text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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|---|---|---|---|---|---|---|---|
import sys
from glob import glob
from setuptools import setup
if sys.version_info[0] != 2 or sys.version_info[1] < 7:
sys.exit("Sorry, only Python 2.7+ supported.")
setup(
name="fast5tools",
version="0.4",
description="Tools for working with fast5 files (nanopore data).",
author="John Urban",
... | JohnUrban/fast5tools | setup.py | Python | mit | 911 | [
"Biopython"
] | 0f0e82b4ae1cc3e0ded955255e09456886c9fc7bc95176f959ec8c4df142fd89 |
#!/usr/bin/python
import json
from threading import Thread
import time
import selenium.webdriver as wd
from config import Config
from util import Checker, Util, Url, Xpath
class Torn:
def __init__(self):
self.timer = 0
self.config = Config()
if self.config.client == Config.PHANTOM:
... | yusufRahmatullah/TornBot | torn.py | Python | mit | 8,322 | [
"VisIt"
] | 27a31080b18ae133323a963948857db2ae9410331dfe1cdf06685c3a1a201629 |
# 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... | psci2195/espresso-ffans | testsuite/python/observable_profileLB.py | Python | gpl-3.0 | 4,742 | [
"ESPResSo"
] | f97dd49275cee72149152e6fdf35fee9f422059bf5fc86446955c03fdab5bb13 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""Tests for the unique domains visited analysis plugin."""
import unittest
from plaso.analysis import unique_domains_visited
from plaso.lib import definitions
from tests.analysis import test_lib
class UniqueDomainsPluginTest(test_lib.AnalysisPluginTestCase):
"""Tes... | kiddinn/plaso | tests/analysis/unique_domains_visited.py | Python | apache-2.0 | 2,201 | [
"VisIt"
] | 68daa9f05e778780a927bed14b5935a94a40911e70b82578cd25323681530351 |
# Copyright (C) 2012,2013,2015,2016
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the ... | kkreis/espressopp | src/FixedQuadrupleList.py | Python | gpl-3.0 | 3,188 | [
"ESPResSo"
] | 058a5aaf92b14d384d6e100f01d722d2d41dd1023fe16701ca1c9419d3007ee5 |
import sys
simulator = ""
print "Has args: %s" % hasattr(sys,"argv")
# Lines from standard PyNN examples
if hasattr(sys,"argv"): # run using python
simulator = sys.argv[-1]
else:
simulator = "neuron" # run using nrngui -python
exec("from pyNN.%s import *" % simulator)
size = 4
inputName = "Input... | rgerkin/neuroConstruct | pythonNeuroML/PyNNUtils/Pop.py | Python | gpl-2.0 | 984 | [
"NEURON"
] | e8a977e4fd00c0bbe98841bee34da258f39e93c9eb6bd4eb4dfc6067fe0fbf2e |
from asap3 import *
from ase.lattice.cubic import *
atoms = FaceCenteredCubic(size=(10, 10, 10), symbol="Cu")
z = atoms.get_atomic_numbers()
z[7]=8
atoms.set_atomic_numbers(z)
try:
atoms.set_calculator(EMT())
except AsapError:
print "Test 1 passed."
else:
print "Test 1 failed."
atoms = FaceCenteredCu... | auag92/n2dm | Asap-3.8.4/Test/Exception.py | Python | mit | 782 | [
"ASE"
] | b889d22fd9f183a5c5d3cb9a2564eea35735b6ec8edb7386d755eafe1e68e4a5 |
# -*- coding: utf-8 -*-
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding field 'UltrasoundScanning.saved_ultrasound_image'
db.add_column(u'patient_ultrasoundscanning', 'sav... | aazhbd/medical_info01 | patient/migrations/0008_auto__add_field_ultrasoundscanning_saved_ultrasound_image.py | Python | bsd-3-clause | 28,937 | [
"VisIt"
] | b00fcb1a89efe033eda5bf3eab2b90e4d49d0e08e3044ab4f4cb17c6fb8a52e2 |
##
# Copyright 2009-2013 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
# the Hercules foundation (htt... | geimer/easybuild-easyblocks | easybuild/easyblocks/a/aladin.py | Python | gpl-2.0 | 14,593 | [
"NetCDF"
] | 50e1269f993fda06ca36c83345609ba5e6ed360330d181cd2b4b5476f109ca70 |
# SummaryOfReadQC/SummaryOfReadQC.py - a self annotated version of rgToolFactory.py generated by running rgToolFactory.py
# to make a new Galaxy tool called SummaryOfReadQC
# User admin@galaxy.org at 04/05/2015 11:13:46
# rgToolFactory.py
# see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
#
# copyright ross... | myoshimura080822/tools_of_preanalysis_on_docker_galaxy | SummaryOfReadQC/SummaryOfReadQC.py | Python | mit | 32,760 | [
"Galaxy"
] | 16120f6ccd9e966c9f2184103ff628f20de22b063741e5a0e61db800cc1e14a0 |
# Copyright 2018 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 a... | google/loaner | loaner/web_app/backend/models/fleet_model_test.py | Python | apache-2.0 | 5,619 | [
"MOE"
] | 230c9e4122cdb3a79e88755c738305e7146df2dc84357281311bc3b0e072ea01 |
"""
Computational Neurodynamics
Exercise 5
(C) Murray Shanahan et al, 2015
"""
import sys
sys.path.append('../Exercise_2')
from IzNetwork import IzNetwork
import numpy as np
import numpy.random as rn
def Sync2Connect(N1, N2):
"""
Constructs two populations of neurons (comprising two layers each) that
oscilla... | pmediano/ComputationalNeurodynamics | Fall2015/Exercise_5/Sync2Connect.py | Python | gpl-3.0 | 4,270 | [
"NEURON"
] | 45dbd327eaaba0b000085befc067b019798dc5b3dcdb7cf0bd86b01a2332afe8 |
from lxml import etree
import xml.sax
import sys
# XML SAX parser
class GenomeHandler(xml.sax.ContentHandler):
# Call when an element starts
def startElement(self, tag, attributes):
if tag == "neuron":
neurons.append(Neuron(attributes["id"], attributes["type"], attributes["activation"]))
elif tag == "connect... | BLueders/ENTM_CSharpPort | src/Scripts/anji2sharpneat.py | Python | gpl-3.0 | 1,963 | [
"NEURON"
] | 76ec3ffcca2df2796763bdd93c098a6e0e8417be8cc55e4a82ae20a696ce184e |
#
# mainTab
#
tab = self.notebook.mainTab
tab.settings['Program'] = 'crystal'
tab.settings['Output file name'] = 'qua_hf_2d_f_ir-int.out'
#
# SettingsTab
#
tab = self.notebook.settingsTab
tab.settings['Eckart flag'] = False
tab.settings['Neutral Born charges'] = False
tab.settings['Sigma value'] = 5
tab.settings['Mass ... | JohnKendrick/PDielec | Examples/Crystal/Quartz/script.py | Python | mit | 2,091 | [
"CRYSTAL"
] | dc69260ffedfd9f297f53eb54c8b517331b2e00c00049187b68d43b3d03dc360 |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | ghchinoy/tensorflow | tensorflow/tools/common/public_api.py | Python | apache-2.0 | 4,920 | [
"VisIt"
] | 87c43f91ef4c8b9278611dc4dad1367a96e3022b6943c652e7452137a027e4f6 |
# jhbuild - a build script for GNOME 1.x and 2.x
# Copyright (C) 2001-2006 James Henstridge
#
# tinderbox.py: build logic for a non-interactive reporting build
#
# 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 So... | rpavlik/jhbuild-vrjuggler | jhbuild/frontends/tinderbox.py | Python | gpl-2.0 | 12,761 | [
"VisIt"
] | e079a399d41eace4bf3d38ee155a8cbeea19611febbd30a01e34986901323ff6 |
from .genotype import Gene
class Innovations(object):
"""Tracks innovations.
Maintains list of gene and neuron mutations, preventing the recreation
of innovations that have already occurred.
"""
def __init__(self):
self.neuron_innov = []
self.gene_innov = []
self.innov = 0
... | jasonb5/pyneat | pyneat/innovations.py | Python | apache-2.0 | 2,829 | [
"NEURON"
] | 1f53ed2553e0f988b29b4837d6da1015feb9ac957d58ac6abe55d84ba14dd2b5 |
import os
import config
head_star_log = ["Sample", "Links","Started job","Started mapping","Finished","Mapping speed [Mr/h]","Input reads [n]","Input read length (mean)","Uniquely mapped [n]","Uniquely mapped [%]","Mapped length","Splices [n]","Splices annotated [n]","Splices GT/AG [n]","Splices: GC/AG [n]","Splices: ... | HudsonAlpha/aRNAPipe | lib/spider_stats.py | Python | mit | 28,193 | [
"HTSeq"
] | d64b0c7d1d1ced44c48404c687e34cc68162f70d6ba0d62242524367a35f562a |
#!/usr/bin/env
"""
Chuckchi_Winds_NARR_model_prep.py
Retrieve NARR winds for one locations
Icy Cape Line, Ckip2
Latitude = 70.8401 Longitude = 163.2054
Filter NARR winds with a triangular filter (1/4, 1/2, 1/4) and output every 3hrs
Provide U, V
Save in EPIC NetCDF standard
"""
#System Stack
import datetim... | shaunwbell/FOCI_Analysis | ReanalysisRetreival_orig/Chuckchi_Winds/Chuckchi_Winds_NARR_model_prep_Vladd.py | Python | mit | 6,206 | [
"NetCDF"
] | d4ceb090719c1ef3c6772e51aa5393fb23380f42530ae414e6942dc842b0096b |
# Copyright 2008-2009 Brian Boyer, Ryan Mark, Angela Nitzke, Joshua Pollock,
# Stuart Tiffen, Kayla Webley and the Medill School of Journalism, Northwestern
# University.
#
# This file is part of django-facebookconnect.
#
# django-facebookconnect is free software: you can redistribute it and/or modify
# it under the te... | ryszard/django-facebookconnect | facebookconnect/models.py | Python | gpl-3.0 | 11,164 | [
"Brian"
] | bf9641b686c8587ef9af820a219329a192732ab91fda4f253f3c1b9c2e3a51a6 |
# vim: tabstop=4 shiftwidth=4 softtabstop=4
# Copyright 2012 Nebula, 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
#
# ... | ikargis/horizon_fod | horizon/base.py | Python | apache-2.0 | 29,614 | [
"VisIt"
] | b4ba5f79fc098bda0b3648efb57a5fc018ed4e6ac6bd9ee138d1afa4fe9ecffa |
# -*- coding: utf-8 -*-
"""
Created on Wed Oct 1 13:41:48 2014
@authors: Luciano Masullo, Federico Barabas
"""
import os
import numpy as np
from scipy import ndimage as ndi
from PIL import Image
import pyqtgraph as pg
from pyqtgraph.Qt import QtCore, QtGui
import ringfinder.utils as utils
from ringfinder.neurosimul... | fedebarabas/ringfinder | ringfinder/ringFinderDeveloper.py | Python | gpl-3.0 | 26,312 | [
"Gaussian",
"NEURON"
] | 4a65f03760cdcf9c620f8a8aadf82e7d6bfe123740636d80bc5c0694fbbad2ea |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | TheTimmy/spack | var/spack/repos/builtin/packages/bwa/package.py | Python | lgpl-2.1 | 2,373 | [
"BWA"
] | 62e7bf4f30affdedf9f688100591d04ebc4eb429890acb67b3ba365bddf04574 |
"""Scraper for the Rhode Island Supreme Court
CourtID: ri
Court Short Name: R.I.
Author: Brian W. Carver
Date created: 2013-08-10
"""
from juriscraper.opinions.united_states.state import ri_p
class Site(ri_p.Site):
def __init__(self, *args, **kwargs):
super(Site, self).__init__(*args, **kwargs)
se... | Andr3iC/juriscraper | opinions/united_states/state/ri_u.py | Python | bsd-2-clause | 786 | [
"Brian"
] | 075c79d6221d18aa57afa46cd3210cbb038addec85d4c6fc890c7892eea61c85 |
import Levenshtein as editdist
import pandas as pd
def observed_wellbc_extraction(line, AD1='GGAAGCCTTGGCTTTTG'):
'''
This function returns the sequence (observed wellbc) before the first adaptor sequence
ToDo, fix alignments to well bc
Parameters
----------
... | erscott/RASLseqTools | RASLseqTools/RASLseqWellbc.py | Python | mit | 8,469 | [
"BLAST"
] | e15653af3be8567e68716a9dc30c5a514cf7f7a0412eec464d16c27347404659 |
# Copyright (c) 2006, 2008-2010, 2013-2014 LOGILAB S.A. (Paris, FRANCE) <contact@logilab.fr>
# Copyright (c) 2014 Brett Cannon <brett@python.org>
# Copyright (c) 2014 Arun Persaud <arun@nubati.net>
# Copyright (c) 2015-2018, 2020 Claudiu Popa <pcmanticore@gmail.com>
# Copyright (c) 2015 Florian Bruhin <me@the-compiler.... | ruchee/vimrc | vimfiles/bundle/vim-python/submodules/pylint/pylint/pyreverse/diadefslib.py | Python | mit | 8,779 | [
"VisIt"
] | 98b4661cb556237f00416ab6b7d7c3d966bb48977b8d60936ca37f4e503c1500 |
#!/usr/bin/env python
'''
ViSAPy example script for generating benchmark corresponding to an in vivo
tetrode recording
'''
#import modules
import uuid
import urllib2
import zipfile
import numpy as np
import h5py
import os
import glob
#workaround for plots on cluster
if not os.environ.has_key('DISPLAY'):
import matp... | espenhgn/ViSAPy | examples/example_in_vivo_tetrode.py | Python | gpl-2.0 | 14,783 | [
"NEURON"
] | 3c54fb80a25bf67822dd20f71992b2979defcde787b2cd1c8866d12245d9ba85 |
#!/usr/bin/env python3
"""
Copyright 2020 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester 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 ... | pwillworth/galaxyharvester | html/postGalaxy.py | Python | gpl-3.0 | 9,350 | [
"Galaxy"
] | f00e59db186f64f9b5d765271dee457832b1751c5b271e7a8fa8a99a747b15fa |
'''
computes an unsupervised combination of multiple kernels
Author : Akhil P M
Kernel types
1. Arc cosine
2. Gaussian
3. Polynomial
4. Sigmoid
'''
from settings import *
def compute_J(N, theta):
if N == 0:
return np.pi - theta
elif N == 1:
return np.sin(theta) + (np.pi - theta) * np.cos(theta)
elif ... | akhilpm/Masters-Project | UMKL/umkl.py | Python | mit | 3,993 | [
"Gaussian"
] | 5acce931c3c70c4f0c9361b4353425f05e21e54359670a062c5bb5d8c3762348 |
import logging
import requests
from lxml import etree
from itertools import chain
from . import TransportRTIProvider
from requests.exceptions import RequestException
from moxie.core.exceptions import ServiceUnavailable
from moxie.core.metrics import statsd
logger = logging.getLogger(__name__)
OPERATOR_KEY = "title"
... | ox-it/moxie | moxie/transport/providers/cloudamber.py | Python | apache-2.0 | 5,840 | [
"Amber"
] | 5a9bfa6c38a2f6e63499d1ca468f5a4a6405bf9e8333c18038c61e162b29124a |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | xzturn/tensorflow | tensorflow/python/autograph/pyct/cfg.py | Python | apache-2.0 | 31,607 | [
"VisIt"
] | 739c005218b7839a7553089d73fbe68d96c91873e63cbd6d5e4fce25859ee341 |
# -*- coding: utf-8 -*-
#
# hl_api_spatial.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License,... | Silmathoron/nest-simulator | pynest/nest/lib/hl_api_spatial.py | Python | gpl-2.0 | 45,069 | [
"NEURON"
] | 888b6924856410cd5c83854da021f2035731bd935c9724354adb0976cf630c7f |
# Copyright 2018 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | tensorflow/tensorflow | tensorflow/python/autograph/pyct/origin_info.py | Python | apache-2.0 | 9,984 | [
"VisIt"
] | 6d008169e2e5447b984ccc0e7848c4fd25a3a4ef243741a4114afba71fe220d1 |
#!/usr/bin/env python3
from reporter.connections import RedcapInstance
from reporter.emailing import RECIPIENT_SCAD_ADMIN
from reporter.application_abstract_reports.redcap.data_quality import (
RedcapMissingData,
RedcapMissingDataWhen,
RedcapInvalidDate,
RedcapRecordInvalidStudyNumber,
Red... | LCBRU/reporter | reporter/uhl_reports/scad/data_quality/redcap.py | Python | mit | 10,903 | [
"VisIt"
] | 071ff134793ba3df573bffec08e31ad76a6882ed0b311a7d637e93d730c208cd |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | psi4/psi4 | psi4/driver/procrouting/libcubeprop/__init__.py | Python | lgpl-3.0 | 937 | [
"Psi4"
] | 0da5b86d341df0e6df0974cecbeccf6ed8679ce9d45fbada38bf5f486fb9db96 |
#!/usr/bin/env python
# ----------------------------------------------------------------------------
# Copyright 2016 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 License at
#
# ... | Jokeren/neon | examples/music_genres.py | Python | apache-2.0 | 4,491 | [
"Gaussian"
] | 15679682e670419965b7406187c5c9d4a98e69bdd930bf9d81b699a50b8b9feb |
# 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... | belliottsmith/cassandra | pylib/cqlshlib/wcwidth.py | Python | apache-2.0 | 15,865 | [
"MOOSE"
] | 3ec6c5ece68394b22d6a257a9e2bbc17f38e81560b268d18a5be7e70e255dd06 |
"""Collection of DIRAC useful list related modules.
By default on Error they return None.
"""
__RCSID__ = "$Id$"
import random
import sys
random.seed()
def uniqueElements(aList):
"""Utility to retrieve list of unique elements in a list (order is kept).
:param aList: list of elements
:type aList: python:li... | andresailer/DIRAC | Core/Utilities/List.py | Python | gpl-3.0 | 3,753 | [
"DIRAC"
] | 8064d05e3ed0a32b7b96c53031f7c7566951c2cce3ac0c4de4ecb80f565f2423 |
#!/usr/bin/env python3
# Copyright 2016-2018 Brian Warner
#
# 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... | OSSHealth/ghdata | workers/facade_worker/facade_worker/facade06analyze.py | Python | mit | 6,594 | [
"Brian"
] | 59b49651896c3dc138b21f74a3129747248b12b961f4fa4e12a47fea39b42ba9 |
"""
.. deprecated:: 0.1
"""
import warnings
warnings.warn("transfer.py is deprecated. Directly operate over slabiter.", DeprecationWarning)
import numpy
from mpi4py import MPI
try:
from numba import jit
except ImportError:
jit = None
pass
class TransferFunction:
""" these a a function of Window Trans... | rainwoodman/pypm | pmesh/transfer.py | Python | gpl-3.0 | 7,913 | [
"Gaussian"
] | 09e8757bb1c16da1c4f8703b6c1ce7d1ca15562bc9b4349e79126b051175b7ba |
import os
import re
import subprocess
import tempfile
import random
import glob
import signal
import threading
from pkg_resources import parse_version
from io import StringIO
import logging as pyLog
import six
import sys
# workaround for python2/3 string handling {{{
try:
from string import strip
except ImportError:... | Try2Code/cdo-bindings | python/cdo.py | Python | gpl-2.0 | 28,245 | [
"NetCDF"
] | 150cf732b08090760f3818177ea09f2dbc5af2488dab5e8558ce909693d6c7d4 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Uses graphlib and topiclib to run the Latent Response Mood Model
Copyright (C) 2011 Joseph Perla
GNU Affero General Public License. See <http://www.gnu.org/licenses/>.
"""
from itertools import izip,chain
from functools import partial
try:
import... | jperla/happynews | model/latentmood.py | Python | agpl-3.0 | 9,713 | [
"Gaussian"
] | 65f599cc9f20bc4995c4eb230fb20a38dd8f6c5b42d121b3b9b777fbcccc27bb |
# Copyright (c) 2003-2016 LOGILAB S.A. (Paris, FRANCE).
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
# Licensed under the GPL: https://www.gnu.org/licenses/old-licenses/gpl-2.0.html
# For details: https://github.com/PyCQA/pylint/blob/master/COPYING
"""handle diagram generation options for class diagram or def... | bgris/ODL_bgris | lib/python3.5/site-packages/pylint/pyreverse/diadefslib.py | Python | gpl-3.0 | 7,986 | [
"VisIt"
] | 266a301f798f2fd16a83a4edc188bb58371a26ad8249ebf4f8f3bb7f8206688d |
"""
utils.py
Utility functions for the *sfc_models* package.
Copyright 2016 Brian Romanchuk
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 ... | brianr747/SFC_models | sfc_models/utils.py | Python | apache-2.0 | 13,490 | [
"Brian"
] | 4c427276365f00c936184bdfb8973ee0f40d28235109f044c3e3ea13a6ebf1a6 |
# -*- coding: utf-8 -*-
from south.utils import datetime_utils as datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding field 'Subscription.administrant'
db.add_column(u'visits_subscri... | clincher/phuketstash | visits/migrations/0003_auto__add_field_subscription_administrant__add_field_payment_administr.py | Python | bsd-3-clause | 9,849 | [
"VisIt"
] | bb6f87b661efde7be2322e6343fa1615c3c5fdb827f3776b472bba1f7e9b7ccf |
# 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 (t... | apache/allura | Allura/allura/controllers/project.py | Python | apache-2.0 | 40,457 | [
"VisIt"
] | 78307a0be78a63309724c643c80d967d6de0cb614d22ea0d26eb7a0e787e6ea1 |
#!/usr/bin/env python
#
#
# FreeType 2 glyph name builder
#
# Copyright 1996-2015 by
# David Turner, Robert Wilhelm, and Werner Lemberg.
#
# This file is part of the FreeType project, and may only be used, modified,
# and distributed under the terms of the FreeType project license,
# LICENSE.TXT. By continuing to u... | hpfmn/MuseScore | thirdparty/freetype/src/tools/glnames.py | Python | gpl-2.0 | 105,237 | [
"FEFF"
] | ea3717ac95f9c3457ed383df5eea9a969988595e7103406acc773e16f1adda9e |
#! /usr/bin/env python
# -*- coding:utf-8
# Convolutional Neural Network (CNN) for recognizing handwritten digits
# Special thanks: Harisson@pythonprogramming.net
'''
File name: cnn_test.py
Author: chimney37
Date created: 12/09/2017
Python Version: 3.62
'''
import tensorflow as tf
from tensorflow.examp... | chimney37/ml-snippets | cnn_test.py | Python | mit | 8,863 | [
"NEURON"
] | 44502f6b761c5d4e52794ad22d23b599d3bb28675e239b4ea0fec0be6b9eb5e2 |
#
# 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 us... | bdrillard/spark | python/pyspark/ml/clustering.py | Python | apache-2.0 | 51,763 | [
"Gaussian"
] | efdba02fd63ffcf90bfc9a6ea96ae18cc710fb5194c969d0f1a7e7d1ddf4fcf5 |
'''
FieldElements.
>>> import moose
on node 0, numNodes = 1, numCores = 8
Info: Time to define moose classes:0
Info: Time to initialize module:0.05
>>> a = moose.IntFire('a')
Created 123 path=a numData=1 isGlobal=0 baseType=IntFire
>>> b = moose.Synapse('a/b')
Created 125 path=a/b numData=1 isGlobal=0 baseType=Synapse... | BhallaLab/moose | moose-examples/snippets/fieldelement.py | Python | gpl-3.0 | 5,722 | [
"MOOSE"
] | cf912ed76884816ed3b5620136252e3af083121c7c4df6141d48257a96e01b86 |
import pymc as pm
import numpy as np
import matplotlib.pyplot as plt
x = np.arange(5,400,10)*1e3
# Parameters for gaussian
amp_true = 0.2
size_true = 1.8
ps_true = 0.1
# Gaussian function
gauss = lambda x,amp,size,ps: amp*np.exp(-1*(np.pi**2/(3600.*180.)*size*x)**2/(4.*np.log(2.)))+ps
f_true = gauss(x=x,amp=amp_true... | Delosari/dazer | working_examples/pymc2_tests.py | Python | mit | 2,582 | [
"Gaussian"
] | 23e669ee936638eb408416f67809178e87b7c24c1ffb18ae4bea885ffdfac7e8 |
"""Total variation deconvolution using PDHG.
Solves the optimization problem
min_x 1/2 ||A(x) - g||_2^2 + lam || |grad(x)| ||_1
Where ``A`` is a convolution operator, ``grad`` the spatial gradient and ``g``
is given noisy data.
For further details and a description of the solution method used, see
https://odlg... | kohr-h/odl | examples/solvers/pdhg_deconvolve.py | Python | mpl-2.0 | 2,847 | [
"Gaussian"
] | 133c643760827054867df3367df697fc519619acc3aee11c941fd92e84ccb9b7 |
print("""simone 11 me
marcel 9 brother
greg 39 dad
heather 38 mom
daizy 9 months dog
brixton 8 months cousin
christy 35 aunt
james ? uncle
anne ? grandma
scott ? grandpa
amber 32 aunt
andy ? uncle
kathy ? grandma
tom
bryn
talley
mike
roberta
john
connie
gerald""")
| sleepinghungry/wwif | students/simone/firstprogram.py | Python | mit | 293 | [
"Amber"
] | b493bf5bcfe0b963521c682d9ec9da378ff9ede181746c3ce6c11c46574e2a4d |
from pathlib import Path
import os
import numpy as np
import netCDF4
import matplotlib.pyplot as plt
from aps.util.nc_index_by_coordinate import tunnel_fast
# Creates the mask over the small regions of 20x20 km size
def create_small_regions_mask():
p = Path(os.path.dirname(os.path.abspath(__file__))).parent
nc... | kmunve/APS | aps/util/edit_region_mask.py | Python | mit | 3,167 | [
"NetCDF"
] | eec648a242ee531687bb5e0ef894697e1b0b9152e58d7b8a0f95b76f8ca5c9f1 |
#!/usr/bin/env vpython
# Copyright (c) 2013 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
# Copyright (C) 2008 Evan Martin <martine@danga.com>
"""A git-command for integrating reviews on Gerrit."""
from __future__ impo... | CoherentLabs/depot_tools | git_cl.py | Python | bsd-3-clause | 206,756 | [
"VisIt"
] | 6021ab4a771d870bb3efd19597396c3febb1c17bd3c3407240f813a6fb2b2d25 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import io
from itertools import chain
import os
import re
import shutil
import subprocess
import sys
import warnings
from setuptools import setup
pkg_name = "chempy"
url = "https://github.com/bjodah/" + pkg_name
license = "BSD"
RELEASE_VERSION = os.environ.get("%s_RELEA... | bjodah/chempy | setup.py | Python | bsd-2-clause | 4,992 | [
"ChemPy"
] | 037cd60e007cc2cb2e4843491fe9c22878f5d48c7f0722c209ecad772325327c |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright: (c) 2014, Brian Coca <briancoca+ansible@gmail.com>
# 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
DOCUMENTATION = r'''
---
module... | j-carl/ansible | lib/ansible/modules/debconf.py | Python | gpl-3.0 | 5,936 | [
"Brian"
] | 0fb4a9ba7c565553000209d053933058e8e7bfd8976877f8dd7e66317646eba0 |
""" Interacts with sqlite3 db
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import six
import sqlite3
import os
import hashlib
import random
import time
import DIRAC
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.FrameworkSystem.private.monitorin... | ic-hep/DIRAC | src/DIRAC/FrameworkSystem/private/monitoring/MonitoringCatalog.py | Python | gpl-3.0 | 19,766 | [
"DIRAC"
] | 5af0a4fb881aee631fe044e947bf0c09eb042f0272b079a86b6084cd93aa533c |
# 2-electron VMC code for 2dim quantum dot with importance sampling
# No Coulomb interaction
# Using gaussian rng for new positions and Metropolis- Hastings
# Energy minimization using standard gradient descent
# Common imports
import os
# Where to save the figures and data files
PROJECT_ROOT_DIR = "Results"
FIGURE... | CompPhysics/ComputationalPhysics2 | doc/src/MCsummary/src/qdotnint.py | Python | cc0-1.0 | 5,849 | [
"Gaussian"
] | fbca57dc6e27732452b8b6799d69820b3b9fe8ac8ee23d89d5f1037be28edec4 |
"""
Copyright (c) 2014 Brian Muller
"""
import sys
from twisted.python import log
INFO = 5
DEBUG = 4
WARNING = 3
ERROR = 2
CRITICAL = 1
class FileLogObserver(log.FileLogObserver):
def __init__(self, f=None, level=WARNING, default=DEBUG):
log.FileLogObserver.__init__(self, f or sys.stdout)
self.l... | jorik041/Network | log.py | Python | mit | 1,705 | [
"Brian"
] | 60c5bd1c6c18be3cc531cd4b57e86f57f25775d2482e42dc3a3ecb39f8cc6879 |
import numpy as np
from numpy import cos, sin, pi
#import gmin_ as GMIN
from pele.potentials import LJ
from pele.angleaxis import RBTopology, RBSystem, RigidFragment, RBPotentialWrapper
def make_otp():
"""this constructs a single OTP molecule"""
otp = RigidFragment()
otp.add_atom("O", np.array([0.0, -2./... | kjs73/pele | pele/angleaxis/_otp_cluster.py | Python | gpl-3.0 | 3,625 | [
"PyMOL"
] | 0aa1fbe2c78e61eaa8dc2afa0bde42bb6a56e870d9b77582cd72628ec28f6335 |
import pytest
import pandas as pd
from neuprint import Client, default_client, set_default_client
from neuprint import (NeuronCriteria as NC,
MitoCriteria as MC,
SynapseCriteria as SC,
fetch_custom, fetch_neurons, fetch_meta,
fetch... | connectome-neuprint/neuprint-python | neuprint/tests/test_queries.py | Python | bsd-3-clause | 9,142 | [
"NEURON"
] | 0bec542539796ae72ae60941cf33f0520fd1a79fbe9d2268a9bb565d7b7f250c |
"""
Views for the verification flow
"""
import datetime
import decimal
import json
import logging
import six
import six.moves.urllib.error # pylint: disable=import-error
import six.moves.urllib.parse # pylint: disable=import-error
import six.moves.urllib.request # pylint: disable=import-error
from course_modes.mo... | cpennington/edx-platform | lms/djangoapps/verify_student/views.py | Python | agpl-3.0 | 52,390 | [
"VisIt"
] | 36ee5331b16db28b59024a692526669a604e87e45fdfe9fdd9add0a5cd570225 |
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
from rest_framework import routers, viewsets
import basil.users.views
... | mesako/basil | config/urls.py | Python | agpl-3.0 | 1,959 | [
"VisIt"
] | 09780eda9265c4f843a17e99857b16672725231ddc90467f981119144a046887 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | alistairlow/tensorflow | tensorflow/contrib/gan/python/eval/python/classifier_metrics_impl.py | Python | apache-2.0 | 17,698 | [
"Gaussian"
] | 5dcd921604fd792d002640c56cdec1c7ea4b2832fcf90df7821c911876d7934c |
from difflib import get_close_matches
from Firefly import logging
from Firefly import aliases
from Firefly.const import (ACTION_LEVEL, ACTION_OFF, ACTION_ON, ALEXA_OFF_REQUEST, ALEXA_ON_REQUEST,
ALEXA_SET_COLOR_REQUEST, ALEXA_SET_COLOR_TEMP_REQUEST, ALEXA_SET_PERCENTAGE_REQUEST,
... | Firefly-Automation/Firefly | Firefly/services/alexa.py | Python | apache-2.0 | 5,602 | [
"Firefly"
] | 71c49c04ebff7ddbf9558ef2b9b0dc7fff585086f73c0848614361b78d840d41 |
# -*- coding: utf-8 -*-
"""
Data Visualization Exercise 02
University of Zurich
Moritz Eck
14-715-296
"""
import numpy as np
from scipy import ndimage
from PIL import Image
from bokeh.plotting import figure, output_file, curdoc
from bokeh.layouts import row, column, widgetbox
from bokeh.models import Div, Tabs, Pan... | meck93/hs17-datavis-ex | ex2/ex2_main.py | Python | mit | 11,625 | [
"Gaussian"
] | e642288d9f40e4f12aab925879d45edef81fbf2e8a97b706b70b42efff28f618 |
"""
Delta printer linear least squares autocalibration.
Most of the code in this package is a pretty straightforward
translation of David Crocker's linear least squares calibration
algorithm: http://escher3d.com/pages/wizards/wizarddelta.php .
For additional information on the algorithm, visit the following
Wikipedia... | Alex2114/Deb-3df | redeem/DeltaAutoCalibration.py | Python | gpl-3.0 | 16,398 | [
"VisIt"
] | 5ff18416410d97e078cf12b367bc1147403e6192e3b4af3a1efbaa5d7d5fb8da |
########################################################################
# File : InProcessComputingElement.py
# Author : Stuart Paterson
########################################################################
""" The simplest of the "inner" CEs (meaning it's used by a jobAgent inside a pilot)
A "InProcess" CE... | ic-hep/DIRAC | src/DIRAC/Resources/Computing/InProcessComputingElement.py | Python | gpl-3.0 | 5,160 | [
"DIRAC"
] | 710fe236e38b8a0a5fe2a26a13023d3fba6c5fbf4fcc56bb1a93360d884079e3 |
# -*- coding: utf-8 -*-
# Copyright 2013 splinter authors. All rights reserved.
# Use of this source code is governed by a BSD-style
# license that can be found in the LICENSE file.
import os
import unittest
from splinter import Browser
from .fake_webapp import EXAMPLE_APP
from .base import WebDriverTests
from selen... | gjvis/splinter | tests/test_webdriver_chrome.py | Python | bsd-3-clause | 1,915 | [
"VisIt"
] | 218d20e1f5ac846303d26867c09f89a057a8e9fab38ef9be0b11d12a08b853b3 |
''' LogStatusAction
'''
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = '$Id$'
from DIRAC import S_ERROR
from DIRAC.ResourceStatusSystem.Client.ResourceStatusClient import ResourceStatusClient
from DIRAC.ResourceStatusSystem.PolicySystem.Action... | yujikato/DIRAC | src/DIRAC/ResourceStatusSystem/PolicySystem/Actions/LogStatusAction.py | Python | gpl-3.0 | 3,927 | [
"DIRAC"
] | 3fff4facd264795704e768e2132960510dd08f3fc86b37ec7cb9ef90e7211008 |
from vtk.web import testing
from vtk.web.testing import WebTest
dependencies_met = True
try:
# import module for scripting HTTP requests from Python
import requests
except:
dependencies_met = False
# =============================================================================
# This test class extends... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/Web/Applications/TestApp/test/test_pv_web_testapp_retrieve_file_check_includes.py | Python | gpl-3.0 | 3,131 | [
"ParaView",
"VTK"
] | 72353316fe06150c9ae69e7a96653b6da08fad8e4a5a7c873e7c0d1351acbc8c |
"""
Contains the data that are sent by the crystal diffraction widget to the viewer.
"""
class MailingBox(object):
def __init__(self, diffraction_result, mueller_result):
self.diffraction_result = diffraction_result
self.mueller_result = mueller_result
| edocappelli/oasys-crystalpy | orangecontrib/oasyscrystalpy/util/MailingBox.py | Python | mit | 275 | [
"CRYSTAL"
] | 0d85f7cd409029199406f78414013bd34714fbcb97aca888b788c09026aea3d4 |
import unittest
import importlib
from mock import Mock
from DIRAC.ConfigurationSystem.Client.Helpers.Resources import getDIRACPlatform, getCompatiblePlatforms
class HelpersTestCase( unittest.TestCase ):
""" Base class for the Helpers test cases
"""
def setUp( self ):
self.gConfigMock = Mock()
self.resou... | andresailer/DIRAC | ConfigurationSystem/Client/Helpers/test/Test_Helpers.py | Python | gpl-3.0 | 3,197 | [
"DIRAC"
] | 1ea10e58f5d17b627d8ee23b34923043c10e80b6497f00bbea28c2b326c784ef |
#!/usr/bin/env python
# multimeter.py
#
# Copyright (C) 2009-2010 The NEST Initiative
'''
This file illustrates recording from a iaf_cond_alpha neuron
using a multimeter.
See multimeter_file.py for an example of how to record to file.
'''
import cynest as nest
import numpy as np
import pylab as pl
nest.ResetKer... | gewaltig/cython-neuron | cynest/examples/multimeter.py | Python | gpl-2.0 | 1,601 | [
"NEURON"
] | a5dfa0fa2495b926453839b59b1ca4e97dc500e230e7d7ac0e1551b407ecdc5d |
#!/usr/bin/env python3
"""
Copyright 2021 Ryan Wick (rrwick@gmail.com)
https://github.com/katholt/Kaptive
Kaptive is a tool which reports information about the K and O types for Klebsiella genome
assemblies. It will help a user to decide whether their Klebsiella sample has a known or novel
locus type, and if novel, ho... | katholt/Kaptive | kaptive.py | Python | gpl-3.0 | 80,980 | [
"BLAST"
] | 7d3bda06e1cc4a9314b0f03371e2c5d37ac756586516b1e46373413152a3ac6c |
# Import the relevant tools
import time # to measure performance
import numpy as np # standard array library
import theano # Autodiff & symbolic calculus library :
import theano.tensor as T # - mathematical tools;
from theano import config, printing # - printing ... | jeanfeydy/lddmm-ot | Simple_script/lddmm_theano.py | Python | mit | 22,467 | [
"DIRAC",
"VTK"
] | 04dbd5ce3c55d6b7521b8f7d64d8c44b3b739e2f18e9e46d4c7f386d472696c9 |
#!/usr/bin/env python
from setuptools import setup, find_packages
from txairbrake import version
setup(
name="txairbrake",
version=version,
description="txairbrake reports exceptions in Twisted code to an airbrake server",
author="Brian Muller",
author_email="bamuller@gmail.com",
license="MIT"... | bmuller/txairbrake | setup.py | Python | mit | 451 | [
"Brian"
] | c192acd8b94a460a2b897eddbcbc3b9accea225771771fa6d041191660740b87 |
#!/usr/bin/env python
import vtk
def main():
colors = vtk.vtkNamedColors()
perlinNoise = vtk.vtkPerlinNoise()
perlinNoise.SetFrequency(2, 1.25, 1.5)
perlinNoise.SetPhase(0, 0, 0)
sample = vtk.vtkSampleFunction()
sample.SetImplicitFunction(perlinNoise)
sample.SetSampleDimensions(65, 65... | lorensen/VTKExamples | src/Python/Filtering/PerlinNoise.py | Python | apache-2.0 | 1,268 | [
"VTK"
] | 7a2eb799a2273bd5eed6f0c51211cdd42f48302b35b298940dcb69b72fd10640 |
from __future__ import division
import csv
import numpy as np
from scipy.stats import rankdata
from hmm import PoissonHMM
def is_outlier(out, thresh=3.5):
"""
only consider positions with variants larger than 2, otherwise will be driven by positionof 0/1/2 mutations (most case)
Returns a boolean arra... | ShenLab/hotspot | Poisson_HMM.py | Python | bsd-3-clause | 7,033 | [
"Gaussian"
] | ec7f76e8b0eecce0c72398687284051b0dd98d9f8a49b415ae89e10454fd3a7a |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
AO-direct CCSD (New in PySCF 1.3)
'''
from pyscf import gto, scf, cc
mol = gto.M(
atom = 'H 0 0 0; F 0 0 1.1',
basis = 'ccpvdz')
mf = scf.RHF(mol).run()
#
# AO-direct CCSD can largely reduce the IO overhead. You need specify .direct... | gkc1000/pyscf | examples/cc/10-ao_direct_ccsd.py | Python | apache-2.0 | 483 | [
"PySCF"
] | b4a6f410dd7afb7b53140d3d10ea789843f919089667a8b4a6b78f1679153e16 |
import pytest, py
import tox
import os
import sys
from py.builtin import print_
from fnmatch import fnmatch
import time
from tox._config import parseconfig
from tox._venv import VirtualEnv
from tox._cmdline import Action
from tox.result import ResultLog
def pytest_configure():
if 'TOXENV' in os.environ:
de... | doismellburning/tox | tox/_pytestplugin.py | Python | mit | 9,979 | [
"VisIt"
] | a61391aceb6b13aba41e6044f8c250bba6c504789ce5c0a9cad629bb40863731 |
#!/bin/env python
import argparse
import datetime
#CDAT
import cdms2
import numpy as np
#Matplotlib libraries
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import matplotlib.dates as mdates
import matplotlib.font_manager as font_manager
from pylab import legend
def plot(title,variable,ifil... | ywang-bom/cwsl-ctools | visualisation/plot_timeseries.py | Python | apache-2.0 | 2,041 | [
"NetCDF"
] | 546ddd96882b4a942e5bc964cfdfd6d24519955707e1cf612fb7bf153f06eb75 |
# -*- coding: utf-8 -*-
"""
Copyright © 2016, N. Niehof, Radboud University Nijmegen
PsiMarginal 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 lat... | NNiehof/Psi-staircase | PsiMarginal.py | Python | gpl-3.0 | 24,439 | [
"Gaussian"
] | eee65d09935df3748f61297fa50f4db0a2cbfe2eec1b0bb44162032ff7f27c70 |
#!/usr/bin/python3
import pandas as pd
import numpy as np
import pdb
import time
import mhyp_enrich as mh
import statsmodels.stats.multitest as mt
import random
from scipy import stats as st
from scipy.stats import beta
def main():
num_MC_samp = 1000000 # Number of Monte-Carlo samples to use
alt = 'two-sided... | joelbader/regulon-enrichment | rnaseq_enrichment_analysis.py | Python | mit | 6,218 | [
"BLAST"
] | 23434eae0c9f2879b9c80079f27842db90c85302b24369b47626419852e24ee9 |
#!/usr/bin/python
"""
pyNEAT
Copyright (C) 2007-2008 Brian Greer
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... | liquidkarma/pyneat | tools/gen_startgenes.py | Python | gpl-2.0 | 2,497 | [
"Brian"
] | 540088f10709981bdf09c0ba60c2eb97189d0453add4a732ad85620b941a3e32 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
class Migration(migrations.Migration):
dependencies = [
('doctor', '0001_initial'),
('room', '0001_initial'),
('medicine_category', '0001_initial'),
]
operations = [
... | godspeedcorporation/clinic | visit/migrations/0001_initial.py | Python | mit | 775 | [
"VisIt"
] | 1b0be22492257b223d4bc20e59528f7985dc1e2582f4ff5e60e4aff1872e99f8 |
#!/usr/bin/env python
"""%prog [options] -s TOPOL -f TRAJECTORY
Generate densities (solvent and bulk) for the system specified by
the structure file TOPOL and the MD TRAJECTORY. Any combination of
TOPOL and TRAJECTORY that can be read by MDAnalysis is acceptable
(e.g. a PSF/DCD or GRO/XTC combination).
At the moment,... | iwelland/hop | scripts/hop-generate-densities.py | Python | lgpl-3.0 | 6,392 | [
"CHARMM",
"Gromacs",
"MDAnalysis"
] | 46f1263105000d7c298f441ddd501cdf875eff1a1a721e8856e860206aad39fe |
# Copyright 2020 The StackStorm Authors.
# Copyright 2019 Extreme Networks, 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 ... | nzlosh/st2 | st2common/st2common/middleware/cors.py | Python | apache-2.0 | 4,133 | [
"GULP"
] | 094b499c20faeb05077a79cfa22b4d0abbfcc9ed405670ed27a4205905e7b1b9 |
#!/usr/bin/env python
__author__ = "Antonio Gonzalez Pena"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Antonio Gonzalez Pena"]
__license__ = "GPL"
__version__ = "1.8.0-dev"
__maintainer__ = "Antonio Gonzalez Pena"
__email__ = "antgonza@gmail.com"
from qiime.plot_semivariogram import hist_bins... | wasade/qiime | tests/test_plot_semivariogram.py | Python | gpl-2.0 | 12,517 | [
"Gaussian"
] | 11900af00636f40cec5886052e86a73e1873bc786435738537f875cd2e7b3d7d |
#!/usr/bin/python3
import sys
sys.path.append('/usr/lib/python3.5/site-packages')
import numpy as np
from pylamp_const import *
#from bokeh.plotting import figure, output_file, show, save
import vtk
#import gr
from scipy.interpolate import griddata
import os
import glob
###
# program to convert pylamp output (npz f... | larskaislaniemi/PyLamp | pylamp_post.py | Python | bsd-2-clause | 7,910 | [
"VTK"
] | 09af94c54ab1945d4a8b1f000379394fcff85fb167a92bbe54727be48083dd72 |
from suspect import MRSData, transformation_matrix
import functools
import numpy
try:
import GERecon
except ModuleNotFoundError as e:
GERecon = e
gerecon_err_msg = "GE P-file functionality requires the GE \"Orchestra for " \
"Python\" package to be installed. For more information, please visit " \
"http... | openmrslab/suspect | suspect/io/ge.py | Python | mit | 10,450 | [
"VisIt"
] | 43cb9b0e8e808cad1820a7f6ca3ab0c9e5202c0ced98cfaabeb358149def1e9a |
# -*- coding: utf-8 -*-
"""
***************************************************************************
OTBUtils.py
---------------------
Date : 11-12-13
Copyright : (C) 2013 by CS Systemes d'information (CS SI)
Email : otb at c-s dot fr (CS SI)
Contrib... | sebastic/QGIS | python/plugins/processing/algs/otb/maintenance/OTBSpecific_XMLcreation.py | Python | gpl-2.0 | 29,105 | [
"Gaussian"
] | 73357cf799b7113ab7d66558b2ffebfaf81754fd3880097774674c1ebe35cbae |
"""
Results for test_glm.py.
Hard-coded from R or Stata. Note that some of the remaining discrepancy vs.
Stata may be because Stata uses ML by default unless you specifically ask for
IRLS.
"""
import numpy as np
from statsmodels.compatnp.py3k import asbytes
import glm_test_resids
import os
from statsmodels.api import... | pprett/statsmodels | statsmodels/genmod/tests/results/results_glm.py | Python | bsd-3-clause | 270,071 | [
"Gaussian"
] | b1df16b96300e7a8aa489f12e4bc4ce8a779079d5091edb0c381909e8014dae4 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Weekly News Output Chooser
# Version: 0.0.1
# (c) 2010 by Sascha Manns <saigkill@opensuse.org>
#
#
# Common Entities for all OWN articles
# This work is licensed under the
# Creative Commons Attribution-ShareAlike 3.0 Unported License
# by Sascha Manns. To view ... | saigkill/opensuse-weekly-news | ja/en/chooser.py | Python | agpl-3.0 | 1,503 | [
"VisIt"
] | d4b85d696741bee8c4e03cbe7f4e8f86372038c4031c1625bde6588237dda3b7 |
# -*- coding: utf-8 -*-
"""
Module for API-related calls.
"""
try:
from urllib import parse as urlparse
except ImportError:
import urlparse
def hostname_tld_migration(hostname):
"""
Migrate transifex.net to transifex.com.
:param hostname: The hostname to migrate (if needed).
:returns: A hos... | devs1991/test_edx_docmode | venv/lib/python2.7/site-packages/txclib/processors.py | Python | agpl-3.0 | 1,562 | [
"VisIt"
] | 569343e7fc05fd6026c81097395834ead61a60ddaa70e1bd957d416bd304397e |
#!/usr/local/bin/env python
# ==============================================================================
# MODULE DOCSTRING
# ==============================================================================
"""
Analyze
=======
YANK Specific analysis tools for YANK simulations from the :class:`yank.yank.AlchemicalP... | choderalab/yank | Yank/analyze.py | Python | mit | 51,715 | [
"MDTraj",
"NetCDF",
"OpenMM"
] | ce63f1a84f710318e363e8486e0d20f5517d5b819dde4ccdccaec0442888bbc4 |
# ----------------------------------------------------------------------------
# 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/alignment/_tabular_msa.py | Python | bsd-3-clause | 81,218 | [
"scikit-bio"
] | 6e03defbdefbd90f4a4159cbeb3a4c49825be0fa427a0dff90de980bb4838df1 |
#!/usr/bin/env python
import os
import re
import logging
import argparse
from Bio.Blast import NCBIXML
def getOptions():
""" Function to pull in arguments """
parser = argparse.ArgumentParser(description="Parse BLASTs XML format to a basic table. This was originally done for the Bloom project, the script may ... | McIntyre-Lab/mcscript | parseBlastXml.py | Python | gpl-3.0 | 2,235 | [
"BLAST"
] | 9213ba433a1d01d0be94d95f293c56967a9ef37e5abf02c3fb129ecb59690357 |
#!/usr/bin/env python3.6
import ast
import sys
class MockChecker(ast.NodeVisitor):
def __init__(self):
self.errors = 0
self.init_module_imports()
def init_module_imports(self):
self.imported_patch = False
self.imported_mock = False
def check_files(self, files):
fo... | somic/paasta | paasta_tools/contrib/mock_patch_checker.py | Python | apache-2.0 | 2,437 | [
"VisIt"
] | 1697fccf71189c2cab9d47d5974e15fd29a91055d2f4d66ea49712c4fc8bd7b4 |
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