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#!/usr/bin/env python
# -*- coding: utf-8 -*-
# pyresample, Resampling of remote sensing image data in python
#
# Copyright (C) 2010-2020 Pyresample developers
#
# 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
... | davidh-ssec/pyresample | pyresample/test/test_geometry.py | Python | lgpl-3.0 | 129,892 | [
"NetCDF"
] | 63d19910c02b331c6d532239b93a5419fcddd02b8bc366db67332ae1a384f21b |
"""Utilities to lazily create and visit candidates found.
Creating and visiting a candidate is a *very* costly operation. It involves
fetching, extracting, potentially building modules from source, and verifying
distribution metadata. It is therefore crucial for performance to keep
everything here lazy all the way dow... | google/material-design-icons | update/venv/lib/python3.9/site-packages/pip/_internal/resolution/resolvelib/found_candidates.py | Python | apache-2.0 | 5,410 | [
"VisIt"
] | 173c4a73385e9771a156238811f18751f510eab3775346e530c52ebbe6e51df5 |
#!/usr/bin/env python
from scipy.stats import norm
from scanpy._utils import check_nonnegative_integers
from itertools import product
import anndata
import numpy as np
import pandas as pd
"""
HashSolo script provides a probabilistic cell hashing demultiplexing method
which generates a noise distribution and signal dis... | theislab/scanpy | scanpy/external/pp/_hashsolo.py | Python | bsd-3-clause | 15,047 | [
"Gaussian"
] | 43626ece34f6c5c1c791fc61392c1ad870aac54b714f4c4c788c9c74445a9f90 |
"""
The :mod:`sklearn.lda` module implements Linear Discriminant Analysis (LDA).
"""
# Authors: Matthieu Perrot
# Mathieu Blondel
import warnings
import numpy as np
from scipy import linalg
from .base import BaseEstimator, ClassifierMixin, TransformerMixin
from .utils.extmath import logsumexp
from .utils.fi... | mrshu/scikit-learn | sklearn/lda.py | Python | bsd-3-clause | 9,304 | [
"Gaussian"
] | 03c7be72fa13f78d18d8954764a91ec7e9ba95f0fecb407460b63e0e43df2003 |
import mykde
class Action(mykde.BaseAction):
name = 'LibreOffice'
description = "LibreOffice with custom settings"
packages = ['libreoffice', 'libreoffice-style-galaxy']
def proceed(self):
# NOTE: the XML config is updated not really nice, because registrymodifications.xcu
# contains... | warvariuc/mykde | packages/vic_kubuntu_14_10/libreoffice/__init__.py | Python | bsd-3-clause | 538 | [
"Galaxy"
] | 019b1148495444ef6525a3e0e8afb7027291f6fcc1fa1827e94d5e0320a41fca |
import vtk
reader = vtk.vtkRectilinearGridReader()
reader.SetFileName("D:/Notebooks_Bogota2017/SS_2017/data/jet4_0.500.vtk")
reader.Update()
output = reader.GetOutput()
xmi, xma, ymi, yma, zmi, zma = output.GetBounds()
# Color Transfer Function and LookUpTable
# Create transfer mapping scalar value to color
#
#
#
#
... | dianafprieto/SS_2017 | scripts/07_NB_Challenge_1.py | Python | mit | 2,714 | [
"VTK"
] | 9f2b79dc86146adf138f20ec01304c97863f98bef3940d706bfb9bae1117f915 |
# encoding: 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 'IndicatorData.generate_percent'
db.delete_column('profiles_indicatordata', 'generate_per... | 216software/Profiles | communityprofiles/profiles/oldmigrations/0013_auto__del_field_indicatordata_generate_percent__add_field_indicator_ge.py | Python | mit | 10,446 | [
"MOE"
] | f50152b1f4f318186a553eaa940c74c371c539aa5cb0df6b9ef05616ef1b6d6d |
import os
os.environ["SERVER_URI"] = "http://orca.beta-1.linewize.net:5001"
from orcaweb import app
app.run(port=8080, debug=True)
| theorcaproject/orca-web | runorcaweb.py | Python | gpl-3.0 | 132 | [
"ORCA"
] | 8cbe78d60a88c28065b0825500b981b4b5e00c3ad1bdf04a42b41ecd958e2918 |
#Created by martin.king@uni.no, 21 Nov 2013.
#This script does range of data values checks
#I will write in the realistic ranges in a csv file.
#Now, the example given below checks tas to be 100<tas<400.
#Needs ncdump, grep, and cdo.
import glob, os
#os.system('module load netcdf')
#os.system('module load cdo')
time... | martin-king/mycfqc | my_qc_step2.py | Python | gpl-3.0 | 1,520 | [
"NetCDF"
] | 97decc262e615c107f0ef92b9c8ca447834f2936f2ce54a685ca434de0e6987f |
# -*- coding: utf-8 -*-
"""Tests for PyNPA."""
import unittest
import pandas as pd
from pybel import BELGraph
from pybel.dsl import ComplexAbundance, Gene, Protein, Rna
from pybel.io.pynpa import to_npa_dfs, to_npa_layers
from pybel.struct.getters import get_tf_pairs
from pybel.testing.utils import n
g1 = Gene("hg... | pybel/pybel | tests/test_io/test_pynpa.py | Python | mit | 3,188 | [
"Pybel"
] | de999e94bfb77c0f037dd59e868beb79f858b01e767f9537612288878f4d9939 |
# -*- coding: utf-8 -*-
"""
Unitary Event (UE) analysis is a statistical method to analyze in a time
resolved manner excess spike correlation between simultaneously recorded
neurons by comparing the empirical spike coincidences (precision of a few ms)
to the expected number based on the firing rates of the neurons
(see... | apdavison/elephant | elephant/unitary_event_analysis.py | Python | bsd-3-clause | 28,494 | [
"NEURON"
] | 0c24cbbc3da94fce3b0a75a5f94c1d5ed4e20aa70f26f5be790e878aca283491 |
import numpy as np
from scipy._lib._util import check_random_state
def rvs_ratio_uniforms(pdf, umax, vmin, vmax, size=1, c=0, random_state=None):
"""
Generate random samples from a probability density function using the
ratio-of-uniforms method.
Parameters
----------
pdf : callable
A ... | WarrenWeckesser/scipy | scipy/stats/_rvs_sampling.py | Python | bsd-3-clause | 7,177 | [
"Gaussian"
] | 24ea8ce12ee3f9541adb6b1c53424c1baa295204a0c14a235f2d468531a17a34 |
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2006-2013, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version 2.1 or l... | jchodera/cclib | src/cclib/bridge/cclib2pyquante.py | Python | lgpl-2.1 | 1,373 | [
"cclib"
] | 8a584426018cd5176882c69f3dd5d58fb7311e7ae0211536ad2e887d513bb4a9 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | kain88-de/mdanalysis | testsuite/MDAnalysisTests/plugins/knownfailure.py | Python | gpl-2.0 | 3,258 | [
"MDAnalysis"
] | b0fff57cf63cd922153c47977dafd44033ee406d7600ea88ca581ec1da084af4 |
from pyscf import lib
import sys
assert len(sys.argv)==2,"""
Usage: chkfile_gaps.py chkfile.
"""
dat=lib.chkfile.load(sys.argv[1],'scf')
nspin=2
print('nspin:',nspin)
if nspin==1:
egy=dat['mo_energy']
occ=dat['mo_occ']
print('Occupations Energies')
last=0.0
count=1
for info in zip(occ,egy):
o,e=in... | bbusemeyer/busempyer | drivers/chkfile_gaps.py | Python | gpl-2.0 | 770 | [
"PySCF"
] | fd883c538d174953eb6bb49c468fda4f8bf686461c6948007d46c4f36d958887 |
"""Retrieve run information describing files to process in a pipeline.
This handles two methods of getting processing information: from a Galaxy
next gen LIMS system or an on-file YAML configuration.
"""
import collections
from contextlib import closing
import copy
import glob
import itertools
import os
import string
... | brainstorm/bcbio-nextgen | bcbio/pipeline/run_info.py | Python | mit | 40,596 | [
"Galaxy"
] | b7ee6932fa62b0d2be4c95163f9a4362579f395f80c79e73a71414157b390e62 |
#!/usr/bin/env python
########################################################################
# File : dirac-admin-allow-site
# Author : Stuart Paterson
########################################################################
"""
Add Site to Active mask for current Setup
Example:
$ dirac-admin-allow-site LCG.IN... | ic-hep/DIRAC | src/DIRAC/Interfaces/scripts/dirac_admin_allow_site.py | Python | gpl-3.0 | 3,305 | [
"DIRAC"
] | 703bda2258720d4f48e370c3b151042aed04e58f4be9cf816f57da269abb9141 |
import numpy
def write_shadow_surface(s,xx,yy,outFile='presurface.dat'):
"""
write_shadowSurface: writes a mesh in the SHADOW/presurface format
SYNTAX:
out = write_shadowSurface(z,x,y,outFile=outFile)
INPUTS:
z - 2D array of heights
x - 1D array of spatial coord... | srio/ShadowOui-Tutorial | SCRIPTS/script21.py | Python | mit | 2,451 | [
"Gaussian"
] | 829750faff94134e198b276cbedf57a813c36815f0223e7b0ff7a953b825d4e6 |
# -*- coding: utf-8 -*-
"""Script used to run an example job against a running Pulsar server.
Exercises various features both the Pulsar client and server.
"""
import optparse
import os
import re
import shutil
import sys
import tempfile
import threading
import time
import traceback
from collections import namedtuple
... | ssorgatem/pulsar | pulsar/client/test/check.py | Python | apache-2.0 | 18,355 | [
"BWA",
"Galaxy"
] | 4311171a61e1b7887ddd683909e876736e7c75bd73d6a38c450450c2558c7e1a |
"""
Generator for Kernel
A word about args: it is organised as two correlated tuples, because the
order of the elements of dicts in Python is arbitrary, meaning that the item
added first might be the last when iterating over the dict.
"""
import numpy
import shogun.Kernel as kernel
from shogun.Features import Combine... | curiousguy13/shogun | tests/integration/generator/kernel.py | Python | gpl-3.0 | 16,052 | [
"Gaussian"
] | 1adf34adf76f3f39c400887129a0a686addcfef87a17347e15e68271aa7756ac |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# resadmin - Resource administration front end
# Copyright (C) 2003-2009 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 the GNU General Public... | heromod/migrid | mig/cgi-bin/resadmin.py | Python | gpl-2.0 | 1,082 | [
"Brian"
] | 430f3b100ba4daa579e23e69596306afbb88d9d821fec24f7162acdd2f063fc1 |
import numpy as np
from msmbuilder.example_datasets import MinimalFsPeptide
from msmbuilder.featurizer import BinaryContactFeaturizer
from msmbuilder.featurizer import ContactFeaturizer
from msmbuilder.featurizer import LogisticContactFeaturizer
import mdtraj as md
import itertools
from numpy.testing.decorators import... | Eigenstate/msmbuilder | msmbuilder/tests/test_contactfeaturizers.py | Python | lgpl-2.1 | 4,286 | [
"MDTraj"
] | d550017924f01103630fc2d5ba7d6fabdee600a29a962077adf02c4900e1675c |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# ---------------------------------------------------------------------
# Copyright (c) 2012 Michael Hull.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are m... | mikehulluk/morphforge | src/morphforgecontrib/simulation/synapse_templates/exponential_form/exp2syn/postsynaptic_mechanisms_exp2syn_modfile_new.py | Python | bsd-2-clause | 3,259 | [
"NEURON"
] | a9078f88fbc73263abe152a3097b87644ee0b047b8ce969c5d952993bebaded6 |
"""The suite of window functions."""
from __future__ import division, print_function, absolute_import
import warnings
import numpy as np
from scipy import special, linalg
from scipy.fftpack import fft
from scipy._lib.six import string_types
__all__ = ['boxcar', 'triang', 'parzen', 'bohman', 'blackman', 'nuttall',
... | witcxc/scipy | scipy/signal/windows.py | Python | bsd-3-clause | 48,621 | [
"Gaussian"
] | 8799c531d57e30f5e1f01c7eebe9c9010fa3dc4af2c18181cd2dbbd03e3331db |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2020, 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.
"""Bridge for using cclib data in PyQuante (http://pyquante.sourceforge.net)."""
import numpy
from cclib.parser... | langner/cclib | cclib/bridge/cclib2pyquante.py | Python | bsd-3-clause | 1,531 | [
"cclib"
] | e84be388f66067251095fedc73440968f7fda5621f978829579f3c0821adcba8 |
# -*- coding: utf-8 -*-
# Copyright 2007-2022 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at y... | jat255/hyperspy | hyperspy/_components/split_voigt.py | Python | gpl-3.0 | 7,868 | [
"Gaussian"
] | 9ba609cfc2c1046b77e666d77c6920c20c0b74d00fafcce56514444520c6f2a3 |
import itertools
import numpy as np
from scipy import ndimage
from dipy.align import floating
from dipy.align.metrics import SSDMetric, CCMetric, EMMetric
from numpy.testing import (assert_array_equal,
assert_array_almost_equal,
assert_raises)
def test_exceptions(... | FrancoisRheaultUS/dipy | dipy/align/tests/test_metrics.py | Python | bsd-3-clause | 10,298 | [
"Gaussian"
] | 27400c351a2a9fe1ecfacd05b04d2775246d81b2468c2568d64845ebde18db3d |
#!/usr/bin/env python
# Copyright 2014-2019 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/fci/direct_spin0_symm.py | Python | apache-2.0 | 13,337 | [
"PySCF"
] | e83c68e41f061212c51f9723e759f6c6a6bb4edf1d58fc7fd50a24cf162a4e5f |
from DIRAC.Core.Utilities.Decorators import executeOnlyIf
class AnyClass(object):
def __init__(self):
self.attr = None
@executeOnlyIf("attr", False)
def withoutSpecificValue(self):
"""Decorator with no specific value"""
return True
@executeOnlyIf("undefined", False)
def w... | DIRACGrid/DIRAC | src/DIRAC/Core/Utilities/test/Test_Decorator.py | Python | gpl-3.0 | 3,143 | [
"DIRAC"
] | f2e2c476493f0e0abefb14d01e2d97887b1453f403b974af7a4ad611bfdd60de |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Licensed to Cloudera, Inc. under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. Cloudera, Inc. licenses this file
# to you under the Apache License, Version 2.0 (... | erickt/hue | apps/useradmin/src/useradmin/tests.py | Python | apache-2.0 | 34,911 | [
"MOE"
] | 3929610e9be4656760ca9706f5339bcb88c2e442d7f3cc6e5fbb7b020f499502 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import print_function
import argparse
import numpy as np
from fractions import Fraction
from phonopy.structure.atoms import atom_data, symbol_map
from vasp.poscar import Poscar
from primitive_axis import PrimitiveAxis
from .band_path import BandPath
phonop... | yuzie007/ph_analysis | ph_analysis/phonopy_conf_creator.py | Python | mit | 11,773 | [
"VASP",
"phonopy"
] | ffc56247de9eea2f14629bd2bf3d89d0394510d70c8d9c4678cb558cefa28398 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module contains the main object used to identify the coordination environments in a given structure.
If you use this module, please cite the following:
David Waroquiers, Xavier Gonze, Gian-Marco Rigna... | richardtran415/pymatgen | pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.py | Python | mit | 95,165 | [
"pymatgen"
] | e4d3bbbaf71185d3f8ece261a3f979cef03a13d8aaadb30133fa0d640ea27c70 |
# -*- coding: utf-8 -*-
"""
Init and user authentication in Earth Engine
"""
import os
import hashlib
import urllib.request
import webbrowser
from qgis.PyQt.QtWidgets import QInputDialog
import logging
# fix the warnings/errors messages from 'file_cache is unavailable when using oauth2client'
# https://github.com/goo... | gena/qgis-earthengine-plugin | ee_auth.py | Python | mit | 2,295 | [
"VisIt"
] | 8f4e5dcaba700fdeec3d774aa8b500b9dbf288ba83b7815f3df05611f7101f78 |
#!/usr/bin/python
from wixlib import *
version = extract_version_information('/home/andres/Projects/CS')
version_stringed = version.replace('.', '_')
version_full = version + '.3'
upgrade_code = '933473B2-62E5-11DC-99EE-0015582877AD'
outdir = '/mnt/vm_1/work'
def gen_b2cs_blender_plugin_msm():
(base, merge, dir)... | baoboa/Crystal-Space | scripts/packaging/msi/genwix_b2cs.py | Python | lgpl-2.1 | 5,477 | [
"CRYSTAL"
] | 1ee1e17cdfcea0a68532bd0f5da6aa6d94f491999e53dd4596d2481f685ce838 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2010 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; either version 2 of the License, or
# (at your optio... | SNoiraud/gramps | gramps/cli/user.py | Python | gpl-2.0 | 7,977 | [
"Brian"
] | d33ef62fce1db18b7fc92d3c0702e517533532fd1cf351b4dee6a324dd83bac7 |
'''Unit test for roman1.py
This program is part of 'Dive Into Python 3', a free Python book for
experienced programmers. Visit http://diveintopython3.org/ for the
latest version.
'''
import roman5
import unittest
class KnownValues(unittest.TestCase):
known_values = ( (1, 'I'),
(2, 'II'),
... | ctasims/Dive-Into-Python-3 | examples/romantest5.py | Python | mit | 5,253 | [
"VisIt"
] | 295ae0bdc70b3269ca061f27aa67d7ceeeea8c5d6413ab4c31bae6a0e8cb4ce7 |
#!/usr/bin/env python
# Copyright 2015 The Kubernetes Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appli... | rrati/kubernetes | cluster/juju/layers/kubernetes-master/reactive/kubernetes_master.py | Python | apache-2.0 | 45,652 | [
"CDK"
] | c4caa18aab0cabbe31cf52da2fa5db13193bc25413403bb149618e02e8119e06 |
#
# Toolbox ia898
#
__version__ = 'ia898 Python Toolbox for Teaching Image Processing version 0.1 12Mar2017'
from ia898.src.affine import affine
from ia898.src.applylut import applylut
from ia898.src.bwlp import bwlp
from ia898.src.colormap import colormap
from ia898.src.conv import conv
from ia898.src.comb import c... | robertoalotufo/ia898 | src/__init__.py | Python | mit | 1,830 | [
"Gaussian"
] | 6df1f828a775d1b00642b92833ee43ca739e611dcb34bcb9214b4cbded1c7aaf |
# 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... | Xeralux/tensorflow | tensorflow/contrib/py2tf/pyct/ast_util.py | Python | apache-2.0 | 3,065 | [
"VisIt"
] | a6a36a524aab5e711795adbaea9887df39d01be58e411560994ae1c501ce0223 |
blacklist = {
"password",
"123456",
"12345678",
"qwerty",
"dragon",
"baseball",
"football",
"letmein",
"monkey",
"696969",
"abc123",
"mustang",
"michael",
"shadow",
"master",
"jennifer",
"111111",
"jordan",
"superman",
"harley",
"123456... | jaredlunde/cargo-orm | cargo/etc/passwords.py | Python | mit | 7,311 | [
"CRYSTAL",
"Jaguar"
] | 6bd74304b97865dcfd466393cecc620bec858ac85b8d75934b82be094a4f1686 |
"""
===============================================
:mod:`ec` -- Evolutionary computation framework
===============================================
This module provides the framework for creating evolutionary computations.
.. Copyright 2012 Inspired Intelligence Initiative
..... | saulshanabrook/pushgp.py | thirdparty/inspyred-1.0/inspyred/ec/ec.py | Python | bsd-3-clause | 36,219 | [
"Gaussian"
] | 4afd323cfae8a6820039c0e086286f486d3d886854e006ee5c77dd0e8b46169f |
#!/usr/bin/env python
#
# ingestPlot.py
#
# TODO: Update the description below
#
# This is a simple plotter for the data coming out of tMSSink, the ingest MS writer simulation app
# that Max wrote to test the write IO issues we are having with scratch2.
#
# It reads in a file created by the tMSSink program, extracts th... | ATNF/askap-benchmarks | current/mpiperf/gatherPlot.py | Python | gpl-2.0 | 4,023 | [
"Galaxy"
] | bcc07f22316c193001c1ba7407133cad4a2245cec90b87630bb904925d25897c |
#!/usr/bin/env python -i
# preceding line should have path for Python on your machine
# split.py
# Purpose: similar to simple.py, but first the world communicator
# is split in two halves and LAMMPS is run only on one partition
# Syntax: split.py in.lammps
# in.lammps = LAMMPS input script
from __future__... | Pakketeretet2/lammps | python/examples/split.py | Python | gpl-2.0 | 1,831 | [
"LAMMPS"
] | 17b960f0142a1cb2195be94d2bf26f9fa15785e3acc8f5ca868e9ca14659538d |
""" Test class for JobWrapper
"""
# pylint: disable=protected-access, invalid-name
# imports
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
import os
import shutil
import pytest
from mock import MagicMock
from DIRAC import gLogger
from DIRAC.DataManagem... | yujikato/DIRAC | src/DIRAC/WorkloadManagementSystem/JobWrapper/test/Test_JobWrapper.py | Python | gpl-3.0 | 4,310 | [
"DIRAC"
] | db9bf9e552f1acad144177f530c38e2baea8042cc137cebf018c8de01bf0a627 |
"""
Series of functions that deal with collapsing bowtie BAM alignment to a
transcriptome where a read can align to many transcripts. Bowtie should be
run as follows:
bowtie -a --best --strata -S -X 400 -p 8 transcriptome.ref -1 1.fastq -2
2.fastq > out.sam
There is a script in scripts that runs the whole pip... | jeffhsu3/genda | genda/parsing/transcriptAlign.py | Python | bsd-3-clause | 402 | [
"Bowtie"
] | d22cca2f742cd2210508a0823d7b05422f486f3ffe3e7426614217f1073a3185 |
#!/usr/bin/env python
# ======================================================================
# == Python script replacing "forbidden" access to standard output ==
# == or standard error in ABINIT source files by statements using ==
# == "std_out" or "std_err" global variables. ==
# == ... | SamKChang/abinit-7.10.5_multipole | developers/maintainers/replace_write6.py | Python | gpl-3.0 | 6,875 | [
"ABINIT"
] | 76706970686c180c795d5009d9b4271d3d611d5e7033935318161bdd3ee1140a |
import struct
import socket
import numpy as np
import yaml
from pysisyphus.calculators import XTB
from pysisyphus.helpers import geom_loader
from pysisyphus.socket_helper import send_closure, recv_closure, get_fmts
def ipi_client(addr, atoms, forces_getter, hessian_getter=None, hdrlen=12):
atom_num = len(atoms... | eljost/pysisyphus | examples/opt/10_h2o_xtb_ipi_server/client.py | Python | gpl-3.0 | 4,764 | [
"xTB"
] | e219b7b50a9080c95931781c4c679ade747a781c7a66dc11eb1fd930a4155501 |
"""Gabor filters banks extraction from standalone modality."""
from __future__ import division
import numpy as np
from scipy.signal import fftconvolve
from .standalone_extraction import StandaloneExtraction
def _sigma_prefactor(bandwidth):
b = bandwidth
# See http://www.cs.rug.nl/~imaging/simplecell.html
... | glemaitre/protoclass | protoclass/extraction/gabor_bank_extraction.py | Python | gpl-2.0 | 9,756 | [
"Gaussian"
] | ff7bc89139aa81dd1cc4173e7aeb06395c458f60f0163cd5a477ba4514ba7b6f |
#!/usr/bin/env python
# Copyright 2013 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""The frontend for the Mojo bindings system."""
import argparse
import imp
import os
import pprint
import sys
# Disable lint check ... | chromium2014/src | mojo/public/tools/bindings/mojom_bindings_generator.py | Python | bsd-3-clause | 7,082 | [
"VisIt"
] | 2b0eb48efc243c58234aa122a903b4bc79d7e50ae38263a5384413d30132b7b3 |
from __future__ import absolute_import
from django.db import models
from django.conf import settings
from django.contrib.auth.models import AbstractBaseUser, UserManager, \
PermissionsMixin
from django.dispatch import receiver
from zerver.lib.cache import cache_with_key, flush_user_profile, flush_realm, \
user... | ashwinirudrappa/zulip | zerver/models.py | Python | apache-2.0 | 49,969 | [
"VisIt"
] | 7531eb82a6fb63afe5cb024728e1e2fd2cbaf5c027938f883478e9083015ca4f |
from chemlab.core import Atom, Molecule, crystal
from chemlab.graphics.qt import display_system
# Molecule templates
na = Molecule([Atom('Na', [0.0, 0.0, 0.0])])
cl = Molecule([Atom('Cl', [0.0, 0.0, 0.0])])
s = crystal([[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]], # Fractional Positions
[na, cl], # Molecules
... | chemlab/chemlab | examples/nacl.py | Python | gpl-3.0 | 517 | [
"CRYSTAL"
] | cd4d01af92252f4fca8a66254cb3fc97f61120f7d362a3cb17a45a60f941c2ca |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements an interface to Thomas Manz's
Chargemol code (https://sourceforge.net/projects/ddec/files) for
calculating DDEC3, DDEC6, and CM5 population analyses.
This module depends on a compiled chargemol execu... | materialsproject/pymatgen | pymatgen/command_line/chargemol_caller.py | Python | mit | 24,507 | [
"VASP",
"pymatgen"
] | 06e97095b1b6542f5a21376b7a6ee0450e8cb5992537583cbdd26f78596d4082 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright: (c) 2016, Brian Coca <bcoca@ansible.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version': '1... | caphrim007/ansible | lib/ansible/modules/system/systemd.py | Python | gpl-3.0 | 19,401 | [
"Brian"
] | b152ac5b358cd79e59bcb136bdd06dc7b939e58f4d13f693d68b334a79a1c2e7 |
# ----------------------------------------------------------------------------
# Copyright (c) 2015--, micronota development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# ---------------------------------------------... | mortonjt/micronota | micronota/bfillings/tests/test_diamond.py | Python | bsd-3-clause | 7,169 | [
"BLAST"
] | abbcde517c40637bc1c80531b2ba5fc1d2b516c217ee49d5b6219467dfdd89ee |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals, absolute_import
import os
import unittest
import mock
import nikola
import nikola.plugins.command.import_wordpress
from .base import BaseTestCase
class BasicCommandImportWordpress(BaseTestCase):
def setUp(self):
self.module = nikola.plugi... | andredias/nikola | tests/test_command_import_wordpress.py | Python | mit | 22,852 | [
"VisIt"
] | ea7fefb99ddf33be545226f9ed32c91c0164d9c1a596a9d9065de552a5c5e417 |
# flake8: noqa
import logging
import time
import hashlib
from collections import Counter
from deepchem.utils.rdkit_utils import MoleculeLoadException, load_molecule
import numpy as np
from scipy.spatial.distance import cdist
from copy import deepcopy
from deepchem.feat import ComplexFeaturizer
logger = logging.getLo... | lilleswing/deepchem | deepchem/feat/complex_featurizers/rdkit_grid_featurizer.py | Python | mit | 49,561 | [
"RDKit"
] | f75234aced18c406cf00db7c0503d424b2577f391363044cff618de040a691a9 |
from __future__ import annotations
import logging
import os
from xia2.Decorators.DecoratorFactory import DecoratorFactory
from xia2.Driver.DriverFactory import DriverFactory
from xia2.Handlers.Phil import PhilIndex
from xia2.Wrappers.CCP4.AimlessHelpers import parse_aimless_xml
logger = logging.getLogger("xia2.Wrapp... | xia2/xia2 | src/xia2/Wrappers/CCP4/Aimless.py | Python | bsd-3-clause | 27,283 | [
"CRYSTAL"
] | 935053360edbba0613bb886df7a3c8ba219ad78f08d9d3adb96214efe49fd020 |
# -*- coding: utf-8 -*-
prefixes = [
u"Sir ",
u"Mr ",
u"Ms ",
u"The Rt Hon "
]
sufixes = [
u" MP",
u"Mr ",
u"Ms ",
u"The Rt Hon "
]
lords_titles = [
u"Lady",
u"Lord",
u"Earl",
u"Baroness",
u"Viscount",
u"Bishop",
u"Countess",
u"Archbishop",
u"Duke",... | spudmind/undertheinfluence | utils/config.py | Python | mit | 40,082 | [
"Brian",
"Desmond"
] | 1c346fb3bd54a3bfce2d0aeff2fa13bc316238d2c9360eb2747aff99c2a845d8 |
from edc_dashboard.subject import RegisteredSubjectDashboard
from bcvp.bcvp_lab.models import SubjectRequisition
from bcvp.bcvp_subject.models import SubjectVisit, SubjectConsent, SubjectLocator
from bcvp.bcvp_subject.models.subject_eligibility import SubjectEligibility
class SubjectDashboard(RegisteredSubjectDashbo... | botswana-harvard/bcvp | bcvp/bcvp_dashboard/classes/subject_dashboard.py | Python | gpl-2.0 | 2,829 | [
"VisIt"
] | 477d78ab20c422bc22eced440be4a435dc26d2959f7be99a997ed647f081e1ab |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under t... | MDAnalysis/mdanalysis | package/MDAnalysis/auxiliary/__init__.py | Python | gpl-2.0 | 19,866 | [
"Gromacs",
"MDAnalysis"
] | e4b9225bce59bac4c4969be8b8a3008d8a3170b93b43a28cb7dea63eb2deb7e7 |
# ==================================================================================================
# Copyright 2011 Twitter, Inc.
# --------------------------------------------------------------------------------------------------
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use thi... | foursquare/commons-old | src/python/twitter/common/util/__init__.py | Python | apache-2.0 | 3,533 | [
"Brian"
] | fdcc35e7d913822b505db492a69879ab5c8c77380072aeb00fc2c3d04e612bf1 |
"""
:mod:`operalib.ridge` implements Operator-valued Naive Online
Regularised Risk Minimization Algorithm (ONORMA)
"""
# Author: Romain Brault <romain.brault@telecom-paristech.fr> with help from
# the scikit-learn community.
# License: MIT
from numpy import eye, empty, ravel, vstack, zeros
from sklearn.base i... | operalib/operalib | operalib/onorma.py | Python | bsd-3-clause | 12,243 | [
"Gaussian"
] | aec1b1c41894b5d2d4846504513d69f88f6342ce022f3da810d81a128f0674c1 |
if inflow == 'log':
kappa = 0.4 # Kappa: von karman constant
us = WS * kappa / np.log(WF.WT[0].H / z0) # friction velocity
#eq inflow ws
WS_inf = gaussN(WF.WT[0].R, Ua, [WF.WT[0].H,us,z0]).sum()
elif inflow == 'pow':
#eq inflow ws
WS_inf = gaussN(WF.WT[0].R, Ua_shear, [WF.WT[0].H,WS,alpha]).su... | rethore/FUSED-Wake | fusedwake/wind_farm_flow.py | Python | agpl-3.0 | 14,014 | [
"Gaussian"
] | eaff0a72feaf9cd72e822a269fef48673e903125ec5262e595a825952311fbd6 |
"""Tests for reporting.views."""
# pylint: disable=invalid-name
import csv
import io
from django.conf import settings
from django.contrib.auth import get_user_model
from django.core.urlresolvers import reverse
from django.test import Client, TestCase
from django.test.utils import override_settings
from model_mommy imp... | ofa/connect | open_connect/reporting/tests/test_views.py | Python | mit | 8,005 | [
"VisIt"
] | 1702e7ee883d69b86f6ec4b3f231c788740a6c75ea3482edb0d0aa4de209cd16 |
"""IO methods for probabilistic predictions."""
import pickle
import os.path
import numpy
import netCDF4
from gewittergefahr.gg_utils import time_conversion
from gewittergefahr.gg_utils import target_val_utils
from gewittergefahr.gg_utils import file_system_utils
from gewittergefahr.gg_utils import error_checking
FIL... | thunderhoser/GewitterGefahr | gewittergefahr/deep_learning/prediction_io.py | Python | mit | 18,173 | [
"NetCDF"
] | c8e52827235fa74d344b4e606f8a0bc0cbbfbf72ea92ec4b9ee8a2794739f9a0 |
#
# Copyright (C) 2004-2008 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
from __future__ import print... | rvianello/rdkit | rdkit/Chem/Pharm3D/UnitTestExcludedVolume.py | Python | bsd-3-clause | 1,193 | [
"RDKit"
] | 3820a2b8fc16808224672e017ea6c138bac012ddee4656b561ef482798f38375 |
#!/usr/bin/env python
#Dan Blankenberg
import sys
from galaxy import eggs
import pkg_resources; pkg_resources.require( "bx-python" )
import bx.align.maf
from galaxy.tools.util import maf_utilities
assert sys.version_info[:2] >= ( 2, 4 )
def __main__():
output_name = sys.argv.pop(1)
input_name = ... | dbcls/dbcls-galaxy | lib/galaxy/datatypes/converters/maf_to_fasta_converter.py | Python | mit | 941 | [
"Galaxy"
] | 6a043b001b17af3e0257735c9b3d9e6822afd16b9b013473ff3739a6ff4459bc |
import sys
from ._utils import fill_nans
from ..schemata import tune, xcorr, stack
from io import BytesIO
from . import images
import numpy as np
from ..schemata import experiment, shared, reso, meso, stack, pupil, treadmill, tune
from flask import render_template, redirect, url_for, flash, request, session, send_from... | fabiansinz/pipecontrol | app/images/views.py | Python | mit | 44,469 | [
"NEURON"
] | 965b66985d0c021b077fa0e56d415ddb08a7d87974c573460173c932e9e69602 |
#S4 app3 - Modelisation et simulation mecanique pour realite virtuelle
#Developpeur - Brian Compagnat - comb2301
# - Adriatik Sermaxhaj - sera1901
#
#Date creation: 2016-07-01
#Derniere modification: 2016-07-02
# Description: Script ajoutant les objets neccessaires et effectuant l'animation d'un train
# à ... | nicolasb565/projects4 | Blender/code/codePython.py | Python | mit | 2,571 | [
"Brian"
] | a4503a154b03d2532c1a2518f41070f91d89e13588bf40e73929739c9ad5f4ab |
from __future__ import division
import re
import pysam
from clipper.src.peaks import readsToWiggle_pysam
import sys
import os
from subprocess import Popen, call, PIPE
from optparse import OptionParser, SUPPRESS_HELP
from numpy import *
from multiprocessing import Pool
#from deap import dtm
import cPickle as pickle
impo... | YeoLab/gscripts | gscripts/rnaseq/oldsplice.py | Python | mit | 25,889 | [
"pysam"
] | b217f2eac089e2497d91df1ced3bf453945aad5341735e46c915697f6d6e0821 |
#############################################################################################
# #
# This class is part of the MLB-Galaxy package, adding some sequence analysis #
# functionality to PSU's Galaxy fra... | vipints/oqtans | oqtans_tools/EasySVM/0.3.3/scripts/poim.py | Python | bsd-3-clause | 5,489 | [
"Galaxy"
] | 557b34edc02ffd18882a9ab1335d715ed21abc0c4cfe78ac6a3a8565e7a190e8 |
# -*- coding: utf-8 -*-
from setuptools import setup
VERSION = '0.1.3'
setup(
name='django-compoundqueryset',
packages=[
'djcompoundqueryset',
],
version=VERSION,
description='Allows for creation of compound querysets in Django.',
url='https://github.com/brianwawok/django-compoundquer... | brianwawok/django-compoundqueryset | setup.py | Python | mit | 1,249 | [
"Brian"
] | ff54051afffb1edbaecafe42e14227b1a7d261f086d39eb69b59974c21f7dc6c |
import pytest
from elliptic.Kernel.Context import Context, ContextException
from elliptic.Kernel.Expression import EllipticNode, Expression
class TestEllipticNode:
def test_unique_id(self):
first_node = EllipticNode()
second_node = EllipticNode()
assert first_node.unique_id != second_no... | padmec-reservoir/ELLIPTIc | tests/unit/test_expression.py | Python | mit | 2,676 | [
"VisIt"
] | 06ae3a2630bb53512e81f3d85883f4370ce259d08c77e60aec9cc5fefbef6d93 |
"""Nexus file reading, writing and inspection."""
# -*- coding: utf-8 -*-
# Copyright 2007-2021 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Fou... | erh3cq/hyperspy | hyperspy/io_plugins/nexus.py | Python | gpl-3.0 | 47,807 | [
"VisIt"
] | d4812803478dca36752836159f5e4e2394fd958e7a692853041eecc7b4aa975e |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Defines SymmetryGroup parent class and PointGroup and SpaceGroup classes.
Shyue Ping Ong thanks Marc De Graef for his generous sharing of his
SpaceGroup data as published in his textbook "Structure of Mater... | mbkumar/pymatgen | pymatgen/symmetry/groups.py | Python | mit | 18,974 | [
"CRYSTAL",
"pymatgen"
] | 8b0f70ca5c8061b3f4def9dc9d056773d7bad5069305dd603bcac3cbb7fd88a2 |
#!/usr/bin/env python
"""
"""
import vtk
def main():
colors = vtk.vtkNamedColors()
fileName = get_program_parameters()
# This example shows how to use decimation to reduce a polygonal mesh. We also
# use mesh smoothing and generate surface normals to give a pleasing result.
#
hawaii = vtk... | lorensen/VTKExamples | src/Python/VisualizationAlgorithms/DecimateHawaii.py | Python | apache-2.0 | 3,105 | [
"VTK"
] | 98e000b44e857f47c5809ec611731beea35668bb214eed7ecf71e7bdf1f1e9fa |
# visit.py
# Updated 2013-06-20 to fix bug on line 38
import inspect
__all__ = ['on', 'when']
def on(param_name):
def f(fn):
dispatcher = Dispatcher(param_name, fn)
return dispatcher
return f
def when(param_type):
# f - actual decorator
# fn - decorated method, i.e. visit
# f... | PrzemekBurczyk/dalvik-compiler | src/visit.py | Python | mit | 1,596 | [
"VisIt"
] | c9d9a865a6fa24c2761faabc244a7f50d67db820e92ace71fac8d78543894a28 |
#coding:utf8
'''
Created on 2011-10-3
@author: lan (www.9miao.com)
'''
import sys,os
if os.name!='nt':#对系统的类型的判断，如果不是NT系统的话使用epoll
from twisted.internet import epollreactor
epollreactor.install()
from twisted.internet import reactor
from twisted.python import log
from firefly.utils import services
fr... | yangdw/PyRepo | src/annotation/Firefly/firefly/test/test_netconnect_server.py | Python | mit | 1,223 | [
"Firefly"
] | d95190ac5208d9818856e067a7f45bb529ff7479a554a9db35c0041ac0231493 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2017-2019 Satpy developers
#
# This file is part of satpy.
#
# satpy 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 Licens... | pytroll/satpy | satpy/readers/seviri_l1b_nc.py | Python | gpl-3.0 | 14,933 | [
"NetCDF"
] | f13ab445e3bff6020e1d41c4741454eac10b4e7b4fa0295de4588d0f75f36daf |
#!/usr/bin/env python
#
# Author: Elvira R. Sayfutyarova <elviras@princeton.edu>
# Qiming Sun <osirpt.sun@gmail.com>
#
'''
Section IV.A of AVAS paper arXiv:1701.07862 [physics.chem-ph]
'''
from functools import reduce
import numpy
from pyscf import gto
from pyscf import scf
from pyscf import mcscf
from pyscf... | sunqm/pyscf | examples/mcscf/43-avas.py | Python | apache-2.0 | 2,392 | [
"PySCF"
] | 4fe58e775c0998e1aefa9a974a4ac16a798a05ffd11e9a5330961ce85b7803d6 |
"""
Testing for the forest module (sklearn.ensemble.forest).
"""
# Authors: Gilles Louppe,
# Brian Holt,
# Andreas Mueller,
# Arnaud Joly
# License: BSD 3 clause
import pickle
from collections import defaultdict
from itertools import combinations
from itertools import product
import numpy ... | valexandersaulys/airbnb_kaggle_contest | venv/lib/python3.4/site-packages/sklearn/ensemble/tests/test_forest.py | Python | gpl-2.0 | 39,405 | [
"Brian"
] | 5025d7965026f0e41b3783e2f67c9d0d32e10b77690f0cf279654133c19a8b66 |
#!/usr/bin/env python
"""
To ensure conda packages are built in the most compatible manner, we can use
a docker container. This module supports using a docker container to build
conda packages in the local channel which can later be uploaded to anaconda.
Note that we cannot simply bind the host's conda-bld directory... | bioconda/bioconda-utils | bioconda_utils/docker_utils.py | Python | mit | 18,673 | [
"Bioconda"
] | 9467d6c52a42e96a55b29f92a60275dcd1308dccae47a86b2a94b8e6df8b8804 |
"""
Module to set up run time parameters for Clawpack.
The values set in the function setrun are then written out to data files
that will be read in by the Fortran code.
"""
import os
import numpy as np
#------------------------------
def setrun(claw_pkg='amrclaw'):
#------------------------------
""... | clawpack/adjoint | examples/acoustics_2d_radial_mixed/adjoint/setrun.py | Python | bsd-2-clause | 11,219 | [
"NetCDF"
] | cbab5a689c179bacfa3e2c62b812fc7e7c7df99807e51b9c6364a68310b23064 |
'''Raster plots for E-I parameter sweeps.
.. currentmodule:: noisefigs.EI_plotting.rasters
Functions
---------
.. autosummary::
EIRaster
plotEIRaster
plotAvgFiringRate
plot_avg_firing_rate_spikes
'''
import logging
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.ticker as ti
i... | MattNolanLab/ei-attractor | noisefigs/noisefigs/EI_plotting/rasters.py | Python | gpl-3.0 | 6,694 | [
"NEURON"
] | b696397d2d3301793cb61eaeaeee208da2fdb84316e97641d8755b87df48cb6a |
import collections
import heapq
import traceback
import weakref
import numpy
import six
import chainer
from chainer import _backprop_utils
from chainer.backends import cuda
from chainer import configuration
from chainer import function_hook
from chainer.utils import experimental
from chainer.utils import type_check
f... | aonotas/chainer | chainer/function_node.py | Python | mit | 38,023 | [
"VisIt"
] | a1a5d0442fed656e89af5288d636215a9fb59caf7845af9823d753b669ce0577 |
# Principal Component Analysis Code :
from numpy import mean,cov,double,cumsum,dot,linalg,array,rank,size,flipud
from pylab import *
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import ro... | tapomayukh/projects_in_python | classification/Classification_with_kNN/Single_Contact_Classification/Feature_Comparison/multiple_features/best_kNN_PCA/test11_cross_validate_objects_1200ms_scaled_method_v_force_motion.py | Python | mit | 4,963 | [
"Mayavi"
] | 853d2c9c1111f6d4e9a1e19d5a509a7a16aa270beb489f34f1099722af7cd8ba |
# Copyright (c) 2011, Apple Inc. All rights reserved.
# Copyright (c) 2009, 2011, 2012 Google Inc. All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must ret... | youfoh/webkit-efl | Tools/Scripts/webkitpy/common/config/committers.py | Python | lgpl-2.1 | 42,297 | [
"Brian"
] | b2c184fa7e2469aaf6f74c3f2dcdbefc70155ba9d9869f90732b22b846e959ca |
from .._shared.utils import skimage_deprecation
from warnings import warn
global _import_warned
warn(skimage_deprecation('The `skimage.filter` module has been renamed '
'to `skimage.filters`. This placeholder module '
'will be removed in v0.13.'))
_import_warned = Tr... | jwiggins/scikit-image | skimage/filter/__init__.py | Python | bsd-3-clause | 2,746 | [
"Gaussian"
] | cf15d89d87ff3db1de7982f1d299463408a85543fd3b4aa664745acebac06c14 |
"""
Enums defined in the Pico Technology SDK v10.6.10.24
"""
from enum import IntEnum
class PicoScopeInfoApi(IntEnum):
"""
Constants that can be passed to the :meth:`~.picoscope.PicoScope.get_unit_info` method.
"""
DRIVER_VERSION = 0x00000000
USB_VERSION = 0x00000001
H... | MSLNZ/msl-equipment | msl/equipment/resources/picotech/picoscope/enums.py | Python | mit | 41,097 | [
"Gaussian"
] | 214c00b9b94215e325d3cff9a642f7e65e9a74a1934af126a612843259a54639 |
'''
modified by Chongxuan Li (chongxuanli1991@gmail.com)
'''
import numpy as np
import sys, os
import theano
import theano.tensor as T
import collections as C
import anglepy as ap
import anglepy.ndict as ndict
import color
from anglepy.misc import lazytheanofunc
import math, inspect
#import theano.sandbox.cuda.rng_c... | zhenxuan00/mmdgm | mlp-mmdgm/anglepy/models/GPUVAE_Z_X.py | Python | mit | 18,867 | [
"Gaussian"
] | 2ea463e1d53f5128cbe3ccece4db005dc72bf53de0175f3fb77e3135a88a1743 |
# -*- coding: utf-8 -*-
#! /usr/bin/env python
""" crypto.cipher.icedoll_test
Tests for icedoll encryption algorithm
Copyright © (c) 2002 by Paul A. Lambert
Read LICENSE.txt for license information.
"""
from crypto.cipher.icedoll import Icedoll
from crypto.cipher.base import noPadding
from binascii ... | TheDSCPL/SSRE_2017-2018_group8 | Projeto/Python/cryptopy/crypto/cipher/icedoll_test.py | Python | mit | 3,918 | [
"Brian"
] | 8d73e262731669e70a2d0ccdc0abf2e341999420cee1250328dfd9572728789d |
#!/usr/bin/env python
# -*- coding:utf-8 -*-
#
# Author: Leann Mak
# Email: leannmak@139.com
# Date: Aug 8, 2016
#
# This is autotest for service module of eater package.
import sys, json
sys.path.append('.')
from nose.tools import *
import os
from sqlite3 import dbapi2 as sqlite3
from promise impo... | tecstack/opback | tests/testEater/testServices.py | Python | apache-2.0 | 16,901 | [
"Elk"
] | 730c8817e8af772d1cba056404e98e314286d003260bdc8eec139da444f57ac5 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | andysim/psi4 | psi4/driver/qmmm.py | Python | gpl-2.0 | 5,571 | [
"Psi4"
] | 26a53d3d8d0c0215f4cc99012b1ef0dadff9e2251ac5273e96cbe4aaf54628ae |
#!/usr/bin/env python2
"""Extension to python-markdown to support LaTeX (rather than html) output.
Authored by Rufus Pollock: <http://www.rufuspollock.org/>
Reworked by Julian Wulfheide (ju.wulfheide@gmail.com) and
Indico Project (indico-team@cern.ch)
Usage:
======
1. Command Line. A script entitled markdown2latex.p... | DavidAndreev/indico | indico/util/mdx_latex.py | Python | gpl-3.0 | 24,957 | [
"Bowtie"
] | 145351123a3fbc5432f99e7503acadfe74e88a462569c9f7eebbc7bba5853d64 |
"""[explorerhat]
API library for Explorer HAT and Explorer HAT Pro, Raspberry Pi add-on boards"""
import atexit
import signal
import time
from sys import exit, version_info
import logging
logger = logging.getLogger(__name__)
try:
from smbus import SMBus
except ImportError:
if version_info[0] < 3:
log... | WayneKeenan/picraftzero | picraftzero/thirdparty/pimoroni/explorerhat/__init__.py | Python | mit | 22,696 | [
"Amber"
] | 5cb509c91f1238d2e638d71735e912f32f289182a99f874d34d4168516627e8f |
""" Please add a file description here"""
from equadratures.distributions.template import Distribution
from equadratures.distributions.recurrence_utils import jacobi_recurrence_coefficients
import numpy as np
from scipy.stats import uniform
RECURRENCE_PDF_SAMPLES = 8000
class Uniform(Distribution):
"""
The cla... | Effective-Quadratures/Effective-Quadratures | equadratures/distributions/uniform.py | Python | lgpl-2.1 | 4,489 | [
"Gaussian"
] | 3b44c982c39e912934e840f0ea4e78b5d978cf7d875c8863a1e8bc91d5f455fb |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: TJ Lane
# Contributors: Robert McGibbon
#
# MDTraj is free sof... | kyleabeauchamp/mdtraj | mdtraj/tests/test_prmtop.py | Python | lgpl-2.1 | 1,596 | [
"MDTraj"
] | 0d92d6a7804805ebefd8cf6335e6295e3c1ee1516c97c28e9e32c96c002bfa3f |
""" codecs -- Python Codec Registry, API and helpers.
Written by Marc-Andre Lemburg (mal@lemburg.com).
(c) Copyright CNRI, All Rights Reserved. NO WARRANTY.
"""#"
import builtins, sys
### Registry and builtin stateless codec functions
try:
from _codecs import *
except ImportError as why:
raise SystemErro... | amrdraz/brython | www/src/Lib/codecs.py | Python | bsd-3-clause | 35,436 | [
"FEFF"
] | 493a59d6ea25348283d35ab6a530dcbc19edf7910e49aa98dddea73100957c4d |
from pywps.Process import WPSProcess
from flyingpigeon.subset import countries # REGION_EUROPE
from flyingpigeon.log import init_process_logger
import logging
logger = logging.getLogger(__name__)
class SegetalfloraProcess(WPSProcess):
"""This process calculates the relative humidity"""
def __init__(self):
... | KatiRG/flyingpigeon | flyingpigeon/processes/wps_segetalflora.py | Python | apache-2.0 | 6,390 | [
"NetCDF"
] | 88f872d2a78f3eb620b2eac99494e6ee8ce6f10b686f77d1cab2104d0d8823c4 |
import logging
from pywps import ComplexInput, ComplexOutput
from pywps import Format
from pywps import LiteralInput
from pywps import Process
from pywps.app.Common import Metadata
from flyingpigeon import plt_ncdata
from flyingpigeon.utils import extract_archive
from flyingpigeon.nc_utils import get_variable
# from ... | bird-house/flyingpigeon | flyingpigeon/processes/wps_plot_spaghetti.py | Python | apache-2.0 | 6,709 | [
"NetCDF"
] | 6ca76588a415fca2432c679f773ec95400e8d5e1386236d11e1c2ba191761dac |
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