Merge branch 'docs'

gideonsimpson · Mar 16, 2024 · c292609 · c292609
2 parents 86de49c + 12b793a
commit c292609
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diff --git a/docs/Project.toml b/docs/Project.toml
@@ -1,6 +1,7 @@
 [deps]
 BasicMD = "f448d96e-cc9b-4179-976a-6795f3ef2db6"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+DocumenterCitations = "daee34ce-89f3-4625-b898-19384cb65244"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
 HypothesisTests = "09f84164-cd44-5f33-b23f-e6b0d136a0d5"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"

diff --git a/docs/make.jl b/docs/make.jl
@@ -9,9 +9,18 @@ if abspath(PROGRAM_FILE) == @__FILE__
 end
 using WeightedEnsemble
 using Documenter
+using DocumenterCitations
+
+bib = CitationBibliography(joinpath(@__DIR__, "src", "refs.bib"); style=:numeric)
+
 makedocs(checkdocs=:none,
          sitename = "WeightedEnsemble.jl",
          modules  = [WeightedEnsemble],
+         format=Documenter.HTML(
+            # ...
+            assets=String["assets/citations.css"],
+            ),
+         plugins=[bib],
          pages=[
                 "Home" => "index.md",
                 "Structures" => "struct1.md",
@@ -21,7 +30,9 @@ makedocs(checkdocs=:none,
                 "Coarse Modeling" => "coarse1.md",
                 "Utility Functions" => "util1.md",
                 "Weighted Ensemble Methods" => "we1.md",
-                "Examples"=>["examples/equil1.md"]
+                "Examples"=>["examples/equil1.md"],
+                "References"=>"refs1.md",
+                "API"=>"api.md"
                ])
 deploydocs(;
     repo="github.com/gideonsimpson/WeightedEnsemble.jl",

diff --git a/docs/src/api.md b/docs/src/api.md
@@ -0,0 +1,4 @@
+# Index
+
+```@index
+```
diff --git a/docs/src/assets/citations.css b/docs/src/assets/citations.css
@@ -0,0 +1,28 @@
+.citation dl {
+    display: grid;
+    grid-template-columns: max-content auto;
+}
+
+.citation dt {
+    grid-column-start: 1;
+}
+
+.citation dd {
+    grid-column-start: 2;
+    margin-bottom: 0.75em;
+}
+
+.citation ul {
+    padding: 0 0 2.25em 0;
+    margin: 0;
+    list-style: none !important;
+}
+
+.citation ul li {
+    text-indent: -2.25em;
+    margin: 0.33em 0.5em 0.5em 2.25em;
+}
+
+.citation ol li {
+    padding-left: 0.75em;
+}
diff --git a/docs/src/index.md b/docs/src/index.md
@@ -36,6 +36,9 @@ stored in an [`Ensemble`](@ref) data structure. The ensemble is evolved,
 successively, in two steps, _selection_ and _mutation_.  As the partilces and
 weights evolve in time, we add a ``t`` subscript to indicate that these quantities change, ``\{(\omega_t^{i},\xi_t^{i}\}``.
 
+This implementation has been used in [aristoff_weighted_2023, webber_splitting_2020](@cite).  It is heavily influenced by the algoirthmic
+description found in [aristoff_optimizing_2020](@cite).  
+
 ### Selection
 During the selection step, particles are resampled from the empirical
 distribution in such a way so as to maintain unbiasedness _and_ reduce variance
@@ -149,16 +152,3 @@ parallelize the selection step.
 ## Acknowledgements
 This work was supported in part by the US National Science Foundation Grants DMS-1818716 and DMS-2111278.
 
-## References
- 1.  Aristoff, D., Copperman, J., Simpson, G., Webber, R. J. & Zuckerman, D. M. Weighted ensemble: Recent mathematical developments. J. Chem. Phys. 158, 014108 (2023).
- 2.  Russo, J. D. et al. WESTPA 2.0: High-Performance Upgrades for Weighted Ensemble Simulations and Analysis of Longer-Timescale Applications. J. Chem. Theory Comput. 18, 638–649 (2022).
- 3.  Aristoff, D. An ergodic theorem for the weighted ensemble method. arXiv:1906.00856 (2021).
- 4.  Webber, R. J., Aristoff, D., & Simpson, G. A splitting method to reduce MCMC variance. arXiv:2011.13899 (2020)
- 5.  Aristoff, D. & Zuckerman, D. M. Optimizing Weighted Ensemble Sampling of Steady States. Multiscale Model. Simul. 18, 646–673 (2020).
- 6.  Huber, G. A. & Kim, S. Weighted-ensemble Brownian dynamics simulations for protein association reactions. Biophysical Journal 70, 97–110 (1996).
- 7.  Douc, R. & Cappe, O. Comparison of resampling schemes for particle filtering. in ISPA 2005. Proceedings of the 4th International Symposium on Image and Signal Processing and Analysis, 2005. 64–69 (IEEE, Zagreb, Croatia, 2005). doi:10.1109/ISPA.2005.195385.
-
-## Index
-```@index
-```
-
diff --git a/docs/src/refs.bib b/docs/src/refs.bib
diff --git a/docs/src/refs1.md b/docs/src/refs1.md
@@ -0,0 +1,4 @@
+# References
+```@bibliography
+*
+```
diff --git a/docs/src/selection/resampling1.md b/docs/src/selection/resampling1.md
@@ -3,7 +3,7 @@
 As it is neccessary to perform resampling, both for determining how many
 offspring each bin should have, and, having determined that, resampling the
 particles within each bin, we have provided several choices here.  These
-methods, and their properties, can be found in Douc et al. (2005).  The provided
+methods, and their properties, can be found in [douc_comparison_2005](@cite).  The provided
 `selection!` functions default to using [`WeightedEnsemble.systematic`](@ref)
 across bins and [`WeightedEnsemble.multinomial`](@ref) within bins.