text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
from __future__ import absolute_import
import math
from collections import namedtuple
from PyQt4.QtGui import (
QWidget, QFrame, QLabel, QListWidget, QScrollArea, QSplitter,
QListView, QVBoxLayout, QGridLayout, QSizePolicy,
QPainter, QBrush, QPen, QPalette
)
from PyQt4.QtCore import Qt, QSize, QRectF, ... | tomazc/orange-bio | orangecontrib/bio/widgets/OWMoleculeVisualizer.py | Python | gpl-3.0 | 30,307 | [
"Pybel"
] | 1a68ad66e2c0a17f6cee8c79822cfa43ea278ab2ee982fb27594883c8de3d2a2 |
from PyQt4 import QtCore, QtGui
from vtk.qt4.QVTKRenderWindowInteractor import QVTKRenderWindowInteractor
import platform
import sip
import types
import vtk
class system:
systemType = platform.system()
AsciiToKeySymTable = ( None, None, None, None, None, None, None,
None, None,
... | rsmz/pyqvtkwidget | PyQVTKWidget.py | Python | gpl-2.0 | 30,206 | [
"VTK"
] | 11bc1646a5028ca30c2cde8781f93ca443550c0b40ee4d7e0f6bae2cec701127 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
r"""rna_pdb_edit_occupancy_bfactor.py - edit occupancy or bfactor in PDB file.
Example::
rna_pdb_edit_occupancy_bfactor.py --occupancy --select A:1-40,B:1-22 \
--set-to 0 \
19_Bujnicki_Human_4_rpr_... | mmagnus/rna-pdb-tools | rna_tools/tools/rna_pdb_edit_occupancy_bfactor/rna_pdb_edit_occupancy_bfactor.py | Python | gpl-3.0 | 6,158 | [
"Biopython"
] | 9182bf763ded49137ca2d7edfff904a417745224b62567baa4c08dd739d0ff6a |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
cc_plugin_ncei/ncei_base.py
'''
from __future__ import print_function
from compliance_checker.base import Result, BaseCheck, BaseNCCheck
from compliance_checker.cf.util import StandardNameTable, units_convertible
from cc_plugin_ncei import util
from cf_units import Uni... | ioos/cc-plugin-ncei | cc_plugin_ncei/ncei_base.py | Python | apache-2.0 | 80,767 | [
"NetCDF"
] | 904ed8a815504b035532141e949a200e13ddd131a8bb3e1972db89dc9517ed29 |
#!/usr/bin/env python
import vtk
def main():
colors = vtk.vtkNamedColors()
colors.SetColor("right_bkg", [0.4, 0.5, 0.6, 1.0])
colors.SetColor("left_bkg", [0.6, 0.5, 0.4, 1.0])
# Create an image
source = vtk.vtkImageSinusoidSource()
source.Update()
normalizeFilter = vtk.vtkImageNorma... | lorensen/VTKExamples | src/Python/ImageData/ImageNormalize.py | Python | apache-2.0 | 2,168 | [
"VTK"
] | 8e29407ca29e3c83e3a40d1bb808332ecc21d816756d9d6c5a9964c6cf532612 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | python/peacock/tests/utils/test_ExeLauncher.py | Python | lgpl-2.1 | 1,034 | [
"MOOSE"
] | 4a521cc7ff2d0cbc819d5404bc116ddd03346e34f57cebc6dd59278d2b747c1f |
"""Test the vtk.mutable() type and test pass-by-reference.
Created on Sept 19, 2010 by David Gobbi
"""
import sys
import vtk
from vtk.test import Testing
class TestMutable(Testing.vtkTest):
def testFloatMutable(self):
m = vtk.mutable(3.0)
n = vtk.mutable(4.0)
m *= 2
self.assertEqu... | b3c/VTK-5.8 | Common/Testing/Python/TestMutable.py | Python | bsd-3-clause | 1,602 | [
"VTK"
] | a6d32090e7b393f70df042b17efbd0880e48dcaa1710730def9c57f2944e357f |
"""
fillerbase Module
Classes to help fill widgets with data
Copyright (c) 2008-10 Christopher Perkins
Original Version by Christopher Perkins 2008
Released under MIT license.
"""
from .configbase import ConfigBase, ConfigBaseError
from .metadata import FieldsMetadata
import inspect
from datetime import datetime
en... | gjhiggins/sprox | sprox/fillerbase.py | Python | mit | 13,428 | [
"VisIt"
] | 30eb96b55ca57d20403257364f82234938551a3dc7e92a6de3969f0b19348449 |
"""
Copyright (c) 2009 John Markus Bjoerndalen <jmb@cs.uit.no>,
Brian Vinter <vinter@nbi.dk>, Rune M. Friborg <rune.m.friborg@gmail.com>.
See LICENSE.txt for licensing details (MIT License).
"""
from pycsp_import import *
import time
@process
def Prefix(cin, cout, prefixItem=None):
t = prefixItem
while... | runefriborg/pycsp | examples/Commstime.py | Python | mit | 1,622 | [
"Brian"
] | bf002c5ea9993380e674b92412e97b9dc41cc7a67616360de498827d894ff1ec |
"""
Code for computing cut-based free energy profiles, and optimal reaction coordinates
within that framework.
This code employs scipy's weave, so C/OMP compatability is required. Most machines
should have this functionality by default.
To Do
-----
> Choose best search method in `optimize`
> Add functionality for sa... | msmbuilder/msmbuilder-legacy | MSMBuilder/cfep.py | Python | gpl-2.0 | 19,701 | [
"MDTraj"
] | e5a4968bbb1e84e6a0b52e76da8fca6dec2fa90c4f18745062ae45adfabf95af |
"""
This file contains the outline of an implementation to load environment modules
(http://modules.sourceforge.net/).
This is a community contributed feature and the core Galaxy team does utilize
it, hence support for it will be minimal. The Galaxy team eagerly welcomes
community contribution and maintenance however.... | jmchilton/pulsar | galaxy/tools/deps/resolvers/modules.py | Python | apache-2.0 | 6,087 | [
"Galaxy"
] | 90c63fa1090a4afe543b02cb0efa2ea2a1e3d6aae2eb4776cc5e63a445c6a22c |
# Copyright 2010-2017, The University of Melbourne
# Copyright 2010-2017, Brian May
#
# This file is part of Karaage.
#
# Karaage 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... | brianmay/karaage | docs/conf.py | Python | gpl-3.0 | 1,895 | [
"Brian"
] | 49411c8fe7f7c7a42eeb17016944c139372e32c72711d21bb22320520a480b89 |
from __future__ import division, absolute_import, print_function
import numpy as np
from numpy.testing import (
TestCase, run_module_suite, assert_, assert_raises, assert_equal,
assert_warns, assert_array_equal, assert_array_almost_equal)
from numpy import random
from numpy.compat import asbytes
import... | nbeaver/numpy | numpy/random/tests/test_random.py | Python | bsd-3-clause | 59,057 | [
"Gaussian"
] | c861d37133229d61b267caeb6535e6790ffc6d695a981ac0d73aaa457171d0d2 |
"""
Copyright (C) 2011 N.D. Price Lab
This program 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, either version 3 of the License, or
(at your option) any later version.
This program is distributed in th... | JohnCEarls/AUREA | src/AUREA/adaptive/ResourceEstimate.py | Python | agpl-3.0 | 5,543 | [
"DIRAC"
] | 9d1698b48490cb7a823da8348bae7b8ff06f9697c5c2d16ffc92a2aee7845142 |
#!/bin/python
import vtk
import math
view = vtk.vtkContextView()
view.GetRenderer().SetBackground(1.0, 1.0, 1.0)
view.GetRenderWindow().SetSize(400, 300)
chart = vtk.vtkChartXY()
view.GetScene().AddItem(chart)
chart.SetShowLegend(True)
arrX = vtk.vtkFloatArray()
arrX.SetName("X Axis")
arrC = vtk.vtkFloatArray()... | trianam/tests | python/vtkPlot.py | Python | gpl-2.0 | 1,708 | [
"VTK"
] | a7045c488a10975428cab3053e5e0a4ccdbeac3673f0067b9c4312505af5b202 |
# Copyright (c) 2011 OpenStack Foundation
# All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless ... | Tesora-Release/tesora-trove | trove/guestagent/db/models.py | Python | apache-2.0 | 42,269 | [
"NAMD"
] | 4991ba3d5c4301fdc2e56838a47535f03eee33be87e928d07b9f583a0e36f7c7 |
# coding=utf-8
# Copyright 2019 Pants project contributors (see CONTRIBUTORS.md).
# Licensed under the Apache License, Version 2.0 (see LICENSE).
from __future__ import absolute_import, print_function
import fileinput
import functools
import json
import os
import re
import subprocess
import sys
from collections impor... | jsirois/pex | pex/pip.py | Python | apache-2.0 | 30,029 | [
"VisIt"
] | edbc2cf6dbe5028088d673ceab2ab54994b23124566679f0037891cf48b5894c |
#! /usr/bin/python
#
# Copyright (C) 2003-2014 ABINIT group
#
# Written by Matthieu Verstraete in python (compatible v1.9).
# This is free software, and you are welcome to redistribute it
# under certain conditions (GNU General Public License,
# see ~abinit/COPYING or http://www.gnu.org/copyleft/gpl.txt... | SamKChang/abinit-7.10.5_multipole | scripts/post_processing/get_irreps.py | Python | gpl-3.0 | 15,644 | [
"ABINIT"
] | e74afa93acbc102abb9adcbc992a63e97ac66c9cdb30a0299f211f27e4ba2954 |
#!/usr/bin/env python
"""
Add an existing transformation to an existing production.
Transformations already belonging to another production cannot be added.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import DIRAC
from DIRAC.Core.... | ic-hep/DIRAC | src/DIRAC/ProductionSystem/scripts/dirac_prod_add_trans.py | Python | gpl-3.0 | 2,507 | [
"DIRAC"
] | 696eb6ce9c1de50a0c623d27f863dc6072505bc7a132a67c981a6493fd84cbb5 |
## INFO ########################################################################
## ##
## formbuilder ##
## =========== ... | petervaro/formbuilder | views.py | Python | gpl-3.0 | 2,482 | [
"VisIt"
] | 5c221a1b909959041e97b57a8e6f37a173db1bd0ba43f0eed06e37d2bf2dc9df |
"""Metrics to assess performance on classification task given class prediction
Functions named as ``*_score`` return a scalar value to maximize: the higher
the better
Function named as ``*_error`` or ``*_loss`` return a scalar value to minimize:
the lower the better
"""
# Authors: Alexandre Gramfort <alexandre.gramf... | bnaul/scikit-learn | sklearn/metrics/_classification.py | Python | bsd-3-clause | 95,205 | [
"Brian"
] | cefcf14b1e39817460dd8d63fa1d21a7de86da6f99f00869e2e39a480a36869c |
#!/usr/bin/env python
import copy
from lsst.sims.catalogs.generation.db import queryDB
from lsst.sims.catalogs.measures.astrometry import Bbox
if __name__ == "__main__":
csize = 10
objects = ("GALAXY",)
myqdb = queryDB.queryDB(chunksize=csize, objtype="GALAXY")
ic = myqdb.getInstanceCatalogById(8574812... | lsst/sims_catalogs_generation | python/lsst/sims/catalogs/generation/deprecated/jobAllocator/simonTest1.py | Python | gpl-3.0 | 430 | [
"Galaxy"
] | a9cc1ada7e65e8165c07c10bc614d86a45977feaf575c13ffa2e81abdb74141b |
"""Metrics to assess performance on regression task.
Functions named as ``*_score`` return a scalar value to maximize: the higher
the better.
Function named as ``*_error`` or ``*_loss`` return a scalar value to minimize:
the lower the better.
"""
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# ... | manhhomienbienthuy/scikit-learn | sklearn/metrics/_regression.py | Python | bsd-3-clause | 41,871 | [
"Gaussian"
] | d6c0c999b5dc5b5c43432042f01c914f84611c2ad6991ffa4a48287ceff9e716 |
# Prepare per-patient clinical data
# TODO: Possibly incorporate Palumbo data
import os
from load_patient_data import load_per_patient_data
import numpy as np
import pandas as pd
pd.options.mode.chained_assignment = None
# Load input data
data, per_patient_dict, per_patient_fields = load_per_patient_data()
# Dictio... | xpspectre/multiple-myeloma | prep_patient_data.py | Python | mit | 8,458 | [
"VisIt"
] | 29e065d6396bb8917ae38441bea864f98af22d9e2237f633433c8296f537434f |
# -*- coding: utf-8 -*-
# YAFF is yet another force-field code.
# Copyright (C) 2011 Toon Verstraelen <Toon.Verstraelen@UGent.be>,
# Louis Vanduyfhuys <Louis.Vanduyfhuys@UGent.be>, Center for Molecular Modeling
# (CMM), Ghent University, Ghent, Belgium; all rights reserved unless otherwise
# stated.
#
# This file is pa... | molmod/yaff | yaff/examples/007_monte_carlo/co2_in_mil53/raspa.py | Python | gpl-3.0 | 1,403 | [
"RASPA"
] | c4a4f250f373b74984219001be7203983fd1155bf22da737f967e481dfcb589b |
#!/usr/bin/env python
import sys
import os
import logging
import plyvel
import argparse
from subprocess import call
from os.path import expanduser
from basta import FileUtils as futils
from basta import TaxTree as ttree
from basta import AssignTaxonomy
from basta import DownloadUtils as dutils
from basta import DBUti... | timkahlke/BASTA | basta/BastaMain.py | Python | gpl-3.0 | 8,636 | [
"BLAST"
] | d84909dbed2699ff0f106281ff22eb3c662e24ab9f911a4f24e8b204326a4690 |
import os
import sys
import vtkAll as vtk
import math
import time
import types
import functools
import numpy as np
from director import transformUtils
from director import lcmUtils
from director.timercallback import TimerCallback
from director.asynctaskqueue import AsyncTaskQueue
from director import objectmodel as om... | patmarion/director | src/python/director/drilldemo.py | Python | bsd-3-clause | 130,003 | [
"VTK"
] | 9aad6bb1d20612a36a3e213bca6a257e38207d6038a79d4eb931ee10f7a19b79 |
#!/usr/bin/env python
#
# $File: AcgtMutator.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can redistribut... | BoPeng/simuPOP | docs/AcgtMutator.py | Python | gpl-2.0 | 1,571 | [
"VisIt"
] | 0ed1f4f94135cd1639567842c8df15399415e62752e5d4436d8d892c5f17ac57 |
import logging
from datetime import datetime
from pathlib import Path
import h5py
import xarray
from numpy.ma import masked_invalid # for pcolormesh, which doesn't like NaN
from matplotlib.pyplot import figure, draw, close
from matplotlib.colors import LogNorm
from matplotlib.ticker import MultipleLocator
from matplot... | scienceopen/gridaurora | gridaurora/plots.py | Python | gpl-3.0 | 17,476 | [
"Gaussian"
] | 27bcd226af78b31c8b11aaadc82629809fb7f60ab4186c2c0ea2d11c1b4d56b8 |
# proxy module
from __future__ import absolute_import
from mayavi.modules.ui.iso_surface import *
| enthought/etsproxy | enthought/mayavi/modules/ui/iso_surface.py | Python | bsd-3-clause | 98 | [
"Mayavi"
] | 4ff3c89b537bc0d28d5e5d3c88e84d792e26aab2886a198ff4268ce156035ede |
#!/usr/bin/python
import mechanize
import bs4
import sys
def parseInput(input):
"""
Returns a tuple of type (input_type, course dep/None, courser num/crn)
given a user unput, parseInput does it's best to understand what is going on
It broadly accepst two types of input
1: CRN
Simple string of numbers
... | devty1023/peepingpete_dead | src/info_retrieve.py | Python | gpl-2.0 | 3,593 | [
"VisIt"
] | c5dd90f9f698581805bc32c22320b80e225b0dbddc73809623dcecf203c6fd09 |
#__docformat__ = "restructuredtext en"
# ******NOTICE***************
# optimize.py module by Travis E. Oliphant
#
# You may copy and use this module as you see fit with no
# guarantee implied provided you keep this notice in all copies.
# *****END NOTICE************
# A collection of optimization algorithms. Version ... | gfyoung/scipy | scipy/optimize/optimize.py | Python | bsd-3-clause | 104,490 | [
"Gaussian"
] | be2fb351a6f9b879daa6bdb33b3d06b7c47becf200c504f828521b76bc22286c |
# This file is part of rhizi, a collaborative knowledge graph editor.
# Copyright (C) 2014-2015 Rhizi
#
# This program 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, either version 3 of... | tlevine/rhizi | src/server/neo4j_cypher_parser.py | Python | agpl-3.0 | 27,434 | [
"VisIt"
] | 789358d3c11c39b891f79baff168c9089d0c84f24af35539b2daf6fe31339182 |
from gmi.mostusedsites.backend.models import Base, DBSession, User, Visit
from sqlalchemy import create_engine
from webtest import TestApp
import gmi.mostusedsites.backend as backend
import pytest
import transaction
@pytest.fixture(scope="session")
def app(request):
settings = {'sqlalchemy.url': 'sqlite:///:memor... | geyer-moldfusz/gmi.most_used_sites.backend | src/gmi/mostusedsites/backend/tests/conftest.py | Python | gpl-3.0 | 1,185 | [
"VisIt"
] | df4038af268e1356731b84c7a57a31e157da2e893a77a9115999ca2a6f5fc05e |
#!/usr/bin/env python
# Copyright 2014-2019 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/scf/uhf.py | Python | apache-2.0 | 39,122 | [
"PySCF"
] | 66e9f5f002103bb62087eb5bbbba0e9861d54780660c6f3433b9cf3a87dbac90 |
import json
import asyncio
import aiohttp
import websockets
from listen.errors import ListenError
from listen.objects import User, Song
from listen.utils import ensure_token
from listen.constants import (
AUTH_URL,
USER,
USER_FAVOURITES,
SONG_FAVOURITES,
SONG_REQUEST,
SOCKET_ENDPOINT
)
class... | GetRektByMe/Listen | listen/client.py | Python | mit | 4,830 | [
"MOE"
] | 5cc777aa9a691ea7118bfdbff0787bd65d9b521a527aee0cc954c01b1402a1d9 |
# http://networkx.github.io/documentation/latest/tutorial/tutorial.html
# http://code.enthought.com/projects/mayavi/
import networkx as nx
import numpy as np
import numpy.ma as ma
import itertools
from mayavi import mlab
# Generate graph to visualize
#H=nx.random_lobster(100,0.9,0.9)
#H=nx.balanced_tree(5, 2)
#H=nx.co... | fromeroj/iimas | distribuida/ejemplo.py | Python | mit | 2,185 | [
"Mayavi"
] | d321c9c18537c5624492ef8d84e33fd9fa22459048330e759153ed69d6589525 |
"""This test checks that the StrainFilter works using the default
built-in EMT calculator."""
import numpy as np
from ase.constraints import StrainFilter
from ase.optimize.mdmin import MDMin
from ase.calculators.emt import EMT
from ase.structure import bulk
cu = bulk('Cu', 'fcc', a=3.6)
class EMTPlus(EMT):
def g... | alexei-matveev/ase-local | ase/test/strain_emt.py | Python | gpl-2.0 | 468 | [
"ASE"
] | f82572200b10918a4660a21ccbfa2282c1e0fd66ede0c264fbe6889c3ea3aa4c |
#default python modules
import os
from datetime import datetime
#external packages
import numpy as np
import pandas as pd
from sklearn.externals import joblib
from sklearn.linear_model import Lasso
from sklearn.model_selection import train_test_split, GridSearchCV
from sklearn.neural_network import MLPClassifier
from s... | joekasp/ionic_liquids | ionic_liquids/test/test_utils.py | Python | mit | 5,560 | [
"RDKit"
] | 70f29e00906c7bd34805dc243990c884259585e332e4408f9b193e74907cdb02 |
# -*- coding: utf-8 -*-
import unittest
import logging
from nose.tools import * # flake8: noqa (PEP8 asserts)
import mock
from framework.auth.core import Auth
from website import settings
import website.search.search as search
from website.search import elastic_search
from website.search.util import build_query
from... | cldershem/osf.io | tests/test_elastic.py | Python | apache-2.0 | 26,984 | [
"Brian"
] | 412024e6c42bfc61c57b1d7693efcddf68872d5c952fc68c0eea6217e0d44ebd |
import os.path
from collections import defaultdict
import numpy as np
import pysam
class Bam(object):
def __init__(self, filename):
""" Basic wrapper for pysam module, to allow the quick pulling of pileups
for a certain region
Arguments:
----------
filename = The full pat... | McIntyre-Lab/papers | newman_events_2017/python_workflow/programs/mclib_Python/bam.py | Python | lgpl-3.0 | 4,148 | [
"pysam"
] | c7b1dde9c97e62a9def97ffec8a0a24dbde0fdf2ce6aee7ff2feb74e18244144 |
from __future__ import unicode_literals
import csv
import itertools
import re
from mptt.forms import TreeNodeMultipleChoiceField
from django import forms
from django.conf import settings
from django.core.validators import URLValidator
from django.urls import reverse_lazy
COLOR_CHOICES = (
('aa1409', 'Dark red')... | snazy2000/netbox | netbox/utilities/forms.py | Python | apache-2.0 | 19,262 | [
"Amber"
] | 9881a3a6f7e4b09082e482f3b48c575c1e5246410fd23d05b5b715688ab7b7d2 |
from mock import Mock
import unittest
from nav.models.manage import Netbox, Room
class MetaClassTestCase(unittest.TestCase):
def setUp(self):
self.maxDiff = None
self.netbox = Mock(name='Netbox', spec=Netbox)
self.netbox.pk = 1337
self.netbox.id = self.netbox.pk
self.netbox... | alexanderfefelov/nav | tests/unittests/netmap/metaclass_testcase.py | Python | gpl-2.0 | 756 | [
"Galaxy"
] | 944d9388732affade78b1950d07977a5f4c7dbe3fcc4e43d744ce13abf540f81 |
#!/usr/bin/env python
"""
MagPy-General: Standard pymag package containing the following classes:
Written by Roman Leonhardt, Rachel Bailey 2011/2012/2013/2014
Written by Roman Leonhardt, Rachel Bailey, Mojca Miklavec 2015/2016
Version 0.2 (starting 28.02.2015)
"""
from __future__ import print_function
# -------------... | leonro/magpy-git | magpy/stream.py | Python | gpl-3.0 | 471,297 | [
"Gaussian",
"NetCDF"
] | efccf840978af3f9a81b504c5bf1d17e20fd2b45452f5fa346620d05a6a85231 |
# Paperwork - Using OCR to grep dead trees the easy way
# Copyright (C) 2012-2014 Jerome Flesch
#
# Paperwork 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
... | Starch/paperwork | src/paperwork/frontend/settingswindow/__init__.py | Python | gpl-3.0 | 38,070 | [
"ADF"
] | ee85e4395184699740d648f7121eeec06072c3858272af4b4039b4d2f9bee2ec |
"""Tornado handlers for WebSocket <-> ZMQ sockets.
Authors:
* Brian Granger
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2008-2011 The IPython Development Team
#
# Distributed under the terms of the BSD License. The full license is in
# the file COPYING, dis... | WillisXChen/django-oscar | oscar/lib/python2.7/site-packages/IPython/html/base/zmqhandlers.py | Python | bsd-3-clause | 6,064 | [
"Brian"
] | 571184f85b5da2ebf58f95c5ab8b374c9c42b4c565659a32f8d078b5e1dd08a1 |
import numpy as np
from .control import model_setup
from .cp_confocal import twod, threed
from .cp_triplet import trip
from .cp_mix import triple_pnum
def CF_Gxyz_gauss_3D3D2DT(parms, tau):
u""" Two three-dimensional and one two-dimensional free diffusion
with a Gaussian laser profile, including a triple... | paulmueller/PyCorrFit | pycorrfit/models/model_confocal_t_3d_3d_2d.py | Python | gpl-2.0 | 5,809 | [
"Gaussian"
] | 4e10b34e505decc97311d303e78876571876ea06cb63cafa30e1bf963554228b |
#!/usr/bin/python
import os, sys # low level handling, such as command line stuff
import string # string methods available
import re # regular expressions
import getopt # comand line argument handling
from low import * # custom functions, written by myself
import anydbm # index databases (file ... | lotharwissler/bioinformatics | python/fasta/generate-fasta-aa-nt.py | Python | mit | 3,295 | [
"Biopython"
] | 9540181e272ad0674ad39e8581e816de3755ba61944ad427746fe85ccff4115c |
# -*- coding: utf-8 -*-
"""
Created on Fri June 23 09:30:00 2017
@author: S.Y. Agustsson
"""
import sys
import numpy as np
from scipy import misc
import matplotlib.pyplot as plt
from matplotlib import cm
import cv2
import pyqtgraph as pg
from PyQt5 import QtWidgets as qw, QtCore as qc, QtGui as qg
import time
# impo... | steinnymir/BeamProfiler | legacy/BeamProfilerLib/gui.py | Python | gpl-3.0 | 14,308 | [
"Gaussian"
] | 352e65797f119cd66570bbe8a9ca1c4ec53ed64fb2d69bbac3e3cb5d15a1acdc |
"""
Foote method for segmentation, published here:
Foote, J. (2000). Automatic Audio Segmentation Using a Measure Of Audio
Novelty. In Proc. of the IEEE International Conference of Multimedia and Expo
(pp. 452-455). New York City, NY, USA.
"""
__author__ = "Oriol Nieto"
__copyright__ = "Copyright 2014, Music and Audi... | urinieto/SegmenterMIREX2014 | foote.py | Python | bsd-3-clause | 1,264 | [
"Gaussian"
] | da8289bd548da9898ffb168b72dc7e35f76f291cb5aace00a85f291c06afca80 |
"""
Slightly more specialized than methods in the ``util.strings`` module,
provides functions for parsing and extracting information from strings
that follow some expected nomenclature. The primary examples of this
information are IDs, names, labels, and other metadata for files and
objects generated either by Illumina... | BenaroyaResearch/bripipetools | bripipetools/parsing/__init__.py | Python | mit | 1,022 | [
"Galaxy"
] | ab007eececc5541ba6448609410dca9c9be6f08d959109bef87c2875468d8a45 |
# -*- coding: utf-8 -*-
"""
Newspaper uses much of python-goose's extraction code. View their license:
https://github.com/codelucas/newspaper/blob/master/GOOSE-LICENSE.txt
Keep all html page extraction code within this file. Abstract any
lxml or soup parsing code in the parsers.py file!
"""
__title__ = 'newspaper'
__a... | srujant/MLNews | newspaper/extractors.py | Python | mit | 36,554 | [
"Brian"
] | efd2c2848b0ecc3d99e24c35e5dec295b7ddc0f54241f3b13b1a402940af29ec |
import copy
import csv
import datetime
import json
import mock
import re
import urllib
import pyquery
from cStringIO import StringIO
from nose.tools import eq_, ok_, assert_raises
from nose.plugins.skip import SkipTest
from django.test.client import RequestFactory
from django.test.utils import override_settings
from ... | pcabido/socorro | webapp-django/crashstats/crashstats/tests/test_views.py | Python | mpl-2.0 | 194,289 | [
"VisIt"
] | 86f49c8f8a16b952649027c134ae7e135f1836e4f006be6c8e65b0462e52e591 |
#!/usr/bin/python
# (c) 2017, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
# most of it copied from AWX's scan_packages module
from __future__ import absolute_import, division, print_function
__metaclass__ = type
DOCUMENTATION = '''
module: package_fac... | nitzmahone/ansible | lib/ansible/modules/package_facts.py | Python | gpl-3.0 | 16,794 | [
"Brian"
] | 341069d9c6507a7093e217b1279b0a7a2d3a80413ade4e06e57bbe3906b862a8 |
#!/usr/bin/env python
import time, os
import random
import writeInputs
import threading as mt
import tarfile
import radical.entk as re
import radical.utils as ru
#os.environ['RADICAL_VERBOSE'] = 'INFO'
os.environ['RADICAL_ENTK_VERBOSE'] = 'INFO'
os.environ['RADICAL_PILOT_DBURL'] = 'mongodb://smush:key1209@ds263816.... | radical-cybertools/radical.repex | old/repex/async_repex.py | Python | mit | 15,118 | [
"Amber"
] | 71e4e7b926854560dc148decba4df98d05c860e8d4930c3426d3e52600398dc4 |
#!/usr/bin/env python
# Copyright (C) 2013-2017 Steven Myint
#
# Permission is hereby granted, free of charge, to any person obtaining
# a copy of this software and associated documentation files (the
# "Software"), to deal in the Software without restriction, including
# without limitation the rights to use, copy, mo... | myint/rstcheck | rstcheck.py | Python | mit | 31,580 | [
"VisIt"
] | 582799299709bf254db679bb20b6c35145882621a6b93e4044d1259761f0ed1c |
# Copyright 2007-2021 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 ... | thomasaarholt/hyperspy | hyperspy/tests/signals/test_eds_sem.py | Python | gpl-3.0 | 15,337 | [
"Gaussian"
] | bf8716fceefc74c8e090cd010699cf3f39a01b59ffe054ff0044f3a43953c635 |
#!/usr/bin/env python
"""Universal feed parser
Handles RSS 0.9x, RSS 1.0, RSS 2.0, CDF, Atom 0.3, and Atom 1.0 feeds
Visit http://feedparser.org/ for the latest version
Visit http://feedparser.org/docs/ for the latest documentation
Required: Python 2.4 or later
Recommended: CJKCodecs and iconv_codec <http://cjkpytho... | Arno-Nymous/pyload | module/lib/feedparser.py | Python | gpl-3.0 | 167,083 | [
"NetCDF",
"VisIt"
] | 525fcb0ccbc1ad3442a3a2cee9428718d954eabf3b5a17ef76a01c34ed5761e3 |
import os
import re
from django.contrib.auth.models import User
from django.db import models
from django.db.models import Q
from django.utils import timezone
from django.utils.html import escape
from django.utils.safestring import mark_safe
from django.utils.translation import ugettext_lazy as _
from djblets.util.db i... | viswimmer1/PythonGenerator | data/python_files/32676780/models.py | Python | gpl-2.0 | 67,150 | [
"VisIt"
] | 6bcd3aedf8cea917dae6fed3fdcae63aaeb8f16b1c953fd2dfa6b8d6b2f76919 |
import datetime
import os
import uuid
import warnings
import zipfile
from typing import Dict, List, Set, Tuple, Union
import dateutil.parser
import geopy
import netCDF4
import numpy as np
import pandas
import pint
import pyresample
import xarray
import xarray.core.variable
from cachetools import TTLCache
from flask_ba... | DFO-Ocean-Navigator/Ocean-Data-Map-Project | data/netcdf_data.py | Python | gpl-3.0 | 40,517 | [
"Gaussian",
"NetCDF"
] | 83aaeb0dd2b59a143a77c481fd734d5d62ad32532b337c526f388d4cb99e96c8 |
#!/usr/bin/python
"""
Copyright (c) 2011-2015 Nathan Boley, Marcus Stoiber
This file is part of GRIT.
GRIT 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... | nboley/grit | grit/proteomics/ORF.py | Python | gpl-3.0 | 10,272 | [
"Biopython",
"pysam"
] | c7f059ac3bbf8d11cd9c1350d385a39ba2302daf8d9e9ebd4c5e2563a390e113 |
import cv2
import numpy as np
import sys
print()
def rectify(h):
h = h.reshape((4,2))
hnew = np.zeros((4,2),dtype = np.float32)
add = h.sum(1)
hnew[0] = h[np.argmin(add)]
hnew[2] = h[np.argmax(add)]
diff = np.diff(h,axis = 1)
hnew[1] = h[np.argmin(diff)]
hnew[3] = h[np.argmax(diff)]
... | Hubert51/AutoGrading | learning/main_v1.py | Python | mit | 28,594 | [
"Gaussian"
] | b306ff57f96a6fa078cd75a6ff3e4cf56873f6f15423e1af3d7844d03f7b41be |
import sys
sys.path.insert(1,"../../../")
import h2o
from tests import pyunit_utils
import random
from h2o.estimators.gbm import H2OGradientBoostingEstimator
def cv_cars_gbm():
# read in the dataset and construct training set (and validation set)
cars = h2o.import_file(path=pyunit_utils.locate("smalldata/junit/c... | madmax983/h2o-3 | h2o-py/tests/testdir_algos/gbm/pyunit_cv_cars_gbm.py | Python | apache-2.0 | 6,995 | [
"Gaussian"
] | e269b17d9d8195a9ceace4b0d8060bac4c3477482bc26f9ae0b3bd83e681ea76 |
# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
from types import IntType
__doc__="Class that maps (chain_id, residue_id) to a residue pr... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/PDB/AbstractPropertyMap.py | Python | apache-2.0 | 3,335 | [
"Biopython"
] | 5aef52b7a43651a08d3d3e03ce3ba77e3906eb901feff8c479147f8f9ec1935c |
# 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
#
# Unless required by appl... | gkc1000/pyscf | pyscf/nao/m_xjl.py | Python | apache-2.0 | 1,736 | [
"PySCF"
] | 88a8d841194a54c013db3d0cb3bb807725390760c14886f7f1caf43c14b7d32f |
"""Python bindings for core 0MQ objects."""
#
# Copyright (c) 2010-2011 Brian E. Granger & Min Ragan-Kelley
#
# This file is part of pyzmq.
#
# pyzmq is free software; you can redistribute it and/or modify it under
# the terms of the Lesser GNU General Public License as published by
# the Free Software ... | IsCoolEntertainment/debpkg_python-pyzmq | zmq/core/__init__.py | Python | lgpl-3.0 | 1,560 | [
"Brian"
] | 9207db77aa5e9391a31724802568bcc9ae6425e261deb7c7cde9f38a3bd309d7 |
"""Crossover classes, that cross the elements in the supplied
atoms objects.
"""
import random
import numpy as np
from ase.ga.offspring_creator import OffspringCreator
class ElementCrossover(OffspringCreator):
"""Base class for all operators where the elements of
the atoms objects cross.
"""
def __... | suttond/MODOI | ase/ga/element_crossovers.py | Python | lgpl-3.0 | 5,533 | [
"ASE"
] | c952c159372b90a6405e1e470cfc5a369b8ad0cb6b5e6be946847a69662f4758 |
'''
An example of using Tilting module with ASE
'''
from __future__ import print_function
import unittest
from ase.lattice.spacegroup import crystal
import set_path
from tilde.core.settings import settings
from tilde.core.api import API
from tilde.parsers import Output
crystal_obj = crystal(
('Sr', 'Ti', 'O',... | ansobolev/tilde | tests/apps/perovskite_tilting/ase_example.py | Python | mit | 1,667 | [
"ASE",
"CRYSTAL"
] | 15055dd51bff5634c4cbcbd564d1c6080c99691260191ad018717257ad66aa2c |
__all__ = ['fixed_quad','quadrature','romberg','trapz','simps','romb',
'cumtrapz','newton_cotes']
from scipy.special.orthogonal import p_roots
from scipy.special import gammaln
from numpy import sum, ones, add, diff, isinf, isscalar, \
asarray, real, trapz, arange, empty
import numpy as np
import math... | teoliphant/scipy | scipy/integrate/quadrature.py | Python | bsd-3-clause | 26,478 | [
"Gaussian"
] | e6bd607da2d3281b8e9c9d0d9c13936e6f9a5d372e3850f5b5d786f9b7306427 |
#!/usr/bin/env python2
desc="""Identify enhanvers (eRNAs) from RNA-Seq.
Enhancers are defined as genomic regions having similar level of expression.
It's rather slow right now, 17h per fish genome (1.5G). Instead consider bam2cov_pool.py approach:
# get 100bp windows of non-coding part of the genome
w=500; awk -F'\t... | lpryszcz/bin | bam2enhancers.py | Python | gpl-3.0 | 4,595 | [
"pysam"
] | caf576930797fa8fb4a362aa486f76f8258f30ee71e57b29fa31e74f1300ffff |
# !usr/bin/env python
# -*- coding: utf-8 -*-
#
# Licensed under a 3-clause BSD license.
#
# @Author: Brian Cherinka
# @Date: 2018-04-04 23:07:41
# @Last modified by: Brian Cherinka
# @Last Modified time: 2018-10-18 14:12:38
from __future__ import absolute_import, division, print_function
import copy
from marvin... | sdss/marvin | python/marvin/utils/datamodel/dap/MPL7.py | Python | bsd-3-clause | 1,180 | [
"Brian"
] | 31d191559ba5735150986b285015566f51e618db052d338502c13188635c56a9 |
from __future__ import absolute_import, division, print_function, unicode_literals
from gratipay.testing import BrowserHarness
class Tests(BrowserHarness):
def test_sign_in_modal_is_hidden_by_default(self):
self.visit('/')
assert not self.css('#sign-in-modal').visible
def test_clicking_sig... | gratipay/gratipay.com | tests/ttw/test_sign_in.py | Python | mit | 923 | [
"VisIt"
] | 71210e0aa8f1bc3f0896e7d326287cd06c57b8203bc9c4bd5a7034b2ce8d2f71 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Author: Andrew Jewett (jewett.aij at g mail)
# http://www.chem.ucsb.edu/~sheagroup
# License: 3-clause BSD License (See LICENSE.TXT)
# Copyright (c) 2012, Regents of the University of California
# All rights reserved.
from ttree_lex import InputError
# Users ... | ganzenmg/lammps_current | tools/moltemplate/src/lttree_styles.py | Python | gpl-2.0 | 9,573 | [
"LAMMPS"
] | 443db80d523f07910cb9acdfacc2ddb429bbec37efa74b9f39ad98a21640902a |
#!/usr/bin/env python
#
# Copyright 2013 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Convert Android xml resources to API 14 compatible.
There are two reasons that we cannot just use API 17 attributes,
so we are ge... | mdakin/engine | build/android/gyp/generate_v14_compatible_resources.py | Python | bsd-3-clause | 11,922 | [
"Galaxy"
] | 0c7cbd438e8eca4d63f6d764f8a12828918850c8e10b77f3306eefca4a519d5d |
#
# Copyright (C) 2007, Mark Lee
#
#http://rl-glue-ext.googlecode.com/
#
# 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... | mguzdial3/MineCode | python-codec/src/rlglue/RLGlue.py | Python | apache-2.0 | 5,110 | [
"Brian"
] | c1f6a89ef5274f9ad1c5648df2b61592689cfdff9ba2d7c4b4fb3ee92bad3429 |
import numpy as np
from math import exp, log
import random
import scipy.stats
import matplotlib.pyplot as plt
from copy import deepcopy
#Feature size
N = 2
#Model parameters
Theta = np.array([random.gauss(0,1) for i in range(N)])
def LogPrior(theta_p):
'''
Return prior pdf. Multivariate gaussian, Cov = diag(... | dmancevo/Bayesian_Classifier | Bayesian_Classifier.py | Python | mit | 2,404 | [
"Gaussian"
] | 5216dabfbea8a0f39afd823178a20b73c6c00e18aac86379aee47592a47b9bbf |
import ConfigParser
import logging
import os
import re
from galaxy import util
from galaxy import web
from galaxy.web.form_builder import build_select_field
from galaxy.webapps.tool_shed.model import directory_hash_id
from tool_shed.dependencies.repository import relation_builder
from tool_shed.util import common_ut... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/tool_shed/util/repository_util.py | Python | gpl-3.0 | 18,642 | [
"Galaxy"
] | 49322a06550093745fb104ec9205a3900a9274ad0eeda07bd12cee97e3480ed4 |
import vtk
def get_program_parameters():
import argparse
description = 'Converts the polydata to imagedata and masks the given imagedata.'
epilogue = '''
Contributed by: Peter Gruber
'''
parser = argparse.ArgumentParser(description=description, epilog=epilogue)
parser.add_argument('fil... | lorensen/VTKExamples | src/Python/PolyData/PolyDataToImageDataStencil.py | Python | apache-2.0 | 2,880 | [
"VTK"
] | 12e645896fba7f8240d5e1765326444b23b2585b11ecf11e1294783c1989af1e |
# -*- coding: utf-8 -*-
#
# This file is part of Invenio.
# Copyright (C) 2013, 2014, 2015 CERN.
#
# Invenio is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License as
# published by the Free Software Foundation; either version 2 of the
# License, or (at your optio... | tiborsimko/invenio-ext | invenio_ext/script/__init__.py | Python | gpl-2.0 | 12,590 | [
"VisIt"
] | 93f9d1660c2b84252f5b2d6e4d9564d16df91e21b47e4f8e33997c19e1dae0ef |
# Copyright (C) 2012-2015 Codethink Limited
#
# 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; version 2 of the License.
#
# This program is distributed in the hope that it will be useful,
# but... | tacgomes/morph | morphlib/cachekeycomputer_tests.py | Python | gpl-2.0 | 6,074 | [
"Brian"
] | c522d945181fd3df9db73637d42caa422fa6b561e67381c1c7f9f8ffa7c7b8ec |
#!/usr/bin/python3
# -*- coding: utf-8 -*-
from setuptools import setup
from os import chdir, makedirs, walk
from os.path import abspath, dirname, join, relpath
from shutil import copy
from subprocess import check_call
def read(path):
with open(path) as f:
return f.read().strip()
# identify and enter ... | brbsix/caffeine-reloaded | setup.py | Python | lgpl-3.0 | 2,082 | [
"Brian"
] | 2c9de1d4ddd9e26f6e9e2d545a2de31d1fe682d3c20b5fe560175de5641df0c9 |
# Copyright 2015 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Dummy benchmarks for the bisect FYI integration tests.
The number they produce aren't meant to represent any actual performance
data of the browser. For m... | was4444/chromium.src | tools/perf/benchmarks/dummy_benchmark.py | Python | bsd-3-clause | 1,656 | [
"Gaussian"
] | 8b518dae4eddd6b21a6f55a53e7c972d14d10b434ea747ab8394894b57e39aa8 |
# Copyright (C) 2017-2020 The Software Heritage developers
# See the AUTHORS file at the top-level directory of this distribution
# License: GNU Affero General Public License version 3, or any later version
# See top-level LICENSE file for more information
import json
import random
from hypothesis import given
from... | SoftwareHeritage/swh-web-ui | swh/web/tests/browse/views/test_revision.py | Python | agpl-3.0 | 11,989 | [
"VisIt"
] | 55974f8bfeac4fdb99d65e6b43ce646f3986face052b73016b96d3fff69b41ab |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | susilehtola/psi4 | psi4/driver/procrouting/proc.py | Python | lgpl-3.0 | 202,663 | [
"Psi4"
] | 9ecc3689916dad8cd9b0e686225f170d8e5a720fa6d32cf0f39f2f3c3338c7fc |
#!/usr/bin/env python3
"""Test the basic properties of the deast module."""
# Copyright © 2017 Timothy Pederick
#
# 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... | perey/deast | tests/test_module.py | Python | apache-2.0 | 1,931 | [
"VisIt"
] | 2a9049f7d8a4fb0f011f1def9187212af3f49e9e1618303faa126e582a361317 |
#!/usr/bin/env python
'''
GOAL:
- this code contains all of the code to make figures for MS paper
REQUIRED MODULES
- LCSbase.py
**************************
written by Gregory Rudnick
June 2018
**************************
'''
###########################
###### IMPORT MODULES
###########################
import LCSba... | rfinn/LCS | python/LCS_MSpaper.py | Python | gpl-3.0 | 116,120 | [
"Galaxy"
] | 634d722a5da89164b3c00c57e6f4e56403277ca1149721207057e2a6f8559d88 |
import numpy as np
from numpy import pi
import wave
import scipy
import scipy.io.wavfile
from scipy import signal
import matplotlib.pyplot as plt
import math
import pygame.sndarray
import time
import pyaudio
SAMPLING_RATE = 192000
SAMPLES_PER_MS = int(SAMPLING_RATE / 1000)
CARRIER_FREQ = 5000
CLOCK_MS = 100
NUM_BIT... | labseven/SigsysFinalProject | signal_functions.py | Python | mit | 10,932 | [
"Gaussian"
] | 76481d33d15d50224652c1ecb20c217d36044af6ce619d25d6db3d166cd8503c |
import tempfile
import textwrap
import os
try:
from StringIO import StringIO
except ImportError:
from io import StringIO
import numpy as np
from nose.tools import ok_, eq_
from mock import patch
import neurom.io as io
from neurom.io.datawrapper import DataWrapper
import neurom.io.neurolucida as nasc
from neu... | liesbethvanherpe/NeuroM | neurom/io/tests/test_neurolucida.py | Python | bsd-3-clause | 8,012 | [
"NEURON"
] | 6a9d52e43273d86af0c469ff6a27dc77d2ef22878344ec675b67e945ea87938a |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
try:
import urllib3
except:
print('BlastPDB requires urllib3')
class BlastPDB:
"""BlastPDB - run Blast online on the PDB database.
This can be used in Jupiter based RNA notebooks, e.g.
https://github.com/mmagnus/rna-pdb-tools/blob/master/rp18.ipynb
... | mmagnus/rna-pdb-tools | rna_tools/BlastPDB.py | Python | gpl-3.0 | 1,141 | [
"BLAST"
] | dc3253268894d422c034bb0a7a57eeccea1f1f20f1b6e1a2357687fa9e01ffcc |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import print_function
#
# PCR-GLOBWB (PCRaster Global Water Balance) Global Hydrological Model
#
# Copyright (C) 2016, Edwin H. Sutanudjaja, Rens van Beek, Niko Wanders, Yoshihide Wada,
# Joyce H. C. Bosmans, Niels Drost, Ruud J. van der Ent, Inge E. M. de... | UU-Hydro/PCR-GLOBWB_model | model/configuration.py | Python | gpl-3.0 | 31,987 | [
"NetCDF"
] | 65020cc0f8398ac6167678e71383ed864cb0dcc5b07ff11486961b75657f0595 |
# -*- encoding: utf-8
# Setup code, stay away
items = []
item = lambda *x: items.append(x)
# News items go here, most recent ones at top. Dates can be either
# strings or time(3) output.
#
# item("INSERT TITLE HERE",
# (1901, 3, 1),
# """
# INSERT TEXT HERE
# """,
# "INSERT AUTHOR HERE")
# ht... | saigkill/gnome-publisher | web/newsitems.py | Python | gpl-3.0 | 16,101 | [
"exciting"
] | e0139236bdbff0d2aa788e513a28beb988a12c5022ff4a161fd82d15a2066566 |
from .mdtraj_json import *
import pytest
import numpy as np
import numpy.testing as npt
from ..simstore.custom_json import bytes_codec, numpy_codec, custom_json_factory
from ..simstore.test_custom_json import CustomJSONCodingTest
from openpathsampling.tests.test_helpers import data_filename
class MDTrajCodingTest(C... | choderalab/openpathsampling | openpathsampling/experimental/storage/test_mdtraj_json.py | Python | lgpl-2.1 | 2,273 | [
"MDTraj"
] | d4849aa73d14c9f4ddc3cfb69809caa66ee076cce471385914e2b2e10a54b24f |
# Copyright 2010-2014 Google
# 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 writing, so... | 2947721120/curly-hockeypuck | src/ortools/linear_solver/linear_solver_natural_api.py | Python | apache-2.0 | 6,999 | [
"VisIt"
] | 8d37607ca7a50ac270e7bcac9815ee928a1a481a39938a5894fe6686290c1ec6 |
########################################################################
# $HeadURL$
# File : ExecutorReactor.py
# Author : Adria Casajus
########################################################################
__RCSID__ = "$Id$"
import time
import threading
from DIRAC import S_OK, S_ERROR, gLogger, rootPath, gConfi... | Sbalbp/DIRAC | Core/Base/ExecutorReactor.py | Python | gpl-3.0 | 8,253 | [
"DIRAC"
] | 3444d1f349b640c43f83a113d5407795d52e163f46c072f8a85c26c02c0a5739 |
from __future__ import division
from builtins import map
from builtins import zip
from builtins import str
from builtins import range
from builtins import object
import json
import numpy as np
import os
try:
from osgeo import ogr
except ImportError:
import ogr
try:
from osgeo import osr
except ImportEr... | mauroalberti/beePen | geosurf/geo_io.py | Python | gpl-3.0 | 23,172 | [
"VTK"
] | 338426cdb662d9c63c6274fc9cb191857553342aba36ce3c919405ea73c320ef |
import cPickle as pickle
galaxies = pickle.load(open('galaxies.pickle','rb'))
galaxies = filter(lambda galaxy: galaxy.ston_I > 30., galaxies)
for galaxy in galaxies:
print int(galaxy.ID), galaxy.RA, galaxy.DEC
| boada/ICD | sandbox/legacy_plot_code/printstuff.py | Python | mit | 216 | [
"Galaxy"
] | 6a81cc708f8175affbe03ce5187a1ae1876c21d39d71f28f6f7d94dc7e88b06f |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2017 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB ... | yashdsaraf/scancode-toolkit | src/licensedcode/index.py | Python | apache-2.0 | 33,611 | [
"VisIt"
] | 86a6d55ce2db93beea5dbca7ec9c332404b8c68b500e1777aa8a1cea98ad08af |
import numpy
import six
import chainer
from chainer.functions.array import permutate
from chainer.functions.array import transpose_sequence
from chainer.functions.rnn import n_step_rnn as rnn
from chainer import initializers
from chainer import link
from chainer.utils import argument
from chainer import variable
def... | pfnet/chainer | chainer/links/rnn/n_step_rnn.py | Python | mit | 12,967 | [
"Gaussian"
] | 9e01e5f2a84ac6bf525b2751f82983ad95882b43494160dee1da74f36854e198 |
#!/usr/bin/env python
from vtk import *
source = vtkRandomGraphSource()
source.DirectedOff()
source.SetNumberOfVertices(10)
source.SetEdgeProbability(0.22)
source.SetUseEdgeProbability(True)
source.AllowParallelEdgesOn()
source.SetStartWithTree(True)
# Connect to the centrality filter.
centrality = vtkBoo... | hlzz/dotfiles | graphics/VTK-7.0.0/Examples/Infovis/Python/boost_mst.py | Python | bsd-3-clause | 1,801 | [
"VTK"
] | 94ace7b2e95e07a7ff16d718e278d1d3cf202f27e67c233fb444e2b23ffdafdd |
import unittest, re, sys
sys.path.extend(['.','..','../..','py'])
import h2o, h2o_cmd, h2o_import as h2i
print "FIX!: Avoiding an RF histogram assertion error on some of these datasets"
DO_RF = False
class Basic(unittest.TestCase):
def tearDown(self):
h2o.check_sandbox_for_errors()
@classmethod
... | 111t8e/h2o-2 | py/testdir_single_jvm/test_parse_many_doublesp_fvec.py | Python | apache-2.0 | 7,474 | [
"Dalton"
] | d7062722c7fd02a744dc317e32a50a26795a952d1ce41adf882e076ab739d4bd |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.