Welcome to `academic-ads-bibtex` documentation!¶

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Introduction¶

The Hugo Academic admin tool allows for the ingestion of BibTeX records to add to the publication list. One easy solution is to use the NASA ADS to retrieve such records from a NASA ADS Library. However, such records often contain LaTeX \newcommand. For example:

@ARTICLE{2016ApJS..226....5L,
   author = {{Ly}, C. and {Malhotra}, S. and {Malkan}, M.~A. and {Rigby}, J.~R. and
        {Kashikawa}, N. and {de los Reyes}, M.~A. and {Rhoads}, J.~E.
        },
    title = "{The Metal Abundances across Cosmic Time (MACT) Survey. I. Optical Spectroscopy in the Subaru Deep Field}",
  journal = {\apjs},
archivePrefix = "arXiv",
   eprint = {1602.01089},
 keywords = {galaxies: abundances, galaxies: distances and redshifts, galaxies: evolution, galaxies: ISM, galaxies: photometry, galaxies: star formation},
     year = 2016,
    month = sep,
   volume = 226,
      eid = {5},
    pages = {5},
      doi = {10.3847/0067-0049/226/1/5},
   adsurl = {https://ui.adsabs.harvard.edu/abs/2016ApJS..226....5L},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}

Here, the journal name is simplified to \apjs. This ends up propagating into Hugo Academic sites. To fix this, this simple pure Python script will convert such aliases into the full journal names. It uses a journal database to conduct the replacement.

Installation¶

There are two ways to get the code:

From PyPi
From source

But first, we recommend creating a separate (virtual) environment to avoid any possible conflicts with existing software that you used. Instructions are provided for conda and virtualenv.

From PyPi¶

Using conda:

(base) $ (sudo) conda create -n bibtex python=3.7
(base) $ conda activate bibtex
(bibtex) $ (sudo) pip install academic-ads-bibtex

Using virtualenv:

(base) $ (sudo) conda install virtualenv  # if not installed
(base) $ mkdir academic-ads-bibtex
(base) $ cd academic-ads-bibtex
(base) $ virtualenv venv
(base) $ source venv/bin/activate
(venv) $ pip install academic-ads-bibtex

From Source¶

Using conda:

(base) $ (sudo) conda create -n bibtex python=3.7
(base) $ conda activate bibtex
(bibtex) $ git clone https://github.com/astrochun/academic-ads-bibtex.git
(bibtex) $ cd academic-ads-bibtex
(bibtex) $ (sudo) python setup.py install

Using virtualenv:

(base) $ (sudo) conda install virtualenv  # if not installed
(base) $ git clone https://github.com/astrochun/academic-ads-bibtex.git
(base) $ cd academic-ads-bibtex
(base) $ virtualenv venv
(base) $ source venv/bin/activate
(venv) $ python setup.py install

Examples¶

The primary script to execute is academic_ads_bibtex. The above installation will include this executable in your python environment paths.

Execution requires only one argument, which is the full path to the BibTeX file. It can be provided with the -f or --filename command-line flag.

$ academic_ads_bibtex -f /full/path/to/my_pubs.bbl

By default:

The code uses the repository-based journal database, bibtex_journals.db. This can be changed by specifying the -d or --db_filename command-line flag.
The revised BibTeX file will be based on the input filename with the prefix changed to include _revised. For example, for the above case, the output file will be /full/path/to/my_pubs_revised.bbl. This can be changed by specifying the -o or --out_filename command-line flag.

A log file is constructed: /full/path/to/academic_ads_bibtex.YYYY-MM-DD.log

License¶

This project is licensed under the GNU GPLv3 License. See the LICENSE file for details.

API Documentation¶

The `Converter` class¶

class academic_ads_bibtex.converter.Convert(filename, db_filename, out_filename, log=None)¶

Bases: object

Main class to perform BibTeX conversion for Academic compatibility

Parameters

filename – str or pathlib.Path object
db_filename – str or pathlib.Path object
out_filename – str or pathlib.Path object
log – LogClass or logger object

Variables

bibtex_content – str (from import_file)
db_dict – dict of journal database (from import_database)
bibtex_revised – str (from replace)

import_file(): Import BibTeX file
import_database(): Import journal database file
replace(): Replace journal abbreviations
write_file(): Write revised BibTeX file

import_database()¶: Import journal database file

import_file()¶: Import BibTeX file

replace()¶: Replace journal abbreviations

write_file()¶: Write revised BibTeX file

The `LogClass` class¶

class academic_ads_bibtex.logger.LogClass(logfile)¶

Bases: object

Main class to log information to stdout and ASCII logfile.

Note: This code is identical to the one used in:: https://github.com/ualibraries/LD_Cool_P

Note: Logging level is set for DEBUG for file and INFO for stdout

To use:: log = LogClass(logfile).get_logger()

Parameters: logfile – str or pathlib.Path object for logging file

get_logger()¶

Welcome to academic-ads-bibtex documentation!¶