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#!/usr/bin/env python
"""
A linting tool to check for xss vulnerabilities.
"""
from __future__ import print_function
import argparse
import ast
import os
import re
import sys
import textwrap
from enum import Enum
class StringLines(object):
"""
StringLines provides utility methods to work with a string in te... | pepeportela/edx-platform | scripts/xss_linter.py | Python | agpl-3.0 | 101,159 | [
"VisIt"
] | c31be62db2e6f81ddb382b45fbebfd41146cbb53d85e44fbc7b541a9056f69f3 |
# -*- coding: cp1252 -*-
"""
#########################################################################
Author: Shalin Shah
Project: DNA Cloud
Graduate Mentor: Dixita Limbachya
Mentor: Prof. Manish K Gupta
Date: 5 November 2013
Website: www.guptalab.org/dnacloud
This module contains code for the main GUI Frame.
########... | shalinshah1993/DNACloud | source/MainFrame.py | Python | mit | 65,081 | [
"VisIt"
] | a7287d4339255678f501f863c18c53b00416bedf7e94d0fb472b914fb6fcfdcf |
"""
Test utils for CCX
"""
import datetime
import pytz
from django.conf import settings
from lms.djangoapps.ccx.overrides import override_field_for_ccx
from lms.djangoapps.ccx.tests.factories import CcxFactory
from student.roles import CourseCcxCoachRole
from student.tests.factories import (
AdminFactory,
)
from ... | solashirai/edx-platform | lms/djangoapps/ccx/tests/utils.py | Python | agpl-3.0 | 3,620 | [
"VisIt"
] | 232bf43ecfe3b7f87280205b9510bb70be93126ba5dff4200529429da7528e83 |
# -*- coding: utf-8 -*-
# Copyright (C) 2004-2016 by
# Aric Hagberg <hagberg@lanl.gov>
# Dan Schult <dschult@colgate.edu>
# Pieter Swart <swart@lanl.gov>
# All rights reserved.
# BSD license.
#
# Authors: Aric Hagberg (hagberg@lanl.gov)
# Dan Schult (dschult@colgate.edu)
# Ben Edward... | cmtm/networkx | networkx/generators/geometric.py | Python | bsd-3-clause | 16,979 | [
"Gaussian"
] | 7aa59ac878274f0cae7beac4985b4e954cae61a42b5d3b6cd002a27e600abd51 |
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | pierrelapointe/scancode-toolkit | tests/licensedcode/test_detect.py | Python | apache-2.0 | 31,217 | [
"VisIt"
] | 5e60bca0a7c22ff6e9e54b0cb5493c0dd832cedea742cf3086c02b4215a97861 |
# Copyright (C) 2012,2013,2017(H)
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the te... | kkreis/espressopp | src/standard_system/Default.py | Python | gpl-3.0 | 2,337 | [
"ESPResSo"
] | 01942db5ded3093f15c5b914cd913cdcfbd4a24898be4030dc53a5af647cbfd4 |
"""
Acceptance tests for Content Libraries in Studio
"""
from ddt import data, ddt
from nose.plugins.attrib import attr
from common.test.acceptance.fixtures.course import XBlockFixtureDesc
from common.test.acceptance.pages.common.auto_auth import AutoAuthPage
from common.test.acceptance.pages.studio.library import Lib... | Stanford-Online/edx-platform | common/test/acceptance/tests/studio/test_studio_library.py | Python | agpl-3.0 | 27,844 | [
"VisIt"
] | aa39c989029988edb55952159ae890bf85006121b708b6b29996a9102fb1c958 |
import subprocess
import os.path as op
from functools import partial
import pytest
import numpy as np
from numpy.testing import assert_allclose, assert_array_equal
from pytest import raises
import scipy.sparse as sps
from scipy.optimize import approx_fprime
from sklearn.datasets import make_regression
from sklearn.p... | pavanramkumar/pyglmnet | tests/test_pyglmnet.py | Python | mit | 16,630 | [
"Gaussian"
] | f46b7138e3c3f5889ff02e6a3dabbddd5463c240a6b4af2918dae42909997c26 |
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are ... | liesbethvanherpe/NeuroM | neurom/core/_neuron.py | Python | bsd-3-clause | 8,633 | [
"NEURON"
] | 49d95f1067807693658c667884f136cec8f2369b4b7953e758697e587ef3cf6b |
# Takes 30 mins with 8 cores in domain-parallel (memory ~500mb, max 1.5gb)
import numpy as np
from ase import Atom, Atoms
from gpaw import GPAW, MixerDif, mpi
from gpaw.lrtddft import LrTDDFT
from gpaw.pes.dos import DOSPES
from gpaw.pes.tddft import TDDFTPES
atoms = Atoms([Atom('C', (7.666263598984184, 7.63778085043... | robwarm/gpaw-symm | gpaw/test/big/pes/PES_CO.py | Python | gpl-3.0 | 1,518 | [
"ASE",
"GPAW"
] | f320c0364982043a553f891b7b1e43f97d7ab735cd1eeee0aede762541702340 |
# Copyright 2012 United States Government as represented by the
# Administrator of the National Aeronautics and Space Administration.
# All Rights Reserved.
#
# Copyright 2012 Nebula, Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the... | Crystal-SDS/dashboard | crystal_dashboard/dashboards/crystal/containers/forms.py | Python | gpl-3.0 | 14,761 | [
"CRYSTAL"
] | a71637f00af4c648ead08588cce7c3adb66949471db1bcfb1c43e8b543d75e60 |
import numpy as np
import pickle
from NO import NaturalOrbitals as NO
from NO import plot_basis
# Import Hamiltonian/overlap matrix. This example has been
# calculated/optimized with GPAW. H and S can be saved to disk
# with dump_hamiltonian_parallel() as pickles and be
# converted to .txt-files.
h = np.loadtxt(... | andersborges/natural-orbitals | CH4_example.py | Python | mit | 1,453 | [
"ASE",
"GPAW"
] | 1ca84ba1d4d94ed25aaa20cff255841ee7467290104dd84beccb73c9f6b0ec60 |
import imp
import os
import marshal
import struct
import sys
import types
from cStringIO import StringIO
from compiler import ast, parse, walk, syntax
from compiler import pyassem, misc, future, symbols
from compiler.consts import SC_LOCAL, SC_GLOBAL, SC_FREE, SC_CELL
from compiler.consts import CO_VARARGS, CO_VARKEYW... | trivoldus28/pulsarch-verilog | tools/local/bas-release/bas,3.9/lib/python/lib/python2.3/compiler/pycodegen.py | Python | gpl-2.0 | 42,252 | [
"VisIt"
] | b1d929badd2c9471b493772c3c226ac2449a5d86069e5d6f393846008fecd29d |
# -*- coding: utf-8 -*-
# Copyright 2020 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | sasha-gitg/python-aiplatform | tests/unit/gapic/aiplatform_v1/test_job_service.py | Python | apache-2.0 | 250,207 | [
"Octopus"
] | 86d0b33fb7284bc1f3f3ef9ee37126704b26b452907cda3523cf1ffa9cc7760f |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Makes sure that all files contain proper licensing information."""
import optparse
import os.path
import subprocess
import sys... | ChromiumWebApps/chromium | tools/checklicenses/checklicenses.py | Python | bsd-3-clause | 16,045 | [
"Galaxy"
] | b51b12d8970de3afb189e06273f86ded5e64ae1a4de8cf34df7206060e755e7d |
"""Unit tests of MQProducer interface in the DIRAC.Resources.MessageQueue.MProducerQ
"""
import unittest
from DIRAC import S_OK
from DIRAC.Resources.MessageQueue.MQProducer import MQProducer
from DIRAC.Resources.MessageQueue.MQConnectionManager import MQConnectionManager
from DIRAC.Resources.MessageQueue.MQConnector im... | DIRACGrid/DIRAC | src/DIRAC/Resources/MessageQueue/test/Test_MQProducer.py | Python | gpl-3.0 | 4,422 | [
"DIRAC"
] | 078e9fc69df87a91d481070458b743b267dc52902856c86b16adbfea38d0ea98 |
#!/usr/bin/env python
# Copyright 2014-2021 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... | sunqm/pyscf | pyscf/cc/uccsd_slow.py | Python | apache-2.0 | 29,020 | [
"PySCF"
] | 20aa1bbb593df2ea4b5711dd5cd0aaa21c5e6d4830b69dd2ee9a5cc0cbc13593 |
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are ... | juanchopanza/NeuroM | neurom/fst/tests/test_neuritefunc.py | Python | bsd-3-clause | 11,131 | [
"NEURON"
] | 1ffb537e40decafabd0ef3206d4c58d41f358c53656772fcee023d5a9f719da7 |
#!/usr/bin/env python
# Copyright (C) 2010 Ion Torrent Systems, Inc. All Rights Reserved
import os
import re
import sys
from optparse import OptionParser
import pysam
import string
#MATCH = 0
#INS = 1
#DEL = 2
#REF_SKIP = 3
#SOFT_CLIP = 4
#HARD_CLIP = 5
#PAD = 6
def get_qref(md, cigar, q... | nh13/TMAP | scripts/util/sam2hpstats.py | Python | gpl-2.0 | 9,643 | [
"pysam"
] | da9aec0495dd547f6e277a4cf0c869c434a5d2d557476a8f3ca7e691bb0f84f0 |
# -*- coding: utf-8 -*-
#!/usr/bin/env python
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007 Johan Gonqvist <johan.gronqvist@gmail.com>
# Copyright (C) 2007-2009 Gary Burton <gary.burton@zen.co.uk>
# Copyright (C) 2007-2009 Stephane Charet... | jralls/gramps | gramps/plugins/webreport/basepage.py | Python | gpl-2.0 | 114,137 | [
"Brian"
] | e66ffab92ab09e7984b1034bded63ab892b5df310953885cd24d6179e86edda9 |
# Copyright (c) 2018 PaddlePaddle 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 app... | PaddlePaddle/Paddle | python/paddle/fluid/tests/unittests/test_gaussian_random_op.py | Python | apache-2.0 | 12,671 | [
"Gaussian"
] | 55e9f402ff8d4e4ec8b69210810af053d7ebe0f99b6bc341f261a539a7e5e617 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | kyleabeauchamp/mdtraj | mdtraj/geometry/tests/test_geometry.py | Python | lgpl-2.1 | 14,869 | [
"MDTraj",
"PyMOL"
] | b82a8a92323f56bbda44122214076489ecff410d69bbe8a1bfd5578474627ab6 |
import functools
import numpy as np
import pandas as pd
from itertools import izip
from collections import OrderedDict
import data_array
import dataset
import groupby
import indexing
import ops
import utils
from common import AbstractArray
def as_variable(obj, strict=True):
"""Convert an object into an Variabl... | takluyver/xray | xray/variable.py | Python | apache-2.0 | 29,152 | [
"NetCDF"
] | b6225090d0b3d0d4e20ade637835e9b430da33e9d066552ec9a5bfbd19affe50 |
import subprocess
import tempfile
import os
import warnings
import shutil
import ensembler
import mdtraj
from PIL import Image, ImageFont, ImageDraw
class PymolRender(object):
def __init__(self, width=640, height=480):
self.width = width
self.height = height
def run_pymol(self, input_filepath... | choderalab/ensembler | ensembler/tools/rendering.py | Python | gpl-2.0 | 8,131 | [
"MDTraj",
"PyMOL"
] | 6d536f68bb28eaae3b89c18ebd63f5467289c4ea19decfa10cba3563329b9f12 |
from learner import ktsp, tst, dirac, tsp
from parser import SOFTParser, GMTParser
from adaptive import ResourceEstimate
from adaptive import LearnerQueue
import random
from testScripts import testTemplate
def getScores(learner):
myfile = open('test' + str(learner) + '.csv')
temp = []
for line in myfile.re... | JohnCEarls/AUREA | scripts/testScripts/testRE.py | Python | agpl-3.0 | 2,777 | [
"DIRAC"
] | dbe845e6df6ca73a2aa97cbca34bf21fc08d70476cd11cdcb37d139911fc4f54 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
urlpatterns = [
url(r'^$', TemplateView.as_view(templ... | sebastian-code/portal | config/urls.py | Python | bsd-3-clause | 1,232 | [
"VisIt"
] | 6f84bb65987e9c25c1a06d094b74771a0f415a94b9ab285ae6b39754099a0b92 |
def run(to_remap_bam, remap_bam, keep_bam, orig_num_file, is_paired_end):
import gzip
import sys
import pysam
to_remap_bam = pysam.Samfile(to_remap_bam, "rb")
remap_bam = pysam.Samfile(remap_bam, "rb")
keep_bam = pysam.Samfile(keep_bam, "wb", template=to_remap_bam)
orig_num_file = gzip.ope... | cdeboever3/WASP | mapping/filter_remapped_reads.py | Python | apache-2.0 | 8,014 | [
"pysam"
] | a8e3370d84dd895a61da880b0edc5f1dd4f7ba7f8adc2266210ad06eef229acf |
import pandas as pd
import numpy as np
import os
from sys import argv
import copy
import json
plot_angle = 0 # plot histogram of maxmimum angle between NN atom vectors.
class POSCAR:
theta = 90 # surface threshold in degree
ninfile = ''
lines = ''
line_list = []
com... | cwandtj/A2P2 | 180419_qCat_SurfAtomExt.py | Python | mit | 23,421 | [
"VASP"
] | cc5a296402efad287f9ef055f65766cf5ed2110cc066d6ca7360d468ccc97015 |
#
# Copyright 2016 The BigDL 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
#
#
from unittest import TestCase
import pytest
import ray
from bigdl.orca import stop_orca_context
fr... | intel-analytics/BigDL | python/orca/test/bigdl/orca/ray/ray_cluster/test_rayctx_local.py | Python | apache-2.0 | 1,330 | [
"ORCA"
] | 747c588a1693f26d1a9ac3112819b5b9337508acedd37fdba75829767f00213c |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright: (c) 2014, Brian Coca <briancoca+ansible@gmail.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
DOCUMENTATION = r'''
---
module... | s-hertel/ansible | lib/ansible/modules/debconf.py | Python | gpl-3.0 | 6,083 | [
"Brian"
] | ab09c5d3d9c5c6277c9f627237a6a40b69282a488e34391f2afbc3f1ce365cf4 |
import os
from flask import request, url_for, Blueprint
from igvjs._config import basedir
err_message = 'pysam is not installed. Please install pysam (pip install pysam) '\
'if you wish to use the alignments service.'
pysam_installed = True
try:
import pysam
from urllib import unquote
except ImportError:
... | igvteam/igv.js-flask | igvjs/alignments.py | Python | mit | 1,642 | [
"pysam"
] | cea56af18d777b8a287fec7f72c28ef6efd005371d546db99372975a9805a336 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# (c) 2014, Ruggero Marchei <ruggero.marchei@daemonzone.net>
# (c) 2015, Brian Coca <bcoca@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
#... | fernandezcuesta/ansible | lib/ansible/modules/files/find.py | Python | gpl-3.0 | 12,982 | [
"Brian"
] | 9727a5203674eee7a7ab2c4c91b387c26083fb38520d86b2572af060fbd2a7ff |
"""
Copyright (C) 2016,2019 Jakub Krajniak <jkrajniak@gmail.com>
This file is distributed under free software licence:
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 ... | MrTheodor/bakery | src/app_args.py | Python | gpl-3.0 | 8,053 | [
"Gromacs"
] | 8dff5fe112e83fc84dffe4f93621f2d0e14d4beff512be278bb0fbedab4dbb7f |
#!/usr/bin/env python
# -*- coding=utf-8 -*-
import os
import sys
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.collections import LineCollection
from matplotlib.gridspec import GridSpec
import pymatgen as mg
from pymatgen.io.vasp.outputs import Vasprun, BSVasprun
from pymatgen.electronic_struct... | gVallverdu/myScripts | VASP/bandstructure.py | Python | gpl-2.0 | 18,000 | [
"VASP",
"pymatgen"
] | 4bb1eb875854e2720efc7259537bd1d9ababfbd00efdb6ebcc3455e7226a864a |
# pylint: disable=missing-docstring
import datetime
import os
import pytz
from django.conf import settings
from lettuce import step, world
from mock import patch
from nose.tools import assert_equal, assert_in, assert_is_none, assert_true
from pytz import UTC
from selenium.common.exceptions import NoAlertPresentExcepti... | Lektorium-LLC/edx-platform | lms/djangoapps/courseware/features/lti.py | Python | agpl-3.0 | 14,313 | [
"VisIt"
] | b1de698d1d8a0990f320945e7beb54122c3415b1803f4ab27bdb50ca875bcb5b |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, subprocess, sys, glob, string
import zipfile
from datetime import date
cwd = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
os.chdir(cwd)
required_module_keys = ['architectures', 'name','version','moduleid','descripti... | jaraen/TiAccurateTimer | iphone/build.py | Python | apache-2.0 | 8,499 | [
"VisIt"
] | 958b2020d64f4d3900b512a649026e1d63b5d3935d621e26c2f298cb45924e43 |
import numpy as np
import mayavi.mlab as mlab
import moviepy.editor as mpy
duration= 2 # duration of the animation in seconds (it will loop)
# MAKE A FIGURE WITH MAYAVI
fig_myv = mlab.figure(size=(220,220), bgcolor=(1,1,1))
X, Y = np.linspace(-2,2,200), np.linspace(-2,2,200)
XX, YY = np.meshgrid(X,Y)
ZZ ... | solvery/lang-features | python/use_lib/video_1/mayavi_1.py | Python | gpl-2.0 | 712 | [
"Mayavi"
] | e1d43f0d82c56d9e4bac26aefe76ed53a4a4505990c9468140fa85da5d16e4be |
from collections.abc import Iterable
import numpy as np
import numba
DEFAULT_CVD_COLS = {
"dist": "dist",
"n_pixels": "n_valid",
"n_contacts": "balanced.sum",
"contact_freq": "balanced.avg",
"smooth_suffix": ".smoothed",
}
def _log_interp(xs, xp, fp):
"""
Interpolate a function in the l... | open2c/cooltools | cooltools/sandbox/expected_smoothing.py | Python | mit | 9,036 | [
"Gaussian"
] | bf223d724cade360ca4ceea7fd3d64bdc5955a47b05af62726be5f64818ef1af |
"""An implementation of the Zephyr Abstract Syntax Definition Language.
See http://asdl.sourceforge.net/ and
http://www.cs.princeton.edu/~danwang/Papers/dsl97/dsl97-abstract.html.
Only supports top level module decl, not view. I'm guessing that view
is intended to support the browser and I'm not interested in the
br... | TathagataChakraborti/resource-conflicts | PLANROB-2015/seq-sat-lama/Python-2.5.2/Parser/asdl.py | Python | mit | 11,306 | [
"VisIt"
] | 66daf07adb228fb20d93ef51cb7d747baa164b0d5e0fa2ba7ec09c36033e1d6b |
# Orientation from Orientation Tensor by Local Polynomial Approximation using Numba JIT Acceleration
#
# Calculates the orientation using an orientation tensor derived from the coefficients of a local polynomial
# approximation (3D 2nd order polynomial using gaussian weighted least squares) as proposed by Farneback.
# ... | waynegm/OpendTect-Plugins | bin/python/wmpy/Experimental/LocalPolynomialApproximation/ex_lpa_dip.py | Python | gpl-3.0 | 3,389 | [
"Gaussian"
] | b9c076e97d93e6549c16cc6264589e2c9e69a3dfae74b7bd35f974892bf35719 |
from ovito import *
from ovito.io import *
from ovito.modifiers import *
import numpy
node = import_file("../../files/NetCDF/sheared_aSi.nc")
import ovito.modifiers
ovito.modifiers.BinAndReduceModifier(property = "Position.X")
modifier = BinAndReduceModifier()
node.modifiers.append(modifier)
print("Parameter defaul... | srinath-chakravarthy/ovito | tests/scripts/test_suite/binandreduce_modifier.py | Python | gpl-3.0 | 1,116 | [
"NetCDF",
"OVITO"
] | caf9a654f8524d48a0b12f75d85093b2a14310f3235605438a21be58668f9607 |
#!/usr/bin/env python3
### VERY MUCH PYTHON 3 !!!
"""
Example for aiohttp.web basic async service
Uses a background timer to print to a logger
exposes an obvious REST endpoint
It's a template!
Made available under the MIT license as follows:
Copyright 2017 Brian Bulkowski brian@bulkowski.org
Permission is hereby ... | bbulkow/MagnusFlora | led/led.py | Python | mit | 8,944 | [
"Brian"
] | ccddf43e70faaa43d7462578b98ac1fd762bb2e6decc0f789001bed7412bb15b |
import numpy as np
from astropy.io import fits
import os
# TODO: rewrite this to have multiple components generated here.
# Having a bundle of test filaments would be very nice.
def make_test_cube(shape=(30,9,9), outfile='test.fits',
sigma=None, seed=0, writeSN=False ):
"""
Generate... | vlas-sokolov/multicube | multicube/astro_toolbox.py | Python | mit | 5,386 | [
"Gaussian"
] | 6c688f6fac06aae1c5e2e6d92c09982b476e23dadd2d3f3b91be2714f861746b |
"""
Featurizes proposed binding pockets.
"""
import numpy as np
import logging
from typing import Dict, List
from deepchem.feat import Featurizer
from deepchem.utils.coordinate_box_utils import CoordinateBox
from deepchem.utils.rdkit_utils import load_molecule
logger = logging.getLogger(__name__)
def boxes_to_atoms... | deepchem/deepchem | deepchem/feat/binding_pocket_features.py | Python | mit | 3,961 | [
"MDTraj"
] | cac86661270a30aeccefcf814d46077501d20193a6ca5a8e659efdb2d33f243f |
# $Id$
#
# Copyright (C) 2002-2006 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
"""Command line tool ... | jandom/rdkit | rdkit/ML/EnrichPlot.py | Python | bsd-3-clause | 14,937 | [
"RDKit"
] | 3f39ed67ea52adb0fdcb53ba11cfca765b91462897a982903639562066634db0 |
from kinko.refs import ArgRef, RefsCollector, FieldRef, ItemRef, extract, CtxRef
from kinko.refs import type_to_query
from kinko.query import Edge, Field, Link
from kinko.nodes import Symbol
from kinko.types import StringType, Record, IntType, Func, ListType, TypeVar
from kinko.utils import VarsGen
from kinko.checker i... | vmagamedov/kinko | tests/test_refs.py | Python | bsd-3-clause | 4,531 | [
"VisIt"
] | 6c07b8b1b095607f0bfcdc88560121f04ca614b19cb454e4823c89a10cf1f452 |
# -*- coding: utf-8 -*-
#
# Name: SkyBiometry Face Detection and Recognition API Python client library
# Description: SkyBiometry Face Detection and Recognition REST API Python client library.
#
# For more information about the API and the return values,
# visit the official documentation at http://www.skybiometry.com/... | Liuftvafas/python-face-client | face_client/face_client.py | Python | bsd-3-clause | 15,038 | [
"VisIt"
] | ed7a8dd0fc510c6b95198b8a11b1b81328f5a945b30c18bb967cd26dcdeeaf0f |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | python/peacock/tests/postprocessor_tab/test_PostprocessorSelectPlugin.py | Python | lgpl-2.1 | 4,053 | [
"MOOSE"
] | e65e49d2538c1fbf2636387a54831847ac298fade3e885f23d57a3858e3fdf61 |
#!/usr/bin/env python
"""
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the term... | jeremiahyan/lammps | examples/PACKAGES/cgdna/util/generate.py | Python | gpl-2.0 | 19,265 | [
"LAMMPS"
] | 58b91c3686e93c41f614edeaf1cff08dfaec139cbda1758b06b327748c8dd8e7 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import functools
import json
import os
import random
import unittest
import warnings
from shutil import which
from monty.json import MontyDecoder
from pymatgen.core.lattice import Lattice
from pymatgen.core.periodic_table im... | materialsproject/pymatgen | pymatgen/transformations/tests/test_standard_transformations.py | Python | mit | 25,335 | [
"VASP",
"pymatgen"
] | b5279856369024b7f80ee9180742062363fd0d9a528fb4369b137c7b53fc73c4 |
# -*- coding: utf-8 -*-
# Copyright 2012 splinter authors. All rights reserved.
# Use of this source code is governed by a BSD-style
# license that can be found in the LICENSE file.
import warnings
from .fake_webapp import EXAMPLE_APP
class MouseInteractionTest(object):
def test_mouse_over(self):
"Sho... | gjvis/splinter | tests/mouse_interaction.py | Python | bsd-3-clause | 2,679 | [
"VisIt"
] | 85f1bdc7fa7cc86c08894bd4cdffe8128ebb835d722e869020eb95b21877f181 |
# -*- coding: utf-8 -*-
from wms.models.style import Style
from wms.models.group import Group
from wms.models.server import Server
from wms.models.variable import Variable
from wms.models.layer import Layer, VirtualLayer
from wms.models.datasets.netcdf import NetCDFDataset
from wms.models.datasets.base import Dataset
... | brianmckenna/sci-wms | wms/models/__init__.py | Python | gpl-3.0 | 534 | [
"NetCDF"
] | c74cd405ff8b394f86b938a38d8754fd979cf2bd0b5d1f592cf2730a98156da7 |
"""
sphinx.application
~~~~~~~~~~~~~~~~~~
Sphinx application class and extensibility interface.
Gracefully adapted from the TextPress system by Armin.
:copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS.
:license: BSD, see LICENSE for details.
"""
import os
import pickle
import p... | sonntagsgesicht/regtest | .aux/venv/lib/python3.9/site-packages/sphinx/application.py | Python | apache-2.0 | 54,085 | [
"VisIt"
] | a2181c104cdc514960d0d7e0829020f464bef3f0cb4b16d1136787f0bb816d4f |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# This module is also sponsored by E.T.A.I. (www.etai.fr)
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version... | jimi-c/ansible | lib/ansible/modules/cloud/vmware/vmware_guest.py | Python | gpl-3.0 | 118,949 | [
"VisIt"
] | a5db625ef1a44fd573bde2022e492fa3a351687e6dc470c13b8afc0ea21d844c |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Installation script for the vlfeat module
"""
import sys, os
from distutils.core import Extension, setup
from distutils.errors import DistutilsFileError
from distutils.command.build_ext import build_ext
import numpy
__version__ = '0.1.1a3'
vlfeat_src = ['vlfeat/vl/... | u1234x1234/pyvlfeat | setup.py | Python | gpl-2.0 | 4,710 | [
"Brian"
] | 94526f62a66e4dcce8ca58878baab4993ffb3b200a554e9f87c7da4365ddd355 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Module containing class to create an ion
"""
import re
from copy import deepcopy
import numpy as np
from monty.json import MSONable
from pymatgen.core.composition import Composition
from pymatgen.util.s... | mbkumar/pymatgen | pymatgen/core/ion.py | Python | mit | 6,401 | [
"pymatgen"
] | 64213dbf127f2e9d3226ff30c19d5e526406a2bab1303daa908e234e33ef3d6b |
"""
Generating Object Catalogue
===========================
These simple functions can be used to generate different types of object catalogues that can then be used
as an input for the VIS simulator.
Please note that the script requires files from the data folder. Thus, you should
place the script to an empty direct... | sniemi/EuclidVisibleInstrument | sources/createObjectCatalogue.py | Python | bsd-2-clause | 18,037 | [
"Galaxy"
] | 6f35d02fe566ea75180c31254d3681227d6fe30b21a87d4c389dabd44cfb0f21 |
#!/usr/bin/python2
import os, glob
os.chdir( '/workspace/Shared/Tech_Projects/ALFRESCO_Inputs/project_data/CODE/tem_ar5_inputs' )
base_dir = '/workspace/Shared/Tech_Projects/ESGF_Data_Access/project_data/data/prepped'
output_base_dir = '/workspace/Shared/Tech_Projects/ALFRESCO_Inputs/project_data/TEM_Data/downscaled'... | ua-snap/downscale | snap_scripts/old_scripts/tem_iem_older_scripts_april2018/tem_inputs_iem/old_code/downscaling_launcher.py | Python | mit | 3,851 | [
"NetCDF"
] | e3d009542d8afedea8ada00fea5a7f46c16fbb04d2958d1f9143bbea96085748 |
"""
A collection of functions to find the weights and abscissas for
Gaussian Quadrature.
These calculations are done by finding the eigenvalues of a
tridiagonal matrix whose entries are dependent on the coefficients
in the recursion formula for the orthogonal polynomials with the
corresponding weighting function over ... | juliantaylor/scipy | scipy/special/orthogonal.py | Python | bsd-3-clause | 23,767 | [
"Gaussian"
] | 7fc4bbf46ba3d4a9727b3a44fd62a4a7f7e02faa01b35286893228aa104a7059 |
# !usr/bin/env python
# -*- coding: utf-8 -*-
#
# Licensed under a 3-clause BSD license.
#
# @Author: Brian Cherinka
# @Date: 2017-08-04 14:21:05
# @Last modified by: Brian Cherinka
# @Last Modified time: 2018-02-23 13:43:43
from __future__ import print_function, division, absolute_import
import os
__version__ = ... | havok2063/SciScript-Python | python/sciserver/__init__.py | Python | apache-2.0 | 4,324 | [
"Brian"
] | 50555e7f0902e706078742db4533e64aa1c9d323d6efc14be39719d293b8d4bb |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2004-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Contribution 2009 by Brad Crittenden <brad [AT] bradcrittenden.net>
# Copyright (C) 2008 Benny Malengier
# Copyright (C) 2010 Jakim Friant
#
# This program is free... | arunkgupta/gramps | gramps/gui/plug/export/_exportassistant.py | Python | gpl-2.0 | 24,209 | [
"Brian"
] | e7d82019bfb2bbb44b95be806f62641cb8ab2a1d465b790b956ae01e1a0c400b |
# -*- coding: utf-8 -*-
from collections import OrderedDict
from gluon import current
from gluon.storage import Storage
from s3 import S3CRUD
def config(settings):
"""
Cumbria Emergency Assistance Centres
"""
T = current.T
settings.base.system_name = T("Cumbria Emergency Assistance Centres... | flavour/eden | modules/templates/CumbriaEAC/config.py | Python | mit | 157,038 | [
"Amber"
] | 64ceca497056ed46e709522c7d9bbdfcdbdf6e300dcf5a44f06c2731834b8242 |
import matplotlib.pyplot as plt
import matplotlib.pylab as pl
import numpy as np
from ClusterSVDD.svdd_primal_sgd import SvddPrimalSGD
from ClusterSVDD.cluster_svdd import ClusterSvdd
def generate_gaussians(datapoints, cluster, noise_frac=0.1, dims=2):
mean_mul = 50.
vars = [4.1, 4.1]
num_noise = np.in... | nicococo/ClusterSvdd | scripts/test_clustersvdd.py | Python | mit | 3,232 | [
"Gaussian"
] | 997e72779ad60db082b0068a650e98499c8fd39fc4353737a07074aab0e8620f |
from time import time
import numpy as np
from scipy import weave
from scipy.constants import g
from trampa import utils
from wavesimlib import spec
from wavesimlib import spread
class OceanSurface(object):
""" Ocean surface simulator class
:param Lx: Scene X size (m)
:param Ly: Scene Y si... | pakodekker/oceansar | misc/ocean.py | Python | gpl-3.0 | 12,210 | [
"Gaussian"
] | 677714e30d5c1de95c6fedfe0c1b28c6554f6608736266e947ef0bf973004fc7 |
import numpy as np
import tempfile
import os
# catalog_name, output_name
sex_params = \
'''
CATALOG_NAME {catalog_name} # name of the output catalog
CATALOG_TYPE ASCII_HEAD # NONE,ASCII,ASCII_HEAD, ASCII_SKYCAT,
# ASCII_VOTABLE, FITS_1.0 or FITS_LDAC
PARAMETERS_NAME ... | nickkonidaris/kpy | SEDM/SexSpectra.py | Python | gpl-2.0 | 4,288 | [
"Galaxy"
] | 8cef22bb7b6e9d755e5bd739cc0e047ee9d5cc219727934e4b3a309ce70d619f |
# Copyright (C) 2015 Henrique Pereira Coutada Miranda
# All rights reserved.
#
# This file is part of yambopy
#
#
import sys
if sys.version_info.major > 2:
from past.builtins import basestring
from yambopy import *
import os
import json
import re
from itertools import product
class YamboAnalyser():
"""
Cla... | palful/yambopy | yambopy/analyse.py | Python | bsd-3-clause | 19,722 | [
"Yambo"
] | 10c84814eaf25ccee25980b5d6adbdee4656c91c1ade356e49f9972462ece255 |
#!/usr/bin/env python
'''
Quantile regression model
Model parameters are estimated using iterated reweighted least squares. The
asymptotic covariance matrix estimated using kernel density estimation.
Author: Vincent Arel-Bundock
License: BSD-3
Created: 2013-03-19
The original IRLS function was written for Matlab by... | yarikoptic/pystatsmodels | statsmodels/regression/quantile_regression.py | Python | bsd-3-clause | 15,069 | [
"Gaussian"
] | 44dbec95cb5e923ef19cf5b3e6a2b7200a983229ad09ae4c702746c9b12abb9c |
# 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 RFgsea(RPackage):
"""Fast Gene Set Enrichment Analysis.
The package implements an ... | iulian787/spack | var/spack/repos/builtin/packages/r-fgsea/package.py | Python | lgpl-2.1 | 1,558 | [
"Bioconductor"
] | a9c7a7ab4f659ad7cf445bc942b3b60c88a30f23440d123970d8942b886f56d4 |
# file findingaids/content/forms.py
#
# Copyright 2012 Emory University Library
#
# 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/LICEN... | emory-libraries/findingaids | findingaids/content/forms.py | Python | apache-2.0 | 6,655 | [
"VisIt"
] | ccdd90d3418b3f494dae7de1c36de87d26f090eb1bd81942f834fce9bc9a23fb |
#!/usr/bin/env python
#-*- coding: utf-8 -*-
""" An example python-meep simulation of a dielectric sphere scattering a broadband impulse,
illustrating the use of the convenient functions provided by meep_utils.py
(c) 2014 Filip Dominec, see http://f.dominec.eu/meep for more information
The simulated models of struc... | FilipDominec/python-meep-utils | ldos.py | Python | gpl-2.0 | 7,825 | [
"Gaussian",
"exciting"
] | eb10c458716a7fdde7d90a7c6cbcaf8d279b7e3a840cf9c82e1f1ee75dabc0e7 |
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import json
import os
import os.path
import re
import sys
import warnings
from collections import defaultdict
try:
from setuptools import setup, find_packages
from setuptools.command.build_py import build_py as BuildPy
... | pmarques/ansible | setup.py | Python | gpl-3.0 | 14,573 | [
"Galaxy"
] | 308d750a1a89c07597f7e7556fcad7b9afbde9a7493d274a5e783990e7b7e31f |
#!/usr/bin/env python
#-*- coding: utf-8 -*-
"""
This is a manual computation of Fourier transform, to verify that the numpy.fft's or scipy's built-in Fast Fourier Transform
behaves as expected also in terms of accumulated power etc.
The curves obtained using the
1) frequency `f'
2) angular frequency `omega'
... | FilipDominec/python-meep-utils | ringdown_analysis.py | Python | gpl-2.0 | 9,788 | [
"DIRAC"
] | d5fb555df507166f1f4165d4cecf31b6184d245d4e067a65b9179dc4be283797 |
# coding: utf-8
from __future__ import unicode_literals
from pymatgen.alchemy.filters import ContainsSpecieFilter, \
SpecieProximityFilter, RemoveDuplicatesFilter, RemoveExistingFilter
from pymatgen.core.lattice import Lattice
from pymatgen.core.structure import Structure
from pymatgen.core.periodic_table import ... | ctoher/pymatgen | pymatgen/alchemy/tests/test_filters.py | Python | mit | 5,195 | [
"pymatgen"
] | ed8ff9d52223eeaa24bb530d79659bbbf00ee7c227ae41898a53460a7b3fa8a1 |
# - coding: utf-8 -
# Copyright (C) 2008-2010 Toms Bauģis <toms.baugis at gmail.com>
# Dual licensed under the MIT or GPL Version 2 licenses.
# See http://github.com/tbaugis/hamster_experiments/blob/master/README.textile
import math
import datetime as dt
import gtk, gobject
import pango, cairo
import re
try:
im... | pacoqueen/cican | formularios/graficas/graphics.py | Python | gpl-3.0 | 76,957 | [
"FLEUR"
] | 6dd933b59c0205b9afb0c7a774433e707ce584adf38c4e16e043dbb405dd59b0 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
from django.conf import settings
import multiselectfield.db.fields
class Migration(migrations.Migration):
dependencies = [
('branch', '0047_merge'),
]
operations = [
migrations.Alter... | MaximeBiset/care4care | branch/migrations/0048_auto_20141204_2054.py | Python | agpl-3.0 | 10,512 | [
"VisIt"
] | e7b2c625c9b2f1cd0c3d531851828bdb505f8784e6dbdc293e1d25856ba6314b |
# Copyright (C) 2014,2015 Nippon Telegraph and Telephone Corporation.
#
# 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 ... | cgasparini/bgp-agent | vendor/github.com/osrg/gobgp/tools/pyang_plugins/bgpyang2golang.py | Python | apache-2.0 | 26,627 | [
"VisIt"
] | 4bf1e7b746a3cc01e04f462c45e1eb3733af0559a70e26c9f9a3b51c9f4db804 |
# -*- coding: utf-8 -*-
#
# AtHomePowerlineServer - networked server for CM11/CM11A/XTB-232 X10 controllers
# Copyright © 2014, 2015 Dave Hocker
#
# 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 Fou... | dhocker/athomepowerlineserver | commands/DeviceDim.py | Python | gpl-3.0 | 1,670 | [
"xTB"
] | 65ee3d735d35283909a58577bc7f7d5f913cbbdf618eb4dd9b1342b3764d9ed5 |
import fileinput, os, time, random, math
from bs_utils.utils import *
from bs_align_utils import *
import gzip
#----------------------------------------------------------------
# Read from the mapped results, return lists of unique / multiple-hit reads
# The function suppose at most 2 hits will be reported in single f... | BioInfoTools/BSVF | bin/BSseeker2/bs_align/bs_single_end.py | Python | lgpl-3.0 | 34,394 | [
"Bowtie"
] | 487cb6ce48af14415add88de31b49b22f819d75ae59d0f135a92f4d6c54b446b |
# pylint: disable=missing-docstring
# pylint: disable=redefined-outer-name
from lettuce import world
import time
import json
import re
import platform
# django_url is assigned late in the process of loading lettuce,
# so we import this as a module, and then read django_url from
# it to get the correct value
import l... | jbassen/edx-platform | common/djangoapps/terrain/ui_helpers.py | Python | agpl-3.0 | 21,620 | [
"VisIt"
] | da3545e4406ef4e10af5f4d0087dd96c37e3ce15f58a9d6dc9dc15819c76da72 |
#!/bin/bash python
# -*- coding:utf-8 -*-
"""
author: janes
date: 2016/04/08
todo: 高级搜索
"""
import logging
import hashlib
import json
import sys
import requests
from exploit import joomla
reload(sys)
sys.setdefaultencoding("utf-8")
logging.basicConfig(level=logging.INFO, format='%(message)s')
class Shadan(obje... | hxer/NetworkScript | shadan/shadan.py | Python | gpl-2.0 | 7,348 | [
"VisIt"
] | c29ceaacce28d3bfad72ae0e412a1d47eca2f6ec8d6f69c6d18e48e1e8ce5aa4 |
# Copyright 2013 OpenStack Foundation
# All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requ... | JioCloud/glance | glance/api/v2/image_members.py | Python | apache-2.0 | 13,074 | [
"Brian"
] | ae9ca6da3500aa4bad36853fc6fed26b85539d4fba170efb41479968e95a4410 |
#!/usr/bin/env python3
"""
CREDITS:
1. Parts of signature() and body() are courtesy of codegen.py
copyright: Copyright 2008 by Armin Ronacher.
license: BSD
2. py2js for inspiration
"""
import ast
from _ast import *
import sys
class Py2Neko(ast.NodeVisitor):
# Eq, NotEq, In and NotIn are in visit_Compa... | narke/py2neko | py2neko.py | Python | mit | 16,799 | [
"VisIt"
] | 89068960a5963d313ad3c895b7ef69558afa3ccec62e021b65e3ef516667c376 |
# This file is part of Buildbot. Buildbot 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, version 2.
#
# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without eve... | seankelly/buildbot | pkg/buildbot_pkg.py | Python | gpl-2.0 | 8,914 | [
"GULP"
] | 4d63894e3e40671a267247a3ba240c5641e2874f8d25af4012d94dc8bb9c1721 |
# -*-python-*-
#
# Copyright (C) 1999-2013 The ViewCVS Group. All Rights Reserved.
#
# By using this file, you agree to the terms and conditions set forth in
# the LICENSE.html file which can be found at the top level of the ViewVC
# distribution or at http://viewvc.org/license-1.html.
#
# For more information, visit h... | marcellodesales/svnedge-console | svn-server/lib/viewvc/vclib/svn/svn_ra.py | Python | agpl-3.0 | 28,986 | [
"VisIt"
] | 63a435004bafab54b7215c2ff8a5b99bbe249e1b95111fd02810a7419a29d0a5 |
"""
This class performs the meshing of the geo file generated in PreMeshingFunctions.py. It allows the use of NetCDF
files as a mesh-size metric on a planar surface or the generation of a mesh with no NetCDF specified. Once the
geo file has been appropriately appended to include the necessary field it meshes the f... | janhui/test_engine | dev/plugins/mesh_netcdf/scripts/MeshOperations.py | Python | lgpl-2.1 | 7,376 | [
"NetCDF"
] | b38b5d095dcfad03b1037f0c4e85470335a68490aec742d0c43a005e48e816bd |
# Create by Lucas Andrade
# On 11 / 09 / 2017
import pandas as pd
import codecs
import numpy as np
from sklearn import svm
from sklearn.svm import SVC
from sklearn.model_selection import cross_val_score
from sklearn.naive_bayes import MultinomialNB
from sklearn.naive_bayes import GaussianNB
from sklearn.ensemble impo... | jarvis-fga/Projetos | Problema 2/lucas/src/text_classification.py | Python | mit | 5,048 | [
"Gaussian"
] | 963b4dc0aa8077eb56aa22bd4a0972ebb22cfbe9c42d37c5023b9f878d2541b6 |
from numpy import *
from pylab import *
eps = 1e-9
def vl_plotframe(frames, color='#00ff00', linewidth=2):
# VL_PLOTFRAME Plot feature frame
# VL_PLOTFRAME(FRAME) plots the frames FRAME. Frames are attributed
# image regions (as, for example, extracted by a feature detector). A
# frame is a vector of D=2,3,.... | DerThorsten/pyvlfeat | vlfeat/plotop/vl_plotframe.py | Python | gpl-2.0 | 5,258 | [
"Brian"
] | 33195138300a0edd4087cd5b2665e9fa814df5041b447f269f345c3a32d6d79b |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | junghans/espressopp | src/analysis/XPressure.py | Python | gpl-3.0 | 1,837 | [
"ESPResSo"
] | 2be08863d240ecac81fc3b6db766103cc7c9a14ee8124ad6506b60cbe68db6a6 |
from ..load.load_utils import get_maf
from ..utils import get_phenolist, get_gene_tuples, pad_gene, PheWebError, vep_consqeuence_category
from .. import conf
from .. import parse_utils
from ..file_utils import get_filepath, get_pheno_filepath, VariantFileReader
from .server_utils import get_variant, get_random_page, g... | statgen/pheweb | pheweb/serve/server.py | Python | agpl-3.0 | 21,494 | [
"VisIt"
] | c60f1c3031192458f7508cec42c722efbc1cecdeb415bbb9e0716c2a7d15e681 |
# display.py -- graphical vtk helper stuff
# -*- coding: utf-8 -*-
#
# Written by Jonathan Kleinehellefort <jk@molb.org>.
#
# Copyright 2008 Lehrstuhl Bildverstehen und wissensbasierte Systeme,
# Technische Universität München
#
# This file is part of RoboView.
#
# RoboView is free software: you can red... | arcoslab/roboview | display.py | Python | gpl-3.0 | 8,122 | [
"VTK"
] | ec062f0f9f716a28cc4481924864236204d4c854d90f629a2ada98fefa78dc73 |
# Orca
#
# Copyright 2005-2008 Sun Microsystems Inc.
# Copyright 2011 The Orca Team
#
# 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 opti... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/mag.py | Python | gpl-3.0 | 1,419 | [
"ORCA"
] | 2affe73d30d99a18999add886edf4f213bbc75500231fc01443a448a8ceedb0c |
###########################################################################################
# Filename:
# Device.py
###########################################################################################
# Project Authors:
# Juhapekka Piiroinen
# Brian Wu
#
# Changes:
# June 14, 2010 by Juhapekka Pi... | antonvino/inmoov-basic | hexapod_scripts_base/maestro_lib.py | Python | mit | 13,426 | [
"Brian"
] | 401dad37bb8415a53ffaddc698129040caab0fac4278d19d58abb4181ad64006 |
"""
Factory used by mayavi to import csv-like files into datasets.
"""
# Author: Gael Varoquaux <gael.varoquaux@normalesup.org>
# Copyright (c) 2008, Enthought, Inc.
# License: BSD Style.
from traits.api import HasTraits, Callable
from traitsui.api import Handler
from mayavi.tools.data_wizards.data_source_wizard imp... | liulion/mayavi | mayavi/tools/data_wizards/csv_source_factory.py | Python | bsd-3-clause | 1,733 | [
"Mayavi"
] | ff8d419fa977c4576bc8b70a3399095a93690f8d5b7a235b036bc9f755ba1114 |
# Copyright 2013-2021 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 RAnnotationdbi(RPackage):
"""Manipulation of SQLite-based annotations in Bioconductor
... | LLNL/spack | var/spack/repos/builtin/packages/r-annotationdbi/package.py | Python | lgpl-2.1 | 1,548 | [
"Bioconductor"
] | 7b6a2be89a19b33b227ba58af9de1e89d6f65ac75682e34c416a92c30ba21204 |
import os
import re
import sys
import ngsutils.support
import pysam
try:
from eta import ETA
except:
pass
def bam_open(fname, mode='r', *args, **kwargs):
if fname.lower()[-4:] == '.bam':
return pysam.Samfile(fname, '%sb' % mode, *args, **kwargs)
return pysam.Samfile(fname, '%s' % mode, *args,... | nitesh1989/tools-iuc | tools/ngsutils/ngsutils/bam/__init__.py | Python | mit | 30,120 | [
"pysam"
] | 6ff0425d56bdd8644373d4f44e1136359a09e6b994a4ede0532eea87bd81929b |
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2006-2014, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version 2.1 or l... | Clyde-fare/cclib | test/testGeoOpt.py | Python | lgpl-2.1 | 13,110 | [
"Molpro",
"NWChem",
"ORCA",
"cclib"
] | 03eb807980aac6145e863032e069c6ab8615ab807064d9badf0a829dcedb15bc |
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | lach76/scancode-toolkit | src/packagedcode/models.py | Python | apache-2.0 | 24,384 | [
"VisIt"
] | 19be407a96b13452aca551c011de1d60ab21e3a16068882228f3cea99834f802 |
from __future__ import print_function
"""Simple and efficient pythonic file-format.
Stores ndarrays as binary data and Python's built-in datatypes (int, float,
bool, str, dict, list) as json.
File layout for a single item::
0: "AFFormat" (magic prefix, ascii)
8: " " (tag, ascii)
24: ve... | suttond/MODOI | ase/io/aff.py | Python | lgpl-3.0 | 12,584 | [
"ASE"
] | 1447ce741db55586e3a0e97e4281c89184c629f52cb227c2e2d1a57434334476 |
#
# iqcalc.py -- image quality calculations on FITS data
#
# Eric Jeschke (eric@naoj.org)
#
# Copyright (c) 2011-2012, Eric R. Jeschke. All rights reserved.
# This is open-source software licensed under a BSD license.
# Please see the file LICENSE.txt for details.
#
import math
import logging
import numpy
import thre... | rupak0577/ginga | ginga/util/iqcalc.py | Python | bsd-3-clause | 14,637 | [
"Gaussian"
] | 7485b335ad89dc57ecc90c24f8c3357b37002b095932b431e1756cb11485009b |
from Module import AbstractModule
class Module(AbstractModule):
def __init__(self):
AbstractModule.__init__(self)
def run(
self, network, antecedents, out_attributes, user_options, num_cores,
out_path):
import os
from genomicode import filelib
from genomicode im... | jefftc/changlab | Betsy/Betsy/modules/normalize_with_rsem.py | Python | mit | 6,505 | [
"Bowtie"
] | 2b6fcc45f66dfdde147a66687d63bffc571904a2c8b6de238f3f126e8422d250 |
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