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#!/usr/bin/env python
"""Look at reads mapping to decoy STR chromosomes and use their pairs to
determine which STR locus they originated from.
Generates counts of reads mapping to the decoy originating each STR locus.
"""
import argparse
import pysam
#from insert_size import parse_bed, span_intervals
import pybedtools... | hdashnow/STRetch-paper | scripts/identify_locus.py | Python | mit | 6,091 | [
"BWA",
"pysam"
] | af385494cf90404cd2e07c904dccad435f8a4fe72cec21cfb3b845bb5350b774 |
"""
Student Views
"""
import datetime
import logging
import uuid
import json
import warnings
from collections import defaultdict
from urlparse import urljoin, urlsplit, parse_qs, urlunsplit
from django.views.generic import TemplateView
from pytz import UTC
from requests import HTTPError
from ipware.ip import get_ip
i... | jjmiranda/edx-platform | common/djangoapps/student/views.py | Python | agpl-3.0 | 104,748 | [
"VisIt"
] | f1b21b2ebadacf47cf35c1c2db24049edfc9362dcb415e5a4f16a3fe04547dfe |
#!/usr/bin/env python
"""
Count total base coverage.
usage: %prog in_file out_file
-1, --cols1=N,N,N,N: Columns for start, end, strand in first file
"""
from galaxy import eggs
import pkg_resources
pkg_resources.require( "bx-python" )
import sys, traceback, fileinput
from warnings import warn
from bx.intervals im... | volpino/Yeps-EURAC | tools/new_operations/gops_basecoverage.py | Python | mit | 1,465 | [
"Galaxy"
] | fa38910599e031fabf2ad93dad6f7a177b367f88634c530e0b7e3f5d65acdee5 |
########################################################################
# $Id$
########################################################################
""" DIRAC FileCatalog Storage Element Manager mix-in class """
__RCSID__ = "$Id$"
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.Utilities.Pfn import pfnun... | miloszz/DIRAC | DataManagementSystem/DB/FileCatalogComponents/SEManager.py | Python | gpl-3.0 | 9,070 | [
"DIRAC"
] | fd4b2400d4194d3e86489e0f3b0164d9347093c53f1c18bd21518453ee297ee8 |
# -*- coding: utf-8 -*-
"""
Created on Thu Sep 06 17:09:00 2012
@author: Shreejoy
"""
import csv
from django.db.models import Count, Q
import numpy as np
from db_functions.normalize_ephys_data import normalize_nedm_val
import neuroelectro.models as m
# TODO: remove neurotree references here
from db_f... | neuroelectro/neuroelectro_org | db_functions/compute_field_summaries.py | Python | gpl-2.0 | 29,893 | [
"NEURON"
] | 7e09d95728d9d7565058f997dc535d0c28e79c422abfa18dd8125a733bcf14dc |
# WV Well Permit Scraper
import re
from datetime import datetime, timedelta
import xlrd
import uuid
from string import Template
from xml.sax.saxutils import escape
from urlparse import urlsplit, urljoin
from random import shuffle
import collections
from scrapy.spider import BaseSpider
from scrapy.contrib... | SkyTruth/scraper | nrc/nrc/spiders/WVPermitScraper.py | Python | mit | 24,761 | [
"Elk"
] | 4082f3978cf4f526b393a2bbe88847d48b63fd12ef61794b71f00a16379f63c4 |
"""
===========================================
Sparse coding with a precomputed dictionary
===========================================
Transform a signal as a sparse combination of Ricker wavelets. This example
visually compares different sparse coding methods using the
:class:`sklearn.decomposition.SparseCoder` esti... | mrshu/scikit-learn | examples/decomposition/plot_sparse_coding.py | Python | bsd-3-clause | 3,846 | [
"Gaussian"
] | 4de5ad7b753633ffe888d3861f91258f38206c5487d7fae03107a9191ce475a4 |
"""
Example builders that read or write files.
"""
__author__ = "Dan Gunter <dkgunter@lbl.gov>"
__date__ = "5/16/14"
from pymatgen.db.builders.core import Builder
class FileCounter(Builder):
"""Count lines and characters in a file."""
def __init__(self, **kwargs):
self.num_lines, self.num_chars = 0,... | materialsproject/pymatgen-db | pymatgen/db/builders/examples/file_builders.py | Python | mit | 1,171 | [
"pymatgen"
] | 9e63fe6d21478434def7d1d755d496b06bfe4653de304f3bd026eb65dc6831a4 |
# Version: 0.19
"""The Versioneer - like a rocketeer, but for versions.
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/python-versioneer/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible with: Python 3.6, 3.7, 3.8, 3.9 and pypy3
* [![Latest Version][pyp... | pbrod/numpy | versioneer.py | Python | bsd-3-clause | 70,146 | [
"Brian"
] | 31636742e75672d116a450ec082af5d9c50d7844570486108a57e02013377b18 |
#pylint: disable=C0111
#pylint: disable=W0621
from lettuce import world, step
from nose.tools import assert_true, assert_equal, assert_in
from terrain.steps import reload_the_page
from selenium.common.exceptions import StaleElementReferenceException
############### ACTIONS ####################
@step('I select Checkl... | abhinavp13/IITBX-edx-platform-dev | cms/djangoapps/contentstore/features/checklists.py | Python | agpl-3.0 | 4,539 | [
"VisIt"
] | 6994611ddd407a3c51bb7cef9fe066fd42e7d85847e5f0531c4d00c006756d9e |
'''
Created on Apr 8, 2011
@author: awblocker
'''
# Load libraries
import re
import sys
import StringIO
import csv
import os
import time
import numpy as np
import pysam
# Define constants
ILLUMINA_REGEXP_PAIRED = re.compile(r"(.*#0/[12]):([^:]*):([^:]*)")
FASTQ_PATTERN = r"@\1\n\2\n+\1\n\3"
BOWTIE_FIELDS = ( "name... | awblocker/paired-end-pipeline | libPipeline.py | Python | apache-2.0 | 8,493 | [
"Bowtie",
"pysam"
] | 4d03799520e39f956b85c5a2848edd882321e52f98f2a126a18415d2bf550267 |
#Author: Miguel Molero <miguel.molero@gmail.com>
__all__=['ReaderVTP']
from vtk import vtkXMLPolyDataReader
from .base import PolyDataBase
class ReaderVTP(PolyDataBase):
def __init__(self, filename):
super(ReaderVTP, self).__init__()
self.filename_ = filename
def _update(self):
read... | mmolero/pcloudpy | pcloudpy/core/io/ReaderVTP.py | Python | bsd-3-clause | 460 | [
"VTK"
] | 6091347cf7370ce631adc8b63e5ec89558361f1fc9aaf61df1518fb98be0624a |
#! /usr/bin/env python
"""
Group fMRI analysis frontend for Lyman ecosystem.
"""
import os
import sys
import time
import shutil
import os.path as op
from textwrap import dedent
import argparse
import matplotlib as mpl
mpl.use("Agg")
import nipype
from nipype import Node, MapNode, SelectFiles, DataSink, IdentityInter... | tuqc/lyman | scripts/run_group.py | Python | bsd-3-clause | 8,643 | [
"Gaussian"
] | 3edda52a0daf64beb00748cb24a6cb6d22aea9a1561b4aa4469e0b931af38680 |
import PythonQt
from PythonQt import QtCore, QtGui
import director.objectmodel as om
import director.visualization as vis
from director import transformUtils
from director import applogic as app
from director import vtkAll as vtk
import numpy as np
class SplineEndEffectorPlanner(object):
def __init__(self, han... | patmarion/director | src/python/director/splinewidget.py | Python | bsd-3-clause | 9,987 | [
"VTK"
] | 505d03aa556cde3cb130a0dd7f7112a6420da29a7f65954189263595bda903fb |
"""
merged implementation of the cache provider
the name cache was not chosen to ensure pluggy automatically
ignores the external pytest-cache
"""
from __future__ import absolute_import, division, print_function
import py
import pytest
import json
from os.path import sep as _sep, altsep as _altsep
class Cache(object... | alexzoo/python | selenium_tests/env/lib/python3.6/site-packages/_pytest/cacheprovider.py | Python | apache-2.0 | 9,009 | [
"VisIt"
] | b4a7e60190af260209c6a30fbf88f9b59736630c2fd295666de836c1c454cc54 |
"""
Spin-projected MP2
"""
import h5py
import numpy as np
import scipy.linalg as slg
from frankenstein import sgscf
from frankenstein.tools.spscf_utils import (sp2block, get_grid, get_Rbeta)
from frankenstein.tools.perf_utils import TIMER
from frankenstein.mp.romp2 import lorentz_regularization
from pyscf import sc... | hongzhouye/frankenstein | mp/spmp2.py | Python | bsd-3-clause | 19,835 | [
"MOE",
"PyMOL",
"PySCF"
] | 8ed36af2a578527abd49c872c2b570cb8243ef0c2d8ca131355434caec3a4504 |
from behave import given, when, then
from app.models.gym_item import GymItem
from app.models.gym import Gym
from app.models.profile import Profile
from app.models.raid_item import RaidItem
from app.models.ex_raid_pokemon import ExRaidPokemon
from datetime import datetime, timedelta
from app.features.steps.page_object_m... | Gimpneek/exclusive-raid-gym-tracker | app/features/steps/gym_list.py | Python | gpl-3.0 | 16,933 | [
"VisIt"
] | a31836e1b33abd062f418379e389f9a1f1f5b878574cf070368494d39d0fb266 |
from pylab import figure,scatter,contour,show,legend,connect
from numpy import array, append, arange, reshape, empty, exp
from modshogun import Gaussian, GMM
from modshogun import RealFeatures
import util
util.set_title('SMEM for 2d GMM example')
#set the parameters
max_iter=100
max_cand=5
min_cov=1e-9
max_em_iter=10... | AzamYahya/shogun | examples/undocumented/python_modular/graphical/smem_2d_gmm.py | Python | gpl-3.0 | 3,771 | [
"Gaussian"
] | 70df3c1b8c5ab3c2e9b34b135f7b497111683de492bd6bb9f976b00a38a8db06 |
"""
CSV response formatting.
"""
from csv import QUOTE_MINIMAL, writer
from io import StringIO
from werkzeug import Response
from werkzeug.utils import get_content_type
from microcosm_flask.formatting.base import BaseFormatter
from microcosm_flask.formatting.encoding import UTF_8, UTF_8_SIG
class CSVFormatter(Base... | globality-corp/microcosm-flask | microcosm_flask/formatting/csv_formatter.py | Python | apache-2.0 | 2,790 | [
"FEFF"
] | c1c4d73c07722eb1733de1647a429ef531e8286e43066dd78368f679cd2bef89 |
# pyresample, Resampling of remote sensing image data in python
#
# Copyright (C) 2010-2021 Pyresample developers
#
# This program is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 3 of the... | pytroll/pyresample | pyresample/kd_tree.py | Python | lgpl-3.0 | 48,667 | [
"Gaussian"
] | 6dd25e5a6ab61c1f6e622be3f8993b2d26795f4bc5c9c878ec9adc84357215df |
import requests
from time import sleep
# ("According to his trusty servant Jeff.", False),
# ("Beautiful toy birds.",False),
# ("Dancing boys can never sing.",True),
# ("Dancing in the moonlight could rock.", True),
# ("Dancing in the moonlight makes me happy.", True),
# ("Dancing in the moonlight suck.", ... | empirical-org/WikipediaSentences | utils/qfragment/qfragment/tests/update_status.py | Python | agpl-3.0 | 9,932 | [
"exciting"
] | 43b6160f5882a75024a322f49350d9d7889e11fd443284e70029f478cdb08e59 |
u"""
Importazione computo/variante/contabilità/prezzario
dal formato XPWE
"""
import logging
from xml.etree.ElementTree import ElementTree, ParseError
from com.sun.star.table import CellRangeAddress
import LeenoUtils
import LeenoFormat
import pyleeno as PL
import LeenoDialogs as DLG
import SheetUtils
import LeenoCo... | giuserpe/leeno | src/Ultimus.oxt/python/pythonpath/LeenoImport_XPWE.py | Python | lgpl-2.1 | 50,155 | [
"CASINO"
] | 079951e927e5a6edca4047403d3cfb58e009f0cb3871bb96c158e31d5b6378d8 |
# !usr/bin/env python
# -*- coding: utf-8 -*-
#
# Licensed under a 3-clause BSD license.
#
# @Author: Brian Cherinka
# @Date: 2018-07-17 23:33:27
# @Last modified by: Brian Cherinka
# @Last Modified time: 2018-07-18 23:09:17
from __future__ import print_function, division, absolute_import
from marvin.utils.datamo... | sdss/marvin | python/marvin/utils/datamodel/vacs/__init__.py | Python | bsd-3-clause | 474 | [
"Brian"
] | 5af6bcf72cc5d0ad5070c9e0aeb30315e1d2244d9f6339ee048f03507e350d93 |
#!/usr/bin/env python
#Guruprasad Ananda
#MAQ mapper for SOLiD colourspace-reads
import sys, os, zipfile, tempfile, subprocess
def stop_err( msg ):
sys.stderr.write( "%s\n" % msg )
sys.exit()
def __main__():
out_fname = sys.argv[1].strip()
out_f2 = open(sys.argv[2].strip(),'r+')
ref_fname = sys... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/tools/solid_tools/maq_cs_wrapper.py | Python | gpl-3.0 | 12,130 | [
"Galaxy"
] | d1a2beea83c3c6bd2066db56cf5a3bda6820f2a6e3fcfb72093e99a1131f1484 |
#!/usr/bin/env python
#pylint: disable=missing-docstring
####################################################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simu... | liuwenf/moose | python/MooseDocs/tests/sqa/test_sqa.py | Python | lgpl-2.1 | 4,711 | [
"MOOSE"
] | 41ef70be58afaa39aea9285f4f50470fcf7f457ef3d42e229eb7ba5f81436a29 |
# 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... | fweik/espresso | testsuite/scripts/samples/test_electrophoresis.py | Python | gpl-3.0 | 2,263 | [
"ESPResSo"
] | 273b94d696cddbb7f445e4a66ae3740da85cc938ef8c43ea98163aa58c772df9 |
"""
This file is part of Giswater 3
The 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.
"""
# -*- coding: utf-8 -*-
import configpars... | Giswater/giswater_qgis_plugin | test/test_giswater.py | Python | gpl-3.0 | 3,202 | [
"VisIt"
] | 38236e954b453d0343f3b4dd6a215a1fe7fe7daf699c25bf798c2c239a4a99d0 |
#! /usr/bin/env python
#
# The purpose of this script is to create a moltemplate lt file for the opls.
# and oplsaa forcefields.
__author__ = 'Jason Lambert and Andrew Jewett'
# (some additional corrections by Miguel Gonzalez, Yue Chun Chiu and others)
__version__ = '0.1'
__date__ = '2016-11-20'
import sys
impor... | andeplane/lammps | tools/moltemplate/src/tinkerparm2lt.py | Python | gpl-2.0 | 24,150 | [
"LAMMPS",
"TINKER"
] | ec14e1105b02b6372ee71cfbdf61c479378e90ab1cfc6494e73d36690b29ef56 |
from __future__ import print_function
from builtins import zip
from builtins import range
import sys
sys.path.insert(1,"../../../")
import h2o
from tests import pyunit_utils
import random
def random_attack():
def attack(family, train, valid, x, y):
kwargs = {}
kwargs['family'] = family
... | nilbody/h2o-3 | h2o-py/tests/testdir_algos/glm/pyunit_DEPRECATED_NOPASS_random_attack_medium.py | Python | apache-2.0 | 5,426 | [
"Gaussian"
] | 8c69aabcd7880a3facd2b5420c8059c1c1975948069acb658704a570b2a8acc4 |
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | vinodpanicker/scancode-toolkit | src/commoncode/fileset.py | Python | apache-2.0 | 6,660 | [
"VisIt"
] | 460937816df416def11373773faa07ef1c371529c5853d0848f544457fdfa4f5 |
import re
from sqlalchemy import and_
from sqlalchemy import bindparam
from sqlalchemy import case
from sqlalchemy import Column
from sqlalchemy import exc
from sqlalchemy import extract
from sqlalchemy import ForeignKey
from sqlalchemy import func
from sqlalchemy import Integer
from sqlalchemy import join
from sqlalc... | zzzeek/sqlalchemy | test/sql/test_external_traversal.py | Python | mit | 96,801 | [
"ADF",
"VisIt"
] | 21c7b852f87111ef27d05cae1142019bae7742dc2e6d86941910c45aa2d18875 |
import json
import re
from collections import defaultdict
from datetime import datetime
from django.db import connection
from django.http import HttpResponse
from django.contrib.auth.models import User
from catmaid.models import UserRole, Treenode, TreenodeConnector, Connector, \
Location, ClassInstanceClas... | htem/CATMAID | django/applications/catmaid/control/node.py | Python | agpl-3.0 | 27,863 | [
"NEURON"
] | 592fe54ff7fe4a1896209021b87eb8cc4b30bc962dcfeea1b115ba6961b3feda |
"""
Testing for the forest module (sklearn.ensemble.forest).
"""
# Authors: Gilles Louppe,
# Brian Holt,
# Andreas Mueller,
# Arnaud Joly
# License: BSD 3 clause
import pickle
from collections import defaultdict
from itertools import combinations
from itertools import product
import numpy ... | beepee14/scikit-learn | sklearn/ensemble/tests/test_forest.py | Python | bsd-3-clause | 39,141 | [
"Brian"
] | 650da30b45cf21bad43ccca8d49d59e2845191e3500f1505c53e75e090dbd2b9 |
# changelog bisection for mercurial
#
# Copyright 2007 Matt Mackall
# Copyright 2005, 2006 Benoit Boissinot <benoit.boissinot@ens-lyon.org>
#
# Inspired by git bisect, extension skeleton taken from mq.py.
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 ... | joewalnes/idea-community | plugins/hg4idea/testData/bin/mercurial/hbisect.py | Python | apache-2.0 | 5,029 | [
"VisIt"
] | b1ba077954925305c60700943aeba174cad3ff88d99d19ee967bcfedaae2dccd |
# -*- coding: utf-8 -*-
#
# 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
#... | sid88in/incubator-airflow | tests/plugins/test_plugin.py | Python | apache-2.0 | 2,918 | [
"Galaxy"
] | a22441adc57af90eff2aa18cf3b0f8855bf006e97a34b208431f73169b479f98 |
from django import template
from django.template.defaulttags import register
register = template.Library()
@register.filter(name='get_language')
def get_language(language_key):
if(language_key == 'nb_NO'):
return 'Norwegian'
else:
return 'English'
@register.filter(name='get_status')
def get_s... | SINTEF-Infosec/Incident-Information-Sharing-Tool | incidents/templatetags/incidents_get_language.py | Python | apache-2.0 | 3,257 | [
"Amber"
] | 1a55834827c99c7fd2fdfe98294efd22166c50a9c70f2a2eb3215c6bad6fc69e |
from brian2 import *
from matplotlib.pyplot import *
start_scope()
eqs = '''
dv/dt = (I-v)/tau : 1
I : 1
tau : second
'''
G = NeuronGroup(3, eqs, threshold='v>1', reset='v = 0')
G.I = [2, 0, 0]
G.tau = [10, 100, 100]*ms
# Comment these two lines out to see what happens without Synapses
S = Synapses(G,... | amarnathmhn/ECEN751_Project2 | BrianSNN/VarSynapse.py | Python | gpl-2.0 | 664 | [
"NEURON"
] | 8430805d150ba0580aa8275a5190fc2376742f5a5bc2b6078e7ffcf8710b5d5d |
# -*- coding: utf-8 -*-
"""
Newspaper uses a lot of python-goose's extraction code. View their
license here: https://github.com/codelucas/newspaper/blob/master/GOOSE-LICENSE.txt
Keep all html page extraction code within this file. PLEASE abstract any
lxml or soup parsing mechanisms in the parsers.py file!
"""
__title_... | cantino/newspaper | newspaper/extractors.py | Python | mit | 30,129 | [
"Brian"
] | 4689d01d482a54591a217e964b52f27386cc2544149f35e0080cda5a9999d9de |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from setuptools import setup, find_packages
from holmes import __version__
tests_require = [
'mock',
'nose',
'coverage',
'yanc',
'preggy',
'tox',
'ipdb',
'coveralls',
'factory_boy',
'sqltap',
'sphinx',
'honcho',
'nose-fo... | holmes-app/holmes-api | setup.py | Python | mit | 2,301 | [
"Octopus"
] | 0aae6d7ef7cc744476b6634552303cec4ef023d229039dc365f1430ad7799233 |
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | gkc1000/pyscf | pyscf/nao/test/test_0020_scipy_gmres.py | Python | apache-2.0 | 2,618 | [
"PySCF"
] | 2c2e25f26c19dd5c7cc083ac94350fc4884dbbeb613d1f2b9ff6e1a8e2def894 |
# 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.
#
"""Code for working with NMR data
This directory currently contains contributions from
Bob Bussell <rgb2003@med.cornell.edu> -- NOEtools and xpktoo... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/NMR/__init__.py | Python | gpl-2.0 | 327 | [
"Biopython"
] | 4e5056f92c8c24c22dbd09a6ae554761e00b33ff4b58229820444b302ae487a6 |
'''
SASSIE: Copyright (C) 2011 Joseph E. Curtis, Ph.D.
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.
... | madscatt/zazzie_1.5 | trunk/sassie/simulate/energy_minimization/namd_minimize.py | Python | gpl-3.0 | 14,848 | [
"NAMD"
] | 3a2d865ea7fa29b23b8f9656575cc87f12eba6f6e62902cc04198292f89aab22 |
"""
This module defines export functions for decision trees.
"""
# Authors: Gilles Louppe <g.louppe@gmail.com>
# Peter Prettenhofer <peter.prettenhofer@gmail.com>
# Brian Holt <bdholt1@gmail.com>
# Noel Dawe <noel@dawe.me>
# Satrajit Gosh <satrajit.ghosh@gmail.com>
# Trevor... | valexandersaulys/airbnb_kaggle_contest | venv/lib/python3.4/site-packages/sklearn/tree/export.py | Python | gpl-2.0 | 15,886 | [
"Brian"
] | fa69610acccc9dfd994cfff51c788c17202ae818c6350d8cb1581fe7676f90e3 |
#
# Copyright (C) 2001-2008 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.
#
""" Exposes functionality for ... | rvianello/rdkit | rdkit/Chem/MolSurf.py | Python | bsd-3-clause | 14,742 | [
"MOE",
"RDKit"
] | 0867c694f1b5d65c0629502726f49477eb9f9b5b1016fa84a9682c512752b9c4 |
# $HeadURL: $
''' CSHelpers
Module containing functions interacting with the CS and useful for the RSS
modules.
'''
from DIRAC import gConfig, gLogger, S_OK, S_ERROR
from DIRAC.Core.Utilities.SitesDIRACGOCDBmapping import getGOCSiteName
from DIRAC.ResourceStatusSystem.Util... | calancha/DIRAC | ResourceStatusSystem/Utilities/CSHelpers.py | Python | gpl-3.0 | 10,316 | [
"DIRAC"
] | a05138e31e26f34a5905a867d1b5ed523f89746d01498be0da23cefe3f9de8d0 |
__author__ = 'Zhouhao Zeng'
import HTSeq
import sys
from optparse import OptionParser
import numpy
def getSummitProfile(ga, summit_pos_set, window_size, resolution, UpstreamExtension, DownstreamExtension):
upstream_num_points = UpstreamExtension / resolution
downstream_num_points = DownstreamExtension / reso... | zhouhaozeng/bioinformatics-codebase | profile/generate_profile_around_summits.py | Python | gpl-3.0 | 5,138 | [
"HTSeq"
] | 5c71c144b7807e2d0358fe7cea37751be8e0ea65ce6e03488c59da2a60ad0487 |
#!/usr/bin/env python2
import pyadcircmodules
import math
print "Reading a mesh"
m = pyadcircmodules.Mesh("../testing/test_files/ms-riv.grd")
m.read()
print "Mesh read successfully"
print " Node at position 2"
print " Node 2 id:",m.node(1).id()
print " Node 2 location: ",m.node(1).x(),",",m.node(1).y(),",",m.node... | zcobell/QADCModules | testing/python_tests/pyadcirc_python2_testcase.py | Python | gpl-3.0 | 3,941 | [
"NetCDF"
] | 6e81f8ed7b923e34288273fd5ffd1797ea29d0719cdc2d9380731bc16cddd17c |
# sql/compiler.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
"""Base SQL and DDL compiler implementations.
Classes provided include:
... | olivierdalang/stdm | third_party/sqlalchemy/sql/compiler.py | Python | gpl-2.0 | 112,433 | [
"VisIt"
] | 1aa6b4384a07898644dfc28c4889f7d0906a32ab78893fec087e394ddf701d1a |
"""
OpenNebula Endpoint base class implementation for the OpenNebula cloud service.
"""
import os
import base64
import ssl
from requests.auth import HTTPBasicAuth
try:
from xmlrpc.client import ServerProxy
except ImportError:
# python2 compat
from xmlrpclib import ServerProxy
# DIRAC
from DIRAC import... | DIRACGrid/DIRAC | src/DIRAC/Resources/Cloud/OpenNebulaEndpoint.py | Python | gpl-3.0 | 9,696 | [
"DIRAC"
] | 4434c008cc9e01489acfea3446eaf8b00ddd158c7d083bc30337eae94b435d39 |
# -*- coding: utf-8 -*-
#
# NURBS-Python documentation build configuration file, created by
# sphinx-quickstart on Fri Mar 10 21:16:25 2017.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
... | orbingol/NURBS-Python | docs/conf.py | Python | mit | 6,225 | [
"VTK"
] | 6272d2c22bce49e508e58ce614e9507a8afc0e1b409a836d168bf46c0709051f |
""" This module loads all the classes from the VTK Parallel library into
its namespace. This is an optional module."""
import os
if os.name == 'posix':
from libvtkParallelPython import *
else:
from vtkParallelPython import *
| sgh/vtk | Wrapping/Python/vtk/parallel.py | Python | bsd-3-clause | 236 | [
"VTK"
] | d4af43f5ac5e3749abfe9190217ebfc1c7d134cb0b8c11c45b25ab9b9c90d852 |
# (c) 2012-2014, Michael DeHaan <michael.dehaan@gmail.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) an... | stacywsmith/ansible | lib/ansible/constants.py | Python | gpl-3.0 | 30,141 | [
"Galaxy",
"MOOSE"
] | 2d9a0a7ff30e9701e0bad8b98c36f7b98cd19cf4d2a76b54936b00ee8cd1868d |
#!/usr/bin/env python
import numpy as np
from ifscube.spectools import get_wl
import pyfits as pf
from scipy.interpolate import interp1d
# import matplotlib as mpl
import matplotlib.pyplot as plt
# import scipy.ndimage as ndim
from scipy.ndimage import gaussian_filter as gf
import subprocess
def perturbation(infile,... | danielrd6/pyslight | pyslight/starlight.py | Python | gpl-3.0 | 8,113 | [
"Gaussian"
] | abc8f0887a7d930fd0697bc1046e3e3e22d36447d47c89fa74460ca7be2d551b |
#!/usr/bin/env python
import os
try:
__IPYTHON__
import sys
del sys.argv[1:]
except:
pass
import srwl_bl
import srwlib
import srwlpy
import math
import srwl_uti_smp
def set_optics(v=None):
el = []
pp = []
names = ['Sample', 'Watchpoint']
for el_name in names:
if el_name == 'Sam... | mkeilman/sirepo | tests/template/srw_generate_data/sample-from-image.py | Python | apache-2.0 | 24,266 | [
"Gaussian"
] | 93986f775beb600fdaea4033798a1f42f7e30f8dc3caa3eb8371f53ec3e2f3df |
from nose.tools import assert_raises
import mitty.benchmarking.creed as creed
class MyRead:
def __init__(self, qname, secondary, paired, read1, unmapped, reference_id, pos, cigarstring):
self.qname, self.is_secondary, self.is_paired, self.is_read1 = qname, secondary, paired, read1
self.is_unmapped, self.re... | latticelabs/Mitty | mitty/tests/benchmarking/creed_test.py | Python | gpl-2.0 | 5,564 | [
"pysam"
] | 1376bb83bb9699ec22c804ecfea1783997de079a0288a3d61adaa8aec9a0125c |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | capoe/espressopp.soap | src/tools/info.py | Python | gpl-3.0 | 2,657 | [
"ESPResSo"
] | af0055d3bc64a5ed668497b76438bb3e814d1e22b456e57cd899296fecafe1f6 |
#!/usr/bin/env python
from compliance_checker.suite import CheckSuite
from compliance_checker.cf import CFBaseCheck, dimless_vertical_coordinates
from compliance_checker.cf.util import is_vertical_coordinate, is_time_variable, units_convertible, units_temporal, NCGraph
from netCDF4 import Dataset
from tempfile import ... | duncombe/compliance-checker | compliance_checker/tests/test_cf.py | Python | apache-2.0 | 36,065 | [
"NetCDF"
] | b1c2cdf508959b5151b09ef47b598bbff41293982ab29da583afd54c886d4f23 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | xguse/scikit-bio | skbio/tree/_tree.py | Python | bsd-3-clause | 88,509 | [
"VisIt",
"scikit-bio"
] | 29e91e0be3db3f73d0d3c8a95fb3327ab5ad4df5413218b612a102ca978d0ca4 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | asimshankar/tensorflow | tensorflow/python/autograph/pyct/ast_util.py | Python | apache-2.0 | 10,787 | [
"VisIt"
] | 84fa8cce2fcdf5962cd8692423e73dc23b6380c85ee9f3fa8b19aa084cfe9699 |
# These are the Qualitas system versions as used in the Promise paper.
# In most cases I got these from the spreadsheet, but for some (noted below)
# this was blank, and I had to get them from Fig 1 of the APSEC 2015 paper.
# In some cases the tag was slightly incorrect, so I edited it.
import os
import sys
# Uses G... | MalloyPower/python-compliance | esem-paper-apr-2017/analysis-code/promise_versions.py | Python | mit | 3,275 | [
"Biopython"
] | f8c352d7acc61323f94385a92f4cffe1bc9d96d6dcf93ea2c362494212bc2824 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Implementation of defect correction methods.
"""
import logging
import matplotlib.pyplot as plt
import numpy as np
import scipy
from scipy import stats
from pymatgen.analysis.defects.core import DefectCorrection
from py... | vorwerkc/pymatgen | pymatgen/analysis/defects/corrections.py | Python | mit | 38,776 | [
"VASP",
"pymatgen"
] | 2f52a4cd2bf15708e392061b4b90a3be2d9d2e6f491a6f39d5d6f3148c21fc2a |
import numpy
from ..mrsobjects import MRSData
def gaussian(time_axis, frequency, phase, fwhm, f0=123.0):
dt = time_axis[1] - time_axis[0]
oscillatory_term = numpy.exp(2j * numpy.pi * (frequency * time_axis) + 1j * phase)
damping = numpy.exp(-time_axis ** 2 / 4 * numpy.pi ** 2 / numpy.log(2) * fwhm ** 2)
... | openmrslab/suspect | suspect/basis/__init__.py | Python | mit | 1,190 | [
"Gaussian"
] | 72988e194834ec353b3d906af9f2175e0dbcaa44f6cad925cdf783a10b450094 |
from __future__ import absolute_import
import random
import math
import bisect
import numpy as np
from draw import Maze
# 0 - empty square
# 1 - occupied square
# 2 - occupied square with a beacon at each corner, detectable by the robot
maze_data = ((1, 1, 0, 0, 2, 0, 0, 0, 0, 1),
(1, 2, 0, 0, 1, 1, 0, 0... | gwario/kogrob_2 | particle_filter.py | Python | bsd-2-clause | 6,561 | [
"Gaussian"
] | 2b49b58aacce0e4f45fa3ca89a89ada4680bdab19ba2f16cdc34ea3dc2a8859d |
"""
High-level user-level commands controlling the entire simulation.
$Id$
"""
__version__='$Revision$'
import cPickle as pickle
import os,sys,re,string,time,platform
import __main__
# gzip module might not have been built (if zlib could not be found when building)
try:
import gzip
except ImportError:
pass
... | jesuscript/topo-mpi | topo/command/basic.py | Python | bsd-3-clause | 31,774 | [
"Gaussian"
] | 1cf32f8ee0e255169190c03b206fe21f1d205e2550b974934844bc923f11e634 |
#!/usr/bin/env python
#-*- coding:utf-8 -*-
'''
Dimension and entropy estimation
If you are looking for a program that reads your signal and issues
a number that says "correlation dimension", you got yourself the
wrong package. We think you are still better off than getting such
a wrong answer. The programs in... | sdia/tisane | dimension_entropy_estimation.py | Python | gpl-3.0 | 5,868 | [
"Gaussian"
] | da59b04e1767a043216be6a1a0d0b955b261798a1164724c9a65df7ea96d55c8 |
import sublime
import sublime_plugin
import os.path
is_sublime_text_3 = int(sublime.version()) >= 3000
if is_sublime_text_3:
from .settings import Settings
from .status_bar import StatusBar
from .insert_in_output_view import insert_in_output_view
from .timeout import set_timeout, defer_sync
else:
... | NicoSantangelo/sublime-gulp | base_command.py | Python | mit | 5,042 | [
"GULP"
] | dc437ae72e4acbf28c00d1d2fa1cc308e3eceb2a24765ac94810352c70637994 |
"""
==================================================
Automatic Relevance Determination Regression (ARD)
==================================================
Fit regression model with Bayesian Ridge Regression.
See :ref:`bayesian_ridge_regression` for more information on the regressor.
Compared to the OLS (ordinary l... | glemaitre/scikit-learn | examples/linear_model/plot_ard.py | Python | bsd-3-clause | 3,912 | [
"Gaussian"
] | 42127006f4f39e1080e804aaaf79b2d5c402f3b32959aee46d180bd4c9e8db28 |
# -*- coding: utf-8 -*-
# Copyright: (c) 2020-2021, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
"""Dependency resolution machinery."""
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
try:
from typing import TY... | bcoca/ansible | lib/ansible/galaxy/dependency_resolution/__init__.py | Python | gpl-3.0 | 2,235 | [
"Galaxy"
] | 72c806a7da846a18881acbf94fe3f804293f6e75d943ac4d8e2e4252864c983e |
class ImportBench(object):
def time_import(self):
"""Benchmark time needed to import MDAnalysis
"""
import MDAnalysis as mda
pass
| MDAnalysis/mdanalysis | benchmarks/benchmarks/import.py | Python | gpl-2.0 | 166 | [
"MDAnalysis"
] | 816854fe204385c8dcdf7a60245daa06397204e078402c8004b88bab76c59d11 |
import unittest
import datetime
from valley.validators import (RequiredValidator, DateTimeValidator,
DateValidator, FloatValidator, IntegerValidator,
MaxLengthValidator, MinLengthValidator,
MaxValueValidator, MinValueValidator,
... | capless/valley | valley/tests/validators.py | Python | gpl-3.0 | 5,597 | [
"Brian"
] | 89efabaa0c9e90ee6a57cf201c834a65064e40ebb0dbb55066d2cc8bb85b0f4a |
import numpy as np
import itertools
import logging
import time
import traceback
from collections import Mapping
from ..conventions import cf_encoder
from ..core.utils import FrozenOrderedDict
from ..core.pycompat import iteritems, dask_array_type, OrderedDict
# Create a logger object, but don't add any handlers. Leav... | petercable/xray | xray/backends/common.py | Python | apache-2.0 | 7,617 | [
"NetCDF"
] | 88e52b385cabd0b9c48ee960e82075cd9343cbf7b0fe47d518f4a027806cd630 |
"""
AWS_SNS v0.01
Copyright 2011 Brian Monkaba
This file is part of ga-bitbot.
ga-bitbot 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 ... | matthusby/ga-bitbot | AWS_SNS.py | Python | gpl-3.0 | 3,493 | [
"Brian",
"VisIt"
] | c6895252ad20963f50a170df18d80ca3b0a52373ec74ee089f2c2ff6457a77b4 |
#!/usr/bin/python3
# -*- coding: utf-8 -*-
"""This file contains code for use with "Think Bayes",
by Allen B. Downey, available from greenteapress.com
Copyright 2012 Allen B. Downey
License: GNU GPLv3 http://www.gnu.org/licenses/gpl.html
"""
"""This file contains class definitions for:
Hist: represents a histogram ... | qrsforever/workspace | python/learn/thinkbayes/thinkbayes.py | Python | mit | 42,651 | [
"Gaussian"
] | aa6dcc265e92f8f12bcf351875194452001ac11357b2b48099419392a9675037 |
from __future__ import print_function
import functools
import numpy as np
# sklearn imports
have_isotonic = False
try:
from sklearn.isotonic import IsotonicRegression
have_isotonic = True
except ImportError:
raise ValueError('unable to import isotonic regression from sklearn, SLOPE subgradient projection... | selective-inference/selective-inference | selectinf/randomized/slope.py | Python | bsd-3-clause | 10,166 | [
"Gaussian"
] | e744601a8709972331dc9c19d92aa1a24fdcb82c1058096f78a53e65803041b2 |
#!/usr/bin/env python
from eyed3.id3 import Tag
from eyed3.id3 import ID3_V1_0, ID3_V1_1, ID3_V2_3, ID3_V2_4
import logging
from eyed3 import log
log.setLevel(logging.DEBUG)
t = Tag()
t.artist = "M.O.P."
t.title = "How About Some Hardcore"
t.album = "To The Death"
t.genre = "Hip-Hop"
t.track_num = (3, 5)
t.disc_num =... | nicfit/eyed3 | examples/tag_example.py | Python | gpl-2.0 | 6,030 | [
"BLAST",
"MOE"
] | 655982deeafea3cedce5eba4a4fdbfe183a870df03341565c565e73f37b0f5cd |
#!/usr/bin/env python
# Copyright 2004 by Michael Hoffman. 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.
from Bio import MissingExternalDependencyError
import sys
if sys.plat... | updownlife/multipleK | dependencies/biopython-1.65/Tests/requires_wise.py | Python | gpl-2.0 | 880 | [
"Biopython"
] | 79e8d5cd24ffa4d384519163098713b9ad5efc0d5d7eea54c3ed9a98366069c6 |
# Apache OCW lib immports
from ocw.dataset import Dataset, Bounds
import ocw.data_source.local as local
import ocw.data_source.rcmed as rcmed
import ocw.dataset_processor as dsp
import ocw.evaluation as evaluation
import ocw.metrics as metrics
import ocw.plotter as plotter
import ocw.utils as utils
import datetime
imp... | jarifibrahim/climate | examples/time_series_with_regions.py | Python | apache-2.0 | 5,382 | [
"NetCDF"
] | e65c5377208edf0013b8d81e71d27eadf3527622584c78f2061260a401ace935 |
import numpy as np
import matplotlib
import matplotlib.pyplot as plt
from fitFunctions import gaussian
import mpfit
import scipy.stats
import smooth
from util.ObsFile import ObsFile
from util.FileName import FileName
def smoothBaseline(baselines,nPtsInMode=400):
modBases = np.array(baselines)
for i in range(le... | bmazin/SDR | Projects/Simulator/checkObsBase.py | Python | gpl-2.0 | 10,226 | [
"Gaussian"
] | 9d6efdb3cdb33cf27069a1439f783bcd924ab02277fb3e798b48208ae5fcb12b |
# -*- coding: utf-8 -*-
"""
Copyright (C) 2013-2014 Team-XBMC
Copyright (C) 2014-2019 Team Kodi
This file is part of service.xbmc.versioncheck
SPDX-License-Identifier: GPL-3.0-or-later
See LICENSES/GPL-3.0-or-later.txt for more information.
"""
import sys
import xbmc # pylint: disable=import... | asavah/xbmc | addons/service.xbmc.versioncheck/resources/lib/version_check/common.py | Python | gpl-2.0 | 9,160 | [
"VisIt"
] | 06da4620b14797365264964be3e24de2cc9b0292a025011b839a8f7f214435de |
# -*- coding: utf-8 -*-
""" Data structures and manipulation of ADCP data
ADCPy allows the user to read raw (unprocessed) data from ADCP
instruments, perform a suite of processing functions and data transformations,
and output summary data and related plots. By providing access to the raw ADCP
velocities, ADCPy all... | esatel/ADCPy | adcpy/adcpy.py | Python | mit | 54,878 | [
"NetCDF"
] | 91aa5496eb08178e921d110242336162a688dccf9e319ebfe140887742ac8ace |
# -*- coding: utf-8 -*-
import datetime
from email.utils import parseaddr
from django.conf import settings
from django.contrib.contenttypes.models import ContentType
from django.http import HttpResponse
from django.test import TestCase, override_settings
from django.utils.timezone import now as timezone_now
from djang... | tommyip/zulip | zerver/tests/test_signup.py | Python | apache-2.0 | 159,968 | [
"VisIt"
] | 98f96d3414bac86ac1c9097454e836506e00e64ac2677357ffc1612646168d31 |
##############################################################################
# adaptiveMD: A Python Framework to Run Adaptive Molecular Dynamics (MD)
# Simulations on HPC Resources
# Copyright 2017 FU Berlin and the Authors
#
# Authors: Jan-Hendrik Prinz
# Contributors:
#
# `adaptiveMD` is free software: ... | thempel/adaptivemd | adaptivemd/engine/engine.py | Python | lgpl-2.1 | 14,873 | [
"MDTraj"
] | 6ebcaff67d5cde474eb4ca0159a385aab2ac2512165158647d8f32681185200d |
"""Next gen sequence alignment with Mosaik.
https://code.google.com/p/mosaik-aligner/
"""
import os
import subprocess
from bcbio.pipeline import config_utils
from bcbio.utils import file_exists
from bcbio.distributed.transaction import file_transaction
galaxy_location_file = "mosaik_index.loc"
def _mosaik_args_from... | a113n/bcbio-nextgen | bcbio/ngsalign/mosaik.py | Python | mit | 4,046 | [
"Bowtie"
] | b190f2417926db5dd0924458c9ea60479d4a65d93fa788617f7e0e0891c1ff05 |
import cgi
from webob import Request, Response
from webob.exc import HTTPNotFound
import json
import functools
import logging
from .validator import validate_args, ValidationError
from .utils import json_encode, is_file, FileIter
from .version import __version__
import threading
from wsgiref.simple_server import make_s... | palnabarun/firefly | firefly/app.py | Python | apache-2.0 | 8,275 | [
"Firefly"
] | 157bf53e8d3bdbd214db5d7f9e0d2029b7a4034c00af58fdc89b9d12d676a84a |
#!/usr/bin/env python
from __future__ import print_function
import vtk
def main():
# Create a square in the x-y plane.
points = vtk.vtkPoints()
points.InsertNextPoint(0.0, 0.0, 0.0)
points.InsertNextPoint(1.0, 0.0, 0.0)
points.InsertNextPoint(1.0, 1.0, 0.0)
points.InsertNextPoint(0.0, 1.0, 0.0... | lorensen/VTKExamples | src/Python/GeometricObjects/PolygonIntersection.py | Python | apache-2.0 | 1,059 | [
"VTK"
] | c99f18592fde7414e135b6e0231031903ecf3a754e5771d92d061618c2946baa |
#!/usr/bin/env python
#PBS -N Cu1000_se
#PBS -e se.err
#PBS -o se.log
#PBS -m ae
#PBS -q long
#PBS -l nodes=1:ppn=1:opteron4
"""Prepares a finished surface MC simulation for atoms MC by filtering and symmetry elimination.
Usage: cd simparentfolder
python surface_end.py direc Tmc Nleft smc_log_file
where Tmc is the te... | auag92/n2dm | Asap-3.8.4/Projects/NanoparticleMC/surface_end.py | Python | mit | 3,636 | [
"ASE"
] | 37039ee35fc35f5d78fa3efde2e467f5be0f21cc3c31009a6ab26fb2cc2a5252 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals, print_function
import os
import re
import json
import warnings
from io import open
from enum import Enum
from pymatgen.core.units import Mass, Length, unitiz... | tallakahath/pymatgen | pymatgen/core/periodic_table.py | Python | mit | 37,149 | [
"CRYSTAL",
"pymatgen"
] | 291211dd6828749c752f8aeb920b3d80e7a6796b07cd3db6a5fee9051ae413e2 |
# Copyright (C) 2003 CAMP
# Please see the accompanying LICENSE file for further information.
from gpaw.grid_descriptor import GridDescriptor
from gpaw.transformers import Transformer
import time
n = 6
gda = GridDescriptor((n,n,n))
gdb = gda.refine()
gdc = gdb.refine()
a = gda.zeros()
b = gdb.zeros()
c = gdc.zeros(... | qsnake/gpaw | gpaw/test/timing.py | Python | gpl-3.0 | 562 | [
"GPAW"
] | 66fab84be0e18701c31f2e1732ebd6afc156187ce2b90a3e7441f69349285995 |
#
# Copyright (C) 2007, Mark Lee
#
#http://rl-glue-ext.googlecode.com/
#
# 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... | shiwalimohan/RLInfiniteMario | system/codecs/Python/src/rlglue/environment/EnvironmentLoader.py | Python | gpl-2.0 | 2,059 | [
"Brian"
] | cd29b9037a861a999e58e7ef6e5c1a678198e00e4dcab1556fb7c469c2d470d7 |
"""
Copyright (C) 2004-2015 Pivotal Software, Inc. All rights reserved.
This program and the accompanying materials are made available under
the terms of the 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
... | rvs/gpdb | src/test/tinc/tincrepo/mpp/models/regress/sql_related/optimizer/regress_optimizer_sql_perf.py | Python | apache-2.0 | 3,961 | [
"ORCA"
] | e5a7bae274b6e9577b16b8d70846af0d7e1af2696f7738cddb473088557feba6 |
# -*- coding: utf-8 -*-
u"""Traits-based GUI for head-MRI coregistration.
Hierarchy
---------
This is the hierarchy of classes for control. Brackets like [1] denote
properties that are set to be equivalent.
::
CoregFrame: GUI for head-MRI coregistration.
|-- CoregModel (model): Traits object for estimating the h... | bloyl/mne-python | mne/gui/_coreg_gui.py | Python | bsd-3-clause | 89,510 | [
"Mayavi"
] | a36b80a6d954a4ffcbbd52df1e273142f8be9fc1d1a8c53b1bde7a3086ad46b7 |
###
### Copyright 2002 Ximian, Inc.
###
### This program 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 Software Foundation.
###
### This program is distributed in the hope that it will be useful,
### but WITHOUT ... | joeshaw/rug | src/rcnewscmds.py | Python | gpl-2.0 | 2,961 | [
"VisIt"
] | faed0757fda43e16632bf9fc3b173230d87e9d46efcfe1d38408626c39d2dc37 |
import ast
import os
from pathlib import Path
import site
import subprocess
import sys
import unittest
from hypothesis import HealthCheck, given, settings
from hypothesmith import from_grammar
from bugbear import BugBearChecker, BugBearVisitor
from bugbear import (
B001,
B002,
B003,
B004,
B005,
... | ambv/flake8-bugbear | tests/test_bugbear.py | Python | mit | 12,868 | [
"VisIt"
] | d56ee8912e265c29afb4fad13cad0c521bec70c31ddf9f10a480ccc9fe245568 |
../../../../share/pyshared/orca/orca_gui_splash.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/orca_gui_splash.py | Python | gpl-3.0 | 50 | [
"ORCA"
] | 228457a1f8407183493577a3ff59d46319cfb6357597762b62bbff2062fac7b6 |
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | gkc1000/pyscf | pyscf/nao/test/test_0023_read_siesta_bulk_spin_nao.py | Python | apache-2.0 | 1,048 | [
"PySCF",
"SIESTA"
] | 92fb979991765cf04c0234cf26cf53fddabb35a8425b684b11be6b3be7661390 |
#!/usr/bin/env python
import sys
import pysam
import argparse
import random
from collections import defaultdict
import logging
FORMAT = '%(levelname)s %(asctime)s %(message)s'
logging.basicConfig(format=FORMAT)
logger = logging.getLogger(__name__)
logger.setLevel(logging.INFO)
def rc(dna):
''' reverse complement... | adamewing/bamsurgeon | bamsurgeon/replacereads.py | Python | mit | 10,398 | [
"pysam"
] | 7493f99286ae1a1c466afa9d26530501849845b16bc05cc5b685d6624bb77f3f |
'''
@file : testFile8.py
@author (A) : Madhu Kumar Dadi.
@project : Social List
@function :
test8(postags) : checks for the presence of Verbs in the hashtag
@postags : list containing pos tags for a hashtag
return : count of Verbs
@Licence :
This work is licensed under the
Creative Commons Attribution-Non... | SummerProject16/project | CMUTweetTagger/testFile8.py | Python | cc0-1.0 | 631 | [
"VisIt"
] | d569aa2d2dea4fc5b2376492c54362aabe8d4cf1d0a59313d840701382b9db38 |
from jasp import *
import uuid
import textwrap
# * Archive and clone
# http://cms.mpi.univie.ac.at/vasp/vasp/Files_used_VASP.html
vaspfiles = ['INCAR', 'STOPCAR', 'stout', 'POTCAR',
'OUTCAR', 'vasprun.xml',
'KPOINTS', 'IBZKPT', 'POSCAR', 'CONTCAR',
'EXHCAR', 'CHGCAR', 'CHG', 'WAVE... | jboes/jasp | jasp/jasp_extensions.py | Python | gpl-2.0 | 50,432 | [
"ASE",
"VASP"
] | a605912fe34b0db30cafa849fd9c001f81f79f1ddff78e515cb61ef2c8f640a5 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# PMDA
# Copyright (c) 2019 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under the GNU Public Licence, v2 or any higher ve... | MDAnalysis/pmda | pmda/test/test_rmsf.py | Python | gpl-2.0 | 2,703 | [
"MDAnalysis"
] | f4795fd1cc27286367d4dea097033f97499960b608d7246f26ebb724935e7094 |
#!/usr/bin/env python
#
# $File: statNeDemographic.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can redis... | BoPeng/simuPOP | docs/statNeDemographic.py | Python | gpl-2.0 | 2,071 | [
"VisIt"
] | 4ad23378295989bbf6f6ccff89bb00736ee0adaa9383bda8b5531914e2775fe7 |
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