text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
"""
the diags_file contains the hits that dagchainer found, the all_file is the full list of blast hits.
this script goes through all of the hits in the dag file and adds any hit from the all_file that is within 'dist' of
any hit in the diag.
"""
from scipy.spatial import cKDTree
import numpy as np
import sys
from cda... | asherkhb/coge | bin/dagchainer_bp/dagtools/find_nearby.py | Python | bsd-2-clause | 3,453 | [
"BLAST"
] | 15c8362e68a0ac754d046fae6a444af73fe6a696da6990f1b0c4541fb4cc21bc |
import datetime
import os
from unittest import mock
from django.conf import settings
from django.contrib.auth.models import Group, Permission
from django.core import mail
from django.core.files.base import ContentFile
from django.http import HttpRequest, HttpResponse
from django.test import TestCase, modify_settings,... | gasman/wagtail | wagtail/admin/tests/pages/test_edit_page.py | Python | bsd-3-clause | 111,997 | [
"VisIt"
] | b22ab3bb53d9591dc87cf7cfec0365dd7196e6db2efcca4cbb4a2b603f8914b9 |
import unittest
import numpy as np
import pysal
import pysal.spreg as EC
PEGP = pysal.examples.get_path
class TestBaseOLS(unittest.TestCase):
def setUp(self):
db = pysal.open(PEGP('columbus.dbf'),'r')
y = np.array(db.by_col("HOVAL"))
self.y = np.reshape(y, (49,1))
X = []
X.... | AlanZatarain/pysal | pysal/spreg/tests/test_ols.py | Python | bsd-3-clause | 4,988 | [
"COLUMBUS"
] | 1e0fad5365b4cd6fcf8ec5f1036e8fa8b6a92f0583f7ba988b54d542b7992d97 |
#!/usr/bin/env python
# Copyright 2014-2020 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/mcscf/mc_ao2mo.py | Python | apache-2.0 | 14,897 | [
"PySCF"
] | 8087b4769b0136a97a2f45b2da38aa64dbd29245c0e5ec81ac3dc1accbec96d9 |
########################################################################
# $HeadURL$
# File : CREAMComputingElement.py
# Author : A.T.
########################################################################
""" CREAM Computing Element
"""
__RCSID__ = "$Id$"
from DIRAC.Resources.Computing.ComputingElement ... | Sbalbp/DIRAC | Resources/Computing/CREAMComputingElement.py | Python | gpl-3.0 | 14,501 | [
"DIRAC"
] | 84cac7460952b2e00d2f42176e58ec5ab60e11a1df4e92c819cce64797bc89bd |
#!/usr/bin/env python
# -----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# ---------------------... | Jorge-C/bipy | skbio/parse/sequences/tests/test_fastq.py | Python | bsd-3-clause | 4,497 | [
"scikit-bio"
] | b0051bd0398faeb8c8836a8f9af7ebd5aef774b1b0d5301ecf698c86cece2562 |
# Orca
#
# Copyright 2006-2008 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... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/scripts/apps/gnome_segv2/script.py | Python | gpl-3.0 | 2,481 | [
"ORCA"
] | d1e9fb2e50a7d6cfe5678aee0b4128e1eff47fc482fe2c58097c72bd8b559c97 |
from radical.entk.appman.wfprocessor import WFprocessor
from radical.entk import Pipeline, Stage, Task
import pytest
from radical.entk.exceptions import *
from Queue import Queue
def test_pending_completed_queue_types():
def create_single_task():
t1 = Task()
t1.environment = ['module load gromacs... | vivek-bala/radical.entk | tests/test_wfprocessor.py | Python | mit | 2,283 | [
"Gromacs"
] | 11b8ad063cf990bc2739d5c20528f823649aee7aa4009cd71e31eaa3275c2ebd |
from urllib2 import urlopen
from bs4 import BeautifulSoup
import requests
#point to FRUS volumes
html = urlopen("http://digicoll.library.wisc.edu/cgi-bin/FRUS/FRUS-idx?type=browse&scope=FRUS.FRUS1")
soup = BeautifulSoup(html, 'html.parser')
with open("frus_section_pdf_urls.txt", "w") as file:
#scrape FRUS volume rel... | thomasgpadilla/webscraping | frus_section_pdf_urls.py | Python | cc0-1.0 | 1,247 | [
"VisIt"
] | 467ea99271749ea1e1910e10a611360ceebef7ea6d7fecbf938d2397f061fc45 |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-os-config | tests/unit/gapic/osconfig_v1/test_os_config_zonal_service.py | Python | apache-2.0 | 200,898 | [
"Octopus"
] | d88293a0b7e5df0dba08dc774bc70cc3dade7b6ef5f7f6a55c0027e4ce1ad6b7 |
import numpy as np
import theano
from theano import config
import theano.tensor as T
from theano.tensor.shared_randomstreams import RandomStreams
import tree_util
class LSTM(object):
def square_weight(self, ndim):
return self.rng.uniform(
low=-np.sqrt(6. / (4 * ndim)),
... | jimmycallin/master-thesis | architectures/nn_discourse_parser/nets/lstm.py | Python | mit | 18,623 | [
"MOE"
] | 9e65efd951ecf9ba30ed50c09635fc9f2f536fa70b32b2cb37c5923e0370d9c4 |
#!/usr/bin/env python
from functools import reduce
import numpy
import scipy.linalg
from pyscf import scf
from pyscf import gto
from pyscf import mcscf, fci
'''
Triplet and quintet energy gap of Iron-Porphyrin molecule
In this example, we use density matrix embedding theory
(ref. Q Sun, JCTC, 10(2014), 3784) to gene... | sunqm/pyscf | examples/mcscf/43-dmet_cas.py | Python | apache-2.0 | 3,787 | [
"PySCF"
] | 5946d30cec2e871f1f2727bcbe53e737037174a4fc2478a23a38dfd827f58652 |
""" converters.py
"""
import common_info
import c_spec
#----------------------------------------------------------------------------
# The "standard" conversion classes
#----------------------------------------------------------------------------
default = [c_spec.int_converter(),
c_spec.float_converter()... | scipy/scipy-svn | scipy/weave/converters.py | Python | bsd-3-clause | 2,720 | [
"VTK"
] | 832a27e6f21827b3f5bef627bc998e83d2f633fa8af084703922a7583b6e5383 |
from bok_choy.page_object import PageObject, PageLoadError, unguarded
from bok_choy.promise import BrokenPromise, EmptyPromise
from .course_page import CoursePage
from ...tests.helpers import disable_animations
from selenium.webdriver.common.action_chains import ActionChains
class NoteChild(PageObject):
url = Non... | franosincic/edx-platform | common/test/acceptance/pages/lms/edxnotes.py | Python | agpl-3.0 | 20,390 | [
"VisIt"
] | 668eb40d49e5e14523dfbcf454a96e86926c95ec81043f1d5494004e8f3cdbdb |
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 mouse=a
import matplotlib
matplotlib.rcParams['figure.facecolor'] = '1.'
matplotlib.use('Agg')
import ants
import numpy as np
import pandas as pd
import os
import imageio
import nipype.pipeline.engine as pe
import nipype.interfaces.utility as niu
import nibabel as... | APPIAN-PET/APPIAN | src/qc.py | Python | mit | 42,641 | [
"Gaussian"
] | 4bb234208762d35786dbf8c117002d379eee4370aacc3575e58ead12e8c05e8f |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# math2html: convert LaTeX equations to HTML output.
#
# Copyright (C) 2009-2011 Alex Fernández
#
# Released under the terms of the `2-Clause BSD license'_, in short:
# Copying and distribution of this file, with or without modification,
# are permitted in any m... | axbaretto/beam | sdks/python/.tox/docs/lib/python2.7/site-packages/docutils/utils/math/math2html.py | Python | apache-2.0 | 182,247 | [
"Bowtie"
] | c9819d929fb5112d63637cfcad69d09f82fca1629caff175367343cd684066e7 |
# Copyright (c) 2009-2021 The Regents of the University of Michigan
# This file is part of the HOOMD-blue project, released under the BSD 3-Clause
# License.
"""Test Image list generation for small box / large move size simulations."""
import hoomd
import pytest
import numpy
@pytest.fixture(scope="function")
def on... | joaander/hoomd-blue | hoomd/hpmc/pytest/test_small_box_3d.py | Python | bsd-3-clause | 4,537 | [
"HOOMD-blue"
] | 55def2a93b2f68dc2e949668542087ffcecebb749b87b1ede1f07be723e1c92b |
# -*- coding: utf-8 -*-
#
# pypgen documentation build configuration file, created by
# sphinx-quickstart on Sun Feb 3 11:35:09 2013.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All ... | ngcrawford/pypgen | doc/conf.py | Python | bsd-3-clause | 8,422 | [
"pysam"
] | b0aeb48c28d193957a8843cb7f97b2573cdd64b8cf63319843ddeb785c55d327 |
# -*- coding:utf-8 -*-
import blog2md
b = blog2md.Blog(
"http://jianyan.me/page/",
first_page_url="http://jianyan.me/",
entry_tag='section',
entry_class='post',
description_tag='p',
)
for index, article in enumerate(b.get_all_articles(), 1):
print index,
article.to_hexo(
content_cla... | EndlessCheng/blog2md | test.py | Python | mit | 3,323 | [
"MOE"
] | 1252f2607b9fbc199b13c6054aed0c90f29a268e32f4b25865650370bc9c486b |
#! /usr/bin/env python3
# -*- coding: utf-8 -*-
import vtk
def main():
cutmesh('patte.stl', ymin=30, ymax=45, step=0.1)
def cutmesh(filename, ymin, ymax, step):
# 1. setup pipeline
# -----------------
# STL mesh
stlmesh = vtk.vtkSTLReader()
stlmesh.SetFileName(filename)
stlmesh.Upda... | rboman/progs | sandbox/vtk/patte/patte.py | Python | apache-2.0 | 5,097 | [
"ParaView",
"VTK"
] | 96d6e730678d49ea56f4ea030b4dd8c889402d51afa78f31fbf7299effef8f05 |
from pysimm import system, lmps, forcefield
def run(test=False):
# use a smiles string to query the pubchem search database and read the mol file returned from the http request
try:
s = system.read_pubchem_smiles('CO')
except:
import os
s = system.read_mol(os.path.join(os.path.dirna... | mefortunato/pysimm | Examples/02_methanol/gaff2/create.py | Python | mit | 892 | [
"LAMMPS"
] | 77c414b1e521107a88e00b98cd0f9c1a205fba95bffc05cae75e85a848a55b55 |
import os
import re
import subprocess
import markdown
import collections
import yaml
import logging
log = logging.getLogger(__name__)
from MooseObjectSyntax import MooseObjectSyntax
from MooseSystemSyntax import MooseSystemSyntax
from MooseTextFile import MooseTextFile
from MooseImageFile import MooseImageFile
from Mo... | katyhuff/moose | python/MooseDocs/extensions/MooseMarkdown.py | Python | lgpl-2.1 | 6,989 | [
"MOOSE"
] | 77c35fd0b45f2cb7bb0d52e4c705f3d5d9b042c53a7d82d643474fc4b9547dfe |
# -*- coding: utf-8 -*-
#
# Copyright © 2016 Mark Wolf
#
# This file is part of scimap.
#
# Scimap 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 lat... | m3wolf/scimap | tests/test_xrd.py | Python | gpl-3.0 | 21,647 | [
"Gaussian"
] | 26c14cec18be703ab9fdc78dd1c76146ea75062b043740bbb93edbc8e23e5677 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/gto/basis/parse_gaussian.py | Python | apache-2.0 | 3,697 | [
"Gaussian",
"NWChem",
"PySCF"
] | 933331e3b8a73a23b9a142bca7a8f0b7f965c3797ed4f635d408128df0e71c9c |
# Copyright (c) 2012 OpenStack Foundation.
#
# 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... | SmartInfrastructures/neutron | neutron/tests/unit/test_policy.py | Python | apache-2.0 | 29,285 | [
"BLAST"
] | c1486e2f5d782a17b62854ff264a7aa905f920f8fe3c3601c382f9fe0e08a1d9 |
#* 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 re
i... | harterj/moose | python/MooseDocs/extensions/autolink.py | Python | lgpl-2.1 | 10,456 | [
"MOOSE"
] | 8b2b3d817a47910d4bc210a0a6b9db7434d59a155c625b1cccba21828c1ff89a |
"""Examine callable regions following genome mapping of short reads.
Identifies callable analysis regions surrounded by larger regions lacking
aligned bases. This allows parallelization of smaller chromosome chunks
through post-processing and variant calling, with each sub-section
mapping handled separately.
Regions ... | Cyberbio-Lab/bcbio-nextgen | bcbio/bam/callable.py | Python | mit | 24,249 | [
"pysam"
] | 35ad99455a0888638c79e6e9e1d253a22e4f97ea0206327a47abd6d3fa7d244f |
#!/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.
"""\
Wrapper script around Rietveld's upload.py that simplifies working with groups
of files.
"""
import json
import optparse
impo... | npe9/depot_tools | gcl.py | Python | bsd-3-clause | 51,770 | [
"VisIt"
] | ee1a7054c1b396c0a10c91a1828ac0c0419a378ac9b7a0efd106aa45cee4c216 |
from __future__ import division
import numpy as np
from scipy.ndimage import gaussian_filter
from scipy.spatial import cKDTree
from hagelslag.util.derived_vars import relative_humidity_pressure_level, melting_layer_height
from hagelslag.util.make_proj_grids import make_proj_grids, read_arps_map_file, read_ncar_map_fi... | djgagne/hagelslag | hagelslag/data/ModelOutput.py | Python | mit | 11,780 | [
"Gaussian"
] | 673788be3e2656dd5b40ae10a1c16d536e5770865f9641947be57c3c84c83144 |
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not use ... | curoverse/libcloud | libcloud/common/google.py | Python | apache-2.0 | 29,438 | [
"VisIt"
] | 86a3ebbc31e8365e089cee0eaa538bd0e866002358d88a747c152a11d0e2ac55 |
"""
Helper functions for connecting to the Quilt Registry.
"""
import json
import os
import platform
import stat
import subprocess
import sys
import time
import botocore.session
import pkg_resources
import requests
from botocore.credentials import (
CredentialProvider,
CredentialResolver,
RefreshableCrede... | quiltdata/quilt-compiler | api/python/quilt3/session.py | Python | apache-2.0 | 8,069 | [
"VisIt"
] | 4e22e24885ed720e8c2211151a4f46ce3d049e3bb1b8fbf269cf1c9e1c32b66b |
# Copyright (C) 2003 CAMP
# Please see the accompanying LICENSE file for further information.
"""This module provides all the classes and functions associated with the
evaluation of exact exchange.
"""
import numpy as np
from gpaw.xc import XC
from gpaw.xc.kernel import XCNull
from gpaw.xc.functional import XCFunct... | ajylee/gpaw-rtxs | gpaw/xc/hybrid.py | Python | gpl-3.0 | 16,469 | [
"ASE",
"GPAW"
] | 6de98cac9a8a810ff8538aefce35c1848e36cf91daad47620ce9e2e75367d46f |
import math
try:
import cupy as xp
except ImportError:
import numpy as xp
from scipy.signal import firwin, kaiserord, windows
class FIR:
def __init__(self, num_chs, L_x, h, D=1):
assert num_chs >= 1, 'Filter must have at least one input channel'
assert h.ndim == 1, 'Impulse response must ... | cuauv/software | hydrocode/modules/common/filt.py | Python | bsd-3-clause | 2,292 | [
"Gaussian"
] | 82855fd029031f61dfc2edb363f60d3b80dfe20528bb7e0bc88c7a6d7876f34e |
"""
To know more or get code samples, please visit my website:
https://morvanzhou.github.io/tutorials/
Or search: 莫烦Python
Thank you for supporting!
"""
# please note, all tutorial code are running under python3.5.
# If you use the version like python2.7, please modify the code accordingly
# 8 - RNN Classifier exampl... | MediffRobotics/DeepRobotics | DeepLearnMaterials/tutorials/kerasTUT/7-RNN_Classifier_example.py | Python | gpl-3.0 | 2,498 | [
"VisIt"
] | 54ccd40fb840fbe07ae4ae282ad70a8efe5236cf6524028875f3293dd11d91cc |
from gpaw import GPAW, restart, FermiDirac
from ase import Atoms
from ase.calculators.test import numeric_force
from gpaw.test import equal
import numpy as np
a = 5.404
bulk = Atoms(symbols='Si8',
scaled_positions=[(0, 0, 0),
(0, 0.5, 0.5),
(0.... | robwarm/gpaw-symm | gpaw/test/si.py | Python | gpl-3.0 | 1,233 | [
"ASE",
"GPAW"
] | 11a0c3250dc67310227f86c87bcf13e5b01af77a622358afb85f53e981293de5 |
#!/usr/bin/python
#
# Copyright(c) 2005 Jason Stubbs <jstubbs@gentoo.org>
# Copyright(c) 2005-2006 Brian Harring <ferringb@gmail.com>
# Copyright(c) 2009-2010 Gentoo Foundation
#
# Licensed under the GNU General Public License, v2
#
# $Header$
"""Provides attributes and methods for a category/... | djanderson/equery | pym/gentoolkit/cpv.py | Python | gpl-2.0 | 6,275 | [
"Brian"
] | 5a4ba79553ba1751aa99428bf2324d9a2d914064d96b61e11b020da60b73bc4f |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, print_function, division
from itertools import islice
import numpy as np
from zarr.compat import PY2, MutableMapping
from zarr.attrs import Attributes
from zarr.core import Array
from zarr.storage import (contains_array, contains_group, init_group,
... | alimanfoo/zarr | zarr/hierarchy.py | Python | mit | 38,195 | [
"VisIt"
] | b8cc8e3cfd6a986ee3720d18a2b9b27ffb63efb907e266ea02357f999d9b6882 |
import collections
import datetime
import itertools
import numbers
import re
import six
import pandas as pd
import toolz
from multipledispatch import Dispatcher
import ibis.common as com
from ibis.compat import PY2, builtins, functools
import ibis.expr.types as ir
class DataType(object):
__slots__ = 'nullable... | deepfield/ibis | ibis/expr/datatypes.py | Python | apache-2.0 | 31,911 | [
"Brian"
] | c50b34803d67c9ed89b38811ef3b08cc7f150e2ac4ad2b4b050407639b6083c6 |
from __future__ import division, print_function
import math, sys, warnings, datetime
from operator import itemgetter
import itertools
import numpy as np
from numpy import ma
import matplotlib
rcParams = matplotlib.rcParams
import matplotlib.artist as martist
from matplotlib.artist import allow_rasterization
import m... | lthurlow/Network-Grapher | proj/external/matplotlib-1.2.1/lib/matplotlib/axes.py | Python | mit | 324,939 | [
"Gaussian"
] | 8e39cc2030aa07c54921839a451f773ea04cc3187fd0c9edbc5ca6c400e68b9f |
# Copyright (c) 2013, GlaxoSmithKline Research & Development Ltd.
# All rights reserved.
#
# 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
# ... | soerendip42/rdkit | rdkit/Chem/Fraggle/FraggleSim.py | Python | bsd-3-clause | 17,058 | [
"RDKit"
] | 080bffb64fa8672c36d48a8df2c72c173dd7f29bbe1326398ab4e22928e39ce1 |
# -*- coding: utf-8 -*-
from __future__ import print_function, division
# Description: class NeuroML for loading NeuroML from single file into MOOSE
# Version 1.0 by Aditya Gilra, NCBS, Bangalore, India, 2011 for serial MOOSE
# Version 1.5 by Niraj Dudani, NCBS, Bangalore, India, 2012, ported to parallel MOOSE
# Versi... | BhallaLab/moose-core | python/moose/neuroml/NeuroML.py | Python | gpl-3.0 | 7,807 | [
"MOOSE"
] | 460c3ecc62bd9067f3b6ac39827d840c653b2c76a82a2d200bcc5b80fdcb8de9 |
#!/usr/bin/env python
# Author: Andrew Jewett (jewett.aij at g mail)
# http://www.chem.ucsb.edu/~sheagroup
# License: 3-clause BSD License (See LICENSE.TXT)
# Copyright (c) 2011, Regents of the University of California
# All rights reserved.
"""
chargepairs_by_type.py reads a LAMMPS data file (or an exce... | Dixon3/lammps | tools/moltemplate/src/chargepairs_by_type.py | Python | gpl-2.0 | 17,074 | [
"LAMMPS"
] | 42ef2cf82115a73730edd2ecb2c24206ad9639488ca726f1b562a2c13a084b89 |
# $Id$
#
# @@ 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.
#
from rdkit import RDConfig
import unittest,os
from rdkit.six.moves import cPickle
from rdki... | soerendip42/rdkit | rdkit/Chem/Fraggle/UnitTestFraggle.py | Python | bsd-3-clause | 1,570 | [
"RDKit"
] | 77cd373b43157e38d4a7bd3bebb67debed3efa66354dde7b9e496f3ad5533f41 |
#!/usr/bin/env python
## category General
## desc Update read names with a suffix (for merging)
'''
Tags each read in a BAM file
Currently supported tags:
-suffix
-xs
-orig-ref
-orig-pos
-orig-cigar
-junction
'''
import sys
import os
from ngsutils.bam import bam_iter, cigar_tostr
import pysam
class BamWr... | ngsutils/ngsutils | ngsutils/bam/tag.py | Python | bsd-3-clause | 6,470 | [
"pysam"
] | 377dab243527774901e49c97adab1c2d25b2e2d6ec75a3ea4e109929b4e2853e |
from flask import Blueprint, current_app, render_template
from flask_login import login_required
main = Blueprint("main", __name__)
# function that is called when you visit /
@main.route("/")
def index():
# access the logger with the logger from api.core and uses the standard logging module
return render_temp... | hilam/ninmah | app/views.py | Python | mit | 446 | [
"VisIt"
] | d9e62125ed3816862e2dde31f8dfa80904dde196290f76041cf4ce8c1b23b884 |
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetTempDir
VTK_TEMP_DIR = vtkGetTempDir()
contr = vtk.vtkMultiProcessController.GetGlobalController()
if not contr:
nranks = 1
rank = 0
else:
nranks = contr.GetNumberOfProcesses()
rank = contr.GetLocalProcessId()
def GetSource(dataTy... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Filters/Parallel/Testing/Python/testTransmit.py | Python | gpl-3.0 | 3,814 | [
"VTK"
] | 4f47647369558055d44f25f8a56762d2e8a2ff6f7a628b7513516714973a68a3 |
import numpy
import math
import scipy.stats
from KabschAlign import *
from IterativeMeansAlign import *
from MDAnalysis import *
#u = MDAnalysis.Universe('../data/ubq_1111.pdb', '../data/UBQ_500ns.dcd', permissive=False);
#u = MDAnalysis.Universe('../../tmp/2V93_1.pdb', '../../tmp/2V93.dcd', permissive=False);
#ca = ... | acadev/pyACA | src/AnharmonicHisto_2V93.py | Python | gpl-2.0 | 2,215 | [
"MDAnalysis"
] | 76c8385bfd6a6737cb3107cb2d0dd97e6b7e47bc0446f344d4adfb922e09aad4 |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publish... | thica/ORCA-Remote | src/ORCA/actions/ScriptsAndInterfaces.py | Python | gpl-3.0 | 17,700 | [
"ORCA"
] | f9fd3e87ed75afea8a667854ad80ddfa977d982f9ccb57a49ce18baaa80f790f |
# Orca
#
# Copyright 2009 Sun Microsystems Inc.
# 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)... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/scripts/apps/ddu/script.py | Python | gpl-3.0 | 5,212 | [
"ORCA"
] | c52a30a1b784a7529d4a867afc1ce48fb630afe75c7d15522e58172b3229690e |
"""Create the Aqueous class to hold the properties of water."""
from __future__ import division
from math import log10, log, pi, sqrt, exp
from .constants import gas_constant, reference_temperature, \
kelvin, elementary_charge, avogadro,\
boltzmann, permittivity, lpm3, pitt... | lewisamarshall/ionize | ionize/Solvent.py | Python | gpl-2.0 | 5,588 | [
"Avogadro"
] | c205c6c28d2f7a88296dccfdbd3892f8ed866a24408fdca4adf9a0d044fd1eb5 |
'''
Implementation of a Hidden Markov Model based on Bishop's Pattern Recognition and Machine Learning book.
'''
import numpy as np
from sklearn.cluster import KMeans
from scipy.stats import norm
# Generate training data?
# Sine waves?
sig1 = np.sin(np.arange(180)*np.pi/180)
sig2 = np.cos((np.arange(180)+30)*np.pi/... | colincsl/StructuredModels | StructuredModels/models/hmm.py | Python | bsd-2-clause | 7,973 | [
"Gaussian"
] | 9b7a9e057083d1cdc875045921826f948a904319567c5ab712a6acfa8d11e8e3 |
#!/bin/python
"""
Program Polaron hop by Aksyonov Dmitry, Skoltech, Moscow
Multiset is not supported yet
"""
import sys, json, os, glob, copy
print('Python version is', sys.version)
from shutil import copyfile
import random
from os.path import expanduser
home = expanduser("~")
sys.path.append(home+'/to... | dimonaks/siman | siman/polaron_hop.py | Python | gpl-2.0 | 2,406 | [
"VASP"
] | cefe2bf58608b16010e4440581a1cb6f8656b93089781e1b266990e9d843d14a |
# ----------------------------------------------------------------------
# Numenta Platform for Intelligent Computing (NuPIC)
# Copyright (C) 2017, Numenta, Inc. Unless you have an agreement
# with Numenta, Inc., for a separate license for this software code, the
# following terms and conditions apply:
#
# This progra... | ywcui1990/nupic.research | projects/sdr_paper/poirazi_neuron_model/run_dim_classification_experiment.py | Python | agpl-3.0 | 4,633 | [
"NEURON"
] | 4aaad7ada07753559d823dacf07ea72b43c0586dd476bc6e8979ad05141c1403 |
"""Tests for the NPS email."""
import datetime
import os
import unittest
from unittest import mock
from urllib import parse
import mongomock
import pymongo
import requests_mock
from bob_emploi.common.python import now
from bob_emploi.frontend.api import user_pb2
from bob_emploi.frontend.server import auth
from bob_e... | bayesimpact/bob-emploi | frontend/server/mail/test/nps_test.py | Python | gpl-3.0 | 9,595 | [
"BLAST"
] | 54bd20d6a134f11c7284c50b86554dbe58f14e670d81398b8f157e300f5dedad |
# Version: 0.19
"""The Versioneer - like a rocketeer, but for versions.
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/python-versioneer/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible with: Python 3.6, 3.7, 3.8, 3.9 and pypy3
* [![Latest Version][pyp... | mrahnis/drapery | versioneer.py | Python | bsd-3-clause | 70,144 | [
"Brian"
] | 75899351026d0035fb8e8a0ad13559224caefc855145342ae3e7db4d47d375ce |
# Module to run tests on turbulent scattering
from __future__ import print_function, absolute_import, division, unicode_literals
# TEST_UNICODE_LITERALS
import numpy as np
import pytest
from astropy import units as u
from astropy import constants as const
from frb.turb_scattering import Turbulence
#def data_path(f... | FRBs/FRB | frb/tests/test_frbtscatt.py | Python | bsd-3-clause | 1,562 | [
"Galaxy"
] | c9078f65c5c7f179be11b11795634e0d9443beded1be634f09c37e664d064c9c |
"""Tasks for flagging out bad or unwanted data.
This includes data quality flagging on timestream data; sun excision on sidereal
data; and pre-map making flagging on m-modes.
"""
from typing import Union
import numpy as np
import scipy.signal
from scipy.ndimage import median_filter
from caput import config, weighted... | radiocosmology/draco | draco/analysis/flagging.py | Python | mit | 53,818 | [
"Gaussian"
] | ba6acddeec8b065a3e8216f1980409f6668344acce9a31b1e2b594790ff9bbf2 |
"""
vasppy: Python utilities for working with VASP inputs and outputs
"""
from setuptools import setup, find_packages
from vasppy import __version__ as VERSION
readme = 'README.md'
long_description = open( readme ).read()
scripts = [ 'check_species',
'murnfit',
'vasp_summary',
'... | bjmorgan/vasppy | setup.py | Python | mit | 1,898 | [
"VASP",
"pymatgen"
] | af1baeb46f6ad14aaecd0d8cd61cb145f88eb83adbcc097be0d2f44fd60aca4d |
##################################################################################
#
# apogee.tools.path: return the path of various APOGEE data files
#
# This file depends on various environment variables that should be set:
#
# - SDSS_LOCAL_SAS_MIRROR: top-level directory with data
# - RES... | jobovy/apogee | apogee/tools/path.py | Python | bsd-3-clause | 49,113 | [
"VisIt"
] | 33df665005dd4ac71990ef504cc170601e4161c6f822fe1fcf5382cd083ee0c1 |
# includes all the modules from the top folder in the python path
import sys
sys.path.insert(0, '../')
from spike_doer import *
from poster import *
from article import *
#fig1b(make=0)
correlation_derivative(make=0)
correlation_maximum_line(make=0)
put_together()
#fig3b_o(make=1)
#fig3b_c(make=0)
#match_to_fix... | zsomko/visualcortex | python/spikes/tester.py | Python | gpl-2.0 | 1,494 | [
"Gaussian"
] | 7b1ef08ac957fce2a00ed1d36fc0d50a924a2ba8e757aa00cbe10df3d6dff6a0 |
#-*- coding:utf-8 -*-
"""
PyHdust *phc* module: physical constants and general use functions
`List of constants`_
.. _`List of constants`: phc_list.html
:license: GNU GPL v3.0 (https://github.com/danmoser/pyhdust/blob/master/LICENSE)
"""
import os as _os
import re as _re
import numpy as _np
import datetime as _dt
... | dbednarski/pyhdust | pyhdust/phc.py | Python | gpl-3.0 | 27,572 | [
"Gaussian"
] | 9cea6bc1319b89b09731c442df768abd2a660795b896c2cbca77a93f2f3c1132 |
# -*- coding: utf-8 -*-
# Copyright © 2012-2017 Roberto Alsina and others.
# 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 t... | gwax/nikola | nikola/__main__.py | Python | mit | 14,321 | [
"VisIt"
] | 397c4940565aaa9e970d6605ab6750bb786e893beefdb0a819c5f4ee035a441c |
#!/usr/bin/env python
## @file
# A file containing functions to plot distributions (spatially and as histograms) of a given variable.
## @namespace distributionPlots
# Plotting functions.
# A set of functions to make quality evaluation plots, comparing a
# source list to a reference list and looking at quantities ... | ATNF/askapsdp | Code/Components/Analysis/evaluation/current/askap/analysis/evaluation/distributionPlots.py | Python | gpl-2.0 | 26,348 | [
"Gaussian"
] | d7870f0952bdb96e70bf50a983fed6885ea1913c9d4475854b7f9989806601a3 |
from astropy.io import fits
import numpy as np
from General import Mathamatics
import math
import jdcal
from scipy.optimize import curve_fit
from scipy import asarray as ar,exp
import matplotlib.pyplot as plt
from astropy.modeling import models,fitting
import jplephem
import de423
import ephem
import astropy.time as as... | tboudreaux/PHY-2002 | GuiFunction.py | Python | lgpl-3.0 | 31,172 | [
"Gaussian"
] | 49f7cec2c2479efbfe1e4812cd8c01975099eb3c1d06792950cc4da00355034e |
# https://wiki.fysik.dtu.dk/gpaw/tutorials/H2/atomization.html#atomization-energy
# Creates: atomization.txt
from __future__ import print_function
from ase import Atoms
from ase.parallel import paropen as open
from gpaw import GPAW, PW, FermiDirac
a = 10. # Size of unit cell (Angstrom)
c = a / 2
# Hydrogen atom:
a... | miroi/open-collection | theoretical_chemistry/software_runs/ase/runs/gpaw-ase/H2_structure_optimization/H2_atomization.py | Python | mit | 1,422 | [
"ASE",
"GPAW"
] | c462fe73f4a5d6a25a795dae1242ad5222eb7dbb409d4ea61df7db78e11bfac2 |
import os, sys, os.path, math, time, random
import ast, re
valid_id = re.compile(r'[a-zA-Z$_]+[a-zA-Z0-9$_]*')
def get_type_name(t):
s = str(t).replace("<_ast.", "").replace("<class '_ast.", "").replace("'>", "")
if "object at" in s:
s = s[:s.find(" ")]
s = s.replace("[", "").replace("]", "").strip()
s = ... | joeedh/webblender | tools/extjs_cc/py_to_js.py | Python | apache-2.0 | 11,738 | [
"VisIt"
] | a79c1479234aa85815d6af2ecfe76fa3d082a7c31981519117ffddc3aad73a05 |
# 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 the G... | espressopp/espressopp | src/interaction/StillingerWeberPairTerm.py | Python | gpl-3.0 | 11,625 | [
"ESPResSo"
] | 8e7404045999c1d41aeb40254b5b58fc9336afbd946f13935933f4a7d131749b |
"""
========================
Reaching Dataset Example
========================
A demonstration of Spykes' functionality using the reaching dataset.
"""
########################################################
import numpy as np
import pandas as pd
from spykes.plot.neurovis import NeuroVis
from spykes.ml.neuropop i... | codekansas/spykes | examples/plot_reaching_dataset_example.py | Python | mit | 12,553 | [
"NEURON"
] | 79fdb04c544dc7f1f4776d733339a3d19de2647debcae5dd54fe153db767a85f |
"""
This module gathers tree-based methods, including decision, regression and
randomized trees. Single and multi-output problems are both handled.
"""
# Authors: Gilles Louppe <g.louppe@gmail.com>
# Peter Prettenhofer <peter.prettenhofer@gmail.com>
# Brian Holt <bdholt1@gmail.com>
# Noel Da... | Djabbz/scikit-learn | sklearn/tree/tree.py | Python | bsd-3-clause | 37,676 | [
"Brian"
] | 713aab59612d670c0d19170a4e93523f17cbe679acfec025645643bf979a6676 |
from __future__ import absolute_import, print_function, unicode_literals
from builtins import dict, str
from copy import deepcopy
import json
import logging
import itertools
import collections
import numpy as np
from matplotlib.colors import LinearSegmentedColormap as colormap
from matplotlib.colors import rgb2hex, hex... | jmuhlich/indra | indra/assemblers/cyjs_assembler.py | Python | bsd-2-clause | 29,624 | [
"Cytoscape"
] | 047c915394a72d9d85a146bcc30601896b09fc33b6cd8486b3e1fc8031bf36ed |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | MBoustani/climate | ocw/data_source/local.py | Python | apache-2.0 | 24,228 | [
"NetCDF"
] | 6c87487d1b7b0ad9430045539497dc77c36fa1542fc60fc55ff3f68c533a8209 |
# ======================================================================
#
# Cosmograil: cosmograil.tools.sexcatalog
#
# sexcatalog module.
#
# Author: Laurent Le Guillou <laurentl@ster.kuleuven.ac.be>
#
# $Id: sexcatalog.py,v 1.1 2005/06/29 13:07:41 hack Exp $
#
# ======================================================... | Pica4x6/numina | numina/util/sexcatalog.py | Python | gpl-3.0 | 27,089 | [
"Gaussian"
] | 6944a3830ea1915a96bf98040755cebcfeeccfa8f656782a814ea8f8849baa1b |
from Firefly import logging
from Firefly.const import (ALIAS_FILE)
import json
class Alias(object):
def __init__(self, alias_file=ALIAS_FILE):
self._alias_file = alias_file
self._aliases = {}
self.read_file()
def read_file(self):
with open(self._alias_file) as file:
self._aliases = json.loa... | Firefly-Automation/Firefly | Firefly/helpers/alias.py | Python | apache-2.0 | 1,857 | [
"Firefly"
] | 062e5899501e270ed4c9532bde3718a4322f7a9bf2696ccb2da7634119987194 |
"""OAuth support functionality
"""
from __future__ import unicode_literals
# Try importing the Python 3 packages first, falling back to 2.x packages when it fails.
try:
from http import server as http_server
except ImportError:
import BaseHTTPServer as http_server
try:
from urllib import parse as urllib_... | search5/nanumlectures | lib/flickrapi/auth.py | Python | apache-2.0 | 17,865 | [
"VisIt"
] | 4a6856e4341b25b1cd6959e9358b31dc709a8f00ea0743e6f366dae9c31d6aca |
# Definition for a binary tree node.
# class TreeNode(object):
# def __init__(self, x):
# self.val = x
# self.left = None
# self.right = None
# 核心思路
# 因为没有BST的性质，所以这里只能常规遍历
# 遍历时候返回：确定p/q的数量 & LCA的结点
# 自底向上遍历，当某个结点的左、右子树已经找齐了，则把LCA结点返回；如果左右子树数量，加上当前节点（如果是pq之一）
# 等于2，则说明当前节点就是LCA
class Solut... | kingsamchen/Eureka | crack-data-structures-and-algorithms/leetcode/lowest_common_ancestor_of_a_binary_tree_q236.py | Python | mit | 1,154 | [
"VisIt"
] | bff02b18e27b889714c83f5f8e698f6ea2a0052c91f09f6688ab4f6b105f0242 |
from datetime import datetime
import itertools
import string
from decimal import Decimal
import re
import dateutil.parser
from gogapi.contentsystem import Build, SecureLinkV2
from gogapi.download import Download
from gogapi.normalization import normalize_system, normalize_language
from gogapi.base import GogObject, M... | Yepoleb/pygogapi | gogapi/product.py | Python | mit | 15,731 | [
"Galaxy"
] | 2c467d2ddaae54a420f562169bc39d11215a72be4569f426d06aadc67eb0e6ce |
#!/usr/local/bin/python
import psycopg2
import sys
from optparse import OptionParser
import socket
def main():
usage="Usage: %prog [options]\n"
usage+="\tFinds the uvfits file location for an Observation ID"
usage+="\tand version,subversion number."
parser = OptionParser(usage=usage)
parser.add... | ryandougherty/mwa-capstone | MWA_Tools/scripts/read_uvfits_loc.py | Python | gpl-2.0 | 2,101 | [
"Bowtie"
] | e554e11d76843f816bb47f5477591d0d03fcfefbb930a47ca2dde856a2fd6282 |
import struct
import json
from concurrent.futures import ThreadPoolExecutor
import random
import tarfile
import os
from scannerpy.common import *
from scannerpy.protobufs import protobufs
def read_advance(fmt, buf, offset):
new_offset = offset + struct.calcsize(fmt)
return struct.unpack_from(fmt, buf, offset)... | scanner-research/scanner | python/scannerpy/profiler.py | Python | apache-2.0 | 13,393 | [
"VisIt"
] | 185d39384adb1e35382ac67c058e41ad90dbb55cebe220bbad0fd16aecb760f8 |
r"""Collection of quadrature methods."""
import logging
from functools import wraps
from .frontend import generate_quadrature
from .sparse_grid import sparse_grid
from .utils import combine
from .chebyshev import chebyshev_1, chebyshev_2
from .clenshaw_curtis import clenshaw_curtis
from .discrete import discrete
from... | jonathf/chaospy | chaospy/quadrature/__init__.py | Python | mit | 2,767 | [
"Gaussian"
] | c2af281d11f8a83acc36fe0093158109f114fc4b495f1d982f482ea82ea35dc2 |
"""Creates simple polygon that outlines all land in the continental U.S.
How to use this script:
[1] Download shapefile from this webpage:
https://github.com/matplotlib/basemap/blob/master/examples/st99_d00.shp
[2] Download the corresponding .dbf and .shx files and put them in the same
directory.
[3] Call t... | thunderhoser/GewitterGefahr | gewittergefahr/scripts/make_conus_polygon.py | Python | mit | 6,270 | [
"NetCDF"
] | bbf79e6aa1156bd98a579edfb1f54277dedd6830483fecd9b792885c33762eac |
# Copyright Cartopy Contributors
#
# This file is part of Cartopy and is released under the LGPL license.
# See COPYING and COPYING.LESSER in the root of the repository for full
# licensing details.
# NOTE: This file must remain Python 2 compatible for the foreseeable future,
# to ensure that we error out properly for... | SciTools/cartopy | setup.py | Python | lgpl-3.0 | 13,905 | [
"NetCDF"
] | 5ccbc8f8138c2c33901100df79334025c68ffbb99faf7262fa43d6f5d69e8165 |
# $Id$
#
# Copyright (C) 2004-2006 Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" unit testing code for MOE-type des... | soerendip42/rdkit | rdkit/Chem/EState/UnitTestVSA.py | Python | bsd-3-clause | 1,739 | [
"MOE",
"RDKit"
] | 98c24959c36bcb8d6b3276e2238e1ce2ca7bbfbc6bc1e531c25c3de501b216bc |
# Copyright (C) 2010-2019 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 v... | espressomd/espresso | samples/visualization_constraints.py | Python | gpl-3.0 | 5,022 | [
"ESPResSo"
] | e919885ff4b31b1deda17f6f2e5984e38740ad83587d8051419374e4f963825a |
from builtins import object
import numpy as np
from cs231n.layers import *
from cs231n.fast_layers import *
from cs231n.layer_utils import *
class ThreeLayerConvNet(object):
"""
A three-layer convolutional network with the following architecture:
conv - relu - 2x2 max pool - affine - relu - affine - sof... | kabrapratik28/Stanford_courses | cs231n/assignment2/cs231n/classifiers/cnn.py | Python | apache-2.0 | 7,265 | [
"Gaussian"
] | cb4c4792e9ac49fc22a43321f060aa09a7b4459f2ab3e6547941ca0acb2eac19 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/prop/ssc/test/test_integral.py | Python | apache-2.0 | 8,290 | [
"PySCF"
] | f52192da9ae41afc2c32be18405600687836d7cc75acd7e4ddac70bab79121e0 |
# Hidden Markov Model Implementation
import math
import pylab as pyl
import numpy as np
import matplotlib.pyplot as pp
import matplotlib.cm as cm
#from enthought.mayavi import mlab
import scipy as scp
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import rospy
import tf
#impo... | tapomayukh/projects_in_python | rapid_categorization/fixed_length_training_data/hmm_force_motion_10_states_scaled_wrt_all_data_two_objects.py | Python | mit | 24,034 | [
"Gaussian",
"Mayavi"
] | aab89e2dff94c88b6f5fd379fdd1cfd1cf14a04230f8685135686a61a42412d5 |
#!/usr/bin/env python3
# Copyright (C) 2020
# Max Planck Institute for Polymer Research & JGU Mainz
# Copyright (C) 2015-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of ... | espressopp/espressopp | examples/vectorization/lennard_jones.py | Python | gpl-3.0 | 15,661 | [
"ESPResSo",
"VMD"
] | 82b7f9c6844da8eb09cf247d1bc574875c9323585830f6ecd6a0c1bd08dba300 |
#!/usr/bin/env python
import torch
from torch.utils.data import DataLoader
import pickle
from rdkit import Chem
from rdkit import rdBase
from tqdm import tqdm
from data_structs import MolData, Vocabulary
from model import RNN
from utils import Variable, decrease_learning_rate
rdBase.DisableLog('rdApp.error')
def pre... | MarcusOlivecrona/REINVENT | train_prior.py | Python | mit | 2,622 | [
"RDKit"
] | cc5bb67867a84256bfe073fdc5823f7d49e04ceb8a5976c21181863058a1d5e3 |
"""
Loadable.Loadable subclass
"""
# This file is part of Munin.
# Munin 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.
# Munin is... | munin/munin | munin/mod/oomph.py | Python | gpl-2.0 | 10,655 | [
"Galaxy"
] | 019570650a3ad4e159ab9ec2b231ce1655e94fbd36766cfb33ec573687a285d0 |
"""
Acceptance tests for course in studio
"""
from nose.plugins.attrib import attr
from common.test.acceptance.tests.studio.base_studio_test import StudioCourseTest
from common.test.acceptance.pages.studio.auto_auth import AutoAuthPage
from common.test.acceptance.pages.studio.users import CourseTeamPage
from common.t... | synergeticsedx/deployment-wipro | common/test/acceptance/tests/studio/test_studio_course_team.py | Python | agpl-3.0 | 15,725 | [
"VisIt"
] | 8256daabcb9c7b42bd533172176b6fbbd31486b2a603e1bf10a46cf363a9cc5a |
import rgz
from astropy.io import ascii,fits
from astropy import wcs
import requests
import numpy as np
from matplotlib import pyplot as plt
from astroML.plotting import hist as histML
subjects,classifications = rgz.load_rgz_data()
# Find the distribution of areas and/or max sizes
rgz_dir = '/Users/willettk/A... | willettk/rgz-analysis | python/compact_sources.py | Python | mit | 2,193 | [
"Galaxy"
] | 3854866fae6d252f65f8d05530c3bb014b6786ad6f2d2d2d40fdd3b6c1663a22 |
# $HeadURL$
"""
DIRAC - Distributed Infrastructure with Remote Agent Control
The LHCb distributed data production and analysis system.
DIRAC is a software framework for distributed computing which
allows to integrate various computing resources in a single
system. At the same time it integrates all kin... | marcelovilaca/DIRAC | __init__.py | Python | gpl-3.0 | 4,852 | [
"DIRAC"
] | 3e7dbeeaf597e8c141bdd10288d911c26e96b6075342bb70e55623042e9f42ee |
'''
@file : combineArff.py
@author (A) : Madhu Kumar Dadi.
@project : Social List
This script combines the arff files obtained from socialList.py and GoogleSearch.py
@Usage : python combineArff.py socialList.arff GoogleSearch.arff
@Licence :
This work is licensed under the
Creative Commons Attribution-NonCommerc... | SummerProject16/project | CMUTweetTagger/combineArff.py | Python | cc0-1.0 | 840 | [
"VisIt"
] | 5945d3dd565b8b54c6bad301071290d82439ea5cf5b4b7fe8ed77d1cac215e9f |
import unittest
import os
import json
import scipy
from io import open
from pymatgen.phonon.dos import CompletePhononDos
from pymatgen.phonon.plotter import PhononDosPlotter, PhononBSPlotter, ThermoPlotter
from pymatgen.phonon.bandstructure import PhononBandStructureSymmLine
test_dir = os.path.join(os.path.dirname(__... | gVallverdu/pymatgen | pymatgen/phonon/tests/test_plotter.py | Python | mit | 3,672 | [
"pymatgen"
] | 53d7a1ed55d94634cb32bde6c6ba5413645910e53ec19b53420a6dc182b741c8 |
import functools
import inspect
import os
import sys
import warnings
from collections import defaultdict
from collections import deque
from types import TracebackType
from typing import Any
from typing import Callable
from typing import cast
from typing import Dict
from typing import Generator
from typing import Generi... | pexip/os-pytest | src/_pytest/fixtures.py | Python | mit | 65,239 | [
"VisIt"
] | 24c5e08b62466425f3977efdf8349c1785c3a1eba6664a98381dfa4dd9da53a5 |
# 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 RMergemaid(RPackage):
"""Merge Maid.
The functions in this R extension are intende... | iulian787/spack | var/spack/repos/builtin/packages/r-mergemaid/package.py | Python | lgpl-2.1 | 1,710 | [
"Bioconductor"
] | 86fa2e9dd77a0be5673f886418859576b19f3ef600c3a88cc6be31584fec2d25 |
"""
Ported by Massimo Vassalli [http://mv.nanoscopy.eu massimo.vassalli@gmail.com]
"""
import numpy as np
def pwc_bilateral(y, soft=True, beta=200.0, width=5, display=True, stoptol=1e-3, maxiter=50):
# Performs PWC denoising of the input signal using hard or soft kernel
# bilateral filtering.
#
# Usage:
# x = pwc_bilat... | waynegm/OpendTect-External-Attributes | Python_3/Jupyter/pwc_bilateral.py | Python | mit | 3,244 | [
"Gaussian"
] | c098579af25649da1494513de32b1ee9d08ad96d6faa4ffb04d69980927535ea |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# Proxy Agent - Agent enabling secured ingoing traffic via a MiG proxy
# without opening services anything other than localhost.
#
# @author Simon Andreas Frimann Lund
#
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter... | heromod/migrid | mig/vm-proxy/deprecated/proxy/mipclient.py | Python | gpl-2.0 | 1,409 | [
"Brian"
] | 293f8be66bcba9e17ae6bff7157e29e39c4b3f7545e121b72f2ef44ca481ea39 |
# -*- coding: utf-8 -*-
#
# Copyright (C) 2006-2010 Edgewall Software
# All rights reserved.
#
# This software is licensed as described in the file COPYING, which
# you should have received as part of this distribution. The terms
# are also available at http://genshi.edgewall.org/wiki/License.
#
# This software consist... | retif/stealthpage | genshi/template/eval.py | Python | gpl-3.0 | 21,099 | [
"VisIt"
] | 062aa9615112f65fd56f8ced800511c491b4ca9db3dba92dfa503c88f63c208b |
# neuron_client
import base64
import sys, socket, select
from Crypto.Cipher import AES
import os
import hashlib
import signal
os.system("clear")
print """
___ ___ __ _________ ___
/ _ \/ -_) // / __/ _ \/ _ \
/_//_/\__/\_,_/_/ \___/_//_/
messenger v 1.2 | susmithHCK
for queries: https://www.askt... | susmithHCK/neuron | neuron.py | Python | gpl-3.0 | 2,779 | [
"NEURON"
] | 94781fec2e1d755aecc27d8627f4abce03b13de1ac7f276a6a6d5ccaddddd1cb |
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