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#!/usr/bin/python
# Schedule targets to remote observatory.
#
# This script should be run by rts2-bb. It creates target on remote observatory.
#
# (C) 2012-2013 Petr Kubanek, Institute of Physics <kubanek@fzu.cz>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | jstrobl/rts2 | src/bb/schedule_target.py | Python | lgpl-3.0 | 2,311 | [
"VisIt"
] | c6ee935cc9ea45403aca9c7fa4701e0dc21751b6f51f4093841c449371815ff3 |
"""
Generate samples of synthetic data sets.
"""
# Authors: B. Thirion, G. Varoquaux, A. Gramfort, V. Michel, O. Grisel,
# G. Louppe, J. Nothman
# License: BSD 3 clause
import numbers
import array
import numpy as np
from scipy import linalg
import scipy.sparse as sp
from collections import Iterable
from ..p... | BiaDarkia/scikit-learn | sklearn/datasets/samples_generator.py | Python | bsd-3-clause | 58,722 | [
"Gaussian"
] | f65f61ab067127a642f46ab3dc54c8b0f6f269e94ebb782e55d98565cf81fa15 |
#!/usr/bin/env python
'''
This module contains helper functions to make plugins simpler to read and write,
centralising common functionality easy to reuse
'''
import os
import re
import cgi
import logging
from tornado.template import Template
from framework.dependency_management.dependency_resolver import BaseCompone... | DarKnight24/owtf | framework/plugin/plugin_helper.py | Python | bsd-3-clause | 17,908 | [
"VisIt"
] | 29d766646826e0738764396f914abd5c8da131302f472c59b0bdb195c6307617 |
from __future__ import division
import numpy as np
from numpy.linalg import solve
def cov_mat(x1, x2, a, b):
return a * np.exp(-b * (x1[:, np.newaxis] - x2)**2)
def reg_cov_mat(x, a, b, c):
return cov_mat(x, x, a, b) + c * np.eye(x.shape[0])
def compute_means_covs(ts, t_ref, gp_parms, winsize=0, mean_shif... | mlds-lab/egk | full_marginal.py | Python | mit | 1,818 | [
"Gaussian"
] | fb7779a12e316eb64e3b9c05e5f1382e76b28e57851e76a7c368a929a3bff571 |
# Default Django settings. Override these with settings in the module
# pointed-to by the DJANGO_SETTINGS_MODULE environment variable.
# This is defined here as a do-nothing function because we can't import
# django.utils.translation -- that module depends on the settings.
gettext_noop = lambda s: s
##########... | hunch/hunch-gift-app | django/conf/global_settings.py | Python | mit | 21,326 | [
"VisIt"
] | 1f270c6261134979bc18c4718a71dfcadf756c485a1006f1f0fec1f851a644bc |
import os
import os.path
import stat
import struct
from .ADFBlockDevice import ADFBlockDevice
from .HDFBlockDevice import HDFBlockDevice
from .RawBlockDevice import RawBlockDevice
from .DiskGeometry import DiskGeometry
from amitools.fs.rdb.RDisk import RDisk
import amitools.util.BlkDevTools as BlkDevTools
class Blk... | FrodeSolheim/fs-uae-launcher | amitools/fs/blkdev/BlkDevFactory.py | Python | gpl-2.0 | 6,367 | [
"ADF"
] | 9add0cbf75b25b9c4f170311efccd3cbc3499d9afb7a4de0820c28b777f5e398 |
########################################################################
# Author: Stuart Paterson
# eMail : Stuart.Paterson@cern.ch
########################################################################
""" The Watchdog class is used by the Job Wrapper to resolve and monitor
the system CPU and memory consumed... | chaen/DIRAC | WorkloadManagementSystem/JobWrapper/WatchdogLinux.py | Python | gpl-3.0 | 2,939 | [
"DIRAC"
] | f9105ed7c7a4ba3a86487ce74175e7e03c7bc50ed1c3a6181bc25818ca4bf3eb |
# 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, software
# d... | github-borat/cinder | cinder/flow_utils.py | Python | apache-2.0 | 5,920 | [
"VisIt"
] | 4b94a16b45e7e1d1d6223e786dcdfceb3ee4123e58f0b6b0fbd4771e61633b9f |
# $HeadURL $
''' PolicyCaller
Module used for calling policies. Its class is used for invoking
real policies, based on the policy name.
'''
from DIRAC import S_ERROR
from DIRAC.ResourceStatusSystem.Utilities import Utils
from DIRAC.ResourceStatusSystem.Command import CommandCal... | Sbalbp/DIRAC | ResourceStatusSystem/PolicySystem/PolicyCaller.py | Python | gpl-3.0 | 2,881 | [
"DIRAC"
] | 42022798b4b632c2b8c6b10c2ba64a401b0d0612b992054adf8c9a19eed231ad |
"""An NNTP client class based on:
- RFC 977: Network News Transfer Protocol
- RFC 2980: Common NNTP Extensions
- RFC 3977: Network News Transfer Protocol (version 2)
Example:
>>> from nntplib import NNTP
>>> s = NNTP('news')
>>> resp, count, first, last, name = s.group('comp.lang.python')
>>> print('Group', name, 'ha... | gkoh/pynab | lib/nntplib.py | Python | gpl-2.0 | 47,582 | [
"Brian"
] | 3db7c6082ab6ecf8a140032c34b54dbe037a17b1a551bc2d90d75351e1a19b9a |
'''
James D. Zoll
4/8/2013
Purpose: Defines logic to parse and insert recipedia data into the database.
License: This is a public work.
'''
# System Imports
import sys
from urllib import urlopen
# Library Imports
from bs4 import BeautifulSoup
# Local Imports
from leapday.models import Good
# Constants and Conf... | Zerack/zoll.me | leapday/tasks/update_recipes.py | Python | mit | 28,732 | [
"Amber",
"CRYSTAL"
] | 285e81fef3f59bcc4d61f83002024f24428a660045d816280f3e254ee0cd390d |
from flask import Flask, render_template, session, request, redirect
import random
app = Flask(__name__)
app.secret_key = 'my_secret_key'
@app.route('/')
def index():
if not 'gold' in session:
session['gold'] = 0
if not 'activities' in session:
session['activities'] = []
return render_temp... | jiobert/python | Cron_Philip/Assignments/flaskolympics/olympics8/server.py | Python | mit | 1,726 | [
"CASINO"
] | cdc6d01e58ea96665b2ca3990930270c6e32bff7befe50be8c66e05c0ce37364 |
import sys
sys.path.insert(1,"../../../")
import h2o
from tests import pyunit_utils
from h2o.estimators.glm import H2OGeneralizedLinearEstimator as glm
# test scoring_history for Gaussian family with validation dataset and cv
def testGLMGaussianScoringHistory():
col_list_compare = ["iterations", "objective", "nega... | h2oai/h2o-3 | h2o-py/tests/testdir_algos/glm/pyunit_PUBDEV_7968_scoring_history_glm_gaussian_cv.py | Python | apache-2.0 | 2,589 | [
"Gaussian"
] | 0e5288f2f4919d7fc5b499c7f6256c1c67f8fc921fd0bafab94389db99a8a213 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | python/jacobiandebug/analyzejacobian.py | Python | lgpl-2.1 | 17,497 | [
"MOOSE"
] | 48ee39ffdb1d983fe414c3d7913c430be9ca39f3b1e9a1c2a5e8ae3a9558a1c3 |
import pytest
import json
from FeedCrowdstrikeFalconIntel import Client
def get_fetch_data():
with open('./test_data.json', 'r') as f:
return json.loads(f.read())
indicators = get_fetch_data()
@pytest.mark.parametrize(
"params, actors_filter, expected",
[
({}, '', '/intel/combined/act... | demisto/content | Packs/FeedCrowdstrikeFalconIntel/Integrations/FeedCrowdstrikeFalconIntel/FeedCrowdstrikeFalconIntel_test.py | Python | mit | 1,832 | [
"Amber"
] | fc57bf7f6a4dfd6afeeeb0e31d75028d7bd0713b503a5ed100721fa590617f18 |
# -*- coding: utf-8 -*-
#
# test_mc_neuron.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,... | sanjayankur31/nest-simulator | testsuite/pytests/test_mc_neuron.py | Python | gpl-2.0 | 7,863 | [
"NEURON"
] | 903f5a9982bfbb59e372587c9f09c6a0e5c580d3a3e4ac93a88fad8391393e0d |
"""
The Data object, used to store and manipulate the data contained in a
single laser ablation files. A core dependency of LAtools.
(c) Oscar Branson : https://github.com/oscarbranson
"""
import re
import itertools
import numpy as np
import matplotlib.pyplot as plt
import matplotlib as mpl
import warnings
import skl... | oscarbranson/latools | latools/D_obj.py | Python | mit | 65,522 | [
"Gaussian"
] | c22d97301090fb85abcf29ab0c06d03279b3dc6cfc2e53e6f994f715c2a86ec2 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 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
#... | jturney/psi4 | psi4/share/psi4/databases/NHTBH.py | Python | lgpl-3.0 | 36,620 | [
"Psi4"
] | a096232cec2d46d046618fdbc73fa613b4293a79a0cc289f8fee95311c0c1dcf |
import logging
import os
import re
from .. import util
from .. import parsing
logger = logging.getLogger(__name__)
class BatchParameterizer(object):
"""
Defines workflow batch parameters for a list of input samples,
given a list of parsed parameters for a Galaxy workflow.
:type sample_paths: list
... | jaeddy/bripipetools | bripipetools/submission/batchparameterize.py | Python | mit | 18,172 | [
"Galaxy",
"HTSeq"
] | d5c586aab1290ed252aba84317a46fbbd5c2b1b61cb899abaf413127f9243d48 |
""" Double beta decay utility converter
Provides a useful tool for converting between different double beta
dacay parameters.
"""
import numpy
from echidna.calc import constants as const
import echidna.test.physics_tests as physics_tests
class DBIsotope(object):
""" Class which calculates expected counts for a... | mjmottram/echidna | echidna/calc/decay.py | Python | mit | 24,391 | [
"Gaussian"
] | 07a5875b7c962b37f7ef1bbd49745dae92570acbabaac45c8770bf1fb70d0698 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2007-2008 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## 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 Fou... | tiagocardosos/stoq | stoqlib/domain/test/test_payment_method.py | Python | gpl-2.0 | 17,961 | [
"VisIt"
] | 0ff2e8b47e78c387a0c2850765544024ad809f5c0479660b08d68b5ec7b59393 |
#
# Copyright 2014, 2021 Lars Pastewka (U. Freiburg)
# 2014 James Kermode (Warwick U.)
#
# matscipy - Materials science with Python at the atomic-scale
# https://github.com/libAtoms/matscipy
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public... | libAtoms/matscipy | scripts/fracture_mechanics/energy_barrier_multiple.py | Python | lgpl-2.1 | 8,330 | [
"ASE",
"Matscipy"
] | cf77a0ec44bdbdc6c1fc01f202939884008acc7ce395f8636bc7adabd011506c |
# Copyright (c) Charl P. Botha, TU Delft.
# All rights reserved.
# See COPYRIGHT for details.
from external.ObjectListView import ColumnDefn, EVT_CELL_EDIT_FINISHING
import itk
from module_kits import itk_kit
import module_utils
import vtk
import wx
####################################################################... | nagyistoce/devide | modules/viewers/comedi_match_modes.py | Python | bsd-3-clause | 22,056 | [
"VTK"
] | e084f813cce40887fd1162a2149fe85019bc2b61a849f915fcc1c8cfc38c6d41 |
# -*- coding: utf-8 -*-
## Copyright 2016 Rasmus Scholer Sorensen, rasmusscholer@gmail.com
##
## This file is part of Nascent.
##
## Nascent 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 Foundati... | scholer/na_strand_model | nascent/graph_visualization/vispy_graph_viewer_app.py | Python | gpl-3.0 | 65,434 | [
"Galaxy",
"Mayavi"
] | 94aa5bb4d49690379a795ff27adf8cfdd62f9b82c6f5027c4907fb8d1219ca96 |
#!/usr/bin/env python
""" Remove the outputs produced by a transformation
"""
import sys
from DIRAC.Core.Base.Script import parseCommandLine
parseCommandLine()
if len( sys.argv ) < 2:
print 'Usage: dirac-transformation-remove-output transID [transID] [transID]'
sys.exit()
else:
transIDs = [int( arg ) for arg i... | andresailer/DIRAC | TransformationSystem/scripts/dirac-transformation-remove-output.py | Python | gpl-3.0 | 906 | [
"DIRAC"
] | e284d5946fc28287ab216327442d8fd88a7fd251c2eef41e07ccc441a27c9004 |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
#
# Imports
#
from __future__ import absolute_import
from future import standard_library
standard_library.install_aliases()
from builtins import str
from builtins import object
import os
import sys
import urllib.request, urllib.parse, urllib.error
import requests
from time... | skipmodea1/plugin.video.nlhardwareinfo | resources/lib/nlhardwareinfo_list_play.py | Python | gpl-3.0 | 12,307 | [
"Galaxy"
] | 61ffc0c4f30e97fc6fc0afd976bb6e96ae23494474b123c6bbe4fe975748bc2d |
from __future__ import print_function
from future import standard_library
standard_library.install_aliases()
from builtins import range
from past.builtins import basestring
import sys, os
sys.path.insert(1, "../../")
import h2o
import imp
import random
import re
import subprocess
from subprocess import STDOUT,PIPE
from... | nilbody/h2o-3 | h2o-py/tests/pyunit_utils/utilsPY.py | Python | apache-2.0 | 25,008 | [
"Gaussian"
] | 24405b83f58bffcb2f529bd75b118cb9c74d0713cb9dade4f80408c11aebafb0 |
# 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, software
# distributed under t... | openstack/mistral | mistral/hacking/checks.py | Python | apache-2.0 | 9,715 | [
"VisIt"
] | b0587dfb8be8bb3b5e02905dcbf68591a860b48cb222b1d919ab48b8be8f0f71 |
"""Bulk Al(fcc) test"""
from ase import Atoms
from ase.visualize import view
from gpaw import GPAW
name = 'Al-fcc'
a = 4.05 # fcc lattice paramter
b = a / 2
bulk = Atoms('Al',
cell=[[0, b, b],
[b, 0, b],
[b, b, 0]],
pbc=True)
view(bulk)
k = 4
calc =... | qsnake/gpaw | doc/exercises/aluminium/Al_fcc.py | Python | gpl-3.0 | 571 | [
"ASE",
"GPAW"
] | 4bb9e0f428b243b880d34fb2af4ae8dcdf37658ff99bafd86514a532f018c759 |
"""A setuptools based setup module.
See:
https://packaging.python.org/guides/distributing-packages-using-setuptools/
https://github.com/pypa/sampleproject
"""
# Always prefer setuptools over distutils
from setuptools import setup, find_packages
import pathlib
here = pathlib.Path(__file__).parent.resolve()
# Get the... | pypa/sampleproject | setup.py | Python | mit | 8,625 | [
"VisIt"
] | a770d8658bfd33575da12474908195a65626ac517abad8ae00e33133aeac9e19 |
from __future__ import print_function, division
import random
from sympy.core.basic import Basic
from sympy.core.compatibility import is_sequence, as_int, range
from sympy.core.function import count_ops
from sympy.core.decorators import call_highest_priority
from sympy.core.singleton import S
from sympy.core.symbol i... | yukoba/sympy | sympy/matrices/dense.py | Python | bsd-3-clause | 43,236 | [
"DIRAC"
] | ef6027a83ddd516793049052091fa1d49afe62b647e33a7bfd340066bdcaa494 |
# -*- coding: utf-8 -*-
"""An implementation of a drug-target-based mechanism enrichment strategy."""
import itertools as itt
import logging
import os
from typing import Iterable, List, Mapping, Optional, TextIO, Tuple, Union
from tqdm import tqdm
from pybel import BELGraph
from pybel.dsl import Gene
from pybel.str... | pybel/pybel-tools | src/pybel_tools/analysis/epicom/algorithm.py | Python | mit | 4,543 | [
"Pybel"
] | 234c3d6918ba44d4b7b68583c1d5940a8fe3bc2e5948228cd3c98e9018cd6688 |
import sys
import urllib
import urlparse
import xbmcgui
import xbmcplugin
import xbmcaddon
import urllib2
import sqlite3
import re
import os
import json,time
from BeautifulSoup import BeautifulSoup as bs
from pftvso import *
import xbmcvfs
try:
from addon.common.addon import Addon
from addon.common.net import N... | natko1412/repo.natko1412 | zips/plugin.video.pftvso/default.py | Python | gpl-2.0 | 68,642 | [
"VisIt"
] | 53ed2dc64405451c09d14526160c00cefabe8e2a7279575ff39dae6a0be4f205 |
"""
Generate coulomb matrices for molecules.
See Montavon et al., _New Journal of Physics_ __15__ (2013) 095003.
"""
from __future__ import print_function
from __future__ import division
from __future__ import unicode_literals
__author__ = "Steven Kearnes"
__copyright__ = "Copyright 2014, Stanford University"
__licen... | bowenliu16/deepchem | deepchem/feat/coulomb_matrices.py | Python | gpl-3.0 | 6,378 | [
"RDKit"
] | a5f3b851b7d911db66b4b30584b5dab9a2750b42c07affb13645923a92da7ddd |
""" I wish who wrote this would have put some doc...
IIUC this is a wrapper around the JobState object. It basically tries to cache
everything locally instead of going to the DB.
"""
import copy
import time
from DIRAC.Core.Utilities import Time, DEncode
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Work... | DIRACGrid/DIRAC | src/DIRAC/WorkloadManagementSystem/Client/JobState/CachedJobState.py | Python | gpl-3.0 | 13,271 | [
"DIRAC"
] | bf1566bfc3b17d0b7843f8520108d3d649edf3d5e7192d6d96e8ad074368699b |
from copy import deepcopy
from warnings import warn
from itertools import chain
from ast import NodeTransformer
from six import iteritems
from .. import Reaction, Metabolite
from .delete import get_compiled_gene_reaction_rules
from ..core.Gene import ast2str
_renames = (
(".", "_DOT_"),
("(", "_LPAREN_"),
... | JuBra/cobrapy | cobra/manipulation/modify.py | Python | lgpl-2.1 | 12,649 | [
"VisIt"
] | b8838d50fbb1bf105923d00cbd240eb0b3ed580cb9c218faa165e4fde79c2325 |
from paraview import simple
from paraview import smtesting
renderView = simple.CreateView('RenderView')
renderView.AxesGrid = 'GridAxes3DActor'
renderView.AxesGrid.Visibility = 1
renderView.AxesGrid.XTitleColor = [0.0, 0.0, 0.0]
renderView.AxesGrid.YTitleColor = [0.0, 0.0, 0.0]
renderView.AxesGrid.ZTitleColor = [0.0,... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/ParaViewCore/ServerManager/Default/Testing/Python/AxesGridTestGridLines.py | Python | gpl-3.0 | 831 | [
"ParaView"
] | d2546e93ca0725817115f52078e940ab4e9ed1f7507e0cbb1afbcc6d8635fedb |
# -*- coding: utf-8 -*-
r"""
.. _disc-filtering:
===================================
Background information on filtering
===================================
Here we give some background information on filtering in general, and
how it is done in MNE-Python in particular.
Recommended reading for practical applications ... | kambysese/mne-python | tutorials/discussions/plot_background_filtering.py | Python | bsd-3-clause | 48,036 | [
"Gaussian"
] | 6a2b94e8c65fb7080e2525fd636279f1b7dc2abb96067949672808c62f0fc7e9 |
'''
GraphQL.js provides a reference implementation for the GraphQL specification
but is also a useful utility for operating on GraphQL files and building
sophisticated tools.
This primary module exports a general purpose function for fulfilling all
steps of the GraphQL specification in a single operation, but also inc... | public-ink/public-ink | server/appengine/lib/graphql/__init__.py | Python | gpl-3.0 | 7,300 | [
"VisIt"
] | 5ce197fa8d3e6d1891482a1b14d3b42674287971cadd32089eeb1d2905ec2a23 |
from __future__ import print_function
import matplotlib.pyplot as plt
import neat
def plot_spikes(spikes, title):
""" Plots the trains for a single spiking neuron. """
t_values = [t for t, I, v, u, f in spikes]
v_values = [v for t, I, v, u, f in spikes]
u_values = [u for t, I, v, u, f in spikes]
... | drallensmith/neat-python | examples/neuron-demo/demo-iznn.py | Python | bsd-3-clause | 2,126 | [
"NEURON"
] | f27b96d058ab60f1b40f59a63183512548c59a9317d46ae3feef3829c35dcd77 |
#!/usr/bin/env python
################################################################################
##
## util.py
## Author: Satoshi Takahama (satoshi.takahama@epfl.ch)
## Nov. 2014
##
## -----------------------------------------------------------------------------
##
## This file is part of APRL-SSP
##
## APRL-SSP... | stakahama/aprl-ssp | util.py | Python | gpl-3.0 | 8,403 | [
"Pybel"
] | 68169b551450341b52a3f25a9e005fbc372d9af9dc8c85d4fbdc01a5f350f723 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under ... | MDAnalysis/mdanalysis | package/MDAnalysis/core/selection.py | Python | gpl-2.0 | 53,364 | [
"Amber",
"CHARMM",
"Gromacs",
"MDAnalysis",
"RDKit",
"VMD"
] | ff9630a7201ba6927f1e94cd7ddd205df2c3fe379e96b3a67bfc9e83d812c5aa |
#!/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... | pli3/Openwebif | plugin/controllers/views/web/signal.py | Python | gpl-2.0 | 5,562 | [
"VisIt"
] | 225339a1cc3aad62e36061468265eef33a292451230a77164c073dc4c488c3f4 |
#
# Copyright (C) 2007 by Greg Landrum
# All rights reserved
#
from __future__ import print_function
import copy
import time
from rdkit import Chem, Geometry
from rdkit.Chem import AllChem
from rdkit.Chem.Subshape import BuilderUtils
from rdkit.Chem.Subshape import SubshapeObjects
from rdkit.six.moves import cPickl... | rvianello/rdkit | rdkit/Chem/Subshape/SubshapeBuilder.py | Python | bsd-3-clause | 4,281 | [
"PyMOL",
"RDKit"
] | 3aa5eb92fe3c8b666c3a56470f06f40b8aa1bfe8fec0e4d24cc256c50c7b5e9d |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Constant-Q transforms"""
import warnings
import numpy as np
from numba import jit
from . import audio
from .fft import get_fftlib
from .convert import cqt_frequencies, note_to_hz
from .spectrum import stft, istft
from .pitch import estimate_tuning
from .._cache import c... | librosa/librosa | librosa/core/constantq.py | Python | isc | 44,406 | [
"Brian"
] | 03d23527a96601eca8c8c22710b34dbcd41599cbf6345f3ae9b751da0d9c515c |
#! /bin/env python
import sys
from six.moves import range
import numpy as np
import xml.dom.minidom
from landlab.io.vtk.encoders import encode
from landlab.io.vtk.vtktypes import SYS_TO_VTK_ENDIAN, NUMPY_TO_VTK_TYPE
class VtkExtent(object):
def __init__(self, shape):
assert(len(shape) <= 3)
se... | csherwood-usgs/landlab | landlab/io/vtk/vtkxml.py | Python | mit | 6,566 | [
"VTK"
] | c86356c1ea8025135f02e93869bc1439df02824e7ac51ac82c77ea7f71e6e1f7 |
#!/usr/bin/env python
# Calculate a table of pairwise energies and forces between "INT" atoms
# in the lipid membrane model described in
# Brannigan et al, Phys Rev E, 72, 011915 (2005)
# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2)
# I realized later this is not what we want becau... | jcarlson23/lammps | tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/moltemplate_files/version_charmm_cutoff/calc_table.py | Python | gpl-2.0 | 2,403 | [
"CHARMM",
"LAMMPS"
] | 38d11c26dd74681aff3b179f921e7e22f4a9c20eabca74947af06ebe8c1d5b8d |
"""
The main client API you'll be working with most often. You'll need to
configure a dropbox.session.DropboxSession for this to work, but otherwise
it's fairly self-explanatory.
"""
import re
import json
from dropbox.rest import ErrorResponse
from dropbox.rest import RESTClient
def format_path(path):
"""Normal... | codecollision/DropboxToFlickr | dropbox/client.py | Python | bsd-3-clause | 24,444 | [
"VisIt"
] | 18cf0b30ec6886b550d92ff8d4939a869413b3bb71c39702772a32d31e1f3a54 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# freezedb - manage frozen archives
# Copyright (C) 2003-2014 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 GNU General Public License as... | heromod/migrid | mig/shared/functionality/freezedb.py | Python | gpl-2.0 | 8,247 | [
"Brian"
] | 2224ca6e147510544d8d8752189fd1db566bc49554408b1ae78cd7d456897ca9 |
#!/usr/bin/env python
import os
import sys
import argparse
import shutil
parser = argparse.ArgumentParser(description='Android system files extractor')
parser.add_argument("-p", "--prefix", metavar="NAME", required=True,
help="Prefix for stored files, e.g. galaxy-s7-us")
SYSTEM_FILES = [
"/... | pytorch/cpuinfo | scripts/arm-linux-filesystem-dump.py | Python | bsd-2-clause | 3,213 | [
"Galaxy"
] | eca1a2584eaa458086aa2ef55e6bc940eab0f0d8abfed86ce95380a7b675bef7 |
#!/usr/bin/python
#
# Copyright (C) 2007, 2009 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 applicabl... | kbdick/RecycleTracker | recyclecollector/scrap/gdata-2.0.18/samples/apps/org_unit_sites.py | Python | gpl-3.0 | 12,293 | [
"VisIt"
] | 851dd5ae4fe5f4716cf9cc18c9ee2a721beced4ef47ac03b7e73e8a8c23aceb0 |
"""
@name: PyHouse/src/Modules/Lighting/_test/test_lighting_actions.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2015-2019 by D. Brian Kimmel
@license: MIT License
@note: Created on Sep 3, 2015
@Summary:
Passed all 5 tests - DBK - 2019-01-20
"""
__updated__ = '2019-1... | DBrianKimmel/PyHouse | Project/src/Modules/House/Lighting/_test/test_actions.py | Python | mit | 2,341 | [
"Brian"
] | 50482a9c8ab3e7ca8775104bd4742287256a78e98553836d0191810d0877e0d2 |
#this program corresponds to special.py
### Means test is not done yet
#E Means test is giving error (E)
#F Means test is failing (F)
#EF Means test is giving error and Failing
#! Means test is segfaulting
#8 Means test runs forever
### test_besselpoly
### test_mathieu_a
### test_mathieu_even_coef
### te... | teoliphant/scipy | scipy/special/tests/test_basic.py | Python | bsd-3-clause | 96,108 | [
"Elk"
] | ba3416c15903ec1a5820b6e82d31cc3e67a24cb17198dd578109d7e2554a0f08 |
""" StorageManagementDB is a front end to the Stager Database.
There are five tables in the StorageManagementDB: Tasks, CacheReplicas, TaskReplicas, StageRequests.
The Tasks table is the place holder for the tasks that have requested files to be staged.
These can be from different systems and have differen... | miloszz/DIRAC | StorageManagementSystem/DB/StorageManagementDB.py | Python | gpl-3.0 | 62,868 | [
"DIRAC"
] | ba795455b2eded5af43230ae2baa1817009e07b535f1b87bb288f7da51c6ebb5 |
""" Module for setting up statistical models
"""
import pylab as pl
import pymc as mc
from pymc import gp
import data
reload(data)
def gp_puzzle_nub(diff_degree=2., amp=1., scale=1.5, steps=100):
""" Generate a puzzle nub connecting point a to point b"""
M, C = uninformative_prior_gp(0., diff_degree, amp, s... | aflaxman/pymc-gp-puzzle | src/models.py | Python | gpl-3.0 | 1,765 | [
"Gaussian"
] | 8227066e34ddba8b43e1c6fda8fef04a9d47e2c7e41cefca0bc194868b3781a4 |
# test_stpsynchan.py ---
#
# Filename: test_stpsynchan.py
# Description:
# Author: Subhasis Ray
# Maintainer:
# Copyright (C) 2010 Subhasis Ray, all rights reserved.
# Created: Mon Jun 13 14:59:06 2011 (+0530)
# Version:
# Last-Updated: Thu Jun 30 12:23:43 2011 (+0530)
# By: Subhasis Ray
# Update #: ... | BhallaLab/moose-thalamocortical | TESTS/pymoose/test_stpsynchan.py | Python | lgpl-2.1 | 7,273 | [
"MOOSE"
] | e6f36c8d9dbd98c19552fb820688f02a4a7bfe9221097d4c90c335376974dbae |
#
# 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.
#
""" Notes about the diverses class of the restriction enzyme im... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/Restriction/Restriction.py | Python | apache-2.0 | 81,064 | [
"Biopython"
] | 939b80c2d0f18125c6f1b175b1ff5dc30a0a29b2663025fc735529615ca241c8 |
"""
mbed SDK
Copyright (c) 2011-2013 ARM Limited
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 wr... | NordicSemiconductor/mbed | workspace_tools/synch.py | Python | apache-2.0 | 11,471 | [
"VisIt"
] | b29ef97999563dfa7b7881c5e02dfaaf8955403ad49c51cc56f43b8b0432428c |
# Script initially by Tom Kazimiers 2013-01-12
# Adapted by Albert Cardona 2013-01-25
#
# The purpose of this script is to connect to a django session
# in a remote computer, and to retrieve information from the database
# such as the skeleton of a neuronal arbor and its synapses
# in the form of a NetworX graph.
from... | catsop/CATMAID | scripts/remote/access.py | Python | gpl-3.0 | 5,805 | [
"NEURON"
] | e0f91c1d67f94b9894b20c2409ee13ab1bf8d03be05b852454062a5dc2c5b97b |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, subprocess, sys, glob, string
import zipfile
from datetime import date
cwd = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
os.chdir(cwd)
required_module_keys = ['architectures', 'name','version','moduleid','descripti... | Inwy/linea-pro | ios/build.py | Python | mit | 8,622 | [
"VisIt"
] | 34bd56d33323873521013eeb0df517423e711038f84e37989178ce6475a7cf0b |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Created oriented text
text0Source = vtk.vtkTextSource()
text0Source.SetText("Text Source with Scalars (default)")
text0Mapper = vtk.vtkPolyDataMapper()
text0Mapper.SetInpu... | hlzz/dotfiles | graphics/VTK-7.0.0/Rendering/FreeType/Testing/Python/text.py | Python | bsd-3-clause | 2,061 | [
"VTK"
] | c910edb78b6d3ef55e36b5de58eb5bf588e1db3f672cd50a377424fa68854eec |
__author__ = 'nzhang-dev'
import unittest
from ctree.frontend import *;
from ctree.transformations import PyBasicConversions
from ctree.transforms import DeclarationFiller
def fib(n):
a, b = 0.0, 1.0
k = "hello"
while n > 0:
a, b = b, a + b
n -= 1
return a
class DeclarationTest(uni... | ucb-sejits/ctree | test/test_transforms/test_declaration_filler.py | Python | bsd-2-clause | 1,649 | [
"VisIt"
] | 3798645cdb150ba96ca85d59ba306de89d7d3e4cd6de39729966cc7807c73fcc |
#!/usr/bin/python
import argparse, sys, os, random, multiprocessing, subprocess, re
from shutil import rmtree, copytree
# This will operate a pipeline to go from
# Pre:
# pacbio_raw .. the path to the bax.h5 or bas.h5 you want to process
# please keep in mind that in this requires the accordingly
... | jason-weirather/Au-public | iron/code/pre-IDP/pre-IDP_step-2_error_correction.py | Python | apache-2.0 | 10,335 | [
"BWA"
] | 036909fda0c2f6ad8fafc3e3c012decb84c8b5f224b4a4de572d16de92fec33a |
#!/usr/bin/env python
# =============================================================================
# MODULE DOCSTRING
# =============================================================================
"""
Factories to manipulate OpenMM System forces.
"""
# ==========================================================... | choderalab/openmmtools | openmmtools/forcefactories.py | Python | mit | 7,743 | [
"MDTraj",
"OpenMM"
] | 189db12acae636422b4c5cd69ad6f549dcf2ac460f953f275322f880524c65dd |
from PyGMO.problem._problem import tsp, tsp_cs, tsp_vrplc, _tsp_encoding
from PyGMO import __extensions__
if __extensions__["gtop"] is True:
from PyGMO.problem._problem_space import tsp_ds
tsp_ds.encoding_type = _tsp_encoding
# Renaming and placing the enums
tsp.encoding_type = _tsp_encoding
tsp_vrplc.encoding... | kartikkumar/pagmo | PyGMO/problem/_tsp.py | Python | gpl-3.0 | 16,114 | [
"VisIt"
] | ac9f1f2a649c3aa72314dc51798771fa8ebb2600d7cf4a04f121623c563db71c |
#generic python modules
import argparse
import operator
from operator import itemgetter
import sys, os, shutil
import os.path
##########################################################################################
# RETRIEVE USER INPUTS
###############################################################################... | jhelie/xvg_conv | xvg_conv.py | Python | gpl-2.0 | 11,696 | [
"Avogadro"
] | fec98b2905e43c398afdb2862629d6af76a6bc0b08c8f2cd7e0a3118d4b32b7a |
import pickle
from math import log, pi, sqrt
import numpy as np
from ase.units import Hartree
from gpaw.utilities.cg import CG
import gpaw.mpi as mpi
class XAS:
def __init__(self, paw, mode="xas", center=None, spin=0):
wfs = paw.wfs
self.orthogonal = wfs.gd.orthogonal
self.cell_cv = np.ar... | qsnake/gpaw | gpaw/xas.py | Python | gpl-3.0 | 24,403 | [
"ASE",
"GPAW",
"Gaussian"
] | 93932791c58acfaf463c95f0296685a0b10e956982e497dfb65fe2978d249365 |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2020, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
"""
Universe Notebook Widget
#########################
To visualize a universe containing atoms, molecules, orbitals, etc., do
the following in a Jupyter notebook environment.
.. co... | exa-analytics/atomic | exatomic/widgets/widget.py | Python | apache-2.0 | 24,671 | [
"ADF",
"Gaussian"
] | 9703f60ea164c8e1c4a46e4b418b52bd5820766a1ee04a04764274114a6ac845 |
from __future__ import print_function
import copy
import numpy as np
from numpy.linalg import pinv
from simplenet import SigmoidLayer, LinearLayer
class MlpTrainer(object):
def __init__(self, mlp_network, learning_rate=1.0):
# Check that this is compatible with pseudoinverse training.
assert len(ml... | rileymcdowell/simplennet | simplenet/trainers/mlp_trainer.py | Python | mit | 5,031 | [
"NEURON"
] | ea2e81fa768e79159e412cad43c3f3bc4d35d8cde32a1980a0502de8732db876 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | test/tools/large_subdomain_gen/large_sub_gen.py | Python | lgpl-2.1 | 1,339 | [
"MOOSE"
] | 6fae116c08b97e773bfa02264a987c27d550c02887468cf3fc941c33f9decf32 |
# Copyright 2014-2018 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
#
# Unless required by appl... | gkc1000/pyscf | pyscf/nao/m_xc_scalar_ni.py | Python | apache-2.0 | 2,141 | [
"PySCF"
] | d8b774665f78d04e2ba2461a4696e2b5d2d8a4a034acb3621ac0676af3c55f00 |
# Copyright (c) 2016, Mike Smith
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import GPy
import numpy as np
import sys #so I can print dots
def get_log_likelihood(inputs,data,clust):
"""Get the LL of a combined set of clusters, ignoring time series offsets.
Get the log likelihood of a clus... | befelix/GPy | GPy/util/cluster_with_offset.py | Python | bsd-3-clause | 6,520 | [
"Gaussian"
] | 306382e3681c054083b266dfd57505ec55b773a46d497e66d884f48e17c8f9b8 |
# Copyright 2020 Department of Computational Biology for Infection Research - Helmholtz Centre for Infection Research
#
# 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 Li... | CAMI-challenge/AMBER | src/utils/labels.py | Python | apache-2.0 | 9,949 | [
"Amber"
] | a332eefd8e1f5739154371600dd2a92cbd471e9300a3c0ef8163e7169f7e36cc |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import logging
import os
import sqlite3
import sys
from collections import OrderedDict, defaultdict
from functools import wraps
from warnings import warn
import numpy as np
import pyproj
import regex
from cf_units import Unit
from compliance_checker import cfutil
from c... | aodn/compliance-checker | compliance_checker/cf/cf.py | Python | apache-2.0 | 220,804 | [
"NetCDF"
] | 5db406b303a8e92a825bb7b6ba0fd9446919f9e62b3773d19ba867aa5a5db399 |
# $HeadURL: $
''' Test_RSS_Command_VOBOXAvailabilityCommand
'''
import mock
import unittest
import DIRAC.ResourceStatusSystem.Command.VOBOXAvailabilityCommand as moduleTested
__RCSID__ = '$Id: $'
################################################################################
class VOBOXAvailabilityCommand_Tes... | Sbalbp/DIRAC | ResourceStatusSystem/Command/test/Test_RSS_Command_VOBOXAvailabilityCommand.py | Python | gpl-3.0 | 3,648 | [
"DIRAC"
] | d240705079f45e98797ca8db351f447c857da384bc3c995156452ac28e3be610 |
#!/usr/bin/python
#
# This source file is part of appleseed.
# Visit http://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2014-2016 Francois Beaune, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any ... | docwhite/appleseed | scripts/runtestsuite/runtestsuite.py | Python | mit | 19,303 | [
"VisIt"
] | 73e3df94cd603a6d0b627488ba066d277d94674b799cca4f9e24443c4e11692a |
#!/home/paulk/software/bin/python
from __future__ import division
from sys import argv,stderr,exit
from math import log
import pysam
import argparse
from cPickle import load
print >> stderr,"Note: the alignment being used is unique-reads against hg19. Please change it if needed (and change this notice)."
"""
Synopsis... | polarise/RP-python | count_in_features_v2.py | Python | gpl-2.0 | 3,441 | [
"pysam"
] | 8f14bfad93e50e7251775839eacd27332ddea310d9dcde1129b145cab702dce7 |
__author__ = "Rick Sherman"
import unittest2 as unittest
from nose.plugins.attrib import attr
from mock import patch
import os
import json
from jnpr.junos import Device
from jnpr.junos.factory.to_json import PyEzJSONEncoder, TableJSONEncoder, TableViewJSONEncoder
from jnpr.junos.op.routes import RouteSummaryTable
fro... | spidercensus/py-junos-eznc | tests/unit/factory/test_to_json.py | Python | apache-2.0 | 3,980 | [
"Firefly"
] | 32a81e2f566096d8b068df9b11c6390591ed72d9e2fda46248864263db319996 |
#
# Copyright 2018 Analytics Zoo Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... | intel-analytics/analytics-zoo | pyzoo/test/zoo/orca/learn/ray/pytorch/test_estimator_pytorch_backend.py | Python | apache-2.0 | 11,605 | [
"ORCA"
] | 9cacb56d00428c2c3e2ef06790d229c112d92371dc9555231aa041424abd5567 |
#!/usr/bin/env python
__author__ = 'H.L.'
import sys
import os
import re
import pysam
import utils
class pairBam(object):
"""
The object will manipulate Hi-C raw sequencing alignment files and generate disired outputs.
"""
_gatc = {'G': 'C', 'A': 'T', 'T': 'A', 'C': 'G', 'g': 'c', 'a': 't', 't': 'a'... | haochenl/hic_input_norm | input.py | Python | gpl-3.0 | 18,804 | [
"pysam"
] | 33fd92a89773f752a618b90fe4428ab8a32022247a12fe14deda7305c184dbb2 |
"""The WaveBlocks Project
This file contains the class which represents an inhomogeneous Hagedorn wavepacket.
@author: R. Bourquin
@copyright: Copyright (C) 2010, 2011, 2012, 2013, 2014, 2016 R. Bourquin
@license: Modified BSD License
"""
from numpy import zeros, complexfloating, array, eye, atleast_2d, angle, squee... | WaveBlocks/WaveBlocksND | WaveBlocksND/HagedornWavepacketInhomogeneous.py | Python | bsd-3-clause | 8,120 | [
"Gaussian"
] | da40fd915995160c145c3a00cd1209f53233c3311fd78460dcc91717e2911789 |
#!/usr/bin/env python
##############################################################################################
#
#
# regrid_emissions_N96e.py
#
#
# Requirements:
# Iris 1.10, time, cf_units, numpy
#
#
# This Python script has been written by N.L. Abraham as part of the UKCA Tutorials:
# http://www.ukca.ac.u... | acsis-project/emissions | emissions/python/timeseries_1960-2020/regrid_BC_fossil_emissions_n96e_greg.py | Python | gpl-3.0 | 19,004 | [
"NetCDF"
] | 7805d3e9070bd7de806f30c4dfefa95576ee7da8c9ab3f30de5822da4e3ffe21 |
# Copyright (C) 2018 Henrique Pereira Coutada Miranda, Alejandro Molina-Sanchez
# All rights reserved.
#
# This file is part of yambopy
#
import xml.etree.ElementTree as ET
from qepy.auxiliary import *
from .lattice import *
from yambopy.plot.plotting import add_fig_kwargs
__all__ = ['PwXML']
HatoeV = 27.2107
class... | henriquemiranda/yambo-py | qepy/pwxml.py | Python | bsd-3-clause | 14,095 | [
"Quantum ESPRESSO"
] | c9b5d761f48c669181671e2c24ebc64e85525becde9f607d36253f2a7389971e |
"""
================================
Image denoising using kernel PCA
================================
This example shows how to use :class:`~sklearn.decomposition.KernelPCA` to
denoise images. In short, we take advantage of the approximation function
learned during `fit` to reconstruct the original image.
We will co... | manhhomienbienthuy/scikit-learn | examples/applications/plot_digits_denoising.py | Python | bsd-3-clause | 5,166 | [
"Gaussian"
] | c4be801bebdcc17a6b4a9084d3fa39db1a76a7a3ecb6841daa258429cfaa1d4d |
# -*- coding: utf-8 -*-
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding field 'ArticleFullTextStat.methods_tag_found'
db.add_column('neuroelectro_articlefulltex... | neuroelectro/neuroelectro_org | neuroelectro/south_migrations/0057_auto__add_field_articlefulltextstat_methods_tag_found__add_field_metad.py | Python | gpl-2.0 | 28,970 | [
"NEURON"
] | 55712e9604be5adb642c192cc24434cee7bfe62597cd8f21bc19b6df13d7decf |
# choco/codegen.py
# Copyright (C) 2006-2016 the Choco authors and contributors <see AUTHORS file>
#
# This module is part of Choco and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""provides functionality for rendering a nodes constructing into module
source code."""
impor... | whiteclover/Choco | choco/codegen.py | Python | mit | 48,648 | [
"VisIt"
] | 5caef7fc130f98ecba026dc34c4d3dac5f1db7d6be1a5bbe4e8f94f1693000d3 |
# coding: utf-8
from __future__ import division, unicode_literals
"""
This module defines classes for point defects
"""
import os
import abc
import json
from bisect import bisect_left
from pymatgen.core.periodic_table import Specie, Element
from pymatgen.core.sites import PeriodicSite
from pymatgen.symmetry.analyze... | rousseab/pymatgen | pymatgen/analysis/defects/point_defects.py | Python | mit | 52,771 | [
"GULP",
"pymatgen"
] | b1ba06d0d01af0a03697dbab74c5a3a57d10ab6a1363c9709d7f43a4fd7d8777 |
#!/usr/bin/env python
# coding=utf-8
# Copyright 2016 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
#
# ... | corona10/grumpy | grumpy-tools-src/grumpy_tools/grumpc.py | Python | apache-2.0 | 6,825 | [
"VisIt"
] | 28a937691def29feafb8fe75fd1610e1b2fa59e8b5252b3eb285088487aa8c7d |
# Copyright 2019 The Oppia 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 applicable ... | prasanna08/oppia | scripts/setup.py | Python | apache-2.0 | 9,945 | [
"VisIt"
] | 62a27f906ce75651b9a7fe6e16f153bf6cff91ac1fdacfac90e827d8acb307f7 |
# -*- coding: utf-8 -*-
"""
MolVS - Molecule Validation and Standardization
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
MolVS is a python tool built on top of RDKit that performs validation and standardization of chemical structures.
"""
from __future__ import print_function
from __future__ import unicode_litera... | mcs07/MolVS | molvs/__init__.py | Python | mit | 837 | [
"RDKit"
] | 0ac4cdb3c42d112864a76dd69558f35f2391e820c21e5a284606cd5ccb55322f |
#!/usr/bin/env python
# -*- coding: iso-8859-1 -*-
# Documentation is intended to be processed by Epydoc.
"""
Introduction
============
The Munkres module provides an implementation of the Munkres algorithm
(also called the Hungarian algorithm or the Kuhn-Munkres algorithm),
useful for solving the Assignment Problem... | djgagne/hagelslag | hagelslag/util/munkres.py | Python | mit | 24,647 | [
"Brian"
] | 9f89c70e20fcad72c2c54148c2ea074fc1f524ca21510e2cc175abe469b9bee3 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | kdmurray91/scikit-bio | skbio/stats/ordination/_principal_coordinate_analysis.py | Python | bsd-3-clause | 6,010 | [
"scikit-bio"
] | 45caee65950de192e1a268ad69ee819f9cc6621f17bdfe5a1c22a4dade0fc116 |
from chemlab.core import Atom, Molecule, crystal,System
from chemlab.graphics.qt import QtViewer
from chemlab.graphics.renderers import BallAndStickRenderer
import numpy as np
#--- PATCH
from chemlab.db import ChemlabDB
from chemlab.libs.ckdtree import cKDTree
cdb = ChemlabDB()
# Those functions have a separate life
... | chemlab/chemlab | examples/silicon.py | Python | gpl-3.0 | 1,565 | [
"CRYSTAL"
] | be4196f2d1aaaae83d6b803b445616d418a36b2559ec29801d188a6acdfa684d |
'''
Created on Jul 31, 2017
@author: lubo
'''
from collections import defaultdict
from sgains.genome import Genome
from termcolor import colored
import os
import glob
import pandas as pd
import numpy as np
import pysam
import traceback
from dask import distributed
class VarbinPipeline(object):
def __init__(self... | KrasnitzLab/sgains | sgains/pipelines/varbin_pipeline.py | Python | mit | 5,372 | [
"pysam"
] | 315ae46abc66f2a65de119eb5c0d3fbd222dfd5ad1ad86d174225b73c3b45111 |
"""
The image module supports basic image loading, rescaling and display
operations.
"""
from __future__ import (absolute_import, division, print_function,
unicode_literals)
from matplotlib.externals import six
from matplotlib.externals.six.moves.urllib.parse import urlparse
from matplotlib.ex... | yuanagain/seniorthesis | venv/lib/python2.7/site-packages/matplotlib/image.py | Python | mit | 51,454 | [
"Gaussian"
] | b8f1c0190b12a119c559f2e93fad1c7b7fae6c7bbf3fc944361bd9c3043b42b1 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Create the RenderWindow, Renderer and both Actors
#
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
iren = vtk.vtkRenderWindowInteractor()
iren.SetR... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Imaging/Hybrid/Testing/Python/shepards.py | Python | gpl-3.0 | 1,559 | [
"VTK"
] | 1ab6dcd734fac7d5f72e26d7afef8454887c5822663769935a396a4159704baa |
# -*- coding: utf-8 -*-
"""Module containing the LinePlot class
This class is intended to extract 1-dimensional data from a ArrayReaderBase
instance and visualize it as a line plot"""
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.dates as mdates
import datetime as dt
from numpy import array, lin... | Chilipp/nc2map | mapos/_lineplot.py | Python | gpl-2.0 | 28,223 | [
"NetCDF"
] | 5c94a710c4c2c703b21f8f84fb3eaf874ffe4cef838d6c9d36c20f4218a7c9f1 |
########################################################################
#
# (C) 2015, Brian Coca <bcoca@ansible.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... | fdupoux/ansible | lib/ansible/galaxy/__init__.py | Python | gpl-3.0 | 2,371 | [
"Brian",
"Galaxy"
] | 4ec5cf3fbbe6aa46f7045f08f06441a9cff75282228a6792b477463dc164b16d |
# pylint: disable=bad-continuation
"""
Certificate HTML webview.
"""
import logging
import urllib
from datetime import datetime
from uuid import uuid4
import pytz
from django.conf import settings
from django.contrib.auth.models import User
from django.http import Http404, HttpResponse
from django.template import Reque... | angelapper/edx-platform | lms/djangoapps/certificates/views/webview.py | Python | agpl-3.0 | 28,569 | [
"VisIt"
] | de82b94b9176bc7738e8a703acf6b3ea261e81c3efb340d32afbfd55c695008d |
# Copyright (c) 2012, GPy authors (see AUTHORS.txt).
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import unittest
import numpy as np
import GPy
class MiscTests(unittest.TestCase):
def setUp(self):
self.N = 20
self.N_new = 50
self.D = 1
self.X = np.random.uniform(-3.... | strongh/GPy | GPy/testing/model_tests.py | Python | bsd-3-clause | 21,946 | [
"Gaussian"
] | 2afc8ea6fde9e4939f236774f1481416b1babab69a75a407135dae359ab3cb71 |
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