JOSS: initial draft for arXiv

CONTRIBUTING.md

@@ -230,6 +230,7 @@ Choose the prefix that best describes the change:
 | `MAINT` | Refactor or maintain code without changing intended behavior |
 | `TST` | Add or improve tests |
 | `DOC` | Update documentation |
+| `JOSS` | Update the JOSS paper or its submission materials |
 | `BLD` | Change packaging, dependencies, or build configuration |
 | `CI` | Change continuous integration workflows |
 | `REL` | Prepare or maintain a release |

joss_paper/Makefile

@@ -0,0 +1,30 @@
+.PHONY: joss arxiv arxiv.pdf
+
+# Build the JOSS PDF without the abstract (default).
+joss:
+	docker run --rm \
+		--volume "$(CURDIR):/data" \
+		--user "$$(id -u):$$(id -g)" \
+		--env JOURNAL=joss \
+		openjournals/inara \
+		-o pdf -- paper.md --metadata=abstract:
+
+# Build the arXiv preprint.
+arxiv:
+	docker run --rm \
+		--volume "$(CURDIR):/data" \
+		--user "$$(id -u):$$(id -g)" \
+		--env JOURNAL=joss \
+		openjournals/inara \
+		-o preprint paper.md
+
+# Compile the arXiv preprint to paper.preprint.pdf.
+arxiv.pdf: arxiv
+	docker run --rm \
+		--volume "$(CURDIR):/data" \
+		--user "$$(id -u):$$(id -g)" \
+		--workdir /data \
+		--env XDG_CACHE_HOME=/tmp \
+		--entrypoint latexmk \
+		openjournals/inara \
+		-xelatex -interaction=nonstopmode -halt-on-error paper.preprint.tex

joss_paper/paper.bib

@@ -0,0 +1,222 @@
+@book{chopin2020introduction,
+  title={An introduction to sequential {Monte Carlo}},
+  author={Chopin, Nicolas and Papaspiliopoulos, Omiros},
+  series={Springer Series in Statistics},
+  year={2020},
+  publisher={Springer},
+  doi={10.1007/978-3-030-47845-2}
+}
+
+@article{delmoral2006smc,
+  title={Sequential {Monte Carlo} Samplers},
+  author={Del Moral, Pierre and Doucet, Arnaud and Jasra, Ajay},
+  journal={Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
+  volume={68},
+  number={3},
+  pages={411--436},
+  year={2006},
+  doi={10.1111/j.1467-9868.2006.00553.x}
+}
+
+@article{karamanis2025persistent,
+  title={Persistent Sampling: Enhancing the Efficiency of Sequential {Monte Carlo}},
+  author={Karamanis, Minas and Seljak, Uro{\v{s}}},
+  journal={Statistics and Computing},
+  volume={35},
+  number={5},
+  pages={144},
+  year={2025},
+  publisher={Springer},
+  doi={10.1007/s11222-025-10682-y}
+}
+
+@article{cabezas2024blackjax,
+  title={{BlackJAX}: Composable {Bayesian} inference in {JAX}},
+  author={Cabezas, Alberto and Corenflos, Adrien and Lao, Junpeng and Louf, R{\'e}mi and Carnec, Antoine and Chaudhari, Kaustubh and Cohn-Gordon, Reuben and Coullon, Jeremie and Deng, Wei and Duffield, Sam and Dur{\'a}n-Mart{\'i}n, Gerardo and Elantkowski, Marcin and Foreman-Mackey, Dan and Gregori, Michele and Iguaran, Carlos and Kumar, Ravin and Lysy, Martin and Murphy, Kevin and Orduz, Juan Camilo and Patel, Karm and Wang, Xi and Zinkov, Rob},
+  journal={arXiv preprint arXiv:2402.10797},
+  url={https://arxiv.org/abs/2402.10797},
+  year={2024}
+}
+
+@article{demasi2026sharpy,
+  title={The Sequential {Monte Carlo} goes {NUTS}: Boosting Gravitational-Wave Inference},
+  author={Demasi, Gabriele and Capurri, Giulia and Lenti, Massimo and Ricciardone, Angelo and Patricelli, Barbara and Frattale Mascioli, Adriano and Piccari, Lorenzo and Albuquerque, Saulo and Guidi, Gianluca M. and Pannarale, Francesco and Stratta, Giulia and Del Pozzo, Walter},
+  journal={arXiv preprint arXiv:2601.02336},
+  url={https://arxiv.org/abs/2601.02336},
+  year={2026}
+}
+
+@article{ashton2019bilby,
+  title={{Bilby}: A user-friendly {Bayesian} inference library for gravitational-wave astronomy},
+  author={Ashton, Gregory and H{\"u}bner, Moritz and Lasky, Paul D. and Talbot, Colm and Ackley, Kendall and Biscoveanu, Sylvia and Chu, Qi and Divarkala, Atul and Easter, Paul J. and Goncharov, Boris and Hernandez Vivanco, Francisco and Harms, Jan and Lower, Marcus E. and Meadors, Grant D. and Melchor, Denyz and Payne, Ethan and Pitkin, Matthew D. and Powell, Jade and Sarin, Nikhil and Smith, Rory J. E. and Thrane, Eric},
+  journal={The Astrophysical Journal Supplement Series},
+  volume={241},
+  number={2},
+  pages={27},
+  year={2019},
+  doi={10.3847/1538-4365/ab06fc}
+}
+
+@article{abrilpla2023pymc,
+  title={{PyMC}: A modern, and comprehensive probabilistic programming framework in {Python}},
+  author={Abril-Pla, Oriol and Andreani, Virgile and Carroll, Colin and Dong, Larry and Fonnesbeck, Christopher J. and Kochurov, Maxim and Kumar, Ravin and Lao, Junpeng and Luhmann, Christian C. and Martin, Osvaldo A. and Osthege, Michael and Vieira, Ricardo and Wiecki, Thomas V. and Zinkov, Robert},
+  journal={PeerJ Computer Science},
+  volume={9},
+  pages={e1516},
+  year={2023},
+  doi={10.7717/peerj-cs.1516}
+}
+
+@misc{smcpy_repo,
+  author = {{NASA Langley Research Center}},
+  title = {{SMCPy}: {Python} module for uncertainty quantification using a parallel sequential {Monte Carlo} sampler},
+  year = {2026},
+  howpublished = {\url{https://github.com/nasa/SMCPy}},
+  note = {Accessed 2026-07-07}
+}
+
+@misc{python_array_api,
+  author = {{Consortium for Python Data API Standards}},
+  title = {{Python} array {API} standard},
+  year = {2026},
+  howpublished = {\url{https://data-apis.org/array-api/latest/}},
+  note = {Accessed 2026-07-07}
+}
+
+@article{williams2026accelerated,
+    author = "Williams, Michael J.",
+    title = "{Accelerated Sequential Posterior Inference via Reuse for Gravitational-Wave Analyses}",
+    eprint = "2511.04218",
+    archivePrefix = "arXiv",
+    primaryClass = "hep-ex",
+    reportNumber = "LIGO-P2500623",
+    doi = "10.1103/5hvn-3lmh",
+    journal = "Physical Review Letters",
+    volume = "137",
+    number = "2",
+    pages = "021410",
+    year = "2026"
+}
+
+
+@article{salomone2025unbiased,
+    author = {Salomone, Robert and South, Leah F and Drovandi, Christopher and Kroese, Dirk P and Johansen, Adam M},
+    title = {Unbiased and consistent nested sampling via sequential {Monte Carlo}},
+    journal = {Journal of the Royal Statistical Society Series B: Statistical Methodology},
+    volume = {87},
+    number = {4},
+    pages = {1221--1238},
+    year = {2025},
+    month = {09},
+    issn = {1369-7412},
+    doi = {10.1093/jrsssb/qkaf015},
+    url = {https://doi.org/10.1093/jrsssb/qkaf015},
+    eprint = {https://academic.oup.com/jrsssb/article-pdf/87/4/1221/63166567/qkaf015.pdf},
+}
+
+@article{dau2022wastefree,
+    author = {Dau, Hai-Dang and Chopin, Nicolas},
+    title = {Waste-Free Sequential {Monte Carlo}},
+    journal = {Journal of the Royal Statistical Society Series B: Statistical Methodology},
+    volume = {84},
+    number = {1},
+    pages = {114--148},
+    year = {2022},
+    month = {02},
+    issn = {1369-7412},
+    doi = {10.1111/rssb.12475},
+    url = {https://doi.org/10.1111/rssb.12475},
+    eprint = {https://academic.oup.com/jrsssb/article-pdf/84/1/114/49324223/jrsssb_84_1_114.pdf},
+}
+
+@misc{williams2026inprep,
+    author = {Williams, Michael J. and Chapman-Bird, Christian E. A. and Costa Barroso, Raissa and Harry, Ian},
+    title = {Robust {Bayesian} inference for massive black hole binaries in {LISA} with sequential {Monte Carlo}},
+    howpublished = {Manuscript in preparation (provisional title)},
+    year = {2026}
+}
+
+@software{sequince,
+  author       = {Michael J. Williams and
+                  Christian Chapman-Bird},
+  title        = {{sequince-dev/sequince}},
+  year         = {2026},
+  publisher    = {Zenodo},
+  doi          = {10.5281/zenodo.23596103},
+  url          = {https://doi.org/10.5281/zenodo.23596103},
+}
+
+@software{sequince_density,
+  author       = {Michael J. Williams},
+  title        = {{sequince-dev/sequince-density}},
+  year         = {2026},
+  publisher    = {Zenodo},
+  doi          = {10.5281/zenodo.23687687},
+  url          = {https://doi.org/10.5281/zenodo.23687687},
+}
+
+@software{sequince_bilby,
+  author       = {Michael J. Williams},
+  title        = {{sequince-dev/sequince-bilby}},
+  year         = {2026},
+  publisher    = {Zenodo},
+  doi          = {10.5281/zenodo.23736054},
+  url          = {https://doi.org/10.5281/zenodo.23736054},
+}
+
+@misc{sequince_examples,
+  author       = {{Sequince contributors}},
+  title        = {{sequince-dev/sequince-examples}},
+  year         = {2026},
+  url          = {https://github.com/sequince-dev/sequince-examples},
+  note         = {Accessed 2026-10-27},
+}
+
+@software{orng,
+  author       = {Michael J. Williams and
+                  Colm Talbot},
+  title        = {{sequince-dev/orng}},
+  year         = {2026},
+  publisher    = {Zenodo},
+  doi          = {10.5281/zenodo.17544786},
+  url          = {https://doi.org/10.5281/zenodo.17544786},
+}
+
+@software{bilby,
+  author       = {Colm Talbot and
+                  Gregory Ashton and
+                  Moritz Hübner and
+                  Matt Pitkin and
+                  Michael J. Williams and
+                  plasky and
+                  asb5468 and
+                  Aditya Vijaykumar and
+                  Rory Smith and
+                  SMorisaki and
+                  John Veitch and
+                  Duncan Macleod and
+                  Nikhil Sarin and
+                  Daniel Williams and
+                  JasperMartins and
+                  MarcArene and
+                  Vivien Raymond and
+                  C P L Berry and
+                  AlexandreGoettel and
+                  Fabian Gittins and
+                  Ceciliogq and
+                  Lorenzo Pompili and
+                  Ivan Markin and
+                  David Keitel and
+                  Hen42rik and
+                  Mick Wright and
+                  oliviawilk and
+                  noahewolfe and
+                  jacobgolomb and
+                  Shichao Wu},
+  title        = {{bilby-dev/bilby}},
+  month        = aug,
+  year         = 2026,
+  publisher    = {Zenodo},
+  doi          = {10.5281/zenodo.14025463},
+  url          = {https://doi.org/10.5281/zenodo.14025463},
+}