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# Copyright (c) 2012 - N.P. de Klein
#
# This file is part of Python Mass Spec Analyzer (PyMSA).
#
# Python Mass Spec Analyzer (PyMSA) is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either ver... | davidmam/pyMSA | build/lib/pyMSA/test/test_plots.py | Python | gpl-3.0 | 3,576 | [
"OpenMS"
] | 28802befe385186dacf0bc835acc34845ab641e53dce3221bf47cf483a727912 |
from lettuce import step, world
from survey.features.page_objects.question_module import QuestionModuleList, NewQuestionModule, EditQuestionModulePage
from survey.models import QuestionModule
@step(u'And I have two question modules')
def and_i_have_two_question_modules(step):
world.health_module = QuestionModule.... | antsmc2/mics | survey/features/question_module-steps.py | Python | bsd-3-clause | 3,047 | [
"VisIt"
] | a301b7fcf77fbeec54967ece16838b243fe11e81b7128df4f1dd63a97a2d5c40 |
"""
Geckoboard decorators.
"""
import base64
import json
from types import ListType, TupleType
try:
from Crypto.Cipher import AES
from Crypto import Random
from hashlib import md5
encryption_enabled = True
except ImportError:
encryption_enabled = False
from functools import wraps
from collection... | rossdeane/flask-geckoboard | flask_geckoboard/decorators.py | Python | mit | 17,376 | [
"Amber"
] | 14d3be302464854567596b77857df45b67399c335593651163e809597c235a65 |
'''Launches browser to visit given urls (local and remote).
Completes short urls like "blacktrash.org" automagically.
$BROWSER environment may be overridden with option "-b".
'''
# $Id$
import optparse, sys
from muttils import pybrowser, util
proginfo = 'Pybrowser - python interface to system browsers'
def run():... | cwarden/muttils | muttils/pybrowsercommand.py | Python | gpl-2.0 | 926 | [
"VisIt"
] | 57b98d40507f93caf9fbd6dc328d97173ebe59c9eba836b0c5fc0e947031b2fe |
# Copyright 2013-present Barefoot 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 required by applicable law or ... | p4lang/p4-hlir | p4_hlir/hlir/table_dependency.py | Python | apache-2.0 | 24,705 | [
"VisIt"
] | 391f109f51712bd000cb22563c13aae07e864d2809fe91ce0837f8d43bb49f4f |
__author__ = 'sibirrer'
from astrofunc.LensingProfiles.gaussian import Gaussian
from astrofunc.LensingProfiles.gaussian_kappa import GaussianKappa
import numpy as np
import numpy.testing as npt
import pytest
class TestGaussian(object):
"""
tests the Gaussian methods
"""
def setup(self):
self.... | sibirrer/astrofunc | test/test_gaussian.py | Python | mit | 4,514 | [
"Gaussian"
] | 4458baae73a8170b9b8806bd8fd0a3906176d36a668f1336c113284c1d28261b |
# 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 of ... | espressopp/espressopp | src/tools/tabulated.py | Python | gpl-3.0 | 1,943 | [
"ESPResSo"
] | 83231884250a0991025448d7551fa37a0da4f3a8dd61d72509c5ea2d8a881c25 |
# Definition for a binary tree node.
# class TreeNode:
# def __init__(self, x):
# self.val = x
# self.left = None
# self.right = None
class Solution:
def hasPathSum(self, root: TreeNode, sum: int) -> bool:
if not root:
return False
def visit(s, n):
... | fy0/my-leetcode | 112. Path Sum/main.py | Python | apache-2.0 | 681 | [
"VisIt"
] | e4a5f9cc6247569e093ee708381737c0c3524cbc3a06134110f89e85d486911d |
import os
import unittest
from __main__ import vtk, qt, ctk, slicer
from slicer.ScriptedLoadableModule import *
import logging
import SimpleITK as sitk
import sitkUtils
import math
import numpy
import LabelStatistics
#
# ComputeT2Star
#
class ComputeT2Star(ScriptedLoadableModule):
"""Uses ScriptedLoadableModule bas... | tokjun/CryoMonitoring | ComputeT2Star/ComputeT2Star.py | Python | bsd-3-clause | 26,949 | [
"VTK"
] | c8a5698dee57734f6c956bf0fc7d7c8b903bd7e74a83f3a1517f6ce29246a330 |
# encoding: utf8
from __future__ import absolute_import, division
from collections import defaultdict, namedtuple
import colorsys
import json
import logging
import mimetypes
import re
import pokedex.db
import pokedex.db.tables as tables
import pkg_resources
from pylons import config, request, response, session, tmpl_... | Sanqui/spline-pokedex | splinext/pokedex/controllers/pokedex.py | Python | mit | 78,359 | [
"CRYSTAL"
] | 7e450e46e0a43d59260ab0bd545fd0e105d2b13e8f0b4bc57090263bcb85ce7f |
########################################################################
# $HeadURL$
# File : BOINCComputingElement.py
# Author : J.Wu
########################################################################
""" BOINC Computing Element
"""
__RCSID__ = "$Id$"
from DIRAC.Resources.Computing.ComputingElement ... | Sbalbp/DIRAC | Resources/Computing/BOINCComputingElement.py | Python | gpl-3.0 | 13,448 | [
"DIRAC"
] | 0081fab1e16ad446d1eee0af26de5a0443a0380502a46dda965559ad07380226 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, print_function, division
import numbers
import itertools
import collections
import numpy as np
from zarr.errors import (err_too_many_indices, err_boundscheck, err_negative_step,
err_vindex_invalid_selection)
def is_integer(x)... | alimanfoo/zarr | zarr/indexing.py | Python | mit | 28,056 | [
"VisIt"
] | 2eec5366063448353e764a56f44576d6233d79097013a9ebaab5cc5502ef3a85 |
"""
The Euclid Visible Instrument Image Simulator
=============================================
This file contains an image simulator for the Euclid VISible instrument.
The approximate sequence of events in the simulator is as follows:
#. Read in a configuration file, which defines for example,
detect... | sniemi/EuclidVisibleInstrument | simulator/simulatorCOSMOS.py | Python | bsd-2-clause | 57,734 | [
"Galaxy",
"Gaussian"
] | 94565fb3fe769547d267d255dcfeb93a6034b83b32cc322f928a8136b4b7e175 |
# sql/elements.py
# Copyright (C) 2005-2015 the SQLAlchemy authors and contributors
# <see AUTHORS file>
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Core SQL expression elements, including :class:`.ClauseElement`,
:class:`.ColumnE... | sunze/py_flask | venv/lib/python3.4/site-packages/sqlalchemy/sql/elements.py | Python | mit | 132,392 | [
"VisIt"
] | 2652b0acbf34dd55673087fe90b6ec133d769e11f7da1f4d135b49494861ac48 |
# coding=utf-8
# main codes, call functions at stokes_flow.py
# Zhang Ji, 20170518
import sys
import petsc4py
petsc4py.init(sys.argv)
import numpy as np
from src.stokes_flow import problem_dic, obj_dic
import src.stokes_flow as sf
from petsc4py import PETSc
from src.geo import *
import pickle
# def print_case_inf... | pcmagic/stokes_flow | try_code/try_forcefreeinpipe.py | Python | mit | 7,866 | [
"VTK"
] | 400eef829b45a41efed7573f1da8ded3ef3bc482934b174bfc905adb1473bbbb |
#!/usr/bin/env python
import pylab as pyl
from mpl_toolkits.axes_grid1 import AxesGrid
import cPickle as pickle
from colsort import colsort
def plot_uvj_vs_icd():
galaxies = pickle.load(open('galaxies.pickle','rb'))
galaxies = filter(lambda galaxy: galaxy.ICD_IH != None, galaxies)
galaxies = filter(lambda ... | boada/ICD | sandbox/plot_sersic_vs_icd_vs_mass_box_width.py | Python | mit | 6,098 | [
"Galaxy"
] | 745bb7553a79e1dcc75e8b9bbef3ba35752a70848cd7b1c13496b5fc31236471 |
from __future__ import division
from __future__ import unicode_literals
__author__ = "Bharath Ramsundar, Evan Feinberg, and Karl Leswing"
__copyright__ = "Copyright 2016, Stanford University"
__license__ = "MIT"
import logging
import os
import shutil
from warnings import warn
import time
import tempfile
import hashli... | ktaneishi/deepchem | deepchem/feat/rdkit_grid_featurizer.py | Python | mit | 49,998 | [
"RDKit"
] | 3b6f79b72a8f8d06f639f20eb03d4cb63aa48b72141d577e1d154677c6ad0e14 |
"""Implementation of the WebSocket protocol.
`WebSockets <http://dev.w3.org/html5/websockets/>`_ allow for bidirectional
communication between the browser and server.
WebSockets are supported in the current versions of all major browsers,
although older versions that do not support WebSockets are still in use
(refer ... | legnaleurc/tornado | tornado/websocket.py | Python | apache-2.0 | 47,962 | [
"VisIt"
] | a6b451f090dbf3042f55b1907f513e80d84872d482dd584ad46e869e8c7a05be |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kratman/psi4public | psi4/driver/p4util/util.py | Python | gpl-2.0 | 19,422 | [
"Psi4"
] | b4bbf78ab44ee5aed217566d7191cb8f322419794391bdbe2524ac963aea8144 |
"""Save pairwise RMSD, TFDs, and E3FP TCs between conformer pairs.
Authors: Seth Axen
E-mail: seth.axen@gmail.com
"""
import argparse
import numpy as np
import rdkit.Chem
from rdkit.Chem import rdMolAlign, TorsionFingerprints
from e3fp.pipeline import params_to_dicts, fprints_from_mol
from e3fp_paper.pipeline import ... | keiserlab/e3fp-paper | project/fingerprint_comparison/random_conformer_pairs/get_pair_rmsds_tfds_tcs.py | Python | lgpl-3.0 | 2,568 | [
"RDKit"
] | 6faee5375c576a7c1d8ac31b0a08bd8254faffd8c5e74c8bffbdd144af7d1dc2 |
#
# ----------------------------------------------------------------------------------------------------
#
# Copyright (c) 2007, 2015, Oracle and/or its affiliates. All rights reserved.
# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
#
# This code is free software; you can redistribute it and/or modify ... | mohlerm/hotspot_cached_profiles | .mx.jvmci/mx_jvmci.py | Python | gpl-2.0 | 37,568 | [
"VisIt"
] | 6f8d922f658ac936b54b8a53d1cc63e9930717f41a9fa764108aa8d6296cf45a |
# (C) 2015, 2016 Elke Schaper @ Vital-IT, Swiss Institute of Bioinformatics
"""
.. moduleauthor:: Elke Schaper <elke.schaper@sib.swiss>
"""
import logging
import GPy
import numpy as np
from hts.data_tasks.gaussian_processes import create_gaussian_process_composite_kernel
LOG = logging.getLogger(__name__)
def... | elkeschaper/hts | hts/data_tasks/prediction.py | Python | gpl-2.0 | 2,141 | [
"Gaussian"
] | 037492f23bd049354e37969081655855856f9dc3bfbe7480a7cead7f499717b7 |
#!/usr/bin/env python
#
# Wrapper script for invoking the jar.
#
# This script is written for use with the Conda package manager and is ported
# from a bash script that does the same thing, adapting the style in
# the peptide-shaker wrapper
# (https://github.com/bioconda/bioconda-recipes/blob/master/recipes/peptide-sha... | colinbrislawn/bioconda-recipes | recipes/wdltool/wdltool.py | Python | mit | 2,506 | [
"Bioconda"
] | ebd951347711fb5e4f1ade1bfbf650301463db66d36a06e5d8b068e95e202bc9 |
# Copyright (c) 2012, Cloudscaling
# 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... | sajeeshcs/nested_quota_final | nova/hacking/checks.py | Python | apache-2.0 | 21,797 | [
"VisIt"
] | fa2b765f28596b5d8de596d82cee608a692982f6cf3ffd17ff90aadaddf9ea98 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Grass(AutotoolsPackage):
"""GRASS GIS (Geographic Resources Analysis Support System), is a... | iulian787/spack | var/spack/repos/builtin/packages/grass/package.py | Python | lgpl-2.1 | 10,428 | [
"NetCDF"
] | 3c0343956d1c70f5ab3db99b4fc7b778f8124ccfc322a4f8fffdc8a91b7850b3 |
__source__ = 'https://leetcode.com/problems/course-schedule/description/'
# https://github.com/kamyu104/LeetCode/blob/master/Python/course-schedule.py
# Time: O(|V| + |E|)
# Space: O(|E|)
#
# Description: Leetcode # 207. Course Schedule
#
# There are a total of n courses you have to take, labeled from 0 to n - 1.
#
# ... | JulyKikuAkita/PythonPrac | cs15211/CourseSchedule.py | Python | apache-2.0 | 10,360 | [
"VisIt"
] | 8bfdf3de8620b676c8383f6d2edb2e48155d6ae142c074e50d18642551f02111 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
def GetRGBColor(colorName):
'''
Return the red, green and blue components for a
color as doubles.
'''
rgb = [0.0, 0.0, 0.0] # black
vtk.vtkNamedColors... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Filters/Core/Testing/Python/StreamPolyData.py | Python | gpl-3.0 | 2,667 | [
"VTK"
] | 864bbb79919c2d989531f611000b3d0c6a000c5e765da205aaa7cebdc35b7aa1 |
# -*- coding: utf-8 -*-
from django.conf import settings
from django.test import TestCase
from zilencer.models import Deployment
from zerver.models import (
get_realm, get_user_profile_by_email,
PreregistrationUser, Realm, ScheduledJob, UserProfile,
)
from zerver.lib.actions import (
create_stream_if_nee... | gkotian/zulip | zerver/test_signup.py | Python | apache-2.0 | 20,333 | [
"VisIt"
] | 3d6a2c7ce48c1a3a17055284f9937438c0420909251c7a840ebcaa3233477485 |
import time
from base_handler import BlogHandler
from models import User
from utility import valid_email, valid_username, valid_password, hash_str
class RegistrationHandler(BlogHandler):
def get(self):
self.render("register.html")
def post(self):
has_error = False
error_list = []
... | ghoshabhi/Multi-User-Blog | handlers/registration_handler.py | Python | mit | 3,696 | [
"VisIt"
] | c7b711527d7dc61aa3398915f9cc80222018d64b97b978e1bfb40c27bb869535 |
import unittest
from chartbeatpy import Chartbeat
class ChartbeatTest(unittest.TestCase):
def setUp(self):
self.beat = Chartbeat("317a25eccba186e0f6b558f45214c0e7", "avc.com")
self.keys = [
Chartbeat.READ, Chartbeat.WRITE, Chartbeat.IDLE
]
def test_histogram(self):
... | michigan-com/chartbeatpy | tests/test_chartbeat.py | Python | mit | 2,386 | [
"VisIt"
] | 5a95c2ff64b2f1b9bf9cf5373bd46cc089f273e199e306d85854ce8b90674f92 |
# coding: utf8
from __future__ import unicode_literals, print_function, division
import re
from collections import defaultdict
from itertools import groupby, chain, combinations
import io
from clld.db.meta import DBSession
from clld.db.models import common
from cdk import models
SOURCE_MAP = {
'WΕR2': 'WER2',
... | clld/cdk | cdk/scripts/util.py | Python | apache-2.0 | 15,401 | [
"CDK"
] | bda6ed9606b29b49146ebc66bc800d2ef29601bb6b5dfa1d6fae75f7b19ae6ec |
"""Workflow for collecting diffraction data from high quality crystals in a cassette."""
import csv
import sys
import math
import optparse
import os
import time
from datetime import datetime
"""
@begin simulate_data_collection @desc Workflow for collecting diffraction data from high quality crystals in a cassette.
@p... | idaks/DataONE-Prov-Summer-2017 | examples/simulate_data_collection/source-scripts/simulate_data_collection.py | Python | apache-2.0 | 11,420 | [
"CRYSTAL"
] | b99a554073c9896d5cc25f98f3402d06a00a33517930b479af6f93ef8b898cab |
"""This module provides several built-in models for incoherent
neutron scattering data fitting.
These functions generate a `Model` class instance from
the **lmfit** package [#]_.
References
----------
.. [#] https://lmfit.github.io/lmfit-py/
"""
import operator
import numpy as np
try:
from lmfit import Comp... | kpounot/nPDyn | nPDyn/lmfit/lmfit_builtins.py | Python | gpl-3.0 | 6,538 | [
"DIRAC",
"Gaussian"
] | 0cc57e3ecaead9efd39ebe224f52754aa9596f395e64a5eb4fef97b362dbb060 |
# coding: utf-8
# # ACS Lab 01 - Scientific Visualization
#
# The first lab of the semester will be structured differently than the rest. The focus of this lab is to familiarize yourself with a wide variety of scientific visualizations. All of the labs this semester will be language agnostic, meaning you can use you... | eitanlees/ISC-5315 | ACS1_Lab_01/ACS1_Lab_01.py | Python | mit | 9,149 | [
"Gaussian"
] | 268ddad696fdc947899444960049ec472129b54fe976a34327fe63a69c102a80 |
import numpy as np
from mdtraj.testing import eq
from msmbuilder.example_datasets import AlanineDipeptide
from msmbuilder.featurizer import AtomPairsFeaturizer, get_atompair_indices
from msmbuilder.featurizer.subset import SubsetAtomPairs, \
SubsetCosPhiFeaturizer, SubsetCosPsiFeaturizer, SubsetFeatureUnion, \
... | dr-nate/msmbuilder | msmbuilder/tests/test_featurizer_subset.py | Python | lgpl-2.1 | 2,780 | [
"MDTraj"
] | 0edee68e8ba8e6894b70a107555b70c45b1b5ce81071da0c1c7a776776ea530d |
import calendar
import datetime
import logging
import uuid
from celery.result import AsyncResult
from django.conf import settings
from django.core.exceptions import ValidationError
from django.db import models
from .fields import BoundingBoxField, RasterRendererField
from .utils import auto_memoize
logger = logging.... | consbio/ncdjango | ncdjango/models.py | Python | bsd-3-clause | 8,338 | [
"NetCDF"
] | 0f985e49a3e5e78ceae5fd82df01938f885b529f9435c5802e3e1f9c74936dfc |
# vim: set expandtab shiftwidth=2 softtabstop=2:
# TODO - BundleAPI eh? - seems to be the class we have to override and mess with to get things imported to ChimeraX
from chimerax.core.toolshed import BundleAPI
class _MyAPI(BundleAPI):
@staticmethod
def get_class(class_name):
if class_name == 'ToolUI':
f... | OniDaito/ChimeraXTempy | src/__init__.py | Python | mit | 1,224 | [
"ChimeraX"
] | b8a1f8f502df13a50883fc69b476e4f4a7389988b3bc903505907774cd18bc5d |
import sys
import git
import pygtk
pygtk.require('2.0')
import gtk
class HelloWorld:
# This is a callback function. The data arguments are ignored
# in this example. More on callbacks below.
def hello(self, widget, data=None):
print "Hello World"
def delete_event(self, widget, event, dat... | DavidAwad/GitTorrent | app.py | Python | mit | 3,405 | [
"VisIt"
] | 47351da47426efdbecfd21909a14f0454bf58d113f375e40e4865c8da11d9a93 |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
#
# Python motu client
#
# Motu, a high efficient, robust and Standard compliant Web Server for Geographic
# Data Dissemination.
#
# http://cls-motu.sourceforge.net/
#
# (C) Copyright 2009-2010, by CLS (Collecte Localisation Satellites) -
# http://www.cls.fr - and Co... | dipapaspyros/bdo_platform | aggregator/connectors/motu/client.py | Python | mit | 13,497 | [
"NetCDF"
] | 5d04ad8af76886ff019650dd3142bcccad484e85ccc6e0a47d587b733688ca27 |
from progressbar import ProgressBar, Percentage, SimpleProgress, Timer, AdaptiveETA, Bar, FormatLabel
import numpy as np
import itertools
import random
from phylo_utils import seq_to_partials
from phylo_utils.markov import TransitionMatrix
from phylo_utils.models import LG, WAG, GTR
from phylo_utils.likelihood import G... | kgori/treeCl | treeCl/utils/misc.py | Python | mit | 7,203 | [
"Biopython"
] | 7cd0d13a8768d9b448b437772f1d4918ba8b653ba676b710ebc19b682833276c |
# sql/visitors.py
# Copyright (C) 2005-2016 the SQLAlchemy authors and contributors
# <see AUTHORS file>
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Visitor/traversal interface and library functions.
SQLAlchemy schema and express... | pcu4dros/pandora-core | workspace/lib/python3.5/site-packages/sqlalchemy/sql/visitors.py | Python | mit | 10,271 | [
"VisIt"
] | e22a46bc092a15a4805a0c8db8a8f1e71fe6b3c188cbd6aafb00b9a63e3e6778 |
# LIBTBX_PRE_DISPATCHER_INCLUDE_SH export PHENIX_GUI_ENVIRONMENT=1
from __future__ import annotations
import json
import math
import os
import sys
import matplotlib
import iotbx.phil
from cctbx import crystal, miller
from cctbx.array_family import flex
from scitbx import matrix
import dials.util
help_message = ""... | dials/dials | command_line/stereographic_projection.py | Python | bsd-3-clause | 15,500 | [
"CRYSTAL"
] | 52ffdd5231f9f41c5f19f00e32c318b481f163b56ad39522688c4f558a4a2a7b |
# Python Imports
import uuid
import os
import json
import time
import re
import numpy as np
now = time.time # shortcut
# Twisted Imports
from twisted.internet import defer, threads, task
from twisted.python import log
from twisted.python.filepath import FilePath
from twisted.logger import Logger
# Octopus Imports
fr... | richardingham/octopus | octopus/blocktopus/experiment.py | Python | mit | 19,197 | [
"Octopus"
] | 7e508557f813f43ae2c82496f06d0d9b7af9d0e776dbf5ff6d372e8e2544bbe6 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2016, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Unit tests for writer xyzwriter module."""
import os
import unittest
import cclib
__filedir__ = os.path.dirname(__f... | Schamnad/cclib | test/io/testxyzwriter.py | Python | bsd-3-clause | 940 | [
"ADF",
"cclib"
] | 468038157364d5011fd7a70bcb100b613ab18a7c26a7dfb2bb13fdcbb8efd227 |
# -*- coding: utf-8 -*-
#
# hl_api_simulation.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 Licen... | SepehrMN/nest-simulator | pynest/nest/lib/hl_api_simulation.py | Python | gpl-2.0 | 11,564 | [
"NEURON"
] | ba2cdca79071153ed2802b3c53b4ee700608094d944bc7462737cc12970e6546 |
import cv2
import numpy as np
COLOR_SWATCH = [
[255, 64, 0], [255, 128, 0], [255, 191, 0],
[255, 255, 0], [191, 255, 0], [128, 255, 0], [64, 255, 0],
[0, 255, 0], [0, 255, 64], [0, 255, 128],
[0, 255, 191], [0, 255, 255], [0, 191, 255],
[0, 128, 255], [0, 64, 255], [0, 0, 255],
[64, 0, 255], [128, 0... | jabeerahmed/testrepo | term1/Lessons/LaneDetection/Helper.py | Python | gpl-2.0 | 4,155 | [
"Gaussian"
] | 41df5150dcc8a74d9b3018a191b3990c8e3ea6de87993e515fa78db1989ba995 |
#!/usr/bin/env python
""" Loads forecast info, fits beta distributions to marginals.
"""
import pandas as pd
import numpy as np
import os
from kernel_regression import KernelRegression
from itertools import izip
__copyright__ = "Copyright 2016, Tue Vissing Jensen"
__credits__ = ["Tue Vissing Jensen"]
__license__ = "M... | TueVJ/RE-Europe_SimpleEnsembles | forecast_marginal_estimator.py | Python | mit | 3,570 | [
"Gaussian"
] | be6b81983e7c1671099cd9fce6a6a0d86a1a2c03b4ff0987e540ad8be1619415 |
import imp
import os
from DIRAC import S_OK, S_ERROR, gConfig, gLogger
from DIRAC.Core.Utilities.CFG import CFG
from DIRAC.ConfigurationSystem.Client.ConfigurationData import gConfigurationData
from DIRAC.ConfigurationSystem.Client.Helpers import CSGlobals
BASECS = "WebApp"
def loadWebAppCFGFiles():
"""
Load Web... | chaen/WebAppDIRAC | Core/ConfMgr.py | Python | gpl-3.0 | 2,773 | [
"DIRAC"
] | abdcb9269c21866ea6cba78c5f8ff6616a7573d6cc89b46e7caa4a371d02eaef |
import ast
import itertools
from ..core.ast_helper import get_call_names
class VarsVisitor(ast.NodeVisitor):
def __init__(self):
self.result = list()
def visit_Name(self, node):
self.result.append(node.id)
def visit_BoolOp(self, node):
for v in node.values:
self.visi... | python-security/pyt | pyt/helper_visitors/vars_visitor.py | Python | gpl-2.0 | 5,270 | [
"VisIt"
] | 4c24a9e5405c1324ff697266828fa2c3242ca43facbf63366886fa4776b10658 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Common functions.
"""
import sys
import logging
import gzip
import numpy as np
import biochem_tools
import os
import fnmatch
__author__ = "David Hoksza"
__email__ = "david.hoksza@mff.cuni.cz"
__license__ = 'X11'
def find_files_recursively(direct... | davidhoksza/bayescreen | common.py | Python | mit | 2,782 | [
"RDKit"
] | 4b6fbc881e56320c8f4614e7066f4ff069bed7f8cc4ab8f9aa3cf9df29b8517c |
"""Bayesian Data Analysis, 3r ed
Chapter 3, demo 1
Visualise the joint density and marginal densities of posterior of normal
distribution with unknown mean and variance.
"""
from __future__ import division
import numpy as np
from scipy import stats
import matplotlib.pyplot as plt
import matplotlib.gridspec as grids... | lenovor/BDA_py_demos | demos_ch3/demo3_1.py | Python | gpl-3.0 | 3,966 | [
"Gaussian"
] | 708b025535fabafe93d6c231a4259f8d1a93a3c4d0de0ce52b027ebb83e92715 |
# encoding: utf-8
from woo.dem import *
import woo.core
import woo.dem
import woo.pyderived
import woo.models
import math
from minieigen import *
nan=float('nan')
try:
from PyQt4.QtGui import *
from PyQt4.QtCore import *
except ImportError: pass
class EllGroup(woo.core.Preprocessor,woo.pyderived.PyWooObject):
'... | eudoxos/woodem | py/pre/ell2d.py | Python | gpl-2.0 | 8,521 | [
"VTK"
] | 9460c80c632c4c59cd116426515deabf8cf6e9dbb33870edebe6370b40e384db |
import os
import sys
import numpy as np
import fitsio
from astrometry.util.fits import *
def floatcompress(fn, truncbits):
I,hdr = fitsio.read(fn, header=True)
print I.shape, I.dtype
assert(I.dtype == np.float32)
F = np.zeros(I.shape, np.uint32)
F.data[:] = I.data
# IEEE -- ASSUME little-endi... | dstndstn/unwise-coadds | merge.py | Python | gpl-2.0 | 6,712 | [
"Gaussian"
] | bb8a16506860c686a6d8bc689e149c231fce098651b64431cf751f43a779d3e9 |
'''Term class hierarchy.'''
# pylint: disable-msg=W0142
from aterm import types
from aterm import compare
from aterm import hash
from aterm import write
from aterm import lists
class Term(object):
'''Base class for all terms.
Terms are non-modifiable. Changes are carried out by returning another term
instance... | mewbak/idc | aterm/term.py | Python | lgpl-2.1 | 6,584 | [
"VisIt"
] | e581651f0c27797fc9af61ce01db0fb7f2d9cdb1f618a63c492b48c3414db683 |
# Clustering.py
#
# Cluster segments
# Version 3.0 14/09/20
# Authors: Stephen Marsland, Nirosha Priyadarshani, Julius Juodakis, Virginia Listanti
# AviaNZ bioacoustic analysis program
# Copyright (C) 2017--2020
# This program is free software: you can redistribute it and/or modify
# it under the terms o... | smarsland/AviaNZ | Clustering.py | Python | gpl-3.0 | 53,528 | [
"Gaussian"
] | 265ce6968f65710170c4a70c005a76c37ab5142fd95f5396632f75fd2c445143 |
# Copyright 2018 David Huberdeau & Peter Kok
#
# 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... | brainiak/brainiak | brainiak/reconstruct/iem.py | Python | apache-2.0 | 45,193 | [
"Gaussian"
] | 378158d4d099bdb90d6f96ff533844ef4cf78d084ca57059fa3a37f06f5d7079 |
from __future__ import print_function
from __future__ import division
from __future__ import absolute_import
from builtins import map
from builtins import zip
from builtins import range
import os
import operator
from math import log
from Bio import motifs
import numpy as np
def get_motif_bg_freq(meme_file):
"""Rea... | saketkc/moca | moca/helpers/meme.py | Python | isc | 6,268 | [
"Biopython"
] | da195e6ad2fb32aa21839a5d5a4beb9e524bb98e1b8b5a8a387a4da71aab7a7a |
# -*- coding: utf-8 -*-
import pytest
from csirtg_indicator.indicator import Indicator
from pprint import pprint
@pytest.fixture
def indicator():
i = {
'indicator': "http://refreshdharan.com/bg/excel2/index.php?userid={dong.keonkwonfinancialconsultd@yahoo.com}",
'itype': 'fqdn',
... | csirtgadgets/csirtg-indicator-py | test/format/test_format_keys.py | Python | mpl-2.0 | 653 | [
"Amber"
] | 440e3ed903a93a35471e548682cbbe8c1e236654e9bd275822c6a90d6e4be4c6 |
#Copyright (C) 2013 Alex Nitz
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 3 of the License, or (at your
# option) any later version.
#
# This program is distributed in the h... | ahnitz/pycbc | pycbc/strain/strain.py | Python | gpl-3.0 | 80,053 | [
"Gaussian"
] | bb2ba3c88d4ffc0a2b04383dd98c8163265af3718f6b13b3210c386ce2c23b1d |
"""
desispec.bootcalib
==================
Utility functions to perform a quick calibration of DESI data
TODO:
1. Expand to r, i cameras
2. QA plots
3. Test with CR data
"""
from __future__ import print_function, absolute_import, division
import numpy as np
import copy
import pdb
import yaml
import glob
import math
i... | desihub/desispec | py/desispec/bootcalib.py | Python | bsd-3-clause | 66,424 | [
"Gaussian"
] | e34fdeb202af140b636b92d0375bb3960ca6c0b284cd095edc4362a14d8b4ca8 |
""" DIRAC FileCatalog mix-in class to manage directory metadata
"""
# pylint: disable=protected-access
__RCSID__ = "$Id$"
import os
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Utilities.Time import queryTime
class DirectoryMetadata:
def __init__(self, database=None):
self.db = database
def setDataba... | fstagni/DIRAC | DataManagementSystem/DB/FileCatalogComponents/DirectoryMetadata.py | Python | gpl-3.0 | 27,739 | [
"DIRAC"
] | 55d7c7ee2466c5b8250e1064144fac49cfadd927f8c8447d7e03ec73c114af24 |
# ----------------------------------------------------------------------
# Numenta Platform for Intelligent Computing (NuPIC)
# Copyright (C) 2016, Numenta, Inc. Unless you have an agreement
# with Numenta, Inc., for a separate license for this software code, the
# following terms and conditions apply:
#
# This progra... | ThomasMiconi/nupic.research | projects/poolingCapacity/layer2_capacity.py | Python | agpl-3.0 | 16,286 | [
"NEURON"
] | ed4c5453be6ec44b3f15549d39481332e1e5554c1ff54b160a8cd9c9c919c9ea |
"""helper.py
Helper functions.
"""
__author__ = "Dilawar Singh"
__copyright__ = "Copyright 2015, Dilawar Singh and NCBS Bangalore"
__credits__ = ["NCBS Bangalore"]
__license__ = "GNU GPL"
__version__ = "1.0.0"
__maintainer__ = "Dilawar Singh"
__email__ ... | dilawar/moose-chemical | utils/helper.py | Python | gpl-2.0 | 3,321 | [
"MOOSE"
] | 4b4d7bbdc89f7a1464f2f6b813bed4f3271f0178b60ebd9dc1d9e7eea22140ce |
from .GlobalData import global_data
from .Projects import all_projects
from .Apps import all_apps
from .Pods import all_pods
from .Task import Task
from .Session import Session
from .CustomizedTask import customizedTask
from .CerberusIntegration import cerberusIntegration
from .utils.SlackIntegration import slackIntegr... | mffiedler/svt | reliability/tasks/TaskManager.py | Python | apache-2.0 | 9,751 | [
"VisIt"
] | 31600a0ebc5fcf73e4624b2e20481ee45ea0f91f96f65974f3ad092d68c9b157 |
# This file is part of MAUS: http://micewww.pp.rl.ac.uk/projects/maus
#
# MAUS is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
# ... | mice-software/maus | tests/py_unit/test_maus_cpp/test_maths/test_polynomial_map.py | Python | gpl-3.0 | 10,671 | [
"MOOSE"
] | d01a2651630457aa62ad70b2407fafa2e400fcc01442ec86791980c013c57f4c |
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'RESTool/ui/design_v2.ui'
#
# Created: Fri May 29 22:07:35 2015
# by: PyQt4 UI code generator 4.11.3
#
# WARNING! All changes made in this file will be lost!
from PyQt4 import QtCore, QtGui
try:
_fromUtf8 = QtCore.QString.fromUtf8
... | Nikola-K/RESTool | RESTool/restoolgui.py | Python | apache-2.0 | 31,410 | [
"VisIt"
] | 1ca841335d595c46cc82c809af431e0066d4ad9097ad3e910176b150f4578a12 |
import unittest
import numpy as np
import pysal.lib
from pysal.model.spreg.twosls import BaseTSLS, TSLS
from pysal.lib.common import RTOL
class TestBaseTSLS(unittest.TestCase):
def setUp(self):
db = pysal.lib.io.open(pysal.lib.examples.get_path("columbus.dbf"),'r')
self.y = np.array(db.by_col("CRIM... | lixun910/pysal | pysal/model/spreg/tests/test_twosls.py | Python | bsd-3-clause | 14,366 | [
"COLUMBUS"
] | 196ba3d7484565af50bf5048b5067fc29000da7523cc36649f18da2d147bc110 |
from ase import Atoms
from ase.io import write
from gpaw import GPAW, Mixer
from ase.data.molecules import molecule
CO = molecule('CO')
CO.set_cell((6., 6., 6.))
CO.center()
calc = GPAW(h=0.2,
nbands=8,
mixer=Mixer(beta=0.1, nmaxold=5, weight=50.0),
txt='CO.txt')
CO.set_calculator... | qsnake/gpaw | doc/exercises/wavefunctions/CO.py | Python | gpl-3.0 | 593 | [
"ASE",
"GPAW"
] | 770c4923f034e49d8d6aaabd0cce8e0a86c26c407a94a3b617b496e4f15998f3 |
from ..utils import *
##
# Minions
class AT_006:
"Dalaran Aspirant"
inspire = Buff(SELF, "AT_006e")
AT_006e = buff(spellpower=1)
class AT_007:
"Spellslinger"
play = Give(ALL_PLAYERS, RandomSpell())
class AT_008:
"Coldarra Drake"
update = Refresh(FRIENDLY_HERO_POWER, {GameTag.HEROPOWER_ADDITIONAL_ACTIVATIO... | beheh/fireplace | fireplace/cards/tgt/mage.py | Python | agpl-3.0 | 770 | [
"BLAST"
] | 556063811b029b9ab1620770c8512355016028b4a28dd7f92dfe9777688d9bf5 |
#!/usr/bin/python
"""
Extracting features from VTK input files.
Authors:
- Forrest Sheng Bao (forrest.bao@gmail.com) http://fsbao.net
Copyright 2012, Mindboggle team (http://mindboggle.info), Apache v2.0 License
For algorithmic details, please check:
Forrest S. Bao, et al., Automated extraction of nested ... | binarybottle/mindboggle_sidelined | fundi_from_pits/libbasin.py | Python | apache-2.0 | 18,234 | [
"VTK"
] | b8a1ac9f3104b48f3a72970362f7850910bbe64f51674829c968ad4d4ea4f6af |
import ddapp.applogic as app
from ddapp import lcmUtils
from ddapp import transformUtils
from ddapp import visualization as vis
from ddapp import filterUtils
from ddapp import drcargs
from ddapp.shallowCopy import shallowCopy
from ddapp.timercallback import TimerCallback
from ddapp import vtkNumpy
from ddapp import obj... | gizatt/director | src/python/ddapp/pointcloudlcm.py | Python | bsd-3-clause | 4,666 | [
"VTK"
] | fa0c646377338a455f1d36b65b5c24c0cc0df68a3670c71573199f3d8559a248 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | fweik/espresso | testsuite/python/lb_get_u_at_pos.py | Python | gpl-3.0 | 3,196 | [
"ESPResSo"
] | a62f28683b478b5e8decc9f49ad629ade589c80c450e01399538a3ae6e537772 |
# coding: utf-8
# In[1]:
# opengrid imports
from opengrid.library import misc, houseprint, caching
from opengrid.library.analysis import DailyAgg
from opengrid import config
c=config.Config()
# other imports
import pandas as pd
import charts
import numpy as np
import os
import datetime as dt
import pytz
BXL = pytz.... | JrtPec/opengrid | opengrid/recipes/electricity_standby.py | Python | apache-2.0 | 10,486 | [
"ADF"
] | 7e0383bfe72f135afb92303fdb4155d8f3067a8bd76f699122c42e001881d766 |
#! /usr/bin/python
"""
COllection of functions and classes to parse and filter hit tables from:
blast
hmmer
last
diamond
infernal
SAM
GFF
"""
import logging
import re
import sys
from edl.util import InputFile, parseExp
logger = logging.getLogger(__name__)
#############
# Constants #
#####... | jmeppley/py-metagenomics | edl/blastm8.py | Python | mit | 46,178 | [
"BLAST",
"BWA"
] | 93c494cd81531103219903c50ead474f33a16d891be2ba028dd504ef52b1c668 |
# Copyright: (c) 2013, James Cammarata <jcammarata@ansible.com>
# Copyright: (c) 2018, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import os.path
import re
import sh... | cchurch/ansible | lib/ansible/cli/galaxy.py | Python | gpl-3.0 | 50,152 | [
"Galaxy"
] | 3be1a9f4e54aa88688105234ae2a588cfdb3e943c9f8f4d5b6a0318aab9bc72e |
#!/usr/bin/env python
# Ryan G. Coleman, Kim A. Sharp, http://crystal.med.upenn.edu,
# ryan.g.coleman ATSYMBOL gmail.com ryangc ATSYMBOL mail.med.upenn.edu
#file takes care of reading .crg files and putting them into dictionary struct
#charge files are column based and look like this:
#NH1 ARG -0.350
#0123456... | ryancoleman/traveldistance | src/charge.py | Python | gpl-2.0 | 2,913 | [
"CRYSTAL"
] | 0f640d1abad436cfa4f076498c106e22c8b592561cfba7e510ef95d6638dc6f0 |
# 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... | AndreasMadsen/tensorflow | tensorflow/contrib/distributions/python/ops/distribution.py | Python | apache-2.0 | 35,525 | [
"Gaussian"
] | 04e67117adc8fd3452783a6ea842e9b6b74b16135e3beaf4055208b2e45e4dd8 |
"""The ants module provides basic functions for interfacing with ants functions.
Change directory to provide relative paths for doctests
>>> import os
>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
>>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
>>> os.chdir(... | iglpdc/nipype | nipype/interfaces/ants/registration.py | Python | bsd-3-clause | 55,946 | [
"Gaussian",
"VTK"
] | dac3135269c121e2005993fbca52c24d81db169683b9527cac7d42d343c911a1 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | andysim/psi4 | psi4/driver/util/filesystem.py | Python | gpl-2.0 | 1,284 | [
"Psi4"
] | 85767998df72d607daf981239b360982f2cb954d1169ca3082d338eaedebe5be |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright (c) 2013 Chris Synan & Dataworlds LLC
# Portions copyright (c) 2012 Stephen P. Smith
#
# Permission is hereby granted, free of charge, to any person obtaining
# a copy of this software and associated documentation files
# (the "Software"), to deal in the Software... | sjmalski/ispresso | ispresso.py | Python | mit | 55,175 | [
"ESPResSo"
] | 166030bf7e8bc3e950c73f5446d17bcc2d7d90fa0bddd61e172ce4f6aec9c0ec |
# This program basically works by calling
# the function websiteRate()
# like this --> websiteRate("http://www.example.com")
# or this --> websiteRate(["http://www.example.com","http://www.otherexample.com",...])
# It returns the number of positive words minus the number of negatives words
# and the number of keywords ... | tiw51/DeepPurple | Stock_Programs/websiteRater.py | Python | apache-2.0 | 5,768 | [
"exciting"
] | df7066fe830f40a30e7cacc676db609b6236f5e5d31b43c653351733a825b42a |
from __future__ import division
import numpy as np
from .kernels import KERNELS
from .utils import nfft_matrix, fourier_sum, inv_fourier_sum
def ndft(x, f_hat):
"""Compute the non-equispaced direct Fourier transform
f_j = \sum_{-N/2 \le k < N/2} \hat{f}_k \exp(-2 \pi i k x_j)
Parameters
----------... | jakevdp/nfft | nfft/core.py | Python | mit | 6,446 | [
"Gaussian"
] | d90a96e67c439e6d525bb954d9a302cf57d780dee4300424cda59d6c0e532ad2 |
import random
import matplotlib.pyplot as plt
import numpy
''' 3_nn.py
simple neural net with 2 neurons
'''
''' -has primitive backprop
-weights deviate in opposite direction of error
-productivity is determined by difference between forward output and target
'''
'''TODO:
-one function to forward through all gat... | wegfawefgawefg/NeuralNetDemos | 3_nn.py | Python | gpl-3.0 | 3,572 | [
"NEURON"
] | 61d53c689a4b69b238b0a5c9c73ec623208135b3e3d2300fc021543e83bf9e32 |
#! /usr/bin/env python3
# -*- 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 requi... | googleapis/python-iap | scripts/fixup_iap_v1_keywords.py | Python | apache-2.0 | 6,634 | [
"VisIt"
] | bd0e2cefb763a1c4bf8094f5b5830d7ca7bf3cf24de42a70915b9328f5105cd5 |
#!/usr/bin/python
"""create simulated data for testing 2d model fit
"""
import matplotlib as mpl
# we do this because sometimes we run this without an X-server, and this backend doesn't need
# one. We set warn=False because the notebook uses a different backend and will spout out a big
# warning to that effect; that's ... | billbrod/spatial-frequency-preferences | sfp/simulate_data.py | Python | mit | 16,900 | [
"Gaussian"
] | c4b7e53e6ff398e9fdfdc786f07adce8ce40767bad413d2810cbd03aad5a357f |
"""
This module contains classes for walking abstract syntax trees and transforming
them.
"""
from .node import Node
class NodeVisitor(object):
"""
Walks the abstract syntax tree, calling the visitor function for every
subtree found.
"""
def __init__(self):
self._visitor_cache = {}
def... | jeffkistler/BigRig | bigrig/parser/visitor.py | Python | bsd-3-clause | 2,223 | [
"VisIt"
] | d2bf0efab32814b4c36fde4ada330bdd07bd8c97064d0b98eb4db511c959ee6c |
#!/usr/bin/env python
import os
import subprocess
import sys
from distutils.command.build import build
from distutils.command.sdist import sdist
from distutils.errors import DistutilsExecError
from distutils.version import StrictVersion
from setuptools.command.build_ext import build_ext
from setuptools.command.install ... | jnavila/openbabel | scripts/python/setup.py | Python | gpl-2.0 | 6,165 | [
"Open Babel",
"Pybel"
] | 3d4a529569a3851429684836eed9efa98e112fd66e29bd75b8fb64d9fa6bcd33 |
"""SCons.Util
Various utility functions go here.
"""
#
# Copyright (c) 2001 - 2016 The SCons Foundation
#
# Permission is hereby granted, free of charge, to any person obtaining
# a copy of this software and associated documentation files (the
# "Software"), to deal in the Software without restriction, including
# wit... | xiaohaidao007/pandoraBox-SDK-mt7620 | staging_dir/host/lib/scons-2.5.0/SCons/Util.py | Python | gpl-2.0 | 50,268 | [
"VisIt"
] | b6df6501ec6a442a17a01626b23459e97f51635e8a172b97ddf4f7d5e90ac129 |
"""Implementation of the WebSocket protocol.
`WebSockets <http://dev.w3.org/html5/websockets/>`_ allow for bidirectional
communication between the browser and server.
WebSockets are supported in the current versions of all major browsers,
although older versions that do not support WebSockets are still in use
(refer ... | saltstack/salt | salt/ext/tornado/websocket.py | Python | apache-2.0 | 48,071 | [
"VisIt"
] | 82b9b00d35c4a3ea0260487a7caa591f29f2f6ae40b843cc35fc00aff34e5013 |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
"""
Run bowtie2 command and skips the manual run of naming intermediate output
files. Bowtie2 help:
<http://bowtie-bio.sourceforge.net/bowtie2/index.shtml>
"""
import sys
import logging
from jcvi.formats.base import BaseFile
from jcvi.utils.cbook import percentage
from j... | tanghaibao/jcvi | jcvi/apps/bowtie.py | Python | bsd-2-clause | 5,219 | [
"Bowtie"
] | 8aa2fae7ef2346fce87dbe40026258d3eda1dee185b313ca2c8c3fee38bf4dd5 |
"""Testing for Gaussian process regression """
# Author: Jan Hendrik Metzen <jhm@informatik.uni-bremen.de>
# Licence: BSD 3 clause
import numpy as np
from scipy.optimize import approx_fprime
from sklearn.gaussian_process import GaussianProcessRegressor
from sklearn.gaussian_process.kernels \
import RBF, Constan... | kashif/scikit-learn | sklearn/gaussian_process/tests/test_gpr.py | Python | bsd-3-clause | 11,870 | [
"Gaussian"
] | f2c0c5c251cf4cba689abf5e8f8e5aae32e86c0e44cd5abe9b53a108c5f0f2ec |
#!/usr/bin/python
import os
import glob
from os import system
from shutil import copyfile
import re
import string
import sys
system('clear') # Clear the screen and start fresh
rs=system('make makestr.x') # need the exit status here...
if rs!=0: sys.exit("\n\nCompilation of makestr.x failed\n")
#tests=glob.glob('tes... | msg-byu/enumlib | support/newtests.py | Python | mit | 1,579 | [
"VASP"
] | 9bea60c13b2a9163768ab00241e959134ea98b3d6c12af4706a1f10a375d3f9c |
# Name: WL_Script.py
#
# Weak-Lensing "Study of Systematics and Classification of Compact Objects" Program I
#
# Type: python script
#
# Description: Central script that develops the whole process of reading images, filtering into galaxies and stars, correcting sizes and shapes, correcting PSF annisotropies, and re-cla... | gcanasherrera/Weak-Lensing | WL_Script.py | Python | gpl-3.0 | 23,947 | [
"Galaxy"
] | 4ee4f6d5136f952ad573e6113eaafe46ab494c4f58de3c60eebba43d4b20e3fc |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
This is a self-generating script that contains all of the iso3166-1 data.
To regenerate, a CSV file must be created that contains the latest data. Here's
how to do that:
1. Visit https://www.iso.org/obp
2. Click the "Country Codes" radio option and click the search bu... | Ali-aqrabawi/ezclinic | lib/django_countries/data.py | Python | mit | 17,825 | [
"BWA",
"VisIt"
] | 51d04f964fc4dabface476a2d4438500b5fa7cd8a487e26ebecaaa0e372bec62 |
""" Python test discovery, setup and run of test functions. """
import fnmatch
import functools
import inspect
import re
import types
import sys
import py
import pytest
from _pytest._code.code import TerminalRepr
from _pytest.mark import MarkDecorator, MarkerError
try:
import enum
except ImportError: # pragma: n... | youtube/cobalt | third_party/web_platform_tests/tools/pytest/_pytest/python.py | Python | bsd-3-clause | 89,406 | [
"VisIt"
] | 7829475370dbb8910798605ae98c04b5b47b7ddf458f829aefcb3cb913380282 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
Ansible module to configure .deb packages.
(c) 2014, Brian Coca <briancoca+ansible@gmail.com>
This file is part of Ansible
Ansible is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Softwa... | smashwilson/ansible-modules-extras | system/debconf.py | Python | gpl-3.0 | 5,256 | [
"Brian"
] | 5f476f2a08e03208635312146e19d3d6b63a6f12983cab40dc5a15c09a44f63c |
"""
(c) RIKEN 2015. All rights reserved.
Author: Keitaro Yamashita
This software is released under the new BSD License; see LICENSE.
"""
from yamtbx.dataproc.auto.command_line import multi_check_cell_consistency
from yamtbx.dataproc.auto.command_line.run_all_xds_simple import run_xds
from yamtbx.dataproc.xds.xds_asci... | keitaroyam/yamtbx | yamtbx/dataproc/auto/command_line/multi_prep_merging.py | Python | bsd-3-clause | 27,305 | [
"CRYSTAL"
] | bb7ba4a40f82ad78b69931f354428fc34607e28ae22f7926067c1f72944e109a |
# Code from Chapter 18 of Machine Learning: An Algorithmic Perspective (2nd Edition)
# by Stephen Marsland (http://stephenmonika.net)
# You are free to use, change, or redistribute the code in any way you wish for
# non-commercial purposes, but please maintain the name of the original author.
# This code comes with n... | Anderson-Lab/anderson-lab.github.io | csc_466_2021_spring/MLCode/Ch18/plotdist.py | Python | mit | 850 | [
"Gaussian"
] | 44fd5644677e0aa365e648ba610da5761e7c8e8f12a93408c2adb02b90d29a5e |
import unittest
import cryptosite
import saliweb.test
import saliweb.backend
import os
import subprocess
class MockCheckCall(object):
def __init__(self):
self.calls = []
def __call__(self, cmd, **keys):
self.calls.append(cmd)
class Tests(saliweb.test.TestCase):
"""Test postprocessing me... | salilab/cryptosite-web | test/backend/test_post.py | Python | lgpl-2.1 | 2,221 | [
"ChimeraX"
] | 8f844deef1a25b70ff6b947c7c39a81751610377bcb089ca8a0bc06ac2c4d674 |
# Copyright 2017 Norman Heckscher. 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 la... | normanheckscher/mnist-multi-gpu | older/model.py | Python | apache-2.0 | 8,993 | [
"Gaussian"
] | 504ecc8c69cc234f86839b025596b6cf04b179671a1aec40208e473d5a9bb008 |
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