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"""
wf_DynamicFramework
-------------------
This is a replacement for the standard pcraster/python DynamicFramwork class.\
It provides extra functionality to simplify linking the models build in the framework
with other models. The provided functionality allows external programs to control
and interrogate the m... | openstreams/wflow | wflow/wf_DynamicFramework.py | Python | gpl-3.0 | 132,587 | [
"NetCDF"
] | 0fa0913e5b46a7b7a6e0a45ace56a93561e3412bc2858826d7e1c9bc0d6b027a |
"""Module implements liveness analysis."""
from cfg import AssignmentNode
from copy import deepcopy
from ast import NodeVisitor, Compare, Call
from analysis_base import AnalysisBase
class LivenessAnalysis(AnalysisBase):
"""Implement liveness analysis rules."""
def __init__(self, cfg):
"""Initialize u... | SW10IoT/pyt | pyt/liveness.py | Python | gpl-2.0 | 2,474 | [
"VisIt"
] | e8b4ba3aeba4f4f8020eab425433cd3efc99b7b65524484092e5106862e94272 |
# -*- coding: utf-8 -*-
# MolMod is a collection of molecular modelling tools for python.
# Copyright (C) 2007 - 2019 Toon Verstraelen <Toon.Verstraelen@UGent.be>, Center
# for Molecular Modeling (CMM), Ghent University, Ghent, Belgium; all rights
# reserved unless otherwise stated.
#
# This file is part of MolMod.
#
#... | molmod/molmod | molmod/io/psf.py | Python | gpl-3.0 | 16,026 | [
"CHARMM",
"CP2K"
] | a57b1729037e39a20e7b1eb583cb2fac50bc120b44db19076214e9efb42a2382 |
# encoding: utf-8
"""
Adf.ly shortener implementation
Needs api key and uid
"""
from ..exceptions import ShorteningErrorException
from .base import BaseShortener
class Adfly(BaseShortener):
api_url = 'http://api.adf.ly/api.php'
def __init__(self, **kwargs):
if not all([kwargs.get('key', False), kwarg... | RuiNascimento/krepo | script.areswizard/pyshorteners/shorteners/adfly.py | Python | gpl-2.0 | 1,065 | [
"ADF"
] | b69ce741b714bf96c9efdb3e858730ebc32e0f3b75d97ec509b20298a9af1d13 |
# Copyright 2013 University of Maryland. All rights reserved.
# Use of this source code is governed by a BSD-style
# license that can be found in the LICENSE.TXT file.
import sys
import time
from selenium.common.exceptions import NoAlertPresentException
import framework
# POC: http://www.exploit-db.com/exploits/... | UMD-SEAM/bugbox | framework/Exploits/DRUPAL_DP0001.py | Python | bsd-3-clause | 2,325 | [
"VisIt"
] | 3dde71de53c1cda88045152db392cd0a692235706938d4bdc60e6b2b96c0ca7c |
# Author: Samuel Genheden samuel.genheden@gmail.com
"""
Program to collect TI results for a list of output
Examples:
collect_ti.py list
"""
import argparse
import os
import numpy as np
def _integrate(filename):
"""
Read a PMF from an Lammps output file and integrate it
"""
lines = []
with open(... | SGenheden/Scripts | Lammps/collect_ti.py | Python | mit | 2,550 | [
"LAMMPS"
] | db66b0434fe2b7d73439af4c5183fa90a772aa9be4ae22a97d681421fdd95371 |
# -*- coding: utf-8 -*-
import unittest
import logging
from nose.tools import * # flake8: noqa (PEP8 asserts)
from framework.auth.core import Auth
from website import settings
import website.search.search as search
from website.search import elastic_search
from website.search.util import build_query
from website.sea... | barbour-em/osf.io | tests/test_elastic.py | Python | apache-2.0 | 20,719 | [
"Brian"
] | e94c96612ee44e694f26bc0c922d43d538b866bda31ad1cec59940488bc4fdc4 |
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Eric Larson <larson.eric.d@gmail.com>
#
# License: Simplified BSD
from copy import deepcopy
import re
import numpy as np
from scipy import linalg
from .cov import read_cov, _get_whitener_data
from .io.constants import FIFF
from .io.pi... | wronk/mne-python | mne/dipole.py | Python | bsd-3-clause | 38,186 | [
"Mayavi"
] | afe09af55627b3c509515b0be0971fbeb2567f84d9d711fda039c8f16cc577ab |
from ..frontend import jit
import numpy as np
@jit
def conjugate(x):
"""
For now we don't have complex numbers so this is just the identity function
"""
return x
@jit
def real(x):
"""
For now we don't have complex types, so real is just the identity function
"""
return x
def _scalar_sign(x):
... | pombredanne/parakeet | parakeet/lib/math.py | Python | bsd-3-clause | 1,470 | [
"Biopython"
] | b11e8fc4f0276fbe94bae26e8b98c102e64ebd5af802c0db4edbb611f5723ba2 |
#! /usr/bin/python
#
# Copyrighted David Cournapeau
# Last Change: Sat Jun 02 07:00 PM 2007 J
# New version, with default numpy ordering.
import numpy as N
import numpy.linalg as lin
from numpy.random import randn
from scipy.stats import chi2
# Error classes
class DenError(Exception):
"""Base class for exception... | jhmadhav/pynopticon | src/em/densities2.py | Python | gpl-3.0 | 8,876 | [
"Gaussian"
] | 663e2aa33a1eb70d814eb973351f686c88e461a07ca9150e27e9705d3466941a |
#!/usr/bin/python
# Copyright 2015 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
# 'top'-like memory/network polling for Android apps.
import argparse
import curses
import os
import re
import sys
import time
from opera... | ds-hwang/chromium-crosswalk | tools/android/appstats.py | Python | bsd-3-clause | 37,289 | [
"Galaxy"
] | a6f5897741a67309e37d4f869f8dd1e0ec67c17b2f2758b1751a3ddd71826261 |
#!/usr/bin/env python3
# Copyright (C) 2012-2019 The ESPResSo project
# Copyright (C) 2011 Olaf Lenz
# Copyright 2008 Marcus D. Hanwell <marcus@cryos.org>
#
# 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 F... | espressomd/espresso | maintainer/git2changelog.py | Python | gpl-3.0 | 4,666 | [
"ESPResSo"
] | e23d580849e4db45c0331ced4232984e8d8c771bcd1a466854fb272564ac4fc8 |
r"""protocols is a module that contains a set of VTK Web related
protocols that can be combined together to provide a flexible way to define
very specific web application.
"""
from time import time
import os, sys, logging, types, inspect, traceback, logging, re
try:
from vtk.vtkWebCore import vtkWebApplication, v... | keithroe/vtkoptix | Web/Python/vtk/web/protocols.py | Python | bsd-3-clause | 11,606 | [
"VTK"
] | 80826b171b3126ee1e2163c853ebe5e0821611bf4fa17f08812c55ae6c719683 |
"""Timeseries plotting functions."""
from __future__ import division
import numpy as np
import pandas as pd
from scipy import stats, interpolate
import matplotlib as mpl
import matplotlib.pyplot as plt
from .external.six import string_types
from . import utils
from . import algorithms as algo
from .palettes import c... | cwu2011/seaborn | seaborn/timeseries.py | Python | bsd-3-clause | 13,239 | [
"NEURON"
] | ee9439b7deb1dd8a99e6cfb87c578de3df2a8f34d29177d1d81358aedd4be091 |
"""This directory is setup with configurations to run the main functional test.
It exercises a full analysis pipeline on a smaller subset of data.
"""
import os
import subprocess
import unittest
import shutil
import contextlib
import collections
import functools
from nose import SkipTest
from nose.plugins.attrib impo... | gifford-lab/bcbio-nextgen | tests/test_automated_analysis.py | Python | mit | 16,978 | [
"Galaxy"
] | 8ebacfc151a45e3a564a4d553de9e8216da9d3e02d9c0885c04df5367ca7a2ed |
import logging
import os
import click
logger = logging.getLogger(__name__)
@click.group()
@click.version_option()
@click.option('-v', '--verbose', type=int, default=0)
def cli(verbose):
"""A genomic data simulator for testing and debugging bio-informatics tools"""
logging.basicConfig(level=[
logging.ERROR,... | sbg/Mitty | mitty/cli.py | Python | apache-2.0 | 30,231 | [
"BWA"
] | 3e614a23038a465232582599f89f3d712f3e20d38b52356640f52c5e079d297d |
# import and init CUDA
import pycuda.autoinit
import pycuda.driver as cuda
import numpy as np
import Image
from pylab import show, imshow
import logging
logging.basicConfig(format='%(levelname)s: %(message)s',
level=logging.WARNING)
# motion energy device code
# SourceModule stored in variable m... | UCI-CARL/MotionEnergy | pyME/pyME/motionenergy.py | Python | mit | 26,322 | [
"Gaussian"
] | 3f6ae503a589febefe379e00d8b9c1deaa6cb2f6423cbb14345423a0b6b06893 |
import itertools
import time
from collections import defaultdict
from datetime import datetime, timedelta
from typing import Callable, Dict, List, Optional, Sequence, Tuple, Union
from django.conf import settings
from django.db import connection
from django.http import HttpRequest, HttpResponse
from django.shortcuts i... | hackerkid/zulip | analytics/views/installation_activity.py | Python | apache-2.0 | 19,623 | [
"VisIt"
] | 1a4e8d3aa6e5cb39c4e9d2b78eb1773d10c9ceb4ff78825dc38065f5969fbd41 |
from pathlib import Path
from datetime import datetime
import numpy as np
from netCDF4 import Dataset
import pytest
from ladim.gridforce.ROMS import Forcing
@pytest.fixture
def nc_files():
# Setup, make netCDF files with time records
for i in range(10):
fname = f"test_file{i:02d}.nc"
ncid = Da... | bjornaa/ladim | test/test_ROMS_forcing.py | Python | mit | 3,662 | [
"NetCDF"
] | 236f54ca0226f9c55e7e22a011b158ea00afd15883f8b2914efd4f7a3da964e2 |
# =============================================================================
#
# Convolution.py
#
# This file is part of ANNarchy.
#
# Copyright (C) 2019 Julien Vitay <julien.vitay@gmail.com>,
# Helge Uelo Dinkelbach <helge.dinkelbach@gmail.com>
#
# This program is free software: you can redistr... | vitay/ANNarchy | ANNarchy/extensions/convolution/Convolve.py | Python | gpl-2.0 | 41,839 | [
"NEURON"
] | c3342615213cbb6735e189b96a120d66b675e96ebf4c060a535689ff83148861 |
#!/usr/bin/python
import HTSeq
import sys
from Bio.Seq import Seq
from Bio.Alphabet import generic_dna
from Bio.Blast import NCBIXML
from Bio.Blast.Applications import NcbiblastnCommandline
from Bio.Blast.Applications import NcbiblastpCommandline
from Counter import Counter # --- Counter.py from python3 is needed to ... | mickaelsilva/pythonscripts | AlleleCalling/cluster_versions/alleleCalling_ORFbased_main.py | Python | gpl-2.0 | 9,262 | [
"BLAST",
"HTSeq"
] | 87d1def22a13e2ea0de17a59c20b353b18d90a0cc6dec3eb70a5033a53cf63fc |
# Copyright 2008-2014 Nokia Solutions and Networks
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable l... | eric-stanley/robotframework | src/robot/model/stats.py | Python | apache-2.0 | 6,017 | [
"VisIt"
] | 059f181f54a231a45174d2dd688b47e95801198e3a5f47ede044009b3a8994d8 |
from copy import copy
from numpy import asarray, diag, dot, exp
from numpy.linalg import pinv, solve
from glimix_core._ep import EPLinearKernel
from ._glmm import GLMM
class GLMMExpFam(GLMM):
r"""Generalised Linear Gaussian Processes implementation.
It implements inference over GLMMs via the Expectation P... | limix/glimix-core | glimix_core/glmm/_expfam.py | Python | mit | 6,734 | [
"Gaussian"
] | 08dbc0e9336f63bf78f20dd7bee86eb55938a9396fe54ab4a3270b29946df6d7 |
# Copyright (C) 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 versio... | fweik/espresso | testsuite/scripts/tutorials/test_active_matter__enhanced_diffusion.py | Python | gpl-3.0 | 1,395 | [
"ESPResSo"
] | 063affbb083310f4f0053911e99e8d4318db634701e75a6c53034f0073b03688 |
from numpy import *
import sortUtils as tech
import XKCD as XKCD
import matplotlib.pyplot as plt
import neuroTools as postdoc
from os import mkdir
from os.path import splitext, dirname,basename, isfile, isdir
from scipy.io import savemat,loadmat
from time import time
import cPickle
import json
from matplotlib ... | mac389/brainpy | lib/Recording.py | Python | gpl-3.0 | 13,114 | [
"Brian"
] | 370795ed0b45320bfcc06227ca69796c18ba1b417e30dc2bb677c9a09c9dba77 |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
#
ANSIB... | alxgu/ansible | lib/ansible/modules/network/avi/avi_ipamdnsproviderprofile.py | Python | gpl-3.0 | 5,896 | [
"VisIt"
] | bd3def9f45d5b3ae5637f47a9b3ed31f52d6170dc95fe8c9e9770a42611646e6 |
#!/usr/bin/env python3
### VERY MUCH PYTHON 3 !!!
"""
Example for aiohttp.web basic server
Uses a background timer to read from a file to update a shared datastructure
Because it's going to be used as a simulator
Made available under the MIT license as follows:
Copyright 2017 Brian Bulkowski brian@bulkowski.org
P... | bbulkow/MagnusFlora | sim/portal_sim_decom.py | Python | mit | 27,153 | [
"Brian"
] | 826f3bb9263afb2c8745cc5e321762e44699016476b480f7738c1b4099e5036e |
# Copyright 2004-2008 by Sebastian Bassi.
# 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.
"""Calculate the thermodynamic melting temperatures of nucleotide sequences."""
impor... | bryback/quickseq | genescript/Bio/SeqUtils/MeltingTemp.py | Python | mit | 7,166 | [
"Biopython"
] | b0eb3a05c8fdf427d3a0e78689d47bc06f501e42a7bea13e9ad8a6e6d389ac47 |
#
# Copyright 2016 The BigDL Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... | intel-analytics/BigDL | python/chronos/src/bigdl/chronos/model/tcn.py | Python | apache-2.0 | 7,817 | [
"ORCA"
] | 4575ddeaacb25637afc6502d2945df11045706720e8fcf6799a0b8b2d19871a4 |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""This script generates an rc file and header (setup_strings.{rc,h}) to be
included in setup.exe. The rc file includes translation... | leighpauls/k2cro4 | chrome/installer/util/prebuild/create_string_rc.py | Python | bsd-3-clause | 9,760 | [
"xTB"
] | e23d690a2e18b619f3bcf6f4962491fc8ddd944d360d43657081437651c83dd5 |
""" :mod: GFAL2_SRM2Storage
=================
.. module: python
:synopsis: SRM2 module based on the GFAL2_StorageBase class.
"""
# pylint: disable=invalid-name
import errno
import json
import gfal2 # pylint: disable=import-error
# from DIRAC
from DIRAC import gLogger, gConfig, S_OK, S_ERROR
from DIR... | andresailer/DIRAC | Resources/Storage/GFAL2_SRM2Storage.py | Python | gpl-3.0 | 8,520 | [
"DIRAC"
] | de38fc3ba57e6eb487bf1a6cca61f037bd1addd8bdeba7b2a267d416534f6e3a |
# Checks all psi4 relevant files for proper boilerplate GNU license.
# This is sold as is with no warrenty-- probably should double check everything
# after running. I am not responsible if you break Psi4.
#
# Do not forget to do share/plugins by hand!
import os
# File type we know how to handle
ftypes = ['cc', 'h', ... | amjames/psi4 | psi4/share/psi4/scripts/apply_license.py | Python | lgpl-3.0 | 3,497 | [
"Psi4"
] | b2167c6ea3755a044afa2588075c5efa3e8dd2bdcabe71c2a1ed7242e89f9667 |
"""
Display information about your smartphone with KDEConnector.
Configuration parameters:
cache_timeout: how often we refresh this module in seconds (default 30)
device: the device name, you need this if you have more than one device
connected to your PC (default None)
device_id: alternatively to ... | ultrabug/py3status | py3status/modules/kdeconnector.py | Python | bsd-3-clause | 8,900 | [
"Galaxy"
] | 202e286e9a69fad2f0b9b0ad646df17668e503e1bcd10be1e097de28c2596ba5 |
from setuptools import setup
import io
# read the contents of your README file
from os import path
this_directory = path.abspath(path.dirname(__file__))
with io.open(path.join(this_directory, 'README.md'), encoding='utf-8') as f:
long_description = f.read()
setup(
name='goodvibes',
packages=['goodvibes'],
v... | bobbypaton/GoodVibes | setup.py | Python | mit | 1,039 | [
"Gaussian"
] | bf29cff2efc2e7abd1eabf3c343006733dc9611eb4b49ed883b5b7e17cae15be |
import numpy as np
import torch
from torch.autograd import Variable
from stats.tensor import tensor
def fit(pdfs, parameters, observations, iter, lr):
"""Estimates the parameters of a mixture model via maximum likelihood maximization.
Uses gradient descent for optimization.
Parameters
----------
... | mlosch/pytorch-stats | stats/estimation/mm.py | Python | mit | 4,418 | [
"Gaussian"
] | 55dfb134ceed8504e41fff2bc120a02d8196db71ac7642fbdc0447660ff9e2f0 |
#!/usr/bin/env python
#
# @file BaseFile.py
# @brief base class for all files to be generated
# @author Frank Bergmann
# @author Sarah Keating
#
# <!--------------------------------------------------------------------------
#
# Copyright (c) 2013-2015 by the California Institute of Technology
# (California, USA)... | hovo1990/deviser | generator/base_files/BaseFile.py | Python | lgpl-2.1 | 22,143 | [
"VisIt"
] | 224809df4bcbbf7fc562031b9684767f8376caaf215274d67d0a76145ed358cb |
# This script reads the carrier database
# and display it along a path in histogram form
# along with a representation of the carriers in energy space
from __future__ import print_function
from __future__ import division
from builtins import range
from past.utils import old_div
from yambopy import *
import matplotlib.... | alexmoratalla/yambopy | scripts/realtime/plot_occ.py | Python | bsd-3-clause | 9,348 | [
"DIRAC"
] | f6176e8112519f5301e42159e72c5a99e385875dde145c8ffd91cda78130615a |
# -*- coding: utf-8 -*-
# Copyright: (c) 2014, Brian Coca <brian.coca+dev@gmail.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
DOCUMENTATION = '''
---
module: getent
short_descrip... | privateip/ansible | lib/ansible/modules/getent.py | Python | gpl-3.0 | 5,521 | [
"Brian"
] | 1c40bfb430509851ce2d98d95a9453780cc8fff9160a61b5d2a58c187dba3f4f |
from vtk import *
import os.path
data_dir = "../../../../VTKData/Data/Infovis/Images/"
if not os.path.exists(data_dir):
data_dir = "../../../../../VTKData/Data/Infovis/Images/"
source = vtkGeoRandomGraphSource()
source.DirectedOff()
source.SetNumberOfVertices(100)
source.SetEdgeProbability(0.00) # produces a tree
s... | collects/VTK | Examples/Infovis/Python/geoview.py | Python | bsd-3-clause | 2,300 | [
"VTK"
] | 9e98441eddf8c8e6be78590f3116ed5adc38176a6fbb1ac36aabcba910e3e4c0 |
# Copyright 2014 Cloudera Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, so... | o0neup/ibis | ibis/sql/compiler.py | Python | apache-2.0 | 27,343 | [
"VisIt"
] | 90b7b6f5a2a29b35a3d4c55adbe8c09b690e674d94c00273e4cd5f4177c2ca43 |
#
# Copyright (c) 2016 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yashdsaraf/scancode-toolkit | src/extractcode/archive.py | Python | apache-2.0 | 29,018 | [
"VisIt"
] | a06404caf027f05aa1704f61f7bbf06a3735075a456d57839e684c0845aff353 |
import utils.archive as archive
import os, sys
import shutil
from pprint import pprint
import importlib
import random
import json
import time
from multiprocessing import Queue, Process
import logging
import logging.handlers
from utils.processes import local_subprocess, mp_pool
#from utils.xutils import convert_unicod... | RAPD/RAPD | src/test2.py | Python | agpl-3.0 | 10,111 | [
"ADF"
] | cea75baf3b4520dd82b4292153ca63f63f62e9cddd32450f3f49c2b3a1b12f57 |
'''
Created on Jul 1, 2011
@author: mkiyer
chimerascan: chimeric transcript discovery using RNA-seq
Copyright (C) 2011 Matthew Iyer
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... | tectronics/chimerascan | chimerascan/deprecated/write_output_v1.py | Python | gpl-3.0 | 7,533 | [
"pysam"
] | 851f13ee7ab4dee597822cf8f5f9a4d1ffd85892db5ef3921f84ca64136cfc09 |
'''Term paths.'''
import itertools
from aterm.factory import factory
from aterm import types
from aterm import visitor
from aterm import project
from aterm import annotation
PRECEDENT = -2
ANCESTOR = -1
EQUAL = 0
DESCENDENT = 1
SUBSEQUENT = 2
class _Transformer(visitor.IncrementalVisitor):
def __init__(self, i... | mewbak/idc | aterm/path.py | Python | lgpl-2.1 | 5,156 | [
"VisIt"
] | fa11ac82113aebe50bd1ad7a3ef6080c9269ff23156394bcc347aded7d3be6aa |
from lib_spm import *
#out_dir = os.path.join('/data42s/comparat/firefly/v1_1_0/figures', 'mass-redshift-presentation')
out_dir = os.path.join(os.environ['HOME'], 'wwwDir', 'firefly')
m_bins = n.arange(-3., 3., 0.01)
p.figure(2, (6.5, 3.5))
p.axes([0.12,0.18,0.8,0.73])
print('eboss')
for imf in imfs:
stellar_mass... | JohanComparat/pySU | spm/bin_SMF/plot_distribution_metals.py | Python | cc0-1.0 | 10,258 | [
"Firefly",
"Galaxy"
] | fee2da742f36c00f95dbadea0f38b19e4c14e1237cae8478b2b9460bfa3dbea5 |
# Copyright (C) 2010, Joao Rodrigues (anaryin@gmail.com)
# 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.
"""
Module with assorted geometrical functions on
macromolecules.
"""
from Bio.PDB import Ent... | SBRG/ssbio | ssbio/biopython/Bio/Struct/Geometry.py | Python | mit | 2,274 | [
"Biopython"
] | 6ed0786b6de3a60a208701d3e555475c1989808bfa98a21851d6dca19467f14b |
"""
Play soundfiles from the disk.
SfMarkerXXX objects use markers features (store in the header) from
an AIFF file to create more specific reading patterns.
"""
"""
Copyright 2009-2015 Olivier Belanger
This file is part of pyo, a python module to help digital signal
processing script creation.
pyo is free softwar... | belangeo/pyo | pyo/lib/players.py | Python | lgpl-3.0 | 20,439 | [
"Gaussian"
] | 0a2886e650b3e500ec88f764e45c9dae3e4842f80c3ff3119e2a9a4591a04ed6 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# readmdict.py
# Octopus MDict Dictionary File (.mdx) and Resource File (.mdd) Analyser
#
# Copyright (C) 2012, 2013, 2015 Xiaoqiang Wang <xiaoqiangwang AT gmail DOT com>
#
# This program is a free software; you can redistribute it and/or modify
# it under the terms of the ... | finalion/WordQuery | src/libs/mdict/readmdict.py | Python | gpl-3.0 | 40,280 | [
"Octopus"
] | b52230034ea452bf72b6df2918521a6e10561b93b22a62993ab365284d3ac3b2 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals, division, print_function
import os
import unittest
import numpy as np
from pymatgen import Structure
from pymatgen.util.testing import PymatgenTest
from pymatgen.io.ab... | sonium0/pymatgen | pymatgen/io/abinitio/tests/test_netcdf.py | Python | mit | 2,917 | [
"pymatgen"
] | bf15e42a7e3cab5e24946f1235e7287242446d857ae868b8e633cb0cd6135815 |
# Copyright (C) 2020 Atsushi Togo
# All rights reserved.
#
# This file is part of phono3py.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# * Redistributions of source code must retain the above copyright
# noti... | atztogo/phono3py | phono3py/phonon/solver.py | Python | bsd-3-clause | 5,731 | [
"phonopy"
] | 699d48efcf93228d3aa7cb3b4841e4524a9122c9035c81dbcb29f80d7bde8451 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
A set of built-in plotting functions to help visualize ``dynesty`` nested
sampling :class:`~dynesty.results.Results`.
"""
import logging
import warnings
import numpy as np
import matplotlib.pyplot as pl
from matplotlib.ticker import MaxNLocator, NullLocator
from matpl... | joshspeagle/dynesty | py/dynesty/plotting.py | Python | mit | 90,999 | [
"Gaussian"
] | 465adc4ffa43217836c9cce17a39bfac5191e2b80ec3ac451b9b343d1c9c398e |
# Copyright 2016 James Hensman
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, so... | jameshensman/VFF | VFF/ssgp.py | Python | apache-2.0 | 6,416 | [
"Gaussian"
] | fa9c241c1dee60a2250ec4676255e540b9303dc77fd9fd02fcb2c55639db50de |
# GromacsWrapper: formats.py
# Copyright (c) 2009-2011 Oliver Beckstein <orbeckst@gmail.com>
# Released under the GNU Public License 3 (or higher, your choice)
# See the file COPYING for details.
"""
Gromacs parameter MDP file format
=================================
The `.mdp file`_ contains a list of keywords that a... | Becksteinlab/GromacsWrapper | gromacs/fileformats/mdp.py | Python | gpl-3.0 | 5,815 | [
"Gromacs"
] | 915c6ed871d25bb58e4fe17c1a05fe8257d7dba8f89d722df50db73cd14e10ed |
'''
* Created by Zhenia Syryanyy (Yevgen Syryanyy)
* e-mail: yuginboy@gmail.com
* License: this code is under GPL license
* Last modified: 2017-02-27
'''
import numpy as np
import os
from feff.libs.dir_and_file_operations import get_folder_name, runningScriptDir
from feff.libs.feff_processing import xftf
def load_expe... | yuginboy/from_GULP_to_FEFF | feff/libs/load_chi_data_file.py | Python | gpl-3.0 | 2,623 | [
"FEFF"
] | 41c6ef36ffa290bd4830ebe9dc41f4c41378f3789018086ec692b1e2a5825af5 |
##
# Copyright 2013 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://vscentrum.be/nl/en),
# the Hercules foundation (http://w... | ULHPC/modules | easybuild/easybuild-easyblocks/easybuild/easyblocks/q/qt.py | Python | mit | 3,382 | [
"VisIt"
] | 203d76f2a58fc02d21e5e4a976d7716e02c5a3f78fd0d994e76148721bff01f3 |
import logging
from multiprocessing import Queue, Lock
import pysam
from PyMaSC.handler.masc_noindex_worker import SingleProcessCalculator
from PyMaSC.handler.masc_worker import NaiveCCCalcWorker, MSCCCalcWorker, NCCandMSCCCalcWorker
from PyMaSC.core.readlen import estimate_readlen
from PyMaSC.utils.progress import M... | ronin-gw/PyMaSC | PyMaSC/handler/masc.py | Python | mit | 8,168 | [
"pysam"
] | 8b3518eb625de32f9b5b7cf288e76d43038ff72b442d0f10d2aa5aff0abca755 |
#!/usr/bin/env python
#coding=utf-8
'''
Created on 01 Ιουλ 2011
@author: tedlaz
'''
class Beverage():
def __init__(self):
self.desc = 'unknown'
def getDesc(self):
return self.desc
def cost(self):
return 0
class Espresso(Beverage):
def __init__(self):
self.desc = 'Espre... | tedlaz/pyted | misthodosia/pyMisthodosia/src/erg.py | Python | gpl-3.0 | 2,076 | [
"ESPResSo"
] | 1d822a6c2beef658339243be56182c55b779c73c3b382aca11960616ff7375eb |
"""This module contains all of the important meta-information for
Hypatia such as the author's name, the copyright and license, status,
and so on.
"""
__author__ = "Lillian Lemmer"
__copyright__ = "Copyright 2015 Lillian Lemmer"
__credits__ = ["Lillian Lemmer"]
__license__ = "MIT"
__maintainer__ = __author__
__site__... | Applemann/hypatia | hypatia/__init__.py | Python | mit | 632 | [
"Brian"
] | 33128007ba8dbc98a7ab5c7d72f56ed5746c1566b74eb388cc319140776c3272 |
# coding: utf-8
# Copyright (c) Henniggroup.
# Distributed under the terms of the MIT License.
from __future__ import division, print_function, unicode_literals, \
absolute_import
"""
Sample LAMMPS workflow that runs MD calculations for a bunch of structures and
subsequently generate their phasediagram.
"""
fro... | henniggroup/MPInterfaces | examples/workflows/lammps_workflow.py | Python | mit | 3,731 | [
"LAMMPS",
"pymatgen"
] | a9f716812857ff5eb3fdd5cd3db10f0d1094adc546626e2e0c6f9afef402ae50 |
"""
Computing integrals.
"""
# TODO:
# FIX GAUSSIAN QUADRATURE
# Include error estimates for each method?
import math
import souffle.utils as utl
import souffle.datatypes as dtt
def trapezoidal(f, a, b, n):
"""
Evaluates the integral of f, with endpoints a and b, using the trapezoidal
rule with n... | pauljxtan/mathsci | souffle/math/integral.py | Python | mit | 2,255 | [
"Gaussian"
] | c0e74aed549e1c78120bbbb69550fb67ec23ac5a1f511f549d6f90db772d3987 |
__all__ = ["GET_FIRST_CLIENT_RECT", \
"GET_LOCATION_IN_VIEW", \
"GET_PAGE_ZOOM", \
"IS_ELEMENT_CLICKABLE", \
"TOUCH_SINGLE_TAP", \
"CLEAR", \
"CLEAR_LOCAL_STORAGE", \
"CLEAR_SESSION_STORAGE", \
"CLICK", \
"EXECUTE_ASYNC_S... | PeterWangIntel/crosswalk-webdriver-python | third_party/atoms.py | Python | bsd-3-clause | 417,522 | [
"ADF",
"ASE"
] | 3b7ef94b7bdb7f97bcc288bb9821213a8bd58a9c0d9556b49133818872895db2 |
"""
Student Views
"""
import datetime
import logging
import uuid
import json
import warnings
from collections import defaultdict
from urlparse import urljoin, urlsplit, parse_qs, urlunsplit
from django.views.generic import TemplateView
from pytz import UTC
from requests import HTTPError
from ipware.ip import get_ip
i... | itsjeyd/edx-platform | common/djangoapps/student/views.py | Python | agpl-3.0 | 107,769 | [
"VisIt"
] | 737d150ee3aa6d62ebb66c2628d3e109a84073f1a026a2733f9af3121db11304 |
"""Random variable generators.
integers
--------
uniform within range
sequences
---------
pick random element
pick random sample
generate random permutation
distributions on the real line:
------------------------------
uniform
... | kozec/SimplePython | src/random.py | Python | lgpl-3.0 | 15,856 | [
"Gaussian"
] | f7bba7a147d7719d3760fd4e2252e48c7383b960e5c67951f673cac318dff9bb |
#! /usr/bin/env python3
# -*- 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 requi... | googleapis/python-area120-tables | scripts/fixup_tables_v1alpha1_keywords.py | Python | apache-2.0 | 6,502 | [
"VisIt"
] | 90ef4d67c093af05c37da78cfbf173e8a4f27049e54a6e0df9b6499446e8adea |
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are ... | wizmer/NeuroM | neurom/check/tests/test_structural_checks.py | Python | bsd-3-clause | 7,517 | [
"NEURON"
] | 1b4d98ee0a35c3d3d32c815d5def2360040776f111d6e76fb8459e941ae39c74 |
# -*- coding: utf-8 -*-
# Copyright (c) 2019 SubDownloader Developers - See COPYING - GPLv3
import argparse
from collections import namedtuple
import logging
from pathlib import Path
from subdownloader import project
from subdownloader.client import ClientType
from subdownloader.client.cli import CliAction
from subdo... | subdownloader/subdownloader | subdownloader/client/arguments.py | Python | gpl-3.0 | 12,582 | [
"VisIt"
] | 65ef148e0d6ad36ef5684a9cfe55f3a3f553a5ca974a57515e540661c72c9e72 |
# $Id$
#
# Copyright (C) 2000-2006 greg Landrum
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" Matrix operations which may or may not come ... | rvianello/rdkit | rdkit/ML/MatOps.py | Python | bsd-3-clause | 813 | [
"RDKit"
] | 41a2cc4aa664ea9fdafe0862499d5f96855d2d2789e77eb334bfad6a3e1e01a2 |
# Load python packages
import re, sys, math
from collections import OrderedDict
# Load Moose packages
from FactorySystem import MooseObject
from ..slides import RemarkSlide, SlideWarehouse
##
# Base class for markdown slide generation
class RemarkSlideSet(MooseObject):
##
# Defines the available properties for t... | mellis13/moose | python/PresentationBuilder/slidesets/RemarkSlideSet.py | Python | lgpl-2.1 | 9,831 | [
"MOOSE"
] | 636129ff0bf4a4499b1ed48e8dd6365878d9adb62921a7214276535ddb2125d7 |
# Copyright 2014 Roberto Brian Sarrionandia
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed t... | sarrionandia/tournatrack | reg_add.py | Python | apache-2.0 | 1,433 | [
"Brian"
] | 6d76afa388427ef06d0fd2869b807faaf80cbe900665a9a0a637f7d3e942a650 |
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
from django.views import defaults as default_views
from neural_exploration.visualize.views import SpikeDataView
urlpatter... | brookefitzgerald/neural-exploration | config/urls.py | Python | mit | 1,721 | [
"VisIt"
] | 51d42cace981dee0589f80a86da7c0249a1d9a1652b27be8cb1e7b2b4242b7ff |
import os
import sys
import datetime
import tensorflow as tf
import numpy as np
import prettytensor as pt
from convolutional_vae_util import deconv2d
from utils import *
class CVAE(object):
'''
CVAE: Convolutional Variational AutoEncoder
Builds a convolutional variational autoencoder that compresses
... | jramapuram/CVAE | cvae.py | Python | mit | 10,644 | [
"Gaussian"
] | b82bd1db56273100e035f474d35ac2269c41a90886560f1f2c620f92158cfa6f |
from pysal.weights import Distance as d
from pysal.weights.util import get_points_array
from pysal.weights import Contiguity as c
from pysal.common import RTOL, ATOL
from pysal.cg.kdtree import KDTree
import numpy as np
import pysal as ps
import unittest as ut
PANDAS_EXTINCT = ps.common.pandas is None
# All instances ... | ljwolf/pysal | pysal/weights/tests/test_Distance.py | Python | bsd-3-clause | 11,865 | [
"COLUMBUS",
"Gaussian"
] | ac71b1d5920237fcd764ac724ef42e390a75e8ab6d5af1ea1b7ec17668c18892 |
#!/usr/bin/env python
# Copyright (C) 2010-2012 Google Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | googlearchive/appengine-recover-unapplied-writes-python | apply_unapplied_writes.py | Python | apache-2.0 | 5,104 | [
"VisIt"
] | 462331a0263a4c2ce177ad666672abd085428fb39a4dc48b943fe9591a919091 |
#################################################################
# #
# Integrate images with MOSFLM and merge with SCALA #
# #
# Copyright: Molecular Images 2007 ... | mifit/miexpert | mi_integrate.py | Python | gpl-3.0 | 36,722 | [
"CRYSTAL"
] | dcc033b0c7468067d54a3f016bfacee01e5fd5f6c269a17b9a13456f806f1f1c |
import os
from commands import getoutput
from glob import glob
def gen_que(comfile, queue = 'gb', gauversion = 'd', QUE_PATH = False):
QUE_EXT = '.q'
text = """#!/bin/bash
### Request number of processors
SET_PROCS_NUM
### Previleges
SET_GRP_NAME
SET_QUE_NAME
### Home directory where the input files are l... | eduardoftoliveira/oniomMacGyver | omg/qtrex.py | Python | gpl-3.0 | 7,009 | [
"Gaussian"
] | 8a13fefd01c35d068a517084ba37a7330c53f374c4adad0fa637c3aa81c0d265 |
# Copyright Iris contributors
#
# This file is part of Iris and is released under the LGPL license.
# See COPYING and COPYING.LESSER in the root of the repository for full
# licensing details.
"""
A package for converting cubes to and from specific file formats.
"""
from iris.io.format_picker import (
FileExtensi... | pp-mo/iris | lib/iris/fileformats/__init__.py | Python | lgpl-3.0 | 4,539 | [
"NetCDF"
] | 7e9fdb7e1c5d73dcfa9810b4377f2a8c8c3a9db41ec7e265e0217d86a4b2bf32 |
import re
import requests
from difflib import SequenceMatcher
from coalib.results.Diff import Diff
from coalib.bears.LocalBear import LocalBear
from coalib.bears.requirements.PipRequirement import PipRequirement
from coalib.results.RESULT_SEVERITY import RESULT_SEVERITY
from coalib.results.Result import Result
from c... | dosarudaniel/coala-bears | bears/general/InvalidLinkBear.py | Python | agpl-3.0 | 5,280 | [
"VisIt"
] | 854d19145de840d6ad029d6e49fc9b8bb92fd84b703e3ba72e226ee7c13cdd1b |
"""Core visualization operations."""
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Eric Larson <larson.eric.d@gmail.com>
# Joan Massich <mailsik@gmail.com>
# Guillaume Favelier <guillaume.favelier@gmail.com>
#
# License: Simplified BSD
import sys
import os
from contextlib im... | pravsripad/mne-python | mne/viz/backends/renderer.py | Python | bsd-3-clause | 11,507 | [
"Mayavi"
] | b8491dd2b7cdc1f7411b3b8652816ac25faa8f427705a862a86ba6ebfc873023 |
# -*- coding: utf-8 -*-
"""Infrared intensities"""
import pickle
from math import sin, pi, sqrt, exp, log
from os import remove
from os.path import isfile
import numpy as np
import ase.units as units
from ase.io.trajectory import PickleTrajectory
from ase.parallel import rank, barrier
from ase.vibrations import Vi... | freephys/python_ase | ase/infrared.py | Python | gpl-3.0 | 10,849 | [
"ASE",
"Gaussian",
"VASP"
] | 1051246c073a796b3cc53ec9facc46911dd62749a3daecc6c3fa37845f2bfc3b |
# Copyright 2003-2009 by Bartek Wilczynski. All rights reserved.
# Revisions copyright 2009 by Peter Cock.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""This module provides code to work with th... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/motifs/applications/_alignace.py | Python | gpl-2.0 | 5,755 | [
"Biopython"
] | 47f28d70c74da1156ea74c99d7692ffd7d1e4ac43428cd0a65d0dfea3c27b290 |
try: paraview.simple
except: from paraview.simple import *
def RequestDataDescription(datadescription):
"Callback to populate the request for current timestep"
if datadescription.GetForceOutput() == True:
for i in range(datadescription.GetNumberOfInputDescriptions()):
datadescription.GetIn... | openmichigan/PSNM | KleinGordon/Programs/KleinGordon3dMpiFFTParaView/pipeline_vtis.py | Python | bsd-2-clause | 6,773 | [
"ParaView"
] | 454b60b1175dc9c99c2e203e70fe10f190f1e54fefb83a610e89adcc7cbc8c6f |
"""This file contains code for use with "Think Stats" and
"Think Bayes", both by Allen B. Downey, available from greenteapress.com
Copyright 2014 Allen B. Downey
License: GNU GPLv3 http://www.gnu.org/licenses/gpl.html
"""
from __future__ import print_function, division
"""This file contains class definitions for:
H... | smorton2/think-stats | code/thinkstats2.py | Python | gpl-3.0 | 70,025 | [
"Gaussian"
] | 524f2df7adee26d00012dd6bc687d7aefc51131f081d9bae675a326f0b28f417 |
"""
Acceptance tests for Studio's Setting pages
"""
from nose.plugins.attrib import attr
from base_studio_test import StudioCourseTest
from ...pages.studio.settings_advanced import AdvancedSettingsPage
@attr('shard_1')
class AdvancedSettingsValidationTest(StudioCourseTest):
"""
Tests for validation feature... | c0710204/edx-platform | common/test/acceptance/tests/studio/test_studio_settings.py | Python | agpl-3.0 | 6,475 | [
"VisIt"
] | 531be978020219f6a0ba691915da9df4cb51a7ff24ef6e0f33a63f58fa50a002 |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, subprocess, sys, glob, string
import zipfile
from datetime import date
cwd = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
os.chdir(cwd)
required_module_keys = ['name','version','moduleid','description','copyright','... | delapecci/titanium-modules | ios7media/build.py | Python | mit | 6,797 | [
"VisIt"
] | c5c1d5154e96bea8890a1ebbc5a88eee3587a306bbde4ee876b20acb91f3478e |
#!/bin/env python
"""
tests for SSHComputingElement module
"""
import os
import shutil
import subprocess32 as subprocess
import shlex
import pytest
import DIRAC
from DIRAC.Resources.Computing.SSHComputingElement import SSHComputingElement
from DIRAC.Resources.Computing.BatchSystems.executeBatch import executeBatchCon... | DIRACGrid/DIRAC | src/DIRAC/Resources/Computing/test/Test_SSHComputingElement.py | Python | gpl-3.0 | 2,459 | [
"DIRAC"
] | 8b41a3a9eb0cabd04daf914a2584b40a6c316c263ad6dfcd37f0d8cf5d3b9da7 |
"""
The B{0install digest} command-line interface.
"""
# Copyright (C) 2011, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from __future__ import print_function
import os, tempfile
from zeroinstall import SafeException, _
from zeroinstall.zerostore import manifest, unpack
from zero... | slovenwd/0install | zeroinstall/cmd/digest.py | Python | lgpl-2.1 | 1,983 | [
"VisIt"
] | c733abcf24fe0656062e229a984c8ae2a8cfd8af35848332a84f26ad6bda390a |
#!/usr/bin/python3
# vim: foldmethod=marker :
# Documentation. {{{
# server.py - machine multiplexing for Franklin {{{
# Copyright 2014-2016 Michigan Technological University
# Copyright 2016 Bas Wijnen <wijnen@debian.org>
# Copyright 2017 Lorin Edwin Parker <lorin.parker@hive13.org>
# Author: Bas Wijnen <wijnen@debian... | mtu-most/franklin | server/server.py | Python | agpl-3.0 | 38,340 | [
"VisIt"
] | 5d082abb6a0bda7b0816e233a39ede88a8acf35d7e699abfbb51758ffe98a17b |
# Copyright 2012, 2013 The GalSim developers:
# https://github.com/GalSim-developers
#
# This file is part of GalSim: The modular galaxy image simulation toolkit.
#
# GalSim 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... | mardom/GalSim | galsim/shapelet.py | Python | gpl-3.0 | 11,288 | [
"Galaxy",
"Gaussian"
] | 4bb77074420b1a80b37e59036fd04f791df83cbd2a93a7e63aacff6b9a66ca58 |
from vtk import *
import os.path
data_dir = "../../../../VTKData/Data/Infovis/SQLite/"
if not os.path.exists(data_dir):
data_dir = "../../../../../VTKData/Data/Infovis/SQLite/"
sqlite_file = data_dir + "SmallEmailTest.db"
# Construct a graph from database tables (yes very tricky)
databaseToGraph = vtkSQLDatabaseGra... | jeffbaumes/jeffbaumes-vtk | Examples/Infovis/Python/databases2.py | Python | bsd-3-clause | 1,219 | [
"VTK"
] | 81eb01794793a39d5d8a98b003e25afa9b151137bbc9a809c2b8102d33efd8c0 |
'''
Dts_Shape.py
Copyright (c) 2003 - 2006 James Urquhart(j_urquhart@btinternet.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 restriction, including
without limitation the rights t... | pchan126/Blender_DTS_30 | DTSPython/Dts_Shape.py | Python | mit | 52,893 | [
"exciting"
] | 728f1caf6e93f8e8137e1ac01b0d148cf022586f1338242259108fad3b6f83f9 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# editor - [insert a few words of module description on this line]
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of th... | heromod/migrid | mig/cgi-bin/editor.py | Python | gpl-2.0 | 1,100 | [
"Brian"
] | 530791734d4622a3cce400fbfacfe7a5e02887de1bfda3695c48d66d9eb0dfb6 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
Created on Apr 28, 2012
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "S... | sonium0/pymatgen | pymatgen/io/tests/test_babel.py | Python | mit | 2,260 | [
"Pybel",
"pymatgen"
] | 9778c08bec9c7422907c91bb7bc923b1fec99f3eef3d519e6bad2922d38d9599 |
# ----------------------------------------------------------------------------
# cocos2d
# Copyright (c) 2008-2012 Daniel Moisset, Ricardo Quesada, Rayentray Tappa,
# Lucio Torre
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided t... | shadowmint/nwidget | lib/cocos2d-0.5.5/cocos/particle_systems.py | Python | apache-2.0 | 10,826 | [
"Galaxy"
] | a8e5776b55dbe81d5a125952111483122eb38ad877de6753934304b43848d994 |
#!/usr/bin/env python
"""
Asymmetric shape integration
Usage:
explore/asymint.py [MODEL] [q-value]
Computes the numerical integral over theta and phi of the given model at a
single point q using different algorithms or the same algorithm with different
precision. It also displays a 2-D image of the theta-phi su... | SasView/sasmodels | explore/asymint.py | Python | bsd-3-clause | 20,630 | [
"Gaussian"
] | 1f47a4551fb720f8dd1022c62aad8879cca70c5c5f24fe2b579746c58612bb6c |
from __future__ import division
import numpy as np
np.seterr(divide='ignore') # these warnings are usually harmless for this code
from matplotlib import pyplot as plt
import copy, os
import pyhsmm
from pyhsmm.util.text import progprint_xrange
SAVE_FIGURES = False
print \
'''
This demo shows the HDP-HSMM in action. I... | bikash/pyhsmm | examples/hsmm.py | Python | mit | 1,985 | [
"Gaussian"
] | 47fbfe1d6ae3178877d2b92b1769e5856d49b16c3417061621f27a78d3a41095 |
import numpy as np
import time
from ..doublyPeriodic import doublyPeriodicModel
from numpy import pi
class model(doublyPeriodicModel):
def __init__(self, name = None,
# Grid parameters
nx = 256, ny = None, Lx = 1e6, Ly = None,
# Solver parameters
t = 0.0,
... | glwagner/py2Periodic | py2Periodic/physics/nearInertialWaves_xy.py | Python | mit | 7,349 | [
"Gaussian"
] | 4543f52e3e7bf17ab4f2c6d06c215beedd23350a2fd21b10c3e9e795ff556183 |
"""Converts Illumina SampleSheet CSV files to the run_info.yaml input file.
This allows running the analysis pipeline without Galaxy, using CSV input
files from Illumina SampleSheet or Genesifter.
"""
import os
import csv
import itertools
import difflib
import glob
import yaml
from bcbio.illumina import flowcell
fro... | Cyberbio-Lab/bcbio-nextgen | bcbio/illumina/samplesheet.py | Python | mit | 5,032 | [
"Galaxy"
] | b632e6f3ed87c30c3fbc1d0875955e5983978b673a38a984d4e54667eb06d52b |
"""Assessment Engine API view functions"""
from datetime import datetime
from flask import (
Blueprint,
abort,
current_app,
flash,
jsonify,
make_response,
redirect,
request,
session,
url_for,
)
from flask_babel import gettext as _
from flask_user import roles_required
from urlli... | uwcirg/true_nth_usa_portal | portal/views/assessment_engine.py | Python | bsd-3-clause | 76,196 | [
"VisIt"
] | b58538db2701f63bbca43eb1641df937e44aa88f3ab288499ae92d5ae73de4f1 |
#!/usr/bin/env python
"""
Read a maf and print the text as a fasta file, concatenating blocks
usage %prog species1,species2 maf_file out_file
"""
#Dan Blankenberg
import sys
from galaxy import eggs
import pkg_resources; pkg_resources.require( "bx-python" )
from bx.align import maf
from galaxy.tools.util import maf_ut... | dbcls/dbcls-galaxy | tools/maf/maf_to_fasta_concat.py | Python | mit | 1,262 | [
"Galaxy"
] | 5e74632921a4bc924aef2f6e98a19ac2ff77f4d313d51517e6a05aed66904c0d |
########################################################################
# $HeadURL $
# File: CleanReqDBAgent.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/05/17 08:31:26
########################################################################
"""Cleaning the RequestDB from obsolete records and kicking assig... | yujikato/DIRAC | src/DIRAC/RequestManagementSystem/Agent/CleanReqDBAgent.py | Python | gpl-3.0 | 6,076 | [
"DIRAC"
] | a1e6c553fd9fcecd7f5e253273f09000f28afa57c5ffcd83ec5c865d37c8ce3d |
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