dunnlab-code

Plugin dunnlab-code from marketplace dunnlab in caseywdunn/dunnlab_code. Commands read from the repo's manifest — 14 days ago.

Skills (12)

• skill-audit

  Audit this repo's skills, summaries, and manual for competing mandates, contradictions, unclear instructions, and descriptions that drift from skill bodies. Use before a release or after changing skill boundaries.

• dunnlab-biblio

  Manage verified manuscript, data, and software citations with Dunn Lab BibTeX conventions and conservative editing of existing references.

• dunnlab-bioinformatics

  Design sequence, phylogenetic, annotation, and comparative analyses using Dunn Lab tool preferences, biological input checks, and identifier conventions. Use for bioinformatics method and tool choices; general workflow architecture belongs to dunnlab-workflow-design.

• dunnlab-codereview

  Code review checklist and process for Dunn Lab projects. Use when reviewing pull requests, auditing code quality, or giving feedback on scripts and analyses.

• dunnlab-coding-defaults

  Dunn Lab language, coding, dependency, testing, documentation, commit, and agent-instruction conventions. Use when writing or reviewing code, committing, or writing user-facing documentation or AGENTS.md. Workflow architecture belongs to dunnlab-workflow-design; repository scaffolding belongs to dun

• dunnlab-hpc

  YCRC HPC cluster reference for the Dunn Lab. Use when writing SLURM batch scripts, configuring job resources, managing storage, or running analyses or coding agents on Bouchet, McCleary, or Misha clusters. Covers partitions, storage, job scheduling, the Bouchet agent partition, and cluster-specific

• dunnlab-manuscript

  Set up, write, revise, and build Dunn Lab manuscripts: prose style, Quarto source in a -ms repository, results staged in the analysis repository and synced in, PDF and Word output, and co-author edits.

• dunnlab-new-project

  Scaffold a new Dunn Lab repository or fill missing project setup: source and test directories, environment, README, and agent instructions. Use for project initialization, not ongoing development or scientific lifecycle management.

• dunnlab-release-cycle

  Run a project on a release cycle: dev and issue branches, GitHub issues, dev_docs/PLAN.md with gates, CHANGELOG, and the release ritual. Use when setting up releases, working through a planned release, or cutting one.

• dunnlab-research-lifecycle

  Plan, explore, distill, and validate scientific analyses, preserving the decisions and evidence behind reported results. Use when organizing research, selecting analyses for a deliverable, or assessing scientific readiness and handoff. Workflow architecture belongs to dunnlab-workflow-design.

• dunnlab-specimens

  Manage field-collected specimen and sample metadata with provenance: identifiers, vouchers, tubes, collecting data, taxonomy, and crosswalks among YPM/LUX, GBIF, iNaturalist, SRA/ENA, and lab records. Use when ingesting, curating, validating, or depositing specimen data.

• dunnlab-workflow-design

  Design or revise computational analysis workflows in any discipline, from exploratory runs to reproducible results, with explicit data flow, reusable computation, and traceable execution.

Slash commands (1)

• /dunnlab-code:dunnlab-check

  Verify that the dunnlab_code plugin is loaded and list available skills

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