text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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# Copyright 2017 reinforce.io. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | lefnire/tensorforce | tensorforce/models/distribution_model.py | Python | apache-2.0 | 11,323 | [
"Gaussian"
] | e318a351f4cdc5fefc69eeb1ff438e7db1d1185c6f0d158d013b0d8ca44a6c9a |
#! /usr/bin/python
#
# Copyright (C) 2003-2021 ABINIT group
#
# Written by Matthieu Verstraete in python (compatible v1.9).
# This is free software, and you are welcome to redistribute it
# under certain conditions (GNU General Public License,
# see ~abinit/COPYING or http://www.gnu.org/copyleft/gpl.txt... | abinit/abinit | scripts/post_processing/get_irreps.py | Python | gpl-3.0 | 15,657 | [
"ABINIT"
] | b911d9dc245b2706b6ffc2ff258fcf2abb18a31feb42482d1b2e5b699b5ab5a7 |
#
# Copyright (C) 2013-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | espressomd/espresso | testsuite/python/langevin_thermostat_stats.py | Python | gpl-3.0 | 9,593 | [
"ESPResSo"
] | e45352effbd6a25ec158627dc081f952f7a4e7de8fdc588c891d07aee092f7b3 |
"""TransformationCleaningAgent cleans up finalised transformations.
.. literalinclude:: ../ConfigTemplate.cfg
:start-after: ##BEGIN TransformationCleaningAgent
:end-before: ##END
:dedent: 2
:caption: TransformationCleaningAgent options
"""
__RCSID__ = "$Id$"
# # imports
import re
import ast
import os
import... | petricm/DIRAC | TransformationSystem/Agent/TransformationCleaningAgent.py | Python | gpl-3.0 | 25,687 | [
"DIRAC"
] | b700928a2c5a321d7c7455c15b500299c9cebd80a27038ff26fcc01194cdb8b3 |
"""
An example on how to read existing CP2K input files directly into the CP2K
object.
"""
from pycp2k import CP2K
# The CP2K object is normally initialized
calc = CP2K()
# This function tries to read the input file in the given path and places its
# contents to the input tree. Notice that this will overwrite any alr... | SINGROUP/pycp2k | examples/example_parse_input.py | Python | lgpl-3.0 | 538 | [
"CP2K"
] | 77988eec3ea50190d324154f102ffaf62de47f101c58d853f2774e5dc462b522 |
# RunCrystal for Mira
import subprocess as sub
from submission_tools import LocalSubmitter
import os
class LocalMiraSubmitter(LocalSubmitter):
"""Abstract submission class. Defines interaction with the queuing system."""
def __init__(self,time='72:00:00',nn=1,np='allprocs',mode=16,queue='batch'):
""" Initializ... | willwheelera/mainline | utils/autogen/Specific/mira.py | Python | gpl-2.0 | 3,799 | [
"CRYSTAL"
] | 22ff4f0ee93d593be507f3e465e81fbe2a17c09db2abfbce2d65f00ab2f19712 |
# -*- coding: utf-8 -*-
'''
Created on 20 Oct 2015
@author: Kimon Tsitsikas
Copyright © 2015-2016 Kimon Tsitsikas and Éric Piel, Delmic
This file is part of Odemis.
Odemis is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License version 2 as published by the Free ... | delmic/odemis | src/odemis/util/peak.py | Python | gpl-2.0 | 20,769 | [
"Gaussian"
] | 4dc65a5bc2937380a767749a4b6b19462999b6697a578d4ed5f32dc2789dcc0f |
#!/usr/bin/python
"""
Script for joining suntans netcdf processor-based output into one file
Object oriented version created December 2013
@author: mrayson
"""
from sunpy import Grid
from netCDF4 import Dataset
import getopt, sys, time
import numpy as np
from multiprocessing import Pool
import pdb
# Globals
gridva... | UT-CWE/Hyospy | Hyospy_ensemble/lib/SUNTANS/SUNTANS/joinsun.py | Python | mit | 15,626 | [
"NetCDF"
] | 24ebc0c3b5437a9c5f17a28be6ea7dd26a06c07180ddd7d681a2c802126462ef |
#!/usr/bin/env python
# CREATED:2013-03-11 18:14:30 by Brian McFee <brm2132@columbia.edu>
# unit tests for librosa.beat
from __future__ import print_function
from nose.tools import nottest, raises, eq_
# Disable cache
import os
try:
os.environ.pop('LIBROSA_CACHE_DIR')
except:
pass
import numpy as np
import ... | r9y9/librosa | tests/test_beat.py | Python | isc | 6,912 | [
"Brian"
] | 576fca10f9a55ca715f0a95a22a4f99ecd02c50812c828d6fafbd2fb4730299d |
from waxy import *
from mywaxy import *
import math
from utils import *
def FileInfo(fname):
var=[]
try:
var=hdf5_load_images(fname)
except IOError:
infostr="File %s not found" % fname
if var:
mn=min([im.min() for im in var['im']])*var['im_scale_shift'][0]+var['im... | bblais/plasticity | plasticity/dialogs/input_params.py | Python | mit | 19,769 | [
"Gaussian"
] | 17d9a5fe63f70a2aa3ec1054bd770a0a3eb890876106380d772842291b3e2641 |
"""
Copyright (C) 2013-2018 Calliope contributors listed in AUTHORS.
Licensed under the Apache 2.0 License (see LICENSE file).
cli.py
~~~~~~
Command-line interface.
"""
import contextlib
import datetime
import itertools
import logging
import os
import pstats
import shutil
import sys
import traceback
import click
... | brynpickering/calliope | calliope/cli.py | Python | apache-2.0 | 10,871 | [
"NetCDF"
] | 012dd6527cb80d9f795c76ad0fa398714b69ca097cc7c50af4eb6406dc78c582 |
from __future__ import print_function
from __future__ import division
from builtins import str
from builtins import range
from past.utils import old_div
import numpy as np
from boututils.file_import import file_import
import sys
if sys.version_info[0]>=3:
message = "polplotslice uses the VTK library through mayavi... | erikgrinaker/BOUT-dev | tools/pylib/boututils/plotpolslice.py | Python | gpl-3.0 | 3,758 | [
"Mayavi",
"VTK"
] | 60e860634f77f59020ead54dc1bf003daeaeecf962e3205061cfa563d4118049 |
import numpy as np
DELTA_FACTOR = 0.01 # Max delta factor for soft mutations
SIGMA_FACTOR = 0.01 # Sigma as factor of max dimensions for gaussian mutations
class Gene(object):
"""Define class to hold gene"""
def __init__(self, size_x, size_y, n_vertices):
"""Initialize gene with all values at zero... | jbmorgado/daliea | daliea/gene.py | Python | gpl-3.0 | 6,871 | [
"Gaussian"
] | f9a9acb07d7bb007d263ededbf1916bbd0851a30afc1306466f8e1be33f4ff39 |
# symcompartment.py ---
#
# Filename: symcompartment.py
# Description:
# Author:Subhasis Ray
# Maintainer:
# Created: Thu Jun 20 17:47:10 2013 (+0530)
# Version:
# Last-Updated: Fri Jul 12 12:10:52 2013 (+0530)
# By: subha
# Update #: 71
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#
# Ch... | BhallaLab/moose-examples | snippets/symcompartment.py | Python | gpl-2.0 | 3,308 | [
"MOOSE"
] | d3830d277ae8b2c4af78669b5e7d3fbd1b8f32559d1318994ce6e0f5af96fdf3 |
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | gkc1000/pyscf | pyscf/nao/__init__.py | Python | apache-2.0 | 1,411 | [
"PySCF"
] | 4ef2a28b1c86415262d43f9e08c11032291ecca56fd818b09d3a2b7575688129 |
import pytest
from tests.utils import Command
from thefuck.rules.gulp_not_task import match, get_new_command
def stdout(task):
return '''[00:41:11] Using gulpfile gulpfile.js
[00:41:11] Task '{}' is not in your gulpfile
[00:41:11] Please check the documentation for proper gulpfile formatting
'''.format(task)
de... | mbbill/thefuck | tests/rules/test_gulp_not_task.py | Python | mit | 852 | [
"GULP"
] | 7c488ad0ba7d3435951258219d8c3630e9ffb20ce1c15c58cd696c8acf436bea |
#!/usr/bin/env python
#
# This program is free software you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation either version 3 of the License, or
# (at your option) any later version.
#
# Written (C) 2012-2013 Heiko Strathmann
#
from ... | curiousguy13/shogun | examples/undocumented/python_modular/statistics_linear_time_mmd.py | Python | gpl-3.0 | 4,125 | [
"Gaussian"
] | 38762a2344af4e48cf6c3e12ae9d9b8195564578cdce7a2cee7001abe94c3c97 |
"""Functionality to query and extract information from aligned BAM files.
"""
import collections
import contextlib
import os
import itertools
import signal
import subprocess
import numpy
import pysam
import toolz as tz
from bcbio import utils
from bcbio.bam import ref
from bcbio.distributed import objectstore
from bc... | mjafin/bcbio-nextgen | bcbio/bam/__init__.py | Python | mit | 19,587 | [
"pysam"
] | 7099f36c917d6d9798957715e9106c953498d47931ca84350ffb7acd9a1d135b |
#!/usr/bin/env python3
#
# Copyright (C) 2016-2018 Zubax Robotics <info@zubax.com>
#
# This program is free software: you can redistribute it and/or modify it under the terms of the
# GNU General Public License as published by the Free Software Foundation, either version 3 of the License,
# or (at your option) any late... | PX4/sapog | tools/drwatson/drwatson_sapog.py | Python | bsd-3-clause | 18,772 | [
"CRYSTAL"
] | d37fc3ee5a6aef8862aae32320a19529ca67835c2e38b7c95c575df089ae2fca |
# tifffile/setup.py
"""Tifffile package setuptools script."""
import sys
import re
from setuptools import setup
buildnumber = ''
with open('tifffile/tifffile.py') as fh:
code = fh.read()
version = re.search(r"__version__ = '(.*?)'", code).groups()[0]
version += ('.' + buildnumber) if buildnumber else ''
desc... | cgohlke/tifffile | setup.py | Python | bsd-3-clause | 3,344 | [
"Napari"
] | f05becf130e5a152aea0fb6c801520edc75ab9833e9f8908e5c30a00f996ed91 |
from __future__ import with_statement
import os
import re
import sys
import time
import signal
import socket
import sqlite3
import hashlib
import logging
import datetime
try:
import json
except ImportError:
import simplejson as json
import yaml
import tornado.web
import tornado.ioloop
import tornado.httpcli... | Yelp/firefly | firefly/data_server.py | Python | isc | 9,130 | [
"Firefly"
] | 06542fd699aa2fd0a1442804c889063a58c07c76b173409151b8f5b9d3cabb20 |
'''
This file contains the HMM definition
'''
try:
import psyco
psyco.full()
except:
pass
import numpy as NUM
import State
import sys
from Def import DEF
ARRAYFLOAT=NUM.float64
ARRAYINT=NUM.int
def _sample_gaussian(mean, covar, n_samples=1):
'''
Generate random samples from a Gaussian distributi... | arthurfait/HMM-3 | hmm/HMM.py | Python | gpl-3.0 | 19,865 | [
"Gaussian"
] | 7cc8feb0015bac21871f889de6d2577616fe3487bda5fce9d6596d235daddf72 |
#!/usr/bin/env python
# coding: utf-8
from datetime import datetime
from HTMLParser import HTMLParser
import argparse
import json
import os
import sys
import urllib2
###############################################################################
# Options
#############################################################... | dhstack/gae-init | magic.py | Python | mit | 6,352 | [
"VisIt"
] | 6693c5a481f0cdd780911c53c420f588d5a7f6e055a94bfa06430eb65d290444 |
"""
I/O for VTU.
<https://vtk.org/Wiki/VTK_XML_Formats>
<https://vtk.org/wp-content/uploads/2015/04/file-formats.pdf>
"""
import base64
import re
import sys
import zlib
import numpy as np
from ..__about__ import __version__
from .._common import info, join_strings, raw_from_cell_data, replace_space, warn
from .._exce... | nschloe/meshio | src/meshio/vtu/_vtu.py | Python | mit | 33,923 | [
"ParaView",
"VTK"
] | 45a7a108adfc4425cbb760c97460c650cdafca59cd42444ea1e60b6b64f8b095 |
"""Visualization helpers."""
from contextlib import contextmanager
import copy
import os.path as op
import numpy as np
from scipy import linalg
from mne import read_proj, read_events, pick_types
from mne.utils import verbose
from mne.viz.utils import tight_layout, plt_show
from ._sss import compute_good_coils
from ... | ktavabi/mnefun | mnefun/_viz.py | Python | bsd-3-clause | 18,227 | [
"Mayavi"
] | 79b310d4a15589edb6bc179768c167d29d5e8f7f2f4aa77d8ee22f561a682ee8 |
#!/usr/bin/env python
# coding: utf-8
default={}
default['lang_default']=u'English'
default['lang_local']=u''
default['menu_dashboard']=u'MY DASHBOARD'
default['menu_dashboard_url']="http://dashboard.hackerdojo.com"
default['menu_events']=u'EVENTS'
default['menu_events_url']="http://events.hackerdojo.com/"
defa... | nasebanal/hd-website | translate/US.py | Python | agpl-3.0 | 2,262 | [
"VisIt"
] | b740fa7b374620490e08060e43c9bf56afdb70a4b6f569345156f9231ce481d7 |
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | pierrelapointe/scancode-toolkit | tests/extractcode/test_extract.py | Python | apache-2.0 | 43,208 | [
"VisIt"
] | 585ef44048a003491222f65d23057b65124df7c36a941716225065042d71fd9b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
E-I network connected with NEST topology
----------------------------------------
Simulation of a network consisting of an excitatory and an inhibitory
neuron population with distance-dependent connectivity.
The code bases on the script
brunel_alpha_nest.py
which... | HBPVIS/VIOLA | test_data/topo_brunel_alpha_nest.py | Python | gpl-2.0 | 44,592 | [
"Gaussian",
"NEURON"
] | c55ba94e4b7af557aec912cadce6b98ca4db0a3ba2c8aca2a8dcf342575392ed |
import pytest
from textwrap import dedent
from parso import load_grammar, ParserSyntaxError
from parso.python.tokenize import tokenize
@pytest.fixture
def grammar():
return load_grammar(version='3.8')
@pytest.mark.parametrize(
'code', [
# simple cases
'f"{1}"',
'f"""{1}"""',
... | snakeleon/YouCompleteMe-x64 | third_party/ycmd/third_party/jedi_deps/parso/test/test_fstring.py | Python | gpl-3.0 | 4,080 | [
"FLEUR"
] | 35664f4a5282564aaaccdbf0aca3fce41e766d097b51b98b4ff9fd1ad148f81c |
#
# FRETBursts - A single-molecule FRET burst analysis toolkit.
#
# Copyright (C) 2013-2016 The Regents of the University of California,
# Antonino Ingargiola <tritemio@gmail.com>
#
"""
This module contains all the main FRETBursts analysis functions.
`burstslib.py` defines the fundamental object `Data()`... | chungjjang80/FRETBursts | fretbursts/burstlib.py | Python | gpl-2.0 | 133,746 | [
"Gaussian"
] | 061edc405545dfb06f21bb3f6ace3f56bff3fcd9526ea75d039c3cfe052f04f9 |
"""Template for a pickaxe run.
This python script provides a skeleton to build Pickaxe runs around
The general format of a script will be:
1. Connect to mongoDB (if desired)
2. Load reaction rules and cofactors
3. Load starting compounds
4. Load Filtering Options
5. Transform Compounds
6. Write resul... | JamesJeffryes/MINE-Database | pickaxe_run_template.py | Python | mit | 17,130 | [
"RDKit"
] | f33d5e94c7c5a142bf44d3beb5dd03a64a849645c28928e881cf7491dc2adcfd |
"""
End-to-end tests for the LMS that utilize the course home page and course outline.
"""
from openedx.core.lib.tests import attr
from ...fixtures.course import CourseFixture, XBlockFixtureDesc
from ...pages.lms.course_home import CourseHomePage
from ...pages.lms.courseware import CoursewarePage
from ..helpers impor... | eduNEXT/edunext-platform | common/test/acceptance/tests/lms/test_lms_course_home.py | Python | agpl-3.0 | 2,937 | [
"VisIt"
] | 7d65b2de5fe2feece6a81ea3ce270d0e527c5afcae0dd38a05d30299f95f9353 |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | tgroh/incubator-beam | sdks/python/apache_beam/runners/dataflow/dataflow_runner_test.py | Python | apache-2.0 | 15,831 | [
"VisIt"
] | 21ca66326889cf848be0599f9017310411ecec15d6f49afd9aa8e965dca429d0 |
# -*- coding: utf-8 -*-
# Generated by Django 1.11 on 2017-06-12 16:42
from __future__ import unicode_literals
from django.conf import settings
from django.db import migrations, models
import django.db.models.deletion
class Migration(migrations.Migration):
initial = True
dependencies = [
migrations... | ashish-padakannaya/TradingPlatform | stockapi/migrations/0001_initial.py | Python | mit | 2,820 | [
"exciting"
] | eb775fa056c71e64c9f8bc79304b0a606ff91866a22e551b610631019e3a0a97 |
# -*- coding: utf-8 -*-
# GromacsWrapper
# Copyright (c) 2009 Oliver Beckstein <orbeckst@gmail.com>
# Released under the GNU Public License 3 (or higher, your choice)
# See the file COPYING for details.
from __future__ import division, absolute_import, print_function
import six
import os.path
import pytest
import g... | Becksteinlab/GromacsWrapper | tests/test_core.py | Python | gpl-3.0 | 2,821 | [
"Gromacs"
] | ee821f76261f34083d37df9c18d850ff6942843a7be831fbfb86aa2ea7d3a7b2 |
from __future__ import division, print_function, absolute_import
import os
from collections import OrderedDict
from itertools import combinations, chain
import sys
from six.moves import urllib
import numpy as np
import pandas as pd
from scipy.spatial.distance import cdist
from rdkit import RDLogger
from rdkit import... | mkukielka/oddt | oddt/toolkits/extras/rdkit/fixer.py | Python | bsd-3-clause | 43,688 | [
"RDKit"
] | d525c952389b6fbcfa0ba63f5968ca4692ce235c4abc0f2daa632ba0fa23a71e |
# Copyright 2015 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... | dongjoon-hyun/tensorflow | tensorflow/python/ops/image_ops_impl.py | Python | apache-2.0 | 108,169 | [
"Gaussian"
] | 21c06e96d2dfd665b212eb7f1cdfde44d051fcf3d6e497b861825412f45c6403 |
#!/usr/bin/env python3
import unittest
from unittest.mock import patch
import numpy as np
import pandas as pd
from tmc import points
from tmc.utils import load, get_out, patch_helper
module_name="src.last_week"
last_week = load(module_name, "last_week")
ph = patch_helper(module_name)
class LastWeek(u... | mohanprasath/Course-Work | data_analysis/uh_data_analysis_with_python/hy-data-analysis-with-python-spring-2020/part04-e15_last_week/test/test_last_week.py | Python | gpl-3.0 | 4,731 | [
"Brian"
] | b039139570b91c082e95a1889bfbd807c7b50f666627cca0f118eca0c49438c6 |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-admin-get-job-pilot-output
# Author : Stuart Paterson
########################################################################
"""
Retrieve the output of the pilot that executed a given job
""... | andresailer/DIRAC | Interfaces/scripts/dirac-admin-get-job-pilot-output.py | Python | gpl-3.0 | 1,386 | [
"DIRAC"
] | 8166e6818f5616f9b743fc35491ca3fe798a11be929b632a413431ffd631696b |
#! /usr/bin/env python
from pyDFTutils.vasp.vasp_utils import read_poscar_and_unsort
import ase.calculators.vasp.create_input
if 'maskcell' not in ase.calculators.vasp.create_input.int_keys:
ase.calculators.vasp.create_input.int_keys.append('maskcell')
from ase.calculators.vasp import Vasp, Vasp2
from ase.dft.kpoi... | mailhexu/pyDFTutils | pyDFTutils/vasp/myvasp.py | Python | lgpl-3.0 | 29,832 | [
"ASE",
"VASP",
"Wannier90"
] | a21e7db09d1f79d9af5468716dd48890e01301a58abba5ede4eaef76edebeb82 |
import argparse
import sys
import pysam
__author__ = 'Rob Edwards'
"""
Read a BAM file and calculate the coverage for each read
"""
if __name__ == '__main__':
parser = argparse.ArgumentParser(description='calculate the coverage of each read in a bam file')
parser.add_argument('-b', help='bam file to pa... | linsalrob/EdwardsLab | JohnMolkili/sequence_coverage.py | Python | mit | 1,471 | [
"pysam"
] | 99a38f746b517b0c901ec70a0995fc9ea6c1f311b6d1cec7329008f176514cce |
# coding: utf-8
# In[95]:
# import libraries
from __future__ import print_function
import csv
import re
from Bio import Entrez
from Bio import SeqIO
from Bio.PDB.Polypeptide import d1_to_index
import numpy as np
import pandas as pd
from rdkit.Chem import AllChem
# In[38]:
def download_info(patterm, database="G... | neilswainston/development-py | synbiochemdev/pablo_ml/seqs_crawling.py | Python | mit | 5,126 | [
"RDKit"
] | ca277e200e9a14844d15c978b6484508420fa34a6f433a945e628450e7f943aa |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RAnnotate(RPackage):
"""Annotation for microarrays.
Using R enviroments for annota... | iulian787/spack | var/spack/repos/builtin/packages/r-annotate/package.py | Python | lgpl-2.1 | 1,247 | [
"Bioconductor"
] | 02cc9700ca8796797169cbc2ae4075ee08536cb08d3e4f013257c12812cfe16f |
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | gkc1000/pyscf | pyscf/nao/m_siesta_ion_xml.py | Python | apache-2.0 | 8,187 | [
"PySCF",
"VisIt"
] | 2577a77c66123105fb9522196ddc2e13b3dccaa1255cbba71ebdfd19dc88ba9a |
### Imports below
import sys
import imp
import vtk
import gdcm
import os
import re
import vtkgdcm
import time
import thread
import threading
import Queue
import numpy
import numpy_support
import dicom
import matplotlib.cm as cm
import matplotlib.pyplot as plt
import matplotlib.image as mpimg
import multiprocessing
fr... | Nefarin/SODM | src/GUI/AppWindow.py | Python | gpl-2.0 | 17,919 | [
"VTK"
] | 7f233e396807bd2c60a7f5bcf22380021dc65033576806cce75cc95373425646 |
"""
==================================
Constants (:mod:`scipy.constants`)
==================================
.. currentmodule:: scipy.constants
Physical and mathematical constants and units.
Mathematical constants
======================
================ ============================================================... | DailyActie/Surrogate-Model | 01-codes/scipy-master/scipy/constants/__init__.py | Python | mit | 11,998 | [
"Avogadro"
] | 79bdc3b21fdb57069bad6e69a28008076f8aabf2ebb3efa4d67ac7e387dd63a3 |
'''
Count the number of proteins in common between the phages and the
bacteria based on blastx
'''
import sys
from phage import Phage
phage=Phage()
try:
f=sys.argv[1]
except:
sys.exit(sys.argv[0] + " <blast output file converted to NC/NC format. Probably phage.genomes.blastx")
count={}
lens=phage.phageSequ... | linsalrob/PhageHosts | code/blastx_all_v_all_coverage.py | Python | mit | 1,115 | [
"BLAST"
] | ae78423fe721fbceabf6c632cab627730b2a8c7a625698ed02b143a43534e779 |
# ----------------------------------------------------------------------------
# Copyright (c) 2016-2022, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ------------------------------------------------... | qiime2/q2-diversity | q2_diversity/_beta/_visualizer.py | Python | bsd-3-clause | 17,650 | [
"scikit-bio"
] | da059da609d9682b8338d16dc3de49709eea1eeda6acf876fab014f924d96f0e |
try:
from AG_fft_tools import correlate2d,fast_ffts
except ImportError:
from image_registration.fft_tools import correlate2d,fast_ffts
import warnings
import numpy as np
__all__ = ['cross_correlation_shifts','cross_correlation_shifts_FITS']
def cross_correlation_shifts(image1, image2, errim1=None, errim2=Non... | dattalab/d_code | imaging/alignment/image_registration/image_registration/cross_correlation_shifts.py | Python | mit | 10,678 | [
"Gaussian"
] | 1ef37d5ff4a6c8cbb77eb7f8f2df3b94b32a9ab5485260d416eadbbf1df97c56 |
#!/usr/bin/env python
"""
Created on Thu Dec 4 11:44:35 2014
Author: Oren Freifeld
Email: freifeld@csail.mit.edu
"""
import numpy as np
from pylab import plt
from cpab.cpa3d.needful_things import *
from cpab.cpaNd import TransformWrapper as TransformWrapperNd
from of.utils import *
from cpab.distributions.Multiscale... | freifeld/cpabDiffeo | cpab/cpa3d/TransformWrapper.py | Python | mit | 11,280 | [
"Gaussian"
] | 29848966d185b1e52d0e3e92bd070552a7e9942ef008cc369bfd38f11c606a53 |
# 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... | pkuyym/Paddle | python/paddle/fluid/layers/nn.py | Python | apache-2.0 | 147,515 | [
"NEURON"
] | b587b0797bf317d8a864dc55e229d5b34a87d6f7557962ea500880b5a8edb117 |
# (C) British Crown Copyright 2013 - 2017, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | zak-k/iris | lib/iris/fileformats/pp_rules.py | Python | gpl-3.0 | 40,992 | [
"NetCDF"
] | 345b0cd4e978803fab21604f67e0419b68b9863f527a48f5d301f2f07fd2c5e7 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
====================================================
Command line script (:mod:`sknano.scripts.nanogen`)
====================================================
CLI to :mod:`sknano.generators` tools.
.. currentmodule:: sknano.scripts.nanogen
This module allows for easy ... | androomerrill/scikit-nano | sknano/scripts/nanogen.py | Python | bsd-2-clause | 13,975 | [
"LAMMPS"
] | 9501cd77cf59739fb6e89e770228f9b097db3819f18fbef88c4edfe4697d061e |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements various equation of states.
Note: Most of the code were initially adapted from ASE and deltafactor by
@gmatteo but has since undergone major refactoring.
"""
import logging
import ... | gmatteo/pymatgen | pymatgen/analysis/eos.py | Python | mit | 19,699 | [
"ASE",
"pymatgen"
] | 1d032072f913a5bae810bbec0dde90371be46e600256945c2519c61cff66c1f5 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import pylid
from collections import Counter
sv = pylid.PyLID(3)
sv.total_ngrams = 264433400
sv.lang = 'sv'
sv.ngrams = Counter({
u'en#': 3176010,
u'#de': 2444732,
u'tt#': 2381964,
u'et#': 2353948,
u'f\xf6r': 2307213,
u'er#': 2272184,
u'att': 1... | dmort27/pylid | pylid/langs/sv.py | Python | mit | 311,552 | [
"ADF",
"ASE",
"BWA",
"CDK",
"EPW",
"Elk",
"MOE",
"VTK",
"xTB"
] | 60de066b79949f2363ceab379b2bf4965ce2009ea7e6f6d836fb7eaac09c8ded |
from ..libmp.backend import xrange
from .functions import defun, defun_wrapped
def _check_need_perturb(ctx, terms, prec, discard_known_zeros):
perturb = recompute = False
extraprec = 0
discard = []
for term_index, term in enumerate(terms):
w_s, c_s, alpha_s, beta_s, a_s, b_s, z = term
h... | GbalsaC/bitnamiP | venv/lib/python2.7/site-packages/sympy/mpmath/functions/hypergeometric.py | Python | agpl-3.0 | 51,556 | [
"Gaussian"
] | a9849c93076020d5871bdda9c85bcd9e87e0129992bfca497ae14d0953b4feff |
import abc
from mdtraj.utils.six import with_metaclass
class AbstractDimReduction(with_metaclass(abc.ABCMeta, object)):
"""
abstract class for defining dimensionality reduction
techniques.
Any subclass of this class can be used with the RedDimPNorm
distance metric
"""
@abc.abstractmetho... | msmbuilder/msmbuilder-legacy | MSMBuilder/reduce/baseclasses.py | Python | gpl-2.0 | 898 | [
"MDTraj"
] | 93177790282cb87b8f075158ef2dad9509243f820f33d668233f4b4801ee072d |
''' IMPORTS '''
import demistomock as demisto
from CommonServerPython import *
from CommonServerUserPython import *
import tweepy
import urllib
import requests
class Client:
def auth(self):
auth = tweepy.OAuthHandler(demisto.params().get('apikey'), demisto.params().get('apikey_secret'))
auth.set_a... | VirusTotal/content | Packs/Twitter/Integrations/Twitter/Twitter.py | Python | mit | 11,568 | [
"VisIt"
] | 91a3f1c0cf5ce4ca4b2ae46646712bf9346e304e10ffae51814f03100233c7b3 |
# First, and before importing any Enthought packages, set the ETS_TOOLKIT
# environment variable to qt4, to tell Traits that we will use Qt.
import os
os.environ['ETS_TOOLKIT'] = 'qt4'
# By default, the PySide binding will be used. If you want the PyQt bindings
# to be used, you need to set the QT_API environment varia... | MSHallOpenSoft/plotter | mayaviPlot.py | Python | gpl-2.0 | 17,765 | [
"Mayavi",
"VTK"
] | 8f9507d232d279e56cf57ddcab196edfcaf1ea647430b108224e6459d05c1d97 |
#!/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... | sunqm/pyscf | pyscf/dft/test/test_libxc.py | Python | apache-2.0 | 14,426 | [
"PySCF"
] | e46335374c6b6f9b182cfba0a9ff0155149e4c05e2727f45e02ed98360e3d22a |
# (C) British Crown Copyright 2010 - 2015, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | mo-g/iris | lib/iris/tests/test_grib_load.py | Python | gpl-3.0 | 28,851 | [
"Gaussian"
] | b4ae8b1b25a26279f84946d98c3c65c38126886e853c5ac412b7f54c6db9bbb8 |
#! /usr/bin/python2.7
# -*- coding: utf-8 -*-
import warnings
import re
import numpy as np
from itertools import izip, count # izip for maximum efficiency: http://stackoverflow.com/questions/176918/finding-the-index-of-an-item-given-a-list-containing-it-in-python
from errval import *
from errvallist import *
from std... | stefantkeller/errorvalues | functions.py | Python | mit | 11,324 | [
"Gaussian"
] | 35884d72a9dbdca61842d42603f4e80a48a0c3a6044facfb76b0d7d3e8fe5eef |
# Copyright (C) 2017,2018
# Max Planck Institute for Polymer Research
# Copyright (C) 2016
# Jakub Krajniak (jkrajniak at gmail.com)
# Copyright (C) 2012,2013,2014,2015
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & F... | espressopp/espressopp | src/interaction/Tabulated.py | Python | gpl-3.0 | 44,816 | [
"ESPResSo"
] | c3c4f40528d3e246c4b3d5abfe48f7c21c7ac6a993d6433ec5858d642cd60549 |
# -*- coding: utf-8 -*-
# Copyright (c) 2016-2017, Zhijiang Yao, Jie Dong and Dongsheng Cao
# All rights reserved.
# This file is part of the PyBioMed.
# 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 PyBioMed source tree.
"""
The s... | gadsbyfly/PyBioMed | PyBioMed/test/test_PyMolecule.py | Python | bsd-3-clause | 12,834 | [
"MOE",
"Pybel",
"RDKit"
] | a2f407f1e31b4972d10f2ddd5e31d88d8461940dbb949113f23da567917434b7 |
#!/usr/bin/python
#load simulated reads
sim=open('sim.20.hsa.fa','r')
data={}
dataseq={}
lendata={}
name=""
for line in sim:
line=line.strip()
if line.startswith(">"):
name=line.replace(">","")
slot=name.split("_")[0].split("-")
data[name]="-".join(slot[0:3])
else:
lendata[n... | lpantano/eggs | mirannotation/check.align.py | Python | gpl-2.0 | 7,496 | [
"Bowtie"
] | bf032e416505f7c53c9548eacd492ff6186c27f9be1323e89820367f8619f2df |
from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os
import logging
log = logging.getLogger( __name__ )
category_name = 'Test 1420 Tool dependency environment variable inheritance'
category_description = 'Test script 1420 for interpolation of inherited environment variables.'
package_atlas_repositor... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/test/tool_shed/functional/test_1420_tool_dependency_environment_inheritance.py | Python | gpl-3.0 | 23,594 | [
"Galaxy",
"RDKit"
] | d4201afdf3ebca5db1be06f0ec97a7f246d9376adec4030a3a22ff1e4d60db71 |
# hu.po
val = {"" : "Project-Id-Version: sheltermanager\nReport-Msgid-Bugs-To: FULL NAME <EMAIL@ADDRESS>\nPOT-Creation-Date: 2013-01-24 10:55+0000\nPO-Revision-Date: 2010-07-17 19:12+0000\nLast-Translator: meggyes <Unknown>\nLanguage-Team: Hungarian <hu@li.org>\nMIME-Version: 1.0\nContent-Type: text/plain; charset=UTF... | aubzen/sheltermanager | src/locale/locale_hu.py | Python | gpl-3.0 | 84,193 | [
"Amber",
"VisIt"
] | 3f704853c5570d350f01dc449aed2921bbb2581d07ad318e553568401bdd8071 |
#!/usr/bin/env python
#coding:utf-8
# Author: Mozman
# Purpose: treemixin provides top level functions for binary trees
# Created: 03.05.2010
# Copyright (c) 2010-2013 by Manfred Moitzi
# License: MIT License
from __future__ import absolute_import
from .walker import Walker
from .treeslice import TreeSlice
class Tr... | Teamxrtc/webrtc-streaming-node | third_party/webrtc/src/chromium/src/third_party/bintrees/bintrees/treemixin.py | Python | mit | 22,453 | [
"VisIt"
] | 7698f4c12ad1784af1e1a9311110e5b5477145102d899a11645bc06dacc08a00 |
from Tkinter import *
import tkMessageBox
from FreesteelPython import *
import code
"""
Keys:
Space: Start/Pause animation playback
Backspace: Reverse playback direction
+/-: Increase/decrease playback speed
Home/End: Go to start/end of animation
Page up/down: 10% step back/forward
... | play113/swer | libactp-read-only/freesteel/test/FreesteelWindow.py | Python | mit | 5,580 | [
"VTK"
] | a52ed1250fe9f95eedf36bfc4b6f0ee0ff536baf67d8f7be87a982cc18dc32cf |
import atomium
from unittest import TestCase
class MmcifFileDictReadingTests(TestCase):
def test_1lol_file_dict(self):
d = atomium.open("tests/integration/files/1lol.cif", file_dict=True)
self.assertEqual(d["entry"], [{"id": "1LOL"}])
self.assertEqual(d["audit_author"], [
{"name":... | samirelanduk/molecupy | tests/integration/test_file_dict_reading.py | Python | mit | 3,936 | [
"CRYSTAL"
] | bf6e1e4f0d802bb0a25190b05bb42b429d08c090ca2f2b92afa7769728d36bb2 |
"""Wrappers and from-mimetype lookup code for archive extractors
@todo: Will unstuff and cabextract handle self-extracting cabs?
(If so, add application/cab to the .exe list)
@todo: Figure out a better syntax for specifying extractor arguments.
(especially destination directories)
"""
__author__ = "Ste... | ssokolow/unball | unball/extractors.py | Python | gpl-2.0 | 28,440 | [
"ADF"
] | f4a1730c15ed8cfbc316ee2c180b3962d5c6b679471305c933a705cc8eb98585 |
#
# gPrime - A web-based genealogy program
#
# Copyright (C) 2009 Benny Malengier
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any lat... | sam-m888/gprime | gprime/plugins/graph/graphplugins.gpr.py | Python | gpl-2.0 | 3,020 | [
"Brian"
] | 6e998bd3bc1b2833fe1f797850b7e42d947ebeee2b3c9632129274d9414c7019 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2016, 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.
"""Unit tests for writer filewriter module."""
import os
import unittest
import cclib
__filedir__ = os.path.dirname(__... | Schamnad/cclib | test/io/testfilewriter.py | Python | bsd-3-clause | 900 | [
"ADF",
"cclib"
] | 06df3c81bf39e01d9eff0c7e7f5b0dfc017294af1869652dbfce06ab8440936e |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
import re
import os
import io
import requests
import warnings
import numpy as np
from astropy.table import Table
import astropy.io.fits as fits
from astroquery.exceptions import NoResultsWarning
__all__ = ['query', 'save_file', 'get_file']
id_parse = re... | ceb8/astroquery | astroquery/ipac/irsa/sha/core.py | Python | bsd-3-clause | 8,485 | [
"VisIt"
] | a0925ae25413468b814b8c1d37aa39538ef34d5e9dd21570ab39c2034dc14a2d |
"""
Sphinx plugins for Django documentation.
"""
import json
import os
import re
from docutils import nodes
from docutils.parsers.rst import directives
from sphinx import addnodes
from sphinx.builders.html import StandaloneHTMLBuilder
from sphinx.domains.std import Cmdoption
from sphinx.util.compat import Directive
fr... | auready/django | docs/_ext/djangodocs.py | Python | bsd-3-clause | 10,813 | [
"VisIt"
] | 990f9bc196dd05719b165e4fd3065a8f7c6ad026e3412c0407acaa9288030305 |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
""" Inspired from https://gist.github.com/RichardBronosky/454964087739a449da04
See http://www.python.org/dev/peps/pep-0008/ for more PEP-8 details
This module's docstring summary line.
This is a multi-line docstring. Paragraphs are separated with blank lines.
Normally ... | fstagni/DIRAC | tests/formatting/pep8_good.py | Python | gpl-3.0 | 3,796 | [
"DIRAC"
] | dbadb12f70781bb170444de88e6d7f469d00be51d04e8ccacb0cccddc67ba482 |
"""
Visit the Twitter developer page and create a new application:
https://dev.twitter.com/apps/new
This will get you a CONSUMER_KEY and CONSUMER_SECRET.
When users run your application they have to authenticate your app
with their Twitter account. A few HTTP calls to twitter are required
to do this. Please see ... | miragshin/twitter | twitter/oauth.py | Python | mit | 4,930 | [
"VisIt",
"exciting"
] | 455581c285a3b309a39d0d4b8262f71bb7969bc85caac3f3e9db64e3738e8bab |
from ase.data.molecules import molecule
from gpaw import GPAW
from gpaw.poisson import PoissonSolver
from gpaw.atom.basis import BasisMaker
from gpaw.test import equal
# Tests basis set super position error correction
# Compares a single hydrogen atom to a system of one hydrogen atom
# and one ghost hydrogen atom. T... | qsnake/gpaw | gpaw/test/lcao_bsse.py | Python | gpl-3.0 | 1,735 | [
"ASE",
"GPAW"
] | 6c348d0f3202d6457242e3d7d5610c76b5e6cc9656e580ad287523e5e95d5ea0 |
from ase import Atoms
from gpaw import FermiDirac, Mixer
from gpaw.transport.calculator import Transport
from gpaw.atom.basis import BasisMaker
from gpaw.poisson import PoissonSolver
import pickle
a = 3.6
L = 7.00
basis = BasisMaker('Na').generate(1, 1, energysplit=0.3)
atoms = Atoms('Na12', pbc=(1, 1, 1), cell=[L,... | qsnake/gpaw | gpaw/test/transport.py | Python | gpl-3.0 | 1,176 | [
"ASE",
"GPAW"
] | 434c6585cb599e7c94f602beb2c537db78153b1bc111a42dce0d86766f958dcb |
#!python
# encoding: utf-8
# ***** BEGIN LICENSE BLOCK *****
# Version: MPL 1.1/GPL 2.0/LGPL 2.1
#
# The contents of this file are subject to the Mozilla Public License
# Version 1.1 (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.... | archifix/settings | sublime/Packages/SublimeCodeIntel/libs/codeintel2/util.py | Python | mit | 28,852 | [
"VisIt"
] | c2733d1ec1a319b629d7624e47336c84769b31a8d9770cde8312eebe4338a330 |
# OpenShot Video Editor is a program that creates, modifies, and edits video files.
# Copyright (C) 2009 Jonathan Thomas
#
# This file is part of OpenShot Video Editor (http://launchpad.net/openshot/).
#
# OpenShot Video Editor is free software: you can redistribute it and/or modify
# it under the terms of the GNU G... | i5o/openshot-sugar | openshot/openshot/blender/scripts/spacemovie_intro.py | Python | gpl-3.0 | 5,460 | [
"Galaxy"
] | 8a7b29ffa72916ecafecebc1c8051fc2b405d22e5727e9085e4804887cfcbc68 |
import json
import functools
from nxtools import logging
from firefly.api import api
from firefly.objects import has_right
from firefly.widgets import FireflyString, FireflySelect
from firefly.qt import QWidget, QHBoxLayout, QFormLayout, QPushButton, QTabWidget
class PlayoutPlugin(QWidget):
def __init__(self, p... | immstudios/firefly | firefly/modules/rundown_plugins.py | Python | gpl-3.0 | 3,356 | [
"Firefly"
] | 2a7f4bc30defa342711acd95c3fd00d1fa2208d86403667955191d29cbb12e1e |
from datetime import datetime, timedelta
from limbo.exceptions import SecurityError, RedirectRequest
import logging
from django.contrib import messages
log = logging.getLogger(__file__)
class rate_limited:
"""
Limits hit on the view to a certain number per hour on the SESSION.
This is really a class that ... | gdoermann/django-limbo | limbo/decorators.py | Python | mit | 2,405 | [
"VisIt"
] | 320d3b950a14103e1c3993cb7084594e5a605e1db4de2cea38e09ca6eb50f649 |
############################################################################
##
## Copyright (C) 2006-2010 University of Utah. All rights reserved.
##
## This file is part of VisTrails.
##
## This file may be used under the terms of the GNU General Public
## License version 2.0 as published by the Free Software Foundat... | VisTrails/vistrails-contrib-legacy | vtksnl/inspectors.py | Python | bsd-3-clause | 9,884 | [
"VTK"
] | 3bdd5b490cc2f0c0acf041d50c29a65b81f929d81d33cf934f0c431ff3792440 |
#!/usr/local/bin/env python
"""
Test iodrivers.py facility.
"""
# =============================================================================================
# GLOBAL IMPORTS
# =============================================================================================
import numpy as np
try:
from openmm imp... | choderalab/openmmtools | openmmtools/tests/test_storage_iodrivers.py | Python | mit | 11,351 | [
"NetCDF",
"OpenMM"
] | 87c1c3ae13a04ed84f1eaeeb04ffd49eeda4fb94487001f2f73660d3d689308c |
from rdkit import Chem
import os
outFile = "AllTestCmpds.txt"
fid = open(outFile, "w")
files = os.listdir(".")
idx = 1
for file in files:
fileName, ext = os.path.splitext(file)
if ext == ".sdf":
print fileName
inMols = Chem.SDMolSupplier(fileName+".sdf")
for mol in inMols:
... | JonnaStalring/AZOrange | tests/standardizationTestSuite/mergeSdf.py | Python | lgpl-3.0 | 398 | [
"RDKit"
] | 70fdf4a615915b1f241e502d733215c36996fddd428003f8400674bdc94e6205 |
# -*- coding: utf-8 -*-
##############################################################################
#
# OpenERP, Open Source Management Solution
# Copyright (C) 2004-2009 Tiny SPRL (<http://tiny.be>).
# Copyright (C) 2010-2014 OpenERP s.a. (<http://openerp.com>).
#
# This program is free software: you ca... | 0k/odoo | openerp/tools/misc.py | Python | agpl-3.0 | 44,983 | [
"VisIt"
] | 864ba0d0a83c92c663077a06167c8d9683299eee6284551b245d8cd30fcab33e |
#
# Copyright 2016 The BigDL Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... | intel-analytics/BigDL | python/chronos/test/bigdl/chronos/autots/deprecated/regression/test_time_sequence_predictor.py | Python | apache-2.0 | 4,826 | [
"ORCA"
] | 97e6f259c6f710102425be4fdfbcdd378b7977f85a21ab5817bb48ec0063aa7d |
import random
from lib.keras_utils import *
from lib.utils import *
from parameters import *
from skimage.transform import ProjectiveTransform
EPS = 1e-10 # Epsilon
MIN_CP = -2. # Minimum power index of c
MAX_CP = 2. # Maximum power index of c
SCORE_THRES = 0.99 # Softmax score threshold to consider success of ... | chawins/aml | lib/OptProjTran.py | Python | mit | 19,964 | [
"Gaussian"
] | f2f64378df1c8dc975c9ebaa78af7db900cfaafcd6f6e8a485c905811bdf7b2c |
# pylint: disable=C0111
# pylint: disable=W0621
from lettuce import world, step
from lettuce.django import django_url
@step('I register for the course "([^"]*)"$')
def i_register_for_the_course(_step, course):
url = django_url('courses/%s/about' % world.scenario_dict['COURSE'].id.to_deprecated_string())
worl... | nanolearning/edx-platform | lms/djangoapps/courseware/features/registration.py | Python | agpl-3.0 | 1,354 | [
"VisIt"
] | e933226425fcf23f53ebb799e8588896bd5be10660d16d11bba47e7accd40798 |
""" core implementation of testing process: init, session, runtest loop. """
from __future__ import absolute_import, division, print_function
import contextlib
import functools
import os
import pkgutil
import six
import sys
import _pytest
from _pytest import nodes
import _pytest._code
import py
from _pytest.config i... | davidszotten/pytest | src/_pytest/main.py | Python | mit | 22,922 | [
"VisIt"
] | f592c2db2defd5ce17152657fef065be8002f0349c356b3f5a3f82572eb05225 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
""" Module for commons shared by tests """
import re
import logging
logging = logging.getLogger('sneakylang')
from sneakylang.err import ParserRollback, MacroCallError
from sneakylang.macro import Macro
from sneakylang.node import Node, TextNode
from sneakylang.parser i... | andrejtokarcik/python-sneakylang | sneakylang/test/module_test.py | Python | bsd-3-clause | 5,234 | [
"VisIt"
] | d3aa88bee4b7581f32892fdc79fdc79eecf3c9e1aacc9ca16781d009ece44613 |
# 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 Foundation, either version 3 of the License, or
# (at your option) any later ve... | thomasaarholt/hyperspy | hyperspy/tests/model/test_chi_squared.py | Python | gpl-3.0 | 3,380 | [
"Gaussian"
] | c0c6e9731044dbf26220da9d232129bc89e744f2a37ef6dfaa005a0209222f9d |
# 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... | ghchinoy/tensorflow | tensorflow/python/autograph/pyct/pretty_printer.py | Python | apache-2.0 | 4,097 | [
"VisIt"
] | c7b7cd328c1c125081e595eea6fa74db2143a26534f1d439fab8914b3c1c9f8b |
# BEGIN_COPYRIGHT
#
# Copyright (C) 2014 CRS4.
#
# This file is part of blast-python.
#
# blast-python 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)
# ... | crs4/blast-python | BlastPython/fasta_stream_from_stream.py | Python | gpl-3.0 | 1,632 | [
"BLAST"
] | 01bb1045cbc799a15cb18f4e9b447956367ad210cd4dff3ca76103746e4b982f |
""" StorageManagementDB is a front end to the Stager Database.
There are five tables in the StorageManagementDB: Tasks, CacheReplicas, TaskReplicas, StageRequests.
The Tasks table is the place holder for the tasks that have requested files to be staged.
These can be from different systems and have differe... | ic-hep/DIRAC | src/DIRAC/StorageManagementSystem/DB/StorageManagementDB.py | Python | gpl-3.0 | 64,349 | [
"DIRAC"
] | 7bf53af65f8e47f5cdf279512ab05d72d9ef758c6db3dbfccb042f9b7ea3556c |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2008 Jerome Rapinat
# Copyright (C) 2008 Benny Malengier
#
# 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... | beernarrd/gramps | gramps/gen/filters/rules/person/_haslds.py | Python | gpl-2.0 | 1,759 | [
"Brian"
] | 92eaa256b426f736e72ad5eaf84e5b23586e3a84503220090141061520b0a215 |
# proxy module
from __future__ import absolute_import
from mayavi.components.source_widget import *
| enthought/etsproxy | enthought/mayavi/components/source_widget.py | Python | bsd-3-clause | 100 | [
"Mayavi"
] | 4e2ef9ae7bca49adb36368ddad08d6cdeca969fcac031c97f749a140a2bf9114 |
# -*- coding: utf-8 -*-
#
# evaluate_quantal_stp_synapse.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST 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 o... | kristoforcarlson/nest-simulator-fork | pynest/examples/evaluate_quantal_stp_synapse.py | Python | gpl-2.0 | 6,184 | [
"NEURON"
] | eabaa9dd48c63469fbcc7650facce0cd605773a3cc1ec88e5799ced72c8d993f |
"""Example to solve 3D aqueous foam pipe flow using rheological
Herschel-Bulkley power law for bulk and wall shear stress dependent
slip velocity law for wall layer
"""
import foam_controlwrapper
from simphony.core.cuba import CUBA
from simphony.api import CUDS, Simulation
from simphony.cuds.meta import api
from simp... | simphony/simphony-openfoam | foam_internalwrapper/examples/aqueous_foam_pipe_flow.py | Python | gpl-2.0 | 4,286 | [
"Mayavi"
] | 6db7b0dbe525ab4baeb46ed5ca2c2d06d1caf58721117055e6ffb6ed57775fa0 |
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