From e2c76a9d1b14c5dfda9cce7ffd2d1c04d9c85b9b Mon Sep 17 00:00:00 2001
From: Rowan Cockett <rowanc1@gmail.com>
Date: Tue, 16 Apr 2024 22:00:32 -0600
Subject: [PATCH] Ignore various references without DOIs

---
 papers/00_texderwalt/main.tex  | 18 +++++++++---------
 papers/00_texderwalt/mybib.bib |  5 ++++-
 papers/00_texderwalt/myst.yml  | 11 +++++++++++
 3 files changed, 24 insertions(+), 10 deletions(-)

diff --git a/papers/00_texderwalt/main.tex b/papers/00_texderwalt/main.tex
index 832eaa3a40..1b4d702f00 100644
--- a/papers/00_texderwalt/main.tex
+++ b/papers/00_texderwalt/main.tex
@@ -55,7 +55,7 @@ \subsection{DOIs in bibliographies}\label{dois-in-bibliographies}
 In order to include a DOI in your bibliography, add the DOI to your bibliography
 entry as a string. For example:
 
-\begin{verbatim}
+\begin{lstlisting}[language=bibtex]
 @book{hume48,
     author = {David Hume},
     year = 1748,
@@ -64,7 +64,7 @@ \subsection{DOIs in bibliographies}\label{dois-in-bibliographies}
     publisher = {Hackett},
     doi = {10.1017/CBO9780511808432}
 }
-\end{verbatim}
+\end{lstlisting}
 
 
 \section{Citing software and websites}\label{citing-software-and-websites}
@@ -85,17 +85,17 @@ \section{Citing software and websites}\label{citing-software-and-websites}
 
 In this paper we not only terraform a desert using the package terradesert \citep{terradesert}, we also catch a sandworm with it.
 To cite a website, the following BibTeX format plus any additional tags necessary for specifying the referenced content is recommended.
-If you are citing a team, ensure that the author name is wrapped in additional braces \texttt{\{Team Name\}}, so it is not treated as an authors first and last names.
+If you are citing a team, ensure that the author name is wrapped in additional braces \texttt{\{Team Name\}}, so it is not treated as an author's first and last names.
 
-\begin{verbatim}
+\begin{lstlisting}[language=bibtex]
 @misc{terradesert,
     author = {{TerraDesert Team}},
-    title = {Code for terraforming a desert},
-    year = {2000},
-    url = {https://terradesert.com/code/},
-    note = {Accessed 1 Jan. 2000}
+    title  = {Code for terraforming a desert},
+    year   = {2000},
+    url    = {https://terradesert.com/code/},
+    note   = {Accessed 1 Jan. 2000}
 }
-\end{verbatim}
+\end{lstlisting}
 
 
 \section{Source code examples}\label{source-code-examples}
diff --git a/papers/00_texderwalt/mybib.bib b/papers/00_texderwalt/mybib.bib
index eeb8a09368..de1bb823dd 100644
--- a/papers/00_texderwalt/mybib.bib
+++ b/papers/00_texderwalt/mybib.bib
@@ -1,10 +1,12 @@
+# Feel free to delete these first few references, which are specific to the template:
+
 @book{hume48,
   author    = "David Hume",
   year      = "1748",
   title     = "An enquiry concerning human understanding",
   address   = "Indianapolis, IN",
   publisher = "Hackett",
-	doi       = {https://doi.org/10.1017/CBO9780511808432},
+  doi       = {https://doi.org/10.1017/CBO9780511808432},
 }
 
 @article{Atr03,
@@ -25,6 +27,7 @@ @misc{terradesert
   note    = {Accessed 1 Jan. 2000}
 }
 
+# These references may be helpful:
 
 @inproceedings{jupyter,
   abstract  = {It is increasingly necessary for researchers in all fields to write computer code, and in order to reproduce research results, it is important that this code is published. We present Jupyter notebooks, a document format for publishing code, results and explanations in a form that is both readable and executable. We discuss various tools and use cases for notebook documents.},
diff --git a/papers/00_texderwalt/myst.yml b/papers/00_texderwalt/myst.yml
index 359cd2f7fc..75ccc6c578 100644
--- a/papers/00_texderwalt/myst.yml
+++ b/papers/00_texderwalt/myst.yml
@@ -24,6 +24,7 @@ project:
       corresponding: true
     - name: Cleopatra
       email: cleopatra@rome.it
+      affiliation: Ptolemaic Kingdom
   keywords:
     - terraforming
     - desert
@@ -31,6 +32,16 @@ project:
   # Add the abbreviations that you use in your paper here
   abbreviations:
     MyST: Markedly Structured Text
+  # It is possible to explicitly ignore the `doi-exists` check for certain citation keys
+  error_rules:
+    - rule: doi-exists
+      severity: ignore
+      keys:
+        - Atr03
+        - terradesert
+        - jupyter
+        - sklearn1
+        - sklearn2
   # A banner will be generated for you on publication, this is a placeholder
   banner: banner.png
   # The rest of the information shouldn't be modified