text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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'''Calculate molecular orbitals module'''
import numpy as np
def molecular_orbital(coords, mocoeffs, gbasis):
'''Return a molecular orbital given the nuclei coordinates, as well as
molecular orbital coefficients and basis set specification as given by the cclib library.
The molecular orbital is repr... | chemlab/chemlab | chemlab/qc/wavefunction.py | Python | gpl-3.0 | 1,482 | [
"cclib"
] | 55a634215a08cf8c94596b479b990338815c045c495d1247caf70249aaf782df |
import sys
import os
import gzip
import argparse
import commands
from timeit import default_timer as timer
parser = argparse.ArgumentParser(description='Gather potential reads for a region')
parser.add_argument('-r', help='Path of the reference fasta file', type=str)
parser.add_argument('--bed', help='Regions to extra... | berguner/svmap | extractreads_fq.py | Python | gpl-3.0 | 7,257 | [
"BWA"
] | 4a17698284ea1bc233d91a00e908d6f273373563c3f3f980e6b0f5b47935400a |
"""Contains the drivers and interface code for pinball machines which
use the Multimorphic R-ROC hardware controllers.
This code can be used with P-ROC driver boards, or with Stern SAM, Stern
Whitestar, Williams WPC, or Williams WPC95 driver boards.
Much of this code is from the P-ROC drivers section of the pyprocgam... | jabdoa2/mpf | mpf/platform/p_roc.py | Python | mit | 55,259 | [
"Brian"
] | c52ab705ffd6c6477c64d916cfaea2c5b22d4ae6efe3591274db5f0e219301bf |
#!/usr/bin/env python
# Copyright (C) 2007, Thomas Leonard
# See the README file for details, or visit http://0install.net.
import sys, os, shutil, tempfile, subprocess
import unittest
from zeroinstall.injector import model, qdom
sys.path.insert(0, '..')
import support
mydir = os.path.realpath(os.path.dirname(__file... | gfxmonk/0release | tests/testrelease.py | Python | lgpl-2.1 | 4,897 | [
"VisIt"
] | 77ed83df319efa7644d2f3b2b12b91e075beb60c37967a7c448ba71698327c5c |
#coding:utf8
'''
Created on 2011-10-17
@author: lan (www.9miao.com)
'''
from firefly.utils import services
from firefly.distributed.root import PBRoot,BilateralFactory
from twisted.internet import reactor
from twisted.python import log
import sys
reactor = reactor
log.startLogging(sys.stdout)
root = PBRoot()
ser... | yangdw/PyRepo | src/annotation/Firefly/firefly/test/test_distributed_root.py | Python | mit | 1,031 | [
"Firefly"
] | 720b58110c48e6f6ccb7229bceb0849c20bfbd3784c3904c1866d24bad22ca02 |
""" Runs few integrity checks
"""
__RCSID__ = "$Id$"
import re
import ast
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.Base.AgentModule import AgentModule
from DIRAC.ConfigurationSystem.Client.Helpers.Operations impor... | calancha/DIRAC | TransformationSystem/Agent/ValidateOutputDataAgent.py | Python | gpl-3.0 | 9,603 | [
"DIRAC"
] | 39b11492f623733e9622b8423f4d514cf455a30323cd0569603e89d53d5f4297 |
#! /usr/bin/env python
########################################################################
# File : dirac-stager-stage-files
# Author : Daniela Remenska
########################################################################
"""
Submit staging requests for a particular Storage Element! Default DIRAC JobID wil... | ic-hep/DIRAC | src/DIRAC/StorageManagementSystem/scripts/dirac_stager_stage_files.py | Python | gpl-3.0 | 2,881 | [
"DIRAC"
] | 6933eea7714523e2b4274291aa9cae406793b482b4772650fa321cd02de9db66 |
from collections import defaultdict, OrderedDict
from functools import wraps
import logging
from django.utils.translation import ugettext_lazy as _
from casexml.apps.case.xml import V2_NAMESPACE
from casexml.apps.stock.const import COMMTRACK_REPORT_XMLNS
from corehq.apps.app_manager.const import (
SCHEDULE_PHASE, S... | qedsoftware/commcare-hq | corehq/apps/app_manager/xform.py | Python | bsd-3-clause | 79,213 | [
"VisIt"
] | 8ebf5570b3f7526d908873d666388c9b86cd7007cadc76eabca8ce149b9c9fd6 |
r"""
QSeq format (:mod:`skbio.io.qseq`)
==================================
.. currentmodule:: skbio.io.qseq
The QSeq format (`qseq`) is a record-based, plain text output format produced
by some DNA sequencers for storing biological sequence data, quality scores,
per-sequence filtering information, and run-specific me... | johnchase/scikit-bio | skbio/io/qseq.py | Python | bsd-3-clause | 9,495 | [
"scikit-bio"
] | caff52063def3e5f277e56e19269cb80818509c33df5c63a80d119ec58a215a2 |
# Copyright (C) 2012,2013,2016
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of ... | espressopp/espressopp | src/tools/topology.py | Python | gpl-3.0 | 8,424 | [
"ESPResSo"
] | 04176869756bd6daf4510531b74cbad77c46cff05fa07da07f90c32c571e372c |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Usage: LaneCorrector.py folder/ cam.avi raw_lidar.npz multilane_points.npz
import bisect
from collections import deque
from colorsys import hsv_to_rgb
import glob
import math
import multiprocessing
import os
import sys
import time
import urllib
import cv2
import matplotlib.... | sameeptandon/sail-car-log | process/LaneCorrector.py | Python | bsd-2-clause | 64,765 | [
"VTK"
] | 2bdd46c742ea4c87e356bc9044161bd4ef5c950380deac0df21929f4ac40b3a2 |
"""
Robust location and covariance estimators.
Here are implemented estimators that are resistant to outliers.
"""
# Author: Virgile Fritsch <virgile.fritsch@inria.fr>
#
# License: BSD 3 clause
import warnings
import numbers
import numpy as np
from scipy import linalg
from scipy.stats import chi2
from . import empi... | bnaul/scikit-learn | sklearn/covariance/_robust_covariance.py | Python | bsd-3-clause | 32,315 | [
"Gaussian"
] | e9031f1971a447b27df6fd63422161cd6ae6137015de5e06e872c9422fbc184a |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import numpy as np
import scipy.linalg
from scipy.spatial.distance import cdist
import matplotlib.pyplot as plt
from . import variogram_models
from . import cor... | rth/PyKrige | pykrige/uk.py | Python | bsd-3-clause | 53,525 | [
"Gaussian"
] | b794a1e22c6e11d1d55f1cb9b878e94548862d84f469d5e4fb4d825a3a780c11 |
import os
from warnings import warn
from collections import Mapping
from .. import yaml_io
import numpy as np
from .. Error import GroupMissingDataError
from . Group import Group, Descriptor
from . Scheme import GroupAdditivityScheme
from . DataDir import get_data_dir
class GroupLibrary(Mapping):
"""Represent li... | VlachosGroup/VlachosGroupAdditivity | pgradd/GroupAdd/Library.py | Python | mit | 12,866 | [
"RDKit"
] | c6fc68e291ed8d9f7967efebb81f8c2a0bb45f09b43cc8b0486156709548d40c |
'''
ModelGenie (c) University of Manchester 2015
ModelGenie is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
| neilswainston/development-py | synbiochemdev/modelgenie/__init__.py | Python | mit | 203 | [
"VisIt"
] | 193611357385da67b913f07b19be086993538e9dfcc6345788b7cc90c5ceb01f |
import json
import re
#!!! This giant block of imports should be something simpler, such as:
# from great_exepectations.helpers.expectation_creation import *
from great_expectations.execution_engine import (
PandasExecutionEngine,
SparkDFExecutionEngine,
SqlAlchemyExecutionEngine,
)
from great_expectations... | great-expectations/great_expectations | contrib/experimental/great_expectations_experimental/expectations/expect_column_values_to_be_valid_urls.py | Python | apache-2.0 | 9,336 | [
"VisIt"
] | 1f9f7f9c66fe76371b663eb06b68b6e2292c9777d05b6cc0c18e846ae1eea788 |
#!/bin/env python
# -*- coding: utf-8 -*-
import os,re, sys, shutil
from Sire.IO import *
from Sire.Mol import *
from Sire.CAS import *
from Sire.System import *
from Sire.Move import *
from Sire.MM import *
from Sire.FF import *
from Sire.Units import *
from Sire.Vol import *
from Sire.Maths import *
from Sire.Base ... | michellab/Sire | wrapper/Tools/deprecated/FDTISingleBound.py | Python | gpl-2.0 | 69,441 | [
"Amber"
] | b6930a65ee6c45fd85de8c1ce3a18df929c42d2a21b25bec602b161ed1196172 |
import crosscat.cython_code.ContinuousComponentModel as ccm
import math
import random
import numpy
import six
from scipy.stats import norm as norm
from crosscat.utils.general_utils import logmeanexp
# FIXME: Using this instead of randrange because randrange is different before
# and after Python 3.2, and we hardcode... | mit-probabilistic-computing-project/crosscat | src/tests/component_model_extensions/ContinuousComponentModel.py | Python | apache-2.0 | 15,258 | [
"Gaussian"
] | 8a74d06c92ac48add6e497e0b48594dd6c3862cc64a2c435f26ef836978f0981 |
""" SandboxHandler is the implementation of the Sandbox service
in the DISET framework
"""
__RCSID__ = "$Id$"
import os
import time
import threading
import tempfile
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.Utilities.File import mkDir
from DIRAC.Core.DISET.RequestHandler import RequestHandler
from... | fstagni/DIRAC | WorkloadManagementSystem/Service/SandboxStoreHandler.py | Python | gpl-3.0 | 19,344 | [
"DIRAC"
] | 9144ec4c152f02738ea16fe6a1487a60739d7fe3f3d184ef2111699fab4ba2fa |
'''
author Kyle Cranmer <kyle.cranmer@nyu.edu>
Define model mu_s*Gaus(x|alpha,sigma)+mu_b*flat(x)
Generate {x} for several {alpha}
Calculate power (expected significance) for some alpha using profile likelihood approach
1) Train NN for alpha=0.
1a) make (histfactory/on the fly) model for NN with alpha variations
-... | cranmer/parametrized-learning | GausSigOnExpBkg_dev.py | Python | bsd-2-clause | 15,753 | [
"Gaussian"
] | f0762e0b553f8f4a754e45c0892de263d556ade4d006d0cd6fe16408ac498366 |
from __future__ import print_function
import astropy
try:
import scipy
from scipy import optimize,sqrt
from scipy.optimize import leastsq
#from scipy.stats.stats import nanmedian,nanmean,_nanmedian
except ImportError:
print("Scipy cold not be loaded. Collapse_gaussfit may fail")
import numpy
from n... | allisony/pyspeckit | pyspeckit/spectrum/collapse_gaussfit.py | Python | mit | 22,602 | [
"Gaussian"
] | 97711a10c0d03b3915a4e54d4ff41a76d3ce9730ec5d0ea265e276ebd1aec1e4 |
from rez.config import config
from rez.packages_ import Package
from rez.serialise import load_from_file, FileFormat, set_objects
from rez.packages_ import create_package
from rez.exceptions import PackageMetadataError, InvalidPackageError
from rez.utils.system import add_sys_paths
from rez.utils.sourcecode import Sour... | cwmartin/rez | src/rez/developer_package.py | Python | lgpl-3.0 | 10,532 | [
"VisIt"
] | d8c546ad61b8894662545e9e52f5389120e1c5bfaadb8680d520bbedd092c3a3 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class REnsembldb(RPackage):
"""Utilities to create and use Ensembl-based annotation databases
... | LLNL/spack | var/spack/repos/builtin/packages/r-ensembldb/package.py | Python | lgpl-2.1 | 3,387 | [
"Bioconductor"
] | 4360daf2884cd8e812d8945768b5f5436cc6c0b41c5a43a87f68aae02e93be4f |
# coding=utf-8
from global_test_case import GlobalTestCase as TestCase
from instance.models import WriteItInstance
from ..models import Confirmation, send_confirmation_email
from ..models import Message, ConfirmationTemplate
from django.core import mail
from subdomains.utils import reverse
from django.contrib.auth.mode... | ciudadanointeligente/write-it | nuntium/tests/confirmation_template_test.py | Python | gpl-3.0 | 12,497 | [
"VisIt"
] | b9d56658a278379e31767792c3de1fca1fb6160cc26a456101867772e5f11907 |
# This file is part of DEAP.
#
# DEAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# DEAP is distributed ... | CG-F16-24-Rutgers/steersuite-rutgers | steerstats/tools/deap/gp.py | Python | gpl-3.0 | 36,560 | [
"ADF"
] | cff50046aa3d2ac0121c15f95caf16ed336e4a3a2e1ccdba742a6054190d1f3f |
#
# Copyright (C) 2017 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 vers... | KonradBreitsprecher/espresso | testsuite/rotate_system.py | Python | gpl-3.0 | 2,399 | [
"ESPResSo"
] | 078356a18aa27692482565d76f83889ce248f9044ba4af86424e30f768859583 |
# -*- coding: utf-8 -*-
# Part of Odoo. See LICENSE file for full copyright and licensing details.
import random
import requests
import string
from lxml import html
from werkzeug import urls
from odoo import tools, models, fields, api, _
URL_MAX_SIZE = 10 * 1024 * 1024
class LinkTracker(models.Model):
""" Lin... | rven/odoo | addons/link_tracker/models/link_tracker.py | Python | agpl-3.0 | 9,635 | [
"VisIt"
] | 2e6d64682381a0c5ee9fe951a986f3cae10f31afb4dceadd98bc35d593786c09 |
# Copyright (c) 2012 Purdue University
# All rights reserved.
#
# Redistribution and use in source and binary forms, with o without ... | lastweek/gem5 | configs/spec2k6_classic/run.py | Python | bsd-3-clause | 9,050 | [
"GAMESS",
"Gromacs",
"NAMD"
] | 8967cea4fa9b5809aca97bbd8655d557c8211b25a3935c4900db82adb699095f |
import unittest
import xidplus
from astropy.io import ascii, fits
from astropy import wcs
import numpy as np
import xidplus
from xidplus import moc_routines
class wcs_update(unittest.TestCase):
def setUp(self):
xidplus.__path__[0]
# Folder containing maps
imfolder = xidplus.__path__[0] + ... | H-E-L-P/XID_plus | tests/test_wcs_update.py | Python | mit | 4,124 | [
"Gaussian"
] | 21bc4c1d143e832041d1eca0493ad2d220ab09ca4f6ae7e68ce70b61d3e2601e |
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2003-2007 Donald N. Allingham
# Copyright (C) 2008-2010 Brian G. Matherly
# Copyright (C) 2007-2010 Jerome Rapinat
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Gener... | pmghalvorsen/gramps_branch | gramps/plugins/rel/rel_ca.py | Python | gpl-2.0 | 31,230 | [
"Brian"
] | 129b8afb02c001d8a784cb4bdd82587b40f1f72e23621aa185d1a776c2cb5816 |
from i3pystatus.core.util import internet, require
from i3pystatus.scores import ScoresBackend
import copy
import json
import pytz
import re
import time
from datetime import datetime
from urllib.request import urlopen
LIVE_URL = 'https://www.nhl.com/gamecenter/{id}'
SCOREBOARD_URL = 'https://www.nhl.com/scores'
API_U... | Arvedui/i3pystatus | i3pystatus/scores/nhl.py | Python | mit | 15,422 | [
"COLUMBUS"
] | 9d6c58f116fd5163bbf608be4e747f22877b2592b2b1523cffcc2855ab780a3f |
#! /usr/bin/env python
import re
import math
import collections
import numpy as np
import time
import operator
from scipy.io import mmread, mmwrite
from random import randint
from sklearn import cross_validation
from sklearn import linear_model
from sklearn.grid_search import GridSearchCV
from sklearn import preproces... | Goodideax/CS249 | predict_gbm_5000.py | Python | bsd-3-clause | 14,603 | [
"Gaussian"
] | e7f2605300f759a2e74e5db1dbfab27b00b60598992bb35776dcf9013f66dcce |
# This file is part of cclib (http://cclib.sf.net), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2006, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version 2.1 or later. You shou... | Clyde-fare/cclib_bak | src/cclib/progress/textprogress.py | Python | lgpl-2.1 | 1,579 | [
"cclib"
] | 803f41f6130f1b3491f2d818b1370ad69bf04ef2a922e5f767f362bba57b3038 |
import sys, re
from Globals import *
from random import randint
from urllib import urlencode
from urllib2 import urlopen
from urlparse import urlunparse
from hashlib import sha1
from os import environ
# Set your proprty id via the environment or simply type it
# below
PROPERTY_ID = environ.get("GA_PROPERTY_ID", "UA... | 7fever/script.pseudotv.live | resources/lib/ga.py | Python | gpl-3.0 | 2,740 | [
"VisIt"
] | 2521c00c3803924cb3f27c7382bae9d738646dd84d007cc7d0c447fd512df1b9 |
""" This module loads all the classes from the VTK IO library into its
namespace. This is a required module."""
from vtkIOPython import *
| b3c/VTK-5.8 | Wrapping/Python/vtk/io.py | Python | bsd-3-clause | 140 | [
"VTK"
] | 53d3be4251f0b543e4062b45367f088c842c34eca40365dffd7a2ae03115a832 |
# -*- coding: utf-8 -*-
#
# Pyplis is a Python library for the analysis of UV SO2 camera data
# Copyright (C) 2017 Jonas Gliss (jonasgliss@gmail.com)
#
# This program is free software: you can redistribute it and/or
# modify it under the terms of the GNU General Public License a
# published by the Free Software Foundat... | jgliss/pyplis | pyplis/model_functions.py | Python | gpl-3.0 | 8,950 | [
"Gaussian"
] | 36ff9fd548c77b59c2317b3bb387518016ae7238affc5d8422cb45ba0376a24c |
#-*- coding: utf-8 -*-
#! /usr/bin/env python
'''
#------------------------------------------------------------
filename: ex_runTensorBoard.py
objectives: provide an example of Tensorboard using the
"lab6_runTFMultiANN_MNIST.py" example.
refs:
- google doc: https ://www.tensorflow.org/get_started/... | jwkanggist/EveryBodyTensorFlow | tf_basic/ex_runTensorBoard.py | Python | unlicense | 5,043 | [
"NEURON"
] | bd5dfcf1d017f766d27e47cdff8bcc9d9750fcc81f17e488ec7f883a5cf9e350 |
#!/bin/env python
# -*- coding: utf-8 -*-
# <nbformat>3.0</nbformat>
# <codecell>
"""
Generates a bed-file for the gaps or contigs for a given fasta file
Splits the sequences on gaps (default: 20 bases)
Output goes to to standard out
Requires Biopython
Lex Nederbragt, September 2013
lex.nederbragt@ibv.uio.no
"""
# ... | lexnederbragt/sequencetools | scaffoldgap2bed.py | Python | unlicense | 4,768 | [
"Biopython"
] | 993336065f375036aa1816aaf07f38b30319680d1636de838906216bdd45f050 |
"""Convenience functions for handling XML.
@since: 1.9
"""
# Copyright (C) 2012, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from xml.dom import Node
def _compare_children(a, b):
"""@rtype: bool"""
ac = a.childNodes
bc = b.childNodes
if ac.length != bc.length:
return Fals... | res2k/0install | zeroinstall/support/xmltools.py | Python | lgpl-2.1 | 1,271 | [
"VisIt"
] | 847901f2259c3f85843eb38f24207b7cf5df918c8a814dff6c4f78c01b400eaf |
# 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 Vesta(Package):
"""VESTA is a 3D visualization program for structural models, volumetric d... | rspavel/spack | var/spack/repos/builtin/packages/vesta/package.py | Python | lgpl-2.1 | 955 | [
"CRYSTAL"
] | 3bda067760cb82f6b5b42755819774c9282c03c9629292ab7b44f505468f3955 |
"""This file contains code used in "Think Stats",
by Allen B. Downey, available from greenteapress.com
Copyright 2012 Allen B. Downey
License: GNU GPLv3 http://www.gnu.org/licenses/gpl.html
"""
import matplotlib.pyplot as pyplot
import thinkplot
import csv
import math
import numpy
import random
import thinkstats2
i... | wavelets/ThinkStats2 | code/heri14.py | Python | gpl-3.0 | 14,158 | [
"Gaussian"
] | 40507ddbb311b49293378d37e91dc41d2e90dfeef407349b0db4e7069fcdeb23 |
"""Gaussian Mixture Model."""
# Author: Wei Xue <xuewei4d@gmail.com>
# Modified by Thierry Guillemot <thierry.guillemot.work@gmail.com>
# License: BSD 3 clause
import numpy as np
from scipy import linalg
from ._base import BaseMixture, _check_shape
from ..utils import check_array
from ..utils.extmath import row_nor... | kevin-intel/scikit-learn | sklearn/mixture/_gaussian_mixture.py | Python | bsd-3-clause | 28,290 | [
"Gaussian"
] | 13f79fb68b9eab3c68abc313533c8541ba2f2feb27b16b35edc73f4a49760da3 |
import os
import shutil, tempfile
import numpy as nm
try:
from enthought.traits.api \
import HasTraits, Instance, Button, Int, Float, Bool, on_trait_change
from enthought.traits.ui.api \
import View, Item, Heading, Group, HGroup, VGroup, Handler, spring
from enthought.traits.ui.editors.... | RexFuzzle/sfepy | sfepy/postprocess/viewer.py | Python | bsd-3-clause | 48,068 | [
"Mayavi",
"VTK"
] | 3c15587f1c9e38622f7d2240680fac661a228f0085b1414466ea21a47210eb86 |
# -*- coding: utf-8 -*-
import os
import time
import shutil
from datetime import datetime
import bisect
import tempfile
import itertools
from math import sqrt
import warnings
import numpy as np
import numpy.ma as ma
import netCDF4 as nc4
import pytz
from pyaxiom.netcdf import EnhancedDataset, EnhancedMFDataset
from py... | ayan-usgs/sci-wms | wms/models/datasets/sgrid.py | Python | gpl-3.0 | 29,603 | [
"NetCDF"
] | 9ffa13c59baca6e8b7da2eded95d5fd35b42c307c16aa18ec5f90a7da657d038 |
#!/usr/bin/python
# spud - keep track of photos
# Copyright (C) 2008-2013 Brian May
#
# 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 l... | brianmay/spud | spud/management/commands/check_all_files.py | Python | gpl-3.0 | 1,128 | [
"Brian"
] | 7b1ac9a8fd1832c0d100749516fb513ebd6ca1a8308aa8390745a7448d74a416 |
# Hop --- a framework to analyze solvation dynamics from MD simulations
# Copyright (c) 2007-2010 Oliver Beckstein <orbeckst@gmail.com>
#
# 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 v... | iwelland/hop | hop/density.py | Python | lgpl-3.0 | 48,917 | [
"CHARMM",
"CRYSTAL",
"Gaussian",
"MDAnalysis",
"VMD"
] | 0bd40f5e24e87d369e87b280ee26d719847e418446536c0d0f3a9c44223d7d3b |
# jsb.plugs.common/koffie.py
#
# Made by WildRover and Junke1990
""" schenk wat koffie! """
## jsb imports
from jsb.lib.commands import cmnds
from jsb.lib.examples import examples
## basic imports
import os
import string
import random
## defines
koffie = []
thee = []
bier = []
wijn = []
fris = []
taart = []
koek... | melmothx/jsonbot | jsb/plugs/common/koffie.py | Python | mit | 13,683 | [
"ESPResSo",
"Elk"
] | 464a2dfc36f75291bc37306adfde04996994f4ba1fcdcb4ea929be2b260957ad |
# -*- coding: utf-8 -*-
import pytest
import inflection
SINGULAR_TO_PLURAL = (
("search", "searches"),
("switch", "switches"),
("fix", "fixes"),
("box", "boxes"),
("process", "processes"),
("address", "addresses"),
("case", "cases"),
("stack", "stacks"),
("wish", "wishes"),
("f... | jpvanhal/inflection | test_inflection.py | Python | mit | 12,044 | [
"Octopus"
] | f92c5085ba83c07192ca12fd024d828a734b7996226893bf9d72e649fc10200b |
import os
import cPickle as pickle
import numpy as np
import matplotlib.pyplot as pl
import tempfile
import smtplib
try:
from email.mime.text import MIMEText
from email.mime.multipart import MIMEMultipart
except ImportError:
from email.MIMEMultipart import MIMEMultipart
from email.MIMEText import MIMET... | robwarm/gpaw-symm | gpaw/test/big/analysis.py | Python | gpl-3.0 | 9,085 | [
"GPAW"
] | 67c55aefdf7325015cb2d6bf20811509c0078d7329ad4ab4331306a83f9269b4 |
# -*- coding: utf-8 -*-
import numpy as np
import scipy.ndimage as snd
__author__ = "Ulysse Rubens <urubens@uliege.be>"
__version__ = "0.1"
def scoremap_transform_edt(binary_mask, mean_radius, alpha):
"""
Compute an exponentially shaped Euclidean distance transform
of a binary mask.
Parameters
... | urubens/CellCounting | cell_counting/preprocessing.py | Python | mit | 2,644 | [
"Gaussian"
] | 9da9be22982d74f82b63185d2bde26b2c97ba2aeb6b06d5e56f9721861734a1b |
# Principal Component Analysis Code :
from numpy import mean,cov,double,cumsum,dot,linalg,array,rank,size,flipud
from pylab import *
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import ro... | tapomayukh/projects_in_python | sandbox_tapo/src/skin_related/BMED_8813_HAP/Features/single_feature/results/cross_validate_categories_BMED_8813_HAP_scaled_method_II_force.py | Python | mit | 4,029 | [
"Mayavi"
] | 8ea779c4840f4efd9fd1072d56fa3438a023c1770b14498467321c240c18eec1 |
# Orca
#
# Copyright (C) 2010 Joanmarie Diggs
# Copyright (C) 2011-2012 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; eith... | ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/scripts/toolkits/WebKitGtk/braille_generator.py | Python | gpl-3.0 | 4,116 | [
"ORCA"
] | d2391de4e4591b3dad7b81f521fb21b237a8cd9f2676947f079851bbb36b9ad2 |
#!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Created on Thu Dec 15 16:41:07 2016
The package REGPHOT is designed for the analysis of resolved galaxy images.
It can run chi squared minimisation using Galfit or pyprofit on single band images as well
as GalfitM on multiband data.
It can run these in batch on a ca... | raphaelshirley/regphot | regphot/__init__.py | Python | mit | 2,669 | [
"Galaxy",
"Gaussian"
] | 32479211ae38d79216ddc3713ebdc93d5ccc868d811d9046e5d6bc634d2e1d43 |
# Copyright 2014-2016 Insight Software Consortium.
# Copyright 2004-2008 Roman Yakovenko.
# Distributed under the Boost Software License, Version 1.0.
# See http://www.boost.org/LICENSE_1_0.txt
"""
Define few unrelated algorithms that work on declarations.
"""
import warnings
from . import declaration_uti... | RayRuizhiLiao/ITK_4D | Modules/ThirdParty/pygccxml/src/pygccxml/declarations/algorithm.py | Python | apache-2.0 | 3,437 | [
"VisIt"
] | 5f900aa9e25d95d82badba8006799919612168617f692b58083a123ff0082c0c |
""" The LSF TimeLeft utility interrogates the LSF batch system for the
current CPU and Wallclock consumed, as well as their limits.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import os
import re
import time
from DIRAC import S_OK, S_ERROR
from ... | yujikato/DIRAC | src/DIRAC/Resources/Computing/BatchSystems/TimeLeft/LSFResourceUsage.py | Python | gpl-3.0 | 9,729 | [
"DIRAC"
] | c3bf6691a89313717d3aee9cc2f327ea3b9b2d3611db63da36878f65ec657708 |
from Sire.MM import *
from Sire.FF import *
from Sire.CAS import *
from Sire.System import *
from Sire.Move import *
from Sire.IO import *
from Sire.Mol import *
from Sire.Maths import *
from Sire.Vol import *
from Sire.Base import *
from Sire.Units import *
from Sire.Qt import *
from nose.tools import assert_almos... | michellab/SireUnitTests | unittests/SireFF/test_forcefields.py | Python | gpl-3.0 | 5,014 | [
"Amber"
] | be0d030d984cf84f916b4d29d4ed3ac62a52e43e795a4aa3941929eb7fe0bc6d |
#!/usr/bin/env python
#
# Copyright 2008 Jose Fonseca
#
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU Lesser General Public License as published
# by the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This ... | Wingless-Archangel/bokken | ui/xdot.py | Python | gpl-2.0 | 97,604 | [
"FLEUR"
] | e98c21a69730c95d2ac6b36c1c2aefb46de5388610fc620a2ebeb2479357f07f |
"""
Common DBM Layer classes
"""
from __future__ import print_function
__authors__ = ["Ian Goodfellow", "Vincent Dumoulin"]
__copyright__ = "Copyright 2012-2013, Universite de Montreal"
__credits__ = ["Ian Goodfellow"]
__license__ = "3-clause BSD"
__maintainer__ = "LISA Lab"
import functools
import logging
import num... | Refefer/pylearn2 | pylearn2/models/dbm/layer.py | Python | bsd-3-clause | 127,303 | [
"Gaussian"
] | aefafa6a34853274795d4b38df53a5037565801405f1df13a86d21a4fb74f235 |
'''
Support package for processing a dbSNP tabix dump from UCSC.
'''
import collections
import sys
import pysam
from ngsutils.support import revcomp
class SNPRecord(collections.namedtuple('SNPRecord', '''bin
chrom
chromStart
chromEnd
name
score
strand
refNCBI
refUCSC
observed
molType
clazz
valid
avHet
avHetSE
func
... | nturaga/tools-iuc | tools/ngsutils/ngsutils/support/dbsnp.py | Python | mit | 3,664 | [
"pysam"
] | 1a2b31ccf65436ce892e173369a2365362640279681a9f579bc026990ec14703 |
__author__ = 'cos'
from fife.extensions import pychan
from dialogs import InfoDialog
from huds import Widget
class GalaxyUI(Widget):
'''
Holds the UI widget showing the planets. It can be extended to form planet selection interfaces.
'''
_UNSELECT, _SELECTABLE, _SELECT, _NOTPOSSIBLE, _SPECIAL = xr... | conan747/fallen-heaven | scripts/gui/universeUI.py | Python | gpl-2.0 | 8,289 | [
"Galaxy",
"VisIt"
] | 106fa8a8c0edccf347fb4c8d03d9405eae4068e158ccd1f9e45dbba67d3e2b10 |
"""Pluralize English nouns (stage 6)
This program is part of "Dive Into Python", a free Python book for
experienced programmers. Visit http://diveintopython.org/ for the
latest version.
Command line usage:
$ python plural6.py noun
nouns
"""
__author__ = "Mark Pilgrim (mark@diveintopython.org)"
__version__ = "$Revis... | tapomayukh/projects_in_python | sandbox_tapo/src/refs/diveintopython-pdf-5.4/diveintopython-5.4/py/plural/stage6/plural6.py | Python | mit | 917 | [
"VisIt"
] | 3445a51ddc56d94b5a396c3690225b41e1fcd0526e8f8334724b6d1945a947fc |
import numpy as np
import random as rand
import sys, os
import copy
import pickle
#from mpi4py import MPI
from pymatgen import Lattice, Structure, Element, PeriodicSite
from pymatgen.io.vasp import Poscar, VaspInput
from pymatgen.analysis.structure_matcher import StructureMatcher, FrameworkComparator
from pymatgen.app... | skasamatsu/py_mc | examples/HAp-bulk/model_setup.py | Python | gpl-3.0 | 8,809 | [
"VASP",
"pymatgen"
] | d2c3106384f09749af470c02728461468e1b2dcda880d44c321429285a6e37dc |
# Copyright (c) 2012, CyberPoint International, LLC
# 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
# notice, this lis... | CyberPoint/libpgm | libpgm/pgmlearner.py | Python | bsd-3-clause | 45,678 | [
"Gaussian"
] | a00d802edcb3911a7d8130c74efb2cbe929f8b87c5470bc70da84e6154537ce8 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Run this test like so:
# vtkpython TestBarGraph.py -D $VTK_DATA_ROOT \
# -B $VTK_DATA_ROOT/Baseline/Charts/
import os
import vtk
import vtk.test.Testing
import math
data_2008 = [10822, 10941, 9979, 10370, 9460, 11228, 15093, 12231, 10160, 9816, 9384, 7892]
data_2009 =... | b3c/VTK-5.8 | Charts/Testing/Python/TestBarGraph.py | Python | bsd-3-clause | 2,353 | [
"VTK"
] | 3485b45f9e678360fc192b2c7cc7c1ebf583bf8e7cf057de15b55329aa5f3a5e |
#!/usr/bin/env python
#
# Copyright (C) 2017 - Massachusetts Institute of Technology (MIT)
#
# 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... | azariven/BioSig_SEAS | SEAS_Main/atmosphere_effects/cloud.py | Python | gpl-3.0 | 16,754 | [
"Gaussian"
] | 429614ab3938e83bff6018f10fca0572e2f2727e301c0c5368be5156f3b0a707 |
import numpy as np
from ase import Atoms
from gpaw import GPAW
from gpaw.tddft import TDDFT
from gpaw.tddft.abc import LinearAbsorbingBoundary
from gpaw.tddft.laser import CWField
atoms = Atoms('Be',[(0,0,0)], pbc=False)
atoms.center(vacuum=6)
calc = GPAW(h=0.35)
atoms.set_calculator(calc)
atoms.get_potential_energy()... | qsnake/gpaw | gpaw/test/be_nltd_ip.py | Python | gpl-3.0 | 1,059 | [
"ASE",
"GPAW"
] | 4b5e7dab3a44dc5647bca770c98ff7c3eac80b4039ea42bcece5c65a417f71b9 |
from kernel_exp_family.estimators.finite.gaussian import KernelExpFiniteGaussian
from kernel_exp_family.estimators.lite.gaussian import KernelExpLiteGaussian
from kernel_exp_family.estimators.parameter_search_bo import BayesOptSearch,\
plot_bayesopt_model_1d
from kernel_exp_family.examples.tools import visualise_fi... | karlnapf/kernel_exp_family | kernel_exp_family/examples/demo_xvalidation_bayes_opt_manual.py | Python | bsd-3-clause | 3,167 | [
"Gaussian"
] | 11d74b4e3b61c5f5496c4ae6f87ab9387f682e8cc5549384f319c79f0f8f347e |
#
# QAPI visitor generator
#
# Copyright IBM, Corp. 2011
#
# Authors:
# Anthony Liguori <aliguori@us.ibm.com>
# Michael Roth <mdroth@linux.vnet.ibm.com>
#
# This work is licensed under the terms of the GNU GPLv2.
# See the COPYING.LIB file in the top-level directory.
from ordereddict import OrderedDict
from qapi ... | HusterWan/qemu-1.7.2-stable | scripts/qapi-visit.py | Python | gpl-2.0 | 14,043 | [
"VisIt"
] | b43a06e13c04e8d6f7dafcd016c51fc83c8cc9e28229a3b9e446117e8b2d2894 |
# 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 pickle
import collections
from pymatgen.core.periodic_table import Element, Specie, DummySpecie, \
PeriodicTable, get_el_sp
from py... | migueldiascosta/pymatgen | pymatgen/core/tests/test_periodic_table.py | Python | mit | 12,703 | [
"pymatgen"
] | a023fb03a793137ebc7f2cb934ee7b08cf087c5d0313e3753865c0035f751f8c |
# coding = utf-8
from builtins import next
from builtins import str
from builtins import zip
from builtins import range
from builtins import object
import os
import random
from itertools import combinations
from math import pi as PI, inf as INF, sin
from numpy import array, cross, argmin, argmax, dot, average
from nump... | Oslandia/albion | elementary_volume/__init__.py | Python | gpl-3.0 | 26,343 | [
"VTK"
] | d956ebe1f472546905a80b61cadcf5f14f66cceca0235a1d74a60bd672fb6481 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module defines site transformations which transforms a structure into
another structure. Site transformations differ from standard transformations
in that they operate in a site-specific manner.
All tr... | mbkumar/pymatgen | pymatgen/transformations/site_transformations.py | Python | mit | 22,807 | [
"CRYSTAL",
"pymatgen"
] | 9e37eedf610c6bf3842175aac5d8cf5ac6a0e75974a848f84784142d95c33c6e |
#
# Copyright (C) 2015 - 2017 Red Hat, Inc.
#
# This copyrighted material is made available to anyone wishing to use,
# modify, copy, or redistribute it subject to the terms and conditions of
# the GNU General Public License v.2, or (at your option) any later version.
# This program is distributed in the hope that it ... | atodorov/anaconda | pyanaconda/ui/gui/spokes/blivet_gui.py | Python | gpl-2.0 | 12,818 | [
"VisIt"
] | 4f611c48c2e5acaf25730ee3bc9472e33c966effa91e6a55c2504de184230dc7 |
#!/usr/bin/env python
########################################################################
# File : dirac-version
# Author : Ricardo Graciani
########################################################################
"""
Print version of current DIRAC installation
Usage:
dirac-version [option]
Example:
$ dira... | DIRACGrid/DIRAC | src/DIRAC/Core/scripts/dirac_version.py | Python | gpl-3.0 | 662 | [
"DIRAC"
] | 6d26dacabcadf0430ce16f195d4e728411a22360bd40815deba4192afbdaaae1 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import os
from pymatgen.core.structure import Molecule
from pymatgen.io.xyz import XYZ
from pymatgen.io.vasp.inputs import Poscar
test_dir = os.path.join(os.path.dirname(__file__), "..", "..",... | mbkumar/pymatgen | pymatgen/io/tests/test_xyz.py | Python | mit | 5,714 | [
"VASP",
"pymatgen"
] | eb0fbcda3688056a2f016e29db709524076c71b6f3a94d63d925abbd9686275b |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | krafczyk/spack | var/spack/repos/builtin/packages/r-abadata/package.py | Python | lgpl-2.1 | 2,068 | [
"Bioconductor"
] | c188d2af77e9401e66139720298ffa28732f14dafaeb960a7235e209607a02e5 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for LibraryContent block in LMS
"""
import ddt
import textwrap
from nose.plugins.attrib import attr
from common.test.acceptance.tests.helpers import UniqueCourseTest, TestWithSearchIndexMixin
from common.test.acceptance.pages.studio.auto_auth import AutoAuthPage
from common... | chrisndodge/edx-platform | common/test/acceptance/tests/lms/test_library.py | Python | agpl-3.0 | 13,659 | [
"VisIt"
] | e48876d8a863fc6db300284cabbf21daeda3dd4b45c831401496cdcc727af268 |
"""Minimal Python 2 & 3 shim around all Qt bindings
DOCUMENTATION
Qt.py was born in the film and visual effects industry to address
the growing need for the development of software capable of running
with more than one flavour of the Qt bindings for Python - PySide,
PySide2, PyQt4 and PyQt5.
1. Bu... | listyque/TACTIC-Handler | thlib/side/Qt.py | Python | epl-1.0 | 58,624 | [
"VisIt"
] | 4db03b284e40a399d4d17f41725841bbfbbcec600b9c2a802bd96d5f2d61b985 |
#!/usr/bin/env python2.7
#Ryan G. Coleman, Brian K. Shoichet Lab
import string
import sys
import optparse
import sybyl2dock
import mol2
import hierarchy
import solv
import clash
import hydrogens
import time
import math
def mol2db2(options):
'''function that does all the actual work you may want to do to convert a... | ryancoleman/mol2db2 | mol2db2.py | Python | gpl-2.0 | 8,590 | [
"Brian"
] | 4d91d6158805b6c659d7bddb50b9a880e947c7f38b3ee6f4aaf2bd4edbb14a82 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2002-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Jerome Rapinat
# Copyright (C) 2008 Benny Malengier
# Copyright (C) 2011 Tim G L Lyons
#
# This program is free software; you can redistribute it ... | SNoiraud/gramps | gramps/gen/filters/rules/citation/_hasnote.py | Python | gpl-2.0 | 1,799 | [
"Brian"
] | 98f1efdbf0fcfdbd2ee673d832eb0eb776cba98a920730c131151cdcfdf2b668 |
################################################################################
#
# Copyright 2015-2020 Félix Brezo and Yaiza Rubio
#
# This program is part of OSRFramework. You can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published by
# the Free Softwa... | i3visio/osrframework | osrframework/wrappers/about.py | Python | agpl-3.0 | 4,647 | [
"VisIt"
] | a96269cc312bbe3f7cac3b5109ad03b3e61dd80985fdc5f91c847960e1fe8333 |
"""Configure file for PyMorph. Authors: Vinu Vikram, Yogesh Wadadekar and Ajit Kembhavi (IUCAA) 2008, Alan Meert (UPenn)"""
###----Specify the input images and Catalogues----###
imagefile = 'j8f643-1-1_drz_sci.fits'
whtfile = 'j8f643-1-1_drz_rms.fits' #The weight image. If it contains the
... | vvinuv/pymorph | test/test_run/config.py | Python | gpl-2.0 | 5,787 | [
"Galaxy"
] | bb1348cc9caeb57d0073b5d89d183f5453dc8e0e2326d678580046763c0b6a12 |
# -*- coding: utf-8 -*-
"""
Created on Thu May 30 18:39:58 2013
@author: jpeacock-pr
"""
#==============================================================================
import matplotlib.pyplot as plt
import numpy as np
import os
import matplotlib.colorbar as mcb
import matplotlib.colors as colors
import mtpy.imagin... | geophysics/mtpy | mtpy/imaging/plotpseudosection.py | Python | gpl-3.0 | 48,915 | [
"Gaussian"
] | 568f7cd8a5332026278c8518db190c2a9902affe8850c2bc45a1978b395a309e |
# Copyright 2012 Viewfinder Inc. All Rights Reserved.
"""Viewfinder notification manager.
The notification manager:
1. Creates notifications for the various operations. Notifications allow the client to
incrementally stay in sync with server state as it changes. Each operation triggers zero,
one, or mo... | liduanw/viewfinder | backend/op/notification_manager.py | Python | apache-2.0 | 42,665 | [
"VisIt"
] | 5ac008423ccd233b26d83590d1b24bac87e4e984bc544d489369c805cebd2c70 |
# -*- coding: utf-8 -*-
#
# sensitivity_to_perturbation.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... | lekshmideepu/nest-simulator | pynest/examples/sensitivity_to_perturbation.py | Python | gpl-2.0 | 8,858 | [
"NEURON"
] | 5f0f1ab7bb575947814ed2a84eb5b71293d6d4ada462b966e81a73f014ca9e30 |
# 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 RAffyplm(RPackage):
"""Methods for fitting probe-level models.
A package that exte... | iulian787/spack | var/spack/repos/builtin/packages/r-affyplm/package.py | Python | lgpl-2.1 | 1,500 | [
"Bioconductor"
] | 9215d940a77468b0d06b1dc845650dd0afef3e27de5cd8a1da05e9403c5bff74 |
# Copyright 2008-2015 Nokia Solutions and Networks
#
# 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 l... | caio2k/RIDE | src/robotide/lib/robot/model/keyword.py | Python | apache-2.0 | 4,556 | [
"VisIt"
] | 08978589282f8adbd4b7006c585cf848b6420b2ad1eb7c33ea9c8934e1818222 |
"""SCons.Util
Various utility functions go here.
"""
#
# Copyright (c) 2001 - 2014 The SCons Foundation
#
# 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
# wit... | engineer0x47/SCONS | engine/SCons/Util.py | Python | mit | 48,908 | [
"VisIt"
] | 9bb6ccfb87fec5b21a533f2d4e1babc758e4b948c1f6a854a01e4773f99d4d03 |
from functools import partial, wraps
from crispy_forms.layout import Layout, HTML
from django.contrib import messages
from django.forms import BaseFormSet
from django.forms.models import formset_factory
from django.http import HttpResponseRedirect
from mezzanine.pages.page_processors import processor_for
from hs_app_... | hydroshare/hydroshare | hs_app_netCDF/page_processors.py | Python | bsd-3-clause | 6,814 | [
"NetCDF"
] | 560c36dc6b94ba76ccba5e4fd2a7e8681b54ee07df96a179ca362585e5f615e3 |
# Copyright (c) Corporation for National Research Initiatives
from BaseEvaluator import BaseEvaluator
import jast
import ImportName
COMMASPACE = ', '
from org.python.compiler import ScopesCompiler, Future, CompilationContext
from org.python.compiler.ScopeConstants import *
import warnings
from org.python.parser imp... | mcarlson/openlaszlo | 3rd-party/tools/jythonc/SimpleCompiler.py | Python | epl-1.0 | 25,652 | [
"VisIt"
] | fd8ea15a8ba72f8e064268fa34d7894b552823d8e2e04378b701754790a98fec |
import os
import sys
import time
import random
jobstates = ['waiting', 'submitted', 'running', 'success', 'FAILED',
'disabled', 'TIMEOUT']
class AGTSJob:
def __init__(self, dir, script, queueopts=None,
ncpus=1, walltime=10 * 60, deps=None, creates=None,
show=None):... | robwarm/gpaw-symm | gpaw/test/big/agts.py | Python | gpl-3.0 | 12,997 | [
"GPAW"
] | 9c2e423627ce2b5da37f7560f2bc4d9625b5fe07b265f9a5bca1135d8abf5f9c |
"""
This is the main Python API for interacting with the JPER system.
If you are building a web API, or consuming information from the system as an external data consumer (i.e. you're not
writing a core module that sits underneath this interface) then you should use this class to validate, create and
consume notificat... | JiscPER/jper | service/api.py | Python | apache-2.0 | 23,362 | [
"Octopus"
] | 7685c9d840cddab9b2382e1b6d0140beae6df917ad98775550c6c7af958b1d80 |
#!/usr/bin/env python
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
from __future__ import print_function
__doc__ = """
This examples performs sifferent kinds of (2D and 3D) plots
of a given activation map.
Needs matplotlib.
Author : Bertrand Thirion... | bthirion/nipy | examples/labs/need_data/viz3d.py | Python | bsd-3-clause | 1,853 | [
"Mayavi"
] | 8608f1c2f5f46db97cde75bb193d3364f3196c09aaa4f870ef08a09cd1913c8d |
# encoding: utf-8
"""
System command aliases.
Authors:
* Fernando Perez
* Brian Granger
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2008-2011 The IPython Development Team
#
# Distributed under the terms of the BSD License.
#
# The full license is in the file... | noslenfa/tdjangorest | uw/lib/python2.7/site-packages/IPython/core/alias.py | Python | apache-2.0 | 9,427 | [
"Brian"
] | a83f3a1aee955f91640ea71d271b45c83b63f27b0b44b0853a0464158642611f |
# -*- coding: utf-8 -*-
# Copyright 2007-2020 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy 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... | dnjohnstone/hyperspy | hyperspy/models/model1d.py | Python | gpl-3.0 | 36,896 | [
"Gaussian"
] | 56062670f8384cecb1b38746de5f48f521c45347f95ea10758e2b60dbeb5f764 |
#!/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... | harterj/moose | modules/combined/examples/geochem-porous_flow/geotes_2D/geotes_2D.py | Python | lgpl-2.1 | 1,202 | [
"MOOSE"
] | 06a1ac14022d5320e05b194519f01e9681b696458bc94fce26b11aeba76d604e |
import sys, os, copy, pickle
import numpy as np
import pandas as pd
import pyneb_parser_castep
from pyneb_parser_castep import deprecate
import pyneb_structureformat
from time import time
def write_supercells2pickle(path,supercells):
# write data from supercell form into a dataframe and write that to disk... | andrew031191/pyneb | pyneb_parser_general.py | Python | lgpl-3.0 | 14,434 | [
"CASTEP",
"VASP"
] | 53cf31ab6be3ae9b323e9757ebfa141e2c8dd3da9e903ec10003f955cbd68373 |
# Mantid Repository : https://github.com/mantidproject/mantid
#
# Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
# NScD Oak Ridge National Laboratory, European Spallation Source
# & Institut Laue - Langevin
# SPDX - License - Identifier: GPL - 3.0 +
from __future__ import (absolute_import, divi... | mganeva/mantid | Framework/PythonInterface/test/python/plugins/algorithms/LRPeakSelectionTest.py | Python | gpl-3.0 | 2,895 | [
"Gaussian"
] | d3a9c6e34170d9e116b96b64910e676258ba2e79933181916d0da29fbf88f71b |
from base import RBM
import units
import parameters
import theano
import theano.tensor as T
import numpy as np
### RBMS ###
class BinaryBinaryRBM(RBM): # the basic RBM, with binary visibles and binary hiddens
def __init__(self, n_visible, n_hidden):
super(BinaryBinaryRBM, self).__init__()
# dat... | gupta-abhay/morb-theano | rbms.py | Python | unlicense | 9,380 | [
"Gaussian"
] | 8cc4d7a5f2861ba4bbc88dfb05c41fa6be808a527dca56e0643875ce53e8b27d |
#!/usr/bin/env python3
# Copyright 2018 The GraphicsFuzz Project Authors
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless requir... | google/graphicsfuzz | build/travis/licenses.py | Python | apache-2.0 | 43,288 | [
"Amber"
] | f5449dfd283ac4b7e246af43e390c48b8cc93180fe53678b69842faea99859f8 |
"""
Quadratic Discriminant Analysis
"""
# Author: Matthieu Perrot <matthieu.perrot@gmail.com>
#
# License: BSD 3 clause
import warnings
import numpy as np
from .base import BaseEstimator, ClassifierMixin
from .externals.six.moves import xrange
from .utils import check_array, check_X_y
__all__ = ['QDA']
class QDA... | soulmachine/scikit-learn | sklearn/qda.py | Python | bsd-3-clause | 7,139 | [
"Gaussian"
] | 055109303f0e312969772984759b34d459419e58b264c9c847bbab3610504068 |
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