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"""
Reading and writing from KlustaKwik-format files.
Ref: http://klusters.sourceforge.net/UserManual/data-files.html
Supported : Read, Write
Author : Chris Rodgers
TODO:
* When reading, put the Unit into the RCG, RC hierarchy
* When writing, figure out how to get group and cluster if those annotations
weren't set. ... | JuliaSprenger/python-neo | neo/io/klustakwikio.py | Python | bsd-3-clause | 17,272 | [
"NEURON"
] | 238ee25c244d4a493788972d9f2f84c4a5fb9255c38870e17b22fbca7b8f6272 |
# Copyright 2007-2016 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy 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 ve... | to266/hyperspy | hyperspy/tests/model/test_set_parameter_state.py | Python | gpl-3.0 | 4,275 | [
"Gaussian"
] | 75f665bcdb5b36c0298c05e758519a5fc15a00df82aab6ebfe9ac22b8e0f5820 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
GridPP and DIRAC: get the CERN@school cluster data.
"""
import os
#...for parsing the arguments.
import argparse
#...for the logging.
import logging as lg
# Import the JSON library.
import json
# The DIRAC imports.
from DIRAC.Core.Base import Script
Script.pars... | gridpp/dirac-getting-started | get_clusters.py | Python | mit | 4,627 | [
"DIRAC"
] | 24614a36177efac30e02b8b2251364a7ac74d38c283db54094a9c947540fe051 |
'''
Author: Aaron Zhang (fenzhang)
Notes:
1. openstack-neutron.spec needs a bunch python libs as BuildRequires.
If they are missing, the rpm_build cmd will fail.
yum install them manually then once on the building server.
'''
import argparse
import ConfigParser
import fnmatch
import os
import re
import subprocess
imp... | CiscoSystems/n1kv-openstack-tools | packaging_v2.py | Python | apache-2.0 | 13,135 | [
"NEURON"
] | 788768d2213863418ad40a5486cf29fe359a2aba53808948300a612b6ccc7e81 |
from Bio import PDB
from Bio.PDB.PDBIO import PDBIO
from Bio.PDB.PDBIO import Select
from Bio.PDB.PDBParser import PDBParser
from Bio.PDB.mmtf import MMTFParser
from Bio.PDB.PDBExceptions import PDBConstructionWarning
import os.path as op
import logging
import warnings
import ssbio.utils
from ssbio.biopython.bp_mmcifpa... | SBRG/ssbio | ssbio/protein/structure/utils/structureio.py | Python | mit | 5,451 | [
"Biopython"
] | aeab81958248a708a3b707d80650ae3fa44dff763ea7e6175ab738a41eeb21a7 |
# Copyright (C) 2016 Alex Nitz
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 3 of the License, or (at your
# option) any later version.
#
# This program is distributed in the ... | sfairhur/pycbc | pycbc/events/stat.py | Python | gpl-3.0 | 33,222 | [
"Gaussian"
] | a476f56e698bfd316a2976c856df70f0f3a7d739ffb16289437c12913f004e4e |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under th... | kain88-de/mdanalysis | package/MDAnalysis/analysis/waterdynamics.py | Python | gpl-2.0 | 44,335 | [
"MDAnalysis"
] | bf0ce1534d45c9de869122505ea69d48587e4ae632a521ebc4e9850bf9193954 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | allenlavoie/tensorflow | tensorflow/contrib/autograph/pyct/transformer.py | Python | apache-2.0 | 2,730 | [
"VisIt"
] | 2e8bd9ee75f7ccabc112638e27447d1fb52e4e7a7cba387a8ac69ff74f0f5075 |
def _plotDirty(self,redo=True, gifStep = -1, stepSize = 1):
Np4 = self.Npix/4
##Do noisy to add different noise every step steps and sample fourier plane from that
thermalNoise = False
customNoise = True
customRMS = .0000000001
gifMode = False
if gifStep == 0:
#... | alexhege/Orbital-APSYNSIM | APSYNSIM_v1.3/SCRIPT/plotdirtygif.py | Python | gpl-3.0 | 8,090 | [
"Gaussian"
] | 2a5bf9e9591dc406f2fe9d56dc66aaa44f17c215eefa3bab0e1126135d7ad7c3 |
from paraview.simple import *
myMedReader=MEDReader(FileName="/home/H87074/WORK/TESTS_AMA/TESTS0/ssll117a/ssll117a.med")
# list of all keys
keys=myMedReader.GetProperty("FieldsTreeInfo")[::2]
# list all the names of arrays that can be seen (including their spatial discretization)
arr_name_with_dis=[elt.split("/")[... | FedoraScientific/salome-paravis | src/Plugins/MEDReader/Doc/HowTo0.py | Python | lgpl-2.1 | 509 | [
"ParaView"
] | 07c661add086b8954d504222a5d83919543e41a92395deef45630464c7c1f676 |
import os
import json
import subprocess
import click
class expander(object):
def __init__(self, M):
self.M = { '${%s}'%k : v for k, v in M.iteritems() }
self.topological_order = []
visiting = set()
visited = set()
level = [0]
def visit(var):
... | sterin/vscode-msbuild-tools | py/msbuild_tools.py | Python | mit | 3,416 | [
"VisIt"
] | 148c212fbf80738081635b8b663317160197a85a40013ec939986df9dafe30df |
# Copyright (c) 2014 Universidade Federal Fluminense (UFF)
# Copyright (c) 2014 Polytechnic Institute of New York University.
# This file is part of noWorkflow.
# Please, consult the license terms in the LICENSE file.
from __future__ import (absolute_import, print_function,
division, unicode_li... | paopao74cn/noworkflow | capture/noworkflow/now/prov_definition/utils.py | Python | mit | 4,896 | [
"VisIt"
] | ce1f698e04e911736cd686ba4819823d4d27047307516237ffab7c0a1816cda5 |
import unittest
import math
import ast
from numpy import array, eye, arange, roll, tile
from openmdao.main.datatypes.array import Array
from openmdao.main.expreval import ExprEvaluator, ConnectedExprEvaluator, \
ExprExaminer
from openmdao.main.printexpr import ExprPrinter, print_node... | HyperloopTeam/FullOpenMDAO | lib/python2.7/site-packages/openmdao.main-0.13.0-py2.7.egg/openmdao/main/test/test_evalexpr.py | Python | gpl-2.0 | 29,921 | [
"VisIt"
] | 422505d590f74c90ab72ab2804c9c561d09f7d1065cb3ee22e53e16917ffd1fe |
import math
import base64
import cairo
import numpy
from project.utils import StringIO
from graph import get_cycles, prune_cycles, get_fused_cycles, sort_fused_cycles, identify_core
from graph import Tree, breadth_first_search, graph_distance
from utils import calculate_bonds
from structure import from_xyz
def bfs_... | crcollins/chemtools-webapp | chemtools/percent.py | Python | mit | 7,373 | [
"Gaussian"
] | 6d79c98d92ba2365bfcb0ad458c20e431f4c32c72f295b9b4773fe6e166fe304 |
source = """
l = k = [1,2,3]
i = a = 0
while i < 2+1*2:
a = a+1
"""
import ast
from astoptimizer import Config, parse_ast, optimize_ast, compile_ast
#~ from astmonkey import visitors, transformers
class Test(ast.NodeVisitor):
def __init__(self):
pass
def visit(self, node):
res = ""
if isinstance(... | librallu/RICM4Projet | parser/testNode.py | Python | gpl-3.0 | 2,821 | [
"VisIt"
] | 9af79b1105f67bec23fc2998fa8009343e3f5bd011041476446b458d12b5381f |
from __future__ import print_function
import fileinput
import os
import shutil
import subprocess
import click
def _get_version():
__version__ = None
with open('flexget/_version.py') as f:
exec(f.read())
if not __version__:
raise click.ClickException('Could not find __version__ from flexge... | antivirtel/Flexget | dev_tools.py | Python | mit | 2,746 | [
"GULP"
] | e596d1dbe7dd6d2c221b5b2501f6d95e515bc593f69731c7ba11e12d3b179ac6 |
# This file is part of xrayutilities.
#
# xrayutilities is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed... | dkriegner/xrayutilities | lib/xrayutilities/simpack/models.py | Python | gpl-2.0 | 81,996 | [
"Gaussian"
] | 89192becbbd04ec8e15961ef72dfca3ded0e43b98c1cd9d4fac72d3f3bdd62ff |
#!/usr/bin/env python
# Author: Pierre de Buyl http://pdebuyl.be/
# License: BSD 3-clause
"""Display the last frame of a dimer simulation, optionally with solvent
species B
"""
from __future__ import print_function, division
import argparse
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument('fi... | pdebuyl-lab/RMPCDMD | experiments/01-single-dimer/view_last_simulation_frame.py | Python | bsd-3-clause | 3,040 | [
"Mayavi"
] | 256775c6ac34524723304835a03a3c7c69c0f248e9dea8fb1f4329aad97e93ba |
#!/usr/bin/env python
"""
GUI framework and application for use with Python unit testing framework.
Execute tests written using the framework provided by the 'unittest' module.
Further information is available in the bundled documentation, and from
http://pyunit.sourceforge.net/
Copyright (c) 1999, 2000, ... | cypsun/FreeCAD | src/Mod/Test/unittestgui.py | Python | lgpl-2.1 | 15,856 | [
"VisIt"
] | b39eb0aff1ecde58915c9130aa3b80f32c1615570d4d2a8ebc875bc31de3c416 |
import datetime
from django.http import HttpResponse
import logging
import numpy as np
import pandas as pd
from pyper import *
import json
import functions
LOG_FILENAME = 'error_log.txt'
pd.set_option('display.max_colwidth', -1)
def getDiffAbund(request, stops, RID, PID):
try:
while True:
i... | manterd/myPhyloDB | functions/analysis/diffabund_graphs.py | Python | gpl-3.0 | 22,843 | [
"Bioconductor"
] | 42ff822ebc9da1625e1abc36e47145fd48d0f66adec8b2d6b73f9407e832eb4b |
# Copyright 2006-2015 by Peter Cock. All rights reserved.
#
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Bio.AlignIO support for "stockholm" format (used in the PFAM database).
You are expecte... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/Bio/AlignIO/StockholmIO.py | Python | apache-2.0 | 23,759 | [
"BioPerl",
"Biopython"
] | fa11a2f096b27575efd028a6c829e8a98960916eaaefe9ed8db302e9b5d1a957 |
#########################################################################################
# Condor.py
# 10.11.2014
# Author: A.T.
#########################################################################################
""" Condor.py is a DIRAC independent class representing Condor batch system.
Condor objects are... | arrabito/DIRAC | Resources/Computing/BatchSystems/Condor.py | Python | gpl-3.0 | 8,122 | [
"DIRAC"
] | 28fde23c4fd29827c30386898f86d3e8251de3451137ff689932fd62f5fb679b |
from __future__ import division, print_function
import math
import warnings
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 matplotlib... | cactusbin/nyt | matplotlib/lib/matplotlib/axes.py | Python | unlicense | 334,492 | [
"Gaussian"
] | d462cc07f616187537fff13b3c482b1aca7e83adb8b8b5f63d5ac68f8efef21d |
"""
izh.py
Python/NEURON GUI for the different celltypes of Izhikevich neuron (versions from 2 publications).
* 2003 Izhikevich artificial neuron model from
EM Izhikevich "Simple Model of Spiking Neurons"
IEEE Transactions On Neural Networks, Vol. 14, No. 6, November 2003 pp 1569-1572
* 2007 Izhikevich artificial ... | nmsutton/MemoryModule | examples/IzhikevichOctave/izhikevich15jun19/izhiGUI.py | Python | mit | 15,133 | [
"NEURON"
] | a78b7a0ec315a43ac3105365efb554ef3568b8d18a6019ddde9668622eb8143f |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
"""This module checks to see if a retrieved sequence is valid, by checking its
base pair count, number of contigs from sequencing, and the validity of its
characters. The sequence is also ran against a reference database containing
sequences for regions that would uniquely... | kevinkle/semantic | superphy/src/upload/python/sequence_validation.py | Python | apache-2.0 | 7,082 | [
"BLAST"
] | 0da3f2e0217c2afcabdb8e2b89fc524ab6dfb07e140b5044c4ac8cf813ad6525 |
# Copyright (C) 2019-2020
# Max Planck Institute for Polymer Research & JGU Mainz
#
# 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 ... | espressopp/espressopp | src/vectorization/interaction/__init__.py | Python | gpl-3.0 | 924 | [
"ESPResSo"
] | 0c1c3ef323422b6af91fc66cf9c6225e37ca6acd77a99bcaf96a76320c6b3902 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2010 Brian G. Matherly
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option... | SNoiraud/gramps | gramps/gui/widgets/progressdialog.py | Python | gpl-2.0 | 23,201 | [
"Brian"
] | 501eb50b69c7f178b83726968679dea78da43a3293d9c51c30389ada85fd9154 |
# Author: Eric Larson <larson.eric.d@gmail.com>
#
# License: BSD (3-clause)
import sys
from mne.utils import run_subprocess
run_script = """
import sys
import mne
out = set()
# check scipy
ok_scipy_submodules = set(['scipy', 'numpy', # these appear in old scipy
'fftpack', 'lib', 'linalg... | olafhauk/mne-python | mne/tests/test_import_nesting.py | Python | bsd-3-clause | 1,371 | [
"Mayavi"
] | f5bd3ecac5ae4a0e8d437291833d84b0530a4b8acc96ad14d08d5fb673970f1f |
# -*- coding: utf-8 -*-
# Generated by Django 1.9.5 on 2016-05-30 12:29
from __future__ import unicode_literals
import django.core.validators
from django.db import migrations, models
import django.db.models.deletion
import registration.models
class Migration(migrations.Migration):
dependencies = [
('ins... | open-craft/opencraft | registration/migrations/0003_auto_20160530_1229.py | Python | agpl-3.0 | 1,459 | [
"VisIt"
] | 88064d3bdb0aaafc6613b41d7034aa2a1ce100c02dcc84727725f8ac09fafb49 |
"""Support the ElkM1 Gold and ElkM1 EZ8 alarm/integration panels."""
from __future__ import annotations
import asyncio
import logging
import re
from types import MappingProxyType
from typing import Any
import async_timeout
import elkm1_lib as elkm1
import voluptuous as vol
from homeassistant.config_entries import SO... | mezz64/home-assistant | homeassistant/components/elkm1/__init__.py | Python | apache-2.0 | 15,249 | [
"Elk"
] | 79c3512f903cfdf5695749b034648db642820d07f8a3b87d1e2b6b2c6c47bb09 |
#!/usr/bin/env python
# Copyright (c) 2005-2010 ActiveState Software Inc.
"""eol -- a tool for working with EOLs in text files
Usage:
eol FILE... # list EOL-style of file(s)
eol -c NAME FILE... # convert file(s) to given EOL-style
eol -f NAME FILE... # find files with the given EOL-style
`e... | phil65/SublimeKodi | libs/eol/eol.py | Python | gpl-3.0 | 29,303 | [
"VisIt"
] | 4f15ce7ac033b76ff429bbd02b236b6b753c1bfb59eb02dab27dc9ec4c2c9f39 |
#!/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... | sunqm/pyscf | pyscf/mcscf/test/test_addons.py | Python | apache-2.0 | 22,066 | [
"ORCA",
"PySCF"
] | 34526a10c9e24d2562c8d68044696b0046d250439e4e13fbe412d78c95bd9543 |
#!/usr/bin/env python
# ----------------------------------------------------------------------------
# Copyright 2015 Nervana Systems Inc.
# 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
#
# ... | nhynes/neon | examples/multi_optimizer.py | Python | apache-2.0 | 2,672 | [
"Gaussian"
] | 3d3e25224a365de784c2e4678f0598c4286142b7b627acdd11ccfdc74a142716 |
import datetime as dt
import os
import sys
import pytest
from click.testing import CliRunner
from freezegun import freeze_time
from khal.cli import main_ikhal, main_khal
from .utils import _get_ics_filepath, _get_text
class CustomCliRunner(CliRunner):
def __init__(self, config_file, db=None, calendars=None,
... | sdx23/khal | tests/cli_test.py | Python | mit | 29,264 | [
"VisIt"
] | d4f2b9ba70921321c9e9c97d2c74ac6acd9df42cd4e23596f916072bad42df3b |
#!/usr/bin/env python2.7
#
# ----------------------------------------------------------------------------------------------------
#
# Copyright (c) 2007, 2015, Oracle and/or its affiliates. All rights reserved.
# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
#
# This code is free software; you can redis... | rschatz/mx | mx_unittest.py | Python | gpl-2.0 | 18,542 | [
"VisIt"
] | 55deb4790400720ece42cd6009b445ea7c3dd8615551bdcf3d3f32e5c7e84a9c |
# [The "BSD license"]
# Copyright (c) 2012 Terence Parr
# Copyright (c) 2012 Sam Harwell
# Copyright (c) 2014 Eric Vergnaud
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistr... | sidhart/antlr4 | runtime/Python3/src/antlr4/tree/Tree.py | Python | bsd-3-clause | 5,760 | [
"VisIt"
] | d0cc78a784c0d506f2cebc8be7c0eb1c2b8e8e0df94f01c81209609cf0a5f9d6 |
import os, sys
from siman import header
from siman.header import db
from siman.geo import create_surface2, stoichiometry_criteria
from siman.calc_manage import get_structure_from_matproj, smart_structure_read
from siman.calc_manage import (clean_history_file, prepare_run, manually_remove_from_struct_des, update_... | dimonaks/siman | siman/matproj_functions.py | Python | gpl-2.0 | 45,013 | [
"Jmol",
"VASP",
"pymatgen"
] | c6d5abe2c41f43b3a8473a9d1a2bdb5569f84424a5823892132a70292246b44d |
# This file is part of Shuup.
#
# Copyright (c) 2012-2017, Shoop Commerce Ltd. All rights reserved.
#
# This source code is licensed under the OSL-3.0 license found in the
# LICENSE file in the root directory of this source tree.
import os
import pytest
from django.core.urlresolvers import reverse
from shuup.testing.u... | suutari-ai/shoop | shuup_tests/browser/front/test_recently_viewed_products.py | Python | agpl-3.0 | 1,998 | [
"VisIt"
] | 1e8ba0d1e018c0c94b8c186a47a45c0ee1e2854f4dc525c4a8a5cfbfc0a2a595 |
#!/usr/bin/python
# -*- coding: UTF-8 -*-
# This file is part of pyAlienFX.
#
# pyAlienFX 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... | cmotc/pyalienfx | pyAlienFX_daemon.py | Python | gpl-3.0 | 13,594 | [
"VisIt"
] | a4de26c7fa6fa97c052821d116517407a2394d69111785ff32a88ca908d624c4 |
#!/usr/bin/env python3
import os,sys,string,subprocess,signal,shutil
#psutil
import argparse
mcdir = sys.path[0]
parser = argparse.ArgumentParser(description='snakemake and metacompass params')
group1 = parser.add_argument_group('required')
#group1.add_argument("-s",'--snakefile', help='metacompass rules file',defau... | marbl/MetaCompass | workflows/go_metacompass.py | Python | artistic-2.0 | 24,774 | [
"BLAST"
] | 079efb881af25457b1d2b4aa09d8a964867569e71df5486971ef5ec1d7188067 |
from galaxy import eggs
eggs.require( "SVGFig" )
import svgfig
MARGIN = 5
LINE_SPACING = 15
class WorkflowCanvas( object ):
def __init__( self ):
self.canvas = svgfig.canvas( style="stroke:black; fill:none; stroke-width:1px; stroke-linejoin:round; text-anchor:left" )
self.text = svgfig.SVG( "g"... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/workflow/render.py | Python | gpl-3.0 | 6,680 | [
"Galaxy"
] | f7a778d017312a992e1888d1ef04909e661cece40276d7650be17562add654d0 |
import sys
sys.path.insert(1, "../../../")
import h2o
import random
def random_attack(ip,port):
def attack(train, valid, x, y):
kwargs = {}
# randomly select parameters and their corresponding values
if random.randint(0,1): kwargs['mtries'] = random.randint(1,len(x))
if ... | weaver-viii/h2o-3 | h2o-py/tests/testdir_algos/rf/pyunit_NOPASS_random_attack_medium.py | Python | apache-2.0 | 3,457 | [
"Gaussian"
] | 9e414c428f2b877b7c9091fe0a39544bf985b64fb5f2963ea8bfe3883ccbe95c |
"""
A number of functions that enhance IDLE on Mac OSX.
"""
import sys
import tkinter
from os import path
import warnings
def runningAsOSXApp():
warnings.warn("runningAsOSXApp() is deprecated, use isAquaTk()",
DeprecationWarning, stacklevel=2)
return isAquaTk()
def isCarbonAquaTk(root)... | MalloyPower/parsing-python | front-end/testsuite-python-lib/Python-3.5.0/Lib/idlelib/macosxSupport.py | Python | mit | 8,487 | [
"VisIt"
] | a2576d3675be95038915f84692a91d8e4060123901835b01e1091e1f50f01df1 |
"""
The InputData Optimizer Executor queries the file catalog for specified job input data and adds the
relevant information to the job optimizer parameters to be used during the scheduling decision.
"""
__RCSID__ = "$Id$"
import time
import pprint
from DIRAC ... | vmendez/DIRAC | WorkloadManagementSystem/Executor/InputData.py | Python | gpl-3.0 | 14,769 | [
"DIRAC"
] | 3a652900db74d05e84d45ccefc692c2b4171cb6bca77ff4c5a76f626145f8f96 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals, division, print_function
import os.path
import collections
from pymatgen.util.testing import PymatgenTest
from pymatgen.io.abinit.pseudos import *
_test_dir = os.pat... | czhengsci/pymatgen | pymatgen/io/abinit/tests/test_pseudos.py | Python | mit | 6,819 | [
"ABINIT",
"pymatgen"
] | c88df410638208a3aba7e7f5df005a4622bc5341bf8b709dd8b7446fd2bdedd0 |
# coding: utf-8
from __future__ import division, unicode_literals
from pymatgen.util.testing import PymatgenTest
from pymatgen.core.periodic_table import Element, Specie
from pymatgen.core.composition import Composition
from pymatgen.core.operations import SymmOp
from pymatgen.core.structure import IStructure, Struct... | yanikou19/pymatgen | pymatgen/core/tests/test_structure.py | Python | mit | 42,055 | [
"pymatgen"
] | 893ef65abc8ebcfd38fd45314970d80ade399759822c04d8d12952701ba1a107 |
"""
Sequential Monte Carlo for approximately constrained Gaussians.
http://arxiv.org/abs/1410.8209
"""
import numpy as np
def sample(white_constraint,
nsample,
proposal_sigma=0.2,
temps=np.linspace(0, 50, 51.)):
"""
Build up an approximately constrained Gaussian
based on... | stefanv/selective-inference | selection/sampling/sequential.py | Python | bsd-3-clause | 2,137 | [
"Gaussian"
] | b1c39709bdf0c0302a80e92b623ba014c2c0b0d6e87bd5b291910fb66b19ff30 |
# -*- coding: utf-8 -*-
"""
Unit tests for instructor.api methods.
"""
import datetime
import ddt
import random
import pytz
import io
import json
import os
import requests
import shutil
import tempfile
from urllib import quote
from django.conf import settings
from django.contrib.auth.models import User
from django.cor... | dkarakats/edx-platform | lms/djangoapps/instructor/tests/test_api.py | Python | agpl-3.0 | 178,337 | [
"VisIt"
] | 0f8e5368cb608dbb477468414199fc908a23a931e76d402d5e9ba8876b06165f |
#=========================================================================
# ast_visitor_test.py
#=========================================================================
# Tests for Python AST Visitors.
import pytest
from ast_visitor import *
from ..ast_helpers import get_method_ast, print_simple_ast
from pymtl ... | Abhinav117/pymtl | pymtl/tools/simulation/ast_visitor_test.py | Python | bsd-3-clause | 11,486 | [
"VisIt"
] | 72180ac942bef3999f0f811a84181ae9525c00194e14aacee308896d4de465d8 |
# Todo: ACDF formula
from __future__ import division
import sys
from math import pi
import numpy as np
from ase.units import Hartree
from ase.utils import prnt
import gpaw.mpi as mpi
from gpaw.xc import XC
from gpaw.xc.tools import vxc
from gpaw.xc.kernel import XCNull
from gpaw.response.pair import PairDensity
from... | robwarm/gpaw-symm | gpaw/xc/exx.py | Python | gpl-3.0 | 10,169 | [
"ASE",
"GPAW"
] | 5dc571f932d72e5cbd7614e4ec10741e125b74f635e67a7150e2cc32ef869931 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | var/spack/repos/builtin/packages/repeatmasker/package.py | Python | lgpl-2.1 | 3,189 | [
"BLAST"
] | 1e6b8c059fa6c4ca84dc8cf4c20b6ddbe027fa76b7a2faf8009d0fee12a75ccb |
__docformat__ = 'reStructuredText'
'''
Script creating the daily met netCDF files (set up in TaskScheduler).
*Author:* kmu
*Created:* 07. jan. 2011
'''
import sys
import os
import logging
import datetime
execfile(os.path.join(os.path.dirname(__file__), "set_pysenorge_path.py"))
from pysenorge.set_environme... | kmunve/pysenorge | pysenorge/themes/run_generate_daily_met.py | Python | gpl-3.0 | 1,611 | [
"NetCDF"
] | 02ccbed2db4a6f8ad60dfb93bd18dc3b23f566e9f3077f70afe917085b1cc067 |
########################################################################
# File : dirac-proxy-init.py
# Author : Adrian Casajus
###########################################################from DIRAC.Core.Base import Script#############
from __future__ import print_function
import sys
import getpass
import DIRAC
fro... | petricm/DIRAC | FrameworkSystem/Client/ProxyUpload.py | Python | gpl-3.0 | 5,982 | [
"DIRAC"
] | aa86ee674ddb4f44abaeaaf1a6dcd5dd3bde009f777a725ebdf666c14306e5fe |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | nolanliou/tensorflow | tensorflow/contrib/py2tf/pyct/ast_util.py | Python | apache-2.0 | 2,876 | [
"VisIt"
] | 3c290a01dc9da812f267e6dcb5c7748cc91e1cfdd277b6a97cfadf29f5d1b3fb |
"""Internal helper files for user output."""
__author__ = "Luc Anselin luc.anselin@asu.edu, David C. Folch david.folch@asu.edu, Jing Yao jingyao@asu.edu"
import textwrap as TW
import numpy as np
import copy as COPY
import diagnostics as diagnostics
import diagnostics_tsls as diagnostics_tsls
import diagnostics_sp as d... | spreg-git/pysal | pysal/spreg/user_output.py | Python | bsd-3-clause | 18,125 | [
"COLUMBUS"
] | 2fb0da4264d036803c47f2194e2b5cedbdfc379573cf7b403a0c0a227e0164f7 |
# coding: utf-8
# 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.
# Maintainer: joaander / All Developers are free to add commands for new
# features
from hoomd.minimize.fire import FIRE
| joaander/hoomd-blue | hoomd/minimize/__init__.py | Python | bsd-3-clause | 298 | [
"HOOMD-blue"
] | 0995571beda28fbbc78f16671c98cfc1ae4441ead20bd1ba518663c06da918d2 |
from Sire.IO import *
from Sire.MM import *
from Sire.System import *
from Sire.Mol import *
from Sire.Maths import *
from Sire.FF import *
from Sire.Move import *
from Sire.Units import *
from Sire.Vol import *
from Sire.Qt import *
import os
amber = Amber()
(molecules, space) = amber.readCrdTop("test/io/waterbox.... | chryswoods/SireTests | unittests/SireMM/testnewgridff.py | Python | gpl-2.0 | 6,593 | [
"Amber"
] | 0f26582a4d8973e56120293b17e256ac7abf8556e3f7d3fa6ce664cf5bb7f6c1 |
"""
Linear dynamical system model for the AP text dataset.
Each document is modeled as a draw from an LDS with
categorical observations.
"""
from __future__ import print_function
import os
import gzip
import time
import numpy as np
import re
from sklearn.feature_extraction.text import CountVectorizer
import matplotli... | fivejjs/pgmult | examples/multinomial_lds_2.py | Python | mit | 7,549 | [
"Gaussian"
] | f051ba0fbfb5dc8a3395ba2d61dc215ed6886f952e0c73c3d2a8a9755e17bfc9 |
#
# Copyright 2001 - 2006 Ludek Smid [http://www.ospace.net/]
#
# This file is part of IGE - Outer Space.
#
# IGE - Outer Space 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 Lice... | OuterDeepSpace/OuterDeepSpace | libs/server/ige/ospace/IAIPiratePlayer.py | Python | gpl-2.0 | 10,211 | [
"Galaxy"
] | db76b180c23187abdbb1fae593d4288a35c58e8c1ffb51de8b6584f1961a6925 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
=====================
Classifier comparison
=====================
A comparison of a several classifiers in scikit-learn on synthetic datasets.
The point of this example is to illustrate the nature of decision boundaries
of different classifiers.
This should be taken with ... | lesteve/scikit-learn | examples/classification/plot_classifier_comparison.py | Python | bsd-3-clause | 5,239 | [
"Gaussian"
] | dc4564c6e249f68cd5cf29b0c725fd7b40bcc01950982e913fdcd24c866321d5 |
# Lint as: python3
"""Common code for computing probabilities."""
import functools
import jax
import jax.numpy as jnp
from jax.scipy import special
from tensorflow_probability.substrates import jax as tfp
tfd = tfp.distributions
def softplus(x, floor, softness=1):
"""See https://en.wikipedia.org/wiki/Rectifier_(n... | HopkinsIDD/EpiForecastStatMech | epi_forecast_stat_mech/statistical_models/probability.py | Python | apache-2.0 | 7,977 | [
"Gaussian"
] | 06441147082b1a5749deff5002bbced21be4464c077e2f082f13f4d8b411bc50 |
""" Visualize average of :mod:`time series <pySPACE.resources.data_types.time_series>` and time domain features
Additional features can be added to the visualization.
"""
import os
import cPickle
import pylab
import matplotlib.font_manager
from matplotlib import colors
from pySPACE.missions.nodes.base_node import Ba... | pyspace/test | pySPACE/missions/nodes/visualization/average_and_feature_vis.py | Python | gpl-3.0 | 40,990 | [
"Gaussian"
] | 1edcb074daa13200fa27979b4b495030c56e963dadaed79b0ff374b710f4b658 |
from iminuit import Minuit
from probfit import UnbinnedLH, gaussian, SimultaneousFit, rename
from matplotlib import pyplot as plt
from numpy.random import randn, seed
seed(0)
width = 2.
data1 = randn(1000)*width + 1
data2 = randn(1000)*width + 2
#two gaussian with shared width
pdf1 = rename(gaussian, ('x', 'mu_1', 's... | mtresch/probfit | doc/pyplots/costfunc/simul.py | Python | mit | 703 | [
"Gaussian"
] | 66a26ff11d0d3a5b99a79c6dca77a4ab839e5f5b5adb30df5820de5a3df84bd4 |
#!/usr/bin/env python
#
# 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
# A... | cmouse/buildbot | worker/setup.py | Python | gpl-2.0 | 4,989 | [
"Brian"
] | a94ee34598b0e334a71b97e68d7fc8d64fc4030d827e871bb07b8f1a685d2bd2 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | mfherbst/spack | var/spack/repos/builtin/packages/r-affycomp/package.py | Python | lgpl-2.1 | 1,724 | [
"Bioconductor"
] | d14102670604425fc56524dc32d91b75838a448d0cb6c02f6ef938c6dc1c8d98 |
#!/usr/bin/env python
# Copyright 2013 The Swarming Authors. All rights reserved.
# Use of this source code is governed under the Apache License, Version 2.0 that
# can be found in the LICENSE file.
import datetime
import hashlib
import json
import logging
import os
import StringIO
import subprocess
import sys
import ... | sgraham/nope | tools/swarming_client/tests/swarming_test.py | Python | bsd-3-clause | 43,645 | [
"VisIt"
] | 0ceb7229f95b1305cb1363d24edb11a5bc8c5ace37544ae5c75b6e05b8e84870 |
#
# vim: ts=4 sw=4 expandtab ai:
#
# Copyright (C) 2008-2011 Exposong.org
#
# ExpoSong 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 version.
#... | Alwnikrotikz/exposong | lib/exposong/main.py | Python | gpl-3.0 | 24,643 | [
"VisIt"
] | 7bfeb1e252703660261925b95bc170b62155c8927355777717236d2c50632293 |
#!/usr/bin/env python
#Adapted from Dan Blankenberg
"""
A wrapper script for running the SeattleSeq writeGenotype jarfile
"""
import sys, optparse, os, tempfile, subprocess, shutil
CHUNK_SIZE = 2**20 #1mb
def cleanup_before_exit( tmp_dir ):
if tmp_dir and os.path.exists( tmp_dir ):
shutil.rmtree( tmp_di... | jhl667/galaxy_tools | tools/SueRichards_lab_tools/writeGenotype.py | Python | apache-2.0 | 6,910 | [
"Galaxy"
] | 186e72306cbbd98787693e5242e1314e09a8bd0956964caec7df27c46085f95f |
import numpy as np
import sys
import unittest
from random import random
from sure import expect
from time import time
from tdigest.merge_digest import MergeDigest
class TestMergeDigest(unittest.TestCase):
def stub_cdf(self, x, data):
n1 = 0
n2 = 0
for el in data:
if el < x:
... | trademob/t-digest | tests/test_merge_digest.py | Python | mit | 4,154 | [
"Gaussian"
] | f3ad868df038106be9a1ba3978e31a6388459eff2e0e6d0f69c8e8e3b5d6370d |
"""
Written by T.R. Maarleveld, Amsterdam, The Netherlands
E-mail: tmd200@users.sourceforge.net
Last Change: Augustus 06, 2014
"""
from __future__ import division, print_function, absolute_import
from . import PyscesInterfaces
class SBML2PSC():
"""
Module that converts SBML models into PSC models if libxml and li... | SystemsBioinformatics/stochpy | stochpy/modules/SBML2PSC.py | Python | gpl-3.0 | 1,116 | [
"PySCeS"
] | 99af3b773bea47959dbc8970a69fa673469cd66a462e71c8c9b6ceb95fcece10 |
import numpy as np
import numpy.linalg as la
from dataset import DataSet
from helpers import to_one_of_n
def gaussian_dataset(ninstances=[50, 50]):
'''
Simple Gaussian dataset with a variable number of instances for up to 3
classes.
'''
mus = [\
[0, 0],
[2, 1],
[5, 6]]
sigmas = [\
[[1, 2],... | breuderink/golem | golem/data.py | Python | bsd-3-clause | 1,000 | [
"Gaussian"
] | 8c02ee5028517c7e6ccf26ccbc7391b854ee0ad9574781f232634c636579f7e0 |
import copy
from SDWLE.cards.base import SecretCard, SpellCard
from SDWLE.cards.minions.mage import SpellbenderMinion, MirrorImageMinion
from SDWLE.constants import CHARACTER_CLASS, CARD_RARITY
from SDWLE.tags.base import BuffUntil, Buff
from SDWLE.tags.card_source import CollectionSource
from SDWLE.tags.condition impo... | jomyhuang/sdwle | SDWLE/cards_copy/spells/mage.py | Python | mit | 12,823 | [
"BLAST"
] | 9b0ad0f2a07b5305edd58fcf0b9261c49a1594a6f2b3c706c8e3f79901a0c9e5 |
#!/usr/bin/env python
# -*- coding=utf-8 -*-
# A Python code for plotting orbital-resolved bandstructure.
# Written by : Internet
# catalyst : Ravindra
# under the eagle eyes of : Rinkle
import sys
import os
import numpy as np
from numpy import array as npa
import matplotlib as... | neelravi/vasp | bandplotting-orb-resolved-bug-removed-without-borders.py | Python | gpl-3.0 | 5,274 | [
"VASP",
"pymatgen"
] | 46fdb99cf457a69defc1801f683539c368f023771810d33da708934cc4acdf33 |
#!/usr/bin/env python
##############################################################################################
#
#
# CMIP6_hybrid_regrid_emissions_N96e.py
#
#
# Requirements:
# Iris 1.10, time, cf_units, numpy
#
#
# This Python script has been written by N.L. Abraham as part of the UKCA Tutorials:
# http://... | acsis-project/emissions | emissions/python/CMIP6_hybrid/CMIP6_hybrid_regrid_NOx_emissions_n96e_greg.py | Python | gpl-3.0 | 19,124 | [
"NetCDF"
] | 9332e8964d66f1e8d45b67e8e445602b706bb528e3182dd528f54e75bed2b7c1 |
from gym_minigrid.minigrid import *
from babyai.levels.verifier import *
from babyai.levels.verifier import (ObjDesc, pos_next_to,
GoToInstr, OpenInstr, PickupInstr, PutNextInstr, BeforeInstr, AndInstr, AfterInstr)
class DisappearedBoxError(Exception):
"""
Error that's thro... | mila-iqia/babyai | babyai/bot.py | Python | bsd-3-clause | 38,494 | [
"VisIt"
] | f8389a2935f02f95f36328f651b888b3e0a661b7a4af6587da57b68d56ba08dc |
import cpp_ast as cpp
import python_ast as ast
import scala_ast as scala
try:
from asp.util import *
except Exception,e:
pass
def is_python_node(x):
return isinstance(x, ast.AST)
def is_cpp_node(x):
return isinstance(x, cpp.Generable)
def is_scala_node(x):
return isinstance(x, scala... | pbirsinger/aspNew | asp/codegen/ast_tools.py | Python | bsd-3-clause | 22,362 | [
"VisIt"
] | 1c4156bf278aa3646881ae0a7123f439b7de551435a7e75c4f0c30ee15d08b16 |
# Copyright (c) Twisted Matrix Laboratories.
# See LICENSE for details.
"""
An example of a proxy which logs all requests processed through it.
Usage:
$ python logging-proxy.py
Then configure your web browser to use localhost:8080 as a proxy, and visit a
URL (This is not a SOCKS proxy). When browsing in this con... | EricMuller/mynotes-backend | requirements/twisted/Twisted-17.1.0/docs/web/examples/logging-proxy.py | Python | mit | 1,413 | [
"VisIt"
] | 3ca76ed999fd1fc005b8df3ca53c827bf663520e6726d35785f142a52ed2ddbc |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/transitions | openlp/plugins/songusage/songusageplugin.py | Python | gpl-2.0 | 11,524 | [
"Brian"
] | 59ff24da2812200bee4fb480f07e1d7bfb80ff0a16eaf710257106e423293c2c |
#!/usr/bin/env python
#
# LSST Data Management System
# Copyright 2016 AURA/LSST.
#
# This product includes software developed by the
# LSST Project (http://www.lsst.org/).
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# t... | yalsayyad/obs_decam | tests/testWcsCards.py | Python | gpl-3.0 | 2,622 | [
"VisIt"
] | 3c2f5854699610d46dae55d49781180750fbb7d305f6f59a98ab9fa7a3d696f2 |
"""
SPADE is the combination of a mining technique and multiple statistical tests
to detect and assess the statistical significance of repeated occurrences of
spike sequences (spatio-temporal patterns, STP).
Given a list of Neo Spiketrain objects, assumed to be recorded in parallel, the
SPADE analysis can be applied a... | apdavison/elephant | elephant/spade.py | Python | bsd-3-clause | 89,889 | [
"NEURON"
] | 3d075b6eca8ed8f0fe5cbe3c0d35b4230dbee9b6a52eb77bc3154158990400ef |
from djangomako.shortcuts import render_to_string
from bellum.common.session.login import must_be_logged
from bellum.common.session import getAccount, getRace
from bellum.province.models import Province, Reinforcement
from bellum.meta import MPBI
from django.db.models import Q
from django.core.exceptions import ObjectD... | piotrmaslanka/bellum | space/ajax/regionmap.py | Python | agpl-3.0 | 1,801 | [
"Galaxy"
] | a67b65453c3e568503f0b6bb5e538f595d97623612e48548a6993e84e1830014 |
import re
from setuptools import setup
__version__ = re.search(r'__version__\s*=\s*[\'"]([^\'"]*)[\'"]',
open('kindel/__init__.py').read()).group(1)
CLASSIFIERS = ['Environment :: Console',
'Environment :: MacOS X',
'Intended Audience :: Science/Research',
... | bede/kindel | setup.py | Python | gpl-3.0 | 1,567 | [
"Biopython"
] | bbd431cc293d0343feb0bb121fde7acb1499720c4742b22544986e426e1016fc |
#!/usr/bin/env python
#from BCBio import GFF
from BCBio import GFF
from Bio import SeqIO
from optparse import OptionParser
import sys
# Arguments #
usage = """ %prog genbank_in_file gff_out_name"""
description = """Description: Use Biopython to convert a genbank to a gff."""
epilog = """"""
version = "0.1"
par... | nyoungb2/CLdb | sandbox/genbank2gff.py | Python | gpl-2.0 | 649 | [
"Biopython"
] | b63c7628435fb988565e11a07bd86defac1f3c759c9b2513cdfc1d83e47371fe |
"""
Customized data batching class based on tensorflow's MNIST helper module
"""
from tensorflow.examples.tutorials.mnist import input_data
import numpy as np;
class MNISTData(object):
class BaseImages(object):
"""
Completely identical to mnist dataset
"""
def __init__(self, data_... | YuhuaBillChen/tf-minist-playground | tf_data.py | Python | apache-2.0 | 4,733 | [
"Gaussian"
] | d728d413714dd7026b2e71408635620fab427be82c060e6175046896cf64de2e |
############################################################################################
# QN-S3VM BFGS optimizer for semi-supervised support vector machines.
#
# This implementation provides both a L-BFGS optimization scheme
# for semi-supvised support vector machines. Details can be found in:
#
# F. Gieseke, A.... | tmadl/semisup-learn | methods/qns3vm.py | Python | mit | 39,965 | [
"Gaussian"
] | 89c9e7e0f38904427cd7fb105518fbc93e4147ed50caac67392ae2782a2688b2 |
# -*- 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-dialogflow | tests/unit/gapic/dialogflow_v2/test_intents.py | Python | apache-2.0 | 121,005 | [
"Octopus"
] | eac9c79c21dfc06d5c158f8fca6a15daf3c7146e88a14c0e1d18105a77c5510e |
"""This module contains classes for generating a Control Flow Graph of a python program.
The class CFG is the main entry point to this module
The method generate_ast(path) can the used to generate input for the CFG class' create method
"""
import ast
import os
from collections import namedtuple, OrderedDict
from copy... | SW10IoT/pyt | pyt/cfg.py | Python | gpl-2.0 | 38,962 | [
"VisIt"
] | c21892510185cf47aa6bf7b1c37630c9468e65fc93ea7843486416d3f37a2ba9 |
#!/usr/bin/env python
"""
CI Status Tool
Used for a quick stats collection on Third Party CIs for various OpenStack
projects.
Example usage:
$ ./ci-status.py -v -u datera-ci \\
-k /home/user/.ssh/id_rsa \\
-c "Datera CI" -a datera-dsvm-full -t 2 \\
-j openstack/cinder \\
... | openstack/third-party-ci-tools | monitoring/ci-status/ci-status.py | Python | apache-2.0 | 26,842 | [
"VisIt"
] | 06b88dccfa6c67aafa9f1256b8cbfea12fe4972f9c15223c4f8006b8816fb0e5 |
# coding: utf-8
from __future__ import unicode_literals
import copy
import glob
import json
import os
from unittest import TestCase
import unittest
from pymatgen import Molecule
from pymatgen.io.qchem import QcTask, QcInput, QcOutput
__author__ = 'xiaohuiqu'
test_dir = os.path.join(os.path.dirname(__file__), "..... | rousseab/pymatgen | pymatgen/io/tests/test_qchem.py | Python | mit | 71,955 | [
"pymatgen"
] | 5a6c01d891aae96e12290e7795d1131aa23d494f5ae6b271d9f28d9abc1bbe99 |
#
# Manta - Structural Variant and Indel Caller
# Copyright (c) 2013-2015 Illumina, Inc.
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# at your option) a... | chapmanb/manta | src/python/lib/workflowUtil.py | Python | gpl-3.0 | 10,379 | [
"BWA"
] | a025e4f31e368b9372e5a5289c98d9404ecca085991a3274b3d1289ac8987104 |
#########################################################################
## This program is part of 'MOOSE', the
## Messaging Object Oriented Simulation Environment.
## Copyright (C) 2014 Upinder S. Bhalla. and NCBS
## It is made available under the terms of the
## GNU Lesser General Public License version 2... | BhallaLab/moose-examples | tutorials/ChemicalOscillators/repressillator.py | Python | gpl-2.0 | 3,118 | [
"MOOSE"
] | 15bef8a0acf71a2c52dc7955e042f3a5aff97c86b48ae6661601867b6bbf49be |
import ase.units as units
import numpy as np
from gpaw.setup import BaseSetup
from gpaw.spline import Spline
from gpaw.basis_data import Basis
class X(BaseSetup):
def __init__(self, e0=-10.0, rc=2.5):
e0 /= units.Hartree
rc /= units.Bohr
self.e0 = e0
self.rc = rc
... | robwarm/gpaw-symm | gpaw/xatom.py | Python | gpl-3.0 | 1,951 | [
"ASE",
"GPAW"
] | 83e32175d92953f0ef00a8ff73be75aa055bf604b9152e484d76ae7def7b9b50 |
from tracker.tests import TrackerTestCase
from django.core import mail
from .models import User
class AccountsTestCase(TrackerTestCase):
def test_in_browser_user_registration_and_confirmation(self):
self.browser.visit('/accounts/register/')
# Test validation
self.assertTrue(self.browse... | danielward/health-tracker | tracker/accounts/tests.py | Python | gpl-2.0 | 3,896 | [
"VisIt"
] | a0b671a69737337500a9eb4a92f2d44d3b3af90ea86fafbfdbb7e47e78c3dc29 |
# coding: utf-8
# Plot T-S diagrams and platform positions using the data from CMEMS.<br>
# For Argo floats, the pressure has to be transformed to depth.
# In[1]:
import numpy as np
import netCDF4
import matplotlib.pyplot as plt
import glob
import os
import seawater
import cmocean
from matplotlib import rcParams
fr... | ctroupin/CMEMS_INSTAC_Training | PythonNotebooks/CommunicationMaterial/plot_TS_diagram_all.py | Python | mit | 9,164 | [
"NetCDF"
] | ced574914bc837c1a14ef127f37b909ac7bd61efd120875c25a237a1606a438f |
import math
from ..libmp.backend import xrange
class QuadratureRule(object):
"""
Quadrature rules are implemented using this class, in order to
simplify the code and provide a common infrastructure
for tasks such as error estimation and node caching.
You can implement a custom quadrature rule by ... | kantel/processingpy | mpmathtest/mpmath/calculus/quadrature.py | Python | mit | 38,334 | [
"Gaussian"
] | 1c5edddfc02c6eee5a77dca5989dd2153e6f92b08d635f083f7598bcd2574dd9 |
# 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... | jarifibrahim/climate | ocw/data_source/local.py | Python | apache-2.0 | 24,799 | [
"NetCDF"
] | 7f40dcc3545900c92d5c51ae0a23ea03edc12cb947d91b6ce4207149ef9b9272 |
# 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 ... | mgeplf/NeuroM | neurom/fst/_neuronfunc.py | Python | bsd-3-clause | 9,686 | [
"NEURON"
] | 11a26e1bffb010307e3ef07d448fdac3f8a85d08f78fca55f46b87cdaf5644c7 |
# sybase/base.py
# Copyright (C) 2010-2020 the SQLAlchemy authors and contributors
# <see AUTHORS file>
# get_select_precolumns(), limit_clause() implementation
# copyright (C) 2007 Fisch Asset Management
# AG http://www.fam.ch, with coding by Alexander Houben
# alexander.houben@thor-solutions.ch
#
# This module is par... | gltn/stdm | stdm/third_party/sqlalchemy/dialects/sybase/base.py | Python | gpl-2.0 | 31,789 | [
"ASE"
] | b2962d98957bd7c456f885332b1d7537cfe4f4610a33de6a79754c2b466d9814 |
"""
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... | mbayon/TFG-MachineLearning | venv/lib/python3.6/site-packages/sklearn/tree/tree.py | Python | mit | 60,518 | [
"Brian"
] | ea321c79046e4bd8c946d6ecc45eb2cd0bd35eebc9286b944470fc8efbbf8200 |
"""Tests for options manager for :class:`Poly` and public API functions. """
from sympy.polys.polyoptions import (
Options, Expand, Gens, Wrt, Sort, Order, Field, Greedy, Domain,
Split, Gaussian, Extension, Modulus, Symmetric, Strict, Auto,
Frac, Formal, Polys, Include, All, Gen, Symbols)
from sympy.polys... | pernici/sympy | sympy/polys/tests/test_polyoptions.py | Python | bsd-3-clause | 11,113 | [
"Gaussian"
] | 6db9b1c84aa25d5afcb5fec1eae711de246aefa8fd934549353a02e89f572640 |
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