From fb1c2895c1e9854d16adc75e770a858be3a2abac Mon Sep 17 00:00:00 2001
From: Chris Barnes <barnesc@janelia.hhmi.org>
Date: Wed, 16 Dec 2020 16:19:49 +0000
Subject: [PATCH 1/4] Fix "help" make recipe

- Remove tabs causing misalignment
- Remove meaningless whitespace which make editing more difficult
---
 Makefile | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/Makefile b/Makefile
index bc995665..dbdc2c02 100644
--- a/Makefile
+++ b/Makefile
@@ -11,19 +11,19 @@ SCRATCHDIR=$(BASEDIR)/scratch
 BIBFILE=$(INPUTDIR)/references.bib
 
 help:
-	@echo ' 																	  '
-	@echo 'Makefile for the Markdown thesis                                       '
-	@echo '                                                                       '
-	@echo 'Usage:                                                                 '
-	@echo '   make install                     install pandoc plugins
-	@echo '   make html                        generate a web version
-	@echo '   make pdf                         generate a PDF file  			  '
-	@echo '   make docx	                       generate a Docx file 			  '
-	@echo '   make tex	                       generate a Latex file 			  '
-	@echo ' 																	  '
-	@echo ' 																	  '
-	@echo 'get local templates with: pandoc -D latex/html/etc	  				  '
-	@echo 'or generic ones from: https://github.com/jgm/pandoc-templates		  '
+	@echo ''
+	@echo 'Makefile for the Markdown thesis'
+	@echo ''
+	@echo 'Usage:'
+	@echo '   make install                     install pandoc plugins'
+	@echo '   make html                        generate a web version'
+	@echo '   make pdf                         generate a PDF file'
+	@echo '   make docx                        generate a Docx file'
+	@echo '   make tex                         generate a Latex file'
+	@echo ''
+	@echo ''
+	@echo 'get local templates with: pandoc -D latex/html/etc'
+	@echo 'or generic ones from: https://github.com/jgm/pandoc-templates'
 
 install:
 	sh $(BASEDIR)/install.sh

From a4592545fd8e7433d937942b2fea1190aa4f050b Mon Sep 17 00:00:00 2001
From: Chris Barnes <barnesc@janelia.hhmi.org>
Date: Wed, 16 Dec 2020 16:25:34 +0000
Subject: [PATCH 2/4] Run help recipe on CI

---
 .travis.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.travis.yml b/.travis.yml
index 75cc0184..7ca5e423 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -37,6 +37,7 @@ before_install:
 
 # Attempt to create a PDF
 script:
+  - make help
   - make pdf
   - cat pandoc.log
   - make html

From 25c8e5e07086c32e3d17937e6c2b51e80285da2d Mon Sep 17 00:00:00 2001
From: Chris Barnes <barnesc@janelia.hhmi.org>
Date: Wed, 16 Dec 2020 16:05:54 +0000
Subject: [PATCH 3/4] docker

---
 Dockerfile | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)
 create mode 100644 Dockerfile

diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 00000000..4fbfd65b
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,26 @@
+FROM pandoc/ubuntu-latex
+
+RUN tlmgr update --self \
+    && tlmgr install truncate \
+    && tlmgr install tocloft \
+    && tlmgr install wallpaper \
+    && tlmgr install morefloats \
+    && tlmgr install sectsty \
+    && tlmgr install siunitx \
+    && tlmgr install threeparttable \
+    && tlmgr install makecell \
+    && tlmgr update l3packages \
+    && tlmgr update l3kernel \
+    && tlmgr update l3experimental
+
+RUN apt-get update \
+    && apt-get install -y python3 python3-pip pandoc-citeproc \
+    && rm -rf /var/lib/apt/lists/*
+
+RUN pip3 install \
+    pandoc-fignos \
+    pandoc-eqnos \
+    pandoc-tablenos \
+    pandoc-secnos \
+    pandoc-shortcaption \
+    fabric

From 75a3acf864407d2cd014f1b1d001dee7ed9f9d55 Mon Sep 17 00:00:00 2001
From: Chris Barnes <barnesc@janelia.hhmi.org>
Date: Wed, 16 Dec 2020 16:30:31 +0000
Subject: [PATCH 4/4] Add docker to Makefile

---
 Makefile | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index dbdc2c02..9d843d6e 100644
--- a/Makefile
+++ b/Makefile
@@ -10,11 +10,14 @@ SCRATCHDIR=$(BASEDIR)/scratch
 
 BIBFILE=$(INPUTDIR)/references.bib
 
+DOCKER_TAG=phd_thesis_markdown
+
 help:
 	@echo ''
 	@echo 'Makefile for the Markdown thesis'
 	@echo ''
 	@echo 'Usage:'
+	@echo '   make docker                      build docker image "$(DOCKER_TAG)"'
 	@echo '   make install                     install pandoc plugins'
 	@echo '   make html                        generate a web version'
 	@echo '   make pdf                         generate a PDF file'
@@ -25,6 +28,9 @@ help:
 	@echo 'get local templates with: pandoc -D latex/html/etc'
 	@echo 'or generic ones from: https://github.com/jgm/pandoc-templates'
 
+docker:
+	docker build --tag "$(DOCKER_TAG)" .
+
 install:
 	sh $(BASEDIR)/install.sh
 
@@ -89,4 +95,4 @@ html:
 	cp -r "$(INPUTDIR)/figures" "$(OUTPUTDIR)/source/figures"
 
 
-.PHONY: help install pdf docx html tex
+.PHONY: help docker install pdf docx html tex