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import wx
import wx.grid
import wx.lib.scrolledpanel
import wx.stc
import os
import os.path
import time
import platform
import multiprocessing
import datetime
import Bio.PDB
import webbrowser
from threading import Thread
from tools import *
class AntibodyPanel(wx.lib.scrolledpanel.ScrolledPanel):
def __init__(self... | schenc3/InteractiveROSETTA | InteractiveROSETTA/scripts/antibody.py | Python | gpl-2.0 | 14,153 | [
"PyMOL"
] | fbcd7efa81898935509fcf098376afe5dd8167a192a02af2f10c9faed95e116f |
#!/usr/bin/env python
#
# 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.
#
# Written (W) 2012 Heiko Strathmann
# Copyrigh... | abhiatgithub/shogun-toolbox | examples/undocumented/python_modular/modelselection_grid_search_krr_modular.py | Python | gpl-3.0 | 5,347 | [
"Gaussian"
] | 545dd4d5346d73d49e1d63dfbc50d8172408adae731704e2d2757ff51e9ebb08 |
from datetime import timedelta
import datetime
from django.utils.translation import ugettext_noop
from django.utils import html
from casexml.apps.case.models import CommCareCase
from django.core.urlresolvers import reverse, NoReverseMatch
from django.utils.translation import ugettext as _
from corehq.apps.reports.stand... | qedsoftware/commcare-hq | custom/apps/crs_reports/reports.py | Python | bsd-3-clause | 11,308 | [
"VisIt"
] | bd47870fa7a5780a6262818fea5f841017b197333c147cac70c2e8a6a5fcbc2d |
import time
t0t=time.time()
from os.path import join
import os
import numpy as n
import glob
import sys
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as p
import astropy.io.fits as fits
from scipy.interpolate import interp1d
from scipy.stats import norm as gaussD
plate = sys.argv[1]
mjd =... | JohanComparat/pySU | spm/bin/combine_model_spectra.py | Python | cc0-1.0 | 10,387 | [
"Firefly"
] | 4ac4fe11fc8c89c37351027eccce379ea1e2a47ccd619245dfb4c6dfcdbc3a85 |
# $Id$
#
# Copyright (C) 2005-2006 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
def ConstructEnsemb... | ptosco/rdkit | rdkit/DataStructs/BitUtils.py | Python | bsd-3-clause | 1,132 | [
"RDKit"
] | 47dd3469bc2f57f9ebfdef83d35deead0b758f45dafc963b1774de44cb997476 |
"""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 ... | wolfram74/numerical_methods_iserles_notes | venv/lib/python2.7/site-packages/tornado/websocket.py | Python | mit | 40,622 | [
"VisIt"
] | 6bfcd3c6efdac39328f7339ce19e9e1c68a9830595f513ad0b5ebaee0f8a9793 |
"""
LISSOM and related sheet classes.
$Id$
"""
__version__='$Revision$'
from numpy import zeros,ones
import copy
import param
import topo
from topo.base.projection import Projection
from topo.base.sheet import activity_type
from topo.base.simulation import EPConnectionEvent
from topo.transferfn.basic import Piecew... | jesuscript/topo-mpi | topo/sheet/lissom.py | Python | bsd-3-clause | 18,697 | [
"Gaussian"
] | e6f4b37fe03040d8e162a04b52ec55426b95140f9a35d287f9377e39f228a23a |
# coding: utf-8
# ## FFT solver for 1D Gross-Pitaevski equation
# We look for the complex function $\psi(x)$ satisfying the GP equation
#
# $ i\partial_t \psi = \frac{1}{2}(-i\partial_x - \Omega)^2\psi+ V(x)\psi + g|\psi|^2\psi $,
#
# with periodic boundary conditions.
#
# Integration: pseudospectral method with ... | brunojulia/ultracoldUB | brightsolitons/Alejandro/bs_v1.py | Python | gpl-3.0 | 14,708 | [
"Gaussian"
] | eb29f61d0f77379523db22e360ed1e90d396e1eee671b6f40de9e5bc6510cf83 |
#!/usr/bin/python2
import optparse
import subprocess
import sys
import shutil
from builds import GporcaBuild, GpcodegenBuild, GporcacodegenBuild
def install_gpdb(dependency_name):
status = subprocess.call("mkdir -p /usr/local/gpdb", shell=True)
if status:
return status
status = subprocess.call(
... | xuegang/gpdb | concourse/scripts/test_gpdb.py | Python | apache-2.0 | 2,056 | [
"ORCA"
] | a3e8bc63f2f8496214f9170539080fbcad5e51257ec19736326966ab84db820f |
from .base import *
class idmapper(object):
"""
cytoscape network interface as shown in CyREST's swagger documentation for 'idmapper'.
:param url: an url of the type 'http://' + host + ':' + str(port) + '/' + version + '/'.
"""
def __init__(self, url):
self.__url = url + 'commands/idmappe... | idekerlab/py2cytoscape | py2cytoscape/cyrest/idmapper.py | Python | mit | 2,018 | [
"Cytoscape"
] | 9ef15af9bff88612da5c77aa3378ba4f00c7e4ba95880fa2a9e8d43f737c6c34 |
#!/usr/bin/env python
import Tkinter
import math, os, sys
import vtk
import vtk.tk
from vtk.tk.vtkTkRenderWidget import *
# Make a root window
root = Tkinter.Tk()
# Add a vtkTkRenderWidget
pane = vtkTkRenderWidget(root,width=400,height=400)
pane.pack(expand='true',fill='both')
# Get the render window from the widge... | andregouws/mrMeshPy | legacy/mrMesh/mrMeshPy/mrMeshRender.py | Python | mit | 819 | [
"VTK"
] | 20711a51f9db2b4842a98ec4a32b74ffb4d69be259fc4fe7424f9e4d34e29514 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import absolute_import
# To make a release follow these steps:
# python setup.py sdist
# twine upload dist/argos-0.2.0rc1.tar.gz
# or better
# rm -rf build dist
# python setup.py bdist_wheel
# twine check dist/*
# twine upload dist/argos-x.y.z-p... | titusjan/argos | setup.py | Python | gpl-3.0 | 4,069 | [
"NetCDF"
] | 080bbb7824eee1b4e7d966c99932597d19373a475a79a249214af4c536a3d08c |
from __future__ import print_function
import nibabel as nib
import numpy as np
import scipy
import scipy.ndimage
from scipy.ndimage.filters import gaussian_filter
def load_data(filename):
""" Return fMRI data corresponding to the given filename and prints
shape of the data array
----------
filenam... | yuchengdong/project-beta-1 | code/utils/data_loading.py | Python | bsd-3-clause | 5,511 | [
"Gaussian"
] | 5a70db389ae00b51bf55f6a092130cfc2db02e1bb731e7a131aa5201c6ad6bcd |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to make it easier to submit
# large numbers of jobs on supercomputers. It provides a python interface to physical input, suc... | pylada/pylada-light | src/pylada/process/__init__.py | Python | gpl-3.0 | 5,719 | [
"CRYSTAL",
"VASP"
] | 837aae7d87e9e5e5d540de411d08c128dcfa7058591479fb74207b90265dea0e |
########################################################################
# File : JobWrapper.py
# Author : Stuart Paterson
########################################################################
""" The Job Wrapper Class is instantiated with arguments tailored for running
a particular job. The JobWrapper starts ... | vmendez/DIRAC | WorkloadManagementSystem/JobWrapper/JobWrapper.py | Python | gpl-3.0 | 62,593 | [
"DIRAC"
] | 39e6e3c6c339d81d1ab84219511b5b701a72be053bac1d506b785309abcbd852 |
"""
Universe configuration builder.
"""
import os
import sys
import logging
import logging.config
from optparse import OptionParser
import ConfigParser
from galaxy.util import string_as_bool, listify
log = logging.getLogger( __name__ )
def resolve_path( path, root ):
"""If 'path' is relative make absolute by prep... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/webapps/tool_shed/config.py | Python | gpl-3.0 | 14,329 | [
"Galaxy"
] | b869f6024a0b7334129cc60d215ca5429c554c0dcf8864daa832a7467d9eb759 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""Tests for the unique domains visited analysis plugin."""
import unittest
from plaso.analysis import unique_domains_visited
from plaso.containers import reports
from plaso.lib import definitions
from tests.analysis import test_lib
class UniqueDomainsPluginTest(test_... | joachimmetz/plaso | tests/analysis/unique_domains_visited.py | Python | apache-2.0 | 2,525 | [
"VisIt"
] | 72275f4e0b28c0e5d2ac8898a55df67c8caf54ff09ea38a84c25b4468eab8791 |
#!/usr/bin/env python
# (C) Copyright IBM Corporation 2004, 2005
# All Rights Reserved.
#
# 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 without limitation
# ... | ArcticaProject/vcxsrv | mesalib/src/mapi/glapi/gen/glX_proto_send.py | Python | gpl-3.0 | 39,193 | [
"Brian"
] | c7c6e262a249792abeb57a01c8781c438e2c7e402e49a56b1314ccf0b3d8d689 |
"""Contains the DataManager base class."""
# data_manager.py
# Mission Pinball Framework
# Written by Brian Madden & Gabe Knuth
# Released under the MIT License. (See license info at the end of this file.)
# Documentation and more info at http://missionpinball.com/mpf
import copy
import logging
import os
import errno... | spierepf/mpf | mpf/system/data_manager.py | Python | mit | 5,227 | [
"Brian"
] | d138a8307adc96ae7fa24663cbd66feab983bc0bca768a910ab838abb18a03bf |
#!/usr/bin/env python
"""
Converts a step5_assembly.{psf,pdb} to a mae file appropriate
for membrane input to dabble
"""
from __future__ import print_function
import os
from vmd import atomsel, molecule
thedir = os.path.abspath(input("Which directory contains step5_assembly.{psf,crd}? > "))
if not os.path.isdir(thedi... | Eigenstate/dabble | convert_step5_to_dabble.py | Python | gpl-2.0 | 1,142 | [
"VMD"
] | 4f7161be86a4f57b773f3569a4250290ee64640a817e8c31f6c1fbc11c525171 |
#!/usr/bin/env python
"""
.. See the NOTICE file distributed with this work for additional information
regarding copyright ownership.
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
... | Multiscale-Genomics/mg-process-fastq | process_chipseq.py | Python | apache-2.0 | 16,373 | [
"BWA"
] | 3be6bd8b04cf48083bbf6f754fbf4bf0452e7a565ecfb9773b785e10f114d8d5 |
# 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)
import sys
class Hdf(AutotoolsPackage):
"""HDF4 (also known as HDF) is a library and multi-object
file format fo... | rspavel/spack | var/spack/repos/builtin/packages/hdf/package.py | Python | lgpl-2.1 | 6,068 | [
"NetCDF"
] | 89c8febe3379de1c7dc055f9e71ce5fa5fda673b94e67bc29303160a150615bc |
# -*- coding: utf-8 -*-
def VtkDibujaPropCells(nmbFilter):
# Dibuja las etiquetas de las líneas.
cc= vtk.vtkCellCenters()
cc.SetInput(nmbFilter) # Centroides de las celdas.
visCells= vtk.vtkSelectVisiblePoints()
visCells.SetInput(cc)
visCells.SetRenderer(renderer)
visCells.SelectionWindowOff()
... | lcpt/xc | python_modules/postprocess/xcVtk/vtk_dibuja_prop_cells.py | Python | gpl-3.0 | 806 | [
"VTK"
] | 7fc80f05a91982deac1b1b9c8b5abd6277888f0641d709f3e57207a7d8347b2c |
from __future__ import print_function
import os
import datetime
import boto
from boto.s3.key import Key
from jinja2 import Environment
# The secret key is available as a secure environment variable
# on travis-ci to push the build documentation to Amazon S3.
AWS_ACCESS_KEY_ID = os.environ['AWS_ACCESS_KEY_ID']
AWS_S... | marscher/mdtraj | tools/ci/speedpack/push-wheels-to-s3.py | Python | lgpl-2.1 | 2,173 | [
"MDTraj"
] | 7aa42bdb5831723926358f16a6e6059040412084366cc4025ef4ba1e2760592b |
# Docstrings for generated ufuncs
#
# The syntax is designed to look like the function add_newdoc is being
# called from numpy.lib, but in this file add_newdoc puts the
# docstrings in a dictionary. This dictionary is used in
# generate_ufuncs.py to generate the docstrings for the ufuncs in
# scipy.special at the C lev... | devs1991/test_edx_docmode | venv/lib/python2.7/site-packages/scipy/special/add_newdocs.py | Python | agpl-3.0 | 56,683 | [
"Gaussian"
] | a300b7d17494fa97ab43a685c6cd1b355c0de6911c96fd2dca283acbab8c3bf4 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# oiddiscover - discover valid openid relying party endpoints for this realm
# Copyright (C) 2003-2015 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the t... | heromod/migrid | mig/shared/functionality/oiddiscover.py | Python | gpl-2.0 | 5,822 | [
"Brian"
] | f8e946b966be791abe4805718e6ebbee4939d600facb47881c3eab99053e5eac |
import os
import time
import yaml
import datetime
import linecache
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from pymatgen import MPRester
from pymatgen.io.cif import CifWriter
from diffpy.Structure import loadStructure
from diffpy.srreal.structureadapter import nosymmetry
from diffpy.srre... | chiahaoliu/pdf_lib | pdf_lib/pdf_lib.py | Python | mit | 10,483 | [
"CRYSTAL",
"pymatgen"
] | 68964a97dd79f0a7abfbd4bb62dbf2c9c0cc9c9b81c787bddb4f8fb3a5a07ccc |
"""
simple, elegant templating
(part of web.py)
Template design:
Template string is split into tokens and the tokens are combined into nodes.
Parse tree is a nodelist. TextNode and ExpressionNode are simple nodes and
for-loop, if-loop etc are block nodes, which contain multiple child nodes.
Each node can emit som... | gabelerner/finkin | api/web/template.py | Python | mit | 45,408 | [
"VisIt"
] | a5cc9cf94bd7989d809c099d7c347e07ca7062296a25380da6aa9e7104c6c7c6 |
###
### This script can be run with pvpython rather than pvbatch, as it does not
### need mpi.
###
### Purpose:
###
### Generate a static image dataset of volume rendering on the ne cooling data
###
### Example usages (assumes you are in directory with this script):
###
### 1) To run on the coarse mesh, time... | Kitware/cinema | scripts/data_generation/ne-cooling/volume-vorticity-custom.py | Python | bsd-3-clause | 8,837 | [
"ParaView",
"VTK"
] | 0d33d4181238296e22015f99068bde374431ba8f0ab4d3b72ee0fd2cc7f1978c |
# $Id$
#
# Copyright (C) 2003-2006 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
import sys
from rdk... | ptosco/rdkit | rdkit/Dbase/DbInfo.py | Python | bsd-3-clause | 5,758 | [
"RDKit"
] | 20f6c1f0bbb158c90ed30ed8b48c506800eb16b78df9afaabe31e842a668230a |
# -*- coding: utf-8 -*-
"""
.. _tut-artifact-ica:
Repairing artifacts with ICA
============================
This tutorial covers the basics of independent components analysis (ICA) and
shows how ICA can be used for artifact repair; an extended example illustrates
repair of ocular and heartbeat artifacts. For conceptu... | wmvanvliet/mne-python | tutorials/preprocessing/40_artifact_correction_ica.py | Python | bsd-3-clause | 29,544 | [
"Gaussian"
] | 3b395eeb808d9411f02752a615b5db5a50ecefb4b671b336e7b0ce57d4771db2 |
#!/usr/bin/env python
import os
try:
__IPYTHON__
import sys
del sys.argv[1:]
except:
pass
import srwl_bl
import srwlib
import srwlpy
import srwl_uti_smp
def set_optics(v=None):
el = []
pp = []
names = ['CRL', 'CRL_Watchpoint', 'Watchpoint', 'Fiber', 'Fiber_Watchpoint2', 'Watchpoint2']
... | mrakitin/sirepo | tests/template/srw_generate_data/boron-fiber-crl-with-3-lenses.py | Python | apache-2.0 | 23,714 | [
"Gaussian"
] | 00cfbe41fa783676f506cc544d3780c4794e4f53fa54619018e065701a396c66 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | magic/services/seds.py | Python | agpl-3.0 | 52,228 | [
"Galaxy"
] | e819d1b8cae5bb75b314ca9f4b3fc83a3d31d6a71dd292c0917551ed2d402848 |
##############################
# Bullet Constraints Builder #
##############################
#
# Written within the scope of Inachus FP7 Project (607522):
# "Technological and Methodological Solutions for Integrated
# Wide Area Situation Awareness and Survivor Localisation to
# Support Search and Rescue (USaR) Teams"
#... | KaiKostack/bullet-constraints-builder | kk_bullet_constraints_builder/gui_buttons.py | Python | gpl-2.0 | 42,281 | [
"VisIt"
] | 02e789966f85e103f7272953a86d675db69f15df4a3ef3ec3d1ec91e75c6ea84 |
"""Analyze python import statements."""
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import ast
import os
from .util import (
display,
ApplicationError,
)
from .data import (
data_context,
)
VIRTUAL_PACKAGES = set([
'ansible.module_utils.six',
])
def get_... | cchurch/ansible | test/lib/ansible_test/_internal/import_analysis.py | Python | gpl-3.0 | 9,016 | [
"VisIt"
] | fbf508e174ea8a778aa0f5048c763a987f3262d01f1462b64a53296a4c2e1d29 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2002 Gary Shao
# Copyright (C) 2007 Brian G. Matherly
# Copyright (C) 2009 Benny Malengier
# Copyright (C) 2009 Gary Burton
#
# This program is free software; you can redistribute i... | jralls/gramps | gramps/gen/plug/docgen/paperstyle.py | Python | gpl-2.0 | 6,300 | [
"Brian"
] | 8db7e1d8b25045ce88b10ae44c7a38fa04496950bf37b8328ea224af276f7db8 |
"""
Unit tests for masquerade.
"""
import json
import pickle
from datetime import datetime
from importlib import import_module
from unittest.mock import patch
import pytest
import ddt
from django.conf import settings
from django.test import TestCase, RequestFactory
from django.urls import reverse
from edx_toggles.tog... | eduNEXT/edunext-platform | lms/djangoapps/courseware/tests/test_masquerade.py | Python | agpl-3.0 | 22,699 | [
"VisIt"
] | d6a77521844ae6cefe0a7c31f5b4757cf00560b42531ef7c0fa5f63932ee98ed |
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not use ... | andrewsomething/libcloud | libcloud/compute/drivers/azure.py | Python | apache-2.0 | 113,227 | [
"VisIt"
] | 4b2e2a383974b55da89f56c160c6a9676ae0cc9814c9de8d02c4e97c65d6b432 |
"""A base class for RPC services and proxies.
Authors:
* Brian Granger
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2012. Brian Granger, Min Ragan-Kelley
#
# Distributed under the terms of the BSD License. The full license is in
# the file COPYING.BSD, dist... | ellisonbg/zpyrpc | zpyrpc/base.py | Python | bsd-3-clause | 2,496 | [
"Brian"
] | b55d007ed023d29477f32d47e6a66e46c11530a53b80993b135b68cd49f92d82 |
# coding=utf-8
# Copyright 2022 The Uncertainty Baselines Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by ap... | google/uncertainty-baselines | baselines/imagenet/sngp.py | Python | apache-2.0 | 21,753 | [
"Gaussian"
] | 80f5a3545846994894917a6ff14bf4e1790c91b80bf72b7613c8d2657840e437 |
""" Main module
"""
import os
import re
import json
import pprint
import datetime
import functools
import traceback
from hashlib import md5
from concurrent.futures import ThreadPoolExecutor
import tornado.web
import tornado.websocket
from tornado import gen
from tornado.web import HTTPError
from tornado.ioloop import... | DIRACGrid/WebAppDIRAC | src/WebAppDIRAC/Lib/WebHandler.py | Python | gpl-3.0 | 16,064 | [
"DIRAC"
] | 72c785c6630ccba7ce32e20684594c233773635acd4a64b9683b64780f5ec788 |
#!/usr/bin/env python
#
# Copyright 2014 Google Inc. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless require... | anthrotype/nototools | nototools/opentype_data.py | Python | apache-2.0 | 10,931 | [
"FEFF"
] | 3480eebe8d4b651ad370038b30367e15f7c3e0413e9e20d40fef2945b5b2ccc9 |
# -*- coding: utf-8 -*-
#
# biseqt documentation build configuration file, created by
# sphinx-quickstart on Sun Nov 8 14:22:42 2015.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# Al... | amirkdv/biseqt | docs/conf.py | Python | bsd-3-clause | 11,019 | [
"pysam"
] | 75357687f5d86a3353f0d143878571c786e484c6162383d098e0db109e120cc0 |
# -*- 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 publi... | thica/ORCA-Remote | src/ORCA/scripttemplates/Template_Keyhandler.py | Python | gpl-3.0 | 2,115 | [
"ORCA"
] | 40472989ef6300896d554933b2cef04c3f15cad7e3329c54ca465b9dcf72ca6f |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | Stargrazer82301/CAAPR | CAAPR/CAAPR_AstroMagic/PTS/pts/eagle/starformation.py | Python | mit | 8,784 | [
"Gaussian"
] | bc08a7efb117da64ec4dacbc36cc941790814da16bc5bb2d2a5d3569e57d2e49 |
#
# Copyright (C) 2013-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | espressomd/espresso | testsuite/python/interactions_non-bonded_interface.py | Python | gpl-3.0 | 8,780 | [
"ESPResSo"
] | f58f80c38f40a2719b5b17e76b8b1e07b67e0d0db5b4e48e58a982a72ca9cd73 |
# -*- coding: utf-8 -*-
import os
class AdoptionCenter:
"""
The AdoptionCenter class stores the important information that a
client would need to know about, such as the different numbers of
species stored, the location, and the name. It also has a method to adopt a pet.
"""
def __init__(self,... | NicovincX2/Python-3.5 | Divers/pets_adoption.py | Python | gpl-3.0 | 9,562 | [
"VisIt"
] | 998f7b14da19e11412414e0f3091390b11bb2e3210a643cc8b2285e8fbfb7b7e |
from collections import deque
from rdkit import Chem
import sys
import tensorflow as tf
import pickle
import os
import fnmatch
import numpy as np
from scipy.spatial.distance import pdist, squareform
import pandas as pd
from deepchem.feat.base_classes import Featurizer
from deepchem.feat.graph_features import atom_f... | rbharath/deepchem | deepchem/feat/adjacency_fingerprints.py | Python | mit | 4,395 | [
"RDKit"
] | c453fdd643118622633b8f12ef6698a659c47a95584a2580f9229f65a6da6644 |
# $Id$
#
# Copyright (C) 2005-2006 Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" uses DSViewer to interact with molec... | bp-kelley/rdkit | rdkit/Chem/DSViewer.py | Python | bsd-3-clause | 12,125 | [
"PyMOL",
"RDKit"
] | a5e9cc1f050dd810590272c5995fa97be9462424b6877039a8d141d53875ecac |
import csv
import xlrd
import xlwt
import subprocess
import ConfigParser
import sys
import os
import string
import random
from datetime import datetime
FILE_CHRCHECKFIRST = ""
PARAM_NUMBER_N = 100
UNIQUE_PRIMERS = set("")
NON_UNIQUE_PRIMERS = set("")
FORBIDDEN_PRIMERS = set("")
def main():
"""Perform primer desi... | zichner/primerDesign | primerDesign.py | Python | mit | 25,518 | [
"BLAST"
] | 7317ba510fc07e41211be0a770d7902afca9bd40896c5d57a5596d1b0ff2ce7c |
import matplotlib as mpl
mpl.use('Agg')
import numpy as np
import pandas as pd
import matplotlib.mlab as mlab
import matplotlib.pyplot as plt
import scipy as sp
from scipy.interpolate import griddata
import seaborn as sns
from scipy.stats import norm
from scipy.stats import uniform
from scipy.stats import multivar... | bmanubay/open-forcefield-tools | single-molecule-property-generation/graph_bl.py | Python | mit | 17,095 | [
"Gaussian"
] | df1d3c31ddf5b40e0245f89e0a44cd6d81d77df54b06ecea49614e3446d132f5 |
import os
import netCDF4 as nc
import numpy
import pyresample
from satistjenesten import io
from satistjenesten import image
# Steps for the IO implementation
@given(u'we process mitiff file {input_filepath}')
def step_impl(context, input_filepath):
context.input_filepath = input_filepath
context.scene = io... | mitkin/satistjenesten | features/steps/steps.py | Python | mit | 1,531 | [
"NetCDF"
] | cac3c6c02b1addf3b4bbfc77dbaf364dd1f2746c16756bd6ce94097e0e51317d |
""" DIRAC.Resources.Storage package """
| DIRACGrid/DIRAC | src/DIRAC/Resources/Storage/__init__.py | Python | gpl-3.0 | 40 | [
"DIRAC"
] | 5068bfac7fb45974f6b786af9bd399184d057851dcfad0eae5f2c6390ee35f59 |
#pylint: disable=C0111
#pylint: disable=W0621
from lettuce import world, step
from lettuce.django import django_url
from course_modes.models import CourseMode
from nose.tools import assert_equal
def create_cert_course():
world.clear_courses()
org = 'edx'
number = '999'
name = 'Certificates'
course... | abo-abo/edx-platform | lms/djangoapps/courseware/features/certificates.py | Python | agpl-3.0 | 8,213 | [
"VisIt"
] | e74a1509ccc12b88660de0c6fe62c1a031ac06bc52b9acf7dbb022f0a0f93fa3 |
# -*- coding: utf-8 -*-
#!/usr/bin/env python
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007 Johan Gonqvist <johan.gronqvist@gmail.com>
# Copyright (C) 2007-2009 Gary Burton <gary.burton@zen.co.uk>
# Copyright (C) 2007-2009 Stephane Charet... | jralls/gramps | gramps/plugins/webreport/addressbooklist.py | Python | gpl-2.0 | 6,358 | [
"Brian"
] | a5fda53318480dd2c7f93a4f2a555dd6bf3e937be25ca65e7b078aa352058fac |
import numpy
from pyproj import Proj
import click
import rasterio
from rasterio.crs import CRS
from rasterio.warp import reproject
from rasterio.enums import Resampling
from trefoil.netcdf.crs import get_crs
from trefoil.netcdf.utilities import copy_variable, copy_dimension, get_fill_value
from trefoil.netcdf.variable... | consbio/clover | trefoil/netcdf/warp.py | Python | bsd-3-clause | 5,979 | [
"NetCDF"
] | 36652e7425fb45c28f71b7f4352e9d6d59d0958fdfe8b27eba0b1e65417916c2 |
import os
import pymc3
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
def hdi_of_mcmc(sample_vec, cred_mass=0.95):
"""
Highest density interval of sample.
"""
assert len(sample_vec), 'need points to find HDI'
sorted_pts = np.sort(sample_vec)
ci_idx_inc = int(np.floor(... | ipashchenko/ra_orbit | changepoint.py | Python | mit | 3,862 | [
"Gaussian"
] | 0ba3265736feab7e8b73210e2459911856e7462c08331f34838655897ba4047c |
# This file is part of DEAP.
#
# DEAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# DEAP is distributed... | PyQuake/earthquakemodels | code/cocobbob/coco/deapbbob/deapbbob.py | Python | bsd-3-clause | 5,055 | [
"Gaussian"
] | d8592c13c42dc724bc6be06d26bdd4c875cff32ced3761cf27cabefe60b6d1c6 |
# The following is a Python translation of a MATLAB file originally written principally by Mike Tipping
# as part of his SparseBayes software library. Initially published on GitHub on July 21st, 2015.
# SB2_PARAMETERSETTINGS User parameter initialisation for SPARSEBAYES
#
# SETTINGS = SB2_PARAMETERSETTINGS(parameter... | jhallock7/SparseBayes-Python | SB2_ParameterSettings.py | Python | gpl-2.0 | 3,373 | [
"Gaussian"
] | e261417b78543776dccfa97cdb89813dc4849fb4e7a89d83dfd0577056f5ef43 |
from pylab import *
import json
nodes = [
{
"fileName": "generators/PoissonGenerator.qml",
"label": "",
"x": 100,
"y": 100,
"engine": {
"fireOutput": 0.0001,
"rate": 300
}
},
# {
# "fileName":"meters/RasterPlot.qml",
# ... | dragly/hodgkin-huxley | tools/generate_massive.py | Python | gpl-3.0 | 2,939 | [
"NEURON"
] | 68ce105b400b3ea65a0c3abb2033c4bdf8d5b12d97f5caf801b92feb8d678be0 |
import os
import itertools
import numpy as np
from scipy.optimize import differential_evolution
from sklearn.decomposition import PCA
from sklearn.neighbors import KernelDensity
from sklearn.model_selection import GridSearchCV
from sklearn.ensemble import IsolationForest
from sklearn.model_selection import cross_val_sc... | tupui/HDR-Boxplot | hdr.py | Python | mit | 8,452 | [
"Gaussian"
] | c04e7a19e75a3743393104821c8ab784063a2f26d1742eeb465498beda92c442 |
from easy.visitors.codegen import CodeGenVisitor
from easy.visitors.constant_folding import ConstantFoldingVisitor
from easy.visitors.pprint import PPrintVisitor
from easy.visitors.symbol_table import SymbolTableVisitor
class Compiler(object):
def __init__(self, ast):
self._ast = ast
def _do_pass(self... | helgefmi/Easy | src/easy/compiler.py | Python | mit | 616 | [
"VisIt"
] | e07e384a8f0b926daf75f4bbd54d8625db968cf1280d0e36070d2e6e8be37a9c |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
from django.conf import settings
import django.core.validators
class Migration(migrations.Migration):
dependencies = [
migrations.swappable_dependency(settings.AUTH_USER_MODEL),
]
operations... | FMI-B20/Yarr | main/migrations/0001_initial.py | Python | mit | 1,995 | [
"VisIt"
] | 9e429d828bc0c2ff41b54607cab87650c2c33cb4e678cd620175db6c32d61c6c |
"""
Implementation of the Brunel 2000 network:
sparsely connected network of identical LIF neurons (Model A).
"""
# This file is part of the exercise code repository accompanying
# the book: Neuronal Dynamics (see http://neuronaldynamics.epfl.ch)
# located at http://github.com/EPFL-LCN/neuronaldynamics-exercises.
# T... | EPFL-LCN/neuronaldynamics-exercises | neurodynex3/brunel_model/LIF_spiking_network.py | Python | gpl-2.0 | 10,560 | [
"NEURON"
] | 1fdd8ac7348f7d64ac73a67606aea1d148c9a9ae58dc3b201880f76cfab9920f |
# $HeadURL$
"""
DIRAC - Distributed Infrastructure with Remote Agent Control
The LHCb distributed data production and analysis system.
DIRAC is a software framework for distributed computing which
allows to integrate various computing resources in a single
system. At the same time it integrates all kin... | rajanandakumar/DIRAC | __init__.py | Python | gpl-3.0 | 4,985 | [
"DIRAC"
] | 2e37dabd0dfe8f24cfbe8a1550ac5d8306fa7c632f448d4c7f13c0de81c51107 |
from __future__ import (absolute_import, division, print_function)
import stresstesting
from mantid.simpleapi import Abins, mtd, DeleteWorkspace
from AbinsModules import AbinsConstants, AbinsTestHelpers
class HelperTestingClass(object):
def __init__(self):
self._temperature = 10 # K
self._sample... | dymkowsk/mantid | Testing/SystemTests/tests/analysis/AbinsTest.py | Python | gpl-3.0 | 14,934 | [
"CASTEP",
"CRYSTAL",
"DMol3",
"Gaussian"
] | ae730d36d6b83861d98fc41dfe211093c1cd50040bd9d3e8fd4b5d3e784f2dda |
#!/usr/bin/env python3
"""Cheap and simple API helper
This program is part of "Dive Into Python", a free Python book for
experienced programmers. Visit http://diveintopython.org/ for the
latest version.
"""
__author__ = "Mark Pilgrim (mark@diveintopython.org)"
__version__ = "$Revision: 1.3 $"
__date__ = "$Date: 2004... | jtraver/dev | python3/sys/apihelper.py | Python | mit | 1,802 | [
"VisIt"
] | 8b8c638db17ba696e8572f2cbdf60e988919c4806f20ecd86464931ef2160735 |
import sys
import os
import platform
import stat
import time
from ddsc.exceptions import DDSUserException
TERMINAL_ENCODING_NOT_UTF_ERROR = """
ERROR: DukeDSClient requires UTF terminal encoding.
Follow this guide for adjusting your terminal encoding:
https://github.com/Duke-GCB/DukeDSClient/blob/master/docs/Unicod... | Duke-GCB/DukeDSClient | ddsc/core/util.py | Python | mit | 16,145 | [
"VisIt"
] | 045bfd7cc3f5d1b777ca0ad8860cc935804986deef7738567ac20cd0d06a2e6e |
# -*- coding: utf-8 -*-
"""
.. note::
Functions for calculating surfaces and analyzing them.
.. moduleauthor:: Adam Gagorik <adam.gagorik@gmail.com>
"""
import langmuir as lm
import numpy as np
try:
import scipy.special as special
import scipy.fftpack as fftpack
import scipy.ndimage as ndimage
imp... | LangmuirSim/langmuir | LangmuirPython/langmuir/surface.py | Python | gpl-2.0 | 29,896 | [
"Gaussian",
"ParaView"
] | 914b0a957753cf3fb93331fe304930b977939db2d84c2bf286b8a596064e0b76 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
urlpat... | nectR-Tutoring/nectr | config/urls.py | Python | mit | 2,898 | [
"VisIt"
] | c1fde64d0961a81256b8c594cffe86a1b08773a1f298567ad44835f149f4fb03 |
import numpy as np
np.seterr(divide='ignore') #ignore errors in log division
np.seterr(all='ignore') #ignore errors in log division
import sys
import time
##########################################################################################
def BGMCMC(LogPosterior,gp,post_args,ch_len,ep,gibbs_index,chain_file... | nealegibson/Infer | src/MCMC_BGibbs.py | Python | gpl-3.0 | 7,699 | [
"Gaussian"
] | 06fe5b2654cc54a6113623ec50c6729205e296945056ba0b5c7f75bcce6dc683 |
import datetime
from django.core.management.base import NoArgsCommand
from django.core.urlresolvers import reverse
from django.db import connection
from django.db.models import Q, F
from askbot.models import User, Post, PostRevision, Thread
from askbot.models import Activity, EmailFeedSetting
from django.utils.translat... | tvenkat/askbot-devel | askbot/management/commands/send_email_alerts.py | Python | gpl-3.0 | 21,935 | [
"VisIt"
] | 4545158c15f26f082960de116a7547deb1f320dce855c416662816d6322b6d42 |
import curses, curses.panel
import sys, os, math, copy
from testData import Test_DATA
class GUI():
DOWN = 1
UP = -1
LEFT = -1
RIGHT = 1
# Planet view options
IDX_PLANET = 0
def __init__(self):
# Variables for game
self.time = 0
# Variables for me... | hydrius/schwarzschild-radius | old/SchwarzschildRadius1/main.py | Python | mit | 10,314 | [
"Galaxy"
] | ec9d8454be1a211a04e6c4104d632bbac7ac625664719b3d6c6cebfe06d155e4 |
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Matti Hamalainen <msh@nmr.mgh.harvard.edu>
# Denis Engemann <denis.engemann@gmail.com>
# Andrew Dykstra <andrew.r.dykstra@gmail.com>
# Mads Jensen <mje.mads@gmail.com>
#
# License: BSD (3-clause)
from copy imp... | yousrabk/mne-python | mne/evoked.py | Python | bsd-3-clause | 53,456 | [
"Mayavi"
] | 292412df39610e31b2ba97ceff611b23d76f39b76b7cfa7c92631cbefda2894f |
# 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... | alsrgv/tensorflow | tensorflow/python/autograph/pyct/cfg_test.py | Python | apache-2.0 | 31,083 | [
"VisIt"
] | 3696c2e8f50e42db984df5c6149e32d50115eb8cfcbff1bf672f6a413364a153 |
""" Class to solve the creation, serialisation etc. of NetCDF files used
in the BioVel Biome-BGC project. The module is used from the
:mod:`ResultEvaluator`.
"""
# Copyright (c) 2014 MTA Centre for Ecological Research
# Distributed under the GNU GPL v3. For full terms see the file LICENSE.
from Scientific.IO... | icce-p/bbgc-ws | BBGCNetCDF.py | Python | gpl-3.0 | 5,082 | [
"NetCDF"
] | b18eddcf8b1fee20e2ef883e29992c193a78e9e311304f7949b7e442577a2d39 |
#!/usr/bin/python
#FILE DESCRIPTION=======================================================
#~ Python script used for post-processing automatization of flow on an
#~ inclined (?textured?) plate (minimal postprocessing to test the results)
#~
#~ NOTES:
#~ - still unfinished BUT improvement
#~ USAGE:
#~ paraF... | MartinIsoz/CFD_oF | 03_texturedPlate/03_pyrTexture/00_Scripts/postProcMinimalV2.py | Python | gpl-2.0 | 6,470 | [
"ParaView"
] | 3c16fb4de454e170d220ddf1fc34893a2c8fb4d5bc22d4dc6feb5ee4a1b6a65d |
from collections import OrderedDict
from numpy import argmax, append, exp, zeros, pi, asarray, argsort, diff, concatenate, int8, where, array, sqrt, square, ones, power, sum, mean, std, linspace, max, round, median, polyfit, vstack, random, greater, less, searchsorted, sort
from numpy i... | Delosari/dazer | bin/lib/Math_Libraries/FittingTools_old.py | Python | mit | 89,714 | [
"Gaussian"
] | ec85710b767f1e8f8273faeb48b73e76e9be896d2c37f1b7c62ef0c21e380dc0 |
r"""smtrace module is used along with vtkSMTrace to generate Python trace for
ParaView. While this module is primarily designed to be used from the ParaView
GUI, Python scripts can use this module too to generate trace from the script
executed.
Typical usage is as follows::
from paraview import smtrace
config... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/Wrapping/Python/paraview/smtrace.py | Python | gpl-3.0 | 54,107 | [
"ParaView",
"VTK"
] | 43d949971bc250fb4bdc974a174096c4115954ab1401e6a4173a60eab30fb78b |
# Copyright (c) Microsoft Corporation.
#
# This source code is subject to terms and conditions of the Apache License, Version 2.0. A
# copy of the license can be found in the LICENSE.txt file at the root of this distribution. If
# you cannot locate the Apache License, Version 2.0, please send an email to
# vsp... | msunardi/PTVS | Python/Product/Pyvot/Pyvot/xl/__init__.py | Python | apache-2.0 | 4,494 | [
"VisIt"
] | 513fe4a2c6b766ed116bdc9c54fcb8f982c50256411a58109b757724f802d10c |
#!/usr/bin/python
#encoding:utf-8
'''
client
'''
import socket, sys, os
import time, json
host = socket.gethostname() # 这里获取的是本地，具体视情况而定
port = 7878
BUF_SIZE = 4096
try:
client = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
except socket.error, e:
print "Error creating socket: %s" % e
sys.exit()
... | hugoxia/Python | heartbeat/client.py | Python | mit | 1,240 | [
"exciting"
] | 56ce8360c3fc13eb527f292c8e444d8a75877e54e1c3b46a682245a81f9246c9 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Kyle A. Beauchamp
# Contributors: Robert McGibbon, John D. Cho... | jchodera/mdtraj | mdtraj/formats/mol2.py | Python | lgpl-2.1 | 9,458 | [
"MDTraj",
"OpenMM"
] | 50c23afc52a7f127d0cd5281db9cb8071bd5eea07efee778c3f0656fc7dc806c |
import itertools
import math
import networkx as nx
import re
from collections import defaultdict
from django.db import connection
from django.http import JsonResponse
from django.shortcuts import get_object_or_404
from rest_framework.decorators import api_view
from catmaid import state
from catmaid.models import Us... | catsop/CATMAID | django/applications/catmaid/control/treenode.py | Python | gpl-3.0 | 43,232 | [
"NEURON"
] | ffa09440ab1ae90c0ed027aca4e25c6668b1d6ffc1b8e7757cac874a4a02968d |
import unittest
from pyramid import testing
class TutorialFunctionalTests(unittest.TestCase):
def setUp(self):
from tutorial import main
app = main({})
from webtest import TestApp
self.testapp = TestApp(app)
def test_home(self):
res = self.testapp.get('/', status=200)... | FedericoStra/pyramid_tutorial | 07_views/tests/test_functional.py | Python | mit | 585 | [
"VisIt"
] | f25718aa7f5c8f381306d15be0a3f999266a4f7fff5a67e0a11c52ddac0e80e6 |
# -*- coding: utf-8 -*-
"""
Created on Thu Jun 30 15:34:39 2016
@author: charlesgulian
"""
import os
curr_dir = os.getcwd()
import numpy as np
import matplotlib.pyplot as plt
import matplotlib
import pysex
import sex_stats
import sex_config
import fits_tools
# Image deconvolution project:
# Main script for data anal... | CharlesGulian/Deconv | Main.py | Python | gpl-3.0 | 17,228 | [
"Gaussian"
] | 010744d03a4727cfd192ab34574b9731cc2448fe650b8085dca258e8bc959053 |
#!/usr/bin/python3
#
# Copyright (c) 2012 Mikkel Schubert <MikkelSch@gmail.com>
#
# 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 without limitation the rights
... | MikkelSchubert/paleomix | paleomix/pipelines/phylo/makefile.py | Python | mit | 29,283 | [
"pysam"
] | 9e0d2e173a80599d1422c54643ddac74976bf6d5ab761abc9858472fbcb8e644 |
#__docformat__ = "restructuredtext en"
# ******NOTICE***************
# optimize.py module by Travis E. Oliphant
#
# You may copy and use this module as you see fit with no
# guarantee implied provided you keep this notice in all copies.
# *****END NOTICE************
# A collection of optimization algorithms. Version ... | chaluemwut/fbserver | venv/lib/python2.7/site-packages/scipy/optimize/optimize.py | Python | apache-2.0 | 116,124 | [
"Gaussian"
] | 984fea8ac17cee5425a39aa88eee83c6bc308a870487ee6ab07dc9f950aa40f5 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | demis001/scikit-bio | skbio/alignment/_lib/__init__.py | Python | bsd-3-clause | 487 | [
"scikit-bio"
] | 0ae76f7accb8293f082864ff0a1ed14333dfde95fbec83a0bbca236f6a21e698 |
# coding: utf-8
from __future__ import unicode_literals
import re
from .common import InfoExtractor
from ..utils import (
ExtractorError,
parse_iso8601,
qualities,
)
class SRGSSRIE(InfoExtractor):
_VALID_URL = r'(?:https?://tp\.srgssr\.ch/p(?:/[^/]+)+\?urn=urn|srgssr):(?P<bu>srf|rts|rsi|rtr|swi):(?:... | akirk/youtube-dl | youtube_dl/extractor/srgssr.py | Python | unlicense | 6,606 | [
"Jaguar"
] | a836d21c725b05d392e72ceb481a3009568e58e3f3884cc482397f487a4e0a72 |
#!/usr/bin/env python
"""
Start a given production
"""
__RCSID__ = "$Id$"
import DIRAC
from DIRAC.Core.Base import Script
Script.setUsageMessage('\n'.join([__doc__.split('\n')[1],
'Usage:',
' %s prodID' % Script.scriptName,
... | fstagni/DIRAC | ProductionSystem/scripts/dirac-prod-start.py | Python | gpl-3.0 | 908 | [
"DIRAC"
] | 4b549f7db67c7027394e8ccf47a1cc0f3c9456bba035d2aeb5651e03c0c12bb1 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import logging
import numpy as np
import itertools
from scipy.spatial import ConvexHull
from pymatgen.analysis.pourbaix.entry import MultiEntry, ion_or_solid_... | johnson1228/pymatgen | pymatgen/analysis/pourbaix/maker.py | Python | mit | 12,869 | [
"pymatgen"
] | f8e820c34c178aeab82fd8efe1e381731741160ca5a3ad92d2c591f1d83635e5 |
# -*- coding: utf-8 -*-
#
# test_growth_curves.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 Lice... | sanjayankur31/nest-simulator | testsuite/pytests/test_sp/test_growth_curves.py | Python | gpl-2.0 | 14,933 | [
"Gaussian"
] | 6ffebc75a4b4c5d47179cab916fd93d67dc01b0a22397796e3ee0bbe0d6684ce |
#######################################################################
#
#
# Next Event Renderer for Dreambox/Enigma-2
# Coded by Vali (c)2010
# Support: www.dreambox-tools.info
#
#
# This plugin is licensed under the Creative Commons
# Attribution-NonCommercial-ShareAlike 3.0 Unported License.
# To view ... | openmips/stbgui | lib/python/Components/Renderer/OMNextEvent.py | Python | gpl-2.0 | 1,770 | [
"VisIt"
] | a4cd8888ddeee44b92772ee5d989419cf476b0311cedcf68f8de3b2b3eb64048 |
from setuptools import setup, find_packages
from os import path
try:
from jupyterpip import cmdclass
except:
import sys
import subprocess
import importlib
subprocess.call([sys.executable, '-m', 'pip', 'install', 'jupyter-pip'])
cmdclass = importlib.import_module('jupyterpip').cmdclass
here = p... | PySCeS/PyscesToolbox | setup.py | Python | bsd-3-clause | 1,776 | [
"PySCeS"
] | 4f950c746607a05b9270d226734b24e32880369e410e9160cd44509b91c6a5db |
#!/usr/bin/env python
from __future__ import print_function
import json
import optparse
import os
import subprocess
import sys
import tempfile
CHUNK_SIZE = 2**20
DEFAULT_DATA_TABLE_NAME = "bowtie_indexes"
def get_id_name(params, dbkey, fasta_description=None):
# TODO: ensure sequence_id is unique and does not ... | mvdbeek/tools-iuc | data_managers/data_manager_bowtie_index_builder/data_manager/bowtie_index_builder.py | Python | mit | 4,110 | [
"Bowtie"
] | 8feb931662c8340951da977c0389b36f6c1864735283f8359ecab3af6d506817 |
import numpy
from chainer.functions.connection import bilinear
from chainer import link
class Bilinear(link.Link):
"""Bilinear layer that performs tensor multiplication.
Bilinear is a primitive link that wraps the
:func:`~chainer.functions.bilinear` functions. It holds parameters ``W``,
``V1``, ``V... | AlpacaDB/chainer | chainer/links/connection/bilinear.py | Python | mit | 4,147 | [
"Gaussian"
] | f28445425feeb1111dfb101b77c949e0cc031909e06c145792e8535af2fd31af |
from matplotlib import rcParams, rc
import numpy as np
import sys
from fitFunctions import gaussian
import scipy.interpolate
import scipy.signal
from baselineIIR import IirFilter
# common setup for matplotlib
params = {'savefig.dpi': 300, # save figures to 300 dpi
'axes.labelsize': 14,
'text.fontsi... | bmazin/SDR | Projects/Simulator/simulateSOS.py | Python | gpl-2.0 | 9,421 | [
"Gaussian"
] | 27427cd102d09725cbd40121bca008cd94dd6f24d34c94adebb7968b7287912e |
import wx
from confmanager import ConfManager
"""Set up some example stuff, so you can get a working example of the classes in action:"""
if __name__ == '__main__':
a = wx.App() # Create the main wx app
c = ConfManager('test') # Make a ConfManager and call it test
c.add_section('people') # Add a section call... | chrisnorman7/confmanager | example.py | Python | mpl-2.0 | 1,841 | [
"VisIt"
] | 8ed4ef332955e43ed310a64ac36eda29d84087acca71a01634609dee3ba261c8 |
# -*- coding: utf-8 -*-
"""INI time-to-first-spike simulator backend with dynamic threshold.
This module defines the layer objects used to create a spiking neural network
for our built-in INI simulator
:py:mod:`~snntoolbox.simulation.target_simulators.INI_ttfs_dyn_thresh_target_sim`.
The coding scheme underlying this... | NeuromorphicProcessorProject/snn_toolbox | snntoolbox/simulation/backends/inisim/ttfs_dyn_thresh.py | Python | mit | 18,549 | [
"NEURON"
] | 33ceaddc92bfaca9108776d714b3f771d9323a7857fbf7a9339115a5940804ea |
""" Test for AccountingDB
"""
import pytest
import DIRAC
DIRAC.initialize() # Initialize configuration
from DIRAC import gLogger
from DIRAC.AccountingSystem.DB.AccountingDB import AccountingDB
gLogger.setLevel("DEBUG")
acDB = AccountingDB()
startTime = 1262200000
middleTime = 1262300000
endTime = 1262400000
key... | DIRACGrid/DIRAC | tests/Integration/AccountingSystem/Test_AccountingDB.py | Python | gpl-3.0 | 2,975 | [
"DIRAC"
] | cb43533904ff2db4eaba009bb69c5d3a097d6601cf2e515cca23dd720771d4e9 |
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