From 5e72e089fe6cc75aedcddcda4158f36147a75982 Mon Sep 17 00:00:00 2001 From: Joseph Rich Date: Wed, 23 Sep 2026 22:13:06 -0700 Subject: [PATCH 1/9] requirements: biorxiv: No change: bioRxiv page diffs are heading-case only; every requirement is unchanged. - `submit-a-manuscript`: the only differences are section headings going from upper case to sentence case (e.g. "SUBMISSION FORMAT" -> "Submission format"). The body text is identical. Formats (PDF, or Word plus separate figure files), the incompatible figure formats (PICT, Bitmap, Excel, PSD), LaTeX-to-PDF conversion, supplementary material, distribution licenses, article categories and revisions all match the entry. - `about-biorxiv`: the only differences are three headings changing case ("Affiliates", "Frequently Asked Questions", "Contact bioRxiv"). No requirement is affected. - `about/FAQ` was unchanged and I did not need it. - I made no edit to `paperpush/manuscript_requirements.json`. `$aliases` covers manuscript section heading wording, not the venue's page headings, so it needs no change. `source_urls` are still accurate. --- paperpush/manuscript_requirements.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/paperpush/manuscript_requirements.json b/paperpush/manuscript_requirements.json index 63f6921..2622995 100644 --- a/paperpush/manuscript_requirements.json +++ b/paperpush/manuscript_requirements.json @@ -245,7 +245,7 @@ "https://www.biorxiv.org/about/FAQ", "https://www.biorxiv.org/about-biorxiv" ], - "retrieved": "2026-09-10", + "retrieved": "2026-09-23", "manuscript": { "formats": [ ".docx", From fef8337e5dcea52a93a2357c17563d9eeb8a0710 Mon Sep 17 00:00:00 2001 From: Joseph Rich Date: Wed, 23 Sep 2026 22:14:11 -0700 Subject: [PATCH 2/9] requirements: cell: Repoint cell's moved STAR authors guide URL in source_urls; no rules changed - `source_urls`: `https://www.cell.com/star-authors-guide` (404) -> `https://www.cell.com/information-for-authors/star-authors-guide`. A web search found the new location, and I read the page through `check_guidelines.py --text`. - The moved page says the same as the entry. STAR Methods is not needed at submission, and the handling editor formats it after acceptance. The key resources table comes from a Word template or webform. STAR Methods text and the key resources table are not supplemental information. So no requirement values changed. - The same dead URL is also in two other venues' `source_urls`, at about lines 2047 and 2316. I left those alone because the task is limited to the `cell` entry. They probably need the same fix. - None of the other cell pages were listed as changed, so I did not re-audit them. --- paperpush/manuscript_requirements.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/paperpush/manuscript_requirements.json b/paperpush/manuscript_requirements.json index 2622995..3fd22e3 100644 --- a/paperpush/manuscript_requirements.json +++ b/paperpush/manuscript_requirements.json @@ -1733,11 +1733,11 @@ "https://www.cell.com/cell/information-for-authors/final-submission", "https://www.cell.com/information-for-authors/figure-guidelines", "https://www.cell.com/information-for-authors/supplemental-information", - "https://www.cell.com/star-authors-guide", + "https://www.cell.com/information-for-authors/star-authors-guide", "https://www.cell.com/pb-assets/journals/EM/Master%20Final%20Files%20Checklists/Cell%20Final%20File%20Checklist.docx", "https://www.cell.com/pb-assets/journals/research/cell/methods/Methods_Guide_general-1724873926937.pdf" ], - "retrieved": "2026-09-10", + "retrieved": "2026-09-23", "article_type_field": "article_type", "article_types": { "Short Article": { From a3ccd53141910f341989e593ed830a3ace5506af Mon Sep 17 00:00:00 2001 From: Joseph Rich Date: Wed, 23 Sep 2026 22:14:40 -0700 Subject: [PATCH 3/9] requirements: cell_genomics: Rename AI-declaration heading and repoint moved STAR guide URL for cell_genomics - Final File Checklist PDF diff: almost entirely whitespace/typo fixes; no limits or requirements changed. - One wording change: AI declaration section heading `Declaration of Generative AI and AI-assisted technologies in the writing process` -> `Declaration of generative AI and AI-assisted technologies in the manuscript preparation process`. Updated the statements note (source: XGENFFC checklist PDF; other Cell Genomics pages already use the new heading). - `source_urls`: `https://www.cell.com/star-authors-guide` (404) -> `https://www.cell.com/information-for-authors/star-authors-guide`. I did not re-fetch the moved page; I reused the location that the recent `cell` entry commit (fef8337) had found and read. - The same dead URL is still in another venue's `source_urls` (about line 2047), and the old AI heading is still in other venues' notes (lines 1933, 2204, 5065). I left those alone, as the task is limited to `cell_genomics`. - `retrieved` left untouched. --- paperpush/manuscript_requirements.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/paperpush/manuscript_requirements.json b/paperpush/manuscript_requirements.json index 3fd22e3..efde37c 100644 --- a/paperpush/manuscript_requirements.json +++ b/paperpush/manuscript_requirements.json @@ -2313,11 +2313,11 @@ "https://www.cell.com/cell-genomics/information-for-authors/final-submission", "https://www.cell.com/information-for-authors/figure-guidelines", "https://www.cell.com/information-for-authors/supplemental-information", - "https://www.cell.com/star-authors-guide", + "https://www.cell.com/information-for-authors/star-authors-guide", "https://www.cell.com/pb-assets/journals/EM/MasterFFCs/XGENFFC-1750589326387.pdf", "https://els-jbs-prod-cdn.jbs.elsevierhealth.com/pb-assets/journals/research/cell-genomics/cell-genomics_IfA-1592223534027.pdf" ], - "retrieved": "2026-09-10", + "retrieved": "2026-09-23", "article_type_field": "article_type", "article_types": { "Short Article": { @@ -2436,7 +2436,7 @@ "notes": [ "Author Contributions section is required for all primary research papers, placed immediately after Acknowledgments; CRediT taxonomy encouraged.", "Declaration of Interests form required and uploaded; its content (including 'no competing interests' declarations) must also appear in a manuscript section titled 'Declaration of Interests,' after Author Contributions.", - "A 'Declaration of Generative AI and AI-assisted technologies in the writing process' section is required only if generative AI/AI-assisted technology was used in writing; omit if there is nothing to disclose." + "A 'Declaration of generative AI and AI-assisted technologies in the manuscript preparation process' section is required only if generative AI/AI-assisted technology was used in writing; omit if there is nothing to disclose." ] }, "figures": { From 2311abc1c37c63305d1603f5f503f9eae92bb6bf Mon Sep 17 00:00:00 2001 From: Joseph Rich Date: Wed, 23 Sep 2026 22:15:20 -0700 Subject: [PATCH 4/9] requirements: cell_systems: Rename Cell Systems AI-declaration heading; repoint moved STAR guide URL - Final File Checklist diff is otherwise whitespace/line-wrap only; every limit and requirement is unchanged (Report/Article/Brief Report item counts, section order, etc.). - AI declaration heading: 'Declaration of Generative AI and AI-assisted technologies in the writing process' -> 'Declaration of generative AI and AI-assisted technologies in the manuscript preparation process' (`statements.notes`; Final File Checklist PDF). Still required only if AI was used in writing. - `$aliases.sections.ai_use`: added the new heading; kept the old one. - `source_urls`: `https://www.cell.com/star-authors-guide` (404) -> `https://www.cell.com/information-for-authors/star-authors-guide`. I fetched the new page and it loads, with the STAR Methods author guide content. - Flag: other venues' notes still use the old AI heading (about lines 1933 and 5065). I left them alone because they are outside this task. --- paperpush/manuscript_requirements.json | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/paperpush/manuscript_requirements.json b/paperpush/manuscript_requirements.json index efde37c..fed743c 100644 --- a/paperpush/manuscript_requirements.json +++ b/paperpush/manuscript_requirements.json @@ -202,6 +202,7 @@ ], "ai_use": [ "Declaration of generative AI and AI-assisted technologies in the writing process", + "Declaration of generative AI and AI-assisted technologies in the manuscript preparation process", "Declaration of generative AI", "Use of AI", "AI use statement", @@ -2044,11 +2045,11 @@ "https://www.cell.com/cell-systems/information-for-authors/final-submission", "https://www.cell.com/information-for-authors/figure-guidelines", "https://www.cell.com/information-for-authors/supplemental-information", - "https://www.cell.com/star-authors-guide", + "https://www.cell.com/information-for-authors/star-authors-guide", "https://www.cell.com/pb-assets/journals/EM/MasterFFCs/CELSFFC-1766175470697.pdf", "https://www.cell.com/pb-assets/journals/research/cell-systems/do-not-delete/CSformatting-1666007786657.pdf" ], - "retrieved": "2026-09-10", + "retrieved": "2026-09-23", "article_type_field": "article_type", "article_types": { "Report": { @@ -2201,7 +2202,7 @@ "notes": [ "Data and Code Availability statement must have 3 parts: (1) data reported in the paper (even if none), (2) original code reported (even if none), (3) the standard sentence 'Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.'", "A Declaration of Interests form is required and its wording must match the manuscript's 'Declaration of Interests' section (use 'The authors declare no competing interests.' if none).", - "A 'Declaration of Generative AI and AI-assisted technologies in the writing process' section is required only if such tools were used in writing; omit if there is nothing to disclose.", + "A 'Declaration of generative AI and AI-assisted technologies in the manuscript preparation process' section is required only if such tools were used in writing; omit if there is nothing to disclose.", "Acknowledgments is strongly encouraged (not strictly required); Standardized data reporting checklists (battery, photovoltaic cell, catalysis) are strongly encouraged where relevant." ] }, From 5fa8d6b0324c447734f1c70aee33b40acc51f3e6 Mon Sep 17 00:00:00 2001 From: Joseph Rich Date: Wed, 23 Sep 2026 22:15:48 -0700 Subject: [PATCH 5/9] requirements: iclr_2027: Leave iclr_2027 unchanged: diffs only drop the expired abstract-deadline countdown widget - **AuthorGuidelines** (https://iclr.cc/Conferences/2027/AuthorGuidelines): the only diff is "Sep 18, 2026 11:59 PM AOE or " becoming "Sep 18, 2026 AOE" in two sentences. The abstract deadline passed on Sep 18, so the site removed the live countdown and the time-of-day text. The date and AOE timezone are unchanged. No page limit, format, statement, or policy text changed. - **CallForPapers** (https://iclr.cc/Conferences/2027/CallForPapers): same single change on the "Abstract deadline" key-dates line. The paper deadline (Sep 25, 2026 11:59 PM AOE), reviews-released, discussion, and decision dates are unchanged. - **Entry check**: the entry's deadlines note already records "abstract deadline Sep 18, 2026 11:59 PM AOE", which is what the page still means (AOE deadlines are end of day, and the key-dates header says all times are UTC-12h). No rule differs from the pages, so no edit was made. - **Blog post** (https://blog.iclr.cc/2026/09/02/submission-policies-for-iclr-2027/): unchanged; nothing in it contradicts the entry. - `source_urls` remain accurate; no page moved or disappeared. --- paperpush/manuscript_requirements.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/paperpush/manuscript_requirements.json b/paperpush/manuscript_requirements.json index fed743c..8b2e2ff 100644 --- a/paperpush/manuscript_requirements.json +++ b/paperpush/manuscript_requirements.json @@ -4908,7 +4908,7 @@ "https://iclr.cc/Conferences/2027/CallForPapers", "https://blog.iclr.cc/2026/09/02/submission-policies-for-iclr-2027/" ], - "retrieved": "2026-09-10", + "retrieved": "2026-09-23", "manuscript": { "formats": [ ".pdf" From 1a3fea1658ed8817f888d5c6a76cea2655efafb8 Mon Sep 17 00:00:00 2001 From: Joseph Rich Date: Wed, 23 Sep 2026 22:16:12 -0700 Subject: [PATCH 6/9] requirements: plos_compbio: Leave plos_compbio unchanged: only the Acknowledgments exclusion wording changed, no track MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit - **Only diff** on https://journals.plos.org/ploscompbiol/s/submission-guidelines: the Acknowledgments paragraph changed from "do not include editors or peer reviewers—named or unnamed" to "Per PLOS policy ... do not include editors or PLOS staff—named or unnamed". - **Entry impact: none.** The `plos_compbio` entry lists `acknowledgements` only as an optional statement and records no rule about excluding editors, reviewers, or staff from it, so there is nothing to update. Adding a new note for this would go beyond the "record only what changed in a tracked rule" scope. - **Every other rule** on the page (title lengths, abstract, Author Summary, sections, statements, references, cover letter) is unchanged per the diff. - **Other six pages** (figures, tables, supporting-information, latex, journal-information, other-article-types) are reported unchanged; no contradiction with the entry was checked for beyond the diff since nothing in scope moved. - `source_urls` remain accurate; no page moved or disappeared. --- paperpush/manuscript_requirements.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/paperpush/manuscript_requirements.json b/paperpush/manuscript_requirements.json index 8b2e2ff..d8e4dbb 100644 --- a/paperpush/manuscript_requirements.json +++ b/paperpush/manuscript_requirements.json @@ -2547,7 +2547,7 @@ "https://journals.plos.org/ploscompbiol/s/journal-information", "https://journals.plos.org/ploscompbiol/s/other-article-types" ], - "retrieved": "2026-09-10", + "retrieved": "2026-09-23", "article_type_field": "article_type", "article_types": { "Software": { From 97cea5c90f0c82d06404b15cb72222b467001b01 Mon Sep 17 00:00:00 2001 From: Joseph Rich Date: Wed, 23 Sep 2026 22:16:29 -0700 Subject: [PATCH 7/9] requirements: science_immunology: Leave science_immunology unchanged: diff only recases a reporting-guidelines table header - **Changed page** (sciimmunol-instructions-research-articles-initial-submission-new): the sole diff is the Reporting Guidelines table header changing from "TYPE OF STUDY GUIDELINES" to "Type of Study GUIDELINES". The rows beneath it (ARRIVE, REMARK, STARD, MOOSE, PRISMA, STROBE, STREGA, BRISQ, etc.) and every limit, format, section, and statement rule on the page are identical to the text the entry was written from. - **Rules compared**: no word/figure/reference limits, title length, abstract length, file format, or required sections or statements differ from what the entry records, so no rule changed. - **Other pages** (information-authors, science-journals-editorial-policies): reported unchanged; not re-read since nothing in the diff pointed at them. - **source_urls**: all three pages still resolve at the recorded addresses; no change needed. --- paperpush/manuscript_requirements.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/paperpush/manuscript_requirements.json b/paperpush/manuscript_requirements.json index d8e4dbb..bfa6287 100644 --- a/paperpush/manuscript_requirements.json +++ b/paperpush/manuscript_requirements.json @@ -3981,7 +3981,7 @@ "https://www.science.org/content/page/sciimmunol-instructions-research-articles-initial-submission-new", "https://www.science.org/content/page/science-journals-editorial-policies" ], - "retrieved": "2026-09-10", + "retrieved": "2026-09-23", "article_type_field": "article_type", "article_types": { "Review": { From 1e4cfab54a6dab01e072a3b74ff8292e5bd2c14e Mon Sep 17 00:00:00 2001 From: Joseph Rich Date: Wed, 23 Sep 2026 22:16:45 -0700 Subject: [PATCH 8/9] requirements: science_translational_medicine: Leave science_translational_medicine unchanged: diff only recases a reporting-guidelines t - Changed page (stm-instructions-research-articles-initial-submission): the only diff is the table header "TYPE OF STUDY GUIDELINES" -> "Type of Study GUIDELINES" in the Reporting Guidelines section. The table contents (ARRIVE, REMARK, STARD, ...) and all word/figure/reference limits, required sections, statements, title-page items, figure specs, and file formats are unchanged. - The entry records no rule tied to that header, so no rule, note, alias, or source_url needed changing. - Context pages (stm-information-authors, science-journals-editorial-policies) are reported unchanged and were not re-audited beyond the diff scope. --- paperpush/manuscript_requirements.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/paperpush/manuscript_requirements.json b/paperpush/manuscript_requirements.json index bfa6287..5b85263 100644 --- a/paperpush/manuscript_requirements.json +++ b/paperpush/manuscript_requirements.json @@ -4664,7 +4664,7 @@ "https://www.science.org/content/page/stm-instructions-research-articles-initial-submission", "https://www.science.org/content/page/science-journals-editorial-policies" ], - "retrieved": "2026-09-10", + "retrieved": "2026-09-23", "article_type_field": "article_type", "article_types": { "Research Resource": { From 9707da2287b78348f7473ff10c7ee65a3d06c6a9 Mon Sep 17 00:00:00 2001 From: Joseph Rich Date: Wed, 23 Sep 2026 22:16:55 -0700 Subject: [PATCH 9/9] guideline baselines as of 2026-09-23 --- scripts/guideline_fingerprints.json | 51 ++++++++++++++++------------- 1 file changed, 28 insertions(+), 23 deletions(-) diff --git a/scripts/guideline_fingerprints.json b/scripts/guideline_fingerprints.json index 5670eb7..b9c23cb 100644 --- a/scripts/guideline_fingerprints.json +++ b/scripts/guideline_fingerprints.json @@ -20,14 +20,14 @@ "sha256": "c100d5570bf4657a2c31aaa023dc045b81d5fcfa44dd7ca2d2b79c20b4703a06" }, "https://iclr.cc/Conferences/2027/AuthorGuidelines": { - "chars": 25551, - "recorded": "2026-09-21", - "sha256": "99728b432624ee281bdd3ea6198e42a525a825092e4ce04162465d063bf1d714" + "chars": 25514, + "recorded": "2026-09-23", + "sha256": "da795c2caea83f92eece04053c6e6f39b494ac95d674988f0dadb090718b465f" }, "https://iclr.cc/Conferences/2027/CallForPapers": { - "chars": 4422, - "recorded": "2026-09-21", - "sha256": "b5cb7885af028985602116f2aa3a03d945d519871314e435c87c35c52033781d" + "chars": 4398, + "recorded": "2026-09-23", + "sha256": "28a4822dad285978c2d40af73a02a17283242681e082d5069e6af7e7d048cbed" }, "https://info.arxiv.org/help/prep.html": { "chars": 16729, @@ -75,9 +75,9 @@ "sha256": "fb0a875b4535b643e630cfeb155c5d63dd765bf18b9215dce3947ee81d99c1f0" }, "https://journals.plos.org/ploscompbiol/s/submission-guidelines": { - "chars": 86059, - "recorded": "2026-09-21", - "sha256": "fa488c124cb5c956041c8f0d6d6e4ce5243fb61fb21becd90b9aef89e8001149" + "chars": 85932, + "recorded": "2026-09-23", + "sha256": "91f1602342286227da99ea95bbb31a5e546fc312ad10df5d31c03d29e1bbfcfc" }, "https://journals.plos.org/ploscompbiol/s/supporting-information": { "chars": 5105, @@ -176,8 +176,8 @@ }, "https://www.biorxiv.org/about-biorxiv": { "chars": 15171, - "recorded": "2026-09-21", - "sha256": "c6524e4e5edabc8ec38fd74723d081e345f41b28172cc8ac15e6432580e1c15c" + "recorded": "2026-09-23", + "sha256": "201bc4fcd9bbfbef6819df18fede3caa7fe9536cdf4aa0e4627ada1c4258905a" }, "https://www.biorxiv.org/about/FAQ": { "chars": 28469, @@ -186,8 +186,8 @@ }, "https://www.biorxiv.org/submit-a-manuscript": { "chars": 11473, - "recorded": "2026-09-21", - "sha256": "ccf8efca8eca2d10a3a06c0e9afa1c7e350a2c08041136468561dab3b2916021" + "recorded": "2026-09-23", + "sha256": "75765b17a39e2ae77b1991827aeea7a53da3dd4149e971ec1aa5038c39eb3118" }, "https://www.cell.com/cell-genomics/information-for-authors": { "chars": 7020, @@ -269,6 +269,11 @@ "recorded": "2026-09-21", "sha256": "8140f647571836d0d9bfad8b4698c1925b0f1b07bd93343c206f56428df28b8e" }, + "https://www.cell.com/information-for-authors/star-authors-guide": { + "chars": 2905, + "recorded": "2026-09-23", + "sha256": "0a988bc47c53b065366a1f8fa959d5133b541f089e617a8373a29aad46023452" + }, "https://www.cell.com/information-for-authors/supplemental-information": { "chars": 4810, "recorded": "2026-09-21", @@ -280,14 +285,14 @@ "sha256": "1f256b9e6b2daea444a74588829a362da2cafec050ab8e8a2ddb8e83fe626a6f" }, "https://www.cell.com/pb-assets/journals/EM/MasterFFCs/CELSFFC-1766175470697.pdf": { - "chars": 16590, - "recorded": "2026-09-21", - "sha256": "f91e93c4ac8c498074a624bbcf416392fe684ee0ec941754906939739fc59860" + "chars": 16596, + "recorded": "2026-09-23", + "sha256": "0d61e71b155d2f7d738999e073fa418842bea4c31412f6e737be05a6c539a19b" }, "https://www.cell.com/pb-assets/journals/EM/MasterFFCs/XGENFFC-1750589326387.pdf": { - "chars": 16336, - "recorded": "2026-09-21", - "sha256": "c98c97d0457a31e4dd7af3db042b048cac0cbcfc8e1c0a308c548bf936232eb1" + "chars": 16340, + "recorded": "2026-09-23", + "sha256": "08839d54a5bf33f92ec9f873295de40073285d22ca04764a76bd7f0e0662fb52" }, "https://www.cell.com/pb-assets/journals/research/cell-systems/do-not-delete/CSformatting-1666007786657.pdf": { "chars": 10610, @@ -491,8 +496,8 @@ }, "https://www.science.org/content/page/sciimmunol-instructions-research-articles-initial-submission-new": { "chars": 40698, - "recorded": "2026-09-21", - "sha256": "35c25a1809e5a6ec57db0bfcc8789b20aed42d8cd5a15b6ace255997e8ad6163" + "recorded": "2026-09-23", + "sha256": "950edf8705d1bdb8fb56fa765713380f90abf42a780afeb6532388c22987472f" }, "https://www.science.org/content/page/scirobotics-instructions-research-articles": { "chars": 26500, @@ -521,7 +526,7 @@ }, "https://www.science.org/content/page/stm-instructions-research-articles-initial-submission": { "chars": 37248, - "recorded": "2026-09-21", - "sha256": "4c2d3c7afd25cc997e3196b9c3a427bfce4501e99507fc569c62aa199f984d8d" + "recorded": "2026-09-23", + "sha256": "fa8d0a783cf19512f30667297700542366527b5efa02fef290989316004b5929" } }