text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific.
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove ... | gratefulfrog/lib | python/chempy/cpv.py | Python | gpl-2.0 | 13,830 | [
"PyMOL"
] | d02b178a9732d4e3cde7b1e5c8066f1d58e0292f0c802c28fd1e563b571110d0 |
#!/usr/bin/env python
# -*- coding: ISO-8859-1 -*-
#
# Kovan's OGBot
# Copyright (c) 2007 by kovan
#
# *************************************************************************
# * *
# * This program is free software; you ca... | tectronics/ogrobot | src/WebAdapter.py | Python | gpl-2.0 | 36,957 | [
"CRYSTAL",
"Galaxy",
"NAMD"
] | 66d2e311d42a1c2cb22e1a000073b14b910142a8e083cd4afec52e9b7ee6eaae |
#!/usr/bin/env python
import numpy
import netCDF4
import argparse
import math
def parseCommandLine():
"""
Parse the command line and invoke operations.
"""
parser = argparse.ArgumentParser(description=
'''
Concatenates monthly data files into a single netcdf file.
''',
epilog='Written ... | adcroft/convert_WOA05 | python/concatenate_data.py | Python | mit | 3,180 | [
"NetCDF"
] | e6052b822f5eb35422cd661a12cb497a4cddb32e10b7132492bbda36643c631d |
"""
@name: Modules/House/Security/motion_sensor.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2019-2019 by D. Brian Kimmel
@license: MIT License
@note: Created on aug 26, 2019
@Summary:
"""
__updated__ = '2019-12-29'
__version_info__ = (19, 8, 1)
__version__ = '.'.join... | DBrianKimmel/PyHouse | Project/src/Modules/House/Security/Motiondetectors/motiondetectors.py | Python | mit | 4,434 | [
"Brian"
] | aed97e72c2ac86a38cb4c78ffcbe9ae27ead7dd1f552aafe1bcefcf9541ea032 |
"""Test buffer protocol for VTK arrays
Python 2.6 introduced a new buffer protocol that can expose raw
memory as a multi-dimensional array. This is used, for example,
by numpy in order to automatically generate arrays from memory
exposed by other python extension modules.
Created on Aug 1, 2015 by David Gobbi... | hlzz/dotfiles | graphics/VTK-7.0.0/Common/Core/Testing/Python/TestBuffer.py | Python | bsd-3-clause | 5,200 | [
"VTK"
] | 2c258a8e7d67d186c3d55747e7a001df6d46c32da05718cf1816ae5d63dcea24 |
# (C) British Crown Copyright 2010 - 2013, 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... | kwilliams-mo/iris | lib/iris/tests/test_pickling.py | Python | gpl-3.0 | 4,374 | [
"NetCDF"
] | 389d6d3588162359177ef332185ac614be1e81ab7528e3b48c9a4a50abb5730f |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module defines classes for point defects.
"""
__author__ = "Bharat Medasani, Nils E. R. Zimmermann"
__copyright__ = "Copyright 2011, The Materials Pr... | xhqu1981/pymatgen | pymatgen/analysis/defects/point_defects.py | Python | mit | 72,613 | [
"GULP",
"pymatgen"
] | d9ed6d4183082fa715d4a8e956f02cabd9244816900c3ba098ec3b9dd8dde496 |
import numpy as np
from scipy.optimize import curve_fit, minimize
from scipy.special import erf
from copy import copy
def CDF_distance(cdf1, cdf2):
"""
Very simple function to return distance between two CDFs.
"""
return np.max( np.abs(cdf2 - cdf1))
def compute_cdf(x, y):
"""
Given x and y d... | aemerick/galaxy_analysis | utilities/functions.py | Python | mit | 11,888 | [
"Gaussian"
] | 3a7ce3399e60c5a7616136375aad131479af1c20b9697d70f983463276ce6e17 |
#!/usr/bin/env python
"""
Artificial Intelligence for Humans
Volume 2: Nature-Inspired Algorithms
Python Version
http://www.aifh.org
http://www.jeffheaton.com
Code repository:
https://github.com/jeffheaton/aifh
Copyright 2014 by Jeff Heaton
Licensed under the Apache License, Versi... | trenton3983/Artificial_Intelligence_for_Humans | vol2/vol2-python-examples/examples/example_conway.py | Python | apache-2.0 | 4,382 | [
"VisIt"
] | d78de31c0e252482a0273806037dfc9d538248c097c7638469ed2f5869c27cfe |
####################################################################
# Rdesigneur example 3.2
# Making a myelinated axon with a propagating action potential.
####################################################################
import numpy as np
import moose
import pylab
import rdesigneur as rd
numAxonSegments = 405
n... | BhallaLab/moose-examples | tutorials/Rdesigneur/ex3.4_myelinated_axon.py | Python | gpl-2.0 | 1,957 | [
"MOOSE",
"NEURON"
] | c9b395a6b97e7d859e1a46445c4b21c720b33d3ed35ab08dfd573a9f920a43f4 |
import cv2
import numpy as np
import math
#import requests
#import json
import time
class Neuron(object):
def __init__(self, weights):
splitted = weights.replace('\n', '').split(' ')
self.weights = [float(x) for x in splitted]
def forward(self, x):
if len(self.weights) != len(x):
... | kazepilot/backbone | network.py | Python | mit | 1,683 | [
"NEURON"
] | 1acf4e759bf89fad14ff0e338e057ed78a6497a26081234da1512f8a53c074ef |
#!/usr/bin/python3-utf8
# -*- coding: utf-8 -*-
import configparser
import datetime
import json
import os
import re
import sqlite3
import sys
import time
import urllib.parse
from classes.template_engine import TemplateEngine
from classes.galaxy_db import GalaxyDB
from classes.xnova_utils import PageDownloader, XNGala... | minlexx/xnova_galaxy_parser | site_uni5/index.py | Python | gpl-3.0 | 15,457 | [
"Galaxy"
] | 26fbcbf49e1403183ab1723e7ed30d5bc87058435f8585929716be60b064d5c5 |
# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# 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.
"""Map the residues of two structures to each other based on a FASTA alignment
file.
"""
... | zjuchenyuan/BioWeb | Lib/Bio/PDB/StructureAlignment.py | Python | mit | 4,024 | [
"Biopython"
] | eb17bdb7cd12f8deceb362ce90ce10e4c15ef4bce66c3b9bb0835ce33a4c216a |
import os
import time
from collections import OrderedDict
from io import BytesIO
from translate.storage import po, poheader, poxliff
def test_parseheaderstring():
"""test for the header parsing function"""
source = r"""item1: one
item2: two:two
this item must get ignored because there is no colon sign in it
... | miurahr/translate | translate/storage/test_poheader.py | Python | gpl-2.0 | 11,321 | [
"MOE"
] | e73e95024590a167243c2c181369b582bdc4193fa582185b4fa53bb6664fdcfa |
# -*- coding: utf-8 -*-
import os
import copy
import logging
import shutil
import time
import mathutils
import bpy
import bmesh
from collections import OrderedDict
from mmd_tools.core import pmx
from mmd_tools.core.bone import FnBone
from mmd_tools.core.material import FnMaterial
from mmd_tools.core.morph import FnMo... | powroupi/blender_mmd_tools | mmd_tools/core/pmx/exporter.py | Python | gpl-3.0 | 56,830 | [
"VMD"
] | bbeac54b35be75e1a4ac01c78205e4d5ed882cfdf08d8b57e226e3144e583f8f |
########################################################################
# File : AgentModule.py
# Author : Adria Casajus
########################################################################
"""
Base class for all agent modules
"""
import os
import threading
import time
import signal
import DIRAC
from DIRAC... | arrabito/DIRAC | Core/Base/AgentModule.py | Python | gpl-3.0 | 18,318 | [
"DIRAC"
] | 379a945f65e5a28bb3a88f9f3fa2fdbf6f09f193873d4a06c16ebe965f547971 |
from pathlib import Path
import shutil
import tempfile
import pytest
from pysisyphus.benchmarks import Benchmark
from pysisyphus.helpers import align_geoms
from pysisyphus.run import run_from_dict
from pysisyphus.testing import using
from pysisyphus.xyzloader import write_geoms_to_trj
Bh = Benchmark(
"birkholz_... | eljost/pysisyphus | tests/test_birkholz_rx/test_birkholz_rx.py | Python | gpl-3.0 | 4,385 | [
"xTB"
] | 333dc76cb2e8f53bebd60e955878849b7f328d8bf70e66b2b9b0373ea403ac6e |
import glob
import pandas as pd
import numpy as np
pd.set_option('display.max_columns', 50) # print all rows
import os
os.chdir("/gpfs/commons/home/biederstedte-934/evan_projects/correct_phylo_files")
normalB = glob.glob("binary_position_RRBS_normal_B_cell*")
mcell = glob.glob("binary_position_RRBS_NormalBCD19pCD27... | evanbiederstedt/RRBSfun | trees/chrom_scripts/normal_chr07.py | Python | mit | 25,843 | [
"MCell"
] | b50595ea7b7920869f80378675c8fa6a2c711b35ea761c2949b1707d0810e8d1 |
# Copyright (c) 2009-2021 The Regents of the University of Michigan
# This file is part of the HOOMD-blue project, released under the BSD 3-Clause
# License.
"""Implement Box."""
import numpy as np
from functools import partial
import hoomd._hoomd as _hoomd
def _make_vec3(vec, vec_factory, scalar_type):
"""Conv... | joaander/hoomd-blue | hoomd/box.py | Python | bsd-3-clause | 14,679 | [
"HOOMD-blue"
] | e952d2fe527253887d594a4a5b8cd6630d05ef2dd108ac71750f2ec35db873b6 |
import argparse
from math import pi as PI, ceil
from pathlib import Path
import sys
from pysisyphus.constants import AMU2KG
from pysisyphus.helpers import geom_loader
from pysisyphus.helpers_pure import get_input, highlight_text
from pysisyphus.io.pdb import geom_to_pdb_str
from pysisyphus.wrapper.packmol import make_... | eljost/pysisyphus | pysisyphus/pack.py | Python | gpl-3.0 | 4,954 | [
"Dalton"
] | dda653fd5eb07e20a8c91db6f448e100cae879869359e6f142851a58cf2fa6d8 |
# -*- coding: utf-8 -*-
from __future__ import (division, absolute_import, unicode_literals,
print_function)
import json
import logging
import os
import re
import subprocess
import warnings
import dlib
import numpy
import pathlib2
import six
import skimage
import skimage.color
import skimage.... | AbdealiJK/file-metadata | file_metadata/image/image_file.py | Python | mit | 36,216 | [
"Gaussian"
] | 4a7b567ed0cbfdb6a7fa458d6fc91f326b549c09f43534cfc15b5094135d2c7b |
# -*- coding: utf-8 -*-
"""Implementation of execution-related magic functions."""
# Copyright (c) IPython Development Team.
# Distributed under the terms of the Modified BSD License.
from __future__ import print_function
from __future__ import absolute_import
import ast
import bdb
import gc
import itertools
import ... | pacoqueen/ginn | extra/install/ipython2/ipython-5.10.0/IPython/core/magics/execution.py | Python | gpl-2.0 | 53,186 | [
"VisIt"
] | ac0eeabd7085e0f866279e47b1cb0bc8dc042e63a9a9e95b2a42f79860d82dff |
#-------------------------------------------------------------------------------
# Name: Point_Circle_Generator
#
# Author: Mark Tingey
#
# Created: 23/01/2019
#-------------------------------------------------------------------------------
##import Statements
import random as rnd
import numpy ... | andrewruba/YangLab | JPC simulations 2019/Figure 9 - fold symmetry and rotation/point_circle_generator.py | Python | gpl-3.0 | 3,749 | [
"Gaussian"
] | eb27f32887bec0900b0d5b5510b8a026ef2ad3e16335491c12740c51c0825894 |
import os
import glob
import warnings
import logging
import re
import atexit
logger = logging.getLogger(__name__)
@atexit.register
def cleanup():
for f in glob.glob('/sys/class/tacho-motor/motor*/command'):
with open(f, 'w') as f:
f.write('stop')
for f in glob.glob('/sys/class/leds/*/trig... | evz/python-ev3 | ev3/ev3dev.py | Python | apache-2.0 | 20,034 | [
"Amber"
] | c412a6fa2f17fb5b66268644b7c44835d01d7159f0121e985fe02b9f1cf412dc |
# -*- coding: utf-8 -*-
"""
Created on Wed Jun 17 17:03:46 2015
new script for doing HDCM C1Roll and C2X calibration automatically
it requires the HDCM Bragg is calibrated and the d111 and dBragg in SRXenergy script are up-to-date
converting to be compatible with bluesky, still editing
@author: xf05id1
"""
import SRX... | NSLS-II-SRX/ipython_ophyd | profile_xf05id1/startup/98-hdcmc1rollc2xcalib.py | Python | bsd-2-clause | 9,969 | [
"CRYSTAL"
] | 11c6a13c248c781a9cb437436c614ac73cdf94ab7543b655e86ec35502d065b2 |
# Principal Component Analysis Code :
from numpy import mean,cov,double,cumsum,dot,linalg,array,rank,size,flipud
from pylab import *
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import ro... | tapomayukh/projects_in_python | classification/Classification_with_kNN/Single_Contact_Classification/Time_Window/test10_cross_validate_categories_400ms.py | Python | mit | 4,371 | [
"Mayavi"
] | 90334323e8bbcc2e651c6a0654755058a4fb87743d4b110dcbfd2f6a14316903 |
# -*- coding: utf-8 -*-
import re
import urllib
from core import httptools
from core import jsontools
from core import scrapertools
from core import tmdb
from core.item import Item
from megaserver import Client
from platformcode import config, logger, platformtools
__modo_grafico__ = config.get_setting(... | alfa-jor/addon | plugin.video.alfa/channels/puyasubs.py | Python | gpl-3.0 | 19,794 | [
"MOE"
] | beeb0baf0441b1e739d5bcf4c724fd87d928a922030892ab27db6d38194f3994 |
## this script is a post process for lammps nanoindent *****
# the motivation for making this script is to find the maximum per atom force and per atom pe of run from dumpfiles
# nano indent output gives the total force felt by a indenter, so bigger the indenter the more force (sum of all atoms below the indenter) will... | msadat/python-scripts | dump2force-vs-displacement.py | Python | gpl-3.0 | 2,532 | [
"LAMMPS"
] | f8325a88ed3e3633894764632fe3d033731b89a312e34a9dea698d5888ac0971 |
from ... import numpy as np
from .. import logging
import scipy.stats
from collections import OrderedDict
import warnings
logger = logging.getLogger('rsdfit.emcee_results')
logger.addHandler(logging.NullHandler())
class EmceeParameter(object):
"""
Class to hold the parameter fitting result
"""
def __i... | nickhand/pyRSD | pyRSD/rsdfit/results/emcee_results.py | Python | gpl-3.0 | 33,251 | [
"Gaussian"
] | 0bece4091d9b76f03962314c8b48367dbd5e14f947aaefae60e1426ab677e5ef |
from __future__ import unicode_literals
from .common import InfoExtractor
class NhkVodIE(InfoExtractor):
_VALID_URL = r'https?://www3\.nhk\.or\.jp/nhkworld/en/vod/(?P<id>.+?)\.html'
_TEST = {
# Videos available only for a limited period of time. Visit
# http://www3.nhk.or.jp/nhkworld/en/vod/ ... | jcoady9/youtube-dl | youtube_dl/extractor/nhk.py | Python | unlicense | 1,968 | [
"VisIt"
] | d53a20720374dd45f864ce1d4b5937f8f196d8f2b7a4ebf3469160fe43c249b0 |
import pandas as pd
import pickle
data_dir = "data/"
gene_id = "uc021pzf.2"
gene_file_suffix = ".gtf"
gene_file = "refGene-chr10-{}-exons".format(gene_id)
cigar_pickle_file = "transcript-{}-cigarIntervals.pickle".format(gene_id)
cyto_file = gene_file + ".cyto"
# load read intervals from serialized file
with open(data... | gorgitko/bioinformatics-chemoinformatics | bioinformatics/exon-joining/03_exons.py | Python | mit | 1,861 | [
"Cytoscape"
] | 2de33796ba9bae6773b922f7f9a6894c652e7398a8b8156e377036a4e35c2e19 |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2008, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | zenoss/Community-Zenpacks | ZenPacks.Imas.SmsFunctions/setup.py | Python | gpl-2.0 | 3,276 | [
"VisIt"
] | 7973017ffd1404895824d168afc98e88516e80c64c0c9d2e41d0d800d8c9d9ab |
# Copyright (c) 2011-2018, wradlib developers.
# Distributed under the MIT License. See LICENSE.txt for more info.
import unittest
import wradlib as wrl
from wradlib.io import dem
from wradlib.io import radolan
from wradlib.io import rainbow
from wradlib.io import CfRadial, OdimH5, create_xarray_dataarray
from wradlib... | kmuehlbauer/wradlib | wradlib/tests/test_io.py | Python | mit | 56,474 | [
"NetCDF"
] | 1cae5bec2eb9513ffdd9bb0fa636b312e0a124d5b30b74df31e2833bae0906c8 |
# 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
#
# Unless required by appl... | gkc1000/pyscf | pyscf/pbc/df/test/test_df_ao2mo.py | Python | apache-2.0 | 7,511 | [
"PySCF"
] | d404519637dfabd178fe50a4e549f59d24e8b5ce8379b199f119c491ff28c6ce |
from distutils.core import setup
setup(name = 'IGCexpansion',
version = '0.3-dev',
author = 'Xiang Ji',
url = 'https://github.com/xji3/IGCexpansion',
#download_url = 'https://github.com/xji3/Genconv/tree/master/IGCexpansion/',
packages = ['IGCexpansion',],
install_requires=[
... | xji3/IGCexpansion | setup.py | Python | gpl-3.0 | 645 | [
"Biopython"
] | 5caebfa87d8e2975c2b10292c3cd8379fe4cf585986e33cdbea541386cd8f639 |
"""
Module of kernels that are able to handle continuous as well as categorical
variables (both ordered and unordered).
This is a slight deviation from the current approach in
statsmodels.nonparametric.kernels where each kernel is a class object.
Having kernel functions rather than classes makes extension to a multiv... | detrout/debian-statsmodels | statsmodels/nonparametric/kernels.py | Python | bsd-3-clause | 6,365 | [
"Gaussian"
] | 8309b11f7b76720660e01d0358751828b36953ef9613b5b371543d990e44ca8b |
#!/usr/bin/env python
'''buildScriptsDocs
Build scripts documentation from the scripts docstrings. The scripts are not
very uniform
'''
import glob
import os
import sys
import subprocess
from DIRAC import rootPath
# Scripts that either do not have -h, are obsolete or cause havoc when called
BAD_SCRIPTS = ['dir... | andresailer/DIRAC | docs/Tools/buildScriptsDocs.py | Python | gpl-3.0 | 5,675 | [
"DIRAC"
] | 0b9f5b5c12e92c5c8d720a2dd77c1e150eb7560345de1536bd21d59614219ddb |
from __future__ import division, print_function
import numpy as np
from bct.utils import cuberoot, binarize, invert
def breadthdist(CIJ):
'''
The binary reachability matrix describes reachability between all pairs
of nodes. An entry (u,v)=1 means that there exists a path from node u
to node v; alterna... | clbarnes/bctpy | bct/algorithms/distance.py | Python | gpl-3.0 | 35,085 | [
"VisIt"
] | 01b7cd971e580f012e51a3b19c79765797316108d5930a7eaa51c9d7b15326ed |
# coding=utf-8
# Copyright 2022 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... | google-research/google-research | poem/core/common.py | Python | apache-2.0 | 8,170 | [
"Gaussian"
] | f9a76acb1a959496aff1530e50c9593ab06a60b21a9d6e2e8c8c70311b98c448 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
def GetRGBColor(colorName):
'''
Return the red, green and blue components for a
color as doubles.
'''
rgb = [0.0, 0.0, 0.0] # black
vtk.vtkNamedColors... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Filters/Core/Testing/Python/reverseNormals.py | Python | gpl-3.0 | 2,227 | [
"VTK"
] | 0d4a9710817e6ce66359cad2482d6fd67d41f84c81e8b36572da2bd6a7110040 |
from keys import *
from simulation_params import *
import nest
import numpy.random as random
# Neuron parameters
hh_neuronparams = {'E_L': -70., # Resting membrane potential in mV
'V_T': -63., # Voltage offset that controls dynamics.
# -63mV ... | research-team/NEUCOGAR | NEST/cube/integration/excitement/synapses.py | Python | gpl-2.0 | 3,707 | [
"NEURON"
] | 21ad5a851e5f4004d56c610b8f4b9e1399d4b16276d3416e93f17b9228ced611 |
#!/bin/env python
#
# Copyright 2013-2014 Graham McVicker and Bryce van de Geijn
#
# 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 ... | gmcvicker/CHT | import_bam_ref_nonref_counts.py | Python | apache-2.0 | 23,722 | [
"pysam"
] | 6cecac51ef4c848ac2c1784a8b70a357af9d0f9ce18a362dcea48e9d54aa3353 |
import math
import unittest
import numpy
import chainer
from chainer import backend
from chainer.backends import cuda
from chainer import functions
from chainer import gradient_check
from chainer import testing
from chainer.testing import attr
from chainer.testing import condition
class CTCTestBase(object):
de... | okuta/chainer | tests/chainer_tests/functions_tests/loss_tests/test_ctc.py | Python | mit | 9,219 | [
"xTB"
] | c437c61952e952a0768b371660d92ecd05414f529aa9483b9a488ac73c25cec0 |
#!/usr/bin/python3
# direct translation of extract_wb in python using as little external deps as possible
from __future__ import print_function
import sys
import os
import xml.etree.ElementTree as ET
import subprocess
import shlex
def eprint(*args, **kwargs):
print(*args, file=sys.stderr, **kwargs)
if len(sys.ar... | LebedevRI/darktable | tools/extract_wb.py | Python | gpl-3.0 | 16,320 | [
"Amber"
] | 9b32a0618c5a2e7fa9f5f16e2f7481a37df8b87872e0b6d28e613d9e108d7646 |
#!/usr/bin/python
########################################################################
# 1 August 2014
# Patrick Lombard, Centre for Stem Stem Research
# Core Bioinformatics Group
# University of Cambridge
# All right reserved.
########################################################################
import os, sy... | pdl30/pychiptools | pychiptools/utilities/count_method.py | Python | gpl-2.0 | 3,571 | [
"HTSeq"
] | cdaaf6af10c8d9fcc45c0833db7a5bc09262d995c50d7ac2cc200ff9cd6883da |
#! /usr/bin/python
# -*- coding: utf-8 -*-
#
# Vladimír Slávik 2008 - 2011
# Python 2.6, 3.1
#
# for Simutrans
# http://www.simutrans.com
#
# code is public domain
#
# read all dat files in all subfolders and rehash them together with images
# into translator-acceptable amount of data
from __future__ import pr... | simutrans/pak128 | tools/extract-objects-translator-reduced.py | Python | artistic-2.0 | 5,276 | [
"VisIt"
] | 2ee38a9873b507c00d3c3d3708da3da8075f02524822ed7651108afe887a47c6 |
# Copyright 2021 DeepMind Technologies Limited.
#
#
# 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agre... | deepmind/deepmind-research | galaxy_mergers/helpers.py | Python | apache-2.0 | 8,748 | [
"Galaxy",
"Gaussian"
] | 911e1b2e8b92f1812cbcb66447ee36fb24b7abaf9dfd0f0d6580fa1cce0eb85a |
# -*- coding: utf-8 -*-
# Copyright 2007-2021 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... | ericpre/hyperspy | hyperspy/_signals/signal2d.py | Python | gpl-3.0 | 36,718 | [
"Gaussian"
] | 7a1b1a99131b43fb3e2b98755cc3d9159f5851ebc686bc60f3a7ae7496ac405c |
"""
Augmenters that perform simple arithmetic changes.
List of augmenters:
* :class:`Add`
* :class:`AddElementwise`
* :class:`AdditiveGaussianNoise`
* :class:`AdditiveLaplaceNoise`
* :class:`AdditivePoissonNoise`
* :class:`Multiply`
* :class:`MultiplyElementwise`
* :class:`Cutout`
... | aleju/ImageAugmenter | imgaug/augmenters/arithmetic.py | Python | mit | 205,414 | [
"Gaussian"
] | 0f4a49f6fa392f6e7ea89cf37a0f4393615959a00e24472f2f7854a8054aa7c2 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | espressomd/espresso | src/python/espressomd/lbboundaries.py | Python | gpl-3.0 | 3,773 | [
"ESPResSo"
] | 985b36e318b2198cbf7a622fb2a064f52f300bec4eced7c19c778966ddf57ede |
'''
@author: David W.H. Swenson
'''
from __future__ import division
from __future__ import absolute_import
from builtins import zip
from past.utils import old_div
from builtins import object
import os
from nose.tools import (assert_equal, assert_not_equal, assert_almost_equal)
from nose.plugins.skip import SkipTest
... | choderalab/openpathsampling | openpathsampling/tests/test_toy_dynamics.py | Python | lgpl-2.1 | 12,312 | [
"Gaussian"
] | a5c1cb5da2872799a16a8f4d7a57e55658be9b8d351b239b5dfb47a96d5c4e03 |
'''The fitting module define some classes to easily perform 1D curve
fitting. This module supports fitting (x, y) data with a general
mechanism. Any fitting function can be provided to the fit method
and a few general purpose fuctions are predefined:
* Gaussian
* Lorentzian
* Cosine
* Vo... | heprom/pymicro | pymicro/xray/fitting.py | Python | mit | 12,900 | [
"Gaussian"
] | d1396a337338b8690c48fc4bef48976dc5240a5e870af8b59ff4ad12a28105bd |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import os
from pymatgen.util.testing import PymatgenTest
from pymatgen.core.lattice import Lattice
from pymatgen.core.structure import Structure
from pymatgen.core.lattice import Lattice
from ... | fraricci/pymatgen | pymatgen/symmetry/tests/test_kpaths.py | Python | mit | 4,487 | [
"pymatgen"
] | f12f859b4b72d2187d17b6cf96e131556064d1a7a02736618aa92692d272976e |
# Principal Component Analysis Code :
from numpy import mean,cov,double,cumsum,dot,linalg,array,rank,size,flipud
from pylab import *
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import ro... | tapomayukh/projects_in_python | classification/Classification_with_kNN/Single_Contact_Classification/Feature_Comparison/multiple_features/results/test10_cross_validate_objects_1200ms_scaled_method_v_force_area.py | Python | mit | 4,597 | [
"Mayavi"
] | 7276b57c98914bfae6791ba6f15fbe1198c46eeb5e83397d099fbd6d63ad939b |
#
# Copyright (C) 2000 greg Landrum
#
""" handles doing cross validation with neural nets
This is, perhaps, a little misleading. For the purposes of this module,
cross validation == evaluating the accuracy of a net.
"""
from rdkit.ML.Neural import Network, Trainers
from rdkit.ML.Data import SplitData
import math
... | bp-kelley/rdkit | rdkit/ML/Neural/CrossValidate.py | Python | bsd-3-clause | 3,924 | [
"RDKit"
] | f05b9b707cea5508662675578b051954a751366df13a3c816c26519da7f69bb6 |
import unittest
import random
import string
import sys
from pyokc import pyokc
class TestSequenceFunctions(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.u1 = pyokc.User(USERNAME1, PASSWORD1)
cls.u2 = pyokc.User(USERNAME2, PASSWORD2)
def test_search_and_visit(self):
... | odkken/pyokc | unittests.py | Python | mit | 2,664 | [
"VisIt"
] | 26f7fb06f6acf8ad348b9c9e8892c25f08399a74ca1b1c0c5a30850f1741abfb |
"""
Views for the verification flow
"""
import datetime
import decimal
import json
import logging
import urllib
from pytz import UTC
from ipware.ip import get_ip
from django.conf import settings
from django.contrib.auth.decorators import login_required
from django.core.mail import send_mail
from django.core.urlresolv... | ahmadiga/min_edx | lms/djangoapps/verify_student/views.py | Python | agpl-3.0 | 58,792 | [
"VisIt"
] | f02ab1a7bbbf1f3d626d59e0e6768a2cdd6342439025db37a5071b5b056418ca |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS.
"""
from flaky import flaky
from textwrap import dedent
from unittest import skip
from nose.plugins.attrib import attr
from bok_choy.promise import EmptyPromise
from bok_choy.web_app_test import WebAppTest
from ..helpers import (
UniqueCourseTest,
Even... | DefyVentures/edx-platform | common/test/acceptance/tests/lms/test_lms.py | Python | agpl-3.0 | 40,301 | [
"VisIt"
] | 6ac46077a3d9d6314b73535011e49918fc1a9c0e4104990a06383c205e5fadcf |
"""This module provides the FourierNoiseDomainExpression class to represent
f-domain (Fourier domain) noise expressions.
Copyright 2014--2022 Michael Hayes, UCECE
"""
from __future__ import division
from .sym import symsimplify
from .functions import sqrt
from .sym import pi, omegasym, fsym
from .state import state
f... | mph-/lcapy | lcapy/noisefexpr.py | Python | lgpl-2.1 | 4,770 | [
"Gaussian"
] | 635e9fdeea487c10522c8373ed022bfe0697b494dcae5e1c8b7b71759a69f78b |
from __future__ import print_function
import itertools
from ctypes import WINFUNCTYPE, POINTER, Structure, c_int, c_void_p, windll, pointer
from ctypes.wintypes import BOOL, HWND, RECT, LPARAM, HDC, HANDLE, DWORD, WCHAR
# Constants
PHYSICAL_MONITOR_DESCRIPTION_SIZE = 128
TRUE = 1
# Enums
MC_COLOR_TEMPERATURE_UNKNO... | cmihai/winmoncon | winmoncon/monitor.py | Python | unlicense | 9,426 | [
"CRYSTAL"
] | ff9e60b896fe8f3b5ac7a332bcd43e80d61ae2e8e4b1af7114a803e026ba4b69 |
# Orca
#
# Copyright 2010 Joanmarie Diggs.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This library i... | pvagner/orca | src/orca/scripts/apps/Instantbird/chat.py | Python | lgpl-2.1 | 7,140 | [
"ORCA"
] | 95c1049dd740988cad0875be165990ed4b57a5c1e0f622c40575b86b37027b0a |
import numpy as np
import array
import os, sys
import re
import time
import multiprocessing
import h5py
import logging
from astropy.table import Table, Column
from astropy import units as u
import argparse
parser = argparse.ArgumentParser()
parser.add_argument("-p","--params", type=str,
help = "Pa... | dunkenj/smpy | scripts/data/fitting.py | Python | mit | 27,412 | [
"Galaxy"
] | ee272494b27c37b581c56d670d69ac4c3d62ffcfe2bef74499adf8b1e3ee90e2 |
# Welcome script to be run asynchronously.
# This script is executed when the GaiaSandbox is first started.
# Created by Toni Sagrista
from gaia.cu9.ari.gaiaorbit.script import EventScriptingInterface
gs = EventScriptingInterface.instance()
# Disable input
gs.disableInput()
gs.cameraStop()
gs.minimizeInterfaceWindow... | vga101/gaiasky | assets/scripts/welcome.py | Python | mpl-2.0 | 888 | [
"Galaxy"
] | 0f590354422e42628db8f2ffa331126b73ed442a9b8b7330ac3a7e42cdd28b27 |
import numpy as np
from mobility import mobility as mob
try:
from pyevtk.hl import gridToVTK
except ImportError:
pass
# Try to import the visit_writer (boost implementation)
try:
# import visit.visit_writer as visit_writer
from visit import visit_writer as visit_writer
except ImportError as e:
print(e)
pa... | stochasticHydroTools/RotationalDiffusion | plot/plot_velocity_field.py | Python | gpl-3.0 | 11,514 | [
"VTK",
"VisIt"
] | 14e4b6745cb958f462fc4ecb8fee0dc68b51b3a831ef7993ce5fae47591fe604 |
from .base import BaseChildResultsVisitor
from copy import copy
from nineml.exceptions import NineMLNotBoundException, NineMLUsageError
class Cloner(BaseChildResultsVisitor):
"""
A Cloner visitor that visits any NineML object (except Documents) and
creates a copy of the object
"""
def __init__(se... | INCF/lib9ML | nineml/visitors/cloner.py | Python | bsd-3-clause | 4,926 | [
"VisIt"
] | 6ada0cd743802b296e3c7d3f591283a839117abb261e27c52099803550759844 |
# -*- coding: utf-8 -*-
#
# Copyright (c), 2016-2019, SISSA (International School for Advanced Studies).
# All rights reserved.
# This file is distributed under the terms of the MIT License.
# See the file 'LICENSE' in the root directory of the present
# distribution, or http://opensource.org/licenses/MIT.
#
# @author ... | brunato/xmlschema | xmlschema/validators/models.py | Python | mit | 18,670 | [
"VisIt"
] | ff426da33f5cf45cfec8b6d7c4fdbc483b58e8f0c86bc93714137fe7fb11af59 |
# Copyright (C) 2012-2013 Wesley Baugh
#
# This work is licensed under the Creative Commons
# Attribution-NonCommercial-ShareAlike 3.0 Unported License.
# To view a copy of this license, visit:
# http://creativecommons.org/licenses/by-nc-sa/3.0/
#
# This file was created using the streaming example from Tweepy
# as a g... | souravsarangi/SeedURLWork | TwitterURLs/twitter_corpus.py | Python | mit | 10,180 | [
"VisIt"
] | 63001ecb36f9c354d18c4357db65280bbcf9b80e580bf214f3fce489d5df9dee |
# Orca
#
# Copyright (C) 2010-2011 The Orca Team
# Copyright (C) 2011-2012 Igalia, S.L.
#
# Author: Joanmarie Diggs <jdiggs@igalia.com>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; e... | pvagner/orca | src/orca/scripts/toolkits/WebKitGtk/script.py | Python | lgpl-2.1 | 24,333 | [
"ORCA"
] | c63531abe1a0d4f20864c9f47b1de7e8d69c1a9eaf6c507aa8899eca4396b5dc |
"""
Grab IRAC bands 3,4 and MIPS mosaics from the web
"""
import os
from time import time
from urllib import urlopen
from multiprocessing import Pool
from functools import partial
def get_url(url, fname, target_dir='galaxy/raw/'):
""" Save a file from the internet
Parameters
----------
url : The url t... | ChrisBeaumont/brut | bubbly/data/scrape.py | Python | mit | 2,957 | [
"Galaxy"
] | bb1923caf45c9264bb5e12450d7ecf7af68da1ec81aee05cfea36c5f126f91d2 |
#!/usr/bin/env python3
import argparse
import atexit
import os
import os.path
import signal
from kalplib import knpm
from kalplib import kutils
from kalplib import kwatchdog
from jnscommons import jnsos
VERSION = '1.2.2'
THREAD_WAIT_TIMEOUT = 1.0 # in seconds
watchdogs = [] # pylint: disable=invalid-name
watchd... | eviljoe/junk-n-stuff | src/kalp.py | Python | mit | 5,951 | [
"GULP"
] | 7d6ae9750c6356a53a079799613498f1edbce2d0d1db2e8efa19006b64dd3ecb |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2002-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; ... | beernarrd/gramps | gramps/gen/filters/rules/person/_regexpname.py | Python | gpl-2.0 | 2,199 | [
"Brian"
] | ea5a065a9d1aadd5f2a1ab7285fa65b00fefccef865b61c9e4373382e441de24 |
""" Module that expose the base class for DIRAC Clients.
This class exposes possible RPC calls, given a url of a service.
"""
import ast
from functools import partial
try:
from functools import partialmethod
except ImportError:
class partialmethod(partial):
def __get__(self, instance, owner):
... | ic-hep/DIRAC | src/DIRAC/Core/Base/Client.py | Python | gpl-3.0 | 8,250 | [
"DIRAC"
] | aa63ab0574fd857badc35e2da0c57e4c7a838ee57086a08c6af79e6462e29816 |
from __future__ import print_function, division
import numpy as np
from numpy import zeros, dot
def omask2wgts_loops(mf, omask, over):
""" Finds weights """
ksn2w = zeros(mf.mo_energy.shape[:])
for k in range(mf.nkpoints):
for s in range(mf.nspin):
for n in range(mf.norbs):
ksn2w[k,s,n] = dot( ... | gkc1000/pyscf | pyscf/nao/m_dos_pdos_ldos.py | Python | apache-2.0 | 3,808 | [
"PySCF"
] | c2d4fbc65494037c654cad5c9f0f73d8caab8d1e18d228347d682bad51287c7c |
#--------------------------------------------------------------------------
# Software: InVesalius - Software de Reconstrucao 3D de Imagens Medicas
# Copyright: (C) 2001 Centro de Pesquisas Renato Archer
# Homepage: http://www.softwarepublico.gov.br
# Contact: invesalius@cti.gov.br
# License: GNU ... | tatiana/invesalius | invesalius/data/volume.py | Python | gpl-2.0 | 25,571 | [
"VTK"
] | 96e1b2ec444a592c3a1647fa93900587f632ca3bc5ff9bf1e399e007aaf04728 |
#!/usr/bin/env python
import os, sys, time, socket, getopt, getpass
import Pyro.core
import shutil
import time
import getopt
# from Bio.Blast import NCBIStandalone
from Bio.Blast import NCBIXML
from Bio.Blast.Applications import NcbiblastpCommandline
from StringIO import StringIO
#from Bio import Fasta
from types impo... | byuphamerator/phamerator-dev | phamerator/blastclient.py | Python | gpl-2.0 | 7,478 | [
"BLAST"
] | 474c7a4d10216421c5b938cf7bff3f54413145b0418f4b2cb9db1242fa9d1aa1 |
pdb_bmrb_map_text = """
SELECT UPPER(pdb_id) || ' ' || string_agg(bmrb_id, ',' ORDER BY bmrb_id) AS string
FROM (SELECT pdb_id, bmrb_id, 'exact' AS link_type, null AS comment
FROM web.pdb_link
UNION
SELECT UPPER("Database_accession_code"), "Entry_ID", 'author', "Relationship"
FROM macromolecules... | uwbmrb/BMRB-API | server/wsgi/bmrbapi/views/sql/db_links.py | Python | gpl-3.0 | 5,526 | [
"BLAST"
] | 23245aa4fa3351aa4d20db93c5b9554ce2d118ba19afbc7ccbc4eed263da7f5b |
"""Pipeline utilities to retrieve FASTQ formatted files for processing.
"""
import os
import shutil
from bcbio import bam, broad, utils
from bcbio.bam import fastq
from bcbio.distributed import objectstore
from bcbio.pipeline import alignment
from bcbio.pipeline import datadict as dd
from bcbio.utils import file_exist... | a113n/bcbio-nextgen | bcbio/pipeline/fastq.py | Python | mit | 5,886 | [
"Bowtie"
] | 1d25bcd607edd20d0466bfdf8589e771fe632d0fb0af7b1e1f749ad89bee20ff |
# 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)
import os
from spack import *
class Rnaquast(Package):
"""Quality assessment of de novo transcriptome assemblies fr... | LLNL/spack | var/spack/repos/builtin/packages/rnaquast/package.py | Python | lgpl-2.1 | 1,420 | [
"BLAST"
] | 1382a6e9feaf953131a809efb8b4df5c2e1c3438a06c46023fb72596b7427e64 |
'''
sbclearn (c) University of Manchester 2018
sbclearn is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
# pylint: disable=invalid-name
# pylint: disable=too-many-arguments
# pylint: disable=wrong-import-order
import itertools... | synbiochem/synbiochem-learn | gg_learn/nicole/nicole.py | Python | mit | 5,781 | [
"VisIt"
] | 0019891aaf8b0e3a3d3706ee272d388ad07f97c4229fe2c1c7c8ced798f28902 |
#!/usr/bin/env python3
"""
Unit tests for MetSim
"""
import os
import subprocess
import tempfile
from collections import OrderedDict
import numpy as np
import pandas as pd
import pytest
import xarray as xr
import metsim.cli.ms as cli
import metsim.metsim
from metsim.metsim import MetSim
from metsim import io
class... | arbennett/MetSim | metsim/tests/test_metsim.py | Python | gpl-3.0 | 15,361 | [
"NetCDF"
] | 67a3153b59868e2910547215fb111b1be05d389f3be6135d21d985a6d8f92d54 |
'''
Created on 03.09.2014
@author: Jan-Hendrik Prinz, David W.H. Swenson
'''
from . import range_logic
import abc
from openpathsampling.netcdfplus import StorableNamedObject
import numpy as np
import warnings
# TODO: Make Full and Empty be Singletons to avoid storing them several times!
def join_volumes(volume_list... | dwhswenson/openpathsampling | openpathsampling/volume.py | Python | mit | 21,931 | [
"OpenMM"
] | d8609a874f37ad776b343d551895b0a069917a79fa1a5bc143282e762bbe42f2 |
#* 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 os, ... | nuclear-wizard/moose | python/peacock/Input/OutputNames.py | Python | lgpl-2.1 | 4,849 | [
"MOOSE"
] | ae4ca919bfc48cb42709a4d8fad3e553510ff60d3c929d1cdeb500a2eeec2731 |
from ase import *
from gpaw import GPAW
from gpaw.utilities import equal
a = 4.8 # => N = 4.8 / 0.2 = 24
loa = Atoms([Atom('C', [a / 2 + .3, a / 2 -.1, a / 2], magmom=2)],
pbc=False,
cell=(a, a, a))
p = []
exx = []
i = 0
for hosts in [1, 4]:
calc = GPAW(convergence={'eigenstates... | qsnake/gpaw | oldtest/exx_parallel.py | Python | gpl-3.0 | 1,132 | [
"ASE",
"GPAW"
] | 0511777454c9e69271cb16f3ded6f5988c477edff5307984aac7a3c116bca382 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
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.views.generic import TemplateView
urlpatterns = [
url(r'^$', TemplateView.as_view(templ... | angryjoe/propertytrack | config/urls.py | Python | bsd-3-clause | 1,235 | [
"VisIt"
] | 83e98e19f44f1b2d52d13438da137c742c87c6d6959c704cb50826400ca13856 |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to make it easier to
# submit large numbers of jobs on supercomputers. It provides a python interface to physical input,
# ... | pylada/pylada-light | src/pylada/espresso/functional.py | Python | gpl-3.0 | 20,437 | [
"CRYSTAL",
"ESPResSo",
"VASP"
] | 90b2d93a8ff1414ad3bd291c14af229d302c2b2ce19e8b23bb1f7092a057a425 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from setuptools import setup
from setuptools.extension import Extension
from seqlib.version import __version__
from Cython.Build import cythonize
ext_modules = [Extension('seqlib.align', ['seqlib/align.pyx'])]
setup(name='seqlib',
version=__version__,
descrip... | kepbod/seqlib | setup.py | Python | mit | 1,265 | [
"pysam"
] | c7ddf4678af42dc3baed4fc8f5477a242f26754161ade6d8d4d631c03c3a5664 |
#===============================================================================
#
# CUDAGenerator.py
#
# This file is part of ANNarchy.
#
# Copyright (C) 2016-2021 Julien Vitay <julien.vitay@gmail.com>,
# Helge Uelo Dinkelbach <helge.dinkelbach@gmail.com>
#
# This program is free software: you can... | vitay/ANNarchy | ANNarchy/generator/Projection/CUDAGenerator.py | Python | gpl-2.0 | 64,614 | [
"NEURON"
] | 954060335c71010452cbfe239530cfe7b3238e2cb683931591ce4a939cd1dcdf |
# ******************************************************
#
# File generated by: neuroConstruct v1.5.1
#
# ******************************************************
import neuron
from neuron import hoc
import nrn
hoc.execute('load_file("TestHDF5.hoc")')
| rgerkin/neuroConstruct | testProjects/TestHDF5/simulations/TestSpikesHDF5Parallel/run_TestHDF5.py | Python | gpl-2.0 | 260 | [
"NEURON"
] | 3c7f5fc73019584564f9bb2d823f4f15ba9d61d4935e9ab9267fc0c406f7b7b6 |
# -*- coding: utf-8 -*-
#
# Copyright 2017 Toyota Research Institute
#
# 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... | dreal/dreal4 | setup.py | Python | apache-2.0 | 7,657 | [
"VisIt"
] | 67878c63763e99f5fbbc491967a45f3d667ee9fcaa9635bafd7f2b55d1e7a9d6 |
#!/usr/bin/python
from __future__ import print_function
import csv
import os
import sys
# Get directory to check as argument
if ( len(sys.argv) > 1 ):
rf_dir = sys.argv[1]
if ( not os.path.isdir(os.path.join("src", rf_dir)) ):
sys.stderr.write("Error: %s is not a directory\n" % rf_dir)
sys.exit(1)
else:
... | jmbeuken/abinit | developers/maintainers/process-orphans.py | Python | gpl-3.0 | 1,195 | [
"ABINIT"
] | 11fefa2ec784e9dcd39e3f23390fb7f32f97ef61c7714351dbeb6d78dc5394d4 |
"""
This is the boilerplate default configuration file.
Changes and additions to settings should be done in the config module
located in the application root rather than this config.
"""
config = {
# webapp2 sessions
'webapp2_extras.sessions': {'secret_key': '3jk4l1j3k4l13jkl34j3kl14'},
# webapp2 authenti... | markap/TravelMap | config/localhost.py | Python | lgpl-3.0 | 4,512 | [
"VisIt"
] | c78681ce99969195e68fd8b772cd0f5d75c2c093d54bb3ae5385de4e84fb4816 |
##############################################################################
# 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/r-dirichletmultinomial/package.py | Python | lgpl-2.1 | 2,070 | [
"Bioconductor"
] | 7e6fd93292d7000b355837a5dd75a5a36025975192bf3576652a1d4810cd1f09 |
# -*- coding: utf-8 -*-
"""
Created on Tue Mar 1 17:57:42 2016
"""
from __future__ import print_function, division
import math
import numpy as np
from datetime import datetime
from scipy.stats import norm
from numpy.linalg import cholesky, inv, slogdet
from warnings import warn
from .EPABC import create_Halton_sequen... | sbitzer/pyEPABC | pyEPABC/PWABC.py | Python | bsd-3-clause | 7,076 | [
"Gaussian"
] | 7c5f1da4fee8c921cf7f7492b4b8eed82703d75db08f9abbe8c5cf79d03b1b07 |
# $HeadURL: $
''' GGUSTicketsCommand
The GGUSTickets_Command class is a command class to know about
the number of active present opened tickets.
'''
import urllib2
from DIRAC import gLogger, S_ERROR, S_OK
from DIRAC.Core.LCG.GGUSTicketsClient ... | marcelovilaca/DIRAC | ResourceStatusSystem/Command/GGUSTicketsCommand.py | Python | gpl-3.0 | 5,609 | [
"DIRAC"
] | 477110ade4b8347d1db990ca60d89fc6652064d398a6055669d4af5284d758ea |
#!/usr/bin/env python3
# -*-coding:Utf-8 -*
"""Use MCMC to find the stellar mass halo mass relation.
Based on the Behroozi et al 2010 paper.
Use a parametrization of the SHMR, plus a given HMF to find the expected SMF and compare it
to the observed SMF with its uncertainties using a likelihod maximisation.
Started o... | Gorbagzog/StageIAP | MCMC_SHMR_old.py | Python | gpl-3.0 | 6,422 | [
"Gaussian"
] | 09e5a04bb6048f7ba7c385fdd06d0a77efc3f7d31b8e7152b9a8f9c64008d9e8 |
# Copyright 2012-2014 Brian May
#
# This file is part of python-tldap.
#
# python-tldap 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.... | brianmay/python-tldap-debian | tldap/ldap_passwd.py | Python | gpl-3.0 | 1,733 | [
"Brian"
] | c0acae8882b430033d08ee846fe5b13f4fb4542337ecd35fc30bc4c6a77c53e8 |
# Copyright notice
# ================
#
# Copyright (C) 2010
# Lorenzo Martignoni <martignlo@gmail.com>
# Roberto Paleari <roberto.paleari@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... | shotgunner/wusstrace | pywuss/visitor/htmlify.py | Python | gpl-3.0 | 3,918 | [
"VisIt"
] | e3690a9136de4e5a0b950e7b4ea05397443cd932777cc4fb25866ada3e53d107 |
"""
Spectroscopy class
This file contains the Spectroscopy class that forms the basis analysis of all
the spectroscopy measurement analyses.
"""
import logging
import numpy as np
import lmfit
import pycqed.analysis_v2.base_analysis as ba
import pycqed.analysis.fitting_models as fit_mods
import pandas as pd
import ma... | QudevETH/PycQED_py3 | pycqed/analysis_v2/spectroscopy_analysis.py | Python | mit | 81,833 | [
"Gaussian"
] | ad5214c357453dc63c6ec17afbc5513882a7a6c13d82e005a4099093149bbf8c |
#-*- coding: utf-8 -*-
import modules.mapcss_lib as mapcss
import regex as re # noqa
from plugins.Plugin import with_options # noqa
from plugins.PluginMapCSS import PluginMapCSS
class Josm_deprecated(PluginMapCSS):
MAPCSS_URL = 'https://josm.openstreetmap.de/browser/josm/trunk/resources/data/validator/deprecate... | tkasp/osmose-backend | plugins/Josm_deprecated.py | Python | gpl-3.0 | 787,125 | [
"CASINO"
] | 4c5c0592a5b90b5115d6881136864d78c407f6043d52bbf1fdefd75b4d5f5899 |
#!/usr/bin/env python
'''
Anh Nguyen <anh.ng8@gmail.com>
2016
'''
from __future__ import print_function
import os, sys
os.environ['GLOG_minloglevel'] = '2' # suprress Caffe verbose prints
import settings
sys.path.insert(0, settings.caffe_root)
import caffe
import numpy as np
from numpy.linalg import norm
import sc... | philkuz/ppgn | sampler.py | Python | mit | 12,786 | [
"Gaussian"
] | 92c91d125ed9722c3edb23d826ef09085db40f4bebcada1681aea3a81957b480 |
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