toolkit-skills

A collection of Claude Code skills for research software development workflows, with a focus on MC2 Center tooling and the Software Gardening Almanack.

Skills

Skills live in .claude/skills/ and are available in any Claude Code session run from this repo. You can also copy them to ~/.claude/skills/ to use them across all your projects.

General dev workflow

Skill	Description	Invocation
commit	Create Conventional Commits from staged/unstaged changes	/commit
review-pr	Review a pull request for correctness, security, and test coverage	/review-pr <pr-number>
fix-issue	Fix a GitHub issue end-to-end (read → implement → test → commit)	/fix-issue <issue-number>

Research software quality

Skill	Description	Invocation
assess-repo	Full sustainability report for any GitHub repo — almanack + JOSS + weighted score + prioritized action items	/assess-repo <github-url> or automatic
improve-repo	Fork a repo, make real engineering improvements (refactoring, tests, CI, docs), show before/after score, and offer to open a PR	/improve-repo <github-url>
almanack-check	Run a Software Gardening Almanack sustainability assessment	/almanack-check <repo> or automatic
joss-review	Assess a repository against JOSS submission criteria	/joss-review <repo> or automatic
notebook-review	Review a Jupyter notebook for reproducibility and clarity	/notebook-review <path> or automatic

CCKP benchmark analysis (for the Bioinformatics paper)

These skills operate on the local ~/cckp-toolkit-workflow/ dataset (956 tools across 10 bioinformatics domains).

Skill	Description	Invocation
almanack-weights	Compute weighted almanack scores using nf-core as gold standard; produces sensitivity analysis for paper	/almanack-weights [output-dir] or automatic
software-deadness	Analyze "dead" software (no commits 2+ years); alive vs dead score comparison, longevity predictors	/software-deadness [output-dir] or automatic
domain-distribution	Star-filtered (≥5) within-domain distribution analysis; tests the 0.1 score threshold hypothesis	/domain-distribution [min-stars] [output-dir] or automatic

Usage

Invoke a skill directly using its slash command:

/almanack-check https://github.com/mc2-center/cckp-toolkit-workflow
/joss-review ./my-research-tool
/commit

Let Claude invoke skills automatically — skills with no disable-model-invocation set will be loaded by Claude when relevant. For example, if you ask "does this repo meet JOSS standards?", Claude will use the joss-review skill automatically.

Skills marked with disable-model-invocation: true (like /commit, /review-pr, /fix-issue) only run when you explicitly invoke them — they have side effects you should control.

Installation

As a plugin

If Claude Code supports your plugin directory, install directly from GitHub:

/plugin install toolkit-skills@mc2-center

Or clone and reference locally:

claude --plugin-dir ./toolkit-skills

Manual (copy skills to your home directory)

cp -r .claude/skills/* ~/.claude/skills/

GitHub MCP server (recommended)

The skills work better with the GitHub MCP server — assess-repo can check files without cloning, improve-repo can create PRs via the API, and review-pr gets richer diff context.

The .mcp.json in this repo configures it automatically. You'll need a GitHub token:

export GITHUB_TOKEN=ghp_...
npx -y @modelcontextprotocol/server-github  # installs the server

Related projects

• mc2-center/cckp-toolkit-workflow — Nextflow pipeline for batch repository quality assessment
• software-gardening/almanack — Python package and handbook for sustainable software development