text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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import sys
import cmd
from cmd import Shortcut, is_string, QuietException
from cmd import fb_module, fb_mask, fb_action,_raising
import copy
from pymol import _cmd
import string
def _feedback(module,mask,_self=cmd): # feedback query routine
# WARNING: internal routine, subject to change
if not hasattr(_self,... | gratefulfrog/lib | python/pymol/feedingback.py | Python | gpl-2.0 | 5,642 | [
"PyMOL"
] | c3920b6ae8ede8b24e1874d71ed3dab826320cdd9c4017a93290eab5e05dd4c4 |
# Copyright 2018 Mycroft AI Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writin... | MycroftAI/adapt | test/ContextManagerTest.py | Python | apache-2.0 | 4,606 | [
"Galaxy"
] | bc2044a0137e3eff7e772fb1dd8b91c74a838f9984dbd4b26d59ea9033d5ab9a |
##############################################################################
# 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... | lgarren/spack | var/spack/repos/builtin/packages/cdo/package.py | Python | lgpl-2.1 | 5,997 | [
"NetCDF"
] | b226835a3c7db67b46aeab597ca0ed059be948a2b447082fcecb22d395d14bf4 |
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Mathieu Blondel <mathieu@mblondel.org>
# Olivier Grisel <olivier.grisel@ensta.org>
# Andreas Mueller <amueller@ais.uni-bonn.de>
# License: BSD
from collections import Sequence
import warnings
import numbers
import numpy as np
imp... | lucidfrontier45/scikit-learn | sklearn/preprocessing.py | Python | bsd-3-clause | 41,723 | [
"Gaussian"
] | 30bb40606bfd1ca8fdf0b877667efd9285f3847a14c4735af3f8eba58b19636d |
#!/usr/bin/env python
# Standard packages
import os
import sys
import argparse
# Third-party packages
from toil.job import Job
# Package methods
from ddb import configuration
from ddb_ngsflow import gatk
from ddb_ngsflow import annotation
from ddb_ngsflow import pipeline
from ddb_ngsflow.align import bwa
from ddb_ng... | dgaston/ddb-ngsflow-scripts | specialist/workflow-myeloma_combined.py | Python | mit | 9,535 | [
"BWA"
] | 0dde017722607ee282b4767ff50caef2f8773b8fcd04f7d238cb2d9a204ed8fb |
#!/usr/bin/env python3
'''Take a prefix and model name run predictions, and generate evaluations for crystal, bestonly,
and all test sets (take max affinity; if pose score is available also consider
max pose score).
Generates graphs and overall CV results. Takes the prefix and (for now) assumes trial 0.
Will evalua... | gnina/scripts | affinity_search/evaluate.py | Python | bsd-3-clause | 9,170 | [
"CRYSTAL"
] | 7f16638c98bc484361b8e1d2f944cd859fe03a2fdac5f4a84dc49c3d5ceca975 |
#
# QAPI types generator
#
# Copyright IBM, Corp. 2011
#
# Authors:
# Anthony Liguori <aliguori@us.ibm.com>
#
# This work is licensed under the terms of the GNU GPLv2.
# See the COPYING.LIB file in the top-level directory.
from ordereddict import OrderedDict
from qapi import *
import sys
import os
import getopt
impor... | mithleshvrts/qemu-kvm-rhel6 | scripts/qapi-types.py | Python | gpl-2.0 | 7,111 | [
"VisIt"
] | 6a0b54b1070b631b6bca5e4e76a00720608f91d9fb7008f8929a05ad5cf13ba8 |
""" DIRAC.ResourceStatusSystem.DB package
"""
| ic-hep/DIRAC | src/DIRAC/ResourceStatusSystem/DB/__init__.py | Python | gpl-3.0 | 46 | [
"DIRAC"
] | 211bdb98fbdad458047255e5dbf67ed33191a64aa8d090edace2fda1faf112b1 |
from django.conf.urls import url, include
from django.views.decorators.cache import cache_page
from django.views.generic import TemplateView
from core import views
urlpatterns = [
# public urls
url(r'^(?P<lang>\w{2})/$',
# Default URL shown on first visit after install
views.initial_edit_view... | adfinis-sygroup/freedomvote | app/core/urls.py | Python | gpl-3.0 | 3,882 | [
"VisIt"
] | 8a240b61cac50ef89c61b3572d077399506bc23ddf6eb4b7115154d468391e71 |
# -*- coding: utf8 -*-
# $Id: __init__.py 6348 2010-06-28 22:08:05Z milde $
# Author: Engelbert Gruber <grubert@users.sourceforge.net>
# Copyright: This module has been placed in the public domain.
"""LaTeX2e document tree Writer."""
__docformat__ = 'reStructuredText'
# code contributions from several people include... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/eggs/docutils-0.7-py2.7.egg/docutils/writers/latex2e/__init__.py | Python | gpl-3.0 | 111,472 | [
"VisIt"
] | 018d30bdd447c55aecb40f6b5aab4b4833a6ade9aa89028896766a8314490bbe |
#!/usr/bin/env python
"""Resort a BAM file karyotypically to match GATK's preferred file order.
Broad's GATK and associated resources prefer BAM files sorted as:
chr1, chr2... chr10, chr11... chrX
instead of the simple alphabetic sort:
chr1, chr10, chr2 ...
This takes a sorted BAM files with an alternative... | Cyberbio-Lab/bcbio-nextgen | scripts/utils/resort_bam_karyotype.py | Python | mit | 3,542 | [
"pysam"
] | 75098739fbf54e77a4905720deb5618c8094814d1e4ab5e5a541c0ff9b397c07 |
import multiprocessing
import platform
import subprocess
import sys
import os
from conans.client.tools.env import environment_append
from conans.errors import ConanException
from conans.model.version import Version
from conans.util.log import logger
from conans.client.tools import which
_global_output = None
def a... | luckielordie/conan | conans/client/tools/oss.py | Python | mit | 13,531 | [
"Jaguar"
] | d007a4128b89cddcf5e8b5304b9a646a670000980cd25275da3be69b32d4c0e4 |
# coding: utf-8
#
# Copyright (C) 2016 Savoir-faire Linux Inc. (<www.savoirfairelinux.com>).
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by the Free Software Foundation, either version 3 of the
# Licens... | sfl-drupal/drupalizer | helpers.py | Python | gpl-3.0 | 7,624 | [
"VisIt"
] | 7b5e4c4bae5a4d6b2c127449f8968529676583b1f808c97283ad4ae873d32702 |
#!/usr/bin/env python
#
# PdbConverter.py
#
# Supports conversion between old and new pdb files
# - ribose descriptor (* <---> ')
# - phosphate group nomenclature (O1P, O2P, O3P <---> OP1, OP2, OP3)
# - residue name position (18 <---> 19 <---> 20)
# - residue flag (ATOM <---> HETATM <---> ATOM/HETATM)
#
# Converion ca... | mmagnus/rna-pdb-tools | rna_tools/tools/mini_moderna3/moderna/PdbConverter.py | Python | gpl-3.0 | 9,166 | [
"Biopython"
] | c1c5eb11a6a56726552156dd5ff80ff7e82ff4a0f683956620ba12e402bf15da |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=80 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# -------------------------------------------------------... | marmyshev/transitions | openlp/plugins/songs/lib/test/test_importing_lots.py | Python | gpl-2.0 | 3,268 | [
"Brian"
] | d544006fba8c31027f970270270d945ce38d7b3648a3d01125772374a185f8d0 |
import os, stat, sys, socket, threading, time, subprocess
from copy import copy
import config, recordfilehandler, cmdlineutils
import commandlinetraffic, fileedittraffic, clientservertraffic, customtraffic
from SocketServer import TCPServer, StreamRequestHandler
try:
from xmlrpclib import Fault, ServerProxy
fr... | emilybache/texttest-runner | src/main/python/lib/capturemock/server.py | Python | mit | 21,906 | [
"Brian"
] | 28eb0b7c4d94a65c82c47c0acfa1f8ee60735a5989f4b3216154fb94f92a1762 |
import warnings
warnings.warn("Bio.expressions was deprecated, as it does not work with recent versions of mxTextTools. If you want to continue to use this module, please get in contact with the Biopython developers at biopython-dev@biopython.org to avoid permanent removal of this module from Biopython", DeprecationWar... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/expressions/blast/wublast.py | Python | apache-2.0 | 15,611 | [
"BLAST",
"Biopython"
] | e54284866be1c4326d440ad7841c95c4f14b8cb9e1a954b9b4c952297e121f0f |
# vim: set expandtab shiftwidth=2 softtabstop=2:
# test_cmd
# based on the python3 unittest boilerplate code
# https://docs.python.org/3.5/library/test.html
#
import unittest
# This might be a bit evil but we need it for now
import sys, os, re
sys.path.insert(0, "../TEMPy")
from TEMPy.StructureParser import P... | OniDaito/ChimeraXTempy | test/test_cmd.py | Python | mit | 13,832 | [
"ChimeraX",
"Gaussian"
] | f81f10e33cdf236402740bcc35f09a421378f6fb32e606edb716a3c7f794bef4 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
###########################################################################
# #
# ESPResSo++ Python script for tabulated GROMACS simulation #
# ... | acfogarty/espressopp | examples/water_gromacs/water.py | Python | gpl-3.0 | 6,266 | [
"ESPResSo",
"Gromacs"
] | b8b1a8a3605c5130ac0a758e54cfef9bde6e569bf878ef9713c52a721a200883 |
#!/usr/bin/env python
"""Converts an EFP potential to the corresponding
Polarizable Embedding potential
"""
import sys
import fileinput
import numpy
def labelize(label):
"""the goal here is to split the label into more
sensible parts (count and atom label)
"""
idx = int(label[1:3])
symbol = l... | cstein/dalton-scripts | scripts/efp2pot.py | Python | bsd-2-clause | 6,622 | [
"GAMESS"
] | cd31aa1b0d8bcc34c24ee7e115b3006be66cdfd4a60bc803b7b3af93eaf3b277 |
from math import sqrt
import gtk
from gettext import gettext as _
from ase.gui.widgets import pack, Help
class Constraints(gtk.Window):
def __init__(self, gui):
gtk.Window.__init__(self)
self.set_title(_('Constraints'))
vbox = gtk.VBox()
b = pack(vbox, [gtk.Button(_('Constrain'))... | grhawk/ASE | tools/ase/gui/constraints.py | Python | gpl-2.0 | 1,497 | [
"ASE"
] | 6c3d272a649629a773b3d6cbe3a23dfdf7a292661c3f59aead8fcb7acd3c8d8e |
# 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... | LUTAN/tensorflow | tensorflow/contrib/distributions/python/ops/distribution.py | Python | apache-2.0 | 38,444 | [
"Gaussian"
] | 568612001044407bf34e5221e6dacb3e44c19b4c4aa797e2db5df26627f25fbe |
# This is the translator that converts Tcl test to python.
# Not all Tcl test are translatable.
# To ensure that a test can be translated :
# 1) do not use Tcl arrays
# 2) do not use string substitution except in variable names
# eg. obj${i} GetOutput is okay
# obj12 GetOutputAs${i} is not okay.
# 3) do not ... | 151706061/activizdotnet | Testing/TclToCsScript/vtkTclToCsConvertor.py | Python | bsd-3-clause | 78,758 | [
"VTK"
] | 3ee25e1456fc26fd13b852e9c6ac236ea4ccd24b52c346e7bace81aeb9317245 |
'''
SCRNA.py is a module file for single cell RNA seq analysis functions.
Functions
---------
Classes
-------
SingleCell: object
This is the principle object in this module. It holds single cell
expression data in multiple forms, transform data, performs analysis
and plots data and results.
TODO:
* wrapper for BA... | MikeDMorgan/scRNAseq | SCRNA.py | Python | mit | 23,697 | [
"ASE",
"Avogadro",
"Bioconductor"
] | 6d12bd76606dc0acf457e0c64944f00ea3e7c75cccec3fb4e630e40e9560af43 |
#! /usr/bin/env python3
# -*- coding: utf-8 -*-
# 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 requi... | sasha-gitg/python-aiplatform | schema/predict/prediction/scripts/fixup_prediction_v1beta1_keywords.py | Python | apache-2.0 | 5,910 | [
"VisIt"
] | ee48bd5d15166a801707470d8e69438e72c1016d89546d9380492194054dfab0 |
#! /usr/bin/python3
entero=10 # numero entero
flotante=10.0 # numero decimal
cadena="Ola Ke ase, pythoneando o ke ase" # una cadena
Booleano=True # un simple booleano
complejo=3+2j # numero complejo
caracter = "a"
print("Este es un valor entero [ %f ] " % entero)
print("Este es un valor flotante [ %d ]" % flotante)
pri... | IntelBUAP/Python3 | codigo9.py | Python | gpl-2.0 | 536 | [
"ASE"
] | 0d249cca7c62b54529509de89796adaf0b5eeabdc70b9955b1ddca108f86ab8d |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 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/utils/databaseform.py | Python | gpl-2.0 | 1,786 | [
"VisIt"
] | abbf488d4a04217cf77865d47c311c8e241bd7fd510d98bdb9a6c4ec983f1b60 |
import pytest
from bricolage.neighbourhood import NetworkNeighbourhood, Collection, \
PopulationNeighbourhood
from bricolage import threshold3, logic2
import numpy as np
# from bricolage.frames import get_population_neighbourhood_fitness
from generate import get_database
np.set_printoptions(linewidth=150)
@pytes... | brettc/bricolage | tests/test_neighbourhood.py | Python | gpl-3.0 | 2,620 | [
"Bowtie"
] | 4d4ff664ccd6578828cd2afff1c3cb3f42bfaed81654b4247b922f2ff8738df3 |
from numpy.random import seed
from scikits.learn.machine.em import GM, GMM, EM
import copy
# To reproduce results, fix the random seed
seed(1)
#+++++++++++++++++++++++++++++
# Meta parameters of the model
# - k: Number of components
# - d: dimension of each Gaussian
# - mode: Mode of covariance matrix: full or... | jhmadhav/pynopticon | src/em/examples/basic_example2.py | Python | gpl-3.0 | 1,355 | [
"Gaussian"
] | c6b9c45e42ef7324843e6d9abda6ab030f64f2ed4fad92a5b0ee5c32936961ca |
"""Rewrite assertion AST to produce nice error messages"""
from __future__ import absolute_import, division, print_function
import ast
import errno
import itertools
import imp
import marshal
import os
import re
import six
import struct
import sys
import types
import atomicwrites
import py
from _pytest.assertion impor... | UK992/servo | tests/wpt/web-platform-tests/tools/third_party/pytest/src/_pytest/assertion/rewrite.py | Python | mpl-2.0 | 35,779 | [
"VisIt"
] | 956f107f89689ac7a8c8c6ac8a5e65fe2c72bfc2a32cb1fbee1dd422c523b239 |
"""
Test topological fingerprints.
"""
import unittest
from rdkit import Chem
from vs_utils.features import fingerprints as fp
class TestCircularFingerprint(unittest.TestCase):
"""
Tests for CircularFingerprint.
"""
def setUp(self):
"""
Set up tests.
"""
smiles = 'CC(... | rbharath/vs-utils | vs_utils/features/tests/test_fingerprints.py | Python | gpl-3.0 | 1,544 | [
"RDKit"
] | 330733a704e369410dbb0d4904c6baeb42eff12d0f0776e4c89ec87fd737d5fd |
# pylint: disable=missing-docstring
import urllib
from lettuce import world
from django.contrib.auth.models import User
from student.models import CourseEnrollment
from xmodule.modulestore.django import modulestore, clear_existing_modulestores
from xmodule.contentstore.django import _CONTENTSTORE
@world.absorb
def c... | solashirai/edx-platform | common/djangoapps/terrain/course_helpers.py | Python | agpl-3.0 | 2,482 | [
"VisIt"
] | 285e65bacdbc8c0af7ccd81cfc12036fefedf5ddf941a6f37e5eeedb71d0f86e |
"""
Course Outline page in Studio.
"""
import datetime
from bok_choy.page_object import PageObject
from bok_choy.promise import EmptyPromise
from selenium.webdriver.support.ui import Select
from selenium.webdriver.common.keys import Keys
from selenium.webdriver.common.action_chains import ActionChains
from .course_p... | eestay/edx-platform | common/test/acceptance/pages/studio/overview.py | Python | agpl-3.0 | 23,729 | [
"VisIt"
] | 98381818044348ce023d12dd3d3eb9c9266a08e73551cf8bbc72b3b7878ef146 |
# - make our own window control for colour-sequence bar
# - this should also have separate (?) line with HSV colour vertices
# - on this line, there should be vertical lines indicating the current
# position of all the opacity transfer function vertices
# - abstract floatcanvas-derived linear function editor into wx_... | chrisidefix/devide | modules/viewers/TransferFunctionEditor.py | Python | bsd-3-clause | 10,762 | [
"VTK"
] | 9552155fd2d158888b0af4b80e8a5b45588ed4b86725d78b839a20a50a640f4d |
from datetime import datetime, timedelta, tzinfo
from registry.models import Passport, Visit
from registry.extensions import db
class TZ(tzinfo):
def utcoffset(self, dt):
return timedelta(hours=1)
def tzname(self, dt):
return "tz"
def dst(self, dt):
return timedelta(0)
tz = TZ(... | arsgeografica/kinderstadt-registry | test/unit/test_chart.py | Python | gpl-3.0 | 2,671 | [
"VisIt"
] | 4921c6b6f60112f4fe9e4de4eaf39d7757282e82f261f6110ebd79f5ea53a40a |
"""This file contains code used in "Think Bayes",
by Allen B. Downey, available from greenteapress.com
Copyright 2012 Allen B. Downey
License: GNU GPLv3 http://www.gnu.org/licenses/gpl.html
"""
import math
import numpy
import cPickle
import numpy
import random
import scipy
import brfss
import thinkplot
import think... | jtrussell/think-bayes-workspace | src/vendor/AllenDowney/variability.py | Python | mit | 13,533 | [
"Gaussian"
] | 208cdbd61c0b9da79adf8879416a6924f503988fbbc4d45b9f3ebf239ab5a8f6 |
#!/usr/bin/python3
# -*- coding: utf-8 -*-
#
#
# Copyright (C) 2015 Bitergia
#
# 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 ve... | sanacl/GrimoireELK | grimoire/elk/discourse.py | Python | gpl-3.0 | 4,026 | [
"Elk"
] | 73fe74c2a0fcf5bb5b79caeae1689e99ad23e5a4fd7502c0a1f451ca484f06dd |
#!/usr/bin/env python
# coding=utf-8
#
# Copyright (c) 2013 Sean Dawson. All rights reserved.
#
# This file is released under the MIT License:
# http://www.opensource.org/licenses/mit-license.php
def dot_product(row, column):
"""Dot product between two vectors.
>>> dot_product([1,2,3], [4,5,6])
32
>... | seanpile/math.py | matrix.py | Python | mit | 18,970 | [
"Gaussian"
] | 28de6b69e34a242c8411b0b6180e907f878dc96aae538435f2d9806cd5ede950 |
# Text formatting abstractions
# Note -- this module is obsolete, it's too slow anyway
# Oft-used type object
Int = type(0)
# Represent a paragraph. This is a list of words with associated
# font and size information, plus indents and justification for the
# entire paragraph.
# Once the words have been added to a... | atmark-techno/atmark-dist | user/python/Lib/lib-old/Para.py | Python | gpl-2.0 | 10,064 | [
"VisIt"
] | 2f724cd41620b3a7fb86f88f37915258df477699c7a2254adbf9a2a81f91092d |
from Tkinter import *
import subprocess
def hello():
print('hello')
def about():
w = Label(root,text="The developer\nfuyunbiyi\nfyby website\nhttp:// www.")
w.pack(side=TOP)
def installMin():
w = Label(root,text="The meanings of these options:\nMin: Install LAMMPS with package MEAM and REAX\nAll... | Rareson/LammpsRelated | misc/oldStuff/aboutGUI/guiV.1.0.0.py | Python | gpl-3.0 | 1,742 | [
"LAMMPS"
] | 28a36d49986a47fd10ac778e61b72421453b5199138e1ada35e52ed464686fb6 |
"""Python support code for JavaScript based widgets.
Authors:
* Brian Granger
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2008-2012 The IPython Development Team
#
# Distributed under the terms of the BSD License. The full license is in
# the file COPYING, d... | cloud9ers/gurumate | environment/share/doc/ipython/examples/widgets/directview/widget.py | Python | lgpl-3.0 | 1,639 | [
"Brian"
] | fd70e8cb1b4f52397f52ff88d7efe74ce4f61a8547b5f7bad15454266bcb2a7f |
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at https://mozilla.org/MPL/2.0/.
from functools import partial
from subprocess import CompletedProcess
import logging
import numpy as np
from sisl.io i... | zerothi/sisl | toolbox/siesta/minimizer/_minimize_siesta.py | Python | mpl-2.0 | 7,798 | [
"SIESTA"
] | bc2c2b4c770b4e46ea81e511820435cc64bfa87c602aeb4a0e5677a0bc3b7ed5 |
"""
Cost layers.
TODO: write more documentation
"""
__docformat__ = 'restructedtext en'
__authors__ = ("Razvan Pascanu "
"KyungHyun Cho "
"Caglar Gulcehre ")
__contact__ = "Razvan Pascanu <r.pascanu@gmail>"
import numpy
import copy
import theano
import theano.tensor as TT
from theano.sa... | ChristosChristofidis/GroundHog | groundhog/layers/cost_layers.py | Python | bsd-3-clause | 43,769 | [
"Gaussian"
] | 5fe5b8c14048248109739e3167065c987f129e05abb1b9833222bf2f5b5a0b0d |
# Docstrings for generated ufuncs
#
# The syntax is designed to look like the function add_newdoc is being
# called from numpy.lib, but in this file add_newdoc puts the
# docstrings in a dictionary. This dictionary is used in
# generate_ufuncs.py to generate the docstrings for the ufuncs in
# scipy.special at the C lev... | sriki18/scipy | scipy/special/add_newdocs.py | Python | bsd-3-clause | 141,444 | [
"Gaussian"
] | 48c94d7d213d1921e6dd2c803990ea52aee80dffaaf9faee708cae4a3fea4376 |
#!/usr/bin/python
#Icefilms.info v1.1.0 - Eldorado
#All code Copyleft (GNU GPL v2) Eldorado and icefilms-xbmc team
############### Imports ############################
#standard module imports
import sys,os
import time,re
import urllib,urllib2,base64
import random
import copy
import threading
import st... | aplicatii-romanesti/allinclusive-kodi-pi | .kodi/addons/plugin.video.icefilms/default.py | Python | apache-2.0 | 135,740 | [
"VisIt"
] | 597e6dcc9bdb428bf2bb6572c4df17b4010e242010ccc84b052f410f64706b0b |
# produces the probability distribution as a sum of three independent
# pdfs
from shapely.geometry import MultiLineString
from shapely.geometry import Point
from shapely.geometry import LineString
import scipy.special as sp
import scipy.stats as st
import numpy as np
from math import *
import sphere as sph
def rd(x... | chebi/prob | mk_prob.py | Python | mit | 3,200 | [
"Gaussian"
] | a02da28bb2e498875a74b3114892e5f1208919034542df735d65663c694ea03c |
# -*- coding: utf-8 -*-
"""Types for PyBEL."""
from typing import Iterable, Mapping, Union
__all__ = [
"Strings",
"EdgeData",
]
Strings = Union[str, Iterable[str]]
EdgeData = Mapping
| pybel/pybel | src/pybel/typing.py | Python | mit | 196 | [
"Pybel"
] | 1a5375f98f43987aff18641e0775bd48a4d485b47fe0294c3e6bff69fa46654d |
RSA = {
"name": "South Africa",
"topLevelDomain": [".za"],
"alpha2Code": "ZA",
"alpha3Code": "ZAF",
"callingCodes": ["27"],
"capital": "Pretoria",
"altSpellings": ["ZA", "RSA", "Suid-Afrika", "Republic of South Africa"],
"region": "Africa",
"subregion": "Southern Africa",
"popula... | SteinRobert/python-restcountries | restcountries/tests/countries_data.py | Python | unlicense | 7,990 | [
"BWA"
] | 5b988c1cdc6c10ead0cc352b79e6589b8b1d0281ddef43a1a2f4209d65463b54 |
#!/usr/bin/env python
# Try to determine how much RAM is currently being used per program.
# Note per _program_, not per process. So for example this script
# will report RAM used by all httpd process together. In detail it reports:
# sum(private RAM for program processes) + sum(Shared RAM for program processes)
# The... | murphydavis/dotfiles | bin/ps-mem.py | Python | mit | 12,467 | [
"Brian"
] | f67d1ff340fb03e7b73be993f05520696d4dc072b4cd63ed801edefaddf1c59a |
# Copyright 2001 by Tarjei Mikkelsen. 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.
# python unittest framework
import unittest
# modules to be tested
from Bio.Pathway import... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_Pathway.py | Python | gpl-2.0 | 7,522 | [
"Biopython"
] | ee8b733ddb7007419a394dc83ca117144bbad8aed21b73a82da24c2aa1b6b19b |
import numpy as np
def read_vtk(filename):
with open(filename) as vtk:
pts, polys = None, None
line = vtk.readline()
while len(line) > 0 and (pts is None or polys is None):
if line.startswith("POINTS"):
_, n, dtype = line.split()
data = vtk.readline().split()
n = int(n)
nel = n*3
while le... | CVML/pycortex | cortex/formats_old.py | Python | bsd-2-clause | 720 | [
"VTK"
] | 217e87bff2d38b6799b37afecc541aaab4b0d874d07f239677bb2ee54eb3f050 |
#!/usr/bin/env python
# -*- coding:utf-8 mode:python; tab-width:4; indent-tabs-mode:nil; py-indent-offset:4 -*-
##
import sqlite3
import re
import sys
import os
import json
import time
def install_with_pip(name):
ins = False
d = {'y': True,
'n': False}
while True:
choice = raw_input('Do... | mattbernst/ebsel | src/EMSL_dump.py | Python | mit | 22,127 | [
"Dalton",
"GAMESS",
"Hyperchem",
"MOLCAS",
"Molpro",
"NWChem",
"TURBOMOLE",
"deMon2k"
] | c295eee47a488bab70e8118bbd5138aacab92d44aac5282a89393f8f44ffb0b4 |
#
# Copyright (C) University College London, 2007-2012, all rights reserved.
#
# This file is part of HemeLB and is provided to you under the terms of
# the GNU LGPL. Please see LICENSE in the top level directory for full
# details.
#
import os.path
import sys
import platform
import re
import numpy
import vtk
try:... | jenshnielsen/hemelb | Tools/setuptool/setup.py | Python | lgpl-3.0 | 7,307 | [
"VTK"
] | 8842803eff5850c999577ea94aec4f83881083e9dbaef72a5420f09060f3c195 |
# ----------------------------------------------------------------------
# Copyright (c) 2016, The Regents of the University of California All
# rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# ... | drichmond/tinker | python/MemoryType.py | Python | bsd-3-clause | 5,128 | [
"TINKER"
] | 8675fa1f88f4250f7f4b5670935526936cb465b8d06234f4be54b32f3798acfa |
import rasterio
import os
import numpy as np
import matplotlib.pyplot as plt
def flat(input_dem, output_dem, elevation):
# Open dem_flat to read in info
dem_flat_in = rasterio.open(input_dem)
dem = dem_flat_in.read(1)
###### Create flat dem
dem_flat = np.array(dem, copy=True, dtype=np.float64)... | Chrismarsh/mesher | examples/data/makedata.py | Python | gpl-3.0 | 4,543 | [
"Gaussian"
] | d8346451502721d26837994569046bcdf0d03483ecc2d01b39cffc33e244d29b |
import numpy as np
from collections import defaultdict
from .base import State, StateStructure, StaticState
import itertools
class IsingState(State):
def __init__(self, spin_list, name='ising'):
"""
:param spin_list: list, 0 and 1's indicating spin
:param name: string, a name string for th... | materialsvirtuallab/veidt | veidt/monte_carlo/state.py | Python | bsd-3-clause | 5,540 | [
"pymatgen"
] | 8685d0a26897d90693c01e0468be58f3f016811662c33aabf109fb5f42bbf684 |
import xml.dom.minidom
from PyQt5 import QtWidgets, QtCore, QtGui
from functions import button_functions
from ui.Ui_aboutwindow import Ui_aboutWindow
import logging
def create_eufar_xml(self, out_file_name):
logging.debug('eufar_metadata_xml.py - create_eufar_xml - starting...')
NAMESPACE_URI1 = "http://www.i... | eufarn7sp/emc-eufar | functions/eufar_metadata_xml.py | Python | bsd-3-clause | 63,144 | [
"NetCDF"
] | cd3a4f0669e3fdbe2c744d008336274aea98420a5504c7e0ae9d95be88fc06eb |
"""
Stack-In-A-WSGI: stackinawsgi.session.service.StackInAWsgiSessionManager
"""
import unittest
import uuid
from stackinabox.services.service import StackInABoxService
from stackinabox.services.hello import HelloService
from stackinawsgi.exceptions import (
InvalidSessionId
)
from stackinawsgi.session.service i... | TestInABox/stackInAWSGI | stackinawsgi/test/test_session_service.py | Python | apache-2.0 | 7,549 | [
"COLUMBUS"
] | 0b7dc09c5aae5f52208fbe0b87e84a57c10f1c641db261740d5d437e574c65c0 |
# Johnny Nguyen
# Combinatorial Optimization Project for CSC 499
# Under the tutelage of Dr. Franc Brglez
# And collaboration with Yang Ho
from itertools import imap
import B.coord
import time
import sys
import os
import pwd
import platform
import random
import util
import core
from config import *
import math
def ma... | fbrglez/gitBed | xProj/B.lightp/pLib/B/lightp.py | Python | gpl-2.0 | 63,066 | [
"VisIt"
] | d16f4b13eed3de7dea9a394338236893aa9e993abc4688c1e3dd8ed2b4a2e417 |
import os
import pytest
import sys
def compile_neuron_mod_dir(pkg_dir):
try:
print('Compiling {}'.format(pkg_dir))
os.system('nrnivmodl {}'.format(pkg_dir))
from neuron import load_mechanisms
load_mechanisms(pkg_dir)
print(' Compilation of support folder mod files successful... | Neurosim-lab/netpyne | tests/examples/utils.py | Python | mit | 840 | [
"NEURON"
] | a3f0c28f99203e396ebc35a64850e45e09decfab9387c8f664ddc2019a003bed |
"""
This is the handler file for installing, activating and updating services. This should only ever be called from core.
"""
import json
from os.path import isfile, join
from typing import Dict
from Firefly import logging
from Firefly.core.const import SERVICE_PACKAGE_FILE, SERVICE_CONFIG_DIR
"""
ServiceConfig is... | Firefly-Automation/Firefly | Firefly/core/service_handler.py | Python | apache-2.0 | 9,762 | [
"Firefly"
] | af18556dfec70545c35198d6c5e39d029d417ad6de8017a7f68fe6160caab7aa |
"""
FEniCS program for the deflection w(x,y) of a membrane:
-Laplace(w) = p = Gaussian function, in a unit circle,
with w = 0 on the boundary.
"""
from dolfin import *
import numpy
if not has_cgal():
import sys
sys.exit(0)
# Set pressure function:
T = 10.0 # tension
A = 1.0 # pressure amplitude
R = 0.3 ... | akshmakov/Dolfin-Fijee-Fork | test/unit/book/python/chapter_1_files/stationary/poisson/membrane1.py | Python | lgpl-3.0 | 2,170 | [
"Gaussian"
] | 7dc3ec8d5e157803c6152a526049428b1dd82dda7c8f9cd2103778529d43ba60 |
from django.shortcuts import render
# Create your views here.
import logging
from django.contrib.auth.decorators import login_required
from django.shortcuts import render
from cenet.models import Neuron, SynapticConn, CENetwork
from cenet.views import ids_phar
from django.db.models import Q
from django.http import Htt... | Si-elegans/Web-based_GUI_Tools | worm_conf/views.py | Python | apache-2.0 | 9,430 | [
"NEURON"
] | 9aed6bbd9d36fb6f7e8030002d8035d1ae10c65b8889368f4804319bec2035bf |
# -*- coding: utf-8 -*-
"""
Output Plugin for Coding Technology MP4 encoder.
Copyright (c) 2006-2008 by Nyaochi
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the Licen... | rinrinne/cueproc-alternative | src/ce_ctmp4.py | Python | gpl-2.0 | 3,659 | [
"VisIt"
] | 9a1fc9938ceea55ab36e78ca8c022980d360ebd8108b72f993c3bc2775c71c2d |
# Copyright 2008-2015 Nokia Solutions and Networks
#
# 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 l... | snyderr/robotframework | src/robot/model/stats.py | Python | apache-2.0 | 6,552 | [
"VisIt"
] | 710d0406c692e18170e8f2ff3265be2c23b6bad202ae522507115ad7c9edd395 |
#!/usr/bin/env python2
#
# Copyright 2001 - 2017 Ludek Smid [http://www.ospace.net/]
#
# This file is part of Outer Space.
#
# Outer Space is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 ... | ospaceteam/outerspace | tests/ai_observer.py | Python | gpl-2.0 | 3,295 | [
"Galaxy"
] | ec790921b128154bdcb987c368adfcbc87eeb732bb29c69aa6fce5cfd5ee533e |
# $Id$
#
# Copyright (c) 2009, Novartis Institutes for BioMedical Research Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above... | AlexanderSavelyev/rdkit | rdkit/Chem/BRICS.py | Python | bsd-3-clause | 30,884 | [
"RDKit"
] | 7ba6e73ea70f2956e70a22397768a8b458d54b7ac5b147b0df5c2bc98b3d463c |
# ========================================================================
#
# Imports
#
# ========================================================================
import numpy as np
# ========================================================================
#
# Function definitions
#
# ================================... | marchdf/dg1d | dg1d/dg.py | Python | apache-2.0 | 3,217 | [
"Gaussian"
] | 887b3ffef30af0a6b61d0a5802e063dce0c1b02584c90feb12adcf3795d2e12d |
"""
cante100 Loader
.. admonition:: Dataset Info
:class: dropdown
The cante100 dataset contains 100 tracks taken from the COFLA corpus. We defined 10 style
families of which 10 tracks each are included. Apart from the style family, we manually
annotated the sections of the track in which the vocals ar... | mir-dataset-loaders/mirdata | mirdata/datasets/cante100.py | Python | bsd-3-clause | 13,954 | [
"VisIt"
] | 0120774b187ed55443bc951bddacb23a2ee12ee15ce3afc2ea263ec7066742fe |
# Copyright (C) 2017
# Gregor Deichmann (TU Darmstadt, deichmann(at)cpc.tu-darmstadt.de)
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either ve... | govarguz/espressopp | src/io/DumpXTC.py | Python | gpl-3.0 | 3,604 | [
"ESPResSo",
"GROMOS",
"Gromacs"
] | ce3e74a70aeaf5672792a808e8faad80445d7ae87ebf5239e27f62838eab141f |
# ################################################################
#
# Active Particles on Curved Spaces (APCS)
#
# Author: Silke Henkes
#
# ICSMB, Department of Physics
# University of Aberdeen
# Author: Rastko Sknepnek
#
# Division of Physics
# School of Engineering, Physics and Mathem... | sknepneklab/SAMoS | analysis/batch_nematic/batch_analyze_nematic_long5_d.py | Python | gpl-3.0 | 2,577 | [
"VTK"
] | 5cf3be7dc120cd2b3d4c0a752b91d115bfd192a008647a30674b0f42039799eb |
# -*- coding: utf-8 -*-
"""
Bok choy acceptance tests for problems in the LMS
"""
from __future__ import absolute_import
from textwrap import dedent
import time
import ddt
from common.test.acceptance.fixtures.course import CourseFixture, XBlockFixtureDesc
from common.test.acceptance.pages.common.auto_auth import AutoA... | jolyonb/edx-platform | common/test/acceptance/tests/lms/test_lms_problems.py | Python | agpl-3.0 | 46,261 | [
"VisIt"
] | dbba19d93fc48d84104d0cf524769134074b765d11dcc94d95bdbd9dd19241ad |
import os
import ase
from dftd_interface import d3_pbc as dftd3
from dftd_interface import d2_pbc as dftd2
import numpy
print 'single cell'
system = ase.read('./test/POSCAR5', format='vasp')
c, d = dftd3(system ,'pbe')
print repr(c)
print d
print 'mupltiple cell'
system = ase.read('./test/POSCAR6', format='vasp')
c, ... | alexei-matveev/ase-local | ase/dftd/test_dftd.py | Python | gpl-2.0 | 456 | [
"ASE",
"VASP"
] | 3ddf31d62a418c02e7964408bb3a5302fde1ee5a895679461c2ba601fff034e2 |
from __future__ import division
from builtins import range
from builtins import object
import numpy as np
from scipy.spatial import cKDTree as KDTree
from numba import jit
class Invdisttree(object):
"""inverse-distance-weighted interpolation using KDTree:
Copied from http://stackoverflow.com/questions/310478... | pycomlink/pycomlink | pycomlink/spatial/idw.py | Python | bsd-3-clause | 5,437 | [
"Gaussian"
] | e8515900f0307528ba827a324c2370b7a7dde999f9e72238da5c576c83a586e3 |
# -*- coding: utf-8 -*-
from __future__ import print_function, division, absolute_import
import llvm
from numba import *
from numba import nodes
from numba.typesystem import is_obj, promote_to_native
from numba.codegen.codeutils import llvm_alloca, if_badval
from numba.codegen import debug
class ObjectCoercer(object... | shiquanwang/numba | numba/codegen/coerce.py | Python | bsd-2-clause | 8,887 | [
"VisIt"
] | 10c6b38e54164d3e52d4d02059739d6aca211e186c20c038188b2248751cc994 |
# Copyright 2018 Google LLC. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... | PAIR-code/interpretability | text-dream/python/helpers/activation_helper.py | Python | apache-2.0 | 6,274 | [
"NEURON"
] | 739c64f2e948481a2e382b4f418da7dd1d7d6c1c5d7f7cbb0dba8526e7b38995 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
"""
This module provides classes to comparsion the structures of the two
molecule. As long as the two molecule have the same bond connection tables,
the molecules are de... | sonium0/pymatgen | pymatgen/analysis/molecule_structure_comparator.py | Python | mit | 7,957 | [
"Dalton",
"pymatgen"
] | dc5b4c9d5a9f5002dd1dc3dda6eb42aaa8fc065b26fa833fc512b4c26d00f3e3 |
from gpaw.mpi import world
from gpaw.blacs import BlacsGrid, Redistributor
if world.size < 2:
raise ValueError('Runs on two or more processors')
grid = BlacsGrid(world, 2, world.size // 2)
desc = grid.new_descriptor(12, 8, 2, 3)
a = desc.zeros()
a[:] = world.rank
subdesc = grid.new_descriptor(7, 7, 2, 2)
b = s... | robwarm/gpaw-symm | gpaw/test/parallel/submatrix_redist.py | Python | gpl-3.0 | 678 | [
"GPAW"
] | c475e40434cffe66011af4151cd89014dfa9401bce29da2e2779c15532120c99 |
# This is a very simple implementation of the UCT Monte Carlo Tree Search algorithm in Python 2.7.
# The function UCT(rootstate, itermax, verbose = False) is towards the bottom of the code.
# It aims to have the clearest and simplest possible code, and for the sake of clarity, the code
# is orders of magnitude less... | rfrerebe/MCTS | python/python.py | Python | gpl-2.0 | 16,150 | [
"VisIt"
] | 2eb466c17327a7993eac89d373f764d638ca1bbe29a8acfcec71b3a7490b4f95 |
# 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... | kobejean/tensorflow | tensorflow/python/autograph/converters/control_flow.py | Python | apache-2.0 | 12,260 | [
"VisIt"
] | 9bcd8391e78efc11c1dc2033a7eb55817eab2592bf1bc42ed15cc2e1e25f0f8d |
"""
grdfilter - Filter a grid in the space (or time) domain.
"""
import xarray as xr
from pygmt.clib import Session
from pygmt.helpers import (
GMTTempFile,
build_arg_string,
fmt_docstring,
kwargs_to_strings,
use_alias,
)
@fmt_docstring
@use_alias(
D="distance",
F="filter",
G="outgrid... | GenericMappingTools/gmt-python | pygmt/src/grdfilter.py | Python | bsd-3-clause | 5,209 | [
"Gaussian",
"NetCDF"
] | c6196dcf6fad3b576fc8d5a35d3eb702a2a54b667296e027209ebbdff14ed20f |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Busco(PythonPackage):
"""Assesses genome assembly and annotation completeness with Benchma... | rspavel/spack | var/spack/repos/builtin/packages/busco/package.py | Python | lgpl-2.1 | 1,773 | [
"BLAST"
] | 63db00e1258a3fc092b255b93751665366f08f6e4e5f2c2c90cb5b8ad60a620b |
import scrapy
from scrapy.selector import Selector
from scrapy.http import FormRequest,Request
from crawlers.items import PrincipalItem
class PrincipalsSpider(scrapy.Spider):
name = "principals"
allowed_domains = ["moe.edu.sg"]
start_urls = (
'http://www.moe.edu.sg/',
)
def start_requ... | jackliusr/scrapy-crawlers | crawlers/crawlers/spiders/principals.py | Python | apache-2.0 | 3,707 | [
"MOE"
] | 05b2ee3d8a0cbe9a093e1c82f62edb49adcb58c38bd3e7a1f26c64d926eee1dd |
# -*- coding: utf-8 -*-
"""
Created on Sat Feb 22 17:25:36 2014
@author: Lukasz Tracewski
Module for identification of kiwi calls
"""
import os
import pickle
import numpy as np
from collections import namedtuple
from utilities import contiguous_regions
from sklearn import preprocessing
from sklearn import svm
Candi... | tracek/Ornithokrites | identification.py | Python | gpl-3.0 | 3,765 | [
"Gaussian"
] | 2a40ae62f34a6a1484e7e0423142ce02df73980f5655d4cdb93ad51c0585e46e |
import RoguePy
from RoguePy.Game.Item import Item
from attack import Attack
from buildsite import BuildSite
import chars
from enemies import *
from entities import Shroom, Node, Enemy
from entities import Construct
import items
import uielements
__author__ = 'jripley'
import sys
import config as cfg
from RoguePy.Inp... | v4nz666/7drl2016 | states/playstate.py | Python | gpl-3.0 | 25,431 | [
"Amber"
] | 808f4a4f85c91ad3d4c25fc0e32bd58e781f02a9b6bde3fc9ac0662617e01301 |
# Copyright (c) 2012 Spotify AB
#
# 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, s... | riga/luigi | setup.py | Python | apache-2.0 | 4,110 | [
"VisIt"
] | 926873b4859848651b64de5911a35cc37d36169e01f52fe48e162aa3feff4b5c |
from datetime import datetime
from contextlib import contextmanager
import numpy as np
import siphon.testing
from siphon.ncss import NCSS, NCSSQuery, ResponseRegistry
from nose.tools import eq_
recorder = siphon.testing.get_recorder(__file__)
class TestNCSSQuery(object):
def test_proj_box(self):
nq = ... | hyoklee/siphon | siphon/tests/test_ncss.py | Python | mit | 5,331 | [
"NetCDF"
] | 432eda34fb52bb36f668db18a673dff05ff926aa450bbb494c45fb2b7e6fd0db |
from degas.analysis_setup import calc_stellar_mass
from astropy.table import Table
from astropy.io import fits
import os
multiDir = os.path.join(os.environ['ANALYSISDIR'],'ancillary_data','multiwavelength')
iracDir = os.path.join(multiDir,'data','irac1','convolved_with_astropy')
MtoLDir = os.path.join(multiDir,'data'... | low-sky/degas | scripts/calc_irac1_mstar.py | Python | gpl-3.0 | 1,158 | [
"Galaxy"
] | 09c5f340bf9e4a1a33c5dae5e7aee0c44a8701514727241e962ad8298ecf3191 |
# -*- coding: UTF-8 -*-
"""Definitions for `Ensembler` class."""
import gc
import sys
import time
import numpy as np
import scipy
from astrocats.catalog.model import MODEL
from astrocats.catalog.quantity import QUANTITY
from emcee.autocorr import AutocorrError
from mosfit.mossampler import MOSSampler
from mosfit.samp... | guillochon/FriendlyFit | mosfit/samplers/ensembler.py | Python | mit | 26,879 | [
"Gaussian"
] | 96e3372ee7fd2883d50f567fedb5ee71ddac98de91c9f0057b9222ca2c8fe205 |
"""
@file
@brief Deals with :epkg:`ImageNet` classes.
"""
from collections import OrderedDict
import numpy
_class_names = {
0: 'tench, Tinca tinca',
1: 'goldfish, Carassius auratus',
2: 'great white shark, white shark, man-eater, man-eating shark, '
'Carcharodon carcharias',
3: 'tiger shark, Ga... | sdpython/ensae_teaching_cs | src/ensae_teaching_cs/data/imagenet_classes.py | Python | mit | 34,378 | [
"Bowtie",
"ESPResSo",
"Jaguar",
"ORCA"
] | ee52ec007c84edf620d0ca77a4da0c3ddab17dbe614ac00c8b78e1833a3781f2 |
import h5py
import numpy
from rdkit import Chem
from steps.preprocessing.shared.tensor2d import tensor_2d_array
from util import data_validation, file_structure, file_util, progressbar, hdf5_util, logger, buffered_queue, misc
class Calculate2DSubstructureLocations:
@staticmethod
def get_id():
return... | patrick-winter-knime/mol-struct-nets | molstructnets/steps/interpretation/calculate2dsubstructurelocations/calculate_2d_substructure_locations.py | Python | gpl-3.0 | 4,923 | [
"RDKit"
] | 767296143959c5c7fd193aa49500515ee6350fccf55bf2b4b7bff407cb384c6c |
r"""
This module provides some testing functionality for paraview and
vtk web applications. It provides the ability to run an arbitrary
test script in a separate thread and communicate the results back
to the service so that the CTest framework can be notified of the
success or failure of the test.... | mspark93/VTK | Web/Python/vtk/web/testing.py | Python | bsd-3-clause | 30,476 | [
"ParaView",
"VTK"
] | 84f80518b55725574fa0e4b19a93b726c4420732b979aa4dc4e3116eecfd495e |
from lib_spm import *
#out_dir = os.path.join('/data42s/comparat/firefly/v1_1_0/figures', 'mass-redshift-presentation')
out_dir = os.path.join(os.environ['HOME'], 'wwwDir', 'firefly')
m_bins = n.arange(5.5, 11.5, 0.01)
p.figure(2, (6.5, 3.5))
p.axes([0.12,0.18,0.8,0.73])
print('eboss')
for imf in imfs:
stellar_ma... | JohanComparat/pySU | spm/bin_SMF/plot_distribution_ages.py | Python | cc0-1.0 | 10,187 | [
"Firefly",
"Galaxy"
] | 2d4b411dddce8c44ac2d97c1547fa895fdf73cb642c8b9703cb18521ac4474b4 |
########################################################################
# File: FTSClient.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/04/08 14:29:43
########################################################################
"""
:mod: FTSClient
.. module: FTSClient
:synopsis: FTS client
.. moduleauthor::... | Sbalbp/DIRAC | DataManagementSystem/Client/FTSClient.py | Python | gpl-3.0 | 16,130 | [
"DIRAC"
] | e599327a52921fd02ccb80319614e3773143bd9655e3a6e8cf6ab86b9a41c880 |
# -*- coding: utf-8 -*-
"""
This example demonstrates a very basic use of flowcharts: filter data,
displaying both the input and output of the filter. The behavior of
he filter can be reprogrammed by the user.
Basic steps are:
- create a flowchart and two plots
- input noisy data to the flowchart
- flowchart con... | robertsj/poropy | pyqtgraph/examples/Flowchart.py | Python | mit | 2,452 | [
"Gaussian"
] | 2e2fbb1b885fb112af69befbc6fdfb1741249bddbf8312ea9c8d35677dd71b63 |
#!/usr/bin/env python
# vim:fileencoding=UTF-8:ts=4:sw=4:sta:et:sts=4:ai
from __future__ import (unicode_literals, division, absolute_import,
print_function)
__license__ = 'GPL v3'
__copyright__ = '2011, Kovid Goyal <kovid@kovidgoyal.net>'
__docformat__ = 'restructuredtext en'
import re, thr... | Eksmo/calibre | src/calibre/ebooks/metadata/sources/base.py | Python | gpl-3.0 | 19,997 | [
"VisIt"
] | abf36ffed58176504e91ea64b1efab0a0e53aff6c6f45380344b02188ff9ad72 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | ctk3b/mdtraj | mdtraj/__init__.py | Python | lgpl-2.1 | 3,391 | [
"Amber",
"CHARMM",
"Gromacs",
"MDTraj",
"NAMD",
"NetCDF"
] | b41224bb839436cfd897cb33ac9f0b92bf519b379ce365fbe3429433b1ae24fa |
# This file is part of DEAP.
#
# DEAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# DEAP is distributed... | DEAP/deap | examples/bbob.py | Python | lgpl-3.0 | 5,040 | [
"Gaussian"
] | b32d096994895b74f2f49fb72c7800efcf54e1c6f39b3cef3521466e95d20cad |
from __future__ import print_function
from builtins import range
from boutdata.collect import collect
import numpy as np
import os
try:
from enthought.mayavi import mlab
from enthought.mayavi.mlab import *
except ImportError:
try:
from mayavi import mlab
from mayavi.mlab import *
except ... | erikgrinaker/BOUT-dev | tools/pylib/boututils/anim.py | Python | gpl-3.0 | 2,466 | [
"Mayavi"
] | fd1a1f5d2209ee0afd5381b79be5f008c39ed91f9af6c5e67423bf47b7c1a34e |
# -*- coding: utf-8 -*-
"""
Generic module for loading netCDF4 files into the pandas format within pysat.
This file may be used as a template for adding pysat support for a new dataset
based upon netCDF4 files, or other file types (with modification).
This routine may also be used to add quick local support for a net... | jklenzing/pysat | pysat/instruments/templates/netcdf_pandas.py | Python | bsd-3-clause | 7,632 | [
"NetCDF"
] | 72f0d17cd64a4ef3b95c136aab7faf4831eeeb72ddd3fe205e428710fc5627bd |
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