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# $Id$
#
# Copyright (C) 2002-2006 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
"""unit testing code f... | AlexanderSavelyev/rdkit | rdkit/Chem/Pharm2D/UnitTestGobbi.py | Python | bsd-3-clause | 5,499 | [
"RDKit"
] | d6772a0809c508a29873d4105695e3c47e26cc9c41a490fa4ab6116667179ee8 |
#
# Honeybee: A Plugin for Environmental Analysis (GPL) started by Mostapha Sadeghipour Roudsari
#
# This file is part of Honeybee.
#
# Copyright (c) 2013-2015, Mostapha Sadeghipour Roudsari <Sadeghipour@gmail.com>
# Honeybee is free software; you can redistribute it and/or modify
# it under the terms of the GNU Ge... | samuto/Honeybee | src/Honeybee_Lookup Daylighting Folder.py | Python | gpl-3.0 | 9,600 | [
"EPW"
] | c345dc8b98c3d6ff7a8f5b45d340afa57770413f613e8786ab61526acea7334e |
#
# This file is part of Sequana software
#
# Copyright (c) 2016 - Sequana Development Team
#
#
# Distributed under the terms of the 3-clause BSD license.
# The full license is in the LICENSE file, distributed with this software.
#
# website: https://github.com/sequana/sequana
# documentation: http://sequana.read... | sequana/sequana | sequana/modules_report/summary.py | Python | bsd-3-clause | 11,824 | [
"Bioconda",
"VisIt"
] | f0d8a2ae79dfed2f31e5666da9be62dbad69d4c7977496b6f09b29b8d47dd7a6 |
from flask import Flask, render_template, session, request, redirect
import random
app = Flask(__name__)
app.secret_key = 'my_secret_key'
@app.route('/')
def index():
if not 'gold' in session:
session['gold'] = 0
if not 'activities' in session:
session['activities'] = []
return render_temp... | authman/Python201609 | Guerrero_Melissa/Assignments/Guerrero_Flask_Olympics/olympics8/server.py | Python | mit | 1,530 | [
"CASINO"
] | 265a66f604b2008f8cef5325800e8ce376316c0d6768306b88e38c89b43e63ef |
#!/usr/bin/env python3
from nxtools import log_traceback
from firefly.application import FireflyApplication
if __name__ == "__main__":
app = FireflyApplication()
try:
app.start()
except Exception:
log_traceback()
| immstudios/firefly | firefly.py | Python | gpl-3.0 | 243 | [
"Firefly"
] | 6651bd75cabb22e9a178f8e23d598c08161b698bc3dec3baac298e7ed5ab79e2 |
# -*- coding: utf-8 -*-
# Copyright (C) 2017 by Pedro Mendes, Virginia Tech Intellectual
# Properties, Inc., University of Heidelberg, and University of
# of Connecticut School of Medicine.
# All rights reserved.
# Copyright (C) 2010 - 2016 by Pedro Mendes, Virginia Tech Intellectual
# Properties, Inc., Universit... | jonasfoe/COPASI | copasi/bindings/python/unittests/Test_CReport.py | Python | artistic-2.0 | 2,748 | [
"COPASI"
] | 4f9f5a339e115d2b3a4ab471783c1e7130109e29db4406c3d48c664896a13731 |
#!/usr/bin/env python
# By Jason Ladner
from __future__ import division
import sys, optparse, os, pysam
#In version 2, added ability to limit calculations to a subset region of the genome
#Provide with a text file that has a header and three tab-delimited columns
#Only the third column is used and should be bam... | jtladner/Scripts | strand_specific_coverage/strand_ratio_counts/strand_ratio_counts_v2.py | Python | gpl-3.0 | 3,435 | [
"pysam"
] | 29ee39ad9f6902d8d061935c844fddd2073c2d43ab849707c3d54630c3266535 |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | alsrgv/tensorflow | tensorflow/tools/compatibility/ast_edits.py | Python | apache-2.0 | 38,290 | [
"VisIt"
] | 5b15b504f7a62b3e8ff9ff05ec907c72ba54f6de1230055068a0a124d96ed396 |
from vtk import *
import sys
import os
import time
myProcId = 0
numProcs = 1
compManager = vtkCompositeManager()
if compManager.GetController():
myProcId = compManager.GetController().GetLocalProcessId()
numProcs = compManager.GetController().GetNumberOfProcesses()
try:
v = vtkMesaRenderer()
if myPro... | arnaudgelas/VTK | Examples/ParallelProcessing/MPI/Python/ParallelCone.py | Python | bsd-3-clause | 2,152 | [
"VTK"
] | 8571f2cef7d9cd575b419cbc5cc09f3f89997ff6fb5aad985795ba1934bf488e |
import os
from bs4 import BeautifulSoup
from decimal import Decimal as D
from ..base import BaseAccountScraper
class AustralianEthicalScraper(BaseAccountScraper):
scrape_code = 'australianethical'
default_currency = 'AUD'
def login(self):
self.browser.visit(
'https://memberservices.... | elbaschid/geldmaschine | geldmaschine/scrapers/au/australian_ethical.py | Python | mit | 1,358 | [
"VisIt"
] | bc6c712d83c19ca2e373bfc784f230cd39509e3b2d0676b6bc73206ed2d7c76b |
"""
Bioconda Bot & Github App
.. autosummary::
:toctree:
chat
commands
config
events
tasks
views
web
worker
"""
| bioconda/bioconda-utils | bioconda_utils/bot/__init__.py | Python | mit | 141 | [
"Bioconda"
] | 647123a3fce9f6a75972760cb56f9e3cc1bbfd4390c9bd2a5c11811aadeb7175 |
#!/usr/bin/env python
"""script to concatenate the dirac.cfg file's Systems sections with the content of the ConfigTemplate.cfg files."""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from collections import OrderedDict
import logging
import os
import re
i... | ic-hep/DIRAC | docs/diracdoctools/cmd/concatcfg.py | Python | gpl-3.0 | 5,548 | [
"DIRAC"
] | 8a33504c882c826351a99b30bdc52bad097c7dcd8cd1c6ab21efd4ba564246d3 |
#!/usr/bin/env python
class configuracion():
"""
Esta clase cumple la función de una base de datos o fichero de configuración, donde se almacenan de
manera temporal las preferencias de uso del ReDA.
"""
color = 0
"""Indica el color de la camisa del interprete, sus posibles valores son 0... | joseguerrero/sembrando | src/presentacion/librerias/configuracion.py | Python | gpl-3.0 | 4,541 | [
"VisIt"
] | 83fa5bde3385de94dcf833155ae8ff0cdbcbd64d90155fbfc8337734805e6bb9 |
#!/usr/bin/env pythonw
#!/usr/bin/env ffmpeg
#################################
# NPR Leveler
# NPR Labs, Copyright 2015
# Provides a platform-agnostic user interface for analyzing and
# adjusting audio files to enforce compliance with EBU Loudness
# standards.
#
# This version is for DEBUGGING PURPOSES ONLY and h... | goldfarb/LVLR | simpler.py | Python | gpl-2.0 | 74,223 | [
"VisIt"
] | e0910cf80c40afb0aff4769fbbd49770a996345a86a4e566babb0f823784a3b1 |
# coding: utf-8
"""
Abinit Flows
"""
from __future__ import unicode_literals, division, print_function
import os
import sys
import time
import collections
import warnings
import shutil
import pickle
from six.moves import map
from atomicfile import AtomicFile
from pprint import pprint
from prettytable import PrettyTa... | yanikou19/pymatgen | pymatgen/io/abinitio/flows.py | Python | mit | 50,423 | [
"ABINIT",
"pymatgen"
] | 62c214e2cb2cd590c869c5db22da7ca5de1a9c36123a91a07ce3dd80ccc14c2d |
import datetime
import unittest
from db.player.player import Player
#from sitescraper.nhl.tsndotca import TsnDotCaScraper
from sitescraper.nhl.scottcullen import ScottCullenScraper
from sitescraper.nhl.cbssportsdotcom import NhlCbsSportsDotComSraper
class HockeyPlayer(Player):
def __init__(self, name=None, team... | jeffdasilva/stattrack | db/player/hockey.py | Python | gpl-2.0 | 12,625 | [
"COLUMBUS"
] | 4c0219e3683ba103de0bdf2a38543ff9ca7619007c44585106d7d856acca1d8b |
"""
hw3_2.py
Monitoring how the ion channels activate
"""
import neuron
# neuron.load_mechanisms('.')
from neuron import h, gui
h.load_file("stdrun.hoc") # load init(), run(), etc.
# Create a cell
soma = h.Section(name="soma")
soma.diam = 15
soma.L = 15
soma.insert("ml")
soma.betaw_ml = 0 # This controls the ha... | shhong/a310_cns_2017 | Assignment_3/hw3_2.py | Python | gpl-3.0 | 1,297 | [
"NEURON"
] | 0b9dc98d6b69226d05aded8b72a54b0aac0eaa342c4c3dda382512e3b530a1c4 |
"""
Plugin for pylint that tells it about flask's extension classes.
"""
from pylint.utils import PyLintASTWalker
from logilab.astng import MANAGER
from logilab.astng import node_classes
def copy_node_info(src, dest):
"""Copy information from src to dest
Every node in the AST has to have line number information.... | pave/pylint_flask_ext | flask_ext_clean.py | Python | mit | 5,123 | [
"VisIt"
] | b63fa8ee3f58ce9f59f7d1ac1c0a170c7f72cb3b32e72cef1c28dcf25ab462a6 |
# Copyright 2014-2019 The PySCF Developers. 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 appl... | gkc1000/pyscf | pyscf/adc/test/test_OH_uadc_ea.py | Python | apache-2.0 | 3,365 | [
"PySCF"
] | 83894d6a57c7cae008d7eed32b0ffec11a415d539a3c1a164169ce88b1130b03 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements classes to perform bond valence analyses.
"""
import collections
import numpy as np
import operator
import os
import functools
from math import exp, sqrt
from monty.serialization imp... | gVallverdu/pymatgen | pymatgen/analysis/bond_valence.py | Python | mit | 21,352 | [
"Gaussian",
"pymatgen"
] | 2e465c3e31a1b6ebfbb1f0504608897b469263e01531179d9b9bff3721831667 |
#!/usr/bin/env python3
# generate 'mandel_polydata.vtp' first !
import vtk
# source
r = vtk.vtkXMLPolyDataReader()
r.SetFileName('mandel_polydata.vtp')
# mapper
mandelMapper = vtk.vtkDataSetMapper()
mandelMapper.SetInputConnection(r.GetOutputPort())
mandelMapper.SetScalarModeToUsePointFieldData()
mandelMapper.Select... | dubrayn/dubrayn.github.io | examples/vtk/vtk_load_polydata.py | Python | mit | 785 | [
"VTK"
] | 1496ba2a641c9ec4de422bb338d3f761f14c0de3c1c02ccbb91009488c747395 |
#!/usr/bin/env python
"""
Copyright (c) 2006-2015 sqlmap developers (http://sqlmap.org/)
See the file 'doc/COPYING' for copying permission
"""
import cookielib
import glob
import inspect
import logging
import httplib
import os
import random
import re
import socket
import string
import sys
import tempfile
import threa... | krintoxi/NoobSec-Toolkit | NoobSecToolkit /tools/inject/lib/core/option.py | Python | gpl-2.0 | 90,227 | [
"VisIt"
] | 49cde81878d81f3df18c356710b83683d003cfbbd4b5e70bbaa716619dd77e49 |
"""A grid plane component.
"""
# Author: Prabhu Ramachandran <prabhu_r@users.sf.net>
# Copyright (c) 2005-2006, Enthought, Inc.
# License: BSD Style.
# Enthought library imports.
from traits.api import Instance, Int, Range
from traitsui.api import View, Group, Item
from tvtk.api import tvtk
# Local imports.
from may... | dmsurti/mayavi | mayavi/components/custom_grid_plane.py | Python | bsd-3-clause | 6,800 | [
"Mayavi"
] | 4ff53635d08a93199afc5f8debef95cd596e01bf74831afdf6163974d4fc1c6a |
# Docstrings for generated ufuncs
#
# The syntax is designed to look like the function add_newdoc is being
# called from numpy.lib, but in this file add_newdoc puts the
# docstrings in a dictionary. This dictionary is used in
# _generate_pyx.py to generate the docstrings for the ufuncs in
# scipy.special at the C level... | pizzathief/scipy | scipy/special/add_newdocs.py | Python | bsd-3-clause | 238,216 | [
"Gaussian"
] | 8792c405ebf61d6afe1d843caa1477b44def8611a4144fe78504bb96b90ea9c0 |
# moose.py ---
# Filename: moose.py
# Description:
# Author: Subhasis Ray
# Maintainer:
# Copyright (C) 2010 Subhasis Ray, all rights reserved.
# Created: Sat Mar 12 14:02:40 2011 (+0530)
# Version:
# Last-Updated: Tue Oct 27 15:00:31 2015 (-0400)
# By: Subhasis Ray
# Update #: 2182
# URL:
# Keywor... | dilawar/moose-full | moose-core/python/moose/moose.py | Python | gpl-2.0 | 13,702 | [
"MOOSE"
] | 91bfe06cff5fb3ec192fecddf38e614a274b5fd5199263cd6ec393678f8cc3de |
#!/usr/bin/env python
import matplotlib.pyplot as plt
import numpy as np
import pickle
import phrases
from scipy import stats
from math import *
import MDAnalysis as MD
from argparse import ArgumentParser
parser = ArgumentParser( description = 'Find Binding Sites in Receptor+Ligand MD simulation')
#
# INPUT FILES
#
pa... | sherpaman/MolToolPy | bin/phrases-analysis.py | Python | gpl-2.0 | 4,412 | [
"MDAnalysis"
] | c13e9bc04fd4021fd71d51932132bbc5d4dab883b0d96d4b1fd2cd3bb4102a35 |
#!/usr/bin/env python
#
# Check OpenStack Neutron Agent Status
# ===
#
# Dependencies
# -----------
# - python-neutronclient and related libraries
#
# Performs API query to determine 'alive' status of all
# (or filtered list of) Neutron network agents. Also has
# ability to warn if any agents have been administratively... | intoximeters/sensu-community-plugins | plugins/openstack/neutron/neutron-agent-status.py | Python | mit | 3,806 | [
"Brian"
] | 382a2e026da9ddd14fc3b8236c18e1fd727fdce527b38864f2bbd747dc879a6d |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Package for analyzing elastic tensors and properties.
"""
from .elastic import * # noqa
from .strain import * # noqa
from .stress import * # noqa
| vorwerkc/pymatgen | pymatgen/analysis/elasticity/__init__.py | Python | mit | 248 | [
"pymatgen"
] | fa11d10932eea7ad6e64062746138e40854daa4add2baf4dc116696e1c9f7335 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2013 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## 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 Foundati... | andrebellafronte/stoq | stoqlib/domain/test/test_image.py | Python | gpl-2.0 | 2,552 | [
"VisIt"
] | 6dd431542274bf3a02de0a828629a1cb3509cd3f76c15b3f4a20f1866ff91714 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# dddheatmap.py
#
# Copyright 2016 Cosmo <cosmo@CosmoSpectre>
#
# 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 L... | CosmoJG/neural-heatmap | ddd-path-length/dddheatmap.py | Python | gpl-3.0 | 7,284 | [
"NEURON"
] | b32d3681b11524eb24980249b6fe7d58d2864cb4560abc677b77b676b7d1908e |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
The maths module provides higher-level interfaces to some of the operations
that can be performed with the fslmaths command-line program.
"""
import os
import numpy as np
from nipype.interfaces... | Leoniela/nipype | nipype/interfaces/fsl/maths.py | Python | bsd-3-clause | 11,588 | [
"Gaussian"
] | 9de12fdf2abbf2ef9898da105ebdc264b9d325c018c344de5b4b8ad94dc221dd |
"""
Viewing Stanford 3D Scanning Repository bunny model
"""
# Copyright (c) 2014, Enthought, Inc.
# Standard library imports
import os
from os.path import join
# Enthought library imports
from mayavi import mlab
### Download the bunny data, if not already on disk ############################
if not os.path.exists('bu... | liulion/mayavi | examples/mayavi/mlab/bunny.py | Python | bsd-3-clause | 1,034 | [
"Mayavi"
] | 5d48de8895a0f96bbbbf9f4d260eaee71c43a0d2b643dee1d1be59abf723edbf |
"""
Spectral energy distributions
===============================
Methods and classes for dealing with spectral energy distributions (SEDs).
"""
import numpy, pylab, os, scipy
from . import lsd # intrapackage reference
import astropy.io.ascii as ascii
class SED:
"""
Class that defines objects storing Spectral en... | rsnemmen/nemmen | nmmn/sed.py | Python | mit | 56,230 | [
"Bowtie"
] | 52853d20b2bbde06508a630103f9a2f32e6f3dbdcdcbc86c0c4daa35c3b21faa |
#!/usr/bin/env python3
#* 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/licenses/lgp... | nuclear-wizard/moose | python/peacock/tests/utils/test_WidgetUtils.py | Python | lgpl-2.1 | 1,300 | [
"MOOSE"
] | 0d89f5c7533ba8d55641a2e972567685342a99fbceca0cb14a8e0e686ad3ea82 |
from __future__ import print_function
__version__ = '0.3.1'
from .common.envcheck import *
from .common.cuda_probe import is_cuda_available
def run_env_check() :
print('CUDA : {}'.format('Available' if is_cuda_available() else 'Not available'))
checker = EnvChecker(__version__)
checker.check()
check... | shinmorino/quant_sandbox | sqaodpy/sqaod/__init__.py | Python | bsd-3-clause | 901 | [
"VisIt"
] | 4f525be1456a52399b0ba01db8f29d6d6c9c41d450c84995cad960c914d83024 |
"""
Vector Autoregression (VAR) processes
References
----------
Lutkepohl (2005) New Introduction to Multiple Time Series Analysis
"""
from __future__ import division, print_function
from statsmodels.compat.python import (range, lrange, string_types, StringIO, iteritems,
cStringIO)
fr... | detrout/debian-statsmodels | statsmodels/tsa/vector_ar/var_model.py | Python | bsd-3-clause | 50,350 | [
"Gaussian"
] | 78a61219c37325bd065a0ab01c024a6a89db1ef86ad529c8fed499a4e074e747 |
import numpy as np
import datetime
from copy import deepcopy
from scipy.io import netcdf
from matplotlib.dates import *
import matplotlib.pyplot
import os
import sys
import Common
class File:
def __init__(self, filename):
self.checkFile(filename)
self.filename = filename
file = netcdf.netcdf_file(... | WFRT/Comps | graphics/files/VerifFile.py | Python | bsd-3-clause | 2,640 | [
"NetCDF"
] | d1c1e6d8fbf53485eeb3cfffc00e88d9544db4ebfef574784f0af26d53d204ca |
# Licensed under GPL version 3 - see LICENSE.rst
'''`Mayavi <http://docs.enthought.com/mayavi/mayavi/>`__ plotting backend
Mayavi is a python package for interactive 3-D displays that uses VTK underneath.
Fuctions in this module display rays or objects in 3D using mayavi. Each of them
requires a ``mayavi.core.scene.Sc... | hamogu/marxs | marxs/visualization/mayavi.py | Python | gpl-3.0 | 9,786 | [
"Mayavi",
"VTK"
] | 9f4be2158ec694c7d61e1d10932bdeac703969c09ff47978a29f5e2160cd70c2 |
langversion = 1
langname = "Norsk"
##updater
# text construct: "Versjon "+version+available+changelog
#example: Version 3 available, click here to download, or for changelog click here
available = " tilgjengelig, trykk her for å laste ned"
changelog = ", eller trykk her for endringsliste"
##world gen
worldify = "fra... | flying-sheep/omnitool | Language/norwegian.py | Python | mit | 3,154 | [
"VisIt"
] | 1e81e5b879c1ae70ed5cdf035402524718663bc5a6b479a5ccf0866315051764 |
# ----------------------------------------------------------------------
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
# http://lammps.sandia.gov, Sandia National Laboratories
# Steve Plimpton, sjplimp@sandia.gov
#
# Copyright (2003) Sandia Corporation. Under the terms of Contract
# DE... | qipa/lammps | python/lammps.py | Python | gpl-2.0 | 6,952 | [
"LAMMPS"
] | 13651a5e421bcfa5391a6d4676bd261144120ea64986649c488260a9d41fbcdb |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | yanchen036/tensorflow | tensorflow/contrib/autograph/converters/break_statements.py | Python | apache-2.0 | 4,651 | [
"VisIt"
] | 6a7fcc64cc589f1c82aad0505420751343839af84bc1ed37c87361ece460d075 |
## \mainpage GOGranny :: A Python library for GO network graph analysis and representation
# \section desc Description
# GOGranny is a python library that uses the Gene Ontology to create a network relating terms
# to each other and proteins to terms. Given a species name or the name of one of the origin
# databases fo... | aswarren/GOGranny | GOGranny/__init__.py | Python | gpl-2.0 | 1,805 | [
"Brian"
] | 7fdb61da1265688d10514c4cc48f65146428f6806bb668555fc9363f45baa42e |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.MDAnalysis.org
# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein
# and contributors (see KATHRYN for the ... | sseyler/PSAnalysis | source/core/path_pair.py | Python | gpl-3.0 | 4,557 | [
"MDAnalysis"
] | 678a45652d91a410e08e26a9ef9af3cd3da89bafef0976566272067bfed7220d |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2006 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publi... | Forage/Gramps | gramps/plugins/tool/rebuild.py | Python | gpl-2.0 | 3,649 | [
"Brian"
] | 6eee8d166dc2c1caff6da5da29ba13e0e50d717af9d3252bc3971f5d51a8b7c9 |
"""
Module that implements the EppClient class
"""
try:
# use gevent if available
import gevent.socket as socket
import gevent.ssl as ssl
except ImportError:
import socket
import ssl
import struct
from collections import deque
import logging
from six import PY2, PY3
from past.builtins import xrang... | cloudregistry/eppy | eppy/client.py | Python | mit | 13,419 | [
"VisIt"
] | 76665e22b5037d846a8521d83bded45418607ec2c7600fe5b27306022e11c89d |
'''This script will concatenate blastn, blastx, and blastp results into
a single csv summary annotation.'''
import argparse
def blastDict(indir):
# Builds dictionary from blast files
annotation = {}
blastn = indir + "blastn.outfmt6"
blastx = indir + "blastx.outfmt6"
blastp = indir + "blastp.outfmt6"
annotation... | icwells/Quoll | bin/blastToCSV.py | Python | gpl-3.0 | 2,939 | [
"BLAST"
] | e65e2244fc7a16bf6635994631d8735ec407f95114607ceaeaacbbf699a3a704 |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to make it easier to submit
# large numbers of jobs on supercomputers. It provides a python interface to physical input, suc... | pylada/pylada-light | src/pylada/crystal/write.py | Python | gpl-3.0 | 19,336 | [
"CASTEP",
"CRYSTAL",
"GULP",
"VASP"
] | cc962743955bc2172cacac6480835a258e4e9b98c9a2536d84203ee9ff656ab4 |
"""
Module simplifying manipulation of XML described at
http://libvirt.org/formatdomain.html
"""
import logging
from autotest.client.shared import error
from virttest import virsh, xml_utils
from virttest.libvirt_xml import base, accessors, xcepts
from virttest.libvirt_xml.devices import librarian
class VMXMLDevices... | kylazhang/virt-test | virttest/libvirt_xml/vm_xml.py | Python | gpl-2.0 | 31,826 | [
"VisIt"
] | ea6e13cd9314408677965c87a20eb5b4715749a60186d017feadd1373ab7c6c2 |
# -*- coding: utf-8 -*-
# Copyright: (c) 2020-2021, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
"""Dependency resolution machinery."""
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import typing as t
if t.TYPE_... | mattclay/ansible | lib/ansible/galaxy/dependency_resolution/__init__.py | Python | gpl-3.0 | 2,142 | [
"Galaxy"
] | fda6143a05e98784442c0832a611dd441c9f3cdc8449f40e639a9869116bbf77 |
# 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 and/or modify
# it under the terms of t... | capoe/espressopp.soap | src/analysis/RDFatomistic.py | Python | gpl-3.0 | 2,047 | [
"ESPResSo"
] | 0b50533edcdff87c4395d216d55611fc66ddb2fd24b402d4ff0e104b00eb781d |
#!/usr/bin/env python
# Copyright (C) 2008 Brian Quinlan
#
# 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.
#
#... | hfiguiere/libopenraw | python/demo/cfa.py | Python | lgpl-3.0 | 2,693 | [
"Brian"
] | 4e225044a75fcbe36e3eba1d750ea566061eb8dc1a2670b9d996f29551f9c9a0 |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to make it easier to submit
# large numbers of jobs on supercomputers. It provides a python interface to physical input, suc... | pylada/pylada-light | tests/vasp/test_vasp_keywords.py | Python | gpl-3.0 | 8,654 | [
"CRYSTAL",
"VASP"
] | 85f9f7bc0bbb8bfdc2adb4452479db0a23f6c83d626cb6ecdf4c336584820a38 |
'''This script demonstrates how to build a variational autoencoder with Keras.
Reference: "Auto-Encoding Variational Bayes" https://arxiv.org/abs/1312.6114
'''
import numpy as np
import matplotlib.pyplot as plt
from scipy.stats import norm
from keras.layers import Input, Dense, Lambda
from keras.models import Model
f... | nwiizo/workspace_2017 | keras_ex/example/variational_autoencoder.py | Python | mit | 3,491 | [
"Gaussian"
] | 24d41b0dd369c9f090bdff3dc927c5e24fbe8c091c49aa101a42b4621d436428 |
from octopus.runtime import *
from octopus.sequence.util import Trigger
from twisted.internet import reactor
def fn ():
print "fn called"
return sequence(
log("fn called"),
set(v, False)
)
v = variable(False, "v", "v")
v2 = variable(False, "v", "v")
o1 = Trigger(v == True, fn)
o2 = Trigger(v2 == True, log("o... | rasata/octopus | examples/test_on.py | Python | mit | 582 | [
"Octopus"
] | f85d014455835b35131a5367ce12d9e2fbee658e8bdc47b3780c1cdd9ece25ef |
"""The ants module provides basic functions for interfacing with ants functions.
Change directory to provide relative paths for doctests
>>> import os
>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
>>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
>>> os.chdir(... | JohnGriffiths/nipype | nipype/interfaces/ants/registration.py | Python | bsd-3-clause | 42,530 | [
"Gaussian",
"VTK"
] | 00250899f1f572043fa01c7f862ba45fc0a4318a8e604ea9b54c7f329e9c42fe |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
=========================================================================
Program: Visualization Toolkit
Module: TestGPURayCastIndependentComponent.py
Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
All rights reserved.
See Copyright... | hlzz/dotfiles | graphics/VTK-7.0.0/Rendering/Volume/Testing/Python/TestGPURayCastIndependentComponent.py | Python | bsd-3-clause | 4,317 | [
"VTK"
] | 40c708f0c0facc55dd824762088c9728acb60b2c4d1dc687db6972a69e19a520 |
import unittest
from create_EGAP_json import (schema_to_spreadsheet_mapping,
make_project_dict,
make_registration_dict,
other_mapping,
)
HEADER_ROW = ['POST DATE',
'ID',
'STATUS',
'TITLE',
'B2 AUTHORS',
'EMAIL',
'B3 ACKNOWLEDGEMENTS',
'B4 FACULTY MEMBER?',
'B5 PROSPECTIVE OR RETROSPECTIVE?',
'B6 EXPERIMENT... | saradbowman/osf.io | scripts/EGAP/EGAP_tests.py | Python | apache-2.0 | 4,472 | [
"Brian"
] | db413300d81bddf462864ba55a0b32bb2adb18fdab7af792fdac89c4e2715b21 |
#!/usr/bin/env python
# This example shows how to construct a surface from a point cloud.
# First we generate a volume using the
# vtkSurfaceReconstructionFilter. The volume values are a distance
# field. Once this is generated, the volume is countoured at a
# distance value of 0.0.
import os
import string
... | hlzz/dotfiles | graphics/VTK-7.0.0/Examples/Modelling/Python/reconstructSurface.py | Python | bsd-3-clause | 2,693 | [
"VTK"
] | 345ab0b69262dfe700c7ef644e403fc2da89e14ea6538b9b151c43eed8f676b3 |
"""SConsAddons.Options.Xerces
Defines options for Xerces project
"""
#
# __COPYRIGHT__
#
# This file is part of scons-addons.
#
# Scons-addons 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 o... | rpavlik/cppdom-old-fork | deps/scons-addons/src/SConsAddons/Options/Xerces.py | Python | lgpl-2.1 | 5,367 | [
"VTK"
] | f5afe3938c92226946ff6f2c087dab5b4019f67de97c266e9889e873fb3dc56f |
# Copyright 2014 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Environment setup and teardown for remote devices."""
import distutils.version
import json
import logging
import os
import random
import sys
from pylib ... | mdakin/engine | build/android/pylib/remote/device/remote_device_environment.py | Python | bsd-3-clause | 13,388 | [
"Galaxy"
] | c5ab2d40cc295d05626882474b77be2487a889f92a9fd6f8bc95d2e3fe3ac67a |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2016 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 ... | kannon92/psi4 | psi4/driver/p4util/exceptions.py | Python | gpl-2.0 | 5,625 | [
"Psi4"
] | 7335f2c7d1fa4e68790d763308df168853fc40d95036f096006cfc19d2be1a9b |
def initialState():
state = {
'carpets':{
'carpet1': {
'name': 'Floral Rug',
'image': 'https://images.konga.com/v2/media/catalog/product//H/N/HNKG-Brown-and-Blue-Floral-Rug---150x230-cm-7530162_1.jpg?h=400&w=400&scale_mode=aspect_fit',
'desc': 'The Hong Kong 33L Brown/Blue is a hand tufted acrylic ru... | AdinoyiSadiq/back-office-tool | baseState.py | Python | mit | 5,124 | [
"exciting"
] | 01e94d50d44887d48a1c5c99eae279e89de4cdb0d2271aedc8a02219c804c01a |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import unittest
import os
from pymatgen.io.feff import Header, FeffTags, FeffLdos, FeffPot, Xmu, \
FeffAtoms
test_dir = os.path.join(os.path.dirname(__file__), "..... | sonium0/pymatgen | pymatgen/io/feff/tests/test_feffio.py | Python | mit | 7,590 | [
"FEFF",
"pymatgen"
] | a6367d88cfc8b4254d842cb898aa7ff8c286c93d653b5b8d056f8255bb19e426 |
# Copyright 2014 Uri Laserson
#
# 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,... | churchlab/ulutil | ulutil/SeqRecordLite.py | Python | apache-2.0 | 4,468 | [
"Biopython"
] | 8e02e49a7a9f4fa8c550010d0f5c7c0941ee0278b435572c0ee40dec6d5186be |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | magic/services/attenuation.py | Python | agpl-3.0 | 16,441 | [
"Galaxy"
] | 91529eb54039d799b650f266192eafa19df0d3931f5efaa18d0792dcbc7794fb |
#!/galaxy/home/mgehrin/hiclib/bin/python
"""
Reads a list of intervals and a set of indexed mafs. For each interval print
the amount covered by each species other than the reference.
usage: %prog maf_files [options] < interval_file
-s, --src=s: Use this src for all intervals
-p, --prefix=p: Prepend this... | bxlab/HiFive_Paper | Scripts/HiCLib/bx-python-0.7.1/build/scripts-2.7/maf_region_coverage_by_src.py | Python | bsd-3-clause | 1,919 | [
"Galaxy"
] | f107c28e4e0b2ebac69ccf5f4850835e180b9cd1f7a4816368972054e7fae31d |
# 2013 derrick.snowden@noaa.gov: initial version of python script for creating
# IOOS glider NetCDF template.
# 2013-07-19 kerfoot@marine.rutgers.edu: modified script to adhere to most
# recent version of CDL template:
# - creation of variables and addition of recommended variable attributes
# - variable at... | acrosby/glidertraj | ioos_glider.py | Python | gpl-3.0 | 56,531 | [
"NetCDF"
] | f342406e17393a8846d5d84e9107d72931317b5bf390b79021315e68f359e847 |
"""
Wrapper for OpenMM Amber potential.
To be consistent with GMIN, units are kcal/mol and angstroms
Requires:
coords.inpcrd and coords.prmtop
"""
# TODO: if BasePotential is imported after simtk imports, it gives a seg fault!!
from pygmin.potentials import BasePotential
from simtk.openmm.app imp... | js850/PyGMIN | pygmin/amber/openmm_potential.py | Python | gpl-3.0 | 4,891 | [
"Amber",
"OpenMM"
] | f9193bb664ba55535bcb112739237030576dd17ead108bceb61a614709a8c887 |
#!/usr/bin/python
"""Test of Orca output when tabbing on a page with imagemaps."""
from macaroon.playback import *
import utils
sequence = MacroSequence()
# Work around some new quirk in Gecko that causes this test to fail if
# run via the test harness rather than manually.
sequence.append(KeyComboAction("<Control>... | pvagner/orca | test/keystrokes/firefox/focus_tracking_imagemap.py | Python | lgpl-2.1 | 2,532 | [
"ORCA"
] | d38ac044e07779c63a60d3f2bdacbfbeb0e05843c583fcf4a963dcc0971c0494 |
"""Dirac notation for states."""
from sympy import Expr
from sympy.printing.pretty.stringpict import prettyForm
from sympy.physics.quantum.qexpr import (
QExpr, dispatch_method
)
__all__ = [
'KetBase',
'BraBase',
'StateBase',
'State',
'Ket',
'Bra',
'TimeDepState',
'TimeDepBra',
... | pernici/sympy | sympy/physics/quantum/state.py | Python | bsd-3-clause | 14,799 | [
"DIRAC"
] | 6f5c492308ec7e2c5a2a94867939c282533eadac9b882ec73ccee79885399017 |
# -*- coding: utf-8 -*-
import numpy as np
from sample import sample2D, sample2DU, sample2DV
from depth import sdepth
class Section(object):
"""Class for handling sections in a ROMS grid
The section is defined by a sequence of nodes, supposedly quite close
The endpoints of the section are nodes
T... | chiluf/roppy | roppy/section.py | Python | mit | 4,290 | [
"NetCDF"
] | 36cd838cce923528fd869e1265cf962fa0c3270cddd4fcddfd5ecb7e2c2ed8ea |
from buildbot.plugins import steps
from buildbot.steps.shell import ShellCommand
from buildbot.locks import WorkerLock
from buildbot.process.properties import Interpolate
class Steps:
def __init__(self,Environ):
# Max number of running builds
build_lock = WorkerLock('build',
maxCount = 2,
... | QEF/q-e_schrodinger | test-suite/buildbot/Udine_farm/worker.py | Python | gpl-2.0 | 20,336 | [
"EPW",
"Wannier90"
] | 9dd0c378954d95903585ed8d86658f366e6d2e81996bc2c26fadac35f28232e9 |
import warnings
import numpy as np
import pandas as pd
from scipy.sparse import csr_matrix, SparseEfficiencyWarning
from scipy.spatial.distance import pdist, squareform
from scvelo.preprocessing.neighbors import get_connectivities, get_neighs
from .utils import normalize
warnings.simplefilter("ignore", SparseEfficie... | theislab/scvelo | scvelo/tools/transition_matrix.py | Python | bsd-3-clause | 7,734 | [
"Gaussian"
] | 9251fea03c59babc94e21c5bc6159ac2b15b4d5b5515bb65acb06be535e51e8e |
# Copyright (C) 2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later versio... | KaiSzuttor/espresso | testsuite/scripts/samples/test_lb_profile.py | Python | gpl-3.0 | 1,280 | [
"ESPResSo"
] | 6e2dfb6835c8e481853605a53e9871d957d90601f546e15eaafdfd0a5f35f1ef |
# squid.py ---
#
# Filename: squid.py
# Description:
# Author: Subhasis Ray
# Maintainer:
# Created: Mon Feb 13 11:35:11 2012 (+0530)
# Version:
# Last-Updated: Thu Sep 20 14:05:27 2012 (+0530)
# By: subha
# Update #: 771
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
# Rewrite of th... | BhallaLab/moose | moose-examples/squid/squid.py | Python | gpl-3.0 | 13,343 | [
"MOOSE"
] | e0be8f6c1b3fd610e4f22069247ce5d289298cb5df213b256108122034537e9a |
#!/usr/bin/en python
from __future__ import print_function
import os
import sys
import glob
import json
import numpy as np
import pandas as pd
from lxml import objectify
def read_xml_sidecar(filepath):
"""
Read a CMTK xml sidecar file.
Returns
=======
lxml.objectify
"""
abs_path = os.path... | sibis-platform/ncanda-datacore | scripts/reporting/check_gradient_tables.py | Python | bsd-3-clause | 6,824 | [
"VisIt"
] | 31130ffba21771d17678155315f31b6eb1023c262bc7f8b50c5cc5ffaa00bbd1 |
#
# ----------------------------------------------------------------------------------------------------
#
# Copyright (c) 2007, 2015, Oracle and/or its affiliates. All rights reserved.
# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
#
# This code is free software; you can redistribute it and/or modify ... | graalvm/mx | mx_spotbugs.py | Python | gpl-2.0 | 7,596 | [
"VisIt"
] | ebd1a657e74852a245e873bb47378a92c48291f88ba64c124c7198093eed4cd6 |
# Contains region-specific attributes for Dubizzle sites
uae = {
'base_url': 'http://uae.dubizzle.com/search',
'cities': {
'code': 'site',
'options': {
'all': '--',
'dubai': '2',
'abudhabi': '3',
'ajman': '14',
'alain': '39',
... | Cyph0n/dubizzle | dubizzle/regions.py | Python | mit | 5,287 | [
"Jaguar"
] | af0f1489023e3700dd5bcfd73371dc3e58d5a6153b69880af07301e687df3693 |
# coding=utf-8
"""
Module for reading binary files in the Blackrock format.
Authors: Michael Denker, Lyuba Zehl
blackrockio
===========
Classes
-------
BlackrockIO - class to enable reading of BlackrockIO files
"""
import datetime
import os
import struct
from neo.io.baseio import BaseIO
import neo
import numpy... | SPP1665DataAnalysisCourse/python-neo | neo/io/blackrockio.py | Python | bsd-3-clause | 83,089 | [
"NEURON"
] | 127c7519c061894a6903a3a02664fde77dba7108db6a1a5c151eee9dbe48d541 |
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yasharmaster/scancode-toolkit | tests/licensedcode/test_match_set.py | Python | apache-2.0 | 4,841 | [
"VisIt"
] | be9c8e8b0abe2fb01e338ad0f4bb3bf7cf1bfaa254ccc5cfe36fd0f7d923218e |
#! /usr/bin/env python
"""Test script for the bsddb C module by Roger E. Masse
Adapted to unittest format and expanded scope by Raymond Hettinger
"""
import os, sys
import copy
import bsddb
import dbhash # Just so we know it's imported
import unittest
from test import test_support
from sets import Set
class TestBSD... | MalloyPower/parsing-python | front-end/testsuite-python-lib/Python-2.4/Lib/test/test_bsddb.py | Python | mit | 9,431 | [
"Brian"
] | e9b778814b2d30a9e0e46be8625aad8385a39a281353498e3323f8ecd74e677f |
#!/usr/bin/python
# vim: et sw=4 ts=4:
# -*- coding: utf-8 -*-
#
# Piwik - free/libre analytics platform
#
# @link http://piwik.org
# @license http://www.gnu.org/licenses/gpl-3.0.html GPL v3 or later
# @version $Id$
#
# For more info see: http://piwik.org/log-analytics/ and http://piwik.org/docs/log-analytics-tool-how-... | bigwhirled/elmsln | core/_nondrupal/piwik/misc/log-analytics/import_logs.py | Python | gpl-3.0 | 85,710 | [
"VisIt"
] | f4c308b3e3be0f9fda9a789fce4045e11508640d003e0daf158ae77a4f9a3f9d |
from DIRAC.AccountingSystem.Client.Types.BaseAccountingType import BaseAccountingType
import DIRAC
class DataOperation(BaseAccountingType):
def __init__(self):
super(DataOperation, self).__init__()
self.definitionKeyFields = [
("OperationType", "VARCHAR(32)"),
("User", "VAR... | DIRACGrid/DIRAC | src/DIRAC/AccountingSystem/Client/Types/DataOperation.py | Python | gpl-3.0 | 1,243 | [
"DIRAC"
] | a9b52ace039fc3971f843b3eaf8afbe37392089291d1e7a11cc3e4400532f200 |
import pysal
from pysal.common import *
import pysal.weights
import numpy as np
from scipy import sparse, float32
import scipy.spatial
import os
import operator
import scipy
__all__ = ['lat2W', 'block_weights', 'comb', 'order', 'higher_order',
'shimbel', 'remap_ids', 'full2W', 'full', 'WSP2W',
'i... | dfolch/pysal | pysal/weights/util.py | Python | bsd-3-clause | 32,056 | [
"COLUMBUS"
] | 81b89c35daa379d7c7db3c9df70bbb51e5004c63b43e8b8b4e530057a82ed696 |
""" Test functions for stats module
"""
from __future__ import division, print_function, absolute_import
import warnings
import re
import sys
import pickle
from numpy.testing import (TestCase, run_module_suite, assert_equal,
assert_array_equal, assert_almost_equal, assert_array_almost_equal,
assert_allclose,... | larsmans/scipy | scipy/stats/tests/test_distributions.py | Python | bsd-3-clause | 94,164 | [
"Gaussian"
] | 2216e6e3c0b879694dbc64e4fe90735351488e1ddee71e36b04e25e2d5f6ba1f |
#
# @file TestWriteSBML.py
# @brief Write SBML 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 generated automatically by convertin... | alexholehouse/SBMLIntegrator | libsbml-5.0.0/src/bindings/python/test/sbml/TestWriteSBML.py | Python | gpl-3.0 | 56,596 | [
"VisIt"
] | de325ef42411253a3c7c7a5c55fcfb1e401e0471152e5cca2e85ef3ca7a0a941 |
"""
Playground: Development of MorphoSphere3D
@authors: Fanny Georgi
"""
import skimage
import math
import cv2
from scipy import ndimage
from skimage import measure,morphology
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
from ggplot import *
from PIL import Image
import re
#import multiproes... | FannyGeorgi/SpheroidRDF3D | MorphoSphere3D/playground.py | Python | gpl-2.0 | 6,778 | [
"Gaussian"
] | c04136696db1e3e37b8d08b9ff797fa3a55441e39b2fb401251b035689b6d72e |
import sys
import time
import zmq
import numpy as np
import matplotlib as mpl
mpl.use('Qt4Agg')
from scipy.ndimage.interpolation import rotate
from scipy.optimize import curve_fit
from matplotlib.gridspec import GridSpec
from PyQt4 import QtCore, QtGui
from matplotlib.figure import Figure
from matplotlib.backends.backe... | cweninger/lcls-monitoring | client.py | Python | gpl-2.0 | 6,253 | [
"Gaussian"
] | d1f0a7a5acfff90c990e8f736670b7f64eb830b3794c660300ab73e802557bfb |
from textwrap import dedent
import tempfile
import yaml
import os
import subprocess as sp
import conda_build.api
def ensure_missing(package):
"""
Delete a package if it exists and re-index the conda-bld dir.
If a package is deleted from the conda-bld directory but conda-index is not
re-run, it remai... | bioconda/bioconda-utils | test/helpers.py | Python | mit | 3,715 | [
"Bioconda"
] | 004c127711dd1609c972daa560750aff3fb9fba38cbd8d623881960386055ecf |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
For UHF method, level shift for alpha and beta spin can be different.
'''
from pyscf import gto, scf
mol = gto.M(
atom = '''
O 0 0. 0
H 0 -2.757 2.587
H 0 2.757 2.587''',
basis = 'ccpvdz',
)
mf = scf.RHF(mol)
mf.level_shift = 0.2... | gkc1000/pyscf | examples/scf/03-level_shift.py | Python | apache-2.0 | 568 | [
"PySCF"
] | 77253f39280b1f09eecf09dafd440548ff05dff1c82bba4d4f66d9628e4bd04b |
#!/usr/bin/env python
## category General
## desc Extracts reads based on regions in a BED file
"""
Extracts reads based on regions in a BED file
Given a BAM file and a BED file, this script will extract only reads that
map to the given BED regions.
Specifically, if a read starts or ends within a BED region, it is ex... | ngsutils/ngsutils | ngsutils/bam/extract.py | Python | bsd-3-clause | 3,276 | [
"pysam"
] | dde73fbd2f0d13dde46c59097673dd5eab94fb1c9be378eeabd558f40aebe8b8 |
"""A Volume file reader"""
# Author: Suyog Dutt Jain <suyog.jain@aero.iitb.ac.in>
# Copyright (c) 2009, Enthought, Inc.
# License: BSD Style.
# Enthought library imports.
from traits.api import Instance, Str
from traitsui.api import View, Group, Item
from tvtk.api import tvtk
# Local imports.
from mayavi.core.source ... | dmsurti/mayavi | mayavi/sources/volume_reader.py | Python | bsd-3-clause | 2,665 | [
"Mayavi",
"VTK"
] | a872e570706eab6b386b3fb13a55cfc35e0d7e383fd5248f653569d572af092a |
# -*- coding:utf-8; python-indent:2; indent-tabs-mode:nil -*-
# Copyright 2013 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/l... | pombredanne/pytype | pytype/pytd/optimize_test.py | Python | apache-2.0 | 18,208 | [
"VisIt"
] | 0e491c253c150e0e43762e77bd953a76f36d981223667ab4e05735a6041938b0 |
# sql/elements.py
# Copyright (C) 2005-2020 the SQLAlchemy authors and contributors
# <see AUTHORS file>
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Core SQL expression elements, including :class:`.ClauseElement`,
:class:`.ColumnE... | graingert/sqlalchemy | lib/sqlalchemy/sql/elements.py | Python | mit | 155,766 | [
"VisIt"
] | 740e9414771b610e6ceb5f6c66ba1ee22d9492455838a268cbd5f318065e56b7 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors: Kyle A Beauchamp
#
# MDTraj is... | dwhswenson/mdtraj | mdtraj/testing/testing.py | Python | lgpl-2.1 | 7,047 | [
"MDTraj"
] | e7c2e4e43f187eac576fdfdb0824eb8a822a20f00c86b479e3e557f57423c01c |
#!/usr/bin/python
# -*- coding: utf-8 -*-
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
#
# Copyright (C) 2017 Lenovo, Inc.
#
# 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 Licens... | caphrim007/ansible | lib/ansible/modules/network/cnos/cnos_factory.py | Python | gpl-3.0 | 3,939 | [
"VisIt"
] | b9e4330e9abb41b6c367356858a64834b47a3c273c1d285c2185800715b51221 |
"""
Submodule: CI
Basic module for various configuration interaction methods
Currently it is simply a wrapper of the ci module in PySCF
"""
from frankenstein.ci.cisd import CISD
| hongzhouye/frankenstein | ci/__init__.py | Python | bsd-3-clause | 181 | [
"PySCF"
] | 25dbdb110bab9ad80930bc62209e4bb0dbe074efb406d49be34a7f2398e1875c |
import argparse
import os
from hmm_kit import HMMModel
import pandas as pd
import numpy as np
from hmm_kit import bwiter
from sklearn.cluster import KMeans
import pickle as pkl
def train_model(input_path, kernel, states, emission=None, transition=None, model_name=None, html=False):
input_dir = os.path.dirname(os... | eranroz/hmm | scripts/simple_hmm.py | Python | mit | 6,325 | [
"Gaussian"
] | a00bc382434410655a859cd7b74e917a692c593cccf62098c41cdf35e997f713 |
#!/usr/bin/python
# This file extracts the raw substitution matrix contents located within
# the same directory, e.g., BLOSUM62, PAM250, and constructs files
# appropriate for inclusion within a C program.
import glob
import os
header = """/**
* @file
*
* @author jeff.daily@pnnl.gov
*
* Copyright (c) 2015 Batte... | dikaiosune/parasail-sys | parasail_c/util/matrices/codegen.py | Python | mit | 5,450 | [
"BLAST"
] | 414a624639b3295a15e9f5e7af8616644547cc582dcf29b83e82b8815550d31d |
from itertools import izip
import vtk
from vtk.util import numpy_support as ns
import numpy as np
from tractography import Tractography
def tractography_from_vtk_files(vtk_file_names):
tr = Tractography()
if isinstance(vtk_file_names, str):
vtk_file_names = [vtk_file_names]
for file_name in vtk... | oesteban/tract_querier | tract_querier/tractography/vtkInterface.py | Python | bsd-3-clause | 16,162 | [
"VTK"
] | 47837f9aa9f1962a226fef7a334c0cd70fa10bfe0ab929dd0d6606a65dc94751 |
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