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"""
Maximum likelihood covariance estimator.
"""
# Author: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Gael Varoquaux <gael.varoquaux@normalesup.org>
# Virgile Fritsch <virgile.fritsch@inria.fr>
#
# License: BSD 3 clause
# avoid division truncation
from __future__ import division
import warnin... | vortex-ape/scikit-learn | sklearn/covariance/empirical_covariance_.py | Python | bsd-3-clause | 9,139 | [
"Gaussian"
] | f7fe3cf31019a357f259b0e43e68d97d177f8c6a8a5bc2d07c5beaf8a3ef93f3 |
import io
import sys
import pytest
from webob import Request, Response
from firefly.app import Firefly, FireflyFunction, ctx
py2_only = pytest.mark.skipif(sys.version_info.major >= 3, reason="Requires Python 2")
py3_only = pytest.mark.skipif(sys.version_info.major < 3, reason="Requires Python 3+")
def square(a):
... | rorodata/firefly | tests/test_app.py | Python | apache-2.0 | 7,999 | [
"Firefly"
] | 450455478fdcbd66ee1e36a2cda2012e2ab168560a53ef1ea809d5fc42f646f2 |
# -*- Mode: Python; coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2005-2011 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 Fre... | tiagocardosos/stoq | stoq/gui/till.py | Python | gpl-2.0 | 22,922 | [
"VisIt"
] | ebeddaea94e61bbeec1264f36d4c73e40150e7fdfc9893f78693999cde282c07 |
# This file is part of xrayutilities.
#
# xrayutilities is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed... | dkriegner/xrayutilities | examples/xrayutilities_experiment_Powder_example_Iron.py | Python | gpl-2.0 | 2,058 | [
"CRYSTAL"
] | 04a42ab36eef0fa4a340e3fffd8f25936bebf42462f64f79d26805e958dd3717 |
# -*- coding: utf-8 -*-
import numpy as np
from iminuit import Minuit
from probfit import AddPdf, BinnedLH, Extended, gen_toy
from probfit.pdf import HistogramPdf
bound = (0, 10)
np.random.seed(0)
bkg = gen_toy(lambda x: x ** 2, 100000, bound=bound) # a parabola background
sig = np.random.randn(50000) + 5 # a Gauss... | iminuit/probfit | doc/pyplots/pdf/histogrampdf.py | Python | mit | 905 | [
"Gaussian"
] | 3e685d021d4c2c5fd39e3885b13482d910ce24af691b0d615e10153002e3ec2d |
import os, time
import numpy as np
from desolvationGrid_util import *
# Most of the heavy lifting is done by these Cython routines
# from desolvationGrid_util:
# enumerate_SAS_points
# set_inside_sphere_to
# increment_inside_sphere
# decrement_inside_sphere
# fraction_r4inv_low_dielectric
# calc_desolvationGrid
def g... | CCBatIIT/AlGDock | Pipeline/desolvationGrid/desolvationGrid.py | Python | mit | 8,261 | [
"Amber"
] | d2be837d7ed66d0315d8574b5a2d405372515a30b3efaa6b42c573c6c62ac26b |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2009 Benny Malengier
#
# 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; eith... | SNoiraud/gramps | gramps/gen/plug/_plugin.py | Python | gpl-2.0 | 2,269 | [
"Brian"
] | 2873bee23e967a0edea4aca038ada60eaf29dbf421247225c7ad5cbaf6b8b66e |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | ashutoshvt/psi4 | psi4/driver/procrouting/findif_response_utils/db_helper.py | Python | lgpl-3.0 | 6,311 | [
"Psi4"
] | a3121fa659d41ee3a3e424dbe19a4b1588264cebca67816f35d1241f0c765e1c |
import numpy as np
import MDAnalysis as mda
from MDAnalysis.coordinates.memory import MemoryReader
from MDAnalysisTests.datafiles import DCD, PSF
from MDAnalysisTests.coordinates.base import (BaseReference,
MultiframeReaderTest)
from MDAnalysis.coordinates.memory import Ti... | alejob/mdanalysis | testsuite/MDAnalysisTests/coordinates/test_memory.py | Python | gpl-2.0 | 7,133 | [
"MDAnalysis"
] | 4ed480e92b4012ac89879f4988662989d249688cd4a23e1c964867797607a807 |
# -*- coding: utf-8 -*-
"""
Regression tests for the Test Client, especially the customized assertions.
"""
from __future__ import unicode_literals
import os
from django.conf import settings
from django.core.exceptions import SuspiciousOperation
from django.core.urlresolvers import reverse
from django.template import... | RaoUmer/django | tests/regressiontests/test_client_regress/tests.py | Python | bsd-3-clause | 48,630 | [
"VisIt"
] | 0ef8fce4af7177570c82f708abffc6e23c2d7e5b7341af1bd82b1489e8ffff83 |
"""Visualization tools for coarse grids, both C/F splittings and aggregation.
Output is either to file (VTK) or to the screen (matplotlib).
vis_splitting: visualize C/F splittings through vertex elements
vis_aggregate_groups: visualize aggregation through groupins of edges, elements
"""
import warnings
impo... | pyamg/pyamg | pyamg/vis/vis_coarse.py | Python | mit | 9,747 | [
"ParaView",
"VTK"
] | 6263a2880e4069c6b6cf0753ea74fdb1097e4c2e5961fe2d38bac578c39a052e |
# Copyright 2008-2015 Nokia Solutions and Networks
#
# 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 l... | caio2k/RIDE | src/robotide/lib/robot/model/testcase.py | Python | apache-2.0 | 2,504 | [
"VisIt"
] | 6079aa00d038b32a1020e086f5b802f0860d1c6424a8784340bf83aec7181b82 |
# ######################################################################
# Copyright (c) 2014, Brookhaven Science Associates, Brookhaven #
# National Laboratory. All rights reserved. #
# #
# @author: Li Li (lili@bnl.g... | tacaswell/scikit-beam | skbeam/core/fitting/tests/test_background.py | Python | bsd-3-clause | 3,709 | [
"Gaussian"
] | f197689b998fbdf8199ffb32fb0841480ce5139535b3930e08bc0e4412149432 |
# -*- coding: utf-8 -*-
"""
Created on Thu May 5 17:12:20 2016
@author: nguyen
"""
import numpy as np
from netCDF4 import Dataset
# Constants
Nh = 96
Nt = 37
sspacing = 4
tspacing = 6
HTLS_sknots = np.arange(0,Nh,sspacing)
HTHS_sknots = np.arange(0,Nh,1)
LTHS_tknots = np.arange(0,Nh,tspacing)
Nl = len(HTLS_sknots)... | linhvannguyen/PhDworks | codes/isotropic/regression/funcs/KRR_rbf_sspacing4_tspacing6.py | Python | mit | 2,903 | [
"NetCDF"
] | bfdc737388aa6b4b0d41728b7dbafeb3bd05d138d2e8337dc6840e8fa8d28bf6 |
import os
import sys
import argparse
import argparse
import logging
import extensions
import database
import commands
import html2latex
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_... | vityurkiv/Ox | python/MooseDocs/__init__.py | Python | lgpl-2.1 | 7,975 | [
"MOOSE"
] | d981ca36466c0877c7ebacedb2edf048452037269eb6ff9614a57a051c13dc5b |
# -*. coding: utf-8 -*-
# Copyright (c) 2008-2012, Noel O'Boyle; 2012, Adrià Cereto-Massagué
# All rights reserved.
#
# This file is part of Cinfony.
# The contents are covered by the terms of the GPL v2 license
# which is included in the file LICENSE_GPLv2.txt.
"""
pybel - A Cinfony module for accessing Open Babel
G... | serval2412/openbabel | scripts/python/pybel.py | Python | gpl-2.0 | 33,954 | [
"Open Babel",
"Pybel"
] | d06220841bd112e766dcfc2f19ec4d54c2e1ac2861e1d92163139e21a84652d5 |
# -*- coding: utf-8 -*-
#
# This file is part of Invenio.
# Copyright (C) 2014, 2015 CERN.
#
# Invenio is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License as
# published by the Free Software Foundation; either version 2 of the
# License, or (at your option) any... | eamonnmag/invenio-search | invenio_search/walkers/facets.py | Python | gpl-2.0 | 3,938 | [
"VisIt"
] | 62b13ccbaae2d899fc9af28c22c9e254f299925c6ffe11f4d0355420edb8175e |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#... | MDAnalysis/mdanalysis | testsuite/MDAnalysisTests/topology/test_pdbqt.py | Python | gpl-2.0 | 1,705 | [
"MDAnalysis"
] | e13b44c89f835c5b3d742aed66c860727ac3cea8c7acba62442b1fbc73164c05 |
# #
# Copyright 2009-2020 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (... | pescobar/easybuild-framework | easybuild/tools/filetools.py | Python | gpl-2.0 | 93,165 | [
"NetCDF"
] | 973ca1be28779958ca502655b038bcbe68b91c15da999628e1ac53cee62b10ee |
"""Machinery for interspersing lines of text with linked and colored regions
The typical entrypoints are es_lines() and html_line().
Within this file, "tag" means a tuple of (file-wide offset, is_start, payload).
"""
import cgi
from itertools import chain
try:
from itertools import compress
except ImportError:
... | pombredanne/dxr | dxr/lines.py | Python | mit | 19,336 | [
"VisIt"
] | 8e15955d8559c06532ea103138e962b2aec885f8933c65fcdedcb8821f017e0f |
from OWWidget import OWWidget
from OWkNNOptimization import *
import orange, math, random
import OWGUI, orngVisFuncts, numpy
from math import sqrt
from orngScaleLinProjData import *
from orngLinProj import *
class FreeVizOptimization(OWWidget, FreeViz):
settingsList = ["stepsBeforeUpdate", "restrain", "differenti... | yzl0083/orange | Orange/OrangeWidgets/OWFreeVizOptimization.py | Python | gpl-3.0 | 22,281 | [
"Gaussian"
] | 78744986b448f0b2368d9fe48fdb54400ed21d5bc2ac8b218252b0c34eb05c8d |
# 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... | jwlawson/tensorflow | tensorflow/contrib/py2tf/convert/call_trees.py | Python | apache-2.0 | 5,766 | [
"VisIt"
] | d06826a687647906bd0ad03fd1c6e2cd48113e6161b183856f74e4c08886f50b |
# Copyright (C) 2016-2019 The ESPResSo project
# Copyright (C) 2014 Olaf Lenz
#
# 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... | KaiSzuttor/espresso | src/python/espressomd/__init__.py | Python | gpl-3.0 | 2,126 | [
"ESPResSo"
] | 0d31ea316a05598b170e8444becf90473777a4fa6298b8cd1723f97fe2171735 |
# Copyright 2009 by Cymon J. Cox. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Command line wrapper for the multiple alignment program PRANK.
"""
from __future__ import pr... | zjuchenyuan/BioWeb | Lib/Bio/Align/Applications/_Prank.py | Python | mit | 10,550 | [
"Biopython"
] | 57fa5b68cf8a6a17ff64253f3ed41ab5dfc6dd108cfd2ce12d1c3d2cd047d0dd |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 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/gui/test/test_stockdecreasewizard.py | Python | gpl-2.0 | 5,583 | [
"VisIt"
] | 4d3887e60f4e472e754c3dfab4da12987f83c18dad1448d23c9dabf38d3dd8be |
from __future__ import annotations
import copy
import logging
import math
import libtbx
from dxtbx.model.experiment_list import Experiment, ExperimentList
from dials.algorithms.indexing import DialsIndexError, DialsIndexRefineError
from dials.algorithms.indexing.indexer import Indexer
from dials.algorithms.indexing.... | dials/dials | algorithms/indexing/stills_indexer.py | Python | bsd-3-clause | 34,055 | [
"CRYSTAL"
] | aab859a5a4302f81cc8a8a3cc906a895b8cc922db7226bc995ed4803c1432ff6 |
# -*- coding: utf-8 -*-
{
"'Cancel' will indicate an asset log entry did not occur": "'cancelar' irá indicar que a entrada de log de ativo não ocorreu",
"A location that specifies the geographic area for this region. This can be a location from the location hierarchy, or a 'group location', or a location that has a bou... | flavour/Turkey | languages/pt-br.py | Python | mit | 271,439 | [
"VisIt"
] | 251e3f6191d905b018c89b8889349085daa6cef99b3ef539b789d3abfcea5d6e |
#!/usr/bin/env python
# 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
#
# U... | gkc1000/pyscf | pyscf/prop/magnetizability/rks.py | Python | apache-2.0 | 7,203 | [
"PySCF"
] | b427cc1159b76d843ab60e3aa40032865348d3f7517365806a0e8ff72a7bca11 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (C) 2014-2015 James Clark <james.clark@ligo.org>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
#... | astroclark/bhextractor | patrec/classify/adhoc_cat.py | Python | gpl-2.0 | 4,977 | [
"Gaussian"
] | c12f1b53ec24040a9a17f3833f41a4bb3d9f8e210e71d07320e1b17e47a34aa1 |
#!/usr/bin/env python
# Copyright 2014 the V8 project authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
# This script retrieves the history of all V8 branches and trunk revisions and
# their corresponding Chromium revisions.
# Requires ... | kingland/go-v8 | v8-3.28/tools/push-to-trunk/releases.py | Python | mit | 16,571 | [
"VisIt"
] | 39c82260b93b132b7458d49da3d6e70a1f275670716bdb3c7f9e6e1315e75691 |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (C) 2011 ~ 2012 Deepin, Inc.
# 2011 ~ 2012 Wang Yong
#
# Author: Wang Yong <lazycat.manatee@gmail.com>
# Maintainer: Wang Yong <lazycat.manatee@gmail.com>
#
# This program is free software: you can redistribute it and/or modify
# it under the... | linuxdeepin/deepin-ui | dtk/ui/button.py | Python | gpl-3.0 | 60,880 | [
"Gaussian"
] | fe47e1e6069fa160a20359be91456feb31a83e31a41013e1902ba361540c4a1b |
""" Top-level module to build or re-build the JSON files for
FRB host galaxies"""
from pkg_resources import resource_filename
import os
import sys
from IPython import embed
import numpy as np
import pandas
from astropy.coordinates import SkyCoord
from astropy import units
from astropath.priors import load_std_pri... | FRBs/FRB | frb/builds/build_path.py | Python | bsd-3-clause | 3,583 | [
"Galaxy"
] | 3ce59b8d4b24882d638a3682fbf6adfe776850dcb3e26383b9970cf0afee6881 |
''' This is a comment
'''
from xml.sax.handler import ContentHandler
<<<<<<< HEAD
from DIRAC.Core.Workflow.Parameter import Parameter
from DIRAC.Core.Workflow.Module import ModuleInstance, ModuleDefinition
from DIRAC.Core.Workflow.Step import StepDefinition, StepInstance
=======
from DIRAC.Core.Workflow.Parameter imp... | avedaee/DIRAC | Core/Workflow/WorkflowReader.py | Python | gpl-3.0 | 5,180 | [
"DIRAC"
] | a5a9f3412e5459af3f1f8319eae19ea4c1ba529d055dd253477bab8cc3e6e88a |
#!/usr/bin/python
import logging
logging.basicConfig(level=logging.INFO, format="%(asctime)s - %(name)s - %(levelname)s - %(message)s")
import pinproc
import procgame.game, sys, os
import procgame.config
import pygame
import time
import thread
import procgame.sound
sys.path.insert(0,os.path.pardir)
from bingo_emulato... | bingopodcast/bingos | bingo_emulator/menu.py | Python | gpl-3.0 | 36,494 | [
"Galaxy"
] | cdb51c15c814d73d304712ffdd2c3e208c1a29187981308d04b396f4a1ef8657 |
from ply import *
keywords = (
'Prefer', 'Patient', 'Visit', 'Blind', 'Click', 'Input', 'Choose',
'Back', 'Forward', 'Accept', 'Auth', 'Dismiss', 'Press', 'Switch',
'Repeat', 'Task', 'End', 'Judge', 'Empty', 'Not', 'True', 'False', 'Page', 'Enter','LoadSmartApp', 'DoGenomicAuth'
)
tokens = keywords + (
... | ideaworld/FHIR_Tester | FHIR_Tester_backend/services/monkey/MonkeyLex.py | Python | mit | 1,169 | [
"VisIt"
] | 30887d33c8c9cc1937b658064becf415c14170a99428975b1dd417db6b0e3129 |
#
# Copyright (C) 2013-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | fweik/espresso | testsuite/python/accumulator_correlator.py | Python | gpl-3.0 | 9,481 | [
"ESPResSo"
] | 98372c265bf0b327a49635555e4c02dce1231f89851e34f6315b46bb33365fbb |
from behave import given, when, then, step
from search.management.commands.create_session import create_pre_authenticated_session
from django.conf import settings
@given('I am a logged-in user')
def given_i_am_logged_in(context):
session_key = create_pre_authenticated_session(email='a@b.c')
## to set a cookie... | golgoth42/golgoth | search/features/steps/dork.py | Python | bsd-2-clause | 1,474 | [
"VisIt"
] | f672a7966e9ec5a6b6355a47a4587986d169d8b8e6507ae3252fad1d4ed802d9 |
# ALL the Scikit-Learn functions
from sklearn.feature_extraction.text import TfidfVectorizer
from sklearn.cross_validation import train_test_split
from sklearn.ensemble import RandomForestClassifier
from sklearn.preprocessing import StandardScaler
from sklearn import linear_model as lm
from sklearn.svm import SVC
from ... | kn-olin/insults | explore.py | Python | gpl-2.0 | 4,130 | [
"Gaussian"
] | c8acf60a6f529ce43b793b2708be1c0d037610806af28937cedaaf2678377ace |
# proxy module
from __future__ import absolute_import
from mayavi.components.implicit_plane import *
| enthought/etsproxy | enthought/mayavi/components/implicit_plane.py | Python | bsd-3-clause | 101 | [
"Mayavi"
] | 13cc7be43331db21ca8662bdd53c9c7e4bc5be1641faa1d2c6189e67a8bba6fd |
from __future__ import division, absolute_import
from struct import unpack as _unpack, pack as _pack
import os.path
from sys import byteorder as _BYTEORDER
import warnings
import numpy as np
from scipy.ndimage import zoom, gaussian_filter
from ._powerfit import blur_points, dilate_points
class Volume(object):
@... | haddocking/powerfit | powerfit/volume.py | Python | apache-2.0 | 20,760 | [
"Gaussian"
] | 16d5a6d49e013f63ff49d06d233d1a0a0e1727916e85908741356473e6c17b35 |
# coding: utf-8
from __future__ import division, unicode_literals
"""
Created on May 1, 2012
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep@gmail.com"
__date__ = "May 1, 2012"
import unittest
import... | yanikou19/pymatgen | pymatgen/electronic_structure/tests/test_plotter.py | Python | mit | 3,173 | [
"pymatgen"
] | 43221c1e798f54b9e0741abe3b0da12e64f4b2abafdb88df99b07918fdd72c9c |
#!/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... | hryamzik/ansible | lib/ansible/modules/network/cnos/cnos_backup.py | Python | gpl-3.0 | 11,453 | [
"VisIt"
] | 6e1f151ceb036b312c22efd49509558a435f83696182abaee0fde2444badddd5 |
"""Universal feed parser
Handles RSS 0.9x, RSS 1.0, RSS 2.0, CDF, Atom 0.3, and Atom 1.0 feeds
Visit https://code.google.com/p/feedparser/ for the latest version
Visit http://packages.python.org/feedparser/ for the latest documentation
Required: Python 2.4 or later
Recommended: iconv_codec <http://cjkpython.i18n.org... | Elandril/SickRage | lib/feedparser/feedparser.py | Python | gpl-3.0 | 156,312 | [
"NetCDF",
"VisIt"
] | c4c5acc93059df9dc71eef6be2200218ab5a5ffc5955f1d0801ad81e0bd245ce |
# -*- coding:utf-8 -*-
#
# Copyright 2012 NAMD-EMAP-FGV
#
# This file is part of PyPLN. You can get more information at: http://pypln.org/.
#
# PyPLN 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 vers... | flavioamieiro/pypln.web | pypln/web/core/admin.py | Python | gpl-3.0 | 899 | [
"NAMD"
] | bc69385f939d8cc62fda7b95078aaf8569dd34eea39381c3e1f7eb29cdd3edef |
#
# Copyright 2018 Analytics Zoo Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... | intel-analytics/analytics-zoo | pyzoo/zoo/friesian/feature/table.py | Python | apache-2.0 | 97,400 | [
"ORCA",
"VisIt"
] | 43fba7f793507af0981a4421f5767914fcee15edc471bbf3b4a4c9e3f9bfd651 |
# Copyright (C) 2003 CAMP
# Please see the accompanying LICENSE file for further information.
import os
import sys
import time
import atexit
import pickle
import numpy as np
from gpaw import debug
from gpaw import dry_run as dry_run_size
from gpaw.utilities import is_contiguous
from gpaw.utilities import gcd
from gp... | robwarm/gpaw-symm | gpaw/mpi/__init__.py | Python | gpl-3.0 | 33,158 | [
"ASE",
"GPAW"
] | 446d7c32fdc1883c52eefcbea072ce151d647926f5b2b2da8ba5aee9252e10a1 |
""" TokenAgent
This agent inspect all elements, and resets their tokens if necessary.
The following options can be set for the TokenAgent.
.. literalinclude:: ../ConfigTemplate.cfg
:start-after: ##BEGIN TokenAgent
:end-before: ##END
:dedent: 2
:caption: TokenAgent options
"""
__RCSID__ = '$Id$'
from date... | andresailer/DIRAC | ResourceStatusSystem/Agent/TokenAgent.py | Python | gpl-3.0 | 6,969 | [
"DIRAC"
] | fb7f7eb1524d598512b96e1d9cb07685537c3c090069f09397f6a730e83c90a1 |
# Settings for Zulip Voyager
### MANDATORY SETTINGS
#
# These settings MUST be set in production. In a development environment,
# sensible default values will be used.
# The user-accessible Zulip hostname for this installation, e.g.
# zulip.example.com
EXTERNAL_HOST = 'zulip.example.com'
# The email address for the ... | Frouk/zulip | zproject/local_settings_template.py | Python | apache-2.0 | 15,172 | [
"VisIt"
] | 99f6d13f233db15a2102aa1a203b87cd014f667d8c7d7fe19b46b103ed48d96b |
import nrrd
import json
import numpy as np
import pickle
import os
import scipy.stats as stats
from scipy.optimize import fsolve
from scipy.special import iv
from scipy.special import factorial2, factorial
from scipy.special import hyp1f1
from sklearn.neighbors.kde import KernelDensity
from sklearn.model_selection imp... | kayarre/Tools | process_VWI_nrrd_4.py | Python | bsd-2-clause | 97,925 | [
"Gaussian"
] | a526c42f228114670215eda577778ee5d43f5ef873a13e355200e36a3078d37c |
########################################################################
# $HeadURL$
# File : MightyOptimizer.py
# Author : Adria Casajus
########################################################################
"""
SuperOptimizer
One optimizer to rule them all, one optimizer to find them,
one optimizer to b... | calancha/DIRAC | WorkloadManagementSystem/Agent/MightyOptimizer.py | Python | gpl-3.0 | 6,295 | [
"DIRAC"
] | c5d4954c7cbb851baf1f4f025239611b90b7ea48d34f67b83044fe06caf3414a |
#!/Library/Frameworks/Python.framework/Versions/2.7/bin/python
# ----------------------------------------
# USAGE:
# ----------------------------------------
# PREAMBLE:
import MDAnalysis
from MDAnalysis.analysis.align import *
import sys
import os
from sel_list import *
from distance_functions import *
# ---------... | rbdavid/RMSD_analyses | PCA_RMSD_One_Ref/RMSD_analysis.py | Python | gpl-3.0 | 4,428 | [
"MDAnalysis"
] | 4fe3a6090fd6c4dc1ef22bebd23a33026dd91d3269e91a4555d6ba05e156fbb3 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Part of the PsychoPy library
# Copyright (C) 2002-2018 Jonathan Peirce (C) 2019-2020 Open Science Tools Ltd.
# Distributed under the terms of the GNU General Public License (GPL).
"""Converting code parameters and components from python (PsychoPy)
to JS (ES6/PsychoJS)
"... | psychopy/versions | psychopy/experiment/py2js.py | Python | gpl-3.0 | 7,669 | [
"VisIt"
] | 9e283a61deebb36b1647d1b71184794f25cec4164417ccd20058dae945bd6230 |
import os
from setuptools import setup, find_packages
# Convert README.md to README.rst automagically
# https://packaging.python.org/en/latest/guides/making-a-pypi-friendly-readme/
# read the contents of your README file
from pathlib import Path
this_directory = Path(__file__).parent
long_description = (this_director... | PeteHaitch/methtuple | setup.py | Python | mit | 1,263 | [
"pysam"
] | 49ddf7842551d9407f0d70662e8a54139ffe20f145907aeb618d6e98491ed7b0 |
# Copyright (C) 2006, Thomas Hamelryck (thamelry@binf.ku.dk)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Wrappers for PSEA, a program for secondary structure assignment.
See this citation for... | zjuchenyuan/BioWeb | Lib/Bio/PDB/PSEA.py | Python | mit | 2,832 | [
"Biopython"
] | 043bdb0fdbf8f577e171cd86796086bc635b1ce6e1c15996e2a9826da8748114 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | jgonthier/psi4 | psi4/driver/pluginutil.py | Python | lgpl-3.0 | 5,886 | [
"Psi4"
] | 105dc0431ee93dd112aff2629ba2f53007fd90e3d2bf3618f8c36e61b8ecc996 |
# -*- coding: utf-8 -*-
# HORTON: Helpful Open-source Research TOol for N-fermion systems.
# Copyright (C) 2011-2015 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... | eustislab/horton | horton/io/test/test_vasp.py | Python | gpl-3.0 | 4,443 | [
"VASP"
] | d1f36b31b846dd99071c29fe78cc39483d324034e4fe40be3129e78f964d7630 |
#!/usr/bin/env python
""" This template will become the job wrapper that's actually executed.
The JobWrapperTemplate is completed and invoked by the jobAgent and uses functionalities from JobWrapper module.
It has to be an executable.
The JobWrapperTemplate will reschedule the job according to certain cri... | hgiemza/DIRAC | WorkloadManagementSystem/JobWrapper/JobWrapperTemplate.py | Python | gpl-3.0 | 8,744 | [
"DIRAC"
] | 4772acc3b2546f46529b7e8fd9848d88d411ebf1970cfc8ad7a45f6144f59118 |
''' This file defines the columns for each table in the Postgres database.
We store our data in multiple schemas. We create one schema for each partner,
(ex: 'noble' and 'kipp_nj'), where each table contains the data from that
individual partner. We also create a 'common' schema where we combine the data
from all pa... | dssg/education-college-public | code/etl/db_schema/SQLtables_cols.py | Python | mit | 16,343 | [
"VisIt"
] | f71624ee67f6b709db973943bb65898cfbbe92d29b68f09d74f11dd9487b335c |
# standard libraries
import os
import setuptools
# third party libraries
pass
# first party libraries
pass
project_name = 'dotedict'
author = 'Brian J Petersen'
author_email = None
def load_file(fname, default=None):
try:
with open(fname, 'rb') as f:
d = f.read()
except:
d = defaul... | brianjpetersen/dotedict | setup.py | Python | mit | 1,073 | [
"Brian"
] | fae8f9ae7a307f8ff28f7440fcd5248059c0d9f2b5022cbe8d3f33ea27a6e1b7 |
##################################################################
# Copyright 2018 Open Source Geospatial Foundation and others #
# licensed under MIT, Please consult LICENSE.txt for details #
##################################################################
"""List of know mimetypes"""
# List of known compl... | bird-house/PyWPS | pywps/inout/formats/__init__.py | Python | mit | 7,158 | [
"NetCDF"
] | f290937869558fa7814d1a9fc633a3bba67f23768b81e07a133a8c072366f64e |
######################################################################
# Copyright 2016, 2021 John J. Rofrano. 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
#
# https:/... | nyu-devops/lab-flask-bdd | features/steps/web_steps.py | Python | apache-2.0 | 6,569 | [
"VisIt"
] | ab8bbeae2b06ee1d091e3dac60e1dadad6d19f25cbfa1eba36704d162da3fb7e |
from vtk import *
addStringLabel = vtkProgrammableFilter()
def computeLabel():
input = addStringLabel.GetInput()
output = addStringLabel.GetOutput()
output.ShallowCopy(input)
# Create output array
vertexArray = vtkStringArray()
vertexArray.SetName("label")
vertexArray.SetNumberOfTuples(output.GetNumbe... | collects/VTK | Examples/Infovis/Python/graph_tree_ring.py | Python | bsd-3-clause | 2,928 | [
"VTK"
] | d6758d7fa5ba2c4ac9ac004cf3d5ac7c24c0efe6dc156a862277d84f62c6d2dc |
import os
import theano
import theano.tensor as T
import numpy as np
from mozi.datasets.mnist import Mnist
from mozi.model import Sequential
from mozi.layers.linear import Linear
from mozi.layers.activation import *
from mozi.layers.noise import Dropout, Gaussian
from mozi.log import Log
from mozi.train_object import... | dksahuji/Mozi | example/mnist_dae.py | Python | mit | 3,060 | [
"Gaussian"
] | a0e6d1f03599b3e7d5b9309565937671a8177416f17ef66d769f548a83f0bea9 |
"""
:mod: DataManager
.. module: DataManager
:synopsis: DataManager links the functionalities of StorageElement and FileCatalog.
This module consists of DataManager and related classes.
"""
# # imports
from datetime import datetime, timedelta
import fnmatch
import os
import time
import errno
# # from DIRAC
import... | Andrew-McNab-UK/DIRAC | DataManagementSystem/Client/DataManager.py | Python | gpl-3.0 | 74,437 | [
"DIRAC"
] | fa09e1725033e5de091292dce0dc455a1fa71641a9e77231419859f3f5c983f0 |
# Lint as: python2, python3
# 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
#
... | xzturn/tensorflow | tensorflow/tools/compatibility/ast_edits.py | Python | apache-2.0 | 40,392 | [
"VisIt"
] | 383f8a57481a7cfd04eb0f21bd2a8e0332be86834ce72532be17bd1b164b1f10 |
#!/usr/bin/env python
"""Copyright 2008 Phidgets Inc.
This work is licensed under the Creative Commons Attribution 2.5 Canada License.
To view a copy of this license, visit http://creativecommons.org/licenses/by/2.5/ca/
"""
__author__ = 'Adam Stelmack'
__version__ = '2.1.4'
__date__ = 'May 02 2008'
#Basi... | jantman/tuxostat | fs_backup/home/tuxostat/devel/Python/PHSensor-simple.py | Python | gpl-3.0 | 3,154 | [
"VisIt"
] | fd32abcd31f856cc17245561515b1784707a951d86ffc9b58a88f94c887bf65a |
from sqlalchemy import create_engine
from sqlalchemy.exc import IntegrityError
from sqlalchemy.orm import sessionmaker
from gmi.mostusedsites.backend.models import Base, User, Visit
import pytest
class TestModels:
def test_user(self, session):
user = User(unique_id='foo')
session.add(user)
... | geyer-moldfusz/gmi.most_used_sites.backend | src/gmi/mostusedsites/backend/tests/test_models.py | Python | gpl-3.0 | 3,037 | [
"VisIt"
] | c4105b1e7c92f12d27d4ee413a9561f7ec2eaf934397f8990120a47749dc2c93 |
# Orca
#
# Copyright 2010 Joanmarie Diggs.
#
# 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.
#
# This library i... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/scripts/apps/Thunderbird/formatting.py | Python | gpl-3.0 | 1,990 | [
"ORCA"
] | fb4a2ecac6f55f34b9d13457162825beb0876862a3091b3a65c861ed478f5ec5 |
#!/usr/bin/env python3
########################################################################
# Solves problem 131 from projectEuler.net.
# Finds the number of primes below 1 millon for which exists an n that
# n ** 3 + (n ** 2) * p is a perfect cube.
# Copyright (C) 2011 Santiago Alessandri
#
# This prog... | sanSS/programming-contests | project-euler/problem131.py | Python | gpl-3.0 | 1,762 | [
"VisIt"
] | 3b8d7b6413f4b764be25f26bd7354d837f6e71c9bec43439c4c2d9f861d7dc7a |
########################################################################
#
# (C) 2013, James Cammarata <jcammarata@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software ... | konstruktoid/ansible-upstream | lib/ansible/cli/galaxy.py | Python | gpl-3.0 | 32,475 | [
"Galaxy"
] | 21eec9714de6e9ef1eafcd12512aade116b27fc157bab944cbb128393df2e82b |
#!/usr/bin/env python
import argparse
import pysam
import numpy as np
import sys
import pdb
import matplotlib.pyplot as plt
ap = argparse.ArgumentParser(description="Summarize various aspects of alignments in SAM format.")
ap.add_argument("sam", help="Input.", nargs="+")
ap.add_argument("-F", help="Exclude these fl... | yunlongliukm/chm1_scripts | SummarizeFromAlignments.py | Python | mit | 3,704 | [
"pysam"
] | 68fbf08bc800fc2aad58dcd61728a073c8b54d4d1dd8221ee824fd9f36754751 |
from __future__ import division, print_function, absolute_import
import sys
def configuration(parent_package='',top_path=None):
from numpy.distutils.misc_util import Configuration
config = Configuration('sids',parent_package,top_path)
config.add_subpackage('helper')
config.add_subpackage('es')
con... | zerothi/siesta-es | sids/setup.py | Python | gpl-3.0 | 547 | [
"SIESTA"
] | cf2e92fe1c8b79fb68dee0884fcfbb181f630e8978165531cbf4f9e2bbb5a7ce |
#!/usr/bin/env python3
"""
Template by pypi-mobans
"""
import os
import sys
import codecs
import locale
import platform
from shutil import rmtree
from setuptools import Command, setup, find_packages
from setuptools import __version__ as setuptools_version
from pkg_resources import parse_version
import pkg_resources... | chfw/moban | setup.py | Python | mit | 7,396 | [
"VisIt"
] | 583557caeeac657e06a9be61b39e9e94fe346647ec4a6658ff4ce5453f5902a8 |
import numpy as np
from ase import Atoms
from ase.visualize.vtk.sources import vtkAtomSource, vtkForceSource, \
vtkVelocitySource
from ase.visualize.vtk.cell import vtkUnitCellModule, vtkAxesModule
from ase.visualize.vtk.grid import vtkAtomicPositions
from ase.visualize.vtk.modu... | grhawk/ASE | tools/ase/visualize/vtk/atoms.py | Python | gpl-2.0 | 4,730 | [
"ASE",
"VTK"
] | 2b492a0ca0470e4839cb423a2afb3443f419a0ff57c23181c02f71291a973031 |
####################################################################################################
# #
# RUN SCRIPT to perform an MD simulation in Sire with OpenMM #
# ... | michellab/Sire | wrapper/Tools/OpenMMMD.py | Python | gpl-2.0 | 69,390 | [
"Amber",
"OpenMM",
"VisIt"
] | 9f0bfd1ce22f7ed110d30eba7d4187629fdc70c4244c5a6573f5237337df6d90 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# (c) 2012 Michal Kalewski <mkalewski at cs.put.poznan.pl>
#
# This file is a part of the Simple Network Simulator (sim2net) project.
# USE, MODIFICATION, COPYING AND DISTRIBUTION OF THIS SOFTWARE IS SUBJECT TO
# THE TERMS AND CONDITIONS OF THE MIT LICENSE. YOU SHOULD H... | mkalewski/sim2net | sim2net/placement/uniform.py | Python | mit | 3,617 | [
"VisIt"
] | c20d9e4ca211024b59dac3552b549d89d8fc0ab20b710f6fb898e2f0bfa147c1 |
"""Tests for QHA calculations."""
import os
import numpy as np
from phonopy import PhonopyQHA
current_dir = os.path.dirname(os.path.abspath(__file__))
ev_vs_v = np.array(
[
[140.030000, -42.132246],
[144.500000, -42.600974],
[149.060000, -42.949142],
[153.720000, -43.188162],
... | atztogo/phonopy | test/qha/test_QHA.py | Python | bsd-3-clause | 5,043 | [
"phonopy"
] | 4d08c8c0335aa449b6575e8820e451c49d4f792a7c733d14720b83339203fb6d |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2017, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Fragment analysis based on parsed ADF data."""
import logging
import random
import numpy
numpy.inv = numpy.linalg.inv... | cclib/cclib | cclib/method/fragments.py | Python | bsd-3-clause | 5,375 | [
"ADF",
"cclib"
] | 2a8de76181c3aefb81ce4461e48852d7dea5d7d4a98eb215db701bf0186edab9 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkPDBReader(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkP... | nagyistoce/devide | modules/vtk_basic/vtkPDBReader.py | Python | bsd-3-clause | 464 | [
"VTK"
] | 886b02382737797e05e7e04bf69fa351c760a1a5113af1382eec7c995c2eaad4 |
# MIT License
#
# Copyright (c) 2017
#
# 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, publish, di... | kellerberrin/OSM-QSAR | OSMProperties.py | Python | mit | 16,637 | [
"RDKit"
] | 31cb3ce0b62bc159398ddc05939d7656159cdf13377f733688888271406ea4be |
import logging
from cStringIO import StringIO
from math import exp
from lxml import etree
from path import path # NOTE (THK): Only used for detecting presence of syllabus
import requests
from datetime import datetime
import dateutil.parser
from lazy import lazy
from xmodule.modulestore import Location
from xmodule.pa... | morenopc/edx-platform | common/lib/xmodule/xmodule/course_module.py | Python | agpl-3.0 | 42,110 | [
"VisIt"
] | e3af1f1c458fe4c3fd343f2423fc626fa263043ade37f315b5c101efcfef449c |
#!/usr/bin/env python3
# B a r a K u d a
#
# L. Brodeau, 2017]
import sys
import numpy as nmp
from PIL import Image
import os
from netCDF4 import Dataset
import datetime
#l_fake_coor = True
l_fake_coor = False
l_nemo_like = True
narg = len(sys.argv)
if not narg in [2, 3]:
print('Usage: '+sys.argv[0... | brodeau/barakuda | python/exec/image_to_netcdf.py | Python | gpl-2.0 | 3,263 | [
"NetCDF"
] | 57772cb51d2e429c18c517a149137eeb82dc7f2ee9fc639ad5e448060b8e49a4 |
""" Collection of utilities for finding paths in the CS
"""
from urllib import parse
from DIRAC.Core.Utilities import List
from DIRAC.ConfigurationSystem.Client.ConfigurationData import gConfigurationData
from DIRAC.ConfigurationSystem.Client.Helpers import Path
def getDIRACSetup():
"""Get DIRAC default setup na... | DIRACGrid/DIRAC | src/DIRAC/ConfigurationSystem/Client/PathFinder.py | Python | gpl-3.0 | 10,836 | [
"DIRAC"
] | 802e1b2e1581cb037accdd97b1798b5441e8ff3e0885cae38f9757c30b52eb95 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
class Migration(migrations.Migration):
dependencies = [
('visit', '0011_location_is_primary'),
]
operations = [
migrations.AddField(
model_name='visit',
name=... | koebbe/homeworks | visit/migrations/0012_visit_status.py | Python | mit | 540 | [
"VisIt"
] | 1c3b30c6a79e45e715528a1dc4aaf219c8e16e40f3fe19a71bfd5d3262186527 |
"""
This module was copied from the scipy project.
In the process of copying, some methods were removed because they depended on
other parts of scipy (especially on compiled components), allowing seaborn to
have a simple and pure Python implementation. These include:
- integrate_gaussian
- integrate_box
- integrate_b... | mwaskom/seaborn | seaborn/external/kde.py | Python | bsd-3-clause | 13,806 | [
"Gaussian"
] | 5327f7c6a8f51b3949e039b0e3c0a0f1c8ad06c30b1ffc720190c9ed512bfaa0 |
# This module contains functions that output a cmd string for calling executables, should be broad/odyssey compatible
import os, sys, subprocess
script_path = os.path.dirname(__file__)
sys.path.append(script_path)
import myos
def start_java_cmd(mem_usage, additional_option):
return 'java -Xmx%sm %s -jar' %(mem_us... | dfernan/de | myutils/execs_commands.py | Python | mit | 5,296 | [
"Bowtie"
] | 726ebd9e5676f2ad3e1e2dfb1069f25246d1a23aa592481fd9f9c0313c656a58 |
"""Minimal Python 2 & 3 shim around all Qt bindings
DOCUMENTATION
Qt.py was born in the film and visual effects industry to address
the growing need for the development of software capable of running
with more than one flavour of the Qt bindings for Python - PySide,
PySide2, PyQt4 and PyQt5.
1. Bu... | duncanskertchly/dm2skin | dependencies/Qt.py | Python | unlicense | 39,781 | [
"VisIt"
] | 2b7ad8537cbf1ee3abdb72a6a67b7d63e34b8bac6bb380750869779d5ee66ad5 |
"""Shared functionality useful across multiple structural variant callers.
Handles exclusion regions and preparing discordant regions.
"""
import collections
from contextlib import closing
import os
import numpy
import pybedtools
import pysam
import toolz as tz
import yaml
from bcbio import bam, utils
from bcbio.dis... | elkingtonmcb/bcbio-nextgen | bcbio/structural/shared.py | Python | mit | 13,523 | [
"pysam"
] | 9d973310bda6213af19276335be0152849f1ce40ad9ac7396878ed9edad92460 |
# -----------------------------------------------------------------------------------------------------
# CONDOR
# Simulator for diffractive single-particle imaging experiments with X-ray lasers
# http://xfel.icm.uu.se/condor/
# -------------------------------------------------------------------------------------------... | FXIhub/condor | condor/source.py | Python | bsd-2-clause | 9,648 | [
"Gaussian"
] | 60cb2497dfdaa946caaff768a98eafeb5d53896c37b2bfe0aabeee3f68c28d9f |
#!/usr/bin/env python
"""Module to create, configure and dispose separate database instances for individual OrthoMCL runs."""
from ConfigParser import SafeConfigParser
import MySQLdb
import collections
from datetime import datetime
import os
import shutil
import logging as log
from shared import resource_filename
_... | ODoSE/odose.nl | orthomcl_database.py | Python | mit | 3,880 | [
"BLAST"
] | d4a2b092646dbfca02bfb56115d18154423f92610c3eea5603996c6bf6c7a9f0 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RBiocgenerics(RPackage):
"""S4 generic functions used in Bioconductor.
The package... | iulian787/spack | var/spack/repos/builtin/packages/r-biocgenerics/package.py | Python | lgpl-2.1 | 986 | [
"Bioconductor"
] | d17ae77c0cd5aa76a8e96a012792aa1c084607f17faa9fbd8b34dba7d943a256 |
import logging
import os
import re
from tweakmark.formatters.base import FormatterBase
logger = logging.getLogger(__name__)
class TerminalFormatterConfig:
def __init__(self, style=None, strict=True, width=None):
style = style or {}
self.width = width
class FormattingState():
def __init__(s... | delins/tweakmark | tweakmark/formatters/terminal_formatter/formatter.py | Python | lgpl-3.0 | 5,894 | [
"VisIt"
] | c0799b8847b86f2dad139887dc7e7b48c5aa00e38178ad3253ff98d7edcc822d |
#
# Copyright (C) 2013,2014,2015,2016 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)... | tbereau/espresso | testsuite/python/magnetostaticInteractions.py | Python | gpl-3.0 | 2,692 | [
"ESPResSo"
] | f25c80d97e8c7f3b2156cf82f27c7fb19f9cb754c093d999c6ee7cfe1b4e5393 |
# Orca
#
# Copyright 2004-2008 Sun Microsystems Inc.
#
# 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.
#
# This... | ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/scripts/apps/Thunderbird/script.py | Python | gpl-3.0 | 15,728 | [
"ORCA"
] | f51be77b61f8dc8d1a99d44cb1302fe453f37b3a3f7376ca7e67ab1c1de742e3 |
import os
import _iso
import numpy as np
from mpl_toolkits.basemap import Basemap, shiftgrid
from matplotlib.mlab import griddata
import matplotlib.colors as colors
from scipy.signal import medfilt2d
import netCDF4
import pyroms
import pyroms_toolbox
from bathy_smoother import *
# Grid dimension
Lm = 140
Mm = 120
lo... | kshedstrom/pyroms | examples/Yellow_Sea/make_YELLOW_grd_v1.py | Python | bsd-3-clause | 3,559 | [
"NetCDF"
] | 43688a711a1a84a94dcafb67dd1680b4bc2129c688652477d2615adcb2a79b92 |
#* 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/lgpl-2.1.html
import os
i... | nuclear-wizard/moose | python/peacock/utils/__init__.py | Python | lgpl-2.1 | 1,231 | [
"MOOSE"
] | 7aa1b1a03dec818eae6ceba5abd2ae7016868dab0e28166da5da8924b5dd3399 |
import os, re
from copy import copy
from difflib import unified_diff
from sqlalchemy import *
from sqlalchemy.orm import *
from model import *
from cStringIO import StringIO
from cgi import FieldStorage
from tw import framework
framework.default_view = 'mako'
#try:
import xml.etree.ElementTree as etree
#except Import... | jokajak/itweb | data/env/lib/python2.6/site-packages/sprox-0.6.10-py2.6.egg/sprox/test/base.py | Python | gpl-3.0 | 5,454 | [
"VisIt"
] | 5dc790a787838924b5e4f883507869ddec47a14db1789867c026493d70cc13b9 |
import pandas as pd
from sklearn.ensemble import RandomForestClassifier
from sklearn.ensemble import GradientBoostingClassifier
from sklearn.ensemble import BaggingClassifier
from sklearn.ensemble import AdaBoostClassifier
from sklearn.ensemble import ExtraTreesClassifier
from sklearn.neural_network import MLPClassifie... | rupakc/Kaggle-Compendium | Walmart Trip Type Challenge/walmart-baseline.py | Python | mit | 2,893 | [
"Gaussian"
] | 23dc70e41332fb1789d5b5e2abf524c01e0db41a045ed09d551bf1247d7c1030 |
from __future__ import print_function
import copy
import warnings
import graphviz
import matplotlib.pyplot as plt
import numpy as np
def plot_stats(statistics, ylog=False, view=False, filename='avg_fitness.svg'):
""" Plots the population's average and best fitness. """
if plt is None:
warnings.warn(... | CodeReclaimers/neat-python | examples/xor/visualize.py | Python | bsd-3-clause | 5,915 | [
"NEURON"
] | 35e6d9dc43bff65bea1f6f087598d840bb977c864f80e4808e294c827e37bd93 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# king_phisher/client/export.py
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, th... | zigitax/king-phisher | king_phisher/client/export.py | Python | bsd-3-clause | 13,884 | [
"VisIt"
] | 86cfe448278240b800e7fa5f0ac12b1c8be31af5c0f213a38cef426f470d32b6 |
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