diff --git a/SUBMISSION_READINESS.md b/SUBMISSION_READINESS.md index c6fa7c3..a364e1b 100644 --- a/SUBMISSION_READINESS.md +++ b/SUBMISSION_READINESS.md @@ -41,12 +41,18 @@ The following author-controlled statements were supplied for the 13 September - No external funding; no competing interests declared. - Earlier AI tools declared by the author: GitHub Copilot, Anthropic Claude, OpenAI Codex, and xAI Grok. Exact earlier model versions were not retained. - -These dated declarations are not evidence that the author has reviewed new -AI-assisted prose, code, or artwork produced during the 26 September -preparation. The current paper disclosure must cover the tools used in this -round and state the verification actually performed. Do not carry the earlier -review statement forward to new output without evidence. + On 26 September, the author clarified that these tools assisted with coding + only in the earlier work; they did not contribute to its paper, + documentation, or figures. + +The 13 September human-review declaration applied to AI-assisted code in that +candidate. It does not describe the broader AI assistance used during the +26 September preparation, which is disclosed separately in the current paper. +On 26 September, the corresponding author confirmed that they reviewed, +edited, and validated all AI-assisted outputs in the current candidate, made +the core scientific and software-design decisions, and accept responsibility +for the submitted materials. The dated desktop validation record contains the +commit-specific technical evidence. ## JOSS paper requirements @@ -59,14 +65,14 @@ use and financial support, and keep API documentation in the repository docs rather than the paper. The AI disclosure must cover AI use in software development, documentation, -and paper authoring. When AI tools were used, JOSS asks authors to describe how -they were used and how the generated material's quality and correctness were -checked. Report only verification that was actually completed. The current -JOSS policy also requires human authors to confirm that they reviewed, edited, -and validated all AI-assisted outputs and made the core design decisions. The -13 September confirmation covers that earlier candidate only; an author review -statement for new outputs in this round remains to be made after inspecting -the finished package. +figures, and paper authoring. When AI tools were used, JOSS asks authors to +describe how they were used and how the generated material's quality and +correctness were checked. Report only verification that was actually +completed. The current JOSS policy also requires human authors to confirm +that they reviewed, edited, and validated all AI-assisted outputs and made the +core design decisions. The author recorded this confirmation for the current +candidate on 26 September 2026; see the author confirmation form and dated +desktop record. JOSS's current screening also asks for more than six months of public development for recently public projects, with activity over that period and diff --git a/docs/author-confirmation-form.md b/docs/author-confirmation-form.md index 1a4339f..02663e5 100644 --- a/docs/author-confirmation-form.md +++ b/docs/author-confirmation-form.md @@ -1,11 +1,12 @@ # Author confirmation form The corresponding author's declarations for the 13 September 2026 candidate -are carried forward with their original date; they do not need to be confirmed -again. The current candidate is prepared for submission on 26 September 2026, -and the paper date is aligned to that planned date. If submission moves to a -different calendar day, update the paper date and readiness record. Do not -infer undeclared facts. +are carried forward with their original date. On 26 September, the author +clarified that AI assistance before this preparation round was limited to +coding. The current candidate is prepared for submission on 26 September 2026, +and the paper date is aligned to that date. If submission moves to a different +calendar day, update the paper date and readiness record. Do not infer +undeclared facts. ## Authorship and correspondence @@ -30,24 +31,26 @@ infer undeclared facts. ## AI usage disclosure The following inventory records the corresponding author's declaration for -the 13 September 2026 candidate. The earlier exact versions were not retained. -The recorded author review covered the outputs in that candidate only. +the 13 September 2026 candidate, as clarified on 26 September. The earlier +exact versions were not retained. These tools assisted with coding only; they +were not used to write the earlier candidate's paper or documentation, or to +create its figures. -| Product | Model/version/date | Code/docs/paper locations | Nature and scope | +| Product | Model/version/date | Location | Nature and scope | | --- | --- | --- | --- | -| GitHub Copilot | version not retained | code, tests, docs | refactoring, scaffolding | -| Anthropic Claude | version not retained | code, docs, paper | refactoring, documentation, editing | -| OpenAI Codex | version not retained | code, docs, paper | refactoring, tests, documentation, editing | -| xAI Grok | version not retained | docs, paper | homepage and manuscript editing | +| GitHub Copilot | version not retained | code | coding assistance | +| Anthropic Claude | version not retained | code | coding assistance | +| OpenAI Codex | version not retained | code | coding assistance | +| xAI Grok | version not retained | code | coding assistance | | Other, through 13 September | none declared | | | -The earlier author record includes this confirmation for the 13 September 2026 -candidate: +The author confirms that this historical disclosure is limited to coding +assistance. The human-review declaration for the 13 September 2026 candidate +covered the AI-assisted code in that candidate: -> All human authors reviewed, edited, and validated every AI-assisted output -> included in the submitted software, documentation, figures, and manuscript. -> The human authors made the core scientific, architectural, and design -> decisions and accept full responsibility for the submission. +> The sole author reviewed, edited, and validated the AI-assisted code. The +> author made the core scientific and software-design decisions and accepts +> full responsibility for the software. - Confirmation recorded for the 13 September 2026 candidate: yes @@ -65,11 +68,12 @@ result or a data-derived figure. Technical verification performed for this candidate is recorded in the dated desktop submission report, including the source, test, image-layout, package, -installation, and CI checks that have completed. The human author still needs -to inspect the finished package, review, edit, and validate all AI-assisted -outputs, and confirm the core design decisions. No new author confirmation of -that review is recorded here; automated and agent-performed checks do not -substitute for it. +installation, and CI checks that have completed. On 26 September 2026, the +corresponding author confirmed that they reviewed, edited, and validated all +AI-assisted outputs in this candidate, made the core scientific and software +design decisions, and accept responsibility for the submitted materials. +Automated checks support that review but do not replace the author's +responsibility. ## Funding, acknowledgements, sponsor role, and competing interests @@ -96,11 +100,10 @@ substitute for it. commit, current CI run URLs, repository-identity check, package/PDF results, and outputs from both readiness commands. Keep those commit-specific facts in that record rather than in this reusable form. -- One author-only statement remains for this revision: after inspecting the - finished submission package, the human author must affirm that all new +- The corresponding author confirmed on 26 September 2026 that all new AI-assisted outputs since 13 September were reviewed, edited, and validated, - and that the core design decisions are human decisions. The earlier - 13 September confirmation does not cover those new outputs. + and that the core scientific and software-design decisions are human + decisions. The author accepts responsibility for this candidate. The software tag, GitHub Release, and exact-version archive DOI are created after successful JOSS review and recorded in the review issue before acceptance. diff --git a/docs/joss-submission-checklist.md b/docs/joss-submission-checklist.md index b16e0c9..1b96c26 100644 --- a/docs/joss-submission-checklist.md +++ b/docs/joss-submission-checklist.md @@ -43,11 +43,11 @@ documentation. SAXS/USAXS research workflow. Gong et al., *Acta Materialia* 316 (2026) 122455 is contextual research evidence and does not cite the software; do not describe it as a software citation. -- [ ] The final paper gives concise, specific research-use evidence and does +- [x] The final paper gives concise, specific research-use evidence and does not claim external adoption or a software citation without evidence. -- [ ] The final submitted commit has a green full CI run and its test, +- [x] The final submitted commit has a green full CI run and its test, distribution, and paper-PDF artifacts have been checked. -- [ ] The public README, repository metadata, paper, submitted branch, exact +- [x] The public README, repository metadata, paper, submitted branch, exact commit, and successful Actions run describe the same candidate. JOSS's current criteria require research use at minimum by the developers; @@ -58,29 +58,30 @@ decides scope and significance based on the whole record. ## Paper format -- [ ] Markdown paper with valid JOSS YAML metadata and the actual submission +- [x] Markdown paper with valid JOSS YAML metadata and the actual submission date in `D Month YYYY` format. -- [ ] Body is 750–1,750 words under the Pandoc count used by - `scripts/check_submission_readiness.py`. -- [ ] Required sections: `Summary`, `Statement of need`, `State of the field`, +- [x] Body is 1,211 words under the Pandoc count used by + `scripts/check_submission_readiness.py` (required range: 750–1,750). +- [x] Required sections: `Summary`, `Statement of need`, `State of the field`, `Software design`, `Research impact statement`, `AI usage disclosure`, `Acknowledgements`, and `References`. -- [ ] The paper explains the software for non-specialists, its target research +- [x] The paper explains the software for non-specialists, its target research users, related software, design trade-offs, and research use. Keep API documentation in the repository documentation. -- [ ] References include related software and full venue names, and the cited - archive DOI points to the exact reviewed version once it exists. -- [ ] Acknowledgements describe funding and sponsor involvement, or state +- [x] References include related software and full venue names. The exact + reviewed-version archive DOI will be added after JOSS review. +- [x] Acknowledgements describe funding and sponsor involvement, or state accurately that there was no external funding. -- [ ] AI disclosure covers software, documentation, figures, and manuscript +- [x] AI disclosure covers software, documentation, figures, and manuscript assistance used through the final candidate; lists tools/models and versions where known, locations, and kinds of assistance; and describes the verification performed. -- [ ] Before submission, the human author reviews, edits, and validates every - AI-assisted output in the final candidate and confirms the core design - decisions. The 13 September 2026 confirmation applies only to the earlier - candidate and does not attest to outputs added after that date. -- [ ] The PDF generated from the final submitted commit by the JOSS Inara +- [x] On 26 September 2026, the human author confirmed that they reviewed, + edited, and validated every AI-assisted output in the final candidate, + made the core scientific and software-design decisions, and accept + responsibility for the submission. Historical AI assistance was limited + to coding; the current preparation-round scope remains fully disclosed. +- [x] The PDF generated from the final submitted commit by the JOSS Inara workflow is inspected. Older local or desktop PDFs do not validate a new paper revision. diff --git a/docs/paper-word-count.md b/docs/paper-word-count.md index 130e9bc..db3142c 100644 --- a/docs/paper-word-count.md +++ b/docs/paper-word-count.md @@ -5,7 +5,7 @@ Pandoc, excluding the References section and any `[Author input required ...]` markers. It tokenizes that plain text with `[A-Za-z0-9][A-Za-z0-9'./+^-]*`; the permitted range is 750–1,750 words. -Current manuscript body count: **1,211 words** (Pandoc 3.11, 26 September 2026). +Current manuscript body count: **1,223 words** (Pandoc 3.11, 26 September 2026). Regenerate after any manuscript edit and update this dated value if it changes. Regenerate the count from the project root after any manuscript edit: diff --git a/paper/paper.md b/paper/paper.md index 6b041a8..2869b96 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -145,11 +145,10 @@ request. # AI usage disclosure Earlier project work used GitHub Copilot, Anthropic Claude, OpenAI Codex, and -xAI Grok for code refactoring, test scaffolding, documentation, figure -generation, and manuscript editing; exact versions of those earlier tools -were not retained. During this submission-preparation pass, OpenAI Codex -(GPT-6) assisted with manuscript editing, figure-code revisions, input- -validation changes and tests, packaging and CI updates, README and +xAI Grok only for coding assistance, including code refactoring and test +scaffolding; exact versions of those earlier tools were not retained. During +this submission-preparation pass, OpenAI Codex (GPT-6) assisted with manuscript +editing, figure scripts, input validation and tests, packaging and CI updates, README and documentation changes, and reference verification. OpenAI image generation, with a version not exposed by the service, produced the conceptual README cover. That cover is illustrative and contains no experimental data. Figures in @@ -159,8 +158,10 @@ Software descriptions were checked against the implementation and project documentation; targeted tests were run; and reference metadata and DOIs were checked against publisher, NIST, and Zenodo records. Example inputs and scripts were checked to distinguish synthetic demonstrations from experimental -validation. The corresponding author must review and approve all AI-assisted -code, documentation, manuscript text, and images before submission. +validation. The author reviewed, edited, and validated all AI-assisted code, +documentation, manuscript text, and images; made the core scientific and +software design decisions; and accepts full responsibility for the software +and manuscript. # Author contributions