | doc/sphinxman/document_plugins.py | Python | gpl-2.0 | 15,256 | [
"Psi4"
] | b33380bd01d82106b63bfa4c5a475f3fa97911c00800fb889413074975b1d2d5 |
# Copyright 2006-2009 by Peter Cock. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""
Bio.SeqIO support module (not for general use).
Unless you are writing a new parser or w... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/SeqIO/Interfaces.py | Python | gpl-2.0 | 10,886 | [
"Biopython"
] | 4defd01b141e7f9766c753f84209a7a3b4ac8a54f7d885f71fd5bfbc9ed5e9e2 |
import tomviz.operators
def median_filter(operator, step_pct, input_image):
import itk
from tomviz import itkutils
median_filter = \
itk.MedianImageFilter.New(Input=input_image)
dimension = input_image.GetImageDimension()
median_radius = itk.Size[dimension]()
median_radius.Fill(1)
... | cryos/tomviz | tomviz/python/SegmentPores.py | Python | bsd-3-clause | 12,672 | [
"VTK"
] | 1255b63f5e26438ec5e14bb380850d9514fcc34f2b6763a93e5e6e59485234f1 |
# -*- coding: utf-8 -*-
#
# MNE documentation build configuration file, created by
# sphinx-quickstart on Fri Jun 11 10:45:48 2010.
#
# This file is execfile()d with the current directory set to its containing
# dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All c... | teonlamont/mne-python | doc/conf.py | Python | bsd-3-clause | 10,883 | [
"Mayavi"
] | 8979d727a948eadaf888834fda4a1ffe4107a3886c50051b4df650afe3955ef7 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | MOA-2011/e2openplugin-OpenWebif | plugin/controllers/views/web/pluginlistread.py | Python | gpl-2.0 | 5,226 | [
"VisIt"
] | bc18136c1f10b99d42a8d3d01b62409289a1f52dd674a75e3b1ea977a9e429ff |
# -*- coding: utf-8 -*-
import sys
import os
sys.path.insert(0, os.path.abspath('..'))
import cdk
| twitter/cdk | tests/context.py | Python | apache-2.0 | 101 | [
"CDK"
] | 370b078c19bc04a2f22e80530e29d0c89edcbdf5d552a4b35eb13f4382c51045 |
# Orca
# Copyright (C) 2014-2015 Synthicity, LLC
# Copyright (C) 2015 Autodesk
# See full license in LICENSE.
"""
Utilities used in testing of Orca.
"""
import numpy as np
import numpy.testing as npt
import pandas as pd
def assert_frames_equal(actual, expected, use_close=False):
"""
Compare DataFrame items ... | SANDAG/orca | orca/utils/testing.py | Python | bsd-3-clause | 2,051 | [
"ORCA"
] | 587c991ae591728480f0f94b2283f45338eedf4129a7d7a652f89cb291818327 |
from __main__ import vtk, qt, ctk, slicer
import Resources
import PythonQt
#
# CMRToolkitWizard
#
class CMRToolkitWizard:
def __init__(self, parent):
parent.title = "CMR Toolkit Wizard"
parent.categories = ["Cardiac MRI Toolkit"]
parent.dependencies = []
parent.contributors = ["Salma Bengali (CARMA)... | carma-center/carma_slicer_extension | CMRToolkitWizard/CMRToolkitWizard.py | Python | bsd-2-clause | 6,887 | [
"Brian",
"VTK"
] | 06a856cfddef3645344fb41e1199b30d8ffd8a56bd35805f7246080bbfbf1ede |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, subprocess, sys, glob, string
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 = ['architectures', 'name','version','moduleid','descripti... | E2010/ios64-parse-titanium | iphone/build.py | Python | mit | 8,510 | [
"VisIt"
] | 49c7f2faa7b8a361cbb476caf952f947b37403033e6a7098d5afa86cd93dbfb0 |
# Developed by Redjumpman for Redbot.
# Standard Library
import asyncio
import calendar
import logging
import re
from typing import Union, Final
from operator import itemgetter
# Casino
from . import utils
from .data import Database
from .games import Core, Blackjack, Double, War
from .utils import is_input_unsuppor... | ARG-TLQ/Red-DiscordBot | cogs/casino/casino.py | Python | gpl-3.0 | 53,536 | [
"CASINO"
] | 4952dde5f950c6eb48b7b2bd0899970891a36317695c1408551d8da5f1f2a771 |
# coding: utf-8
from __future__ import unicode_literals
import base64
import datetime
import hashlib
import json
import netrc
import os
import random
import re
import socket
import sys
import time
import math
from ..compat import (
compat_cookiejar,
compat_cookies,
compat_etree_fromstring,
compat_getp... | Tithen-Firion/youtube-dl | youtube_dl/extractor/common.py | Python | unlicense | 118,732 | [
"VisIt"
] | 52811f3c7458964dfc01c00b30f57676e28067e4d7a7a3c52b24e37b2bc42c61 |
##############################################################
# Iris Verweij
# First Feature extraction test
# April 25, 2016
###############################################################
import cv2
import numpy as np
from matplotlib import pyplot as plt
from numpy import arange, sqrt, exp, pi, meshgrid, arctan, ze... | CivilizationAlpha/CyberFarming | extractfeatures.py | Python | gpl-2.0 | 8,784 | [
"Gaussian"
] | 2828d29f553a2331f0010d99f2731cf25434c45ace4a91b550006341818b8bc9 |
"""
@file sobel_demo.py
@brief Sample code using Sobel and/or Scharr OpenCV functions to make a simple Edge Detector
"""
import sys
import cv2
def main(argv):
## [variables]
# First we declare the variables we are going to use
window_name = ('Sobel Demo - Simple Edge Detector')
scale = 1
delta = 0... | zzjkf2009/Midterm_Astar | opencv/samples/python/tutorial_code/ImgTrans/SobelDemo/sobel_demo.py | Python | mit | 1,924 | [
"Gaussian"
] | 0df73da93da91d850f56d5f78d13cf7eab926acc719a24969f71e31dc2be28bc |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors: Kyle A Beauchamp, Ravi Ramanat... | leeping/mdtraj | mdtraj/geometry/dihedral.py | Python | lgpl-2.1 | 23,763 | [
"MDTraj"
] | 9b5dc4d350d69b3280ff92239e4fcc598fbe04bf142f892cff55cc8f0095278b |
from django.db import models
class Portal(models.Model):
portal_id = models.IntegerField()
class LandingPage(models.Model):
portal = models.ForeignKey(Portal)
url = models.URLField(max_length=500)
title = models.CharField(max_length=200)
class Visitor(models.Model):
ip_address = models.IPAddressF... | jcrugzz/lpvisualization | lpVis/models.py | Python | bsd-3-clause | 996 | [
"VisIt"
] | 52f5d8551d76e527c5728f77af6b3e4cc0c041806796ee9ec1f11f3d0a2d1cb8 |
import random, string, sys
courses = ["0170", "0320", "0330", "0510"]
category_names = ["homeworks", "labs", "exams", "projects"]
students = []
categories = []
assignments = []
topics = []
questions = []
num_students = 100
num_assignments = 100
num_topics = 1000
num_questions = 3000
num_visits = 10000
category_file_... | bwallace722/SignMeUp2.0 | data/python_generated/populateData.py | Python | gpl-2.0 | 3,115 | [
"VisIt"
] | fbf9e0c429cca65b6d779de861b0138fea63ab0accfd27e6832312168ff0ae6b |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkGAMBITReader(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.v... | nagyistoce/devide | modules/vtk_basic/vtkGAMBITReader.py | Python | bsd-3-clause | 476 | [
"VTK"
] | 1d283886c5f404186572ecab518ff6f7074293ee8f748d483577b5a5545a8864 |
# -*- coding: utf-8 -*-
"""
train_utils.py: Utilities needed by PyMP for training.
Contains an enum with the available training methods, as
well as their implementations.
"""
from __future__ import division
import copy
import enum
import logging
import numpy
# a set of required params for validation
validation_params... | VHarisop/PyMP | pymp/train_utils.py | Python | gpl-3.0 | 16,672 | [
"NEURON"
] | 96919ddf2798557e9434e1eb4151b2ae103528be27f0ed5d29aae70f0985e8ad |
#!/usr/bin/env python
"""
Classes encapsulating decypher tool.
James E Johnson - University of Minnesota
"""
import pkg_resources
import logging, os, string, sys, tempfile, glob, shutil, types, urllib
import shlex, subprocess
from optparse import OptionParser, OptionGroup
from stat import *
log = logging.getLogger( ... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/tools/sr_assembly/velveth_wrapper.py | Python | gpl-3.0 | 2,284 | [
"Galaxy"
] | 341fcafccb7e59df09e9e6682400426ebb67f3f21a56fae60b166bbd43db99ca |
"""
This module contains all the array handling code for TVTK.
The most important functions provided by this module involve the
conversion of numpy arrays/Python lists to different VTK data arrays
and vice-versa.
Warning: Numpy Character arrays will not work properly since there
seems no unique one-to-one VTK data ar... | liulion/mayavi | tvtk/array_handler.py | Python | bsd-3-clause | 27,489 | [
"VTK"
] | cc4b9b4fdb319fa83e3a70c10d6a053c4788b7ef0767030793ca6ffcae1dc63d |
# -*- coding: utf-8 -*-
##
## This file is part of Invenio.
## Copyright (C) 2011, 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 yo... | lnielsen/invenio | invenio/legacy/bibauthorid/templates.py | Python | gpl-2.0 | 181,082 | [
"VisIt"
] | 7777bd04cebec24dec5dac42a3a6354856a5a804218fbda88d0eb0aad822b40d |
# Copyright 2017 Raytheon BBN Technologies
#
# 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
try:
from QGL import *
from QGL import co... | BBN-Q/Auspex | src/auspex/qubit/single_shot_fidelity.py | Python | apache-2.0 | 9,613 | [
"Gaussian"
] | 0a4bb538fc7f81edcac5ec67cd89b8589dcc4eb2e10658503e655333de495b3d |
import ternary
import numpy as np
import pandas as pd
from functions import *
import sys
from functools import reduce
from sklearn.manifold import *
from sklearn.cluster import *
from sklearn.linear_model import *
from sklearn.ensemble import *
from pylab import *
import _pickle as cPickle
from skimage.filters import g... | gviejo/ThalamusPhysio | python/main_test_final_classification_XGB_KL.py | Python | gpl-3.0 | 15,477 | [
"Gaussian"
] | b717417651f892e1be9a5d18ef5a991619f9ee94c5d0ee04ef4c6a4b62eba191 |
from views import *
from lookups import *
import requests
import re
from utils import *
import itertools
from config import config
if config.IMPORT_PYSAM_PRIMER3:
import pysam
import csv
#hpo lookup
import orm
def individuals_update(external_ids):
patients_db=get_db(app.config['DB_NAME_PATIENTS'])
users_db... | logust79/phenopolis | views/my_patients.py | Python | mit | 5,768 | [
"pysam"
] | 02fa81ae3b55d75a12bd505b15164ec2c6cb3287002f4204c18b34ef06c52ba1 |
# pylint: disable=line-too-long, no-member
from __future__ import division
from builtins import str # pylint: disable=redefined-builtin
import csv
import calendar
import datetime
import io
import json
import os
import tempfile
import time
from zipfile import ZipFile
from past.utils import old_div
import arrow
imp... | audaciouscode/PassiveDataKit-Django | generators/pdk_web_visit.py | Python | apache-2.0 | 6,182 | [
"VisIt"
] | 17f9d8fc3af13d9f4d7696afed72a42ea96d383e9ea8fd09c3624b6285d38327 |
# Generated from lists.g4 by ANTLR 4.5.2
from antlr4 import *
# This class defines a complete generic visitor for a parse tree produced by listsParser.
class listsVisitor(ParseTreeVisitor):
# Visit a parse tree produced by listsParser#lst.
def visitLst(self, ctx):
return self.visitChildren(ctx)
... | arminnh/c-to-p-compiler | resources/antlr-introduction/solution/listsVisitor.py | Python | mit | 697 | [
"VisIt"
] | f3e2b700397c804cc27a66887540c247f761ae3b70dc09997b2dbb24da591473 |
#!/usr/bin/python
#
# Copyright 2010 Brian Dolbec <brian.dolbec@gmail.com>
# Copyright(c) 2010, Gentoo Foundation
# Copyright 2003-2004 Karl Trygve Kalleberg
# Licensed under the GNU General Public License, v2
#
# $Header: $
"""Gentoo's installed packages analysis and repair tool"""
# Move to Imports section after P... | dol-sen/gentoolkit | pym/gentoolkit/enalyze/__init__.py | Python | gpl-2.0 | 3,107 | [
"Brian"
] | f8dc50525cc8e2592a868eb427fafd19ba73d5e561f1f31e2040dc29764942f7 |
"""
Pyinvoke tasks.py file for automating releases and admin stuff.
Author: Shyue Ping Ong
"""
import datetime
import glob
import json
import os
import re
import subprocess
import webbrowser
import requests
from invoke import task
from monty.os import cd
from pymatgen.core import __version__ as CURRENT_VER
@task
d... | materialsproject/pymatgen | tasks.py | Python | mit | 10,137 | [
"pymatgen"
] | 457b064eee5acc7a3d93880b1288491d0176389e881a24f7e208ac8998f9e2e7 |
"""
awot.io.read_latmos_falcon
=========================
Grouping of scripts designed to process (French)
Falcon distributed by LATMOS.
Note: This has only been tested with DYNAMO data files, versions
may change and another function may be needed.
"""
# Load the needed packages
from netCDF4 import Dataset, num2date... | adlyons/AWOT | awot/io/read_latmos_falcon.py | Python | gpl-2.0 | 12,726 | [
"NetCDF"
] | e0ad5e69da64ca76768032c7832d43e3aef31cf826d9b952c8add6f4b719d33c |
'''
Build new DetCI io interface
'''
from .high_level import main_ci_read
from .tools import molpro_mo_order_ci
from .psi4 import psi4_detci
from .tmol import tmol_escf, tmol_tddft
from .gamess import gamess_cis, gamess_tddft
from .molpro import molpro_mcscf
from .gaussian import gaussian_tddft
__all__ = ['main_ci_re... | orbkit/orbkit | orbkit/detci/ci_read/__init__.py | Python | lgpl-3.0 | 462 | [
"GAMESS",
"Gaussian",
"Molpro",
"Psi4"
] | db196dcce2bb9beb895cd917e0d254ed6f639d8ba5f5511e0a0a7f535110d42c |
#!/usr/bin/python
#
# This source file is part of appleseed.
# Visit http://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2010-2013 Francois Beaune, Jupiter Jazz Limited
# Copyright (c) 2014-2015 Francois Beaune, The appleseedhq Organi... | Vertexwahn/appleseed | scripts/convertmany.py | Python | mit | 5,687 | [
"VisIt"
] | a8203b8176a40820d1d6acb8b7ba188a4eceb8beaffad06348e41c8093c84519 |
import numpy as np
import pickle
from aeropy.filehandling.vtk import generate_points
directory = 'D:\\GitHub\\AeroPy\\examples\\JAXA_files\\processed\\'
filename = 'fuselage'
n = 200
data = []
upper = []
lower = []
for i in range(n):
print(i)
data_i = np.genfromtxt(directory+filename+'_%i.csv' % i, delimiter... | leal26/AeroPy | examples/3D_fitting/output_process.py | Python | mit | 1,139 | [
"VTK"
] | 687eefc3dd3715b8129b644af4bd1fd7029ce22b9049294d4ec0f7b6d65f11c1 |
'''
Numerical example for the Continuous No-Regret Algorithm with Gaussian loss functions
@author: Maximilian Balandat, Walid Krichene
@date: Dec 20, 2014
'''
from ContNoRegret.Domains import S
from ContNoRegret.Distributions import Uniform
from ContNoRegret.LossFunctions import GaussianLossFunction
from ContNoRegret... | Balandat/cont_no_regret | old_code/GaussLoss_ex_both.py | Python | mit | 1,802 | [
"Gaussian"
] | 469a1527e9da7edb4936079422bfcefcaa0dc7a3d533323eaf2790f86b22d08c |
import re
import docclass
def sample_train(classifier):
classifier.train('Nobody owns the watter.', 'good')
classifier.train('the quick rabbit jumps fences', 'good')
classifier.train('buy pharmaceuticals now', 'bad')
classifier.train('make quick money at the online casino', 'bad')
classifier.train... | rokujyouhitoma/tips | classifier/test.py | Python | mit | 1,611 | [
"CASINO"
] | 1640f9b6db483f65f2397331289549d93ce98a1e2372f768fb6c19dcee7f81b8 |
#! /usr/bin/env python
"""
This script performs event averaging for particle
spectra and anisotropic flow coefficients calculated
from event-by-event simulations
v_n is analyzed up to n = 6
Format for particle_XXX_vndata.dat file:
n_order real_part real_part_err imag_part imag_part... | chunshen1987/hadronic_afterburner_toolkit | ebe_scripts/average_event_spvn_h5.py | Python | mit | 73,061 | [
"Psi4"
] | 10b24c29658d8db0bff7aaa76d318c5ac6b23cca49f9cf7166b0eb81fba6205e |
__RCSID__ = "$Id$"
import os
from DIRAC import S_OK, S_ERROR, rootPath
from DIRAC.ConfigurationSystem.Client.Config import gConfig
from DIRAC.Core.Security import Locations, X509Chain
gBaseSection = "/REST"
def getOption( path, defaultValue = "" ):
return gConfig.getValue( "%s/%s" % ( gBaseSection, path ), defaul... | DIRACGrid/RESTDIRAC | ConfigurationSystem/Client/Helpers/RESTConf.py | Python | gpl-3.0 | 2,173 | [
"DIRAC"
] | 4fcd6bff119353ea230abbf60e65ca93a83623c13281342af93e11a7ff944da4 |
import io
import json
stat_names = [
'durability',
'armor_durability',
'enchantability',
'harvest_level',
'harvest_speed',
'melee_damage',
'magic_damage',
'attack_speed',
'armor',
'armor_toughness',
'magic_armor',
'ranged_damage',
'ranged_speed',
'chargeability',... | SilentChaos512/SilentGems | scripts/make_gear_parts.py | Python | lgpl-3.0 | 6,605 | [
"Amber"
] | 54b6542f611b3d8c671190fa8457874b90d21c3e59a2769895a7545c3d483146 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import numpy as np
import scipy.stats as stats
from pymatgen.core.spectrum import Spectrum
from pymatgen.util.testing import PymatgenTest
class SpectrumTest(PymatgenTest):
def setUp(self... | gmatteo/pymatgen | pymatgen/core/tests/test_spectrum.py | Python | mit | 3,473 | [
"pymatgen"
] | 8df744ba796368956434904f71f15ffc15af83446cc7925a6dc56a3d1c6e8dc8 |
# -*- coding: utf-8 -*-
import json
import networkx as nx
from networkx.readwrite import json_graph
from django.http import HttpRequest, JsonResponse
from catmaid.models import UserRole, ClassInstanceClassInstance
from catmaid.control.authentication import requires_user_role
def get_annotation_graph(project_id=None... | catmaid/CATMAID | django/applications/catmaid/control/object.py | Python | gpl-3.0 | 1,868 | [
"NEURON"
] | 3550cf28b39f42bd8729a968a88470f99a2288fef1f40a16d8e7ab6bf1c389cf |
import numpy as np
from lmfit import minimize, Parameters
from spectral_cube import OneDSpectrum
def gaussfunc_gh(paramsin, x):
'''
Code adapted from http://research.endlessfernweh.com/curve-fitting/
'''
try:
amp = paramsin['amp'].value
center = paramsin['center'].value
sig =... | e-koch/CubeAnalysis | cube_analysis/spectral_fitting/gausshermite.py | Python | mit | 2,175 | [
"Gaussian"
] | 62836bc2c02861ba09e328d1aecbbb3281274a91b628d7908413527ee6f46ca8 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | python/MooseDocs/test/common/test_get_requirements.py | Python | lgpl-2.1 | 4,729 | [
"MOOSE"
] | 3d34550c3834abf54c257e6342c7d0b27df4123be7a11b37b294e9c8b5e80dbd |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
import sys
import gzip
import pandas as pd
import re
import os
def main():
# Options
# in_blast = "../blast-multiplexed-seqs/4out_blast-output-parsed_head.tsv.gz"
# in_demux = "../parse-demux-assignments/demultiplexed_prob0.05_assingments_head.tsv.gz"
i... | edm1/error-aware-demultiplexer | extras/demulitplexer-threshold-analysis-150311/compare_demux_to_blast/1_merge-blast-demux.py | Python | mit | 1,066 | [
"BLAST"
] | 190c4de2eb0bfc41cf055c653267d67c6c6a42737ab7694cba71fe78e747a449 |
# Copyright 2009-2014 Eucalyptus Systems, Inc.
#
# 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; version 3 of the License.
#
# This program is distributed in the hope that it will be useful,
# b... | eucalyptus/eucalyptus-database-server | eucadb/euca_db_factory.py | Python | bsd-2-clause | 1,105 | [
"VisIt"
] | df2f9ec5a1e604906cc90aab690bdafd7989951bef04025e8a672162bbf83b96 |
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Denis Engemann <denis.engemann@gmail.com>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Eric Larson <larson.eric.d@gmail.com>
# Mainak Jas <mainak@neuro.hut.fi>
# Mark Wronkiewicz <wronk.mark@gmail.com>
#
# Lice... | rkmaddox/mne-python | mne/viz/tests/test_3d.py | Python | bsd-3-clause | 36,270 | [
"Mayavi"
] | 5f3d96d3855ad666f260bdd6995cada44350f3b4d5f4269eee5dd9af8a33b177 |
from __future__ import annotations
import pytest
import iotbx.mtz
from cctbx import sgtbx
from cctbx.array_family import flex
from dxtbx.model import Experiment, ExperimentList, Scan
import dials.pychef
def test_observations():
miller_indices = flex.miller_index(
((1, 2, 3), (-1, 2, 3), (1, -2, 3), (4,... | dials/dials | tests/pychef/test_pychef.py | Python | bsd-3-clause | 3,950 | [
"CRYSTAL"
] | ee3ecb11bb53e44bcbb2545a77dd15090263c72793b3e2a875a5e577dbedf777 |
# 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 RRots(RPackage):
"""Reproducibility-Optimized Test Statistic
Calculates the Reprod... | LLNL/spack | var/spack/repos/builtin/packages/r-rots/package.py | Python | lgpl-2.1 | 1,117 | [
"Bioconductor"
] | a4d96332e721abef0494d3789e51d0bc4cd7e5f69c7e09e7d47f9a8b417ccf9e |
"""
This test currently fails. The database is not available.
"""
import os
import unittest
from rdkit import RDConfig
from rdkit.Dbase.DbConnection import DbConnect
from rdkit.ML import InfoTheory
import pickle
RDConfig.usePgSQL = 0
def feq(v1, v2, tol2=1e-4):
return abs(v1 - v2) <= tol2
def getFingerprin... | ptosco/rdkit | rdkit/ML/InfoTheory/UnitTestBitRanker.py | Python | bsd-3-clause | 4,584 | [
"RDKit"
] | cc5aa293410684e807f3ff2f0d0803cb4d1693869918e1c45c49a60fd320538f |
# -*- coding: utf-8 -*-
import rnftools.lavender
import rnftools.utils
import gzip
import os
import pysam
import re
import textwrap
import bs4
from svg42pdf import svg42pdf
###########
###########
### BAM ###
###########
###########
class Bam:
"""Class for a BAM file.
Args:
panel (rnftools.lavender.Panel)... | karel-brinda/rnftools | rnftools/lavender/Bam.py | Python | mit | 34,600 | [
"pysam"
] | 83f58bfc2e98d0e9cdbef091edd43ae1c8a7a3b5ea410cc71c675e3a9e8cc2d9 |
"""Traits-based GUI for head-MRI coregistration"""
# Authors: Christian Brodbeck <christianbrodbeck@nyu.edu>
#
# License: BSD (3-clause)
import os
from ..externals.six.moves import queue
import re
from threading import Thread
import traceback
import warnings
import numpy as np
from scipy.spatial.distance import cdis... | jniediek/mne-python | mne/gui/_coreg_gui.py | Python | bsd-3-clause | 55,137 | [
"Mayavi"
] | 8c775a11afc3349f6c074fe1fc684c87dd778fd31e55e52a7157034389bf187e |
# Lint as: python3
# Copyright 2020 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 ... | gunan/tensorflow | tensorflow/python/eager/gradient_input_output_exclusions.py | Python | apache-2.0 | 12,655 | [
"VisIt"
] | c03f9a64326de21389cab355ea3c0971dcd3c2bf4e30d1c385d4e31d730c1fcc |
import os
import glob
import shutil
import numpy as np
#import pyfits
import astropy.io.fits as pyfits
import scipy.linalg
import matplotlib.pyplot as plt
import threedhst
import threedhst.prep_flt_files
import threedhst.catIO as catIO
import threedhst.eazyPy as eazy
import unicorn
def goods_ers():
"""
GOOD... | gbrammer/unicorn | candels.py | Python | mit | 143,004 | [
"VisIt"
] | de2b3583f7f5726d079164cfb26722794e79ecd9e3e8cf079fb600dc00493478 |
#!/usr/bin/env python
"""
Calculate the mean and dispersion of a data set with errors using MCMC sampling of a Gaussian likelihood function.
"""
import os
import warnings
from collections import OrderedDict as odict
import logging
import numpy as np
import emcee
import scipy.stats
try:
from dsphsim import __versi... | kadrlica/dsphsim | dsphsim/vdisp.py | Python | mit | 10,629 | [
"Gaussian"
] | 870e5de9c70db7573974f7ea4eb817022958eabfaaab3f444d1e1408f36079ef |
"""Simulation to examine the P(reject) as the parameters for each problem are
varied. What varies will depend on the problem."""
__author__ = 'wittawat'
import fsic.data as data
import fsic.feature as fea
import fsic.indtest as it
import fsic.glo as glo
import fsic.util as util
import fsic.kernel as kernel
import ... | wittawatj/fsic-test | fsic/ex/ex2_prob_params.py | Python | mit | 26,966 | [
"Gaussian"
] | 694f8580a0098643e6efdf208924c4a72abba92492d82d35deba7c906eb0b70e |
from __future__ import division, print_function, absolute_import
from copy import deepcopy
from sklearn.base import clone
from sklearn.metrics import accuracy_score, roc_auc_score, mean_squared_error
import numpy
import pandas
from scipy.special import expit
from six.moves import cPickle
from ..estimators import Cla... | vkuznet/rep | rep/test/test_estimators.py | Python | apache-2.0 | 8,915 | [
"Gaussian"
] | 71776be6d11e16407053ccdcf9b07c3cc27e79d9d8cf45b3b010d8f2a947ea67 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2008 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## 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 F... | andrebellafronte/stoq | stoqlib/gui/slaves/domainslavemapper.py | Python | gpl-2.0 | 1,350 | [
"VisIt"
] | 7cba93ef333a8e403798dd769e7cb8bb5d56b7fca96515cf975f18f19e90b6ec |
try:
import scipy
except ImportError:
from ase.test import NotAvailable
raise NotAvailable('This test needs scipy module.')
import numpy as np
from ase.io import read, PickleTrajectory
from ase.lattice import bulk
from ase.calculators.emt import EMT
a0 = 3.52 / np.sqrt(2)
c0 = np.sqrt(8 / 3.0) * a0
print ... | conwayje/ase-python | ase/test/hcp.py | Python | gpl-2.0 | 1,132 | [
"ASE"
] | c8d433ae87a375967565dcc5154916144b2719181504f651a85a84fbc3962d9a |
#!/usr/bin/python
# Filename: climate.py
#
# Code by Martin Jucker, distributed under an GPLv3 License
#
# This file provides helper functions that can be useful as pre-viz-processing of files and data
############################################################################################
#
from __future__ import... | mjucker/aostools | climate.py | Python | gpl-3.0 | 102,878 | [
"NetCDF"
] | 91fd1d614793420f808496ab6a800ac43bee5bed1f67e62864b54e5d143ccbc1 |
#!/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/cc/uccsd_slow.py | Python | apache-2.0 | 28,879 | [
"PySCF"
] | f895f7900aa4700faa78a5dfb3e8db4d5c392d9e05803d46e64ebd3e615ad249 |
import feathermodules
import pydoc
advice_text = {"ecb":
"""
=== ECB MODE ===
Analysis identified that two or more blocks in one of the samples matched. This is incredibly unlikely unless Electronic Code Book mode (ECB) is in use. ECB has a number of known vulnerabilities and is considered dangerous to use.
ECB revea... | nccgroup/featherduster | featherduster/advice.py | Python | bsd-3-clause | 14,178 | [
"VisIt"
] | e60e59d32bafb2b1b09700c9959ed6efe8b8b660cdb9b1c56fad3f981f1dab08 |
#!/usr/bin/env python
"""
Rejects version numbers in DESCRIPTION files which:
- Have more or less than 3 dot-separated segments
- Have any non-numeric characters within those segments
- Have a y (in x.y.z) that is even in devel or odd in release
- Have a lower version number than before
- Change x or y in release
If... | Bioconductor/DESCRIPTION_hook | check_for_bad_version.py | Python | artistic-2.0 | 11,068 | [
"Bioconductor"
] | 75baf7acf14964a2defd19593d18a0cf22bd07b71427073c25728cd42b366378 |
import datetime
import os
import re
from typing import Optional
class ExifProxy:
"""Object accessing EXIF info in a friendly, @property-friendly way.
All properties are user-friendly strings
"""
def __init__(self, a_dict):
self._data = a_dict
@property
def camera(self) -> str:
... | janpipek/chagallpy | chagallpy/image_info.py | Python | mit | 5,729 | [
"Galaxy"
] | 04e94f0fae400797e3fc46f457831d7c1d479135c20cfdfa5ad989f81c63ee5b |
# Cell cycle classification and feature selection - perform feature selection and prediction with internal and external cross-validation; results are saved as figures and in a hdf5 file.
#
########
######## PACKAGE LOADING
########
from __future__ import print_function
import h5py
import sys
import os
from os.path im... | PMBio/cyclone | py/core/cyclone.py | Python | apache-2.0 | 31,486 | [
"Gaussian"
] | ecdcdef4649eaa2299342e5d5a96eab400a5f9baac9c71c4153cfa5f1db1835f |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import logging
import itertools
import numpy as np
import re
from monty.json import MSONable
from pymatgen.core.composition import Composition
from pymatgen.e... | aykol/pymatgen | pymatgen/analysis/reaction_calculator.py | Python | mit | 20,114 | [
"pymatgen"
] | 61cb8b1b4a48512ed42cfec238eca69e2d86c31fc139f9332153d077e918cc0d |
#coding=utf-8
from flask import Flask, redirect, render_template, request, Response
from codepy import menulog
import anydbm as dbm
import shelve
import os, sys
import urllib
from datetime import datetime
import time
import urllib2
import hashlib
app = Flask(__name__)
visit = 0
visitHome = 0
startTime = time.time()
... | arcsun/neteaseMenu | mock.py | Python | apache-2.0 | 1,436 | [
"VisIt"
] | 473b6b5f799d59db1ecaa32c56850d1a5de082390e9d4efa698b45e8236194a2 |
"""
pymc.distributions
A collection of common probability distributions for stochastic
nodes in PyMC.
"""
from __future__ import division
from .dist_math import *
from numpy.random import uniform as runiform, normal as rnormal
__all__ = ['Uniform', 'Flat', 'Normal', 'Beta', 'Exponential', 'Laplace',
'T',... | kyleam/pymc3 | pymc/distributions/continuous.py | Python | apache-2.0 | 16,718 | [
"Gaussian"
] | 5e97e8d2463c27066be115bad1aeeabf9cc873af3521803947082f1734441840 |
"""
Functions for adding decorations (axes, colorbar, outlines..) to the
pipeline in a procedural way.
"""
# Author: Gael Varoquaux
# Copyright (c) 2007, 2008, 2009, Enthought, Inc.
# License: BSD Style.
import operator
import numpy as np
# Enthought library imports.
from traits.api import String, CFloat, Instance,... | liulion/mayavi | mayavi/tools/decorations.py | Python | bsd-3-clause | 19,544 | [
"Mayavi",
"VTK"
] | 59d3f776abbac8c872dd29f0f7e5d1857ec760c5f3f2832c58018caa96836ada |
# -*- coding: utf-8 -*-
"""
Created on Sat Jun 17 16:07:09 2017
@author: Owner
"""
# -*- coding: utf-8 -*-
"""
Created on Fri Jun 16 08:53:24 2017
Ida Storm
Depeloping tools that will take a point data set as input. The point dataset
will have a field for year/data as well as a field with names of the... | ScandinavianSection-UCLA/hGIS_ETK | Repeat_visit/repeatVisit_code_final.py | Python | gpl-3.0 | 3,638 | [
"VisIt"
] | 2c40e03d960ed20557fca4b3ac96f3d52a7a47e4f6cefe89ac0314f78c30ea47 |
#!/usr/bin/env python
# Author: Subhasis Ray
# 2008-09-05 10:02:31 UTC
import sys
sys.path.append("/home/subha/lib/python2.5/site-packages")
sys.path.append("/home/subha/lib/python2.5/site-packages/neuron")
import time
import pylab
import numpy
import neuron
import moose
#time_file = open("runtime.txt", "w")
clas... | BhallaLab/moose-thalamocortical | DEMOS/pymoose/ray_bhalla_2008/mus_nrn/moosenrn.py | Python | lgpl-2.1 | 9,185 | [
"MOOSE",
"NEURON"
] | 5f349e1391f59d8c071ce55c988b734df7ed96a19c3b3df933c86dcaa258a736 |
"""
Notifications for Android TV notification service.
For more details about this platform, please refer to the documentation at
https://home-assistant.io/components/notify.nfandroidtv/
"""
import logging
import io
import base64
import requests
from requests.auth import HTTPBasicAuth
from requests.auth import HTTPDi... | tinloaf/home-assistant | homeassistant/components/notify/nfandroidtv.py | Python | apache-2.0 | 10,035 | [
"Amber"
] | 98ac7a9e818a994dc63706e3273cbe2e4f96627abf88dbfc26e8317d616690e9 |
#!/usr/bin/env python
"""Testing script for write-math symbol classifier."""
# Core Library modules
import json
import logging
import sys
# Third party modules
import numpy
# Local modules
from ..classify import classify_segmented_recording as evaluate
from ..datasets import mfrdb
from ..utils import less_than
log... | MartinThoma/hwrt | hwrt/datasets/mfrdb_eval.py | Python | mit | 2,473 | [
"MOOSE"
] | 7944a486304dc163fe8731dd55f5b04bb67583287905ef9d5b2bce1da8cd4b55 |
# -*- coding: utf-8 -*-
"""
Build the scaffold PDB to be used as the basis of the final parameterized
model. Also need to store data about regions to be completed.
"""
'''
SASSIE: Copyright (C) 2011 Joseph E. Curtis, Ph.D.
This program is free software: you can redistribute it and/or modify
it under the t... | madscatt/zazzie_1.5 | trunk/sassie/build/pdbrx/scaffold_builder.py | Python | gpl-3.0 | 12,777 | [
"CHARMM"
] | 8985b82ae5b20c9faf4b7f8f237c7ab56cc3d7a6871d65d90e94793df6e63913 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | Stargrazer82301/CAAPR | CAAPR/CAAPR_AstroMagic/PTS/pts/modeling/fitting/bestmodellauncher.py | Python | mit | 9,551 | [
"Galaxy"
] | 565aa6ce61614d1d96eae01489d512a434510b0712b70abd14f1b26898c4779e |
#!/usr/bin/env python
# This file is part of the Printrun suite.
#
# Printrun 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.
#
# Prin... | 3DP-Unlimited/3DP-Printrun | pronsole.py | Python | gpl-3.0 | 61,053 | [
"Firefly"
] | dfd551767ec87f4d9f01cd676b58dec15ce094342f33d996f035b206bc30ed3e |
#!/usr/bin/env python
"""This test ensures that the mapper does not change the LookupTable
that may be shared among different mappers. Specifically, the vtkMapper
and vtkScalarsToColorsPainter classes use the LookupTable to map scalars
to colors. When they do this they set the LookupTable's Alpha ivar.
They should d... | spthaolt/VTK | Rendering/Testing/Python/TestMapperLUT.py | Python | bsd-3-clause | 6,402 | [
"VTK"
] | e29a6997b4e3dcaf6303ffe2535e6eb8bc8073259ac38cfab1b690a43e95aad8 |
# -*- coding: utf-8 -*-
# HORTON: Helpful Open-source Research TOol for N-fermion systems.
# Copyright (C) 2011-2015 The HORTON Development Team
#
# This file is part of HORTON.
#
# HORTON is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by th... | eustislab/horton | horton/meanfield/test/common.py | Python | gpl-3.0 | 19,966 | [
"Gaussian"
] | b31565aa722e841c565a4fca6170b9ed58fb2ae1250ed6432a1c43daef415f09 |
# -*- 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-access-approval | tests/unit/gapic/accessapproval_v1/test_access_approval.py | Python | apache-2.0 | 111,587 | [
"Octopus"
] | bb6c2e3b64ed521343e8e55bb5cc4c3255708cf1be8bcd7970cbe313b4bce1cb |
# -*- coding: utf-8 -*-
# Copyright (C) 2009 Canonical
#
# Authors:
# Michael Vogt
#
# 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; version 3.
#
# This program is distributed in the hope that... | pombreda/https-gitorious.org-appstream-software-center | softwarecenter/backend/reviews/__init__.py | Python | gpl-3.0 | 28,962 | [
"exciting"
] | 350a4bc0007ce6fcb571def0a16535a18fcf1f0e06af5bceecefd5498ae572e1 |
"""Utility functions for plotting M/EEG data
"""
from __future__ import print_function
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Denis Engemann <denis.engemann@gmail.com>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Eric Larson <larson.eric.d@gmail.com>
# ... | jaeilepp/eggie | mne/viz/utils.py | Python | bsd-2-clause | 12,829 | [
"Mayavi"
] | 4cdc59d0db7362481e069130867ed679cfee59552e1bb92ffc0db1a4c13bc892 |
#!/usr/bin/env python
# encoding: utf-8
'''
Licensed under a 3-clause BSD license.
Revision History:
Initial Version: 2016-02-17 17:46:57
Last Modified On: 2016-02-17 17:46:57 by Brian
'''
from __future__ import print_function
from __future__ import division
from brain.api.base import BrainBaseView
from brai... | albireox/marvin | python/marvin/api/base.py | Python | bsd-3-clause | 1,423 | [
"Brian"
] | cb7b7330b7916cf022651286bed6f36f6cbc1770f622902c70714c14757a24a1 |
"""
Dataset loading utilities
Portions of this module derived from
http://scikit-learn.org/stable/modules/classes.html#module-sklearn.datasets
"""
import numpy as np
import requests
import tarfile
import os
from six.moves import urllib
from scipy.io import loadmat
from scipy.spatial.distance import cdist
from unipat... | NICTA/revrand | revrand/utils/datasets.py | Python | apache-2.0 | 7,269 | [
"Gaussian"
] | bf7286b6324866f3df6aeae676f2e338f9ad027f052b9afe6640a0909ac0472d |
# Python Core
from datetime import datetime, timedelta
# Django
from django.db import models
from django.contrib.auth.models import User
from django.utils.translation import ugettext_lazy as _
from django.contrib.contenttypes.models import ContentType
from django.contrib.contenttypes import generic
from django.core.ur... | arctelix/django-notification-automated | notification/backends/website.py | Python | mit | 7,271 | [
"VisIt"
] | f454c9c3ebb6f18b96df9fe423d01017a50d0d3a20c23908289a0b9cfff2853d |
# -*- coding: utf-8 -*-
#-------------------------------------------------------------------------------
# Name: zdde.py
# Purpose: Python based DDE link with ZEMAX server, similar to Matlab based
# MZDDE toolbox.
# Licence: MIT License
# This file is subject to the terms and co... | ng110/PyZDDE | pyzdde/zdde.py | Python | mit | 493,200 | [
"Gaussian"
] | 8e47e0f0c657fb6d2abe415806e1993b3f146fe51d5b597beb64ad9bf9ba612b |
# -*- coding: utf-8 -*-
#
# Copyright © 2014 René Samselnig
#
# This file is part of Database Navigator.
#
# Database Navigator 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, ... | resamsel/dbnavigator | src/dbmanagr/args.py | Python | gpl-3.0 | 5,176 | [
"VisIt"
] | 930ec991c53e9e711ad746870bcda65f27ab94b20d8684d4b377dc6679e63dfe |
#!/opt/local/bin/pypy
#!/usr/bin/python
import sys
from collections import deque, defaultdict
import multiprocessing
class defaultlist(list):
def __init__(self, fx):
self._fx = fx
def _fill(self, index):
while len(self) <= index:
self.append(self._fx())
def __setitem__(self, index, value):
self._fill(inde... | mabrowning/PuzzleCompetition | parse.py | Python | gpl-3.0 | 7,966 | [
"VisIt"
] | ecf2aabc523ebbbb88ee17f255713000013624d85aa83af66bc17de58ad05e69 |
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