text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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from typing import Dict, Iterable, Optional
from iota import AdapterSpec, Address, BundleHash, ProposedTransaction, Tag, \
TransactionHash, TransactionTrytes, TryteString, TrytesCompatible
from iota.adapter import BaseAdapter, resolve_adapter
from iota.commands import CustomCommand, core, extended
from iota.crypto... | iotaledger/iota.lib.py | iota/api_async.py | Python | mit | 57,097 | [
"VisIt"
] | 1404b0f1b73d3a6e67c51338698a951db1aae5556cdae2703e23a342852050e0 |
# Copyright (c) 2015, Frappe Technologies Pvt. Ltd. and Contributors
# License: GNU General Public License v3. See license.txt
import frappe
from frappe import _
from frappe.utils import format_date, get_datetime
from erpnext.utilities.transaction_base import TransactionBase
class MaintenanceVisit(TransactionBase)... | frappe/erpnext | erpnext/maintenance/doctype/maintenance_visit/maintenance_visit.py | Python | gpl-3.0 | 4,558 | [
"VisIt"
] | 929e8e094b6b1984843942bb2eb9abae44573b3c7d72309708f266deed5f0008 |
# coding: utf-8
from __future__ import division, unicode_literals
'''
Created on Sep 23, 2011
'''
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2011, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep@gmail.com"
__date__ = "Sep 23, 2011"
import os
import rand... | rousseab/pymatgen | pymatgen/transformations/tests/test_standard_transformations.py | Python | mit | 16,832 | [
"VASP",
"pymatgen"
] | a7b4ac8babda210137ea31f08eee882671cd3f0b99d6e0dd2ee18072b59eabf6 |
# force floating point division. Can still use integer with //
from __future__ import division
# other good compatibility recquirements for python3
from __future__ import absolute_import
from __future__ import print_function
from __future__ import unicode_literals
# This file is used for importing the common utilities ... | prheenan/BioModel | EnergyLandscapes/Inverse_Boltzmann/Python/Code/InverseBoltzmannUtil.py | Python | gpl-2.0 | 13,659 | [
"Gaussian"
] | c1e53aae3dd330c650f9f5ceb96126b411fbc5d45a0d9544d57b6a78daaa0287 |
# shamelessly copied from pliExpertInfo (Vali, Mirakels, Littlesat)
from enigma import iServiceInformation, iPlayableService
from Components.Converter.Converter import Converter
from Components.Element import cached
from Components.config import config
from Tools.Transponder import ConvertToHumanReadable
from Tools.Ge... | kingvuplus/italysat-enigma2 | lib/python/Components/Converter/PliExtraInfo.py | Python | gpl-2.0 | 24,998 | [
"Galaxy"
] | 445b1f21cbb1f74f6a5ab925c1f7207d002bca5ff1630db9f998508670e2506c |
"""The tasks module provides a simple light-weight alternative to threads.
When you have a long-running job you will want to run it in the background,
while the user does other things. There are four ways to do this:
- Use a new thread for each task.
- Use callbacks from an idle handler.
- Use a recursive mainloop... | pombredanne/zero-install | zeroinstall/support/tasks.py | Python | lgpl-2.1 | 11,127 | [
"VisIt"
] | 11f34404497f8c5684b5337e90474bdc917eff258cffa199e1086a81f84604ef |
# -*- coding: utf-8 -*-
import os
import sys
def check_cclib(cclib):
"""Make sure we are importing code from a subdirectory, which should exist
and should have been updated just before running this script. Note that
this script does not assume any version in the module and just takes
what it finds...... | cclib/cclib | doc/sphinx/docs_common.py | Python | bsd-3-clause | 518 | [
"cclib"
] | 867bb35f4f836a06b862595771a8f0cce94a2ec27e22359100b5a2fc78baf694 |
import os
import time
import tarfile
import xml.sax
import numpy as np
from gpaw.mpi import broadcast as mpi_broadcast
from gpaw.mpi import world
from gpaw.io import FileReference
intsize = 4
floatsize = np.array([1], float).itemsize
complexsize = np.array([1], complex).itemsize
itemsizes = {'int': intsize, 'float... | ajylee/gpaw-rtxs | gpaw/io/tar.py | Python | gpl-3.0 | 8,152 | [
"GPAW"
] | 89a4dc57f72eda0c2a4233aa72d545a348cb48dc12520a700b8d73e685691e42 |
# -*- coding: utf-8 -*-
import os
import re
import uuid
import urllib
import logging
import datetime
import urlparse
from collections import OrderedDict
import warnings
import pytz
import blinker
from flask import request
from django.core.urlresolvers import reverse
from HTMLParser import HTMLParser
from modularodm i... | barbour-em/osf.io | website/project/model.py | Python | apache-2.0 | 89,823 | [
"VisIt"
] | d3eaaf5b7f66fde6c856be16676c94826a37a56de7b56abe17b27b8b431c0ae3 |
from nutils import *
from nutils.testing import *
import math, re
@parametrize
class gauss(TestCase):
# Gaussian quadrature and exact integration on different element types
maxdegree=7
exclude=frozenset()
def setUp(self):
super().setUp()
self.monomials = numpy.mgrid[ (slice(self.maxdegree),)*self.ndi... | wijnandhoitinga/nutils | tests/test_quadrature.py | Python | mit | 2,061 | [
"Gaussian"
] | 75fb0a6b551668869e934a180e0bdd5a7b2251def037a94fc4ab21593cb1dbba |
from ovito import *
from ovito.io import *
from ovito.data import *
import numpy
node = import_file("../../files/LAMMPS/bonds.data.gz", atom_style = 'bond')
print(node.source)
node.source.create_bond_property(BondProperty.Type.Color)
node.source.create_user_bond_property("MyProperty", "int", 2)
values = numpy.ones(no... | srinath-chakravarthy/ovito | tests/scripts/test_suite/bond_properties.py | Python | gpl-3.0 | 812 | [
"LAMMPS",
"OVITO"
] | 991344e19594edff0f844968e251833e73f72f362ef0a1da3cf2b74d20c1363c |
# -*- coding: utf-8 -*-
# Author: Óscar Nájera
# License: 3-clause BSD
"""
========================
Backreferences Generator
========================
Reviews generated example files in order to keep track of used modules
"""
from __future__ import print_function
import ast
import os
# Try Python 2 first, otherwise ... | emmanuelle/multi-diffusion | doc/ext/sphinx_gallery/backreferences.py | Python | bsd-3-clause | 6,128 | [
"VisIt"
] | f1d9280eda20357479b3d8441f830c10f8a606dd57418042c3d670ab42971421 |
#
# Copyright 2016 The BigDL Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... | intel-analytics/BigDL | python/chronos/src/bigdl/chronos/autots/model/auto_tcn.py | Python | apache-2.0 | 6,024 | [
"ORCA"
] | 5687c07d08750c212cbff81c24f4a1f0be2ff41c50976440ea8173fdbccac6e3 |
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2006-2014, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version 2.1 or later. ... | chrisjsewell/PyGauss | pygauss/cclib_patch/parser/gausscomparser.py | Python | gpl-3.0 | 3,617 | [
"Gaussian",
"cclib"
] | 4119716d8da58b36fcf737ae743f7331fc756ee32ffc61eeb1442cbb02130fcf |
#!/usr/bin/env python2
# -*- coding: utf-8 -*-
# Copyright 2017 The Chromium OS Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Autosuspend udev rule generator
This script is executed at build time to generate udev rules. The
resu... | phomes/systemd | tools/chromiumos/gen_autosuspend_rules.py | Python | gpl-2.0 | 7,260 | [
"Octopus"
] | c3af8118b0c6baf94910359059cabdec00d7dbd4c94ce422a231ce9e604ec82a |
#!/usr/bin/python
import os
cwd=os.getcwd()
cwd = cwd + '/'
f1= open(cwd + 'dsb_script.py',"w+")
f2= open(cwd +'dsb_temp_script.py',"r")
f5= open(cwd +'dsb_temp_glmol.py',"r")
f4= open(cwd +'dsb_script_gl.py',"w+")
inf_t=[]
inp= open(cwd +'inputfile.txt',"r")
with inp as ins:
ins = [line.rstrip('\n') for line in ins]... | S-John-S/MAT | dsb_main.py | Python | mit | 1,968 | [
"PyMOL"
] | e380e5f9be9b30ed5d0d328522d24afc90b1472d98e5a3cc6414ba39e4b2b92d |
"""
Sheet classes.
A Sheet is a two-dimensional arrangement of processing units,
typically modeling a neural region or a subset of cells in a neural
region. Any new Sheet classes added to this directory will
automatically become available for any model.
$Id$
"""
__version__='$Revision$'
# Imported here so that all ... | ioam/svn-history | topo/sheet/__init__.py | Python | bsd-3-clause | 7,841 | [
"NEURON"
] | 0e34e4c74e7ad6ddad9e76ba403e18099f00c6281a87eaa9038789d3e69ecbe4 |
# encoding: utf-8
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Removing unique constraint on 'IndicatorData', fields ['indicator', 'feature', 'time']
db.delete_unique(... | ProvidencePlan/Profiles | communityprofiles/profiles/oldmigrations/0004_remove_indicatordata_time.py | Python | mit | 10,759 | [
"MOE"
] | 97edf714757b42a233d72d1ed8f0861142207162cff092de8c128644d13d747b |
# -*- coding: utf-8 -*-
# This file is part of MOOSE simulator: http://moose.ncbs.res.in.
# MOOSE 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... | dharmasam9/moose-core | python/moose/moose_config.py | Python | gpl-3.0 | 1,820 | [
"MOOSE"
] | 275f063802ddc4cd1dc4503c0e27af52b9fb495774f468aa43108348095cf665 |
import sys
import pysam
samfile = pysam.Samfile( "ex1.bam", "rb" )
print "###################"
# check different ways to iterate
print len(list(samfile.fetch()))
print len(list(samfile.fetch( "chr1", 10, 200 )))
print len(list(samfile.fetch( region="chr1:10-200" )))
print len(list(samfile.fetch( "chr1" )))
print len(... | genome-vendor/chimerascan | chimerascan/pysam/tests/example.py | Python | gpl-3.0 | 3,206 | [
"pysam"
] | fe0b1fb87e899b4cceea4f742ee7d379255615a6b60fcf51b364fde6bcc859a6 |
"""
This module implements the base functionality for MCMC-based samplers for NNs.
"""
import logging
import numpy as np
import scipy as sp
import tensorflow as tf
from sampler import Sampler, SampleStats
GRADIENT_CLIP_VALUE = 1e5
class MCMC_sampler(Sampler):
"""
Base class for MCMC (HMC/LD) -based samplers ... | myshkov/bnn-analysis | models/mcmc_sampler.py | Python | mit | 21,351 | [
"Gaussian"
] | 437127eac9345cc6e795fcc7f87c45f700cda0d470da5d372b57aeb47c87ab44 |
#
# This source file is part of appleseed.
# Visit http://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2012-2013 Esteban Tovagliari, Jupiter Jazz Limited
# Copyright (c) 2014-2017 Esteban Tovagliari, The appleseedhq Organization
#
# P... | gospodnetic/appleseed | src/appleseed.python/__init__.py | Python | mit | 1,430 | [
"VisIt"
] | 882aa59abfe6095cae328b39b070ff64a2033ec1f87fad639a97ae86075493f3 |
# 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... | ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/phonnames.py | Python | gpl-3.0 | 2,822 | [
"ORCA"
] | a689e713c4d7500c84b43e2e4f0d0579b6652d4463955a02399b69df16c7304c |
# -*- coding: iso-8859-1 -*-
############################################################
# Example 1: Simple basin hopping
############################################################
import numpy as np
import pele.potentials.lj as lj
import pele.basinhopping as bh
from pele.takestep import displace
natoms = 12
# r... | kjs73/pele | examples/basinhopping_no_system_class/1_basic.py | Python | gpl-3.0 | 714 | [
"PyMOL"
] | 65c7b4298c36fe10774ad800be5dc1a1f1f741539e415293f3672abd71587dba |
# -*- coding: utf-8 -*-
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Mathieu Blondel <mathieu@mblondel.org>
# Robert Layton <robertlayton@gmail.com>
# Andreas Mueller <amueller@ais.uni-bonn.de>
# Philippe Gervais <philippe.gervais@inria.fr>
# Lars Buitinck ... | carrillo/scikit-learn | sklearn/metrics/pairwise.py | Python | bsd-3-clause | 44,120 | [
"Gaussian"
] | 2effb95bdcb991fc19165ad9aa5c9c6a732d8c586a13f387bd90cc801fb9ad94 |
'''
Sort entries in a tabular BLAST output file in reverse order.
-----------------------------------------------------------
(c) 2013 Allegra Via and Kristian Rother
Licensed under the conditions of the Python License
This code appears in section 8.4.2 of the book
"Managing Biological Data with Python".
... | raymonwu/Managing_Your_Biological_Data_with_Python_3 | 08-sorting_data/8.4.2_sort_blast_output.py | Python | mit | 883 | [
"BLAST"
] | 20a014fa3864852431e335d6c0590554c61978153377574be9bbb4291fc4d42d |
from math import sqrt
import pylab as plt
from ase import Atoms
from gpaw import GPAW
# Lattice constant
a = 5.475
atoms = Atoms(symbols='Si4',
scaled_positions=[(.0, .0, .0),
(.5, .5, .5),
(.0, .5, .75),
(... | qsnake/gpaw | doc/exercises/dos/dos_Si.py | Python | gpl-3.0 | 768 | [
"ASE",
"GPAW"
] | 2eef58618c0307fa0fe1c4406d3bc9a2207df93c8dbf8fe0be81b0aafa71b65a |
"""
JobReport class encapsulates various methods of the job status reporting blah, blah, blah...
"""
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.Utilities import Time, DEncode
from DIRAC.Core.DISET.RPCClient import RPCClient
from DIRAC.RequestManagementSystem.Client.Operation import Operation
__RCSID_... | Andrew-McNab-UK/DIRAC | WorkloadManagementSystem/Client/JobReport.py | Python | gpl-3.0 | 5,984 | [
"DIRAC"
] | ed7c61b86fbb0094df42e2be1239a87242a0d71b81d00fc5c24ae044acdcfb76 |
import copy
import exchange
import lan
from lan import ast_buildingblock as ast_bb
from processing import collect_array as ca
from processing import collect_device as cd
from processing import collect_gen as cg
from processing import collect_id as ci
from processing import collect_loop as cl
class Stencil(object):
... | dikujepsen/OpenTran | v3.0/framework/transformation/stencil.py | Python | mit | 4,516 | [
"VisIt"
] | 10afea3b7cb596cde37ca912f49ba60c1d15e0ff5912893a218a9e7b5aa34aa7 |
#!/usr/bin/env python
import fnmatch
import os
from argparse import ArgumentParser
import json
import subprocess
def combine_known_symbols(kn1, kn2):
for key, value in kn2.items():
if key not in kn1:
kn1[key] = value
else:
kn1[key] += value
return kn1
def parse_folde... | MartinThoma/write-math | tools/language_model/language-model-building/parse_folder.py | Python | mit | 1,918 | [
"MOOSE"
] | 18400fca9ccac09d574947e819ca50395ce6217814b81ff77d94c193bcd5e15b |
# !usr/bin/env python2
# -*- coding: utf-8 -*-
#
# Licensed under a 3-clause BSD license.
#
# @Author: Brian Cherinka
# @Date: 2017-02-12 17:38:51
# @Last modified by: Brian Cherinka
# @Last Modified time: 2017-03-25 16:08:37
from __future__ import print_function, division, absolute_import
from flask_testing impor... | bretthandrews/marvin | python/marvin/tests/web/__init__.py | Python | bsd-3-clause | 3,851 | [
"Brian"
] | dadbc8a9b1da4d0160e5d1c200c8c836475025c6202b9412d294d23f322f4696 |
###########################################################################
#
# Copyright 2020 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/l... | google/starthinker | dags/airflow_dag.py | Python | apache-2.0 | 4,871 | [
"VisIt"
] | 90eaca74fb72c9293d190122c67156ede3827f437a1f8cb79efb20e15e397b68 |
hucs = [['01','New England'],
['0101','St. John'],
['010100','St. John'],
['01010001','Upper St. John'],
['01010002','Allagash'],
['01010003','Fish'],
['01010004','Aroostook'],
['01010005','Meduxnekeag'],
['0102','Penobscot'],
['010200','Penobscot'... | IMDProjects/IM_Climate | IM_Climate_py/hucs.py | Python | mit | 103,491 | [
"CRYSTAL",
"Elk"
] | 2a93baf26cd79ac641612cf615194d2d8d647d3a165e10052185f26527cfc409 |
#!/usr/bin/env python
#
# Read Output of a CP2K BSSE Calculation and Calculate the Interaction Energy.
# Only for 2 Component System A-B with 5 Subcalculations in one Output.
import os, shutil
from scm.plams import *
def main(name, assign):
try:
if isinstance(config['default_jobmanager'], JobManager):
... | patrickmelix/Python4ChemistryTools | cp2k-bsse.py | Python | mit | 2,654 | [
"CP2K"
] | 730eb1a780adc71b89dc00dcbe730ea9e265c88cb2fd19dfe7d2474e31ef1a7e |
"""ll.py - Implementation of an LL(1) (Left to right Leftmost) parser generator
"""
# Copyright 2012 Erich Blume <blume.erich@gmail.com>
# ===========================
#
# This file is part of pcc
#
# pcc is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as pu... | eblume/pcc | pcc/ll.py | Python | gpl-3.0 | 14,433 | [
"GULP"
] | 6aefb19bfc23c451c33d30c4ab6985530ba99c7c0359f15f5127ec29bb9056dd |
"""
Student Views
"""
import datetime
import logging
import uuid
import json
import warnings
from collections import defaultdict
from pytz import UTC
from requests import HTTPError
from ipware.ip import get_ip
from django.conf import settings
from django.contrib.auth import logout, authenticate, login
from django.cont... | mjirayu/sit_academy | common/djangoapps/student/views.py | Python | agpl-3.0 | 92,243 | [
"VisIt"
] | 6040889533cc42b58c1fe9b3a3d355c9cff4e76924d9715a6abe72b37e6558c6 |
# -*- coding: utf-8 -*-
from south.utils import datetime_utils as datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding field 'SurveyQuestionResponse.positive_response'
db.add_column(u... | myvoice-nigeria/myvoice | myvoice/survey/migrations/0013_auto__add_field_surveyquestionresponse_positive_response.py | Python | bsd-2-clause | 12,899 | [
"VisIt"
] | ba92bf33ae1eecb8bc6b3d5d70201616b87237fe4aeb60f39caf974711be24a2 |
import unittest
from nose.tools import (assert_in, assert_raises, assert_equals)
import io
import logging
import numpy
from sknn.mlp import MultiLayerPerceptron as MLP
from sknn.mlp import Regressor as MLPR
from sknn.mlp import Classifier as MLPC
from sknn.mlp import Layer as L
import sknn.mlp
class TestTrainingPr... | jgdwyer/ML-convection | sknn_jgd/tests/test_training.py | Python | apache-2.0 | 5,275 | [
"Gaussian"
] | e713c9ebc899cdf97abad85a22141d01276a4b23dd21108a5471fac79127c8e2 |
#!/usr/bin/env python
"""
ParseBlast.py
takes as input an xml results file
creates a csv summary results file
can pass file handles for results files
instead of file paths if running over
multiple files
BLAST against the swissprot database and it returns the protein gi number
BLAST agai... | ajrichards/htsint | htsint/blast/ParseBlast.py | Python | bsd-3-clause | 4,046 | [
"BLAST"
] | c76eb3420f2ddd579aed3765af64e8daf913f99f42a81a15bfd976d34d9a8097 |
""" The gateway service is used for forwarding service calls to the appropriate services.
For this to be used, the following CS option is required:
DIRAC
{
Gateways
{
my.site.org = dips://thisIsAn.url.org:9159/Framework/Gateway
}
}
At the same time, this same gateway ser... | Andrew-McNab-UK/DIRAC | Core/DISET/private/GatewayService.py | Python | gpl-3.0 | 20,150 | [
"DIRAC"
] | cd423a8dc1fa76cc34960bf50961fa1c9cd8c57381d04a24cf069adb5a01577c |
#!/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/symm/test/test_geom.py | Python | apache-2.0 | 38,355 | [
"PySCF"
] | 366b5e14691b3a43a9b75c60fe3f3580980b3c999835736713f247b5cd0899a0 |
# Copyright 2014-2016 by Marco Galardini. 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.
"""This module provides classes to work with Phenotype Microarray data.
More informatio... | zjuchenyuan/BioWeb | Lib/Bio/phenotype/phen_micro.py | Python | mit | 37,132 | [
"Biopython"
] | c8c33dff3e78e4e56b4385ee76363dc03c151d32361784da6e008c2678c23127 |
# Principal Component Analysis Code :
from numpy import mean,cov,double,cumsum,dot,linalg,array,rank,size,flipud
from pylab import *
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import ro... | tapomayukh/projects_in_python | classification/Classification_with_kNN/Single_Contact_Classification/Final/best_kNN_PCA/objects/24/test11_cross_validate_objects_24_1200ms.py | Python | mit | 4,613 | [
"Mayavi"
] | 3bcf98f0a18856900ec1584d61c62cb536ead186af98cab634798605c881a000 |
#!/usr/local/bin/python -i
# preceeding line should have path for Python on your machine
# vizplotgui_gl.py
# Purpose: viz running LAMMPS simulation via GL tool with plot and GUI
# Syntax: vizplotgui_gl.py in.lammps Nfreq compute-ID
# in.lammps = LAMMPS input script
# Nfreq = plot data point and viz... | val-github/lammps-dev | python/examples/vizplotgui_gl.py | Python | gpl-2.0 | 4,375 | [
"LAMMPS"
] | 722ef0e0572c84740642c433f686bca6a620fadda60ddf83d2b50e6c86a408f4 |
import numpy as np
import copy
import pdb
import os
import time
import matplotlib
matplotlib.use('Agg')
import matplotlib.pylab as plt
from .context import pep, vfe
from .context import pep_tmp as pep
from test_utils import check_grad
np.random.seed(42)
def test_gpr_pep_gaussian():
N_train = 20
M = 5
D =... | thangbui/geepee | tests/test_grads_pep.py | Python | mit | 4,943 | [
"Gaussian"
] | 0d9faa6381ecd2ecd4c23bdab2a422d8838c37d561236b354e9ff1dc73996959 |
"""Header value parser implementing various email-related RFC parsing rules.
The parsing methods defined in this module implement various email related
parsing rules. Principal among them is RFC 5322, which is the followon
to RFC 2822 and primarily a clarification of the former. It also implements
RFC 2047 encoded w... | ruibarreira/linuxtrail | usr/lib/python3.4/email/_header_value_parser.py | Python | gpl-3.0 | 103,875 | [
"CRYSTAL"
] | dca7c0c707195c5266980131bc81246ca3cb1015b69ddc47f14209b1ab38e812 |
"""
Trying to build a network with shared connections:
>>> from random import random
>>> n = buildSharedCrossedNetwork()
Check if the parameters are the same:
>>> (n.connections[n['a']][0].params == n.connections[n['a']][1].params).all()
True
>>> (n.connections[n['b']][0].params == n... | iut-ibk/Calimero | site-packages/pybrain/tests/unittests/test_shared_connections.py | Python | gpl-2.0 | 2,444 | [
"NEURON"
] | 1455933431d20916a0e8e9a322c1308449df2dd8f6882fbf468cb45e97bd1331 |
# Copyright (c) 2017, The MITRE Corporation. All rights reserved.
# See LICENSE.txt for complete terms.
"""
STIX Extension for AIS Data Markings
Unlike the other marking extensions, the AIS marking extension is not loaded
automatically, since AIS markings are not a part of the published STIX 1.x
specifications. They ... | STIXProject/python-stix | stix/extensions/marking/ais.py | Python | bsd-3-clause | 12,265 | [
"Amber"
] | c9d092f78e59da8d712065b51291128a0a29a7042424eca431cbe95b5c728dc8 |
# Online haptic_map implementation
import pylab as pyl
import numpy as np
import matplotlib.pyplot as pp
#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
import os
#import hrl_lib.mayavi2_util as mu
i... | tapomayukh/projects_in_python | rapid_categorization/haptic_map/online_haptic_map_taxel_based.py | Python | mit | 16,270 | [
"Gaussian",
"Mayavi"
] | f5db77a2a8ea05410c80edcac957a1221bcc932cea949a659b11ea824af10413 |
from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os
repository_name = 'filtering_0410'
repository_description = 'Galaxy filtering tool for test 0410'
repository_long_description = 'Long description of Galaxy filtering tool for test 0410'
'''
1. Create a repository in the tool shed owned by test_user... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/test/tool_shed/functional/test_0410_repository_component_review_access_control.py | Python | gpl-3.0 | 13,119 | [
"Galaxy"
] | f5ed46c2749809379e61c12d7c8d79d43ab65b6db367fdb27875c1adeb08c706 |
import matplotlib.pyplot as plt
from matplotlib import cm
import pandas as pd
from sklearn.neighbors import kneighbors_graph
import networkx as nx
import numpy as np
from sklearn import preprocessing
# Function to do some comparison between professionals and students
def plot_stud_prof(prof_stack="", stud_stack="", pr... | mdeff/ntds_2017 | projects/reports/stackoverflow_recommendation/helper_functions.py | Python | mit | 9,671 | [
"BWA"
] | 3cbf94923e33d2d2798d9502de345c0738d4eec2d921d56a843c74a765ab6b5c |
#
# QAPI parser test harness
#
# Copyright (c) 2013 Red Hat Inc.
#
# Authors:
# Markus Armbruster <armbru@redhat.com>
#
# This work is licensed under the terms of the GNU GPL, version 2 or later.
# See the COPYING file in the top-level directory.
#
from qapi import *
from pprint import pprint
import os
import sys
c... | coloft/qemu | tests/qapi-schema/test-qapi.py | Python | gpl-2.0 | 1,749 | [
"VisIt"
] | 6e70fbf39f4c5ad9b077d113c3242ffa39b37bb70a3bae169527492396730bbe |
"""
Created on 30/01/2013
@author: thom
"""
import random
import logging
import numpy as np
from rdkit.Chem import AllChem as Chem
import xml.etree.cElementTree as ElementTree
from population import Population
from molecule import Molecule # only used to get canonical SMILES representation for a molecule
class M... | th0mmeke/toyworld | molecular_population.py | Python | gpl-3.0 | 8,174 | [
"RDKit"
] | 33b40426f4127f7fad35400db132e1c3dd46ed20909ebe873b02690507272527 |
from collections import OrderedDict
import numpy as np
from robosuite.environments.manipulation.single_arm_env import SingleArmEnv
from robosuite.models.arenas import TableArena
from robosuite.models.objects import BoxObject
from robosuite.models.tasks import ManipulationTask
from robosuite.utils.mjcf_utils import Cu... | ARISE-Initiative/robosuite | robosuite/environments/manipulation/stack.py | Python | mit | 20,724 | [
"Gaussian"
] | 44010f02d0aacb718510f9f548b2483b6d31ee2a67c092905d0452d78bedb896 |
"""
Test a variety of different buttons.
"""
from aloe.testing import FeatureTest
from aloe_webdriver.tests.base import feature
# pylint:disable=line-too-long
class TestSteps(FeatureTest):
"""Test steps."""
@feature()
def test_press_of_submit_button_by_name(self):
"""
Given I visit tes... | aloetesting/aloe_webdriver | aloe_webdriver/tests/test_buttons.py | Python | mit | 4,147 | [
"VisIt"
] | 9ea98c5b3e5179419e109e6d6ddf22b271101ed2849651d7efaaebd9a335de5e |
# Modified: Richar J. Hall, 07/2010 rjhall@berkeley.edu
# Author: Pawel A.Penczek, 09/09/2006 (Pawel.A.Penczek@uth.tmc.edu)
# Copyright (c) 2000-2006 The University of Texas - Houston Medical School
#
# This software is issued under a joint BSD/GNU license. You may use the
# source code in this file under either licens... | mcianfrocco/Cianfrocco_et_al._2013 | 3D_projection_matching_EMAN2/functions.py | Python | mit | 43,859 | [
"Gaussian"
] | 64f8bb82945bedb2c4e104285cf01deea2f644799e5b0bb8290cf2514db15501 |
"""Test generation helpers
Intended to functionalize common tasks when working with the pytest_generate_tests hook.
When running a test, it is quite often the case that multiple parameters need to be passed
to a single test. An example of this would be the need to run a Provider Add test against
multiple providers. W... | akarol/cfme_tests | cfme/utils/testgen.py | Python | gpl-2.0 | 13,742 | [
"VisIt"
] | 80a310d6e49a67d9dfa65ceb0be32871d70df778a72816bf528a9da56994a1b3 |
"""Wrapper for launching pdbquery"""
"""
This file is part of RAPD
Copyright (C) 2017, Cornell University
All rights reserved.
RAPD is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, version 3.
RAPD is dis... | RAPD/RAPD | src/plugins/mr/commandline.py | Python | agpl-3.0 | 10,746 | [
"ADF"
] | acfc3a731a3ea09d024c1b4ab054d004082bb0f66fb8205128c55de1b39fb151 |
# Stub models file
from dimagi.ext.couchdbkit import Document
# ensure our signals get loaded at django bootstrap time
from . import signals
from corehq.apps.users.models import CommCareCase
from custom.succeed.reports import VISIT_SCHEDULE, LAST_INTERACTION_LIST, PM3
import fluff
from custom.utils.utils import flat_fi... | puttarajubr/commcare-hq | custom/succeed/models.py | Python | bsd-3-clause | 2,931 | [
"VisIt"
] | 68d317fb0604cca9fff20c940f8c3534cee34eb416856287f2d580e1681fda09 |
from unittest import TestCase
from StringIO import StringIO
from mock import MagicMock
from apetools.commands.ipconfig import Ipconfig
from apetools.connections.localconnection import OutputError
output = """
Windows IP Configuration
Wireless LAN adapter Wireless Network Connection 3:
Media State . . . . . . .... | rsnakamura/oldape | tests/testunits/testcommands/testipconfig/testipconfig.py | Python | apache-2.0 | 4,225 | [
"FEFF"
] | 66ad0a9241634601823ddf15691a7b4a333bd5a77aa01dde885aa132e8ca680d |
from django.db import models
from edc_base.model_fields.custom_fields import OtherCharField
from edc_base.model_managers import HistoricalRecords
from ..managers import CurrentSiteManager
from edc_base.model_validators import date_not_future
from edc_constants.choices import YES_NO_NA
from edc_visit_tracking.managers i... | botswana-harvard/ambition-subject | ambition_subject/models/follow_up.py | Python | gpl-3.0 | 2,214 | [
"VisIt"
] | 51f586773dc6ae609129eca957d21140e2679b17b13e5a3a0e769a46359e2c11 |
import pickle
import time
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from scipy.interpolate import interp1d, Rbf
from scipy.io import loadmat, savemat
import sys, os
sys.path.append("./")
from Utils.RK4 import RK4
from Utils.boxgrid import boxgrid
from Utils.compare import compare
f... | CDNoyes/EDL-Py | EntryGuidance/AAS20.py | Python | gpl-3.0 | 14,106 | [
"Gaussian"
] | 77c449bbfab877c4e0efc403869a223a393652d8fc102e9ded530dbb183dfb4a |
from datetime import date, timedelta
import warnings
from pyluach.dates import GregorianDate
from .core import UnitedStates
from ..registry_tools import iso_register
class HebrewHolidays:
hebrew_calendars = {}
@classmethod
def get_hebrew_calendar(cls, gregorian_year):
"""
Build and cach... | novapost/workalendar | workalendar/usa/florida.py | Python | mit | 4,158 | [
"COLUMBUS"
] | a8128a01f7ad57e7d5c4613c90fdb63f4686d93f795fd816959185563cfd0155 |
# Copyright (C) 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 versio... | mkuron/espresso | testsuite/scripts/samples/test_p3m.py | Python | gpl-3.0 | 1,006 | [
"ESPResSo"
] | 2e97c6c9e5844d4b16d6325e49759365e6e3601684fed9484ec25ed73107d551 |
# Bookmark plugin for Exaile media player
# Copyright (C) 2009-2011 Brian Parma
#
# 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) any later... | Zarokka/exaile | plugins/bookmarks/__init__.py | Python | gpl-2.0 | 10,244 | [
"Brian"
] | f52aac99f7959029736b0a75e2fa39b1e4015f4f57a3a86cd881b87620feae7d |
import sys, os, glob
if not os.path.exists('output'):
os.mkdir('output')
SCRIPT = '../nesoni_scripts/nesoni'
def run_nesoni(command, same_python=True):
full_command = '%s %s' % (SCRIPT, command)
if same_python:
full_command = sys.executable + ' ' + full_command
print
print 'Running:'
... | Victorian-Bioinformatics-Consortium/nesoni | test/test_nesoni_consensus.py | Python | gpl-2.0 | 1,422 | [
"Bowtie"
] | acda74f0a998dc469351c44db6e173366a14f3f6ab36875af928a13fa07e8d20 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#... | MDAnalysis/mdanalysis | testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py | Python | gpl-2.0 | 9,893 | [
"MDAnalysis"
] | 96c87afe81c758aca78bc5f5fe67cc0a60ceed5a78c829c35f803777de6616ae |
# Copyright 2020, The TensorFlow Federated Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law o... | tensorflow/federated | tensorflow_federated/python/learning/model_update_aggregator.py | Python | apache-2.0 | 12,865 | [
"Gaussian"
] | 1aba37ca2aa09d01f9f90bc58e3bf7b0289c46d29fbb2f7126533d88bd449a9b |
from math import fsum, sqrt
from copy import copy
from pyelectro import analysis
from traceHandler import sizeError
import efel
import numpy as np
import scipy
import inspyred
from inspyred import ec
from inspyred.ec import emo
from inspyred.ec import variators
from inspyred.ec import observers
import modelHandler
impo... | KaliLab/optimizer | optimizer/fitnessFunctions.py | Python | lgpl-2.1 | 52,265 | [
"ASE",
"NEURON"
] | 6c612f9fba107e0b53f39023a2336e0a5742a38962a93bd580950808a7551e91 |
########################################################################
#
# (C) 2013, James Cammarata <jcammarata@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software ... | hryamzik/ansible | lib/ansible/cli/galaxy.py | Python | gpl-3.0 | 33,565 | [
"Galaxy"
] | 9a8dec4d12fce7b156128b2df8f82a110efef710104c43cf647c270d8c3222f5 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Reditools(PythonPackage):
"""REDItools: python scripts for RNA editing detection by RNA-Se... | LLNL/spack | var/spack/repos/builtin/packages/reditools/package.py | Python | lgpl-2.1 | 3,487 | [
"BWA",
"pysam"
] | 522470655cdecc1f80bacb080e8d27d8cdb4d3c2317dc355b24ee5ea8eb843e0 |
'''
This is the primary module for user-interaction with the :mod:`hmf` package.
The module contains a single class, `MassFunction`, which wraps almost all the
functionality of :mod:`hmf` in an easy-to-use way.
'''
version = '1.4.6'
###############################################################################
# So... | tbs1980/hmf | hmf/hmf.py | Python | mit | 29,047 | [
"TINKER"
] | db93d7de9a75276f9ca6866429befca38fc56f368c61b05a3fda60262a1bd8f8 |
"""I/O functions that operate on omics ExpressionSet objects.
Supported:
* I/O from/to Bioconductor ExpressionSet (RData)
* I/O from/to HDF5 storage (Pandas dataframes)
Input:
* RData2ExpressionSet(RData, assay='exprs', fFactors='auto', pFactors='auto')
* HDF52ExpressionSet(HDF5, assay='exprs', fData='fData',... | choyichen/omics | omics/io/ExpressionSetIO.py | Python | mit | 6,917 | [
"Bioconductor"
] | 23dc2b5a55727955a198bcf79edb59ba41c3ee832a6acaa7b1e339536845fc6f |
#!/usr/bin/env python
'''
Spherical symmetry needs to be carefully treated in the atomic calculation.
The default initial guess may break the spherical symmetry. To preserve the
spherical symmetry in the atomic calculation, it is often needed to tune the
initial guess and SCF model.
See also 31-cr_atom_rohf_tune_ini... | gkc1000/pyscf | examples/scf/31-v_atom_rohf.py | Python | apache-2.0 | 2,028 | [
"PySCF"
] | c3fda4f87ea2b66757115b5dbc798eb90387ffed00c2668b263a83fe920cdd79 |
"""This module defines an ASE interface to FHI-aims.
Felix Hanke hanke@liverpool.ac.uk
Jonas Bjork j.bjork@liverpool.ac.uk
"""
import os
import numpy as np
from ase.units import Hartree
from ase.io.aims import write_aims, read_aims
from ase.data import atomic_numbers
from ase.calculators.calculator import FileIOCal... | suttond/MODOI | ase/calculators/aims.py | Python | lgpl-3.0 | 25,262 | [
"ASE",
"DIRAC",
"FHI-aims"
] | 0a972e69fe26b75eff63bb1c3b62ad00b9fb56d625f7dddf68933518b9351618 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundati... | tiagocardosos/stoq | stoqlib/gui/test/test_creditcheckhistorysearch.py | Python | gpl-2.0 | 2,838 | [
"VisIt"
] | 9d9cd12579bddccdd16bbd07d1d465390ca45f0b8b8257356ee70bfc189a3192 |
# coding: utf-8
from __future__ import unicode_literals
import itertools
import re
from .common import InfoExtractor
from ..utils import (
clean_html,
dict_get,
ExtractorError,
float_or_none,
get_element_by_class,
int_or_none,
js_to_json,
parse_duration,
parse_iso8601,
try_get,... | rbrito/pkg-youtube-dl | youtube_dl/extractor/bbc.py | Python | unlicense | 60,023 | [
"VisIt"
] | a893f4a1468f765b1002f3bb560c7b7fe2881e417b9a511f5d60564ae95b9740 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import unittest
import os
from pymatgen.analysis.pourbaix.entry import PourbaixEntry, IonEntry, MultiEntry
from pymatgen.analysis.pourbaix.entry import PourbaixEntryIO
... | setten/pymatgen | pymatgen/analysis/pourbaix/tests/test_entry.py | Python | mit | 6,029 | [
"pymatgen"
] | 9c0193fb679ac73b88a1bc45e9061c30199c9f6480c9e1b1d23ff3c60ac2af57 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from malepierre.characters.views import CharacterViewSet
... | EliotBerriot/malepierre | config/urls.py | Python | bsd-3-clause | 1,510 | [
"VisIt"
] | a925c30cfb30c6f55dd2f57b1c6551e44139b9b43089898de70b2892499fb6e3 |
"""
=================
:mod:`crossovers`
=================
.. Copyright 2012 Aaron Garrett
.. 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 restrict... | aarongarrett/inspyred | inspyred/ec/variators/crossovers.py | Python | mit | 18,622 | [
"Gaussian"
] | 32c6beadb296fa4e252bb048ab48e80bed33d84573a43c23d0b2ccb7a97d3263 |
#!/usr/bin/env python
# easyFig.py Written by: Mitchell Sullivan mjsull@gmail.com
# Supervisor: Dr. Scott Beatson and Dr. Nico Petty University of Queensland
# Version 2.2.3 08.11.2016
# License: GPLv3
import os
import subprocess
from math import ceil, hypot
import threading
import time
import struct
import base64... | TAMU-CPT/galaxy-tools | tools/gbk_viz/Easyfig.py | Python | gpl-3.0 | 914,274 | [
"BLAST",
"VisIt"
] | e6d236996cae6c5a9f143d3ff048a2f23550526cae4b87954dddbc0857b76128 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
################################################################################
#
# ChemPy - A chemistry toolkit for Python
#
# Copyright (c) 2010 by Joshua W. Allen (jwallen@mit.edu)
#
# Permission is hereby granted, free of charge, to any person obtaining a
# co... | jwallen/ChemPy | chempy/thermo.py | Python | mit | 24,040 | [
"ChemPy"
] | 5e7dadf85f333953b6d35d9049bbe9b8b870b5cfa2fbc0536d011ae08183ea69 |
# Copyright 2009 Brian Quinlan. All Rights Reserved.
# Licensed to PSF under a Contributor Agreement.
"""Execute computations asynchronously using threads or processes."""
__author__ = 'Brian Quinlan (brian@sweetapp.com)'
from serge.blocks.concurrent.futures._base import (FIRST_COMPLETED,
... | smmosquera/serge | blocks/concurrent/futures/__init__.py | Python | lgpl-3.0 | 839 | [
"Brian"
] | 46d9dcc05721a93d1ce88306046b35bfccddcff45e7aeef9b1fdb59d11b01256 |
#
# This source file is part of appleseed.
# Visit http://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2017 Petra Gospodnetic, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaining a co... | aytekaman/appleseed | sandbox/tests/test scenes/many light sampling/generators/4_point_lights_test_scene.py | Python | mit | 8,605 | [
"VisIt"
] | e5211b66bd4c6f17338a3895c124def743ad93e1e3794e3ba4645e3660b098a7 |
from ase.tasks.main import run
atoms, task = run("nwchem molecule O2 O -p task=gradient")
atoms, task = run('nwchem molecule O2 O -s')
ae = 2 * task.data['O']['energy'] - task.data['O2']['energy']
assert abs(ae - 6.605) < 1e-3
| alexei-matveev/ase-local | ase/test/nwchem/nwchem_cmdline.py | Python | gpl-2.0 | 228 | [
"ASE",
"NWChem"
] | 1c446877f4d080e58180341f6bb720c03e86dfede899dcafd02f3c12650c0339 |
import serial
import inspect
import time
import itertools
from util import two_byte_iter_to_str, to_two_bytes
# Message command bytes - straight from Firmata.h
DIGITAL_MESSAGE = 0x90 # send data for a digital pin
ANALOG_MESSAGE = 0xE0 # send data for an analog pin (or PWM)
DIGITAL_PULSE = 0x91 # SysE... | hatchetation/pyFirmata | pyfirmata/pyfirmata.py | Python | bsd-3-clause | 18,886 | [
"CRYSTAL"
] | f4bec138938b581f06d35160ef1a96b4921fa1756744359471222cb357a903a6 |
#galaxy.py
from __future__ import division
import numpy
import math
import matplotlib
import matplotlib.pyplot
import time
import pickle
import sys
from custom import loopProgress
from custom import rotate
from custom import build_distance_matrix
from custom import partitionData
class galaxy (object):
def __init... | LynnCo/galaxySim | galaxy.py | Python | mit | 9,254 | [
"Galaxy"
] | 4d868316b657b2a60c7026316cf3fc28c445e5d21d6e20d8c30e48ced98050a7 |
# CREATED:2015-02-17 14:41:28 by Brian McFee <brian.mcfee@nyu.edu>
# this function is lifted wholesale from matploblib v1.4.2,
# and modified so that images are stored explicitly under the tests path
from __future__ import (absolute_import, division, print_function,
unicode_literals)
import si... | ruohoruotsi/librosa | tests/mpl_ic.py | Python | isc | 11,814 | [
"Brian"
] | 4bbefb01035e659bd609e4a0d14f1c3bf64c2fd302fdf01bbcac50d155370fe0 |
##############################################################################
# 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... | matthiasdiener/spack | var/spack/repos/builtin/packages/mfem/package.py | Python | lgpl-2.1 | 21,451 | [
"NetCDF"
] | f34172ba624097c302ff5457244c9824dab62be832c8de7f1c7b098f1da42e97 |
#!/usr/bin/env python
# find_differential_primers.py
#
# A Python script that identifies pairs of forward and reverse primers which
# are capable of amplifying either individual organisms, or a particular
# family of organisms, from a set of genome sequences. Primers are expected
# to be located within CDS features, i... | alainr85/bio_primers | find_differential_primers/find_differential_primers.py | Python | gpl-3.0 | 83,235 | [
"BLAST",
"Biopython"
] | 34b1b8419fe51782860983c91c840f4f25e9dc9101b4689070ccb3a8184dc494 |
"""
=================================
Gaussian Mixture Model Ellipsoids
=================================
Plot the confidence ellipsoids of a mixture of two Gaussians with EM
and variational Dirichlet process.
Both models have access to five components with which to fit the
data. Note that the EM model will necessari... | BerkeleyAutomation/vtsc | scripts/examples/plot_gmm.py | Python | mit | 2,870 | [
"Gaussian"
] | 30d3eff81a9b3f3edd550c5e95ceee850be439e534b2ad7bfe4ce58495bf91f0 |
import pandas
import os
import os.path
##--------------------------------------------------------------------
## Simulation suite
## - "swissface"
## - "fluxnet"
## - "fluxnet2015"
## - "fluxnet_cnmodel"
## - "gcme"
## - "campi"
## - "campi_cmodel"
## - "fluxnet_fixalloc"
## - "atkin"
## - "atkinfull"
## - "olson"
## ... | stineb/sofun | get_sitelist_simsuite.py | Python | lgpl-2.1 | 1,708 | [
"NetCDF"
] | 659699c2402fed697dc0701740c246a7fa8057f311fa074ff606dceadd53f952 |
''' <h1> Library for specular magnetic x-ray reflectivity</h1>
The magnetic reflectivity is calculated according to: S.A. Stephanov and S.K Shina PRB 61 15304.
Note: The documentation is not updated from the interdiff model!
<h2>Classes</h2>
<h3>Layer</h3>
<code> Layer(b = 0.0, d = 0.0, f = 0.0+0.0J, dens = 1.0, magn_a... | joshp123/genx | models/xmag.py | Python | gpl-3.0 | 26,324 | [
"Gaussian"
] | b4c6f57683121ea79158c3381eecec98220f8d4d026f019ec60dd4bcb3feed53 |
#!/usr/bin/env python
#Copyright (C) 2013 by Glenn Hickey
#
#Released under the MIT license, see LICENSE.txt
import unittest
import sys
import os
import argparse
import logging
import itertools
import copy
from teHmm.common import runShellCommand
from teHmm.common import runParallelShellCommands
from teHmm.track impo... | glennhickey/teHmm | bin/teHmmBenchmark.py | Python | mit | 26,622 | [
"Gaussian"
] | cf4cd7cab6ef8682d654d6d09abd8022fd934f07ebb96ae5ce787e0199c0fde5 |
#!/usr/bin/env python
import os, sys, glob, gzip, math
from optparse import OptionParser
# Make sure to set the proper PYTHONPATH before running this script:
import FileUtils
import Fasta, AnalyzeSequence, Variant
def getPercentiles(hist = {}, pctiles = [ 1,5,10,25, 50, 75, 90, 95, 99]):
vals = sorted(hist.keys())... | genome/dindel-tgi | python/mergeOutputPooled.py | Python | gpl-3.0 | 22,740 | [
"VisIt"
] | 9ffc512a6b2de6486d90218bfa8c3e32370643cdd98e5f9106daf2a23a5183ec |
# -*- coding: utf-8 -*-
#
# Copyright © 2017 Mark Wolfman
#
# This file is part of Xanespy.
#
# Xanespy 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) an... | canismarko/xanespy | xanespy/fitting.py | Python | gpl-3.0 | 18,115 | [
"Gaussian"
] | a3b732a132b6b87ccce812fbbb9e93c7008457f9c68cc26ad9d8282dfcce0d59 |
#!/usr/bin/env python3
#pylint: disable=missing-docstring
#* 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
... | nuclear-wizard/moose | python/chigger/tests/annotations/time_annotation_change.py | Python | lgpl-2.1 | 1,218 | [
"MOOSE"
] | 8e6a2687d0ec3fb8321ae83d861df8e6c4fefced0b02f995a061f529aa751a5e |
# 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... | eadgarchen/tensorflow | tensorflow/contrib/timeseries/python/timeseries/state_space_models/varma.py | Python | apache-2.0 | 8,893 | [
"Gaussian"
] | 03dc363362f05267f2e6b977013235098dab655ab6ef57554c1208d39993d93f |
tests = [("python", "testPickers.py", {}), ("python", "testMaxMin.py", {})]
longTests = []
if __name__ == '__main__':
import sys
from rdkit import TestRunner
failed, tests = TestRunner.RunScript('test_list.py', 0, 1)
sys.exit(len(failed))
| rvianello/rdkit | Code/SimDivPickers/Wrap/test_list.py | Python | bsd-3-clause | 249 | [
"RDKit"
] | a525a832b2cbbd3e654521fa59df64a88973c8d85d7b3394baddd55df50616e6 |
#!/usr/bin/env python3
"""
This is to assign functional annotation to gene models using a wide variety of evidence. Meant to
support unlimited hierarchy rules, this utility relies on a user-created configuration file.
Current limitations:
- Rules are evaluated on a per-gene basis, so no rules are currently possible... | jorvis/Attributor | assign_functional_annotation.py | Python | apache-2.0 | 52,345 | [
"BLAST"
] | 53c50376c16b00f87ee6c064de46867831f1dce7e3fa9d86e7fb64a611d4b738 |
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