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import os
from flask import Flask, url_for, request, render_template, jsonify, send_file
from werkzeug.utils import secure_filename
import deepchem as dc
import subprocess
from shutil import copyfile
import csv
import rdkit
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import Draw
STATIC_DIR = ... | deepchem/deepchem-gui | gui/app.py | Python | gpl-3.0 | 8,020 | [
"RDKit"
] | ba90d6b1f8a77147a62fdc984205db052fd55458bfaf686e23831f3fed5f6bc0 |
"""Module containing the nextera pipeline."""
import logging
from pathlib import Path
import pysam
import toolz
from pyim.external.bowtie2 import bowtie2
from pyim.external.cutadapt import cutadapt, cutadapt_summary
from pyim.external.util import flatten_arguments
from pyim.model import Insertion
from pyim.util.path... | jrderuiter/pyim | src/pyim/align/aligners/nextera.py | Python | mit | 10,533 | [
"Bowtie",
"pysam"
] | 673540427a634d798478ed2647e1f03cfc4b868b63c7e5fa2904e9c7ceb855dc |
"""
Create db from gdf files to be able to then select neuron spike times.
Best use case:
1. run simulation
2. create sqlite db of spike times with indexing
3. use this db many times
Creating index for db will dominate insertions for larger set of spike times.
[TODO] Check how much slower things are if index is crea... | espenhgn/ViSAPy | ViSAPy/gdf.py | Python | gpl-2.0 | 8,440 | [
"NEURON"
] | b22a844f41d03d6a3eff3e4b9f7e3f208fdb4d3066529d78d4ac0f3c713be3e2 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
def GetRGBColor(colorName):
'''
Return the red, green and blue components for a
color as doubles.
'''
rgb = [0.0, 0.0, 0.0] # black
vtk.vt... | hlzz/dotfiles | graphics/VTK-7.0.0/Rendering/Core/Testing/Python/rendererSource.py | Python | bsd-3-clause | 3,438 | [
"VTK"
] | 097d6a01ba731e3f465ceaa84569315cc97a9cd90499b485bf526c5eb9245640 |
# Simple python code for automatically bonusing workers on mTurk.
# Written by Desmond Ong (github.com/desmond-ong), 15 July 2013. Send comments to dco@stanford.edu.
# version 1.2, updated Jul 22, 2015
# Instructions:
# 1) replace "filename" with the name of the input file,
# 2) write the bonus message to particip... | desmond-ong/amtBonusScript | bonusScript.py | Python | mit | 4,369 | [
"Desmond"
] | be1255ea4c324fca21bec40ae14d8c8b4c62eeb86fa4e1d76bc9c1fb20f7ad48 |
"""cpassdb - Config"""
__author__ = "Brian Wiborg <baccenfutter@c-base.org>"
__license__ = "GNU/GPLv2"
import os
STORAGE_ROOT = os.path.expanduser('~/.cpassdb')
OBJECTS_DIR = 'objects'
TIMESTAMP_FORMAT = 'YYYYMMDDHHmmss'
DEFAULT_TTL = 30
PROTOCOL_IDLE_TIMEOUT_SECONDS = 15
ADMIN_GROUP = 'wheels'
GNUPG_PATH = os.path.... | baccenfutter/cpassdb | cpassdb/config.py | Python | gpl-2.0 | 368 | [
"Brian"
] | 419a194e24019b68da040685c8e10d9e4d90d76f7849647f7a7b5aeece6b89c3 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This package implements modules for input and output to and from CREST
"""
| gmatteo/pymatgen | pymatgen/io/xtb/__init__.py | Python | mit | 190 | [
"pymatgen"
] | 90c8aee366ecce18ef4a0c161562c1ea9f24063b5056960ec932d57137ae14e6 |
from __future__ import absolute_import
from __future__ import print_function
import os
import numpy as np
import matplotlib.pyplot as plt
import datetime
import clawpack.visclaw.colormaps as colormap
import clawpack.visclaw.gaugetools as gaugetools
import clawpack.clawutil.data as clawdata
import clawpack.amrclaw.da... | mandli/surge-examples | sandy/setplot.py | Python | mit | 10,948 | [
"NetCDF"
] | de21a4d632b3704ff42734ba3f168236b666a5f92c664d5a96e933bb84cdbcbe |
"""
General API for testing dataset objects
"""
from __future__ import print_function
from __future__ import division
from __future__ import unicode_literals
__author__ = "Bharath Ramsundar"
__copyright__ = "Copyright 2016, Stanford University"
__license__ = "GPL"
import unittest
import tempfile
import os
import shut... | bowenliu16/deepchem | deepchem/data/tests/__init__.py | Python | gpl-3.0 | 3,608 | [
"Gaussian"
] | 074a646eaae53197be216c18015c71fa3707bbafc969cf1e5eee83dbe3885ec5 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import json
import os
import unittest
import warnings
import numpy as np
from monty.json import MontyDecoder
from pymatgen.analysis.xas.spectrum import XAS, site_weighted_spectrum
from pymatgen.core import Element
from pymat... | vorwerkc/pymatgen | pymatgen/analysis/xas/tests/test_spectrum.py | Python | mit | 5,982 | [
"pymatgen"
] | 5ba724b14273bb266c98a82e1429fde795035efbb2317c448a330cd54d44eb4a |
#!/usr/bin/python
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it ... | andysim/psi4 | doc/sphinxman/document_driver.py | Python | gpl-2.0 | 4,584 | [
"Psi4"
] | fe1a256f01030cac87038bea694704e7a0bf9ebb831e1cb241d3703f1dd34511 |
# Copyright 2021 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | GoogleCloudPlatform/python-docs-samples | composer/workflows/gke_operator.py | Python | apache-2.0 | 10,478 | [
"VisIt"
] | bfa8f09ffdadf61a046ff812b90bc180e2ae92657dbc085c85ea1b7dcb5579a7 |
import os
from boxbranding import getMachineBrand, getMachineName
import xml.etree.cElementTree
from datetime import datetime
from time import ctime, time, strftime, localtime, mktime
from bisect import insort
from enigma import eActionMap, quitMainloop
from Components.config import config
from Components.TimerSanity... | popazerty/openhdf-enigma2 | PowerTimer.py | Python | gpl-2.0 | 41,102 | [
"ASE"
] | c128a780f00f0178ac3305fc42d3f5db70b53bf564faf1b8d89f63c73d833e94 |
"""
Utility functions for transcripts.
++++++++++++++++++++++++++++++++++
"""
import os
import copy
import json
import requests
import logging
from pysrt import SubRipTime, SubRipItem, SubRipFile
from lxml import etree
from HTMLParser import HTMLParser
from xmodule.exceptions import NotFoundError
from xmodule.contents... | ahmadiga/min_edx | common/lib/xmodule/xmodule/video_module/transcripts_utils.py | Python | agpl-3.0 | 24,420 | [
"FEFF"
] | 3c868b7d5a45a73dd534182b5c104a3fefb59caa2317e899f1561dc366463256 |
# -*- coding: utf-8 -*-
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Mathieu Blondel <mathieu@mblondel.org>
# Robert Layton <robertlayton@gmail.com>
# Andreas Mueller <amueller@ais.uni-bonn.de>
# Philippe Gervais <philippe.gervais@inria.fr>
# Lars Buitinck
... | manhhomienbienthuy/scikit-learn | sklearn/metrics/pairwise.py | Python | bsd-3-clause | 73,354 | [
"Gaussian"
] | e12565a397f86ef67c86258997023cc4bcb9219cb983a94d4969007d71d4a326 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the courseware unit bookmarks.
"""
import json
from nose.plugins.attrib import attr
import requests
from ...pages.studio.auto_auth import AutoAuthPage as StudioAutoAuthPage
from ...pages.lms.auto_auth import AutoAuthPage as LmsAutoAuthPage
from ...pages.lms.bookmarks imp... | solashirai/edx-platform | common/test/acceptance/tests/lms/test_bookmarks.py | Python | agpl-3.0 | 23,733 | [
"VisIt"
] | 6c3594bb0c82b416a187a26967d4a5237b201b498fa3a712f810dc92c588a838 |
#! /usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requi... | googleapis/python-eventarc-publishing | scripts/fixup_eventarc_publishing_v1_keywords.py | Python | apache-2.0 | 6,018 | [
"VisIt"
] | 20e4cf7b9ef443120d5f8f04d22ee11314c189449beafe67369c0fd8caabe1c4 |
'''
Code to generate LTSA for the car project
Brian Gravelle
'''
MAX_CARS = 4
file = open("testfile.txt","w")
file.write("wait response do not use!!")
file.write("\n")
file.write("\n")
file.write("\n")
lower_priority = \
"""{2}receive_request[{0}][ID][Lanes] -> send_permission[ID][{0}] -> WAIT_RESPONSE{1}[ll2][ll3... | mastino/Internet_of_Thrones | final/ltsa/gen.py | Python | gpl-3.0 | 4,090 | [
"Brian"
] | 987fc675ec45dea4459448e12a34c8f3658875be9d60ba494dc8a78230b646fd |
# copyright 2003-2013 LOGILAB S.A. (Paris, FRANCE), all rights reserved.
# contact http://www.logilab.fr/ -- mailto:contact@logilab.fr
#
# This file is part of astroid.
#
# astroid 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
#... | pylint-bot/astroid-unofficial | astroid/manager.py | Python | gpl-2.0 | 11,763 | [
"VisIt"
] | dd93f7e583fb7aa16f3785ec4401ff83cf7d4fc0b6267945e8a68165406a8010 |
# -*- coding: utf-8 -*-
# squidgui.py ---
#
# Filename: squidgui.py
# Description:
# Author:
# Maintainer:
# Created: Mon Jul 9 18:23:55 2012 (+0530)
# Version:
# Last-Updated: Tue May 3 00:18:47 2016 (-0400)
# By: subha
# Update #: 1078
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary: ... | BhallaLab/moose | moose-examples/squid/squid_demo.py | Python | gpl-3.0 | 44,883 | [
"MOOSE"
] | 992799fdf8b27bb54eb76e249712a30693c4a74f1335479e7309a34a7a20b54d |
#!/usr/bin/python
#Audio Tools, a module and set of tools for manipulating audio data
#Copyright (C) 2008-2012 Brian Langenberger
#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... | Excito/audiotools | audiotools/delta.py | Python | gpl-2.0 | 9,448 | [
"Brian"
] | 5933107cef1a897b7cd09e09ecb11c7f152e2334c4cc09828afa4335ecd4bc3a |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Much of this code adapted from dynesty.plotting (Josh Speagle)
import numpy as np
from scipy.ndimage import gaussian_filter as norm_kde
try:
import matplotlib.pyplot as pl
from matplotlib.ticker import MaxNLocator, NullLocator
from matplotlib.ticker import... | bd-j/prospector | prospect/plotting/corner.py | Python | mit | 23,308 | [
"Gaussian"
] | a0147c209b6f59fa4157ffd8b9584078405d35804deb930db8c1512959349476 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Interface with command line GULP.
http://projects.ivec.org
WARNING: you need to have GULP installed on your system.
"""
__author__ = "Bharat Medasani, Wenhao Sun"
__copyright__ = "Copyright 2013, The Materials Project"
__... | materialsproject/pymatgen | pymatgen/command_line/gulp_caller.py | Python | mit | 27,411 | [
"GULP",
"pymatgen"
] | fb1929df8f39415bb9b1a2ccd19d5d95ad5313a2ea86329b643db0a95efc0f07 |
# -*- coding: utf-8 -*-
#
# This file is part of Invenio-Client.
# Copyright (C) 2014 CERN.
#
# Invenio-Client is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License as
# published by the Free Software Foundation; either version 2 of the
# License, or (at your opt... | inveniosoftware/invenio-client | invenio_client/contrib/cds.py | Python | gpl-2.0 | 2,282 | [
"VisIt"
] | e611714d7caad13241acbefa196ff5c1fffdc55b78b4d879cf8f3ff0a3318807 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# (c) 2015, Heyo
#
# 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) a... | ravibhure/ansible | lib/ansible/modules/windows/win_nssm.py | Python | gpl-3.0 | 6,003 | [
"ADF"
] | fa0ce13e77f980b02c051f4a25116f54bd8011c9d9541ab534b95070bf051589 |
"""edc_pharmacy URL Configuration
The `urlpatterns` list routes URLs to views. For more information please see:
https://docs.djangoproject.com/en/1.10/topics/http/urls/
Examples:
Function views
1. Add an import: from my_app import views
2. Add a URL to urlpatterns: url(r'^$', views.home, name='home')
Cla... | botswana-harvard/ba-namotswe | ba_namotswe/urls.py | Python | gpl-3.0 | 2,610 | [
"VisIt"
] | 43ad7fd303f330d04daa4f0673baf10af7d520f8bfd57356d3476d4864df05d7 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RGoseq(RPackage):
"""Gene Ontology analyser for RNA-seq and other length biased data.
... | iulian787/spack | var/spack/repos/builtin/packages/r-goseq/package.py | Python | lgpl-2.1 | 1,312 | [
"Bioconductor"
] | 3912ce7c1530b8c0b97ca7cc87f8b3bb85bc2fd4ccf041e3f12fb63a7d7b170b |
from rope.base import libutils
from rope.base import pyobjects, exceptions, stdmods
from rope.refactor import occurrences
from rope.refactor.importutils import importinfo
class ImportInfoVisitor(object):
def dispatch(self, import_):
try:
method_name = "visit" + import_.import_info.__class__.__... | python-rope/rope | rope/refactor/importutils/actions.py | Python | lgpl-3.0 | 14,313 | [
"VisIt"
] | fb191a0022f642b9754b61c34b704285310300a74422aabdce21f355f5307053 |
#==============================================================================
# import packages
#==============================================================================
import numpy as np
import mayavi.mlab as mlab
from tvtk.api import tvtk
import csv
import math
from mayavi.filters.mask_points import MaskPoi... | grongen/point-cloud-visualization | plotcloud3d.py | Python | gpl-3.0 | 36,535 | [
"Mayavi"
] | b6070f7f4269871aeae6957425294fae730271a7078732d4b3b7853c708eb8e6 |
# Loading libraries
from scipy.io import loadmat
import h5py
from time import strptime
from calendar import timegm
import pysam
print pysam.__version__
print pysam.__file__
# /nfs/software/cn/el6.5/python/envs/.virtualenvs/cpython279/lib/python2.7/site-packages/RSeQC-2.6.2-py2.7-linux-x86_64.egg
# pip install --ta... | cbcrg/pergola | test/c_elegans_data_test/read_worm_data_dev.py | Python | gpl-3.0 | 9,914 | [
"pysam"
] | 898c6eb17c7e91b9dd4a83325bb7a50cb3e0e974696b87f9185ccf3bc3b8eb61 |
#!/usr/bin/python3
"""perceptron.py: Predicts whether some data belongs to one class or another."""
__author__ = 'Andrei Muntean'
__license__ = 'MIT License'
import numpy as np
class Perceptron:
def __init__(self, learning_rate = 1):
self.learning_rate = learning_rate
def train(self, data, labels, maximum_ite... | andreimuntean/Perceptron | Perceptron/perceptron.py | Python | mit | 1,909 | [
"NEURON"
] | 986733d92e4aa67245e51e32e761c6813ce670a7b06ce8472b7155589f130665 |
# -*- coding: utf-8 -*-
#
# Name: face.com Python API client library
# Description: face.com REST API Python client library.
#
# For more information about the API and the return values,
# visit the official documentation at http://developers.face.com/docs/api/.
#
# Author: Tomaž Muraus (http://www.tomaz-muraus.info)
#... | pizzapanther/Church-Source | dependencies/face_client/face_client.py | Python | gpl-3.0 | 11,111 | [
"VisIt"
] | 20795acb5d86cd330a04c445d1f789611522ac29764bc505dfc3404c6f0f4f81 |
from frappe import _
def get_data():
return [
{
"label": _("Sales Pipeline"),
"icon": "fa fa-star",
"items": [
{
"type": "doctype",
"name": "Lead",
"description": _("Database of potential customers."),
},
{
"type": "doctype",
"name": "Opportunity",
"description": _... | patilsangram/erpnext | erpnext/config/crm.py | Python | gpl-3.0 | 3,615 | [
"VisIt"
] | 20ca58443771c9a246f19b5743239729954ec57169b467732303a03eb41863ee |
#!/usr/bin/env python
import os
import sys
import time
import logging
import numpy as np
import pandas as pd
from datetime import datetime
from sklearn.ensemble import RandomForestClassifier
from sklearn.model_selection import RandomizedSearchCV
from sklearn.preprocessing import MinMaxScaler
from moloi.config_processi... | DentonJC/virtual_screening | moloi/bin/rf.py | Python | gpl-3.0 | 4,657 | [
"RDKit"
] | fa6fd939c75c3c15f40233962559c66b251a2160e1fc2f8c90013f41edecf481 |
#
# Copyright 2018 Analytics Zoo 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 to... | intel-analytics/analytics-zoo | pyzoo/test/zoo/orca/learn/ray/pytorch/conftest.py | Python | apache-2.0 | 1,280 | [
"ORCA"
] | 682af61fc1f8d57771626dd5b23107625a4e330a7d2dacb47d71112a41b3bfa8 |
"""
==================================================
Automatic Relevance Determination Regression (ARD)
==================================================
Fit regression model with Bayesian Ridge Regression.
See :ref:`bayesian_ridge_regression` for more information on the regressor.
Compared to the OLS (ordinary l... | RPGOne/Skynet | scikit-learn-0.18.1/examples/linear_model/plot_ard.py | Python | bsd-3-clause | 2,828 | [
"Gaussian"
] | 411f31846b536d3610cc9c215f91b850a6ed59f5d3cefc3bdc22421775f2e90e |
# Copyright 2004-2017 Tom Rothamel <pytom@bishoujo.us>
#
# 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 to use, copy, modify, m... | kfcpaladin/sze-the-game | renpy/display/dragdrop.py | Python | mit | 25,608 | [
"VisIt"
] | 8ccb5c2a94f60bd1f9a0b7492c3437ccf272340c1fdbf49e7f00d8b54ba3ea12 |
# Natural Language Toolkit: Probability and Statistics
#
# Copyright (C) 2001 University of Pennsylvania
# Author: Edward Loper <edloper@gradient.cis.upenn.edu>
# Trevor Cohn <tacohn@cs.mu.oz.au> (additions)
# URL: <http://nltk.sf.net>
# For license information, see LICENSE.TXT
#
# $Id: probability.py,v 1.1.1.2... | ronaldahmed/robot-navigation | neural-navigation-with-lstm/MARCO/nltk/probability.py | Python | mit | 60,530 | [
"Gaussian"
] | 41bd63550b6481e81e967d0d51a03586832bc7e6673163c01471e4333246d670 |
#
# Copyright (C) 2013-2018 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... | hmenke/espresso | testsuite/python/observables.py | Python | gpl-3.0 | 7,120 | [
"ESPResSo"
] | 1dd94b7fbe2b0f2f74c66b4a42cad9f90aff417a6c1767b20c4b00c04166bc01 |
import numpy as np
from scipy.io import netcdf
def genNetCDF(wavelength, stI, stQ, stU, stV, sigmaI, sigmaQ, sigmaU, sigmaV, boundary, height, obsTheta, obsGamma, mask, pars, outputFile):
"""
This routine generates a NetCDF file with the observations ready for Hazel-MPI
Args:
wavelength (float): array of siz... | aasensio/pyAndres | genNetCDF.py | Python | mit | 3,845 | [
"NetCDF"
] | 81109225fc069d104d2a24448afdce4d8deee700c53ae44ff8f782b6d9b58905 |
"""Install Fall3d-6.2 on Linux platform
An environment variable, FALL3DHOME, may be specified to determine
the location of the Fall3d installation.
If it is not specified, Fall3d will be installed within the AIM source tree.
"""
#----------------------------------------
# Auxiliary modules and functions
#------------... | GeoscienceAustralia/PF3D | source/aim/install_fall3d.py | Python | gpl-3.0 | 14,568 | [
"NetCDF"
] | 95e3eb9e213c20b9bbd63d8dd5dea1f4518d5f1c90b68d68253e3c91f24969e1 |
# -*- coding: utf-8 -*-
# * Authors:
# * TJEBBES Gaston <g.t@majerti.fr>
# * Arezki Feth <f.a@majerti.fr>;
# * Miotte Julien <j.m@majerti.fr>;
"""
User and user datas listing views
"""
import logging
from sqlalchemy import (
or_,
distinct,
)
from autonomie_base.models.base import DBSESSION
f... | CroissanceCommune/autonomie | autonomie/views/user/lists.py | Python | gpl-3.0 | 6,931 | [
"VisIt"
] | 93e3ea7406b1aab5db594349d8d622ff58291446e64b2e7b6642a19bea12b5d7 |
# Copyright (C) 2018 Charlie Hoy, Collin Capano
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 3 of the License, or (at your
# option) any later version.
#
# This program is dis... | tdent/pycbc | pycbc/inference/models/marginalized_gaussian_noise.py | Python | gpl-3.0 | 26,761 | [
"Gaussian"
] | f2583720d339aaca777fe599b4e8e477758c750c11accd8e6303bf7bd4f36843 |
Classes and Object-oriented programming: examples from Python, Java and Javascript.
Among the most important programming paradigms is the object-oriented programming. Object oriented is
based on the idea of using 'objects' to build different applications. We can think of an object as a
container that contains attrib... | TamerKhraisha/webpage.github.io | python-java-javascript.py | Python | mit | 15,987 | [
"VisIt"
] | fc37a00b12e4064f0ef58df1bcd629902271da4b0ac4b03c7b5cd0f14595e7b7 |
# Copyright (C) 2015 Henrique Pereira Coutada Miranda, Alejandro Molina Sanchez, Alexandre Morlet, Fulvio Paleari
# All rights reserved.
#
# This file is part of yambopy
#
#
from yambopy import *
import os
#
# by Henrique Miranda
#
def pack_files_in_folder(folder,save_folder=None,mask='',verbose=True):
"""
Pac... | henriquemiranda/yambopy | yambopy/recipes.py | Python | bsd-3-clause | 17,973 | [
"Yambo"
] | 935da6add191e268181e86b92d4a6dd2bc3e5a4f94cb73ad069406700b7a3731 |
""" Just listing the possible Properties
This module contains list of Properties that can be assigned to users and groups
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
#: A host property. This property is used::
#: * For a host to ... | ic-hep/DIRAC | src/DIRAC/Core/Security/Properties.py | Python | gpl-3.0 | 2,097 | [
"DIRAC"
] | 4fe66bd3369927f682b5216f8b4ef599dc3960babbb3fa6f301739946217aeb0 |
import sys
if sys.hexversion < 0x2060000:
raise NotImplementedError('Python < 2.6 not supported.')
import ez_setup
ez_setup.use_setuptools()
from setuptools import setup
with open('README.rst') as file:
long_description = file.read()
setup(name='pydons',
version='0.2.5',
description='Python dat... | coobas/pydons | setup.py | Python | mit | 1,438 | [
"NetCDF"
] | 9825d9bae8f256dd91489952edaa2790fc6029070f61877f9cbeccccfd67401b |
""" NormalizeStaticIf adds support for static guards. """
from pythran.analyses import (ImportedIds, HasReturn, IsAssigned, CFG,
HasBreak, HasContinue, DefUseChains, Ancestors,
StaticExpressions, HasStaticExpression)
from pythran.passmanager import Transforma... | serge-sans-paille/pythran | pythran/transformations/normalize_static_if.py | Python | bsd-3-clause | 16,623 | [
"VisIt"
] | db9df9b4173fb3e880e6ad75086d443f7e0697a4dcc66ac839948561628f8721 |
#!/usr/bin/env python
# imports
from __future__ import print_function
import os, subprocess, shutil
import _config as config
def run_command(command, logfile='runlog.log'):
'''runs a process and reports its output and status
Gets:
command -> a list of arguments, e.g. ['ls' , '-l']
logfi... | resal81/PyTopol | test/systems/cmp_namd_gmx.py | Python | gpl-3.0 | 14,655 | [
"Gromacs",
"NAMD"
] | 75c31c3d88d8ef18a399bd573747d8c71dade8591241b5b7c0f92adfeadbb97e |
# Benchmark the calculation of Ramachandran phi/psi angles from a PDB file
import time
import MDAnalysis as mda
pdb_filepath = "data/1AKE.pdb"
u = mda.Universe(pdb_filepath)
def ramachandran():
phi_angles = []
psi_angles = []
for res in u.residues:
try:
phi = res.phi_selection()
... | jgreener64/pdb-benchmarks | MDAnalysis/ramachandran.py | Python | mit | 744 | [
"MDAnalysis"
] | 21cf340adaea3c38984b870b63c317de66db6ce9b1eb36cc659d7e12993d4919 |
## This file is part of Invenio.
## Copyright (C) 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012, 2014 CERN.
##
## Invenio 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, ... | jmartinm/invenio | modules/websession/lib/websession_templates.py | Python | gpl-2.0 | 119,669 | [
"VisIt"
] | 689a7d24b07911a1005b4ec6f75f55cefc5333284d5852046bdf98a4defa3cb6 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Create the RenderWindow, Renderer and both Actors
#
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.SetMultiSamples(0)
renWin.AddRenderer(ren)
iren =... | hlzz/dotfiles | graphics/VTK-7.0.0/Filters/Core/Testing/Python/probe.py | Python | bsd-3-clause | 2,456 | [
"VTK"
] | 4d21e5607697003c91a74cfd631cb141d469d77c798ddda0d7b54cb4d4d4c8a8 |
import doctest
import inspect
import os
import re
from datetime import datetime
from types import SimpleNamespace
from unittest.mock import Mock, patch
from django.test import SimpleTestCase, TestCase
import attr
from dateutil.tz import tzoffset, tzutc
from lxml import etree
from nose.tools import assert_equal, asser... | dimagi/commcare-hq | corehq/motech/openmrs/tests/test_atom_feed.py | Python | bsd-3-clause | 23,450 | [
"VisIt"
] | 91488d8ff052b5b5d6bc103b2c9657f82f13ad00ef8c234f5ce16b28b7f48670 |
# Delete the last n messages sent by the bot
# Very useful for cleaning up after testing
# Manually interacts with Slack's API through res.robot.slack_client.api_call
import itertools
import json
import logging
from espresso.main import robot
@robot.respond(r"(?i)delete your last (?P<howmany>[0-9]*) messages")
def d... | ratchetrobotics/espresso | plugins/deletemessages.py | Python | bsd-3-clause | 1,095 | [
"ESPResSo"
] | 5004e5e086555a261a5096866a203ba5c06cff7dddae61b89bbd66808bd99973 |
"""
Test combination of multiple experiments and reflections files.
"""
from __future__ import annotations
import copy
import os
import procrunner
import pytest
from dxtbx.model.experiment_list import ExperimentListFactory
from dxtbx.serialize import load
import dials.command_line.combine_experiments as combine_e... | dials/dials | tests/command_line/test_combine_experiments.py | Python | bsd-3-clause | 15,490 | [
"CRYSTAL"
] | 1e4dc479d2d5b9663ea40bd9f83aae3d6389d3154ec9788e3d8614159aec2760 |
import numpy as np
from numpy.matrixlib.defmatrix import matrix, asmatrix
# need * as we're copying the numpy namespace
from numpy import *
__version__ = np.__version__
__all__ = np.__all__[:] # copy numpy namespace
__all__ += ['rand', 'randn', 'repmat']
def empty(shape, dtype=None, order='C'):
"""
Return a ... | GbalsaC/bitnamiP | venv/lib/python2.7/site-packages/numpy/matlib.py | Python | agpl-3.0 | 9,494 | [
"Gaussian"
] | e5383f9fa588303d5f2f0ad8ed46781449d34cf6b681b9bfdebe81f2e05f8d41 |
"""Mayavi/traits GUI visualization elements."""
# Authors: Christian Brodbeck <christianbrodbeck@nyu.edu>
#
# License: BSD (3-clause)
import numpy as np
from mayavi.mlab import pipeline, text3d
from mayavi.modules.glyph import Glyph
from mayavi.modules.surface import Surface
from mayavi.sources.vtk_data_source impor... | jaeilepp/mne-python | mne/gui/_viewer.py | Python | bsd-3-clause | 11,226 | [
"Mayavi"
] | 76b21e956d1ee53c658aafef37634f90cb356b712110b7ee8dfc0c9610a56d9f |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class NetcdfCxx4(AutotoolsPackage):
"""NetCDF (network Common Data Form) is a set of software li... | rspavel/spack | var/spack/repos/builtin/packages/netcdf-cxx4/package.py | Python | lgpl-2.1 | 2,756 | [
"NetCDF"
] | 743b1fa0e314cd2b9404d314577fd38ef2d8c58219974a9f68c2311d353bd15c |
#pylint: disable=missing-docstring
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/... | nuclear-wizard/moose | python/chigger/utils/LegendOptions.py | Python | lgpl-2.1 | 3,315 | [
"MOOSE",
"VTK"
] | 62195e0b2af3c7c7ea2ff4a6a99e85bd3bfc9e252ab7da018c81ed4a6eaa01dd |
"""
DIRAC.Resources package
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
| yujikato/DIRAC | src/DIRAC/Resources/__init__.py | Python | gpl-3.0 | 162 | [
"DIRAC"
] | 0f6e8ecda42389c2c43a9029445910f0ab7f52cc0b8ef93239c757112e186ba9 |
import json
import logging
from difflib import ndiff
import waffle
from django import forms
from django.conf import settings
from django.core.exceptions import ObjectDoesNotExist
from django.forms.widgets import CheckboxSelectMultiple
from django.template.loader import render_to_string
from django.utils import transla... | jwhitlock/kuma | kuma/wiki/forms.py | Python | mpl-2.0 | 37,759 | [
"VisIt"
] | 12622de5a7d831f69169045c25ab28b4b9993c70e29dd8749bf813e429fc5e55 |
"""
====================================================================
K-means clustering and vector quantization (:mod:`scipy.cluster.vq`)
====================================================================
Provides routines for k-means clustering, generating code books
from k-means models, and quantizing vectors ... | mortonjt/scipy | scipy/cluster/vq.py | Python | bsd-3-clause | 25,312 | [
"Gaussian"
] | 860a4b11ba3bc6e3c2e2ef214629499b1b652030ec719b9416ee6792bdbce5a3 |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import random
from collections import defaultdict, deque
from typing import Any, Text, List, Dict
from rasa_core.events import UserUttered, ActionExecuted
from rasa_cor... | deepak02/rasa_core | rasa_core/training_utils/visualization.py | Python | apache-2.0 | 11,796 | [
"VisIt"
] | 065a9a3d58986a52e762c6a0ac15fed0d3d88b4a95117883fe280deb906e49dd |
#! /usr/bin/env python3
import textwrap
import re
def regex_rules(words, extract=0):
"""A function which returns the regular expression (regex) pattern for the
provided keywords.
Parameters
----------
words : list
A list of keywords or regex patterns.
extract : int, default 0
... | JQGoh/jqlearning | Analysis/StringPatternsWithKeywords/main.py | Python | gpl-3.0 | 3,448 | [
"VisIt"
] | 4b5d999342d3632f733b2fb33aa6305b3134487e495eb553fd6d57859381ec91 |
# -*- coding: utf-8 -*-
"""Tests for reserved field handling in header
"""
from vcfpy import header
# INFO for (small) variants ---------------------------------------------------
def test_info_aa():
assert header.RESERVED_INFO["AA"]
assert header.RESERVED_INFO["AA"].type == "String"
assert header.RESER... | bihealth/vcfpy | tests/test_reserved_fields.py | Python | mit | 15,248 | [
"ADF"
] | 7cf8177c15680f08ca65d061cfa8bcf7452bd39037055fad223669b06926cc99 |
# Original Author: iwatobipen
#
# 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.
"""
This script performs fast clustering of SMILES
Clustering method is repeated bi section, the m... | bp-kelley/rdkit | Contrib/Fastcluster/fastcluster.py | Python | bsd-3-clause | 2,364 | [
"RDKit"
] | f7b91d17de7a41c238b69f5d54c41709118b6da9789a1cb40ac1a35261980e49 |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publish... | thica/ORCA-Remote | src/ORCA/utils/TypeConvert.py | Python | gpl-3.0 | 16,124 | [
"ORCA"
] | 271aa1260fc149d733e4b4358ebef69e2c42a089a156382da2d0c73da5169c8b |
#!/usr/bin/env python
"""
==================
ModEM
==================
# Generate files for ModEM
# Generate data file for ModEM
# by Paul Soeffky 2013
# revised by LK 2014
# revised by JP 2014
# edited by AK 2016
# revised by JP 2017
# revised by AK 2017 to bring across functionality from ak branch
"""
#============... | MTgeophysics/mtpy | legacy/modem.py | Python | gpl-3.0 | 358,776 | [
"ParaView",
"VTK"
] | 4ef61cf6aef154a575c4484788c731968c1f8114ef0d67f8a5db08fdc3907fce |
# Copyright 2019 The TensorFlow Hub 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 ap... | tensorflow/hub | tensorflow_hub/tools/make_nearest_neighbour_index/embedding_generator.py | Python | apache-2.0 | 4,754 | [
"Gaussian"
] | a486fa28d49a3a742bcf3a6c7783e627ffc0f2557a9307bcbee3b45947641e77 |
import os
path=os.path.join(os.path.expanduser('~'),'.noma/')
fin = open(path+'savefile.txt','r')
savedfile=fin.readlines()
fin.close()
i=0
a=len(savedfile)
while i<a:
savedfile[i]=savedfile[i][:-1]
i+=1
from Tkinter import *
root = Tk()
root.title("Preferences")
####
def parabutton(event=None):
firstpage()
def fi... | marmy28/NOMA | saving.py | Python | gpl-2.0 | 26,562 | [
"VMD"
] | 2513545f8012230c5fb52c03eaf55a620c610deebe79e16e6bc59bedb57f9aed |
# Checks all psi4 relevant files for proper boilerplate GNU license.
# This is sold as is with no warrenty-- probably should double check everything
# after running. I am not responsible if you break Psi4.
#
# Do not forget to do share/plugins by hand!
import os
# File type we know how to handle
ftypes = ['cc', 'h', ... | kratman/psi4public | psi4/share/psi4/scripts/apply_license.py | Python | gpl-2.0 | 3,531 | [
"Psi4"
] | 817e4660ca44edf1177bf3b633bbd26371cf18ec5fc581c548cf7b6a043cc285 |
#!/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2014, Georgios Is. Detorakis (gdetor@gmail.com) and
# Nicolas P. Rougier (nicolas.rougier@inria.fr)
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided th... | gdetor/SI-RF-Structure | DiCarloProtocol/dicarlo-learning.py | Python | gpl-3.0 | 9,758 | [
"Gaussian"
] | 8794cfb6d5b5afee21796b4e74405eca99b7eebb826dce7f0cdffbb34be08068 |
"""Support code for working with Shippable."""
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import os
import re
import time
from .. import types as t
from ..config import (
CommonConfig,
TestConfig,
)
from ..git import (
Git,
)
from ..http import (
HttpCli... | 2ndQuadrant/ansible | test/lib/ansible_test/_internal/ci/shippable.py | Python | gpl-3.0 | 10,042 | [
"Octopus"
] | d02abd8638ddf731011fc24a89b7646414de1fb3cee5a575f1d26e313f2aa014 |
#!/usr/bin/env python3
import argparse
import multiprocessing
from itertools import product
import requests
parser = argparse.ArgumentParser(description="Warm up the tile cache.")
parser.add_argument(
"--url",
type=str,
required=True,
help="Root URL to Navigator instance. Ex: https://navigator.oceans... | DFO-Ocean-Navigator/Ocean-Data-Map-Project | scripts/pregen_tiles.py | Python | gpl-3.0 | 3,057 | [
"Gaussian"
] | cccb764d4089161647ca00867f33909eab2bf66f796e150125c9ed40a24fb304 |
#!/usr/bin/env python
########################################################################
# File : dirac-wms-job-get-output-data
# Author : Stuart Paterson
########################################################################
"""
Retrieve the output data files of a DIRAC job
"""
import DIRAC
from DIRAC.Core... | ic-hep/DIRAC | src/DIRAC/Interfaces/scripts/dirac_wms_job_get_output_data.py | Python | gpl-3.0 | 1,317 | [
"DIRAC"
] | 027ab3748c451f0185fac1cdd286aed3e65b2faf85cf817f717d438b225e2704 |
"""
API for initiating and tracking requests for credit from a provider.
"""
import datetime
import logging
import pytz
import uuid
from django.db import transaction
from lms.djangoapps.django_comment_client.utils import JsonResponse
from openedx.core.djangoapps.credit.exceptions import (
UserIsNotEligible,
... | rismalrv/edx-platform | openedx/core/djangoapps/credit/api/provider.py | Python | agpl-3.0 | 15,435 | [
"VisIt"
] | 349bf20a119dacfbcedcbbfa4272422215860b859ede01896d4f04cc7386983e |
'''test methods related to vagrant'''
from behave import *
import ConfigParser
config = ConfigParser.ConfigParser()
config.read('config/uat.cfg')
remote_user = config.get("vagrant", "user")
vagrant_build_dependencies = "ruby,ruby-devel,ruby-libvirt,rubygem-ruby-libvirt,libvirt,libvirt-devel,rubygem-bundler,rubygem-bu... | jlebon/UATFramework | steps/vagrant.py | Python | gpl-2.0 | 5,287 | [
"CDK"
] | 0032dc9a68c2cff06ae604a6f171eebab47efcd88b88f8e486f0e77224960d5a |
#-*- coding:utf-8 -*-
"""
This file is part of openexp.
openexp 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.
openexp is distributed in ... | SCgeeker/OpenSesame | openexp/_canvas/canvas.py | Python | gpl-3.0 | 31,992 | [
"Gaussian"
] | 024f07d7432568e80927d6c1a32b1f0fcc1436085c932d6aad8a0c4f994a85d9 |
""" Job accounting type.
Filled by the JobWrapper (by the jobs) and by the agent "WorloadManagement/StalledJobAgent"
"""
import DIRAC
from DIRAC.AccountingSystem.Client.Types.BaseAccountingType import BaseAccountingType
class Job(BaseAccountingType):
def __init__(self):
super(Job, self).__init__()
... | DIRACGrid/DIRAC | src/DIRAC/AccountingSystem/Client/Types/Job.py | Python | gpl-3.0 | 2,185 | [
"DIRAC"
] | 2b9d76ce8f5eb5fb8338a3692f90d6c7e28cf3e1fe1072a0c67c3cd0f66f1253 |
# Storage filtering classes
#
# Copyright (C) 2013 Red Hat, Inc.
#
# This copyrighted material is made available to anyone wishing to use,
# modify, copy, or redistribute it subject to the terms and conditions of
# the GNU General Public License v.2, or (at your option) any later version.
# This program is distributed... | projectatomic/anaconda | pyanaconda/ui/gui/spokes/filter.py | Python | gpl-2.0 | 26,603 | [
"VisIt"
] | 9adc0948fba718e00039f061e38dc64bba303fa327c6aa1d5117de0d00c6c919 |
# -*- coding: utf-8 -*-
import moose
import re
def fixPath(path):
path = re.sub(r'/+', '/', path)
return path
def test_path():
paths = [ '/a'
, '//a'
, '/a/b'
, '/a/b/'
, '//a//b/////'
, '/a/./b'
, '///a/././b'
]
expe... | dilawar/moose-core | tests/core/test_moose_paths.py | Python | gpl-3.0 | 986 | [
"MOOSE"
] | bac4beef5ffcd33255f02564e3adc2cc001ac9258ec93e735d9ae498521a4313 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# ---------------------------------------------------------------------
# Copyright (c) 2012 Michael Hull.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are m... | mikehulluk/morphforge | src/morphforge/simulation/neuron/objects/neuronobject.py | Python | bsd-2-clause | 2,027 | [
"NEURON"
] | a9e79dad9ac614b270df92c75e9559393ab58dd272b5888ce46b9682048a40c1 |
#!/usr/bin/python
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 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... | CDSherrill/psi4 | doc/sphinxman/document_plugins.py | Python | lgpl-3.0 | 15,221 | [
"Psi4"
] | f3a5db21290d7d57cb1839b674a9944d2a679dffe39b300850ab61950cbb4bfe |
#!/usr/bin/env python
#import argparse
#from glob import glob
dhdhd
from os.path import join as jp
from os.path import abspath
import os
import sys
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('-s', "--samples", help="Samples.txt file with sample ID.", required=True)
parser.add_argument('-b',... | shendri4/fox_wgs | bam2vcf_GATK_pipeline.py | Python | apache-2.0 | 2,643 | [
"BWA"
] | 148bb935ccbf597a52813ef5bc2483239dbec59a2fe4d51d3693ca40c438f84f |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class PyMdanalysis(PythonPackage):
"""MDAnalysis is a Python toolkit to analyze molecular dynami... | iulian787/spack | var/spack/repos/builtin/packages/py-mdanalysis/package.py | Python | lgpl-2.1 | 4,107 | [
"Amber",
"Biopython",
"CHARMM",
"DL_POLY",
"Gromacs",
"LAMMPS",
"MDAnalysis",
"NAMD",
"NetCDF"
] | c6daf2450c2f1cfab9a82334211b373cd7bab739dc3d6d9ed8c44488f2be7c58 |
#!/homes/dthybert/software/Python-2.7.5/python
import pysam
import scipy.stats
import sys
import argparse
class GenomeSegment:
def __init__(self,size, chr,start):
self.chr=chr
self.start=start
self.windowsSmoothing=5
self.lstPos=[0]*size
self.lstNbRead=[0]*size
self.lstFraction=[0.0]*size
self.lstNor... | tk2/assembly-eval | consistent/GetconsistantRegions.py | Python | mit | 8,960 | [
"pysam"
] | c1496f2bb12dc139177a6a139b7a4ac97aefd14eed701c64cc0234923377ef28 |
# -*- coding: utf-8 -*-
"""Tests for the query parser"""
from unittest import TestCase
from nose.tools import eq_
from dxr.plugins import plugins_named
from dxr.query import query_grammar, QueryVisitor
class VisitorTests(TestCase):
"""Make sure ``QueryVisitor`` is putting together sane data structures."""
... | jbradberry/dxr | tests/test_query_parser.py | Python | mit | 7,592 | [
"VisIt"
] | b4fe640df0369f98df6375d94dca31421dc744e3606169382e63b4098fe535ef |
""" SiteInspectorAgent
This agent inspect Sites, and evaluates policies that apply.
The following options can be set for the SiteInspectorAgent.
.. literalinclude:: ../ConfigTemplate.cfg
:start-after: ##BEGIN SiteInspectorAgent
:end-before: ##END
:dedent: 2
:caption: SiteInspectorAgent options
"""
import d... | DIRACGrid/DIRAC | src/DIRAC/ResourceStatusSystem/Agent/SiteInspectorAgent.py | Python | gpl-3.0 | 6,013 | [
"DIRAC"
] | 9d9fe3ad83e0cc2337187146c0a62dbfe26fe2902708987fb3c73489d41c500a |
#!/usr/bin/env python
########################################################################
# File : dirac-proxy-init.py
# Author : Adrian Casajus
########################################################################
"""
Creating a proxy.
Example:
$ dirac-proxy-init -g dirac_user -t --rfc
Enter Certifica... | ic-hep/DIRAC | src/DIRAC/FrameworkSystem/scripts/dirac_proxy_init.py | Python | gpl-3.0 | 10,817 | [
"DIRAC"
] | fa889b6cd1e4714e439a937d409a33b880ce99f2a9231524af52c78861789efe |
import numpy as np
def affine_forward(x, w, b):
"""
Computes the forward pass for an affine (fully-connected) layer.
The input x has shape (N, d_1, ..., d_k) and contains a minibatch of N
examples, where each example x[i] has shape (d_1, ..., d_k). We will
reshape each input into a vector of dime... | 5hubh4m/CS231n | Assignment2/cs231n/layers.py | Python | mit | 17,409 | [
"NEURON"
] | bed646f539feadbcc90c9f69b46d735e773149ece387cc82f6582242e6aa673f |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright: (c) 2014, Ruggero Marchei <ruggero.marchei@daemonzone.net>
# Copyright: (c) 2015, Brian Coca <bcoca@ansible.com>
# Copyright: (c) 2016-2017, Konstantin Shalygin <k0ste@k0ste.ru>
# Copyright: (c) 2017, Ansible Project
# GNU General Public License v3.0+ (see COPYING... | t794104/ansible | lib/ansible/modules/files/find.py | Python | gpl-3.0 | 16,464 | [
"Brian"
] | a7fd8b74172aed9207f417fc54c4ee7f02650d3cb5f7c71927fa2cbf8b4251ee |
import base64
import os
import re
import shutil
import subprocess
import tempfile
import urllib
from contextlib import contextmanager
from typing import Any, Dict, Iterable, Iterator, List, Optional, Sequence, Set, Tuple, Union
from unittest import TestResult, mock
import lxml.html
import orjson
from django.apps impor... | showell/zulip | zerver/lib/test_classes.py | Python | apache-2.0 | 50,855 | [
"VisIt"
] | b6afb97df4e6c999a1633d0182538c6201d7604fee453f47df366f7c3ca8a072 |
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2002 Bruce J. DeGrasse
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007-2009 Brian G. Matherly
# Copyright (C) 2007 Robert Cawley <rjc@cawley.id.au>
# Copyright (C) 2008-2009 James Friedmann <jfriedm... | gramps-project/addons-source | DetDescendantReport-images/detdescendantreporti.py | Python | gpl-2.0 | 55,465 | [
"Brian"
] | 98db80548dd353f94220ff96283f3f4688f8d3687e8c2e3da3fc2d01d311d70c |
from setuptools import setup
setup(
name='ipyaudio',
version='0.0',
description='Bridge PortAudio, IPython interactive widgets, and DSP callbacks',
author='Brian McFee',
author_email='brian.mcfee@nyu.edu',
url='http://github.com/bmcfee/ipyaudio',
download_url='http://github.com/bmcfee/ipyau... | bmcfee/ipyaudio | setup.py | Python | mit | 903 | [
"Brian"
] | fdb65b1f8e2c769e3b2bb64d0acb275118381e89f52ef69ea44b4a814ec4404b |
# -*- coding: utf-8 -*-
from __future__ import division, print_function
import os
import math
import time
import itertools
import functools
import collections
import sys
import platform
import warnings
import re
from functools import reduce
import threading
import six
import vaex.utils
# import vaex.image
import numpy... | maartenbreddels/vaex | packages/vaex-core/vaex/dataframe.py | Python | mit | 282,160 | [
"Gaussian"
] | 460ab1acb9ef710939ef541cb63a8682e9379ddd74877bb13348d22630eb9dc3 |
#!/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/e2openplugin-OpenWebif | plugin/controllers/views/mobile/movies.py | Python | gpl-2.0 | 8,429 | [
"VisIt"
] | 86257ac1e02a8c8ccf7d705a59f704d80df61bbf27f599c48f8b13dba6585cf6 |
#!/usr/bin/python
usage = """a script that tests the basic functionality of our modules"""
#=================================================
import os
import sys
sys.path.append("/home/reed/LIGO/BAYESburst/bayesburst/")
import numpy as np
import healpy as hp
import utils
import detector_cache
import time
import ... | reedessick/bayesburst | methods_tests.py | Python | gpl-2.0 | 66,937 | [
"Gaussian"
] | c8f39d32f0d0c9987180d3614ca8ed24398f2cb4f6d6706c24c5b9112bb3bc5c |
#
# Copyright (C) 2013-2018 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... | mkuron/espresso | testsuite/python/rigid_bond.py | Python | gpl-3.0 | 1,942 | [
"ESPResSo"
] | 17c7ffc5add56efa67054b78c29cd7ac7d04783c8d4147bfe42b00f8be300bf5 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kratman/psi4public | psi4/driver/qcdb/__init__.py | Python | gpl-2.0 | 1,840 | [
"CFOUR",
"ORCA",
"Psi4"
] | 0ea860fcfd840ffce3a22483d3cd0c9a2530257a7f19ab1e95023a95d760deb9 |
__author__ = 'Thomas Rueckstiess, ruecksti@in.tum.de'
from scipy import random
from pybrain.structure.modules.neuronlayer import NeuronLayer
from pybrain.tools.functions import expln, explnPrime
from pybrain.structure.parametercontainer import ParameterContainer
class GaussianLayer(NeuronLayer, ParameterContainer):
... | comepradz/pybrain | pybrain/structure/modules/gaussianlayer.py | Python | bsd-3-clause | 1,579 | [
"Gaussian"
] | 8853682203cc1834a280af420514dbd218e0ab332f935d72cd203ecda97ddc3c |
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