Merge pull request #31

Prevent duplicate labels in :alpha style

From branch `mg/alphastyle`

NEWS.md

@@ -3,6 +3,22 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [Unreleased]
+
+### Fixed
+
+* Do not try include a year when rendering a reference if the underlying BibTeX entry has no `year` field.
+* Avoid duplicate labels in `:alpha` style. This is implemented via the new stateful `AlphaStyle()`, but is handled automatically.
+* With the alphabetic style (`:alpha`/`AlphaStyle`), include up to 4 names in the label, not 3 (but 5 or more names results in 3 names and "+"). Also, include the first letter of a "particle" in the label, e.g. "vWB08" for a first author "von Winckel". Both of these are consistent with LaTeX's behavior.
+
+### Added
+
+* New `style=AlphaStyle()` that generates unique citation labels. This can mostly be considered internal, as `style=:alpha` is automatically upgraded to `style=AlphaStyle()`.
+
+### Internal Changes
+
+* Added an internal function `init_bibliography!` that is called at the beginning of the `ExpandBibliography` pipeline step. This function is intended to initialized internal state either of the `style` object or the `CitationBibliography` plugin object before rendering any `@bibliography` blocks. This is used to generate unique citation labels for the new `AlphaStyle()`. For the other builtin styles, it is a no-op. Generally, `init_bibliography!` can help with implementing custom "stateful" styles.
+
 
 ## [Version v1.0.0][1.0.0] - 2023-07-12
 

docs/latex/Makefile

@@ -1,6 +1,6 @@
 .PHONY: all clean
 
-ALL = numeric.pdf authoryear.pdf rmp.pdf prb.pdf
+ALL = numeric.pdf authoryear.pdf rmp.pdf prb.pdf alpha.pdf
 
 all: $(ALL)
 
@@ -28,6 +28,12 @@ prb.pdf: prb.tex
 	pdflatex $<
 	pdflatex $<
 
+alpha.pdf: alpha.tex
+	pdflatex $<
+	bibtex $(basename $<)
+	pdflatex $<
+	pdflatex $<
+
 clean:
 	@rm -f ${ALL}
 	@rm -f *.aux

docs/latex/alpha.tex

@@ -0,0 +1,63 @@
+\documentclass[aps,pra,onecolumn,noshowpacs,superscriptaddress,preprintnumbers,%
+kamsmath,amssymb,notitlepage,letterpaper]{revtex4-2}
+
+\def\Author{Michael Goerz}
+\def\Title{Demo of the standard RevTeX numeric citation style}
+
+\usepackage{natbib}
+\usepackage[utf8]{inputenc}
+\usepackage{caption}
+\captionsetup{justification=raggedright, singlelinecheck=true}
+\usepackage[
+  pdftitle={\Title},
+  pdfauthor={\Author},
+  colorlinks=true, linkcolor=black, urlcolor=black, citecolor=black,
+  bookmarksopen=false, breaklinks=true, plainpages=false, pdfpagelabels
+]{hyperref}
+
+\begin{document}
+
+\title{\Title}
+\author{\Author}
+\date{\today}
+
+\maketitle
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\begin{itemize}
+  \item \verb|\cite{GoerzQ2022}| renders as ``\cite{GoerzQ2022}''.
+  \item \verb|\citet{GoerzQ2022}| renders as ``\citet{GoerzQ2022}''.
+  \item \verb|\citep{GoerzQ2022}| renders as ``\citep{GoerzQ2022}''.
+  \item \verb|\cite[Eq.~(1)]{GoerzQ2022}| renders as ``\cite[Eq.~(1)]{GoerzQ2022}''.
+  \item \verb|\citet[Eq.~(1)]{GoerzQ2022}| renders as ``\citet[Eq.~(1)]{GoerzQ2022}''.
+  \item \verb|\citep[Eq.~(1)]{GoerzQ2022}| renders as ``\citep[Eq.~(1)]{GoerzQ2022}''.
+  \item \verb|\citet*{GoerzQ2022}| renders as ``\citet*{GoerzQ2022}''.
+  \item \verb|\citep*{GoerzQ2022}| renders as ``\citep*{GoerzQ2022}''.
+  \item \verb|\citet*[Eq.~(1)]{GoerzQ2022}| renders as ``\citet*[Eq.~(1)]{GoerzQ2022}''.
+  \item \verb|\citep*[Eq.~(1)]{GoerzQ2022}| renders as ``\citep*[Eq.~(1)]{GoerzQ2022}''.
+  \item \verb|\citet{WinckelIP2008}| renders as ``\citet{WinckelIP2008}''.
+  \item \verb|\Citet{WinckelIP2008}| renders as ``\Citet{WinckelIP2008}''.
+  \item \cite{GraceJMO2007}, \cite{GraceJPB2007}, \cite{GrondPRA2009a}, and \cite{GrondPRA2009b}
+\end{itemize}
+
+Further commands that we do not support in markdown:
+
+\begin{itemize}
+  \item \verb|\citenum{GoerzQ2022}| renders as ``\citenum{GoerzQ2022}''.
+  \item \verb|\citealt{GoerzQ2022}| renders as ``\citealt{GoerzQ2022}''.
+  \item \verb|\citealp{GoerzQ2022}| renders as ``\citealp{GoerzQ2022}''.
+  \item \verb|\citealt*{GoerzQ2022}| renders as ``\citealt*{GoerzQ2022}''.
+  \item \verb|\citealp*{GoerzQ2022}| renders as ``\citealp*{GoerzQ2022}''.
+  \item \verb|\citealt*[Eq.~(1)]{GoerzQ2022}| renders as ``\citealt*[Eq.~(1)]{GoerzQ2022}''.
+  \item \verb|\citealp*[Eq.~(1)]{GoerzQ2022}| renders as ``\citealp*[Eq.~(1)]{GoerzQ2022}''.
+  \item \verb|\Citealt{WinckelIP2008}| renders as ``\Citealt{WinckelIP2008}''.
+  \item \verb|\Citealp{WinckelIP2008}| renders as ``\Citealp{WinckelIP2008}''.
+\end{itemize}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+\bibliographystyle{alpha}
+\bibliography{../src/refs}
+
+\end{document}

docs/src/gallery.md

@@ -82,6 +82,24 @@ Style = :alpha
 Canonical = false
 ```
 
+Note that the `:alpha` style is able to automatically disambiguate labels:
+
+```@bibliography
+Pages = []
+Style = :alpha
+Canonical = false
+
+GraceJMO2007
+GraceJPB2007
+```
+
+This works because the `DocumenterCitations` automatically upgrades `style=:alpha` to the internal
+
+```@docs
+DocumenterCitations.AlphaStyle
+```
+
+
 ## [Custom styles](@id custom_styles)
 
 In the following, we show two examples for user-defined styles. See the [notes on customization](@ref customization) on how to generally define a custom style.

docs/src/internals.md

@@ -27,7 +27,7 @@ ExpandCitations
 
 ## [Customization](@id customization)
 
-A custom style can be created by defining methods for functions listed below that specialize for a user-defined `style` argument to [`CitationBibliography`](@ref). If the `style` is identified by a simple name, e.g. `:mystyle`, the method should specialize on `Val{:mystyle}`, see the [examples for custom styles](@ref custom_styles). Beyond that, e.g., if the `style` needs to implement options or needs to maintain internal state to manage unique citation labels, `style` can be an object of a custom type.
+A custom style can be created by defining methods for the functions listed below that specialize for a user-defined `style` argument to [`CitationBibliography`](@ref). If the `style` is identified by a simple name, e.g. `:mystyle`, the methods should specialize on `Val{:mystyle}`, see the [examples for custom styles](@ref custom_styles). Beyond that, e.g., if the `style` needs to implement options or needs to maintain internal state to manage unique citation labels, `style` can be an object of a custom type. The builtin [`DocumenterCitations.AlphaStyle`](@ref) is an example for such a "stateful"  style, initialized via a custom [`init_bibliography!`](@ref) method.
 
 
 ```@docs
@@ -36,6 +36,7 @@ bib_sorting
 format_bibliography_label
 format_bibliography_reference
 format_citation
+init_bibliography!
 ```
 
 ## Debugging

docs/src/refs.bib

@@ -312,6 +312,8 @@ @article{GoerzQ2022
     Doi = {10.22331/q-2022-12-07-871},
     Pages = {871},
     Volume = {6},
+    eprint = {2205.15044},
+    Archiveprefix = {arXiv},
 }
 
 @article{RaithelQST2022,
@@ -427,3 +429,59 @@ @manual{SciPy
     year = {2001--},
     url = {https://docs.scipy.org/doc/scipy/},
 }
+
+
+@article{LapertPRA09,
+    Author = {Lapert, M. and Tehini, R. and Turinici, G. and Sugny, D.},
+    Title = {Monotonically Convergent Optimal Control Theory of Quantum Systems with Spectral Constraints on the Control Field},
+    Journal = pra,
+    Year = {2009},
+    Doi = {10.1103/PhysRevA.79.063411},
+    Pages = {063411},
+    Volume = {79},
+}
+
+
+@article{GraceJMO2007,
+    Author = {Grace, Matthew D. and Brif, Constantin and Rabitz, Herschel and Lidar, Daniel A. and Walmsley, Ian A. and Kosut, Robert L.},
+    Title = {Fidelity of optimally controlled quantum gates with randomly coupled multiparticle environments},
+    Journal = jmo,
+    Year = {2007},
+    Doi = {10.1080/09500340701639615},
+    Pages = {2339},
+    Volume = {54},
+}
+
+
+@article{GraceJPB2007,
+    Author = {Grace, Matthew and Brif, Constantin and Rabitz, Herschel and Walmsley, Ian A and Kosut, Robert L and Lidar, Daniel A},
+    Title = {Optimal control of quantum gates and suppression of decoherence in a system of interacting two-level particles},
+    Journal = jpb,
+    Year = {2007},
+    Doi = {10.1088/0953-4075/40/9/s06},
+    Pages = {S103},
+    Volume = {40},
+}
+
+
+@article{GrondPRA2009b,
+    Author = {Grond, Julian and von Winckel, Gregory and Schmiedmayer, J\"org and Hohenester, Ulrich},
+    Title = {Optimal control of number squeezing in trapped {Bose-Einstein} condensates},
+    Journal = pra,
+    Year = {2009},
+    Doi = {10.1103/PhysRevA.80.053625},
+    Pages = {053625},
+    Volume = {80},
+}
+
+
+@article{GrondPRA2009a,
+    Author = {Grond, Julian and Schmiedmayer, J\"org and Hohenester, Ulrich},
+    Title = {Optimizing number squeezing when splitting a mesoscopic condensate},
+    Journal = pra,
+    Year = {2009},
+    Doi = {10.1103/PhysRevA.79.021603},
+    Pages = {021603},
+    Volume = {79},
+}
+

docs/src/syntax.md

@@ -19,7 +19,7 @@ In `[…](@cite)`, the following variations can be used instead of `@cite`:
 
 Lastly, capitalizing the `c` in `@citet` or `@citet*` ensures that the first letter of the citation is capitalized so that it can be used at the beginning of a sentence, e.g., [WinckelIP2008](@Citet) (`[WinckelIP2008](@Citet)`) versus [WinckelIP2008](@citet) (`[WinckelIP2008](@citet)`).
 
-The [natbib](https://mirrors.rit.edu/CTAN/macros/latex/contrib/natbib/natnotes.pdf) commands `@citealt`, `@citealp`, and `@citenum` commands are also recognized. They are not supported by any of the built-in style, but  may be handled by [custom styles](@ref customization).
+The [natbib](https://mirrors.rit.edu/CTAN/macros/latex/contrib/natbib/natnotes.pdf) commands `@citealt`, `@citealp`, and `@citenum` commands are also recognized. They are not supported by any of the built-in styles, but  may be handled by [custom styles](@ref customization).
 
 See the [Citation Style Gallery](@ref gallery) for examples of all the possible combinations.
 
@@ -82,7 +82,7 @@ Renders a bibliography for *all* references included in the `.bib` file, not jus
 
 ### [Multiple `@bibliography` blocks](@id canonical)
 
-It is possible to have multiple `@bibliography` blocks. However, there can only be one "canonical" bibliography target for any citation (the location where a citation links to). Any `@bibliography` block will automatically skip entries that have already been rendered in an earlier `@bibliography` block. Thus, for two consecutive
+It is possible to have multiple `@bibliography` blocks. However, there can only be one "canonical" bibliography target for any citation (the location where a citation links to). Any `@bibliography` block will automatically skip entries that have already been rendered in an earlier canonical `@bibliography` block. Thus, for two consecutive
 
 ~~~markdown
 ```@bibliography

src/DocumenterCitations.jl

@@ -10,8 +10,7 @@ using Documenter.Expanders
 using Documenter.Writers.HTMLWriter
 
 using Markdown
-using Bibliography
-using Bibliography: xyear, xlink, xtitle
+using Bibliography: Bibliography, xyear, xlink, xtitle
 using OrderedCollections: OrderedDict, OrderedSet
 using Unicode
 
@@ -79,8 +78,12 @@ function CitationBibliography(bibfile::AbstractString=""; style=nothing, cached=
         # The message is only to transition users through the breaking change
         # in 1.0. It can be removed in any future 1.1 release.
         style = :numeric
+        @debug "Using default style=$(repr(style))"
+    elseif style == :alpha
+        @debug "Auto-upgrading :alpha to AlphaStyle()"
+        style = AlphaStyle()
     end
-    entries = import_bibtex(bibfile)
+    entries = Bibliography.import_bibtex(bibfile)
     if length(bibfile) > 0
         if !isfile(bibfile)
             error("bibfile $bibfile does not exist")
@@ -115,6 +118,36 @@ in its docstring.
 """
 struct Example end
 
+
+"""
+"Smart" alphabetic citation style (relative to the "dumb" `:alpha`).
+
+```julia
+style = AlphaStyle()
+```
+
+instantiates a style for [`CitationBibliography`](@ref) that avoids duplicate
+labels. Any of the entries that would result in the same label will be
+disambiguated by appending the suffix "a", "b", etc.
+
+Any bibliography that cites a subset of the given `entries` is guaranteed to
+have unique labels.
+"""
+struct AlphaStyle
+
+    # BibTeX key (entry.id) => rendered label, e.g. "GraceJMO2007" => "GBR+07b"
+    label_for_key::Dict{String,String}
+    # The internal field `label_for_key` is set by `init_bibliography!` at the
+    # beginning of the `ExpandBibliography` pipeline step.
+
+    AlphaStyle() = new(Dict{String,String}())
+
+end
+
+
+Base.show(io::IO, ::AlphaStyle) = print(io, "AlphaStyle()")
+
+
 include("citations.jl")
 include("bibliography.jl")
 include("formatting.jl")