text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
"""
Acceptance tests for Studio.
"""
import uuid
from selenium.webdriver.common.keys import Keys
from common.test.acceptance.fixtures.course import CourseFixture, XBlockFixtureDesc
from common.test.acceptance.pages.common.auto_auth import AutoAuthPage
from common.test.acceptance.pages.studio import LMS_URL
from com... | cpennington/edx-platform | common/test/acceptance/tests/studio/test_studio_general.py | Python | agpl-3.0 | 10,173 | [
"VisIt"
] | 0aa16ee685a93314723969f760c2fee3528b2696d3039ff2a6aba85cbbee904b |
########################################################################
# File: RequestDB.py
# Date: 2012/12/04 08:06:30
# pylint: disable=no-member
########################################################################
""" Frontend for ReqDB
:mod: RequestDB
=======================
.. module: Request... | andresailer/DIRAC | RequestManagementSystem/DB/RequestDB.py | Python | gpl-3.0 | 33,776 | [
"DIRAC"
] | 96406885c35cbb05e5e3e5fdb861ee260a2787273382f3cb9f3694689ba2ebc1 |
#!python
"""\
Easy Install
------------
A tool for doing automatic download/extract/build of distutils-based Python
packages. For detailed documentation, see the accompanying EasyInstall.txt
file, or visit the `EasyInstall home page`__.
__ http://peak.telecommunity.com/DevCenter/EasyInstall
"""
import sys, os.path, ... | stanbellcom/webapp_politik | sites/all/modules/annotator/lib/store-plugin/pyenv/lib/python2.7/site-packages/distribute-0.6.10-py2.7.egg/setuptools/command/easy_install.py | Python | gpl-2.0 | 64,060 | [
"VisIt"
] | 418a81586e186c9b22e346ed8bee68b4556aedd8b42c62b6a6f369d3433000f2 |
import neurolab as nl
import numpy as np
x = np.linspace(-7, 7, 20)
y = np.sin(x) * 0.5
size = len(x)
inp = x.reshape(size,1)
tar = y.reshape(size,1)
# Input is in range [-7,7]. Input layer has 1 neuron.
# Hidden layer has 5 neurons. Output layer has 1 neuron.
net = nl.net.newff([[-100, 100]],[5, 1])
erro... | lisiyuan656/Gesture-Recognizer | tutorials/mlp_tutorial.py | Python | gpl-2.0 | 755 | [
"NEURON"
] | 9ce0a9f2b630b05da260bd1d19997628a912b81ad90c203259a6ae8ac44f4b31 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import
import pytest
import re
import responses
import six
from symbolic import SourceMapTokenMatch
from mock import patch
from requests.exceptions import RequestException
from sentry import http
from sentry.lang.javascript.processor import (
discover_sour... | gencer/sentry | tests/sentry/lang/javascript/test_processor.py | Python | bsd-3-clause | 25,956 | [
"VisIt"
] | e6cbce2aff4e3fc3160219fd9e9238933793a6adc3d0e9bd1d0a4eb9df81b7b9 |
from __future__ import division
from __future__ import print_function
from __future__ import absolute_import
from __future__ import unicode_literals
import os
import zlib
import json
import shutil
import urllib
import zipfile
import hashlib
import tempfile
import unittest
import pkg_resources
import fs_uae_launcher.fs... | uhef/fs-uae-gles | launcher/fs_uae_launcher/LaunchHandler.py | Python | gpl-2.0 | 38,057 | [
"ADF"
] | 904353964b647b118764539161973ded0aa7f64a3a5f262262dedcfa32e93484 |
# Copyright 2020 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | google/neural-light-transport | nlt/util/img.py | Python | apache-2.0 | 7,482 | [
"Gaussian"
] | ccdd1d4b8a4271103ffb9ce221c1435da79d1b5dbefc622677803305ddda1110 |
#! /usr/bin/env python2
import argparse
from RecBlastUtils import *
import csv_transformer
import taxa_to_taxid
from uuid import uuid4
import part_one
import part_two
import part_three
from RecBlastFigures import *
# this will be the stand alone version of RecBlast for linux.
__version__ = "1.1.2"
# flags:
# DEBUG ... | neuhofmo/RecBlast | RecBlast.py | Python | mit | 17,000 | [
"BLAST"
] | b1f1c482ea604980d5143df61cbb544d7fbf78536d011cf2e9f799dc0ce9c6c3 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 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
#... | psi4/psi4 | psi4/driver/qcdb/__init__.py | Python | lgpl-3.0 | 1,871 | [
"CFOUR",
"ORCA",
"Psi4"
] | d56febc6c7dcc6ad97f83ad1d911743aa55f917efaf3a23cb2b4f8c253014013 |
# -*- coding: utf-8 -*-
# <nbformat>3.0</nbformat>
# <headingcell level=1>
# Plotting a CF-1.6 Time Series file with Iris
# <codecell>
import iris
import matplotlib.pyplot as plt
import iris.quickplot as qplt
%matplotlib inline
# <codecell>
url='http://comt.sura.org/thredds/dodsC/comt_1_archive_full/inundation_tr... | rsignell-usgs/notebook | IRIS/Iris_time_series_plot.py | Python | mit | 844 | [
"NetCDF"
] | 8ba9333fb9e409fca275c5b353023cc1a14284dec25e69543afd5041fc667883 |
#!/usr/bin/python
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
#
# See COPYING file distributed along with the PyMVPA package for the
# copyright and license terms.
#
#... | nno/surfing | python/afni_surface_alphasim.py | Python | bsd-2-clause | 17,918 | [
"Gaussian"
] | 0d107c81d6828802594fb492ca1f728521bccd593a5622712125ad902ed10a2c |
#!/usr/bin/env python
# The MIT License (MIT)
#
# Copyright (c) 2014 Sidhartha Goyal, Shirish Goyal
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without li... | arlissc/phageParser | setup.py | Python | mit | 1,428 | [
"Biopython"
] | f77aa5942c4d27337a04d7528d9547ef71837332971b2177541364375be67e21 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2003-2006 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publi... | jralls/gramps | gramps/plugins/gramplet/leak.py | Python | gpl-2.0 | 9,078 | [
"Brian"
] | a87304fb8152f022f171b8890bf1643afe8e3e32d79c0e8aba0a1e7006e2bb66 |
# -*- coding: utf-8 -*-
"""Main IPython class."""
#-----------------------------------------------------------------------------
# Copyright (C) 2001 Janko Hauser <jhauser@zscout.de>
# Copyright (C) 2001-2007 Fernando Perez. <fperez@colorado.edu>
# Copyright (C) 2008-2011 The IPython Development Team
#
# Distribu... | lancezlin/ml_template_py | lib/python2.7/site-packages/IPython/core/interactiveshell.py | Python | mit | 132,017 | [
"VisIt"
] | 66fbd9fd60f210b3fc717fb12ac48a544c053678c7bc705a1e36b9aff4a91b36 |
from ctypes import Structure, POINTER
import time as time_module
from datetime import date
from datetime import datetime
from datetime import timedelta as delta
import numpy as np
import xarray as xr
from operator import attrgetter
import progressbar
from parcels.compiler import GNUCompiler
from parcels.field import ... | OceanPARCELS/parcels | parcels/particleset.py | Python | mit | 45,542 | [
"NetCDF"
] | bdc1a8ddf000681fb36e627816b12e5e4579c749c0913c432849eafae4e884fb |
###############################################################################
##
## Copyright (C) 2011-2014, NYU-Poly.
## Copyright (C) 2006-2011, University of Utah.
## All rights reserved.
## Contact: contact@vistrails.org
##
## This file is part of VisTrails.
##
## "Redistribution and use in source and binary for... | Nikea/VisTrails | vistrails/packages/vtk/vtkviewcell.py | Python | bsd-3-clause | 38,492 | [
"VTK"
] | 824b26d164163691e017746e1d618027aadc0f2685ebb735220b50aba1ad2fee |
import sys
import os
import io
import psycopg2
import xml.etree.ElementTree as ET
from lxml import etree
import math
from collections import Counter
from operator import itemgetter
import datetime
import collections
#For use with Tr-ConLL
def block(ch):
'''
Return the Unicode block name for ch, or None if ch ... | grantdelozier/TopoCluster | experimental/TestResolver_TRCONLL.py | Python | apache-2.0 | 34,390 | [
"FEFF"
] | 662eee7e6bc32edb624eaa5b9e91277a1ca97617076268f9705289df43e5d475 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import warnings
import numpy as np
import os
import logging
from enum import Enum, unique
from collections import namedtuple
from scipy.stats import gaussian_kde
from scipy.signal import argrelextrema
from ... | dongsenfo/pymatgen | pymatgen/analysis/magnetism/analyzer.py | Python | mit | 46,776 | [
"VASP",
"pymatgen"
] | ca2df98e0a3a302faed2415210c84f0df7439a6d7125c2028d4809eb4b3f0575 |
from traits.api import HasTraits, Instance, on_trait_change
from traitsui.api import View, Group, Item
from mayavi.core.api import Engine
from mayavi.core.ui.api import MayaviScene, MlabSceneModel, \
SceneEditor
################################################################################
class MyApp(H... | HPCGISLab/STDataViz | WorkingVersion/LibTry/MayaviGUI/Multiple engines Example.py | Python | bsd-3-clause | 1,734 | [
"Mayavi",
"VTK"
] | b69ccd333ff5e4d175c2e3448e41897d9987447d682ee83f552c6bf21bcc9e56 |
"""Some test functions for bivariate interpolation.
Most of these have been yoinked from ACM TOMS 792.
http://netlib.org/toms/792
"""
import numpy as np
from .triangulate import Triangulation
class TestData(dict):
def __init__(self, *args, **kwds):
dict.__init__(self, *args, **kwds)
self.__dic... | alephu5/Soundbyte | environment/lib/python3.3/site-packages/matplotlib/delaunay/testfuncs.py | Python | gpl-3.0 | 21,009 | [
"Gaussian"
] | c2e2b4d5e1ec0cee1fe4a07b2f4c33386d52d51f05e4f4f694cf50742e053b1c |
##
# Copyright 2009-2020 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... | pescobar/easybuild-easyblocks | easybuild/easyblocks/o/openfoam.py | Python | gpl-2.0 | 21,822 | [
"ParaView"
] | 8890090ba62434e877c9954721f4c5ffc389b448276e2f8c1c9a86c90dcd7c61 |
#!/usr/bin/env python
__author__ = 'Mike McCann,Duane Edgington,Danelle Cline'
__copyright__ = '2018'
__license__ = 'GPL v3'
__contact__ = 'duane at mbari.org'
__doc__ = '''
Master loader for all CANON May-June Campaign 2019
Mike McCann, Duane Edgington, Danelle Cline
MBARI 22 May 2019
@var __date__: Date of last s... | duane-edgington/stoqs | stoqs/loaders/CANON/loadCANON_may2019.py | Python | gpl-3.0 | 14,754 | [
"NetCDF"
] | adfa3118d41db511fb93217f73a3c6710f402571511674a7a12cd875e1267ab5 |
# 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/euca-python-lib | eucalib/util.py | Python | bsd-2-clause | 1,420 | [
"VisIt"
] | 41c6347a8caa4c8716b5f8e767b62938664156566479585c1b9f07b3f5dd2aa2 |
#!/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 = ['name','version','moduleid','description','copyright','... | DianthuDia/TiCustomAlert | build.py | Python | mit | 6,533 | [
"VisIt"
] | 72fe90745de98337e65cfa2d3192495478590597440e9bd6a3e53e42e6414ffb |
""" X509Certificate is a class for managing X509 certificates alone
"""
__RCSID__ = "$Id$"
import GSI
import os
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Utilities import Time
from DIRAC.Core.Utilities import DErrno
from DIRAC.ConfigurationSystem.Client.Helpers import Registry
# List of OIDs used in handling VO... | fstagni/DIRAC | Core/Security/pygsi/X509Certificate.py | Python | gpl-3.0 | 8,526 | [
"DIRAC"
] | f3f6207b1676c152d1d0b07837c4de2785211ea0a653cd369cfeb9eec03090e4 |
# -*- coding: utf-8 -*-
#
# test_rate_neuron.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the Licens... | hakonsbm/nest-simulator | pynest/nest/tests/test_rate_neuron.py | Python | gpl-2.0 | 4,919 | [
"NEURON"
] | 8f676d6e58565e6ce70e12d0403f320509742100ce9a8659bd652ecc75fc0b1a |
import numpy as np
def wcentroid(image, xcoords, ycoords, sigma=None, tol=1.e-4, maxnits=100, info=False, warn=True):
"""Find the weighted (or unweighted if sigma is not set) centroid of an
image.
This is defined relative to user-specified x and y coordinates for the
image, specifed as arrays, as gene... | plazas/wfirst-detectors-vnl | code/moments.py | Python | mit | 13,940 | [
"Gaussian"
] | e823687ae92020ac77a93522c4be81df5f9118ad621aaa40e706acfd86cad9c6 |
# Version: 0.14
"""
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, and pypy
* [![Latest Version]
(https://pypip.in/version/versioneer/badge.svg?style=flat)
](ht... | Winterflower/khmer | versioneer.py | Python | bsd-3-clause | 40,384 | [
"Brian"
] | 5ccd8fdbe05208c2ef8eb423fd05ba6a4a0650032985917c5d3632f637079f5d |
# Copyright 2018 DT42
#
# This file is part of BerryNet.
#
# BerryNet 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.
#
# BerryNet is d... | DT42/BerryNet | berrynet/bndyda/pipeline.py | Python | gpl-3.0 | 15,708 | [
"Galaxy"
] | 9467631980bda13bf75539a21c279861417d0aa2c9f01ceb381c7c4ebdbaa367 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# (c) 2016, Brian Coca <bcoca@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License... | britcey/ansible | lib/ansible/modules/system/systemd.py | Python | gpl-3.0 | 18,567 | [
"Brian"
] | 170e864ed34172c7ba77409eea5c3e0eb0dbf4112ee94b00b6835bafebb41c2c |
#
# This program is free software you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation either version 3 of the License, or
# (at your option) any later version.
#
# Written (C) 2012 Heiko Strathmann
#
from numpy import *
from pylab i... | JingheZ/shogun | examples/undocumented/python_modular/graphical/statistics_hsic.py | Python | gpl-3.0 | 6,169 | [
"Gaussian"
] | 78002784fd29cc7fead2c5faa794b0844615f19778147310406175a222a53d7b |
#===============================================================================
#
# tensorboard/Logger.py
#
# This file is part of ANNarchy.
#
# Copyright (C) 2013-2020 Julien Vitay <julien.vitay@gmail.com>,
# Helge Uelo Dinkelbach <helge.dinkelbach@gmail.com>
#
# This program is free software: yo... | vitay/ANNarchy | ANNarchy/extensions/tensorboard/Logger.py | Python | gpl-2.0 | 12,742 | [
"NEURON"
] | 6f42a74184ca40b2ab0999d6114fdadfbbe9d7778999205bd871829412390a94 |
'''
Classes for dropout prediction models
11/12/2014
Sebastien Boyer
Updated to get rid of reliance on csv files in favor of accessing database
directly
5/28/15
Ben Schreck
'''
import numpy as np
#import csv
import os
from preprocess_data import *
import flatten_featureset
from statistical_feat import *... | EDUlib/eTracesX | Stopout-Prediction/classes.py | Python | agpl-3.0 | 24,875 | [
"Gaussian"
] | 155d2a38d57cbc40042a60f4f36776a811caafd1b00a72e3c0e644d7aaabed77 |
# 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 agreed ... | google-research/ott | ott/tools/gaussian_mixture/gaussian.py | Python | apache-2.0 | 4,361 | [
"Gaussian"
] | ff8c771cc2f445771054436727d38cd1829f12429ed8a2e6d1e012746e5e21ee |
# Written by Max Theiler, max.theiler@gmail.com
# 2/5/2016
# This script for parsing the output file timers.txt,
# and writing it as a csv file comprehensible to the
# pie chart tools created by Brian Broom-Peltz.
# It also includes in the comments a crude mini-tutorial
# on python's regex tools.
# "re" is the best... | dpaiton/OpenPV | pv-core/python/timers_txt_to_csv.py | Python | epl-1.0 | 2,725 | [
"Brian"
] | b73a335597039639cb1da322dba4fe482df9d1eb28cac7a4fabf044223448798 |
# -*- coding: utf-8 -*-
from typing import Any, DefaultDict, Dict, List, Optional, Set, Tuple, Union
from collections import namedtuple, defaultdict
from itertools import chain, islice
from functools import partial
from networkx import Graph, single_source_shortest_path
from django.db import connection
from django.h... | tomka/CATMAID | django/applications/catmaid/control/analytics.py | Python | gpl-3.0 | 16,051 | [
"NEURON"
] | 6a36e1122b18d9b62662db727f6140f370c466c5ddcb8b0bd4c7655124ff8fb0 |
#!/usr/bin/env python
########################################################################
# $Header: $
########################################################################
"""
Remove the given file or a list of files from the File Catalog
Example:
$ dirac-dms-remove-catalog-files /formation/user/v/vhamar... | ic-hep/DIRAC | src/DIRAC/DataManagementSystem/scripts/dirac_dms_remove_catalog_files.py | Python | gpl-3.0 | 2,411 | [
"DIRAC"
] | c0e5172f3acd021214658b4dd5acdfa499454cd2dc62d983139ff8dc8e9f4095 |
"""
@created_at 2014-06-09
@author Exequiel Fuentes <efulet@gmail.com>
@author Brian Keith <briankeithn@gmail.com>
"""
# Se recomienda seguir los siguientes estandares:
# 1. Para codificacion: PEP 8 - Style Guide for Python Code (http://legacy.python.org/dev/peps/pep-0008/)
# 2. Para documentacion: PEP 257 - Docst... | efulet/laberinto | laberinto/lib/opciones.py | Python | mit | 2,292 | [
"Brian"
] | 1e498470388cbe7f80c4a74f025d07d49854e83fa9dfb5a2b622515c1bc62e0d |
import sys
from DIRAC import S_OK, S_ERROR
from email.mime.text import MIMEText
from email.mime.multipart import MIMEMultipart
STATE_MAP = { 0: 'RUNNING',
1: 'REBOOTING',
2: 'TERMINATED',
3: 'PENDING',
4: 'UNKNOWN',
5: 'STOPPED',
6: '... | xianghuzhao/VMDIRAC | VMDIRAC/Resources/Cloud/Utilities.py | Python | gpl-3.0 | 786 | [
"DIRAC"
] | 965032cdf89a60706dc0e5688b4e8d1ac05364f3aa3ee9e441bac05a931db0a2 |
import datetime
import re
import secrets
import time
from datetime import timedelta
from typing import (
AbstractSet,
Any,
Callable,
Dict,
List,
Optional,
Pattern,
Sequence,
Set,
Tuple,
TypeVar,
Union,
)
import django.contrib.auth
import orjson
from bitfield import BitFi... | rht/zulip | zerver/models.py | Python | apache-2.0 | 153,908 | [
"VisIt"
] | 9283e21396102cc822d5f5d70c4ff3d182da6fbf2b2593362f358b9bc9d9a327 |
"""
Linter classes containing logic for checking various filetypes.
"""
from __future__ import absolute_import
import ast
import os
import re
import textwrap
import io
from xsslint import visitors
from xsslint.reporting import ExpressionRuleViolation, FileResults, RuleViolation
from xsslint.rules import RuleSet
from ... | ESOedX/edx-platform | scripts/xsslint/xsslint/linters.py | Python | agpl-3.0 | 67,990 | [
"VisIt"
] | eebe1e8112758abcd0967dd102febab60452c8ab30d7b65c96a641b6aabfb3a9 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Encyclopedia Brown, user reviews"""
import sys
import os
import datetime
import pickle
import csv
import pprint
LOCALES = ['NYC', 'Paris', 'Bangkok', 'Sydney', 'Rio', 'Accra']
def initialize_reviewdict():
"""initializes the text file to an empty dictionary.""... | slb6968/Encyclopedia-Brown | reviews.py | Python | gpl-2.0 | 3,391 | [
"VisIt"
] | d1da5226ca2784a48bc166fc427047f2545733af0718f0808dbae84c6a0f35d5 |
"""Basic setuptools script for DIRACDocs."""
import os
import glob
# Actual setuptools
from setuptools import setup, find_packages
# Find the base dir where the setup.py lies
BASE_DIR = os.path.abspath(os.path.join(os.path.dirname(__file__), 'diracdoctools'))
# Take all the packages but the scripts and tests
ALL_PAC... | fstagni/DIRAC | docs/setup.py | Python | gpl-3.0 | 970 | [
"DIRAC"
] | 7efb84be53655723c94e77dcb8747bd0e09e73a3992ebf4a4fe73f6e6a7ab811 |
#!/usr/bin/env python
#
# $File: statHeteroFreq.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can redistri... | BoPeng/simuPOP | docs/statHeteroFreq.py | Python | gpl-2.0 | 1,443 | [
"VisIt"
] | 374f7544927e85300a664f81ae6ebd775a69a2b3ce6cf72eea65589848f377b9 |
import os
os.environ.setdefault('DJANGO_SETTINGS_MODULE','dd3.dd3.settings')
from datetime import datetime
import django
print(django.get_version())
from dd3.visitor.models import Apache
import pytz
def add_apache_logs():
apache = Apache()
apache.date = datetime.now().replace(tzinfo=pytz.utc)
apache.visit = 44
... | za/dd3 | populate.py | Python | apache-2.0 | 355 | [
"VisIt"
] | a338338913e0d0245e5db2a1e9af36e034e07e29eed63f2c79aa31b2cfd65e45 |
"""
Force field methods.
"""
from .uff import UFF_DATA
from .uff4mof import UFF4MOF_DATA
from .dreiding import DREIDING_DATA
from .uff_nonbonded import UFF_DATA_nonbonded
from .BTW import BTW_angles, BTW_dihedrals, BTW_opbends, BTW_atoms, BTW_bonds, BTW_charges
from .Dubbeldam import Dub_atoms, Dub_bonds, Dub_angles, D... | peteboyd/lammps_interface | lammps_interface/ForceFields.py | Python | mit | 187,746 | [
"CHARMM",
"Gaussian",
"LAMMPS"
] | b3e129a25db1c84895c5d7a2091bdd5f5619e7c629257cdf1ebc3379aa833966 |
# Copyright (c) 2014, the GREAT3 executive committee (http://www.great3challenge.info/?q=contacts)
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without modification, are permitted
# provided that the following conditions are met:
#
# 1. Redistributions of source code must retain... | barnabytprowe/great3-public | inputs/galdata/combine_image_info.py | Python | bsd-3-clause | 4,085 | [
"Galaxy"
] | 431bc175d46e6457a80f56800986262dce14a720976ab8b6e9bf4272b3e7952e |
import re
from collections import OrderedDict
from ase.io import read
def symbol_number(symbols):
"""
symbols can be also atoms. Thus the chemical symbols will be used.
Fe Fe Fe O -> {Fe1:0 Fe2:1 Fe3:2 O1:3}
"""
try:
symbs=symbols.copy().get_chemical_symbols()
except Exception:
... | mailhexu/pyDFTutils | pyDFTutils/ase_utils/symbol.py | Python | lgpl-3.0 | 1,165 | [
"ASE"
] | ab329dfb651b81887e5a1dcd387da24e5f14af0f076b7bd9b025789b903d9f3e |
#!/usr/bin/env python
# File created on 07 Jul 2012
from __future__ import division
__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.8.0-dev"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
from ... | wasade/qiime | qiime/parallel/align_seqs.py | Python | gpl-2.0 | 4,989 | [
"BLAST"
] | 5e4b6da26f6a6141166ee768b807aa06e1350faed5eeb67cf2c1992943ef4814 |
from unittest import TestCase
import unittest
import pygem.igeshandler as ih
import numpy as np
import filecmp
import os
class TestIgesHandler(TestCase):
def test_iges_instantiation(self):
iges_handler = ih.IgesHandler()
def test_iges_default_infile_member(self):
iges_handler = ih.IgesHandler()
assert i... | fsalmoir/PyGeM | tests/test_igeshandler.py | Python | mit | 7,106 | [
"VTK"
] | 4cedc0156d2042e97faefba83fd04d1a558f4ea00f779565d31c224347e4532a |
"""
.. _tut_compute_covariance:
Computing covariance matrix
===========================
"""
import os.path as op
import mne
from mne.datasets import sample
###############################################################################
# Source estimation method such as MNE require a noise estimations from the
# rec... | wronk/mne-python | tutorials/plot_compute_covariance.py | Python | bsd-3-clause | 6,745 | [
"Gaussian"
] | 6dd379ec1266f3e986327b43c25cff093bb7f3cf3b3d4e2d960a10b4627aa5e0 |
# 4-body improper interactions
# This file is part of ForceSolve, Copyright (C) 2008-2015 David M. Rogers.
#
# ForceSolve 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,... | frobnitzem/forcesolve | cg_topol/pimprop.py | Python | gpl-3.0 | 6,115 | [
"CHARMM"
] | 2b53fd9684abb0ada6a49c70a643f8dafcb32075f6b213f650a53d576a750bf2 |
class GraphNode(object):
"""
Graph's Node is a base cluster.
"""
def __init__(self, name):
# Name of the node
self.__name = name
#links (edges)
self.__links = set()
def add_name(self, name):
self.__name = name
@property
def... | abramovd/Newster | newster/structures/Graph.py | Python | mit | 2,224 | [
"VisIt"
] | 85ddba9564c3f4d6136195be1ce3ec0465e74ca192fa6f1cba6ab5efe618b12d |
# region gplv3preamble
# The Medical Simulation Markup Language (MSML) - Simplifying the biomechanical modeling workflow
#
# MSML has been developed in the framework of 'SFB TRR 125 Cognition-Guided Surgery'
#
# If you use this software in academic work, please cite the paper:
# S. Suwelack, M. Stoll, S. Schalck, N.Sch... | CognitionGuidedSurgery/msml | src/msml/sortdef.py | Python | gpl-3.0 | 6,629 | [
"VTK"
] | c145a290a7c392e1e6a21b5219de962930e09225924fd635286dbd272361957e |
"""
Introduction
============
The Munkres module provides an implementation of the Munkres algorithm
(also called the Hungarian algorithm or the Kuhn-Munkres algorithm),
useful for solving the Assignment Problem.
Assignment Problem
==================
Let *C* be an *n*\ x\ *n* matrix representing the costs of each of... | camielv/wildlife-monitoring | src/modules/utils/munkres.py | Python | lgpl-2.1 | 24,828 | [
"Brian"
] | ccd543afa6f8e8bf9c881edf57aa54f790a6b287f71d04b054185e21a3a52bb8 |
# 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... | deepakgupta1313/models | differential_privacy/dp_sgd/dp_optimizer/utils.py | Python | apache-2.0 | 10,661 | [
"Gaussian"
] | fc58679ee617226e6955d10a9daa9a977eeb63f332feb65650b5995bce6c0ff2 |
import sys, os, string, threading, gconf
import pygtk, gtk
sys.path.append(os.path.join(os.path.dirname(__file__), '..'))
from ui.ui import gladeFile
from utils.utils import *
from phamerator_manage_db import *
import logger
import config
import ConfigParser
import urllib2
import cairo
import gconf
class Phage:
def ... | byuphamerator/phamerator-dev | phamerator/dialogs/dialogs.py | Python | gpl-2.0 | 43,817 | [
"BLAST"
] | d3817e7b3e8c47706a4adb52442337d131ab929fa175c939ee23aed5cd7ed30a |
from ase import *
from ase.parallel import paropen
from gpaw import *
from gpaw.mpi import serial_comm
from gpaw.xc.rpa_correlation_energy import RPACorrelation
import numpy as np
ws = np.array([0.5*i for i in range(2001)])
ecut = 50
calc = GPAW('N2.gpw', communicator=serial_comm, txt=None)
rpa = RPACorrelation(calc... | ajylee/gpaw-rtxs | doc/tutorials/rpa/frequency.py | Python | gpl-3.0 | 608 | [
"ASE",
"GPAW"
] | a93f6d2b10e08b7445b5fcd5ea2e4ab547a5f7d72338f23bdfacb5a41b21b60f |
__author__ = 'Robert Meyer'
from pypet.tests.testutils.ioutils import unittest, run_suite, make_temp_dir, get_log_config, \
parse_args
from pypet.tests.testutils.data import TrajectoryComparator
from pypet import Environment
import time
import os
try:
import brian
from brian import ms, mV, NeuronGroup, Sy... | nigroup/pypet | pypet/tests/integration/briantests/network_test.py | Python | bsd-3-clause | 7,893 | [
"Brian",
"NEURON"
] | 734218179d6ee7750d508de962921861d7e2b7cb4e4748bdfa7426cc5b52dd29 |
# Copyright 2002 Gary Strangman. All rights reserved
# Copyright 2002-2016 The SciPy Developers
#
# The original code from Gary Strangman was heavily adapted for
# use in SciPy by Travis Oliphant. The original code came with the
# following disclaimer:
#
# This software is provided "as-is". There are no expressed or... | scipy/scipy | scipy/stats/_stats_py.py | Python | bsd-3-clause | 329,502 | [
"DIRAC"
] | d190ef13b5dc3aa3844cc0a504bc2298fbb2d5e8464aadf33c4d676a082835f4 |
# -*- coding: utf-8 -*-
# Copyright 2007-2016 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at... | magnunor/hyperspy | hyperspy/model.py | Python | gpl-3.0 | 75,168 | [
"Gaussian"
] | 242028ab73c93a778d9bf88f98a388a40c755cb788a4cdc0e18632cbe56571d3 |
# -*- 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-compute | tests/unit/gapic/compute_v1/test_target_ssl_proxies.py | Python | apache-2.0 | 127,851 | [
"Octopus"
] | 47444fdb54bf1ac995cf567defb227c59ffdef6722f93247bd365550b7b1827a |
from __future__ import print_function
def test_pandas(h2kc, project, df):
"""
"""
import qcdb
try:
if project == 'dhdft':
print("""\n Checks from dhdft project:\n""")
digits = 4
# B3LYP
qcdb.compare_values(-2.8732, h2kc * df['B3LYP-CP-a... | loriab/qcdb | qcdb/pandas_test.py | Python | lgpl-3.0 | 180,801 | [
"Psi4"
] | 67018212985d13d796c349b072649d7e7268c64492eab142f6258cbb47b4d456 |
from flask import Flask, render_template, session, request, redirect
import random
app = Flask(__name__)
app.secret_key = 'my_secret_key'
@app.route('/')
def index():
if not 'gold' in session:
session['gold'] = 0
if not 'activities' in session:
session['activities'] = []
return render_temp... | jiobert/python | raj_chetan/flask_olympics/olympics7/server.py | Python | mit | 1,266 | [
"CASINO"
] | e89c8b51b7e69fa710e1875b3a4ece6a8abe8cfa2fecdfaf44b106e4eeaeb724 |
# 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
#
# Unless required by appl... | gkc1000/pyscf | pyscf/nao/test/nao/ae_fii/test_ae_fii.py | Python | apache-2.0 | 2,162 | [
"PySCF"
] | 0b15c4111de4430460944498291c6e85213842969d0867bb76f7a0353149f8e0 |
from bs4 import BeautifulSoup
from collections import defaultdict
from operator import itemgetter
from repreader import RepReader
import urllib
import urllib2
import cookielib
import re
import time
import requests
import sys
import itertools
#Lists the top ten users by rep given
class TopRepGivers(RepReader):
def _... | rbonick/care-tags_scripts | care_tags_repmeter/topreps.py | Python | mit | 3,533 | [
"VisIt"
] | d5b76c617b95cb7970cdd149d1698cce904b62f26f039dbefe683af2db1498a1 |
# NOTE: User roles are not managed here. Visit PlanetLab to change user roles.
user_list = [('Stephen', 'Stuart', 'sstuart@google.com'),
('Chris', 'Ritzo', 'critzo@opentechinstitute.org'),
('Josh', 'Bailey', 'joshb@google.com'),
('Nathan', 'Kinkade', 'kinkade@measurementlab... | critzo/operator | plsync/users.py | Python | apache-2.0 | 680 | [
"VisIt"
] | 9a1bc7e8433dfcbcf1c5b8dbf1fb3ca70b603b37f8e827d9039ed087a57ecec5 |
#import plotly.plotly as py
#from plotly.tools import FigureFactory as FF
#import plotly.graph_objs as go
import sys
import os
import json
import pandas as pd
import numpy as np
from scipy.stats.stats import pearsonr
#fix dictionary - fabs getting added to seedfree?
#MSH->MLH linear like yeast (and maybe other well ... | aGitHasNoName/PERCscripts | pearsonDF.py | Python | gpl-3.0 | 3,477 | [
"scikit-bio"
] | ff1d4f5eab4ac7f315c72aefd41de5e2c9f5628a7540ad4b8153d192e011b9f6 |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | wangsheng1001/incubator-singa | test/python/test_tensor.py | Python | apache-2.0 | 5,642 | [
"Gaussian"
] | a8dde75e305c248c5ede7bd7c12c84ee7c762e561286b610edc9577ca2d28eb0 |
# Copyright (C) 2015 OLogN Technologies AG
#
# This source file is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License version 2
# as published by the Free Software Foundation.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY W... | smartanthill/plugin-handler-compiler | smartanthill_phc/writer.py | Python | gpl-2.0 | 26,879 | [
"VisIt"
] | 99c9faac623448622e927c4047a67876604e6848a2b9339030d82af1e044b7db |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Functional tests using WebTest."""
import httplib as http
import logging
import unittest
import markupsafe
import mock
from nose.tools import * # flake8: noqa (PEP8 asserts)
import re
from framework.mongo.utils import to_mongo_key
from framework.auth import cas
from f... | amyshi188/osf.io | tests/webtest_tests.py | Python | apache-2.0 | 42,212 | [
"VisIt"
] | 0ef3dbae5326af1d83d017ce4325d93570f548ef3790208da82f48d30872fcb8 |
# SimpleCV Cameras & Devices
#load system libraries
from SimpleCV.base import *
from SimpleCV.ImageClass import Image, ImageSet, ColorSpace
from SimpleCV.Display import Display
from SimpleCV.Color import Color
from collections import deque
import time
import ctypes as ct
import subprocess
import cv2
import numpy as np... | vdt/SimpleCV | SimpleCV/Camera.py | Python | bsd-3-clause | 119,588 | [
"VisIt"
] | 018456e3d4a3bb7b7f429cb7c2acad5216248c45deb79734156beef9b62ddeee |
from rdkit import six
#-------------------------------------------------------------------------
# Color
#-------------------------------------------------------------------------
class Color:
"""This class is used to represent color. Components red, green, blue
are in the range 0 (dark) to 1 (full intens... | jandom/rdkit | rdkit/sping/colors.py | Python | bsd-3-clause | 6,870 | [
"RDKit"
] | 2f282c1b984d56aea0e9bbc0391e5bc239b46c3cea7f6f1bee89f9f4159e0e87 |
#/* FILE INFORMATION
#** Based mostly on the traub91proto.g by Dave Beeman
#** Main difference is addition of Glu and NMDA channels
#** The 1991 Traub set of voltage and concentration dependent channels
#** Implemented as tabchannels by : Dave Beeman
#** R.D.Traub, R. K. S. Wong, R. Miles, and H. Michelson
#** Jou... | dilawar/moose-full | moose-examples/snippets/MULTI/proto18.py | Python | gpl-2.0 | 19,126 | [
"MOOSE"
] | f3f4a16a1cf43988bbbf311aae441af3e19098c3ed47842030b7caee6217d1a4 |
import numpy as np
import matplotlib.pyplot as plt
from unsharp import *
from stack_functions import *
im1_fname = 'orange.jpg'
im2_fname = 'apple.jpg'
im1 = plt.imread(im1_fname)
if im1.mean() >= 1.0:
im1 = im1/255.
im2 = plt.imread(im2_fname)
if im2.mean() >= 1.0:
im2 = im2/255.
#if np.max(mask) > 1.0:
#... | rachelalbert/CS294-26_code | project3_code/part_3/main.py | Python | mit | 1,228 | [
"Gaussian"
] | f674934f3f69dbce498d65ebdb89854788007bec7304dd686b6e2dd15dc6c959 |
#
# @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 program is free software; you can redistribute it and/or modify
# it under the terms of ... | kratman/psi4public | psi4/driver/qcdb/basislistdunning.py | Python | gpl-2.0 | 33,130 | [
"Psi4"
] | 8d91daf59668f221a5abb29f39d8d871fb82e47b04018210a5581f4354e88988 |
# Copyright 2017 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... | ghchinoy/tensorflow | tensorflow/contrib/timeseries/python/timeseries/math_utils.py | Python | apache-2.0 | 44,149 | [
"Gaussian"
] | 096ebd10da8d41413a1b80ca84f934b82de377c47774b502e8afab9c2c638765 |
"""
Created on Jun 1, 2012
"""
__author__ = "Shyue Ping Ong, Stephen Dacek"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyue@mit.edu"
__date__ = "Jun 1, 2012"
import datetime
import glob
import os
import shutil
import unittest
from pyma... | materialsproject/custodian | custodian/vasp/tests/test_handlers.py | Python | mit | 39,371 | [
"VASP",
"pymatgen"
] | 9aa539823d1ebe9f7e02d05221f1ae3ddfd0507c1610e014502949bd95eaecf9 |
# To be run from the [TARGET] directory, or
# the parent directory with the multi_target option
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('--clean_dock_not_complex', action='store_true', \
default=False, \
help='Removes docking results if there is not an AMBER complex')
parser.add_argu... | CCBatIIT/AlGDock | Pipeline/count.py | Python | mit | 5,891 | [
"Amber"
] | 88c96b70e54ced34a8b82a72efdea35cd304db3e8a3effb01f5b4797dd9558ec |
#! /usr/bin/env python
# Test for the adapting exponential integrate and fire model according to
# Brette and Gerstner (2005) J. Neurophysiology.
# This script reproduces figure 2.C of the paper.
# Note that Brette&Gerstner give the value for b in nA.
# To be consistent with the other parameters in the equations, b mu... | gewaltig/cython-neuron | cynest/examples/brette-gerstner-fig-2c.py | Python | gpl-2.0 | 1,053 | [
"NEURON"
] | 246c3afa01819bd2009af548f1f6533dc0fb50f09f74d5e8cf38147df0319adb |
from ovito import *
from ovito.data import *
# The number of particles we are going to create.
num_particles = 3
# Create the particle position property.
pos_prop = ParticleProperty.create(ParticleProperty.Type.Position, num_particles)
pos_prop.marray[0] = (1.0, 1.5, 0.3)
pos_prop.marray[1] = (7.0, 4.2, 6.0)
pos_prop... | srinath-chakravarthy/ovito | tests/scripts/test_suite/create_new_particle_property.py | Python | gpl-3.0 | 1,892 | [
"OVITO"
] | 2660cb106368dd29ffb9b3fd3640e1ecc3a98b4163e9bdda10c908339b4a84e9 |
#!/usr/bin/env python
"""
Encapsulate the properties of a dwarf galaxy.
"""
import copy
from collections import OrderedDict as odict
import numpy as np
import logging
from dsphsim.velocity import GaussianVelocity
from dsphsim.velocity import PhysicalVelocity
from dsphsim.velocity import velocityFactory
from ugali.an... | kadrlica/dsphsim | dsphsim/dwarf.py | Python | mit | 3,600 | [
"Galaxy"
] | 290d8c925600f8ce4b3d9a1f7689998c3b06f5a069f15c19351dc9fa1800d0e5 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | skosukhin/spack | var/spack/repos/builtin/packages/redundans/package.py | Python | lgpl-2.1 | 2,428 | [
"BWA"
] | 1a427b21ee501b84a2b432b6554101bbdd110cd52c498791d31bec575884eb75 |
from plotly.basedatatypes import BaseTraceHierarchyType as _BaseTraceHierarchyType
import copy as _copy
class Marker(_BaseTraceHierarchyType):
# class properties
# --------------------
_parent_path_str = "splom"
_path_str = "splom.marker"
_valid_props = {
"autocolorscale",
"cauto"... | plotly/python-api | packages/python/plotly/plotly/graph_objs/splom/_marker.py | Python | mit | 55,063 | [
"Bowtie"
] | 52d1b81f133084c2c82025bb326b7c5d2b7e9af590b80244acb908ea9c368d51 |
# -*- coding: utf-8 -*-
# Copyright 2007-2022 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at y... | jat255/hyperspy | hyperspy/tests/model/test_fit_component.py | Python | gpl-3.0 | 5,756 | [
"Gaussian"
] | 90fde2e627a0fdd5ad7ec7b3817eebfb6b7d03fb85ce3218ca6ab52b2aec2a50 |
from __future__ import absolute_import, print_function
import numpy
import pandas as pd
from gtfspy.gtfs import GTFS
from .event import Event
from .heap import EventHeap
from .spreading_stop import SpreadingStop
class Spreader(object):
"""
Starting from a specific point and time, get complete single source
... | CxAalto/gtfspy | gtfspy/spreading/spreader.py | Python | mit | 7,465 | [
"VisIt"
] | f117dec824ac9ed18464c0df5be9a022dcfac902485afdd87f3aadb9d0f9c4c1 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright 2008-2009 Zuza Software Foundation
#
# This file is part of Pootle.
#
# 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... | lehmannro/pootle | pootle/settings.py | Python | gpl-2.0 | 8,584 | [
"VisIt"
] | b9d954c8fe7526dbf648d58b0ffcd4b7d3ced6dac6ef7424883ccd889b224c41 |
########################################################################
# $HeadURL$
# File : SiteDirector.py
# Author : A.T.
########################################################################
""" The Site Director is a simple agent performing pilot job submission to particular sites.
"""
try:
import has... | sposs/DIRAC | WorkloadManagementSystem/Agent/SiteDirector.py | Python | gpl-3.0 | 46,031 | [
"DIRAC"
] | 8f9e96cb21cc56476500a35930f8a57ee84705366a732a57801a67bc6871d858 |
#!/usr/bin/env python
# bsaseq_megamapper executer
# by Nikolaus Obholzer, Jan 2012
"""
usage: %prog [options]
-x, --galaxyDir=x: Galaxy root directory
"""
import sys, re, tempfile, subprocess
import os, shutil
from galaxy import eggs
from rpy import *
import pkg_resources; pkg_resources.require( "bx-python" )
fr... | maxplanck-ie/Megamapper | custom/hapmap_sd.py | Python | bsd-3-clause | 1,625 | [
"Galaxy"
] | b1fb444ed130382e23ef045fc3961fd4dcb60ec6070228632e42d176033562aa |
"""
Details of how the data model objects are mapped onto the relational database
are encapsulated here.
"""
import logging
import pkg_resources
from sqlalchemy import and_, asc, Boolean, Column, DateTime, desc, ForeignKey, Integer, MetaData, not_, Numeric, select, String, Table, TEXT, Unicode, UniqueConstraint
from ... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/model/mapping.py | Python | gpl-3.0 | 125,012 | [
"Galaxy"
] | e8227db2791e76abca77e874e8b921b7f08caddb454d25147c5f0bc5b12a69f0 |
""" JSON schema definitions for splice
* default schema:
the imageURI and enhancedImageURI are not re-used, Splice versions prior to
1.1.23 use this schema
* compact schema:
the imageURI and enhancedImageURI are re-used, a "URI id" to "URI" mapping
is stored in the "assets" property
"""
ISO_8061_patte... | ncloudioj/splice | splice/schemas.py | Python | mpl-2.0 | 6,921 | [
"VisIt"
] | 327da5e0acdecfe9db054d287935eb8b4b34ba9ebaf29feaab92a460323b824e |
"""
gmagoon 05/03/10: new class for MM4 parsing, based on mopacparser.py, which, in turn, is based on gaussianparser.py from cclib, described below:
cclib (http://cclib.sf.net) is (c) 2006, the cclib development team
and licensed under the LGPL (http://www.gnu.org/copyleft/lgpl.html).
"""
__revision__ = "$Revisi... | faribas/RMG-Java | source/cclib/parser/mm4parser.py | Python | mit | 11,929 | [
"Avogadro",
"cclib"
] | c0c93af2a1b51f3f6c2d3ccbf719475e33b17a0f5f264f03b5415eddc6eae87a |
#!/usr/bin/env python2.7
#
# ----------------------------------------------------------------------------------------------------
#
# Copyright (c) 2007, 2015, Oracle and/or its affiliates. All rights reserved.
# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
#
# This code is free software; you can redis... | dougxc/mx | mx_findbugs.py | Python | gpl-2.0 | 3,894 | [
"VisIt"
] | 2935208fedd6f7c727e36d44e2506e5ede6179354dc843e413663ba219faed73 |
from graph import *
class PathFinder:
"""
Class container for pathfinding solution.
"""
def __init__(self):
self.canPassHomeNodes = False
self.useCyclicBFS = False
# convert the complex Graph object to a simple dictionary to
# faciliate pathfinding without cycles
def _Grap... | kondrak/graph_bfs_solver | pathFinding.py | Python | mit | 3,973 | [
"VisIt"
] | 92f91209264c16a76b8fe1838d293c1e34b268c2a8b6e467486a787ae59f83b5 |
'''
TODO:
table for .fastq file locations
table for bowtie parameters
table for .bam/.sam files
table for cufflink parameters
table for cuffdiff parameters
'''
import sys
sys.path.append('C:/Users/dmccloskey-sbrg/Documents/GitHub/SBaaS_base')
from SBaaS_base.postgresql_settings import postgresql_settings
from SBaaS_b... | dmccloskey/SBaaS_rnasequencing | SBaaS_rnasequencing/main.py | Python | mit | 5,500 | [
"Bowtie"
] | 958a48c1e1cf83b8195071aea8b6c76210f13555b2d8a1f442e0f0c2db2c3308 |
import logging
import re
import cgi
from django.conf import settings
from django.contrib.sites.models import Site
from django.core.exceptions import ImproperlyConfigured
from django.shortcuts import redirect
from wiki.core.exceptions import NoRootURL
from wiki.models import URLPath, Article
from courseware.courses im... | abo-abo/edx-platform | lms/djangoapps/course_wiki/views.py | Python | agpl-3.0 | 4,581 | [
"VisIt"
] | 212f1f0802046c086a7245e05d45b7452ca0a9500dd726ae6d63a70aba77a2ee |
from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os
repository_name = 'freebayes_0010'
repository_description = "Galaxy's freebayes tool"
repository_long_description = "Long description of Galaxy's freebayes tool"
'''
1. Create repository freebayes_0020 and upload only the tool XML.
2. Upload the to... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py | Python | gpl-3.0 | 10,731 | [
"Galaxy"
] | d7e0e9628148fb7168440cdee69678ad5d53f1fcdd78d9b08f6c21b968733868 |
# coding=utf-8
# Copyright 2022 The Google Research 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 applicab... | google-research/google-research | light_field_neural_rendering/src/utils/model_utils.py | Python | apache-2.0 | 3,150 | [
"Gaussian"
] | 4f53078c4fada79b4689f17876c2204fb783625e142a4def7b2ffd7b01fa2ad2 |
from django.contrib.admin import SimpleListFilter
class BlastHitsFilter(SimpleListFilter):
title = 'BLAST hits'
parameter_name = 'hits'
def lookups(self, request, model_admin):
return (
('none', 'No hits'),
('some', 'Hits'),
)
def queryset(self, req... | eco32i/tweed | tasm/filters.py | Python | bsd-3-clause | 474 | [
"BLAST"
] | 221a3cd87f4a7e612249502f87c9a49aaf9ceb424ee60d82399abb37e5ffea5b |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | wscullin/spack | var/spack/repos/builtin/packages/psi4/package.py | Python | lgpl-2.1 | 4,595 | [
"Psi4"
] | 5e9aef6e8330d55d5bdaf80b8abf2b2d42eeb2d7882e922bc4144693724b391a |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.