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#!/usr/bin/python
"""
a standalone utility to convert mmp or mmpz files to midi files
(basically used to tinker with the mmp format)
authors: Mohamed Abdel Maksoud (mohamed at amaksoud.com), Alexis Archambault
licence: GPL2
"""
import sys
import getopt
import zlib
import xml.etree.ElementTree as etree
from midiutil.M... | mohamed--abdel-maksoud/mmp2midi | mmp2midi.py | Python | gpl-2.0 | 5,527 | [
"TINKER"
] | 0b333527ab10f21841b534a8961e93360cea8d5e98604095bac59c9ba2acdecc |
# ECWMF-CLIM-WAVE.PY
# ------------------------------------------------------------------
# This program will compute daily climatology from hourly renalaysis data
# obtained at the ECWMF portal
# input: filename [fname]
# output: filename [cfile(s)]
# SCS domain (90E-137E,7S-30N), recommended ECMWF resolution=0.25
#... | luuquanghung1982/python | earthscience/ecwmf-clim-wave.py | Python | gpl-3.0 | 7,220 | [
"NetCDF"
] | dbb42b0debfd84bea86a5a0ec6b40c3e8b83024b781191b7d484d96521e2a523 |
# script to identify skipped exons in circRNA bam files
import pysam
import pybedtools
import tempfile
import os
class detect_skipped_exons(object):
def __init__(self, outfolder, sample, bedfile, tmp_folder, platform, cpus):
self.folder = outfolder + sample
self.sample = sample
self.out... | dieterich-lab/FUCHS | FUCHS/detect_skipped_exons.py | Python | gpl-3.0 | 7,926 | [
"pysam"
] | 361e0508b52c8d891dd0cbccc6f3ec430043af82b57b926702dc2982debaf6c7 |
'''Count the number of hits to each of the phages in the different metagenomes'''
import sys,os,re
from phage import Phage
import gzip
# get a list of all phages
phage=Phage()
phages=phage.phageTaxonomyString()
count={}
for p in phages:
count[p] = {}
# read the sizes of all the metagenomes. This will be slow but... | linsalrob/PhageHosts | code/count_phage_mg_hits.py | Python | mit | 2,846 | [
"BLAST"
] | 69dd60cb6079bdfef62cd0c7d661cfe06387838d666d6373f00d1cedb0583424 |
import networkx as nx
import numpy as np
import random as ra
from collections import defaultdict
from functools import partial
from math import ceil,floor
from probability import CPD,fast_space_iterator,JointDistribution
def generateSubGraphs(numgraphs = 2, nodespersub = 5, interconnects = 0):
kernel = lambda x: x... | binarybana/samcnet | samcnet/generator.py | Python | mit | 4,624 | [
"Gaussian"
] | 9c8d7a2a8e2dbc68c2ec1016811913c3632ce5b32757d56a1a9c83cb18364f51 |
import metakit, re, pickle, string, os.path
import rdatabase
import gourmet.gglobals as gglobals
from gourmet import keymanager,shopping,convert
from gourmet.defaults import lang as defaults
from gourmet.gdebug import *
from gettext import gettext as _
import gourmet.version
import shutil
class RecData (rdatabase.RecD... | Linutux/Gourmet | gourmet/legacy_db/db_09/rmetakit.py | Python | gpl-2.0 | 29,271 | [
"Brian"
] | 28b9c36d6a1449c1cab4b0c63c86b67db527dcdff8042b3a41660f77ffed1f1a |
"""
Linear Discriminant Analysis and Quadratic Discriminant Analysis
"""
# Authors: Clemens Brunner
# Martin Billinger
# Matthieu Perrot
# Mathieu Blondel
# License: BSD 3-Clause
from __future__ import print_function
import warnings
import numpy as np
from scipy import linalg
from .extern... | vibhorag/scikit-learn | sklearn/discriminant_analysis.py | Python | bsd-3-clause | 25,845 | [
"Gaussian"
] | d085a0080504607c6587164b3ebf6aa403d59cf2356ca176676302dcfc1c29f8 |
# Copyright (C) 2010-2019 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... | KaiSzuttor/espresso | samples/visualization_npt.py | Python | gpl-3.0 | 2,542 | [
"ESPResSo"
] | dd38f841c6843697e81ba82e5b4d348210bca2f49e2d52515309c6054ed1ef04 |
""" This is the RFIO StorageClass """
__RCSID__ = "$Id$"
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Resources.Utilities.Utils import checkArgumentFormat
from DIRAC.Resources.Storage.StorageBase import StorageBase
from DIRAC.Core.Utilities.Subprocess ... | sposs/DIRAC | Resources/Storage/RFIOStorage.py | Python | gpl-3.0 | 40,340 | [
"DIRAC"
] | 86cccce2388bc72194561155cb7cbc2d70ca466a19a678ea2e17b62ac4ae56a0 |
#!/usr/bin/env python
########################################################################
# File : tornado-start-all
# Author : Louis MARTIN
########################################################################
# Just run this script to start Tornado and all services
# Use CS to change port
from __future__ i... | yujikato/DIRAC | src/DIRAC/Core/Tornado/scripts/tornado_start_all.py | Python | gpl-3.0 | 2,231 | [
"DIRAC"
] | bba932d64de51435f26cd4da83fb15c236612948642cdb4ea5446664059605c6 |
#########################################################################
# Name: FeedBackLoopProcessor
#
# FileName: fblp.py
#
# Version: 1.0
#
# Usage: This program periodically inspects a mailbox for incoming
# feedback loop mail in ARF (Abuse Report Format). When it
# finds an abuse report, it extract... | vimmaniac/iemfbl | fblp.py | Python | lgpl-3.0 | 6,321 | [
"VisIt"
] | 2592ea10719959af2cfd51dbd77c8d1bdacba97a44c958e4066e04708b89035e |
#!/usr/bin/python
"""
Tracking of rotating point.
Rotation speed is constant.
Both state and measurements vectors are 1D (a point angle),
Measurement is the real point angle + gaussian noise.
The real and the estimated points are connected with yellow line segment,
the real and the measured points ar... | eirTony/INDI1 | to/lang/OpenCV-2.2.0/samples/python/kalman.py | Python | mit | 3,942 | [
"Gaussian"
] | 5b45e9aa5fabff44db1739812f389f13423101bdf7beac185d107cd2a4a479a1 |
tableData = [['apples', 'oranges', 'cherries', 'banana'],
['Alice', 'Bob', 'Carol', 'David'],
['dogs', 'cats', 'moose', 'goose']]
def printTable(tableData):
colWidths = [0]*len(tableData)
for col in range(len(tableData)):
for row in range(len(tableData[0])):
if len(tableData[col][row... | disasterisk/itc110 | assignment6.py | Python | mit | 591 | [
"MOOSE"
] | 0bc2af0c002663e8b6506464abbcf9f365c029aa1d6ccd719c2d4ef29fa7232a |
'''
PathwayGenie (c) GeneGenie Bioinformatics Ltd. 2018
PathwayGenie is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
# pylint: disable=consider-using-set-comprehension
# pylint: disable=invalid-name
# pylint: disable=wrong-im... | neilswainston/PathwayGenie | pathway_genie/export.py | Python | mit | 3,027 | [
"VisIt"
] | b4ae451087d5d013e7ddc48cbf87e759d70005075e6d6d4d760a92cc9c1617a1 |
# Copyright 2018 The TensorFlow Probability Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law o... | tensorflow/probability | tensorflow_probability/examples/vae.py | Python | apache-2.0 | 18,856 | [
"Gaussian"
] | 76abb25e905434ec5792ee3a332b8d112a270441ad8a59003e5bfde49b12ada9 |
import warnings
from sympy import Basic, Symbol, Integer
from sympy.core.sympify import sympify, converter, SympifyError
from sympy.core.basic import S
from sympy.polys import Poly, roots, cancel
from sympy.simplify import simplify
from sympy.utilities import any
from sympy.printing import sstr
import random
class ... | mattpap/sympy-polys | sympy/matrices/matrices.py | Python | bsd-3-clause | 67,835 | [
"DIRAC",
"Gaussian"
] | 33951d2691c2b93829336274e2b401e300225f5d721f9e07d4121a4bc45e4047 |
import enum
import sys
import unittest
from enum import Enum, IntEnum, unique, EnumMeta
from pickle import dumps, loads, PicklingError, HIGHEST_PROTOCOL
pyver = float('%s.%s' % sys.version_info[:2])
try:
any
except NameError:
def any(iterable):
for element in iterable:
if element:
... | viridia/coda | third-party/python/enum34-1.0/enum/test_enum.py | Python | apache-2.0 | 60,233 | [
"MOE"
] | eeb96e50d299ee7e2dbb61b1e7b879d67816408a433ed2e2c1896f7c3ae651fc |
"""Event tracking backend that sends events to woopra.com"""
from __future__ import absolute_import
from track.backends import BaseBackend
from woopra import WoopraTracker
import logging
LOG = logging.getLogger(__name__)
class WoopraBackend(BaseBackend):
"""
Event tracker backend that send events to woopra... | Learningtribes/edx-platform | common/djangoapps/track/backends/woopra.py | Python | agpl-3.0 | 5,739 | [
"VisIt"
] | 7926e525ee2777b1c07ccfb3e4581e229929cc6549a865475751ee7d994cbb0c |
#!/usr/bin/env python
"""
lib.py
Library of utilities for ocean models, imported into the namespace
when importing the model module
Written by Brian Powell on 10/18/13
Copyright (c)2010--2021 University of Hawaii under the MIT-License.
"""
import numpy as np
import seapy
import scipy.constants
# Define ref... | powellb/seapy | seapy/model/lib.py | Python | mit | 11,643 | [
"Brian"
] | 6b5f2a41cdf648bcbddd6531ea37e0b6c6736a21ca8e7f131bbdb82a1da80534 |
import numpy as np
import tensorflow as tf
from tensorflow.contrib import rnn
def _print_success_message():
print('Tests Passed')
def test_create_lookup_tables(create_lookup_tables):
with tf.Graph().as_default():
test_text = '''
Moe_Szyslak Moe's Tavern Where the elite meet to drink
... | marko911/deep-learning | tv-script-generation/problem_unittests.py | Python | mit | 12,202 | [
"MOE"
] | 7f6e3e1a79bfc80e79b0063fd8844539070bb82e26026a25b13a16276294b581 |
#!/usr/bin/env python
#-*- coding:utf-8 -*-
#
# This file is part of the NNGT project to generate and analyze
# neuronal networks and their activity.
# Copyright (C) 2015-2019 Tanguy Fardet
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License a... | Silmathoron/NNGT | nngt/lib/constants.py | Python | gpl-3.0 | 1,450 | [
"NEURON"
] | 0ef6f042ea826aaf22857ca75632cbeb0e686db8961ebf1f64a7d326d62b1733 |
#
# Copyright (C) 2013-2019 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... | psci2195/espresso-ffans | testsuite/python/correlation.py | Python | gpl-3.0 | 2,046 | [
"ESPResSo"
] | b5639260e14ef50d04f471714cbae907938420cea03e8446ac1acf5d1387cf3f |
from __future__ import annotations
from typing import TYPE_CHECKING, Callable, Dict, Tuple, Any, cast
import functools
import numpy as np
import math
import types
import warnings
# trapezoid is a public function for scipy.integrate,
# even though it's actually a NumPy function.
from numpy import trapz as trapezoid
fro... | anntzer/scipy | scipy/integrate/_quadrature.py | Python | bsd-3-clause | 33,320 | [
"Gaussian"
] | 5a912122c8b7ceb9cf80188fe14cd0f0a01506a0ff71d8615d2de53232154fef |
import os
import csv
import pandas as pd
# ------------ Part1: Check the metfile
def check_metfile(input_file, output_file):
''' Functie die een metfile leest en dan checkt of de profielinformatie en de metingen genoeg elementen hebben. En
allemaal een afsluiting. Geeft een excelbestand terug met daarin de pr... | tijhuisingenieurs/gistools | tools/check_metfile.py | Python | gpl-3.0 | 6,207 | [
"Elk"
] | dbd3fbd150adb60882aaa54dd1b28211aec38964940d3efeea140efa85091361 |
# Mantid Repository : https://github.com/mantidproject/mantid
#
# Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
# NScD Oak Ridge National Laboratory, European Spallation Source
# & Institut Laue - Langevin
# SPDX - License - Identifier: GPL - 3.0 +
# pylint: disable=no-init,too-few-public-meth... | mganeva/mantid | Framework/PythonInterface/plugins/algorithms/LoadCIF.py | Python | gpl-3.0 | 18,605 | [
"CRYSTAL"
] | d935f20df2536552a6c7511b0eb1d4d4be3fc8c083c9d5c9721891cd8a2f3e66 |
import logging
from django.shortcuts import get_object_or_404,render
from .forms import MyForm
#from .forms import MyFormbool
from django.urls import reverse
# Create your views here.
from django.http import HttpResponseRedirect, HttpResponse
from django.template import loader
#my package
from datamanagerpkg import Pro... | CARPEM/GalaxyDocker | data-manager-hegp/analysisManager/analysismanager/sequencer/views.py | Python | mit | 31,062 | [
"Galaxy"
] | d4b2547838e7f8d9ff3b651686a7a8c19c535d9a57d3873517f8c78b76a49f7f |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright 2013 The Plaso Project Authors.
# Please see the AUTHORS file for details on individual 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 L... | cvandeplas/plaso | plaso/parsers/bencode_parser_test.py | Python | apache-2.0 | 5,358 | [
"Brian"
] | 20930f19da9057fef499679779c1376c4cd618c48fc2c265848b6bd6867d9ed4 |
import os
import warnings
# cmr calls all available methods in ase.atoms detected by the module inspect.
# Therefore also deprecated methods are called - and we choose to silence those warnings.
warnings.filterwarnings('ignore', 'ase.atoms.*deprecated',)
from ase.test import NotAvailable
# if CMR_SETTINGS_FILE is mis... | suttond/MODOI | ase/test/cmr/reactions_xsimple.py | Python | lgpl-3.0 | 2,265 | [
"ASE"
] | 3bf311801b47ba261b506a61bc3095d3ccc01d4d6be04c27410350521ff18c8f |
#!/usr/bin/env python
# vim:fileencoding=UTF-8:ts=4:sw=4:sta:et:sts=4:fdm=marker:ai
from __future__ import (unicode_literals, division, absolute_import,
print_function)
__license__ = 'GPL v3'
__copyright__ = '2013, Kovid Goyal <kovid at kovidgoyal.net>'
__docformat__ = 'restructuredtext en'
... | sss/calibre-at-bzr | src/calibre/db/tests/writing.py | Python | gpl-3.0 | 16,188 | [
"MOOSE"
] | a97e2c14425e552072a7a49415d7d8c363b4bfc894d7e78220bb24835d528fef |
#!/usr/bin/env python
#Copyright 2012
#Ganesh Katrapati <ganesh.katrapati@gmail.com>
#This file is part of MinQL.
#MinQL 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 ... | neshkatrapati/MinQL | python/minqli.py | Python | gpl-3.0 | 4,903 | [
"exciting"
] | f460e82087a5c56555e3fd355b8050e1bb7d8e0e59252fbbd813cb71a39c97b4 |
"""Configuration file for eruption scenario
Scenario Name: Mount Galunggung
This scenario is based on the observed eruptive characteristics of the 1982 Mount Galunggung eruption in West Java, Indonesia. The eruption date is present day and the wind profile is ex... | GeoscienceAustralia/PF3D | testing/galunggung.py | Python | gpl-3.0 | 3,461 | [
"Gaussian"
] | 6b79c189a8be195eaf3c322f0160aec2f2febab31ee03b0e640111152aec60fe |
# -*- coding: utf-8 -*-
"""Resources for PyBEL."""
CHEBI_URL = "https://raw.githubusercontent.com/pharmacome/conso/d67144bc27a21626a514837b3b4382413dd6866b/external/chebi-names.belns"
EC_URL = (
"https://raw.githubusercontent.com/pharmacome/conso/d67144bc27a21626a514837b3b4382413dd6866b/external/ec-code.belns"
)
... | pybel/pybel | src/pybel/resources/resources.py | Python | mit | 1,619 | [
"Pybel"
] | 1dd1636ef57a4760a0eb1601e505be573f46c6e60809267bc164403968326457 |
#!/usr/bin/env python
#
# Electrum - lightweight Bitcoin client
# Copyright (C) 2011 thomasv@gitorious
#
# 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... | kepppu/electrum-n900 | wallet.py | Python | gpl-3.0 | 33,276 | [
"VisIt"
] | 4d6fdbbf51c790f4d170f924d1c5d66f86643704c6e7284d730453232600d721 |
"""Test class for Repository CLI
:Requirement: Repository
:CaseAutomation: Automated
:CaseLevel: Component
:CaseComponent: Repositories
:Assignee: chiggins
:TestType: Functional
:CaseImportance: High
:Upstream: No
"""
from random import choice
from string import punctuation
import pytest
import requests
from f... | SatelliteQE/robottelo | tests/foreman/cli/test_repository.py | Python | gpl-3.0 | 108,047 | [
"Galaxy"
] | 9bc430c7a8ffa351acc5beb3f5393f94bc510ac07270931ad7a8f6db15764a37 |
import pytest
import os
from lissero.scripts.Serotype import SerotypeDB
from lissero.scripts.Blast import Blast
from lissero.scripts.Sample import Sample
from lissero.scripts.Sample import Samples
BLAST_OUTFMT = '6 qaccver saccver length slen pident'
test_folder = os.path.dirname(os.path.realpath(__file__))
db_folder... | MDU-PHL/LisSero | tests/test_SampleClass.py | Python | gpl-2.0 | 2,595 | [
"BLAST"
] | 683e31ac649f359ebec9d73d3315e06c089b1c386caac41b34b677fe64decfc4 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Module containing classes to generate grain boundaries.
"""
import numpy as np
from fractions import Fraction
from math import gcd, floor, cos
from functools import reduce
from pymatgen import Structure, L... | gVallverdu/pymatgen | pymatgen/analysis/gb/grain.py | Python | mit | 117,980 | [
"CRYSTAL",
"pymatgen"
] | 3120a863fa3c57bfa526e0c6011362f6d410acd5e5aa194ad544fc620ac1ae88 |
from pycparser import c_ast
from pycparser import parse_file
class FuncDefVisitor(c_ast.NodeVisitor):
def __init__(self):
self.decls = {}
def visit_Decl(self, node):
if isinstance(node.type, c_ast.FuncDecl):
self.decls[node.name] = node.type.args
def parse_header(lib, names):
... | seibert/blaze-core | blaze/module/cheader.py | Python | bsd-2-clause | 537 | [
"VisIt"
] | 21d17a4bd03c197d3a8978e7f4fe6c8de20bb5bb4cd69b51625208cd55948397 |
# ----------------------------------------------------------------------------
# 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/stats/tests/test_composition.py | Python | bsd-3-clause | 52,056 | [
"scikit-bio"
] | ae301a3e844d2e170604451c2537110e249a731bdb6b0b0c7d9ce9408785be3f |
# Copyright (c) 2012 ARM Limited
# All rights reserved.
#
# The license below extends only to copyright in the software and shall
# not be construed as granting a license to any other intellectual
# property including but not limited to intellectual property relating
# to a hardware implementation of the functionality ... | SanchayanMaity/gem5 | src/python/m5/SimObject.py | Python | bsd-3-clause | 57,035 | [
"VisIt"
] | ed0fa32fae794f9df332df3d3776acc9fcfb4e994e46374334ae267b8890f59b |
# 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.
import os.path
import Bio.PDB.mmCIF.MMCIFlex
from UserDict import UserDict
__doc__="Turn ... | NirBenTalLab/proorigami-cde-package | cde-root/usr/lib64/python2.4/site-packages/Bio/PDB/MMCIF2Dict.py | Python | mit | 5,078 | [
"Biopython"
] | a8dd55d71ef3353c56e91a750b1b4785049eda88bf69f070e3384f7f2a5d4fe2 |
# Orca
#
# Copyright 2006-2009 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... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/scripts/apps/nautilus/__init__.py | Python | gpl-3.0 | 843 | [
"ORCA"
] | 89149c8ab094e3867728a76970c21f7ade89c89988e4fab7ce62e358bfa5b345 |
#! /usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Module: netcdf_to_shape.py
Created on Sun Jul 28 15:51:04 2013
@author: gcoombes
Dexcription: Create a shapefile of contours or probability regions from teh netcdf data
"""
### IMPORTS ###
from __future__ import print_function
import sys, os
import time
from itertoo... | gjcoombes/banks | banks/shape/xcyshape.py | Python | mit | 5,816 | [
"NetCDF"
] | 543df80aa769c2efff495097cbc5a5d7a29028e6c32e1d3d2281a71c3fe52c26 |
import numpy as np
from gpaw import debug
from gpaw.utilities.lapack import general_diagonalize
class MatrixDescriptor:
"""Class representing a 2D matrix shape. Base class for parallel
matrix descriptor with BLACS."""
def __init__(self, M, N):
self.shape = (M, N)
def __nonzero__(s... | robwarm/gpaw-symm | gpaw/matrix_descriptor.py | Python | gpl-3.0 | 24,015 | [
"GPAW"
] | 681ee6cebec5b55a78d7a1e2a0622239280bb98d604404c0dc4c471d6ff67f33 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkDataSetToDataObjectFilter(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | chrisidefix/devide | modules/vtk_basic/vtkDataSetToDataObjectFilter.py | Python | bsd-3-clause | 512 | [
"VTK"
] | 0b100cf23d1aa351a8917799466166cb3a3405a8f440c29ddd922df836bf53dc |
"""Convert to and from Roman numerals"""
__author__ = "Mark Pilgrim (f8dy@diveintopython.org)"
__version__ = "1.4"
__date__ = "8 August 2001"
__copyright__ = """Copyright (c) 2001 Mark Pilgrim
This program is part of "Dive Into Python", a free Python tutorial for
experienced programmers. Visit http://diveint... | Orav/kbengine | kbe/src/lib/python/Doc/tools/roman.py | Python | lgpl-3.0 | 2,766 | [
"VisIt"
] | 90561c88d5b201e1f49388fb58631f175fa61adf817a32f63ad2a5dc12bc899d |
'''
Created on Feb 4, 2017
@author: Jake
'''
import math
from Connection import *
class Neuron(object):
inCons = []
outCons = []
neuronID = None
neuronType = None
value = None
def __init__(self):
self.inCons = []
self.outCons = []
self.neuronID = 0
self... | JakeShulman/G-Neat | Neuron.py | Python | apache-2.0 | 1,908 | [
"NEURON"
] | 6fc6af05b0332c1acebbe0f2a1a5ed3aff6aac76bf5c7ef842e0e7503c6a6351 |
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
import unittest
from DIRAC.tests.Utilities.utils import cleanTestDir
from DIRAC import gLogger
from DIRAC.Interfaces.API.Dirac import Dirac
from DIRAC.DataManagementSystem.Client.DataManager import DataManager... | yujikato/DIRAC | src/DIRAC/tests/Utilities/IntegrationTest.py | Python | gpl-3.0 | 1,097 | [
"DIRAC"
] | f8d2f724122616ea3f0f5203ad7ae21a84b10a98264cf867aab1e84b5b0f34bd |
from __future__ import division, print_function, absolute_import
from copy import deepcopy
from sklearn.base import clone
from sklearn.metrics import accuracy_score, roc_auc_score, mean_squared_error
import numpy
import pandas
from scipy.special import expit
from six.moves import cPickle
from ..estimators import Cla... | yandex/rep | rep/test/test_estimators.py | Python | apache-2.0 | 8,936 | [
"Gaussian"
] | 167b11005c3ad9f0363cfb1b5f52ef4582f83c56dc1d77326f6f9a758452dbb6 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2017 Lenovo, Inc.
#
# 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
# ... | Tatsh-ansible/ansible | lib/ansible/modules/network/lenovo/cnos_interface.py | Python | gpl-3.0 | 26,957 | [
"VisIt"
] | 661c0ba9ecb2a2668a62214a32be4b535454ec8e3ba147440daff1ef5bcb9642 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import subprocess as sp
from Bio import SeqIO
from .make_paths import get_blast_db_path
def fastq_to_fasta(fastq_path):
""" Yields out fasta records from fastq file """
with open(fastq_path) as input_handle:
for record in SeqIO.parse(input_handle, 'fast... | TheCulliganMan/cgap | cgap/format_srdb.py | Python | gpl-3.0 | 875 | [
"BLAST",
"Biopython"
] | 1e7b2bf7e0b8a18c711b99af65b7978906da459bf3698bf2905fb0f7649270c4 |
# -*- coding: utf-8 -*-
"""
NeuroTools.signals.spikes
==================
A collection of functions to create, manipulate and play with spikes signals.
Classes
-------
SpikeTrain - object representing a spike train, for one cell. Useful for plots,
calculations such as ISI, CV, mean rate(), ... | meduz/NeuroTools | src/signals/spikes.py | Python | gpl-2.0 | 111,706 | [
"NEURON"
] | a82b84003d2a4a79a4a72edc94c46e4ec15bbbc15c9672d718c4e4876b2b6bcf |
"""
Written by : Raizan
Date : April 5th, 2015
Script for renaming files uploaded by AnimeChiby.com
Two patterns covered in this script: Mediafire and Mega
Rename files in a folder to "[Anime Title] [#Episode].mkv"
Example: "637_smc_19_hd_hs_acb.mkv" to "Sailor Moon Crystal 19.mkv"
"""... | Raizan/ACBFileRenamer | acb_rename_script.py | Python | mit | 3,644 | [
"CRYSTAL"
] | c64102048b09a44f1af2694597711333a14238ad4965a293b9809cbf90cf5a23 |
from PeacockActor import PeacockActor
import vtk
from vtk.util.colors import peacock, tomato, red, white, black
class ExodusActor(PeacockActor):
def __init__(self, renderer, data, type, index):
PeacockActor.__init__(self, renderer)
self.data = data
self.type = type
self.index = index
self.solid... | gleicher27/Tardigrade | moose/gui/vtk/ExodusActor.py | Python | lgpl-2.1 | 1,384 | [
"VTK"
] | 83e2992199830ad2a1cad06ca0ff7de49265f8c53dc6c5e862d2a3e8961e8d33 |
#!/usr/bin/python
# coding: utf-8
#----------------------------------------------------------------
# Author: Max Geislinger
# Description: este algoritmo descreve a sétima implementação de OpenCV
# Function: Digital Image -> Transform HSV -> Binary Image -> Erosion Binary -> Find area -> Find Coordinates
# Function ... | xamgeis/RoboPi | AlexaPi/MOVIMENTO_HORIZONTAL.py | Python | mit | 9,324 | [
"Gaussian"
] | eafc2f8f70c9da049e939baef715214d56849d7082990b8b229b59ecb70afde1 |
"""Ansible specific plyint plugin for checking deprecations."""
# (c) 2018, Matt Martz <matt@sivel.net>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
# -*- coding: utf-8 -*-
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import dat... | privateip/ansible | test/lib/ansible_test/_util/controller/sanity/pylint/plugins/deprecated.py | Python | gpl-3.0 | 11,848 | [
"VisIt"
] | 9c2e19d2a3e4d3ada41ee7b00625fa9a4a1993078d8cff2cf9454126611441bc |
#
# Copyright (C) 2004-2006 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.
#
import argparse
import csv
import os
import sys... | bp-kelley/rdkit | rdkit/Chem/ChemUtils/SDFToCSV.py | Python | bsd-3-clause | 2,519 | [
"RDKit"
] | fae1e53fdbb54960218e83369ddeb36b361edbddb60e9dd90c077f40b0a450a0 |
#!/usr/bin/env python
"""Utility classes and functions for SAMPLing analysis."""
# =============================================================================
# GLOBAL IMPORTS
# =============================================================================
import os
import csv
import glob
import json
import operat... | MobleyLab/SAMPL6 | host_guest/Analysis/Scripts/pkganalysis/sampling.py | Python | mit | 24,658 | [
"Amber",
"Gromacs",
"NAMD",
"OpenMM"
] | 560573970db303024f022febd1f429f076845580197aa30a94e25416e9b65ebe |
# 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.
"""The Bio.Nexus contains a NEXUS file parser and objects to model this data."""
| Ambuj-UF/ConCat-1.0 | src/Utils/Bio/Nexus/__init__.py | Python | gpl-2.0 | 249 | [
"Biopython"
] | 40d1024e4bab8575357489baac455ebd6d5b61a16bc71cd37398403cd8b4cf5f |
# -*- coding: utf-8 -*-
""" Tests for student account views. """
import re
from unittest import skipUnless
from urllib import urlencode
import json
import mock
import ddt
import markupsafe
from django.conf import settings
from django.core.urlresolvers import reverse
from django.core import mail
from django.contrib im... | B-MOOC/edx-platform | lms/djangoapps/student_account/test/test_views.py | Python | agpl-3.0 | 18,469 | [
"VisIt"
] | 0d2a689fd6f7bf78b18ce5d170f8531b3cf3cabda669a0dd994b4df3b2f1d606 |
#!/usr/bin/env python
#-*- coding:utf-8 -*-
# test_generation2.py
# This file is part of the NNGT module
# Distributed as a free software, in the hope that it will be useful, under the
# terms of the GNU General Public License.
"""
Test the new methods of the :mod:`~nngt.generation` module.
"""
import os
import nu... | Silmathoron/NNGT | testing/test_generation2.py | Python | gpl-3.0 | 12,950 | [
"Gaussian"
] | 022d069e51ad945bcb81e505c21521db4cd11e1782c987ba4a53c8b3c9327dde |
#!/usr/bin/env python
"""
Usage: update_site.py [options]
Updates a server's sources, vendor libraries, packages CSS/JS
assets, migrates the database, and other nifty deployment tasks.
Options:
-h, --help show this help message and exit
-e ENVIRONMENT, --environment=ENVIRONMENT
T... | yvan-sraka/wprevents | bin/update_site.py | Python | bsd-3-clause | 4,635 | [
"GULP"
] | 9069617fd40bbc06c3aae883834a2ccad7a0a3f1ef3ce8f3d631a8dd218461cd |
# Copyright 2011 Nicholas Bray
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing... | ncbray/pystream | bin/analysis/cfg/dom.py | Python | apache-2.0 | 4,326 | [
"VisIt"
] | c7fb06faebb4b224ea6ca8368a7d6a7e2bae738f1c6eda1138687e87c67891a7 |
# Copyright (c) 2003-2013 LOGILAB S.A. (Paris, FRANCE).
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
#
# 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, o... | Shouqun/node-gn | tools/depot_tools/third_party/pylint/checkers/design_analysis.py | Python | mit | 14,962 | [
"VisIt"
] | cd0ea72fc201d6cfac8d932541d5ca9096b8babc08319fdf3249cc047df14926 |
###############################################################################
#
# Copyright (c) 2011 Ruslan Spivak
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, inc... | slideclick/slimit | src/slimit/visitors/minvisitor.py | Python | mit | 14,179 | [
"VisIt"
] | b8f642c529e8c236df7a9920ed873cc6e093122dd3096726c0432a60bbb09166 |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""The fsl module provides classes for interfacing with the `FSL
<http://www.fmrib.ox.ac.uk/fsl/index.html>`_ command line tools. This
was written to work with FSL version 4.1.4.
Examples
--------
See the... | sgiavasis/nipype | nipype/interfaces/fsl/utils.py | Python | bsd-3-clause | 84,310 | [
"Gaussian",
"VTK"
] | 24ed50c039cca601c95a39fe5e04dc15f5f7184b004cd6d5bd50e2c9df795c37 |
# Copyright 2008-2012 Nokia Siemens Networks Oyj
#
# 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... | Senseg/robotframework | src/robot/reporting/resultwriter.py | Python | apache-2.0 | 4,098 | [
"VisIt"
] | 67a845e6f9a353a1630f4690faf2cb2b7c057856d613c5642d3a29b15d75f1d6 |
"""
forked from github.com/python-acoustics
GPLv3
"""
from __future__ import annotations
import numpy as np
def ms(x: np.ndarray) -> np.ndarray:
"""Mean Square value of signal `x`.
input
-----
* x: signal vector
output
------
* Mean square of `x`.
"""
return (abs(x) ** 2).mean... | scivision/soothing-sounds | src/soothingsounds/signal_acoustics.py | Python | gpl-3.0 | 812 | [
"Gaussian"
] | 54817a1bdc1f4399209028f378a287b7d8d641165e91df7f55aabc05db63c213 |
'''
Write to a text file
-----------------------------------------------------------
(c) 2013 Allegra Via and Kristian Rother
Licensed under the conditions of the Python License
This code appears in section 3.4.1 of the book
"Managing Biological Data with Python".
----------------------------------------... | raymonwu/Managing_Your_Biological_Data_with_Python_3 | 03-data_columns/write_text_file.py | Python | mit | 454 | [
"NEURON"
] | d588db40fe0e5cd0cce2e3299cc5c82d2d2b8bd8531a4840edd6e74a3e9c13a7 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2020, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Test scan logfiles in cclib"""
import os
import unittest
import numpy
import cclib
from skip import s... | cclib/cclib | test/data/testScan.py | Python | bsd-3-clause | 7,204 | [
"Jaguar",
"MOLCAS",
"ORCA",
"TURBOMOLE",
"cclib"
] | c7c4462b09ed18ec98f9d64e09417f03c4091b3fa024121c407ecd6903a01bad |
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from neuron import h
import numpy as np
import sys
n3dpoints = {} #has sec name and the first and last coordinates of its location
def retrieve_coordinate(sec):
sec.push()
x, y, z, d = [],[],[],[]
area = 0
tot_points = 0
connec... | ccluri/L5Pyr | morph_compare.py | Python | gpl-3.0 | 2,604 | [
"NEURON"
] | fe38803d097fbaff21ed2bb15ff3eef7ef11bbaef8eb4d307fe96c94b1d4e59a |
#
# Code to parse the interesting bits of a PAML results file that contains
# statistics for several trees. Note, this approach contains some hacks that
# are probably specific to multiple-tree CODEML files, Biopython has a module
# for handling other PAML outputs, and it probably a better starting point for
# 'normal'... | xji3/IGCCodonSimulation | Parse_multitree_paml.py | Python | mit | 6,166 | [
"Biopython"
] | 7e4e80cfe0f04cff0f68a63bdc9bc2aed71a795f5277a1bc33a576993694ed45 |
# Copyright (C) 2004-2008 Paul Cochrane
#
# 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.
#
# This program is distribut... | paultcochrane/pyvisi | pyvisi/renderers/gnuplot/camera.py | Python | gpl-2.0 | 4,799 | [
"VTK"
] | ecbc843766be869b765a981f348de57f8418fdb4e4f4600b68e0776a4be033d1 |
# -*- coding: utf-8 -*-
"""
molvs.validations
~~~~~~~~~~~~~~~~~
This module contains all the built-in :class:`Validations <molvs.validations.Validation>`.
"""
from __future__ import print_function
from __future__ import unicode_literals
from __future__ import division
import logging
from rdkit import Chem
from .er... | mcs07/MolVS | molvs/validations.py | Python | mit | 7,188 | [
"RDKit"
] | 0376ad6128f05dcc2e8aeedcceedaa5b7e2c5e3e537e47a3e504cafbc2904d89 |
# -*- coding: utf-8 -*-
import time
import unittest
import logging
import functools
from nose.tools import * # flake8: noqa (PEP8 asserts)
import mock
from framework.auth.core import Auth
from website import settings
import website.search.search as search
from website.search import elastic_search
from website.search... | njantrania/osf.io | tests/test_elastic.py | Python | apache-2.0 | 27,583 | [
"Brian"
] | aa5fd693faad20b49d20c8f1325b355f496f51918fd63987f1d47f2509273fcc |
"""
Copyright (c) 2015 Andreea Georgescu
Created on Wed Nov 19 00:18:55 2014
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.
... | Andreea-G/Codds_DarkMatter | src/Data/CDMSSi2012.py | Python | gpl-2.0 | 3,725 | [
"Gaussian"
] | 4b008a56fe670d02332c748307faa725a2a4215bbe943e859cac283830802aad |
from pymol import cmd
from pymol import cgo
from chempy import models
import cProfile
import RMF
colors = {}
periodic_table = [
"INV", "H", "He", "Li", "Be", "B", "C", "N", "O",
"F", "Ne", "Na", "Mg", "Al", "Si", "P", "S", "Cl", "Ar", "K", "Ca",
"Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn", "... | salilab/rmf | plugins/pymol/plugin.py | Python | apache-2.0 | 6,324 | [
"ChemPy",
"PyMOL"
] | ccd319ee9e07ee042940e7d25028793b98b2d10a314000373bcc6498559579ab |
'''
This component constantly polls a pygame camera device,
when a message is received on its input it outputs an image.
Created on 29/11/2009
@author: Brian Thorne
'''
import logging
import numpy
from scipysim import Source, Actor, Channel, Event, LastEvent
import logging
verbose = True
LOG_FILENAME = None
logging.b... | mm318/scipysim-nogui | scipysim/actors/io/VideoSnapshot.py | Python | gpl-3.0 | 4,553 | [
"Brian"
] | 3d2e78e3c75e051c1fa46e94f5e69e3d05ee9fa1d045c3e3d262422d24870895 |
#!/usr/bin/env python
################################################################################
# Copyright (C) 2014, 2015 GenAP, McGill University and Genome Quebec Innovation Centre
#
# This file is part of MUGQIC Pipelines.
#
# MUGQIC Pipelines is free software: you can redistribute it and/or modify
# it und... | ccmbioinfo/mugqic_pipelines | pipelines/rnaseq/rnaseq.py | Python | lgpl-3.0 | 50,141 | [
"BWA",
"Bioconductor",
"HTSeq"
] | 1e79b18188297ff24f772efac3c1b7387dc74cca7ab941e4199b173a03ff3d65 |
# This component assembles an analysis recipe for the annual adaptive comfort component
#
# Honeybee: A Plugin for Environmental Analysis (GPL) started by Mostapha Sadeghipour Roudsari
#
# This file is part of Honeybee.
#
# Copyright (c) 2013-2015, Chris Mackey <Chris@MackeyArchitecture.com>
# Honeybee is free softw... | samuto/Honeybee | src/Honeybee_Adaptive Comfort Analysis Recipe.py | Python | gpl-3.0 | 35,407 | [
"EPW"
] | fef72d502ae82f1f7c03fce06c84af3e5d42b335dd245320a903a782bd2fe996 |
# Copyright (C) 2010-2019 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... | fweik/espresso | samples/visualization_constraints.py | Python | gpl-3.0 | 5,030 | [
"ESPResSo"
] | f88e73ad54957b1f1a90e73ee01816b2f9658169392ca156756a704ef8cf783b |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
This module defines tools to perform aperture photometry.
"""
import warnings
import numpy as np
from astropy.nddata import NDData, StdDevUncertainty
from astropy.table import QTable
import astropy.units as u
from astropy.utils.exceptions import Astr... | astropy/photutils | photutils/aperture/photometry.py | Python | bsd-3-clause | 9,796 | [
"Gaussian"
] | 92fca9e1b13fa0e65484a7565149f8f4facdd692ea57b3f7d49d7d750b298766 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2017, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Test configuration interaction (CI) logfiles in cclib"""
import os
import unittest
import numpy
__filedir__ = os.pa... | gaursagar/cclib | test/data/testCI.py | Python | bsd-3-clause | 5,927 | [
"GAMESS",
"Gaussian",
"Jaguar",
"cclib"
] | ba7fa665799427e441ff36db642984c6427adb99b4e57f5e8cff5142af099e21 |
import re
from thefuck.utils import for_app
from thefuck.system import open_command
@for_app('yarn', at_least=2)
def match(command):
return (command.script_parts[1] == 'help'
and 'for documentation about this command.' in command.stdout)
def get_new_command(command):
url = re.findall(
r'... | mlk/thefuck | thefuck/rules/yarn_help.py | Python | mit | 431 | [
"VisIt"
] | 33f60180d0b5fcd7d14c7d6cf690b2896ea714179c3e4ba4e8c1d8d4c8f1de84 |
# pylint: disable = R0904, R0913, C0103
# ----------------------------------------------------------------------------
# Copyright 2014 Nervana Systems 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... | ypkang/neon | neon/backends/backend.py | Python | apache-2.0 | 61,394 | [
"Gaussian"
] | 5a742d81b6ac8b4687e85134c089d2bdbed87a60a9377fe0d213d33ebade2615 |
"""
Mecode
======
### GCode for all
Mecode is designed to simplify GCode generation. It is not a slicer, thus it
can not convert CAD models to 3D printer ready code. It simply provides a
convenient, human-readable layer just above GCode. If you often find
yourself manually writing your own GCode, then mecode is for y... | razeh/mecode | mecode/main.py | Python | mit | 35,815 | [
"Mayavi"
] | 4d37bf712e84e01b49f20c3724e3cdcb60a7c20c0dbe67e6ae938541795cbdd1 |
#!/usr/bin/env python
# -*- coding: latin-1 -*-
#
# Copyright 2016-2021 Blaise Frederick
#
# 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/LICEN... | bbfrederick/rapidtide | rapidtide/helper_classes.py | Python | apache-2.0 | 48,595 | [
"Gaussian"
] | 4ff19d7f58af450b93a8550d5e3821d785b78c53708f2b6ef9c0f107988ff3af |
# multicomp_lif.py ---
#
# Filename: multicomp_lif.py
# Description: Leaky Integrate and Fire using regular neuronal compartment
# Author: subha
# Maintainer:
# Created: Fri Feb 7 16:26:05 2014 (+0530)
# Version:
# Last-Updated:
# By:
# Update #: 0
# URL:
# Keywords:
# Compatibility:
#
#
# Co... | dilawar/moose-full | moose-examples/snippets/multicomp_lif.py | Python | gpl-2.0 | 6,179 | [
"MOOSE",
"NEURON"
] | f1985e328dfb572a97c194ac17d0e4b7e2e651c323810ab5db208b89f4fb6c8a |
#!/usr/bin/env python
"""A kernel that creates a new ASCII file with a given size and name.
"""
__author__ = "The ExTASY project <vivek.balasubramanian@rutgers.edu>"
__copyright__ = "Copyright 2015, http://www.extasy-project.org/"
__license__ = "MIT"
from copy import deepcopy
from radical.ensemblemd.exceptions... | radical-cybertools/ExTASY | examples/coam-on-stampede/kernel_defs/coco.py | Python | mit | 5,628 | [
"NetCDF"
] | 351bb95ea81757a8bf15646a846f1bd10eb100f5846b4f45157525ce74bffb39 |
# -*- coding: utf-8 -*-
"""configuration module for MPContribs Flask API"""
import os
import datetime
import json
import gzip
formulae_path = os.path.join(
os.path.dirname(__file__), "contributions", "formulae.json.gz"
)
with gzip.open(formulae_path) as f:
FORMULAE = json.load(f)
VERSION = datetime.datetime... | materialsproject/MPContribs | mpcontribs-api/mpcontribs/api/config.py | Python | mit | 5,326 | [
"pymatgen"
] | 212dac4662e5219903bba36e3da2699d5226459f2a67de411d7f90fa5c9eba88 |
#!/usr/bin/env python3
# coding=UTF-8
import os.path
import numpy as np
from scipy import constants
from MeshedFields import *
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('file', help='the file name of the watch point HDF5 file')
parser.add_argument('-Ex', help="plot Ex at given time", dest... | lehnertu/TEUFEL | scripts/plot_MeshedField.py | Python | gpl-3.0 | 6,044 | [
"VTK"
] | 9aeba62fe0736c650ec054d13f696525ade95f2d3a55d7600a6cee65bbab22f5 |
#!/usr/bin/env python
'''
subtracts BAM (or SAM) files based on sequence names
(for example, use to remove reads that also map rRNA)
outputs to alignments_filtered.BAM
by default, looks in alignments.BAM for .bam files
and expects corresponding files in mapped/alignments.BAM
ignores the species folder name i.e. mappe... | benjschiller/seriesoftubes | scripts/subtract_bam.py | Python | artistic-2.0 | 4,304 | [
"pysam"
] | df1deb62951b8b7bb21881f4899b521290ee45a5c45b2b55b9b41623d2bbeded |
import fresh_tomatoes
import media
# Create instances of favorite movies
# Each movie variable consist of 4 arguments
casino_royale = media.Movie("Casino Royale",
"Armed with a licence to kill, Secret Agent James"
" Bond sets out on his first mission as 007 and"
... | rmews/python-movie-website | movies/entertainment.py | Python | mit | 3,265 | [
"CASINO",
"Galaxy"
] | c8573a5fcf2245cd24f43c649ef4a86f9f1df391ae7fab61c876b26d38cd090f |
"""
Learns unregularized linear regression weights using stochastic gradient
descent.
==============
Copyright Info
==============
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 ... | bdol/bdol-ml | linear_regression/unregularized_regression/run_unregularized_regression.py | Python | lgpl-3.0 | 2,055 | [
"Brian"
] | 96aca4ab67628235e0fabec3b4eb4944023b1fa3411000d811b7444f39049bc4 |
import glob
import pandas as pd
import numpy as np
pd.set_option('display.max_columns', 50) # print all rows
import os
os.chdir("/gpfs/commons/home/biederstedte-934/evan_projects/correct_phylo_files")
normalB = glob.glob("binary_position_RRBS_normal_B_cell*")
mcell = glob.glob("binary_position_RRBS_NormalBCD19pCD27... | evanbiederstedt/RRBSfun | epiphen/cll_tests/total_cells.py | Python | mit | 32,920 | [
"MCell"
] | 302aed6abfa16fec38490fcb3f0025d21141d6b4e4874f0cabe45e83ef54f4e3 |
# -*- coding: utf-8 -*-
"""
(c) 2012-2021 Martin Wendt; see https://github.com/mar10/pyftpsync
Licensed under the MIT license: https://www.opensource.org/licenses/mit-license.php
"""
import time
from datetime import timedelta
from ftpsync.cli_common import (
common_parser,
creds_parser,
matcher_parser,
... | mar10/pyftpsync | ftpsync/scan_command.py | Python | mit | 4,354 | [
"VisIt"
] | 8b8d979fceabbe984d0997b9c117ad3c1145fe91c0268f4e43321e6d6f8a81be |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright: (c) 2015, Heyo
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
# this is a windows documentation stub. actual code lives in the .ps1
# file of the same name
ANSIBLE_METADATA = {'metadata_version': '1.1',
... | simonwydooghe/ansible | lib/ansible/modules/windows/win_nssm.py | Python | gpl-3.0 | 6,757 | [
"ADF"
] | 6ac8ed9f288b32fc33fe81cf5090ef384db8706caf3f9fae9b86a0396e19ca7b |
#!/usr/bin/env python
#
# Wrapper script for starting the Biopet JAR package
#
# This script is written for use with the Conda package manager and is copied
# from the peptide-shaker wrapper. Only the parameters are changed.
# (https://github.com/bioconda/bioconda-recipes/blob/master/recipes/peptide-shaker/peptide-shak... | joachimwolff/bioconda-recipes | recipes/biopet/biopet.py | Python | mit | 3,302 | [
"Bioconda"
] | d72a7b61d65dac230fdfc92a20acb85e3534349e160722af35b7179cb9650227 |
#!/usr/env/python
"""
Short description.
flow_accum_to_n.py: Implementation a route-to-multiple drainage stack alorithm.
Algorithm for route to multiple (N) flow accumulation. Inspiration for data
structures and attempting O(n) efficiency taken from Braun and Willet(2013).
Algorithm constructs drainage area and (o... | ManuSchmi88/landlab | landlab/components/flow_accum/flow_accum_to_n.py | Python | mit | 21,057 | [
"VisIt"
] | 54f6234ea0e8dd86cc25e16f3879ecd15ec5e54cc826e091ac2ba0cddfcea391 |
# -*- coding: utf-8 -*-
{
"A location that specifies the geographic area for this region. This can be a location from the location hierarchy, or a 'group location', or a location that has a boundary for the area.": 'この地域を地理的に指定するロケーション。これはロケーションの階層構造のうちの一つか、ロケーショングループの一つか、この地域の境界に面するロケーションです。',
"Acronym of the organ... | bobrock/eden | languages/ja.py | Python | mit | 353,167 | [
"VisIt"
] | 376c77cec6ee7018920811d6a75d714f33b8148595918d68220e3e6ffc7578a2 |
"""This demo program solves the equations of static linear elasticity
for a gear clamped at two of its ends and twisted 30 degrees."""
# Copyright (C) 2007 Kristian B. Oelgaard
#
# This file is part of DOLFIN.
#
# DOLFIN is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser Gen... | alogg/dolfin | demo/undocumented/elasticity/python/demo_elasticity.py | Python | gpl-3.0 | 2,995 | [
"VTK"
] | 60964158da8b6a4c8b66b67b04150e17388a1d779c29047ad4e64501404ce32c |
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