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#!/usr/bin/env python3
"""Check that we have the minimum requirements for running atram."""
import re
import sys
import subprocess
from functools import reduce
from distutils.version import LooseVersion
from shutil import which
RESULTS = {}
def test_format(name, value):
"""Format test results."""
RESULTS[n... | juliema/aTRAM | util_check_requirements.py | Python | bsd-3-clause | 4,156 | [
"BLAST",
"BWA",
"Biopython"
] | cc91e7b5383ef806335fb33a7aa133c389aca5f9d33525f8a07b8f44d19895b0 |
# ECWMF-CLIM-WIND.PY
# ------------------------------------------------------------------
# This program will compute daily climatology from hourly renalaysis data
# obtained at the ECWMF portal
# input: filename [fname]
# output: filename [cfile(s)]
# SCS domain (90E-137E,7S-30N), recommended ECMWF resolution=0.25
#... | luuquanghung1982/python | earthscience/ecwmf-clim-wind.py | Python | gpl-3.0 | 6,109 | [
"NetCDF"
] | 72a92950b3c49c6b972e3b65f3669ad0b82eb4eccb7b8e407a1bfaf0f1f10df0 |
# -*- coding: utf-8 -*-
#
# This file is part of the python-chess library.
# Copyright (C) 2012-2018 Niklas Fiekas <niklas.fiekas@backscattering.de>
#
# 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 Foundat... | Diceling/pythonprototyping | newchessbot/chess/pgn.py | Python | gpl-2.0 | 36,215 | [
"VisIt"
] | b4522e5437634192ea3134b3a16f1260e7794ab54db0a9a766c576e677184009 |
# vim: tabstop=4 shiftwidth=4 softtabstop=4
# Copyright (c) 2012 OpenStack, LLC.
# 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... | fajoy/nova | nova/tests/compute/test_resource_tracker.py | Python | apache-2.0 | 31,647 | [
"exciting"
] | 1ac5578ca7289644334c72df6f121976e98c92bce62c37bfcb235b666fa26698 |
'''
Created on 30.04.2017
@author: Mr. Jones
'''
from slimit.visitors.ecmavisitor import ECMAVisitor
from slimit.visitors.scopevisitor import ScopeTreeVisitor
from slimit import ast,lexer
from slimit.scope import VarSymbol, FuncSymbol, Symbol
from jimplify.fproxy.jscript import JScript
'''ECMAVisitor chang... | mrj0n3s/jimplify | Jimplify/jimplify/slimitmodifications.py | Python | mit | 8,748 | [
"VisIt"
] | bba9fe0e6e69256f0e3c02432877c0a5b998556bf48ed1b6e7dd835b1cd07b54 |
###############################################################################
# Backport concurrent.futures for python2.7/3.3
#
# author: Thomas Moreau and Olivier Grisel
#
# adapted from concurrent/futures/_base.py (17/02/2017)
# * Do not use yield from
# * Use old super syntax
#
# Copyright 2009 Brian Quinlan. Al... | TNT-Samuel/Coding-Projects | DNS Server/Source/Lib/site-packages/joblib/externals/loky/_base.py | Python | gpl-3.0 | 20,706 | [
"Brian"
] | b50d411ba76c451003eed04cd2a805d225618d10c67ace48334a9f25e3037aa8 |
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2015 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier (bgoli@users.sourceforge.net)
Triple-J Group for Molecular Cell Physiology
Stellenbosch University, South Africa.
Permiss... | asttra/pysces | pysces/kraken/KrakenNET.py | Python | bsd-3-clause | 15,322 | [
"PySCeS"
] | 0da84776d4e7ec374aef68db912e67646ae0b6f1e596bfeea32bb38a3161433c |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Shows a Ez field in a photonic crystal waveguide.
A simple example showing the Ez field in a two-dimensional
photonic crystal waveguide.
"""
import os, sys
new_path = os.path.abspath('../')
sys.path.append(new_path)
from gmes import *
space = Cartesian(size=(16,8,... | aitatanit/gmes | examples/phc_waveguide.py | Python | gpl-3.0 | 968 | [
"CRYSTAL"
] | 37538b143cd68e4612f3f608896f57e1e19a6c755d20f1ba16cf0ed935334389 |
# In this module all the static files are specified that are required by the
# CATMAID front-end. The configuration is separated in libraries and CATMAID's
# own files:
#
# Libraries: To add a new library, add a new entry into the libraries_js
# dictionary and, if needed, add the libraries CSS files to sourcefiles
# tu... | htem/CATMAID | django/projects/mysite/pipelinefiles.py | Python | agpl-3.0 | 3,595 | [
"Cytoscape"
] | 38476f2f67e23fa33ad79c82e206cd6d6bf9c71692a98301fc474caa5df10fe5 |
# -*- coding: utf-8 -*-
#########################################################################
## This program is part of 'MOOSE', the
## Messaging Object Oriented Simulation Environment.
## Copyright (C) 2014 Upinder S. Bhalla. and NCBS
## It is made available under the terms of the
## GNU Lesser General ... | upibhalla/moose-core | tests/python/test_Xreacs4.py | Python | gpl-3.0 | 3,365 | [
"MOOSE"
] | 0d51213766a7e77057bd6229db572850e8aaf39dbe8498a2ac91e00b6204375e |
# methods for determining why a read didn't map
# stuff to try:
# - blast to ref
# - assemble
# - check complexity
# - contamination (align to alternative)
class ReadAlign( object ):
def __init__( self ):
pass
def blast( self, read ):
pass
def assemble( self, read ):
pass
def complexity( self, ... | supernifty/mgsa | mgsa/bio/read_realign.py | Python | mit | 378 | [
"BLAST"
] | 8dae3b17928d0b7cb79fa52d53eab4471c011bf41b093d01d40a5d4501dd0c3b |
# Licensed to the StackStorm, Inc ('StackStorm') under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not use th... | alfasin/st2 | st2common/st2common/hooks.py | Python | apache-2.0 | 13,890 | [
"GULP"
] | b5bc5631ac041c48955a3f47a30ad31b115dc184af6e2f89fe2ecbecac02be7e |
#!/usr/bin/python
########################################################################
# 28 Apr 2014
# Patrick Lombard, Centre for Stem Stem Research
# Core Bioinformatics Group
# University of Cambridge
# All right reserved.
########################################################################
import argparse... | pdl30/pynoncode | pynoncode/alignment.py | Python | gpl-2.0 | 8,971 | [
"Bowtie",
"HTSeq",
"pysam"
] | eb2af966d49406425130b1bb4753b2c0a90d2833c7f25351f3ce2fe50b21fbbf |
""" Collection of utilities function
"""
import os
import time
from DIRAC.ConfigurationSystem.Client.Helpers.CSGlobals import getVO, getCSExtensions
from DIRAC.Core.Workflow.Module import ModuleDefinition
from DIRAC.Core.Workflow.Parameter import Parameter
from DIRAC.Core.Workflow.Step import StepDefinition
#######... | arrabito/DIRAC | Workflow/Utilities/Utils.py | Python | gpl-3.0 | 3,562 | [
"DIRAC"
] | d4b0a5cfa13c3249030e038af3c46626188536332d9cbc69114bdc3f3681c227 |
""" Unit tests for the Dirac interface module
"""
# pylint: disable=no-member, protected-access, missing-docstring
from __future__ import print_function
import logging
from pprint import pformat
import pytest
from mock import MagicMock, call
from DIRAC.Interfaces.API.Dirac import Dirac
from DIRAC import S_OK
logging... | fstagni/DIRAC | Interfaces/API/test/Test_DIRAC.py | Python | gpl-3.0 | 4,103 | [
"DIRAC"
] | f34da0d72b52cca155fad5437f6d8c38f1b6aa6ed93c778ff36e4a9a202c578f |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2011 Async Open Source
##
## This program is free software; you can redistribute it and/or
## modify it under the terms of the GNU Lesser General Public License
## as published by the Free Software Foundation; either version 2
## of the License, or... | andrebellafronte/stoq | stoqlib/lib/process.py | Python | gpl-2.0 | 2,394 | [
"VisIt"
] | bc69fc9b8106802de9217903788e5a7fbeb6dd1affc43967e6b338d1311b6239 |
#!/usr/bin/env python
#
# Extracts summary info from a log file that compiles and executes test suite
# queries. Creates a CSV (comma-separated values) summary.
#
# Usage:
#
# perfsummary.py [ <log-file-name> ] [ --baseLog <base-log-file-name> ]
#
# Log files must have queries that were executed with timing on.
#
# Log... | 50wu/gpdb | concourse/scripts/perfsummary.py | Python | apache-2.0 | 12,313 | [
"ORCA"
] | 87031e1f955bbaacfa06ea9169d413b1c7d34f386d7c6de4c1ab0a467676c604 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# secret_key.py
#
# Copyright (C) 2011-2013 Linaro Limited
# Author: Zygmunt Krynicki <zygmunt.krynicki@linaro.org>
# Copyright 2013 Neil Williams <codehelp@debian.org>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | OSSystems/lava-server | lava_server/settings/secret_key.py | Python | agpl-3.0 | 2,347 | [
"VisIt"
] | fb5f1980eefb355c8e8416f365e14b95fd025c223cefa4056d3f5925b24da2c2 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# ChemCoord documentation build configuration file, created by
# sphinx-quickstart on Tue Jan 12 23:12:55 2016.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# ... | mcocdawc/chemcoord | docs/source/conf.py | Python | lgpl-3.0 | 10,556 | [
"ASE",
"pymatgen"
] | cbf6b70d1c6ccafdaad0c879abf55fe7da42da9fe3ec0f8f1dfbf3c70b5db622 |
""" I wish who wrote this would have put some doc...
IIUC this is a wrapper around the JobState object. It basically tries to cache
everything locally instead of going to the DB.
"""
import copy
import time
from DIRAC.Core.Utilities import Time, DEncode
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Wor... | arrabito/DIRAC | WorkloadManagementSystem/Client/JobState/CachedJobState.py | Python | gpl-3.0 | 11,529 | [
"DIRAC"
] | a6622109475b05104cf8ed5e3e9e45e99d725f2e4707c4bb8848d12b29cbe83f |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | xguse/scikit-bio | skbio/stats/ordination/_canonical_correspondence_analysis.py | Python | bsd-3-clause | 8,342 | [
"scikit-bio"
] | edc20ac24213bcbdf38bf0747f20768e77aa4b085b86ea423da5d3a92b2f157d |
# kcell.py
# python3
import numpy as np
import pandas as pd
from sklearn import model_selection, svm, metrics, cluster, tree, ensemble
from sklearn.preprocessing import MinMaxScaler
from sklearn.decomposition import PCA
import re
import kkeras
import klstm
param_d = {"n_cv_flt": 2, "n_cv_ln": 3, "cv_activation": "r... | jskDr/jamespy_py3 | kcellml.py | Python | mit | 30,408 | [
"VASP"
] | 276bdf70a3e852be940e7080f955da5a1817984f0db418c2702f5fc12590f8fd |
# This program computes the delay between the different gene segments using the
# convolved Gaussian process framework for RNA pol-II dynamics
#
# This code supports parallel computations
#
# Ciira wa Maina, 2013
# Dedan Kimathi University of Technology.
# Nyeri-Kenya
import sys
import os
import numpy as np
import ... | ciiram/PyPol_II | ParPyPolII.py | Python | bsd-3-clause | 7,158 | [
"Gaussian"
] | 5900972e1cc5d3662d80f43fcdc6e375ea46fa9af10bcc08c4994f293200e22c |
from __future__ import absolute_import
from django.test import TestCase
from .models import (Building, Child, Device, Port, Item, Country, Connection,
ClientStatus, State, Client, SpecialClient, TUser, Person, Student,
Organizer, Class, Enrollment)
class SelectRelatedRegressTests(TestCase):
def test_re... | LethusTI/supportcenter | vendor/django/tests/regressiontests/select_related_regress/tests.py | Python | gpl-3.0 | 6,537 | [
"Brian"
] | 4bcc09ca71b2dd3b13a2fba5209854a10bf58f221fc7b927d1491489f91bba4a |
# 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... | Xeralux/tensorflow | tensorflow/contrib/py2tf/pyct/transformer.py | Python | apache-2.0 | 2,709 | [
"VisIt"
] | 945a178f5a96f1d654d62de6c07dc990fcdec4f6c65cc001106b88dcdc0c2f61 |
#!/usr/bin/env python
#
# License: BSD
# https://raw.githubusercontent.com/stonier/py_trees/devel/LICENSE
#
##############################################################################
# Documentation
##############################################################################
"""
Library of common methods for t... | stonier/py_trees_suite | py_trees/tests.py | Python | bsd-3-clause | 1,793 | [
"VisIt"
] | 9fac0b328d88d04708d29f1ff61e1032c4bb0ca3fd8441275990063c9261e7d4 |
# encoding: utf-8
"""
The Base Application class for IPython.parallel apps
Authors:
* Brian Granger
* Min RK
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2008-2011 The IPython Development Team
#
# Distributed under the terms of the BSD License. The full lice... | marcoantoniooliveira/labweb | oscar/lib/python2.7/site-packages/IPython/parallel/apps/baseapp.py | Python | bsd-3-clause | 9,995 | [
"Brian"
] | bef5ada97d14db021f23c34a63fbceb476b068feefedfc7de8f31ca3a3dbe82a |
#!/usr/bin/env python
# -- Content-Encoding: UTF-8 --
"""
Beans to store the description of compositions and components
:author: Thomas Calmant
:license: Apache Software License 2.0
:version: 3.0.0
..
Copyright 2014 isandlaTech
Licensed under the Apache License, Version 2.0 (the "License");
you may not ... | isandlaTech/cohorte-devtools | qualifier/deploy/cohorte-home/repo/cohorte/composer/beans.py | Python | apache-2.0 | 6,657 | [
"VisIt"
] | 724cfd6182a3c0e6ba5b0757389c67ef55da745ab9ac0f058fa7095477708f78 |
from __future__ import absolute_import, division, print_function
from jaspyx.visitor import BaseVisitor
class Attribute(BaseVisitor):
def visit_Attribute(self, node):
self.visit(node.value)
self.output('.%s' % node.attr)
| ztane/jaspyx | jaspyx/visitor/attribute.py | Python | mit | 243 | [
"VisIt"
] | 4130cd05272829e43b1c20d8636501844c9f2898150809f9ffa4e4919a5768b3 |
import numpy
from chainer import backend
from chainer import initializer
# Original code forked from MIT licensed keras project
# https://github.com/fchollet/keras/blob/master/keras/initializations.py
class Normal(initializer.Initializer):
"""Initializes array with a normal distribution.
Each element of t... | ktnyt/chainer | chainer/initializers/normal.py | Python | mit | 4,690 | [
"Gaussian"
] | 54aa85cae5ad0493dcc83032bec4dca464097a747b1cf09d867b051b0f74f2c1 |
# ======================================================================
# USER-GFMD - Elastic half-space methods for LAMMPS
# https://github.com/Atomistica/user-gfmd
#
# Copyright (2011-2016,2021)
# Lars Pastewka <lars.pastewka@imtek.uni-freiburg>,
# Tristan A. Sharp and others.
# See the AUTHORS file in the top... | Atomistica/user-gfmd | tests/TEST_Hertz_fcc111_64x37_2/eval.py | Python | gpl-2.0 | 2,980 | [
"LAMMPS"
] | 78bf8280dd1ccff1002175f430493c148d63c627a2e95e3e3f11d98a0b3a253b |
from jinja2.ext import Extension
import os
from pyjade import Parser, Compiler as _Compiler
from pyjade.runtime import attrs, iteration
from jinja2.debug import fake_exc_info
from pyjade.utils import process
ATTRS_FUNC = '__pyjade_attrs'
ITER_FUNC = '__pyjade_iter'
class Compiler(_Compiler):
def visitCodeBlock(se... | glennyonemitsu/MarkupHiveServer | src/pyjade/ext/jinja.py | Python | mit | 3,707 | [
"VisIt"
] | d21f95e4ab7dcc422e8cc2e871245a6140d165023b18c9675b62c94e9a7971cb |
# 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... | theflofly/tensorflow | tensorflow/python/data/experimental/kernel_tests/rejection_resample_test.py | Python | apache-2.0 | 5,144 | [
"DIRAC"
] | 863942ccc541ccb46931dbc536f58a62fa511f048412ce9914fee520e3da2a3b |
import numpy as np
import scipy
import scipy.ndimage
def zap( ecounts2d, nsig_cull_transient=8, nsig_cull_static=10, niter=1 ):
"""
Routine for identifying static and transient bad pixels in a spectroscopic data cube.
Inputs:
ecounts2d - NxMxK data cube where N is cross-dispersion, M is dispersion, K... | tomevans/utils | bad_pixels.py | Python | gpl-2.0 | 4,667 | [
"Gaussian"
] | 757ebfb64a226677fe5316d9b085d987589e4be3d9cc36a75e0b7b396a0e6202 |
# Todd Miller jmiller@stsci.edu
from __future__ import (absolute_import, division, print_function,
unicode_literals)
import six
from six.moves import tkinter as Tk
from six.moves import tkinter_filedialog as FileDialog
import os, sys, math
import os.path
# Paint image to Tk photo blitter ex... | unnikrishnankgs/va | venv/lib/python3.5/site-packages/matplotlib/backends/backend_tkagg.py | Python | bsd-2-clause | 40,267 | [
"FLEUR"
] | 9cfc931c69f764618df4b334391ba8210fed53016c91057526d67bbeec84a202 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import copy
import glob
import json
import os
import unittest
import sys
from pymatgen import Molecule
from pymatgen.io.qchem import QcTask, QcInput, QcOutput, QcNucVel... | setten/pymatgen | pymatgen/io/tests/test_qchem.py | Python | mit | 86,318 | [
"pymatgen"
] | 181b5980dc1713f47341eafd42fb0b55e99fda2cb2fac4863128f2e652d0cb8c |
# Author: Virgile Fritsch <virgile.fritsch@inria.fr>
#
# License: BSD 3 clause
import numpy as np
import scipy as sp
import warnings
from . import MinCovDet
from ..utils.validation import check_is_fitted, check_array
from ..metrics import accuracy_score
from ..base import OutlierMixin
class EllipticEnvelope(MinCovDe... | BiaDarkia/scikit-learn | sklearn/covariance/elliptic_envelope.py | Python | bsd-3-clause | 7,621 | [
"Gaussian"
] | 2713c0f8ab26ae80675c35581d6e7b4299fe03a79746471b197c8528da37e56f |
#!/usr/bin/env python
#
# Copyright (C) 2014
# Brian Caswell <bmc@lungetech.com>
# Narf Industries <info@narfindustries.com>
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the "Software"),
# to deal in the Software without res... | f0rki/cb-multios | original-challenges/Mixology/poller/for-release/machine.py | Python | mit | 4,203 | [
"Brian"
] | 5a61db1a4f69fd8e3e855683c7a0bc81c6c3e6d3ca72d5e9deebd78ea61557d8 |
#
# Created by Greg Landrum (greg.landrum@t5informatics.com), Feb 2016
#
from flask import Flask,make_response,request,jsonify
from rdkit import Chem
from rdkit import rdBase
from rdkit.Chem import rdDepictor
from rdkit.Chem.Draw import rdMolDraw2D
from io import StringIO
import json,sys
Chem.WrapLogs()
app = Flask(_... | nbateshaus/chem-search | mol-renderer/render.py | Python | bsd-3-clause | 3,423 | [
"RDKit"
] | d44cb7100519cffb10bd733fda213aa926631f2ff695f497951f02771c3c5dcd |
#-------------------------------------------------------------------------------
# Cloud-COPASI
# Copyright (c) 2013 Edward Kent.
# All rights reserved. This program and the accompanying materials
# are made available under the terms of the GNU Public License v3.0
# which accompanies this distribution, and is available... | edkent/cloud-copasi | cloud_copasi/web_interface/pools/task_tools.py | Python | gpl-3.0 | 6,420 | [
"COPASI"
] | dd5d587c6fc249f00c702622a3ea7c20c4cb2848584468ecea8781496bab2bc2 |
'''
Author: Juan Jose Conti <jjconti@gmail.com>
This module can parse Python files looking for uses of the % operator.
The % operator is mainly used for string formatting operations.
Use:
python wrapstrings.py file.py funcName
'''
import ast
class RewriteMod(ast.NodeTransformer):
def visit_BinOp(self,... | jjconti/taint-mode-py | wrapstrings/wrapstrings.py | Python | gpl-3.0 | 1,189 | [
"VisIt"
] | a66237d0a066b3cfe11236937d25139b2f7a2b72c61dce41916145bb8b713ebc |
#!/usr/bin/env python
# Copyright 2014-2018 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
#
# U... | gkc1000/pyscf | pyscf/cc/eom_gccsd.py | Python | apache-2.0 | 26,847 | [
"PySCF"
] | 40b621a7479e12cc845e49201f27fadf5b87ca20312cb15fc6a50d8f1ab9f7ac |
"""scandir, a better directory iterator and faster os.walk(), now in the Python 3.5 stdlib
scandir() is a generator version of os.listdir() that returns an
iterator over files in a directory, and also exposes the extra
information most OSes provide while iterating files in a directory
(such as type and stat infor... | vicky2135/lucious | oscar/lib/python2.7/site-packages/scandir.py | Python | bsd-3-clause | 24,476 | [
"VisIt"
] | eb9b22d3d2df1f1637241fd9d983402130c3843a69664e7899c9ae87d618799f |
from random import choice
# If the code is not Cython-compiled, we need to add some imports.
from cython import compiled
if not compiled:
from mazelib.solve.MazeSolveAlgo import MazeSolveAlgo
class Tremaux(MazeSolveAlgo):
""" The Algorithm
0. Every time you visit a cell, mark it once.
1. When you hit... | theJollySin/mazelib | mazelib/solve/Tremaux.py | Python | gpl-3.0 | 4,973 | [
"VisIt"
] | 845e4ee58051e2ea0a2e37f648631134166778bd79c959821adb1e3b68cb667e |
# Copyright 2016 Battelle Energy Alliance, 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 agr... | brianmoose/civet | ci/views.py | Python | apache-2.0 | 41,361 | [
"MOOSE"
] | be567782810962cfa445856be903e84d33ac76a1044af53875648f15554d9571 |
# -*- coding: utf-8 -*-
"""
Created on Sat Jun 11 14:49:53 2016
@author: nebula
"""
import numpy as np
from swc2vtk.vtkgenerator import VtkGenerator
if __name__ == '__main__':
filename = 'rot_cube.vtk'
vtkgen = VtkGenerator()
pi = 3.141592
# pos = np.array([[0, 0, 0], [0, 2, 0], [4, 2, 0], [5, 5, 5]... | DaisukeMiyamoto/swc2vtk | examples/test_rotcube.py | Python | apache-2.0 | 719 | [
"VTK"
] | 31fd6cd589234d7a31e8adbf6654eee334abbfccaa7cde8c7fc28c6183b1e663 |
# 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... | alivecor/tensorflow | tensorflow/contrib/data/python/kernel_tests/sql_dataset_op_test.py | Python | apache-2.0 | 13,427 | [
"MOE"
] | cb66888b50678b7c3974b942db2434087ebc593966c59063751b27d5245a9c45 |
# -*- coding: utf-8 -*-
"""
Regression tests for the Test Client, especially the customized assertions.
"""
from __future__ import unicode_literals
import datetime
import itertools
import os
from django.contrib.auth.models import User
from django.contrib.auth.signals import user_logged_in, user_logged_out
from django... | mattrobenolt/django | tests/test_client_regress/tests.py | Python | bsd-3-clause | 67,062 | [
"VisIt"
] | fcfed000111517cd7b9666c481a577533b946cf1156974fc51c73e62776b3a78 |
from gamedef import *
from random import gauss
from random import randint
from random import random
from math import exp
import maps
# cost of unlocking given level
def cost(index):
if 0 == index:
return 0
times = LEVELS[index-1]['toPlay']
# times to play x optimal earnings for each weather group
... | nadvamir/gofish-lite | gofish_project/gofish/engine/level.py | Python | apache-2.0 | 3,521 | [
"Gaussian"
] | f22421aa5ec0544f7d91271b96ed8ddd3fe371d9e5605212ff3c0b13c1de7375 |
#!/usr/bin/env python
from __future__ import (absolute_import, division,
print_function, unicode_literals)
import sys
import os
import importlib
from natsort import natsorted
from amptk import amptklib
from pkg_resources import get_distribution
__version__ = get_distribution('amptk').version
d... | nextgenusfs/ufits | amptk/amptk.py | Python | bsd-2-clause | 46,442 | [
"BLAST"
] | 1d9fbfcde901e2bf6d72ca56bb615a1b39e7e742de1106030b2aa15af1831288 |
# Copyright 2018 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... | jendap/tensorflow | tensorflow/python/keras/layers/kernelized_test.py | Python | apache-2.0 | 16,617 | [
"Gaussian"
] | 8dd6efeddf12eeed62bc2713f174bff3d6cdf7fbf853f9e8f106f1f652e59f1e |
import numpy as np
from ase.optimize.optimize import Dynamics
from ase.optimize.fire import FIRE
from ase.units import kB
from ase.parallel import world
from ase.io.trajectory import Trajectory
class BasinHopping(Dynamics):
"""Basin hopping algorythm.
After Wales and Doye, J. Phys. Chem. A, vol 101 (1997) 5... | suttond/MODOI | ase/optimize/basin.py | Python | lgpl-3.0 | 4,539 | [
"ASE",
"GPAW"
] | a864ccd6475df8c4608f7c1b138613fb950af09d850681e5fb8bcf0c519ffa36 |
import unittest
import tempfile
import os
import numpy as np
import six
import caffe
def simple_net_file(num_output):
"""Make a simple net prototxt, based on test_net.cpp, returning the name
of the (temporary) file."""
f = tempfile.NamedTemporaryFile(mode='w+', delete=False)
f.write("""name: 'testne... | jwyang/JULE-Caffe | python/caffe/test/test_net.py | Python | mit | 2,927 | [
"Gaussian"
] | 736ae857988c2dd2fc1362ccbd63fae70d24b952c191be1abfd189261c6ae6e9 |
#!/usr/bin/env python3
# THIS FILE IS PART OF THE CYLC SUITE ENGINE.
# Copyright (C) 2008-2019 NIWA & British Crown (Met Office) & Contributors.
#
# 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... | trwhitcomb/cylc | cylc/flow/scheduler.py | Python | gpl-3.0 | 81,088 | [
"BLAST"
] | 75967c05c25f86ee00fa7ee16b06e5320bb5d1b246e9bc8dedbae6f441aaa0ef |
from __future__ import unicode_literals
import re
from .common import InfoExtractor
from ..compat import (
compat_str,
compat_HTTPError,
)
from ..utils import (
ExtractorError,
find_xpath_attr,
)
class NBCIE(InfoExtractor):
_VALID_URL = r'https?://www\.nbc\.com/(?:[^/]+/)+(?P<id>n?\d+)'
_TE... | Nikoli/youtube-dl | youtube_dl/extractor/nbc.py | Python | unlicense | 8,062 | [
"Brian"
] | 720b18590e52b0889eda3f497ab7d05c1f3f2c42da3d9df51e5a790be5b4a8d8 |
"""
Import utilities
Exported classes:
ImportManager Manage the import process
Importer Base class for replacing standard import functions
BuiltinImporter Emulate the import mechanism for builtin and frozen modules
DynLoadSuffixImporter
"""
# note: avoid importing non-builtin modules
import... | MalloyPower/parsing-python | front-end/testsuite-python-lib/Python-2.2/Lib/imputil.py | Python | mit | 25,399 | [
"BLAST"
] | 1a8aa9d8caa8b9b7a75a5ee0e2874abdc519a72d217c3b31033c70599ecd9120 |
#!/usr/bin/env python
description = ">> New automated psf version"
usage = "%prog image [options] "
# ###############################################################
# EC 2012 Feb 20
# modified by SV for lsc
################################################################
import os, sys, shutil, subprocess, string
... | svalenti/agnkey | trunk/bin/agnpsf.py | Python | mit | 31,751 | [
"Gaussian"
] | 0f0666690f4759094a045f4afd6c999128e47c0d859cbf6bbcf59e2457243164 |
from ase import Atom, Atoms
from gpaw import GPAW
from gpaw.test import equal
a = 4.05
d = a / 2**0.5
bulk = Atoms([Atom('Al', (0, 0, 0)),
Atom('Al', (0.5, 0.5, 0.5))], pbc=True)
bulk.set_cell((d, d, a), scale_atoms=True)
h = 0.25
calc = GPAW(h=h,
nbands=2*8,
kpts=(2, 2, 2),
... | qsnake/gpaw | gpaw/test/davidson.py | Python | gpl-3.0 | 1,021 | [
"ASE",
"GPAW"
] | 882902a71ae395d9c3b4d61e9fc2797f680a7d94fe5e94d1937f656351283683 |
# -*- coding: utf-8 -*-
# HORTON: Helpful Open-source Research TOol for N-fermion systems.
# Copyright (C) 2011-2017 The HORTON Development Team
#
# This file is part of HORTON.
#
# HORTON is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by th... | FarnazH/horton | horton/scripts/test/test_atomdb.py | Python | gpl-3.0 | 9,266 | [
"CP2K",
"ORCA"
] | 6b551216f3015dd737b5c9dcdb93b0a53446250c33d9cc89b197d8e05310c35e |
import re
import socket
import tempfile
import unittest
from contextlib import closing
import numpy as np
from numpy.testing import assert_array_almost_equal
from shyft.api import Calendar
from shyft.api import DtsClient
from shyft.api import DtsServer
from shyft.api import IntVector
from shyft.api import UtcTimeVect... | jfburkhart/shyft | shyft/tests/api/test_dtss.py | Python | lgpl-3.0 | 27,837 | [
"NetCDF"
] | 4c2fb13ef00fdff399254480b7e1b13dcd5f2b1102e9180102d5ed04d0134958 |
'''
Created on 4 Sep 2015
@author: maxz
'''
import unittest
import numpy as np
import GPy
class BGPLVMTest(unittest.TestCase):
def setUp(self):
np.random.seed(12345)
X, W = np.random.normal(0,1,(100,6)), np.random.normal(0,1,(6,13))
Y = X.dot(W) + np.random.normal(0, .1, (X.shape[0], W.s... | avehtari/GPy | GPy/testing/minibatch_tests.py | Python | bsd-3-clause | 13,011 | [
"Gaussian"
] | 4d0869128f6febb7b45bc59d0b1fd7f4cf03e9a100eae92997745d02cc3ea46e |
#!/usr/bin/env python
import glob
import numpy as np
try:
from setuptools import setup
have_setuptools = True
except ImportError:
from distutils.core import setup
have_setuptools = False
try:
from Cython.Build import cythonize
have_cython = True
except ImportError:
have_cython = False
kwa... | bhermanmit/openmc | setup.py | Python | mit | 1,926 | [
"VTK"
] | d9538a61128f78c32ae4a82f8a7bc722728ac33e2e4cfaa7ba166dc46c756120 |
import numpy as np
from alis import almsgs
from alis import alfunc_base
msgs=almsgs.msgs()
class PowerLaw(alfunc_base.Base) :
"""
Returns a 1-dimensional gaussian of form:
p[0] = amplitude
p[1] = x offset
p[2] = dispersion (sigma)
"""
def __init__(self, prgname="", getinst=False, atomic=Non... | rcooke-ast/ALIS | alis/alfunc_powerlaw.py | Python | gpl-3.0 | 5,082 | [
"Gaussian"
] | 9e6c087af17a08532292edd914b14ae89717e601991c037fc155e17e8a01e3a1 |
# -*- coding: utf-8 -*-
#########################################################################
# Programm : Avantes spectro python library for UNIX/LINUX system #
# Path : /home/Pi/control_commands/avaspec.py #
# #
... | smarrazzo/pyava | avaspec.py | Python | mit | 15,792 | [
"CRYSTAL"
] | 30f28c2ac54050cd4d4dd2845ad18f7e2255fa7273b7a04aadbec1f34ac6e256 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/transitions | openlp/plugins/alerts/forms/__init__.py | Python | gpl-2.0 | 3,320 | [
"Brian"
] | 86b958ae77f3ba6ade60d873ffa3b1f66ef82faaed196c6e491e87204f7edbb3 |
#!/usr/bin/env python
# This example demonstrates how to use a programmable filter and how
# to use the special vtkDataSetToDataSet::GetOutput() methods
import vtk
from math import *
# We create a 100 by 100 point plane to sample
plane = vtk.vtkPlaneSource()
plane.SetXResolution(100)
plane.SetYResolution(100)
# We ... | sgh/vtk | Examples/Modelling/Python/expCos.py | Python | bsd-3-clause | 2,367 | [
"VTK"
] | 4f0258f56ad6d8e88db28c461d63aad1ca6f1882028301036705e240955ddc2d |
# -*- coding: utf8 -*-
# pylint: disable-msg=C0103 # Disable naming style messages
# Pymetar (c) 2002-2012 Tobias Klausmann
"""
PyMETAR is a python module and command line tool designed to fetch Metar
reports from the NOAA (http://www.noaa.gov) and allow access to the
included weather information.
"""
# This program is... | theswitch/pymetar3 | pymetar.py | Python | gpl-2.0 | 37,244 | [
"CRYSTAL"
] | bac006d1894ba8a8d641ddf3ad42648282a8367f01196b9231ac8d9f62f1b2f8 |
#!/usr/bin/env python
"""
Created on Wed May 7 11:30:31 2014
Author: Oren Freifeld
Email: freifeld@csail.mit.edu
"""
import numpy as np
from gpu.gaussian import calc_signal_err_per_sample
from gpu.gaussian import calc_ll_per_sample
#from cpab.distributions.CpaCovs import CpaCovs
from _ScaleDependentLogLikelihoo... | freifeld/cpabDiffeo | cpab/cpa2d/model/transformations/register/_ScaleDependentLogLikelihoodGaussian.py | Python | mit | 3,769 | [
"Gaussian"
] | 2c78b951c37923ee646e685e6853f3cb789c250fb2afd71c986b04532225966c |
from common import Modules, data_strings, load_yara_rules, PEParseModule, ModuleMetadata, is_ip_or_domain
class dexter(PEParseModule):
def __init__(self):
md = ModuleMetadata(
module_name="dexter",
bot_name="Dexter",
description="Point of sale malware designed to extrac... | bwall/bamfdetect | BAMF_Detect/modules/dexter.py | Python | mit | 1,265 | [
"Brian"
] | 080a728798408645d50ef789891bf7784d8814acc18d71811f2ad7d12ca97832 |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
from pyscf import gto
'''
Specify symmetry.
Mole.symmetry can be True/False to turn on/off the symmetry (default is off),
or a string to specify the symmetry of molecule. symmetry_subgroup keyword
can be set to generate a subgroup of the detected... | gkc1000/pyscf | examples/gto/13-symmetry.py | Python | apache-2.0 | 1,264 | [
"PySCF"
] | 56c196eaefd46eb51ff62fc33dbd803f571c323d55b8b8547a4c2001ea80fa1c |
# 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, software
# d... | theanalyst/cinder | cinder/flow_utils.py | Python | apache-2.0 | 5,869 | [
"VisIt"
] | 847a8f013e70180a47844f38ba8528ad6efd3ab661530164bc352ead97be9f95 |
# Copyright (C) 2010-2018 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 v... | mkuron/espresso | testsuite/python/analyze_distance.py | Python | gpl-3.0 | 4,417 | [
"ESPResSo"
] | 0a60659b4ae53b6272b75939ea6bd06f3215a94fdf0a495928cec3c1cc0bad34 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2001 Jesper Zedlitz
# Copyright (C) 2004-2006 Donald Allingham
# Copyright (C) 2007 Johan Gonqvist <johan.gronqvist@gmail.com>
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
#
# This program is free so... | arunkgupta/gramps | gramps/plugins/textreport/numberofancestorsreport.py | Python | gpl-2.0 | 9,288 | [
"Brian"
] | 9de25cc99255f9fd172141a210e71cd51d7afeb4a232e25318172aa708584cb4 |
from Products.CMFCore.permissions import DeleteObjects, ModifyPortalContent
from Products.CMFCore.utils import getToolByName
from Products.Five.browser.pagetemplatefile import ZopeTwoPageTemplateFile
from Products.ZCatalog.Catalog import AbstractCatalogBrain
from opencore.browser.formhandler import OctopoLite, action
f... | socialplanning/opencore | opencore/project/browser/contents.py | Python | gpl-3.0 | 14,797 | [
"Octopus"
] | 118e1269724ca1a48622f53224168c38cef43968186661146907e077c309d991 |
"""
MIT License
Copyright (c) 2017 cgalleguillosm
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, merge,... | cgalleguillosm/accasim | accasim/utils/data_fitting.py | Python | mit | 9,977 | [
"Gaussian"
] | a8b260228f8f2953d869a847fae9e99ededac95e903b66b4146759768d54c6e1 |
import os
import sys
import argparse
import argparse
import logging
import extensions
import database
import commands
import utils
# Check for the necessary packages, this does a load so they should all get loaded.
if utils.check_configuration(['yaml', 'mkdocs', 'markdown', 'markdown_include', 'mdx_math']):
sys.e... | katyhuff/moose | python/MooseDocs/__init__.py | Python | lgpl-2.1 | 9,963 | [
"MOOSE"
] | 6f1a100a6ad0cc5075196fc9a00b759bfde1b1c83e504b5ef6521c691b06738d |
#This follows the tutorials at
#https://casaguides.nrao.edu/index.php/VLA_Continuum_Tutorial_3C391-CASA4.6
#https://casaguides.nrao.edu/index.php?title=First_Look_at_Self_Calibration
import os
#+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
# Constants and definitions
#-----------------... | kkozarev/mwacme | src/imaging_113-114.py | Python | gpl-2.0 | 9,306 | [
"Gaussian"
] | a080ed58ddf01782fb7007fbb065631bad20b306cd51ffd5c1c08380652f9062 |
# Copyright 2015 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... | apark263/tensorflow | tensorflow/python/ops/image_ops_impl.py | Python | apache-2.0 | 120,291 | [
"Gaussian"
] | 8775856d8b0fc24ef5d47dd31843d41032aab852e0449f5f74d5b8146706a49b |
"""
This is the base class for generating a biasing potential
for expanded ensemble simulation
"""
import openmoltools
import simtk.openmm as openmm
import simtk.openmm.app as app
import simtk.unit as units
import logging
_logger = logging.getLogger()
_logger.setLevel(logging.INFO)
class BiasEngine(object):
"""
... | choderalab/perses | perses/bias/bias_engine.py | Python | mit | 5,401 | [
"Amber",
"OpenMM"
] | 5861fe05c77d07e4622f701c98932859263a1fb862001f7bb298874c0d4d8b3d |
'''Main functions for PyMOLProbity plugin.'''
from __future__ import absolute_import
from __future__ import print_function
import logging
import os
import re
import subprocess
import tempfile
from pymol import cmd #cgo, cmd, plugins
from pymol import CmdException
# import colors
# from commands import command_line... | jaredsampson/pymolprobity | pymolprobity/main.py | Python | mit | 28,634 | [
"PyMOL"
] | 8307d915392c3cfc7dc69ed85c12af67a1523b238c3460f396b33b869f13a038 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | skosukhin/spack | var/spack/repos/builtin/packages/r-deseq/package.py | Python | lgpl-2.1 | 2,157 | [
"Bioconductor"
] | 94669b77d8feab8fb7cc13d6b88480054df31c74d62d3ab4f7e1c14c15b9d46c |
#!/opt/datafax/PHRI/python27
#
# Copyright 2017-2019, Population Health Research Institute
# Copyright 2017-2019, Martin Renters
#
# This file is part of the DataFax Toolkit.
#
# The DataFax Toolkit is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publish... | mrenters/DFtoolkit | dfpython/make_closeout_db.py | Python | gpl-3.0 | 9,116 | [
"VisIt"
] | 61e22cfc1410aeed00d2d9a232b866e5fed002f0c2f7f1f3c7b34012982f0f24 |
"""
desisim.pixelsplines
====================
Pixel-integrated spline utilities.
Written by A. Bolton, U. of Utah, 2010-2013.
"""
from __future__ import absolute_import, division, print_function
import numpy as n
from scipy import linalg as la
from scipy import sparse as sp
from scipy import special as sf
def compu... | desihub/desisim | py/desisim/pixelsplines.py | Python | bsd-3-clause | 15,653 | [
"Gaussian"
] | 551cc9901446326753d13d1997038220cc3ed415823c3824fb8f6ebb44a93f5a |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''Views tests for the OSF.'''
from __future__ import absolute_import
import unittest
import json
import datetime as dt
import mock
import httplib as http
import math
import time
from nose.tools import * # noqa PEP8 asserts
from tests.test_features import requires_search... | reinaH/osf.io | tests/test_views.py | Python | apache-2.0 | 178,509 | [
"Brian"
] | 38c6d3c25835ea804da0d83a4b184cb0cc9e9e9ab208d606a6bcbf727ae4d2af |
#!/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.vtkNamedColors... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Rendering/Core/Testing/Python/cowHair2.py | Python | gpl-3.0 | 2,709 | [
"VTK"
] | 76d52c7f0ebbf4d45cd703ec654ec5badb6285b6229b7c38c9e168871f9520ec |
"""
ODE simulation of the neuron models in Theano
"""
import theano
import theano.tensor as T
import theano.sandbox.rng_mrg
import collections
import numpy as np
import numpy.random as npr
def simulate_theano(S, dt, enc, bth, Nstd, x0=None, tau_c=0.01, model='fhn',
resp_out=True, states_out=False... | ctn-archive/hunsberger-neco2014 | scripts/neurons.py | Python | gpl-3.0 | 6,629 | [
"NEURON"
] | 13f91bb159ccf473420c75da7142b2cc025da2b4beec27eb1231750c5078b415 |
# Copyright (C) 2003 CAMP
# Please see the accompanying LICENSE file for further information.
"""A replacement for the ``time.clock()`` function.
From the clock man page::
Note that the time can wrap around. On a 32bit system
where CLOCKS_PER_SEC equals 1000000 this function will
return the sam... | ajylee/gpaw-rtxs | gpaw/utilities/timing.py | Python | gpl-3.0 | 9,706 | [
"GPAW"
] | ba25c671f76e5071b90b874a297e3637657e3a71867cf7221f5ac161c700f5e2 |
import os.path
#!/usr/bin/env python
#
#
# A file which can be used to generate NEURON mod files (and hoc files to test them)
# from **SIMPLE** SBML files. The only SBML elements which are currently supported are:
#
# listOfCompartments
# listOfSpecies
# listOfParameters
# listOfReactions
# ... | pgleeson/TestArea | models/SBMLDemo/cellMechanisms/VarSynSBML/SBML2NEURON.py | Python | gpl-2.0 | 19,212 | [
"NEURON"
] | af9c62103a2158d9e165f5a85aaa90dd8b43ee1a6bb0cd3dd9cae667c449e8c6 |
'''
Created on Aug 5, 2014
@author: gearsad
'''
import vtk
from SceneObject import SceneObject
class CameraScreen(SceneObject):
'''
A template for loading complex models.
'''
# The camera texture
cameraVtkTexture = None
def __init__(self, renderer, screenDistance, width, height):
... | GearsAD/semisorted_arnerve | sandbox/bot_vis_platform_post3b/scene/CameraScreen.py | Python | mit | 1,927 | [
"VTK"
] | af4270d86ab077a3829cffe5bc678d8b81b923145a98ef2ee185ef749edb4b51 |
#!/usr/bin/env python
"""
Featurize molecules and save features to disk. Featurizers are exposed as
subcommands, with __init__ arguments as subcommand arguments.
"""
__author__ = "Steven Kearnes"
__copyright__ = "Copyright 2014, Stanford University"
__license__ = "BSD 3-clause"
import argparse
import inspect
import j... | rbharath/pande-gas | vs_utils/scripts/featurize.py | Python | bsd-3-clause | 13,096 | [
"RDKit"
] | 41031820d3ba2410f98004ed8cceff3989facb657e91d357c5646196648a67a6 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# parallel https://code.google.com/p/pysam/issues/detail?id=105
# import pp
import argparse
import multiprocessing as mp
import os
from datetime import datetime
from pynnotator import settings
from subprocess import run
class Dbnsfp(object):
def __init__(self, vcf_... | raonyguimaraes/pynnotator | pynnotator/helpers/dbnsfp.cyvcf2.py | Python | bsd-3-clause | 5,997 | [
"pysam"
] | a84a96367c2f6a3d5b55af97b5ca26e808b84932556285d032ab1185dd90c8e4 |
#!/usr/bin/env python
###############################################################################
#
# __template__.py - Description!
#
###############################################################################
# #
# This program is free software: you can redistribute it and/or modify #
# it under the terms of ... | JoshDaly/scriptShed | get_fasta_from_pairs.trackm.py | Python | gpl-2.0 | 5,316 | [
"Biopython"
] | 83d2dd03d0497e0c4937faecd7cd600e4d002a6a0ac57aef793242797a5b422d |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals, division, print_function
import os
import tempfile
from pymatgen.util.testing import PymatgenTest
from pymatgen.io.abinit.abiinspect import *
_test_dir = os.path.join(... | migueldiascosta/pymatgen | pymatgen/io/abinit/tests/test_abiinspect.py | Python | mit | 3,774 | [
"ABINIT",
"pymatgen"
] | 031d40b89b522de177648d984d03795847261b4b0e4df3000249d95162f1e4e0 |
'''
The one parameter exponential family distributions used by GLM.
'''
# TODO: quasi, quasibinomial, quasipoisson
# see http://www.biostat.jhsph.edu/~qli/biostatistics_r_doc/library/stats/html/family.html
# for comparison to R, and McCullagh and Nelder
import numpy as np
from scipy import special
from . import links ... | hlin117/statsmodels | statsmodels/genmod/families/family.py | Python | bsd-3-clause | 39,410 | [
"Gaussian"
] | be7bfe54085642ed3adcacfc82be88fdb1c628a0a2fc25096a872f969164dd5f |
"""
Browser set up for acceptance tests.
"""
# pylint: disable=no-member
# pylint: disable=unused-argument
from base64 import encodestring
from json import dumps
from logging import getLogger
import requests
from django.conf import settings
from django.core.management import call_command
from lettuce import after, b... | ahmedaljazzar/edx-platform | common/djangoapps/terrain/browser.py | Python | agpl-3.0 | 10,334 | [
"VisIt"
] | 038b22c7cff3482070189ed788bfd6d7ebad5f283731c69b542c427568c0da5f |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module is used for analysis of materials with potential application as
intercalation batteries.
"""
__author__ = "Anubhav Jain, Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
import itertoo... | materialsproject/pymatgen | pymatgen/apps/battery/insertion_battery.py | Python | mit | 22,061 | [
"pymatgen"
] | 2e9a088fe2a8c5c44d3ebcce9b4fdc0d9932947977f5662b918aac2f98053e97 |
from ..Error import MolQueryError
from rdkit import Chem
from collections import defaultdict
import operator as op
"""
Written by Geun Ho Gu 8/4/2016
MolQuery class is equipped with enhanced query comparison over
RDkit query comparison.
This module uses a graph description language called R.I.N.G.
Rangarajan, S., Kamin... | VlachosGroup/VlachosGroupAdditivity | pgradd/RDkitWrapper/MolQuery.py | Python | mit | 24,302 | [
"RDKit"
] | bffd6c1673041d878a3901760c9120f618a5c5dd6fef321f400aa5ce48d5b8d8 |
# SCons Builder Engine Tools V2.23
import os
import os.path
import re
import fnmatch
import string
import copy
from butils import Version
import SCons
import SCons.Util
import SCons.Errors
import SCons.Node.FS
from types import IntType
from SCons.Script import \
Environment, AddMethod, ARGUMENTS, Configure, \
... | paeschli/scons-builder | btools.py | Python | gpl-2.0 | 59,652 | [
"VisIt"
] | b3b40452f4fc08627560463e6a62001066ef362abf53fd94f69c23bf06f43a6f |
import pygame
import screen
from .. import networking
from .. import game
ship_tracks_bitmaps = (
[0x001400, 0x001400, 0x043804, 0x087008, 0x489038, 0x489038, 0x087008, 0x043804],
[0x043804, 0x001400, 0x001400, 0x043804, 0x087008, 0x489038, 0x489038, 0x087008],
[0x087008, 0x043804, 0x001400, 0x001400, 0x0... | scarabeusiv/openmoo2 | oldmess/gui/main_screen.py | Python | gpl-2.0 | 9,710 | [
"Galaxy"
] | 12b561d6e065497e6fb561d071ef70c0c28ed11852e0906a545c319fa7d5e051 |
"""
It is used to test the MonitoringReporter.
It requires MonitoringDB which is based on elasticsearch and MQ which is optional...
CS (not strictly necessary):
Systems
{
Monitoring
{
Certification
{
Databases
{
MonitoringDB
{
Host = localhost
Port = 9200
... | DIRACGrid/DIRAC | tests/Integration/Monitoring/Test_MonitoringReporter.py | Python | gpl-3.0 | 24,543 | [
"DIRAC"
] | fe40059fd28c4c782bd73579e57c949373a9284cbc390ff9bec2721802d9ce47 |
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