@pikaa-ai/pikaa 0.3.23 → 0.3.25

package/skills/autoskill/SKILL.md

@@ -1,233 +0,0 @@
----
-name: autoskill
-description: Observe the user's screen via screenpipe, detect repeated research workflows, match them against existing scientific-agent-skills, and draft new skills (or composition recipes that chain existing ones) for the patterns not yet covered. Use when the user asks to analyze their recent work and propose skills based on what they actually do. Requires the screenpipe daemon (https://github.com/screenpipe/screenpipe) running locally on port 3030 — the skill has no other data source and will refuse to run if screenpipe is unreachable. All detection runs locally; only redacted cluster summaries reach the LLM.
-allowed-tools: Read Write Edit Bash
-license: MIT license
-metadata:
-  version: "1.3"
-  skill-author: K-Dense Inc.
-  openclaw:
-    requires:
-      bins:
-      - screenpipe
-    primaryEnv: SCREENPIPE_TOKEN
-    envVars:
-    - name: SCREENPIPE_TOKEN
-      required: true
-      description: Auth token for the local screenpipe daemon.
-    - name: ANTHROPIC_API_KEY
-      required: false
-      description: For Claude API calls during skill drafting.
-    - name: FOUNDRY_API_KEY
-      required: false
-      description: Optional Foundry access for drafting.
----
-
-# autoskill
-
-> **Requires a running [screenpipe](https://github.com/screenpipe/screenpipe) daemon.** This skill has no alternate data source — it reads exclusively from the local screenpipe HTTP API (default `http://localhost:3030`). If the daemon isn't running, `run()` raises `ScreenpipeUnreachable` with install instructions.
-
-> **Network access & environment variables.** This skill makes authenticated HTTP requests to (a) the user's local screenpipe daemon on loopback, and (b) the user-configured LLM backend — one of `http://localhost:1234/v1` (LM Studio, default), `https://api.anthropic.com` (opt-in Claude), or a user-supplied BYOK Foundry gateway. The skill reads three environment variables — `SCREENPIPE_TOKEN`, `ANTHROPIC_API_KEY`, `FOUNDRY_API_KEY` — and uses each only to authenticate to the single endpoint its name implies. No other network destinations, no telemetry, no data egress to any third party.
-
-## Overview
-
-Turn the user's own workflow history — captured passively by the local [screenpipe](https://github.com/screenpipe/screenpipe) daemon — into new skills. This skill is on-demand: the user invokes it with a time window, it queries screenpipe's local HTTP API, clusters repeated workflow patterns, compares each pattern against the existing skills in this repo, and produces a staged folder of proposals the user can review, edit, and promote.
-
-## When to Use This Skill
-
-Invoke this skill when the user asks to:
-- "Analyze my last 4 hours / day / week and propose new skills."
-- "Look at what I've been doing and tell me what's not covered yet."
-- "Draft a skill from my recent workflow."
-- "Find composition recipes for workflows I repeat."
-
-Do **not** invoke it for one-off questions about screenpipe itself, for real-time screen queries, or without an explicit user request — the skill analyzes sensitive local content and must stay explicitly user-triggered.
-
-## Privacy Posture
-
-- **Screenpipe handles app/window filtering at capture time.** Install a starter deny-list by copying `references/screenpipe-config.yaml` into the user's screenpipe config. Sensitive apps (password managers, messaging, banking) are never OCR'd in the first place.
-- **Raw OCR never leaves the machine.** `scripts/fetch_window.py` pulls data over localhost HTTP. `scripts/cluster.py` reduces the timeline to app/duration/title summaries. `scripts/redact.py` strips emails, API keys, bearer tokens, and phone numbers as defense-in-depth before any cluster summary reaches the LLM.
-- **LLM backend defaults to `local`.** The recommended setup is [LM Studio](https://lmstudio.ai/) running `Gemma-4-31B-it` — strong reasoning at a size that fits on most workstation GPUs, and no data ever leaves your machine. Cloud backends (`claude`, `foundry`) are opt-in and documented in `config.yaml` for users who explicitly want them. Detection and embeddings always run locally regardless of backend choice.
-- **Dry-run mode** (`--plan`) prints the exact timeline that will be analyzed before any LLM call.
-- **TLS for localhost** (optional, for corporate policy): see `references/https-proxy.md` for the Caddy pattern.
-
-## Prerequisites
-
-### 1. Screenpipe daemon
-
-Either install the official release or build from source. Either way the daemon binds HTTP on `localhost:3030` by default.
-
-**From source** (recommended if you want the CLI daemon without the desktop GUI):
-
-```bash
-git clone --depth 1 https://github.com/mediar-ai/screenpipe.git
-cd screenpipe
-cargo build -p screenpipe-engine --release
-# System deps (macOS): cmake + full Xcode.app (not just Command Line Tools).
-#   brew install cmake
-#   # if xcodebuild plug-ins error: sudo xcodebuild -runFirstLaunch
-./target/release/screenpipe doctor   # confirm permissions + ffmpeg
-./target/release/screenpipe record --disable-audio --use-pii-removal
-```
-
-First run will prompt for macOS Screen Recording permission. Grant it and relaunch.
-
-### 2. Screenpipe API token
-
-The local API now requires bearer auth. Retrieve your token and export it:
-
-```bash
-export SCREENPIPE_TOKEN=$(screenpipe auth token)
-```
-
-(Or set `screenpipe.token` directly in `config.yaml` — env var is preferred since it keeps secrets out of version control.)
-
-### 3. Python environment
-
-Via `pipenv` from the repo root:
-
-```bash
-pipenv install httpx pyyaml sentence-transformers
-```
-
-The embedding model (`sentence-transformers/all-MiniLM-L6-v2`, ~80 MB) downloads on first run.
-
-### 4. Local LLM (default path) — LM Studio
-
-- Install [LM Studio](https://lmstudio.ai/).
-- Download `Gemma-4-31B-it` (or another strong reasoning model; adjust `local.model` in `config.yaml`).
-- Load it via the CLI for headless use (no GUI required):
-
-```bash
-lms load gemma-4-31b-it --context-length 131072 --gpu max -y
-lms status   # confirm server running on :1234
-```
-
-### 5. Cloud LLM backends (optional, opt-in)
-
-Only if you explicitly opt out of local:
-- `claude`: set `ANTHROPIC_API_KEY`, flip `backend: claude` in `config.yaml`.
-- `foundry`: set `FOUNDRY_API_KEY`, flip `backend: foundry`, set `foundry.endpoint` to your corporate gateway URL.
-
-## Architecture
-
-```
-screenpipe daemon (user-installed)
-        │  HTTP on localhost:3030
-        ▼
-scripts/fetch_window.py    → normalized timeline events
-scripts/redact.py          → regex scrub (defense-in-depth)
-scripts/cluster.py         → sessions + clusters (local only)
-scripts/match_skills.py    → top-k vs existing 135 skills (local embeddings)
-scripts/synthesize.py      → LLM judge: reuse / compose / novel
-        │
-        ▼
-~/.autoskill/proposed/<timestamp>/        (default; override with --out)
-  ├── report.md
-  ├── composition-recipes/<name>/SKILL.md
-  └── new-skills/<name>/SKILL.md
-
-scripts/promote.py         → user-approved proposal → skills/<name>/
-```
-
-## Workflow
-
-The skill ships a unified CLI at `scripts/autoskill.py` with three subcommands:
-
-```bash
-python scripts/autoskill.py doctor   --config config.yaml --skills-dir ../
-python scripts/autoskill.py run      --start ... --end ... --config config.yaml
-python scripts/autoskill.py promote  --proposed ~/.autoskill/proposed/<ts> --skills-dir ../ --name <skill>
-```
-
-### 0. Preflight with `doctor`
-
-Before a full run, verify every dependency in one shot:
-
-```bash
-python scripts/autoskill.py doctor \
-  --config skills/autoskill/config.yaml \
-  --skills-dir skills
-```
-
-The report covers `config` (backend choice valid), `skills_dir` (exists), `screenpipe` (reachable + authed), and `llm` (LM Studio serving or API key present). Non-zero exit on any failure, with the offending line marked `error`.
-
-### 1. Run the pipeline
-
-```bash
-export SCREENPIPE_TOKEN=$(screenpipe auth token)
-python scripts/autoskill.py run \
-  --start "2026-04-17T00:00:00Z" \
-  --end   "2026-04-17T23:59:59Z" \
-  --config skills/autoskill/config.yaml \
-  --skills-dir skills
-```
-
-Proposals land in `~/.autoskill/proposed/<timestamp>/` by default, keeping experimental output out of the skills repo. Pass `--out PATH` to override.
-
-Internally:
-1. **Fetch** — `fetch_window` paginates screenpipe's `/search` endpoint, normalizes events to `{ts, app, window_title, text, content_type}`.
-2. **Redact** — `redact` scrubs emails, API keys, bearer tokens, phones from OCR text and window titles as defense-in-depth over screenpipe's own PII removal.
-3. **Cluster** — `segment_sessions` splits on idle gaps (default 10 min) and drops short sessions; `cluster_sessions` groups sessions by app-signature and keeps clusters of size `min_cluster_size` (default 2).
-4. **Match** — `load_skill_descriptions` reads frontmatter from every `SKILL.md` in `skills/`; `top_k_matches` ranks each cluster against all skills using local `sentence-transformers` embeddings (cosine similarity).
-5. **Synthesize** — `synthesize` prompts the configured LLM backend to classify each cluster as `reuse`, `compose`, or `novel` and emit a SKILL.md body where appropriate.
-6. **Report** — writes `<out_dir>/<ts>/report.md`, plus `new-skills/<name>/SKILL.md` or `composition-recipes/<name>/SKILL.md` for each proposal.
-
-Add `--dry-run` to stop after clustering; this skips the LLM (and the sentence-transformers load), writing only `plan.md` for inspection.
-
-### 2. Review and promote
-
-Open `~/.autoskill/proposed/<ts>/report.md`, edit drafts in place, delete anything you don't want. Then:
-
-```bash
-python scripts/autoskill.py promote \
-  --proposed ~/.autoskill/proposed/2026-04-17T14-30-00 \
-  --skills-dir skills \
-  --name zotero-pubmed-helper
-```
-
-`promote` moves the directory into `skills/<name>/`, refusing to overwrite an existing skill. Exits non-zero with a friendly error if the proposal isn't found or the target already exists.
-
-## Configuration
-
-See `config.yaml` for the full shape. Default values (local-first):
-
-```yaml
-backend: local
-local:
-  endpoint: http://localhost:1234/v1   # LM Studio's Developer server
-  model: Gemma-4-31B-it
-
-screenpipe:
-  url: http://localhost:3030           # or https://screenpipe.local via Caddy
-
-cluster:
-  min_session_minutes: 5
-  idle_gap_minutes: 10
-  min_cluster_size: 2
-```
-
-To opt into a cloud backend:
-
-```yaml
-backend: claude                         # or foundry
-claude:
-  model: claude-opus-4-7
-```
-
-## Composition recipes vs new skills
-
-- **compose**: the LLM judged that chaining existing skills covers the workflow. The emitted SKILL.md is intentionally thin — frontmatter + a "Workflow" section that invokes existing skills in order. The same agent runtime that discovered the skill can then invoke it end-to-end.
-- **novel**: no combination of existing skills covers it. A fuller SKILL.md is drafted, still following repo conventions (frontmatter, Overview, When to Use, Workflow). The user should always review new-skill drafts before promoting.
-
-## Testing
-
-The skill is covered by a small pytest suite at `tests/autoskill/` in the repository root. Each script is unit-tested in isolation with dependency injection (mock HTTP transport, stub backend, stub embedder):
-
-```bash
-python -m pytest tests/autoskill -v
-```
-
-## Composition with other skills in this repo
-
-The autoskill's embedding index covers all 135 sibling skills. Workflows that look like scientific writing will match `scientific-writing` / `literature-review` / `citation-management`; figure work will match `scientific-schematics` / `generate-image` / `infographics`; slide prep matches `scientific-slides` / `pptx`; etc. When a cluster scores high against two or three sibling skills the emitted composition recipe names them explicitly, so the user's future agent invocations use the optimized paths already documented in this repo.

package/skills/benchling-integration/SKILL.md

@@ -1,229 +0,0 @@
----
-name: benchling-integration
-description: Benchling Python SDK and REST API integration for registry entities, inventory, ELN entries, workflows, Benchling Apps, and Data Warehouse queries. Use when automating lab data with benchling-sdk or the v2 API.
-license: MIT
-allowed-tools: Read Write Edit Bash
-compatibility: Requires a Benchling account, tenant URL, and API key or OAuth app credentials. Install benchling-sdk with uv pip install.
-metadata:
-  version: "1.4"
-  skill-author: K-Dense Inc.
-  openclaw:
-    primaryEnv: BENCHLING_API_KEY
-    envVars:
-    - name: BENCHLING_TENANT_URL
-      required: true
-      description: Benchling tenant base URL.
-    - name: BENCHLING_API_KEY
-      required: false
-      description: API key auth (alternative to OAuth).
-    - name: BENCHLING_CLIENT_ID
-      required: false
-      description: OAuth app client id.
-    - name: BENCHLING_CLIENT_SECRET
-      required: false
-      description: OAuth app client secret.
-    - name: BENCHLING_PROD_TENANT_URL
-      required: false
-      description: Production tenant URL (multi-env setups).
-    - name: BENCHLING_PROD_API_KEY
-      required: false
-      description: Production API key (multi-env setups).
-    - name: BENCHLING_STAGING_TENANT_URL
-      required: false
-      description: Staging tenant URL (multi-env setups).
-    - name: BENCHLING_STAGING_API_KEY
-      required: false
-      description: Staging API key (multi-env setups).
----
-
-# Benchling Integration
-
-## Overview
-
-Benchling is a cloud platform for life sciences R&D. Access registry entities (DNA, RNA, proteins), inventory, electronic lab notebooks, and workflows programmatically via the Python SDK and REST API.
-
-**Version note:** Examples target **benchling-sdk 1.25.0** (latest stable on PyPI). Docs: [benchling.com/sdk-docs](https://benchling.com/sdk-docs/). Platform guide: [docs.benchling.com](https://docs.benchling.com/).
-
-## When to Use This Skill
-
-This skill should be used when:
-- Working with Benchling's Python SDK or REST API
-- Managing biological sequences (DNA, RNA, proteins) and registry entities
-- Automating inventory operations (samples, containers, locations, transfers)
-- Creating or querying electronic lab notebook entries
-- Building workflow automations or Benchling Apps
-- Syncing data between Benchling and external systems
-- Querying the Benchling Data Warehouse for analytics
-- Setting up event-driven integrations with AWS EventBridge
-
-## Core Capabilities
-
-Seven capability areas, each with code, are in
-[references/core_capabilities.md](references/core_capabilities.md):
-
-1. **Authentication and setup** — API key and OAuth app auth; see
-   [references/authentication.md](references/authentication.md).
-2. **Registry and entity management** — DNA and AA sequences, custom entities, schemas,
-   and registration.
-3. **Inventory management** — containers, boxes, plates, locations, and transfers.
-4. **Notebook and documentation** — entries, day-to-day notes, and structured tables.
-5. **Workflows and automation** — tasks, flowcharts, and assay runs.
-6. **Events and integration** — EventBridge subscriptions; see
-   [references/eventbridge.md](references/eventbridge.md).
-7. **Data warehouse and analytics** — SQL access to the warehouse.
-
-Endpoint and SDK detail is in
-[references/api_endpoints.md](references/api_endpoints.md) and
-[references/sdk_reference.md](references/sdk_reference.md).
-
-## Best Practices
-
-### Error Handling
-
-The SDK automatically retries failed requests:
-```python
-# Automatic retry for 429, 502, 503, 504 status codes
-# Up to 5 retries with exponential backoff
-# Customize retry behavior if needed
-from benchling_sdk.retry import RetryStrategy
-
-benchling = Benchling(
-    url=tenant_url,
-    auth_method=ApiKeyAuth(api_key),
-    retry_strategy=RetryStrategy(max_retries=3),
-)
-```
-
-### Pagination Efficiency
-
-Use generators for memory-efficient pagination:
-```python
-# Generator-based iteration
-for page in benchling.dna_sequences.list():
-    for sequence in page:
-        process(sequence)
-
-# Check estimated count without loading all pages
-total = benchling.dna_sequences.list().estimated_count()
-```
-
-### Schema Fields Helper
-
-Use the `fields()` helper for custom schema fields:
-```python
-# Convert dict to Fields object
-custom_fields = benchling.models.fields({
-    "concentration": "100 ng/μL",
-    "date_prepared": "2025-10-20",
-    "notes": "High quality prep"
-})
-```
-
-### Forward Compatibility
-
-The SDK handles unknown enum values and types gracefully:
-- Unknown enum values are preserved
-- Unrecognized polymorphic types return `UnknownType`
-- Allows working with newer API versions
-
-### Security Considerations
-
-- Never commit API keys or OAuth secrets to version control
-- Read only named environment variables (`BENCHLING_TENANT_URL`, `BENCHLING_API_KEY`, etc.)
-- Route network calls exclusively to your tenant URL
-- Rotate keys if compromised; use OAuth for multi-user production apps
-- Grant minimal necessary permissions for apps in the Developer Console
-
-## Resources
-
-### references/
-
-Detailed reference documentation for in-depth information:
-
-- **authentication.md** - Comprehensive authentication guide including OIDC, security best practices, and credential management
-- **sdk_reference.md** - Detailed Python SDK reference with advanced patterns, examples, and all entity types
-- **api_endpoints.md** - REST API endpoint reference for direct HTTP calls without the SDK
-- **eventbridge.md** - EventBridge setup, event payload schema, rule examples, Lambda handler, validation, and recovery
-
-Load these references as needed for specific integration requirements.
-
-## Common Use Cases
-
-**1. Bulk Entity Import:**
-```python
-# Import multiple sequences from FASTA file
-from Bio import SeqIO
-
-for record in SeqIO.parse("sequences.fasta", "fasta"):
-    benchling.dna_sequences.create(
-        DnaSequenceCreate(
-            name=record.id,
-            bases=str(record.seq),
-            is_circular=False,
-            folder_id="fld_abc123"
-        )
-    )
-```
-
-**2. Inventory Audit:**
-```python
-# List all containers in a specific location
-containers = benchling.containers.list(
-    parent_storage_id="box_abc123"
-)
-
-for page in containers:
-    for container in page:
-        print(f"{container.name}: {container.barcode}")
-```
-
-**3. Workflow Automation:**
-```python
-# Update all pending tasks for a workflow
-tasks = benchling.workflow_tasks.list(
-    workflow_id="wf_abc123",
-    status="pending"
-)
-
-for page in tasks:
-    for task in page:
-        # Perform automated checks
-        if auto_validate(task):
-            benchling.workflow_tasks.update(
-                task_id=task.id,
-                workflow_task=WorkflowTaskUpdate(
-                    status_id="status_complete"
-                )
-            )
-```
-
-**4. Data Export:**
-```python
-# Export all sequences with specific properties
-sequences = benchling.dna_sequences.list()
-export_data = []
-
-for page in sequences:
-    for seq in page:
-        if seq.schema_id == "target_schema_id":
-            export_data.append({
-                "id": seq.id,
-                "name": seq.name,
-                "bases": seq.bases,
-                "length": len(seq.bases)
-            })
-
-# Save to CSV or database
-import csv
-with open("sequences.csv", "w") as f:
-    writer = csv.DictWriter(f, fieldnames=export_data[0].keys())
-    writer.writeheader()
-    writer.writerows(export_data)
-```
-
-## Additional Resources
-
-- **Official Documentation:** https://docs.benchling.com
-- **Python SDK Reference:** https://benchling.com/sdk-docs/
-- **API Reference:** https://benchling.com/api/reference
-- **Support:** [email protected]

package/skills/bgpt-paper-search/SKILL.md

@@ -1,75 +0,0 @@
----
-name: bgpt-paper-search
-description: Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server. Returns 25+ fields per paper including methods, results, sample sizes, quality scores, and conclusions. Use for literature reviews, evidence synthesis, and finding experimental details not available in abstracts alone.
-license: MIT
-compatibility: Requires the BGPT MCP server configured in the agent host (npx mcp-remote or npx bgpt-mcp), internet access to bgpt.pro, and an optional BGPT API key for paid usage.
-metadata:
-  version: "1.1"
-  skill-author: BGPT
-  website: https://bgpt.pro/mcp
-  github: https://github.com/connerlambden/bgpt-mcp
----
-
-# BGPT Paper Search
-
-## Overview
-
-BGPT is a remote MCP server that searches a curated database of scientific papers built from raw experimental data extracted from full-text studies. Unlike traditional literature databases that return titles and abstracts, BGPT returns structured data from the actual paper content — methods, quantitative results, sample sizes, quality assessments, and 25+ metadata fields per paper.
-
-## When to Use This Skill
-
-Use this skill when:
-- Searching for scientific papers with specific experimental details
-- Conducting systematic or scoping literature reviews
-- Finding quantitative results, sample sizes, or effect sizes across studies
-- Comparing methodologies used in different studies
-- Looking for papers with quality scores or evidence grading
-- Needing structured data from full-text papers (not just abstracts)
-- Building evidence tables for meta-analyses or clinical guidelines
-
-## Setup
-
-BGPT is a remote MCP server — no local installation required. Configure it in your agent's MCP settings before use; this skill instructs the agent to call the `search_papers` MCP tool and does not enable MCP access by itself.
-
-### Claude Desktop / Claude Code
-
-Add to your MCP configuration:
-
-```json
-{
-  "mcpServers": {
-    "bgpt": {
-      "command": "npx",
-      "args": ["mcp-remote", "https://bgpt.pro/mcp/sse"]
-    }
-  }
-}
-```
-
-### npm (alternative)
-
-```bash
-npx bgpt-mcp
-```
-
-## Usage
-
-Once the BGPT MCP server is configured, call its `search_papers` tool via the agent's MCP interface (not via Bash):
-
-```
-Search for papers about: "CRISPR gene editing efficiency in human cells"
-```
-
-The server returns structured results including:
-- **Title, authors, journal, year, DOI**
-- **Methods**: Experimental techniques, models, protocols
-- **Results**: Key findings with quantitative data
-- **Sample sizes**: Number of subjects/samples
-- **Quality scores**: Study quality assessments
-- **Conclusions**: Author conclusions and implications
-
-## Pricing
-
-- **Free tier**: 50 searches per network, no API key required
-- **Paid**: $0.01 per result with an API key from [bgpt.pro/mcp](https://bgpt.pro/mcp)
-