Manuscript fails to build: pandoc-manubot-cite invalid api version 1.20

[habi]

I've updated my rootstock-derived manuscript with some issued mentioned from the journal editorial check.

On push, the manuscript fails to build with this error:

TypeError: ('invalid api version', [1, 20])
Error running filter pandoc-manubot-cite:
Filter returned error status 1
Error: Process completed with exit code 83.

Prior to this change, my manuscript built just fine, I guess/hope the problem is unrelated to my changes.

How can I make it build again?

[fmsabatini]

Hi, I was having the same problem:
https://github.com/fmsabatini/sPlotOpen_Manuscript/actions/runs/354512839
I updated rootstock and it now seems to work
https://github.com/manubot/rootstock/blob/master/SETUP.md#merging-upstream-rootstock-changes

[dhimmel]

Thanks for the quick reports! This issue was caused by the release of panflute 2.0.3, which dropped support for older versions of the Pandoc data structure.

How to fix this:

1. add panflute=1.12.5 as a conda dependency in build/environment.yml (as in aaefe9a).
2. upgrade rootstock to the latest version using the instructions here

1 is easier, 2 is preferable. Am happy to help if you run into issues. I could even submit a PR to do 2.

[dhimmel]

To clarify the extent of the problem, all manuscript instances running old versions of Rootstock will begin failing. I think we've only had an issue like this once before. It's severe and points to the importance of reproducible computational environments. Switching from conda to docker would add an extra layer of protection, so that is on our roadmap.

[habi]

Thanks for the super-quick response and fix.
The preferable fix 2 worked well: habi/zmk-tooth-cohort-method-manuscript#11 now I'm off to re-submitting an updated PDF :)

[habi]

To clarify the extent of the problem, all manuscript instances running old versions of Rootstock will begin failing.

I think it's an important issue to tackle, but it seems that upgrading to the newest rootstock version isn't that involved.

[dhimmel]

I think it's an important issue to tackle, but it seems that upgrading to the newest rootstock version isn't that involved.

Yeah, it can depend on the number of conflicts that arise. For very old manuscripts, it can be a bit daunting.

@fmsabatini very cool manuscript at https://fmsabatini.github.io/sPlotOpen_Manuscript/. Feel free to add it to https://github.com/manubot/catalog.

[fmsabatini]

Will do!
Thanks for the indications, and for maintaining Manubot. With 160 coauthors, I'm really loving it

[agitter]

@dhimmel this issue is going to affect a lot of manuscripts. Should we make a more prominent announcement in this repository? Maybe pin this issue or even update the readme.

Thanks for fixing the underlying error quickly.