text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
"""
This module defines input sets for CP2K and is a work in progress. The structure/philosophy
of this module is based on the Vasp input sets in Pymatgen. These sets are meant to contain
tested parameters that will result in successful, reproducible, consistent calculations without
need for intervention 99% of the tim... | materialsproject/pymatgen | pymatgen/io/cp2k/sets.py | Python | mit | 48,941 | [
"CP2K",
"Gaussian",
"VASP",
"pymatgen"
] | d4180d0b612ef79f21b37e828399e739593e45fe83c3086469fd05e2de29f777 |
#! /usr/bin/env python
__RCSID__ = "$Id$"
from DIRAC.Core.Base.Script import parseCommandLine
parseCommandLine()
from DIRAC.Resources.Storage.StorageElement import StorageElement
from DIRAC.Resources.Utilities import Utils
from DIRAC.Core.Utilities.File import getS... | avedaee/DIRAC | Resources/Storage/TestStorageElement.py | Python | gpl-3.0 | 36,561 | [
"DIRAC"
] | 73c667ce2ae35c851f20e29b3ffd7b31cb7ffaa742f5f91a3aed6f2634187cb5 |
#
# Copyright (C) 2017 Peter Gedeck
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
'''
Collection of utilities to be used with descriptors
'''
i... | rdkit/rdkit | rdkit/Chem/ChemUtils/DescriptorUtilities.py | Python | bsd-3-clause | 1,916 | [
"RDKit"
] | 644bb67ddb0452448cf8825581cac3d6ffa19e7b21dc2d844b45bcb704e58f60 |
#
# Copyright (C) 2018-2019 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... | KaiSzuttor/espresso | testsuite/python/actor.py | Python | gpl-3.0 | 3,068 | [
"ESPResSo"
] | e8163be19bb1355d6cda76b24d9a70aadd260f4050ef327a81e29f3ebac4f20c |
############################################################################
# GE class representing SGE batch system
# 10.11.2014
# Author: A.T.
############################################################################
""" Torque.py is a DIRAC independent class representing Torque batch system.
Torque objec... | yujikato/DIRAC | src/DIRAC/Resources/Computing/BatchSystems/GE.py | Python | gpl-3.0 | 7,196 | [
"DIRAC"
] | d0370b6ce64f45a738cf3848f3fc7405f6a7efc8590884a77270153aaa144199 |
# revset.py - revision set queries for mercurial
#
# Copyright 2010 Matt Mackall <mpm@selenic.com>
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 or any later version.
import re
import parser, util, error, hbisect, phases
import node
import heapq
impo... | hekra01/mercurial | mercurial/revset.py | Python | gpl-2.0 | 110,473 | [
"VisIt"
] | f35f471eec47bb30375fd5690f1f145fb76f3c84c248b635c6455f87c7ab3f54 |
try:
# try C library _cbor.so
from ._cbor import loads, dumps, load, dump
except:
# fall back to 100% python implementation
from .cbor import loads, dumps, load, dump
from .cbor import Tag, CBOR_TAG_CBOR, _IS_PY3
class ClassTag(object):
'''
For some CBOR tag_number, encode/decode Python class... | DisposaBoy/GoSublime | gosubl/vendor/cbor_py/cbor/tagmap.py | Python | mit | 4,748 | [
"Brian"
] | 00e5041219848fa3945074b3090258749faa255e7b8d1547aaa3735297e247e1 |
import openpathsampling as paths
import numpy as np
class TrajectorySegmentContainer(object):
"""Container object to analyze lists of trajectories (or segments).
For the most part, this imitates a list. It supports most list behaviors
(addition, iteration, etc). However, as a list of lists, it contains a
... | jhprinz/openpathsampling | openpathsampling/analysis/trajectory_transition_analysis.py | Python | lgpl-2.1 | 15,511 | [
"VisIt"
] | ba1a255446fe20d74718fb70ea15eb4acda8c2d53f3d8025407586c89b9fab6f |
"""This module generates the tvtk (Traited VTK) wrapper classes for
VTK classes.
"""
# Author: Prabhu Ramachandran
# Copyright (c) 2004-2015, Enthought, Inc.
# License: BSD Style.
from __future__ import print_function
import sys
import vtk
import types
import textwrap
import keyword
import copy
# Local imports (the... | dmsurti/mayavi | tvtk/wrapper_gen.py | Python | bsd-3-clause | 57,223 | [
"VTK"
] | 1e533c9338eda9d7177a4cc1159def75986be03098fbcfb13ccff8e1c7b7ab99 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2006 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 Lesser General Public License as published by
## the Free Software F... | andrebellafronte/stoq | stoqlib/domain/test/test_transaction.py | Python | gpl-2.0 | 5,640 | [
"VisIt"
] | f4897b2627aa47c51b8f002e16ff115b5e08c0886f6a6b00ba8ba935f81f87cf |
from django.core.urlresolvers import reverse
from django.db import models
from edc_base.audit_trail import AuditTrail
from edc_base.model.models.base_uuid_model import BaseUuidModel
from edc_visit_tracking.models import BaseVisitTracking
from edc_visit_tracking.constants import VISIT_REASON_NO_FOLLOW_UP_CHOICES
from ... | botswana-harvard/edc-bhp074 | bhp074/apps/eit_maternal/models/maternal_visit.py | Python | gpl-2.0 | 1,592 | [
"VisIt"
] | e97363ba5429623fbee35125956784f593df71320521885ca63d1afea8679540 |
from __future__ import annotations
import os
from cctbx import sgtbx
from dxtbx.model import Crystal
from dxtbx.model.experiment_list import ExperimentListFactory
from iotbx.xds import integrate_hkl, spot_xds
from libtbx.phil import parse
from rstbx.cftbx.coordinate_frame_helpers import align_reference_frame
from sci... | dials/dials | command_line/import_xds.py | Python | bsd-3-clause | 17,160 | [
"CRYSTAL"
] | f3f4379d461b2bd641666e6aa82c7b249169fa85302520d1cceb059965ced917 |
class CrystalProject:
"""
Project to use for crystal
"""
def __init__(self, project_id, project_name, description, domain_name, enabled, crystal_enabled):
"""
:param project_id: project id
:param project_name: project name
:param description: project description
... | Crystal-SDS/dashboard | crystal_dashboard/dashboards/crystal/projects/projects/models.py | Python | gpl-3.0 | 691 | [
"CRYSTAL"
] | ee922727afa0b60991de86c357f250d3d7bfc510c74ef96b81aed114e83478d6 |
'''
This module contains the one-parameter exponential families used
for fitting GLMs and GAMs.
These families are described in
P. McCullagh and J. A. Nelder. "Generalized linear models."
Monographs on Statistics and Applied Probability.
Chapman & Hall, London, 1983.
'''
#from statsmodels.family.family im... | hlin117/statsmodels | statsmodels/genmod/families/__init__.py | Python | bsd-3-clause | 514 | [
"Gaussian"
] | ca17866047832c76d1f58e3e9a319e333482b02899711f225b7abf39df61310f |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | rahul003/mxnet | example/image-classification/common/fit.py | Python | apache-2.0 | 13,460 | [
"Gaussian"
] | 740dbec2ecf0045fd592ea6c81e002f8dcc03e783175639d152401e6550f41ba |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Copyright (c) 2017, Ivan Luchko and Project Contributors
Licensed under the terms of the MIT License
https://github.com/luchko/latticegraph_designer
This module contains the definition of the app MainWindow.
class MainWindow(QMainWindow, Ui_MainWindow):
... | luchko/latticegraph_designer | latticegraph_designer/app/main.py | Python | mit | 19,862 | [
"CRYSTAL"
] | 6093e6ca2d7aaef7b55eeb9c5391da6f5189345a5c57c667a37197b93bb3e7d7 |
#!/usr/bin/env python
# Copyright 2014-2020 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/mrpt/test/test_nevpt2.py | Python | apache-2.0 | 4,409 | [
"PySCF"
] | c47233504e18887f27642b775276907c46404b76759cefc800b27a3f97b15817 |
# -*- coding: utf-8 -*-
__version__ = '0.9'
__authors__ = u'Konrad Talik, Stanisław Jastrzębski'
__copyright__ = 'Copyright 2013-2015,\
Jagiellonian University Robotics Interest Group'
__license__ = 'MIT'
__maintainer__ = 'Konrad Talik'
__email__ = 'konradtalik@gmail.com'
__about__ = """This simula... | uj-robotics/krakrobot2016-online | simulator/misc/defines.py | Python | mit | 2,047 | [
"VisIt"
] | 331778901f5e5a6afe2af0c1bb3c935bfa42ba3f70355b754fd56a7a951aee49 |
# -*- coding: utf-8 -*-
# Twisted Imports
from twisted.enterprise import adbapi
from twisted.internet import reactor, defer
from twisted.logger import Logger
from twisted.python import log, filepath, urlpath
from twisted.web import server, static, resource, guard, http
from twisted.web.template import flatten
from twi... | richardingham/octopus | octopus/blocktopus/server/server.py | Python | mit | 17,316 | [
"Octopus"
] | 21e9a2de32e920242534e572539f87e82458991b5a6c632c3d80c36c823344c3 |
#!/usr/bin/env python3
# ******************************************************************************
# $Id: gdal_proximity.py 124baa7f71f15396a661014a81b6c5b0c82c8004 2020-10-14 17:29:39 +0300 Idan Miara $
#
# Name: gdalproximity
# Project: GDAL Python Interface
# Purpose: Application for computing raster ... | grueni75/GeoDiscoverer | Source/Platform/Target/Android/core/src/main/jni/gdal-3.2.1/swig/python/osgeo/utils/gdal_proximity.py | Python | gpl-3.0 | 7,868 | [
"NetCDF"
] | 7017e3bb063fc9de0cd4d26481b94d9ad3c36f6386c23b90519f7a8abd77c7af |
#### PATTERN | WEB #################################################################################
# -*- coding: utf-8 -*-
# Copyright (c) 2010 University of Antwerp, Belgium
# Author: Tom De Smedt <tom@organisms.be>
# License: BSD (see LICENSE.txt for details).
# http://www.clips.ua.ac.be/pages/pattern
############... | EricSchles/pattern | pattern/web/__init__.py | Python | bsd-3-clause | 136,733 | [
"VisIt"
] | ae66fe350250d146f8e0eef32d6d4c6da7ee5cc179b81ebd295132a59e1013b2 |
#!/usr/bin/env python
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
... | smadha/tika | tika-parsers/src/main/resources/org/apache/tika/parser/recognition/tf/inceptionapi.py | Python | apache-2.0 | 19,624 | [
"VisIt"
] | 361d758bc03ef5c41867fa3796c08678b553362acaffd42e1ef199ef81027f77 |
# -*- coding: utf8
"""Random Projection transformers
Random Projections are a simple and computationally efficient way to
reduce the dimensionality of the data by trading a controlled amount
of accuracy (as additional variance) for faster processing times and
smaller model sizes.
The dimensions and distribution of Ra... | eickenberg/scikit-learn | sklearn/random_projection.py | Python | bsd-3-clause | 21,651 | [
"Gaussian"
] | 63088c97a232df45675cdab2c92f8e4fc99e969e6e489f080498b095e3c50bf9 |
from itertools import chain
from contextlib import contextmanager
from collections import namedtuple, deque, defaultdict
from .refs import ArgRef, FieldRef, ItemRef, Reference, is_from_arg, CtxRef
from .nodes import Tuple, Number, Keyword, String, List, Symbol, Placeholder
from .nodes import NodeVisitor, NodeTransform... | vmagamedov/kinko | kinko/checker.py | Python | bsd-3-clause | 23,824 | [
"VisIt"
] | 4126e0a8b881c0a46ea3f42ce68be38607ad590413e2feaedb385445ccb97a52 |
"""
analysis/network.py
Functions to plot and analyze connectivity-related results
Contributors: salvadordura@gmail.com
"""
from __future__ import print_function
from __future__ import division
from __future__ import unicode_literals
from __future__ import absolute_import
from builtins import open
from builtins impo... | thekerrlab/netpyne | netpyne/analysis/network.py | Python | mit | 51,620 | [
"NEURON"
] | fed865231587c60ad53adcfd45d5ddfdf59421c759ec42d09c620d9fb4b3a9c3 |
"""Retrieve indexed genomes using Galaxy's rsync server resources.
http://wiki.galaxyproject.org/Admin/Data%20Integration
"""
from xml.etree import ElementTree
from fabric.api import *
from fabric.contrib.files import *
# ## Compatibility definitions
server = "rsync://datacache.g2.bx.psu.edu"
index_map = {"bowtie"... | joemphilips/cloudbiolinux | cloudbio/biodata/galaxy.py | Python | mit | 8,503 | [
"BWA",
"Bowtie",
"Galaxy"
] | 480bc9fb44dc12782608ecd23c4a305d128bb4c3c34d1149e4297922d074f252 |
from __future__ import absolute_import, division, print_function
import functools
import sys
import warnings
from collections import Mapping, defaultdict
from distutils.version import LooseVersion
from numbers import Number
import numpy as np
import pandas as pd
import xarray as xr
from . import (
alignment, du... | jcmgray/xarray | xarray/core/dataset.py | Python | apache-2.0 | 136,388 | [
"NetCDF"
] | 733ec41ef7b9e2e775bedc18e93d4f8876d55af9087e3410395a8cbfc3895a77 |
# (c) 2012-2014, Michael DeHaan <michael.dehaan@gmail.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) an... | civisanalytics/ansible | lib/ansible/constants.py | Python | gpl-3.0 | 28,972 | [
"Galaxy",
"MOOSE"
] | 2835ea5775beb4bdb9ebec4445705e8c088c9b1db3a6f2b66d5adba3c9dec77a |
#-*- coding:utf-8 -*-
"""
This file is part of openexp.
openexp is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
openexp is distributed in ... | amazinger2013/OpenSesame | openexp/_canvas/xpyriment.py | Python | gpl-3.0 | 10,518 | [
"Gaussian",
"VisIt"
] | 92c6c46ffde4863ad18e72fb6e639767c6683efe65ff92c597eddcfff98be994 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under th... | kain88-de/mdanalysis | package/MDAnalysis/coordinates/TRZ.py | Python | gpl-2.0 | 19,766 | [
"MDAnalysis"
] | 9cade73a4e7584177ccc2c3ea545e9d61442ce4aeaaabb4cd4023a8c5bb4863d |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2019, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Unit tests for general file writer."""
import inspect
import os
import unittest
import cclib
__filedir__ = os.path.... | cclib/cclib | test/io/testfilewriter.py | Python | bsd-3-clause | 881 | [
"ADF",
"cclib"
] | 5c6c64ff0cf395e7abe7da0f26350ba248fc6ba580c6d7c29eabfb4a254663e0 |
## This file is part of Invenio.
## Copyright (C) 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012, 2014 CERN.
##
## Invenio is free software; you can redistribute it and/or
## modify it under the terms of the GNU General Public License as
## published by the Free Software Foundation; either version 2 of the
## License, ... | lnielsen/invenio | invenio/legacy/websession/templates.py | Python | gpl-2.0 | 122,398 | [
"VisIt"
] | a07ad9b93d879b990407992e4663588f5350e0fac7700fbf868bf2f5111c50a2 |
import ast
import sys
from pyflakes import checker
from pyflakes.test.harness import TestCase, skipIf
class TypeableVisitorTests(TestCase):
"""
Tests of L{_TypeableVisitor}
"""
@staticmethod
def _run_visitor(s):
"""
Run L{_TypeableVisitor} on the parsed source and return the visi... | lmregus/Portfolio | python/design_patterns/env/lib/python3.7/site-packages/pyflakes/test/test_checker.py | Python | mit | 6,047 | [
"VisIt"
] | feca5986e292e614eb58e873ac46f32bb19e13a24808e2adf28dec6abb5ce99f |
from crop import Region, Point
import numpy
import cli
import code
import cv2
import os
from scipy import ndimage as scind
@cli.Plugin.register
class CropLocal(cli.Plugin):
''' Crops out an image by looking for a single region of low uniformity
This method of cropping
is moderately slo... | SeanTater/tscan | tscan/crop_local.py | Python | gpl-3.0 | 3,311 | [
"Gaussian"
] | 85c55ab603bdc80bd4c8c87f83508a3849c6da2e1c5886fcef8f6a702c3434c4 |
"""Generate Java code from an ASDL description."""
# TO DO
# handle fields that have a type but no name
import os, sys, traceback
import asdl
TABSIZE = 4
MAX_COL = 100
def reflow_lines(s, depth):
"""Reflow the line s indented depth tabs.
Return a sequence of lines where no line extends beyond MAX_COL
... | RandallDW/Aruba_plugin | plugins/org.python.pydev.parser/src/org/python/pydev/parser/jython/ast/asdl_java.py | Python | epl-1.0 | 19,782 | [
"VisIt"
] | 7f981d74e8af2d11116068454dcb5a1d125782fadaec98dd5a2cadeb090657e1 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
urlpatterns = [
url(r'^$', TemplateView.as_view(templ... | atiro/culture-board | config/urls.py | Python | bsd-3-clause | 1,330 | [
"VisIt"
] | ecd959e8d665b0a9b737a89102eaa87ff9996a139845c538c79e32f8f3c16f35 |
# (C) 2012, Michael DeHaan, <michael.dehaan@gmail.com>
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any la... | junegunn/ansible | plugins/callbacks/osx_say.py | Python | gpl-3.0 | 2,764 | [
"exciting"
] | 2aa11409d7256a77b1244932eef8d9a995e12f04aa9293163572c6bf7aa448df |
# -*- coding: utf-8 -*-
"""Constants for PyBEL.
This module maintains the strings used throughout the PyBEL codebase to promote consistency.
"""
from .config import connection
def get_cache_connection() -> str:
"""Get the preferred RFC-1738 database connection string.
1. Check the environment variable ``P... | pybel/pybel | src/pybel/constants.py | Python | mit | 18,553 | [
"Pybel"
] | 6beeae05f3a3aae3b98ff8bbd5bbad472feb0f79d4592977863ad9b10b81a83e |
"""Driver for gradient calculations."""
from __future__ import absolute_import, print_function, division
import six.moves.builtins as builtins
import logging
import time
import warnings
import numpy # for numeric_grad
from six import itervalues
import theano
from theano import gof
from theano.gof import utils, Vari... | JazzeYoung/VeryDeepAutoEncoder | theano/gradient.py | Python | bsd-3-clause | 81,055 | [
"VisIt"
] | 9a7be706bdae4d0b58718b09cfc999c4b5b6e3a148257ee4792d337ab2324959 |
# -*- coding: utf-8
from yade import ymport,utils,pack,export,qt,bodiesHandling
import gts,os
# for plotting
from math import *
from yade import plot
############################
### DEFINING PARAMETERS ###
############################
#GEOMETRIC :dimension of the rectangular box
a=.2 # side dimension
h=.1 # h... | anna-effeindzourou/trunk | examples/anna_scripts/tilt/tilttest_cylinders.py | Python | gpl-2.0 | 8,699 | [
"ParaView"
] | b70076df1a50f7abd25d95805536153743c96e20a2e4caf6925b54f3223503bf |
#/###################/#
# Import modules
#
#ImportModules
import ShareYourSystem as SYS
#/###################/#
# Build the model
#
#Definition an instance
MyRater=SYS.RaterClass(
).mapSet(
{
'RatingUnitsInt':3,
}
).brian(
)
#/###################/#
# Print
#
#Definition the AttestedStr
print('MyRater is... | Ledoux/ShareYourSystem | Pythonlogy/draft/Rater/01_ExampleCell.py | Python | mit | 901 | [
"Brian"
] | 4bfb79b2482afe504c743b91b3af14a51cf7bc06e1bb91dff6a114d1821471d1 |
# PyVision License
#
# Copyright (c) 2006-2008 David S. Bolme
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistributions of source code must retain the above copyright
# notice, thi... | tigerking/pyvision | src/pyvision/point/DetectorCorner.py | Python | bsd-3-clause | 7,990 | [
"Gaussian"
] | e87986e0cc22be08a3279b8f4db543f4a5c29384628d05befdb218d092255dee |
import sys, os
sys.path.append(f"{os.path.dirname(__file__)}")
sys.path.append(f"{os.path.dirname(__file__)}/../repESP_old")
import cube_helpers
import numpy as np
from scipy.ndimage.morphology import distance_transform_edt as scipy_edt
import argparse
def grid_point_nearest_atom(field, atom):
"""Returns indice... | jszopi/repESP | scripts/cavity.py | Python | gpl-3.0 | 2,559 | [
"Gaussian"
] | 9ee99c4db93cc2cb949ca342737ab6646ebd808bc65884872255639dcd5b8566 |
'''
This defines a bridge between Python and Spider.
Adapted from http://www.wadsworth.org/spider_doc/spider/proc/spyder.py
Example usage
-------------
.. sourcecode:: py
>>> from spider.core.spider_session import Session
>>> spi = Session(ext='dat')
>>> spi.invoke("[size]=117")
>>> size = spi[... | ezralanglois/arachnid | arachnid/core/spider/spider_session.py | Python | gpl-2.0 | 33,805 | [
"Gaussian"
] | 36fe65177c4bf02055e0100dd494e46d5c7dcb114920983be107391d85774efc |
# -*- coding: utf-8 -*-
##############################################################################
#
# OpenERP, Open Source Management Solution
# Copyright (C) 2004-today OpenERP SA (<http://www.openerp.com>)
#
# This program is free software: you can redistribute it and/or modify
# it under the terms o... | quanvm009/codev7 | openerp/addons/project/project.py | Python | agpl-3.0 | 74,633 | [
"VisIt"
] | 8a1ae6059ecaea4cb654cf043cdc6130d14c1bf37fa923687e4fa581918928d7 |
# Gabor function fitter.
#
# Copyright (C) 2010-2011 Huang Xin
#
# See LICENSE.TXT that came with this file.
from __future__ import division
import math
import numpy as np
from mpfit import mpfit
from gaussfitter import gaussfit
def onedgabor(x,H,A,dx,w,l,p):
"""
Returns a 1-dimensional gabor of form
g = ... | chrox/RealTimeElectrophy | Experimenter/DataProcessing/Fitting/gaborfitter.py | Python | bsd-2-clause | 7,970 | [
"Gaussian"
] | 2e762f1c8c6c334fd6b7271eda75a2493f5c095e85bc13f1ac38bbef17b36d85 |
# -*- coding: utf-8 -*-
# flake8:noqa
# pylint: skip-file
# id:01.20140505
# original at https://gist.github.com/798546
unicode_to_tex = {
u"\u0020": b"\\space ",
u"\u0023": b"\\#",
u"\u0024": b"\\textdollar ",
u"\u0025": b"\\%",
u"\u0026": b"\\&",
u"\u0027": b"\\textquotesingle ",
u"\u0... | jonasjberg/autonameow | autonameow/vendor/isbnlib/_data/data4tex.py | Python | gpl-2.0 | 78,089 | [
"Bowtie"
] | e90151502fe0289557946463f170d72bca47bba16b7d0fcf813de8f2908b4855 |
# The MIT License (MIT)
#
# Copyright (c) 2014 Richard Moore
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, mod... | ricmoo/pycoind | pycoind/util/piecewise.py | Python | mit | 12,310 | [
"VisIt"
] | c4e666e25aa11088eafe95bad7d3f77601035c3a66745c7b096e61c9aa342881 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | corburn/scikit-bio | skbio/sequence/tests/test_sequence.py | Python | bsd-3-clause | 119,853 | [
"scikit-bio"
] | 9bf0faaf59217ef5e5c5cb81108fe3e4437f010d79fd882da76c98968b8e9626 |
#* 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/lgpl-2.1.html
import os
i... | nuclear-wizard/moose | python/MooseDocs/extensions/autolink.py | Python | lgpl-2.1 | 9,495 | [
"MOOSE"
] | 2273c4dead358051b9278e0eabc8e18c356dc29148cafb3be382531b33d0539c |
"""
Test for common server leaks.
"""
import json
import re
from typing import Dict, Union
from urllib.parse import urlparse
from tldextract import extract
import requests
from requests.exceptions import ConnectionError
from requests.models import Response
from concurrent.futures import ThreadPoolExecutor
test_name =... | PrivacyScore/PrivacyScore | privacyscore/test_suites/serverleak.py | Python | gpl-3.0 | 7,184 | [
"VisIt"
] | 02d0ad4c3811f24dd898663dded59a1f29596090e99168c3c34c0abe7ea1df63 |
#!/usr/bin/env python
import argparse
import numpy as np
from mapTools import *
from plotTools import addContourf
from utilities import vtkWriteDataStructured2d, writeLog
import matplotlib.pyplot as plt
'''
Description:
Author: Mikko Auvinen
mikko.auvinen@helsinki.fi
University of Helsinki &
... | saskartt/P4UL | pyRaster/rasterToVtk.py | Python | mit | 2,045 | [
"VTK"
] | 15281b79bfa53b91b544a1f3c039667382cff9fd71662455b07a5221a4314658 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import rdkit
from rdkit.Chem import AllChem
from rdkit import DataStructs
__license__ = "X11"
METADATA = {
"id": "method_rdkit_ecfp8_1024_tanimoto",
"representation": "ecfp8_1024",
"similarity": "tanimoto"
}
def _compute_fingerprint(molecule):
return Al... | skodapetr/lbvs-environment | methods/ecfp/ecfp8_1024_tanimoto.py | Python | mit | 1,396 | [
"RDKit"
] | 805b57832c4c27e775e45bd0008fa98baecd84f18de14b3c47a798d776db2a28 |
# Version: 0.11
"""
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, and pypy
[]... | eusoubrasileiro/fatiando_seismic | versioneer.py | Python | bsd-3-clause | 35,319 | [
"Brian"
] | c6ec2a35bd3d3178518423c587b105491d3bb1f62b31ea04027d1c5615f7400e |
#!/usr/bin/env python
import vtk
def main():
colors = vtk.vtkNamedColors()
numTuples = 12
bitter = vtk.vtkFloatArray()
bitter.SetNumberOfTuples(numTuples)
crispy = vtk.vtkFloatArray()
crispy.SetNumberOfTuples(numTuples)
crunchy = vtk.vtkFloatArray()
crunchy.SetNumberOfTuples(numTu... | lorensen/VTKExamples | src/Python/Plotting/SpiderPlot.py | Python | apache-2.0 | 2,754 | [
"VTK"
] | 17fc4e1131163cb6bf4399db0fe9b94ebadfac2288c726eb94e7da1e0307fcf1 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2016 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kannon92/psi4 | psi4/driver/qcdb/psiutil.py | Python | gpl-2.0 | 8,258 | [
"Psi4"
] | 5a465904a26280bb7ba8142cc18545bf2940ea5902110106ab4717c0a3d28413 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# File: steering-filter.py
import argparse
import numpy as np
import tensorflow as tf
import cv2
from scipy.signal import convolve2d
from six.moves import range, zip
import multiprocessing
from tensorpack import *
from tensorpack.utils import logger
from tensorpack.utils.... | haamoon/tensorpack | examples/DynamicFilterNetwork/steering-filter.py | Python | apache-2.0 | 9,719 | [
"Gaussian"
] | fc09b0576fff4cd3157be8e4609f093791c40476eff0a605366b914310e27e91 |
"""
Copyright 2017 BlazeMeter Inc.
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software... | greyfenrir/taurus | bzt/requests_model.py | Python | apache-2.0 | 17,668 | [
"VisIt"
] | 611657bf3dddb6ed979cade6ce0fec5bc2eb8dc7c2b5bb92f361edbe8e4261c7 |
"""An NNTP client class based on RFC 977: Network News Transfer Protocol.
Example:
>>> from nntplib import NNTP
>>> s = NNTP('news')
>>> resp, count, first, last, name = s.group('comp.lang.python')
>>> print 'Group', name, 'has', count, 'articles, range', first, 'to', last
Group comp.lang.python has 51 articles, rang... | remybaranx/qtaste | tools/jython/lib/Lib/nntplib.py | Python | gpl-3.0 | 18,776 | [
"Brian"
] | 55e1196c6b1aeddf4077503f093b3270d1a62200ef27fd868e6a45ec64c7dc66 |
#!/usr/bin/env python
'''
File name: main_ripp_mod.py
Author: Guillaume Viejo
Date created: 16/08/2017
Python Version: 3.5.2
'''
import sys
import numpy as np
import pandas as pd
import scipy.io
from functions import *
# from pylab import *
# import ipyparallel
from multiprocessing import Pool
import os
impor... | gviejo/ThalamusPhysio | python/main_make_ISOMAP_NO_HD_plot.py | Python | gpl-3.0 | 4,550 | [
"Gaussian"
] | e9520c06238fb8a399a64532356904d11128d76be19c43eef733b8f2f6388bda |
import atexit
import base64
import cPickle
import codecs
import collections
import datetime
import gc
import glob
import hashlib
import os
import random
import shutil
import sqlite3
import time
import zlib
import threading
import scandir
from itertools import izip, cycle
import chardet.universaldetector
def xor_cryp... | lukasmonk/lucaschess | Code/Util.py | Python | gpl-2.0 | 38,732 | [
"SIESTA"
] | be08241bdd992345d73e098181972e2138946bbe4379a18c7be948224eb311ed |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | jensreeder/scikit-bio | skbio/io/_registry.py | Python | bsd-3-clause | 27,393 | [
"scikit-bio"
] | 88e86be4505885f054fc056c380f710140c7f7a822666c805e69fc6cb8e5ff09 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import unittest
import os
import numpy as np
from pymatgen.core.sites import PeriodicSite
from pymatgen.core.operations import SymmOp
from pymatgen.io.vasp.i... | setten/pymatgen | pymatgen/symmetry/tests/test_analyzer.py | Python | mit | 28,190 | [
"VASP",
"pymatgen"
] | df7e4e09ece4a506ce5f4af990a55739f9120134b168b7eabbe0a008ef6c86dc |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | mengxn/tensorflow | tensorflow/tools/compatibility/tf_upgrade.py | Python | apache-2.0 | 26,394 | [
"VisIt"
] | 7efaca5d948510de627d8806911b8d316b238906e9fbeb30a51571b8120750f8 |
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Provides an interface to start and stop Android emulator.
Assumes system environment ANDROID_NDK_ROOT has been set.
Emulator: The class provides t... | patrickm/chromium.src | build/android/pylib/utils/emulator.py | Python | bsd-3-clause | 14,142 | [
"Galaxy"
] | 5ae7dc24ac23e6ea83ad0dc3829239c1f236e3772a2923175c459dca65985798 |
from ase.io.opls import OPLSff, OPLSStructure
s = OPLSStructure('172_ext.xyz')
opls = OPLSff('172_defs.par')
opls.write_lammps(s, prefix='lmp')
| misdoro/python-ase | doc/ase/io/write_lammps.py | Python | gpl-2.0 | 145 | [
"ASE"
] | 0d80c13be677fd9d8cd33b8e687114e020bddd91b09577eb1627dcbfcfb5246a |
####################################################################################################
# neuropythy/optimize/core.py
# Code for optimizing functions; made with the intention of optimizing functions on the cortical
# surface using gradient descent or a gradient-aware method.
# By Noah C. Benson
import os,... | noahbenson/neuropythy | neuropythy/optimize/core.py | Python | agpl-3.0 | 50,543 | [
"Gaussian"
] | 7e7c306a0daa20c3e2089dc79697362909ba197ad02d768ec315e0e5e37abc6a |
########################################################################
# $HeadURL$
# File : ComputingElementFactory.py
# Author : Stuart Paterson
########################################################################
""" The Computing Element Factory has one method that instantiates a given Computing Element
... | Sbalbp/DIRAC | Resources/Computing/ComputingElementFactory.py | Python | gpl-3.0 | 2,612 | [
"DIRAC"
] | 2c8edccbde9e659e48d5e9bd72ea66cd2db16162d12c2d291f959ea1b64a3d15 |
# Created on Fri Sep 7 19:15:32 2018
# Author: XiaoTao Wang
import os, subprocess, io
from runHiC.utilities import cleanFile, sleep, extract_chrom_sizes
from runHiC.filtering import create_frag, stats_pairs, stats_samfrag
from runHiC.quality import outStatsCache
from pairtools import _fileio, _headerops
##### functi... | XiaoTaoWang/HiC_pipeline | runHiC/mapping.py | Python | gpl-3.0 | 16,543 | [
"BWA"
] | 671c9881b2efd7bb4bcf613ffbec52818dbb258b8aac78c853b258c949e2eca0 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | psi4/psi4 | psi4/driver/qcdb/basislistdunning.py | Python | lgpl-3.0 | 40,068 | [
"Psi4"
] | 7598cb5d1c8c73b170c2819e12206636443dda60f7084726362392d57dc2bcd5 |
from flask import Flask, jsonify, abort, make_response, request, url_for
app = Flask(__name__)
books = [
{
'id': 1,
'title': u'Python Cookbook',
'tags': [u'Python', u'Algorithms', u'Development'],
'authors': [u'David Beazley', u'Brian K. Jones'],
'publishing': [u"O'Reilly",... | rafaelhenrique/rest-with-bdd | app.py | Python | lgpl-3.0 | 3,044 | [
"Brian"
] | 15149aafb0b8d749f5cacab9a361201f335ec58d122fdb5529cf586ca11c25dd |
#
# Copyright (C) 2000-2006 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" module containing machin... | adalke/rdkit | rdkit/ML/__init__.py | Python | bsd-3-clause | 340 | [
"RDKit"
] | 661ec323e51a81afcef676bd9d7f67553a65cbaeaca7c4580157eb52aea94f55 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# 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)
#... | MDAnalysis/mdanalysis | testsuite/MDAnalysisTests/topology/test_altloc.py | Python | gpl-2.0 | 2,165 | [
"MDAnalysis"
] | 9313f1cedaedf751fb5c987f2f8401119fe23e61f3b4ab54a8d1c70d52a0d5b3 |
import numpy as np
import os
try:
import netCDF4 as netCDF
except:
import netCDF3 as netCDF
import matplotlib.pyplot as plt
import time
from datetime import datetime
from matplotlib.dates import date2num, num2date
import pyroms
import pyroms_toolbox
import _remapping
class nctime(object):
pass
def remap_clm(... | dcherian/pyroms | examples/Arctic2/remap_clm.py | Python | bsd-3-clause | 5,495 | [
"NetCDF"
] | 3377fe4141014402a507b81da9011e1b4b280bbb806b7d79da494e8e1af76ce5 |
# Copyright 2016 Raytheon BBN Technologies
#
# 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
try:
from QGL import *
from QGL import co... | BBN-Q/Auspex | src/auspex/qubit/pulse_calibration.py | Python | apache-2.0 | 65,298 | [
"Gaussian"
] | 671843fc3e6a2a10c2b6fdf9c9c43f4dea6425e884474b49d54a1d488c413108 |
#!/usr/bin/env python3
import argparse
import sys
import numpy as np
import scipy.ndimage as sn # contains the filters
from mapTools import readNumpyZTile, saveTileAsNumpyZ
'''A script for filtering rasters.
Jukka-Pekka Keskinen
jukka-pekka.keskinen@fmi.fi
Finnish Meteorological Insitute
2020-2021
'''
#=arg parser===... | mjsauvinen/P4UL | pyRaster/filterRaster.py | Python | mit | 2,890 | [
"Gaussian"
] | c2c3cd85000a4cdb15636d9f7455b1af2324d577545c3bd4bdd0bb808c136463 |
"""Test module for Dashboard UI
:Requirement: Dashboard
:CaseAutomation: Automated
:CaseLevel: Acceptance
:CaseComponent: UI
:TestType: Functional
:CaseImportance: High
:Upstream: No
"""
from nailgun import entities
from requests.exceptions import HTTPError
from robottelo import manifests
from robottelo.api.util... | elyezer/robottelo | tests/foreman/ui/test_dashboard.py | Python | gpl-3.0 | 28,492 | [
"VisIt"
] | cfb480867a7064896dd810e5c997d305306d2372701bf08c985783ede7e32255 |
#!/usr/bin/env python
#
# Copyright 2008,2009,2011,2012 Free Software Foundation, Inc.
#
# This file is part of GNU Radio
#
# GNU Radio 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, or (at ... | DanielG/gr-osmosdr | apps/osmocom_siggen_base.py | Python | gpl-3.0 | 19,104 | [
"Gaussian"
] | cd999bb8be061ec406e79ba028773836799db28382d02aec517533f988814b0b |
#!/usr/bin/env python
"""
Mixture of route endpoints and supporting functions.
"""
from flask import jsonify, request, current_app, url_for, g
from ooiservices.app.models import User
from ooiservices.app.uframe import uframe as api
from ooiservices.app.main.authentication import auth
from ooiservices.app.main.errors i... | asascience-open/ooi-ui-services | ooiservices/app/uframe/controller.py | Python | apache-2.0 | 67,103 | [
"NetCDF"
] | c8020665ca04abf410fefec33d07837623f7f4e79380e965b9b68e19cce80a2c |
# TD quantum dynamics with TD Gauss-Hermite basis
# Two basis only
# Test anharmonic system
import numpy as np
from math import *
import numba
Ntraj = 1000
print('Number of trajectories = {} \n'.format(Ntraj))
dt = 0.004
am = 1.0
# initial values has to be stored to compute autocorrelation function
x0 = -1.... | binghongcha08/pyQMD | GHQT/Erhenfest/QtVP.py | Python | gpl-3.0 | 15,079 | [
"Gaussian"
] | f91a874f1360a681589ddb7c6ba6d33c801926300b288bb6ef82aeff0e8b2333 |
#!/usr/bin/env python
from __future__ import division
import sys
from galaxy import eggs
import pkg_resources; pkg_resources.require( "bx-python" )
from bx.arrays.array_tree import *
from bx.arrays.wiggle import IntervalReader
BLOCK_SIZE = 100
def main():
input_fname = sys.argv[1]
out_fname = sys.argv[2... | volpino/Yeps-EURAC | lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py | Python | mit | 709 | [
"Galaxy"
] | cf5948a5098e8469046334ec7959a6580ee42a7efd5a2ae260f9206d473e6a87 |
#! /usr/bin/env python
#
# Copyright (C) 2011-2014 Alexandre Gramfort
# Michael Waskom
# Scott Burns
# Martin Luessi
# Eric Larson
descr = """PySurfer: cortical surface visualization using Python."""
import os
# deal with ... | diego0020/PySurfer | setup.py | Python | bsd-3-clause | 3,134 | [
"Mayavi"
] | fefced4fc4e9440168166bb5d8fe898cc759fa399dd009cb33c6ef233b022cf4 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import numpy as np
from monty.os.path import which
from pymatgen.core.lattice import Lattice
from pymatgen.core.structure import Structure, Molecule
from pymatgen.transformations.site_transformations import ... | vorwerkc/pymatgen | pymatgen/transformations/tests/test_site_transformations.py | Python | mit | 13,736 | [
"pymatgen"
] | 5cc2a01ebd4c50a96b86f7ce7c8a57c97729641ecec7249825c9acd9c284df1a |
###########################################################################
#
# Copyright 2020 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/l... | google/starthinker | dags/anonymize_query_dag.py | Python | apache-2.0 | 5,032 | [
"VisIt"
] | 61c68623017d6ea62b4b182e76f0d96edaa0a1c73e54cef88a8d1db4552dcae5 |
""" This is a module to handle generic ASE (gui) defaults from a ~/.ase/gui.py configuration file, if it exists.
It is imported when opening ag and can then be modified at runtime, if necessary.
syntax for each entry:
gui_default_settings['key'] = value
"""
gui_default_settings = {
'gui_graphs_string' : 'i, e - E... | slabanja/ase | ase/gui/defaults.py | Python | gpl-2.0 | 570 | [
"ASE"
] | 8eb97585d482dbbd0e740d8bb883a9556cf97677591b5ebbfea12ba68b1b4204 |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses... | amenonsen/ansible | lib/ansible/modules/network/avi/avi_analyticsprofile.py | Python | gpl-3.0 | 32,479 | [
"VisIt"
] | 46e80b4f1831554f9e6212d140dbdade1aa7d15dd4146c8414776f15385f6101 |
__author__ = 'waroquiers'
import abc
from monty.json import MSONable
class AbstractEnvironmentNode(MSONable):
"""
Abstract class used to define an environment as a node in a graph.
"""
COORDINATION_ENVIRONMENT = 0
NUMBER_OF_NEIGHBORING_COORDINATION_ENVIRONMENTS = 1
NUMBER_OF_NEIGHBORING_CES ... | mbkumar/pymatgen | pymatgen/analysis/chemenv/connectivity/environment_nodes.py | Python | mit | 9,331 | [
"pymatgen"
] | 4acc17e0d1ee4d0b9f29e672df1193a52b7a3e45701caa98adaa6e007659188c |
""" It is used to test Plotting utilities used to create different plots.
"""
# pylint: disable=invalid-name,wrong-import-position
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import os
import math
import operator
from functools import reduce
# sut
fr... | yujikato/DIRAC | tests/Integration/AccountingSystem/Test_Plots.py | Python | gpl-3.0 | 12,069 | [
"DIRAC"
] | 386c38909d2b010a225cbd76fcddf39a764754ea5f588e690269c8ef254f371f |
import shutil
import sys
import os
import re
import io
import traceback
from pybtex.plugin import find_plugin
from pybtex.database import BibliographyData, parse_file
from pybtex.database.input.bibtex import UndefinedMacro as undefined_macro_exception
import MooseDocs
from MooseCommonExtension import MooseCommonExtens... | stimpsonsg/moose | python/MooseDocs/extensions/MooseBibtex.py | Python | lgpl-2.1 | 6,820 | [
"MOOSE"
] | b607662e06feadab5e8bc926bd2a73b437123d0a85a9aa52dcfa05c44fd9f11c |
from django.db import models
# from edc_base.audit_trail import AuditTrail
from edc_base.model.models import BaseUuidModel
from edc_constants.choices import YES_NO
from edc_constants.constants import NOT_APPLICABLE
from edc_export.models import ExportTrackingFieldsMixin
from edc_sync.models import SyncModelMixin, Sync... | botswana-harvard/tshilo-dikotla | td_infant/models/infant_arv_proph.py | Python | gpl-2.0 | 2,846 | [
"VisIt"
] | 5dbf9003ddec700a8395d837c13a55c290c71d327a93979a6f6be7030b6a2c3d |
# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# 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.
"""Half-sphere exposure and coordination number calculation."""
from __future__ import pr... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/PDB/HSExposure.py | Python | gpl-2.0 | 11,542 | [
"Biopython",
"PyMOL"
] | 79cadd09846e0771ce0a3cda2ff1e70e66b146836719ce2ec549ba955a050c58 |
import tempfile
import warnings
import numpy
from openfisca_core import commons, periods
from openfisca_core.errors import CycleError, SpiralError
from openfisca_core.indexed_enums import Enum, EnumArray
from openfisca_core.periods import Period
from openfisca_core.tracers import FullTracer, SimpleTracer, TracingPara... | openfisca/openfisca-core | openfisca_core/simulations/simulation.py | Python | agpl-3.0 | 18,837 | [
"VisIt"
] | fad0225fc4113484841c7c78bdc34b4aa7f836ce7e11f1628204a71d99282680 |
#!/usr/bin/env python
#*******************************************************************
#* File: UniformRngTestCase.py
#* Description:
#* Author: Subhasis Ray
#* E-mail: ray dot subhasis at gmail dot com
#* Created: 2008-09-19 10:21:51
#*************************************... | BhallaLab/moose-thalamocortical | pymoose/tests/randnum/UniformRngTestCase.py | Python | lgpl-2.1 | 3,063 | [
"MOOSE"
] | f1a832ed34cd65a3df11e1f791c92c51137420271c23889aea0d82d04133928e |
# Copyright 2012, 2013 The GalSim developers:
# https://github.com/GalSim-developers
#
# This file is part of GalSim: The modular galaxy image simulation toolkit.
#
# GalSim 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... | mardom/GalSim | galsim/fits.py | Python | gpl-3.0 | 45,237 | [
"Galaxy"
] | 52caae3ccf2d969bfe96938db5834336cdbf1ffd0c45995d16358bb9dd683e93 |
# This component assembles an analysis recipe for the annual adaptive comfort component
#
# Honeybee: A Plugin for Environmental Analysis (GPL) started by Mostapha Sadeghipour Roudsari
#
# This file is part of Honeybee.
#
# Copyright (c) 2013-2020, Chris Mackey <Chris@MackeyArchitecture.com>
# Honeybee is free softw... | mostaphaRoudsari/Honeybee | src/Honeybee_PMV Comfort Analysis Recipe.py | Python | gpl-3.0 | 39,754 | [
"EPW"
] | 44bd2d409a086f7a51fa5a18917ff0e0773a75eb15bdb36d46330cf32483047f |
import os.path
import shutil
import tarfile
import json
from django.conf import settings
from django.http import HttpResponse
from django.db.models import Count
from catmaid.control.authentication import requires_user_role
from catmaid.control.common import get_relation_to_id_map, id_generator
from catmaid.control.cr... | htem/CATMAID | django/applications/catmaid/control/treenodeexport.py | Python | agpl-3.0 | 21,531 | [
"NEURON"
] | 0679826f9c1963063524c263850f4ef2635fc784338eff9f8dae2fce67936de1 |
import os
from setuptools import setup, find_packages
from packageinfo import VERSION, NAME
with open('README.rst', 'r') as readme:
README_TEXT = readme.read()
def write_version_py(filename=None):
if filename is None:
filename = os.path.join(
os.path.dirname(__file__), 'simlammps', 'ver... | simphony/simphony-lammps-md | setup.py | Python | bsd-2-clause | 860 | [
"LAMMPS"
] | 60e23ceb5097b743216806bb61b38b418d179d98e104a2f73e553f8be5833027 |
#!/usr/bin/python
#Audio Tools, a module and set of tools for manipulating audio data
#Copyright (C) 2007-2012 Brian Langenberger
#This program is free software; you can redistribute it and/or modify
#it under the terms of the GNU General Public License as published by
#the Free Software Foundation; either version 2... | Excito/audiotools | audiotools/py_encoders/shn.py | Python | gpl-2.0 | 9,916 | [
"Brian"
] | e9967db4514ba09c369aeb92e970fdf7728ee5756172b2780dda7d1d3bb2fd4a |
##############################################################################
##############################################################################
# Estimating the Value-at-Risk for a portfolio of oil futures
# using a stochastic volatility (SV) model with alpha-stable log-returns.
#
# The SV model is inferr... | compops/gpo-abc2015 | scripts-paper/example3-gpoabc.py | Python | mit | 4,316 | [
"Gaussian"
] | 320202e04d67c3fe0c9b0a98a0e61bb3e323574d0b4b75c5aa5fe4aaee66e998 |
from hermes2d import Linearizer, Solution
def sln2png(sln, filename):
"""
Creates a nice png image of the Solution sln.
"""
plot_sln_mayavi(sln)
from enthought.mayavi.mlab import savefig
savefig(filename)
def plot_sln_mpl(sln, method="default", just_mesh=False, axes=None):
"""
Plots th... | hanak/hermes2d | python/hermes2d/plot.py | Python | gpl-2.0 | 10,970 | [
"Mayavi",
"VTK"
] | b7dfd36faf66a32fb7c6beef92bb3e86a5cbda86e25dc0579c1219aac2c942a8 |
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