psyclaw 0.28.0 → 0.28.2

package/vendor/nature-skills/skills/nature-shared/journal-formats/nature.md

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+# Nature Article submission requirements
+
+Canonical shared rules for an original-research **Article submitted to the
+flagship journal Nature**. Do not apply these numbers automatically to Nature
+Portfolio subjournals. Their author instructions can differ substantially.
+
+## Contents
+
+1. Authority and stage gate
+2. Editorial fit
+3. Initial-submission file preflight
+4. Article structure and limits
+5. Administrative and authorship checks
+6. Displays, Extended Data and Supplementary Information
+7. Reporting, availability and specialist routing
+8. Submission modes and related work
+9. Final-submission boundary
+10. Official sources
+
+## 1. Authority and stage gate
+
+Before applying a rule, record the stage:
+
+- `initial_submission`: before the first editorial decision; Nature permits
+  reasonable formatting flexibility.
+- `revision`: after review; follow the handling editor's instructions in
+  addition to the public guide.
+- `accepted_in_principle`: production-quality text, figures, Extended Data,
+  Supplementary Information, forms and declarations are requested.
+- `proof`: production corrections only; not a new manuscript rewrite.
+
+Do not reject an otherwise reviewable initial submission merely because it has
+not yet been converted to final production house style. Still run the readiness
+checks below because they reduce avoidable delays and expose missing policy
+items.
+
+## 2. Editorial fit
+
+A Nature Article should:
+
+- report original scientific research whose main results and conclusions are
+  not published or simultaneously submitted elsewhere
+- be of outstanding scientific importance
+- reach a conclusion of interest to an interdisciplinary readership
+- present results that are novel and arresting, with immediate and
+  far-reaching implications
+
+Additional fit tests:
+
+- a large-dataset paper should provide a comprehensively validated dataset or
+  a significant technical advance or scientific insight
+- a solely technical paper needs significant impact for a research community
+- a therapeutic paper without new mechanism needs a substantial effect on an
+  important disease
+
+Treat these as editorial-fit criteria, not formatting promises. Flag weak fit
+instead of inflating significance language.
+
+## 3. Initial-submission file preflight
+
+For a standard initial submission:
+
+- submit through Nature's online manuscript system
+- prefer manuscript text and figures together in one Microsoft Word or PDF
+  file, up to 30 MB
+- place each figure legend on the same page as its figure
+- include line numbers; number every line in a supplied PDF
+- include titles for cited articles and datasets in the reference list
+- before acceptance, submit a PDF for a TeX/LaTeX manuscript
+- ensure figures have enough resolution for referees, while recognizing that
+  production-quality files are not required at this stage
+
+If the submission uses separate files, record why and verify every display is
+cited and present.
+
+## 4. Article structure and limits
+
+### Required sequence
+
+Audit the manuscript in this order:
+
+1. title
+2. authors
+3. affiliations and present addresses
+4. bold summary paragraph
+5. main text
+6. main references
+7. tables
+8. figure legends
+9. Methods, including separate Data Availability and Code Availability
+   statements where applicable
+10. Methods references
+11. acknowledgements
+12. funding statement
+13. author contributions
+14. competing-interests declaration
+15. additional information, including Supplementary Information and
+    corresponding-author lines
+16. Extended Data figure and table legends
+
+### Initial manuscript styling
+
+- write in English using Oxford English Dictionary spelling conventions
+- use double spacing
+- Microsoft Word without style tags is preferred
+- a standard font, preferably 12 pt Times New Roman, is recommended for the
+  manuscript text
+- use normal text or Symbol font for ordinary mathematical and Greek symbols;
+  reserve equation editors for formulae that cannot be set reliably as text
+
+### Title
+
+- no more than two printed lines, equivalent to 75 characters including spaces
+- normally avoid numbers, acronyms, abbreviations and punctuation
+- avoid technical terms and active verbs
+- retain enough detail for indexing while remaining intelligible outside the
+  immediate field
+
+### Summary paragraph
+
+- fully referenced and ideally no more than about 200 words
+- written for readers outside the discipline
+- avoid numbers, abbreviations, acronyms and measurements unless essential
+- use the sequence: broad field, background/rationale, main conclusion
+  introduced by `Here we show` or an equivalent, then general context and how
+  the work moves the field forward
+
+### Main text and display budget
+
+- typical six-page Article: about 2,500 words and four modest display items
+- typical eight-page Article: about 4,300 words and five or six modest display
+  items
+- a modest display item plus legend occupies about one-quarter page; a large
+  composite can require a corresponding reduction in text
+- up to about 50 main-text references within the page budget
+- subheadings may contain up to 40 characters including spaces
+- the title, author list, acknowledgements and references do not count toward
+  the main-text word count
+
+### Methods
+
+- include every element needed to interpret and replicate the results
+- write concisely; the section typically does not exceed 3,000 words but may be
+  longer when necessary
+- use short bold method headings and consider dedicated statistics, reagents
+  and animal-model subsections
+- do not place figures or tables in Methods; route essential displays to
+  Extended Data or, exceptionally, Supplementary Information
+- continue Methods-reference numbering after the main-text references
+- cite deposited step-by-step protocols and mention them in Methods
+
+### References, tables and end notes
+
+- number references sequentially in order of first appearance across text,
+  tables, legends, Methods and Extended Data
+- use superscript citations in text unless confusion with another superscript
+  is likely
+- list only one publication per reference number
+- remove linked fields produced by EndNote or similar software
+- normally include only published or accepted work and recognized preprints;
+  describe work in preparation in the text rather than the reference list
+- include titles for cited articles and datasets
+- list all authors unless there are more than five; then give the first author
+  followed by `et al.`
+- give each table a short title sentence, with details in table footnotes
+- keep acknowledgements brief; do not thank anonymous referees or editors and
+  avoid effusive praise
+- declare funding separately only when the work is within scope of, and arose
+  directly from, the named grant
+- include an individual author-contribution statement and a competing-interests
+  statement
+- identify equal contributors directly below the address list when there are up
+  to three; describe larger equal-contribution groups in the author-
+  contributions statement
+- place present addresses immediately below the author list
+
+## 5. Administrative and authorship checks
+
+### Corresponding author
+
+Before submission, confirm that the corresponding author:
+
+- has included all authors in the author list
+- has confirmed that every author agrees with the list order and submission
+- is prepared to manage all journal and coauthor communication
+- is identified with an asterisk in the manuscript
+- is named for correspondence and material requests
+
+### Cover letter
+
+For flagship Nature, the initial cover letter is **optional**. If supplied:
+
+- explain the importance of the work and its fit for Nature briefly
+- do not repeat the abstract or introduction
+- use it for confidential information that should not go to referees, including
+  relevant conflicts and related work in press or under consideration
+- do not treat a missing optional cover letter as a submission blocker
+
+### AI and LLM use
+
+- an LLM or other AI system cannot be an author
+- human authors retain responsibility for originality, accuracy and integrity
+- document LLM use in Methods or, if Methods is unavailable, a suitable
+  alternative section
+- apply the current Nature Portfolio risk framework and disclosure rules in
+  `../core/ethics.md`
+
+## 6. Displays, Extended Data and Supplementary Information
+
+### Figures and legends at initial submission
+
+- embed figures with the manuscript when practical
+- high-resolution production files are not required initially, but data must be
+  assessable by referees
+- keep each legend below 250 words
+- begin with a brief title sentence, then describe what is depicted rather than
+  restating results or methods
+- make the figure and legend understandable in isolation where possible
+
+Use the Nature-specific figure reference in `nature-figure` for final dimensions,
+editable formats, accessibility, image integrity and the distinction between
+main-figure and Extended Data uploads.
+
+### Extended Data
+
+- place integral supporting data in no more than ten multi-panel Extended Data
+  figures or tables
+- consider a simple schematic when the main conclusion involves a complex
+  process unfamiliar to nonspecialists
+- at initial submission, Extended Data may appear as regular display items or
+  within Supplementary Information
+- accepted papers require formal Extended Data formatting
+
+### Supplementary Information
+
+Use Supplementary Information only for peer-reviewed material essential to the
+paper's conclusion that is too large, impractical or specialized for print.
+Prefer Extended Data for ordinary figures and small tables.
+
+When SI is present, audit:
+
+- the categories Supplementary Methods, Tables, Discussion, Equations, Notes,
+  Data, Video and Audio
+- numbering separate from main-text and Extended Data displays
+- a `SIGuide.doc` containing each file title and a summary of no more than
+  50 words; video/audio titles and legends may be up to 100 words
+- no more than ten files where possible
+- up to 30 MB per sound/video or combined PDF and no more than 150 MB total
+- every SI item is cited in the manuscript and every file uses an accepted
+  format
+
+Current accepted SI formats include PDF, Word, plain text, RTF, WordPerfect,
+PostScript/EPS, HTML, Excel, QuickTime, WAV, MPEG/MP4/MP3 and supported systems-
+biology markup formats such as SBML/XML/OWL. Keep SI images at or below
+640 × 480 pixels. If a required item cannot meet the format or size contract,
+contact the handling editor rather than silently converting or omitting it.
+
+## 7. Reporting, availability and specialist routing
+
+- include a Data Availability statement and, for central custom code or
+  algorithms, a separate Code Availability statement
+- make supporting data and central code available to editors and referees when
+  requested
+- route exact repository, accession, restriction and materials checks to
+  `nature-data`
+- route Nature's exact statistical checklist to `nature-statistics`
+- require a completed reporting summary for life sciences, behavioural and
+  social sciences, and ecology, evolution and environmental sciences
+- check for field-specific physical-science reporting summaries, including
+  solar cells and claims of lasing
+- open `../core/research-compliance.md` for human, animal, clinical, image,
+  structure, chemistry, taxonomy, geological, archaeological or
+  palaeontological research
+
+## 8. Submission modes and related work
+
+- disclose related manuscripts with overlapping authorship that are under
+  consideration, under appeal or in press
+- include copies of those manuscripts as clearly marked separate files
+- preprints are permitted: the original submitted version may be posted at any
+  time; the accepted version may be posted six months after publication; the
+  copyedited published Nature version may not be posted to a preprint server or
+  another website
+- double-anonymized review is optional; authors must remove identifying
+  information and are responsible for successful anonymization
+- reviewer suggestions should be independent and include contact details;
+  Nature normally permits requests to exclude one or two competing groups
+- a presubmission enquiry, when used, needs a broad-readership cover paragraph,
+  a fully referenced summary paragraph and a reference list
+
+## 9. Final-submission boundary
+
+Do not apply accepted-in-principle production requirements as initial-submission
+blockers. After an editor requests final files, separately audit:
+
+- final accepted text and production-quality main and Extended Data files
+- text/figure file separation and TeX/LaTeX conversion requirements
+- final Supplementary Information and `SIGuide.doc`
+- requested forms, declarations and licence workflow
+- production figure specifications and unprocessed life-science gel/blot images
+
+## 10. Official sources
+
+Verified 2026-08-08:
+
+- Initial submission: <https://www.nature.com/nature/for-authors/initial-submission>
+- Formatting guide: <https://www.nature.com/nature/for-authors/formatting-guide>
+- Editorial criteria and processes: <https://www.nature.com/nature/for-authors/editorial-criteria-and-processes>
+- Supplementary Information: <https://www.nature.com/nature/for-authors/supp-info>
+- Forms and declarations: <https://www.nature.com/nature/for-authors/forms-and-declarations>
+- Final submission: <https://www.nature.com/nature/for-authors/final-submission>
+- Nature Portfolio reporting standards: <https://www.nature.com/nature-portfolio/editorial-policies/reporting-standards>
+- Nature Portfolio AI policy: <https://www.nature.com/nature-portfolio/editorial-policies/ai>

package/vendor/nature-skills/skills/nature-shared/manifest.yaml

@@ -0,0 +1,52 @@
+name: nature-shared
+version: 1.6.0
+description: >
+  Declarative manifest for shared Nature reference modules. This package is not
+  a standalone workflow; installed Nature skills use it to load exact shared
+  core or journal-format files on demand.
+
+# Design note: never preload the whole shared package. Requesting skills should
+# load only the specific file listed below and then return to their own workflow,
+# output format, and QA rules.
+
+always_load: []
+
+core:
+  on_demand:
+    - condition: shared ethics, safety, authorship, disclosure, or non-invention guardrails are needed
+      path: core/ethics.md
+    - condition: human or animal ethics, clinical research, reporting summaries, image integrity, structures, chemistry, taxonomy, geological, archaeological, or palaeontological compliance is involved
+      path: core/research-compliance.md
+    - condition: classifying paper type, article genre, or manuscript family before applying a writing/reader workflow
+      path: core/paper-type-taxonomy.md
+    - condition: shared reader workflow is explicitly requested by another Nature skill
+      path: core/reader-workflow.md
+    - condition: maintaining terminology consistency across paper reading, polishing, writing, or slide generation
+      path: core/terminology-ledger.md
+    - condition: auditing an existing or multi-round-revised manuscript for accumulated drift — terminology/unit/number variants, headline counts that do not reconcile with the Methods, claims contradicted by the paper's own tables, over- or under-claiming, tense parallelism, and prose that restates displays
+      path: core/consistency-sweep.md
+    - condition: drafting, restructuring, compressing, or reviewer-revising scientific main text — classify results as core/support/qualification/robustness/heterogeneity/provenance/alternative inference/edge case; allocate evidence across main text, captions, and SI; run paragraph-necessity, deletion, statistics-location, and claim-repetition checks
+      path: core/main-text-discipline.md
+    - condition: drafting, restructuring, or polishing Results or Discussion for flagship Nature, Nature Communications, Nature Machine Intelligence, or another Nature Portfolio title; auditing claim escalation, evidence-bound local interpretation, diagnostic perturbation, necessary recap versus redundant re-demonstration, or cross-Results synthesis
+      path: core/nature-results-discussion.md
+    - condition: drafting, restructuring, or polishing any scientific Discussion; sequencing anchor, positioning, interpretation, contribution, limitations, and future work; calibrating modal verbs or hedging to evidence strength; or auditing whether Discussion repeats Results
+      path: core/discussion-argument-language.md
+    - condition: drafting, restructuring, or polishing an Introduction for flagship Nature, Nature Communications, Nature Machine Intelligence, or another Nature Portfolio title; building a fast problem funnel, exact knowledge gap, literature tension, question-first novelty, compact study roadmap, or Introduction–Results alignment audit
+      path: core/nature-introduction.md
+    - condition: drafting, restructuring, or polishing an abstract for flagship Nature, Nature Communications, Nature Machine Intelligence, or another Nature Portfolio title; compressing the manuscript into a discovery-centred evidence chain; selecting one main claim, one or two decisive supports, optional core numbers, and a bounded field-level payoff
+      path: core/nature-abstract.md
+
+journal_formats:
+  on_demand:
+    - condition: formatting, initial-submission readiness, or stage-aware checking for a flagship Nature Article
+      path: journal-formats/nature.md
+    - condition: formatting or checking output for Nature Communications conventions
+      path: journal-formats/nat-comms.md
+    - condition: formatting, article-type selection, initial-submission readiness, or stage-aware checking for Nature Machine Intelligence
+      path: journal-formats/nature-machine-intelligence.md
+
+quality_tools:
+  consistency_script: scripts/check_consistency.py
+  use_when: auditing an existing full manuscript or a manuscript revised over multiple rounds
+  purpose: warn about terminology variants, equivalent lengths expressed in different units, and equal numeric values reported at different precision
+  script_resolution: resolve relative to the nature-shared package directory, never the user working directory

package/vendor/nature-skills/skills/nature-shared/scripts/check_consistency.py

@@ -0,0 +1,273 @@
+#!/usr/bin/env python3
+"""Find mechanically detectable consistency risks in manuscript text files."""
+
+from __future__ import annotations
+
+import argparse
+import json
+import re
+from dataclasses import asdict, dataclass
+from decimal import Decimal, InvalidOperation
+from pathlib import Path
+from typing import Iterable, Sequence
+
+
+DEFAULT_TERM_GROUPS = {
+    "self-reference": ("this study", "this work", "this paper", "this article"),
+    "standard-deviation": ("standard deviation", "SD", "Std"),
+}
+
+LENGTH_FACTORS_METRES = {
+    "um": Decimal("0.000001"),
+    "mm": Decimal("0.001"),
+    "cm": Decimal("0.01"),
+    "m": Decimal("1"),
+}
+
+
+@dataclass(frozen=True)
+class Finding:
+    code: str
+    message: str
+    evidence: tuple[str, ...]
+
+
+@dataclass(frozen=True)
+class Occurrence:
+    path: Path
+    line: int
+    value: str
+
+    def label(self) -> str:
+        return f"{self.path}:{self.line}: {self.value}"
+
+
+def read_sources(paths: Sequence[Path]) -> dict[Path, str]:
+    return {
+        path: path.read_text(encoding="utf-8", errors="replace")
+        for path in paths
+    }
+
+
+def visible_lines(text: str) -> Iterable[tuple[int, str]]:
+    """Yield lines after removing Markdown fences and unescaped LaTeX comments."""
+    in_fence = False
+    for line_number, raw_line in enumerate(text.splitlines(), 1):
+        if re.match(r"^\s*```", raw_line):
+            in_fence = not in_fence
+            continue
+        if in_fence:
+            continue
+        line = re.sub(r"(?<!\\)%.*$", "", raw_line)
+        yield line_number, line
+
+
+def phrase_pattern(phrase: str) -> re.Pattern[str]:
+    escaped = re.escape(phrase).replace(r"\ ", r"\s+")
+    prefix = r"(?<![\w-])" if phrase[0].isalnum() else ""
+    suffix = r"(?![\w-])" if phrase[-1].isalnum() else ""
+    return re.compile(prefix + escaped + suffix, re.IGNORECASE)
+
+
+def find_phrase_occurrences(
+    sources: dict[Path, str], phrase: str
+) -> list[Occurrence]:
+    pattern = phrase_pattern(phrase)
+    occurrences: list[Occurrence] = []
+    for path, text in sources.items():
+        for line_number, line in visible_lines(text):
+            for match in pattern.finditer(line):
+                occurrences.append(Occurrence(path, line_number, match.group(0)))
+    return occurrences
+
+
+def check_term_groups(
+    sources: dict[Path, str], groups: dict[str, tuple[str, ...]]
+) -> list[Finding]:
+    findings: list[Finding] = []
+    for group_name, variants in groups.items():
+        present: list[tuple[str, list[Occurrence]]] = []
+        for variant in variants:
+            occurrences = find_phrase_occurrences(sources, variant)
+            if occurrences:
+                present.append((variant, occurrences))
+        if len(present) < 2:
+            continue
+        counts = ", ".join(f"{variant}={len(items)}" for variant, items in present)
+        evidence = tuple(
+            occurrence.label()
+            for _, items in present
+            for occurrence in items[:3]
+        )
+        findings.append(
+            Finding(
+                code="TERM_VARIANTS_PRESENT",
+                message=f"term group '{group_name}' uses multiple variants: {counts}",
+                evidence=evidence,
+            )
+        )
+    return findings
+
+
+NUMBER_PATTERN = re.compile(r"(?<![\w.])([+-]?(?:\d+\.\d+|\d+))(?![\w.])")
+
+
+def decimal_places(token: str) -> int:
+    unsigned = token.lstrip("+-")
+    return len(unsigned.partition(".")[2]) if "." in unsigned else 0
+
+
+def check_numeric_precision(sources: dict[Path, str]) -> list[Finding]:
+    values: dict[Decimal, dict[int, list[Occurrence]]] = {}
+    for path, text in sources.items():
+        for line_number, line in visible_lines(text):
+            for match in NUMBER_PATTERN.finditer(line):
+                token = match.group(1)
+                try:
+                    value = Decimal(token)
+                except InvalidOperation:
+                    continue
+                places = decimal_places(token)
+                values.setdefault(value, {}).setdefault(places, []).append(
+                    Occurrence(path, line_number, token)
+                )
+
+    findings: list[Finding] = []
+    for value, precision_groups in values.items():
+        if len(precision_groups) < 2:
+            continue
+        precision_summary = ", ".join(
+            f"{places} decimal place(s)={len(items)}"
+            for places, items in sorted(precision_groups.items())
+        )
+        evidence = tuple(
+            occurrence.label()
+            for _, items in sorted(precision_groups.items())
+            for occurrence in items[:3]
+        )
+        findings.append(
+            Finding(
+                code="NUMERIC_PRECISION_VARIANT",
+                message=f"numeric value {value} appears at multiple precisions: {precision_summary}",
+                evidence=evidence,
+            )
+        )
+    return findings
+
+
+LENGTH_PATTERN = re.compile(
+    r"(?<![\w.])([+-]?(?:\d+\.\d+|\d+))\s*(?:\\,\s*)?"
+    r"(?:\\(?:mathrm|text)\s*\{\s*)?(μm|µm|um|mm|cm|m)(?:\s*\})?"
+    r"(?![A-Za-z])",
+    re.IGNORECASE,
+)
+
+
+def normalized_unit(unit: str) -> str:
+    unit = unit.lower()
+    return "um" if unit in {"μm", "µm"} else unit
+
+
+def check_equivalent_length_units(sources: dict[Path, str]) -> list[Finding]:
+    values: dict[Decimal, dict[str, list[Occurrence]]] = {}
+    for path, text in sources.items():
+        for line_number, line in visible_lines(text):
+            for match in LENGTH_PATTERN.finditer(line):
+                number, raw_unit = match.groups()
+                unit = normalized_unit(raw_unit)
+                metres = Decimal(number) * LENGTH_FACTORS_METRES[unit]
+                values.setdefault(metres, {}).setdefault(unit, []).append(
+                    Occurrence(path, line_number, match.group(0))
+                )
+
+    findings: list[Finding] = []
+    for metres, unit_groups in values.items():
+        if len(unit_groups) < 2:
+            continue
+        counts = ", ".join(
+            f"{unit}={len(items)}" for unit, items in sorted(unit_groups.items())
+        )
+        evidence = tuple(
+            occurrence.label()
+            for _, items in sorted(unit_groups.items())
+            for occurrence in items[:3]
+        )
+        findings.append(
+            Finding(
+                code="EQUIVALENT_LENGTH_UNIT_VARIANT",
+                message=f"equivalent length {metres} m appears in multiple units: {counts}",
+                evidence=evidence,
+            )
+        )
+    return findings
+
+
+def parse_term_group(value: str) -> tuple[str, tuple[str, ...]]:
+    name, separator, raw_variants = value.partition("=")
+    variants = tuple(item.strip() for item in raw_variants.split("|") if item.strip())
+    if not separator or not name.strip() or len(variants) < 2:
+        raise argparse.ArgumentTypeError(
+            "term groups must use NAME=variant one|variant two with at least two variants"
+        )
+    return name.strip(), variants
+
+
+def run_checks(
+    paths: Sequence[Path],
+    term_groups: dict[str, tuple[str, ...]] | None = None,
+) -> list[Finding]:
+    sources = read_sources(paths)
+    findings = check_term_groups(sources, term_groups or {})
+    findings.extend(check_numeric_precision(sources))
+    findings.extend(check_equivalent_length_units(sources))
+    return findings
+
+
+def build_parser() -> argparse.ArgumentParser:
+    parser = argparse.ArgumentParser(
+        description="Find terminology, numeric-precision, and equivalent-unit variants."
+    )
+    parser.add_argument("paths", nargs="+", type=Path)
+    parser.add_argument(
+        "--term-group",
+        action="append",
+        default=[],
+        type=parse_term_group,
+        metavar="NAME=TERM|VARIANT",
+        help="Add a manuscript-specific terminology group. Repeat as needed.",
+    )
+    parser.add_argument(
+        "--no-default-term-groups",
+        action="store_true",
+        help="Disable the built-in self-reference and standard-deviation groups.",
+    )
+    parser.add_argument("--json", action="store_true", dest="as_json")
+    parser.add_argument(
+        "--fail-on-findings",
+        action="store_true",
+        help="Return exit status 1 when warnings are found.",
+    )
+    return parser
+
+
+def main(argv: list[str] | None = None) -> int:
+    args = build_parser().parse_args(argv)
+    groups = {} if args.no_default_term_groups else dict(DEFAULT_TERM_GROUPS)
+    groups.update(dict(args.term_group))
+    findings = run_checks(args.paths, groups)
+
+    if args.as_json:
+        print(json.dumps([asdict(item) for item in findings], ensure_ascii=False, indent=2))
+    elif findings:
+        for finding in findings:
+            print(f"{finding.code}\t{finding.message}")
+            for item in finding.evidence:
+                print(f"  {item}")
+    else:
+        print("No mechanical consistency warnings found.")
+
+    return 1 if findings and args.fail_on_findings else 0
+
+
+if __name__ == "__main__":
+    raise SystemExit(main())