Add support for biorXiv and HAL preprint servers

NEWS.md

@@ -15,8 +15,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 
 * New `style=AlphaStyle()` that generates unique citation labels. This can mostly be considered internal, as `style=:alpha` is automatically upgraded to `style=AlphaStyle()`.
-* Support for `eprint` field. It is recommended to add the arXiv ID in the `eprint` field for any article whose DOI is behind a paywall.
-* Support for `note` field.
+* Support for `eprint` field. It is recommended to add the arXiv ID in the `eprint` field for any article whose DOI is behind a paywall [[#32][]]
+* Support for non-arXiv preprint servers BiorXiv and HAL [[#35][], [#36][]]
+* Support for `note` field. [[#20][]]
 
 ### Changed
 
@@ -55,3 +56,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 [Unreleased]: https://github.com/JuliaDocs/DocumenterCitations.jl/compare/v1.0.0...HEAD
 [1.0.0]: https://github.com/JuliaDocs/DocumenterCitations.jl/compare/v0.2.12...v1.0.0
+[#36]: https://github.com/JuliaDocs/DocumenterCitations.jl/pull/36
+[#35]: https://github.com/JuliaDocs/DocumenterCitations.jl/issues/35
+[#32]: https://github.com/JuliaDocs/DocumenterCitations.jl/pull/32
+[#20]: https://github.com/JuliaDocs/DocumenterCitations.jl/issues/20

docs/src/refs.bib

@@ -420,7 +420,7 @@ @article{ImamogluPRE2015
     Pages = {022714},
     Volume = {91},
     Number = {2},
-    arxiv = {1408.5798},
+    eprint = {1408.5798},
 }
 
 @unpublished{Evans1983,
@@ -531,6 +531,71 @@ @article{Wilhelm2003.10132
     Doi = {10.48550/ARXIV.2003.10132},
 }
 
+@article{TuriniciHAL00640217,
+    Title = {Quantum control},
+    Author = {Turinici, Gabriel},
+    Journal = {HAL:hal-00640217},
+    Year = {2012},
+    Url = {https://hal.science/hal-00640217},
+}
+
+@article{SauvagePRXQ2020,
+    Author = {Sauvage, Frédéric and Mintert, Florian},
+    Title = {Optimal Quantum Control with Poor Statistics},
+    Journal = prxq,
+    Year = {2020},
+    Doi = {10.1103/prxquantum.1.020322},
+    Pages = {020322},
+    Volume = {1},
+    Number = {2},
+    eprint = {hal-03612955},
+    Archiveprefix = {HAL},
+}
+
+
+@article{LarrouyPRX2020,
+    Author = {Larrouy, Arthur and Patsch, Sabrina and Richaud, Rémi and Raimond, Jean-Michel and Brune, Michel and Koch, Christiane P. and Gleyzes, Sébastien},
+    Title = {Fast Navigation in a Large Hilbert Space Using Quantum Optimal Control},
+    Journal = prx,
+    Year = {2020},
+    Doi = {10.1103/physrevx.10.021058},
+    Pages = {021058},
+    Volume = {10},
+    Number = {2},
+    eprint = {hal-02887773},
+    Archiveprefix = {Hal},
+}
+
+@phdthesis{BrionPhd2004,
+    Author = {Brion, Etienne},
+    Title = {Contrôle Quantique et Protection de la Cohérence par effet Zénon, Applications à l'Informatique Quantique},
+    School = {Université Pierre et Marie Curie - Paris VI},
+    eprint = {tel-00007910v2},
+    Archiveprefix= {hal},
+    Year = {2014},
+}
+
+@article{Vecheck2022.09.09.507322,
+    Author = {Amy M. Vecheck and Cameron McNamee and Renee Reijo Pera and Robert J. Usselman},
+    Title = {Quantum Biology in Cellular Migration},
+    Year = {2022},
+    Doi = {10.1101/2022.09.09.507322},
+    journal = {bioRxiv:2022.09.09.507322}
+}
+
+@article{KatrukhaNC2017,
+    Author = {Katrukha, Eugene A. and Mikhaylova, Marina and van Brakel, Hugo X. and van Bergen en Henegouwen, Paul M. and Akhmanova, Anna and Hoogenraad, Casper C. and Kapitein, Lukas C.},
+    Title = {Probing cytoskeletal modulation of passive and active intracellular dynamics using nanobody-functionalized quantum dots},
+    Journal = natcom,
+    Year = {2017},
+    Doi = {10.1038/ncomms14772},
+    Pages = {14772},
+    Volume = {8},
+    Number = {1},
+    eprint = {089284},
+    Archiveprefix = {biorxiv},
+}
+
 @misc{QCRoadmap,
     editor = {Todd Heinrichs},
     title = {Quantum Computation Roadmap},

docs/src/syntax.md

@@ -195,10 +195,24 @@ Some tips to keep in mind when editing a `.bib` file to be used with `Documenter
 * You do not need to use [braces to protect capitalization](https://texfaq.org/FAQ-capbibtex). `DocumenterCitations` is not always able to remove such braces. But, unlike `bibtex`, `DocumenterCitation` will preserve the capitalization of titles.
 * Use a consistent scheme for citation keys. Shorter keys are better.
 * All entries should have a `Doi` field, or a `Url` field if no DOI is available.
-* If the published paper (`Doi` link) is not open-access, but a version of the paper is available on the [arXiv](https://arxiv.org), include the arXiv ID as `eprint` in the BibTeX entry. In the rendered bibliography, there will be a link to `https://arxiv.org/abs/<ID>`.
-* It is not necessary to define `Archiveprefix` in the `.bib` file. A missing `Archiveprefix` is assumed to be `arXiv`.
-* For documents that are available only as an arXiv eprint, the best result is obtained with a BibTeX entry using the `@article` class, with, e.g., `arXiv:2003.10132` in the `Journal` field, and, e.g., `10.48550/ARXIV.2003.10132` in the `Doi` field (but no `eprint` field).
 * Use `@string` macros for abbreviated journal names, with the caveat of [#31](https://github.com/Humans-of-Julia/BibParser.jl/issues/31) and [#32](https://github.com/Humans-of-Julia/BibParser.jl/issues/32) in the [BibParser.jl issues](https://github.com/Humans-of-Julia/BibParser.jl/issues).
 
 
 You may be interested in using (or forking) the [`getbibtex` script](https://github.com/goerz/getbibtex) to generate consistent `.bib` files.
+
+
+### Preprint support
+
+If the published paper (`Doi` link) is not open-access, but a version of the paper is available on a preprint server like the [arXiv](https://arxiv.org), your are strongly encouraged to add the arXiv ID as `Eprint` in the BibTeX entry. In the rendered bibliography, the preprint information will be shown and automatically link to `https://arxiv.org/abs/<ID>`.
+If necessary, you may also add a `Primaryclass` field to indicate a category, see ["BibTeX and Eprints" in the arXiv documentation](https://info.arxiv.org/help/hypertex/bibstyles/index.html).
+
+Note that unlike in [default](https://tex.stackexchange.com/questions/386078/workaround-for-missing-archiveprefix-in-bib-entry) BibTeX, it is not necessary to define `Archiveprefix` in the `.bib` file. A missing `Archiveprefix` is assumed to be `arXiv`. The field name `Eprinttype` (which in BibTeX is an alias for `Archiveprefix`) is currently not yet supported, nor is `Eprintclass` as an alias for `Primaryclass`.
+
+For documents that are available *only* as an arXiv eprint, the best result is obtained with a BibTeX entry using the `@article` class, with, e.g., `arXiv:2003.10132` in the `Journal` field, and, e.g., `10.48550/ARXIV.2003.10132` in the `Doi` field (but no `Eprint` field) [Wilhelm2003.10132](@cite).
+
+Beyond arXiv, other preprint servers are supported. The `Archiveprefix` field for non-arXiv preprints is mandatory. For any defined `Archiveprefix`, `Eprint`, and `Primaryclass` fields, the rendered bibliography will include the preprint information in the format `ArchivePrefix:Eprint [Primaryclass]`. However, only certain preprint servers (known `ArchivePrefix`) will automatically be linked. Besides arXiv, the currently supported preprint servers are:
+
+* [BiorXiv](https://www.biorxiv.org). The `Archiveprefix` is `biorXiv`. The `Eprint` ID should be the final part of the DOI, e.g. `2022.09.09.507322` [KatrukhaNC2017](@cite).
+* [HAL](https://hal.science). The `Archiveprefix` is `HAL`. The `Eprint` ID should include the prefix (usually `hal-`, but sometimes `tel-`, etc.), e.g., Refs [SauvagePRXQ2020](@cite) and [BrionPhd2004](@cite).
+
+If you would like support for any additional preprint server, [please open an issue](https://github.com/JuliaDocs/DocumenterCitations.jl/issues/new/choose).

src/formatting.jl

@@ -301,24 +301,42 @@ end
 
 
 function format_eprint(entry)
+
     eprint = entry.eprint.eprint
     if isempty(eprint)
         return ""
     end
     archive_prefix = entry.eprint.archive_prefix
     primary_class = entry.eprint.primary_class
+
+    # standardize prefix for supported preprint repositories
     if isempty(archive_prefix) || (lowercase(archive_prefix) == "arxiv")
         archive_prefix = "arXiv"
     end
+    if lowercase(archive_prefix) == "hal"
+        archive_prefix = "HAL"
+    end
+    if lowercase(archive_prefix) == "biorxiv"
+        archive_prefix = "biorXiv"
+    end
+
     text = "$(archive_prefix):$eprint"
     if !isempty(primary_class)
         text *= " [$(primary_class)]"
     end
+
+    # link url for supported preprint repositories
     link = ""
     if archive_prefix == "arXiv"
         link = "https://arxiv.org/abs/$eprint"
+    elseif archive_prefix == "HAL"
+        link = "https://hal.science/$eprint"
+    elseif archive_prefix == "biorXiv"
+        link = "https://www.biorxiv.org/content/10.1101/$eprint"
     end
+
     return linkify(text, link)
+
 end
 
 

test/test_formatting.jl

@@ -89,6 +89,24 @@ end
 end
 
 
+@testset "format_biliography_reference (preprints)" begin
+    bib = CitationBibliography(joinpath(@__DIR__, "..", "docs", "src", "refs.bib"),)
+    bib0 = CitationBibliography(joinpath(splitext(@__FILE__)[1], "preprints.bib"))
+    merge!(bib.entries, bib0.entries)
+    html(key) = format_bibliography_reference(Val(:numeric), bib.entries[key])
+    @Test html("LarrouyPRX2020") ==
+          "A. Larrouy, S. Patsch, R. Richaud, J.-M. Raimond, M. Brune, C. P. Koch and S. Gleyzes. <i>Fast Navigation in a Large Hilbert Space Using Quantum Optimal Control</i>. <a href='https://doi.org/10.1103/physrevx.10.021058'>Phys. Rev. X <b>10</b>, 021058 (2020)</a>. <a href='https://hal.science/hal-02887773'>HAL:hal-02887773</a>."
+    @Test html("TuriniciHAL00640217") ==
+          "G. Turinici. <a href='https://hal.science/hal-00640217'><i>Quantum control</i></a>. HAL:hal-00640217 (2012)."
+    @Test html("BrionPhd2004") ==
+          "E. Brion. <i>Contrôle Quantique et Protection de la Cohérence par effet Zénon, Applications à l'Informatique Quantique</i>. Phd thesis, Université Pierre et Marie Curie - Paris VI (2014). <a href='https://hal.science/tel-00007910v2'>HAL:tel-00007910v2</a>."
+    @Test html("KatrukhaNC2017") ==
+          "E. A. Katrukha, M. Mikhaylova, H. X. van Brakel, P. M. van Bergen en Henegouwen, A. Akhmanova, C. C. Hoogenraad and L. C. Kapitein. <i>Probing cytoskeletal modulation of passive and active intracellular dynamics using nanobody-functionalized quantum dots</i>. <a href='https://doi.org/10.1038/ncomms14772'>Nat. Commun. <b>8</b>, 14772 (2017)</a>, <a href='https://www.biorxiv.org/content/10.1101/089284'>biorXiv:089284</a>."
+    @Test html("NonStandardPreprint") ==
+          "M. Tomza, M. H. Goerz, M. Musiał, R. Moszynski and C. P. Koch. <i>Optimized production of ultracold ground-state molecules: Stabilization employing potentials with ion-pair character and strong spin-orbit coupling</i>. <a href='https://doi.org/10.1103/PhysRevA.86.043424'>Phys. Rev. A <b>86</b>, 043424 (2012)</a>, xxx-preprint:1208.4331."
+end
+
+
 @testset "format_bibliography_reference(:authoryear)" begin
     bib = CitationBibliography(joinpath(@__DIR__, "..", "docs", "src", "refs.bib"),)
     html(key) = format_bibliography_reference(Val(:authoryear), bib.entries[key])

test/test_formatting/preprints.bib

@@ -0,0 +1,18 @@
+% Additionally to the main .bib file
+@string{pra = "Phys. Rev. A"}
+
+% https://github.com/Humans-of-Julia/BibParser.jl/issues/32
+@string{XXXclearparser = ""}
+
+@article{NonStandardPreprint,
+    Author = {Tomza, Micha\l{} and Goerz, Michael H. and Musia\l{}, Monika and Moszynski, Robert and Koch, Christiane P.},
+    Title = {Optimized production of ultracold ground-state molecules: Stabilization employing potentials with ion-pair character and strong spin-orbit coupling},
+    Journal = pra,
+    Year = {2012},
+    Doi = {10.1103/PhysRevA.86.043424},
+    Pages = {043424},
+    Volume = {86},
+    eprint = {1208.4331},
+    Archiveprefix = {xxx-preprint},
+}
+