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import unittest
import numpy as np
from deepchem.feat import OneHotFeaturizer
from deepchem.feat.molecule_featurizers.one_hot_featurizer import ZINC_CHARSET
class TestOneHotFeaturizert(unittest.TestCase):
"""
Test OneHotFeaturizer.
"""
def test_onehot_featurizer(self):
"""
Test simple one hot encod... | lilleswing/deepchem | deepchem/feat/tests/test_one_hot_featurizer.py | Python | mit | 2,017 | [
"RDKit"
] | 53175b9644500eee5be1e2898a207726caed1d70896f420dfb24d19fde33cab6 |
#!/usr/bin/env python
###############################################################################
#
# ptgraph2.py - generate protein topology graphs from PDB atomic co-ordinates
# plus STRIDE or DSSP information.
#
# File: ptgraph2.py
# Author: Alex Stivala
# Created: July 2007
#
# $Id: ptgraph2.py 4642 2013-04... | NirBenTalLab/proorigami-cde-package | cde-root/local/munk/data/phd/phd/ptgraph/ptgraph2.py | Python | mit | 347,701 | [
"Biopython",
"PyMOL"
] | e98ff09649096f076e63fd4efc837e072dca7ee7321f7d6c6f49b48f453a85fe |
# MIT License
#
# Copyright (c) 2017, Stefan Webb. All Rights Reserved.
#
# 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 us... | stefanwebb/tensorflow-models | tensorflow_models/models/vae_expconcrete_made_prior_iw.py | Python | mit | 17,788 | [
"Gaussian"
] | 78d9378b0ae50cb8363c48ed9ea92ed7959fbbddd1992e5390f9299f5c139362 |
# -*- coding: utf-8 -*-
# Copyright 2013-2014 Victor Amin, http://vamin.net/
"""MESS.DB match module
This module contains the match tool class and load function.
"""
from __future__ import print_function
from __future__ import unicode_literals
import argparse
import csv
import codecs
import json
import logging
impo... | vamin/MESS.DB | mess/tools/match.py | Python | agpl-3.0 | 18,329 | [
"Pybel"
] | 9be4dcb17414df1b22b6909b7b364c7040962b40d2e03e8bbc71e8f737718c74 |
from rapidsms.webui.utils import render_to_response
from django.contrib.auth.decorators import login_required, permission_required
from models import *
@login_required
@permission_required("harvard.can_view")
def index(req):
template_name="harvard/index.html"
# will store number of sucesses, failures per ... | commtrack/temp-rapidsms | apps/harvard/views.py | Python | lgpl-3.0 | 2,375 | [
"VisIt"
] | fe17f6fcf691317ad7a61886ad9ad614c75bcdc8cc9d487c829674449627e770 |
# Copyright 2007-2016 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later ... | vidartf/hyperspy | hyperspy/tests/signal/test_eds_sem.py | Python | gpl-3.0 | 13,067 | [
"Gaussian"
] | 3c420f4766f22ae94908a1766a2e6660f909afe361e2191f4d2b2455995bdcdf |
"""
=================================================================
Image feature extraction and manipulation (:mod:`medpy.features`)
=================================================================
.. currentmodule:: medpy.features
This package contains various functions for feature extraction and
manipulation in ... | lfrdm/medpy | medpy/features/__init__.py | Python | gpl-3.0 | 6,483 | [
"Gaussian"
] | a975bb7cf642202bf63c8caa22f24f6c58232a18e117d61a12f183c43fa4a71e |
#!/usr/bin/python
__author__ = 'K. Voss'
__version__ = '0.1'
import numpy as np
import scipy as sp
from numpy.core.getlimits import finfo
from scipy import ndimage
import matplotlib.pyplot as plt
import mahotas
#import unittest
import ConfigParser
import logging
import os
##### Importing constants
config = ConfigP... | kvoss/pylsm | src/lsmethod.py | Python | mit | 15,007 | [
"DIRAC",
"Gaussian"
] | b8fb6c0fc23584b5ec7ec80e7725406d7d1d00e6529872352aa98e6abaa31d54 |
# Copyright 2017 Google Inc. 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 law or ag... | KaranToor/MA450 | google-cloud-sdk/lib/googlecloudsdk/command_lib/search_help/table.py | Python | apache-2.0 | 2,996 | [
"VisIt"
] | 44ee2fbe1808f226cf659ece4ec710320a9aad02a58fbd8bf48c2b40978b56a8 |
"""Fallaxy (ansible-galaxy) plugin for integration tests."""
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import os
import uuid
from . import (
CloudProvider,
CloudEnvironment,
CloudEnvironmentConfig,
)
from ..util import (
find_executable,
display,
)
f... | k0ste/ansible | test/lib/ansible_test/_internal/cloud/fallaxy.py | Python | gpl-3.0 | 5,719 | [
"Galaxy"
] | 91fe17f01826b9929ac40c8760e1e7a84beb4118aa8f39d8a5498a77270bd103 |
"""
A collection of utility functions and classes. Originally, many
(but not all) were from the Python Cookbook -- hence the name cbook.
This module is safe to import from anywhere within matplotlib;
it imports matplotlib only at runtime.
"""
from __future__ import (absolute_import, division, print_function,
... | unnikrishnankgs/va | venv/lib/python3.5/site-packages/matplotlib/cbook.py | Python | bsd-2-clause | 83,917 | [
"Gaussian"
] | 51d0f3aa65552d528e02758b16263d5af20bfc6d6cce0f1d2d513ec31947e7f8 |
# coding: utf-8
from anki.find import Finder
from tests.shared import getEmptyDeck
def test_parse():
f = Finder(None)
assert f._tokenize("hello world") == ["hello", "world"]
assert f._tokenize("hello world") == ["hello", "world"]
assert f._tokenize("one -two") == ["one", "-", "two"]
assert f._tok... | rubyu/anki | tests/test_find.py | Python | agpl-3.0 | 10,620 | [
"Octopus"
] | 9c48258d201e5ea480befd9adfeb463b20f957a1ebe65ef695f40f2a5c03a771 |
# Copyright (C) 2020(H)
# Jozef Stefan Institute
# Max Planck Institute for Polymer Research
# Copyright (C) 2012,2013,2016
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPRe... | espressopp/espressopp | src/tools/pdb.py | Python | gpl-3.0 | 9,039 | [
"CRYSTAL",
"ESPResSo"
] | 55f6eaf0200721e345a6239264027ef41a379149b66f7ade264ebd5613a696b8 |
# -*- coding: utf-8 -*-
"""
Setup file for the ase-espresso package.
"""
from setuptools import setup
MAIN_PACKAGE = "aseqe"
DESCRIPTION = "Python API for the Quantum Espresso software"
LICENSE = "GPLv3"
URL = "https://github.com/lmmentel/ase-espresso"
AUTHOR = "Lukasz Mentel"
EMAIL = "lmmentel@gmail.com"
VERSI... | lmmentel/ase-espresso | setup.py | Python | gpl-3.0 | 1,724 | [
"ASE",
"ESPResSo",
"Quantum ESPRESSO"
] | b6e8c22ab98dbbbfe0b491c036c6ce5a8ca32019c7910bce6d13b722edabac7d |
# -*- coding: utf-8 -*-
##
## This file is part of Invenio.
## Copyright (C) 2010, 2011, 2012, 2013, 2016, 2021 CERN.
##
## 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 version 2 of the
## ... | inspirehep/invenio | modules/bibupload/lib/batchuploader_engine.py | Python | gpl-2.0 | 33,404 | [
"VisIt"
] | 39cb460da7c1d029eb5b6f7a61f21c57c92f1ef6a8f0cbcb11b4362fc03a0a7f |
"""
=========================
Bayesian Ridge Regression
=========================
Computes a :ref:`bayesian_ridge_regression` on a synthetic dataset.
Compared to the OLS (ordinary least squares) estimator, the coefficient
weights are slightly shifted toward zeros, wich stabilises them.
As the prior on the weights is... | joshbohde/scikit-learn | examples/linear_model/plot_bayesian_ridge.py | Python | bsd-3-clause | 2,489 | [
"Gaussian"
] | 7514611eb2c9801a33b50694b53f2f2c053c5adfff8689227bc6487fbef226dd |
"""A host of different carrier peak interpolation techniques."""
import numpy as np
from scipy.optimize import curve_fit
def _dirichlet_kernel(xdata, block_len, carrier_len):
# pylint: disable=invalid-name
N, W = block_len, carrier_len
xdata = np.array(xdata, dtype=np.float64)
with np.errstate(divide... | swkrueger/Thrifty | thrifty/experimental/carrier_interpolators.py | Python | gpl-3.0 | 2,989 | [
"Gaussian"
] | 317428c6fcdec250f483eb8b815756dde56cabc1f7debb0b957a8eba77070f54 |
#! /usr/bin/python
import MDAnalysis
import sys
from pylab import *
my_traj = sys.argv[1]
myTitle = sys.argv[2]
u = MDAnalysis.Universe(my_traj,my_traj)
OH = u.selectAtoms("segid B and resid 18 and name OH")
xArr = []
yArr = []
zArr = []
data = []
for ts in u.trajectory:
xArr.append(OH.coordinates()[0,0])
... | demharters/git_scripts | calc_movement_OH.py | Python | apache-2.0 | 795 | [
"MDAnalysis"
] | 22e5fff448cd93f61e3b66a3c32980ba215f526e9a53cafda9974c8051e035e6 |
#!/usr/bin/env python
# Copyright (C) 2011-2012, 2014, 2016, 2017 The PISM Authors
# script to generate figure: results from SeaRISE experiments
# usage: if UAFX_G_D3_C?_??.nc are result NetCDF files then do
# $ slr_show.py -m UAFX
# try different netCDF modules
try:
from netCDF4 import Dataset as CDF
except:
... | talbrecht/pism_pik | examples/std-greenland/slr_show.py | Python | gpl-3.0 | 3,919 | [
"NetCDF"
] | 5e5f84e0ee01b34d698e45d0acbabc8ce5e335a8114bd439ee3aae901268dea1 |
# Python function that implements a loop of short runs
# calls back to LAMMPS via "lmp" instance
# lammps() must be called with ptr=lmpptr for this to work
def loop(N,cut0,thresh,lmpptr):
print "LOOP ARGS",N,cut0,thresh,lmpptr
from lammps import lammps
lmp = lammps(ptr=lmpptr)
natoms = lmp.get_natoms()
fo... | ganzenmg/lammps_current | examples/python/funcs.py | Python | gpl-2.0 | 831 | [
"LAMMPS"
] | 9fb27662437978d32f014855cd1d4f1dae122b9f634f6ce508932b503c1d3348 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2017 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | dwhswenson/mdtraj | tests/test_geometry.py | Python | lgpl-2.1 | 15,738 | [
"MDTraj",
"PyMOL"
] | 8e6d51dfc7844cb89cd5d3a8ae138cb8cd19d452875153d0f9d31b7c92a7b945 |
########################################################################
# $HeadURL $
# File: PfnTestCase.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2011/12/14 15:07:01
########################################################################
""" :mod: PfnTestCase
=======================
.. module: ... | Sbalbp/DIRAC | Core/Utilities/test/PfnTestCase.py | Python | gpl-3.0 | 3,168 | [
"DIRAC"
] | 7e8cd4ce4c3cc75005342142180d01756c49a16f3f13a0ed68b3d3389a0e8282 |
import os
import re
import datetime
import pdb
import logging
import copy
import comicsite.utils.query
from django import forms
from django.conf import settings
from django.contrib import messages
from django.contrib.auth.models import Group,User,Permission
from django.contrib.contenttypes.models import ContentType
fr... | cpatrick/comic-django | django/comicmodels/models.py | Python | apache-2.0 | 44,758 | [
"VisIt"
] | 5a9502883e8d5fab3f08cc86e7f71043d5ed83caeaeea589565c11380af4595f |
import cv2
import numpy as np
from math import pi
from math import atan2
#with help from : https://github.com/galenballew/SDC-Lane-and-Vehicle-Detection-Tracking/blob/master/Part%20I%20-%20Simple%20Lane%20Detection/P1.ipynb
def grayscale(img):
"""Applies the Grayscale transform
This will return an image with ... | djorna/I-See-Pi | sidewalk_detection.py | Python | mit | 8,845 | [
"Gaussian"
] | 1809bb816ce20135755952bad13d0fadd9fbaaeef7ce4a025433225b9a27a5db |
# libraries
import argparse
import logging
import re
import sys
import os.path
import time
import random
from datetime import *
from selenium import webdriver
# prog imports
import user
import dblog
import conf
import datamgr
import handlers
import selfies
import historian
class dirtyboots( ):
"""
Management ... | m-kal/DirtyBoots | src/dirtyboots.py | Python | gpl-3.0 | 26,792 | [
"VisIt"
] | 68ac192d5591e62387dc9a078cccfb4bbba4cddf2d7d77036d6ea91f7bd02f41 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# (c) 2015, Heyo
#
# 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 Software Foundation, either version 3 of the License, or
# (at your option) a... | e-gob/plataforma-kioscos-autoatencion | scripts/ansible-play/.venv/lib/python2.7/site-packages/ansible/modules/windows/win_nssm.py | Python | bsd-3-clause | 5,858 | [
"ADF"
] | 4ca89c2f2271bf2f240ac5518cde12afdbeff7fa595c3bc988aad6de4681d83c |
import os
import tarfile
from flyingpigeon.subset import clipping
from flyingpigeon.subset import countries, countries_longname
from pywps.Process import WPSProcess
import logging
class ClippingProcess(WPSProcess):
def __init__(self):
WPSProcess.__init__(
self,
identifie... | sradanov/flyingpigeon | flyingpigeon/processes/wps_subset.py | Python | apache-2.0 | 4,262 | [
"NetCDF"
] | e40bce748de74bdfc800690c16d0fc3d4d75d8294eb4de28fc5e322c2e986e34 |
import numpy as np
from cs231n.layers import *
from cs231n.layer_utils import *
class TwoLayerNet(object):
"""
A two-layer fully-connected neural network with ReLU nonlinearity and
softmax loss that uses a modular layer design. We assume an input dimension
of D, a hidden dimension of H, and perform classific... | machinelearningnanodegree/stanford-cs231 | solutions/vijendra/assignment2/cs231n/classifiers/fc_net.py | Python | mit | 17,207 | [
"Gaussian"
] | b52606c6cc4888447d4d0b664f0f398de1054aca166aac8c22e8ad60fea3afea |
import numpy as np
from .base import BaseTransformer
import mdtraj as md
from .utils import get_square_distances
from .utils import get_neighbors
from . import FeatureTrajectory
import copy
class Coordination(BaseTransformer):
r"""
Use the effective coordination number to compute inner
products.
... | schwancr/water-features | features/coordination.py | Python | gpl-2.0 | 1,862 | [
"MDTraj"
] | 4fea7ee00be4c8ec336e1fb4f737ae449b0ff100081f98155cbd671886c990f1 |
#!/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... | lothian/psi4 | psi4/share/psi4/basis/primitives/dunning_prepend_and_checknew.py | Python | lgpl-3.0 | 2,192 | [
"Molpro",
"Psi4"
] | 6fb729b6a6eaaeaef152799550e9d0907cb8c333756a983d7faebe88547346a7 |
import unittest
from nose.tools import (assert_true, assert_in, assert_raises, assert_equal)
import io
import numpy
import logging
import sknn
from sknn.mlp import Regressor as MLPR
from sknn.mlp import Layer as L, Convolution as C
class LoggingTestCase(unittest.TestCase):
def setUp(self):
self.buf = i... | jgdwyer/ML-convection | sknn_jgd/tests/test_rules.py | Python | apache-2.0 | 5,933 | [
"Gaussian"
] | f554e8ac5566fd3fd6414b8fe3c8d1f8fd6441487fab59b7a2c20be3e0fbe2ca |
from __future__ import print_function
import numpy as np
from numpy import linalg
from ase.transport.selfenergy import LeadSelfEnergy, BoxProbe
from ase.transport.greenfunction import GreenFunction
from ase.transport.tools import subdiagonalize, cutcoupling, dagger,\
rotate_matrix
class TransportCalculator:
... | suttond/MODOI | ase/transport/calculators.py | Python | lgpl-3.0 | 15,407 | [
"ASE"
] | 84b57af8a44f8879b3c0008d713763832aeadd68d2b4029860bc32cbc2d67d1a |
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
from __future__ import unicode_literals
from xml.etree.ElementTree import ElementTree
from pymatgen.core.periodic_table import Element
import os
from io import StringIO
import sys
import shutil
import string
f... | willwheelera/mainline | utils/autogen/xyz2crystal.py | Python | gpl-2.0 | 8,364 | [
"pymatgen"
] | 57f397af20e8cd3dfdbbc197b9ea6e2fe8e97c9f5183ce57ba8fdd58ef120b6a |
# coding: utf-8
from __future__ import division, unicode_literals
"""
Created on Mar 15, 2012
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep@gmail.com"
__date__ = "Mar 15, 2012"
import unittest
imp... | Dioptas/pymatgen | pymatgen/transformations/tests/test_site_transformations.py | Python | mit | 9,321 | [
"pymatgen"
] | 5a51f88454dd455ba36f89946cf8798181e2fd8176604e683428d1f4e73acd5c |
# -*- coding: utf-8 -*-
from __future__ import print_function, division, unicode_literals, absolute_import
import os
import re as regex
from ..base import TraitedSpec, CommandLineInputSpec, CommandLine, File, traits, isdefined
from ..traits_extension import str
"""This script provides interfaces for BrainSuite comma... | carolFrohlich/nipype | nipype/interfaces/brainsuite/brainsuite.py | Python | bsd-3-clause | 75,684 | [
"ADF",
"Gaussian"
] | 63becc04f17ab5b3018526386756ce26bc8f807f6847b59cb30f9ffd08830296 |
"""This is an example app, demonstrating usage."""
import os
from flask import Flask
from flask_jsondash.charts_builder import charts
app = Flask(__name__)
app.config['SECRET_KEY'] = 'NOTSECURELOL'
app.config.update(
JSONDASH_FILTERUSERS=False,
JSONDASH_GLOBALDASH=True,
JSONDASH_GLOBAL_USER='global',
)
... | christabor/flask_jsondash | example_app/app.py | Python | mit | 1,164 | [
"VisIt"
] | d5c634ab78c480df754115cf132a4198ac5ef8256c41fad5c8d643194240263c |
# Copyright 2003-2008 by Leighton Pritchard. All rights reserved.
# Revisions copyright 2008-2009 by Peter Cock.
# 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.
#
# Contact: Leighton Pritchard,... | asherkhb/coge | bin/last_wrapper/Bio/Graphics/GenomeDiagram/_AbstractDrawer.py | Python | bsd-2-clause | 19,549 | [
"Biopython"
] | 8f452be6d079a06ae8fe67803f97a3d911cb54a2bcdf1402904f254a6d77f502 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | krafczyk/spack | var/spack/repos/builtin/packages/r-oligoclasses/package.py | Python | lgpl-2.1 | 2,347 | [
"Bioconductor"
] | cb2073cd3fab8594a1c2d1624e3ca984280287dfd7c588bb7a1cfd67745b326c |
###
# Copyright 2016 Miler T. Lee, University of Pittburgh
# This file is part of the RESA Suite
#
# RESA Suite 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 op... | MTLeeLab/RESA | bam_seq_convert.py | Python | gpl-3.0 | 2,436 | [
"pysam"
] | 59a49febddbe44adcb88a8030b52ac1668211f253da5b259f6832a5ce2473222 |
from __future__ import unicode_literals
from django.test import TestCase
from django.utils import six
from .models import (Building, Child, Device, Port, Item, Country, Connection,
ClientStatus, State, Client, SpecialClient, TUser, Person, Student,
Organizer, Class, Enrollment, Hen, Chick, A, B, C)
class Se... | oscaro/django | tests/select_related_regress/tests.py | Python | bsd-3-clause | 9,454 | [
"Brian"
] | 8092d1124e8844b850a554cd17c78ae04ec7dff9d1b8f877148037ddddfa672a |
"""
This script tests the scf module.
"""
import os
import numpy as np
import pytest
from frankenstein.be import BE
@pytest.mark.parametrize(
"geom, basis, fsites, frank, incore, nibath, solver, jac, B0, bad_con, "
"good_con, e_ps_ref",
[
# Frankenstein BE, FCI solver
("geom/h10.zmat", "st... | hongzhouye/frankenstein | tests/be_test.py | Python | bsd-3-clause | 7,599 | [
"PyMOL",
"PySCF"
] | 6438888a59183c0e6584e035c3c9f806d55994b1ea64b2a0074a3b4aaf5a4c5a |
#!/usr/bin/env python
'''
plebdisc.py
DESCRIPTION
===========
ENVIRONMENTAL VARIABLES
=======================
ZRPATH : Path to the directory with ZRTOOLS binary directory
to setset in bash:
>> export ZRPATH=<your ZRPATH>
if not set, it will be the installation directory... | bootphon/ZRTools | plebdisc_tools/plebdisc.py | Python | gpl-3.0 | 23,880 | [
"Gaussian"
] | 6f4abe7e4c3dcd0f1fecdf493fc6e9799dec78c3afe4d6848b499ee506c49986 |
#
# Copyright (c) 2017, 2021, Oracle and/or its affiliates. All rights reserved.
# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
#
# This code is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License version 3 only, as
# published by the Free Softwar... | graalvm/fastr | mx.fastr/mx_fastr_edinclude.py | Python | gpl-2.0 | 6,243 | [
"VisIt"
] | d067c0d21a1ac4c003efa3a2d95beaadf56b04e803194a1173208c2844fd28d9 |
# coding=utf-8
from __future__ import unicode_literals
import json
import pytz
import six
from datetime import datetime, date, timedelta
from django.core.files.base import ContentFile
from django.core.urlresolvers import reverse
from django.conf import settings
from django.db.models import Value as DbValue
from djang... | onaio/rapidpro | temba/contacts/tests.py | Python | agpl-3.0 | 210,520 | [
"Amber",
"VisIt"
] | 4912a0e9c047f4b4e49a30a97fcb779758ffeddc74f3e2730a08da93c711c3c2 |
../../../../../../../share/pyshared/orca/scripts/apps/gajim/script.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/scripts/apps/gajim/script.py | Python | gpl-3.0 | 69 | [
"ORCA"
] | 593bf0319d622de0b45028bd3cd51ec5818dacf905910d657eecf9f877c44802 |
#!/usr/bin/python
# filename: msa.py
#
# Copyright (c) 2015 Bryan Briney
# License: The MIT license (http://opensource.org/licenses/MIT)
#
# 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 with... | briney/abtools | abtools/phylogeny/msa.py | Python | mit | 2,450 | [
"Biopython"
] | a268b6d6cb07c5b966114fd73a9f03d1c13889c0d363fcb4dae90ceb128bde95 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import print_function
from __future__ import with_statement
from acq4.devices.DAQGeneric import DAQGeneric, DAQGenericTask, DAQGenericTaskGui
from acq4.util.Mutex import Mutex
#from acq4.devices.Device import *
from acq4.util import Qt
import time
import num... | pbmanis/acq4 | acq4/devices/MockClamp/MockClamp.py | Python | mit | 14,294 | [
"NEURON"
] | 736d0a626673d833d7709a635a9abc5369b173feaf489ad1de5491ac7c41d6da |
"""Phonopy loader."""
# Copyright (C) 2018 Atsushi Togo
# All rights reserved.
#
# This file is part of phonopy.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# * Redistributions of source code must retain the abo... | atztogo/phonopy | phonopy/cui/load.py | Python | bsd-3-clause | 12,151 | [
"CRYSTAL",
"VASP",
"phonopy"
] | a17310accabd9016aff7e5f317cfea6bcf4438b5743ab740d9eb9c0877898a67 |
#!/usr/bin/env python
from setuptools import setup, find_packages
setup(name='django-spillway',
version='0.8.1',
description='Geodata extensions for Django REST Framework',
long_description=open('README.rst').read(),
author='Brian Galey',
author_email='bkgaley@gmail.com',
url='http... | bkg/django-spillway | setup.py | Python | bsd-3-clause | 1,094 | [
"Brian"
] | 0002939d73cf13608e7f3ff8850b3cc6d591ffeeaa284c14c388e2cfe5562483 |
""" cpfigure.py - provides a frame with a figure inside
CellProfiler is distributed under the GNU General Public License.
See the accompanying file LICENSE for details.
Copyright (c) 2003-2009 Massachusetts Institute of Technology
Copyright (c) 2009-2015 Broad Institute
All rights reserved.
Please see the AUTHORS fi... | sstoma/CellProfiler | cellprofiler/gui/cpfigure.py | Python | gpl-2.0 | 91,475 | [
"Gaussian"
] | 3b8cebe5bceee4993790de7618aff9fab1a3ee8200d7c758e72d7891c8f6ddd1 |
"""
fillerbase Module
Classes to help fill widgets with data
Copyright (c) 2008-10 Christopher Perkins
Original Version by Christopher Perkins 2008
Released under MIT license.
"""
from .configbase import ConfigBase, ConfigBaseError
from .metadata import FieldsMetadata
import inspect
from datetime import datetime
fro... | TurboGears/sprox | sprox/fillerbase.py | Python | mit | 13,478 | [
"VisIt"
] | 39f835d4eafd149387bd41431deb06e9d15e36ccb0e68af324439eaff5806ba6 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides utility classes for io operations.
"""
import codecs
import errno
import os
import re
import tempfile
from monty.io import zopen
__author__ = "Shyue Ping Ong, Rickard Armiento, Anub... | davidwaroquiers/pymatgen | pymatgen/util/io_utils.py | Python | mit | 6,233 | [
"pymatgen"
] | 4d415e596c61534b2c31495651ff7cf7f3b10578f4cabef9fca317443a4e88e2 |
from enum import Enum
class Parse(Enum):
BYTES = 1
ASCII = 2
DOL = 3 # Data Object List
DEC = 4 # Decimal encoded in hex
DATE = 5 # Date encoded in hex digits as [0xYY 0xMM 0xDD]
INT = 6 # Decode bytes as an integer
COUNTRY = 7 # Decode bytes as an ISO country code
CURRENCY = 8 #... | russss/python-emv | emv/protocol/data_elements.py | Python | mit | 10,828 | [
"ADF"
] | 72e453778511f94974d7e816356a3f8714ed4af8de5009719d54b5c64da009fd |
"""Unit tests for the pylint checkers in :mod:`pylint.extensions.check_docs`,
in particular the parameter documentation checker `ParamDocChecker`
"""
from __future__ import division, print_function, absolute_import
import unittest
import sys
import astroid
from astroid import test_utils
from pylint.testutils import C... | justathoughtor2/atomicApe | cygwin/lib/python2.7/site-packages/pylint/test/extensions/test_check_docs.py | Python | gpl-3.0 | 19,656 | [
"VisIt"
] | ddc3d58df48361c85dd5ec0cd06d4edf4dc1c5e97a6956a7f60927c1e8c84105 |
# -*- coding: utf-8 -*-
"""The optimizer tries to constant fold expressions and modify the AST
in place so that it should be faster to evaluate.
Because the AST does not contain all the scoping information and the
compiler has to find that out, we cannot do all the optimizations we
want. For example, loop unrolling do... | sserrot/champion_relationships | venv/Lib/site-packages/jinja2/optimizer.py | Python | mit | 1,457 | [
"VisIt"
] | 8102e5318cef42196e873980205035b574b473081660e8e9acdfa04d170756c7 |
"""
A simple wrapper for writing tarballs as a stream.
"""
import os
import logging
import tarfile
from galaxy.exceptions import ObjectNotFound
log = logging.getLogger( __name__ )
class StreamBall( object ):
def __init__( self, mode, members=None ):
self.members = members
if members is None:
... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/util/streamball.py | Python | gpl-3.0 | 1,740 | [
"Galaxy"
] | 884663a532eea3577f21057ac8660791a105ca8b67c52430bd6c9269eb10fc0f |
import json
import numpy as np
import pytest
from pandas import DataFrame, Index, Series, json_normalize
import pandas._testing as tm
from pandas.io.json._normalize import nested_to_record
@pytest.fixture
def deep_nested():
# deeply nested data
return [
{
"country": "USA",
"... | jreback/pandas | pandas/tests/io/json/test_normalize.py | Python | bsd-3-clause | 27,430 | [
"COLUMBUS"
] | 580bb7e4daf5d0753a9d6af9696c24f963afda202d03ae2f2fa2db2d923c7979 |
# -*- coding: utf-8 -*-
from django.db import migrations
from django.contrib.postgres.operations import TrigramExtension
forward = """
CREATE INDEX class_instance_name_trgm_idx
ON class_instance USING gin (name gin_trgm_ops);
"""
backward = """
DROP INDEX class_instance_name_trgm_idx;
"""
class Mi... | tomka/CATMAID | django/applications/catmaid/migrations/0058_add_pg_trgm_ext_and_class_instance_name_index.py | Python | gpl-3.0 | 1,229 | [
"NEURON"
] | 6376d237e939d21e92c6b8988c9cd4417edd53c3d0555c9cad017760223380b4 |
'''\
a piddle wrapper for wxPython DeviceContexts
piddleWxDc.py
By Paul and Kevin Jacobs
History -
1.0 Many fixes and the rest of required piddle functionality added.
0.5 Much work done by Jeffrey Kunce on image support and code factoring.
PiddleWxDc adds Piddle-compatible methods to any wxPython DeviceCont... | adalke/rdkit | rdkit/sping/WX/pidWxDc.py | Python | bsd-3-clause | 9,638 | [
"RDKit"
] | 58999d46af9cb35491b820cd6aa1269b228ef1fcb4d44d9e20b4b72d7d239e40 |
#########################################################################
## This program is part of 'MOOSE', the
## Messaging Object Oriented Simulation Environment.
## Copyright (C) 2014 Upinder S. Bhalla. and NCBS
## It is made available under the terms of the
## GNU Lesser General Public License version 2... | dilawar/moose-full | moose-examples/snippets/bidirectionalPlasticity.py | Python | gpl-2.0 | 2,861 | [
"MOOSE"
] | 4adc813b6c899826d0da6c4d9d779b5e24531ee851e29860b3cdf2947cb2e5dc |
"""
Tests for Gaussian Process Hyperparameter Optimization.
These tests fails every so often. I think it's when the Gaussian
process optimizer doesn't find an optimal point. This is still a
valuable test suite so leaving it in despite the flakiness.
"""
import numpy as np
import sklearn
import deepchem as dc
import un... | lilleswing/deepchem | deepchem/hyper/tests/test_gaussian_hyperparam_opt.py | Python | mit | 6,768 | [
"Gaussian"
] | 691fdf9d517f457da04d22ab923244a0dffcac6be6091bc71b63c4ea045b5ace |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes to interface with the Crystallography Open
Database. If you use data from the COD, please cite the following works (as
stipulated by the COD developers)::
Merkys, A., Vaitk... | dongsenfo/pymatgen | pymatgen/ext/cod.py | Python | mit | 5,029 | [
"CRYSTAL",
"pymatgen"
] | 1464555f0b6d22dfa773627c19fa1372451230de98f8a17511672c4554d97fbb |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import platform
import re
import unittest
import warnings
import random
import sys
from pymatgen import SETTINGS, __version__ as pmg_version
from pymatgen.ext.matproj import MPRester, MPRestError, TaskType
from ... | mbkumar/pymatgen | pymatgen/ext/tests/test_matproj.py | Python | mit | 21,564 | [
"pymatgen"
] | 79f2c6a1f499a1e6920cb33f11824366d15ae158457adf42633638a2bf137c3d |
# Copyright 2008-2015 Nokia Solutions and Networks
#
# 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 l... | fingeronthebutton/RIDE | src/robotide/lib/robot/model/modifier.py | Python | apache-2.0 | 2,081 | [
"VisIt"
] | 92d91d7750bb5bc5419f3822085a818ee8982a66ea84e20793ca91a3a699c378 |
import os
from os.path import join
from tempfile import mkstemp
from netCDF4 import Dataset
from datetime import datetime, date
import numpy as np
import logging
import matplotlib
matplotlib.use('Agg') # use this if no xserver is available
from matplotlib import pyplot as plt
from matplotlib.colors import Normalize
... | KatiRG/flyingpigeon | flyingpigeon/visualisation.py | Python | apache-2.0 | 22,328 | [
"NetCDF"
] | a85cddd141fc55ed21fe8a8920d3bc0866b19f6ee48ce0beffd3619755bcda8f |
#!/usr/bin/python
#
# pyLirc, lirc (remote control) module for python
# Copyright (C) 2003 Linus McCabe <pylirc.linus@mccabe.nu>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Found... | offlinehacker-playground/pylirc2 | pylirc_test.py | Python | lgpl-2.1 | 2,750 | [
"Brian"
] | 968776d87a2c94040a3b234e7f5b9017a8126ec8937c79ada793cae81eff7c40 |
import numpy as np
import os
from gpaw.io.hdf5_highlevel import File, HyperslabSelection
from gpaw.mpi import world, rank, size
# data to be written
attrs = {'int' : 42, 'float' : 6.2, 'complex' : 1.0 + 2.0j,
'bool1' : False, 'bool2' : True, 'data' : np.array(((1,2),(3,4)))}
datasize = 4
data = {}
for dtype ... | robwarm/gpaw-symm | gpaw/test/fileio/hdf5_simple.py | Python | gpl-3.0 | 2,748 | [
"GPAW"
] | be35737d2f5531f87ba032e9bbcbd9423f257453c98e98f08937d9e1128a3f6d |
#!/usr/bin/python
# vim: fileencoding=utf-8
#
# The Qubes OS Project, https://www.qubes-os.org/
#
# Copyright (C) 2014-2015
# Marek Marczykowski-Górecki <marmarek@invisiblethingslab.com>
# Copyright (C) 2015 Wojtek Porczyk <woju@invisiblethingslab.com>
#
# This program is free software; you can redi... | v6ak/qubes-core-admin | tests/basic.py | Python | gpl-2.0 | 31,918 | [
"Amber"
] | 9de299de9a01ce0196c66e0da5457dc8a9f8f4e139d2f6343cb04fe831996163 |
# -*- coding: utf-8 -*-
"""
Difference frequency generation module
Defines:
- The dfg_problem, a class which can be intergrated by the pyNLO ODESolve
- The fftcomputer, which handles FFTs using pyFFTW
- A helper class, dfg_results_interface, which provides a Pulse-class based
wrapper around the dfg r... | ycasg/PyNLO | src/pynlo/interactions/ThreeWaveMixing/DFG_integrand.py | Python | gpl-3.0 | 28,773 | [
"CRYSTAL",
"Gaussian"
] | cafc6ac415c9ffef2e5f0391a8bf25ccd5a25ae5878c1de9fe8c4d5067d6a5dc |
"""Copyleft 2010 Forrest Sheng Bao http://fsbao.net
PyEEG, a Python module to extract EEG features, v 0.02_r2
Project homepage: http://pyeeg.org
**Data structure**
PyEEG only uses standard Python and numpy data structures,
so you need to import numpy before using it.
For numpy, please visit http://numpy.scipy.org
... | gilestrolab/pyrem | scripts/pyeeg.py | Python | gpl-3.0 | 22,999 | [
"VisIt"
] | a7cfb370c7c0be6132e25fc2bf387c9649101b8c1fce40833673cfefd3f250b5 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Gary Burton
#
# 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 v... | pmghalvorsen/gramps_branch | gramps/gen/plug/menu/_menu.py | Python | gpl-2.0 | 4,321 | [
"Brian"
] | b199c7c69927c540a511db3a59409b59e168be037d5e961b28c87acca97de2e6 |
../../../../../../../share/pyshared/orca/scripts/apps/gcalctool/speech_generator.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/scripts/apps/gcalctool/speech_generator.py | Python | gpl-3.0 | 83 | [
"ORCA"
] | 53236bdd2b14f05c6c233ae503c1e551e382e37b26b56a6ee5c02c3e64462fed |
import os.path
import pickle
from datetime import datetime as ddt
import numpy as np
import pandas as pd
import xarray as xr
from . import constants as c
from .util import ParcelModelError
from .thermo import rho_air
from .version import __version__ as ver
#: Acceptable output formats
OUTPUT_FORMATS = ["nc", "obj", ... | darothen/parcel_model | pyrcel/output.py | Python | bsd-3-clause | 9,077 | [
"NetCDF"
] | ed4ca59e402b6c6b8d569b09bdcfa2193cdd27275ef88d6be98d21b8f45350d5 |
#!/usr/bin/env python
from __future__ import absolute_import, division, print_function
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COP... | Kleptobismol/scikit-bio | skbio/diversity/alpha/tests/test_gini.py | Python | bsd-3-clause | 2,260 | [
"scikit-bio"
] | 849f0e042d6b398928c8767aecbeb3071215063a3a9b89f3e4150e871bb4c93a |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# genjobscriptsh - helpers for sh jobs
# Copyright (C) 2003-2014 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License... | heromod/migrid | mig/server/genjobscriptsh.py | Python | gpl-2.0 | 40,385 | [
"Brian"
] | 4d9f7e852a4c5ac3cd43691d8de6c76d5bc448744470cf65fd884d3723abf65e |
#
# @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
#... | jturney/psi4 | psi4/driver/schema_wrapper.py | Python | lgpl-3.0 | 23,560 | [
"Gaussian",
"Psi4"
] | 507bf65b0a2e77666e78e755f040f616e7632c08bf018f59af743f8a8c141dc6 |
"""mbe.fragment: a class for dealing with Fragments and other standalone
functions."""
import os
import sympy
from toolz import frequencies
from . import utils
class Fragment(object):
"""A fragment is a molecule that can be combined with another
fragment.
"""
def __init__(self):
self.fxyz ... | berquist/mbe | mbe/fragment.py | Python | mpl-2.0 | 11,226 | [
"Q-Chem"
] | 47fe950100f568275473db9b4a95ac75e9c72eddae97b4077f0d72c101247c39 |
import os
import tensorflow as tf
import numpy as np
from text_loader import TextLoader
from model import Model
from parameters import model_params
from midi_interaction import MusicLoader
os.environ['TF_CPP_MIN_LOG_LEVEL'] = '2'
def train():
""" Train Action """
# Our model
model = Model(model_params)
... | ArnoGranier/MusicRNN | train.py | Python | mit | 4,603 | [
"NEURON"
] | b863eb9df3d61a4ee995d9e528532381f1bddc0e2b1e84b53daa4decfe4f1bd5 |
#from opengmcore import _opengmcore.adder as adder
from opengmcore import *
from __version__ import version
from functionhelper import *
from _inf_param import _MetaInfParam , InfParam
from _visu import visualizeGm
from _misc ... | recarroll/opengm | src/interfaces/python/opengm/__init__.py | Python | mit | 9,919 | [
"VisIt"
] | 611a5bb7d73b074e10834e3f6f2a23f73f21533da655fd56b1f2fbe70ad865ac |
#! /usr/bin/env python
"""
Implementation of the STIM map from [PAI19]
.. [PAI19]
| Pairet et al, 2019
| STIM map: detection map for exoplanets imaging beyond asymptotic Gaussian residual speckle noise**
| *MNRAS, 487, 2262*
| `doi:10.1093/mnras/stz1350 <http://doi.org/10.1093/mnras/stz1350>`_
"... | vortex-exoplanet/VIP | vip_hci/metrics/stim.py | Python | mit | 2,081 | [
"Gaussian"
] | 3df4bf313a5a8989f28018d9e9c730d914bbf2fe4aefd20eac15fef06a8492d3 |
# Orca
#
# Copyright 2006-2008 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/pronunciation_dict.py | Python | gpl-3.0 | 2,799 | [
"ORCA"
] | 848bceae459366c568e8304d22dfd070087dd0ae7cf27973ad592fe54c438681 |
# Installation source spoke classes
#
# Copyright (C) 2011, 2012 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 ... | vathpela/anaconda | pyanaconda/ui/gui/spokes/installation_source.py | Python | gpl-2.0 | 72,645 | [
"VisIt"
] | cefa9a4079608788ea0d3b769a5c50156fca8e2337793eaf799219abb4234ed8 |
#!/usr/bin/python
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2016 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it ... | kannon92/psi4 | doc/sphinxman/document_efpfrag.py | Python | gpl-2.0 | 5,068 | [
"Psi4"
] | 687ee8bb071199273c8186048bd109bcf3851605f32c15ec4771504d3b5c1cfc |
from astropy.io import fits as pyfits
# Conversion table from full filter names to single-letter abbreviations
# used in STARDUST and other S.Rodney code
FilterAlpha = {'unknown': '?',
'F225W': 'S', 'F275W': 'T', 'F336W': 'U', 'F390W': 'C',
'F350LP': 'W',
'F435W': 'B', 'F47... | srodney/hstphot | hstphot/util.py | Python | bsd-3-clause | 12,158 | [
"Gaussian"
] | da3b5259dd23c4a8c40f2e5c48560526d2f783c36e63e84d45d0dbbc3d555641 |
# 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 glob
import itertools
import logging
import math
import os
import re
import warnings
import xml.etree.cElementTree as ET
from collection... | Bismarrck/pymatgen | pymatgen/io/vasp/outputs.py | Python | mit | 151,442 | [
"CRYSTAL",
"VASP",
"pymatgen"
] | b2e1b9f5c67ab3f10c6e85cfb659e46c6ea4abb56eaccd0b31eceb56847a30fb |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | karllessard/tensorflow | tensorflow/python/ops/image_ops_impl.py | Python | apache-2.0 | 218,567 | [
"Gaussian"
] | fbfce9b47fcbeca4cbea6ebc3e1769d1f57868452ef7df359d1f2553af43e9e5 |
#import string
from django.core.urlresolvers import reverse
from django.shortcuts import render, redirect, get_object_or_404
from django.core import serializers
from django.http import HttpResponse, HttpResponseRedirect
# from django.contrib import messages
from django.contrib.auth import authenticate, login, logo... | avoajaugochukwu/suaveproject | suave/views.py | Python | mit | 13,467 | [
"BLAST"
] | d08660ceab50bb06d97ecdc7cd0b626fafe94989ab6f649fc3b68a3b8fec17ad |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes to define a phonon band structure.
"""
import collections
import numpy as np
from monty.json import MSONable
from pymatgen.core.lattice import Lattice
from pymatgen.core.stru... | richardtran415/pymatgen | pymatgen/phonon/bandstructure.py | Python | mit | 24,100 | [
"CRYSTAL",
"phonopy",
"pymatgen"
] | 23175008e17b05597b3f4cd3e0b1642a525d34f10c2a750b81d004d176b90e40 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | krafczyk/spack | lib/spack/spack/url.py | Python | lgpl-2.1 | 30,733 | [
"HOOMD-blue",
"VTK"
] | 42d27f013f6c15c59ea3bdfcbe504d1cf8f004972c2d3c629131d9db825271c6 |
# Google Material Design Colors as rgb or hex dictionaries
color_names = ["indigo", "red", "yellow", "brown", "orange",
"green", "blue", "amber", "pink", "light-blue",
"lime", "blue-grey", "deep-orange", "grey", "cyan",
"deep-purple", "purple", "teal", "light-green"]
color_subnames = ... | nre-aachen/GeMpy | gempy/colors.py | Python | mit | 31,153 | [
"Amber"
] | ecbd9d46cc256264b6e2188fe3ade9a5e541403828d68b1dc95b6094ee0dbeb0 |
import sys
import traceback
import logging
import re
import itertools
import string
import cStringIO
import ho.pisa as pisa
import pyPdf
import isodate
import cherrypy
import httpagentparser
from cgi import FieldStorage, escape
import turbogears, sendmail
from hubspace import inplace_i18n
from turbogears import contro... | thehub/hubspace | hubspace/controllers.py | Python | gpl-2.0 | 274,457 | [
"VisIt"
] | e7601c374aeea5881ad387a23d037e44b72b9fcbcfeb5a407d926f94cbc30d6c |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
CCSD density matrix
'''
import numpy
from pyscf import gto, scf, cc, ao2mo
mol = gto.M(
atom = 'H 0 0 0; F 0 0 1.1',
basis = 'ccpvdz')
mf = scf.RHF(mol).run()
mycc = cc.CCSD(mf).run()
#
# CCSD density matrix in MO basis
#
dm1 = mycc.m... | gkc1000/pyscf | examples/cc/01-density_matrix.py | Python | apache-2.0 | 1,066 | [
"PySCF"
] | 9557ee269365961371f45f849794d5be51420dcb88b24c7eac28d3cc68abfc25 |
"""Custom initializers for non-ResNet weights."""
import mxnet as mx
import numpy as np
from mxnet.util import is_np_array
@mx.init.register
class SegmentedXavier(mx.init.Xavier):
"""
Returns an initializer performing "Xavier" initialization independently for
each segment of weights.
Parameters
-... | mlperf/training_results_v0.7 | NVIDIA/benchmarks/ssd/implementations/mxnet/ssd/initializer.py | Python | apache-2.0 | 3,274 | [
"Gaussian"
] | 14fd922c59705017979f49967b67c66e91421ae6508a7d6bb16e0599cd36d387 |
#!/usr/bin/env python
""""
Simple implementation of http://arxiv.org/pdf/1502.04623v2.pdf in TensorFlow
Example Usage:
python draw.py --data_dir=/tmp/draw --read_attn=True --write_attn=True
Author: Eric Jang
"""
import tensorflow as tf
from tensorflow.examples.tutorials import mnist
import numpy as np
import os
... | ericjang/draw | draw.py | Python | apache-2.0 | 8,365 | [
"Gaussian"
] | 4457ac9fc1808bbbf3c01f1ab666c464e55a27d54dcb23eee62622fafd386714 |
#!/usr/bin/env python
"""leastsq_fit.py
This example shows how to fit a PDF to data via the method of
least-squares.
"""
import matplotlib.pyplot as plt
import numpy as np
import statspy as sp
import scipy.stats
# Define the true PDF (gaussian signal on top of an exponentially falling bkg)
pdf_true_sig = sp.PF("pd... | bruneli/statspy | examples/leastsq_fit.py | Python | bsd-3-clause | 2,739 | [
"Gaussian"
] | 2777e44f70dcf575f00f543c030fea7cec0782a6fa0be6a3b007770ab04de695 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# configuration - [insert a few words of module description on this line]
# Copyright (C) 2003-2011 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the te... | heromod/migrid | mig/grsfs-fuse/fs/core/configuration.py | Python | gpl-2.0 | 4,366 | [
"Brian"
] | a456f8640862b248ee969415aa0bdace0b549baa16fbdaf6b76290a8a25e0a20 |
# File: install.py
# Author: Brian A. Vanderburg II
# Purpose: An install builder to install subdirectories and files
# Copyright: This file is placed in the public domain.
##############################################################################
# Requirements
#############################... | Nils-TUD/Escape | source/tools/install.py | Python | gpl-2.0 | 6,809 | [
"Brian"
] | dffc88e808c9e05a2900b91ccd650ea3726a4a52dd21a4f022791ef5510239a3 |
# helper functions
import numpy as np
import matplotlib.pyplot as plt
import os
import pandas as pd
from diffpy.Structure import loadStructure
from pyobjcryst.crystal import CreateCrystalFromCIF
from diffpy.srreal.bondcalculator import BondCalculator
from diffpy.srreal.pdfcalculator import PDFCalculator
from diffpy.... | chiahaoliu/pdf_lib | pdf_lib/pdf_helper.py | Python | mit | 3,994 | [
"CRYSTAL"
] | 73e8d098bfbf2adf3d79f9cc67b8ec315853ba91724806d1e28057a08d8e2ad5 |
"""An NNTP client class based on RFC 977: Network News Transfer Protocol.
Example:
>>> from nntplib import NNTP
>>> s = NNTP('news')
>>> resp, count, first, last, name = s.group('comp.lang.python')
>>> print 'Group', name, 'has', count, 'articles, range', first, 'to', last
Group comp.lang.python has 51 articles, rang... | MalloyPower/parsing-python | front-end/testsuite-python-lib/Python-2.1/Lib/nntplib.py | Python | mit | 18,078 | [
"Brian"
] | 941928e5c9d4f1d58e6e3f06fa5c1ae396ed4c99dedca7bd57e4d118ef9d290d |
#!/usr/bin/env python3.5
# coding=utf-8
"""Threaded gps client"""
from __future__ import print_function
from threading import Thread
from time import sleep
try: # This kludge to get around imports with files and directories the same name.
import agps3 # Python 3
except ImportError:
from . import agps3 # Py... | wadda/gps3 | gps3/agps3threaded.py | Python | mit | 3,509 | [
"MOE"
] | 21777c595f2ed7a0485bac17082c79516e23d08c7726d2598939cfd69b6c1443 |
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