docs: JOSS paper for PyAutoLens-Assistant

paper/.gitignore

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+/paper.pdf

paper/README.md

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+# PyAutoLens-Assistant JOSS paper
+
+This directory contains the PyAutoLens-Assistant paper for submission to the
+[Journal of Open Source Software](https://joss.theoj.org/). It is hosted with the
+software it describes, and is the sibling of the PyAutoLens-JAX paper in
+`PyAutoLens/paper_jax/`.
+
+## Files
+
+- `paper.md` — manuscript and JOSS metadata.
+- `paper.bib` — bibliography cited by the manuscript. Entries are copied verbatim
+  from `../wiki/literature/bibliography/autolens_literature.bib` so the paper and
+  the literature wiki cannot drift apart.
+- `paper.pdf` — local build output; do not commit it.
+
+## Drafting checklist
+
+- Confirm the full author list, affiliations, ORCIDs, corresponding author, and
+  submission date. The current block mirrors the PyAutoLens-JAX paper.
+- Keep the manuscript within the current JOSS target of 750–1750 words.
+- Replace every drafting comment (`State of the field`, `Research impact
+  statement`, `Acknowledgements`) with specific, evidenced prose.
+- Compare against other domain-specific scientific AI assistants and
+  general-purpose coding assistants in “State of the field”.
+- **Report real benchmark results.** The `Benchmark examples` section is written
+  in the future tense because `../benchmarks/RESULTS.md` currently records no runs
+  for any benchmark. Once the suite has been run, replace that prose with measured
+  outcomes — do not claim results the repository cannot evidence.
+- The paper describes **three representative** benchmarks; the repository ships
+  **four** prompts (the fourth is `hard_group_multi.md`). This framing is
+  deliberate. If the fourth is later described, update the wording in both places.
+- Verify every bibliography entry resolves and is the intended paper.
+- Keep the AI usage disclosure accurate as the manuscript evolves.
+
+The current format requirements are documented in the
+[JOSS paper guide](https://joss.readthedocs.io/en/latest/paper.html).
+
+## Build the paper
+
+From the `autolens_assistant` repository root, compile with the official JOSS
+Inara image:
+
+```bash
+docker run --rm \
+  --volume "$PWD/paper:/data" \
+  --user "$(id -u):$(id -g)" \
+  --env JOURNAL=joss \
+  openjournals/inara
+```
+
+The generated PDF is written to `paper/paper.pdf`.

paper/paper.bib

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+% Bibliography for the PyAutoLens-Assistant JOSS paper.
+% Entries are copied verbatim from the assistant literature bibliography
+% (wiki/literature/bibliography/autolens_literature.bib) so they stay consistent
+% with the wiki. Verify every entry before submission.
+
+@article{Casey2023,
+archivePrefix = {arXiv},
+arxivId = {2211.07865},
+author = {Casey, Caitlin M. and Kartaltepe, Jeyhan S. and Drakos, Nicole E. and Franco, Maximilien and Harish, Santosh and Paquereau, Louise and Ilbert, Olivier and Rose, Caitlin and Cox, Isabella G. and Nightingale, James W. and Robertson, Brant E. and Silverman, John D. and Koekemoer, Anton M. and Massey, Richard and McCracken, Henry Joy and Rhodes, Jason and Akins, Hollis B. and Allen, Natalie and Amvrosiadis, Aristeidis and Arango-Toro, Rafael C. and Bagley, Micaela B. and Bongiorno, Angela and Capak, Peter L. and Champagne, Jaclyn B. and Chartab, Nima and {Ch{\'{a}}vez Ortiz}, {\'{O}}scar A. and Chworowsky, Katherine and Cooke, Kevin C. and Cooper, Olivia R. and Darvish, Behnam and Ding, Xuheng and Faisst, Andreas L. and Finkelstein, Steven L. and Fujimoto, Seiji and Gentile, Fabrizio and Gillman, Steven and Gould, Katriona M. L. and Gozaliasl, Ghassem and Hayward, Christopher C. and He, Qiuhan and Hemmati, Shoubaneh and Hirschmann, Michaela and Jahnke, Knud and Jin, Shuowen and Khostovan, Ali Ahmad and Kokorev, Vasily and Lambrides, Erini and Laigle, Clotilde and Larson, Rebecca L. and Leung, Gene C. K. and Liu, Daizhong and Liaudat, Tobias and Long, Arianna S. and Magdis, Georgios and Mahler, Guillaume and Mainieri, Vincenzo and Manning, Sinclaire M. and Maraston, Claudia and Martin, Crystal L. and McCleary, Jacqueline E. and McKinney, Jed and McPartland, Conor J. R. and Mobasher, Bahram and Pattnaik, Rohan and Renzini, Alvio and Rich, R. Michael and Sanders, David B. and Sattari, Zahra and Scognamiglio, Diana and Scoville, Nick and Sheth, Kartik and Shuntov, Marko and Sparre, Martin and Suzuki, Tomoko L. and Talia, Margherita and Toft, Sune and Trakhtenbrot, Benny and Urry, C. Megan and Valentino, Francesco and Vanderhoof, Brittany N. and Vardoulaki, Eleni and Weaver, John R. and Whitaker, Katherine E. and Wilkins, Stephen M. and Yang, Lilan and Zavala, Jorge A.},
+doi = {10.3847/1538-4357/acc2bc},
+eprint = {2211.07865},
+issn = {0004-637X},
+journal = {ApJ},
+number = {1},
+pages = {31},
+title = {{COSMOS-Web: An Overview of the JWST Cosmic Origins Survey}},
+volume = {954},
+year = {2023}
+}
+
+@article{Nightingale2021,
+author = {Nightingale, James. and Hayes, Richard and Kelly, Ashley and Amvrosiadis, Aristeidis and Etherington, Amy and He, Qiuhan and Li, Nan and Cao, XiaoYue and Frawley, Jonathan and Cole, Shaun and Enia, Andrea and Frenk, Carlos and Harvey, David and Li, Ran and Massey, Richard and Negrello, Mattia and Robertson, Andrew},
+doi = {10.21105/joss.02825},
+issn = {2475-9066},
+journal = {J. Open Source Softw.},
+number = {58},
+pages = {2825},
+title = {{PyAutoLens: Open-Source Strong Gravitational Lensing}},
+volume = {6},
+year = {2021}
+}
+
+@article{EuclidCollaboration2025,
+archivePrefix = {arXiv},
+arxivId = {2503.15324},
+author = {{Euclid Collaboration} and Walmsley, M. and Holloway, P. and Lines, N. E. P. and Rojas, K. and Collett, T. E. and Verma, A. and Li, T. and Nightingale, J. W. and Despali, G. and Schuldt, S. and Gavazzi, R. and Melo, A. and Metcalf, R. B. and Andika, I. T. and Leuzzi, L. and Manj{\'{o}}n-Garc{\'{i}}a, A. and Pearce-Casey, R. and Vincken, S. H. and Wilde, J. and Busillo, V. and Tortora, C. and Barroso, J. A. Acevedo and Dole, H. and Ecker, L. R. and Pearson, J. and Marshall, P. J. and More, A. and Saifollahi, T. and Gracia-Carpio, J. and Baeten, E. and Cornen, C. and Johnson, L. C. and Macmillan, C. and Kruk, S. and Remmelgas, K. A. and Cl{\'{e}}ment, B. and Degaudenzi, H. and Courbin, F. and Bovy, J. and Casas, S. and Dannerbauer, H. and Diego, J. M. and Finner, K. and Galan, A. and Giocoli, C. and Hogg, N. B. and Jahnke, K. and Katona, J. and Kov{\'{a}}cs, A. and {De Leo}, C. and Mahler, G. and Millon, M. and Nagam, B. C. and Nugent, P. and de Murieta, A. 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+eprint = {2503.15324},
+journal = {https://arxiv.org/abs/2503.15324},
+title = {{Euclid Quick Data Release (Q1): The Strong Lensing Discovery Engine A -- System overview and lens catalogue}},
+url = {http://arxiv.org/abs/2503.15324},
+year = {2025}
+}
+
+@article{Minor2021,
+archivePrefix = {arXiv},
+arxivId = {2011.10627},
+author = {Minor, Quinn and Gad-Nasr, Sophia and Kaplinghat, Manoj and Vegetti, Simona},
+doi = {10.1093/mnras/stab2247},
+eprint = {2011.10627},
+issn = {13652966},
+journal = {MNRAS},
+number = {2},
+pages = {1662--1683},
+title = {{An unexpected high concentration for the dark substructure in the gravitational lens SDSSJ0946+1006}},
+volume = {507},
+year = {2021}
+}
+
+@article{LSSTDarkEnergyScienceCollaboration2012,
+archivePrefix = {arXiv},
+arxivId = {1211.0310},
+author = {{LSST Dark Energy Science Collaboration}},
+eprint = {1211.0310},
+journal = {arXiv preprint arXiv:1211.0310},
+pages = {133},
+title = {{Large Synoptic Survey Telescope: Dark Energy Science Collaboration}},
+url = {http://arxiv.org/abs/1211.0310},
+year = {2012}
+}
+
+@article{Vegetti2010,
+archivePrefix = {arXiv},
+arxivId = {0910.0760},
+author = {Vegetti, S. and Koopmans, L. V.E. and Bolton, A. and Treu, T. and Gavazzi, R.},
+doi = {10.1111/j.1365-2966.2010.16865.x},
+eprint = {0910.0760},
+isbn = {063114806X},
+issn = {00358711},
+journal = {MNRAS},
+month = {nov},
+number = {4},
+pages = {1969--1981},
+title = {{Detection of a dark substructure through gravitational imaging}},
+volume = {408},
+year = {2010}
+}