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#!/usr/bin/env python
# ***********************************************************
# File: vasp2cif[.py]
# Description: a tool to make CIF format files out of
# VASP POSCAR+POTCAR/OUTCAR files.
# Output files acquire a .cif extension
# example: POSCAR --> POSCAR.cif
#
# ... | egplar/vasp2cif | vasp2cif.py | Python | apache-2.0 | 17,299 | [
"CRYSTAL",
"VASP"
] | a4e6655782930cae5ce9f6539aa4c6420bf391b5939563504582cac8508555bb |
#Take eigenvalues in espresso format and print
import numpy as np
from natsort import natsorted
import glob
from numpy import linalg as la
import pylab
import matplotlib.pyplot as plt
import scipy
from scipy import interpolate as ipl
import colormath
from colormath.color_objects import sRGBColor, XYZColor, AdobeRGBC... | QEF/postqe | postqe/eig2spectra.py | Python | lgpl-2.1 | 2,938 | [
"ESPResSo"
] | 2a9a4f830265a2746d88e6c09ffc3eea029177339dcedf93cab65dfe5a790b60 |
from __future__ import print_function
import sys
import vtk
from vtk.test import Testing
def load_geojson(input_string, feature_properties={}):
'''Parses input_string with vtkGeoJSONReader, returns vtkPolyData
feature_properties is a dictionary of name-default_values
to attach as cell data in the returned vtkP... | mspark93/VTK | IO/GeoJSON/Testing/Python/TestGeoJSONReader.py | Python | bsd-3-clause | 3,165 | [
"VTK"
] | bb13c6765cbce0056881e8d67c1325702ce50c106e069fc21d41a1d9470c3faa |
# Copyright 2012 Hewlett-Packard Development Company, L.P.
#
# 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 applicabl... | rahulunair/nova | nova/tests/unit/policy_fixture.py | Python | apache-2.0 | 7,114 | [
"TINKER"
] | ea8d79c7112714dcff6ac82dc81a1ceb5ca031d79942fd752dfcff2ebf3f0b47 |
from __future__ import print_function
import pytesseract
import atexit
import copy
import errno
import subprocess
import os
os.environ['TZ'] = 'US/Eastern'
from com.dtmilano.android.viewclient import ViewClient
import os.path as osp
from Tkinter import *
from PIL import Image, ImageTk
import re
import socket
import s... | kenshay/ImageScript | ProgramData/SystemFiles/Python/Lib/site-packages/spyderlib/main.py | Python | gpl-3.0 | 145,518 | [
"CRYSTAL"
] | c451ab044073d505c41c89a7e68f343697db660277e6047683e3adaeb1bcc1e1 |
#!/usr/bin/python
import sys
import os
import re
from PyQt5 import QtCore as Qc
from PyQt5 import QtGui as Qg
from PyQt5 import QtWidgets as Qw
from PyQt5 import QtWebEngineWidgets as Qwkit
INIT_URL = "https://alexandria-library.space/files/"
CDIR = os.path.dirname(os.path.realpath(__file__))
VERSION = '0.6'
class Fw... | tedlaz/qwget | src/python-qwget-0.6/qwget/qwget.py | Python | gpl-3.0 | 7,642 | [
"VisIt"
] | 1d29db3343fc0685643d6b0ad4274494ee226de06d2158220132a78e16f7a9bc |
#!/usr/bin/python
# -*- coding: utf-8 -*-
import datetime
import os.path
import socket
import psycopg2
import sys
import errno
import logging
import traceback
from netCDF4 import Dataset
import numpy
import urllib2 as urllib
# Variables de sistema
HOME_PATH = '/home/aisuser/'
APP_PATH = HOME_PATH + 'netcdf/'
BASE_PAT... | stregoika/aislib | scb_netcdf/netcdf_ais_temp.py | Python | gpl-3.0 | 10,572 | [
"NetCDF"
] | 3e52d97e6d95fba523712196fefa34c8d8bb5d873aef1878ddc723e3f9afc045 |
# ==================================================================================================
# Copyright 2011 Twitter, Inc.
# --------------------------------------------------------------------------------------------------
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use thi... | foursquare/commons-old | tests/python/twitter/common/lang/singleton_test.py | Python | apache-2.0 | 3,243 | [
"Brian"
] | 4d236ea219d787417baebcc080a5243b1e59a9fc7500befd4f1f45c3cc816882 |
"""
Functionality common to cli modules
"""
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import ga4gh.server
import ga4gh.schemas.protocol as protocol
# the maximum value of a long type in avro = 2**63 - 1
# (64 bit signed integer)
# http://avro.apache... | david4096/ga4gh-server | ga4gh/server/cli/__init__.py | Python | apache-2.0 | 1,204 | [
"pysam"
] | b674e3875d7bee5869ac93a395b7c7ad2dad4c2acd9a9c06b33ab780c089208d |
# pt_BR.po
val = {"" : "Project-Id-Version: sheltermanager\nReport-Msgid-Bugs-To: FULL NAME <EMAIL@ADDRESS>\nPOT-Creation-Date: 2013-01-24 10:55+0000\nPO-Revision-Date: 2014-01-28 19:25+0000\nLast-Translator: Júlio Cezar Santos Pires <Unknown>\nLanguage-Team: Brazilian Portuguese <pt_BR@li.org>\nMIME-Version: 1.0... | aubzen/sheltermanager | src/locale/locale_pt_BR.py | Python | gpl-3.0 | 88,857 | [
"Amber",
"VisIt"
] | 8dfb3050358d05bc769bbff23d9f36cd3937ada58a96771f21c149650c3a4b45 |
# -*- coding: utf-8 -*-
from math import sqrt, pi, acos
import gtk
import numpy as np
from ase.data import chemical_symbols as symbols
from ase.data import atomic_names as names
from ase.gui.widgets import pack
from ase.gui.languages import translate as _
def formula(Z):
hist = {}
for z in Z:
if z i... | freephys/python_ase | ase/gui/status.py | Python | gpl-3.0 | 2,287 | [
"ASE"
] | baeb9ed3921a41f60f18c12a68b49e6441dded238d7eb3949ed2e6a0a7ffae1d |
import pandas as pd
from sklearn.ensemble import RandomForestClassifier
from sklearn.ensemble import GradientBoostingClassifier
from sklearn.ensemble import BaggingClassifier
from sklearn.ensemble import AdaBoostClassifier
from sklearn.ensemble import ExtraTreesClassifier
from sklearn.neural_network import MLPClassifie... | rupakc/Kaggle-Compendium | Poker Rule Induction/poker-baseline.py | Python | mit | 2,761 | [
"Gaussian"
] | 0babe9810879c0bb917730b4f14ee1c295a0bdb64991d4e1c0179f9ab9086346 |
import numpy as np
import batoid
from .utils import bilinear_fit, fieldToDirCos
def _reciprocalLatticeVectors(a1, a2, N):
norm = 2*np.pi/(a1[0]*a2[1] - a1[1]*a2[0])/N
b1 = norm*np.array([a2[1], a2[0]])
b2 = norm*np.array([a1[1], a1[0]])
return b1, b2
def dkdu(
optic, theta_x, theta_y, wavelengt... | jmeyers314/jtrace | batoid/analysis.py | Python | bsd-2-clause | 29,548 | [
"Gaussian"
] | e99289f49514b1d603f3e53544ee9af13d586e8601b651229d47b1ff58d57980 |
# This code is meant to be run after loading the model in 'Axon.g'.
# 'Axon.g' loads 2 identical copies of an linear, passive neuron.
#
# These are helper functions to scale passive parameters Cm, Rm, Ra,
# diameter and length. By default the second copy ('/axon1') is
# modified.
#
# After scaling a passive parameter, ... | BhallaLab/moose-thalamocortical | DEMOS/axon-passive/Axon.py | Python | lgpl-2.1 | 1,610 | [
"MOOSE",
"NEURON"
] | 0141916f4cbd95b55acf1c29d5bd4d4a3f9b0da6a33c3f0418eebfe9f0275187 |
# Authors:
# Martin Kosek <mkosek@redhat.com>
# Pavel Zuna <pzuna@redhat.com>
#
# Copyright (C) 2010 Red Hat
# see file 'COPYING' for use and warranty information
#
# 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 Fr... | hroncok/freeipa | ipalib/plugins/dns.py | Python | gpl-3.0 | 168,403 | [
"VisIt"
] | 0134bf03633490be6874a1d4ffdf2a18880abee752daa8a5a901e9d727bff460 |
""" This module loads all the classes from the VTK Hybrid library into
its namespace. This is an optional module."""
from vtkHybridPython import *
| b3c/VTK-5.8 | Wrapping/Python/vtk/hybrid.py | Python | bsd-3-clause | 149 | [
"VTK"
] | f2898ac3affe12d1ab0772f6e1d009cc174f58f31232510503c4eb07898d2153 |
#!/home/paulk/software/bin/python
from __future__ import division
from sys import argv,exit,stderr
from subprocess import Popen,PIPE
from key_functions import parse_lines
import pysam
f = open(argv[1])
t = pysam.Tabixfile("resources/Homo_sapiens.GRCh37.66.gtf.gz")
for row in f:
if row[0] == 'u': continue
l = row.st... | polarise/RP-python | add_exons_to_flanking_intron_file.py | Python | gpl-2.0 | 617 | [
"pysam"
] | 902efacb1999d932f03764573169c0212cc137ff105c4fb62ac984de6961960f |
from os.path import exists, join
import shutil
import tempfile
import time
from pulsar.managers.queued import QueueManager
from pulsar.managers.stateful import StatefulManagerProxy
from pulsar.tools.authorization import get_authorizer
from .test_utils import TestDependencyManager
from galaxy.util.bunch import Bunch
f... | jmchilton/pulsar | test/persistence_test.py | Python | apache-2.0 | 1,535 | [
"Galaxy"
] | 47b5efdaa71d0dbbe05118eb4e84af035cd4a6e795a7b8b3d37474470a3150da |
#!/usr/bin/env python
# Copyright 2015 The Kubernetes Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appli... | ingvagabund/contrib | hack/verify-flags-underscore.py | Python | apache-2.0 | 8,924 | [
"VisIt"
] | aa029b48b73e80e4a118b1b0ebd148b4d5398898efdca56a7a85af7b94d7c34d |
#!/usr/bin/env python
#
# uses meshio:
# https://github.com/nschloe/meshio
#
# install with:
# pip install -U meshio
#
# this script reads in a Gmsh file (in Gmsh-ASCII format) and outputs SPECFEM-readable mesh files
#
# Boundary surfaces must be defined prior when generating the mesh as Physical Surfaces in Gmsh.
... | geodynamics/specfem3d | utils/Cubit_or_Gmsh/Gmsh2specfem.py | Python | gpl-3.0 | 28,443 | [
"VTK"
] | 2d3e1642cc7e1c0d37547ff89f148115bc0eebea51941ab038a81cb87c91a21a |
import os
from pymatgen.io.vasp.inputs import Incar
from twod_materials.stability.startup import get_magmom_string, INCAR_DICT
def run_major_axis_anisotropy_calculations(submit=True):
"""
Perform static calculations with the magnetic axis along
100, 010, and 001.
Kwargs:
submit (bool): Whet... | ashtonmv/twod_materials | twod_materials/magnetism/startup.py | Python | gpl-3.0 | 2,063 | [
"VASP",
"pymatgen"
] | 8283de5ccef8df6f507a936a8c0cd403cd84cc5a9809f9b1de54563af42eadff |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import warnings
"""
Created on Mar 19, 2012
"""
__author__ = "Shyue Ping Ong, Stephen Dacek"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep@... | materialsproject/pymatgen | pymatgen/entries/tests/test_compatibility.py | Python | mit | 86,846 | [
"pymatgen"
] | 4406934d45aa427d2a1ecb697946e6302fee6bd2a04f9dcfc167c4beea5b44d8 |
""" :mod: DErrno
==========================
.. module: DErrno
:synopsis: Error list and utilities for handling errors in DIRAC
This module contains list of errors that can be encountered in DIRAC.
It complements the errno module of python.
It also contains utilities to manipulate these err... | Andrew-McNab-UK/DIRAC | Core/Utilities/DErrno.py | Python | gpl-3.0 | 11,641 | [
"DIRAC"
] | 5cfffdcddd84976c0a22928c35f005c738e2327d9a47278fc6be7505d551da42 |
from operator import attrgetter
import numpy as np
from neupy.utils import format_data
from neupy.exceptions import StopTraining
from neupy.algorithms.base import BaseNetwork
from neupy.core.properties import (NumberProperty, ProperFractionProperty,
IntProperty)
__all__ = ('Growin... | itdxer/neupy | neupy/algorithms/competitive/growing_neural_gas.py | Python | mit | 14,513 | [
"NEURON"
] | e76fc8dd2c5aaff77d1aa10315b7e25f3d195eb93f170f1e01559562bc802cc3 |
"""
Integrates download callbacks with an external mainloop.
While things are being downloaded, Zero Install returns control to your program.
Your mainloop is responsible for monitoring the state of the downloads and notifying
Zero Install when they are complete.
To do this, you supply a L{Handler} to the L{policy}.
"... | slovenwd/0install | zeroinstall/injector/handler.py | Python | lgpl-2.1 | 9,362 | [
"VisIt"
] | ee6556dbdc46a79881227248cab1fc55598cea21a6c174af0dc555816cba3b36 |
#!/usr/bin/env python
'''
Online example from :
http://www.vtk.org/Wiki/VTK/Examples/Python/Graphs/EdgeWeights
Going to heavly comment out the steps to understand how to edit
this into what we need to make other graphs
'''
import vtk # Manditory on all python VTK
import random
g = vtk.vtkMutableUndirecte... | espinm2/interactive-vtk | pysrc/NonPlanarGraph.py | Python | mit | 1,328 | [
"VTK"
] | c3d161fcc8cbeb59a444721615394b5b32c310a0f9717efc5e6b4927a624b5f3 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for Student's Profile Page.
"""
from flaky import flaky
from contextlib import contextmanager
from datetime import datetime
from bok_choy.web_app_test import WebAppTest
from nose.plugins.attrib import attr
from ...pages.common.logout import LogoutPage
from ...pages.lms.acc... | Shrhawk/edx-platform | common/test/acceptance/tests/lms/test_learner_profile.py | Python | agpl-3.0 | 31,732 | [
"VisIt"
] | a6ee851dcedcd523c187dfc22db5649f91ee735dc60ec5b1b9581f340a6f21a0 |
""" The MJF utility calculates the amount of wall clock time
left for a given batch system slot or VM. This is essential for the
'Filling Mode' where several jobs may be executed in the same slot.
Machine Job/Features are used following HSF-TN-2016-02 if available.
Otherwise values are filled in using ... | chaen/DIRAC | Core/Utilities/MJF.py | Python | gpl-3.0 | 6,573 | [
"DIRAC"
] | 2bd8d3dc035bf84eaf1341d41dd010be56c413e4b34f929d190871cb3465d6db |
# -*- coding: utf-8 -*-
"""
Applied Mathematics for Computer Science.
Homework1 -- Curve Fitting.
@author: LiBin 11531041
@date: 2016 - 5 - 23.
"""
import numpy as np
import matplotlib.pyplot as plt
# Function of computing the regression parameters
def Compute_PolyCurFit( x, y, M, par_lambda ):
... | tracer9/Applied_Math | Homework_1.py | Python | apache-2.0 | 4,623 | [
"Gaussian"
] | a2b2d5a4cf3b0ed7b53870160669372ec913d1dd1a4ef20fbc2b8c2e19a19ce7 |
# Author: Travis Oliphant, 2002
#
# Further updates and enhancements by many SciPy developers.
#
from __future__ import division, print_function, absolute_import
import math
import warnings
from collections import namedtuple
import numpy as np
from numpy import (isscalar, r_, log, sum, around, unique, asarray,
... | raoulbq/scipy | scipy/stats/morestats.py | Python | bsd-3-clause | 82,440 | [
"Gaussian"
] | 707da7c761af62eb8a4a2d2ab337269e29f43a78cc9145190e4c7ff2e46a00f2 |
# From https://bitbucket.org/arjones6/sphinx-numfig/
from docutils.nodes import figure, caption, Text, reference, raw, SkipNode, Element
from sphinx.roles import XRefRole
# Element classes
class page_ref(reference):
pass
class num_ref(reference):
pass
# Visit/depart functions
def skip_page_ref(self, nod... | mhunter1/OpenMx | docs/source/ext/numfig.py | Python | apache-2.0 | 3,328 | [
"VisIt"
] | 675f2255576bc8ee9f61583fb0d303a8cafc2e23efa6f6f746f177ee2e57132c |
# -*- Mode: python; coding: utf-8 -*-
from __future__ import division, print_function
#from __future__ import with_statement
LAYOUT_ALGORITHM = 'neato' # ['neato'|'dot'|'twopi'|'circo'|'fdp'|'nop']
REPRESENT_CHANNELS_AS_NODES = 1
DEFAULT_NODE_SIZE = 1.0 # default node size in meters
DEFAULT_TRANSMISSIONS_MEMORY = 5 # ... | named-data-ndnSIM/ns-3-dev | src/visualizer/visualizer/core.py | Python | gpl-2.0 | 71,202 | [
"FLEUR"
] | 6a375bd519625aeb03216ab6e168dda4759942153c4de5ac29b3ffe825bccb34 |
"""
===================================
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... | DailyActie/Surrogate-Model | 01-codes/scikit-learn-master/examples/neighbors/plot_kde_1d.py | Python | mit | 5,103 | [
"Gaussian"
] | 8713965ed4eb323cc0098c643e19dc99f6524144e30b385c8b9b836519af4b2b |
# -*- coding: utf-8 -*-
"""Implementation of execution-related magic functions."""
# Copyright (c) IPython Development Team.
# Distributed under the terms of the Modified BSD License.
import ast
import bdb
import builtins as builtin_mod
import gc
import itertools
import os
import shlex
import sys
import time
import ... | unnikrishnankgs/va | venv/lib/python3.5/site-packages/IPython/core/magics/execution.py | Python | bsd-2-clause | 53,438 | [
"VisIt"
] | e2b7221537f1caced114b661e50d9e21622b6d37bd9328d215f0e8d003d913ed |
# Copyright 2014-2020 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | sunqm/pyscf | pyscf/agf2/ragf2_slow.py | Python | apache-2.0 | 8,709 | [
"PySCF"
] | d2c2dd20429594087c1b9196db35626d2b69ad878f9a70a6044206d50289287b |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | TheTimmy/spack | var/spack/repos/builtin/packages/r-nlme/package.py | Python | lgpl-2.1 | 1,662 | [
"Gaussian"
] | d80196aa80b3395ae12c895ce7bbd7cff164c362748b69d6e051e5f75dc57fa8 |
#!/usr/bin/env python
# Copyright 2012 Google Inc. All Rights Reserved.
"""Tests for grr.lib.objectfilter."""
import unittest
from grr.lib import objectfilter
attr1 = "Backup"
attr2 = "Archive"
hash1 = "123abc"
hash2 = "456def"
filename = "boot.ini"
class DummyObject(object):
def __init__(self, key, value):
... | MiniSEC/GRR_clone | lib/objectfilter_test.py | Python | apache-2.0 | 17,281 | [
"Desmond"
] | 540aef7660976a7b718e72972c1c03eb4243dc983f95f772bf4208925dc24715 |
"""
Process an input dataset into a format suitable for machine learning.
"""
from __future__ import division
from __future__ import unicode_literals
import os
import gzip
import pandas as pd
import numpy as np
import csv
import numbers
import tempfile
from rdkit.Chem import rdmolfiles
from rdkit.Chem import rdmolops
f... | Agent007/deepchem | deepchem/data/data_loader.py | Python | mit | 10,562 | [
"RDKit"
] | dce0bd527ad52798015eccdaa2f429ecbbd177bf16319a7ed35cf2a038c6353f |
"""
Provides analysis of site symmetries.
"""
import numpy as np
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer as sga
from pymatgen.core.operations import SymmOp
def get_site_symmetries(struc, precision=0.1):
"""
Get all the point group operations centered on each atomic site
in the form [[po... | mbkumar/pymatgen | pymatgen/symmetry/site_symmetries.py | Python | mit | 2,982 | [
"pymatgen"
] | 9314d2093c84ae4d6d63fdcff2cc4bf5ca4850b5f985dd12eedf1f31e01f5a0a |
# -*- coding: utf-8 -*-
# graphutil.py ---
#
# Filename: graphutil.py
# Description:
# Author: Subhasis Ray
# Maintainer:
# Created: Sun Mar 18 13:42:28 2012 (+0530)
# Version:
# Last-Updated: Wed Mar 28 18:27:26 2012 (+0530)
# By: subha
# Update #: 103
# URL:
# Keywords:
# Compatibility:
#
#
# Commentar... | dharmasam9/moose-core | python/moose/graphutil.py | Python | gpl-3.0 | 5,869 | [
"MOOSE"
] | db0e973681970e8cd7131df18d317ab844d44e9b5adfd5ea676014da8a13c480 |
# -*- coding: utf-8 -*-
"""
pyflot.graph
This module implements the main classes.
:copyright: (c) 2011 by Brian Luft
:license: MIT, see LICENSE for more details.
"""
import collections
from datetime import date
from functools import partial
from itertools import chain
import inspect
import json
impor... | unbracketed/python-flot-utils | pyflot/graph.py | Python | mit | 6,335 | [
"Brian"
] | 7e820fce4cee005f2e33f207d3370e2a7d4bd03c23a04795c2feb2a19f1e1f77 |
#!/usr/bin/env python
# Copyright 2017 Battelle Energy Alliance, 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 appl... | idaholab/raven | scripts/copy_plugins_tests.py | Python | apache-2.0 | 1,982 | [
"MOOSE"
] | eed91f783e955245fe76b67c1050c65694f30178f977e0e5d440a73149979fdf |
# Copyright 2010-2017, The University of Melbourne
# Copyright 2010-2017, Brian May
#
# This file is part of Karaage.
#
# Karaage 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... | brianmay/karaage | karaage/projects/urls.py | Python | gpl-3.0 | 2,344 | [
"Brian"
] | 898617aa4c21877c441aef0608ad1101b72302af9131645d73aca71671cad6f6 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# create pipeline
#
leader = vtk.vtkLeaderActor2D()
leader.GetPositionCoordinate().SetCoordinateSystemToNormalizedViewport()
leader.GetPositionCoordinate().SetValue(0.1, 0.1... | hlzz/dotfiles | graphics/VTK-7.0.0/Rendering/Core/Testing/Python/TestLeaderActor2D.py | Python | bsd-3-clause | 2,074 | [
"VTK"
] | 03b9375eb5193b1ae2e95a236ae50a8cffecb7cccd6f3cc3010710b46e79ac73 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 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
#... | dgasmith/psi4 | psi4/driver/qcdb/dbwrap.py | Python | lgpl-3.0 | 174,506 | [
"Gaussian",
"Psi4",
"PyMOL"
] | 178bd107f75057a2052977382f54a40ff843c32ce64a733d90d6d592e0a759c3 |
#!/usr/bin/env python -u
# Take the Gaussian components and use them to examine the gas characteristics at each position.
#
# Author James Dempsey
# Date 26 Mar 2017
from __future__ import print_function, division
import argparse
import csv
import datetime
import glob
import math
import os
import re
from string im... | jd-au/magmo-HI | examine_gas.py | Python | apache-2.0 | 49,896 | [
"Gaussian"
] | 9f937c51bebe8e5fe17a4462bf466f51a28a78940264f5fbeb096122be6380e4 |
# Copyright (C) 2004-2008 Paul Cochrane
#
# 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 later version.
#
# This program is distribut... | paultcochrane/pyvisi | examples/imageOnPlane.py | Python | gpl-2.0 | 3,538 | [
"VTK"
] | c51ea76aec58db16a8adfabba59c86e81f3421f0a1b06f467a6562a32db73b01 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import os
import warnings
from pymatgen.apps.borg.hive import VaspToComputedEntryDrone, \
SimpleVaspToComputedEntryDrone, GaussianToComputedEntryDrone
from pymatgen.entries.computed_entrie... | mbkumar/pymatgen | pymatgen/apps/borg/tests/test_hive.py | Python | mit | 4,773 | [
"pymatgen"
] | e80d120ad2e2d65156328e0544ad3ef0c25d9c0da8090592e6abea00ab8b1a0b |
#!/usr/bin/env python
# vim: set fileencoding=utf-8 ts=8 sw=4 tw=0 :
# Copyright (c) 2017 Tiziano Müller <tiziano.mueller@chem.uzh.ch>.
#
# 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 ... | dev-zero/cp2k-tools | cp2k_tools/generator/cli.py | Python | apache-2.0 | 1,081 | [
"CP2K"
] | 6c32ee29936de10c62a371e782099374fe774949fb58c32afaa70da155d10b58 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkOutlineSource(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.... | nagyistoce/devide | modules/vtk_basic/vtkOutlineSource.py | Python | bsd-3-clause | 473 | [
"VTK"
] | a1218735c9c864b48272522ff2a54a22c26e921447bd202ed36bb1235a4d32d9 |
"""
This tools copied from biean.hearing and aim for creating filters coefficient.
Unilike biran cascade of filter are represented like matlab sosfilter and scipy (>0.15) sos filter:
dim = (ncascade x 6) = (ncascade x [b0, b1, b2, a0, a1, a2])
In case of multiple channel the filter is
dim = (nchannel x ncascade x 6)... | samuelgarcia/HearingLossSimulator | hearinglosssimulator/filterfactory.py | Python | mit | 4,508 | [
"Brian"
] | 545e62e13727ab9a1dad0d572dc77fe56dfe3389009d987a079b74ba6d188c98 |
"""Download DayMet data in a box and convert it to Amanzi-style HDF5.
DayMet is downloaded in box mode based on lat-lon bounds, then converted to
hdf5 files that ATS knows how to read.
"""
import requests
import datetime
import logging
import h5py, netCDF4
import sys, os
import numpy as np
VALID_YEARS = (1980,2018)
... | amanzi/ats-dev | tools/utils/daymet_to_ats_box.py | Python | bsd-3-clause | 9,515 | [
"NetCDF"
] | 1c4874a6023ba14816e93f6c564648193fe0d9b33fdd633892ea26b0051f2334 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkPlaneSource(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vt... | nagyistoce/devide | modules/vtk_basic/vtkPlaneSource.py | Python | bsd-3-clause | 469 | [
"VTK"
] | d62489a2e3122f4309535ad9d739c32b44df3b1e6600bc87857494cc2d31c295 |
# $HeadURL$
__RCSID__ = "$Id$"
from DIRAC.FrameworkSystem.private.logging.Logger import Logger
from DIRAC.FrameworkSystem.private.standardLogging.LoggingRoot import LoggingRoot
# old logging system
# gLogger = Logger()
# new logging system
gLogger = LoggingRoot()
def getLogger():
return gLogger
| Andrew-McNab-UK/DIRAC | FrameworkSystem/Client/Logger.py | Python | gpl-3.0 | 302 | [
"DIRAC"
] | 1f110e709596eb1e5ebc38e77ebda6660f8c0cc516ea6b2beb59d41a0c3ca77b |
import json
import io
from bcpp_referral.referral import Referral
from decimal import Decimal
from django.apps import apps as django_apps
from django.test import TestCase
from django.utils import timezone
from edc_constants.constants import YES
from edc_metadata.models import CrfMetadata, RequisitionMetadata
from edc_... | botswana-harvard/bcpp-subject | bcpp_subject/tests/create_bhs_members.py | Python | gpl-3.0 | 9,813 | [
"VisIt"
] | eacceefead1a141511a6a95a57785e11d7233a3c504a917f0cb661785a657351 |
# coding=utf-8
# Copyright 2018 The Google AI Language Team Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by ... | google-research/language | language/bert_extraction/steal_bert_qa/data_generation/preprocess_thief_dataset_squad.py | Python | apache-2.0 | 6,656 | [
"Gaussian"
] | 9657c3cca5c87e79ed57f9576a1664a5053ec53b6993e77e269b8f90637ecd6c |
#
# @BEGIN LICENSE
#
# pylibefp/wrapper/exceptions.py:
#
# Copyright (c) 2017-2019 The Psi4 Developers
#
# All rights reserved. Use of this source code is governed by a
# BSD-style license that can be found in the LICENSE file.
#
# @END LICENSE
#
"""Module with non-generic exceptions classes."""
from . import e... | loriab/pylibefp | pylibefp/exceptions.py | Python | bsd-3-clause | 2,071 | [
"Psi4"
] | aa52438dd637285d9309fd0660882443478644cbe8bfb46511da8019a77525bf |
# coding=utf-8
"""Descriptors, factory classes etc for the Radiance library."""
import warnings
import os
try:
basestring
from collections import Iterable
except NameError:
basestring = str
from typing import Iterable
__all__ = ['RadiancePath', 'RadianceNumber', 'RadianceBoolFlag',
'Radiance... | ladybug-tools/honeybee | honeybee_plus/radiance/datatype.py | Python | gpl-3.0 | 32,641 | [
"EPW"
] | 714d219d2dd0fe5053be7581b5d60d4ee0b41f58418c8d1574b3272073758871 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | kkreis/espressopp | src/integrator/VelocityVerlet.py | Python | gpl-3.0 | 1,806 | [
"ESPResSo"
] | 4fe35087f70faee8c8e38f9d0901b9d42fa189511b740294f1d1823b94f16282 |
# Gaussian mixture model using PyMC3
# Based on https://github.com/aloctavodia/BAP/blob/master/code/Chp6/06_mixture_models.ipynb
import superimport
import pymc3 as pm
import numpy as np
import scipy.stats as stats
import pandas as pd
import theano.tensor as tt
import matplotlib.pyplot as plt
import arviz as az
import... | probml/pyprobml | scripts/gmm_chooseK_pymc3.py | Python | mit | 3,503 | [
"Gaussian"
] | 5a5cc6dcf41cbaf6e40c4f25843a3864d362bcc416a07b556736df87801d4d85 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
#
#
# 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... | fernandezcuesta/ansible | lib/ansible/modules/network/avi/avi_snmptrapprofile.py | Python | gpl-3.0 | 3,396 | [
"VisIt"
] | 6afcf70add765c12593236b23a37305c4a3d404e8f93fe0a4edbb506f1c4c823 |
"""
Migration 35
- Remove builtin damage patterns and target profiles from the database
"""
import sqlalchemy
dmgPatterns = (
'Uniform',
'[Bombs]Concussion Bomb',
'[Bombs]Electron Bomb',
'[Bombs]Scorch Bomb',
'[Bombs]Shrapnel Bomb',
'[Exotic Plasma]Baryon',
'[Exotic Plasma]Meson',
'[... | DarkFenX/Pyfa | eos/db/migrations/upgrade35.py | Python | gpl-3.0 | 5,614 | [
"Jaguar"
] | 49a075711719eb35b36cbb178dce25b38d7d2a9013bd7fac1ccb65cbb3708e4a |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
class Migration(migrations.Migration):
dependencies = [
('visit', '0075_visit_created'),
]
operations = [
migrations.AddField(
model_name='staff',
name='secon... | koebbe/homeworks | visit/migrations/0076_staff_secondary_schools.py | Python | mit | 456 | [
"VisIt"
] | 5df3cef4264edca876a39394aeb5b750a846ec4147bc68ad40f3bb4eab9ed063 |
#!/usr/bin/env python
oneline = "writing pp-data in vtk format automatically, saving memory"
docstr = """this is the docstr of LIGGGHTSPostProcessing"""
from dump import dump
from math import floor
from math import ceil
import vtk
import glob
import multiprocessing
import sys
import time
import os
import exceptions
... | CFDEMproject/LPP | src/lpp.py | Python | gpl-2.0 | 7,656 | [
"VTK"
] | 2bfec4b6bfd983da6049dd6cfc084dcb9cc89bc1734a5a04f49657fab747853c |
__version_info__ = ('0', '2', '0')
__version__ = '.'.join(__version_info__)
__author__ = "Brian O'Connor"
__license__ = 'MIT'
__copyright__ = "(c) 2015 by Brian O'Connor"
import logging
from flask import current_app, _app_ctx_stack as stack
from flask.ext.login import current_user
__all__ = ['FeatureManager']
log ... | btoconnor/flask-feature | flask_feature.py | Python | mit | 1,408 | [
"Brian"
] | 44e305a1ee9be9b3076a9fd0662437abe36f9dd51d8ba105d0ab9c695fa1e465 |
#! coding: utf-8
import copy
import inspect
import sys
from sqlalchemy import exc
from sqlalchemy import sql
from sqlalchemy import testing
from sqlalchemy import util
from sqlalchemy.sql import column
from sqlalchemy.sql.base import DedupeColumnCollection
from sqlalchemy.testing import assert_raises
from sqlalchemy.... | wujuguang/sqlalchemy | test/base/test_utils.py | Python | mit | 86,279 | [
"MOE"
] | 5198ad7364eb6dead210ffc3589e668121adeb0f841ba15af436aecbe062508e |
import sys
import os
import glob
import yt
import numpy as np
from numpy import *
import astropy
from astropy.cosmology import Planck13 as cosmo
import findGalaxyProps as fGP
def _stars(pfilter, data):
return data[(pfilter.filtered_type, "particle_type")] == 2
#this gets dark matter particles in zoom region only... | gsnyder206/vela-yt-sunrise | enzoGalaxyProps.py | Python | gpl-3.0 | 5,983 | [
"Galaxy"
] | 3f8365dbc4a721efac1015827ed52be8ea7e1fd4a98af27f3c00ff8d710d019b |
# $HeadURL: $
''' ResourceStatusClient
Client to interact with the ResourceStatusDB.
'''
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.DISET.RPCClient import RPCClient
#from DIRAC.ResourceStatusSystem.DB.ResourceStatusDB impo... | Sbalbp/DIRAC | ResourceStatusSystem/Client/ResourceStatusClient.py | Python | gpl-3.0 | 20,832 | [
"DIRAC"
] | f0d3f6a74f5bbbf6e23eb21af2a3eb236f7ef1e5d3d5dfb9a6cce5322069f461 |
#!/usr/bin/env python
# Copyright 2014-2018 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... | sunqm/pyscf | pyscf/pbc/cc/test/test_kuccsd.py | Python | apache-2.0 | 11,351 | [
"PySCF"
] | 97f92224c3cc16b12e5a82113d6aeea2b9f9539c4e7bcea6fa8e32df6eba286b |
#!/usr/bin/python
from __future__ import print_function
import os, sys
PRII='priism-4.2.7'
PRI_DIR=os.path.expanduser('~')
if sys.platform == 'darwin':
if os.path.exists('/Applications/%s' % PRII):
PRI_DIR='/Applications'
elif os.path.exists(os.path.expanduser('~/%s' % PRII)):
PRI_DIR=os.path.... | macronucleus/chromagnon | Chromagnon/PriCommon/priismCommands.py | Python | mit | 6,042 | [
"Gaussian"
] | 9f54225d0305f0b8725b1feb05a40370a80054425e67225534c870536c54d1cf |
""" Test class for Job Cleaning Agent
"""
# imports
from __future__ import absolute_import
import pytest
from mock import MagicMock
# DIRAC Components
from DIRAC.WorkloadManagementSystem.Agent.JobCleaningAgent import JobCleaningAgent
from DIRAC import gLogger
gLogger.setLevel('DEBUG')
# Mock Objects
mockReply = Mag... | fstagni/DIRAC | WorkloadManagementSystem/Agent/test/Test_Agent_JobCleaningAgent.py | Python | gpl-3.0 | 5,700 | [
"DIRAC"
] | 50a7b3d015e0a22aefcc415fc271be249a34be66e53d9fcbeabe4786a83c3669 |
import numpy as np
from srxraylib.plot.gol import plot
import scipy.constants as codata
#inputs BM18-EBS
distance_bm = 180.0 # 220.0
beta_bm = 1.814
eta_bm = 0.018
#inputs ID19-EBS
distance_und = 155.0
beta_und = 6.9
eta_und = 0.0017
undulator_length = 2.0
#inputs ID19-ESRF
distance_und_present = 155.0
beta_und_pr... | srio/shadow3-scripts | bm18_coherence_length.py | Python | mit | 3,233 | [
"Gaussian"
] | a4bdd2756fb1cd38d4a6616f5df7ff17dcdb050de2272a5185086d7ff679c799 |
# -*- coding:Utf-8 -*-
"""
.. currentmodule:: pylayers.network.network
Node Class
==========
.. autoclass:: Node
:members:
Network Class
==============
.. autoclass: Network
:members:
PNetwork Class
==============
SimPy Process compliant version of the Network class
.. autoclass:: PNetwork
:members... | pylayers/pylayers | pylayers/network/network.py | Python | mit | 63,263 | [
"Mayavi"
] | 38e4f89a86d18505112db07a6209f512da1b998106b8dea7343e4e648c8482cf |
# Copyright (C) 2010-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | hmenke/espresso | testsuite/python/lb.py | Python | gpl-3.0 | 9,910 | [
"ESPResSo"
] | 44cc20f4b24b16ceef3f67d71ee10c5ba8e837a6cd483d45e8d884994b6b0afb |
#
# @file TestSyntaxChecker.py
# @brief SyntaxChecker unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Sarah Keating
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatically by converting the file lo... | TheCoSMoCompany/biopredyn | Prototype/src/libsbml-5.10.0/src/bindings/python/test/sbml/TestSyntaxChecker.py | Python | bsd-3-clause | 4,304 | [
"VisIt"
] | e2f5c0caaab669f83f1d0e3a56962862a0cd89510d3bfb52e3079b85528642e0 |
# -*- coding: utf-8 -*-
# Copyright 2007-2021 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at... | erh3cq/hyperspy | hyperspy/tests/component/test_components.py | Python | gpl-3.0 | 24,341 | [
"Gaussian"
] | c6367a4682357fae0efb2b8b8452caba52b9e439f4fbb6f4b0f7ceb78fa085ec |
import urllib.request as ur
import urllib.parse as up
import json
serviceurl = "http://python-data.dr-chuck.net/geojson?"
# This API only accepts the university in a list of its accepted ones.
# This API uses the same parameters (sensor and address) as the Google API.
# This API also has no rate limit so you can test... | crookedreyes/py4e-specialization | course-3/chapter-13/assing2-week6.py | Python | lgpl-2.1 | 998 | [
"VisIt"
] | e3f54075aef81591f9ef8e141ec62b921493c59be0c67d6226359acafb0c4f49 |
""" Visualization demonstrating extending an existing plot class and adding
additional functionality on top.
"""
from plots.value_plot import ValuePlot
from plots.base_plot import registered_plot
@registered_plot
class DogePlot(ValuePlot):
""" DogePlot class. Same as ValuePlot except for some text drawn on top.... | chairmanmeow50/Brainspawn | brainspawn/plots/dogeplot.py | Python | bsd-3-clause | 1,613 | [
"NEURON"
] | 3e50611fa89a4a45d7faac164ee493fd6d4601e645c1b5cd260eb05fd7e2fa37 |
# -*- coding: utf-8 -*-
""" Qt Standalone Layout editor
.. automodule::
:members:
"""
import sys, os, random
if 'QT_API' in os.environ:
if os.environ['QT_API'] != 'pyqt':
saveQTAPI = os.environ['QT_API']
os.environ['QT_API'] = 'pyqt'
else:
saveQTAPI = ''
os.environ['QT_API'] = 'pyq... | dialounke/pylayers | pylayers/gui/editor.py | Python | mit | 51,243 | [
"Mayavi"
] | 86d4050071cc5a5fa238d1ab9da5eaa78777a53a61bae4e09d8821b520703b92 |
# (c) 2014, Brian Coca, Josh Drake, et al
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
... | opoplawski/ansible | lib/ansible/plugins/cache/base.py | Python | gpl-3.0 | 1,495 | [
"Brian"
] | 57d2abc8760cc8ad6ba72dee5b9078cf561fe60815b1188bbdc98f1b200c734e |
# -*- coding: utf-8 -*-
"""Utility functions for plotting M/EEG data."""
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Denis Engemann <denis.engemann@gmail.com>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Eric Larson <larson.eric.d@gmail.com>
# Mainak Jas <mainak... | cjayb/mne-python | mne/viz/utils.py | Python | bsd-3-clause | 129,999 | [
"Mayavi"
] | d6ec3dea64f0b7d66481ca4099addabf728c6e6d08a07cdc66239961f9685c35 |
########################################################################
# File : StalledJobAgent.py
########################################################################
""" The StalledJobAgent hunts for stalled jobs in the Job database. Jobs in "running"
state not receiving a heart beat signal for more than stalle... | vmendez/DIRAC | WorkloadManagementSystem/Agent/StalledJobAgent.py | Python | gpl-3.0 | 20,169 | [
"DIRAC"
] | db12366813c916a810016aa8b703c12d5e99bcf66d3cfba923b93b1a568782b0 |
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Mathieu Blondel <mathieu@mblondel.org>
# Olivier Grisel <olivier.grisel@ensta.org>
# Andreas Mueller <amueller@ais.uni-bonn.de>
# Eric Martin <eric@ericmart.in>
# Giorgio Patrini <giorgio.patrini@anu.edu.au>
# Lic... | ClimbsRocks/scikit-learn | sklearn/preprocessing/data.py | Python | bsd-3-clause | 69,939 | [
"Gaussian"
] | 1a4f16650ffa0031c8e7ae5f22a241d1ec4e2ae0adc1a7d9605dd777e07964a4 |
# -*- coding: utf-8 -*-
'''
Created on Aug 23, 2013
@author: shywel
'''
#===============================================================================
# QUIZ
#
# # Define a procedure, is_friend, that takes
# # a string as its input, and returns a
# # Boolean indicating if the input string
# # is the name of a frie... | shywel/gateando-python | src/courses/search-engine/es/lesson-2/MoreFriends.py | Python | gpl-3.0 | 1,605 | [
"MOE"
] | 5cd547f4e16393d8019f53d7775624be16e1123ba6305601bc7f90ceb9002375 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
File: CIRCfinder.py
Author: Xiao-Ou Zhang
Email: kepbod@gmail.com
Github: https://github.com/kepbod
Description: A pipeline to map junction reads for circular intronic RNAs (ciRNAs)
"""
import sys
import argparse
import os
import os.path
import subprocess
import loggi... | JinfengChen/CIRCfinder | CIRCfinder.py | Python | mit | 4,692 | [
"Bowtie"
] | 8ce8b839c0eb569be732c0a6f22d7a6fcc66b31d16bf56a9aee3685fb8d47731 |
#* 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
| harterj/moose | python/peacock/PostprocessorViewer/plugins/__init__.py | Python | lgpl-2.1 | 308 | [
"MOOSE"
] | 8afd79f04e21e586f4fb6b8e26932b330d4a6b4b4790c540e86e77c522cec726 |
import os.path
import numpy as np
import itertools
# This python module is containing definitions useful for
# generating test patterns.
import Tools
# This function is generating patterns for an addition
def writeTests(config,format):
# In this test, we can use the same inputs for several tests.
# For insta... | JonatanAntoni/CMSIS_5 | CMSIS/DSP/Testing/PatternGeneration/Example.py | Python | apache-2.0 | 3,493 | [
"Gaussian"
] | 8ae93dc94f57a11de13bb0c4816abdd4ebd563fcdbdcaa96e8a37f2ef85b33c3 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | theflofly/tensorflow | tensorflow/python/autograph/converters/conditional_expressions.py | Python | apache-2.0 | 1,409 | [
"VisIt"
] | 43ec943be3076c7ff84e88b6d262cd528c31a806b124d4b4690a384ee5b0ab4b |
""" PilotAgentsDB class is a front-end to the Pilot Agent Database.
This database keeps track of all the submitted grid pilot jobs.
It also registers the mapping of the DIRAC jobs to the pilot
agents.
Available methods are:
addPilotTQReference()
setPilotStatus()
deletePilot()
clearPilo... | petricm/DIRAC | WorkloadManagementSystem/DB/PilotAgentsDB.py | Python | gpl-3.0 | 36,529 | [
"DIRAC"
] | c4fc5508e54e3f91009f986a3b66d9df340d6e7dfbf860da7b9992d659934c75 |
# -*- coding: utf-8 -*-
import unittest
import logging
from nose.tools import * # flake8: noqa (PEP8 asserts)
import mock
from framework.auth.core import Auth
from website import settings
import website.search.search as search
from website.search import elastic_search
from website.search.util import build_query
from... | lyndsysimon/osf.io | tests/test_elastic.py | Python | apache-2.0 | 27,030 | [
"Brian"
] | a88d70f4db82337fa737e03c903013f79f2e87045a671017ba7ad53a15439e54 |
from margin.mappers.abstractMapper import AbstractMapper
from sonLib.bioio import system
import os
class Minimap2(AbstractMapper):
def run(self, args="-ax map-ont -N 0"):
localReferenceFastaFile = os.path.join(self.getLocalTempDir(), "ref.fa") #Because BWA builds these crufty index files, copy to a tempora... | benedictpaten/marginAlign | src/margin/mappers/minimap2.py | Python | mit | 745 | [
"BWA"
] | 721d9eac82c5abb67412faa726128fb32a2c33c4628fc23c74be9c04680b770c |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | Achuth17/scikit-bio | skbio/alignment/_pairwise.py | Python | bsd-3-clause | 42,137 | [
"BLAST",
"scikit-bio"
] | 97812110415ce654809f5e29c9ae678597c6e9de0172060af17cf535f99ae9c2 |
## Absolute location where all raw files are
RAWDATA_DIR = '/home/cmb-06/as/skchoudh/dna/Dec_12_2016_Penalva_Musashi1_U251/RNA-Seq'
## Output directory
OUT_DIR = '/home/cmb-06/as/skchoudh/rna/Dec_12_2016_Penalva_Musashi1_U251'
## Absolute location to 're-ribo/scripts' directory
SRC_DIR = '/home/cmb-panasas2/skchoud... | saketkc/ribo-seq-snakemake | configs/Dec_12_2016_Penalva_Musashi1_U251.py | Python | bsd-3-clause | 2,378 | [
"HTSeq",
"pysam"
] | d9659ddbbcb36b90f4ea42263936ab6593af6f70dcddc0c7045da2ddc8e996f8 |
from paraview import simple
from tonic import camera
def update_camera(viewProxy, cameraData):
viewProxy.CameraFocalPoint = cameraData['focalPoint']
viewProxy.CameraPosition = cameraData['position']
viewProxy.CameraViewUp = cameraData['viewUp']
simple.Render(viewProxy)
def create_spherical_camera(v... | Kitware/tonic-data-generator | python/tonic/paraview/__init__.py | Python | bsd-3-clause | 760 | [
"ParaView"
] | 8d3c25f00ea999e9780be299d3c7232d9131754431d43d8d4f1eb9cce3d78a1c |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | BackupTheBerlios/espressopp | src/interaction/CoulombKSpaceP3M.py | Python | gpl-3.0 | 4,758 | [
"ESPResSo"
] | c8081a76e34fc972e86be93090b1047b278ed78809c5231ad883f4c75de9a451 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | eagle/plotgreybodyfit.py | Python | agpl-3.0 | 4,926 | [
"Galaxy"
] | 12dd1b257661b0e82b2415436586a49a079ce5a1d3f51b12ca65bc0a0600dfe1 |
'''
CodonGenie (c) University of Manchester 2016
CodonGenie is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
# pylint: disable=exec-used
import setuptools
with open('README.md', 'r') as fh:
_LONG_DESCRIPTION = fh.read()
... | synbiochem/CodonGenie | setup.py | Python | mit | 876 | [
"VisIt"
] | c79944991f9ca90261c9ec3fe4bdac8df67c6311ea94a13a822c6dd49c1be9b6 |
import sys
from ase import Atoms
from gpaw import GPAW, FermiDirac
from gpaw import KohnShamConvergenceError
from gpaw.utilities import devnull, compiled_with_sl
from ase.structure import molecule
# Calculates energy and forces for various parallelizations
tolerance = 4e-5
parallel = dict()
basekwargs = dict(mode... | robwarm/gpaw-symm | gpaw/test/parallel/fd_parallel_kpt.py | Python | gpl-3.0 | 4,423 | [
"ASE",
"GPAW"
] | 8c96b5bb9140915df368b015f401161ef1d3b632941b8c4bcef5cba81770be3a |
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'about.ui'
#
# Created: Thu Aug 29 22:57:47 2013
# by: PyQt4 UI code generator 4.10.3
#
# WARNING! All changes made in this file will be lost!
from PyQt4 import QtCore, QtGui
try:
_fromUtf8 = QtCore.QString.fromUtf8
except Attribut... | beastwood/synctity | about_ui.py | Python | gpl-3.0 | 4,346 | [
"Brian"
] | af982bea628c9b32b31920a04a5d3870d21c2c758d6d145dc1235fa754c30f2e |
#!/usr/bin/env python
from __future__ import print_function
## @package sam_compare
# This script compares two SAM files (sequence alignment maps) and
# generates counts for similarly mapped reads.
# Translated to python from an existing perl script.
# @author Oleksandr Moskalenko <om@hpc.ufl.edu>
# @version 0.1... | McIntyre-Lab/mcscript | sam_compare.py | Python | gpl-3.0 | 33,586 | [
"ASE"
] | 867fafabded50840efdcb2c686f1380eaad65e1d849f6b0704247f3a9ae4b298 |
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