@pikaa-ai/pikaa 0.3.23 → 0.3.25

package/skills/scanpy/SKILL.md

@@ -1,303 +0,0 @@
----
-name: scanpy
-description: Standard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, visualization, and converting R-friendly single-cell formats such as Seurat or SingleCellExperiment RDS files into h5ad for Scanpy. Best for exploratory scRNA-seq analysis with established workflows. For deep learning models use scvi-tools; for data format questions use anndata.
-license: BSD-3-Clause
-metadata:
-  version: "1.5"
-  skill-author: K-Dense Inc.
----
-
-# Scanpy: Single-Cell Analysis
-
-## Overview
-
-Scanpy is a scalable Python toolkit for analyzing single-cell RNA-seq data, built on AnnData. Apply this skill for complete single-cell workflows including quality control, normalization, dimensionality reduction, clustering, marker gene identification, visualization, and trajectory analysis. Current stable release: **scanpy 1.12.x** (January 2026).
-
-## Installation
-
-Requires Python **3.12+** (scanpy 1.12 dropped Python ≤3.11) and anndata **≥0.10**.
-
-```bash
-uv pip install "scanpy[leiden]"
-```
-
-The `[leiden]` extra installs `python-igraph` and `leidenalg`, required for Leiden clustering. For reproducible environments, pin a version: `uv pip install "scanpy[leiden]==1.12.1"`.
-
-For large or out-of-core datasets, many functions support [Dask](https://docs.dask.org/) arrays (experimental):
-
-```bash
-uv pip install "scanpy[leiden]" dask
-```
-
-See the [Using dask with Scanpy](https://scanpy.scverse.org/en/stable/tutorials/experimental/dask.html) tutorial. For GPU-accelerated scanpy-like operations, use [rapids-singlecell](https://rapids-singlecell.readthedocs.io/) as a separate package.
-
-If the input is an R-native single-cell object (`.rds`, `.RData`, Seurat, or SingleCellExperiment), first convert it to `.h5ad` with R tooling, then load it with Scanpy. Read `references/r_interop.md` for agent-run installation and conversion instructions across macOS, Linux, and Windows.
-
-For AnnData structure and I/O details, use the **anndata** skill. For probabilistic models and batch correction, use **scvi-tools**.
-
-## When to Use This Skill
-
-This skill should be used when:
-- Analyzing single-cell RNA-seq data (.h5ad, 10X, CSV formats)
-- Working with R-friendly single-cell datasets (`.rds`, `.RData`, Seurat, SingleCellExperiment) that need conversion to `.h5ad`
-- Performing quality control on scRNA-seq datasets
-- Creating UMAP, t-SNE, or PCA visualizations
-- Identifying cell clusters and finding marker genes
-- Annotating cell types based on gene expression
-- Conducting trajectory inference or pseudotime analysis
-- Generating publication-quality single-cell plots
-
-## Script Toolkit (prefer these over writing code from scratch)
-
-This skill bundles ready-to-run CLI scripts in `scripts/` for every common step. **Run these instead of hand-writing scanpy code** — they handle file loading by extension, figure setup, sensible defaults, raw-count preservation, and progress logging. Each reads and writes `.h5ad`, so they chain together, and each has its own `--help`. Only drop down to writing scanpy code when a task isn't covered by a script or needs unusual customization.
-
-All scripts use a shared `scripts/_common.py` helper (loading, saving, figure config) — keep it alongside the others. Run from the skill directory or pass full paths; figures default to `./figures/`.
-
-| Script | Purpose | Typical call |
-|--------|---------|--------------|
-| `run_pipeline.py` | **Full workflow in one command**: load → QC → normalize → HVG → PCA → (batch) → UMAP → Leiden → markers | `python scripts/run_pipeline.py raw.h5ad -o processed.h5ad` |
-| `inspect_data.py` | Summarize an unknown dataset (shape, obs/var, layers, what's already computed, raw vs normalized) | `python scripts/inspect_data.py data.h5ad` |
-| `convert.py` | Load any format (10x dir/.h5, csv, loom, mtx) and write `.h5ad` | `python scripts/convert.py 10x_dir/ -o data.h5ad` |
-| `qc_analysis.py` | QC metrics, before/after plots, filtering, optional Scrublet doublets | `python scripts/qc_analysis.py raw.h5ad -o qc.h5ad --scrublet` |
-| `preprocess.py` | Normalize, log1p, HVG, optional scale/regress (keeps `counts` layer + `raw`) | `python scripts/preprocess.py qc.h5ad -o norm.h5ad` |
-| `reduce_dimensions.py` | PCA + variance plot, neighbors, UMAP, optional t-SNE | `python scripts/reduce_dimensions.py norm.h5ad -o red.h5ad` |
-| `batch_correct.py` | Integration: harmony / bbknn / combat | `python scripts/batch_correct.py red.h5ad -o int.h5ad --method harmony --batch-key sample` |
-| `cluster.py` | Leiden (or louvain) at one or many resolutions | `python scripts/cluster.py red.h5ad -o clu.h5ad --resolution 0.3 0.6 1.0` |
-| `find_markers.py` | `rank_genes_groups` + per-group CSVs + marker plots | `python scripts/find_markers.py clu.h5ad --groupby leiden -o clu.h5ad` |
-| `annotate.py` | Map clusters → cell types from JSON/CSV; optional marker reference dotplot | `python scripts/annotate.py clu.h5ad -o ann.h5ad --mapping map.json` |
-| `score_genes.py` | Score gene signatures (JSON) and/or cell-cycle phase | `python scripts/score_genes.py ann.h5ad -o scored.h5ad --gene-sets sigs.json` |
-| `pseudobulk.py` | Aggregate counts by sample × cell type → matrix for pydeseq2 | `python scripts/pseudobulk.py ann.h5ad --by sample cell_type --out-prefix pb` |
-| `subset.py` | Subset by obs values or gene list (optionally clear stale embeddings) | `python scripts/subset.py ann.h5ad -o tcells.h5ad --obs cell_type --keep "T cells"` |
-| `plot.py` | Generate umap/tsne/pca/violin/dotplot/heatmap/etc. from a processed object | `python scripts/plot.py ann.h5ad --kind dotplot --genes CD3D CD14 --groupby cell_type` |
-
-### One-shot end-to-end run
-
-```bash
-# Counts → clustered, marker-annotated object + figures + marker CSVs
-python scripts/run_pipeline.py raw.h5ad -o processed.h5ad \
-    --resolution 0.5 --n-top-genes 2000 --scrublet
-# With multi-sample integration:
-python scripts/run_pipeline.py raw.h5ad -o processed.h5ad --batch-key sample --batch-method harmony
-# Reproducible parameters via JSON (keys mirror flag names with underscores):
-python scripts/run_pipeline.py raw.h5ad -o processed.h5ad --config params.json
-```
-
-### Step-by-step chain (when you need to inspect/iterate between stages)
-
-```bash
-python scripts/qc_analysis.py        raw.h5ad  -o qc.h5ad   --scrublet
-python scripts/preprocess.py         qc.h5ad   -o norm.h5ad --n-top-genes 2000
-python scripts/reduce_dimensions.py  norm.h5ad -o red.h5ad  --n-pcs 40
-python scripts/cluster.py            red.h5ad  -o clu.h5ad  --resolution 0.3 0.5 0.8
-python scripts/find_markers.py       clu.h5ad  -o clu.h5ad  --groupby leiden --use-raw
-# inspect results/markers/*.csv, decide labels, write a mapping JSON, then:
-python scripts/annotate.py           clu.h5ad  -o ann.h5ad  --mapping celltypes.json
-```
-
-The sections below document the underlying scanpy calls each script performs — read them when customizing beyond the script flags.
-
-## Quick Start
-
-### Basic Import and Setup
-
-```python
-import scanpy as sc
-import pandas as pd
-import numpy as np
-
-# Configure settings
-sc.settings.verbosity = 3
-sc.settings.set_figure_params(dpi=80, facecolor='white')
-sc.settings.figdir = './figures/'
-sc.settings.autosave = True  # Preferred over per-plot save= (deprecated in scanpy 1.12)
-```
-
-### Loading Data
-
-```python
-# From 10X Genomics
-adata = sc.read_10x_mtx('path/to/data/')
-adata = sc.read_10x_h5('path/to/data.h5')
-
-# From h5ad (AnnData format)
-adata = sc.read_h5ad('path/to/data.h5ad')
-
-# From CSV
-adata = sc.read_csv('path/to/data.csv')
-```
-
-For R-native files, do not try to parse Seurat `.rds` directly in Python. Convert first:
-
-```bash
-# See references/r_interop.md for installing R and conversion packages.
-Rscript convert_rds_to_h5ad.R input.rds output.h5ad
-```
-
-```python
-adata = sc.read_h5ad('output.h5ad')
-```
-
-### Understanding AnnData Structure
-
-The AnnData object is the core data structure in scanpy:
-
-```python
-adata.X          # Expression matrix (cells × genes)
-adata.obs        # Cell metadata (DataFrame)
-adata.var        # Gene metadata (DataFrame)
-adata.uns        # Unstructured annotations (dict)
-adata.obsm       # Multi-dimensional cell data (PCA, UMAP)
-adata.raw        # Raw data backup
-
-# Access cell and gene names
-adata.obs_names  # Cell barcodes
-adata.var_names  # Gene names
-```
-
-## Standard Analysis Workflow
-
-The seven steps, with code and the parameters that matter at each, are in
-[references/analysis_workflow.md](references/analysis_workflow.md):
-
-1. **Quality control** — filter cells and genes; inspect mitochondrial fraction and counts
-   before choosing thresholds rather than copying defaults.
-2. **Normalization and preprocessing** — normalize, log-transform, select highly variable
-   genes, and keep `.raw` for later plotting.
-3. **Dimensionality reduction** — PCA, then the neighbour graph, then UMAP.
-4. **Clustering** — Leiden at a resolution chosen for the question, not the default.
-5. **Marker gene identification** — ranked genes per cluster.
-6. **Cell type annotation** — mapping clusters to types from markers.
-7. **Save results** — writing the annotated `AnnData`.
-
-Common follow-on tasks — publication plots, trajectory inference, pseudobulk differential
-expression between conditions, gene set scoring, and batch correction — are in the same
-file. See also [references/standard_workflow.md](references/standard_workflow.md) and
-[references/plotting_guide.md](references/plotting_guide.md).
-
-## Key Parameters to Adjust
-
-### Quality Control
-- `min_genes`: Minimum genes per cell (typically 200-500)
-- `min_cells`: Minimum cells per gene (typically 3-10)
-- `pct_counts_mt`: Mitochondrial threshold (typically 5-20%)
-
-### Normalization
-- `target_sum`: Target counts per cell (default 1e4)
-
-### Feature Selection
-- `n_top_genes`: Number of HVGs (typically 2000-3000)
-- `min_mean`, `max_mean`, `min_disp`: HVG selection parameters
-
-### Dimensionality Reduction
-- `n_pcs`: Number of principal components (check variance ratio plot)
-- `n_neighbors`: Number of neighbors (typically 10-30)
-
-### Clustering
-- `resolution`: Clustering granularity (0.4-1.2, higher = more clusters)
-
-## Common Pitfalls and Best Practices
-
-1. **Always save raw counts**: `adata.raw = adata` before filtering genes
-2. **Check QC plots carefully**: Adjust thresholds based on dataset quality
-3. **Use Leiden clustering**: `sc.tl.louvain` is deprecated in scanpy 1.12
-4. **Try multiple clustering resolutions**: Find optimal granularity
-5. **Validate cell type annotations**: Use multiple marker genes
-6. **Use `use_raw=True` for gene expression plots**: Shows normalized counts from `.raw`
-7. **Check PCA variance ratio**: Determine optimal number of PCs
-8. **Save intermediate results**: Long workflows can fail partway through
-9. **Pseudobulk for DE**: Do not treat `rank_genes_groups` p-values as rigorous DE between conditions
-10. **Save plots via settings**: Use `sc.settings.autosave` instead of deprecated `save=` on plot functions
-11. **Convert R objects before Scanpy**: Use R packages to convert Seurat or SingleCellExperiment `.rds` files to `.h5ad`, preserving counts, metadata, and gene identifiers
-
-## Bundled Resources
-
-### scripts/ (CLI toolkit)
-A composable set of `.h5ad`-in/`.h5ad`-out scripts covering the whole workflow plus a one-command end-to-end pipeline. See the **Script Toolkit** section above for the full table and chaining examples. Each script has `--help`. Files:
-
-- `_common.py` — shared loading/saving/figure helpers imported by the others (not a CLI)
-- `run_pipeline.py` — full pipeline in one command (flags or `--config` JSON)
-- `inspect_data.py`, `convert.py` — explore and load/convert any input format
-- `qc_analysis.py`, `preprocess.py`, `reduce_dimensions.py`, `batch_correct.py`, `cluster.py` — pipeline steps
-- `find_markers.py`, `annotate.py`, `score_genes.py`, `pseudobulk.py` — markers, annotation, scoring, DE prep
-- `subset.py`, `plot.py` — subset by metadata/genes; generate any standard plot
-
-**Default to these scripts before writing scanpy code from scratch.**
-
-### references/standard_workflow.md
-Complete step-by-step workflow with detailed explanations and code examples for:
-- Data loading and setup
-- Quality control with visualization
-- Normalization and scaling
-- Feature selection
-- Dimensionality reduction (PCA, UMAP, t-SNE)
-- Clustering (Leiden)
-- Doublet detection (scrublet) and pseudobulk aggregation
-- Marker gene identification
-- Cell type annotation
-- Trajectory inference
-- Differential expression
-
-Read this reference when performing a complete analysis from scratch.
-
-### references/api_reference.md
-Quick reference guide for scanpy functions organized by module:
-- Reading/writing data (`sc.read_*`, `adata.write_*`)
-- Preprocessing (`sc.pp.*`)
-- Tools (`sc.tl.*`)
-- Plotting (`sc.pl.*`)
-- AnnData structure and manipulation
-- Settings and utilities
-
-Use this for quick lookup of function signatures and common parameters.
-
-### references/plotting_guide.md
-Comprehensive visualization guide including:
-- Quality control plots
-- Dimensionality reduction visualizations
-- Clustering visualizations
-- Marker gene plots (heatmaps, dot plots, violin plots)
-- Trajectory and pseudotime plots
-- Publication-quality customization
-- Multi-panel figures
-- Color palettes and styling
-
-Consult this when creating publication-ready figures.
-
-### references/r_interop.md
-Agent runbook for installing R on macOS, Linux, and Windows, installing CRAN/Bioconductor conversion packages, inspecting `.rds`/`.RData` inputs, converting Seurat or SingleCellExperiment objects to `.h5ad`, and validating the result in Scanpy.
-
-### assets/analysis_template.py
-Complete analysis template providing a full workflow from data loading through cell type annotation. Copy and customize this template for new analyses:
-
-```bash
-cp assets/analysis_template.py my_analysis.py
-# Edit parameters and run
-python my_analysis.py
-```
-
-The template includes all standard steps with configurable parameters and helpful comments.
-
-### assets/ JSON templates
-Edit-and-pass templates so you don't author config/mappings from scratch:
-- `assets/pipeline_config.json` — parameter set for `run_pipeline.py --config`
-- `assets/celltype_mapping.json` — cluster → cell-type map for `annotate.py --mapping`
-- `assets/gene_signatures.json` — gene-set signatures for `score_genes.py --gene-sets`
-
-## Additional Resources
-
-- **Official scanpy documentation**: https://scanpy.scverse.org/en/stable/
-- **Scanpy tutorials**: https://scanpy.scverse.org/en/stable/tutorials/index.html
-- **Release notes**: https://scanpy.scverse.org/en/stable/release-notes/index.html
-- **scverse ecosystem**: https://scverse.org/ (related tools: squidpy, scvi-tools, cellrank)
-- **R interoperability**: https://www.bioconductor.org/packages/release/bioc/html/zellkonverter.html and https://mojaveazure.github.io/seurat-disk/
-- **Best practices**: Luecken & Theis (2019) "Current best practices in single-cell RNA-seq"
-
-## Tips for Effective Analysis
-
-1. **Start with the template**: Use `assets/analysis_template.py` as a starting point
-2. **Run QC script first**: Use `scripts/qc_analysis.py` for initial filtering
-3. **Consult references as needed**: Load workflow and API references into context
-4. **Iterate on clustering**: Try multiple resolutions and visualization methods
-5. **Validate biologically**: Check marker genes match expected cell types
-6. **Document parameters**: Record QC thresholds and analysis settings
-7. **Save checkpoints**: Write intermediate results at key steps

package/skills/scholar-evaluation/SKILL.md

@@ -1,296 +0,0 @@
----
-name: scholar-evaluation
-description: Provide qualitative-first, evidence-traceable developmental review of scholarly works and audit low-stakes research-assessment rubrics with optional local quality controls. Never use for ranking people or consequential decisions.
-license: MIT
-compatibility: Requires Python 3.11+ for optional bundled standard-library CLIs. All tooling is local JSON/CSV processing with no network, credentials, external models, or subprocesses.
-allowed-tools: Read Write Bash Glob Python
-metadata:
-  version: "2.1"
-  skill-author: K-Dense Inc.
----
-
-# Scholar Evaluation
-
-## Purpose
-
-Provide developmental, evidence-traceable feedback on a **scholarly work**:
-paper, draft, protocol, literature synthesis, or research idea. Use
-qualitative judgment first. Optional scores only describe how submitted
-evidence maps to a predeclared bounded rubric.
-
-This skill also audits whether a low-stakes assessment process documents its
-construct, provenance, rater quality, uncertainty, traceability, sensitivity,
-fairness, accessibility, privacy, and human governance.
-
-## Hard safety boundary
-
-Never use this skill to automate, recommend, materially influence, or score:
-
-- hiring, promotion, or tenure;
-- admissions;
-- grants or other funding;
-- prizes, honors, or awards;
-- discipline, dismissal, or sanctions; or
-- any other high-impact personnel decision.
-
-Never rank people. Never reduce a person to a composite score. Never infer
-ability, character, integrity, protected traits, future performance, or worth.
-A nominal human-in-the-loop does not remove this boundary.
-
-If asked for a prohibited use, stop. Offer developmental comments on a
-scholarly work or a process-only audit that does not process applications,
-compare people, recommend an outcome, or advise a decision.
-
-Do not issue publication-readiness, accept/reject, or “top-tier” judgments.
-
-Read `references/responsible_assessment.md` before any organizational use.
-
-## ScholarEval status
-
-The referenced ScholarEval project is an **experimental
-literature-grounded research-idea evaluation framework**, not validated
-psychometrics.
-
-The verified primary record is Moussa et al., *ScholarEval: Research Idea
-Evaluation Grounded in Literature*, arXiv:2510.16234v2, revised 2026-02-28.
-It reports a retrieval-augmented soundness/contribution framework, a
-117-idea four-discipline dataset, coverage experiments, and a user study.
-
-Do not generalize those results to person assessment, consequential decisions,
-all disciplines, or this skill's rubric. No peer-reviewed publication status
-was verified during the dated review. See `references/source_ledger.md`.
-
-## Metric and prestige policy
-
-Do not score or infer quality from:
-
-- Journal Impact Factor or other journal measures;
-- h-index, publication counts, or citation counts;
-- altmetrics or attention;
-- journal, conference, venue, institution, employer, or geographic prestige;
-- author affiliation, reputation, network, or career path.
-
-The rubric validator rejects common proxy-measure criteria.
-
-If a qualified reviewer mentions an indicator descriptively outside the
-scoring tools, record its exact purpose, source, coverage, field and time
-effects, uncertainty, missingness, biases, gaming risk, and why it does not
-directly measure quality. Never hide indicators inside an opaque composite.
-
-## Data boundary
-
-Bundled scripts accept only strict local JSON/CSV containing pseudonymous IDs,
-bounded ratings, statuses, uncertainty, and local references.
-
-Do not put raw private applications, CVs, letters, reviewer identities,
-contact details, protected attributes, or source-document text in inputs,
-outputs, logs, examples, or prompts. Keep source content in the authorized
-records system and use opaque local references.
-
-Allowed classifications are:
-
-- `synthetic`
-- `public_scholarly_work`
-- `deidentified_low_stakes`
-
-No script searches the web, loads environment files, reads credentials, calls a
-model, executes supplied text, deserializes executable objects, or launches a
-process.
-
-Use Bash only to invoke the documented local `python3` commands.
-
-## Workflow
-
-### 1. Confirm allowed use and authorization
-
-Record:
-
-- developmental purpose;
-- unit of assessment: `scholarly_work`;
-- work type, stage, discipline, language, and audience;
-- authorized source location and data classification;
-- accountable committee owner;
-- conflicts and recusals;
-- accessibility and accommodation process;
-- appeal or correction route; and
-- data purpose, access, retention, and deletion.
-
-Stop on a prohibited decision context or unnecessary private data.
-
-### 2. Define the construct before criteria
-
-State:
-
-- what quality or support is being examined;
-- excluded constructs;
-- intended interpretation;
-- contexts where the interpretation does not travel;
-- evidence requirements; and
-- known limitations.
-
-Start with values and disciplinary context, not available metrics.
-
-### 3. Adapt and validate the rubric
-
-Begin with `assets/rubric_template.json`, then obtain qualified disciplinary,
-assessment-methods, stakeholder, accessibility, privacy, and fairness review.
-
-The template deliberately records content validity as `not_established`.
-Do not change that status without documented evidence for the exact intended
-use.
-
-Validate structure:
-
-```bash
-PYTHONDONTWRITEBYTECODE=1 python3 scripts/validate_rubric.py \
-  --rubric assets/rubric_template.json
-```
-
-Read `references/evaluation_framework.md` for construct, anchor, validity, and
-rater guidance.
-
-### 4. Build traceable evidence records
-
-Reviewers may read an authorized work outside the scripts. Record only stable
-local locators and claim references in
-`assets/evidence_manifest_template.json`.
-
-For every criterion, distinguish:
-
-- observed evidence from interpretation;
-- supporting from contrary evidence;
-- available from unavailable evidence;
-- `missing` from `not_applicable`; and
-- uncertainty from absence.
-
-Failure to find prior work does not prove novelty.
-
-### 5. Rate independently
-
-Use `assets/evaluation_template.json`. Each criterion must be:
-
-- `rated` with an anchor score, bounded uncertainty, evidence IDs, and a local
-  rationale reference;
-- `missing` with null score/uncertainty and a rationale reference; or
-- `not_applicable` with null score/uncertainty and a rationale reference.
-
-Do not encode missing or not-applicable as zero. Raters should train, calibrate,
-disclose conflicts, rate independently, and document disagreement.
-
-### 6. Run local quality checks
-
-Bounded scoring, without labels or recommendation:
-
-```bash
-PYTHONDONTWRITEBYTECODE=1 python3 scripts/calculate_scores.py \
-  --rubric assets/rubric_template.json \
-  --evaluation assets/evaluation_template.json
-```
-
-Evidence traceability:
-
-```bash
-PYTHONDONTWRITEBYTECODE=1 python3 scripts/check_traceability.py \
-  --rubric assets/rubric_template.json \
-  --evaluation assets/evaluation_template.json \
-  --evidence assets/evidence_manifest_template.json
-```
-
-Inter-rater agreement:
-
-```bash
-PYTHONDONTWRITEBYTECODE=1 python3 scripts/summarize_agreement.py \
-  --rubric assets/rubric_template.json \
-  --ratings assets/ratings_template.csv
-```
-
-Weight sensitivity requires two or more distinct scholarly-work evaluation
-files:
-
-```bash
-PYTHONDONTWRITEBYTECODE=1 python3 scripts/weight_sensitivity.py \
-  --rubric assets/rubric_template.json \
-  --evaluation /tmp/work-a-evaluation.json \
-  --evaluation /tmp/work-b-evaluation.json
-```
-
-Process controls:
-
-```bash
-PYTHONDONTWRITEBYTECODE=1 python3 scripts/check_process.py \
-  --process assets/process_checklist_template.json
-```
-
-The checklist template is intentionally unconfirmed and fails closed.
-Instructions and exact schemas are in `references/local_tooling.md`.
-
-### 7. Synthesize qualitative findings
-
-Lead with criterion-level evidence, not the composite. For each criterion:
-
-1. cite evidence references;
-2. state `rated`, `missing`, or `not_applicable`;
-3. explain the anchor interpretation;
-4. report score and uncertainty only if rated;
-5. note disagreements and context;
-6. identify strengths and limitations; and
-7. offer non-prescriptive improvement options.
-
-Generate an empty-reference scaffold if useful:
-
-```bash
-PYTHONDONTWRITEBYTECODE=1 python3 scripts/generate_report_scaffold.py \
-  --rubric assets/rubric_template.json \
-  --evaluation assets/evaluation_template.json \
-  --output /tmp/developmental-report-scaffold.json
-```
-
-The scaffold does not read source documents or draft findings.
-
-### 8. Human review and release
-
-Before releasing an organizational report, a qualified accountable human
-committee must verify:
-
-- construct and rubric provenance;
-- content-validity evidence and limits;
-- rater training, agreement, inter-rater reliability evidence, and drift;
-- evidence traceability and source access;
-- missingness, not-applicable rationales, and uncertainty;
-- weight sensitivity and order instability;
-- disciplinary and subgroup bias review;
-- conflicts and recusals;
-- accessibility and accommodations;
-- privacy, minimization, retention, and output controls; and
-- correction or appeal information.
-
-Document dissent. Do not imply consensus, validity, or precision beyond the
-evidence. Periodically evaluate the evaluation and retire harmful criteria.
-
-## Interpretation rules
-
-- A score is an ordinal rubric summary, not a natural measurement.
-- Normalization does not repair incomplete evidence.
-- The bundled uncertainty range is not a confidence interval.
-- Agreement does not establish reliability, validity, fairness, or correctness.
-- Stable results under tested weights do not establish validity.
-- The overall score never overrides criterion evidence or qualified judgment.
-- No output is a decision recommendation.
-
-## Bundled resources
-
-- `references/responsible_assessment.md` — safety, metrics, governance,
-  accessibility, privacy, and bias.
-- `references/evaluation_framework.md` — ScholarEval boundary, construct,
-  criteria, anchors, validity, and interpretation.
-- `references/local_tooling.md` — strict schemas, formulas, commands, and
-  output behavior.
-- `references/source_ledger.md` — authoritative sources and publication-status
-  verification dated 2026-07-23.
-- `references/security_validation.md` — baseline remediation, validation, and
-  residual security-scan record.
-- `assets/rubric_template.json` — bounded rubric template.
-- `assets/evaluation_template.json` — rating template.
-- `assets/evidence_manifest_template.json` — traceability template.
-- `assets/process_checklist_template.json` — fail-closed process checklist.
-- `assets/ratings_template.csv` — synthetic agreement data.