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#!/usr/bin/python
#
# Copyright 2012 Google Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... | miketoth/RESTful-notifications-server | oauth2.py | Python | apache-2.0 | 12,268 | [
"VisIt"
] | bda4e0f5c60bfae9c2fb272b2d87b76ee4c5559d4518b5e3c39a52f2e8383e2d |
# -*- coding: utf-8 -*-
from __future__ import print_function, division, absolute_import
import ast
import ast as ast_module
try:
import __builtin__ as builtins
except ImportError:
import builtins
import types
from numba import functions, PY3
from numba import nodes
from numba.nodes.metadata import annotate, qu... | shiquanwang/numba | numba/visitors.py | Python | bsd-2-clause | 14,579 | [
"VisIt"
] | 628612917a8cbc0f68a1bfc1ac5c39b68d8ed015bd7c54f7c5245f51ca59bd3d |
#!/usr/bin/env python
"""
Artificial Intelligence for Humans
Volume 2: Nature-Inspired Algorithms
Python Version
http://www.aifh.org
http://www.jeffheaton.com
Code repository:
https://github.com/jeffheaton/aifh
Copyright 2014 by Jeff Heaton
Licensed under the Apache License, Versi... | PeterLauris/aifh | vol2/vol2-python-examples/examples/example_flock.py | Python | apache-2.0 | 7,379 | [
"VisIt"
] | 72458886567f23f815ba42f4867bf66e37b730ce8edc78cc29274217a4943c1c |
########################################################################
# File: File.py
# Date: 2012/08/03 15:02:53
########################################################################
"""
:mod: File
.. module: File
:synopsis: RMS operation file
operation file
"""
# Disable invalid names warning
# pylint: disa... | petricm/DIRAC | RequestManagementSystem/Client/File.py | Python | gpl-3.0 | 5,389 | [
"DIRAC"
] | b9f2d8c133b3796282dc76b7b792cc04fab2311defed7a3d3bda013ee4f616ca |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the Account Settings page.
"""
from datetime import datetime
from unittest import skip
from bok_choy.page_object import XSS_INJECTION
from nose.plugins.attrib import attr
from pytz import timezone, utc
from common.test.acceptance.pages.common.auto_auth import AutoAuthP... | lduarte1991/edx-platform | common/test/acceptance/tests/lms/test_account_settings.py | Python | agpl-3.0 | 20,507 | [
"VisIt"
] | fa6ab45937bf5a19bbd3729c2bdb3babfa8ed224af3931687a8e8d6f7e6ecd3e |
#!/usr/bin/env python
# encoding: utf-8
################################################################################
#
# RMG - Reaction Mechanism Generator
#
# Copyright (c) 2002-2009 Prof. William H. Green (whgreen@mit.edu) and the
# RMG Team (rmg_dev@mit.edu)
#
# Permission is hereby granted, free of cha... | faribas/RMG-Py | rmgpy/cantherm/input.py | Python | mit | 15,255 | [
"Gaussian"
] | 00f8c16a0e76691f9d42959ba07e1670618131a359cb0a13e6c0ef53ee5419ab |
import logging
import os
from efforia.jade import Compiler as _Compiler, Parser
from efforia.jade.runtime import attrs
from efforia.jade.exceptions import CurrentlyNotSupported
from efforia.jade.utils import process
from django.conf import settings
from django.contrib.markup.templatetags.markup import markdown
class... | efforia/eos-dashboard | pandora-ckz/pandora/jade/ext/django/__init__.py | Python | lgpl-3.0 | 2,351 | [
"VisIt"
] | 18f36c40cef16e321d33bba78d1f28e123fb62c5c20254710c6e432b03ee7d90 |
import logging
import sys
from datetime import datetime, timedelta
from django.contrib.auth.models import User
from django.core.mail import send_mass_mail
from django.core.management.base import BaseCommand
from django.template import loader
from django.utils.timezone import utc, make_aware
logger = logging.getLogger... | voutilad/courtlistener | cl/users/management/commands/cl_welcome_new_users.py | Python | agpl-3.0 | 2,443 | [
"Brian"
] | 440a8d633634151b7904dc6182487377ccac8f12156839df90299ed8057e1c2d |
import unittest, itertools, os, copy, shutil
from mock import Mock
from DIRAC import gLogger
class ModulesTestCase( unittest.TestCase ):
""" Base class for the Modules test cases
"""
def setUp( self ):
gLogger.setLevel( 'DEBUG' )
# import sys
# sys.modules["DIRAC"] = DIRAC.ResourceStatusSystem.test.... | avedaee/DIRAC | Workflow/Modules/test/Test_Modules.py | Python | gpl-3.0 | 28,447 | [
"DIRAC"
] | 3b7cc451687ba24f9534ab33e29d5afb8d07026b5e17065257c86ddb88ab4d09 |
#!/usr/bin/env python
"""
Retrieves site mask logging information.
"""
########################################################################
# File : dirac-admin-site-mask-logging
# Author : Stuart Paterson
########################################################################
__RCSID__ = "$Id$"
import DI... | andresailer/DIRAC | Interfaces/scripts/dirac-admin-site-mask-logging.py | Python | gpl-3.0 | 1,183 | [
"DIRAC"
] | 97c11334954f74bccb1bbd24232ae5895235f8991b6aab809b2f5e3c44963675 |
'''
This script performs a parameter sweep over the weight/conductance values of connections
among a network of MLIs and PKJs. It measures the error of the fit of mean and CV of the
ISIs by finding the single neuron among MLIs and PKJs that is closest to the prototypes
reported by Hausser and Clark (1997).
'''
import ... | blennon/MLI_PKJ_net | MLI_PKJ_net/parameter_search/mli_pkj_param_sweep_closest.py | Python | mit | 3,399 | [
"Brian",
"NEURON"
] | e6f2023f2b19a09abf438c5e6692e412ecbe123aa17e5e7517724ede127dd501 |
#!/usr/bin/python
# (c) 2017, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
# most of it copied from AWX's scan_packages module
from __future__ import absolute_import, division, print_function
__metaclass__ = type
DOCUMENTATION = '''
module: package_fac... | j-carl/ansible | lib/ansible/modules/package_facts.py | Python | gpl-3.0 | 15,115 | [
"Brian"
] | a566b3870338b23c460e0d0cfe65f13643d842ca2b63269491f2fe42744882f1 |
"""Tracker for zero-copy messages with 0MQ."""
#-----------------------------------------------------------------------------
# Copyright (C) 2013 Brian Granger, Min Ragan-Kelley
#
# This file is part of pyzmq
#
# Distributed under the terms of the New BSD License. The full license is in
# the file COPYING.BSD, d... | IsCoolEntertainment/debpkg_python-pyzmq | zmq/sugar/tracker.py | Python | lgpl-3.0 | 4,012 | [
"Brian"
] | 170c7870c016b76d361fa09f40b811748745f33c1d515415463151048a1e3fcb |
#!/usr/bin/python
# -*- coding: utf-8 -*-
##########################################################################
# OpenWebif: owbranding
##########################################################################
# Copyright (C) 2014 - 2020 E2OpenPlugins
#
# This program is free software; you can redistribute it an... | rdamas/e2openplugin-OpenWebif | plugin/controllers/models/owibranding.py | Python | gpl-3.0 | 27,142 | [
"Galaxy"
] | 7ff8aab1e0426343a61335f405c95a0694bbb82421b5bd68d48e815f843203ea |
# ################################################################
#
# Active Particles on Curved Spaces (APCS)
#
# Author: Silke Henkes
#
# ICSMB, Department of Physics
# University of Aberdeen
# Author: Rastko Sknepnek
#
# Division of Physics
# School of Engineering, Physics and Mathem... | sknepneklab/SAMoS | analysis/batch_nematic/batch_analyze_nematic_R40a.py | Python | gpl-3.0 | 2,362 | [
"VTK"
] | e4ee1d586363e80430475cc2d531e7dadbaaa2528c87fef3085887ffe978a36c |
import sys
import os
import vtk
BLUE = "\033[0;34m"
BLUE_BOLD = "\033[1;34m"
RED = "\033[0;31m"
RED_BOLD = "\033[1;31m"
GREEN = "\033[0;32m"
GREEN_BOLD = "\033[1;32m"
YELLOW = "\033[0;33m"
YELLOW_BOLD = "\033[1;33m"
CYAN = "\033[0;36m"
CYAN_BOLD = "\033[1;36m"
NC = "\033[0m"
NC_BOLD = "\033[1m"
# Convert time, retur... | PrinceNgattaiLam/Trafic | TraficLib/fiberfileIO.py | Python | apache-2.0 | 5,961 | [
"VTK"
] | 622057a0f0a69af9eced6b4a862216f14d0456de4211c8ec34a1b8af9ba595a3 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | wdwvt1/scikit-bio | skbio/io/format/_base.py | Python | bsd-3-clause | 7,758 | [
"scikit-bio"
] | 14c49227488624784b80a6241b263de2b6770423d164fd79236b1d7aeb99bf66 |
import pytest
import capybara
from capybara.tests.app import AppError
class TestReset:
def test_removes_cookies(self, session):
session.visit("/set_cookie")
session.visit("/get_cookie")
assert session.has_text("test_cookie")
session.reset()
session.visit("/get_cookie")
... | elliterate/capybara.py | capybara/tests/session/test_reset.py | Python | mit | 3,112 | [
"VisIt"
] | f03a902fa371ec1e01c17e8e7bcc210927c09db1b26723557f1c1babcef802fc |
#!/usr/bin/env python
#
# $File: polygamous.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can redistribute... | BoPeng/simuPOP | docs/polygamous.py | Python | gpl-2.0 | 1,492 | [
"VisIt"
] | 41b4fdf8ea622567b3cb6deb8c5da8bf7c03147eddc85c3001263278673f2748 |
from __future__ import annotations
import math
import warnings
from collections import namedtuple
import numpy as np
from numpy import (isscalar, r_, log, around, unique, asarray, zeros,
arange, sort, amin, amax, atleast_1d, sqrt, array,
compress, pi, exp, ravel, count_nonzero, si... | WarrenWeckesser/scipy | scipy/stats/morestats.py | Python | bsd-3-clause | 128,655 | [
"Gaussian"
] | 401370170de07fbaf30a53c6b709c525a7187521bd72aec5fa4cec2dd7f6bf6c |
#
# gPrime - A web-based genealogy program
#
# Copyright (C) 2000-2006 Donald N. Allingham
# Copyright (C) 2009 Brian G. Matherly
# Copyright (C) 2009 Peter G. Landgren
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published... | sam-m888/gprime | gprime/constfunc.py | Python | gpl-2.0 | 5,103 | [
"Brian"
] | 97d7cad006a61e70da062b947e8796da25199ea4b70d24ee75ce58b90d9ff4c1 |
"""
Course Outline page in Studio.
"""
import datetime
from bok_choy.page_object import PageObject
from bok_choy.promise import EmptyPromise
from selenium.webdriver import ActionChains
from selenium.webdriver.support.ui import Select
from selenium.webdriver.common.keys import Keys
from ..common.utils import click_cs... | Learningtribes/edx-platform | common/test/acceptance/pages/studio/overview.py | Python | agpl-3.0 | 35,446 | [
"VisIt"
] | fbc8fc62525da5de7599d85f6ecf9f83653868f1679ee11d61744b901fcd2feb |
# *SymmetryFinder*: platform-independent symmetry finder, wrapping Spglib code
# *SymmetryHandler*: symmetry inferences for 0D-, 1D-, 2D- and 3D-systems
# Author: Evgeny Blokhin
from numpy.linalg import det
from ase.atoms import Atoms
from ase.geometry import cell_to_cellpar
import spglib as spg
class SymmetryFin... | tilde-lab/tilde | tilde/core/symmetry.py | Python | mit | 6,756 | [
"ASE",
"CRYSTAL"
] | 5d8d97404605fe8e9456c15dd8438d3ab09037533160629e6075d89b160dbba2 |
import numpy as np
import sys, time, os
import h5py as h5
import matplotlib.pyplot as plt
import pycuda.driver as cuda
from pycuda.compiler import SourceModule
import pycuda.gpuarray as gpuarray
from pycuda.reduction import ReductionKernel
from pycuda.elementwise import ElementwiseKernel
currentDirectory = os.getcwd(... | bvillasen/phyGPU | nBody/nBody.py | Python | gpl-3.0 | 12,402 | [
"Galaxy"
] | 0cc3a00fccec578f5f3f559390b5d59285bbd21a593de1b33c15d5efddf5a028 |
# Compiled by Charles Harris, dated October 3, 2002
# updated to 2002 values by BasSw, 2006
# Updated to 2006 values by Vincent Davis June 2010
"""
Fundamental Physical Constants
------------------------------
These constants are taken from CODATA Recommended Values of the Fundamental
Physical Constants 2010.
Object... | sargas/scipy | scipy/constants/codata.py | Python | bsd-3-clause | 81,178 | [
"Avogadro",
"VisIt"
] | 76e027b675121c523044c4030742de4bc1db294d691961209999607585579dc0 |
# -*- coding: utf-8 -*-
# Este arquivo é parte do programa Blocos
# Blocos é um software livre; você pode redistribui-lo e/ou
# modifica-lo dentro dos termos da Licença Pública Geral GNU como
# publicada pela Fundação do Software Livre (FSF); na versão 3 da
# Licença, ou (na sua opinião) qualquer versão.
#
# Este... | yantrabuddhi/blocos | blockcanvas/canvas.py | Python | gpl-3.0 | 19,312 | [
"FLEUR"
] | 91c5ab8abcff67cee66b7213d53823a5fc1bb5f58ec2f48e91b155f393569025 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2006 Brian Matherly
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) ... | pmghalvorsen/gramps_branch | gramps/gen/mime/_winmime.py | Python | gpl-2.0 | 3,649 | [
"Brian"
] | d28497c3e75030a1fb3959c3bb3909f076a57d8ad91c1642fea42ab2fd7fac29 |
# Created by DrLecter, based on DraX' scripts
# This script is part of the L2J Official Datapack Project
# Visit us at http://www.l2jdp.com/
# See readme-dp.txt and gpl.txt for license and distribution details
# Let us know if you did not receive a copy of such files.
import sys
from com.l2scoria.gameserver.model.ques... | zenn1989/scoria-interlude | L2Jscoria-Game/data/scripts/village_master/dark_elven_change_2/__init__.py | Python | gpl-3.0 | 4,673 | [
"VisIt"
] | 308b645c962229f750735345599557920891c6c62484db0f23d6e9fc9076c806 |
import warnings
warnings.warn("pymatgen.phasediagram and submodules has been moved to "
"pymatgen.analysis.phase_diagram This stub will be "
"removed in pmg 2018.01.01.")
from pymatgen.analysis.phase_diagram import *
| setten/pymatgen | pymatgen/phasediagram/entries.py | Python | mit | 247 | [
"pymatgen"
] | de20b5a212ea0533ca85cc2969f7176a0792e19ae4abe7deb15eafba5af9f5bd |
## Copyright (c) 2001-2013, Scott D. Peckham
##
## Jan 2013. Fixed bug in create_initial_DEM() (PLANE option)
## Jan 2009 (converted from IDL)
## September, October, November 2009
## February 2010 (local time-stepping)
## August 2010 (updated to use new model_output, conventions, etc.)
## Sep to Nov 2011 (mi... | mdpiper/topoflow | topoflow/components/erode_base.py | Python | mit | 121,888 | [
"Gaussian"
] | 3875afcdd516c6b07c9b69a03114719004b67d4f9f74a4b0291df82a952a9c88 |
import os
import os.path
from typing import Tuple
import bokeh
import bokeh.io
import bokeh.model
import bokeh.plotting
import bokeh.util.platform
import matplotlib.pyplot as plt
import pyproj
from bokeh.models import ColumnDataSource, Circle
from bokeh.tile_providers import STAMEN_TERRAIN
from netCDF4 import Dataset
... | DeDop/dedop | dedop/ui/compare.py | Python | gpl-3.0 | 12,663 | [
"NetCDF"
] | 35e66c2defe332abd12a23c4f0fd13f16db54e107ea8e06f9f2d2dba2aa40936 |
import os
import sys
import time
from math import sin, cos, radians, atan2, degrees
import numpy as np
class DevNull:
def write(self, string):
pass
def flush(self):
pass
def seek(self, offset, whence=0):
return 0
def tell(self):
return 0
def close(self):
... | PHOTOX/fuase | ase/ase/utils/__init__.py | Python | gpl-2.0 | 6,003 | [
"ASE"
] | 7aa6469573a8252d3b530b88570d6b6dfcd8fd64ecaf15ae323981fe5feb2543 |
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 import defaults as default_views
from wagtail.wagtailcore import urls as wagtail_urls
from wagtail.wagtailadm... | bruecksen/impacts-world | config/urls.py | Python | mit | 1,678 | [
"VisIt"
] | c84a70e88719bd547290f928ba093748a564d25e10990cff5a403785f666ae3a |
# util/langhelpers.py
# Copyright (C) 2005-2022 the SQLAlchemy authors and contributors
# <see AUTHORS file>
#
# This module is part of SQLAlchemy and is released under
# the MIT License: https://www.opensource.org/licenses/mit-license.php
"""Routines to help with the creation, loading and introspection of
modules, cl... | sqlalchemy/sqlalchemy | lib/sqlalchemy/util/langhelpers.py | Python | mit | 61,911 | [
"VisIt"
] | f7198ef31d22f84b760ae3218da3df5928afe7dd59944b4262acb229375d2290 |
"""
========================================
Special functions (:mod:`scipy.special`)
========================================
.. currentmodule:: scipy.special
Nearly all of the functions below are universal functions and follow
broadcasting and automatic array-looping rules.
.. seealso::
`scipy.special.cython_s... | jamestwebber/scipy | scipy/special/__init__.py | Python | bsd-3-clause | 27,407 | [
"Gaussian"
] | 8bc1e0541707820c5065a19a3eae3cb3ac177d9483efd4f9f7037808fb297f61 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from pymatgen.transformations.transformation_abc import AbstractTransformation
"""
This module defines classes for point defect transformations on structures
"""
__author__ = "Danny Broberg, Shyam Dwaraknath"
... | blondegeek/pymatgen | pymatgen/transformations/defect_transformations.py | Python | mit | 1,904 | [
"pymatgen"
] | 741d2794d3b7e131cafaa4064bacc5ac0f0f55c10516f769cdcac3253cbed6e8 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2002-2007 Donald N. Allingham
# Copyright (C) 2007-2009 Brian G. Matherly
# Copyright (C) 2009 Benny Malengier
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publish... | Forage/Gramps | gramps/gen/filters/rules/event/_hassourcecount.py | Python | gpl-2.0 | 1,773 | [
"Brian"
] | a1aa9aa5ed2904bb9c891eeaf0f7181336a4eef0f25a26713522bf20e623ee67 |
#
# Copyright (C) 2001,2002,2003 greg Landrum and Rational Discovery LLC
#
""" Functionality for ranking bits using info gains
**Definitions used in this module**
- *sequence*: an object capable of containing other objects which supports
__getitem__() and __len__(). Examples of these include lists, tupl... | rdkit/rdkit | rdkit/ML/InfoTheory/BitRank.py | Python | bsd-3-clause | 5,487 | [
"RDKit"
] | b620ff6adaf707aad116c53972c636c9b2c5cdd21297df57348401213cd5475b |
#!/usr/bin/python
#import numpy
#from mayavi.mlab import *
import numpy as np
from enthought.mayavi import mlab
# x, y, z = np.ogrid[-10:10:20j, -10:10:20j, -10:10:20j]
# s = np.sin(x*y*z)/(x*y*z)
# src = mlab.pipeline.scalar_field(s)
# mlab.pipeline.iso_surface(src, contours=[s.min()+0.1*s.ptp(), ], opacity=0.3)
#... | eriser/marsyas | src/apps/carfac/carfac_3d.py | Python | gpl-2.0 | 677 | [
"Mayavi"
] | 03abda10143ac3edd5b6ffc0d5fe7352d450829e15003128105e3605104c5c78 |
# 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... | Xeralux/tensorflow | tensorflow/contrib/factorization/python/ops/gmm_ops.py | Python | apache-2.0 | 20,311 | [
"Gaussian"
] | 8c12a45710e7c94ed7157f89157a792d0decd3ae78318d5703c6679a33dfea19 |
# GENERATED FILE - DO NOT EDIT THIS FILE UNLESS YOU ARE A WIZZARD
#pylint: skip-file
from heat.engine import properties
from heat.engine import constraints
from heat.engine import attributes
from heat.common.i18n import _
from avi.heat.avi_resource import AviResource
from avi.heat.avi_resource import AviNestedResource... | ypraveen/avi-heat | avi/heat/resources/se_properties.py | Python | apache-2.0 | 53,305 | [
"ADF"
] | 4fc4dd0743e80bb5673824e9886f06fd12101f151976ab6ac681adfe3f8da5ee |
import logging
from cStringIO import StringIO
from math import exp
from lxml import etree
from path import path # NOTE (THK): Only used for detecting presence of syllabus
import requests
from datetime import datetime
import dateutil.parser
from lazy import lazy
from xmodule.modulestore import Location
from xmodule.se... | apigee/edx-platform | common/lib/xmodule/xmodule/course_module.py | Python | agpl-3.0 | 40,844 | [
"VisIt"
] | 78d2ce4b27b87b3ded26fcff474167d0de3571d14e036e794e17f549378244a4 |
# coding: utf-8
from __future__ import division, unicode_literals
"""
This module is used for analysis of materials with potential application as
intercalation batteries.
"""
__author__ = "Anubhav Jain, Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Anu... | Dioptas/pymatgen | pymatgen/apps/battery/insertion_battery.py | Python | mit | 20,583 | [
"pymatgen"
] | 80e346c954a1a0fcf260bda7c74205177b033d90bc4176f2c7cbd8c74e595c82 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
reader = vtk.vtkBMPReader()
reader.SetFileName("" + str(VTK_DATA_ROOT) + "/Data/masonry.bmp")
# set the window/level
viewer = vtk.vtkImageViewer2()
viewer.SetInputConnection... | hlzz/dotfiles | graphics/VTK-7.0.0/Imaging/Core/Testing/Python/TestMapToWindowLevelColors2.py | Python | bsd-3-clause | 446 | [
"VTK"
] | 4ac1fb41d773e881334f15e218f492a9dc61068df5ef0182247168d3388cbbb9 |
from math import sqrt, ceil
import numpy as np
from pychemia.utils.serializer import PyChemiaJsonable, generic_serializer
"""
Definition of the set of k-points in reciprocal space
"""
__author__ = "Guillermo Avendano-Franco"
__copyright__ = "Copyright 2014"
__version__ = "1.1"
__maintainer__ = "Guillermo Avendano-Fra... | MaterialsDiscovery/PyChemia | pychemia/crystal/kpoints.py | Python | mit | 12,819 | [
"pymatgen"
] | 59b91858424d9d20236d4415884c5b05fd9902d1a96ec271c699ff43d713b381 |
#!/usr/bin/env
"""
NARR_daily_WindsTemp_atheight.py
Retrieve NARR winds for one locations at designated pressure level (height)
Filter NARR winds with a triangular filter (1/4, 1/2, 1/4) and output every 3hrs
Provide U, V
Save in EPIC NetCDF standard
"""
#System Stack
import datetime
import argparse
#Scienc... | shaunwbell/FOCI_Analysis | NARR_daily_WindsTemp_atheight.py | Python | mit | 8,476 | [
"NetCDF"
] | 8561711c2b561545d2a51bca426d56e9c283e12ec9512e87710c27d16c9de2c7 |
#!/usr/bin/env python
"""wxpyblast.py: A graphical interface to BioPython's NCBI Blast interface"""
__author__ = "Adam Caldwell"
__copyright__ = "(C) 2012 Adam Caldwell"
__license__ = "GPL"
__version__ = "11"
__maintainer__ = "Adam Caldwell"
__email__ = "adam.caldwell@gmail.com"
import sys, datetime, getopt, re, thr... | accaldwell/wxpyblast | wxpyblast.py | Python | gpl-3.0 | 14,732 | [
"BLAST",
"Biopython"
] | 6deaccc8d8d90394178036fb8e1957a03c5426b97b32cdc7bc4baa9bed7d8dea |
# 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... | kkreis/espressopp | src/tools/topology.py | Python | gpl-3.0 | 6,325 | [
"ESPResSo"
] | 506446caef93393173948cf50e4441d050535793f51257aaec8cb5476f3cef7b |
# encoding: utf-8
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Changing field 'Protein.name'
db.alter_column('neuroelectro_protein', 'name', self.gf('django... | lessc0de/neuroelectro_org | neuroelectro/south_migrations/0003_auto__chg_field_protein_name.py | Python | gpl-2.0 | 4,345 | [
"NEURON"
] | cd4a3e52083c4a49db5e1ed5bc144b3bec0704f2a29b4c4ac2e9a818255a6b08 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements more advanced transformations.
"""
import numpy as np
from fractions import Fraction
from math import gcd
from itertools import groupby, product
from string import ascii_lowercase
fr... | tschaume/pymatgen | pymatgen/transformations/advanced_transformations.py | Python | mit | 82,376 | [
"CRYSTAL",
"pymatgen"
] | 754c6a4b60fe876aef8f290e19032f1557c380beda3718cec58ce7a4618e7a18 |
#!/usr/bin/env python
from ase.io import read
from ase.constraints import FixAtoms
from ase.calculators.siesta import Siesta
from ase.md import VelocityVerlet
from ase import units
# Read in the geometry from a xyz file, set the cell, boundary conditions and center
atoms = read('geom.xyz')
atoms.set_cell([7.66348,7.66... | conwayje/ase-python | doc/exercises/siesta2/siesta2.py | Python | gpl-2.0 | 991 | [
"ASE",
"SIESTA"
] | 1381fa5b011efd1d022bab6d6515166a788f4ea237bd481dfc7d225f2ca059f0 |
import numpy as np
from scipy import signal
from scipy.signal import convolve, fftconvolve
def cwt(data, wavelet, widths):
"""
Continuous wavelet transform.
Performs a continuous wavelet transform on `data`,
using the `wavelet` function. A CWT performs a convolution
with `data` using the `wavelet... | xkortex/SigFlux | sigflux/wave/custom_cwt.py | Python | mit | 1,608 | [
"Gaussian"
] | 270057107e2c48f6060132cb1946561872a4693bb5e51bbfd520324315fda76c |
import copy
import random
import numpy as np
from Hypothesis import Hypothesis
class VectorHypothesis(Hypothesis):
"""Store n-dimensional vectors (defaultly with Gaussian proposals)."""
def __init__(self, value=None, n=1, proposal=None, propose_scale=1.0, propose_n=1):
self.n = n
self.propose... | ebigelow/LOTlib | LOTlib/Hypotheses/VectorHypothesis.py | Python | gpl-3.0 | 3,282 | [
"Gaussian"
] | 5dbdfb31e781830278fb8c09d7edc9d7656c36de30c3a3f36cb76d5452a35808 |
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
import os, subprocess
from zeroinstall.gui import dialog
from io import BytesIO
from zeroinstall import _
from zeroinstall.injector import model, selections, qdom
from zeroinstall.gui.gui import glib
XMLNS_0COMPILE... | linuxmidhun/0install | zeroinstall/gui/compile.py | Python | lgpl-2.1 | 3,271 | [
"VisIt"
] | 90888d2ebac8c9f6a0a333add6a6df8eb1248ba4484f72ead43fe1343add3eb0 |
import nest
import numpy.random as random
from property import *
# E_L
L2_EL_mu = -79.3
L2_EL_sigma = 4.27 / 4
L3_EL_mu = -79.3
L3_EL_sigma = 4.27 / 4
L4_EL_mu = -71.8
L4_EL_sigma = 4.20 / 4
L5A_EL_mu = -69.9
L5A_EL_sigma = 4.18 / 4
L5B_EL_mu = -68.5
L5B_EL_sigma = 3.98 / 4
L6_EL_mu = -69.9
L6_EL_sigma = 4.18 / 4... | research-team/robot-dream | somatosensory_columns/parameters.py | Python | mit | 6,123 | [
"NEURON"
] | 8ee758b59dac2c67b1d5017c91ac2776d95ffe28e7930209fe0108d98cbe7a83 |
"""
Topological fingerprints.
"""
from __future__ import division
from __future__ import unicode_literals
__author__ = "Steven Kearnes"
__copyright__ = "Copyright 2014, Stanford University"
__license__ = "MIT"
from deepchem.feat import Featurizer
class CircularFingerprint(Featurizer):
"""
Circular (Morgan) fing... | ktaneishi/deepchem | deepchem/feat/fingerprints.py | Python | mit | 3,331 | [
"RDKit"
] | fc31d61ef710dbfe453cda34b8177574b384a4c839073b029300bd9dc714360d |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | modules/level_set/test/tests/reinitialization/viewer.py | Python | lgpl-2.1 | 624 | [
"MOOSE",
"VTK"
] | 8a9dda42fa195ca2b7d77c9482c5ca2894c8b341ed32ac0c955b813273a89a83 |
from pylons import request
import dirac.lib.credentials as credentials
from DIRAC.Core.DISET.RPCClient import RPCClient
from DIRAC.Core.DISET.TransferClient import TransferClient
from DIRAC.FrameworkSystem.Client.UserProfileClient import UserProfileClient
def __prepareArgs( kwargs ):
if ( 'static' not in kwargs or ... | DIRACGrid/DIRACWeb | dirac/lib/diset.py | Python | gpl-3.0 | 1,262 | [
"DIRAC"
] | 766edd313d7209023822ac3efb9ce14babd8d9216a48ed9bc23841d31457a0ef |
import sys
from modelBuild import *
from constants import *
from PyQt4.QtGui import QPixmap, QImage, QPen, QGraphicsPixmapItem, QGraphicsLineItem
from PyQt4.QtCore import pyqtSignal
from kkitUtil import *
from setsolver import *
from PyQt4 import QtSvg
from moose import utils
class GraphicalView(QtGui.QGraphicsView):... | dilawar/moose-full | moose-gui/plugins/kkitViewcontrol.py | Python | gpl-2.0 | 58,605 | [
"MOOSE"
] | 86d99060ad9638c5ae0a84f2418bfba191fec76fc9c845c099784a747694c1ef |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements input and output processing from PWSCF.
"""
import re
from collections import defaultdict
from monty.io import zopen
from monty.re import regrep
from pymatgen.core.lattice import Lattice
from pym... | vorwerkc/pymatgen | pymatgen/io/pwscf.py | Python | mit | 19,731 | [
"CRYSTAL",
"pymatgen"
] | 75969324a28a488b91c55dc31668bef78ff297d7b0279120bc245406bd3c25c5 |
#
# Copyright (c) 2017 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yasharmaster/scancode-toolkit | tests/scancode/test_cli.py | Python | apache-2.0 | 23,264 | [
"VisIt"
] | 40d1d0fc34e1525817786da716924a9e9daa974e9065d7681d0869bcc328d69d |
import pysam
import numpy as np
class BedGraphFile:
def __init__(self,bedgraph):
self.tbx = pysam.Tabixfile(bedgraph)
def read(self, chrom, start, end, empty = np.nan):
out = np.ones(end-start)*empty
if chrom in self.tbx.contigs:
for row in self.tbx.fetch(chrom,start,end, ... | GreenleafLab/NucleoATAC | pyatac/bedgraph.py | Python | mit | 679 | [
"pysam"
] | 0e76bf7cb6e0973c261229eb6a8a8294d1883bb2d8e5235c0d6daa36fc156a02 |
from collections import OrderedDict, defaultdict, namedtuple, Counter
from collections.abc import Iterable
from copy import deepcopy
from numbers import Real
from pathlib import Path
import re
import warnings
from xml.etree import ElementTree as ET
import numpy as np
import openmc
import openmc.data
import openmc.che... | mit-crpg/openmc | openmc/material.py | Python | mit | 46,463 | [
"Avogadro"
] | 0dabe84e68ca5591f14384c6076f7d0b229ddd2d7ee81d797216cf045d099fa8 |
#############################################################################
# $HeadURL$
#############################################################################
""" ..mod: FTSRequest
=================
Helper class to perform FTS job submission and monitoring.
:deprecated:
"""
# # imports
import sys... | Sbalbp/DIRAC | DataManagementSystem/Client/FTSRequest.py | Python | gpl-3.0 | 37,278 | [
"DIRAC"
] | 86ede491e803c10cb2c5053b18401eab2d4087a0229a0dac0849caab01ccb9c9 |
# ----------------------------------------------------------------------
# Numenta Platform for Intelligent Computing (NuPIC)
# Copyright (C) 2014-2016, Numenta, Inc. Unless you have an agreement
# with Numenta, Inc., for a separate license for this software code, the
# following terms and conditions apply:
#
# This p... | lscheinkman/nupic | src/nupic/algorithms/anomaly_likelihood.py | Python | agpl-3.0 | 28,338 | [
"Gaussian"
] | ad892402b6263abd684d34e27d29a6f860a2f17f0ded42402ee9208c56283b9a |
#* 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
def levensh... | nuclear-wizard/moose | python/mooseutils/levenshtein.py | Python | lgpl-2.1 | 1,746 | [
"MOOSE"
] | f763438598f94c197ff9abb301828c23f6c21c9c0d9bdb94ab6c082504355c1f |
# -*- coding: UTF-8 -*-
## Copyright 2013 Luc Saffre
## This file is part of the Lino project.
## Lino 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)... | MaxTyutyunnikov/lino | lino/modlib/cal/workflows/faggio.py | Python | gpl-3.0 | 1,894 | [
"VisIt"
] | a99db0b31275903197563b725656fbbfad06139dc6a6e4d527f9066c3ecc3d91 |
# -*- coding: utf-8 -*-
#
# IntroPython_Winter_2016 documentation build configuration file, created by
# sphinx-quickstart on Sat Jan 9 18:16:31 2016.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogener... | Heroes-Academy/Intro-to-Python-Spring-2016 | docs/source/conf.py | Python | mit | 8,352 | [
"Brian"
] | 2af8dcbfe123bd2d415d6cffecd1f8d146d3b81739ae0e15dcc05c62f1eddf26 |
#!/usr/bin/env python
#pylint: disable=missing-docstring
####################################################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simu... | yipenggao/moose | python/MooseDocs/tests/common/file_tree/test_file_tree.py | Python | lgpl-2.1 | 9,403 | [
"MOOSE"
] | 26347ccd229d2faf96fbea9b06185b07fa55196e7bed126a1667762127fe2117 |
#!/usr/bin/env python
# ***** BEGIN LICENSE BLOCK *****
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this file,
# You can obtain one at http://mozilla.org/MPL/2.0/.
# ***** END LICENSE BLOCK *****
import copy
import os
import pla... | kartikgupta0909/build-mozharness | mozharness/mozilla/testing/testbase.py | Python | mpl-2.0 | 26,610 | [
"VisIt"
] | fc8dece35c6c3c7c85c7664adcd1b37fd032744c8429bf199e3d1819f263c081 |
'''
This module launches single point propagations...
'''
import numpy as np
import pandas as pd
import itertools as it
from collections import namedtuple
import quantumpropagator.h5Reader as hf
import quantumpropagator.Propagator as Pr
import quantumpropagator.EMPulse as pp
import quantumpropagator.GeneralFunctions ... | acuzzio/GridQuantumPropagator | src/quantumpropagator/SinglePointPropagator.py | Python | gpl-3.0 | 5,751 | [
"MOLCAS"
] | a490862851dfc135f48a184f46a868eace272748cad46c30c71338f5b6fdda8f |
"""
A VTK RenderWindowInteractor widget for wxPython. Note that wxPython
comes with its own wxVTKRenderWindow in wxPython.lib.vtk. Try both
and see which one works better for you.
Find wxPython info at http://wxPython.org
Created by Prabhu Ramachandran, April 2002
Based on wxVTKRenderWindow.py
Fixes and updates... | sgh/vtk | Wrapping/Python/vtk/wx/wxVTKRenderWindowInteractor.py | Python | bsd-3-clause | 19,105 | [
"VTK"
] | 02920493eb215fa749b741a7070f8ab92dd3d7e88b7654f0558213881cbbf5c1 |
#! -*- coding: utf-8 -*-
import os
import re
from bs4 import BeautifulSoup
from decimal import Decimal as D
from ..base import BaseAccountScraper
class MlpAccountScraper(BaseAccountScraper):
scrape_code = 'mlp'
default_currency = 'EUR'
BALANCE_RE = re.compile(r'[0-9]{,3}(.[0-9]{3})*,[0-9]{2}')
def... | elbaschid/geldmaschine | geldmaschine/scrapers/de/mlp.py | Python | mit | 2,159 | [
"VisIt"
] | e5b1ac9335ed001dabbc15d81de8b06d5851b68dd34622da55873fec3c55cacb |
# Copyright (C) 2015 Henrique Pereira Coutada Miranda
# All rights reserved.
#
# This file is part of yambopy
#
#
"""
Create, read and write yambo input files
Read, modify and write yambo databases
Analyse results from yambo calculations
Modules:
io
- YamboIn: read, write and manipulate yambo input files
... | henriquemiranda/yambopy | yambopy/__init__.py | Python | bsd-3-clause | 2,164 | [
"Yambo"
] | 6e6870fc1c68f7eff4833037ab2699a31b81ea49d410902501eec514f62ee57a |
from pathlib import Path
from sbmlutils.converters import copasi
from sbmlutils.test import REPRESSILATOR_SBML
def test_write_ids_to_names(tmp_path: Path) -> None:
outfile = tmp_path / "out.xml"
copasi.write_ids_to_names(REPRESSILATOR_SBML, outfile)
assert outfile
| matthiaskoenig/sbmlutils | src/sbmlutils/test/converters/test_copasi.py | Python | lgpl-3.0 | 280 | [
"COPASI"
] | fd2779800ba39472f19243632f43b810434e38046da5c04dc6db6c35025fdde5 |
# (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... | CitizenB/ansible | lib/ansible/constants.py | Python | gpl-3.0 | 18,621 | [
"Galaxy",
"MOOSE"
] | 28c9b010849df85acc08363b0088e9747ec7ac584c3e807f537622a1462400ad |
# -*- coding: utf-8 -*-
# devices.py
#
# Copyright 2014-2015 BitVault, Inc. dba Gem
from __future__ import unicode_literals
from .config import *
from .wrappers import Wrapper
from .errors import *
class Devices(Wrapper):
"""A wrapper class for user.devices.create -- not an actual collection"""
def create(... | GemHQ/round-py | round/devices.py | Python | mit | 1,740 | [
"VisIt"
] | 838f6b72fac0b3dc5e61836192f6894b0c5e74066436407be3672a208de7635c |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2017, 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.
"""Test coupled cluster logfiles"""
import os
import unittest
import numpy
__filedir__ = os.path.realpath(os.path.dirna... | cclib/cclib | test/data/testCC.py | Python | bsd-3-clause | 1,015 | [
"cclib"
] | 48124825124cbf09ee4ab10287386bc131d479a62b546dafa74b1392be397972 |
"""
Migration script to create table for storing tool tag associations.
"""
from sqlalchemy import *
from sqlalchemy.orm import *
from migrate import *
from migrate.changeset import *
from galaxy.model.custom_types import *
import datetime
now = datetime.datetime.utcnow
import logging
log = logging.getLogger( __nam... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/model/migrate/versions/0077_create_tool_tag_association_table.py | Python | gpl-3.0 | 1,446 | [
"Galaxy"
] | 0f6a409e48d69b80ee97b23b0340259587a89acc936497bf58ca0222e19694af |
from django.conf.urls import url
import crystal_dashboard.dashboards.crystal.swift_monitoring.views as views
urlpatterns = [
url(r'^$', views.CrystalDashboard.as_view(), name='index'),
]
| Crystal-SDS/dashboard | crystal_dashboard/dashboards/crystal/swift_monitoring/urls.py | Python | gpl-3.0 | 192 | [
"CRYSTAL"
] | e623faa22bac6485005dfde799c2e631c98a17fda25a2d76d312db26e30792e7 |
import six
import chainer
import chainer.functions as F
from chainer.functions.loss.vae import gaussian_kl_divergence
import chainer.links as L
class VAE(chainer.Chain):
"""Variational AutoEncoder"""
def __init__(self, n_in, n_latent, n_h):
super(VAE, self).__init__()
with self.init_scope():... | aonotas/chainer | examples/vae/net.py | Python | mit | 2,150 | [
"Gaussian"
] | c2ae436fa87d3179c6432a230fb4c701f9e437ffe212c143fab7d3ba7aa27c33 |
# -*- encoding: utf-8
from sqlalchemy.test.testing import eq_
import datetime
import os
import re
import warnings
from sqlalchemy import *
from sqlalchemy import types, exc, schema
from sqlalchemy.orm import *
from sqlalchemy.sql import table, column
from sqlalchemy.databases import mssql
from sqlalchemy.dialects.mssql... | dbbhattacharya/kitsune | vendor/packages/sqlalchemy/test/dialect/test_mssql.py | Python | bsd-3-clause | 60,719 | [
"ASE"
] | 442c60990725796d6c9ff75c4a4a832626e06a77e79c343afd97f0f9593964cd |
# Copyright (c) 2018 PaddlePaddle 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 app... | QiJune/Paddle | python/paddle/fluid/initializer.py | Python | apache-2.0 | 18,543 | [
"Gaussian"
] | 3fb836eaf36bc5436d532509ac771140228e2c4d13f604bd487e3adb1e7195a1 |
# Copyright (c) Twisted Matrix Laboratories.
# See LICENSE for details.
"""
This example demonstrates how to run a reverse proxy.
Run this example with:
$ python reverse-proxy.py
Then visit http://localhost:8080/ in your web browser.
"""
from twisted.internet import reactor
from twisted.web import proxy, server... | EricMuller/mynotes-backend | requirements/twisted/Twisted-17.1.0/docs/web/examples/reverse-proxy.py | Python | mit | 438 | [
"VisIt"
] | ab3a67f6dea60c44493e2fb52520a5fec1fb0093682a3c53ba2a41d1f7cc4897 |
# -*- coding: latin-1 -*-
# Copyright (C) 2009-2014 CEA/DEN, EDF R&D
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later ... | FedoraScientific/salome-hexablock | src/TEST_PY/test_unit/test_sphere.py | Python | lgpl-2.1 | 1,610 | [
"VTK"
] | 03451365434388d60988140d7b9c951f7c11fbb66535c464c817ba5a03e88295 |
# -*- coding: utf-8 -*-
"""
Copyright (C) <2010> Autin L. TSRI
This file git_upy/hostHelper.py is part of upy.
upy 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 Lic... | corredD/upy | hostHelper.py | Python | gpl-3.0 | 169,185 | [
"PyMOL"
] | 98b1d40333dfa9eb8e217e033285a0ad27ac302880557a37196ad4a772d1c880 |
#!/usr/bin/env python
# vim: ai ts=4 sts=4 et sw=4
from datetime import date, datetime
from strings import ENGLISH as STR
from django.core.exceptions import ObjectDoesNotExist, MultipleObjectsReturned
import rapidsms
from rapidsms.message import Message
from rapidsms.connection import Connection
from rapidsms.parser... | genova/rapidsms-senegal | apps/poll/app.py | Python | bsd-3-clause | 6,984 | [
"BLAST"
] | e56a00e7b204854a7f57c30bbb3a27efe6a3dacc382544153451f66b15f7776c |
# creates: fcc100.png fcc110.png bcc100.png fcc111.png bcc110.png bcc111.png hcp0001.png fcc111o.png bcc110o.png bcc111o.png hcp0001o.png ontop-site.png hollow-site.png fcc-site.png hcp-site.png bridge-site.png
import os
from ase import Atoms
from ase.io import write
from ase.lattice.surface import (fcc100, fcc110, bc... | slabanja/ase | doc/ase/surface.py | Python | gpl-2.0 | 1,561 | [
"ASE"
] | a8a12fce0c444b02d5478aee4a5b041fe8203bb08050e684ec59f2b940d3ec2b |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals, division, print_function
"""
Error handlers for errors originating from the Submission systems.
"""
__author__ = "Michiel van Setten"
__copyright__ = " "
__version__ =... | sonium0/pymatgen | pymatgen/io/abinitio/scheduler_error_parsers.py | Python | mit | 13,085 | [
"pymatgen"
] | 2a914c355412738d7939ed4a301a5d79aba4ae294dd8a92668c6e7b8dbe4c7dd |
#/**********************************************************************
#** This program is part of 'MOOSE', the
#** Messaging Object Oriented Simulation Environment.
#** Copyright (C) 2014 Upinder S. Bhalla. and NCBS
#** It is made available under the terms of the
#** GNU Lesser General Public License versi... | dilawar/moose-full | moose-examples/snippets/RandSpikeStats.py | Python | gpl-2.0 | 3,665 | [
"MOOSE"
] | 5ca87583450551e81bfb04c8f6e4774ea43d60c1423918ea5596b086933af9cc |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/transitions | openlp/plugins/presentations/lib/presentationcontroller.py | Python | gpl-2.0 | 14,497 | [
"Brian"
] | d6bb8854da1d09ecb976fe90ee99f28fd2f72c794c01609e30ca6ee866713f63 |
'''
Taken from http://www.djangosnippets.org/snippets/214/
WTForm (What The Form)
======================
WTForm is an extension to the django forms library allowing
the developer, in a very flexible way, to layout the form
fields using <fieldset>s and columns
WTForm was built with the well-documented YUI Grid CSS[1]... | intelligenia/django-cmsutils | cmsutils/forms/wtform.py | Python | lgpl-3.0 | 13,861 | [
"VisIt"
] | 9af31a85e4896bf541697a73c10b887812b0f167b5198119988f339a1698703c |
from scipy.optimize import nnls
import multiprocessing as mp
from ctc_filters import *
from ggplot import *
from astropy.coordinates import Distance
from astropy import units as u
import seaborn as sns
'''
Perform non negative least square SED fitting using
the Assef et al. 2010 templates and extinction laws
#self.bui... | CTJChen/ctc_astropylib | xservs/xmmobj.py | Python | apache-2.0 | 9,547 | [
"Galaxy"
] | 75b8972b3b6cb313aade830b39974932c0180461517eef0d020b746147ccfb2f |
#!/usr/bin/env python
"""
GUI framework and application for use with Python unit testing framework.
Execute tests written using the framework provided by the 'unittest' module.
Further information is available in the bundled documentation, and from
http://pyunit.sourceforge.net/
Copyright (c) 1999, 2000, ... | Fat-Zer/FreeCAD_sf_master | src/Mod/Test/unittestgui.py | Python | lgpl-2.1 | 15,996 | [
"VisIt"
] | 81bdd6953eee5c3f5f44fd8674fd102aaaa9e6b372660fb9f10be750026e89d6 |
import mimpy.mesh.hexmesh as hexmesh
import mimpy.mfd.mfd as mfd
import numpy as np
res_mfd = mfd.MFD()
res_mfd.set_compute_diagonality(True)
res_mfd.set_m_e_construction_method(0)
#Define the permeability function
def K(p, i, j, k):
return np.eye(3)
#The exact solution.
def u(p):
return p[0]**2 + p[1]**2 +... | ohinai/mimpy | examples/hexmesh/example1/hexmesh_example_1.py | Python | bsd-3-clause | 1,798 | [
"VTK"
] | 67e6eb4af876d847525b2ed003c6e9d7e6290309ff1a14af333f86bfe2aaabc1 |
from __future__ import division
import unittest
from .checks import *
from .knownfailure import *
from nose import SkipTest
from nose.plugins.attrib import attr
from pymc3.tests.test_distributions import (build_model,
Domain, product, R, Rplus, Rplusbig, Unit, Nat, NatSmall,
I, Simplex, Vector, PdMatrix)
fr... | superbobry/pymc3 | pymc3/tests/test_distributions_random.py | Python | apache-2.0 | 25,637 | [
"exciting"
] | 5124ec789371bffdb26f785d81e2d29d9ea5ff87fa7549fb635c96970a765cb4 |
## -*- coding: utf-8 -*-
## Copyright (c) 2015-2018, Exa Analytics Development Team
## Distributed under the terms of the Apache License 2.0
#"""
#PW Input Composer
###########################
#
#"""
#from exa import TypedProperty
#from exatomic.qe.base_composer import PWCPComposer
#
#
#class PWInput(PWCPComposer):
# ... | alexvmarch/atomic | exatomic/qe/pw/composer.py | Python | apache-2.0 | 566 | [
"Quantum ESPRESSO"
] | d956cc0d9f43f8ec1c2cba88448dc2ea714e0b2c869f7af08dd9d04725c01987 |
"""
@name: Modules/House/Hvac/thermostat.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2018-2019 by D. Brian Kimmel
@note: Created on Aug 28, 2019
@license: MIT License
@summary: Handle the hvac thermostat
"""
__updated__ = '2019-12-02'
__version_info__ = (19, 10, 11... | DBrianKimmel/PyHouse | Project/src/Modules/House/Hvac/thermostat.py | Python | mit | 4,780 | [
"Brian"
] | 28fb4099ff3464f5bb318b9758ed2d8ecaa276a2bce05d10fa1085770b92361c |
"""
Filter VCF and output only SNP calls in a sequence context where there
is a different homopolymer either side of the site, one of which is the same base as the ALT
allele, and one is the ref e.g. ref sequence is AAAAATTTTT and SNP is T-->A or A --> A.
"""
import sys
import pysam
a = pysam.Fastafile(sys.argv[1])
t... | andyrimmer/Platypus | scripts/removeJoiningHPs.py | Python | gpl-3.0 | 1,398 | [
"pysam"
] | 437fdc087d15683ea02762f73df925926e005657550938b3bf898ee8f25530ce |
# Copyright (c) 2003-2013 LOGILAB S.A. (Paris, FRANCE).
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
#
# This program is free software; you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
# Foundation; either version 2 of the License, o... | hkupty/python-mode | pymode/libs/pylama/lint/pylama_pylint/pylint/checkers/design_analysis.py | Python | lgpl-3.0 | 15,085 | [
"VisIt"
] | bd1fb88fa88263dc2d0ed5c2899a7a643664e1840221bd6ba29e7a2e4ae5d721 |
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