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pytopsscrape

Python Interface for the TOPS webform (OPLIB opacities)

https://github.com/tboudreaux/pytopsscrape

Science Score: 54.0%

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    Scientific vocabulary similarity
    Low similarity (17.7%) to scientific vocabulary

Keywords

astronomy
Last synced: 7 months ago · JSON representation ·

Repository

Python Interface for the TOPS webform (OPLIB opacities)

Basic Info
  • Host: GitHub
  • Owner: tboudreaux
  • License: mit
  • Language: HTML
  • Default Branch: master
  • Homepage:
  • Size: 21 MB
Statistics
  • Stars: 2
  • Watchers: 2
  • Forks: 2
  • Open Issues: 0
  • Releases: 1
Topics
astronomy
Created over 3 years ago · Last pushed 11 months ago
Metadata Files
Readme License Citation

README.md

pyTOPSScrape

Liscence DOI

A tool for scraping OPLIB opacities from the TOPS web form and converting them into a format more similar to that used by OPAL

Documentation

This README provides a basic overview; however, more in depth documentation, including detailed descriptions of command line arguments and file formats may be found in the following links

Official Documentation (mirror)

PDF Documentation

Overview

The TOPS webform provides access to some of the most up to date high temperature radiative opacities. However, entering compositions manually into a webpage can be a chore. Especially when one needs opacities for a variety of rescaled compositions as is often the case when working stellar evolution programs.

pyTOPSScrape aims to address this by providing a simple interface to query the TOPS webform for n tables rescaled from a base composition. Moreover, pyTOPSScrape can transform the parameterization of opacities from mass density and temperature to R and temperature. Additionally, pyTOPSScrape will automatically merge tables from rescaled compositions into a single table mimicking the form of high temperature opacity tables already used by the Dartmouth Stellar Evolution Program (DSEP).

The primary interface for pyTOPSScrape is a bash script included with the package an example use of which follows

bash generateTOPStables GS98.abun rescalings.dat -d ./rawOutput -o GS98.opac -j 20

Further examples and the data files needed to run them may be found in the examples directory of this repository.

In addition to this bash script pyTOPSScrape provides a programmatic interface made up of primarily the pyTOPSScrape.api.call and pyTOPSScrape.api.TOPS2OPAL functions. These can be called individually if you wish to implement your own custom converter function (In that case you would use call and then some custom function in place of TOPS2OPAL)

Install

Prerequisites

  • python >= 3.8
  • mechanize >= 0.4.5
  • scipy >= 1.5.2
  • tqdm >= 4.50.2
  • beautifulsoup4 >= 4.8.2
  • importlib_resources >= 5.2.0

pip

If you install with pip all the dependencies should be automatically installed. bash pip install pyTOPSScrape

Source

bash git clone https://github.com/tboudreaux/pytopsscrape.git cd pytopsscrape python setup.py install

Current Potential Issues

There seem to be small variations in the results I get from the web form for the same inputs between queries. I have yet to track down if this is on my end of on there end but be aware of this. (This also makes some of the tests fail as I am doing a character to character check and not a numeric similarity within threshold check)

Examples

There are examples of the command line interface and the python interface in the examples directory of this repository. It is recommended you look at those before querying your own opacity files. The command line examples are all shell scripts with names that describe that they are examples of while the python interface example is in the form of a Jupyter notebook in the examples/Notebooks directory. If you do not have jupyter installed on your computer you should be able to view the .ipynb file on Github.

Owner

  • Name: Emily Boudreaux
  • Login: tboudreaux
  • Kind: user
  • Location: Dartmouth College

I am a Fifth Year Graduate Student at Dartmouth College studying Astrophysics. My research focuses on numerical models of stellar evolution.

Citation (CITATION.cff) 

cff-version: 1.1.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Boudreaux"
  given-names: "Thomas"
  orcid: "https://orcid.org/0000-0002-2600-7513"
title: pyTOPSScrape
version: 1.0
date-released: 2022-09-19
url: "https://github.com/tboudreaux/pytopsscrape"

GitHub Events

Total
  • Push event: 1
  • Fork event: 1
Last Year
  • Push event: 1
  • Fork event: 1

Committers

Last synced: about 3 years ago

All Time
  • Total Commits: 112
  • Total Committers: 1
  • Avg Commits per committer: 112.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Thomas Boudreaux t****s@b****m 112
Committer Domains (Top 20 + Academic)
boudreauxmail.com: 1

Issues and Pull Requests

Last synced: 8 months ago

All Time
  • Total issues: 0
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 0
  • Total pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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Packages

  • Total packages: 1
  • Total downloads:
    • pypi 9 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 4
  • Total maintainers: 1
pypi.org: pytopsscrape

Python bindings around TOPS webform for OPLIB opacities

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 9 Last month
Rankings
Dependent packages count: 6.6%
Average: 26.7%
Forks count: 30.5%
Dependent repos count: 30.6%
Stargazers count: 39.1%
Maintainers (1)
tboudreaux
Last synced: 8 months ago

Dependencies

setup.py pypi
  • beautifulsoup4 >=4.9.3
  • importlib_resources >=5.2.0
  • mechanize >=0.4.5
  • numpy >=1.19.2
  • scipy >=1.5.2
  • tqdm >=4.50.2