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#=============================================================================#
# MODEL DEFINITION FILE #
#=============================================================================#
import numpy as np
#----------------------------------------------------------... | crpurcell/RM-tools | RMtools_1D/deprecated/models_mc/m6.py | Python | mit | 6,807 | [
"Gaussian"
] | 688f04f883a98b918675a0edc45a1ef51ec14f7e18b2573316b3ec628c5bc1ba |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
Created on Nov 10, 2012
@author: shyue
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2011, The Materials Project"
__version__ = "0.1"
__m... | migueldiascosta/pymatgen | pymatgen/core/tests/test_composition.py | Python | mit | 16,674 | [
"pymatgen"
] | 14e3d9ccd1d7c58e6380d71f2c0d1a4d4c61f04105a6b2ef688d44e31c8a5f33 |
import Bio.SeqIO as sio
from Bio.Alphabet import IUPAC
from Bio import motifs
import numpy as np
import re
import os
L = {'A': 0,
'a': 0,
'C': 1,
'c': 1,
'G': 2,
'g': 2,
'T': 3,
't': 3
}
def _getOneHotSeq(seq):
"""Convert Biopython Seq to one-hot encoding.
.. note:: ... | schulter/crbm | secomo/sequences.py | Python | gpl-3.0 | 3,530 | [
"Biopython"
] | 2f25ad6251a89aaa8b44233309cf15d29dacf369d5876115efe56c46fbe4fa79 |
import logging
logger = logging.getLogger(__name__)
from netCDF4 import Dataset
def set_basic_md(resource):
"""
basis meta data
:param resource: netCDF file where basic meta data should be set
"""
import sys
from datetime import datetime as dt
py_version = sys.version
creation_date = dt.strftime( ... | sradanov/flyingpigeon | flyingpigeon/metadata.py | Python | apache-2.0 | 9,754 | [
"NetCDF"
] | 18850415273e5186dd7125178ac2c032707fec839fb2a7ef4e71fed7d54e3c3e |
'''
Created on Aug 22, 2014
@author: David Zwicker <dzwicker@seas.harvard.edu>
contains functions that are useful for image analysis
'''
from __future__ import division
import functools
import numpy as np
from scipy import ndimage
import cv2
from utils.data_structures.cache import cached_property
def subpixe... | david-zwicker/video-analysis | video/analysis/image.py | Python | bsd-3-clause | 13,979 | [
"Gaussian"
] | a464cd7354d424d891268c3679dfe949c2c0a63417a4c20e22078221c0729972 |
import hyperchamber as hc
import numpy as np
import hypergan as hg
from hypergan.distributions.uniform_distribution import UniformDistribution
from hypergan.gan_component import ValidationException
from unittest.mock import MagicMock
from tests.mocks import MockDiscriminator, mock_gan
gan = mock_gan()
distribution = ... | 255BITS/HyperGAN | tests/distributions/test_uniform_distribution.py | Python | mit | 1,656 | [
"Gaussian"
] | 69a8853c5a54e5fe3ffd98bcf3744b1c4aa7faa13a5d5c39eeda737c2db170e5 |
"""Functions for escaping and unescaping strings (for URLs, filenames, etc).
The underscore escaping functions are useful when generating directory names
which should be reasonably human-readable, and not contain characters which are
likely to confuse programs (e.g. ":" doesn't work on Windows, "#" confuses
cmake, "="... | michel-slm/0install | zeroinstall/support/escaping.py | Python | lgpl-2.1 | 1,637 | [
"VisIt"
] | 75b307add7a82b3b586ed62ee258edf2aa83fe3703515ed4c4039ddd238c928a |
from __future__ import print_function, absolute_import, division
from future.builtins import *
from future import standard_library
standard_library.install_aliases()
# Copyright 2017 Autodesk Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | Autodesk/molecular-design-toolkit | moldesign/data/data.py | Python | apache-2.0 | 2,786 | [
"GAMESS",
"PySCF"
] | 983ede182cb3f8da2bfd534834011413aaf9220f2185b9170adf4a9d036c6885 |
#!/usr/bin/env python2
# Copyright (C) 2016
# Max Planck Institute for Polymer Research
#
# 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 ver... | acfogarty/espressopp | examples/adress/hadress_tetraliquid/hadress_tetraliquid_FEC/hadressPressureFEC.py | Python | gpl-3.0 | 8,976 | [
"CRYSTAL",
"ESPResSo"
] | 2ce037255d9a474f12fbe29c4454df2d402ecb7f27a8d70f25d09cb1ea2e477f |
#!/usr/bin/python
#
# This source file is part of appleseed.
# Visit https://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2014-2018 Francois Beaune, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any... | Biart95/appleseed | scripts/runtestsuite/runtestsuite.py | Python | mit | 21,256 | [
"VisIt"
] | 22d783c59720498af86bcf9fa5b7f2afb04a85f71d7f4d175c7be636e097b853 |
"""rbf - Radial basis functions for interpolation/smoothing scattered Nd data.
Written by John Travers <jtravs@gmail.com>, February 2007
Based closely on Matlab code by Alex Chirokov
Additional, large, improvements by Robert Hetland
Some additional alterations by Travis Oliphant
Interpolation with multi-dimensional ta... | lhilt/scipy | scipy/interpolate/rbf.py | Python | bsd-3-clause | 12,011 | [
"Gaussian"
] | fb1ff2827e1ee5897c6864c307b3b2d5e06155cb2fd4c21edec1a87e41046265 |
input_name = '../examples/navier_stokes/stabilized_navier_stokes.py'
output_name = 'test_stabilized_navier_stokes.vtk'
from tests_basic import TestInput
class Test( TestInput ):
pass
| RexFuzzle/sfepy | tests/test_input_stabilized_navier_stokes.py | Python | bsd-3-clause | 188 | [
"VTK"
] | 461dfbe98643ef4ad96976328a647b61fe30b40520a3a3d9a261c1f1887009b5 |
#####################################################################################
#
# Copyright (c) Crossbar.io Technologies GmbH
#
# Unless a separate license agreement exists between you and Crossbar.io GmbH (e.g.
# you have purchased a commercial license), the license terms below apply.
#
# Should you enter ... | NinjaMSP/crossbar | crossbar/adapter/mqtt/test/test_protocol.py | Python | agpl-3.0 | 16,012 | [
"FEFF"
] | 23c84cb704b40d30ab8df06acc86e484097cf67b8c2549377a10fd2a337f6b94 |
#!/usr/bin/env python
# Exercise 43: Basic Object-Oriented Analysis and Design
# Class Hierarchy
# * Map
# - next_scene
# - opening_scene
# * Engine
# - play
# * Scene
# - enter
# * Death
# * Central Corridor
# * Laser Weapon Armory
# * The Bridge
# * Escape Pod
# * Human
# - attack
# - defend
#... | Akagi201/learning-python | lpthw/ex43.py | Python | mit | 9,133 | [
"BLAST"
] | 17edca621e7a7e3e480954ebb84aedf68c187608c976149643d648d162727d9c |
# Copyright (C) 2010-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | mkuron/espresso | samples/visualization_lbboundaries.py | Python | gpl-3.0 | 1,774 | [
"ESPResSo"
] | 2329380d8f2c00aec0f1b64e1e681dcac154353c5d3df17fe1ed1758d0313980 |
import pysam
import sys
import gzip
import os
import logging
import argparse
import xml.etree.ElementTree as ET
import subprocess
from CountXmlUtils import readCountXmlQueryLocationInFeatures
DEBUG = False
NOT_DEBUG= not DEBUG
if DEBUG:
genomeListFile="/scratch/cqs/shengq2/vickers/20191112_smallRNA_3018-KCV_76_mous... | shengqh/ngsperl | lib/SmallRNA/getBacteriaCount2.py | Python | apache-2.0 | 4,363 | [
"pysam"
] | 7e6dae339942bfbb0a6c7300312bc442054c23bca95236bcad799fedbb5806e9 |
# Lint as: python3
# Copyright 2018 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 ... | tensorflow/lingvo | lingvo/tasks/mt/base_config.py | Python | apache-2.0 | 27,164 | [
"Gaussian"
] | 83b5d51f16716f422b1aa1fc28069c6e5a2711dbdbea0ac905b820d3bf8f5911 |
""" VOMS2CSSyncronizer is a helper class containing the logic for synchronization
of the VOMS user data with the DIRAC Registry
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
from collections import defaultdict
from DIRAC import... | ic-hep/DIRAC | src/DIRAC/ConfigurationSystem/Client/VOMS2CSSynchronizer.py | Python | gpl-3.0 | 26,822 | [
"DIRAC"
] | 267038e18c79bb631257a9fb885d16127ad61b9ee32e69b106290a1e9125d6e7 |
#!/usr/bin/env python
import argparse
import os
import matplotlib as mpl
havedisplay = "DISPLAY" in os.environ
if not havedisplay:
mpl.use('Agg')
import numpy as np
import pylab as plt
from crrlpy import crrls
from crrlpy.models import rrlmod
from crrlpy import synthspec as synth
def power_law(freq, Tc, nu):
... | astrofle/CRRLpy | scripts/make_spec.py | Python | mit | 7,100 | [
"Gaussian"
] | dad9589c723018d989a084e175ea73ab23d8954e0bab3f6c5dcf0d804d1c6aca |
#!/usr/bin/env python
from __future__ import print_function, division
import bayesloop as bl
import numpy as np
import sympy.stats as stats
class TestTwoParameterModel:
def test_fit_1cp_1bp_2hp(self):
# carry out fit
S = bl.ChangepointStudy()
S.loadData(np.array([1, 2, 3, 4, 5]))
... | christophmark/bayesloop | tests/test_changepointstudy.py | Python | mit | 4,717 | [
"Gaussian"
] | 8751c018f44203e7309eb53e1ebd63efe42825ccb0d7457e881e560e5291873a |
"""
Description of the video:
Mimic of Star Wars' opening title. A text with a (false)
perspective effect goes towards the end of space, on a
background made of stars. Slight fading effect on the text.
"""
import numpy as np
from skimage import transform as tf
from moviepy.editor import *
from moviepy.video.tools.dr... | kerimlcr/ab2017-dpyo | ornek/moviepy/moviepy-0.2.2.12/examples/star_worms.py | Python | gpl-3.0 | 4,827 | [
"Galaxy"
] | 18b0d85485c76cebc6cb220c94e3e44686f6bcf330c1d80329272e6a308b8fd7 |
#
# @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/procrouting/mcscf/mcscf_solver.py | Python | lgpl-3.0 | 14,309 | [
"Psi4"
] | c5fee228dd6e5d16ad5538cd28d0933dcebeaede8d728403cc4be77a583017ee |
# -*- coding: utf-8 -*-
##
## This file is part of Invenio.
## Copyright (C) 2011, 2012 CERN.
##
## Invenio is free software; you can redistribute it and/or
## modify it under the terms of the GNU General Public License as
## published by the Free Software Foundation; either version 2 of the
## License, or (at your opt... | MSusik/invenio | invenio/legacy/bibauthorid/webapi.py | Python | gpl-2.0 | 111,703 | [
"VisIt"
] | 24ee05ec31bbd2b1af92964296112c3bbce77e492765e62b95ed23894534cac7 |
#!/usr/bin/python
# coding: UTF-8
#--------------------------------------------------------------------------------------------------
# This script use python
# adding quick-reference comment in ./model/***.param files.
#-------------------------------------------------------------------------------------------------... | kawai125/md_fdps | script/param_file_comment.py | Python | mit | 6,604 | [
"CHARMM"
] | a16c2d80ec3cae91c6c4bc867f7c571c316fb79e6918c4de8863db2ee0b21798 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2002-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2011 Tim G L Lyons
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publ... | arunkgupta/gramps | gramps/gen/filters/rules/citation/__init__.py | Python | gpl-2.0 | 1,994 | [
"Brian"
] | c89131734d80c4ed6ca9d8d6d4e91348961f49ff6cbe1a3053bb8dae29bbb38d |
# Copyright 2015 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 applic... | b4dawn75/cifar10-dist | cifar10.py | Python | mit | 15,143 | [
"Gaussian"
] | 9a9131e95959c256fb0b43e6745d1f5a64e01c2673fd13f7e69666f399da8f25 |
#!/usr/bin/python -W all
"""
findRoutes.py: find longest route with an index of the available train rides
usage: findRoutes.py [-b beam-size] [-f firstStation] [-h] [-H history-file] [-i] [-n] [-s time] [-S] < traintrips.txt
note: expected input line formats:
1. hash sign distance start-station end-station... | eriktks/kmtrein | findRoute.py | Python | apache-2.0 | 23,335 | [
"VisIt"
] | acc4b2c0a6231bc57b0dfd59878fd36c16b1c4085f71b340f12429b25338670a |
#!/usr/bin/env python
# standard library
import itertools
import random
# third party
import dendropy as dpy
import numpy as np
from tree_distance import PhyloTree
# treeCl
from .errors import optioncheck
from .constants import ISPY3
from .utils import fileIO, weighted_choice
from .utils.decorators import lazyprop
f... | kgori/treeCl | treeCl/tree.py | Python | mit | 53,894 | [
"Brian"
] | cd73b12dbc9894fd2411aae894ee7afb117c5c8fa36de46bd4694674660bb7f7 |
# -*- 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-pubsublite | tests/unit/gapic/pubsublite_v1/test_subscriber_service.py | Python | apache-2.0 | 49,675 | [
"Octopus"
] | 4ae9ec57c400911c1cd6c203e632c4667ce433252468c40f614540738b3bc3ae |
#Author: Ajayrama Kumaraswamy(ajayramak@bio.lmu.de)
#Date: 3 March 2014
#Place: Dept. of Biology II, LMU, Munich
#********************************************List of Dependencies*******************************************************
#The following code has been tested with the indicated versions on 64bit Linux and P... | ajayramak/BlenderSWCVizualizer | blenderHelper.py | Python | apache-2.0 | 24,404 | [
"NEURON"
] | 8a55a88d6ca822adf4fbf29b1fde5e2a957a73d9f82bdaf68410d62393607b8f |
#!/usr/bin/env python
# -*- coding:utf-8 -*-
from random import shuffle
import os
class Blackjack(object):
def __init__(self):
self.money = 2000.00
def creat_deck(self, deck=1):
'''
Create card function, it is possible to create a deck with more cards.
Increases the difficulty... | Bhyan/blackjack | blackjack/blackjack.py | Python | mit | 3,037 | [
"CASINO"
] | 00b099b48f8b392eddb24fcff87bce824a4808c9052230d3ff11eb17e5a00124 |
"""Sensor that can display the current Home Assistant versions."""
from datetime import timedelta
import logging
from pyhaversion import HaVersion, HaVersionChannel, HaVersionSource
from pyhaversion.exceptions import HaVersionFetchException, HaVersionParseException
import voluptuous as vol
from homeassistant.componen... | w1ll1am23/home-assistant | homeassistant/components/version/sensor.py | Python | apache-2.0 | 4,721 | [
"TINKER"
] | 8158fe6ea6c5ba6da86525085cab63bec1899b02d0ca746b2b2fd208ac52c737 |
# This file is part of PyEMMA.
#
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
#
# PyEMMA 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 versi... | markovmodel/PyEMMA | pyemma/coordinates/data/featurization/featurizer.py | Python | lgpl-3.0 | 41,564 | [
"MDTraj"
] | d43317af4f31921d6c5f60b0b26389cb4f38d9fb7ae7766f489128dfff8d697e |
## This file is part of Scapy
## See http://www.secdev.org/projects/scapy for more informations
## Copyright (C) Philippe Biondi <phil@secdev.org>
## This program is published under a GPLv2 license
"""
Packet sending and receiving with libdnet and libpcap/WinPcap.
"""
import time,struct,sys
import socket
if not sys.p... | guedou/scapy-codecov | scapy/arch/pcapdnet.py | Python | gpl-2.0 | 25,041 | [
"VisIt"
] | ff1d259e3e82ded3f158292cb4b15b363bbfae9a17ae47124f2a67f75e3b4437 |
"""!
@brief Neural and oscillatory network module. Consists of models of bio-inspired networks.
@authors Andrei Novikov (pyclustering@yandex.ru)
@date 2014-2020
@copyright BSD-3-Clause
"""
import math
from enum import IntEnum
class initial_type(IntEnum):
"""!
@brief Enumerator of types of ... | annoviko/pyclustering | pyclustering/nnet/__init__.py | Python | gpl-3.0 | 15,896 | [
"Gaussian"
] | 6ce39d85fc47caccfffe87e82d723c8b29ebb15c0e87fdc51a468181d6c9119d |
#!/usr/bin/python
#
# Copyright (C) 2014, Jaguar Land Rover
#
# This program is licensed under the terms and conditions of the
# Mozilla Public License, version 2.0. The full text of the
# Mozilla Public License is at https://www.mozilla.org/MPL/2.0/
#
#
# Reads signed certificate, validates signature and prints pa... | afan1/rvi_core | python/rvi_sign.py | Python | mpl-2.0 | 1,105 | [
"Jaguar"
] | 9fb78306e732c36e9ae5da6d77e821181c95c3c98dce4df86e880925a5417a73 |
# Eidolon Biomedical Framework
# Copyright (C) 2016-8 Eric Kerfoot, King's College London, all rights reserved
#
# This file is part of Eidolon.
#
# Eidolon 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, eit... | ericspod/Eidolon | eidolon/ImageAlgorithms.py | Python | gpl-3.0 | 35,574 | [
"Gaussian"
] | 425f8d49fa081db78c2e71ab5b06558a1403503abe97c1ca9a9f11afd8e4dbdf |
# 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... | xuleiboy1234/autoTitle | tensorflow/tensorflow/contrib/distributions/python/ops/mvn_full_covariance.py | Python | mit | 7,246 | [
"Gaussian"
] | 65843b23232bc61569c3e5bbe89358e19cf10a4d1084d2fac5b7ac1e5c118aa3 |
# -*- coding: UTF-8 -*-
"""
``BlastXMLmerge``
-----------------------
:Authors: Menachem Sklarz
:Affiliation: Bioinformatics core facility
:Organization: National Institute of Biotechnology in the Negev, Ben Gurion University.
A module for running ``BlastXMLmerge.py``, available from github at https://github.com/jh... | bioinfo-core-BGU/neatseq-flow_modules | neatseq_flow_modules/searching/BlastXMLmerge.py | Python | gpl-3.0 | 5,721 | [
"BLAST"
] | ba46211f7a784a085506c60a9ca7b35de6ae5c2363c1d7e33847d51084f04479 |
import ast
import json
import os
import re
import sys
from functools import partial
from importlib import import_module
from optparse import make_option
from shutil import copyfile
from django.conf import settings
from django.core.management.base import BaseCommand
from django.db.models.fields import NOT_PROVIDED, Dat... | symmetricapi/django-symmetric | symmetric/management/commands/generatebackbonemodels.py | Python | mit | 34,070 | [
"VisIt"
] | a80ad7f60a7709b7447eff1c373f91c5b4a98cc5017fffea72b0615e032670f2 |
import logging
logger = logging.getLogger('Collections')
import copy
import scipy
import SloppyCell
import SloppyCell.Utility as Utility
import SloppyCell.KeyedList_mod as KeyedList_mod
KeyedList = KeyedList_mod.KeyedList
if SloppyCell.HAVE_PYPAR:
import pypar
class ExperimentCollection(dict):
"""
Expe... | GutenkunstLab/SloppyCell | SloppyCell/Collections.py | Python | bsd-3-clause | 19,564 | [
"Gaussian"
] | aa72492f40c54114a20c4bd8323ea2e9f07ac9274d953c3cadad87b0c56ed44b |
"""Abstraction for dealing with products and the files they contain."""
import os
from xml.dom.minidom import parseString
from .coda_aware import CODA_Aware
class Product(CODA_Aware):
"""A CODA product, composed mainly of NetCDF files."""
def __init__(self, uuid, work_dir=""):
self.files = []
... | erget/Presence | codaPresence/product.py | Python | mit | 1,964 | [
"NetCDF"
] | 67aca25bc9e675b254a89bb6599413c0a652de46dfab7509873e42eb5cf96bf6 |
#
# Copyright (c) 2020, 2020, 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 redistribute it and/or modify it
# under the terms of the GNU General Public License version 2 only, as
# published by the Free Softwar... | smarr/Truffle | espresso/mx.espresso/mx_espresso_benchmarks.py | Python | gpl-2.0 | 12,162 | [
"ESPResSo",
"VisIt"
] | b53935d4ab8b4f2bc5df5befdc1c7dfc84f89ef6f27dd446176daeecd34dc9e1 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import datetime as dt
from spack import *
class Lammps(CMakePackage, CudaPackage):
"""LAMMPS stands for Large-scale ... | LLNL/spack | var/spack/repos/builtin/packages/lammps/package.py | Python | lgpl-2.1 | 12,617 | [
"LAMMPS",
"NetCDF"
] | 2d9a5ad52744d2cf277c4a8162e42ed1c8e7838a7f6baac358e8eff770b90ed7 |
from __future__ import division, print_function
import sys
sys.path.append("../lib")
import logging
import theano
import theano.tensor as T
from theano import tensor
from blocks.bricks.base import application, lazy
from blocks.bricks.recurrent import BaseRecurrent, recurrent
from blocks.bricks import Random, Initia... | drewlinsley/draw_classify | draw/fast_draw.py | Python | mit | 19,059 | [
"Gaussian"
] | 1ee25eabcbd0ca3db455959268e4722a6d1dd7d3f464b83beedf396626519106 |
"""
Sample Controller File
A Controller should be in charge of responding to a request.
Load models to interact with the database and load views to render them to the client.
Create a controller using this template
"""
from system.core.controller import *
import random
from time import strftime
class Welcome(Contro... | authman/Python201609 | Ron_Miller/Assignments/NinjaGold_pylot/app/controllers/Welcome.py | Python | mit | 1,855 | [
"CASINO"
] | e0a36b348d4f10760353a6332b3c68431ef2880222b8e50da87ae75b04f4ff28 |
#!/usr/bin/python
##
# Massimiliano Patacchiola, Plymouth University (2016)
#
# Implementation of hebbian connection and hebbian network classes.
#
import numpy as np
class HebbianNetwork:
"""HebbianNetwork
This is an implementation of the hebbian network class.
The Hebbian Network is considered as an ... | mpatacchiola/pyERA | pyERA/hebbian.py | Python | mit | 19,526 | [
"Gaussian"
] | 2b5d3f8f7ecbd432b8495a19aa4e6009abe08646a9b279840927e14e0a867e25 |
# -*- coding: utf-8 -*-
"""
Editor de Spyder
Este es un archivo temporal
"""
#
# Esto en [pyspark | GoogleCloud] NO hace falta (ya hay una seasión de spark lanzada y un sparkContext creado):
# C:\Archivos de programa\Google\Cloud SDK>gcloud compute instances start cluster-jjtzapata-m cluster-jjtzapata-... | jjtoharia/KaggleOutbrain | pySpark/temp_spark.py | Python | mit | 32,616 | [
"Galaxy"
] | 5ec00fb4f31055492b614cee64cd8ac799d6af0dcfff759e726dd84f30bbed4e |
"""\
CGBF.py Perform basic operations over contracted gaussian basis
functions. Uses the functions in PGBF.py.
References:
OHT = K. O-ohata, H. Taketa, S. Huzinaga. J. Phys. Soc. Jap. 21, 2306 (1966).
THO = Taketa, Huzinaga, O-ohata, J. Phys. Soc. Jap. 21,2313 (1966).
This program is part of the PyQuante qua... | berquist/PyQuante | PyQuante/CGBF.py | Python | bsd-3-clause | 6,833 | [
"Gaussian"
] | 0e956c6e282bde66b6ced7f9dc2646b23223aa30857b601dce3563169581a58b |
# Write the benchmarking functions here.
# See "Writing benchmarks" in the asv docs for more information.
import os
import sys
import py_entitymatching as mg
p = mg.get_install_path()
datasets_path = os.sep.join([p, 'datasets', 'example_datasets'])
class TimeBlockTablesElect... | anhaidgroup/py_entitymatching | benchmarks/benchmark_rule_based_blocker.py | Python | bsd-3-clause | 7,542 | [
"VisIt"
] | 445cd6581893460a04c166b05d97ab85cd4b66d2a75eb0476577b3466b208172 |
import json
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.http import HttpResponse
from catmaid.control.authentication import requires_user_role
fro... | catsop/CATMAID | django/applications/catmaid/control/analytics.py | Python | gpl-3.0 | 10,572 | [
"NEURON"
] | a7e9b8070988f21710541069bb8797ce50de7b515357448dec420e74db9f2e28 |
# dulwich doesn't return the symref where remote HEAD points, so we monkey
# patch it here
from dulwich.errors import GitProtocolError
from dulwich.protocol import extract_capabilities
from edenscm.mercurial import url, util as hgutil
try:
from edenscm.mercurial import encoding
hfsignoreclean = encoding.hfsi... | facebookexperimental/eden | eden/hg-server/edenscm/hgext/hggit/compat.py | Python | gpl-2.0 | 3,104 | [
"FEFF"
] | 2b0374d79a67154b2c6606e2a9d52275b562973cf2bc323d0412fddcc2253069 |
from math import sqrt
from ase import Atoms
from ase.optimize.lbfgs import LBFGS
from ase.constraints import StrainFilter, UnitCellFilter
from ase.io import Trajectory
from ase.optimize.lbfgs import LBFGS
from ase.optimize.mdmin import MDMin
try:
from asap3 import EMT
except ImportError:
pass
else:
a = 3.6
... | suttond/MODOI | ase/test/unitcellfilter.py | Python | lgpl-3.0 | 945 | [
"ASE"
] | a8dfb87f5e4da101d1aca365e271c20ce4fdec6ede6490ef80757e41c10cd424 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkHyperOctreeToUniformGridFilter(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,... | nagyistoce/devide | modules/vtk_basic/vtkHyperOctreeToUniformGridFilter.py | Python | bsd-3-clause | 525 | [
"VTK"
] | d96e1157718846f2235045393bb3619a00b444116bc8d8397d0c93c1c14997db |
# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# 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.
"""Polypeptide-related classes (construction and representation).
Simple example with mul... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/PDB/Polypeptide.py | Python | gpl-2.0 | 14,399 | [
"Biopython"
] | 4ee51f3d60376867d5e646bc26590aa2cac39948265560c8ae7cb32b7452b2fd |
# -*- coding: utf-8 -*-
# Licensed under a 3-clause BSD style license - see LICENSE.rst
# Author: Pauli Virtanen, 2016
from __future__ import (absolute_import, division, print_function,
unicode_literals)
import math
from .util import inf, nan
def compute_stats(samples, number):
"""
... | pv/asv | asv/statistics.py | Python | bsd-3-clause | 11,359 | [
"Gaussian"
] | 5ba259a28f93ad1b81249d0166bda71cd26ab9cad30e19e99ebf747286c7c908 |
#!/usr/bin/env python
#
# E-Mail post-processing script for NZBGet
#
# Copyright (C) 2013-2017 Andrey Prygunkov <hugbug@users.sourceforge.net>
#
# 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; e... | ta264/nzbget | scripts/EMail.py | Python | gpl-2.0 | 10,326 | [
"VisIt"
] | e427ada1acf3855da21e1ed4c882518f97caf8e4380838fb80621a03cbed72e8 |
# Orca
#
# Copyright 2005-2009 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | h4ck3rm1k3/orca-sonar | src/orca/scripts/apps/soffice/braille_generator.py | Python | lgpl-2.1 | 9,347 | [
"ORCA"
] | 71c0e24204258bce13110fc4c5da7db71f106d129515168f8603f62f43b9db0e |
#mccabe complexity: ["error", 31]
from django.contrib.postgres.aggregates import ArrayAgg
from django.core.cache import cache
from django.db.models import F, Q, Count
from django.http import HttpResponse, JsonResponse
from django.shortcuts import render, redirect
from django.utils.decorators import method_decorator
fro... | protwis/protwis | signprot/views.py | Python | apache-2.0 | 66,370 | [
"CRYSTAL"
] | b9c27f7a2e86c533fce341c2750b04561c2652af0c3f85dd619378ba8f2b541d |
# changelog bisection for mercurial
#
# Copyright 2007 Matt Mackall
# Copyright 2005, 2006 Benoit Boissinot <benoit.boissinot@ens-lyon.org>
#
# Inspired by git bisect, extension skeleton taken from mq.py.
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 ... | seewindcn/tortoisehg | src/mercurial/hbisect.py | Python | gpl-2.0 | 9,244 | [
"VisIt"
] | bc7c43ed70ae1942d1c3b1c959de6b79f6b8f10bb68adf57dcb793ffc093f680 |
"""A quick DOM implementation.
Python's xml.dom is very slow. The xml.sax module is also slow (as it imports urllib2).
This is our light-weight version.
"""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import _
from xml.parsers import expat
c... | pombredanne/zero-install | zeroinstall/injector/qdom.py | Python | lgpl-2.1 | 3,375 | [
"VisIt"
] | c30f2cbaa7ca865ee8f901cafa1dc93937607f87833c2d6c6c72fe51badf5a0e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright @ 2014 Mitchell Chu
from __future__ import (absolute_import, division, print_function,
with_statement)
from datetime import datetime
import os
from os.path import exists, isdir, join
from torndsession.driver import SessionDriver
from... | MitchellChu/torndsession | torndsession/filesession.py | Python | mit | 3,165 | [
"VisIt"
] | bfc8c369790faa7aed972534a302bee8b83c2cebe1db9ea98018923ba10733ef |
# coding=utf-8
import ast
import traceback
from collections import OrderedDict
class SampleCodeValidator(ast.NodeVisitor):
"""
Class that checks if a string is a valid and "safe" Python expression
What is considered "safe" for this class is limited to the context of generating
provider method sample... | joke2k/faker | faker/sphinx/validator.py | Python | mit | 5,769 | [
"VisIt"
] | d66b7cd2987c88103a3ba5c2365af4f6512037087776684c309630c57f10a09a |
# Copyright 2019 Brian Quinlan
#
# 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writin... | brianquinlan/learn-machine-learning | lunarlander/play.py | Python | mit | 2,796 | [
"Brian"
] | 607d4b6b7b0fab9094f65f0d910d2999e5ddbae8baefa75ff5c586387d0986c2 |
#!/usr/bin/env python
# -*- coding : utf8 -*-
""" Container for working with files in FDF, XV, MDE, OUT format
"""
import os
import re
import glob
from collections import OrderedDict
import xml.dom.minidom as xml
import numpy as np
import const
import errors
# --- Methods ---
def data2file(data, title, file_name... | ansobolev/shs | shs/sio.py | Python | mit | 19,561 | [
"SIESTA"
] | 2f35891ff6cc3581d672237ebb5f375bc24865993b6d7ec66749e09b9e186391 |
#!/usr/bin/env python3
# Copyright 2015 The Kubernetes 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 appl... | michelle192837/test-infra | hack/boilerplate/verify_boilerplate.py | Python | apache-2.0 | 7,683 | [
"VisIt"
] | 4a619c18ca2c12512fc5d3e9ed65e1185b74211710f9e8756be7061f1c84c5d5 |
'''
thevideo urlresolver plugin
Copyright (C) 2014 Eldorado
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.
This program is di... | azumimuo/family-xbmc-addon | script.mrknow.urlresolver/lib/urlresolver9/plugins/thevideo.py | Python | gpl-2.0 | 2,850 | [
"VisIt"
] | a149ba4ecf3dd2b30c876f341e79d9e9c58276d19f5b50b5c1935bdf56606905 |
#! /usr/bin/env python
from ase.utils.geometry import rotate
from ase.io import read
from ase.geometry.cell import cellpar_to_cell, cell_to_cellpar
from pyDFTutils.ase_utils.symbol import get_symdict,symbol_number,symnum_to_sym
from pyDFTutils.ase_utils.ase_utils import scaled_pos_to_pos,force_near_0,pos_to_scaled_pos... | mailhexu/pyDFTutils | pyDFTutils/perovskite/octahedra.py | Python | lgpl-3.0 | 21,324 | [
"ASE"
] | 1256f77a01d7f51613a7ab53ec3377f11ff3f1cac25f2cf93adda79ee6bf33cc |
# $Id$
#
# Copyright (C) 2003-2006 Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" Unit Test code for Fragment Descript... | adalke/rdkit | rdkit/Chem/UnitTestFragmentDescriptors.py | Python | bsd-3-clause | 8,371 | [
"RDKit"
] | c9e0d30a04c9b757c4bc058d92fdd52cd25de5a7a73cd8a9bafac488e4921896 |
# #############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2014 Stanford University and the Authors
#
# Authors: Matthew Harrigan
# Contributors: Carlos Xavier Hernandez
#
# MDTraj i... | gph82/mdtraj | tests/test_selection.py | Python | lgpl-2.1 | 10,441 | [
"MDTraj"
] | 23b314749d45001f5f6cd6911f2c89aa49f796519be87142ba5ceba4c67ffe1d |
#!/usr/bin/env python
#
# extras_dictcursor - test if DictCursor extension class works
#
# Copyright (C) 2004-2010 Federico Di Gregorio <fog@debian.org>
#
# psycopg2 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... | pcu4dros/pandora-core | workspace/lib/python3.5/site-packages/psycopg2/tests/test_extras_dictcursor.py | Python | mit | 17,434 | [
"GULP"
] | caccfc44a1effd590ed8f0702fae3d0fe1522f68d7a8bff0a3e9d77c5c3caf2a |
#!/usr/bin/env python
import os
import sys
from libcl import NMRclust
from libbuild import make_ligprotein
from libindex import reindexing_file
to_one_letter = {'GLY':'G', 'ALA':'A', 'SER':'S', 'THR':'T', 'CYS':'C', 'VAL':'V', 'LEU':'L', 'ILE':'I', 'MET':'M', 'PRO':'P', 'PHE':'F', 'TYR':'Y', 'TRP':'W', 'ASP':'D',... | seoklab/GalaxyPPDock | lib/libzdock.py | Python | gpl-3.0 | 10,468 | [
"Galaxy"
] | ea9a34ebee4985ec646a20701acaa75696b6c123b097d31cf0cc94db0b3720ab |
# Natural Language Toolkit: Probability and Statistics
#
# Copyright (C) 2001-2008 University of Pennsylvania
# Author: Edward Loper <edloper@gradient.cis.upenn.edu>
# Steven Bird <sb@csse.unimelb.edu.au> (additions)
# Trevor Cohn <tacohn@cs.mu.oz.au> (additions)
# URL: <http://nltk.sf.net>
# For licens... | hectormartinez/rougexstem | taln2016/icsisumm-primary-sys34_v1/nltk/nltk-0.9.2/nltk/probability.py | Python | apache-2.0 | 61,472 | [
"Gaussian"
] | b741a552ad9664a7adb12ecc1cad153fac0067bebfefb4b32603d40a4c24125a |
from scipy.optimize import curve_fit
from numpy import *
import matplotlib.pyplot as plt
# Create a function
# ==> First encounter with *whitespace* in Python <==
def gaussian(x, a, b, c):
val = a * exp(-(x - b)**2 / c**2)
return val
# Generate fake data.
# Note: functions in random package, array arithmetic ... | azariven/BioSig_SEAS | bin/dev/random_code.py | Python | gpl-3.0 | 1,048 | [
"Gaussian"
] | b339187f674cbb6ba477c2bab2a9baebe64b169248c0eea7d066f3d6df10fa34 |
## Copyright 2015-2021 PyPSA Developers
## You can find the list of PyPSA Developers at
## https://pypsa.readthedocs.io/en/latest/developers.html
## PyPSA is released under the open source MIT License, see
## https://github.com/PyPSA/PyPSA/blob/master/LICENSE.txt
"""Functions for importing and exporting data.
"""
... | PyPSA/PyPSA | pypsa/io.py | Python | mit | 43,000 | [
"NetCDF"
] | 775376b33a16bc3b3162123b33c30dba336a9c0ce575ba2fa1fd3a67358df87c |
# -*- coding: utf-8 -*-
# <nbformat>3.0</nbformat>
# <codecell>
from __future__ import division
from pandas import *
import os, os.path
import sys
import numpy as np
sys.path.append('/home/will/HIVReportGen/AnalysisCode/')
sys.path.append('/home/will/PySeqUtils/')
os.chdir('/home/will/HIVVariation/')
from GeneralSeq... | JudoWill/ResearchNotebooks | SonyaSpots.py | Python | mit | 9,724 | [
"VisIt"
] | c1832708c31c308f98401f6e098fef503ea3543addf4bebfd84a452d6c4b97c7 |
#$Id: common.py,v 1.49 2010-12-29 12:13:04 jorn Exp $
# Import modules from standard Python library
import sys,os.path,UserDict,re,xml.dom.minidom,datetime
# Import additional third party modules
import numpy
import xmlstore.xmlstore
def get_py2exe_datafiles():
from distutils.filelist import findall
def add... | BoldingBruggeman/gotm | gui.py/xmlplot/common.py | Python | gpl-2.0 | 59,700 | [
"NetCDF"
] | 2d0ebbee2caf5008bcdaec22244168bdd1b285718d55e4b427fc5a526585ceb6 |
from util import *
from InputParameters import InputParameters
from MooseObject import MooseObject
class Tester(MooseObject):
@staticmethod
def validParams():
params = MooseObject.validParams()
# Common Options
params.addRequiredParam('type', "The type of test of Tester to create for this test.")
... | mellis13/moose | python/TestHarness/testers/Tester.py | Python | lgpl-2.1 | 9,581 | [
"VTK"
] | f3d11f02ef87073f4bf4ad771a55c79335d9387e8c2782ea759dd38757324823 |
"""Examine callable regions following genome mapping of short reads.
Identifies callable analysis regions surrounded by larger regions lacking
aligned bases. This allows parallelization of smaller chromosome chunks
through post-processing and variant calling, with each sub-section
mapping handled separately.
Regions ... | SciLifeLab/bcbio-nextgen | bcbio/bam/callable.py | Python | mit | 21,478 | [
"pysam"
] | 32497aa88bd91fcf62df67acb587018bafd2bbcd5e52678756538d75d3f86e92 |
from collections import OrderedDict
from ase.io import read
from ase.units import Bohr
from pyDFTutils.ase_utils import symbol_number
from pyDFTutils.ase_utils.kpoints import ir_kpts
from pyDFTutils.wannier90.wannier import read_basis
import pythtb
import os
import numpy as np
from green import green_J
class exchang... | mailhexu/pyDFTutils | pyDFTutils/wannier90/wann_green_J.py | Python | lgpl-3.0 | 7,727 | [
"ASE",
"Wannier90"
] | a42b5140b46e7b5bab5e016f54c3f7b69bf6f0dd6269fdca34c77216ad447842 |
# -*- coding: utf-8
# Copyright (C) 2012 - 2013, A. Murat Eren
#
# This program is free software; you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free
# Software Foundation; either version 2 of the License, or (at your option)
# any later version.
#
# Pl... | jooolia/oligotyping | Oligotyping/utils/blast.py | Python | gpl-2.0 | 14,512 | [
"BLAST",
"Biopython"
] | 22ac195da66e3c684600d2734eb53a42c49fb9c1e4411062321083089e2b09f7 |
# -*- coding: utf-8 -*-
'''
RVIC parameter file development driver
'''
import os
import numpy as np
import pandas as pd
from logging import getLogger
from .core.log import init_logger, close_logger, LOG_NAME
from .core.multi_proc import error
from .core.utilities import make_directories, copy_inputs, strip_invalid_char... | UW-Hydro/RVIC | rvic/parameters.py | Python | gpl-3.0 | 26,943 | [
"NetCDF"
] | 099f29e98fe080c39aab33d2aefbbf8fab1dc3ca80ef5a49015fd86d882b15d0 |
from abc import ABCMeta, abstractmethod
from matplotlib.backends.backend_qt5agg import (
NavigationToolbar2QT, FigureCanvasQTAgg as FigureCanvas)
from matplotlib.figure import Figure
__all__ = ["VtkVisualizer", "MplVisualizer"]
try:
import vtk
from vtk.qt.QVTKRenderWindowInteractor import *
class QV... | cklb/PyMoskito | pymoskito/visualization.py | Python | bsd-3-clause | 3,666 | [
"VTK"
] | 0c0faa1ed49e07725a82896595795a266d1205ae0935a79ad569b7c9edec54c3 |
"""
Simple demo showing how to use a more complicated kernel. This fits the data of
CO_2 levels at Mauna Loa; see chapter 5 of Rasmussen and Williams. Note that we
don't fit the hyperparameters as the values given below are reasonable and this
would just take some time.
"""
import os
import numpy as np
import matplotl... | mwhoffman/pygp | pygp/demos/maunaloa.py | Python | bsd-2-clause | 1,546 | [
"Gaussian"
] | 7ac9f3c4b1ec150bb4200f69103e408a831a19e4b816a1e26ba32bd6cabf8ddb |
# Copyright (c) 2016-present, Facebook, 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... | Yangqing/caffe2 | caffe2/python/layers/random_fourier_features.py | Python | apache-2.0 | 4,001 | [
"Gaussian"
] | 017fc7a0b7f0ef6438fd8c2c66c2ac786ead76e2c03120b5f6e9d7df5af871e9 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | rmcgibbo/psi4public | psi4/driver/driver.py | Python | lgpl-3.0 | 110,664 | [
"Gaussian",
"Psi4"
] | e566c19c06d7e164015392e5327d66ff5aad44f5e67dd4cdd2f2dec5d6359670 |
# ar.po
val = {" days." : "",
"(all)" : "",
"(any)" : "",
"(anyone)" : "",
"(available)" : "",
"(blank)" : "",
"(both)" : "",
"(everyone)" : "",
"(master user, not editable)" : "",
"(no change)" : "",
"(no deduction)" : "",
"(none)" : "",
"(unknown)" : "",
"(use system)" : "",
"({0} given, {1} remaining)" : "",
"1 tre... | bobintetley/asm3 | src/asm3/locales/locale_ar.py | Python | gpl-3.0 | 109,086 | [
"Amber",
"VisIt"
] | 9f8a1705c3e2c2a1a1af298b0355632db8523d0b80ecebb4b29920114b42cadc |
"""
@name: Modules/House/Hvac/hvac_actions.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2015-2019 by D. Brian Kimmel
@license: MIT License
@note: Created on Sep 11, 2015
@Summary:
"""
__updated__ = '2019-10-11'
# Import system type stuff
# Import PyMh files
from Mod... | DBrianKimmel/PyHouse | Project/src/Modules/House/Hvac/hvac_actions.py | Python | mit | 591 | [
"Brian"
] | 114cfa44994d58fd3542fa160edca6fc265c20dae7657d4b096d5a52c29117b0 |
# 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/m_siesta_ev2ha.py | Python | apache-2.0 | 647 | [
"PySCF"
] | 06283c81b38c94d35a9dc006d118e4ecae5e2628870854206ba3053a1b052ae3 |
##
# 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/n/netcdf.py | Python | gpl-2.0 | 6,966 | [
"NetCDF"
] | 1caf6f4c74529e88ad11be1304cbc7caf9c103e6789005e12371e6bf8e154cb7 |
'''
COMP 1021 Assignment 1
Written by: JOO, Minhyung
Student ID: 20173164
Email: mjoo@stu.ust.hk OR melody10511@gmail.com
'''
import pygame.midi # Import the midi module for playing music
import time # Import the time module for the time.sleep function
import turtle # Import the turtle module for t... | RavenJoo/comp1021 | Music.py | Python | mit | 10,475 | [
"CRYSTAL"
] | d2b106f0b0e1542591932adad837d903d65ef3a65e9df702685d38dddc97693a |
#!/usr/bin/env python
# Copyright 2015 The Kubernetes 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
#
# Unle... | manansaraf/kubernetes | hack/verify-flags-underscore.py | Python | apache-2.0 | 8,838 | [
"VisIt"
] | ea125b824abea9f8f1e57d4b008addbd5e1511037f94e2d4a0faca8b3f798987 |
import pandas as pd
from sklearn.ensemble import RandomForestClassifier
from sklearn.ensemble import GradientBoostingClassifier
from sklearn.ensemble import BaggingClassifier
from sklearn.ensemble import AdaBoostClassifier
from sklearn.ensemble import ExtraTreesClassifier
from sklearn.neural_network import MLPClassifie... | rupakc/Kaggle-Compendium | Eye Movements Verfication and Identification Competition/eye-baseline.py | Python | mit | 2,455 | [
"Gaussian"
] | b8ad285c3522d2e479cd0290c6db3cda7977afce6c38506f18412c91be13d2bc |
"""feedfinder: Find the Web feed for a Web page
http://www.aaronsw.com/2002/feedfinder/
Usage:
feed(uri) - returns feed found for a URI
feeds(uri) - returns all feeds found for a URI
>>> import feedfinder
>>> feedfinder.feed('scripting.com')
'http://scripting.com/rss.xml'
>>>
>>> feedfinder.fe... | AllMyChanges/allmychanges.com | allmychanges/downloaders/utils/feedfinder.py | Python | bsd-2-clause | 13,164 | [
"Brian"
] | 569f2f1789a2e6e6a3864d14738f730c39fe7c7fba73b339243bd7fa6e832ba4 |
# Copyright (C) 2009 by Eric Talevich (eric.talevich@gmail.com)
# Based on Bio.Nexus, copyright 2005-2008 by Frank Kauff & Cymon J. Cox.
# 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 pa... | bryback/quickseq | genescript/Bio/Phylo/NewickIO.py | Python | mit | 9,674 | [
"Biopython"
] | 85897dbe09bafadb9409f199b9cd077c26b45ca05e19eb85ddf513bb7dfbd02a |
import numpy as np
from ase import Atom, Atoms
from ase.structure import bulk
from ase.units import Hartree, Bohr
from gpaw import GPAW, FermiDirac
from gpaw.response.bse import BSE
GS = 1
bse = 1
df = 1
check_spectrum = 1
if GS:
a = 6.75 * Bohr
atoms = bulk('C', 'diamond', a=a)
calc = GPAW(h=0.2,
... | qsnake/gpaw | gpaw/test/bse_diamond.py | Python | gpl-3.0 | 1,629 | [
"ASE",
"GPAW"
] | a20bbc7a4afeeb1eb57c3e572800a80d7e4ea7e52c5c3ca0e378d598a0b16a69 |
###########################################################################
##
## Copyright (C) 2006-2010 University of Utah. All rights reserved.
##
## This file is part of VisTrails.
##
## This file may be used under the terms of the GNU General Public
## License version 2.0 as published by the Free Software F... | VisTrails/vistrails-contrib-legacy | titan/__init__.py | Python | bsd-3-clause | 2,615 | [
"VTK"
] | 5e316b88bdac167827ad8ad4a14369ddaaffb43d4200c83aed424a27ccb35273 |
# plot a simple molecule; requires pillow
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import Draw
comp = Chem.MolFromSmiles('CN1C=NC2=C1C(=O)N(C)C(=O)N2C')
comp.UpdatePropertyCache(strict=False)
AllChem.Compute2DCoords(comp)
Draw.MolToFile(comp, 'test_pillow_caffeine.png')
| guowei-he/bioconda-recipes | recipes/rdkit/2016.03.3/run_test.py | Python | mit | 300 | [
"RDKit"
] | 0286c25a1c7b85dc1a41bef5578d4f3a62334558a0b3917ebf3733c971b49d4c |
#! /usr/bin/python
'''
Demuxes miR from chimeric CLEAR-CLIP reads.
'''
import argparse
import operator
import pysam
import sys
from Bio import SeqIO
from collections import defaultdict
from itertools import tee
from itertools import islice
from itertools import izip
from StringIO import StringIO
def determine_chime... | dkdeconti/CLEAR-CLIP_chimera-masking | demux.py | Python | mit | 4,511 | [
"pysam"
] | 13fecf995613ce2df33829a9042c85decae220de27e987b4551a0c50ccff5930 |
# Copyright (C) 2018 Henrique Pereira Coutada Miranda
# All rights reserved.
#
# This file is part of yambopy
#
"""
Scripts to manipulate Quantum Espresso input files
Also able to read output files in xml format (datafile.xml or datafile-schema.xml)
"""
import os
class qepyenv():
PW = "pw.x"
PH = "ph.x"
... | henriquemiranda/yambo-py | qepy/__init__.py | Python | bsd-3-clause | 665 | [
"Quantum ESPRESSO"
] | 611925ecc47ad16a1c3aa57cc1e39254ee483898fc391e8d192b8923df364809 |
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