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Does anyone know how to cite the developmental version of Avogadro 2 version 1.98 mentioned here or unpublished software in general?

I have found a BibTeX citation here though this is for a generic version of Avogadro.

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3 Answers 3

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Doing what the authors prefer

Sometimes the authors will have strong preferences for how they want their work to be cited, so I would often try to ask the authors how they would like me to cite an "unreleased" or "unpublished" or "development" version of their software. You can see my answer to: How may I install the latest version of a software? for more information about such software versions.

When the authors don't respond

It is not always easy to get a response from the original authors though, and their response might be that they do not have strong preferences for how they want their development versions to be cited, so often you will have to make a decision yourself (which is fine, and even when the authors do have strong preferences, they'll find that a lot of people accidentally or intentionally botch their preferred BibTeX format anyway).

Finding the best BibTeX entry for the software

I disagree with the URL that you provided for the Avogadro2 BibTeX entry. It didn't seem right, and then when I looked more closely, I found that it was from "Cite Bay" which seems to be a name borrowed from Pirate Bay. When seeking the authors' preferred way to cite something, I always recommend to look for something on their own website or GitHub page. I didn't see anything immediately at https://two.avogadro.cc/, and even the README of the GitHub page didn't have anything, but then I saw "Cite this repository" on the right-hand side, which gave me the following when I selected "BibTeX" as my preferred format:

@software{Hanwell_Avogadro,
author = {Hanwell, Marcus and Hutchison, Geoffrey},
license = {BSD-3-Clause},
title = {{Avogadro}},
url = {https://github.com/openchemistry/avogadrolibs}
}

This is must more likely to be the way that the authors want you to cite it, because it's what they provided on their own GitHub page.

Version numbers or no version numbers?

There's ways to add a version number, or a "retrieved on ___" date for software, just like on other "dynamic" things such as websites. However the above BibTeX entry is the one that the authors likely prefer, and it doesn't mention any specific version number.

Some authors might want you to specify the specific version number so that they can track how many citations each version is getting, or so that they can get multiple highly cited versions on their Google Scholar, or because of changes in co-authorship from version to version, or for whatever reasons they have (there's many reasonable reasons for this). Some authors might want citations no matter what the version, to all go to one place.

For your case (Avogadro2)

I personally would follow the authors' preference and use their suggested BibTeX entry, then in the paper when mentioning the software, I would say something like: "We used the nightly build from 31 February 2023" or "We built the 31 February 2023 version of the GitHub repository from source and used that".

In one of my papers I actually did this at least two times:

"To calculate these integrals, we have used a locally modified version of MOLCAS [34] in order to support larger basis sets."

"The calculations are performed using thedeveloper version of the software NECI [38]"

Reference [34] was just the standard most-recent reference for the OpenMolcas software (our local modification of it would have been done slightly before or around the time that the name "OpenMolcas" was first made, in case you're wondering why we wrote MOLCAS instead of OpenMolcas at the time).

Reference [38] was just the standard reference for NECI at the time, which was the same reference for the developer version on BitBucket and the public version on GitHub, so the distinction was made in the text rather than in the BibTeX entry.

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    $\begingroup$ Instead of referring to a date, you should also refer to the precise revision. In the case of git, the commit hash. This makes it absolutely clear what you built and used. $\endgroup$
    – Polygnome
    Aug 28, 2023 at 12:27
  • $\begingroup$ Wait, what link are you suggesting to exist between Cite Bay and The Pirate Bay? $\endgroup$ Aug 28, 2023 at 14:14
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    $\begingroup$ Seconding @Polygnome , from the perspective of a software person: please, please identify the precise version of the software you used. If you built it yourself, please identify it using the most friendly identifier that is precise: If you built whatever happened to be current at the time, that's probably a git commit ID. If you built a specific version you could use a version number instead. I can't imagine why a software author would want you to cite with no indication of the specific version, but if they do, you should ignore it. Don't add to the reproducibility crisis in science, please. $\endgroup$ Aug 28, 2023 at 20:15
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    $\begingroup$ Much as we've forgotten it, the purpose of a citation is to precisely identify the thing cited, for the benefit of the reader. It is NOT to aggrandize the publisher of the cited work in some database. $\endgroup$ Aug 28, 2023 at 20:18
  • $\begingroup$ @GlennWillen if you have an alternative answer, please post it as such. $\endgroup$ Aug 29, 2023 at 2:35
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GitHub has added support for CITATION files. Unfortunately, GitHub's support isn't great. It suggests the following BibTeX:

@software{Hanwell_Avogadro,
author = {Hanwell, Marcus and Hutchison, Geoffrey},
license = {BSD-3-Clause},
title = {{Avogadro}},
url = {https://github.com/openchemistry/avogadrolibs}
}

The problem is that anything citing Avogadro should also cite the original Avogadro paper.

@article{Hanwell2012,
  doi = {10.1186/1758-2946-4-17},
  url = {https://doi.org/10.1186/1758-2946-4-17},
  year = {2012},
  month = aug,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {4},
  number = {1},
  author = {Marcus D Hanwell and Donald E Curtis and David C Lonie and Tim Vandermeersch and Eva Zurek and Geoffrey R Hutchison},
  title = {Avogadro: an advanced semantic chemical editor,  visualization,  and analysis platform},
  journal = {Journal of Cheminformatics}
}

and for Avo2, work on the CML support:

@article{deJong2013,
  doi = {10.1186/1758-2946-5-25},
  url = {https://doi.org/10.1186/1758-2946-5-25},
  year = {2013},
  month = may,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {5},
  number = {1},
  author = {Wibe A de Jong and Andrew M Walker and Marcus D Hanwell},
  title = {From data to analysis: linking {NWChem} and Avogadro with the syntax and semantics of Chemical Markup Language},
  journal = {Journal of Cheminformatics}
}

@NikeDattani's answer does a nice job talking about citing particular builds for software in general.

Avogadro creates Zenodo DOI for each release, e.g. Version 1.97

And upon the release of Avogadro 2.0, we'll certainly have a paper submission for that, and probably also for Chemical JSON.

Suffice to say, I need to write up a few things for the README and website.

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First, follow what the publisher says.

Failing that, follow your house style.

Failing that ask for - if you have to, demand - a style meeting in your house.

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