merges https://github.com/manubot/rootstock/pull/470
closes https://github.com/manubot/rootstock/issues/469



Co-authored-by: Daniel Himmelstein <daniel.himmelstein@gmail.com>

merges https://github.com/manubot/rootstock/pull/456

DataCite content negotiation is no longer used directly for DOIs.
DOI metadata resolution should experience fewer failures,
but certain fields might experience regressions.

The following fields in metadata.yaml are now supported:

manubot-randomize-author-order: true
manubot-randomize-author-order-seed: "set a custom seed here, otherwise use HEAD git commit hash"

Adds a fallback provider for DOI Content Negotiation to improve
reliability of DOI metadata lookup.

merges https://github.com/manubot/rootstock/pull/454

adds SPELLCHECK & MANUBOT_USE_DOCKER options to
GitHub Actions triggered by workflow_dispatch.

merges https://github.com/manubot/rootstock/pull/448

Includes a full environment upgrade by removing all versions in
environment.yml and allowing the conda resolver to select
compatible versions. Notable upgrades include:

python 3.7.8 --> 3.10.0
pandoc 2.14 --> 2.16.2
weasyprint 0.42.3 --> 53.4

merges https://github.com/manubot/rootstock/pull/452

merges https://github.com/manubot/rootstock/pull/447
closes https://github.com/manubot/rootstock/issues/446

merges https://github.com/manubot/rootstock/pull/450

https://github.com/conda-forge/miniforge
https://conda-forge.org/

closes https://github.com/manubot/rootstock/issues/451
merges https://github.com/manubot/rootstock/pull/453

The ,, operator was introduced in bash 4.0,
but bash on macOS is still version 3.2.

merges https://github.com/manubot/rootstock/pull/449
closes https://github.com/manubot/rootstock/issues/440

MANUBOT_USE_DOCKER=true instructs Manubot to use Docker for PDF export.
Defaults to DOCKER_RUNNING (whether Docker is running on the system).

merges https://github.com/manubot/rootstock/pull/445

https://github.blog/changelog/2021-11-10-github-actions-input-types-for-manual-workflows/

merges https://github.com/manubot/rootstock/pull/444

Switches CURIE support and resolution from the Identifiers.org
database to the Bioregistry, which is open source and community
curated.

See https://github.com/manubot/manubot/commit/0205bd6c10d81d40d51989e23c04d8d68214ba47

merges https://github.com/manubot/rootstock/pull/439
closes https://github.com/manubot/rootstock/issues/437

merges https://github.com/manubot/rootstock/pull/438

fixes 09776607

merges https://github.com/manubot/rootstock/pull/436

* allows ad-hoc builds of main that can set BUILD_DOCX=true
* upgrade manubot to fix GitHub Actions URLs
* build.sh: set variable defaults and lowercase

merges https://github.com/manubot/rootstock/pull/427



Co-authored-by: Daniel Himmelstein <daniel.himmelstein@gmail.com>
Co-authored-by: Anthony Gitter <agitter@users.noreply.github.com>

merges https://github.com/manubot/rootstock/pull/384
refs https://github.com/manubot/rootstock/issues/249

merges https://github.com/manubot/rootstock/pull/419
closes https://github.com/manubot/rootstock/issues/418



Co-authored-by: Daniel Himmelstein <daniel.himmelstein@gmail.com>
Co-authored-by: Anthony Gitter <agitter@users.noreply.github.com>

merges https://github.com/manubot/rootstock/pull/417
closes https://github.com/manubot/rootstock/issues/401

merges https://github.com/manubot/rootstock/pull/415

merges https://github.com/manubot/rootstock/pull/409

* moves repeated and shared/generic functions to separate "core" plugin
* reorganizes html.yaml config into first and third party plugins
* removes functionality to set plugin options from url
* reformats plugins with Prettier (eg 4 space tabs to 2 space)
* removes anonymizer wrapper. Just make <script> tag into module to keep scope local
  and avoid function name conflicts. this reduces the indent of the whole script by one level.
* moves plugin specific CSS to plugins themselves
* adds scite plugin (uncomment to enable)

merges https://github.com/manubot/rootstock/pull/404
refs https://github.com/manubot/manubot/issues/123

merges https://github.com/manubot/rootstock/pull/399
closes https://github.com/manubot/rootstock/issues/349



Co-authored-by: Anthony Gitter <agitter@users.noreply.github.com>

merges https://github.com/manubot/rootstock/pull/389
closes https://github.com/manubot/rootstock/issues/388

> The `set-env` command is deprecated and will be disabled on
November 16th. Please upgrade to using Environment Files.
For more information see:
https://github.blog/changelog/2020-10-01-github-actions-deprecating-set-env-and-add-path-commands/

merges https://github.com/manubot/rootstock/pull/385

Pin panflute dependency
We use panflute to build custom pandoc filters. Panflute versions
only work with specific versions of the Pandoc AST.
We need to pin pandoc/panflute to a version pair that is known to
work together.

Pin versions of additional explicit manubot dependencies, as of
https://github.com/manubot/manubot/blob/01d69f066eaf6554111e6bcf197f7ee1fcfb240b/setup.py#L65-L80

CI: use conda-incubator/setup-miniconda on GH actions
https://github.com/conda-incubator/setup-miniconda
appears to have replaced https://github.com/goanpeca/setup-miniconda.
The later is currently 31 commits behind.

merges https://github.com/manubot/rootstock/pull/383

pandoc-eqnos upgrade addresses the following error:
UnboundLocalError: local variable 'ret' referenced before assignment
https://github.com/tomduck/pandoc-eqnos/issues/43

Hold back pandoc due to the lack of panflute support.

Switch commands in build/README.md to be relative to the repo root.

merges https://github.com/manubot/rootstock/pull/378
closes https://github.com/manubot/rootstock/pull/377
refs https://github.com/manubot/rootstock/pull/375

merges https://github.com/manubot/rootstock/pull/375
supersedes https://github.com/manubot/rootstock/pull/373



By default, these plugins are disabled. Enable in
`build/pandoc/defaults/html.yaml`.

Co-authored-by: Matthew Turk <matthewturk@gmail.com>

merges https://github.com/manubot/rootstock/pull/372
closes https://github.com/manubot/rootstock/issues/369

merges https://github.com/manubot/rootstock/pull/374

From https://github.com/manubot/rootstock/runs/1212860980#step:2:10:

> Warning: The `set-env` command is deprecated and will be disabled soon.
> Please upgrade to using Environment Files.
> For more information see:
> https://github.blog/changelog/2020-10-01-github-actions-deprecating-set-env-and-add-path-commands/

https://docs.github.com/en/free-pro-team@latest/actions/reference/workflow-commands-for-github-actions#setting-an-environment-variable

merges https://github.com/manubot/rootstock/pull/371
closes https://github.com/manubot/rootstock/issues/368

https://stackoverflow.com/a/55283209/4651668
https://stackoverflow.com/a/18035947/4651668

merges https://github.com/manubot/rootstock/pull/366

clarifies that
1. OWNER can be an organization!
2. no additional configuration is needed for github actions.

merges https://github.com/manubot/rootstock/pull/356

merges https://github.com/manubot/rootstock/pull/348
closes https://github.com/manubot/rootstock/issues/344

Update docx files that can be supplied to Pandoc via --reference-doc.

Recreate build/themes/default.docx from scratch (via a blank pandoc output).
Improves aesthetic and fixes issues like invisible table gridlines.

Add build/themes/nih-grant.docx that produces documents that adhere
to many of the National Institutes of Health (NIH) formatting requirements.
https://grants.nih.gov/grants/how-to-apply-application-guide/format-and-write/format-attachments.htm

merges https://github.com/manubot/rootstock/pull/346
closes https://github.com/manubot/rootstock/issues/155
supersedes https://github.com/manubot/rootstock/pull/158
tested via https://github.com/manubot/manubot/pull/110
refs https://twitter.com/csl_styles/status/1270049414200074243



Add a space delimiter across the style.
Fixes some references where there is a missing space after the title,
when authors are missing.

Set second-field-align="flush"
This option is not supported by pandoc yet, but it more closely resembles
hanging-indent="true", which pandoc is currently using to layout the
bibliography.

Co-authored-by: Rintze M. Zelle <rintze.zelle@gmail.com>

merges https://github.com/manubot/rootstock/pull/345

Enhancements related to Hypothes.is annotations plugin at build/plugins/hypothesis.html.
Adds button to load hypothesis plugin, rather than automatically loading it.
closes https://github.com/manubot/rootstock/issues/281 

PDF build / print page view will no longer include annotations by default,
since hypothesis not loaded until activated.
closes https://github.com/manubot/rootstock/issues/280

Fix overlap of hypothesis sidebar and table of contents plugin on small screens.
closes https://github.com/manubot/rootstock/issues/306

Change default font sizes of h1 through h6 to be larger than base text size,
breaking with browser precedent
closes https://github.com/manubot/rootstock/issues/293

merges https://github.com/manubot/rootstock/pull/342

Includes major updates to how citations are processed by the pandoc-manubot-cite filter.
See the following commit messages for more information:

- https://github.com/manubot/manubot/commit/7055bcc6524fdf1ef97d838cf0158973e2061595
- https://github.com/manubot/manubot/commit/47b03e0c202e6a0561e6548ba08a4ad790f56eee

Removes requirement to prefix certain citekeys with raw: or tag:
Removes support for deprecated `content/citation-tags.tsv`.
Switches from tag to alias terminology for citation aliases. 
closes https://github.com/manubot/manubot/issues/120

Removes pandas and jsonref dependencies, which are no longer needed.