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#!/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 October 2010
Mike McCann
MBARI 22 April 2012
@var __date__: Date of last svn commit
@undocumented: __doc__ parser
@status:... | mikemccann/stoqs | loaders/CANON/loadCANON_october2010.py | Python | gpl-3.0 | 4,979 | [
"NetCDF"
] | 54482bf1e5dafa3b046325d1b20c6582e03246510f26b9c684f5b376eef3bced |
#!/bin/env python
from netCDF4 import Dataset, num2date
from local_utils import get_month_slice, get_day_slice
import numpy as np
DATA_DIR = '/snfs4/assessment/brooke/20Century/z500_Members/'
LATS = 91
LONS = 180
GRIDS = [(lat, lon) for lat in range(LATS) for lon in range(LONS)]
ENSEMBLE = 0
for year in range(2012, ... | abuddenb/agu2015 | calc_daily_anom_1.py | Python | mit | 2,486 | [
"NetCDF"
] | 9cbcb2111d7b534da2fba5061ff04963d134b2cc555ad2397a5761ab08f2be74 |
"""
Procedures for fitting marginal regression models to dependent data
using Generalized Estimating Equations.
References
----------
KY Liang and S Zeger. "Longitudinal data analysis using
generalized linear models". Biometrika (1986) 73 (1): 13-22.
S Zeger and KY Liang. "Longitudinal Data Analysis for Discrete and
... | phobson/statsmodels | statsmodels/genmod/generalized_estimating_equations.py | Python | bsd-3-clause | 98,301 | [
"Gaussian"
] | f654cad57912e9d0427cd19921550eb1d9b15c3e8cd7b19cd8bc4744dab34fd1 |
from setuptools import setup, find_packages
setup(
name='amber-state-machine',
version='0.0.1',
description='Amber State Machine',
long_description='Amber State Machine',
# The project's main homepage.
url='',
# Author details
author='Henri Korpela',
author_email='',
# Choo... | Hicks48/amber-state-machine-python | setup.py | Python | mit | 906 | [
"Amber"
] | e1865de8cfb163d37c9fcca92e9c17e640c6b09117d5d8841df8ee8595cca446 |
#!/usr/bin/env python
# encoding: utf-8
'''
Created by Brian Cherinka on 2016-05-23 00:13:58
Licensed under a 3-clause BSD license.
Revision History:
Initial Version: 2016-05-23 00:13:58 by Brian Cherinka
Last Modified On: 2016-05-23 00:13:58 by Brian
'''
from __future__ import print_function
from __future__... | bretthandrews/marvin | python/marvin/db/ArrayUtils.py | Python | bsd-3-clause | 1,759 | [
"Brian"
] | b540c81118c7a94b580ca2209669e2b50f48542908ff17d4b40ec3943083520b |
import functools, copy
import numpy as np
import regreg.api as rr
from ..randomized.randomization import randomization
class CV(object):
def __init__(self, loss, folds, lam_seq, objective_randomization=None, epsilon=None):
(self.loss,
self.folds,
self.lam_seq,
self.objective_r... | selective-inference/selective-inference | selectinf/algorithms/cv.py | Python | bsd-3-clause | 8,237 | [
"Gaussian"
] | ae9049de595492c5b97869d016d6c6c94ee2b79eb4a115f9347545411f70821f |
# -*- coding: utf-8 -*-
"""
Copyright (C) 2010 by Indifex (www.indifex.com), see AUTHORS.
License: BSD, see LICENSE for details.
For further information visit http://code.indifex.com/transifex-client
"""
VERSION = (0, 7, 0, 'final')
def get_version():
version = '%s.%s' % (VERSION[0], VERSION[1])
if VERSION... | zaabalonso/Transifex_Client_wui_interface | txclib/__init__.py | Python | gpl-2.0 | 474 | [
"VisIt"
] | 6d8570ab990b52c2d442c8d4047d0d3d9b8fb032ee110ac084631d26bab3df7f |
# 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 RXvector(RPackage):
"""Foundation of external vector representation and manipulation in
... | LLNL/spack | var/spack/repos/builtin/packages/r-xvector/package.py | Python | lgpl-2.1 | 1,979 | [
"Bioconductor"
] | 475ab807d4654bf8679b77af0a034cebd0a07e25771f023558321e6ca9bbbacb |
#!/usr/bin/env python3
"""Script to create the text generated based on the seventeenth chapter of
Joyce's Ulysses, 'Ithaca.' It relies on a simply formatted text file that
summarizes an automated analysis of 'Ithaca' performed by the script at
/UlyssesRedux/scripts/utility-scripts/get-chapter-17-stats.py, which classif... | patrick-brian-mooney/UlyssesRedux | chapter_scripts/ch17.py | Python | gpl-3.0 | 4,783 | [
"Brian"
] | 13aa9c535b52d38c37de108567432dc30aeaf2a4b10231043bb08fb7317e5a1a |
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at https://mozilla.org/MPL/2.0/.
"""
VASP
====
carSileVASP
doscarSileVASP
eigenvalSileVASP
chgSileVASP
locpotSileVASP
outSileVASP
"""... | zerothi/sisl | sisl/io/vasp/__init__.py | Python | mpl-2.0 | 466 | [
"VASP"
] | 3d08f586410ef84856e63b15405e4870369a6701cb1b215f85d36fb44bb85d16 |
# Adopted form SfePy project, see http://sfepy.org
# Thanks to Robert Cimrman
import sys
from copy import copy
import os.path as op
import numpy as nm
from .base import (
complex_types,
dict_from_keys_init,
assert_,
is_derived_class,
insert_static_method,
output,
get_default,
get_defau... | mjirik/dicom2fem | dicom2fem/meshio.py | Python | bsd-3-clause | 86,767 | [
"VTK"
] | e042a83a6995c8303f31bc7ac3cdaec40f8d62b85568a1d81a676df47dd7e322 |
#!/usr/bin/env python3
from setuptools import setup
with open("README.md", "r", encoding="utf-8") as fh:
long_description = fh.read()
setup(
name="braid",
version="0.14.1",
author="Brian House",
author_email="email@brian.house",
description="A musical notation system and sequencer for monopho... | brianhouse/braid | setup.py | Python | gpl-3.0 | 747 | [
"Brian"
] | 2673ce19b55c1ed8e54b89515d1f4db743903b726c9d56325aa9f2a7f5b0661f |
#! /usr/bin/env python
from Asap import *
from Asap.Dynamics.VelocityVerlet import VelocityVerlet
from Asap.Dynamics.Langevin import Langevin
from Asap.Setup.Lattice.Cubic import FaceCenteredCubic
import sys, cPickle, time, commands, os, re
import RandomArray
from Numeric import *
from Asap.testtools import ReportTest... | auag92/n2dm | Asap-3.8.4/Test/Timing/LennardJonesTiming.py | Python | mit | 2,494 | [
"ASE"
] | 5cf3841587597c99b65d0ae87e61c4a1989985870d5db6b5c8fb1aceaa6975bc |
# http://pyrocko.org - GPLv3
#
# The Pyrocko Developers, 21st Century
# ---|P------/S----------~Lg----------
from __future__ import absolute_import, print_function
import sys
import math
import time
import numpy as num
import logging
from .qt_compat import qc, qg, qw, use_pyqt5
from .marker import Marker, PhaseMarke... | pyrocko/pyrocko | src/gui/util.py | Python | gpl-3.0 | 20,353 | [
"VTK"
] | 5f667a50462f8efdcb0031d48b9a1390c4250868f95ee783fa5df87857ed2f91 |
# Author: Prabhu Ramachandran <prabhu [at] aero . iitb . ac . in>
# Copyright (c) 2008, Enthought, Inc.
# License: BSD Style.
# Enthought library imports.
from tvtk.tools.tvtk_doc import TVTKFilterChooser, TVTK_FILTERS
# Local imports.
from mayavi.filters.filter_base import FilterBase
from mayavi.core.common import ... | dmsurti/mayavi | mayavi/filters/user_defined.py | Python | bsd-3-clause | 3,082 | [
"Mayavi"
] | c6be6ba599ff7a677d6dca4a337e653cac986e8c709105108554a645e4303621 |
#! /usr/bin/env python3
import argparse
import asyncio
import ast
import sys
from colorama import init as colorama_init, Fore, Style
class NotSupportedNodeError(ValueError): pass
def attr2str(node):
if isinstance(node, ast.Attribute):
if isinstance(node.value, ast.Attribute):
value = attr2s... | lablup/coroutine-check | check.py | Python | mit | 7,691 | [
"VisIt"
] | 8495ca9d65687edbfa6e60714c420c979dc1d27c2530f8f4023dd46dd7f5550a |
"""
weather.py - Willie Yahoo! Weather Module
Copyright 2008, Sean B. Palmer, inamidst.com
Copyright 2012, Edward Powell, embolalia.net
Copyright 2013, Ross Mulcare, rossmulcare.net
Licensed under the Eiffel Forum License 2.
http://willie.dftba.net
"""
from willie import web
from willie.module import commands, exampl... | mulcare/willie-modules | weather.py | Python | unlicense | 6,157 | [
"COLUMBUS"
] | cb328d2f962b306d382be4c7a5c20b40a5201728484c0b1eb7dd25185bc39a01 |
#!/usr/bin/env python
#-*- coding:UTF-8 -*-
#
# @author Ritashugisha
# @contact ritashugisha@gmail.com
#
# This file is part of OmniTube.
#
# OmniTube 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 ve... | ritashugisha/OmniTube | OmniAuth.py | Python | gpl-3.0 | 4,544 | [
"VisIt"
] | e86afd56e944a9b3b4abc21eb43dd10f098bca7c9e48128d32323f9913265d69 |
#!/usr/bin/env python
"""mockjson.py: Library for mocking JSON objects from a template."""
__author__ = "James McMahon"
__copyright__ = "Copyright 2012, James McMahon"
__license__ = "MIT"
try:
import simplejson as json
except ImportError:
import json
import random
import re
import string
import sys
from dat... | JamesMcMahon/mockjson.py | mockjson.py | Python | mit | 5,486 | [
"Brian"
] | d0cb89263433c04f0f81788ca7a1fdd5454a10ebbd029687226517d83ff2dd75 |
# $Id$
#
# Copyright (C) 2003 Rational Discovery LLC
# All Rights Reserved
#
from rdkit import RDConfig
import sys,os,types
from rdkit import Chem
from rdkit.VLib.Filter import FilterNode
class SmartsFilter(FilterNode):
""" filter out molecules matching one or more SMARTS patterns
There is a count associate... | soerendip42/rdkit | rdkit/VLib/NodeLib/SmartsMolFilter.py | Python | bsd-3-clause | 2,727 | [
"RDKit"
] | 270a0ad4b6f327a9218f7119e353858ff40cb5fddf988d2cc03d1bf3b2fb737c |
# fig)a2.py ---
#
# Filename: fig)a2.py
# Description:
# Author:
# Maintainer:
# Created: Thu Jun 27 12:06:52 2013 (+0530)
# Version:
# Last-Updated: Sun Jun 25 15:09:51 2017 (-0400)
# By: subha
# Update #: 31
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#
# Change log:
# ... | BhallaLab/moose-examples | traub_2005/py/fig_a2_fs.py | Python | gpl-2.0 | 3,561 | [
"MOOSE"
] | 935312de568229bfe7a8b4a2cfaf7ea2e1ae0217fe1ec0c35429d55f5ad2a688 |
#!/usr/bin/python
#FILE DESCRIPTION=======================================================
#~ Python script used for foam case construction (as automatic, as
#~ possible)
#~
#~ NOTES:
#~ - mesh grading in z direction
#~ USAGE:
#~ - modify and run the script
#~ TO DO:
#LICENSE=======================... | MartinIsoz/CFD_oF | 04_perforatedPlate/21_noTextureZigZagPerforationV2/00_Scripts/caseConstructorMappedV1.py | Python | gpl-2.0 | 23,061 | [
"ParaView"
] | b696975ba77138889d4efce68a0145fe8e3bdb020f4dac05b7897b2ee4c33d07 |
"""
Import utilities
Exported classes:
ImportManager Manage the import process
Importer Base class for replacing standard import functions
BuiltinImporter Emulate the import mechanism for builtin and frozen modules
DynLoadSuffixImporter
"""
# note: avoid importing non-builtin mo... | lovelysystems/pyjamas | pyjd/imputil.py | Python | apache-2.0 | 27,018 | [
"BLAST"
] | c910d240c19b1ac49610e931cdbf304ff280e535cd8428171e521df9053b6771 |
from dalton.config.loader import YamlFileSecurityGroupsConfigLoader
from dalton.config.models import Rule, SecurityGroup
| signal/dalton | dalton/config/__init__.py | Python | apache-2.0 | 121 | [
"Dalton"
] | 56fc3d855db8ee4e5cefe51cdf55d3a077e1efa2297fc3804d3dea5cad7bd2e0 |
"""
vtkImageImportFromArray: a NumPy front-end to vtkImageImport
Load a Numeric Python array into a VTK image.
To use this class, you must have the LLNL Numeric Python distribution
(http://numpy.sf.net)
Methods:
GetOutput() -- connect to VTK image pipeline
SetArray() -- set the array to load in
Convert pytho... | sgh/vtk | Wrapping/Python/vtk/util/vtkImageImportFromArray.py | Python | bsd-3-clause | 4,423 | [
"VTK"
] | 8027b8b726dc2dea9058066f7e815da8efdbfccadb8d2dedd41ddf44e686427f |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# Copyright (C) 2021 The SymbiFlow Authors.
#
# Use of this source code is governed by a ISC-style
# license that can be found in the LICENSE file or at
# https://opensource.org/licenses/ISC
#
# SPDX-License-Identifier: ISC
from fpga_interchange.interchange_capnp impor... | SymbiFlow/symbiflow-xc-fasm2bels | fasm2bels/lib/interchange.py | Python | isc | 30,257 | [
"VisIt"
] | 24e947def29fb6ab50b7ca9f701c24984cf3087699a65776951636642e89bb75 |
# -*- 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... | andrebellafronte/stoq | stoqlib/domain/test/test_purchase.py | Python | gpl-2.0 | 26,967 | [
"VisIt"
] | 4da38a3a5f328aa6cb427e0e88dacd239ac104ce8e0cbf2c43710f73efcf8281 |
# Copyright 2013-2020 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 RTmixclust(RPackage):
"""Time Series Clustering of Gene Expression with Gaussian Mixed-Eff... | iulian787/spack | var/spack/repos/builtin/packages/r-tmixclust/package.py | Python | lgpl-2.1 | 1,567 | [
"Bioconductor",
"Gaussian"
] | 9e77342319ef10c7b0a1a8de29d3a791c5f2b4d8449b5b7c4bc55e5466a01a6e |
#!/usr/bin/python3
# -*- coding: utf-8 -*-
'''Pychemqt, Chemical Engineering Process simulator
Copyright (C) 2009-2017, Juan José Gómez Romera <jjgomera@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 Softwar... | jjgomera/pychemqt | tools/UI_Tables/chooseFluid.py | Python | gpl-3.0 | 65,195 | [
"Gaussian"
] | 8a10a9899a93e3f57c93f5c55baebf64efa057604126094341b7fcbbbb2c1a39 |
# -*- coding: utf-8 -*-
#
# This file is part of Invenio-Query-Parser.
# Copyright (C) 2014 CERN.
#
# Invenio-Query-Parser 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 ... | egabancho/invenio-query-parser | invenio_query_parser/walkers/pypeg_to_ast.py | Python | gpl-2.0 | 4,120 | [
"VisIt"
] | 9983af9c1ba89609d875c53150f08b88db4a52430519ce9d32a952c46df3e0a8 |
"""
Tools for dealing with ROMS model output
See Octant project as well
Created on Fri Mar 08 15:09:46 2013
@author: mrayson
"""
import numpy as np
import sys
from netCDF4 import Dataset, MFDataset, num2date
from datetime import datetime, timedelta
import matplotlib.pyplot as plt
from scipy import in... | UT-CWE/Hyospy | Hyospy_ensemble/lib/SUNTANS/DataIO/romsio.py | Python | mit | 65,146 | [
"NetCDF"
] | c50796eefcdf96379840739534b954d2bcd138d6ae6f6851e1f36fd3f692efdd |
####################################################################
#
# Configuration related utilities
#
####################################################################
from DIRAC import S_OK, S_ERROR, gLogger, gConfig
from DIRAC.ConfigurationSystem.Client.Helpers import Registry, Operations
from DIRAC.Framewor... | xianghuzhao/VMDIRAC | VMDIRAC/Resources/Cloud/ConfigHelper.py | Python | gpl-3.0 | 5,227 | [
"DIRAC"
] | 24aeacb3f852d79dd047e2aa3e21e2c710ef2c786d6680de85f0d708362f025a |
import os
import shutil
import copy
#import codepy.cgen
import asp.codegen.cpp_ast as CppAst
import asp.codegen.ast_tools as CppAstTools
from tinycu_converter import CppLambda
import codepy
#############################################################################
from cpp_analysis_config import *
###############... | richardxia/asp-multilevel-debug | asp/analysis/cpp_instrument.py | Python | bsd-3-clause | 27,550 | [
"VisIt"
] | edbe8de22b32cb838558dea9b8e1b094ad4c622f744d6a627dfe61dba4100f9b |
"""@package DisplacementKernels
This module defines an interface to read and use InputGen projects
See C++ InputGen project for more details on Projects
"""
from numpy import vectorize
import math
import numpy as np
from scipy import stats
class DisplacementKernel(stats.rv_continuous):
"""Python representation o... | amonszpart/globOpt | evaluation/packages/displacementKernels.py | Python | apache-2.0 | 4,205 | [
"DIRAC"
] | dd04c49983c6d10c9d77f0fdaa9296ba644bcff83dbe8d68756836bf26002970 |
# -*- coding: utf-8 -*-
# Copyright 2022 Google 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... | googleapis/python-monitoring-metrics-scopes | tests/unit/gapic/monitoring_metrics_scope_v1/test_metrics_scopes.py | Python | apache-2.0 | 79,522 | [
"Octopus"
] | 9d5be1c1a12ed1967e538e66212e5615cf2c1596c5a8e63aadc52ba875315fe4 |
#!/usr/bin/env python
import sys
import numpy as np
import matplotlib.pyplot as plt
from matplotlib import animation
import argparse
import netCDF4 as nc
"""
#This script is a trial and makes a fluid animation using netcdf data.
"""
def main():
parser = argparse.ArgumentParser()
parser.add_argument('i... | scottc234/fluids_movie | make_movie.py | Python | apache-2.0 | 1,299 | [
"NetCDF"
] | 8200235d8791465860658c0f7191994e7d1f1878ab30700e323366e1f44077ce |
"""
Contains the main interface in the Universe class
"""
import cgi
import os
import urllib
from paste.httpexceptions import HTTPNotFound, HTTPBadGateway
from galaxy.web.base.controller import BaseUIController, UsesHistoryDatasetAssociationMixin, UsesHistoryMixin
from galaxy import managers
from galaxy import web
f... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/webapps/galaxy/controllers/root.py | Python | gpl-3.0 | 23,710 | [
"Galaxy"
] | 5e1cb83ac47ef56c7192dc0508fae9aa39261f5f2a9127fbc34d078195743f14 |
"""
Django settings for amber project.
Generated by 'django-admin startproject' using Django 1.11.5.
For more information on this file, see
https://docs.djangoproject.com/en/1.11/topics/settings/
For the full list of settings and their values, see
https://docs.djangoproject.com/en/1.11/ref/settings/
"""
# Build pat... | Taywee/amberherbert.com | amber/settings/base.py | Python | mit | 4,304 | [
"Amber"
] | 5b18095017f6819fdab38a35cff1c15b7216658c507cdf4c5a24e4551742b250 |
from sfepy.base.base import *
from sfepy.fem.mesh import Mesh
from sfepy.fem.meshio import MeshIO
from sfepy.solvers.ts import TimeStepper
from sfepy.base.ioutils import get_trunk, write_dict_hdf5
def dump_to_vtk(filename, output_filename_trunk=None, step0=0, steps=None):
"""Dump a multi-time-step results file int... | olivierverdier/sfepy | sfepy/postprocess/time_history.py | Python | bsd-3-clause | 5,385 | [
"VTK"
] | 8f7fdb940087aff5edf04900ede41595f1714678f760a720f6f6071a6235a218 |
from MuLexer import MuLexer
from MuParser import MuParser
from MyMuVisitor import MyMuVisitor, MuRuntimeError, MuSyntaxError
from MyMuTypingVisitor import MyMuTypingVisitor, MuTypeError
import argparse
import antlr4
# Main file for Lab 4, CAP, october 2017
enable_typing = False
def main():
# command line
pa... | lauregonnord/cap-labs | TP04/Mu-evalntype/Main.py | Python | gpl-3.0 | 1,150 | [
"VisIt"
] | a54aa7ff682c2a50840b5c6f9ad9e8095a6402baa0405f5642168e205fc3529c |
cards = {
"Abomination": 0,
"Abusive Sergeant": 2,
"Acidic Swamp Ooze": 2,
"Acidmaw": 1,
"Acolyte of Pain": 1,
"Al'Akir the Windlord": 0,
"Alarm-o-Bot": 1,
"Aldor Peacekeeper": 2,
"Alexstrasza": 0,
"Alexstrasza's Champion": 0,
"Amani Berserker": 2,
"Ancestor's Call": 0,
... | Templarrr/hearthtools | data/nastya_collection.py | Python | cc0-1.0 | 18,044 | [
"BLAST",
"TINKER"
] | f734b88a4faa9633d0878132545518e91fe4f04d6acbcd044b6f35e9633812a0 |
"""Copyright 2012 Phidgets Inc.
This work is licensed under the Creative Commons Attribution 2.5 Canada License.
To view a copy of this license, visit http://creativecommons.org/licenses/by/2.5/ca/
"""
__author__ = 'Adam Stelmack'
__version__ = '2.1.8'
__date__ = 'May 17 2010'
import threading
from ctypes ... | danielsuo/mobot | src/move/PhidgetsPython/Phidgets/Devices/InterfaceKit.py | Python | mit | 23,361 | [
"VisIt"
] | a1882c698ff7339a07fa3ea5f26e4c58f06c925fa66c9bdcee1e639afbfd942e |
#!/usr/bin/env python
# -*- coding: utf-8 -*
import numpy as np
import skimage
from skimage import morphology
import scipy.ndimage.filters as filters
import math
import SimpleITK as sitk
def preprocess_brain(img, spacing, modality, image_orientation, atlas_orientation='pir'):
"""Perform all preprocessing steps a... | neurodata/ndreg | ndreg/preprocessor.py | Python | apache-2.0 | 13,526 | [
"Gaussian"
] | 23fd3d5863011e94aa72ea85663f5020c456225c97f8f58be21e35574cd8cdd3 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# This file is part of convertdate.
# http://github.com/fitnr/convertdate
# Licensed under the GPL-v3.0 license:
# http://opensource.org/licenses/MIT
# Copyright (c) 2016, fitnr <fitnr@fakeisthenewreal>
# source: Wikipedia
# month 13 is the Sansculottides
french_republic... | mpercich/Calendarize | ios/dateparser/lib/python2.7/site-packages/convertdate/data/french_republican_days.py | Python | mit | 8,040 | [
"FLEUR"
] | 6d894b848c49417946fe8bb2d5333ee06174345ebd5bd50955a4217f1fde9555 |
import cv2
import numpy as np
cap = cv2.VideoCapture(0)
while( cap.isOpened() ) :
# Checks if the capturing is on
ret,image = cap.read()
# returns true and value of captured frame
gray = cv2.cvtColor(image,cv2.COLOR_BGR2GRAY)
#converts image to gray scale
blur = cv2.GaussianBlur(gray,(5,5),0)
... | Mnw2212/DANI | handtest.py | Python | gpl-2.0 | 3,039 | [
"Gaussian"
] | f1794bc1f31b4d115345c87e10c9480372db6396bfc02c0fd48b88ee61fcf1be |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
"""
SYNOPSIS
.
DESCRIPTION
EXAMPLES
python inverse_document.py
EXIT STATUS
0 program exit normal
1 program had problem on execution
AUTHOR
Theofilis George <theofilis.g@gmail.com>
LICENSE
This program is free software: you ca... | theofilis/tutorial-information-retrieval | latent_sematic_index.py | Python | gpl-3.0 | 3,084 | [
"TINKER"
] | 219bfa153e813d5ce0ad4611ecadf38dbe636ff35d25fed89206ea7f26330c1f |
"""Check that energy is correct even after wrapping through periodic boundary conditions.
"""
from ase.lattice.cubic import FaceCenteredCubic
from asap3 import *
from asap3.testtools import *
import random
ref_atoms = FaceCenteredCubic(size=(7,7,7), symbol="Cu", pbc=(True, False, True))
ref_atoms.set_calculator(EMT()... | auag92/n2dm | Asap-3.8.4/Test/PBCwrap.py | Python | mit | 1,518 | [
"ASE"
] | 29c230da9aae0aac6e184d26c2cb61d30a798b247df82cfd7a5b0ffe4a235e23 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""usage: blobtools map2cov -i FASTA [-b BAM...] [-a CAS...]
[-o PREFIX] [-c]
[-h|--help]
Options:
-h --help show this
-i, --infile FASTA FASTA ... | DRL/blobtools | lib/map2cov.py | Python | gpl-3.0 | 1,644 | [
"pysam"
] | 677374610c00e780df93a35c8ba672003a730bd8d643f3592ff61061f1d88ff7 |
"""Defines a base Visitor class for all the outputs.
This class does almost all of the lifting for output generation. It's super
important; don't gloss this one over.
"""
from io import IOBase
from collections import ChainMap
import sys
from os import makedirs
import os.path
import contextlib
from .util import prin... | NJDFan/register-maps | registermaps/visitor.py | Python | gpl-3.0 | 10,036 | [
"VisIt"
] | 7045b0979c1f6597cc2b4aa60ac39fa6dca7f0ab07462daac0757aa5ecd7a221 |
# -*- python -*-
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2003-2005 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
#
# This program is free software; you can redistribute it and/or modify
# it under... | arunkgupta/gramps | gramps/plugins/rel/rel_it.py | Python | gpl-2.0 | 21,032 | [
"Brian"
] | 4784e0f68ec3c4171608f7b86c2ee7b2cdacfc69c9f5c26a6762378657161904 |
##
# Copyright 2009-2020 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | pescobar/easybuild-easyblocks | easybuild/easyblocks/n/neuron.py | Python | gpl-2.0 | 9,088 | [
"NEURON"
] | f7074019490f7f912b015a6a6789e35df7a9b3c2d7f2ab1d4839619df4ac13b1 |
from lutris.runners.runner import Runner
from lutris.util.display import get_current_resolution
class fsuae(Runner):
human_name = "FS-UAE"
description = "Amiga emulator"
platforms = [
'Amiga 500',
'Amiga 500+',
'Amiga 600',
'Amiga 1000',
'Amiga 1200',
'Amiga... | RobLoach/lutris | lutris/runners/fsuae.py | Python | gpl-3.0 | 5,405 | [
"ADF"
] | a894b1fb203ce0c4953dd9b1b45e7712c3f4ba15e235aa5b477a45f22e193cab |
'''
Read a basis set file in a given format
'''
import os
import bz2
from ..skel import create_skel
from ..validator import validate_data
from ..compose import _whole_basis_types
from .turbomole import read_turbomole
from .g94 import read_g94
from .nwchem import read_nwchem
from .gbasis import read_gbasis
from .dalton... | MOLSSI-BSE/basis_set_exchange | basis_set_exchange/readers/read.py | Python | bsd-3-clause | 4,993 | [
"CFOUR",
"Dalton",
"MOLCAS",
"Molpro",
"NWChem",
"TURBOMOLE",
"deMon2k"
] | 272425718f7bb44d5a78a6e47f197e5b19ef62205d0714b58367dacccc0db855 |
# Copyright (C) 2013,2014 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... | mgusenbauer/espresso | src/core/gen_featureconfig.py | Python | gpl-3.0 | 3,808 | [
"ESPResSo"
] | 803432cc0eb2a566adcac8cd59165c30cd0e90502bcd7a5f9681eb9a9449fac8 |
import unittest
import numpy as np
from pymicro.crystal.lattice import Lattice, HklDirection, HklPlane, Symmetry
from pymicro.crystal.microstructure import Orientation
from pymicro.xray.laue import select_lambda, diffracted_vector, gnomonic_projection_point, gnomonic_projection, index
from pymicro.xray.detectors import... | heprom/pymicro | pymicro/xray/tests/test_Laue.py | Python | mit | 8,732 | [
"CRYSTAL"
] | dd4776b202b0aa3c3640b24ada3ffa9bdc2f27b6779ffa64b1e00a0b095c1d94 |
#Seance: a bioinformatics pipeline for reference-based phylogenetic analysis
#Copyright (C) 2014 Alan Medlar (amedlar@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 Foundation, either version 3 ... | ajm/seance | seance/main.py | Python | gpl-3.0 | 28,714 | [
"BLAST"
] | e7b71e4dc86187154dc354d5d0a09b6e115446b948c23ec53409e874b121d79b |
from collections import namedtuple
__all__ = ['tarjan',
'tarjan_iter',
'tarjan_recursive']
""" Context used to implement the algorithm without recursion in @tarjan
and @tarjan_iter """
TarjanContext = namedtuple('TarjanContext',
['g', # the graph
... | Inoryy/py-tarjan | src/__init__.py | Python | agpl-3.0 | 5,523 | [
"VisIt"
] | 5f200b5f49e33a2a04886730d352e2c7c85e0a5a1ab5f8a1580607c97dede3f2 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/Openwebif | plugin/controllers/views/web/streamsubservices.py | Python | gpl-2.0 | 5,579 | [
"VisIt"
] | f0ee8a9ffa6f27d3abcfdbb1cc9278d9493bd941de42a4b6d05f886b429d34dc |
#!/usr/bin/python
import os
import sys
import tempfile
if '--dir' in sys.argv:
i = sys.argv.index('--dir')
dir = sys.argv[i + 1]
else:
dir = None
if '--email' in sys.argv:
i = sys.argv.index('--email')
email = sys.argv[i + 1]
else:
email = None
if '--nodoc' in sys.argv:
i = sys.argv.index... | askhl/ase | tools/sphinx.py | Python | gpl-2.0 | 4,307 | [
"ASE"
] | 1a7de4f8b2f33112e801b35a159b03c660230d045e77ce0928618b3d60b1d487 |
""" The TimeLeft utility allows to calculate the amount of CPU time
left for a given batch system slot. This is essential for the 'Filling
Mode' where several VO jobs may be executed in the same allocated slot.
The prerequisites for the utility to run are:
- Plugin for extracting information from lo... | fstagni/DIRAC | Core/Utilities/TimeLeft/TimeLeft.py | Python | gpl-3.0 | 9,578 | [
"DIRAC"
] | d792d487cc49c96e30a63b7d08fd6d96f19bd160cc23ba2a1081c21bd21915fd |
"""The tasks module provides a simple light-weight alternative to threads.
When you have a long-running job you will want to run it in the background,
while the user does other things. There are four ways to do this:
- Use a new thread for each task.
- Use callbacks from an idle handler.
- Use a recursive mainloop... | res2k/0install | zeroinstall/support/tasks.py | Python | lgpl-2.1 | 13,783 | [
"VisIt"
] | 37e5fa85fc11f3904af7b3956f1be3ed241a377dca0672876f98708ab9dc9062 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# The MIT License (MIT)
#
# Copyright (c) 2014 Siyuan Ren (netheril96@gmail.com)
#
# 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 restr... | coldze/autojsoncxx | autojsoncxx.py | Python | mit | 19,165 | [
"VisIt"
] | 839d24772474da8f3ebf4a1983abd0371824e448af3382bea9df51d0a3c5d41f |
# Copyright (c) Charl P. Botha, TU Delft
# All rights reserved.
# See COPYRIGHT for details.
from typeModules.transformStackClass import transformStackClass
import cPickle
from module_base import ModuleBase
from module_mixins import FilenameViewModuleMixin
import module_utils
import wx
import vtk
class transformStack... | nagyistoce/devide | modules/insight/transformStackWRT.py | Python | bsd-3-clause | 3,873 | [
"VTK"
] | d1d913b46c7e59250875e1949e6368d39f304ceb1bef666674e409a6f850d867 |
# -*- coding: utf-8 -*-
"""
Copyright (C) 2014 TopCoder Inc., All Rights Reserved.
This Python module provides a template of script for ParaView to load multiple data files.
This script could NOT run directly, but should be treated as a template and run after edited some fields.
@author: caoweiquan322
@version: 1.0
... | NREL/OpenWARP | source/openwarpgui/bundled/paraview/paraview_script_template.py | Python | apache-2.0 | 1,313 | [
"ParaView",
"VTK"
] | a5b64616fa8af9478c46f38f84318ce12369dab0e69da774f9cf7a9c3e807144 |
# -*- coding: utf-8 -*-
'''filtering test mixins'''
from inspect import ismodule
from twoq.support import port
class MSliceQMixin(object):
def test_first(self):
manq = self.qclass(5, 4, 3, 2, 1).first()
self.assertFalse(manq.balanced)
manq.sync()
self.assertTrue(manq.balanced)
... | lcrees/twoq | twoq/tests/man/filtering.py | Python | bsd-3-clause | 9,554 | [
"MOE"
] | 7fbcb3a2345c9dbaceb6ad500d53787aabc1249be5d4ff672582302a5835bf99 |
from math import sqrt,log
import numpy as np
from matplotlib import pyplot
import rft1d
eps = np.finfo(float).eps
def here_hotellingsT2(y):
N = y.shape[0]
m = np.matrix( y.mean(axis=0) )
T2 = []
for ii,mm in enumerate(m):
W = np.matrix( np.cov(y[:,ii,:].T, ddof=1) ) #estimated cov... | 0todd0000/rft1d | rft1d/examples/val_upx_3_T2_set.py | Python | gpl-3.0 | 2,078 | [
"Gaussian"
] | 5c9df7bd492887cd7dbcafbb37f9ebaffef348f9a67c21af3d70799d119eb6e7 |
# -*- coding: utf-8 -*-
"""
The :mod:`sklearn.metrics.pairwise` submodule implements utilities to evaluate
pairwise distances, paired distances or affinity of sets of samples.
This module contains both distance metrics and kernels. A brief summary is
given on the two here.
Distance metrics are a function d(a, b) such... | liberatorqjw/scikit-learn | sklearn/metrics/pairwise.py | Python | bsd-3-clause | 42,629 | [
"Gaussian"
] | 4f54cc8df44e4333f7c499879d7a6d843e3d9c59831417b09caec83529387e40 |
"""Miscellaneous utilities."""
from functools import reduce
import os
import os.path as op
import subprocess
import warnings
import numpy as np
from mne import pick_types, pick_info, make_sphere_model, DipoleFixed, Epochs
from mne.channels import make_standard_montage, make_dig_montage
from mne.fixes import _get_args... | kambysese/mnefun | mnefun/_utils.py | Python | bsd-3-clause | 6,487 | [
"Mayavi"
] | 6ab815222eca09e9e0b1a6df815a82b89b53d963a3aa523c5ac9bf3d862937f1 |
import os, sys
import urllib
import Globals
from AccessControl import ClassSecurityInfo
from DateTime import DateTime
from OFS.SimpleItem import SimpleItem
from Acquisition import aq_base
from Products.Archetypes.Referenceable import Referenceable
from OFS.PropertyManager import PropertyManager
from Products... | erikriver/eduIntelligent-cynin | products/ATRatings/RatingsTool.py | Python | gpl-3.0 | 13,993 | [
"Gaussian"
] | e3fea02fbfae9452ec71c90d75e0b16e391f1f168d2d2591ce9ce65ad584d2bb |
# Copyright 2010 by Tiago Antao <tiagoantao@gmail.com>. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
from __future__ import print_function
import os
import shutil
import tem... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_PopGen_DFDist.py | Python | gpl-2.0 | 4,586 | [
"Biopython"
] | c0deefbbf23537a79963b7dbaa9cd30187dfaf61a40d2d41a5fc42c586bc505e |
"""
:Author: Engelbert Gruber
:Contact: grubert@users.sourceforge.net
:Revision: $Revision$
:Date: $Date$
:Copyright: This module has been placed in the public domain.
LaTeX2e document tree Writer.
"""
__docformat__ = 'reStructuredText'
# code contributions from several people included, thanks to all.
# some named: ... | crystalspace/CS | docs/support/docutils/writers/latex2e.py | Python | lgpl-2.1 | 75,909 | [
"VisIt"
] | cdd9ec759a69760ea5a83f388b4be8fdccebc34ea67b006346510376e3d0dbd0 |
#!/usr/bin/env python
# -*- coding: iso-8859-1 -*-
#
# Impressive, a fancy presentation tool
# Copyright (C) 2005-2008 Martin J. Fiedler <martin.fiedler@gmx.net>
# portions Copyright (C) 2005 Rob Reid <rreid@drao.nrc.ca>
# portions Copyright (C) 2006 Ronan Le Hy <rlehy@free.fr>
# portions Copyright (C) 2007 Luke Campag... | leeper/Impressive | impressive-geekq.py | Python | gpl-2.0 | 140,647 | [
"VisIt"
] | 1fe56d4b72f675230a633663abca78b28ccce2cb14b05bd088bacf4eaebcac09 |
import itertools
import numpy as np
from ase import Atoms, Atom, visualize
from ase.utils.distance import distance
# artificial structure
org = Atoms([
Atom('C', [-1.75072, 0.62689, 0.00000]),
Atom('O', [0.58357, 2.71652, 0.00000]),
Atom('P', [-5.18268, 1.36522, 0.00000]),
Atom('N', [-... | grhawk/ASE | tools/ase/test/distance.py | Python | gpl-2.0 | 1,788 | [
"ASE"
] | a601a4b46324f29a1770f781cd196baa7a1f420a4cca310f7ac11c2dd7e9f286 |
"""
sender - SimplE Neuron DEleteR
Deletes the least significant neurons.
Outgoing value of neuron is defined as sum of absolute values of
weights outgoing from neuron divided by sum of absolute values of
weights outgoing from entire layer.
Ingoing value of neuron is defined as sum of absolute ... | heurezjusz/Athena | athenet/algorithm/simple_neuron_deleter2.py | Python | bsd-2-clause | 4,013 | [
"NEURON"
] | 3f2cfcacfa45e815ddfb37fcba0fe93b97f7458b24b2c479d6663300f47849ac |
#!/usr/bin/env python3
# PYTHON_ARGCOMPLETE_OK
# ======================================================================
# matscipy - Python materials science tools
# https://github.com/libAtoms/matscipy
#
# Copyright (2019) Johannes Hoermann, University of Freiburg
#
# This program is free software: you can redistribut... | libAtoms/matscipy | matscipy/cli/electrochemistry/pnp.py | Python | lgpl-2.1 | 10,487 | [
"Matscipy"
] | be1257f3fb6d9d86d4658debecd1e39ce70dd489a7ffa4bca5afbb791b2a216a |
import treeCl
"""
The first point of call is the treeCl.Collection class.
This handles loading your data, and calculating the trees
and distances that will be used later.
This is how to load your data. This should be a directory
full of sequence alignments in fasta '*.fas' or phylip
'*.phy' formats. These can also be... | DessimozLab/treeCl | example.py | Python | mit | 4,565 | [
"Gaussian"
] | 20b98a2673ab2c44097254d36e36087d0c7da53602800fa617c3a59dd0507848 |
# Copyright 2013-2020 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 RXde(RPackage):
"""XDE: a Bayesian hierarchical model for cross-study analysis of
d... | iulian787/spack | var/spack/repos/builtin/packages/r-xde/package.py | Python | lgpl-2.1 | 1,423 | [
"Bioconductor"
] | 3004b3e1ff21a9a33277b6ecf8d7ddb92c1ccbef8512d8c415dc69f6d8174e6a |
#!/usr/bin/env python
#
# AST.py
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License version 2 as
# published by the Free Software Foundation.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; witho... | amohanta/thug | src/AST/AST.py | Python | gpl-2.0 | 10,154 | [
"VisIt"
] | 1b30236bffdf38dd3e3b1dc4ecd180c1d6b394217b83021e3051c4f800b280dd |
#
# Copyright 2013-2020 Universidad Complutense de Madrid
#
# This file is part of PyEmir
#
# SPDX-License-Identifier: GPL-3.0+
# License-Filename: LICENSE.txt
#
"""Combination routines"""
from __future__ import division
import datetime
import functools
import logging
import uuid
import numpy
from astropy.io import... | nicocardiel/pyemir | emirdrp/processing/combine.py | Python | gpl-3.0 | 13,969 | [
"Gaussian"
] | 02f34790fce3ca606ec320d71c32cfdc4a5561338c44cec280d745c15a417009 |
# coding=utf-8
# Copyright 2022 The Tensor2Tensor 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... | tensorflow/tensor2tensor | tensor2tensor/models/research/moe.py | Python | apache-2.0 | 27,293 | [
"MOE"
] | 5a280799c9c47c2df29f6c4aa054b88dcf8be339e000efb6e9c59679efb75259 |
# -*- coding: utf-8 -*-
# This program is free software; you can redistribute it and/or modify it under
# the terms of the (LGPL) GNU Lesser 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 distri... | ovnicraft/suds | tests/test_cache.py | Python | lgpl-3.0 | 39,849 | [
"Firefly"
] | 9eb7c764fa257cdd10b901176a7d61888e38ffc09503bff0e35cd9244e57b40d |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2014 Stanford University and the Authors
#
# Authors: Peter Eastman, Robert McGibbon
# Contributors: Kyle A. Beaucha... | mdtraj/mdtraj | mdtraj/core/topology.py | Python | lgpl-2.1 | 60,859 | [
"MDTraj",
"OpenMM",
"VMD"
] | 26bfb397bf925c1bac38c65a15ff6079a70046de942e63804fc46357f180117b |
# Copyright 2007-2016 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later ... | CodeMonkeyJan/hyperspy | hyperspy/tests/signal/test_eels.py | Python | gpl-3.0 | 8,249 | [
"Gaussian"
] | 93b2226bc8c6f42f6df89d676c09883e34b0cf4198e7b78841db292b120fd2b3 |
##
# Copyright 2013-2021 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | akesandgren/easybuild-easyblocks | easybuild/easyblocks/g/gromacs.py | Python | gpl-2.0 | 36,255 | [
"Gromacs"
] | 31b6f697803d3221003cbcb86ba332cd2d214f975bd13708b1b99c64d974cc42 |
#!/usr/bin/env python3
# Copyright (C) 2015-2017(H)
# Max Planck Institute for Polymer Research
#
# 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, eit... | espressopp/espressopp | examples/lennard_jones_93_wall/lennard_jones_93_wall.py | Python | gpl-3.0 | 6,473 | [
"ESPResSo"
] | cb3c86bb44b3fae0d700b85bec62230010f77343ee481faabf278255bde36332 |
#!/usr/bin/env python
# encoding: utf-8
# Thomas Nagy, 2005-2008 (ita)
"base for all c/c++ programs and libraries"
import os, sys, re
import TaskGen, Task, Utils, preproc, Logs, Build, Options
from Logs import error, debug, warn
from Utils import md5
from TaskGen import taskgen, after, before, feature
from Constants ... | oneman/xmms2-oneman-old | wafadmin/Tools/ccroot.py | Python | lgpl-2.1 | 18,542 | [
"VisIt"
] | 6372523a1ce41b0a97be6e022b7b3f13beb821d92fb96dd8b01ff08d789b6996 |
from __future__ import absolute_import
from __future__ import print_function
import unittest2 as unittest
import os
import numpy as np
from pymatgen.util.testing import PymatgenTest
from pymatgen.core.surface import generate_all_slabs
from pymatgen.analysis.adsorption import *
from pymatgen.symmetry.analyzer import S... | aykol/pymatgen | pymatgen/analysis/tests/test_adsorption.py | Python | mit | 3,135 | [
"pymatgen"
] | 75e0afede4190b4b4fc37f06a7b29b9860cf0ebd8c2dfe092adf7d476f68ce48 |
# -*- 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.
"""Population analyses based on cclib data."""
import logging
import numpy
from .calculationmethod import ... | gaursagar/cclib | src/cclib/method/population.py | Python | bsd-3-clause | 2,928 | [
"cclib"
] | cb937d0fb5c6560b3136c0cc0a315cec175bedaa937a9660006e1b3d38013f8e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import (absolute_import, division,
print_function, unicode_literals)
from collections import OrderedDict
import numpy as np
from .eos import EOSFactory
from phonopy.qha.eos import EOSFit
__author__ = 'Yuji Ikeda'
def calculate_rmse... | yuzie007/ph_analysis | ph_analysis/eos/eos_fitting.py | Python | mit | 2,363 | [
"phonopy"
] | c328b5155ef688d3067c287c5f3bf752542d4df20da0a4e468ba42d60d8951b8 |
#
# Copyright 2020-2021 Lars Pastewka (U. Freiburg)
# 2020 Jan Griesser (U. Freiburg)
#
# 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 GNU General Public ... | libAtoms/matscipy | tests/test_hessian_finite_differences.py | Python | lgpl-2.1 | 4,264 | [
"ASE",
"Matscipy"
] | 0acf0b28a02dbe613170bb60e6e39cf860f94ec837cf20ffe3e0df45b85816c6 |
import os
import os.path as op
import time
from copy import copy
import numpy as nm
from sfepy.base.base import dict_from_keys_init, select_by_names
from sfepy.base.base import output, get_default, Struct, IndexedStruct
import sfepy.base.ioutils as io
from sfepy.base.conf import ProblemConf, get_standard_keywords
fro... | RexFuzzle/sfepy | sfepy/discrete/problem.py | Python | bsd-3-clause | 50,787 | [
"VTK"
] | 40bbac844fed9a926810c5ea98a049cf0114fe258a3509137a1ac691e36b434d |
'''
@file : testFile10.py
@author (A) : Madhu Kumar Dadi.
@project : Social List
@function :
test10(postags) : checks for the presence of Pronouns in the hashtag
@postags : list containing pos tags for a hashtag
return : count of Pronouns
@Licence :
This work is licensed under the
Creative Commons Attribu... | SummerProject16/project | CMUTweetTagger/testFile10.py | Python | cc0-1.0 | 623 | [
"VisIt"
] | 49c3c69e807ca53144a899a0b5dc44ca8bce90b9416615e332f2c1877f5ed3a9 |
#!/usr/bin/python
# Filename: filter_fastq.py
# Version: 2015-05-14
# Description: Program to remove invalid data records from fastq files.
# References: http://en.wikipedia.org/wiki/FASTQ_format
# http://www.bioperl.org/wiki/Fastq
# http://maq.sourceforge.net/fastq.shtml
# Author: ... | brianhigh/filter-fastq | filter_fastq.py | Python | gpl-3.0 | 3,846 | [
"BioPerl",
"Brian"
] | 0b5584da0378f9f16293e3b93604215aaeb938e78867558af4fdb8a9cf6feb11 |
import numpy as np
from mdt import CompartmentTemplate, CompositeModelTemplate, FreeParameterTemplate, ProtocolParameterTemplate, \
LibraryFunctionTemplate
from mdt.model_building.parameter_functions.transformations import ScaleTransform
from mdt.utils import voxelwise_vector_matrix_vector_product, create_covarianc... | cbclab/MDT | mdt/data/components/standard/composite_models/qmt.py | Python | lgpl-3.0 | 15,518 | [
"Gaussian"
] | a135b46d317993e82996330ec906cba4b4ecbacfa0b03422a436344e6e64d596 |
# Copyright (C) 2011-2012 CRS4.
#
# This file is part of Seal.
#
# Seal 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.
#
# Seal is dis... | QwertyManiac/seal-cdh4 | seal/lib/aligner/bwa/bwa_core.py | Python | gpl-3.0 | 20,060 | [
"BWA"
] | 7f380c55f54bd8cb09b9ee5ef69729c55bd40174d996f86fdd2af18bf9c132e8 |
""" Test for WMS clients
"""
# pylint: disable=protected-access, missing-docstring, invalid-name, line-too-long
from __future__ import print_function
import os
import unittest
import importlib
import StringIO
from mock import MagicMock
from DIRAC.DataManagementSystem.Client.test.mock_DM import dm_mock
from DIRAC imp... | fstagni/DIRAC | WorkloadManagementSystem/Client/test/Test_Client_WorkloadManagementSystem.py | Python | gpl-3.0 | 6,691 | [
"DIRAC"
] | ca7ed9c719a8537aee657367fc6d4853f945bd488166a4d428f86b9be84880f3 |
import time
import logging as alog # axis log
alog.basicConfig()
from math import cos, radians
from numpy import arange
from emotion import Controller
from emotion import settings
from emotion import log as elog
from emotion.log import bcolors
from emotion.controller import add_axis_method
from emotion.axis import Ax... | esrf-emotion/emotion | emotion/controllers/PiezoJack.py | Python | gpl-2.0 | 20,192 | [
"CRYSTAL"
] | 897235e6945b6d505cb7a525ea49bfa4814e6e2391f0a505dda8d548543e4974 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/ao2mo/test/bz_nr.py | Python | apache-2.0 | 2,517 | [
"PySCF"
] | 52b3b2ccc061b9d68cfccbc79d6fec40a67f90c0316e052d370782d1a9808c53 |
import os
from bcbio.rnaseq import (featureCounts, cufflinks, oncofuse, count, dexseq,
express, variation, gtf, stringtie)
from bcbio.ngsalign import bwa, bowtie2, alignprep
import bcbio.pipeline.datadict as dd
from bcbio.utils import filter_missing
from bcbio.log import logger
def rnaseq_var... | hjanime/bcbio-nextgen | bcbio/pipeline/rnaseq.py | Python | mit | 9,841 | [
"BWA"
] | bfdf2382d657adc094ae2175739fe5b5d32e61aa478af0259e1177f782e605d4 |
# Authors: Jan Cholasta <jcholast@redhat.com>
#
# Copyright (C) 2014 Red Hat
# see file 'COPYING' for use and warranty information
#
# 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 versi... | pspacek/freeipa | ipaserver/install/ipa_cacert_manage.py | Python | gpl-3.0 | 13,511 | [
"VisIt"
] | c906a66cf90019ad9589dcdb3ec9a77cb8c09ab0868ef159d58f1d02ae4f4967 |
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