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""" Top-level module to build or re-build the JSON files for
FRB host galaxies"""
from pkg_resources import resource_filename
import os
import sys
import warnings
from IPython import embed
import numpy as np
from astropy.coordinates import SkyCoord
from astropy import units
from astropy.table import Table
from astr... | FRBs/FRB | frb/builds/old_build_hosts.py | Python | bsd-3-clause | 97,489 | [
"Galaxy",
"Gaussian"
] | 774b8c85a6a921e94c79eb764422129d5158248714f6a9ec323529ceaef7ba74 |
# -*- coding: utf-8 -*-
"""
Tools for modifying suntans boundary condition files
Examples:
---------
Example 1) Modify the boundary condition markers with a shapefile:
------------------------------------------------------------------
>>from sunboundary import modifyBCmarker
>># Path to the ... | UT-CWE/Hyospy | Hyospy_ensemble/lib/SUNTANS/SUNTANS/sunboundary.py | Python | mit | 31,633 | [
"NetCDF"
] | 786533f2cafbe02cac771d67affc574b898082d53c181ee805bb5b8e2d947ecb |
#Si4707_I2C.py - Python library for controling the Silicon Labs Si4707 in I2C mode (BeagleBone Black)
#
#This file is a conversion of the provided Arduino code for AIW Industries Si4707
#breakout module with the following license information
#------------------------------------------------------------------------
... | gerrypower/weather_radio | raspberrypi/si4707_i2c.py | Python | gpl-3.0 | 36,798 | [
"CRYSTAL"
] | 530060a839abed141c78202bb2a7bd4f541f3a4804cac02e5784827ad19193fb |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2004 Martin Hawlisch
# Copyright (C) 2005-2008 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011 Michiel D. Nauta
#
# This program is free software; you can redistribut... | SNoiraud/gramps | gramps/plugins/export/exportvcard.py | Python | gpl-2.0 | 12,897 | [
"Brian"
] | 52c5e78499dbea4b060ffcccc9a10d185bb9d49116a193741da8579659de53f7 |
import copy
import logging
import lib.const as C
import lib.visit as v
from .. import util
from ..meta import class_nonce, register_class, class_lookup
from ..meta.program import Program
from ..meta.clazz import Clazz
from ..meta.method import Method
from ..meta.field import Field
from ..meta.statement import Stateme... | plum-umd/java-sketch | java_sk/rewrite/generator.old.py | Python | mit | 5,184 | [
"VisIt"
] | 5a8f75cc843e448683fbaee172185599a20cd7e604708e8ad1b0248e8b77daee |
#ImportModules
import ShareYourSystem as SYS
#Definition
MyBrianer=SYS.BrianerClass(
).set(
'-Populations',
[
(
'ManagingBeforeSetVariable',
{
'NeurongroupingBrianKwargVariablesDict':
{
'model':
'''
dv/dt = (ge+gi-(v+49*mV))/(20*ms) : volt
dge/dt = -ge/(5*ms) : volt
... | Ledoux/ShareYourSystem | Pythonlogy/draft/Simulaters/Brianer/draft/03_ExampleDoc.py | Python | mit | 1,598 | [
"Brian"
] | d004b7fc32a3b8d6ebdfabfa34c25ed7657bf68df84ba45a7a988a51e64ea2a2 |
#!/usr/bin/env python
"""
Sequence utilities and genome annotation methods
Created November 2013
Copyright (C) Damien Farrell
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; e... | dmnfarrell/epitopepredict | epitopepredict/sequtils.py | Python | apache-2.0 | 22,497 | [
"BLAST",
"Biopython"
] | e73880ee7b4cf4371ec8f4f3afa037bac1eccb33a827539c08331621c1570c37 |
from __future__ import division, absolute_import, print_function
import numpy as np
from numpy.matrixlib.defmatrix import matrix, asmatrix
# need * as we're copying the numpy namespace (FIXME: this makes little sense)
from numpy import *
__version__ = np.__version__
__all__ = np.__all__[:] # copy numpy namespace
__a... | MSeifert04/numpy | numpy/matlib.py | Python | bsd-3-clause | 9,727 | [
"Gaussian"
] | 581d457a8abc3f94499e2d0dd8be0261fa6fa68f9327bb352709401555ee05f9 |
"""
A function for asking the user for their Twitter API keys.
"""
import requests
from requests_oauthlib import OAuth1
from urllib.parse import parse_qs
def handshake():
# Default empty keys
consumer_key = ""
consumer_secret = ""
access_token = ""
access_token_secret = ""
bearer_token = i... | hugovk/twarc | twarc/handshake.py | Python | mit | 4,047 | [
"VisIt"
] | 5f09f95c9a41863ac2f2db19945fb1dacb076928c04297c0e0c0eea0771191d8 |
from ase.lattice.surface import fcc100, add_adsorbate
from ase.constraints import FixAtoms
from ase.calculators.emt import EMT
from ase.dimer import DimerControl, MinModeAtoms, MinModeTranslate
# Set up a small "slab" with an adatoms
atoms = fcc100('Pt', size = (2, 2, 1), vacuum = 10.0)
add_adsorbate(atoms, 'Pt', 1.61... | slabanja/ase | ase/test/dimer_method.py | Python | gpl-2.0 | 1,376 | [
"ASE"
] | ed14a8561768d5895e495559f9a8e3bb0e8b822716806880c7d83740a997d05a |
##
# Copyright 2009-2020 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | pescobar/easybuild-easyblocks | easybuild/easyblocks/t/tinker.py | Python | gpl-2.0 | 6,190 | [
"TINKER"
] | ce7583cd1222d4dbc05ba829bcd99825c0ab0d0c7360572dec42f8a634b7bca5 |
# 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/tools/info.py | Python | gpl-3.0 | 2,653 | [
"ESPResSo"
] | 288d46ff536733d070061e47f08e6ce8234b268b9ecf61d36d891f106ea8fbf0 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
import unittest
from pymatgen.io.shengbte import Control
from pymatgen.util.testing import PymatgenTest
test_dir = os.path.join(PymatgenTest.TEST_FILES_DIR, "shengbte")
this_dir = os.path.dirname(os.path.abspath(_... | vorwerkc/pymatgen | pymatgen/io/tests/test_shengbte.py | Python | mit | 4,265 | [
"pymatgen"
] | 615174ffb56c700810c9174ae5041f9d3009a19f0c3eb1509b287dfb42b0e2a1 |
#! /usr/bin/python
import re;
import os;
import sys;
import subprocess;
import multiprocessing;
import fnmatch
import numpy as np;
SCRIPT_PATH = os.path.dirname(os.path.realpath(__file__));
tools_path = '%s/../tools' % (SCRIPT_PATH);
SAMSCRIPTS = '%s/../tools/samscripts/src/' % (SCRIPT_PATH);
# sys.path.append('%s/.... | isovic/graphmap-reproduce | src/run-realdata.py | Python | mit | 97,163 | [
"BWA"
] | 38b54eb4fa960751bc2bfc88ab4e115e583fa318149d2faf4844e7e4bb6528d0 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Code for making plots for background classifiers (muon/random_noise/neutrinos).
"""
from matplotlib import pyplot as plt
from matplotlib.backends.backend_pdf import PdfPages
import numpy as np
from orcanet_contrib.plotting.utils import get_mc_info_and_other_datasets
... | ViaFerrata/DL_pipeline_TauAppearance | orcanet_contrib/plotting/bg_classifier.py | Python | agpl-3.0 | 20,479 | [
"Gaussian"
] | e1f38bc852370d6efa4ddb3f34d6451265661ed96b9985a888faf527940223d4 |
# -*- coding: utf-8 -*-
# Copyright 2007-2016 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... | hyperspy/hyperspy | hyperspy/io_plugins/jeol.py | Python | gpl-3.0 | 46,158 | [
"ADF"
] | 3280a032bf312d29811fb2d564cc0d4229490f1319b6bbfef1ccd9c63fac0a76 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
## all SI units
########################################################################################
## Plot the firing rate vs current injection curve for a Cerebellar Granule Cell neuron
## Author: Aditya Gilra
## Creation Date: 2012-07-12
## Modification Date: 2012-07-12... | dilawar/moose-full | moose-examples/neuroml/GranuleCell/FvsI_Granule98.py | Python | gpl-2.0 | 2,295 | [
"MOOSE",
"NEURON"
] | f6e7d5eca89963174a78dc815812aae2c78fe42a706a87469abfdfe44a765594 |
#
# ----------------------------------------------------------------------------------------------------
#
# Copyright (c) 2015, Oracle and/or its affiliates. All rights reserved.
# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
#
# This code is free software; you can redistribute it and/or modify it
# u... | olpaw/mx | mx_compat.py | Python | gpl-2.0 | 5,586 | [
"VisIt"
] | c2f3745389af93c934a4837766b1ccda3cb425b338e300a5630671a2b27ce3bc |
# Copyright 2020 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... | keras-team/keras | keras/engine/keras_tensor.py | Python | apache-2.0 | 26,629 | [
"VisIt"
] | facb01d29d8b70bbb2557134cddeed37c2f601adf3a63864ae7a7358a0952cb0 |
# -*- coding: latin-1 -*-
"""
Hydrogen Models
---------------
Hydrogen in HII regions is typically assumed to follow Case B recombination
theory.
The values for the Case B recombination coefficients are given by `Hummer &
Storey (1987)
<http://adsabs.harvard.edu/cgi-bin/nph-bib_query?bibcode=1987MNRAS.224..801H&db_ke... | vlas-sokolov/pyspeckit | pyspeckit/spectrum/models/hydrogen.py | Python | mit | 11,468 | [
"Gaussian"
] | aa14bc81c8c73786fd53007b713b1842a48b9c42fe8d7ce424a60323315ba791 |
#!/usr/bin/env python
#
# @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 redistri... | lothian/psi4 | psi4/share/psi4/fsapt/copy_pymol.py | Python | lgpl-3.0 | 1,344 | [
"Psi4",
"PyMOL"
] | 45885551fb6d50e3adff3e1b2428b6ddb3f9124b37ffc702cfa4b02374778b72 |
from abc import ABC, abstractmethod
import re
import logging
import serial
from serial.tools import list_ports
from .exceptions import (
ControllerNotConnectedException,
ControllerPortNotOpenException
)
from .utils import (
Observable, Observer, Event,
Visitor
)
LOGGER = logging.getLogger(__name__)
#... | glibersat/brewpiv2 | brewpiv2/controller.py | Python | agpl-3.0 | 7,809 | [
"VisIt"
] | 3d5531a3ab875ea7171b2ee226ee38027c7e514a150e9bf1d528a4ccd0f16966 |
#
# Copyright (C) 2015-2017 University of Oxford
#
# This file is part of msprime.
#
# msprime 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... | shajoezhu/msprime | msprime/simulations.py | Python | gpl-3.0 | 53,800 | [
"DIRAC"
] | 7ebf6689b62023154217d69c24468fe9b520ab437e595069d7b12461691283d3 |
# -*- coding: utf-8 -*-
from ev3.lego import TouchSensor
from ev3.lego import ColorSensor
from ev3.lego import InfraredSensor
from override import m_over as Motor
from override import mm_over as MMotor
from ev3.ev3dev import LED
from ev3.ev3dev import Tone
from ev3.ev3dev import Key
import time
import signal
import sy... | KMPSUJ/lego_robot | modules/Robot.py | Python | mit | 3,972 | [
"Amber"
] | ec415090201c74d3e1191c560238e2305259ecc6420eef082a83a0335ecf7673 |
# coding: utf-8
from __future__ import unicode_literals
import re
from .mtv import MTVServicesInfoExtractor
from ..utils import update_url_query
class NickIE(MTVServicesInfoExtractor):
# None of videos on the website are still alive?
IE_NAME = 'nick.com'
_VALID_URL = r'https?://(?:(?:www|beta)\.)?nick(?... | phihag/youtube-dl | youtube_dl/extractor/nick.py | Python | unlicense | 8,073 | [
"VisIt"
] | bb8d400d0958e42272da42acdecb1ed7473b7e3670858544879332beb3bebd05 |
"""
raven.middleware
~~~~~~~~~~~~~~~~~~~~~~~~
:copyright: (c) 2010-2012 by the Sentry Team, see AUTHORS for more details.
:license: BSD, see LICENSE for more details.
"""
import galaxy.eggs; galaxy.eggs.require( "raven" )
from raven import Client
from raven.utils.wsgi import get_current_url, get_headers, \
get_env... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/web/framework/middleware/sentry.py | Python | gpl-3.0 | 2,288 | [
"Galaxy"
] | b39d46f378c5a911d0d3cb9285ddca308d669d1f30a4940b1cf43ab118765b84 |
#!/usr/bin/env python
# encoding: utf-8
"""Description: sync the configuration db with single xml files.
load configuration from xml file, insert to db.
or load configuration from db, save to xml file.
"""
__version__ = "0.1"
__author__ = "@boqiling"
from simplexml import loads, dumps
from configuration import PGEMCo... | fanmuzhi/UFT | src/UFT/backend/config_io.py | Python | gpl-3.0 | 5,824 | [
"CRYSTAL"
] | 4894d85e38114f79e47398931755d9103a655160739db5689c74344846bb7f43 |
#!/usr/bin/env python
try:
from setuptools import setup
except ImportError:
from distutils.core import setup
setup(name='bio-APRICOT',
version='1.3.3',
description=('Sequence-based identification and characterization '
'of protein classes'),
author='Malvika Sharan',
... | malvikasharan/APRICOT | setup.py | Python | isc | 963 | [
"Biopython"
] | 3c9df47032f26582bfde7e36e4b97d4781838678daeaefdbd571f63d5f246143 |
"""Check if spin-symmetry is conserved"""
from ase import Atoms
from ase.calculators.nwchem import NWChem
def main():
"""Check is independence of alignment is conserved"""
energies = []
cr_atom = Atoms('Cr', positions=[(0, 0, 0)], pbc=False)
for orientation in range(2):
imm = 6 * (-1) ** orien... | suttond/MODOI | ase/test/nwchem/nwchem_spin_symmetry.py | Python | lgpl-3.0 | 865 | [
"ASE",
"NWChem"
] | 5d0a82acb55291c4f8a01e4cf8c9defc6dadf891ba679e4cf846cfc8f3bfd052 |
#!/usr/bin/env python
#
# Copyright 2013 Tristan Bereau and Christian Kramer
#
# 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... | MMunibas/FittingWizard | scripts/calc_Multipole_Gauss_MEP_comp.py | Python | bsd-3-clause | 11,908 | [
"Gaussian"
] | a1e12fd4f3366d009027e872e3febf6ff4c497e0218d9776a19b391166a2ae01 |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to
# make it easier to submit large numbers of jobs on supercomputers. It
# provides a python interface to physical input, ... | pylada/pylada-light | src/pylada/ipython/launch/asone_script.py | Python | gpl-3.0 | 3,459 | [
"CRYSTAL",
"VASP"
] | a94520f490099abe4d86df7a46d1871157086464bbcf3a00cbc99e92372ae2f2 |
from __future__ import print_function
from rdkit import RDConfig
import os.path
from rdkit.six.moves import cPickle
from rdkit import Chem
from rdkit.Chem import Descriptors
descrs = ['BertzCT', 'Chi0', 'HallKierAlpha', 'Ipc', 'Kappa3', 'LabuteASA', 'SMR_VSA1', 'SMR_VSA10',
'SMR_VSA2', 'SMR_VSA3', 'SMR_VSA4'... | rvianello/rdkit | rdkit/Chem/test_data/BuildDescrsTestSet.py | Python | bsd-3-clause | 1,794 | [
"RDKit"
] | f5e27dd6c665a95c4ea217124092c6af31931bbee52c1e33531c37d6c85048a6 |
# coding:utf-8
"""
@file: game.py
@author: lyn
@contact: tonylu716@gmail.com
@python: 3.3
@editor: PyCharm Mac
@create: 2017/1/11 20:00
@description:
保存德州扑克游戏逻辑
"""
import time
from itertools import combinations
from .compare import CompareModel
from .judge import JudgeModel
from .patterns ... | lyn716/deep_stack | utils/game.py | Python | apache-2.0 | 11,188 | [
"CASINO"
] | c5107ca011363986ba57bf292975723c1c6c9bcdc056c201f502453720aa9aa3 |
""" core implementation of testing process: init, session, runtest loop. """
import enum
import fnmatch
import functools
import importlib
import os
import sys
import attr
import py
import _pytest._code
from _pytest import nodes
from _pytest.config import directory_arg
from _pytest.config import hookimpl
from _pytest.... | randyzingle/tools | kub/services/archive/cdk/python/sample-app/.env/lib/python3.6/site-packages/_pytest/main.py | Python | apache-2.0 | 24,506 | [
"VisIt"
] | e873b9c90c09e5a49c09ab8e71796fb1e4b9fbcdd05a79459f28fb40678ae30d |
'''@package docstring
@author: Jyh-Miin Lin (Jimmy), Cambridge University
@address: jyhmiinlin@gmail.com
Created on 2013/1/21
================================================================================
This file is part of pynufft.
pynufft is free software: you can redistribute it and/or modify
it u... | jyhmiinlin/cineFSE | CsTransform/pynufft2.py | Python | gpl-3.0 | 57,898 | [
"Mayavi"
] | 9a404c85fea85119f6014002c3808199d86e2b8ebb46034532626d016d68a846 |
# -*- coding: utf-8 -*-
'''
IMProToo
Improved MRR Processing Tool
Python toolkit to read, write and process MRR Data. Raw Data, Average and
Instantaneous Data are supported.
Copyright (C) 2011-2021 Maximilian Maahn, U Leipzig
maximilian.maahn_AT_uni-leipzig.de
https://github.com/maahn/IMProToo
This program is free ... | aronnem/IMProToo | IMProToo/core.py | Python | gpl-3.0 | 134,704 | [
"NetCDF"
] | 6a459cbdf9c17c1387552cfc45f23f957a3f8b83506908d2e374ad264933720b |
# (C) British Crown Copyright 2014 - 2016, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | arulalant/UMRider | others/ncmrwfIRIS/_load_convert.py | Python | gpl-2.0 | 82,618 | [
"Gaussian"
] | cc4ec9496f92530d4cee2079dd238f3c3d55c04c21e390450bb6cbca5276ce9c |
# -*- 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 required by applicable law or... | googleapis/python-grafeas | tests/unit/gapic/grafeas_v1/test_grafeas.py | Python | apache-2.0 | 149,238 | [
"Octopus"
] | 3581b1b1ba4cb71afc06238f582c4bcac549009f097202d3af5a5fb9e8d19fa2 |
#!/usr/bin/env python
# for python 2 / 3 compatibility
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
try :
range = xrange
except NameError :
pass
try :
import ConfigParser as configparser
except Import... | andyofmelbourne/crappy-crystals | process/forward_model.py | Python | gpl-3.0 | 5,324 | [
"CRYSTAL"
] | 6e6ad7a9b684b4cc3a6306c61c2f43c6b6c65f934a9a90f59fa26c0647f3aed3 |
"""Support for Google - Calendar Event Devices."""
from datetime import datetime, timedelta, timezone
from enum import Enum
import logging
import os
from googleapiclient import discovery as google_discovery
import httplib2
from oauth2client.client import (
FlowExchangeError,
OAuth2DeviceCodeError,
OAuth2We... | sander76/home-assistant | homeassistant/components/google/__init__.py | Python | apache-2.0 | 14,245 | [
"VisIt"
] | fdb6612d63bccfb9ff7ac2b9a2f8e0338316e96704ff9808536d8f2f5072f72d |
# encoding: utf8
from quantiphy import (
Quantity, add_constant, set_unit_system,
QuantiPhyError, IncompatibleUnits, UnknownPreference, UnknownConversion,
UnknownUnitSystem, InvalidRecognizer, UnknownScaleFactor, InvalidNumber,
ExpectedQuantity, MissingName,
)
import pytest
def test_constants():
Q... | KenKundert/quantiphy | tests/test_constants.py | Python | mit | 11,945 | [
"Gaussian"
] | 3d827f7d9e94181b1f4fdcb03bfce9f6422f5c3e8447a647532de01df5945dad |
# $Id$
#
# Copyright (C) 2003-2008 Greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
from rdkit import Chem... | rdkit/rdkit-orig | rdkit/Chem/FragmentCatalog.py | Python | bsd-3-clause | 2,388 | [
"RDKit"
] | dc31ee0262c8b8adf07838c6d9297b35fbfe04fd8545b70f5ccd1aa61c7fed5d |
try:
import unittest2 as unittest
except ImportError:
import unittest
from Ivy.io.fasta import Fasta
from Ivy.helper import find_app_root
import os
import os.path
import pysam
class TestFasta(unittest.TestCase):
def setUp(self):
path = 'sample/hg19_mock.fasta'
self.mock_fasta = os.path.joi... | soh-i/Ivy | src/Ivy/tests/test_fasta.py | Python | gpl-2.0 | 1,733 | [
"pysam"
] | fa36292d25652534bbd10d039b72a24179eed9ce0826ca9add02fb2a62d7003c |
from typing import List
import bgmi.config
from bgmi.config import BANGUMI_MOE_URL, SHARE_DMHY_URL
ACTION_ADD = "add"
ACTION_FETCH = "fetch"
ACTION_FILTER = "filter"
ACTION_DELETE = "delete"
ACTION_UPDATE = "update"
ACTION_CAL = "cal"
ACTION_CONFIG = "config"
ACTION_DOWNLOAD = "download"
ACTION_LIST = "list"
ACTION_M... | codysk/BGmi | bgmi/lib/constants.py | Python | mit | 12,070 | [
"MOE"
] | e384006181a4d7519c101d0ec8837d0ca70f0fa13c156092cdf28a983413025a |
from python.src.neural_networks.neural_network_utils import NeuralNetworkUtils
from python.src.neurons.neurons import NeuronType
import math
import random
# http://home.agh.edu.pl/~vlsi/AI/backp_t_en/backprop.html
# http://www.cse.unsw.edu.au/~cs9417ml/MLP2/
class TrainingResult(object):
def __init__(self, epo... | DomenicD/dom_ml_playground | python/src/learning_algorithms/backpropagation.py | Python | mit | 3,948 | [
"NEURON"
] | 1b81e643827bc672112285c46b50aa5c8afdc89062250ae7cfae75671817be52 |
# Copyright 2013-2020 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 *
import os
class Paraview(CMakePackage, CudaPackage):
"""ParaView is an open-source, multi-platfo... | iulian787/spack | var/spack/repos/builtin/packages/paraview/package.py | Python | lgpl-2.1 | 16,115 | [
"NetCDF",
"ParaView",
"VTK"
] | a0ddc9dd3e6073797de6039c27d1bc456a5b1f9043dacb154d7671778d305369 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# generated by wxGlade 0.6.3 on Mon Sep 15 19:43:15 2008
import wx
import os
from matplotlib import use
use('WXAgg')
from pylab import *
from pdf2py import data,channel,listparse, pdf, readwrite
from mri import img, viewmri, transform, mr2vtk, vtkview, sourcesolution2img
... | badbytes/pymeg | gui/wx/wxpymeg_v20.py | Python | gpl-3.0 | 122,045 | [
"VTK"
] | f326d7a12ade7e31fc850ab14aa1ba4911effe5c0cd2e8a81fecdfe87cc99783 |
# -*- coding: utf-8 -*-
from flask import Blueprint, render_template, request, redirect, flash, \
url_for, abort, json
from flask.ext.login import login_required
from octopus.case import queries
from octopus.case.forms import EditCoreCaseForm, NewCaseForm, CaseTagsForm, \
CaseStaffForm, CaseFileForm, PageDownForm
... | quaintm/octopus | octopus/case/views.py | Python | bsd-3-clause | 5,202 | [
"Octopus"
] | b6a876194b6a3724d526558a036e3773d7302aa742bf5aede247a0e8fd190b4f |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2018 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | amjames/psi4 | psi4/driver/p4util/python_helpers.py | Python | lgpl-3.0 | 12,610 | [
"Psi4"
] | 36658c23a55fcf052227940f7d96f7799546649b5d6bba477943d5ab54017696 |
#!/usr/bin/env python
import subprocess as sp
import psycopg2, os, glob
from datetime import datetime
PATH_TO_LOG = '/tmp/current_beam.log'
PATH_TO_PNGS = '/var/beam_images/'
env = os.getenv('EOR_ENV', "dev")
if env == "prod":
GET_OBS_INFO = '/home/ubuntu/MWA_Tools/scripts/get_observation_info.py'
elif env =="sta... | ryandougherty/mwa-capstone | MWA_Tools/eorlive_v2/scripts/generate_beam_image.py | Python | gpl-2.0 | 1,915 | [
"Bowtie"
] | f0936b9a1b6dd1cdd76b926f71422cebbf237bc7d63ebbbc52fc29353ae23636 |
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yasharmaster/scancode-toolkit | tests/commoncode/test_timeutils.py | Python | apache-2.0 | 4,708 | [
"VisIt"
] | 3d3ece8dff5434d7b8876666e20ea0e807ef1d72e8c8dc63a11f86cf4db09e6c |
#!/usr/bin/env python
########################################
#Globale Karte fuer tests
# from Rabea Amther
########################################
# http://gfesuite.noaa.gov/developer/netCDFPythonInterface.html
import math
import numpy as np
import pylab as pl
import Scientific.IO.NetCDF as IO
import matplotlib as... | CopyChat/Plotting | Python/climate_change/global_changes_tas_rcp85.py | Python | gpl-3.0 | 7,729 | [
"NetCDF"
] | 8a4a85756bc5f9d10ee3de67b0b62c12577a9544ce7b21abcabfc7831edc3140 |
# ----------------------------------------------------------------------
# Numenta Platform for Intelligent Computing (NuPIC)
# Copyright (C) 2013, Numenta, Inc. Unless you have an agreement
# with Numenta, Inc., for a separate license for this software code, the
# following terms and conditions apply:
#
# This progra... | numenta/nupic.vision | src/nupic/vision/image/__init__.py | Python | agpl-3.0 | 15,369 | [
"Gaussian"
] | 8709515352330f73b9e4253a0c8db0318487fd57b2c1c4b5f8ba628cc7cec2e4 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2007 Async Open Source
##
## This program is free software; you can redistribute it and/or
## modify it under the terms of the GNU Lesser General Public License
## as published by the Free Software Foundation; either version 2
## of the License, or... | andrebellafronte/stoq | stoqlib/drivers/__init__.py | Python | gpl-2.0 | 901 | [
"VisIt"
] | 264b9da6dfe2a1ea585b373d05f9ca092d9d9d08e906cd0948ca6a76d0072486 |
#-*- coding:utf-8 -*-
from docutils import nodes
from docutils.parsers import rst
def setup(app):
app.add_node(youtube,
html=(visit, depart))
app.add_directive('youtube', YoutubeDirective)
class youtube(nodes.General, nodes.Element):
pass
def visit(self, node):
url = u'//www.youtub... | indigits/sparse-plex | docs/extensions/youtube.py | Python | apache-2.0 | 919 | [
"VisIt"
] | 140867d74253da04efb936bdc3020b27829b49ee8a671e3b9a85168a2f3e8055 |
"""
Galaxy Quotas
"""
import logging
import galaxy.util
log = logging.getLogger(__name__)
class NoQuotaAgent( object ):
"""Base quota agent, always returns no quota"""
def __init__( self, model ):
self.model = model
self.sa_session = model.context
def get_quota( self, user, nice_size=Fals... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/quota/__init__.py | Python | gpl-3.0 | 7,212 | [
"Galaxy"
] | bbfb08bb9bd77fcb28ad68449b64d131b98a0336c6150ea83aedf08b2912fefe |
##
## Biskit, a toolkit for the manipulation of macromolecular structures
## Copyright (C) 2004-2012 Raik Gruenberg & Johan Leckner
##
## 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 v... | ostrokach/biskit | Biskit/Fold_X.py | Python | gpl-3.0 | 10,386 | [
"FoldX"
] | f6fa537d2020f8b74420db2ebb3eb1d790fdf3e9755ddcac3e27c10ee4f93fc9 |
import numpy as np
from deepchem.utils.typing import RDKitMol
from deepchem.utils.data_utils import pad_array
from deepchem.feat.base_classes import MolecularFeaturizer
from deepchem.feat.molecule_featurizers.atomic_coordinates import AtomicCoordinates
class BPSymmetryFunctionInput(MolecularFeaturizer):
"""Calcula... | lilleswing/deepchem | deepchem/feat/molecule_featurizers/bp_symmetry_function_input.py | Python | mit | 1,663 | [
"RDKit"
] | 80921ba20e7ac1303d9f74bfaa55bae93bcaf9615f40e1ffb988fddbd4c9bcf9 |
# -*- coding: utf-8 -*-
''' Geometric entities representation (k-points,lines,surfaces,bodies,...)
'''
__author__= "Luis C. Pérez Tato (LCPT) , Ana Ortega (AO_O) "
__copyright__= "Copyright 2016, LCPT, AO_O"
__license__= "GPL"
__version__= "3.0"
__email__= "l.pereztato@ciccp.es, ana.ortega@ciccp.es "
import vtk
from p... | lcpt/xc | python_modules/postprocess/xcVtk/CAD_model/vtk_CAD_graphic.py | Python | gpl-3.0 | 3,028 | [
"VTK"
] | 19430154c8b156e4d9a7b761aec8c00abd7a0798ee6199f41bc79b7d72269271 |
from django.utils.translation import ugettext_lazy as _
from crystal_dashboard.dashboards.crystal import dashboard
import horizon
class Filters(horizon.Panel):
name = _("Filters")
slug = "filters"
dashboard.CrystalController.register(Filters)
| Crystal-SDS/dashboard | crystal_dashboard/dashboards/crystal/filters/panel.py | Python | gpl-3.0 | 255 | [
"CRYSTAL"
] | 1fe64faf93ab85e5e21e650ac620b0d02986a866da33abbfa6f4a067f9e91991 |
import pprint
import tempfile
from DIRAC import gConfig, gLogger
from DIRAC.Resources.Catalog.FileCatalog import FileCatalog
from DIRAC.ConfigurationSystem.Client.Helpers.Registry import getVOForGroup
from DIRAC.ConfigurationSystem.Client.Helpers.Operations import Operations
from DIRAC.FrameworkSystem.Client.ProxyMana... | DIRACGrid/WebAppDIRAC | src/WebAppDIRAC/WebApp/handler/JobLaunchpadHandler.py | Python | gpl-3.0 | 8,851 | [
"DIRAC"
] | c909fbf9c319754b193a2f160290670394163fb5538f4805e8a4caba2ab59310 |
import config
import datetime
import os
import sys
import bio
# set these
insertion = True
mapper = 'bwa'
#mapper = 'bwa_indel'
#mapper = 'bowtie2_indel'
fasta = 'hiv'
# all good
if insertion:
tmpl = 'batch/find_longest_indel_tandem.cfg'
start = 20
else:
tmpl = 'batch/find_longest_deletion_tandem.cfg'
start... | supernifty/mgsa | mgsa/find_longest_indel.py | Python | mit | 1,618 | [
"BWA"
] | 2c8e1eef3aa92b5dbe9eacfa3e9383b686107752c1f898d8ee8271b7857b7f57 |
# Copyright 2019 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... | karllessard/tensorflow | tensorflow/python/keras/layers/kernelized.py | Python | apache-2.0 | 11,153 | [
"Gaussian"
] | bfe3ff4db4355a25280f5845566a634f6d7369ddfcfbfa5ac3119f89533d8c40 |
# Copyright (C) 2013 by Eka A. Kurniawan
# eka.a.kurniawan(ta)gmail(tod)com
#
# 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; version 2 of the License.
#
# This program is distributed in the hop... | ekaakurniawan/hppNeuroDock | PyNeuroDock/Atom.py | Python | gpl-3.0 | 33,265 | [
"Dalton",
"Gaussian"
] | 2641a66c4a5daeb21554332712585a943f61f1336c8f7bcffb6dae5ded0b5def |
'''
bilat-filter.py
Experiment with OpenCV for FITS files.
http://docs.opencv.org/trunk/doc/py_tutorials/py_tutorials.html
Author: S.T. Castle
Created: 20150213
'''
import numpy as np
import cv2
import fileinput
from matplotlib import pyplot as plt
import sys
from fits-proc import FitsProc
def main():
for file... | castlest/shell-detection | fits-algs/convolutions-plot.py | Python | bsd-3-clause | 1,711 | [
"Gaussian"
] | 94694cd3c4056ba492e7ed271cabc292b638faa07417af901605a0b16c77f1fb |
##############################################################################
##############################################################################
# Example code for
# quasi-Newton particle Metropolis-Hastings
# for a linear Gaussian state space model
#
# Please cite:
#
# J. Dahlin, F. Lindsten, T. B. Sch\"{... | compops/qpmh2-sysid2015 | state/kalman.py | Python | gpl-3.0 | 7,543 | [
"Gaussian"
] | 3994984e5069bb54edfe6ea4ce61020f704707f128a2aab9fb38161c24a1a69f |
"""
End-to-end test for cohorted courseware. This uses both Studio and LMS.
"""
import json
from nose.plugins.attrib import attr
from studio.base_studio_test import ContainerBase
from ..pages.studio.settings_group_configurations import GroupConfigurationsPage
from ..pages.studio.auto_auth import AutoAuthPage as Stud... | zadgroup/edx-platform | common/test/acceptance/tests/test_cohorted_courseware.py | Python | agpl-3.0 | 9,754 | [
"VisIt"
] | 23a9da8577d064014d51aaf71b3b4b4dcb374b7f613a5ff77bb696d6ee64df8f |
# Lint as: python3
# Copyright 2020 The TensorFlow Probability 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 ... | tensorflow/probability | spinoffs/inference_gym/inference_gym/targets/ill_conditioned_gaussian.py | Python | apache-2.0 | 4,270 | [
"Gaussian"
] | b3fb1be9117d0ce980f32d898494405008d3b1fae9bfdb75cbc959b1406658f1 |
# 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/tools/vmd.py | Python | gpl-3.0 | 4,751 | [
"ESPResSo",
"VMD"
] | 524d405b38ae26eefdbac472945d7db6e6521348b17b4f22685167a3a2817d86 |
"""Berendsen NPT dynamics class."""
import numpy as np
from ase.md.nvtberendsen import NVTBerendsen
import ase.units as units
class NPTBerendsen(NVTBerendsen):
"""Berendsen (constant N, P, T) molecular dynamics.
This dynamics scale the velocities and volumes to maintain a constant
pressure and temp... | askhl/ase | ase/md/nptberendsen.py | Python | gpl-2.0 | 5,991 | [
"ASE"
] | 8f53de3035d0dcf1c8ddc2db8366218e19620221e951f55de2f7857847b46d55 |
'''dedup_grouped_bam - Deduplicate a BAM file using the UMI groups from umi_tools group
=======================================================================================
:Author: Tom Smith
:Release: $Id$
:Date: |today|
:Tags:
Purpose
-------
The purpose of this script is to sensibly deduplicate reads where
mul... | k3yavi/alevin | testing/src-py/dedup_grouped_bam.py | Python | gpl-3.0 | 12,086 | [
"pysam"
] | d35c392d5adad5060925375768f6750f4b34df7c068afca3c92b92adda1b007f |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Debugging parameters
sze = 300
reader = vtk.vtkExodusIIReader()
reader.SetFileName(VTK_DATA_ROOT + "/Data/disk_out_ref.ex2")
reader.UpdateInformation()
reader.SetPointResultArraySt... | SimVascular/VTK | Filters/SMP/Testing/Python/TestSMPContourGridWithSpanSpace.py | Python | bsd-3-clause | 1,153 | [
"VTK"
] | db94f9b4a9dbb3db45bbbab99a183e133d98099b9c96a122331d5ec3618b3fd0 |
#!/Users/nicolasf/anaconda/bin/python
# -*- coding: utf-8 -*-
# ==================================================================================
# code get_daily_TRMM.py
# Description: download TRMM 3B42 RT binary files for
# TAGS:3B42:... | nicolasfauchereau/ICU | maps/TRMM/get_daily_TRMM.py | Python | bsd-3-clause | 3,303 | [
"NetCDF"
] | 8eeb632a59a6a1ed3915920e4a1de98583e1805543246c948727ad175e70152f |
#!/usr/bin/env python
#
# ingestPlot.py
#
# TODO: Update the description below
#
# This is a simple plotter for the data coming out of tMSSink, the ingest MS writer simulation app
# that Max wrote to test the write IO issues we are having with scratch2.
#
# It reads in a file created by the tMSSink program, extracts th... | ATNF/askap-benchmarks | current/mpiperf/writePlot.py | Python | gpl-2.0 | 4,023 | [
"Galaxy"
] | 33101d4f69efb2a0b98513348d42f2c6e44ef9113fde4c58bc02419e890c07e5 |
##############################################################################
# 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/cblas/package.py | Python | lgpl-2.1 | 2,364 | [
"BLAST"
] | 0dfbc4bb71772d25846a62e42837aa3b41dfa70dc3c10cb5ad7a50d27b564f80 |
#!/usr/bin/env python
import numpy as np
import gzip
import argparse
parser = argparse.ArgumentParser(description='Reads CP2K PDOS files')
parser.add_argument('file', type=argparse.FileType('r'), help='PDOS output file to read.')
# range options
parser.add_argument('--limit', default=-1, type=int,
help='The max... | ferchault/euston | src/tools/es_cp2kpdos.py | Python | lgpl-3.0 | 10,777 | [
"CP2K",
"Gaussian"
] | 99a4c3792c167164d4388073e54ca7ee3fa736979ee6f2314e33128a687bb407 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 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
#... | jH0ward/psi4 | psi4/driver/procrouting/mcscf/__init__.py | Python | lgpl-3.0 | 953 | [
"Psi4"
] | 312f6d9b0ddf4a724535c00f74fd79cc920e862697aff8c811207cb5002bab32 |
#!/usr/bin/python
'''USAGE: annotate_fasta.py Fasta BLASToutput annotatedFasta
This script annotates a fasta file with sequence names determined from a BLAST of that file.
'''
import sys
fasta_file = open(sys.argv[1],'r')
output_file = open(sys.argv[3],'w')
# Write dictionary from BLAST output
with open(sys.argv[2],'... | mjenior/Blog_scripts | annotate_fasta.py | Python | mit | 2,061 | [
"BLAST"
] | 9822070ca513e510119748a40e3db370b074c8d8c695e988ccf8d8e046531034 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# 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.
... | davidobrien1985/ansible-modules-core | windows/win_lineinfile.py | Python | gpl-3.0 | 6,279 | [
"Brian"
] | 442aa176db7d34ec8a279037581aab1facbb2cda706f75aa6ffcc1478861bece |
#
# Copyright 2016 The BigDL 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 applicable law or agreed to in ... | intel-analytics/BigDL | python/orca/src/bigdl/orca/data/image/parquet_dataset.py | Python | apache-2.0 | 16,354 | [
"ORCA"
] | aa70d3e19cc748b9e2f534a0e560182f0e3f748332d2a22799614efd7a97003a |
"""
Displays Agg images in the browser, with interactivity
"""
from __future__ import (absolute_import, division, print_function,
unicode_literals)
# The WebAgg backend is divided into two modules:
#
# - `backend_webagg_core.py` contains code necessary to embed a WebAgg
# plot inside of a web... | yuanagain/seniorthesis | venv/lib/python2.7/site-packages/matplotlib/backends/backend_webagg.py | Python | mit | 12,216 | [
"VisIt"
] | 716b70f23e781b57ea5d074ac21479047f9931eaa7e89640f2260fb7f5bb61ba |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import re
import signal
import sys
import json
from html.parser import HTMLParser
from collections import OrderedDict
from xml.etree import ElementTree
from urllib.parse import urlencode
from urllib.request import urlopen
import multiprocessing
from multiprocessing.pool im... | Frozen-Developers/android-periodic-table | build_db.py | Python | gpl-3.0 | 30,099 | [
"CRYSTAL"
] | adbb2973621426ae1f1b3eec3efa9b02bafa5d140d8d1f1017e7eab7241de43a |
"""
DataWriter.py
"""
from DataController import DataController
from DataReader import DataReader
from vtk import vtkMetaImageWriter
from vtk import vtkXMLImageDataWriter
class DataWriter(DataController):
"""
DataWriter writes an image data object to
disk using the provided format.
"""
def __init__(self):
sup... | berendkleinhaneveld/Registrationshop | core/data/DataWriter.py | Python | mit | 1,183 | [
"VTK"
] | 346ca1b1c857ed50130a07e1e1a1b14ea23c639b913f50f236033995d493b13d |
# -*- coding: utf-8 -*-
# Copyright 2016 Onestein (<http://www.onestein.eu>)
# License AGPL-3.0 or later (http://www.gnu.org/licenses/agpl.html).
from odoo import fields, models
class ResPartner(models.Model):
_inherit = 'res.partner'
type = fields.Selection(selection_add=[('visit', 'Visit Address')])
| VitalPet/addons-onestein | partner_contact_type_visit/models/res_partner.py | Python | agpl-3.0 | 315 | [
"VisIt"
] | 0139abf12c65ad54280646a27dd2461bac6c5c3e28d1940587026d34126a4377 |
#!/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... | gkc1000/pyscf | pyscf/pbc/tdscf/kuhf.py | Python | apache-2.0 | 12,812 | [
"PySCF"
] | 0742f5a536b2eed5d7023d0ee1a0750e73d4460e5d4f547e71ff471e0ae85016 |
#!/usr/bin/env python
# encoding: utf-8
#| Copyright Inria May 2015
#| This project has received funding from the European Research Council (ERC) under
#| the European Union's Horizon 2020 research and innovation programme (grant
#| agreement No 637972) - see http://www.resibots.eu
#|
#| Contributor(s):
#| - Jean-Bap... | jbmouret/limbo | waf_tools/xcode.py | Python | gpl-3.0 | 12,550 | [
"Gaussian"
] | 066c969dc927909724c1547d1f9ba69464603a349664bfc021407d00535de32d |
from pyscf.pbc.gto import Cell
from pyscf.pbc.scf import RHF
from pyscf.pbc.tdscf import TDHF
from pyscf.pbc.tdscf.rhf_slow import PhysERI, PhysERI4, PhysERI8, TDRHF
from pyscf.tdscf.common_slow import eig
from test_common import retrieve_m, retrieve_m_hf, assert_vectors_close
import unittest
from numpy import testin... | gkc1000/pyscf | pyscf/pbc/tdscf/test/test_rhf_slow.py | Python | apache-2.0 | 3,697 | [
"PySCF"
] | 7c85496b0e0f9e53a3d34fde80a5fbbd63e665f892961877c2fbda20e20a091d |
import sys, os, re
import numpy, math
import HTSeq
###########################################
def addBin(array1, binLen):
binNum = math.ceil( float(len(array1)) / float(binLen) ) ## NOT math.floor
binNum = int(binNum)
array2 = numpy.zeros( binNum, dtype='float64' )
for i in range(0, binNum):
... | CTLife/SomeRecords | test/HTSeq_Genes_Full.py | Python | gpl-3.0 | 10,186 | [
"HTSeq"
] | a833a92c8ae7076a332621f65831f77af6a88e6c41493b879e651fc0068247fa |
import telepot
import time
import requests
import urllib
import urllib2
import json
from watson_developer_cloud import NaturalLanguageClassifierV1
#natural_language_classifier = NaturalLanguageClassifierV1(
# username = ''
# password= ''
#)
welcomeMsg = 'Welcome to TravelBot. It sends you latest ticket prices,temprat... | xorforce/ibmHack-delhi | 1.py | Python | mit | 2,858 | [
"VisIt"
] | 1d228cf32d9edef0088f434eac0e1dd8a4cd884f5998c391a0df0ad62ba20890 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import os
from pathlib import Path
import json
import gzip
import numpy as np
import warnings
from shutil import copyfile, copyfileobj
from monty.tempfile import ScratchDir
import xml.etree.c... | tschaume/pymatgen | pymatgen/io/vasp/tests/test_outputs.py | Python | mit | 74,981 | [
"VASP",
"pymatgen"
] | 9fc744992c005852d2ba5f741842723d0fdf83074fc1415b362b787ad6b60d1a |
"""Contains the Slide parent class."""
# display.py
# Mission Pinball Framework
# Written by Brian Madden & Gabe Knuth
# Released under the MIT License. (See license info at the end of this file.)
# Documentation and more info at http://missionpinball.com/mpf
import logging
import uuid
from mpf.system.timing import... | spierepf/mpf | mpf/media_controller/core/slide.py | Python | mit | 16,188 | [
"Brian"
] | 669335a26939e3f4f454dd51abde4d34e1c0a901ab71f76052cba8c3d6cea8e5 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
################################################################################
# Copyright (C) 2012 Travis Shirk <travis@pobox.com>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publi... | gaetano-guerriero/eyeD3-debian | examples/tag_example.py | Python | gpl-3.0 | 6,923 | [
"BLAST",
"MOE"
] | 7a741abcb77945865a983a6245539dd54009afe6a67e710f9906bf055f85847b |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# This software (including its Debian packaging) is available to you under the terms of the GPL-3, see
# "/usr/share/common-licenses/GPL-3".
# Software is created and maintained by Laboratory of Biomolecular Systems Simulation at University of Gdansk.
# Contributors:
# - ... | tomaszmakarewicz/Dynamics | tests/gromacs_ver_test.py | Python | gpl-3.0 | 1,075 | [
"Gromacs"
] | 57b3ceb4df03f33a068e3cd54928814888748066f93a73523564aba088f5cbf7 |
"""Galaxy (ansible-galaxy) plugin for integration tests."""
from __future__ import annotations
import os
import tempfile
from ....config import (
IntegrationConfig,
)
from ....docker_util import (
docker_cp_to,
)
from ....containers import (
run_support_container,
)
from . import (
CloudEnvironment... | mahak/ansible | test/lib/ansible_test/_internal/commands/integration/cloud/galaxy.py | Python | gpl-3.0 | 6,374 | [
"Galaxy"
] | 193e078eb4fbb2623e399f8d917bbb3f6930645216c5f93270f4c97b25c889e3 |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | unnikrishnankgs/va | venv/lib/python3.5/site-packages/tensorflow/models/differential_privacy/privacy_accountant/tf/accountant.py | Python | bsd-2-clause | 17,541 | [
"Gaussian"
] | 2f0c4ed0da7fdfeb13afbc48db556ca1846224ca7a32044476d47a5954e42b96 |
# -*- coding:utf-8 -*-
#
# My Utilities
#
# Class ContourInfo
# def __init__(self):
# def calc_all(self):
# def contour_sorting_by_area(self, reverse=False):
# def delete_contour_info(self, idx):
# def check_inclusion(self, canvas, idx_small, idx_big, disp=False):
# def delete_co... | kdg1016/SVHNClassifier | data/HoonUtils.py | Python | gpl-3.0 | 39,868 | [
"Gaussian"
] | 5ac7559debd80a4486baeef342700b4f50e1bf5875784d423fddaf9e6cffa456 |
# LOFAR AUTOMATIC IMAGING PIPELINE
# awimager
# The awimager recipe creates based an image of the field of view. Based on
# nine concatenated and measurementsets each spanning 10 subbands
# The recipe contains two parts: The call to awimager
# and secondairy some functionality that calculates settings (for awimager)
# ... | kernsuite-debian/lofar | CEP/Pipeline/recipes/sip/nodes/imager_awimager.py | Python | gpl-3.0 | 26,112 | [
"Gaussian"
] | 50b188c3b3f5530affd8610cd62ca4fcbbc8e99bbb47adad11fd1b18449ba208 |
#!/usr/bin/env python
from __future__ import print_function
import vtk
class MyInteractorStyle(vtk.vtkInteractorStyleTrackballCamera):
def __init__(self,parent=None):
self.AddObserver("MiddleButtonPressEvent",self.middleButtonPressEvent)
self.AddObserver("MiddleButtonReleaseEvent",self.middleButt... | saullocastro/pyNastran | pyNastran/gui/vtk_examples/mouse_events.py | Python | lgpl-3.0 | 1,161 | [
"VTK"
] | 85d693e8ada21a2620f7d3026ff30bf3ec86085cb27374ae1602f40bf7086119 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import filecmp
import os
import re
import shutil
import unittest
import pandas as pd
from pymatgen.core.lattice import Lattice
from pymatgen.core.structure import Structure
from pymatgen.io.lammps.data import ... | gmatteo/pymatgen | pymatgen/io/lammps/tests/test_inputs.py | Python | mit | 4,354 | [
"Gaussian",
"LAMMPS",
"pymatgen"
] | 345f2e2b02a901ef45072125ade31deda6b778bfbfdfa0636c316be91171341a |
# -*- coding: utf-8 -*-
import os, sys; sys.path.insert(0, os.path.join("..", ".."))
import unittest
import random
import subprocess
from pattern import en
#---------------------------------------------------------------------------------------------------
class TestInflection(unittest.TestCase):
def setUp(self... | piskvorky/pattern | test/test_en.py | Python | bsd-3-clause | 39,004 | [
"Octopus"
] | ae03f285f65d5f7bcf13b92f76e0c0021bfc3dd8d9505f2be64dad5b9011d158 |
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