Manubot upgrade required to fix broken builds

[dhimmel]

Greetings Manubot manuscript user. On 2020-11-09, most Manubot manuscripts started encountering errors when building. This does not endanger the existing manuscript, but does make it so changes to the manuscript won't be automatically published by continuous integration.

The error occurs during pandoc-manubot-cite filter execution, when panflute detects an incompatible Pandoc version and raises TypeError: ('invalid api version', [1, 20]). The issue was triggered when version 2 of panflute was released, which dropped support for older Pandoc versions. We (the Manubot maintainers) had forgotten to pin the panflute dependency, so CI installs the most recent version from PyPI, which happens to be incompatible. See manubot/rootstock#387 for more information.

The suggested fix is to update to the latest version of manubot/rootstock, as described in SETUP: Merging upstream rootstock changes. We are happy to review upgrade pull requests (just mention it here). In addition, if you are having trouble upgrading, let us know and we can open a pull request to do so.

Upgrading to the current rootstock will also resolve manubot/rootstock#388, which relates to the following message you might have seen in your GitHub Actions CI logs:

The set-env command is deprecated and will be disabled on November 16th.

Thanks for being an early adopter of Manubot!

[apeltzer]

Thanks @dhimmel - we'll be looking into the issue and update here. Doesn't sound too difficult to get this working again

[jfy133]

@dhimmel we believe the upstream merged worked and GitHub pages apparently successfully deployed. Would be cool that you could check that it looks ok, as we personally didn't see any issues previously.

The githubpages version is at apeltzer.github.io/eager2-paper

[dhimmel]

Would be cool that you could check that it looks ok

Yep looks good. Don't see any problems with the merge commit 9444db7.

Looking at the CI logs, one of the cited URLs (https://nf-co.re/eager/docs) returns a 404:

we have written documentation and tutorials [@url:https://nf-co.re/eager/docs] that also gives guidance on how to run the pipeline

But this is a separate issue.

[jfy133]

Yeah, that link has changed since we submitted the manuscript so all good from there.

Thanks for checking!