drug-discovery-prompts/upstream/K-Dense-AI-scientific-agent-skills/skills/hypogenic/references/configuration.md

title, task, lineage_type, upstream_source, upstream_sha, imported_at, prompt_class, upstream_changes, author, validated

title	task	lineage_type	upstream_source	upstream_sha	imported_at	prompt_class	upstream_changes	author	validated
Configuration		import	https://github.com/K-Dense-AI/scientific-agent-skills/blob/757b63b1/skills/hypogenic/references/configuration.md	757b63b1	2026-07-24	prompt	accepted	upstream	false

Configuration

Reviewed against hypogenic 0.3.5 and source commit 8c3800ccae155e333fac5b530afa8abdaac38300 on 2026-07-23.

Two schemas, two purposes

Do not merge these layers or imply that upstream enforces the local policy.

Upstream task config

hypogenic.tasks.BaseTask reads YAML with these fields:

• required: task_name, train_data_path, val_data_path, test_data_path, prompt_templates;
• optional: label_name (defaults to label) and ood_data_path;
• dataset paths are resolved relative to the config file;
• basic generation uses prompt templates named observations, batched_generation, and inference;
• adaptive and literature workflows need additional templates.

The exact prompt keys vary by workflow. Start from a config in the pinned dataset revision rather than inventing keys. The upstream config does not select a model/provider, store credentials, approve network access, impose token/cost caps, or redact logs.

assets/task_config.example.yaml demonstrates only the basic source shape. It is not a claim that an arbitrary task is ready to run.

Validate JSON task configs without dependencies:

python3 scripts/validate_config.py task --input task_config.json --root .

For YAML, use only the reviewed parser version:

uv run --with "pyyaml==6.0.2" \
  python scripts/validate_config.py task \
  --input task_config.yaml \
  --root . \
  --check-data-files

The loader uses yaml.SafeLoader, rejects duplicate keys, non-string mapping keys, aliases, anchors, explicit tags, non-JSON scalar types, excessive depth, and oversized files. Package help paths do not import PyYAML.

Local run policy

assets/run_config.example.json is a safety and reproducibility overlay used only by this skill's validator/planner. HypoGeniC does not read it.

Required sections:

• data: task config, dataset manifest, output directory, and locked test policy;
• provider: exact wrapper type, model, credential variable name, data destination, and local model path where applicable;
• limits: requests, per-request input/output tokens, total tokens, cost, concurrency, split sizes, and bank size;
• pricing: user-reviewed current token rates, review date, and source;
• execution: fixed to plan_only, no external authorization, separate confirmation required, and test split not sent;
• logging: INFO or higher, prompt/response redaction required, credential inclusion forbidden.

Provider mapping verified from the pinned source:

wrapper type	credential name	declared data destination
gpt	OPENAI_API_KEY	openai_api
claude	ANTHROPIC_API_KEY	anthropic_api
huggingface	none	local_process
vllm	none	local_process

For both local types, the policy requires a reviewed relative local_model_path. This is stricter than upstream: a model ID with no local path can trigger a Hub download. A local path does not by itself prove the artifact is trustworthy; record its source revision, license, hashes, and review status separately.

Credential rules

• Put only the environment variable name in config.
• Never put a credential value in YAML/JSON, source control, a prompt, a log, or a generated report.
• Do not load or search .env files. Do not traverse parent directories looking for secrets. Do not print a variable to prove it exists.
• --check-env reads only the validated provider-specific name and emits present: true/false; it never includes the value.
• Use project-scoped, least-privilege credentials and provider-side budget/rate controls. Rotate after suspected exposure.

python3 scripts/validate_config.py run \
  --input reviewed_run_config.json \
  --root . \
  --check-env \
  --check-paths

The command is local-only. Presence is not proof that the key has the desired project, retention, region, rate-limit, or spend policy.

Pricing and budget semantics

The example intentionally leaves prices null. Fill them only after reviewing the provider's current pricing page for the exact model and date. The planner computes:

max_requests × (
  max_input_tokens_per_request × input_rate +
  max_output_tokens_per_request × output_rate
) / 1,000,000

This is a conservative arithmetic bound, not tokenizer output. It excludes local compute, retries beyond the request cap, caching discounts, tiered pricing, storage, data transfer, taxes, and provider-specific features. The pinned upstream CLI has no hard dollar-budget enforcement; use provider-side limits as well.

Prompt templates are untrusted content

Prompt files can contain malicious or irrelevant instructions. The local validator checks structure only and never renders a template. During an approved run:

• delimit dataset/literature content as quoted data;
• instruct the model not to follow embedded instructions;
• do not allow prompt text to choose tools, providers, paths, or credentials;
• do not interpolate untrusted values into shell commands or Python code;
• keep test data out of generation and selection prompts.