upgrade pandoc to version 2.14 #425

dhimmel · 2021-05-29T15:43:45Z

supersedes #386

new citeproc filter name upgrade pandoc-xnos packages refs tomduck/pandoc-fignos#85 upgrade panflute to 2.0.5 includes fix to manubot#386 (comment): Element "MetaList" received "CSL_Item" but expected <class 'panflute.base.MetaValue'> pandoc html: disable document-css in template From pandoc 2.11 (2020-10-11) changelog: > Add CSS to default HTML template (#6601, Mauro Bieg). This greatly improves the default typography in pandoc’s HTML output. The CSS is sensitive to a number of variables (e.g. mainfont, fontsize, linestretch): see the manual for details. To restore the earlier, more spartan output, you can disable this with -M document-css=false. pandoc 2.11.3 https://github.com/jgm/pandoc/releases/tag/2.11.3

dhimmel · 2021-05-29T15:44:07Z

Could also make this pandoc 2.14 if conda-forge/pandoc-feedstock#90 is merged soon.

AppVeyorBot · 2021-05-29T15:46:45Z

AppVeyor build 1.0.234 for commit 57c9d4a is now complete.

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AppVeyorBot · 2021-05-29T15:53:21Z

AppVeyor build 1.0.235 for commit 0881325 is now complete.

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AppVeyorBot · 2021-05-29T16:01:21Z

AppVeyor build 1.0.236 for commit a6d315c is now complete.

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dhimmel · 2021-05-29T16:11:06Z

This PR updates pandoc and it appears the tooltip plugin stops working. Take a look at https://ci.appveyor.com/api/buildjobs/v8df0g3o4vq6pagw/artifacts/manuscript-1.0.236-a6d315c.html.

The HTML for citations looks the same to me. With pandoc 2.13:

<p>Citation by DOI <span class="citation" data-cites="IhliSZDo">[<a href="#ref-IhliSZDo" role="doc-biblioref">1</a>]</span>.</p>

Before:

rootstock/manuscript.html

Line 233 in 5be899e

    
           <p>Citation by DOI <span class="citation" data-cites="IhliSZDo">[<a href="#ref-IhliSZDo" role="doc-biblioref">1</a>]</span>.</p>

But the HTML for references has changed. Now:

<h2 class="page_break_before" id="references">References</h2>
<!-- Explicitly insert bibliography here -->
<div id="refs" class="references csl-bib-body" role="doc-bibliography">
<div id="ref-IhliSZDo" class="csl-entry" role="doc-biblioentry">
<div class="csl-left-margin">1. </div><div class="csl-right-inline"><strong>Sci-Hub provides access to nearly all scholarly literature</strong> <div class="csl-block">Daniel S Himmelstein, Ariel Rodriguez Romero, Jacob G Levernier, Thomas Anthony Munro, Stephen Reid McLaughlin, Bastian Greshake Tzovaras, Casey S Greene</div> <em>eLife</em> (2018-03-01) <a href="https://doi.org/ckcj">https://doi.org/ckcj</a> <div class="csl-block">DOI: <a href="https://doi.org/10.7554/elife.32822">10.7554/elife.32822</a> · PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/29424689">29424689</a> · PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5832410">PMC5832410</a></div></div>
</div>

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Lines 457 to 465 in 5be899e

    
           <h2 class="page_break_before" id="references">References</h2> 
        
           <!-- Explicitly insert bibliography here --> 
        
           <div id="refs" class="references hanging-indent" role="doc-bibliography"> 
        
           <div id="ref-IhliSZDo"> 
        
           <p>1. <strong>Sci-Hub provides access to nearly all scholarly literature</strong> <br /> 
        
           Daniel S Himmelstein, Ariel Rodriguez Romero, Jacob G Levernier, Thomas Anthony Munro, Stephen Reid McLaughlin, Bastian Greshake Tzovaras, Casey S Greene<br /> 
        
           <em>eLife</em> (2018-03-01) <a href="https://doi.org/ckcj">https://doi.org/ckcj</a> <br /> 
        
           DOI: <a href="https://doi.org/10.7554/elife.32822">10.7554/elife.32822</a> · PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/29424689">29424689</a> · PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5832410">PMC5832410</a></p> 
        
           </div>

@vincerubinetti would you be able to take a look and see if the tooltip plugin needs any changes for the new HTML? If so, you can make a PR into this PR

AppVeyorBot · 2021-05-31T22:15:02Z

AppVeyor build 1.0.242 for commit fd7ff49 is now complete.

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dhimmel · 2021-05-31T22:15:51Z

I upgraded pandoc in this PR to 2.14 (release notes) which includes jgm/pandoc@3f09f53. We can use more recent HTML to prototype the tooltip updates.

Adding this note: the tooltip plugin doesn't have to work with both the new and old HTML. Working with the new alone is sufficient if that simplifies things.

vincerubinetti · 2021-05-31T22:18:35Z

@dhimmel will do this tomorrow 🤖

AppVeyorBot · 2021-05-31T23:14:59Z

AppVeyor build 1.0.243 for commit fe18096 is now complete.

Found 52 potential spelling error(s). Preview:

content/02.delete-me.md:44:adipiscing
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vincerubinetti · 2021-06-01T18:34:32Z

Some notes as I work through this:

rootstock/build/plugins/tooltips.html

Line 232 in 95bf5b2

"data-glow",

needs to add "class".

rootstock/build/plugins/tooltips.html

Line 339 in 95bf5b2

if (id.indexOf("ref-") === 0) target = target.querySelector("p");

change querySelector("p") to querySelector(":nth-child(2)")

Table references are also broken:

"jump to" plugin broken for references:

And references CSS needs some tweaking. Indent is too large, and no spacing between entries.

vincerubinetti · 2021-06-01T20:21:16Z

@dhimmel can you give me access to push commits to dhimmel:pandoc-2.13. There are more changes required here than I thought. Or perhaps you can do this PR as a branch instead of a fork.

dhimmel · 2021-06-02T02:11:26Z

@vincerubinetti perhaps you can create a branch based off of this PR's branch and then make as many commits as you'd like to that branch. I can then make the PR from your branch to dhimmel:pandoc-2.13.

Do you have your own fork of rootstock currently? If you have your own fork that you've cloned locally, then you can do:

git checkout -b dhimmel-pandoc-2.13 main
git pull https://github.com/dhimmel/manubot-rootstock.git pandoc-2.13
# make commits
# push

I want to avoid adding extra branches to this repo, since that can hamper the demonstrative nature of it. Let me know if you hit any snags. Happy to jump on a quick call to debug any git issues.

vincerubinetti · 2021-06-02T21:27:49Z

Sorry for the delay, I needed to get Manubot actually running on my Windows machine before I could tackle this (was able to do that with WSL).

One thing I noticed is this (with all plugins and themes disabled):

id's are supposed to be unique to the document. This is an error in the table-nos plugin and I believe is what is causing the double anchors and buttons.

Edit: posting this here because not 100% sure it's table-nos and not something else in the manubot pandoc config

vincerubinetti · 2021-06-02T22:29:39Z

#427

dhimmel · 2021-06-03T16:27:13Z

Closing this, since we can merge #427 instead

upgrade environment

0881325

CSL style: remove handing indent

a6d315c

update pandoc to 2.14

fd7ff49

dhimmel changed the title ~~upgrade pandoc to version 2.13~~ upgrade pandoc to version 2.14 May 31, 2021

manubot deleted a comment from AppVeyorBot May 31, 2021

USAGE: document curly-brace citation keys

fe18096

This was referenced Jun 3, 2021

Upgrade pandoc to 2.14 and fix plugin breaks #427

Merged

Table IDs are duplicated in HTML output on the <div> and <table> elements tomduck/pandoc-tablenos#31

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upgrade pandoc to version 2.14 #425

upgrade pandoc to version 2.14 #425

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upgrade pandoc to version 2.14 #425

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