text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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"""
Copyright (C) 2016 Quinn D Granfor <spootdev@gmail.com>
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
version 2, as published by the Free Software Foundation.
This program is distributed in the hope that it will be useful, but
... | MediaKraken/MediaKraken_Deployment | source/common/common_docker.py | Python | gpl-3.0 | 22,042 | [
"Elk"
] | 4587b9f18ae9e2de02e7d570971ce4bcd12f222ea712c0ec020ca876ea1215b9 |
from __future__ import unicode_literals
import sys
import comtypes
from comtypes import GUID
import ctypes
import os
from itertools import takewhile
import logging
logging.basicConfig(filename=r'D:\bogo.log', level=logging.DEBUG)
# We aren't interested in DEBUG messages from comtypes
comtypes_logger = logging.getLogg... | BoGoEngine/bogo-win | bogo_server.py | Python | gpl-3.0 | 11,014 | [
"ASE"
] | 9daadcd14ca3d3f497491df32862d618668f4300629e13b0fd1b135d86b3f6a0 |
"""
Functions related to 2D gaussian functions and comparing ellipticities
derived either analytically or using quadrupole moments.
:requires: NumPy
:requires: matplotlib
:author: Sami-Matias Niemi
:contact: smn2@mssl.ucl.ac.uk
:version: 0.2
"""
import matplotlib
matplotlib.use('PDF')
import matplotlib.pyplot as plt... | sniemi/EuclidVisibleInstrument | support/gaussians.py | Python | bsd-2-clause | 7,161 | [
"Gaussian"
] | ed5c0dc56abc30064c6cff3d9654f045cd99c9cfe942f5f1088a22436d1ce85f |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Setup for jsonextended."""
import io
from importlib import import_module
from setuptools import setup, find_packages
with open('requirements.txt') as handle:
requirements = handle.read().splitlines()
with open('test_requirements.txt') as handle:
test_requireme... | chrisjsewell/jsonextended | setup.py | Python | mit | 2,162 | [
"CRYSTAL"
] | 2e126726d75069083f821e1bc3d3bc1c2a4946fb1765babc77eb06b40c13908b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from typing import NamedTuple
from typing import Optional
from typing import Set
import src.api.global_ as gl
import src.api.symboltable.symboltable
import src.api.utils
import src.api.symboltable
import src.api.check as chk
from src import symbols
from src.ast import No... | boriel/zxbasic | src/api/optimize.py | Python | gpl-3.0 | 19,483 | [
"VisIt"
] | c9a499c3b1f8d50d7b20be872629986caf050baf2fd3f35c6de5e8bc5b4ff460 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# ---------------------------------------------------------------------
# Copyright (c) 2012 Michael Hull.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are m... | mikehulluk/morphforge | src/morphforge/simulation/neuron/hocmodbuilders/__init__.py | Python | bsd-2-clause | 2,143 | [
"NEURON"
] | 757ced23f173ddee491ff94269f01b38cb316a89940cae5b501dd0c07173ec2a |
# Copyright (c) 2003-2013 LOGILAB S.A. (Paris, FRANCE).
# Copyright (c) 2009-2010 Arista Networks, Inc.
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
# 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
# ... | tlksio/tlksio | env/lib/python3.4/site-packages/pylint/checkers/base.py | Python | mit | 37,578 | [
"VisIt"
] | d35ca1c64609cb5653862a144df93eecb3fc1b3025dbe98e1a270f3d71d56d7e |
import tensorflow as tf
from tensorflow.contrib import rnn as rnn_cell
import numpy as np
import io
from util.tf_utils import tf_confusion_metrics
import inspect
import util.eval as eval
class Model:
"""
-- Copied from RNN TODO update to FC --
Tensorflow graph using ful
Tensorflow Graph using Fully ... | TUM-LMF/fieldRNN | cnn_model.py | Python | mit | 10,879 | [
"NEURON"
] | a4617f51a1d26ab8d7909342c73b7d881cc3c44783954161420aea4f8b1a51f9 |
"""
/******************************************************************************
This source file is part of the Avogadro project.
Copyright 2013 Kitware, Inc.
This source code is released under the New BSD License, (the "License").
Unless required by applicable law or agreed to in writing, software
di... | wadejong/avogadrolibs | avogadro/qtplugins/quantuminput/inputGenerators/apbs.py | Python | bsd-3-clause | 3,447 | [
"Avogadro"
] | 3f32011dedcbf1c0701aa03c633a284c7a11ca2ea3c73a3438cace24e5d40e8e |
# coding: utf-8
from __future__ import unicode_literals
import numpy as np
import unittest
import os
from pymatgen.analysis.structure_analyzer import VoronoiCoordFinder, \
solid_angle, contains_peroxide, RelaxationAnalyzer, VoronoiConnectivity, \
oxide_type
from pymatgen.io.vasp.inputs import Poscar
from pym... | rousseab/pymatgen | pymatgen/analysis/tests/test_structure_analyzer.py | Python | mit | 8,139 | [
"VASP",
"pymatgen"
] | d9d304ad1e3881d340a74a260a07a6414b75211694120d41760192e96b52ed92 |
""" VOMS2CSSyncronizer is a helper class containing the logic for synchronization
of the VOMS user data with the DIRAC Registry
"""
__RCSID__ = "$Id$"
from collections import defaultdict
from DIRAC import S_OK, S_ERROR, gLogger, gConfig
from DIRAC.Core.Security.VOMSService import VOMSService
from DIRAC.Core.Uti... | chaen/DIRAC | ConfigurationSystem/Client/VOMS2CSSynchronizer.py | Python | gpl-3.0 | 19,777 | [
"DIRAC"
] | 99a1bd8c15c18ccaa91e9e13e0b475073978f2ddbc58c5388666aaf0cb517559 |
import datetime
import json
from flask import Flask, g, render_template, flash, redirect, url_for, request, jsonify, abort, send_from_directory, session
from flask.ext.login import LoginManager, UserMixin, login_user, login_required, logout_user, current_user
from flask.ext.babel import Babel, get_locale, get_timezone... | buckket/weltklang | lib/rfk/site/__init__.py | Python | bsd-3-clause | 17,628 | [
"VisIt"
] | 0ad7b8a5c207662143b2f6199928f35ee9e993398d3527249935e275e593e434 |
''' Use this file to hand register multiple depth cameras with the 3D visualizer
Procedure:
1) Modify the scrip below for your files
2) After adding points, click the mayavi button in the window and add Transformation to the scene. Drag the second points to the transformation.
3) Manually match the two scenes
4) Click... | colincsl/pyKinectTools | pyKinectTools/utils/AlignCameras.py | Python | bsd-2-clause | 7,960 | [
"Mayavi"
] | 3ad16b0653dca2714dc6faafb474df1297b1e52b951965d9bf323d787827e739 |
# .. coding: utf-8
# $Id: __init__.py 7745 2014-02-28 14:15:59Z milde $
# Author: Engelbert Gruber, Günter Milde
# Maintainer: docutils-develop@lists.sourceforge.net
# Copyright: This module has been placed in the public domain.
"""LaTeX2e document tree Writer."""
__docformat__ = 'reStructuredText'
# code contributi... | havard024/prego | venv/lib/python2.7/site-packages/docutils/writers/latex2e/__init__.py | Python | mit | 124,479 | [
"VisIt"
] | f7b907e5eb9dfd17bef49ec0d229309bba022f53e262dac0739cf2f17b884c87 |
# Copyright (c) 2016. Mount Sinai School of Medicine
#
# 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 o... | hammerlab/isovar | test/testing_helpers.py | Python | apache-2.0 | 1,658 | [
"pysam"
] | 41a012bfb4d9900c053f9f714e2dc688e2c36b6074b3be4cf56bd0326ed26604 |
"""Functions for finding chains in a graph."""
import networkx as nx
from networkx.utils import not_implemented_for
@not_implemented_for("directed")
@not_implemented_for("multigraph")
def chain_decomposition(G, root=None):
"""Returns the chain decomposition of a graph.
The *chain decomposition* of a graph w... | SpaceGroupUCL/qgisSpaceSyntaxToolkit | esstoolkit/external/networkx/algorithms/chains.py | Python | gpl-3.0 | 6,573 | [
"VisIt"
] | 98659562848b309a52a072bc8e401ed8250602a8c17d336c2f823feee3b34d14 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright (C) 2014-2016 Simone Donadello
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) an... | simondona/img-fft-filter-bec-tn | libraries/fitting.py | Python | gpl-3.0 | 7,664 | [
"Gaussian"
] | 88738df7593baabd2341056fbfcc132c01d061531ae04b8950fa6877a2a9b105 |
"""
Contains a variety of sensory models, specifically models for the
visual pathway.
"""
import topo
import param
import numbergen
import lancet
import numpy
import imagen
from imagen.patterncoordinator import PatternCoordinator, PatternCoordinatorImages
from topo.base.arrayutil import DivideWithConstant
from topo.... | ioam/topographica | topo/submodel/earlyvision.py | Python | bsd-3-clause | 15,036 | [
"Gaussian"
] | bf669af306e46e01435c2e99b16a50c2d9958f6485032dc9d9bb87c8eb73bb8c |
import numpy as np
from sklearn.utils.testing import (assert_allclose, assert_raises,
assert_equal)
from sklearn.neighbors import KernelDensity, KDTree, NearestNeighbors
from sklearn.neighbors.ball_tree import kernel_norm
def compute_kernel_slow(Y, X, kernel, h):
d = np.sqrt(((Y... | depet/scikit-learn | sklearn/neighbors/tests/test_kde.py | Python | bsd-3-clause | 4,720 | [
"Gaussian"
] | 08fb640bf21f8b0fc0e4c81c30b4e8c9bf8ba04ecce8ee95ce9bc00ae20a8a3f |
"""
The utility functions used in ORCA calculations are collected.
Notice some functions are general so that they can be used for other DFT tools.
"""
def findStrings(afile,substr):
lines=[]
with open(afile) as astr:
for line in astr:
if substr in line:
lines.append(line)
return lines
def findFinalEnergy... | jskDr/jamespy_py3 | jorca.py | Python | mit | 1,132 | [
"ORCA"
] | 3849f4c1b643ad6ae9b2128c88ef46a8112198218f94265fc5ff98f10365106e |
###########################################################################
# Mean prediction from Gaussian Processes based on classifier_libsvm_minimal_modular.py
###########################################################################
from numpy import *
from numpy.random import randn
from shogun.Features import *... | ratschlab/ASP | examples/undocumented/python_modular/regression_gaussian_process_modular.py | Python | gpl-2.0 | 1,012 | [
"Gaussian"
] | 9adb4e90c6ccb81f8fa9c922a7930fca1aade720c0e8ba4c1ee46e62786c4c64 |
#!/usr/bin/env python
import sys
import subprocess
from setuptools import setup, find_packages
def check_bwa():
p = subprocess.Popen(['bwa'], stderr=subprocess.PIPE)
for line in p.stderr:
line = line.decode()
if line.startswith('Version:'):
major, minor, sub = line.strip().split()[... | adamewing/tebreak | setup.py | Python | mit | 2,813 | [
"BWA",
"pysam",
"scikit-bio"
] | e443e24f8546f8bb45b6fb1710e000cd1f94ce020a8ec4644615c14bb4923fb8 |
# -*- coding: utf-8 -*-
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
Built-in distribution-creation functions.
"""
from warnings import warn
import numpy as np
from astropy import units as u
from .core import Distribution
__all__ = ['normal', 'poisson', 'uniform']
def normal(center, *, std=... | bsipocz/astropy | astropy/uncertainty/distributions.py | Python | bsd-3-clause | 6,437 | [
"Gaussian"
] | c52c1a0fc56b735ae4564e411721ce58c40daeccb1f417d4845e9c1c178863e0 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007 Zsolt Foldvari
# Copyright (C) 2008-2009 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; eithe... | SNoiraud/gramps | gramps/plugins/docgen/gtkprint.py | Python | gpl-2.0 | 20,880 | [
"Brian"
] | de3f058e14e231ae1d54b59ba44a470cd9fed047c30a100b25b0da52488b77b0 |
import sgmllib
import Bio.File
"""
The LocusLink site is:
http://www.ncbi.nlm.nih.gov/LocusLink/
Parses a Locus web page.
"""
import warnings
warnings.warn("Bio.LocusLink was deprecated, as NCBI's LocusLink was superceded by Entrez Gene. If you still need this module, please get in touch with the Biopython developers... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/LocusLink/web_parse.py | Python | apache-2.0 | 26,686 | [
"Biopython"
] | 7cf57d65cd640cbc1003d7c9d5f6c8171613f4edf81f1bcff1d94696581f3a1d |
#!/usr/bin/env python
################################################################################
# Copyright (C) 2014, 2015 GenAP, McGill University and Genome Quebec Innovation Centre
#
# This file is part of MUGQIC Pipelines.
#
# MUGQIC Pipelines is free software: you can redistribute it and/or modify
# it und... | ccmbioinfo/mugqic_pipelines | bfx/blast.py | Python | lgpl-3.0 | 3,916 | [
"BLAST"
] | 25114f00809092ca5cb24679ff0950eae36f0031e8e8f0fd5cea40890685b40b |
#########
# BatPrepare.py
# Lithium-ion-batteries will loose their capacity, if they were stored full powered.
# This program will rotate the propellers of the drone (but not make it flight), till battery reached 50% capacity.
# Dependencies: a POSIX OS, PS-Drone-API 2.0 beta or higher.
# (w) J. Philipp de Graaff, www.... | reixd/ps-drone | tools/batPrepare.py | Python | artistic-2.0 | 2,122 | [
"VisIt"
] | 7a591910615a4ad54064c598f781b2e75aa4315e9fce3af6ebe4be808cf51002 |
# 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 yambopy import *
import matplotlib.gridspec as gridspec
from scipy.optimize import curve_fit
import os
############
# SETTIN... | alexandremorlet/yambopy | scripts/realtime/plot_occ2.py | Python | bsd-3-clause | 7,553 | [
"DIRAC"
] | edf26ecc4492eab6cb8656914ac8484cdb5de57c254c4206b6aa3a97db1e9f0f |
#
# Copyright (C) 2013-2019 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... | KaiSzuttor/espresso | testsuite/python/mpiio.py | Python | gpl-3.0 | 4,479 | [
"ESPResSo"
] | 8d7a0c73123414891197720ebb4e58d8e55d4709f0bd5ad52433306d0741402d |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RRnaseqmap(RPackage):
"""rnaSeq secondary analyses
The rnaSeqMap library provides ... | LLNL/spack | var/spack/repos/builtin/packages/r-rnaseqmap/package.py | Python | lgpl-2.1 | 1,493 | [
"Bioconductor"
] | 30804a63f179094568dc0faab60bf8698228424a772b615fe953c6008e7c6aa8 |
# Copyright (c) 2012 OpenStack Foundation
# All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless ... | zhimin711/nova | nova/tests/unit/compute/test_resource_tracker.py | Python | apache-2.0 | 56,861 | [
"exciting"
] | 0e23503459e6743a27ea11a4ad3e2e57b66d7119e25a4b840e1efb477d0cdd89 |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publish... | thica/ORCA-Remote | src/ORCA/vars/Access.py | Python | gpl-3.0 | 6,419 | [
"ORCA"
] | f6ebcca25569c8deb21f28b8650c7a5d8d22d3c91cb7d9f69571c7a6ffabb963 |
import tkSimpleDialog
import tkMessageBox
from pymol.wizard import Wizard
from pymol import cmd, preset
import os,sys
cwd = os.getcwd() #ensure pymol can find libraries
sys.path.append(cwd)
import selector_prot
import p3d.protein
import p3d.geo
cmd.set_wizard(selector.selector('{name}','{chain}','{resid}','{resid2}')... | tmorrell/SamStruct | inputs/pymol_view_prot.py | Python | gpl-2.0 | 749 | [
"PyMOL"
] | a1ad37ad94d59216bfa33ecf871962b4fb4dc6d97961369b4ab71e282d2808d5 |
# -*- coding: utf-8 -*-
#
# ase-espresso documentation build configuration file, created by
# sphinx-quickstart on Wed Nov 25 10:09:02 2015.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
... | lmmentel/ase-espresso | docs/source/conf.py | Python | gpl-3.0 | 10,437 | [
"ASE",
"ESPResSo"
] | 8319fe091dbe45e0193de264396c1b2a0ac95544ad8e023ef1a606e436dd5141 |
# 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 | d3pm/images/utils.py | Python | apache-2.0 | 10,056 | [
"Gaussian"
] | 85bb0023b21d980ef2a5a545910941e7dd531c16f2cec63899678162a44cced0 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
'''
Created on Mar 5, 2012
'''
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Sh... | sonium0/pymatgen | pymatgen/alchemy/tests/test_transmuters.py | Python | mit | 4,528 | [
"pymatgen"
] | 3bfa497c09a950bedfb00a3d32a7386fac3e37d7ea87fedf02457a4d9a17d492 |
# -*- coding: utf-8 -*-
""" Chemical Signalling model loaded into moose can be save into Genesis-Kkit format """
__author__ = "Harsha Rani"
__copyright__ = "Copyright 2017, Harsha Rani and NCBS Bangalore"
__credits__ = ["NCBS Bangalore"]
__license__ = "GNU GPL"
__version__ =... | BhallaLab/moose-core | python/moose/genesis/writeKkit.py | Python | gpl-3.0 | 39,455 | [
"MOOSE"
] | 70293b9dbb9c2ce00638f0c317e72255bb6f7650be9c2a0462c293f16d188c29 |
# qsub -- utilities for batch submission systems
# Copyright (c) 2010 Oliver Beckstein <orbeckst@gmail.com>
# Made available under GNU Pulic License v3.
"""
:mod:`gromacs.qsub` -- utilities for batch submission systems
=============================================================
The module helps writing submission s... | PicoCentauri/GromacsWrapper | gromacs/qsub.py | Python | gpl-3.0 | 18,105 | [
"Gromacs"
] | a3cc64931cb15cc1d35a27289ab8b7f46287ed07a351a558bb616d6206599bc7 |
#+
#
# This file is part of h5py, a low-level Python interface to the HDF5 library.
#
# Copyright (C) 2008 Andrew Collette
# http://h5py.alfven.org
# License: BSD (See LICENSE.txt for full license)
#
# $Date$
#
#-
"""
Provides high-level Python objects for HDF5 files, groups, and datasets.
Objects in t... | qsnake/h5py | h5py/highlevel.py | Python | bsd-3-clause | 56,170 | [
"VisIt"
] | c9b97e1c6921fb3063710570386492b4add31678832bf722465dad82d4c67225 |
import tempfile
import numpy as np
from pygmin.systems import AtomicCluster
from pygmin.potentials.ljpshiftfast import LJpshift
from pygmin.utils.xyz import write_xyz
from pygmin.mindist import CoMToOrigin
__all__ = ["BLJCluster"]
class BLJCluster(AtomicCluster):
"""
define the System class for a binary Lenn... | js850/PyGMIN | pygmin/systems/bljcluster.py | Python | gpl-3.0 | 5,755 | [
"PyMOL"
] | dd4dc35f61c0c4b6788b606e011c5278eaa0cc30ffaadff2b1bf23c0353ef094 |
"""
This module contain solvers for all kinds of equations:
- algebraic or transcendental, use solve()
- recurrence, use rsolve()
- differential, use dsolve()
- nonlinear (numerically), use nsolve()
(you will need a good starting point)
"""
from __future__ import print_function, division
fr... | jaimahajan1997/sympy | sympy/solvers/solvers.py | Python | bsd-3-clause | 123,374 | [
"Gaussian"
] | 97e38f46cae7f0f43950e661cf113f3785b14f37172b7c4dc67b9367a4bf43cc |
#! /usr/bin/python2
import subprocess
import sys
import os
import time
from subprocess import PIPE
import socket
default_params = ''
output_file_prefix = 'output'
if len(sys.argv) > 1:
output_file_prefix = sys.argv[1]
#
# SCENARIO
#
# 0: radial dam break
# 1: gaussian
# 2: balanced steady state u
# 3: balanced ste... | schreiberx/sweet | archive/benchmarks_plane/rexi_tests_stfc/test_nxq/params.py | Python | mit | 5,377 | [
"Gaussian"
] | 65519e408684877a4b6656f6a1013f184964f77a5477fd99741b0f4959504d26 |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | jhseu/tensorflow | tensorflow/python/autograph/core/converter.py | Python | apache-2.0 | 13,320 | [
"VisIt"
] | e22dc79a355f2461bbb8a889476065d1ff01ad708446fa2b76746d5e67551017 |
# -*- coding: utf-8 -*-
# YAFF is yet another force-field code.
# Copyright (C) 2011 Toon Verstraelen <Toon.Verstraelen@UGent.be>,
# Louis Vanduyfhuys <Louis.Vanduyfhuys@UGent.be>, Center for Molecular Modeling
# (CMM), Ghent University, Ghent, Belgium; all rights reserved unless otherwise
# stated.
#
# This file is pa... | molmod/yaff | yaff/pes/scaling.py | Python | gpl-3.0 | 7,782 | [
"CRYSTAL"
] | c58e6a8a9dd61af53570bf45483a4ea27baaed525391d006af3b3bf67b614bd5 |
import functools
import inspect
import sys
import warnings
from collections import defaultdict
from collections import deque
from collections import OrderedDict
from typing import Dict
from typing import List
from typing import Tuple
import attr
import py
import _pytest
from _pytest._code.code import FormattedExcinfo... | alfredodeza/pytest | src/_pytest/fixtures.py | Python | mit | 56,037 | [
"VisIt"
] | 19949c2d61701327e9dac4b8b3acb9f59686a2d2d67d1ad2f74836d46c668ecb |
# -*- coding: utf-8 -*-
#------------------------------------------------------------
# pelisalacarta - XBMC Plugin
# Canal para filmenoi
# http://blog.tvalacarta.info/plugin-xbmc/pelisalacarta/
#------------------------------------------------------------
import urlparse,urllib2,urllib,re
import os, sys
from core im... | superberny70/plugin.video.pelisalacarta-3-9X | pelisalacarta/channels/filmenoi.py | Python | gpl-3.0 | 5,966 | [
"ADF"
] | 6749a3b26122cfb4132e8d741ba1391056fc19fa7314fafa0f828b6894204241 |
import time
import os
import matplotlib.pyplot as plt
import numpy as np
import seaborn as sns
import mbuild as mb
import metamds as mds
import mdtraj as md
def build_monolayer(chain_length, n_molecules, **kwargs):
from mbuild.examples import AlkaneMonolayer
pattern = mb.Random2DPattern(n_molecules)
mon... | iModels/demos | demos/monolayer/monolayer.py | Python | mit | 2,860 | [
"MDTraj"
] | b93a0c02eee88f079eae49e3b1cb042f0ee83ed02704b2f0afc7d0899f02a879 |
# This file is part of Buildbot. Buildbot 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, version 2.
#
# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without eve... | denny820909/builder | lib/python2.7/site-packages/buildbot-0.8.8-py2.7.egg/buildbot/status/web/waterfall.py | Python | mit | 33,047 | [
"VisIt"
] | 559d2e307402c1e5a11d69d73ad0789d0592dda288ef3669eb4136bb9c6f1538 |
################################################################################
# #
# Copyright (C) 2010-2018 The ESPResSo project #
# ... | hmenke/espresso | doc/tutorials/06-active_matter/EXERCISES/enhanced_diffusion.py | Python | gpl-3.0 | 5,115 | [
"ESPResSo"
] | 6a01fa560a37c082e4a40dc76d02c3dd0edf9e54b5830a840cac796be5b8e247 |
"""
Overview
--------
This module implements the Multiple Imputation through Chained
Equations (MICE) approach to handling missing data in statistical data
analyses. The approach has the following steps:
0. Impute each missing value with the mean of the observed values of
the same variable.
1. For each variable in t... | bert9bert/statsmodels | statsmodels/imputation/mice.py | Python | bsd-3-clause | 45,391 | [
"Gaussian"
] | 362ec9c64bb6dd25928aed5df7cf257c2becf0a48137c069e6e87fcff89baabd |
"""
.. _tut_forward:
Head model and forward computation
==================================
The aim of this tutorial is to be a getting started for forward
computation.
For more extensive details and presentation of the general
concepts for forward modeling. See :ref:`ch_forward`.
"""
import mne
from mne.datasets i... | teonlamont/mne-python | tutorials/plot_forward.py | Python | bsd-3-clause | 8,449 | [
"Mayavi"
] | 52c9b4122dae3c49b7f37111bea44271fa76f5d15926066c6ead3a5553469e0e |
from sympy import Basic, Symbol, Integer, C, S, Dummy, Rational, Add, Pow
from sympy.core.numbers import Zero
from sympy.core.sympify import sympify, converter, SympifyError
from sympy.core.compatibility import is_sequence
from sympy.polys import Poly, roots, cancel
from sympy.simplify import simplify as sympy_simplif... | GbalsaC/bitnamiP | venv/lib/python2.7/site-packages/sympy/matrices/matrices.py | Python | agpl-3.0 | 103,046 | [
"DIRAC",
"Gaussian"
] | 0a35b942d30310507bceeeb9f85455e68b135579a2bc43a8923d6f9f3878013a |
import sys
import random
import time
import readline
import obj
import utils
import entities
def personInteraction():
entities.player.location = entities.getLocation('Interact')
personType = random.randint(1, 3)
if personType == 1:
person = [random.choice(entities.enemies), random.choice(entities.... | V1Soft/textbasedgame | locations.py | Python | gpl-3.0 | 10,127 | [
"VisIt"
] | f62e9f14d4038fe8a3bbacb39a8c88c33fca0dd4ed9e346676110d6637bf931c |
""" ProxyManagementAPI has the functions to "talk" to the ProxyManagement service
"""
import os
import datetime
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.ConfigurationSystem.Client.Helpers import Registry
from DIRAC.Core.Utilities import ThreadSafe, DIRACSingleton
from DIRAC.Core.Utilities.DictCache import D... | fstagni/DIRAC | FrameworkSystem/Client/ProxyManagerClient.py | Python | gpl-3.0 | 19,222 | [
"DIRAC"
] | 29428fb95f26f5c7fdc640b5de59da95499ca9911086ef2c94c7636ba87999c4 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2013, Christoph Reimann
crystalExe = '/home/chr/sys/bin/Pcrystal09'
crystalVersion = 'CRYSTAL09 v2.0.1'
mpi = '/home/chr/sys/openmpi-1.4.1/bin/mpirun -np 8'
copyCmd = 'cp'
grepCmd = 'grep'
# basis set restrictions
exponentLowerLimit = 0.2
import minuit
im... | chrr/Pcrystal09_bsopt | Pcrystal09_bsopt.py | Python | bsd-2-clause | 14,025 | [
"CRYSTAL"
] | 59bff4bda24fbbdfa39fa1e50d9f6065e236fda5e2621d671051fcefb8823d5c |
#!/usr/bin/env python3
"""
Clean IMGT germline fasta files for IgBLAST database build
"""
import Bio
from pkg_resources import parse_version
from sys import argv
from Bio import SeqIO
from Bio.SeqRecord import SeqRecord
# Get input and output file names
in_file = argv[1]
out_file = argv[2]
# Load sequences into memor... | psathyrella/partis | packages/immcantation/scripts/clean_imgtdb.py | Python | gpl-3.0 | 987 | [
"Biopython"
] | df740f45227292cf32a5aa362de410f185ef5e95b3eefa2df6320dfd914eae2d |
#!/usr/bin/python
# -*- mode: python; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-
#
# $Id$
#
# Copyright (c) Erik Lindahl, David van der Spoel 2003-2007.
# Coordinate compression (c) by Frans van Hoesel.
# Python wrapper (c) by Roland Schulz
#
# IN contrast to the rest of Gromacs, XDRFILE is distr... | kmtu/xdrfile-d | src/python/sample.py | Python | bsd-2-clause | 1,977 | [
"Gromacs"
] | b976279f16423f3f3b0084559a1a0a0f1cd14de7c3f56067b8f835f697d5dfaf |
# maxentropy.py: Routines for fitting maximum entropy models.
# Copyright: Ed Schofield, 2003-2006
# License: BSD-style (see LICENSE.txt in main source directory)
# Future imports must come before any code in 2.5
from __future__ import division
__author__ = "Ed Schofield"
__version__ = '2.1'
__changelog__ = """
This... | stefanv/scipy3 | scipy/maxentropy/maxentropy.py | Python | bsd-3-clause | 67,591 | [
"Gaussian"
] | 4f7c9b06ff19268b92d97f3b356b491510d35b3000fffcaa3afd86a068f6e1d4 |
#pylint: disable=C0111
#pylint: disable=W0621
from lettuce import world, step
from django.contrib.auth.models import User
from lettuce.django import django_url
from student.models import CourseEnrollment
from common import course_id, course_location
from problems_setup import PROBLEM_DICT
TEST_SECTION_NAME = 'Test Se... | syjeon/new_edx | lms/djangoapps/courseware/features/navigation.py | Python | agpl-3.0 | 6,853 | [
"VisIt"
] | db5f36a8d58f6c85d6e3907257524be6a7c9840c4154bd0d28364d69deb3a4bc |
"""Transform a string with Python-like source code into SymPy expression. """
from __future__ import print_function, division
from .sympy_tokenize import \
generate_tokens, untokenize, TokenError, \
NUMBER, STRING, NAME, OP, ENDMARKER
from keyword import iskeyword
import ast
import re
import unicodedata
im... | alephu5/Soundbyte | environment/lib/python3.3/site-packages/sympy/parsing/sympy_parser.py | Python | gpl-3.0 | 27,927 | [
"VisIt"
] | 5a134f7e5f72ad3612abba19102e951365535d9196e47cb5c93ceab130f8695d |
# Copyright 2013 Cloudbase Solutions SRL
# Copyright 2013 Pedro Navarro Perez
# 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... | javacruft/networking-hyperv-debian | hyperv/neutron/hyperv_neutron_agent.py | Python | apache-2.0 | 14,932 | [
"VisIt"
] | d1fdf7849476b22d3b29392311db5712b605b97cac9fb3c735dbacf5ad1ff357 |
import sublime
import sublime_plugin
import traceback
import codecs
import os
from datetime import datetime
from threading import Thread
import signal, subprocess
import json
import webbrowser
is_sublime_text_3 = int(sublime.version()) >= 3000
if is_sublime_text_3:
from .base_command import BaseCommand
from .... | nickgzzjr/sublime-gulp | gulp.py | Python | mit | 16,770 | [
"GULP"
] | adf62676d903a4f3ca89f90147cbd9fb03507a293152eb2e0a1304fda44ae904 |
#!/usr/bin/env python
__author__ = 'Mike McCann,Duane Edgington,Reiko Michisaki,Danelle Cline'
__copyright__ = '2017'
__license__ = 'GPL v3'
__contact__ = 'duane at mbari.org'
__doc__ = '''
Master loader for all KISS/CANON April season activities in 2017
Mike McCann, Duane Edgington, Danelle Cline
MBARI 7 April 2017... | stoqs/stoqs | stoqs/loaders/CANON/loadCANON_april2017.py | Python | gpl-3.0 | 20,155 | [
"NetCDF"
] | 45ef867c2d9d66e853ed39c7e233cdbd6804041bb700a8dd512d077a71198cda |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | casawa/mdtraj | mdtraj/tests/test_xml.py | Python | lgpl-2.1 | 1,353 | [
"MDTraj"
] | e3ce7a44b5bf40b3dc5caf71ee8154757a88d45b06f815f9db3df302027a4fc7 |
from ase import Atoms
from gpaw import GPAW, FermiDirac
k = 7
kT = 0
h = 0.18
a = 5.4
b = a/2
atoms = Atoms('Si2',
positions=([0, 0, 0],
[b/2, b/2, b/2]),
cell=([0, b, b],
[b, 0, b],
[b, b, 0]),
pbc=True)
c... | qsnake/gpaw | gpaw/test/big/dfpt/Si_AH.py | Python | gpl-3.0 | 548 | [
"ASE",
"GPAW"
] | e02ceabe5129f96a98e78bbae6736fc4b404bb3ea980038acc1b024f08b5eada |
#!/usr/bin/env python3
#* 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/lgp... | nuclear-wizard/moose | python/MooseDocs/test/tree/test_syntax_tree.py | Python | lgpl-2.1 | 2,774 | [
"MOOSE"
] | 09be17eaec1052cad968a858ddeab54f2b97cb7c013e7fbde7fd953d9244b92c |
#-------------------------------------------------------------------------------
# Name: output
# Purpose: Encapsulation of parsing/handling of data from computation
# textual output.
#
# Author: Brian Skinn
# bskinn@alum.mit.edu
#
# Created: 16 Feb 2015
# Copyright: ... | bskinn/opan | opan/output.py | Python | mit | 26,931 | [
"Brian",
"ORCA"
] | bf5f13cc9545d8cdc7e0f88c6a08620eb19b5b3a684ef84fb03894242630c0cf |
""" This is a test of the chain
SiteStatus -> ResourceStatusClient -> ResourceStatusDB
It supposes that the DB is present, and that the service is running
"""
# pylint: disable=invalid-name,wrong-import-position
from datetime import datetime
import unittest
import sys
import DIRAC
DIRAC.initialize() # Init... | DIRACGrid/DIRAC | tests/Integration/ResourceStatusSystem/Test_SiteStatus.py | Python | gpl-3.0 | 5,867 | [
"DIRAC"
] | dde91a631335164e313f8353e96fb27e7b5630948a53987ef44f1c5a45ff8f7c |
# -*- coding: utf-8 -*-
from south.utils import datetime_utils as datetime
from south.db import db
from south.v2 import DataMigration
from django.db import models
class Migration(DataMigration):
def forwards(self, orm):
"Write your forwards methods here."
# Note: Don't use "from appname.models imp... | myvoice-nigeria/myvoice | myvoice/clinics/migrations/0039_initial_data_state_lga_lga2_lgatemp.py | Python | bsd-2-clause | 13,520 | [
"VisIt"
] | a2e087460f89ae2127d1af3b33a921134b67c18730dd03a3225fe13b66c3a6e5 |
# This file is part of PyEMMA.
#
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
#
# PyEMMA 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 vers... | gph82/PyEMMA | pyemma/coordinates/tests/test_save_trajs.py | Python | lgpl-3.0 | 6,916 | [
"MDTraj"
] | d822eb1f6a9190b57c4450841199b3e89244914d740f64e8e67a613829c864c9 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2013 David Doukhan <doukhan@limsi.fr>
# This file is part of TimeSide.
# TimeSide is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or... | ANR-DIADEMS/timeside-diadems | timeside/plugins/diadems/limsi_diarization.py | Python | gpl-2.0 | 8,304 | [
"Gaussian"
] | 268f0e8b4e7743a7f7d2900c4238d9e7d7851be56eadd96e22b10844a27a9cd3 |
# Copyright (C) 2010-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later ... | mkuron/espresso | testsuite/python/dipolar_mdlc_p3m_scafacos_p2nfft.py | Python | gpl-3.0 | 7,409 | [
"ESPResSo"
] | 8f34595fd119ccd0553beaf54cd00cc1784c851fac1c2132a37bda4097db0042 |
import re
import click
import six
from httpie.context import Environment
from httpie.core import main as httpie_main
from parsimonious.exceptions import ParseError, VisitationError
from parsimonious.grammar import Grammar
from parsimonious.nodes import NodeVisitor
from six import BytesIO
from six.moves.urllib.parse i... | Yegorov/http-prompt | http_prompt/execution.py | Python | mit | 11,589 | [
"VisIt"
] | e48a4baf3c549dfab8ff9fc1c62c9cdb1c40a00322e1edacebf35edce59c95e2 |
"""
Test LMS Notes
"""
from unittest import skip
import random
from uuid import uuid4
from datetime import datetime
from nose.plugins.attrib import attr
from common.test.acceptance.tests.helpers import UniqueCourseTest, EventsTestMixin
from common.test.acceptance.fixtures.course import CourseFixture, XBlockFixtureDesc
... | louyihua/edx-platform | common/test/acceptance/tests/lms/test_lms_edxnotes.py | Python | agpl-3.0 | 60,053 | [
"VisIt"
] | b952c56f874a107c3cbb0fd80ed18c9e628d6e930e564a7804d08e4fae77d50e |
import sys
import maya.OpenMaya as OpenMaya
import maya.OpenMayaMPx as OpenMayaMPx
import maya.cmds as cmds
kPluginNodeName = "MitsubaRoughCoatingShader"
kPluginNodeClassify = "/shader/surface"
kPluginNodeId = OpenMaya.MTypeId(0x8700F)
class roughcoating(OpenMayaMPx.MPxNode):
def __init__(self):
OpenMayaM... | hpd/MitsubaForMaya | plug-ins/mitsuba/materials/roughcoating.py | Python | mit | 7,843 | [
"Amber"
] | 3593436990da693a49b9ebc6ace50467664f09d254b1b7929b63f1dc27d421ed |
"""Universal feed parser
Handles RSS 0.9x, RSS 1.0, RSS 2.0, CDF, Atom 0.3, and Atom 1.0 feeds
Visit https://code.google.com/p/feedparser/ for the latest version
Visit http://packages.python.org/feedparser/ for the latest documentation
Required: Python 2.4 or later
Recommended: iconv_codec <http://cjkpython.i18n.org... | boompieman/iim_project | project_python2/lib/python2.7/site-packages/pattern/web/feed/feedparser.py | Python | gpl-3.0 | 167,911 | [
"NetCDF",
"VisIt"
] | 1c369a00338df4c6fbfd5b9c0aafb638b857c4f355cdac46a0f17a44256f6549 |
import hashlib
import numpy as np
from cryspy import numbers as nb
from cryspy import geo as geo
from cryspy import blockprint as bp
from cryspy import tables
class Drawable():
def __init__(self, name, pos):
assert isinstance(name, str), \
"First argument of crystal.Drawable.__init__(...) must ... | tobias-froehlich/cryspy | cryspy/crystal.py | Python | gpl-3.0 | 26,189 | [
"CRYSTAL"
] | b47f63b611843193a9c325322c41acd11c6f2abb7f89f36c051ce23ec82a8972 |
#!/usr/bin/env python
import argparse
import copy
import logging
import re
import sys
from BCBio import GFF
logging.basicConfig(level=logging.INFO)
log = logging.getLogger(name='blastxml2gff3')
__author__ = "Eric Rasche"
__version__ = "0.4.0"
__maintainer__ = "Eric Rasche"
__email__ = "esr@tamu.edu"
__doc__ = """
B... | yhoogstrate/tools-iuc | tools/blastxml_to_gapped_gff3/blastxml_to_gapped_gff3.py | Python | mit | 9,199 | [
"BLAST"
] | 4efa24a1e00eb63403d4463aee1eb70fb144cb95a5dd265c63c7aea7fec48f2c |
"""Testing for Gaussian process regression """
# Author: Jan Hendrik Metzen <jhm@informatik.uni-bremen.de>
# License: BSD 3 clause
import numpy as np
from scipy.optimize import approx_fprime
from sklearn.gaussian_process import GaussianProcessRegressor
from sklearn.gaussian_process.kernels \
import RBF, Constan... | zorroblue/scikit-learn | sklearn/gaussian_process/tests/test_gpr.py | Python | bsd-3-clause | 13,791 | [
"Gaussian"
] | 4d8bbeb18d27f09dbb559e3330f2da6d1ef9d7e84e5aba83d86c77a63ef637e9 |
"""
Training costs for unsupervised learning of energy-based models
"""
import functools
import logging
import numpy as np
import sys
from theano import scan
import theano.tensor as T
from theano.compat.six.moves import zip as izip
from pylearn2.compat import OrderedDict
from pylearn2.costs.cost import Cost, DefaultD... | junbochen/pylearn2 | pylearn2/costs/ebm_estimation.py | Python | bsd-3-clause | 10,143 | [
"CDK"
] | 6d694d622a914dfbac1be90ec5c992dc29d488af25bba070318c34079f9afc85 |
#!/usr/bin/env python
#JSON {"lot": "RKS/6-31G(d)",
#JSON "scf": "CDIISSCFSolver",
#JSON "er": "cholesky",
#JSON "difficulty": 7,
#JSON "description": "Basic RKS DFT example with hybrid MGGA exhange-correlation functional (TPSS)"}
import numpy as np
from horton import * # pylint: disable=wildcard-import,unused-wi... | QuantumElephant/horton | data/examples/hf_dft/rks_water_hybmgga.py | Python | gpl-3.0 | 3,707 | [
"Gaussian"
] | 3d28612510d909969ff24e689f29a0bf972aac8a9bbc3f83a0e8bf2599ba5eec |
#pylint: disable=missing-docstring
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/... | harterj/moose | python/chigger/filters/BoxClipper.py | Python | lgpl-2.1 | 1,241 | [
"MOOSE",
"VTK"
] | a7cf17442fba320dc544a1930e2cf8903cf93d098353d0baaad2ffa27badd63e |
"""
An efficient implementation of the triple-plane view showing 3 cut planes
on volumetric data, and side views showing each cut, with a cursor to
move the other cuts.
This is an example of complex callback interaction. It builds on the
:ref:`example_volume_slicer` but has more complex logic. You should try
to unders... | LTS5/connectomeviewer | cviewer/visualization/volume/volume_slicer_advanced.py | Python | bsd-3-clause | 11,268 | [
"Mayavi",
"VTK"
] | 369d9bc29d78b53e01ca6381598f9e06a05ca1fe82235cac98f62cea939c45a8 |
# -*- coding: utf-8 -*-
# imports here
from aiida.parsers.exceptions import OutputParsingError
#
from aiida.orm.data.folder import FolderData
from aiida.orm.data.parameter import ParameterData
from aiida.orm.data.structure import StructureData
from aiida.orm.data.array import ArrayData
#
from aiida.parsers.plugins.vas... | abelcarreras/aiida_extensions | plugins/parsers/vasp/instruction/data/array_data_parser.py | Python | mit | 3,324 | [
"VASP",
"pymatgen"
] | 272195dc25cadd074db7fde495772afbe62eab401975c4027dc877dc061dc44c |
# ***** BEGIN LICENSE BLOCK *****
# Version: MPL 1.1/GPL 2.0/LGPL 2.1
#
# The contents of this file are subject to the Mozilla Public License Version
# 1.1 (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.mozilla.org/MPL/
#
# Softwa... | centrumholdings/buildbot | buildbot/db/connector.py | Python | gpl-2.0 | 44,327 | [
"Brian"
] | 38b57d0ad4d3c20fdc0bf92d06349cbf53dd96613e4d10e88672957d23fc7d91 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements classes and methods for processing LAMMPS output
files (log and dump).
"""
import glob
import re
from io import StringIO
import numpy as np
import pandas as pd
from monty.io import zopen
from mont... | vorwerkc/pymatgen | pymatgen/io/lammps/outputs.py | Python | mit | 5,940 | [
"LAMMPS",
"pymatgen"
] | 476f8849b041764da5e54eb0f68fd283817e7e02d480fbe12d09bdbe01f0e33a |
# -*- python -*-
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2003-2005 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
#
# This program is free software; you can redistribute it and/or modify
# it under... | SNoiraud/gramps | gramps/plugins/rel/rel_it.py | Python | gpl-2.0 | 21,059 | [
"Brian"
] | e3eb8e6930f5d464a94048c7ab492d723c4521afc342b86e9b07edc146e27ba5 |
import os
from os.path import join
import logging
import glob
import csv
from collections import namedtuple
import sys
import pprint
import pickle
import multiprocessing
cpu_count = multiprocessing.cpu_count()
# Project working directory, where samples will be linked to
samples_path = '/path/to/working_directory'
# ... | d-quinn/bio_quinn2013 | SNP_calling/DGRP_all/mglobals.py | Python | mit | 4,959 | [
"Bowtie"
] | b777e32a53a735c8c14fe0982b8305005ef197314b0b0211a6e40606028b1866 |
# Copyright 2019 Google Inc. 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 applicable law or... | googlegenomics/gcp-variant-transforms | gcp_variant_transforms/libs/header_merger_test.py | Python | apache-2.0 | 9,036 | [
"pysam"
] | 9946cac251443b38535281cae295bcca9dde8eb2b75ff978a2b345e4d8b4c1e5 |
# Copyright 2009 Brian Quinlan. All Rights Reserved.
# Licensed to PSF under a Contributor Agreement.
"""Implements ProcessPoolExecutor.
The follow diagram and text describe the data-flow through the system:
|======================= In-process =====================|== Out-of-process ==|
+----------+ +-... | prefetchnta/questlab | bin/x64bin/python/37/Lib/concurrent/futures/process.py | Python | lgpl-2.1 | 28,719 | [
"Brian"
] | f7bc62f4da1cc04912b6da0e772a106a4f3b63a87a7fac2720448c782266d097 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the G... | espressopp/espressopp | src/interaction/LennardJonesGromacs.py | Python | gpl-3.0 | 9,755 | [
"ESPResSo"
] | cf6e572935974f436c556a1f3e72ce05f087e8434fadea504a15b0d9d38e6c38 |
__author__ = 'Mikhail Pedrosa <mikhailj.pedrosa@gmail.com> e Arthur Costa <arthur.opa@gmail.com>'
__description__ = 'Methods for Plot Images, Vector and Graphs'
__version__ = '0.1'
__date__ = '13/04/2015'
import pyart
import matplotlib.pyplot as plt
from filters import *
from memory_profiler import profile
#@profile... | mikhailpedrosa/radar_wind-field | graphical.py | Python | gpl-2.0 | 9,193 | [
"Gaussian"
] | 1c08f0608627e91fa9c81fb70d2e880a5d367d5ef9a77510a57a015b81ad1a1d |
#!/galaxy/home/mgehrin/hiclib/bin/python
"""
Tool for filtering a tabular data file. Fields are separated by tabs, the
header line is denoted by a '#' in the first byte, comments are denoted by
a '#' at the start of any subsequent line.
Expressions can use column names as well as numbers. The -c options allows
cutti... | bxlab/HiFive_Paper | Scripts/HiCLib/bx-python-0.7.1/build/scripts-2.7/table_filter.py | Python | bsd-3-clause | 2,263 | [
"Galaxy"
] | 8cccee71e1170f3272ab6cc851cecb18a11b9fa41d0da4ac78fa9ea7f54e1766 |
#! /usr/bin/env python3
"""Main ProPhyle file.
Author: Karel Brinda <kbrinda@hsph.harvard.edu>
Licence: MIT
Example:
Download sequences:
$ prophyle download bacteria
Create an index for k=10 and the small testing bacterial tree:
$ prophyle index -k 10 -s 0.1 ~/prophyle/bacteria.nw ~/proph... | karel-brinda/prophyle | prophyle/prophyle.py | Python | mit | 48,225 | [
"BWA"
] | ffe9a11b202539a90a99448d2935ffba9055831a9e9d115c158d5f57240d08ee |
# Placeholder because units moved
# Remove this in version 1.0
from __future__ import absolute_import
import warnings
with warnings.catch_warnings():
warnings.simplefilter('always', DeprecationWarning)
warnings.warn(("units has moved to MDAnalysis.units "
"and will be removed from here in re... | kain88-de/mdanalysis | package/MDAnalysis/core/units.py | Python | gpl-2.0 | 394 | [
"MDAnalysis"
] | ece0995e2f588c98dcbe547071ac084acaa9d1f262b47555214d8724d3c6209a |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import numpy as np
import unittest
import os
from pymatgen.analysis.find_dimension import find_dimension
from pymatgen.io.vasp.inputs import Poscar
from pymatgen.io.vas... | nisse3000/pymatgen | pymatgen/analysis/tests/test_find_dimension.py | Python | mit | 1,109 | [
"VASP",
"pymatgen"
] | 14274f369ae8f5946b0dc90cc83115ea3af00aa498a000e69abf628946d36c33 |
#!/usr/bin/env python
import sys
from g03 import *
from g09 import *
from g16 import *
from gamess import *
from nwchem import *
from orca import *
from qchem import *
from xyz import *
def guess(filename):
'''Returns the correct class needed to parse filename, if it exists.'''
#
# Dictionary of unique ... | dpadula85/ExSPy | stable/QM_parser/parser/guess.py | Python | gpl-3.0 | 1,657 | [
"GAMESS",
"Gaussian",
"NWChem",
"ORCA"
] | 9ef2edd70a263b27f55376b4a14467f05ae5d8bf6833ea7d5ad21ec4a025601a |
import logging
from functools import reduce
import nanoget.utils as ut
import pandas as pd
import sys
import pysam
import re
from Bio import SeqIO
import concurrent.futures as cfutures
from itertools import repeat
def process_summary(summaryfile, **kwargs):
"""Extracting information from an albacore summary file.... | wdecoster/nanoget | nanoget/extraction_functions.py | Python | gpl-3.0 | 18,527 | [
"pysam"
] | d42461c32e146c526faff721abac5bd8269946b2ccdf2e4cfe10c1ecc139732a |
#!/usr/bin/env python
# encoding: utf-8
################################################################################
#
# RMG - Reaction Mechanism Generator
#
# Copyright (c) 2009-2011 by the RMG Team (rmg_dev@mit.edu)
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of thi... | faribas/RMG-Py | rmgpy/molecule/symmetry.py | Python | mit | 20,083 | [
"RDKit"
] | cc788b55124cb248691f2445c33f4acf85897cf600e0241131206890a13c0c61 |
# -*- coding: utf-8 -*-
"""
Bok choy acceptance tests for LTI xblock
"""
from __future__ import absolute_import
import os
from common.test.acceptance.pages.lms.instructor_dashboard import (
GradeBookPage,
InstructorDashboardPage,
StudentAdminPage
)
from common.test.acceptance.pages.lms.progress import Pro... | ESOedX/edx-platform | common/test/acceptance/tests/lms/test_lms_lti.py | Python | agpl-3.0 | 22,185 | [
"VisIt"
] | e3bc1033dcde5f52f8dcc9dae16831c25862d6277582e49e8d036a33167cdfd6 |
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