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# ============================================================================
#
# Copyright (C) 2007-2012 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | jeroendierckx/Camelot | camelot/admin/action/document_action.py | Python | gpl-2.0 | 2,912 | [
"VisIt"
] | ba8bb2f52515032bed979152609236204fc51ad1d9f022ff60d08ed24cb72663 |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publish... | thica/ORCA-Remote | src/ORCA/settings/setttingtypes/SettingInputHelper.py | Python | gpl-3.0 | 2,180 | [
"ORCA"
] | 886d84aaf7c8dd4188973a47ada05f6ce0038411717077a9999fc74e6b60036e |
#!/cluster/home2/mglerner/anaconda3/bin/python
#!/usr/bin/env python
'''
Combine hbond output from a series of ptraj runs into one data set.
'''
import sys, os
from optparse import OptionParser
from pypat import md_analysis_utils
get_resinum_to_resi_map = md_analysis_utils.get_resinum_to_resi_map
from pypat import hb... | LernerLabs/PyPAT | drivers/combine_hbonds.py | Python | apache-2.0 | 5,495 | [
"Amber"
] | 4ec56e0ffb64d12c681ccf8cc686bf597405bc5e5d61a9b9dc55a457158f43ed |
"""
@author David W.H. Swenson
"""
from __future__ import absolute_import
from builtins import object
from .test_helpers import (CallIdentity, raises_with_message_like,
make_1d_traj)
import pytest
import numpy as np
from openpathsampling.integration_tools import unit, HAS_SIMTK_UNIT
impor... | dwhswenson/openpathsampling | openpathsampling/tests/test_volume.py | Python | mit | 16,488 | [
"OpenMM"
] | 4bc4f229662698c247d1c714870f6507ea59da22a83c28922286e7a7fdd0e19b |
#!/usr/bin/env python
# to run the script with the correct version of uvcdat:
# source /usr/local/uvcdat/1.4.0/bin/setup_runtime.sh
import cdms2
from cdms2 import MV2
import numpy
import glob
import sys
import os
from os import path
import shutil
import re
import string
import random
import gc
import logging
import ... | BrunoCombal/climate | make_ensembleMean_tyx.py | Python | gpl-2.0 | 24,108 | [
"NetCDF"
] | 2ee4538a18c621ca49533868a201dc99ade424fd107a3f53aa219766c532c319 |
import os
from os.path import join, abspath, exists
import shutil
import subprocess
from ideFoam.inputFiles import getFileClass, getFilePath
from pythonScripts.fsTools import getFoamTimeFolders
def cleanCase(case, clean):
"""Clean case directory
clean = True => Remove directory
clean = "i" => Interac... | BV-DR/foamBazar | ideFoam/ofCase.py | Python | gpl-3.0 | 9,102 | [
"ParaView"
] | 82c387373a873ee8125b889596febd43ecaaeacbf88dec68ae5b0ab017d501cd |
#!/usr/bin/env python
# Script by Jason Kwong
# Checks for dual W+Y antigenic specificity of Neisseria meningitidis
# Use modern print function from python 3.x
from __future__ import print_function
# Modules
import argparse
from argparse import RawTextHelpFormatter
import sys
import os
from Bio.Seq import Seq
from Bi... | MDU-PHL/meningotype | meningotype/menwy.py | Python | gpl-3.0 | 2,583 | [
"BLAST",
"Biopython"
] | 71df1b0165083bc9543274f4369a7bfc68654faccbb62a37283d5ff15f6d4164 |
sf_day = 0x00000000
sf_dawn = 0x00000001
sf_night = 0x00000002
sf_clouds_0 = 0x00000000
sf_clouds_1 = 0x00000010
sf_clouds_2 = 0x00000020
sf_clouds_3 = 0x00000030
sf_no_shadows = 0x10000000
sf_HDR = 0x20000000 # this will generate HDR-shaded skyboxes, you should make a LDR version of... | disperse/ripping-yarns | module_data-1.166/Skyboxes.py | Python | mit | 5,360 | [
"VisIt"
] | 7c2de9728f3d638f2b089a8b73e0838e987d7c58d5a6b542e595d4fcc8d1dcee |
#! /usr/bin/env python
# Validate non-LTE excitation calculation by solving the water
# radiative transfer benchmark problem presented at the RT workshop
# at Leiden in 2004. This problem considers the excitation of
# 2-level ortho-water in an isothermal, uniform gas cloud. Two
# dynamical cases are considered -- a st... | itahsieh/sparx-alpha | bin/sparx-validate-leiden.py | Python | gpl-3.0 | 23,217 | [
"Gaussian"
] | 86bbae59492777c246c7b313d35cefc2a80191e008c3ed720b2a20429b18eb57 |
''' This script launches a 3d propagation from a h5 file. '''
import pickle
import glob
import numpy as np
import os
import sys
from argparse import ArgumentParser
from collections import namedtuple
from quantumpropagator import (fromFsToAu,
printDict,stringTransformation3d,retrieve_hdf5_data,
loadInp... | acuzzio/GridQuantumPropagator | Scripts/ThreeDPropagator.py | Python | gpl-3.0 | 8,572 | [
"Gaussian"
] | c4e18220517c12bf934c5c99bc83ba5bab74a282a9ef020e9d781bb28b9288ee |
import random
import matplotlib.pyplot as plt
import numpy
''' 1_nn.py
simple neural net
'''
''' -has primitive backprop
-weights deviate in direction of derivative
-productivity is determined by difference between forward output and target
'''
# forward propogation
def forwardGate( inp, weight ):
return ( inp *... | wegfawefgawefg/NeuralNetDemos | 2_nn.py | Python | gpl-3.0 | 3,075 | [
"NEURON"
] | 65e332eaa2517f4b2c888bdbdab6937f75108aa328a94ac8e9a95c1cce9f8393 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | MOA-2011/enigma2-plugin-extensions-openwebif | plugin/controllers/views/web/moviemove.py | Python | gpl-2.0 | 5,222 | [
"VisIt"
] | 36457dfdf546d1c999673367a5e68cca9117880b23a3976fea046abda5add49b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
import unittest
from pymatgen.analysis.path_finder import NEBPathfinder, ChgcarPotential
from pymatgen.io.vasp import Poscar, Chgcar
from pymatgen.core.periodic_table import Element
from numpy import mean
__author__ = 'Ziqin (Shaun) Rong'
__version__ = '0.1'
__... | gVallverdu/pymatgen | pymatgen/analysis/tests/test_path_finder.py | Python | mit | 2,147 | [
"VASP",
"pymatgen"
] | 212b44c5271b95978ba795084fcfb4c08a8aec5fcc9e5cdf1a3eea8e9227103e |
# freeseer - vga/presentation capture software
#
# Copyright (C) 2011, 2013 Free and Open Source Software Learning Centre
# http://fosslc.org
#
# 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 Foundati... | Freeseer/freeseer | src/freeseer/plugins/videoinput/usbsrc/__init__.py | Python | gpl-3.0 | 5,256 | [
"VisIt"
] | ec79ca34f2c4a60caa13810f8bd0e092450b8eb821e34a64b5a395bab3a764e9 |
"""
#####################################################################
Copyright (C) 2001-2014, Michele Cappellari
E-mail: michele.cappellari_at_physics.ox.ac.uk
Updated versions of the software are available from my web page
http://purl.org/cappellari/software
If you have found this software useful for your
rese... | jakeown/GAS | GAS/voronoi_2d_binning.py | Python | mit | 27,815 | [
"Galaxy"
] | 33b6cede6a3f115d53361c82448f7613e325f1355745bf811ab46fc505ba33e3 |
''' python modules '''
''' own modules '''
from sge.sge import SGE
class BWA(SGE):
def __init__(self):
pass | mlesche/deep_seq_pipeline | deep_seq_pipeline/src/sge/aligner/bwa.py | Python | mit | 116 | [
"BWA"
] | d329b72f19c99c18a0a899b9b2ec561c1c152cfdc8e77490792f63a2f5ad039a |
#* 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
from FileTe... | harterj/moose | python/TestHarness/testers/Exodiff.py | Python | lgpl-2.1 | 4,462 | [
"MOOSE"
] | 010edffb8ee14edbbd6bdc943738419c11ab25a6b5f3643c663d40da835f2718 |
#-*- coding:utf-8 -*-
# Copyright (C) 2013-2014 Germán Poo-Caamaño <gpoo@gnome.org>
#
# 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) any l... | mjbrender/MailingListStats | pymlstats/tests/test_analyzer.py | Python | gpl-2.0 | 8,551 | [
"Brian"
] | e30305eb195cbf4796d0b708d72a8771c05602dad55b1837b362b28112d54c58 |
"""
This script is based on the followying Pysurfer Source:
https://pysurfer.github.io/auto_examples/plot_basics.html#sphx-glr-auto-examples-plot-basics-py
You need to install Pysurfer (which uses Mayavi & Matplotlib for the visualization):
https://pysurfer.github.io/
NOTE: The plot is not 100% accurate. I think bra... | iELVis/iELVis | iELVis_PYTHON/pysurf_elec_plot.py | Python | gpl-3.0 | 1,613 | [
"Mayavi"
] | e2c2629b17c152e3884bf6f5b818beeeef57b72a45468e1b1b618db96aaccff1 |
# -*- coding: utf-8 -*-
#
# hl_api.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (a... | PedroTrujilloV/nest-simulator | pynest/nest/hl_api.py | Python | gpl-2.0 | 46,938 | [
"NEURON",
"VisIt"
] | e6db15c7f627dec9c7b1083eb7d6cf129db095ba8ecee0c5de76eb55f155bbf6 |
# Demonstrates the creation of some simple objects
# To be run using "Tools -> Python Shell -> Run Script" inside of paraFoam
# assumes that one OpenFOAM-case is opened
from PyFoam.Paraview import readerObject
from PyFoam.Paraview.SimpleSources import Point,Sphere,Cube,Text,Line,Plane,Arrow,Glyph
from PyFoam.Paravi... | takaakiaoki/PyFoam | examples/paraview3/testSimpleSources.py | Python | gpl-2.0 | 952 | [
"ParaView"
] | b86f39a3fb440d71c43448989b2faaa2d3384d8c296c531d93d05a750765e8f2 |
#!/usr/bin/env python
'''
This example shows how to use P-junction screening in the SGX module.
P-junction screening (pjs in the module) allows the SGX method to
achieve linear scaling for large systems.
'''
from pyscf import gto
from pyscf import scf
from pyscf import dft
from pyscf import sgx
import time
mol = gto... | sunqm/pyscf | examples/sgx/01-pscreen_large_mol.py | Python | apache-2.0 | 1,054 | [
"PySCF"
] | ae723642a5ebd82588c94638315d9281f3c1c5c07155a81235b364db02a8835a |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | MBoustani/climate | ocw/tests/test_utils.py | Python | apache-2.0 | 10,288 | [
"NetCDF"
] | e55404fc21494f76409d2255313b0667fbd4f16ddb85f7899c2d677d92b5c1e8 |
# coding: utf-8
"""
Acceptance tests for Studio's Setting pages
"""
from __future__ import unicode_literals
import os
from mock import patch
from nose.plugins.attrib import attr
from base_studio_test import StudioCourseTest
from bok_choy.promise import EmptyPromise
from common.test.acceptance.fixtures.course import X... | jzoldak/edx-platform | common/test/acceptance/tests/studio/test_studio_settings.py | Python | agpl-3.0 | 37,473 | [
"VisIt"
] | 6dcadd6e3206f61afe86ebaed24e3d038f05f6a525d3ec625498b923a001a7ee |
# Copyright (C) 2003 CAMP
# Please see the accompanying LICENSE file for further information.
from math import pi
import sys
import numpy as np
from numpy.fft import fftn, ifftn, fft2, ifft2
from gpaw.transformers import Transformer
from gpaw.fd_operators import Laplace, LaplaceA, LaplaceB
from gpaw import PoissonC... | qsnake/gpaw | gpaw/dfpt/poisson.py | Python | gpl-3.0 | 22,456 | [
"GPAW",
"Gaussian"
] | d564c45aa747ec3eebbcb3e91039d10dab1335742c9f0ba140107617d89b44bd |
#!python
DOMAINMAP = '''
qgp\d{2} * duke.edu
lqcd\d{2} * duke.edu
neutrino-\d{2} * duke.edu
neuron-\d{2} * duke.edu
neutron-\d{2} * duke.edu
nano\d{2} * duk... | CI-Connect/connect-client | connect/lib/connect/extensions/disabled/historygram.py | Python | apache-2.0 | 3,044 | [
"NEURON"
] | d7ca3f3fd194eefc2c1dffe05a4c015f3f56e5ca8b7ff4446ac45873a28332aa |
"""
game.py
Copyright 2016 Brian Romanchuk
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... | brianr747/Simple4Xpygame | server/game.py | Python | apache-2.0 | 18,099 | [
"Brian",
"Galaxy"
] | b2e379308ae1d67a895051bf25f96b57e0979be2d1e7b80076bf79faad5ab4bf |
from __future__ import print_function, division
from sympy.core.add import Add
from sympy.core.compatibility import as_int, is_sequence, range
from sympy.core.exprtools import factor_terms
from sympy.core.function import _mexpand
from sympy.core.mul import Mul
from sympy.core.numbers import Rational
from sympy.core.nu... | kaushik94/sympy | sympy/solvers/diophantine.py | Python | bsd-3-clause | 99,225 | [
"Gaussian"
] | f630a7e0d78621b1437be4a2db4d8c0cbaa8a0428a28a799bd0905979f3a54f0 |
"""
Module to set up run time parameters for Clawpack.
The values set in the function setrun are then written out to data files
that will be read in by the Fortran code.
"""
from __future__ import absolute_import
from __future__ import print_function
import os
import numpy as np
#CC=os.environ['CC']
try:
CLAW =... | clawpack/adjoint | examples/chile10_CrescentCity/setrun.py | Python | bsd-2-clause | 20,947 | [
"NetCDF"
] | 87bcd4657bfdafdb626b56c90308f2dcb29717347af00e086bc436be69ff54a4 |
# coding: utf-8
from __future__ import division, print_function, unicode_literals, \
absolute_import
import unittest
import random
import os
import tempfile
import numpy as np
from monty.os.path import which
from pymatgen import Lattice, Structure, Element
from veidt.describer.atomic_describer import \
Bisp... | materialsvirtuallab/veidt | veidt/describer/tests/test_atomic_describer.py | Python | bsd-3-clause | 6,664 | [
"LAMMPS",
"pymatgen"
] | f5797f043f4ff1115dc648eea3cf1657fbe9cdfb60f22bd20a2f3e4b56852f78 |
"""This Module is designed to safely move a file.
Author: Brian Lindsay
Author Email: tekemperor@gmail.com
"""
import os
import sys
import errno
def move(source, destination, itr_pre="_", itr_post="", itr_pad=0):
"""Try to move a file iteratively.
Attempts to move a file, appends increasing number if unsuc... | tekemperor/datename | datename/safemove.py | Python | mit | 3,610 | [
"Brian"
] | fed5757b41433da37ab4e957f593230d492d964e3a0ceeb1a859b274ca70d48b |
#!/usr/bin/env python3
import argparse
import errno
from html5lib import (HTMLParser, serializer, treebuilders, treewalkers)
import os
import re
import sys
import time
import urllib.error
import urllib.request
from xml.dom.minidom import Node
def log_if_v(msg):
if args.verbose:
print('[DEBUG] %s' % msg, fi... | t3nsor/quora-backup | converter.py | Python | gpl-2.0 | 12,936 | [
"Brian"
] | 1699037d10631104375ff271f16dd9da0d47db3b30515e517fab16ea73fdbeb5 |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, subprocess, sys, glob, string
import zipfile
from datetime import date
cwd = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
os.chdir(cwd)
required_module_keys = ['architectures', 'name','version','moduleid','descripti... | jasper-lyons/ti-uxcam | ios/iphone/build.py | Python | mit | 8,489 | [
"VisIt"
] | 15f865cbaecfd5a1cee4007e48ecf2d2372d0a829d33bee89810ffa2a781e8c5 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import unittest
import sys
from pymatgen.analysis.defects.point_defects import *
from pymatgen.core.structure import Structure
from pymatgen.core.periodic_table import ... | migueldiascosta/pymatgen | pymatgen/analysis/defects/tests/test_point_defects.py | Python | mit | 23,964 | [
"GULP",
"pymatgen"
] | b1295c97aef74c63738506418e9ef92af8c661ca6c725800cacee4bf688c42bd |
#from opengmcore import _opengmcore.adder as adder
from opengmcore import *
from __version__ import version
from functionhelper import *
from _inf_param import _MetaInfParam , InfParam
from _visu import visualizeGm
from _misc ... | joergkappes/opengm | src/interfaces/python/opengm/__init__.py | Python | mit | 10,979 | [
"VisIt"
] | d4c9cb8e54bc21eaa182b849b93a1f048fe1e02657707d06f171a82f19934aa6 |
#!/usr/bin/env python
'''
SEQUENTIAL TONE GENERATOR
Generate various audio waveforms, including:
- noise (white, pink)
- sine, square, sweep
- silence
Write to .wav @ 16kHz, 16-bit
TODO:
- Argument parser
- class waveform():
'''
import numpy as np
import wave
import struct
from scipy.signal import chirp
from scipy.s... | yunque/tongen | polytongen.py | Python | cc0-1.0 | 5,514 | [
"Gaussian"
] | fdabe3799c331dac8d7f66ca1ce0a4b906d0c645c3f3995af2dbd19488b24ca6 |
from math import atan2
from math import cos
from math import pi
from math import sin
from numpy import asarray
from numpy import atleast_1d
from numpy import atleast_2d
from numpy import cross
from numpy import diff
from numpy import dot
from numpy import linspace
from numpy import loadtxt
from numpy impo... | aurmarsan/pyturbo | UVParametrizationFilter.py | Python | mit | 11,939 | [
"ParaView",
"VTK"
] | f7f0e122d519ac5816bd9e3cefa0a146ce03c196ce4fee43f712a859e91bdd4e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2013,2014 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version... | olenz/espresso | samples/python/cellsystem_test.py | Python | gpl-3.0 | 1,182 | [
"ESPResSo"
] | bddc3db79fff32b4dcbcb971bb2f21602bdf953109b3896f6aeb662385b64de6 |
import unittest
import saliweb.test
import re
# Import the saxsmerge frontend with mocks
saxsmerge = saliweb.test.import_mocked_frontend("saxsmerge", __file__,
'../../frontend')
def get_summary_file():
return """garbage line
Merge file
General
Filename: merged... | salilab/saxsmerge | test/frontend/test_results.py | Python | lgpl-2.1 | 4,544 | [
"Gaussian"
] | bbf1848be0c649eaa60e427aab41ef4610e49a4717025ef2a9d6222768b97dc2 |
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# This script tests vtkBandedPolyDataContourFilter (BPDCF)
# Create 8 renderers, each showing a 4-point polydata with
# a different combinations of (poly)vertices, (poly)lines,
# triangles, quads, with a ... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Filters/Modeling/Testing/Python/TestBandedContourFilter2.py | Python | gpl-3.0 | 5,198 | [
"VTK"
] | 971b6a08df5e71314e37c75c3a2873b706cc1df7ecd932a8456d2fcd22b0a66e |
#pylint: disable=C0103,R0903,W0232
"""
Classes and constants for representing thermodynamic variables.
"""
import sys
from sympy import Float, Symbol
from pycalphad.io.grammar import parse_chemical_formula
class Species(object):
"""
A chemical species.
Attributes
----------
name : string
... | tkphd/pycalphad | pycalphad/variables.py | Python | mit | 13,959 | [
"pycalphad"
] | 4ec6f672933915672ac46708283ac7e82a697771db8fd82a6e96c2dc6aa3960a |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2017 Lenovo, Inc.
#
# 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
# ... | bjolivot/ansible | lib/ansible/modules/network/lenovo/cnos_bgp.py | Python | gpl-3.0 | 19,399 | [
"VisIt"
] | 036d9540af3f1d250f276c787811cdf1f93cacf7b13a72abf933937470e0dc4f |
# coding: utf-8
"""
Vericred API
Vericred's API allows you to search for Health Plans that a specific doctor
accepts.
## Getting Started
Visit our [Developer Portal](https://developers.vericred.com) to
create an account.
Once you have created an account, you can create one Application for
Production and an... | vericred/vericred-python | test/test_drug_coverages_api.py | Python | apache-2.0 | 10,086 | [
"VisIt"
] | 0f9ba06c2091dfa8786a406533eed3a3ba6b53399b8a622255b5eef24d4a94c1 |
"""Simple test for the grid plane and outline module.
"""
# Author: Prabhu Ramachandran <prabhu_r@users.sf.net>
# Copyright (c) 2005, Enthought, Inc.
# License: BSD Style.
# Standard library imports.
from os.path import abspath
from StringIO import StringIO
import copy
# Local imports.
from common import TestCase, g... | liulion/mayavi | integrationtests/mayavi/test_grid_plane.py | Python | bsd-3-clause | 3,791 | [
"Mayavi",
"VTK"
] | c0dd25a6de98a976bcea263b714342ad39f55fd2df785157d0d2dcf31e38bd89 |
#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* Copyright (c) Schrodinger, LLC.
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove this copyright notice.
#F* -------... | gratefulfrog/lib | python/pymol/editing.py | Python | gpl-2.0 | 70,567 | [
"CRYSTAL",
"ChemPy",
"PyMOL"
] | fe8fe082e4b4654c0198ed568a9b75359be6a5f331910b6bf39613085e63a5f0 |
#!/usr/bin/env python
import sys
import vtk
from vtk.util import numpy_support
import netCDF4 as nc
import numpy as np
import matplotlib.pyplot as plt
"""
Notes:
- this looks useful http://stackoverflow.com/questions/7666981/how-to-set-data-values-on-a-vtkstructuredgrid
"""
def main():
with nc.Dataset('grid... | nicjhan/mom-particles | vtk/mask.py | Python | gpl-2.0 | 1,948 | [
"VTK"
] | dfd849f01e84a533f6b782542dc4b7fcac5fd9c500c265decc4ca8b577af21fa |
# This is the main AMT script that should be executed and will do the following:
# * Create a HIT
# * Wait for the HIT to become reviewable
# * Process assignments once the HIT is reviewable
# * Check whether their input code is one that we gave them.
# * If yes, pay them, if not, reject them.
# NOT... | macilath/CrowdMix | amt/AMTscript.py | Python | mit | 6,706 | [
"VisIt"
] | 88b07804c3600200cdf87fb4cdceb081fd94fc4728300831cdc109f455ef3c06 |
"""An NNTP client class based on RFC 977: Network News Transfer Protocol.
Example:
>>> from nntplib import NNTP
>>> s = NNTP('news')
>>> resp, count, first, last, name = s.group('comp.lang.python')
>>> print 'Group', name, 'has', count, 'articles, range', first, 'to', last
Group comp.lang.python has 51 articles, rang... | trivoldus28/pulsarch-verilog | tools/local/bas-release/bas,3.9/lib/python/lib/python2.3/nntplib.py | Python | gpl-2.0 | 19,693 | [
"Brian"
] | 83ca60ec8cff09b9fe7a3b24f5fd1c4395a18846cb5fe4d877258ee7a1f29168 |
"""
Automated fitting script.
A minimal run must specify an input.json and a datasets folder containing input files.
"""
from __future__ import print_function
import os
import argparse
import logging
import multiprocessing
import sys
import json
import warnings
import numpy as np
import yaml
import dask
import dist... | PhasesResearchLab/ESPEI | espei/espei_script.py | Python | mit | 12,427 | [
"pycalphad"
] | 6a80331c69138271d13a0a4d06ec890a6b465e4a244f81aafe4cb539f383d401 |
"""
======================================
Probability calibration of classifiers
======================================
When performing classification you often want to predict not only
the class label, but also the associated probability. This probability
gives you some kind of confidence on the prediction. However,... | DailyActie/Surrogate-Model | 01-codes/scikit-learn-master/examples/calibration/plot_calibration.py | Python | mit | 4,791 | [
"Gaussian"
] | c28fca70516a3f4d143fcf2ad870fd0cf32efa23bad5cd4a23ee49a0ce0f9b9e |
# Orca
#
# Copyright 2005-2009 Sun Microsystems Inc.
#
# 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 version.
#
# This... | h4ck3rm1k3/orca-sonar | src/orca/braille_generator.py | Python | lgpl-2.1 | 18,667 | [
"ORCA"
] | 34f1a65c21b5af0b65a3a89ebb3ad7055402b1175c9d7e7e0be0bd0a295814cf |
#!/usr/bin/env python3
########################################################################
# Solves problem 19 from projectEuler.net.
# Finds the number of Sundays that were first of the month during
# the 20th century.
# Copyright (C) 2010 Santiago Alessandri
#
# This program is free software: you can... | sanSS/programming-contests | project-euler/problem019.py | Python | gpl-3.0 | 1,376 | [
"VisIt"
] | 93dd96ff5a369f024daa196de6923b18731b85501cec13933cb4e3bf4c92cbb8 |
import os
import external.cclib as cclib
import logging
from subprocess import Popen
import re
from rmgpy.molecule import Molecule
from qmdata import CCLibData
from molecule import QMMolecule
class Gaussian:
"""
A base class for all QM calculations that use Gaussian.
Classes such as :class:`Gaussian... | chatelak/RMG-Py | rmgpy/qm/gaussian.py | Python | mit | 19,411 | [
"Gaussian",
"MOPAC",
"cclib"
] | df642a4c29af2f4e20c71ac3bd5ee68d490175fc5b50721bd1c977fdb3f24667 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import re
import numpy as np
import warnings
from pymatgen.core.operations import SymmOp
from pymatgen import Element, Molecule, Composition
from monty.io imp... | aykol/pymatgen | pymatgen/io/gaussian.py | Python | mit | 53,484 | [
"Gaussian",
"pymatgen"
] | ca79636d3a425c58ee35c6ae89f66b4c25edd101cec0d69b15982b4d9a22ff60 |
# -*- coding: utf-8 -*-
# Copyright 2017 Vojtech Vozab
#
# 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... | V17/bigaussian | bigaussian.py | Python | gpl-3.0 | 13,343 | [
"DIRAC",
"Gaussian"
] | 7022ddb6cb5d4c8872e7bbd72311f5dd4837cc77ea409cbdfa5433f2928bafb0 |
"""
Data-driven tests for reads
"""
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import collections
import os
import ga4gh.backend as backend
import ga4gh.datamodel as datamodel
import ga4gh.datamodel.datasets as datasets
import ga4gh.datamodel.reads as... | macieksmuga/server | tests/datadriven/test_reads.py | Python | apache-2.0 | 18,970 | [
"pysam"
] | b749f414983af01d793211d1a72378bbb1f9018d2f350a0fa2bc7bacca4409f0 |
import tempfile
from WebAppDIRAC.Lib.WebHandler import WebHandler, asyncGen
from DIRAC import gConfig, gLogger
from DIRAC.ConfigurationSystem.Client.Helpers.Operations import Operations
from DIRAC.ConfigurationSystem.Client.Helpers.Registry import getVOForGroup
class JobLaunchpadHandler(WebHandler):
AUTH_PROPS = "... | zmathe/WebAppDIRAC | WebApp/handler/JobLaunchpadHandler.py | Python | gpl-3.0 | 9,524 | [
"DIRAC"
] | d32e2acaa1f3b6221048681cea50b03e47aa24f667dd3a62d28852a7dd77e7ab |
#!/usr/bin/env python
import numpy as np
import matplotlib.pyplot as plt
from xmitgcm import open_mdsdataset
import scipy.io.netcdf as netcdf
import f90nml
import glob,os,re
import intergrid
import cartopy.crs as ccrs
from cartopy.mpl.gridliner import LONGITUDE_FORMATTER, LATITUDE_FORMATTER
plt.ion()
dir0 = '/home/b... | Herpinemmanuel/Oceanography | diag_caml.py | Python | mit | 3,474 | [
"NetCDF"
] | 8082d400f2a73bbce5f8ab7510d197d41b60981697316b9d96720c63b2733a74 |
#
# The Qubes OS Project, https://www.qubes-os.org/
#
# Copyright (C) 2010-2015 Joanna Rutkowska <joanna@invisiblethingslab.com>
# Copyright (C) 2014-2015 Wojtek Porczyk <woju@invisiblethingslab.com>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser Genera... | nrgaway/qubes-core-admin | qubes/dochelpers.py | Python | gpl-2.0 | 15,881 | [
"VisIt"
] | 31e2bed5d89e3418835c6343b4043c2de3444a8eef1182f0dc69cec6fe98bb7c |
from __future__ import absolute_import
# coding: utf-8 -*-
from flask import url_for
import pytest
from firefly.models.topic import Category
@pytest.mark.usefixtures('client_class')
class TestCategory:
def setup(self):
categories = []
for x in range(3):
categories.append(
... | mozillazg/firefly | tests/test_category.py | Python | mit | 1,593 | [
"Firefly"
] | b42f6ffe43779158a0b2804fa43283aba42751fd2200f6fad132ffb7e5d21452 |
#!/usr/bin/env python
# -*- encoding: utf-8 -*-
import sys
import BioClasses
import cPickle
import pysam
import scipy
def main():
# load data from the GTF pic
with open( "/home/paul/Resources/H_sapiens/test.hg19.chr.pic" ) as f:
genes = cPickle.load( f )
# load the indexed FASTA file
fastafile = pysam.Fastafi... | polarise/python-bioclasses | test/test_UTR.py | Python | gpl-2.0 | 756 | [
"pysam"
] | 1e1a8ba6955e5f0ba85432ca08111469d9f66348b3abef1a7d9f2182709bd090 |
class TestEntryList(object):
def test_blog_page_entries(self, browser, site_url):
browser.visit(site_url + '/blog/')
entries = browser.find_by_css('.page-content')
assert browser.status_code == 200
assert len(entries) > 0
def test_entry_page_search(self, browser, site_url):
... | APSL/puput | tests/functional/test_entry_list.py | Python | mit | 2,068 | [
"VisIt"
] | bbb0d0b706935c2b1ce50220e7f10a38f6a59341b388ec023766fd1b82dbba33 |
"""
Measuring a shape of an object
==============================
Simple class to measure weighted quadrupole moments, size, and ellipticity of an object.
Can be used for example to verify weak lensing mission requirements.
:requires: NumPy (tested with 1.9.1)
:author: Sami-Matias Niemi
:contact: s.niemi@icloud.com
... | sniemi/ShapeMeasurement | shapeMeasurements.py | Python | bsd-2-clause | 17,431 | [
"Gaussian"
] | 66175d4f9d7bed3d18c5fa77d7dfcb54e118532ec4cae1de55783a31df128b94 |
#
# 1D sample netCDF file generation test suite
# Author: Ashley Hall
# Last modified: 27 Apr 2014
#
# This file is part of Climate Analyser.
#
# Climate Analyser 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 Foundatio... | climate-analyser-team/sample_data_generator | tests/test_gen2D.py | Python | gpl-3.0 | 1,413 | [
"NetCDF"
] | 6e4f14d7c45b4ce451f561c0574b48c9809ef808efb1c64ddde9e2d6a9811db7 |
#!/usr/bin/env python
# Collect quality parsimonious SNPs from vcf files
# and output alignment files in fasta format.
import argparse
import multiprocessing
import os
import queue
import shutil
import sys
import time
from collections import OrderedDict
from datetime import datetime
import pandas
import vcf
def ge... | abretaud/tools-iuc | tools/vsnp/vsnp_get_snps.py | Python | mit | 24,525 | [
"Galaxy"
] | b81cce5dca23249a4423a0e949a6a54639177544cea8521541dc2977fa824497 |
# -*- Mode: Python; test-case-name: flumotion.test.test_feedcomponent010 -*-
# vi:si:et:sw=4:sts=4:ts=4
#
# Flumotion - a streaming media server
# Copyright (C) 2004,2005,2006,2007 Fluendo, S.L. (www.fluendo.com).
# All rights reserved.
# This file may be distributed and/or modified under the terms of
# the GNU Genera... | offlinehacker/flumotion | flumotion/component/feedcomponent010.py | Python | gpl-2.0 | 37,566 | [
"GULP"
] | 0e9f91171c286e932207aa54971d365244ca1e002dc73548e6d4e5ce32f6092d |
from __future__ import unicode_literals
import os
import warnings
import yaml
__author__ = "Pymatgen Development Team"
__email__ ="pymatgen@googlegroups.com"
__maintainer__ = "Shyue Ping Ong"
__maintainer_email__ ="shyuep@gmail.com"
__date__ = "May 14 2017"
__version__ = "4.7.6"
SETTINGS_FILE = os.path.join(os.path... | tallakahath/pymatgen | pymatgen/__init__.py | Python | mit | 2,773 | [
"CRYSTAL",
"pymatgen"
] | 809ed04183f1dbaf9dfbd0e69d648dea19dc0d4c6c076f14644d301474a90816 |
input_name = '../examples/diffusion/poisson_iga.py'
output_name = 'test_poisson_iga.vtk'
from tests_basic import TestInput
class Test(TestInput):
pass
| RexFuzzle/sfepy | tests/test_input_poisson_iga.py | Python | bsd-3-clause | 156 | [
"VTK"
] | ae0c36325d43403774df6b7d3044b0909f7c57277a4dcf39adda612d1274cd7a |
import os
basedir = os.path.abspath(os.path.dirname(__file__))
SQLALCHEMY_DATABASE_URI = 'sqlite:///' + os.path.join(basedir, 'zignet.db')
SECRET_KEY = 'siesta-har-5-onkler' | Rabbit-Development/Zignet | zignet/config.py | Python | mit | 174 | [
"SIESTA"
] | af2df9d6d184a736706d4e99cbdb9806227db248b427cdc2a205bec54f497a19 |
#!/usr/bin/env python
# Copyright (c) 2011 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Downloads web pages with fillable forms after parsing through a set of links.
Used for collecting web pages with forms. Used as... | plxaye/chromium | src/chrome/tools/webforms_aggregator.py | Python | apache-2.0 | 28,920 | [
"VisIt"
] | 44ca3abe9e65c1c25418142e39c2ed6126e6e0946983abf9868db3e7716e6883 |
"""
Module to set up run time parameters for Clawpack -- AMRClaw code.
The values set in the function setrun are then written out to data files
that will be read in by the Fortran code.
"""
from __future__ import absolute_import
from __future__ import print_function
import os
import numpy as np
#-------------... | mandli/coastal | examples/geoclaw/benchmark_3/setrun.py | Python | mit | 13,811 | [
"NetCDF"
] | af9b5d56bbd2ad066df08a334568aad5065dfdeaf5a7b398791f0ecfe56646ee |
#!/bin/env python
# -*- coding: utf-8 -*-
from Sire.IO import *
from Sire.System import *
from Sire.Mol import *
from Sire.MM import *
from Sire.FF import *
from Sire.CAS import *
from Sire.Maths import *
from Sire.Analysis import *
from Sire.System import *
from Sire.Base import *
from Sire.Cluster import *
from Sire... | chryswoods/Sire | wrapper/Tools/WaterView.py | Python | gpl-2.0 | 21,873 | [
"Amber"
] | 1f3147f77dc8ed04f9b417173921311a4b15ab656c0240b6a365317062e633f2 |
"""
bace dataset loader.
"""
import os
import deepchem as dc
from deepchem.molnet.load_function.molnet_loader import TransformerGenerator, _MolnetLoader
from deepchem.data import Dataset
from typing import List, Optional, Tuple, Union
from deepchem.molnet.load_function.bace_features import bace_user_specified_f... | lilleswing/deepchem | deepchem/molnet/load_function/bace_datasets.py | Python | mit | 5,238 | [
"CRYSTAL"
] | 88e3d9ff770f0b0c88b5c71989abe9843dd3113d99fb0777b7b98055182af906 |
#pylint: disable=redefined-builtin
from __future__ import (absolute_import, division, print_function)
from six.moves import range
import re
import numpy as np
import dos.load_helper as load_helper
def parse_castep_file(file_name, ir_or_raman):
"""
Read frequencies from a <>.castep file
@param file_name... | wdzhou/mantid | scripts/Inelastic/dos/load_castep.py | Python | gpl-3.0 | 5,644 | [
"CASTEP"
] | cd62439f53db9497b676e7ca5d1a6ce52794f21d2e88595d74860d1d03202572 |
"""Rewrite assertion AST to produce nice error messages"""
from __future__ import absolute_import, division, print_function
import ast
import errno
import itertools
import imp
import marshal
import os
import re
import six
import struct
import sys
import types
import py
from _pytest.assertion import util
# pytest cac... | rmfitzpatrick/pytest | _pytest/assertion/rewrite.py | Python | mit | 36,199 | [
"VisIt"
] | d7084919d40f2f73ae522fcd4f746e97f644536bf44a6ea51570a149780f7116 |
# -*- coding: utf-8 -*-
"""
Tests for tipfy utils
"""
from __future__ import with_statement
import unittest
import werkzeug
from tipfy import RequestHandler, Request, Response, Rule, Tipfy
from tipfy.app import local
from tipfy.utils import (xhtml_escape, xhtml_unescape, json_encode,
json_decode, render_jso... | pombreda/tipfy | tests/utils_test.py | Python | bsd-3-clause | 7,382 | [
"MOE"
] | 7b4ce10c7989ae5752e52faae07482d89061ba28b14e60b0e5b32e169682cc85 |
#
# $Id: tex2libplot.py,v 1.5 2002/08/18 22:04:07 mrnolta Exp $
#
# Copyright (C) 2000 Mike Nolta <mike@nolta.net>
#
# 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 Lic... | nolta/biggles | biggles/libplot/tex2libplot.py | Python | gpl-2.0 | 11,761 | [
"Bowtie"
] | 80a21f1ff8de207fe5764dca258f7cd6e403a454a1ad540ddc401adcfe01e2fe |
# Author: Prabhu Ramachandran <prabhu_r at users dot sf dot net>
# Copyright (c) 2006, Enthought, Inc.
# License: BSD Style.
# Enthought library imports.
from traits.api import Instance
from tvtk.api import tvtk
# Local imports
from mayavi.filters.filter_base import FilterBase
from mayavi.core.pipeline_info import Pi... | dmsurti/mayavi | mayavi/filters/mask_points.py | Python | bsd-3-clause | 2,222 | [
"Mayavi",
"VTK"
] | 695ca3842abd6f3fa3467e016d9cd99e2b3dcc034b2b8d025d513157d4ae6308 |
#!/usr/bin/env python
# Copyright 2014-2019 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/prop/magnetizability/uks.py | Python | apache-2.0 | 8,171 | [
"PySCF"
] | abfa7229c1cd0735522dcafe013aaff6c87650e8957544241ca93f5a70ddb569 |
#!/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 | framework/doc/content/media/porous_flow/flux_limiters.py | Python | lgpl-2.1 | 1,187 | [
"MOOSE"
] | 524ed357eb02beb150942927fd249321570e22d0e85c7d5b1af28ba60bf8d5cf |
# -*- coding: utf-8 -*-
import pytest
from csirtg_indicator.format.ztable import Table
from csirtg_indicator.indicator import Indicator
@pytest.fixture
def indicator():
i = {
'indicator': "example.com",
'itype': 'fqdn',
'provider': "me.com",
'tlp': "amber",
... | csirtgadgets/csirtg-indicator-py | test/format/test_table.py | Python | mpl-2.0 | 937 | [
"Amber"
] | 11d386ce32a11369cc68ab3d0a7b7e911fe979b71846089478de7ccb80c17219 |
import numpy as np
from .utils.carrier import Carrier
from .utils.validation import check_random_state
def sigmoid(array, sharpness):
return 1. / (1. + np.exp(-sharpness * array))
def simulate_pac(n_points, fs, high_fq, low_fq, low_fq_width, noise_level,
high_fq_amp=0.5, low_fq_amp=0.5, random... | RPGOne/Skynet | pactools-master/pactools/simulate_pac.py | Python | bsd-3-clause | 3,602 | [
"Gaussian"
] | 9d8021fe9a78065de73d3f4191b9a50dd999ad9fefd1511ef0f3042601ce1ea8 |
import math
from chainer.functions.activation import softplus
from chainer.functions.math import exponential
from chainer.functions.math import sum
def gaussian_kl_divergence(mean, ln_var, reduce='sum'):
"""Computes the KL-divergence of Gaussian variables from the standard one.
Given two variable ``mean`` r... | rezoo/chainer | chainer/functions/loss/vae.py | Python | mit | 6,485 | [
"Gaussian"
] | e15af5d117389e57e2ba74668656088335efa7a537805652c2d617fdc697b844 |
# 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.
#
import sys
# Add path to Bio
sys.path.append('../..')
"""Dynamic Programming algorithms for general usage.
This module contains classes which imple... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/HMM/DynamicProgramming.py | Python | gpl-2.0 | 12,827 | [
"Biopython"
] | e955a784aebe4b9498a1948c909a138ba2373c2b804e1a27fa1f8d63901c47d3 |
# Cowboy: A person on the map that can move around and interact within the saloon.
# DO NOT MODIFY THIS FILE
# Never try to directly create an instance of this class, or modify its member variables.
# Instead, you should only be reading its variables and calling its functions.
from typing import Optional
from games.s... | siggame/Joueur.py | games/saloon/cowboy.py | Python | mit | 5,142 | [
"SIESTA"
] | 8b5e3b021c92e6cf7befb35c84ad036ea5af43e4efe223d31bd9faceb2238d9d |
"Helper to quickly build instruction's semantic side effects"
import inspect
import ast
import re
from future.utils import PY3
import miasm.expression.expression as m2_expr
from miasm.ir.ir import IRBlock, AssignBlock
class MiasmTransformer(ast.NodeTransformer):
"""AST visitor translating DSL to Miasm expressi... | serpilliere/miasm | miasm/core/sembuilder.py | Python | gpl-2.0 | 13,186 | [
"VisIt"
] | fc3baced219615c2227a5a5cd50ee3a62b2f1c990aa366bbedd709ae22801fd6 |
"""Contains Timing and Timer classes"""
# timing.py
# Mission Pinball Framework
# Written by Brian Madden & Gabe Knuth
# Released under the MIT License. (See license info at the end of this file.)
# Documentation and more info at http://missionpinball.com/mpf
import logging
import time
class Timing(object):
"""... | spierepf/mpf | mpf/system/timing.py | Python | mit | 8,456 | [
"Brian"
] | f9bff4c1919f478d3f2f61fa1051623d85cbcab3332ff16e0fb7b441e58bd490 |
#!/usr/bin/python3.5
# -*- coding: utf-8 -*-
# @package run_multiblast.py
# @author Sebastien Ravel
"""
The run_multiblast script
=========================
:author: Sebastien Ravel
:contact: sebastien.ravel@cirad.fr
:date: 08/07/2016
:version: 0.1
Script description
------------------
This Programme run 1 b... | sravel/scripts | local/run_multiblast.py | Python | gpl-3.0 | 8,285 | [
"BLAST"
] | 9dd9d53356b23317637740cdc660eb001b248a6a6684e533639c5cf5d3157b9b |
# Portions Copyright (c) Meta Platforms, Inc. and affiliates.
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2.
# posix.py - Posix utility function implementations for Mercurial
#
# Copyright 2005-2009 Matt Mackall <mpm@selenic.com> and others
#
# This... | facebookexperimental/eden | eden/scm/edenscm/mercurial/posix.py | Python | gpl-2.0 | 35,862 | [
"FEFF"
] | a290ac2fbeaf96fe154c701c4f50da0296ae929cfdfef5e33cb3172988257048 |
#!/usr/bin/env python
# __*__ coding: utf8 __*__
#
# This file is a part of Siesta Help Scripts
#
# (c) Andrey Sobolev, 2012
#
import numpy as np
import scipy.spatial as ss
from ngbr import model_ngbr
from vp import vp
# Functions:
def vp_vertex(pt, pbc, vc, vc_inv):
''' Finds Voronoi polihedon vertex as the c... | ansobolev/shs | shs/voronoi/numpy/voronoi.py | Python | mit | 24,014 | [
"Mayavi",
"SIESTA"
] | 3e1e39995540a4e1662d50c5a72449450ddab66f9879dbb16f3130035bb52364 |
#! /usr/bin/env python
import numpy as np
import ase.io
import ase.units as units
from matscipy.fracture_mechanics.crack import thin_strip_displacement_y
import quippy
import sys
import params
from minim import constrained_minim
def shrink_cell(atoms):
"""
Shrink Atoms cell to match min-max in every directi... | marcocaccin/MLTI | step1_TI/make_crack.py | Python | gpl-3.0 | 5,453 | [
"ASE",
"Matscipy"
] | 83d6aa63ee41cd0a19e824494bf0f026477895ebcf29ee456748976331c05eb4 |
# sql/compiler.py
# Copyright (C) 2005-2020 the SQLAlchemy authors and contributors
# <see AUTHORS file>
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Base SQL and DDL compiler implementations.
Classes provided include:
:class:`.c... | graingert/sqlalchemy | lib/sqlalchemy/sql/compiler.py | Python | mit | 147,508 | [
"VisIt"
] | fdfca26f0e1d59ea4636b03c02a5fa051db13a721035716514773d2dbc09b896 |
"""
.. module:: CXPhasing2.py
:platform: Unix
:synopsis: Implements phase retrieval algorithms.
.. moduleauthor:: David Vine <djvine@gmail.com>
"""
import os
import numpy as np
import scipy as sp
import pylab
import time
import math
import pdb
from numpy.random import uniform
import multiprocessing as mp
imp... | jbgastineau/cxphasing | cxphasing/CXPhasing2.py | Python | mit | 38,868 | [
"Gaussian"
] | ce9b10e4fa5f3a0b381dc0b0429bdb87a6bd265e1a3b74a4c4347765c0eb105b |
''' TaskManager contains WorkflowsTasks and RequestTasks modules, for managing jobs and requests tasks
'''
__RCSID__ = "$Id$"
COMPONENT_NAME = 'TaskManager'
import time, types, os
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.Security.ProxyInfo ... | miloszz/DIRAC | TransformationSystem/Client/TaskManager.py | Python | gpl-3.0 | 24,466 | [
"DIRAC"
] | 43d9cd347a589f5ca79ca095bde252cd28d157369dd8b6dd4ded7c1956577f54 |
# -*- coding: utf-8 -*-
# Generated by Django 1.11 on 2017-09-02 20:29
from __future__ import unicode_literals
import os
from graphviz import Digraph
from django.db import migrations
from django.core.files.base import ContentFile
from django.contrib.contenttypes.management import create_contenttypes
from bayesian_ne... | math-a3k/django-ai | django_ai/examples/migrations/0006_clustering_bn_example.py | Python | lgpl-3.0 | 5,210 | [
"Gaussian"
] | 04579627dd8105f42d276950c642a1ebdb189562c2138a3491106117995c48fc |
# -*- coding: utf-8 -*-
# ####################################################################
# Copyright (C) 2005-2019 by the FIFE team
# http://www.fifengine.net
# This file is part of FIFE.
#
# FIFE is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
#... | fifengine/fifengine | engine/python/fife/extensions/fife_utils.py | Python | lgpl-2.1 | 3,290 | [
"Brian"
] | d450a4f23d12455d6341f12944a5ab29f48e5f7dc0a05674c9c934b9c3536fc5 |
#
# Copyright 2012-2014 John Whitlock
#
# 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 writ... | tulsawebdevs/django-multi-gtfs | multigtfs/tests/test_feed.py | Python | apache-2.0 | 33,956 | [
"CASINO"
] | 2e5655e1a658012bc37ae41864e1d03fd746d0ce555f80a769c5895d2e2e0b3f |
import os
import csv
import luigi
import logging
import tarfile
import pandas as pd
from rdkit import Chem
from sklearn.externals import joblib
from sklearn.multiclass import OneVsRestClassifier
from sklearn.naive_bayes import MultinomialNB
from sklearn.preprocessing import MultiLabelBinarizer
from chembl_release_utils... | chembl/target_predictions | target_prediction.py | Python | apache-2.0 | 19,903 | [
"RDKit"
] | 70df907a24b69bd7c3c4dcba1371e3deb9b6da7ff2ac242aa036a7587b3f6191 |
import pylab as p
import numpy as np
import sys, time
sys.path.append("../../")
sys.path.append('../')
from channel_config import ChannelConfig
#Contour refinement functions
import matplotlib._cntr as cntr
import numpy.ma as ma
from scipy.optimize import fsolve
import scipy.optimize.lbfgsb as solver
from utils import... | singleswitch/ticker | experiments/simulations/ticker_click_noise_numerical.py | Python | mit | 45,765 | [
"Gaussian"
] | ed7aa27ff10423c8c7c945c4c90a95e47dcde811ab37d4d1569322acf4d91a92 |
#!/usr/bin/env python
# Copyright (c) 2020, Michael Boyle
# See LICENSE file for details: <https://github.com/moble/spherical_functions/blob/master/LICENSE>
"""Script and/or library to calculate optimal translation and boost from Horizons.h5
See docstrings below for more detail.
To use this function from another scr... | moble/scri | scri/SpEC/com_motion.py | Python | mit | 21,901 | [
"Psi4"
] | 7e6d128d96b6954dcec41f132d13fc32b8a1ce0a798c4715c683776511f29a05 |
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