Update environment and documentation (#81)

Pandoc upgraded to v2.0.0.1

Swap anaconda packages to conda-forge

Update build.sh for pandoc 2.0

WeasyPrint was not renderring MathJax, so use --webtex to convert
equations to SVGs for PDF output. See
Kozea/WeasyPrint#59

USAGE.md

@@ -120,7 +120,7 @@ For guidance on what CSL JSON should be like for different document types, refer
 ## 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).
-`metadata.yaml` should contain the manuscript `title`, `authors` list, and `keywords`.
+`metadata.yaml` should contain the manuscript `title`, `authors` list, `keywords`, and language (`lang`).
 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.
 For example, setting the `TZ` environment variable to `Etc/UTC` directs the Manubot to use Coordinated Universal Time.
@@ -147,7 +147,7 @@ If you experience any issues with the Manubot or would like to contribute to its
 
 For additional examples, check out existing manuscripts that use the Manubot:
 
-+ Satoshi Nakamoto's Bitcoin Whitepaper ([source](https://github.com/dhimmel/bitcoin-whitepaper/), [manuscript](https://dhimmel.github.io/bitcoin-whitepaper/))
++ Satoshi Nakamoto's Bitcoin Whitepaper ([source](https://github.com/dhimmel/bitcoin-whitepaper/), [manuscript](https://dhimmel.github.io/bitcoin-whitepaper/), [commentary](https://steemit.com/manubot/@dhimmel/how-i-used-the-manubot-to-reproduce-the-bitcoin-whitepaper))
 + The Sci-Hub Coverage Study ([source](https://github.com/greenelab/scihub-manuscript), [manuscript](https://greenelab.github.io/scihub-manuscript/))
 + A Report for the Vagelos Scholars Program by Michael Zietz ([source](https://github.com/zietzm/Vagelos2017), [manuscript](https://zietzm.github.io/Vagelos2017/))
 + The Deep Review ([source](https://github.com/greenelab/deep-review), [manuscript](https://greenelab.github.io/deep-review/))

build/build.sh

@@ -28,13 +28,12 @@ echo "Exporting HTML manuscript"
 pandoc --verbose \
   --from=markdown \
   --to=html5 \
-  --filter pandoc-fignos \
-  --filter pandoc-eqnos \
-  --filter pandoc-tablenos \
+  --filter=pandoc-fignos \
+  --filter=pandoc-eqnos \
+  --filter=pandoc-tablenos \
   --bibliography=$BIBLIOGRAPHY_PATH \
   --csl=$CSL_PATH \
   --metadata link-citations=true \
-  --smart \
   --mathjax \
   --css=github-pandoc.css \
   --include-in-header=build/assets/analytics.js \
@@ -44,30 +43,41 @@ pandoc --verbose \
 
 # Create PDF output
 echo "Exporting PDF manuscript"
-weasyprint \
-  --verbose \
-  --presentational-hints \
-  webpage/index.html \
-  output/manuscript.pdf
+ln --symbolic content/images images
+pandoc \
+  --from=markdown \
+  --to=html5 \
+  --pdf-engine=weasyprint \
+  --pdf-engine-opt=--presentational-hints \
+  --filter=pandoc-fignos \
+  --filter=pandoc-eqnos \
+  --filter=pandoc-tablenos \
+  --bibliography=$BIBLIOGRAPHY_PATH \
+  --csl=$CSL_PATH \
+  --metadata link-citations=true \
+  --webtex=https://latex.codecogs.com/svg.latex? \
+  --css=webpage/github-pandoc.css \
+  --output=output/manuscript.pdf \
+  $INPUT_PATH
+rm --recursive images
 
 # Create DOCX output when user specifies to do so
 if [ "$BUILD_DOCX" = "true" ];
 then
     echo "Exporting Word Docx manuscript"
-    ln --symbolic content/images images
     pandoc --verbose \
     --from=markdown \
     --to=docx \
-    --filter pandoc-fignos \
-    --filter pandoc-tablenos \
+    --filter=pandoc-fignos \
+    --filter=pandoc-eqnos \
+    --filter=pandoc-tablenos \
     --bibliography=$BIBLIOGRAPHY_PATH \
     --csl=$CSL_PATH \
     --metadata link-citations=true \
-    --reference-docx=$DOCX_PATH \
-    --smart \
+    --reference-doc=$DOCX_PATH \
+    --resource-path=.:content \
     --output=output/manuscript.docx \
     $INPUT_PATH
-    rm --recursive images
 fi
 
 echo "Build complete"

build/environment.yml

@@ -1,28 +1,27 @@
 name: manubot
 channels:
-  - anaconda
   - conda-forge
 dependencies:
-  - anaconda::jinja2=2.9.6
-  - anaconda::pandas=0.20.3
-  - anaconda::python=3.6.2
-  - anaconda::pyyaml=3.12
-  - anaconda::requests=2.14.2
   - conda-forge::cairo=1.14.6
   - conda-forge::cffi=1.10.0
-  - conda-forge::pandoc=1.19.2
+  - conda-forge::jinja2=2.9.6
+  - conda-forge::pandas=0.21.0
+  - conda-forge::pandoc=2.0.0.1
+  - conda-forge::python=3.6.3
+  - conda-forge::pyyaml=3.12
+  - conda-forge::requests=2.18.4
   - conda-forge::watchdog=0.8.3
   - pip:
     - errorhandler==2.0.1
     - ghp-import==0.5.5
     - git+https://github.com/greenelab/manubot@367f0b5c8046e5ce2f1e5a0ef555ec29a4aefd59
     - opentimestamps-client==0.5.0
     - opentimestamps==0.1.0
-    - pandoc-eqnos==0.16
-    - pandoc-fignos==0.20
-    - pandoc-tablenos==0.16
+    - pandoc-eqnos==0.18.1
+    - pandoc-fignos==0.21.1
+    - pandoc-tablenos==0.17.1
     - pybase62==0.3.2
     - pysha3==1.0.2
     - python-bitcoinlib==0.8.0
     - requests-cache==0.4.13
-    - weasyprint==0.40
+    - weasyprint==0.41

content/metadata.yaml

@@ -4,6 +4,7 @@ keywords:
   - markdown
   - publishing
   - manubot
+lang: en-US
 author_info:
   -
     github: johndoe