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"""
Copyright (C) <2010> Autin L.
This file ePMV_git/demo/loading_stat.py is part of ePMV.
ePMV 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
(... | corredD/ePMV | demo/loading_stat.py | Python | gpl-3.0 | 6,167 | [
"CRYSTAL"
] | 6b10170883d786cf5633481e55dd65b0c6d62e88291f26a7bc3eb2b23921ebbe |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS.
"""
import urllib
from datetime import datetime, timedelta
from textwrap import dedent
import pytz
from common.test.acceptance.fixtures.course import CourseFixture, CourseUpdateDesc, XBlockFixtureDesc
from common.test.acceptance.pages.common.auto_auth import A... | teltek/edx-platform | common/test/acceptance/tests/lms/test_lms.py | Python | agpl-3.0 | 45,460 | [
"VisIt"
] | f0257be101c47735d8efc11e7c4030c2e4e6eaacce9cb0c98b60ca2bd331e4a5 |
"""Generate self-contained HTML reports from MNE objects."""
# Authors: Alex Gramfort <alexandre.gramfort@inria.fr>
# Mainak Jas <mainak@neuro.hut.fi>
# Teon Brooks <teon.brooks@gmail.com>
#
# License: BSD (3-clause)
import base64
from io import BytesIO
from mne.proj import read_proj
import os
impor... | rkmaddox/mne-python | mne/report.py | Python | bsd-3-clause | 88,561 | [
"Mayavi"
] | 9551d3596f6c588c66e2be2bcd4b8853f6776126b16a3209dc353586258bb85d |
"""
This module simulations that can be run.
They MUST provide a step() function thet steps forward 1 ms.
They MUST log what they output, and return this with get_output()
The exception is "main_simulation_run", the one which creates and
runs every other sim.
"""
#FIXME/TODO?: Move to new-style class?
class NemoSimulat... | nico202/pyNeMo | libs/simulations.py | Python | gpl-2.0 | 11,461 | [
"NEURON"
] | 6efe740f5aeeb88850ec1fb3a8724822d834f5278a77291b57d3b88831aa86ce |
#__docformat__ = "restructuredtext en"
# ******NOTICE***************
# optimize.py module by Travis E. Oliphant
#
# You may copy and use this module as you see fit with no
# guarantee implied provided you keep this notice in all copies.
# *****END NOTICE************
# A collection of optimization algorithms. Version ... | rmcgibbo/scipy | scipy/optimize/optimize.py | Python | bsd-3-clause | 95,968 | [
"Gaussian"
] | 2b470bd2afd3da6d6670e0dd57cc0dade15a5e962e4a8a82a0c389df29f3b550 |
"""Guess the MIME type of a file.
This module defines two useful functions:
guess_type(url, strict=True) -- guess the MIME type and encoding of a URL.
guess_extension(type, strict=True) -- guess the extension for a given MIME type.
It also contains the following, for tuning the behavior:
Data:
knownfi... | harmy/kbengine | kbe/res/scripts/common/Lib/mimetypes.py | Python | lgpl-3.0 | 20,999 | [
"NetCDF"
] | 1a8a0dc4d8771c50821875f98242dbb01b074302ed01039942ceb35203b843c2 |
# coding=utf-8
# Copyright 2022 The Google Research 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 applicab... | google-research/google-research | depth_from_video_in_the_wild/randomized_layer_normalization.py | Python | apache-2.0 | 2,463 | [
"Gaussian"
] | 40b00bdfeeab55ad85a63cd7943ed4a5a17dc1b4c9e519445fac51f5ee42ea28 |
__doc__="""
pliu 20150511
python module for a ChIP-seq experiment that contains
replicates of ChIP-seq data for target and/or control
"""
import os
import sys
import multiprocessing as mp
import Util
class ChIPSeqExperiment:
def __init__(self):
self.param = None ## reference to input paramet... | pliu55/RSEM | pRSEM/ChIPSeqExperiment.py | Python | gpl-3.0 | 8,875 | [
"Bowtie"
] | d3ff2d0d2775efe38418bcfd907be8e375fa5cc4145c37e1ec4266dbc7e19d39 |
# gpaw-python Segmentation faults
# when gpaw-python and numpy are linked to different blas
import numpy as np
import sys
from math import sqrt
from ase import Atom, Atoms
from gpaw import GPAW
from gpaw import ConvergenceError
kpts = (2,1,1)
a=1.42
c=3.355
# AB stack
atoms = Atoms('C4',[
(1/3.0,1/3.0... | qsnake/gpaw | gpaw/test/numpy_zdotc_graphite.py | Python | gpl-3.0 | 784 | [
"ASE",
"GPAW"
] | c17320621650ab9d7df96ccc21baef228546e050904382b64b1443e1a51826da |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Trinity(MakefilePackage):
"""Trinity, developed at the Broad Institute and the Hebrew Univ... | LLNL/spack | var/spack/repos/builtin/packages/trinity/package.py | Python | lgpl-2.1 | 4,808 | [
"BLAST",
"Bowtie"
] | 2d59d8e629267484f17a4d5fd8e1bdb5784356c8d1f7dd9aff82582e20901883 |
#please add any of the toy examples you build with comprehensions here
students = ['Andrew', 'Casey', 'Nate', 'Jordan', 'Jimmy']
student_list = [' '.join(student) for student in students]
# print(student_list)
fish_tuple = ('blowfish', 'clownfish', 'catfish', 'octopus')
fish_list = [fish for fish in fish_tuple if f... | developerQuinnZ/this_will_work | student-work/andrew_k_telleria/week_2/day_1/working_with_csvs/comprehensions.py | Python | mit | 926 | [
"Octopus"
] | 8453b720e1c96d17027022cca23f0dc863cbdb89bea00aa559002f91bd4bd10f |
"""Script to combine ReferenceGenomes into a single one.
"""
import os
from Bio import SeqIO
from Bio.Alphabet.IUPAC import ambiguous_dna
from main.models import Chromosome
from main.models import Dataset
from main.models import ReferenceGenome
from utils.import_util import add_dataset_to_entity
from utils import ge... | woodymit/millstone | genome_designer/utils/combine_reference_genomes.py | Python | mit | 5,326 | [
"Biopython"
] | 47aa0cf0cb9d753f977bd6ee9efda86d7d654aa01a8f677a603a8b088c3b7a3f |
"""\
pyints.py Python implementations of work functions for Gaussian
integrals in the PyQuante package.
The equations herein are based upon
'Gaussian Expansion Methods for Molecular Orbitals.' H. Taketa,
S. Huzinaga, and K. O-ohata. H. Phys. Soc. Japan, 21, 2313, 1966.
[THO paper].
The accompanying module ci... | gabrielelanaro/pyquante | PyQuante/pyints.py | Python | bsd-3-clause | 13,117 | [
"Gaussian"
] | 164f3f3346802d28cf6769894633af039064a525d8646ab825861aaeb4b30f4f |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
import unittest
import warnings
import numpy as np
from monty.serialization import loadfn
from pymatgen.electronic_structure.core import OrbitalType, Spin
from pymatgen.io.vasp import Vasprun
from p... | gmatteo/pymatgen | pymatgen/electronic_structure/tests/test_boltztrap2.py | Python | mit | 14,994 | [
"VASP",
"pymatgen"
] | a9bddea9919c5b059b30e85b56a8b39d5b4b14298f2b5f5de18ae85a0c66de08 |
#!/usr/bin/env python
"""Parser for Google chrome/chromium History files."""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import itertools
from future.moves.urllib import parse as urlparse
from past.builtins import... | demonchild2112/travis-test | grr/core/grr_response_core/lib/parsers/chrome_history.py | Python | apache-2.0 | 4,569 | [
"VisIt"
] | aa42596dec8c2ece0a89d798a9aa81f8b489ed37437cdaebae2ffad8c96558fc |
import sys
from numpy import *
set_printoptions(precision=2)
def add_noise_gaussian(M, sigma):
N = random.normal(0, sigma, M.shape)
M += N
def add_noise_uniform(M, rng):
N = (random.rand(M.shape) * rng) - (rng/2.0)
M += N
def main():
rt = matrix(loadtxt("rt.txt"))
print("original params:\n", rt, "... | ivankreso/stereo-vision | scripts/sba_tester/add_noise.py | Python | bsd-3-clause | 539 | [
"Gaussian"
] | 0736f0dcfff84601337a58533982e83ce19cc610c51f9fb7896c3712fbc85387 |
#!/usr/bin/env python
# Copyright 2015.
# Michael A. DeJesus, Chaitra Ambadipudi, and Thomas R. Ioerger.
#
#
# This file is part of TRANSIT.
#
# TRANSIT 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 Foun... | mad-lab/transit | src/pytpp/tpp_tools.py | Python | gpl-3.0 | 56,453 | [
"BWA"
] | 41664f1d1d67b88c38aa0150128470693bcc92e206998b048a4347945d54ae5d |
#!/usr/bin/env python
# CREATED:2013-03-08 15:25:18 by Brian McFee <brm2132@columbia.edu>
# unit tests for librosa.filters
#
# This test suite verifies that librosa core routines match (numerically) the output
# of various DPWE matlab implementations on a broad range of input parameters.
#
# All test data is generated... | stefan-balke/librosa | tests/test_filters.py | Python | isc | 13,255 | [
"Brian"
] | d8f2997969dda8763b5f1b45e38ccbec114c375254c397d390d9873daec9d48f |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides objects for extracting timing data from the ABINIT output files
It also provides tools to analye and to visualize the parallel efficiency.
"""
from __future__ import unicode_literals, di... | czhengsci/pymatgen | pymatgen/io/abinit/abitimer.py | Python | mit | 29,938 | [
"ABINIT",
"pymatgen"
] | bceec660a54e99136047468dfb066431a4e1f97945174b0926badcb1a6462ef3 |
import logging
from unittest import TestCase
import uuid
from mock import patch
from brainiak.prefixes import MemorizeContext
from brainiak.utils.sparql import *
from tests.mocks import mock_schema, triplestore_config
class MockSchemaTestCase(TestCase):
maxDiff = None
def test_mock_schema(self):
c... | bmentges/brainiak_api | tests/unit/test_utils_sparql.py | Python | gpl-2.0 | 54,276 | [
"Galaxy"
] | ecd5ca9c8da44a3c1a72979dd87553cdb2e881839027c13f0546f9d62978892f |
import sys
import os
import vtk
import imgtools
# Make sure we have enough arguments passed by the user
if len(sys.argv) < 3:
print("usage:\npython main.py <input folder> <output folder>")
exit()
input_folder_name = sys.argv[1]
output_folder_name = sys.argv[2]
# Check if the input directory exists
if not os.path... | zibneuro/convert | vol2mesh/main.py | Python | bsd-3-clause | 3,489 | [
"Gaussian",
"VTK"
] | d51d709a1d5134427391ffd47aa09252b719ee01753b6254439d9629e98faa92 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | BackupTheBerlios/espressopp | src/storage/DomainDecompositionNonBlocking.py | Python | gpl-3.0 | 2,572 | [
"ESPResSo"
] | f5e05e398aeff8892601a08cf51680f10c6ed5ca63679094efcff4572bee994b |
#
# Copyright 2015 The AMP HTML 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 applic... | DistroScale/amphtml | validator/validator_gen_js.py | Python | apache-2.0 | 26,585 | [
"VisIt"
] | 692709b22d3e5db4573c64018dfe1bd0570666c88e2da6f838a018f38aeb6856 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | andysim/psi4 | psi4/driver/procrouting/proc_table.py | Python | gpl-2.0 | 10,293 | [
"CFOUR",
"Psi4"
] | e8ea710ac5a8e2470125741000128a4b873000061e6ac7eb2935846314f98725 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | kdmurray91/scikit-bio | skbio/io/format/tests/test_stockholm.py | Python | bsd-3-clause | 43,046 | [
"scikit-bio"
] | cf9cdae851a411fcc33fd0f4aed36b8fc4307883619a7418dacfb3e5ca000c30 |
#
# Copyright (c) 2004 Conectiva, Inc.
#
# Written by Anders F Bjorklund <afb@users.sourceforge.net>
#
# This file is part of Smart Package Manager.
#
# Smart Package Manager 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 Softwar... | 64studio/smart | smart/interfaces/qt4/channels.py | Python | gpl-2.0 | 31,129 | [
"CRYSTAL"
] | c68ec7522feb4299134d3f726ef201fa8cb706f257fafa2cdf4e05a3bf330f1c |
import numpy as np
import matplotlib.pyplot as plt
from kernels import GaussianKernel
# generate the center of the gaussian and the grid
x_q = np.random.uniform(-1,1,2)
x_p = np.meshgrid(np.linspace(-5,5,100),np.linspace(-5,5,100))
x_p_0 = np.reshape(x_p[0],(-1,1))
x_p_1 = np.reshape(x_p[1],(-1,1))
# generate a rando... | pvarin/Dynamics-LGP | src/testGaussianKernel.py | Python | mit | 1,004 | [
"Gaussian"
] | 354edd8ee420ba330f457b06c0a1d684799e0d802b225c5eedc12f39f0c3d839 |
## Copyright (C) 2005-2006 Graham I Cummins
## 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 version.
##
## This program is d... | gic888/MIEN | nmpml/pprocs.py | Python | gpl-2.0 | 4,147 | [
"NEURON"
] | 2bdc9b029deac9e26cc5ca1b0a0e79b68b9d7897e07645f59f24e3dd95de5b0d |
"""
Collection of physical constants and conversion factors.
Most constants are in SI units, so you can do
print '10 mile per minute is', 10*mile/minute, 'm/s or', 10*mile/(minute*knot), 'knots'
The list is not meant to be comprehensive, but just a convenient list for everyday use.
"""
from __future__ import division... | mbayon/TFG-MachineLearning | venv/lib/python3.6/site-packages/scipy/constants/constants.py | Python | mit | 8,252 | [
"Avogadro"
] | 1b6271b5f36fd69353a65937af2e85c3e92fe4913ff3a88b67c111f9b554f6ea |
import logging
from pylons import request, response, session, tmpl_context as c
from zkpylons.lib.helpers import redirect_to
from pylons.decorators import validate
from pylons.decorators.rest import dispatch_on
from formencode import validators, htmlfill, ForEach, Invalid
from formencode.variabledecode import NestedV... | neillc/zookeepr | zkpylons/controllers/person.py | Python | gpl-2.0 | 23,348 | [
"VisIt"
] | 11802c798d929cf3b0bc1599d1f57ffbff6bcab6c30cac62f53b3855573e676f |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/transitions | openlp/plugins/images/__init__.py | Python | gpl-2.0 | 2,239 | [
"Brian"
] | 1e698129343a5406897c61d84edd2e702e1e35611450c5a21db71b4b34669841 |
import pathlib
import diffhtml
import flask
from flask import request
from markupsafe import Markup
app = flask.Flask(
'Diff-HTML Demo',
template_folder=pathlib.Path(__file__).parent.joinpath('templates'),
)
DEFAULT_A = """
I am the very model of a modern Major-General,
I've information vegetable, animal,... | uranusjr/diffhtml | demo/app.py | Python | isc | 1,395 | [
"MOE"
] | 55e200f670ebb4f3ec576635923b5ddc0e197a5c9989f1edfa54bcfb93e3cb0c |
"""
Service handler for FTS3DB using DISET
.. literalinclude:: ../ConfigTemplate.cfg
:start-after: ##BEGIN FTS3Manager
:end-before: ##END
:dedent: 2
:caption: FTS3Manager options
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$... | ic-hep/DIRAC | src/DIRAC/DataManagementSystem/Service/FTS3ManagerHandler.py | Python | gpl-3.0 | 6,992 | [
"DIRAC"
] | 01421b262f8dd630b0dcb1fb33a87fddcd5d76f694ed1c533f841eda5d23babe |
# tr.contrib.learn , classifier, prediction
# 1. Dataset
# 2. Classifier
# 3. Train
# 4. Evaluate
# 5. Predict
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import tensorflow as tf
import numpy as np
IRIS_TRAINING = "iris_training.csv"
IR... | Wonjuseo/Project101 | 1/1-8. iris_clasification.py | Python | apache-2.0 | 1,586 | [
"NEURON"
] | d8b5272da74a9f1aed3b401a470148b3dae601246fd7280d10f05753a6aa693c |
"""
A first test for the ELBO on the catalysis problem.
The target is consisted of an uninformative prior and a Gaussian likelihood.
The approximating mixture has two components.
Author:
Panagiotis Tsilifis
Date:
6/12/2014
"""
import numpy as np
import matplotlib.pyplot as plt
import os
import cPickle as ... | ebilionis/variational-reformulation-of-inverse-problems | unittests/test_optimize_catalysis_full_dmnl.py | Python | gpl-2.0 | 6,880 | [
"Gaussian"
] | 4160249658fba749aa1cc88599f0a8e63757daa603d9bc58f53413008b9d8c86 |
# Copyright (c) 2000 Autonomous Zone Industries
# This file is licensed under the
# GNU Lesser General Public License v2.1.
# See the file COPYING or visit http://www.gnu.org/ for details.
__revision__ = "$Id: counterparties.py,v 1.12 2003/03/28 13:41:18 myers_carpenter Exp $"
"""
Implements counter party ob... | zooko/egtp_new | egtp/counterparties.py | Python | lgpl-2.1 | 29,891 | [
"VisIt"
] | 4723408338d8cbabb0023a604d04e1672e56dddd6270c0fbab10bf20af37d170 |
# 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... | fweik/espresso | testsuite/python/ek_common.py | Python | gpl-3.0 | 2,361 | [
"ESPResSo"
] | a1e91afb9f7248089003d4e38410750e36eb95d62f5cbebdb9b17f4c02df2e33 |
from django.db import models, migrations
from django.utils.text import slugify
from django.utils.timezone import now
from successstories.utils import get_field_list, convert_to_datetime
MARKER = '.. Migrated from Pages model.\n\n'
DEFAULT_URL = 'https://www.python.org/'
normalized_company_names = {
'dlink': 'D-L... | manhhomienbienthuy/pythondotorg | successstories/migrations/0006_auto_20170726_0824.py | Python | apache-2.0 | 3,773 | [
"Mayavi"
] | 53eb86f156f40b46a568016d96398156235d765ca2b3da780d011e87e7a1ba31 |
# QUANTCONNECT.COM - Democratizing Finance, Empowering Individuals.
# Lean Algorithmic Trading Engine v2.0. Copyright 2014 QuantConnect Corporation.
#
# 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 Lic... | AlexCatarino/Lean | Algorithm.Python/NLTKSentimentTradingAlgorithm.py | Python | apache-2.0 | 2,830 | [
"VisIt"
] | 14a57cd322299f836d7d3de2510ae86ebc8de935b3eb6e7e66cc025c7cc6ee74 |
# pylint: disable=missing-docstring
# pylint: disable=redefined-outer-name
from lettuce import world, step
from common import course_location
from problems_setup import PROBLEM_DICT
from nose.tools import assert_in
@step(u'I am viewing a course with multiple sections')
def view_course_multiple_sections(step):
cr... | nttks/edx-platform | lms/djangoapps/courseware/features/navigation.py | Python | agpl-3.0 | 5,623 | [
"VisIt"
] | 83580bfe12b15f305233ea4bd6ed16efaf58b6298fc2490f33716a7efd2ca1a1 |
#-------------------------------------------------------------------------------
# Copyright (c) 2011, Kafti team
#
# Released under the MIT license. See the LICENSE file for details.
#-------------------------------------------------------------------------------
# R0904: Too many public methods (%s/%s) Used when... | kafti/pynasl | pynasl/visitors/ast2py/translator.py | Python | mit | 12,328 | [
"VisIt"
] | 5f402428d89ec91375f8e1d851ef5d8125c9837b9a72f9b1ab8d505b96ca43c5 |
"""
Pymatgen-db is a database add-on for the Python Materials Genomics (pymatgen)
materials analysis library. It enables the creation of Materials
Project-style MongoDB databases for management of materials data and
provides a clean and intuitive web ui for exploring that data. A query engine
is also provided to enable... | migueldiascosta/pymatgen-db | matgendb/__init__.py | Python | mit | 542 | [
"pymatgen"
] | 4f9c4a64d097b2d423aac64df7e23b789af84fbc182d6c0e30646e225ce55771 |
'''
:Tags: Python
Usage
========================================================
Enrichment analysis (Gene set enrichment analysis(GSEA))
========================================================
This pipeline is a wrapper of script runGSEA.py (enrichment analysis
by using GSEA. Further description is provided below.)... | CGATOxford/CGATPipelines | CGATPipelines/pipeline_enrichment.py | Python | mit | 24,658 | [
"Cytoscape"
] | 3e4c37f40ca7519063f72a31e40429e49df8b884f3c5d6d0a0577a544a0663b6 |
# -*- coding: utf-8 -*-
"""
InaSAFE Disaster risk assessment tool developed by AusAid and World Bank
- **Functionality related to shake events.**
Contact : ole.moller.nielsen@gmail.com
.. note:: This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public Lice... | wonder-sk/inasafe | realtime/shake_event.py | Python | gpl-3.0 | 71,808 | [
"VisIt"
] | 1ee4df7eab87186e11ef13b9a9dba432d975273290c7c8e2725a678463f3592d |
import altair as alt
import urllib.parse
import pandas as pd
from IPython.display import display, HTML
def plot_with_yoy(df, col, title):
height = 150
return alt.Chart(df.reset_index(), height=height).mark_bar().encode(
x='Year:O',
y=alt.Y(f'{col}:Q',
axis=alt.Axis(title=f'Num... | ciyer/outlier | public/articles/2021-review/plots.py | Python | gpl-3.0 | 10,777 | [
"Gaussian"
] | 8d09d62a41eff2df2e34070d6ca0f21633b36632e3a64d6254065f7b45ca6337 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# (c) 2018, Chris Houseknecht <@chouseknecht>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version': '1.1',
... | agaffney/ansible | test/support/integration/plugins/modules/k8s.py | Python | gpl-3.0 | 9,564 | [
"Galaxy"
] | 51ad27cfce42a31112bad7e36ee8127863e445d98c3674ac7234bdcb1ff8b5cb |
# -*- coding: utf-8 -*-
# Copyright (c) 2015, ESS LLP and contributors
# For license information, please see license.txt
from __future__ import unicode_literals
import frappe
from frappe.model.document import Document
import json
from frappe.utils import getdate, add_days
from frappe import _
import datetime
from frap... | chdecultot/erpnext | erpnext/healthcare/doctype/patient_appointment/patient_appointment.py | Python | gpl-3.0 | 14,261 | [
"VisIt"
] | a39f0908e822ded5c9acc1bd6976be861c9bd413ce6269733a7d775b1306649a |
"""
Accessibility tests for Studio Library pages.
Run just this test with:
SELENIUM_BROWSER=phantomjs paver test_bokchoy -d accessibility -t test_studio_library_a11y.py
"""
from ..tests.studio.base_studio_test import StudioLibraryTest
from ..pages.studio.library import LibraryEditPage
class StudioLibraryAxsTest(Stud... | playm2mboy/edx-platform | common/test/acceptance/accessibility/test_studio_library_a11y.py | Python | agpl-3.0 | 940 | [
"VisIt"
] | 3c0c8202fc4c600aba6eebd5dc95c9cc49baa3720c003a0715e4e241e314c86d |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | capoe/espressopp.soap | src/integrator/VelocityVerletOnRadius.py | Python | gpl-3.0 | 1,955 | [
"ESPResSo"
] | 2d3008924e8054a96f54ece97a67d13b6de1c210f572dadaa4ec355dea38c2d4 |
import lb_loader
import numpy as np
import pandas as pd
import simtk.openmm as mm
from simtk.openmm import app
from simtk import unit as u
from openmmtools import integrators, testsystems
pd.set_option('display.width', 1000)
n_steps = 3000
temperature = 300. * u.kelvin
masses = [1.0, 2.0, 3.0, 3.5, 4.0]
data = []
for... | kyleabeauchamp/HMCNotes | code/obsolete/generate_hmr_data.py | Python | gpl-2.0 | 1,507 | [
"OpenMM"
] | 3c9a4be35de75bf382280255662d27cb10f8e18e6c22dd73759b9f71bdc6129a |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | magic/sources/list.py | Python | agpl-3.0 | 5,682 | [
"Galaxy"
] | e71fbbd23f93f21cac8cd31431f06f4c0512ba9ec5baa2485fad6a261f62e271 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2007 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program 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 F... | andrebellafronte/stoq | stoqlib/reporting/payment.py | Python | gpl-2.0 | 3,858 | [
"VisIt"
] | a943c93cdc1b1a1d1e8deed6db729fc0155d892cbdbcbb446e910cb4012cd3d5 |
########################################################################
#
# Copyright 2014 Johns Hopkins University
#
# 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... | idies/pyJHTDB | examples/threshold.py | Python | apache-2.0 | 9,437 | [
"Mayavi"
] | b3a9739ae820524621d9ec1981080470146badab2aed172077c21ee05e2ca727 |
"""
Description:
Provides a simple VTK widget for pyGtk. This embeds a
vtkRenderWindow inside a GTK widget. This is based on
vtkTkRenderWidget.py. The GtkVTKRenderWindowBase class provides the
abstraction necessary for someone to use their own interaction
behaviour. The method names are similar to those ... | collects/VTK | Wrapping/Python/vtk/gtk/GtkVTKRenderWindow.py | Python | bsd-3-clause | 17,606 | [
"VTK"
] | 7317a21e0cc909c01e0c8280dd5f0f40a02599649f7926340e5748fc7475818e |
# Copyright (C) 2012 Victor Semionov
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice, this
# list of conditions and ... | vsemionov/npamp | npamp/core.py | Python | bsd-2-clause | 19,527 | [
"ASE"
] | f47a8efc446aa64cbfee97975b8f8e9ebf0c1ba5f66d25228e6c919ddabb42dc |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals, division, print_function
import unittest
from pymatgen.io.abinitio.launcher import ScriptEditor
class ScriptEditorTest(unittest.TestCase):
def test_base(self):
... | sonium0/pymatgen | pymatgen/io/abinitio/tests/test_launcher.py | Python | mit | 671 | [
"pymatgen"
] | 4ac8f1d2a79538f1515c1d0679c5d58e2ef0d0c2ca0e67d87842e90ed0b9ff36 |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import numpy as np
__doc__ = """
PyKrige
=======
Code by Benjamin S. Murphy and the PyKrige Developers
bscott.murphy@gmail.com
Summary
-------
Function... | rth/PyKrige | pykrige/variogram_models.py | Python | bsd-3-clause | 2,172 | [
"Gaussian"
] | f763536ca84a599f085b6a93fdccdb447f3059373e71d99f1b81e96acdf16f90 |
#--------------------------------------------------------------------------
# Software: InVesalius - Software de Reconstrucao 3D de Imagens Medicas
# Copyright: (C) 2001 Centro de Pesquisas Renato Archer
# Homepage: http://www.softwarepublico.gov.br
# Contact: invesalius@cti.gov.br
# License: GNU ... | fabio-otsuka/invesalius3 | invesalius/gui/dicom_preview_panel.py | Python | gpl-2.0 | 29,268 | [
"VTK"
] | a537a1c78a652e387d955b462a4d8e2ff2c71791e13a95e8a6b961cdd1b256e3 |
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.contrib.auth.decorators import login_required
from django.urls import path, re_path
from django.views.defaults import (
bad_request,
page_not_found,
... | KlubJagiellonski/pola-backend | pola/config/urls.py | Python | bsd-3-clause | 3,355 | [
"VisIt"
] | 1e1e6f382ae701b2f029b19fa57bc51eecd232a1035daaa4f546cb67cfbbc037 |
# ----------------------------------------------------------------------
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
# http://lammps.sandia.gov, Sandia National Laboratories
# Steve Plimpton, sjplimp@sandia.gov
#
# Copyright (2003) Sandia Corporation. Under the terms of Contract
# DE... | timattox/lammps_USER-DPD | python/lammps.py | Python | gpl-2.0 | 36,940 | [
"LAMMPS"
] | 2b246ffcd1ac3fd4ab68779a0b634aad5275472436f4f4346468d5d0c940c739 |
#
# Copyright (C) 2013,2014 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... | KonradBreitsprecher/espresso | samples/wang_landau_reaction_ensemble.py | Python | gpl-3.0 | 3,440 | [
"ESPResSo"
] | 0c22ec5e39953ca057e8392acb72d4e2312a339074b343dcc458081b4f6b21b0 |
# Copyright 2016 Autodesk Inc.
#
# 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 writing... | tkzeng/molecular-design-toolkit | moldesign/models/pyscf.py | Python | apache-2.0 | 21,691 | [
"Molpro",
"PySCF"
] | 99518db0b93010658ec3e2f067b4864eb91e2b96b4fa2a66eaec614f86b138ae |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Enumerator with the libxc identifiers.
This is a low level object, client code should not interact with LibxcFunc directly
but use the API provided by the Xcfunc object defined in core.xcfunc.py.
Part of thi... | mbkumar/pymatgen | pymatgen/core/libxcfunc.py | Python | mit | 13,158 | [
"pymatgen"
] | 58ffc7057f1d1373b4023c9800247c762ad2188edbd6cedb9a3e65cf41adb9e2 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | marscher/mdtraj | MDTraj/io.py | Python | lgpl-2.1 | 12,268 | [
"MDTraj"
] | 301e7a24828f2e187830ba553e7eb86fcc0ccd49e88cef255cc2025bd7a07306 |
#!/usr/bin/env python
# Based heavily on the Bowtie 2 data manager wrapper script by Dan Blankenberg
from __future__ import print_function
import argparse
import os
import shlex
import subprocess
import sys
from json import dumps, loads
DEFAULT_DATA_TABLE_NAME = "hisat2_indexes"
def get_id_name(params, dbkey, fasta... | Delphine-L/tools-iuc | data_managers/data_manager_hisat2_index_builder/data_manager/hisat2_index_builder.py | Python | mit | 3,596 | [
"Bowtie"
] | f245571d33186f34a5fb99b83f92e7e3716eaeece26826d52c4bfa13581872c9 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import pylid
from collections import Counter
ro = pylid.PyLID(3)
ro.total_ngrams = 60720033
ro.lang = 'ro'
ro.ngrams = Counter({
u'#de': 618454,
u'de#': 480736,
u're#': 470485,
u'te#': 467717,
u'#\xeen': 458944,
u'are': 447940,
u'le#': 399364,
... | dmort27/pylid | pylid/langs/ro.py | Python | mit | 206,035 | [
"ASE",
"BWA",
"EPW",
"Elk",
"MOE"
] | 5555892242234169a55bf8178e3106740fba158dd07245eb8564f26c9b89709e |
#!/usr/bin/env python
__author__ = 'Mike McCann'
__copyright__ = '2011'
__license__ = 'GPL v3'
__contact__ = 'mccann at mbari.org'
__doc__ = '''
Master loader for all CANON activities in September 2010
Mike McCann
MBARI 22 April 2012
'''
import os
import sys
parentDir = os.path.join(os.path.dirname(__file__),... | josephmfaulkner/stoqs | stoqs/loaders/CANON/loadCANON_september2010.py | Python | gpl-3.0 | 2,213 | [
"NetCDF"
] | f49c89d32bdecbe339f654e9dbec9bb723aaecff4004a72362dfe5bee989f0e9 |
#
# mainTab
#
tab = self.notebook.mainTab
tab.settings['Program'] = 'abinit'
tab.settings['Output file name'] = 'Na2SO42.out'
#
# SettingsTab
#
tab = self.notebook.settingsTab
tab.settings['Eckart flag'] = True
tab.settings['Neutral Born charges'] = False
tab.settings['Sigma value'] = 2
tab.settings['Mass definition'] ... | JohnKendrick/PDielec | Examples/AbInit/Na2SO42/script.py | Python | mit | 1,924 | [
"ABINIT"
] | c0582754cc2b6f21b3549185dacb7b4bb6a8b3faadca03d6b78d03c479ae57e3 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | skosukhin/spack | var/spack/repos/builtin/packages/r-affycoretools/package.py | Python | lgpl-2.1 | 2,633 | [
"Bioconductor"
] | 2ecc9a975df5ea08582c2ea2a29407d90fa4f043806add5fcc9f17b5e649b617 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2013 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program 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 F... | tiagocardosos/stoq | stoqlib/gui/wizards/workorderquotewizard.py | Python | gpl-2.0 | 15,716 | [
"VisIt"
] | ee0b5f588647384d9f2c79d9005ccaf1690cf0238a43dbd91473078287f71eec |
#!/usr/bin/env python
from datetime import datetime, timedelta
from collections import OrderedDict
import calendar
import sys
from ecmwfapi import ECMWFDataServer
import time
start_time = time.time()
server = ECMWFDataServer()
def retrieve_interim():
"""
A function to demonstrate how to iterate effi... | joelfiddes/toposubv2 | test/eraRetrievePLEVEL.py | Python | gpl-3.0 | 3,645 | [
"NetCDF"
] | 44218c0a76e24b816a46e459049ea36d38ebe9060469247da854f1d9f99de5d2 |
#! /usr/bin/env python
"""
@name: src/install.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2016-2017 by D. Brian Kimmel
@license: MIT License
@note: Created May 11, 2016
@Summary: Install.
This is run after the user 'pyhouse' is created and functional.
"""
# Imp... | DBrianKimmel/PyHouse_Install | install.py | Python | mit | 2,484 | [
"Brian"
] | f8873ef119f0d80423fb821aaf1ce9744da41265165845cb077e856f9a5eccb6 |
r"""
File I/O (:mod:`skbio.io`)
==========================
.. currentmodule:: skbio.io
This package provides I/O functionality for skbio.
Supported file formats
----------------------
For details on what objects are supported by each format,
see the associated documentation.
.. currentmodule:: skbio.io.format
.. au... | anderspitman/scikit-bio | skbio/io/__init__.py | Python | bsd-3-clause | 7,859 | [
"scikit-bio"
] | f83091fd2f4b5120b6c7127189858a7c49b256f0a8d105404b113989f76f7dbc |
import numpy as np
class GeneticAlgorithm(object):
"""
Implement a simple generational genetic algorithm as described in the instructions
"""
def __init__(self, chromosomeShape,
errorFunction,
elitism=1,
populationSize=25,
mutationProbabi... | DominikDitoIvosevic/Uni | AI/lab4/geneticAlgorithm.py | Python | mit | 5,684 | [
"Gaussian"
] | 0884264d38b7803ceb3cd23cd2da1c94698ecbb58063d346f0d80107dceccce0 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
DOCUMENTATION = '''
---
module: svc
author: Brian Coca
version_added:
short_description: Manage daemontools services.
description:
- Controls daemontools services on remote hosts using the svc utility.
options:
name:
required: true
description:
... | adematte/ansible-modules-extras | system/svc.py | Python | gpl-3.0 | 8,662 | [
"Brian"
] | 6a2a3646493ce0a5bc1b743ceb8b9212afa9d8acbe456ac63a1efa2772d4c745 |
"""Get useful information from live Python objects.
This module encapsulates the interface provided by the internal special
attributes (co_*, im_*, tb_*, etc.) in a friendlier fashion.
It also provides some help for examining source code and class layout.
Here are some of the useful functions provided by this module:... | batermj/algorithm-challenger | code-analysis/programming_anguage/python/source_codes/Python3.5.9/Python-3.5.9/Lib/inspect.py | Python | apache-2.0 | 114,199 | [
"VisIt"
] | d78f4ab5fc55f1f58611ebc0337f7e68a14011ffa8dd5f270ab883ba84405bce |
from __future__ import print_function
"""Lattice data - Face Centered Cubic"""
import numpy as np
from ase.cluster.data.symmetry import *
# Definition of symmetries
basesymmetries = [np.matrix([[-1, 0, 0], # Mirror x-axis
[0, 1, 0],
[0, 0, 1]]),
... | suttond/MODOI | ase/cluster/data/fcc.py | Python | lgpl-3.0 | 10,315 | [
"ASE"
] | 7f3d7f939a7b8326750bcdff7f85845a8a92d422dccf10cdf0f0a58c423da4e9 |
from ovito import *
assert(len(ovito.version) == 3)
print(ovito.version_string)
print(ovito.gui_mode)
print(ovito.headless_mode)
# Progress display
progress = ovito.get_progress_display()
if progress is not None:
print(progress.canceled) | srinath-chakravarthy/ovito | tests/scripts/test_suite/global_namespace.py | Python | gpl-3.0 | 243 | [
"OVITO"
] | 9d84a161941e4bcdc9f2ae84eaebff2888c4ce4cf5cd116ecbbf40099587d40e |
# Script control setup area
# script info
__script__.title = 'KKB Plot and Reduction 14.1.2017 BATCH'
__script__.version = '2.0'
# 2019-06-16 Add sample file temperature in batch file
from math import sqrt, sin, exp
from datetime import datetime, timedelta
from bisect import bisect_left
from __builtin... | Gumtree/Kookaburra_scripts | Internal/KKB-Plot and Reduction - export specifc q-values.py | Python | epl-1.0 | 57,383 | [
"CRYSTAL"
] | 42f7d7755fb27d08408a4c5182c722c0bf3c013716770600e4db9e9f27968cb1 |
# -*- coding: utf-8 -*-
#########################################################################
#
# Copyright (C) 2018 OSGeo
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 ... | timlinux/geonode | geonode/tests/bdd/e2e/fixtures/browser.py | Python | gpl-3.0 | 1,392 | [
"VisIt"
] | a1f0cdaf9982f47ab24e6689eafa477924d2502ddc2ebd26f96317ff9dd1c4bb |
from rdkit import DataStructs
from rdkit import RDConfig
from rdkit import Chem
from rdkit.Chem import ChemicalFeatures, rdDistGeom, AllChem
from rdkit import Geometry
import unittest, os
def lstFeq(l1, l2, tol=1.e-4):
if (len(list(l1)) != len(list(l2))):
return 0
for i in range(len(list(l1))):
if not feq... | ptosco/rdkit | Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py | Python | bsd-3-clause | 7,163 | [
"RDKit"
] | 14ab81bfbbcad905c9bad277f7ef2ae5e1e2b4eda30125bdc46801d712a38df0 |
#!/usr/bin/python
"""MouseMorph, an automatic mouse MR image processor
Simple image processing functions, and tools for working with groups of NIfTI images.
With loop_and_save(), you can apply any compatible function to an entire directory of images.
Most of these were composed to fulfil a specific need. All should... | nmpowell/mousemorph | mousemorph/mm_functions.py | Python | bsd-3-clause | 135,180 | [
"Gaussian"
] | 0e57f39d2722bcd5203ccb345e4829c8b2bc71d3ab1349726c944eea2db33cf5 |
"""
Performs filtering methods
Todo:
1) Set intersection of species/translation sequences
2) Set intersection of 50 kb regions
3) Set intersections of all context genes present
4) Set intersection of key context genes present
5) Use e-values for tie breakers
"""
from bx.intervals import *
from collections import defa... | idoerg/BOA | src/filter/interval_filter.py | Python | gpl-3.0 | 5,118 | [
"BLAST"
] | 55a60229ba5ebea8e315782201811f8f6c6610b8044e1edf5820162154c4d37e |
#Copyright (C) 2013 Alex Nitz
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 3 of the License, or (at your
# option) any later version.
#
# This program is distributed in the h... | tjma12/pycbc | pycbc/strain/strain.py | Python | gpl-3.0 | 73,950 | [
"Gaussian"
] | 05df2501a1208e320311459dd4c17c7105acfc88da1fff060de84fcfd1e237c4 |
"""Test passing arguments of various types
Created on Sept 19, 2010 by David Gobbi
"""
import sys
import vtk
from vtk.test import Testing
arrays = [
vtk.vtkFloatArray,
vtk.vtkDoubleArray,
vtk.vtkSignedCharArray,
vtk.vtkShortArray,
vtk.vtkIntArray,
vtk.vtkLongArray,
vtk.vtkTypeInt64Array,
vtk.vtkIdTyp... | SimVascular/VTK | Common/Core/Testing/Python/TestArrayArguments.py | Python | bsd-3-clause | 3,853 | [
"VTK"
] | 95b40c4f40dc1267eabfc28b317a217db1f6a8bafcaf8d6c27bc7a15d5746b2e |
# FreeCAD TemplatePyMod module
# (c) 2010 Werner Mayer LGPL
"""
The module can be executed with:
FreeCAD -P <path_to_file> Automation.py
FreeCADCmd -P <path_to_file> Automation.py
"""
import FreeCAD, Part
def makeSnapshotWithGui():
from PyQt4 import QtGui
import FreeCADGui
def getMainWindow():
to... | JonasThomas/free-cad | src/Mod/TemplatePyMod/Automation.py | Python | lgpl-2.1 | 2,259 | [
"CRYSTAL"
] | df00d72ea7142273d5c9646abf3868a363af6de3e73d07acd1c5c1e6f34456f4 |
def gauss_kern(size, sizey=None):
""" Returns a normalized 2D gauss kernel array for convolutions """
size = int(size)
if not sizey:
sizey = size
else:
sizey = int(sizey)
#print size, sizey
x, y = mgrid[-size:size+1, -sizey:sizey+1]
g = exp(-(x**2/float... | ActiveState/code | recipes/Python/576764_Convolving_Gaussian/recipe-576764.py | Python | mit | 1,494 | [
"Gaussian"
] | 32066d3d16fcd042943919416478acf577b38ccdf0c8ee6d658952db4c042338 |
"""
Instructor Dashboard Views
"""
import logging
import datetime
import uuid
import pytz
from django.contrib.auth.decorators import login_required
from django.views.decorators.http import require_POST
from django.utils.translation import ugettext as _
from django_future.csrf import ensure_csrf_cookie
from django.vie... | xiandiancloud/edxplaltfom-xusong | lms/djangoapps/instructor/views/instructor_dashboard.py | Python | agpl-3.0 | 19,208 | [
"VisIt"
] | 1f85ae93700ce70c14951f3f190c5bd4e5606bb9aa57f6594d2996c2dd7ec8d8 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Author: Andrew Jewett (jewett.aij at g mail)
# http://www.chem.ucsb.edu/~sheagroup
# License: 3-clause BSD License (See LICENSE.TXT)
# Copyright (c) 2012, Regents of the University of California
# All rights reserved.
"""
ltemplify.py
The "ltemplify.py" script... | CFDEMproject/LAMMPS | tools/moltemplate/src/ltemplify.py | Python | gpl-2.0 | 94,070 | [
"LAMMPS"
] | 23039c655e9a86148f16a040b0839be1be41e6fd1c1d4f90dec5119d9db174ef |
# Copyright 2010-2017 Luc Saffre
# License: BSD (see file COPYING for details)
from __future__ import unicode_literals
from builtins import str
from django.db import models
from lino.mixins.polymorphic import Polymorphic
from django.utils.encoding import python_2_unicode_compatible
@python_2_unicode_compatible
class... | khchine5/book | lino_book/projects/mti/app/models.py | Python | bsd-2-clause | 1,826 | [
"VisIt"
] | 27bee94d67b62dc1af055999e9e254219afb560a0148ca05bc20ceb80b659dd0 |
#!/usr/bin/env python
import unittest
import warnings
import numpy as np
from pymatgen.core.lattice import Lattice
from pymatgen.core.operations import SymmOp
from pymatgen.symmetry.groups import PointGroup, SpaceGroup, _get_symm_data
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Virt... | vorwerkc/pymatgen | pymatgen/symmetry/tests/test_groups.py | Python | mit | 7,543 | [
"pymatgen"
] | f2e08c805cdb2dd0e1301d34f74eb8b770dbee3384981fd91437894a55c40790 |
# -*- coding: utf-8 -*-
# flake8: noqa
from __future__ import print_function
from pandas.compat import map, reduce, range, lrange
from pandas.io.common import urlopen
from pandas.io import json
import pandas
import numpy as np
import warnings
warnings.warn("\n"
"The pandas.io.wb module is moved to a s... | pjryan126/solid-start-careers | store/api/zillow/venv/lib/python2.7/site-packages/pandas/io/wb.py | Python | gpl-2.0 | 12,802 | [
"BWA"
] | 933369299b19b77405a4f3567d4b4df637c1daedef3c44f2a429067f9ae5ea7e |
import numpy as np
from skimage.transform import SimilarityTransform, estimate_transform, matrix_transform
import matplotlib.pyplot as plt
import scipy
from skimage.filters import gaussian
def plot_closest_points(image_points, edge_points, closest_edge_points):
plt.plot(edge_points[:, 0], edge_points[:, 1], 'r+')... | jrdurrant/insect_analysis | vision/measurements/subspace_shape.py | Python | gpl-2.0 | 4,784 | [
"Gaussian"
] | d246b36b4b257d7e38c06f50086e7567be3ecdfc34ce2e081750ac8a0d212003 |
#
# Author: Henrique Pereira Coutada Miranda
# Run a Silicon groundstate calculation using Quantum Espresso
#
from __future__ import print_function
import os
import sys
import argparse
from qepy import *
scf_kpoints = [2,2,2]
nscf_kpoints = [2,2,2]
dg_kpoints = [4,4,4]
prefix = 'si'
matdyn = 'matdyn.x'
q2r = 'q2... | henriquemiranda/yambo-py | tutorial/si/gs_si.py | Python | bsd-3-clause | 7,964 | [
"CRYSTAL",
"Quantum ESPRESSO"
] | 82eee783cdcf3864823bcac0a0727775f54791ce1f06d30fd749f791a9adfacf |
import numpy as np
from ._nl_means_denoising import (
_nl_means_denoising_2d,
_nl_means_denoising_3d,
_fast_nl_means_denoising_2d,
_fast_nl_means_denoising_3d)
def denoise_nl_means(image, patch_size=7, patch_distance=11, h=0.1,
multichannel=True, fast_mode=True):
"""
Perfo... | pratapvardhan/scikit-image | skimage/restoration/non_local_means.py | Python | bsd-3-clause | 5,397 | [
"Gaussian"
] | 5f6fbb437bedecdf98726ac5e97981014c9e0a70bb50ecb051e2a39ec92d7564 |
import datetime
from django.core.exceptions import ImproperlyConfigured
from django.test import TestCase, override_settings, skipUnlessDBFeature
from django.test.utils import requires_tz_support
from django.utils import timezone
from .models import Artist, Author, Book, BookSigning, Page
def _make_books(n, base_dat... | tysonclugg/django | tests/generic_views/test_dates.py | Python | bsd-3-clause | 35,527 | [
"MOOSE"
] | 1c84a8902d7c885e1db6f935a8d323cc85352895bd4cf329d6b8226d8d844105 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
## Description Tool for generating a SDFile from diverse sources
##
## Authors: Inés Martínez (mmartinez4@imim.es)
## Manuel Pastor (manuel.pastor@upf.edu)
##
## Copyright 2015 Manuel Pastor
##
## This file is part ... | manuelpastor/phitools | phitools/getSDF.py | Python | gpl-3.0 | 3,751 | [
"RDKit"
] | 8153218ddb0f7d50521e876c62dafd9ce0412728a7df445a376944fa9d85fb35 |
""" Priority corrector for the group and ingroup shares
"""
__RCSID__ = "$Id$"
from DIRAC.Core.Utilities import ObjectLoader
from DIRAC.ConfigurationSystem.Client.Helpers.Operations import Operations
from DIRAC.WorkloadManagementSystem.private.correctors.BaseCorrector import BaseCorrector
from DIRAC import gLogger, ... | sposs/DIRAC | WorkloadManagementSystem/private/SharesCorrector.py | Python | gpl-3.0 | 4,589 | [
"DIRAC"
] | d676e0f562b93582b3576d897cc88d2a2486e57299eb1fdd709ca59942bcf4f5 |
"""
Reading of ordinary SIESTA output files
"""
import numpy as _np
import os as _os, os.path as _osp
import sids.siesta.fdf as _fdf
import sids.helper.units as _unit
import sids.simulation as _sim
import ascii_tbt as _tbt
class FileASCIIError(Exception):
""" Error for reading SIESTA files """
pass
def read(... | zerothi/siesta-es | sids/siesta/io/ascii.py | Python | gpl-3.0 | 6,183 | [
"SIESTA"
] | b10af6691ed3be2720d5be9dc7e4f2e844c63ed9a1b7879c60f3ec0938a9a4cb |
#
# @file TestSyncAnnotation.py
# @brief tests for improved syncAnnotation functions
#
# @author Akiya Jouraku (Python conversion)
# @author Sarah Keating
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatically by c... | TheCoSMoCompany/biopredyn | Prototype/src/libsbml-5.10.0/src/bindings/python/test/annotation/TestSyncAnnotation.py | Python | bsd-3-clause | 61,263 | [
"VisIt"
] | 351c3ed10dea26fc5d3eb60a28662f90962d825e86b1679c7ccff49a59137b33 |
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