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 |
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"""Fortran/C symbolic expressions
References:
- J3/21-007: Draft Fortran 202x. https://j3-fortran.org/doc/year/21/21-007.pdf
"""
# To analyze Fortran expressions to solve dimensions specifications,
# for instances, we implement a minimal symbolic engine for parsing
# expressions into a tree of expression instances. A... | simongibbons/numpy | numpy/f2py/symbolic.py | Python | bsd-3-clause | 53,009 | [
"VisIt"
] | 8ac6d03959b6bc15b7a8ed3b4c4136dd7571b37ad6719c8f6a084feffae22f97 |
# -*- coding: utf-8 -*-
"""
mchem.build
~~~~~~~~~~~
Functions for building the database.
:copyright: Copyright 2014 by Matt Swain.
:license: MIT, see LICENSE file for more details.
"""
from __future__ import print_function
from __future__ import unicode_literals
from __future__ import division
import gzip
import log... | mcs07/mongodb-chemistry | mchem/build.py | Python | mit | 2,697 | [
"RDKit"
] | 075b4df0799b9941e06af25048cac923b81dc90bafd9b9cf104aecb6f8477ff5 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkTemporalInterpolator(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | nagyistoce/devide | modules/vtk_basic/vtkTemporalInterpolator.py | Python | bsd-3-clause | 515 | [
"VTK"
] | c945a1dc9c3d23425b7c9358dccac8c7e94325b8192b95494bcc41e1a94f3340 |
##########################################################################
#
# Copyright 2010 VMware, Inc.
# All Rights Reserved.
#
# 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 res... | surround-io/apitrace | retrace/retrace.py | Python | mit | 24,408 | [
"VisIt"
] | 1ae50497b1abf2d9f0d92d6dbea926ad699fd0a315ec9aaafe473e46ddcc7021 |
#
# Copyright (C) 2015 - 2017 Red Hat, Inc.
#
# This copyrighted material is made available to anyone wishing to use,
# modify, copy, or redistribute it subject to the terms and conditions of
# the GNU General Public License v.2, or (at your option) any later version.
# This program is distributed in the hope that it ... | vathpela/anaconda | pyanaconda/ui/gui/spokes/blivet_gui.py | Python | gpl-2.0 | 11,981 | [
"VisIt"
] | 9614ad6e586953a8d2856239293ab75ccce90625974e451350a68c473bc714e1 |
########################################################################
# $Id$
########################################################################
__RCSID__ = "$Id$"
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.DataManagementSystem.DB.FileCat... | miloszz/DIRAC | DataManagementSystem/DB/FileCatalogComponents/FileManager.py | Python | gpl-3.0 | 32,590 | [
"DIRAC"
] | c2d2f6d70491453f355b09f1bec47f17e666021c623c1f2afe7298f5701814d4 |
#! /usr/bin/env python
"""Write structured grids to NetCDF files.
Write netcdf
++++++++++++
.. autosummary::
:toctree: generated/
~landlab.io.netcdf.write.write_netcdf
"""
import os
import warnings
import six
import numpy as np
try:
import netCDF4 as nc4
except ImportError:
warnings.warn('Unable ... | csherwood-usgs/landlab | landlab/io/netcdf/write.py | Python | mit | 22,121 | [
"NetCDF"
] | c1516ffe064732f50b142794d2fd3d27130e13ae0f324dd5896411a1840e99f1 |
"""Leetcode 85. Maximal Rectangle
Hard
URL: https://leetcode.com/problems/maximal-rectangle/
Given a 2D binary matrix filled with 0's and 1's, find the largest rectangle
containing only 1's and return its area.
Example:
Input:
[
["1","0","1","0","0"],
["1","0","1","1","1"],
["1","1","1","1","1"],
["1","0","0... | bowen0701/algorithms_data_structures | lc0085_maximal_rectangle.py | Python | bsd-2-clause | 2,585 | [
"VisIt"
] | c198251b51db2580663545bef1b6b9e93248fcc88a7caab8396903b855bb8526 |
""" The CS! (Configuration Service)
"""
__RCSID__ = "$Id$"
from DIRAC.Core.Utilities.ReturnValues import S_OK, S_ERROR
from DIRAC.ConfigurationSystem.private.ServiceInterface import ServiceInterface
from DIRAC.Core.DISET.RequestHandler import RequestHandler
from DIRAC.Core.Utilities import DErrno
gServiceInterface =... | arrabito/DIRAC | ConfigurationSystem/Service/ConfigurationHandler.py | Python | gpl-3.0 | 3,918 | [
"DIRAC"
] | a6eebe2f5687a0f2bc72d3f0eb58ca24b6a59e67e9fccf5f84b2f6700cf1a83f |
#!/usr/bin/python
# script for generating 4 fasta files 21nt and 25nt, forward and reverse, before weblogo analysis
# version 3-2-2012
# Usage fasta_sorter.py <bowtie input> <output1> <output2> <output3> <output4>
import sys, re, os
def antipara (sequence):
antidict = {"A":"T", "T":"A", "G":"C", "C":"G"}
revseq =... | drosofff/tools-artbio | unstable/local_tools/fasta_sorter.py | Python | mit | 1,613 | [
"Bowtie"
] | 366243917c19ccf99699cb30d4ef89efc4b71ac6869d05d6455872275f407e3f |
"""The suite of window functions."""
from __future__ import division, print_function, absolute_import
import warnings
import numpy as np
from scipy import special, linalg
from scipy.fftpack import fft
from scipy._lib.six import string_types
__all__ = ['boxcar', 'triang', 'parzen', 'bohman', 'blackman', 'nuttall',
... | ales-erjavec/scipy | scipy/signal/windows.py | Python | bsd-3-clause | 53,971 | [
"Gaussian"
] | a19e165f52ec07573f29e0f9a0896207d9598fd523ea6f9ea1c5731aad305d7c |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | python/MooseDocs/test/tree/test_html.py | Python | lgpl-2.1 | 1,056 | [
"MOOSE"
] | cdfba73bf8db15a678bdb742348deb516a346ab12025b2df3f05f35f7cc57e4c |
import copy
import inspect
import os
import sys
import threading
import traceback
from collections import namedtuple, defaultdict
from .common import fail, warn
from .constopt import ConstantOptBase
from .errors import Errors, Warnings, InterpretError
from .env import env
from .graph import Graph
from .ir import Ctx, L... | ktok07b6/polyphony | polyphony/compiler/pure.py | Python | mit | 28,462 | [
"VisIt"
] | 9dc9cda611ef1ec93d47aead4e503bdc0d3eacac165c53aed1e2698f39139c6b |
import random
from math import *
landmarks = [[20.0, 20.0], [80.0, 80.0], [20.0, 80.0], [80.0, 20.0]]
world_size = 100.0
T = 20
class robot:
def __init__(self):
self.x = random.random()*world_size
self.y = random.random()*world_size
self.orientation = random.random()*2.0*pi
self.forward_noise = 0.0
se... | ResByte/SLAM | particle_filter.py | Python | gpl-2.0 | 3,153 | [
"Gaussian"
] | 67cbdda4f458b21c910817df2b02b801f579f2c0ad5a3d670f7e72f6004c2e16 |
#start_imports
from random import Random
from time import time
from math import pi
from inspyred import ec
from inspyred.ec import terminators
import numpy as np
from matplotlib import pyplot
#end_imports
# The problem in concern is the of fitting a of
# appropriate order among a lis of 2D points.
# X = ... | hargup/ga_curve_fitting | curve_fitting.py | Python | gpl-3.0 | 11,076 | [
"Gaussian"
] | 68c7c308c5d9c0f37835e01f370331059eeaa15054b1a7861a705405690d1c29 |
"""
This file contains view functions for wrapping the django-wiki.
"""
import cgi
import logging
import re
from django.conf import settings
from django.shortcuts import redirect
from django.utils.translation import ugettext as _
from opaque_keys.edx.locations import SlashSeparatedCourseKey
from wiki.core.exceptions i... | miptliot/edx-platform | lms/djangoapps/course_wiki/views.py | Python | agpl-3.0 | 4,350 | [
"VisIt"
] | 0b265de5a67e5e87b7d29a4e66f103b99d43a5626a1d0129cbc890f139647c5d |
#
# @file TestXMLAttributes.py
# @brief TestXMLAttributes unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Ben Bornstein
#
# $Id: TestXMLAttributes.py 11441 2010-07-09 02:22:23Z mhucka $
# $HeadURL: https://sbml.svn.sourceforge.net/svnroot/sbml/trunk/libsbml/src/bindings/python/test/xml/TestXM... | alexholehouse/SBMLIntegrator | libsbml-5.0.0/src/bindings/python/test/xml/TestXMLAttributes.py | Python | gpl-3.0 | 5,144 | [
"VisIt"
] | f10f4e8b7b8551accdfced8f120b67aaaf19169d0539d300ed800e7ffc10d6ab |
"""Test OpenBabel Python bindings
On Windows or Linux, you can run these tests at the commandline
in the build folder with:
"C:\Program Files\CMake 2.6\bin\ctest.exe" -C CTestTestfile.cmake
-R pybindtest -VV
The runtime directory is ${CMAKE_SRC_DIR}/test.
You could also "ch... | dkoes/openbabel | test/testbindings.py | Python | gpl-2.0 | 47,513 | [
"Pybel",
"TURBOMOLE"
] | be7d0b71fd9e70bf5c277e248d190bf59719cc7a3753150d7e9ce39c2e0b79d6 |
"""
===================================
Simple 1D Kernel Density Estimation
===================================
This example uses the :class:`sklearn.neighbors.KernelDensity` class to
demonstrate the principles of Kernel Density Estimation in one dimension.
The first plot shows one of the problems with using histogram... | chrsrds/scikit-learn | examples/neighbors/plot_kde_1d.py | Python | bsd-3-clause | 5,514 | [
"Gaussian"
] | 1e507c12ce643a63cd4002a412fdcf5a45a7e08b26fe255cfccb6d249433d818 |
from __future__ import print_function
import numpy as np
from heapq import nlargest
from time import time
import marshal
# TODO - FEATURES:
## TODO: sparse permanence like in the temporal_pooler
## TODO: boosting: firing uses b_dec boosting_factor, which restores by b_inc per cycle
## TODO: TEST dynamic threshold (ra... | mobarski/sandbox | cortex/spatial.py | Python | mit | 8,704 | [
"NEURON"
] | 215983389a5740669108fb52d8af67be33fc86013f6860dd5e97b17daa2daefb |
from pylab import *
from ase import *
from hotbit import *
from box.grids import GridData
from ase.data.molecules import molecule
atoms = molecule('C6H6')
calc = Hotbit(SCC=True,width=0.05,txt='benzene.cal')
atoms.set_calculator(calc)
atoms.center(vacuum=3)
atoms.get_potential_energy()
#view(atoms)
r = atoms.get_posit... | pekkosk/hotbit | examples/benzene_STM.py | Python | gpl-2.0 | 751 | [
"ASE"
] | efd6cea80d2b5eeb1402843b901745edf83333f7de2b85c40833630b9f3ac794 |
import numpy.lib.stride_tricks
import numpy as np
from scipy.fft import rfft2 as rfft2_, irfft2 as irfft2_, fftshift as fftshift_
from numpy import ma
from scipy.signal import convolve2d as conv_
from numpy import log
"""This module contains a pure python implementation of the basic
cross-correlation algorithm for PIV... | OpenPIV/openpiv-python | openpiv/pyprocess.py | Python | gpl-3.0 | 43,261 | [
"Gaussian"
] | 77e234a86cf99feac20f6a6aae835c7875849a433a59f1ab4c8b9fa3c3b98815 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# License AGPLv3 (https://www.gnu.org/licenses/agpl-3.0-standalone.html)
"""
This script helps to create a new branch for a new Odoo version from the
another existing branch, making the needed changes on contents.
Installation
============
For using this utility, you nee... | OCA/maintainer-tools | tools/migrate_branch.py | Python | agpl-3.0 | 14,171 | [
"VisIt"
] | 7fac74118cfc0a9ef1765c9d644ecaf89c11f8932c35680a8d9da0092f79fd7e |
## \file
## \ingroup tutorial_roofit
## \notebook
## Multidimensional models: multi-dimensional pdfs with conditional pdfs in product
##
## `pdf = gauss(x,f(y),sx | y ) * gauss(y,ms,sx)` with `f(y) = a0 + a1*y`
##
## \macro_code
##
## \date February 2018
## \authors Clemens Lange, Wouter Verkerke (C++ version)
impo... | root-mirror/root | tutorials/roofit/rf305_condcorrprod.py | Python | lgpl-2.1 | 2,551 | [
"Gaussian"
] | 5a2f9a2ff25d069ae8c4fbb5314ad9e5b8cf4ee4e0ae2efd823f8cfc115bce9b |
import pytest
import vtk
import pyvista
from pyvista import colors
@pytest.fixture
def default_theme():
return pyvista.themes.DefaultTheme()
def test_backwards_compatibility():
try:
color = (0.1, 0.4, 0.7)
pyvista.rcParams['color'] = color
assert pyvista.rcParams['color'] == color
... | akaszynski/vtkInterface | tests/test_theme.py | Python | mit | 12,894 | [
"VTK"
] | 283084bffa481632231ee4e1b40d2c07d85c4be89163cc409b100721dafc34bf |
#!/usr/bin/env python
##
## See COPYING file distributed along with the ncanda-data-integration package
## for the copyright and license terms
##
"""
Check Missing Scans
===================
- Take as input a csv file containing subject id, visit, and validation type.
- Then query redcap to see if scan information is... | sibis-platform/ncanda-data-integration | scripts/redcap/obsolete/check_missing_scans.py | Python | bsd-3-clause | 3,558 | [
"VisIt"
] | 45a7ab0947794c3d1f81be0cf0a71bb94d7a58d54e3bd0e5da6acf935d8cd2c5 |
#!/usr/bin/env python3
"""Use this to actually run the iterative mapper. But first make sure you made a header file with make_header.py"""
import time
from LoLIM.utilities import logger
from LoLIM.iterativeMapper.iterative_mapper import read_header, iterative_mapper
## these lines are anachronistic and should be fi... | Bhare8972/LOFAR-LIM | LIM_scripts/iterativeMapper/examples/run_mapper.py | Python | mit | 1,318 | [
"Brian"
] | 36dae8460a5031bf436e29850378b1a624f92ec7a242ad5ee6cb76acfebc7b49 |
# 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.io.lobster import Cohpcar, Icohplist
from pymatgen.electronic_structure.core import Spin, Orbital
fro... | gpetretto/pymatgen | pymatgen/io/tests/test_lobster.py | Python | mit | 12,985 | [
"pymatgen"
] | 7690aa264dbc31b5f276aa77873cbe85439511ea782abea2bf4c3b961e442554 |
import argparse
import os
import sys
new_path = [ os.path.join( os.getcwd(), "lib" ) ]
new_path.extend( sys.path[1:] )
sys.path = new_path
from galaxy.util import asbool
from galaxy import eggs
eggs.require( 'boto' )
import boto
from tool_shed.util.basic_util import INSTALLATION_LOG
class BucketList( object ):
... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/tool_shed/scripts/check_s3_for_empty_tool_dependency_installation_paths.py | Python | gpl-3.0 | 7,921 | [
"Galaxy"
] | e6fe032876e8ee123ac34d7455110f4cfb845f35fa6f4b7d56c1d0682869899c |
import matplotlib.pylab as plt
import numpy as np
import scipy.special as special
import scipy.constants as constants
import scipy.integrate as integrate
################################################################################
hbarc = 0.1973269664036767; # in GeV nm
#c = constants.c*100.0 # cm/s
c = 3e10 # c... | mattbellis/dark-matter-models | dm_models.py | Python | mit | 24,599 | [
"Avogadro"
] | 1c4d9f9d3272e05c11f07717d8f772a2d8e1157fd7c94bcb6377b72b25ef2e2a |
#!/usr/bin/env python
import uuid
import subprocess
import shlex
import csv
import sys
import time
from sklearn.base import BaseEstimator,RegressorMixin, ClassifierMixin
from sklearn.datasets import load_svmlight_file,dump_svmlight_file
import libsvm
import libsvm.svmutil
import numpy as np
import scipy.sparse
import... | niitsuma/gpusvm | python/svm2classcuda.py | Python | bsd-3-clause | 9,346 | [
"Gaussian"
] | 2e5d8e5a59ad8c746e30f58d09067ef772bf3a951b2a01820cecee8062b3c37a |
#* 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 uuid... | harterj/moose | python/MooseDocs/extensions/floats.py | Python | lgpl-2.1 | 6,225 | [
"MOOSE"
] | b33bfcb3b3ec873eaf63348f39997e7741273e6aafe517503593338d547bdb20 |
"""Communication Module
"""
#------------------------------------------------------------------------
# Copyright (c) 2015 SGW
#
# Distributed under the terms of the New BSD License.
#
# The full License is in the file LICENSE
#------------------------------------------------------------------------
import numpy as n... | sgwoodjr/velvet | velvet/commfunc.py | Python | bsd-3-clause | 5,557 | [
"Gaussian"
] | 06f40ec81af46543ff072adf4f36f4233a78335aec6a058d3f7f346a92b1f27a |
"""
A setuptools based setup module.
See:
https://packaging.python.org/en/latest/distributing.html
https://github.com/pypa/sampleproject
"""
# Always prefer setuptools over distutils
from setuptools import setup, find_packages
from os import path
from RiboCode import __version__
import sys
if sys.version_info[0] ... | xzt41/RiboCode | setup.py | Python | mit | 4,449 | [
"Biopython",
"HTSeq",
"pysam"
] | a6f4b1344c135a37f039e1794c72b2012fec77cf448a4094c5fdb4fa86722d45 |
# Copyright 2018 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | mlperf/training_results_v0.7 | Google/benchmarks/minigo/implementations/minigo-research-TF-tpu-v4-128/gtp_cmd_handlers.py | Python | apache-2.0 | 12,133 | [
"VisIt"
] | 30d69f32483b4f59d01b41901db837494692ee4e3d83163dd71df6c2c3435cdd |
#!/usr/bin/python
'''
NAMEGEN.PY V1.0
Got it working, generating the names from one or many of several databases,
being Goblin, Western (m+f), Elf (m+f), Orc, and Greek Gods. Also is cross-
platform (only checks for which backslash it should use), which should save time
between two files. Currently the names are genera... | jackshanson/DnD-namegen | namegen.py | Python | mit | 17,101 | [
"Gaussian"
] | 3a2f7f384219ff33827a593efbd62faecb0cc396c1556086c4d8bfc539092120 |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to
# make it easier to submit large numbers of jobs on supercomputers. It
# provides a python interface to physical input, ... | pylada/pylada-light | src/pylada/ipython/launch/array_script.py | Python | gpl-3.0 | 3,366 | [
"CRYSTAL",
"VASP"
] | bdd3e68ebde50218ba5e4e2802281d91d8c8880555f608447e1d6370c00def09 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# demonstrates the use of vtkPropAssembly
# create four parts: a top level assembly and three primitives
#
sphere = vtk.vtkSphereSource()
sphereMapper = vtk.vtkPolyDataMapper()
sphere... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Rendering/Core/Testing/Python/propAssembly.py | Python | gpl-3.0 | 2,332 | [
"VTK"
] | 9a9d5a97c1ea7b7952725c9933a332484d4e6a9c45a9771fa43768a5b3533aef |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
import itertools
import pytest
import numpy as np
from numpy.testing import assert_allclose
from astropy.convolution.utils import discretize_model
from astropy.modeling.functional_models import (
Gaussian1D, Box1D, MexicanHat1D, Gaussian2D, Box2D, M... | bsipocz/astropy | astropy/convolution/tests/test_discretize.py | Python | bsd-3-clause | 6,122 | [
"Gaussian"
] | a9d56a3c4e62479316bedf1b6b618f42e29c24a8264b948b926f30f7dab85239 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/transitions | openlp/plugins/songusage/forms/songusagedeleteform.py | Python | gpl-2.0 | 3,932 | [
"Brian"
] | 49a7a81a1a0b92d87c9f0bd8f5127b9882a97dab26baa1a05edb0298575f5fd3 |
# Copyright 2021 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | google-research/crest | third_party/data_util.py | Python | apache-2.0 | 16,831 | [
"Gaussian"
] | 074a4d7d09f71e3e356975808c734b24566d0ad65d10f91bc8cb70fe712859d7 |
import sys
# Load in the files from arguments.
blastfile = sys.argv[1]
ravifile = sys.argv[2]
keyfile = sys.argv[3]
# Generate the result file.
resultfile = sys.argv[2] + '.results'
# Load in BLAST results, and choose the lowest evalue result(s)
# Store the evalue into the zeroth position, and then all matching ac... | pandeyravi15/SGMBL | script/singularblast_f.py | Python | gpl-3.0 | 3,851 | [
"BLAST"
] | 88dd85b155d024ece57ea50bf88220cf75050a8f5bf262a30833374c27a181e6 |
import vtk
import numpy as np
def _max_length(strings):
if not strings: return 0
return max(len(s) for s in strings)
def _fields_repr(self, indent=4):
indent_str = ' '*indent
field_names = list(self._fields)
field_names.sort()
fill_length = _max_length(field_names) + 1
s = type(self).__n... | patmarion/director | src/python/director/fieldcontainer.py | Python | bsd-3-clause | 3,427 | [
"VTK"
] | 8f23a431aad7b6e7760c9d35b329077c8c97e37994bf25f3f5cb323df87b9892 |
""" WMSHistory corrector for the group and ingroup shares
"""
__RCSID__ = "$Id$"
import datetime
import time as nativetime
from DIRAC.WorkloadManagementSystem.private.correctors.BaseCorrector import BaseCorrector
from DIRAC.Core.Utilities import Time
from DIRAC.AccountingSystem.Client.ReportsClient import ReportsClie... | Sbalbp/DIRAC | WorkloadManagementSystem/private/correctors/WMSHistoryCorrector.py | Python | gpl-3.0 | 8,726 | [
"DIRAC"
] | 6ea533c04b17d0cd19f38c825f91f989c114817586ea5513d4becafa0e52905c |
"""
.. moduleauthor:: Gilbert Maitre <gilbert.maitre@hevs.ch>
The :mod:`gridsim.electrical` module implements the electrical part of the
gridsim simulator. It basically manages Consuming-Producing-Storing (CPS)
Elements, which consume (positive sign) and/or produce (negative sign) a
certain amount of energy (``delta_e... | gridsim/gridsim | gridsim/electrical/__init__.py | Python | gpl-3.0 | 1,140 | [
"Gaussian"
] | 460e8cc7279342194e86bbe3844e8492993538f387caefe4c22ba56b7c51b324 |
"""
====================================================================
Linear and Quadratic Discriminant Analysis with confidence ellipsoid
====================================================================
Plot the confidence ellipsoids of each class and decision boundary
"""
print(__doc__)
from scipy import lin... | kashif/scikit-learn | examples/classification/plot_lda_qda.py | Python | bsd-3-clause | 4,952 | [
"Gaussian"
] | 4be867a985850a2c47ef5cc0a287f6184810d1fe88d79997ad06ca3a29fad974 |
# This file is part of Androguard.
#
# Copyright (c) 2012 Geoffroy Gueguen <geoffroy.gueguen@gmail.com>
# 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://... | subho007/androguard | androguard/decompiler/dad/basic_blocks.py | Python | apache-2.0 | 11,199 | [
"VisIt"
] | 1d13381502088017a645a4dafecb78d013589868e72eb045f7b7cb30e8d757dc |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# stopexe - [insert a few words of module description on this line]
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of t... | heromod/migrid | mig/cgi-bin/stopexe.py | Python | gpl-2.0 | 1,102 | [
"Brian"
] | aa931a5ef100acae2b6cd9dc5d41240cb74e1b6eb52dccff9ecf4fd361567185 |
#Just a copy of the version in python 2.5 to be used if it's not available in jython 2.1
"""Simple XML-RPC Server.
This module can be used to create simple XML-RPC servers
by creating a server and either installing functions, a
class instance, or by extending the SimpleXMLRPCServer
class.
It can also be used to hand... | goodwinnk/intellij-community | python/helpers/pydev/_pydev_imps/_pydev_SimpleXMLRPCServer.py | Python | apache-2.0 | 21,572 | [
"Brian"
] | 87a86546c8c75345440a6c7fb21b2e2adcb806971af94ea0c9a196d612bb1adb |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""The freesurfer module provides basic functions for interfacing with
freesurfer tools.
Change directory to provide relative paths for doctests
>>> import os
>>> filepath = os.path.dirname( os... | rameshvs/nipype | nipype/interfaces/freesurfer/model.py | Python | bsd-3-clause | 41,924 | [
"Gaussian"
] | 3a36129fccbc3ec4c3fa9a9951646be983e64e1e21852abaf03f4c7fc7efda8a |
from matplotlib.matlab import *
x = randn(10000) # some gaussian noise
subplot(211) # a subplot
hist(x, 100) # make a histogram
grid(True) # make an axes grid
ylabel('histogram')
# now do the regression...
x = arange(0.0, 2.0, 0.05)
y = 2+ 3*x + 0.2*randn(len(x)) # y is a linear function of x + nse
# the bestfit li... | sniemi/SamPy | sandbox/src1/tests/histog.py | Python | bsd-2-clause | 622 | [
"Gaussian"
] | f0d00e6784e93530ec57fad54105db86d98688b2f8554880422edc8f92d7da94 |
#! /usr/bin/env python
import os
import time
import datetime
import StringIO
import numpy as np
from sqlalchemy import and_
import matplotlib.pyplot as plt
from matplotlib.backends.backend_agg import FigureCanvasAgg as FigureCanvas
from matplotlib.dates import DateFormatter
from matplotlib.ticker import MaxNLocator
... | pomeslab/sumcoresg | data_collector.py | Python | gpl-2.0 | 15,460 | [
"ORCA"
] | 6c0da570898258ea46f0537b6eed5e614e5d6b907d8f5eeba154a4f85d232791 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import numpy as np
from pymatgen.core import Lattice
from pymatgen.electronic_structure.core import Magmom, Orbital, Spin
class SpinTest(unittest.TestCase):
def test_init(self):
... | gmatteo/pymatgen | pymatgen/electronic_structure/tests/test_core.py | Python | mit | 5,467 | [
"pymatgen"
] | 62ece5df8614728ae7c55ac349ad711553adc9d2e0bc0ff561bc65a2f9a5d7bc |
#!/usr/bin/env python
########################################################################
# File : dirac-jobexec
# Author : Stuart Paterson
########################################################################
""" The dirac-jobexec script is equipped to execute workflows that
are specified via their XML... | DIRACGrid/DIRAC | src/DIRAC/WorkloadManagementSystem/scripts/dirac_jobexec.py | Python | gpl-3.0 | 4,179 | [
"DIRAC"
] | 5484abf772fae3a177b085a6b8ca84d41631bc76499fd36284ec43ff0bca81af |
# -*- coding: utf-8 -*-
import logging
import re
from django.apps import apps
from django.core.exceptions import ValidationError
from osf.utils import sanitize
logger = logging.getLogger(__name__)
def has_anonymous_link(node, auth):
"""check if the node is anonymous to the user
:param Node node: Node whic... | erinspace/osf.io | website/project/model.py | Python | apache-2.0 | 2,775 | [
"VisIt"
] | 682f51dbb17e828ff2d8190e2cbaff166097d926a4c5faac7a1f0f0527be4e16 |
import os
import subprocess
import jinja2
import json
import openchemistry as oc
def run_calculation(geometry_file, output_file, params, scratch_dir):
# Read in the geometry from the geometry file
# This container expects the geometry file to be in .xyz format
with open(geometry_file) as f:
xyz_st... | OpenChemistry/mongochemdeploy | docker/psi4/src/run.py | Python | bsd-3-clause | 2,467 | [
"Psi4"
] | 0e204597c89c9c509b35260abd587eab971841a4cdbc74762f064f5007add2c5 |
# -*- 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
from django.views import defaults as default_views
urlpat... | hbutau/dzidzo | config/urls.py | Python | bsd-3-clause | 1,308 | [
"VisIt"
] | 63e5e1b19d08cc0a636ff36aea4532c5f1a873d89dda23655210a1621f48434b |
#!/usr/bin/env python
import MDAnalysis, argparse
from MDAnalysis.analysis.rms import rmsd
import MDAnalysis.analysis
import os
from os.path import splitext, basename
#This finds the most distinct set of frames. Does not perform alignment, just rmsd.
def compute_cluster_sizes(current, model, selection):
"""Given a... | dkoes/md-scripts | diversemdselect.py | Python | bsd-3-clause | 2,641 | [
"MDAnalysis"
] | 982cc7d0de9480bb2c9c31bc8e3c966100bcdef84d9451a889c51529f115bf1b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import math
import operator as op
EMSG = {
"point_init": "Wrong initialization argument: %s.",
"point_sub": "Could not subtract points.",
"point_add": "Addtion is not defined for Point and %s",
"vector_prod": "The cross product is only d... | dreadworks/college-cg | t1-raytracer/geometry.py | Python | mit | 13,275 | [
"Gaussian"
] | 1adb9b3433f39835ecfd4085d53a88a681bf3f8879b4fda2081c98da76c5c159 |
# 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
# distribu... | jarrodmcc/OpenFermion | src/openfermion/utils/_sparse_tools_test.py | Python | apache-2.0 | 55,877 | [
"Gaussian"
] | bcc6bab652b881bdce6474b444aa4f4733ec6c97e725dfe83a1941993249d0bf |
import pysam
import sys
import csv
import os
import argparse
from quicksect import IntervalNode
from random import randint, seed
def getOverlap(a, b):
return max(0, min(a[1], b[1]) - max(a[0], b[0]))
def is_rRNA(read,chr):
find_list_rRNA=find(read.reference_start, read.reference_end , tree_rRNA[chr])
... | smangul1/gprofile | gprofileSE.py | Python | apache-2.0 | 10,871 | [
"pysam"
] | 2fe5448f63620366dc7b2a99d69d9d8a5287e03df61218b2f6c9df9b9954d91e |
# Sample module in the public domain. Feel free to use this as a template
# for your modules (and you can remove this header and take complete credit
# and liability)
#
# Contact: Brian Carrier [carrier <at> sleuthkit [dot] org]
#
# This is free and unencumbered software released into the public domain.
#
# Anyone is f... | esaunders/autopsy | pythonExamples/reportmodule.py | Python | apache-2.0 | 4,635 | [
"Brian"
] | 0df71aea81b7a196eb02cdc54d1c2ab5f8701cbf0de09148b8f8ed927fb889f6 |
# coding: utf-8
r"""face.py module of aocutils"""
import logging
import OCC
# import OCC.BRepBuilderAPI
from OCC.Core.BRep import BRep_Tool, BRep_Tool_Surface
from OCC.Core.BRepTopAdaptor import BRepTopAdaptor_FClass2d
# import OCC.BRepFill
if OCC.VERSION[0] == '7':
from OCC.Core.Geom import Geom_Curve, Handle_G... | guillaume-florent/aoc-utils | aocutils/brep/face.py | Python | lgpl-3.0 | 19,751 | [
"Gaussian"
] | 5ba037792a0c1af1b1351a71e5ec580c4c19869ce8f39c7b907fa70d0297eb76 |
import os
import platform
try:
import paraview.simple as pv
except ImportError:
print("Py: ParaView module not imported - is ParaView in the python path?")
def pvd_to_mp4(sim_dir, path_to_movies, movie_name='movie', representation='Surface', num_regions=0):
###############################
# Validate... | fcooper8472/useful_scripts | immersed_boundary.py | Python | bsd-3-clause | 9,331 | [
"ParaView"
] | a4b0ca7362de805e80a27bcf0fa0b816038d02a2052c8b34a642ff747bc1a703 |
"""
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 3 of the License, or
(at your option) any later version.
Written (W) 2013 Heiko Strathmann
"""
from numpy import int32, array
from n... | karlnapf/kameleon-mcmc | kameleon_mcmc/gp/mcmc/PseudoMarginalHyperparameterDistributionDiffusion.py | Python | bsd-2-clause | 2,998 | [
"Gaussian"
] | 30e49bc9914cb4b3effd879a7a418035c517b97f4d1073b7ed3902a57bce984b |
# Copyright 2016 Mingbo Cai, Princeton Neuroscience Instititute,
# Princeton University
#
# 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... | TuKo/brainiak | tests/reprsimil/test_brsa.py | Python | apache-2.0 | 29,837 | [
"Gaussian"
] | 93e8f883d97a77d989b27acf6e5522c0e53e5fc80d4fe3c6c5cffe5bb3fc0241 |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
Second order SCF with QM/MM charges is available
'''
import numpy
from pyscf import gto, scf, qmmm
mol = gto.M(atom='''
C 1.1879 -0.3829 0.0000
C 0.0000 0.5526 0.0000
O -1.1867 -0.2472 0.0000
H -1.9237 0.3850 0.0000... | gkc1000/pyscf | examples/qmmm/11-newton.py | Python | apache-2.0 | 711 | [
"PySCF"
] | 82544afefba8a29b7e0ce0eba2d97f092aa47364e1122f887ee3e61b6d896e60 |
#!/usr/bin/env python
"""
Wrapper for antsApplyTransforms to make it more like the old WarpImageMultiTransform
COMMAND:
antsApplyTransforms
antsApplyTransforms, applied to an input image, transforms it according to a
reference image and a transform (or a set of transforms).
OPTIONS:
-d, -... | sujason/thomas | WarpImageMultiTransform.py | Python | mit | 5,695 | [
"Gaussian"
] | 96a8caa998832f2575939f4b9fb2cdc6641391d1d25a503ce05451377d0d9b36 |
"""
Code has been reformated (and modified in some details) by Christian Schwartz
Author: Aaron MacDonald
Date: June 14, 2007
Description: An implementation of the precise permissive field
of view algorithm for use in tile-based games.
... | cschwartz/pycrpg | src/algorithms/fov.py | Python | gpl-2.0 | 10,615 | [
"VisIt"
] | 4f4df3f59761a3f411d0888bb65bfaf6e6f64657bb7bae12e621506313f5a649 |
#!/usr/bin/env python3
"""K. Miernik 2012
k.a.miernik@gmail.com
Distributed under GNU General Public Licence v3
This module is inteded to be loaded in an interactive interpreter session.
The ipython is strongly recommended. The pydamm is a python replacement for
DAMM programm.
"""
import math
import numpy as np
impo... | ntbrewer/Pyspectr | Pyspectr/pydamm.py | Python | gpl-3.0 | 59,304 | [
"Gaussian"
] | 446c30f4ac4f7edb8dd8e9cbaa89dd99b18eebe423c6259a5c37996d1b25b3d3 |
# This file is part of cclib (http://cclib.sf.net), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2006, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version 2.1 or later. You shou... | Clyde-fare/cclib_bak | src/cclib/progress/qt4progress.py | Python | lgpl-2.1 | 1,311 | [
"cclib"
] | a8852f9b28724c18d2a76966d7dacf7034f7a4e81acfcdf6230b33ce041446a3 |
# GromacsWrapper: xpm.py
# Copyright (c) 2012 Oliver Beckstein <orbeckst@gmail.com>
# Copyright (c) 2010 Tsjerk Wassenaar <tsjerkw@gmail.com>
# Released under the GNU Public License 3 (or higher, your choice)
# See the file COPYING for details.
"""
Gromacs XPM file format
=======================
Gromacs stores matrix ... | PicoCentauri/GromacsWrapper | gromacs/fileformats/xpm.py | Python | gpl-3.0 | 10,379 | [
"Gromacs"
] | 2001084f42f80be507e60cd0f00f83a55615b03f8043096b710795a8eb681209 |
"""
shortcircuit.py
Adapted from pseudo code written by Shaun Cooper
Written By: Brian O'Dell September, 2017
A small script written in python to test if the language
uses short circuit evaluation when executing conditionals with and
If a language does, then the helper function is not called w... | brian-o/CS-CourseWork | CS471/Program2/shortcircuit.py | Python | gpl-3.0 | 935 | [
"Brian"
] | a0a258d9e92c94424d62618ca8163c7b225361655c777d625a7872a0a35aaad8 |
import time
from django.core.urlresolvers import reverse
from django.test import LiveServerTestCase
from django.conf import settings
from nose.plugins.attrib import attr
from nose.plugins.skip import SkipTest
from splinter.browser import Browser
@attr('e2e')
class E2ETestCase(LiveServerTestCase):
def setUp(self,... | hobson/totalgood | totalgood/utils/test_helpers.py | Python | mit | 1,104 | [
"VisIt"
] | 15669e8468096acfe14677f913056442fd385d0ac15d3d0069365effbeff7e9b |
#!/usr/bin/env python
"""
Simple script that uses Biopython AlignIO to convert
between various file formats for sequence alignments.
See documentation online at:
http://biopython.org/wiki/AlignIO
"""
# This program is free software: you can redistribute it and/or
# modify it under the terms of the GNU General Publi... | jrjhealey/bioinfo-tools | x2phy.py | Python | gpl-3.0 | 4,530 | [
"Biopython"
] | ef8218f0539f36e2be723dbb72d30dea0b080acf9fdca729911cdd9b7036c447 |
from Sire.IO import *
from Sire.MM import *
from Sire.System import *
from Sire.Mol import *
from Sire.Maths import *
from Sire.FF import *
from Sire.Move import *
from Sire.Units import *
from Sire.Vol import *
from Sire.Qt import *
import os
coul_cutoff = 20 * angstrom
lj_cutoff = 10 * angstrom
amber = Amber()
(... | chryswoods/SireTests | unittests/SireMM/testgridff2.py | Python | gpl-2.0 | 3,699 | [
"Amber"
] | f53e0d7f4c8b30ac90de424c5540902059c06222bcf99a89b0a897ff1ec78734 |
# ##########################################################################
#
# Example to submit DDSim job to ILCDirac, as an User job.
#
# To submit,
# python subddsim.py
#
# A. Miyamoto, 1-July-2019
#
# ###########################################################################
from DIRAC.Core.Base import ... | akiyamiyamoto/Tutorial | grid/ilcdirac/ddsim/subddsim.py | Python | gpl-3.0 | 4,435 | [
"DIRAC"
] | b12a292fb17ce145f0dfd3703de8eabba4947ae1fb717da2864e4e8b540822b3 |
# -*- coding: utf-8 -*-
import datetime
import json
import os
from django.conf import settings
from django.core.urlresolvers import reverse
import mock
from nose.tools import eq_, ok_
from pyquery import PyQuery as pq
import mkt
from mkt.constants.applications import DEVICE_TYPES
from mkt.files.tests.test_models imp... | tsl143/zamboni | mkt/submit/tests/test_views.py | Python | bsd-3-clause | 39,244 | [
"exciting"
] | a70fd135b681f30570f2ed5961bfddc60ecef93bd860ed9e9742d243026316f4 |
# -*- coding: utf-8 -*-
import netCDF4
import numpy as np
from netCDF4 import num2date, date2num
EPOCH_UNITS = "seconds since 1970-1-1 00:00:00+0:00"
def var_to_dict(standard_name, data, units, long_name):
"""
Convert variable information to a dictionary.
"""
d = {}
d["data"] = data[:]
d["uni... | josephhardinee/PyDisdrometer | pydsd/io/common.py | Python | lgpl-2.1 | 1,627 | [
"NetCDF"
] | 9de882e196531b893bfe3f55193d0266d3fa4c0dda541d9dc93bf4c47fb4f16c |
# savemodel.py ---
#
# Filename: savemodel.py
# Description:
# Author: subha
# Maintainer:
# Created: Wed Oct 29 00:08:50 2014 (+0530)
# Version:
# Last-Updated:
# By:
# Update #: 0
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#
# Change log:
#
#
#
#
# This program is... | dilawar/moose-full | moose-examples/snippets/savemodel.py | Python | gpl-2.0 | 1,327 | [
"MOOSE"
] | 9b7494c659b64d04d55c31686a1e7e76acc28c86867ad3fff815909ad0c9399e |
# Copyright 2021 DeepMind Technologies Limited. 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 ... | deepmind/mctx | mctx/_src/tree.py | Python | apache-2.0 | 5,371 | [
"VisIt"
] | 76feea8b47ddc4bca11c9fa4c15dcfdf18d25f232a76f778b3a4d48e8adbaec9 |
from __future__ import division
import numpy as np
import scipy.interpolate as intpl
from pySDC.core.Collocation import CollBase
from pySDC.core.Errors import CollocationError
class EquidistantSpline_Right(CollBase):
"""
Implements equidistant nodes with right end point included and spline interpolation
... | danielru/pySDC | pySDC/implementations/collocation_classes/equidistant_spline_right.py | Python | bsd-2-clause | 3,164 | [
"Gaussian"
] | 3d6ba5a7bc1ffd6d6e01a1de719f6df7cc2674951dec2f30caab7abc50ba2b30 |
"""
Dependency management for tools.
"""
import os.path
import logging
log = logging.getLogger( __name__ )
from .resolvers import INDETERMINATE_DEPENDENCY
from .resolvers.galaxy_packages import GalaxyPackageDependencyResolver
from .resolvers.tool_shed_packages import ToolShedPackageDependencyResolver
from galaxy.uti... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/tools/deps/__init__.py | Python | gpl-3.0 | 4,543 | [
"Galaxy"
] | 1bdb962e03035aca9634b56233433e9d48398a00fa5a6186f836fdf5d9420384 |
# -*- coding: utf-8 -*-
"""Classes for handling input/output prompts.
Authors:
* Fernando Perez
* Brian Granger
* Thomas Kluyver
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2008-2011 The IPython Development Team
# Copyright (C) 2001-2007 Fernando Per... | boompieman/iim_project | project_python2/lib/python2.7/site-packages/IPython/core/prompts.py | Python | gpl-3.0 | 16,172 | [
"Brian"
] | 7d26d49d9325f78769d68e9cfcccf6ea530e3b1670b4d7413388e5d58bd1c6a3 |
# ## Copyright (c) 2013, GPy authors (see AUTHORS.txt).
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
import itertools, logging
from ..kern import Kern
from ..core.parameterization.variational import NormalPosterior, NormalPrior
from ..core.parameterization import Param, Parameterized... | TianpeiLuke/GPy | GPy/models/mrd.py | Python | bsd-3-clause | 14,604 | [
"Gaussian"
] | d7ef0bc2ce605e719ca56cd29bb89c6ead822675fe4ce0d893fc8f23c9e869bc |
import stdlib
import netCDF4
import wrappers
from wrappers import base
from utilities import geometry
from dateutil import parser
import datetime
import numpy
# http://www.hydro.washington.edu/~jhamman/hydro-logic/blog/2013/10/12/plot-netcdf-data/
class Wrapper(base.BaseWrapper):
"""
Wrapper for NetCDF data ... | Castronova/EMIT | wrappers/netcdf.py | Python | gpl-2.0 | 4,346 | [
"NetCDF"
] | 15c23fb58d16f1e6ef32e47ba3184ccdc4b44ca03e06acb94fc21e61c5920845 |
"""
Copyright 2016 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 agreed to in writing, software
di... | haeusser/tensorflow | tensorflow/contrib/semisup/python/semisup/train_imagenet.py | Python | apache-2.0 | 6,880 | [
"VisIt"
] | a832ea06cb7806181bd2f42bd1091ed55aa50cbc26ab390bab0583207ec31cf1 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2018 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
#... | amjames/psi4 | psi4/driver/driver.py | Python | lgpl-3.0 | 119,607 | [
"Gaussian",
"Psi4"
] | 4cb36d9c8be611d5820a92f36274c8a05d6075c2912885c27c011fd899b0ebaf |
__author__ = 'Brian Wickman'
__version__ = '0.8.3'
__license__ = 'MIT'
import sys
from .base import Environment
from .basic import Boolean, Enum, Float, Integer, String
from .choice import Choice
from .composite import Default, Empty, Required, Struct
from .container import List, Map
from .naming import Namable, Ref... | wickman/pystachio | pystachio/__init__.py | Python | mit | 406 | [
"Brian"
] | cd3cd8a03f73f65dd3a4d8c38be5618c8fee9a37dead0dd3398302ae9c165c8b |
#!/usr/bin/env python
import argparse
import pysam
import sys
import Tools
import pdb
DELTA = 50
def Close(a, b):
return (abs(a-b) < DELTA)
# ---*==========*-----
# --*===*----------
fromTo = 0
contains = 1
partial = 2
def Order(aln, boundaries):
tb = boundaries[aln.tName]
qb = bo... | yunlongliukm/chm1_scripts | SamCons.py | Python | mit | 11,518 | [
"pysam"
] | a626682f04870f6607b353b4902c331b94d5fb3ad43aab3c593398e2c946fc2d |
# -*- coding: utf-8 -*-
from . import constants
# Note: the factor 10000 appearing in metal and qepw units is due to the following:
# 1e(2*(-19) + 2*(-10) -2*(-12) -(-23) -3*(-10) -15) = 1e4
# e_SI ang ps kB ang fs
# since the multiplicative factor would be
# [(charge*1e-19)**2] [velocity*... | lorisercole/thermocepstrum | sportran/current/units/electric.py | Python | gpl-3.0 | 2,208 | [
"DL_POLY",
"GPUMD",
"LAMMPS",
"Quantum ESPRESSO"
] | c9ec6be004da307454f92a80f7baa1602637c650f4a1c794669ec6c9873b4e4f |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
def test_uccsd_8():
"""Test projective unlinked UCCSD on H4 using RHF/STO-3G orbitals"""
import pytest
import forte.proc.scc as scc
import forte
import psi4
ref_energy = -1.9976233094 # from Jonathon
geom = """
H 0.0 0.0 0.0
H 0.0... | evangelistalab/forte | tests/pytest/sparse_ci/srcc/test_uccsd_8.py | Python | lgpl-3.0 | 1,064 | [
"Psi4"
] | 14d4c336bf97ca91df894bd1d5198c9b5ab89f3fc9b3d771ebf7b598d0b85f9c |
""" tests for the JobDB module """
# pylint: disable=protected-access, missing-docstring
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
import unittest
from mock import MagicMock, patch
from DIRAC import S_OK
MODULE_NAME = "DIRAC.WorkloadManagementSyst... | yujikato/DIRAC | src/DIRAC/WorkloadManagementSystem/DB/tests/Test_JobDB.py | Python | gpl-3.0 | 1,090 | [
"DIRAC"
] | c32e7aebbd3c6fce3eda3ce344216cb8298414c4bdab66dbe7637e171eb58f78 |
import Scientific
try:
if Scientific.__version__ < 2.8:
print 'your ScientifPython version is: ',Scientific.__version__
print 'ScientificPython 2.8 or greater required for numpy support in NetCDF'
raise Exception
except AttributeError:
print 'It appears your ScientificPython has no ver... | conwayje/ase-python | ase/calculators/jacapo/utils/__init__.py | Python | gpl-2.0 | 413 | [
"NetCDF"
] | 41ec0f2428047ac3adf3942a6e9f4d3e18d94d7ee10e28aae89b20854c9e9180 |
"""Weight of Evidence"""
import numpy as np
import pandas as pd
from sklearn.base import BaseEstimator
from category_encoders.ordinal import OrdinalEncoder
import category_encoders.utils as util
from sklearn.utils.random import check_random_state
__author__ = 'Jan Motl'
class WOEEncoder(BaseEstimator, util.Transform... | scikit-learn-contrib/categorical-encoding | category_encoders/woe.py | Python | bsd-3-clause | 11,566 | [
"Gaussian"
] | c2a0f2c35984613db030f50667c2046e548f06527f0173a672cc71be0079f49d |
#!/usr/bin/env python
"""Demo of the most fundamental Tkinter and Pmw widgets"""
from Tkinter import *
import tkMessageBox, tkFileDialog, tkColorChooser
import Pmw
import string, sys, os
class InputFields:
"""
Demonstrate typical widgets for input data: entry, slider,
option menu, checkbutton, radiobuttons... | sniemi/SamPy | sandbox/src1/TCSE3-3rd-examples/src/py/gui/demoGUI.py | Python | bsd-2-clause | 33,712 | [
"VisIt"
] | 2b4a4d1d50620d0b2ab160c7747f408f8310d31259a32e2b4ed1b2e27bfca2ad |
#!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates.
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
"""
This file contains a list of all the tasks, their id and task name, description and the
tags associated with them.
""... | facebookresearch/ParlAI | parlai/tasks/task_list.py | Python | mit | 58,760 | [
"CASINO"
] | 8723112a967c1075fb28b76b694df7e8bc6b182b06d03eaa3e148475cc547a54 |
########################################################################
#
# (C) 2015, Brian Coca <bcoca@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation... | alxgu/ansible | lib/ansible/galaxy/__init__.py | Python | gpl-3.0 | 2,000 | [
"Brian",
"Galaxy"
] | a9957e678dfdc62e956bac6b1ff264abd01f1fd249f4fd10e6a45b5f2b262a7e |
# Copyright 2010 by Tiago Antao. All rights reserved.
# 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.
"""
Large file parsing of Genepop files
The standard parser loads the whole file into memory. T... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/PopGen/GenePop/LargeFileParser.py | Python | gpl-2.0 | 3,937 | [
"Biopython"
] | c2a2ede780a8e2a2bd6ee37718ff4280c5b00390cc4fced20616153d51885280 |
import unittest
from test.support import (verbose, refcount_test, run_unittest,
strip_python_stderr)
import sys
import time
import gc
import weakref
try:
import threading
except ImportError:
threading = None
### Support code
#########################################################... | firmlyjin/brython | www/tests/unittests/test/test_gc.py | Python | bsd-3-clause | 29,494 | [
"VisIt"
] | 07bf39a97081b3bc0417cac418baeb5854067dc95319748e790143648f2fb50c |
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