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# -*- coding: utf-8 -*-
"""
Created on Wed Jan 13 09:41:53 2016
@author: Radu
"""
# -*- coding: utf-8 -*-
"""
Created on Tue Jan 12 10:34:07 2016
@author: Radu
"""
from interneuron import Interneuron
from neuron import h
class Ia_in(Interneuron): #### Inherits from Cell
"""Two-section cell: A soma with active... | penguinscontrol/Spinal-Cord-Modeling | CPG/ia_in.py | Python | gpl-2.0 | 376 | [
"NEURON"
] | be31eccde1c059020aeabec71417c608fdd0b6e4ef8beeedc207ebf02bfba4a0 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from sys import exit
from random import randint
class Scene(object):
def enter(self):
print "This scene is not yet configured. Subclass it and implement enter()."
exit(1)
class Engine(object):
def __init__(self, scene_map):
s... | renweizhukov/LearningPythonTheHardWay | ex43.py | Python | lgpl-3.0 | 9,213 | [
"BLAST"
] | a546de9d6036b7aad14991f17855524a1713830f4dec3e436540cd9af90c1822 |
'''
ÄãÒ²¿ÉÒÔʵʱµØѹËõ»ò½âѹËõÊý¾Ý, Èç ÏÂÀý Ëùʾ.
'''
import zlib
encoder = zlib.compressobj()
data = encoder.compress("life")
data = data + encoder.compress(" of ")
data = data + encoder.compress("brian")
data = data + encoder.flush()
print repr(data)
print repr(zlib.decompress(data)) | iamweilee/pylearn | zlib-example-3.py | Python | mit | 290 | [
"Brian"
] | 2bdb6d646b64a753ec8dea8ddb7b0e2d206022873a7df6b444c67c695cd3ce76 |
import sys
sys.path.insert(1,"../../")
import h2o
from tests import pyunit_utils
from h2o.estimators.gbm import H2OGradientBoostingEstimator
def metric_accessors():
cars = h2o.import_file(path=pyunit_utils.locate("smalldata/junit/cars_20mpg.csv"))
r = cars[0].runif()
train = cars[r > .2]
valid = car... | h2oai/h2o-dev | h2o-py/tests/testdir_misc/pyunit_metric_accessors.py | Python | apache-2.0 | 41,699 | [
"Gaussian"
] | 16e931cf00ed116ecfe9295d2076a154b01e071a06d8d648c27d1d46af1a1ef0 |
# -*- coding: utf-8 -*-
"""
stellarPYL - python stellar spectra processing software
Copyright (c) 2016 Brunston Poon
@file: tools
This program comes with absolutely no warranty.
"""
import numpy as np
from PIL import Image
from matplotlib import pyplot as plt
#required for plotIntensityWLambda2
from mpl_toolkits.axes_... | brupoon/stellarpy | tools.py | Python | mit | 15,686 | [
"Brian"
] | bdfab794178f40a7a4a70b53c81089ef4accdd42e7ffb563c3546bd6538d1f07 |
"""
GFcalc module
Code to compute the lattice Green function for diffusion; this entails inverting
the "diffusion" matrix, which is infinite, singular, and has translational
invariance. The solution involves fourier transforming to reciprocal space,
inverting, and inverse fourier transforming back to real (lattice) sp... | DallasTrinkle/Onsager | onsager/GFcalc.py | Python | mit | 26,630 | [
"CRYSTAL"
] | 51144668619c6ade3c2eb1dc16e7d15ecb55c41d57794e8de666d763813920bb |
"""Interface module.
The interface module handles all functions typically needed by the user in an
interactive environment such as IPython. Many are also used by the
custom IPython shell defined in pybdsf.
"""
from __future__ import print_function
from __future__ import absolute_import
try:
# For Python 2, use r... | lofar-astron/PyBDSF | bdsf/interface.py | Python | gpl-3.0 | 47,239 | [
"Gaussian"
] | 028740d877667276933a0f7a985545735db28fd78ec2869227aa010f337290fe |
#!/usr/bin/python
'''
File defining a python class for snowpit data
November 2016, Simon Filhol
'''
import numpy as np
import pandas as pd
import os
import snowpyt.CAAMLv6_xml as cxv6
from snowpyt.snowflake.sf_dict import snowflake_symbol_dict
import snowpyt.snowflake.sf_dict as sfd
from matplotlib import pyplot ... | ArcticSnow/snowpyt | snowpyt/.ipynb_checkpoints/pit_class-checkpoint.py | Python | mit | 29,826 | [
"CRYSTAL"
] | daf6bd8ed01f489a4dd52c600a454a901a2bcf5740cde8bd75fe4c9957ab8853 |
# -*- coding: utf-8 -*-
r"""
Convert html from text cells in the notebook into ReStructuredText
This is called by sws2rst
- Pablo Angulo Ardoy (2011-02-25): initial version
"""
#**************************************************
# Copyright (C) 2011 Pablo Angulo
#
# Distributed under the terms of the GPL License
#***... | PhysikOnline-FFM/sagenb | sagenb/misc/comments2rst.py | Python | gpl-3.0 | 14,609 | [
"VisIt"
] | cc9cc93650cc722612497f3bbfc76a47ec73899e001bdda92e61e1450708d568 |
"""Kernels for Gaussian process regression and classification.
The kernels in this module allow kernel-engineering, i.e., they can be
combined via the "+" and "*" operators or be exponentiated with a scalar
via "**". These sum and product expressions can also contain scalar values,
which are automatically converted to... | DailyActie/Surrogate-Model | 01-codes/scikit-learn-master/sklearn/gaussian_process/kernels.py | Python | mit | 66,380 | [
"Gaussian"
] | aa628ea6b9fd1d402cdf543e0880245b6aaf57012ab3d2bfaf08f919f0f296e5 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2001-2006 Donald N. Allingham
# Copyright (C) 2008 Brian Matherly
# Copyright (C) 2008 Gary Burton
# Copyright (C) 2010 Jakim Friant
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the... | Forage/Gramps | gramps/gui/plug/__init__.py | Python | gpl-2.0 | 1,925 | [
"Brian"
] | 588cc79a3bba15313aedc8749b617bd2e14100f3ec49ccef57c77a8b8a1d0e1b |
# -*- coding: utf-8 -*-
# Generated by Django 1.10.4 on 2017-02-19 17:41
from __future__ import unicode_literals
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('core', '0002_auto_20170101_2054'),
]
operations = [
migrations.AlterField(
... | BridgeCityBicycleCoop/workstand | core/migrations/0003_auto_20170219_1741.py | Python | mit | 620 | [
"VisIt"
] | f37f1a91d5286f54905856a661e6ed42dfac039377f8b80aacd6515af959c051 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module is intended to be used to compute Pourbaix diagrams
of arbitrary compositions and formation energies. If you use
this module in your work, please consider citing the following:
General formalism for solid-aque... | materialsproject/pymatgen | pymatgen/analysis/pourbaix_diagram.py | Python | mit | 42,475 | [
"pymatgen"
] | 9b11b73bc816b3701ea9c43e50914068263163d518b65880e73ee774d895c08b |
# Copyright (c) 2016, Diego Alonso Cortez, diego@mathisart.org
# Code released under the BSD 2-Clause License
# Inspired by: Michael Nielsen, Mocha
# http://neuralnetworksanddeeplearning.com
# https://github.com/pluskid/Mocha.jl
import numpy as np
import abc # Define "skeleton" classes that do nothing but ... | etale-cohomology/unicorns | activation_functions.py | Python | bsd-2-clause | 7,428 | [
"Gaussian",
"NEURON"
] | a09b77581b620981a485c98ab3ca469ca8ed0145c308fd40a46836b6868f9322 |
# -*- coding: utf-8 -*-
# Copyright: (c) 2019, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
# Make coding more python3-ish
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import os
import functools
import pytest
i... | ansible/ansible | test/units/galaxy/test_role_install.py | Python | gpl-3.0 | 6,393 | [
"Galaxy"
] | 7149045d4bfe2d591582ae19d128c232ea024f1434a9fd003e164b10299cee7b |
import unittest
import datetime
from mock import Mock
from DIRAC.DataManagementSystem.Agent.RequestOperations.ReplicateAndRegister import ReplicateAndRegister
from DIRAC.RequestManagementSystem.Client.File import File
class ReqOpsTestCase( unittest.TestCase ):
""" Base class for the clients test cases
"""
def s... | avedaee/DIRAC | DataManagementSystem/Agent/RequestOperations/test/test_RequestOperations.py | Python | gpl-3.0 | 3,139 | [
"DIRAC"
] | 64ffd5a2fd228e1fe62aa064928dc84fe31b2e66fc8acca42f4c5888c1902bf8 |
#!/usr/bin/env python
import os
from flask import Flask, render_template, request, abort
from tornado.wsgi import WSGIContainer
from tornado.httpserver import HTTPServer
from tornado.ioloop import IOLoop
import requests
app = Flask(__name__)
FLAG = os.environ.get('FLAG', None)
if FLAG is None:
raise ValueError('F... | HackUCF/workshops-http | http50/challenge.py | Python | agpl-3.0 | 934 | [
"VisIt"
] | 298cd4f484f6b7e143e41b0c39e7aea59fcc91c850351deedf5031fe8e8ae4be |
# coding: utf-8
from __future__ import unicode_literals
"""
This module provides classes to define everything related to band structures.
"""
__author__ = "Geoffroy Hautier, Shyue Ping Ong, Michael Kocher"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "1.0"
__maintainer__ = "Geoffroy Hautier"... | yanikou19/pymatgen | pymatgen/electronic_structure/bandstructure.py | Python | mit | 40,971 | [
"CRYSTAL",
"pymatgen"
] | 5c003eb3faeadaa48a7d742a66ebda05ec4aa45181acbfc8652cd2098073ef46 |
#
# Author: Henrique Pereira Coutada Miranda
# Tests for yambopy
# Si
#
from __future__ import print_function
import matplotlib
import unittest
import sys
import os
import shutil
import argparse
import subprocess
import filecmp
import shutil as sh
import yambopy
from yambopy import *
from qepy import *
reference_dir =... | henriquemiranda/yambo-py | yambopy/integration_tests/itest_si_bse.py | Python | bsd-3-clause | 9,038 | [
"Yambo"
] | 3c72ffd1851a9c0a61275762bdd92e76ffd354aa2571ed01043bda207d8d17fb |
"""A quick DOM implementation.
Python's xml.dom is very slow. The xml.sax module is also slow (as it imports urllib2).
This is our light-weight version.
"""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from xml.parsers import expat
import zeroinstall
from zer... | michel-slm/0install | zeroinstall/injector/qdom.py | Python | lgpl-2.1 | 4,532 | [
"VisIt"
] | bd6cb227b918c9bfc253bfddc7a351a9197af7aa8bab6b60d2329aa7fc645bea |
import re
import sys
from collections import namedtuple, Counter, OrderedDict
from operator import itemgetter
from math import log
from Bio import SeqIO
from RecBlast import print, merge_ranges
from RecBlast.Search import id_search
from itertools import chain, islice
import mygene
from pathlib import Path
from RecBlast... | docmanny/RecBlast | RecBlast/Auxilliary.py | Python | mit | 40,401 | [
"BLAST"
] | f9425a7526dc8f259482cc235c933af3ce6dafc01854bffd8e9b819d97dde3ac |
#!/usr/bin/env python
# Copyright (c) 2014, the GREAT3 executive committee (http://www.great3challenge.info/?q=contacts)
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without modification, are permitted
# provided that the following conditions are met:
#
# 1. Redistributions of ... | barnabytprowe/great3-public | validation/count_objects.py | Python | bsd-3-clause | 8,267 | [
"Galaxy"
] | 8dce08552c26460042a828705b7cccb5c085706f1cbe2487f33f5a7b652d7836 |
# 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... | kkreis/espressopp | src/interaction/Quartic.py | Python | gpl-3.0 | 4,275 | [
"ESPResSo"
] | 9f43e5cbece5f55142af3761b21c635ff3a6fe70e732d252d128ce9f97532dcd |
"""
This module contains cost functions to use with deep Boltzmann machines
(pylearn2.models.dbm).
"""
__authors__ = ["Ian Goodfellow", "Vincent Dumoulin"]
__copyright__ = "Copyright 2012, Universite de Montreal"
__credits__ = ["Ian Goodfellow"]
__license__ = "3-clause BSD"
__maintainer__ = "LISA Lab"
import numpy as... | skearnes/pylearn2 | pylearn2/costs/dbm.py | Python | bsd-3-clause | 60,267 | [
"Gaussian"
] | 987bc89b5f13497423611f645a1a9d3ec585101ab1dd5d642628b868325021c4 |
"""functions used to construct different architectures
"""
import tensorflow as tf
import numpy as np
FLAGS = tf.app.flags.FLAGS
tf.app.flags.DEFINE_float('weight_decay', 0.0005,
""" """)
def _activation_summary(x):
"""Helper to create summaries for activations.
Creates a summary ... | ChrysLiang/singapore_weather_prediction | layer_def.py | Python | mit | 4,412 | [
"Gaussian"
] | 74dffa6f1eddadb8987498a286a50ebe658889aa24480668d1548203fc6cb30a |
"""
It is used to test the database modules...
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import unittest
import DIRAC.MonitoringSystem.private.DBUtils as moduleTested
__RCSID__ = "$Id$"
###########################################################... | ic-hep/DIRAC | src/DIRAC/MonitoringSystem/DB/test/Test_monitoringdb.py | Python | gpl-3.0 | 2,863 | [
"DIRAC"
] | c171ad887f8dec66496598e14313a874818f0ecb77899ba3b2a122e4c979c262 |
# Standard Library
import time
from contextlib import contextmanager
# Third Party Stuff
import splinter
from PIL import Image, ImageChops
from selenium.webdriver.support.ui import WebDriverWait
from selenium.webdriver.support import expected_conditions as EC
from selenium.common.exceptions import TimeoutException, We... | psjinx/html2latex | src/html2latex/webkit2png.py | Python | mit | 2,510 | [
"VisIt"
] | 86a34ea25dbdd954064a57a01adf8d95641db2019ff674429f86785ce53c797f |
# Copyright Anne M. Archibald 2008
# Released under the scipy license
from numpy.testing import (assert_equal, assert_array_equal, assert_,
assert_almost_equal, assert_array_almost_equal,
assert_allclose)
from pytest import raises as assert_raises
import pytest
fro... | nmayorov/scipy | scipy/spatial/tests/test_kdtree.py | Python | bsd-3-clause | 50,109 | [
"VisIt"
] | 2ab81964393c012801e84ba4276126e44bc79d0e2ad92c85af2354efec5566c4 |
import ee
from ee_plugin import Map
from ee_plugin.contrib import palettes
dem = ee.Image("AHN/AHN2_05M_RUW").convolve(ee.Kernel.gaussian(0.5, 0.3, 'meters'))
extrusion = 3
weight = 0.7
palette = palettes.crameri['oleron'][50]
rgb = dem.visualize(**{'min': 0, 'max': 3, 'palette': palette })
hsv = rgb.unitScale(0, 25... | gena/qgis-earthengine-plugin | examples/palettes_crameri_oleron_dem.py | Python | mit | 791 | [
"Gaussian"
] | a0e476d1725b193493e0de848d76234df7ee4f05ccc0aee59ca4359edb1006f8 |
# -*- coding: utf-8 -*-
#
# cclib documentation build configuration file, created by
# sphinx-quickstart on Thu Jan 30 14:44:27 2014.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All c... | hainm/cclib.github.io | sphinx/conf.py | Python | lgpl-2.1 | 8,177 | [
"cclib"
] | 5df2fddba6b55dc4f439a584b5c9a32ed5d954073b9319a8f26a9d301898c1a9 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
import subprocess
import shutil
import warnings
import glob
import numpy as np
from pymatgen.io.vasp.outputs import Chgcar
from pymatgen.io.vasp.inputs import Potcar
from monty.dev import requires
... | dongsenfo/pymatgen | pymatgen/command_line/bader_caller.py | Python | mit | 18,751 | [
"VASP",
"pymatgen"
] | 8d5934d4ec30f098a4138b1efea9e89d3b65c243ee5af3c887dcf8136808b0d2 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Moving sky plot to bottom of object spectrum plot, added badlines
# stuff,restricted z range
# for cross correlation to slider z +/-0.3
#
# Adding xcsao button - need shady iraf import shenanigans, otherwise iraf
# causes feedback between tk
# widgets and variables to n... | boada/redshiftCode | visualTemplateRedshift5.py | Python | mit | 41,270 | [
"Galaxy"
] | 3e1be91d7d88f1d0135d050c07ca502f80fe9f0b274ecc38852862e150312948 |
#!/usr/bin/env python
"""Find the functions in a module missing type annotations.
To use it run
./functions_missing_types.py <module>
and it will print out a list of functions in the module that don't
have types.
"""
import argparse
import ast
import importlib
import os
NUMPY_ROOT = os.path.dirname(os.path.join(
... | charris/numpy | tools/functions_missing_types.py | Python | bsd-3-clause | 3,195 | [
"VisIt"
] | 033380bd4ad8ff3ff79d8d0647d06d1edfda330416757ae979535f86553257dd |
# pylint: disable=missing-docstring
# pylint: disable=redefined-outer-name
# pylint: disable=unused-argument
from lettuce import world, step
from common import course_location
from problems_setup import PROBLEM_DICT
from nose.tools import assert_in
@step(u'I am viewing a course with multiple sections')
def view_cour... | antoviaque/edx-platform | lms/djangoapps/courseware/features/navigation.py | Python | agpl-3.0 | 5,405 | [
"VisIt"
] | 2b6b40353e12c635232b78a0a58493f6b1e6ca6856c2dd147090a34116197708 |
import unittest
from tvtk.api import tvtk
from simphony_mayavi.core.cell_collection import CellCollection
class TestCellCollection(unittest.TestCase):
def setUp(self):
self.cells = [
[0, 1, 2, 3],
[4, 5, 6, 7, 8, 9, 10, 11],
[2, 7, 11],
[1, 4],
... | simphony/simphony-mayavi | simphony_mayavi/core/tests/test_cell_collection.py | Python | bsd-2-clause | 3,792 | [
"VTK"
] | 9b7e29392e7ccb59d6af62ebd1db00a86291c204a8e494642b2783064671790f |
#
# mainTab
#
tab = self.notebook.mainTab
tab.settings['Program'] = 'vasp'
tab.settings['Output file name'] = 'OUTCAR'
#
# SettingsTab
#
tab = self.notebook.settingsTab
tab.settings['Eckart flag'] = False
tab.settings['Neutral Born charges'] = False
tab.settings['Sigma value'] = 2.0
tab.settings['Mass definition'] = 'a... | JohnKendrick/PDielec | Examples/Vasp/F-Apatite/script.py | Python | mit | 2,418 | [
"VASP"
] | e22ccc9eb721d5ee24d460c2090a0aab97627ca9ab37d6e1ac7334ce6a3de0b2 |
''' This script reads and make operations on cubes '''
from collections import namedtuple
from argparse import ArgumentParser
import numpy as np
import pandas as pd
import os
def vmd_watch_cube(fn):
'''
This function will launch VMD to display a cube.
'''
cwd = os.getcwd()
vmd_script = fn + "vmds... | acuzzio/GridQuantumPropagator | Scripts/old_semiuseless/ReadCube.py | Python | gpl-3.0 | 2,737 | [
"VMD"
] | e0024823b4ed8c97cf27265a03e1f7dfc7ef6fb782bd2130a1b59424189f03de |
import os
import warnings
from numba import errors
def get_numbapro_envvar(envvar, default=None):
# use vanilla get here so as to use `None` as a signal for not-set
value = os.environ.get(envvar)
if value is not None:
url = ("http://numba.pydata.org/numba-doc/latest/reference/"
"de... | jriehl/numba | numba/cuda/envvars.py | Python | bsd-2-clause | 1,105 | [
"VisIt"
] | 26b08bc0d5af7fa72a7daa98e1aafe31eac209debf40dae8dbc89f2c3ae3ed0f |
######################################################################
# Copyright (C) 2013 Jaakko Luttinen
#
# This file is licensed under Version 3.0 of the GNU General Public
# License. See LICENSE for a text of the license.
######################################################################
####################... | nipunreddevil/bayespy | bayespy/utils/tests/test_linalg.py | Python | gpl-3.0 | 6,989 | [
"Gaussian"
] | 41b12d3f67c56509cd07000167690206f4dbec00c2132139e24bba4b5008cd64 |
from telegram.ext import Updater,CommandHandler,MessageHandler,Filters,CallbackQueryHandler,InlineQueryHandler
from telegram import InlineKeyboardButton, InlineKeyboardMarkup,InlineQueryResultArticle,InputTextMessageContent,ParseMode
import telegram,logging,time,re
from PyDictionary import PyDictionary
import nltk
impo... | aaqaishtyaq/doc-the-bot | bot.py | Python | mit | 4,734 | [
"VisIt"
] | 5b671b67492ee85ba1bac14c497caf2096ac8d3c22c1eb5bceaa955e861ff2ed |
#ptmcmc analysis support
#John Baker (2019)
#Find at github.com/johngbaker/ptmcmc
#
#Provides class for holding chain data
import sys
import os
import numpy as np
import math
import subprocess
import argparse
import matplotlib
import matplotlib.pyplot as plt
import matplotlib.colors as colors
import matplotlib.cm as c... | JohnGBaker/ptmcmc | python/ptmcmc_analysis.py | Python | apache-2.0 | 23,022 | [
"Gaussian"
] | fbfd951e36bd4f4fd282a08b2d932b1f588f04b0018b1f1a8699ea751efc4c9a |
# -*- coding: utf-8 -*-
from tasty.tastyc import bases
from tasty.tastyc.transformation import BasicTastyTransformer
from collections import defaultdict
from ast import *
import copy
from gmpy import mpz
from tasty import state
from tasty.tastyc.bases import (has_parent_node, get_fqnn, add_keyword,
CALL_TYPE_CT... | tastyproject/tasty | tasty/tastyc/pass_dispatching.py | Python | gpl-3.0 | 11,946 | [
"VisIt"
] | cbc243e5f7fe83ba7d36570ce5b2c9c34b0b272b3b07c70689c69854c93d29f0 |
from flopy.utils.flopy_io import get_url_text
class acdd:
"""Translate ScienceBase global metadata attributes to CF and ACDD
global attributes.
see:
https://www.sciencebase.gov/catalog/
http://cfconventions.org/cf-conventions/v1.6.0/cf-conventions.html#description-of-file-contents
http://w... | brclark-usgs/flopy | flopy/export/metadata.py | Python | bsd-3-clause | 8,389 | [
"NetCDF"
] | 17094bc2d71e062e47b609e4b99d012fce8304b429b697eaf27e2d0abc80755b |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This package provides the modules to perform FEFF IO.
FEFF: http://feffproject.org/feffproject-feff.html
"""
from .inputs import * # noqa
from .outputs import * # noqa
| gmatteo/pymatgen | pymatgen/io/feff/__init__.py | Python | mit | 287 | [
"FEFF",
"pymatgen"
] | c1eac4de55467a1e0848397fd2a270a2ba247a4de05bb4dcb1bf38544492188f |
# -*- coding: utf-8 -*-
# Licensed under a 3-clause BSD style license - see LICENSE.rst
from __future__ import (absolute_import, division, print_function,
unicode_literals)
import numpy as np
from astropy import log
import astropy
import astropy.units as u
from .utils import validate_data_table... | cdeil/naima | naima/core.py | Python | bsd-3-clause | 11,339 | [
"Gaussian"
] | c446303372cc9b06658491be654248ed8211c3bc0cf4463428be2baf81bedb7b |
"""
Signal handling functions for use with external commerce service.
"""
import logging
from urlparse import urljoin
from django.conf import settings
from django.contrib.auth.models import AnonymousUser
from django.core.mail import EmailMultiAlternatives
from django.dispatch import receiver
from django.utils.translat... | GbalsaC/bitnamiP | lms/djangoapps/commerce/signals.py | Python | agpl-3.0 | 7,258 | [
"VisIt"
] | c6efbb22a051cace028a610d845e309e512164e0d6765c3e281486af9a47145b |
"""
This test is designed to check protocol/server performances with a database
Configuration and how to run it are explained in the documentation
"""
from DIRAC.Core.Tornado.Client.ClientSelector import RPCClientSelector
from time import time
from random import random
import sys
import os
class Transaction(objec... | ic-hep/DIRAC | tests/Integration/TornadoServices/perf-test-DB/test_scripts/v_perf.py | Python | gpl-3.0 | 1,057 | [
"DIRAC"
] | 2fc7060fcf35ff0a818455d0ea5364889ca77a720747a02c5cb2556568f45acb |
"""
Character Inclusion Abstract Domain
===================================
Non-relational abstract domain to be used for **string analysis**.
The set of possible string values of a program variable in a program state
is represented by the sets of characters that must and may form the string.
:Authors: Radwa Sherif A... | caterinaurban/Lyra | src/lyra/abstract_domains/string/character_domain.py | Python | mpl-2.0 | 9,807 | [
"VisIt"
] | a475fe3eb49a12be4f1626149fdbbda40c7c5ca48e6b46b218da0515399366c1 |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses... | kvar/ansible | lib/ansible/modules/network/avi/avi_role.py | Python | gpl-3.0 | 3,407 | [
"VisIt"
] | 295d8524f2d99494effce067c6fc13cfb42aa4bf77cb2bd3bdce372e0d2655fc |
#!/usr/bin/python
# -*- coding: utf-8 -*-
__author__ = 'Chengwei Luo (cluo@broadinstitute.org)'
__version__ = '0.1.0'
__date__ = 'Dec 2013'
USAGE = \
"""
refMapping2readBins.py takes a mapping against reference genomes BAM file
and split it down to bins of reads belong to certain level of taxa (e.g., all species)
f... | luo-chengwei/utilitomics | WGS/refMapping2readBins.py | Python | gpl-3.0 | 4,662 | [
"pysam"
] | 7368e179491f564836102358df1b5ac67bc69051a8b636e12e1013fe3cb6983b |
from __future__ import print_function
#include <vtkVersion.h
#include <vtkSmartPointer.h
#include <vtkPointData.h
#include <vtkIdTypeArray.h
#include <vtkDataSetSurfaceFilter.h
#include <vtkRendererCollection.h
#include <vtkProperty.h
#include <vtkPlanes.h
#include <vtkObjectFactory.h
#include <vtkPolyDataMapper.h
#inc... | saullocastro/pyNastran | pyNastran/gui/vtk_examples/highlight_selected_points.py | Python | lgpl-3.0 | 4,900 | [
"VTK"
] | 01d4c994739c7ca64c1ec3b69c91c35d05c0f51620068a0dbf90634e5a2edde0 |
# gear_profile_macro.py
# the macro to generate a gear_profile.
# created by charlyoleg on 2013/08/27
#
# (C) Copyright 2013 charlyoleg
#
# This file is part of the Cnc25D Python package.
#
# Cnc25D is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publis... | charlyoleg/Cnc25D | cnc25d/tests/gear_profile_macro.py | Python | gpl-3.0 | 6,930 | [
"VisIt"
] | f9bc0193fd9f3f5b11b418c369b1cd77796413ef1087089c10ab0d4011c91b53 |
# Storage filtering classes
#
# Copyright (C) 2013 Red Hat, Inc.
#
# This copyrighted material is made available to anyone wishing to use,
# modify, copy, or redistribute it subject to the terms and conditions of
# the GNU General Public License v.2, or (at your option) any later version.
# This program is distributed... | fabiand/anaconda | pyanaconda/ui/gui/spokes/filter.py | Python | gpl-2.0 | 24,108 | [
"VisIt"
] | 6b97dae9f85f155da8881dd6ebb16c01ac7e8cf8bc2cdcc5e3c04c58f18f3bf1 |
'''
For blastn searches we are going to calculate the percent coverage of
the phage genome and score the longest coverage as the best hit. It
doesn't matter where the hits are on the bacterial genome.
We are going to use a cutoff of 0.001 E value
'''
import sys,os,re
from phage import Phage
phage=Phage()
try:
... | linsalrob/PhageHosts | code/blastn_all_v_all.py | Python | mit | 2,055 | [
"BLAST"
] | 1f218e552de86f6c1b7993d016f76e3cbcb02b213d1767584b90ab59c3d12e7e |
# -*- coding: UTF-8 -*-
# -----------------------------------------------------------------------------
# xierpa server
# Copyright (c) 2014+ buro@petr.com, www.petr.com, www.xierpa.com
#
# X I E R P A 3
# Distribution by the MIT License.
#
# ---------------------------------------------------------------... | petrvanblokland/Xierpa3 | xierpa3/contributions/filibuster/content/modernmedia.py | Python | mit | 4,328 | [
"VisIt"
] | cd7080ec57bc2fd2fcd558b78d8e45f28db60bd2209d0737f6c533324883b44f |
'''
Created on 2013-08-13, adapted on 2013-09-13
This module provides a class that contains definitions of source and target datasets and methods to process
variables in these datasets.
The class is designed to be imported and extended by modules that perform more specific tasks.
Simple methods for copying and avera... | aerler/GeoPy | src/processing/process.py | Python | gpl-3.0 | 48,018 | [
"NetCDF"
] | a7198588c790f4ccebe34792ba6c901b1eae54420b37488b9e28a17a50d42904 |
#!/usr/bin/env python
import sys
sitePython = "@SITEPYTHON@"
if sitePython:
sys.path.insert( 0, "@SITEPYTHON@" )
from DIRAC.Core.Base import Script
Script.parseCommandLine()
from DIRAC.WorkloadManagementSystem.JobWrapper.JobWrapper import JobWrapper, rescheduleFailedJob
from DIRAC.WorkloadManagementSystem.Client.J... | rajanandakumar/DIRAC | WorkloadManagementSystem/JobWrapper/JobWrapperTemplate.py | Python | gpl-3.0 | 5,300 | [
"DIRAC"
] | 3b48dc49ac08ad3681171b6a92558147a23e715f0dbd3e0da5103db555cbfd94 |
# Here is a simple example. As shown it will run in non-parallel mode; comments indicate what to do for parallelization.
from lmc import *
## for MPI
#from mpi4py import MPI
#mpi_rank = MPI.COMM_WORLD.Get_rank()
### Define some parameters.
x = Parameter(name='x')
y = Parameter(name='y')
### This is the object that w... | abmantz/lmc | examples/simple_hoodOpen.py | Python | lgpl-3.0 | 2,965 | [
"Gaussian"
] | 95b9b7251bb6e045319d28f836e941fa0684cb34f7385f6eab854b11f6e15172 |
from __future__ import unicode_literals
import re
from .common import InfoExtractor
from ..utils import (
int_or_none,
parse_iso8601,
)
class IGNIE(InfoExtractor):
"""
Extractor for some of the IGN sites, like www.ign.com, es.ign.com de.ign.com.
Some videos of it.ign.com are also supported
"... | fluxw42/youtube-dl | youtube_dl/extractor/ign.py | Python | unlicense | 8,789 | [
"Brian"
] | 0d4f62e232ec12266a60acd895fa40cc5cab25922285e82101db1f61dbfe5285 |
import IMP
import IMP.test
import IMP.core
import IMP.atom
import IMP.algebra
class Tests(IMP.test.TestCase):
"""Test the CHARMMAtom decorator"""
def test_create(self):
"""Check creation of CHARMMAtom decorators"""
m = IMP.Model()
p = IMP.Particle(m)
IMP.atom.Atom.setup_parti... | shanot/imp | modules/atom/test/test_charmm_atom.py | Python | gpl-3.0 | 1,282 | [
"CHARMM"
] | 5522a9b9a19bf02eaabc6def88c83809c6f8874dac478da8420cda8e307c723e |
"""
Computes quantities associated with the Gaussian linear state space model.
References
----------
https://lectures.quantecon.org/py/linear_models.html
"""
from textwrap import dedent
import numpy as np
from numpy.random import multivariate_normal
from scipy.linalg import solve
from numba import jit
from .util im... | oyamad/QuantEcon.py | quantecon/lss.py | Python | bsd-3-clause | 13,254 | [
"Gaussian"
] | ee4baeae92e1794a3ca533cd2e4dd6a9d852906b3d3200fececcf7a3d8126d8b |
from pyramid.config import Configurator
# we must make sure custom models are known at database initialization!
from cdk import models
_ = lambda s: s
_('Unitvalue')
_('Unitvalues')
_('Unit Values')
_('Sentence')
_('Sentences')
def main(global_config, **settings):
""" This function returns a Pyramid WSGI appli... | clld/cdk | cdk/__init__.py | Python | apache-2.0 | 445 | [
"CDK"
] | 18cc98df3d0b88e840eae350e97cb437d4d81bae22e29910eb79ead182137cdf |
############ To get POV-Ray specific objects In and Out of Blender ###########
import bpy
from bpy_extras.io_utils import ImportHelper
from bpy_extras import object_utils
from math import atan, pi, degrees, sqrt, cos, sin
from bpy.props import (
StringProperty,
BoolProperty,
IntProperty,
... | Microvellum/Fluid-Designer | win64-vc/2.78/Python/bin/2.78/scripts/addons/render_povray/primitives.py | Python | gpl-3.0 | 71,790 | [
"Avogadro"
] | 8c9a77b461c7e4b1b1d5124e9b043b67d807eacdad0697648725aae21bbfb2b9 |
"""
test_TimedArray.py
This file is part of ANNarchy.
Copyright (C) 2018-2020 Helge Uelo Dinkelbach <helge.dinkelbach@gmail.com>,
Copyright (C) 2019 Alex Schwarz <alex.schwarz@informatik.tu-chemnitz.de>
This program is free software: you can redistribute it and/or modify
it under the terms o... | vitay/ANNarchy | tests/Unittests/test_TimedArray.py | Python | gpl-2.0 | 4,706 | [
"NEURON"
] | cebd9e46156629c65feb09a804ad295b4677721b491b8d90db5b9f991dfb7c82 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | gregcaporaso/scikit-bio | skbio/sequence/_grammared_sequence.py | Python | bsd-3-clause | 24,488 | [
"scikit-bio"
] | d6da76b293adffebaaee6dfd65b203a77cd16af90e015cf9e8f30c0e17fbe7b0 |
#
# libtcod 1.5.1 python wrapper
# Copyright (c) 2008,2009,2010 Jice & Mingos
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright... | fiddlerwoaroof/yinjar | libtcodpy.py | Python | bsd-3-clause | 59,053 | [
"Amber"
] | f3548d1cae931d22cd3a0c9afb06634f3c76d8c60243e721984162b00977907f |
# Copyright (C) 2010-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later ... | hmenke/espresso | testsuite/python/dipolar_mdlc_p3m_scafacos_p2nfft.py | Python | gpl-3.0 | 7,748 | [
"ESPResSo"
] | 5b8e57f5135143038f98822c82d6c1f192b9dfd5de9974d0255b6bcf2ccde331 |
#-*- coding: utf8
# Author: David C. Lambert [dcl -at- panix -dot- com]
# Copyright(c) 2013
# License: Simple BSD
"""The :mod:`random_layer` module
implements Random Layer transformers.
Random layers are arrays of hidden unit activations that are
random functions of input activation values (dot products for simple
ac... | jmgore75/Python-ELM | random_layer.py | Python | bsd-3-clause | 18,978 | [
"Gaussian"
] | 44c30f7ac998e606bede4f444f350b503a3eb0e757970df8d30cadbedc2082d6 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""Tools and helper functions for abinit calculations"""
from __future__ import unicode_literals, division, print_function
import os
import six
import re
import collections
import shutil
import operator
import ... | aykol/pymatgen | pymatgen/io/abinit/utils.py | Python | mit | 27,783 | [
"ABINIT",
"NetCDF",
"pymatgen"
] | cbd2edb6c00b61eefccfad9473301de943ebf1e5612c0938a65ab355e272b8ec |
#!/usr/bin/env python
# Script: dump2xyz.py
# Purpose: convert a LAMMPS dump file to XYZ format
# Syntax: dump2xyz.py dumpfile Nid Ntype Nx Ny Nz xyzfile
# dumpfile = LAMMPS dump file in native LAMMPS format
# Nid,Ntype,Nx,Ny,Nz = columns #s for ID,type,x,y,z
# (usuall... | SGenheden/lammps | tools/python/dump2xyz.py | Python | gpl-2.0 | 906 | [
"LAMMPS"
] | 80bf84b891c674426500410eb96aaa01403da64d1ca9f5cf4739c2685cc5cf9c |
# -*- coding: utf-8 -*-
# Copyright 2007-2011 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy 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... | pburdet/hyperspy | hyperspy/model.py | Python | gpl-3.0 | 76,034 | [
"Gaussian"
] | a29ebf23c8f6f1991b24f3cafde8d755bf2a389d9443c9be4a51ff816b31e0f3 |
#!/usr/bin/env python3
#* 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/licenses/lgp... | nuclear-wizard/moose | python/postprocessing/tests/test_combine_csv.py | Python | lgpl-2.1 | 5,272 | [
"MOOSE"
] | 73f65fb9ded1b14d83c782f5785e3d10e1e62717af06b2a2a731ab114f7ea3f8 |
#
# Copyright (C) 2008, Brian Tanner
#
#http://rl-glue-ext.googlecode.com/
#
# Licensed under the Apache License, Version 2.0 (the "License"
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requir... | chaostrigger/rl-library | projects/packages/examples/mines-sarsa-python/sample_experiment.py | Python | apache-2.0 | 5,470 | [
"Brian"
] | 7285b97e0de5dcad24e75dbb03a0fbde829a0af032998670e3ff1867b68eefc1 |
from __future__ import print_function
import psi4
from psi4.driver import qcdb
#! A test of the basis specification. Various basis sets are specified outright and in blocks, both
#! orbital and auxiliary. Constructs libmints BasisSet objects through the constructor that calls
#! qcdb.BasisSet infrastructure. Checks th... | amjames/psi4 | tests/python/mints9/input.py | Python | lgpl-3.0 | 9,016 | [
"Psi4"
] | 5afe55815ad683ac3e35937ba972876351225b3d71fe5d787de15ffa77ed79eb |
""" Storage Factory Class - creates instances of various Storage plugins from the Core DIRAC or extensions
This Class has three public methods:
getStorageName(): Resolves links in the CS to the target SE name.
getStorage(): This creates a single storage stub based on the parameters passed in a dict... | ic-hep/DIRAC | src/DIRAC/Resources/Storage/StorageFactory.py | Python | gpl-3.0 | 19,372 | [
"DIRAC"
] | 1dec9a1b4d7cb20e89310decdefdff434bf78fe99b5da1fd98751b9e35e33d40 |
import inspect
import os
import sys
import textwrap
import types
import warnings
from .formatting import format_filename, format_variable
from .moduleshim import ModuleShim
class XTracebackFrame(object):
FILTER = ("__builtins__", "__all__", "__doc__", "__file__", "__name__",
"__package__", "__path... | 005/xtraceback | xtraceback/xtracebackframe.py | Python | mit | 8,117 | [
"xTB"
] | 8f66cedace2b83c1bf98340a260b748b3c9b44e63f9a889f29064d761b110ab5 |
# -*- mode: Python; indent-tabs-mode: nil -*- #
import awe
import numpy as np
import sys
import os
#-----Simulation Default Values-----
iterations = 5
nwalkers = 4
nstates = 100
restarts = float('inf')
maxreps = 50
#-----WQ Default Values-----
wq_port = 9123
wq_fast_abort_multiplier = -1.0
#-----Get u... | jeffkinnison/awe-wq | share/awe/awe-ala.py | Python | gpl-2.0 | 4,953 | [
"Gromacs"
] | 849a7a226569889b0f7151fb122ed8356ff9fa647ecb141827a2c3707ec28ddd |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | rmcgibbo/psi4public | psi4/share/psi4/databases/RSE42.py | Python | lgpl-3.0 | 77,097 | [
"Psi4"
] | 8794a24aec8bf612124d06d81496d2f3d45cc5ffa32d19221bef0ff98b5398f2 |
from __future__ import print_function
import tensorflow as tf
import numpy as np
import unittest
import Henbun as hb
from scipy.special import loggamma
from Henbun._settings import settings
float_type = settings.dtypes.float_type
np_float_type = np.float32 if float_type is tf.float32 else np.float64
class test_bimixtu... | fujii-team/Henbun | testing/test_densities.py | Python | apache-2.0 | 3,044 | [
"Gaussian"
] | 77cdf4ad44be87033ea332cabe5e41359de19db972b728df904256f7a72e90a1 |
#!/usr/bin/env python
# File: plot_selected_vs_z_hist.py
# Created on: Mon Aug 20 21:04:20 2012
# Last Change: Fri 28 Sep 2012 10:21:27 AM CDT
# Purpose of script: <+INSERT+>
# Author: Steven Boada
import pylab as pyl
from mk_galaxy_struc import mk_galaxy_struc
galaxies = mk_galaxy_struc()
low =[]
med=[]
high=[]
ap... | boada/ICD | sandbox/legacy_plot_code/plot_selected_vs_z_hist.py | Python | mit | 1,076 | [
"Galaxy"
] | ee6931b3a6ea56ce58a63b010d48928f4fa930e8351254cddb4c80a434e6a15b |
#!/usr/bin/env python
"""
This is the main function to call for disambiguating between BAM files
from two species that have alignments from the same source of fastq files.
It is part of the explant RNA/DNA-Seq workflow where an informatics
approach is used to distinguish between e.g. human and mouse or rat RNA/DNA rea... | gifford-lab/bcbio-nextgen | bcbio/pipeline/disambiguate/run.py | Python | mit | 16,821 | [
"BWA",
"pysam"
] | 3d2347be6b7bfc5d4ff317a2c2b0da85713390e17e63f58d31bbe2ea80c76689 |
tests=[
("testExecs/test.exe","",{}),
]
longTests=[]
if __name__=='__main__':
import sys
from rdkit import TestRunner
failed,tests = TestRunner.RunScript('test_list.py',0,1)
sys.exit(len(failed))
| soerendip42/rdkit | Code/DataStructs/test_list.py | Python | bsd-3-clause | 213 | [
"RDKit"
] | c227b11acb68b976984e8cc9efa65732c0e279c9f73da99c18fcaf7be6edf32e |
########################################################################
# File : LocalComputingElement.py
# Author : Ricardo Graciani, A.T.
########################################################################
""" LocalComputingElement is a class to handle non-grid computing clusters
Allows direct submission to... | ic-hep/DIRAC | src/DIRAC/Resources/Computing/LocalComputingElement.py | Python | gpl-3.0 | 14,211 | [
"DIRAC"
] | 925492662a37fce72ec7a3bd1ede7618e4636acb60dd85df23f3954a19baa585 |
from __future__ import (absolute_import, division, print_function)
import os
import numpy as np
from mantid import config, mtd, logger
from mantid.kernel import StringListValidator, Direction
from mantid.api import PythonAlgorithm, MultipleFileProperty, FileProperty, \
WorkspaceGroupProperty, FileAction, Progress
... | dymkowsk/mantid | Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/IndirectILLEnergyTransfer.py | Python | gpl-3.0 | 17,557 | [
"CRYSTAL"
] | 8d2218b0874e08e76b2c44425348255bd51eb6647a47dd581a5d046f7353bbbc |
# Copyright (c) 2017 Gyula Istvan Geza Jozsa, Paolo Serra, Kshitij Thorat, Sphesihle Makhatini, NRF (Square Kilometre Array South Africa) - All Rights Reserved
import matplotlib
import types
matplotlib.use('Agg')
"""
Class Sunblocker
Taylored towards method phazer, aimed at removing solar interference from interferom... | gigjozsa/sunblocker | sunblocker/sunblocker.py | Python | gpl-2.0 | 56,562 | [
"Gaussian"
] | 43d6bc4b8417cac532add415508a2f009055e8080ead92c5e58147e57b3432bf |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | jhseu/tensorflow | tensorflow/python/autograph/converters/control_flow.py | Python | apache-2.0 | 20,253 | [
"VisIt"
] | 5f7f3f3535b2046a22698770162f25da8c504b2d3399ef29c560c420d3b416ef |
# -*- 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/mediaplugin.py | Python | gpl-2.0 | 5,654 | [
"Brian"
] | 614f0e89eac3578cc7292fc95c4742a4c2687b4b00b4c518728acb77a630e022 |
# Copyright 2012, 2013 The GalSim developers:
# https://github.com/GalSim-developers
#
# This file is part of GalSim: The modular galaxy image simulation toolkit.
#
# GalSim is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software... | mardom/GalSim | devel/modules/test_psfcorr_masks.py | Python | gpl-3.0 | 5,612 | [
"Galaxy",
"Gaussian"
] | 36125bb1aa37a962e59f5d2f722fbada2f4b74bc409782948d267fa1707f351d |
QUOTES = [
"500 bucks. Is Zapp Brannigan okay? 600 bucks.",
"500 real dollars? That's an outrage! Professor, I can take care of that waste for only 499 and one hundred cents.",
"1947 can bite my shiny, metal...",
"$500, you say?",
"'singing' Just tell me why! There must be robots worse than I. Then... | pschmitt/bender-bot | bender/plugins/quote/quotes.py | Python | gpl-3.0 | 56,348 | [
"BLAST",
"CASINO",
"Galaxy",
"VisIt"
] | 91276b8ea49a70572064632c654b065cea9521391b3be07e5f272342ea77079a |
##############################################################################
# Copyright (c) 2013-2016, 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/repeatmasker/package.py | Python | lgpl-2.1 | 3,192 | [
"BLAST"
] | 529eca9ebe7253dce1cd9e803e72fbeb352ac7bca48a3ce6d764cf726f1b5d7b |
# Copyright (C) 2012,2013,2016
# 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 modify
# it under the terms... | fedepad/espressopp | src/interaction/__init__.py | Python | gpl-3.0 | 4,135 | [
"ESPResSo"
] | e0daa74003044f91ae0ae17545a928d9abdccfc08f36f3d2439111c88348195e |
"""
Acceptance tests for Studio related to the asset index page.
"""
import os
from common.test.acceptance.fixtures.base import StudioApiLoginError
from common.test.acceptance.fixtures.config import ConfigModelFixture
from common.test.acceptance.pages.studio.asset_index import AssetIndexPage, AssetIndexPageStudioFront... | procangroup/edx-platform | common/test/acceptance/tests/studio/test_studio_asset.py | Python | agpl-3.0 | 12,814 | [
"VisIt"
] | 4003295c7561b595b25429c29b333edb6fc0f2c86bf9820eab87397082175711 |
#
# @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/driver/p4util/exceptions.py | Python | lgpl-3.0 | 7,442 | [
"Psi4"
] | ef7e115901646b790a891fb2bdbf037da77934a02127347b6ccef9da674d45c9 |
"""Next-gen alignments with TopHat a spliced read mapper for RNA-seq experiments.
http://tophat.cbcb.umd.edu
"""
import os
import shutil
import sys
from contextlib import closing
import glob
import subprocess
import numpy
import pysam
try:
import sh
except ImportError:
sh = None
from bcbio.pipeline import c... | Cyberbio-Lab/bcbio-nextgen | bcbio/ngsalign/tophat.py | Python | mit | 15,056 | [
"Bowtie",
"pysam"
] | 108a74a7d98fa76fcb394be10dedaaa5bee544d743f038241752d94775fc178e |
#!/usr/bin/env python3
#
# Python script that tries to check, if a BBS sky model file
# is syntactically correct
#
# File: checkBBSskymodel.py
# Author: Sven Duscha (duscha@astron.nl)
# Date: 2011-02-18
# Last change: 2011-02-24
#
# This file parses a BBS sky model file .sky or .model and... | kernsuite-debian/lofar | CEP/Calibration/BBSControl/scripts/checkBBSskymodel.py | Python | gpl-3.0 | 15,923 | [
"Gaussian"
] | 3799d30c1308bb70d86283d7758e4319b848f6d779bf25653f408657155ba5a7 |
########################################################################
# $HeadURL$
########################################################################
""" ProfileManager manages web user profiles
in the DISET framework
"""
__RCSID__ = "$Id$"
import types
from DIRAC.Core.DISET.RequestHandler import Request... | Andrew-McNab-UK/DIRAC | FrameworkSystem/Service/UserProfileManagerHandler.py | Python | gpl-3.0 | 6,203 | [
"DIRAC"
] | 1289e885ed38f96e6d2ea7cf1a042260e715740563f56fb1b2074eeec3614b32 |
# -*- coding: UTF-8 -*-
# @author JoseMariaRomeroARK visit my gitHub site at: https://github.com/JoseMariaRomeroARK
import Utilidades
from VentanaMain import createNewMain
from VentanAux import createNew
archivoCon = open(Utilidades.getRuta()+"DesOrg.txt","r")
lineas = list()
for linea in archivoCon:
... | JoseMariaRomeroARK/Movil-Music-Mananger-M3 | Execute.py | Python | cc0-1.0 | 474 | [
"VisIt"
] | 47557e0e2877c30a5a1a5ed4ae695bbed952e27ce28633c0fad23d751e1b375e |
'''
Some helper functions for parsing basis set files
'''
import re
import regex
from ..misc import transpose_matrix
floating_re_str = r'[-+]?\d*\.\d*(?:[dDeE][-+]?\d+)?'
floating_re = re.compile(floating_re_str)
floating_only_re = re.compile('^' + floating_re_str + '$')
integer_re_str = r'[-+]?\d+'
integer_re = re.c... | MOLSSI-BSE/basis_set_exchange | basis_set_exchange/readers/helpers.py | Python | bsd-3-clause | 19,511 | [
"MOLCAS"
] | a3ae9cb37b3be24233cdfd8f9920dcee428ef93e412ce085c2a82fab211c3d37 |
import numpy as np
from numpy import cos, sin
from robot import Robot
from potential_field import PotentialField
import matplotlib.pyplot as plt
import matplotlib.path as mpath
import matplotlib.lines as mlines
import matplotlib.patches as mpatches
import matplotlib.animation as animation
from matplotlib.collections im... | ozanarkancan/path-planning | main.py | Python | mit | 11,015 | [
"Gaussian"
] | a038ffe3a24dbaec887bc9f75ca0969355fc36e9e3d0d8f6689dc98acb799cd3 |
# -*- 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/gamess.py | Python | gpl-3.0 | 4,539 | [
"GAMESS"
] | 3042fc7bd74fcca2f14b694ccf4eca33085d35ed52b8dea4a26abfcb037d7fbc |
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