Skip to content

JOSS paper: paper.md + paper.bib (#101) - #102

Merged
neuromechanist merged 6 commits into
mainfrom
feature/issue-101-joss-paper
Jul 11, 2026
Merged

JOSS paper: paper.md + paper.bib (#101)#102
neuromechanist merged 6 commits into
mainfrom
feature/issue-101-joss-paper

Conversation

@neuromechanist

Copy link
Copy Markdown
Member

Closes #101.

Summary

Adds the Journal of Open Source Software (JOSS) submission for pyAMICA: paper.md
(~880 words) and paper.bib (17 references, all DOIs verified). Also addresses
repository items a JOSS reviewer checks alongside the paper.

What is included

  • paper.md: Summary, Statement of need, Implementation and validation, State
    of the field, Acknowledgements. Sole author (S. Y. Shirazi), SCCN/UCSD.
  • paper.bib: AMICA (Palmer et al.), natural gradient (Amari), Newton-ICA
    (Palmer et al. 2008), ICLabel, EEGLAB, Infomax, extended Infomax, FastICA,
    Picard, MNE, PyTorch, NumPy, SciPy, MLX, and the two other Python AMICA
    reimplementations. All journal DOIs resolved against the publisher.
  • README: de-WIP'd; reflects validated Fortran parity, GPU backends, docs;
    install via uv sync.
  • getting-started: install from source (a PyPI release name is deferred).
  • LICENSE: copyright year 2023-2026.
  • sample_data/ATTRIBUTION.md: provenance/licenses for the bundled SCCN/EEGLAB
    test artifacts (Fortran binary, sample EEG, loadmodout15.m).

Process (per the no-shortcuts standard)

  • Drafted with the manuscript-writing skill; polished with humanizer.
  • Independent paper-review (JOSS reviewer). Findings addressed: the novelty
    claim was reframed after a landscape check found two other public Python AMICA
    packages (now cited); missing methods citations added (natural gradient,
    Newton-ICA, ICLabel); the drop-in claim scoped to single-model (multi-model
    round-trips with a self-consistent layout); the test-suite wording corrected
    to "synthetic data is never the basis of a correctness claim"; "dipolar"
    glossed for non-specialists.

Remaining before actual JOSS submission (author action)

  • ORCID: paper.md still has a placeholder; the corresponding author's real
    ORCID must replace it.
  • Archived release (Zenodo/Software Heritage) with a matching version, and
    the PyPI distribution name, to be arranged at the transfer/release step.

Tested: paper is not code; all 17 citation keys resolve to bib entries; docs
build is exercised by the existing docs workflow.

@neuromechanist

Copy link
Copy Markdown
Member Author

Updated per author request:

  • Co-authors added: Arnaud Delorme (ORCID 0000-0002-0799-3557; SCCN/UCSD + CNRS, University of Toulouse) and Scott Makeig (ORCID 0000-0002-9048-8438; SCCN/UCSD) added to paper.md and CITATION.cff. Makeig moved from the acknowledgements to the author list; the acknowledgement now credits Palmer and Kreutz-Delgado.
  • Corresponding-author ORCID set to the real value (0000-0001-5557-259X).
  • README modernized: leads with the scikit-learn AMICA API, a backend/precision guide (CPU/CUDA float64, float32, MLX on Apple Silicon), and the EEGLAB write_amica_output/loadmodout15 round-trip; the legacy NumPy CLI is kept as a subsection and the full parameter reference points to the docs.

Remaining before actual JOSS submission (release/transfer step): an archived release (Zenodo/Software Heritage) with a matching version, and the PyPI distribution name (deferred).

@neuromechanist
neuromechanist merged commit d4f43e6 into main Jul 11, 2026
7 checks passed
@neuromechanist
neuromechanist deleted the feature/issue-101-joss-paper branch July 11, 2026 08:39
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

JOSS paper: paper.md + paper.bib

1 participant