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|---|---|---|---|---|---|---|---|
"""
Acceptance tests for the teams feature.
"""
import json
import ddt
from nose.plugins.attrib import attr
from uuid import uuid4
from ..helpers import UniqueCourseTest
from ...fixtures import LMS_BASE_URL
from ...fixtures.course import CourseFixture
from ...fixtures.discussion import (
Thread,
MultipleThrea... | tiagochiavericosta/edx-platform | common/test/acceptance/tests/lms/test_teams.py | Python | agpl-3.0 | 47,439 | [
"VisIt"
] | a3e1fb86000c7525c6c63aed3f699fe01cef0a0f94bf970e72679dda7b108c66 |
import tempfile
from pele.landscape import DoubleEndedConnect, DoubleEndedConnectPar
from pele import basinhopping
from pele.storage import Database
from pele.takestep import RandomDisplacement, AdaptiveStepsizeTemperature
from pele.utils.xyz import write_xyz
from pele.optimize import lbfgs_cpp
from pele.transition_st... | js850/pele | pele/systems/basesystem.py | Python | gpl-3.0 | 17,853 | [
"PyMOL"
] | 55e0965d14b1bf6614920c8430e45b6a606332485944f3eebb56b80a3100f48a |
from cifsdk.format.cifcsv import Csv
def test_format_csv():
data = [
{
'observable': "example.com",
'provider': "me.com",
'tlp': "amber",
'confidence': "85",
'reporttime': '2015-01-01T00:00:00Z',
'tags': ['botnet', 'malware']
... | csirtgadgets/cif-sdk-py | test/test_csv.py | Python | lgpl-3.0 | 853 | [
"Amber"
] | dc636fdbb13d0ccb00a2722fb935ce4608649c17949d85244a170d3c48bbe55a |
"""Module symbol-table generator"""
from . import ast
from .consts import SC_LOCAL, SC_GLOBAL, SC_FREE, SC_CELL, SC_UNKNOWN
from .misc import mangle
import types
import sys
MANGLE_LEN = 256
class Scope:
# XXX how much information do I need about each name?
def __init__(self, name, module, klass=None):
... | minghuascode/pyj | pyjs/src/pyjs/lib_trans/pycompiler/symbols.py | Python | apache-2.0 | 14,441 | [
"VisIt"
] | 21804abba13342ff14e8cae49fd93d9f2d917406dced428b12aa6ae41ff482e0 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import json
import pytz
import six
from datetime import datetime, timedelta
from django.conf import settings
from django.core.urlresolvers import reverse
from django.utils import timezone
from django_redis import get_redis_connection
from django.db impor... | pulilab/rapidpro | temba/msgs/tests.py | Python | agpl-3.0 | 105,258 | [
"VisIt"
] | 81d83aa082461c796f44a9977b71f716afadc4e41af3e87e3cf847b3d07066f9 |
"""Test for WMS clients."""
# pylint: disable=protected-access, missing-docstring, invalid-name
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
import pytest
from mock import MagicMock
from DIRAC import S_OK, S_ERROR
from DIRAC.WorkloadManagementSystem.Cl... | yujikato/DIRAC | src/DIRAC/WorkloadManagementSystem/Client/test/Test_Client_DownloadInputData.py | Python | gpl-3.0 | 10,844 | [
"DIRAC"
] | 6001f316d96a20c535c7a185d19d433d4a22b0ef3f6003b23479824f5fcee4e1 |
# -*- coding: utf-8 -*-
from pgradd.RINGParser.Reader import Read
from rdkit import Chem
import unittest
class TestRINGParser(unittest.TestCase):
def test_molquery(self):
testmol = Chem.MolFromSmiles('CCC')
s = """
fragment a{
C labeled c1
C labeled c2 single bond ... | VlachosGroup/VlachosGroupAdditivity | pgradd/tests/test_RINGparser_RDkitwrapper_test.py | Python | mit | 12,902 | [
"RDKit"
] | 9e91061cdd9f2a0169b3efb047cedee1752ce36424e02c87436e0f548a1ca83d |
# Copyright (C) 2013, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from __future__ import print_function
import os
import shutil
from os.path import join, relpath
from repo import archives, cmd
from zeroinstall import SafeException
def handle(args):
cmd.find_config()
config = c... | bastianeicher/0repo | repo/cmd/reindex.py | Python | lgpl-2.1 | 2,103 | [
"VisIt"
] | 8f8cdbc9c43c75fb5df46472c92f2dbd7657e39eb0ac9a1a6fc8b6d19cedb9b6 |
# ----------------------------------------------------------------------
# Numenta Platform for Intelligent Computing (NuPIC)
# Copyright (C) 2016, Numenta, Inc. Unless you have purchased from
# Numenta, Inc. a separate commercial license for this software code, the
# following terms and conditions apply:
#
# This pro... | EricSB/nupic | src/nupic/regions/AnomalyLikelihoodRegion.py | Python | agpl-3.0 | 4,853 | [
"Gaussian"
] | 7cb1523ed16a03ceeae2d72b7edc71df2ec9d478112bddf9169385de51f5ee1b |
from __future__ import absolute_import
input_name = '../examples/linear_elasticity/elastic_shifted_periodic.py'
output_name = 'test_elastic_shifted_periodic.vtk'
from tests_basic import TestInput
class Test(TestInput):
pass
| rc/sfepy | tests/test_input_elastic_shifted_periodic.py | Python | bsd-3-clause | 229 | [
"VTK"
] | 5f04762f45089e28d83ed68780fc96108f75ac96509540ab6042cfd5bb3bed13 |
# -*- coding: utf-8 -*-
from django.test import TestCase, override_settings
from django.core.management import call_command
from django.shortcuts import get_object_or_404
from django.contrib.auth.models import User
from django.contrib.auth.hashers import make_password
from helpdesk.models import Queue, Ticket, TicketC... | rossp/django-helpdesk | helpdesk/tests/test_get_email.py | Python | bsd-3-clause | 37,282 | [
"VisIt"
] | 3db1322a8713b902f40215c38056be38f6953744fb21b6854d463712fe658c42 |
# Copyright 2008-2015 Nokia Solutions and Networks
#
# 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 l... | snyderr/robotframework | src/robot/model/testcase.py | Python | apache-2.0 | 2,883 | [
"VisIt"
] | fbe4fd0003ecd8786a876e212bfd12ad384f193f391bf25e2b4b0255c4ee8576 |
#!/usr/bin/python
import os, sys # low level handling, such as command line stuff
import string # string methods available
import re # regular expressions
import getopt # comand line argument handling
from low import * # custom functions, written by myself
import anydbm # index databases (file ... | lotharwissler/bioinformatics | python/kegg/kegg-enzyme2ko.py | Python | mit | 2,761 | [
"Biopython"
] | 5c8fd74c7c48abd76fd61af1d11f2d6fabc72b26b190e384d477b3bc753b222f |
#----------------------------------------------------------
#Example to run a multi-dimensional GP analysis with pyaneti
#Barragan O., 2021
#This analysis reproduces the RV analysis of K2-100 presented in
#http://dx.doi.org/10.1093/mnras/stz2569
#----------------------------------------------------------
#------------... | oscaribv/pyaneti | inpy/example_timeseries_k2100/input_fit.py | Python | gpl-3.0 | 5,723 | [
"Gaussian"
] | 2c9a4c57a0bff43077ab549acc63b17a5ebb9bb58344f23e8b089f9a344bf67d |
#!/usr/bin/env python
"""I am a(n) adjective noun."""
import random
import sys
VOWELS = ('a', 'e', 'i', 'o', 'u')
ADJECTIVES = [
'alphabetical',
'apple-eyed',
'carbon-based',
'cheery-eyed',
'couch-like',
'earl-grey',
'flubbery',
'half-silvered',
'inconvenient',
'kitten-sitt... | dbarella/i-am-a | i_am.py | Python | mit | 2,153 | [
"Octopus"
] | 63483b6a9abcf6059cf4f0a302470ec1e10e220bb2e2be97bc14347179c220af |
from DIRAC import gLogger
from DIRAC.Core.Base.Client import Client, createClient
@createClient("WorkloadManagement/VirtualMachineManager")
class VMClient(Client):
def __init__(self, *args, **kwargs):
super(VMClient, self).__init__(*args, **kwargs)
self.log = gLogger.getSubLogger("WorkloadManageme... | ic-hep/DIRAC | src/DIRAC/WorkloadManagementSystem/Client/VMClient.py | Python | gpl-3.0 | 401 | [
"DIRAC"
] | f9ca5c193c0d578e7858735d8aed27a07c0737ace9ed7a75d3b7c605eb649edd |
# creates: transport_setup.png
import numpy as np
from ase import Atoms
from ase.data.molecules import molecule
from ase.io import write
a = 3.92 # Experimental lattice constant
sqrt = np.sqrt
cell = np.array([[a / sqrt(3), 0., 0.],
[ 0., a / sqrt(2), 0.],... | grhawk/ASE | tools/doc/ase/transport/transport_setup.py | Python | gpl-2.0 | 2,462 | [
"ASE"
] | 7debf0a32acf5badeaf505d91fe620f93db2280d45bb6ba8c881c56079cf101e |
########################################################################
# $HeadURL$
# File : CondorComputingElement.py
# Author : R.Graciani
########################################################################
import os, stat, tempfile, shutil
from DIRAC.Resources.Computing.LocalComputingElement import LocalCom... | sposs/DIRAC | Resources/Computing/CondorComputingElement.py | Python | gpl-3.0 | 770 | [
"DIRAC"
] | 4f2d258e00577b4f599c43ddb202f3b7e11b0f00d4e22cba8fdc639d920bdd0a |
import abc
import datetime
import enum
import typing
import jsii
import jsii.compat
import publication
from jsii.python import classproperty
import aws_cdk.core
import aws_cdk.cx_api
__jsii_assembly__ = jsii.JSIIAssembly.load("@aws-cdk/assets", "1.15.0", __name__, "assets@1.15.0.jsii.tgz")
@jsii.data_type(jsii_type=... | randyzingle/tools | kub/services/archive/cdk/python/sample-app/.env/lib/python3.6/site-packages/aws_cdk/assets/__init__.py | Python | apache-2.0 | 9,336 | [
"CDK"
] | f6a16670d1aacbcf83ba2a9b30d8b1ddb59dac114ea141517dd26e010fee7887 |
#
#
#Custom filename tags to distinguish from other runs
project = "Project"
runVers = "Run"
#Default plot
#Select ONE only:
#makePlot = "structure"
#makePlot = "sed"
makePlot = "spectrum"
#makePlot = "ldc"
#makePlot = "ft"
#makePlot = "tlaLine"
#Spectrum synthesis mode
# - uses model in Restart.py... | sevenian3/ChromaStarPy | T4300g45CaIIHK.py | Python | mit | 2,744 | [
"Gaussian"
] | 5238ad792835f28e5f80676fceb60b357ea7d23ead810cb8999b9ceafaaac3ae |
#!@PYTHON_EXECUTABLE@
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 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 redistri... | CDSherrill/psi4 | psi4/run_psi4.py | Python | lgpl-3.0 | 14,074 | [
"Psi4"
] | 53f38e5d81abcc69eb8c150b49658f5025beab5c84fb15dc44c2e0d261b42c83 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
#
#
# 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... | e-gob/plataforma-kioscos-autoatencion | scripts/ansible-play/.venv/lib/python2.7/site-packages/ansible/modules/network/avi/avi_alertconfig.py | Python | bsd-3-clause | 11,682 | [
"VisIt"
] | 5eba1f7e425727b804ce0788fb5c21216f8bd8bc0aafbbe3d2bcea0f2487c92e |
'''
Created on 2014-01-26
A script to extract time-series averaged over the area defined by a collection of shapes (shapefiles).
Adapted from regrid.py.
@author: Andre R. Erler, GPL v3
'''
# external imports
import os # check if files are present
import numpy as np
from importlib import import_module
fr... | aerler/GeoPy | src/processing/shpavg.py | Python | gpl-3.0 | 22,539 | [
"NetCDF"
] | ae2c0937077f7f68ff5f267f4ae436cbcf4824a88f6a3a938db31c59ff96e197 |
#!/usr/bin/env python
########################################################################
# File : dirac-wms-job-delete
# Author : Stuart Paterson
########################################################################
"""
Delete DIRAC job from WMS, if running it will be killed
Example:
$ dirac-wms-job-delete ... | DIRACGrid/DIRAC | src/DIRAC/Interfaces/scripts/dirac_wms_job_delete.py | Python | gpl-3.0 | 2,108 | [
"DIRAC"
] | 3c90d18333fe7835974d3cbd358de08de44e2a5ead08cccf16c7148abec95613 |
# -*- coding: utf-8 -*-
"""
Connection screen
Texts in this module will be shown to the user at login-time.
Muddery will look at global string variables (variables defined
at the "outermost" scope of this module and use it as the
connection screen. If there are more than one, Muddery will
randomize which one it displ... | emergebtc/muddery | templates/example/server/conf/connection_screens.py | Python | bsd-3-clause | 1,277 | [
"VisIt"
] | 944dd27fcfecfb525dae2a8a813c4e775fbbb51394685c8fbcb1c43fe5845f08 |
#! /usr/bin/python3
import argparse
import sys
import csv
import lib.sqlite_interface as misc
import re
import pandas
# =========
# CONSTANTS
# =========
MISSING_DATA = 'MISSING'
# ==================
# EXPORTED FUNCTIONS
# ==================
def parse(parent, *args, **kwargs):
""" Handles arguments for the 'qu... | zbwrnz/blastdbm | lib/query.py | Python | unlicense | 8,969 | [
"BLAST"
] | cead84e4c23162a2fde7f7d86aaed9457317dbc757812388db2b09be99e0cff1 |
import numpy as np
from copy import deepcopy
from typing import List, Tuple, Optional, Union, Dict
from .config.cfg import SweepConfig
from .config.schema import fill_validate_metric
from .run import SweepRun, RunState
from .params import HyperParameter, HyperParameterSet
from sklearn import gaussian_process as sklea... | wandb/client | wandb/sweeps/bayes_search.py | Python | mit | 17,615 | [
"Gaussian"
] | 4b77d34171341820ea6f4e7ef668f7c1f45b4f80b69d9dcf43d3627111e995e2 |
"""A web analytics application."""
import os
import datetime
from flask import Flask
from flask_bcrypt import Bcrypt
from flask_login import LoginManager
from flask_sqlalchemy import SQLAlchemy
from .extensions import geo_ip
from .extensions import encoding
app = Flask(__name__, instance_relative_config=True)
app.c... | bmweiner/crumby | crumby/__init__.py | Python | mit | 1,643 | [
"VisIt"
] | 9572632a0cdca4983f151892cf2919bdad41b4ccf4db3f24c0a0b27bcbcd8fe4 |
#!/usr/bin/env python
"""
multiple stimulus demo
"""
############################
# Import various modules #
############################
import VisionEgg
VisionEgg.start_default_logging(); VisionEgg.watch_exceptions()
from VisionEgg.Core import *
from VisionEgg.Dots import DotArea2D
from VisionEgg.Gratings impor... | visionegg/visionegg | demo/multi_stim.py | Python | lgpl-2.1 | 11,928 | [
"Gaussian"
] | daff1937b7440086d5ab954b948a7a3e682dace81157c35d7f65b037abe305ef |
# coding=utf-8
"""
InaSAFE Disaster risk assessment tool developed by AusAid -
**IS Utilities implementation.**
Contact : ole.moller.nielsen@gmail.com
.. note:: 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... | borysiasty/inasafe | safe/utilities/utilities.py | Python | gpl-3.0 | 12,014 | [
"VisIt"
] | 27a35b222f15c03e5161553f0062929bd5d79e8f8415086673684328aae667e6 |
import os
from datetime import datetime
from django.test import SimpleTestCase
from django.utils.functional import lazystr
from django.utils.html import (
conditional_escape, escape, escapejs, format_html, html_safe, json_script,
linebreaks, smart_urlquote, strip_spaces_between_tags, strip_tags, urlize,
)
from... | frankvdp/django | tests/utils_tests/test_html.py | Python | bsd-3-clause | 11,654 | [
"ADF"
] | 58ba322a807a916edf27834aa4f8d043978202e0fa6bb55b7ea5701681b87e58 |
#!@TARGET_PYTHON@
# This file is part of LilyPond, the GNU music typesetter.
#
# LilyPond 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 versi... | sehe/Lilypond | scripts/etf2ly.py | Python | gpl-3.0 | 33,743 | [
"GULP"
] | 48066eb157206a068d455b56245e2a6dcf24cd4da0b6639d7ccfc688e5fb0720 |
#!/usr/bin/env python
# -*- coding: iso-8859-1 -*-
# Documentation is intended to be processed by Epydoc.
"""
Introduction
============
The Munkres module provides an implementation of the Munkres algorithm
(also called the Hungarian algorithm or the Kuhn-Munkres algorithm),
useful for solving the Assignment Problem... | wasit7/toi | python/munkres-1.0.7/munkres.py | Python | bsd-3-clause | 24,745 | [
"Brian"
] | b7012b63a20322be2904157e3f8ab7c51f805134ed26f1622808a8973e98e3b5 |
import fnmatch
import os
import pandas as pd
import cPickle as pickle
import subprocess
import csv
'''This program takes accepted_hits.bam files from tophat and turns them into
counts and creates matrix file of cells/conditions and counts using htseq:
http://www-huber.embl.de/HTSeq/doc/overview.html
The files are sort... | idbedead/RNA-sequence-tools | Count_Parsing/sort_htseq_count_single.py | Python | mit | 6,529 | [
"HTSeq"
] | b60fa6976062b666cb224066ff6fb6b7fdb255c36763c4ecbea295c6be30fc59 |
# coding=utf-8
"""
Tests for the course home page.
"""
from datetime import datetime, timedelta
import ddt
import mock
import six
from django.conf import settings
from django.http import QueryDict
from django.urls import reverse
from django.utils.http import urlquote_plus
from django.utils.timezone import now
from e... | eduNEXT/edunext-platform | openedx/features/course_experience/tests/views/test_course_home.py | Python | agpl-3.0 | 44,799 | [
"VisIt"
] | 7e485be94d1391334691b8509f2d9c8ddd83910abfb28a77d37f6c5d9b7b4d8b |
"""
Acceptance tests for the Import and Export pages
"""
from nose.plugins.attrib import attr
from datetime import datetime
from flaky import flaky
from abc import abstractmethod
from bok_choy.promise import EmptyPromise
from common.test.acceptance.tests.studio.base_studio_test import StudioLibraryTest, StudioCourse... | itsjeyd/edx-platform | common/test/acceptance/tests/studio/test_import_export.py | Python | agpl-3.0 | 16,975 | [
"VisIt"
] | 072ee50df42f2934bcad404d32259a7de40ecfd5e47be18b92ad4ba596c852bc |
import os
import errno
import logging
from .log import getLogger
from .var import IS_WINDOWS
__all__ = ['mkdirp', 'get_mtime', 'try_remove', 'samefile', 'rename', 'rmtree', 'lisdir']
def mkdirp(p):
try:
os.makedirs(p)
except OSError as e:
if e.errno != errno.EEXIST: raise
def get_mtime(path):
'''
Note: we re... | timbertson/gup | python/gup/util.py | Python | lgpl-2.1 | 2,174 | [
"VisIt"
] | 1f732d8125f1f1dda836bc48e6c171d6ae1b80bc4284d9c81b1b8c8788608e68 |
__author__ = 'sunwj'
import os
import httplib
import json
from datetime import datetime
from cms.aliyun_oss_handler import *
from cms import cms_model
from cms import service_config
from cms.image_processor import ImageProcessor
from cms import cms_service
config = service_config.config
logger = config.getlogger("... | swenker/studio | shijing_img/source/wshelper.py | Python | apache-2.0 | 9,857 | [
"VisIt"
] | da61c54bdd9745ac37802ff48971cefd5c2e9c9d474fc6863b92844e1713190e |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# vim:fenc=utf-8
#
# Copyright © 2017 Malcolm Ramsay <malramsay64@gmail.com>
#
# Distributed under terms of the MIT license.
"""Testing the dynamics module."""
import numpy as np
import quaternion
from hypothesis import HealthCheck, assume, given, settings
from hypothesi... | malramsay64/MD-Molecules-Hoomd | test/dynamics_test.py | Python | mit | 8,955 | [
"Gaussian"
] | 89f02f6f529e8b6517b04a4ebaf196890de98eb79c6f7f23d720e5078b476958 |
#
# Copyright (C) 2013-2018 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... | mkuron/espresso | samples/p3m.py | Python | gpl-3.0 | 6,406 | [
"ESPResSo"
] | a98c6c18fc89895e3ae8ce298233f7b349e519a2bd3cdb18cf158654bd084295 |
import campaign_lib
from campaign_lib import *
gosshawkspeech1={"intro":[("Gosshawk","Good day Captain. Are you looking for work?"),
("Burrows","Maybe -- you're hiring?"),
("Gosshawk","Indeed. My name is Captain Gosshawk, I'm a Privateer for myself. I've got my fi... | ermo/privateer_wcu | modules/galagoss.py | Python | gpl-2.0 | 29,352 | [
"Galaxy",
"VisIt",
"exciting"
] | 922fbf743d7a33b3b47f7ec57170ec5e94b8a4b97aa195b19c55a191bde607a3 |
# -*- coding: utf-8 -*-
""" Incident Reporting System - Model
@author: Sahana Taiwan Team
@author: Fran Boon
"""
if deployment_settings.has_module("irs"):
# Staff as component of Incident Reports
if deployment_settings.has_module("vehicle"):
link_table = "irs_ireport_vehicle_human_resource"
... | flavour/porto | models/05_irs.py | Python | mit | 32,652 | [
"VisIt"
] | a756784740dccb792c4d5e13a7cacc1b4f811807e28445a41a04ece0af3b606e |
#!/usr/bin/env python
# -*- coding: utf-8
"""This file contains Kegg related classes."""
import os
import shutil
import glob
import re
import copy
import statistics
import json
import time
import hashlib
import pandas as pd
import numpy as np
from scipy import stats
import anvio
import anvio.db as db
import anvio.uti... | merenlab/anvio | anvio/kegg.py | Python | gpl-3.0 | 357,559 | [
"VisIt"
] | 62709bf219e034ff9039839fc5e7f4dd2b6d5264ceb9626688b55ed3e811cfa9 |
"""
A robot exclusion rules parser for Python by Philip Semanchuk
Full documentation, examples and a comparison to Python's robotparser module
reside here:
http://NikitaTheSpider.com/python/rerp/
Comments, bug reports, etc. are most welcome via email to:
philip@semanchuk.com
Simple usage examples:
import ro... | rboulton/robotexclusionrulesparser | robotexclusionrulesparser.py | Python | bsd-3-clause | 29,498 | [
"VisIt"
] | dff09f952ab5d15475e1f86f65721b97194c047029c552547cb6b7bd5eb1ecfa |
# Hidden Markov Model Implementation
import pylab as pyl
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy as scp
import scipy.ndimage as ni
import scipy.io
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import rospy
#import hrl_lib.mayavi2_util as mu
imp... | tapomayukh/projects_in_python | classification/Classification_with_HMM/Single_Contact_Classification/simulation_results/Combined/hmm_crossvalidation_force_10_states.py | Python | mit | 13,035 | [
"Gaussian",
"Mayavi"
] | de352672864c35c2969264d5acf50260108effebe351603f4d965c74fbbc7a3f |
#!/usr/bin/env python
import sys
# WE RELY ON THESE BEING SET !!!
# set default verbose level
# verbose = os.environ.get('RADICAL_PILOT_VERBOSE', 'REPORT')
# os.environ['RADICAL_PILOT_VERBOSE'] = verbose
# set default URL to IMP Mongo DB
# path_to_db = os.environ.get(
# 'RADICAL_PILOT_DBURL', "mongodb://ensembl... | jrossyra/adaptivemd | examples/rp/test_simple.py | Python | lgpl-2.1 | 2,935 | [
"OpenMM"
] | 7e58bc6aef99d34cd47cbead6bd6ebf6e5f25ed5ba0dc595636fcd1c538489c0 |
#!/usr/bin/env python
# Iridium browser OSX translations clean up script
# Copyright (C) 2015 struktur AG <opensource@struktur.de>
# 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 versio... | guorendong/iridium-browser-osx | trim_xtb.py | Python | gpl-2.0 | 3,046 | [
"xTB"
] | e1544614144a027da39f5af78e807cd4873e15f934c09005b9014eba8f40d577 |
"""Smooth sine projected maps with Gaussian kernels"""
import argparse
from multiprocessing import Pool
import numpy as np
from astropy import constants as const
from astropy.io import fits
from opstats.modeling import gaussian_smooth
from opstats.utils import check_dir, HERA_ANT_DICT
from opstats.utils import MWA_FR... | piyanatk/sim | scripts/smooth_sine_maps.py | Python | mit | 2,943 | [
"Gaussian"
] | b58d702ca3396c4f3b7c333fa9a1f89f35c5a45a7e1c945afe5b97e2a72e9340 |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publish... | thica/ORCA-Remote | src/ORCA/ActionType.py | Python | gpl-3.0 | 3,470 | [
"ORCA"
] | 01a9256b54bd7706a22bbf92e2dddb06b01d183ef585ba044284ff5893f81fd4 |
#! /usr/bin/env python
#
# Copyright (c) 2004 Theodore A. Roth
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright
# notice, thi... | michelangelo/Cumae | external/avr-libc-2.0.0/devtools/cr_check.py | Python | mit | 3,518 | [
"VisIt"
] | d719eef93422b61f0282caf1c35c4e3a2a5edc3ab6778a6c9aa7aa16f8a49948 |
#!/usr/bin/python
# Guillermo Torres MSc,
# ggtorrese@unal.edu.co, guigotoe@gmail.com
# Bioinformatic Research Group
# Biotechnology Institute of National University of Colombia
# last update: Dic 2014
# * Working file; retrieve info about PIS and SS to analyse their behavior
# * Nmax of PIS corrected
# update: Ju... | guigotoe/HISS | scripts/CrSo/CrSo_wkv.py | Python | gpl-3.0 | 15,831 | [
"BLAST",
"Biopython"
] | 236afc1729f7163a0f3c75b9e51ea0614fb522e0a516eb1e982b7489626201a5 |
## unit tests for python synapse client
############################################################
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
from collections import OrderedDict
from datetime import datetime as ... | kkdang/synapsePythonClient | tests/unit/unit_test_annotations.py | Python | apache-2.0 | 6,536 | [
"MOOSE"
] | ce8e9fdeb946cfe2287808bad74ae31341f6f0872d6dd759a36720122e1d1ab9 |
# Copyright 2018 The TensorFlow Probability Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law o... | tensorflow/probability | tensorflow_probability/python/bijectors/real_nvp.py | Python | apache-2.0 | 17,808 | [
"Gaussian"
] | df01e82603b6e4a7e00846dd6edc803ea23cc956ded53a87b0138c2664b3913a |
import sys, glob
import matplotlib
import matplotlib.pyplot as plt
import numpy as np
from collections import defaultdict
usage = """python src/plot_metrics.py folder
the folder should contain models_iters_[topic].(type|word)scores,
along with lexscores.csv
e.g. python src/plot_metrics.py naima_11to24m"""
DO_ONLY = {... | SnippyHolloW/contextual_word_segmentation | src/plot_metrics.py | Python | mit | 14,073 | [
"Gaussian"
] | b6eee0af2752f585c0234844202da1fe74c68b0a8e7601318d0bb965c88b9500 |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publi... | thica/ORCA-Remote | src/ORCA/BaseConfig.py | Python | gpl-3.0 | 17,316 | [
"ORCA"
] | 74d6553098e86c5202f66797922d6a757295d44bff1e445fe79acf9b79244ace |
#!/usr/bin/python2.4
# Copyright (c) 2006-2008 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.
'''Unit tests for grd_reader package'''
import os
import sys
if __name__ == '__main__':
sys.path.append(os.path.join(os.path... | kuiche/chromium | tools/grit/grit/grd_reader_unittest.py | Python | bsd-3-clause | 3,565 | [
"xTB"
] | 047355dbaae2bef92ad4515e11bfd9527d2f93ce6dc54f22503a80ad79911c13 |
#!/usr/bin/env python
################################################################################
#
# A bunch of regression type tests for the builder and parser.
#
################################################################################
ident = '$Id: SOAPtest.py,v 1.19 2004/04/01 13:25:46 warnes Exp $'
... | cmsdaq/hltd | lib/SOAPpy-py3-0.52.24/tests/SOAPtest.py | Python | lgpl-3.0 | 138,717 | [
"MOOSE"
] | fb84bd9a1d906a66a4ae340e0f263d8f0dd35e01ca4f267ad9dd13b3d89cf6a4 |
# -*- coding: utf-8 -*-
import os
import subprocess
import shutil
import tempfile
from chempy import Reaction, ReactionSystem, Substance
from ..graph import rsys2dot, rsys2graph
from ..testing import requires, skipif
try:
dot_missing = subprocess.call(["dot", "-?"]) != 0
except OSError:
dot_missing = True
... | bjodah/chempy | chempy/util/tests/test_graph.py | Python | bsd-2-clause | 1,631 | [
"ChemPy"
] | 283c539b96edb94f5de74e5fc267208a09cec86415631883923c1f7aa61e7716 |
#!/usr/bin/env python
from __future__ import print_function
from __future__ import division
import sys, os
import datetime
import argparse
import pickle
import netCDF4 as nc
import numpy as np
import yaml
import scipy.ndimage as nd
from scipy.integrate import odeint
from scipy import interpolate as interp
from collec... | nicjhan/mom-particles | mom_particles.py | Python | gpl-2.0 | 17,555 | [
"NetCDF"
] | 6c3f9c56a52402fd991af2f531660231d495f703d48fa2fea28ad1dbe30023d2 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
import argparse
if __name__ == '__main__':
# Arguments parsing
parser = argparse.ArgumentParser(description='')
# -i / --input_sam
parser.add_argument('-i', '--input_sam',
metavar='INSAM',
type=argparse.Fi... | ppericard/matamog | scripts/filter_sam_based_on_blast.py | Python | agpl-3.0 | 1,740 | [
"BLAST"
] | 10e4e24a3397eea67d6a3b4c8830a4ae8e92ae9d277d3c408cd5d37e4923eaf5 |
import os
import sys
import unittest
from pathlib import Path
from monty.tempfile import ScratchDir
from pymatgen.core.periodic_table import Element
from pymatgen.io.phonopy import *
from pymatgen.util.testing import PymatgenTest
try:
from phonopy import Phonopy
from phonopy.file_IO import parse_FORCE_CONSTA... | richardtran415/pymatgen | pymatgen/io/tests/test_phonopy.py | Python | mit | 7,420 | [
"phonopy",
"pymatgen"
] | 34e3eb2dd091999bf5e1831e8f431236af2a0845bdb11103d16308b948fd3996 |
###AltAnalyze
#Copyright 2005-2008 J. David Gladstone Institutes, San Francisco California
#Author Nathan Salomonis - nsalomonis@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 with... | wuxue/altanalyze | AltAnalyze_BACKUP_6888.py | Python | apache-2.0 | 569,185 | [
"Cytoscape",
"pysam"
] | 4ec711f54492ae9600d5d2eb44bd14bfde02885ff62ce6d4efd5019a3533c14a |
#!/usr/bin/env python
# Parallel Python setup script
# For the latest version of the Parallel Python
# software visit: http://www.parallelpython.com
"""
Standard build tool for python libraries.
"""
import os.path
from distutils.core import setup
from pp import version as VERSION
LONG_DESCRIPTION = """
Parallel Pyt... | wiehan-a/pp-features | setup.py | Python | bsd-3-clause | 1,767 | [
"VisIt"
] | 43a31c4a6fe9ec3b5eaee0d8f12c4530bf319f5d10fef9cdd60c411d8f2546eb |
# Unit tests for cache framework
# Uses whatever cache backend is set in the test settings file.
import copy
import io
import os
import pickle
import re
import shutil
import tempfile
import threading
import time
import unittest
import warnings
from unittest import mock
from django.conf import settings
from django.core... | mlavin/django | tests/cache/tests.py | Python | bsd-3-clause | 91,516 | [
"Brian"
] | f4c7fd29018c0085d9e48e35fdef90a963a2e8a4c50bfd3ee685d3c5caec0770 |
import os, sys
import unittest
from tilde.core.api import API
from tilde.core.settings import BASE_DIR, EXAMPLE_DIR
class Test_API(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.sample = API()
def test_count_classifiers(self):
available_classifiers = []
path = os.path... | tilde-lab/tilde | tests/unit/api_test.py | Python | mit | 2,083 | [
"CRYSTAL",
"VASP"
] | 8e90ccdc2efbde615b75b2451982b4ef66f9f44e017cc039aee85983f5ddf8fb |
"""
TODO
"""
import numpy as _np
def radiation_length(material) -> float:
"""
Args:
material:
Returns:
"""
a: float = material.atomic_a
z: float = material.atomic_z
return 716.4 * a * (1 / (z * (z + 1) * (_np.log(287 / _np.sqrt(z)))))
def scattering_length(material) -> float:
... | chernals/georges | georges/fermi/mcs.py | Python | gpl-3.0 | 4,036 | [
"Avogadro"
] | 393bf56e2336db3e11aecb338668ee92b9132b2a302646ce95f60496756aecc3 |
from mmp_tracer_api import MMPRaytracer, objID
from mmp_mie_api import MMPMie
from comsol_api import MMPComsolDummy
from mupif import Property, PropertyID, FieldID, ValueType
import logging
import os
if not os.path.isdir('runFolder'):
os.mkdir('runFolder')
os.chdir('runFolder')
if __name__ == '__main__':
log... | ollitapa/MMP-TracerApi | Tests/LocalTest/localTest.py | Python | apache-2.0 | 4,539 | [
"VTK"
] | 1826ac7d01fc3bbd60d4b5d437b5e7ada39ba6dca418399d9f38a30e48309919 |
"""HTTPS module based on the GFAL2_StorageBase class."""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
# from DIRAC
from DIRAC.Resources.Storage.GFAL2_StorageBase import GFAL2_StorageBase
from DIRAC import gLogger
class GFAL2_HTTPSStorage(GFAL2_StorageBa... | ic-hep/DIRAC | src/DIRAC/Resources/Storage/GFAL2_HTTPSStorage.py | Python | gpl-3.0 | 1,019 | [
"DIRAC"
] | 3514059b3017ed1c863c32751e8d33b34569cbb11ef9800b210206678986db1f |
#!/usr/bin/env python
#
# Copyright 2007 Google Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law o... | levibostian/myBlanky | googleAppEngine/google/appengine/tools/sdk_update_checker.py | Python | mit | 15,221 | [
"VisIt"
] | d5fc00d95377855a683c90037934ab8f78edb04532d6f2437e6e57eda16b8752 |
# 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 RBiomart(RPackage):
"""Interface to BioMart databases (i.e. Ensembl).
In recent ye... | rspavel/spack | var/spack/repos/builtin/packages/r-biomart/package.py | Python | lgpl-2.1 | 2,004 | [
"Bioconductor"
] | 2ad0c74e08bddc93840de4f080a2b827cd43e82e6a5f2a64ec993eac00e2dc23 |
# ------------------------------------------------------------------------------
# Name: h5cube_cmdline
# Purpose: Tests for the command line interface to h5cube
#
# Author: Brian Skinn
# bskinn@alum.mit.edu
#
# Created: 29 Aug 2016
# Copyright: (c) Brian Skinn 2016
# License: T... | bskinn/h5cube | h5cube/test/h5cube_cmdline.py | Python | mit | 14,519 | [
"Brian"
] | d67607046dab2801cde369b1a7e1cc75dc043bab37d9f6967fa83584a18d41a9 |
#!/usr/bin/env python
# Run this file to generate the min and max counts used in
# test_description.json
import os
import numpy as np
def run_sims():
num_seeds = 100
mcell_name = "mcell"
mdl_name = "main_no_dg.mdl"
print("Begin running MCell simulations")
for i in range(1, num_seeds+1):
... | mcellteam/nutmeg | tests/dynamic_geometry_rxns/analyze.py | Python | bsd-2-clause | 3,641 | [
"MCell"
] | db55b06ecfebbb2b9bcd3171653fb994f0ab756447b8bd68a1ca4c19474a9766 |
"""
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Copyright (C) 2015 National Institutes of Health
This library is free software; you can redistribute it and/or
modify it under the ... | cnerger/wnd-charm | wndcharm/FeatureSpacePredictionExperiment.py | Python | lgpl-2.1 | 40,763 | [
"ASE"
] | d7680276d13a83d34375734814af4a1904a20c060076715c2397149ea8cf6509 |
from .base import *
class styles(object):
"""
cytoscape session interface as shown in CyREST's swagger documentation.
:param url: an url of the type 'http://' + host + ':' + str(port) + '/' + version + '/'.
"""
def __init__(self, url):
self.__url = url + 'commands/styles'
self.___... | idekerlab/py2cytoscape | py2cytoscape/cyrest/styles.py | Python | mit | 19,897 | [
"Cytoscape"
] | 7c86ff45e747c2ff62caed5f261a093f7b1b4d3fd1e64ddfdce40eb5e0e193a9 |
"""A Multivariate Normal Distribution."""
__authors__ = "Ian Goodfellow"
__copyright__ = "Copyright 2010-2012, Universite de Montreal"
__credits__ = ["Ian Goodfellow"]
__license__ = "3-clause BSD"
__maintainer__ = "LISA Lab"
__email__ = "pylearn-dev@googlegroups"
import warnings
try:
from scipy.linalg import choles... | JazzeYoung/VeryDeepAutoEncoder | pylearn2/pylearn2/distributions/mnd.py | Python | bsd-3-clause | 4,113 | [
"Gaussian"
] | 25cc5de2769bfe0b302bfc50f4f732e7162b6ffbbf3fd0ad94fd1ef96ca05908 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/Openwebif | plugin/controllers/views/web/serviceplayable.py | Python | gpl-2.0 | 5,413 | [
"VisIt"
] | 132aa7776dd12c3b0794f0eac44542f7200da5069523024a722ea57491152471 |
# Copyright (c) 2012 Google Inc. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
from __future__ import with_statement
import errno
import filecmp
import os.path
import re
import tempfile
import sys
# A minimal memoizing decorator. It'll blo... | kans/birgo | tools/gyp/pylib/gyp/common.py | Python | apache-2.0 | 15,488 | [
"VisIt"
] | b8d82062e7177022345f4fbb18bdb35860494d9a69d10ae044d46c25083a54e8 |
"""Guess the MIME type of a file.
This module defines two useful functions:
guess_type(url, strict=True) -- guess the MIME type and encoding of a URL.
guess_extension(type, strict=True) -- guess the extension for a given MIME type.
It also contains the following, for tuning the behavior:
Data:
knownfiles -- list ... | yotchang4s/cafebabepy | src/main/python/mimetypes.py | Python | bsd-3-clause | 20,956 | [
"NetCDF"
] | 8e48a1d7fef64970622959ba0fffcd514ecf8131764b5273ad6fdfe241585529 |
#
# Copyright (C) 2009, Brian Tanner
#
# http://rl-glue-ext.googlecode.com/
#
# Licensed under the Apache License, Version 2.0 (the "License")
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requ... | evenmarbles/rlglued | examples/mines-sarsa-example/sample_mines_environment.py | Python | bsd-3-clause | 8,581 | [
"Brian"
] | de8a75497fe51fe5dc3ec5740cae9bff547d77cd588b2859c1a1c79e99be3173 |
""" 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... | DIRACGrid/DIRAC | src/DIRAC/Core/Security/test/Test_X509Certificate.py | Python | gpl-3.0 | 11,585 | [
"DIRAC"
] | 6cde75cc5fb749ea5939cbdf49c3fffb24b84ab1a3794f522664fe66df0fd4d4 |
import os
import tempfile
import unittest
from pyepw.epw import TypicalOrExtremePeriods, TypicalOrExtremePeriod, EPW
class TestTypicalOrExtremePeriods(unittest.TestCase):
def setUp(self):
self.fd, self.path = tempfile.mkstemp()
def tearDown(self):
os.remove(self.path)
def test_create_ty... | rbuffat/pyepw | tests/test_typical_or_extreme_periods.py | Python | apache-2.0 | 2,262 | [
"EPW"
] | cfda493f91d8b04087543caa06ded741d4829c2599bbf05cff6b3567be08d0ee |
import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt
from matplotlib.patches import Ellipse
from matplotlib.ticker import MaxNLocator
import itertools as itt
def setfigdefaults():
mpl.rcParams['axes.linewidth'] = 1
mpl.rcParams['font.size'] = 14
#mpl.rcParams['font.family'] = 'sans-serif... | tianhuil/isaac-thedataincubator-project | analysis/myplotting.py | Python | apache-2.0 | 4,762 | [
"Gaussian"
] | c0a69f1bd679c29594e7da3ba1fdcbc87cdcf3d34c6d8833085cb5f1450eb463 |
#!/usr/bin/env python
import roslib
import rospy
import smach
import smach_ros
import sys
import time
from geometry_msgs.msg import Pose
from hlpr_speech_recognition.speech_listener import SpeechListener
from hlpr_speech_msgs.srv import SpeechService
#from hlpr_speech_synthesis import speech_synthesizer
from hlpr_... | kirmani/hlpr_cadence | third_party/hlpr_hello_world/scripts/manipulation_states.py | Python | mit | 15,593 | [
"exciting"
] | 3c4d1138f0c60b438cb8ff68a106fa2f0f400063a138b8f25bf13d30d78ec35d |
#!/usr/bin/env python
"""Usage::
$ rna_align_find_seq_in_alignment.py -a pistol_noPk.sto -s hcf.fa
('Match:', 'HCF12C_58327/229-301')
ID: HCF12C_58327/229-301
Name: HCF12C_58327
Description: HCF12C_58327/229-301
Number of features: 0
/start=229
/end=301
/accession=HCF12C_58327
... | m4rx9/rna-pdb-tools | rna_tools/tools/rna_alignment/rna_align_find_seq_in_alignment.py | Python | mit | 2,174 | [
"Biopython"
] | 74b6dd9897e3fae11cf833fd567bdd9534e3213d2747b300cac27ca9750b53a1 |
from __future__ import division, print_function
__author__ = "adrn <adrn@astro.columbia.edu>"
# Standard library
import os
# Third-party
from six.moves.urllib.request import urlretrieve, urlopen
from six.moves.urllib.error import URLError
__all__ = ['fetch_notMNIST', 'fetch_GalaxyZoo']
def fetch_data(data_url, cac... | astroNN/astroNN | astronn/data.py | Python | mit | 4,399 | [
"Galaxy"
] | 27ac59e17f2a91d1aa6441a4e1bdfe7163863648a7ab84b35206ae4f51e07e08 |
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yashdsaraf/scancode-toolkit | src/commoncode/system.py | Python | apache-2.0 | 3,745 | [
"VisIt"
] | 1ead992fecf33dd050bd76e7e71f53b462589738d4a29d727aaed3472c0ec2e9 |
# Module 'os' -- OS routines for NT, Posix, or UEFI depending on what system we're on.
#
# Copyright (c) 2015, Daryl McDaniel. All rights reserved.<BR>
# Copyright (c) 2011 - 2012, Intel Corporation. All rights reserved.<BR>
# This program and the accompanying materials are licensed and made available under
# th... | google/google-ctf | third_party/edk2/AppPkg/Applications/Python/Python-2.7.10/PyMod-2.7.10/Lib/os.py | Python | apache-2.0 | 27,611 | [
"VisIt"
] | 6cd52e7dff1a25787d05dc4d38daddebf74822c1a67c52104d6e7bd73afdd106 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import print_function, division, absolute_import
try:
import cPickle as pickle
except ImportError:
import pickle
from collections import OrderedDict
from functools import reduce
from itertools import product
from operator import add
import os
imp... | chemreac/chemreac | chemreac/tests/test_integrate.py | Python | bsd-2-clause | 12,589 | [
"ChemPy"
] | 55ffae0c943c1aa84bd0464384949a2c2b56ea28622f9377a11334297584ee0b |
#! python
# encoding: utf-8
# Wellcome Trust Sanger Institute and Imperial College London
# Copyright (C) 2020 Wellcome Trust Sanger Institute and Imperial College London
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by t... | sanger-pathogens/gubbins | python/scripts/extract_gubbins_clade.py | Python | gpl-2.0 | 4,295 | [
"Biopython"
] | eb9f26a3b9cc9527706b06f52cbf42ef37bc62bcf5181651dbe382f83dbb441e |
import sys
import cudamat as cm
from cudamat import cudamat_conv_gemm as cc
from cudamat import gpu_lock2 as gpu_lock
import h5py
import os
import numpy as np
import matplotlib.pyplot as plt
plt.ion()
from time import sleep
import pdb
import datetime
import time
import config_pb2
from google.protobuf import text_form... | y0ast/unsupervised-videos | util.py | Python | mit | 4,232 | [
"Gaussian"
] | 68a82dc5b4a3f92b7039ad6136d6c79bbeaea9a1f8d1a2f945831b122e2431b1 |
#
# Copyright (C) 2013,2014,2015,2016 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... | tbereau/espresso | samples/python/minimal-polymer.py | Python | gpl-3.0 | 1,764 | [
"ESPResSo"
] | aef00650677062dca9d984c241af7a9fec2f65a276d503e0e126b988d3509351 |
#!/ysr/bin/env python
from __future__ import division
import utils as utils
import numpy as np
import numpy.random as npr
import theano
import theano.tensor as T
import time
from HelperFuncs import to_fX
def my_batched_dot(A, B):
"""
Compute: [np.dot(A[i,:,:], B[i,:,:]) for i in range(A.shape[0])]
"""
... | capybaralet/Sequential-Generation | MotionRenderers.py | Python | mit | 12,755 | [
"Gaussian"
] | 6945b8308e6a1593916c558d4a6c9b7bc79fb7b40f8167fd7786cab106dc0589 |
"""
PySCeS - Python Simulator for Cellular Systems
(http://pysces.sourceforge.net)
Copyright (C) B.G. Olivier, J.M. Rohwer, J.-H.S. Hofmeyr
Stellenbosch, 2004-2015.
Triple-J Group for Molecular Cell Physiology
Stellenbosch University, South Africa
Author: Brett G. Olivier
PySCeS is Open Source Software dist... | asttra/pysces | pysces/nleq2/4.2/__init__.py | Python | bsd-3-clause | 423 | [
"PySCeS"
] | 8f422b2aad907e7e578d01a0845c3684d41afc4d53b8b566e0a40ec2297b330b |
# -*- coding: utf-8 -*-
# Copyright 2010 Dirk Holtwick, holtwick.it
#
# 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 ... | bakaat/xhtml2pdf | xhtml2pdf/parser.py | Python | apache-2.0 | 25,104 | [
"VisIt"
] | 2369d01abf7aafd9a88e4b3351f92765b2fee7b1a0a348c252ad58b241f215cc |
##
# Copyright 2009-2015 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
# the Hercules foundation (htt... | ULHPC/modules | easybuild/easybuild-easyblocks/easybuild/easyblocks/n/netcdf_fortran.py | Python | mit | 2,740 | [
"NetCDF"
] | 7f7df4adfd269a10b3944c729fea8ed8c0fcf38e75745f5b97eb93dfa28f6f51 |
# urls.py in blog project for potato
# created by Puneet Chawla (pchawla@buffalo.edu)
from django.conf.urls.defaults import *
handler500 = 'djangotoolbox.errorviews.server_error'
urlpatterns = patterns('',
('^_ah/warmup$', 'djangoappengine.views.warmup'),
# blank url for home page
url(r'^$', 'blog.views.home... | thisispuneet/potato-blog | urls.py | Python | bsd-3-clause | 1,013 | [
"VisIt"
] | 6c90dd7dc956c8c4a54d56bb80344a1fb658bbc6f1cf495cedcc834fff18caa7 |
# -*- coding: utf-8 -*-
from __future__ import print_function, absolute_import, division
from collections import defaultdict
import numpy as np
from pyodesys.util import import_
from pyodesys.core import integrate_chained
from pyodesys.symbolic import ScaledSys, TransformedSys, symmetricsys, PartiallySolvedSystem, g... | bjodah/pyodesys | pyodesys/native/tests/_tests.py | Python | bsd-2-clause | 16,492 | [
"ChemPy"
] | e581c6061f3bb598619247a17cf9007ba1859af89a62e511339dcc06d9e44e9c |
"""Global fixtures"""
import smtplib
from os.path import join
import pytest
from hdx.api.configuration import Configuration
from hdx.api.locations import Locations
@pytest.fixture(scope="session")
def fixturesfolder():
return join("tests", "fixtures")
@pytest.fixture(scope="session")
def configfolder(fixtures... | OCHA-DAP/hdx-python-api | tests/hdx/conftest.py | Python | mit | 44,829 | [
"BWA"
] | c4a6f9123a5a42c6b607a9bde55b54bdabfabe60776abe6a3733c066298fb975 |
__author__ = 'aniket'
"""
*
* ================================
*
* Author List:
* Filename:
* Date:
* Functions:
* Global Variables:
* Dependent library files:
*
* e-Yantra - An MHRD project under National Mission on Education using
* ICT(NMEICT)
*
**********************************************... | amirajdhawan/eYSIP_2015_Depth_Mapping_Kinect | Research/MyProjects/Kinect.py | Python | cc0-1.0 | 34,635 | [
"Gaussian"
] | 60d0802475fa27a6c78b21fe0c5f22472839611ac867def30d13ce5b917d1b2a |
""" Storage plug-ins related utilities
"""
__RCSID__ = "$Id$"
import errno
from DIRAC import S_OK
from DIRAC.Core.Utilities.DErrno import DError
def checkArgumentFormat( path ):
""" returns {'/this/is/an/lfn.1':False, '/this/is/an/lfn.2':False ...}
"""
if isinstance( path, basestring ):
return S_OK( {pat... | vmendez/DIRAC | Resources/Storage/Utilities.py | Python | gpl-3.0 | 664 | [
"DIRAC"
] | 668c008d57afe6d3db5edb844a717cb6ebe24ccc7a8a4b20a920a4b744c4fecb |
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