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"""Nonlinear transform coding."""
import matplotlib.pyplot as plt
import numpy as np
import tensorflow as tf
import tensorflow_compression as tfc
import tensorflow_probability as tfp
from toy_sources import compression_model
tfpd = tfp.distributions
@tf.custom_gradient
def st_round(inputs):
return tf.round(inputs... | tensorflow/compression | models/toy_sources/ntc.py | Python | apache-2.0 | 14,474 | [
"Gaussian"
] | 7ef8c4d335541e1bb3b367e09ff9705d2f53bd130265ddbfe0e0f3377d27186c |
#
# Trees.py
#
# Copyright 2005 by Frank Kauff & Cymon J. Cox. 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.
#
# Tree class handles phylogenetic trees. Provides a set of method... | JohnReid/bioinf-utilities | python/corebio/seq_io/_nexus/Trees.py | Python | mit | 29,775 | [
"Biopython"
] | 3742a53b9d6456c0f6991f9348168126223dd47329c1b632c974748d2db57c5b |
""" Class for the LCG File Catalog Client
"""
import DIRAC
from DIRAC import S_OK, S_ERROR, gLogger, gConfig
from DIRAC.Resources.Utilities.Utils import checkArgumentFormat
from DIRAC.Resources.Catalog.FileCatalogueBase import F... | calancha/DIRAC | Resources/Catalog/LcgFileCatalogClient.py | Python | gpl-3.0 | 65,146 | [
"DIRAC"
] | d80111a42a50a8ba368703c187be2f00e8d10bbf16383d9dd4bdbaeeeeedd07c |
from requests_oauthlib import OAuth2Session
from bs4 import BeautifulSoup
import json, re
# The CLIENT_SECRETS_FILE variable specifies the name of a file that contains
# the OAuth 2.0 information for this application, including its client_id and
# client_secret. You can acquire an OAuth 2.0 client ID and client secret... | CravateRouge/Shaz2You | shaz2you.py | Python | gpl-3.0 | 5,738 | [
"VisIt"
] | 0b036d3f8d62ff14f9947f0875e4598d27bee099e561d7a391432fb5aab11b89 |
# 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... | lukeiwanski/tensorflow | tensorflow/contrib/autograph/converters/builtin_functions.py | Python | apache-2.0 | 2,541 | [
"VisIt"
] | 035319b42d3b60a517c484d0e449c3486ab4910c70a0616e361ab8157dfe3461 |
import numpy as np
from cs231n.layers import *
from cs231n.layer_utils import *
def affine_bn_relu_forward(X, W, b, gamma, beta, bn_param):
"""
Convenience layer that perorms an affine -> batch norm -> ReLU
Inputs:
- X: Input to the affine layer
- W, b: Weights for the affine layer
- gamma, beta: weights... | HaoMood/cs231n | assignment2/assignment2/cs231n/classifiers/fc_net.py | Python | gpl-3.0 | 16,815 | [
"Gaussian"
] | ea9b6ee7d95d65229c9ca8d475dc79613df3beb851ff584df6513cf344d2dacd |
from __future__ import nested_scopes
"""
################################################################################
#
# SOAPpy - Cayce Ullman (cayce@actzero.com)
# Brian Matthews (blm@actzero.com)
# Gregory Warnes (Gregory.R.Warnes@Pfizer.com)
# Christopher Blunck (blunck@... | marco-mariotti/selenoprofiles | libraries/SOAPpy/Client.py | Python | gpl-2.0 | 17,054 | [
"Brian"
] | ad74416492ab28f8a2657e7d42e684859179d813b32d391f72ac3d374417ac53 |
#! /usr/bin/env python
"""
This script performs event averaging for particle
spectra and anisotropic flow coefficients calculated
from event-by-event simulations
v_n is analyzed up to n = 6
Format for particle_XXX_vndata.dat file:
n_order real_part real_part_err imag_part imag_part... | chunshen1987/hadronic_afterburner_toolkit | ebe_scripts/average_event_spvn_h5_minimumbias.py | Python | mit | 104,915 | [
"Psi4"
] | 6e6615718dd6930fc3949d32f5837c85cab8f06de58a9c3a122522a02cb1fb63 |
import matplotlib.pyplot as plt
import numpy as np
from matplotlib.pyplot import Rectangle # Used to make dummy legend
# Open CSV File from Simulation
datafileS = open('../HIIregionFiles/3DHiiRegions.csv', 'r')
csvFileS = []
for row in datafileS:
csvFileS.append(row.strip().split(','))
# Save Galactic Radius Info ... | WillArmentrout/galSims | tests/completeness/Completeness_TwoPanel_B2.py | Python | gpl-2.0 | 24,438 | [
"Galaxy"
] | 5dcad128e396f15a185d5bb31a9296ba7f1c091c89384960770de08af14cdb4d |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# MLN Parameter Learning Tool
#
# (C) 2012-2015 by Daniel Nyga
# 2006-2007 by Dominik Jain
#
# Permission is hereby granted, free of charge, to any person obtaining
# a copy of this software and associated documentation files (the
# "Software"), to deal in the Software wit... | danielnyga/pracmln | python3/pracmln/mlnlearn.py | Python | bsd-2-clause | 48,186 | [
"Gaussian"
] | e09fe99963d0cd14e9fb8852295a53051fc573d0374be35da28ff001628060f1 |
import netCDF4
import urllib2
import logging
import numpy as np
import pandas as pd
from collections import OrderedDict
from datetime import datetime, timedelta
import xml.etree.ElementTree as ElementTree
class Dataset:
'''OpenDAP dataset object
Similar to netCDF4.Dataset but approaches OpenDAP directory... | openearth/opendap-python | OpenDAP/opendap.py | Python | gpl-3.0 | 14,021 | [
"NetCDF"
] | e1418bb92caa316a4388ba405e294b995c6c1fb7185ce6e8087013cce6d31c0a |
import numpy as np
from ase.io.pupynere import NetCDFFile
class Reader:
def __init__(self, filename, comm):
self.nc = NetCDFFile(filename)
def dimension(self, name):
return self.nc.dimensions[name]
def __getitem__(self, name):
value = getattr(self.nc, name)
if isinsta... | robwarm/gpaw-symm | gpaw/io/netcdf.py | Python | gpl-3.0 | 1,965 | [
"ASE"
] | 35825d158db68311623da186e0527d3cfcf032c4607590353a950164f7b6d4fb |
'''
@file : precision.py
@author (A) : Madhusai Ravada.
@project : Social List
program to find the precision of search results in google
This work is licensed under the
Creative Commons Attribution-NonCommercial-ShareAlike 4.0
International License. To view a copy of this license,
visit http://creativecommons.org/lic... | SummerProject16/project | CMUTweetTagger/precision.py | Python | cc0-1.0 | 1,843 | [
"VisIt"
] | e785e441cbda4159b85931d8613ceb60844f1c47e32a305b941ce9d62082f006 |
#########################################################################
## This program is part of 'MOOSE', the
## Messaging Object Oriented Simulation Environment.
## Copyright (C) 2015 Upinder S. Bhalla. and NCBS
## It is made available under the terms of the
## GNU Lesser General Public License version 2... | dilawar/moose-full | moose-examples/paper-2015/Fig2_elecModels/Fig2D.py | Python | gpl-2.0 | 3,755 | [
"MOOSE",
"NEURON"
] | 9cb49ad096c7782e47afcaccc694fb8ae40a5954c8d1841305a7d2e04d96061c |
import sys
sys.path.append('..')
import numpy as np
np.random.seed(888)#for experiment repetibility
import ANN_classifier as ann
import os
import sys
import utils.dataset_manupulation as dm
import utils.utils as utl
import argparse
import warnings
warnings.simplefilter("ignore", DeprecationWarning)
parser = argparse.A... | vespero89/Snoring_Challenge | Supervectors/gridsearch_ANN.py | Python | gpl-3.0 | 7,609 | [
"Gaussian"
] | 1c55ac7c8537d27e7ded33b12a92db97a019e9e69be2c2b007aade73fdce2a45 |
#!/usr/bin/env python3
########################################################################
# Solves problem 142 from projectEuler.net.
# ???
# Copyright (C) 2011 Santiago Alessandri
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public L... | sanSS/programming-contests | project-euler/problem142.py | Python | gpl-3.0 | 1,119 | [
"VisIt"
] | 629d1db1eca553cc74f7102a1186ae53746ef92faeab3a7b47e5e17b37a5599a |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
# Author: Pauli Virtanen, 2016
import math
import operator
from .util import inf, nan, is_na
def compute_stats(samples, number):
"""
Statistical analysis of measured samples.
Parameters
----------
samples : list of float
L... | airspeed-velocity/asv | asv/statistics.py | Python | bsd-3-clause | 15,930 | [
"Gaussian"
] | e1c3a380f13ea20f432eb9d721883e1cd7b042fb62b7fac4d70bf03c7827dbc1 |
from __future__ import division
import numpy as np
import matplotlib
matplotlib.use("Agg")
import matplotlib.pyplot as plt
import matplotlib.animation as animation
import matplotlib.patches as patches
import matplotlib.path as path
import subprocess
plt.style.use('classic')
# Parameters for animation
aL=4
cH=0.25
lam... | letsgoexploring/signalingAnimation | code/signalingAnimationPoolingHighType.py | Python | mit | 4,856 | [
"Brian"
] | 6fda422d074659f1b38acd7776f6c50124938105343a45e2bbf3078cc0c807f1 |
"""
Test LogRecord Creation
- createLogRecord
- debug, verbose, info, warn, notice, error, fatal, always
"""
__RCSID__ = "$Id$"
import pytest
from DIRAC.FrameworkSystem.private.standardLogging.LogLevels import LogLevels
from DIRAC.FrameworkSystem.private.standardLogging.test.TestLogUtilities import gLogger, gLogge... | ic-hep/DIRAC | src/DIRAC/FrameworkSystem/private/standardLogging/test/Test_Logging_CreationLogRecord.py | Python | gpl-3.0 | 2,998 | [
"DIRAC"
] | c38fecb0a1fa3ec3b35c906512e4a341bad2af6d82a12b6d8a356198e1e8caf0 |
#!/usr/bin/python
# 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.
#
# Ansible is distributed... | GustavoHennig/ansible | lib/ansible/modules/cloud/amazon/cloudwatchevent_rule.py | Python | gpl-3.0 | 14,942 | [
"Dalton"
] | 142d1fd4bc63b913c77ac50fd6f69a4d30a0d506ae296324338b7648a6fd2183 |
# $Id$
#
# Copyright (C) 2003-2006 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.
#
"""basic unit testing code for the rdk... | soerendip42/rdkit | rdkit/Chem/UnitTestChemv2.py | Python | bsd-3-clause | 5,913 | [
"RDKit"
] | 43a1dd9a0e6d79f778fb7035016277f4e6a70a7473851c20d037256041a676de |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
A simple example to run FCI
'''
import pyscf
mol = pyscf.M(
atom = 'H 0 0 0; F 0 0 1.1', # in Angstrom
basis = '6-31g',
symmetry = True,
)
myhf = mol.RHF().run()
#
# create an FCI solver based on the SCF object
#
cisolver = pyscf... | sunqm/pyscf | examples/fci/00-simple_fci.py | Python | apache-2.0 | 744 | [
"PySCF"
] | 67a305739a57d21021b7ae9ef44058b75fcb90a47f6566d83ff29fb844a7d4d5 |
#!/usr/bin/python2.5
# Copyright (C) 2007 Google Inc.
#
# 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 la... | jonpetersen/transitfeed-1.2.12 | schedule_viewer.py | Python | apache-2.0 | 19,268 | [
"VisIt"
] | 8fd9ccc24f7e37f88e5cdcffc1d733effb129d53f9da24833eea25bbe88f4a8b |
from __future__ import print_function
"""bundletrajectory - a module for I/O from large MD simulations.
The BundleTrajectory class writes trajectory into a directory with the
following structure::
filename.bundle (dir)
metadata.pickle Data about the file format, and about which
... | suttond/MODOI | ase/io/bundletrajectory.py | Python | lgpl-3.0 | 33,982 | [
"ASE"
] | f86c2f4a73f440fa965da0c45b4cb37346362b5bd0dad75873e2542f89348d87 |
########################################################################
#
# Wrappers for algorithms in DEAP library (http://deap.readthedocs.org/en/latest/api/algo.html)
#
########################################################################
import wx
from wx.lib.agw.floatspin import FloatSpin as wxFloatSpin
fro... | dibondar/PyPhotonicReagents | libs/gui/deap_algorthims_tabs.py | Python | bsd-3-clause | 8,460 | [
"Gaussian"
] | 43f8aebc4ece2af9e78d9a47ab87178887e9b6aa38f3586b444c73962bf0c98b |
import os
from typing import Optional
import libcst
from libcst import Annotation, BaseExpression, FunctionDef, Name, Subscript
from libcst.metadata import SyntacticPositionProvider
BASE_DIR = 'django-stubs'
fpath = os.path.join(BASE_DIR, 'core', 'checks', 'model_checks.pyi')
with open(fpath, 'r') as f:
contents... | snakeleon/YouCompleteMe-x64 | third_party/ycmd/third_party/jedi_deps/jedi/jedi/third_party/django-stubs/scripts/catch_non_abstract_annotation.py | Python | gpl-3.0 | 3,606 | [
"VisIt"
] | 6d34b8e282ab2ea4caf3edae2c51df83af9dd431fd25e5e7db2ddf320ba6c83f |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publish... | thica/ORCA-Remote | src/ORCA/actions/WidgetControl.py | Python | gpl-3.0 | 29,473 | [
"ORCA"
] | 25036650f8f47cfb776b1ad7e12b0d9f144db26a67db1440256ece96f5c7751b |
import multiprocessing
import os
import platform
import shutil
import subprocess
import sys
import threading
import warnings
import inspect
import pickle
import weakref
from itertools import chain
from io import StringIO
import numpy as np
from numba import njit, jit, generated_jit, typeof
from numba.core import type... | stonebig/numba | numba/tests/test_dispatcher.py | Python | bsd-2-clause | 69,584 | [
"VisIt"
] | d9881816d803c8f8aebc2a6bc213633f9cd58dfe21086cd6a59d28df13f5c344 |
# ============================================================================
#
# Copyright (C) 2007-2010 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... | kurtraschke/camelot | camelot/view/controls/delegates/__init__.py | Python | gpl-2.0 | 4,566 | [
"VisIt"
] | 256697a6447f7ab794539539e421b5070374372a5541c82af245490e4793b1a1 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals, division, print_function
import os
import tempfile
from pymatgen.util.testing import PymatgenTest
from pymatgen.io.abinitio.abiinspect import *
#test_dir = os.path.jo... | sonium0/pymatgen | pymatgen/io/abinitio/tests/test_abiinspect.py | Python | mit | 2,469 | [
"pymatgen"
] | af785f45d4e4b15c28709060aca1e8e4d5fb313be5d47590383beb082457eb58 |
# Author: Prabhu Ramachandran
# License: BSD style
# Copyright (c) 2004, Enthought, Inc.
"""Tests for vtk_parser.py.
Note that the `test_parse_all` parses every single class in
VTK-Python. It organizes the methods and also tries to obtain the
method signature for every method in every class. If this runs
without cr... | dmsurti/mayavi | tvtk/tests/test_vtk_parser.py | Python | bsd-3-clause | 13,056 | [
"VTK"
] | f71a1d01700695b86f184be99c511b1ae3d0bb54b0559c63f84ada884a6acdcc |
#!/usr/bin/env python
"""Clean and prepare a set of genomes for CWL usage and upload.
bcbio with CWL can read directly from a reference genome folder
without using Galaxy location files. This allows both local and
remote usage on object stores (Arvados, DNAnexus, SevenBridges, Synapse, S3).
This copies from an existi... | a113n/bcbio-nextgen | scripts/utils/bcbio_prep_cwl_genomes.py | Python | mit | 2,642 | [
"BWA",
"Galaxy"
] | 8f320e88238064a3ca7c3b0bd0a012d345df18ebe767b96f576317c999171baa |
class InputDeck(object):
"""Parse the input section for an ORCA job, either an entire input
file or a section of the output file.
"""
def __init__(self):
return
| berquist/orcaparse | orcaparse/inputdeck.py | Python | mpl-2.0 | 186 | [
"ORCA"
] | f239180b97feb5b2cec0cd9a283716a7b903b5b7bc9d8253359bba04e1f6102c |
from vtk . numpy_interface import dataset_adapter as dsa
from vtk . numpy_interface import algorithms as algs
import h5py as h5
f1=h5.File("/pkg/etc/clion/system/cmake/generated/2774870a/2774870a/Debug/example/em/tokamak0007.h5")
x=f1["/record/0/H"][:]['p']['v']
coords=algs.make_vector(x[:,0],x[:,1],x[:,2])
pts=vtk.vtk... | simpla-fusion/SimPla | scripts/PostProcesse/pv_prog_source.py | Python | bsd-3-clause | 411 | [
"VTK"
] | 42a1fb7e0fa82a13fae87f3d30c5d05a20dfbe46b5d09625f78ebbaa84cf0428 |
#!/usr/bin/env python
"""
Easy Install
------------
A tool for doing automatic download/extract/build of distutils-based Python
packages. For detailed documentation, see the accompanying EasyInstall.txt
file, or visit the `EasyInstall home page`__.
__ https://setuptools.readthedocs.io/en/latest/easy_install.html
""... | wildchildyn/autism-website | yanni_env/lib/python3.6/site-packages/setuptools/command/easy_install.py | Python | gpl-3.0 | 85,973 | [
"VisIt"
] | 7abb84e11e097ce4f1d3fd210d830c125a6ea77dd0927d0fe3895c9603fc740d |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
Module to test fitting routines
"""
from __future__ import (absolute_import, unicode_literals, division,
print_function)
import os.path
import numpy as np
from numpy import linalg
from numpy.testing.utils import assert_allcl... | piotroxp/scibibscan | scib/lib/python3.5/site-packages/astropy/modeling/tests/test_fitters.py | Python | mit | 13,133 | [
"Gaussian"
] | 7f69a97b9cd3967e389ea30788f22d66adc105b90a32476433e461bc986366b5 |
# coding: utf-8
# ## ***Plotting brightness temperatures in a Lambert Conformal Conic map projection***
# In this notebook we're going to continue working with http://clouds.eos.ubc.ca/~phil/Downloads/a301/MYD021KM.A2005188.0405.005.2009232180906.h5. We will also need to go to Laadsweb and do a wildcard search on
#... | dennissergeev/classcode | notebooks/satellite_basemap_h5.py | Python | cc0-1.0 | 10,423 | [
"NetCDF"
] | b84e309ed693794ffa99a191d98918f7cef64097c62161805716fc8dfbc3a0d1 |
#!/usr/bin/env python
########################################################################
# File : dirac-admin-delete-user
# Author : Adrian Casajus
########################################################################
"""
Remove User from Configuration
Example:
$ dirac-admin-delete-user vhamar
"""
from ... | ic-hep/DIRAC | src/DIRAC/Interfaces/scripts/dirac_admin_delete_user.py | Python | gpl-3.0 | 1,571 | [
"DIRAC"
] | 44c9ff70ea185625e40e4a724f86a2a7c47a8c72a5ab7d07f696bcf8d76bc3d0 |
# 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... | rabipanda/tensorflow | tensorflow/contrib/py2tf/converters/control_flow.py | Python | apache-2.0 | 5,422 | [
"VisIt"
] | 2b8bca365069884ad6ee17b5bd55d10af59a6a1d01c621e1c9729cd594858c55 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2009 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## 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 F... | tiagocardosos/stoq | stoqlib/reporting/production.py | Python | gpl-2.0 | 2,042 | [
"VisIt"
] | b941e5f3a9902d953fe2d072444e5765bc0fff42c1b4ab06a5cc9bc25be6a915 |
#!/usr/bin/env python
'''do sims of cells, LFP, and output data'''
#import modules
import uuid
import numpy as np
import h5py
import os
from glob import glob
#workaround for plots on cluster
if not os.environ.has_key('DISPLAY'):
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
from scipy.... | espenhgn/ViSAPy | examples/example_in_vitro_MEA/example_in_vitro_MEA.py | Python | gpl-2.0 | 11,523 | [
"NEURON"
] | 856a0f878aa80174fa172e229104d08bbfc9076e1d1d2749dd607b42d531b528 |
import os
from glob import glob
from nose.tools import (assert_equal, assert_not_equal, assert_is_not_none)
from qiutil.collections import concat
import qixnat
from qipipe.staging.iterator import iter_stage
from ... import (ROOT, PROJECT)
from ...helpers.logging import logger
from ...helpers.staging import subject_sour... | ohsu-qin/qipipe | test/unit/staging/test_iterator.py | Python | bsd-2-clause | 6,389 | [
"VisIt"
] | 2c1ee5f4cf3a46f757cd4ab9f574c54c7df54d7e9b3d2343f1807b39ee1746a3 |
""" Visit https://developer.github.com/v3/repos/statistics/
for API tips.
This code builds the HISTORY.rst file using the GitHub API
"""
# I like extra spaces inside parens and sometimes camelCase
# pylint: disable=C0326, C0325
# pylint: disable=C0103
import requests
import os
import datetime
import getp... | sonofeft/Tk_Nosy | history_from_github_api.py | Python | gpl-3.0 | 1,888 | [
"VisIt"
] | 183c1809e26e6d5cf891e508e01b26f32c63e853474ac4693b15c68c3ff67589 |
from datetime import datetime
from dateutil.relativedelta import relativedelta
from collections import Counter
from itertools import groupby
from operator import attrgetter, itemgetter
from django.db.models import Count, Sum, Q, OuterRef, Subquery
from django.utils import timezone
from django_countries.fields import ... | UKTradeInvestment/export-wins-data | mi/views/base_view.py | Python | gpl-3.0 | 28,891 | [
"Amber"
] | f45082aa1d4a82b32d3f47e420b3cedf28ac49ac8d10ee1910b8fad4fd9a958f |
# -*- coding: utf-8 -*-
"""
Created on Thu Jun 11 10:08:31 2015
This file is part of pyNLO.
pyNLO 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 optio... | ycasg/PyNLO | src/pynlo/light/beam.py | Python | gpl-3.0 | 7,929 | [
"CRYSTAL",
"Gaussian"
] | 35f6a6456282000c7124a24095cd32406401c00a4c5913a66d482b4e8c10de6d |
# $Id$
#
# Copyright (C) 2003-2006 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.
#
""" Calculation of topo... | adalke/rdkit | rdkit/Chem/GraphDescriptors.py | Python | bsd-3-clause | 19,951 | [
"RDKit"
] | 6c49d5948cd035c4b82d751018172df44aabc9d3dd1c945a812280248634e235 |
"""
cats: cat sequence
"""
DOCLINES = __doc__.split("\n")
from setuptools import setup,find_packages
CLASSIFIERS = [
'Development Status :: 3 - Alpha',
'Intended Audience :: Science/Research',
'License :: OSI Approved :: BSD License',
'Programming Language :: Python',
'Programming Language :: Pyth... | khughitt/cats | setup.py | Python | bsd-2-clause | 1,346 | [
"Biopython"
] | 4e7afb25426cd65d263574adcf6056bfecd4f47176e727a935824577b6b957c2 |
import networkx as nx
import random
import heapq
import numpy as np
import EoN
from collections import defaultdict
from collections import Counter
#######################
# #
# Auxiliary stuff #
# #
#######################
def _truncated_exponential_(rate, T):
r'''ret... | springer-math/Mathematics-of-Epidemics-on-Networks | EoN/simulation.py | Python | mit | 162,236 | [
"Amber"
] | 6eb759337fec6676cdeef1e469de27b492d54d990e9f455626e55cb533077a78 |
import numpy as np
import matplotlib.pyplot as plt
import networkx as nx
pairs = [("openmm", "yank"), ("cmake", "openmm"), ("cuda", "openmm"), ("fftw3f", "openmm"), ("swig", "openmm"), ("mpi4py", "yank"), ("netcdf4", "yank"),
("numpy", "mdtraj"), ("scipy", "mdtraj"), # ("mdtraj", "mixtape"), ("sklearn", "mixtape"),
(... | kyleabeauchamp/FullStack | src/make_graph.py | Python | gpl-2.0 | 1,173 | [
"MDTraj",
"OpenMM"
] | d9834e6704cfaecc1e160cd871e26fdb4cd4f0ccdd0d90e931f4657406e2055b |
# $HeadURL$
"""
Collection of DIRAC useful operating system related modules
by default on Error they return None
"""
__RCSID__ = "$Id$"
from types import StringTypes
import os
import multiprocessing
import DIRAC
from DIRAC.Core.Utilities.Subprocess import shellCall, systemCall
from DIR... | rajanandakumar/DIRAC | Core/Utilities/Os.py | Python | gpl-3.0 | 6,064 | [
"DIRAC"
] | efdfdd7efdbc3e6e3dc49050e16b6111a57b1a4fb8e4a392cc547a6cc68580ef |
"""
@name: Modules/House/Hvac/hvac.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2015-2019 by D. Brian Kimmel
@license: MIT License
@note: Created on Jul 12, 2015
@Summary:
This is the controlling portion of a complete HVAC system.
PyHouse.House.Hvac.
... | DBrianKimmel/PyHouse | Project/src/Modules/House/Hvac/hvac.py | Python | mit | 2,674 | [
"Brian"
] | 4dc31869392484be850d38300a486817a87952c7d2ab9ff35aa239bdbd30892d |
from __future__ import absolute_import
from contextlib import contextmanager
from capybara.version import __version__
app = None
""" object: The WSGI-compliant app to test. """
app_host = None
""" str: The default host to use when giving a relative URL to visit. Must be a valid URL. """
default_driver = "werkzeug"... | elliterate/capybara.py | capybara/__init__.py | Python | mit | 8,368 | [
"VisIt"
] | f9abe0b724393e1d155c8c0018bb0c65dc3a5a99e19372cca537313cad5d7b21 |
# Copyright (C) 2000 Greg Landrum
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2 of the License, or (at your option) any later version.
#
# This library is distri... | rdkit/rdkit-orig | rdkit/sping/SVG/pidSVG.py | Python | bsd-3-clause | 23,791 | [
"RDKit"
] | f6293766f4d5298dffc8f6e99f71e640a86bb38190089895c80ae5881ac159d8 |
# ***************************************************************************
# * Copyright (c) 2019 Bernd Hahnebach <bernd@bimstatik.org> *
# * *
# * This file is part of the FreeCAD CAx development system. *
# * ... | sanguinariojoe/FreeCAD | src/Mod/Fem/femtest/app/test_femimport.py | Python | lgpl-2.1 | 7,670 | [
"VTK"
] | dfc8402051b1b25450afe37ae48acff3877fd13d21ab1f414742dbb56c16821e |
"""
from py2neo import neo4j, ogm, node, rel
from cuorewebpage.Model.Calendar import Calendar
from cuorewebpage.Model.Event import Event
from datetime import datetime
from cuorewebpage.Model.Project import Project
from cuorewebpage.Model.Task import Task, STS_OPEN, STS_IN_PROG
from cuorewebpage.Model.Workspace import ... | cuoretech/dowork | dowork/Model/database_populate.py | Python | apache-2.0 | 7,444 | [
"exciting"
] | c6a675f25d589c198eb321cf29e62cebde1cdb2f8a9a21b5d5fd9f170d3b2c9b |
import sys, logging, os, time, datetime, errno
log = logging.getLogger( __name__ )
log.setLevel(logging.DEBUG)
handler = logging.StreamHandler( sys.stdout )
format = "%(name)s %(levelname)s %(asctime)s %(message)s"
formatter = logging.Formatter( format )
handler.setFormatter( formatter )
log.addHandler( handler )
fro... | volpino/Yeps-EURAC | lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py | Python | mit | 37,520 | [
"Galaxy"
] | 676955d6c57d70701946ec8fc8795c90f45940b55ca280365cdc766383099a8c |
import dateutil.parser
import demistomock as demisto # noqa: F401
from CommonServerPython import * # noqa: F401
from typing import Any, Dict, Union, Optional, Tuple
DEMISTO_OCCURRED_FORMAT = '%Y-%m-%dT%H:%M:%SZ'
DEMISTO_INFORMATIONAL = 0.5
ORCA_API_TIMEOUT = 30 # Increase timeout for ORCA API
ORCA_API_LIMIT = 500... | demisto/content | Packs/Orca/Integrations/Orca/Orca.py | Python | mit | 12,360 | [
"ORCA"
] | 7adbe055bb73a6fdc7373d79cd6d4e316582ebf75756d301a21aeeadae9b018b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
A tool generate AUTHORS. We started tracking authors before moving to git, so
we have to do some manual rearrangement of the git history authors in order to
get the order in AUTHORS.
"""
from __future__ import unicode_literals
from __future__ import print_function
imp... | lindsayad/sympy | bin/authors_update.py | Python | bsd-3-clause | 2,770 | [
"Brian"
] | acc8ecc67ccabb42e031238a85d59b624d9afc67a3286dc78133bdac9066660a |
# Copyright (c) 2018 PaddlePaddle 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 app... | PaddlePaddle/Paddle | python/paddle/fluid/tests/unittests/test_random_seed.py | Python | apache-2.0 | 18,017 | [
"Gaussian"
] | a410412f51ce07338c8e181358505a3e6fbc4f75e008e0d56226ddce67a2db7c |
# -*- coding: utf-8 -*-
"""
The :mod:`sklearn.naive_bayes` module implements Naive Bayes algorithms. These
are supervised learning methods based on applying Bayes' theorem with strong
(naive) feature independence assumptions.
"""
# Author: Vincent Michel <vincent.michel@inria.fr>
# Minor fixes by Fabian Pedre... | wlamond/scikit-learn | sklearn/naive_bayes.py | Python | bsd-3-clause | 30,852 | [
"Gaussian"
] | 761b5a9ad01056bc325d53a34b083c649ea2a5d8a0c8e7cee33b878a0ecafd6f |
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'battery_window_qt.ui'
#
# Created by: PyQt5 UI code generator 5.6
#
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore, QtGui, QtWidgets
class Ui_CognitiveBattery(object):
def setupUi(self, CognitiveBattery... | sho-87/cognitive-battery | designer/battery_window_qt.py | Python | mit | 21,548 | [
"VisIt"
] | cf68afabcfaf97c0e3a7bfc42a811b05bd4dfdd6f59fd819a25f2b8f8279aa80 |
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at https://mozilla.org/MPL/2.0/.
import numpy as np
from ..sile import add_sile, sile_fh_open, SileError
from .sile import SileSiesta
from sisl._array ... | zerothi/sisl | sisl/io/siesta/eig.py | Python | mpl-2.0 | 10,158 | [
"Gaussian",
"SIESTA"
] | a421a04fdc3ca6bee63626c1fcdcbd4c9ed1c081fdd4ddd920cba5b1d61f73e0 |
#!/usr/bin/python
#
# Copyright 2015 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required b... | coxmediagroup/googleads-python-lib | examples/adwords/v201502/advanced_operations/add_text_ad_with_upgraded_urls.py | Python | apache-2.0 | 4,027 | [
"VisIt"
] | 92e92fda23fb56cd6cfe42059c2c8d4fc448e37dcde7a7920ba8543c0416bbaa |
'''
Created on 2013-05-02
@author: brian
'''
import pygame
from pygame.locals import *
class Quit:
def __init__(self, player):
self.player = player
self.quit = None
self.finished = False
self.player.log.append('Quit? (Y/N)')
def nextStep(self):
if(self.finished):
... | Greymerk/python-rpg | src/actions/quit.py | Python | gpl-3.0 | 819 | [
"Brian"
] | db03f3fff4a8a2caeeed6b9fb02e700c14cfa524c7e03d6553f2835ab57c8fa0 |
#!/usr/bin/env ganga
import getpass
from distutils.util import strtobool
import os
import re
DoneBkgs=['nobkg']
for fname in os.listdir("PotentialBackgrounds"):
channel=fname[6:14]
if re.search("MC_12_1.*py",fname)>0 and not channel in DoneBkgs:
DoneBkgs.append(channel)
print fname
pola... | Williams224/davinci-scripts | ksteta3pi/BackJobSubmit.py | Python | mit | 2,516 | [
"DIRAC"
] | 2496c9d5340aa1bb8eea575bc76e781fb70fcd395c0110dc11526692075cb4b1 |
# Copyright 2018 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... | tensorflow/privacy | tensorflow_privacy/privacy/analysis/rdp_accountant_test.py | Python | apache-2.0 | 9,435 | [
"Gaussian"
] | 5caf13774970986caa9a52b4676cae445c978efa759fe19a584a0da9f62bfd62 |
from __future__ import absolute_import
from __future__ import print_function
import numpy as np
import math
from . import mesh
from six.moves import map
from six.moves import range
from six.moves import zip
class VoroMesh(mesh.Mesh):
""" The voro mesh loads data from
voro++ voronoi generator by Chris H. Ryc... | ohinai/mimpy | mimpy/mesh/voromesh.py | Python | bsd-3-clause | 10,799 | [
"VTK"
] | f3b4520dc97ad2c3bde163aa85130961ce9f2629f482a0d3887d0ef8f9675f1d |
# -*- coding: utf-8 -*-
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Deleting field 'PatientAdmission.fourth_visit'
db.delete_column(u'admission_patientadmission', 'fourth_vis... | aazhbd/medical_info01 | admission/migrations/0002_auto__del_field_patientadmission_fourth_visit__del_field_patientadmiss.py | Python | bsd-3-clause | 7,912 | [
"VisIt"
] | beac424acff125306f96c6709b5b1397edaa56059a51a4355949b5ad5bd1fcc6 |
import functools
import logging
import os
from typing import TYPE_CHECKING, Dict, List, Optional, Set, Tuple, cast
from pip._vendor.packaging.utils import canonicalize_name
from pip._vendor.packaging.version import parse as parse_version
from pip._vendor.resolvelib import BaseReporter, ResolutionImpossible
from pip._v... | google/material-design-icons | update/venv/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/resolver.py | Python | apache-2.0 | 12,085 | [
"VisIt"
] | de1967ad9925b33154c06405177de72e410ef24c73e2f677fee2a9fcbf18be61 |
# First feature extraction method
from features_extraction.methods.first_feature_extraction import features as first_features
from features_extraction.methods.first_feature_extraction import values as first_values
# Second feature extraction method
from features_extraction.methods.second_feature_extraction import feat... | benitesf/Skin-Lesion-Analysis-Towards-Melanoma-Detection | features_extraction/feature_extraction.py | Python | mit | 5,846 | [
"Gaussian"
] | 236b74deb1ab011271a07c8920b35ecba2259333f1c3647489e0fc5e9f7565b6 |
#! /usr/bin/env python
"""
Module with the MCMC (``emcee``) sampling for NEGFC parameter estimation.
"""
__author__ = 'O. Wertz, Carlos Alberto Gomez Gonzalez, V. Christiaens'
__all__ = ['mcmc_negfc_sampling',
'chain_zero_truncated',
'show_corner_plot',
'show_walk_plot',
'... | carlgogo/vip_exoplanets | vip_hci/negfc/mcmc_sampling.py | Python | bsd-3-clause | 53,793 | [
"Gaussian"
] | 4c765bd7e04ce0aa06425060ecfc4b34e3afa04a9c7fdd0a93522936940d9231 |
# $Id$
#
# Copyright (C) 2007-2009 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.
#
import sqlalchemy
from rdkit import Chem
from rdki... | rvianello/rdkit | rdkit/Chem/MolDb/Loader_sa.py | Python | bsd-3-clause | 6,245 | [
"RDKit"
] | b4496818e6ad94883ad6ba53b7d2756ac2ed40b66d46373cc6275c21f0a31252 |
"""
@name: Modules/web/web_webs.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2013-2020 by D. Brian Kimmel
@license: MIT License
@note: Created on Sep 27, 2013
@summary: Handle all of the information for a house.
"""
__updated__ = '2019-12-30'
# Import system type s... | DBrianKimmel/PyHouse | Project/src/Modules/Computer/Web/web_webs.py | Python | mit | 1,740 | [
"Brian"
] | 6e37fa4f8cacf48c35f9768ce964dfe347628c50936f72623d8f0c10f47f7ccf |
# Copyright (c) 2015, Frappe Technologies Pvt. Ltd. and Contributors
# License: GNU General Public License v3. See license.txt
from __future__ import unicode_literals
import frappe
from frappe.utils import add_days, getdate, cint, cstr
from frappe import throw, _
from erpnext.utilities.transaction_base import Transa... | aruizramon/alec_erpnext | erpnext/support/doctype/maintenance_schedule/maintenance_schedule.py | Python | agpl-3.0 | 8,940 | [
"VisIt"
] | 311aa0063d50bb6e2b826ccf84929094c1930eff8d8c70b8a28ef51e5d6c550a |
'''
Created on 2013-09-28, revised 2014-06-17, added daily output 2020-05-04
A script to average WRF output; the default settings are meant for my 'fineIO' output configuration and
process the smaller diagnostic files.
The script can run in parallel mode, with each process averaging one filetype and domain, producing... | aerler/WRF-Tools | Python/wrfavg/wrfout_average.py | Python | gpl-3.0 | 79,623 | [
"NetCDF"
] | f1df7aa470a160bbf174fbf4dca00f84a675a0362c2605bdacab322f17474ca7 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
Created on Tue Sep 27 10:11:22 2016
@author: etienne
Functions to calculate the nematic order parameter from ordering tensor (see arXiv:1409.3542v2) and
the smectic A order parameter (see The Journal of chemical physics 138(20), 204901 (2013).)
from a LAMMPS output with Ga... | EtiCui/Msc-UdeS | dataAnalysis/nematic_sma_OP.py | Python | mit | 11,728 | [
"LAMMPS"
] | cfaf5e19219b9ff2e8fde8242196714aac75d680f7fe95886954382d79c22b5f |
# coding=utf-8
"""
InaSAFE Disaster risk assessment tool developed by AusAid -
**IS Utilities implementation.**
Contact : ole.moller.nielsen@gmail.com
.. note:: 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 Fre... | drayanaindra/inasafe | safe_qgis/utilities/utilities.py | Python | gpl-3.0 | 23,842 | [
"VisIt"
] | 20a500a64a92d46a4e0ccdf7510b7dcf838be803bfca3c9790aa71a899f66532 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Example implementation.
If run, access token
"""
import string
import simplejson
from yammer import Yammer, YammerError
try:
from example_local_settings import *
except ImportError:
pass
__author__ = 'Jonas Nockert'
__license__ = "MIT"
__version__ = '0.2'... | lemonad/python-yammer-oauth | example.py | Python | mit | 5,957 | [
"VisIt"
] | 01ef3366185b92513fef9df9c27dac935a142d84013a287788b8990d7699f326 |
# -*- coding: utf-8 -*-
# Dioptas - GUI program for fast processing of 2D X-ray diffraction data
# Principal author: Clemens Prescher (clemens.prescher@gmail.com)
# Copyright (C) 2014-2019 GSECARS, University of Chicago, USA
# Copyright (C) 2015-2018 Institute for Geology and Mineralogy, University of Cologne, Germany
... | erangre/Dioptas | dioptas/model/util/PeakShapes.py | Python | gpl-3.0 | 1,278 | [
"Gaussian"
] | cdaa9e0355e88d5f6ab3dd3827bb3f11f85882c3a14df03eb099d87950e83699 |
#!/usr/bin/env python
import re
import sys
import json
import os
badtests = []
testfail = re.compile(r'^\s*(?P<num>\d+) - (?P<name>\w+(?:-\w+)*) \(Failed\)\s*$')
with open('full_ctest_output.dat', 'r') as outfile:
ctestout = outfile.readlines()
ctest_exit_status = int(ctestout[0])
if len(ctestout[1:]) == 0:
... | ashutoshvt/psi4 | devtools/scripts/ci_print_failing.py | Python | lgpl-3.0 | 1,808 | [
"CFOUR"
] | 85f006e2533bed1d4e51beb9b91372c0ef597121b4479e0a6159b9888a7a7593 |
# This file is part of DEAP.
#
# DEAP 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 later version.
#
# DEAP is distributed ... | fmder/deap | deap/gp.py | Python | lgpl-3.0 | 37,228 | [
"ADF"
] | 7ecd9a7664def1f2ec090cb656465032ea026d69585e5fac47b10a9146fee241 |
"""
Social conveyer
Randall Ung
Creates GUI to control behavioral and imaging devices for in vivo calcium
imaging. Script interfaces with Arduino microcontroller and imaging devices.
"""
from Tkinter import *
import tkMessageBox
import tkFileDialog
import collections
import serial
import serial.tools.list_ports
impo... | rlung/conveyer | social-run/social_free_roam.py | Python | gpl-3.0 | 35,006 | [
"NEURON"
] | b98a1ea8e852c3afc43154e7d3fcb04aaa6feb93a141cb35d4ac5f3287fe2e04 |
# -*- coding: utf-8 -*-
{
"'Cancel' will indicate an asset log entry did not occur": "'Abbrechen' wird angeben, dass ein Asset Log Eintrag nicht eingetreten ist",
"A location that specifies the geographic area for this region. This can be a location from the location hierarchy, or a 'group location', or a location that... | flavour/Turkey | languages/de.py | Python | mit | 255,451 | [
"VisIt"
] | 34ab2850527e9e2a53f94f202f2e6bb657016c259366fafa7d003966a3a717a6 |
import simtk.openmm.app.element as elem
class Element(elem.Element):
"""An Element represents a chemical element.
The simtk.openmm.app.element module contains objects for all the standard chemical elements,
such as element.hydrogen or element.carbon. You can also call the static method Element.getBySymbo... | iModels/foyer | foyer/element.py | Python | mit | 1,566 | [
"OpenMM"
] | dbe38d9bace88d11cd549cf15b1ba974e09faa5f172a683dd85d10e2aa74652d |
''' DIRAC.ResourceStatusSystem.DB package
'''
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = '$Id$'
| yujikato/DIRAC | src/DIRAC/ResourceStatusSystem/DB/__init__.py | Python | gpl-3.0 | 175 | [
"DIRAC"
] | fdafbbb2d6904194238ff896d9d1e29cec3799799f504b4a83a80aa8378cfdb5 |
from nanopore.mappers.abstractMapper import AbstractMapper
from sonLib.bioio import system
import os
class Bwa(AbstractMapper):
def run(self, args=""):
localReferenceFastaFile = os.path.join(self.getLocalTempDir(), "ref.fa") #Because BWA builds these crufty index files, copy to a temporary directory
... | mitenjain/nanopore | nanopore/mappers/bwa.py | Python | mit | 974 | [
"BWA"
] | e27e12bd5ea5d8dc1d80e0b9307de38bc30fb688a9657f2cc64f474cd10806f2 |
# -*- coding: utf-8 -*-
import logging
import os
import re
import socket
import sys
import traceback
import webbrowser
import functools
from typing import Set
import django
from django.conf import settings
from django.core.management.base import BaseCommand, CommandError, SystemCheckError
from django.core.management.c... | django-extensions/django-extensions | django_extensions/management/commands/runserver_plus.py | Python | mit | 22,111 | [
"VisIt"
] | ac2072b8443a2729b629a92622aca5397848dbbd762b2fc03538a171451a6346 |
import sys
import os.path
sys.path.append(os.path.join( % CMAKE_BINARY_DIR%, "lib"))
execfile(os.path.join( % PROJECT_SOURCE_DIR%, "plugins", "pymol", "plugin.py"))
| salilab/rmf | plugins/pymol/loader-template.py | Python | apache-2.0 | 167 | [
"PyMOL"
] | 5841e2ab3dbe4b3c965deb05855e40ddc709ac942f69a4fd25b7ce56226aad04 |
from behave import *
use_step_matcher("parse")
@when('I list teams filtered by "{search}"')
def step_impl(context, search):
url = context.get_url('/teams/list_teams/?search_box=' + search)
context.browser.visit(url)
@when('I list teams')
def step_impl(context):
context.browser.visit(context.get_url('/te... | Marcelpv96/SITWprac2017 | sportsBetting/features/steps/list_teams.py | Python | gpl-3.0 | 715 | [
"VisIt"
] | 9af9aadbd5ac18a9ddcaa43f6344f4a86bc5dbc51300426ddaf39e32d54268cf |
#!/usr/bin/env python
import argparse
import binascii
import copy
import datetime
import hashlib
import json
import logging
import os
import shutil
import struct
import subprocess
import tempfile
import xml.etree.ElementTree as ET
from collections import defaultdict
from Bio.Data import CodonTable
logging.basicConfig(... | loraine-gueguen/tools-iuc | tools/jbrowse/jbrowse.py | Python | mit | 53,695 | [
"BLAST",
"Galaxy"
] | 1c11720d08963acdc2c5122deb379f0da9cbc9f5afca816ba1b861806d59ca6d |
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2015 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier (bgoli@users.sourceforge.net)
Triple-J Group for Molecular Cell Physiology
Stellenbosch University, South Africa.
Permiss... | asttra/pysces | pysces/PyscesWeb.py | Python | bsd-3-clause | 14,488 | [
"PySCeS"
] | 177c1755d8504b85ab3e5eaee2f733ea985bc6a7ee7b522dd3b2cace0dbccdf6 |
import logging
from cStringIO import StringIO
from math import exp
from lxml import etree
from path import path # NOTE (THK): Only used for detecting presence of syllabus
import requests
from datetime import datetime
import dateutil.parser
from lazy import lazy
from xmodule.seq_module import SequenceDescriptor, Seque... | UQ-UQx/edx-platform_lti | common/lib/xmodule/xmodule/course_module.py | Python | agpl-3.0 | 50,646 | [
"VisIt"
] | 341e36cf82d1531450d5ee78939f14bd2f6c91d9722dffcc8c57c89ee64f17ed |
from __future__ import print_function, division, absolute_import
import numpy as np
import re
import types
import warnings
import functools
import collections
from mdtraj.utils.six import PY3
from mdtraj.utils.six.moves import copyreg, xrange
if PY3:
from itertools import filterfalse as ifilterfalse
else:
from... | msmbuilder/msmbuilder-legacy | MSMBuilder/utils.py | Python | gpl-2.0 | 10,220 | [
"MDTraj"
] | d98f91dc35fc203672bc1159acd056d7ff5b71059960ea94f6a64451ca0867c5 |
#
#
# File to test current configuration of CA1Pyramidal cell project.
#
# To execute this type of file, type '..\..\..\nC.bat -python XXX.py' (Windows)
# or '../../../nC.sh -python XXX.py' (Linux/Mac). Note: you may have to update the
# NC_HOME and NC_MAX_MEMORY variables in nC.bat/nC.sh
#
# Author:... | pgleeson/TestArea | models/LarkumEtAl2009/pythonScripts/RunTestsDescret2.py | Python | gpl-2.0 | 2,561 | [
"NEURON"
] | 0fe571fc5d12bc51e29fca381f67bbd5b5b2d51cfb7c3ef0e839b13d32634bc3 |
#!/usr/bin/env python
# coding=utf-8
"""Examples of using the cmd2 table creation API"""
import functools
import sys
from typing import (
Any,
List,
)
from cmd2 import (
EightBitBg,
EightBitFg,
Fg,
ansi,
)
from cmd2.table_creator import (
AlternatingTable,
BorderedTable,
Column,
... | python-cmd2/cmd2 | examples/table_creation.py | Python | mit | 11,090 | [
"Brian"
] | d586693f4f114dc1e3501233752d59dec8b2b1a71fb0adc559dd9fcfdf6f2d46 |
# Copyright (C) 2010-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | mkuron/espresso | samples/h5md.py | Python | gpl-3.0 | 2,031 | [
"ESPResSo"
] | ae9815108ae98f6a0084a146b566427dfb5f2ef85e347161f0c23a76c8983e7f |
# Orca
#
# Copyright 2010 Consorcio Fernando de los Rios.
# Author: Javier Hernandez Antunez <jhernandez@emergya.es>
# Author: Alejandro Leiva <aleiva@emergya.es>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the ... | ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/orca_gui_profile.py | Python | gpl-3.0 | 4,155 | [
"ORCA"
] | e3a8a26eb76eb861e087d8d46f5b7d2b71aee1a7b1823078ddf70d62a8d51cda |
#
# pymatgen documentation build configuration file, created by
# sphinx-quickstart on Tue Nov 15 00:13:52 2011.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All configuration values h... | materialsproject/custodian | docs_rst/conf.py | Python | mit | 9,561 | [
"pymatgen"
] | 9a45184ad450435d761d41e26b198461a4c847d86a8a9e1e21d5dbb98ca4eee9 |
""" This is the guy that parses and interprets the local configuration options.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import re
import os
import sys
import six
import getopt
import DIRAC
from DIRAC import gLogger
from DIRAC... | yujikato/DIRAC | src/DIRAC/ConfigurationSystem/Client/LocalConfiguration.py | Python | gpl-3.0 | 28,163 | [
"DIRAC"
] | 6d3bc5d4247b2423c8faafe64ce1640a7f8d6430b955c0805a5a48ce2cf37abb |
"""
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of ... | Yukarumya/Yukarum-Redfoxes | testing/mozbase/mozlog/mozlog/formatters/html/xmlgen.py | Python | mpl-2.0 | 9,161 | [
"VisIt"
] | 5a022c9d969378bd6d54d4785ab50286b13abf1f9f6c1fe5e8ffdfc7d97e780b |
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