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yaml-to-bibtex.py is fragile #11

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rougier opened this issue Apr 27, 2020 · 4 comments
Open

yaml-to-bibtex.py is fragile #11

rougier opened this issue Apr 27, 2020 · 4 comments

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@rougier
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rougier commented Apr 27, 2020

The yaml-to-bibtex script seems to be quite fragile and will break fro any typo in the yaml file (see for example #10). We need to make it more robust. Any taker ?
broukema added a commit to broukema/RBG08_rep that referenced this issue Jul 28, 2020
@broukema
DOI: oadoi.org; ArXiv identifiers; URL display
ee98e5d 
This commit changes the DOI links in the references to open
access DOI oadoi.org for the link and displays the DOI identifier
in the text. Related changes: \sloppy option for references is
inserted, to avoid having text extending into the margin;
(most) URL texts are made copy/pastable by redefining \nolinkurl
to print text without alteration.

The text appearance of the eprint identifers was wrong because
it inserted a space into the identifier; see
https://arxiv.org/help/arxiv_identifier . This is fixed in
this commit.

The display of URLs is enabled in this commit. Linking to the URL
archives is good, but the original URLs should be shown too -
archives can themselves be sometimes unavailable, not only URLs.

TODO: A better version of the URL fix still needs to be considered.
(Examples where the text URL is unusable in Roukema 2020
ReScience C, 6, 1, ReScience#11 = https://zenodo.org/record/3956058 are
ref [12] with
`https : / / techcrunch . com / 2019 / 07 / 29 / github - ban -`
and ref [24] with `https : / / gcc . gnu . org /`.)

* modified:   rescience.cls

This commit was cherry-picked from the original d4cc1fc.
@broukema broukema mentioned this issue Jul 28, 2020
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@schackartk
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I might like to take a stab at it (article.py as well). Are you using any code formatters or formal linters at this time?

I would like to start off by using a formatter (I would elect black, but happy to use whatever), and make sure it passes pylint and flake8. Then add type annotations and check with mypy.

I think those checks will get it pretty far in terms of robustness. From there, I would like to add more parsing checks and some unit tests (e.g. lastname and abbrvname extraction tests). Are there any objections to this proposal?

@rougier
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rougier commented Feb 14, 2023

Thanks for the proposal. We're actually transitioning to a new system (JOSS) where metadata will be entered at time of submission. Hopefully we won't need the script anymore. But I retain your proposal in case things do not work as expected.

@schackartk
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Thanks! On that note, how soon do you think the transition will be complete? I have a replication I would like to submit soon and was wondering if it would be best to wait until after the transition?

@rougier
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rougier commented Mar 27, 2023

Sorry for the delay. We have an early protype and I hope we'll make the transition by end of June but difficult to say. If you can wait a few more weeks, I should have a better timeline (don't hesitate to ping me in this thread).

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