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 |
|---|---|---|---|---|---|---|---|
#!/usr/bin/env python
# $HeadURL$
"""
Perform initial sanity checks on WN, installs and configures DIRAC and runs
Job Agent to execute pending workload on WMS.
It requires dirac-install script to be sitting in the same directory.
"""
__RCSID__ = "$Id$"
import os
import sys
import getopt
import urllib2
import stat
i... | SuperDIRAC/DIRAC | WorkloadManagementSystem/PilotAgent/dirac-pilot.py | Python | gpl-3.0 | 28,246 | [
"DIRAC"
] | 26ffd822646934ee612a57e2f30bf9fc01c4be38d7fe59b019b115e383a1cb15 |
# coding: utf-8
"""
Vericred API
Vericred's API allows you to search for Health Plans that a specific doctor
accepts.
## Getting Started
Visit our [Developer Portal](https://developers.vericred.com) to
create an account.
Once you have created an account, you can create one Application for
Production and an... | vericred/vericred-python | test/test_zip_county_response.py | Python | apache-2.0 | 10,047 | [
"VisIt"
] | 2f59c5dbf7b13875eb4044e9f3786601a5cdc06ba5ad04eef9225b7fab584214 |
import math
import operator
from collections import defaultdict
from numpy.core.multiarray import zeros
from tabfile import TabFile
class CharDict(defaultdict):
"""
CharDict is a generalized dictionary that inherits defaultdict.
default values are 0. Accepts any keys.
"""
def __init__(self, dict={... | benjschiller/seriesoftubes | bioplus/motif.py | Python | artistic-2.0 | 13,949 | [
"Biopython"
] | 1c5a73df924f767974f9df17d6469e1b7ebe3d28f4b09a6041811835003c981d |
#! /usr/bin/env python
from ppclass import pp
########
## ppclass allows for getting fields very easily from a netcdf file
## ... this is contained in the "f" attributes of the pp object
## ... and the "l" attributes of the pp object contains useful information
## ... two methods getf() and getfl() are helpful shortcu... | aymeric-spiga/planetoplot | examples/ppclass_additional/easy_get_field.py | Python | gpl-2.0 | 2,209 | [
"NetCDF"
] | 64a41c77f1b2b64d927f43e68de21c9c0d528ea65650db0234852ed0a8dd013b |
# -*- coding: utf-8 -*-
"""
Created on Tue Aug 30 08:57:31 2016
@author: nicholas
"""
import sys
import logging
import os
import unittest
from riboSeed.riboSeed import NgsLib, nonify_empty_lib_files
logger = logging
@unittest.skipIf((sys.version_info[0] != 3) or (sys.version_info[1] < 5),
"Subpro... | nickp60/riboSeed | tests/test_NgsLib.py | Python | mit | 5,902 | [
"BWA"
] | 218db59aa5dbf84dca43830fd2dfde68c7bfa2ce9ffe43b24ccec48ace5cafb2 |
from django.contrib import admin
from collections import OrderedDict
from edc.export.actions import export_as_csv_action
from edc.subject.appointment.admin import BaseAppointmentModelAdmin
from bhp074.apps.eit_lab.models import MaternalRequisition
from ..models import MaternalVisit
from ..forms import MaternalVisitF... | botswana-harvard/edc-bhp074 | bhp074/apps/eit_maternal/admin/maternal_visit_admin.py | Python | gpl-2.0 | 2,145 | [
"VisIt"
] | dd565972b4976c02215f25ae89430bdb832f82d8e156d049e32206a697d81458 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# 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)
#
# Released under t... | MDAnalysis/mdanalysis | package/MDAnalysis/lib/picklable_file_io.py | Python | gpl-2.0 | 15,899 | [
"MDAnalysis"
] | 6cb99208694e02848698c9bae59cd8f23fba4d274522834d0895b1725e89947b |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | zhreshold/mxnet | example/distributed_training-horovod/resnet50_imagenet.py | Python | apache-2.0 | 17,959 | [
"Gaussian"
] | a7f2e22497e1aa4576ff039449de51ca9f53be046f3d68d1c872c72efa7b4ffd |
#===============================================================================
# LICENSE XOT-Framework - CC BY-NC-ND
#===============================================================================
# This work is licenced under the Creative Commons
# Attribution-Non-Commercial-No Derivative Works 3.0 Unported Li... | SMALLplayer/smallplayer-image-creator | storage/.xbmc/addons/net.rieter.xot.smallplayer/resources/libs/cache/cachedhttpresponse.py | Python | gpl-2.0 | 4,532 | [
"VisIt"
] | 5813f3cae9ab82405d6d04acb94819a3d5f80a7fe7db7f8cfae5e9e94a085193 |
import numpy as np
from .shared import StaticContainerStore, StaticContainer, unmask_quantity
from openpathsampling.netcdfplus import WeakLRUCache
import openpathsampling as paths
variables = ['statics']
lazy = ['statics']
storables = ['statics']
dimensions = ['n_atoms', 'n_spatial']
_length_unit = "simtk(unit.nano... | choderalab/openpathsampling | openpathsampling/engines/features/statics.py | Python | lgpl-2.1 | 3,355 | [
"MDTraj",
"OpenMM"
] | 8c504bf228be85ac5d78d3dd94ea5e2b2e50e1ac1483f8b3f1c3b62e813dc9f1 |
# -*- coding: utf-8 -*-
"""
trueskill
~~~~~~~~~
The video game rating system.
:copyright: (c) 2012-2015 by Heungsub Lee
:license: BSD, see LICENSE for more details.
"""
from __future__ import absolute_import
from itertools import chain
import math
from six import iteritems
from six.moves import map,... | Ninjakow/TrueSkill | lib/trueskill/__init__.py | Python | gpl-3.0 | 27,585 | [
"Gaussian"
] | 5172cb3abb1a2de21a501dc6bb74b7f7d1b593f39f0d19bd1a6c0134f5825980 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
urlpatterns = [
url(r'^about/$', TemplateView.as_view... | JadsonReis/osmcha-django | config/urls.py | Python | gpl-3.0 | 1,228 | [
"VisIt"
] | dfc5574e676b125dfab7a098ed9c8bf63c83d174a80a8a1556df248cbf584e87 |
import os
from .stl_general_test import CStlGeneral_Test, CTRexScenario
from trex_stl_lib.api import *
import pprint
def avg (values):
return (sum(values) / float(len(values)))
# performance report object
class PerformanceReport(object):
GOLDEN_NORMAL = 1
GOLDEN_FAIL = 2
GOLDEN_BETTER = 3
de... | kisel/trex-core | scripts/automation/regression/stateless_tests/stl_performance_test.py | Python | apache-2.0 | 14,351 | [
"Elk"
] | 5f037992447dcb94528e6e980809d28b2c0fee97a4ca1eea6f319d21d1b37305 |
#! /usr/bin/env python
import re
import math
import collections
import numpy as np
import time
import operator
from scipy.io import mmread, mmwrite
from random import randint
from sklearn import cross_validation
from sklearn import linear_model
from sklearn.grid_search import GridSearchCV
from sklearn import preproces... | Goodideax/CS249 | predict_svm_combine_1000.py | Python | bsd-3-clause | 14,603 | [
"Gaussian"
] | bb3bb566631be81e639ce523d48fb8bcef8454075d8c5a5b4e59ca8006002908 |
# coding: utf-8
from __future__ import division, unicode_literals
'''
Created on Oct 24, 2012
@author: shyue
'''
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2011, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep@gmail.com"
__status__ = "Production"
__dat... | Dioptas/pymatgen | pymatgen/analysis/tests/test_bond_valence.py | Python | mit | 2,450 | [
"pymatgen"
] | 2f4b2c86133d411dc54140c09db1b1121b3397a9d2ec6e9d04da2dd57fcc0f1c |
# -*- coding: utf-8 -*-
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import textwrap
import py
import pytest
from _pytest.config import PytestPluginManager
from _pytest.main import EXIT_NOTESTSCOLLECTED
from _pytest.main import EXIT_OK
from _pytest.main... | cloudera/hue | desktop/core/ext-py/pytest-4.6.11/testing/test_conftest.py | Python | apache-2.0 | 19,666 | [
"VisIt"
] | 8f964641b09ac376cb669e34c22dbebec369f601aca2edf5f8055604d239b99d |
import os, sys, re
import optparse
import shutil
import pandas
import numpy
import subprocess
#import time
#####################################
#This is the wrapper for luciphor2.
#It will be responsible for taking command line arguments and building a
#configuration file for running of luciphor2 to help localize PTM... | wohllab/milkyway_proteomics | galaxy_milkyway_files/tools/wohl-proteomics/luciphor2/luciphor_wrapper.py | Python | mit | 32,505 | [
"Galaxy"
] | c11766ca47439895d1fd65c55e9b0b183b60347cf5d54a716ee60a433dc8d229 |
import ast
import datetime
import re
import time
from collections import defaultdict
from datetime import timedelta
from typing import (
AbstractSet,
Any,
Callable,
DefaultDict,
Dict,
Iterable,
List,
Optional,
Sequence,
Set,
Tuple,
TypeVar,
Union,
)
import django.con... | brainwane/zulip | zerver/models.py | Python | apache-2.0 | 128,981 | [
"VisIt"
] | f86c70a5bb374a148889db0b2bf2a7d994902dbb43bbcb186099b9372beb13c7 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Yambo(AutotoolsPackage):
"""Yambo is a FORTRAN/C code for Many-Body calculations in solid
... | iulian787/spack | var/spack/repos/builtin/packages/yambo/package.py | Python | lgpl-2.1 | 5,358 | [
"ABINIT",
"NetCDF",
"Yambo"
] | 5f239bf882fe25bd770360bdcf2731f28e943368043fb4e18e0bffd9cceb7020 |
import numpy as np
from meshio import Mesh
from meshio.vtk_io import vtk_to_meshio_type
def read(filetype, filename):
import vtk
from vtk.util import numpy as numpy_support
def _read_data(data):
"""Extract numpy arrays from a VTK data set."""
# Go through all arrays, fetch data.
... | nschloe/meshio | tests/legacy_reader.py | Python | mit | 6,813 | [
"VTK"
] | 47d0ae5f360636c44bad8a73aa62ca0fc6371f62c3449ca3ccd33bcc28a4ecf0 |
from __future__ import print_function
import time
from numpy import pi, sin, cos, linspace
from bokeh.browserlib import view
from bokeh.document import Document
from bokeh.models.glyphs import Line
from bokeh.models import (
Plot, DataRange1d, LinearAxis, Range1d,
ColumnDataSource, PanTool, WheelZoomTool
)
f... | akloster/bokeh | examples/glyphs/line_animate.py | Python | bsd-3-clause | 1,296 | [
"VisIt"
] | 4bd090e72513a17ab07614580414c815837906ccff070b9ad0543f4695bfd375 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 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
#... | jH0ward/psi4 | psi4/driver/procrouting/findif_response_utils/db_helper.py | Python | lgpl-3.0 | 6,374 | [
"Psi4"
] | ea7628867d398b90e92e8f52e7b66c49e95a32ad4779171811365982059bbde2 |
import numpy
import pylab
import moose
import time
def main():
"""
This example implements a reaction-diffusion like system which is
bistable and propagates losslessly. It is based on the NEURON example
rxdrun.py, but incorporates more compartments and runs for a longer time.
The system is implemen... | BhallaLab/moose-examples | snippets/rxdReacDiffusion.py | Python | gpl-2.0 | 2,651 | [
"MOOSE",
"NEURON"
] | 69ddbcfdd9480544c0172a7fd56df24b934a4861e2babc53e34ad91a97bfa75f |
from common2 import *
# NAME IDEA -> pooling/random/sparse/distributed hebbian/horde/crowd/fragment/sample memory
# FEATURES:
# + boost -- neurons with empty mem slots learn faster
# + noise --
# + dropout -- temporal disabling of neurons
# + decay -- remove from mem
# + negatives -- learning to avoid detecting some... | mobarski/sandbox | rsm/v9le/v5.py | Python | mit | 8,419 | [
"NEURON"
] | 7656ff0172adf122ea32e874fb283769242a7d4811d5bc2fe0e01ef715937d81 |
"""Substitution matrices and associated functions.
Several of these are originally imported from BioPython.
Substitution matrices are similarity and not distance matrices.
Matrices are represented in two ways in this module and there are
converters that go from one to the other:
(1) Parameters called "subst" are ... | agartland/seqdistance | matrices.py | Python | mit | 4,539 | [
"Biopython"
] | 5bdb403e4a30c2a58ceb7b1eeeb4af3b0e5d9f244392365b76ebcd61cff90a15 |
#!/usr/bin/env python
__author__ = 'Mike McCann,Duane Edgington,Reiko Michisaki'
__copyright__ = '2015'
__license__ = 'GPL v3'
__contact__ = 'duane at mbari.org'
__doc__ = '''
Master loader for all CANON activities in May 2015
Mike McCann and Duane Edgington
MBARI 11 May 2015
@var __date__: Date of last svn ... | stoqs/stoqs | stoqs/loaders/CANON/loadCANON_may2015.py | Python | gpl-3.0 | 17,046 | [
"NetCDF"
] | 6ae054fea7bb2d367b7cc9a16135316a171aa0145bb050341f32c519d6ca0a1c |
import dbus as _dbus
from razer.client.devices import RazerDevice as __RazerDevice, BaseDeviceFactory as __BaseDeviceFactory
from razer.client.devices.firefly import RazerFirefly as __RazerFirefly
from razer.client.devices.keyboard import RazerKeyboardFactory as __RazerKeyboardFactory
from razer.client.devices.mice imp... | z3ntu/razer-drivers | pylib/razer/client/device.py | Python | gpl-2.0 | 2,599 | [
"Firefly"
] | c614b52b22f1741b37ecad15270bf12bf867df3737e56a2f1285963da97d371c |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | demis001/scikit-bio | skbio/stats/_misc.py | Python | bsd-3-clause | 935 | [
"scikit-bio"
] | 923af26a0ccb685eeaf9b684057f8e57194da1e129237a835020ff4d4af68bc2 |
# -*- coding: iso-8859-15 -*-
# ISO-3166 alpha country codes - ver 1
ISO3166CountryCodesAlpha= { "ABW":"Aruba",\
"AFG":"Afghanistan",\
"AGO":"Angola",\
"AIA":"Anguilla",\
"ALA":"Åland Islands",\
"ALB":"Albania",\
"AND":"Andorra",\
"ANT":"Netherlands Antilles",\
"ARE":"United Arab Emirate... | kaosbeat/datakamp | RFIDIOt-master/rfidiot/iso3166.py | Python | mit | 16,392 | [
"BWA"
] | 8364efd8fea1dfb6ce361618eec50718d2809cb42e52b2d61f8e8810abc09ddc |
#!/usr/bin/env python
#David Hoover, based on gatk by Dan Blankenberg
"""
A wrapper script for running the GenomeAnalysisTK.jar commands.
"""
import sys, optparse, os, tempfile, subprocess, shutil
from binascii import unhexlify
GALAXY_EXT_TO_GATK_EXT = { 'gatk_interval':'intervals', 'bam_index':'bam.bai', 'gatk_dbsn... | mr-c/tools-iuc | tools/gatk2/gatk2_wrapper.py | Python | mit | 7,377 | [
"Galaxy"
] | 80d509564f52bb0bd464c36c615e525a9cdbcb92062ea47a32c6134aa7e9fa10 |
"""
Base class for factories for adding objects to the pipeline.
"""
# Author: Gael Varoquaux <gael.varoquaux@normalesup.org>
# Copyright (c) 2007, Enthought, Inc.
# License: BSD Style.
import warnings
from auto_doc import make_doc
from traits.api import HasPrivateTraits, Str, TraitError,\
Instance, Any... | liulion/mayavi | mayavi/tools/pipe_base.py | Python | bsd-3-clause | 7,617 | [
"Mayavi",
"VTK"
] | b9d2dfc4e878e937aed669a43b89e69e623790572e470e74086253423a434e1d |
# coding:utf-8
"""
视频抓取脚本
"""
# coding:utf-8
"""
数据库配置
"""
from urllib import quote
from pymongo import MongoClient
DEBUG = False
# mongo
NEW_USER = "username"
NEW_PASSWORD = quote("password")
if DEBUG:
NEW_HOST_PORT = "ip:port"
else:
NEW_HOST_PORT = "ip:port"
NEW_DATABASE = "db_name"
NEW_MONGO_URL = "mongodb:... | China-00-com/china-00-com-movie | spiders/video_spider.py | Python | gpl-3.0 | 26,182 | [
"MOE"
] | f32fe0d215d00f4f23c77bbf2ed42e9dce568aa0e84f4527e3d9fda09f5edd9d |
# Copyright 2018 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... | frreiss/tensorflow-fred | tensorflow/python/distribute/input_lib.py | Python | apache-2.0 | 110,264 | [
"VisIt"
] | 8e75d4f3521b6afa769a03ce167c951c1e4d61ec46590ad908666518e1b0bc3f |
"""
Deployment file to facilitate releases of pymatgen.
Note that this file is meant to be run from the root directory of the pymatgen
repo.
"""
__author__ = "Shyue Ping Ong"
__email__ = "ongsp@ucsd.edu"
__date__ = "Sep 1, 2014"
import glob
import os
import json
import webbrowser
import requests
import re
import subp... | Dioptas/pymatgen | fabfile.py | Python | mit | 4,612 | [
"pymatgen"
] | 96f4288050e2f6ec0268d7a34cba278cdecc9ebd0daec1554f6d8f2d8d6c99e3 |
# Orca
#
# Copyright 2005-2009 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/orca_gtkbuilder.py | Python | gpl-3.0 | 5,479 | [
"ORCA"
] | 327b462cac8b3ceb74ab913c18ad4daa1ad002a832444e63a527ae409e07b50d |
#!/usr/bin/env python
#Retreives data from UCSC and stores in a file. UCSC parameters are provided in the input/output file.
import urllib, sys, os, gzip, tempfile, shutil
from galaxy import eggs
#from galaxy.datatypes import data
from galaxy.util import gzip_magic
assert sys.version_info[:2] >= ( 2, 4 )
def stop_err... | dbcls/dbcls-galaxy | tools/experimental/data_source.py | Python | mit | 2,363 | [
"Galaxy"
] | 498425d6b4d5716cfacd3b704c7484656bc132e7c567d0cce998d3ab154771e8 |
"""
__init__.py
State Estimation and Analysis for PYthon
Module for working with oceanographic data and models
Copyright (c)2010--2021 University of Hawaii under the MIT-License.
Requires the following packages: joblib, rich, cartopy, numpy_groupies
Import classes include:
- :class:`~seapy.environ... | powellb/seapy | seapy/__init__.py | Python | mit | 1,330 | [
"NetCDF"
] | cc7cca627a6a8aebf162b92967089b2bc3a80090970ccff66a14ad6c8a885a7b |
# -*- coding: utf-8 -*-
import order
import re
class ParseConfig(object):
"""
This class parse a template file of a configuration file for a server application.
the `self.input` of the instance variable is the template file for the server application.
the `self.abstract` of the instance variable is a intermediat... | KNCT-KPC/RapidHouse | rapidhouse/lib/parseconfig.py | Python | mit | 3,514 | [
"VisIt"
] | 850d947d4898f5ee295e24a6f3f3427e978d7d6761565dc467ee0f241f4d89dc |
from random import *
# sig : doc
rrand_dists = {
# (a, b) : in half-open or close interval, "depending on rounding" (???)
'uniform': uniform,
# (low=0.0, high=1.0, mode=None) : low and hight are bounds. for mode wikipedia /Triangular_distribution
'triangular': triangular,
'normal': [
# (mu... | ransomw/dotfiles | pyutils/cookbook/plot_random.py | Python | apache-2.0 | 657 | [
"Gaussian"
] | 062138aea0cc0572026227249ee3768f9bf2b3ce1fa5af5cbc238bfac7ab67bb |
#
# plots.py -- Utility functions for plotting.
#
# Eric Jeschke (eric@naoj.org)
#
# Copyright (c) Eric R. Jeschke. All rights reserved.
# This is open-source software licensed under a BSD license.
# Please see the file LICENSE.txt for details.
#
import numpy
import matplotlib as mpl
from matplotlib.figure import Figu... | Cadair/ginga | ginga/util/plots.py | Python | bsd-3-clause | 12,879 | [
"Gaussian"
] | d92ca9cf3e02c4fee60c99eaed87252887d9f0f453d846b6109836e96b347a81 |
# 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... | fweik/espresso | testsuite/scripts/tutorials/test_convert.py | Python | gpl-3.0 | 14,187 | [
"ESPResSo"
] | 1cd84ceb5a7e4733d0262ea6a50bd4056a3e4614277d741d5756e8a82143513b |
# -*- coding: utf-8 -*-
import tweepy
def performOauthDance(auth):
print('Please visit:', auth.get_authorization_url())
verifier = input('Verification token:')
try:
auth.get_access_token(verifier)
print('\n'.join([
'Authentication data is:',
'ACCESS_TOKEN=%s' % auth... | runjak/hoodedfigure | oauthDance.py | Python | mit | 483 | [
"VisIt"
] | e4209638aba9070bfe5459d349a0da719704536b23300a6819b6fd3229401089 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | var/spack/repos/builtin/packages/r-snprelate/package.py | Python | lgpl-2.1 | 2,803 | [
"Bioconductor"
] | 73841b59fbbe4ea15fddbf460c3d110b226a435451b2fe66b5722dfa0405764e |
import sys
import pyranges as pr
import pandas as pd
def get_fasta(gr, path=None, pyfaidx_fasta=None):
"""Get fasta sequence.
Parameters
----------
gr : PyRanges
Coordinates.
path : str
Path to fasta file. It will be indexed using pyfaidx if an index is not found
pyfaidx_f... | biocore-ntnu/pyranges | pyranges/get_fasta.py | Python | mit | 3,179 | [
"Bioconda"
] | 9c44533c81533dfdda72ce4018434e00fe8baf834042bcf1be646b79dc3790b9 |
#
# Copyright 2018 Analytics Zoo 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... | intel-analytics/analytics-zoo | pyzoo/test/zoo/chronos/forecaster/test_seq2seq_forecaster.py | Python | apache-2.0 | 8,709 | [
"ORCA"
] | e2bebd990c6e2d412023336d00bbdb5d13351b27c7df1ae7f4cfb848d20ff338 |
#!/usr/bin/env python
# Generate a number of FLML files from a base directory
# manipulating various parameters to explore parameter
# space
# Ouput structure is:
# output_dir/
# template (copied in if not already here)
# runs/
# 1/
# run.flml
# other defined files
# 2
# 3
# dire... | FluidityProject/multifluids | scripts/create_param_sweep.py | Python | lgpl-2.1 | 7,778 | [
"NetCDF"
] | 293b9dbaa7f1cabe1f4e6e7b2c6ac49f80961a8e947fab83927603f59a03648e |
""" core implementation of testing process: init, session, runtest loop. """
import py
import pytest, _pytest
import inspect
import os, sys, imp
try:
from collections import MutableMapping as MappingMixin
except ImportError:
from UserDict import DictMixin as MappingMixin
from _pytest.mark import MarkInfo
tra... | c0710204/mirrorsBistu | pypi/bandersnatch/lib/python2.7/site-packages/_pytest/main.py | Python | mit | 22,859 | [
"VisIt"
] | 94df7d5b2cb7df463bf31fb802af1951fa488491cef29c27fb8cf06c140a46b5 |
from unittest import TestCase
from pymatgen.util.sequence import get_chunks, PBarSafe
class SequenceUtilsTest(TestCase):
def setUp(self):
self.sequence = list(range(100))
def test_get_chunks(self):
lengths = [len(chunk) for chunk in get_chunks(self.sequence, 30)]
self.assertTrue(all(... | gVallverdu/pymatgen | pymatgen/util/tests/test_sequence.py | Python | mit | 639 | [
"pymatgen"
] | 8944cf93106f6de65cc09b74b6cd683de2ce4d8d48c76e6589ec8bdaf56428d3 |
#!/usr/bin/env python
# Reports a beta diversity matrix for tabular input file
# using scikit-bio
# Daniel Blankenberg
import io
import optparse
import sys
from skbio import TreeNode
from skbio.diversity import beta_diversity
__VERSION__ = "0.0.1"
DELIMITER = '\t'
NEEDS_TREE = ['unweighted_unifrac', 'weighted_un... | loraine-gueguen/tools-iuc | tools/scikit-bio/scikit_bio_diversity_beta_diversity.py | Python | mit | 3,695 | [
"scikit-bio"
] | 80334950bfeff7ac91089ad2372fc30935a77b4c6ff9daab6842de77223a379e |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#**************************************************************************
#
# $Id: PGG_Simulator.py $
# $Revision: v18 $
# $Author: epichler $
# $Date: 2014-11-07 $
# Type: Python program.
#
# Comments: Runs a Public Goods Game simulator.
#
# Usage:
# Use the `-h' flag for fu... | avishapiro/public-goods-game-simulator | src/PGG_Simulator.py | Python | lgpl-3.0 | 16,592 | [
"Gaussian"
] | 66b8f24cc265ce23536f7c3b923ef3422ef60ef968c37f5e39c7d67bc860e7ee |
#!/usr/bin/python
"""
Transform FreeSurfer surfaces to the original space of a given image.
Copyright 2011 Arno Klein (arno@mindboggle.info) after
https://gist.github.com/1459725 by Satrajit Ghosh
Apache License, Version 2.0
"""
import os, sys
import numpy as np
import nibabel as nb
from tvtk.api imp... | binarybottle/mindboggle_sidelined | freesurfer_to_native_space_OLD_gifti.py | Python | apache-2.0 | 4,961 | [
"Mayavi",
"VTK"
] | 4b1c201d1aa295e65c9c06cd911e712109e50150374da46f77e006d6e4ecc399 |
# Mantid Repository : https://github.com/mantidproject/mantid
#
# Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
# NScD Oak Ridge National Laboratory, European Spallation Source
# & Institut Laue - Langevin
# SPDX - License - Identifier: GPL - 3.0 +
import unittest
from mantid.simpleapi import... | mganeva/mantid | scripts/test/VesuvioProfileTest.py | Python | gpl-3.0 | 12,366 | [
"Gaussian"
] | ce9262c2279004de43e06c709b0f87c8f9505c5cf23a44368841f91aee5c7d88 |
# Orca
#
# Copyright 2010 Joanmarie Diggs, Mesar Hameed.
#
# 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.
#
# ... | h4ck3rm1k3/orca-sonar | src/orca/scripts/toolkits/Gecko/keymaps.py | Python | lgpl-2.1 | 4,099 | [
"ORCA"
] | 6c3a20872dee7de76120a87e97dec6cd1ef9dec5a388ef243d1c5912c4aaaf62 |
from qcodes.instrument.base import Instrument
from qcodes.utils import validators as vals
from qcodes.instrument.parameter import ManualParameter
import numpy as np
class NoiseParametersCZ(Instrument):
'''
Noise and other parameters for cz_superoperator_simulation_new
'''
def __init__(self, name, *... | DiCarloLab-Delft/PycQED_py3 | pycqed/instrument_drivers/virtual_instruments/noise_parameters_CZ_new.py | Python | mit | 7,569 | [
"Gaussian"
] | 41592b1d8ea32a0d9ac990ea24067e0904711e14d5d202ad533b5b91354413c8 |
# ----------------------------------------------------------------------
# Numenta Platform for Intelligent Computing (NuPIC)
# Copyright (C) 2017-2018, Numenta, Inc. Unless you have an agreement
# with Numenta, Inc., for a separate license for this software code, the
# following terms and conditions apply:
#
# This p... | neuroidss/nupic.research | htmresearch/frameworks/location/path_integration_union_narrowing.py | Python | agpl-3.0 | 23,428 | [
"Gaussian"
] | d9e52327d58e3818346a4e8521b2048f8ab1cfa6ef3b837b46db439d3e0b658e |
##############################################################################
# Copyright (c) 2013-2017, 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... | wscullin/spack | var/spack/repos/builtin/packages/r-go-db/package.py | Python | lgpl-2.1 | 1,691 | [
"Bioconductor"
] | 3890d4b51208be9b6fa71d5cbbe8dcd18d8368291441426b33467d030d22f45c |
# 24.05.2007, c
# last revision: 25.02.2008
from sfepy import data_dir
from sfepy.fem.periodic import *
filename_mesh = data_dir + '/meshes/2d/special/channels_symm944t.mesh'
if filename_mesh.find( 'symm' ):
region_1 = {
'name' : 'Y1',
'select' : """elements of group 3""",
}
region_2 = {
... | olivierverdier/sfepy | examples/navier_stokes/stokes.py | Python | bsd-3-clause | 4,109 | [
"VTK"
] | e89da51952d7d404ac169c7423be38d5fabb024223163b1cb58a1405ff548386 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, division, print_function
import os
import py.path
import pytest
import sys
import _pytest.pytester as pytester
from _pytest.pytester import HookRecorder
from _pytest.pytester import CwdSnapshot, SysModulesSnapshot, SysPathsSnapshot
from _pytest.config impo... | tareqalayan/pytest | testing/test_pytester.py | Python | mit | 13,187 | [
"Brian"
] | 7c9a593c29108603a336d9547624f0333cec67a79fafbee6a0f12b709131d4d9 |
#########################################################################
## This program is part of 'MOOSE', the
## Messaging Object Oriented Simulation Environment.
## Copyright (C) 2014 Upinder S. Bhalla. and NCBS
## It is made available under the terms of the
## GNU Lesser General Public License version 2... | dilawar/moose-full | moose-examples/snippets/gssaCylinderDiffusion.py | Python | gpl-2.0 | 6,418 | [
"MOOSE"
] | e0fda5259d53f7e69eb1f24f2a72cd47d03e398f7024f2a391fbfb8f2107259e |
# (c) 2014 Michael DeHaan, <michael@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 Foundation, either version 3 of the License, or
# (at your option) any later ve... | ravello/ansible | v2/ansible/playbook/role/metadata.py | Python | gpl-3.0 | 3,133 | [
"Galaxy"
] | affb12a32979165828ffe3e5fd570a484d0a0bba7e6f975d04ba7e02a8ea4486 |
from pymol.wizard import Wizard
from pymol import cmd
import pymol
class Annotation(Wizard):
def get_event_mask(self):
return Wizard.event_mask_scene+Wizard.event_mask_state+Wizard.event_mask_frame
def do_scene(self):
self.cmd.dirty_wizard()
def do_frame(self,frame):
... | gratefulfrog/lib | python/pymol/wizard/annotation.py | Python | gpl-2.0 | 2,654 | [
"ChemPy",
"PyMOL"
] | 242217a5a1edc9dfacb71c3822a33bb66564417418455dd20a254dabab420b78 |
import sys
sys.path.insert(1, "../../../")
import h2o, tests
def distribution_behaviorGBM():
#Log.info("==============================")
#Log.info("Default Behavior - Gaussian")
#Log.info("==============================")
eco = h2o.import_file(path=tests.locate("smalldata/gbm_test/ecology_model.csv"))
... | kyoren/https-github.com-h2oai-h2o-3 | h2o-py/tests/testdir_algos/gbm/pyunit_loss_behaviorGBM.py | Python | apache-2.0 | 2,973 | [
"Gaussian"
] | 575db2075f13e2917d7ec8ac6716adcff9b31bfcd44326e1332eca531b73ff37 |
#!/usr/bin/env python
import vtk
import numpy as np
from vmtk import vmtkscripts
import argparse
import copy
import sys
# extract region boundaries
class GetBoundaries():
def __init__(self, args):
self.Surface = None
self.InputFile = args.surface
self.OutputFile = args.file_out
... | kayarre/Tools | vmtk/get_boundary.py | Python | bsd-2-clause | 19,895 | [
"VTK"
] | f4bcd9cd44918efdd2ab3f0b01b319bae6230f97e64aa311bc21df079d5e26c1 |
# Copyright 2007 by Tiago Antao <tiagoantao@gmail.com>.
# Revisions copyright 2014 by Melissa Gymrek <mgymrek@mit.edu>.
# 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... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/Bio/PopGen/SimCoal/Controller.py | Python | apache-2.0 | 11,919 | [
"Biopython"
] | d9efbcedd621e0001693a5180d4ecef16e9dca912dc872ae3ce18166e81fc77f |
#!/usr/bin/env python
'''
setup board.h for chibios
'''
import argparse, sys, fnmatch, os, dma_resolver, shlex
parser = argparse.ArgumentParser("chibios_pins.py")
parser.add_argument(
'-D', '--outdir', type=str, default=None, help='Output directory')
parser.add_argument(
'hwdef', type=str, default=None, help=... | dgrat/ardupilot | libraries/AP_HAL_ChibiOS/hwdef/scripts/chibios_hwdef.py | Python | gpl-3.0 | 32,533 | [
"CRYSTAL"
] | 16e129c3932074f192c777ea47e955e4200b95f4a0f43660c8ab803312aab1da |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from rauth import OAuth2Service
print '\n\n##############################################################'
print '################## PYTHON MONEYBIRD OAUTH2 ###################'
print '##############################################################'
print(
"\nBefore yo... | sanderkwantes/moneybird-python-api | tools/get_access_token.py | Python | mit | 4,463 | [
"VisIt"
] | 9658a5d54787107d6082e15f71eb0d3206adb37493b45eaf7d1c816f114489ea |
import numpy as np
import random
from scipy.ndimage import zoom
from skimage.util import view_as_blocks
import tensorflow as tf
import sys
sys.path.append('../..')
from util import load_images, load_regions
def _float_feature(value):
return tf.train.Feature(float_list=tf.train.FloatList(value=value))
def _int64_fe... | gvanhorn38/active_neurofinder | baselearners/tf/generate_inputs.py | Python | mit | 6,259 | [
"NEURON"
] | 22bfb0671692b47ddd6caec8ec9fd5594eb9f15de394be0fc370805efc8a80db |
# Orca
#
# Copyright 2012 Igalia, S.L.
#
# Author: Joanmarie Diggs <jdiggs@igalia.com>
#
# 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 o... | chrys87/orca-beep | src/orca/orca_gui_navlist.py | Python | lgpl-2.1 | 5,857 | [
"ORCA"
] | de38758f87eb049bd84a14c615c6c0a363ccf5d06a7701dc05ea347b4ae17e55 |
"""
Methods for interpolating data from structured data sets on Thetis fields.
Simple example of an atmospheric pressure interpolator:
.. code-block:: python
def to_latlon(x, y, positive_lon=False):
# Converts mesh (x,y) points to coordinates used in the atm data
lon, lat = coordsys_spcs.spcs2lo... | tkarna/cofs | thetis/interpolation.py | Python | mit | 31,094 | [
"NetCDF"
] | 1aa9164af59dd034291167ee68430ccefbbb6193739a71eb51d8b99702571a5d |
# This file is part of DmpBbo, a set of libraries and programs for the
# black-box optimization of dynamical movement primitives.
# Copyright (C) 2018 Freek Stulp
#
# DmpBbo 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 ... | stulp/dmpbbo | python/dmp/Dmp.py | Python | lgpl-2.1 | 15,749 | [
"Gaussian"
] | 28c335a9bd003bd753e68563f835ac5fee37399432d299c5b7433932975a48c6 |
'''
Created on 24 Nov 2015
@author: wnm24546
'''
from scipy.constants import c, h, k, pi
from scipy.optimize import curve_fit
from collections import OrderedDict
import numpy as np
from Lucky.LuckyExceptions import BadModelStateException
#k is kb
class CalculationService(object):
def __init__(self, pp):
... | mtwharmby/lucky | Lucky/src_Mike_GUI_Total/Lucky/Calculations.py | Python | apache-2.0 | 20,095 | [
"Gaussian"
] | dab88bda50e83c5f74bd456d13ac943888cfc5e502b8046d549230eaa836ee6b |
#!/home/elsa/Ureka/variants/common/bin/python
from mpl_toolkits.mplot3d import Axes3D
from matplotlib import cm
from matplotlib.ticker import LinearLocator
from matplotlib.mlab import griddata
import matplotlib.pyplot as plt
import numpy as np
##By Elsa Johnson
##Heat filter algorithm by Sam Gerber (originally written... | ElsaMJohnson/pythonprograms | ThreeDGalaxy/proc_3dgal.py | Python | mit | 8,283 | [
"Gaussian"
] | be3564772b43a3cf8850d334bb46984102a4db17fbda44e0ccd7507d38675281 |
#!/usr/bin/env python
#
# Copyright 2014 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.
"""
Utilities for the modular DevTools build.
"""
from os import path
import os
try:
import simplejson as json
except ImportErr... | danakj/chromium | third_party/WebKit/Source/devtools/scripts/modular_build.py | Python | bsd-3-clause | 7,037 | [
"VisIt"
] | 0fe78828d015498d55675992fd43ef0cd05f53e74e933c951f11e086903bca15 |
########################################################################
#
# (C) 2015, Brian Coca <bcoca@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation... | hkariti/ansible | lib/ansible/galaxy/role.py | Python | gpl-3.0 | 15,068 | [
"Brian",
"Galaxy"
] | 4521e8243ecaacefb820eccb0a007288f16a41a57bd00cafc5b2dd20c706065d |
# 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... | fweik/espresso | testsuite/scripts/tutorials/test_lattice_boltzmann_part2.py | Python | gpl-3.0 | 1,748 | [
"ESPResSo"
] | 4afeff5540f88d8964e32ce0ca81344ceb1bafe647709258943c1ec021ecb993 |
#!/usr/bin/env python
# coding: utf-8
"""Tools for 3D displays with VTK."""
# Copyright (C) 2017-2019 Matthieu Ancellin
# See LICENSE file at <https://github.com/mancellin/capytaine>
from typing import Union
from capytaine.meshes.meshes import Mesh
from capytaine.meshes.collections import CollectionOfMeshes
from capy... | mancellin/capytaine | capytaine/ui/vtk/helpers.py | Python | gpl-3.0 | 2,679 | [
"VTK"
] | 3630282932026581d7d103f650a6819fc9db0f3eed590947668be5a8daac992a |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | Stargrazer82301/CAAPR | CAAPR/CAAPR_AstroMagic/PTS/pts/eagle/plotgreybodyfit.py | Python | mit | 4,909 | [
"Galaxy"
] | 4f560531b6b2b988ec67e1d3d176a758e8a4240b2f87ead0300f1d79316fc60c |
#!/usr/bin/python
# -*- coding: utf-8 -*-
import os
import re
from HTMLParser import HTMLParseError
from time import time
from urlparse import urlparse
import requests
from bs4 import BeautifulSoup
from app import logger
from http_cache import http_get
from http_cache import is_response_too_large
from oa_local impor... | Impactstory/oadoi | webpage.py | Python | mit | 58,365 | [
"ORCA"
] | 1acd6c7a4debd6af6ad1a91936ce46aabd33f1c37024a703617ceece25d3f2ad |
#!/usr/bin/env python
import os
import sys
import json
import pychemia
filename = None
if len(sys.argv) == 2:
filename = sys.argv[1]
else:
print('Enter the JSON filename to store the data')
exit(1)
dirs = [x for x in os.listdir('.') if os.path.isdir(x)]
ret = []
for idir in dirs:
if os.path.isfile(i... | MaterialsDiscovery/PyChemia | scripts/relax_to_json.py | Python | mit | 1,785 | [
"CRYSTAL",
"VASP"
] | d3d6d4a6f625e2b5f063d724c2a3e25e47e8f83d1f1ebf2ba6cecc3d71673621 |
from simphony.api import CUBA
def get_box(particle_data_containers,
command_format=False,
change_existing=False):
""" Get simulation box commands
Using CUBA.VECTOR and CUBA.ORIGIN, return the
string used by LAMMPS to define the simulation box in
the LAMMPS data file or as a co... | simphony/simphony-lammps-md | simlammps/config/domain.py | Python | bsd-2-clause | 3,957 | [
"LAMMPS"
] | 59e27bbf79098b82cfb2a8ff6d893a60ed6532a19f9a13aacfc955a41268346d |
# Copyright (C) 2013-2021 The Debsources developers
# <qa-debsources@lists.alioth.debian.org>.
# See the AUTHORS file at the top-level directory of this distribution and at
# https://salsa.debian.org/qa/debsources/blob/master/AUTHORS
#
# This file is part of Debsources. Debsources is free software: you can
# redistrib... | Debian/debsources | lib/debsources/tests/test_webapp.py | Python | agpl-3.0 | 27,718 | [
"VisIt"
] | 5d0491ed988e05c75718b04c2106e62ca5e020313e25bccb7f8f8b10ed5f06e0 |
# Copyright (c) 2001 Autonomous Zone Industries
# This file is licensed under the
# GNU Lesser General Public License v2.1.
# See the file COPYING or visit http://www.gnu.org/ for details.
"""
Sends and receives buffers on TCP connections.
"""
__revision__ = "$Id: TCPConnection.py,v 1.12 2003/03/09 18:54:57 z... | zooko/egtp_new | egtp/TCPConnection.py | Python | lgpl-2.1 | 31,090 | [
"VisIt"
] | 1ca7b569036a4c029ce1026ce2fafb9251fa397930044068686db17c8158b98c |
#!/usr/bin/env python
##############################################################################################
#
#
# CMIP6_hybrid_regrid_emissions_N96e.py
#
#
# Requirements:
# Iris 1.10, time, cf_units, numpy
#
#
# This Python script has been written by N.L. Abraham as part of the UKCA Tutorials:
# http://... | acsis-project/emissions | emissions/python/CMIP6_hybrid/CMIP6_hybrid_regrid_iC4H10_emissions_n96e_360d.py | Python | gpl-3.0 | 17,251 | [
"NetCDF"
] | 3467d7fa7af239e36ca3de7903c06e6f7f24aaa3c644d5465bec16deb7995444 |
import ocl
import camvtk
import time
import vtk
import datetime
import math
def drawPoints(myscreen, clpoints, ccpoints):
c=camvtk.PointCloud( pointlist=clpoints, collist=ccpoints)
c.SetPoints()
myscreen.addActor(c )
def drawFiber(myscreen, f, fibercolor):
inter = f.getInts()
print("fiber has ", ... | aewallin/opencamlib | examples/python/fiber/fiber_13_onetri_cutter_comparison.py | Python | lgpl-2.1 | 5,644 | [
"VTK"
] | 2b8d556303ae6564e1c79cfe460be88a5c22d5db263f66e9a408706b8cf73993 |
####
# This sample is published as part of the blog article at www.toptal.com/blog
# Visit www.toptal.com/blog and subscribe to our newsletter to read great posts
####
import asyncio
import logging
import os
from time import time
import aiohttp
from download import setup_download_dir, get_links
logging.basicConfig(... | volker48/python-concurrency | async_imgur.py | Python | mit | 2,279 | [
"VisIt"
] | 82a0c53a93a8d953555cd2ddabe6699e817c3702c1fd0f890e407208200e0617 |
"""
Obtains filepaths from examples for testing.
"""
import os
test_dir = os.path.dirname(os.path.abspath(__file__))
examples_dir = os.path.join(test_dir, "..", "examples")
def get_example_filename(*filename):
program = filename[0].lower()
# Make sure we have written these programs
if program not in ["... | dgasmith/EEX_scratch | tests/eex_find_files.py | Python | bsd-3-clause | 798 | [
"Amber",
"Gromacs",
"LAMMPS"
] | e8f8f9d13b6c353c522507275e01a1811d97603761f7f88b1d1482b823d93365 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | demis001/scikit-bio | skbio/alignment/_exception.py | Python | bsd-3-clause | 658 | [
"scikit-bio"
] | 404d7eb2314bc2f59345307a84ac7eb5ebd420095d2dddc8beb950ce9ec1d19d |
#
# Copyright (c) 2013, Scott J Maddox
#
# This file is part of SimplePL.
#
# SimplePL 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) ... | scott-maddox/simplepl | src/simplefit/main_window.py | Python | agpl-3.0 | 14,092 | [
"Gaussian"
] | 9c4e7b5cd5982550d50dc65647dafc9958da049b675c7324dd116bf55e1fc60a |
#!/usr/bin/env python
# encoding: utf-8
# === IMPORTANT ====
# NOTE: In order to support non-ASCII file names,
# your system's locale MUST be set to 'utf-8'
# CAVEAT: DOESN'T work with proxy, the underlying reason being
# the 'requests' package used for http communication doesn't seem
# to work ... | Zocalos/bypy | bypy.py | Python | mit | 114,113 | [
"VisIt"
] | 9e7d1f3c80577443111ee8af1385af8f952fc274996a1fd21835bd6637a4fbc7 |
#!/usr/bin/env python
#Copyright 2013 Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000, there is a non-exclusive license for use of this work by or on behalf of the U.S. Government. Export of this program may require a license from the United States Government.
import pymongo
import sys, string, tim... | sandialabs/grandmaster | processing/updateUPCmodel.py | Python | apache-2.0 | 4,285 | [
"VTK"
] | 0636796ebb85ebc03a9e357b9692654d9604e4a6f0f2279700fcd229b9821aa2 |
###
### This script demonstrates the use of the new generic cinema io api to create
### a small dataset based on the disk_out_ref Exodus II file. Three contours
### are created and images are captured from a small set of camera angles. Due
### to the fact that all the data array values are radially symmetric, we cho... | Kitware/cinema | scripts/data_generation/generateSimpleDiskOut.py | Python | bsd-3-clause | 5,767 | [
"ParaView"
] | 564b2599f0193292c6f9b78ec17231d60b974712fd0e570f3987f59802eb4eb5 |
#Caoimhe Harvey
from skyscanner.skyscanner import Flights
flights_service = Flights('<Your API Key>')
# http://stackoverflow.com/questions/7047790/how-can-i-input-data-into-a-webpage-to-scrape-the-resulting-output-using-python
#QPX Express API Key
QAPI_key = 'AIzaSyC74E3Vu_dY0ZfxMIhQlXonC8yklxhVYqU'
#user_airports ... | caoimheharvey/Backpacking_Solution | tsp_backpacking.py | Python | mit | 2,128 | [
"VisIt"
] | 403f247f897c74a0804ea9d5a891878a426bced3fb3243ee41765e78e8b25152 |
# Copyright (c) 2018, Henrique Miranda
# All rights reserved.
#
# This file is part of the yambopy project
#
from yambopy import *
from netCDF4 import Dataset
class YamboStaticScreeningDB(object):
"""
Class to handle static screening databases from Yambo
This reads the databases ``ndb.em1s*``
Ther... | henriquemiranda/yambo-py | yambopy/dbs/em1sdb.py | Python | bsd-3-clause | 7,055 | [
"Yambo"
] | 5ab3a2576f5bddcd8e79227f7c2bcdd907e7f6ffb0a89b8136f1579b3c2161ca |
#!/usr/bin/env python -u
#############################################################################################
#
# Python script to demonstrate interacting with CASDA's TAP and SODA implementations to
# retrieve cutout images in bulk.
#
# This script does a TAP query to get the image cubes for a given schedul... | csiro-rds/casda-samples | cutouts.py | Python | apache-2.0 | 6,363 | [
"Galaxy"
] | bb9b7e70f1e37360462a8c651bc6107692cb8d97fab284e322871b51908eb148 |
#! /usr/bin/env python
#
# Copyright (C) 2011, 2012, 2013, 2014 David Maxwell
#
# This file is part of PISM.
#
# PISM 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 y... | talbrecht/pism_pik06 | examples/inverse/pismi.py | Python | gpl-3.0 | 20,733 | [
"NetCDF"
] | b700da27a849cdc0dfde6594901a47213ff68c1e206076213338638cc8f1a896 |
# Author: Travis Oliphant, 2002
#
# Further updates and enhancements by many SciPy developers.
#
from __future__ import division, print_function, absolute_import
import math
import warnings
from collections import namedtuple
import numpy as np
from numpy import (isscalar, r_, log, around, unique, asarray,
... | jlcarmic/producthunt_simulator | venv/lib/python2.7/site-packages/scipy/stats/morestats.py | Python | mit | 94,486 | [
"Gaussian"
] | 8d533d697bc4bcb4895b1092dadce94e07a33280b92041ef6f16b57c432913a1 |
# Copyright 2012, 2013 The GalSim developers:
# https://github.com/GalSim-developers
#
# This file is part of GalSim: The modular galaxy image simulation toolkit.
#
# GalSim 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... | mardom/GalSim | examples/MeasMoments.py | Python | gpl-3.0 | 3,251 | [
"Galaxy",
"Gaussian"
] | 56e459949428d3583ce1e87e405c05da901b18b42b41337457223497d7261dd2 |
# 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.
"""Output of PDB files."""
from Bio.Data.IUPACData import atom_weights # Allowed Elements... | bryback/quickseq | genescript/Bio/PDB/PDBIO.py | Python | mit | 6,035 | [
"Biopython"
] | 552744126cdacfd5060f07c8eaea83004e9801457e3c56e8bbd5a41613b09d66 |
import fnmatch
import tempfile
from contextlib import contextmanager
from os import makedirs
from os import unlink
from os.path import (
abspath,
basename,
dirname,
exists,
join,
sep,
)
from re import compile, escape
from typing import Any, Dict, List, Type
from galaxy.util.bunch import Bunch
... | natefoo/pulsar | pulsar/client/action_mapper.py | Python | apache-2.0 | 28,849 | [
"Galaxy"
] | ea955699b309b47bf40cd50423ad8defb95860246bfea79c105e86058a2e2e1f |
# -*- coding: utf-8 -*-
"""
Automated optimization of simulation of Basket cell
"""
__version__ = 0.1
from neuron import h
import neuron
import numpy as np
from neurotune import optimizers
from neurotune import evaluators
from neurotune import controllers
import os
import sys
class Simulation(object):
"""
S... | vellamike/neurotune | examples/example_1/optimization.py | Python | bsd-3-clause | 8,119 | [
"NEURON"
] | 619914e34a232977244e8e52c06c99e77f566773919b6a46f168e616517aef94 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.