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import numpy
import math
import re
import csv
import os
from __main__ import vtk, qt, ctk, slicer
from random import randint
from slicer.ScriptedLoadableModule import *
class MeshStats(ScriptedLoadableModule):
def __init__(self, parent):
ScriptedLoadableModule.__init__(self, parent)
parent.title = ... | luciemac/MeshStats | MeshStats.py | Python | apache-2.0 | 28,111 | [
"VTK"
] | 4422c6a5e2a4ab141fbd1f37824a958631f14163f69156a3376cfb05278edc74 |
import requests
import json
import re
files_endpt = "https://api.gdc.cancer.gov/files"
filters = {
"op": "and",
"content":[
{
"op": "in",
"content":{
"field": "cases.project.primary_site",
"value": ["Lung"]
}
},
{
"op": "in",
... | NCIP/gdc-docs | docs/API/Users_Guide/scripts/Download_Files_Filter.py | Python | apache-2.0 | 1,664 | [
"HTSeq"
] | 80eb6973d1849b01c2f00ec3d82c0be78fa75f202ada0b2a23dcd28a443bf679 |
import numpy as np
import pytest
from pysisyphus.helpers import geom_loader, imag_modes_from_geom
def test_imag_modes_from_geom(this_dir):
# Obtained at the xtb-GFN2 level of theory
H = np.loadtxt(this_dir / "calculated_final_cart_hessian")
geom = geom_loader("lib:hcn_iso_ts_opt_xtb.xyz")
geom._hessi... | eljost/pysisyphus | tests/test_imag_modes_from_geom/test_imag_modes_from_geom.py | Python | gpl-3.0 | 581 | [
"xTB"
] | 5666c1695da0d36324ebac8121061d23cf8d55c9ce8516ffec0eeb03030719e7 |
#Copyright ReportLab Europe Ltd. 2000-2017
#see license.txt for license details
#history http://www.reportlab.co.uk/cgi-bin/viewcvs.cgi/public/reportlab/trunk/reportlab/platypus/paraparser.py
__version__='3.3.0'
__doc__='''The parser used to process markup within paragraphs'''
import string
import re
import sys
import ... | sandeepkoduri/GAE-html-to-pdf | libs/reportlab/platypus/paraparser.py | Python | mit | 48,983 | [
"VisIt"
] | daacd6397c33b233e465eea8cf775ca7a0099d58bceaafad6b82cc4aabd2bbab |
from __future__ import print_function, division, absolute_import
from . import imgaug as ia
from .parameters import StochasticParameter, Deterministic, Binomial, Choice, DiscreteUniform, Normal, Uniform, FromLowerResolution
from abc import ABCMeta, abstractmethod
import random
import numpy as np
import copy as copy_mod... | bookus/VideoClassification | imgaug/augmenters.py | Python | gpl-3.0 | 237,095 | [
"Gaussian"
] | efe7747e3d14ad88724dfd76551edc23dcdc2237c353f6934b132eee71f976c1 |
import os, sys; sys.path.insert(0, os.path.join("..", ".."))
from pattern.web import Crawler, DEPTH, BREADTH, FIFO, LIFO
# This example demonstrates how to use the Crawler class for web crawling.
# -------------------------------------------------------------------------------------------------
# First, we need a su... | EricSchles/pattern | examples/01-web/13-crawler.py | Python | bsd-3-clause | 6,213 | [
"VisIt"
] | 13f015818b652d6f6f26733667476539694f983e3c48cfcf203d3898e48420fa |
""" Test case for DIRAC.Core.Utilities.File module
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
##
# @author Krzysztof.Ciba@NOSPAMgmail.com
# @date 2011/01/17 14:01:18
# @brief Definition of FileTestCase class.
# imports
import os
from os.path import... | yujikato/DIRAC | src/DIRAC/Core/Utilities/test/Test_File.py | Python | gpl-3.0 | 4,473 | [
"DIRAC"
] | 6cc31343484d63bac9d4f1a2deaee424f3c59d887c498aab9780f04a9368b541 |
# Copyright (C) 2020 Atsushi Togo
# All rights reserved.
#
# This file is part of phono3py.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# * Redistributions of source code must retain the above copyright
# noti... | atztogo/phono3py | phono3py/phonon3/fc3.py | Python | bsd-3-clause | 30,797 | [
"phonopy"
] | 7ee4c6b68431dc32088436f8392651c9a946c7ef9a210d3cce239cb911843262 |
# -*- python -*-
# Copyright (C) 1998,1999,2000 by the Free Software Foundation, Inc.
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) an... | baxterbln/servcup | install/templates/mail/etc/mailman/mm_cfg.py | Python | apache-2.0 | 4,315 | [
"VisIt"
] | 6a6b5c1e43a1ad47f165094b987bffbd1fba98641b0d13cd314134265ac88204 |
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2010 Craig J. Anderson
# Copyright (C) 2014 Paul Franklin
#
# This program is free software; you can redistri... | pmghalvorsen/gramps_branch | gramps/plugins/drawreport/ancestortree.py | Python | gpl-2.0 | 45,087 | [
"Brian"
] | affa60d20d5b4d26197fd7ee88239b7f515e0ba9d7407a1d4401badb439bf20d |
"""
This file contains Django middleware. For more information visit
https://docs.djangoproject.com/en/dev/topics/http/middleware/.
"""
import logging
from django.http import Http404
from django.template.response import TemplateResponse
from django.utils.deprecation import MiddlewareMixin
from opaque_keys import Inv... | edx/edx-analytics-dashboard | analytics_dashboard/courses/middleware.py | Python | agpl-3.0 | 1,701 | [
"VisIt"
] | ac4941d993a55e7862da6b687327927ca40817465ab49858897f909b4390a6e0 |
import os, shutil, urllib, StringIO, re, gzip, tempfile, shutil, zipfile
from galaxy import datatypes, jobs
from galaxy.datatypes import sniff
from galaxy import model, util
import sys, traceback
import logging
log = logging.getLogger( __name__ )
class UploadToolAction( object ):
# Action for uploading files
... | dbcls/dbcls-galaxy | lib/galaxy/tools/actions/upload.py | Python | mit | 18,992 | [
"Galaxy"
] | 5148af14c9e1c27b62ade3bcdb5dbb62efb8338f2f3c998945fa71ac224cea6e |
"""
Common code for basic electronic structure examples.
Notes
-----
The same code should work also with a 3D (box) mesh, but a very fine mesh would
be required. Also in the 2D case, finer mesh and/or higher approximation order
means higher accuracy.
Try changing C, F and L parameters in square.geo and regenerate th... | RexFuzzle/sfepy | examples/quantum/quantum_common.py | Python | bsd-3-clause | 2,734 | [
"VTK"
] | 88078a0e997ee85c51ab84c041d570e56f2fa3b24bedc78509b2db27da1f2c7a |
"""
@name: PyHouse/src/Modules/Families/Insteon/_test/test_Insteon_HVAC.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2014-2020 by D. Brian Kimmel
@license: MIT License
@note: Created on Dec 6, 2014
@Summary:
Passed all 2 tests - DBK - 2015-07-29
"""
__updated__ = '20... | DBrianKimmel/PyHouse | Project/src/Modules/House/Family/Insteon/_test/test_insteon_light.py | Python | mit | 6,285 | [
"Brian"
] | ca74f3033c400f7236c9ed1948a67f9c4930ba041983f16f816d7277b5edac0d |
import scipy as sci
from scipy import linalg
import numpy as np
from tensortools.tensors import KTensor
# TODO - refactor this code to take an arbitrary random generator.
def _check_random_state(random_state):
"""Checks and processes user input for seeding random numbers.
Parameters
----------
rand... | ahwillia/tensortools | tensortools/data/random_tensor.py | Python | mit | 5,863 | [
"Gaussian"
] | d6a34b8b50d5690e32ad3e7fe328034fa0f97975e408c63c4be5582985ac3d87 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/transitions | openlp/plugins/songusage/forms/__init__.py | Python | gpl-2.0 | 2,211 | [
"Brian"
] | 67dddb5816c5b9072340384f388041b32de914cbaba953d1ddde05567c3990a7 |
"""
Module extracts metadata from NetCDF file to complete the required HydroShare NetCDF
Science Metadata
References
reprojection
http://gis.stackexchange.com/questions/78838/how-to-convert-projected-coordinates-to-
lat-lon-using-python
datatype
http://docs.scipy.org/doc/numpy/reference/arrays.dtypes.html
... | hydroshare/hydroshare | hs_file_types/nc_functions/nc_meta.py | Python | bsd-3-clause | 17,093 | [
"NetCDF"
] | a48e964e29720b582ef2d6aa49608d5e2688f99754b16bc07b11fd7e2dba5dd2 |
"""The tasks module provides a simple light-weight alternative to threads.
When you have a long-running job you will want to run it in the background,
while the user does other things. There are four ways to do this:
- Use a new thread for each task.
- Use callbacks from an idle handler.
- Use a recursive mainloop... | dabrahams/zeroinstall | zeroinstall/support/tasks.py | Python | lgpl-2.1 | 11,789 | [
"VisIt"
] | 32fbff0a85143718f6074be7f097383a9819b3077e2d4342fb577bc919755370 |
# Wrapper for the shortest augmenting path algorithm for solving the
# rectangular linear sum assignment problem. The original code was an
# implementation of the Hungarian algorithm (Kuhn-Munkres) taken from
# scikit-learn, based on original code by Brian Clapper and adapted to NumPy
# by Gael Varoquaux. Further impr... | grlee77/scipy | scipy/optimize/_lsap.py | Python | bsd-3-clause | 3,183 | [
"Brian"
] | be09ac762f9c563940249d0932a2a9cbe7435fa1ff8febe4b4fc63043469d6f9 |
# harvest images for the given collection
# by this point the isShownBy value for the doc should be filled in.
# this should point at the highest fidelity object file available
# from the source.
# use brian's content md5s3stash to store the resulting image.
import os
import sys
import datetime
import time
import urlp... | mredar/harvester | harvester/image_harvest.py | Python | bsd-3-clause | 14,549 | [
"Brian"
] | 846f20eac700a5a0cc8f9be5b37de5382c29a01f1adcdf0858d3318ed051a2a9 |
"""
API operations on annotations.
"""
import logging
from galaxy import web
from galaxy.model.item_attrs import UsesAnnotations
from galaxy.util.sanitize_html import sanitize_html
from galaxy.web.base.controller import BaseAPIController, HTTPNotImplemented, UsesHistoryDatasetAssociationMixin, UsesHistoryMixin, UsesSto... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/webapps/galaxy/api/annotations.py | Python | gpl-3.0 | 2,586 | [
"Galaxy"
] | a5dc203638e47056aedecd4a785547ed841a2b1f12f315dcda982c5cd207e9fb |
# Copyright 2015 Dalton Nikitas
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in wri... | rhiw/yggdrasil | scripts/python/setup_client.py | Python | apache-2.0 | 3,441 | [
"Dalton"
] | 94315ce4e48c3cd37ffa3b02beded7877073a05005830c55c53951c3f9c2694f |
#!/usr/bin/env python
# Copyright (c) 2012 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.
"""Makes sure that all files contain proper licensing information."""
import json
import optparse
import os.path
import subproces... | geminy/aidear | oss/qt/qt-everywhere-opensource-src-5.9.0/qtwebengine/src/3rdparty/chromium/tools/checklicenses/checklicenses.py | Python | gpl-3.0 | 24,761 | [
"Galaxy"
] | 5851b405ec4208dd5b1b327490979ca82b39ca3a55714be583fbbbe249dc51f1 |
import pickle
import numpy as np
import matplotlib.pyplot as plt
from ase.utils.eos import EquationOfState
import ase.units as units
results = []
K = range(3, 13)
for k in K:
A, data = pickle.load(open('eos-%d.pckl' % k))
for energies, xcname in zip(data, ['PBE', 'LDA', 'PBE0']):
eos = EquationOfState(... | robwarm/gpaw-symm | doc/tutorials/pbe0/results.py | Python | gpl-3.0 | 1,730 | [
"ASE"
] | 432ea8371b4d7eb944303b0c7d33a9b1415ce0b9dad2970d0ccab564831e3b16 |
from __future__ import division, print_function
import os
import numpy as np
__all__ = ['exp_kern', 'gauss_kern', 'make_conv_file']
def make_conv_file(kern_name, width_param, size, outdir='default',
norm=True, fmt='%.8f', **kwargs):
"""
Make a convolution file for given kernel.
Param... | johnnygreco/hugs | hugs/sextractor/_kernels.py | Python | mit | 5,167 | [
"Gaussian"
] | cf5c387ea9f7705cb04c76ba620ff97fc8e650a5e9c16ddb8222019c47e8487c |
#!/usr/bin/env python
# ui.py
#
# Copyright (C) 2014 Kano Computing Ltd.
# License: http://www.gnu.org/licenses/gpl-2.0.txt GNU General Public License v2
#
#
# Kano Burner UI back-end
#
# The UI base class handles all the PyQt front-end and uses a VerticalContainer
# as a layout manager.
#
# The application's window c... | ektor5/kano-burners | src/common/ui.py | Python | gpl-2.0 | 7,441 | [
"VisIt"
] | ba520e5ca236c246d596239e9842008200bb2d879ebe25a9e42bee71041da41f |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | annarev/tensorflow | tensorflow/python/autograph/converters/break_statements.py | Python | apache-2.0 | 5,865 | [
"VisIt"
] | 0e7a0ddfc9fcdd7e677d0e556035ea6e1a53ac7b41eff2d9cfe075070d3f3329 |
# -*- coding: utf-8 -*-
import os
import re
import shutil
import threading
import logging
import copy
from datetime import datetime, timedelta
from core.lib.io.file import create_folder_with_permissions, listdir_fullpath
from core.lib.utils.extended_collections import DotDict
from core.lib.utils.log import log_format_... | schmidtfederico/PRinde | core/modules/simulations_manager/ForecastManager.py | Python | gpl-2.0 | 21,741 | [
"NetCDF"
] | 70890773afb5e55faf972d62bf643c0a409feb523d0923dec8b2e5a4eeb93a3b |
from osmnames.database.functions import exec_sql, exists
from osmnames import settings
from osmnames import logger
from osmnames.logger import logged_check_call
from osmnames.helpers import run_in_parallel
log = logger.setup(__name__)
def import_wikipedia():
if exists("SELECT * FROM information_schema.tables WHE... | philippks/OSMNames | osmnames/import_wikipedia/import_wikipedia.py | Python | gpl-2.0 | 3,253 | [
"Brian"
] | d3555981c24f5e83b85b6e57a0fb8a311a7bd90861e327be8785b669aa329bd9 |
##############################################################################
# Copyright (c) 2013-2018, 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... | EmreAtes/spack | var/spack/repos/builtin/packages/r-rhtslib/package.py | Python | lgpl-2.1 | 2,020 | [
"Bioconductor"
] | 3d91b302c94d6594d3f13dd839b462415f0ef9397b2d01468bb18d3797b0e62f |
from WebAppDIRAC.Lib.WebHandler import WebHandler, asyncGen, WErr
from DIRAC import gConfig, S_OK
from DIRAC.Core.Utilities import Time
from DIRAC.Core.DISET.RPCClient import RPCClient
import json
import datetime
class ComponentHistoryHandler( WebHandler ):
AUTH_PROPS = 'authenticated'
@asyncGen
def web_getIns... | zmathe/WebAppDIRAC | WebApp/handler/ComponentHistoryHandler.py | Python | gpl-3.0 | 6,028 | [
"DIRAC"
] | 3b38d50708fec76c92d210719aa208a522b911c0725573d5d09b2ddf64203dd4 |
"""Tests for pickaxe.py using pytest."""
# pylint: disable=redefined-outer-name
# pylint: disable=protected-access
import hashlib
import os
import re
import subprocess
from filecmp import cmp
from pathlib import Path
import pymongo
import pytest
from pymongo.errors import ServerSelectionTimeoutError
from rdkit.Chem i... | JamesJeffryes/MINE-Database | tests/test_unit/test_pickaxe.py | Python | mit | 13,418 | [
"RDKit"
] | 434a1002e61e61182df9e6c3d1f5edee9f7a88de928a4318db99e36818284712 |
#!/usr/bin/env/python
"""
We treat each silica atom as its own residue. As a consequence,
we have more than 10000 residues in the system.
The silly PDB format only allows up to 9999 residues. We solve
this issue by manually creating a .gro file, which allows for
up to 99999 residues
"""
from __future__ import print_f... | jmborr/confinedBSA | simulation/silica/cristobalite/confineBSA/poretop/nobonds/adaptPDB.py | Python | mit | 1,589 | [
"MDAnalysis"
] | 8924524029442fbd52f2e5a52fcc8f6cca7bf00acfa734c52d8185daa0b92d29 |
import os
import unittest
try:
import phonopy
from phonopy.phonon.dos import TotalDos
except ImportError as ex:
print(ex)
phonopy = None
TotalDos = None
from pymatgen.io.phonopy import get_gruneisen_ph_bs_symm_line, get_gruneisenparameter
from pymatgen.phonon.gruneisen import Gruneisen... | materialsproject/pymatgen | pymatgen/phonon/tests/test_gruneisen.py | Python | mit | 5,287 | [
"phonopy",
"pymatgen"
] | 06add0e9dd009904b4bbe24d2a2a2e8f71dbb0e0bce089ea2959fb91f87a1ee6 |
input_name = '../examples/diffusion/poisson_functions.py'
output_name = 'test_poisson_functions.vtk'
from testsBasic import TestInput
class Test(TestInput):
pass
| olivierverdier/sfepy | tests/test_input_poisson_functions.py | Python | bsd-3-clause | 167 | [
"VTK"
] | 3e58eae109086203bb544f082c73d19c9ddbe9f73ec4d40f8cdef054d8aee371 |
#!/usr/bin/python
import fileinput
import sys
import re
import math
import numpy as np
nlsRE = re.compile("^Nonlinear System:\n$")
varlistFullRE = re.compile("^\s*Variables:\s*\{([^}]+)\}")
varlistStartRE = re.compile("^\s*Variables:\s*\{([^}]+)")
varlistEndRE = re.compile("^\s*([^}]+)\}")
varlistContRE = re.compile("... | karpeev/xcontact | tests/jacobian/analyzejacobian.py | Python | lgpl-2.1 | 4,628 | [
"MOOSE"
] | 5e5b7fcb7e6b66aacf05902742c55af8ff7b7c001bb52dabb5544d68a394c2f7 |
"""An NNTP client class based on RFC 977: Network News Transfer Protocol.
Example:
>>> from nntplib import NNTP
>>> s = NNTP('news')
>>> resp, count, first, last, name = s.group('comp.lang.python')
>>> print 'Group', name, 'has', count, 'articles, range', first, 'to', last
Group comp.lang.python has 51 articles, rang... | atmark-techno/atmark-dist | user/python/Lib/nntplib.py | Python | gpl-2.0 | 14,397 | [
"Brian"
] | 3881fcbd30f544d6ddd6edcf679296608115f5ac1f9a105a33fc93a2592f81cf |
from unittest import skipUnless
from bok_choy.web_app_test import WebAppTest
from acceptance_tests import (
APPLICATION_NAME,
ENABLE_ERROR_PAGE_TESTS,
PLATFORM_NAME,
SUPPORT_EMAIL,
)
from acceptance_tests.pages import (
AccessDeniedErrorPage,
NotFoundErrorPage,
ServerErrorPage,
Service... | edx/edx-analytics-dashboard | acceptance_tests/test_error_pages.py | Python | agpl-3.0 | 1,176 | [
"VisIt"
] | b0a56f1cc73819207c76df9f8700ab930a5bb087dc979c95bc6df0b46eec9410 |
# ################################################################
#
# Active Particles on Curved Spaces (APCS)
#
# Author: Silke Henkes
#
# ICSMB, Department of Physics
# University of Aberdeen
# Author: Rastko Sknepnek
#
# Division of Physics
# School of Engineering, Physics and Mathem... | sknepneklab/SAMoS | analysis/batch_nematic/batch_analyze_nematic_R40d.py | Python | gpl-3.0 | 2,363 | [
"VTK"
] | c0c725faeadce449cfff4da5b7e583c7a5fdcd8a031e1ab7e165d8b9d01a8308 |
# Copyright 2008-2015 Nokia Solutions and Networks
#
# 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 l... | snyderr/robotframework | src/robot/result/executionerrors.py | Python | apache-2.0 | 1,541 | [
"VisIt"
] | 413e3d80870d80b9f8119ced43f22d4b65d7e9264eeb6952c217d84a472683de |
# coding: utf-8
import os
import unittest
import pytest
from pymatgen.analysis.fragmenter import Fragmenter
from pymatgen.analysis.graphs import MoleculeGraph
from pymatgen.analysis.local_env import OpenBabelNN, metal_edge_extender
from pymatgen.core.structure import Molecule
from pymatgen.util.testing import Pymatg... | gmatteo/pymatgen | pymatgen/analysis/tests/test_fragmenter.py | Python | mit | 6,766 | [
"pymatgen"
] | 9d0c134d702edb38bdbea08a3e27ec4f4067098df75be36b7de17d48330eeb38 |
# -*- coding: utf-8 -*-
from __future__ import division
import numpy as np
from scipy.ndimage import map_coordinates
from scipy.interpolate import UnivariateSpline, splrep, splev
from scipy.optimize import leastsq
import abel
from abel import _deprecated, _deprecate
##################################################... | PyAbel/PyAbel | abel/tools/circularize.py | Python | mit | 13,798 | [
"Gaussian"
] | 73d82f69e178fa2687aae9514a496202fdba2013e46f1840073efdac6a0bf81e |
# ---------------------------------------------------------------------------- #
# #
# 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 ... | speksofdust/BeyondDreams | beyonddreams/item/consumables.py | Python | gpl-3.0 | 10,106 | [
"CRYSTAL"
] | 9778bdd12f3760ac7a481f9a702b7e0fb0cfc5774b5b95388250f70213dde01f |
#!/Library/Frameworks/Python.framework/Versions/2.7/bin/python
# ----------------------------------------
# USAGE:
# ----------------------------------------
# PREAMBLE:
import MDAnalysis
from MDAnalysis.analysis.align import *
import sys
# ----------------------------------------
# VARIABLE DECLARATION
pdb = sys.a... | rbdavid/RMSD_analyses | PCA_RMSD_FrameVsFrame/Write_traj_single_system.py | Python | gpl-3.0 | 2,792 | [
"MDAnalysis"
] | 94baedfc09eab64a6c61a2384191cce5c19192717db742ebf87601ad38521c6d |
import numpy as np
from .making_abundances import abundance_to_mass_fraction_normed_to_solar,abundance_to_mass_fraction
class PRIMORDIAL_INFALL(object):
def __init__(self,elements,solar_table):
'''
This class calculates the chemical abundance fractions and can be used to provide primordial or solar scaled materia... | jan-rybizki/Chempy | Chempy/infall.py | Python | mit | 6,103 | [
"ChemPy"
] | d1c124a092957a283f112fe1ef7266a4773e0a1b8b01986ecb661c63a10ac9b1 |
#!/usr/bin/pythonTest
# -*- coding: utf-8 -*-
#
# File functions Info
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
... | netvigator/myPyPacks | pyPacks/File/Info.py | Python | gpl-2.0 | 6,358 | [
"MOE"
] | 609310be76339bffcb931423b83f5e83bdc48b14b20e0e0e0518ea99bdedb18b |
#!/usr/local/bin/python
"""
SUNTANS NetCDF plotting GUI
"""
import os
import wx
# The recommended way to use wx with mpl is with the WXAgg
# backend.
#
import matplotlib
matplotlib.use('WXAgg')
# Set some default parameters
matplotlib.rcParams['text.color']='white'
matplotlib.rcParams['savefig.facecolor']='black'
ma... | UT-CWE/Hyospy | Hyospy_ensemble/lib/SUNTANS/SUNTANS/sunplotpy.py | Python | mit | 25,164 | [
"NetCDF"
] | 1a5fcfd227d0ed1e04a43f6aab8b4cd051cfea05eeefdbc53488e13572b6afae |
from sklearn import metrics, preprocessing, pipeline, \
feature_extraction, decomposition, model_selection
import sklearn
import pandas as pd
import numpy as np
from time import gmtime, strftime
import numpy.random as rng
# from multiprocessing.dummy import Pool
# import concurrent.futures
import tensorf... | ifuding/Kaggle | SVPC/Code/philly/keras_train.py | Python | apache-2.0 | 23,757 | [
"Gaussian"
] | 2727201d3c508b372b75973deb04bf3b70a9943becea644ddf77db4e48dd2546 |
"""
=====================================
Blind source separation using FastICA
=====================================
An example of estimating sources from noisy data.
:ref:`ICA` is used to estimate sources given noisy measurements.
Imagine 3 instruments playing simultaneously and 3 microphones
recording the mixed si... | chenyyx/scikit-learn-doc-zh | examples/zh/decomposition/plot_ica_blind_source_separation.py | Python | gpl-3.0 | 2,228 | [
"Gaussian"
] | cabb655a7ec2734907e09c78975cee299137971d04333fa5243825cbc7507b33 |
#!/usr/bin/env python
# CREATED:2014-01-18 14:09:05 by Brian McFee <brm2132@columbia.edu>
# unit tests for util routines
# Disable cache
import os
try:
os.environ.pop('LIBROSA_CACHE_DIR')
except:
pass
import matplotlib
matplotlib.use('Agg')
import numpy as np
import scipy.sparse
np.set_printoptions(precision=... | Cortexelus/librosa | tests/test_util.py | Python | isc | 23,905 | [
"Brian"
] | 44d3faf1be70c78d7d7fc6cca6dd22566b97ca274f1f6ba1cee4f344fb1ceb49 |
#!/usr/bin/env python
##############################################################################################
#
#
# regrid_emissions_N96e.py
#
#
# Requirements:
# Iris 1.10, time, cf_units, numpy
#
#
# This Python script has been written by N.L. Abraham as part of the UKCA Tutorials:
# http://www.ukca.ac.u... | acsis-project/emissions | emissions/python/timeseries_1960-2020/regrid_iC5H12_emissions_n96e_greg.py | Python | gpl-3.0 | 18,761 | [
"NetCDF"
] | 83e89898015d735179b6e82037b4a2ffd835d5234db240bc487ddc6e2129d5fb |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
import unittest
from shutil import which
from pymatgen.command_line.critic2_caller import Critic2Analysis, Critic2Caller
from pymatgen.core.structure import Structure
from pymatgen.util.testing import PymatgenTest
... | materialsproject/pymatgen | pymatgen/command_line/tests/test_critic2_caller.py | Python | mit | 5,771 | [
"pymatgen"
] | d8881bdc0bcfb334667ac7de8f39b8b228a5aac0f0c0c40d5418fb151f431e1b |
# -*- coding: utf-8 -*-
"""Tests for inference functions."""
import unittest
from pybel import BELGraph
from pybel.constants import *
from pybel.dsl import protein
from pybel_tools.mutation.inference import infer_missing_two_way_edges
class TestMutationInference(unittest.TestCase):
def test_infer_missing_two_w... | pybel/pybel-tools | tests/test_mutation/test_inference.py | Python | mit | 1,121 | [
"Pybel"
] | 48af6c8eff8598be1f69a4c88f517ba6da4f7de0743222f52c5d5e72b87aa438 |
# amplicon.py - classes for fitting amplicon distributions from PSDs
#
# v 1.1.1
# rev 2017-11-29 (MS: minor bug fix)
# Notes:
import scipy.optimize
import scipy.special
import scipy.stats
import numpy as np
import pandas as pd
from . import extra_tools
def func_logis(x, inter, asym, xmid, scal):
""" Return logi... | parklab/PaSDqc | PaSDqc/amplicon.py | Python | mit | 11,243 | [
"Gaussian"
] | c4c514b4a3852b348026c6cd95e9763ea116b42d69bc702d425679398cf4abf3 |
''' Script to check the correctness of the analysis. The analysis is done on raw data and all results are compared to a recorded analysis.
'''
import os
import shutil
import unittest
from testbeam_analysis import result_analysis
from testbeam_analysis.tools import analysis_utils, test_tools
testing_path = os.path.dir... | SiLab-Bonn/testbeam_analysis | testbeam_analysis/testing/test_result_analysis.py | Python | mit | 4,580 | [
"Gaussian"
] | fc7ccdaccc2a68f871502c0a5abffb4fe46edf5b5536137add93ea7ba8d25a11 |
#!/usr/bin/env python
########################################################################
# File : dirac-executor
# Author : Adria Casajus
########################################################################
__RCSID__ = "$Id$"
""" This is a script to launch DIRAC executors
"""
import sys
from DIRAC.Config... | fstagni/DIRAC | Core/scripts/dirac-executor.py | Python | gpl-3.0 | 1,649 | [
"DIRAC"
] | 07888e54ba964333f5bbfdee8a2d679fe298975d2b84ad876363e224eda29fc5 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#... | MDAnalysis/mdanalysis | testsuite/MDAnalysisTests/coordinates/test_writer_registration.py | Python | gpl-2.0 | 2,340 | [
"MDAnalysis"
] | bd5b70d30d6305fa5aa216db23873d614c18ce932ad59ae65af6fc73989a2070 |
########################################################################
# File: FTSClient.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/04/08 14:29:43
########################################################################
"""
:mod: FTSClient
.. module: FTSClient
:synopsis: FTS client
.. moduleauthor:: K... | sposs/DIRAC | DataManagementSystem/Client/FTSClient.py | Python | gpl-3.0 | 15,606 | [
"DIRAC"
] | 824bf16af2df72a83838b80f6f8b3ac83f0180600371733185889a74fdfdea4a |
"""
=================================================
Linear fascicle evaluation (LiFE)
=================================================
Evaluating the results of tractography algorithms is one of the biggest
challenges for diffusion MRI. One proposal for evaluation of tractography
results is to use a forward model t... | sinkpoint/dipy | doc/examples/linear_fascicle_evaluation.py | Python | bsd-3-clause | 11,596 | [
"Gaussian"
] | 9d0fcd2e8e922eb6714d804ba214b1425fab1be4403ffe8cfd7897a08afa363e |
"""
Test the Studio help links.
"""
from nose.plugins.attrib import attr
from unittest import skip
from common.test.acceptance.fixtures.course import XBlockFixtureDesc
from common.test.acceptance.tests.studio.base_studio_test import StudioCourseTest, ContainerBase
from common.test.acceptance.pages.studio.index import... | prarthitm/edxplatform | common/test/acceptance/tests/studio/test_studio_help.py | Python | agpl-3.0 | 47,918 | [
"VisIt"
] | c3ed64bf5773fec321cb9a4b294e2a4f05a9b5a6b03c235644173d8521a140be |
#!/usr/bin/env python3
"""Example for vasp.
[Notes from Dan]
1 - a python code that runs and creates a tar file - it writes the tar file directly,
rather than creating the contents and then tarring them, though someone likely could
change this to create the contents directly with some work.
2 - if we open th... | swift-lang/swift-e-lab | parsl/tests/integration/test_apps/vasp/vasp_example.py | Python | apache-2.0 | 3,255 | [
"VASP"
] | cb97c0f7530d6df72359957247846eab24aea98dd847de95e9b149a11a5db162 |
# Copyright 2014-2015 Dietrich Epp.
# This file is part of SGGL. SGGL is licensed under the terms of the
# 2-clause BSD license. For more information, see LICENSE.txt.
import os
import xml.etree.ElementTree as etree
import collections
import io
import re
API_LIST = 'gl:core', 'gl:compatibility', 'gles1', 'gles2'
NO... | depp/sggl | glgen/__init__.py | Python | bsd-2-clause | 22,123 | [
"VisIt"
] | dbe02e58a03ed102a0039424f28684cbc22ead6e94af8f9bdb15d9c22114f3c7 |
# The purpose of this test is to detect a change in the _metric_json of MetricsBase objects. Many of the metric
# accessors require _metric_json to have a particular form.
import sys
sys.path.insert(1, "../../")
import h2o, tests
def metric_json_check():
df = h2o.import_file(path=tests.locate("smalldata/logr... | kyoren/https-github.com-h2oai-h2o-3 | h2o-py/tests/testdir_misc/pyunit_metric_json_check.py | Python | apache-2.0 | 10,421 | [
"Gaussian"
] | b5b354ec5a2796a147a4a17a721b3d00da16d81e2b10f603958d20fe1273280e |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2018 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | amjames/psi4 | tests/make_cmake_files.py | Python | lgpl-3.0 | 1,863 | [
"Psi4"
] | 6758c5fe0abf7543eac40aaa0418308b2a8c033ad0683d8eb381d02f2e3e9dda |
from __future__ import print_function
from builtins import range
"""
SECTION 1 : Load and setup data for training
the datasets has separated to two file from originai datasets:
iris_train.csv = datasets for training purpose, 80% from the original data
iris_test.csv = datasets for testing purpose, 20% from the origin... | rianrajagede/simplesamplecode | Lasagne/iris_lasagne.py | Python | mit | 3,469 | [
"NEURON"
] | b719b437da1534bd27c5a0cde61f2ecaf42ac71e6fbf4613566cb0ab73436409 |
# Copyright 2015 Amazon.com, Inc. or its affiliates. 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. A copy of
# the License is located at
#
# http://aws.amazon.com/apache2.0/
#
# or in the "license" file acc... | LockScreen/Backend | venv/lib/python2.7/site-packages/awscli/shorthand.py | Python | mit | 14,650 | [
"VisIt"
] | 6c9b56bd54ba3776e8fd7783db14168349c3367234eb06b19b76c90b9b3aa9e9 |
import json
import keystoneclient
import logging
import time
import unittest
import yaml
import paramiko
from uuid import uuid4
from nose import SkipTest
from string import letters
import keystoneclient.v2_0.client as ksclient
import heatclient
from heatclient.client import Client as heat_client
from neutronclient.ne... | pombredanne/RPC-Heat-ELK | tests/unittest_example.py | Python | apache-2.0 | 6,743 | [
"Elk"
] | d71a5d7b3788424e88853d0764f3487ec38909f38e8a77d33d0b6fd89976dbd7 |
#!/usr/bin/env python3
# ver 0.1 - coding python by Hyuntae Jung on 6/1/2017
import argparse
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
description='Initial coordiante of FRP (freely rotated poymer, no angle potential) for MC or MD simulation')
## args
#parser... | jht0664/Utility_python_gromacs | MonteCarlo/python/initial-pol.py | Python | mit | 6,342 | [
"Gromacs"
] | 8033a29e6303cb86ec0700fc7f3f4896bb228540aa5ac3b59d22becfdca7763a |
# sql/compiler.py
# Copyright (C) 2005-2017 the SQLAlchemy authors and contributors
# <see AUTHORS file>
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Base SQL and DDL compiler implementations.
Classes provided include:
:class:`.c... | Widiot/simpleblog | venv/lib/python3.5/site-packages/sqlalchemy/sql/compiler.py | Python | mit | 108,248 | [
"VisIt"
] | fe6751e92ddf9b9d55d37f01fbc1d31bca056ed92f6998b816960b15d8ae894c |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
# -*- coding: utf-8 -*-
"""
desitarget.brightmask
=====================
Module for studying and masking bright sources in the sweeps
.. _`Tech Note 2346`: https://desi.lbl.gov/DocDB/cgi-bin/private/ShowDocument?docid=2346
.. _`Tech Note 2348`: https://de... | desihub/desitarget | py/desitarget/brightmask.py | Python | bsd-3-clause | 42,013 | [
"Galaxy"
] | c3fd183b883e4b60403b8e8b552768caca3fa640bb603f395c1b775ed09b1d23 |
"""Echo module based on the GFAL2_StorageBase class."""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import os
import random
import time
from timeit import default_timer
# from DIRAC
from DIRAC.Resources.Storage.GFAL2_StorageBase import GFAL2_StorageBas... | ic-hep/DIRAC | src/DIRAC/Resources/Storage/EchoStorage.py | Python | gpl-3.0 | 4,903 | [
"DIRAC"
] | 1c4460297b86d1e06e8a2d19ebab59818a4bb185b2c7b1c80205ea7f7265e86e |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import numpy as np
from numpy.testing import assert_allclose
import abel
def test_hansenlaw_shape():
n = 21
x = np.ones((n, n), dtype='float32')
recon = abel.hansenlaw.hansenlaw_transform(x, dir... | PyAbel/PyAbel | abel/tests/test_hansenlaw.py | Python | mit | 3,867 | [
"Gaussian"
] | e5f7840bec3d02e9f3dbb4af06ef1532a9ec58c4044eacce35c9d2cf48d35dfd |
import numpy as np
from numpy.testing import assert_equal, assert_raises, assert_almost_equal
from skimage.measure import LineModel, CircleModel, EllipseModel, ransac
from skimage.transform import AffineTransform
from skimage.measure.fit import _dynamic_max_trials
from skimage._shared._warnings import expected_warnings... | michaelaye/scikit-image | skimage/measure/tests/test_fit.py | Python | bsd-3-clause | 8,327 | [
"Gaussian"
] | 9428e31ce196b0c4fd15924b9c3d2b902404d5b37e1ddfa4536b622d577700e1 |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publish... | thica/ORCA-Remote | src/ORCA/Screen_Init.py | Python | gpl-3.0 | 20,966 | [
"ORCA"
] | 203167795ef926e544de1fd9099676d0ccf0686f1c8b023348754b7842f8ed14 |
#!/usr/bin/env python
# This example shows how to use cutting (vtkCutter) and how it
# compares with extracting a plane from a computational grid.
import vtk
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Read some data.
pl3d = vtk.vtkMultiBlockPLOT3DReader()
pl3d.SetXYZFileName(VTK_DATA... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Examples/VisualizationAlgorithms/Python/CutCombustor.py | Python | gpl-3.0 | 2,643 | [
"VTK"
] | f280e708a6640ea11327b66cc80ceb7fbb28e2f484cbb19ac13f3bae26f7a530 |
import psycopg2 as dbapi2
from flask import render_template
from flask import redirect
from flask import url_for
class Polo_Store:
def About_Page(self):
return render_template('index.html')
def __init__(self, key):
self.key = key
return
def show_water_polo_page(self):
wit... | itucsdb1525/itucsdb1525 | Polo_Store.py | Python | gpl-3.0 | 15,645 | [
"Brian"
] | 464db66670ac30651cd856120c20dcb89a6907fb0a4f255ff6bf0a85f63c395a |
# -*- coding: utf-8 -*-
# <nbformat>3.0</nbformat>
# <headingcell level=2>
# Try using Xray to convert CSV to netcdf
# <codecell>
import pandas as pd
import xray
%matplotlib inline
# <codecell>
url = 'http://www.cpc.ncep.noaa.gov/products/precip/CWlink/'
ao_file = url + 'daily_ao_index/monthly.ao.index.b50.curre... | rsignell-usgs/notebook | csv2netcdf.py | Python | mit | 1,313 | [
"NetCDF"
] | f33c000d62892cf2348eb5b9454faccb36861f52fea3b9aea148874b3aa0e33c |
#!/usr/bin/env python
from __future__ import division
from __future__ import print_function
import os
import sys
import matplotlib as mpl
mpl.use('Agg')
import numpy as np
import matplotlib.pyplot as plt
from datetime import datetime, timedelta
from scipy import fftpack
from scipy.linalg impo... | meteoswiss-mdr/precipattractor | pyscripts/growthdecay/nowcast.py | Python | gpl-3.0 | 34,351 | [
"Gaussian",
"NetCDF"
] | d484fb359eadaebc82d20e46c5c8c2a709ef9bddb14a82a75c3937ab403d7915 |
# Copyright 2021 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 agreed to in writing, so... | googlecodelabs/migrate-python2-appengine | mod4b-rundocker/main.py | Python | apache-2.0 | 1,413 | [
"VisIt"
] | 06d228fcbc2bf25eaf983aae3e36e64c392501387c22849adb744f04f05c0a92 |
# -*- coding: utf-8 -*-
"""
Created on Wed Feb 22 16:28:11 2017
Updated on Sun Mar 19 08:52:55 2017
@author: Mohammed Yusuf Khan
"""
from selenium import webdriver
import time
#import codecs
url='https://twitter.com/WalkingDead_AMC'
#open the browser and visit the url
driver = webdriver.Chrome('chromedriver.exe')
d... | getmykhan/PythonforDataAnalytics | Web Scrapping/twitter.py | Python | gpl-3.0 | 2,276 | [
"VisIt"
] | 01da541bf674a035dd69b79f4fb30a2ecc1a8c87c0fde6b1e73933c9e488605b |
import logging
from pip._vendor.packaging.utils import canonicalize_name
from pip._internal.exceptions import (
DistributionNotFound,
InstallationError,
InstallationSubprocessError,
MetadataInconsistent,
UnsupportedPythonVersion,
UnsupportedWheel,
)
from pip._internal.models.wheel import Wheel... | pantsbuild/pex | pex/vendor/_vendored/pip/pip/_internal/resolution/resolvelib/factory.py | Python | apache-2.0 | 18,946 | [
"VisIt"
] | a2f39e31d002daf86c6592d96ccaa78ac65aa010e517c77ae1f25da5509232da |
# Copyright 2009 by Tiago Antao <tiagoantao@gmail.com>. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""
This module allows to control GenePop.
"""
import os
import re
im... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/PopGen/GenePop/Controller.py | Python | gpl-2.0 | 33,106 | [
"Biopython"
] | 4b34ad5d942a2594899442bcf305fc3fe7ca1eaa9bb7149e3f547956a91ae3d6 |
# Copyright (c) 2012, CyberPoint International, LLC
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright
# notice, this lis... | CyberPoint/libpgm | build/lib.linux-x86_64-2.7/libpgm/nodedata.py | Python | bsd-3-clause | 7,032 | [
"Gaussian"
] | 7b1cfcaa787a85e9f3e47a383eaeadbeb69f0b0a63d35d30e966b363eac7a534 |
import wx
import os
import os.path
import sys
import platform
import subprocess
import multiprocessing
import psutil
from tools import *
# If this fails, it is probably because PyRosetta is not being imported
try:
from daemon import daemonLoop
except:
if (platform.system() == "Windows"):
addon = "\n\nDe... | schenc3/InteractiveROSETTA | InteractiveROSETTA/scripts/protocols.py | Python | gpl-2.0 | 50,752 | [
"PyMOL"
] | 47a05fe3e822b3522588d76cc5d40ba6e21626a59596518a3d83bcbef9ed4eef |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""Tests for the Mozilla Firefox history database plugin."""
import collections
import unittest
from plaso.formatters import firefox as _ # pylint: disable=unused-import
from plaso.lib import eventdata
from plaso.lib import timelib
from plaso.parsers import sqlite
from plaso... | ostree/plaso | tests/parsers/sqlite_plugins/firefox.py | Python | apache-2.0 | 9,746 | [
"VisIt"
] | 5b31fae780a2bdb3badb2d44bf963e477b14308693a2276c1bc485a1a4b9924c |
#!/usr/bin/env python
#
# extras_dictcursor - test if DictCursor extension class works
#
# Copyright (C) 2004-2010 Federico Di Gregorio <fog@debian.org>
#
# psycopg2 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... | thiriel/maps | venv/lib/python2.7/site-packages/psycopg2/tests/test_extras_dictcursor.py | Python | bsd-3-clause | 15,904 | [
"GULP"
] | 6e3868dc2f52d729adaeb38461dec8c3e8d1443d2dd17c1c355c0769bd4974d5 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
from setuptools import setup, find_packages
from sphinx.setup_command import BuildDoc
__description__ = """Python package for Gaussian process regression in python
========================================================
demo_gpr.py explains how to perform basic regression ... | PMBio/pygp | setup.py | Python | gpl-2.0 | 1,257 | [
"Gaussian"
] | e45eef30015ae9b9dcf0641c6ce8fdfb512d675e14fc385fa78bafa5a66e21ef |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkImageConvolve(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.... | nagyistoce/devide | modules/vtk_basic/vtkImageConvolve.py | Python | bsd-3-clause | 489 | [
"VTK"
] | 0bdd4f3a0f374e4ef8629f7170873d4521c4dd37b802214e31a6363ce9b7c8e3 |
from __future__ import print_function
# Most of this code is:
# (c) 2005 Ian Bicking and contributors; written for Paste (http://pythonpaste.org)
# Licensed under the MIT license: http://www.opensource.org/licenses/mit-license.php
# The server command includes the additional header:
# For discussion of daemonizing:
... | ssorgatem/pulsar | galaxy/util/pastescript/serve.py | Python | apache-2.0 | 36,420 | [
"Galaxy"
] | 8041143b219bbb4c535a0cc564cd970538de16a8fe18dbb3d41b18ad330c95d8 |
from copy import copy
from functools import partial
from typing import cast, List, Optional
from pytest import mark, raises
from graphql.language import (
Node,
FieldNode,
NameNode,
SelectionNode,
SelectionSetNode,
parse,
visit,
BREAK,
REMOVE,
SKIP,
ParallelVisitor,
Vis... | graphql-python/graphql-core | tests/language/test_visitor.py | Python | mit | 62,563 | [
"VisIt"
] | a46f833e802d232c4b6d99e963fdc04264352caed757e79781cf7dc33f351e9a |
from google.protobuf import text_format
from .caffe import get_caffe_resolver
from .errors import KaffeError, print_stderr
from .layers import LayerAdapter, LayerType, NodeKind, NodeDispatch
from .shapes import make_tensor
class Node(object):
def __init__(self, name, kind, layer=None):
self.name = name
... | lcy-seso/models | fluid/image_classification/caffe2fluid/kaffe/graph.py | Python | apache-2.0 | 14,027 | [
"VisIt"
] | f04fbb56ba819944168135fe237b4403508a2cbd8cfb38639115f80d1b125501 |
import sys
import os
import nest
import BasalGanglia
import Reward
import json
import simulation_parameters
import utils
import numpy as np
import time
import tempfile
import mynest
os.environ['MPLCONFIGDIR'] = tempfile.mkdtemp()
import matplotlib
matplotlib.use('Agg')
import pylab as pl
# Load BCPNN synapse and bias... | pierreberthet/bg_dopa_nest | test.py | Python | gpl-2.0 | 1,108 | [
"NEURON"
] | b703831bf725c35c93bc82f4a595d09947795598e4b4eb3269c850c1eeb3d471 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | andreaso/ansible | lib/ansible/modules/network/avi/avi_pkiprofile.py | Python | gpl-3.0 | 4,754 | [
"VisIt"
] | 212bafe6a7056d04d404816ff55ca690470abad1d0c965d0c6d8d99da441ddbd |
# 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... | Omkar20895/climate | ocw/data_source/local.py | Python | apache-2.0 | 29,273 | [
"NetCDF"
] | a35fbfd69e935d3fe20fefcf86105a7ad6c81f1fc578bfebbacd41fcc5e845ca |
########################################################################
# $HeadURL: $
########################################################################
""" The RequestCleaning agent removes the already executed requests from the database after
a grace period.
:deprecated:
"""
from DIRAC import gL... | sposs/DIRAC | RequestManagementSystem/Agent/RequestCleaningAgent.py | Python | gpl-3.0 | 2,363 | [
"DIRAC"
] | 1adeeb29dfc8fcb34f2d85e46101582a3bfb42f5bbe035883cd795bfe3049c09 |
# coding=utf-8
# 1. generate velocity and force nodes of sphere using MATLAB,
# 2. for each force node, get b, solve surrounding velocity boundary condition (pipe and cover, named boundary velocity) using formula from Liron's paper, save .mat file
# 3. read .mat file, for each boundary velocity, solve associated bounda... | pcmagic/stokes_flow | try_code/try_pipe_cover.py | Python | mit | 10,652 | [
"VTK"
] | b7cd6e8d804d7109a6be444eff07e3855655c70f1da5d879fda80d2ff7cb9e80 |
"""DIRAC RPC Server."""
import logging
#from types import FunctionType
import rpyc
from rpyc.utils.server import ThreadedServer
from daemonize import Daemonize
from DIRAC.Interfaces.API.Job import Job
from DIRAC.Interfaces.API.Dirac import Dirac
logger = logging.getLogger(__name__) # pylint: disable=invalid-name
#... | alexanderrichards/LZProduction | lzproduction/rpc/DiracRPCServer.py | Python | mit | 2,947 | [
"DIRAC"
] | 393785f917a1e1acbc8f375dbfde938bd94de01b257a952dfd1a326c08ba3041 |
"""
Functions to generate simulated galaxy templates.
J. Moustakas
2014 Dec
"""
from os import getenv
from os.path import join
import specter.io as io
import numpy as np
class filter:
"""
Define the filter class. Could add additional functions
to compute the filter effective wavelength, the Vega
ze... | forero/desisim | py/desisim/templates.py | Python | bsd-3-clause | 2,807 | [
"Galaxy"
] | eb6a75cd8dff09013e3830aa9a10a386438e74daedff1841ff6d03e4432c1297 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
Tutorial on analyzing climate networks using Python.
Uses the Python packages ``core`` and ``climate`` providing all kinds of tools
related to climate networks. Written as part of a diploma / phd thesis in
Physics by Jonathan F. Donges (donges@pik-potsdam.de) at Universit... | leftaroundabout/pyunicorn | examples/tutorials/climate_network.py | Python | bsd-3-clause | 5,038 | [
"NetCDF"
] | 1b416325f2e6984eb2ed1b48a8050160690779705716cfc3334d18f2d6a12c65 |
# -*- coding: utf-8 -*-
"""
Miscellaneous utility code for VAR estimation
"""
from statsmodels.compat.pandas import frequencies
from statsmodels.compat.python import asbytes
import numpy as np
import pandas as pd
import scipy.linalg.decomp as decomp
import scipy.stats as stats
import statsmodels.tsa.tsatools as tsa
... | jseabold/statsmodels | statsmodels/tsa/vector_ar/util.py | Python | bsd-3-clause | 9,611 | [
"Gaussian"
] | 4dd54e67df8e598c20d2e452797fd7a10e2329068f5c6f63f9a0100b6c29f1ec |
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