Changelog

All notable changes to this project are documented here. The format follows Keep a Changelog and the project uses Semantic Versioning.

[Unreleased]

Added

• Eval suites for all 281 skills (evals/<skill>/evals.json): realistic prompts plus near misses naming the better skill. Suites for adapted skills were generated from each SKILL.md and are marked pending review.
• Import-time enrichment of adapted skills (tools/enrich.py): oversized skills split into references/, dead links repaired, category-specific agent operating procedures (environment check, small first run, validation, failure-recovery table, integrity rules) and computed related-skill handoffs.
• Trigger-rich description overrides for 84 adapted skills (third_party/description-overrides.yaml, generated by tools/generate_skill_data.py and validated).
• Offline smoke tests for every skill script: all 497 compile; 327 standard-library CLIs run --help on every CI OS (tests/test_skill_scripts_smoke.py).
• tools/trigger_bench.py --sample N --seed S for reproducible subsamples with the paid Claude router.

Changed

• Marketing residue (GitHub star counts, user numbers) is stripped from imported skills.
• The 500-line SKILL.md budget is now enforced for every skill (the size baseline is empty).
• Adapted-skill quality rose from a mean of 80.9 to 95.2. Claude-router trigger accuracy on a 100-prompt sample of all evals is hit@3 0.96 with no false triggers.

Fixed

• openpiv/run_example.py explains a missing dependency instead of raising a traceback.

[1.1.0] - 2026-10-01

Added

• unslop-academic-writing: removes AI slop from research prose (stock vocabulary, empty emphasis, hedge stacks, formulaic signposting, monotone rhythm) with a zero-dependency linter for Markdown, LaTeX, text and Word files.
• Skill verification tooling: static quality rubric (tools/skill_quality.py), trigger-routing benchmark (tools/trigger_bench.py, BM25 and Claude routers), with-vs-without-skill task benchmark with a blind judge (benchmarks/task_evals), labeled citation-verification benchmark and a human-vs-model slop benchmark.
• benchmarks.yml workflow: quality and routing gates on every PR, weekly citation benchmark, manual paid benchmarks.
• Documentation site restructure: getting started, guides (papers, theses, no-slop writing, systematic reviews, skills by field), reference (CLI, architecture, benchmarks, security, contributing), FAQ, JSON-LD metadata.
• Generated llms.txt for AI search engines and agents.
• .editorconfig, .pre-commit-config.yaml, Makefile, SUPPORT.md, GOVERNANCE.md.

Changed

• Repository moved to KalarisLabs/research-agent-skills; code owner @saynchowdhury.
• Journal-format and other original skills gained numbered workflows and explicit integrity rules.
• Sharper descriptions for cover-letter-to-editor and rebuttal-and-response-to-reviewers to prevent mis-triggering.

[1.0.0] - 2026-10-01

Added

• 278 agent skills across 19 categories: research writing, journal formats, literature review, ideation and design, data science, visualization, knowledge graphs and RAG, scientific databases, life sciences, chemistry, clinical research, physical sciences, lab automation, research automation and ML research engineering.
• 21 original skills, including journal formats (Nature Portfolio, Science, Cell Press, IEEE, ACM, Elsevier, Springer LNCS, PLOS, APA 7, arXiv), citation verification, BibTeX hygiene, systematic reviews (PRISMA 2020), reference-manager interop, paper-corpus RAG, research knowledge graphs, abstracts and titles, reviewer responses, cover letters, reproducibility statements and a research skill creator.
• research-agent-skills CLI: one-command install for Claude Code, Codex, Cursor, Gemini CLI, Copilot, OpenCode, Windsurf and .agents/skills harnesses, with checksum verification, integrity checks (doctor), update and uninstall.
• Standalone install.sh / install.ps1 installers with SHA-256 verification.
• Security CI: spec validation, prompt-injection lint, Cisco AI Defense skill-scanner, CodeQL, Semgrep, Bandit, TruffleHog, OSV/pip-audit/npm audit, zizmor, actionlint, OpenSSF Scorecard, signed releases with build provenance.

Fixed

• Windows console crashes (cp1252) in skill scripts that print non-ASCII text.
• experimental-design: fractional allocation ratios no longer silently drop an arm.
• analytical-method-validation: ragged CSV rows exit cleanly with code 2; JSON and CSV inputs are normalized identically.
• arbor: set-evidence validates status; node lists sort n1..n10 numerically.
• deeptools: BAM index detection no longer breaks when a parent directory contains .bam.
• Doubled uv uv pip install commands.