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# Authors : Denis A. Engemann <denis.engemann@gmail.com>
# Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
#
# License : BSD 3-clause
from copy import deepcopy
import math
import numpy as np
from scipy import fftpack
# XXX explore cuda optimazation at some point.
from ..io.pick import pick_type... | effigies/mne-python | mne/time_frequency/_stockwell.py | Python | bsd-3-clause | 9,583 | [
"Gaussian"
] | 5eae42ad9b188546c3920e9cd42e8fe7173c798cf2f06292a1b9270b20c061b3 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/fci/addons.py | Python | apache-2.0 | 30,183 | [
"PySCF"
] | 4cd9be98feb1d5d4c55906ab3883f630bfc88bd00a583207634aca1b4fb2213d |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/e2-openwbif | plugin/controllers/views/web/mediaplayercurrent.py | Python | gpl-2.0 | 6,093 | [
"VisIt"
] | 65109212caa821534b1d44d9f4a9000611601d0e028780498f4d784accd0b6e9 |
#!/usr/bin/env python
""" create rst files for documentation of DIRAC """
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import os
import shutil
import socket
import sys
import logging
import glob
from diracdoctools.Utilities import writeLinesToFile, mkd... | ic-hep/DIRAC | docs/diracdoctools/cmd/codeReference.py | Python | gpl-3.0 | 16,069 | [
"DIRAC"
] | 689b1e09b085f9ee2c761683f674f86c56d10c5324d4796f15fcf37ca850e01a |
# -*- coding: utf-8 -*-
# MolMod is a collection of molecular modelling tools for python.
# Copyright (C) 2007 - 2019 Toon Verstraelen <Toon.Verstraelen@UGent.be>, Center
# for Molecular Modeling (CMM), Ghent University, Ghent, Belgium; all rights
# reserved unless otherwise stated.
#
# This file is part of MolMod.
#
#... | molmod/molmod | molmod/io/__init__.py | Python | gpl-3.0 | 1,923 | [
"CP2K",
"CPMD",
"CRYSTAL",
"GAMESS",
"Gromacs",
"LAMMPS"
] | 1abe0bac391c9e0f545955e051cffe38b6d847a0c48fd723d5ee1dbbb09ee772 |
from Functions import Normal, FunctionsError
import numpy as np
import pylab as pl
def test_normal():
xarr = np.arange(-25, 25, 0.1)
arr = np.indices([50, 50]) - 25
d3arr = np.indices([50, 50, 50]) - 25
# create a 1-D gaussian
g1d = Normal(xarr, 10, 5, 15)
pl.figure(figsize=(10, 10))
pl.... | crawfordsm/pyspectrograph | PySpectrograph/unit_tests/ut_Functions.py | Python | bsd-3-clause | 1,203 | [
"Gaussian"
] | 39898d105cda397a7c00f2a82502bab5e1f400bc07933cdce77ef2bf30e82515 |
#
#@BEGIN LICENSE
#
# PSI4: an ab initio quantum chemistry software package
#
# 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 2 of the License, or
# (at your option) any later ver... | spring01/libPSI | lib/python/qcdb/libmintsmolecule.py | Python | gpl-2.0 | 96,230 | [
"Elk",
"Psi4"
] | 6e11a98bffce2afe8868c3577ddaf08eea9c46d6cd416611ad39ebc276881f88 |
# coding: utf-8
from __future__ import division, unicode_literals
"""
This module defines classes for point defects
"""
import os
import abc
import json
from bisect import bisect_left
from pymatgen.core.periodic_table import Specie, Element
from pymatgen.core.sites import PeriodicSite
from pymatgen.symmetry.analyze... | yanikou19/pymatgen | pymatgen/analysis/defects/point_defects.py | Python | mit | 52,397 | [
"GULP",
"pymatgen"
] | 9af831f3565a823e8f230b85db251c763ac860ee5c3abf8cf25f31f2227f7aad |
from setuptools import setup, find_packages
setup(
name = "zpyrpc",
version = "0.1",
packages = find_packages(),
install_requires = ['tornado','pyzmq'],
author = "Brian Granger",
author_email = "ellisonbg@gmail.com",
description = "Zippy fast and simple RPC based on ZeroMQ and Python",
... | ellisonbg/zpyrpc | setup.py | Python | bsd-3-clause | 437 | [
"Brian"
] | 1897cb6cdf8587041ab6dbfa0813301116205eb8380a55b7bd8ea87381963dd4 |
import requests
import time
from bs4 import BeautifulSoup
def parse_source(html, encoding='utf-8'):
parsed = BeautifulSoup(html, from_encoding=encoding)
return parsed
def get_price(item, sizzle):
resp = requests.get(item[1], timeout=3)
resp.raise_for_status()
parsed = parse_source(resp.content, ... | DryTuna/lowr | url_scraper.py | Python | mit | 2,062 | [
"Galaxy"
] | 6806f38ce507d49453cd1f84e62e69f03eb4017387c9127941989bc568d17a35 |
#!/usr/bin/env python
##############################################################################################
#
#
# CMIP6_hybrid_regrid_emissions_N96e.py
#
#
# Requirements:
# Iris 1.10, time, cf_units, numpy
#
#
# This Python script has been written by N.L. Abraham as part of the UKCA Tutorials:
# http://... | acsis-project/emissions | emissions/python/CMIP6_hybrid/CMIP6_hybrid_regrid_nC5H12_emissions_n96e_greg.py | Python | gpl-3.0 | 18,843 | [
"NetCDF"
] | 53b2ddcdbffad1acac2694aaff3ac4ff12a062c54785db67443c6d9b49414916 |
#!/usr/bin/env python
# https://github.com/svenkreiss/PyROOTUtils/blob/master/PyROOTUtils/Graph.py
__author__ = "Kyle Cranmer <kyle.cranmer@nyu.edu"
__version__ = "0.1"
'''
This is a research work in progress.
Define model mu_s*Gaus(x|alpha,sigma)+mu_b*flat(x)
Generate {x} for several {alpha}
Calculate power (expec... | cranmer/parametrized-learning | GausSigOnExpBkg.py | Python | bsd-2-clause | 17,679 | [
"Gaussian"
] | f671a75644e1e54126522f8a50f1acfe94ef639527277ae332b52383bb36f3fa |
import numpy as np
import copy
import warnings
from scipy.fftpack import fftshift,fft2
from scipy.ndimage.measurements import center_of_mass
import matplotlib.pyplot as plt; plt.ioff()
import matplotlib.cm as cm
from matplotlib.colors import SymLogNorm
from astropy.cosmology import Planck15
from .class_utils import *
f... | jspilker/visilens | visilens/plot_images.py | Python | mit | 13,902 | [
"Gaussian"
] | 2f2ce6c7686f36f03857c7713c3b9cbc10591235d9e78d6577fc7f253d4d6c28 |
import re
from typing import List, Union, Optional
from functools import lru_cache
from xml.etree import ElementTree as ET # type: ignore
from xmlschema.validators import ( # type: ignore
XsdAttribute,
XsdAtomicBuiltin,
XsdAtomicRestriction,
XsdComplexType,
XsdElement,
XsdGroup,
XsdSimpleT... | SymbiFlow/uxsdcxx | uxsdcxx/schema.py | Python | apache-2.0 | 10,772 | [
"VisIt"
] | f530783ef1a59f52e08225114942d793b58bca850677cfced0260033c0b9da46 |
#!/usr/bin/env python
"""
Created on 2015-09-26T12:13:49
"""
from __future__ import division, print_function
import sys
import argparse
import re
import time
try:
import numpy as np
except ImportError:
print('You need numpy installed')
sys.exit(1)
import pandas as pd
from splinter.browser import Browser
i... | mattgiguere/doglodge | code/splinter_scrape_ta_hotels.py | Python | mit | 13,661 | [
"VisIt"
] | b7048dea34c54fd218da7b177dce9299502e5c9fefaac9d375db2af5e87e7ffe |
#################################################################
# Class DirectoryListing
# Author: A.T.
# Added 02.03.2015
#################################################################
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
__RCSID__ = "$Id$"
... | yujikato/DIRAC | src/DIRAC/DataManagementSystem/Client/DirectoryListing.py | Python | gpl-3.0 | 6,662 | [
"DIRAC"
] | 214518557da0855056aa43e50e6f48da75b23b3c3a553572ba540ba6c1b6c088 |
# Copyright 2014 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
from recipe_engine.types import freeze
DEPS = [
'adb',
'depot_tools/bot_update',
'chromium',
'chromium_android',
'chromium_tests',
... | eunchong/build | scripts/slave/recipes/android/perf.py | Python | bsd-3-clause | 10,066 | [
"Galaxy"
] | 8f797d9722ae8b54bcfd6a6df482b154d0be00761e12ace027df228aa4e1e0f5 |
import logging
import numpy as np
from openmmtools.integrators import PeriodicNonequilibriumIntegrator
from openmmtools.utils import get_fastest_platform
from pkg_resources import resource_filename
from simtk import unit
from simtk import openmm
import os
import pathlib
import time
from perses.app.relative_point_mutati... | choderalab/perses | examples/barnase-barstar-neq-switching/run_example.py | Python | mit | 7,774 | [
"OpenMM"
] | 8138a6f22efe77f6308103d875dce8c1f3cecc350e2f5d45910daded042d7e47 |
import itertools
import logging
import re
import time
import urllib
from collections import defaultdict
from datetime import datetime, timedelta
from decimal import Decimal
from typing import Any, Callable, Dict, List, \
Optional, Set, Tuple, Type, Union, cast
import pytz
from django.conf import settings
from dj... | rishig/zulip | analytics/views.py | Python | apache-2.0 | 51,902 | [
"VisIt"
] | f9e5ad30dd24caf2b9535ea9769abdbad127fefe808e104acb665a14223082fc |
title = 'Inverter'
#Put SPICE device models used in the simulations here.
models="""
.model 2N3906 PNP(Is=455.9E-18 Xti=3 Eg=1.11 Vaf=33.6 Bf=204 Ise=7.558f
+ Ne=1.536 Ikf=.3287 Nk=.9957 Xtb=1.5 Var=100 Br=3.72
+ Isc=529.3E-18 Nc=15.51 Ikr=11.1 Rc=.8508 Cjc=10.13p Mjc=.6993
+ ... | Ttl/evolutionary-circuits | examples/inverter.py | Python | mit | 5,157 | [
"xTB"
] | e54ff0cfe4036edd9a435fc5ecd48efde4c2c6fd13841bafbeda00e1ed1c0d6e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# This file is part of the SPORCO package. Details of the copyright
# and user license can be found in the 'LICENSE.txt' file distributed
# with the package.
"""
Colour ℓ2-TV Denoising
======================
This example demonstrates the use of class :class:`.tvl2.TVL2Den... | bwohlberg/sporco | examples/scripts/tv/tvl2den_clr.py | Python | bsd-3-clause | 2,775 | [
"Gaussian"
] | 9309d4372bc78d92c9c7640014d1ee1910ed3bf210353ed467f33efa2bf95ac5 |
'''<b>Example2a</b> - An example of an image processing function.
<hr>
This example deconvolves the image with a Gaussian. Given a point spread
function that is an accurate representation of how optics aberations map
a point to pixels in an image, the deconvolution with that point spread
function uses the information i... | LeeKamentsky/CellProfiler | tutorial/example2a_imageprocessing.py | Python | gpl-2.0 | 7,915 | [
"Gaussian"
] | 59ef63b0d54b745ee4cabf3f4ad4b877ed6bf6fa83e54811f535fb6a4ef43997 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | psci2195/espresso-ffans | testsuite/python/lb.py | Python | gpl-3.0 | 16,968 | [
"ESPResSo"
] | 3afd32407c9e4440624904dce5a56cb213cc0d9f1a3b19c0c83402ad1a4cea08 |
# TODO: Add the map (select subsection of nasa map based on longitude & lattitude), color & scale points, fetch from web using urlib (http://webservices.rm.ingv.it/fdsnws/event/1/query?starttime=2015-10-04+00%3A00%3A00&endtime=2015-10-11+23%3A59%3A59&minmag=2&maxmag=10&minlat=35&maxlat=48&minlon=6&maxlon=19&minversion=... | RDeckers/ScientificVisualization-1TD389 | Assignments/Project/main.py | Python | gpl-3.0 | 4,875 | [
"VTK"
] | cca93d287fdb2bd8af7f6d2798f704fb120852c3c6647186aec6be1052309de3 |
import numpy as np
from time import time, ctime
from datetime import timedelta
from ase.lattice import bulk
from ase.units import Hartree
from gpaw import GPAW, FermiDirac
from gpaw.response.gw import GW
from gpaw.mpi import serial_comm, world, rank
from gpaw.wavefunctions.pw import PW
starttime = time()
a = 5.431
at... | robwarm/gpaw-symm | gpaw/test/gw_planewave.py | Python | gpl-3.0 | 1,176 | [
"ASE",
"GPAW"
] | 83c066d75430de0b7b924108e3ecd47c9e96a9841a62cd9c3d278c2f29f5c0b3 |
# Copyright (c) 2013, Web Notes Technologies Pvt. Ltd. and Contributors
# License: GNU General Public License v3. See license.txt
from __future__ import unicode_literals
import frappe
from frappe.utils import add_days, getdate, cint
from frappe import throw, _
from erpnext.utilities.transaction_base import Transacti... | suyashphadtare/test | erpnext/support/doctype/maintenance_schedule/maintenance_schedule.py | Python | agpl-3.0 | 9,794 | [
"VisIt"
] | 68d2257749e27407841a097382989be66b1a543f1f781b095fb6696117e79376 |
"""
Robots in Grid: Problem 8.2 from CTCI
A robot is in the upper left corner of a grid with r rows and c cols
The robot can move right or down. It is trying to get to the lower right corner
Some coordinates are off-limits. These are denoted as 0, otherwise 1.
Design an algorithm to find a path from top left to botto... | jackchi/interview-prep | dynamic programming/robot_in_grid.py | Python | mit | 1,493 | [
"VisIt"
] | 1abecbd79d7dc2f648e9b5641cf61b98ff684bd74da15b8bf7a29148a5e09c2d |
# Copyright (c) 2012-2014, GPy authors (see AUTHORS.txt).
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
from .gp import GP
from .parameterization.param import Param
from ..inference.latent_function_inference import var_dtc
from .. import likelihoods
from GPy.core.parameterization.varia... | esiivola/GPYgradients | GPy/core/sparse_gp.py | Python | bsd-3-clause | 6,354 | [
"Gaussian"
] | d1dd2c926cf969f795537bc60083eb78714b7ef491e218ce3794311f7a27c8e6 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2002 Gary Shao
# Copyright (C) 2007 Brian G. Matherly
# Copyright (C) 2009 Benny Malengier
# Copyright (C) 2009 Gary Burton
#
# This program is free software; you can redistribute i... | pmghalvorsen/gramps_branch | gramps/gen/plug/docgen/tablestyle.py | Python | gpl-2.0 | 7,029 | [
"Brian"
] | 4d5cb2ac6d89503242d280838886ded72d2794a5dd1574d6c2a851aba08d93d8 |
import numpy as np
from ase.units import Hartree
from gpaw.transport.tools import aa1d, interpolate_array, \
collect_atomic_matrices, distribute_atomic_matrices
# ---------------------------------------
# side | | side
# o o| o o o o o o o... | qsnake/gpaw | gpaw/transport/surrounding.py | Python | gpl-3.0 | 12,584 | [
"ASE",
"GPAW"
] | b5d1c2dbc0ea773d9af1cbe05292bcc23c69e0bb40372d53f28a7a339be7a508 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
This software is part of Frog, a chemo informatics class able to build
3D coordinates for small compounds
Copyright (C) 2006-2007 P. Tuffery, B.O. Villoutreix, Th. Bohme Leite, D. Gomes, M. Miteva, J. Chomilier
Frog2 (C) 2009-2010 by P. Tuffery, M. Miteva, ... | tuffery/Frog2 | www_iMolecule.py | Python | gpl-3.0 | 32,527 | [
"PyMOL"
] | 5b649717f24b2db11002b4fff50ceeab4692f2873aebb8f3238e0a992ef0bb45 |
# 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 | tests/test_optics.py | Python | gpl-3.0 | 19,715 | [
"Galaxy"
] | 9d7172bcb00917bd49fc69865544e847afefc70aa72b167b730feacbeebca440 |
#!/usr/bin/env python
#
# @file ValidatorCodeFile.py
# @brief class for generating code file for the given class
# @author Frank Bergmann
# @author Sarah Keating
#
# <!--------------------------------------------------------------------------
#
# Copyright (c) 2013-2018 by the California Institute of Technology
... | sbmlteam/deviser | deviser/code_files/ValidatorCodeFile.py | Python | lgpl-2.1 | 17,946 | [
"VisIt"
] | 8649e079954a810600df188baeb86964f36c51900fb6f686ba620cd57f94e8c7 |
"""
Integration tests for singletask vector feature models.
"""
import os
import deepchem as dc
import numpy as np
from sklearn.ensemble import RandomForestRegressor
def test_singletask_sklearn_rf_ECFP_regression_API():
"""Test of singletask RF ECFP regression API."""
X = np.random.rand(100, 5)
y = np.random.ra... | lilleswing/deepchem | deepchem/models/tests/test_api.py | Python | mit | 5,338 | [
"RDKit"
] | 3a2556ba29c2d1566b96ec01b595d1c85dbbd31f8edb55fa592e32023b365d2c |
""" This is a test of using WMSClient and several other functions in WMS
In order to run this test we need the following DBs installed:
- JobDB
- JobLoggingDB
- TaskQueueDB
- SandboxMetadataDB
And the following services should also be on:
- OptimizationMind
- JobManager
- SandboxSt... | ic-hep/DIRAC | tests/Integration/WorkloadManagementSystem/Test_Client_WMS.py | Python | gpl-3.0 | 24,095 | [
"DIRAC"
] | 40a44591180a8adc3500f1a719ab70495029df7da2b55d595d80734d03b6d732 |
# The MIT License (MIT)
#
# Copyright (c) 2015 Simon Marchi <simon.marchi@polymtl.ca>
#
# 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 r... | simark/pygdbmi | pygdbmi/cli/pprint.py | Python | mit | 2,376 | [
"VisIt"
] | 06f3d1c5c28f9f579a19bf905e0a162cee061c6b8de04d60b23a4d58f19acd4a |
from typing import Any, Dict, List, Optional, Tuple, Union
import json
import logging
import os
import yaml
import re
from ..config import ACResource, Config
from ..utils import parse_yaml, parse_json, dump_json, parse_bool
from .dependency import DependencyManager, IngressClassesDependency, SecretDependency, Servic... | datawire/ambassador | python/ambassador/fetch/fetcher.py | Python | apache-2.0 | 19,357 | [
"VisIt"
] | 5c55490a203781cc719da467f7b2d247cc15cdf6725d089b7172637ed13814a0 |
#!/usr/bin/env python
# -*- coding:utf-8 mode:python; tab-width:4; indent-tabs-mode:nil; py-indent-offset:4 -*-
##
import os
import string
import sys
from structures import BasisSetEntry
class Converter(object):
def __init__(self):
self._prepare_element_data()
def _prepare_element_data(self):
... | mattbernst/ebsel | src/conversion.py | Python | mit | 20,448 | [
"GAMESS",
"Gaussian",
"NWChem",
"Psi4"
] | 4e66cd80b91adda7b3b670af65d1bfd58fa52ee0cb3e5a875e07387b8b2b2ec6 |
from __future__ import print_function
import logging
import string
import os
from math import log as mlog2
from collections import Counter, defaultdict
from seqcluster.libs.read import map_to_precursors, precursor_sequence, map_to_precursor_biopython
from seqcluster.libs.utils import safe_dirs
from progressbar import... | lpantano/seqcluster | seqcluster/libs/report.py | Python | mit | 4,778 | [
"Biopython"
] | 4099db374d98bc1bf0a58ea85e0911b0339c3693956001c400f500a061d56113 |
# ----------------------------------------------------------------------------
# cocos2d
# Copyright (c) 2008-2011 Daniel Moisset, Ricardo Quesada, Rayentray Tappa,
# Lucio Torre
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the... | eevee/cocos2d-mirror | cocos/cocosnode.py | Python | bsd-3-clause | 28,041 | [
"VisIt"
] | 2bfdb1117a9a923ff89749633cfe8f323c3c778cc006a962159e4b3117e8ecee |
# Copyright 2016 Netherlands eScience Center
#
# 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 t... | 3D-e-Chem/python-modified-tanimoto | tests/test_db.py | Python | apache-2.0 | 12,244 | [
"CRYSTAL",
"RDKit"
] | 9bb50b45ad6e63597d01e4fd953983be7eb393abb467afe92848b7a7509531fc |
"""
This source is very simple: if there is a -OH, the compounds are inactive. Else, they are active. So the substructures
encoding this -OH should have a big influence in properly predicting the molecules in this specific source. If I check
the picture, these are the substructures that most change weight and could enc... | sdvillal/manysources | manysources/analyses/acridones_boumendjel.py | Python | bsd-3-clause | 18,663 | [
"RDKit"
] | 18a9382f6f85407252dabf8338893076abc01064824300bfe506ecef6d9acdf5 |
# -*- coding: utf-8 -*-
"""
Created on Mon Nov 19 16:39:13 2018
A much faster PRF fitter, with the caveat that the psf model is hardcoded.
psffit.py can fit an arbitrary PSF model to an image. The cost of this flexibility
is that it must perform numerical intergration to calculate the flux in each pixel.
This is slo... | barentsen/dave | diffimg/fastpsffit.py | Python | mit | 4,310 | [
"Gaussian"
] | 3a07a4800307848c68aff163f7a47516e73638dcc861b4a6d060e3d7d744ddcd |
"""
Class for spherical harmonic coefficients of the gravitational potential.
"""
import numpy as _np
import matplotlib as _mpl
import matplotlib.pyplot as _plt
from mpl_toolkits.axes_grid1 import make_axes_locatable as _make_axes_locatable
import copy as _copy
import warnings as _warnings
import xarray as _xr
from... | MarkWieczorek/SHTOOLS | pyshtools/shclasses/shgravcoeffs.py | Python | bsd-3-clause | 169,176 | [
"COLUMBUS",
"NetCDF"
] | fee240e77aae202b501b07be7beb5c5b23e1b3d16b4f2b7c753a9c22f2e4d5c5 |
#!/usr/bin/env python3
from setuptools import setup
with open('README.rst') as fh:
long_description = fh.read()
setup(
name='tacl',
version='5.0.0',
description='Text analyser for corpus linguistics',
long_description=long_description,
author='Jamie Norrish',
author_email='jamie@artefact... | ajenhl/tacl | setup.py | Python | gpl-3.0 | 1,237 | [
"Biopython"
] | faf5a9dab643577bf060ad9e4cafad5d7c57b9e38bcfb5161df503fd3b33ec18 |
import numpy as np
from .layers import SparseGP_MPI
from GPy.core import Parameterized
from GPy.core import SparseGP
from GPy import likelihoods
from GPy import kern
from GPy.core.parameterization.variational import NormalPosterior, VariationalPosterior
from GPy.util.initialization import initialize_latent
from deep... | zhenwendai/DeepGP | deepgp/layers/mrd.py | Python | bsd-3-clause | 12,468 | [
"Gaussian"
] | 763d68eb0a84e2b7da58d6e968598d9611a4e531eab943fad26f614f469421b3 |
# $HeadURL$
"""
NovaImage
The NovaImage provides the functionality required to use
a OpenStack cloud infrastructure, with NovaAPI DIRAC driver
Authentication is provided by user/password attributes
"""
# File : NovaImage.py
# Author : Victor Mendez ( vmendez.tic@gmail.com )
# DIRAC
from DIRAC import gLo... | myco/VMDIRAC | WorkloadManagementSystem/Client/NovaImage.py | Python | gpl-3.0 | 6,716 | [
"DIRAC"
] | e6b8139b4bb8a6f0fa5119608eee41032dc80ae532a1805c081a1cc5ee0253e9 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
if __name__ == '__main__':
import nose
nose.main()
import unittest
import os.path
import string
import random
from io import StringIO
from nose.tools import *
from src.preprocessing import split, remove_stops
from src.corpora import GeneralCorpus
# datapath is ... | cscorley/doc2vec-feature-location | tests/test_preprocessing.py | Python | bsd-3-clause | 8,669 | [
"ASE"
] | 529faa63a27b849a4cb82da66beeab897d3bf7a85eff30dc9347c6c5bc1c9259 |
"""
This code reads in an input files containing the wells,
bimolecular products, transition states and
barrierless reactions and creates a PES plot
"""
from __future__ import print_function, division
import os
import sys
import matplotlib
matplotlib.use('TkAgg')
from matplotlib import pylab as plt
import matplotlib.im... | rubenvdvijver/PESViewer | pesviewer/pesviewer.py | Python | mit | 43,740 | [
"Pybel",
"RDKit"
] | cfe470b764db53bedb3fac8fbc9d8c2d75ff92354ca5407a5a8eeb40ad3f0f66 |
from __future__ import (absolute_import, division, print_function,
unicode_literals)
from .scale import scale
from copy import deepcopy
CRAYON_COLORS = {
"red": "#ed0a3f",
"maroon": "#c32148",
"scarlet": "#fd0e35",
"brick red": "#c62d42",
"english vermilion": "#cc474b",
... | yhat/ggplot | ggplot/scales/scale_color_crayon.py | Python | bsd-2-clause | 10,469 | [
"BLAST"
] | c5f79524a3f88502773aca3c8c8d61819a944b235adc3c158053c24179026b93 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Support for reading XCrysDen files.
"""
from pymatgen.core.periodic_table import Element
__author__ = "Matteo Giantomassi"
__copyright__ = "Copyright 2013, The Materials Project"
__version__ = "0.1"
__mai... | gmatteo/pymatgen | pymatgen/io/xcrysden.py | Python | mit | 3,842 | [
"CRYSTAL",
"pymatgen"
] | b58e822cdd0e1552f01f60a20a9ebb7f872e8bde41704b4282b1a6021cc8a5f2 |
import numpy as np
def S(i,j,A,B,a,b):
''' Recursive definition of Hermite Gaussian coefficients.
Returns a float.
a: orbital exponent on Gaussian 'a' (e.g. alpha in the text)
b: orbital exponent on Gaussian 'b' (e.g. beta in the text)
i,j: orbital angular momentum number on Gaussia... | fhqgfss/MoHa | moha/system/integral/overlap.py | Python | mit | 2,434 | [
"Gaussian"
] | dfd181b9a231712b699ee63266e957cb70acc8f623377516242210d86dd504b7 |
from pygr.seqdb import *
db=BlastDB('sp') # OPEN SWISSPROT BLAST DB
s=Sequence(str(db['CYGB_HUMAN'][40:-40]),'boo')
m=db.blast(s) # DO BLAST SEARCH
myg=db['MYG_CHICK']
for i in m[s][myg]:
print repr(i.srcPath),repr(i.destPath),i.blast_score,i.percent_id
| ctb/pygr | tests/oldtests/old/blasttest.py | Python | bsd-3-clause | 260 | [
"BLAST"
] | e9f0f35c5dc0ea1261ed1cb17d30fc4391799d95c569a30ecc2dfd5accf6502d |
##### NEED TO FIX DIVISION OPERATOR!!!!!
from __future__ import division
#http://docs.python.org/release/2.2.3/whatsnew/node7.html
#The most controversial change in Python 2.2 heralds the start of an effort to fix an old design flaw that's been in Python from the beginning. Currently Python's division operator, /,... | andreasbastian/pyControl | pyControl.py | Python | gpl-3.0 | 5,421 | [
"BLAST"
] | 5656cb1a063f46f80807dff1f9e6a5364aa1ce18843e9e6185eb4c103047ff22 |
import random
import pytest
import numpy as np
import moldesign as mdt
from moldesign import units as u
from . import helpers
registered_types = {}
def typedfixture(*types, **kwargs):
"""This is a decorator that lets us associate fixtures with one or more arbitrary types.
We'll later use this type to dete... | tkzeng/molecular-design-toolkit | moldesign/_tests/test_mm.py | Python | apache-2.0 | 4,019 | [
"OpenMM"
] | 27eb2b38219011bb43cb924cc22e11755d1efe1804875e1032bbaac6f09dbd24 |
try:
from django.urls import reverse
except ImportError:
from django.core.urlresolvers import reverse
from tastypie import authorization
from tastypie.authentication import MultiAuthentication
from crits.events.event import Event
from crits.events.handlers import add_new_event
from crits.core.api import CRITsA... | Magicked/crits | crits/events/api.py | Python | mit | 4,204 | [
"Amber"
] | 5da47ef254bdd8d7c36a8de627e4aca52646e200be2467b716b8a189e6cebd1a |
import pathlib
import shutil
import tempfile
import traceback
from typing import Union, List, Dict
from flask_login import current_user
from wand.image import Image
import cairosvg
import plotly.io as pio
import os
import msgpack
import dash_bootstrap_components as dbc
import dash_html_components as html
import pandas... | BiRG/Omics-Dashboard | omics/omics_dashboard/dashboards/dashboard_model.py | Python | mit | 13,327 | [
"ORCA"
] | 1d38df64d91e0d130d1d41857fe5bd8be2ba3489877386addf962d9b7c2da714 |
from __future__ import absolute_import
from __future__ import print_function
from . import base
from .. import nodes
class Importer(base.NodeTransformer):
def __init__(self, callback):
self.callback = callback
def visit_Import(self, node):
if isinstance(node.uri, nodes.StringNode):
... | colossalbit/cssypy | cssypy/visitors/importers.py | Python | bsd-3-clause | 895 | [
"VisIt"
] | 9a027c853ea383691eddadef2d7248cf40f11f9bc31015078e5c24e5969c6439 |
"""Dimer: Diffusion along rows"""
from __future__ import print_function
import numpy as np
from math import sqrt
from ase import Atoms, Atom
from ase.io import Trajectory
from ase.constraints import FixAtoms
from ase.optimize import QuasiNewton
from ase.calculators.emt import EMT
from ase.dimer import DimerControl, M... | misdoro/python-ase | doc/tutorials/selfdiffusion/dimer_along.py | Python | gpl-2.0 | 2,116 | [
"ASE"
] | c0ccc800466a39f7384e2598a5955e934826ea356ac96ba9129a190528d5b02e |
import datetime
import copy
import util
import re
import logging
from fullpattern import FullPattern
from patternatom import PatternAtom
from grouptemplate import GroupTemplate
term_names = ['Michaelmas','Lent','Easter']
multispace_re = re.compile(r" +")
# XXX within term
class Year:
def __init__(self,starts):
... | ieb/timetables | python/lib/year.py | Python | agpl-3.0 | 3,914 | [
"BLAST"
] | 08299b1916a5e02d3b6add85f62b9244556c72f06177c425bf8bfd7399516429 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors: Kyle A Beauchamp
#
# MDTraj is... | casawa/mdtraj | mdtraj/geometry/distance.py | Python | lgpl-2.1 | 8,619 | [
"MDTraj"
] | c2070f8525a18d8ffa93c4633b83e83701da7b0b6d0506b63be286ad3a3e1b38 |
#got the following from http://stackoverflow.com/questions/434287/what-is-the-most-pythonic-way-to-iterate-over-a-list-in-chunks
from itertools import izip_longest
from octree_node import OctreeNode
def grouper(iterable, n, fillvalue=None):
nathan_args = [iter(iterable)] * n
return izip_longest(*nathan_args, f... | dayo7116/PointMan-Renderer | server/read_octopus.py | Python | gpl-3.0 | 2,482 | [
"Octopus"
] | d70419e473280a41754447e36b9f9ed103e4f0a0899a72a7aba31345ab2801cd |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
#
# 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; ... | pmghalvorsen/gramps_branch | gramps/plugins/quickview/all_events.py | Python | gpl-2.0 | 4,290 | [
"Brian"
] | 121be2b777956cf332cf1c0a805ef4dbf35ae595d5887d2f110f0c33f5c381e8 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
## Contributors for this file:
## - Yann Le Boulanger <asterix@lagaule.org>
## - Nikos Kouremenos <kourem@gmail.com>
##
## Copyright (C) 2003-2004 Yann Le Boulanger <asterix@lagaule.org>
## Vincent Hanquez <tab@snarc.org>
## Copyright (C) 2005 Yann L... | pacoqueen/bbinn | gajim-0.9.1/src/common/migrate_logs_to_dot9_db.py | Python | gpl-2.0 | 10,162 | [
"VisIt"
] | 21c706701e108929621f4ba8041f5d243f1e7c501f42d7142f43a732839f5e5f |
#
# Copyright (C) 2013-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | psci2195/espresso-ffans | samples/wang_landau_reaction_ensemble.py | Python | gpl-3.0 | 4,506 | [
"ESPResSo"
] | 666037eac82151a83a6eae9de9d895db0aeba82ea955239fb6859d9bf9b32dcd |
import numpy as np
import matplotlib.pyplot as plt
from scipy import ndimage
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.image as mplimg
from matplotlib.colors import LogNorm
from numpy import fft
def get_photon_positions(image, cdf, cdf_indexes, nphot=1):
"""
Uses an inverse CDF lookup to find ... | davidwhogg/DiffractionMicroscopy | code/toyproblems/generate_images.py | Python | mit | 14,588 | [
"Gaussian"
] | 4d29a10084d8083d97c41a8ff495c3d658fc70072ef968157c75cb8e131b2b76 |
from __future__ import print_function
# Copyright (C) 2010, Jesper Friis
# (see accompanying license files for details).
"""
A module for ASE for simple creation of crystalline structures from
knowledge of the space group.
"""
import numpy as np
import ase
from ase.atoms import string2symbols
from .spacegroup impor... | suttond/MODOI | ase/lattice/spacegroup/crystal.py | Python | lgpl-3.0 | 6,084 | [
"ASE",
"CRYSTAL"
] | 040ebbdd23434e79af9046a7db647ad29232c872d7f201db0938f6f4dc03250c |
# Copyright 2020 Tensorforce Team. 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 applicable la... | reinforceio/tensorforce | tensorforce/agents/dpg.py | Python | apache-2.0 | 13,083 | [
"Gaussian"
] | 148f21777b533f8e78dcf52abca62d5b3d6ae8405ad7b56632eddaf58b5a9bb7 |
import unittest
import pysal.lib
import numpy as np
from pysal.model.spreg import probit as PB
from pysal.lib.common import RTOL
class TestBaseProbit(unittest.TestCase):
def setUp(self):
db=pysal.lib.io.open(pysal.lib.examples.get_path("columbus.dbf"),"r")
y = np.array(db.by_col("CRIME"))
y... | lixun910/pysal | pysal/model/spreg/tests/test_probit.py | Python | bsd-3-clause | 5,218 | [
"COLUMBUS"
] | bc6240554cc1639ed83d31061d94790eb2f4d2a6fcabb904d06a2104ed84cb14 |
# Copyright Yair Benita Y.Benita@pharm.uu.nl
# Biopython (http://biopython.org) license applies
"""Simple protein analysis.
Example::
X = ProteinAnalysis("MAEGEITTFTALTEKFNLPPGNYKKPKLLYCSNGGHFLRILPDGTVDGTRDRSDQHIQLQLSAESVGEVYIKSTETGQYLAMDTSGLLYGSQTPSEECLFLERLEENHYNTYTSKKHAEKNWFVGLKKNGSCKRGPRTHYGQKAILFLPLPV")
... | zjuchenyuan/BioWeb | Lib/Bio/SeqUtils/ProtParam.py | Python | mit | 10,925 | [
"Biopython"
] | 33c966f0e581f9a6cd02d01e255e0c4cafb65b201721db0900a0390c9ae04bb3 |
# encoding: utf8
from __future__ import unicode_literals
BASE_EXCEPTIONS = [
"0-day",
"0-days",
"1000Base-T",
"100Base-T",
"100Base-T4",
"100Base-TX",
"10BASE-F",
"10Base-T",
"1,1-diméthylhydrazine",
"11-septembre",
"11-Septembre",
"120-cellules",
"1,2,3-tris-nitrooxy-propane",
"1,2-diazine",
"1,2-dichloropropane",
... | banglakit/spaCy | spacy/fr/_tokenizer_exceptions_list.py | Python | mit | 513,597 | [
"FLEUR",
"Jaguar"
] | bdac9c4a4e235a45b07d1f54272e19d43cf5b9afb903062c4bc87a5e0c87e2fc |
# Copyright (c) 2012 OpenStack Foundation
# All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless ... | eayunstack/nova | nova/tests/compute/test_resource_tracker.py | Python | apache-2.0 | 61,239 | [
"exciting"
] | 1eb701970b4ad65a7aefbdb6b2f4f2ac5029cc76579c0af8e22c2699c76b91a9 |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2009, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | zenoss/ZenPacks.community.VMwareESXMonitor | ZenPacks/community/VMwareESXMonitor/migrate/ChangeESXPluginName.py | Python | gpl-2.0 | 1,518 | [
"VisIt"
] | bba759929b33bfc34378fcd78f465e10124177315fcd36f18faa517741b71fc1 |
#!/usr/bin/env python
##
## @file printModel.py
## @brief Prints some information about the top-level model
## @author Sarah Keating
## @author Ben Bornstein
## @author Michael Hucka
##
## This file is part of libSBML. Please visit http://sbml.org for more
## information about SBML, and the latest version of... | dilawar/moose-full | dependencies/libsbml-5.9.0/examples/python/printSBML.py | Python | gpl-2.0 | 2,284 | [
"VisIt"
] | 1972f3ed8856a05cfacba16bea1d0b19412c23d52aca0aa2fc8b33dc5c3e0173 |
# Copyright (c) 2006-2015 LOGILAB S.A. (Paris, FRANCE) <contact@logilab.fr>
# Copyright (c) 2011-2014 Google, Inc.
# Copyright (c) 2012 FELD Boris <lothiraldan@gmail.com>
# Copyright (c) 2014-2016 Claudiu Popa <pcmanticore@gmail.com>
# Copyright (c) 2014-2015 Michal Nowikowski <godfryd@gmail.com>
# Copyright (c) 2015 M... | arju88nair/projectCulminate | venv/lib/python3.5/site-packages/pylint/lint.py | Python | apache-2.0 | 56,715 | [
"VisIt"
] | 1f714dfdb7d4061e844d2fa8375e8a1ee6abf5a21b3156f938a3c50f81a8170f |
import os
import sys
msg = "\nThe GDK rendering GTK matplotlib backend is missing or not installed properly.\n"
msg += "See http://matplotlib.org/faq/usage_faq.html#what-is-a-backend.\n"
msg += "Is the PYTHONPATH environment variable set correctly?\n"
msg += "Please verify your installation by running on the command l... | askhl/ase | ase/test/dependency_backend_gdk.py | Python | gpl-2.0 | 1,583 | [
"ASE"
] | 3d048786215af161b556b41275db10c6d0802ef0fab7c5c7ad78f8fcc1d6802b |
from distutils.core import setup
setup(
name = 'gefes',
version = '0.0.1',
description = 'Genome Extraction From Environmental Sequencing',
long_description = open('README.txt').read(),
license = 'MIT',
url = 'http://github.com/limno/g... | inodb/gefes | setup.py | Python | mit | 638 | [
"Biopython"
] | 24b313af2aa368dec0291668e7f3a7c70ebac13432695e30eb194e75abffcaf2 |
#!/usr/bin/python
"""
UnitCell v2.0.0 Jeff W. Doak jeff.w.doak@gmail.com
Class to read in, store, and manipulate crystallographic unit cell data.
This class is used in a variety of other classes that manipulate VASP input and
output files to parse the unit cell associated with a VASP calculation.
"""
import os
imp... | jeffwdoak/UnitCell | UnitCell/unitcell.py | Python | mit | 47,850 | [
"CRYSTAL",
"GULP",
"LAMMPS",
"VASP"
] | 30113e9751ef9f3030f45e5ae279200a1a8800cc202446e0681a086b9b84d9db |
#
# comment_collector_visitor.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at you... | kperun/nestml | pynestml/visitors/comment_collector_visitor.py | Python | gpl-2.0 | 12,724 | [
"NEURON"
] | b1be49daa4e994981e40fd01eb0a0851bbcd3c23f2552d093641fde3b9eea377 |
import os
import sys
import time
import logging
import datetime
import numpy as np
from data import *
from time import clock
from parameters import *
from collections import defaultdict
spike_generators = {} # dict name_part : spikegenerator
spike_detectors = {} # dict name_part : spikedetector
multimeters = {} ... | research-team/NEUCOGAR | NEST/cube/dopamine/integrated/scripts/func.py | Python | gpl-2.0 | 9,657 | [
"NEURON"
] | 4f29d1c7f6e4475c9db98dabd92cdbe084f3e353eff2d6edb04ecac8a0683808 |
import os
import catmaid
from django.core.management.base import BaseCommand, CommandError
from django.db import connection, transaction
from catmaid.models import ClassInstance
from catmaid.control.skeleton import update_skeleton_id
class Command(BaseCommand):
help = 'Change the ID of a skeleton, optionally als... | catmaid/CATMAID | django/applications/catmaid/management/commands/catmaid_change_skeleton_id.py | Python | gpl-3.0 | 1,275 | [
"NEURON"
] | 5c6e165b7a4cae41bfd4a23422c68b8545f366f2eb22455597569ecfde5dc0ae |
import numpy as np
import pyscf.pbc
from pyscf.pbc import cc as pbccc
import pyscf.tools as tools
import pyscf.pbc.tools.pbc as tools
import ase.dft.kpoints
import pyscfdump
import shutil
def run_kccsd(mf):
cc = pbccc.KCCSD(mf)
cc.verbose = 7
cc.ccsd()
return cc
def run_krccsd(mf):
cc = pbccc.K... | hande-qmc/hande | test_suite/fciqmc/np4/Ne-complex-k311/integral_generation/Ne_molcryst_new.py | Python | lgpl-2.1 | 5,104 | [
"ASE",
"CRYSTAL",
"PySCF"
] | f904a8dfedea3d553b6a65a9653a40ddf2eacd70be6e8c1e84e423d3dc425ed8 |
# Copyright (c) 2015, Frappe Technologies Pvt. Ltd. and Contributors
# License: GNU General Public License v3. See license.txt
from __future__ import unicode_literals
import frappe
import json
import frappe.utils
from frappe.utils import cstr, flt, getdate, comma_and
from frappe import _
from frappe.model.mapper impor... | treejames/erpnext | erpnext/selling/doctype/sales_order/sales_order.py | Python | agpl-3.0 | 14,834 | [
"VisIt"
] | 0b13019d899c9183534ec4b100a652ca15c99d3cac2586e3ce90189cceec8a87 |
from __future__ import unicode_literals
import base64
import datetime
import hashlib
import json
import netrc
import os
import re
import socket
import sys
import time
import xml.etree.ElementTree
from ..compat import (
compat_cookiejar,
compat_http_client,
compat_urllib_error,
compat_urllib_parse_urlp... | Celthi/youtube-dl-GUI | youtube_dl/extractor/common.py | Python | mit | 41,110 | [
"VisIt"
] | d9780064f3155a51c38becc990d9f853a799aeb313f59eb52fbf1cae57ee7546 |
# Principal Component Analysis Code :
from numpy import mean,cov,double,cumsum,dot,linalg,array,rank,size,flipud
from pylab import *
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy as scp
import scipy.ndimage as ni
import scipy.io
import roslib; roslib.load_manifes... | tapomayukh/projects_in_python | sandbox_tapo/src/skin_related/AI_Surface_Recognition/src/k_NN_objects.py | Python | mit | 4,499 | [
"Mayavi"
] | 47882f6c95699fe38ffc3a6ac15cf6d82ad138b3e8cb25bd2afcc478522624f5 |
# -*- coding: utf-8 -*-
#
# event.py
# GSSHApy
#
# Created by Alan D Snow, 2017.
# BSD 3-Clause
from datetime import datetime, timedelta
import logging
import os
from pytz import utc
from RAPIDpy import RAPIDDataset
from ..grid import ERAtoGSSHA, GRIDtoGSSHA, HRRRtoGSSHA, NWMtoGSSHA
from ..util.context import tmp... | CI-WATER/gsshapy | gsshapy/modeling/event.py | Python | bsd-3-clause | 27,588 | [
"NetCDF"
] | 18d68e48da40c988aa1c9895022c7a3b7d2724b7dfeb1c260a218dcc4e26bc08 |
#
# Copyright 2016 The BigDL 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 ... | intel-analytics/BigDL | python/chronos/test/bigdl/chronos/data/utils/test_cycle_detection.py | Python | apache-2.0 | 1,089 | [
"ORCA"
] | c6a1d6cacf99813c0026bea4f2a9a4162558b5632148346cd30e7c67649bd7ea |
import nest
import pylab as plt
import numpy as np
"""
Reproduce result of the pairing experiment from Pfister-Gerstner (2006) with the triplet model.
"""
nest.Install("stdpmodule")
nest.set_verbosity("M_WARNING")
def generateSpikes(neuron, times):
"""Trigger spike to given neuron at specified times."""
dela... | zifeo/nest-stdpmodule | examples/PfisterGerstnerPairing_connection.py | Python | gpl-2.0 | 2,909 | [
"NEURON"
] | df5db5b5156d4cba38e3c654ca16809627445a0fc6e5274a99c44aae0a9d94f9 |
# -*- coding: utf-8 -*-
"""
Regression tests for the Test Client, especially the customized assertions.
"""
from __future__ import unicode_literals
import os
import itertools
from django.core.urlresolvers import reverse, NoReverseMatch
from django.template import TemplateSyntaxError, Context, engines
from django.test... | runekaagaard/django-contrib-locking | tests/test_client_regress/tests.py | Python | bsd-3-clause | 65,959 | [
"VisIt"
] | 9cb6106f0d5f2a3f2a9cebd3c35b65f39082995ed2ee98be456bc5cb3bf2ccaa |
#!/usr/bin/env python
'''
experiments on toy datasets
author: Ke Sun < sunk [dot] edu [at] gmail [dot] com >
suppored by University of Geneva
'''
from __future__ import print_function
import matplotlib.pyplot as plt
import numpy as np
import spacetime
import scipy.io
import sys
def teapot():
mat = scipy.io.load... | sunk/spacetime | toy.py | Python | bsd-2-clause | 1,817 | [
"Gaussian"
] | 03070f24d679d0ffbdafc49d12169dfc64ff57fe1304767feb1c2f4496afab0c |
"""
================================================
Segmenting the picture of greek coins in regions
================================================
This example uses :ref:`spectral_clustering` on a graph created from
voxel-to-voxel difference on an image to break this image into multiple
partly-homogeneous regions.... | sergeyf/scikit-learn | examples/cluster/plot_coin_segmentation.py | Python | bsd-3-clause | 4,226 | [
"Brian",
"Gaussian"
] | b8aaf70709cd75e59d5877389ef65495ff78a2b79968652b72e3be2cb1fa570c |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2015 Gerald Kunzmann <gerald@gkunzmann.de>
# Copyright (C) 2013-2016 Paul Franklin
#
# This program is free softw... | jralls/gramps | gramps/plugins/textreport/familygroup.py | Python | gpl-2.0 | 38,932 | [
"Brian"
] | 57d8999c90a4bc2a529bc820f1efdfad9ce1b817580776bf4936be324e44a2cc |
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2020 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier (bgoli@users.sourceforge.net)
Triple-J Group for Molecular Cell Physiology
Stellenbosch University, South Africa.
Permission to us... | bgoli/pysces | pysces/PyscesPlot2.py | Python | bsd-3-clause | 52,114 | [
"PySCeS"
] | 90c78f894b7f928b530eed8be6599d6f2ba4aed77c9ee6b3921540de12dde977 |
from tater.base.visitor import Visitor
class DataVisitor(Visitor):
def get_nodekey(self, obj):
return obj.__class__.__name__
def get_children(self, obj):
if isinstance(obj, dict):
for k, v in obj.items():
yield k
yield v
if isinstance(obj, ... | twneale/visitors | visitors/ext/visitors.py | Python | bsd-3-clause | 676 | [
"VisIt"
] | 35d5ed2b944e3648d59bf64034f7e4deaa16610f607d17606a749ad1062a6bea |
import datetime
from itertools import count
import os
curdir = os.path.join(os.getcwd(), os.path.dirname(__file__))
import threading
import time
import cherrypy
from cherrypy._cpcompat import next, ntob, quote, xrange
from cherrypy.lib import httputil
gif_bytes = ntob(
'GIF89a\x01\x00\x01\x00\x82\x00\x01\x99"\x1e... | heytcass/homeassistant-config | deps/cherrypy/test/test_caching.py | Python | mit | 12,587 | [
"VisIt"
] | 22a8b0317def94fe863f194170028659392238fe7d28a80db90ce9cfe2ea5dbd |
# Copyright 2016 Battelle Energy Alliance, LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... | idaholab/civet | ci/DebugViews.py | Python | apache-2.0 | 7,629 | [
"MOOSE",
"VTK"
] | db8cb3cd8b48dc846cf6b06684eb0db858df476ad0455aa493e6fc08ad0f9550 |
"""Next gen sequence alignments with Bowtie2.
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
"""
import os
from bcbio.pipeline import config_utils
from bcbio.distributed.transaction import file_transaction
from bcbio.provenance import do
from bcbio import bam, utils
from bcbio.pipeline import datadict as dd
fr... | biocyberman/bcbio-nextgen | bcbio/ngsalign/bowtie2.py | Python | mit | 6,907 | [
"Bowtie",
"Galaxy"
] | 996a93fdb971ddd78c9d3fc2002e4177b4d8ff8360d7fad663593e05f37b7965 |
"""
Test netcd time interpolation
"""
from thetis.interpolation import *
import numpy as np
from scipy.interpolate import interp1d
import netCDF4
import pytest
import os
@pytest.fixture()
def dataset(request):
# create random time series on regular intervals
np.random.seed(2)
x_scale = 100.
ndata = 3... | tkarna/cofs | test/interpolation/test_netcdftimeinterp.py | Python | mit | 5,195 | [
"NetCDF"
] | 1c6d834dc475a72536eda68a4811e769bd3063b77242cc2ad6f7465af0bf9bf9 |
#pylint: disable=missing-docstring
####################################################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment ... | liuwenf/moose | python/MooseDocs/common/moose_docs_import.py | Python | lgpl-2.1 | 3,857 | [
"MOOSE"
] | 3606092687a4afdd656afc640cfc720ce4f6fad32f5dab89af4e71ee3bb1f66f |
#!/usr/bin/env python
__RCSID__ = "$Id$"
import DIRAC
from DIRAC.Core.Base import Script
groupName = None
groupProperties = []
userNames = []
def setGroupName( arg ):
global groupName
if groupName or not arg:
Script.showHelp()
DIRAC.exit( -1 )
groupName = arg
def addUs... | Andrew-McNab-UK/DIRAC | Interfaces/scripts/dirac-admin-add-group.py | Python | gpl-3.0 | 2,637 | [
"DIRAC"
] | 0e7acbffe01cb06f4f01960a71f154dfa4765a6781b05a0ad51e164369f938f0 |
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