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from rdkit import Chem
from rdkit.Chem import rdMolDescriptors
from rdkit.Chem import rdPartialCharges
from collections import namedtuple
class LigDescr(object):
__version__ = "09.2016"
"""This module analyses various properties of the ligand molecule such as charges, logP and MR.
It also detects rotatable bonds.
... | ldomic/lintools | lintools/ligand_description.py | Python | gpl-3.0 | 2,908 | [
"RDKit"
] | 14d8a5a811e5c5d0a1f4065c2d794dde1f4c44fdad43756378a3d2a130f9156a |
import os
import re
import shutil
import sys
try:
from setuptools import setup
setup_params = {
'entry_points': {
'console_scripts': [
'virtualenv=virtualenv:main',
'virtualenv-%s.%s=virtualenv:main' % sys.version_info[:2]
],
},
'z... | michael-go/heroku-buildpack-go | vendor/virtualenv-1.11.6/setup.py | Python | mit | 2,975 | [
"Brian"
] | 536ab03d4a7dec6a96e615463fcb1f7df81e544eefdc8f38c71a65c7975b90f6 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# Copyright (C) 2015-2018 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 l... | dicortazar/ceres | setup.py | Python | lgpl-3.0 | 2,835 | [
"Elk"
] | 8a6bd1796b5c68dfb958a0f8677cbc370a63fce229d70777cb28d4d8bc1f9835 |
"""
Non-linear activation functions for artificial neurons.
"""
import theano.tensor.nnet
# sigmoid
def sigmoid(x):
"""Sigmoid activation function :math:`\\varphi(x) = \\frac{1}{1 + e^{-x}}`
Parameters
----------
x : float32
The activation (the summed, weighted input of a neuron).
Retur... | Richi91/nntools | lasagne/nonlinearities.py | Python | mit | 5,364 | [
"NEURON"
] | 50a5b07e8e2ad935b4d8aab5a39fa1b5c6e1c1fa1322a53c7b1f3d4cdb30f2f1 |
"""
View for Courseware Index
"""
# pylint: disable=attribute-defined-outside-init
from datetime import datetime
from django.conf import settings
from django.contrib.auth.decorators import login_required
from django.contrib.auth.models import User
from django.core.context_processors import csrf
from django.core.urlreso... | caesar2164/edx-platform | lms/djangoapps/courseware/views/index.py | Python | agpl-3.0 | 22,674 | [
"VisIt"
] | 8fb97a696b3a894470095315eb848c8159a01d675d65fadc6787ca447500dafc |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | dmlc/tvm | python/tvm/contrib/cutlass/build.py | Python | apache-2.0 | 17,047 | [
"VisIt"
] | c81f731b8799cd1a82453397f497643378a78f0649d08e95314253596b87bc1b |
"""
cclib (http://cclib.sf.net) is (c) 2006-2010, the cclib development team
and licensed under the LGPL (http://www.gnu.org/copyleft/lgpl.html).
"""
__revision__ = "$Revision: 888 $"
__version__ = "1.0"
import parser
import progress
import method
import bridge
# The test module can be imported if it was installed w... | faribas/RMG-Java | source/cclib/__init__.py | Python | mit | 369 | [
"cclib"
] | 3e4ebe6333eacf55a1b94f1dc93aa50d5dbef923d0867a780d64755f528e33b1 |
#-------------------------------------------------------------------------------
# Cloud-COPASI
# Copyright (c) 2013 Edward Kent.
# All rights reserved. This program and the accompanying materials
# are made available under the terms of the GNU Public License v3.0
# which accompanies this distribution, and is available... | edkent/cloud-copasi | cloud_copasi/web_interface/pools/condor_tools.py | Python | gpl-3.0 | 14,261 | [
"COPASI"
] | bb7e7cbe4e57e1916d3a45eb311243699cdd3b1e770ddfeb95934c35f2a63e1a |
# -*- coding: utf-8 -*-
"""
This file is part of pyCMBS.
(c) 2012- Alexander Loew
For COPYING and LICENSE details, please refer to the LICENSE file
"""
"""
Module that contains relevant classes for diagnostic plots
# TODO implement writing of statistics to an ASCII file as export
# TODO implement taylor plots
# TODO ... | pygeo/pycmbs | pycmbs/plots/plots_basic.py | Python | mit | 129,727 | [
"NetCDF"
] | 803655eff759f5c58a3111da70f18825d289fa75f537af1a69defb32f9e67bc9 |
"""
# Notes:
- This simulation seeks to emulate the COBAHH benchmark simulations of (Brette
et al. 2007) using the Brian2 simulator for speed benchmark comparison to
DynaSim. However, this simulation includes CLOCK-DRIVEN synapses, for direct
comparison to DynaSim's clock-driven architecture. The synaptic connec... | asoplata/dynasim-benchmark-brette-2007 | output/Brian2/brian2_benchmark_COBAHH_clocksyn_hidens_32000/brian2_benchmark_COBAHH_clocksyn_hidens_32000.py | Python | gpl-3.0 | 3,781 | [
"Brian"
] | 03b6bdfa5ad32632f05bb8d4be24f8ff706853a21c06b47b8198a7eaa58e91b4 |
from cvxopt import spmatrix, printing, amd
import chompack as cp
printing.options['width'] = 17
# Define sparse matrix
I = range(17) + [2,2,3,3,4,14,4,14,8,14,15,8,15,7,8,14,8,14,14,15,10,12,13,16,12,13,16,12,13,15,16,13,15,16,15,16,15,16,16]
J = range(17) + [0,1,1,2,2,2,3,3,4,4,4,5,5,6,6,6,7,7,8,8,9,9,9,9,10,10,10,11... | cvxopt/chompack | examples/symbolic_factorization.py | Python | gpl-3.0 | 1,261 | [
"NAMD"
] | 1d6a2ee654354f0943ed2b933af5409ee865b3276f9790309a0965ad7a350528 |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2008, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | zenoss/ZenPacks.vmware.VirtualMachines | setup.py | Python | gpl-2.0 | 3,287 | [
"VisIt"
] | 4a6ee9424fa6ba89e70527f289026b58675b13b699fa02bccac53417b2b1ca3a |
'''
:Authors: Fan Zhang(zfwise@gwu.edu), supported by GWU computer science department
:Date: 3/2013
:Note: Matrix operations over finite fields
'''
def GaussEliminationinGroups(m):
#The code was original found at: http://ine.scripts.mit.edu/blog/2011/05/gaussian-elimination-in-python/
#Here is an exam... | lferr/charm | charm/toolbox/matrixops.py | Python | lgpl-3.0 | 2,886 | [
"Gaussian"
] | 065ba725eb74cdc318a4766e5c616c2bf2e062df6a608bb39431f803a5ec7cff |
'''
Computes the similarity between neuron properties of different property classes.
E.g. compares neurotransmitters (GABA) with proteins (GAD67, and ephys (FS) with proteins (PV)
Similarity rules inter (between) neuron property classes are explicited in the following format:
(['onto_id1', 'onto_id2', ...], #0: e... | renaud/neuroNER | similarity/similarity_inter.py | Python | lgpl-3.0 | 2,135 | [
"NEURON"
] | 93490ee3d46b14dcb99cbd506f5857e3399a6d8d32e22ab8dce467e6c6edf7e2 |
from abapy.mesh import RegularQuadMesh
from abapy.indentation import IndentationMesh
import numpy as np
def tensor_function(x, y, z, labels):
"""
Vector function used to produced the displacement field.
"""
r0 = 1.
theta = .5 * np.pi * x
r = y + r0
s11 = z + x
s22 = z + y
s33 = x**2
s12 = y**2
s1... | lcharleux/abapy | doc/example_code/mesh/Mesh-dump2vtk.py | Python | gpl-2.0 | 1,191 | [
"VTK"
] | bc11b8439766e3490e547b8bf78f7f927fc11bbf954ce21e23ca7ca72bae9afe |
"""
NCBI sra class
"""
import logging
import binascii
from galaxy.datatypes.data import nice_size
from galaxy.datatypes.binary import Binary
log = logging.getLogger(__name__)
class Sra(Binary):
""" Sequence Read Archive (SRA) """
file_ext = 'sra'
def __init__( self, **kwd ):
Binary.__init__( self... | JuPeg/tools-artbio | tools/sra-tools/sra.py | Python | mit | 1,412 | [
"Galaxy"
] | 17cfa09ca46648b71dec4e23db54f414783add6b9367529971a028139bd875ae |
# Paperwork - Using OCR to grep dead trees the easy way
# Copyright (C) 2012-2014 Jerome Flesch
#
# Paperwork is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
... | openpaperwork/paperwork | paperwork-gtk/src/paperwork/frontend/settingswindow/__init__.py | Python | gpl-3.0 | 39,579 | [
"ADF"
] | 4df0070626ccbef6689fea42b431423f2331da4a19de7e8ae32b0d63d00e83ea |
from __future__ import print_function
import unittest
import IMP.rmf
import IMP.test
import IMP.core
import RMF
from IMP.algebra import *
class Tests(IMP.test.TestCase):
def test_navigation(self):
"""Test loading and saving of rigid bodies implicitly"""
for suffix in IMP.rmf.suffixes:
... | shanot/imp | modules/rmf/test/test_rigid_body_round_trip.py | Python | gpl-3.0 | 26,900 | [
"Gaussian"
] | 7c4b50685b421aeaaeaeddb443de2dbdcdd214415f86d1a2092274a428d6728f |
# mako/ast.py
# Copyright (C) 2006-2014 the Mako authors and contributors <see AUTHORS file>
#
# This module is part of Mako and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""utilities for analyzing expressions and blocks of Python
code, as well as generating Python from AS... | grepme/CMPUT410Lab01 | virt_env/virt1/lib/python2.7/site-packages/Mako-1.0.0-py2.7.egg/mako/ast.py | Python | apache-2.0 | 6,702 | [
"VisIt"
] | 18243f948e7ed06b56ef399e0e8473d4cb6d1fa964e77b9953ce0398c749d9e7 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/e2-openwbif | plugin/controllers/views/ajax/eventdescription.py | Python | gpl-2.0 | 4,479 | [
"VisIt"
] | 1c85d952b2155248a9e1db780aea35f1b9dc40d6f816a0cf8678014cf3e24cfc |
""" Cache
This module provides a generic Cache extended to be used on RSS, RSSCache.
This cache features a lazy update method. It will only be updated if it is
empty and there is a new query. If not, it will remain in its previous state.
However, Cache class internal cache: DictCache sets a validity to its entries.
Af... | yujikato/DIRAC | src/DIRAC/ResourceStatusSystem/Utilities/RSSCacheNoThread.py | Python | gpl-3.0 | 14,414 | [
"DIRAC"
] | 46c1e380d28220318db75622ea221074e7ceeb9e63900391d7ec77319c58fcaf |
# coding=utf-8
# Copyright 2014 Pants project contributors (see CONTRIBUTORS.md).
# Licensed under the Apache License, Version 2.0 (see LICENSE).
from __future__ import (absolute_import, division, generators, nested_scopes, print_function,
unicode_literals, with_statement)
import os
from conte... | fkorotkov/pants | tests/python/pants_test/backend/python/test_python_chroot.py | Python | apache-2.0 | 10,535 | [
"VisIt"
] | 247404a84774734d2b1dee19f5d67bf34908c30052100e13ffd68e00d31a405e |
## Python Implementation of Smooth Incremental Graphical Lasso Estimation (SINGLE) algorithm ##
#
#
#
from choose_h import *
from fitSINGLE import *
from plotSINGLE import plotSINGLE
#import spams
import numpy
class SINGLE():
'''Class for SINGLE objects
INPUT:
- data: numpy array of multivariat... | piomonti/pySINGLE | pySINGLE/SINGLE.py | Python | mit | 3,690 | [
"Gaussian"
] | 638d56138ea69718ba86fe78b7c6bbc081a88a0d748b869548b8a8f3141de232 |
# -*- coding: utf-8 -*-
#
# Moonstone is platform for processing of medical images (DICOM).
# Copyright (C) 2009-2011 by Neppo Tecnologia da Informação LTDA
# and Aevum Softwares LTDA
#
# This file is part of Moonstone.
#
# Moonstone is free software: you can redistribute it and/or modify
# it under the terms of the GN... | aevum/moonstone | src/moonstone/bloodstone/utils/msmath.py | Python | lgpl-3.0 | 8,682 | [
"VTK"
] | 0284da01f6ee11ca8bb8a9737dad213874ba6486bcb86f81cfb6327dfffd242c |
#!/usr/bin/env python
import sys
sitePython = "@SITEPYTHON@"
if sitePython:
sys.path.insert( 0, "@SITEPYTHON@" )
from DIRAC.Core.Base import Script
Script.parseCommandLine()
#######################################################################################################################
# $Id$
# Generated by Jo... | avedaee/DIRAC | WorkloadManagementSystem/JobWrapper/JobWrapperTemplate.py | Python | gpl-3.0 | 5,625 | [
"DIRAC"
] | 98bba8a06b016805d85ef712300a0066324e6e8cc7f05dc60696247d74c07054 |
"""The module contains implementations of approximate posteriors."""
import logging
import matplotlib.pyplot as plt
import numpy as np
import scipy.stats as ss
from elfi.methods.bo.utils import minimize
logger = logging.getLogger(__name__)
# TODO: separate the likelihood to its own class
class BolfiPosterior:
... | lintusj1/elfi | elfi/methods/posteriors.py | Python | bsd-3-clause | 7,764 | [
"Gaussian"
] | df96dcfa2fa6307e64aca67cee4170378a207aaea477693c509f90a7ddcc269b |
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Daniel Strohmeier <daniel.strohmeier@tu-ilmenau.de>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
#
# License: BSD (3-clause)
import warnings
import math
import numpy as np
from ..io.pick import pick_channels_cov
from ..forwar... | teonlamont/mne-python | mne/simulation/evoked.py | Python | bsd-3-clause | 4,582 | [
"Gaussian"
] | d6c528efb9f3b4619361f27f27796985fd61e7cfaff5966d107579f775ca689e |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from pymatgen.core.tensors import SquareTensor
from collections import namedtuple
from pymatgen.core.units import FloatWithUnit
from pymatgen.core.periodic_table import Specie
from pymatgen.core.structure imp... | fraricci/pymatgen | pymatgen/analysis/nmr.py | Python | mit | 8,157 | [
"pymatgen"
] | 215e698ed138c8ec6a64d62518c552ab03809a8b9f7aaeec474867d162afe832 |
from deskbar.core.Utils import load_base64_icon
from deskbar.core.Web import MateURLopener, Account, AccountDialog, ConcurrentRequestsException
from deskbar.defs import VERSION
from gettext import gettext as _
import deskbar
import deskbar.interfaces.Action
import deskbar.interfaces.Match
import deskbar.interfaces.Modu... | benpicco/mate-deskbar-applet | deskbar/handlers/twitter.py | Python | gpl-2.0 | 12,390 | [
"VisIt"
] | 217c958ee051c38e75a06d1a7d4ee60916f59fef8abd973f46eec46361cc2c3d |
"""
Acceptance tests for Studio related to the split_test module.
"""
import math
from unittest import skip
from nose.plugins.attrib import attr
from selenium.webdriver.support.ui import Select
from xmodule.partitions.partitions import Group
from bok_choy.promise import Promise, EmptyPromise
from ...fixtures.course ... | defance/edx-platform | common/test/acceptance/tests/studio/test_studio_split_test.py | Python | agpl-3.0 | 46,849 | [
"VisIt"
] | e9d2afbab72c61a1b37c5039e45d6a4ad087c37ee311ba15a11834a7e728bc2d |
from DIRAC import S_OK, S_ERROR
from DIRAC.WorkloadManagementSystem.Splitters.BaseSplitter import BaseSplitter
class InputDataBySESplitter( BaseSplitter ):
AFTER_OPTIMIZER = "InputDataResolution"
def splitJob( self, jobState ):
result = jobState.getManifest()
if not result[ 'OK' ]:
return result
... | avedaee/DIRAC | WorkloadManagementSystem/Splitters/InputDataBySESplitter.py | Python | gpl-3.0 | 1,967 | [
"DIRAC"
] | 48dd758b34e1b3fc606147d52374f1ffcc37cbb9d12195d5c01903d054e958f0 |
import os
import sys
import nest
import time
import logging
import datetime
import numpy as np
import nest.topology as tp
import matplotlib.pyplot as plt
from collections import defaultdict
from parameters import *
from time import clock
from data import *
dictPosition_NeuronID = {} # position (1,0,1) : 6 neuron ID
... | research-team/NEUCOGAR | NEST/auditory/scripts/func.py | Python | gpl-2.0 | 9,656 | [
"NEURON"
] | 78f498a145af913ba20f5e412b83bafda58b0381f5774c59135392763de6b38c |
# sql/compiler.py
# Copyright (C) 2005-2015 the SQLAlchemy authors and contributors
# <see AUTHORS file>
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Base SQL and DDL compiler implementations.
Classes provided include:
:class:`.c... | brianv0/sqlalchemy | lib/sqlalchemy/sql/compiler.py | Python | mit | 100,189 | [
"VisIt"
] | 38a7b5409f7a57b8f443e2b2f00c0d7ec2ac64c68dec41a9a1499b34255e4c36 |
import krylov
import meshplex
import meshzoo
import numpy as np
from scipy.sparse.linalg import LinearOperator
import pyfvm
def test():
mu = 5.0e-2
V = -1.0
g = 1.0
class Energy:
"""Specification of the kinetic energy operator."""
def __init__(self):
self.subdomains = [N... | nschloe/pyfvm | examples/ginzburg_landau_example_test.py | Python | gpl-3.0 | 2,779 | [
"VTK"
] | 431133f1ebe71eb9209cd8fde88e8d1dacafeff9dfa532b1e199c0600cc33531 |
#
# AtHomePowerlineServer - networked server for CM11/CM11A/XTB-232 X10 controllers
# Copyright (C) 2014 Dave Hocker
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, version 3 of the Lic... | dhocker/athomepowerlineserver | database/__init__.py | Python | gpl-3.0 | 387 | [
"xTB"
] | e2e682cdf91b3d27f1f08abfe145000d4e65722ea63b1249d75f095f24ded8e0 |
# $Id$
#
# Copyright (C) 2003-2008 Greg Landrum and Rational Discovery LLC
# All Rights Reserved
#
from __future__ import print_function
import bisect
from rdkit import DataStructs
from rdkit.DataStructs.TopNContainer import TopNContainer
class GenericPicker(object):
_picks = None
def MakePicks(self, force=Fa... | rvianello/rdkit | rdkit/SimDivFilters/SimilarityPickers.py | Python | bsd-3-clause | 7,333 | [
"RDKit"
] | 187b7c24c0245f88e835d6c8a45585e3e7dcf01dbbbf8644c54533230dcb18c8 |
#!/usr/bin/env python
from __future__ import print_function
import os
import string
import subprocess
import sys
from pulsar.main import (
ArgumentParser,
DEFAULT_APP_YAML,
DEFAULT_INI
)
try:
import pip
except ImportError:
pip = None
try:
import virtualenv
except ImportError:
virtualenv ... | jmchilton/pulsar | pulsar/scripts/config.py | Python | apache-2.0 | 8,876 | [
"Galaxy"
] | 01eea49f3cbccbe786b20fbdf55f652cbc95b354e69698b77a0c51ab80985153 |
#!/usr/bin/python
# Copyright 2012, SIL International
# All rights reserved.
#
# 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 License, or
# (at y... | silnrsi/graide | lib/graide/waterfall.py | Python | lgpl-2.1 | 3,693 | [
"VisIt"
] | d7c44966602844dc016a039e01141261f9f72ff398d4e330d9eb017f07915c8f |
# coding: utf-8
# # 데이터 시각화
# In[1]:
from __future__ import division, print_function
# ## 주요 내용
#
# 데이터 분석을 위해 가장 기본적으로 할 수 있고, 해야 하는 일이 데이터 시각화이다.
# 데이터를 시각화하는 것은 어렵지 않지만, 적합한 시각화를 만드는 일은 매우 어려우며,
# 많은 훈련과 직관이 요구된다.
#
# 여기서는 데이터를 탐색하여 얻어진 데이터를 시각화하는 기본적인 방법 네 가지를 배운다.
#
# * 선그래프
# * 막대그래프
# * 히스토그램
# * 산점도
... | liganega/Gongsu-DataSci | previous/notes2017/W05/GongSu12_Data_Visualization.py | Python | gpl-3.0 | 12,527 | [
"Gaussian"
] | ae68514ca9d857553fe2d8bf3b0d9bb0ba23ec3336bcbb02832d5ec8307e2f55 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | gregcaporaso/scikit-bio | skbio/sequence/tests/test_rna.py | Python | bsd-3-clause | 2,083 | [
"scikit-bio"
] | d0266067ebe15dc39ce5aa8793ae0fd32ce7e9c93252375851a8ea38d2d64e18 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
from pyhit ... | nuclear-wizard/moose | python/peacock/Input/InputTreeWriter.py | Python | lgpl-2.1 | 3,455 | [
"MOOSE"
] | 27f0049ed559bb93af67d047079f46872cb9f718d895037e23855cfdd972e614 |
import base64
import hashlib
import json
import os
import re
import socket
import sys
import netrc
import xml.etree.ElementTree
from ..utils import (
compat_http_client,
compat_urllib_error,
compat_urllib_parse_urlparse,
compat_str,
clean_html,
compiled_regex_type,
ExtractorError,
Rege... | MiLk/youtube-dl | youtube_dl/extractor/common.py | Python | unlicense | 24,455 | [
"VisIt"
] | e1ee9e37271426070ac046f8d654ab174b1876544249e2423f07e829b71f6c9a |
# Multi-class (Nonlinear) SVM Example
#----------------------------------
#
# This function wll illustrate how to
# implement the gaussian kernel with
# multiple classes on the iris dataset.
#
# Gaussian Kernel:
# K(x1, x2) = exp(-gamma * abs(x1 - x2)^2)
#
# X : (Sepal Length, Petal Width)
# Y: (I. setosa, I. virginica... | benjaminoh1/tensorflowcookbook | Chapter 04/multiclass_svm.py | Python | mit | 5,539 | [
"Gaussian"
] | 80485f4f87c5b599fbb0ed212327135894d044bdfea8c67c50c7a5eef5ef65ce |
from cardboard import types
from cardboard.ability import (
AbilityNotImplemented, spell, activated, triggered, static
)
from cardboard.cards import card, common, keywords, match
@card("Midnight Covenant")
def midnight_covenant(card, abilities):
def midnight_covenant():
return AbilityNotImplemented
... | Julian/cardboard | cardboard/cards/sets/champions_of_kamigawa.py | Python | mit | 63,627 | [
"BLAST"
] | 614707af68a148ecf025ce7ea9555738da2fd5077d113fb1585b873f09cc3b93 |
import json
import os
import re
from random import randint
import sys
import warnings
import xml
import xml.etree.ElementTree as ET
from Bio import BiopythonWarning
from Bio import SeqIO
from Bio._py3k import Request as _Request
from Bio._py3k import urlopen as _urlopen
from Bio._py3k import urlencode as _urlencode
fr... | carlosp420/bold | bold/api.py | Python | bsd-3-clause | 27,773 | [
"Biopython"
] | 57ab6353739fee2d0725d414606b8e8aec90e394473a24e9dfeedf3e87b4c4f2 |
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Matti Hamalainen <msh@nmr.mgh.harvard.edu>
# Denis A. Engemann <denis.engemann@gmail.com>
#
# License: BSD (3-clause)
import os
from os import path as op
import sys
from struct import pack
from glob import glob
import numpy as... | trachelr/mne-python | mne/surface.py | Python | bsd-3-clause | 39,201 | [
"Mayavi"
] | ecbd1689e46d3587c091a615be3ff61d064efe09bbf6e8c22ed4eb547c6747ba |
# -*- encoding: utf-8 -*-
# Copyright (C) 2010 LangaCore
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, version 3 of the License.
#
# This program is distributed in the hope that it will be u... | ambv/django-crystal-small | setup.py | Python | lgpl-3.0 | 2,338 | [
"CRYSTAL"
] | fcbe926ad0286d780fcd8b6d810de45afd80f404df3fade5d4740f129ed682fc |
"""Tests for algorithms for partial fraction decomposition of rational
functions. """
from sympy.polys.partfrac import (
apart_undetermined_coeffs,
apart_full_decomposition,
apart,
apart_list_full_decomposition,
apart_list, assemble_partfrac_list
)
from sympy import (S, Poly, E, pi, I, Matrix, Eq,... | wolfram74/numerical_methods_iserles_notes | venv/lib/python2.7/site-packages/sympy/polys/tests/test_partfrac.py | Python | mit | 5,309 | [
"Gaussian"
] | ba28ab7ae162121a08b2423f0bc8383a268099e1910925288e4ce2589d663983 |
# -*- encoding: utf-8 -*-
# Copyright 2013 Red Hat, Inc.
# 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 re... | openstack/watcher | watcher/api/controllers/v1/audit.py | Python | apache-2.0 | 28,050 | [
"VisIt"
] | d2bbc95fb8674263af67781ccb563137144ca3f65638c1d1724b2867f926d720 |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""Interfaces to assorted Freesurfer utility programs.
Change directory to provide relative paths for doctests
>>> import os
>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
>>> d... | FredLoney/nipype | nipype/interfaces/freesurfer/utils.py | Python | bsd-3-clause | 45,062 | [
"Gaussian",
"VTK"
] | bab6adfee387b6f2b02539bb10dd4d3361e69c20a3bfd8bcd1ba63ecfd636318 |
#
# gPrime - A web-based genealogy program
#
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2008 Jerome Rapinat
# Copyright (C) 2008 Benny Malengier
# 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 Lice... | sam-m888/gprime | gprime/filters/rules/citation/_hasgallery.py | Python | gpl-2.0 | 1,814 | [
"Brian"
] | f495a7eeb4e9ad9e23c889d68d76ea08af7b9d7df8fc10613f5eba21bc44ddd4 |
# The Hazard Library
# Copyright (C) 2012-2014, GEM Foundation
#
# 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
# License, or (at your option) any later version.
... | larsbutler/oq-hazardlib | openquake/hazardlib/gsim/base.py | Python | agpl-3.0 | 38,674 | [
"Gaussian"
] | a595a9c787d008fed6728641ef099acc8a51587111a8775ff8cfe9ebab582106 |
import ocl
import camvtk
import time
import vtk
import datetime
import math
def drawPoints(myscreen, clpoints, ccpoints):
c=camvtk.PointCloud( pointlist=clpoints, collist=ccpoints)
c.SetPoints()
myscreen.addActor(c )
def drawFiber(myscreen, f):
#myscreen.addActor( camvtk.Line(p1=(f.p1.x,f.p1.y,f.p1.... | aewallin/opencamlib | examples/python/fiber/fiber_01.py | Python | lgpl-2.1 | 2,899 | [
"VTK"
] | 25d5c30f712f2659c91d5de997400913fa20db735ccf956b7837717b7fdaeee7 |
"""
Manage Galaxy eggs
"""
import os, sys, shutil, tarfile, zipfile, zipimport, subprocess, ConfigParser, glob, urllib2, shutil
from types import ModuleType
import logging
log = logging.getLogger( __name__ )
import pkg_resources
# we MUST have the top level galaxy dir for automatic egg fetching
# within tools. i d... | volpino/Yeps-EURAC | lib/galaxy/eggs/__init__.py | Python | mit | 25,034 | [
"Galaxy"
] | 8095eecfa1773ca8f7ca07ea202ef643420f7c0708cb9af59ffa18be46123304 |
"""
Forest of trees-based ensemble methods.
Those methods include random forests and extremely randomized trees.
The module structure is the following:
- The ``BaseForest`` base class implements a common ``fit`` method for all
the estimators in the module. The ``fit`` method of the base ``Forest``
class calls th... | shyamalschandra/scikit-learn | sklearn/ensemble/_forest.py | Python | bsd-3-clause | 100,128 | [
"Brian"
] | 0b9856aad2e1eab90be280d8b86237f8bdc9549161ad93e3e4edf7c2a3063be4 |
"""
sphinx.writers.texinfo
~~~~~~~~~~~~~~~~~~~~~~
Custom docutils writer for Texinfo.
:copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS.
:license: BSD, see LICENSE for details.
"""
import re
import textwrap
import warnings
from os import path
from typing import Iterable, cast
from ... | lmregus/Portfolio | python/design_patterns/env/lib/python3.7/site-packages/sphinx/writers/texinfo.py | Python | mit | 57,753 | [
"VisIt"
] | 927ed26a80e81ef41d6cd19ac3177503e05a6881c3236b1cb04918282f225832 |
# (c) 2014 Michael DeHaan, <michael@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later ve... | xen0l/ansible | lib/ansible/playbook/role/requirement.py | Python | gpl-3.0 | 8,577 | [
"Galaxy"
] | aba18eda29f225b76c62a0e12862098027a7ac80817a3eae047247b5faebfaa0 |
'''
Runs unit tests for classification routines.
To run the unit tests, type the following from the system command line:
# python -m spectral.tests.classifiers
'''
from __future__ import absolute_import, division, print_function, unicode_literals
import os
import numpy as np
import spectral as spy
from numpy.te... | spectralpython/spectral | spectral/tests/classifiers.py | Python | gpl-2.0 | 7,461 | [
"Gaussian"
] | 679a0d08255891cbfd139c2cfc2e6364119f02978c3ea530ffac3be510ae4673 |
# coding=UTF-8
#
# BigBrotherBot(B3) (www.bigbrotherbot.net)
# Copyright (C) 2012 <courgette@bigbrotherbot.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; either version 2 of the License... | AusTac/parma | b3/parsers/csgo.py | Python | gpl-2.0 | 43,562 | [
"MOE"
] | 75b7a32cbf03381fdc1f887034539e03d8a737f6cd4716c9a2bdeb2247a38a5c |
#!/usr/bin/env python
"""
Copyright 2014 Jirafe, 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 applicab... | concerned3rdparty/jirafe-python | jirafe/models/Cart.py | Python | mit | 2,042 | [
"VisIt"
] | 5c592abe16a4894d86eefd430cadb28cf198dc6f19596b4b3946292e640f756b |
#
# Copyright (c) 2009-2015, Jack Poulson
# All rights reserved.
#
# This file is part of Elemental and is under the BSD 2-Clause License,
# which can be found in the LICENSE file in the root directory, or at
# http://opensource.org/licenses/BSD-2-Clause
#
import El, time
n0 = 25
n1 = 25
numLambdas = 3
startLam... | justusc/Elemental | examples/interface/BPDN.py | Python | bsd-3-clause | 2,587 | [
"Gaussian"
] | 1d72202fb1a11887f68545f25cd1abc0d0598cd47322a5a0a6546e443b0b5abf |
r"""*JSON schema to validate inventory dictionaries*.
This module is part of ``sphobjinv``,
a toolkit for manipulation and inspection of
Sphinx |objects.inv| files.
**Author**
Brian Skinn (bskinn@alum.mit.edu)
**File Created**
7 Dec 2017
**Copyright**
\(c) Brian Skinn 2016-2022
**Source Repository**
... | bskinn/sphobjinv | src/sphobjinv/schema.py | Python | mit | 1,759 | [
"Brian"
] | 9fbd0fa3f6d0895c54c4dda2241dd7ebc20d770d162fec701ef5612aad636d75 |
r"""
Empty Files (:mod:`skbio.io.format.emptyfile`)
==============================================
.. currentmodule:: skbio.io.format.emptyfile
This format exists to make debugging simpler, often an empty file is a mistake
which can take an embarrasing amount of time to notice. This format has only
a sniffer and no r... | jairideout/scikit-bio | skbio/io/format/emptyfile.py | Python | bsd-3-clause | 1,269 | [
"scikit-bio"
] | cadaa9728cf88a0eb08d3da73c90b399d6538c96992894c7f8577e9d2c78982e |
"""An implementation of the Zephyr Abstract Syntax Definition Language.
See http://asdl.sourceforge.net/ and
http://www.cs.princeton.edu/~danwang/Papers/dsl97/dsl97-abstract.html.
Only supports top level module decl, not view. I'm guessing that view
is intended to support the browser and I'm not interested in the
br... | MicroTrustRepos/microkernel | src/l4/pkg/python/contrib/Parser/asdl.py | Python | gpl-2.0 | 11,304 | [
"VisIt"
] | 3b8abec3936865f8616594edb401e674c53983a055c49589efe4be8359adb7e6 |
#! /usr/bin/env python3
"""
Sets up an Ubuntu 14.04 x64 server to be a Counterblock Federated Node.
NOTE: The system should be properly secured before running this script.
TODO: This is admittedly a (bit of a) hack. In the future, take this kind of functionality out to a .deb with
a postinst script to do all of... | Bluejudy/bluejudy_build | setup_federated_node.py | Python | mit | 44,159 | [
"Brian"
] | dcb7a0d986ab72aea4e159be4700b62c746af17ad20030aea9debef50b00e242 |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-compute | tests/unit/gapic/compute_v1/test_accelerator_types.py | Python | apache-2.0 | 68,228 | [
"Octopus"
] | a80eab28694eef6d57566f10d02afd684f127eb4abbecb438cd5bd329db1c04b |
"""
Script to call nucleosome positions-- track making, nucleosome calling, and nfr calling!
@author: Alicia Schep
"""
##### IMPORT MODULES #####
# import necessary python modules
#import matplotlib as mpl
#mpl.use('PS')
import multiprocessing as mp
import numpy as np
import traceback
import itertools
import pysam
fro... | GreenleafLab/NucleoATAC | nucleoatac/run_nuc.py | Python | mit | 7,361 | [
"pysam"
] | e6b04bfe0087cb9717e679f65a2ef52433fa1add3d86c3c1723c176b78999ea8 |
"""
Copyright (c) 2011-2015 Nathan Boley
This file is part of GRIT.
GRIT 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.
GRIT is distribut... | nboley/grit | grit/build_transcripts.py | Python | gpl-3.0 | 21,993 | [
"pysam"
] | 2e309cc532dd929479b09041699688e6117f8a24e8e54b1b04e34f8354498bbd |
"""
Tests for the error model.
"""
from __future__ import annotations
import math
import numpy as np
import pytest
from cctbx.sgtbx import space_group
from libtbx import phil
from dials.algorithms.scaling.error_model.engine import ErrorModelRefinery
from dials.algorithms.scaling.error_model.error_model import (
... | dials/dials | tests/algorithms/scaling/test_error_model.py | Python | bsd-3-clause | 10,389 | [
"CRYSTAL"
] | 52313c8e26b557fe1c2c40acb0f86ac0230f0355d6a842b685053c06b23228a5 |
# Copyright 2012 by Wibowo Arindrarto. 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.
"""Tests for SearchIO BlatIO parsers."""
import os
import unittest
from Bio import Biopy... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_SearchIO_blat_psl.py | Python | gpl-2.0 | 55,644 | [
"BLAST",
"Biopython"
] | f477d83afe750c46e132e71e0e5c9784be469f51a95ca7c95a1fd159f6db3be1 |
import ConfigParser
import os
from log import Log
DEPLOY_CONFIG = "../deploy.cfg"
class DeployConfig:
'''
The deploy config class.
'''
def __init__(self, file_name):
self.config_file = os.path.abspath(file_name)
self.config_parser = ConfigParser.SafeConfigParser()
self.config_parser.optionxform =... | zhoffice/minos | client/deploy_config.py | Python | apache-2.0 | 5,246 | [
"Galaxy"
] | 5593f7641bc2207929dba6255bba784be540c61122f3550afc14ba2aa0f7cf6f |
import numpy as np
import scipy.misc
import os, sys
import scipy.ndimage as nd
from sklearn import neighbors
## Gabor filter
def generateGabors(angles, size=[20,20], rho=1):
# angles in degrees
if type(angles) != list:
angles = [angles]
width = size[0]
height = size[1]
xsbase = np.array(range(width)).T
xs = ... | colincsl/pyKinectTools | pyKinectTools/algs/STIP.py | Python | bsd-2-clause | 2,187 | [
"Gaussian"
] | 6d03b6bfd720aaa908f47234289e1cd1636906f9f127a3ba85d6aad72e4c73e5 |
import sys
from ase.build import molecule, fcc111, add_adsorbate
from ase.optimize import QuasiNewton
from ase.constraints import FixAtoms
from ase.calculators.emt import EMT
from ase.vibrations import Vibrations
sys.path.append("../..")
from __init__ import AnharmonicModes
slab = fcc111('Al', size=(2, 2, 2), vacuu... | keldLundgaard/ase-anharmonics | examples/rotate_on_surface/rotate_mol_on_surface.py | Python | lgpl-2.1 | 1,095 | [
"ASE"
] | b0bccad70b1b47687e5d3e740af4298f4624bcc12c558068ef1b2f6861385a28 |
# (c) 2014, Brian Coca, Josh Drake, et al
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
... | M0ses/ansible | v2/ansible/plugins/cache/memcached.py | Python | gpl-3.0 | 5,898 | [
"Brian"
] | 1bf49604363f0fa36655801d4835990820a5819ffb939d15266a680edd0465f7 |
# This file is vendored from Autorelease
import os
import ast
import sys
import fnmatch # Py 2
from setuptools import setup
def _glob_glob_recursive(directory, pattern):
# python 2 glob.glob doesn't have a recursive keyword
# this implements for the specific case that we want an exact match
# See also h... | dwhswenson/contact_map | setup.py | Python | lgpl-2.1 | 4,674 | [
"VisIt"
] | 5cf58c6e4ec38945bce4b311f69065a0b79581f81d911c9a4780e9bbf6b47b88 |
"""
This module contains the Abstract Syntax Tree nodes built from parser.
"""
from collections import namedtuple
Location = namedtuple("Location", "file line column")
class BaseNode(object):
def __init__(self, parent=None, children=None, location=None):
self.parent = parent
self.children = [] if... | codebrainz/treegen | libtreegen/nodes.py | Python | mit | 5,406 | [
"VisIt"
] | a44d4acba6671181e68fe42b54c9bddb4a0719a63fca21cf60a8ad845fc13793 |
#!/usr/bin/python
# Copyright 2008 Squiffle
#
# Script to help find those 3 pieces in prime-numbered sectors.
# TODO : Clean up UI if user makes a mistake
# Of course ideally, we'd use the number of times each sector appears
# as the "value" of visiting it, and the number of turns to get there
# as the "cost" and we... | UEWBot/ssw-scripts | possible_primes.py | Python | gpl-3.0 | 5,016 | [
"VisIt"
] | fd230c5eb974d7343061eb44816dfe42bf390174fd459cb8eae89cf8cd105576 |
# Copyright 2012-2013 Jose Blanca, Peio Ziarsolo,
# COMAV-Univ. Politecnica Valencia
# This file is part of seq_crumbs.
# seq_crumbs 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
# Li... | JoseBlanca/seq_crumbs | crumbs/utils/optional_modules.py | Python | gpl-3.0 | 4,117 | [
"BLAST",
"Biopython",
"pysam"
] | b08898013384d24528808b6efb46ae99efc3b85258cfdfc8e66bab2a98e734a8 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import
from django.conf import settings
from django.http import HttpResponse
from django.test import TestCase
from mock import patch
from fakeldap import MockLDAP
from zilencer.models import Deployment
from zerver.views import do_change_password, create_homepag... | peguin40/zulip | zerver/tests/test_signup.py | Python | apache-2.0 | 48,243 | [
"VisIt"
] | af96d339082fe0853e2549e0c99754275241b2277f07872b3b48c41e9645dcd8 |
#
# @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/driver_util.py | Python | lgpl-3.0 | 16,594 | [
"Psi4"
] | e7030776f8f14a4cf2b7ad9d10cb4484432c617277eca769b9a348c9ecbcf9e8 |
"""
====================================
Outlier detection on a real data set
====================================
This example illustrates the need for robust covariance estimation
on a real data set. It is useful both for outlier detection and for
a better understanding of the data structure.
We selected two sets o... | RPGOne/Skynet | scikit-learn-c604ac39ad0e5b066d964df3e8f31ba7ebda1e0e/examples/applications/plot_outlier_detection_housing.py | Python | bsd-3-clause | 5,578 | [
"Gaussian"
] | 913bd62941d92a775959d1ccf39aee205a1d29aeda0773a8b43991068cf3afe4 |
#!/usr/bin/env python
import sys, getopt
import glob, os
# MergeHash can maybe go on the hour queue
JobParams = {
'CreateHash': {
'outfile': """CreateHash_Job.q""",
'header': ["""#BSUB -J CreateHash""","""#BSUB -o PROJECT_HOME/Logs/CreateHash-Out.out""","""#BSUB -e PROJECT_HOME/Logs/CreateHash-Err.err""","""#BS... | scottdaniel/LatentStrainAnalysis | LSFScripts/create_jobs.py | Python | mit | 11,904 | [
"BLAST"
] | 92ae57c64496a2643393eba6a31d4ca7f4827ca9d922d72780b43d2c9debd25f |
#!/usr/bin/env python
# CREATED:2013-08-22 12:20:01 by Brian McFee <brm2132@columbia.edu>
'''Music segmentation using timbre, pitch, repetition and time.
'''
import argparse
import logging
import sys
import numpy as np
import scipy.signal
import scipy.linalg
import librosa
import msaf
from msaf.algorithms.interface ... | urinieto/msaf | msaf/algorithms/olda/segmenter.py | Python | mit | 10,238 | [
"Brian"
] | f6735fc04da9775be7fed87021880c288a14874ba23e204aa30611159910a49f |
""" Encapsulate here the logic for matching jobs
Utilities and classes here are used by MatcherHandler
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id"
import time
from DIRAC import gLogger
from DIRAC.FrameworkSystem.Client.Monit... | yujikato/DIRAC | src/DIRAC/WorkloadManagementSystem/Client/Matcher.py | Python | gpl-3.0 | 15,528 | [
"DIRAC"
] | 0c82dc449da4672fba6279af8f81d27a0500eaea42a3f62da5ad2c1a77d89732 |
# Copyright 2016 Google Inc. 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 ag... | KaranToor/MA450 | google-cloud-sdk/lib/googlecloudsdk/third_party/appengine/googlecron/GrocParser.py | Python | apache-2.0 | 45,082 | [
"Brian"
] | 041c8c5384bf8ca7af8e5e94a5e5845928695ade585bdca6da08ed96899a8728 |
"""Test Axis device."""
from copy import deepcopy
import json
from unittest import mock
import axis as axislib
from axis.api_discovery import URL as API_DISCOVERY_URL
from axis.applications import URL_LIST as APPLICATIONS_URL
from axis.applications.vmd4 import URL as VMD4_URL
from axis.basic_device_info import URL as ... | tchellomello/home-assistant | tests/components/axis/test_device.py | Python | apache-2.0 | 13,621 | [
"VMD"
] | 27ec2d1d65af932a698dd61c7227ddbd0d489ed9298aff5641a1278e12f3c837 |
# (C) British Crown Copyright 2010 - 2018, Met Office
#
# This file is part of Iris.
#
# Iris 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 l... | dkillick/iris | lib/iris/tests/__init__.py | Python | lgpl-3.0 | 47,007 | [
"NetCDF"
] | c952ff95c32cd1b93962641be29b3ea0acc58a63d162740ce763f36e4f57b7d0 |
# This file is part of Merlin.
# Merlin is the Copyright (C)2008,2009,2010 of Robin K. Hansen, Elliot Rosemarine, Andreas Jacobsen.
# Individual portions may be copyright by individual contributors, and
# are included in this collective work with permission of the copyright
# owners.
# This program is free software; ... | ellonweb/merlin | Hooks/ships/rprod.py | Python | gpl-2.0 | 4,275 | [
"CRYSTAL"
] | 8510873e71386f80da44253cb1c0697864dec577aa8dd19c01c0ed6b95d3fe13 |
def processSNPVcfStartLine(SNPVcfStartLine, SNPVcfStartFile, refCol, altCol):
# Get the chromosome, position on the chromosome, reference allele, and alternate allele from a line of a vcf file
if SNPVcfStartLine == "":
# At the end of the vcf file, so stop
return ["", 0, "", "", True]
SNPVcfStartLineElements = S... | imk1/IMKTFBindingCode | bwaSNPExtractor.py | Python | mit | 12,379 | [
"BWA"
] | 56602c31bfb39a24aa205794a21c7ad77a9fc1f0fd35ef538e0bc651b770374e |
import numpy as np
import matplotlib.pyplot as plt
import abel
transforms = [
("basex", abel.basex.basex_transform),
(r"daun\ (degree=1)", lambda *args, **kwargs:
abel.daun.daun_transform(*args, degree=1, **kwargs)),
(r"daun\ (degree=3)", lambda *args, **kwargs:
ab... | PyAbel/PyAbel | doc/transform_methods/comparison/fig_gaussian/gaussian.py | Python | mit | 2,745 | [
"Gaussian"
] | 4b4fb1b30e6e263c0ee3810b29767073b2e6c0b87a5371ab73b2e62f72d923e5 |
#!/usr/bin/env python
"""
Installer script to install the LAMMPS python package and the corresponding
shared library into either the system-wide site-packages tree, or - failing
that - into the corresponding user tree. Called from the 'install-python'
build target in the conventional and CMake based build systems
"""
... | rbberger/lammps | python/install.py | Python | gpl-2.0 | 4,487 | [
"LAMMPS"
] | d955a95c17454337651696e041b7c932e4cf565d6f3224760f461fd011a7d9e8 |
"""setuptools.command.bdist_egg
Build .egg distributions"""
from distutils.errors import DistutilsSetupError
from distutils.dir_util import remove_tree, mkpath
from distutils import log
from types import CodeType
import sys
import os
import re
import textwrap
import marshal
from setuptools.extern import six
from pk... | google/material-design-icons | update/venv/lib/python3.9/site-packages/setuptools/command/bdist_egg.py | Python | apache-2.0 | 18,185 | [
"VisIt"
] | 9e77d5f0087c2110bf21fbf92e86bd15dc4beba3156f20d7c32f9fa0ff35d333 |
# -*- coding: utf-8 -*-
import requests
from bs4 import BeautifulSoup, Comment
import schedule
import time
from terminaltables import AsciiTable
from termcolor import colored, cprint
import sys
import os
# Method to visit home page of cricbuzz and get urls of matches
def get_list_of_Matches():
r = requests.get(... | LinuxTerminali/crickbuzz_cricket_score | cricket.py | Python | mit | 16,961 | [
"VisIt"
] | 6ef079876a0dffe6ca7a5d6da83cd974606364e3f1c88f673043b2085b7981a6 |
import os
import re
import copy
from .helpers import save_json, load_json
from .collector import Cluster, CollectionSimple
from .content import SimpleContent
def create_person(name_tag, people, cluster_pos, root, skipped, ambi, auto_create=True, letter_index_dirs=True):
"""
a People object is loaded in the ca... | charlesbrandt/medley | medley/person.py | Python | mit | 19,255 | [
"VisIt"
] | ccce47bacb4df08230d1ceb33dddc7ad21481dd54328998c5b6220670c0385ac |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2010-2011, Monash e-Research Centre
# (Monash University, Australia)
# Copyright (c) 2010-2011, VeRSI Consortium
# (Victorian eResearch Strategic Initiative, Australia)
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modificati... | wettenhj/mytardis | tardis/tardis_portal/forms.py | Python | gpl-3.0 | 32,093 | [
"Brian"
] | d09978c5183b99e8808b8e9698b05a4de9819be8fbb6d6236718de5c6bd70c35 |
from builtins import range
import numpy as np
def affine_forward(x, w, b):
"""
Computes the forward pass for an affine (fully-connected) layer.
The input x has shape (N, d_1, ..., d_k) and contains a minibatch of N
examples, where each example x[i] has shape (d_1, ..., d_k). We will
reshape each ... | ALEXKIRNAS/DataScience | CS231n/assignment2/cs231n/layers.py | Python | mit | 29,145 | [
"NEURON"
] | 004ce8c21d1286e80db599fa917acd35f133f7d486486b2e17e89f9c5a103be5 |
"""
Plotting utility functions
"""
import copy
import enum
import matplotlib as mpl
import matplotlib.gridspec as gridspec
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import scipy.stats.kde as kde
import seaborn as sns
from ..util import EMAError, get_module_logger
# .. codeauthor:: jhkw... | quaquel/EMAworkbench | ema_workbench/analysis/plotting_util.py | Python | bsd-3-clause | 25,247 | [
"Gaussian"
] | 8110f386ab423ea263552e5736d20158a7c4a1471dc7516823dd09917fae5390 |
#!/usr/bin/python
# Copyright: (c) 2020, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
ANSIBLE_METADATA = {
'metadata_version': '1.1',
'status': ['preview'],
... | Shaps/ansible | test/integration/targets/ansible-galaxy-collection/library/setup_collections.py | Python | gpl-3.0 | 4,381 | [
"Galaxy"
] | 220cd18c18c493f66e0f2b39980626151a24f9cb564ebdd1de884f553c70020b |
""" unit tests for Transformation Clients
"""
# pylint: disable=protected-access,missing-docstring,invalid-name
import unittest
import json
import mock
from DIRAC.RequestManagementSystem.Client.Request import Request
from DIRAC.TransformationSystem.Client.TaskManager import TaskBase, RequestTasks
from DIRAC.Transfor... | chaen/DIRAC | TransformationSystem/Client/test/Test_Client_TransformationSystem.py | Python | gpl-3.0 | 12,352 | [
"DIRAC"
] | c20b401e372da44638efc3a507ca3e7f45972b7b2aa348530343d3dce7a54647 |
from math import sqrt
from math import factorial
from operator import *
from numpy import *
### Defining the DeltaJ function that will be used in Wigner6J
def DeltaJ(a, b, c):
Total = 0
while True:
if (a+b-c) < 0:
break
elif (a-b+c) < 0:
break
elif (-a+b+c) < 0:
break
elif (a+b+c+1) < 0:
bre... | karamarielynch/hfs-sim | hfs_creation.py | Python | mit | 6,948 | [
"Gaussian"
] | 6ebfe8ada57411910d6c0ac2abfc73f7026c67d15bb8db68137e5df0e0aa8294 |
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