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#!/opt/moose/miniconda/bin/python
#* 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/l... | nuclear-wizard/moose | modules/combined/test/tests/inelastic_strain/elas_plas/plot_cycled_stress.py | Python | lgpl-2.1 | 1,045 | [
"MOOSE"
] | 4d0a33498029abc0a412505e88edc4ecf3a2279484961ee46278d3d47d459d0f |
"""Setup script for Bokeh."""
#-----------------------------------------------------------------------------
# Copyright (c) 2012 - 2014, Continuum Analytics, Inc. All rights reserved.
#
# Powered by the Bokeh Development Team.
#
# The full license is in the file LICENCE.txt, distributed with this software.
#---------... | canavandl/bokeh | setup.py | Python | bsd-3-clause | 19,428 | [
"GULP"
] | 0bf8a29ed93a7aed6a6c332019a4663f14b733ee2260fb03af4e60b3c2c371f8 |
# 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... | vathpela/anaconda | pyanaconda/ui/gui/spokes/advanced_storage.py | Python | gpl-2.0 | 32,436 | [
"VisIt"
] | 976f9a119406d466e5c60cef6998cece73e6af378dc8ddb2b505edcca080b432 |
# narrowcommands.py - command modifications for narrowhg extension
#
# Copyright 2017 Google, Inc.
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 or any later version.
from __future__ import absolute_import
import itertools
import os
from mercurial.i... | smmribeiro/intellij-community | plugins/hg4idea/testData/bin/hgext/narrow/narrowcommands.py | Python | apache-2.0 | 24,400 | [
"VisIt"
] | fa215b4cb45706991f416726c350483c910a6c9ae9e8b0ba64befc5d517e5cba |
import errno
import multiprocessing
import os
import platform
import shutil
import subprocess
import sys
import threading
import warnings
import inspect
import pickle
import weakref
from itertools import chain
from io import StringIO
import numpy as np
from numba import njit, jit, generated_jit, typeof
from numba.cor... | sklam/numba | numba/tests/test_dispatcher.py | Python | bsd-2-clause | 69,292 | [
"VisIt"
] | 5132e430af9254d90b6a5ff17dd4852885b8b7c6a7bca3580eccf93a240e3858 |
__doc__ = \
"""
Example of a script that perfoms histogram analysis of an activation
image, to estimate activation Z-score with various heuristics:
* Gamma-Gaussian model
* Gaussian mixture model
* Empirical normal null
This example is based on a (simplistic) simulated image.
Note : We do not want a 'zscore... | yarikoptic/NiPy-OLD | examples/neurospin/histogram_fits.py | Python | bsd-3-clause | 3,063 | [
"Gaussian"
] | aa98be2d645447a735c68970b4561e53dea7827093bd448ac5ab00a51ac1b7e6 |
from math import pi
import numpy as np
from ase.atoms import Atoms
def make_test_dft_calculation():
a = b = 2.0
c = 6.0
atoms = Atoms(positions=[(0, 0, c / 2)],
symbols='H',
pbc=(1, 1, 0),
cell=(a, b, c),
calculator=TestCalculator()... | freephys/python_ase | ase/calculators/test.py | Python | gpl-3.0 | 2,468 | [
"ASE"
] | 231295059ce28de2b32c94e2d60b06e687554da2327888f45ab1e4536cd424f3 |
from __future__ import division
"""
Script to wrap around nosetests to only run on files modified in the past 10
commits as well as 10% of all files.
"""
import os
import sys
import subprocess
import random
import time
run_ratio = 1 #1/10
try:
files_changed = []
for parent, sub, files in os.walk("pymatgen"... | matk86/pymatgen | run_circle.py | Python | mit | 2,154 | [
"pymatgen"
] | 058a6559dd6c7d3de7f8d679c94d2d4f10dfdc5679936a7678616ac3a2f29e45 |
# -*- coding: utf-8 -*-
##
## This file is part of CDS Invenio.
## Copyright (C) 2002, 2003, 2004, 2005, 2006, 2007, 2008 CERN.
##
## CDS Invenio is free software; you can redistribute it and/or
## modify it under the terms of the GNU General Public License as
## published by the Free Software Foundation; either versio... | ppiotr/Bibedit-some-refactoring | modules/webjournal/lib/webjournal_config.py | Python | gpl-2.0 | 19,402 | [
"VisIt"
] | e75048b08f5f8678c06c8b8355927c03a33d6559fad72df7f3977586df345cbc |
import pytest
import os
def str_to_bool(val):
try:
val = val.lower()
except AttributeError:
val = str(val).lower()
if val == 'true':
return True
elif val == 'false':
return False
else:
raise ValueError("Invalid input value: %s" % val)
@pytest.fixture(scope... | ceph/ceph-ansible | tests/conftest.py | Python | apache-2.0 | 6,505 | [
"Octopus"
] | cd80bbc3f9732824fe8ca659ed3a3386f8ce39117528f85c5f11335b176bbbac |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under th... | kain88-de/mdanalysis | package/MDAnalysis/topology/__init__.py | Python | gpl-2.0 | 12,792 | [
"Amber",
"CHARMM",
"DL_POLY",
"GAMESS",
"Gromacs",
"HOOMD-blue",
"LAMMPS",
"MDAnalysis"
] | 030d8b9c2a059d973c36bdffcfb7dbac3be0c7060b86a3604ad6dbc6dbeeca31 |
#!/usr/bin/env python
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistri... | ashutoshvt/psi4 | psi4/share/psi4/fsapt/fsaptdiff.py | Python | lgpl-3.0 | 4,127 | [
"Psi4"
] | 7dd5accba4e4e81a5983f69ede15475cff033d24bbf953a36465654988ae78db |
'''GFF3 format (:mod:`skbio.io.format.gff3`)
=========================================
.. currentmodule:: skbio.io.format.gff3
GFF3 (Generic Feature Format version 3) is a standard file format for
describing features for biological sequences. It contains lines of
text, each consisting of 9 tab-delimited columns [1]_.... | gregcaporaso/scikit-bio | skbio/io/format/gff3.py | Python | bsd-3-clause | 18,537 | [
"scikit-bio"
] | cefe160162a66c934e757ed8a96fa23b2f33e7cc8e58586defadf198226be4b4 |
########################################################################
# File : ServerUtils.py
# Author : Ricardo Graciani
########################################################################
"""
Provide uniform interface to backend for local and remote clients.return
There's a pretty big assumption here: ... | andresailer/DIRAC | WorkloadManagementSystem/Client/ServerUtils.py | Python | gpl-3.0 | 1,235 | [
"DIRAC"
] | 8e488e9962198dbb2a2c88f42eef06bcf0b95b09bf596feb1c705fb25cc9ebfe |
## INFO ########################################################################
## ##
## COUBLET ##
## ======= ... | petervaro/coublet | widgets/button.py | Python | mit | 4,715 | [
"VisIt"
] | 2d828f020cc15609714b736aa40a8685b2d352edf1d1b587bc1de2b11d8a3b1a |
##!/usr/bin/env python
#-*- coding:utf-8 -*-
"""
Tools for field stars
:author: D. Bednarski
:license: GNU GPL v3.0 (https://github.com/danmoser/pyhdust/blob/master/LICENSE)
"""
import os
import re
import csv
import copy
import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt
#import matplotlib.c... | dbednarski/pyhdust | pyhdust/fieldstars.py | Python | gpl-3.0 | 125,153 | [
"Gaussian"
] | bea33e754c9694eb54d6bf5ea4ef818963c208aaf2474e12f49367ae85b7db7c |
import os
# Mongo information
datastore_host='localhost'
datastore_port=27017
# Logging
import logging
log_level=logging.DEBUG
# Application Settings
import uuid
app_settings = dict(app_name='blinx_api',
compress_response=True,
cookie_secret='<You should fill this in>',
... | blinxin/blinx_api | blinx_api/settings.py | Python | gpl-2.0 | 1,208 | [
"VisIt"
] | e6df5c3c8b034115c87b9a5c213586f5cafd1c9a518395c04b666b8664cce1e5 |
# encoding: utf-8
"Module for displaying information about the system."
import gtk
from gettext import gettext as _
from ase.gui.widgets import pack
singleimage = _("Single image loaded.")
multiimage = _("Image %d loaded (0 - %d).")
ucconst = _("Unit cell is fixed.")
ucvaries = _("Unit cell varies.")
format = _("""... | grhawk/ASE | tools/ase/gui/quickinfo.py | Python | gpl-2.0 | 1,703 | [
"ASE"
] | 500ce6a4b83870fc32d3e55fb6131dd7fef96e966e97c46460b051d4599ae96e |
#!/usr/bin/env python
#-*- coding:utf-8 -*-
#---------------------------------------------------------------
# ReStructuredText to FoLiA Converter
# by Maarten van Gompel
# KNAW Humanities Cluster &
# Centre for Language and Speech Technology (Radboud University Nijmegen)
# proycon AT anaproy DOT nl
#
# Lice... | proycon/foliatools | foliatools/rst2folia.py | Python | gpl-3.0 | 30,332 | [
"VisIt"
] | 2f5e44dd72d13168297c478feb7101748430e24376c73b1e06ef5c3dd7aad6d5 |
#
# @file TestSBMLError.py
# @brief SBMLError unit tests, C++ version
#
# @author Akiya Jouraku (Python conversion)
# @author Sarah Keating
#
# $Id$
# $HeadURL$
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatically ... | alexholehouse/SBMLIntegrator | libsbml-5.0.0/src/bindings/python/test/sbml/TestSBMLError.py | Python | gpl-3.0 | 4,822 | [
"VisIt"
] | 9982a3f2b97f0e60207e795fb8a7c0c527be0554064a65d5dbcf2fab6b4bd95a |
#### filter fasta by cutoff .py ####
#
# input a gene predictions (fasta) file
# and a set of BLAST validation data
# (gene predictions blasted against DB)
# and a list of KOG <-> gene ID mappings
# from the reference.
#
# output a fasta file
# containing only those predicted genes
# which have hits to the validation D... | lonelyjoeparker/real-time-phylogenomics | wales_analyses/phylogenome_wales/SNAP-predicted/filter_fasta_by_cutoff.py | Python | gpl-2.0 | 3,468 | [
"BLAST"
] | 4900dcd40140ecc34986dfa0bcdc62c5d7bc64bfe515c2311834f941fdf2e7fb |
import numpy as np;
from sklearn.svm import SVC;
import sklearn.preprocessing as preprocessing;
from sklearn.externals import joblib;
from sklearn.metrics import recall_score, accuracy_score, confusion_matrix, classification_report
import os
import sys
import dataset_manupulation as dm
import utils
import arff
import ... | vespero89/Snoring_Challenge | Supervectors/gridsearch_FUNCT.py | Python | gpl-3.0 | 7,135 | [
"Gaussian"
] | 9ecb7300909676ac922df9b68f5bbd240efad9af49e25009afa43f26f4d07e73 |
#!/usr/bin/env python
########################################################################
# $HeadURL$
########################################################################
""" Enable using one or more Storage Elements
"""
__RCSID__ = "$Id$"
import DIRAC
from DIRAC.Core.Base import Script
read = True
write = Tr... | Sbalbp/DIRAC | DataManagementSystem/scripts/dirac-admin-allow-se.py | Python | gpl-3.0 | 7,128 | [
"DIRAC"
] | c74b6b100972fd8f12076c0a0d26180cc088e3566dd1b2ff33ac8dd33f2854bf |
#!/usr/bin/env python
# Copyright 2014-2019 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/prop/nmr/rhf.py | Python | apache-2.0 | 13,891 | [
"Gaussian",
"PySCF"
] | 00dfcd4fad09c3e25c751018cff03159caec6b80c20a970c653c75160c6ffd9e |
"""HandleImport transformation takes care of importing user-defined modules."""
from pythran.passmanager import Transformation
from pythran.tables import cxx_keywords, MODULES, pythran_ward
import ast
import importlib
import inspect
def add_filename_field(node, filename):
for descendant in ast.walk(node):
... | hainm/pythran | pythran/transformations/handle_import.py | Python | bsd-3-clause | 15,181 | [
"VisIt"
] | 17afc5214ca7bcdb908d04faf2b6a1ce5e1001f81d7ecf53f947203c3dc8f808 |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, sys, glob, string
import zipfile
from datetime import date
try:
import json
except:
import simplejson as json
cwd = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
os.chdir(cwd)
required_module_keys = ['name','versi... | benbahrenburg/benCoding.Map | build.py | Python | apache-2.0 | 6,428 | [
"VisIt"
] | 73e129c74ec8a638370b2b62c807748484d3e9221a8e483027e6fa255c12df3e |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Classes for reading/manipulating/writing QChem input files.
"""
import logging
import sys
from typing import Dict, List, Optional, Tuple, Union
from monty.io import zopen
from monty.json import MSONable
from pymatgen.cor... | vorwerkc/pymatgen | pymatgen/io/qchem/inputs.py | Python | mit | 28,528 | [
"Q-Chem",
"pymatgen"
] | 7ffdda08f1cf5e3e76d0cc216e4adc948c2850650a82c8f7abb715e8579cc13d |
"""
Tests for ORA (Open Response Assessment) through the LMS UI.
"""
import json
from unittest import skip
from bok_choy.promise import Promise, BrokenPromise
from ..pages.lms.peer_confirm import PeerConfirmPage
from ..pages.lms.auto_auth import AutoAuthPage
from ..pages.lms.course_info import CourseInfoPage
from ..p... | martynovp/edx-platform | common/test/acceptance/tests/test_ora.py | Python | agpl-3.0 | 16,016 | [
"VisIt"
] | 79c389000b358484453fb49ee37292df1359bd5d48ae00a432e33e3b794473a5 |
"""
Provides factory methods to assemble the Galaxy web application
"""
import logging, atexit
import os, os.path
from inspect import isclass
from paste.request import parse_formvars
from paste.util import import_string
from paste import httpexceptions
from paste.deploy.converters import asbool
import flup.middlewar... | dbcls/dbcls-galaxy | lib/galaxy/web/buildapp.py | Python | mit | 9,983 | [
"Galaxy"
] | c89cc3705ea3b55115ea8be3b69e2b0b09752cc4daee4e44c8c4e29e662318ab |
# -*- coding: utf-8 -*-
"""
Generators for random graphs.
"""
# Copyright (C) 2004-2015 by
# Aric Hagberg <hagberg@lanl.gov>
# Dan Schult <dschult@colgate.edu>
# Pieter Swart <swart@lanl.gov>
# All rights reserved.
# BSD license.
from collections import defaultdict
import itertools
import math
import... | dmoliveira/networkx | networkx/generators/random_graphs.py | Python | bsd-3-clause | 31,442 | [
"VisIt"
] | bb4b1bde39d73486c7c188ecb35d3ee7fb778f766ab02d1b2b8f6d572b0fda30 |
import moose
import pylab
import rdesigneur as rd
moogList = []
### Remove comment from line below if you want to display the 3-d cell view.
moogList = [['#', '1', '.', 'Vm', 'Membrane potential', -0.065, -0.055]]
rdes = rd.rdesigneur(
turnOffElec = False,
chemDt = 0.002,
chemPlotDt = 0.02,
diffusionL... | BhallaLab/moose-examples | tutorials/Rdesigneur/ex10.2_spine_Ca_influx_to_branched_neuron.py | Python | gpl-2.0 | 2,506 | [
"MOOSE"
] | 3489df37bbfc4a4969a42ab70359c3db3ea02a6d72a831072b71f3bc28467f61 |
# -*- coding: utf-8 -*-
# for more info please visit http://www.iptvxtra.net
import sys,xbmc,os,shutil,xbmcaddon
# ------------------------------------------------------------------------------------------------------------------------------------------- wiederherstellen der DE Settings - START
try:
sxUser = ... | noba3/KoTos | addons/plugin.video.iptvxtra-de-more/default.py | Python | gpl-2.0 | 17,491 | [
"VisIt"
] | 59adc0d8f8f9d00e375f0b6c0baf081ec4e0233f7efd419dc6e3d238266deec6 |
# coding: utf-8
from collections import defaultdict
from operator import itemgetter
import os
import random
import string
import sys
import time
import h2o
import numpy as np
import pandas as pd
from sklearn.linear_model import LogisticRegressionCV
from sklearn.ensemble import RandomForestClassifier
from sklearn.cros... | roaminsight/roamresearch | BlogPosts/Categorical_variables_in_tree_models/tree_categorical_variables.py | Python | apache-2.0 | 11,127 | [
"Gaussian"
] | a2b00b6221adbae06fb87c590c165ef6c8511937b14b357ed391c69e32d503f8 |
from scipy import signal
import numpy as np
import pandas as pd
import time
def gaussian_filter(_df, _len=16, _sigma=1.6):
cols = np.empty((len(_df.index), len(_df.columns)))
cols.fill(np.nan)
header = []
for column in _df:
header.append(column)
cols[:,len(header)-1] = gaussian_filtere... | degoldschmidt/ribeirolab-codeconversion | python/tracking_project/tracking/preprocessing/filtering.py | Python | gpl-3.0 | 634 | [
"Gaussian"
] | b49b50523df8316379198c2a6b86b36faff6490b4d49d18aa60ed72b10e538b1 |
#!/usr/bin/python
# Copyright (c) 2013, Thomas Rast <trast@inf.ethz.ch>
#
# 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, version 2 of the License.
#
# This program is distributed in the hope t... | trast/evilmergediff | evil-base-diffdiff.py | Python | gpl-2.0 | 7,025 | [
"Octopus"
] | 1cc1c539e0795574f990762b4c78b770a0405621c3d64a1e565c11e0efe256c5 |
import threading
import logging
import socket
from urllib2 import urlopen
from itertools import chain
from datetime import timedelta
from lxml import etree
from molly.apps.places import get_entity
from molly.apps.places.models import Route, EntityType, StopOnRoute, Source, Entity
from molly.apps.places.providers impo... | mollyproject/mollyproject | molly/apps/places/providers/cloudamber.py | Python | apache-2.0 | 10,209 | [
"Amber"
] | 0521801f08331a028f59403fac9eaed395d6193c75956f29655d1a226eaf7159 |
"""
Feature calculations.
"""
import logging
import types
import numpy as np
import multiprocessing
from typing import Any, Dict, List, Iterable, Sequence, Tuple, Union
logger = logging.getLogger(__name__)
class Featurizer(object):
"""Abstract class for calculating a set of features for a datapoint.
This class ... | miaecle/deepchem | deepchem/feat/base_classes.py | Python | mit | 11,262 | [
"CRYSTAL",
"RDKit",
"matminer",
"pymatgen"
] | 9ed6deffb6d7df9f2e9f50d0ea07f6770e3bbc708d91ae64d805662b89d17aeb |
# $Id$
#
# Copyright (C) 2003-2006 Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
import os
import io
import unittest
fro... | soerendip42/rdkit | rdkit/Chem/UnitTestCatalog.py | Python | bsd-3-clause | 9,124 | [
"RDKit"
] | 0beebb81df828581f1211ac79f0a7c580faa8954712d9699d0ca5fc3459a03dd |
"""
Functions for transforming flow cytometer data to MEF units.
"""
import os
import functools
import collections
import six
import packaging
import packaging.version
import numpy as np
import scipy
from scipy.optimize import minimize
import matplotlib.pyplot as plt
import sklearn
if packaging.version.parse(sklearn... | taborlab/FlowCal | FlowCal/mef.py | Python | mit | 48,430 | [
"Gaussian"
] | 9fc52a77e127ab4784be8c71f7a22adf74c336f0b10b137a3f52398cad94b0c9 |
import numpy as np
import pylab as pl
from lmfit import minimize, Parameters, Parameter,\
report_fit, Model, CompositeModel
from lmfit.models import StepModel, GaussianModel, LorentzianModel, ConstantModel, RectangleModel, LinearModel
def gaussian(x, height, center, width, offset):
return (hei... | DiamondLightSource/auto_tomo_calibration-experimental | old_code_scripts/simulate_data/fit_data.py | Python | apache-2.0 | 3,625 | [
"Gaussian"
] | cf96d58034399628b331ac18db1b87da53c02cb2d5242788ad2f1edf603b75a1 |
""" Contains the GI (General Illumination) parent classes. """
# gi.py
# Mission Pinball Framework
# Written by Brian Madden & Gabe Knuth
# Released under the MIT License. (See license info at the end of this file.)
# Documentation and more info at http://missionpinball.com/mpf
import logging
from mpf.system.devices ... | jabdoa2/mpf | mpf/devices/gi.py | Python | mit | 3,293 | [
"Brian"
] | 63e470950f4bb118ae6fe191253d88dd2d6f4f4d733b9f07af01c5a9c0729829 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkVectorText(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtk... | nagyistoce/devide | modules/vtk_basic/vtkVectorText.py | Python | bsd-3-clause | 467 | [
"VTK"
] | c81bf6799bab415dcef8ab24e08901eab2437151480e2ca708dc2460d0090ed8 |
r"""
Alignments (:mod:`skbio.alignment`)
===================================
.. currentmodule:: skbio.alignment
This module provides functionality for computing and manipulating sequence
alignments. DNA, RNA, and protein sequences can be aligned, as well as
sequences with custom alphabets.
Data Structures
----------... | gregcaporaso/scikit-bio | skbio/alignment/__init__.py | Python | bsd-3-clause | 6,612 | [
"scikit-bio"
] | 9632a5824eb0c0a15b36125a7eae7891f7f7b9f5e633f1966751e4f3ae576e31 |
__doc__ = """Code by Benjamin S. Murphy
bscott.murphy@gmail.com
Dependencies:
numpy
scipy
matplotlib
Cython
Classes:
OrdinaryKriging: Convenience class for easy access to 2D Ordinary Kriging.
References:
P.K. Kitanidis, Introduction to Geostatistcs: Applications in Hydrogeology,
... | yejingxin/PyKrige | pykrige/ok.py | Python | bsd-3-clause | 33,614 | [
"Gaussian"
] | ef783e8827514c503adb0c4b8e453d9673829e45fb537de11d3031d96b6cccf4 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
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.generic import TemplateView
from django.views import defaults as default_views
urlpat... | redmoonlas/textinsight | config/urls.py | Python | bsd-3-clause | 1,435 | [
"VisIt"
] | eae1b18014ba6898de6a6e81f45e06edb60a49e7fb7918575d618afa2eb12efe |
# -*- coding: utf-8 -*-
#
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2006-2014, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Pub... | ghutchis/cclib | src/cclib/parser/gamessukparser.py | Python | lgpl-2.1 | 28,809 | [
"GAMESS",
"Gaussian",
"cclib"
] | 863c7e78f72b6565f16f13bbbf159ab5c1bfe1206e59fa4e58c853dac44217ac |
import numpy as np
import scipy as scipy
import lxmls.classifiers.linear_classifier as lc
import sys
from lxmls.distributions.gaussian import *
class MultinomialNaiveBayes(lc.LinearClassifier):
def __init__(self,xtype="gaussian"):
lc.LinearClassifier.__init__(self)
self.trained = False
se... | iarroyof/lxmls-toolkit | lxmls/classifiers/multinomial_naive_bayes.py | Python | mit | 2,763 | [
"Gaussian"
] | fe8bbe7bb5b4ab8dcb5171e372525ebef14f7aac92f30ef3d0651bbf513d0b05 |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
"""
A script that does unsupervised learning on
Spatial Transcriptomics datasets (matrix of counts)
It takes a list of datasets as input and outputs (for each given input):
- a scatter plot with the predicted classes (coulored) for each spot
- the spots plotted onto t... | SpatialTranscriptomicsResearch/st_analysis | scripts/unsupervised.py | Python | mit | 21,532 | [
"Gaussian"
] | 005c517c15bd6eaeeebb47ffba63e8dbcb48fafb9dc3745b9e03029df6d05825 |
import math
import numpy as np
from .utils.io import saveswc
from collections import Counter
from random import gauss
from random import random
from random import randrange
from scipy.spatial.distance import cdist
class SWC(object):
def __init__(self, soma=None):
self._data = np.zeros((1, 8))
if... | RivuletStudio/rivuletpy | rivuletpy/swc.py | Python | bsd-3-clause | 13,080 | [
"VisIt"
] | edad5d08003204b7d493ea0de7b06ed96678b3236ff3ece476b156b39caa47af |
"""Window manager which controls any pop up windows from MPF. Used to display
game information, status, tests, keyboard-to-switch mapping, on screen DMD,
etc."""
# window.py
# Mission Pinball Framework
# Written by Brian Madden & Gabe Knuth
# Released under the MIT License. (See license info at the end of this file.)
... | spierepf/mpf | mpf/media_controller/core/window.py | Python | mit | 5,357 | [
"Brian"
] | 482eb85b2ecced3228e151de8417647badbdabae87ee01c3d6dea4183287bedf |
import json
from octopus.server.server_command import ServerCommand
SERVER_HOST = 'localhost'
SERVER_PORT = '2480'
class PluginExecutor(object):
def __init__(self, server_host = SERVER_HOST, server_port = SERVER_PORT):
self.command = ServerCommand(server_host, server_port)
def execute(self, pluginna... | octopus-platform/octopus | python/octopus-tools/octopus/server/plugin_executor.py | Python | lgpl-3.0 | 615 | [
"Octopus"
] | 8a9f0a9f903f00f787f1e74fac93e35758180600f5e000f72ce90a001d2d6d36 |
# -*- coding: utf-8 -*-
#
# biodoop-blast documentation build configuration file, created by
# sphinx-quickstart on Sun Jul 17 14:32:07 2011.
#
# 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.
#... | crs4/biodoop-blast | docs/conf.py | Python | gpl-3.0 | 7,383 | [
"BLAST"
] | 58d71c488dbcf64df1889791c0cf0e993a4de41599e3da7a112e9c102b435a41 |
from __future__ import print_function, division
from sympy import (Add, ceiling, divisors, factor_list, factorint, floor, igcd,
ilcm, Integer, integer_nthroot, isprime, Matrix, Mul, nextprime,
perfect_power, Poly, S, sign, solve, sqrt, Subs, Symbol, symbols, sympify,
Wild)
from sympy.core.function import ... | Arafatk/sympy | sympy/solvers/diophantine.py | Python | bsd-3-clause | 83,608 | [
"Gaussian"
] | be27cd4729973b0961651e3ad6517644ebd797556f41bcfe14e233b92ed4ce88 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
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.generic import TemplateView
from django.views import defaults as default_views
urlpat... | arruda/revolution | config/urls.py | Python | mit | 1,354 | [
"VisIt"
] | d786e35dc39e24019d662fc6cf53fe80cca4ea3df62062286c9159ae42e0d820 |
#!/usr/bin/env python
import sys
import argparse
import glob
import re
import vtk
import vtktools
def parse_args(argv):
parser = argparse.ArgumentParser(
prog="vtu2ensight",
description="""This converts a vtu file to a ensight file. If applied to checkpointed files, use rename_checkpoint f... | rjferrier/fluidity | tools/vtu2ensight.py | Python | lgpl-2.1 | 5,336 | [
"VTK"
] | b87ce5e094b4641ca84aab7ad38b0ddbe3b58888a820bc1a37f8d1c6eb187ed9 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
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.generic import TemplateView
from django.views import defaults as default_views
urlpat... | shanenater/shanecookie | config/urls.py | Python | bsd-3-clause | 1,282 | [
"VisIt"
] | a6f695922166a8c7f3124ee6d99b63eb86cec3b47519dd5af2ab85ca4f35aa07 |
from vtk import *
source = vtkRandomGraphSource()
source.SetNumberOfVertices(10)
#source.SetStartWithTree(True)
source.SetIncludeEdgeWeights(True)
source.SetGeneratePedigreeIds(True)
# selection source
sel1 = vtkSelectionSource()
#vtkSelectionNode :: SELECTIONS,GLOBALIDS,PEDIGREEIDS,VALUES,INDICES,
# ... | spthaolt/VTK | Examples/Infovis/Python/graph_selection_subtract.py | Python | bsd-3-clause | 2,194 | [
"VTK"
] | 884cf97db05e4b3a8071a5975b9182a7f4d53fc4f9728530e8a5b92d8cd45620 |
#!/usr/bin/python2.7
import pysam
import glob
import os
from time import time
from time import sleep
import subprocess
import multiprocessing as mp
from optparse import OptionParser
# -------------------------------------------------
parser = OptionParser()
parser.add_option("--sambamba", dest="sambamba", help="Path... | jdeligt/Genetics | Count_Telomeric_Sequence_Reads.py | Python | mit | 4,708 | [
"pysam"
] | fae7920047e6b8b4f52c5a8f7625f4be6674b6c7e8a577c8710a26e923e1cff7 |
from numbers import Integral
from functools import wraps
import numpy
from scipy import signal
def record(method):
@wraps(method)
def recorded_method(recorder, *args, **kwargs):
# If this isn't being called from within a recorded method,
# then we should add the call to the object's record. W... | senderle/svd-noise | noise.py | Python | mit | 12,253 | [
"Gaussian"
] | e6a342af94df5e754fecd91af9aa794a43cef8d63592f5230c7894a3f26ff181 |
"""This file implements the gym environment of minitaur.
"""
import math
import time
import os, inspect
currentdir = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe())))
parentdir = os.path.dirname(os.path.dirname(currentdir))
os.sys.path.insert(0, parentdir)
import gym
from gym import spaces
fr... | MTASZTAKI/ApertusVR | plugins/physics/bulletPhysics/3rdParty/bullet3/examples/pybullet/gym/pybullet_envs/minitaur/envs/minitaur_gym_env.py | Python | mit | 25,379 | [
"Gaussian"
] | cdacbad7be157b8fcceccefdc74e580658ec425f635fd12c3da728115408bc1f |
# Copyright 2022 The Scenic Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in w... | google-research/scenic | scenic/dataset_lib/coco_dataset/coco_eval.py | Python | apache-2.0 | 12,814 | [
"VisIt"
] | 1b5300b1f7ba03359828c478fd17f7e8398eaf93231e0fb6f86e1416afdc8ad1 |
#!/usr/bin/python
#
# Copyright (c) 2016 Matt Davis, <mdavis@ansible.com>
# Chris Houseknecht, <house@redhat.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Soft... | cmvelo/ansible | contrib/inventory/azure_rm.py | Python | gpl-3.0 | 32,093 | [
"Galaxy"
] | 64c2f8b35c5f3054d5d491b0f3b74fed7ce22b55e6dd2b9beae79bc1d81d0cb6 |
#
import os
import numpy as np
import healpy as hp
import astropy.io.fits as pyfits
from multiprocessing import Pool
import matplotlib as mpl
mpl.use('Agg')
import matplotlib.pyplot as plt
from quicksipManera import *
import fitsio
from random import random
### ------------ A couple of useful conversions -----------... | legacysurvey/pipeline | validationtests/desi_image_validation.py | Python | gpl-2.0 | 60,916 | [
"Galaxy"
] | 0ed8b575330b3b843bb51eba52f340d8e764b37743ac1e10187004ed5a25fccd |
# -*- coding: utf-8 -*-
#
# Buildbot documentation build configuration file, created by
# sphinx-quickstart on Tue Aug 10 15:13:31 2010.
#
# 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.
#
# Al... | mitya57/debian-buildbot | docs/conf.py | Python | gpl-2.0 | 10,762 | [
"Brian"
] | 79868484738f9f20fac6964b05cc6cbe4df738051e72d24d4885794d9c6ecab6 |
import numpy as np
import matplotlib.pyplot as plt
import astropy.io.fits as fits
import astropy.table as table
from astropy import units as u, constants as c
import ppxf_util as util
from ppxf import ppxf
from scipy import ndimage
import manga_tools as m
import os
import pickle as pk
# for sampling
import emcee
imp... | zpace/MaNGA-fitting | MaNGA_stars_gas_fit.py | Python | mit | 19,438 | [
"Galaxy",
"Gaussian"
] | 08cbcae06206dfae0acddaa0888f7b27403072e8e90f2952ae0aa6048d2cd6cb |
import numpy as np
import matplotlib.pyplot as plt
from matplotlib import collections
from matplotlib.patches import Circle
import networkx as nx
from skimage import img_as_float, morphology
from skimage.color import gray2rgb
def _normalise_image(image, *, image_cmap=None):
image = img_as_float(image)
if imag... | jni/skan | src/skan/draw.py | Python | bsd-3-clause | 13,467 | [
"Gaussian"
] | a53ada6f0b1538c8d15281b5dce083a468d4daf8033d0bdbcd9ca70d1a8c2867 |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, subprocess, sys, glob, string
import zipfile
from datetime import date
cwd = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
os.chdir(cwd)
required_module_keys = ['name','version','moduleid','description','copyright','... | timanrebel/Facebook | iphone/build.py | Python | mit | 7,584 | [
"VisIt"
] | 0e878b305f810e59704147a3c917fd1ed267d38aa2dbf39cb78e6318d278b22c |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 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
#... | lothian/psi4 | psi4/driver/p4util/__init__.py | Python | lgpl-3.0 | 1,255 | [
"Psi4"
] | 0f623875a0e903053106a8d70fd22cbef671a0ced0c6c1857495c2b877f1af6e |
import re
import sys
from circlator import program, common
from circlator import __version__ as circlator_version
import shutil
import pyfastaq
class Error (Exception): pass
prog_to_env_var = {
'samtools': 'CIRCLATOR_SAMTOOLS',
'spades': 'CIRCLATOR_SPADES',
'canu': 'CIRCLATOR_CANU',
}
prog_to_version_cmd... | martinghunt/circlator | circlator/external_progs.py | Python | gpl-3.0 | 3,423 | [
"BWA"
] | d936af282c639d000f4536785488fae6810b9f91eedabf6003436577ad794c45 |
"""
Death Streams Addon
Copyright (C) 2017 Mr.Blamo
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.
... | repotvsupertuga/tvsupertuga.repository | script.vodextende/scrapers/2ddl_scraper.py | Python | gpl-2.0 | 10,345 | [
"ADF"
] | 480f563ecebe798d0467b001c88822e8b7ef14855fb59e30ecfeeab1d55220ff |
from __future__ import absolute_import
import numpy as np
from sklearn.base import BaseEstimator
from . import metrics
from .rank_correlation import spearman_correlation, kendalltau_correlation
def _init_coefs(X, method="corrcoef"):
if method == "corrcoef":
return np.corrcoef(X, rowvar=False), 1.0
e... | skggm/skggm | inverse_covariance/inverse_covariance.py | Python | mit | 11,604 | [
"Gaussian"
] | c648682167e3e07477f0343875b76c98e2acb4cc981e71b50e9c5c6c1ec3101c |
from __future__ import division, print_function, absolute_import
import unittest
import os
from math import floor
from src.utilities import split_file, count_lines
from src.parse_journal.parse_worker import JournalParsingWorker
import json
class TestParsing(unittest.TestCase):
def create_test_data(self):
... | robert-giaquinto/text-analysis | src/tests/test_parse_worker.py | Python | mit | 8,115 | [
"VisIt"
] | 1d06184ae8600a44215b8b5c5b941193a7af246e1ffe1a73095aa6b3c6c1c550 |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
#
ANSIB... | simonwydooghe/ansible | lib/ansible/modules/network/avi/avi_l4policyset.py | Python | gpl-3.0 | 4,150 | [
"VisIt"
] | 2c163015d6b7c9d461c358f1d1ce0bbf706f6290e8e0245676f96321e34f54fc |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright: (c) 2016, Brian Coca <bcoca@ansible.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version': '1... | skg-net/ansible | lib/ansible/modules/system/systemd.py | Python | gpl-3.0 | 19,072 | [
"Brian"
] | 9230527ba9e834f8a2a46e5c97ee95dec318f21cd29b8cdc9dd7471b4d4af5ab |
# -*- coding: utf-8 -*-
"""
Simple Counter
~~~~~~~~~~~~~~
Instrumentation example that gathers method invocation counts
and dumps the numbers when the program exists, in JSON format.
:copyright: (c) 2014 by Romain Gaucher (@rgaucher)
:license: Apache 2, see LICENSE for more details.
"""
import sys
from eq... | neuroo/equip | examples/counter/counter_instrument.py | Python | apache-2.0 | 2,808 | [
"VisIt"
] | 9ce84285ac4c637f32aa909f0d3e64d8177e1cefe40e2639af322dafd7167476 |
from argparse import ArgumentParser
ap = ArgumentParser()
ap.add_argument('-pn', '--planet_name', required=True, type=str, help='Directory Name for the Planet (i.e. GJ1214).')
ap.add_argument('-c', '--channel', required=True, type=str, help='Channel number string (i.e. ch1 or ch2).')
ap.add_argument('-ad', '--aor_dir'... | exowanderer/ExoplanetTSO | Exoplanet_TSO_-_Photometric_Extraction_Pipeline.py | Python | gpl-3.0 | 12,708 | [
"Gaussian"
] | d0db554448e3c67118ad9f7871151ffb2051ab0250bac91168c53831b0c4b101 |
# This file is part of BurpyHooves.
#
# BurpyHooves 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.
#
# BurpyHooves is distributed in... | SparklerPone/muckbot | modules/buh.py | Python | gpl-3.0 | 1,785 | [
"BLAST"
] | 6f04cd5748a6d59d08701ba8f83555370a0f3e63c8ef921442d7d7633b88d28b |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | mlperf/training_results_v0.6 | Fujitsu/benchmarks/resnet/implementations/mxnet/3rdparty/horovod/examples/mxnet/common/fit.py | Python | apache-2.0 | 13,466 | [
"Gaussian"
] | d1c6570ddf5547ddfa9b022a01a9a761752f9be0d8350872f0b941aed44d26d0 |
#!/usr/bin/env python
"""
Easy Install
------------
A tool for doing automatic download/extract/build of distutils-based Python
packages. For detailed documentation, see the accompanying EasyInstall.txt
file, or visit the `EasyInstall home page`__.
__ https://setuptools.readthedocs.io/en/latest/easy_install.html
""... | BitWriters/Zenith_project | zango/lib/python3.5/site-packages/setuptools/command/easy_install.py | Python | mit | 85,933 | [
"VisIt"
] | 0f977f4be88be71f24de422b14de41844eaac21a2dacc43e9be4058403d62bef |
#!/usr/bin/env python
# Copyright 2015 The Kubernetes Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appli... | antoineco/kubernetes | cluster/juju/layers/kubernetes-worker/reactive/kubernetes_worker.py | Python | apache-2.0 | 37,693 | [
"CDK"
] | 88cc6c94174fbe966c5f3fe2115c10b5207239ad91919051a54b8e7a9a8ff5f3 |
import ConfigParser
import commands
from optparse import OptionParser
import os
import string
import sys
import time
import types
SHELL_TYPE_BASH = "bash"
SHELL_TYPE_TCSH = "tcsh"
class Installer(object):
def __init__(self, commandLine):
self.AZOrangeInstallDir = None
self.commandLineArguments = ... | AZCompTox/AZOrange | install/install.py | Python | lgpl-3.0 | 62,982 | [
"CDK",
"RDKit"
] | 1ec29cc4312a2000aedf7c5397139c30c276faf43ecbaa7e7bcaba6625ea6545 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Author: Vincent Dubourg <vincent.dubourg@gmail.com>
# (mostly translation, see implementation details)
# License: BSD style
"""
A module that implements scalar Gaussian Process based prediction (also
known as Kriging).
Contains
--------
GaussianProcess: The main cl... | ominux/scikit-learn | sklearn/gaussian_process/__init__.py | Python | bsd-3-clause | 1,189 | [
"Gaussian"
] | 6c146ca3c3c9fa705062d79545c7f5dac82f516ab2629ae338d8d9f5db44b4da |
#%%#############################################################################
# filterAndAggregate.py
# Copyright (c) 2017, Joshua J Hamilton and Katherine D McMahon
# Affiliation: Department of Bacteriology
# University of Wisconsin-Madison, Madison, Wisconsin, USA
# URL: http://http://mcmahonlab.wisc.... | joshamilton/Hamilton_acI_2017 | code/mapping/05filterAndAggregate.py | Python | mit | 6,718 | [
"HTSeq"
] | 2b5d26d7a2e08d6e24328908990f8823dc05239fd91a47b0752e858ad4a933b0 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import json
import os
import tempfile
import unittest
import warnings
import numpy as np
from pymatgen.core.structure import Structure
from pymatgen.electronic_structure.core import Orbital, Spin
from pymatge... | gmatteo/pymatgen | pymatgen/io/lobster/tests/test_lobster.py | Python | mit | 115,785 | [
"Gaussian",
"VASP",
"pymatgen"
] | 6d732eb01aa8935f2a2d467fc05d61dde5c9196b91a778b36058cdcdd20bdc9b |
#!/usr/bin/python
########################################################################
# 27 April 2015
# Patrick Lombard, Centre for Stem Stem Research
# Core Bioinformatics Group
# University of Cambridge
# All right reserved.
########################################################################
import subpro... | pdl30/pyatactools | pyatactools/atac_profiler.py | Python | gpl-2.0 | 22,058 | [
"HTSeq",
"pysam"
] | 3572f6da7c6e9ce111595f3979e9fe4991fe316e87144055c1b82cf35f90f9aa |
# -*- 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/text/gui/qt/textproperties.py | Python | lgpl-3.0 | 7,252 | [
"VTK"
] | 65ff2577c91c7b3b05e330e97db3dc496b0e736beafd80f08a450b5410345ea6 |
import fnmatch
import os
import pandas as pd
import cPickle as pickle
import csv
from collections import OrderedDict
#list of file paths with mapped hits
pats = ['/netapp/home/idriver/count-picard_combined_ips17_BU3']
#output path
path = '/netapp/home/idriver/count-picard_combined_ips17_BU3'
#base name for final ou... | idbedead/RNA-sequence-tools | Count_Parsing/count_matrix_stats.py | Python | mit | 3,657 | [
"HTSeq"
] | 09928e96a1f3420b47e06e0131aea4cb959730c17e8eea343a40494eb2c54f88 |
""" This is a test of the FileCatalogDB
It supposes that the DB is present.
"""
# pylint: disable=invalid-name,wrong-import-position
import unittest
import itertools
import os
import sys
from DIRAC.Core.Base import Script
Script.parseCommandLine()
from DIRAC.DataManagementSystem.DB.FileCatalogDB import FileCat... | andresailer/DIRAC | tests/Integration/DataManagementSystem/Test_FileCatalogDB.py | Python | gpl-3.0 | 56,699 | [
"DIRAC"
] | 797022c2771e9932020f0705009bcc2602649dbcad3884d04ef88e246c23a795 |
from __future__ import print_function, division
import numpy as np
#########################################
### Generators ###
# Functions which return next value in a sequence upon each call
def squares():
""" Generator which returns the square value of every integer, starting with 1. """
i = 1
wh... | dvida/UWO-PA-Python-Course | Lecture 8/L8_lecture.py | Python | mit | 7,179 | [
"Galaxy"
] | 3f3b30db21d72503cbb74a1546e4d00c9dde5d88d0689750960ca04e23fc0fda |
# Copyright (C) 2003 CAMP
# Please see the accompanying LICENSE file for further information.
import numpy as np
from gpaw import debug
from gpaw.utilities import is_contiguous
import _gpaw
class Spline:
def __init__(self, l, rmax, f_g):
"""Spline(l, rcut, list) -> Spline object
The integer l ... | robwarm/gpaw-symm | gpaw/spline.py | Python | gpl-3.0 | 2,507 | [
"GPAW"
] | e6e0080040f4ae18101060a88b84257c7f2d8f1cc04d2b5dca603ff33527a2b2 |
#
# Copyright (C) 2012-2013 Aleabot
#
# 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 is distributed i... | aleabot/aleabot | src/alea/breakfast.py | Python | gpl-3.0 | 2,991 | [
"VisIt"
] | 1ae5d18c7c72c90132078140f404d8730a6d72e166862d26f1732ada8e5e3a9b |
"""
fitpack --- curve and surface fitting with splines
fitpack is based on a collection of Fortran routines DIERCKX
by P. Dierckx (see http://www.netlib.org/dierckx/) transformed
to double routines by Pearu Peterson.
"""
# Created by Pearu Peterson, June,August 2003
from __future__ import division, print_function, abs... | Universal-Model-Converter/UMC3.0a | data/Python/x86/Lib/site-packages/scipy/interpolate/fitpack2.py | Python | mit | 48,477 | [
"Gaussian"
] | 423cca9b2d77da107d042b8178a72f3de860510d5240e4c14b383cf6e4c7f29f |
"""Read and write notebook files as XML.
Authors:
* Brian Granger
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2008-2011 The IPython Development Team
#
# Distributed under the terms of the BSD License. The full license is in
# the file COPYING, distributed a... | noslenfa/tdjangorest | uw/lib/python2.7/site-packages/IPython/nbformat/v2/nbxml.py | Python | apache-2.0 | 6,765 | [
"Brian"
] | 919fbe71a5ed11dc07a8439c6635bb4bbcea4100fa301477f0451f767386b70e |
# (C) British Crown Copyright 2014 - 2018, Met Office
#
# This file is part of Iris.
#
# Iris 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 3 of the License, or
# (at your option) any l... | dkillick/iris | lib/iris/tests/unit/fileformats/netcdf/test__load_cube.py | Python | lgpl-3.0 | 7,516 | [
"NetCDF"
] | 27f5d494841c6956dd719192d052acb22e2d8404a1cc4f47690a825ba1144930 |
# Copyright 2001 by Tarjei Mikkelsen. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""BioPython Pathway module.
Bio.Pathway is a lightweight class library designed to suppor... | bryback/quickseq | genescript/Bio/Pathway/__init__.py | Python | mit | 10,881 | [
"Biopython"
] | bda20a16d89121fb0a3ee72083d6ad7198df10a30874d921075314244bacb9dd |
""" JobMonitoringHandler is the implementation of the JobMonitoring service
in the DISET framework
The following methods are available in the Service interface
"""
from __future__ import print_function
__RCSID__ = "$Id$"
from datetime import timedelta
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.DISET.Re... | fstagni/DIRAC | WorkloadManagementSystem/Service/JobMonitoringHandler.py | Python | gpl-3.0 | 21,262 | [
"DIRAC"
] | 954a5f640d4ff8b725210fbfe224f259df441023fd890cc5d1d006ef59e916d1 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# (c) 2014, Ruggero Marchei <ruggero.marchei@daemonzone.net>
# (c) 2015, Brian Coca <bcoca@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
#... | napkindrawing/ansible | lib/ansible/modules/files/find.py | Python | gpl-3.0 | 12,849 | [
"Brian"
] | 4ae4d4d7080105f9ba9629e2eab2d7b3795a8a4dbef5d573819a6cab34cc661a |
# Copyright 2017 juramote contributors (see README)
#
# Permission is hereby granted, free of charge, to any person obtaining a copy of
# this software and associated documentation files (the "Software"), to deal in
# the Software without restriction, including without limitation the rights to
# use, copy, modify, mer... | PromyLOPh/juramote | juramote/com.py | Python | mit | 15,556 | [
"ESPResSo"
] | 586c192dad52a06dc463df24d62c272c77a5e4097b9529af07bacec07db2354e |
#!/usr/bin/env python
""" Tests the MySQL class
"""
# FIXME: to bring back to life
import time
import DIRAC
from DIRAC.Core.Utilities.MySQL import MySQL
nThread = 3
nRetrieval = 100000
DIRAC.gLogger.initialize('test_MySQL', '/testSectionVerbose')
# DIRAC.gLogger.initialize('test_MySQL','/testSection')
class MyDB(... | fstagni/DIRAC | tests/Integration/FIXME_Test_MySQL.py | Python | gpl-3.0 | 7,059 | [
"DIRAC"
] | a22d839b2d486e8030c7b3eb549d04ed98ad1011689de1dc7c17c896b03a01fc |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals, print_function
import abc
import re
import os
import glob
import shutil
import warnings
from itertools import chain
from copy import deepcopy
import six
impo... | nisse3000/pymatgen | pymatgen/io/vasp/sets.py | Python | mit | 77,824 | [
"VASP",
"pymatgen"
] | bc211262c2660e347edd50e357cf51f05ad2f7bd762c3f75a4b5c1f72dd25645 |
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