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# this program corresponds to special.py
### Means test is not done yet
# E Means test is giving error (E)
# F Means test is failing (F)
# EF Means test is giving error and Failing
#! Means test is segfaulting
# 8 Means test runs forever
### test_besselpoly
### test_mathieu_a
### test_mathieu_even_coef
##... | pbrod/scipy | scipy/special/tests/test_basic.py | Python | bsd-3-clause | 132,344 | [
"Elk"
] | 4f1ddce0a7b151c58fd00ed0e05996c45981048dfe48eecbe2a9597bbc434dd0 |
# Copyright (C) 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 versio... | pkreissl/espresso | testsuite/scripts/samples/test_MDAnalysisIntegration.py | Python | gpl-3.0 | 1,919 | [
"ESPResSo",
"MDAnalysis"
] | db85f2a53aa791f6e6b00edec3ca3a4394b3d53a19ecafcc5c67f32e6c929471 |
'''
Created on 2012-11-10
@author: Andre R. Erler
'''
## imports
from numpy import array, arange, zeros, diff
import os, re, sys
# netcdf stuff
from netcdf import Dataset, add_coord, copy_dims, copy_ncatts, copy_vars
# data root folder
from socket import gethostname
hostname = gethostname()
if hostname=='komputer':
... | aerler/WRF-Tools | Python/archive/avgWRF.py | Python | gpl-3.0 | 10,011 | [
"NetCDF"
] | 643ef817c828bb59397b16cfbc110c915813e8f75e010412f3794cae0c6797b3 |
import os
from setuptools import setup
def read(fname):
return open(os.path.join(os.path.dirname(__file__), fname)).read()
setup(
name='scRNApipe',
version='0.1.0',
description='Package for analysing scRNA-seq in Transcript Tag Counting data.',
long_description=read('README.md'),
author='Stavr... | MarinusVL/scRNApipe | setup.py | Python | mit | 1,056 | [
"pysam"
] | 41f60a9c4c9e66899738e664e7b5745315a8bd26971aab116d9893b2edb83c86 |
# -*- coding: utf-8 -*-
# Copyright (C) 2017-2018 CIRCL Computer Incident Response Center Luxembourg (smile gie)
# Copyright (C) 2017-2018 Christian Studer
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published... | TheDr1ver/MISP | app/files/scripts/stix2misp.py | Python | agpl-3.0 | 28,747 | [
"Galaxy"
] | 827b87a179cff0925fb23dff4894d9ecbcc6b840bad08b4b2b518374d841c948 |
__author__ = 'dalton'
from player import Player
class Action():
def __init__(self, method, name, hotkey, **kwargs):
self.method = method
self.name = name
self.hotkey = hotkey
self.kwargs = kwargs
def __str__(self):
return '{}: {}'.format(self.hotkey, self.name)
clas... | dalrrard/text-adventure-tut | adventuretutorial/actions.py | Python | mit | 1,299 | [
"Dalton"
] | 49e7722b9fa278b288573668ce2bc29bed49483437dbdcfe758917b2bdc9db6f |
# python imports
import os
# rasmus imports
from rasmus import util
# compbio imports
from . import fasta
# NCBI BLASTALL 2.2.10 -m 8 tab-delimited output
# Fields:
# 0. Query id,
# 1. Subject id,
# 2. % identity,
# 3. alignment length,
# 4. mismatches,
# 5. gap openings,
# 6. q. start,
# 7. q. end,
# 8. s. start,
... | abhishekgahlot/compbio | compbio/blast.py | Python | mit | 12,417 | [
"BLAST"
] | 88c5184c59b65e921d8543f21660647a39014b2b2174795ca1f3c9f4997526d0 |
# Apache HTTP requests manipulation module
import requests
import json
import os
# The REST server url
#REST_URL = 'https://ccdirac06.in2p3.fr:9178'
REST_URL = 'https://dirac.ba.infn.it:9910'
###########################################
# Get the access token first
# GET request parameters
params = {'response_type':'... | SuperDIRAC/TESTDIRAC | sample-script/rest/list_groups.py | Python | gpl-3.0 | 895 | [
"DIRAC"
] | 4e6a808eb29541af121ae5c834378b3b249d42225cc3ee2342f429add5b45060 |
'''This script will download current NCBI refSeqs, upload any new entries to
the MySQL database, and create new BLAST databases.'''
import argparse
import MySQLdb
import os
from subprocess import Popen
from shlex import split
from datetime import datetime
from getpass import getpass
from dbIO import *
from flatFileCl... | icwells/Kiwi | bin/updateDatabases.py | Python | gpl-3.0 | 4,244 | [
"BLAST"
] | d680cfb764b269c9321804a6a7376405b77e902e961227165d785e0d75e3734b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Li-aung "Lewis" Yip
minecraft@penwatch.net
Requires:
plac (command line argument parsing)
unshortenit (adf.ly resolving)
"""
STARTUP_SCRIPT_TEMPLATE = """#!/bin/bash
java -Xmx2G -XX:MaxPermSize=256M -jar {fn} nogui"""
import sys
import os
import json
from ope... | LiaungYip/Cat-Herder | cat_herder.py | Python | mit | 5,092 | [
"ADF"
] | ce831f05ca899824664bac51789a2c255592441cda91a54dc9eb5c65d8117c3d |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2020, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
"""
Two Body Properties Computations
#####################################
"""
import numpy as np
import numba as nb
import pandas as pd
from IPython.display import display
from ipyw... | exa-analytics/atomic | exatomic/algorithms/angles.py | Python | apache-2.0 | 2,542 | [
"ADF"
] | 32ed10b7a1c02b23c36ea6d0ae0af6e0e9d0e67209117af42799fec2cd1a59c6 |
# Copyright 2018 The TensorFlow Probability Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law o... | tensorflow/probability | tensorflow_probability/python/optimizer/sgld.py | Python | apache-2.0 | 12,237 | [
"Gaussian"
] | d79f3a21f5a08c34c1d99b0e9f6c649d988f25c45827b5a445e58b8b3110fff2 |
"""
Views for the verification flow
"""
import datetime
import decimal
import json
import logging
import urllib
from pytz import UTC
from ipware.ip import get_ip
from django.conf import settings
from django.contrib.auth.decorators import login_required
from django.core.mail import send_mail
from django.core.urlresolv... | pomegranited/edx-platform | lms/djangoapps/verify_student/views.py | Python | agpl-3.0 | 59,238 | [
"VisIt"
] | a4dfbbd94581960c62b27f1bc1fc99ba61ce3546dad9b9b29d329b4f310c90ed |
# -*- coding: utf-8 -*-
"""Tests."""
from datetime import timedelta
import uuid
import unittest
try:
from unittest import mock
except ImportError: # Python 2 fallback.
import mock
import django.test
from django.conf import settings
from django.contrib.auth import hashers
from django.core.management import cal... | novapost/django-ticketoffice | django_ticketoffice/tests.py | Python | bsd-3-clause | 21,230 | [
"VisIt"
] | 8f67cf1550db872fcd648fd2038b9b6491164af44181cf861cecdfc2f4a20782 |
# copyright 2003-2013 LOGILAB S.A. (Paris, FRANCE), all rights reserved.
# contact http://www.logilab.fr/ -- mailto:contact@logilab.fr
#
# This file is part of logilab-astng.
#
# logilab-astng is free software: you can redistribute it and/or modify it
# under the terms of the GNU Lesser General Public License as publis... | yorvic/.vim | bundle/python-mode/pylibs/pylama/checkers/pylint/logilab/astng/builder.py | Python | gpl-3.0 | 8,667 | [
"VisIt"
] | 014916ce1e3ac2e55192f870916857117a25a6ab473855642531ac99e1214040 |
# $Id$
# vmd remote control --- client/server scripts to run VMD from python
# Copyright (c) 2007-2009 Oliver Beckstein <orbeckst@gmail.com>
# Released under the GNU Lesser Public License, version 3 or later.
#
# using asynchat/asyncore to talk to a VMD server process
# (see http://www.python.org/doc/current/lib/module... | pslacerda/GromacsWrapper | vmd/control.py | Python | gpl-3.0 | 10,586 | [
"VMD"
] | 1413990298fd81afa3990a1b1c55597ef8cbbb4ba6d165bbb6b7d400175078c0 |
# mako/pyparser.py
# Copyright (C) 2006-2013 the Mako authors and contributors <see AUTHORS file>
#
# This module is part of Mako and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Handles parsing of Python code.
Parsing to AST is done via _ast on Python > 2.5, otherwise th... | akuchling/book-diary-tools | books.d/mako/pyparser.py | Python | bsd-3-clause | 19,213 | [
"VisIt"
] | ba4da1975bbd175958ef06e493a9333a27ece1ae6fb5f33ba6d0b0a79930e446 |
"""Qt module for VTK/Python.
Example usage:
import sys
import PyQt5
from PyQt5.QtWidgets import QApplication
from vtk.qt.QVTKRenderWindowInteractor import QVTKRenderWindowInteractor
app = QApplication(sys.argv)
widget = QVTKRenderWindowInteractor()
widget.Initialize()
widget.Start()
... | keithroe/vtkoptix | Wrapping/Python/vtk/qt/__init__.py | Python | bsd-3-clause | 937 | [
"VTK"
] | 6cab17ef7b84d368e0f52893162ee3cabb6d71ba28d4ba30df7b8f499e0a1bab |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | skosukhin/spack | var/spack/repos/builtin/packages/r-agimicrorna/package.py | Python | lgpl-2.1 | 1,926 | [
"Bioconductor"
] | ae5167eafa807c02f4e08080786ae924922a7961fd66321a19b848186adafd98 |
import itertools
import random
from typing import Tuple
import inflect
from arrow import Arrow, get
import data
import markup
import navigation
from captains import Captain
from ships import EnemyShip, OurShip
from utils import begins_with_vowel
PERSONALITIES = {
"good": data.personality_good,
"bad": data.p... | eoinnoble/captains-log | travel.py | Python | unlicense | 10,899 | [
"VisIt"
] | dd084f114f43a2b668f2f9f30bd63c742af448e0346b5f4c0ea971b40d097c24 |
# Copyright 2013 by David Arenillas and Anthony Mathelier. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Provides read access to a JASPAR5 formatted database.
This modules re... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/motifs/jaspar/db.py | Python | gpl-2.0 | 25,742 | [
"Biopython"
] | dc899d9fc81b4a15fa51acfa2a96d22984356b552d71cdc5ef2d878cb871ad57 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/e2-openwbif | plugin/controllers/views/web/mediaplayercmd.py | Python | gpl-2.0 | 5,206 | [
"VisIt"
] | 8540bc99916b1f8b1c28a8b3d43011e48e6875707a8150346bd91a8bd83ecc8c |
""" Module for dealing with VOMS (Virtual Organization Membership Service)
"""
import os
import stat
import tempfile
import shlex
import shutil
from DIRAC import S_OK, S_ERROR, gConfig, rootPath, gLogger
from DIRAC.Core.Utilities import DErrno
from DIRAC.Core.Security.ProxyFile import multiProxyArgument, deleteMultiPr... | DIRACGrid/DIRAC | src/DIRAC/Core/Security/VOMS.py | Python | gpl-3.0 | 14,023 | [
"DIRAC"
] | 2b90cd23e7ea9aec9138c21e918b55762797db19d8c2dd78bd4f1c0b3f2e14c3 |
# Copyright (c) 2016, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are ... | eleftherioszisis/NeuroM | neurom/io/neurolucida.py | Python | bsd-3-clause | 10,000 | [
"NEURON"
] | 9d93f49ba735cd8465da3f936ddfe68d4265bf6c9f1e1829c65c5a0834949f71 |
import json
from twistes.compatability import urlencode, quote
from mock import MagicMock
from twisted.internet.defer import inlineCallbacks
from twisted.trial.unittest import TestCase
from twisted.web._newclient import ResponseNeverReceived
from twistes.client import Elasticsearch
from twistes.consts import HttpMetho... | avihad/twistes | tests/test_elasticsearch.py | Python | apache-2.0 | 22,573 | [
"BLAST"
] | e6276239869addf5b5aef860eb98f04fca8b21e3eb5e8a63416b50ee257d2cf7 |
"""
Example of an elaborate dialog showing a multiple views on the same data, with
3 cuts synchronized.
This example shows how to have multiple views on the same data, how to
embedded multiple scenes in a dialog, and the caveat in populating them
with data, as well as how to add some interaction logic on an
ImagePlane... | liulion/mayavi | examples/mayavi/interactive/volume_slicer.py | Python | bsd-3-clause | 8,673 | [
"Mayavi",
"VTK"
] | 7d8852e7642be5f9c21cfb8585b70ec1544148d39e1f44f6797263e426d3adf8 |
import unittest
import chainmap
class TestInit(unittest.TestCase):
def test_accept_n_dicts(self):
chainmap.ChainMap()
chainmap.ChainMap({})
chainmap.ChainMap({}, {})
chainmap.ChainMap({}, {}, {})
def test_get_item(self):
cm = chainmap.ChainMap({"a": 1}, {"a": 2, "b": 3... | sblondon/chainmap | tests.py | Python | lgpl-3.0 | 4,651 | [
"Brian"
] | f750857ec87ae959bea4bfda4e074b671f2701ce5b22ff5710ce527e450684d5 |
#
# 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... | dbtsai/spark | python/pyspark/ml/tests/test_training_summary.py | Python | apache-2.0 | 25,470 | [
"Gaussian"
] | bc6fb42d45d6b294e96e9769f935938ffe8abfd2f31c663496970e2331bba5d4 |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-compute | tests/unit/gapic/compute_v1/test_snapshots.py | Python | apache-2.0 | 125,352 | [
"Octopus"
] | 284df45e93cc8342233b0ce1630ccf565d7294cc0560c9c61c94b0bb8c29ac94 |
"""
NetCDF reader/writer module.
This module is used to read and create NetCDF files. NetCDF files are
accessed through the `netcdf_file` object. Data written to and from NetCDF
files are contained in `netcdf_variable` objects. Attributes are given
as member variables of the `netcdf_file` and `netcdf_variable` objects... | maciejkula/scipy | scipy/io/netcdf.py | Python | bsd-3-clause | 33,546 | [
"NetCDF"
] | fffe3807e54f9c405d7bdd82b711541b2b8be3667626769a17a0d0cde6b99897 |
"""HTSeq is a package to process high-throughput sequencing data.
See http://www-huber.embl.de/users/anders/HTSeq for documentation.
"""
import itertools, warnings, os
try:
from _HTSeq import *
except ImportError:
if os.path.isfile( "setup.py" ):
raise ImportError( "Cannot import 'HTSeq' when working dir... | detrout/python-htseq | HTSeq/__init__.py | Python | gpl-3.0 | 32,996 | [
"Bowtie",
"HTSeq",
"pysam"
] | dda5bd49c32803bcc6ef09dadaea137d362ffc9c656601d9e082a73f5f7549a6 |
# sql/elements.py
# Copyright (C) 2005-2014 the SQLAlchemy authors and contributors <see AUTHORS file>
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Core SQL expression elements, including :class:`.ClauseElement`,
:class:`.ColumnEle... | michaelBenin/sqlalchemy | lib/sqlalchemy/sql/elements.py | Python | mit | 119,161 | [
"VisIt"
] | 224eeb0681889b09d7e3b8cf70589d81c1a24aa198f8818ac97295433eecdc7e |
########################################################################
# File : JobWrapper.py
# Author : Stuart Paterson
########################################################################
""" The Job Wrapper Class is instantiated with arguments tailored for running
a particular job. The JobWrapper starts ... | marcelovilaca/DIRAC | WorkloadManagementSystem/JobWrapper/JobWrapper.py | Python | gpl-3.0 | 62,456 | [
"DIRAC"
] | 43434001512495a2649897846064d18c53e75fd857901dd6648c95692dddce7f |
# -*- coding: utf-8 -*-
# Copyright (C) 2003-2007 CAMP
# Copyright (C) 2007-2008 CAMd
# Please see the accompanying LICENSE file for further information.
"""This module defines a PAW-class.
The central object that glues everything together!"""
import numpy as np
from ase.units import Bohr, Hartree
from ase.dft imp... | ajylee/gpaw-rtxs | gpaw/paw.py | Python | gpl-3.0 | 32,087 | [
"ASE",
"GPAW"
] | 98169ac6560b4dfffbb68d7f145bd225388ba7f311bf9de892914861a5deb986 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from setuptools import setup
import numpy
with open('README.rst') as readme_file:
readme = readme_file.read()
requirements = [
"pandas>=0.23",
"numpy>=1.16.0",
"matplotlib>=2.0.0",
"scikit-learn>=0.24.2",
"scipy>=1.6.0",
"splinecalib>=0.0.2"
]... | numeristical/introspective | setup.py | Python | mit | 1,358 | [
"Brian"
] | 0865033a8e327c787b84085f62f5866f2a3c5bbfd9f71a22a8e39afcb4869c07 |
#!/usr/bin/env python
import random
import math
from . import RANDOPT_RNG
"""
Here we implement the sampling strategies.
"""
class Sampler(object):
"""
Base class for all samplers.
Note: This class should not be directly instanciated.
"""
def __init__(self, *args, **kwargs):
self.rng... | seba-1511/randopt | randopt/samplers.py | Python | apache-2.0 | 7,696 | [
"Gaussian"
] | 165a5264b1214276a462941f3fc31209dcb03e4a05a4a0dd74848f8d2d735a4a |
"""
setup.py
~~~~~~~~~~~~~
:copyright: (c) 2016-2019 Sander Bollen
:license: GPL-3.0
"""
from os.path import abspath, dirname, join
from setuptools import setup, find_packages
readme_file = join(abspath(dirname(__file__)), "README.md")
with open(readme_file) as desc_handle:
long_desc = desc_handle.read()
setup... | sndrtj/wisecondor | setup.py | Python | gpl-3.0 | 1,265 | [
"Biopython",
"pysam"
] | c22443b0da23508aa10f45a13690206993fc2bf67344a1a6abd3aa5e044fdcd6 |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
import unittest
import pbtest
from time import sleep
from selenium.common.exceptions import (
NoSuchElementException,
StaleElementReferenceException,
TimeoutException
)
from selenium.webdriver.common.keys import Keys
from selenium.webdriver.support.ui import... | EFForg/privacybadgerchrome | tests/selenium/widgets_test.py | Python | gpl-3.0 | 12,642 | [
"VisIt"
] | 35a71c6508a1a503a05e2228c3b751e26b8eb5fa88509ec50fa7d685c1288a9c |
# Copyright (C) 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 versio... | espressomd/espresso | testsuite/scripts/samples/test_visualization_constraints.py | Python | gpl-3.0 | 1,581 | [
"ESPResSo"
] | 6feca1feea36a4940b2e59afc394e1fa5e49a4ba31a51d53bfa7d83650943689 |
""" This module attempts to make it easy to create VTK-Python
unittests. The module uses unittest for the test interface. For more
documentation on what unittests are and how to use them, please read
these:
http://www.python.org/doc/current/lib/module-unittest.html
http://www.diveintopython.org/roman_d... | hlzz/dotfiles | graphics/VTK-7.0.0/Wrapping/Python/vtk/test/Testing.py | Python | bsd-3-clause | 18,475 | [
"VTK"
] | 3aca95ad209bdb7bd072a5667c64a7a2d4ea78213806107965e04f54d154b72d |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, division, print_function, unicode_literals
import mock
import time
import unittest
import logging
import functools
from nose.tools import * # noqa: F403
import pytest
from framework.auth.core import Auth
from website import settings
import website.sea... | baylee-d/osf.io | osf_tests/test_elastic_search.py | Python | apache-2.0 | 61,588 | [
"Brian"
] | b65c092820d5cb5468093e66f95af7e2fd377851555fac03837e034a7d42f700 |
import ast
import os
from ..base_test_case import BaseTestCase
from ..test_utils import get_modules_and_packages
from pyt.core.ast_helper import get_call_names_as_string
from pyt.core.project_handler import get_directory_modules
class ImportTest(BaseTestCase):
def test_import(self):
path = os.path.normp... | python-security/pyt | tests/cfg/import_test.py | Python | gpl-2.0 | 30,799 | [
"MOOSE"
] | 9fa99448afc41bf9d283f1bf6c620c11e8356feac036b4a9e393af54ffca6dc2 |
"""Bayesian Gaussian Mixture Models and
Dirichlet Process Gaussian Mixture Models"""
from __future__ import print_function
# Author: Alexandre Passos (alexandre.tp@gmail.com)
# Bertrand Thirion <bertrand.thirion@inria.fr>
#
# Based on mixture.py by:
# Ron Weiss <ronweiss@gmail.com>
# Fabian Ped... | herilalaina/scikit-learn | sklearn/mixture/dpgmm.py | Python | bsd-3-clause | 35,825 | [
"Gaussian"
] | 52225b7fdc215a738fb0bda7baabadf934e8e730a198d4b5d8f7ef8ac31b58b3 |
# -*- coding: utf-8 -*-
#
# hl_api_models.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 of the License, ... | sanjayankur31/nest-simulator | pynest/nest/lib/hl_api_models.py | Python | gpl-2.0 | 5,440 | [
"NEURON"
] | 899c7f5534d69ad1705c731094dacf3ccae390cd08b9c88658d4944ae1590524 |
"""
Base Pair splitting for supported files in galaxy
Currently vcf is supported
looking at impute2 + shapeit data
@Author James Boocock
"""
import logging
import math
import os
import shutil
import time
#For the creation of the tasks
from galaxy import model
log = logging.getLogger(__name__)
def ... | smilefreak/NesiGridSelection | grid_selection/clustering/parallelism/bp.py | Python | mit | 10,481 | [
"Galaxy"
] | 173515806a4223cdd76bc0abb2750d602663173d7688d5d866f2f5803626dbfe |
# This file is part of wger Workout Manager.
#
# wger Workout Manager is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# wger W... | rolandgeider/wger | wger/exercises/tests/test_muscles.py | Python | agpl-3.0 | 4,675 | [
"VisIt"
] | 3bdcfa97edea194d764283685bba4bd9161ee689b84bc7e8e7d372216843ed9a |
# -*- coding: utf-8 -*-
"""
Created on Thu May 7 19:32:22 2015
"""
__author__ = 'Chaya D. Stern'
import numpy as np
import simtk.openmm as mm
from simtk.unit import Quantity, nanometers, kilojoules_per_mole, picoseconds
from mdtraj import Trajectory
from torsionfit import parameters as par
class DataBase(Traje... | ChayaSt/Torsions | torsionfit/database/database.py | Python | gpl-2.0 | 5,885 | [
"CHARMM",
"MDTraj",
"OpenMM"
] | 77a41745ea0a6767a1a39b5bb25f735cd6ff13446d8d3f56b02c1967ff734db9 |
# -*- 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/converters/OpenMMParser.py | Python | gpl-2.0 | 6,474 | [
"MDAnalysis",
"OpenMM"
] | 2062d784c36de9166d6058774d19c62b63ab231bf763d1b95632b8043f60dcd9 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import math
import itertools
import warnings
from six.moves import map, zip
import numpy as np
from numpy.linalg import inv
from numpy import pi, dot, transpo... | aykol/pymatgen | pymatgen/core/lattice.py | Python | mit | 42,053 | [
"ABINIT",
"CRYSTAL",
"pymatgen"
] | 988f460eec492be91b768398788aa83ca5105f39b61e52aeb5b2b3eeca43ce82 |
#! /usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requi... | googleapis/python-resource-settings | scripts/fixup_resourcesettings_v1_keywords.py | Python | apache-2.0 | 6,086 | [
"VisIt"
] | 84b08e7f973c4668cafd997906d0604bbe040c0c423aa7b116cc5a8826fcc7b8 |
import numpy as np
import pytest
from context import GAMESS_OPTIONS
import ppqm
from ppqm import chembridge, gamess, tasks
from ppqm.gamess import GamessCalculator
def _get_options(scr):
gamess_options = {"scr": scr, **GAMESS_OPTIONS}
return gamess_options
def test_optimization(tmpdir):
gamess_options... | ppqm/ppqm | tests/test_gamess.py | Python | mit | 10,871 | [
"GAMESS"
] | 0fc77e1f88f46bd3b3d7a19bf827fe4df4ec36ef621f79a86e65b00bee3d438b |
# coding: utf-8
from __future__ import division, unicode_literals, print_function
import logging
import math
import os
import subprocess
import tempfile
import time
import numpy as np
from monty.dev import requires
from monty.json import jsanitize, MSONable
from monty.os import cd
from monty.os.path import which
fro... | gpetretto/pymatgen | pymatgen/electronic_structure/boltztrap.py | Python | mit | 107,576 | [
"BoltzTrap",
"VASP",
"pymatgen"
] | acb6d911d8bef5734403d56cd9b2c4b24e4c2d15bb3959912831f6254976835a |
#!/usr/bin/env python
import sys
from cutlass import iHMPSession
from settings import auth
from settings import NodeRetrievalFiles
from cutlass_utils import log_it, format_query
from cutlass_search import retrieve_nodes, retrieve_query_all
log = log_it('retrieve_osdf_nodes')
log.info('Starting metadata download fro... | TheJacksonLaboratory/osdf_submit | scripts/retrieve_osdf_nodes.py | Python | gpl-3.0 | 1,940 | [
"VisIt"
] | c676cedf3bc4311eb11d463ee9c24102600d46366ef37dee6f092ba6ffcb654a |
"""
ex20170221_Model_PC.py
Build Model PC from Godley & Lavoie (Chapter 4)
Uses the model builder from the sfc_models.gl_book sub-package.
Copyright 2017 Brian Romanchuk
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 ... | brianr747/SFC_models | sfc_models/examples/scripts/ex20170221_Model_PC.py | Python | apache-2.0 | 2,108 | [
"Brian"
] | c0d53d9afab3894d9a249a05d15aacd56307630eee4580b3ac8d350d61299463 |
""" CurveGraph represents simple line graphs with markers.
The DIRAC Graphs package is derived from the GraphTool plotting package of the
CMS/Phedex Project by ... <to be added>
"""
from DIRAC.Core.Utilities.Graphs.PlotBase import PlotBase
from DIRAC.Core.Utilities.Graphs.GraphUtilities import (
darkenColo... | DIRACGrid/DIRAC | src/DIRAC/Core/Utilities/Graphs/CurveGraph.py | Python | gpl-3.0 | 5,403 | [
"DIRAC"
] | 9fa0f6cd6968e7e9d65634a56904ef09e3d15eae1e00eb53f922fda764323c50 |
import pysam
import collections
import multiprocessing
import functools
import subprocess
import pandas as pd
from ngs_python.bam.pysam_bam import PysamBAM
class PysamVariants(PysamBAM):
def _variant_basecalls(
self, bam, filterfunc, chrom, pos, ref, var
):
# Create base tuple for ... | adam-rabinowitz/ngs_python | bam/pysam_variants.py | Python | gpl-2.0 | 12,369 | [
"pysam"
] | 87684f064fdbcd6de3fb96dbbbb9aae8eb5f553d296766eb2aa17d2da8f73387 |
"""
===============================
Plot classification probability
===============================
Plot the classification probability for different classifiers. We use a 3
class dataset, and we classify it with a Support Vector classifier, L1
and L2 penalized logistic regression with either a One-Vs-Rest or multinom... | DailyActie/Surrogate-Model | 01-codes/scikit-learn-master/examples/classification/plot_classification_probability.py | Python | mit | 2,873 | [
"Gaussian"
] | d948d278af7b5b08143389030ba1565741e1eee829951ac606f42def3e5dcfda |
#from .... import graph
from skgraph import graph
from scipy.spatial.distance import pdist
import numpy as np
import sys
from numpy.linalg import norm
def gaussianKernel(X,Y,beta):
Z=[X,Y]
return np.exp(-beta * pdist(Z, 'sqeuclidean'))
def linearKernel(X,Y):
Xnum=np.array(X)
Ynum=np.array(Y)
Xnu... | nickgentoo/scikit-learn-graph | skgraph/tree/tree_kernels_ST_new.py | Python | gpl-3.0 | 15,875 | [
"Gaussian"
] | b5d21f8706dab5d0d19643dac1abe3ad8885c74ee5afb37f545a325ab12c9ff4 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | corburn/scikit-bio | skbio/sequence/_sequence.py | Python | bsd-3-clause | 80,443 | [
"scikit-bio"
] | a9479b17c35205a03791f8b3f61361919bf726f4e5d7760e30262811dcf326a4 |
"""
A simple gui for multiple functions fitting in veusz application using lmfit modules
"""
from PyQt4.QtGui import QTreeWidget, QLabel, QLineEdit, QPushButton, QComboBox, QGridLayout, QWidget, QTreeWidgetItem
from PyQt4.QtCore import Qt
from lmfit import Model
def gauss(x,y0,A,xc,w):
from numpy import exp, log... | yubaub/python_tools | veusz_mfit.py | Python | gpl-3.0 | 6,349 | [
"Gaussian"
] | d10408e2960576a39520abb966da9db479cf5e8452b2a67b2a87c492da0fe963 |
"""
Copyright (C) 2012 Alan J Lockett
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute,... | hypernicon/pyec | pyec/distribution/ec/mutators.py | Python | mit | 25,601 | [
"Gaussian"
] | e2f71c0ba20dd2bde8a74d1c3db95186d39dd4ffe1bd35f029fd19c8c074ecec |
#!/usr/bin/env python
""" Return explanation and options for each parameter.
ip.get_params_info(1) or ip.get_params_info("project_dir")
return the same result. If not argument, a summary of the available
parameters and their numbered references is returned.
Parameter info is stored as a dict of tupl... | dereneaton/ipyrad | ipyrad/core/paramsinfo.py | Python | gpl-3.0 | 21,970 | [
"BWA"
] | 12f82ec09c1cbc3b2f31c342e7a79361281d20e4b9bf1b16f6ab013b39715b25 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, division, print_function
import os
import py.path
import pytest
import sys
import _pytest.pytester as pytester
from _pytest.pytester import HookRecorder
from _pytest.pytester import CwdSnapshot, SysModulesSnapshot, SysPathsSnapshot
from _pytest.config impo... | peterjoel/servo | tests/wpt/web-platform-tests/tools/third_party/pytest/testing/test_pytester.py | Python | mpl-2.0 | 13,295 | [
"Brian"
] | bc89f899e1a450fa5a195841b3db2aa0c0a0b74f8c3d29e6d57368fe5a4dde78 |
# -*- coding: utf-8 -*-
# Generated by Django 1.9.5 on 2016-05-03 18:44
from __future__ import unicode_literals
from django.conf import settings
import django.contrib.gis.db.models.fields
from django.db import migrations, models
import django.db.models.deletion
import phonenumber_field.modelfields
class Migration(mi... | RideQuest/rideshare-backend | rideshare/rideshare_profile/migrations/0001_initial.py | Python | mit | 2,609 | [
"Jaguar"
] | b7df98703a5310a9bc74f57f960afdd493efd30e0d13c28a7ffa7980b62b44ae |
"""Requests meme metadata (memetadata) from memegenerator's API
"""
from models import *
import requests
import json
import sys
import os
base_data_uri = "http://version1.api.memegenerator.net/Instances_Select_ByNew"
base_gen_uri = "http://version1.api.memegenerator.net/Generators_Search"
meme_names = ['Futurama', ... | ezig/meme-simulator | memetadata.py | Python | bsd-3-clause | 3,215 | [
"Brian"
] | 6d02d74dc116051e0bd0112299209cb7e83dd327da228925e7c1b65aa80570a7 |
'''
Created on 2013-05-23
@author: brian
'''
import pygame
from pygame.color import THECOLORS
from src.util import Vector2
from cell import Cell
class Viewport(object):
size = 17
def __init__(self, surface, pos, world, player, images):
self.images = images
self.surface = surface
self.pos = pos
self.world... | Greymerk/python-rpg | src/gui/viewport.py | Python | gpl-3.0 | 3,531 | [
"Brian"
] | df39b4049d9ef6bf2df3131bd094d9cfdafc6aa49b8f7b67ca6f8efdb10a5686 |
import numpy as np
import matplotlib.pyplot as plt
import scipy.interpolate as spi
import scipy.signal as sps
import mosasaurus.gaussian as g
reload(g)
import mosasaurus.smooth as smooth
# STEP 3: Fit sky background with out-of-spectra data
def fitbg(dataim, mask, x1, x2, deg=1, threshold=5, isrotate=False, isplots=F... | zkbt/mosasaurus | mosasaurus/optspex.py | Python | mit | 30,291 | [
"Gaussian"
] | 665938c459eb6debd10f070ac0958c66a4b3339c262b4aaa090a22ea969184f2 |
from __future__ import print_function
import sys
import random
import os
import numpy as np
import scipy
import math
from scipy import stats
from builtins import range
import time
sys.path.insert(1, "../../../../")
import h2o
from tests import pyunit_utils
from h2o.estimators.glm import H2OGeneralizedLinearEstimator... | YzPaul3/h2o-3 | h2o-py/tests/testdir_dynamic_tests/testdir_algos/glm/pyunit_glm_gaussian_large.py | Python | apache-2.0 | 63,087 | [
"Gaussian"
] | 5af02afef993b6683fd80a7967d33ea3ecd25a4c044904159bb8ef7076287cdf |
#!/usr/bin/env python
'''
from acoular import __file__ as bpath, WNoiseGenerator, PointSource,\
Mixer, WriteH5, TimeSamples, PowerSpectra
from acoular import L_p, Calib, MicGeom, PowerSpectra, EigSpectra, \
RectGrid, BeamformerBase, BeamformerEig, BeamformerOrth, BeamformerCleansc, \
TimeSamples, MaskedTimeSa... | waynezv/ANN | ANN.py | Python | mit | 22,434 | [
"VisIt"
] | 1efdffbd82365246c9be1fa29399455f83fd4c418faaeb31b9c8f2649cb111cc |
# Orca
#
# Copyright 2005-2008 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/bookmarks.py | Python | gpl-3.0 | 8,579 | [
"ORCA"
] | dd045880bc8c6e08282c45aba511b7510b937ecbb6e349b41bfdd07811358d9a |
"""Undocumented Module"""
__all__ = ['unique', 'indent', 'nonRepeatingRandomList',
'writeFsmTree', 'StackTrace', 'traceFunctionCall', 'traceParentCall',
'printThisCall', 'tron', 'trace', 'troff', 'getClassLineage', 'pdir',
'_pdir', '_is_variadic', '_has_keywordargs', '_varnames', '_getcode',
'Signature', 'doc', 'adju... | toontownfunserver/Panda3D-1.9.0 | direct/showbase/PythonUtil.py | Python | bsd-3-clause | 144,615 | [
"Gaussian"
] | 4462673cfc315515a74630ab4490e64d4f26d3ddc5b08ee459844f538384e832 |
# -*- coding: utf-8 -*-
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding model 'Publisher'
db.create_table('neuroelectro_publisher', (
('id', self.g... | neuroelectro/neuroelectro_org | neuroelectro/south_migrations/0055_auto__add_publisher__add_field_journal_publisher.py | Python | gpl-2.0 | 27,500 | [
"NEURON"
] | 226054de60247d5b6397e3f0bd7797d63635776ab47d58599bd369d75ffb0c05 |
import os
import os.path
import argparse
import shutil
import subprocess as s
import yaml
import sys
parser = argparse.ArgumentParser(description='This is a wrapper to set up and run the bpipe command')
parser.add_argument('pipeline',metavar = 'pipeline',nargs='+',
help = 'the name of the bpipe pipeline script ... | lauringlab/variant_pipeline | bin/variantPipeline.py | Python | apache-2.0 | 5,915 | [
"Bowtie"
] | c7ebb86d209103bbb38d0ef92038a5ded8c9cd4a819327dfab4ee1c16ea16e8c |
# $Id$
#
# Copyright (C) 2006 greg Landrum
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
from rdkit import RDConfig
import unittest,sys,os,ma... | soerendip42/rdkit | rdkit/Chem/FeatMaps/UnitTestFeatMapUtils.py | Python | bsd-3-clause | 8,522 | [
"RDKit"
] | f81fe1f0d5323e7765aeb74511ee3cb30ecf700d7472be159bdf359bc55fecd8 |
"""
Maximum likelihood covariance estimator.
"""
# Author: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Gael Varoquaux <gael.varoquaux@normalesup.org>
# Virgile Fritsch <virgile.fritsch@inria.fr>
#
# License: BSD 3 clause
# avoid division truncation
import warnings
import numpy as np
from scipy... | ndingwall/scikit-learn | sklearn/covariance/_empirical_covariance.py | Python | bsd-3-clause | 10,549 | [
"Gaussian"
] | 76b80d6ee7d98704827bee89f292a5579a8b64f90cb583b2bde364e27667d204 |
from __future__ import print_function
__author__ = """Alex "O." Holcombe, Charles Ludowici, """ ## double-quotes will be silently removed, single quotes will be left, eg, O'Connor
import time, sys, platform, os
from math import atan, atan2, pi, cos, sin, sqrt, ceil, radians, degrees
import numpy as np
import psychopy, ... | alexholcombe/dot-jump | dataRaw/Fixed Cue/test_dot-jump21Nov2016_13-46.py | Python | gpl-3.0 | 26,091 | [
"Gaussian"
] | 81d252c900168615670e71dd38efe6f7228ca952e83a71852ec5577ed7c301d6 |
import numpy as np
from pyRSD.rsd._cache import Cache, cached_property, parameter
import itertools
from collections import OrderedDict
from six import string_types
import xarray as xr
from . import indexing, tools
def is_array_like(d, shape):
return not np.isscalar(d) and np.shape(d) == shape
def is_square(d):
... | nickhand/pyRSD | pyRSD/rsdfit/data/covariance_matrix.py | Python | gpl-3.0 | 61,229 | [
"Gaussian"
] | 33118582aa63ff4d5b34d17f23ab6c469fed35bbfe6813e0dbaa553228ddf0d0 |
from django.contrib import admin
from .models import Visit, RANGES
class RangeFilter(admin.SimpleListFilter):
title = 'Range'
parameter_name = 'range'
def lookups(self, request, model_admin):
return enumerate(RANGES)
def queryset(self, request, queryset):
if self.value() or self.valu... | joedborg/fusilier | register/admin.py | Python | agpl-3.0 | 521 | [
"VisIt"
] | dd4d9d9207c263e5bf95e2481c25f1638aa95035838dbd74c7575309126bd05d |
import controller
import wx
import dataStructures.user_data
import os, sys, random, traceback
from gui.error_window import ErrorHandler
# reroute the user config file
dataStructures.user_data.configFile = dataStructures.user_data.apdir + "\\testuser.pyTray"
# setup paths
files = os.path.abspath(os.path.dirname(os.p... | tschalch/pyTray | src/test/unittest.py | Python | bsd-3-clause | 13,869 | [
"CRYSTAL"
] | 009deea6e22ee7f452cec6b7985884b48b3492fa28ec8b6afdcb762e566ee44f |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/ci/__init__.py | Python | apache-2.0 | 2,505 | [
"PySCF"
] | 1ea36c530bbc6e547008d8f9dc1ca5b19cded7a5edf8a5ddd6611609716cbb24 |
""" This is the StorageElement class.
"""
# # custom duty
import copy
import datetime
import errno
import os
import re
import sys
import threading
import time
from functools import reduce
# # from DIRAC
from DIRAC import gLogger, gConfig, siteName
from DIRAC.Core.Utilities import DErrno
from DIRAC.Core.Utilities.F... | petricm/DIRAC | Resources/Storage/StorageElement.py | Python | gpl-3.0 | 50,757 | [
"DIRAC"
] | 03aaca295e11dd2bb702b8531cafbfa7b65436e9e5e63bb47b7ea19c2ac3fd3d |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/e2-openwbif | plugin/controllers/views/mobile/control.py | Python | gpl-2.0 | 10,644 | [
"VisIt"
] | b7ee634ecd6a6c2db641ab23d368ca61a4c515e02b7bf48297f33dec7e72364c |
import errno
import json
import logging
import os
import shutil
import string
from collections import namedtuple
from tempfile import NamedTemporaryFile
from urllib.request import Request, urlopen
from urllib.error import HTTPError, URLError
from uuid import uuid4
import paramiko
from dateutil import parser
from djang... | hydroshare/hydroshare | hs_core/views/utils.py | Python | bsd-3-clause | 64,206 | [
"NetCDF"
] | b2ee349b888a9fa52e6f52c6f7399aa01f208f34859af2740481a44f19ce5235 |
#-----------------------------------------------------------------
# pycparser: c_lexer.py
#
# CLexer class: lexer for the C language
#
# Copyright (C) 2008-2011, Eli Bendersky
# License: BSD
#-----------------------------------------------------------------
import re
import sys
import ply.lex
from ply.lex import TOK... | kk1987/pycparser | pycparser/c_lexer.py | Python | bsd-3-clause | 12,545 | [
"NAMD"
] | acc08b94b95dab09d50b622af0cbb46cdd4df9890416785256ec4f5da8d2516f |
# INPUT FILE for adco_transect_preprocessor
# Set options in this file in order to use process adcp transects using the
# For further information on setting these options, the ADCP Python Documentation
#
# IMPORTANT: This options file is uses Python 2.X code convenctions, meaning:
# 1) there may not be any tab chara... | esatel/ADCPy | adcpy/trn_pre_input_GEO20090106.py | Python | mit | 5,440 | [
"NetCDF"
] | bb56c26eeef398314754bcd84be8585f6efc9800d6a90f014c4d8d592242c37f |
########################################################################
# File : ProcessMonitor.py
# Author : Stuart Paterson
########################################################################
""" The Process Monitor utility allows to calculate cumulative CPU time and memory
for a given PID and it's proce... | Andrew-McNab-UK/DIRAC | Core/Utilities/ProcessMonitor.py | Python | gpl-3.0 | 18,446 | [
"DIRAC"
] | ffe59d83f809915c4438f423e3468d07b1ce44ac36a05583d9b64dfae6c3a618 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
ANSIBLE_METADATA = {'metadata_version': '1.1',
'status': ['preview'],
'supported_by': 'community'}
DOCUMENTATION = r'''
---
module: win_linein... | bregman-arie/ansible | lib/ansible/modules/windows/win_lineinfile.py | Python | gpl-3.0 | 6,640 | [
"Brian"
] | c12f817171dfb6b4fa404e7c5b278892d257dada8253d3b2acc6768ed7ba512c |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
__author__ = 'Michael Liao'
'''
Build release package.
'''
import os, re
from datetime import datetime
from fabric.api import *
# linux user:
env.user = 'root'
# linux hosts:
# env.hosts = ['www.liaoxuefeng.com', 'www.liaoxuefeng.com:23']
# linux mysql user and passw... | AnXi-TieGuanYin-Tea/itranswarp.js | fabfile.py | Python | apache-2.0 | 5,750 | [
"GULP"
] | 953a76c95491321a4f084f80bb78b20b6e819e3afe8cfda9ae99ac442464c76c |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# This file is part of Radicale Server - Calendar Server
# Copyright © 2009-2013 Guillaume Ayoub
#
# This library 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, eit... | bouttier/Radicale | setup.py | Python | gpl-3.0 | 3,060 | [
"VisIt"
] | 81cfc3be0c815b85c35c05390edce4cb99b8f9361dd262ee4b78b65dc1cf6bf9 |
"""Module that can start 3Di-specific tasks."""
from __future__ import division
from osgeo import gdal
import math
import os
import shutil
import tempfile
from flooding_lib.tools.importtool.models import InputField
from flooding_lib.models import Result, ResultType, Scenario
from flooding_lib.util.files import tempo... | lizardsystem/flooding-lib | flooding_lib/tasks/process_imported_3di_scenario.py | Python | gpl-3.0 | 5,394 | [
"NetCDF"
] | b9d883bc90922f62975830275c15846da6b78c2ec139ea14927f5585030b6c9e |
""" DIRAC FileCatalog component representing a simple directory tree
"""
import os
from DIRAC import S_OK, S_ERROR
from DIRAC.DataManagementSystem.DB.FileCatalogComponents.DirectoryManager.DirectoryTreeBase import DirectoryTreeBase
class DirectorySimpleTree(DirectoryTreeBase):
"""Class managing Directory Tree as... | DIRACGrid/DIRAC | src/DIRAC/DataManagementSystem/DB/FileCatalogComponents/DirectoryManager/DirectorySimpleTree.py | Python | gpl-3.0 | 4,620 | [
"DIRAC"
] | 9ccc097ef92523db65c278f100cf7edbc17b18bb7efea7d9effe904ef9fd68de |
"""Linear advection (i.e. translation) in 1D.
Optimal solution provided by Kalman filter (ExtKF).
System is typically used with a relatively large size (Nx=1000),
but initialized with a moderate wavenumber (k),
which a DA method should hopefully be able to exploit.
The system (and the impact on the DA) can also be ad... | nansencenter/DAPPER | dapper/mods/LA/__init__.py | Python | mit | 4,265 | [
"Gaussian"
] | 4ed9bb22e40b00f40281b3728743973a05df6b71d07c895fc97390be917fe9ff |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | jensreeder/scikit-bio | skbio/stats/distance/tests/test_base.py | Python | bsd-3-clause | 23,515 | [
"scikit-bio"
] | bd9397512b656b800cf83857a80856dbd847708a5c87f88f4fb00824cce9b916 |
#!/usr/bin/env python
# vim: tabstop=8 expandtab shiftwidth=4 softtabstop=4
import sys
import subprocess
import os
import random
from src.dependency_checker import check_dependencies
from src.fasta_reader import FastaReader
from src.gff_reader import GFFReader
from src.boulder_io_formatter import BoulderIOFormatter
fr... | genomeannotation/capn_primer | capn_primer.py | Python | mit | 9,357 | [
"BLAST"
] | 762f15e34356978266f1275620e968aee1362ec13539661410d9f4ad931a7efc |
from __future__ import absolute_import
from __future__ import division
import tensorflow as tf
import numpy as np
from six.moves import range
from datetime import datetime
def zero_nil_slot(t, name=None):
"""
Overwrites the nil_slot (first row) of the input Tensor with zeros.
The nil_slot is a dummy slo... | Amber819/chatbot_AM | memn2n/memn2n_dialog.py | Python | mit | 9,508 | [
"Gaussian"
] | 7b75fe3367d152b7de6d3e2a7e0a94834fd90447710c5764d0743bcbe7e7b980 |
"""
This stores the basic class and function dependencies of the
apmapflow module.
#
Written By: Matthew Stadelman
Date Written: 2016/02/26
Last Modifed: 2017/03/03
#
"""
#
########################################################################
#
import logging
import os
import re
import subprocess
import scipy as sp
... | stadelmanma/netl-ap-map-flow | apmapflow/ap_map_flow.py | Python | gpl-3.0 | 22,414 | [
"ParaView",
"VTK"
] | b54053d44d798c8189e1fe37fb8193ee49d933d5cd040653b6665fbf6f54f05e |
###############################################################################
# Caleydo - Visualization for Molecular Biology - http://caleydo.org
# Copyright (c) The Caleydo Team. All rights reserved.
# Licensed under the new BSD license, available at http://caleydo.org/license
######################################... | Caleydo/caleydo_server | phovea_server/mainapp.py | Python | bsd-3-clause | 5,232 | [
"VisIt"
] | fef378376b5723d205bf53016f184eebbab7ef7eb491c9b1622a80f7ffd3dbee |
#
# 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.
#
import unittest
from rdki... | bp-kelley/rdkit | rdkit/Chem/Pharm3D/UnitTestExcludedVolume.py | Python | bsd-3-clause | 1,156 | [
"RDKit"
] | 6c58c113c58782693f4029b224d5e478bcd444e29ab566a2d4cf629ca6788e2b |
# Copyright 2019 DeepMind Technologies Limited
#
# 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 agr... | deepmind/open_spiel | open_spiel/python/algorithms/policy_gradient.py | Python | apache-2.0 | 21,924 | [
"Gaussian"
] | 6e365c2426301e4bd632b9ff98b7f5557bbb47ebaab580bd8a5dc38b53e2de9c |
from ase.atoms import string2symbols
abinitio_energies = {
'CO_gas': -626.611970497,
'H2_gas': -32.9625308725,
'CH4_gas': -231.60983421,
'H2O_gas': -496.411394229,
'CO_111': -115390.445596,
'C_111': -114926.212205,
'O_111': -115225.106527,
'H_111': -1... | rybrogaard/catmap | tutorials/1-generating_input_file/generate_input.py | Python | gpl-3.0 | 5,099 | [
"ASE"
] | b5189818f5fd6de6fd8158be6405a359cba3a5f18ea82e0618e2f9ed5bda13a7 |
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