merge conflicts

Author: deep1401

.agents/skills/lab-autoresearch/SKILL.md

@@ -0,0 +1,32 @@
+---
+name: lab-autoresearch
+description: Autonomous experiment loop on top of the Transformer Lab `lab` CLI — pick an idea, queue a job, score it, keep or discard, repeat. Use when the user types `/lab-autoresearch`, says "run autoresearch", "optimize X in a loop", "set up autoresearch for …", or asks to run an autonomous experimentation / optimization loop against Transformer Lab.
+allowed-tools: Bash(lab *), Bash(curl *lab.cloud*), Bash(curl *localhost:8338*)
+---
+
+# /lab-autoresearch
+
+This skill is the entry point for the autonomous experiment loop. The full spec lives in the `transformerlab-cli` skill — this skill exists so that typing `/lab-autoresearch` resolves to a real skill instead of falling through.
+
+## What to do
+
+1. **Read the spec first.** The authoritative workflow, subcommands (`init <goal>`, `run`, `finalize`), experiment-notes template, loop rules (parallelism, fire-and-advance, stale-job sweep, keep/discard policy, run-description discipline), and natural-language → `lab` mapping all live in:
+
+   `.claude/skills/transformerlab-cli/references/autoresearch.md`
+
+   (or, in the source repo, `.agents/skills/transformerlab-cli/references/autoresearch.md`)
+
+2. **Then use the `transformerlab-cli` skill** for every `lab` command the loop issues. That skill has the command reference, troubleshooting, and the rule that you must use `lab` (not raw `curl`) for normal operations.
+
+## Quick orientation
+
+The loop is layered on the `lab` CLI:
+
+- One **experiment** per session, one **job** per iteration.
+- A job's `-m/--description` is the iteration note; its `score` dict (set via `lab.finish(score=…)`) is the result; `lab job discard` is the keep/discard flag.
+- For hyperparameter fan-out, prefer the task's `sweeps:` block over manually queuing N jobs.
+- The session plan (objective, files in scope, constraints, backlog, what's been tried) is written to **experiment notes** via `lab notes` — there is no local `autoresearch.md` file.
+
+Everything beyond `init` / `run` / `finalize` (status, keep/discard, sweeps, ideas, stopping running jobs, exiting the loop) is just the agent running the right `lab` call in response to natural-language requests — no dedicated subcommand needed.
+
+**Do not improvise the loop without reading `references/autoresearch.md` first.** The rules around parallelism, fire-and-advance, and stale-job sweeps are load-bearing and not derivable from the `lab` CLI alone.

.agents/skills/react-doctor/SKILL.md

@@ -0,0 +1,32 @@
+---
+name: react-doctor
+description: Use when finishing a feature, fixing a bug, before committing React code, or when the user wants to improve code quality or clean up a codebase. Checks for score regression. Covers lint, dead code, accessibility, bundle size, architecture diagnostics.
+version: "1.0.0"
+---
+
+# React Doctor
+
+Scans React codebases for security, performance, correctness, and architecture issues. Outputs a 0–100 health score.
+
+## After making React code changes:
+
+Run `npx -y react-doctor@latest . --verbose --diff` and check the score did not regress.
+
+If the score dropped, fix the regressions before committing.
+
+## For general cleanup or code improvement:
+
+Run `npx -y react-doctor@latest . --verbose` (without `--diff`) to scan the full codebase. Fix issues by severity — errors first, then warnings.
+
+## Command
+
+```bash
+npx -y react-doctor@latest . --verbose --diff
+```
+
+| Flag        | Purpose                                       |
+| ----------- | --------------------------------------------- |
+| `.`         | Scan current directory                        |
+| `--verbose` | Show affected files and line numbers per rule |
+| `--diff`    | Only scan changed files vs base branch        |
+| `--score`   | Output only the numeric score                 |

.agents/skills/transformerlab-cli/SKILL.md

@@ -120,6 +120,25 @@ Add a new task from a local directory containing `task.yaml`, or from a Git repo
 
 **JSON output:** Returns the created task object.
 
+### `task edit <task_id>`
+
+Update an existing task on the server. Three modes:
+
+| Option | Description |
+|---|---|
+| (no flag) | Interactive — fetches current `task.yaml`, opens `$EDITOR`, validates and PUTs it back. YAML-only. |
+| `--from-file <path>` | Replace **only** `task.yaml` from the given path. Leaves `main.py` and other attachments untouched on the server. |
+| `--from-dir <path>` | Replace `task.yaml` **and** sibling files (e.g. `main.py`, configs). Zips the directory, uploads, and applies. **Use this whenever the task's `run` references a script file you've also modified — `--from-file` alone will desync the YAML from the script.** |
+| `--no-interactive` | Skip confirmation prompt (required in automated contexts) |
+| `--dry-run` | With `--from-dir`, preview the upload without submitting |
+| `--timeout <seconds>` | Request timeout for fetch/validate/save (default: 300) |
+
+`--from-file` and `--from-dir` are mutually exclusive.
+
+### `task upload <task_id> <path>`
+
+Upload additional files (or a whole directory) into an existing task without touching `task.yaml`. Useful when you want to add an attachment to a task whose YAML is already correct.
+
 ### `task delete <task_id>`
 
 Delete a task by ID.
@@ -234,7 +253,7 @@ Stop a running job.
 
 Launch the interactive job monitor TUI (Textual app).
 
-**Warning:** This launches a full terminal UI. **Never use in automated or agent contexts.** Use `job list` + `job machine-logs` instead.
+**Warning:** This launches a full terminal UI. **Never use when operating as an AI agent or in non-interactive automation.** Use `job list`, `job info`, and `job task-logs` instead.
 
 ---
 

.agents/skills/transformerlab-cli/references/autoresearch.md

@@ -128,7 +128,7 @@ curl -s -H "Authorization: Bearer API_KEY" -H "X-Team-Id: TEAM_ID" \
 - `provider delete` → add `--yes`
 - `task gallery` → use `--import GALLERY_ID` instead of browsing
 
-**Never use these commands in automated contexts:**
+**Never use these commands when operating as an AI agent or in non-interactive automation:**
 - `job monitor` (launches TUI)
 - `task interactive` (blocks for interactive session)
 

.agents/skills/transformerlab-cli/references/commands.md

@@ -228,3 +228,7 @@ test-results/
 
 docs/superpowers/*
 .superpowers/
+
+/tmp/
+/temp/
+.claude/scheduled_tasks.lock

.agents/skills/transformerlab-cli/references/troubleshooting.md

@@ -0,0 +1,21 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.15.0
+    hooks:
+      - id: ruff
+        name: ruff check (api, cli, lab-sdk)
+        args: [--fix, --line-length=120]
+        files: ^(api|cli|lab-sdk)/.*\.py$
+      - id: ruff-format
+        name: ruff format (api, cli, lab-sdk)
+        args: [--line-length=120]
+        files: ^(api|cli|lab-sdk)/.*\.py$
+
+  - repo: local
+    hooks:
+      - id: npm-format
+        name: npm run format (prettier)
+        entry: npm run format
+        language: system
+        pass_filenames: false
+        files: ^(src|transformerlab-docs)/.*\.(js|jsx|ts|tsx|json|css|scss|md|mdx|ya?ml)$

.gitignore

@@ -32,6 +32,7 @@
 - **Node v22** (v23+ is not supported)
 - **Python**: Managed via conda (`~/.transformerlab/envs/transformerlab`). Install with `cd api && ./install.sh`.
 - **npm deps**: `npm install` (includes `dotenv-cli`, `cross-env`, `concurrently` used by scripts)
+- **pre-commit hooks**: Run `pip install pre-commit && pre-commit install` once after cloning. This wires up `.pre-commit-config.yaml` so `ruff check --fix`, `ruff format`, and `npm run format` run automatically on every commit.
 
 ## Architecture
 

.pre-commit-config.yaml

@@ -0,0 +1,55 @@
+"""add_user_experiment_access_table
+
+Revision ID: 46378c10f132
+Revises: 6ccd4a4d9ca1
+Create Date: 2026-05-04 13:23:27.122716
+
+"""
+
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+from transformerlab.db.migration_utils import table_exists
+
+
+# revision identifiers, used by Alembic.
+revision: str = "46378c10f132"
+down_revision: Union[str, Sequence[str], None] = "6ccd4a4d9ca1"
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    connection = op.get_bind()
+    if not table_exists(connection, "user_experiment_access"):
+        op.create_table(
+            "user_experiment_access",
+            sa.Column("id", sa.Integer(), autoincrement=True, nullable=False),
+            sa.Column("user_id", sa.String(), nullable=False),
+            sa.Column("team_id", sa.String(), nullable=False),
+            sa.Column("experiment_id", sa.String(), nullable=False),
+            sa.Column(
+                "last_opened_at",
+                sa.DateTime(),
+                server_default=sa.text("(CURRENT_TIMESTAMP)"),
+                nullable=False,
+            ),
+            sa.PrimaryKeyConstraint("id"),
+            sa.UniqueConstraint(
+                "user_id",
+                "team_id",
+                "experiment_id",
+                name="uq_user_experiment_access",
+            ),
+        )
+        op.create_index(
+            "idx_user_experiment_access_user_team",
+            "user_experiment_access",
+            ["user_id", "team_id"],
+        )
+
+
+def downgrade() -> None:
+    op.drop_index("idx_user_experiment_access_user_team", table_name="user_experiment_access", if_exists=True)
+    op.drop_table("user_experiment_access", if_exists=True)