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import json
import os
import unittest
import warnings
from sympy import Number, Symbol
from pymatgen.analysis.surface_analysis import (
NanoscaleStability,
SlabEntry,
SurfaceEnergyPlotter,
WorkFunctionAnalyzer,
)
from pymatgen.analysis.wulff import WulffShape
from pymatgen.entries.computed_entries imp... | gmatteo/pymatgen | pymatgen/analysis/tests/test_surface_analysis.py | Python | mit | 22,561 | [
"pymatgen"
] | 2c02bf7fa5c170338812b9eb9da8297495b8997b7a7dae561f8fce72407a3b4a |
# Copyright 2002 Gary Strangman. All rights reserved
# Copyright 2002-2016 The SciPy Developers
#
# The original code from Gary Strangman was heavily adapted for
# use in SciPy by Travis Oliphant. The original code came with the
# following disclaimer:
#
# This software is provided "as-is". There are no expressed or... | person142/scipy | scipy/stats/stats.py | Python | bsd-3-clause | 257,101 | [
"DIRAC"
] | eb51209a3e4b70a325a1add66e16f974195b0a94fa080121019c79e16f4a4c02 |
# Copyright 2021 Google LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | google-research/vmoe | vmoe/nn/vit_moe_test.py | Python | apache-2.0 | 4,412 | [
"MOE"
] | 916abee7cfbe4a4a7927351f6627425ad9b12890e29431f23e37683e06c8ad92 |
# (c) 2012, Michael DeHaan <michael.dehaan@gmail.com>
#
# This file is part of Ansible
#
# Ansible 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 lat... | pmarques/ansible | lib/ansible/template/safe_eval.py | Python | gpl-3.0 | 5,976 | [
"VisIt"
] | d666bb79328859b39a1b333d26d8e7464f4d62d0e1c84cf3c3619c20d99d7a0a |
BOARDS = {
'arduino': {
'digital': tuple(x for x in range(14)),
'analog': tuple(x for x in range(6)),
'pwm': (3, 5, 6, 9, 10, 11),
'use_ports': True,
'disabled': (0, 1) # Rx, Tx, Crystal
},
'arduino_mega': {
'digital': tuple(x for x in range(54)),
'an... | jochasinga/pyFirmata | pyfirmata/boards.py | Python | mit | 727 | [
"CRYSTAL"
] | b3b1cad217bacc211e06ee7b670aec88a8929348349813d29794e065a3e98cdb |
import re
from tests import factories as f
from wye.base.constants import WorkshopLevel
outbox_len = 0
def create_user(password):
user = f.create_user()
user.set_password(password)
user.save()
return user
def login(browser, url, user, password):
browser.visit(url)
browser.fill('login', user... | shankisg/wye | tests/functional/workshop/base.py | Python | mit | 1,398 | [
"VisIt"
] | 83684199e484600e5647073cc48a0227c1d23c5a21cedcd70528b96d89d4d074 |
"""
This is the window manager part of pySSN
pySSN is available under the GNU licence providing you cite the developpers names:
Ch. Morisset (Instituto de Astronomia, Universidad Nacional Autonoma de Mexico)
D. Pequignot (Meudon Observatory, France)
Inspired by a demo code by:
Eli Bendersky (eliben@gmail.c... | mvfcopetti/pySSN | pyssn/qt/pyssn_qt.py | Python | gpl-3.0 | 219,113 | [
"Gaussian"
] | 7fa8867df663a7f7d75ea5ec56735ffe854d5afcb2399879cac2a8b4a1c9f573 |
##
# Copyright 2009-2015 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 (htt... | torbjoernk/easybuild-easyblocks | easybuild/easyblocks/n/netcdf.py | Python | gpl-2.0 | 6,256 | [
"NetCDF"
] | 3298dcbcb91e40a65cb8cd489e9858631e82cd4c77ee9983331237275002e58d |
#User provided customizations for the gpaw setup
compiler = 'cc'
mpicompiler = 'cc'
mpilinker= 'cc'
extra_compile_args = ['-std=c99']
libraries = []
scalapack = True
hdf5 = True
define_macros += [('GPAW_NO_UNDERSCORE_CBLACS', '1')]
define_macros += [('GPAW_NO_UNDERSCORE_CSCALAPACK', '1')]
define_macros += [("GPAW_A... | robwarm/gpaw-symm | doc/install/Cray/customize_louhi.py | Python | gpl-3.0 | 365 | [
"GPAW"
] | 2ee33f3aa2d94a8aa4dcd0a6d17d945e1ad4546e3b7afcae01dc3d9ab38e37db |
# -*- coding: utf-8 -*-
#
# Name: face.com Python API client library
# Description: face.com REST API Python client library.
#
# For more information about the API and the return values,
# visit the official documentation at http://developers.face.com/docs/api/.
#
# Author: Tomaž Muraus (http://www.tomaz.me)
# License:... | Kami/python-face-client | face_client/face_client.py | Python | bsd-3-clause | 14,348 | [
"VisIt"
] | ca56433e11e380d809f2172645c6144ce9c080211cd1f08805f8f13dc1539191 |
# $HeadURL: $
''' CSHelpers
Module containing functions interacting with the CS and useful for the RSS
modules.
'''
from DIRAC import S_OK, S_ERROR
from DIRAC.ConfigurationSystem.Client.Helpers.Resources import getGOCSiteName
from DIRAC.ResourceStatusSystem.Utilit... | sposs/DIRAC | ResourceStatusSystem/Utilities/CSHelpers.py | Python | gpl-3.0 | 3,673 | [
"DIRAC"
] | 9a0cd8b7362fef15b3bec05a3409c85423ba52c80966047b969646b18487e771 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
from os.path import getmtime, exists
import time
import types
import __builtin__
from Cheetah.Version import MinCompatibleVersion as RequiredCheetahVersion
from Cheetah.Version import MinComp... | johm/infoshopkeeper | inventoryserver/CartTemplate.py | Python | gpl-2.0 | 7,132 | [
"VisIt"
] | cc08075bee3b58972b3d37d51b17287c5c3145544adcb00371172bb8a95ed7b0 |
# 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 | dereg.py | Python | apache-2.0 | 2,082 | [
"Brian"
] | 4a01736607dcd64100f28dedbfb6636b4c65558888d075a3447364ecff514935 |
__author__ = 'rhythmicstar'
import copy
import gffutils
import pandas as pd
import numpy as np
from .util import separate, splitstart, splitend
species1DB = gffutils.FeatureDB('/Users/rhythmicstar/projects/exon_evolution//'
'gencode.v19.annotation.humanrbfox2and'
... | jessicalettes/orthoexon | orthoexon/table.py | Python | bsd-3-clause | 28,805 | [
"BLAST"
] | d36eae21a62f5f0397853b00369f9eb6b0632575f2e9d3d8a8a1fb7b175a1906 |
from ase.structure import molecule
from ase.calculators.emt import EMT
from ase.optimize import QuasiNewton
from ase.vibrations import Vibrations
from ase.thermochemistry import IdealGasThermo
atoms = molecule('N2')
atoms.set_calculator(EMT())
dyn = QuasiNewton(atoms)
dyn.run(fmax=0.01)
electronicenergy = atoms.get_po... | askhl/ase | doc/ase/thermochemistry/nitrogen.py | Python | gpl-2.0 | 713 | [
"ASE"
] | a8d2e3542465bc69fa4231e492a2afb4582a8a6b652c161d4636907b33e2d17f |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module provides classes for representing species substitution
probabilities.
"""
from six.moves import zip
__author__ = "Will Richards, Geoffroy Hau... | sonium0/pymatgen | pymatgen/structure_prediction/substitution_probability.py | Python | mit | 9,015 | [
"pymatgen"
] | ab123671a5890610849b24ee7b023a96cf598fef2b3be995ac5c8802679790fb |
# -*- coding: utf-8 -*-
"""Assemble a BEL graph as an `ideogram <https://github.com/eweitz/ideogram>`_ chart in HTML.."""
import random
from typing import Any, Mapping, Optional, TextIO
from IPython.display import Javascript
from pybel import BELGraph
from pybel.dsl import CentralDogma
from pybel.io.jinja_utils imp... | pybel/pybel-tools | src/pybel_tools/assembler/ideogram/assembler.py | Python | mit | 3,475 | [
"Pybel"
] | 9f5ae26a81a6ed5003b68fce74796346ffe02261f78cce0397441cfc66c5084a |
"""Tests for user-friendly public interface to polynomial functions. """
from sympy.polys.polytools import (
Poly, PurePoly, poly,
parallel_poly_from_expr,
degree, degree_list,
LC, LM, LT,
pdiv, prem, pquo, pexquo,
div, rem, quo, exquo,
half_gcdex, gcdex, invert,
subresultants,
resu... | sahilshekhawat/sympy | sympy/polys/tests/test_polytools.py | Python | bsd-3-clause | 106,021 | [
"Gaussian"
] | b029b73620cb254e5092ecc4301c97f76e5c085f5f42ed370f02fb18381f4ec4 |
# Copyright 2018 The TensorFlow Probability 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 o... | tensorflow/probability | tensorflow_probability/python/distributions/mvn_tril.py | Python | apache-2.0 | 9,711 | [
"Gaussian"
] | 281d7a6203ccf291e73782dee9108c1e2245dbf61cfa73f0cd886da41e98bc5f |
import numpy as np
import theano
import theano.tensor as T
from theano.sandbox.rng_mrg import MRG_RandomStreams
from mozi.layers.template import Template
floatX = theano.config.floatX
theano_rand = MRG_RandomStreams()
class Sigmoid(Template):
def _test_fprop(self, state_below):
return T.nnet.sigmoid(stat... | dksahuji/Mozi | mozi/layers/activation.py | Python | mit | 3,869 | [
"NEURON"
] | 61b3d78b987b77c88b50d67848ca2208d788bd1329d3338cc35b8d549dc760c7 |
# ----------------------------------------------------------------------------
# pyglet
# Copyright (c) 2006-2008 Alex Holkner
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# * Redistribu... | jpaalasm/pyglet | pyglet/graphics/__init__.py | Python | bsd-3-clause | 26,045 | [
"VisIt"
] | f34146baddf71fc01ddc7ac5bfbd73b482be8acf2c3de587a2bf79c0f81b1b78 |
__author__ = 'Luca Parmesan'
import imp
import csv
from platform import architecture, system
from warnings import warn
from os import getcwd
class OpalKelly:
"""A simplified version of the Opal Kelly class"""
if system() == 'Windows':
if architecture()[0] == '32bit':
ok = imp... | mcspritz/pyOpalKellyWrapper | OpalKelly.py | Python | gpl-2.0 | 16,393 | [
"CRYSTAL"
] | 95a3d2c320fc99dd717feaa473789f085f24b57de73234d498f414442a2c3be3 |
'''
==============================================================
Group - Group reads based on their UMI and mapping coordinates
==============================================================
*Identify groups of reads based on their genomic coordinate and UMI*
The group command can be used to create two types of out... | CGATOxford/UMI-tools | umi_tools/group.py | Python | mit | 10,510 | [
"pysam"
] | cce79de2ce5087014ac2829d4ab2abfa6d5b76fd803c26eeefc2f3bbff2f5561 |
""" This module contain solvers for all kinds of equations:
- algebraic, use solve()
- recurrence, use rsolve()
- differential, use dsolve()
- transcendental, use tsolve()
- nonlinear (numerically), use nsolve()
(you will need a good starting point)
"""
from sympy.core.sympify import s... | tovrstra/sympy | sympy/solvers/solvers.py | Python | bsd-3-clause | 28,803 | [
"Gaussian"
] | b6f057523a66675a52c98ff37ae9f0cb0e61e4f659f981a8a4c7259fb4f6ba6f |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | kain88-de/mdanalysis | testsuite/MDAnalysisTests/coordinates/test_trj.py | Python | gpl-2.0 | 5,312 | [
"MDAnalysis"
] | 230a9f7b4c7b67ecb56c8ab6cade47d895e79ee03e029ca6be6b6b552bd8d50d |
#
# Copyright (c) 2015 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... | retrography/scancode-toolkit | tests/commoncode/test_fileutils.py | Python | apache-2.0 | 17,989 | [
"VisIt"
] | 77cb3c82d38b49e30e1ce75f8cc398a7cf3f77d34c880b7eeb3fe59705e67d81 |
# Copyright (C) 2017
# Jakub Krajniak (jkrajniak at gmail.com)
# Copyright (C) 2012,2013,2017
# 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 soft... | espressopp/espressopp | src/analysis/Temperature.py | Python | gpl-3.0 | 3,008 | [
"ESPResSo"
] | a5c3d984f1c6892e7395ea763730e9d4b82b5e9ea4573c501d375442d31504c4 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2010 Radim Rehurek <radimrehurek@seznam.cz>
# Licensed under the GNU LGPL v2.1 - http://www.gnu.org/licenses/lgpl.html
"""
Module for Latent Semantic Indexing.
This module actually contains several algorithms for decomposition of large corpora, a
combin... | samantp/gensimPy3 | gensim-develop/gensim/models/lsimodel.py | Python | gpl-3.0 | 33,665 | [
"Gaussian"
] | 10517a412f1178f93d2b5c83661bfc1b00c8c06837ab7266e9291f4b6405b305 |
# paths.py
#
# Created by Brett H. Andrews on 12 Jun 2017.
import os
from os.path import join
from functools import reduce
import click
import numpy as np
@click.command()
@click.option('--stackname', default='dr7_M0.1e')
@click.option('--binnames', default=None, multiple=True)
@click.option('--path_mzr', default=... | bretthandrews/stacking | stacking/paths.py | Python | bsd-3-clause | 3,624 | [
"Galaxy"
] | d61d2aa32c2272aef5866fe76e2665e2069a805360881a9a0b16a8f53218b21c |
# eliteBonusGunshipExplosionVelocity2
#
# Used by:
# Ship: Jaguar
type = "passive"
def handler(fit, src, context):
fit.modules.filteredChargeBoost(lambda mod: mod.charge.requiresSkill("Missile Launcher Operation"), "aoeVelocity",
src.getModifiedItemAttr("eliteBonusGunship2"), s... | bsmr-eve/Pyfa | eos/effects/elitebonusgunshipexplosionvelocity2.py | Python | gpl-3.0 | 369 | [
"Jaguar"
] | b20b30b58807c734d29edd17f6fab98fb3d8af24ae9ec1165ee74189f048502f |
../../../../../../../share/pyshared/orca/scripts/apps/gnome-terminal/script.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/scripts/apps/gnome-terminal/script.py | Python | gpl-3.0 | 78 | [
"ORCA"
] | 94c5826a92e7d5d58ffb5b8ceea71544186540640eebf542d2835acea29f4cbd |
# -*- coding: utf-8 -*-
"""
/***************************************************************************
QGIS Web Processing Service Plugin
-------------------------------------------------------------------
Date : 09 November 2009
Copyright : (C) 2009 by Dr. Horst Duester
email ... | sourcepole/qgis-wps-client | wpslib/processdescription.py | Python | gpl-2.0 | 27,991 | [
"NetCDF"
] | fc47d98d39e70d5329e6c320e61bbdb78eaf3513881d1c238b93d3c1afe4df48 |
# -*- coding: utf-8 -*-
################################################################################
###
### ReadLAMMPSDump - v0.1.8 - May 03, 2018
###
################################################################################
###
### a package to read LAMMPS Dump files
### (it assumes that the data colu... | lorisercole/thermocepstrum | sportran/i_o/read_lammps_dump.py | Python | gpl-3.0 | 19,676 | [
"LAMMPS"
] | c4c61551e68fece25b1ac6e1bb9b95ca8174b5b7d0b52646751850b1b890e66f |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import time
# !! This is the configuration of Nikola. !! #
# !! You should edit it to your liking. !! #
# ! Some settings can be different in different languages.
# ! A comment stating (translatable) is used to denote those.
# ! There are two ways to... | decause/decauseblog | new_site/conf.py | Python | agpl-3.0 | 36,539 | [
"VisIt"
] | 995c58f697cec9db7726e56df4d9825e6358f045e8143c121dbf69eb37e77ff9 |
#!/usr/bin/env python
"""
vm-manager.py manager the openstack VM
Usage: vm-manager.py [options]
Options:
-n, --node=NODE_NAME one of the node name: gitserver
-c, --config=CONFIG_FILE needed config information like openstack
-i, --id=BUILD_ID unique id for the VM name, mo... | larrycai/costa-ci | cloud_manager.py | Python | mit | 12,356 | [
"ADF"
] | c4119d3b90ad13fde94d8ffcb1d9fe5ab9555da44a7d9a77b98140c1caa1cc88 |
../../../../../../../share/pyshared/orca/scripts/apps/xfwm4/__init__.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/scripts/apps/xfwm4/__init__.py | Python | gpl-3.0 | 71 | [
"ORCA"
] | 4b87523a4a20755ba64e50a32187712be5734dc3cad5690d075bc844e4fb4a85 |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# vim:fenc=utf-8
#
# Copyright © 2017 Malcolm Ramsay <malramsay64@gmail.com>
#
# Distributed under terms of the MIT license.
"""Test the simulation module."""
import gc
import os
import subprocess
from pathlib import Path
import gsd.hoomd
import hoomd
import pytest
from... | malramsay64/MD-Molecules-Hoomd | test/simulation_test.py | Python | mit | 6,460 | [
"CRYSTAL"
] | 7ee8c49b115da8f393c7ba0fb5b4010d79e02ea4b8ca5d5b6d404a7695dcd531 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import os.path
import numpy as np
import matplotlib.pyplot as plt
import abel
# This example demonstrates a BASEX transform of an image obtained... | huletlab/PyAbel | examples/example_basex_photoelectron.py | Python | mit | 2,702 | [
"Gaussian"
] | 247c19d852026c4ae418c2c0efc2c24d3a1e9dd90aca1d38552013defc74acba |
"""
.. module::
:platform: Unix
:synopsis: ???
.. moduleauthor: Jan Hajic <hajicj@gmail.com>
"""
import cPickle
import numpy
import safire.utils
import theano
import theano.tensor as TT
from theano.tensor.shared_randomstreams import RandomStreams
from safire.learning.models.autoencoder import Autoencoder
c... | hajicj/safire | safire/learning/models/sparse_denoising_autoencoder.py | Python | gpl-3.0 | 8,323 | [
"NEURON"
] | 825a5b46df49bb3bd049e7ec5df25b313c8a9b39271e2af41d1921ff395d6715 |
#!/usr/bin/env python
#------------------------------------------------------------
# Script compares efficiency of automatic derivatives vs
# analytical in mpfit.py
# Vog, 31 okt 2011
#------------------------------------------------------------
import numpy
from matplotlib.pyplot import figure, show, rc
from kapteyn... | kapteyn-astro/kapteyn | doc/source/EXAMPLES/kmpfit_gauest_multicomp.py | Python | bsd-3-clause | 3,462 | [
"Gaussian"
] | 3104781e2c33de66e42f16f39985fafad1f65a1260d216a06c3e19f1da038b85 |
from __future__ import print_function, unicode_literals, absolute_import, division
import logging
logger = logging.getLogger(__name__)
import numpy as np
import warnings
from mako.template import Template
from gputools import OCLArray, OCLProgram, OCLElementwiseKernel
from gputools.core.ocltypes import assert_bufs_... | maweigert/gputools | gputools/convolve/generic_separable_filters.py | Python | bsd-3-clause | 11,149 | [
"Gaussian"
] | 3aa301af376d3ab3e98fe5d62f0c2cd8c69e6d2e759b26c4903cc9db9488cd63 |
# Copyright (c) 2006-2007, 2009-2014 LOGILAB S.A. (Paris, FRANCE) <contact@logilab.fr>
# Copyright (c) 2009 Mads Kiilerich <mads@kiilerich.com>
# Copyright (c) 2010 Daniel Harding <dharding@gmail.com>
# Copyright (c) 2012-2014 Google, Inc.
# Copyright (c) 2012 FELD Boris <lothiraldan@gmail.com>
# Copyright (c) 2013-202... | ruchee/vimrc | vimfiles/bundle/vim-python/submodules/pylint/pylint/checkers/utils.py | Python | mit | 51,031 | [
"Brian"
] | 80f4f6817633c1047da2b042c80a644e9a9c18a5ed007a5786668e72bf85431f |
# 2D example of viewing aggregates from SA using VTK
from pyamg.aggregation import standard_aggregation
from pyamg.vis import vis_coarse, vtk_writer
from pyamg.gallery import load_example
from pyamg import *
from scipy import *
# retrieve the problem
data = load_example('unit_square')
A = data['A'].tocsr()
V = data['v... | pombreda/pyamg | Examples/WorkshopCopper12/task2.3.py | Python | bsd-3-clause | 1,357 | [
"ParaView",
"VTK"
] | c0990c3a306706e1416e0896a6f0696509928b65f6ca295c949783d15542d81f |
# Copyright (C) 2008 CSC - Scientific Computing Ltd.
"""This module defines an ASE interface to VASP.
Developed on the basis of modules by Jussi Enkovaara and John
Kitchin. The path of the directory containing the pseudopotential
directories (potpaw,potpaw_GGA, potpaw_PBE, ...) should be set
by the environmental fl... | freephys/python_ase | ase/calculators/vasp.py | Python | gpl-3.0 | 44,651 | [
"ASE",
"VASP"
] | 8ec1e5cc4fe7ad5b7947d5b2ceacb8403764ce373edd0db32a06489b11ddaed6 |
#!/usr/bin/env python
# ----------------------------------------------------------------------------
# Copyright 2014 Nervana Systems 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
#
# ... | kfoss/neon | neon/params/tests/test_val_init.py | Python | apache-2.0 | 4,967 | [
"Gaussian"
] | fcb0de445b46233cdb6c9e046468b67218a95548792a1bf5e546e9991a5d0331 |
""" Client for the SandboxStore.
Will connect to the WorkloadManagement/SandboxStore service.
"""
import os
import tarfile
import hashlib
import tempfile
import re
from io import BytesIO, StringIO
from DIRAC import gLogger, S_OK, S_ERROR, gConfig
from DIRAC.Core.Tornado.Client.ClientSelector import TransferClien... | DIRACGrid/DIRAC | src/DIRAC/WorkloadManagementSystem/Client/SandboxStoreClient.py | Python | gpl-3.0 | 14,808 | [
"DIRAC"
] | 62374a8f02260f1cd5c69faf718f352655494418f4c30bd5b27f75f303a7b00b |
# -*- coding: utf-8 -*-
##
## This file is part of Invenio.
## Copyright (C) 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 CERN.
##
## Invenio is free software; you can redistribute it and/or
## modify it under the terms of the GNU General Public License as
## published by the Free Software Foundation; either ve... | pombredanne/invenio | modules/bibupload/lib/batchuploader_webinterface.py | Python | gpl-2.0 | 15,550 | [
"VisIt"
] | 3e8822f126b2c3b60523c6cde949c0211b0d44a3c1eb7e2a876c675b35345a79 |
"""
Specializers for various sorts of data layouts and memory alignments.
These specializers operate on a copy of the simplified array expression
representation (i.e., one with an NDIterate node). This node is replaced
with one or several ForNode nodes in a specialized order.
For auto-tuning code for tile size and Op... | markflorisson/minivect | minivect/specializers.py | Python | bsd-2-clause | 56,778 | [
"VisIt"
] | dadc27d6154a00659b4ed30cbca211a13681b6f22ed3e23533870112daea5332 |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to
# make it easier to submit large numbers of jobs on supercomputers. It
# provides a python interface to physical input, ... | pylada/pylada-light | tests/process/test_pool.py | Python | gpl-3.0 | 2,948 | [
"CRYSTAL",
"VASP"
] | 6f3d289d3f8e51553649ff1e903e6366be222b87aa6649e5a2c40cb34b51f545 |
# Copyright 2021 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, so... | googlecodelabs/migrate-python2-appengine | mod1b-flask/main.py | Python | apache-2.0 | 1,472 | [
"VisIt"
] | 93084f90849977e567bc018cda6ceaa6e8285c3ff1b4151df1eb6454626bdf65 |
# -*- coding: utf-8 -*-
"""
Copyright (c) 2013 wgx731 <wgx731@gmail.com>
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
'Software'), to deal in the Software without restriction, including
without limitation the rights to use, copy,... | fxyzj/xiaohuangji | tests/test_visit.py | Python | mit | 1,845 | [
"VisIt"
] | 8d0111476b937e88abee52d49e6bfd3d3c197a61c9e9c8aabb6121ef64242f81 |
#
# 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/licensedcode/match_seq.py | Python | apache-2.0 | 4,607 | [
"VisIt"
] | ed886362936b0bce304888107d32929b87a84f810d44d9c9cb74214273cfe71e |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""Functional tests using WebTest."""
import datetime as dt
from rest_framework import status as http_status
import logging
import unittest
import markupsafe
import mock
import pytest
from nose.tools import * # noqa: F403
import re
from django.utils import timezone
from... | mfraezz/osf.io | tests/test_webtests.py | Python | apache-2.0 | 55,101 | [
"VisIt"
] | 8ecf48e9b4e9a091e4a114c082f639478a93bad8aed79f92566f23d5cf58f99f |
"""Class for calibrating the color-based red-sequence model.
"""
import os
import numpy as np
import fitsio
import time
import esutil
from scipy.optimize import least_squares
from ..configuration import Configuration
from ..fitters import MedZFitter, RedSequenceFitter, RedSequenceOffDiagonalFitter, CorrectionFitter, E... | erykoff/redmapper | redmapper/calibration/redsequencecal.py | Python | apache-2.0 | 55,079 | [
"Galaxy"
] | 26722be2854a7ae3554243a7d40395c93d3f040442c8b554f3eb72011c9f99fa |
#!/usr/bin/env python
traindat = '../data/fm_train_real.dat'
testdat = '../data/fm_test_real.dat'
parameter_list=[[traindat,testdat,1.9],[traindat,testdat,1.7]]
def kernel_io (train_fname=traindat,test_fname=testdat,width=1.9):
from shogun import CSVFile
from tempfile import NamedTemporaryFile
import shogun as sg
... | lambday/shogun | examples/undocumented/python/kernel_io.py | Python | bsd-3-clause | 955 | [
"Gaussian"
] | dda3db11e39a3cd188ab302b721b86a94f99b901ab1b4c5eeadb7355aeb80ffc |
from __future__ import absolute_import
import numpy as np
from mdtraj.testing import eq
from numpy.testing import assert_approx_equal
from numpy.testing import assert_array_almost_equal
from sklearn.pipeline import Pipeline
from sklearn.decomposition import PCA as PCAr
from msmbuilder.example_datasets import AlanineD... | mpharrigan/mixtape | msmbuilder/tests/test_decomposition.py | Python | lgpl-2.1 | 6,977 | [
"MDTraj"
] | 8314bc4fd095998ce992312d32e1eeb8c7570ed8ba6a6f9eb47a2af288b4b110 |
import os, sys, shutil, re, glob, time, commands
_part_filename = '._%s%03d'
_part_filename_wildcard = '._*[0-9][0-9][0-9]'
_registered_command_line_options = [
('--help',
'Print all options to the doconce program.'),
('--debug',
"""Write a debugging file _doconce_debugging.log with lots
of intermed... | sjsrey/doconce | lib/doconce/misc.py | Python | bsd-3-clause | 366,370 | [
"Gaussian"
] | 1ad7247f4f485809b11202cbf95765ffd895c5133bfab3c33f40c472280d247a |
# Principal Component Analysis Code :
from numpy import mean,cov,double,cumsum,dot,linalg,array,rank,size,flipud
from pylab import *
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import ro... | tapomayukh/projects_in_python | sandbox_tapo/src/skin_related/BMED_8813_HAP/Scaling/best_kNN_PC/cross_validate_categories_kNN_PC_BMED_8813_HAP_scaled_method_II.py | Python | mit | 4,435 | [
"Mayavi"
] | 001c2d9d9b72286d1e22a941fce72b434549f24c0e17511f197da280af43501a |
#
# Provides a convenience Ontology class that implements a high-level interface
# for interacting with an OWL ontology.
#
# Python imports.
from labelmap import LabelMap
from obohelper import isOboID, oboIDToIRI
from ontology_entities import _OntologyClass, _OntologyDataProperty
from ontology_entities import _Ontolog... | biocodellc/biocode-fims-configurator | bin/ontobuilder/ontology.py | Python | gpl-3.0 | 20,578 | [
"Elk"
] | d073345bb0fec6684f6a6519c2065239627a6b4a680dd16c57dc8e3cb9441436 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License
"""
This module implements reading and writing of ShengBTE CONTROL files.
"""
import warnings
from typing import Any, Dict, List, Optional, Union
import numpy as np
from monty.dev import requires
from monty.js... | davidwaroquiers/pymatgen | pymatgen/io/shengbte.py | Python | mit | 9,232 | [
"CRYSTAL",
"ESPResSo",
"VASP",
"pymatgen"
] | 7ba3db8a72381ac21c298a18b0e248dc7fcd3e9a8108beb0692640e9f22966b3 |
""" YES, oor no? """
import datetime
import logging
def yesorno(team, teamdates, date2=None):
"""
Input: team/city/etc, teamdates and date
Returns: True/False
"""
yesterday = datetime.datetime.now() - datetime.timedelta(days=1)
yesterday = yesterday.strftime("%Y-%m-%d")
chosen_team = g... | martbhell/wasthereannhlgamelastnight | src/nhlhelpers.py | Python | mit | 13,252 | [
"COLUMBUS"
] | 97f4c7729f455223a75c5d48eb45cad0d747a30acf9eee939d1682113ad48006 |
# Copyright 2002 by Yves Bastide and Brad Chapman.
# Copyright 2007 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.
"""Functions to calculate assorted sequen... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/SeqUtils/CheckSum.py | Python | gpl-2.0 | 4,470 | [
"BioPerl",
"Biopython"
] | d4103903bef65bcfea1fb4c39d2a84c95efafaaedd24d095493ed5fcdc3c9246 |
#!/usr/bin/env python3
import sys
import os
import mdtraj
if "-h" in sys.argv or "--help" in sys.argv:
print("Takes MD coordinate filename, outputs dummies.gro")
sys.exit(os.EX_OK)
gro = mdtraj.load(sys.argv[1])
for i in range(1, 6):
dummy_index = next(gro.top.atoms_by_name("D{0}".format(i))).index
... | jag1g13/pdb2lmp | scripts/make_sugar_dummies.py | Python | mit | 856 | [
"MDTraj"
] | cf8a36cf99793bcbbaca3b3c005cc50f33c5be0a9c9f04a2e80faad58856e242 |
import numpy as np
import shutil
import os
import mdtraj as md
from mdtraj.utils import enter_temp_directory
from mdtraj.utils.delay_import import import_
import tempfile
from distutils.spawn import find_executable
import simtk.unit as units
PACKMOL_PATH = find_executable("packmol")
HEADER_TEMPLATE = """
# Mixture
... | Clyde-fare/openmoltools | openmoltools/packmol.py | Python | gpl-2.0 | 10,513 | [
"MDTraj",
"OpenMM"
] | de3646d8a8d468e81cdb1aaf042c58dafcf29589d2fc9654cda7e762afc96002 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes for calculating the ewald sum of a structure.
"""
import bisect
from copy import copy, deepcopy
from datetime import datetime
from math import log, pi, sqrt
from typing import ... | gmatteo/pymatgen | pymatgen/analysis/ewald.py | Python | mit | 28,207 | [
"GULP",
"pymatgen"
] | ee2e6e739805361d7039113f62a79ddffc2ea4da531d0c709fd0a0bc1356f9d6 |
#!/usr/bin/env python
"""
This example demonstrates how to use boolean combinations of implicit
functions to create a model of an ice cream cone.
"""
import vtk
def main():
colors = vtk.vtkNamedColors()
# Create implicit function primitives. These have been carefully placed to
# give the effect that w... | lorensen/VTKExamples | src/Python/VisualizationAlgorithms/IceCream.py | Python | apache-2.0 | 3,833 | [
"VTK"
] | 2f4ad9322cf97300198f280c15e770181a77108ac58aae6b9d0cb8c7259d8bdc |
from __future__ import annotations
import os
def parse_integrate_lp_updates(filename):
"""Parse the integrate.lp file to get the values for any updated
parameters."""
if not os.path.split(filename)[-1] == "INTEGRATE.LP":
raise RuntimeError("input filename not INTEGRATE.LP")
with open(filena... | xia2/xia2 | src/xia2/Wrappers/XDS/XDSIntegrateHelpers.py | Python | bsd-3-clause | 4,449 | [
"CRYSTAL"
] | 0300140978575fac6907b4cadb08c42973f5be3e8efec58c1f93a86fc04ffdd9 |
#! /usr/bin/python
"""Copyright 2011 Phidgets Inc.
This work is licensed under the Creative Commons Attribution 2.5 Canada License.
To view a copy of this license, visit http://creativecommons.org/licenses/by/2.5/ca/
"""
__author__="Adam Stelmack"
__version__="2.1.8"
__date__ ="13-Jan-2011 4:28:27 PM"
#Basic imports... | danielsuo/mobot | src/move/Python/Analog-simple.py | Python | mit | 3,861 | [
"VisIt"
] | c31a7eed8b9b06449b795c07e8c1a20d66ef1aec3d45a7531d9419ef7e2a00f3 |
"""Perform validation of final calls against known reference materials.
Automates the process of checking pipeline results against known valid calls
to identify discordant variants. This provides a baseline for ensuring the
validity of pipeline updates and algorithm changes.
"""
import collections
import contextlib
im... | biocyberman/bcbio-nextgen | bcbio/variation/validate.py | Python | mit | 30,594 | [
"pysam"
] | 78d23ac34789ab5ab3ee852d5ddc510824482c8300447e7af636849881fa33c5 |
""" Tornado-based HTTPs ResourceManagement service.
"""
from DIRAC import gLogger
from DIRAC.Core.Tornado.Server.TornadoService import TornadoService
from DIRAC.ResourceStatusSystem.Service.ResourceManagementHandler import ResourceManagementHandlerMixin
sLog = gLogger.getSubLogger(__name__)
class TornadoResourceMan... | DIRACGrid/DIRAC | src/DIRAC/ResourceStatusSystem/Service/TornadoResourceManagementHandler.py | Python | gpl-3.0 | 399 | [
"DIRAC"
] | 70c20a81402eadcde9904a7de9c0a683af1436765d28970ebbc32a97d1fb2113 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
###############################################################################
# $Id: basic_test.py 33758 2016-03-21 09:06:22Z rouault $
#
# Project: GDAL/OGR Test Suite
# Purpose: Test basic GDAL open
# Author: Even Rouault <even dot rouault at mines dash paris dot or... | nextgis-extra/tests | lib_gdal/gcore/basic_test.py | Python | gpl-2.0 | 20,412 | [
"exciting"
] | e9605dc64a9a6c418fe5faac83c7049ab2a0615f73dd81b40dc35063b4680311 |
import codecs
import tkinter
from PluginBot import BYTE
from PluginBot import PRIVMSG
from PluginBot import getUser
from PluginBot import getMessage
from random import randint
def version():
codecs.register(lambda name: codecs.lookup("utf-8") if name == "cp65001" else None)
return "PrivMsg - v1.0"
def plugin_main(... | tommai78101/IRCBot | plugins/privmsg.py | Python | mit | 11,344 | [
"exciting"
] | 7f36d660381bd16f0b1b649e8aee17db1a752911249da213a3e7bdf56a88a661 |
# coding: utf-8
"""
Test the coordinates class that represents the plane of orbit of the Sgr dwarf galaxy.
"""
from __future__ import absolute_import, unicode_literals, division, print_function
__author__ = "adrn <adrn@astro.columbia.edu>"
import os
import pytest
import numpy as np
import astropy.coordinates as... | abonaca/gary | gary/coordinates/tests/test_sgr.py | Python | mit | 1,962 | [
"Galaxy"
] | 3a62306f79231a75f6a0782b93ef498e074d523e8ba288294c0634d56a7f91ac |
###########################################################################
#
# Copyright 2020 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
#
# https://www.apache.org/l... | google/starthinker | dags/bulkdozer_dag.py | Python | apache-2.0 | 5,689 | [
"VisIt"
] | 1ce176f7886540beaa2d57e6d142761bbc2c63cec40eeb13893154205661bec0 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Parsers for Qchem output files.
"""
import copy
import logging
import math
import os
import re
import warnings
from typing import Union, List, Dict, Any
import networkx as nx
import numpy as np
import pan... | gmatteo/pymatgen | pymatgen/io/qchem/outputs.py | Python | mit | 76,797 | [
"Q-Chem",
"pymatgen"
] | edd1546a73e380dadbd04d6bb2423fa99f9e5843cf2b4bd684dd88f4910ae360 |
import UWG
import os
# Gets path of current directory
CURR_DIRECTORY = os.path.abspath(os.path.dirname(__file__))
# To run UWG provide the following inputs
epw_directory = os.path.join(CURR_DIRECTORY,"epw") # EPW file directory
epw_filename = "SGP_Singapore.486980_IWEC.epw" # EPW file name
uwg_param_directory =... | saeranv/UWG_Python | resources/quickstart.py | Python | gpl-3.0 | 587 | [
"EPW"
] | 8d9bde47d61f27ac73efd87feed76656b2d90211a89789b602bf07929ab32970 |
import OOMP
OOMP.oompAddDetail(category="type",code="ANTE",name="Antenna")
OOMP.oompAddDetail(category="type",code="BAHO",name="Battery Holder")
OOMP.oompAddDetail(category="type",code="BAPI",name="Badge Pin")
OOMP.oompAddDetail(category="type",code="BREB",name="Breadboard")
OOMP.oompAddDetail(category="type",code="BU... | oomlout/oomlout-OOMP | OOMPdetailsType.py | Python | cc0-1.0 | 4,439 | [
"CRYSTAL"
] | 4e541550caaaab230496af08463308f53723881e65dec3a35788fa0a9bb5e217 |
import time
from org.gumtree.gumnix.sics.control.events import DynamicControllerListenerAdapter
from org.gumtree.gumnix.sics.control import IStateMonitorListener
from org.gumtree.gumnix.sics.io import SicsProxyListenerAdapter
from org.eclipse.swt.events import DisposeListener
from org.eclipse.swt.widgets import Ty... | Gumtree/Kookaburra_scripts | Internal/Initialise.py | Python | epl-1.0 | 11,361 | [
"Gaussian"
] | 82661620e8b6300ccd6cd0fb7e55f6ee2d59dfe79bfb449a804cc41ed324e147 |
"""Scraper for the Supreme Court of Vermont
CourtID: vt
Court Short Name: VT
Author: Brian W. Carver
Date created: 18 Aug 2013
Reviewer: Mike Lissner
"""
import re
from datetime import datetime
from lxml import html
from juriscraper.OpinionSite import OpinionSite
class Site(OpinionSite):
def __init__(self):
... | brianwc/juriscraper | opinions/united_states/state/vt.py | Python | bsd-2-clause | 2,133 | [
"Brian"
] | d259c2799bb3789536b4afac01f5e551fd5d3f4ecd6c1ad5f9a49fb4b23600ed |
"""Retrieve run information describing files to process in a pipeline.
This handles two methods of getting processing information: from a Galaxy
next gen LIMS system or an on-file YAML configuration.
"""
import collections
from contextlib import closing
import copy
import glob
import itertools
import os
import string
... | Cyberbio-Lab/bcbio-nextgen | bcbio/pipeline/run_info.py | Python | mit | 33,207 | [
"Galaxy"
] | a63bec0b723e098bb751fa5a312d7776be647cec7b2092e7a63a001aed996d28 |
import vtkAll as vtk
from shallowCopy import shallowCopy
import numpy as np
try:
from vtk.util import numpy_support
except ImportError:
from paraview import numpy_support
def numpyToPolyData(pts, pointData=None, createVertexCells=False):
pd = vtk.vtkPolyData()
pd.SetPoints(vtk.vtkPoints())
# Makes... | mitdrc/director | src/python/director/vtkNumpy.py | Python | bsd-3-clause | 2,294 | [
"ParaView",
"VTK"
] | f592de5c4f2c142bf9a99adb5cf7f4f55c3294fbd105df53e55e25482719edb5 |
#!/usr/bin/env python
import argparse
import copy
import io
import logging
import os
import sys
import time
import traceback
import pyexiv2
# import Image
import numpy as np
import matplotlib as mpl
from numpy.f2py.auxfuncs import throw_error
from logging import exception
if os.environ.get('DISPLAY', '') == '':
... | stevemarple/AuroraWatchNet | software/server/awnetd/awnet_plot.py | Python | gpl-2.0 | 34,245 | [
"Amber",
"VisIt"
] | 96602ec7738370011d8eb489df5627272a27bb6fa6c306e7b4525f86ee5fdb1d |
# -*- coding: utf-8 -*-
"""Tests for data structures in PyBEL."""
import os
import random
import tempfile
import unittest
from io import StringIO
import pybel
import pybel.examples
from pybel import BELGraph
from pybel.constants import CITATION_TYPE_PUBMED, IDENTIFIER, NAMESPACE
from pybel.dsl import hgvs, protein
f... | pybel/pybel | tests/test_struct/test_struct_graph.py | Python | mit | 8,814 | [
"Pybel"
] | ccf8bd6da249c2da84331897b0e8fcc407d8cfb2c3060cb4483cab396784fb16 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
The full program is explained in the attached ReadMe.md
Copyright (C) 2013 warehouseman.com
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free S... | martinhbramwell/gspread_HelloOAuthWorld | authorize_SMTP.py | Python | agpl-3.0 | 11,313 | [
"VisIt"
] | 906f1f58e6ebe089d54b80f3aa07990fd17e07fbc75d863ac685b79c968ec9c9 |
'''Term creation.'''
import antlr
from aterm import exception
from aterm import term
from aterm import lexer
from aterm import parser
class _Singleton(type):
'''Metaclass for the Singleton design pattern. Based on
http://aspn.activestate.com/ASPN/Cookbook/Python/Recipe/102187
'''
def __init__(mcs, name, bases... | mewbak/idc | aterm/factory.py | Python | lgpl-2.1 | 5,214 | [
"VisIt"
] | 61cd3c239cdbcc56771f182fd8e2f05b9ba8c82a6e2ccf175763eedd2f511a7d |
# runs after the job (and after the default post-filter)
import sets, os
from galaxy import jobs
def exec_before_process(app, inp_data, out_data, param_dict, tool=None):
"""Sets the name of the data"""
dbkeys = sets.Set( [data.dbkey for data in inp_data.values() ] )
if len(dbkeys) != 1:
raise Exce... | jmchilton/galaxy-central | tools/operations/operation_filter.py | Python | mit | 1,016 | [
"Galaxy"
] | a8305ee6f7b1341f8129a21f2d539ab730b34e86437c458a9dd664ff5640aa0e |
#importing modules
from datetime import datetime, timedelta
import pandas as pd
import quandl
import DBUpdateConfig
from sqlalchemy import create_engine
from tqdm import tqdm
import math
import sys
def getNatureAndColor(row):
open = row.Open
close = row.Close
low = row.Low
high = row.High
body_le... | ashish-padakannaya/TradingPlatform | jobs/DBUpdateScript.py | Python | mit | 14,157 | [
"exciting"
] | 049e397b686fcb3a5fd306948de97eb654b17e084083d6b5a3aa706d754694d7 |
#!/usr/bin/env python
import sys,os,re
import argparse
import subprocess as sub
parser = argparse.ArgumentParser()
parser.add_argument("-i", "--input_file", help="fasta formatted file containing the contigs", required=True)
parser.add_argument("-f", "--forward_reads", help="forward reads used to generate the assembly... | waoverholt/waoverholt.github.io | assets/internal_files/calc_contig_stats.py | Python | mit | 6,810 | [
"Bowtie"
] | 3eb3c353ab6c974d8d166da148ac13ae36cc723bd15f38a601b99a6660aa0a74 |
"""Data flow analysis based on miasm intermediate representation"""
from builtins import range
from collections import namedtuple
from future.utils import viewitems, viewvalues
from miasm.core.utils import encode_hex
from miasm.core.graph import DiGraph
from miasm.ir.ir import AssignBlock, IRBlock
from miasm.expressio... | commial/miasm | miasm/analysis/data_flow.py | Python | gpl-2.0 | 55,696 | [
"VisIt"
] | c1ab24d88d6d7a9f5229069344a4abd648c845fb75907139fa0286064aafdba6 |
# -*- coding: utf-8 -*-
#
# hl_api_server.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST 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, ... | lekshmideepu/nest-simulator | pynest/nest/server/hl_api_server.py | Python | gpl-2.0 | 15,681 | [
"NEURON"
] | 46de919de9eb92cde317d0b1f2fb037cb92bcd887d513f4160952f5b0306fca9 |
from __future__ import print_function, absolute_import, division
import os
import shutil
import tempfile
from nose.plugins.skip import SkipTest
import numpy as np
import sklearn.datasets
from sklearn.externals.joblib import dump
from numpy.testing.decorators import skipif
from osprey.dataset_loaders import (DSVDatase... | pandegroup/osprey | osprey/tests/test_dataset_loader.py | Python | apache-2.0 | 6,459 | [
"MDTraj"
] | d834bb12575a51d8dc2da729ee7da9bb0439a67857f0bd28dc6ddf2eef276e2e |
import click
from parsec.cli import pass_context, json_loads
from parsec.decorators import custom_exception, json_output
@click.command('create_quota')
@click.argument("name", type=str)
@click.argument("description", type=str)
@click.argument("amount", type=str)
@click.argument("operation", type=str)
@click.option(
... | galaxy-iuc/parsec | parsec/commands/quotas/create_quota.py | Python | apache-2.0 | 1,401 | [
"Galaxy"
] | c9525d19ecf59ecc171908168503aa6076e6b85e90e6fb881a7b137289a81479 |
# ################################################################
#
# Active Particles on Curved Spaces (APCS)
#
# Author: Rastko Sknepnek
#
# Division of Physics
# School of Engineering, Physics and Mathematics
# University of Dundee
#
# (c) 2013
#
# This program cannot be used, ... | sknepneklab/SAMoS | utils/InitialAnalysis/vtktools.py | Python | gpl-3.0 | 10,740 | [
"ParaView",
"VTK"
] | 645b97acf8bea599e48e8a51aec0b64d4111a5f4499dedb1cc838d3c7ad6bf73 |
# -*- coding: utf-8 -*-
# Infrared on Android devices using build in transmitter
"""
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 ... | thica/ORCA-Remote | src/interfaces/ir_on_android/interface.py | Python | gpl-3.0 | 7,271 | [
"ORCA"
] | bd43042c4f47c23d511c2185b57f466d02a0244b02edde906e35d6879b090310 |
# -*- coding: utf-8 -*-
import sys, logging
import numpy as np
from math import ceil
from gseapy.stats import multiple_testing_correction
from joblib import delayed, Parallel
def enrichment_score(gene_list, correl_vector, gene_set, weighted_score_type=1,
nperm=1000, seed=None, single=False, sca... | BioNinja/gseapy | gseapy/algorithm.py | Python | mit | 31,007 | [
"VisIt"
] | 6a24c93e9266d6eae4c89fc3dfe51624952b722d2618727933e37b6d516fcd5c |
from bugle.shortcuts import render, redirect, get_object_or_404
from forms import BlastForm
from models import Blast, ImageUpload
from search import query_to_q_object
from django.contrib.auth.models import User
from django.http import HttpResponse, Http404
from django.utils import dateformat
from django.template import... | devfort/bugle | bugle_project/bugle/views.py | Python | bsd-2-clause | 10,222 | [
"BLAST"
] | ec665aa2d7f58d856c04b0c7a8154a2bee68ab4740ca7b0b3d133e74595577c2 |
'''Setup script for theia.'''
from setuptools import setup, find_packages
setup(
#General
name = "theia",
version = "0.1.3",
author = u"Rapha\u00EBl Duque",
description = "3D Gaussian beam tracing and visualization",
license = "GNU GPLv3+",
url = "http://theia.hopto.org",
#Requires and entr... | bandang0/theia | setup.py | Python | gpl-3.0 | 505 | [
"Gaussian"
] | 27fad8e8b5fb0860b9bb8ff5e82bc916ad4eb7edb550737bce78f81a407dd365 |
# Copyright 2012 Viewfinder Inc. All Rights Reserved.
"""Viewfinder viewpoint.
Viewpoints are collections of episodes. Every user has a 'default'
viewpoint which contains all uploaded episodes. Viewpoints of type
'event' are created when a user shares episodes. Additional viewpoints
of type 'thematic' may be created ... | 0359xiaodong/viewfinder | backend/db/viewpoint.py | Python | apache-2.0 | 23,638 | [
"VisIt"
] | 5a7c86bb1cd554b6df20fab7c24f9d97bbc8ce9d5e42459ccec15290eaf821a5 |
import itertools
from collections import defaultdict, namedtuple
from copy import copy
from .block import Block
from .common import Tagged, fail
from .errors import Errors
from .env import env
from .graph import Graph
from .loop import LoopNestTree
from .symbol import Symbol
from .synth import make_synth_params
from .... | ktok07b6/polyphony | polyphony/compiler/scope.py | Python | mit | 23,258 | [
"VisIt"
] | fb565ac97768d119dd9088935b8dbceb971cbc4d4131a0cb6e26ccd35c635f3f |
#!/usr/bin/env python
import Bio.PDB
import warnings
from Bio import BiopythonWarning
warnings.simplefilter('ignore', BiopythonWarning)
import sys
import os
import re
import tempfile
import numpy as np
from Bio.SVDSuperimposer import SVDSuperimposer
from math import sqrt
from argparse import ArgumentParser
import iter... | bjornwallner/DockQ | DockQ.py | Python | gpl-3.0 | 29,613 | [
"Biopython"
] | a6bb88a691bf6fa7083983c1b8a5bf145447b94ddb4d6675041601ead7ef4c6c |
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