text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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if ( ('PFVFLOW' in features) and ('TWOPHASEFLOW' in features) ):
from yade import pack
from yade import export
from yade import timing
from yade import plot
import time
from math import *
num_spheres=1000# number of spheres
young=1e6
compFricDegree = 3 # initial contact friction during the ... | cosurgi/trunk | scripts/checks-and-tests/checks/check_TwoPhaseFlowEngine_PressureInjection.py | Python | gpl-2.0 | 13,370 | [
"VTK"
] | f2f32c6cd4d996a79c08508abefd6be36acdcbed8f9a40e84e6c241cba4ad55d |
#!/usr/bin/python2.5
# Copyright 2010 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 or ... | pet-finder/pet-finder | tests/server_tests.py | Python | apache-2.0 | 170,203 | [
"VisIt"
] | ccee82d1aeea1ab9fc9c7e7f5087ed51e7fc9a0fe1d67e8979d81ebcc0e6216b |
# Author: Travis Oliphant
# 1999 -- 2002
from __future__ import division, print_function, absolute_import
import warnings
import threading
from . import sigtools
from scipy._lib.six import callable
from scipy._lib._version import NumpyVersion
from scipy import linalg
from scipy.fftpack import (fft, ifft, ifftshift, ... | rmcgibbo/scipy | scipy/signal/signaltools.py | Python | bsd-3-clause | 87,008 | [
"Gaussian"
] | 4980d5552d692ae7d22da081a0449f0301e24a67457e677de8cdf8f8768b6b09 |
"""
ocl_gts v0.01
pyopencl genetic trade simulator
Copyright 2011 Brian Monkaba
This file is part of ga-bitbot.
ga-bitbot 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 Li... | bshyong/ga-bitbot | ocl_gts.py | Python | gpl-3.0 | 19,100 | [
"Brian"
] | d54942b5e9970f33d2f9f5ccc173df6d2347c9105667c0687176d566e8fbb8a2 |
# -*- coding: utf-8 -*
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Running SageNB Tests
Functions for running SageNB tests. This can also be used a script.
NOTE:
The SageNB tests tests assume a Selenium server or Grid hub is running
with the options given in :mod:`sagenb.testing.notebook_test_case` or
set by :... | topisani/sagenb | sagenb/testing/run_tests.py | Python | gpl-3.0 | 8,898 | [
"VisIt"
] | fe638daf92ab3a43b3132a0c051f30cadb9649bd6a89a22e32b22c8a45d48594 |
# Copyright (c) 2012 OpenStack Foundation
# All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless ... | CloudServer/nova | nova/tests/unit/compute/test_resource_tracker.py | Python | apache-2.0 | 58,490 | [
"exciting"
] | 64c026185d4c2ae46ef31eb54ce23b0a54745ecb1880b8d4a45413d1c3563ede |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# HORTON: Helpful Open-source Research TOol for N-fermion systems.
# Copyright (C) 2011-2016 The HORTON Development Team
#
# This file is part of HORTON.
#
# HORTON is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public Licens... | crisely09/horton | scripts/horton-esp-gen.py | Python | gpl-3.0 | 4,975 | [
"Gaussian"
] | afc2c97e92c4b2125497ed077773c82dd5ea8c12e964e78b32ea0430d4a42f92 |
# -*- coding: utf-8 -*-
u"""
.. module:: fabfile
Be aware, that becaus fabric doesn't support py3k You need to execute this
particular script using Python 2.
"""
import contextlib
from fabric.api import cd
from fabric.api import env
from fabric.api import prefix
from fabric.api import run
env.user = 'root'
env.host... | magul/wysadzulice.pl | fabfile.py | Python | mit | 847 | [
"GULP"
] | 1dcfbe29fdc4705359457019c383e2de50611746aa12469f74b9548bee28d653 |
../../../../../../../share/pyshared/orca/scripts/apps/soffice/script_utilities.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/scripts/apps/soffice/script_utilities.py | Python | gpl-3.0 | 81 | [
"ORCA"
] | 96ebfd2458aeddb3f60c9925e83ccd1cb2dfb2187252afa8c041a3078ef5e91c |
import unittest
from simphony import engine as engine_api
from simphony.api import CUDS
from simphony.engine import EngineInterface, create_wrapper
from simlammps.lammps_wrapper import LammpsWrapper
# TODO: Use an enum instead, defined in a proper place
_LAMMPS = 'LAMMPS'
class TestPluginIntegration(unittest.Test... | simphony/simphony-lammps-md | simlammps/tests/test_plugin_integration.py | Python | bsd-2-clause | 1,116 | [
"LAMMPS"
] | 30a76e7fa4171d265cb43523d9d36005bb509ba1b52117960fbf0458b45c1b8b |
#
# co_co_buffer_not_assigned.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
# (at you... | kperun/nestml | pynestml/cocos/co_co_buffer_not_assigned.py | Python | gpl-2.0 | 2,249 | [
"NEURON"
] | a8d11fc609c03e7d0c908c64e93971a876a8150fe885468da32e9d9f2b71c186 |
# coding: utf-8
# In[2]:
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.Alphabet import generic_dna
from numpy import random
from math import floor
from random import randint
import warnings
# In[39]:
# subsampling a genome according to the exponential, with mean=~ 1kbp
# In[11]:
def make_subsample(gen... | lonelyjoeparker/real-time-phylogenomics | wales_analyses/in-silico-reference-genome-digest/In silico genome skimming.py | Python | gpl-2.0 | 4,842 | [
"BLAST"
] | de6902e78e534f1756ea0fd9497bfe3f97d6d0d23e5995eda975bd7798afab07 |
""" The Job Scheduling Executor takes the information gained from all previous
optimizers and makes a scheduling decision for the jobs.
Subsequent to this jobs are added into a Task Queue and pilot agents can be submitted.
All issues preventing the successful resolution of a site candidate are dis... | ic-hep/DIRAC | src/DIRAC/WorkloadManagementSystem/Executor/JobScheduling.py | Python | gpl-3.0 | 29,885 | [
"DIRAC"
] | a5b13c37ffabb8c4da6028b4375d8095ac6ddd50b074c9588a4e8e200d48b766 |
"""
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... | ak2703/edx-platform | lms/djangoapps/instructor/views/instructor_dashboard.py | Python | agpl-3.0 | 26,997 | [
"VisIt"
] | f0c1011926566f6148aa34587bc45c64837696150ae7aea61087e949a9ce1e24 |
# coding: utf-8
# # Handwritten Digit Recognition with Theano
#
# In this tutorial we will train a feed forward network / multi-layer-perceptron (MLP) to recognize handwritten digits using pure Theano.
# For a long version see: http://deeplearning.net/tutorial/mlp.html
#
#
#
# ## Layout
# The layout of our netw... | nreimers/deeplearning4nlp-tutorial | 2015-10_Lecture/Lecture2/code/2_MNIST_solution.py | Python | apache-2.0 | 9,372 | [
"NEURON"
] | 814e6144e8ccb15a4650c2d483d73ca1904d36259d665765fc51085eb253ff0b |
"""
PDBBind binding pocket dataset loader.
"""
from __future__ import print_function
from __future__ import division
from __future__ import unicode_literals
import os
import numpy as np
import pandas as pd
import shutil
import time
import re
from rdkit import Chem
import deepchem as dc
def compute_binding_pocket_fea... | Agent007/deepchem | examples/binding_pockets/binding_pocket_datasets.py | Python | mit | 6,311 | [
"RDKit"
] | 87a5ce67a58c4a5e8ba392f0531d0b0323e8dc2622ffd6c983477605570aa0dd |
# linearizedGP -- Implementation of extended and unscented Gaussian processes.
# Copyright (C) 2014 National ICT Australia (NICTA)
#
# This file is part of linearizedGP.
#
# linearizedGP is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by... | NICTA/linearizedGP | linearizedGP/GP.py | Python | gpl-3.0 | 18,915 | [
"Gaussian"
] | c8543d3d056ea82aa316a28f592c354877f89bbccc036698d548646baba247d2 |
"""
UI-level acceptance tests for OpenAssessment.
"""
import ddt
import os
import unittest
import time
from functools import wraps
from pyinstrument import Profiler
from nose.plugins.attrib import attr
from bok_choy.web_app_test import WebAppTest
from bok_choy.promise import BrokenPromise, EmptyPromise
from auto_auth ... | nttks/edx-ora2 | test/acceptance/tests.py | Python | agpl-3.0 | 55,483 | [
"VisIt"
] | ccd8aa80d00e8a9b3effcdee2cb0fa7d2bf2e478865b541653782fb5c24fe0e9 |
#!/usr/bin/env python
"""Transport exersice
This file should do the same as pt_h2_lcao.py, but extracts the Hamiltonians
manually instead of using gpawtransport, which currently does not work
"""
from ase import Atoms
from gpaw import GPAW, Mixer, FermiDirac
from gpaw.lcao.tools import remove_pbc, get_lcao_hamiltonia... | robwarm/gpaw-symm | doc/exercises/transport/pt_h2_lcao_manual.py | Python | gpl-3.0 | 2,820 | [
"ASE",
"GPAW"
] | 1eacbadfe137e6b0c346ccf5deef95d8ad06f9fa0313ae0ecfcb0d362f30ce0e |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/item_title | openlp/plugins/media/lib/__init__.py | Python | gpl-2.0 | 2,206 | [
"Brian"
] | df28e9d2bddbe49adc8876b2fd708bab39ec8ab1d72f97b2d0eeca02c830ea63 |
# vim: tabstop=4 shiftwidth=4 softtabstop=4
# Copyright 2011 OpenStack Foundation
# All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apach... | jessicalucci/NovaOrc | nova/tests/api/openstack/test_xmlutil.py | Python | apache-2.0 | 28,151 | [
"VisIt"
] | 2f987b325d60b493703022b09b186d71338b97068060989d1081a20db9e0a555 |
"""
Non-linearity I: Detection Chain
================================
This simple script can be used to study the error in the non-linearity correction that can be tolerated given the
requirements.
The following requirements related to the non-linearity have been taken from GDPRD.
R-GDP-CAL-058: The contribution of ... | sniemi/EuclidVisibleInstrument | analysis/nonlinearityCalibration.py | Python | bsd-2-clause | 16,305 | [
"Gaussian"
] | 4bc7ab8601d3accaa14616bbd2dbcb659ed15ede3af133208e6e8dbcad1859df |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
A Flow is a container for Works, and works consist of tasks.
Flows are the final objects that can be dumped directly to a pickle file on disk
Flows are executed using abirun (abipy).
"""
from __future__ impo... | setten/pymatgen | pymatgen/io/abinit/flows.py | Python | mit | 106,096 | [
"ABINIT",
"pymatgen"
] | 1bfc5ade35f8d5de69ee9889856aa802ccd0d746774661a66f81c283997add6e |
import os
import tempfile
import shutil
import yaml
import mdtraj
from subprocess import Popen, PIPE
from ensembler.core import get_most_advanced_ensembler_modeling_stage, default_project_dirnames
from ensembler.core import model_filenames_by_ensembler_stage, get_valid_model_ids, mpistate
from ensembler.core import Yam... | danielparton/ensembler | ensembler/validation.py | Python | gpl-2.0 | 10,250 | [
"MDTraj"
] | 6d8dedef2ed6af8bf69b44806d92b16f7f874f4898335173cd149fdb06b2400c |
# coding: utf8
{
'!langcode!': 'nl',
'!langname!': 'Nederlands',
'"update" is an optional expression like "field1=\'newvalue\'". You cannot update or delete the results of a JOIN': '"update" is een optionele expressie zoals "veld1=\'nieuwewaarde\'". Je kan de resultaten van een JOIN niet updaten of verwijderen.',
... | ccpgames/eve-metrics | web2py/applications/admin/languages/nl.py | Python | mit | 28,530 | [
"Elk"
] | 57d8dffad294d9744d41ceef5a0077367c1fc7f234451cd5fb50d97b8f3dd357 |
"""
Performance test created using multi-mechnize to analyze time
for update processing with MySQL.
"""
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
import random
import string
import time
from DIRAC.WorkloadManagementSystem.DB.JobDB import JobDB
def r... | yujikato/DIRAC | tests/Performance/MySQLJobMonitoring/test_scripts/update.py | Python | gpl-3.0 | 950 | [
"DIRAC"
] | 0569ee544e90799e85b4529f17c71064faadc31b853721c2b99a5f0f69aaca71 |
#!/usr/bin/env python3
'''Manual DDNS testing'''
from dnstest.utils import *
from dnstest.test import Test
t = Test()
def check_soa(master, prev_soa):
soa_resp = master.dig("ddns.", "SOA")
compare(prev_soa, soa_resp.resp.answer, "SOA changed when it shouldn't")
def verify(master, zone, dnssec):
if not ... | jkadlec/knot-dns-zoneapi | tests-extra/tests/ddns/basic/test.py | Python | gpl-3.0 | 22,405 | [
"Elk"
] | eaf7cff5a67d96a3481d6c4f0ed01f07d30f57a20494e664e8c12c0e92e2ebc7 |
from .NeuroML import NeuroML, loadNeuroML_L123
from .NetworkML import NetworkML
from .MorphML import MorphML
from .ChannelML import ChannelML
import tempfile
import logging
debug_ = False
if debug_:
logging.basicConfig(level=logging.DEBUG,
format='%(asctime)s %(name)-12s %(levelname)-8s %(message)s',
... | subhacom/moose-core | python/moose/neuroml/__init__.py | Python | gpl-3.0 | 931 | [
"MOOSE"
] | 437c55a9ac82fc5d78aac8d4628c6b252300777bdc1d349286795ccd272aafed |
# ============================================================================
#
# Copyright (C) 2007-2012 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | jeroendierckx/Camelot | camelot/bin/camelot_admin.py | Python | gpl-2.0 | 9,511 | [
"VisIt"
] | a284dffbf35fc1641241cc53601f84544545cc510346a06454c37841f06d39f7 |
# (c) 2014, Brian Coca, Josh Drake, et al
# (c) 2017 Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
DOCUMENTATION = '''
cache: redis
short_description: Use Redis... | maartenq/ansible | lib/ansible/plugins/cache/redis.py | Python | gpl-3.0 | 4,208 | [
"Brian"
] | db16fb36b000a8151d318e621c595881118a6f2912d860b019d35d41bb691673 |
import logging
import os
from pyjade import Compiler as _Compiler, Parser, register_filter
from pyjade.runtime import attrs
from pyjade.exceptions import CurrentlyNotSupported
from pyjade.utils import process
from django.conf import settings
class Compiler(_Compiler):
autocloseCode = 'if,ifchanged,ifequal,ifnote... | char101/pyjade | pyjade/ext/django/compiler.py | Python | mit | 3,357 | [
"VisIt"
] | b457795cae054bb9d17573836a02fa1fd9ed79f2251eb4fec53a2569f57a2a91 |
#
# @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 redistribute it and/or modify
#... | CDSherrill/psi4 | psi4/share/psi4/databases/JSCH.py | Python | lgpl-3.0 | 287,170 | [
"Psi4"
] | b5dae590126a0f7751dbe3986318edde0994adc98225757d3e838f1aa6545039 |
# -*- coding: utf-8 -*-
"""
Created on Sun Nov 27 14:03:34 2011
@author: Shreejoy
"""
#!/usr/bin/python
# -*- coding: utf-8 -*-
from SPARQLWrapper import SPARQLWrapper, JSON, XML, N3, RDF
import re
from pubapp.models import Neuron
# get all subclasses of kir channels
sparql = SPARQLWrapper("http://... | lessc0de/neuroelectro_org | neurolex_integration/get_neuron_types.py | Python | gpl-2.0 | 1,218 | [
"NEURON"
] | 666a696d6956f73599bdf6ccecabbe1c1bc0b248c76ba44f7b032db42565ef64 |
from toee import *
from utilities import *
from combat_standard_routines import *
def san_dialog( attachee, triggerer ):
if (attachee.leader_get() != OBJ_HANDLE_NULL):
triggerer.begin_dialog( attachee, 330 ) ## burne in party
elif (game.global_vars[909] == 32 and attachee.map != 5016 and attachee.map != 5018):
... | GrognardsFromHell/TemplePlus | tpdatasrc/co8fixes/scr/py00004burne.py | Python | mit | 4,926 | [
"Amber"
] | 6683608fd3929004d10bee0a25debb641a678039534d7e3a6f16d5e0b62b8c89 |
# From: Bayesian Models for Astrophysical Data, Cambridge Univ. Press
# (c) 2017, Joseph M. Hilbe, Rafael S. de Souza and Emille E. O. Ishida
#
# you are kindly asked to include the complete citation if you used this
# material in a publication
#
# Code 10.11 Beta model in Python using Stan, for accessing the
# ... | astrobayes/BMAD | chapter_10/code_10.11.py | Python | gpl-3.0 | 2,333 | [
"Galaxy"
] | bff55fd58506f08544f0f90507a7f7c13349e640701c9f85bfcac28ad356929d |
"""
Synthetic Minority Over-Sampling Technique for Regression with Gaussian Noise
https://github.com/nickkunz/smogn
"""
from smogn.box_plot_stats import box_plot_stats
from smogn.phi_ctrl_pts import phi_ctrl_pts
from smogn.phi import phi
from smogn.smoter import smoter
__all__ = [
"box_plot_stats",
"phi_ctr... | nickkunz/smogn | smogn/__init__.py | Python | gpl-3.0 | 354 | [
"Gaussian"
] | 2552e3a0448465f2abaa225e8637ca6e48e23763ce323b8ce66fbae158c78970 |
from parsimonious.grammar import Grammar
from parsimonious.nodes import *
from decimal import Decimal
# ===================================================================
class ReplacementVisitor(NodeVisitor):
def __init__(self, data={}):
self._data = data
# default node handler ------------------... | DanielBaird/prosemaker | egg/dwb.prosemaker/src/dwb/prosemaker/replacementparser.py | Python | apache-2.0 | 4,684 | [
"VisIt"
] | 15d224cf83df4fbad5771dd239e6676d42c3c5359285263aa53ebb733199e31a |
# Copyright (C) 2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later versio... | espressomd/espresso | testsuite/scripts/tutorials/test_active_matter.py | Python | gpl-3.0 | 1,884 | [
"ESPResSo"
] | b18e579ec6ed30c6ed7817b421e4ca8f7f87ae21fd067587f06e454f488db441 |
"""
Acceptance tests for the certificate web view feature.
"""
from nose.plugins.attrib import attr
from common.test.acceptance.fixtures.certificates import CertificateConfigFixture
from common.test.acceptance.fixtures.course import CourseFixture, CourseUpdateDesc, XBlockFixtureDesc
from common.test.acceptance.pages.c... | lduarte1991/edx-platform | common/test/acceptance/tests/lms/test_certificate_web_view.py | Python | agpl-3.0 | 10,347 | [
"VisIt"
] | 157db1a83dd024e8778c7ad238e25490b648f631c1998e3608566e3dcf93de48 |
"""
PyQt5.6 python3
Convert html to pdf with qt print
"""
from PyQt5.QtWidgets import *
from PyQt5.QtGui import *
from PyQt5.QtPrintSupport import QPrinter
html = '''
<?xml version='1.0' encoding='utf-8'?>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta name="author" content="Brian W. Kernighan, Denni... | tcp813/mouTools | qt/html2pdf.py | Python | mit | 3,566 | [
"Brian"
] | 7ac40d96d9675a795f83dbcaeaeb75cb46f283e5e08233ec4761fc68832a431a |
# default python modules
import os
from datetime import datetime
# external packages
import numpy as np
import pandas as pd
from sklearn.externals import joblib
from sklearn.linear_model import Lasso
from sklearn.model_selection import train_test_split, GridSearchCV
from sklearn.neural_network import MLPClassifier
from... | joekasp/ionic_liquids | ionic_liquids/utils.py | Python | mit | 9,003 | [
"RDKit"
] | e6a95237aff690be9683701814b0e18ed7c0068483922fcb5e5330234e528e43 |
#!/usr/bin/env python
"""
This python script generates the py_class_impl! macro.
"""
from collections import namedtuple
import sys, os
PY2 = (os.getenv('PY') == '2')
header = '''
// Copyright (c) 2016 Daniel Grunwald
//
// Permission is hereby granted, free of charge, to any person obtaining a copy of this
// softw... | naufraghi/rust-cpython | src/py_class/py_class_impl.py | Python | mit | 30,720 | [
"VisIt"
] | bc66151026a2837507c1ae6f3ea76aad3b29fddc91a8eb524f3d6997a4c631ed |
""" DowntimeCommand module will look into GOC DB to find announced downtimes for RSS-managed sites and resources.
If found, downtimes are added to the internal RSS cache using ResourceManagementClient.
GOCDB downtimes that are modified or deleted are also synced.
"""
__RCSID__ = '$Id$'
import urllib2
import ... | fstagni/DIRAC | ResourceStatusSystem/Command/DowntimeCommand.py | Python | gpl-3.0 | 13,816 | [
"DIRAC"
] | b951a27282144daa139378f1bdf1d0a6c1a381368df88808f4637000ee7eb725 |
# -*- coding: utf-8 -*-
"""
Created on Sun Aug 19 13:23:54 2018
@author: butenko
"""
import warnings
warnings.filterwarnings("ignore")
from dolfin import *
from pandas import read_csv
import numpy as np
import os
import subprocess
import pickle
import time as tm
from tissue_dielectrics import DielectricProperties
p... | andreashorn/lead_dbs | ext_libs/OSS-DBS/OSS_platform/Math_module_floating_MPI.py | Python | gpl-3.0 | 14,099 | [
"NEURON"
] | e13e50c743b31766f7762191f2ad03d3d55e589587ff98abc4b6b49895014ea9 |
"""
Courseware page.
"""
import re
from bok_choy.page_object import PageObject, unguarded
from bok_choy.promise import EmptyPromise
from selenium.webdriver.common.action_chains import ActionChains
from common.test.acceptance.pages.lms import BASE_URL
from common.test.acceptance.pages.lms.bookmarks import BookmarksPa... | a-parhom/edx-platform | common/test/acceptance/pages/lms/courseware.py | Python | agpl-3.0 | 24,820 | [
"VisIt"
] | d3b96d4dd37c0cb1792ed056d38766c137e83d33864c6cd832b6987c33380b85 |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2020, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
'''
Plotter
#################
This is supposed to be a collection of classes and functions to aid in plotting
'''
from bokeh.plotting import output_notebook, show, figure
from bokeh.... | exa-analytics/atomic | exatomic/plotter/plot.py | Python | apache-2.0 | 4,657 | [
"Gaussian"
] | 6c98f522997cf191d7dec40ecee0aa3dac7a40f8cd9576c3d5a6d4eec79f0b50 |
from django.shortcuts import render_to_response, redirect
from django.template import RequestContext
from django.template.loader import render_to_string
from django.core.mail import send_mail, mail_managers, EmailMessage
from django.contrib.auth.decorators import login_required
from django.contrib import messages
from ... | copelco/Durham-Open-Data-Catalog | OpenDataCatalog/contest/views.py | Python | mit | 5,451 | [
"VisIt"
] | 7ecbdf61304e07ee35e2022b990f8177c6dfa27de5774db7ea7105376440dc97 |
import os
from ase import Atoms, Atom
from ase.io import write
from ase.calculators.jacapo import Jacapo
atoms = Atoms([Atom('H',[0,0,0])],
cell=(2,2,2),
pbc=True)
calc = Jacapo('Jacapo-test.nc',
pw=200,
nbands=2,
kpts=(1,1,1),
spinp... | grhawk/ASE | tools/ase/test/jacapo/jacapo.py | Python | gpl-2.0 | 575 | [
"ASE"
] | 62a05c656081d0b9dc3fb7f964253c2417f568fc1313dc416f193010e69a950a |
#! /usr/bin/env python
from MDAnalysis import *
import numpy
import math
import sys
my_traj = sys.argv[1]
u = Universe("init.pdb",my_traj)
v = Universe("init.pdb")
end = my_traj.find('.pdb')
fout_name = my_traj[0:end] + '_dist_kink.dat'
a1 = u.selectAtoms("segid A and resid 62:78")
b1 = u.selectAtoms("segid B and ... | demharters/git_scripts | dist_mhcii_kink.py | Python | apache-2.0 | 512 | [
"MDAnalysis"
] | 973416491fd3c8e61152d907fb3fa14002debce2a2f2794b21561bd1739df815 |
from __future__ import division, print_function, unicode_literals
__author__ = 'setten'
import os
import unittest
from pymatgen.util.testing import PymatgenTest
from pymatgen.core.structure import Structure
from pymatgen.matproj.rest import MPRester, MPRestError
from pymatgen.io.gwwrapper.datastructures import GWSpe... | yanikou19/pymatgen | pymatgen/io/gwwrapper/tests/test_helpers.py | Python | mit | 3,782 | [
"VASP",
"pymatgen"
] | c711d3c731c921cf6f6de68033a88b83185656ccfe0380738a8259bbae80034e |
from __future__ import division, print_function
import numpy as np
from bct.utils import BCTParamError, binarize, get_rng
from bct.utils import pick_four_unique_nodes_quickly
from .clustering import number_of_components
def latmio_dir_connected(R, itr, D=None, seed=None):
'''
This function "latticizes" a dire... | clbarnes/bctpy | bct/algorithms/reference.py | Python | gpl-3.0 | 58,967 | [
"Gaussian"
] | fed9adb0271e6be00f82bbb04a69043dedbc4364735b064f29e96bba1474fb39 |
# LIBTBX_SET_DISPATCHER_NAME dials.import
from __future__ import annotations
import logging
import pickle
from collections import namedtuple
import dxtbx.model.compare as compare
from dxtbx.imageset import ImageGrid, ImageSequence
from dxtbx.model.experiment_list import (
Experiment,
ExperimentList,
Expe... | dials/dials | command_line/dials_import.py | Python | bsd-3-clause | 34,891 | [
"CRYSTAL"
] | c1c34b7f3521c21e36a887c7c281ca41c27bd99b0af70b575c0f5db3b29ab4b4 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | Kleptobismol/scikit-bio | skbio/stats/distance/tests/test_bioenv.py | Python | bsd-3-clause | 9,846 | [
"scikit-bio"
] | 26cc695dfa811a98255979fb9173a7baf0f4c6dd040c0d5bef241cca412b4d6c |
# coding=utf-8
# Copyright 2022 The Google Research 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 applicab... | google-research/google-research | poem/cv_mim/train_base.py | Python | apache-2.0 | 8,343 | [
"Gaussian",
"MOE"
] | f608d7b4fbc76575a8efa6f1ca932f8857f87945558530f0eb07ed22647e3cec |
""" 2-input XOR example using Izhikevich's spiking neuron model. """
from __future__ import print_function
import os
import matplotlib.pyplot as plt
from matplotlib import patches
from neatsociety import population, iznn, visualize
from neatsociety.config import Config
# Network inputs and expected outputs.
xor_inputs... | machinebrains/neat-python | examples/xor/xor2_spiking.py | Python | bsd-3-clause | 5,293 | [
"NEURON"
] | 70a4153eb9bd4cc72b0d014d5193c906b0981edc11d63774a6e58456703a6779 |
#! /usr/bin/env python
# This version uses NEST's RandomConvergentConnect functions.
import cynest as nest
import cynest.raster_plot
import time
from numpy import exp
nest.ResetKernel()
startbuild = time.time()
dt = 0.1 # the resolution in ms
simtime = 1000.0 # Simulation time in ms
delay = 1.5 # syn... | QJonny/CyNest | cynest/examples/brunel-delta-nest.py | Python | gpl-2.0 | 3,818 | [
"NEURON"
] | e0b853fc7554ce37fe17c865ed7989f4b02730ae9ea5e1ee39331467d169b8fa |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
from DIRAC import gConfig
from DIRAC.ConfigurationSystem.Client.Helpers.Path import cfgPath
gBaseLocalSiteSection = "/LocalSite"
def gridEnv():
"""
Return location of gridenv file... | ic-hep/DIRAC | src/DIRAC/ConfigurationSystem/Client/Helpers/Local.py | Python | gpl-3.0 | 428 | [
"DIRAC"
] | b6f49e6f640ba0636205ea9de6604d5055ff3b6b02c4cc4050327d49d7e1c44f |
#!/usr/bin/env python
import logging
import json
import time
import multiprocessing
import Queue
from cbtestlib.membase.api.rest_client import RestConnection
from cbtestlib.membase.api.exception import ServerUnavailableException
from tabula.table import Table
from tabula.section import Section
from seriesly import Se... | couchbaselabs/cbtop | libcbtop/visit_cb.py | Python | apache-2.0 | 8,502 | [
"VisIt"
] | 80656020fb4e69b24d727edd52151ad06ce0b1173caa43315d91e525ee0faa52 |
from hyperopt import fmin, tpe, hp
import lb_loader
import pandas as pd
import simtk.openmm.app as app
import numpy as np
import simtk.openmm as mm
from simtk import unit as u
from openmmtools import hmc_integrators, testsystems
pd.set_option('display.width', 1000)
n_steps = 1000
platform_name = "CUDA"
precision = "mi... | kyleabeauchamp/HMCNotes | code/optimize/test_optimize_hyper_ghmc.py | Python | gpl-2.0 | 2,473 | [
"OpenMM"
] | 0274afe98e36b784baa7a5a4e66e8c8aa97a36d0c2e7120bce1e3a04a4bc35b8 |
import warnings
import operator
import sys
import functools as ft
from functools import reduce
import numpy as np
import xarray as xr
import pandas as pd
import dask.array as dsar
from dask import delayed
import scipy.signal as sps
import scipy.linalg as spl
from .detrend import detrend as _detrend
__all__ = [
... | xgcm/xrft | xrft/xrft.py | Python | mit | 44,138 | [
"Gaussian"
] | 93565710a23f18696643181cd2cd756015bcfb4b5780e4b77124acf4943344da |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# A script to test the threshold filter.
# Values above 2000 are set to 255.
# Values below 2000 are set to 0.
# Image pipeline
imageCanvas = vtk.vtkImageCanvasSource2D()
imageCanvas.... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Imaging/Core/Testing/Python/TestSkeleton2D.py | Python | gpl-3.0 | 3,308 | [
"VTK"
] | dd41ca2309899febbc1365041732c3d8d8c00cc6ea8545dd0973ace48c430ac9 |
# -*- coding: utf-8 -*-
#
# hl_api_info.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... | hesam-setareh/nest-simulator | pynest/nest/lib/hl_api_info.py | Python | gpl-2.0 | 7,504 | [
"VisIt"
] | 6616dd5794d7d803daa338a16f035a1777c8f1e385db7ed12a98465a96b7e13c |
#!/usr/bin/python
import h2o
def get_model_property(model, summary=True, validation_metrics=False,
mean_residual_deviance=False, columns=False, categorical_col_domains=False,
parameters=False, all_output=False):
"""
A convenience function to return a property from a model, since they
are held in d... | Prooffreader/pyprooff | pyprooff/h2o.py | Python | mit | 13,301 | [
"Gaussian"
] | d9b888054efcf13a02b6881f00bec17f5321960d94ef4c287136a9549d41b7aa |
# bayesiandb.py
# old bailey
#
# naive bayesian learner
# adapted from Segaran, Programming Collective Intelligence, Ch. 6
# persists training info in SQLite DB
from pysqlite2 import dbapi2 as sqlite
stopwords = ['a', 'about', 'above', 'across', 'after', 'afterwards']
stopwords += ['again', 'against', 'all'... | williamjturkel/Digital-History-Hacks--2005-08- | bayesiandb.py | Python | mit | 11,273 | [
"CASINO"
] | 866f822cda295f305c544d03da0e9056388d3bdd31fb3517d3807a7d52abe925 |
#! /usr/bin/python
# -*- coding: iso-8859-15 -*-
from openturns import *
from openturns.viewer import ViewImage
triang = Triangular(1.0, 2.0, 4.0)
norm = Normal(-1.0, 1.0)
norm2 = Normal(3.0, 1.0)
aCollection = DistributionCollection(3)
aCollection[0] = Distribution(triang)
aCollection[1] = Distribution(norm)
aCollec... | dbarbier/privot-doc | src/UseCasesGuide/script_kernelSmoothing.py | Python | lgpl-2.1 | 5,963 | [
"Gaussian"
] | a970dc3591a93afdb4fd083d12e7494529833ece60708af97945f9b943f3f134 |
from django.core.urlresolvers import reverse
from django.utils.safestring import mark_safe
from django.utils.translation import ugettext_noop, ugettext_lazy as _
from corehq.apps.accounting.models import SoftwarePlanEdition as Edition, SoftwareProductType as Product, FeatureType
DESC_BY_EDITION = {
Edition.COMMUNI... | SEL-Columbia/commcare-hq | corehq/apps/accounting/user_text.py | Python | bsd-3-clause | 17,631 | [
"VisIt"
] | 42a807575a28d494ef383dab5f25fa7229453ff8602147f7a04a862cff37544f |
#!/usr/bin/python
# Copyright(C) 2013 David Ream
# Released under Biopython license. http://www.biopython.org/DIST/LICENSE
# Do not remove this comment
import os
import argparse
import time
import sys
from Bio import Entrez
# This exists to make the main function easier to read. It contains code to run the argument... | idoerg/BOA | tools/download_script.py | Python | gpl-3.0 | 2,402 | [
"Biopython"
] | 386e899473e3486c8c9d334bf7b4fd39a727a0936979d636982dc7b06b35ddd1 |
from django.conf.urls import patterns, include, url, static
from django.conf import settings
from django.contrib import admin
admin.autodiscover()
urlpatterns = patterns('',
# Examples:
# url(r'^$', 'collabCTF.views.home', name='home'),
# url(r'^blog/', include('blog.urls')),
url(r'^$', 'collabCTF.vi... | HackUCF/collabCTF | collabCTF/urls.py | Python | mit | 2,840 | [
"VisIt"
] | 0a99f3e31e80ddca5fb441d9a1af07fe0019e7ef4f949614c6cc4ac1800cca2e |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Create the RenderWindow, Renderer and interactive renderer
#
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
# make sure to have the sa... | hlzz/dotfiles | graphics/VTK-7.0.0/Filters/General/Testing/Python/TestRandomAttributeGenerator.py | Python | bsd-3-clause | 1,472 | [
"VTK"
] | 4f371cd1977a8c189d761c8329058fe57b12d2e048e52345c9000532aef544c5 |
"""
General helper functions that don't fit neatly under any given category.
They provide some useful string and conversion methods that might
be of use when designing your own game.
"""
from __future__ import division, print_function
from builtins import object, range
from future.utils import viewkeys, raise_
impor... | ergodicbreak/evennia | evennia/utils/utils.py | Python | bsd-3-clause | 52,956 | [
"VisIt"
] | 27e9c62a9d1623ee4fe459e9e9a623fbd5c49ab1f50a41eab83f93f2ebac6953 |
from ecell4.reaction_reader.decorator2 import species_attributes, reaction_rules
from ecell4.reaction_reader.network import generate_reactions
k1 = 0.1
k2 = 0.2
k3 = 0.3
k4 = 0.4
@species_attributes
def attributegen():
S(e,y=zero) | 1
kinase(s) | 2
pptase(s) | 3
ATP() | 4
ADP() | 5
@rea... | navoj/ecell4 | python/samples/reaction_reader/catalysis/catalysis.py | Python | gpl-2.0 | 3,761 | [
"Avogadro"
] | dbb09a22f4b9ee0e72b29df542125aab9ed716c124e142805c712d3156512b1f |
#!/usr/bin/env python2.7
#coding=utf-8
#author@alingse
#2014.11.08
from __future__ import print_function
import argparse
#import rapidjson as json
import json
import sys
log = print
def get_id_from_id_line(id_line):
return id_line.strip()
#return id_line.strip().decode('utf-8')
#return id_line.strip()[-... | alingse/crawler-common | dodata/filter_data_by_id.py | Python | apache-2.0 | 5,515 | [
"VisIt"
] | d2d6e41b319068a9d882e6d453d561eb467fb81ce88f59c7d21e70737ca31fe8 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | lukeiwanski/tensorflow | tensorflow/contrib/autograph/converters/ifexp.py | Python | apache-2.0 | 1,631 | [
"VisIt"
] | 38358565595485dbb146ca00c736e4d58162220c7be52dc1905706eb1382ada1 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | alejob/mdanalysis | testsuite/MDAnalysisTests/analysis/test_lineardensity.py | Python | gpl-2.0 | 1,939 | [
"MDAnalysis"
] | 2a9c3b76216343c188d2f4327baf774d6323d7cf403ca63f79aca3c1f116c589 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals, print_function
import os
import re
import json
import warnings
from io import open
from enum import Enum
from pymatgen.core.units import Mass, Length, unitiz... | setten/pymatgen | pymatgen/core/periodic_table.py | Python | mit | 40,961 | [
"CRYSTAL",
"pymatgen"
] | 15e17d4a11cc28762aea2e9a9976867a889b76917d12cfbac11ce3a6d40e0d7b |
########################################################################
# $HeadURL $
# File: File.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2012/08/03 15:02:53
########################################################################
"""
:mod: File
.. module: File
:synopsis: RMS operation file
.. moduleau... | calancha/DIRAC | RequestManagementSystem/Client/File.py | Python | gpl-3.0 | 8,188 | [
"DIRAC"
] | febe71573f9dfdd6210a2eacfb692feab27554f81bc2c226e173f3862e1294eb |
import cython
cython.declare(PyrexTypes=object, Naming=object, ExprNodes=object, Nodes=object,
Options=object, UtilNodes=object, LetNode=object,
LetRefNode=object, TreeFragment=object, EncodedString=object,
error=object, warning=object, copy=object)
import PyrexTypes
import... | openilabs/falconlab | env/lib/python2.7/site-packages/Cython/Compiler/ParseTreeTransforms.py | Python | mit | 115,717 | [
"VisIt"
] | ddb2ccc2bb78d6d564b0c11fe411dffda8438a5f8e8a98c16c2294454a5c89b9 |
#
# GMSK modulation and demodulation.
#
#
# Copyright 2005-2007,2012 Free Software Foundation, Inc.
#
# This file is part of GNU Radio
#
# GNU Radio 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 v... | Gabotero/GNURadioNext | gr-digital/python/gmsk.py | Python | gpl-3.0 | 11,094 | [
"Gaussian"
] | 36c8baa2eee86c00b78af9c8ea933beff0823d908aa68111d75cbef3235e0bb5 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kratman/psi4public | psi4/share/psi4/databases/HTR40.py | Python | gpl-2.0 | 41,536 | [
"Psi4"
] | 98f66fdda7c86ac88c84517d6d5c09e2ffd945bf650167fd0cfd2ba1cf8e2e0b |
#!/usr/bin/python
# -*- coding: utf-8 -*-
############################################################################
#
# Copyright (C) 2010-2015
# Christian Kohlöffel
# Jean-Paul Schouwstra
#
# This file is part of DXF2GCODE.
#
# DXF2GCODE is free software: you can redistribute it and/or modif... | Poofjunior/dxf2gcode | dxf2gcode.py | Python | gpl-3.0 | 46,284 | [
"VisIt"
] | b6387b1a9da68a0dde60bf0f243702ba2352986c46086f99d3653c3468945bd0 |
# -*- coding: utf-8 -*-
#
# Copyright (C) 2004-2009 Edgewall Software
# Copyright (C) 2004 Daniel Lundin <daniel@edgewall.com>
# Copyright (C) 2004-2006 Christopher Lenz <cmlenz@gmx.de>
# Copyright (C) 2006 Jonas Borgström <jonas@edgewall.com>
# Copyright (C) 2008 Matt Good <matt@matt-good.net>
# All rights reserved.
#... | moreati/trac-gitsvn | trac/web/session.py | Python | bsd-3-clause | 20,065 | [
"VisIt"
] | f8e5129799a4d6cae087d78b4bc494cea5e0df13097b0a6812fcf43c2acf3403 |
from models import Base, CityModel, StateModel, UserModel, VisitModel
from sqlalchemy import create_engine
from sqlalchemy.orm import sessionmaker
engine = create_engine('mysql://:@localhost/test', echo=False)
# allow our db models (Base) to be accessible via the session
Base.metadata.bind = engine
DBSession = sessi... | boxofgoobers/rv-rest-api | services.py | Python | mit | 7,553 | [
"VisIt"
] | ea280bbc295108525903aab3d8bfc95b02b306ab06426b64faa9b39eae2ed752 |
#!/usr/bin/env python
# -*- coding:utf-8 -*-
# @author:Hieda no Chiaki <i@wind.moe>
import logging
from src.md5 import md5
try:
import configparser
except ImportError:
import ConfigParser
logging.basicConfig(level=logging.INFO)
def uid():
try:
config = configparser.ConfigParser()
except:
... | forblackking/PyBiu | src/sign.py | Python | apache-2.0 | 854 | [
"MOE"
] | 28d33ba356faf44a9ad93fd4b1fd0bbdd995ab552395e0abdd62796516eb2913 |
# remotefilelogserver.py - server logic for a remotefilelog server
#
# Copyright 2013 Facebook, Inc.
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 or any later version.
from __future__ import absolute_import
import errno
import os
import stat
import ... | smmribeiro/intellij-community | plugins/hg4idea/testData/bin/hgext/remotefilelog/remotefilelogserver.py | Python | apache-2.0 | 14,542 | [
"VisIt"
] | b893af18cf0396d3d16e39aa1b8024307a6dd30bfbdc3c5bc668851e0285cefc |
"""
neural_network v0.01
Feed forward neural network class library
Copyright 2011 Brian Monkaba
This file is part of ga-bitbot.
ga-bitbot 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 vers... | OndroNR/ga-bitbot | libs/neural_network.py | Python | gpl-3.0 | 10,579 | [
"Brian",
"NEURON"
] | bc5e7c16d49ce303d3268c08999e0a93da8d69d1175737e1a9cbc91521f34727 |
__RCSID__ = "$Id: UsersAndGroups.py 34413 2011-02-19 06:10:18Z rgracian $"
"""
Update Users and Groups from VOMS on CS
"""
import os
from DIRAC.Core.Base.AgentModule import AgentModule
from DIRAC.ConfigurationSystem.Client.CSAPI import CSAPI
from DIRAC.FrameworkSystem.Client.NotificationC... | sposs/DIRAC | ConfigurationSystem/Agent/UsersAndGroups.py | Python | gpl-3.0 | 16,314 | [
"DIRAC"
] | 3d1f5480a6e7585e373e8d42d712cfbb3b9937afc319caf8960771b26bc24026 |
import glob
import os
import pickle
import sys
import numpy as np
import subprocess as sp
from morphct.definitions import SINGLE_ORCA_RUN_FILE
from morphct.code import helper_functions as hf
class orcaError(Exception):
def __init__(self, file_name):
self.string = "".join(["No molecular orbital data presen... | matty-jones/MorphCT | morphct/code/transfer_integrals.py | Python | gpl-3.0 | 39,487 | [
"ORCA"
] | 2556d13535983c461d8a67ce58fe1a917d39519d7237971d903c536a8ea94942 |
##
# Copyright 2013-2021 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://www.vscentrum.be),
# Flemish Research Foundation (F... | boegel/easybuild-easyblocks | easybuild/easyblocks/p/psi.py | Python | gpl-2.0 | 11,600 | [
"Psi4"
] | 5a9cda75e0ed2d9a1b37812136d83e5bfaee9eda20e6232b7f3c46b3eb85d885 |
#!/usr/bin/env python
"""Download Stx1a gene sequences from Genbank
Example:
$ python blast_stx1a_genes.py .
"""
import argparse
import csv
import logging
import os
import re
from Bio import SeqIO
from utils import DownloadUtils, SubtypeParser, GeneFilter
from blast import Blast
__author__ = "Matthew Wh... | superphy/insilico-subtyping | phylotyper/data/download/blast_stx1a_genes.py | Python | apache-2.0 | 4,135 | [
"BLAST"
] | 670dfa6ac33c5e5ec49d16c7ba4c1036bcde7fbe8b18605052f9372fe8409127 |
# 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
import sys
from spack import *
class Roms(MakefilePackage):
"""ROMS is a free-surface, terrain-following,... | LLNL/spack | var/spack/repos/builtin/packages/roms/package.py | Python | lgpl-2.1 | 5,319 | [
"NetCDF"
] | ac3e3e5f12530870a3f27034017d26a2cbecfba75c550592ab11870557816aa1 |
'''
Broken (piecewise continuous) random field generation using rft1d.randn1d
Note:
When FWHM gets large (2FWHM>nNodes), the data should be padded
using the *pad* keyword.
'''
import numpy as np
from matplotlib import pyplot
import rft1d
#(0) Set parameters:
np.random.seed(12345)
nResponses = 5
nNodes = 1... | 0todd0000/rft1d | rft1d/examples/random_fields_broken_1.py | Python | gpl-3.0 | 862 | [
"Gaussian"
] | ecf0f83a202f9a375f3ca2939a0d2de30dcb4d24bb419905bdee0622bc81bc64 |
# Copyright 2015 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... | keras-team/keras | keras/activations.py | Python | apache-2.0 | 18,941 | [
"Gaussian"
] | a2c5e27b2d1570c2bb8a93d8ac98af3d6b0f53584beca67f8720e907e3b7a42f |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
def GetRGBColor(colorName):
'''
Return the red, green and blue components for a
color as doubles.
'''
rgb = [0.0, 0.0, 0.0] # black
vtk.vt... | hlzz/dotfiles | graphics/VTK-7.0.0/IO/Geometry/Testing/Python/motor.py | Python | bsd-3-clause | 4,880 | [
"VTK"
] | 25f402d6dd6cd1ac432aad05b3b71bb726cf3fdf828c00f9116653894c895109 |
# Copyright (c) 2017 Brian Ginsburg, Julie Rutherford-Fields
# This work is available under the "3-clause ('new') BSD License”.
# Please see the file COPYING in this distribution
# for license terms.
import os
from app import db
from app.models import User, Message
import nltk
# create the database and create the tee... | thuselem/teergrube | init_app.py | Python | bsd-3-clause | 728 | [
"Brian"
] | 800639f3d3070fe1b08b04737057fe934311c563010fd5984eb7b09342a29f90 |
import csv
from datetime import datetime
import time
DATE_FORMAT="%Y-%m-%dT%H:%M:%S"
OFFSET = float(_Offset.GetValue(0))
DATE = _Date.GetValue(0)
NDate = _Date.GetValue(1)
if (NDate):
DATE = NDate
POINTFILENAME = _PointFile.GetValue(0)
def ReadPointFile(pointFile):
#we have finnished reading the triangle file, no... | sherizadeh/PVGPlugins | Readers/EPSReader/EPSRequestData.py | Python | bsd-2-clause | 5,366 | [
"VTK"
] | ad0713adf8a8d4dda07e43d3f59ab7aafcff9342ee0754013db3a49448840757 |
"""
@name: Modules/Core/occupancy.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2020-2020 by D. Brian Kimmel
@license: MIT License
@note: Created on Feb 2, 2020
@summary:
Mode: vacation, Away, Home
Guests: True
Sleeping: False
"""
# ## END DBK
| DBrianKimmel/PyHouse | Project/src/Modules/Core/occupancy.py | Python | mit | 296 | [
"Brian"
] | eaadf2f345d4f8ec8b8994013c13aad5ab42bde5ddb7bc5f347bd12aa435ec0d |
#!/usr/bin/env python
from __future__ import unicode_literals, division, print_function, absolute_import
import re
import os
import sys
from abirules_tools import find_abinit_toplevel_directory
re_markers = re.compile("^(<<<<<<< TREE|=======|>>>>>>> MERGE-SOURCE)$")
re_fbktop = re.compile("fallbacks$")
re_fbkdir =... | abinit/abinit | abichecks/scripts/check-conflict-markers.py | Python | gpl-3.0 | 2,893 | [
"ABINIT"
] | 3512b29587f23da1e9294caa9b706c838bb10bfbd14e3e7f1b92e5224f247e78 |
#! /usr/bin/local/python
# -*- coding: utf-8 -*-
import sys
import os
import math
import pysam
import breakmer.utils as utils
__author__ = "Ryan Abo"
__copyright__ = "Copyright 2015, Ryan Abo"
__email__ = "ryanabo@gmail.com"
__license__ = "MIT"
class FilterValues:
"""
"""
def __init__(self):
sel... | a-bioinformatician/BreaKmer | breakmer/caller/sv_caller.py | Python | mit | 40,683 | [
"BLAST",
"pysam"
] | 560c8b49e13db1b22ab02b29fad18a67cdbae3cb8fb1f69d2da21c0c45651c07 |
import numpy as np
import scipy.ndimage.interpolation
import scipy.ndimage.filters
try:
import seaborn as sns
sns.set()
from matplotlib import pyplot as plt
except ImportError:
pass
from utils import RNG, plot_greyscale_image
from utils.dataset import load_mnist
def get_transformation(transformation... | monsta-hd/ml-mnist | ml_mnist/augmentation.py | Python | mit | 5,439 | [
"Gaussian"
] | 144918b57cf01f82eeb52d99e4617830e722506d0c996588fcc0526b8ea96001 |
"""
Test Help links in LMS
"""
from __future__ import absolute_import
from common.test.acceptance.fixtures.course import CourseFixture
from common.test.acceptance.pages.lms.instructor_dashboard import InstructorDashboardPage
from common.test.acceptance.tests.discussion.helpers import CohortTestMixin
from common.test.a... | jolyonb/edx-platform | common/test/acceptance/tests/lms/test_lms_help.py | Python | agpl-3.0 | 5,071 | [
"VisIt"
] | 0bd9af5703824477488ca0f1b35513c173f3b59c26195818edc4f50d5904c992 |
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