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#python-encoding: UTF-8
from csc.nl.ja.util import *
from csc.nl.ja.properties import *
class JaTreeNode():
''' Things common to tree nodes '''
def __init__(self):
self.parent = None
def __str__(self):
return self.surface
def bredth_first(self, return_filter = None, access_fil... | pbarton666/buzz_bot | djangoproj/djangoapp/csc/nl/ja/tree.py | Python | mit | 7,043 | [
"VisIt"
] | a05bd391d29608978971925facdfa2917fb83604c1a245ccdbe76f24aed34c76 |
#########################
# Classes and Functions #
#########################
class Foldon:
numRes = 0
residuelist = []
numNativeContacts = 0
nativefoldoncontactlist = []
def __init__(self,residuelist):
self.residuelist = residuelist
self.numRes = len(self.residuelist)
self.... | luwei0917/awsemmd_script | script/formulateKineticModel.py | Python | mit | 37,537 | [
"LAMMPS"
] | 46f27fb5727e58a300d44df1326898325ff6ea563d9691ad5071207a0df6ec8d |
import logging
from .. import DataType
from .save_tab import SaveTab
from ..utilities.gui_handler import GuiHandler
from ..utilities.pyqrgraph import Pyqtgrah as PyqtgraphUtilities
class SaveLoadDataTab(SaveTab):
def sample(self):
"""record all the parameters of the Load Data tab / Sample accordion tab"... | ornlneutronimaging/iBeatles | src/iBeatles/session/save_load_data_tab.py | Python | mit | 5,824 | [
"CRYSTAL"
] | 5da7d911b5bb46292c5da1f15b6ee6681a4353ce79d408e38e56520318095e80 |
# import internals
import sys, os, itertools, operator, warnings
# import PIL as the image loader
import PIL.Image
file_extensions = {".asc": "ASCII",
".ascii": "ASCII",
".tif": "GeoTIFF",
".tiff": "GeoTIFF",
".geotiff": "GeoTIFF",
... | karimbahgat/PythonGis | pythongis/raster/loader.py | Python | mit | 24,912 | [
"ADF",
"NetCDF"
] | 6ddcaf91db74775b8f29826bb2b41f504e4fcefaca272997837f2bdabe736dfe |
"""
Calculations relating to absorption lines.
"""
from __future__ import (absolute_import, division, print_function,
unicode_literals)
from .voigt import voigt
from ..data.atomic import get_atomdat
from astropy.units import km, s, angstrom, cm, Quantity
from astropy.constants import m_e, c... | cwfinn/igmtools | igmtools/calculations/absorption.py | Python | bsd-3-clause | 8,468 | [
"Gaussian"
] | 2c0e6b5cb84f6e78d6570ebe478a1d6e1b9b437ab1bee47a6e73536d801ca214 |
#!/usr/bin/env python
"""profile_rallapck.py:
Last modified: Sat Jan 18, 2014 05:01PM
"""
__author__ = "Dilawar Singh"
__copyright__ = "Copyright 2013, NCBS Bangalore"
__credits__ = ["NCBS Bangalore", "Bhalla Lab"]
__license__ = "GPL"
__version__ = "1.0.0"
__maintai... | subhacom/moose-core | tests/python/Rallpacks/profile_rallapck.py | Python | gpl-3.0 | 3,546 | [
"MOOSE"
] | 4ae6df6eed37c5f463bcfe63a6ea6d6ab72669b33a7c4082e1832b0e9f2f2fe2 |
from octopus.sequence.runtime import *
v = variable(0, "v", "v")
s = sequence(
loop_while(v < 5, sequence(
log("v = " + v),
set(v, v + 1)
)),
set(v, 0),
loop_while(v < 2, sequence(
log("v = " + v),
set(v, v + 1)
), min_calls = 5),
log("Done")
)
run(s)
| richardingham/octopus | examples/test_while.py | Python | mit | 270 | [
"Octopus"
] | 99b1fc96f1592c4bfc1ad491472fc0c25b9c1195f526766530d97941d27e7873 |
import numpy as np
import pandas as pd
from scipy.stats import norm
import statsmodels.api as sm
import matplotlib.pyplot as plt
import scripts.common_functions as cmfunc
import sklearn.neighbors as nb
from sets import Set
import warnings
warnings.simplefilter('ignore')
def getCSVData(dataPath):
try:
da... | kimhungGCZ/combinedAL | study_armi_4_with_decay_tsingData.py | Python | agpl-3.0 | 12,137 | [
"Gaussian"
] | d192e64e2fd091530bc7bbfd70520839ca91e72268bcdf341bdd60dae77a983c |
"""
Helper methods for generating k8s API objects.
"""
import base64
import ipaddress
import json
import operator
import os
import re
from urllib.parse import urlparse
from kubernetes.client.models import V1Affinity
from kubernetes.client.models import V1Container
from kubernetes.client.models import V1ContainerPort
f... | yuvipanda/jupyterhub-kubernetes-spawner | kubespawner/objects.py | Python | bsd-3-clause | 34,883 | [
"VisIt"
] | d6be3cdd6dbce8a71b0ab0b7bb580879649af053f01fef6605fc4759696fc75c |
import pytest
from .utils import *
from .addons import using
from qcelemental.testing import compare_values
import psi4
pytestmark = [pytest.mark.quick, pytest.mark.mdi]
@pytest.mark.smoke
@using("mdi")
def test_mdi_water():
psi4.geometry("""
0 1
O
H 1 1.0
H 1 1.0 2 104.5
""")
psi4.set... | lothian/psi4 | tests/pytests/test_mdi.py | Python | lgpl-3.0 | 4,166 | [
"Psi4"
] | a28e4c3411136db98f33ba83eb41e32615bd00782a62adb4dfac05dd2b954a57 |
"""Provides some utilities widely used by other modules"""
import bisect
import collections
import collections.abc
import operator
import os.path
import random
import math
import functools
from itertools import chain, combinations
# ______________________________________________________________________________
# Fun... | SnShine/aima-python | utils.py | Python | mit | 22,773 | [
"Gaussian"
] | b93693967e53012afe86dfd19abea034c0981d2c38eb53b5aa5170b80a3d9526 |
import eva
import eva.tests
import eva.tests.schemas
import eva.adapter
import eva.exceptions
import eva.job
from unittest import mock
import httmock
import datetime
class TestFimexAdapter(eva.tests.BaseTestAdapter):
adapter_class = eva.adapter.FimexAdapter
config_ini = \
"""
[adapter]
fimex_parameters = {{r... | metno/EVA | eva/tests/adapters/test_fimex.py | Python | gpl-2.0 | 2,035 | [
"NetCDF"
] | e9a83a696d9604a300ad28c647571be74904ae55e5de32464dea4bd7a6863054 |
from collections import deque
import time
import requests
# Constants
BRAZIL = 'br'
EUROPE_NORDIC_EAST = 'eune'
EUROPE_WEST = 'euw'
KOREA = 'kr'
LATIN_AMERICA_NORTH = 'lan'
LATIN_AMERICA_SOUTH = 'las'
NORTH_AMERICA = 'na'
OCEANIA = 'oce'
RUSSIA = 'ru'
TURKEY = 'tr'
# Platforms
platforms = {
BRAZIL: 'BR1',
EUR... | reeth/LoLPi | riotwatcher/riotwatcher.py | Python | mit | 21,212 | [
"CRYSTAL"
] | f1f4f7169d55ae4c88b088c106b9e45f9f203f10b3d33eafa0f8ad5d43d791ab |
"""
----------------------------------------------------------------------
Authors: Stephan Nell
----------------------------------------------------------------------
Unit tests for the Blur Manager
----------------------------------------------------------------------
"""
import pytest
import cv2
import os
from hutts... | javaTheHutts/Java-the-Hutts | src/unittest/python/test_blur_manager.py | Python | bsd-3-clause | 4,063 | [
"Gaussian"
] | 97ebfba782c7aa225f68e566095e8e8d38024f03fa0c0be116c894e33de358ae |
"""
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... | xingyepei/edx-platform | lms/djangoapps/instructor/views/instructor_dashboard.py | Python | agpl-3.0 | 29,074 | [
"VisIt"
] | 608f6fff5f18e3dad1c79179949443ae53aa11b7f49730333c56eb8908994fcc |
"""
Policy Gradients
1. Sample paths.
2. Process paths (compute advantage, baseline, rewards, etc)
3. Run the paths through the policy (function approximator)
4. Compute gradients/update policy model weights
5. Profit?!?!
How we optimize the policy
--------------------------
L(theta) = sum t=0 to T-1 log policy(acti... | domluna/deep-rl-gym-tutorials | policy_gradients/vpg.py | Python | mit | 8,321 | [
"Gaussian"
] | 6157755d7055085ee55611e498e4e97e6732fcf61141ba9a7da66c11b21f1b11 |
import numpy as np
### Functions for you to fill in ###
def polynomial_kernel(X, Y, c, p):
"""
Compute the polynomial kernel between two matrices X and Y::
K(x, y) = (<x, y> + c)^p
for each pair of rows x in X and y in Y.
Args:
X - (n, d) NumPy array (n datapoint... | xunilrj/sandbox | courses/MITx/MITx 6.86x Machine Learning with Python-From Linear Models to Deep Learning/project3/mnist/part1/kernel.py | Python | apache-2.0 | 1,287 | [
"Gaussian"
] | 8e301e065f84e3bd6a772586a4c8e02385a421eaa725e9dc29a532dc3a54068c |
# -*- coding: utf-8 -*-
"""
***************************************************************************
dataobject.py
---------------------
Date : August 2012
Copyright : (C) 2012 by Victor Olaya
Email : volayaf at gmail dot com
****************************... | nirvn/QGIS | python/plugins/processing/tools/dataobjects.py | Python | gpl-2.0 | 13,831 | [
"NetCDF"
] | 863257d438bcd4696ff4bced405a00ba5199b226677df5aecbb208a7ee3b9629 |
import os
import re
import pytest
from cookiecutter.exceptions import FailedHookException
import sh
import yaml
from binaryornot.check import is_binary
PATTERN = r"{{(\s?cookiecutter)[.](.*?)}}"
RE_OBJ = re.compile(PATTERN)
@pytest.fixture
def context():
return {
"project_name": "My Test Project",
... | trungdong/cookiecutter-django | tests/test_cookiecutter_generation.py | Python | bsd-3-clause | 10,205 | [
"GULP"
] | 205cd5eac405a8640a5badc05e61434b64192451c81533cae4ad4fbebe35cd1a |
#!/usr/bin/env python
# Copyright (C) 2012,2013,2015(H),2016
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or mo... | cgchemlab/chemlab | tools/convert_gromacs2espp.py | Python | gpl-3.0 | 4,036 | [
"ESPResSo",
"Gromacs"
] | 5edebe4aa4413ef65c6313a99d09b90ad401b0d3af433e34aad1930b1c30c8f6 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# delres - Deletes a resource
# Copyright (C) 2003-2010 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publi... | heromod/migrid | mig/cgi-bin/delres.py | Python | gpl-2.0 | 1,063 | [
"Brian"
] | c0ed971ce5ad365c27ee1fffed69c5e940609f39650f06eab62f6aaad1a8662b |
# -*- coding: utf-8 -*-
"""
Application setup script
To build package:
python3 setup.py bdist_wheel sdist
python2 setup.py bdist_wheel clean
To run tests in an virtualenv:
python setup.py test
To run tests directly with verbose output:
python -m pytest -vv
"""
# Python 2 forwards-compatibility
from __future__ impor... | brbsix/pip-utils | setup.py | Python | gpl-3.0 | 2,885 | [
"Brian"
] | 814a6b19f63aac305c07f292f2eb2a84ac13e6623ae5a5d1581c95ec9e67124a |
# -*- coding: utf-8 -*-
'''
This file is part of O4erednik.
O4erednik 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 version.
... | xomachine/O4erednik | modules/g03.py | Python | gpl-3.0 | 4,192 | [
"Gaussian"
] | dfdcb2c19bf10b045c1119ce43280251ec3207812d19cd8a020c943376375a88 |
"""User-friendly public interface to polynomial functions. """
from sympy import (
S, Basic, I, Integer, Add, Mul, sympify, ask,
)
from sympy.core.decorators import (
_sympifyit,
)
from sympy.polys.polyclasses import (
GFP, DMP, SDP, ANP, DMF,
)
from sympy.polys.polyutils import (
dict_from_basic,
... | tarballs-are-good/sympy | sympy/polys/polytools.py | Python | bsd-3-clause | 74,557 | [
"Gaussian"
] | 39ef848d5e0cb17a3d9f7e01ab9396d7f7bf1777c7373fbebaff7db91d1dca38 |
"""
"""
__author__ = "Xun Li <xunli@asu.edu> "
__all__ = ["DensityMap",'DensityMapQueryDialog','KDEConfigDialog']
import os,time
import wx
import wx.combo
import random
import numpy as np
import scipy
from math import exp,pi,ceil,floor,sqrt
import pysal
import stars
from ShapeMap import ShapeMap, GradientColorSchem... | GeoDaCenter/CAST | stars/visualization/maps/DensityMap.py | Python | gpl-3.0 | 36,615 | [
"Gaussian"
] | d2054d235050bb4f95b8fcc98dcf6b45f6ecc18c2027ae5ca87c6a28de49a6ae |
"""Gaussian processes classification."""
# Authors: Jan Hendrik Metzen <jhm@informatik.uni-bremen.de>
#
# License: BSD 3 clause
import warnings
from operator import itemgetter
import numpy as np
from scipy.linalg import cholesky, cho_solve, solve
from scipy.optimize import fmin_l_bfgs_b
from scipy.special import erf... | ElDeveloper/scikit-learn | sklearn/gaussian_process/gpc.py | Python | bsd-3-clause | 31,542 | [
"Gaussian"
] | 7e168549256d74e822d8eb66c35ee55837d5dc1731422ffff23a3201e5049218 |
from django.conf.urls import url,patterns,include
from moto.moe.api import views,views2
from moto.moe.api import search
from rest_framework.authentication import SessionAuthentication
# urls
urlpatterns = patterns('',
url(r'^post/$', views.Post.as_view() ,name='post'),
url(r'^posts/$', views.PostList.as_view() ... | bung87/moto-moe | moto/moe/api/urls.py | Python | mit | 1,296 | [
"MOE"
] | 15fbf17f1dc98018879e6393fb7972d5d971cbf588a862e1b4db6974173343ae |
#!/usr/bin/env python
# Creates plots to illustrate the marginalization algorithm.
import argparse
import numpy as np
import matplotlib.pyplot as plt
import galsim
import bashes
def main():
# Parse command-line args.
parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)... | deepzot/bashes | examples/plotnll.py | Python | mit | 5,703 | [
"Galaxy"
] | 5e0a45c6646266a290be4b7d11eff4cde75fb4a4324ac3d7c9cdb0d6948c4a09 |
# -*- coding: utf-8 -*-
#!/usr/bin/env python
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007 Johan Gonqvist <johan.gronqvist@gmail.com>
# Copyright (C) 2007-2009 Gary Burton <gary.burton@zen.co.uk>
# Copyright (C) 2007-2009 Stephane Charet... | sam-m888/gramps | gramps/plugins/webreport/introduction.py | Python | gpl-2.0 | 3,854 | [
"Brian"
] | f8c9f9051496872358427cac677ca3407cfde355dfe4a1fd3f766fa2e5b7bd29 |
"""
The Job Wrapper Class is instantiated with arguments tailored for running
a particular job. The JobWrapper starts a thread for execution of the job
and a Watchdog Agent that can monitor its progress.
.. literalinclude:: ../ConfigTemplate.cfg
:start-after: ##BEGIN JobWrapper
:end-before: ##END
:caption: JobW... | DIRACGrid/DIRAC | src/DIRAC/WorkloadManagementSystem/JobWrapper/JobWrapper.py | Python | gpl-3.0 | 70,891 | [
"DIRAC"
] | f7199e6688809653a96df1a42710f355195d1703eee1ec563aea1d0359d0b0b4 |
# 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... | krikru/tensorflow-opencl | tensorflow/python/ops/gradients_impl.py | Python | apache-2.0 | 34,088 | [
"VisIt"
] | 835f89fe9a59e1604f4e158860b6e8e1c7ff72e34814b347ce7ee2350164fc62 |
from setuptools import setup, Command
class my_clean(Command):
description = "Removes the generated files from the directory"
user_options = []
def initialize_options(self):
pass
def run(self):
import os
import shutil
try:
os.remove('MANIFEST')
... | atjacobs/PeakUtils | setup.py | Python | mit | 1,345 | [
"Gaussian"
] | a7ab0fc624ea244da8fb0160ba39d321ac3aab583da33f0a5f8be9ea2d22c13b |
# ----------------------------------------------------------------------
# Numenta Platform for Intelligent Computing (NuPIC)
# Copyright (C) 2014-2015, Numenta, Inc. Unless you have an agreement
# with Numenta, Inc., for a separate license for this software code, the
# following terms and conditions apply:
#
# This p... | sambitgaan/nupic | src/nupic/algorithms/anomaly_likelihood.py | Python | agpl-3.0 | 24,698 | [
"Gaussian"
] | 7651687529b62e0dd8481e896014c2cc245a5ffd60bac54245090be5341240af |
import numpy as np
import cv2
class ColourTracker():
HSV_all = [np.array( [ 0, 0, 0 ], np.uint8 ),
np.array( [ 179, 255, 255 ], np.uint8 )]
def __init__( self,
hsv_slice = None,
use_contours = True,
show_images = False,
... | glenn20/mollie-robot | rpi/colourtracker.py | Python | gpl-2.0 | 6,303 | [
"Gaussian"
] | 552ee9bd062c7a732af611cc66a69897dd2a7982c2f6ea5239f77207a24007ab |
import os
import random
import requests
from cloudbot import hook
from cloudbot.util.http import parse_soup
search_url = "https://www.dogpile.com/search"
CERT_PATH = 'dogpile.crt'
HEADERS = {
'User-Agent': 'Mozilla/5.0 (Linux; Android 4.0.4; Galaxy Nexus Build/IMM76B) AppleWebKit/535.19 '
'(KH... | tiredtyrant/CloudBot | plugins/dogpile.py | Python | gpl-3.0 | 2,007 | [
"Galaxy"
] | 39be52a4e8bcfbe08f9cf9fcc419e5b1c4bb6f10385e3ec6d0e43a8408aa8980 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, division, print_function, unicode_literals
WINE_CLASSIFICATIONS = {'1er Cru', '1er Cru Classé', '1er Grand Cru', '2ème Cru Classé', '2ème Vin',
'4ème Cru Classé', 'Cru Classé', 'Grand Cru', 'Non Classé'}
WINE_PACKING_TYPE = {'OCB06... | nedlowe/amaas-core-sdk-python | amaascore/assets/enums.py | Python | apache-2.0 | 3,334 | [
"Jaguar"
] | 58dd22e0d8cc19775ff50f989a545df9f7abede9940a76fcfde655b9cde74b84 |
# -*- coding: utf-8 -*-
from __future__ import print_function, division
# This example demonstrates random (Poisson) synaptic input to a cell.
# Copyright (C) Upinder S. Bhalla NCBS 2018
# Released under the terms of the GNU Public License V3. No warranty.
# Changelog:
# Thursday 20 September 2018 09:53:27 AM IST
# - ... | BhallaLab/moose-core | tests/core/test_rdesigneur_random_syn_input.py | Python | gpl-3.0 | 1,571 | [
"MOOSE"
] | 9b9ec8f8956f486426a36afe0b93a42bd26c9fc37f7e6a89057b369713b72747 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
################################################################################
#
# RMG - Reaction Mechanism Generator
#
# Copyright (c) 2002-2017 Prof. William H. Green (whgreen@mit.edu),
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu)
#
# ... | Molecular-Image-Recognition/Molecular-Image-Recognition | code/rmgpy/data/thermo.py | Python | mit | 101,127 | [
"VisIt"
] | 319649cf5b56788953ecf76fa8470b45e368883f7089790fa9b8928e447829dd |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | rangadi/incubator-beam | sdks/python/apache_beam/runners/runner.py | Python | apache-2.0 | 14,033 | [
"VisIt"
] | ec80ad4ff4e6e37d5174ab52599efbcffd8f145e845c888204c6fe9fa4e08e7e |
# Orca
#
# Copyright 2010 Joanmarie Diggs.
# Copyright 2014-2015 Igalia, S.L.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) an... | GNOME/orca | src/orca/scripts/web/script_utilities.py | Python | lgpl-2.1 | 199,261 | [
"ORCA"
] | d57180b1976b466418094a361c9fb21723609cce598bf71185deb4b75808f599 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""Tools to compute equations of states with different models."""
from __future__ import unicode_literals, division, print_function
import collections
import numpy as np
import pymatgen.core.units as units
fro... | aykol/pymatgen | pymatgen/analysis/eos.py | Python | mit | 11,338 | [
"pymatgen"
] | 50a5256877b7fe8c82b1cbe8bddd51bea64601581231c059b3f0677b82710f3b |
#!/usr/bin/env python3
"""
refguide_check.py [OPTIONS] [-- ARGS]
- Check for a NumPy submodule whether the objects in its __all__ dict
correspond to the objects included in the reference guide.
- Check docstring examples
- Check example blocks in RST files
Example of usage::
$ python refguide_check.py optimize... | abalkin/numpy | tools/refguide_check.py | Python | bsd-3-clause | 37,850 | [
"Gaussian"
] | 3a9c00232eac0b037fba62a98c7641a80a29632e2c9bbe0fe2d3c911e304acd7 |
# 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)
from spack import *
class RGenomicalignments(RPackage):
"""Representation and manipulation of short genomic alignmen... | LLNL/spack | var/spack/repos/builtin/packages/r-genomicalignments/package.py | Python | lgpl-2.1 | 3,120 | [
"Bioconductor"
] | 8a5af2fb1f389753db59050d9bce21c60a85eda686281e50019ef11d9c59ef37 |
#!/usr/bin/env python3
# coding:utf-8
"""
### Author: Mogu ###
This file contains Memory manager Class.
Python don't set Memory Limit.We need to set Memory Limit to protect our Machine from a pending state.
# Environment:
Python3.5.1
# Requirements:
# References:
1) in Ch13.4 Python Coookbook,Third edition [B... | Moguf/cafepy | cafepy/utils/cafepy_memory_manager.py | Python | gpl-3.0 | 836 | [
"Brian"
] | 87a33e6610593150354b8103771795e135aa092a39bd6cf0e98ceb3848b448c3 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/gto/basis/parse_bfd_pp.py | Python | apache-2.0 | 5,431 | [
"PySCF"
] | 7f43f35efacae3d5c94bb86cfc8ae493fa8d64c94464ecbf5fd5488b42b4c673 |
#!/usr/bin/python
#
# This source file is part of appleseed.
# Visit http://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2010-2013 Francois Beaune, Jupiter Jazz Limited
# Copyright (c) 2014-2016 Francois Beaune, The appleseedhq Organi... | docwhite/appleseed | scripts/convertmany.py | Python | mit | 5,687 | [
"VisIt"
] | 4c24bfb2cbdae8ffb0a41230ee9be1b81e5f72b15c9d738bb49638bb41abe74c |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2002-2006 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2011 Tim G L Lyons
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publ... | pmghalvorsen/gramps_branch | gramps/gen/filters/rules/event/__init__.py | Python | gpl-2.0 | 2,334 | [
"Brian"
] | ae867bc8e420c5eff5d6f6b621b1312e02ef8687a6b31bda191d64d923c0d87f |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import access.rest
import creditor.rest
import members.rest
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views import defaults as default... | rambo/asylum | project/config/urls.py | Python | mit | 2,768 | [
"VisIt"
] | 03295a574353977d9b77414a5f49a306b35dec84049a93dcc8d1067c3949305a |
#!/usr/bin/env python
# ----------------------------------------------------------------------------
# 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.
# ---------------------... | Jorge-C/bipy | setup.py | Python | bsd-3-clause | 2,620 | [
"scikit-bio"
] | fc41cafb27c57230dd2824cd8b62c5fbfccef00d842a6a1d2425d0f747658261 |
# This file is part of OpenHatch.
# Copyright (C) 2010 Parker Phinney
# Copyright (C) 2009, 2010 OpenHatch, Inc.
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published by
# the Free Software Foundation, either version 3 of the ... | waseem18/oh-mainline | mysite/project/tests.py | Python | agpl-3.0 | 18,369 | [
"VisIt"
] | e9ae7e296d9678f3c46c429a15dd16bb8dabd7452149756d95ecfc4c3db68c6d |
from flask_wtf import Form
from wtforms import StringField, PasswordField
from wtforms.validators import DataRequired
from octopus.models import User
class LoginForm(Form):
username = StringField('Username', validators=[DataRequired()])
password = PasswordField('Password', validators=[DataRequired()])
def __i... | quaintm/octopus | octopus/public/forms.py | Python | bsd-3-clause | 978 | [
"Octopus"
] | 5d6034ec1a04842100a60764a4bf1b3c8950675d5671afe29daf00bbf29ababf |
#
# Copyright (c) 2009-2015, Jack Poulson
# All rights reserved.
#
# This file is part of Elemental and is under the BSD 2-Clause License,
# which can be found in the LICENSE file in the root directory, or at
# http://opensource.org/licenses/BSD-2-Clause
#
import El
m = 250
n = 500
lambda1 = 3
lambda2 = 4
displ... | birm/Elemental | examples/interface/ENDense.py | Python | bsd-3-clause | 1,420 | [
"Gaussian"
] | 636a121f1202887f530c8b12442dfe735c127b9c4d63b3fc756ed70d36abe3e9 |
"""
Useful support routines (for internal use).
These functions aren't really Zero Install specific; they're things we might
wish were in the standard library.
@since: 0.27
"""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import _, logger
imp... | timdiels/0install | zeroinstall/support/__init__.py | Python | lgpl-2.1 | 4,694 | [
"VisIt"
] | b296def5d398a48817ac845a00c3a98696d0b33641b69a4c8cc9cb2e7f5470f8 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
# ... | SKIRT/PTS | magic/tests/Sources_real/config.py | Python | agpl-3.0 | 1,493 | [
"Galaxy"
] | 7c15723c10ad9d642210e36e7e5d0b45a71d5b8f5ea4ebc530b9aa03d2ec6a7c |
# -*- coding: utf-8 -*-
"""
Simblin Test Views
~~~~~~~~~~~~~~~~~~
Test the different views of the blogging application.
:copyright: (c) 2010 by Eugen Kiss.
:license: BSD, see LICENSE for more details.
"""
from __future__ import with_statement
import datetime
import flask
from simblin.extensions i... | eugenkiss/Simblin | test/test_views.py | Python | bsd-3-clause | 15,595 | [
"MOE"
] | d01dfdffaa99f73c45c409d5ee5329db577f6ca497fcc2e64b426b53dcfa3e4e |
from .base import *
from .edf import EDFRawReader
from .eeg import EEGReader
from .events import *
from .hdf5 import H5RawReader
from .index import JsonIndexReader
from .netcdf import NetCDF4XrayReader
from .params import ParamsReader
from ptsa.data.readers.base import BaseRawReader
from .tal import *
from .binary impo... | maciekswat/ptsa_new | ptsa/data/readers/__init__.py | Python | gpl-3.0 | 375 | [
"NetCDF"
] | 63db9b69e1064fc9c1f55e90bbdc780e3d04f7c3f79537cf440d0428e2b7df66 |
# -*- Mode: Python; coding: utf-8; indent-tabs-mode: nil; tab-width: 4 -*-
### BEGIN LICENSE
# Copyright (C) 2014 Brian Douglass bhdouglass@gmail.com
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License version 3, as published
# by the Free Softwa... | bhdouglass/agui | agui/awidgets/combobox.py | Python | gpl-3.0 | 2,044 | [
"Brian"
] | fe7db65657d1c6747b2db602e8176cfe3fd7c14614bb3a24e6c8292a03b374f6 |
# coding: utf-8
from __future__ import unicode_literals, division, print_function
import os
from pymatgen.util.testing import PymatgenTest
from pymatgen.core.structure import Structure
from pymatgen.core.units import Ha_to_eV
from pymatgen.io.abinitio.abiobjects import *
import warnings
test_dir = os.path.join(os.... | Dioptas/pymatgen | pymatgen/io/abinitio/tests/test_abiobjects.py | Python | mit | 4,074 | [
"pymatgen"
] | 0283c2a3d118667809403aec58f379d675977eba4a69fa3b23c7653dc295be37 |
"""K-means clustering"""
# Authors: Gael Varoquaux <gael.varoquaux@normalesup.org>
# Thomas Rueckstiess <ruecksti@in.tum.de>
# James Bergstra <james.bergstra@umontreal.ca>
# Jan Schlueter <scikit-learn@jan-schlueter.de>
# Nelle Varoquaux
# Peter Prettenhofer <peter.prettenh... | clemkoa/scikit-learn | sklearn/cluster/k_means_.py | Python | bsd-3-clause | 60,864 | [
"Gaussian"
] | 247042974416581f923adaa96b2e50de5f7a0b576bb87d0040246cbf024fb386 |
from itertools import chain
import sympy
from ...componentclass.visitors.queriers import (
ComponentClassInterfaceInferer,
ComponentRequiredDefinitions, ComponentExpressionExtractor,
ComponentDimensionResolver)
from .base import BaseDynamicsVisitor
from nineml.exceptions import NineMLStopVisitException
from... | INCF/lib9ML | nineml/abstraction/dynamics/visitors/queriers.py | Python | bsd-3-clause | 7,234 | [
"VisIt"
] | 98178443a88a084b740f354bdc0797f3eaa4e7eea62690255bb7e059d78ee025 |
"""Main entrypoint for modeler commands."""
import argparse
from modeler.train import train
from modeler.gen import gen
def main():
"""Execute the modeler commandline interface."""
parser = argparse.ArgumentParser(
description="Train and run the music generator.""",
)
subparsers = parser.add... | crestonbunch/neural-namer | modeler/commands.py | Python | mit | 3,357 | [
"Brian"
] | a5cde3cb4eeaebdda5deb0e9bb4da2f3ccd7081a76e9714a74ccb15649a711ab |
import ast
from .expression_printer import ExpressionPrinter
class ModulePrinter(ExpressionPrinter):
"""
Builds the smallest possible exact representation of an ast
"""
def __init__(self, indent_char='\t'):
super(ModulePrinter, self).__init__()
self.indent_char = indent_char
def... | listyque/TACTIC-Handler | thlib/side/python_minifier/module_printer.py | Python | epl-1.0 | 18,645 | [
"VisIt"
] | 4982588e5bcd38ee0f03f2886a73cffb766882791cc5a83c1a1db15bb8d52d92 |
class Solution:
# @param {integer} numCourses
# @param {integer[][]} prerequisites
# @return {boolean}
def canFinish(self, numCourses, prerequisites):
graph = {i: set() for i in range(numCourses)}
for after, before in prerequisites:
graph[before].add(after)
... | rahul-ramadas/leetcode | course-schedule/Solution.27729680.py | Python | mit | 1,098 | [
"VisIt"
] | 28f84e5e1052313c7e85748a49be42a6917f46cb2e7b9a95bcab4180be2df37e |
# coding: utf-8
"""
django find&replace
~~~~~~~~~~~~~~~
:copyleft: 2015 by find&replace team, see AUTHORS for more details.
:created: 2015 by JensDiemer.de
:license: GNU GPL v3 or above, see LICENSE for more details.
"""
from __future__ import absolute_import, print_function
import os
import doc... | jedie/djangocms-find_and_replace | find_and_replace/tests/test_doctest.py | Python | gpl-3.0 | 2,605 | [
"VisIt"
] | eb7de3384964e0d8dcf9a39b4e9ef51e62febce31a589a19b59fbd8ff53e3718 |
# Copyright 2016 Battelle Energy Alliance, LLC
#
# 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 agr... | idaholab/civet | ci/recipe/tests/test_RecipeCreator.py | Python | apache-2.0 | 20,485 | [
"MOOSE"
] | a6ba4add00550eb7fd8d5a646aa607874d4aeea91e3b6ba8659d9b5eab414ab3 |
# Orca
#
# Copyright 2004-2008 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | GNOME/orca | src/orca/scripts/apps/Thunderbird/script.py | Python | lgpl-2.1 | 14,866 | [
"ORCA"
] | de8bc52fb983d3b4104d23ab79625074e044547e0465d661c8b98bee8277c2a1 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | fedepad/espressopp | src/interaction/VSpherePair.py | Python | gpl-3.0 | 4,449 | [
"ESPResSo"
] | e3a8fe2047c0bae91e59fea1ac99c9be38eb85e03058a851b02576051f44dce1 |
# coding=utf-8
from __future__ import division
import os
from .dt import Date
from .analysisperiod import AnalysisPeriod
from .datacollection import HourlyContinuousCollection
from .datacollection import MonthlyCollection
from .datatype import angle, distance, energyflux, energyintensity, generic, \
illuminance, ... | ladybug-analysis-tools/ladybug-core | ladybug/epw.py | Python | gpl-3.0 | 79,466 | [
"EPW"
] | cd5c40145593aeaee548b6ba8b2d5c1736c2c9796d57a18f2b704e1f0534e6d9 |
#!/usr/bin/env python
"""
Creates graph of three modeled hydrology-related time series from a single file.
"""
# example from grid-sequencing example:
# $ ./hydro-tsshow.py foo.png ts_routing-decoupled.nc
from numpy import *
import pylab as plt
import sys
try:
import netCDF4 as netCDF
except:
print "netCDF... | citibeth/twoway | pism/std-greenland/hydro/hydro-tsshow.py | Python | gpl-3.0 | 1,603 | [
"NetCDF"
] | daa3e8574c67447a0ce46d2c5ec9e9b98c6e92999f9584389fd2682a3efdbb54 |
# -*- coding: utf-8 -*-
#
# Moonstone is platform for processing of medical images (DICOM).
# Copyright (C) 2009-2011 by Neppo Tecnologia da Informação LTDA
# and Aevum Softwares LTDA
#
# This file is part of Moonstone.
#
# Moonstone is free software: you can redistribute it and/or modify
# it under the terms of the GN... | aevum/moonstone | src/moonstone/ilsa/plugins/mark/multislicecontour.py | Python | lgpl-3.0 | 12,283 | [
"VTK"
] | 46845f474238603dc81e38d15315243058c0dda2873f20804fc54206b5cad9db |
#!/usr/bin/env python
from sys import argv, exit
from getopt import getopt, GetoptError
# @package nccmp
# Compares NetCDF files by absolute max norms of difference of variables
##
# Without options,
# \code
# nccmp.py foo.nc bar.nc
# \endcode
# compares all the variables in \c foo.nc and \c bar.nc.
##
# Option \c -v ... | talbrecht/pism_pik07 | util/nccmp.py | Python | gpl-3.0 | 5,018 | [
"NetCDF"
] | 6aa4b9376ff4c23aeed98a50c4e5810f68adb7cf4ec47325a511503d7b5caefd |
"""A test that subscribes to NumPy arrays.
Uses REQ/REP (on PUB/SUB socket + 1) to synchronize
"""
#-----------------------------------------------------------------------------
# Copyright (c) 2010 Brian Granger
#
# Distributed under the terms of the New BSD License. The full license is in
# the file COPYING.BSD... | yyt030/pyzmq | examples/pubsub/subscriber.py | Python | bsd-3-clause | 1,937 | [
"Brian"
] | fb5c3854b939232dd45dcac3352c0b0293d8268fd7fa8d1d7f5f3dcc8fc8b125 |
"""
Tools for integration with miscellaneous non-required packages.
"""
import importlib
import logging
def error_if_no(name, package_name, has_package):
if not has_package:
raise RuntimeError(name + " requires " + package_name
+ ", which is not installed")
def _chain_import(*... | openpathsampling/openpathsampling | openpathsampling/integration_tools.py | Python | mit | 2,366 | [
"MDTraj",
"OpenMM"
] | dc89d4fb49928e8a3272579aee9b598aa312dd527ccc414e3e76c0141b2050f8 |
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 = 300
platform_name = "CUDA"
precision = "mix... | kyleabeauchamp/HMCNotes | code/optimize/test_optimize_hyper_xhmc_respa_manualgroups.py | Python | gpl-2.0 | 2,230 | [
"OpenMM"
] | 64a871e70c8626001b2f5cf49ddc7224db258d836c46e17a475b4ddefce6e8e6 |
##
# 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... | hpcuantwerpen/easybuild-easyblocks | easybuild/easyblocks/n/netcdf4_python.py | Python | gpl-2.0 | 3,956 | [
"NetCDF"
] | 0517a78b66842143a1211747a7a009e687cc921bd695bae4366b463e1b674d92 |
#pylint: disable=missing-docstring
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/... | nuclear-wizard/moose | python/chigger/exodus/ExodusSource.py | Python | lgpl-2.1 | 15,541 | [
"MOOSE",
"VTK"
] | 72545c4931d1fbe86b1dc93003cb971ac1dbc0b360c883565b4e8f074c12f5a7 |
"""Code for converting notebooks to and from the v2 format.
Authors:
* Brian Granger
* Jonathan Frederic
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2008-2011 The IPython Development Team
#
# Distributed under the terms of the BSD License. The full license i... | unnikrishnankgs/va | venv/lib/python3.5/site-packages/nbformat/v2/convert.py | Python | bsd-2-clause | 1,999 | [
"Brian"
] | 434b1a98b4a5a4a456d275ee658e1b3530115e6b98f02945fb8d92934512138e |
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | gkc1000/pyscf | pyscf/nao/m_rsphar_vec.py | Python | apache-2.0 | 1,228 | [
"PySCF"
] | bd26d749f43204a54d404b2dd43f9e86b012c667cdd2354edea08ea364d03524 |
# -*- coding : utf8 -*-
""" Siesta help scripts, (c) Andrey Sobolev 2011
"""
__version__ = 0.2
import atomtype
| ansobolev/shs | shs/__init__.py | Python | mit | 114 | [
"SIESTA"
] | 27d8b83116fd9f4c476f8eff58f317486c3fe386a7f63279dd86f44ebfde909f |
import inspect
import os
import subprocess
from io import StringIO
from os.path import splitext
from subprocess import run
from datasize import DataSize
import chemcoord as cc
import numpy as np
import re
from chemopt.configuration import (conf_defaults, fixed_defaults,
substitute_d... | mcocdawc/chemopt | src/chemopt/interface/molpro.py | Python | lgpl-3.0 | 7,455 | [
"Molpro"
] | 661fea64fa591b97e9e4ed187db1dd71d78ce8c1699ed1f16f450cd8ec51f6a7 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import os
import warnings
from pymatgen.core.structure import Molecule
from pymatgen.analysis.graphs import MoleculeGraph
from pymatgen.analysis.local_env import OpenBabelNN
from pymatgen.analy... | dongsenfo/pymatgen | pymatgen/analysis/tests/test_functional_groups.py | Python | mit | 5,338 | [
"Pybel",
"pymatgen"
] | a606e45272226806ea6e66f9d72a7c805fc2b86d3ccba7963057a9787049df9d |
#! /usr/bin/env python
"""
Script to run blast on Genbank/EMBL files without having to first convert to fasta.
Written by Bryan Wee.
Version 0.0.1 - 20150425
"""
from __future__ import print_function
import sys, os
import argparse
import re
import subprocess
from argparse import RawTextHelpFormatter
from Bio impo... | bawee/bwast | bwast.py | Python | gpl-2.0 | 8,970 | [
"BLAST",
"Biopython"
] | a0455609e557b94838994128d08cd9de32db00e0bdd21737a80808f59703b01a |
#
# QAPI types generator
#
# Copyright IBM, Corp. 2011
#
# Authors:
# Anthony Liguori <aliguori@us.ibm.com>
#
# This work is licensed under the terms of the GNU GPL, version 2.
# See the COPYING file in the top-level directory.
from ordereddict import OrderedDict
from qapi import *
import sys
import os
import getopt
... | xorstream/unicorn | qemu/scripts/qapi-types.py | Python | gpl-2.0 | 11,045 | [
"VisIt"
] | ff217eb124300913459996e624d517311d4602ded65d4dd9fad2246535b5a3bd |
"""
The autotable module provides a simple interface to store data from simulation
runs into efficient HDF5 files onto the filesystem.
These files can later be opened
* in Python: PyTables (http://www.pytables.org/)
* in Matlab: hdf5read( <filename>, <tablename> )
* in pure C or C++: libhdf5 (http://www.hdfgroup.o... | Saran-nns/SORN | utils/autotable.py | Python | mit | 5,979 | [
"Gaussian"
] | e88f8575a1e4935318da818d42ad2c85a847b4af8e084e27b9bc357713152a4c |
import sys
sys.path.insert(1, "../../../")
import h2o, tests
def pyunit_make_glm_model():
# TODO: PUBDEV-1717
pros = h2o.import_file(h2o.locate("smalldata/prostate/prostate.csv"))
model = h2o.glm(x=pros[["AGE","DPROS","DCAPS","PSA","VOL","GLEASON"]], y=pros["CAPSULE"], family="gaussian", alpha=[0])
new... | printedheart/h2o-3 | h2o-py/tests/testdir_algos/glm/pyunit_NOPASS_make_glm_model.py | Python | apache-2.0 | 794 | [
"Gaussian"
] | 6db5723257417c9128832c39fa7703cb7f59c988335c3f15ffb234205ccca438 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 16.3.8
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | halberom/ansible | lib/ansible/modules/network/avi/avi_healthmonitor.py | Python | gpl-3.0 | 6,086 | [
"VisIt"
] | 412c935146b8791ae6188f6659ae84bf25a780b48fb947e5ce014eeb744e614b |
"""
Detecting peaks in arrays.
detect_peaks(): peak and trough detection with a relative threshold.
detect_dynamic_peaks(): peak and trough detection with a dynamically adapted threshold.
accept_peak(): make detect_peaks() return index/time and size of peaks.
accept_peak_size_threshold(): adapt the dection threshold ... | jfsehuanes/thunderfish | thunderfish/peakdetection.py | Python | gpl-3.0 | 32,802 | [
"Gaussian"
] | e4d6c706764ad1b7332c04d41f901932e9dc158f230a1561542f45612c48e54f |
from pymol import cmd
class Wizard:
event_mask_pick = 1
event_mask_select = 2
event_mask_key = 4
event_mask_special = 8
event_mask_scene = 16 # scene changed
event_mask_state = 32 # state changed
event_mask_frame = 64 # frame changed
event_mask_dirty = 128 # anything ... | gratefulfrog/lib | python/pymol/wizard/__init__.py | Python | gpl-2.0 | 2,111 | [
"PyMOL"
] | f7c96a2145ee01b8f0ec266ed0a78cefc532dad5383b357f2d244734e11ab05c |
# vim:fileencoding=utf-8:noet
from __future__ import (unicode_literals, division, absolute_import, print_function)
import sys
import os
from functools import partial
from collections import namedtuple
from time import sleep
from powerline.segments import shell, tmux, pdb, i3wm
from powerline.lib.vcs import get_fallb... | Luffin/powerline | tests/test_segments.py | Python | mit | 73,725 | [
"FEFF"
] | 726387b87aaa27d82043e40a266d59d9f886a5884ad73e72325066e4868550b2 |
"""
Student Views
"""
import datetime
import logging
import uuid
import json
import warnings
from collections import defaultdict
from urlparse import urljoin
from pytz import UTC
from requests import HTTPError
from ipware.ip import get_ip
from django.conf import settings
from django.contrib.auth import logout, authen... | Endika/edx-platform | common/djangoapps/student/views.py | Python | agpl-3.0 | 101,504 | [
"VisIt"
] | bdb0ca7b30418c6602c2e5ca22839e075a3d90d0d6f84c8be15d0b469d5525e2 |
#!/usr/bin/env python2.7
#
# Copyright (C) 2014 INRA
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program ... | frederic-mahe/FROGS | tools/affiliation_OTU.py | Python | gpl-3.0 | 17,760 | [
"BLAST"
] | 240c8213b9ff8824dae47be1468f3d83d2b6dae27486b82ec4b38ec5c1857656 |
def _countdown_(n):
if n < 0:
print('blast off!')
else:
print(n)
countdown(n-1)
k = int(input('enter number you want to countdown: '))
_countdown_(k)
t = input('enter string you want to repeat: ')
num = int(input('enter number of times it will show: '))
def _print_(s,n):
... | HangYang0204/VBA | resursive.py | Python | mit | 400 | [
"BLAST"
] | 98e19fdc3ee340840744ad81c30e523ff6ef6ead1d9355bb1192def5ead3e69d |
import mykde
class ActionPackage(mykde.ActionPackage):
author = 'Victor Varvaryuk <victor.varvariuc@gmail.com>'
version = 2
description = """
TODO:
xnview - unpack to ~/apps/ and create .desktop file in Graphics category
clip2net
galaxy icons libreoffice, enter key behavior in calc
"""
| warvariuc/mykde | packages/__init__.py | Python | bsd-3-clause | 301 | [
"Galaxy"
] | 18d4f8a3fc30c94154c0ab2d85895004119cdce7f651a7bd710b6d92ed21ee39 |
from __future__ import absolute_import, division, print_function
# ----------------------------------------------------------------------------
# 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 ... | Kleptobismol/scikit-bio | skbio/tree/_nj.py | Python | bsd-3-clause | 10,945 | [
"scikit-bio"
] | 22434390cfe3f76bf1d623f8f2a251a926cd04da2aee4bd259387c24dcd1d65d |
import numpy as np
from itertools import izip
import MDAnalysis
from MDAnalysis.core.log import ProgressMeter
import sys
import os.path
class PDBToTraj(object):
def __init__(self, universe, filename=None, infix='_conv',
targetdir=os.path.curdir, format='dcd'):
self.universe = universe
... | sseyler/PSAnalysis | source/coord2traj.py | Python | gpl-3.0 | 5,017 | [
"MDAnalysis"
] | 97a608a53bd51010adacab14daae437a45e29f13e13d33e3b6ccd7309d7dafde |
import numpy as np
import collections
class Hopfield():
"""
The hopfield network in the simplest case of AMIT book in attractor neural network
"""
def __init__(self, n_dim=3, T=0, prng=np.random):
self.prng = prng
self.n_dim = n_dim
self.s = np.sign(prng.normal(size=n_dim))
... | h-mayorquin/hopfield_sequences | hopfield.py | Python | mit | 9,780 | [
"NEURON"
] | bcda459ed6930e569f663ebc932e28cdea5fac06b6b8f2dad89b9e16d03abb07 |
#!/usr/bin/env python3
import os
import sys
import logging
import runner
import collections
import tempfile
import shutil
import re
from fasta_clean_name import read_fasta_file_handle, format_seq
logger = logging.getLogger(__name__)
def index_ref(indexdb_bin_path, input_fasta_ref_path, output_basepath, max_mem, ver... | bonsai-team/matam | scripts/compute_abundance.py | Python | agpl-3.0 | 6,190 | [
"BLAST"
] | f482e233119fe87767affd074f6a49ea5ff2911d1502c314675c91011fcb9d4e |
#!/usr/bin/env python
"""
Visual check to the label sequences used for training and testing SVMs.
Usage: python seq_consensus_viz.py in.fasta fig1.pdf
Requirements:
BioPython:- http://biopython.org
pylab:- http://wiki.scipy.org/PyLab
numpy:- http://numpy.org
"""
import sys
from Bio import SeqIO
def... | vipints/genomeutils | visual_analytics/seq_consensus_viz.py | Python | bsd-3-clause | 2,451 | [
"Biopython"
] | 8f4c7b161d8beecb35c989025cb3d1c7e19e8836a1a6f9eabf18ea4d18cebcea |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | skosukhin/spack | var/spack/repos/builtin/packages/r-ggbio/package.py | Python | lgpl-2.1 | 3,562 | [
"Bioconductor"
] | a6e9cef62f4a6f37c3792eb4ec86c7d46f4d4216d6658279b7b15010a7af3205 |
# compiler.py
# Copyright (C) 2005, 2006, 2007, 2008, 2009, 2010 Michael Bayer mike_mp@zzzcomputing.com
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Base SQL and DDL compiler implementations.
Classes provided include:
:class:`~sq... | cnelsonsic/Liquor-Cabinet | sqlalchemy/sql/compiler.py | Python | gpl-3.0 | 61,821 | [
"VisIt"
] | 0563129d8694533679f47161e104d84d76f7cc010a436ba145be6b1bd757b3a1 |
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