text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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""" This module helps customize the mayavi install. It tries to import
any `site_mayavi.py` (anywhere on `sys.path`) or `user_mayavi.py`. The
`user_mayavi.py` script is found in the users `~/.mayavi2` directory
and this directory is also injected into the path.
It is the users responsibility to import the mayavi reg... | dmsurti/mayavi | mayavi/core/customize.py | Python | bsd-3-clause | 3,952 | [
"Mayavi"
] | d71579ea9a173cd18e8183d0706cd6de6adffe615a1170988a7fdf3a93d26ee7 |
#!/usr/bin/env python3
#pylint: disable=missing-docstring
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
... | nuclear-wizard/moose | python/chigger/tests/geometric/line_source/line_source_data.py | Python | lgpl-2.1 | 645 | [
"MOOSE"
] | 7d10250b5891896b7263d82c6b88e87215e308f31ae186b19bb3e570252c9531 |
#%% addViscous.py
"""
Viscous correction code to augment Cart3D solutions.
Alexander Ward
April 2017
"""
#http://www.dtic.mil/dtic/tr/fulltext/u2/a045367.pdf
from math import exp, log, asin, sin
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
from scipy.optimize import brentq... | AlexanderWard1/VC3D | Integral Methods/addViscous_Bowcutt.py | Python | mit | 61,090 | [
"ParaView",
"VTK"
] | 0aa3c0bb5c397017d135aff32de5bb0dd1f38ce36d1b21f8150bf29127dffedd |
#! python3
# Check FLAC files for tag consistency. Used when ripping CDs to make sure
# the resulting files are cleaned up and ready for moving to the master tree
# of audio files.
#
# Can perform the following checks:
#
# * Check that all required tags are present in all FLAC tracks.
# * Check that tags which should... | plucid/dBpa-scripts | CheckFlacTags.py | Python | mit | 34,767 | [
"Brian"
] | 757b643d020218c05268bae633841384f92ab66f7791b60a2e8cdea75736da07 |
'''
plot.py
Functions to plot xvg data generated by gromacs "gmx energy" package
'''
from sys import argv
import seaborn as sns
import matplotlib.pyplot as plt
xvg = "/home/antonio/Docbox/gromacs_automatizer/test/potential.xvg"
#xvg = argv[1]
#----| BASIC FUNCTIONS |----#
def load2dXVG(xvg_name):
'''
Get d... | gustalima/gromacs_automatizer | plot.py | Python | gpl-3.0 | 1,942 | [
"Gromacs"
] | cb668863ed73bdbee3c6cabff877fb888b9ec20c56688011e0c5dc56e8810485 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright: (c) 2015, René Moser <mail@renemoser.net>
# 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':... | alxgu/ansible | lib/ansible/modules/net_tools/ipify_facts.py | Python | gpl-3.0 | 2,944 | [
"VisIt"
] | 7e7a42910ab6ee5a4bedcc3197453920046c20a21ed70a270395c16eb81a411f |
"""
parser.http.movieParser module (imdb package).
This module provides the classes (and the instances), used to parse the
IMDb pages on the www.imdb.com server about a movie.
E.g., for Brian De Palma's "The Untouchables", the referred
pages would be:
combined details: http://www.imdb.com/title/tt0094226/referen... | logituit/Recbot | PY/imdb/parser/http/movieParser.py | Python | mit | 90,920 | [
"Brian"
] | f47894ded09bbcbc37e1736fc63f935d452525c294b240399d9b575f09103e1b |
#
# libtcod 1.6.3 Python wrapper
# Copyright (c) 2008,2009,2010,2012,2013,2016,2017 Jice & Mingos & rmtew
# 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 mus... | bopace/artifice | src/libtcodpy/__init__.py | Python | mit | 100,027 | [
"Amber"
] | 36f2bb9a30a89df050cd26b530b589c8622fafa37ea8d925f6ab9d57d61efa24 |
## INFO ########################################################################
## ##
## formbuilder ##
## =========== ... | petervaro/formbuilder | form.py | Python | gpl-3.0 | 3,592 | [
"VisIt"
] | abbd160043e246a71d792f164db1e603634f4a10836a1b2cb8c684fc1c6de411 |
# ========================== Start Copyright Notice ========================== #
# #
# Copyright 2014 F.D.I.S. #
# This file is part of Kinetic Gunner: Gunner of Angst ... | CertainlyUncertain/Kinetic-Gunner-Gunner-of-Angst | netMgr.py | Python | gpl-3.0 | 2,584 | [
"VisIt"
] | 961208af75fadfb84c66d53f456bd6f2ae7f327e21e03e961ae9478939478a9b |
from __future__ import print_function, division
import numpy as np
import sys
from scipy.optimize import fmin
from scipy.special import erf
import scipy.stats
from copy import deepcopy
# Constants
kb = 0.00831447215 # kJ/(K*mol)
class Jarz(object):
'''Jarzynski estimator.
Description...
Parameters
... | dseeliger/pmx | pmx/estimators.py | Python | lgpl-3.0 | 23,063 | [
"Gaussian"
] | 6daca56247c21fa6b23ce70a28239979a8cfab11d4d3de0d1061abdd63ee9c58 |
# Copyright 2019 Arie Bregman
#
# 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 agree... | bregman-arie/rhoci | rhoci/api/job.py | Python | apache-2.0 | 5,401 | [
"Elk"
] | a14573d109f95b759aea077c2efc54664db345eb27137bf7c0900e91470ca885 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Part of the PsychoPy library
# Copyright (C) 2002-2018 Jonathan Peirce (C) 2019-2022 Open Science Tools Ltd.
# Distributed under the terms of the GNU General Public License (GPL).
"""Functions and classes related to array handling
"""
__all__ = ["createXYs",
... | psychopy/psychopy | psychopy/tools/arraytools.py | Python | gpl-3.0 | 16,591 | [
"Gaussian"
] | 19e07d7b4de1dea4747f76add63cba5cce70f0bf40719f5fed6ff9094cbafa71 |
#!/usr/bin/env python
import lxml.etree as ET
import subprocess
import sys
import os
import shutil
import argparse
import datetime
import time
import csv
import uuid
from glob import glob
from ififuncs import create_csv
from ififuncs import append_csv
from ififuncs import send_gmail
from ififuncs import hashlib_manifes... | kieranjol/IFIscripts | legacy_scripts/makedpx.py | Python | mit | 11,528 | [
"Brian"
] | c8b942caa0fe34e01c26b443fe8dda61c1fc7fd5dffec9c05a1c82f2a6ccb3dc |
# Copyright 2010-2017, The University of Melbourne
# Copyright 2010-2017, Brian May
#
# This file is part of Karaage.
#
# Karaage 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... | Karaage-Cluster/karaage | karaage/plugins/kgapplications/management/commands/application_cleanup.py | Python | gpl-3.0 | 2,647 | [
"Brian"
] | b04ee97a87dbc50d1656f0f46e2de26cdf9e7adee99782f4cfdc253ba6b40054 |
"""Schemas to valid user input.
Index
-----
.. currentmodule:: nanoqm.workflows.schemas
.. autosummary::
{autosummary}
API
---
{autodata}
"""
__all__ = [
'schema_cp2k_general_settings',
'schema_derivative_couplings',
'schema_single_points',
'schema_distribute_absorption_spectrum',
'schema_dis... | SCM-NV/qmworks-namd | nanoqm/workflows/schemas.py | Python | mit | 10,214 | [
"CP2K",
"CRYSTAL",
"NAMD"
] | b8693fe24f477a4256135f83f898c8f0e88a4bf740c930a7fb20cca731ebaa48 |
'''
Code to calculate clusters using a Dirichlet Process
Gaussian mixture model.
Requires scikit-learn:
http://scikit-learn.org/stable/
'''
import numpy
from sklearn import mixture
FILENAME = "mcdonalds-normalized-data.tsv"
# Note: you'll have to remove the last "name" column in the file (or
# some other such th... | bharcode/Kaggle | DirichletProcesses/dpgmm.py | Python | gpl-2.0 | 516 | [
"Gaussian"
] | 44654a190a39d88407716c343334e764edb88ae0aef74256f2dd163efc4ac3d0 |
# vim: tabstop=4 shiftwidth=4 softtabstop=4
# Copyright (c) 2012 OpenStack Foundation
# All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.a... | imsplitbit/nova | nova/tests/compute/test_resource_tracker.py | Python | apache-2.0 | 38,692 | [
"exciting"
] | aa10a30629b986c9bc3d1de3cb5204683b0869d84c845ebea532a48d2406c417 |
#!/usr/bin/python
# file: formatter.py
# author: Andrea Vedaldi
# description: Utility to format MATLAB comments.
# Copyright (C) 2007-12 Andrea Vedaldi and Brian Fulkerson.
# All rights reserved.
#
# This file is part of the VLFeat library and is made available under
# the terms of the BSD license (see th... | ducha-aiki/mods | vlfeat/docsrc/formatter.py | Python | gpl-2.0 | 18,970 | [
"Brian"
] | 9a7390f46d674f5bbba24edfbfbc1ad4adec506ddb3aff4744311ed10c1b4bd9 |
# Generated from ShExDoc.g4 by ANTLR 4.5.1
from antlr4 import *
if __name__ is not None and "." in __name__:
from .ShExDocParser import ShExDocParser
else:
from ShExDocParser import ShExDocParser
# This class defines a complete generic visitor for a parse tree produced by ShExDocParser.
class ShExDocVisitor(P... | hsolbrig/shexypy | shexypy/shexyparser/parser/ShExDocVisitor.py | Python | mit | 11,828 | [
"VisIt"
] | cc384b34d749388a2ddc424f34cb1abd06356fddfcfaebef0a397a2007c0c786 |
"""Plot the result of sampling clusters
{{header}}
"""
# ? include "plot_header.template"
# ? from "plot_macros.template" import xdg_open with context
import numpy as np
import seaborn as sns
from matplotlib import pyplot as plt
from msmbuilder.io import load_trajs, load_generic
sns.set_style('ticks')
colors = sns... | mpharrigan/mixtape | msmbuilder/project_templates/cluster/sample-clusters-plot.py | Python | lgpl-2.1 | 2,612 | [
"VMD"
] | a9a44f99c4701721d88c874db16e6244cccd8bbe2909f5d5a1f86eae21a13d7a |
import itertools
import os
from collections import (
defaultdict,
Mapping
)
from concurrent.futures import ProcessPoolExecutor
import pandas as pd
import pysam
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt # noqa: E402
from matplotlib.backends.backend_pdf import PdfPages # noqa: E40... | bardin-lab/readtagger | readtagger/plot_coverage.py | Python | mit | 5,120 | [
"pysam"
] | f282ab5f0cb25cc673217fa625fccadce00d22f1bb372daa91ce23221d8c8065 |
#!/usr/bin/env
"""
UP_HRV2OISST_model_prep.py
DataSource: ftp://ftp.cdc.noaa.gov/Datasets/noaa.oisst.v2.highres/
NOAA High Resolution SST data provided by the NOAA/OAR/ESRL PSD,
Boulder, Colorado, USA, from their Web site at http://www.esrl.noaa.gov/psd/
"""
#System Stack
import datetime
import sys
#Scienc... | shaunwbell/FOCI_Analysis | ReanalysisRetreival_orig/UnimakPass/UP_HRV2OISST_model_prep.py | Python | mit | 8,998 | [
"NetCDF"
] | bdd68003ad4b5eda3c99bda0435a0f741cae3593f454162dbe0393dd906db5f3 |
# ============================================================================
#
# Copyright (C) 2007-2010 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | kurtraschke/camelot | camelot/view/export/desktop_service.py | Python | gpl-2.0 | 1,481 | [
"VisIt"
] | eebd211e0411f01bb2def5954940e8db81d52f8c846d16921e5b1f8844573713 |
from __future__ import print_function
__author__ = """Alex "O." Holcombe, Charles Ludowici, """ ## double-quotes will be silently removed, single quotes will be left, eg, O'Connor
import time, sys, platform, os
from math import atan, atan2, pi, cos, sin, sqrt, ceil, radians, degrees
import numpy as np
import psychopy, ... | alexholcombe/dot-jump | dataRaw/Fixed Cue/test_dot-jump25Oct2016_10-53.py | Python | gpl-3.0 | 25,090 | [
"Gaussian"
] | 60e810fcb51ee30c84c1589a2cd0f99766db4739b3c022e08e8295c1b5910f0a |
# Contour Copyright (C) 2013-2014 Hiroyuki Sakai
#
# This file is part of Contour.
#
# Contour 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 optio... | HiroyukiSakai/Contour | contour/models.py | Python | gpl-3.0 | 6,772 | [
"Gaussian"
] | 8230e1f00cd8627e5e807822c3adde9bddc00f03c125e70a516368b00b2ac603 |
#
# Copyright 2016 The BigDL Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... | intel-analytics/BigDL | python/chronos/test/bigdl/chronos/data/utils/test_public_dataset.py | Python | apache-2.0 | 5,094 | [
"ORCA"
] | 03ae6060cebe331c2f500d42ac8e9e7967a37f72e14c6f829eae037583b2e552 |
# Author: David Goodger
# Contact: goodger@users.sourceforge.net
# Revision: $Revision: 21817 $
# Date: $Date: 2005-07-21 22:39:57 +0200 (Thu, 21 Jul 2005) $
# Copyright: This module has been placed in the public domain.
"""
Parser for Python modules. Requires Python 2.2 or higher.
The `parse_module()` function take... | baoboa/Crystal-Space | docs/support/docutils/readers/python/moduleparser.py | Python | lgpl-2.1 | 25,839 | [
"CRYSTAL",
"VisIt"
] | 1e29e147e33973ba1240f66082a146afa1d1327a768b983a8dd379b3c99e6c25 |
import pytest
import ast
import symtab
import hpcs_builtins
from annotators import *
from typing import *
@pytest.fixture
def annotator():
return TypeAnnotator()
class TestTypeAnnotation:
def setup_method(self, method):
self.annotator = TypeAnnotator()
self.ast = ast.parse(method.__doc__)
... | Jokymon/hpcs | test/test_typeannotation.py | Python | gpl-3.0 | 3,762 | [
"VisIt"
] | 0dd1aa54531c61acd14e0636592acd41ea9d524b73054ca1d696e4a0771beb31 |
from Kernel import Kernel
from Gaussian import Gaussian | aerialhedgehog/VyPy | trunk/VyPy/regression/gpr/kernel/__init__.py | Python | bsd-3-clause | 58 | [
"Gaussian"
] | 07e3136878159303e0ca31f6b38a19398ed96ab8351b4dd264e903569d8f4505 |
# $HeadURL$
""" ElementStatus base class for the helpers
Each RSS Status helper extends this class, providing four methods per cache.
* get<elementType>Statuses
* get<elementType>Status
* isUsable<elementType>
* getUsable<elementType>
"""
# DIRAC
from DIRAC ... | avedaee/DIRAC | ResourceStatusSystem/Utilities/ElementStatus.py | Python | gpl-3.0 | 7,799 | [
"DIRAC"
] | 72f4d985cfc33a95af18e29bed244238e9ff9a49604ab44cff8cb977e5d80c51 |
# Copyright: (c) 2017, Brian Coca <bcoca@ansible.com>
# Copyright: (c) 2018, Ansible Project
# 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
import argparse
from operator import attrget... | roadmapper/ansible | lib/ansible/cli/inventory.py | Python | gpl-3.0 | 15,528 | [
"Brian"
] | edd17f7cce1f6dc9067a57ea40896aaee2ced6cd96e26e33cfa068ab34ff4554 |
''' http://www.biopython.org/DIST/docs/api/Bio.KDTree.KDTree%27-module.html '''
def photoz(list):
import sys, pyfits, os
file = os.environ['sne'] + '/cosmos/cosmos_zphot_mag25.nums.fits'
hdulist = pyfits.open(file)
table = hdulist["OBJECTS"].data
r = []
for i in list[0]:
r.append(... | deapplegate/wtgpipeline | non_essentials/kdtree/kdtree2.py | Python | mit | 1,929 | [
"Biopython"
] | af4377ad39855892f70c5e3380988e0d23c0669ab0541f98200313e8bb97c0f2 |
"""Module to test the output of the Mirth Connect channels
NB - this module does NOT provoke actual processing of the test set,
but relies on a persisted copy of the post process database to be
available. To create said file - run::
process_testfiles_via_mirth
(and go get some coffee while you wait...)
The tes... | pbugni/pheme.warehouse | pheme/warehouse/tests/test_mirth_processing.py | Python | bsd-3-clause | 41,610 | [
"VisIt"
] | eae9513556ed369317b94443ba92e44b6c8778d6f1edd57e3472afca87fa69fa |
#!/usr/bin/env python
# Copyright (C) 2006 Imperial College London and others.
#
# Please see the AUTHORS file in the main source directory for a full list
# of copyright holders.
#
# Prof. C Pain
# Applied Modelling and Computation Group
# Department of Earth Science and Engineering
# Imperial Col... | FluidityProject/multifluids | scripts/fl_mayavi_animate.py | Python | lgpl-2.1 | 5,950 | [
"Mayavi",
"VTK"
] | 7181226440a52269b07ac2484cfbb92710062d57368ea709d4ea0886be53c6d9 |
#file: import_problem.py
#from __future__ import print_function, division
#import os as os
import time as time
#import pyzdde.zdde as pyz # PROBLEM
#import matplotlib.pyplot as plt # PROBLEM
#import iutils.opticsutils.foptics as fou # PROBLEM
#import iutils.plotutils.mplutils as mpu # P... | indranilsinharoy/zArrayTrace | import_problem.py | Python | mit | 2,170 | [
"Mayavi"
] | 6c2d6afce14f06cd93bb7ae233edc7f13ae9c3e20897a0a92f3f9c8f4fbdde83 |
# -*- coding: utf-8 -*-
# Part of Odoo. See LICENSE file for full copyright and licensing details.
"""
Miscellaneous tools used by OpenERP.
"""
from functools import wraps
import cPickle
import cProfile
from contextlib import contextmanager
import subprocess
import logging
import os
import passlib.utils
import re
im... | be-cloud-be/horizon-addons | server/openerp/tools/misc.py | Python | agpl-3.0 | 40,141 | [
"VisIt"
] | 825a1af5ab0e07ba27353c2108aab9232fd41333c55cffa794ba2b36aa21cafd |
"""Gaussian process-based minimization algorithms."""
import numpy as np
from sklearn.utils import check_random_state
from .base import base_minimize
from ..utils import cook_estimator
from ..utils import normalize_dimensions
def gp_minimize(func, dimensions, base_estimator=None,
n_calls=100, n_ran... | scikit-optimize/scikit-optimize | skopt/optimizer/gp.py | Python | bsd-3-clause | 11,787 | [
"Gaussian"
] | 20e4816ae03357945c90bce23299005197e33391c928e946de8995f2959e429f |
#!/usr/bin/python -tt
# 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 distributed in the hope that i... | rpm-software-management/yum | yum/i18n.py | Python | gpl-2.0 | 20,860 | [
"NetCDF"
] | 9eef4bf1e24ea695f0bb7e44e03d21268d7dd927c8a2564bf68809afe125ef41 |
from datetime import datetime
import json
import uuid
from psycopg2._psycopg import DATETIME
from openerp import netsvc
from openerp.osv import fields, osv
import logging
import datetime
_logger = logging.getLogger(__name__)
class atom_event_worker(osv.osv):
_name = 'atom.event.worker'
_auto = False
def _... | 3dfxsoftware/cbss-addons | bahmni_atom_feed/atom_feed_client.py | Python | gpl-2.0 | 11,817 | [
"VisIt"
] | 58a62ce2133c0150d12d2decab3188e77fa7dd4a724b7746d5c06ea077638ffc |
class ASTVisitor():
def visit(self, astnode):
'A read-only function which looks at a single AST node.'
pass
def return_value(self):
return None
class ASTNode(object):
def __init__(self):
self.parent = None
self._children = []
@property
def children(self)... | mc-hammertimeseries/cs207project | pype/ast.py | Python | mit | 4,504 | [
"VisIt"
] | adcd3660455bd9a300272816993e34d66616f2f098101e916c0966c900d5f005 |
# MIT License
#
# Copyright (c) 2016 Bing Huang and Anders S. Christensen
#
# 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 u... | qmlcode/qml | qml/slatm.py | Python | mit | 5,503 | [
"Gaussian"
] | bda4101af33ff4841ee40206151a45f825fedef7b5a51fe3a82a33684107d091 |
__author__ = 'USER'
import random
from common import math_util
class NeuralNetwork:
@property
def output_matrix(self):
return self._output_matrix
@output_matrix.setter
def output_matrix(self, __output_matrix):
self._output_matrix = __output_matrix
@output_matrix.deleter
def ou... | ParkJinSang/Logle | learning/mlp/neuralnetwork.py | Python | mit | 8,413 | [
"NEURON"
] | 358358048eb2bde7d13c3b41512855740367fe54cdb8c89173e50658d908bd3d |
# 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 Votca(CMakePackage):
"""VOTCA is a software package which focuses on the analysis of mole... | LLNL/spack | var/spack/repos/builtin/packages/votca/package.py | Python | lgpl-2.1 | 2,236 | [
"ESPResSo",
"Gromacs",
"LAMMPS"
] | f86a489ea415d3700e51b9ca27aaca2b3066c30bc183f5f1242ef7b26d87a303 |
# 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... | junghans/espressopp | src/integrator/ExtAnalyze.py | Python | gpl-3.0 | 2,446 | [
"ESPResSo"
] | 9a16497b3016e03b5f8eb02126cb11a35db9d0a68be4a4d91d31e64920a0d97b |
#!/usr/bin/env python
#
# $File: PyQuanTrait.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can redistribut... | BoPeng/simuPOP | docs/PyQuanTrait.py | Python | gpl-2.0 | 2,087 | [
"VisIt"
] | 3d2358e216d6ce65c6a8855c93fb7df9ee89060688f88de218a6659286b03cd6 |
from ase.structure import molecule
from gpaw import GPAW
a = 8.0
h = 0.2
energies = {}
resultfile = open('results-%.2f.txt' % h, 'w')
for name in ['H2O', 'H', 'O']:
system = molecule(name)
system.set_cell((a, a, a))
system.center()
calc = GPAW(h=h,
txt='gpaw-%s-%.2f.txt' % (name, h))... | robwarm/gpaw-symm | doc/exercises/water/h2o.py | Python | gpl-3.0 | 631 | [
"ASE",
"GPAW"
] | a23254b8fcba2aa4a09287f7d49a231ab8cd32252ea3e3ee974ed86d7eb73380 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | CDSherrill/psi4 | psi4/driver/procrouting/sapt/sapt_sf_terms.py | Python | lgpl-3.0 | 10,386 | [
"Psi4"
] | 8433d35c6302187b051ba3bcf83d8f662c71c2dfe7ca7f9656c1c12dee54da00 |
#################################################################
# Importing samtools, bcftools, and htslib
#
# For each package PKG:
#
# rm -rf PKG
# python import.py PKG path/to/download/PKG-X.Y
import fnmatch
import os
import re
import itertools
import shutil
import sys
import hashlib
EXCLUDE = {
"samtools":... | pysam-developers/pysam | devtools/import.py | Python | mit | 10,243 | [
"pysam"
] | b0caedda86bb58abb984b4ae5e6c7e4ec3c02fe5dee3283dec6d81715c779b18 |
# 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... | annarev/tensorflow | tensorflow/python/ops/nn_impl.py | Python | apache-2.0 | 99,524 | [
"Gaussian"
] | f1c34b4851a5cf723332f966ad04547a1fced25ee0f4d6591bcb17d6f559c446 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
import copy... | nuclear-wizard/moose | python/peacock/Input/ParameterInfo.py | Python | lgpl-2.1 | 4,414 | [
"MOOSE"
] | 63e5a1a8382245ef0f5dd70720245f09e59966c6a68e8a5ff2c0810fcc62fa6f |
#!/usr/bin/env python
# -----------------------------------------------------------------------------
# Copyright (c) 2013, The Deblur Development Team.
#
# Distributed under the terms of the BSD 3-clause License.
#
# The full license is in the file LICENSE, distributed with this software.
# --------------------------... | amnona/deblur | setup.py | Python | bsd-3-clause | 2,025 | [
"scikit-bio"
] | 6f19fd4410941bbbf14352894f039795a9fc7d1970fe0ae64ede227c2f040b71 |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | alec-heif/MIT-Thesis | spark-bin/python/pyspark/ml/clustering.py | Python | mit | 41,715 | [
"Gaussian"
] | ff86d5ed25c736bcfe8085da2bb5ced7c83031f1b6097c6bbb6d5cf394977c4a |
"""
Execute each notebook as a test, reporting an error if any cell throws an exception.
Adapted from https://gist.github.com/minrk/2620876.
"""
from __future__ import print_function
import os
import sys
import socket
from distutils.spawn import find_executable as _find_executable
import pytest
try:
import nbform... | rmcgibbo/mdtraj | examples/test_examples.py | Python | lgpl-2.1 | 3,093 | [
"OpenMM"
] | a8361e76faadd3ab409ccb6fd1a34e4ca97d4c6589d050cdad50c1a6a2b1000f |
"""
A simple VTK widget for PyQt or PySide.
See http://www.trolltech.com for Qt documentation,
http://www.riverbankcomputing.co.uk for PyQt, and
http://pyside.github.io for PySide.
This class is based on the vtkGenericRenderWindowInteractor and is
therefore fairly powerful. It should also play nicely with the
vtk3DWi... | dmsurti/mayavi | tvtk/pyface/ui/qt4/QVTKRenderWindowInteractor.py | Python | bsd-3-clause | 21,119 | [
"CRYSTAL",
"VTK"
] | 23b693ec5af221b6c693613927a7c95e4a17f0c7620a3895f1ca0845e0a8b75d |
# -*- coding: utf-8 -*-
"""
Tools for trend analysis.
Author: R. Lombaert
"""
import os
import operator
from numpy import array
import numpy as np
from numpy.random import normal
from matplotlib import pyplot as plt
import cc.path
from cc.modeling.objects import Transition
from cc.plotting import Plotting2
from cc... | MarieVdS/ComboCode | cc/statistics/TrendAnalysis.py | Python | gpl-3.0 | 79,115 | [
"Gaussian"
] | f1a56cd55c2d63a72972ee4048a8e7b056948a0c8dc1b1a39768a0e532ae0106 |
"""
Viewing Stanford 3D Scanning Repository dragon model
"""
# Copyright (c) 2014-2015, Enthought, Inc.
# Standard library imports
import os
from os.path import join
# Enthought library imports
from mayavi import mlab
### Download the dragon data, if not already on disk ############################
if not os.path.exi... | dmsurti/mayavi | examples/mayavi/mlab/dragon.py | Python | bsd-3-clause | 1,143 | [
"Mayavi"
] | e8101ecbb41b2e43cb8d251dd4c4f6171408fc0e1ef22cae69183d53a1c983d3 |
import os
import warnings
# cmr calls all available methods in ase.atoms detected by the module inspect.
# Therefore also deprecated methods are called - and we choose to silence those warnings.
warnings.filterwarnings('ignore', 'ase.atoms.*deprecated',)
import numpy as np
def array_almost_equal(a1, a2, tol=np.finfo(... | JConwayAWT/PGSS14CC | lib/python/multimetallics/ase/test/cmr/rw.py | Python | gpl-2.0 | 1,209 | [
"ASE"
] | 091cecb6d31927ccbbff9bf184918b4bf1193a87728d8f9712d7e42a43a4327f |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2017, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""A writer for chemical markup language (CML) files."""
try:
import openbabel as ob
has_openbabel = True
except ... | gaursagar/cclib | src/cclib/io/cmlwriter.py | Python | bsd-3-clause | 3,725 | [
"cclib"
] | fd40807fda301787ba5ed7d5bd2c3a90cc4b58fd0e22975048b54bfc88a6107f |
# Copyright (C) 2013 The ESPResSo project
# Copyright (C) 2012 Olaf Lenz
#
# 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
# (a... | gizeminci/espresso | config/gen_sampleconfig.py | Python | gpl-3.0 | 1,710 | [
"ESPResSo"
] | c8f54330aa2d2538acf779ac81352949b9ae1aa427bc8ab88beb96638ad92d6b |
import csv
import random
from time import time
from src.genetic_algorithm import GA
from src.hw1.NeuralNetwork import NeuralNetwork
from src.hw1.Utils.utilities import get_seeds, generate_network
seed_train_set, seed_test_set, seed_train_expected, seed_test_expected = get_seeds("formatted_seeds.txt", 35)
test_data = ... | juanpablos/CC5114-Projects | Tarea 3/Main.py | Python | mit | 2,203 | [
"NEURON"
] | 3d670419f8e7859a68bbde7c639e18c647e130f4bed79b24377fa934d5a1df71 |
# (C) British Crown Copyright 2010 - 2016, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | SusanJL/iris | lib/iris/fileformats/cf.py | Python | gpl-3.0 | 44,968 | [
"NetCDF"
] | 863173195a655154bc78f0c92812eef163a5d1e3e53777d21ef441d3ed577fdf |
'''
libChEBIpy (c) University of Manchester 2015
libChEBIpy is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
from ._base_object import BaseObject
class Reference(BaseObject):
'''Class representing a ChEBI reference.'''
... | libChEBI/libChEBIpy | libchebipy/_reference.py | Python | mit | 1,107 | [
"VisIt"
] | 3077121cd3464fc736b1f00c6c75f06a2a905e9d23026a4236d65c545d2be5fd |
# Copyright 2016 Capital One Services, LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in... | RyanWolfe/cloud-custodian | tests/test_resolver.py | Python | apache-2.0 | 4,328 | [
"Galaxy",
"MOOSE"
] | d1d3d8e6f19f18833c1d4a3184902802dbaf29027e2e28c5aef198c9e4d07ab6 |
# ----------------------------------------------------------------------------
# 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/alignment/_pairwise.py | Python | bsd-3-clause | 44,605 | [
"BLAST",
"scikit-bio"
] | b3005859fb6c543bea05b33c237b4dd042b0846a086353062c935e6678f8c89b |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/item_title | openlp/plugins/bibles/lib/osis.py | Python | gpl-2.0 | 9,953 | [
"Brian"
] | d261c774fb222a560690d8a1f5eaec214183d8ed4536c7bb4b4132c1428f9998 |
from pymicro.view.vtk_utils import *
from pymicro.view.vtk_anim import *
from pymicro.view.scene3d import Scene3D
from pymicro.crystal.microstructure import Orientation
from pymicro.crystal.lattice import Lattice
s3d = Scene3D(display=True, ren_size=(600, 600))
euler_angles = np.array([142.8, 32.0, 214.4])
(phi1, Phi,... | heprom/pymicro | examples/animation/euler_angles_anim.py | Python | mit | 5,222 | [
"CRYSTAL",
"VTK"
] | 63fb549134292abff85aaa1a9a86dbe79550cebbb65dfec9d83e09757b209103 |
"""rbf - Radial basis functions for interpolation/smoothing scattered Nd data.
Written by John Travers <jtravs@gmail.com>, February 2007
Based closely on Matlab code by Alex Chirokov
Additional, large, improvements by Robert Hetland
Some additional alterations by Travis Oliphant
Permission to use, modify, and distrib... | Eric89GXL/scipy | scipy/interpolate/rbf.py | Python | bsd-3-clause | 10,649 | [
"Gaussian"
] | 830aed6d9b8c1867545d70d551098636685153175995efb09cdf87ad866630a1 |
#
# QAPI types generator
#
# Copyright IBM, Corp. 2011
#
# Authors:
# Anthony Liguori <aliguori@us.ibm.com>
#
# This work is licensed under the terms of the GNU GPLv2.
# See the COPYING.LIB file in the top-level directory.
from ordereddict import OrderedDict
from qapi import *
import sys
import os
import getopt
impor... | duythanhphan/qemu | scripts/qapi-types.py | Python | gpl-2.0 | 8,980 | [
"VisIt"
] | 3b9b3b32f10c849cbc58543391436b77440a1c73913193384dc6880838f13bdb |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under th... | kain88-de/mdanalysis | package/MDAnalysis/coordinates/memory.py | Python | gpl-2.0 | 14,541 | [
"MDAnalysis"
] | 34d5d6174ea19de86a1de2d1b4fb74e94a625050ab0eb49b2d8b5bd2a6f4363b |
# -*- Mode: Python; coding: utf-8; indent-tabs-mode: nil; tab-width: 4 -*-
### BEGIN LICENSE
# Copyright (C) 2014 Brian Douglass bhdouglass@gmail.com
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License version 3, as published
# by the Free Softwa... | bhdouglass/agui | agui/backends/gtk/extras/popup.py | Python | gpl-3.0 | 1,012 | [
"Brian"
] | 7df8e187af9e0c7b9781fd0a01eaf33677b775081ad4b56feb63ab1f22f7bc62 |
import matplotlib
import matplotlib.pyplot as plt
import matplotlib.patches
import numpy as np
import Nsound as ns
def main():
matplotlib.rc('font', size = 24)
matplotlib.rc('figure', figsize = [16, 6])
matplotlib.rcParams.update({'figure.subplot.left' : 0.09 })
matplotlib.rcParams.update({'figure.... | weegreenblobbie/sd_audio_hackers | 20160626_spectrograms_explained/media/make_plots.py | Python | mit | 4,732 | [
"Gaussian"
] | cee711ef6ef4f95c7d975c0a30b6fb39240092fb94116c74f8dea0721f6b8c1d |
#!/usr/bin/python
"""Test of Orca bookmarks
"""
from macaroon.playback import *
import utils
sequence = MacroSequence()
########################################################################
# We wait for the focus to be on the Firefox window as well as for focus
# to move to the frame.
#
sequence.append(WaitForW... | h4ck3rm1k3/orca-sonar | test/keystrokes/firefox/orca_bookmarks.py | Python | lgpl-2.1 | 4,788 | [
"ORCA"
] | 84309bcd389e1187ac3a31623640bbfea78af5e251bb4d4c9e20ed132347c57e |
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
from collections import namedtuple
from scipy.optimize import curve_fit
from scipy import asarray as ar,exp
from matplotlib.pyplot import subplot2grid
from scipy.stats import linregress
import statsmodels.api as sm
"""
To save list of all parroqui... | lucidjuvenal/quis-custodiet | stats/ecdata.py | Python | gpl-3.0 | 10,335 | [
"Gaussian"
] | 7e473e0cf823bf1db00f07a8eebac2d27ad6ed946bd0a1a39d3cc053ec5d18b4 |
"""Components for loading and unloading data using `Storm`_.
See :ref:`Using LoadableFixture<using-loadable-fixture>` for examples.
.. _Storm: https://storm.canonical.com/
"""
from fixture.loadable import DBLoadableFixture
from fixture.util import _mklog
stlog = _mklog('fixture.loadable.storm')
class StormMedium... | patrickod/fixture | fixture/loadable/storm_loadable.py | Python | lgpl-2.1 | 2,295 | [
"VisIt"
] | eec62a19d7233f799800f9cf3c230f8479cb5ea0d7b55de73780a8276a4cecf0 |
# 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/interaction/DihedralPotential.py | Python | gpl-3.0 | 2,349 | [
"ESPResSo"
] | cc3d69ba9c954a0e57f3bebb7d86126c3b234b42ce6d83040929327a439df447 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Test suite for sloth.raytracing - shadow part"""
import os
import sys
import math
import unittest
from sloth.utils.bragg import bragg_ev
from sloth.raytracing.shadow_utils import plot_energy_histo, plot_footprint, plot_image
HAS_SHADOW = False
try:
import Shadow
... | maurov/xraysloth | sloth/raytracing/test/test_shadow.py | Python | bsd-3-clause | 4,353 | [
"CRYSTAL"
] | 7ef92c6ef87f3c20a43ddd7fffab8ca6c2a642b63296327026e49216eaf7670c |
# -*- coding: utf-8 -*-
import subprocess as sb
import sys
import logging
from distutils.dir_util import copy_tree
import os
from tqdm import tqdm
logging.basicConfig(level=logging.INFO,
format='%(levelname)-5s @ %(asctime)s:\n\t %(message)s \n',
datefmt='%a, %d %b %... | pinellolab/haystack_bio | haystack/haystack_common.py | Python | agpl-3.0 | 9,089 | [
"Bioconda"
] | df4e9bce7ad30b7f6213058eb84de0fdd2327609673e9eca696432fa3363212a |
from rdkit import RDConfig
import gzip
import os.path
import pickle
from rdkit import Chem
from rdkit.Chem import Crippen
Crippen._Init()
def runIt(inFileName, outFileName, smiCol=0, maxMols=-1, delim=','):
inF = gzip.open(inFileName, 'r')
outF = open(outFileName, 'wb+')
mols = []
nDone = 0
for line in inF... | ptosco/rdkit | rdkit/Chem/test_data/BuildCrippenTestSet.py | Python | bsd-3-clause | 1,005 | [
"RDKit"
] | 5a069915d9a367c0430d97edd6ab9d6df5054948966feec2a8a2830aefa29a12 |
import os
import cPickle as pickle
__all__ = ["Experiment", "experiments", "series", "filterInfo", "the"]
# os.walk from Python 2.6, which adds support for followlinks.
def walk(top, topdown=True, onerror=None, followlinks=False):
"""Directory tree generator.
For each directory in the directory tree rooted a... | KMU-embedded/mosbench-ext | mparts/analyze.py | Python | mit | 7,691 | [
"VisIt"
] | 5b3b969667847575f66517699d87c5b3f7ea41fa54b623c39b0f4c3ae86bd45b |
import os
import nest
import logging
import datetime
from time import clock
from parameters import *
from data import *
times = []
spikegenerators = {} # dict name_part : spikegenerator
spikedetectors = {} # dict name_part : spikedetector
multimeters = {} # dict name_part : multimeter
SYNAPSES = 0
FORM... | vitaliykomarov/NEUCOGAR | nest/GDP/scripts/func.py | Python | gpl-2.0 | 12,382 | [
"NEURON"
] | d89ceacdf4871995ecf1aab1e2bb52d1a13693f3c88c2c9300f1dc2200ef0696 |
"""
Acquisition functions based on the probability or expected value of
improvement.
"""
# future imports
from __future__ import division
from __future__ import absolute_import
from __future__ import print_function
# global imports
import numpy as np
import scipy.stats as ss
# local imports
from ..utils import param... | jhartford/pybo | pybo/bayesopt/policies/improvement.py | Python | bsd-2-clause | 3,291 | [
"Gaussian"
] | 80723b9659dc6cbde6fb1ca87e156c969b9fe7621302c6467b7fc723382f4065 |
#!/bin/python
from pylab import *
from math import exp, sqrt
from image import *
from filters import *
from nibabel import load
def exp2d():
R = 50
I = circle_image3(300, 300, 1, R)
S = []
R = []
kernel_radius = array([2, 2, 0])
for sigma in linspace(1, 11, 5):
I1 = add_gaussian_nois... | facundoq/ipim | tp1/py/test_bilateral.py | Python | gpl-3.0 | 4,633 | [
"Gaussian"
] | e5094aa5f12eafb0a46cad826cb175de039cbd4f12036fd9d67bc115008d7cdc |
# Copyright (C) 2011-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | hmenke/espresso | testsuite/python/ek_eof_one_species_y_nonlinear.py | Python | gpl-3.0 | 11,836 | [
"ESPResSo"
] | e82f217bd8064f479a56901ac97dc0c4189a8ea273873e94c57f2e62a8498e0d |
"""
test_GlobalOperations.py
This file is part of ANNarchy.
Copyright (C) 2021 Helge Uelo Dinkelbach <helge.dinkelbach@gmail.com>
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 Founda... | vitay/ANNarchy | tests/Unittests/test_GlobalOperations.py | Python | gpl-2.0 | 7,962 | [
"NEURON"
] | 17e93d397eb3c89368e4320db230da06a6752c52dba7eb41138c08550e77b25b |
from __future__ import print_function
import getdist.plots as plots
import matplotlib.pyplot as plt
import numpy as np
from getdist.gaussian_mixtures import Mixture2D, Mixture1D, Gaussian1D, Gaussian2D, make_2D_Cov
default_nsamp = 10000
def simFiles(prob, file_root, sample_lengths=[1000, 2000, 5000, 10000, 20000, 5... | ClaudioNahmad/Servicio-Social | Parametros/CosmoMC/CosmoMC-master/python/getdist_tests/test_distributions.py | Python | gpl-3.0 | 14,699 | [
"Gaussian"
] | 98f2a7283428fa496eb91845a0d134117a316965a57f5ae060235aa994a300d1 |
#
# Author: Henrique Pereira Coutada Miranda
# Run a Silicon groundstate calculation using Quantum Espresso
#
from __future__ import print_function, division
import sys
from qepy import *
import argparse
from schedulerpy import *
kpoints = [12,12,1]
kpoints_double = [24,24,1]
qpoints = [3,3,1]
layer_separation = 12
pw... | henriquemiranda/yambopy | tutorial/bn/gs_bn.py | Python | bsd-3-clause | 8,018 | [
"CRYSTAL",
"Quantum ESPRESSO"
] | cfe54b6c2e354e9d1067b27bd5472aaf18ee872e2a1d785d79e9c9bbff263148 |
"""Simulating individual cycles, of different types."""
import numpy as np
from scipy.signal import sawtooth
from scipy.stats import norm
from neurodsp.sim.info import get_sim_func
from neurodsp.utils.data import compute_nsamples
from neurodsp.utils.checks import check_param_range, check_param_options
from neurodsp.u... | voytekresearch/neurodsp | neurodsp/sim/cycles.py | Python | apache-2.0 | 15,139 | [
"Gaussian"
] | 3c7604c1e3a9926c22e5eff46eca63cd9f7597547eb1e6e16405bc9129d56e55 |
#!/usr/bin/python
#
# Copyright 2010 Brian Dolbec <brian.dolbec@gmail.com>
# Copyright(c) 2010, Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
#
"""Provides support functions to enalyze modules"""
from gentoolkit import errors
from gentoolkit.keyword import reduce_keywords
from ... | zmedico/gentoolkit | pym/gentoolkit/enalyze/lib.py | Python | gpl-2.0 | 11,122 | [
"Brian"
] | 142283d0f69789ac0254b53e8b2a86a47054f2319c32f5228efea43973bcc9d6 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 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/gui/editors/shortcutseditor.py | Python | gpl-2.0 | 5,622 | [
"VisIt"
] | 9c216302c45201eada3b3d34aaf071ecf6d4e8a4aa3f5001e529d5d5a9a4d0a0 |
#
# Copyright 2014-2015, 2017, 2020-2021 Lars Pastewka (U. Freiburg)
# 2014 James Kermode (Warwick U.)
#
# matscipy - Materials science with Python at the atomic-scale
# https://github.com/libAtoms/matscipy
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GN... | libAtoms/matscipy | tests/test_idealbrittlesolid.py | Python | lgpl-2.1 | 3,378 | [
"ASE",
"Matscipy"
] | 768e92f51bb502f9b4a9865c93cb718a67bef06541efd7ca0a226b16f4e07c9f |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# ---------------------------------------------------------------------
# Copyright (c) 2012 Michael Hull.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are m... | mikehulluk/morphforge | src/morphforge/traces/tracetypes/tracepiecewise.py | Python | bsd-2-clause | 5,584 | [
"VisIt"
] | d53fa769b94d3012dfb00c4d7e213da139ca362904ed782eebb2696edadcceb6 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sat Mar 25 20:42:44 2017
@author: Yefee
"""
from .share_constant import *
# sec in siderial day ~ sec
sday = SHR_CONST_SDAY
# earth rot ~ rad/sec
omega = SHR_CONST_OMEGA
# radius of earth ~ m
rearth = SHR_CONST_REARTH
# acceleration of gravity ~ m/s^2
g... | Yefee/xcesm | xcesm/config/cesmconstant.py | Python | apache-2.0 | 2,003 | [
"Avogadro"
] | b8c648aa605c7719c7f7b700701cd9b38285d421fbfc394980fe31eca8e0504b |
import numpy as np
import scipy.signal
from scipy.ndimage.morphology import binary_erosion
from scipy.ndimage.morphology import white_tophat
from scipy.ndimage.filters import gaussian_filter
# dictionary describing options available to tune this algorithm
options = {
"best_size":{"purpose":"The estimate of the pea... | AbsoluteIntegrator/Absolute_Integrator | Absolute_Integrator/peak_finding/ranger.py | Python | mit | 6,616 | [
"Gaussian"
] | ea1395bfc041f351d50fad7a3961bbe20ca621936e8afb8c1ef5e414d9139d3d |
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.urls import path
from django.views import defaults as default_views
from gobgift.api.views import FacebookLogin, GoogleLogin
from gobgift.core.views import ... | kimond/gobgift | config/urls.py | Python | mpl-2.0 | 2,608 | [
"VisIt"
] | da2280bc8230d4e469854236373079ccd6814d1c79cf7a668b7c472be4a0b4e4 |
import os
import sys
import setuptools
import shutil
__where__ = os.path.dirname(os.path.abspath(__file__))
with open(os.path.join(__where__, 'exfoliate', 'VERSION.txt'), 'rb') as f:
__version__ = f.read().decode('ascii').strip()
# would prefer to just use markdown, but not compatible with setuptools; see the f... | brianjpetersen/exfoliate | setup.py | Python | mit | 2,763 | [
"Brian"
] | 3234f641dd2910980ca5d7de6dc5172ceaa12305cdcd4044364d9180627c80e0 |
#! /bin/env python
import os
import xml.dom.minidom
from collections import namedtuple
from xml.etree.ElementTree import ElementTree
import numpy as np
from six.moves import xrange
from ...grids import UnstructuredField
from .vtk import (
InvalidEncodingError,
InvalidFormatError,
assemble_vtk_elements,
... | csdms/coupling | deprecated/printers/vtk/vtu.py | Python | mit | 8,567 | [
"VTK"
] | 0c57a41352534869a8cf505b46aa9cd2b69848d9b915e496af399cb648bb4118 |
##############################################################################
# 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... | EmreAtes/spack | var/spack/repos/builtin/packages/py-gpaw/package.py | Python | lgpl-2.1 | 4,617 | [
"ASE",
"GPAW"
] | 0563ef47ee1053cca39931f3ff53d3435ea9d872ba14bd041b66b5dd34f67f0e |
import functools
from nose.tools import raises
from unittest import TestCase
from wadl2rst.nodes.base import BaseNode
class TestBaseNode(TestCase):
def setUp(self):
self.single_node = FakeNode(None, "test", {})
self.parent_node = FakeNode(None, "parent", {})
self.child_node = FakeChil... | annegentle/wadl2rst | test/unit/nodes/base_test.py | Python | apache-2.0 | 2,571 | [
"VisIt"
] | a0a30d89069afe4be9820c1ac89bc4aa1e2b3f0f7f42194048eb37f91618547f |
#
#@BEGIN LICENSE
#
# PSI4: an ab initio quantum chemistry software package
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later ver... | spring01/libPSI | lib/python/gaussian_n.py | Python | gpl-2.0 | 6,843 | [
"Gaussian",
"Psi4"
] | 96ed6a44ebacb70627f1ee5986bbac5064356fd57333db0aed833bd3ea999365 |
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