PAPER: Add JOSS paper for submission

- paper/paper.md: JOSS manuscript (~1580 words)
- paper/paper.bib: 33 references (all verified)
- .gitignore: track paper sources, exclude build artifacts

Author: Axect

.gitignore

@@ -21,5 +21,10 @@ example_data/*.parquet
 src/bin/*
 outputs/
 
-# JOSS paper
-paper/
+# JOSS paper build artifacts
+paper/*.pdf
+paper/*.latex
+paper/*.csl
+paper/*.png
+paper/*.yaml
+paper/jats/

paper/paper.bib

@@ -0,0 +1,305 @@
+% ===== Peroxide itself =====
+@software{peroxide,
+  author       = {Kim, Tae-Geun},
+  title        = {{Peroxide: Rust numeric library containing linear algebra, numerical analysis, statistics, and machine learning tools}},
+  version      = {0.41.0},
+  year         = {2026},
+  publisher    = {Zenodo},
+  doi          = {10.5281/zenodo.10815823},
+  url          = {https://github.com/Axect/Peroxide}
+}
+
+% ===== Papers citing Peroxide =====
+@misc{neural_hamilton,
+  author  = {Kim, Tae-Geun and Park, Seong Chan},
+  title   = {Neural {Hamilton}: Can {A.I.} Understand {Hamiltonian} Mechanics?},
+  year    = {2024},
+  eprint  = {2410.20951},
+  archiveprefix = {arXiv},
+  url     = {https://arxiv.org/abs/2410.20951},
+  note    = {Code: \url{https://github.com/Axect/Neural_Hamilton}}
+}
+
+@misc{hyperboliclr,
+  author  = {Kim, Tae-Geun},
+  title   = {{HyperbolicLR}: Epoch insensitive learning rate scheduler},
+  year    = {2024},
+  eprint  = {2407.15200},
+  archiveprefix = {arXiv},
+  url     = {https://arxiv.org/abs/2407.15200},
+  note    = {Code: \url{https://github.com/Axect/HyperbolicLR}}
+}
+
+@article{jho2026,
+  author  = {Jho, Yongsoo and Kim, Tae-Geun and Park, Jong-Chul and Park, Seong Chan and Park, Yeji},
+  title   = {Primordial Black Holes as a Factory of Axions: Extragalactic Photons from Axions},
+  journal = {Progress of Theoretical and Experimental Physics},
+  year    = {2026},
+  doi     = {10.1093/ptep/ptag011}
+}
+
+% ===== Independent citations of Peroxide =====
+@article{comitini2025,
+  author  = {Comitini, Giorgio and Siringo, Fabio},
+  title   = {Screened massive expansion of {QCD} at finite temperature: Two-loop approximation},
+  journal = {Physical Review D},
+  volume  = {111},
+  pages   = {054012},
+  year    = {2025},
+  doi     = {10.1103/PhysRevD.111.054012}
+}
+
+@inproceedings{steuteville2024,
+  author    = {Steuteville, Robin and Baker, Chad},
+  title     = {Implementing Ordinary Differential Equation Solvers in {Rust} Programming Language for Modeling Vehicle Powertrain Systems},
+  booktitle = {SAE Technical Paper 2024-01-2148},
+  year      = {2024},
+  doi       = {10.4271/2024-01-2148}
+}
+
+% ===== ODE method references =====
+@article{bogacki1989,
+  author  = {Bogacki, Przemyslaw and Shampine, Lawrence F.},
+  title   = {A 3(2) pair of {Runge-Kutta} formulas},
+  journal = {Applied Mathematics Letters},
+  volume  = {2},
+  number  = {4},
+  pages   = {321--325},
+  year    = {1989},
+  doi     = {10.1016/0893-9659(89)90079-7}
+}
+
+@techreport{fehlberg1969,
+  author      = {Fehlberg, Erwin},
+  title       = {Low-order classical {Runge-Kutta} formulas with stepsize control and their application to some heat transfer problems},
+  institution = {NASA},
+  number      = {TR R-315},
+  year        = {1969}
+}
+
+% ===== Foundational references from source code =====
+@book{griewank2008,
+  author    = {Griewank, Andreas and Walther, Andrea},
+  title     = {Evaluating Derivatives: Principles and Techniques of Algorithmic Differentiation},
+  edition   = {2nd},
+  publisher = {SIAM},
+  year      = {2008},
+  doi       = {10.1137/1.9780898717761}
+}
+
+@book{butcher2016,
+  author    = {Butcher, John C.},
+  title     = {Numerical Methods for Ordinary Differential Equations},
+  edition   = {3rd},
+  publisher = {John Wiley \& Sons},
+  year      = {2016},
+  doi       = {10.1002/9781119121534}
+}
+
+@article{dormand1980,
+  author  = {Dormand, J. R. and Prince, P. J.},
+  title   = {A family of embedded {Runge-Kutta} formulae},
+  journal = {Journal of Computational and Applied Mathematics},
+  issn    = {0771-050X},
+  volume  = {6},
+  number  = {1},
+  pages   = {19--26},
+  year    = {1980},
+  doi     = {10.1016/0771-050X(80)90013-3}
+}
+
+@article{tsitouras2011,
+  author  = {Tsitouras, Ch.},
+  title   = {Runge-{Kutta} pairs of order 5(4) satisfying only the first column simplifying assumption},
+  journal = {Computers \& Mathematics with Applications},
+  volume  = {62},
+  number  = {2},
+  pages   = {770--775},
+  year    = {2011},
+  doi     = {10.1016/j.camwa.2011.06.002}
+}
+
+@article{akima1970,
+  author  = {Akima, Hiroshi},
+  title   = {A new method of interpolation and smooth curve fitting based on local procedures},
+  journal = {Journal of the ACM},
+  volume  = {17},
+  number  = {4},
+  pages   = {589--602},
+  year    = {1970},
+  doi     = {10.1145/321607.321609}
+}
+
+@book{knott2000,
+  author    = {Knott, Gary D.},
+  title     = {Interpolating Cubic Splines},
+  publisher = {Birkh\"{a}user Boston},
+  year      = {2000},
+  doi       = {10.1007/978-1-4612-1320-8}
+}
+
+@article{laurie1997,
+  author  = {Laurie, Dirk P.},
+  title   = {Calculation of {Gauss-Kronrod} quadrature rules},
+  journal = {Mathematics of Computation},
+  volume  = {66},
+  number  = {219},
+  pages   = {1133--1145},
+  year    = {1997},
+  doi     = {10.1090/S0025-5718-97-00861-2}
+}
+
+@book{piessens1983,
+  author    = {Piessens, Robert and de Doncker-Kapenga, Elise and \"{U}berhuber, Christoph W. and Kahaner, David K.},
+  title     = {{QUADPACK}: A Subroutine Package for Automatic Integration},
+  publisher = {Springer-Verlag},
+  year      = {1983},
+  doi       = {10.1007/978-3-642-61786-7}
+}
+
+@book{press2007,
+  author    = {Press, William H. and Teukolsky, Saul A. and Vetterling, William T. and Flannery, Brian P.},
+  title     = {Numerical Recipes: The Art of Scientific Computing},
+  edition   = {3rd},
+  publisher = {Cambridge University Press},
+  year      = {2007}
+}
+
+% ===== Python ecosystem references =====
+@article{scipy,
+  author  = {Virtanen, Pauli and Gommers, Ralf and Oliphant, Travis E. and others},
+  title   = {{SciPy} 1.0: Fundamental algorithms for scientific computing in {Python}},
+  journal = {Nature Methods},
+  volume  = {17},
+  pages   = {261--272},
+  year    = {2020},
+  doi     = {10.1038/s41592-019-0686-2}
+}
+
+@article{numpy,
+  author  = {Harris, Charles R. and Millman, K. Jarrod and van der Walt, St\'{e}fan J. and others},
+  title   = {Array programming with {NumPy}},
+  journal = {Nature},
+  volume  = {585},
+  pages   = {357--362},
+  year    = {2020},
+  doi     = {10.1038/s41586-020-2649-2}
+}
+
+% ===== Competing Rust crates =====
+@article{diffsol,
+  author  = {Robinson, Martin and Allmont, Alex},
+  title   = {diffsol: A {Rust} crate for solving differential equations},
+  journal = {Journal of Open Source Software},
+  volume  = {11},
+  number  = {117},
+  year    = {2026},
+  doi     = {10.21105/joss.09384}
+}
+
+@software{faer,
+  author  = {Quinones, Sarah},
+  title   = {faer: Low-level linear algebra routines in pure {Rust}},
+  url     = {https://github.com/sarah-quinones/faer-rs},
+  version = {0.24.0},
+  year    = {2026}
+}
+
+@software{argmin,
+  author  = {Kroboth, Stefan},
+  title   = {argmin: A pure {Rust} optimization framework},
+  url     = {https://github.com/argmin-rs/argmin},
+  version = {0.11.0},
+  year    = {2025}
+}
+
+@article{numdual,
+  author  = {Rehner, Philipp and Bauer, Gernot},
+  title   = {Application of Generalized (Hyper-) Dual Numbers in Equation of State Modeling},
+  journal = {Frontiers in Chemical Engineering},
+  volume  = {3},
+  year    = {2021},
+  url     = {https://www.frontiersin.org/article/10.3389/fceng.2021.758090},
+  doi     = {10.3389/fceng.2021.758090}
+}
+
+@misc{adtrait,
+  author        = {Liang, Chen and Wang, Qian and Xu, Andy and Rakita, Daniel},
+  title         = {ad-trait: A Fast and Flexible Automatic Differentiation Library in {Rust}},
+  year          = {2025},
+  eprint        = {2504.15976},
+  archiveprefix = {arXiv},
+  url           = {https://arxiv.org/abs/2504.15976}
+}
+
+@software{autodiff_elrnv,
+  author  = {Larionov, Egor},
+  title   = {autodiff: Automatic differentiation via operator overloading for {Rust}},
+  url     = {https://github.com/elrnv/autodiff},
+  year    = {2023}
+}
+
+@software{nalgebra,
+  author  = {Crozet, S\'{e}bastien},
+  title   = {nalgebra: General-purpose linear algebra library for {Rust}},
+  url     = {https://github.com/dimforge/nalgebra},
+  version = {0.34.1},
+  year    = {2025}
+}
+
+@software{polars,
+  author  = {Vink, Ritchie},
+  title   = {Polars: Blazingly fast {DataFrames} in {Rust}, {Python}, {Node.js}, {R} and {SQL}},
+  url     = {https://github.com/pola-rs/polars},
+  version = {0.53.0},
+  year    = {2026}
+}
+
+@software{russell,
+  author  = {Pedroso, Dorival M.},
+  title   = {Russell: {Rust} Scientific Library},
+  url     = {https://github.com/cpmech/russell},
+  version = {1.10.0},
+  year    = {2025}
+}
+
+
+@software{matrixmultiply,
+  author  = {Sverdrup, Ulrik},
+  title   = {matrixmultiply: General matrix multiplication of f32 and f64 in {Rust}},
+  url     = {https://github.com/bluss/matrixmultiply},
+  version = {0.3.10},
+  year    = {2025}
+}
+
+@software{splines_crate,
+  author  = {Sabadie, Dimitri},
+  title   = {splines: Spline interpolation library for {Rust}},
+  url     = {https://sr.ht/~hadronized/splines/},
+  version = {5.0.0},
+  year    = {2025}
+}
+
+@software{bspline_crate,
+  author  = {Usher, Will},
+  title   = {bspline: {B}-spline interpolation for {Rust}},
+  url     = {https://github.com/Twinklebear/bspline},
+  year    = {2022}
+}
+
+@software{netcdf,
+  author  = {{NSF Unidata}},
+  title   = {{NetCDF}: Network Common Data Form [software]},
+  publisher = {UCAR/NSF Unidata Program Center},
+  address = {Boulder, CO},
+  doi     = {10.5065/D6H70CW6},
+  url     = {https://www.unidata.ucar.edu/software/netcdf/},
+  year    = {2026}
+}
+
+@software{parquet,
+  author  = {{Apache Software Foundation}},
+  title   = {{Apache Parquet}},
+  url     = {https://parquet.apache.org/},
+  year    = {2026}
+}