skill-authoring

name	skill-authoring
description	Create or update a Codex skill that packages reusable workflows, references, scripts, and assets for repeated tasks. Use when turning notebooks, tutorials, analyses, or domain procedures into a triggerable local skill for other agents, or when deciding whether a notebook subset or branch should update an existing skill instead of creating a duplicate one.

Skill Creator

Create skills that are short, reusable, and biased toward execution.

Core Rules

1. Optimize for another agent using the skill, not for a human reading documentation.
2. Keep SKILL.md small. Put details into references/, deterministic logic into scripts/, and templates into assets/.
3. Put trigger conditions in frontmatter description, not in the body.
4. Prefer procedures and selection rules over long explanations.
5. Source-ground every interface-specific claim against real code, help(...), or -h/--help before writing it into the skill.
6. Include only information another agent is unlikely to infer reliably from general knowledge.
7. Default to capability-first naming. Do not let a sample dataset, species, notebook title, or one published figure become the skill identity unless the workflow is truly specific to that artifact.
8. In generated skill documentation, prefer repo-relative paths or import paths. Do not bake local absolute source-code paths from one machine into SKILL.md or references/.
9. Keep reusable skill content environment-agnostic. Do not encode local environment names such as omictest into SKILL.md or references/; if local validation depends on them, keep that only in the review harness, acceptance harness, or calling prompt.
10. Treat local validation configuration as review-harness data, not as part of the reusable skill itself.
11. Do not generate a scripts/ directory by default. Add scripts only when they carry reusable deterministic logic or a necessary bounded smoke utility that would otherwise make the skill less reliable.

Skill Shape

Each skill should follow this structure:

skill-name/
├── SKILL.md
├── scripts/        # executable helpers for repeated or fragile steps
├── references/     # selectively loaded reference material
└── assets/         # templates, starter files, static resources

Use only the folders that are needed. Do not add extra docs like README.md, CHANGELOG.md, or process notes.

What Belongs Where

Put in SKILL.md

• Skill purpose
• Triggering scope
• The minimum workflow another agent should follow
• Selection rules for which reference or script to use
• Constraints, assumptions, and validation requirements

Put in references/

• API notes
• domain conventions
• notebook-specific biological background
• long examples
• parameter tables

Put in scripts/

• notebook extraction helpers
• format conversion
• deterministic preprocessing
• repeated analysis setup
• validation utilities

Put in assets/

• starter notebooks
• report templates
• plotting styles
• canned config files

Do not treat reviewer-only local execution settings as normal skill content. Machine-specific interpreter paths, local cache locations, and one-user environment bootstrapping belong in the local review harness or the calling prompt, not in the reusable skill body.

Writing Frontmatter

Frontmatter should contain only:

---
name: skill-name
description: What the skill does and when to use it.
---

Write the description so the agent can trigger the skill correctly from user intent alone.

Good description properties:

• names the task
• names the artifacts involved
• names the situations that should trigger the skill
• includes common synonyms users may say

Writing the Body

Use imperative instructions. Assume the reader is a capable coding agent with limited context.

Prefer this body structure:

# Skill Name

## Goal

One short paragraph.

## Quick Workflow

1. Inspect the source artifacts.
2. Select the relevant reference or script.
3. Execute the transformation.
4. Validate the output.

## Resource Map

- Read `references/x.md` when ...
- Run `scripts/y.py` when ...

## Constraints

- Keep ...
- Avoid ...

## Validation

- Check ...
- Compare ...

Notebook To Skill Workflow

Use this workflow when the source material is an ipynb tutorial.

Step 1: Identify the reusable task

Extract the repeated capability behind the notebook, not the notebook itself.

Examples:

• "fit a vector field on dynamo tutorial data"
• "run Jacobian / acceleration / curvature analysis on a simulated motif"
• "preprocess AnnData and prepare layers for downstream dynamo analysis"

If a notebook mixes several capabilities, split them into separate skills or into one skill with clearly separated references.

Step 1.1: Reuse existing skills before creating a new one

Check whether the notebook is:

• a subset of an existing skill
• a branch of an existing skill
• a downstream stage that can extend an existing skill cleanly
• a presentation or validation layer on top of an existing skill

If so, prefer updating the existing skill over creating a duplicate skill.

Use a new skill only when the notebook introduces a stable, independently triggerable job with a different input contract, backend, or compute profile.

When reusing an existing skill:

• preserve the existing trigger surface unless it is wrong
• add the new branch or subset as a clearly named selection rule or reference note
• avoid copying the same execution spine into a second skill
• move notebook-specific deltas into references/ or assets/acceptance.json

Step 1.2: Partition notebook capabilities before writing anything

Before drafting a skill, write a capability partition for the notebook:

• core executable job
• optional downstream analysis jobs
• optional visualization or reporting jobs
• notebook-only pedagogy or presentation material

Treat this partition as mandatory for complex notebooks. Do not skip directly from "read notebook" to "write one big skill".

Good partition examples:

• preprocessing
• model fitting
• downstream interpretation
• visualization / export

Step 1.3: Decide whether this should be one skill or several

Default to splitting when the notebook contains multiple stable jobs that users could request independently.

Split into multiple skills when at least one of these is true:

• a stage can be triggered by a realistic user request without the earlier stages
• a stage has a different input contract from the earlier stage
• a stage is mostly visualization, export, or reporting on top of an already-computed result
• a stage introduces a different model family, backend, or compute profile
• a stage would significantly bloat SKILL.md or trigger language if kept in the same skill

Keep one skill only when most of these are true:

• the stages share one tight input contract
• the user usually wants the stages together as one job
• the later stages are not independently useful without the earlier outputs
• splitting would create thin wrapper skills with little standalone value

If you keep one skill for a broad notebook, the body must still expose the partition clearly with stage selection rules. Do not hide multiple jobs behind a single "run the workflow" instruction.

If the notebook is mostly a subset, branch, or variant of an existing skill, treat that as a reuse signal first, not a split signal. The default move is to update the existing skill with the new branch rules and validation, then only split when the new work is independently triggerable and materially different.

Step 1.5: Choose the right abstraction level

Before naming the skill, separate three layers explicitly:

• stable job or analysis family
• data modality or input contract
• worked example dataset, species, or notebook title

In almost all cases:

• use the stable job as the skill identity
• use the data modality as a constraint or scope note
• demote the worked example to references/, validation, or an example section

Prefer names like:

• dynamo-conventional-rna-velocity
• dynamo-vector-field-analysis
• gene-id-conversion

Avoid names like:

• zebrafish-workflow
• figure-2-pipeline
• tutorial-200-skill

Only keep the example dataset or species in the skill name when changing the example would materially break the workflow or invalidate the interpretation.

Step 2: Separate stable logic from tutorial narration

Classify notebook content into four buckets:

• reusable procedure
• required biological or domain assumptions
• one-off exposition or teaching text
• display-only output

Only the first two usually belong in the skill.

For complex notebooks, apply this bucketization per partitioned capability, not just once across the whole notebook.

Step 3: Extract the execution spine

The skill should preserve the minimal sequence another agent must reproduce:

1. input assumptions
2. required imports and data shape expectations
3. preprocessing
4. core analysis calls
5. postprocessing or storage conventions
6. validation checks

Do not copy the notebook cell-by-cell unless the exact order is fragile and necessary.

Step 3.5: Inspect the real callable interface before documenting it

If the notebook relies on concrete functions, methods, classes, or CLIs, inspect the live interface before writing the skill:

1. read the source or run help(...)
2. capture inspect.signature(...) and parameter defaults
3. extract parameter-level doc details when available
4. detect branch-like parameters such as method, backend, or mode
5. inspect if / match branches so notebook coverage does not hide unmentioned features

If the target is importable Python code, run scripts/inspect_python_interface.py. If the target is a command-line tool, inspect -h or --help.

Step 4: Move long notebook context out of SKILL.md

Use references/ for:

• mathematical background
• motif-specific explanations
• differences between old and new APIs
• alternative branches in the tutorial
• expected figures and interpretation notes

Path rule:

• use repo-relative paths like docs/tutorials/notebooks/200_zebrafish.ipynb
• or import paths like dynamo.preprocessing.Preprocessor
• do not record machine-specific absolute paths like /Users/alice/.../dynamo/preprocessing/Preprocessor.py in generated skill docs
• if local review needs a concrete interpreter such as python_path, keep that in the local review harness, scorer workflow, or calling prompt rather than promoting it into the reusable skill
• if a repository-level acceptance harness needs a named environment, keep that requirement in the local harness rather than treating it as part of the reusable skill contract

Use scripts/ only when one of these is true:

• the skill needs a reusable deterministic helper that another agent would otherwise have to retype or reconstruct repeatedly
• the skill needs a compatibility shim, extractor, or interface inspection helper that stabilizes execution across requests
• the repository needs a bounded smoke utility for acceptance or reviewer-side empirical validation

Do not use scripts/ for:

• short code snippets that already fit cleanly in SKILL.md
• notebook-specific narration or one-off exposition
• local environment bootstrapping, interpreter selection, or cache setup that belongs in the review harness
• worked-example-only logic unless the script is explicitly marked as a local smoke or example utility

If a script depends on a worked example dataset, notebook-specific labels, or fixed genes:

• name it as a smoke, example, or validation utility
• keep it out of the main trigger surface
• explain that it validates the workflow on one bounded example, not that it defines the reusable skill contract

Step 5: Encode trigger language from how users actually ask

For notebook-derived skills, descriptions should include both the task and the artifact style.

Examples:

• "Use when converting a dynamo tutorial or analysis notebook into a reusable execution workflow."
• "Use when an agent needs to run the mixture-of-gaussian simulation, compute analytical Jacobian-derived quantities, or reconcile old tutorial API names with current dynamo code."

Default trigger-writing rule:

• lead with the capability
• include the data modality or artifact style only if it narrows execution meaningfully
• mention the source notebook or example dataset as adaptation context, not as the main trigger surface

Good:

• "Run or adapt a conventional spliced/unspliced RNA velocity workflow in dynamo. Use when analyzing conventional scRNA-seq AnnData, reproducing a related tutorial, or selecting between preprocessing, kinetics, vector-field, and fate stages."

Weak:

• "Run the zebrafish notebook."

Weak because it triggers on a worked example, not on the stable job another agent actually needs.

Step 6: Add compatibility notes only when they unblock execution

Notebook-based skills often need a short compatibility section for drift such as:

• renamed functions
• removed parameters
• changed motif names
• old plotting keys
• old embedding slots

Keep this compact. Put full migration details into references/compatibility.md.

Step 7: Validate against a fresh execution path

Before finalizing the skill, confirm that another agent could execute the workflow without relying on the original notebook narrative.

Validation should check:

• the skill can be triggered from a realistic user request
• the core workflow can be followed without opening the full notebook unless necessary
• references are actually sufficient
• scripts run or are at least structurally correct
• output names and storage locations are explicit
• function signatures, defaults, doc-derived constraints, and branch options were checked against the live interface
• the skill still makes sense if the original example dataset or species name is removed from the user request
• the reusable skill is not secretly coupled to one reviewer's local interpreter path or machine setup
• any generated script is either a reusable helper or a clearly labeled bounded smoke utility, not notebook residue copied into a file

Step 7.2: Handle long-running or GPU-heavy notebooks pragmatically

Do not block skill generation on a full end-to-end run when the notebook's main path is expensive, GPU-bound, or training-heavy.

For these notebooks, validate the reusable execution spine with a representative smoke path instead:

• import and construct the main model or trainer successfully
• run one small fixture, one batch, one step, or one short epoch
• confirm the key branch parameters reach the intended code path
• confirm expected output schema, checkpoint keys, or artifact names
• document any full-scale prerequisites such as GPU, long wall-clock time, or large datasets

Do not pretend a representative smoke is a full reproduction. State clearly when:

• full training was not run
• final quality metrics were not reproduced
• GPU or long-duration execution is still required for the real workload

Step 7.3: Use a bounded validation budget

Use a default local validation budget unless the user explicitly asks for a full expensive run.

Recommended default budget:

• aim for a representative validation path that finishes within roughly 10 minutes wall-clock
• prefer much shorter checks when a smaller smoke path can validate the same execution contract
• if the notebook exceeds that budget, downshift to a smaller fixture, fewer steps, smaller model, or partial stage check

Only exceed the default budget when:

• the user explicitly wants a full run
• the shorter smoke path would fail to validate the core execution contract

Step 7.4: Declare validation_budget in acceptance.json

Every acceptance.json must include a validation_budget block that encodes the cost profile and enforcement rules. This is machine-readable: run_skill_acceptance.py uses it to stop runaway smoke runs.

Schema:

"validation_budget": {
  "smoke_mode": "full",
  "max_wall_seconds": 300,
  "skip_reason": ""
}

Fields:

• smoke_mode: one of "full" | "import_only" | "skip"
  • "full": run all smoke commands (default)
  • "import_only": only run smoke commands tagged with "tier": "import"; skip all others
  • "skip": skip all smoke commands entirely; skip_reason must be non-empty
• max_wall_seconds: aggregate wall-clock cap across all smoke commands; remaining commands are skipped once the cap is reached
• skip_reason: required when smoke_mode is "skip"; state why empirical validation is not feasible (e.g. GPU required, requires 1 TB dataset)

For individual smoke commands, add an optional "tier" field:

• "tier": "import": lightweight import or constructor check; runs in both "full" and "import_only" modes
• "tier": "full" (default if omitted): full smoke; only runs in "full" mode

Cost-profile decision rules:

Notebook cost	smoke_mode	max_wall_seconds	Notes
Cheap (< 2 min total)	"full"	omit or 300	Normal path
Moderate (2–5 min total)	"full"	300	Cap aggregate time
Expensive (> 5 min, no GPU)	"import_only"	120	Write at least one tier: "import" command
GPU-required or infeasible	"skip"	omit	Provide skip_reason

When smoke_mode is "import_only", write at least one smoke command with "tier": "import" that validates imports, constructor calls, and interface availability without running real computation.

Step 7.5: Run an anti-overfitting check

Before shipping the skill, ask these questions:

• If the user asked for the workflow without naming the tutorial dataset, would this skill still trigger?
• If the example dataset were replaced with another compatible dataset, would most of SKILL.md still hold?
• Are dataset-specific grouping columns, lineage labels, or plotting genes presented as defaults only because the notebook used them?

If any answer is "no", the skill is probably overfit to the notebook. Move the example-specific material into:

• references/source-notebook-map.md
• references/compatibility.md
• a worked example section
• acceptance smoke commands

For local validation settings, move them even further out:

• the calling prompt
• the local scorer or reviewer workflow
• a repository-level harness that is explicitly marked as local-only

For long-running workflows, also move these out of the reusable skill body when possible:

• batch-size reductions used only for local smoke checks
• one-step or one-epoch validation shortcuts
• local GPU / CUDA assumptions

Design Heuristics For ipynb-Derived Skills

Prefer one skill per stable job. Do not build a single skill that tries to cover every notebook in a project.

Good candidates for one skill:

• a repeated simulation workflow
• one analysis family
• one plotting/reporting pipeline
• one data ingestion pattern
• one stable modality-constrained workflow with multiple example datasets
• one tightly coupled end-to-end job whose later stages are not independently triggerable

Bad candidates:

• an entire tutorial collection with unrelated goals
• a notebook whose value is mostly pedagogy rather than reusable execution
• a workflow that depends heavily on interactive interpretation at every step
• a skill whose name and trigger language are mostly the name of one sample dataset
• a notebook that really contains multiple independently triggerable jobs but was compressed into one broad skill

Recommended Deliverables For Notebook Conversion

When converting a notebook into a skill, aim for:

1. SKILL.md with the distilled workflow
2. references/source-notebook-map.md mapping notebook sections to skill resources
3. references/source-grounding.md summarizing signature/docstring/source inspection for critical interfaces
4. references/compatibility.md for API drift, if needed
5. scripts/ helpers for repeated extraction or setup, if needed
6. assets/acceptance.json with sample requests, required sections, required terms, optional smoke commands, and a validation_budget block declaring smoke_mode and max_wall_seconds
7. optional additional assets/ templates only if they save substantial repeated effort

If the notebook is a subset or branch of an existing skill, update that existing skill's deliverables instead of creating a parallel duplicate set unless the new job truly needs a new trigger surface.

Resource Map

• Read references/source-grounding.md when the skill documents concrete function signatures, defaults, docstrings, or CLI flags.
• Run scripts/inspect_python_interface.py when a notebook depends on importable Python callables and branch-like parameters may hide unexercised behavior.

Review Checklist

Before finishing, check the skill against this list:

• Frontmatter uses only name and description
• Description is strong enough to trigger correctly
• SKILL.md is procedural and not tutorial-heavy
• Large details moved to references/
• scripts/ was added only when it materially improves reuse or bounded validation
• Any generated script is clearly a reusable helper or an explicitly labeled smoke / validation utility
• Worked-example-specific script logic is not presented as the core reusable workflow
• Critical function and CLI behavior was checked against source, help(...), or -h/--help
• Branch-like parameters such as method or backend were audited for unmentioned options
• The skill name and description describe the stable capability, not just the notebook example
• Example dataset, species, and notebook-title details were demoted out of the main trigger surface unless they are execution-critical
• A counterfactual request without the notebook's proper nouns would still trigger the skill correctly
• If the notebook is a subset or branch of an existing skill, the existing skill was updated instead of duplicated
• Complex notebooks were explicitly partitioned into capabilities before deciding whether to emit one skill or several
• Independently triggerable notebook stages were split unless there is a strong coupling reason not to
• SKILL.md and references/ do not depend on machine-specific absolute source paths
• assets/acceptance.json prefers environment names such as conda_env over machine-specific interpreter paths
• reviewer-only local validation configuration is not presented as if it were part of the reusable skill contract
• Old notebook API drift is captured where necessary
• Validation steps are explicit
• assets/acceptance.json encodes concrete acceptance checks beyond scoring
• assets/acceptance.json includes a validation_budget block with smoke_mode matching the notebook's cost profile
• Expensive or GPU-required notebooks use smoke_mode: "import_only" or "skip" with at least one tier: "import" smoke command or a non-empty skip_reason

Editing Existing Skills

When updating an existing skill:

1. Keep the existing trigger surface unless there is a clear triggering bug.
2. Remove duplicated explanations before adding new content.
3. Prefer tightening the workflow over expanding prose.
4. If the source notebook changed, update compatibility notes and resource mapping first.
5. Re-check whether the current description still matches what the skill actually does.