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__author__ = 'tylin'
__version__ = '1.0.1'
# Interface for accessing the Microsoft COCO dataset.
# Microsoft COCO is a large image dataset designed for object detection,
# segmentation, and caption generation. pycocotools is a Python API that
# assists in loading, parsing and visualizing the annotations in COCO.
# Ple... | Zardinality/TF_Deformable_Net | lib/pycocotools/coco.py | Python | mit | 14,960 | [
"VisIt"
] | fe08522d4c941f0434f156d59805d7199fc31ec77fe9afd4c9ccbfe90f0d872f |
from ase.test import NotAvailable
import warnings
# cmr calls all available methods in ase.atoms detected by the module inspect.
# Therefore also deprecated methods are called - and we choose to silence those warnings.
warnings.filterwarnings('ignore', 'ase.atoms.*deprecated',)
# if CMR_SETTINGS_FILE is missing, cmr r... | grhawk/ASE | tools/ase/test/cmr/reactions_run.py | Python | gpl-2.0 | 1,533 | [
"ASE"
] | 661a2f8d23a46b975d520418f8518cc84ec47af5c92f5626eb5992af8966e238 |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
import os
import numpy as np
import tables
import bob.ip.gabor
from joblib import Parallel, delayed
from braincode.util import configParser
from braincode.math import make_2d_gaussian, ridge
from braincod... | sealhuang/brainCodingToolbox | braincode/prf/vim1_pro.py | Python | bsd-3-clause | 23,373 | [
"Gaussian"
] | 2984f58b1185cf9da07603c39234f2b2d6194ed348c4db25df336c685cbd6f6d |
"""
Migration script to add the sample_dataset table and remove the 'dataset_files' column
from the 'sample' 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 *
from galaxy.util.json ... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py | Python | gpl-3.0 | 3,725 | [
"Galaxy"
] | addb266aac6a6561fd22d4804a6f4e926629293878e5bf49c380d72b267a3ef5 |
"""
============================================================================
Comparing anomaly detection algorithms for outlier detection on toy datasets
============================================================================
This example shows characteristics of different anomaly detection algorithms
on 2D d... | chrsrds/scikit-learn | examples/plot_anomaly_comparison.py | Python | bsd-3-clause | 6,338 | [
"Gaussian"
] | ac18b752d1c678258035d28cfdc0654dac8aaaa686ef6542ceb5466ed70fe76c |
#!/usr/bin/env python
#
# This file is a part of pindel.
# Copyright (C) 2013 DNAnexus, Inc.
#
# This program is free software: you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
# Foundation, either version 3 of the License, or (at your option... | dnanexus/pindel | src/pindel.py | Python | gpl-3.0 | 29,868 | [
"BWA"
] | fd1b52b4bf64449c0a97fc38d8b323720fa8f89476e1fa953e60d831ca02b4db |
# ----------------------------------------------------------------------------
# Copyright (c) 2016-2022, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ------------------------------------------------... | qiime2/qiime2 | qiime2/core/type/tests/test_grammar.py | Python | bsd-3-clause | 23,783 | [
"scikit-bio"
] | 97d948d1d5bd58fcf0fdd1ed1e08355199bfe2d414cadc7767a6c89094854ea9 |
import logging as log
import numpy as np
import os
import pylab as plt
__MAYAVI__ = False
try:
os.environ["QT_API"] = "pyqt"
from mayavi import mlab
__MAYAVI__ = True
except:
try:
os.environ["QT_API"] = "pyside"
from mayavi import mlab
__MAYAVI__ = True
except:
log.i... | Joshuaalbert/IonoTomo | src/ionotomo/plotting/mayavi_tools.py | Python | apache-2.0 | 5,519 | [
"Mayavi"
] | e8a75465f300cfd6a4e79cfe14ea19910aded794682de467071157afd2c46321 |
#-----------------------------------------------------------------
# pycparser: func_calls.py
#
# Using pycparser for printing out all the calls of some function
# in a C file.
#
# Eli Bendersky [http://eli.thegreenplace.net]
# License: BSD
#-----------------------------------------------------------------
from __futur... | CtheSky/pycparser | examples/func_calls.py | Python | bsd-3-clause | 1,240 | [
"VisIt"
] | 6f0cb944e2f837bb0382b38f4c14059f0c730b1adcb0f2aef798dfac4b03f1cc |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS Instructor Dashboard.
"""
import ddt
from nose.plugins.attrib import attr
from bok_choy.promise import EmptyPromise
from ..helpers import UniqueCourseTest, get_modal_alert, EventsTestMixin
from ...pages.common.logout import LogoutPage
from ...pages.lms.auto_au... | waheedahmed/edx-platform | common/test/acceptance/tests/lms/test_lms_instructor_dashboard.py | Python | agpl-3.0 | 59,759 | [
"VisIt"
] | 3ebc87804ff3e3bf399cb66f4a5a7b79e464b54e7ed35545bab40ae6c11233d9 |
#####################################################################
# Ryuretic: A Modular Framework for RYU #
# !/mininet-wifi/Ryuretic/ICMP_Send.py #
# Author: #
# Jacob Cox (jcox70@gatech.edu) ... | Ryuretic/RAP | mininet-wifi/Ryuretic/ICMP_Send.py | Python | apache-2.0 | 3,478 | [
"VisIt"
] | 60871b5b31631f9f84377ca57cbacd89550293579b59fb07b9c61061366a3058 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# This file is part of the SPORCO package. Details of the copyright
# and user license can be found in the 'LICENSE.txt' file distributed
# with the package.
"""
Gaussian White Noise Restoration via CSC
========================================
This example demonstrates th... | bwohlberg/sporco | examples/scripts/csc/gwnden_gry.py | Python | bsd-3-clause | 4,341 | [
"Gaussian"
] | 985c04b4ac682f9f43b1e49e80057dc0627e656b8d6c6bbc71af769bae1eeef9 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | jart/tensorflow | tensorflow/contrib/autograph/pyct/compiler.py | Python | apache-2.0 | 6,492 | [
"VisIt"
] | adef431d988b8cb7e6a407253eb741dea819a313bfb9ea02fe0cdd95e5d02c60 |
"""
Copyright (c) 2014 Brian Muller
"""
import sys
from twisted.python import log
DEBUG = 5
INFO = 4
WARNING = 3
ERROR = 2
CRITICAL = 1
levels = {"debug": 5, "info": 4, "warning": 3, "error": 2, "critical": 1}
class FileLogObserver(log.FileLogObserver):
def __init__(self, f=None, level="info", default=DEBUG):
... | OpenBazaar/Network | log.py | Python | mit | 1,794 | [
"Brian"
] | dc99d15d81b04675069e26a7402bb0b11628e63e72ca4c924b2fb51ef8a090a6 |
#!/usr/bin/python
"""
BACnet Virtual Link Layer Service
"""
import sys
import struct
from .settings import settings
from .debugging import ModuleLogger, DebugContents, bacpypes_debugging
from .udp import UDPDirector
from .task import OneShotFunction, OneShotTask, RecurringTask
from .comm import Client, Server, bind... | JoelBender/bacpypes | py27/bacpypes/bvllservice.py | Python | mit | 48,796 | [
"ASE"
] | b0f2cead3a066bc32ee6fcc6d47bb9e9d7971bdf2448d2befb8490545c35f3a5 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2017, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Building the density matrix from data parsed by cclib."""
import logging
import random
import numpy
fr... | cclib/cclib | cclib/method/density.py | Python | bsd-3-clause | 2,896 | [
"cclib"
] | f16bd79e3167acf854bd4898a4b63f668f0030fd3f52c6eeb433eabe65e7b5d4 |
#!/usr/bin/env python
__author__ = 'Mike McCann'
__copyright__ = '2013'
__license__ = 'GPL v3'
__contact__ = 'mccann at mbari.org'
__doc__ = '''
Loader for data from OceanSITES GDAC
Mike McCann
MBARI 28 October 2014
@var __date__: Date of last svn commit
@undocumented: __doc__ parser
@status: production
@lic... | josephmfaulkner/stoqs | stoqs/loaders/OceanSITES/load_moorings.py | Python | gpl-3.0 | 4,887 | [
"NetCDF"
] | e83d9cc7b9910efd453bd886cc1744c06506685b5d48d314e24da9ceed985f6b |
#!/usr/bin/python
""" Classes and functions for fitting tensors """
from __future__ import division, print_function, absolute_import
import warnings
import functools
import numpy as np
import scipy.optimize as opt
from dipy.utils.six.moves import range
from dipy.utils.arrfuncs import pinv, eigh
from dipy.data impo... | StongeEtienne/dipy | dipy/reconst/dti.py | Python | bsd-3-clause | 61,706 | [
"Gaussian"
] | 89f8d48a4d6c80dcc3fd1c250deb6f0416f19b4d9ac8421cc984099a79a4e19d |
#!/usr/bin/env python
import urllib
import sys
import os
##### totalannotation.py by DJ Barshis
##### This script takes an input fasta file of sequence names and sequences, and blast results files of blasts against
##### nr (parsed .txt with 1 hit per line) and swissprot and tremble (in -outfmt 7) uniprot databases
... | cuttlefishh/papers | vibrio-fischeri-transcriptomics/code/python/totalannotation_v1-1.py | Python | mit | 12,403 | [
"BLAST"
] | 643025039213ebabf3f7714b753caa77fc127d2e6877e1e08e5e94c8540ced34 |
import astropy.units as uu
import astropy.cosmology as co
aa = co.Planck13
from scipy.interpolate import interp1d
import numpy as n
import matplotlib
#matplotlib.use('pdf')
matplotlib.rcParams['font.size']=12
import matplotlib.pyplot as p
import glob
import sys
from scipy.optimize import curve_fit
import cPickle
from o... | JohanComparat/nbody-npt-functions | bin/bin_DF/test_scripts/halo-bias-fit.py | Python | cc0-1.0 | 18,813 | [
"TINKER"
] | 009cbb9105e0fdebd13f7717b4cc16596c246c1054f8ba787cd92bc8d6f12769 |
#!/usr/bin/env python
########################################################################
# File : dirac-admin-get-pilot-info
# Author : Ricardo Graciani
########################################################################
"""
Retrieve available info about the given pilot
Example:
$ dirac-admin-get-pilo... | DIRACGrid/DIRAC | src/DIRAC/Interfaces/scripts/dirac_admin_get_pilot_info.py | Python | gpl-3.0 | 4,545 | [
"DIRAC"
] | 1019d64cae3828573933839411b7b7dab0f956b29ccc907c054ea3a1731d2fb3 |
""" Module for DM Halo calculations
"""
from __future__ import print_function, absolute_import, division, unicode_literals
import numpy as np
import pdb
from IPython import embed
import warnings
from pkg_resources import resource_filename
from scipy.interpolate import InterpolatedUnivariateSpline as IUS
from scipy.... | FRBs/DM | frb/halos.py | Python | bsd-3-clause | 39,183 | [
"Galaxy",
"Gaussian",
"TINKER"
] | 4f596eb48433d508d9d39473b053d914bf35c8e1fb42d2fcd2b5c4ab76943d56 |
"""
This is a template config file that can be used to build a Hodgkin-Huxley neuron
model.
"""
global man
from HH_neuron import get_model
## ----- ----- ----- ----- ----- ----- ##
## SET INITIAL CONDITIONS ##
## ----- ----- ----- ----- ----- ----- ##
path = 'models/'
## ----- ----- ----- ----- -----... | akuefler/fovea | examples/HH_neuron/model_config.py | Python | bsd-3-clause | 2,504 | [
"NEURON"
] | 8d0a28f2ee39818bdefbbf8240f30b6acc6a538379837a44e249a7e09622ef37 |
from warnings import warn
import numpy as np
from pgmpy.utils import _check_1d_array_object, _check_length_equal
from pgmpy.base import HAS_PANDAS
if HAS_PANDAS:
import pandas
class BaseGradLogPDF(object):
"""
Base class for evaluating gradient log of probability density function/ distribution
Cla... | sandeepkrjha/pgmpy | pgmpy/sampling/base.py | Python | mit | 16,434 | [
"Gaussian"
] | b51174c1cf3622df709985283746118ee24dfb32edbe2f4e22cac9889280bad3 |
# 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/pdb.py | Python | gpl-3.0 | 9,525 | [
"CRYSTAL",
"ESPResSo",
"LAMMPS"
] | 5a69647598fc003454f9a25038efe1978ba20259bd6baae0b1903735e6179275 |
import datetime
def load_movie_fixtures():
from camelot.model.fixture import Fixture
from model import Movie, VisitorReport
from camelot.core.files.storage import StoredImage, Storage
storage = Storage(upload_to='covers')
movies = [
[
u'The Shining',
u'The tide of... | kurtraschke/camelot | example/fixtures.py | Python | gpl-2.0 | 8,867 | [
"Brian",
"CASINO",
"COLUMBUS",
"VisIt"
] | e1e199d928ca3ae1f8e09f7c691e54507a5bd5e6b7e72138cfd4c80a42ccd307 |
#!/usr/bin/env python
"""
hawaii.py
State Estimation and Analysis for PYthon
Utilities for dealing with data around Hawaii
Examples
--------
Assume you have longitude, latitude, and sst values:
>>> m=seapy.hawaii()
>>> m.pcolor(lon,lat,sst,vmin=22,vmax=26,cmap=plt.cm.bwr)
>>> m.land()... | ocefpaf/seapy | seapy/hawaii.py | Python | mit | 2,156 | [
"Brian"
] | aac21e10e4948de36bc9ff00247a87f28f3233b42d3820868456550503b7abfa |
import opencor as oc
import sys
sys.dont_write_bytecode = True
import utils
if __name__ == '__main__':
# Test the van der Pol 1928 model using different solvers
utils.run_simulations('van_der_pol_model_1928.cellml', 'van der Pol 1928 model')
| agarny/opencor | src/plugins/support/PythonSupport/tests/data/vanderpol1928tests.py | Python | gpl-3.0 | 254 | [
"OpenCOR"
] | 8f4a77bbf6c2be80a9feb6dc5cfe95ca8ac2ca9cae24c8f960092f3e11dc2a28 |
#!/usr/bin/env ipython
"""
Analisis of sheath-from-icme for Auger Low Energy data
"""
from pylab import *
from numpy import *
from scipy.io.netcdf import netcdf_file
from datetime import datetime, time, timedelta
#------------ shared libraries:
"""
--- antes de modificar cosas, tener en cuenta los bugs en:
'../../shar... | jimsrc/seatos | icmes/src/tt_icme.py | Python | mit | 3,948 | [
"NetCDF"
] | de41d029e9c84e4d18f6af9660a372a6afadfa4147914a5ea96043e383ad9905 |
#! /usr/bin/env python
import os
import numpy as np
from numpy.testing import assert_array_almost_equal
from nose.tools import assert_true, assert_equal, assert_raises
try:
from nose.tools import assert_list_equal
except ImportError:
from landlab.testing.tools import assert_list_equal
from landlab.testing.too... | decvalts/landlab | landlab/grid/tests/test_raster_grid/test_save.py | Python | mit | 2,568 | [
"NetCDF"
] | 7017cdfa4a2769f63fc36f90fe1a8c8bae66e4248b891c138f2aade0ad9866ec |
#
# Copyright (C) 2007-2017 Greg Landrum
#
# @@ 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.
#
""" General descriptor testing code
"""
from __future__... | rvianello/rdkit | rdkit/Chem/UnitTestDescriptors.py | Python | bsd-3-clause | 5,766 | [
"RDKit"
] | ddcc7000873c1396b39d25cd95361c39c7ab7fad2fc7e72938f5aab11fed899a |
#
# Copyright (c) 2016 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/scancode/test_interrupt.py | Python | apache-2.0 | 2,661 | [
"VisIt"
] | 60c7283326e61a234ad249297d68e1fd767d26ab217545f6d0558eb215897eac |
# This module is to process fasta files and some utils.
# download bigWigSummary binary file:
# http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigSummary
import pysam
import itertools
import subprocess
import numpy as np
class FastaFile:
"""docstring for FastaFile"""
def __init__(self, fasta_file):... | huangyh09/brie | brie/utils/fasta_utils.py | Python | apache-2.0 | 7,957 | [
"pysam"
] | e53525e411e49fa6899c8c1cb0636fb9107d62204ac22de2f39cab36dd148847 |
# ============================================================================
#
# Copyright (C) 2007-2012 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | jeroendierckx/Camelot | camelot/container/chartcontainer.py | Python | gpl-2.0 | 5,737 | [
"VisIt"
] | 054ad8689ef83cc0e9e23644a6757584d5c949bc2d018909bcfa43ecf086201a |
import pytest
import numpy as np
import psi4
from .utils import compare_arrays
def test_export_ao_elec_dip_deriv():
h2o = psi4.geometry("""
O
H 1 1.0
H 1 1.0 2 101.5
symmetry c1
""")
rhf_e, wfn = psi4.energy('SCF/cc-pVDZ', molecule=h2o, return_wfn=True)
mints = psi4.... | jgonthier/psi4 | tests/pytests/test_mints.py | Python | lgpl-3.0 | 3,178 | [
"Psi4"
] | 7ccf2a0c762f4c4fb3ec76a35a19fc1a2d894503486ded35d2ead47ab0190a67 |
#!/usr/bin/env python
# Script to generate TVTK files from CitcomS hdf files
# author: Martin Weier
# Copyright (C) 2006 California Institue of Technology
#
# 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
# ... | geodynamics/citcoms | visual/Mayavi2/original_plugins/Citcoms_Hdf2Vtk.py | Python | gpl-2.0 | 22,127 | [
"VTK"
] | 893f39d1fc4b0c4693fa2758d010a9047aaedd0e7fd051839f756473f4816b95 |
#!/usr/bin/env python3
from yat.parser import Parser, Scanner
from yat.model import Scope
from yat.printer import PrettyPrinter
if __name__ == "__main__":
import sys
for filename in sys.argv[1:]:
program = Parser().parse(Scanner(filename), False)
printer = PrettyPrinter()
for stmt in p... | krinkinmu/yat | format.py | Python | mit | 360 | [
"VisIt"
] | 7b8aaf3881a8b5b68b15ace00a298fe9d765050bc721508f73749cf586ebdf12 |
import os
import numpy as np
import matplotlib.pyplot as plt
"""Plotting script for BF panels, with optional multiple RV2 cases.
Needed Stuff
------------
Files named data/KICBFOut_ID.txt
where KIC is the star name and ID is from 1-N visits
the columns should be uncorrected RV (km/s), BF amplitude, Gaussian fit
File... | savvytruffle/cauldron | BF_multipane_plotter.py | Python | mit | 3,632 | [
"Gaussian",
"VisIt"
] | 4cee08c9351dd66e8240253fcc7edcc3520706a36f88641374a78feae94bc8a3 |
########################################################################
# $HeadURL $
# File: CleanReqDBAgent.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/05/17 08:31:26
########################################################################
"""Cleaning the RequestDB from obsolete records and kicking assig... | ic-hep/DIRAC | src/DIRAC/RequestManagementSystem/Agent/CleanReqDBAgent.py | Python | gpl-3.0 | 6,355 | [
"DIRAC"
] | 1f0190b19aaad9fb10d2d6d78ffca5a7d6de6084967e6b6bcbff5b59ae41afee |
import os
import shutil
import os.path as op
import pysam
# from collections import Counter
from bcbio.utils import splitext_plus, file_exists, safe_makedir, chdir
from bcbio.provenance import do
from bcbio.distributed.transaction import file_transaction, tx_tmpdir
from bcbio import broad
from bcbio.bam import index
... | chapmanb/bcbio-nextgen | bcbio/wgbsseq/align.py | Python | mit | 2,886 | [
"pysam"
] | 907eb24a3c157df0a5af70102c275fcd1e76b63cf72389aa505d1c2b22dd18cb |
# -*- coding: utf-8 -*-
from collections import OrderedDict, defaultdict
from functools import reduce
from itertools import chain, product
from operator import mul, add
import copy
import math
import warnings
from .util.arithmeticdict import ArithmeticDict
from .util._expr import Expr
from .util.periodic import mass_... | bjodah/aqchem | chempy/chemistry.py | Python | bsd-2-clause | 53,172 | [
"ChemPy"
] | ec36b454857d0ac64e50596cf42beda1b88d7848e916129153a63f1e076b2c80 |
# (c) 2013-2014, Michael DeHaan <michael.dehaan@gmail.com>
# (c) 2015 Toshio Kuratomi <tkuratomi@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either... | pmarques/ansible | lib/ansible/executor/module_common.py | Python | gpl-3.0 | 65,799 | [
"VisIt"
] | 9b5ceadf61d3898255e0315e644a50114a2907b2d19ef24d2a6354355617164c |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Licensed under the GNU LGPL v2.1 - http://www.gnu.org/licenses/lgpl.html
# Based on Copyright (C) 2016 Radim Rehurek <radimrehurek@seznam.cz>
"""Lda Sequence model, inspired by `David M. Blei, John D. Lafferty: "Dynamic Topic Models"
<https://mimno.infosci.cornell.edu/... | mattilyra/gensim | gensim/models/ldaseqmodel.py | Python | lgpl-2.1 | 62,874 | [
"Gaussian"
] | c6555596dccbf4f61d7dee0ef974e2d9cf73a9cd878654555175a3c1e8733fed |
# -*- coding: utf-8 -*-
#
# Moonstone is platform for processing of medical images (DICOM).
# Copyright (C) 2009-2011 by Neppo Tecnologia da Informação LTDA
# and Aevum Softwares LTDA
#
# This file is part of Moonstone.
#
# Moonstone is free software: you can redistribute it and/or modify
# it under the terms of the GN... | aevum/moonstone | src/moonstone/bloodstone/scenes/slicewidget.py | Python | lgpl-3.0 | 3,195 | [
"VTK"
] | 31bff104979b5e94d6a9d2899030c23b9743a7ced8437ee2a8557fbb9048eb83 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | KaiSzuttor/espresso | samples/visualization_interactive.py | Python | gpl-3.0 | 2,777 | [
"ESPResSo"
] | ed79d3dc6644da3e8076e035e22d636f6379730bc1dccce8ad434c7dea2fd451 |
#!python
# coding=utf-8
import os
import unittest
from pyaxiom.netcdf import EnhancedDataset, EnhancedMFDataset
import logging
from pyaxiom import logger
logger.level = logging.INFO
logger.handlers = [logging.StreamHandler()]
class EnhancedDatasetTests(unittest.TestCase):
def setUp(self):
netcdf_file... | axiom-data-science/pyaxiom | pyaxiom/tests/test_enhanced_dataset.py | Python | mit | 10,238 | [
"NetCDF"
] | 7d95f3a7ec33f45765d31459ad72a2de58c80acef56a13d88f3208cc1a7ff26e |
# -*- coding: utf-8 -*-
"""Functions for FIR filter design."""
from __future__ import division, print_function, absolute_import
from math import ceil, log
import operator
import warnings
import numpy as np
from numpy.fft import irfft, fft, ifft
from scipy.special import sinc
from scipy.linalg import (toeplitz, hankel... | gertingold/scipy | scipy/signal/fir_filter_design.py | Python | bsd-3-clause | 47,327 | [
"Brian"
] | 9f1d2b69714c97c87e7713e8d758bb5fc041f6c06b8eea8a49431af172a68704 |
"""
Sigma_MonteCarlo
"""
import numpy as np
from scipy import interpolate
import halomodel as hm
import matplotlib.pyplot as plt
from matplotlib import rc, rcParams
rc('text', usetex=True)
rcParams['text.latex.preamble']=[r"\usepackage{amsmath}"]
CosPar={'Omega_M':0.3, 'Omega_L':0.7, 'Omega_b':0.045, 'Omega_nu':1e-5,... | guangtunbenzhu/BGT-Cosmology | Examples/LRG-MgII/Sigma_MonteCarlo.py | Python | mit | 52,418 | [
"Galaxy"
] | 2b01f0ddfdeff708af6af57e8bac843e15db8a5802ffcdea16a5a84c3c35068c |
"""
Test courseware search
"""
import json
import uuid
from nose.plugins.attrib import attr
from common.test.acceptance.fixtures.course import XBlockFixtureDesc
from common.test.acceptance.pages.common.auto_auth import AutoAuthPage
from common.test.acceptance.pages.common.logout import LogoutPage
from common.test.ac... | miptliot/edx-platform | common/test/acceptance/tests/lms/test_lms_cohorted_courseware_search.py | Python | agpl-3.0 | 12,266 | [
"VisIt"
] | 48203dd837f94e4416b4fc6f48eb74a4c3ea51bea1af95436f8aabd3c923bc4e |
#!/usr/bin/env python3
try:
from setuptools import setup
from setuptools.command.build_ext import build_ext as _build_ext
except:
print(
'''
[!] Warning: unable to import setuptools.setup. Please visit your package
manager and install pip3 (or setuptools for python3, thought this hasn't been
tested. On Deb... | MusicVisualizationUMass/TeamNameGenerator | setup.py | Python | mit | 1,944 | [
"VisIt"
] | 322edbd7ea8c312a3528fbcd4086ea510cdde2b7b62aa92cec09f1f2cd6e3790 |
from rdkit import Chem
from ..RDkitWrapper.GenRxnNet import GenerateRxnNet
from ..RINGParser.Reader import Read
def enumerate_res_struc(mol):
"""
Generates resonance structures. Structure with minimum number of radical
electrons is outputted
Arguments:
- mol: Input. It can be smiles or mol
... | VlachosGroup/VlachosGroupAdditivity | pgradd/GroupAdd/FindResStruc.py | Python | mit | 4,177 | [
"RDKit"
] | a93657186ec006bceaf56186951b0affd476b8c2a222711c4eaa89b99ec34fb1 |
# Version: 0.15 + modifications to avoid the need for setup.cfg to exist.
"""
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, and pypy
* [![Latest Version]
(http... | matplotlib/fcpy | versioneer.py | Python | bsd-2-clause | 62,700 | [
"Brian"
] | cf341b47ebeabb18bfc08210b919aa46a5cc33f5e22ae9fa2cd8a488f97870f3 |
import os
import json
import logging
import pandas as PD
from netCDF4 import Dataset
from ..util.date import fromJ2000
logger = logging.getLogger('pyrsss.mag.repository')
CONFIG_JSON = os.path.expanduser('~/etc/intermagnet.json')
"""
Path to INTERMAGNET repository JSON configuration file.
"""
def get_config(fnam... | butala/pyrsss | pyrsss/mag/repository.py | Python | mit | 4,772 | [
"NetCDF"
] | 56e96e5f3d7915aa78b6b189ea428ed477d297dc370721a59bceaf10d1f91652 |
from sys import argv
from os import mkdir, path
import time
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.ticker import FormatStrFormatter
from matplotlib.font_manager import FontProperties
# Timing Decorator
def timeFunction(f):
def wrap(*args):
time1 = time.time()
ret = f(*ar... | CompPhysics/ComputationalPhysics2 | doc/src/MCsummary/src/sampling.py | Python | cc0-1.0 | 8,050 | [
"Gaussian"
] | d51bc9865c73b47b94217cf7964d523f748a2d8342a695f2e461f961c79ef05d |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Create the RenderWindow, Renderer and both Actors
#
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
iren = vtk.vtkRenderWindowInteractor(... | timkrentz/SunTracker | IMU/VTK-6.2.0/Filters/Hybrid/Testing/Python/depthSort.py | Python | mit | 2,377 | [
"VTK"
] | 53a666eaecd2bc791adfcd34d7449e60aef2d49a077c797426a87055f4053a6b |
# Mantid Repository : https://github.com/mantidproject/mantid
#
# Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
# NScD Oak Ridge National Laboratory, European Spallation Source
# & Institut Laue - Langevin
# SPDX - License - Identifier: GPL - 3.0 +
from __future__ import (absolute_import, divi... | mganeva/mantid | scripts/SCD_Reduction/BVGFitTools.py | Python | gpl-3.0 | 28,253 | [
"Gaussian"
] | fef53699fdb14059b2c7f77a669b90255a8a8a46444669ee7bd7b2eac0c17460 |
# -*- coding: utf-8 -*-
from __future__ import division
import numpy as np
from scipy.stats import multivariate_normal
from pgmpy.factors.continuous import ContinuousFactor
class LinearGaussianCPD(ContinuousFactor):
u"""
For, X -> Y the Linear Gaussian model assumes that the mean
of Y is a linear funct... | sandeepkrjha/pgmpy | pgmpy/factors/continuous/LinearGaussianCPD.py | Python | mit | 4,320 | [
"Gaussian"
] | cca8df132c2f3dcaf1a855de8cd0a0c87b230faed23b75c95793e9468df32236 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals, division, absolute_import, print_function
from builtins import * # noqa pylint: disable=unused-import, redefined-builtin
from past.builtins import basestring
import logging
import re
import time
from datetime import datetime, timedelta
from dateutil.pa... | poulpito/Flexget | flexget/plugins/internal/api_trakt.py | Python | mit | 52,915 | [
"VisIt"
] | c68ef0bd2507602a93b786bbc7e91cd6e2cd40876a7ce1b7982de4607880df87 |
# this is a collection of speckle generating routines taken from:
# https://github.com/fperakis/Speckles-simulations
import numpy as np
from scipy.ndimage.filters import gaussian_filter
def sample2ddist(asicshape,kbar,dist):
"""
samples photons from a 2D distribution
"""
#Definitions
na... | dkazanc/TomoPhantom | Wrappers/Python/tomophantom/supp/speckle_routines.py | Python | apache-2.0 | 4,055 | [
"Gaussian"
] | 12e08a3b367fe06eaa5724f37774571eed9a634b83a81a7ba6213c1751e80b08 |
import sys
sys.path.append("/Applications/VisIt.app/Contents/Resources/2.8.0/darwin-x86_64/lib/site-packages")
import os
import visit
import alpha
filesPath = "aztec.llnl.gov:/g/g14/damewood/scratchd/2014_Trilayer/vasp"
visit.Launch(vdir="/Applications/VisIt.app/Contents/Resources/bin/")
# Volume plot
visit.OpenDatab... | ldamewood/figures | scripts/Trilayer3D.py | Python | mit | 3,715 | [
"VASP",
"VisIt"
] | 6614d30248f3d1b82dc9deb52be0b004be3e694d70f94aa8e621df66487d94c8 |
../../../../../../../share/pyshared/orca/scripts/apps/gnome-screensaver-dialog/__init__.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/scripts/apps/gnome-screensaver-dialog/__init__.py | Python | gpl-3.0 | 90 | [
"ORCA"
] | 750b809ebaa45ebd56d5d5a4eb715fbd4793e11d03dc695a820c49c715938d93 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | SamStudio8/scikit-bio | skbio/diversity/alpha/_gini.py | Python | bsd-3-clause | 3,741 | [
"scikit-bio"
] | 9f6065c77f0c8170e59762274c06843b837ac372ca49eba037821c1886a7125a |
import os
from __main__ import vtk, qt, ctk, slicer
import logging
import numpy
import time
import pickle
from math import *
import json
from slicer.ScriptedLoadableModule import *
from slicer.util import VTKObservationMixin
class ModelAddedClass(VTKObservationMixin):
def __init__(self, anglePlanes):
VTKO... | JuliaLopinto/AnglePlanes-Extension | AnglePlanes/AnglePlanes.py | Python | apache-2.0 | 84,912 | [
"VTK"
] | 96cd1080225a283a8a50b6f238a2e4510c92976dfe45e04355df891bc8a8fcff |
import unittest
from jamenson.runtime import multimethod as MM
from jamenson.runtime.multimethod import (MultiMethodError, only, before, after, around,
InconsistenCallSignature, InvalidMethodArguments,
NoSuchMethod, MultiMethod, Inval... | matthagy/Jamenson | jamenson/tests/runtime/multimethod.py | Python | apache-2.0 | 13,206 | [
"ADF"
] | 102ab3e295dd0a36a7d4668bc4c9e8f37aa3f702277ca840ef8919fc23c33a3e |
# Copyright (c) 2012-2014, GPy authors (see AUTHORS.txt).
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
from .. import kern
from ..likelihoods import Gaussian
from ..core.parameterization.variational import NormalPosterior, NormalPrior
from ..inference.latent_function_inference.var_dtc... | TianpeiLuke/GPy | GPy/models/bayesian_gplvm_minibatch.py | Python | bsd-3-clause | 11,292 | [
"Gaussian"
] | d5bad00aac8eee8100793ed94ac4343bb66047cfba74d6380cd8f6f024968e24 |
#! /usr/bin/python
"""
Converts SOLiD data to Sanger FASTQ format.
usage: %prog [options]
-i, --input1=i: Forward reads file
-q, --input2=q: Forward qual file
-I, --input3=I: Reverse reads file
-Q, --input4=Q: Reverse qual file
-o, --output1=o: Forward output
-r, --output2=r: Reverse output
usage: ... | volpino/Yeps-EURAC | tools/next_gen_conversion/solid_to_fastq.py | Python | mit | 2,540 | [
"Galaxy"
] | fd532105692d95e60dee17b51b833165696709ac646eb2e21e4805f6b3719522 |
#!/usr/bin/python
# -*- coding: utf-8
#-------------------------------------------------------------------
#This class is made to work as a interface to database
#for other widgets
#
#
#crator: Markus Peltola, last update 24.2.2013
#-------------------------------------------------------------------
'''
This file ... | mape90/VetApp | models/sqlhandler.py | Python | gpl-3.0 | 19,645 | [
"VisIt"
] | dd9f2b706def424b352531f56ce19b12ce5b1d550b0b4a9f7c259150310c8d10 |
from pympler.asizeof import asizeof
import prometheus_client as prom
class SimMonitor:
def __init__(self,
reporter_order=(
'hdf5_reporter',
'dashboard_reporter',
),
):
self.reporter_order = reporter_order
## progress... | ADicksonLab/wepy | jigs/prom/source/lysozyme_we.py | Python | mit | 8,920 | [
"OpenMM"
] | 23cd9d5cf65003c37d8065bac91c9f48f7b383cb4aba2b2e71c31af8a0057bee |
# from io import StringIO
import os
import numpy as np
from aston.trace.trace import Chromatogram
from aston.tracefile.netcdf import write_netcdf
def test_write_netcdf():
d = np.array([[0.1, 0.2, 0.1, 0.1],
[0.5, 0.6, 0.5, 0.4]]).T
t = np.array([0, 1, 2, 3])
df = Chromatogram(d, t, ['A',... | bovee/Aston | aston/test/test_tracefile_export.py | Python | bsd-3-clause | 426 | [
"NetCDF"
] | d449960aafa088c1c6b6200fc29c0d012b30d119aec9db5a61cce0f8056d5722 |
#!/usr/bin/env python
import sys
import os
import re
import argparse
from datetime import (datetime, timedelta)
import pytz
import random
import math
from decimal import Decimal
from bunch import (Bunch, bunchify)
from mongoengine import connect
from qiutil import uid
from qiutil.file import splitexts
from qirest_clien... | ohsu-qin/qirest | qirest/test/helpers/seed.py | Python | bsd-2-clause | 37,577 | [
"VisIt"
] | 764b0d05ca31910877958f4368a22b87f8f5990b5f2b892cb9f764b328af9059 |
# Copyright 2000-2002 Brad Chapman.
# Copyright 2004-2005 by M de Hoon.
# Copyright 2007-2010 by Peter Cock.
# All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Provides objects ... | bryback/quickseq | genescript/Bio/Seq.py | Python | mit | 85,002 | [
"Biopython"
] | 6e3f8ba9818f73a2528229fc41a300a075fefe88bbf03f806334130199782dea |
'''
Python Oauth client for Twitter
modified to work with other oAuth logins like LinkedIn (Ben Adida)
Used the SampleClient from the OAUTH.org example python client as basis.
props to leahculver for making a very hard to use but in the end usable oauth lib.
'''
import urllib.request
import webbrowser
from . import... | benadida/helios-server | helios_auth/auth_systems/oauthclient/client.py | Python | apache-2.0 | 6,080 | [
"VisIt"
] | 875732fcc9c4cabb0293c044ba08b589b79dfcdcc3b25778660f169ff38848f1 |
# coding: utf8
{
'"update" is an optional expression like "field1=\'newvalue\'". You cannot update or delete the results of a JOIN': '"update" é uma expressão opcional como "field1=\'newvalue\'". Não é possível atualizar ou excluir os resultados de uma junção',
'# of International Staff': '# De equipe internacional'... | flavour/rgims_as_diff | languages/pt-br.py | Python | mit | 301,907 | [
"VisIt"
] | b6a884cbed58770e45e373b5eb2ecc218a147e4f79f63fd0866b517567482c3a |
# -*- coding: utf-8 -*-
'''
Metadata driver for ESRI GRIDs
B{Format specification}:
- U{http://home.gdal.org/projects/aigrid/aigrid_format.html}
'''
# Copyright (c) 2015 Australian Government, Department of the Environment
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
... | tectronics/metageta | metageta/formats/esrigrid.py | Python | mit | 4,783 | [
"ADF"
] | 857b62f2b45a8b5784295d132d68c546245e68e3dcce683d55e61bf30d8a9620 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# modificadorX-AMBER.py
#
# Copyright 2015 Carlos Eduardo Sequeiros Borja <casebor@gmail.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 Found... | casebor/labioscripts | python/modificadorX-AMBER.py | Python | gpl-3.0 | 3,686 | [
"Amber"
] | 34a901ddf08412bc6c5f1671cf7f442a0bfaf4c53bd4b1e3e9f3de23a3758a82 |
#!/usr/bin/env python3
"""The influence of windowing of log. bandlimited sweep signals when using a
Kaiser Window by fixing beta (=2) and fade_out (=0).
fstart = 100 Hz
fstop = 5000 Hz
"""
import sys
sys.path.append('..')
import measurement_chain
import plotting
import calculation
import generation
import... | franzpl/sweep | log_sweep_kaiser_window_bandlimited_script5/log_sweep_kaiser_window_bandlimited_script5_1.py | Python | mit | 2,187 | [
"DIRAC"
] | 1538e81e688db77fab888dd5b62e515b8d84c7d7f77663e428063a39d7453498 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# xmlrpcsslclient - XMLRPC client with HTTPS user certificate support
# Copyright (C) 2003-2015 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of... | heromod/migrid | mig/user/xmlrpcsslclient.py | Python | gpl-2.0 | 17,791 | [
"Brian"
] | 35d1039423ae59c4023fae62fc06f4e5519888339f5ea9962d0d23557cdf71aa |
##
# Copyright 2009-2015 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://vscentrum.be/nl/en),
# the Hercules foundation (htt... | ULHPC/modules | easybuild/easybuild-easyblocks/easybuild/easyblocks/w/wrf.py | Python | mit | 15,062 | [
"NetCDF"
] | 6562e3191e27e808fd0e0d63f0920820cec4047db36775a4a820d9c1586f1647 |
#!/usr/bin/env python
#-*- coding: utf-8 -*-
"""
Webhook automated Dota 2 match parsing service for Discord
Users can register their IDs via a chatbot and the Dota bot
will look for local JSON files in the botdata/shared folder.
JSON files are where Dota player IDs are stored, as well as
the last match they played fo... | sleibrock/discord-bots | bots/dota-bot.py | Python | mit | 11,549 | [
"CRYSTAL"
] | 0bda3a99c30b338fc825b95425b3a2be9bee58d2e644c77f22ba2d5a728133bb |
from __future__ import absolute_import, division, print_function
from operator import add
from itertools import chain
def inc(x):
return x + 1
def ishashable(x):
""" Is x hashable?
Example
-------
>>> ishashable(1)
True
>>> ishashable([1])
False
"""
try:
hash(x)
... | hainm/dask | dask/core.py | Python | bsd-3-clause | 10,280 | [
"VisIt"
] | e479bb8b2e2cf2ad39653a2fb42a8114e3fc29adc745de3036562fc6ec0a0734 |
from os import makedirs
from os.path import join, dirname, exists
from string import Template
from galaxy.util.bunch import Bunch
from galaxy.objectstore import build_object_store_from_config
from .test_utils import TempDirectoryTestCase
from .test_utils import skip
class MockDataset:
def __init__(self, id):
... | galaxyproject/pulsar | test/pulsar_objectstore_test.py | Python | apache-2.0 | 5,299 | [
"Galaxy"
] | 0d209fc4683e868d712b196c392d264e7d6847221626f8c0672a406392a4485e |
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Mathieu Blondel <mathieu@mblondel.org>
# Olivier Grisel <olivier.grisel@ensta.org>
# Andreas Mueller <amueller@ais.uni-bonn.de>
# Eric Martin <eric@ericmart.in>
# License: BSD 3 clause
from itertools import chain, combina... | shikhardb/scikit-learn | sklearn/preprocessing/data.py | Python | bsd-3-clause | 42,619 | [
"Gaussian"
] | b10eb3e20fba4ac3e99fac4ab2fb13b6d81661f0e1d9a3fb87e6001a38c474f5 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2005-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
#
# 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; ... | gramps-project/gramps | gramps/gui/dbloader.py | Python | gpl-2.0 | 19,861 | [
"Brian"
] | bac7621044a3701dedcb1377cb118a19128b4739795785c8628c952fefe9ad6b |
import os
import sys
from string import index,split
from traceHandler import Trace
class externalHandler():
"""
Handles models which are using a simulator other than Neuron.
:param command: the command string which should be executed
.. note::
The command must consist of the following parts:
... | vellamike/optimizer | optimizer/modelHandler.py | Python | lgpl-2.1 | 14,825 | [
"NEURON"
] | 7b0a44026c0faabc884fec84a8a7ae78c4fd705a9d0799739da5e335bb291ede |
# Copyright (c) 2010 Luke McCarthy <luke@iogopro.co.uk>
#
# This is free software released under the MIT license.
# See COPYING file for details, or visit:
# http://www.opensource.org/licenses/mit-license.php
#
# The file is part of FSMonitor, a file-system monitoring library.
# https://github.com/shaurz/fsmonitor
imp... | shaurz/fsmonitor | fsmonitor/linux.py | Python | mit | 6,986 | [
"VisIt"
] | e90c342b8e75ffb4731c4554f9c0b6423d0e7d557a5b697780586e2f926ffe5c |
#!/usr/bin/env python3
import os, re, sys
from glob import glob
from argparse import ArgumentParser
parser = ArgumentParser(prog='check-styles.py',
description="Check style table completeness")
parser.add_argument("-v", "--verbose",
action='store_true',
... | agiliopadua/lammps | doc/utils/check-styles.py | Python | gpl-2.0 | 11,468 | [
"LAMMPS"
] | 51a063eddae6167d0e63ca5ff05d2cb87f329235f739a1e7bc8b702b0d8b1874 |
"""Gaussian Mixture Model."""
# Author: Wei Xue <xuewei4d@gmail.com>
# Modified by Thierry Guillemot <thierry.guillemot.work@gmail.com>
# License: BSD 3 clause
import numpy as np
from scipy import linalg
from .base import BaseMixture, _check_shape
from ..externals.six.moves import zip
from ..utils import check_arra... | aabadie/scikit-learn | sklearn/mixture/gaussian_mixture.py | Python | bsd-3-clause | 27,463 | [
"Gaussian"
] | 7c03aa944cc2fefe170dc5cf1a3c22e5bda10392b7165f11e235271e91c85974 |
##---------------------------------------------------------------------------
# R1_conv_ncdf.py
# G.Urbancic
#
# Takes raw .dat files:
# (1) removes NaN values and replace by interpolation
# (2) converts flags into decimal format
# (3) saves data into NetCDF
##---------------------------------------------... | GUrbancic/ABOA_gust | R1_conv_ncdf.py | Python | mit | 4,756 | [
"NetCDF"
] | 312b7afa632f021ae880f898ef75e953c60f680eb93aa8cd52b765d262bb5f23 |
#!/usr/bin/env python
"""
Retrieve status of DIRAC jobs
"""
__RCSID__ = "$Id$"
import os
import json
from DIRAC.Core.Base import Script
from DIRAC.Core.Utilities.Time import toString, date, day
from COMDIRAC.Interfaces.Utilities.DCommands import ArrayFormatter
# TODO: how to import job states from JobDB in cl... | calancha/COMDIRAC | Interfaces/scripts/dstat.py | Python | gpl-3.0 | 5,671 | [
"DIRAC"
] | dcb2b0d4c009a677a778660c95005d5c7c35d755c86e82795409a89f5b137a0b |
# -*- coding: utf-8 -*-
# MolMod is a collection of molecular modelling tools for python.
# Copyright (C) 2007 - 2019 Toon Verstraelen <Toon.Verstraelen@UGent.be>, Center
# for Molecular Modeling (CMM), Ghent University, Ghent, Belgium; all rights
# reserved unless otherwise stated.
#
# This file is part of MolMod.
#
#... | molmod/molmod | molmod/unit_cells.py | Python | gpl-3.0 | 15,006 | [
"CRYSTAL"
] | 7b3629a386b420b8d0dd38492f42150ff83f6efaa49aed15af3d978bd0c3092a |
import numpy as np
from scipy.spatial.distance import euclidean
from wepy.runners.openmm import GET_STATE_KWARG_DEFAULTS
from wepy.resampling.distances.distance import Distance
from wepy.boundary_conditions.receptor import UnbindingBC
from openmm_systems.test_systems import LennardJonesPair
from wepy_tools.sim_maker... | ADicksonLab/wepy | src/wepy_tools/sim_makers/openmm/lennard_jones.py | Python | mit | 2,496 | [
"OpenMM"
] | eb2e8844234ed23a0c835c77540e946dff5326d9090e37c2496bff5aa02c0bc9 |
import os
import warnings
# cmr calls all available methods in ase.atoms detected by the module inspect.
# Therefore also deprecated methods are called - and we choose to silence those warnings.
warnings.filterwarnings('ignore', 'ase.atoms.*deprecated',)
from ase.test import NotAvailable
try:
import cmr
except Im... | JConwayAWT/PGSS14CC | lib/python/multimetallics/ase/test/cmr/cmr_rw.py | Python | gpl-2.0 | 898 | [
"ASE"
] | 5c4a94d4857940849280743c7cc4ac918620bddcd0068f93bc15f44de992e8f1 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module contains the object used to describe the possible bonded atoms based on a Voronoi analysis.
"""
__author__ = "David Waroquiers"
__copyright__ = "Copyright 2012, The Materials Project"
__credits__ = "Geoffroy H... | materialsproject/pymatgen | pymatgen/analysis/chemenv/coordination_environments/voronoi.py | Python | mit | 44,126 | [
"pymatgen"
] | 91487e059e72e61ee422bb7348e6faa77e9cc7116c39dfd011c53d0b809affe2 |
#!/usr/bin/env python
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistri... | dgasmith/psi4 | psi4/share/psi4/fsapt/copy_pymol2.py | Python | lgpl-3.0 | 1,339 | [
"Psi4",
"PyMOL"
] | 321ff5403fd9248967591542fcce19b1c5f183d0f0f2ed223b433df7d1b298cd |
# Copyright 2014-2020 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | sunqm/pyscf | pyscf/agf2/test/test_ragf2_h2o.py | Python | apache-2.0 | 7,115 | [
"PySCF"
] | 8a7020d5e173c925072c50e5755c6a7103079d978efb12177adb0399af346a17 |
import os
import copy
import bs4
import jinja2
import logging
log = logging.getLogger(__name__)
import MooseDocs
from MooseDocsNode import MooseDocsNode
class MooseDocsMarkdownNode(MooseDocsNode):
"""
Node for converting
"""
def __init__(self, md_file=None, syntax=None, parser=None, navigation=None, template=... | paulthulstrup/moose | python/MooseDocs/commands/MooseDocsMarkdownNode.py | Python | lgpl-2.1 | 7,064 | [
"MOOSE"
] | 432288615e23157c0b6809d1f87a51485dbd85f0562fe17fb5c46b93d19da8be |
# $Id: TemplateExpand.py 1053 2008-07-30 12:03:29Z landrgr1 $
#
# Created by Greg Landrum August, 2006
#
#
from __future__ import print_function
from rdkit import RDLogger as logging
logger = logging.logger()
logger.setLevel(logging.INFO)
from rdkit import Chem
from rdkit.Chem import Crippen
from rdkit.Chem import All... | soerendip42/rdkit | rdkit/Chem/ChemUtils/TemplateExpand.py | Python | bsd-3-clause | 14,189 | [
"RDKit"
] | 8bfaab5f92fbd56429bd2b88d14995f0841cb18c98172159497b645ef8666841 |
"""
Kive-style bowtie2
Run bowtie2 on paired-end FASTQ data sets with user-supplied *.bt2
bowtie2 SAM format output to <stdout> for redirection via subprocess.Popen
Sort outputs by refname.
Convert to CSV format and write to file.
"""
import argparse
import csv
import logging
import os
import sys
from micall.core imp... | cfe-lab/MiCall | micall/core/prelim_map.py | Python | agpl-3.0 | 5,979 | [
"Bowtie"
] | fd57469526f88656ded437627df69743d24eef755a3e8ca78042404a92123db2 |
from django.db import models
from django.utils import timezone
import datetime
# Create your models here.
class Visit(models.Model):
url = models.CharField(max_length=256)
date = models.DateTimeField(editable=False)
visitor = models.ForeignKey('Visitor')
# Possibly extend this class in the future to m... | joeyuan19/flaming-bear | PersonalSite/analytics/models.py | Python | apache-2.0 | 2,475 | [
"VisIt"
] | 7d02464e11f69b1aff44ecde98d5ffcee3bab0498dbf27cc19669a85abe7d86f |
# 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... | shakamunyi/tensorflow | tensorflow/contrib/distributions/python/ops/normal.py | Python | apache-2.0 | 9,259 | [
"Gaussian"
] | aed703bea7d89931dca187adda2da9df2471e6d6a2ba7f2a7a03a01b909128de |
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