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# encoding: utf8
from spline.tests import TestController, url
from splinext.pokedex.controllers.pokedex_search import MoveSearchForm
class TestMoveSearchController(TestController):
def do_search(self, **criteria):
u"""Small wrapper to run a move search for the given criteria."""
return self.app.g... | veekun/spline-pokedex | splinext/pokedex/tests/test_move_search.py | Python | mit | 12,954 | [
"FLEUR"
] | 7ed67bd2447ff7c57c7ef42848ba22aa5cdc161e912fd4e7f383e81443479fee |
from datetime import datetime
import numpy as np
from matplotlib.dates import date2num
def ensure_float(value):
"""Make sure datetime values are properly converted to floats."""
try:
# the last 3 boolean checks are for arrays with datetime64 and with
# a timezone, see these SO posts:
... | cphyc/matplotlib-label-lines | labellines/utils.py | Python | mit | 3,290 | [
"VisIt"
] | ddce696a2b3082fea6fa7c66fb25591ba16562c642eb87147cbc91b25693cae3 |
#!/usr/bin/env python
import argparse
import binascii
import copy
import datetime
import hashlib
import json
import logging
import os
import shutil
import struct
import subprocess
import tempfile
import xml.etree.ElementTree as ET
from collections import defaultdict
from Bio.Data import CodonTable
logging.basicConfig(... | TAMU-CPT/galaxy-tools | tools/jbrowse/jbrowse-iuc/jbrowse.py | Python | gpl-3.0 | 52,353 | [
"BLAST",
"Galaxy"
] | fb23b764f0502b17bb8d0cf7144640db10299174a06e36e58e48d168479dbe7e |
# Copyright 2016 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... | cg31/tensorflow | tensorflow/contrib/distributions/python/ops/distribution.py | Python | apache-2.0 | 32,482 | [
"Gaussian"
] | 62956e3ddda8a7b6cf5de52bf3e7ada76cd5e7751286f25f2f29d2f70c565319 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals, division, print_function
"""
Tools to compute equations of states with different models.
Adapted from ASE and deltafactor.
"""
import logging
import numpy as np
from... | aykol/pymatgen | pymatgen/analysis/eos_2.py | Python | mit | 11,006 | [
"ASE",
"pymatgen"
] | 843c9a1c236d8121de127b0e53ed8cf7a0eb4f867e565b44c06762f19e2626dd |
import datetime
import re
import urllib2
from bs4 import BeautifulSoup
from regional_poll_interpolator import RegionalPollInterpolator
party_names = {
'Cons.': 'cpc',
'NDP': 'ndp',
'Liberal': 'lpc',
'BQ': 'bq',
'Green': 'gpc',
'Other': 'oth',
}
province_code_to_region = {
'10': 'ATL',
... | GooseDad/Test | riding_poll_model.py | Python | apache-2.0 | 17,419 | [
"MOOSE"
] | 3512c22ccb9a6dea79b538f175d7854676177750a2a8fdc875b4beecd93537f2 |
import numpy as np
import urllib
import os
import argparse
from sklearn.cross_validation import train_test_split
from astroML.plotting import setup_text_plots
import empiriciSN
from MatchingLensGalaxies_utilities import *
from astropy.io import fits
import GCRCatalogs
import pandas as pd
from GCR import GCRQuery
sys.pa... | LSSTDESC/Twinkles | utils/catalog_production/add_om10_properties.py | Python | mit | 15,129 | [
"Galaxy"
] | 61cc3b5352bdbeff2031a7cdff545f3d015a744472e6cd553840055e5fe367a5 |
import os
import sys
import time
from datetime import datetime
from django.conf import settings
from django.contrib.staticfiles.testing import StaticLiveServerTestCase
from selenium import webdriver
from selenium.common.exceptions import WebDriverException
from selenium.webdriver.support.ui import WebDriverWait
from .... | jrwiegand/tdd-project | functional_tests/base.py | Python | mit | 4,894 | [
"VisIt"
] | 0442480de3a40580805b4bcb7238e53638840fb72a8df6b8cf43829fbc352af0 |
from arrow.arrow import Arrow
from django import forms
from django.apps import apps as django_apps
from django.core.exceptions import ObjectDoesNotExist
from edc_base import get_utcnow
from edc_form_validators.form_validator import FormValidator
from edc_visit_tracking.constants import MISSED_VISIT
from ..constants im... | botswana-harvard/edc-appointment | edc_appointment/form_validators/appointment_form_validator.py | Python | gpl-2.0 | 8,738 | [
"VisIt"
] | 0a01b7fc6153e2867b6918854b181165ae0293427e026732ab42b2a5b45cfc25 |
#! /usr/bin/env python
# -*- coding: UTF8 -*-
from collections import *
from Bio import SeqIO
import os
import time
from Bio.Blast import NCBIXML
from sys import stdout
import sqlite3
import csv
import sys
import datetime
import hashlib
import multiprocessing
import traceback
qq = str(sys.argv[1])
indiv = qq.split("/... | egeeamu/voskhod | bin/voskhod_validate_assembly.py | Python | gpl-3.0 | 14,974 | [
"BLAST"
] | 2b69dc0a014516446667ef4b9555b9b6b4c1a0d2d377af066ecd0f0c9f74426e |
#!/usr/bin/env python
# generate Python Manifest for the OpenEmbedded build system
# (C) 2002-2010 Michael 'Mickey' Lauer <mlauer@vanille-media.de>
# (C) 2007 Jeremy Laine
# licensed under MIT, see COPYING.MIT
import os
import sys
import time
VERSION = "2.6.6"
__author__ = "Michael 'Mickey' Lauer <mlauer@vanille-me... | nx111/openembeded_openpli2.1_nx111 | contrib/python/generate-manifest-2.6.py | Python | mit | 14,822 | [
"VisIt"
] | f679a15d0545e1277351e391dbe303bcd2b8831ce7b99b4a982ff591417f1494 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 16.3.8
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | civisanalytics/ansible | lib/ansible/modules/network/avi/avi_virtualservice.py | Python | gpl-3.0 | 20,706 | [
"VisIt"
] | 83bdd2e0ae751889b552b6ad8b0cef9a1e4bd7c7e4e8a97afde86de12bc14b2f |
########################################################################
# This example demonstrates periodic synaptic input to a cell.
# Copyright (C) Upinder S. Bhalla NCBS 2018
# Released under the terms of the GNU Public License V3. No warranty.
######################################################################... | BhallaLab/moose-examples | tutorials/Rdesigneur/ex5.1_periodic_syn_input.py | Python | gpl-2.0 | 803 | [
"MOOSE"
] | 98854c883944db7594650539bdf9d8cd4830d5e3f9ad7a9287e529764ac920b1 |
"""Module gaul2srl
This will group gaussians in an island into sources. Will code callgaul2srl.f here, though
it could probably be made more efficient.
img.sources is a list of source objects, which are instances of the class Source
(with attributes the same as in .srl of fbdsm).
img.sources[n] is a source.
source.g... | lofar-astron/PyBDSF | bdsf/gaul2srl.py | Python | gpl-3.0 | 34,945 | [
"Gaussian"
] | bd619ba7f2c638426870f4adb5a7ce00b8711d3dfc2f6f33b7b5cf3a32cdad87 |
'''
synbiochem (c) University of Manchester 2017
synbiochem is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
# pylint: disable=invalid-name
# pylint: disable=too-many-arguments
# pylint: disable=too-many-locals
import math
fr... | synbiochem/synbiochem-learn | gg_learn/keras/__init__.py | Python | mit | 7,003 | [
"VisIt"
] | 61eaf23857f6375ba32f248ad7787177798c65907abb9b84430a2248e41a7c8b |
# 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... | szha/mxnet | python/mxnet/contrib/text/embedding.py | Python | apache-2.0 | 31,527 | [
"VisIt"
] | fbed79118172ea7399f79ed7f5fed11f2d04b78c761fe3b7b5257514c2316374 |
#!/usr/bin/env python
"""loader.py:
"""
__author__ = "Dilawar Singh"
__copyright__ = "Copyright 2015, Dilawar Singh and NCBS Bangalore"
__credits__ = ["NCBS Bangalore"]
__license__ = "GNU GPL"
__version__ = "1.0.0"
__maintainer__ = "Dilawar Singh"
__email__ ... | BhallaLab/benchmarks | neuro_morpho/bug/swc_loader.py | Python | gpl-2.0 | 2,080 | [
"MOOSE",
"NEURON"
] | dcafb94217c6e0737c7d7d4d01bdbb6082ab71351d758e9708637f9d18ad5582 |
# -*- Mode: Python; coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2011-2013 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Fre... | andrebellafronte/stoq | stoq/gui/shell/shellwindow.py | Python | gpl-2.0 | 45,650 | [
"VisIt"
] | 39db3ce4431028328ab04f0ca32a1006239a0d6ca3473340f29f7c2ef4b0406c |
#!/usr/bin/env python
"""
https://github.com/kudkudak
Featurization using rdkit descriptors.
Trivial wrapper around rdkit.Chem.Descriptors that includes embedding procedure
See main for example usage.
"""
import pandas as pd
from rdkit import Chem
from rdkit.Chem import AllChem
from mordred import Calculator, desc... | DentonJC/virtual_screening | moloi/descriptors/mordred_descriptor.py | Python | gpl-3.0 | 2,834 | [
"RDKit"
] | 1ce00a8c42cd1675f257ddd59408e58d414b1f2a2e3ab96d9d88ffd68dc31ba5 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
##############################################################################
## Filename: extract_host.py
## Version: $Revision$
## Description: Extract host spectrum from reference cube
## Author: $Author$
## $Id$
#####################################... | snfactory/extract-star | scripts/extract_host.py | Python | mit | 11,597 | [
"Galaxy"
] | c899e0fe94f0da38544b512bf7383bcd98c960bf3c0a903118ff21b11d3b16d0 |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses... | brandond/ansible | lib/ansible/modules/network/avi/avi_role.py | Python | gpl-3.0 | 3,395 | [
"VisIt"
] | a67d99a018654c7356bd5ec8291acca6959290e84516b1a04c7686c6b7f78d2f |
from copy import copy
from ipdb import set_trace as pause
from math import ceil, sqrt
from matplotlib import pyplot as plt
import matplotlib.gridspec as gridspec
import numpy as np
import random
import time
from base import create_mnist_patternsets, Minibatch, Network, Patternset
from utils.utils import imagesc, isfun... | gregdetre/evendeeper | rbm/rbm.py | Python | mit | 16,944 | [
"CDK"
] | bb307639abe4d0860e1160d323a115d57cdec9078c4b25b2466955c9c3f32d63 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Uses graphlib and topiclib to run sLDA
Copyright (C) 2011 Joseph Perla
GNU Affero General Public License. See <http://www.gnu.org/licenses/>.
"""
global final_output
from itertools import chain,izip
from functools import partial
import jsondata
try... | jperla/happynews | model/slda.py | Python | agpl-3.0 | 7,470 | [
"Gaussian"
] | 3528176a7cbee75f1f3c9fceb35cf6389cf4d99b9199e84391b6ce988bf5c4eb |
import urllib2
from bs4 import BeautifulSoup # import required modules for web scraping
names=["GPS", "NFLX", "GRPN", "INTC", "AAPL", "MOLG", "WAIR", "OTIV", "AMDA", "ARUN", "ICLDW", "AAPL", "GOOG", "BABA"]
def calc(names): # method declaration
for i in names: # loop start to use the ... | codypilot/SQLToPython | BeautifulSoup.py | Python | mit | 1,818 | [
"VisIt"
] | 1d1d76f0821574f017af88a5ca5814ad0a42472d144de58d751a4827bd9991fa |
# -*- coding: utf-8 -*-
#
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2017, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public v... | berquist/cclib | cclib/method/orbitals.py | Python | bsd-3-clause | 1,916 | [
"cclib"
] | 640ce82038e8704d97d657d51b365e18968c0266cdb78f9c4910cf785e2a92a4 |
"""
Unit tests for masquerade.
"""
import json
import pickle
from mock import patch
from nose.plugins.attrib import attr
from datetime import datetime
from django.core.urlresolvers import reverse
from django.test import TestCase, RequestFactory
from django.utils.timezone import UTC
from capa.tests.response_xml_factor... | synergeticsedx/deployment-wipro | lms/djangoapps/courseware/tests/test_masquerade.py | Python | agpl-3.0 | 18,408 | [
"VisIt"
] | bb6023ef16934d23969845e546a8fa7e5651ca1f2e38eb0984c653ad72f6535e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
## Copyright 2015 Rasmus Scholer Sorensen, rasmusscholer@gmail.com
##
## This program is free software: you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundation, either version ... | scholer/na_strand_model | nascent/nascent_sim/dom_anneal_sim.py | Python | gpl-3.0 | 64,535 | [
"Biopython"
] | bea1428b8bd8978e217d864cf6211b3dfb0ccbb24ca8a12636e708c06e79984d |
# 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 +
# pylint: disable=no-name-in-module
from __fu... | mganeva/mantid | Framework/PythonInterface/plugins/algorithms/FindEPP.py | Python | gpl-3.0 | 5,918 | [
"Gaussian"
] | 27b78944f400f616af90de9ce1fa6787b6cc20b73d8afdbef02ddea08035b560 |
# -*- coding: utf-8 -*-
"""SQLite parser plugin for Google Chrome history database files."""
from dfdatetime import posix_time as dfdatetime_posix_time
from dfdatetime import webkit_time as dfdatetime_webkit_time
from plaso.containers import events
from plaso.containers import time_events
from plaso.lib import defini... | joachimmetz/plaso | plaso/parsers/sqlite_plugins/chrome_history.py | Python | apache-2.0 | 51,315 | [
"VisIt"
] | d6c5ea1d155ae7f6d2363cf674bffd0e95f45df5875a54e7b093861e19b32271 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2005-2014 Async Open Source
##
## This program 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
## of the Licens... | andrebellafronte/stoq | stoqlib/lib/kiwilibrary.py | Python | gpl-2.0 | 1,354 | [
"VisIt"
] | d540e9eb9858400a84a5a3a40be7b9ecd5d09e2a7eea91a22f6967d64a976519 |
""" This contains unit tests to make sure that the migration between PyGSI and M2Crypto is as smooth as possible
The test covers only the method exposed by the PyGSI version for the time being.
We are not testing:
* generateProxyRequest -> boils down to testing X509Request
* setCertificate -> not used... | ic-hep/DIRAC | src/DIRAC/Core/Security/test/Test_X509Certificate.py | Python | gpl-3.0 | 11,694 | [
"DIRAC"
] | 823e70bafc279f0b38d0706e3de4172783ad0e18a910da882aeee271b052813d |
"""
------------
PyMine 1.0.1
------------
PyMine lets you integrate and visualize biological data used for drug discovery using PyMOL.
------------
REQUIREMENTS
------------
1) Ubuntu 11.04 or above OR Mac OS X 10.7 or above
2) Pymol 1.7 or above
3) PyMine 1.0.1
------------
INSTALLATION
------------
1) Download an... | zhijunlilab/PyMine | pymine.py | Python | mit | 46,678 | [
"PyMOL"
] | a30c00063dfb1b22549c6234dd1364e056ec94dfb2b898c2844cebc08e075114 |
# Copyright (c) 2012 Spotify AB
#
# 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, s... | lungetech/luigi | setup.py | Python | apache-2.0 | 2,954 | [
"VisIt"
] | f95606f7f7b17a2e87ff4352cfe9d92c198b58d80abf50e6ccabeed16c4ba031 |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses... | alexlo03/ansible | lib/ansible/modules/network/avi/avi_virtualservice.py | Python | gpl-3.0 | 28,097 | [
"VisIt"
] | 8648ba9abb2c0f7f10030415e6fe50021675b849cc4a6aa8dc58adc9ce26922e |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2011, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | zenoss/ZenPacks.zenoss.CloudStack | ZenPacks/zenoss/CloudStack/facades.py | Python | gpl-2.0 | 2,180 | [
"VisIt"
] | 692338826eddebbf13ca6a90a3a27afb6615c5f7cfff8b06209e73c889575422 |
###############################################################################
# volumina: volume slicing and editing library
#
# Copyright (C) 2011-2014, the ilastik developers
# <team@ilastik.org>
#
# This program is free software; you can redistribute it and/or
# modify it und... | jakirkham/volumina | volumina/view3d/volumeRendering.py | Python | lgpl-3.0 | 7,286 | [
"VTK"
] | 3c896b6384a771df15c01632bf48eb509f7ab2f764c1c3d4779bc845dd49be86 |
import sys
import commands
from pybedtools import *
from Bio import SeqIO
from pyfaidx import Fasta
# lets try g
# test with bedtools, can try this with pybedtools
#commands.getoutput("bedtools getfasta -fi test.fasta -bed test.gff -fo testout.txt")
#commands.getoutput("cat")
# test with biopython; will learn librar... | jlevy44/Joshua-Levy-Synteny-Analysis | OtherFiles/AdditionalAnalysisScripts/test1.py | Python | mit | 3,712 | [
"Biopython"
] | d0bb3c26e67222d61c9d023470afacba32ed07503c78d679603313fcf0c5729c |
#!/usr/bin/env python
########################################################################
# File : dirac_accounting_decode_fileid
# Author : Adria Casajus
########################################################################
"""
Decode Accounting plot URLs
Usage:
dirac-accounting-decode-fileid [options] ... | yujikato/DIRAC | src/DIRAC/AccountingSystem/scripts/dirac_accounting_decode_fileid.py | Python | gpl-3.0 | 1,512 | [
"DIRAC"
] | 3607d58a7450644265a146aea21b768e0362c1ede854679430844e99877c8018 |
'''
FTDCheat - An automated part unlocker for the game From The Depths
Copyright (c) 2015 Rob Nelson <nexisentertainment@gmail.com>
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 restric... | N3X15/ftdcheat | ftdcheat.py | Python | mit | 10,232 | [
"CRYSTAL"
] | 89fde24422ae036fa97fae9075bb5106b58a251ebcad16fd50444a8287d1cd43 |
import random
import unittest
from egginst.main import name_version_fn
from enstaller.utils import canonical, cname_fn, comparable_version
class TestUtils(unittest.TestCase):
def test_canonical(self):
for name, cname in [
('NumPy', 'numpy'),
('MySql-python', 'mysql_python'),
... | ilanschnell/ironpkg | tests/test_utils.py | Python | bsd-3-clause | 1,609 | [
"VTK"
] | f1bbb1802fb9dcf4b8c81479e85c53f4bd75cd6fb31fee84e885d3ab41e39cc9 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# @Author: Brian Cherinka, José Sánchez-Gallego, and Brett Andrews
# @Date: 2018-07-24
# @Filename: test_rss.py
# @License: BSD 3-clause (http://www.opensource.org/licenses/BSD-3-Clause)
#
# @Last modified by: José Sánchez-Gallego (gallegoj@uw.edu)
# @Last modified time: ... | albireox/marvin | python/marvin/tests/tools/test_rss.py | Python | bsd-3-clause | 8,135 | [
"Brian",
"Galaxy"
] | a8bf44c5fde113455775046d4c0e7004967a1b4cf83a56342b6c0b358c363c30 |
'''Body Composition is a Slicer module that allows to segment different parts of the lungs in a manual or semi-automatic basis
with the help of a customized Slicer Editor.
It also performs a set of operations to analyze the different structures of
the volume based on its label map, like Area, Mean, Std.Dev., etc.
First... | acil-bwh/SlicerCIP | Scripted/CIP_Calibration/CIP_Calibration.py | Python | bsd-3-clause | 19,806 | [
"VTK"
] | 4b964a03f905c65347aca9a0055f40bb7089e3fdc6da5daf6c348ea62e716d66 |
#!/usr/bin/env python
import sys
import argparse
import os
from measureTractsFunctions import printToCSV
def main():
parser = argparse.ArgumentParser(description='computes various tract measures including FA and mode and saves the data to a ".csv"')
parser.add_argument('-i', '--input', dest='files', nargs='+',... | reckbo/ppl | pipeline-lib/measuretracts/measureTracts.py | Python | bsd-3-clause | 1,896 | [
"VTK"
] | b3288da0caff6c69ff69bda269a0ccf00d0fd59f4cf8341d17438b07c91ee2d2 |
from copy import copy
from collections import OrderedDict
import numpy as np
import pandas as pd
from sklearn.metrics import average_precision_score, auc, roc_auc_score
from sklearn.metrics import precision_recall_curve
from sklearn.linear_model import LogisticRegressionCV
from sklearn.cross_validation import Stratifi... | roaminsight/roamresearch | BlogPosts/Average_precision/average_precision_post_code.py | Python | apache-2.0 | 10,740 | [
"Gaussian"
] | f7fcbf233499c678c8ac7818b1cf0cdcd92104980d114301bffedc6b4a470df3 |
# dirstate.py - working directory tracking for mercurial
#
# Copyright 2005-2007 Matt Mackall <mpm@selenic.com>
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 or any later version.
import errno
from node import nullid
from i18n import _
import scmutil... | jordigh/mercurial-crew | mercurial/dirstate.py | Python | gpl-2.0 | 29,447 | [
"VisIt"
] | 391ba82bf2ebe489642c95c8d9946b0d80727c5f17bebeee5320d06be9182ff7 |
# coding=utf-8
# Copyright 2014 Pants project contributors (see CONTRIBUTORS.md).
# Licensed under the Apache License, Version 2.0 (see LICENSE).
from __future__ import (absolute_import, division, generators, nested_scopes, print_function,
unicode_literals, with_statement)
import os
import sub... | landism/pants | tests/python/pants_test/backend/python/test_python_chroot.py | Python | apache-2.0 | 10,612 | [
"VisIt"
] | d45d28108a1c4c0c5e082d1d5403885d2e19863f58715069c7d56b8a54d7b491 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for access page from menu of biz feature
"""
from flaky import flaky
from bok_choy.web_app_test import WebAppTest
from nose.plugins.attrib import attr
from . import PLAT_COMPANY_CODE, PLATFORMER_USER_INFO, GaccoBizTestMixin
from ...pages.biz.ga_dashboard import DashboardPa... | nttks/edx-platform | common/test/acceptance/tests/biz/test_ga_menu_access.py | Python | agpl-3.0 | 8,854 | [
"VisIt"
] | 7b1d4ded155fb13db941689056c30d09ba7afe2af721dc183a9c41b4bd2d61c0 |
# -*- coding: utf-8 -*-
##
## This file is part of Invenio.
## Copyright (C) 2013, 2014 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 opt... | MSusik/invenio | invenio/modules/workflows/testsuite/test_workflows.py | Python | gpl-2.0 | 29,716 | [
"Galaxy"
] | 31a0d06d395f4738ebfffb4e31579bae2b73d8cbcd8fa9826e7c5741bc099e64 |
###############################################################################
##
## Copyright (C) 2011-2014, NYU-Poly.
## Copyright (C) 2006-2011, University of Utah.
## All rights reserved.
## Contact: contact@vistrails.org
##
## This file is part of VisTrails.
##
## "Redistribution and use in source and binary for... | Nikea/VisTrails | vistrails/packages/spreadsheet/spreadsheet_sheet.py | Python | bsd-3-clause | 24,298 | [
"VTK"
] | 648e3f8bd956fe0db3deafcc0748af155ea297371024a6d7c3e1854114af7960 |
##############################################################################
# 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... | tmerrick1/spack | var/spack/repos/builtin/packages/plumed/package.py | Python | lgpl-2.1 | 7,313 | [
"Amber",
"ESPResSo"
] | b3fc33194ea4d3c93a68aa74de38d72b72187e92e3184b68972007725803b858 |
# $Id$
#
# Copyright (C) 2003-2006 Greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" class definitions f... | bp-kelley/rdkit | rdkit/Chem/Fingerprints/SimilarityScreener.py | Python | bsd-3-clause | 5,016 | [
"RDKit"
] | 1992c3401fff3b4d8966d946954c2da7a348e6cc8d92ada02570a5f6ba0860ba |
import re
import numpy as np
from .base import IOHandler, FeatureNotAvailable
from .gro_map import gro_to_cl
from ...core.system import System
from ...db import ChemlabDB
symbol_list = ChemlabDB().get('data', 'symbols')
symbol_list = [s.lower() for s in symbol_list]
class GromacsIO(IOHandler):
'''Handler for... | GabrielNicolasAvellaneda/chemlab | chemlab/io/handlers/gro.py | Python | gpl-3.0 | 6,479 | [
"Gromacs"
] | c861b047ca6b15ddd4d6f02588491365ba890de9d2708fb027b1edc77dda308d |
"""
Instructor Dashboard Views
"""
import logging
import datetime
from opaque_keys import InvalidKeyError
from opaque_keys.edx.keys import CourseKey
import uuid
import pytz
from django.contrib.auth.decorators import login_required
from django.views.decorators.http import require_POST
from django.utils.translation imp... | IndonesiaX/edx-platform | lms/djangoapps/instructor/views/instructor_dashboard.py | Python | agpl-3.0 | 31,077 | [
"VisIt"
] | 2786a01a6d5aaa13763d923e1be0cce82a885f659ff719ed8a9df8be52072a35 |
# coding: utf-8
from __future__ import division, unicode_literals
"""
Unit tests for StructureNL (SNL) format
"""
__author__ = "Anubhav Jain"
__credits__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Anubhav Jain"
__email__ = "ajain@lbl.gov"
__date_... | Dioptas/pymatgen | pymatgen/matproj/tests/test_snl.py | Python | mit | 9,705 | [
"pymatgen"
] | 9f2892ba97d4a60e39f1088815eb3f3b2cab6443031ed3fd49c381ab630ee082 |
#
# 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 us... | lxsmnv/spark | python/pyspark/ml/clustering.py | Python | apache-2.0 | 48,858 | [
"Gaussian"
] | 2f3366937361728aab1795131596aad116b5cc01fceb216f2ffa58e611612658 |
#
# Copyright Capita Translation and Interpreting 2013
#
# This file is part of Pipeline Creation Language (PCL).
#
# Pipeline Creation Language (PCL) 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 ve... | ianj-als/pcl | src/pclc/parser/expressions.py | Python | gpl-3.0 | 10,653 | [
"VisIt"
] | c9be63245cd6283c96df9cd91c0b42fb37e4641d9ab34745963ee55d6639d134 |
#!/usr/bin/env python
##############################################################################################
#
#
# regrid_emissions_N96e.py
#
#
# Requirements:
# Iris 1.10, cf_units, numpy
#
#
# This Python script has been written by N.L. Abraham as part of the UKCA Tutorials:
# http://www.ukca.ac.uk/wiki... | acsis-project/emissions | emissions/python/periodic_1960/regrid_NH3_emissions_n96e_360d_1960.py | Python | gpl-3.0 | 6,995 | [
"NetCDF"
] | 2d36f4dd31ced477c4ee7719ed5b6c7f4de21dea3d1a7b1c0f2256d24c2d4a97 |
# -*- coding: utf-8 -*-
"""Compiles nodes from the parser into Python code."""
from collections import namedtuple
from functools import update_wrapper
from itertools import chain
from keyword import iskeyword as is_python_keyword
from markupsafe import escape
from markupsafe import Markup
from . import nodes
from ._c... | sserrot/champion_relationships | venv/Lib/site-packages/jinja2/compiler.py | Python | mit | 66,284 | [
"VisIt"
] | 4daf56d4b8ade78db022d0075e50dc834b043ac143322ac276514f1c0bab838a |
from SquareDist import squaredist
import numpy as np
def kernelmatrix(x1, x2, param, kernel='linear'):
'''
Input:
x1, x2: collections of points on which to compute the Gram matrix
kernel: can be 'linear', 'polynomial' or 'gaussian'
param: is [] for the linear kernel, the exponent of the polynomial... | ACarfi/Regularization-networks | regularizationNetworks/KernelMatrix.py | Python | mit | 710 | [
"Gaussian"
] | f408e0ebf0192ae57dbe38a991920abea2a30aac3ebbc9be81c495a9ecee04ae |
# Version: 0.17
"""The Versioneer - like a rocketeer, but for versions.
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, 3.5, and pypy
* [![Latest Version]
(https... | dask/distributed | versioneer.py | Python | bsd-3-clause | 68,349 | [
"Brian"
] | c061dbf11b99239ba55a941a8caeb57192da28d7bffaf4a55ea694aa9c357ef6 |
"""
Sign Abstract Domain
====================
Non-relational abstract domain to be used for **numerical analysis**.
The set of possible numerical values of a program variable in a program state
is represented by their sign (negative, zero, positive, ...).
:Author: Jérôme Dohrau and Caterina Urban
"""
from collections... | caterinaurban/Lyra | src/lyra/abstract_domains/numerical/sign_domain.py | Python | mpl-2.0 | 19,823 | [
"VisIt"
] | 6fe97878dcf226d7065bbc6fd3171dbc87e4c3eeb62cb3d6bf7db8584770012d |
# -*- coding: utf-8 -*-
##
## This file is part of Harvesting Kit.
## Copyright (C) 2013, 2014 CERN.
##
## Harvesting Kit 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, o... | kaplun/harvesting-kit | harvestingkit/oup_package.py | Python | gpl-2.0 | 11,863 | [
"VisIt"
] | 650090adfe5fd29c05dbc753b76b81e8d07130bd8349d865bc5c9055c378b821 |
from distutils.core import setup
setup(
name = 'rigolds1000de',
packages = ['rigolds1000de'], # this must be the same as the name above
version = '0.1.1',
description = 'A way to connect to your Rigol DS1000D/E Series oscilloscope over USB.',
author = 'Brian Perrett',
author_email = 'perrettbrian@gmail.com'... | aplstudent/Rigol-DS1000DE | setup.py | Python | mit | 609 | [
"Brian"
] | 5ed549fca1fcffa206ac1fb1159e751f65d0525dddd5408978738c69cd04e34e |
import sys
import os
import pysam
import tempfile
def get_bamfile(bam):
bmode = 'rb'
if bam.endswith(('.sam', '.SAM')):
bmode = 'r'
elif bam.endswith(('.cram', '.CRAM')):
bmode = 'rc'
return pysam.AlignmentFile(bam, bmode)
def get_align_output(output, template=None, header=None):
i... | gantzgraf/bacta | bacta/alignment_file_utils.py | Python | gpl-3.0 | 1,751 | [
"pysam"
] | b429bd4959217aa15ba5b1385b12d6fc0c6057df045290d7e739ca0bccd9108f |
# -*- coding: utf-8 -*-
"""
This file is part of labella.py.
Python rewrite of the VPSC code included in Labella.js.
Originally modified from:
https://github.com/tgdwyer/WebCola/blob/master/WebCola/src/vpsc.ts
Author: G.J.J. van den Burg
License: Apache-2.0
"""
from sys import maxsize
class PositionStats(obj... | GjjvdBurg/labella.py | labella/vpsc.py | Python | apache-2.0 | 11,263 | [
"VisIt"
] | e6f521f47bd6413ea70dc3475aaa9c1ef0993725c9e8c93fe9a9c5504f7077cf |
# -*- coding: utf-8 -*-
#
# ht_poisson.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST 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
... | INM-6/nest-git-migration | pynest/examples/HillTononi/ht_poisson.py | Python | gpl-2.0 | 3,406 | [
"NEURON"
] | a845d32613b7ffb174b4e94ecdfd9e8400e73abb83c934b57ec2e8765899b5b2 |
# coding: utf-8
from __future__ import division, unicode_literals
"""
Classes for reading/manipulating/writing FEFF files.
http://leonardo.phys.washington.edu/feff/
XANES and EXAFS input files, and the xmu.dat, ldos.dat output files are
available, for non-spin case at this time. FEFF input file has parameter tags,
p... | rousseab/pymatgen | pymatgen/io/feff/__init__.py | Python | mit | 44,152 | [
"FEFF",
"pymatgen"
] | 640a45266d47d5da3c6c6a70def3bae37da67e389a15acfde9a2e57fa5508088 |
########################################################################
# $HeadURL $
# File: RequestDB.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2012/12/04 08:06:30
########################################################################
""" :mod: RequestDB
=======================
.. module: Request... | rajanandakumar/DIRAC | RequestManagementSystem/DB/RequestDB.py | Python | gpl-3.0 | 32,300 | [
"DIRAC"
] | 10b2287f6818074f9692c942409148a3a1408e342ba05eeef96dc484456fab59 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# ramaplot.AmberForceField.py
#
# Copyright (C) 2015 Karl T Debiec
# All rights reserved.
#
# This software may be modified and distributed under the terms of the
# BSD license. See the LICENSE file for details.
"""
Reads and represents AMBER-format force fields
"""
#... | ASinanSaglam/Ramaplot | AmberForceField.py | Python | bsd-3-clause | 38,302 | [
"Amber"
] | f99b8d9ff0ed675fe7992a26666af9301cc079830fae624c0af99dcfd60f4593 |
# Copyright 2010 by Kyle Ellrott. 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.
from Bio.Application import _Option, AbstractCommandline, _Switch, _Argument
import os
class ... | midnighteuler/PySIFTER | PySIFTER/ThirdPartyWrappers/biopython_temp/_Hmmer.py | Python | gpl-3.0 | 3,658 | [
"Biopython"
] | 68638f83335222d97f570c63c1812d2fd8e72003bdcf2af35fd2b19b7639ab35 |
"""
This is the client of the Monitoring service based on Elasticsearch.
"""
from DIRAC.Core.Base.Client import Client, createClient
from DIRAC.Core.Utilities.Plotting.FileCoding import codeRequestInFileId
@createClient("Monitoring/Monitoring")
class MonitoringClient(Client):
"""
.. class:: MonitoringClient
... | DIRACGrid/DIRAC | src/DIRAC/MonitoringSystem/Client/MonitoringClient.py | Python | gpl-3.0 | 3,122 | [
"DIRAC"
] | a2d04b31811ef4a756ad4c231317f57993965fa925b9115ded046751e42eea7f |
from pysam.libchtslib import *
from pysam.cutils import *
import pysam.cutils as cutils
import pysam.cfaidx as cfaidx
from pysam.cfaidx import *
import pysam.ctabix as ctabix
from pysam.ctabix import *
import pysam.csamfile as csamfile
from pysam.csamfile import *
import pysam.calignmentfile as calignmentfile
from py... | dannon/pysam | pysam/__init__.py | Python | mit | 6,266 | [
"pysam"
] | ee4fa7c5067b6ea0d740037f72a77a1b05a7c59177d400098257754855e6bff2 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import os
from spack import *
class Vmd(Package):
"""VMD provides user-editable materials which can be applied
... | LLNL/spack | var/spack/repos/builtin/packages/vmd/package.py | Python | lgpl-2.1 | 2,393 | [
"VMD"
] | 07e159198039021b8cb34e564193eefd528212aabf1d9525b85def3c3ddc6fdf |
#
# Code to read, write and edit VCF files
#
# VCF lines are encoded as a dictionary with these keys (note: all lowercase):
# 'chrom': string
# 'pos': integer
# 'id': string
# 'ref': string
# 'alt': list of strings
# 'qual': integer
# 'filter': None (missing value), or list of keys (strings); empty list... | pkaleta/pysam | pysam/VCF.py | Python | mit | 47,621 | [
"pysam"
] | f383723f5c42fa12c1638d6d956ffc24d9055eb5010b9fe7981cc1dbce9f8478 |
# - Coding UTF8 -
#
# Networked Decision Making
# Development Sites (source code):
# http://code.google.com/p/global-decision-making-system/
# http://github.com/NewGlobalStrategy/NetDecisionMaking
#
# Demo Sites (Google App Engine)
# http://netdecisionmaking.appspot.com
# http://globaldecisionmaking.appspot.com
... | NewGlobalStrategy/NetDecisionMaking | controllers/admin.py | Python | mit | 15,531 | [
"VisIt"
] | 515cd7d3ce04320ebafb58e9dd97c091069bf337a9eb25d00d241fed4e76fddf |
#
# 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 n... | apache/climate | mccsearch/code/mainProg.py | Python | apache-2.0 | 4,630 | [
"NetCDF"
] | 5522dcdc0f557b4dc235d7f4a22e13b6efbd0ae2a592b9cec7157f8bde5b3a56 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | BackupTheBerlios/espressopp | src/check/__init__.py | Python | gpl-3.0 | 908 | [
"ESPResSo"
] | fedf3a4475620534052f5706172f130855badad8905cb9dec94b9408f5d6d009 |
# -*- coding: utf-8 -*-
#!/usr/bin/env python
"""
PyGSLIB.gslib, Module to interface GSLIB programs. This includes the
standard programs available at
http://www.statios.com/software/gslib77_ls.tar.gz and non-standard GSLIB
programs provided by contributors.
Note
----
The original Fortran 77 code was modi... | opengeostat/pygslib | pygslib/gslib/__init__.py | Python | mit | 70,925 | [
"Gaussian",
"VTK"
] | 7d718977c7f2e344527de36cbbfdced98bda92aa7a014b05677ffc244cb71921 |
# -*- coding: utf-8 -*-
"""
Generators for random graphs.
"""
# Copyright (C) 2004-2016 by
# Aric Hagberg <hagberg@lanl.gov>
# Dan Schult <dschult@colgate.edu>
# Pieter Swart <swart@lanl.gov>
# All rights reserved.
# BSD license.
from __future__ import division
import itertools
import math
import ran... | SanketDG/networkx | networkx/generators/random_graphs.py | Python | bsd-3-clause | 34,237 | [
"VisIt"
] | 4970adf94e7d780b7170d03f0c0375402d676ab76bb829e536882f86e664ffbc |
########################################################################
#
# algorithms.py - This file is part of the Spectral Python (SPy)
# package.
#
# Copyright (C) 2001-2010 Thomas Boggs
#
# Spectral Python is free software; you can redistribute it and/
# or modify it under the terms of the GNU General P... | ohspite/spectral | spectral/algorithms/algorithms.py | Python | gpl-2.0 | 58,890 | [
"Gaussian"
] | 2e4567d98f64881cf5d7e873c7f9fe95615f7c1b12e9660c535f0970b8589b48 |
# Copyright (c) 2003-2016 LOGILAB S.A. (Paris, FRANCE).
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
# Licensed under the GPL: https://www.gnu.org/licenses/old-licenses/gpl-2.0.html
# For details: https://github.com/PyCQA/pylint/blob/master/COPYING
"""exceptions handling (raising, catching, exceptions classes... | bgris/ODL_bgris | lib/python3.5/site-packages/pylint/checkers/exceptions.py | Python | gpl-3.0 | 15,802 | [
"VisIt"
] | 8789e9ae606cb90244f3a62ab8ce1a2208d7c2fa16750464155c455086f0a201 |
# Orca
#
# Copyright (C) 2010-2013 Igalia, S.L.
#
# Author: Alejandro Pinheiro Iglesias <apinheiro@igalia.com>
# 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 S... | h4ck3rm1k3/orca-sonar | src/orca/scripts/toolkits/clutter/script.py | Python | lgpl-2.1 | 5,276 | [
"ORCA"
] | c798971c973eaf9d372636554fe68e2d76ae9ac18fa30d489242326f78075839 |
#
# vsmtpd/connection.py
#
# Copyright (C) 2011 Damien Churchill <damoxc@gmail.com>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3, or (at your option)
# any later version.
#... | damoxc/vsmtpd | vsmtpd/connection.py | Python | gpl-3.0 | 21,121 | [
"exciting"
] | e1d9c488e8d6a9039bef9bdf099eec1102519cdc834b214831aecb0c77dac38e |
import re
import networkx as nx
from networkx.algorithms.components.connected import connected_components
from datetime import date
import lib.util as util
import csv
import sys
import numpy as np
import lib.config as config
from itertools import izip_longest as zip_longest
sys.path.append('../lib')
def message_numbe... | rohangoel96/IRCLogParser | IRCLogParser/lib/analysis/network.py | Python | mit | 33,360 | [
"VisIt"
] | b2c98d180f421ed076c7c22b2deee82d152c51dd192072b953b0f4c559091249 |
# -*- coding: utf-8 -*-
# Copyright © 2012-2022 Roberto Alsina, Chris Warrick and others.
# Permission is hereby granted, free of charge, to any
# person obtaining a copy of this software and associated
# documentation files (the "Software"), to deal in the
# Software without restriction, including without limitation... | getnikola/nikola | nikola/plugins/command/theme.py | Python | mit | 14,493 | [
"VisIt"
] | 658bc6f27a1f936afff97fdc7597fb082cc1bda385dabd331c15d06746ccd88b |
# Copyright 2000 by Jeffrey Chang. 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.
"""Collection of modules for dealing with biological data in Python.
The Biopython Project is ... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/Bio/__init__.py | Python | apache-2.0 | 3,763 | [
"Biopython"
] | fa4accfa74ff6805b1130c632400ca959aa7f52c63fa888e0181c9578c3921ed |
from __future__ import print_function
import time,gzip,random,os,sys
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.RDLogger import logger
logger = logger()
tests=[1]*1001
if len(sys.argv)>1:
tests=[0]*1001
tests[1]=1
for x in sys.argv[1:]:
x = int(x)
tests[x] = 1
ts = []
... | adalke/rdkit | Regress/Scripts/new_timings.py | Python | bsd-3-clause | 4,872 | [
"RDKit"
] | 667334c45255ce52f35fb3d3a5d0f1e5ca9d5931e4d1e5f92b3ed3a29996024d |
"""
Compliance Checker suite runner
"""
import sys
import inspect
import itertools
from netCDF4 import Dataset
from lxml import etree as ET
from compliance_checker.base import BaseCheck, fix_return_value, Result
from owslib.sos import SensorObservationService
from owslib.swe.sensor.sml import SensorML
import urllib.pa... | webtrike/compliance-checker | compliance_checker/suite.py | Python | apache-2.0 | 16,436 | [
"NetCDF"
] | d29998b069e725358f5137ace3d2240ca26fd1622d6f7c4f6ae93b2b001f1582 |
# (c) 2012-2014, Michael DeHaan <michael.dehaan@gmail.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) an... | fdupoux/ansible | lib/ansible/constants.py | Python | gpl-3.0 | 18,670 | [
"Galaxy",
"MOOSE"
] | 231b462e54d5ec41d4fd21a399378b049ebde5c9fa8b266197e4aaca8b4d28a4 |
#!/bin/env python
"""
Show request given its ID, a jobID or a transformation and a task
"""
import datetime
import os
from DIRAC.Core.Base.Script import Script
def convertDate(date):
try:
value = datetime.datetime.strptime(date, "%Y-%m-%d")
return value
except Exception:
pass
try:
... | DIRACGrid/DIRAC | src/DIRAC/RequestManagementSystem/scripts/dirac_rms_request.py | Python | gpl-3.0 | 11,269 | [
"DIRAC"
] | 2df454ecbd909beb94098325c1ed10152f97e4f58cd40e69bf09fccedb5a58fb |
import numpy as np
from galaxy_analysis.plot.plot_styles import *
fsize = 17
rc('text', usetex=False)
rc('font', size=fsize)#, ftype=42)
import matplotlib as mpl
mpl.use('Agg')
import matplotlib.pyplot as plt
import glob
import deepdish as dd
import sys
import os
import yt
# some general plot styles for consistenc... | aemerick/galaxy_analysis | plot/plot_enrich.py | Python | mit | 16,808 | [
"Galaxy"
] | 4558526c959f71bbaf4e71e27a224f4188377f9e3c3c397c4433322b969ecf48 |
import re
from .torque import Torque
__all__ = ('SlurmTorque',)
class SlurmTorque(Torque):
""" A CLI job executor for Slurm's Torque compatibility mode. This differs
from real torque CLI in that -x command line is not available so job status
needs to be parsed from qstat table instead of XML.
"""
... | galaxyproject/pulsar | pulsar/managers/util/cli/job/slurm_torque.py | Python | apache-2.0 | 907 | [
"Galaxy"
] | 480719c055b2962da8bd78563c8437667e5d1691cee7b6f4322156c8d02028f3 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# 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 Graaf, Jannis M. Hoch,
# Kor de Jong,... | UU-Hydro/PCR-GLOBWB_model | model/groundwater.py | Python | gpl-3.0 | 53,479 | [
"NetCDF"
] | e9ba0e88a24f098f27f5f9dec4c13be081b3ac2fbadcc3b6730c3ba4f84d9683 |
"""Functions to plot epochs data."""
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Denis Engemann <denis.engemann@gmail.com>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Eric Larson <larson.eric.d@gmail.com>
# Jaakko Leppakangas <jaeilepp@student.jyu.fi>
# ... | rkmaddox/mne-python | mne/viz/epochs.py | Python | bsd-3-clause | 42,905 | [
"Gaussian"
] | 7347385c007f8bf7f1a6d53f8675000931b7c55210cb36ae3524627b31631fa0 |
import numpy as np
import pymc
from . import poles
from . import distributions
from . import rotations
class APWPath(object):
def __init__(self, name, paleomagnetic_pole_list, n_euler_poles):
for p in paleomagnetic_pole_list:
assert (isinstance(p, poles.PaleomagneticPole))
self._nam... | ian-r-rose/mcplates | mcplates/apw_path.py | Python | gpl-3.0 | 17,929 | [
"Gaussian"
] | b087f29da2c653a1cedf73e946a369c8ee7f39f9aabd9c1a4f7856d1d384b27e |
import os
import funcsigs
from decorator import decorator
import re
def bucket_url_and_key(gs_path):
m = re.search("(gs://.+?)/.+$", gs_path)
if m:
gs_bucket_path = m.group(1)
key = gs_path.replace(gs_bucket_path + "/", "")
return gs_bucket_path, key
else:
raise ValueErro... | LPM-HMS/COSMOS-2.0 | cosmos/util/task_helpers.py | Python | gpl-3.0 | 6,604 | [
"Bioconda"
] | 7d4ad34672a022c92bc026c1a46b83ec00f620ff3a76e230fe5618c303c3ff21 |
from ast import *
__author__ = 'Mathias Claus Jensen'
__Maintainer__ = 'Mathias Claus Jensen'
__all__ = ['ExtractVisitor']
ATOMIC_SOURCES = ['SQLSource', 'CSVSource']
AGGREGATED_SOURCES = ['JoiningSource']
WRAPPERS = ['ConnectionWrapper']
DIM_CLASSES = ['Dimension']
FT_CLASSES = ['FactTable']
MODIFY_LIST = ATOMIC_SOU... | Betaboxguugi/P6 | code/framework/reinterpreter/extract_visitor.py | Python | gpl-3.0 | 6,094 | [
"VisIt"
] | d0d895d0a1089ddec02415dbee54b261c98bf77a160e3ce89333e61b0feb657f |
from SimpleHTTPServer import SimpleHTTPRequestHandler
from json import loads
from random import randint
from re import search as re_search
from urllib import unquote
class TinyHandler(SimpleHTTPRequestHandler, object):
the_number = randint(1, 99999)
def __init__(s... | elespike/burp-cph | tinyweb.py | Python | mit | 4,789 | [
"VisIt"
] | 9457ed73d3f56f96bf334193d89e510553bf9935ae040b1246141c755cbc7f15 |
from miscfunc import clear,sanitize,getBool
from command import Command,sanitizeCommand
#from mainfunctions import *
from player import Player
from questionnaire import questionnaire
from quests import Quest
import random
from rooms import Room
from standardrooms import possRooms
from standarditems import *
i... | natemacfadden/math121 | ReedGame/main.py | Python | mit | 48,974 | [
"exciting"
] | bb230731256f4afb8ea54d2d7d229748bc9b1ec06367b0e2c037675bbad88c9f |
# Compiled by Charles Harris, dated October 3, 2002
# updated to 2002 values by BasSw, 2006
# Updated to 2006 values by Vincent Davis June 2010
# Updated to 2014 values by Joseph Booker, 2015
"""
Fundamental Physical Constants
------------------------------
These constants are taken from CODATA Recommended Values of ... | gfyoung/scipy | scipy/constants/codata.py | Python | bsd-3-clause | 116,010 | [
"Avogadro",
"VisIt"
] | e6d9f278b7643025568d85d6ad6b4481bc32963a208d914d5ceddab9d15992b0 |
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