@pikaa-ai/pikaa 0.3.1 → 0.3.4

package/skills/scientific-writing/references/citation_styles.md

@@ -1,92 +0,0 @@
-# Citation Integrity and Reference Formatting
-
-## Verification before style
-
-Formatting cannot repair an unverified reference. For every cited source:
-
-1. Open the source or authoritative bibliographic record.
-2. Confirm the cited proposition at a precise locator.
-3. Confirm authors or organization, title, publication state, venue, year, and version.
-4. Copy identifiers exactly from the verified record.
-5. Record corrections, retractions, expressions of concern, updates, and preprint status.
-6. Assign an evidence ID and human verification record.
-
-Do not cite a source that was not read for the proposition. Do not copy a DOI, PMID,
-quotation, or reference from generated text, a search snippet, or another article
-without verification. ICMJE assigns authors responsibility for reference accuracy and
-rejects AI-generated material as a primary source [SW-S01].
-
-## Quotations and paraphrases
-
-- Verify every quotation character-for-character and record a stable locator.
-- Preserve context, qualifications, and negation.
-- Mark changes, omissions, or translations according to venue policy.
-- Paraphrase from understanding, not by superficial word substitution.
-- Obtain permissions where copyright or license terms require them.
-- For personal communications or unpublished information, obtain required permission
-  and follow current journal policy [SW-S01].
-
-## Source choice
-
-Prefer the original source for a reported method, dataset, result, policy, or guideline.
-Use a review for synthesis when it actually supports the synthesized claim. Clearly
-identify preprints and other non-peer-reviewed versions. Check that a later correction
-or published version does not supersede the cited record.
-
-Do not use citation counts, venue prestige, recency, or a target percentage of recent
-references as a substitute for relevance and evidentiary fit.
-
-## Identifiers
-
-The local checker validates syntax and duplicates only. It does not resolve identifiers
-and cannot establish that an identifier belongs to the recorded work.
-
-Supported local checks include:
-
-- DOI;
-- PMID;
-- PMCID;
-- ISBN checksum;
-- HTTP or HTTPS URL shape;
-- duplicate normalized titles and identifiers.
-
-After the local check, a human must compare each identifier with the opened source.
-
-## NLM and journal styles
-
-For biomedical references, use *Citing Medicine* and NLM's sample references for the
-relevant source type [SW-S20, SW-S21]. These cover articles, books, datasets, software,
-and online material. The current target journal's instructions override generic style
-examples.
-
-For APA, AMA, Chicago, IEEE, ACS, Vancouver-derived, or publisher-specific styles:
-
-- use the current official manual or journal style;
-- render from verified structured metadata;
-- check author truncation, title case, journal abbreviation, version, date, locator,
-  and identifier rules;
-- inspect the rendered list manually after conversion.
-
-Do not invent a complete-looking example reference. Templates should use explicit
-fields or evidence IDs until verified metadata exists.
-
-## Citation audit
-
-Before submission:
-
-- every factual or numeric claim maps to verified evidence IDs;
-- each in-text citation maps to a source-manifest record;
-- every reference-list entry is cited unless the venue explicitly permits a
-  bibliography;
-- citation ordering and repeated citation behavior match the target style;
-- reused figures, tables, datasets, software, protocols, and standards are attributed;
-- direct quotations have locators and permissions where needed;
-- duplicate and malformed identifiers are resolved;
-- no retracted or corrected status is concealed.
-
-Run:
-
-```bash
-python3 scripts/audit_claims.py manuscript.md claims.csv source_manifest.json
-python3 scripts/check_references.py source_manifest.json
-```

package/skills/scientific-writing/references/cli_reference.md

@@ -1,113 +0,0 @@
-# Local CLI Reference
-
-All bundled commands use only the Python standard library. They:
-
-- accept explicit UTF-8 JSON, CSV, or Markdown files;
-- reject symbolic-link inputs;
-- cap file size, records, fields, JSON nodes, and nesting;
-- make no network calls;
-- read no environment variables or `.env` files;
-- perform no dynamic evaluation or pickle loading;
-- report issue codes, IDs, and line numbers without echoing manuscript or source text.
-
-Run from the skill directory with Python 3.11 or newer.
-
-## Scaffold
-
-```bash
-python3 scripts/scaffold_manuscript.py \
-  --output-dir ./draft-workspace \
-  --document-id local-draft \
-  --study-design randomized_trial \
-  --guideline consort-2025
-```
-
-The output directory must not exist. The command never overwrites files. Generated
-documents are explicitly incomplete and not submission-ready.
-
-## Manifest validation
-
-```bash
-python3 scripts/validate_manifest.py manuscript_manifest.json --kind manuscript
-python3 scripts/validate_manifest.py source_manifest.json --kind source
-python3 scripts/validate_manifest.py source_manifest.json --kind source --require-verified
-```
-
-The validator checks structure, IDs, verification gates, confidentiality status, and
-required-statement status. It does not read files named inside the manifest.
-
-## Reporting-guideline routing and coverage
-
-```bash
-python3 scripts/select_reporting_guidelines.py select --study-design systematic_review
-python3 scripts/select_reporting_guidelines.py check reporting_coverage.json
-```
-
-Selection and coverage are non-scoring. Open the official guideline after selection.
-
-## Claim and citation audit
-
-```bash
-python3 scripts/audit_claims.py manuscript.md claims.csv source_manifest.json
-```
-
-Required CSV headers:
-
-```text
-claim_id,section,claim_kind,claim_text_sha256,evidence_ids,verification_status,uncertainty,analysis_intent
-```
-
-Separate multiple evidence IDs with semicolons in CSV. Use inline Markdown markers:
-
-```text
-[claim:C001] [evidence:E001,E002]
-```
-
-The audit also flags numeric content without a claim marker.
-
-## Numeric and methods-results consistency
-
-```bash
-python3 scripts/check_consistency.py consistency_manifest.json
-```
-
-The command checks duplicate concepts across sections, units, percentages against
-numerators and denominators, sample sizes, evidence IDs, declared methods, outcome
-mappings, and confirmatory or exploratory status.
-
-## Reference identifiers and duplicates
-
-```bash
-python3 scripts/check_references.py source_manifest.json
-```
-
-The command checks local syntax and duplicates for DOI, PMID, PMCID, ISBN, URL, and
-normalized title. It never resolves an identifier; a human must compare each value with
-the opened source.
-
-## Authorship and disclosure
-
-```bash
-python3 scripts/validate_authorship.py authorship.json
-```
-
-The command checks human authorship criteria, exact CRediT role names, corresponding
-author and guarantor IDs, final approval, hashed declarations, AI disclosure, human
-verification, journal-policy review, and authorization gates for restricted material.
-
-## Language, placeholder, and confidentiality lint
-
-```bash
-python3 scripts/lint_manuscript.py manuscript.md \
-  --manifest manuscript_manifest.json
-```
-
-Possible sensitive-content findings are review prompts, not a de-identification
-certificate. The linter intentionally fails on unresolved placeholders.
-
-## Exit behavior
-
-- exit `0`: no error-level findings;
-- exit `1`: invalid input or one or more error-level findings.
-
-Warnings still require human review. JSON output is deterministic for the same inputs.

package/skills/scientific-writing/references/evidence_workflow.md

@@ -1,94 +0,0 @@
-# Evidence and Provenance Workflow
-
-## Core separation
-
-Drafting and evidence verification are different activities.
-
-- **Drafting** organizes language from already recorded evidence IDs. A draft may remain
-  incomplete and uncertain.
-- **Verification** requires an accountable human to open the source, confirm the exact
-  support and locator, check bibliographic metadata, and record who verified it and
-  when.
-- A fluent sentence is not evidence. Search snippets, generated summaries, memory, and
-  another paper's reference list are discovery aids, not verified support.
-
-## Registries
-
-The scaffold creates five linked records:
-
-1. `source_manifest.json` assigns each source an `E` ID and records identifiers,
-   location, confidentiality class, and verification state.
-2. `claims.csv` assigns each claim a `C` ID, stores a hash rather than raw claim text,
-   and maps the claim to one or more verified `E` IDs.
-3. `consistency_manifest.json` binds numeric facts, methods, outcomes, analysis intent,
-   units, denominators, sample sizes, and result locations.
-4. `authorship.json` records human authorship criteria, CRediT roles, accountability,
-   declarations, and AI use.
-5. `reporting_coverage.json` records high-level coverage without scoring or certifying
-   the manuscript.
-
-These registries contain metadata, not full source documents. Do not paste unpublished
-manuscripts, peer-review files, PHI, sensitive datasets, proprietary content, or source
-documents into them.
-
-## Claim markers
-
-Append machine-readable markers to every factual or numeric assertion while drafting:
-
-```text
-[claim:C001] [evidence:E001,E002]
-```
-
-An alternative citation marker is `[@E001]`. Keep the claim and evidence markers on the
-same line until the audit passes. A final publisher conversion may replace evidence IDs
-with rendered citations only after preserving an auditable mapping.
-
-## Verification procedure
-
-For each source:
-
-1. Open the authoritative source or record.
-2. Confirm title, author or organization, publication state, year, and identifiers.
-3. Record the exact supporting location, such as section, page, table, figure, or
-   registry field.
-4. Confirm that the source supports the claim's direction, population, intervention or
-   exposure, outcome, time point, and uncertainty.
-5. Record caveats, retractions, corrections, expressions of concern, or version status.
-6. Mark the source verified only after a named human completes the check.
-
-For each claim:
-
-1. Classify it as factual, numeric, method, result, interpretive, or declaration.
-2. Hash the normalized claim text and store the hash in `claims.csv`.
-3. Map it to verified evidence IDs.
-4. Record uncertainty and whether the analysis was confirmatory, exploratory,
-   descriptive, or not applicable.
-5. Keep unsupported or conflicting claims out of submission-ready prose. If useful,
-   retain them in a clearly marked unresolved-issues log.
-
-## Drafting gates
-
-Do not infer or complete missing:
-
-- citations, identifiers, quotations, or source locators;
-- data values, denominators, units, sample sizes, or statistical results;
-- methods, protocol details, analysis decisions, or deviations;
-- approvals, consent, registrations, author contributions, conflicts, funding, or
-  availability statements.
-
-Use explicit missing states. Preserve negative, null, adverse, unexpected, and
-inconclusive findings. Never convert absence of evidence into evidence of no effect.
-
-## Final audit
-
-Run:
-
-```bash
-python3 scripts/validate_manifest.py source_manifest.json --kind source --require-verified
-python3 scripts/audit_claims.py manuscript.md claims.csv source_manifest.json
-python3 scripts/check_consistency.py consistency_manifest.json
-python3 scripts/check_references.py source_manifest.json
-```
-
-Tool output contains IDs and line numbers, not manuscript or source text. A passing
-machine audit supports review; it does not replace human scientific judgment.

package/skills/scientific-writing/references/figures_tables.md

@@ -1,94 +0,0 @@
-# Optional Figures and Tables
-
-Figures and tables are optional. Include a display only when it communicates verified
-evidence more clearly than prose and the target venue permits it. This skill does not
-generate images, schematics, graphical abstracts, or synthetic scientific visuals.
-
-## Provenance gate
-
-Each display needs a record containing:
-
-- stable display ID and version;
-- source data or evidence IDs;
-- code, query, or manual transformation used;
-- accountable creator and reviewer;
-- date generated or revised;
-- analysis population, exclusions, and sample size;
-- units, scales, denominators, and uncertainty definitions;
-- license, attribution, and permission status for reused material;
-- documented adjustments, cropping, compositing, or preprocessing.
-
-Do not recreate missing source data from a screenshot or published graphic. Do not
-alter an image in a way that hides, removes, duplicates, or misrepresents information.
-Retain original files and an audit trail.
-
-## Choosing a form
-
-Use:
-
-- prose for a small number of directly relevant values;
-- a table when exact values and multidimensional comparison matter;
-- a figure when pattern, distribution, relationship, sequence, or spatial information
-  matters.
-
-Avoid duplicating the same information in prose, a table, and a figure. There is no
-universal minimum, maximum, or display-per-word rule.
-
-## Tables
-
-Check:
-
-- title and notes define population, time point, analysis set, units, and abbreviations;
-- rows and columns preserve denominators and distinguish missing from zero;
-- percentages can be recomputed from the recorded numerator and denominator;
-- precision is consistent with the measurement and analysis;
-- uncertainty and statistical quantities are named, not implied by symbols alone;
-- values match the abstract, prose, figures, supplements, and consistency registry;
-- cells remain accessible as text rather than an image when the venue allows.
-
-## Figures
-
-Check:
-
-- axes, scales, transformations, units, and reference lines are explicit;
-- truncated or nonlinear scales are visible and justified;
-- individual observations or distributions are shown when scientifically appropriate;
-- uncertainty is defined;
-- group sizes and exclusions are available;
-- legends identify all encodings;
-- colors, shapes, line styles, labels, or patterns provide redundant cues;
-- image panels include scale and orientation information where relevant;
-- the final exported file matches current journal format and size instructions.
-
-Do not add significance stars or trend lines unless they map to a verified analysis.
-
-## Captions and alt text
-
-A caption should state what is shown, define panels and encodings, identify the analysis
-population, units, uncertainty, and relevant methods, and link to evidence IDs during
-drafting.
-
-Alt text should:
-
-- identify the display type and purpose;
-- summarize the principal visible pattern without adding a new conclusion;
-- describe axes, groups, direction, and uncertainty needed to understand the display;
-- avoid repeating the full caption or listing every data point;
-- be reviewed manually with the final display.
-
-Automated accessibility checks do not verify scientific correctness. Inspect contrast,
-color independence, reading order, label size, keyboard or screen-reader behavior where
-applicable, and legibility at final size.
-
-## Flow diagrams
-
-Use the current official flow-diagram resource for the selected guideline, such as
-CONSORT 2025 or PRISMA 2020 [SW-S07, SW-S10]. Populate it only from verified counts.
-Reconcile every branch and denominator with the methods, results, and registry.
-
-## Final manual review
-
-An accountable human should compare each display against source data and analysis
-output, inspect permissions and confidentiality, verify captions and alt text, and
-confirm the rendered export. Passing a file-format or consistency check does not certify
-the display.

package/skills/scientific-writing/references/imrad_structure.md

@@ -1,114 +0,0 @@
-# Manuscript Structure and Consistency
-
-IMRAD is a useful default for many original-research reports, but the study design,
-reporting guideline, article type, and current journal instructions control the final
-structure [SW-S01, SW-S06].
-
-## Title and abstract
-
-The title should identify the work accurately without adding novelty, causality, design,
-or population claims that the manuscript does not support.
-
-Draft the abstract after the main text. Mirror, do not reinterpret:
-
-- objective or question;
-- design, setting, population or material, and key methods;
-- analysis population and prespecified primary result;
-- estimate, uncertainty, denominator, and harms where relevant;
-- conclusion limited to the reported evidence.
-
-Structured versus unstructured format is a venue decision. Do not apply a universal
-format. Any number in the abstract must match the same concept and analysis set in the
-main text and consistency registry.
-
-## Introduction
-
-Build a short evidence chain:
-
-1. verified context;
-2. what is known and uncertain;
-3. the specific gap;
-4. the objective, question, or prespecified hypothesis.
-
-Do not claim that no prior work exists unless a suitable search verifies that claim.
-Avoid previewing unsupported results or inflating significance.
-
-## Methods
-
-Methods should permit evaluation and, where feasible, reproduction. Cover the elements
-applicable to the design:
-
-- design, setting, dates, and protocol or registration;
-- participants, specimens, datasets, or source population;
-- eligibility, selection, sampling, exclusions, and analysis populations;
-- interventions, exposures, comparators, materials, instruments, and versions;
-- outcomes, predictors, thresholds, time points, and measurement methods;
-- bias controls, randomization, allocation, and masking where applicable;
-- sample-size rationale;
-- missing data, transformations, covariates, multiplicity, sensitivity analyses, and
-  statistical or computational methods;
-- confirmatory, exploratory, and descriptive status;
-- ethics, consent, privacy, data governance, and approvals only when verified;
-- data, code, materials, and protocol access conditions.
-
-Record deviations and timing. Never reconstruct a method from a result merely to make
-the paper appear consistent.
-
-## Results
-
-Follow the declared objectives and outcomes. Report:
-
-- participant, sample, or record flow;
-- exclusions, missingness, attrition, and analysis populations;
-- descriptive information needed for interpretation;
-- prespecified primary and secondary results;
-- estimates with units, denominators, sample sizes, and uncertainty;
-- exploratory, sensitivity, subgroup, negative, null, adverse, unexpected, and
-  inconclusive findings with correct labels;
-- protocol or analysis deviations that affect interpretation.
-
-Describe results before interpretation unless the venue combines Results and
-Discussion. Do not equate a threshold crossing with scientific or practical importance.
-
-## Discussion
-
-Start from the verified findings, then:
-
-- answer the objective at the supported level of certainty;
-- compare with verified prior evidence;
-- consider alternative explanations;
-- distinguish statistical, scientific, clinical, and practical interpretation;
-- explain limitations and likely consequences;
-- bound generalizability to the studied population, material, setting, and period;
-- identify implications without prescribing action beyond the evidence.
-
-Do not introduce new results, methods, approvals, or citations that bypass verification.
-
-## Declarations and end matter
-
-Treat each statement as data, not boilerplate:
-
-- author contributions and accountability;
-- acknowledgments and permissions;
-- funding and the funder's role;
-- competing interests;
-- ethics, consent, and registration;
-- data, code, materials, and protocol availability;
-- AI-use disclosure;
-- references, figure legends, tables, and supplements.
-
-Use verified or explicit not-applicable states. Never generate an approval identifier,
-grant number, registration, author role, conflict declaration, or availability promise.
-
-## Cross-section audit
-
-Before submission, compare:
-
-- objective ↔ outcome ↔ result ↔ conclusion;
-- methods ↔ results;
-- abstract ↔ main text ↔ tables ↔ figures ↔ supplement;
-- units, denominators, sample sizes, labels, and time points;
-- registration and protocol ↔ manuscript;
-- in-text citations ↔ source manifest ↔ reference list.
-
-Run `scripts/check_consistency.py` and complete a manual scientific review.

package/skills/scientific-writing/references/journal_policies.md

@@ -1,56 +0,0 @@
-# Journal and Publisher Policy Review
-
-Generic guidance never overrides the target journal's current instructions.
-
-## Capture a dated policy record
-
-Before drafting and again before submission, record:
-
-- journal, article type, and policy URL;
-- date accessed;
-- word, abstract, reference, table, figure, and supplement limits;
-- required structure and reporting guideline;
-- registration, protocol, and analysis-plan requirements;
-- ethics, consent, participant privacy, and image requirements;
-- authorship, contributor, acknowledgment, and change-of-authorship rules;
-- funding, conflicts, and sponsor-role disclosures;
-- data, code, materials, and repository policies;
-- preprint, prior dissemination, duplicate submission, and copyright policies;
-- AI use by authors and any restrictions on external tools;
-- peer-review model and confidentiality;
-- file, accessibility, and submission-system requirements.
-
-Do not guess an absent policy. Ask the journal or leave the decision unresolved.
-
-## Official examples
-
-- JAMA's current Instructions for Authors illustrate article-type-specific requirements
-  and should be consulted directly for a JAMA submission [SW-S25].
-- JAMA's AI guidance illustrates author disclosure, human responsibility, and
-  confidentiality limits for peer review [SW-S24].
-- Nature Portfolio's reporting and availability policy illustrates venue requirements
-  for data, materials, code, protocols, restrictions, and access [SW-S22].
-- Nature Portfolio's authorship policy illustrates publisher-specific accountability
-  and contribution statements [SW-S23].
-- PLOS Biology's data policy illustrates how sharing expectations interact with
-  consent, privacy, legal, ethical, and sensitive-data restrictions [SW-S26].
-
-These are examples, not defaults for other journals. Publisher-level policy and
-journal-level instructions may both apply.
-
-## Submission review
-
-Perform a manual comparison against the live instructions:
-
-1. Select the exact article type.
-2. Confirm the latest reporting guideline and extensions.
-3. Verify every required statement from source records.
-4. Confirm whether checklists or flow diagrams must be uploaded.
-5. Confirm data, code, and materials deposits actually exist and are accessible as
-   stated.
-6. Confirm author order, corresponding author, CRediT roles, and approvals.
-7. Confirm AI-use disclosure wording and location with the human authors.
-8. Verify files, anonymization, accessibility, permissions, and metadata.
-9. Save the access date and policy URLs in the submission record.
-
-Passing local tools does not establish venue compliance.

package/skills/scientific-writing/references/professional_report_formatting.md

@@ -1,82 +0,0 @@
-# Safe Formatting for Reports and Manuscripts
-
-## Content before presentation
-
-The former LaTeX style and demonstration report were removed. They could turn
-plausible-looking placeholder findings into a polished PDF. This version uses
-format-neutral Markdown and JSON/CSV registries so incompleteness remains visible.
-
-Do not format a draft as submission-ready while any verification gate is incomplete.
-Visual polish is not evidence.
-
-## Workflow
-
-1. Create a local scaffold.
-2. Draft and verify content in Markdown.
-3. Run manifest, claim, reference, consistency, authorship, coverage, and lint checks.
-4. Obtain accountable human approval.
-5. Copy the verified content into the current venue template.
-6. Re-run checks that remain applicable and inspect the rendered output manually.
-
-For a journal or conference, use its current author instructions and official template.
-For an institutional report or thesis, use the institution's controlled template.
-
-## Fail-closed placeholder policy
-
-Permitted draft markers are intentionally conspicuous, such as `[[TODO:...]]`. The
-language linter treats them as errors. Never replace an unresolved marker with generic
-boilerplate, a guessed number, a fabricated statement, or an invented citation.
-
-Keep:
-
-- `submission_ready` false;
-- the draft banner visible;
-- missing declaration statuses explicit;
-- human and confidentiality gates incomplete;
-
-until the underlying records are verified.
-
-## Headings and navigation
-
-- Use a single title and logical heading levels.
-- Preserve heading order when converting formats.
-- Include lists of tables or figures only when useful or required.
-- Use stable internal labels for tables, figures, appendices, and supplements.
-- Ensure generated bookmarks and reading order match the visible structure.
-
-## Typography and layout
-
-- Use the venue's prescribed font, spacing, margins, page size, and line numbering.
-- Do not use color, weight, or position as the only carrier of meaning.
-- Keep equations, symbols, units, subscripts, and superscripts intact through
-  conversion.
-- Check widows, orphans, clipped content, broken links, and misplaced floats manually.
-
-## Tables, figures, and accessibility
-
-Follow `figures_tables.md`. Verify alt text, captions, provenance, permissions, color
-independence, reading order, label legibility, and final-size rendering. Do not create a
-decorative visual simply to make a report appear complete.
-
-## References and declarations
-
-References must render from verified metadata. After conversion, inspect identifier
-links, special characters, author order, and citation order.
-
-Declarations must come from validated records. A style template must never supply a
-default ethics approval, consent statement, funding source, conflict statement, author
-contribution, data or code promise, or AI disclosure.
-
-## Archival handoff
-
-Retain:
-
-- the verified Markdown source;
-- the structured registries;
-- the exact venue template version;
-- conversion instructions and software versions;
-- the final rendered file;
-- validator outputs and human approval record.
-
-Do not archive sensitive source documents alongside a public manuscript package unless
-authorization, consent, law, contracts, and policy permit it.