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# -*- coding: utf-8 -*-
"""
Output Plugin for Helix MP3 encoder
Copyright (c) 2006-2008 by Nyaochi
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 yo... | rinrinne/cueproc-alternative | src/ce_hmp3.py | Python | gpl-2.0 | 2,706 | [
"VisIt"
] | a22c2156979b0bedaa8e4ad1e94ebd6a8b0cd2a4d83ed20be9bbd138569d66f1 |
# -*- coding: utf-8 -*-
"""
Authors: Gonzalo E. Espinoza-Dávalos
Contact: g.espinoza@un-ihe.org, gespinoza@utexas.edu
Repository: https://github.com/gespinoza/davgis
Module: davgis
Description:
This module is a python wrapper to simplify scripting and automation of common
GIS workflows used in water resources.
"""
fr... | wateraccounting/SEBAL | hants_old/wa_gdal/davgis/functions.py | Python | apache-2.0 | 29,458 | [
"NetCDF"
] | 167dbb923464018cd8e8a8115a11fe21d291f51214b7563cda07acacf33cf893 |
""" ProxyManager is the implementation of the ProxyManagement service
in the DISET framework
"""
import types
import os
from DIRAC import gLogger, S_OK, S_ERROR, gConfig, rootPath
from DIRAC.Core.DISET.RequestHandler import RequestHandler
from DIRAC.Core.Utilities.File import mkDir
from DIRAC.FrameworkSystem.priv... | andresailer/DIRAC | FrameworkSystem/Service/SecurityLoggingHandler.py | Python | gpl-3.0 | 2,090 | [
"DIRAC"
] | 2e5140628ced611804a39968e16e1f106bb7d2376e68901ae28554c8874a133c |
# -*- coding: utf-8 -*-
# vim: set fileencoding=utf-8 :
# vim: set foldmethod=marker commentstring=\ \ #\ %s :
#
# Author: Taishi Matsumura
# Created: 2016-06-29
#
# Copyright (C) 2015 Taishi Matsumura
#
from pylab import *
close('all')
class Neuron(object):
def __init__(self, N, dt):
self.N = N
... | matsu490/RealtimeSimulation | old/realtimeHH.py | Python | mit | 4,791 | [
"NEURON"
] | 1844f4ae16975bf25d6bdd1a1f1eac2964ddc207ff403f79e02d84f7f2c49877 |
trace = lambda x: None # or print
visit = lambda x: print(x, end=', ')
# breadth-first by items: add to end
def sumtree(L): # Breadth-first, explicit queue
tot = 0
items = list(L) # Start with copy of top level
while ite... | simontakite/sysadmin | pythonscripts/learningPython/sumtree2.py | Python | gpl-2.0 | 2,753 | [
"VisIt"
] | e80917415ac66b2c701df46177b753a012b21a1d35bf4724098ed9f47a28a4eb |
# -*- coding: utf-8 -*-
"""rallpacks_cable_hhchannel.py:
A cable with 1000 compartments with HH-type channels in it.
Last modified: Wed May 21, 2014 09:51AM
"""
__author__ = "Dilawar Singh"
__copyright__ = "Copyright 2013, NCBS Bangalore"
__credits__ = ["NCBS Bangalore", "Bhalla Lab"]... | dharmasam9/moose-core | tests/python/Rallpacks/rallpacks_cable_hhchannel.py | Python | gpl-3.0 | 7,771 | [
"MOOSE"
] | d22b26e8be87f4ca6cfdd79f4d866361bdc9df2c72d408246b8c4d76a1c898ea |
import pytest
from pkg_resources import resource_filename
from berny import Berny, geomlib, optimize
from berny.solvers import MopacSolver
@pytest.fixture
def mopac(scope='session'):
return MopacSolver()
def ethanol():
return geomlib.readfile(resource_filename('tests', 'ethanol.xyz')), 5
def aniline():
... | azag0/pyberny | tests/test_optimize.py | Python | mpl-2.0 | 825 | [
"MOPAC"
] | 49baea9e0e531127143fbed9d6a2c3b193182f4bc6255f6532521a83086c43d5 |
# -*- coding: iso-8859-1 -*-
# Copyright (C) 2007-2014 CEA/DEN, EDF R&D
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any la... | FedoraScientific/salome-paravis | src/Plugins/MEDReader/Test/testMEDReader7.py | Python | lgpl-2.1 | 4,157 | [
"ParaView"
] | aa12cdcbb4a96a543122640f280c799f31285e622cf30c2aab20576c585c9337 |
"""
Utility code that provides classes helpful in choosing a suitable TVTK
class. It does this by providing a list of all the classes along with
the option to be able to search for the documentation.
The nice thing about the UI is that it performs some kind of completion
on names typed by the user, plus it allows us... | liulion/mayavi | tvtk/tools/tvtk_doc.py | Python | bsd-3-clause | 13,568 | [
"Mayavi",
"VTK"
] | 3ea29bdb332ae4e0a10979a6e8363b003673b2469f86f1c73ff2b44f4489032b |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | MOA-2011/enigma2-plugin-extensions-openwebif | plugin/controllers/views/web/serviceplayable.py | Python | gpl-2.0 | 5,414 | [
"VisIt"
] | e61ff799385c9bca00f4fd380f89093435b2f94af3a74e553cfbabdbe398e714 |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# vim:fenc=utf-8
# Copyright © xh
# CreateTime: 2016-06-03 13:55:13
# this is the py version of blast
import sys
#import networkx as nx
from math import log10
import os
#from subprocess import getoutput
if sys.version_info.major == 2:
from commands import getoutput
... | Rinoahu/fastclust | bin/find_orth.py | Python | gpl-3.0 | 19,015 | [
"BLAST",
"VisIt"
] | 562bda55b8b7a63f56ab2df8f20827a4054425c8911deeb13247eda1e8090ee4 |
# FermiLib plugin to interface with Psi4
#
# Copyright (C) 2017 ProjectQ-Framework (www.projectq.ch)
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
... | ProjectQ-Framework/FermiLib-Plugin-Psi4 | fermilibpluginpsi4/_version.py | Python | lgpl-3.0 | 853 | [
"Psi4"
] | 44bb89f96f9a66b2ebe1f0f4ed2431bce8c3937d10eafc751db2ad0f1af8d055 |
# Encoding utf-8
# Written for Python 3.6
import sys
import pymatgen.io.nwchem as nwchem
"""
Quick script to study the total energy change of the system during an
optimization.
"""
if sys.argv[1]:
filename = sys.argv[1]
print('\nAnalyzing energies in ' + filename + '...\n')
else:
OSError('No target output... | mbercx/cage | cage/scripts/energyAnalysis.py | Python | mit | 513 | [
"NWChem",
"pymatgen"
] | 9f8bf2b620cebe96f61cda88dbc6e3f64691db49934325290466efb4d3c196b8 |
from django import forms
from edc_constants.constants import YES, NO, NOT_APPLICABLE
from .base_infant_model_form import BaseInfantModelForm
from ..models import InfantFeeding
class InfantFeedingForm(BaseInfantModelForm):
def clean(self):
cleaned_data = super(InfantFeedingForm, self).clean()
se... | TshepangRas/tshilo-dikotla | td_infant/forms/infant_feeding_form.py | Python | gpl-2.0 | 6,922 | [
"VisIt"
] | 77429c13b7252c9eefacb4a214bf9b69d11e08a90e7590670e44f2a14d088dac |
#!/usr/bin/env python3
import sys
import hashlib
import re
import math
from itertools import count, islice, starmap
import itertools
import wave
import struct
import argparse
import re
# Identitione
# Definitions:
# tone: collection of sounds that make an identifying audio bite i.e. an identitone
# sound: collection ... | brainwater/identitone | identitone.py | Python | gpl-2.0 | 9,561 | [
"Galaxy"
] | 3e6bd45e9370313aef0b50d85665739bade37ccb065d88cc2e1f49950f65897d |
# Copyright 2018, The TensorFlow Federated 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 applicable law o... | tensorflow/federated | tensorflow_federated/tools/python_package/setup.py | Python | apache-2.0 | 5,411 | [
"VisIt"
] | ebb043d3b5d8be98ad6dbc601d881bfea02ef0e26452d5d555240f401b6e6dbf |
from rllab.envs.base import Env
from rllab.envs.base import Step
from rllab.spaces import Box
import numpy as np
class MultiMod2DEnv(Env):
"""
This is a single time-step MDP where the action taken corresponds to the next state (in a 2D plane).
The reward has a multi-modal gaussian shape, with the mode mea... | florensacc/snn4hrl | envs/point/multiMod2D_env.py | Python | mit | 2,207 | [
"Gaussian"
] | 73b5b7876a82d578e3b102c6cd85009d9d37ce23981a1d3b60d3ff6ebc272901 |
# Copyright 2013 Devsim 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, s... | devsim/devsim | examples/mobility/gmsh_mos2d_kla.py | Python | apache-2.0 | 5,542 | [
"VTK"
] | c841a41d86ecac390fe99d49e7bdcea7feecc9ec2f2fad511c1c9becf8544c30 |
import sys
import numpy
import pychemia
if pychemia.HAS_MAYAVI:
from mayavi.mlab import quiver
if not pychemia.HAS_MAYAVI:
sys.exit(1)
def test_quiver3d():
x, y, z = numpy.mgrid[-2:3, -2:3, -2:3]
r = numpy.sqrt(x ** 2 + y ** 2 + z ** 4)
u = y * numpy.sin(r) / (r + 0.001)
... | MaterialsDiscovery/PyChemia | tests/test_code_vasp_03.py | Python | mit | 486 | [
"Mayavi"
] | 8cdc0ac81f0ce9d1c4095686691ee4e51fe4959e6c57ccb201648d43c644d24a |
#!/usr/bin/python
# Copyright 2003-2010 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
from __future__ import print_function
__author__ = "Thomas de Grenier de Latour (tgl), " + \
"modular re-write by: Brian Dolbec (dol-sen)"
__email__ = "degrenier@easyconnect.fr, " + \
"bri... | dol-sen/gentoolkit | pym/gentoolkit/eclean/cli.py | Python | gpl-2.0 | 18,377 | [
"Brian"
] | 3e097e164ca84423ab3413c796bb237b26d996a9f5098c71ed0343dce0a56d39 |
"""Classes to perform GridSearch on the custom kernels defined in
:mod:`kcat.kernels.functions`.
Their interface is very similar to scikit-learn's
`GridSearchCV <http://scikit-learn.org/stable/modules/generated/sklearn\
.grid_search.GridSearchCV.html#sklearn.grid_search.GridSearchCV>`_,
and the same parameters should ... | Alkxzv/categorical-kernels | kcat/kernels/search.py | Python | mit | 8,564 | [
"Elk"
] | 0ce1bf026f1f97a1adf136384bf97ed23e865a2e801e932d80db349ce22bb2b6 |
"""
Example of plotting a 3D vector field
There are still problems here with getting the angles exactly right....
"""
# set up some data to plot
from Numeric import *
dim = 10
# initialise the positions of the vectors
x = zeros((dim,dim), typecode=Float)
y = zeros((dim,dim), typecode=Float)
z = zeros((dim,dim), ty... | paultcochrane/pyvisi | examples/renderers/povray/arrowPlot3D.py | Python | gpl-2.0 | 4,475 | [
"VTK"
] | f295a761d13661a6177e8c2e126d9c98026014469b60b3d44cefc28397041b33 |
#!/usr/bin/python3
import gi
gi.require_version('Cvc', '1.0')
gi.require_version('Gtk', '3.0')
from gi.repository import Gtk, Cvc, GdkPixbuf, Gio
from SettingsWidgets import SidePage, GSettingsSoundFileChooser
from xapp.GSettingsWidgets import *
CINNAMON_SOUNDS = "org.cinnamon.sounds"
CINNAMON_DESKTOP_SOUNDS = "org.c... | glls/Cinnamon | files/usr/share/cinnamon/cinnamon-settings/modules/cs_sound.py | Python | gpl-2.0 | 32,421 | [
"ORCA"
] | 388fabf8b0ce13f4362571d7223701ac6e9fe2550328273e517059440b6f6357 |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
"""
Array of data parsers for bioinformatics file formats, such as: GFF3, BED, SAM/BAM, VCF, PSL, AGP, FASTA/FASTQ, BLAST, etc.
"""
from jcvi.apps.base import dmain
if __name__ == "__main__":
dmain(__file__)
| tanghaibao/jcvi | jcvi/formats/__main__.py | Python | bsd-2-clause | 262 | [
"BLAST"
] | aa010f3240c71b0bf121a2fec26f4d981c7fbe7b7a79471d9013e576d70ab043 |
from plotly.basedatatypes import BaseTraceType as _BaseTraceType
import copy as _copy
class Densitymapbox(_BaseTraceType):
# class properties
# --------------------
_parent_path_str = ""
_path_str = "densitymapbox"
_valid_props = {
"autocolorscale",
"below",
"coloraxis",
... | plotly/python-api | packages/python/plotly/plotly/graph_objs/_densitymapbox.py | Python | mit | 74,226 | [
"Gaussian"
] | 67cb174749fe3b3d36a62ad558489d11d21e5ce85da752c450034f81648fc0b9 |
import pandas as pd
import itertools as it
import seaborn as sns
import numpy as np
from pymea import matlab_compatibility as mc
from matplotlib import pyplot as plt
from matplotlib import mlab as mlab
import random
from datetime import datetime, timedelta
from pymea import supplement_to_plotting as psupp
import math
... | ktyssowski/mea_analysis | pymea/plotting.py | Python | mit | 45,754 | [
"NEURON"
] | 1e30a1401156711bddb52cebdf988656e5c45e92bf4f5bee006748998e6e2488 |
# coding=utf-8
import ast
class RewriteAddToSub(ast.NodeTransformer):
def visit_Add(self, node):
node = ast.Sub()
return node
node = ast.parse('2 + 6', mode='eval')
node = RewriteAddToSub().visit(node)
print eval(compile(node, '<string>', 'eval'))
| dongweiming/web_develop | chapter15/section2/ast_transformer.py | Python | gpl-3.0 | 273 | [
"VisIt"
] | f3bc8ab077a95508a87db271ab79ba4cd86107b89faa11439a2417c8f31b79ef |
# Copyright 2018 The TensorFlow Probability 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 applicable law o... | tensorflow/probability | tensorflow_probability/python/vi/mutual_information_test.py | Python | apache-2.0 | 9,306 | [
"Gaussian"
] | 606a2d1cc6fe6ede71d23e10cc05e756e07fb971c5ba76b434ed2a1beb3dbb68 |
# Copyright 2008 Brian Boyer, Ryan Mark, Angela Nitzke, Joshua Pollock,
# Stuart Tiffen, Kayla Webley and the Medill School of Journalism, Northwestern
# University.
#
# This file is part of Crunchberry Pie.
#
# Crunchberry Pie is free software: you can redistribute it and/or modify
# it under the terms of the GNU Gene... | brianboyer/newsmixer | pie/authentication/templatetags/facebook.py | Python | gpl-3.0 | 4,610 | [
"Brian"
] | 90c4ee25d169fb1a5296c68e052858d23c9609bfefea92213d3093d952b1a307 |
'''
AST Rewrite Pass to join Else nodes
'''
from ..util.dispatch import method_store, multimethod
from .. import node
class JoinElse(object):
_store = method_store()
@multimethod(_store)
def visit(self, n):
pass
@visit.d(node.Block)
def _(self, n):
self.scan(n.exprs)
@visit... | dacjames/mara-lang | bootstrap/mara/passes/join_else.py | Python | mit | 946 | [
"VisIt"
] | fa832770e30fc01777d3dfc40de78d92e59a0bcaa059f9f67f7e7559cc9e501c |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# PyNNLess -- Yet Another PyNN Abstraction Layer
# Copyright (C) 2015 Andreas Stöckel
#
# 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, e... | hbp-sanncs/pynnless | examples/multiple_neurons.py | Python | gpl-3.0 | 1,961 | [
"NEURON"
] | 547cdd0afafdff26448f58b7fe6be15ed636ca55bb473e36e16c5fcc180a7d45 |
# Imports
import os
import h5py
import numpy as np
from collections import Counter, defaultdict, namedtuple
from gatktool import tool
# Keras Imports
import keras.backend as K
# Package Imports
from . import defines
from . import tensor_maps
READ_ELEMENTS = 8
Read = namedtuple("Read", "seq qual cigar reverse mate_r... | ksthesis/gatk | src/main/python/org/broadinstitute/hellbender/vqsr_cnn/vqsr_cnn/inference.py | Python | bsd-3-clause | 17,194 | [
"pysam"
] | dca083ec3f34541ec9da9c57470b4c3d268856c99a60997804a47901a778dd28 |
# -*- coding: utf-8 -*-
'''
Production Configurations
- Use djangosecure
- Use Amazon's S3 for storing static files and uploaded media
- Use sendgird to sendemails
- Use MEMCACHIER on Heroku
'''
from configurations import values
# See: http://django-storages.readthedocs.org/en/latest/backends/amazon-S3.html#settings
... | mikemitr/test-for-brian-criswell | test-for-brian-criswell/config/production.py | Python | bsd-3-clause | 4,374 | [
"Brian"
] | 97332cadbf2656686c69dd0066ac42d8f46785bd36bb137a20a3d4b8b972c113 |
#!/usr/bin/python
# -*- coding: UTF-8 -*-
from __future__ import unicode_literals # Tenho dúvidas se necessário.
#
#title : frases_curtas.py
#description : This script will make scraping the web
# : for use in social networks
#author : @Py3in
#date start : 20151113
#last up... | py3in/social_frases | social_frases.py | Python | gpl-2.0 | 2,867 | [
"VisIt"
] | 2d71613d5ddf0db4070ec13775873b4926de2fb3d44c2aa16265499dbd0723ba |
"""
===========================================
Sparse coding with a precomputed dictionary
===========================================
Transform a signal as a sparse combination of Ricker wavelets. This example
visually compares different sparse coding methods using the
:class:`sklearn.decomposition.SparseCoder` esti... | marcocaccin/scikit-learn | examples/decomposition/plot_sparse_coding.py | Python | bsd-3-clause | 3,876 | [
"Gaussian"
] | 41678f73ba12dd7e8d4a5a30d8f663b8695ba861f2b983fff4b388790d36ea7b |
"""
FeedFinder
==============
Tries to find feeds for
a given URL.
This is essentially a rewrite
of feedfinder.py,
originally by Mark Pilgrim
and Aaron Swartz.
Credits from the original:
Abe Fettig for a patch to sort Syndic8 feeds by popularity
Also Jason Diamond, Brian Lalor for bug reporting and patches
Original... | jakemadison/FeedEater | feedeater/controller/feedfinder_new.py | Python | agpl-3.0 | 6,640 | [
"Brian"
] | a589c0fed2ddda77c98ddab88b747dede34b4019f69432441899df45f8c340c2 |
# encoding: utf-8
# Wellcome Trust Sanger Institute and Imperial College London
# Copyright (C) 2020 Wellcome Trust Sanger Institute and Imperial College London
#
# 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 Sof... | sanger-pathogens/gubbins | python/scripts/extract_clade.py | Python | gpl-2.0 | 4,276 | [
"Biopython"
] | de344b81cbedef3896d28c8d3a66de29021bdc0caa78de05cc648673ce109173 |
# 4455770 Dennis Verheijden KI
# 4474139 Remco van der Heijden KI
# multiAgents.py
# --------------
# Licensing Information: Please do not distribute or publish solutions to this
# project. You are free to use and extend these projects for educational
# purposes. The Pacman AI projects were develop... | ScaleRunner/PacmanAI | 6 - Contest/competitionAgents.py | Python | mit | 13,362 | [
"VisIt"
] | 9258c7a7e98655ac5727278e550a36ada615bae813027f508c9b8a14580377a5 |
# -*- 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... | Fedik/gramps | gramps/plugins/webreport/source.py | Python | gpl-2.0 | 13,250 | [
"Brian"
] | f5f0772e2ee02bb3fa03e9b46fd92f60d5dce536ce0b30a2b9ee114c365ea681 |
def read_aims(filename):
"""Import FHI-aims geometry type files.
Reads unitcell, atom positions and constraints from
a geometry.in file.
"""
from ase import Atoms
from ase.constraints import FixAtoms, FixCartesian
import numpy as np
atoms = Atoms()
fd = open(filename, 'r')
li... | conwayje/ase-python | ase/io/aims.py | Python | gpl-2.0 | 10,341 | [
"ASE",
"FHI-aims"
] | 9c45d5c200057153bd83b9d6072c20d09aec8325f4931d2c2ee6f2be9148dee3 |
# -*- coding: utf-8 -*-
# flake8: noqa: E741
import gzip
import re
import subprocess
import time
import os
import shutil
from datetime import datetime, timedelta, timezone
from io import BytesIO, StringIO
from pathlib import Path
from unittest import mock
from flaky import flaky
from flask import session, escape, url_... | freedomofpress/securedrop | securedrop/tests/test_source.py | Python | agpl-3.0 | 35,531 | [
"VisIt"
] | e76f391ca20a4c564a35d708678fef915e83f3adb9a6868f06839a6f328cd4ac |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
from pyscf import gto
from pyscf import scf
'''
Density fitting method by decorating the scf object with scf.density_fit function.
There is no flag to control the program to do density fitting for 2-electron
integration. The way to call density f... | gkc1000/pyscf | examples/scf/20-density_fitting.py | Python | apache-2.0 | 1,784 | [
"Gaussian",
"PySCF"
] | 807097fd11fc17b15170f246cf66ae4c34cd18aa73c2e68c7ed8856ad0b60c15 |
# Copyright (C) 2013-2015 MetaMorph Software, Inc
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this data, including any software or models in source or binary
# form, as well as any drawings, specifications, and documentation
# (collectively "the Data"), to deal in the Data ... | pombredanne/metamorphosys-desktop | metamorphosys/META/src/Python27Packages/PCC/PCC/estimate_complexity.py | Python | mit | 5,167 | [
"Gaussian"
] | e71c7bfa4739c6694ccfbf137568ca81dab2e59269acc30da828eb6449b87427 |
# Auto generated configuration file
# using:
# Revision: 1.19
# Source: /local/reps/CMSSW/CMSSW/Configuration/Applications/python/ConfigBuilder.py,v
# with command line options: TTbar_Tauola_13TeV_cfi.py --conditions auto:startup -n 1000 --eventcontent FEVTDEBUG --relval 9000,100 -s GEN,SIM --datatier GEN-SIM --no_e... | rovere/productions | TTbar_Tauola_13TeV_cfi_py_GEN_SIM.py | Python | gpl-3.0 | 5,681 | [
"Gaussian"
] | 63b32047610beec05c2382795f7b25d1fafedba0e4d23a888c61d3ab021e7c08 |
"""
# Copyright (C) 2007 Rob King (rob@e-mu.org)
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# ... | derivativeinc/liveapi | src/LiveTelnet/LiveTelnet.py | Python | lgpl-2.1 | 8,633 | [
"VisIt"
] | 55cb6bfe5814104bc3178e3eaafd51c9e746770f20afb27061763a15875d8b1c |
# $Id: ShowFeats.py 537 2007-08-20 14:54:35Z landrgr1 $
#
# Created by Greg Landrum Aug 2006
#
#
_version = "0.3.2"
_usage = """
ShowFeats [optional args] <filenames>
if "-" is provided as a filename, data will be read from stdin (the console)
"""
_welcomeMessage = "This is ShowFeats version %s" % (_version)
... | bp-kelley/rdkit | rdkit/Chem/Features/ShowFeats.py | Python | bsd-3-clause | 11,904 | [
"PyMOL",
"RDKit"
] | 363ea4bd1dd97bad1d6cbcd41f95ddefb19f10c1e038f34f4fd8c6c39ba8321a |
from werkzeug.wsgi import ClosingIterator
def all_casings(input_string):
"""
Permute all casings of a given string.
A pretty algorithm, via @Amber
http://stackoverflow.com/questions/6792803/finding-all-possible-case-permutations-in-python
"""
if not input_string:
yield ""
else:
... | anush0247/Zappa | zappa/middleware.py | Python | mit | 2,639 | [
"Amber"
] | 0a47ceb214983c43914d5d0805f4de06e54a01ea86ad4e010f0b3391c9b7ede9 |
import vigra
from vigra import graphs
from vigra import numpy
import pylab
# parameter
filepath = '12003.jpg' # input image path
sigmaGradMag = 5.0 # sigma Gaussian gradient
superpixelDiameter = 10 # super-pixel size
slicWeight = 10.0 # SLIC color - spatial weight
beta = 0.5 # node vs edge wei... | dstoe/vigra | vigranumpy/examples/graph_agglomerative_clustering.py | Python | mit | 2,298 | [
"Gaussian"
] | c4070d1ab1d222cea54d3c43afae8007fe970dbd58d6f85259a021f9984f39d7 |
# Copyright (C) 2014
# Pierre de Buyl
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it ... | MrTheodor/espressopp | src/bc/SlabBC.py | Python | gpl-3.0 | 2,456 | [
"ESPResSo"
] | b6cc0e1c0f106f4ed6a7cb7b5c439759045fef25edcb62e5e187fe8a24c00c33 |
import logging
import numpy as np
import nibabel as nib
import scipy.ndimage as ndimage
from six import string_types
from .check import check_img
from nilearn._utils import check_niimg
from nilearn.image.image import new_img_like, _fast_smooth_array
log ... | Neurita/boyle | boyle/nifti/smooth.py | Python | bsd-3-clause | 9,313 | [
"Gaussian"
] | ad0e8bb4ffc002b836744f814e299580fae1d1ba99af0a91f2d3aea12ea51bd5 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkExtractEdges(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.v... | nagyistoce/devide | modules/vtk_basic/vtkExtractEdges.py | Python | bsd-3-clause | 484 | [
"VTK"
] | 1a9a4783dd0ad97c0ff2fcf6a80672c14cdb4133a831a0d0c56624f63684110a |
from galaxy.util import bunch
import logging
log = logging.getLogger( __name__ )
#class Bunch( dict ):
# """
# Bunch based on a dict
# """
# def __getattr__( self, key ):
# if key not in self:
# raise AttributeError(key)
# return self[key]
#
# def __setattr__( self, key, value ... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/web/framework/formbuilder.py | Python | gpl-3.0 | 3,315 | [
"Galaxy"
] | b4b850784de190818b3fc5c11d82f69ca1cab76445108e29109fa1fb8ea818f1 |
"""Constants used by AnsibleLint."""
import os.path
import sys
# mypy/pylint idiom for py36-py38 compatibility
# https://github.com/python/typeshed/issues/3500#issuecomment-560958608
if sys.version_info >= (3, 8):
from typing import Literal # pylint: disable=no-name-in-module
else:
from typing_extensions impo... | ansible/ansible-lint | src/ansiblelint/constants.py | Python | mit | 3,254 | [
"Galaxy"
] | 37551a5c69c9697831fb8f14c9c4fc8345962eaac692a2b4273d50529272af98 |
# $Id$
#
# Copyright (C) 2006 Greg Landrum
#
# @@ 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.
#
from rdkit.Chem import ChemicalFeatures
class FeatMap... | rvianello/rdkit | rdkit/Chem/FeatMaps/FeatMapPoint.py | Python | bsd-3-clause | 3,283 | [
"RDKit"
] | 6f429f09c80f37e862bb7b0cbc7d6eb65e1f68897a50e2a1d27bea4648ffe121 |
import requests
import h2o
import h2o_test_utils
from h2o_test_utils import ModelSpec
from h2o_test_utils import GridSpec
def build_and_test(a_node, pp, datasets, algos, algo_additional_default_params):
####################################################################################################
# Bui... | nilbody/h2o-3 | py/rest_tests/test_models.py | Python | apache-2.0 | 13,539 | [
"Gaussian"
] | fda95b98b26b183c825c2ae107836a54e792ac7d7af8b1d9394ad9e44fe497a2 |
"""
Spatial transformer layer, compatible with keras APIs
"""
import keras.backend as K
import numpy as np
from keras.layers import Layer
from keras.models import Model
def standardize_coords(coords, maxes, dim):
"""
standardize_coords - standardizes the coordinates in a mesh grid between -1 and 1 for each
... | taimir/keras-layers | klayers/transform/spatial_transform.py | Python | mit | 20,259 | [
"Gaussian"
] | 01266de11955f38dddae0172969a4021a5e2f82034dcb9c23ecf4c6b4e5eb873 |
"""
Octave (and Matlab) code printer
The `OctaveCodePrinter` converts SymPy expressions into Octave expressions.
It uses a subset of the Octave language for Matlab compatibility.
A complete code generator, which uses `octave_code` extensively, can be found
in `sympy.utilities.codegen`. The `codegen` module can be us... | NikNitro/Python-iBeacon-Scan | sympy/printing/octave.py | Python | gpl-3.0 | 23,630 | [
"DIRAC"
] | 1d6a9a560f0b3b1cdfe357425702141c850cab108f3c430537db9f0bcaa17102 |
# This module provides classes that represent graphics objects to be
# output to VMD. This module is as compatible as possible with module
# VRML. Important differences:
# - No general polygon objects.
# - Only the 'diffuse color' attribute of materials is used for rendering.
# Warning: loading cubes into VMD is very s... | OS2World/DEV-PYTHON-UTIL-ScientificPython | src/Lib/site-packages/Scientific/Visualization/VMD.py | Python | isc | 16,889 | [
"VMD"
] | 63eec6b90613e4ccf849ebc70be8219758781310316b5e8036321ce51f89e808 |
from __future__ import print_function
from __future__ import unicode_literals
from __future__ import division
import random
from datetime import timedelta
from dateutil.relativedelta import relativedelta
from collections import namedtuple
import numpy as np
import pandas as pd
from faker import Faker
from tqdm impor... | madgik/exareme | Exareme-Docker/src/mip-algorithms/KAPLAN_MEIER/generate_fake_cohort.py | Python | mit | 2,865 | [
"VisIt"
] | d3e46bd428031d7ed049d547909535655f403c4dc83c7ec739da09a8e1b98eee |
try:
from paraview.vtk import vtkFiltersVerdict
from paraview.vtk import vtkFiltersGeneral
from paraview.vtk import vtkCommonTransforms
from paraview.vtk import vtkFiltersGeometry
from paraview.vtk import vtkFiltersExtraction
except:
import vtk as vtkFiltersVerdict
import vtk as vtk... | aurmarsan/pyturbo | extractions.py | Python | mit | 7,599 | [
"ParaView",
"VTK"
] | 84b38bac4441c7d5810869af17bcce4812e3d9a01594b58e8715d66af490f9a7 |
from os.path import basename
from os.path import join
from os.path import dirname
from os import sep
from ..util import PathHelper
COMMAND_VERSION_FILENAME = "COMMAND_VERSION"
class ClientJobDescription(object):
""" A description of how client views job - command_line, inputs, etc..
**Parameters**
com... | jmchilton/pulsar | pulsar/client/staging/__init__.py | Python | apache-2.0 | 6,153 | [
"Galaxy"
] | 50850db7c04d0ce12191234fe5a6f441aeb4064b9932f83c22c2726a3f9a9059 |
#
# @file TestModifierSpeciesReference.py
# @brief ModifierSpeciesReference unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Ben Bornstein
#
# $Id$
# $HeadURL$
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generat... | alexholehouse/SBMLIntegrator | libsbml-5.0.0/src/bindings/python/test/sbml/TestModifierSpeciesReference.py | Python | gpl-3.0 | 3,969 | [
"VisIt"
] | ec0d2fdd648f0dd769f3c1a697042ce081ffa995e5646e3969addf33a1caee91 |
# Copyright (c) 2012 OpenStack Foundation
# 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 ... | NeCTAR-RC/nova | nova/tests/unit/compute/test_resource_tracker.py | Python | apache-2.0 | 59,930 | [
"exciting"
] | 3bca63903929ffa36bcfd9e00a7cb0fa3ab6bb7e694110256ae6abc8ec44680b |
""" Priority corrector for the group and in-group shares
"""
__RCSID__ = "$Id$"
from DIRAC.Core.Utilities import ObjectLoader
from DIRAC.ConfigurationSystem.Client.Helpers.Operations import Operations
from DIRAC.WorkloadManagementSystem.private.correctors.BaseCorrector import BaseCorrector
from DIRAC import gLogger,... | andresailer/DIRAC | WorkloadManagementSystem/private/SharesCorrector.py | Python | gpl-3.0 | 4,590 | [
"DIRAC"
] | 9337ee987db7c17a477f12f3c3b1ed4b5bb34fbf73ab62b40bc370e98f723c86 |
"""
Generate samples of synthetic data sets.
"""
# Authors: B. Thirion, G. Varoquaux, A. Gramfort, V. Michel, O. Grisel,
# G. Louppe, J. Nothman
# License: BSD 3 clause
import numbers
import array
import numpy as np
from scipy import linalg
import scipy.sparse as sp
from ..preprocessing import MultiLabelBin... | rishikksh20/scikit-learn | sklearn/datasets/samples_generator.py | Python | bsd-3-clause | 56,558 | [
"Gaussian"
] | d92bb995f62e25cfec9b5ec3edee0b78359067787bcba92811090235bf784e3b |
# Copyright 2013 anthony cantor
# This file is part of pyc.
#
# pyc 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.
#
# pyc is distr... | cantora/pyc | pyc_ir.py | Python | gpl-3.0 | 13,196 | [
"VisIt"
] | ec8593d653e3915b1d98fcb49b2d84487603089ddd79a790d4038c0986263dec |
#!/usr/bin/env python
import randopt as ro
import time
def loss(x):
# time.sleep(1)
return x**2
if __name__ == '__main__':
e = ro.Experiment('simple_example', {
'alpha': ro.Gaussian(mean=0.0, std=1.0, dtype='float'),
})
# Sampling parameters
for i in range(100):
e.sam... | seba-1511/randopt | examples/simple.py | Python | apache-2.0 | 690 | [
"Gaussian"
] | 7958d5006bd1e76c743b1f623c7ffae06d6029b3e31e55920f4a6f4f06c54789 |
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from scipy.optimize import curve_fit
from scipy import stats
from pandas.tools.plotting import scatter_matrix
from scipy.optimize import curve_fit
from matplotlib.colors import LogNorm
df = pd.read_csv('/Users/tylern/Homework/PHYS723/project/LHC/CM... | tylern4/tylern4.github.io | OpenData/Upsilon/Upsilon.py | Python | mit | 10,224 | [
"Gaussian"
] | beef99a835e4d4d261bf0a850d32e899263e48fc4ede2d341165ddde9fb0e69c |
#!/usr/bin/env python
import sys
def convert(filename):
lines = open(filename).readlines()
t1 = ''.join(lines)
first = True
for i in range(len(lines)):
line = lines[i]
if line.startswith('from ASE'):
if first:
lines[i] = 'from ase import *\n'
... | freephys/python_ase | tools/ASE2ase.py | Python | gpl-3.0 | 2,843 | [
"ASE"
] | 890a5825faa7974bf1f8937f31db3c76fa01f446a1237bfeac2c19263a10d45f |
"""
Copyright (C) 2015, Jaguar Land Rover
This program is licensed under the terms and conditions of the
Mozilla Public License, version 2.0. The full text of the
Mozilla Public License is at https://www.mozilla.org/MPL/2.0/
Maintainer: Rudolf Streif (rstreif@jaguarlandrover.com)
Author: Anson Fan (afan1@jagualand... | afan1/rvi_backend | web/dynamicagents/models.py | Python | mpl-2.0 | 8,875 | [
"Jaguar"
] | 0c622175db833de4deb0fa0935f384a534a23baf99180a6291bd45831bbbc1dc |
import sys
tests = [("testExecs/main.exe", "", {}), ]
longTests = []
if __name__ == '__main__':
import sys
from rdkit import TestRunner
failed, tests = TestRunner.RunScript('test_list.py', 0, 1)
sys.exit(len(failed))
| rvianello/rdkit | Code/Numerics/EigenSolvers/test_list.py | Python | bsd-3-clause | 228 | [
"RDKit"
] | 9758b5338bd10e2c197d4e88056bee3af56a96f4570e9206e2ff642bad0c4cbe |
# -*- 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
urlpatterns = [
url(r'^$', TemplateView.as_view(templ... | Ibtiss4m/sendprismApp | config/urls.py | Python | bsd-3-clause | 1,230 | [
"VisIt"
] | 3af7313588b36eeb3543ccb8d6b45a2b4411d7d0d3139fd8335e99e62257b5c1 |
"""
Thesaurus-API
~~~~~~~~~~~~~
An api for thesaurus.com. See the README for instructions.
A pythonic poem authored by Robert.
Inspiration and help from others (see credits).
If there's anything in here you don't understand or want me to change, just
make an issue or send me an email at robert <at> robertism <dot> c... | Manwholikespie/thesaurus-api | thesaurus/thesaurus.py | Python | mit | 19,571 | [
"VisIt"
] | 59d5c47ec6cda16a765e33ee38ec0f1940997f0b45605df305fc75e78800b529 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkPointSetAlgorithm(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | nagyistoce/devide | modules/vtk_basic/vtkPointSetAlgorithm.py | Python | bsd-3-clause | 495 | [
"VTK"
] | 833aa93a2d2e40b8bf6ccc287f41b39bf5961d5cd8a99083d64168beec498f92 |
# -*- coding: utf-8 -*-
"""Tests for gam.AdditiveModel and GAM with Polynomials compared to OLS and GLM
Created on Sat Nov 05 14:16:07 2011
Author: Josef Perktold
License: BSD
Notes
-----
TODO: TestGAMGamma: has test failure (GLM looks good),
adding log-link didn't help
resolved: gamma doesn't fai... | hlin117/statsmodels | statsmodels/sandbox/tests/test_gam.py | Python | bsd-3-clause | 9,820 | [
"Gaussian"
] | 755a019fa7700353a5f367cd3404dc762b17773c7ddecc3fa778bc924ccf0ab8 |
# The MIT License (MIT)
# Copyright (c) 2016, 2017 by the ESA CCI Toolbox development team and contributors
#
# 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 wi... | CCI-Tools/cate-core | cate/core/cdm.py | Python | mit | 16,383 | [
"NetCDF"
] | 40198511574ff1f232d5af53f7ecdd8c3ab716ecb3f3c15418e2bce01dd9ac0a |
"""
@name: Modules/Computer/Communication/communication.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2017-2019 by D. Brian Kimmel
@note: Created on Jan 9, 2017
@license: MIT License
@summary:
"""
__updated__ = '2019-10-11'
# Import system type stuff
# Import PyMh fi... | DBrianKimmel/PyHouse | Project/src/Modules/Computer/Communication/communication.py | Python | mit | 1,191 | [
"Brian"
] | 855564abde18a72aad5bb6bceab810af0159e05620d76cc0dedf3442a8ee1cee |
#!/usr/bin/env python
# encoding: utf-8
from logs import *
logger = logging.getLogger(__name__)
from common import *
from game_art import Art
class __CentralLoggers(object):
"""dumping ground for messy loggers
from central"""
def __init__(self):
pass
def logger_attr_set(self,attr,val):
... | flipdazed/SoftwareDevelopment | actors.py | Python | gpl-3.0 | 38,455 | [
"VisIt"
] | f5fbb160c7f38ba85244fbd65cc9bf28f0e487d550a44ae86fc5a5846e5c1f6e |
#!/usr/bin/env python
import numpy as np
import scipy.interpolate as spi
import scipy.optimize as spo
import bulk_run_phonons
import fit_beta_V
import process_PVT_castep
import bm3_eos as eos
import earthref
import ionic_model
earth_model = earthref.EarthModel(earthref.ak135)
# Define constants
eps0 = 8.854187817E... | andreww/isofrac | alpha_geotherm_6.py | Python | bsd-3-clause | 12,556 | [
"CASTEP"
] | 19220fe397c9883d322dac70b298420574923f11e9a04b502e15dab331d4446f |
# textrender.py
# module to render text, tries to understand a basic LateX-like syntax
# Copyright (C) 2003 Jeremy S. Sanders
# Email: Jeremy Sanders <jeremy@jeremysanders.net>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as... | OpenReliability/OpenReliability | veusz/utils/textrender.py | Python | gpl-2.0 | 48,574 | [
"Bowtie"
] | c8411a57c3dd75e42997913d67167a969727ad74d424b8586fb0dadb868a0a15 |
#!/usr/bin/env python
from __future__ import division
__author__ = "Marek Rudnicki"
import numpy as np
from neuron import h
import waves as wv
def record_voltages(secs):
vecs = []
for sec in secs:
vec = h.Vector()
vec.record(sec(0.5)._ref_v)
vecs.append(vec)
return vecs
def plot... | timtammittee/thorns | thorns/nrn.py | Python | gpl-3.0 | 1,042 | [
"NEURON"
] | 436052c78bdc7f84d350de92bf1e727e3c456b3a7bf433a5a6ec9cbb0795b156 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Licensed to Cloudera, Inc. under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. Cloudera, Inc. licenses this file
# to you under the Apache License, Version 2.0 (... | yongshengwang/builthue | apps/useradmin/src/useradmin/test_ldap_deprecated.py | Python | apache-2.0 | 31,025 | [
"MOE"
] | 62f6073a33768991995fa59be9a97a52a21a2cd408f772e917922dc76bda9374 |
#
# @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 | psi4/driver/procrouting/mcscf/augmented_hessian.py | Python | lgpl-3.0 | 5,801 | [
"Psi4"
] | ffcd6da7f11f012c609c6684836f1363755f6ef4ec98fdfb06c350df8e6383b6 |
"""
Testing for the forest module (sklearn.ensemble.forest).
"""
# Authors: Gilles Louppe,
# Brian Holt,
# Andreas Mueller,
# Arnaud Joly
# License: BSD 3 clause
import pickle
from collections import defaultdict
from itertools import product
import numpy as np
from sklearn.utils.testing im... | eickenberg/scikit-learn | sklearn/ensemble/tests/test_forest.py | Python | bsd-3-clause | 22,872 | [
"Brian"
] | 02ce38d1f4b2c8fb0c2288832052f977c25a3a8e75eaa5cd37b2d170e888b1f5 |
#!/usr/bin/env python
import unittest
import warnings
import numpy as np
from pymatgen.core.lattice import Lattice
from pymatgen.core.operations import SymmOp
from pymatgen.symmetry.groups import PointGroup, SpaceGroup, _get_symm_data
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Virt... | davidwaroquiers/pymatgen | pymatgen/symmetry/tests/test_groups.py | Python | mit | 7,233 | [
"pymatgen"
] | 45676f89281262a6655f5d9bf58249e060855f4b41c68292c5c96cb09b05f021 |
# -*- coding: utf-8 -*-
"""
Unit tests for instructor.api methods.
"""
import datetime
import functools
import io
import json
import random
import shutil
import tempfile
import ddt
import pytz
from django.conf import settings
from django.contrib.auth.models import User
from django.core import mail
from django.core.fil... | pepeportela/edx-platform | lms/djangoapps/instructor/tests/test_api.py | Python | agpl-3.0 | 227,176 | [
"VisIt"
] | a05ce79b0837199f6295b5e9aeca8e75b2396f7dbfda91b1db9e37af567acd05 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# (c) 2016, techbizdev <techbizdev@paloaltonetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version':... | alxgu/ansible | lib/ansible/modules/network/panos/_panos_security_rule.py | Python | gpl-3.0 | 20,230 | [
"Galaxy"
] | 5a93d6cde5714403e8cc0c031e7b66f0139cb13638935fff47a08afd801b10ba |
#!/usr/bin/env python
"""
Get informations for a given production
Example:
$ dirac-prod-get 381
"""
import DIRAC
from DIRAC.Core.Base.Script import Script
@Script()
def main():
# Registering arguments will automatically add their description to the help menu
Script.registerArgument("prodID: Production ID")... | DIRACGrid/DIRAC | src/DIRAC/ProductionSystem/scripts/dirac_prod_get.py | Python | gpl-3.0 | 1,488 | [
"DIRAC"
] | 1ff02858af1b9cceb1d05bb0e546200df4b5bb565d0c2d43e918775378de4936 |
# Copyright (c) Charl P. Botha, TU Delft
# All rights reserved.
# See COPYRIGHT for details.
# TODO:
# * this module is not sensitive to changes in its inputs... it should
# register observers and run _createPipelines if/when they change.
from imageStackRDR import imageStackClass
from module_base import ModuleBase
... | chrisidefix/devide | modules/insight/transform2D.py | Python | bsd-3-clause | 8,857 | [
"VTK"
] | e16a73014adb524dd40284243a2e8b4051a46d3deac1ddf84d715a6219b21d1c |
# (c) 2012, Michael DeHaan <michael.dehaan@gmail.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any lat... | jordiclariana/ansible | lib/ansible/template/safe_eval.py | Python | gpl-3.0 | 4,626 | [
"VisIt"
] | f31482f7e60021e0e6aaa28f2a6fc97b4047e0fba27f0cd50d91cf17ab18d018 |
from __future__ import unicode_literals
import datetime
import json
import pytz
import uuid
from calendar import timegm
from hashlib import sha1
from urlparse import urlparse
from django.core.urlresolvers import reverse
from django.test import TestCase
from django.test.client import FakePayload
from django.utils.enc... | njl/pycon | pycon/pycon_api/tests.py | Python | bsd-3-clause | 21,334 | [
"MOE"
] | d9f1a46c1cd2df522bf44f2a5481ea207524a5c8feae6e3f7f0286c848016ceb |
from __future__ import (absolute_import, division, print_function)
try:
import pathos.multiprocessing as mp
PATHOS_FOUND = True
except ImportError:
PATHOS_FOUND = False
import numpy as np
import six
import os
from mantid.api import AlgorithmFactory, FileAction, FileProperty, PythonAlgorithm, Progress, Wor... | wdzhou/mantid | Framework/PythonInterface/plugins/algorithms/Abins.py | Python | gpl-3.0 | 34,058 | [
"CASTEP",
"CRYSTAL"
] | 0e3612e57454ca828d49d4f236eb78396f0624b4f0c4c13635c454df5cdf90b6 |
#!/usr/bin/env python -Es
"""
Script to set up a custom genome for bcbio-nextgen
"""
import argparse
from argparse import ArgumentParser
import os
import toolz as tz
from bcbio.utils import safe_makedir, file_exists, chdir
from bcbio.pipeline import config_utils
from bcbio.distributed.transaction import file_transacti... | lpantano/bcbio-nextgen | scripts/bcbio_setup_genome.py | Python | mit | 11,347 | [
"Galaxy"
] | c7281d606187e7517b7ba9267b3791de5d2d22cee2adef70c40f0fd07712a81a |
# -*- coding: utf-8 -*-
"""
Created on Mon Oct 17 17:57:40 2016
@author: jdorvinen
"""
import numpy as np
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt
# <codecell>
# Model data fit: alpha=1.498, beta=-0.348, gamma=1.275
# Callaghan et al. used: alpha=21.46, beta=1.08, gamma=1.07
a = 12*1.49... | jdorvi/MonteCarlos_SLC | calculate_gap.py | Python | mit | 1,836 | [
"Mayavi"
] | 370966dc87dedb9e0e1d25bb15282eb2a388e140cfbebd337868a79100d88cad |
# Copyright 2019 The TensorNetwork 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 applicable law or agreed ... | google/TensorNetwork | tensornetwork/linalg/initialization.py | Python | apache-2.0 | 8,131 | [
"Gaussian"
] | d3ff28236a1b8027a1fb7b97b238e8be24f4398059d7e2f69d063f1ad20bc960 |
##################################################################
# SSURGO_to_csv.py Apr 2015
# ritvik sahajpal (ritvik@umd.edu)
#
##################################################################
import constants, logging, os, us, csv, pdb, glob
import numpy as np
import pandas as pd
def open_or_die(path_file, per... | ritviksahajpal/EPIC | SSURGO/SSURGO_to_csv.py | Python | mit | 12,793 | [
"NetCDF"
] | 28bdffd09c32d756fc6325bb8b271b1848120f429deb59e012a60030e0d13751 |
#input essential info:
#1.server info
#2.user name + user password
#3.initial environment
from urlparse import urlparse
from splinter import Browser
import threading,json,random,re,time,getpass
#constant
arrFiled = []
i = 0
while i < 18:
i = i + 1
arrFiled.append("http://ts3.travian.com/build.php?id=" + str(... | laboratoryyingong/TravianPlugin | TravianPlugin.py | Python | mit | 7,256 | [
"VisIt"
] | a7176854393897e19380ead16c9454871b4a76e8750d70e95481d840ce4eb099 |
"""Base classes for parameters of algorithms with biomod functionality"""
from zope.interface import provider
from zope.schema.vocabulary import SimpleVocabulary, SimpleTerm
from zope.schema.interfaces import IVocabularyFactory
brt_var_monotone_vocab = SimpleVocabulary([
SimpleTerm(-1, '-1', u'-1'),
SimpleTe... | chuijbers/org.bccvl.compute | src/org/bccvl/compute/vocabularies.py | Python | gpl-2.0 | 1,153 | [
"Gaussian"
] | a8d51a65cedcea3273cd68afa8dc64ff09edb85deb1713921ce1896017a225f3 |
"""
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 this ... | jellybean4/yosaipy2 | yosaipy2/core/subject/abcs.py | Python | apache-2.0 | 28,464 | [
"VisIt"
] | e0e640f80c4aed37bdb1065b92de4c4fa2c3d89eef36c1bf6ed9be30130a2679 |
#!/usr/bin/env ccp4-python
"""Useful manipulations on PDB files"""
# Python imports
from collections import defaultdict
import copy
import logging
import os
import re
import sys
import unittest
import iotbx.file_reader
import iotbx.pdb
from ample.util import ample_util, pdb_model, residue_map, sequence_util
logger ... | linucks/ample | ample/util/pdb_edit.py | Python | bsd-3-clause | 46,394 | [
"CRYSTAL"
] | 5ce6987f0d7852caf85611559c5fb827c0c2602489d5b17248ecd845e338ac11 |
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