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# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | alejob/mdanalysis | testsuite/MDAnalysisTests/analysis/test_contacts.py | Python | gpl-2.0 | 14,483 | [
"MDAnalysis"
] | f60a7d1b576ff2e9fc510f76aa253be7a8bc2c8c7c9f184e16807872a71cde0b |
# 2-electron VMC code for 2dim quantum dot with importance sampling
# Using gaussian rng for new positions and Metropolis- Hastings
# Added energy minimization
# Common imports
from math import exp, sqrt
from random import random, seed, normalvariate
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits... | CompPhysics/ComputationalPhysics2 | doc/src/MCsummary/src/qdoteminim.py | Python | cc0-1.0 | 5,916 | [
"Gaussian"
] | bccdb1ddbcabcd778f43adf4fdd17126fe42d6f4f1963d3735f1543139d81c76 |
#===============================================================================
# LICENSE XOT-Framework - CC BY-NC-ND
#===============================================================================
# This work is licenced under the Creative Commons
# Attribution-Non-Commercial-No Derivative Works 3.0 Unported Lic... | SMALLplayer/smallplayer-image-creator | storage/.xbmc/addons/net.rieter.xot.smallplayer/resources/libs/progwindow.py | Python | gpl-2.0 | 27,145 | [
"VisIt"
] | 56cd71ae87976575c579dd768751366c34df9d38ce8f90cae0de135bc427e86d |
"""
menu.py
Class instance used to create menu for ARTview app.
"""
import numpy as np
import pyart
import os
import sys
from ..core import Variable, Component, common, QtGui, QtCore, componentsList
class Menu(Component):
'''Class to display the MainMenu.'''
Vradar = None #: see :ref:`shared_variable`
... | jjhelmus/artview | artview/components/menu.py | Python | bsd-3-clause | 23,563 | [
"NetCDF"
] | b807ad3dbcdabfec7175543e8c338174f0d84de08a21bbe13c131740b5e52bc0 |
# For this assignment you are asked to fit classification models to data from the Bank Marketing Study
# Focus is on Logistic Regression and Naive Bayes
# Set seed value for random number generators to obtain reproducible results
RANDOM_SEED = 85
# import packages
import numpy as np
import pandas as pd
from sklearn.l... | sgranitz/nw | predict422/naive-bayes_logistic-regression.py | Python | mit | 8,238 | [
"Gaussian"
] | 33af756104b59f7f8520be54c4130183fbbbb81c6a95668b2211b1497393712b |
import os.path as op
import pytest
import mne
from mne.datasets import testing
from mne.io.pick import pick_channels_cov
from mne.utils import (check_random_state, _check_fname, check_fname,
_check_subject, requires_mayavi, traits_test,
_check_mayavi_version, _check_info_i... | adykstra/mne-python | mne/utils/tests/test_check.py | Python | bsd-3-clause | 5,145 | [
"Mayavi"
] | 5e46ffa0963d6c1f611ec94b432069f28074fc7727a84067b805a75c93d8084f |
#!/usr/bin/env python
import math, numpy as np
#from enthought.mayavi import mlab
import matplotlib.pyplot as pp
import matplotlib.cm as cm
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import rospy
import tf
#import hrl_lib.mayavi2_util as mu
import hrl_lib.viz as hv
import... | tapomayukh/projects_in_python | sandbox_tapo/src/skin_related/Cody_Data/point_tracker.py | Python | mit | 4,448 | [
"Mayavi"
] | 8a49055e3c6fdd25408ce070054ae4d1a97252b652aa2741d4e0929d8d1ab1af |
# Hidden Markov Models
#
# Author: Ron Weiss <ronweiss@gmail.com>
# and Shiqiao Du <lucidfrontier.45@gmail.com>
# API changes: Jaques Grobler <jaquesgrobler@gmail.com>
"""
The :mod:`sklearn.hmm` module implements hidden Markov models.
**Warning:** :mod:`sklearn.hmm` is orphaned, undocumented and has known
numerical s... | mrshu/scikit-learn | sklearn/hmm.py | Python | bsd-3-clause | 46,104 | [
"Gaussian"
] | 70e957ae654d0c18a2d35d4ae39d83649a64a4d8700509a2cd9957576c2a31b0 |
import logging
import threading
import time
import re
from collections import defaultdict
from typing import Optional, Union
import pytz
from doctor_schedule.models import ScheduleResource
from laboratory.settings import SYSTEM_AS_VI, SOME_LINKS, DISABLED_FORMS, DISABLED_STATISTIC_CATEGORIES, DISABLED_STATISTIC_REPOR... | moodpulse/l2 | api/views.py | Python | mit | 90,702 | [
"VisIt"
] | 098de92b0ec2d7b5ef302701da59263a282372235e9c80535e2b2d7c51722af8 |
#!/usr/bin/env python3
import unittest
import sys
import os
from raw_data_parsers.play_by_play.general import row_type, get_kicking_offense
class TestPlayByPlay(unittest.TestCase):
def __set_kicking_consts(self):
"""Set play stings to be used by the kicking tests."""
# Turnovers
self.ki... | chizarlicious/Football-Data-Converter | code/tests/play_by_play/test_general.py | Python | gpl-3.0 | 4,105 | [
"MOE"
] | 2e709db29ededf4fb0e1cd5dfff6fd3226e71c585c93a2d01f9335db2cad8af7 |
"""
Unit tests for the `ambient` module of ``TAMOC``
Provides testing of all of the functions, classes and methods in the `ambient`
module. These tests rely on data stored in the ``./data`` folder and will
write data to and read data from the ``./test/output`` folder.
"""
# S. Socolofsky, July 2013, Texas A&M Univers... | socolofs/tamoc | tamoc/test/test_ambient.py | Python | mit | 29,724 | [
"NetCDF"
] | bfa2dba33a097d0f9ef96b4cbdb6c2fcc5cebfb071205e9093889cfc7c046e83 |
"""Module for easy compartmental implementation of a BRIAN2 network.
Build parts of a network via subclassing :class:`~pypet.brian2.network.NetworkComponent` and
:class:`~pypet.brian2.network.NetworkAnalyser` for recording and statistical analysis.
Specify a :class:`~pypet.brian2.network.NetworkRunner` (subclassing o... | SmokinCaterpillar/pypet | pypet/brian2/network.py | Python | bsd-3-clause | 28,901 | [
"Brian",
"NEURON"
] | 6a9c44cab43245ce31624e9d7726ab1d4f738f27329ad1c1f752f9758b8cc986 |
# -*- coding: utf-8 -*-
# Copyright 2012 splinter authors. All rights reserved.
# Use of this source code is governed by a BSD-style
# license that can be found in the LICENSE file.
from __future__ import unicode_literals
import mimetypes
import re
import time
import warnings
import lxml.html
from lxml.cssselect im... | cobrateam/splinter | splinter/driver/zopetestbrowser.py | Python | bsd-3-clause | 14,435 | [
"VisIt"
] | b846da6d226d88684ad6e21d94df4ae321a32fa1753084074e3640165acac951 |
#!/usr/bin/env python
#simple calculcation done for Stellaris key contest among friends
#optimistic_const was question about number from 1 to 5
#quiz score from 0-100 here https://www.space.com/17791-milky-way-galaxy-quiz-trivia.html
#bad_luck was question about number from 1 to 1000
#also on https://repl.it/I59h/2 so ... | Pulecz/simple-games | calculate_quiz.py | Python | gpl-3.0 | 2,139 | [
"Galaxy"
] | 8f14e04ab7acf00b3a14cf09ae5ed94045e7bf9fcacb8b92ea603cd14c2ab71c |
#!/usr/bin/env python
"""
tidal_energy.py
State Estimation and Analysis for PYthon
Module to compute tidal energy from a column of data.
Written by Brian Powell on 03/30/16
Copyright (c)2017 University of Hawaii under the MIT-License.
Notes
-----
Barotropic to Baroclinic conversion is given by:
.. math::
C=1... | ocefpaf/seapy | seapy/tidal_energy.py | Python | mit | 9,529 | [
"Brian"
] | c66ba5358b0c0c53434046ff6e08ac9d2f6028db2f7cf4461337552701c798b8 |
"""
SALTS XBMC Addon
Copyright (C) 2014 tknorris
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.
T... | JamesLinEngineer/RKMC | addons/plugin.video.salts/scrapers/rlssource_scraper.py | Python | gpl-2.0 | 3,523 | [
"ADF"
] | d14fe3d97760a89d5ad822885d99f33a26cacb893fb28d6d86726bf9248dc76c |
'''
Created on Jun 16, 2016
@author: Jose Pedro Matos
'''
import datetime as dt
import numpy as np
import matplotlib.pyplot as plt
import os
import warnings
import ntpath
import tempfile
import gzip
import shutil
import sys
import re
import geojson
import json
import struct
from urllib import request
from multiproces... | JosePedroMatos/Tethys | timeSeries/satelliteData.py | Python | mit | 51,779 | [
"NetCDF"
] | 901edc44b9295976d68cfe786d1b2bb44297c07e2b09960b3d779ca6e5de7ce8 |
"""
Loadable subclass
"""
# This file is part of Munin.
# Munin 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 later version.
# Munin is distribut... | munin/munin | munin/mod/cost.py | Python | gpl-2.0 | 3,309 | [
"CRYSTAL"
] | 5ccd0f88a8be06aebe06312bbe487bbee14165009a3dd4d94927799fc5c4c8be |
from __future__ import absolute_import, division, print_function
from itertools import chain
from .utils_test import add, inc # noqa: F401
def ishashable(x):
""" Is x hashable?
Examples
--------
>>> ishashable(1)
True
>>> ishashable([1])
False
"""
try:
hash(x)
... | jeffery-do/Vizdoombot | doom/lib/python3.5/site-packages/dask/core.py | Python | mit | 11,612 | [
"VisIt"
] | f48b2fa1fc437cb9a9ae527bc5b2241dc41a24e93552e44277a883e1c4f7fc5a |
#
# Author: Henrique Pereira Coutada Miranda
# Run a IP calculation using yambo
#
from __future__ import print_function
import sys
from yambopy import *
from qepy import *
import argparse
from schedulerpy import *
import matplotlib.pyplot as plt
#parse options
parser = argparse.ArgumentParser(description='Test the yam... | alexmoratalla/yambopy | tutorial/bn/ip_bn.py | Python | bsd-3-clause | 3,433 | [
"Yambo"
] | ae12322553ad114ecd87e00a79a376ef8fe420ce99af26171ade4253946d7e27 |
# -*- coding: utf-8 -*-
"""
Created on 2 Jul 2019
@author: Thera Pals & Éric Piel
Copyright © 2019-2021 Thera Pals, 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 So... | delmic/odemis | src/odemis/driver/focustracker.py | Python | gpl-2.0 | 16,925 | [
"Gaussian"
] | f8f20439dfc09243b528b9f23489d49c93cd82ef02c370b867bb38e0b3ad371b |
# Copyright 2003-2008 by Leighton Pritchard. 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.
#
# Contact: Leighton Pritchard, Scottish Crop Research Institute,
# ... | bryback/quickseq | genescript/Bio/Graphics/GenomeDiagram/_Feature.py | Python | mit | 9,482 | [
"Biopython"
] | e4ed86e0008b30d3127938d000a165d1307f622bafd6e7480efd5895d59ff75d |
import random
from datetime import date, time, timedelta
from decimal import Decimal
from unittest import skipUnless
from django.conf import settings
from django.db.models import F, Func, Value
from django.db.models.functions import Concat
from django.test import TestCase
from django.utils import timezone
from djang... | aykut/django-bulk-update | tests/tests.py | Python | mit | 32,938 | [
"CRYSTAL"
] | 0236a3f180cc5ecd68687ba2fc17b0321a36ca77627c617fefe23db513d3104f |
#######################################################################
# Tests for IlluminaData.py module
#######################################################################
from bcftbx.IlluminaData import *
import bcftbx.utils
import unittest
import cStringIO
import tempfile
import shutil
class MockIlluminaData:... | fw1121/genomics | bcftbx/test/test_IlluminaData.py | Python | artistic-2.0 | 57,652 | [
"Galaxy"
] | cf4533ec0e52c44836e61b0832650abbfcf1d21c804fc78bf8454b20758e8e1e |
"""Sample aospy object library using the included example data."""
from datetime import datetime
import os
import aospy
from aospy import Model, Proj, Region, Run, Var
from aospy.data_loader import DictDataLoader
from aospy.internal_names import LAND_MASK_STR, LON_STR
rootdir = os.path.join(aospy.__path__[0], 'test'... | spencerkclark/aospy | aospy/examples/example_obj_lib.py | Python | apache-2.0 | 3,244 | [
"NetCDF"
] | 7656c8f878d5097268814224a9b9c159b94cd2eea523278b41649ed08e99c0a3 |
import os
voldir = "/projects/mindboggle/data/sulci_volumes/"
surfdir = "/Applications/freesurfer/subjects/Brainvisa62/"
files = os.listdir(surfdir)
for f in files:
for hemi in ['lh','rh']:
if hemi == 'lh':
hemicap = 'L'
else:
hemicap = 'R'
vol = voldir+hemicap+'B... | binarybottle/mindboggle_sidelined | run_label_vol2surf.py | Python | apache-2.0 | 607 | [
"VTK"
] | 18a79da77e88df6412669565bf57d8b63d2400aceb8765344b203c8a4406f213 |
"""
Tests related to the cohorting feature.
"""
from uuid import uuid4
from .helpers import BaseDiscussionMixin
from .helpers import CohortTestMixin
from ..helpers import UniqueCourseTest
from ...pages.lms.auto_auth import AutoAuthPage
from ...fixtures.course import (CourseFixture, XBlockFixtureDesc)
from ...pages.lm... | jruiperezv/ANALYSE | common/test/acceptance/tests/discussion/test_cohorts.py | Python | agpl-3.0 | 5,708 | [
"VisIt"
] | 577914c3d51f46b0c2c99ae2519d73d75678f78213a8d5eda7ecbd4e136fceda |
# $Id: nodes.py 6351 2010-07-03 14:19:09Z gbrandl $
# Author: David Goodger <goodger@python.org>
# Copyright: This module has been placed in the public domain.
"""
Docutils document tree element class library.
Classes in CamelCase are abstract base classes or auxiliary classes. The one
exception is `Text`, for a text... | akiokio/centralfitestoque | src/.pycharm_helpers/docutils/nodes.py | Python | bsd-2-clause | 64,876 | [
"VisIt"
] | dad2253736a10d4bda25d80e251b6fc99802b1c6f2a66d32250a36d377d37a8a |
from django.test import TestCase
from restclients.upass import get_upass_url, get_upass_status
from restclients.models.upass import UPassStatus
from restclients.exceptions import DataFailureException
from restclients.test import fdao_upass_override
@fdao_upass_override
class UPassTest(TestCase):
def test_javerage... | uw-it-aca/uw-restclients | restclients/test/upass.py | Python | apache-2.0 | 3,953 | [
"ORCA"
] | 0821fe0b06179379df018a760144bc77a8671315fa430403e6ac54df90285077 |
# Zeobuilder is an extensible GUI-toolkit for molecular model construction.
# Copyright (C) 2007 - 2009 Toon Verstraelen <Toon.Verstraelen@UGent.be>, Center
# for Molecular Modeling (CMM), Ghent University, Ghent, Belgium; all rights
# reserved unless otherwise stated.
#
# This file is part of Zeobuilder.
#
# Zeobuilde... | woutersmet/Zeosummer | share/plugins/molecular/g03zmat.py | Python | gpl-3.0 | 5,998 | [
"Gaussian"
] | f66e49628301dec9136dfc4f36775c253d8d5e7483f640f82ed9e172adf72f19 |
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Matti Hämäläinen <msh@nmr.mgh.harvard.edu>
# Denis Engemann <denis.engemann@gmail.com>
# Andrew Dykstra <andrew.r.dykstra@gmail.com>
# Teon Brooks <teon.brooks@gmail.com>
# Daniel McCloy <dan.mccloy@gmail.com>
#
#... | olafhauk/mne-python | mne/channels/channels.py | Python | bsd-3-clause | 66,166 | [
"Mayavi"
] | 3d7119239190df92ee0602f0785ab37b6bd1b46bb5b901d0ad1dbfbcc3c9653b |
# $Id$
#
# Copyright (C) 2005-2006 Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
from __future__ import print_function
... | soerendip42/rdkit | rdkit/Chem/ChemUtils/BulkTester.py | Python | bsd-3-clause | 1,982 | [
"RDKit"
] | 82225f1b201aeb6769a267df23ebb3c79cce1528d0e327a374fe9650ff39a603 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from Foundation import objc
from Foundation import NSBundle
from AppKit import NSImage
haskellBundleIdentifier = 'org.purl.net.mkhl.haskell'
def iconForName(name):
"""Return the NSImage instance representing a `name` item."""
bundle = NSBundle.bundleWithIdentifie... | mkhl/haskell.sugar | src/Itemizers.py | Python | mit | 1,446 | [
"ESPResSo"
] | ed8c3de4ae89e5a09a4d9331daa8e53d1fd36b3eca08a1803ef7e415faa52ef3 |
# Hidden Markov Model Implementation
import pylab as pyl
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy as scp
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import rospy
#import hrl_lib.mayavi2_util as mu
import hrl_lib.viz ... | tapomayukh/projects_in_python | classification/Classification_with_HMM/Single_Contact_Classification/force_codes/resolution/hmm_crossvalidation_force_6.py | Python | mit | 16,210 | [
"Gaussian",
"Mayavi"
] | e8d8fb54e57372a4dbcabf4a5f709d4f92711885cf6344356d2d991f77b4fa52 |
import sys, shutil
sys.path.insert(1, "../../../")
import h2o
def cars_checkpoint(ip,port):
cars = h2o.upload_file(h2o.locate("smalldata/junit/cars_20mpg.csv"))
predictors = ["displacement","power","weight","acceleration","year"]
response_col = "economy"
distribution = "gaussian"
# build first mo... | weaver-viii/h2o-3 | h2o-py/tests/testdir_algos/gbm/pyunit_NOPASS_error_checkpointGBM.py | Python | apache-2.0 | 2,486 | [
"Gaussian"
] | a548b778eb09b08fe0690fbec41e5aa0c287212dcaa9ab9b2bf0d6e6fa2e8fc1 |
#!/usr/bin/env python
# pmx Copyright Notice
# ============================
#
# The pmx source code is copyrighted, but you can freely use and
# copy it as long as you don't change or remove any of the copyright
# notices.
#
# ----------------------------------------------------------------------
# pmx is Copyright (C... | tectronics/pmx | scripts/analyze_crooks.py | Python | lgpl-3.0 | 24,517 | [
"Gaussian"
] | d2f70efd7f82db889638c4ef888e49bdaaf851e8945154d6ccb2dbaa2d0b984a |
"""
This module gathers tree-based methods, including decision, regression and
randomized trees. Single and multi-output problems are both handled.
"""
# Authors: Gilles Louppe <g.louppe@gmail.com>
# Peter Prettenhofer <peter.prettenhofer@gmail.com>
# Brian Holt <bdholt1@gmail.com>
# Noel Da... | imaculate/scikit-learn | sklearn/tree/tree.py | Python | bsd-3-clause | 40,425 | [
"Brian"
] | 3be9abe35888aeba0a73543d606e36d249e5553c2a829de41fae578c9b66cc90 |
import json
import time
import requests
mappings = requests.get('http://firefly.ukcod.org.uk/~mark/ynr-post-mapping.json').json()
post_id_lookup = {m['old']: m['new'] for m in mappings}
mapit_ids = requests.get('https://mapit.mysociety.org/areas/WMC').json().keys()
locations = {}
for mapit_id in mapit_ids:
time... | andylolz/ge2015-results-bot | gen_locations.py | Python | mit | 619 | [
"Firefly"
] | 028eba7800f4409c25173bf91ce51009f4c55f54119a00831761e8082de54def |
# Copyright 2013-2021 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)
"""Tests Spack's ability to parse the name and version of a package
based on its URL.
"""
import os
import pytest
from ... | LLNL/spack | lib/spack/spack/test/url_parse.py | Python | lgpl-2.1 | 26,545 | [
"BLAST",
"Gromacs",
"HOOMD-blue",
"Jmol",
"Octopus",
"OpenKIM",
"VTK",
"VisIt"
] | c59d6d03055f74c38ea95b2233953e5650de99c053832025c565e18a60e7de37 |
"""
Tests for Django views.
"""
from django.contrib.auth.models import User
from django.core.urlresolvers import reverse
from django.test import Client
from django.test import TestCase
from main.models import AlignmentGroup
from main.models import Chromosome
from main.models import Project
from main.models import Ref... | woodymit/millstone_accidental_source | genome_designer/main/tests/test_views.py | Python | mit | 6,929 | [
"BWA"
] | e17be15d34859f79899c627e52edfb22bcba5f09493f91a0abc9a99f78b7e463 |
import pysam
samfile = pysam.Samfile( "test.sam", "r" )
for alignedread in samfile.fetch('2L', 100, 120):
print alignedread
samfile.close()
| humberto-ortiz/dmel-ercc | samtest.py | Python | gpl-3.0 | 147 | [
"pysam"
] | e285ad93e2f10732daff14eb68d8421c0c4e3356a30088c4439694488f584eb1 |
# coding=utf-8
# Copyright 2022 The ML Fairness Gym 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 applicab... | google/ml-fairness-gym | distributions_test.py | Python | apache-2.0 | 2,755 | [
"Gaussian"
] | 738d7eea295229bb593e167d0415589b83a7cdad23dccb664fb8987f93be1b33 |
"""\
fermi_dirac.py: Utilities for finite temperature Fermi-Dirac occupations.
This program is part of the PyQuante quantum chemistry program suite.
Copyright (c) 2004, Richard P. Muller. All Rights Reserved.
PyQuante version 1.2 and later is covered by the modified BSD
license. Please see the file LICENSE tha... | berquist/PyQuante | PyQuante/fermi_dirac.py | Python | bsd-3-clause | 3,757 | [
"DIRAC"
] | d61d8bbab8c29162942c404633ad7b32b416cd9165425d7fe5b3cad8e07ff3e6 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the courseware unit bookmarks.
"""
import json
import requests
from ...pages.studio.auto_auth import AutoAuthPage as StudioAutoAuthPage
from ...pages.lms.auto_auth import AutoAuthPage as LmsAutoAuthPage
from ...pages.lms.bookmarks import BookmarksPage
from ...pages.lms.c... | IndonesiaX/edx-platform | common/test/acceptance/tests/lms/test_bookmarks.py | Python | agpl-3.0 | 23,679 | [
"VisIt"
] | fa4a5978aa8456781bcfa780cad69732d91a8b7b0e8fc2ec57753291bc54e69d |
"""
The following contains a database of small molecules
Data for the G2/97 database are from
Raghavachari, Redfern, and Pople, J. Chem. Phys. Vol. 106, 1063 (1997).
See http://www.cse.anl.gov/Catalysis_and_Energy_Conversion/Computational_Thermochemistry.shtml for the original files.
All numbers are experimental valu... | grhawk/ASE | tools/ase/data/g2.py | Python | gpl-2.0 | 1,764 | [
"ASE"
] | a3e6d415fb7d99f242bb9f24dfd02ad74dd8a89e29fe31a2721bbc9130f1eaca |
# Author: Yang Long <longyang_123@yeah.net>
#
# License: LGPL-2.1
import numpy as np
import time
from .Constraint import Constraints
from .MultiCandidate import MultiCandidates
from . import MultiUtils
class MultiGA:
'''
NSGA-II
'''
def __init__(self,func,targetsize,nvars,LB=None,UB=None,IntCon=None... | longyangking/Husky | Husky/GA/MultiGA.py | Python | lgpl-2.1 | 15,032 | [
"Gaussian"
] | a2c5c202e676591df07d87ba85c278a71f60aed3f73dd20e8099aad514d06caf |
"""
@name: Modules/Core/Config/import_tools.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com>
@copyright: (c) 2019-2019 by D. Brian Kimmel
@license: MIT License
@note: Created on Oct 19, 2019
@Summary: This handles
"""
__updated__ = '2020-01-06'
__version_info__ = (19, 11, 28)
__versio... | DBrianKimmel/PyHouse | Project/src/Modules/Core/Config/import_tools.py | Python | mit | 2,581 | [
"Brian"
] | 08d0943482945ab1ca7042e7aae7611ce4049336b3f6f441f111204f19b775be |
#
# 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... | lukecwik/incubator-beam | sdks/python/apache_beam/runners/interactive/pipeline_instrument_test.py | Python | apache-2.0 | 35,015 | [
"VisIt"
] | 58a461ed072456d357b3231d8b7a0ed9e1d0c6064157e570a15ba0a6de44585b |
# coding: utf-8
# Copyright (c) Materials Virtual Lab
# Distributed under the terms of the BSD License.
import numpy as np
class Preprocessing(object):
"""
Preprocessing class used for spectrum preprocessing.
"""
def __init__(self, spectrum):
"""
Create an Preprocessing object
... | materialsvirtuallab/veidt | veidt/elsie/preprocessing.py | Python | bsd-3-clause | 5,913 | [
"pymatgen"
] | 003c142ee620c8e747479f8f695afeb171640802b4afa32678d6818328830947 |
from setuptools import setup, find_packages
with open('README.md') as readme_file:
readme = readme_file.read()
exec(open('graftm/version.py').read()) # loads __version__
setup(name='graftm',
version=__version__,
author='Joel Boyd, Ben Woodcroft',
description='GraftM is a pipeline used for ident... | geronimp/graftM | setup.py | Python | gpl-3.0 | 1,093 | [
"Biopython"
] | 75331dadf850f34a5aaa2a2ef7bfdc0aa4c2565a51892c96f4a5981782c1170b |
# this module contains functions for doing complex Gaussian math. Right
# now everything is hard coded for adiabatic/diabatic representation, but
# it shouldn't be hard to modify for DGAS
import cmath
import math
import types
import numpy as np
from pyspawn.fmsobj import fmsobj
from pyspawn.traj import traj
# comp... | blevine37/pySpawn17 | pyspawn/complexgaussian.py | Python | mit | 6,103 | [
"Gaussian"
] | 137e35bc9e42c2b73a638520393d75fe0f0aabfea12d52e9e5b82954d93e086d |
"""
Module to handle gamma matrices expressed as tensor objects.
Examples
========
>>> from sympy.physics.hep.gamma_matrices import GammaMatrix as G, LorentzIndex
>>> from sympy.tensor.tensor import tensor_indices
>>> i = tensor_indices('i', LorentzIndex)
>>> G(i)
GammaMatrix(i)
N... | kaushik94/sympy | sympy/physics/hep/gamma_matrices.py | Python | bsd-3-clause | 24,227 | [
"DIRAC"
] | c07b9914029210452488b4581fb467d23a72db4d6e4247131ee36a0aff602d75 |
#
# -*- coding: utf-8 -*-
#
# Python-Based Truss Solver
# =============================================================
#
# Author: Robert Grandin
#
# Date: Fall 2007 (Creation of original Fortran solution in AerE 361)
# October 2011 (Python implementation)
# November 2014 (Clean-u... | rgrandin/MechanicsTools | truss/truss_solver.py | Python | bsd-3-clause | 22,478 | [
"ParaView",
"VTK"
] | 37c20a8b534a6a3778f5fed949bee30063572d9f9d4f86f89bb5eac1e5a6150d |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
from django.conf import settings
class Migration(migrations.Migration):
dependencies = [
migrations.swappable_dependency(settings.AUTH_USER_MODEL),
('cenet', '0005_auto_20160801_1639'),
]... | Si-elegans/Web-based_GUI_Tools | rtw_ui/migrations/0001_initial.py | Python | apache-2.0 | 1,674 | [
"NEURON"
] | d76c41f1560705b1d9c41595e277f6b57ce47a8278714424477527a1ab4dd4d9 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
<<<<<<< HEAD
from __future__ import division, unicode_literals
"""
Classes for reading/manipulating/writing FEFF files.
http://leonardo.phys.washington.edu/feff/
XANES and EXAFS input files, and the xmu.dat, l... | Bismarrck/pymatgen | pymatgen/io/feff/__init__.py | Python | mit | 44,572 | [
"FEFF",
"pymatgen"
] | 0ba15de29cd944329fd3a4e3bd043ea3f0c923b28be89f7c33070507304f230a |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
This script computes the permanence and the number of switches of a discrete trait on the tree
trunk.
## Example
$ python3 trunktraitevolution.py -i input_tree.tree --input-format nexus --feature location
## Arguments:
#### mandatory arguments:
1. -i INPU... | gattil/phylo-tools | trunktraitevolution.py | Python | mit | 11,842 | [
"VisIt"
] | 7e0c648856aee4798bd8db747dd4a51e226d9ca0f8cd1e75063aa2b30c07feb1 |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
"""
VTKBot is an IRC bot
Copyright (C) 2010 Mathias De Maré
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; version 2
of the License, no other.
This pro... | Mathiasdm/VTKBot | core.py | Python | gpl-2.0 | 13,180 | [
"VTK"
] | 733ae752c693fa661b550396e217ce2a39f0af50ac77376acf22e7e4a248788f |
# verification of the implementation
------------------------------------
# for AGNs
# reproduce the plots from Bongiorno et al. 2010
# writes plots in data/eRoMok/
python reproduce_bongiorno_2010.py
BOX = MD10 or NUGC
#writes a summary file containing all information for each snapshot
#---------------------------
... | JohanComparat/nbody-npt-functions | bin/bin_SMHMr/run_analysis.py | Python | cc0-1.0 | 3,414 | [
"Galaxy"
] | 2377285a8ca4b5ff0bcc5d212becf0d00535ce063382de9920fca115eff087ae |
#!/usr/bin/env python
# encoding: utf-8
import numpy as np
# -------- GLOBAL SCALAR DEFINITIONS --------------
# excitation - initial conditoons
ex_type = 'plane'
alambda = 0.1 # wavelength
t_ex_sig = 1.0*alambda # width in time (pulse only)
x_ex_sig = 1.0*alambda # width in the x-direction (pulse)
toff_ex... | nthakkar/emclaw | deprecated/maxwell_2d_homogeneous/maxwell_interlayer.py | Python | gpl-2.0 | 8,040 | [
"Gaussian"
] | fc12e604f48fdbcd2bac24e9d8d312acf68d939948efc2a64b948c967524fcc3 |
import os, sys
import re
import math
import numpy
from collections import defaultdict
import pysam
from grit.files.reads import RNAseqReads
import multiprocessing
import queue
from grit.lib.multiprocessing_utils import ProcessSafeOPStream, fork_and_wait
import gzip, io
import pickle
DATA_BASE_DIR = os.path.abspat... | nboley/regulatory_network_tools | src/build_labeled_graph.py | Python | gpl-3.0 | 13,124 | [
"pysam"
] | 0142c59235653a92fd4b046465783330cfbeb8a7e4ca45630939965d78f6f248 |
import warnings
import torch
from gpytorch import settings
from gpytorch.distributions import MultitaskMultivariateNormal
from gpytorch.lazy import BlockDiagLazyTensor
from gpytorch.likelihoods import Likelihood
from ..approximate_gp import ApproximateGP
from ..gp import GP
class _DeepGPVariationalStrategy(object)... | jrg365/gpytorch | gpytorch/models/deep_gps/deep_gp.py | Python | mit | 6,446 | [
"Gaussian"
] | ba8209f6ce46f3d5f11f6f4e3eafd1db17474a0e04acb42a1081d7aec093d7a9 |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | ppries/tensorflow | tensorflow/contrib/distributions/python/ops/distribution.py | Python | apache-2.0 | 33,977 | [
"Gaussian"
] | 2dc946d78360d99f6637ab01b600eb55caf49199e2866d9fd9de422153369f64 |
import os
import numpy as np
import MMTK
class Grid:
"""
Class to read and write alchemical grids.
Data is a dictionary with
spacing - the grid spacing, in Angstroms.
counts - the number of points in each dimension.
vals - the values.
All are numpy arrays.
"""
def __init__(self):
pass
def r... | luizcieslak/AlGDock | AlGDock/IO.py | Python | mit | 14,740 | [
"Amber",
"NetCDF",
"VMD"
] | 71a55a40577dc00d55848a0e0907eb49edcc4fe6f0af05cbf5c72107da03c96d |
#!/usr/bin/env python
import vtk
def main():
colors = vtk.vtkNamedColors()
g = vtk.vtkMutableUndirectedGraph()
# Create 3 vertices
v1 = g.AddVertex()
v2 = g.AddVertex()
v3 = g.AddVertex()
# Create a fully connected graph
g.AddEdge(v1, v2)
g.AddEdge(v2, v3)
g.AddEdge(v1... | lorensen/VTKExamples | src/Python/Graphs/LabelVerticesAndEdges.py | Python | apache-2.0 | 1,646 | [
"VTK"
] | a1c73f8b5082e949138c98e8e9670efed182ffd643153fd4c889a48a601f7a82 |
import ast
import itertools
import multiprocessing
def get_imports(fs, root_path, parent_span):
# TODO: consider crawling over the main project files only; ignore
# examples, tests, etc
py_paths = (path for path in fs.walk(root_path) if path.endswith(".py"))
py_srces = fs.batch_open(py_paths, parent_s... | sourcegraph/python-langserver | langserver/imports.py | Python | mit | 2,232 | [
"VisIt"
] | ccdbb44c43420bb2ace8003b7e1b16fda1c451285019753dadb68c77df0ad5e3 |
import numpy
import cPickle
import theano
import theano.tensor as T
from mlp.logistic_sgd import LogisticRegression
from dA.AutoEncoder import AutoEncoder
from SdA import SdA
from numpy.linalg import norm
from theano.tensor.shared_randomstreams import RandomStreams
from extract_datasets import extract_unlabeled_chu... | lzamparo/SdA_reduce | theano_models/SdA/test_pickle_SdA.py | Python | bsd-3-clause | 10,938 | [
"Gaussian"
] | 4da143c4938582a97dfcd6e833c76c773a967fe4f868f88706c8f773bf0d2a55 |
#!/usr/bin/env python3
from olctools.accessoryFunctions.accessoryFunctions import MetadataObject
from genemethods.geneseekr.geneseekr import GeneSeekr
from genemethods.geneseekr.blast import BLAST
import multiprocessing
from glob import glob
from time import time
import os
test_path = os.path.abspath(os.path.dirname(_... | OLC-Bioinformatics/GeneSeekr | tests/test_blastp.py | Python | mit | 7,385 | [
"BLAST"
] | aeeab2b97db2cdc56ae9f8e57271305aa8c47d998e13424857f6049b39afc81e |
# This is the instrument-specific file for the PS5000 series of instruments.
#
# pico-python is Copyright (c) 2013-2014 By:
# Colin O'Flynn <coflynn@newae.com>
# Mark Harfouche <mark.harfouche@gmail.com>
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are pe... | arunpersaud/pico-python | picoscope/ps5000a.py | Python | bsd-2-clause | 23,542 | [
"Gaussian"
] | 95f1a313613770beed4d4bf79feab07660ded6c96fa9bf12038e3c17bae47fb9 |
from netCDF4 import Dataset
import magic
import numpy as np
import pandas as pd
import matplotlib.pylab as plt
import warnings
try:
import gdal
except ModuleNotFoundError:
warnings.warn('gdal not found, this will probably result in prublems (with respect to landuse) further down the road')
def read_file(fnam... | hagne/hysplit-py | hysplit_py/land_use_map.py | Python | gpl-3.0 | 6,848 | [
"NetCDF"
] | 5b711428897475d0e764df4c274fd66fde2904f561a808b52c83e4df9cf93adf |
""" @package antlr3.tree
@brief ANTLR3 runtime package, tree module
This module contains all support classes for AST construction and tree parsers.
"""
# begin[licence]
#
# [The "BSD licence"]
# Copyright (c) 2005-2008 Terence Parr
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or... | avatar29A/pyfuzzy | antlr3/tree.py | Python | mit | 78,283 | [
"VisIt"
] | 033ecb8b87de9d8162c0791bb99d3bde20fe8c64b974f4f8b7760e622031172a |
# Copyright 1999 by Jeffrey Chang. 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.
"""Index.py
This module provides a way to create indexes to text files.
Classes:
Index D... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/Index.py | Python | gpl-2.0 | 4,948 | [
"Biopython"
] | 0422d8ab9a21f7a7bac20f69d9850ebe71376834b92e9ad8753d00d5e6c0ef33 |
#!/usr/bin/python2.6
# -*- coding: utf8 -*-
"""
"""
__author__ = "Jérôme Samson"
__copyright__ = "Copyright 2014, Mikros Image"
import os
import sys
import csv
import datetime
import logging
from logging import handlers
from optparse import OptionParser
try:
import simplejson as json
except ImportError:... | mikrosimage/OpenRenderManagement | src/pulitools/stats/grab_usage_stats.py | Python | bsd-3-clause | 4,543 | [
"Octopus"
] | 2ba62d2d4474d8a7ed5105db6aa7fb966c78a002dbf259b4b07f3a7bffb5b323 |
#! /usr/bin/env python
import sys
from Settings import Settings
from HTML import HTML
import logging
import Tools.web as web
from Assigner import ParserAssigner
import Tools.IO as IO
from Top import Top
#DONE read/write E and gradients from/to .xyz file; make plots if E/dE available
#DONE rearrange geometry optimizat... | mtthwflst/terse | terse.py | Python | mit | 5,906 | [
"Gaussian",
"Jmol",
"cclib"
] | cc7e7456f11db5a1e04efa454e7b4d1f68e6a0dd44cf9f2b56f37b531893eddc |
# -*- coding: utf-8 -*-
#
# Moonstone is platform for processing of medical images (DICOM).
# Copyright (C) 2009-2011 by Neppo Tecnologia da Informação LTDA
# and Aevum Softwares LTDA
#
# This file is part of Moonstone.
#
# Moonstone is free software: you can redistribute it and/or modify
# it under the terms of the GN... | aevum/moonstone | src/moonstone/ilsa/plugins/text/text.py | Python | lgpl-3.0 | 2,543 | [
"VTK"
] | f6376d51460647d98c1d02744ca3632b053207be88033f7ce723c24584c897ad |
# -*- coding: UTF8 -*-
# Este arquivo é parte do programa Enplicaw
# Copyright 2013-2015 Carlo Oliveira <carlo@nce.ufrj.br>,
# `Labase <http://labase.selfip.org/>`__; `GPL <http://is.gd/3Udt>`__.
#
# Enplicaw é um software livre; você pode redistribuí-lo e/ou
# modificá-lo dentro dos termos da Licença Pública Geral GNU... | cetoli/enplicaw | src/enplicaw/enplicaw.py | Python | gpl-2.0 | 15,050 | [
"NEURON"
] | 3d7d9373dc8a2ef10c963c4340266730eb8caca9ad2f0b183977b609a3bc66c6 |
"""
Traits View definition file.
The view trait of the parent class is extracted from the model definition
file. This file can either be exec()ed or imported. See
core/base.py:Base.trait_view() for what is currently used. Using exec()
allows view changes without needing to restart Mayavi, but is slower than
importi... | dmsurti/mayavi | mayavi/core/ui/lut_manager.py | Python | bsd-3-clause | 4,874 | [
"Mayavi"
] | 5877b6742142dba315f820be51c1483178b4a20181a44086009132eb90089ec5 |
from AritVisitor import AritVisitor
from AritParser import AritParser
class UnknownIdentifier(Exception):
pass
class MyAritVisitor(AritVisitor):
def __init__(self):
self._memory = dict() # store id -> values
def visitNumberAtom(self, ctx):
try:
value = int(ctx.getText())
... | lauregonnord/cap-labs | TP03/arith-visitor/MyAritVisitor.py | Python | gpl-3.0 | 1,520 | [
"VisIt"
] | 3e1af03c08bf91718ddfaa72f6f5316ba8be54f125977fc8934dd18e0ab1da69 |
# Author: Suyog Dutt Jain <suyog.jain@aero.iitb.ac.in>
# Prabhu Ramachandran <prabhu_r@users.sf.net>
# Copyright (c) 2008-2015, Enthought, Inc.
# License: BSD Style.
# Standard library imports.
from os.path import abspath
from io import BytesIO
import numpy
import unittest
from numpy import array
# Enthought... | dmsurti/mayavi | mayavi/tests/test_builtin_image.py | Python | bsd-3-clause | 4,187 | [
"Gaussian",
"Mayavi"
] | 2ae96f920c8a68a54c529ef0475d5d6a9ba1e8bb266852fd89e4c2fc4ca7a795 |
# Publisher and subscriber design pattern example.
# More information about this design pattern can be found at:
# http://wiki.wxpython.org/ModelViewController
# http://wiki.wxpython.org/PubSub
from invesalius.pubsub import pub as Publisher
# The maintainer of Pubsub module is Oliver Schoenborn.
# Since the end of 20... | paulojamorim/invesalius3 | docs/devel/example_pubsub.py | Python | gpl-2.0 | 2,140 | [
"VTK"
] | 19fa49816c5edd163ae7b40b6c16e6f5abc3436285ea92fde3b4c3b8c167ad8f |
########################################################################
# File : Watchdog.py
# Author: Stuart Paterson
########################################################################
""" The Watchdog class is used by the Job Wrapper to resolve and monitor
the system resource consumption. The Watchdog... | yujikato/DIRAC | src/DIRAC/WorkloadManagementSystem/JobWrapper/Watchdog.py | Python | gpl-3.0 | 38,791 | [
"DIRAC"
] | c069e947d8e64055fff3c9d22a357284f99858250deb5a0a6c15bbe61428e1d1 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import sys
import itertools
import json
import platform
import re
import warnings
from time import sleep
from monty.json import MontyDecoder, MontyEncoder
from copy import deepcopy
from pymatgen import SETT... | dongsenfo/pymatgen | pymatgen/ext/matproj.py | Python | mit | 55,884 | [
"ABINIT",
"VASP",
"pymatgen"
] | a4cf6aa8e4eb528c6026ed2661f77cf0ee421afec9a40ee04d8cbb7c2dacde63 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | CDSherrill/psi4 | psi4/driver/p4util/p4regex.py | Python | lgpl-3.0 | 1,207 | [
"Psi4"
] | 9291304be731477462987fd776fb9ce4140dc4fd3cc7fbfa6473b18d974d9ae4 |
from grid_exper import *
from plastk.plot import GPlot
from Scientific.IO.NetCDF import NetCDFFile as CDF
for c in exp.conditions:
names = pkl.files_matching('*%s*%s*-episodes.cdf'%(c['agent_name'],c['grid_name']))
files = [CDF(f) for f in names]
c['data'] = [f.variables['length'][:,0] for f in files]
pl... | ronaldahmed/robot-navigation | neural-navigation-with-lstm/MARCO/plastk/examples/grid_exper_analyze.py | Python | mit | 721 | [
"NetCDF"
] | bf3570d40d0c1f3fa6ab443b4c78f9bedbfbabcc8089ae924c657968eb9490ff |
"""
Utility functions for working with bam files.
"""
import os
import shutil
import subprocess
from django.conf import settings
import pysam
import numpy as np
from utils import convert_fasta_to_fastq
BWA_BINARY = os.path.join(settings.TOOLS_DIR, 'bwa/bwa')
def clipping_stats(bam_path, sample_size=1000):
BA... | churchlab/millstone | genome_designer/utils/bam_utils.py | Python | mit | 7,468 | [
"BWA",
"pysam"
] | a7cecc7143bb94c7794bb636819eda3397ad7072a0ddabec4e8e4292372d9fcb |
# import vtk wrapped version that will raise exceptions for error events
import vtkwithexceptions as vtk
import imp
import tempfile
from visomics.vtk.common import LoadInput, SerializeOutput, parse_json
from celery import Celery
from celery import task, current_task
from celery.result import AsyncResult
celery = Cel... | Visomics/Visomics | AnalysisServer/visomics/vtk/python.py | Python | apache-2.0 | 1,183 | [
"VTK"
] | 5ae5fc935eba6ef03536193daad6d9792199bc6bf4a8d1cc528d7dc1e05b4086 |
#!/usr/bin/env python
"""Compile tests."""
from bowtie import App
from bowtie.control import Nouislider
from bowtie.visual import Plotly
from bowtie.tests.utils import reset_uuid
def callback(*_):
"""dummy function"""
# pylint: disable=unused-argument
def test_build(build_reset, monkeypatch):
"""Tests the ... | jwkvam/bowtie | bowtie/tests/test_compile.py | Python | mit | 580 | [
"Bowtie"
] | cfefaa2a671b6bf8f904fc84d12d757eae0e29773c6d7d576188f0748f7d8bfa |
#
# Copyright (c) SAS Institute Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in w... | fedora-conary/conary | conary_test/localtest/errorstest.py | Python | apache-2.0 | 2,422 | [
"VisIt"
] | 7b84433854ca6cce45ed99f8da77c267437609be378d1bb7dcd2368b81da4896 |
#-------------------------------------------------------------------------------
# Copyright (c) 2011 Anton Golubkov.
# All rights reserved. This program and the accompanying materials
# are made available under the terms of the GNU Lesser Public License v2.1
# which accompanies this distribution, and is available at
#... | anton-golubkov/Garland | src/ipf/ipftype/ipfsmoothingtype.py | Python | lgpl-2.1 | 1,155 | [
"Gaussian"
] | 665984de54dd25f72aa460aba945932dd97944f876d5d207b402e9eab0147584 |
# proxy module
from __future__ import absolute_import
from mayavi.filters.tube import *
| enthought/etsproxy | enthought/mayavi/filters/tube.py | Python | bsd-3-clause | 88 | [
"Mayavi"
] | 5539a483e312f97b78dc375dbf4affbe25da44067fe019792fa4b7decd899b3f |
# -*- coding: utf-8 -*-
"""
Acceptance tests for CMS Video Module.
"""
import os
from mock import patch
from nose.plugins.attrib import attr
from unittest import skipIf
from ...pages.studio.auto_auth import AutoAuthPage
from ...pages.studio.overview import CourseOutlinePage
from ...pages.studio.video.video import Vid... | ahmadiga/min_edx | common/test/acceptance/tests/video/test_studio_video_module.py | Python | agpl-3.0 | 11,780 | [
"VisIt"
] | d1e7e0bf8795cb8ba8beedb75e38cb6bfd8e36f3b7829e48b5c985ac424225e9 |
# Copyright 2021, 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 agreed to in writing... | google-research/mint | mint/core/base_model_util.py | Python | apache-2.0 | 8,036 | [
"Gaussian"
] | 51871c993e46a57b75cea2026e41c5b1d595f1c44b71b7722e764487316486e4 |
from vtk import *
from math import *
# -----------------------------------------------------------------------------
# Set of helper functions
# -----------------------------------------------------------------------------
def normalize(vect, tolerance=0.00001):
mag2 = sum(n * n for n in vect)
if abs(mag2 - 1... | keithroe/vtkoptix | Web/Python/vtk/web/camera.py | Python | bsd-3-clause | 8,442 | [
"VTK"
] | 3d148d3d5ab7225290587824c1d1d925bef3f5d3fe5deeb9821154e5ab06d2b2 |
import pysam
import sys
import gzip
import os
import logging
import argparse
import xml.etree.ElementTree as ET
import subprocess
from CountXmlUtils import readCountXmlQueryLocationInFeatures
DEBUG = False
NOT_DEBUG= not DEBUG
if DEBUG:
genomeListFile="/scratch/stein_lab/shengq2/20200226_4233_4263_michelle_smallRNA... | shengqh/ngsperl | lib/SmallRNA/getBacteriaCount.py | Python | apache-2.0 | 4,574 | [
"pysam"
] | 0b474d17aa2e226b72ae319287ec3578014149193935ff7dddcb368b33ae5ca5 |
import logging
import os
import threading
from mako.template import Template
from galaxy import web
from galaxy.util import json
from galaxy.util import rst_to_html
from galaxy.util import unicodify
import tool_shed.util.shed_util_common as suc
from tool_shed.util import basic_util
from tool_shed.util import common_... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/tool_shed/util/readme_util.py | Python | gpl-3.0 | 7,015 | [
"Galaxy"
] | 3c0c6f5e7b17301885df2426f501516b0b0c47248e2ecdb6af9f6dc71ac281f4 |
"""
################################################################################
# Copyright (c) 2003, Pfizer
# Copyright (c) 2001, Cayce Ullman.
# Copyright (c) 2001, Brian Matthews.
#
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provid... | intip/da-apps | plugins/da_centrallogin/modules/soappy/SOAPpy/SOAPBuilder.py | Python | gpl-2.0 | 20,377 | [
"Brian"
] | f074d9dd249fb56fac0242553b75b920d219538b195320bf46b1c0b08f6b24ad |
from __future__ import print_function
import argparse
import os
import random
from collections import defaultdict
import pysam
import mirtop.libs.logger as mylog
import mirtop.libs.do as runner
parser = argparse.ArgumentParser()
parser.add_argument("--fa",
help="File with mature sequences.", req... | miRTop/mirtop | scripts/make_unique.py | Python | mit | 2,935 | [
"pysam"
] | e633d7c2cad8d5c2edb9ff73735dd5db3d112f906b8775be8a4b4fb81b53031f |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2005-2013 Async Open Source
##
## This program is free software; you can redistribute it and/or
## modify it under the terms of the GNU Lesser General Public License
## as published by the Free Software Foundation; either version 2
## of the Licens... | andrebellafronte/stoq | stoqlib/gui/utils/printing.py | Python | gpl-2.0 | 14,009 | [
"VisIt"
] | a097201c052a984ec20a890f86050632fa2f9bb5ab97580818e5d4aef11529f3 |
#!/usr/bin/python
'''
Script to find trade routes (and LuvSats) from an SSW sector map
'''
# Copyright 2008, 2015-2016 Squiffle
# TODO: Figure out shortest trade and mining routes as well as most profitable.
# TODO: Add command-line options for max_trade_routes, max_mine_routes, min_buy_routes and routes_to_print.
#... | UEWBot/ssw-scripts | ssw_trade_routes.py | Python | gpl-3.0 | 37,002 | [
"VisIt"
] | 8d1bec7ad2134673d261461c4ef1d00d032a5d600df294ca9362dd6774c9c46f |
"""
Robust location and covariance estimators.
Here are implemented estimators that are resistant to outliers.
"""
# Author: Virgile Fritsch <virgile.fritsch@inria.fr>
#
# License: BSD 3 clause
import warnings
import numbers
import numpy as np
from scipy import linalg
from scipy.stats import chi2
from . import empir... | valexandersaulys/airbnb_kaggle_contest | venv/lib/python3.4/site-packages/sklearn/covariance/robust_covariance.py | Python | gpl-2.0 | 29,653 | [
"Gaussian"
] | 2e95ba77da0b87311502f21f08359d991e02add37cfdc92f32d35c09e24fe079 |
#!/usr/bin/python
"""Test of sayAll output."""
from macaroon.playback import *
import utils
sequence = MacroSequence()
sequence.append(utils.StartRecordingAction())
sequence.append(KeyComboAction("KP_Add"))
sequence.append(utils.AssertPresentationAction(
"1. KP_Add to do a SayAll",
["SPEECH OUTPUT: 'Hello w... | pvagner/orca | test/keystrokes/firefox/say_all_bug_591351_1.py | Python | lgpl-2.1 | 969 | [
"ORCA"
] | b23acae7bb669e3deddff5bcd0e4653c7447a80037ea4e7e11cb3e8ac4ae545e |
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