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#
# Copyright (C) 2001 greg Landrum
#
""" unit testing code for MLData sets
"""
import unittest
import cPickle
from rdkit.ML.Data import MLData,DataUtils
from rdkit import RDConfig
class TestCase(unittest.TestCase):
def setUp(self):
#print '\n%s: '%self.shortDescription(),
pass
def setUpQuantLoad... | rdkit/rdkit-orig | rdkit/ML/Data/UnitTestMLData.py | Python | bsd-3-clause | 5,394 | [
"RDKit"
] | fa5e0edf9ed5dea1adc1fe65fa922c03f4c0dc19dbda05487a5cb2957e6fea75 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# stopallexes - [insert a few words of module description on this line]
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms ... | heromod/migrid | mig/cgi-bin/stopallexes.py | Python | gpl-2.0 | 1,123 | [
"Brian"
] | 5b4b0431f02e0888f1e4042951a27fdda58944491c1100b4626691b60e03be57 |
import pytest
import os
import glob
from fireworks.core.rocket_launcher import rapidfire
from abipy.electrons.gsr import GsrFile
from abiflows.fireworks.workflows.abinit_workflows import InputFWWorkflow, ScfFWWorkflow
from abiflows.fireworks.tasks.abinit_tasks import ScfFWTask, OUTDIR_NAME, INDIR_NAME, TMPDIR_NAME
fro... | davidwaroquiers/abiflows | abiflows/fireworks/integration_tests/itest_scf.py | Python | gpl-2.0 | 6,191 | [
"ABINIT"
] | b7315d2d1c41409e0fe1b2c38c8df1b7897d933508360f6b8b6be4703f0d84f6 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | kain88-de/mdanalysis | testsuite/MDAnalysisTests/plugins/capture_err.py | Python | gpl-2.0 | 4,484 | [
"MDAnalysis"
] | 909d9d7d458dccdcd9b8e89695675ef7375ae4ec879f06bc7c79e495c7d2a7a4 |
# Copyright 2008 by Peter Cock. 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 __future__ import print_function
import os
from Bio._py3k import StringIO
from Bio import S... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_AlignIO.py | Python | gpl-2.0 | 14,811 | [
"Biopython"
] | 489a18f5428c7da8db7875d097fa98e88ff983514dc5af9fcff8eb06cb72d2d6 |
# Copyright 2019 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | google-research/computation-thru-dynamics | experimental/lfads_cc/distributions.py | Python | apache-2.0 | 4,001 | [
"Gaussian"
] | 4428cf3c047520c5be9070f04606be12f527f809f59d893a472ec54eea0dd869 |
#!/usr/bin/env python
########################################################################
# File : dirac_admin_add_shifter
# Author : Federico Stagni
########################################################################
"""
Adds or modify a shifter, in the operations section of the CS
"""
from DIRAC.Core.Base... | DIRACGrid/DIRAC | src/DIRAC/ConfigurationSystem/scripts/dirac_admin_add_shifter.py | Python | gpl-3.0 | 1,463 | [
"DIRAC"
] | cd4952958f5c7710789c5810244b4f67f8b70da53e729abeae4d571370f282f2 |
#!/usr/bin/env python
# usage: norm.py <filename>
# calculates norm of cube file
from asetk.format.cube import Cube
import asetk.atomistic.constants as constants
import numpy as np
import argparse
# Define command line parser
parser = argparse.ArgumentParser(
description='Calculates norm of Gaussian cube file.')
... | ltalirz/asetk | scripts/cube-norm.py | Python | mit | 689 | [
"Gaussian"
] | d7159821c91943c8e033209c03dc104ac53e7bc01b628105d9a2e849ecd4bb82 |
# Copyright 2015 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... | sbc100/yapf | yapf/yapflib/pytree_unwrapper.py | Python | apache-2.0 | 13,537 | [
"VisIt"
] | d20e3f8dd0f1a66fa936a7ca0339d6c620d3701163c89952b3e131eed78211f2 |
#!/usr/local/bin/python
# -*- coding: utf-8 -*-
# pylint: disable=invalid-name
import inspect
import numpy as np
import scipy
import scipy.stats as stats
from scipy.optimize import curve_fit
from app.log import logger
def exponential_est(x, a, b, c):
return a * np.exp(b * x) + c
def gaussian(x, a, b, c):
... | peterhil/ninhursag | app/api/analysis.py | Python | mit | 6,372 | [
"Gaussian"
] | efaf5014839c3443a0913f4d24987327f6ae4cc0749f5ce6d09cce753a744f2b |
import math
import os
import subprocess as sub
import sys
from shutil import which
from acpype.params import Pi
def find_bin(abin):
return which(abin) or ""
def checkOpenBabelVersion():
"check openbabel version"
import warnings
import openbabel as obl
warnings.filterwarnings("ignore")
ret... | alanwilter/acpype | acpype/utils.py | Python | gpl-3.0 | 8,518 | [
"Amber"
] | a6b417dc0eacc00424dfe78d4f7ea8830caf43c454981b157f8bc977079938aa |
# -*- coding: utf-8 -*-
# @Author: Amar Prakash Pandey
# @Date: 2016-03-24
# @Email: amar.om1994@gmail.com
# @Github username: @amarlearning
# @Last Modified by: Amar Prakash Pandey
# @Last Modified date: 2016-08-01
# MIT License. You can find a copy of the License
# @http://amarlearning.mit-license.org
... | amarlearning/PyStalker | stalker.py | Python | mit | 12,959 | [
"VisIt"
] | c196e3ee8350bdc91c0d6545f1a1c94ecfbfb07ef9cf8e1794e5b72cf1d69dc1 |
# -*- coding: utf-8 -*-
# Generated by Django 1.9.1 on 2016-02-20 22:21
from __future__ import unicode_literals
from django.db import migrations, models
import django.db.models.deletion
class Migration(migrations.Migration):
initial = True
dependencies = [
]
operations = [
migrations.Creat... | kdechant/eamon | adventure/migrations/0001_initial.py | Python | mit | 9,327 | [
"BLAST"
] | 4e44b2b05352a0fcf1a9826d21a90a2c2d28354e33544dd17f133d38ba347dea |
from galaxy import exceptions
from galaxy import web
from galaxy import model
import logging
log = logging.getLogger( __name__ )
ERROR_MESSAGE_UNKNOWN_SRC = "Unknown dataset source (src) %s."
ERROR_MESSAGE_NO_NESTED_IDENTIFIERS = "Dataset source new_collection requires nested element_identifiers for new collection."
... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/managers/collections_util.py | Python | gpl-3.0 | 4,861 | [
"Galaxy"
] | ca63af6aed9cc1cab3b1d3b06ecba2c08a0b256668a8d5ab6d84a0e2c69aac85 |
import logging
from cStringIO import StringIO
from math import exp
from lxml import etree
from path import path # NOTE (THK): Only used for detecting presence of syllabus
import requests
from datetime import datetime
import dateutil.parser
from lazy import lazy
from xmodule.modulestore import Location
from xmodule.pa... | yokose-ks/edx-platform | common/lib/xmodule/xmodule/course_module.py | Python | agpl-3.0 | 42,971 | [
"VisIt"
] | 83020d33de84f21693a14d9bbb39eda7239c11f64bb267c8643a84d0cd18290f |
#!/usr/bin/env python
#--------------------------------------------------------------------
# load module
#
import time
start_time = time.time()
import sys
import os
import numpy as np
import scipy.io.netcdf as nio
from netCDF4 import Dataset as NCDataset
# from Scientific.IO.NetCDF import NetCDFFile as NCDataset # No... | TheEarnest/Spectral_nudging | models/CAM4/func_change_CAM_yymm.py | Python | gpl-3.0 | 1,270 | [
"NetCDF"
] | de047045eb59aa22412db61e1f76bd5abfcfe031f70aab532787401004e0b29a |
# 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)
class Opencv(CMakePackage, CudaPackage):
"""OpenCV (Open Source Computer Vision Library) is an open source computer
... | LLNL/spack | var/spack/repos/builtin/packages/opencv/package.py | Python | lgpl-2.1 | 19,931 | [
"VTK"
] | a3f501a6d7140b996d9e623ae0e128f0fa4b573d411f00ca3dd709df5606e620 |
# coding=utf-8
"""
InaSAFE Disaster risk assessment tool developed by AusAid -
**IS Utilities implementation.**
Contact : ole.moller.nielsen@gmail.com
.. note:: This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Fre... | opengeogroep/inasafe | safe_qgis/utilities/utilities.py | Python | gpl-3.0 | 26,783 | [
"VisIt"
] | 14985bffb78305dcd1e34776075e773563fd7c737e29c641903581fffcf20431 |
import json
import aiohttp
async def version_check(ev):
version_url = 'https://api.lucia.moe/data/version'
async with aiohttp.ClientSession() as session:
async with session.get(version_url) as version_data:
data = await version_data.read()
data = json.loads(data)
official_... | AXAz0r/apex-sigma-core | sigma/modules/core_functions/system/version_check.py | Python | gpl-3.0 | 1,064 | [
"MOE"
] | 475c82388cd6a63a815bbc9f3b1bd1351f3bcfc2609616d5edd0b8a12101ebe8 |
# -*- coding: utf-8 -*-
import json
import os.path
import shutil
import tarfile
from typing import Dict, List, Optional
from django.conf import settings
from django.core.exceptions import ImproperlyConfigured
from django.http import HttpRequest, JsonResponse
from django.db.models import Count
from catmaid.control.au... | tomka/CATMAID | django/applications/catmaid/control/treenodeexport.py | Python | gpl-3.0 | 22,218 | [
"NEURON"
] | dc4afb8459bf895b27e8863c5f70c6009a7580c94131158eb6ed6beaf4f4f2a4 |
# -*- coding: utf-8 -*-
"""
Created on Tue Sep 12 22:21:56 2017
Based on: GSFLOW_print_PRMSparamfile4.m
@author: gcng
"""
import numpy as np # matlab core
import os # os functions
import pandas as pd # for data structures and reading in data from text file
#from ConfigParser import SafeConfigParser
import settings_t... | UMN-Hydro/GSFLOW_pre-processor | python_scripts/GSFLOW_print_PRMSparamfile_Shullcas_test.py | Python | gpl-3.0 | 43,726 | [
"CRYSTAL"
] | 641c71e7ac7e2c7535fabd0fb10e2648e6e36427fe0867347dd317e1657e07cc |
# Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import torch
from pyro.ops.gamma_gaussian import (
GammaGaussian,
gamma_and_mvn_to_gamma_gaussian,
gamma_gaussian_tensordot,
matrix_and_mvn_to_gamma_gaussian,
)
from pyro.ops.gaussian import (
Gaussian,
gau... | uber/pyro | pyro/distributions/hmm.py | Python | apache-2.0 | 54,999 | [
"Gaussian"
] | af2821cab33d2fc2e43a35b7604831b2ed171228bb37eea0d62bd2f48dfd5fe1 |
#
# 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/ml/gcp/recommendations_ai_test.py | Python | apache-2.0 | 7,200 | [
"VisIt"
] | 020355fa93668bade47a22470ba594f3a3b00eaeec24c8b40d20778228a4d088 |
#!/usr/bin/env python
########################################################################
# File : dirac-proxy-info.py
# Author : Adrian Casajus
########################################################################
from DIRAC.Core.Utilities.ReturnValues import S_OK
class Params(object):
proxyLoc = Fals... | Andrew-McNab-UK/DIRAC | FrameworkSystem/scripts/dirac-proxy-info.py | Python | gpl-3.0 | 5,829 | [
"DIRAC"
] | f95fcc73b7a6a8e1d63e68c2801694d731eca051764106bf75add5391094f681 |
""" DIRAC Basic MySQL Class
It provides access to the basic MySQL methods in a multithread-safe mode
keeping used connections in a python Queue for further reuse.
These are the coded methods:
__init__( host, user, passwd, name, [maxConnsInQueue=10] )
Initializes the Queue and tries to connect to... | miloszz/DIRAC | Core/Utilities/MySQL.py | Python | gpl-3.0 | 61,578 | [
"DIRAC"
] | b2d8969b35c5f767b7d9e060ca51578db3323dfa7a9305bf8377b050f7b861c8 |
__author__ = 'ddeconti'
import FileHandler
import numpy
import sys
from bokeh.plotting import figure, output_file, show, VBox, HBox
from rdkit import DataStructs
from sklearn.cluster import KMeans
from sklearn.decomposition.pca import PCA
from sklearn.metrics import silhouette_score
def train_pca(pains_fps, num_co... | dkdeconti/PAINS-train | training_methods/clustering/kmeans_clustering_of_pca_reduction.py | Python | mit | 4,434 | [
"RDKit"
] | 4cc86d90162f7ac952f99040f63b8ebe83853a043b4ee12bf963fd9f3d69c2e3 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
This module implements classes (called Fitters) which combine optimization
algorithms (typically from `scipy.optimize`) with statistic functions to perform
fitting. Fitters are implemented as callable classes. In addition to the data
to fit, the ``__c... | dhomeier/astropy | astropy/modeling/fitting.py | Python | bsd-3-clause | 71,041 | [
"Gaussian"
] | b68a935a93c38ff8dd16e8dd89b5918b35cc942c9e5c555080c1c38cb3c6bb53 |
#
# Copyright (C) 2010 Cardapio Team (tvst@hotmail.com)
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# ... | daboross/cardapio | src/OptionsWindow.py | Python | gpl-3.0 | 17,527 | [
"FLEUR"
] | 0d1cf03343ac2de537172f857cd9d29a819ceecfab67a3c1d05bb50ff1943471 |
#!/usr/bin/env python
import pyscf
from pyscf.tools import c60struct
from benchmarking_utils import setup_logger, get_cpu_timings
log = setup_logger()
for bas in ('6-31g**', 'cc-pVTZ'):
mol = pyscf.M(atom=[('C', r) for r in c60struct.make60(1.46,1.38)],
basis=bas,
max_memory=4... | sunqm/pyscf | examples/2-benchmark/c60.py | Python | apache-2.0 | 543 | [
"PySCF"
] | 8da01c32aaed135e50aa27c2d2a7d447a5e0bbed709395d4eeac4cce5bd93957 |
# -*- coding: utf-8 -*-
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.path import Path
import matplotlib.patches as patches
#from mayavi import mlab # Some strange error messages if we do like that
#import mayavi # This way we haven't error messages, but it doesn't work.
# Finally I... | lcpt/xc | python_modules/postprocess/reports/graph_material.py | Python | gpl-3.0 | 5,995 | [
"Mayavi"
] | e20615771ec1a89922795c239dcf93a0abce854d4d986a3932563c40a0375cee |
#pylint: disable=C0111
#pylint: disable=W0621
from lettuce import world, step
from django.contrib.auth.models import User
from lettuce.django import django_url
from student.models import CourseEnrollment
from common import course_id, course_location
from problems_setup import PROBLEM_DICT
TEST_SECTION_NAME = 'Test Se... | PepperPD/edx-pepper-platform | lms/djangoapps/courseware/features/navigation.py | Python | agpl-3.0 | 7,020 | [
"VisIt"
] | d6a1d801d47791443f80e4787f3d873801431def280cfae941ab60395cc7bb1b |
"""
===========================================
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... | depet/scikit-learn | examples/decomposition/plot_sparse_coding.py | Python | bsd-3-clause | 3,846 | [
"Gaussian"
] | 571bf8cc670d88f484f98d7c2b39c7f0cad56ac4dc108f23b4f2965b0e1c4764 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# vgridaccess - user access in VGrids
# Copyright (C) 2003-2014 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License ... | heromod/migrid | mig/shared/vgridaccess.py | Python | gpl-2.0 | 34,475 | [
"Brian"
] | cdda24aaecfe7f2685c77f6d3da472193f4b0a2bc321e628343c166469aeecb8 |
# -*- coding: UTF-8 -*-
import numpy as np
import numpy.random as rnd
from numpy.fft import fft, rfft
## Genration of the fractional Gaussian noise with theh circulant matrix method
## of Dietrich, Newsam 1997.
## Inputs: N : number of samples
## H : Hurst parameter (0 < H < 1)
## [seed] : the initial... | ivannz/study_notes | year_14_15/course_project/code/python/synthfbmcircul.py | Python | mit | 5,644 | [
"Gaussian"
] | 5f7a6be1aa5523cfbc22b349048870e831ab8d585b3de7411bb59d76b1efceac |
#!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Created on Thu Oct 12 18:47:30 2017
@author: tianzixie
"""
import numpy as np
import math
def gaussian(sigma,ksize):
array=np.zeros(ksize)
c=0
for x in range (ksize):
ya=(x-int(ksize/2))*(x-int(ksize/2))
... | tianzixie/CAP5415_PA1 | Answers/code/Answer1 of gaussian function.py | Python | mit | 686 | [
"Gaussian"
] | fada807bb2f6af739608b1bc9c02bdc1b7a90cf35567789b58faed18aa202aaa |
import sqlite3
db = sqlite3.connect('groomsmen.sqlite')
c = db.cursor()
c.execute('DROP TABLE groomsmen;')
c.execute('''CREATE TABLE groomsmen (name text, last_name text, pronunciation text, phone text, email text, paid int, party_paid int, tux int, march int, bridesmaid text);''')
c.execute("INSERT INTO groomsmen VAL... | hochbrian/bridal_party | build_db.py | Python | gpl-3.0 | 1,058 | [
"Brian"
] | 39b1846ece969b0f76fd588e23b29a61b814221e17fa595d662450c412a64608 |
import numpy as np
import pytest
import psi4
def test_cc_polaroptrot():
# cc29 + polarizabilities + tensors
mol = psi4.geometry("""
O -0.028962160801 -0.694396279686 -0.049338350190
O 0.028962160801 0.694396279686 -0.049338350190
H 0.350498145881 -0.9106456... | lothian/psi4 | tests/pytests/test_ccresponse.py | Python | lgpl-3.0 | 8,969 | [
"Psi4"
] | c96f2ca6bd57e39d91dc03fe8bfa374f9f9a1b3b8ad303dad7c264f1c605bc01 |
# Hidden Markov Models
#
# Author: Ron Weiss <ronweiss@gmail.com>
# and Shiqiao Du <lucidfrontier.45@gmail.com>
# API changes: Jaques Grobler <jaquesgrobler@gmail.com>
# Modifications to create of the HMMLearn module: Gael Varoquaux
"""
The :mod:`hmmlearn.hmm` module implements hidden Markov models.
"""
import string... | emmaggie/hmmlearn | hmmlearn/hmm.py | Python | bsd-3-clause | 27,264 | [
"Gaussian"
] | e02fc9e26e75072b4e73343c8ff984b0a63e7559657173f2f5c7743ce0582dc9 |
"""Splinter plugin for pytest.
Provides easy interface for the browser from your tests providing the `browser` fixture
which is an object of splinter Browser class.
"""
import codecs
import functools # pragma: no cover
try:
from httplib import HTTPException
except ImportError:
from http.client import HTTPExce... | miohtama/pytest-splinter | pytest_splinter/plugin.py | Python | mit | 20,308 | [
"VisIt"
] | dc54786d3a87c2112d0ad0406dc691943b311d8caf6d57505a53ec2ec6b3eadf |
import sys
import re
import numpy as np
from ase.visualize import view
from ase.structure import molecule
from ase.units import Hartree
from gpaw import GPAW
from gpaw.mpi import rank, world
from gpaw.test import equal
from gpaw.gauss import Gauss
from gpaw.lrtddft import LrTDDFT, photoabsorption_spectrum
from gpaw.... | robwarm/gpaw-symm | gpaw/test/lrtddft3.py | Python | gpl-3.0 | 3,918 | [
"ASE",
"GPAW"
] | ff366a2ed8679a0c75e18ab99aa91f9c8fc9bdafe18cd168e6cd9584ae7993e3 |
from asap3 import *
from ase import units
from ase.lattice.cubic import FaceCenteredCubic
import numpy as np
import matplotlib.pyplot as plt
import time
repeat = 25
AsapThreads()
#set_verbose(1)
atoms = FaceCenteredCubic(size=(50,50,50), symbol='Cu')
atoms.set_calculator(EMT())
lgv = Langevin(atoms, 5*units.fs, 0.0... | auag92/n2dm | Asap-3.8.4/Debug/TestRnd.py | Python | mit | 1,203 | [
"ASE"
] | a0a386600909fd3601acdf98c61b5da8a2adece88b37548aa24309bce572891c |
"""Python tools and wrappers for the PINY molecular simulations package."""
from __future__ import absolute_import
# if the interface is not built, fail nicely
try:
from .piny import PINYEmpirical
except ImportError:
pass
# if ASE is available, add support for it
try:
import ase
except ImportError:
... | yuhangwang/PINY | python/piny/__init__.py | Python | epl-1.0 | 418 | [
"ASE"
] | 84fb91446c8b460069f18a385dfaec69dd87c0f0fe5ed92eed5ea7c34ba542af |
##############################################################################
# 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: ... | jrossyra/adaptivemd | adaptivemd/mongodb/object.py | Python | lgpl-2.1 | 23,869 | [
"MDTraj"
] | 48d3348b4b842633e378671604ec9c4ad5c6d1b749b4482b16faaecd896b2570 |
import ocl
import camvtk
import time
import vtk
def filter_path(path,tol):
f = ocl.LineCLFilter()
f.setTolerance(tol)
for p in path:
p2 = ocl.CLPoint(p.x,p.y,p.z)
f.addCLPoint(p2)
f.run()
return f.getCLPoints()
def adaptive_path_drop_cutter(s, cutter, path):
apdc = o... | JohnyEngine/CNC | opencamlib/scripts/pycam_bench.py | Python | apache-2.0 | 6,421 | [
"VTK"
] | f628d74722476cc8c3704ae22dac95617139ed19cf4af245f59d260184d33cc6 |
import os
import glob
import sys
import shutil
import unittest
import luigi
import ratatosk.job
import ratatosk.lib.tools.gatk
import ratatosk.lib.align.bwa
from ratatosk.config import get_config
localconf = "pipeconf.yaml"
local_scheduler = '--local-scheduler'
process = os.popen("ps x -o pid,args | grep ratatoskd | g... | percyfal/ratatosk | test/test_job.py | Python | apache-2.0 | 1,292 | [
"BWA"
] | c6b1e57fe4e5090c2797e9f476b17f2c6d1bcf457129222d564a9cf51cd78edb |
"""
Sphinx extension that automatically and recursively generates .rst files containing autodoc/autosummary
directives for a hierarchy of Python modules.
"""
__copyright__ = "Copyright (C) 2019 Ben Spiller"
__author__ = "Ben Spiller"
__license__ = "Apache 2.0"
__version__ = "1.0.dev"
__all__ = ['AutoDocGen', 'setup... | xpybuild/xpybuild | docs/ext/sphinx_autodocgen/__init__.py | Python | apache-2.0 | 14,434 | [
"VisIt"
] | ed834c820bd8a5db4f9b73b2326f355e718921a0eda562a8056ed5b80b86e1c1 |
# This file is part of pybootchartgui.
# pybootchartgui 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.
# pybootchartgui is dis... | mmeeks/bootchart | pybootchartgui/gui.py | Python | gpl-2.0 | 12,541 | [
"FLEUR"
] | 8c7a6f60a9855b3ea4e5188c7724795b9ef0d6015d185ef26d1d11b0c5a6f1c5 |
"""
NASA Sloan Atlas dataset size reduction
---------------------------------------
The NASA Sloan Atlas dataset is contained in a ~0.5GB available at
http://www.nsatlas.org/data
This function fetches a ~50MB subset of that data. This subset is created
using the code that can be found at examples/datasets/truncate_n... | astroML/astroML | astroML/datasets/nasa_atlas.py | Python | bsd-2-clause | 2,062 | [
"Galaxy"
] | 3d62fb2fb8ad8d9bd65d941c91d3fb16a3225d481e0b094d12c567863c6cf907 |
# -*- coding: utf-8 -*-
"""
Unit tests for instructor.api methods.
"""
import codecs
import datetime
import ddt
import functools
import random
import pytz
import io
import json
import requests
import shutil
import tempfile
from urllib import quote
from django.conf import settings
from django.contrib.... | nttks/edx-platform | lms/djangoapps/instructor/tests/test_api.py | Python | agpl-3.0 | 246,544 | [
"VisIt"
] | 8d95c5a9410cd9e4afc8917285e734585ef2087f596e30dc1a12bb4ad063aba5 |
import sys
from collections import namedtuple
from mitmflib.ua_parser import user_agent_parser
PY2 = sys.version_info[0] == 2
PY3 = sys.version_info[0] == 3
if PY3:
string_types = str
else:
string_types = basestring
MOBILE_DEVICE_FAMILIES = (
'iPhone',
'iPod',
'Generic Smartphone',
'Generi... | CiuffysHub/MITMf | mitmflib-0.18.4/mitmflib/user_agents/parsers.py | Python | gpl-3.0 | 7,156 | [
"Galaxy"
] | 02ba5db2257f3b4414c37a31384bd86c50c3a9bc153955cfc93b5dff23e70e19 |
""" InfoGetter
Module used to map the policies with the CS.
"""
import copy
from DIRAC import S_OK, S_ERROR, gConfig, gLogger
from DIRAC.ResourceStatusSystem.Utilities import RssConfiguration, Utils
def getPoliciesThatApply(decisionParams):
"""
Method that sanitizes the input parameters and returns the p... | DIRACGrid/DIRAC | src/DIRAC/ResourceStatusSystem/Utilities/InfoGetter.py | Python | gpl-3.0 | 11,151 | [
"DIRAC"
] | 60207baa3ea36e3bd28087d07d6ce676b82c14df78bc48ff987d02f83f3d02bd |
import moose
from pylab import *
from moose.utils import *
import numpy as np
inputGiven = 1
moose.Neutral('/elec')
pg = moose.PulseGen('/elec/inPulGen')
pgTable = moose.Table('/elec/inPulGen/pgTable')
moose.connect(pgTable, 'requestOut', pg, 'getOutputValue')
pg.firstDelay = 10e-3
pg.firstWidth = 2e-03
pg.firstLevel... | BhallaLab/moose | moose-examples/hopfield/test.py | Python | gpl-3.0 | 2,198 | [
"MOOSE"
] | 3c154d52f3e50bdf512da4d3f83db81d81afbed099b590c763c0028df74a09fd |
# --------------------------------------------------------------------------------------------
# Copyright (c) Microsoft Corporation. All rights reserved.
# Licensed under the MIT License. See License.txt in the project root for license information.
# --------------------------------------------------------------------... | yugangw-msft/azure-cli | src/azure-cli/azure/cli/command_modules/sql/custom.py | Python | mit | 185,289 | [
"VisIt"
] | 1abb9b2eff86379bd99d23050d673b85f453b59fcbbc39cb9583fb109a6fa96a |
#
# Copyright 2012 Brian R. D'Urso
#
# This file is part of Python Instrument Control System, also known as Pythics.
#
# Pythics 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 Lic... | LunarLanding/Pythics | pythics/vv.py | Python | gpl-3.0 | 9,148 | [
"Brian"
] | 7224b566146b05200500c1425136912b254e34f0449e29eacc6bc9218a9f5300 |
from mayavi.mlab import *
from mayavi.modules.outline import Outline
from mayavi.modules.surface import Surface
it=38;iesp=0
#data = core.gui.guiShow.arr3
data = core.transReader.readUCN(core,'Mt3dms',it,0,'Tracer')
data= data[:,-1::-1,:]
xm,ym,zm = getMesh3Dcenters(core)
xm = (xm-amin(xm))/(amax(xm)-amin(xm))
ym = (y... | ORTI3D/ORTI3D_code | iliblast/scriptMayavi.py | Python | gpl-3.0 | 610 | [
"Mayavi"
] | 067a665f83d9e7ebe9d6a4e6f8f758fd6057d02cd71fb0407458eb7da378fb06 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#... | MDAnalysis/mdanalysis | testsuite/MDAnalysisTests/core/test_index_dtype.py | Python | gpl-2.0 | 2,783 | [
"MDAnalysis"
] | 0161f7f142413122105d99162ed795e67987461df4aeb643a38fdd9b77af57ee |
import abc
import copy
import logging
import itertools
import os
import uuid
import sys
import time
import datetime
import signal
import subprocess
import re
import multiprocessing
import signal
from yapsy.PluginManager import PluginManager
from yapsy.IPluginLocator import IPluginLocator
from threading import Thread
f... | sebhtml/assembly | lib/assembly/plugins.py | Python | mit | 27,318 | [
"BWA"
] | b19047d71c83ecc47417d3391ed328b0050efc040e87c7628d730cb922996908 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright: (c) 2014, Brian Coca <brian.coca+dev@gmail.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
DOCUMENTATION = '''
---
module: ge... | s-hertel/ansible | lib/ansible/modules/getent.py | Python | gpl-3.0 | 4,244 | [
"Brian"
] | 9b10eae5e54273785fd819e202fd0a78694f2b6015a18b4f2862d4e9f3af923d |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals, division, print_function
import unittest
import os
import warnings
import numpy as np
from pymatgen.io.cif import CifParser, CifWriter, CifBlock
from pymatgen.io.vasp... | czhengsci/pymatgen | pymatgen/io/tests/test_cif.py | Python | mit | 40,792 | [
"VASP",
"pymatgen"
] | b6350659757a4b759b3ce1fbfc046e53015809264ba6419a53aaa06507ce5195 |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2018, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
"""
Universe trait functions
#########################
"""
##########
# traits #
##########
import re
import numpy as np
import pandas as pd
from exatomic.base import sym2radius, sy... | avmarchenko/exatomic | exatomic/widgets/traits.py | Python | apache-2.0 | 5,116 | [
"Jmol"
] | a2ac9e50f024229173ab2d78fa556278fc4e6cf7444e5ef1b9a5d32bc4e81f11 |
# -*- coding: utf-8 -*-
# vim: tabstop=4 shiftwidth=4 softtabstop=4
#
# Copyright (C) 2013-2021 GEM Foundation
#
# OpenQuake is free software: you can redistribute it and/or modify it
# under the terms of the GNU Affero General Public License as published
# by the Free Software Foundation, either version 3 of the Licen... | gem/oq-engine | openquake/hazardlib/geo/surface/multi_old.py | Python | agpl-3.0 | 29,109 | [
"Brian"
] | ed92a052aaceb69367fadd13885c4108524babc7fab49757b2419f12c52ee309 |
"""Define the Multioutput Gaussian Process model.
Author:
Ilias Bilionis
Date:
11/20/2012
1/29/2013 (Made it conform to MarkovChainMonteCarlo class so that it can
be used in conjuction with uq.random.SequentialMonteCarlo.)
1/31/2013 (Added sample_prediction.)
1/2/2013 (Adde... | ebilionis/py-best | best/gp/_multioutput_gaussian_process.py | Python | lgpl-3.0 | 50,867 | [
"Gaussian"
] | e83bc585f5d0fe452ac9c2bcb823c02cd4a4a43460e5640d8d72ac296d6b034a |
#
# This file is part of GreatFET
#
import array
import struct
from ..board import GreatFETBoard
from ..programmers.firmware import DeviceFirmwareManager
from ..errors import DeviceNotFoundError
class GreatFETLegacy(GreatFETBoard):
""" Class representing legacy-firmware (pre-libgreat) GreatFET boards.
This c... | dominicgs/GreatFET-experimental | host/greatfet/boards/legacy.py | Python | bsd-3-clause | 15,113 | [
"CRYSTAL"
] | 971ca21a6572db0f212e7086a833d515a2e4160ab22722662609bca2e17e24a7 |
#
# 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... | shaneknapp/spark | python/pyspark/ml/regression.py | Python | apache-2.0 | 93,425 | [
"Gaussian"
] | 4700a2ad164b950bd3bb507ee8fae68b8eac3cdb3471500728b8c5a079c1207e |
# mako/_ast_util.py
# Copyright (C) 2006-2014 the Mako authors and contributors <see AUTHORS file>
#
# This module is part of Mako and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""
ast
~~~
The `ast` module helps Python applications to process trees of the Pyth... | grepme/CMPUT410Lab01 | virt_env/virt1/lib/python2.7/site-packages/Mako-1.0.0-py2.7.egg/mako/_ast_util.py | Python | apache-2.0 | 25,652 | [
"VisIt"
] | cbbd14c9df4fc7d133ebe08f6d0970b8feed3494b44ea98fe341d89a067c3c72 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | kyleabeauchamp/mdtraj | mdtraj/geometry/hbond.py | Python | lgpl-2.1 | 16,087 | [
"MDTraj"
] | 52bed0528dff56c05fd0b9e34d1c2af35226664e05335e4b88340b34f0c25d63 |
import math
import numpy as np
from typing import Any, Tuple
try:
import torch
from torch import Tensor
import torch.nn as nn
import torch.nn.functional as F
except ModuleNotFoundError:
raise ImportError('These classes require Torch to be installed.')
class ScaleNorm(nn.Module):
"""Apply Scale Normalizati... | peastman/deepchem | deepchem/models/torch_models/layers.py | Python | mit | 32,024 | [
"RDKit"
] | 8e5bdf9f4e76adac7b62ca88823de2a3f4fab535d047890230b6979481e32df7 |
#!/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, names=None, want_final_propagation=True):
el = []
pp = []
if not names:
names = ['Aperture', 'Apert... | radiasoft/sirepo | tests/template/srw_generate_data/tabulated-undulator-example.py | Python | apache-2.0 | 23,615 | [
"Gaussian"
] | 16719d5c6f41d7d0612fd10ce11987a83da01c36e1ab670b363690faefe6bf78 |
# $HeadURL$
#
""" SystemLoggingDB class is a front-end to the Message Logging Database.
The following methods are provided
insertMessage()
getMessagesByDate()
getMessagesByFixedText()
getMessages()
"""
__RCSID__ = "$Id$"
import re
import os
import sys
from types import ListType, StringTypes
fro... | calancha/DIRAC | FrameworkSystem/DB/SystemLoggingDB.py | Python | gpl-3.0 | 27,062 | [
"DIRAC"
] | f30d19154611ff899dd0c7d15e88f1394a02e56c723a56ee0c44ea20a920e725 |
if __name__ == "__main__":
import sys,os
append_path = os.path.abspath(sys.argv[0])[:-22]
print("Append to PYTHONPATH: %s" % (append_path))
sys.path.append(append_path)
import time,logging
import subprocess
from Top import Top
from Tools.IO import is_readable
from Interface.FchkGaussian import FchkGaus... | talipovm/terse | terse/Interface/Isosurface.py | Python | mit | 1,823 | [
"Gaussian"
] | f76844c96c51052803e214705fff03975be07dd224efb77f63aad6d4407bfb5e |
#!/usr/bin/env python
"""
--------------------------------------------------------------------------------
(c) 2017 Julian Rees
License: GNU GPLv3
Description: Print the HOMO and LUMO numbers of an ORCA output file.
Run: python gethomolumo.py filename
Arguments: filename - file name with extension
Dependencies: no... | julianrees/scripts | python/gethomolumo.py | Python | gpl-3.0 | 1,386 | [
"ORCA"
] | 346e996b700411bf31f824db3acf675a06f514b7ba151b2d5b176c53b5492b43 |
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Generic presubmit checks that can be reused by other presubmit checks."""
from __future__ import print_function
import os as _os
_HERE = _os.path.di... | endlessm/chromium-browser | third_party/depot_tools/presubmit_canned_checks.py | Python | bsd-3-clause | 60,066 | [
"VisIt"
] | 204477d423130bba92a1051f68b02421774405375d468e131de3713ba3ce9e2d |
import numpy as np
from scipy.ndimage import gaussian_filter, gaussian_laplace
import itertools as itt
import math
from math import sqrt, hypot, log
from numpy import arccos
from ..util import img_as_float
from .peak import peak_local_max
from ._hessian_det_appx import _hessian_matrix_det
from ..transform import integ... | paalge/scikit-image | skimage/feature/blob.py | Python | bsd-3-clause | 16,868 | [
"Gaussian"
] | 6314997896e6824b696f455b249e81ae5ea96a37e05698f51c9156a1c2e64b51 |
# -*- coding: utf-8 -*-
# @Author: YangZhou
# @Date: 2017-06-18 22:00:07
# @Last Modified by: YangZhou
# @Last Modified time: 2017-06-26 22:43:57
import numpy as np
from numpy.linalg import norm
import time
from functools import wraps
np.set_printoptions(precision=3, suppress=True)
def fn_timer(function):
@wr... | vanceeasleaf/aces | aces/f.py | Python | gpl-2.0 | 11,900 | [
"ASE"
] | eeaf4ce94b5644c02010087c60bab39f4fb3ddca8a67c1ef6466fd467e3fe376 |
# 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 u... | jarifibrahim/climate | ocw/tests/test_local.py | Python | apache-2.0 | 16,629 | [
"NetCDF"
] | 7b04627b83b51fb6a58469ac7fda9e5d9df7a7d82f9d110409285f19cb610879 |
#
# @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
#... | evangelistalab/forte | forte/proc/orbital_helpers.py | Python | lgpl-3.0 | 10,879 | [
"Psi4"
] | aa98111b69017cdaca96da97fb81174ad7e600a5e4dd923d4739fd77d93cab12 |
"""
API for initiating and tracking requests for credit from a provider.
"""
import datetime
import logging
import uuid
import pytz
from django.db import transaction
from edx_proctoring.api import get_last_exam_completion_date
from openedx.core.djangoapps.credit.exceptions import (
UserIsNotEligible,
CreditP... | ahmedaljazzar/edx-platform | openedx/core/djangoapps/credit/api/provider.py | Python | agpl-3.0 | 16,186 | [
"VisIt"
] | 6796cadbeb95fa48b0a717b4d2abf99a6690e392d8bacb4cbfd8c8daeb37e54e |
# $HeadURL$
__RCSID__ = "$Id$"
import sys
import os
import getopt
import types
import DIRAC
from DIRAC import gLogger
from DIRAC import S_OK, S_ERROR
from DIRAC.ConfigurationSystem.Client.ConfigurationData import gConfigurationData
from DIRAC.ConfigurationSystem.private.Refresher import gRefresher
from DIRAC.Configu... | sposs/DIRAC | ConfigurationSystem/Client/LocalConfiguration.py | Python | gpl-3.0 | 17,789 | [
"DIRAC"
] | 37564e244b42b0ff6f97a8b990d94b9d0af93d4c71b8205e1c44fd21796cdd57 |
#!/usr/bin/env python
__author__ = "Kishori M Konwar"
__copyright__ = "Copyright 2013, MetaPathways"
__credits__ = ["r"]
__version__ = "1.0"
__maintainer__ = "Kishori M Konwar"
__status__ = "Release"
"""Contains general utility code for the metapaths project"""
try:
import os, re
from shutil import rmtree
... | Koonkie/MetaPathways_Python_Koonkie.3.0 | libs/python_modules/pipeline/sampledata.py | Python | mit | 10,317 | [
"BLAST",
"BWA"
] | 08346c971c369b4bd87c999f065b8d036c7db39878640ea4e9bd9787fcccec33 |
#
# 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... | retrography/scancode-toolkit | src/commoncode/__init__.py | Python | apache-2.0 | 1,777 | [
"VisIt"
] | 09e851b89c7ddd1e6591cfee365fb4982cdad890b13310f0cf0fb5a48b3d7fed |
#!/usr/bin/env python
'''
Load all long time series MBARI OASIS Mooring data
Mike McCann
MBARI 4 October 2018
'''
import os
import sys
sys.path.insert(0, os.path.join(os.path.dirname(__file__), "../"))
sys.path.insert(0, os.path.join(os.path.dirname(__file__), "../../"))
if 'DJANGO_SETTINGS_MODULE' not in os.environ... | stoqs/stoqs | stoqs/loaders/OceanSITES/load_oasis.py | Python | gpl-3.0 | 2,201 | [
"NetCDF"
] | a6d523c0567921c62d845a94a1827c8bcad55d1efdcd635614558d0a26bc3b8e |
"""
pygments.lexers._asy_builtins
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
This file contains the asy-function names and asy-variable names of
Asymptote.
Do not edit the ASYFUNCNAME and ASYVARNAME sets by hand.
TODO: perl/python script in Asymptote SVN similar to asy-list.pl but only
for function and... | sonntagsgesicht/regtest | .aux/venv/lib/python3.9/site-packages/pygments/lexers/_asy_builtins.py | Python | apache-2.0 | 27,287 | [
"Gaussian"
] | 594e4eaea279aac038b814b21a83ae26c576e458ac79ee5752c3eebe91c8ec86 |
#
# Copyright 2016 The BigDL Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... | intel-analytics/BigDL | python/orca/src/bigdl/orca/learn/tf2/estimator.py | Python | apache-2.0 | 4,518 | [
"ORCA"
] | aa5f9d7c2eb2480c4512e077d346d9286878ebcf2be2ad9f015067c6d7daf73c |
import functools
import json
import logging
import random
import re
import string # pylint: disable=W0402
import fnmatch
import unicodedata
from textwrap import dedent
from external_auth.models import ExternalAuthMap
from external_auth.djangostore import DjangoOpenIDStore
from django.conf import settings
from d... | TsinghuaX/edx-platform | common/djangoapps/external_auth/views.py | Python | agpl-3.0 | 42,147 | [
"Brian"
] | e1db212d29906ba7bd1d66abce8d2a9d52eabd7119b346bf8f7a811228d82890 |
from .log_utils import logger
try:
from ._ffi_xcursors import ffi
except ImportError:
# PyPy < 2.6 compaitibility
import cffi
if cffi.__version_info__[0] == 0:
from .ffi_build import xcursors_ffi as ffi
else:
raise ImportError("No module named libqtile._ffi_xcursors, be sure to run ... | cortesi/qtile | libqtile/xcursors.py | Python | mit | 4,956 | [
"FLEUR"
] | 7de0cda0c07d3b47ca21e4e54a20848ef7c698a3205bee4dd79bdf54a2ecd118 |
'''
Hodgkin-Huxley equations (1952)
We calculate the extracellular field potential at various places.
'''
import os
import matplotlib
matplotlib.use('Agg')
from brian2 import *
from scipy import stats
name = os.path.basename(__file__).replace('.py', '')
codefolder = os.path.join('code', name)
print('runing example {... | brian-team/brian2cuda | examples/compartmental/lfp_cpp.py | Python | gpl-2.0 | 3,384 | [
"NEURON"
] | 22a75ca496b3456fd00141e346c5998c53e170deb230065d8924a253b1bc2765 |
from setuptools import setup, find_packages
from distutils.extension import Extension
import numpy
USE_CYTHON = True
try:
from Cython.Build import cythonize
except Exception:
USE_CYTHON = False
ext = '.pyx' if USE_CYTHON else '.c'
extensions = [Extension("tmhmm.hmm", ["tmhmm/hmm" + ext])]
if USE_CYTHON:
... | ml-lab/tmhmm.py | setup.py | Python | mit | 805 | [
"scikit-bio"
] | 24f934570ef7a1f7e7e00ac90e3143b0597dc9f1eac1a7925aa1469980cc74d4 |
#!/usr/bin/env python
##############################################################################################
#
#
# regrid_emissions_N96e.py
#
#
# Requirements:
# Iris 1.10, cf_units, numpy
#
#
# This Python script has been written by N.L. Abraham as part of the UKCA Tutorials:
# http://www.ukca.ac.uk/wiki... | acsis-project/emissions | emissions/python/timeslice/regrid_aircNO_n96e_360d_1960-1974.py | Python | gpl-3.0 | 8,694 | [
"NetCDF"
] | 6bdf0ac4ac7e9d27f2676797a4506797f27926cfa3b3a18cd232fd5bb5dd0a48 |
#! /usr/bin/env python
# ==========================================================================
# Shows the distribution of significances in a given significance map.
#
# Copyright (C) 2018-2020 Andreas Specovius
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GN... | ctools/ctools | examples/show_significance_distribution.py | Python | gpl-3.0 | 16,186 | [
"Gaussian"
] | 8ca21cb8a16a9a72c8dda60c68655f79e2cf571312f0b203a58ce46d99f70cb9 |
#
# @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
#... | jgonthier/psi4 | psi4/driver/driver.py | Python | lgpl-3.0 | 115,939 | [
"CFOUR",
"Gaussian",
"Molpro",
"Psi4"
] | 7453550e2a8e80415481a0f8c4514f35983e77423c3ccfe5df0c131a409740d8 |
# Copyright 2017 Canonical Ltd.
# Licensed under the LGPLv3, see LICENCE file for details.
import json
from collections import namedtuple
import macaroonbakery.bakery as bakery
ERR_INTERACTION_REQUIRED = 'interaction required'
ERR_DISCHARGE_REQUIRED = 'macaroon discharge required'
class InteractionMethodNotFound(Ex... | go-macaroon-bakery/py-macaroon-bakery | macaroonbakery/httpbakery/_error.py | Python | lgpl-3.0 | 8,215 | [
"VisIt"
] | 996e3f69d759f44dfc9d36d73c5cdf1c754d9bc9d80088b37f14f534177759ad |
#!/usr/bin/env python
"""
obsgen.py
State Estimation and Analysis for PYthon
Module to process observations:
obsgen : class to convert from raw to ROMS observations using
specific subclasses
Written by Brian Powell on 08/15/15
Copyright (c)2017 University of Hawaii under the MIT-License.
"... | ocefpaf/seapy | seapy/roms/obsgen.py | Python | mit | 50,369 | [
"Brian",
"NetCDF"
] | fe91628b787534a7a8c8ca9775b2b6721c2cb6c551953f440625498891b2f599 |
#!/usr/bin/env python
"""
Created on 2015-09-22T16:24:28
"""
from __future__ import division, print_function
import sys
import time
import argparse
try:
import numpy as np
except ImportError:
print('You need numpy installed')
sys.exit(1)
import pandas as pd
from splinter.browser import Browser
import con... | mattgiguere/doglodge | code/splinter_scrape_bf.py | Python | mit | 6,873 | [
"VisIt"
] | 64515b711cfbfdf9cf4c0e4fa6d12da39ebf59db5eb3fc51b032dc70d8c02311 |
#!/usr/bin/env python
########################################################################
# File : dirac-admin-show-task-queues
# Author : Ricardo Graciani
########################################################################
"""
Show details of currently active Task Queues
Usage:
dirac-admin-show-task-... | yujikato/DIRAC | src/DIRAC/WorkloadManagementSystem/scripts/dirac_admin_show_task_queues.py | Python | gpl-3.0 | 3,286 | [
"DIRAC"
] | 76122735a56eb9e523e04af5d12a687de4e879ed3dde3f6038d2de9aca58870c |
#!/usr/bin/env python
# coding=utf-8
# aeneas is a Python/C library and a set of tools
# to automagically synchronize audio and text (aka forced alignment)
#
# Copyright (C) 2012-2013, Alberto Pettarin (www.albertopettarin.it)
# Copyright (C) 2013-2015, ReadBeyond Srl (www.readbeyond.it)
# Copyright (C) 2015-2017, A... | danielbair/aeneas | aeneas/syncmap/smfxml.py | Python | agpl-3.0 | 3,040 | [
"VisIt"
] | 3e6321337127badd57e3183c6a1aacf5661239e9f64390b1f4dbe81f6c713b04 |
#!/usr/bin/env python
# Family size distribution of DCS from various steps of the Galaxy pipeline
#
# Author: Monika Heinzl & Gundula Povysil, Johannes-Kepler University Linz (Austria)
# Contact: monika.heinzl@edumail.at
#
# Takes a TXT file with tags of reads that were aligned to certain regions of the reference genom... | nsoranzo/tools-iuc | tools/fsd/fsd_beforevsafter.py | Python | mit | 15,840 | [
"Galaxy",
"pysam"
] | d6226e9522d09a9044d78c503d0658f4e05bb71516e7f591b1b3e2e02dfd5b6d |
__author__ = 'Jiashun'
import re
import time
starts = time.clock()
hg19 = open("/2_disk/xiaojs/python/blast/hg19.fa")
i = 0
for line in hg19:
if re.match(r">(.*)", line):
if i > 0:
fin = open('/2_disk/xiaojs/python/blast/chrom/chromosome'+str(i)+'.txt', 'w')
chrom = re.... | JiaShun-Xiao/python-implement-fast-BLAST-Basic-Local-Alignment-Search-Tool | chromosome.py | Python | mit | 692 | [
"BLAST"
] | 756ae6b7f4466332d489a34cd41e569a39c4bce9407631100eda5e7c70020c3b |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
This program reads .csv files with the simulated galaxies and saves it in the correct format for BEAGLE to load and
run,
This version has many improvements in terms of generating the catalogs.
@author: Maria Luiza L. Dantas
@date: 2017.05.29
@ve... | mdastro/Challenge | Coding/photo_catalogue.py | Python | mit | 9,391 | [
"Galaxy"
] | 69887a0d4bfae419dba07c7895104867159768916d107b5bf382626fdcffb5db |
__author__ = "Amaral LAN"
__copyright__ = "Copyright 2017-2018, Amaral LAN"
__credits__ = ["Amaral LAN"]
__license__ = "GPL"
__version__ = "1.1"
__maintainer__ = "Amaral LAN"
__email__ = "amaral@northwestern.edu"
__status__ = "Production"
import pymongo
from bs4 import BeautifulSoup
from splinter import Browser
from t... | lamaral1968/maintaining_latex_cv | scrape_google_scholar_citations.py | Python | mit | 5,688 | [
"VisIt"
] | 5643e0979a33212f384e1455ee2e950cbf43c03ca6f5e5476556d86c97a7fed7 |
import pickle
# import cPickle
import cv2
import numpy as np
import sys
import urllib
from build_model import extract_image_features
from skimage import io
def classify_image_url(img_url):
# with open('mole_random_forest_classifer.pk1', 'rb') as fid:
clf = pickle.load(open('mole_random_forest_classifier.pk1', 'rb... | agadiraju/SeniorDesign | analyze_image.py | Python | mit | 3,077 | [
"VisIt"
] | 0b45012ece9edb2f888f572ba3f05cc3075110ccd213aeab2298a382de16ec6f |
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