From ed698f3d7f5f91e137c1536f4851eabf0f124242 Mon Sep 17 00:00:00 2001
From: Stefan Krastanov <stefan@krastanov.org>
Date: Sun, 17 Sep 2023 19:09:13 -0400
Subject: [PATCH] fix documenter

---
 docs/make.jl            |  6 +++---
 docs/src/references.bib | 15 ++++++++-------
 src/entanglement.jl     |  4 ++--
 3 files changed, 13 insertions(+), 12 deletions(-)

diff --git a/docs/make.jl b/docs/make.jl
index b706a6153..48920028c 100644
--- a/docs/make.jl
+++ b/docs/make.jl
@@ -15,13 +15,13 @@ ENV["COLUMNS"] = 80
 bib = CitationBibliography(joinpath(@__DIR__,"src/references.bib"),style=:authoryear)
 
 makedocs(
-bib,
+plugins = [bib],
 doctest = false,
 clean = true,
 sitename = "QuantumClifford.jl",
-format = Documenter.HTML(),
+format = Documenter.HTML(size_threshold_ignore = ["API.md"]),
 modules = [QuantumClifford, QuantumClifford.Experimental.NoisyCircuits, QuantumInterface],
-strict = Documenter.except(:missing_docs),
+warnonly = [:missing_docs],
 authors = "Stefan Krastanov",
 pages = [
 "QuantumClifford.jl" => "index.md",
diff --git a/docs/src/references.bib b/docs/src/references.bib
index 1514cf4e7..d260be4d7 100644
--- a/docs/src/references.bib
+++ b/docs/src/references.bib
@@ -158,12 +158,13 @@ @article{gullans2020dynamical
   publisher={APS}
 }
 
-@misc{hein2006entanglement,
-	title = {Entanglement in Graph States and its Applications},
-	url = {http://arxiv.org/abs/quant-ph/0602096},
-	journaltitle = {arXiv preprint arXiv:quant-ph/0602096},
-	author = {Hein, M. and Dür, W. and Eisert, J. and Raussendorf, R. and Nest, M. Van den and Briegel, H.-J.},
-	year = {2006},
+@article{hein2006entanglement,
+  title={Entanglement in graph states and its applications},
+  author={Hein, Marc and D{\"u}r, Wolfgang and Eisert, Jens and Raussendorf, Robert and Nest, M and Briegel, H-J},
+  journal={arXiv preprint quant-ph/0602096},
+  url={https://arxiv.org/abs/quant-ph/0602096},
+  doi={10.48550/arXiv.quant-ph/0602096},
+  year={2006}
 }
 
 % Encoding circuits
@@ -223,4 +224,4 @@ @article{nahum2017quantum
 	journal = {Physical Review X},
 	author = {Nahum, Adam and Ruhman, Jonathan and Vijay, Sagar and Haah, Jeongwan},
   year = {2017}
-}
\ No newline at end of file
+}
diff --git a/src/entanglement.jl b/src/entanglement.jl
index 78f48612c..fafeec4dd 100644
--- a/src/entanglement.jl
+++ b/src/entanglement.jl
@@ -195,8 +195,8 @@ end
 """
 Get bipartite entanglement entropy by first converting the state to a graph and computing the rank of the adjacency matrix.
 
-Based on [hein2006entanglement](@cite).
-"""
+Based on "Entanglement in graph states and its applications".
+""" # TODO you should use [hein2006entanglement](@cite) instead of "Entanglement in graph states and its applications", but Documenter is giving the weirdest error if you do so...
 function entanglement_entropy(state::AbstractStabilizer, subsystem::AbstractVector, algorithm::Val{:graph})
     graph = Graphs.Graph(state)
     adjmat = Graphs.adjacency_matrix(graph)