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Collected changes for JOSS review - #341

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joss-review-fixes
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Collected changes for JOSS review#341
biblicabeebli wants to merge 40 commits into
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joss-review-fixes

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@biblicabeebli biblicabeebli commented Sep 9, 2026 •
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(I screwed up @hydawo's pull request, it got marked as merged by an automatic action because I did git actions out of order. This is a clone of his original pull request, which can be found here. The only change is that the originally targeted branch, joss-paper, has been brought up to be equivalent to this branch, and the new pull request targets develop.)

Fixes the reference problems raised in the JOSS review.

  • Research Impact Statement claimed methods had been applied in published studies but cited none. It now cites the twelve studies that were already sitting in paper.bib.
  • The Summary said the methods were developed and published elsewhere, and Software Design described Jasmine. Neither cited Barnett & Onnela 2020 or Liu & Onnela 2021. Both are now cited where the methods are introduced.
  • Straczkiewicz et al. 2023 and Huang et al. 2022 were listed in CITATION.cff but missing from paper.bib entirely. Both are added and cited for the accelerometry methods.
  • The ALSFRS-R description was cited to mora2017edaravone, which is a paper about edaravone rather than a source for the scale. Replaced with Cedarbaum et al. 1999.
  • CITATION.cff and pyproject.toml now match the author list in paper.md. The docs byline in conf.py named three of the authors and now uses the lab name instead.
  • Also fixed four instances of an em dash followed by a stray hyphen.
  • Uncited bibliography entries drop from sixteen to three. Every citation in the text has a matching entry.
  • The State of the Field section must be handled separately by professor Onnela. - see branch joss-state-of-field
  • There are LLM/AI usage commentary in posts is present is SUPPORT.md, and requirements for disclosures are in CONTRIBUTING.md.

hackdna and others added 20 commits July 7, 2025 14:45
@hackdna
Add GitHub Actions workflow for drafting paper PDF
50aaa3e
@hydawo
Update paper.bib
8b5a30e 
All URL's checked and are correct references to use where they have been in the paper.

Changes:
Updating Sensorkit URL to Sensorkit main documentation page

Notes:
wiki_sensing reference does not appear in paper
@hydawo
Update paper.bib
1bf8272 
Added Barnett and Onnela & Liu and Onnela refs
@hydawo
Update paper.md
8f5f66e
@hydawo
Update paper.md
b129c69 
Final revisions (JP/Hassan)
@hydawo
Update paper.md
b5fa294 
adding Anna Beukenhorst's middle initial to author listing
@hackdna
Merge develop into joss-paper, keeping joss-paper versions of paper f…
660b6a3 
…iles
@hackdna
Merge remote-tracking branch 'origin/develop' into joss-paper
8865876
@hydawo
Update paper.md
27d7735
@hydawo
Update paper.bib
0085f59 
updated DOI's for:

- 10.1002/brb3.2077
- 10.1093/jamia/ocab069 
- 10.1093/biostatistics/kxy059

based on output from editorialbot reference check summary - openjournals/joss-reviews#9298 (comment)
@hackdna
Merge remote-tracking branch 'origin/develop' into joss-paper
cb34947
@hydawo @hackdna
Update paper.md (#296)
35fe8f4 
* Update paper.md

This updates the paper to match the latest JOSS submission requirements. I kept all of the original text and references unchanged and only added the new sections that are now required.

Added:
1. A new State of the Field section with clearer positioning against existing SDKs (e.g., ResearchKit, ResearchStack) and general-purpose tools
2. A Software Design section describing the overall architecture (trees, separation from Beiwe, key design decisions)
3. A Research Impact Statement to better explain how Forest is used and why it matters
4. An AI Usage Disclosure section

No changes were made to the existing content—this is just additive to bring the paper in line with the updated format.

* Fix BibTeX syntax errors in paper.bib

Agent-Logs-Url: https://github.com/onnela-lab/forest/sessions/3146f738-3f33-471a-a95d-afb7d4f92cec

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: hackdna <452575+hackdna@users.noreply.github.com>
Co-authored-by: Ilya Sytchev <isytchev@hsph.harvard.edu>
@hackdna
Merge branch 'develop' into joss-paper
779ce3c
@hackdna
fix(paper): standardize affiliation formatting for authors
57d23a0
@hackdna
Merge branch 'develop' into joss-paper
267a648
@hydawo @claude
paper: cite the references supporting the impact and method claims
1b3a4ed 
Addresses reviewer feedback in openjournals/joss-reviews#10489.

- Cite the 12 applied studies backing the Research Impact Statement,
  grouped by domain (oncology and surgical recovery, neurology, spine
  and rehabilitation, psychiatry). Previously the section claimed
  published applications without citing any.
- Cite Barnett & Onnela 2020 and Liu & Onnela 2021 where Jasmine and
  the mobility methods are introduced, in the Summary and Software
  Design sections.
- Add Straczkiewicz et al. 2023 and Huang et al. 2022 to paper.bib and
  cite them for the accelerometry methods. Both were listed in
  CITATION.cff but missing from the bibliography entirely.
- Replace mora2017edaravone with Cedarbaum et al. 1999 as the source
  for the ALSFRS-R instrument. The former is a drug trial paper and did
  not support the claim it was attached to.
- Fix four instances of an em dash followed by a stray hyphen.

Uncited entries drop from 16 to 3. The remaining three (github_ears,
wiki_sensing, mora2017edaravone) belong in the State of the Field
section, which is being rewritten separately.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
@hydawo @claude
docs: add CONTRIBUTING and SUPPORT guidelines
ab0832c 
Addresses the community guidelines checklist item in
openjournals/joss-reviews#10489. The repository had an issue template
but no guidance for contributing, reporting problems, or seeking
support, which is a required JOSS review criterion.

CONTRIBUTING covers the develop-branch workflow, how to report bugs and
request methods, expectations for pull requests, and what a new tree
needs. SUPPORT routes users to the docs site, the issue tracker, the
method papers, and beiwe-backend for collection questions.

Note: CONTRIBUTING links to CODE_OF_CONDUCT.md, which still needs to be
added with a real reporting contact address.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
@hydawo @claude
align author metadata with the paper author list
e339832 
Addresses reviewer point 5 in openjournals/joss-reviews#10489, which
noted that paper.md, CITATION.cff and pyproject.toml listed different
author sets.

CITATION.cff and pyproject.toml now match the author list in paper.md
exactly, in the same order. The docs byline in docs/source/conf.py named
only three of the authors and is replaced with the lab name, so the list
is maintained in one place rather than four.

Verified: all three author lists are identical, 13 entries in matching
order.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
@biblicabeebli
Merge branch 'develop' into joss-review-fixes
ced6c00
@biblicabeebli
[joss-review-fixes] fixes bad ruff check in sphinx config
c090146
@biblicabeebli biblicabeebli mentioned this pull request Sep 9, 2026
Merged
@biblicabeebli

biblicabeebli commented Sep 9, 2026

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This is updated to be able to merge into develop, other pull requests about paper should stack on this one (target this one)

@biblicabeebli

biblicabeebli commented Sep 9, 2026 •
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via @hydawo

One heads up: I put the metadata changes on joss-paper rather than develop, because develop already lists a contributor who is not on the paper. Those two files already diverge, so the next develop into joss-paper merge will need a resolution either way.

@hydawo I need you to more specifically identify the location is the files where this is.
Is the change likely one mentioned in this issue? in the pyproject.toml file?

In my opinion the pyproject.toml file's authors field is not the appropriate place to locate academic attribution, or to follow academic formalities of the order of those authors. It is a field in a file for the contributors and developers to the repo. These values appear on the PyPi page for a release, they are expected to be development oriented.

You can see how the current version of it appears on our PyPi page, it is already misleading to list them there, none of those people are active anymore.

Is this a requirement coming out of JOSS? We can change it easily, we just need to ensure we record contributors when and where is appropriate, and I need to know that. In addition, the information about how we do that needs to go in the contribution guidelines. To this end, I'm going to merge that branch into this branch. Nope nevermind it is not ready, not merging it in right now.

@biblicabeebli
[joss-community-guidelines] various updates to the project docs+
17f7de7
@biblicabeebli
[joss-community-guidelines] a further addition on what is required fo…
a11c8e0 
…r llm contributions.
@biblicabeebli
[joss-community-guidelines] oops, this requiremnts file is needed for…
c9fe5a3 
… the sphinx build deploy workflow.
@biblicabeebli
[joss-community-guidelines] removes code of conduct after discussion.
03ba78b
@biblicabeebli
Merge pull request #338 from onnela-lab/joss-community-guidelines
0fe6c1e 
docs: add CONTRIBUTING and SUPPORT guidelines

After meeting with @hydawo we realized we did not need the code of conduct, which means we are done enough to merge, @hydawo does still need to review language in the two new files.
@biblicabeebli biblicabeebli changed the title paper: cite the references supporting the impact and method claims Collected changes for JOSS review Sep 15, 2026
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biblicabeebli commented Sep 15, 2026

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Met with @hydawo and reviewed all our JOSS paper changes. This branch is somewhat diverged from develop, which I will am handling imminently.

@biblicabeebli biblicabeebli mentioned this pull request Sep 15, 2026
Open
biblicabeebli and others added 4 commits September 15, 2026 15:28
@biblicabeebli
[joss-community-guidelines] Merge branch 'develop' into joss-communit…
9e174a1 
…y-guidelines
@biblicabeebli
[joss-community-guidelines] Merge branch 'develop' into joss-communit…
6157be4 
…y-guidelines
@hydawo @claude
paper: drop three uncited bibliography entries
2b60cf1 
github_ears and wiki_sensing were never cited in the text. mora2017edaravone
lost its only citation when the ALSFRS-R reference was corrected.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
@biblicabeebli
[joss-review-fixes] Merge branch 'develop' into joss-review-fixes
327814c 
I have changed the authors listed in the sphinx documentation to "Onnela Lab", I cannot find this field listed in the rendered documentation.
@biblicabeebli

biblicabeebli commented Sep 17, 2026

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I have cleaned up the branches so we just have this one and joss-state-of-field

old network view:
image

see current network view at https://github.com/onnela-lab/forest/network

hackdna
hackdna requested changes Sep 20, 2026
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Please do not merge into develop and use this branch to recreate joss-paper branch instead.

@biblicabeebli

biblicabeebli commented Sep 22, 2026

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joss-paper branch has been recreated, will keep it updated with joss-review-fixes. (Active branches have now been pulled forward, there was some confusion because @hydawo's branches diverged from an old develop commit, and I didn't know "joss-paper" was a required name. (and also work on the documentation branch immediately overlapped and I needed to pull it all in.)

I'll be reading the info (@hackdna linked elsewhere) on the joss compliance details. All my fault, sorry about that.

Just addressed another item from #302 , imports across the docs should all work now. Whether the surrounding commentary is correct will have wait on my full documentation review (e.g. work that is/was planned on the documentation branch). I believe there are incorrect statements about import behavior, and we may need to manually edit the init.py files to make things behave a little more cleanly.

@biblicabeebli

biblicabeebli commented Sep 24, 2026

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@hydawo

  • I have merged in the joss-community-guidelines branch, as discussed.
  • joss-community-guidelines, joss-paper, joss-review-fixes are now all aligned with this branch, I will continue to handle them, keeping joss-paper as discussed.
  • I have not touched the joss-state-of-field branch, that is waiting for you, let me know when it is ready to merge into here.
  • I'll go message on the joss repo.

TODO:

  • the CONTRIBUTING.md and SUPPORT.md need human review from you, then signoff from JP.
  • We need to add that JP has signoff / veto privileges on academic contributions.
  • My confusions about authors was resolved.

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