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Branch: master
Commits on Mar 15, 2019
  1. HTML: fix auto setting for TOC plugin, revert margin to 0.75in

    vincerubinetti authored and dhimmel committed Mar 15, 2019
    Merges #193
Commits on Mar 14, 2019
  1. HTML plugins: lightbox, tooltips, toc tweaks

    vincerubinetti authored and dhimmel committed Mar 14, 2019
    Merges #191
Commits on Mar 13, 2019
  1. CSS: background colors, alignment classes, print control

    vincerubinetti authored and dhimmel committed Mar 13, 2019
    Merges #188
    Miscellaneous changes to default.html style including background colors,
    text/page alignment classes, print control styles.
    Switch margins to 0.75 inches to reduce pages needed to print manuscript.
  2. Update content/ to show formatting

    vincerubinetti authored and dhimmel committed Mar 13, 2019
    Merges #169
Commits on Mar 12, 2019
  1. HTML: add modular plugins for webpage interactivity

    vincerubinetti authored and dhimmel committed Mar 12, 2019
    Merges #179
    Closes #185
    Improves #165
    Adds plugins that can be included in the pandoc build commands
    to enable various interactive frontend features. Plugins are located in
    `build/plugins/` and consist of:
    - accordion (new)
    - analytics (modified)
    - anchors (replaced)
    - hypothesis (modified)
    - jump-to-first (new)
    - lightbox (new)
    - link-highlight (new)
    - math (modifies how MathJax is loaded)
    - table-of-contents (new)
    - table-scroll (new)
    - tooltips (new)
  2. Update rootstock manual JSON CSL in example reference

    agitter authored and dhimmel committed Mar 12, 2019
    Merges #186
Commits on Mar 8, 2019
  1. HTML: default theme updates

    vincerubinetti authored and dhimmel committed Mar 8, 2019
    Merges #178
    Various aesthetic updates, refactoring, edits for plugins, and additional comments
Commits on Mar 2, 2019
  1. CI: only deploy on push TRAVIS_EVENT_TYPE

    dhimmel committed Mar 2, 2019
    Merges #184
    Previously, ci/ could be run for push, api, or cron builds,
    but not for pull_request builds. This commit further restricts when
    deployment is run to just push builds.
Commits on Feb 28, 2019
  1. Fix random string & psutil install

    slochower authored and dhimmel committed Feb 28, 2019
    Merges #182
    Update to replace the correct random string
    Fix missing x86_64-conda_cos6-linux-gnu-gcc in psutil install by installing
    psutil using conda.
    .travis.yml: one configuration option per line (non-functional whitespace change)
Commits on Feb 13, 2019
  1. Relocate repository to manubot/rootstock

    dhimmel committed Feb 13, 2019
Commits on Feb 6, 2019
  1. shortDOI support & update environment on 2019-02-06

    dhimmel committed Feb 6, 2019
    Merges #174
    * Environment update on 2019-02-06
    Does not upgrade weasyprint or cairo, due to the following error during
    WeasyPrint execution:
    OSError: dlopen() failed to load a library: cairo / cairo-2 / cairo-gobject-2
    Specify cairocffi dependency in environment.yml, since v0.9 from PyPI
    seemed to trigger the OSError.
    * Add shortDOI support & usage
    Update repo to
    greenelab/manubot relocated to manubot/manubot as per
    manubot/manubot#94. still references greenelab/manubot,
    however it is not worth creating merge conflicts to
    update just this.
Commits on Feb 1, 2019
  1. HTML themes: rewrite default.html with new style

    vincerubinetti authored and dhimmel committed Feb 1, 2019
    Merges #171
    Various display improvements, simplified code structure with modern
    best practices.
Commits on Jan 29, 2019
  1. Explicit fill color in icon SVGs

    vincerubinetti authored and dhimmel committed Jan 29, 2019
    Merges #172
    Fixes issue that fill="currentColor" did not work as expected because SVGs
    are loaded from URLs rather than defined inline. Hence, revert to specifying
    a specific color.
Commits on Jan 28, 2019
  1. Update frontmatter author icons

    vincerubinetti authored and dhimmel committed Jan 28, 2019
    Merges #166
    Improves formatting and centering of icons.
    Uses github and twitter icons from
  2. Refactor HTML assets to build/themes & build/plugins

    vincerubinetti authored and dhimmel committed Jan 28, 2019
    Merges #168
    Refs #163
Commits on Jan 22, 2019
  1. CSS improvements to github-pandoc.css

    vincerubinetti authored and dhimmel committed Jan 22, 2019
    Merges #159
    When printing, hide hypothesis toolbar and fix page margins.
    Fix pandoc syntax highlighting quirk: long width code boxes
    overflow outside of container.
    Fix superscript size issue documented at
    greenelab/meta-review#88 (comment)
Commits on Jan 21, 2019
  1. front-matter: omit null or empty author fields

    dhimmel committed Jan 21, 2019
    Merges #161
Commits on Jan 3, 2019
  1. Update environment & examples on 2019-01-03

    dhimmel committed Jan 3, 2019
    Merges #153
    Updates pandoc to v2.5.
Commits on Dec 18, 2018
  1. Upgrades on 2018-12-18 including wikidata citation support

    dhimmel committed Dec 18, 2018
    Merges #151
    * Upgrade manubot python package with Wikidata citations
    * Remove DataCite DOI from
    * Add additional manuscripts to USAGE examples
Commits on Dec 11, 2018
  1. webpage utility: upgrade preexisting timestamps

    dhimmel committed Dec 11, 2018
    Merges #150
    Attempt to upgrade preexisting timestamps during continuous
    deployment, such that manually upgrading incomplete timestamps
    should no longer be necessary.
    Add two mutually exclusive arguments to
    --ots-cache and --no-ots-cache for configuring the OTS client
    Disable timestamp caching for (i.e. on Travis CI)
Commits on Nov 20, 2018
  1. Enable ISBN citation support

    dhimmel committed Nov 20, 2018
    Merges #149
    * Enable ISBN citaiton support
    * Update URL citation
    Previous URL citation contained "?", therefore requiring a citation tag.
Commits on Nov 16, 2018
  1. add checkout command to rootstock upgrade

    dhimmel and agitter committed Nov 16, 2018
    Merges #148
    Co-Authored-By: Daniel Himmelstein <>
    Co-Authored-By: Anthony Gitter <>
Commits on Nov 15, 2018
  1. Update manubot to v0.2.1 with PMCID fix

    dhimmel committed Nov 15, 2018
    Merges #147
    Update manubot version on 2018-11-15 to
    Includes migration of PMCID citations to Literature Citation Exporter.
    Update conda-forge dependencies
Commits on Nov 12, 2018
  1. Add pango to conda environment

    dhimmel committed Nov 12, 2018
    Closes #144
    Merges #146
    pango is required by WeasyPrint during the PDF build. While usually
    built-in to the OS on Linux, it is not pre-installed on macOS.
    macOS were installing pango using homebrew, which led to a
    segmentation fault error.
    Pango is available on conda-forge for linux and mac:
    Adding pango to environment.yml prevents conda environment
    installation on Windows, but has the benefits of standardizing
    the pango version on linux and mac platforms and preventing the
    mac homebrew issue.
Commits on Nov 9, 2018
  1. Support BUILD_PDF=false environment variable

    dhimmel committed Nov 9, 2018
    Merges #145
    Closes #122
    * Add BUILD_PDF environment variable
    BUILD_PDF is considered "true" unless specifically set to "false" tolerate missing output/manuscript.pdf
    Refs #144 (comment)
    ots stamp in do not fail if BUILD_PDF=false
    * Delete existing images symlink in PDF build script
    When an images directory exists, do not create a symbolic link with
    source images/images. More info in ln documentation:
    Ignore /images temporary symlink
Commits on Nov 2, 2018
  1. Ignore OS specific files

    dhimmel committed Nov 2, 2018
    Merges #142
Commits on Oct 30, 2018
  1. Enable raw citations & small USAGE updates

    dhimmel committed Oct 30, 2018
    Merges #141
    * Update USAGE with current URLs & recs
    Use HTTPS URLs where possible
    Switch SVG embedding solution from, which is shutting
    down, to the native GitHub solution.
    * Enable raw citations
    Update with raw citation example.
    Also update citations in
Commits on Oct 23, 2018
  1. Bugfix environment updates on 2018-10-23

    dhimmel committed Oct 23, 2018
    Merges #140
    Closes #136
    Updates Manubot to fix empty date-parts issue
    Fix opentimestamps incompatible pinned versions
Commits on Oct 9, 2018
  1. Case sensitive environment variables in setup instructions

    agitter committed Oct 9, 2018
    Merges #138
    Closes #137
    * Case sensitive environment variables
    * Update phrasing borrowing dhimmel ideas
    * Change account to username
Commits on Oct 8, 2018
  1. Update & environment on 2018-10-08

    dhimmel committed Oct 8, 2018
    Merges #135
    Closes manubot/manubot#59
    * suggested citation & acknowledgments
    Mostly copied from
    * Update environment on 2018-10-08
    Updates to
    which is slightly past the manubot v0.2.0 release.
    jsonschema & jsonref should have been added to the environment
    previousely since they are required by manubot for JSON schema
    validation, but were not added.
    Do not upgrade to Python 3.7 due to collections DeprecationWarnings
    in several packages. Fixed warning in
    gazpachoking/jsonref#26, but several remain.
    * Travis CI: update miniconda to 4.5.11
Commits on Oct 6, 2018
  1. CSL: display="block" every other group

    dhimmel committed Oct 6, 2018
    Merges #134
    Previous blocks were causing a blank line after the author line before
    the journal-date-URL line in markdown output. Placing blocks at every
    other line seems to be the solution required for pandoc-citeproc / pandoc
    to properly place the newlines.
Commits on Aug 31, 2018
  1. Upgrade manubot & environment on 2018-08-22

    dhimmel authored and agitter committed Aug 31, 2018
    Merges #132
    * Upgrade manubot to use process subcommand
    * Upgrade environment to latest versions on 2018-08-22
    * CSL style: block to display identifiers
Commits on Aug 3, 2018
  1. CSS: figure & table caption alignment

    dhimmel committed Aug 3, 2018
    Merges #131
    Closes #130
    * Left-align table caption text
    * figure img style: center img, left-align text
Commits on Jul 10, 2018
  1. Add 3 additional example manuscripts to

    dhimmel committed Jul 10, 2018
    Merges #127
    Add TFSEE, global emissions, & yt 3.0 manuscripts
Commits on Jun 18, 2018
  1. build/ minor fix to build instructions

    agitter authored and dhimmel committed Jun 18, 2018
    Merges #125
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