DOC: Add JOSS paper draft - #968
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Draft of a JOSS submission following the current (750-1750 word) paper requirements: Summary, Statement of need, State of the field, Software design, Research impact statement, and AI usage disclosure. Includes a pipeline visualization figure generated from the physics-simulation docs example, and a BibTeX file with full venue names. Two TODOs remain: the SATP publication citation and financial-support acknowledgements.
- Fix framework-agnostic claim (function bodies/signatures, not imports) - Soften retrofit and SLURM-scale claims - Cite all named tools (Airflow, Luigi, mpi4py, Adaptive Scheduler, executorlib JOSS paper, pipefunc-executorlib, SATP, aiida-dynamic-workflows) - Correct coverage claim to >99.9% (Codecov: 99.95%) - Date the download/community statistics (as of June 2026) - Name AI tools explicitly in the disclosure (Claude Code, Codex) - Resolve all remaining TODO placeholders
- Mark Xarray/Zarr integrations as optional - Note the code example is condensed (full version in docs) - Tie coverage/typing claims to CI and Codecov - Source the download statistics - Note open-source adopters are independent of the author - Describe SATP citation as a methodology repository
ConTeXt (the JOSS PDF engine) mis-renders the graphviz SVG, causing overlapping text. Switch to a vector PDF figure, which embeds cleanly.
Add the on-demand single-output execution mode (calling the pipeline directly, optionally supplying intermediate results) alongside the parallel map-reduce mode.
Add a partial reduction (charge[:, j] -> avg_over_V_left[j]) alongside the full scalar reduction, demonstrating that mapspec reduces over a chosen axis while keeping others. Regenerate the figure accordingly.
Replace the placeholder charge/reduction with a real linear-electrostatics model: induced charge Q = C_left*V_left + C_right*V_right, with the capacitances derived from geometry and dielectric. The partial reduction now fits dQ/dV_left to recover the mutual capacitance (2D->1D), and the full reduction reports the peak induced charge. Verified the exact snippet runs and recovers the analytic capacitance; regenerate the figure.
Collapse the capacitance computation to one line, drop redundant inline comments now covered by the prose, and remove verbose annotations. Same behavior and figure; ~8 fewer lines.
- Correct overhead to 10 us with hardware/benchmark context (matches docs) - Lead Research impact with independent adoption; downloads now support it - Merge a redundant framework-agnostic sentence in Statement of need - Polish the Zarr citation
State the GitHub/Discord facts directly rather than asserting an active community, which is harder to defend.
- Fix broken affiliations block: index 2 was referenced but undefined. Restore TU Delft (affiliation) + IonQ (current address) per intent. - Name the Adaptive Scheduler backend for SLURM submission.
Single affiliation (IonQ), index 1; removes the dangling index-2 reference.
The FAQ this line links to states ~10 us on an M4; update the README to match and stay consistent with the JOSS paper.
The SATP-Methodology repo is a reproducible research manuscript (Mitchell & Aletta, soundscape circumplex translations) whose data analysis runs on pipefunc. Update the citation and prose to reflect that it is a real study producing results with pipefunc, not just a methodology repo.
Add the Applied Acoustics paper (doi 10.1016/j.apacoust.2024.110109) for the study and keep the reproducible-analysis repo as a separate reference, since the pipefunc-based repo postdates the paper (to be confirmed with the authors).
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✅ PR Title Formatted CorrectlyThe title of this PR has been updated to match the correct format. Thank you! |
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Adds a draft paper for submission to JOSS in
paper/.Still TODO: