Update Manubot on 2018-11-06

Updates through manubot/rootstock@135f451

.gitignore

@@ -25,5 +25,17 @@ __pycache__/
 # Don't make budgets public
 budgets/
 
-# Stupid Mac Folder crap
-.DS_Store
+# Operating system specific files
+
+## Linux
+*~
+.Trash-*
+
+## macOS
+.DS_Store
+._*
+.Trashes
+
+## Windows
+Thumbs.db
+[Dd]esktop.ini

.travis.yml

@@ -5,7 +5,7 @@ branches:
   only:
     - master
 before_install:
-  - wget https://repo.continuum.io/miniconda/Miniconda3-4.5.4-Linux-x86_64.sh
+  - wget https://repo.continuum.io/miniconda/Miniconda3-4.5.11-Linux-x86_64.sh
     --output-document miniconda.sh
   - bash miniconda.sh -b -p $HOME/miniconda
   - source $HOME/miniconda/etc/profile.d/conda.sh

SETUP.md

@@ -9,10 +9,12 @@ Setup is supported on Linux and macOS, but [**not on Windows**](https://github.c
 
 First, you must configure two environment variables (`OWNER` and `REPO`).
 These variables specify the GitHub repository for the manuscript (i.e. `https://github.com/OWNER/REPO`).
+Make sure that the case of `OWNER` matches how your username is displayed on GitHub.
+In general, assume that all commands in this setup are case-sensitive.
 **Edit the following commands with your manuscript's information:**
 
 ```sh
-# GitHub account (change from greenelab)
+# GitHub username (change from greenelab)
 OWNER=greenelab
 # Repository name (change from manubot-rootstock)
 REPO=manubot-rootstock

USAGE.md

@@ -1,18 +1,18 @@
 # Manubot usage guidelines
 
-This repository uses the [Manubot](https://github.com/greenelab/manubot) to automatically produce a manuscript from its source.
+This repository uses [Manubot](https://github.com/greenelab/manubot-rootstock) to automatically produce a manuscript from the source in the [`content`](content) directory.
 
 ## Manubot markdown
 
 Manuscript text should be written in markdown files, which should be located in [`content`](content) with a digit prefix for ordering (e.g. `01.`, `02.`, etc.) and a `.md` extension.
 
-For basic formatting, check out the [CommonMark Help](http://commonmark.org/help/) page for an introduction to the formatting options provided by standard markdown.
-In addition, manubot supports an extended version of markdown, tailored for scholarly writing, which includes [Pandoc's Markdown](http://pandoc.org/MANUAL.html#pandocs-markdown) and the extensions discussed below.
+For basic formatting, check out the [CommonMark Help](https://commonmark.org/help/) page for an introduction to the formatting options provided by standard markdown.
+In addition, Manubot supports an extended version of markdown, tailored for scholarly writing, which includes [Pandoc's Markdown](https://pandoc.org/MANUAL.html#pandocs-markdown) and the extensions discussed below.
 
 Within a paragraph in markdown, single newlines are interpreted as whitespace (same as a space).
 A paragraph's source does not need to contain newlines.
 However, "one paragraph per line" makes the git diff less precise, leading to less granular review commenting, and makes conflicts more likely.
-Therefore, we recommend using [semantic linefeeds](http://rhodesmill.org/brandon/2012/one-sentence-per-line/ "Semantic Linefeeds. Brandon Rhodes. 2012") — newlines between sentences.
+Therefore, we recommend using [semantic linefeeds](https://rhodesmill.org/brandon/2012/one-sentence-per-line/ "Semantic Linefeeds. Brandon Rhodes. 2012") — newlines between sentences.
 We have found that "one sentence per line" is preferable to "word wrap" or "one paragraph per line".
 
 ### Tables
@@ -30,7 +30,7 @@ Table: Caption for this example table. {#tbl:example-id}
 
 Support for table numbering and citation is provided by [`pandoc-tablenos`](https://github.com/tomduck/pandoc-tablenos).
 Above, `{#tbl:example-id}` sets the table ID, which creates an HTML anchor and allows citing the table like `@tbl:example-id`.
-For easy creation of markdown tables, check out the [Tables Generator](http://www.tablesgenerator.com/markdown_tables) webapp.
+For easy creation of markdown tables, check out the [Tables Generator](https://www.tablesgenerator.com/markdown_tables) webapp.
 
 ### Figures
 
@@ -45,11 +45,11 @@ This figure can be cited in the text using `@fig:example-id`.
 In context, a figure citation may look like: `Figure {@fig:example-id}B shows …`.
 
 For images created by the manuscript authors that are hosted elsewhere on GitHub, we recommend using a [versioned](https://help.github.com/articles/getting-permanent-links-to-files/) GitHub URL to embed figures, thereby preserving exact image provenance.
-When embedding SVG images hosted on GitHub, passing the URL through [RawGit](https://rawgit.com/) is necessary.
-An example of a URL that has been passed through RawGit is:
+When embedding SVG images hosted on GitHub, it's necessary to append `?sanitize=true` to the `raw.githubusercontent.com` URL.
+For example:
 
 ```
-https://cdn.rawgit.com/greenelab/scihub/572d6947cb958e797d1a07fdb273157ad9154273/figure/citescore.svg
+https://raw.githubusercontent.com/greenelab/scihub/572d6947cb958e797d1a07fdb273157ad9154273/figure/citescore.svg?sanitize=true
 ```
 
 Figures placed in the [`content/images`](content/images) directory can be embedded using their relative path.
@@ -59,19 +59,19 @@ For example, we embed an [ORCID](https://orcid.org/) icon inline using:
 ![ORCID icon](images/orcid.svg){height="13px"}
 ```
 
-The bracketed text following the image declaration is interpreted by Pandoc's [`link_attributes`](http://pandoc.org/MANUAL.html#extension-link_attributes) extension.
+The bracketed text following the image declaration is interpreted by Pandoc's [`link_attributes`](https://pandoc.org/MANUAL.html#extension-link_attributes) extension.
 For example, the following will override the figure number to be "S1" and set the image width to 5 inches:
 
 ```md
 {#fig:supplement tag="S1" width="5in"}
 ```
 
-We recommend always specifying the width of SVG images (even if just `width="100%"`), since otherwise SVGs may not render properly in the [WeasyPrint](http://weasyprint.org/) PDF export.
+We recommend always specifying the width of SVG images (even if just `width="100%"`), since otherwise SVGs may not render properly in the [WeasyPrint](https://weasyprint.org/) PDF export.
 
 ### Citations
 
-Manubot supports Pandoc [citations](http://pandoc.org/MANUAL.html#citations) via `pandoc-citeproc`.
-However, Manubot performs automated citation processing and metadata retrieval on raw citations.
+Manubot supports Pandoc [citations](https://pandoc.org/MANUAL.html#citations) via `pandoc-citeproc`.
+However, Manubot performs automated citation processing and metadata retrieval on in-text citations.
 Therefore, citations must be of the following form: `@source:identifier`, where `source` is one of the options described below.
 When choosing which source to use for a citation, we recommend the following order:
 
@@ -80,6 +80,8 @@ When choosing which source to use for a citation, we recommend the following ord
 3. PubMed ID, cite like `@pmid:26158728`.
 4. _arXiv_ ID, cite like `@arxiv:1508.06576v2`.
 5. URL / webpage, cite like `@url:http://openreview.net/pdf?id=Sk-oDY9ge`.
+6. For references that do not have any of the persistent identifiers above, use a raw citation like `@raw:old-manuscript`.
+Metadata for raw citations must be provided manually.
 
 Cite multiple items at once like:
 
@@ -109,20 +111,32 @@ The Manubot workflow requires the bibliographic details for references (the set
 The Manubot attempts to automatically retrieve metadata and generate valid citeproc JSON for references, which is exported to `output/references.json`.
 However, in some cases the Manubot fails to retrieve metadata or generates incorrect or incomplete citeproc metadata.
 Errors are most common for `url` references.
-For these references, you can manually specify the correct citeproc in [`content/manual-references.json`](content/manual-references.json), which will override the automatically generated reference data.
-To do so, create a new citeproc record that contains the field `"standard_citation"` with the appropriate reference identifier as its value.
+For these references, you can manually specify the correct CSL Data in [`content/manual-references.json`](content/manual-references.json), which will override the automatically generated reference data.
+To do so, create a new CSL JSON Item that contains the field `"standard_citation"` with the appropriate reference identifier as its value.
 The identifier can be obtained from the `standard_citation` column of `citations.tsv`, which is located in the `output` branch or in the `output` subdirectory of local builds.
 As an example, `manual-references.json` contains:
 
 ```json
 "standard_citation": "url:https://github.com/greenelab/manubot-rootstock"
 ```
 
+The metadata for `raw` citations must be provided in `manual-references.json` or an error will occur.
+For example, to cite `@raw:private-message` in a manuscript, a corresponding CSL Item in `manual-references.json` is required, such as:
+
+```json
+{
+  "type": "personal_communication",
+  "standard_citation": "raw:private-message",
+  "title": "Personal communication with Doctor X"
+}
+```
+
+All references provided in `manual-references.json` must provide values for the `type` and `standard_citation` fields.
 For guidance on what CSL JSON should be like for different document types, refer to [these examples](https://github.com/aurimasv/zotero-import-export-formats/blob/a51c342e66bebd97b73a7230047b801c8f7bb690/CSL%20JSON.json).
 
 ## Manuscript metadata
 
-[`content/metadata.yaml`](content/metadata.yaml) contains manuscript metadata that gets passed through to Pandoc, via a [`yaml_metadata_block`](http://pandoc.org/MANUAL.html#extension-yaml_metadata_block).
+[`content/metadata.yaml`](content/metadata.yaml) contains manuscript metadata that gets passed through to Pandoc, via a [`yaml_metadata_block`](https://pandoc.org/MANUAL.html#extension-yaml_metadata_block).
 `metadata.yaml` should contain the manuscript `title`, `authors` list, `keywords`, and `lang` ([language tag](https://www.w3.org/International/articles/language-tags/ "W3C: Language tags in HTML and XML")).
 Additional metadata, such as `date`, will automatically be created by the Manubot.
 Manubot uses the [timezone](https://en.wikipedia.org/wiki/List_of_tz_database_time_zones) specified in [`build.sh`](build/build.sh) for setting the manuscript's date.
@@ -167,3 +181,20 @@ For additional examples, check out existing manuscripts that use the Manubot (so
 + The Manubot 2018 Development Proposal ([source](https://github.com/greenelab/manufund-2018), [manuscript](https://greenelab.github.io/manufund-2018/))
 
 If you are using the Manubot, feel free to submit a pull request to add your manuscript to the list above.
+
+## Citing Manubot
+
+To cite the Manubot project or for more information on its design and history, see `@url:https://greenelab.github.io/meta-review/`:
+
+> **Open collaborative writing with Manubot**<br>
+Daniel S. Himmelstein, David R. Slochower, Venkat S. Malladi, Casey S.
+Greene, Anthony Gitter<br>
+_Manubot Preprint_ (2018) <https://greenelab.github.io/meta-review/>
+
+## Acknowledgments
+
+We would like to thank the contributors and funders whose support makes the Manubot project possible.
+Specifically, Manubot development has been financially supported by:
+
+- the **Alfred P. Sloan Foundation** in [Grant G-2018-11163](https://sloan.org/grant-detail/8501) to [**@dhimmel**](https://github.com/dhimmel).
+- the **Gordon & Betty Moore Foundation** ([**@DDD-Moore**](https://github.com/DDD-Moore)) in [Grant GBMF4552](https://www.moore.org/grant-detail?grantId=GBMF4552) to [**@cgreene**](https://github.com/cgreene).

build/assets/style.csl

@@ -51,7 +51,7 @@
       <group display="block">
         <text macro="author"/>
       </group>
-      <group display="block" delimiter=" ">
+      <group delimiter=" ">
         <text macro="venue" font-style="italic"/>
         <date variable="issued" prefix="(" suffix=")">
           <date-part name="year"/>
@@ -60,7 +60,7 @@
         </date>
         <text variable="URL"/>
       </group>
-      <group delimiter=" · ">
+      <group display="block" delimiter=" · ">
         <text variable="DOI" text-case="lowercase" prefix="DOI: "/>
         <text variable="PMID" prefix="PMID: "/>
         <text variable="PMCID" prefix="PMCID: "/>

build/environment.yml

@@ -6,23 +6,25 @@ dependencies:
   - conda-forge::cffi=1.11.5
   - conda-forge::ghp-import=0.5.5
   - conda-forge::jinja2=2.10
+  - conda-forge::jsonschema=2.6.0
   - conda-forge::pandas=0.23.4
-  - conda-forge::pandoc=2.2.2
-  - conda-forge::python=3.6.6
-  - conda-forge::pyyaml=3.12
+  - conda-forge::pandoc=2.3.1
+  - conda-forge::python=3.6.5
+  - conda-forge::pyyaml=3.13
   - conda-forge::requests=2.19.1
   - conda-forge::watchdog=0.8.3
   - pip:
     - errorhandler==2.0.1
-    - git+https://github.com/greenelab/manubot@66a6efc6f4b84153a813aa423ec00725ed1417c5
+    - git+https://github.com/greenelab/manubot@a008126b39e3bd4b80ebaa5af9f9fa2f30b3a670
+    - jsonref==0.2
     - opentimestamps-client==0.6.0
-    - opentimestamps==0.4.0
+    - opentimestamps==0.3.0
     - pandoc-eqnos==1.3.0
     - pandoc-fignos==1.3.0
     - pandoc-tablenos==1.3.0
     - pandoc-xnos==1.1.1
     - pybase62==0.4.0
     - pysha3==1.0.2
-    - python-bitcoinlib==0.10.1
+    - python-bitcoinlib==0.9.0
     - requests-cache==0.4.13
     - weasyprint==0.42.3