Upgrade manubot & environment on 2018-08-22

.travis.yml

@@ -5,7 +5,7 @@ branches:
   only:
     - master
 before_install:
-  - wget https://repo.continuum.io/miniconda/Miniconda3-4.4.10-Linux-x86_64.sh
+  - wget https://repo.continuum.io/miniconda/Miniconda3-4.5.4-Linux-x86_64.sh
     --output-document miniconda.sh
   - bash miniconda.sh -b -p $HOME/miniconda
   - source $HOME/miniconda/etc/profile.d/conda.sh

build/assets/style.csl

@@ -1,4 +1,4 @@
-<?xml version="1.0" encoding="utf-8"?>
+<?xml version="1.0" encoding="utf-8"?>
 <style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="never" default-locale="en-US">
   <!-- This style was edited with the Visual CSL Editor (http://editor.citationstyles.org/visualEditor/) -->
   <info>
@@ -10,7 +10,7 @@
       <name>Daniel Himmelstein</name>
       <email>[email protected]</email>
     </author>
-    <updated>2017-09-04T20:54:02+00:00</updated>
+    <updated>2018-08-22T19:08:46+00:00</updated>
     <rights license="https://creativecommons.org/publicdomain/zero/1.0/legalcode">This work is dedicated to the public domain via CC0 1.0</rights>
   </info>
   <macro name="author">
@@ -51,7 +51,7 @@
       <group display="block">
         <text macro="author"/>
       </group>
-      <group delimiter=" ">
+      <group display="block" delimiter=" ">
         <text macro="venue" font-style="italic"/>
         <date variable="issued" prefix="(" suffix=")">
           <date-part name="year"/>
@@ -60,6 +60,12 @@
         </date>
         <text variable="URL"/>
       </group>
+      <group delimiter=" · ">
+        <text variable="DOI" text-case="lowercase" prefix="DOI: "/>
+        <text variable="PMID" prefix="PMID: "/>
+        <text variable="PMCID" prefix="PMCID: "/>
+        <text variable="ISBN" prefix="ISBN: "/>
+      </group>
     </layout>
   </bibliography>
 </style>

build/build.sh

@@ -7,7 +7,7 @@ export LC_ALL=en_US.UTF-8
 
 # Generate reference information
 echo "Retrieving and processing reference metadata"
-manubot \
+manubot process \
   --content-directory=content \
   --output-directory=output \
   --cache-directory=ci/cache \

build/environment.yml

@@ -2,27 +2,27 @@ name: manubot
 channels:
   - conda-forge
 dependencies:
-  - conda-forge::cairo=1.14.10
-  - conda-forge::cffi=1.11.2
+  - conda-forge::cairo=1.14.12
+  - conda-forge::cffi=1.11.5
   - conda-forge::ghp-import=0.5.5
   - conda-forge::jinja2=2.10
-  - conda-forge::pandas=0.22.0
-  - conda-forge::pandoc=2.1.1
-  - conda-forge::python=3.6.4
+  - 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::requests=2.18.4
+  - conda-forge::requests=2.19.1
   - conda-forge::watchdog=0.8.3
   - pip:
     - errorhandler==2.0.1
-    - git+https://github.com/greenelab/manubot@27456594c407f3fed35804db4bcf3b5bba88a716
-    - opentimestamps-client==0.5.1
-    - opentimestamps==0.2.0.1
-    - pandoc-eqnos==1.2.0
-    - pandoc-fignos==1.2.0
-    - pandoc-tablenos==1.2.0
-    - pandoc-xnos==1.0.1
-    - pybase62==0.3.2
+    - git+https://github.com/greenelab/manubot@66a6efc6f4b84153a813aa423ec00725ed1417c5
+    - opentimestamps-client==0.6.0
+    - opentimestamps==0.4.0
+    - 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==0.9.0
+    - python-bitcoinlib==0.10.1
     - requests-cache==0.4.13
-    - weasyprint==0.42.2
+    - weasyprint==0.42.3