text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
import numpy as np
from skimage import img_as_float
import scipy
import scipy.linalg
from scipy.interpolate import RectBivariateSpline, interp2d
from skimage.filters import sobel
def active_contour(image, snake, alpha=0.01, beta=0.1,
w_line=0, w_edge=1, gamma=0.01,
bc='... | rjeli/scikit-image | skimage/segmentation/active_contour_model.py | Python | bsd-3-clause | 8,077 | [
"Gaussian"
] | 9dd86b0fd0935860945f346c06cea38ccca87c3b52bed5f85e0b7cfcd471c663 |
#
# Copyright (C) 2014 Seiji Matsuoka
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
from rdkit.Chem.Draw.canvasbase import CanvasBase
try:
f... | rvianello/rdkit | rdkit/Chem/Draw/qtCanvas.py | Python | bsd-3-clause | 3,567 | [
"RDKit"
] | cdda531a8fe86dfbc768bbbe2fccf9ad9552b3afdc4f27fbdda401645308f322 |
__author__ = "Marcos da Silva Ramos"
__credits__ = ["Anuvrat Singh"]
__email__ = "ms.ramos@outlook.com"
__license__ = "GPLv2"
import pickle
import urllib.request
import bs4
import os
import hashlib
import shutil
import threading
WRITE_COUNTDOWN = 100
FREE_APP_TOKEN = 'Kostenlos' # 'free' in german
STATE_DIR = "state... | msramos/play-crawler | discoverer.py | Python | gpl-2.0 | 11,671 | [
"VisIt"
] | a38da89697a28193fa8c5d549df5ae629ca92d7c7739359fd44e7e4d75eb3c74 |
# Copyright: 2005-2009 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# Author(s): Brian Harring (ferringb@gentoo.org)
__all__ = ["Mapping", "MutableMapping", "UserDict", "ProtectedDict",
"LazyLoad", "slot_dict_class"]
import sys
import weakref
class Mapping(object):
"""
In p... | Neuvoo/legacy-portage | pym/portage/cache/mappings.py | Python | gpl-2.0 | 10,178 | [
"Brian"
] | bd1f502a03a4797ac42b90d55c7a424962984b05cc19509a0535571790bae042 |
'''
development-py (c) University of Manchester 2017
development-py is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
# pylint: disable=too-few-public-methods
import sys
import cobra
from cobra.util.solver import linear_reacti... | neilswainston/development-py | synbiochemdev/fba/analyse.py | Python | mit | 2,258 | [
"VisIt"
] | d41937e678f7dc63f81defb702087414532a116462818e7892249bbfed46a534 |
# Implementation of TODOC algorithm.
# Adapted from https://github.com/ajriddle/Work-Files/blob/master/cps_fcns.py.
import numpy as np
from scipy.interpolate import interp1d
from scipy.optimize import curve_fit
def create_cross_correlations(observation, template1, template2):
"""Create cross correlations c1, c2,... | jason-neal/companion_simulations | misc/todcor.py | Python | mit | 13,678 | [
"Gaussian"
] | a6bec2255cb108448a24c1153f18f2eaad15ec35ea5971d112d9cbede6d3b817 |
VALIDATORS = [
'CSE HTML Validator Lite Online (http://online.htmlvalidator.com/php/onlinevallite.php)',
'CSSCheck/1.2.2', 'Cynthia 1.0', 'HTMLParser/1.6', 'P3P Validator',
'Jigsaw/2.2.5 W3C_CSS_Validator_JFouffa/2.0', 'W3C_Validator/1.654',
'W3C_Validator/1.606', 'W3C_Validator/1.591', 'W3C_Validator/1... | rangertaha/uagent | uagent/uastrings.py | Python | mit | 1,036,215 | [
"Galaxy",
"ORCA"
] | 253ebc33098beaa1a8e56ffcb0a73cecd4c1027f06d8c05bf69d486760e06265 |
# This file is part of Androguard.
#
# Copyright (C) 2014 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
... | xysec/androguard | androguard/decompiler/dad/ast.py | Python | apache-2.0 | 23,816 | [
"VisIt"
] | e81cb80ac0217f4b9cc8ec6f209cef971f0bdf3c26db5bba881034412714c05e |
from abc import abstractmethod
from contextlib import closing
import importlib
import os
import urllib2
from urlparse import urlparse
from bioblend.cloudman import CloudManInstance
from package_helpers import get_cluster_password, get_registry_location
import services
import util
import yaml
def str_to_class(fq_clas... | gvlproject/gvldash | gvldash/util/packages.py | Python | bsd-3-clause | 5,759 | [
"Galaxy"
] | 2bb74d83a72356223b985f05b84a3d55e8105be60e2d5118b5a057dbd148999a |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
from collections import namedtuple
from monty.json import MSONable
"""
A module to perform NMR data analysis/processing.
"""
__author__ = "Xiaohui Qu"
__cop... | matk86/pymatgen | pymatgen/analysis/nmr.py | Python | mit | 4,047 | [
"VASP",
"pymatgen"
] | f9ac9e15be9466d7b8894b239d2b0f6e6990129c1894d4d100c4792c9d42f689 |
# Copyright 2000 by Jeffrey Chang. 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.
"""Collection of modules for dealing with biological data in Python.
The Biopython Project is ... | bryback/quickseq | genescript/Bio/__init__.py | Python | mit | 2,859 | [
"Biopython"
] | c7c6890b599b1cebc46614d4602d852a9448e8be184f29a312486bc2eb1b0095 |
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Eric Larson <larson.eric.d@gmail.com>
# Oleh Kozynets <ok7mailbox@gmail.com>
# Guillaume Favelier <guillaume.favelier@gmail.com>
# jona-sassenhagen <jona.sassenhagen@gmail.com>
# Joan Massich <mailsik@gmail.com>
#... | kambysese/mne-python | mne/viz/_brain/_brain.py | Python | bsd-3-clause | 135,345 | [
"Mayavi",
"VTK"
] | 6f42c8e325bf1a955eae6424f15b431d159e7d37a7fa2c40ccc93a816c0cf219 |
import urllib
import random
import io
import discord
import wap
from PIL import Image, ImageDraw, ImageFont
from xml.etree import ElementTree
from jshbot import utilities, data, configurations, plugins, logger
from jshbot.exceptions import ConfiguredBotException
from jshbot.commands import (
Command, SubCommand,... | jkchen2/JshBot-plugins | wolframquery/wolframquery.py | Python | mit | 17,031 | [
"VisIt"
] | 7090d76ceea26e41e7623af814d3a0056e1d12be5540e23784946f821d80f133 |
"""Handle running, parsing and manipulating metrics available through Picard.
"""
import contextlib
import glob
import json
import os
import subprocess
from bcbio.utils import tmpfile, file_exists
from bcbio.distributed.transaction import file_transaction
from bcbio.broad.picardrun import picard_rnaseq_metrics
import... | a113n/bcbio-nextgen | bcbio/broad/metrics.py | Python | mit | 21,780 | [
"pysam"
] | f0ce976142358e18aee231f64c29bed3d63ee5a80f9876da2267be8067c44113 |
from jenks import classes as jenks_classes
from profiles.utils import values_to_lists
default_neg_colors = ['#f00', '#f99']
default_pos_colors = ['#EDF8FB', '#B2E2E2', '#66C2A4', '#2CA25F', '#006D2C']
def classes_and_colors(data, negative_colors=default_neg_colors, positive_colors=default_pos_colors):
""" Break ... | 216software/Profiles | communityprofiles/profiles/choropleth.py | Python | mit | 3,580 | [
"MOE"
] | fea9db85ce4209a1fe21836af5a3adf09ca56e322bd38cd2b02381368f2b566e |
# Copyright (c) 2016 Jamie Bull
# =======================================================================
# Distributed under the MIT License.
# (See accompanying file LICENSE or copy at
# http://opensource.org/licenses/MIT)
# =======================================================================
"""Run functions f... | jamiebull1/eppy | eppy/runner/run_functions.py | Python | mit | 10,811 | [
"EPW"
] | 170facd828a8fe6867f258067cdbd31d3f086d8096d16a7ca75b3d9cf2b73257 |
# 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/analysis/MeanSquareDispl.py | Python | gpl-3.0 | 2,666 | [
"ESPResSo"
] | 5463aec64c7e53f3f7b762e0ae1a8baaa83375fc4b17361a7ffa970cc884af31 |
"""
Classes encapsulating galaxy tools and tool configuration.
"""
import pkg_resources;
pkg_resources.require( "simplejson" )
import logging, os, string, sys, tempfile, glob, shutil
import simplejson
import sha, hmac, binascii
from UserDict import DictMixin
from galaxy.util.odict import odict
from galaxy.util.bun... | dbcls/dbcls-galaxy | lib/galaxy/tools/__init__.py | Python | mit | 83,056 | [
"Galaxy",
"VisIt"
] | ad8e95c651e0e09d3a63be7716f0c95ee327cc0138fba6a587d1aca8500fcf32 |
"""
VTK type converter.
This module handles conversion between VTK C++ and VTK Python objects
so that one can write inline C++ code to manipulate VTK Python
objects. It requires that you have VTK and the VTK-Python wrappers
installed. It has been tested with VTK 4.0 and above. You will need
to call inline with incl... | lesserwhirls/scipy-cwt | scipy/weave/vtk_spec.py | Python | bsd-3-clause | 4,142 | [
"VTK"
] | 73036d128669b6f9012534eaafa5bb66b341fbaa35a27f0c0194b7fe2bd7c4c2 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | anderspitman/scikit-bio | skbio/stats/ordination/_principal_coordinate_analysis.py | Python | bsd-3-clause | 5,743 | [
"scikit-bio"
] | 99f8030086a28ea3e6d28060997655335862c76b50ff686c82d330577eb4feec |
# -*- coding: utf-8 -*-
# (c) 2016, Adrian Likins <alikins@redhat.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 you... | k0ste/ansible | test/units/cli/test_galaxy.py | Python | gpl-3.0 | 56,931 | [
"Galaxy"
] | f745bec4fccc501801b2f23bdbfa24464b9cad0ef99f8b85d49bf6f6b42d8ea7 |
from edc_base.modelform_validators import FormValidator
from bcpp_subject_form_validators import ReproductiveHealthFormValidator
from ..constants import ANNUAL
from ..models import ReproductiveHealth
from .form_mixins import SubjectModelFormMixin
class ReproductiveHealthForm (SubjectModelFormMixin):
form_valida... | botswana-harvard/bcpp-subject | bcpp_subject/forms/reproductive_health_form.py | Python | gpl-3.0 | 636 | [
"VisIt"
] | 57d2b554826eafcbeeca6153d0d810c57231772a8066370953d329fe963c8ef0 |
../../../../../../../share/pyshared/orca/scripts/apps/Instantbird/__init__.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/scripts/apps/Instantbird/__init__.py | Python | gpl-3.0 | 77 | [
"ORCA"
] | b0b9209614e75a89421eb496421c84a0eb75041557ac238136d8d21485a41f43 |
#!/usr/bin/env python
# python modules
import argparse
# qt modules
import gaussian
import amber
PARSER = argparse.ArgumentParser(
description = 'Create many gaussian input files from a model file and a mdcrd',
formatter_class = argparse.RawTextHelpFormatter)
PARSER.add_argument('gaucom',
h... | eduardoftoliveira/oniomMacGyver | omg/dock++/md2oniom.py | Python | gpl-3.0 | 1,695 | [
"Amber",
"Gaussian"
] | 014a61f030ac04db25480537239face45c1d7abd520ba13b8dfc75879b7d1983 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | TheTimmy/spack | var/spack/repos/builtin/packages/nccmp/package.py | Python | lgpl-2.1 | 1,948 | [
"NetCDF"
] | 875e95f26318caad8108fec3be787a1e1116ee39f2a090a550fe63e545882a28 |
##
# Copyright 2015-2021 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | hpcuantwerpen/easybuild-easyblocks | easybuild/easyblocks/m/molpro.py | Python | gpl-2.0 | 11,863 | [
"Molpro"
] | d790e7d09eea4862f528b0e87da49085bb12c3d70e41c90b251cc559649dea74 |
from __future__ import print_function
# PythTB python tight binding module.
# December 22, 2016
__version__='1.7.1'
# Copyright 2010, 2012, 2016 by Sinisa Coh and David Vanderbilt
#
# This file is part of PythTB. PythTB is free software: you can
# redistribute it and/or modify it under the terms of the GNU General
#... | mailhexu/pyDFTutils | pyDFTutils/wannier90/pythtb_forj.py | Python | lgpl-3.0 | 153,581 | [
"ABINIT",
"CRYSTAL",
"ESPResSo",
"FLEUR",
"SIESTA",
"VASP",
"WIEN2k",
"Wannier90"
] | e2d0f47559e5dfe08cef65a56494f7c98c28d93efb7667594ea595fc375dc1dc |
import sys
import openpyxl
import pyfastaq
import pymummer
import pysam
from circlator import external_progs, __version__
from circlator import __version__ as circlator_version
def get_all_versions(filehandle, raise_error=True, debug=False, assembler=None):
if filehandle is not None:
print('Circlator vers... | sanger-pathogens/circlator | circlator/versions.py | Python | gpl-3.0 | 1,354 | [
"pysam"
] | 77a506f072ec2feaaa5e1921fce622379051d31c9c3a7fa569f4f5cbd59f315d |
#!/usr/bin/env python
#
# Copyright 2007 Google Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law o... | SRabbelier/Melange | thirdparty/google_appengine/google/appengine/tools/appcfg.py | Python | apache-2.0 | 108,208 | [
"VisIt"
] | 2f16e60525dc038fc7f124c158d718a8688f11299f2ce44eb48176a7a42778ca |
#
# tsne.py
#
# Implementation of t-SNE in Python. The implementation was tested on Python 2.5.1, and it requires a working
# installation of NumPy. The implementation comes with an example on the MNIST dataset. In order to plot the
# results of this example, a working installation of matplotlib is required.
# The ... | jodaiber/semantic_compound_splitting | visualization_and_test/tsne.py | Python | apache-2.0 | 5,303 | [
"Gaussian"
] | 8c831ee0519b0007682862475fdcbbe48ff69b68af39dc811bdee95c211d5781 |
# (C) British Crown Copyright 2010 - 2018, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | duncanwp/iris | lib/iris/tests/test_plot.py | Python | lgpl-3.0 | 33,675 | [
"NetCDF"
] | 4d3921dda42f0005f7c972c91909d826ac30617e130964835043963543f59e47 |
#!/usr/bin/env python
"""
----------------------------------------------------------------------------
ovf2vtk: convert OOMMF vector-field file into vtk-vector field file
SYNTAX: ovf2vtk [OPTIONS] infile outfile
OPTIONS:
[--add xy ]
adding a scalar component to the outfile showing the
... | fangohr/ovf2vtk | ovf2vtk/bin/winovf2vtk.py | Python | bsd-2-clause | 14,891 | [
"VTK"
] | 67dfcc2a813b99f6f559fb556d492ec9060d457e9358b3dcc6e5b7cb44e756b8 |
import sys
BDE_PILOT_SRC = '..'
sys.path.append(BDE_PILOT_SRC)
from netcdf_subset import netCDF_subset
from netCDF4 import Dataset, num2date, date2num
from operator import attrgetter
from argparse import ArgumentParser
if __name__ == '__main__':
parser = ArgumentParser(description='Extract variables from netcd... | iaklampanos/bde-pilot-2 | wrf-docker/scripts/breakdown.py | Python | apache-2.0 | 1,280 | [
"NetCDF"
] | dcc63dd163b6ff44a3180be947b3fe8124d0162fe19ad0e8219efcf4e06b5c81 |
# (C) British Crown Copyright 2010 - 2013, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | kwilliams-mo/iris | lib/iris/fileformats/__init__.py | Python | gpl-3.0 | 6,316 | [
"NetCDF"
] | 3be3d7dfdbbefdf21c0ef15251028e123beeedc9895e243cc79db944e7ae14e2 |
from __future__ import print_function
from __future__ import division
import numpy as np
import torch
class GPRRFA:
"""Random Feature Approximation for Gaussian Process Regression
Estimation and prediction of Bayesian linear regression models
Basic usage::
R = GPRRFA()
hyp = R.estimate(... | amarquand/nispat | pcntoolkit/model/rfa.py | Python | gpl-3.0 | 7,985 | [
"Gaussian"
] | dba0de586ab044ebf5a9517f268ee15efc259bc4cf06a591b6fbc6ba89890c23 |
#!/usr/bin/env python3
"""
Created on Mon Sep 23 21:17:43 2019.
@author: mtageld
"""
import numpy as np
from PIL import Image
from skimage.color import rgb2gray
from histomicstk.annotations_and_masks.annotation_and_mask_utils import \
get_image_from_htk_response
from histomicstk.annotations_and_masks.masks_to_ann... | DigitalSlideArchive/HistomicsTK | histomicstk/saliency/cellularity_detection_superpixels.py | Python | apache-2.0 | 23,492 | [
"Gaussian"
] | fe27eaaa2ff826e01922627fb08dc3782c04c8fd39a0908a772124dedf2b6ab9 |
import numpy as np
from datetime import datetime
import netCDF4 as netCDF
import pyroms
import pyroms_toolbox
## load 2-dimentional interannual discharge data
## from 1948-2007. See Dai and Trenberth (2002) and Dai et al. (2009)
print 'Load interannual discharge data'
nc_data = netCDF.Dataset('/archive/u1/uaf/kat... | kshedstrom/pyroms | examples/Arctic_runoff/compute_daitren_remap_weights.py | Python | bsd-3-clause | 4,079 | [
"NetCDF"
] | 05b9737bdca4162e5467edb7fcfca84d6abe2131ba4af071206026f13e981ac3 |
import warnings
import numpy as np
from ._felzenszwalb_cy import _felzenszwalb_grey
def felzenszwalb(image, scale=1, sigma=0.8, min_size=20):
"""Computes Felsenszwalb's efficient graph based image segmentation.
Produces an oversegmentation of a multichannel (i.e. RGB) image
using a fast, minimum spannin... | chintak/scikit-image | skimage/segmentation/_felzenszwalb.py | Python | bsd-3-clause | 3,016 | [
"Gaussian"
] | 013938379629f5a2bdb74b3a396bd0bb339ac236a0b074fff5bf26274bed4762 |
import vtk
# import matplotlib.cm as cm
import sys
LABEL_NAMES = [
'olfactory bulb',
'cerebral cortex',
'lateral septal nuclei',
'striatum',
'globus pallidus',
'thalamus',
'hypothalamus',
'hippocampal formation',
'superior colliculus',
'inferior colliculus',
'cerebellum',
... | neuroinformatics/bah2016_registration | visualize/draw_intensity.py | Python | apache-2.0 | 5,862 | [
"VTK"
] | 0ae77989d34777351d34da0194a842405aeee38fdf1a85794c5046e275292c32 |
"""Dirac notation for states."""
from __future__ import print_function, division
from sympy import (cacheit, conjugate, Expr, Function, integrate, oo, sqrt,
Tuple)
from sympy.core.compatibility import u
from sympy.printing.pretty.stringpict import prettyForm, stringPict
from sympy.physics.quantum.q... | hrashk/sympy | sympy/physics/quantum/state.py | Python | bsd-3-clause | 28,917 | [
"DIRAC"
] | 0b0cd42a32084cf5e4ca246c33e3a421d546cfdc94de1d86ec83209c2efbcc73 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
ren1 = vtk.vtkRenderer()
renWin1 = vtk.vtkRenderWindow()
renWin1.AddRenderer(ren1)
importer = vtk.vtk3DSImporter()
importer.SetRenderWindow(renWin1)
importer.ComputeNormalsOn()
impor... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Filters/Hybrid/Testing/Python/largeImageParallel.py | Python | gpl-3.0 | 1,596 | [
"VTK"
] | def6952c27336f2215c688f62337920a59dc12002561f0ce0eee715c63ba2ab2 |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Moves C++ files to a new location, updating any include paths that point
to them, and re-ordering headers as needed. If multipl... | hujiajie/chromium-crosswalk | tools/git/move_source_file.py | Python | bsd-3-clause | 9,341 | [
"VisIt"
] | 7cef836332779288df836c27f15e6224197e549a8448c4f676320a73128b4c1f |
# Copyright 2016 The LUCI Authors. All rights reserved.
# Use of this source code is governed under the Apache License, Version 2.0
# that can be found in the LICENSE file.
"""Implements a Checker object which can be used in place of `assert` to check
conditions inside tests, but with much more debugging information, ... | luci/recipes-py | recipe_engine/internal/test/magic_check_fn.py | Python | apache-2.0 | 23,804 | [
"VisIt"
] | e3bfaeb611c67c026da58b39c0a2b7ea9f72d040a1718b619e2ac92446dcd7a3 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | MOA-2011/e2openplugin-OpenWebif | plugin/controllers/views/mobile/control.py | Python | gpl-2.0 | 10,663 | [
"VisIt"
] | 9bb6c5c3395f59fefefc7354598040eeec19a095f3e02ddd7513cb4649235d87 |
#!/usr/bin/env python
import theano as th
import theano.tensor as tt
import numpy as np
import utils
import dynamics_th
import dynamics
import features
from irl import load_data
class Feature(object):
def __init__(self, f):
self.f = f
def __call__(self, *args):
return self.f(*args)
def... | yuhangc/HRI_planner | scripts/IRL/features_th.py | Python | apache-2.0 | 7,282 | [
"Gaussian"
] | fa696d5bba7c080b045ba9282c331d8380277958c0b5db48894a8c8ad206c0c8 |
#!/usr/bin/env python3
"""
day01.py
Day one of the 2016 Advent of Code.
Instructions: http://adventofcode.com/2016/day/1
copyright 2017 noticemesen.py
gitlab: gitlab.com/noticemesenpy
github: github.com/noticemesenpy
********************************************************************************
This program is f... | noticemesenpy/advent_of_code | day01/day01_b.py | Python | gpl-3.0 | 4,605 | [
"VisIt"
] | da5b9a57ceec63810225cea2ff277e2645898fd8940d0d773c69c8e9ed2aa802 |
'''
PathwayGenie (c) GeneGenie Bioinformatics Ltd. 2018
PathwayGenie is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
def get_designs(filename):
'''Reads design file from DOE.'''
designs = []
with open(filename) ... | neilswainston/PathwayGenie | plasmid_genie/doe.py | Python | mit | 500 | [
"VisIt"
] | f05e4a794adefb9daabd990b9192a79bf04c6ff7b31b0e7dae98db144cac89c5 |
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at https://mozilla.org/MPL/2.0/.
r"""
TBtrans
=======
File objects for interaction with the `TBtrans`_ code.
The TBtrans code is a tight-binding transp... | zerothi/sisl | sisl/io/tbtrans/__init__.py | Python | mpl-2.0 | 2,452 | [
"SIESTA"
] | b8778c5a8b7f8604ecc654f1fcd871681d2df5e0eb0ac8d259b4b4692609d83d |
"""Tornado handlers logging into the notebook.
Authors:
* Brian Granger
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2011 The IPython Development Team
#
# Distributed under the terms of the BSD License. The full license is in
# the file COPYING, distributed ... | noslenfa/tdjangorest | uw/lib/python2.7/site-packages/IPython/html/auth/login.py | Python | apache-2.0 | 2,006 | [
"Brian"
] | a04caaa716a35f79e6a066fbc692dd9006588f45e5e0dbb7d5ed0df66331de7e |
from __future__ import absolute_import, division, print_function
class TubeCalibFitParams(object):
# This class is to take the fitting method and parameters for fitting the peaks crated by the calibration slits etc
# and to deliver them to TubeCalib, so it can fit the peaks appropriately
# Author: Karl Palmen ISIS
... | ScreamingUdder/mantid | scripts/Calibration/tube_calib_fit_params.py | Python | gpl-3.0 | 2,644 | [
"Gaussian"
] | 64a9eb381b7d37c76a40fc38c367dea75d050f2d759ee7c01b9fc656109f35a5 |
"""MPF plugin allows a machine to be controlled by an OSC client."""
# osc.py
# Mission Pinball Framework
# Written by Brian Madden & Gabe Knuth
# Released under the MIT License. (See license info at the end of this file.)
# Documentation and more info at http://missionpinball.com/mpf
# This code requires pyOSC, htt... | jabdoa2/mpf | mpf/plugins/osc.py | Python | mit | 17,136 | [
"Brian"
] | 3f83cb7ef64f55f7d3f1f8a3e4d6796b791375408bd717e7eab5bbca50ba0253 |
"""
R
d<-read.table("stats.log",h=T)
library(ggplot2)
library(reshape2)
d.m<-melt(d,id=c("nframes","red"))
ggplot(d.m, aes(x=red, y=value)) + geom_point() + geom_line() + facet_grid(variable~.,scale="free")
"""
from yamtbx.dataproc import crystfel
from yamtbx.dataproc.crystfel.command_line import split_stats
from iot... | keitaroyam/yamtbx | yamtbx/dataproc/crystfel/command_line/stats_stream_savememory.py | Python | bsd-3-clause | 11,238 | [
"CRYSTAL"
] | ae166286773cfd83b65d9dab6904dc4d0144c0fe589c1919b83bbb82eaec3e83 |
import ovito
from ovito.io import *
from ovito.vis import *
import os
import glob
import sys
import re
from os.path import join
print("Hello, this is OVITO %i.%i.%i" % ovito.version)
rs = RenderSettings(
filename = '/tmp/image.png',
size = (320,240),
background_color = (1.0, 1.0, 1.0)
)
rs.renderer.antial... | jorgehog/Deux-kMC | scripts/felix_cav/ovitoviz.py | Python | gpl-3.0 | 1,694 | [
"OVITO"
] | 0e7eaf6a4390f407da0781b62596f9867a350431020e6e35230a3c158462fc20 |
from __future__ import unicode_literals
import sys
import os
import warnings
import ruamel.yaml as yaml
__author__ = "Pymatgen Development Team"
__email__ ="pymatgen@googlegroups.com"
__maintainer__ = "Shyue Ping Ong"
__maintainer_email__ ="shyuep@gmail.com"
__version__ = "2017.11.9"
SETTINGS_FILE = os.path.join(os... | setten/pymatgen | pymatgen/__init__.py | Python | mit | 2,748 | [
"CRYSTAL",
"pymatgen"
] | c592bfb734cae2589fcb61de04c0ae9215c590315810c6cc56a2b3263b219e9c |
import os
import sys
import multiprocessing
import numpy as np
from pandas import DataFrame
import matplotlib.gridspec as gridspec
import pylab as pl
import seaborn as sns
from Bio import SeqIO, Seq, motifs
from Bio.Alphabet import IUPAC
import HTSeq
from .Signal import Signal, get_signals
from .Profile import Profile... | guma44/MetaProfile | MetaProfile/MetaProfiler.py | Python | isc | 8,462 | [
"HTSeq"
] | f19f42ef42c4364c00b46441e43fd508017bd90ba9b5a57bf8179bebbd3cbab2 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# spell - [insert a few words of module description on this line]
# Copyright (C) 2003-2015 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the... | heromod/migrid | mig/shared/functionality/spell.py | Python | gpl-2.0 | 7,912 | [
"Brian"
] | 271670beb3a1e528780db02466e8d71ec8e36fe24365210b11b5730e43d2c1a0 |
"""
# Notes:
- This simulation seeks to emulate the CUBA benchmark simulations of (Brette
et al. 2007) using the Brian2 simulator for speed benchmark comparison to
DynaSim. However, this simulation does NOT include synapses, for better
comparison to Figure 5 of (Goodman and Brette, 2008).
- The time taken to si... | asoplata/dynasim-benchmark-brette-2007 | Brian2/brian2_benchmark_CUBA_nosyn_compiled_8000.py | Python | gpl-3.0 | 2,140 | [
"Brian"
] | 59c14cd98af3a173beb841df6c385aed9926e9e2d8d8ff9c5205c07b2956f032 |
###################################################
######## Programmable filter script ########
###################################################
# Author: Matthieu Heitz
# Output DataSet Type = Same as Input
############# Properties for auto-generated XML #############
Name = 'ApplyPoseTransformToPointCloud'
L... | Kitware/ParaViewTangoRecorder | ParaViewPlugins/ApplyPoseTransformToPointCloud.py | Python | apache-2.0 | 7,769 | [
"ParaView",
"VTK"
] | cdde1b5b3700806e0ffc5d04af9b5535a81359f2608a5dc4af32e216ffe8213a |
from __future__ import print_function
import datetime
import functools
import os
import re
import sublime
import sublime_plugin
import sys
class Prefs:
@staticmethod
def load():
settings = sublime.load_settings('PHPUnit.sublime-settings')
Prefs.folder_search_hints = settings.get('top_folder_h... | Starli0n/f_sublime-phpunit | phpunit.py | Python | bsd-3-clause | 41,397 | [
"VisIt"
] | 9729003ca6328651c65fc6eb819027a3d6fb47bc49a26ba7ca7b0b8d9df5f72b |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkImageMapToRGBA(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk... | nagyistoce/devide | modules/vtk_basic/vtkImageMapToRGBA.py | Python | bsd-3-clause | 491 | [
"VTK"
] | aa1a1488d85b071601f5ab54c5b9cd8d390ac9b9312c83e7f34b6b890613fb06 |
#!/usr/bin/env python
import vtk
def main():
def NumberOfTriangles(pd):
"""
Count the number of triangles.
:param pd: vtkPolyData.
:return: The number of triangles.
"""
cells = pd.GetPolys()
numOfTriangles = 0
idList = vtk.vtkIdList()
for i ... | lorensen/VTKExamples | src/Python/VisualizationAlgorithms/PineRootDecimation.py | Python | apache-2.0 | 3,819 | [
"VTK"
] | 868abe502e9829c8f762a323bb55716bd3a398ef550f6f2b3d68e8d247e26f83 |
########################################################################
# File: Operation.py
# Date: 2012/07/24 12:12:05
########################################################################
"""
:mod: Operation
.. module: Operation
:synopsis: Operation implementation
Operation implementation
"""
# Disable inva... | Andrew-McNab-UK/DIRAC | RequestManagementSystem/Client/Operation.py | Python | gpl-3.0 | 10,275 | [
"DIRAC"
] | 0e3842b48902a1a7e6e7958b0ceb0192866721a68f64a933548ae7f7cfb7c6ee |
#!/usr/bin/env python
#
# @file ValidatorClassFunctions.py
# @brief class to create functions for validator classes
# @author Frank Bergmann
# @author Sarah Keating
#
# <!--------------------------------------------------------------------------
#
# Copyright (c) 2013-2015 by the California Institute of Technolo... | hovo1990/deviser | generator/java_code_files/java_functions/ValidatorClassFunctions.py | Python | lgpl-2.1 | 24,258 | [
"VisIt"
] | b418ad310984b928e1ecd9998c1713ba63b352ca3f5f819aac217f93a9a31125 |
# -*- coding: utf-8 -*-
# These tests don't work at the moment, due to the security_groups multi select not working
# in selenium (the group is selected then immediately reset)
from textwrap import dedent
import fauxfactory
import pytest
from riggerlib import recursive_update
from widgetastic.utils import partial_matc... | lkhomenk/integration_tests | cfme/tests/cloud/test_provisioning.py | Python | gpl-2.0 | 27,684 | [
"VisIt"
] | be264629dd335bc017b1a6e03b7f38c51bea864dddb031931926782c7443341e |
"""
Extended math utilities.
"""
# Authors: G. Varoquaux, A. Gramfort, A. Passos, O. Grisel
# License: BSD
import numpy as np
from scipy import linalg
from . import check_random_state
from . import deprecated
from .fixes import qr_economic
def norm(v):
v = np.asarray(v)
__nrm2, = linalg.get_blas_funcs(['nrm... | cdegroc/scikit-learn | sklearn/utils/extmath.py | Python | bsd-3-clause | 9,320 | [
"Gaussian"
] | 609360fe3f04e67b4a6fa50b0ef164e611f0715f8bcbe602ab824ff162b1653a |
from warnings import warn
import numpy as np
import pandas as pd
from pandas import DataFrame, Series
from shapely.geometry import box
from shapely.geometry.base import BaseGeometry
from .array import GeometryArray, GeometryDtype
def is_geometry_type(data):
"""
Check if the data is of geometry dtype.
... | geopandas/geopandas | geopandas/base.py | Python | bsd-3-clause | 115,336 | [
"Bowtie"
] | 30a645e1677156e52a55d7b76243704552c1c665a16714684df3f59089033859 |
# -*- coding: utf-8 -*-
#
# Moonstone is platform for processing of medical images (DICOM).
# Copyright (C) 2009-2011 by Neppo Tecnologia da Informação LTDA
# and Aevum Softwares LTDA
#
# This file is part of Moonstone.
#
# Moonstone is free software: you can redistribute it and/or modify
# it under the terms of the GN... | aevum/moonstone | src/moonstone/bloodstone/scenes/multisliceimageplane.py | Python | lgpl-3.0 | 88,658 | [
"VTK"
] | 62e6bceb0f3bf1cb6c3a672c73f7248de3dd7160be178863efb7b05665101210 |
# Copyright (c) 2005 Gavin E. Crooks <gec@compbio.berkeley.edu>
#
# This software is distributed under the MIT Open Source License.
# <http://www.opensource.org/licenses/mit-license.html>
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentat... | go-bears/Final-Project | weblogo-3.4_rd/corebio/seq.py | Python | mit | 23,704 | [
"Biopython"
] | 71d399496eb5f12bdb6dfe360513d315186a2e728fe1900c0dad72ed703e1d39 |
# This file is part of cclib (http://cclib.sf.net), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2006, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version 2.1 or later. You shou... | Clyde-fare/cclib_bak | src/cclib/bridge/__init__.py | Python | lgpl-2.1 | 795 | [
"cclib"
] | 4adf8976b129098f60df4b5686e5df55c8a69567c0ea1f07e520397282402dbb |
## Script from Robin that creates Bins of the genome to allow for faster runs
from Bio import SeqIO
import argparse
import numpy as np
import os
parser = argparse.ArgumentParser(
prog='splitfasta2.py',
usage='''python splitfasta2.py --fasta [Genome fasta file] --path [Path of genome file] --pieces [No. of p... | jasdumas/DouglasFir | splitfasta2.py | Python | gpl-2.0 | 1,536 | [
"Biopython"
] | a10fc6a3ab1ffe7ec497dc65964b05bde20143a6a7510c9e66b9aae3121c8aa5 |
# Copyright 2017 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... | yanchen036/tensorflow | tensorflow/contrib/autograph/converters/ifexp.py | Python | apache-2.0 | 1,634 | [
"VisIt"
] | 00fc65e1ca3d9c03d20396e85cedbc5a497b0ddde993202eb6573d90bf3c1fcc |
import random
import numpy as np
from operator import itemgetter
from ase.ga.offspring_creator import OffspringCreator
from ase.ga.utilities import get_distance_matrix, get_nndist
from ase import Atoms
class Mutation(OffspringCreator):
"""Base class for all particle mutation type operators.
Do not call this ... | askhl/ase | ase/ga/particle_mutations.py | Python | gpl-2.0 | 16,481 | [
"ASE"
] | 631ef3eba91c05b0c2af383cab28486d812a56ef9b41ccac11044628d8ed384d |
import movie_class
import movie_website
iron_man = movie_class.Movie(
"Iron Man",
"https://upload.wikimedia.org/wikipedia/en/7/70/Ironmanposter.JPG",
"https://www.youtube.com/watch?v=8hYlB38asDY")
incredible_hulk = movie_class.Movie(
"The Incredible Hulk",
"https://upload.wikimedia.org/wikipedia/e... | JSBCCA/pythoncode | early_projects/movie_project/movie.py | Python | mit | 3,020 | [
"Galaxy"
] | b3f965d34de08aa93f7d53e04c0ae55f1ab3de505a3ec04d35f5fe2006be7fd1 |
# -*- coding: utf-8 -*-
# Copyright 2019 The GraphicsFuzz Project 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless requi... | google/graphicsfuzz | gfauto/gfauto/fuzz_glsl_amber_test.py | Python | apache-2.0 | 17,372 | [
"Amber"
] | f915b3cada827fdd8a4d91cd1253ea8c6577806a2e6254d1102b6c77ed7b71f6 |
class NonLocalFunctionalFactory:
"""Factory class.
NonLocalFunctionalFactory is used by xc_functional.py, when the
functional starts with words GLLB.
It contains a method called get_functional_by_name, which takes
the xc-name for non-local functional and returns the corresponding
NonLocalF... | qsnake/gpaw | gpaw/xc/gllb/nonlocalfunctionalfactory.py | Python | gpl-3.0 | 3,759 | [
"GPAW"
] | 2c96ed980343d61b3a414bb862fb27ce4cded7d6a51a696d3e1c52f20f1ee799 |
# This file is part of wger Workout Manager.
#
# wger Workout Manager 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 Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# wger W... | rolandgeider/wger | wger/core/tests/test_temporary_users.py | Python | agpl-3.0 | 7,379 | [
"VisIt"
] | fa48db46cab399cc2d9a7aedac0a43559699862a3a415d4600e6f0ef3ecc4877 |
# -*- coding: utf-8 -*-
# imports here
from aiida.parsers.exceptions import OutputParsingError
#
from aiida.orm.data.parameter import ParameterData
#
from aiida.parsers.plugins.vasp.instruction import BaseInstruction
__copyright__ = u'Copyright © 2016, Mario Zic, Trinity College Dublin. All Rights Reserved.'
__licens... | abelcarreras/aiida_extensions | plugins/parsers/vasp/instruction/error/default_error_parser.py | Python | mit | 1,974 | [
"VASP"
] | f46effba57b7d54e4b4cb1573682fe1aea8a55bd6188039a15b28ae1d8c7962f |
#! /usr/bin/python
import math
import os, sys
ncs_lib_path = ('../../../')
sys.path.append(ncs_lib_path)
import ncs
def run(argv):
calcium_channel = {
#type of channel
"type": "calcium_dependent",
#starting value, Unit: none
"m_initial": 0.0,
#Unit: mV
"reversal_potential": -80,
"m_power": 2,
#cond... | BrainComputationLab/ncs | python/samples/models/lif/regular_spiking_lif.py | Python | bsd-2-clause | 1,992 | [
"NEURON"
] | 8f48626ca629651e0eb1b16ac67d3dddbed6b88c5fffe1663473452a4a4d5a25 |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Makes sure files have the right permissions.
Some developers have broken SCM configurations that flip the executable
permission... | chromium/chromium | tools/checkperms/checkperms.py | Python | bsd-3-clause | 14,880 | [
"xTB"
] | c4bce70762a1574857e5cc914489694a5c961f5fd4b8180608b6560a236a06c3 |
import numpy as np
import fir_filter
import gauss_pulse
import comms_filters
import json
class modulator
def __init__(self, modulation_type, samples_per_symbol, pulse_factor, pulse_length, config, filename):
"""
Create the generic modulator object and specify the modulation parameters.
"""
#... | phase4ground/DVB-receiver | modem/python/library/modulator.py | Python | gpl-3.0 | 3,566 | [
"Gaussian"
] | 27f3f52f54a424e40436e8b3b06320f445cceeeba6cdc4ff7e8d9ffd64cd47c1 |
# This file is part of the myhdl library, a Python package for using
# Python as a Hardware Description Language.
#
# Copyright (C) 2003-2013 Jan Decaluwe
#
# The myhdl library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public License as
# published by t... | palashahuja/myhdl | myhdl/_intbv.py | Python | lgpl-2.1 | 16,320 | [
"VisIt"
] | 011f54f4e08db0def5f6704da97cc7000852aba0895b2ba3ac64b76ee89691a0 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2018 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | amjames/psi4 | psi4/driver/qcdb/molparse/chgmult.py | Python | lgpl-3.0 | 26,251 | [
"Psi4"
] | 7a6b3dc45906dbe0fef6172627776222a6cc4e95f283abb5bde34a8a8a5305a8 |
import logging, os, sys
from galaxy.util.odict import odict
from galaxy.util.bunch import Bunch
from galaxy import util, jobs, model
from galaxy.forms.forms import form_factory
from galaxy.external_services.service import ExternalServiceActionsGroup
from elementtree.ElementTree import XML
from galaxy.sample_tracking.da... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/sample_tracking/external_service_types.py | Python | gpl-3.0 | 6,273 | [
"Galaxy"
] | 5ad250fd8d0c7702c328dd78e92f09a101f915a9f247bd57f1037f9f4ff1a55a |
########################################################################
# $HeadURL $
# File: File.py
# Date: 2012/08/03 15:02:53
########################################################################
"""
:mod: File
.. module: File
:synopsis: RMS operation file
operation file
"""
# Disable invalid names warning
#... | andresailer/DIRAC | RequestManagementSystem/Client/File.py | Python | gpl-3.0 | 5,524 | [
"DIRAC"
] | 95b99145c80976adfd452cfd672218d53ec9b54bf73fde3e45fc4fa425282a17 |
import numpy as np
import pandas as pd
# from matplotlib.pyplot import plot,show,draw
import scipy.io
import sys
sys.path.append("../")
from functions import *
from pylab import *
from sklearn.decomposition import PCA
import _pickle as cPickle
import matplotlib.cm as cm
import os
import matplotlib.gridspec as gridspec
... | gviejo/ThalamusPhysio | python/main_test_CORR_HD_AUTO_SWR.py | Python | gpl-3.0 | 3,914 | [
"Gaussian"
] | 4cdf1f69ea098f62fe0e2770a07732b03909998851deeb2c6f2341282820e008 |
from sqlalchemy import (
Column, String, BigInteger, Integer, ForeignKey, DateTime, Boolean)
from sqlalchemy import func
from sqlalchemy.ext.declarative import declarative_base
from sqlalchemy.orm import relationship, backref, scoped_session, sessionmaker
from zope.sqlalchemy import ZopeTransactionExtension
import ... | geyer-moldfusz/gmi.most_used_sites.backend | src/gmi/mostusedsites/backend/models.py | Python | gpl-3.0 | 2,010 | [
"VisIt"
] | bd5f08fc071c6246e62176435e59e6b6c3377a7f90f044928126e21aff67f8c1 |
"""Estimate tumor purity and frequency using copy number and allele freqencies with BubbleTree.
http://www.bioconductor.org/packages/release/bioc/html/BubbleTree.html
http://www.bioconductor.org/packages/release/bioc/vignettes/BubbleTree/inst/doc/BubbleTree-vignette.html
"""
from __future__ import print_function
impor... | biocyberman/bcbio-nextgen | bcbio/heterogeneity/bubbletree.py | Python | mit | 18,974 | [
"Bioconductor",
"pysam"
] | f6e7a4f2a02c68443d0edac9b907430a0faed6cf5c09361918f1910d9d9b755b |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import json
import glob
import itertools
import logging
import math
import os
import re
import warnings
from pathlib import Path
import xml.etree.cElementTree as ET
from collections import defaultdict
from io ... | dongsenfo/pymatgen | pymatgen/io/vasp/outputs.py | Python | mit | 186,606 | [
"CRYSTAL",
"VASP",
"VisIt",
"pymatgen"
] | 5ca908cb9f230261806df057a6c9e1aba590509abe5ec586fbe3c12a8f4fa869 |
# 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/math/psd_kernels/schur_complement.py | Python | apache-2.0 | 22,193 | [
"Gaussian"
] | f94af24b90653e58c15675b8508bd1ca86faded37443c17fe4640dd6f9ad0382 |
#@+leo-ver=4-thin
#@+node:paul.20120216232750.10758:@shadow utils.py
#@@language python
#@@tabwidth -4
#@+others
#@+node:paul.20120216232750.10759:utils declarations
"""Some utilities that speed up common operations"""
import sys
import os
import pygame
import subprocess
import serge
import serge.render
import serge.... | smmosquera/serge | blocks/.leo_shadow/xutils.py | Python | lgpl-3.0 | 13,508 | [
"VisIt"
] | 745fc9ab7c3d704b97c99ea143a05b318140ccefeda47bc9e8e085a86f26f356 |
#!/usr/bin/env python
# coding: utf-8
import os
from numpy.distutils.core import Extension, setup
########################
# Fortran extensions #
########################
Delhommeau_source = [
"capytaine/green_functions/Delhommeau_f90/constants.f90",
"capytaine/green_functions/Delhommeau_f90/old_Pr... | mancellin/capytaine | setup.py | Python | gpl-3.0 | 3,857 | [
"VTK"
] | a4b59038171c93ae9e5b24a580e7fd426b02a2c2ad398af6145bdd27b132d26a |
import numpy
import cupy
from cupy._core import internal
from cupyx.scipy.ndimage import _util
from cupyx.scipy import special
def _get_output_fourier(output, input, complex_only=False):
types = [cupy.complex64, cupy.complex128]
if not complex_only:
types += [cupy.float32, cupy.float64]
if outpu... | cupy/cupy | cupyx/scipy/ndimage/_fourier.py | Python | mit | 9,527 | [
"Gaussian"
] | 202f7f6c647a40273b1fb80728c7bc76e002a32c96f816315bc3fe3703adcfaa |
from pympler.asizeof import asizeof
import prometheus_client as prom
class SimMonitor:
def __init__(self,
tag="",
reporter_order=(
'hdf5_reporter',
'dashboard_reporter',
),
):
self.tag = tag
self.rep... | ADicksonLab/wepy | jigs/trio_mapper/source/lysozyme_we.py | Python | mit | 11,203 | [
"OpenMM"
] | 441c46f65eecfcc1057a6a3befb9cbeb9a04509bc184f7cdc2280bedb1ebe635 |
#########################################################################################
# $HeadURL$
# LSF.py
# 10.11.2014
# Author: A.T.
#########################################################################################
""" LSF.py is a DIRAC independent class representing LSF batch system.
LSF objects are... | Sbalbp/DIRAC | Resources/Computing/BatchSystems/LSF.py | Python | gpl-3.0 | 5,765 | [
"DIRAC"
] | bdfbdc940f7422a2e969970608945366f8b72bdbe8b820d83e16972af116c55a |
"""Migration script to change repository.type column value from generic to unrestricted."""
from sqlalchemy import *
from sqlalchemy.orm import *
from migrate import *
from migrate.changeset import *
# Need our custom types, but don't import anything else from model
from galaxy.model.custom_types import *
import sys... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/webapps/tool_shed/model/migrate/versions/0021_change_repository_type_value.py | Python | gpl-3.0 | 1,180 | [
"Galaxy"
] | 17fb8e4c87b52287f98ff8a3e62b541723b63d3934fedc29ea24ae37a1d3620c |
# csymbol.py
# This file contains the symbol and Full Form of the symbol
def stockSym():
return {"ADBL":"Agricultural Development Bank Ltd",
"BOK":"Bank of Kathmandu",
"CBL":"Civil Bank Ltd",
"CCBL":"Century Commercial Bank Ltd.",
"CTBNL":"Commerz and Trust Bank Ne... | acsudeep/nepserate | nepserate/csymbol.py | Python | mit | 21,463 | [
"CRYSTAL"
] | 2492e6fbc39232a06bf0cffc990a18c328865cb6af636a63fba83cf00571f3c6 |
""" pytest of Core.Utilities.Dictionaries
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import pytest
# sut
from DIRAC.Core.Utilities.Dictionaries import breakDictionaryIntoChunks
@pytest.mark.parametrize(
"aDict, chunkSize, expectedSizes",
... | ic-hep/DIRAC | src/DIRAC/Core/Utilities/test/Test_Dictionaries.py | Python | gpl-3.0 | 976 | [
"DIRAC"
] | 545f59b1239587cb400556875bcf771eeb3ce40cf0005a3313849f6a8a2c0332 |
#! /usr/bin/env python
"""
This program plots the energies of each kohn-sham state along the MD trajectory
Note that you have to provide the location of the folder where the NAMD
hamiltonian elements are stored using the -p flag
"""
import numpy as np
import matplotlib.pyplot as plt
import glob
import argparse
import... | felipeZ/nonAdiabaticCoupling | scripts/hamiltonians/plot_mos_energies.py | Python | mit | 2,075 | [
"NAMD"
] | 928dcf2cb8d4d952cf6d8e165c7d01bb61ca73a7b5aad79dc7c9e6d8aa3954b6 |
['1a0s', 'FOBS::f_obs is None::i_obs is None']
['1am7', 'FOBS::f_obs is None::i_obs is None']
['1av2', 'I(+),SIGI(+),I(-),SIGI(-)::f_obs is None::i_obs is None']
['1axg', 'FOBS::f_obs is None::i_obs is None']
['1b26', 'FOBS::f_obs is None::i_obs is None']
['1b7b', 'FOBS::f_obs is None::i_obs is None']
['1b8d', 'FOBS::f... | youdar/work | work/MTRIX/MTRIX_r_calc_error_list.py | Python | mit | 5,003 | [
"CRYSTAL"
] | dc8b4b617bf1b5132088da09003afe58ecbbabf9d65b3a9dd434637f6c7caa1c |
import subprocess
import os
from os import listdir
#========== gsnap alignment ==========================
def gsnap_Db(fa,db_path,db_name,annotation):
"""
This function builds index for genome
"""
cmd = ('gmap_build -D {db_path} -d {db_name} {fa}').format(db_path=db_path,db_name=db_name,fa=fa)
sub... | shl198/Pipeline | Human_GATK_vari_call/f02_aligner_command.py | Python | mit | 10,339 | [
"BLAST",
"BWA"
] | 80ddcf333496bd0267af4e27084b0cab168588eb05487d44e69b4d96f674b77f |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.