Error running filter pandoc-manubot-cite

[thorowitz]

I just made a minor tweak to a manuscript file, and now I get an "all checks have failed" error when I try to merge the pull request. If I read this correctly, it seems to be a failure in the pandoc-manubot-cite process, but I am mystified because I have not changed any citations. I have copied the relevant part of the job error message below:

[INFO] Running filter pandoc-manubot-cite 
Traceback (most recent call last): 
File "/usr/share/miniconda3/envs/manubot/bin/pandoc-manubot-cite", line 8, in <module> 
sys.exit(main()) 
File "/usr/share/miniconda3/envs/manubot/lib/python3.7/site-packages/manubot/pandoc/cite_filter.py", line 222, in main 
doc = pf.load(input_stream=args.input) 
File "/usr/share/miniconda3/envs/manubot/lib/python3.7/site-packages/panflute/io.py", line 58, in load 
doc = json.load(input_stream, object_hook=from_json) 
File "/usr/share/miniconda3/envs/manubot/lib/python3.7/json/__init__.py", line 296, in load 
parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw) 
File "/usr/share/miniconda3/envs/manubot/lib/python3.7/json/__init__.py", line 361, in loads 
return cls(**kw).decode(s) 
File "/usr/share/miniconda3/envs/manubot/lib/python3.7/json/decoder.py", line 337, in decode 
obj, end = self.raw_decode(s, idx=_w(s, 0).end()) 
File "/usr/share/miniconda3/envs/manubot/lib/python3.7/json/decoder.py", line 353, in raw_decode 
obj, end = self.scan_once(s, idx) 
File "/usr/share/miniconda3/envs/manubot/lib/python3.7/site-packages/panflute/elements.py", line 1371, in from_json 
return _res_func[tag](c) 
File "/usr/share/miniconda3/envs/manubot/lib/python3.7/site-packages/panflute/table_elements.py", line 391, in table_from_json 
caption = Caption(*c[1][1], short_caption=c[1][0]) 
IndexError: list index out of range 
Error running filter pandoc-manubot-cite: 
Filter returned error status 1 
Error: Process completed with exit code 83.

[agitter]

This isn't an error you caused, it has to do with the Manubot build environment changing in an unexpected way. The two solutions in #387 (comment) will fix this. If you want to upgrade rootstock to the latest version and get stuck, we can help with a pull request.

[thorowitz]

Thanks! Implemented solution #1, and that worked.

[thorowitz]

I'm trying to update the rootstock, and have run into difficulties. My pull request failed checks at "set environment variables" with the following errors:
Error: Unable to process command '::set-env name=TRIGGERING_SHA_7::cd0f78e' successfully.

Error: The set-envcommand is disabled. Please upgrade to using Environment Files or opt into unsecure command execution by setting theACTIONS_ALLOW_UNSECURE_COMMANDSenvironment variable totrue. For more information see: https://github.blog/changelog/2020-10-01-github-actions-deprecating-set-env-and-add-path-commands/

[agitter]

This is caused by the an old version of the "Set Environment Variables" step and the setup-miniconda action in the GitHub Actions workflow. Is your .github/workflows/manubot.yaml file in sync with the manubot/rootstock version?

Did you execute the git pull --no-ff --no-rebase --no-commit rootstock master step to get the latest version of rootstock before updating your manuscript?

[thorowitz]

manubot.yml is bot yet in sync. That's part of the whole package of changes I'm trying to push.

I did execute git pull --no-ff --no-rebase --no-commit rootstock master

[agitter]

Perhaps something happened in a recent or prior merge such that parts of manubot.yaml are not being updated in your pull request. The easiest solution might be to manually copy these parts of manubot.yaml from rootstock into your version:

rootstock/.github/workflows/manubot.yaml

Lines 17 to 21 in 97b2948

	- name: Set Environment Variables
	run: |
	TRIGGERING_SHA=${GITHUB_PULL_REQUEST_SHA:-$GITHUB_SHA}
	echo "TRIGGERING_SHA_7=${TRIGGERING_SHA::7}" >> $GITHUB_ENV
	echo "TRIGGERING_SHA: $TRIGGERING_SHA"

and

rootstock/.github/workflows/manubot.yaml

Line 35 in 97b2948

uses: conda-incubator/setup-miniconda@v2

If you want help with this, I could make a pull request in your repository.

[thorowitz]

Yes, that would be great if you could create a pull request!

t

[thorowitz]

Thanks for creating the pull request. I successfully merged it. However, I'm still getting the Unable to process command '::set-env name=TRIGGERING_SHA_7::a79967e' successfully. error.

[agitter]

The problem is that the pull request was not merged into your master branch. You'll need to reopen #167 and then merge that to master. It was closed, not merged.

[thorowitz]

I'm not entirely sure what happened there, but it seems to be working again. Thanks!

[agitter]

After you reopened pull request 167 in your repository, I merged it to master. That applied the rootstock updates to your main builds. You should be all set now.