wotann 0.5.81 → 0.5.84

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "wotann",
-  "version": "0.5.81",
+  "version": "0.5.84",
   "description": "WOTANN — The All-Father of AI Agent Harnesses",
   "type": "module",
   "main": "dist/index.js",
@@ -62,7 +62,6 @@
     "tokens:check": "node scripts/generate-tokens.mjs --check",
     "sounds:generate": "node scripts/generate-sound-cues.mjs",
     "sounds:check": "node scripts/generate-sound-cues.mjs --check-only",
-    "prepare": "node scripts/build-typescript.mjs && chmod +x dist/index.js",
     "prepublishOnly": "npm run build:clean",
     "postinstall": "node -e \"try { require('node:fs').chmodSync('dist/index.js', 0o755); } catch {}\"",
     "wotann": "tsx src/index.ts",

package/skills/scientific/LICENSE.md

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 K-Dense Inc.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

package/skills/scientific/adaptyv/SKILL.md

@@ -0,0 +1,211 @@
+---
+name: adaptyv
+author: "K-Dense, Inc."
+description: "How to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieval. Use this skill whenever the user mentions Adaptyv, Foundry API, protein binding assays, protein screening experiments, BLI/SPR assays, thermostability assays, or wants to submit protein sequences for experimental characterization. Also trigger when code imports `adaptyv`, `adaptyv_sdk`, or `FoundryClient`, or references `foundry-api-public.adaptyvbio.com`."
+---
+
+# Adaptyv Bio Foundry API
+
+Adaptyv Bio is a cloud lab that turns protein sequences into experimental data. Users submit amino acid sequences via API or UI; Adaptyv's automated lab runs assays (binding, thermostability, expression, fluorescence) and delivers results in ~21 days.
+
+## Quick Start
+
+**Base URL:** `https://foundry-api-public.adaptyvbio.com/api/v1`
+
+**Authentication:** Bearer token in the `Authorization` header. Tokens are obtained from [foundry.adaptyvbio.com](https://foundry.adaptyvbio.com/) sidebar.
+
+When writing code, always read the API key from the environment variable `ADAPTYV_API_KEY` or from a `.env` file — never hardcode tokens. Check for a `.env` file in the project root first; if one exists, use a library like `python-dotenv` to load it.
+
+```bash
+export FOUNDRY_API_TOKEN="abs0_..."
+curl https://foundry-api-public.adaptyvbio.com/api/v1/targets?limit=3 \
+  -H "Authorization: Bearer $FOUNDRY_API_TOKEN"
+```
+
+Every request except `GET /openapi.json` requires authentication. Store tokens in environment variables or `.env` files — never commit them to source control.
+
+## Python SDK
+
+Install: `uv add adaptyv-sdk` (falls back to `uv pip install adaptyv-sdk` if no `pyproject.toml` exists)
+
+**Environment variables** (set in shell or `.env` file):
+```bash
+ADAPTYV_API_KEY=your_api_key
+ADAPTYV_API_URL=https://foundry-api-public.adaptyvbio.com/api/v1
+```
+
+### Decorator Pattern
+
+```python
+from adaptyv import lab
+
+@lab.experiment(target="PD-L1", experiment_type="screening", method="bli")
+def design_binders():
+    return {"design_a": "MVKVGVNG...", "design_b": "MKVLVAG..."}
+
+result = design_binders()
+print(f"Experiment: {result.experiment_url}")
+```
+
+### Client Pattern
+
+```python
+from adaptyv import FoundryClient
+
+client = FoundryClient(api_key="...", base_url="https://foundry-api-public.adaptyvbio.com/api/v1")
+
+# Browse targets
+targets = client.targets.list(search="EGFR", selfservice_only=True)
+
+# Estimate cost
+estimate = client.experiments.cost_estimate({
+    "experiment_spec": {
+        "experiment_type": "screening",
+        "method": "bli",
+        "target_id": "target-uuid",
+        "sequences": {"seq1": "EVQLVESGGGLVQ..."},
+        "n_replicates": 3
+    }
+})
+
+# Create and submit
+exp = client.experiments.create({...})
+client.experiments.submit(exp.experiment_id)
+
+# Later: retrieve results
+results = client.experiments.get_results(exp.experiment_id)
+```
+
+## Experiment Types
+
+| Type | Method | Measures | Requires Target |
+|---|---|---|---|
+| `affinity` | `bli` or `spr` | KD, kon, koff kinetics | Yes |
+| `screening` | `bli` or `spr` | Yes/no binding | Yes |
+| `thermostability` | — | Melting temperature (Tm) | No |
+| `expression` | — | Expression yield | No |
+| `fluorescence` | — | Fluorescence intensity | No |
+
+## Experiment Lifecycle
+
+```
+Draft → WaitingForConfirmation → QuoteSent → WaitingForMaterials → InQueue → InProduction → DataAnalysis → InReview → Done
+```
+
+| Status | Who Acts | Description |
+|---|---|---|
+| `Draft` | You | Editable, no cost commitment |
+| `WaitingForConfirmation` | Adaptyv | Under review, quote being prepared |
+| `QuoteSent` | You | Review and confirm the quote |
+| `WaitingForMaterials` | Adaptyv | Gene fragments and target ordered |
+| `InQueue` | Adaptyv | Materials arrived, queued for lab |
+| `InProduction` | Adaptyv | Assay running |
+| `DataAnalysis` | Adaptyv | Raw data processing and QC |
+| `InReview` | Adaptyv | Final validation |
+| `Done` | You | Results available |
+| `Canceled` | Either | Experiment canceled |
+
+The `results_status` field on an experiment tracks: `none`, `partial`, or `all`.
+
+## Common Workflows
+
+### 1. Submit a Binding Screen (Step by Step)
+
+```python
+# 1. Find a target
+targets = client.targets.list(search="EGFR", selfservice_only=True)
+target_id = targets.items[0].id
+
+# 2. Preview cost
+estimate = client.experiments.cost_estimate({
+    "experiment_spec": {
+        "experiment_type": "screening",
+        "method": "bli",
+        "target_id": target_id,
+        "sequences": {"seq1": "EVQLVESGGGLVQ...", "seq2": "MKVLVAG..."},
+        "n_replicates": 3
+    }
+})
+
+# 3. Create experiment (starts as Draft)
+exp = client.experiments.create({
+    "name": "EGFR binder screen batch 1",
+    "experiment_spec": {
+        "experiment_type": "screening",
+        "method": "bli",
+        "target_id": target_id,
+        "sequences": {"seq1": "EVQLVESGGGLVQ...", "seq2": "MKVLVAG..."},
+        "n_replicates": 3
+    }
+})
+
+# 4. Submit for review
+client.experiments.submit(exp.experiment_id)
+
+# 5. Poll or use webhooks until Done
+# 6. Retrieve results
+results = client.experiments.get_results(exp.experiment_id)
+```
+
+### 2. Automated Pipeline (Skip Draft + Auto-Accept Quote)
+
+```python
+exp = client.experiments.create({
+    "name": "Auto pipeline run",
+    "experiment_spec": {...},
+    "skip_draft": True,
+    "auto_accept_quote": True,
+    "webhook_url": "https://my-server.com/webhook"
+})
+# Webhook fires on each status transition; poll or wait for Done
+```
+
+### 3. Using Webhooks
+
+Pass `webhook_url` when creating an experiment. Adaptyv POSTs to that URL on every status transition with the experiment ID, previous status, and new status.
+
+## Sequences
+
+- Simple format: `{"seq1": "EVQLVESGGGLVQPGGSLRLSCAAS"}`
+- Rich format: `{"seq1": {"aa_string": "EVQLVESGGGLVQ...", "control": false, "metadata": {"type": "scfv"}}}`
+- Multi-chain: use colon separator — `"MVLS:EVQL"`
+- Valid amino acids: A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y (case-insensitive, stored uppercase)
+- Sequences can only be added to experiments in `Draft` status
+
+## Filtering, Sorting, and Pagination
+
+All list endpoints support pagination (`limit` 1-100, default 50; `offset`), search (free-text on name fields), and sorting.
+
+**Filtering** uses s-expression syntax via the `filter` query parameter:
+- Comparison: `eq(field,value)`, `neq`, `gt`, `gte`, `lt`, `lte`, `contains(field,substring)`
+- Range/set: `between(field,lo,hi)`, `in(field,v1,v2,...)`
+- Logic: `and(expr1,expr2,...)`, `or(...)`, `not(expr)`
+- Null: `is_null(field)`, `is_not_null(field)`
+- JSONB: `at(field,key)` — e.g., `eq(at(metadata,score),42)`
+- Cast: `float()`, `int()`, `text()`, `timestamp()`, `date()`
+
+**Sorting** uses `asc(field)` or `desc(field)`, comma-separated (max 8):
+```
+sort=desc(created_at),asc(name)
+```
+
+**Example:** `filter=and(gte(created_at,2026-01-01),eq(status,done))`
+
+## Error Handling
+
+All errors return:
+```json
+{
+  "error": "Human-readable description",
+  "request_id": "req_019462a4-b1c2-7def-8901-23456789abcd"
+}
+```
+The `request_id` is also in the `x-request-id` response header — include it when contacting support.
+
+## Token Management
+
+Tokens use Biscuit-based cryptographic attenuation. You can create restricted tokens scoped by organization, resource type, actions (read/create/update), and expiry via `POST /tokens/attenuate`. Revoking a token (`POST /tokens/revoke`) revokes it and all its descendants.
+
+## Detailed API Reference
+
+For the full list of all 32 endpoints with request/response schemas, read `references/api-endpoints.md`.