Keep links to bibliography and links to DOI?

[gabrielastro]

Hello!

Thanks a lot for this very helpful file! I get

pdfTeX warning (dest): name{cite.Smith+2000} has been referenced but does not e
xist, replaced by a fixed one

and the clickable links in the document point to "page 0", as hovering reveals, instead of to the bibliography.

Also, in the compact bibliography, is there a way of keeping the DOI links (to the published paper or at least the arXiv version), as for instance with yahapj? I am using bibtex and pdflatex, by the way, and my bibfile entries are from NASA ADS.

A few more small things:

• If easy, could you provide the option of removing "References" at the beginning (I commented it out by hand) and then not put a \textbullet~ before the first element? I am doing the latter by hand with: sed -i '0,/\\textbullet~/{s///}' main.bbl (thanks to an elegant GNU-sed answer)
• One more way to compactify is by replacing "Smith et al. 2010, arXiv e-prints, arXiv:1001.1001" with "Smith et al. 2010, arXiv:1001.1001". This too I am doing by hand, actually with a combined bash alias:

alias Th="pdflatex main.tex && bibtex main.bbl && sed -i '0,/\\\textbullet~/{s///}; s/, arXiv e-prints//g' main.bbl && pdflatex main.tex && pdflatex main.tex"

Maybe this could be baked in too…

In any case, thanks a lot!

[gabrielastro]

A few more things:

• Treat the period at the end of "et~al." not as a sentence full stop because it is not right and also adds more space. This one too, I am currently changing with sed e.g. {et~al.} 2010 into et al.\ 2010 but a change at the source would be better. Unfortunately, I do not not the bibtex language…
• Do not put a period at the end of the record. For this, I am currently removing periods at the ends of the lines but a few entries are longer and the period there is from "Vol." or "ed.", so that is not perfect.
• The single-author entries have an initial for the first name. This should be removed, no, to be consistent? Or at least an option would be nice.
• One could argue that letting "et al." mean "et alium" ("and one other") in the case of two-author papers is a bit of a cheat… Could the two-author papers be kept as "A & B" (again just the last names)?

Could maybe @aschmiedeke (who worked on #2) help? Thanks!

[keflavich]

These are some reasonably suggestions. You're right about "et alium" being silly, but I do plan to coauthor a paper with some:

I don't know bibtex well enough to just quickly make these changes, but if I get around to re-learning it and hacking more, I can try for some of these. Otherwise, PRs are welcome if you come up with any fixes.

[gabrielastro]

😄 I am sure you will have blooming success! Oops, I should have checked my Latin… "alius" it would be.

Thanks for your prompt answer! Unfortunately, I know no bibtex so cannot really help. I see that @lmytime has a fork with what looks like some improvements, so maybe he would be able to help!

By the way, \usepackage{microtype} also helps a bit to save space, as I saw recommended on a forum.

[lmytime]

Hi @gabrielastro , I make some improvements for self-use. It can keep links to the bibliography but I do not keep DOI items. I can help with these when I have spare time.

[gabrielastro]

Thank you very much! Indeed, I see now that the links to the bibliography work, which is a very nice improvement. (@keflavich, maybe you could pull this?) Please let me know whenever you have had time for the other points.

[keflavich]

@lmytime I'd be happy to merge in changes if you want to make a pull request. If you prefer to keep your fork independent, though, that's fine - maybe we should at least add links to it in the README here?

[lmytime]

@keflavich I re-hacked the .bst file from the newest version AAS template and improved a lot. Almost all files have been replaced. So it could not be better if you add a link to my repository: https://github.com/lmytime/tex_compact_bib
But if you prefer, I can make a pull request.

@gabrielastro I have included many suggestions you listed above. Please check my repository. Also, you can check the .bst file. I made many detailed comments for each code I changed from the original AAS .bst file. You can search MLi and tune any if you want.

[keflavich]

@lmytime I linked you from the README:
https://github.com/keflavich/tex_compact_bib/blob/master/README.rst

[gabrielastro]

@lmytime Thanks a lot for your improvements and for the helpful comments in the .bst files! (Sorry for the delay but I was and am travelling.) It is really good. Two things:

• There is an extra dot after one- or two-author entries (e.g., "Ulrich. 1976" or "Smith & Lemaître. 1917")
• I tried modifying the .bst files to have "… et al.\ YYYY" but it does not work (I get an extra dot) and I do not know bibtex… Would that be possible too?

[gabrielastro]

Two more items for @lmytime (I wanted to add it to your fork but apparently one cannot):

• I did not realise that I did not test arXiv entries but I still get "XX et al. 2024, arXiv e-prints, arXiv:NNNN" instead of just "XX et al. 2024, arXiv:NNNN".
• Is it possible to have the first author's name in bold as a compromise in legibility? But only if this is easy to do.
  In any case, thanks again!

[gabrielastro]

One more thing (for @lmytime, @aschmiedeke, @keflavich, or anyone else who understands .bst files well enough): The style of ApJ, on which tex_compact_bib is based, is to sort alphabetically by first author, then by co-author(s)'(s) name(s), and then by year. (A&A, for comparison, sorts by first author's name and then directly by year and not by the name(s) of further author(s).) This leads to papers in tex_compact_bib style that in general seem to be sorted randomly for a given author, which looks strange especially for several "et al." papers. I am not sure how difficult it would be to:

• sort only by first author and year,
• and only for several papers in one year then sort by second author, and only then have the "et al." papers (but be careful 😉).
  Thanks!

[gabrielastro]

To fix the extra dot, to simplify the "arXiv" entries, and to add \ after "et al.", one can do for now:

sed -i 's/}\./}/g; s/, arXiv e-prints//g; s/{et~al\.} /et~al.\\ /g' main.bbl

This thus fixes most of the issues above (and no guarantees but it does seem robust to long names, line breaks, etc.). In case this can be of use to anyone…

To do this with Overleaf, you need to add the .bbl file to the project and in your document to include it and comment out the bibliography:

% \bibliography{papers.bib}
\input{main.bbl}

Of course, if you add or remove references, do not forget to un-/-uncomment those lines, re-run sed, and re-upload the .bbl file. (I get the .bbl file by downloading the project on my computer with git and compiling locally.) By the way, the .bbl file added by hand to Overleaf will not get overwritten, just shadowed, by Overleaf's version when compiling with an active \bibliography{} command.

[lmytime]

Thanks @gabrielastro , I will consider including your suggestion when I have time.

[keikun555]

@lmytime when using the numeric version I found that the years were becoming "????" even though they were present in the .bib file. Did a quick scan and I think https://github.com/lmytime/tex_compact_bib/blob/master/aas_compact-numeric.bst#L856 needs to say "year" instead of "year.addlink". Making this change seems to have worked for me.

Also @keflavich I believe there's an extra ")" in the link to @lmytime 's branch.

[gabrielastro]

To add to this, @lmytime, I finally dug a bit into the .bst style file and fixed the repetitive "arXiv e-prints, arXiv:…": after the FUNCTION {first.page} … block, put (replacing also the current FUNCTION {format.journal}:

FUNCTION {or}
{
{ pop$ #1 }
’skip$
if$
}

%%%%%%%%%%% Comment by MLi: The original codes will show arXiv paper as `arXiv, arXiv:xxxx.xxxxx`. We cancel the duplicate of arXiv.
%%%%% addition by GDM: add the case that the journal is "arXiv e-prints"
%%%%%  and introduce the "or" function (thanks to the bibtex manual!)
FUNCTION {format.journal}
{ journal empty$
  journal "arXiv" =
  or
  journal "arXiv e-prints" =
  or
    { "" }
    { journal }
  if$
}
%%%%%%%%%%%

I had not realised but from arXiv, sometimes the journal is "arXiv", sometimes "arXiv e-prints", and that was the problem. The or function makes it more elegant. Thanks to the manual! Reverse Polish notation is really not so bad after all :).