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DOC: Add JOSS paper draft - #968

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DOC: Add JOSS paper draft#968
basnijholt wants to merge 21 commits into
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joss-paper

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@basnijholt

@basnijholt basnijholt commented Jun 10, 2026

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Adds a draft paper for submission to JOSS in paper/.

Still TODO:

  • Cite the SATP publication if it exists (otherwise keep the repo link)
  • Refresh download/star counts right before submission

@codecov

codecov Bot commented Jun 10, 2026

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Codecov Report

✅ All modified and coverable lines are covered by tests.
see 2 files with indirect coverage changes

🚀 New features to boost your workflow:
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

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.
@codspeed-hq

codspeed-hq Bot commented Jun 10, 2026

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Merging this PR will not alter performance

✅ 6 untouched benchmarks


Comparing joss-paper (c596b9d) with main (cc84ed9)

Open in CodSpeed

- 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 Correctly

The title of this PR has been updated to match the correct format. Thank you!

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