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# vim: set expandtab shiftwidth=2 softtabstop=2:
# nmi
# "score" - compute the nmi score using tempy
#
from TEMPy.MapParser import MapParser
from TEMPy.ScoringFunctions import ScoringFunctions
from TEMPy.StructureParser import PDBParser
from TEMPy.StructureBlurrer import StructureBlurrer
from TEMPy.class_arg import... | OniDaito/ChimeraXTempy | src/nmi.py | Python | mit | 7,191 | [
"ChimeraX"
] | 4aa695fa26ac8dbbae3e0a4ed74982493bd2159c729b59f6919a2d3fba601a0e |
from ovito.io import import_file
from ovito.modifiers import ConstructSurfaceModifier
# Load a particle structure and construct its geometric surface:
node = import_file("simulation.dump")
mod = ConstructSurfaceModifier(radius = 2.9)
node.modifiers.append(mod)
node.compute()
# Query computed surface properties:
print... | srinath-chakravarthy/ovito | doc/python/example_snippets/construct_surface_modifier.py | Python | gpl-3.0 | 761 | [
"OVITO",
"VTK"
] | eae798285655b90db22e2fabe6153b6bddc418c5cfc1e394f63ffa6bcd64bd58 |
../../../../../../../share/pyshared/orca/scripts/toolkits/WebKitGtk/structural_navigation.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/scripts/toolkits/WebKitGtk/structural_navigation.py | Python | gpl-3.0 | 92 | [
"ORCA"
] | d4665a72da678bbbeecfe872e0b8d2ff2a693bfe8b3e6e5cacd7d5e18bddb76b |
"""Generate the quadrature nodes and weights in Clenshaw-Curtis quadrature."""
try:
from functools import lru_cache
except ImportError: # pragma: no coverage
from functools32 import lru_cache
import numpy
import chaospy
from .hypercube import hypercube_quadrature
def clenshaw_curtis(order, domain=(0., 1.),... | jonathf/chaospy | chaospy/quadrature/clenshaw_curtis.py | Python | mit | 3,825 | [
"Gaussian"
] | aa378554025dabd2740221c5adf634ef4c71ae66a09f8e23e98f4a8fbbed487f |
# $Id$
#
# Copyright (c) 2010, Novartis Institutes for BioMedical Research Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above... | rdkit/rdkit-orig | rdkit/Chem/UnitTestFunctionalGroups.py | Python | bsd-3-clause | 6,699 | [
"RDKit"
] | 10ca4b17838dd3d55cceff2e831d8671d80a7e76b667e50a9a03775f47058ae5 |
#!/usr/bin/env python
# encoding: utf-8
# Stdlib:
from time import time
# Internal:
from gi.repository import Moose
# External:
from gi.repository import GLib
class Heartbeat:
'''Count the elapsed song time without querying MPD.
It simply looks for signals and calculates the current song position on
a... | studentkittens/snobaer | snobaer/heartbeat.py | Python | lgpl-3.0 | 5,354 | [
"MOOSE"
] | bfe71c1a26eb1e45e0cce9bb110e9de905b5fd4116da014b7c6cbb1b8c199bdb |
""" GraphData encapsulates input data for the DIRAC Graphs plots
The DIRAC Graphs package is derived from the GraphTool plotting package of the
CMS/Phedex Project by ... <to be added>
"""
__RCSID__ = "$Id$"
import time
import datetime
import numpy
from matplotlib.dates import date2num
from DIRAC.Core.U... | hgiemza/DIRAC | Core/Utilities/Graphs/GraphData.py | Python | gpl-3.0 | 17,723 | [
"DIRAC"
] | 9d98c0859bdc7851b3cf2f1907a887c3bf771a8629cb83802f926015360bbb5e |
"""
netParams.py
High-level specifications for M1 network model using NetPyNE
Contributors: salvadordura@gmail.com
"""
from netpyne import specs
import pickle, json
netParams = specs.NetParams() # object of class NetParams to store the network parameters
netParams.version = 49
try:
from __main__ import cf... | thekerrlab/netpyne | examples/PTcell/netParams.py | Python | mit | 9,565 | [
"Elk"
] | 59555a2e1e6418dcb8e83ca944ecf7eef194fa589bdd92e8ec710007a6097a6e |
import re
import os
import json
from scrapy.spider import BaseSpider
from scrapy.selector import HtmlXPathSelector
from scrapy.http import Request, FormRequest, HtmlResponse, TextResponse
from scrapy.utils.response import get_base_url
from scrapy.utils.url import urljoin_rfc
from urllib import urlencode
import hashlib... | 0--key/lib | portfolio/Python/scrapy/orange/swisscom.py | Python | apache-2.0 | 2,683 | [
"Galaxy"
] | f7c3378668534a85d8226d189e60fd96e332690d8f3bc33d9cad371839ece80e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# From https://gist.github.com/lepture/2011858
#
# Copyright (c) 2012, lepture.com
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# * Redistributions of source code ... | michaeljoseph/pymoji | pymoji/emoji.py | Python | apache-2.0 | 8,018 | [
"Bowtie",
"Octopus"
] | 64a7120120c3c06acf9e577589cf7ffb8f4c55bd9d36fea6a3c8d71cd875d956 |
# Copyright 2014, Brian Coca <bcoca@ansible.com>
# Copyright 2017, Ken Celenza <ken@networktocode.com>
# Copyright 2017, Jason Edelman <jason@networktocode.com>
# Copyright 2017, Ansible Project
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of ... | romain-dartigues/ansible | lib/ansible/plugins/filter/mathstuff.py | Python | gpl-3.0 | 8,065 | [
"Brian"
] | c03e0f6018117496afb15950dd7bfb6d72d4fbe981fb36c4dc577c0283efd08f |
'''
Created on Aug 5, 2014
@author: gearsad
'''
import vtk
from InteractorSuperclass import InteractorSuperclass
class Interactor1stPersonUser(InteractorSuperclass):
'''
Inherit the VTK class vtkInteractorStyleUser and extend it to be a 1st-person camera for the observer.
Ref: http://www.vtk.org/doc/nigh... | GearsAD/semisorted_arnerve | sandbox/bot_vis_platform_oculus/scene/Interactor1stPersonUser.py | Python | mit | 6,049 | [
"VTK",
"VisIt"
] | bd3effbce769291628f2a8d70d61b66b889ca6ba9583fafaf6ea4a7b57ffd43c |
#!/usr/bin/env python2
"""
EMIRGE: Expectation-Maximization Iterative Reconstruction of Genes from the Environment
Copyright (C) 2010-2016 Christopher S. Miller (christopher.s.miller@ucdenver.edu)
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public... | epruesse/EMIRGE | emirge_amplicon.py | Python | gpl-3.0 | 82,875 | [
"BLAST",
"Biopython",
"Bowtie",
"pysam"
] | 8a2fb6666455f422bc59063b72c1748d095f242ae6b5cd2b1d087b81dfb6225a |
"""The cl.oquence kernel programming language."""
import ast as _ast # http://docs.python.org/library/ast.html
import cypy
import cypy.astx as astx
import cypy.cg as cg
version = cypy.Version("cl.oquence", (("Major", 1), ("Minor", 0)), "alpha")
"""The current :class:`version <cypy.Version>` of cl.oquence (1.0 alpha).... | cyrus-/ace | clq/__init__.py | Python | lgpl-3.0 | 21,497 | [
"VisIt"
] | 11f1cf5b296cd8e2c729a02f9baed0f82a4e8bf2141aed5295f2e7dc90e5e9db |
import os, sys, traceback
import xml.etree.ElementTree as xml
##
# Stores error information needed for printing diff messages
class XMLError(object):
##
# Constructor.
# @param err A one line error message
# @param msg A detailed message describing the error
def __init__(self, err, msg):
s... | stimpsonsg/moose | python/TestHarness/XMLDiffer.py | Python | lgpl-2.1 | 11,919 | [
"VTK"
] | d7c205dc185ef60d4bd18aa6b9a7c18a98a111dcbe8f143b4ab5a26559aa5870 |
# -*- coding: utf-8 -*-
#
# Copyright 2008 - 2019 Brian R. D'Urso
#
# This file is part of Python Instrument Control System, also known as Pythics.
#
# Pythics 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, e... | dursobr/Pythics | pythics/start.py | Python | gpl-3.0 | 27,005 | [
"Brian"
] | c20f023f62bcec64cd451b62f37ef6b4f5c472fd7a9341066cd823f7a07d6946 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 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
#... | jturney/psi4 | psi4/driver/qcdb/libmintsbasisset.py | Python | lgpl-3.0 | 65,736 | [
"CFOUR",
"Gaussian",
"Psi4"
] | 584e5577fa119f2f5dbd7f576f662e3267ca53abbef11e4c65d558d8d662a5a5 |
"""Learn to estimate functions from examples. (Chapters 18-20)"""
from utils import (
removeall, unique, product, mode, argmax, argmax_random_tie, isclose,
dotproduct, vector_add, scalar_vector_product, weighted_sample_with_replacement,
weighted_sampler, num_or_str, normalize, clip, sigmoid, print_table, D... | sofmonk/aima-python | learning.py | Python | mit | 37,159 | [
"NEURON"
] | 04917ad67b21ab38a421c4e4ff60736d397970a7b204262c4f08608d6b84402a |
##############################################################################
# Copyright (c) 2013-2018, 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... | krafczyk/spack | var/spack/repos/builtin/packages/rsem/package.py | Python | lgpl-2.1 | 1,887 | [
"Bowtie"
] | b397566980b89f6637356ab7ecf47b5f71b6c134545feba96ef38a7c317bcead |
"""Cronjob like scheduling abstraction in Python.
This module contains the functionality used by the Kodi Alarm clock
addon and is largely based on a Stackoverflow answer by
Brian on http://stackoverflow.com/questions/
373335/suggestions-for-a-cron-like-scheduler-in-python/374207#374207"""
from datetime import dateti... | remigius42/script.service.alarmclock | resources/lib/cronjobs.py | Python | gpl-3.0 | 3,455 | [
"Brian"
] | ff4bdbd6f732c5cffd44388a1e50092eb44e6b4f51ed4e5c6d2f82ef05d4ba60 |
from __future__ import print_function
import traceback
import sys
import threading
from contextlib import contextmanager
from stat import S_IXOTH
from os import pardir, stat, chmod, access, X_OK, pathsep, environ
from os import makedirs, listdir
from os.path import join, dirname, isfile, split
from os.path import exi... | ssorgatem/pulsar | test/test_utils.py | Python | apache-2.0 | 12,876 | [
"Galaxy"
] | d8540ac419692ec35087b58a0b919b640c3e60d0ed7668a21db378a054e88bb8 |
import warnings
import hashlib
import io
import json
import jsonschema
import pandas as pd
from toolz.curried import pipe as _pipe
from .schema import core, channels, mixins, Undefined, SCHEMA_URL
from .data import data_transformers
from ... import utils, expr
from .display import renderers, VEGALITE_VERSION, VEGAEM... | altair-viz/altair | altair/vegalite/v4/api.py | Python | bsd-3-clause | 89,700 | [
"Gaussian"
] | 945f6823c07b7ffc4bc637444e70b57a2d336a5d5805c98048e7c11feedc43b1 |
# This file is part of OpenDrift.
#
# OpenDrift 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, version 2
#
# OpenDrift is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without ev... | OpenDrift/opendrift | opendrift/models/basemodel.py | Python | gpl-2.0 | 238,459 | [
"Gaussian",
"NetCDF"
] | ac19b9de9ee942b6cf6bbe2c3fe8545657c3d6f14a2d4085542d17762469a3f9 |
# Copyright 2012, Nachi Ueno, NTT MCL, Inc.
# 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
#
# Unles... | noironetworks/neutron | neutron/tests/unit/agent/linux/test_iptables_firewall.py | Python | apache-2.0 | 105,760 | [
"FEFF"
] | 943a64f8ad62abe7664102cb46d7c8c6cd3b06b08e602e14c92c7b51fde49370 |
import glob
import logging
import os
import subprocess
from plugins import BaseAligner
from yapsy.IPlugin import IPlugin
from assembly import get_qual_encoding
logger = logging.getLogger(__name__)
class Bowtie2Aligner(BaseAligner, IPlugin):
def run(self):
"""
Map READS to CONTIGS and return alignm... | kbase/assembly | lib/assembly/plugins/bowtie2.py | Python | mit | 2,436 | [
"Bowtie"
] | f7f9f633e2535bd7588b4e35184a1875c53f7af9e86658cf1b78c9d03f5a1657 |
#!/usr/bin/env python
# -*- encoding: utf-8 -*-
# CREATED:2015-02-15 10:06:03 by Brian McFee <brian.mcfee@nyu.edu>
"""Helpful tools for deprecation"""
import warnings
from inspect import signature, isclass, Parameter
from functools import wraps
from decorator import decorator
__all__ = ["moved", "deprecated", "depre... | librosa/librosa | librosa/util/decorators.py | Python | isc | 3,722 | [
"Brian"
] | 49919ee294d5655309cadd1dcc7ca463aed8daf79abacdff92e33c0d96ace536 |
# ######################################################################
# Copyright (c) 2014, Brookhaven Science Associates, Brookhaven #
# National Laboratory. All rights reserved. #
# #
# @author: Li Li (lili@bnl.g... | tacaswell/scikit-xray | skbeam/core/cdi.py | Python | bsd-3-clause | 13,332 | [
"Gaussian"
] | e4ca460e53b600bc006c1b46c123ca59a84204331cc8ee41f0725d656437f4f1 |
"""
CBMPy: fluxmodules main module
This module contains convenience methods for module related computations.
For most users this is the only relevant module.
=====================
PySCeS Constraint Based Modelling (http://cbmpy.sourceforge.net)
This program is free software: you can redistribute it and/or modify
it u... | SystemsBioinformatics/cbmpy | cbmpy/fluxmodules/fluxmodules.py | Python | gpl-3.0 | 6,629 | [
"PySCeS"
] | b864e7d393c482e1a2629f3825bb3e1bad1c14d776312e72058cb36fd0f5aa4a |
#!/usr/bin/env python
"""
Stop a given production
Usage:
dirac-prod-stop prodID
Arguments:
prodID: Production ID (mandatory)
Example:
$ dirac-prod-stop 381
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import DIRAC
from DIR... | yujikato/DIRAC | src/DIRAC/ProductionSystem/scripts/dirac_prod_stop.py | Python | gpl-3.0 | 970 | [
"DIRAC"
] | 6620d41fd686f9d672cfd1fc8ed5927553fd9b899ff8ad50cfb3fc6fb0425404 |
#***********************************************************************
# This code is part of CmplServer
#
# Copyright (C) 2013, 2014
# Mike Steglich - Technical University of Applied Sciences
# Wildau, Germany
#
# CmplServer is a project of the Technical University of
# Applied Sciences Wildau and t... | Mangara/ArboralExplorer | lib/Cmpl/cmplServer/cmplServer/cmplServerHandler.py | Python | apache-2.0 | 4,038 | [
"VisIt"
] | 77f89f64a1d484cec59958e59031d79ac52e16938537a7e5e6b50399e86b3656 |
'''
Created on Feb 1, 2017
@author: Alexandre Day
Purpose:
Perform density clustering on gaussian mixture
'''
from fdc import FDC
from sklearn.datasets import make_blobs
from sklearn.preprocessing import StandardScaler
from sklearn.metrics import normalized_mutual_info_score as nmi
from fdc import plotti... | alexandreday/fast_density_clustering | example/example3.py | Python | bsd-3-clause | 1,001 | [
"Gaussian"
] | b91e5024171fb7bd665b8d65f380d4c7ab6b76744e1bb96368fdcddc8d8bae98 |
# Copyright (C) 2003 CAMP
# Please see the accompanying LICENSE file for further information.
"""K-point/spin combination-descriptors
This module contains classes for defining combinations of two indices:
* Index k for irreducible kpoints in the 1st Brillouin zone.
* Index s for spin up/down if spin-polarized (othe... | robwarm/gpaw-symm | gpaw/kpt_descriptor.py | Python | gpl-3.0 | 27,162 | [
"ASE",
"GPAW"
] | 5e961c4396f4f4370b6b1d3f0bbe2749d4149c7904d8b6af8f86c01f7634d254 |
"""
The dao for pymatgen.
"""
print(
"""
The 道 of Pymatgen
1. Great code enables great materials science.
2. Comprehensive tests ensure robustness.
3. Clear documentation leads to more usage.
4. More usage improves code quality (and increases citations).
5. Even complex scientific ideas can be broken down in... | vorwerkc/pymatgen | pymatgen/dao.py | Python | mit | 715 | [
"pymatgen"
] | 0d9829ef98900aa1a0a402ff50135c578fed68f7902a9d33544a1aed2bd0412c |
# c: 14.12.2007, r: 03.11.2008
import os
import numpy as nm
from sfepy import data_dir
from sfepy.base.base import output, pause, debug, Struct
from sfepy.fem import MeshIO
from sfepy.homogenization.utils import get_volume
from gen_mesh import gen_concentric
is_3D = False
generate_2D = False
fig_suffix = '.pdf'
if ... | olivierverdier/sfepy | examples/phononic/band_gaps_rigid.py | Python | bsd-3-clause | 13,078 | [
"VTK"
] | 7dc7a03dfd066cff4029eefc317989a7cef0ac1058e780cbc65fa80bef5bd392 |
# CamJam EduKit 1 - Basics
# Worksheet 7 - Traffic Lights Template
# Import Libraries
import os
import time
from gpiozero import LED, Button, Buzzer
# Set up variables for the LED, Buzzer and switch pins
# Define a function for the initial state (Green LED on, rest off)
# (If you have the second 'pedestrian LEDs, t... | CamJam-EduKit/EduKit1 | CamJam EduKit 1 - GPIO Zero/Code (GPIO Zero)/7-TrafficLights.py | Python | mit | 2,470 | [
"Amber"
] | f21d90e4b11c3848e1635642e36a1f2fd6212f8f7da65083fb3c797c955dfdb4 |
#!/usr/bin/env python3
"""
Expansion module integrating with VMware NSX Defender.
"""
import argparse
import base64
import configparser
import datetime
import hashlib
import io
import ipaddress
import json
import logging
import pymisp
import sys
import vt
import zipfile
from urllib import parse
from typing import Any, ... | VirusTotal/misp-modules | misp_modules/modules/expansion/vmware_nsx.py | Python | agpl-3.0 | 22,825 | [
"Galaxy"
] | c6e1df5412714092c23d4300a157f12ed3d7dc14717c944d8ae8dc01b810fa9b |
#
# Copyright 2010, 2011 Brian R. D'Urso
#
# Pythics 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.
#
# Pythics is distributed i... | dursobr/Pythics | pythics/instruments/SRS_SR830.py | Python | gpl-3.0 | 2,596 | [
"Brian"
] | 0fc5d6f1693bdfb489f8c826bdb0200272a60be4d8283b6c3a0ecc5c66989d0e |
"""
Module to set up run time parameters for Clawpack -- classic code.
The values set in the function setrun are then written out to data files
that will be read in by the Fortran code.
"""
import os
import numpy as np
#------------------------------
def setrun(claw_pkg='classic'):
#---------------------------... | amath574w2015/am574-class | homeworks/hw3/expflux/setrun.py | Python | bsd-3-clause | 6,996 | [
"NetCDF"
] | 3747982baa1f5432da37b2ff847c3d993c0dc8749ae33f022ce58659003def74 |
# 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
#
# Unless required by appl... | sunqm/pyscf | pyscf/pbc/df/__init__.py | Python | apache-2.0 | 937 | [
"PySCF"
] | 8602eefa6af2b122e730515557d994c1e977291f738014b4adaea152896e01b2 |
"""
Tests the imports and exports of the Molecule object.
"""
import json
import numpy as np
import pytest
import qcelemental as qcel
from . import portal as ptl
def test_molecule_constructors():
### Water Dimer
water_psi = ptl.data.get_molecule("water_dimer_minima.psimol")
ele = np.array([8, 1, 1, 8,... | psi4/DatenQM | qcfractal/interface/tests/test_molecule.py | Python | bsd-3-clause | 5,746 | [
"Psi4"
] | 2c466d30ef1391e2a2bfad845ef2b0511ba13e1bb058e908759a4d22d96c8d93 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
__version__ = '0.6.4'
from octopus.core import Octopus, TimeoutError, ResponseError # NOQA
from octopus.tornado_core import TornadoOctopus # NOQA
| heynemann/octopus | octopus/__init__.py | Python | mit | 196 | [
"Octopus"
] | 8f68dad7cb68891ea0d7fdf509123c6681982427e060080ef59e62a26982a460 |
# this script starts a new AIMS calculation. Ethylene, SA2-CASSCF(2/2).
import numpy as np
import pyspawn
import pyspawn.general
import pyspawn.process_geometry as pg
import pyspawn.dictionaries as dicts
import sys
# terachemserver port
if sys.argv[1]:
port = int(sys.argv[1])
else:
"Please provide a port numb... | blevine37/pySpawn17 | examples/ethylene_sacasscf/start_c2h4.py | Python | mit | 4,064 | [
"Gaussian",
"TeraChem"
] | dce61c0a98063e5ab3a781a735cb36bf8674ef0eecf0282b1512c46b09b2c3ae |
from geckopush import geckopush
import unittest
import json
# Declare initial dashboard widget and test values.
d = geckopush.Dashboard(api_key="api-key-123")
widget_key = "Widget-Key"
# Monkey patch urlopen method to append the url and headers to return dict.
def dummy_urlopen(url):
mock_api_return = {
... | patleeman/geckopush | tests/unit_test.py | Python | mit | 14,360 | [
"Amber"
] | 56eacea06e046ec9e63ee8901782cd124f21ad2b8942a4a86b0df3507c9cf8d1 |
"""
pybsm - python library for the BSM-SG pysical model.
"""
RELEASE = (0, 1, 0)
VERSION = RELEASE[0:2]
VERSION_STR = '.'.join((str(x) for x in VERSION))
__version__ = RELEASE_STR = '.'.join((str(x) for x in RELEASE))
# __all__ = ['galaxy', 'particles']
| supergravity-org/pybsm | pybsm/__init__.py | Python | gpl-3.0 | 260 | [
"Galaxy"
] | 81fd79a18a7fa31be54126eecd46878e7cbdc5d8f7b736fd0a9bc11d0efbc933 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class PyCfgrib(PythonPackage):
"""Python interface to map GRIB files to the NetCDF Common Data M... | LLNL/spack | var/spack/repos/builtin/packages/py-cfgrib/package.py | Python | lgpl-2.1 | 1,507 | [
"NetCDF"
] | 36c15334aa1dd909c14aa43386d3edfacd46635cee262e5700db38625f3dd54e |
######## What the script does:
######## provides preprocessing functions for medical text
#########################
import re
import string
import pickle
printable = set(string.printable)
def sanitize(txt):
return filter(lambda c: c in printable, txt)
try:
stopwords=pickle.load(open('Stopwords.pk','rb'))
exc... | yhalpern/anchorExplorer | Parsing.py | Python | bsd-2-clause | 5,309 | [
"VisIt"
] | ed0068b19bde9cd7b83157e923935f52ac8949c4581c1eb1db270081d056d538 |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import textwrap
import py
import pytest
from _pytest.config import PytestPluginManager
from _pytest.main import EXIT_NOTESTSCOLLECTED
from _pytest.main import EXIT_OK
from _pytest.main import EXIT_USAGEERROR
... | pfctdayelise/pytest | testing/test_conftest.py | Python | mit | 18,429 | [
"VisIt"
] | 3cc3eafe7f2edeed67397a3ffc4b8b1637a56484de00730d81ce631648dd8d63 |
# Run tests with nosetests
import corex
import numpy as np
from functools import partial, update_wrapper
verbose = False
seed = 3
def generate_data(n_samples=100, group_sizes=[2], dim_hidden=2, missing=0):
Y_true = [np.random.randint(0, dim_hidden, n_samples) for _ in group_sizes]
X = np.hstack([np.repeat(Y_... | aaronplasek/CorEx | test_corex.py | Python | gpl-2.0 | 4,334 | [
"Gaussian"
] | b6c556fd0189c25ba53035dbe5024372bdf6501ba94fee2794ae61830b3047fc |
# -*- coding: utf-8 -*-
from __future__ import print_function
import os
import sys
import time
import subprocess
from paver.easy import *
from os.path import islink, isfile,join,basename,dirname,exists,relpath,abspath
from paver.setuputils import setup
try:
from paver.virtual import bootstrap, virtualenv
except I... | demis001/raslpipe | pavement.py | Python | mit | 23,467 | [
"Bioconductor"
] | fd14c2bcf2111b1a0f5d1be4ecad2e403dbe82db129e0007883302c6cce2a1dc |
"""
Migration script to create a new 'sequencer' table
"""
from sqlalchemy import *
from sqlalchemy.orm import *
from migrate import *
from migrate.changeset import *
from sqlalchemy.exc import *
from galaxy.model.custom_types import *
import datetime
now = datetime.datetime.utcnow
import logging
log = logging.getL... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/model/migrate/versions/0063_sequencer_table.py | Python | gpl-3.0 | 2,026 | [
"Galaxy"
] | d9acaf8b1e87cf54ba2822003f5e1bf0940df56d3d62e16fd09650000be89fe2 |
"""
Instructor Dashboard Views
"""
import logging
import datetime
from opaque_keys import InvalidKeyError
from opaque_keys.edx.keys import CourseKey
import uuid
import pytz
from django.contrib.auth.decorators import login_required
from django.views.decorators.http import require_POST
from django.utils.translation imp... | caesar2164/edx-platform | lms/djangoapps/instructor/views/instructor_dashboard.py | Python | agpl-3.0 | 32,750 | [
"VisIt"
] | 022063698dddc9c106bff4f72e0fb80cbd504758cbdb94ff0ead6c0d360b8227 |
"""Handle installation and updates of bcbio-nextgen, third party software and data.
Enables automated installation tool and in-place updates to install additional
data and software.
"""
from __future__ import print_function
import argparse
import collections
import contextlib
import datetime
import dateutil
from distu... | a113n/bcbio-nextgen | bcbio/install.py | Python | mit | 37,903 | [
"BWA",
"Bioconda",
"Bowtie",
"Galaxy"
] | 11d7ea10686273fd0d6fdb007336352ea37a9763886a5555a4168e749e849a10 |
from __future__ import division
from menpo.transform import AlignmentSimilarity
from menpo.model.pdm import PDM, OrthoPDM
from menpo.fit.gradientdescent import RegularizedLandmarkMeanShift
from menpo.fit.gradientdescent.residual import SSD
from menpo.fitmultilevel.base import MultilevelFitter
from menpo.fitmultilevel.... | jabooth/menpo-archive | menpo/fitmultilevel/clm/base.py | Python | bsd-3-clause | 7,116 | [
"Gaussian"
] | a918410aa3b379cdf83f759becf031f6a0bf3bb633754fd01d2cfc82c988cf7c |
""" X509Certificate is a class for managing X509 certificates
Proxy RFC: https://tools.ietf.org/html/rfc38200
X509RFC: https://tools.ietf.org/html/rfc5280
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import datetime
import os
im... | yujikato/DIRAC | src/DIRAC/Core/Security/m2crypto/X509Certificate.py | Python | gpl-3.0 | 14,715 | [
"DIRAC"
] | 71e1f156dc54c6df3b8fa7fd20e75a283b467cabf4220b42c81c2c1961d10090 |
"""Loader for MSG, netcdf format.
"""
from ConfigParser import ConfigParser
from mpop import CONFIG_PATH
import os
import numpy.ma as ma
from numpy import array as np_array
from numpy import nan as np_nan
from glob import glob
from mpop.projector import get_area_def
import datetime
try:
import h5py
except ImportE... | mraspaud/mpop | mpop/satin/msg_seviri_hdf.py | Python | gpl-3.0 | 12,369 | [
"NetCDF"
] | 8c21cd7d47e6ad82e18f85b25f6ba2129964824a98a011d08469070202695427 |
# -*- coding: utf-8 -*-
# This file is part of the Horus Project
__author__ = 'Jesús Arroyo Torrens <jesus.arroyo@bq.com>'
__copyright__ = 'Copyright (C) 2014-2016 Mundo Reader S.L.'
__license__ = 'GNU General Public License v2 http://www.gnu.org/licenses/gpl2.html'
import cv2
import math
import numpy as np
import sc... | bqlabs/horus | src/horus/engine/algorithms/laser_segmentation.py | Python | gpl-2.0 | 8,419 | [
"Gaussian"
] | 1c3287a2136b6692c9eded4eef2af1cfe57626d7bafa4b445eb07fb379eb21e1 |
#!/usr/bin/env python
__author__ = 'Mike McCann,Duane Edgington,Danelle Cline'
__copyright__ = '2018'
__license__ = 'GPL v3'
__contact__ = 'duane at mbari.org'
__doc__ = '''
Master loader for all CANON May-June Campaign 2019
Mike McCann, Duane Edgington, Danelle Cline
MBARI 22 May 2019
@var __date__: Date of last s... | stoqs/stoqs | stoqs/loaders/CANON/loadCANON_may2019.py | Python | gpl-3.0 | 16,982 | [
"NetCDF"
] | 8864f918c780803b0407fbbb3a26d7a949799a97600d0fb256994429b0a55380 |
import pytest
from pysisyphus.benchmarks import Benchmark
from pysisyphus.calculators.PySCF import PySCF
# from pysisyphus.helpers_pure import filter_fixture_store
from pysisyphus.optimizers.RFOptimizer import RFOptimizer
from pysisyphus.testing import using
def calc_getter(charge, mult):
return PySCF(basis="sto... | eljost/pysisyphus | tests/test_baker/test_baker.py | Python | gpl-3.0 | 1,721 | [
"PySCF"
] | e29b694ca19cb5e7c8d22f5b512ef603f52ab95811c7e77f68b5353bf0351d12 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class F3d(CMakePackage):
"""A fast and minimalist scriptable 3D viewer."""
homepage = "http... | LLNL/spack | var/spack/repos/builtin/packages/f3d/package.py | Python | lgpl-2.1 | 559 | [
"VTK"
] | c6a732071b632c06359de31d85ecc827e583bd038f9f78953342e23191729410 |
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
'''The <output> and <file> elements.
'''
from __future__ import print_function
import os
from grit import xtb_reader
from grit.node import base
clas... | scheib/chromium | tools/grit/grit/node/node_io.py | Python | bsd-3-clause | 3,329 | [
"xTB"
] | 30f224ef57ac90bd3a5a628f9b443f324c2613b6cf547adf7abfe9195e00acc4 |
########################################################################
# $HeadURL$
########################################################################
"""
:mod: FTSMonitorAgent
=====================
The FTSMonitorAgent takes FTS Requests from the TransferDB and monitors their execution
using FTSRequest ... | avedaee/DIRAC | DataManagementSystem/Agent/FTSMonitorAgent.py | Python | gpl-3.0 | 17,035 | [
"DIRAC"
] | 88f90422a87c6f67f7cb88814bf22b494dcc0c45d1f2ddb83386c4d6ee5a48e6 |
# Copyright 2017 Antoine Miech 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 applicable law o... | antoine77340/Youtube-8M-WILLOW | frame_level_models.py | Python | apache-2.0 | 48,254 | [
"Gaussian"
] | d3aa58dd9ea710a5a4754436f0001308c7d6f9cda548e65d41c673d825567f3c |
#! /usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requi... | googleapis/python-compute | scripts/fixup_compute_v1_keywords.py | Python | apache-2.0 | 20,432 | [
"VisIt"
] | 22498df3d5f36426ae065d68cd60594444496b60ced452dc1818650a45c340e1 |
#!/usr/bin/env python
"""
replicate file in the FileCatalog
Can work in two modes.
In the first mode, yuser provides the destination SE with option "-D".
In the second mode, when no destination is given, drepl will look for COMDIRAC configuration options "replication_scheme" and "replication_ses".
If found, those va... | pigay/COMDIRAC | Interfaces/scripts/drepl.py | Python | gpl-3.0 | 3,366 | [
"DIRAC"
] | e8e93bbeccbdbba13f8b357951cce8a907e4f6987bccbfc3fef5e3af61398654 |
#
# Dalton Burke, CU Denver
#
# CONUS = [-124.7844079,-66.9513812,24.7433195,49.3457868]
from __future__ import absolute_import
from utils import ensure_dir, symlink_unless_exists
from .downloader import download_url, DownloadError, get_dList
# fast searching of dList
from bisect import bisect
from datetime import d... | vejmelkam/wrfxpy | src/ingest/level0_source.py | Python | mit | 36,889 | [
"Dalton"
] | 81050ef567626c360040df0f1b3305f45edf6f89e6348d1a91c0170d28d1b3df |
# $HeadURL$
__RCSID__ = "$Id$"
from DIRAC import S_OK, S_ERROR, gConfig
from DIRAC.ConfigurationSystem.Client.Helpers.Path import cfgPath
gBaseLocalSiteSection = "/LocalSite"
def gridEnv():
"""
Return location of gridenv file to get a UI environment
"""
ret... | Sbalbp/DIRAC | ConfigurationSystem/Client/Helpers/Local.py | Python | gpl-3.0 | 392 | [
"DIRAC"
] | 817d10cda55ceb7df721330604ba1a4554397d5650e2b04ac87c320df7845394 |
#
# Copyright 2014-2015 Universidad Complutense de Madrid
#
# This file is part of Numina
#
# SPDX-License-Identifier: GPL-3.0+
# License-Filename: LICENSE.txt
#
from __future__ import (absolute_import, unicode_literals, division,
print_function)
import numpy as np
from numpy.testing import as... | nicocardiel/numina | numina/array/tests/test_fwhm.py | Python | gpl-3.0 | 1,818 | [
"Gaussian"
] | 03881d42e149319c07630a2b6a582e2ed7178a7d241b3c8615f95d0d5447dab1 |
r"""
================================================================
Robust covariance estimation and Mahalanobis distances relevance
================================================================
An example to show covariance estimation with the Mahalanobis
distances on Gaussian distributed data.
For Gaussian dis... | DailyActie/Surrogate-Model | 01-codes/scikit-learn-master/examples/covariance/plot_mahalanobis_distances.py | Python | mit | 6,231 | [
"Gaussian"
] | 9dfb0b518c4842d31aafc1b85a1b20a78b6c7c47f7bd4b0124dc0207d5a2e9ea |
""" This module loads all the classes from the VTK VolumeRendering library into
its namespace. This is an optional module."""
from vtkVolumeRenderingPython import *
| b3c/VTK-5.8 | Wrapping/Python/vtk/volumerendering.py | Python | bsd-3-clause | 167 | [
"VTK"
] | 6a910a27e71081b812cb7c765d37d58be5067d928e8a10501c2cf6cc464e7d28 |
"""Use first Brillouin zone (Wigner–Seitz cell) to locate q-points."""
# Copyright (C) 2013 Atsushi Togo
# All rights reserved.
#
# This file is part of phonopy.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# * R... | atztogo/phonopy | phonopy/structure/brillouin_zone.py | Python | bsd-3-clause | 4,584 | [
"phonopy"
] | 30e341a0c285beaaa89bfbc292e945e9951848f0803f33ec9bbcbe9d89d9bdcf |
###
# Copyright (c) 2010, Daniel Folkinshteyn
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright notice,
# this list of cond... | tecan/xchat-rt | plugins/scripts/encryption/supybot-bitcoin-marketmonitor-master/OTCOrderBook/config.py | Python | gpl-2.0 | 3,613 | [
"VisIt"
] | b351dacb4bd075b795e6be0fbd446fc4b9b433056797317d029b09c19846daed |
#!/usr/bin/env python
"""
Install.py tool to build the GPU library
used to automate the steps described in the README file in this dir
"""
from __future__ import print_function
import sys, os, subprocess, shutil
from argparse import ArgumentParser
sys.path.append('..')
from install_helpers import get_cpus
parser = ... | jeremiahyan/lammps | lib/gpu/Install.py | Python | gpl-2.0 | 5,134 | [
"LAMMPS"
] | 589abb464fde2768584fe1d7e16d03ad3d5947588acb7d476b365861d75f5d34 |
"""
Base classes for job runner plugins.
"""
import os
import time
import string
import logging
import datetime
import threading
import subprocess
from Queue import Queue, Empty
import galaxy.jobs
from galaxy.jobs.command_factory import build_command
from galaxy import model
from galaxy.util import DATABASE_MAX_STRI... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/jobs/runners/__init__.py | Python | gpl-3.0 | 26,277 | [
"Galaxy"
] | 1190ab253a8d609b474f9673e45411c3c320f3d12c3953c325181a81eb52817e |
# encoding: utf-8
import json
import nose
import datetime
import sqlalchemy.orm as orm
import ckan.plugins as p
import ckan.lib.create_test_data as ctd
import ckan.model as model
import ckan.tests.legacy as tests
import ckan.tests.helpers as helpers
import ckan.tests.factories as factories
from ckan.common import c... | NicoVarg99/daf-recipes | ckan/ckan/ckan/ckanext/datastore/tests/test_upsert.py | Python | gpl-3.0 | 22,942 | [
"Galaxy"
] | 7b9c9a6ce175c69f40d894ba6b492ebaae8c20d7e93c32456c5aa4ae1d051df7 |
# Copyright (c) 2012 Spotify AB
#
# 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, s... | hadesbox/luigi | setup.py | Python | apache-2.0 | 2,911 | [
"VisIt"
] | 2053dfaccf63cc6276f799f3924276606f2ae12a45be32bc01e681dc952f6f19 |
# Copyright 2014 Google Inc. 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 applicable law or ag... | hunse/cuda-convnet2 | layer.py | Python | apache-2.0 | 83,382 | [
"Gaussian",
"NEURON"
] | 084df6139955a8cea96ae121e2cda24545ab15a0110f7a2cd06611f1790540a7 |
# __Author__: 'Brian Westerman'
# __Date__: 2/15/16
# __File__: view.py
import numpy as np
class View:
# constructor
def __init__(self):
# automatically resets the view
self.reset()
def reset(self,
vrp=np.matrix([0.5, 0.5, 1]),
vpn=np.matrix([0, 0, -1]),
... | bhwester/computer-science-projects | data_analysis_and_visualization_system/view.py | Python | mit | 6,811 | [
"Brian"
] | b6fc1a9795420b94419d48dc02875a8ac7f7c0abd511f49b15e1e63a1b844d97 |
# Copyright (C) 2009 by Eric Talevich (eric.talevich@gmail.com)
# 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.
"""PhyloXML reader/parser, writer, and associated functions.
Instantiates tree elements... | zjuchenyuan/BioWeb | Lib/Bio/Phylo/PhyloXMLIO.py | Python | mit | 33,305 | [
"Biopython"
] | 3fbfbd6a3f49089d13f92cdeb4dfe687c6770a4a215d9509a07a39526bfa304b |
import numpy as np
from scipy import stats
from scipy.special import expit
from scipy.stats import multivariate_normal
def exp_cosh(H):
beta = 1.0
return 0.5 * np.exp(beta * H)/np.cosh(beta * H)
def gaussian(H):
#import ipdb; ipdb.set_trace()
a = 1
cov = np.diag(np.repeat(a, H.shape[1]))
re... | noashin/kinetic_ising_model_neurons | spikes_activity_generator.py | Python | mit | 3,550 | [
"Gaussian",
"NEURON"
] | 2403154facdd0b0cdb34376fd2305c4e97546f4e3516ccc1689c65430660c81c |
"""
Base file for YAPWAF application
"""
import yapwaf as Y
import conf.env as env
import conf.db as db
import conf.routes as routes
# For testing purposes, add a user to the database
from app.models.user import User
Y.Base.metadata.create_all(Y.engine)
user = User('Brian', 'Stack')
Y.session.add(user)
Y.session.commi... | bis12/yapwaf | examples/hello/hello.py | Python | mit | 354 | [
"Brian"
] | 12542c5526ae73a5a301d7ac71da9019d2583b45ee153e19970c1ecbd9578915 |
# -*- coding: utf-8 -*-
"""
Created on Wed Mar 30 20:08:47 2016
@author: boldingd
"""
import SnnBase
import Stdp
import DopamineStdp
import random
class Cluster:
def __init__(self):
self.neurons = []
def add_neuron(self, neuron):
self.neurons.append(neuron)
def create_p... | boldingd/BadSnn | SpikingNetwork.py | Python | bsd-3-clause | 5,110 | [
"NEURON"
] | f1d5aae7be79db61179678bc0c4adb2776a8bf04e79e603a21295c18effc4a59 |
#!/usr/bin/env python -i
infile = 'in.simple'
me = 0
from lammps import lammps
lmp = lammps()
# run infile one line at a time
lines = open(infile,'r').readlines()
for line in lines: lmp.command(line)
lmp.command("run 10")
x = lmp.gather_atoms("x",1,3)
epsilon = 0.1
x[0] += epsilon
lmp.scatter_atoms("x",1,3,x)
lmp.... | crtrott/lammps | test/lib_python/in.simple-001.py | Python | gpl-2.0 | 512 | [
"LAMMPS"
] | a3c77a5845dcc1cce388c70940a2bfedfb3a551f7465d4a49266f53ba2cf364b |
#! /usr/bin/env python
# CSS Localiser (CSS Localizer)
# Version 1.0
#
# Copyright (C) Ben McGinnes, 2014
# Email: ben@adversary.org
# GPG Key: 0x321E4E2373590E5D
# License: GPLv3 or any later version
# Website: https://github.com/adversary-org/stylish-styles
# Bitcoin: 17VvZDeLjhiH1ccU6rZWLZc41UiZd8eh6F
#
# Take... | adversary-org/stylish-styles | localise/localize.py | Python | gpl-3.0 | 5,123 | [
"Amber"
] | ad7435faa40e3360560bce7f846c06d486cb9cd4e09861db5022af3f73849f04 |
import os, sys, getopt
try:
from PyQt4 import QtCore, QtGui
QtCore.Signal = QtCore.pyqtSignal
QtCore.Slot = QtCore.pyqtSlot
except ImportError:
try:
from PySide import QtCore, QtGui
QtCore.QString = str
except ImportError:
raise ImportError("Cannot load either PyQt or PySide... | gleicher27/Tardigrade | moose/gui/vtk/ExodusRenderer.py | Python | lgpl-2.1 | 4,695 | [
"VTK"
] | b24b0d254d86d4a1f446555da6a40b3702bc815bc47f47624677357fe8f9b8d3 |
"""
Copyright (c) 2015 Andreea Georgescu
Created on Wed Nov 19 00:18:55 2014
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.
... | SamWitte/Codds_DarkMatter | src/Data/DAMA2010Na.py | Python | gpl-2.0 | 1,823 | [
"Gaussian"
] | ee883136419b3df0148dcdaefb6c782dd510131056edca549e0553a7307eeeeb |
"""Support for package tracking sensors from 17track.net."""
import logging
from datetime import timedelta
import voluptuous as vol
from homeassistant.components.sensor import PLATFORM_SCHEMA
from homeassistant.const import (
ATTR_ATTRIBUTION,
ATTR_LOCATION,
CONF_PASSWORD,
CONF_SCAN_INTERVAL,
CONF... | fbradyirl/home-assistant | homeassistant/components/seventeentrack/sensor.py | Python | apache-2.0 | 10,883 | [
"VisIt"
] | efdd262925dda82df82a206654fbe077514d0129096360ddda8f650536c28d4e |
# coding: utf-8
# Copyright 2017 CERN. This software is distributed under the
# terms of the GNU General Public Licence version 3 (GPL Version 3),
# copied verbatim in the file LICENCE.md.
# In applying this licence, CERN does not waive the privileges and immunities
# granted to it by virtue of its status as an Intergo... | dquartul/BLonD | unittests/beam_profile/test_beam_profile_object.py | Python | gpl-3.0 | 12,422 | [
"Gaussian"
] | 6df566c2ab07e84b569a8114ec6ea737191486d49cf4fb32e563457d2002f603 |
import base64
import json
from django.contrib.auth import get_user_model
from django.http import HttpRequest
from django.core.exceptions import ImproperlyConfigured
from django.conf import settings
from django.test import TestCase
from django.core.urlresolvers import reverse
from django.test.client import Client
from ... | boedy1996/SPARC | geonode/geoserver/tests.py | Python | gpl-3.0 | 15,606 | [
"VisIt"
] | 1de41f7834eeb4dacdc718d99772a09e04d6b04e0c07fb27b593da001457c556 |
import logging
import yaml
from .bot import Espresso
config = yaml.load(file('botconfig.yaml', 'r'))
logging.basicConfig(level=getattr(logging, config['logging']['level']),
format="%(levelname)s from %(filename)s at %(asctime)s | %(message)s")
logging.debug("config is %s", config)
robot = Espre... | ratchetrobotics/espresso | espresso/main.py | Python | bsd-3-clause | 332 | [
"ESPResSo"
] | 81ec9390ac5ead78c992e1d7fd65756cbc183ffdebe33a03c15b5d7808bd879c |
# Copyright 2008 Brian Boyer, Ryan Mark, Angela Nitzke, Joshua Pollock,
# Stuart Tiffen, Kayla Webley and the Medill School of Journalism, Northwestern
# University.
#
# This file is part of Crunchberry Pie.
#
# Crunchberry Pie is free software: you can redistribute it and/or modify
# it under the terms of the GNU Gene... | brianboyer/newsmixer | social/settings.example.py | Python | gpl-3.0 | 2,370 | [
"Brian"
] | 55cf65763710158364da1f411516ba31f4fac00b0164974122f5fdd9c274d5fc |
#! /usr/bin/python
# -*- coding: utf-8 -*-
from itertools import chain
from MyHearthStone import ext
from MyHearthStone.ext import blank_minion
from MyHearthStone.ext import std_events, std_triggers
from MyHearthStone.ext import enc_common
from MyHearthStone.ext import Spell, Hero, HeroPower, Enchantment
from MyHeart... | fyabc/MiniGames | HearthStone2/MyHearthStone/data/packages/basic/basic_druid.py | Python | mit | 6,554 | [
"CRYSTAL"
] | f21ca22fe75f5b8e071529355b6a8b52de3738a4dbb21310ec26a9b1f5f9b191 |
import numpy as np
import parabem
from parabem.pan2d import vortex_2, vortex_2_v
from parabem.vtk_export import VtkWriter
from parabem.utils import check_path
source = parabem.Vector2(0, 0)
direction = parabem.Vector2(1, 0)
n = 20
a = np.linspace(-10, 10, n).tolist()
b = [parabem.Vector2(i, j) for i in a for j in a]
... | booya-at/paraBEM | examples/vtk/vtk_vortex_2.py | Python | gpl-3.0 | 775 | [
"VTK"
] | 9ec2857e473bb2e8e643aa30aa53234f7caa299f46ae8ead2c3470b5d959ceb3 |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2020, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
#import os
#from unittest import TestCase
#from exatomic import Universe
#from exatomic.gaussian import Output, Input
#from exatomic.gaussian.inputs import _handle_args
#class Test... | exa-analytics/atomic | exatomic/gaussian/tests/test_inputs.py | Python | apache-2.0 | 1,613 | [
"Gaussian"
] | 4a1416ced33f8b127964eb174ba11e6a0ce7f99400d92dace11ee40e757353b0 |
import os
import sys
import math
import collections
## Distribution ########################################################################################
class Distribution(object):
def __init__(self):
raise NotImplementedError("Subclasses should override.")
@classmethod
def mleEstimate(cls, ... | ashkonf/MixedNaiveBayes | src/distributions.py | Python | mit | 13,124 | [
"Gaussian"
] | 94ee169dcfd5a5127069e394d07ec66c72a9f35128fbe8f91389ba6f19df24a5 |
from Errors import error, message
import ExprNodes
import Nodes
import Builtin
import PyrexTypes
from Cython import Utils
from PyrexTypes import py_object_type, unspecified_type
from Visitor import CythonTransform, EnvTransform
class TypedExprNode(ExprNodes.ExprNode):
# Used for declaring assignments of a specifi... | Teamxrtc/webrtc-streaming-node | third_party/webrtc/src/chromium/src/third_party/cython/src/Cython/Compiler/TypeInference.py | Python | mit | 20,732 | [
"VisIt"
] | 1dcfedb1ffe1ddd26a2a4f5a0efe7d5273250c02d8fd9276f036dd522428fdb7 |
#
# 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 us... | ron8hu/spark | python/pyspark/mllib/clustering.py | Python | apache-2.0 | 36,951 | [
"Gaussian"
] | 1de707560e50c0ae16b37aa71c2c4fd78dee33d3c1ad732ee30f8619a0c24ad1 |
#!/usr/bin/python
# script preparing tab file to plot in R for small RNA profiling
# version 1 29-1-2012
# Usage plotter.py <bowtie input> <min size> <max size> <normalization factor> <tabular output>
import sys
def acquisition (file2parse, sizerange):
F = open (file2parse)
plus_table = {}
minus_table = {}
f... | mvdbeek/tools-artbio | unstable/local_tools/plotter.py | Python | mit | 1,722 | [
"Bowtie"
] | 3b7754702a69ce59f24e05bbb8b6e010cbad3d3bf2e0c7ae4f82718990d3dc51 |
import json
import uuid
from datetime import timedelta, datetime
import responses
from django.contrib.auth.models import User
from django.test import TestCase
from django.db.models.signals import post_save
from django.conf import settings
from django.core.cache import cache
from rest_framework import status
from rest... | praekelt/familyconnect-registration | registrations/tests.py | Python | bsd-3-clause | 66,498 | [
"VisIt"
] | bc49471160614e67223530e31c953182713ca1a5c2e073c4d76ff6ad9f17cdec |
# Python test set -- part 1, grammar.
# This just tests whether the parser accepts them all.
from test_support import *
print '1. Parser'
print '1.1 Tokens'
print '1.1.1 Backslashes'
# Backslash means line continuation:
x = 1 \
+ 1
if x <> 2: raise TestFailed, 'backslash for line continuation'
# Backslash does no... | atmark-techno/atmark-dist | user/python/Lib/test/test_grammar.py | Python | gpl-2.0 | 13,663 | [
"GULP"
] | 4c201bfd81d165e65528bf0f00ac87adcf9dee1932464de01837a8d61779c51d |
"""
Just-in-time compilation support.
"""
import abc
import copy
import os
import re
import ast
import logging
import inspect
import hashlib
import json
from collections import namedtuple
import tempfile
import ctree
from ctree.nodes import Project
from ctree.analyses import VerifyOnlyCtreeNodes
from ctree.frontend ... | mbdriscoll/ctree | ctree/jit.py | Python | bsd-2-clause | 14,292 | [
"VisIt"
] | 0f8c175c13cd14fac5840bb46e55f096c0d8c728b88afffd8ab6595f5b28183c |
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