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Branch: master
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 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 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 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 Apr 5, 2018
  1. remove long args incompatible with macOS

    dhimmel committed Apr 5, 2018
    Merges #123
    Refs #120
Commits on Mar 29, 2018
  1. CSL: do not collapse numeric citations

    dhimmel committed Mar 29, 2018
    Change style of citations from [1–4] to [1,2,3,4]
    Merges #121
Commits on Feb 26, 2018
  1. front matter: hyperlink permalink for brevity

    dhimmel committed Feb 26, 2018
    Merges #114
Commits on Feb 17, 2018
  1. include execution (#113)

    dhimmel committed Feb 17, 2018
    Most autobuild users will want to automatically update the webpage. See discussion at
    #101 (comment)
    Update README to better document autobuild.
Commits on Feb 16, 2018
  1. Versioned webpage using commit directories (#101)

    dhimmel committed Feb 16, 2018
    Closes #96
Commits on Feb 15, 2018
  1. Fix name with space issue (#110)

    dhimmel committed Feb 15, 2018
    git's config was being set to first names only, since
    names are space separated. Add quotes to prevent this.
Commits on Feb 6, 2018
  1. Update environment on 2018-02-06 (#108)

    dhimmel committed Feb 6, 2018
    Fix upstream issues:
    Extra brackets around citations in figure captions
    WeasyPrint 0.42 gets stuck
    Updated pandoc-xnos with better semantic versioning
Commits on Feb 1, 2018
  1. Webpage: specify letter page size in CSS (#107)

    dhimmel committed Feb 1, 2018
    Closes #105
Commits on Jan 14, 2018
  1. Environment updates on 2018-01-14 (#100)

    dhimmel committed Jan 14, 2018
    Upgrade Manubot with citations.tsv error message improvements
    Upgrade to weasyprint v0.42
  2. environment: explicitly set pandoc-xnos version (#99)

    dhimmel committed Jan 14, 2018
    Pinning pandoc-eqnos, pandoc-fignos, and pandoc-tablenos, but
    allowing them to trigger the installation of the latest pandoc-xnos
    version (which is a dependency) caused issues. See
    greenelab/deep-review#774 (comment)
Commits on Jan 11, 2018
  1. Enable PubMed ID citations (#98)

    dhimmel committed Jan 11, 2018
Commits on Jan 9, 2018
  1. MAINT: update packages on 2018-01-09

    dhimmel committed Jan 9, 2018
    Update pandoc to 2.1
    Reference 2018 development proposal in
    Remove temporarily broken DOI:
Commits on Dec 7, 2017
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