Fix Ubuntu installation with latest pandoc (citeproc), Fix tlmgr use with TinyTex

.travis.yml

@@ -11,12 +11,14 @@ language: bash
 
 os:
   - osx
-  # - linux  # https://tex.stackexchange.com/questions/313768/why-getting-this-error-tlmgr-unknown-directive
+  - linux  # https://tex.stackexchange.com/questions/313768/why-getting-this-error-tlmgr-unknown-directive
 
-# env:
-  # global:
+env:
+  global:
     # - PATH=$TRAVIS_BUILD_DIR/usr/bin/:$PATH
     # - PATH=/Library/TeX/texbin:$PATH
+    - PATH="$PATH:$HOME/bin"
+    - PATH="$PATH:$HOME/.local/bin"
 
 python:
   # We don't actually use the Travis Python, but this keeps it organized.
@@ -29,8 +31,9 @@ python:
 addons:
   apt:
     packages:
-    - texlive
+    # - texlive
     - xzdec
+    - python3-pip
     update: true
   homebrew:
     casks:
@@ -45,7 +48,10 @@ before_install:
       eval "$(/usr/libexec/path_helper)"
       sudo tlmgr update --self
     elif [ "$TRAVIS_OS_NAME" = "linux" ]; then
-      tlmgr init-usertree
+      wget -qO- "https://yihui.org/tinytex/install-bin-unix.sh" | sh
+      sudo env PATH=$PATH tlmgr update --self
+      TEMP_DEB="$(mktemp)" && wget -O "$TEMP_DEB" 'https://github.com/jgm/pandoc/releases/download/2.11.4/pandoc-2.11.4-1-amd64.deb' && sudo dpkg -i "$TEMP_DEB"
+      rm -f "$TEMP_DEB"
       echo MSG FROM JO:
       echo on linux we cannot update apt installed texlive
       echo next steps to fix see commit msg: https://github.com/tompollard/phd_thesis_markdown/pull/100/commits/85fd9e7ac413a34066b79f1e49b3e1d3efdeac00
@@ -95,17 +101,17 @@ install:
   # Installs both python and texlive dependencies
   - make install
   # For debug
-  - cat /usr/local/texlive/2020/texmf-var/web2c/tlmgr.log
-  - conda list
-  - pip list
-  - python --version
-  - pandoc --version
-  - tlmgr --version
-  - latex --version
-  - echo $PATH
-  - which tlmgr
-  - which latex
-  - find /usr/local/texlive/2020/ -type f -name "l3backend*"
+  # - cat /usr/local/texlive/2020/texmf-var/web2c/tlmgr.log
+  # - conda list
+  # - pip list
+  # - python --version
+  # - pandoc --version
+  # - tlmgr --version
+  # - latex --version
+  # - echo $PATH
+  # - which tlmgr
+  # - which latex
+  # - find /usr/local/texlive/2020/ -type f -name "l3backend*"
 
 # Attempt to create all document output types
 script:
@@ -116,10 +122,10 @@ script:
   - make pdf
   - cat pandoc.pdf.log
   # Debugging the mac error
-  - find /usr/local/texlive/2020/ -type f -name "l3backend*"
+  # - find /usr/local/texlive/2020/ -type f -name "l3backend*"
   - make html
   - cat pandoc.html.log
   - make docx
-  - cat pandoc.docx.log
+  # - cat pandoc.docx.log
   - make all
-  - cat pandoc.*.log
+  # - cat pandoc.*.log

README.md

@@ -11,6 +11,7 @@ If you have used this template in your work, please cite the following publicati
 > Tom Pollard et al. (2016). Template for writing a PhD thesis in Markdown. Zenodo. http://dx.doi.org/10.5281/zenodo.58490
 
 ## Quickstart
+### Mac
 If you're a mac user and you have conda and brew installed, run the following in your terminal to install and generate the example outputs:
 ```bash
 # get texlive
@@ -27,6 +28,29 @@ conda activate phd
 make install
 ```
 
+### Ubuntu
+On Ubuntu, texlive installed with apt is not working, use an installer like below and make sure it is not installed with apt:
+```bash
+# get TinyTex and make sure PATH is set
+wget -qO- "https://yihui.org/tinytex/install-bin-unix.sh" | sh
+PATH="$PATH:$HOME/bin"
+PATH="$PATH:$HOME/.local/bin"
+
+# update tlmgr and packages
+sudo env PATH=$PATH tlmgr update --self
+
+# Install pip
+sudo apt install python3-pip
+
+# Install latest pandoc (apt version too old, needs at least 2.11.*)
+TEMP_DEB="$(mktemp)" &&
+wget -O "$TEMP_DEB" 'https://github.com/jgm/pandoc/releases/download/2.11.4/pandoc-2.11.4-1-amd64.deb' &&
+sudo dpkg -i "$TEMP_DEB"
+rm -f "$TEMP_DEB"
+
+# Install required python and texlive packages
+make install
+```
 ## Why write my thesis in Markdown?
 
 Markdown is a super-friendly plain text format that can be easily converted to a bunch of other formats like PDF, Word and LaTeX. You'll enjoy working in Markdown because:

install_linux.sh

@@ -2,17 +2,34 @@
 
 set -e  # makes the script fail as soon as one command fails
 
-sudo tlmgr install truncate
-sudo tlmgr install tocloft
-sudo tlmgr install wallpaper
-sudo tlmgr install morefloats
-sudo tlmgr install sectsty
-sudo tlmgr install siunitx
-sudo tlmgr install threeparttable
-sudo tlmgr update l3packages
-sudo tlmgr update l3kernel
-sudo tlmgr update l3experimental
-sudo tlmgr update l3backend
+sudo env PATH=$PATH tlmgr install truncate
+sudo env PATH=$PATH tlmgr install tocloft
+sudo env PATH=$PATH tlmgr install wallpaper
+sudo env PATH=$PATH tlmgr install morefloats
+sudo env PATH=$PATH tlmgr install sectsty
+sudo env PATH=$PATH tlmgr install siunitx
+sudo env PATH=$PATH tlmgr install threeparttable
+sudo env PATH=$PATH tlmgr update l3packages
+sudo env PATH=$PATH tlmgr update l3kernel
+sudo env PATH=$PATH tlmgr update l3experimental
+sudo env PATH=$PATH tlmgr update l3backend
+sudo env PATH=$PATH tlmgr install mathspec
+sudo env PATH=$PATH tlmgr install xltxtra
+sudo env PATH=$PATH tlmgr install realscripts
+sudo env PATH=$PATH tlmgr install eso-pic
+sudo env PATH=$PATH tlmgr install ctable
+sudo env PATH=$PATH tlmgr install listings
+sudo env PATH=$PATH tlmgr install pdfpages
+sudo env PATH=$PATH tlmgr install bbold
+sudo env PATH=$PATH tlmgr install cleveref
+sudo env PATH=$PATH tlmgr install fancyhdr
+sudo env PATH=$PATH tlmgr install ulem
+sudo env PATH=$PATH tlmgr install setspace
+sudo env PATH=$PATH tlmgr install makecell
+sudo env PATH=$PATH tlmgr install pdflscape
+sudo env PATH=$PATH tlmgr install caption
+
+#
 # Would it be simpler to just update all packages? (takes ~10m)
 # sudo tlmgr update --all
 pip install pandoc-fignos pandoc-eqnos pandoc-tablenos pandoc-secnos pandoc-shortcaption