From 7d1c827e049ea440b3d68f93ac2ae0913d29c981 Mon Sep 17 00:00:00 2001
From: Daniel Himmelstein <daniel.himmelstein@gmail.com>
Date: Fri, 9 Aug 2019 13:34:42 -0400
Subject: [PATCH 1/3] Update environment on 2019-08-09

---
 build/environment.yml | 14 +++++++-------
 ci/install.sh         |  2 +-
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/build/environment.yml b/build/environment.yml
index fa807dba..1308d40a 100644
--- a/build/environment.yml
+++ b/build/environment.yml
@@ -7,19 +7,19 @@ dependencies:
   - cffi=1.12.3
   - ghp-import=0.5.5
   - jinja2=2.10
-  - jsonschema=3.0.1
-  - pandas=0.24.2
-  - pandoc=2.7.2
+  - jsonschema=3.0.2
+  - pandas=0.25.0
+  - pandoc=2.7.3
   - pango=1.40.14
   - pip=19.1
-  - psutil=5.6.2
+  - psutil=5.6.3
   - python=3.6.7
   - pyyaml=5.1
   - requests=2.22.0
-  - watchdog=0.8.3
+  - watchdog=0.9.0
   - pip:
     - errorhandler==2.0.1
-    - git+https://github.com/manubot/manubot@2a99f4af4a352d2e082988d364e01e2e2809a87b
+    - git+https://github.com/manubot/manubot@1b885c614634d6e88565ebcf5052b6884132ab32
     - jsonref==0.2
     - opentimestamps-client==0.6.0
     - opentimestamps==0.3.0
@@ -27,7 +27,7 @@ dependencies:
     - pandoc-fignos==1.4.2
     - pandoc-tablenos==1.4.2
     - pandoc-xnos==1.2.0
-    - pybase62==0.4.0
+    - pybase62==0.4.1
     - pysha3==1.0.2
     - python-bitcoinlib==0.9.0
     - requests-cache==0.5.0
diff --git a/ci/install.sh b/ci/install.sh
index 252d8892..72833087 100755
--- a/ci/install.sh
+++ b/ci/install.sh
@@ -6,7 +6,7 @@
 set -o errexit \
     -o pipefail
 
-wget https://repo.continuum.io/miniconda/Miniconda3-4.6.14-Linux-x86_64.sh \
+wget https://repo.continuum.io/miniconda/Miniconda3-4.7.10-Linux-x86_64.sh \
     --output-document miniconda.sh
 bash miniconda.sh -b -p $HOME/miniconda
 source $HOME/miniconda/etc/profile.d/conda.sh

From 1f541a845a1861fc29074a4e1f0a1bf474a84aeb Mon Sep 17 00:00:00 2001
From: Daniel Himmelstein <daniel.himmelstein@gmail.com>
Date: Fri, 9 Aug 2019 13:39:21 -0400
Subject: [PATCH 2/3] Update front-matter to use ci_source.manuscript_url

---
 content/00.front-matter.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/content/00.front-matter.md b/content/00.front-matter.md
index 0f1b87af..459eede4 100644
--- a/content/00.front-matter.md
+++ b/content/00.front-matter.md
@@ -12,7 +12,7 @@ _A DOI-citable version of this manuscript is available at <https://doi.org/DOI_H
 <small><em>
 This manuscript
 {% if ci_source is defined -%}
-([permalink](https://{{ci_source.repo_owner}}.github.io/{{ci_source.repo_name}}/v/{{ci_source.commit}}/))
+([permalink]({{ci_source.manuscript_url}}))
 {% endif -%}
 was automatically generated
 {% if ci_source is defined -%}

From b07d870959f583f0fb6424dd1648d3795411999b Mon Sep 17 00:00:00 2001
From: Daniel Himmelstein <daniel.himmelstein@gmail.com>
Date: Thu, 29 Aug 2019 17:31:07 -0400
Subject: [PATCH 3/3] check if ci_source.manuscript_url is defined

---
 content/00.front-matter.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/content/00.front-matter.md b/content/00.front-matter.md
index 459eede4..e762800b 100644
--- a/content/00.front-matter.md
+++ b/content/00.front-matter.md
@@ -11,7 +11,7 @@ _A DOI-citable version of this manuscript is available at <https://doi.org/DOI_H
 {## Template to insert build date and source ##}
 <small><em>
 This manuscript
-{% if ci_source is defined -%}
+{% if ci_source is defined and ci_source.manuscript_url is defined -%}
 ([permalink]({{ci_source.manuscript_url}}))
 {% endif -%}
 was automatically generated