From af52dea6154ea825bc6c75b4779bcbd82e3c52ca Mon Sep 17 00:00:00 2001
From: Daniel Himmelstein <daniel.himmelstein@gmail.com>
Date: Fri, 17 Jan 2020 15:57:48 -0500
Subject: [PATCH] Tweaks following up GitHub Actions

---
 .github/workflows/manubot.yaml | 1 -
 README.md                      | 2 +-
 SETUP.md                       | 2 +-
 USAGE.md                       | 3 ++-
 ci/deploy.sh                   | 7 ++-----
 5 files changed, 6 insertions(+), 9 deletions(-)

diff --git a/.github/workflows/manubot.yaml b/.github/workflows/manubot.yaml
index 355c20f4..b56123ac 100644
--- a/.github/workflows/manubot.yaml
+++ b/.github/workflows/manubot.yaml
@@ -35,6 +35,5 @@ jobs:
         env:
           MANUBOT_SSH_PRIVATE_KEY: ${{ secrets.MANUBOT_SSH_PRIVATE_KEY }}
           BUILD_WEB_URL: https://github.com/${{ github.repository }}/commit/${{ github.sha }}/checks
-          COMMIT_MESSAGE: ${{ github.event.head_commit.message }}
         shell: bash --login {0}        
         run: bash ci/deploy.sh
diff --git a/README.md b/README.md
index fd26266f..d806e795 100644
--- a/README.md
+++ b/README.md
@@ -4,7 +4,7 @@
 
 [![HTML Manuscript](https://img.shields.io/badge/manuscript-HTML-blue.svg)](https://manubot.github.io/rootstock/)
 [![PDF Manuscript](https://img.shields.io/badge/manuscript-PDF-blue.svg)](https://manubot.github.io/rootstock/manuscript.pdf)
-[![GitHub Actions Status](https://github.com/manubot/rootstock/workflows/manubot/badge.svg)](https://github.com/manubot/rootstock/actions)
+[![GitHub Actions Status](https://github.com/manubot/rootstock/workflows/Manubot/badge.svg)](https://github.com/manubot/rootstock/actions)
 [![Travis Build Status](https://travis-ci.com/manubot/rootstock.svg?branch=master)](https://travis-ci.com/manubot/rootstock)
 <!-- usage note: delete CI badges above for services not used by your manuscript -->
 
diff --git a/SETUP.md b/SETUP.md
index 0af07ca0..3035f61f 100644
--- a/SETUP.md
+++ b/SETUP.md
@@ -123,7 +123,7 @@ cat ci/deploy.key.txt && echo
 Next, go to the GitHub repository settings page (URL echoed above).
 Click "Add a new secret".
 For "Name", enter `MANUBOT_SSH_PRIVATE_KEY`.
-Next, copy-paste the content of `deploy.key.txt` into "Value"
+Next, copy-paste the content of `ci/deploy.key.txt` into "Value"
 (printed above by `cat`, including any trailing `=` characters if present).
 
 ### GitHub Actions
diff --git a/USAGE.md b/USAGE.md
index d93e244c..7cae369b 100644
--- a/USAGE.md
+++ b/USAGE.md
@@ -131,6 +131,7 @@ Citing a DOI containing parentheses [@doi:my-doi].
 
 This syntax is also used by [`pandoc-url2cite`](https://github.com/phiresky/pandoc-url2cite).
 Make sure to place these link reference definitions in their own paragraphs.
+These paragraphs can be in any of the content Markdown files.
 
 Another method for defining tags is to define `pandoc.citekey-aliases` in `metadata.yaml`:
 
@@ -141,7 +142,7 @@ pandoc:
     tag:my-doi: doi:10.1016/S0022-2836(05)80360-2
 ```
 
-For backwards compatability, tags can also be defined in `content/citation-tags.tsv`.
+For backwards compatibility, tags can also be defined in `content/citation-tags.tsv`.
 If `citation-tags.tsv` defines the tag `study-x`, then this study can be cited like `@tag:study-x`.
 This method is deprecated.
 
diff --git a/ci/deploy.sh b/ci/deploy.sh
index 5ef1ed60..e3c103aa 100755
--- a/ci/deploy.sh
+++ b/ci/deploy.sh
@@ -61,7 +61,8 @@ manubot webpage \
 
 # Commit message
 MESSAGE="\
-$(git log --max-count=1 --format='%s') [ci skip]
+$(git log --max-count=1 --format='%s')
+[ci skip]
 
 This build is based on
 https://github.com/$REPO_SLUG/commit/$COMMIT.
@@ -69,10 +70,6 @@ https://github.com/$REPO_SLUG/commit/$COMMIT.
 This commit was created by the following CI build and job:
 $BUILD_WEB_URL
 $JOB_WEB_URL
-
-The full commit message that triggered this build is copied below:
-
-$COMMIT_MESSAGE
 "
 
 # Deploy the manubot outputs to output