text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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import numpy as np
import tensorflow as tf
import elbow.util as util
from elbow.conditional_dist import ConditionalDistribution
from elbow.parameterization import unconstrained, positive_exp, simplex_constrained, unit_interval
from elbow.transforms import Logit, Simplex, Exp, TransformedDistribution
from elbow.elemen... | davmre/bayesflow | elbow/models/symmetry_qs.py | Python | bsd-3-clause | 13,010 | [
"Gaussian"
] | 120b574089cdcb8e622664723352baa649093be280b42471022db2c807cd31b0 |
# Copyright 2014->future! Mikko Korpela
#
# 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 agree... | tangkun75/pabot | pabot/result_merger.py | Python | apache-2.0 | 4,229 | [
"VisIt"
] | f3adb1decade6ef6fabaab22df1b5e88be969904268fa826c5f2471a9bc7a0f4 |
''' Test_RSS_Policy_JobRunningWaitingRatioPolicy
'''
import unittest
import DIRAC.ResourceStatusSystem.Policy.JobRunningWaitingRatioPolicy as moduleTested
################################################################################
class JobRunningWaitingRatioPolicy_TestCase( unittest.TestCase ):
def setUp( ... | andresailer/DIRAC | ResourceStatusSystem/Policy/test/Test_RSS_Policy_JobRunningWaitingRatioPolicy.py | Python | gpl-3.0 | 3,638 | [
"DIRAC"
] | e04fc862e1ae7b03d3ee5ae358562a9b01069f0ae26058aa86f81504fba187e5 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | MOA-2011/enigma2-plugin-extensions-openwebif | plugin/controllers/views/ajax/current.py | Python | gpl-2.0 | 32,041 | [
"VisIt"
] | e0d514c51e1ca5766aba1d190ea1c6897ce2e129f73f6f0f2b2b922f494247fa |
#!/usr/bin/env python3
## INFO ########################################################################
## ##
## cutils ##
## ====== ... | matt-hayden/cutils | pycutils/cutils/ccom.py | Python | gpl-3.0 | 14,831 | [
"VisIt"
] | 602838a55809d48c5253d7802a7b8cfc38b4d5747fdb68c427286ec7a0f2aaba |
# Placeholder because log moved
# Remove this in version 1.0
from __future__ import absolute_import
import warnings
with warnings.catch_warnings():
warnings.simplefilter('always', DeprecationWarning)
warnings.warn(("log has moved to MDAnalysis.lib.log "
"and will be removed from here in rele... | kain88-de/mdanalysis | package/MDAnalysis/core/log.py | Python | gpl-2.0 | 394 | [
"MDAnalysis"
] | 80b03569d42af9f34fd63f346e8088deeacad22d2d4dd9081349adb725848f13 |
import vtkAll as vtk
from ddapp import botpy
import math
import numpy as np
import drc as lcmdrc
def getTransformFromNumpy(mat):
'''
Given a numpy 4x4 array, return a vtkTransform.
'''
m = vtk.vtkMatrix4x4()
for r in xrange(4):
for c in xrange(4):
m.SetElement(r, c, mat[r][c])
... | rdeits/director | src/python/ddapp/transformUtils.py | Python | bsd-3-clause | 5,695 | [
"VTK"
] | 18fcf84106c13fdbd5cc212542c59524478aa51476a463b0788fa39d8b03362d |
from p03_ParseSam import get_name
def annotateBlast(blastFile,anno_type):
"""
This function annotates the results got by running all sorts of
blast algorithm. It adds the names of reference genomes
* blastFiles: str. blast file name
* anno_type: str. 'nucleotide' or 'protein'
out... | shl198/Pipeline | DetectVirusPipeline/p04_ParseBlast.py | Python | mit | 5,713 | [
"BLAST"
] | d7c690a2520dc3ba83a5966037d14a1cb9126fd17294196b48409119ba330fc1 |
'''
Go through a given fasta file (later - mod for sets of fastas),
and output a new fasta file, with sequences containg unknown, or non standard AA
removed; too short sequences removed.
Later, can be used to filter sequences whose ID is a classname; (keeping those
with a minimum amount of examples, e.g. 30+ samples ... | ddofer/ProFET | ProFET/feat_extract/FastaFilter.py | Python | gpl-3.0 | 4,999 | [
"Biopython"
] | c6e9f7db0c1aabdd5ebff5e5e8a289af91a70d99a5f84742e5f9dfb099c25318 |
from django.db import models
from api.models import Service
class Application(models.Model):
"""
Application
"""
GROUP_CHOICES = (
('xms', 'xms'),
('sms', 'sms'),
('ws', 'ws'),
('farm', 'farm'),
('cube', 'active-pivot'),
('cube', 'active-pivot'),
... | vyourtaev/ally | ui/models.py | Python | gpl-3.0 | 1,511 | [
"Elk"
] | 731a90645ac9f55e728831b064334e0101f86a6358e4ec557c7978ea8689a72c |
import datetime
rcParams = {'font.family':'Times',
'axes.2D.tickson':True,
'axes.2D.title.fontscale':2.0,
'axes.2D.label.fontscale':2.0,
'axes.2D.x.title':"x-coordinate [m]",
'axes.2D.y.title':"z-coordinate [m]",
'axes.3D.tickson':False,
... | amanzi/ats-dev | tools/visit_ats/visit_ats/visit_rcParams.py | Python | bsd-3-clause | 5,950 | [
"VisIt"
] | 618eb8437b7d5d66adfd98b94244f09ababfd488a6923f4eac12a46b3c655654 |
#!/usr/bin/python
import sys
import ncs
def Run(argv):
sim = ncs.Simulation()
excitatory_parameters = sim.addModelParameters("label_excitatory",
"izhikevich",
{
"a"... | BrainComputationLab/ncs | python/samples/sample.py | Python | bsd-2-clause | 2,686 | [
"NEURON"
] | 24100765c9ee884b9e10caca7f949fd2681986e813a5f549b46737430055522c |
""" VirtualMachineDB Integration Tests
"""
import unittest
from DIRAC.Core.Base.Script import parseCommandLine
parseCommandLine()
from DIRAC.WorkloadManagementSystem.DB.VirtualMachineDB import VirtualMachineDB
class VirtualMachineDBInstanceTests(unittest.TestCase):
"""This tests the instance related database ... | ic-hep/DIRAC | tests/Integration/WorkloadManagementSystem/Test_VirtualMachineDB.py | Python | gpl-3.0 | 10,968 | [
"DIRAC"
] | 32a073f6a28aec74b5f0e1d062808a1c2f9a08a0486723e0d4b05234b00cb272 |
# Copyright 2007-2016 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy 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 ... | to266/hyperspy | hyperspy/tests/signal/test_eds_tem.py | Python | gpl-3.0 | 11,890 | [
"Gaussian"
] | 6a2dfafef529c55b5e1ee965e192e50ad7130098979d93cb56a4e6ee54103bd2 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# cSpell: disable
# author : Santosh
# e-mail : kcraj2[AT]gmail[DOT]com
# Date created : 15 Feb 2018
# Last modified : 15 Feb 2018
"""
Gaussian Linear Classifier with Uncertainty (GLCU)
"""
import os
import sys
import argparse
import tempfile
import numpy as np
import s... | skesiraju/pylibs | pylibs/clf/glc_models.py | Python | gpl-3.0 | 23,704 | [
"Gaussian"
] | 6fc3fadd0913ed85e848f21841ace8ed799e16fac3fe92c88cd75263db94f2e4 |
#!/usr/bin/env python
"""
renumber the integers at the beginning of ever line in the file
to make sure these numbers are contiguous.
The file is read from sys.stdin.
This program does not parse an entire LAMMPS data file.
The text from the "Atoms" section
(or "Bonds", or "Angles", or "Dihedrals", or... | quang-ha/lammps | tools/moltemplate/moltemplate/renumber_DATA_first_column.py | Python | gpl-2.0 | 2,188 | [
"LAMMPS"
] | ddfd613cefc42530d7ef2e5d868d44c28a09eedf74b190f2da82ae9db27c506f |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# distbase - [insert a few words of module description on this line]
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of ... | heromod/migrid | mig/shared/distbase.py | Python | gpl-2.0 | 16,203 | [
"Brian"
] | 21a3b3c0f4c2040dd32bc989223c2937f737d9bf27c9463d5d1e4cd7a567232e |
"""Component Supervision Agent for monitoring agent, executor or service behaviour and intervene if
necessary.
This agent is designed to supervise the Agents, Executors and Services, and restarts them in case
they get stuck. It can only control components running on the same machine as the agent. One agent
per server ... | DIRACGrid/DIRAC | src/DIRAC/FrameworkSystem/Agent/ComponentSupervisionAgent.py | Python | gpl-3.0 | 26,291 | [
"DIRAC"
] | 7f111511538b3b74886e0d6876fbcd8d3f2edb430bb7b787785be9c27c2a6456 |
#! /usr/bin/python
# -*- coding: utf-8 -*-
# import sys
import os
import sys
import os.path
import numpy as np
import logging
logger = logging.getLogger(__name__)
import sklearn
import sklearn.mixture
# path_to_script = os.path.dirname(os.path.abspath(__file__))
# sys.path.append(os.path.join(path_to_script, "./exte... | mjirik/imtools | imtools/ml/gmmcl.py | Python | mit | 2,873 | [
"Gaussian"
] | a92b0da9f8bd5477f829c463ff21c56297cbf4b8e429b1804ad8519014957c2a |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-analytics-data | tests/unit/gapic/data_v1beta/test_beta_analytics_data.py | Python | apache-2.0 | 89,259 | [
"Octopus"
] | 02fe8e114ed2b1903ebaf2b60727c99d9184eba0bc3d5ce378480640cb1e3f59 |
# 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=invalid-name
#
# TUBE CALIBR... | mganeva/mantid | scripts/Calibration/Examples/TubeCalibDemoWish0.py | Python | gpl-3.0 | 1,800 | [
"Gaussian"
] | b639d73e822df293e8d49c788a87b28e7a44032ca7869f35f0ce963b4e7826ed |
from enum import Enum
import arrow
class Region(Enum):
brazil = "BR"
europe_north_east = "EUNE"
europe_west = "EUW"
japan = "JP"
korea = "KR"
latin_america_north = "LAN"
latin_america_south = "LAS"
north_america = "NA"
oceania = "OCE"
turkey = "TR"
russia = "RU"
@prope... | 10se1ucgo/cassiopeia | cassiopeia/data.py | Python | mit | 20,473 | [
"CRYSTAL"
] | 74d0507dbd288b596cadae0b52089d328f0ff540f634ae603fc4c6060899b120 |
# -*- coding: utf-8 -*-
"""
===============================================
Defining a Custom Preprocessor and Extrapolator
===============================================
Here you will be creating trivial preprocessor and and exztrqapolatoirs
following the API.
"""
##################################################... | Cadair/solarbextrapolation | examples/plot_define_and_run_trivial_preprocessor_and_extrapolator.py | Python | mit | 3,965 | [
"Mayavi"
] | ef63450f3fd19308515a9b8d368fa0560d3859b8648f8c7ec9d881eb09595a33 |
from argparse import *
from sys import *
from os.path import *
from paraview.simple import *
from paraview.servermanager import *
parser = ArgumentParser(description = 'Process the arguments')
parser.add_argument('inputFile', help = 'Path to the input file (NetCDF compilant)')
parser.add_argument('outputDir', help = 'P... | fercook/SciViz | Voxels/NETCDF_2_VTK_2_Blender/job/vtk/paraview/NC2VTKVoxel.py | Python | gpl-2.0 | 9,248 | [
"NetCDF",
"ParaView",
"VTK"
] | db92c0138133dce8e809e09832b120a778c7db9c0bdb72588961d739f788a2ef |
# ANTLR Tree -> AST
# antlr4 -Dlanguage=Python3 Cstar.g4
# python3 main.py test.cx
# nLine = x.start.line
# как работает импорт
# в defs[] создается запись вида {isa: import, unit: *ast, id: ID} (по сути - линк)
# он имеет ID определенный в импортирующем модуле (import as ID)
# и ссылается на откомпиленный AST/ASG
#... | ammaaim/cx | main.py | Python | mit | 7,652 | [
"VisIt"
] | 28b070a9c94d2415bf801b576da0ba161e4bced6879f5f9c26f80c1f5e38d1ab |
# -*- coding: utf-8 -*-
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import numpy as np
import abel
import os
from glob import glob
import scipy
from scipy.special import eval_legendre
from scipy import ndimage
###... | DanHickstein/pyBASEX | abel/linbasex.py | Python | gpl-2.0 | 20,440 | [
"Gaussian"
] | 9a74003f4483f0e8738c2d92cf32742a631f5c79cd07bee0eef95f6e0e7d4006 |
# 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... | piiswrong/mxnet | example/ssd/dataset/pycocotools/coco.py | Python | apache-2.0 | 19,564 | [
"VisIt"
] | 450e4d4f8fd2c1358b0ec482074a886b6e2fee03e69a2e229cc871cddd7c16ae |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# -----------------------------------------------------------------------------
# Copyright INRIA
# Contributors: Nicolas P. Rougier (Nicolas.Rougier@inria.fr)
#
# DANA is a computing framework for the simulation of distributed,
# asynchronous, numerical and adaptive models... | rougier/dana | examples/oja.py | Python | bsd-3-clause | 3,086 | [
"Gaussian",
"NEURON"
] | a44b23e9a332fa3ee39fae74f540d8ce7b382c452c5aa2804ec834f077a0a30d |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
SCF analytical nuclear gradients calculation. SCF gradients object can be
created by calling .nuc_grad_method() or .Gradients() for pyscf-1.6.1 and
newer.
'''
from pyscf import gto, scf
mol = gto.M(
atom = [
['O' , 0. , 0. , 0]... | gkc1000/pyscf | examples/grad/01-scf_grad.py | Python | apache-2.0 | 743 | [
"PySCF"
] | b1edc72008ce9ce6ade98a22821b6d42b410aed20b509c7645079333a19d93fb |
# coding: utf-8
"""
Vericred API
Vericred's API allows you to search for Health Plans that a specific doctor
accepts.
## Getting Started
Visit our [Developer Portal](https://developers.vericred.com) to
create an account.
Once you have created an account, you can create one Application for
Production and an... | vericred/vericred-python | test/test_providers_geocode_response.py | Python | apache-2.0 | 10,103 | [
"VisIt"
] | 817f4b6d699c918ee8dedd4949ce733f7ab0a773a48abb89d66c5a47d0b2bfd6 |
#
# Copyright (C) 2013,2014,2015,2016 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)... | Smiljanic/espresso | testsuite/python/magnetostaticInteractions.py | Python | gpl-3.0 | 4,563 | [
"ESPResSo"
] | f07272d120745a6c8c7de97978069a36c872cfe57a4d0c036e0b775df5289a5a |
import pytest
HOME_URL = "https://radiant-stream-4011.herokuapp.com/"
@pytest.mark.webtest
def test_warm_up_calculator(browser):
browser.visit(HOME_URL)
title = browser.find_by_tag("title").first
assert title.html == "Warm Up Calculator"
# submit data
browser.fill_form({
"plates": "55... | drewverlee/warm_up_calculator | tests/test_live_website.py | Python | mit | 524 | [
"VisIt"
] | e11383dfe705fe4802dbf784158d844eb312267bf778aa4d13487355b87c60b6 |
"""
Topological fingerprints.
"""
from typing import Dict
import numpy as np
from deepchem.utils.typing import RDKitMol
from deepchem.feat.base_classes import MolecularFeaturizer
class CircularFingerprint(MolecularFeaturizer):
"""Circular (Morgan) fingerprints.
Extended Connectivity Circular Fingerprints compu... | peastman/deepchem | deepchem/feat/molecule_featurizers/circular_fingerprint.py | Python | mit | 5,057 | [
"RDKit"
] | 7e8049229671af70cf06f1f2d0e72127215784845276a4934a25349d9fbf7e18 |
from setuptools import setup, find_packages
setup(name='geopy',
version='0.93',
description='Python Geocoding Toolbox',
author='Brian Beck',
author_email='exogen@gmail.com',
url='http://exogen.case.edu/projects/geopy/',
download_url='http://geopy.googlecode.com/svn/trunk/',
pa... | AdaptiveApplications/carnegie | tarc_bus_locator_client/geopy/setup.py | Python | mit | 949 | [
"Brian"
] | 5e5fa99af5fa24d575441c73a0dfbbe4a44f22234c99923b5da466fdfa1c003f |
#
# @file TestL3LocalParameter.py
# @brief L3 Local Parameter unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Sarah Keating
#
# $Id$
# $HeadURL$
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generat... | alexholehouse/SBMLIntegrator | libsbml-5.0.0/src/bindings/python/test/sbml/TestL3LocalParameter.py | Python | gpl-3.0 | 6,143 | [
"VisIt"
] | 9935e31a440baabede17039fef6327614c9fdaecb99ec066b569d0b36289f617 |
import logging
import datetime
import tempfile
from dirac.lib.base import *
from dirac.lib.diset import getRPCClient, getTransferClient
from dirac.lib.credentials import getProperties
from dirac.lib.sessionManager import *
from DIRAC.AccountingSystem.Client.ReportsClient import ReportsClient
from DIRAC.FrameworkSystem... | DIRACGrid/DIRACWeb | dirac/controllers/web/siteMap.py | Python | gpl-3.0 | 5,229 | [
"DIRAC"
] | d698f7da067e3762cc60397f73fce8f3eef2787b73bdb678be4f6d6b8695d097 |
import matplotlib.pyplot as plt
from i_Clustering.KMeans import KMeans
from Opt.Methods import *
from Opt.Functions import *
from Util.Util import DataUtil
from Util.Bases import ClassifierBase, RegressorBase
# Example1: Use GradientDescent & Wolfe to minimize l2_norm of (x^2 + 1)^2 using "Automatic Differe... | carefree0910/MachineLearning | Opt/Test.py | Python | mit | 9,188 | [
"Gaussian"
] | f98fed969795a30ad403a1c59546e9f34e919ea8248c36074192e6c3df114ff3 |
"""
Beta diversity measures (:mod:`skbio.diversity.beta`)
=====================================================
.. currentmodule:: skbio.diversity.beta
This package provides implementations of beta diversity measures for computing
sample dissimilarity. Users of this package should also explore
``scipy.spatial.distanc... | gregcaporaso/scikit-bio | skbio/diversity/beta/__init__.py | Python | bsd-3-clause | 1,017 | [
"scikit-bio"
] | 7f445f49f936d9e711752523adfc63aa876ddf0cc51a479e10885e580cefe455 |
# vim: ft=python fileencoding=utf-8 sts=4 sw=4 et:
# Copyright 2016-2021 Florian Bruhin (The Compiler) <mail@qutebrowser.org>
#
# This file is part of qutebrowser.
#
# qutebrowser 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 S... | qutebrowser/qutebrowser | qutebrowser/browser/browsertab.py | Python | gpl-3.0 | 43,551 | [
"VisIt"
] | 457edd45fa1c258bbf3c8faeda092a03e38daec83f4a68d0fce969b1348d9492 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/item_title | openlp/core/ui/themeform.py | Python | gpl-2.0 | 27,079 | [
"Brian"
] | c73fa05273d6ea063232ce0815f26f10cb7a8d6b7ff7e540ef68e9d6d59975bd |
import re
import pandas as pd
import numpy as np
import pytest
import numpy.testing as npt
import pandas.api.types as pdtypes
from plydata import (define, create, sample_n, sample_frac, select,
rename, distinct, arrange, group_by, ungroup,
group_indices, summarize, query, do,... | has2k1/plydata | plydata/tests/test_dataframe.py | Python | bsd-3-clause | 44,743 | [
"ADF",
"Jaguar"
] | 442e63cc34cd48fd55084812c2c7d73ae505d29869b852260ca3ff8b45d2edf6 |
from .owldatarangevisitor import OWLDataRangeVisitor
class OWLDataVisitor(OWLDataRangeVisitor):
"""Marker class"""
def visit(self, node):
"""
:param node: an object of one of the following classes:
- owlapy.model.OWLLiteral
- owlapy.model.OWLFacetRestriction
:r... | patrickwestphal/owlapy | owlapy/model/owldatavisitor.py | Python | gpl-3.0 | 940 | [
"VisIt"
] | 24d84d6d2e35ce4321ccc9401fc523fde03f964385bcedbe624d2ca16b40d96c |
"""
This module use used to predict genes with Genemark and then annotate them using
the function findGenes.
"""
"""
Copyright 2010 Jarl Haggerty
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
ht... | jarl-haggerty/profelis | src/main/jython/profelis/genemark.py | Python | apache-2.0 | 3,522 | [
"BLAST"
] | 99fee3c54d4eb66f7096ef9f7698c23d21a83f6c8574057b70fe6a7949f3bfcc |
import datetime
from django.db import models
class SurveyQuerySet(models.query.QuerySet):
def active(self):
return self.filter(active=True)
class SurveyManager(models.Manager):
query_set_class = SurveyQuerySet
def get_query_set(self):
return self.query_set_class(self.model, using=self... | myvoice-nigeria/myvoice | myvoice/survey/models.py | Python | bsd-2-clause | 8,820 | [
"VisIt"
] | 38cfc78e6cf5cf86c117ffbe0b5dcfe006caa7e97e52effca53a4b1f09996175 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | lgarren/spack | var/spack/repos/builtin/packages/r-yaqcaffy/package.py | Python | lgpl-2.1 | 1,795 | [
"Bioconductor"
] | 071feb0e16b9b1a3a249d39daf71ee6c341f8d8a18a0efae3677ba98299fd8a0 |
import inspect
__all__ = ['GenericVisitor']
class GenericVisitor(object):
"""
A generic visitor.
To define handlers, subclasses should define :data:`visit_Foo`
methods for each class :data:`Foo` they want to handle.
If a specific method for a class :data:`Foo` is not found, the MRO
of the c... | opesci/devito | devito/tools/visitors.py | Python | mit | 4,134 | [
"VisIt"
] | 6a39a8531bc8b21eb979b3b6bb5b545f9e78530df89b911eb7975c11e2d10589 |
# -*- coding: utf-8 -*-
# Licensed under a 3-clause BSD style license - see PYFITS.rst
import copy
import collections
from io import StringIO, BytesIO
import pytest
import numpy as np
from astropy.io import fits
from astropy.io.fits.verify import VerifyWarning
from astropy.utils.exceptions import AstropyUserWarning... | larrybradley/astropy | astropy/io/fits/tests/test_header.py | Python | bsd-3-clause | 115,346 | [
"BLAST"
] | 66e966b91040f8c9e0c41ad147bbaab87f09e9b3875419fc3fa5cd59c718ee23 |
import numpy as np
from ase.cluster.cubic import SimpleCubicFactory
# The L1_2 structure is "based on FCC", but is really simple cubic
# with a basis.
class AuCu3Factory(SimpleCubicFactory):
"A factory for creating AuCu3 (L1_2) lattices."
atomic_basis = np.array([[0., 0., 0.],
[0... | grhawk/ASE | tools/ase/cluster/compounds.py | Python | gpl-2.0 | 485 | [
"ASE"
] | 5de5f88c1aa8a8656cc957a5c2b1ae1ca8e8ac6ecd37328b778758f9f81e11d5 |
import threading
from pymol.wizard import Wizard
from pymol import cmd
import pymol
import types
import time
class Benchmark(Wizard):
def bench_fn(self,action):
time.sleep(0.5)
self.cmd.do("_ wizard benchmark,%s"%action)
def report(self,name,value):
ver = self.cmd.get_version()[0... | gratefulfrog/lib | python/pymol/wizard/benchmark.py | Python | gpl-2.0 | 11,456 | [
"PyMOL"
] | dc0d13e324e60df99af543ce7a8700b1bb2980ec453e71457f2f16d7c6635500 |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | karllessard/tensorflow | tensorflow/python/autograph/converters/logical_expressions.py | Python | apache-2.0 | 4,493 | [
"VisIt"
] | a60ffe8dcea7e26331cd7cb55dfbf4527e2691234f87842c8c8ba0edaa367838 |
# Copyright (C) 2013, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from __future__ import print_function
import urlparse
import httplib
import ftplib
from zeroinstall import SafeException
def get_http_size(url, ttl = 3):
address = urlparse.urlparse(url)
if url.lower().startswit... | gfxmonk/0repo | repo/urltest.py | Python | lgpl-2.1 | 1,945 | [
"VisIt"
] | b305224549e2c75ce1653cbd5e3f7984d0dc70a9adc8bec3801487284da45f11 |
# Orca
#
# Copyright 2005-2009 Sun Microsystems Inc.
# Copyright 2010 Orca Team.
# Copyright 2014 Igalia, S.L.
#
# 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 th... | ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/scripts/toolkits/Gecko/script.py | Python | gpl-3.0 | 116,104 | [
"ORCA"
] | b77e0456aaac1046aa9bdd224621ad5a11ddcc23634b0e00484e272d520f09fc |
"""
Routines related to stochastic optimization techniques
"""
from .annealing import SimulatedAnnealing
from .bee import BeeAlgorithm
from .firefly import FireFly
from .genetic import GeneticAlgorithm
from .grey import GreyWolf
from .harmony import HarmonySearch
from .swarm import ParticleSwarm
from .mhm import Minim... | MaterialsDiscovery/PyChemia | pychemia/searcher/__init__.py | Python | mit | 422 | [
"Firefly"
] | 68ac6000b99717675b90698676c291bfea2f547426a7c637774a5fba32c0055f |
"""
TensorFlow implementations some NN architectures.
Copyright 2016 Deepak Subburam
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later ve... | Fenugreek/comprehend | networks.py | Python | gpl-3.0 | 62,098 | [
"CDK",
"Gaussian"
] | b93dd910b60f8923aae992acaa925bb480ec3040cc90b359016dbadcbfdb9cf6 |
from __future__ import division
import operator
import numpy as np
from scipy import stats, interpolate
#==============================================================================
# This library module is full of functions and classes to compute the maximum
# mutual information (Capacity) between an input (x) (vol... | rzarcone/CAEs | Jesse_Funcs/blahut.py | Python | bsd-2-clause | 14,032 | [
"Gaussian"
] | a4fd389540edbb6bdfe9d076c397f48106ba58bf80d5341996e2edce5322f0f8 |
# -*- coding: utf-8 -*-
import logging
import numpy as np
import os
import pandas as pd
import pkg_resources
import sys
from til_core.config import Config
from til_france.tests.base import ipp_colors
colors = [ipp_colors[cname] for cname in ['ipp_very_dark_blue', 'ipp_dark_blue', 'ipp_medium_blue', 'ipp_light_blue'... | TaxIPP-Life/til-france | til_france/data/data/hsm_dependance_niveau.py | Python | gpl-3.0 | 6,299 | [
"Gaussian"
] | 17ccfcf842b8dfdd0b8d0fadd827e75351998fd639e8b716fa8e3a75bf945e10 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2012 Radim Rehurek <radimrehurek@seznam.cz>
# Copyright (C) 2017 Mohit Rathore <mrmohitrathoremr@gmail.com>
# Licensed under the GNU LGPL v2.1 - http://www.gnu.org/licenses/lgpl.html
"""This module implements functionality related to the `Term Frequency -... | mattilyra/gensim | gensim/models/tfidfmodel.py | Python | lgpl-2.1 | 17,431 | [
"VisIt"
] | ba6092cf78d3288b144936fe0c1572860c3d26c04d3515e2507eb28c912e700d |
# -*- coding: utf-8 -*-
# Copyright 2014 by Ambuj Kumar, Kimball-Braun lab group, University of Florida.
# All rights reserved. This code is part of the ConCat distribution and governed
# by its license. Please see the LICENSE file that should have been included
# as part of this package.
#
# Bug reports welcome: ambuj... | Ambuj-UF/ConCat-1.0 | src/coevolution.py | Python | gpl-2.0 | 74,059 | [
"Biopython"
] | fdd3cda7536bf77ba4f9d9372b9711923017ddd6e4806e45429404d7fc89a251 |
'''
Basic models for decomposing large-scale stacked profiles
'''
import numpy as np
from astropy.modeling import models, fitting
from scipy.interpolate import InterpolatedUnivariateSpline
from scipy.special import erf
from scipy.optimize import curve_fit
from functools import partial
from astropy.convolution import ... | e-koch/CubeAnalysis | cube_analysis/spectral_stacking_models.py | Python | mit | 29,199 | [
"Galaxy",
"Gaussian"
] | 784ca7de875706f44a83b98988c1f41baeedad7a8d52be44d3135ee368b40fc0 |
""" RemoveNestedFunctions turns nested function into top-level functions. """
from pythran.analyses import GlobalDeclarations, ImportedIds
from pythran.passmanager import Transformation
from pythran.tables import MODULES
import ast
class _NestedFunctionRemover(Transformation):
def __init__(self, pm, ctx, global... | hainm/pythran | pythran/transformations/remove_nested_functions.py | Python | bsd-3-clause | 3,432 | [
"VisIt"
] | ab6c5b949c7660f10f71c845226d7529f63b00c1b3da6b25c1f27d4bc99efd06 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011 Tim G L Lyons
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Fr... | arunkgupta/gramps | gramps/gen/plug/__init__.py | Python | gpl-2.0 | 2,671 | [
"Brian"
] | cb0d4bb9dc64eea243232e41debd3afad4c3dd0b6e35a02adaa7151726d26057 |
import logging
import os
import os.path as op
import sys
from copy import copy, deepcopy
import cobra.flux_analysis
import cobra.manipulation
import numpy as np
import pandas as pd
from Bio import SeqIO
from cobra.core import DictList
from slugify import Slugify
import ssbio.core.modelpro
import ssbio.databases.ncbi
... | SBRG/ssbio | ssbio/pipeline/atlas.py | Python | mit | 42,034 | [
"BLAST",
"Biopython"
] | 5ab6119dd51305b4c3b5a999d65976a39f496b75dbc5e40041c84fd30d9db516 |
#
# Copyright 2015-2021 Universidad Complutense de Madrid
#
# This file is part of Numina
#
# SPDX-License-Identifier: GPL-3.0+
# License-Filename: LICENSE.txt
#
import numpy as np
from numpy.polynomial import Polynomial
from ..display.matplotlib_qt import set_window_geometry
from ..display.pause_debugplot import pau... | guaix-ucm/numina | numina/array/wavecalib/peaks_spectrum.py | Python | gpl-3.0 | 8,947 | [
"Gaussian"
] | f11ff3bd3a7955aaf512547170cef1f3b838e1f06b9897be56c9af407a69c785 |
from __future__ import division, print_function
import numpy as np
from numpy.ctypeslib import ndpointer
from ctypes import c_double, c_float, c_int, c_uint
from .vl_ctypes import (LIB, c_to_np_types, np_to_c_types, vl_size, vl_index,
vl_epsilon_f)
from .utils import as_float_image
_imconvcol ... | DLlearn/vlfeat-ctypes | vlfeat/imsmooth.py | Python | bsd-3-clause | 3,570 | [
"Gaussian"
] | 206ba1a486c487da898dd6845b79dc04baf7341f652bdd00c12b28d6058575df |
# iCraft is Copyright 2010 both
#
# The Archives team:
# <Adam Guy> adam@adam-guy.com AKA "Adam01"
# <Andrew Godwin> andrew@aeracode.org AKA "Aera"
# <Dylan Lukes> lukes.dylan@gmail.com AKA "revenant"
# <Gareth Coles> colesgareth2@hotmail.com... | TheArchives/Nexus | core/entities/aborg.py | Python | bsd-2-clause | 6,608 | [
"VisIt"
] | a70af06b7854f582e62561f9cace0e5c23c7aa892d661742e56a6478eb65c1ac |
#! /usr/bin/env python
from MDAnalysis import *
#from MDAnalysis.analysis.align import *
import numpy
import math
import sys
my_traj = sys.argv[1]
end = my_traj.find('.pdb')
u = Universe("init.pdb",my_traj)
v = Universe("init.pdb")
# residues
a1 = u.selectAtoms("segid L and (resid 205)")
#31,32,52,... | demharters/git_scripts | dist_DA10_EPOR-cterm.py | Python | apache-2.0 | 1,713 | [
"MDAnalysis"
] | dc3c3448681794db75d5c6aea312c165c2ac85740b6ff1765830298e86ac84e0 |
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Mathieu Blondel <mathieu@mblondel.org>
# Olivier Grisel <olivier.grisel@ensta.org>
# Andreas Mueller <amueller@ais.uni-bonn.de>
# Eric Martin <eric@ericmart.in>
# Giorgio Patrini <giorgio.patrini@anu.edu.au>
# Lic... | f3r/scikit-learn | sklearn/preprocessing/data.py | Python | bsd-3-clause | 67,092 | [
"Gaussian"
] | 1e6e14cf39aeb90a097d7b308b8ec329caffefd4fe99df4d367cfa1f4ed29718 |
# -*- coding: utf-8 -*-
import h5py
import numpy as np
from keras import backend as K
from keras import optimizers
from keras.models import load_model
from keras.layers import BatchNormalization, Conv3D
import warnings
from datetime import datetime
import re
import os
from functools import reduce
from util.Loggers imp... | StefReck/Km3-Autoencoder | scripts/util/run_cnn.py | Python | mit | 55,670 | [
"NEURON"
] | 01b11c6b932a610c69d675c50cafd4c46aac9e0f8ffb5a7eea0b99778a728d26 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Defines the classes relating to 3D lattices.
"""
import math
import itertools
import warnings
from functools import reduce
import collections
from fractions import Fraction
from typing import List, Union,... | mbkumar/pymatgen | pymatgen/core/lattice.py | Python | mit | 63,139 | [
"ABINIT",
"CRYSTAL",
"pymatgen"
] | 7229b39e4571eeb6b7d1e41429d8ad8863b4e486ce30f3cee0980507e99ddfbd |
"""
Statistics.
"""
import numpy as np
class MultivariateNormal(object):
"""
MultivariateNormal represents a multivariate normal (or "Gaussian")
distribution parametrised in terms of a mean and covariance. The mean is a
length-N vector and the covariance is a NxN matrix.
If mean is unspecified, i... | rjw57/starman | starman/stats.py | Python | mit | 1,782 | [
"Gaussian"
] | 8f054251604ae788d0c1a20dce9a0e0ce1fa4efae0f6ce749d1b3b6dcc23126d |
# -*- coding: utf-8 -*-
"""
General utilities
"""
import obspy.signal.filter
import numpy as np
from numpy.lib.stride_tricks import as_strided
from numpy.fft import rfft, irfft, rfftfreq
import os
import glob
import shutil
import pickle
import shapefile
import matplotlib.pyplot as plt
from matplotlib.patches import Po... | boland1992/seissuite_iran | build/lib/ambient/ant/psutils.py | Python | gpl-3.0 | 20,148 | [
"Gaussian"
] | eda0658803f8ad3e3af1fb1452ae8c187481006d78cd81c59810b6b126717fbb |
# coding: utf-8
from __future__ import unicode_literals
import pytest
from mock import Mock
from attrdict import AttrDict
from ariadne.actions import Visit, Action, FillForm
@pytest.fixture
def ctx_browser():
""" :return: Context with mocked browser. """
mock = Mock()
context = AttrDict({
'brow... | tricoder42/python-ariadne | tests/test_actions.py | Python | mit | 2,882 | [
"VisIt"
] | 2eeeb24c982a9e54ce975e6a38b7b2b971b8524e99a927f910ece5ba41f6b60a |
"""
This examples are outdated and need to be adopted to the new client!!!
Before the start, you have to configure connection settings in conf.json file.
Use our DEMO user to get an overview:
{
...
"username": "guest",
"password": "pass",
"host": "predata.g-node.org",
"port": 80,
...
}
The da... | G-Node/python-gnode-client | gnodeclient/examples/overview.py | Python | lgpl-2.1 | 6,915 | [
"NEURON"
] | 3c53d109461eecc691974eea6215b7d9813308597b48dc9f616e3873652f9a43 |
import sys
import subprocess
import json
import re
import pandas as pd
from pandas import ExcelWriter
_id_offset_pattern = re.compile(u'id=(\d+)&offset=(\d+)')
def _decode_list(data):
rv = []
for item in data:
if isinstance(item, unicode):
item = item.encode('utf-8')
elif isinsta... | teng-lin/teng-lin.github.io | scripts/scrape_linkedin.py | Python | mit | 4,038 | [
"VisIt"
] | e50a855dded1bd37a8838aa6211c40cbe4e342d8a6948828515889c391086f1c |
# -*- coding: utf-8 -*-
"""Get public registrations for staff members.
python -m scripts.staff_public_regs
"""
from collections import defaultdict
import logging
from modularodm import Q
from website.models import Node, User
from website.app import init_app
logger = logging.getLogger('staff_public_regs')
STAFF... | ticklemepierce/osf.io | scripts/staff_public_regs.py | Python | apache-2.0 | 1,355 | [
"Brian"
] | 37cf4661195822788a093e6ce5c4193628e72175c06ab598bd76dfd520758612 |
from __future__ import print_function
from builtins import object
import json
import re
from compiler.js import split_name, escape_package, get_package, mangle_package, escape
from compiler.js.component import component_generator
from collections import OrderedDict
root_type_package = 'core'
root_type_name = 'CoreObj... | pureqml/qmlcore | compiler/js/generator.py | Python | mit | 9,604 | [
"VisIt"
] | bfe467909e4c2d4be946a9b01c5c4830d98ebb1eb1d1b5ab65bd5944b17db399 |
# 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... | mistercrunch/panoramix | superset/charts/schemas.py | Python | apache-2.0 | 44,436 | [
"Gaussian"
] | 508c8e91e208d02c8050f0fcaaa1fd2d443ef0c2a6fb5359ee8abc9a1cacbfcc |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 Async Open Source
##
## This program is free software; you can redistribute it and/or
## modify it under the terms of the GNU Lesser General Public License
## as published by the Free Software Foundation; either version 2
## of the License, or... | andrebellafronte/stoq | stoqlib/l10n/sv/sv.py | Python | gpl-2.0 | 2,528 | [
"VisIt"
] | d1de661d835e0549e6472704d1e66d9ca3c4ec7b0f98a0fb6553d2505fe69282 |
import os
_basedir = os.path.abspath(os.path.dirname(__file__))
DEBUG = False
SECRET_KEY = ''
# URL of the ElasticSearch instance that contains the AVResearcher
# broadcasts index
ES_SEARCH_HOST = 'localhost'
ES_SEARCH_PORT = 9200
ES_SEARCH_URL_PREFIX = ''
ES_SEARCH_INDEX = 'avresearcher'
# URL of the ElasticSearc... | beeldengeluid/audiovisual-researcher | settings.py | Python | apache-2.0 | 10,507 | [
"VisIt"
] | 2da82bb428edb321e11d5d0d091946adf693fc47e72caf8e3e23976dad856e04 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | Achuth17/scikit-bio | skbio/alignment/tests/test_ssw.py | Python | bsd-3-clause | 31,721 | [
"scikit-bio"
] | 46072a0565b5d55be5e28ae31d58d09dfffefdf30756d1ff25dad3fd194c83aa |
""" Schemas for structural stacks. """
import datajoint as dj
from datajoint.jobs import key_hash
import matplotlib.pyplot as plt
import numpy as np
import scanreader
from scipy import signal
from scipy import ndimage
from scipy import optimize
import itertools
from . import experiment, notify, shared, reso, meso
anat... | jakereimer/pipeline | python/pipeline/stack.py | Python | lgpl-3.0 | 135,867 | [
"Gaussian"
] | 7d9991f624d173e76890fa171b0bb99f985e63b84b53ef8b8ce89c087ecfb0bf |
'''
Created on 1/12/2009
@author: brian
'''
from scipysim.actors import Siso, Channel, Event, LastEvent
import unittest
class Decimator(Siso):
'''
This actor takes a source and only passes on every Nth value
'''
def __init__(self, input_channel, output_channel, reduction_factor=5):
'''
... | mm318/scipysim-nogui | scipysim/actors/signal/decimator.py | Python | gpl-3.0 | 2,139 | [
"Brian"
] | f0e6ae3f65eedb3db2fecbdb5b5bba2717ee1748896286feb48e90a4f82d001b |
r"""OS routines for NT or Posix depending on what system we're on.
This exports:
- all functions from posix, nt or ce, e.g. unlink, stat, etc.
- os.path is either posixpath or ntpath
- os.name is either 'posix', 'nt' or 'ce'.
- os.curdir is a string representing the current directory ('.' or ':')
- os.pardir... | Microvellum/Fluid-Designer | win64-vc/2.78/python/lib/os.py | Python | gpl-3.0 | 35,545 | [
"VisIt"
] | 8deb17248221fac37a23098d941075408e64fa3d99e0029f5c9863b20457b6b1 |
#!/usr/bin/env python
import numpy
numpy.seterr(all='raise')
from sys import stdout
from ase import Atoms, Atom
from ase.constraints import FixAtoms
from ase.cluster.icosahedron import Icosahedron; Icosahedron
from ase.cluster.octahedron import Octahedron; Octahedron
from ase.io import write, read
from ase.optimize imp... | SamChill/ligandizer | ligandizer.py | Python | bsd-2-clause | 8,276 | [
"ASE"
] | a4b7879098fbec6adaf9e954e746b38ea14fdea80c2a5c225ee2d2d4aca7ddd6 |
#! /usr/bin/env python
#
# update_po - a gramps tool to update translations
#
# Copyright (C) 2006-2006 Kees Bakker
# Copyright (C) 2006 Brian Matherly
# Copyright (C) 2008 Stephen George
# Copyright (C) 2012
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of t... | pmghalvorsen/gramps_branch | po/update_po.py | Python | gpl-2.0 | 23,742 | [
"Brian"
] | f918887293ce8eb6e2582f115613139af478dfb600e684e4076028439583dee3 |
from common import Modules, data_strings, load_yara_rules, PEParseModule, ModuleMetadata, is_ip_or_domain
import struct
class abaddon(PEParseModule):
def __init__(self):
md = ModuleMetadata(
module_name="abaddon",
bot_name="Abaddon",
description="Point of sale malware d... | bwall/bamfdetect | BAMF_Detect/modules/abaddonpos.py | Python | mit | 1,415 | [
"Brian"
] | 779095528fa0cb62796a719dfe46c7974ad8046263322ba761a04c8a043cbae6 |
"""
Time series interpolation and smoothing
"""
import numpy as np
from scipy.interpolate import PPoly, PchipInterpolator, UnivariateSpline
from . import convert
from . import weighted_linear_model
from importlib import reload
weighted_linear_model = reload(weighted_linear_model)
convert = reload(convert)
def predict... | danmackinlay/branching_process | branching_process/nonlattice/design.py | Python | mit | 11,165 | [
"DIRAC"
] | de2a34e2d42ea3ce6ded291afff36bffe8464ef18e82502c363f6a5c5756f2b2 |
# 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 use ... | watermelo/libcloud | libcloud/security.py | Python | apache-2.0 | 3,583 | [
"VisIt"
] | 183968b195dcc4a124a62ab147ffc64fdb250959bec759f4279668533c96f27e |
import os
import re
import sys
from hq.hquery.syntax_error import HquerySyntaxError
from pytest import raises
sys.path.insert(0, os.path.abspath('../..'))
from ..common_test_util import expected_result
from test.hquery.hquery_test_util import query_html_doc
def test_explicit_child_axis():
html_body = """
<... | rbwinslow/hq | test/hquery/test_axes.py | Python | mit | 10,650 | [
"MOE"
] | ba9e183f5cfeda7f8459b4b0d8d84075e94fb8f4f537604d1738d26a3f0089cc |
#!/usr/bin/python3
"""paleomix rmdup_collapsed [options] < sorted.bam > out.bam
The rmdup_collapsed filters a BAM file for PCR duplicates unpaired reads under
the assumption that any unpaired read have been generated by the merging of
overlapping paired-end reads, and thereby represent the complete template
sequence. ... | MikkelSchubert/paleomix | paleomix/tools/rmdup_collapsed.py | Python | mit | 8,667 | [
"pysam"
] | b5f6a17d5484bc7a3f710aa814dd72dce3b857557dacecb1d8a90e0528b17229 |
# Copyright (C) 2010-2014 CEA/DEN, EDF R&D
#
# 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 library ... | FedoraScientific/salome-paravis | src/VTKWrapping/getwrapclasses.py | Python | lgpl-2.1 | 5,042 | [
"ParaView",
"VTK"
] | f2ba6d45cf5aeb5947380935034d07f2b877f9d9f7ed125569ae2a8d6a930e30 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module implements an XRD pattern calculator.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = ... | aykol/pymatgen | pymatgen/analysis/diffraction/xrd.py | Python | mit | 14,998 | [
"CRYSTAL",
"pymatgen"
] | 0a9126c493d819d58a2c77223aa6cb5c60e38a4f0c6455e2d3460f59217b7e6d |
"""This module parses the VTK methods, obtains the argument and return
type information, and organizes them.
"""
# Author: Prabhu Ramachandran
# Copyright (c) 2004-2015, Enthought, Inc.
# License: BSD Style.
from __future__ import print_function
import collections
import re
import types
# Local imports (these are r... | dmsurti/mayavi | tvtk/vtk_parser.py | Python | bsd-3-clause | 27,635 | [
"VTK"
] | 873aa54725087e5637d743995a40670c4b7409487d06de8d69308cbaece4590f |
import pytest
import mbuild as mb
import mbuild.formats.gomc_conf_writer as gomc_control
from mbuild.formats.charmm_writer import Charmm
from mbuild.lattice import load_cif
from mbuild.tests.base_test import BaseTest
from mbuild.utils.io import get_fn, has_foyer
@pytest.mark.skipif(not has_foyer, reason="Foyer packa... | iModels/mbuild | mbuild/tests/test_gomc_conf_writer.py | Python | mit | 294,149 | [
"CHARMM"
] | 433776525e71e1487453c7820e2ce2e67db48f51c30286a4623b0e63206a7619 |
# Copyright (C) 2012,2013,2016
# 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 terms... | MrTheodor/espressopp | testsuite/esutil/PTestCollectives.py | Python | gpl-3.0 | 1,935 | [
"ESPResSo"
] | 70611933f6a50336e5274034fe9b1f8c68878563ac8c612fd9377f6573ea0c5e |
# -*- coding: utf-8 -*-
from __future__ import print_function
from six.moves import zip
"""
Description:
Input: event / site data previously analyzed by photostim
Output:
- per-event probability of being direct / evoked / spont
- per-site probability of having evoked / direct input
- per-cell measurem... | acq4/acq4 | acq4/analysis/modules/MapAnalyzer/MapAnalyzer.py | Python | mit | 42,680 | [
"Gaussian"
] | fdb76091d05c9e4a4f7e6ec7880772ce491f23db117b0ce5474bf3770bd5cdb2 |
# Copyright (c) 2014. Mount Sinai School of Medicine
#
# 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... | hammerlab/immuno | setup.py | Python | apache-2.0 | 2,074 | [
"Biopython"
] | fce70f5e3fffc3deae8c11c489c8ec45b7de6648e91961aad3698114030a4411 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import unittest
import os
import json
from io import open
import matplotlib
matplotlib.use("pdf") # Use non-graphical display backend during test.
from monty... | czhengsci/pymatgen | pymatgen/electronic_structure/tests/test_plotter.py | Python | mit | 15,076 | [
"BoltzTrap",
"VASP",
"pymatgen"
] | aadf4d4b9a7d731c5866bdb222a2451f73452f14bf7a2681cf98ff843ae1dbb4 |
import pickle
from io import BytesIO
import numpy as np
import scipy.sparse
from sklearn.datasets import load_digits
from sklearn.cross_validation import cross_val_score
from sklearn.externals.six.moves import zip
from sklearn.utils.testing import assert_almost_equal
from sklearn.utils.testing import assert_array_equ... | soulmachine/scikit-learn | sklearn/tests/test_naive_bayes.py | Python | bsd-3-clause | 12,584 | [
"Gaussian"
] | 5fefd29e00666b3977508a63c7e18ac866d03d9df7eef490c62fb366a29230a7 |
#!/usr/bin/env python
#
# Copyright (c) 2021 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.
"""The script runs password change tests present in PasswordChangeFixtureTest.
Example Steps:
1. Fill arguments in config... | chromium/chromium | components/autofill_assistant/android/internal/tools/password_change_tests_runner/runner.py | Python | bsd-3-clause | 6,400 | [
"VisIt"
] | 6886ea317396fc8e235432ab1ac1227dfdd6d90841deba58f6f0a18169e95dc7 |
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