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from test import test_support
import unittest
import codecs
import sys, StringIO
class Queue(object):
"""
queue: write bytes at one end, read bytes from the other end
"""
def __init__(self):
self._buffer = ""
def write(self, chars):
self._buffer += chars
def read(self, size=-1... | mancoast/CPythonPyc_test | cpython/242_test_codecs.py | Python | gpl-3.0 | 27,615 | [
"FEFF"
] | ecc615e6afdf477a19e7d19eb822871eb15911b39c8a1e443357863ed5245241 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RCner(RPackage):
"""CNE Detection and Visualization.
Large-scale identification an... | iulian787/spack | var/spack/repos/builtin/packages/r-cner/package.py | Python | lgpl-2.1 | 2,204 | [
"Bioconductor"
] | 65376e86d7f79401c085d5e56328300abfdc2de7a2bd4008bdde1da7ee5a930c |
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2008-2011 Kees Bakker
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2013-2017 Alois Poettker <alois.poettker@gmx.de>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms ... | ennoborg/gramps | gramps/plugins/importer/importprogen.py | Python | gpl-2.0 | 78,972 | [
"Brian"
] | be87e24cbbba12ee7b22ae27d4b97f13c99c27c9f189dd451f07a3e5cd2a7c8e |
# import numpy as np
# import pandas as pd
#
# # base = library('base') -- import packages from R
# from rpy2.robjects.packages import importr as library
# # R.R('x <- 1') AND R.Array('...') etc -- the core interface
# import rpy2.robjects as R
# # Not clear what this does yet, but allows numpy->R easily?
# import rp... | amloewi/css-blockmodels | testing_rpy2.py | Python | mit | 1,545 | [
"Gaussian"
] | b9be0eeb69e4d9fa093217df0a60430560915a45f7de76fbce944e191d68c109 |
import matplotlib.pyplot as plt
import numpy as np
from grids import DartmouthPMS, PISA, Baraffe15, Seiss
# grid = DartmouthPMS(age_range=[1, 200], mass_range=[0.5, 2.5])
# grid = PISA(age_range=[1, 100], mass_range=[0.5, 2.0])
grid = Baraffe15(age_range=[1, 100], mass_range=[0.5, 1.4])
# grid = Seiss(age_range=[1, 1... | iancze/ScottiePippen | george_tracks.py | Python | mit | 3,812 | [
"Gaussian"
] | 81e1ed38ffaaeb060012072c0bcb6eda9542172e8e2eaba34f1db8706014774a |
#!/usr/bin/env python
#Copyright (C) 2014 by Glenn Hickey
#
#Released under the MIT license, see LICENSE.txt
import unittest
import sys
import os
import argparse
import logging
import numpy as np
import math
import copy
from teHmm.track import TrackList
from teHmm.trackIO import readTrackData, getMergedBedIntervals
f... | glennhickey/teHmm | bin/setTrackScaling.py | Python | mit | 8,621 | [
"Gaussian"
] | 238ab7e445c98af488dd1a33b2ea5c93c73724a320b2ed77e0f2cf43ab75084e |
# Licensed under GPL version 3 - see LICENSE.rst
import numpy as np
from astropy.io import ascii
from .base import FlatOpticalElement, FlatStack
from ..math.utils import norm_vector, e2h, h2e
class FlatBrewsterMirror(FlatOpticalElement):
'''Flat mirror operated at the Brewster angle.
Calculation of the Fres... | hamogu/marxs | marxs/optics/multiLayerMirror.py | Python | gpl-3.0 | 7,308 | [
"Gaussian"
] | c5e627d2e61157ac5535a6b2e01621ca4925c86507aa224328602f389a6e03a7 |
'''Connor-specific classes for working with alignments'''
from __future__ import print_function, absolute_import, division
import connor.utils as utils
class PairedAlignment(object):
'''Represents the left and right aligns from a single paired sequence.'''
def __init__(self,
left_alignment,
... | umich-brcf-bioinf/Connor | connor/consam/alignments.py | Python | apache-2.0 | 6,938 | [
"pysam"
] | b62fb4d1dbd7f70aa22e47fb4ed38d27b5a3fd44738021cad5dc27dc1321f8c3 |
"""
This integration tests will perform basic operations on a storage element, depending on which protocols are available.
It creates a local hierarchy, and then tries to upload, download, remove, get metadata etc
Potential problems:
* it might seem a good idea to simply add tests for the old srm in it. It is not :-)
... | Andrew-McNab-UK/DIRAC | tests/Integration/Resources/Storage/Test_Resources_GFAL2StorageBase.py | Python | gpl-3.0 | 12,158 | [
"DIRAC"
] | 1accf30eee90111b6c1e18b6e26a59b0096590064906b82d1579006a605f0858 |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | kwhitehall/climate | ocw/tests/test_local.py | Python | apache-2.0 | 7,933 | [
"NetCDF"
] | e9b36b50be900a5b41d1c13ff564880fd9a0c26ae16a2cdc475a0e2ec5542f51 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes to handle the calculation of the IR spectra
This implementation is adapted from Abipy
https://github.com/abinit/abipy
where it was originally done by Guido Petretto and Matteo Gi... | fraricci/pymatgen | pymatgen/phonon/ir_spectra.py | Python | mit | 8,288 | [
"ABINIT",
"pymatgen"
] | 9268011e29d0607131533f36efc1094cd70439a6eeb0c72948fd8f14756c750e |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
import django.db.models.deletion
import C4CApplication.models.member
class Migration(migrations.Migration):
dependencies = [
]
operations = [
migrations.CreateModel(
name='Branch... | dsarkozi/care4care-sdp-grp4 | Care4Care/C4CApplication/migrations/0001_initial.py | Python | agpl-3.0 | 7,094 | [
"VisIt"
] | f254fb11d28b43611cc0d73c5f7e0cb022d7a6ba88052f67071fafb9ba5fc3dd |
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | GoogleCloudPlatform/terraform-google-secured-data-warehouse | helpers/wrapped-key/wrapped_key.py | Python | apache-2.0 | 6,617 | [
"VisIt"
] | 3d7ca8f9f817436667677b6929a69aea9812663f2615f5d375f52cc7e3de5e82 |
#
# Copyright 2015 The AMP HTML 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 applic... | yandex-pcode/amphtml | validator/validator_gen_js.py | Python | apache-2.0 | 35,927 | [
"VisIt"
] | c2b2d75453b459faf8c6bad300293bb6982e694b3848467dce33a38c6519e9b5 |
rows = [
{'fname': 'Brian', 'lname': 'Jones', 'uid': 1003},
{'fname': 'David', 'lname': 'Beazley', 'uid': 1002},
{'fname': 'John', 'lname': 'Cleese', 'uid': 1001},
{'fname': 'Big', 'lname': 'Jones', 'uid': 1004}
]
from operator import itemgetter
rows_by_fname = sorted(rows, key=itemgetter('fname'))
ro... | likeleon/Python | cookbook/1.13 일반 키로 딕셔너리 리스트 정렬.py | Python | gpl-2.0 | 724 | [
"Brian"
] | 14e3fe77dee2013b01bafe8a52793abaf5cf1973af89d9cd4a7033a5aa237792 |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | rednaxelafx/apache-spark | python/pyspark/ml/tests/test_training_summary.py | Python | apache-2.0 | 25,473 | [
"Gaussian"
] | c20010202c99cfc73e089c2b28820be45dfcb044059573fda828c1246731b6a1 |
from PyOpenWorm import DataUser,Neuron,Network
import neuroml as N
class NeuroML(DataUser):
@classmethod
def generate(cls, o, t=2):
"""
Get a NeuroML object that represents the given object. The ``type`` determines what content is included in the NeuroML object:
:param o: The object to... | mwatts15/PyOpenWorm | PyOpenWorm/my_neuroml.py | Python | mit | 1,345 | [
"NEURON"
] | 2c03fe12d3641fc8a37bc07962ab081ef172360bd4491f3d86aec8c829c34dfe |
#!/usr/bin/env python
from peacock.utils import Testing
from PyQt5 import QtCore, QtWidgets
from peacock.Input.ParameterInfo import ParameterInfo
class TestAddVariableAndBlock(Testing.PeacockAppImageTestCase):
"""
Tests that if variables are added that GUI maintains it selections
"""
qapp = QtWidgets.Q... | Chuban/moose | python/peacock/tests/peacock_app/check_add_variables_and_blocks/test_AddVariableAndBlock.py | Python | lgpl-2.1 | 4,079 | [
"VTK"
] | d9fb9604545677421b6681284158635d88a43f8e304bdb8268c541f8041b5053 |
"""
Classes for reading, parsing, and writing workflow batch submit files for
Globus Galaxy.
"""
import logging
import re
from collections import OrderedDict
from .. import parsing
logger = logging.getLogger(__name__)
class WorkflowBatchFile(object):
def __init__(self, path, state='template'):
"""
... | BenaroyaResearch/bripipetools | bripipetools/io/workflowbatch.py | Python | mit | 5,966 | [
"Galaxy"
] | d146abe11199076d04ced80f935533f9eb18f3d08f333a68d1ff5518005c37fa |
#!/usr/bin/env python
#pylint: disable=missing-docstring
#################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment #
# #... | Chuban/moose | python/chigger/tests/vector/vector_x.py | Python | lgpl-2.1 | 1,170 | [
"MOOSE"
] | 4b597960fb77b34e96bc5720c9905a5fa87132abce1eb6562fc83781e990c1c1 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright (C) 2017-2018 CIRCL Computer Incident Response Center Luxembourg (smile gie)
# Copyright (C) 2017-2018 Christian Studer
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public Li... | devnull-/MISP | app/files/scripts/stix2/misp2stix2.py | Python | agpl-3.0 | 60,904 | [
"Galaxy"
] | 5963a0650353baff5f54718dff30919175cff0cc46517adffe9da45c73b82536 |
# -*- coding: utf-8 -*-
# ****************************************************************************
# Copyright 2015-2017 Lukasz Mentel
#
# This file is distributed under the terms of the
# GNU General Public License. See the file 'COPYING'
# in the root directory of the present distribution,
# or http://www.gnu.or... | lmmentel/ase-espresso | espresso/__init__.py | Python | gpl-3.0 | 600 | [
"ESPResSo"
] | 0f82e5dc6126ca26ea644674847d6e19a7da51f23664e8b6741b6645d80c9373 |
#!/usr/bin/env python
"""
This script uses matplotlib to compare reference output file(s) with data in tabular form
with the corresponding file(s) generated by the automatic test.
Multiple files can be specified via the command line interface.
Example:
pltdiff.py t88o_DS2_PHDOS
Usage: pltdiff.py file1 [file2, ..... | abinit/abinit | developers/pltdiff.py | Python | gpl-3.0 | 5,645 | [
"ABINIT"
] | 56d0bfd030a6c6bb1407a4804d1245c3c201d0a91059a9e502e0032475356291 |
###########################################################################
#
# 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/sdf_to_bigquery_dag.py | Python | apache-2.0 | 6,653 | [
"VisIt"
] | c41766344ca8cb09025b19f7c124401d409fe5dd4f24bface233ae4402fb3d26 |
from numpy import infty
from numpy.random import uniform
from queueing_tool.queues.choice import _choice, _argmin
class Agent(object):
"""The base class for an agent.
``Agents`` are the objects that move throughout the network.
``Agents`` are instantiated by a queue, and once serviced the
``Agent`` ... | djordon/queueing-tool | queueing_tool/queues/agents.py | Python | mit | 6,408 | [
"VisIt"
] | 38860cf5dea69193eedf71ddd93e9cb60a78430c3a3f90424896c1c8bdf5d19e |
# setup.py ---
#
# Filename: setup.py
# Description:
# Author: subha
# Maintainer:
# Created: Sun Dec 7 20:32:02 2014 (+0530)
# Version:
# Last-Updated: Wed Mar 2 12:23:55 2016 (-0500)
# By: Subhasis Ray
# Update #: 32
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#
# Change log:
#
#
#
#... | rahulgayatri23/moose-core | setup.py | Python | gpl-3.0 | 14,427 | [
"MOOSE",
"NEURON"
] | 5cfaddf5f388eb24e6fe096d9568d4217a4b6271d0f956f995893d5ffea265e6 |
from django.core.urlresolvers import reverse
from django.conf import settings
from django.http import HttpResponseRedirect
from django.views.generic import RedirectView, TemplateView, FormView
from analytics.models import Visit
from .api import RedisProject, RedisRedirect
from .forms import SlugForm
THRESHOLD = getat... | yetizzz/zzz | src/hydra/views.py | Python | bsd-2-clause | 3,649 | [
"VisIt"
] | 5c0b7d4f8865f739f8e4cc8a29533d2c68cf24a86914294db56ee146569d9848 |
# Segment ground voxels
# May 2016 - Martijn Koopman
# ToDo: Clean code; Pass variable dims to function GetArrValue() and SetArrValue() as arguments.
# ToDo: Clean code; Use for loop to iterate over neighbours.
from collections import deque
# User defined parameter:
vertical_footspan = 1 # Number o... | martijnkoopman/thesis | 2_2_segmentation.py | Python | gpl-3.0 | 7,586 | [
"VTK"
] | 85e6997ae6b34acdd0c019b66d587a58b88ceb19664b93914a572e0521f3178f |
from .ast import *
class PrettyPrint(ASTVisitor):
def __init__(self):
pass
def visit(self, node):
print (node.__class__.__name__)
class CheckSingleAssignment(ASTVisitor):
def __init__(self):
self.assignment_table=[]
def visit(self, node):
if isinstance(node, ASTProgram):
for child in ... | cs207-project/pype-package | pype/semantic_analysis.py | Python | mit | 1,876 | [
"VisIt"
] | 9fd2b496ec58e0731bebeb438fcb657b1aa6a5d8ac671544277e8595a235ca54 |
# hg.py - hg backend for convert extension
#
# Copyright 2005-2009 Matt Mackall <mpm@selenic.com> and others
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 or any later version.
# Notes for hg->hg conversion:
#
# * Old versions of Mercurial didn't tr... | ya790206/temp_hg | hgext/convert/hg.py | Python | gpl-2.0 | 17,175 | [
"Octopus"
] | 441ef0eca12b6b84cc2b876e384976ac453473de3b6e8293b129b956b4526ded |
"""
vtk renderer scenes
"""
import vtk
from math import exp, sqrt, sin, cos
def create_renderer():
"""
vtk renderer with a sample scene
"""
quadric = vtk.vtkQuadric()
quadric.SetCoefficients(.5, 1, .2, 0, .1, 0, 0, .2, 0, 0)
sample = vtk.vtkSampleFunction()
sample.SetSampleDimensions(50,... | viz4biz/PyDataNYC2015 | tutorial/scenes.py | Python | apache-2.0 | 7,094 | [
"VTK"
] | 85e9a392d1406ca581c07855ed5728df57bb58eadf0ae6fad40ce12842d1271e |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 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
#... | psi4/psi4 | psi4/driver/qcdb/align.py | Python | lgpl-3.0 | 6,553 | [
"Psi4"
] | 6ed58e265d0b8116ce34b0c50d39af9fe83ab3de4029c6972635012e1ba0a2a0 |
"""Implements HOT-SAX."""
import numpy as np
from saxpy.znorm import znorm
from saxpy.sax import sax_via_window
from saxpy.distance import euclidean
def find_discords_hotsax(series, win_size=100, num_discords=2, alphabet_size=3,
paa_size=3, znorm_threshold=0.01, sax_type='unidim'):
"""HOT... | seninp/saxpy | saxpy/hotsax.py | Python | gpl-2.0 | 4,860 | [
"VisIt"
] | 2293d81f2b391e7d47ea21c73436590c88da1ace91b1090e9a3ffe8ed68e22c8 |
#!/usr/bin/env python
#JSON {"lot": "UHF/cc-pVDZ",
#JSON "scf": "PlainSCFSolver",
#JSON "linalg": "CholeskyLinalgFactory",
#JSON "difficulty": 2,
#JSON "description": "Basic UHF example with Cholesky decomposition of the ERI"}
from horton import *
# Load the coordinates from file.
# Use the XYZ file from HORTON's... | crisely09/horton | data/examples/hf_dft/uhf_methyl_cholesky.py | Python | gpl-3.0 | 1,864 | [
"Gaussian"
] | 7034c89fa8417af00057c83f04114454be09969f673a6063e6ea65153746d81f |
#!/usr/bin/env python
# Copyright (C) 2011 Atsushi Togo
# All rights reserved.
#
# This file is part of phonopy.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# * Redistributions of source code must retain the ab... | quanshengwu/wannier_tools | utility/phonopyTB/phonon_hr.py | Python | gpl-3.0 | 19,854 | [
"ABINIT",
"CRYSTAL",
"Elk",
"SIESTA",
"VASP",
"WIEN2k",
"Wannier90",
"phonopy"
] | 03f90c825fcec40e0bf4ee7984c4fb20e6deb396cc276619cf1b3453b50aa12d |
"""
@name: Modules/House/Family/hue/hue_device.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2017-2020 by D. Brian Kimmel
@note: Created on Dec 18, 2017
@license: MIT License
@summary:
"""
from Modules.Core.Utilities.debug_tools import PrettyFormatAny
__updated__ = '20... | DBrianKimmel/PyHouse | Project/src/Modules/House/Family/Hue/hue_device.py | Python | mit | 4,806 | [
"Brian"
] | 9f45f3c1bdbd77f70b3c5c2ecae72900c81e798ad553d308d9902f33e0f0ddfb |
# 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, ... | keras-team/reservoir_nn | reservoir_nn/utils/image_operations.py | Python | apache-2.0 | 24,209 | [
"Gaussian"
] | 3fefa93d83e098354eb734afc20bb5476eb35be448f34d73081a44e52d6ef2e0 |
"""
Use GDM to obtain maximally entangled orbitals
"""
import numpy as np
import scipy.linalg as slg
from frankenstein.pyscf_be.fragpart import get_boys_orbs
from pyscf.lib import logger
from pyscf import lo
def kernel(me, C0=None):
me.ov, me.C = me.get_init_guess(C0)
optimizer = me.get_optimizer()
m... | hongzhouye/frankenstein | pyscf_be/maxent_orb.py | Python | bsd-3-clause | 10,021 | [
"PySCF"
] | 8f865638791dc21ee56a829ef28be29189914966230520b335d561959c3ff135 |
#!/usr/bin/python
#
# Copyright 2010 Brian Dolbec <brian.dolbec@gmail.com>
# Copyright 2010 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
#
# $Header$
from __future__ import print_function
__version__= "0.0.1"
__author__ = "Brian Dolbec"
__email__ = "brian.dolbec@gmail.com"
fro... | djanderson/equery | pym/gentoolkit/test/eclean/test_clean.py | Python | gpl-2.0 | 3,903 | [
"Brian"
] | 3cfa9c02fea1d09800ff5df6fd3aee87dc896c96e586763c4ac9d5e4c791b0ae |
# -*- coding: utf-8 -*-
r"""Tests special functions
"""
import numpy as np
import pytest
from neutronpy import functions
from scipy.integrate import simps
def test_gauss_norm():
"""Test 1d gaussian
"""
p = np.array([0., 0., 1., -30., 3., 1., 30., 3.])
x = np.linspace(-1e6, 1e6, 8e6 + 1)
y = funct... | pseudocubic/neutronpy | tests/test_functions.py | Python | mit | 1,970 | [
"Gaussian"
] | 9dea4a84328ed9761af62fa0215f36677537931b4878b9cd89daa2d2f5e5da54 |
import matplotlib.pyplot as plt
import numpy as np
import pytest
from pysisyphus.calculators.AnaPot import AnaPot
from pysisyphus.calculators.PySCF import PySCF
from pysisyphus.drivers import run_opt
from pysisyphus.helpers import geom_loader
from pysisyphus.tsoptimizers import *
from pysisyphus.testing import using
... | eljost/pysisyphus | tests/test_tsopt/test_tsopt.py | Python | gpl-3.0 | 2,177 | [
"PySCF"
] | 9daf24a140fccd45675422e5d1c868b8ce9b3c4aff374317ff3de903d9767e7d |
#!/usr/bin/env python3
# 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.
'''
Checks a policy_templates.json file for conformity to its syntax specification.
'''
import argparse
import ast
import json
imp... | chromium/chromium | components/policy/tools/syntax_check_policy_template_json.py | Python | bsd-3-clause | 82,546 | [
"VisIt"
] | 7c90635dc79edc6416708197d15d4eeb32744969410baa90075ef79e2a7415d0 |
# -*- coding: ISO-8859-15 -*-
# =============================================================================
# Copyright (c) 2004, 2006 Sean C. Gillies
# Copyright (c) 2007 STFC <http://www.stfc.ac.uk>
#
# Authors :
# Dominic Lowe <d.lowe@rl.ac.uk>
#
# Contact email: d.lowe@rl.ac.uk
# ========================... | bird-house/OWSLib | owslib/coverage/wcs100.py | Python | bsd-3-clause | 18,987 | [
"NetCDF"
] | e52eaedc4a6d6f29993ce56724418c89a32026bd01fe4a3ce62ac04128a6381b |
""" The HTCondor TimeLeft utility interrogates the HTCondor batch system for the
current CPU consumed, as well as its limit.
"""
__RCSID__ = "$Id$"
import os
from DIRAC import S_OK, S_ERROR
from DIRAC.Resources.Computing.BatchSystems.TimeLeft.TimeLeft import runCommand
from DIRAC.Resources.Computing.BatchSystems... | yujikato/DIRAC | src/DIRAC/Resources/Computing/BatchSystems/TimeLeft/HTCondorResourceUsage.py | Python | gpl-3.0 | 2,437 | [
"DIRAC"
] | 3b3f9f0c2534980bbfaa647fdeff9538c8979395a8f4876b461dd0a35816af0a |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkConeSource(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtk... | chrisidefix/devide | modules/vtk_basic/vtkConeSource.py | Python | bsd-3-clause | 467 | [
"VTK"
] | 8163dad8f4202a0ab70d286c2d0d586a3d2b7b50e7103bd3c2fa93b3c717edf5 |
#
# Restriction Analysis Libraries.
# Copyright (C) 2004. Frederic Sohm.
#
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
# this script is used to produce the dictionary which will con... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/Restriction/_Update/RestrictionCompiler.py | Python | apache-2.0 | 35,222 | [
"Biopython"
] | ac0bc0f29cb406f434c133f69006f9855c61fcdec2b409c0d97484068975756d |
# ################################################################
# slidenc is a data visualization tool
# Copyright (C) 2011-2014 Stefan Riha
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, ... | poidl/slidenc | slidenc/reader.py | Python | gpl-3.0 | 22,511 | [
"NetCDF"
] | 9911ca68a9f8a5ac0cce529833b2437dbea370274572d58ab9fa0ccf2ec3603f |
"""
Covariance estimators using shrinkage.
Shrinkage corresponds to regularising `cov` using a convex combination:
shrunk_cov = (1-shrinkage)*cov + shrinkage*structured_estimate.
"""
# Author: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Gael Varoquaux <gael.varoquaux@normalesup.org>
# Virgile ... | huzq/scikit-learn | sklearn/covariance/_shrunk_covariance.py | Python | bsd-3-clause | 22,312 | [
"Gaussian"
] | 80d7afcd62a9424baac69c8f53961dc9188525ccd863f076d64f7710964d4241 |
'''
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be... | akellehe/biclustering | bicluster.py | Python | gpl-3.0 | 7,989 | [
"Gaussian"
] | 4a122a13343f820f184130a15789fb7655b23708339b52cfa5f8b82531178daf |
'''
The settings for OSMC are handled by the OSMC Settings Addon (OSA).
In order to more easily accomodate future changes and enhancements, each OSMC settings bundle (module) is a separate addon.
The module can take the form of an xbmc service, an xbmc script, or an xbmc module, but it must be installed into the u... | srmo/osmc | package/mediacenter-addon-osmc/src/script.module.osmcsetting.pioverclock/resources/osmc/OSMCSetting.py | Python | gpl-2.0 | 9,682 | [
"VisIt"
] | d04b6cf4b9a66b7670e8d47eebedafda41a86d5a9211bcc58250129fb70fd763 |
"""loader_moose.py:
Load a SWC file in MOOSE.
"""
__author__ = "Dilawar Singh"
__copyright__ = "Copyright 2015, Dilawar Singh and NCBS Bangalore"
__credits__ = ["NCBS Bangalore"]
__license__ = "GNU GPL"
__version__ = "1.0.0"
__maintainer__ = "Dilawar Singh"
_... | BhallaLab/benchmarks | moose_nrn_equivalence_testing/comparision_with_simple_HH_model_additional_mechanism/loader_moose.py | Python | gpl-2.0 | 5,681 | [
"MOOSE"
] | f1b89fb0f15fba0ff7c851ccac03e6c8f001a8e4ce6ef5f227ea50ec673e2b2f |
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are ... | wizmer/NeuroM | neurom/check/neuron_checks.py | Python | bsd-3-clause | 13,385 | [
"NEURON"
] | bf9aae50db5d5b8b79c4e174ba69b24862764e1b8c2c0458944beb59498e9a95 |
# Copyright (C) 2018 ABRT Team
# Copyright (C) 2018 Red Hat, Inc.
#
# This file is part of faf.
#
# faf 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) ... | abrt/faf | src/pyfaf/storage/migrations/versions/9301a426f19d_associates_to_opsys.py | Python | gpl-3.0 | 2,989 | [
"ORCA"
] | e817e9dab67343be75559628c623b3e6d0d847571ec86f54fb66171aac19cddf |
"""
Test the about xblock
"""
import datetime
import pytz
from ccx_keys.locator import CCXLocator
from django.conf import settings
from django.core.urlresolvers import reverse
from django.test.utils import override_settings
from mock import patch
from nose.plugins.attrib import attr
from opaque_keys.edx.locations impo... | MakeHer/edx-platform | lms/djangoapps/courseware/tests/test_about.py | Python | agpl-3.0 | 25,177 | [
"VisIt"
] | 659ee4364f6f84093911712658db2c18991e838c04ced4e088ffd4aadc68ecdb |
from __future__ import print_function
from collections import Iterable
from copy import deepcopy, copy
from functools import total_ordering
from numbers import Number
import os
import re
import itertools
import math
from math import sin, cos, pi
import numpy as np
from grendel import type_checking_enabled, sanity_che... | spring01/libPSI | lib/python/grendel/chemistry/molecule.py | Python | gpl-2.0 | 83,661 | [
"VisIt"
] | 7cdb017a778f063e228eb9ad465ce17feb1de414e870a8df1050c97525622053 |
# -*- coding: utf-8 -*-
# gcompris - piano_composition.py
#
# Copyright (C) 2012 Beth Hadley
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at ... | keshashah/GCompris | src/piano_composition-activity/piano_composition.py | Python | gpl-2.0 | 33,713 | [
"VisIt"
] | 19eb5f5cb9eba22b319e4cd1eaafbc520df3ee03b0179c1c5a35885259fa0c6d |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
import math
import numpy as np
from .core import Kernel1D, Kernel2D, Kernel
from .utils import has_even_axis, raise_even_kernel_exception
from astropy.modeling import models
from astropy.modeling.core import Fittable1DModel, Fittable2DModel
from astropy... | MSeifert04/astropy | astropy/convolution/kernels.py | Python | bsd-3-clause | 33,186 | [
"Gaussian"
] | 4212f00534cb1f11c971bbee1bb3a63b07e4eeb7347e5d1819b0fc307dadf08d |
# From <http://www.djangosnippets.org/snippets/661/>
#
# Copyright (c) 2009 Brian Beck
#
# 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... | mzdaniel/oh-mainline | mysite/search/templatetags/search.py | Python | agpl-3.0 | 9,132 | [
"Brian"
] | 5965db48531bc6385aba88ff14ced32841940bc48e8a0927c4db0f3edbc4e715 |
import PyOpenWorm
from time import time
from PyOpenWorm.neuron import Neuron
PyOpenWorm.connect(configFile='PyOpenWorm/default.conf')
t0 = time()
print("Neurons:")
print(", ".join(sorted(Neuron().name.get())))
print("Receptors:")
print(", ".join(sorted(Neuron().receptor.get())))
tot = time() - t0
print ("Took {} seco... | gsarma/PyOpenWorm | examples/42-loading-neurons-is-very-slow.py | Python | mit | 338 | [
"NEURON"
] | 6ba4fbd36a3cb4281fe5a59c24ceed81311a77d226b76e28ce62f87621b0192f |
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Matti Hamalainen <msh@nmr.mgh.harvard.edu>
# Denis Engemann <denis.engemann@gmail.com>
# Andrew Dykstra <andrew.r.dykstra@gmail.com>
# Mads Jensen <mje.mads@gmail.com>
#
# License: BSD (3-clause)
from copy imp... | antiface/mne-python | mne/evoked.py | Python | bsd-3-clause | 48,644 | [
"Mayavi"
] | cbf04b4d544e646cd4e7c628274f9896b0806d0b48c16704de8c8d7d763ba3eb |
#!/usr/bin/env python
"""
Copyright (c) 2006-2013 sqlmap developers (http://sqlmap.org/)
See the file 'doc/COPYING' for copying permission
"""
import os
import sys
from optparse import OptionError
from optparse import OptionGroup
from optparse import OptionParser
from optparse import SUPPRESS_HELP
from lib.core.com... | golismero/golismero | tools/sqlmap/lib/parse/cmdline.py | Python | gpl-2.0 | 36,761 | [
"VisIt"
] | fad430d938b291d79fba1af9b263ee8a91ad36f58d93c2eec63724abdc1a6f3a |
from random import uniform, gauss
class Neuron:
def __init__(self, n):
self.w = []
for i in range(n):
self.w.append(uniform(-1.0, 1.0))
def feed(self, x):
result = 0
for w_el, x_el in zip(self.w, x):
result += w_el * x_el
return result
def... | lucekdudek/si | lab02/Neuron.py | Python | apache-2.0 | 1,097 | [
"NEURON"
] | 70689237dee1f751274eae998954238c89003b126d3041b8ba8c97ef585f22bf |
from testcase import testcase
from testcase import visitor
class Tc2Tet(visitor.Visitor):
tcTemplate = u"""Testcase General Information
TC_ID {tcid}
QC_ID {qcid}
Title {title}
Author {author}
Created {created}
Purpose {purpose}
Usage {usage}
"""
functionTemplate = u"""function::{name}
{name}:description
{des... | zhongzhu/searchmyworkspace | src/tc2tet.py | Python | gpl-3.0 | 3,506 | [
"VisIt"
] | 61c8f636bbb91d560784986eda97dfc64a40ec5676835cb3bbcfbcc2793fda9b |
# thic code is used to test prepare tracto
import numpy as np
from MNNparcellation import Prepare_tractogram as PT
from MNNparcellation import Region_preparation as RP
from MNNparcellation.inc.CSParcellation import Parcellation as CSP
from termcolor import colored
import os
import h5py
import scipy
import warnings
warn... | BBELAOUCHA/dMRIParcellation | test/test_preparetracto.py | Python | bsd-3-clause | 3,130 | [
"VTK"
] | 5ba380b012a44e021668b988a727d1186668885b39fd8a71f58f7a68d5dd4fb9 |
"""
Support and standalone functions for Robust Linear Models
References
----------
PJ Huber. 'Robust Statistics' John Wiley and Sons, Inc., New York, 1981.
R Venables, B Ripley. 'Modern Applied Statistics in S'
Springer, New York, 2002.
"""
from statsmodels.compat.python import callable, range
import numpy as n... | hlin117/statsmodels | statsmodels/robust/scale.py | Python | bsd-3-clause | 8,313 | [
"Gaussian"
] | d0fb604b33728a90a0632e0fa8e62bc58b910799e28b291269703249e37ff1ba |
#!/usr/bin/env python
#pylint: disable=missing-docstring
#################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment #
# #... | Chuban/moose | python/chigger/tests/mesh_only/mesh_only.py | Python | lgpl-2.1 | 1,159 | [
"MOOSE"
] | 6007eae46aaec616b3543ce0488db9d3037454100a59dc2a2f01eb3005e661af |
#! /usr/bin/python
#usage: reorder_pdb.py template trajectory_frame
# takes naming and ordering from template structure and applies it to trajectory frame.
# This is necessary for analysis with X3DNA
import sys,os
from MDAnalysis import *
my_templateFile = sys.argv[1]
my_trajFile = sys.argv[2]
my_index = my_trajFil... | demharters/git_scripts | reorder_pdb.py | Python | apache-2.0 | 2,562 | [
"MDAnalysis"
] | 634a3f4fa2ebe1cf274e97f5ed50be5ca728c8953136d483514f8ac56a3e0efb |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module defines classes representing non-periodic and periodic sites.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Material... | migueldiascosta/pymatgen | pymatgen/core/sites.py | Python | mit | 18,138 | [
"pymatgen"
] | 1c0bb79a0f4adba516bf902195634e2a89ef35253a994f0e952c0c31d9d1229e |
import pytest
from numpy.testing import assert_equal
import mmtf
from unittest import mock
import MDAnalysis as mda
from MDAnalysis.core.groups import AtomGroup
from MDAnalysisTests.topology.base import ParserBase
from MDAnalysisTests.datafiles import MMTF, MMTF_gz, MMTF_skinny, MMTF_skinny2
class MMTFBase(ParserBas... | MDAnalysis/mdanalysis | testsuite/MDAnalysisTests/topology/test_mmtf.py | Python | gpl-2.0 | 4,702 | [
"MDAnalysis"
] | 9659c2cc4ffbd91a21694c89bc946b6671e849dc7f01fdec936ab835217d95d7 |
"""
The Galaxy web application framework
"""
from framework import url_for
from framework.decorators import error
from framework.decorators import expose
from framework.decorators import json
from framework.decorators import json_pretty
from framework.decorators import require_login
from framework.decorators import req... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/web/__init__.py | Python | gpl-3.0 | 942 | [
"Galaxy"
] | 0f74208ab257e056aa91912173c7ba9eea9f025b3abb446025e258d875088c9d |
## @file setup.py
## @brief Python distutils code for COPASI Python module
##
from distutils.core import setup, Extension
setup(name = "COPASI",
version = "%COPASI_VERSION%",
description = "COPASI Python API",
long_description = ("COPASI is a software application for... | jonasfoe/COPASI | InnoSetup/setup.py | Python | artistic-2.0 | 1,207 | [
"COPASI"
] | e5064a8919f09c5f1843da298394e6439290d55c1a5c14ce89e5bbb3bb019933 |
import sys
import os.path as op
sys.path.insert(0, op.join(op.dirname(__file__), ".."))
from fileindex import FileIndex
class FastQEntry(object):
__slots__ = ('name', 'seq', 'l3', 'qual', 'fpos')
def __init__(self, fh):
self.name = fh.readline().rstrip('\r\n')
self.seq = fh.readline().rstrip('\... | shashidhar22/bio-playground | fileindex/examples/fastq_file.py | Python | mit | 805 | [
"Bowtie"
] | 9e3eae7d08330cd157feb3c7be212472e4fb8bc7a8f078406ac7044bc31c9e9a |
#!/usr/bin/env python
# Demonstrate how to use the vtkBoxWidget to control volume rendering
# within the interior of the widget.
import vtk
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Load a volume, use the widget to control what's volume
# rendered. Basically the idea is that the vtk... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Examples/GUI/Python/VolumeRenderWithBoxWidget.py | Python | gpl-3.0 | 4,079 | [
"VTK"
] | 6f20a3318e5ed83504f8932bd5306d5d73a6985bdf637527c11bfba7e2763801 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module contains the main object used to identify the coordination environments in a given structure.
If you use this module, please cite the following:
David Waroquiers, Xavier Gonze, Gian-Marco Rign... | dongsenfo/pymatgen | pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.py | Python | mit | 98,069 | [
"pymatgen"
] | b7465458ca391322d8ba2bd9b96be52ec5ba6324d94e9184a9feec1aa1d48dc8 |
import numpy as np
import xarray as xr
import datetime as dt
import json
from netCDF4 import Dataset, num2date
from pathlib import Path
class SeNorgeDomain:
# TODO: write docs
def __init__(self):
# XGEO grid set-up
self.senorge_x_left = -75000.0
self.senorge_x_right = 1119000.0
... | kmunve/APS | aps/aps_io/warning_region.py | Python | mit | 10,606 | [
"NetCDF"
] | 12b0515173d419fc5884b0f0af1460491c80e34a7d5cee8e8e4e86ab43c98dea |
import numpy as np
from numpy.testing import assert_array_almost_equal
import pytest
from sklearn.neighbors.kd_tree import (KDTree, NeighborsHeap,
simultaneous_sort, kernel_norm,
nodeheap_sort, DTYPE, ITYPE)
from sklearn.neighbors.dist_metr... | chrsrds/scikit-learn | sklearn/neighbors/tests/test_kd_tree.py | Python | bsd-3-clause | 7,931 | [
"Gaussian"
] | 9e1a18c4c9d868917e979a7f3d1db38adc25d9fd866e705aea986a64314a8beb |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Licensed under the GNU LGPL v2.1 - http://www.gnu.org/licenses/lgpl.html
# Based on Copyright (C) 2016 Radim Rehurek <radimrehurek@seznam.cz>
"""
Inspired by the Blei's original DTM code and paper.
Original DTM C/C++ code: https://github.com/blei-lab/dtm
DTM Paper: h... | pombredanne/gensim | gensim/models/ldaseqmodel.py | Python | lgpl-2.1 | 42,430 | [
"Gaussian"
] | 59d92c0d56bee85d417fbbac4e0832d0cebcd2fe90629908fcdcf6798e0abaa2 |
import lib.env
from lib.loghelper import Logger
from lib.sitkaAPI import APIGet
from lib.progressbar import ProgressBar
import sqlite3
import argparse
import os
import sys
import traceback
import json
from lib.exception import DataException, MissingException, NetworkException
def metric_downloader(workbench, outputfo... | SouthForkResearch/CHaMP_Metrics | scripts/measurement_downloader.py | Python | gpl-3.0 | 4,537 | [
"VisIt"
] | a41f90ea5862a8c272168361a5dcf6cb9fb169b9fb45bce1a7c86c37c9dd84f1 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import unittest
import os
from pymatgen import Molecule
from pymatgen.io.gaussian import GaussianInput, GaussianOutput
from pymatgen.electronic_structure.core ... | johnson1228/pymatgen | pymatgen/io/tests/test_gaussian.py | Python | mit | 13,759 | [
"Gaussian",
"pymatgen"
] | f322ffaf7b1ab230eda4a0e634cf952cbf7880f21f49bf592cd8b353863771f9 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""Tests for the Popularity Contest (popcontest) parser."""
import unittest
from plaso.lib import definitions
from plaso.parsers import popcontest
from tests.parsers import test_lib
class PopularityContestUnitTest(test_lib.ParserTestCase):
"""Tests for the popcontes... | Onager/plaso | tests/parsers/popcontest.py | Python | apache-2.0 | 5,176 | [
"ORCA"
] | 43d597057b2aa3b743c9ec36220390c0ec6ab6eee55f2331d27976154f1e7173 |
"""
Acceptance tests for Studio related to the acid xblock.
"""
from bok_choy.web_app_test import WebAppTest
from common.test.acceptance.pages.studio.auto_auth import AutoAuthPage
from common.test.acceptance.pages.studio.overview import CourseOutlinePage
from common.test.acceptance.pages.xblock.acid import AcidView
fr... | chrisndodge/edx-platform | common/test/acceptance/tests/studio/test_studio_acid_xblock.py | Python | agpl-3.0 | 6,989 | [
"VisIt"
] | 827a1a83739e6a72eebb472ab0b61734370591b2ad1d3dc7fe388327e6158cc4 |
"""Finite-horizon tabular Maximum Causal Entropy IRL.
Follows the description in chapters 9 and 10 of Brian Ziebart's `PhD thesis`_.
.. _PhD thesis:
http://www.cs.cmu.edu/~bziebart/publications/thesis-bziebart.pdf
"""
import collections
import warnings
from typing import Any, Iterable, Mapping, Optional, Tuple, T... | HumanCompatibleAI/imitation | src/imitation/algorithms/mce_irl.py | Python | mit | 20,092 | [
"Brian"
] | 5e4849d34702168902a7edf769411a8abc5290ccdee45b26d97f5c823092755c |
#!/usr/bin/env python3
# Copyright (C) 2016-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, eit... | espressopp/espressopp | examples/tabulated_potential/table_interpolation.py | Python | gpl-3.0 | 6,241 | [
"ESPResSo"
] | df1ad2352d8bfaeb821cf52774b0fa2545a1414eacbc5787b0386a939f8e4fa7 |
# Orca
#
# Copyright 2019 Igalia, S.L.
# Author: Joanmarie Diggs <jdiggs@igalia.com>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your opt... | GNOME/orca | src/orca/scripts/switcher/script_utilities.py | Python | lgpl-2.1 | 2,606 | [
"ORCA"
] | 1b761022baba5292c3767ec86ec3099c1d4d93065e01792e5e5c56626f70b14f |
#!/usr/bin/env python
#------------------------------------------------------------
# Script which demonstrates how to use the Kolmogorov-Smirnov
# goodness of fit test
#
# Vog, 17 Feb 2012
#------------------------------------------------------------
import numpy
from matplotlib.pyplot import figure, show, rc
from k... | kapteyn-astro/kapteyn | doc/source/EXAMPLES/kmpfit_goodnessoffit2.py | Python | bsd-3-clause | 7,197 | [
"Gaussian"
] | 7716466727c5226d614ad85b25233e3d1401ea19824044a8903b2a903a7a52f0 |
# -*- coding: utf-8 -*-
#
# pulsepacket.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, or... | zifeo/nest-simulator | pynest/examples/pulsepacket.py | Python | gpl-2.0 | 10,471 | [
"Gaussian",
"NEURON"
] | c08d72a6ebca51a2d9c714ef00eeccedaf4a8083786e1bd8302dd22a266740bd |
# Copyright (C) 2021 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later versio... | espressomd/espresso | testsuite/scripts/tutorials/test_error_analysis_part2.py | Python | gpl-3.0 | 3,717 | [
"ESPResSo"
] | 7a33af600f8af15302d96d8b2f2d22b4cde153fab80b8e663bf8f89fe78cd258 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
#########
Reporting
#########
*Created on Thu Jun 8 14:40 2017 by A. Pahl*
Tools for creating HTML Reports."""
import time
import base64
import os.path as op
from string import Template
from io import BytesIO as IO
import pandas as pd
from rdkit.Chem import AllChe... | mpimp-comas/cellpainting | cellpainting/reporting.py | Python | mit | 18,606 | [
"RDKit"
] | cca91a10eaffc79321e738ee25f10e7c9fa757753f5dd31ebc27e251711e6826 |
# This file is taken unchanged from the server repo at dropbox/python_linters/analysis.py
from __future__ import absolute_import
import ast
import re
class AnalysisVisitor(object):
def __init__(self, linters, path):
self.items = []
self.path = path
self.ancestors = []
def path_f... | dropbox/changes | linters/analysis.py | Python | apache-2.0 | 7,759 | [
"VisIt"
] | 96dedeac6a92f7f99d80bcbd719568033835a6dce9b92be1d0e4e6d652f2c72b |
# Copyright (c) 2013, GlaxoSmithKline Research & Development Ltd.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# ... | rvianello/rdkit | Contrib/mmpa/create_mmp_db.py | Python | bsd-3-clause | 10,129 | [
"RDKit"
] | 4d00255e666097554d579ff6587cb08ee09b2617bff585efc0021e9d802cc513 |
from ase import *
from ase.dft.bee import BEEF_Ensemble
from gpaw import GPAW
from gpaw.cluster import Cluster
from gpaw.test import equal
import numpy as np
xc = 'mBEEF'
conv = {'eigenstates':1.e-6, 'density':1.e-6, 'energy':1.e-6}
h = 0.18
tol1 = 1.e-3
tol2 = 1.e-1
# N2 molecule
n2 = Cluster(Atoms('N2',[[0.,0.,0.],... | robwarm/gpaw-symm | gpaw/test/mbeef.py | Python | gpl-3.0 | 1,119 | [
"ASE",
"GPAW"
] | cfebd1c07dbaeae3f5d98bac38dd835ea93f8f8c5ca9ac952b454648426858e7 |
#-*- coding:utf-8 -*-
#
# Copyright (C) 2013 Fabrice Desclaux
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# Thi... | commial/miasm | miasm/ir/ir.py | Python | gpl-2.0 | 31,023 | [
"VisIt"
] | 526e82b07da5ebc0cb43b1e6ffdc0cd6ee770a612064fa11f680b48f5e740dfb |
#!/usr/bin/env python
# Copyright 2014-2020 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/mcscf/chkfile.py | Python | apache-2.0 | 2,219 | [
"PySCF"
] | 74ca43f5a2184688e452a481a0d421902f837fdd87549e34af516c36e18acf83 |
"""PAM Measurements Module"""
import logging
import math
import bpy
logger = logging.getLogger(__package__)
class PAMMeasureLayer(bpy.types.Operator):
"""Calculates neuron quantity across the active object"""
bl_idname = "pam.measure_layer"
bl_label = "Measure layer"
bl_description = "Calculates n... | MartinPyka/Parametric-Anatomical-Modeling | pam/tools/measure.py | Python | gpl-2.0 | 2,842 | [
"NEURON"
] | 212da35107a00801ae6e3ada1c7c7ab7f8fb6b76e33407da7cccbaff55db6676 |
from sonLib.bioio import system
import os, sys, glob, time
from optparse import OptionParser
from margin.utils import samToBamFile
import pysam
class Fastaseq():
"""
fasta reader
"""
def __init__(self):
self.id = None
self.seq = ''
self.length = ''
@staticmethod
... | isovic/marginAlign | scripts/createAssemblyHub.py | Python | mit | 8,155 | [
"pysam"
] | b7878ab40117dc20c68a061b0cd38f9fab05653f84ab3f7e5ff28f335d4cf110 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# admin.py
#
# Copyright 2014 Gary Dalton <gary@ggis.biz>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the Licen... | gary-dalton/Twenty47 | twenty47/admin.py | Python | mit | 17,181 | [
"Dalton"
] | dd567f949231ca762741b86c21321b60268c3dbb15e7003ec85beab0a6d4a9f6 |
"""
Retrieve output sandbox for a DIRAC job
"""
import DIRAC
from DIRAC.Core.Base import Script
import os
from COMDIRAC.Interfaces import DSession
class Params:
def __init__ ( self, session ):
self.__session = session
self.outputDir = None
self.outputData = False
self.outputSandbox = False
s... | pigay/COMDIRAC | Interfaces/scripts/doutput.py | Python | gpl-3.0 | 4,188 | [
"DIRAC"
] | 15cee799cff394d8991c97cb18ba2d8be2d115497bf467caac5c67e90095080b |
"""
Instructor Dashboard Views
"""
import logging
import datetime
import uuid
import pytz
from django.contrib.auth.decorators import login_required
from django.views.decorators.http import require_POST
from django.utils.translation import ugettext as _
from django_future.csrf import ensure_csrf_cookie
from django.vie... | wwj718/ANALYSE | lms/djangoapps/instructor/views/instructor_dashboard.py | Python | agpl-3.0 | 20,045 | [
"VisIt"
] | 5a470e63f5fe73f63420c360cd2c0e6e458f0b9fad2097aef216dbf7804bc795 |
try:
from neuron import h, rxd
except ImportError as e:
print( "[INFO ] Failed to import neuron. Quitting ..." )
quit()
import numpy
from matplotlib import pyplot
import time
# needed for standard run system
h.load_file('stdrun.hoc')
dend = h.Section()
dend.nseg = 501
# WHERE the dynamics will take ... | BhallaLab/moose-examples | paper-2015/Fig3_chemModels/Fig3_NEURON.py | Python | gpl-2.0 | 948 | [
"NEURON"
] | 4e06b32d7718880c0671c4bcef8b41ef4404704ffd9cf715816d732af79e2e45 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals, division, absolute_import
from datetime import timedelta, datetime
import pytest
from builtins import * # pylint: disable=unused-import, redefined-builtin
from flexget.manager import Session
from flexget.plugins.api_tvmaze import APITVMaze, TVMazeLook... | qvazzler/Flexget | tests/test_tvmaze.py | Python | mit | 19,305 | [
"Firefly"
] | 354fe9de70da65b4373a35a4670f6359cdd3c7091f3de6b72fa584c46a783c0b |
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