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Update rootstock #306
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Update rootstock #306
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merges manubot/rootstock#399 closes manubot/rootstock#349 Co-authored-by: Anthony Gitter <[email protected]>
merges manubot/rootstock#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 manubot/rootstock#419 closes manubot/rootstock#418 Co-authored-by: Daniel Himmelstein <[email protected]> Co-authored-by: Anthony Gitter <[email protected]>
merges manubot/rootstock#427 Co-authored-by: Daniel Himmelstein <[email protected]> Co-authored-by: Anthony Gitter <[email protected]>
merges manubot/rootstock#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 manubot/rootstock#444 Switches CURIE support and resolution from the Identifiers.org database to the Bioregistry, which is open source and community curated. See manubot/manubot@0205bd6
merges manubot/rootstock#449 closes manubot/rootstock#440 MANUBOT_USE_DOCKER=true instructs Manubot to use Docker for PDF export. Defaults to DOCKER_RUNNING (whether Docker is running on the system).
closes manubot/rootstock#451 merges manubot/rootstock#453 The ,, operator was introduced in bash 4.0, but bash on macOS is still version 3.2.
merges manubot/rootstock#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 manubot/rootstock#454 adds SPELLCHECK & MANUBOT_USE_DOCKER options to GitHub Actions triggered by workflow_dispatch.
Adds a fallback provider for DOI Content Negotiation to improve reliability of DOI metadata lookup.
merges manubot/rootstock#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"
merges manubot/rootstock#470 closes manubot/rootstock#469 Co-authored-by: Daniel Himmelstein <[email protected]>
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This reverts commit 139a0a6.
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This was referenced Aug 11, 2022
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[ci skip] This build is based on ee2e934. This commit was created by the following CI build and job: https://github.com/AlexsLemonade/OpenPBTA-manuscript/commit/ee2e934a9be7cdc77d883c031cf763e10ed49035/checks https://github.com/AlexsLemonade/OpenPBTA-manuscript/actions/runs/2842849213
github-actions bot
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Aug 11, 2022
[ci skip] This build is based on ee2e934. This commit was created by the following CI build and job: https://github.com/AlexsLemonade/OpenPBTA-manuscript/commit/ee2e934a9be7cdc77d883c031cf763e10ed49035/checks https://github.com/AlexsLemonade/OpenPBTA-manuscript/actions/runs/2842849213
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Lots of changes here, but most all of them are from directly following the instructions at https://github.com/manubot/rootstock/blob/main/SETUP.md#merging-upstream-rootstock-changes
Locally, everything still builds and looks nice, but faster and with fewer errors. Not included in this PR is the reason for the change, which was to properly support manual references, which didn't seem to work as expected before. I had actually hoped that biorxiv reference updates would be included somehow, but they appear not to be, so manual references it will be.
Sadly, the docx SVG size is also not fixed☹️
Hopefully this will also build properly in CI.