claude-turing 4.8.0 → 4.8.1

package/commands/init.md

@@ -1,6 +1,6 @@
 ---
 name: init
-description: Initialize a new ML project with the Turing autoresearch harness. Scaffolds the full experiment infrastructure — immutable evaluation pipeline, agent-editable training code, structured logging, convergence detection hooks, and a Python virtual environment. Use --plan to generate a research plan.
+description: Initialize a new ML project with the Turing autoresearch harness. Scaffolds the full experiment infrastructure — immutable evaluation pipeline, agent-editable training code, structured logging, convergence detection hooks, and a uv-managed Python environment. Use --plan to generate a research plan.
 argument-hint: "[project_name] [--plan]"
 allowed-tools: Read, Write, Edit, Bash(*), Grep, Glob, WebSearch, WebFetch
 ---
@@ -23,7 +23,7 @@ Ask the user for the following (or accept from `$ARGUMENTS` if provided as JSON)
 Once you have all 6 values, delegate to the unified scaffolding script:
 
 ```bash
-python3 <templates_dir>/scripts/scaffold.py \
+uv run python <templates_dir>/scripts/scaffold.py \
     --project-name "<project_name>" \
     --target-metric "<target_metric>" \
     --metric-direction "<metric_direction>" \
@@ -38,7 +38,7 @@ The scaffold script handles everything in a single atomic operation:
 - Creates data/, experiments/, models/ directories
 - Sets up agent memory at `.claude/agent-memory/ml-researcher-{project_name}/MEMORY.md`
 - Configures Claude Code hooks in `.claude/settings.local.json`
-- Creates Python virtual environment and installs requirements
+- Runs `uv sync` from the ML directory when uv is available
 - Verifies all placeholders were replaced (fails loudly if any remain)
 
 ## Locating Templates
@@ -57,7 +57,7 @@ node_modules/claude-turing/templates/
 Example command:
 
 ```bash
-python3 ~/.claude/commands/turing/templates/scripts/scaffold.py \
+uv run python ~/.claude/commands/turing/templates/scripts/scaffold.py \
     --project-name "<project_name>" \
     --target-metric "<target_metric>" \
     --metric-direction "<metric_direction>" \
@@ -71,7 +71,7 @@ python3 ~/.claude/commands/turing/templates/scripts/scaffold.py \
 
 Report what was created:
 - The separation: READ-ONLY (`prepare.py`, `evaluate.py`) vs AGENT-EDITABLE (`train.py`)
-- Next steps: add data to the configured data source path, run `python prepare.py`, then `/turing:train`
+- Next steps: add data to the configured data source path, run `uv run python prepare.py`, then `/turing:train`
 - The taste-leverage loop: `/turing:try` to inject hypotheses, `/turing:brief` for intelligence reports
 
 ## Research Plan Generation (--plan flag)

package/commands/leak.md

@@ -9,9 +9,9 @@ Actively probe for data leakage. The #1 cause of "too good to be true" results.
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -21,7 +21,7 @@ Actively probe for data leakage. The #1 cause of "too good to be true" results.
 
 3. **Run leakage scan:**
    ```bash
-   python scripts/leakage_detector.py $ARGUMENTS
+   uv run python scripts/leakage_detector.py $ARGUMENTS
    ```
 
 4. **Checks performed:**

package/commands/lit.md

@@ -9,9 +9,9 @@ Search the literature for papers, baselines, and related work.
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -23,7 +23,7 @@ Search the literature for papers, baselines, and related work.
 
 3. **Run literature search:**
    ```bash
-   python scripts/literature_search.py $ARGUMENTS
+   uv run python scripts/literature_search.py $ARGUMENTS
    ```
 
 4. **Report results:**

package/commands/logbook.md

@@ -2,7 +2,7 @@
 name: logbook
 description: Generate a research logbook showing the full experiment narrative — hypotheses proposed, experiments run, decisions made, and progress over time. Outputs HTML (with interactive chart) or markdown.
 argument-hint: "[--since YYYY-MM-DD] [--format html|markdown] [--output path]"
-allowed-tools: Read, Bash(python scripts/*:*, source .venv/bin/activate:*, mkdir:*), Grep, Glob
+allowed-tools: Read, Bash(uv run python scripts/*:*, uv sync:*, mkdir:*), Grep, Glob
 ---
 
 Generate a research logbook that captures the full narrative of the experiment campaign.
@@ -11,7 +11,7 @@ Generate a research logbook that captures the full narrative of the experiment c
 
 1. **Generate the logbook:**
    ```bash
-   source .venv/bin/activate && python scripts/generate_logbook.py
+   uv run python scripts/generate_logbook.py
    ```
 
    **With options from `$ARGUMENTS`:**
@@ -22,13 +22,13 @@ Generate a research logbook that captures the full narrative of the experiment c
    **Common usage:**
    ```bash
    # HTML logbook with interactive trajectory chart
-   source .venv/bin/activate && python scripts/generate_logbook.py --output logbook.html
+   uv run python scripts/generate_logbook.py --output logbook.html
 
    # Markdown for embedding in docs or READMEs
-   source .venv/bin/activate && python scripts/generate_logbook.py --format markdown --output logbook.md
+   uv run python scripts/generate_logbook.py --format markdown --output logbook.md
 
    # Last week's activity
-   source .venv/bin/activate && python scripts/generate_logbook.py --since 2026-03-24 --output logbook.html
+   uv run python scripts/generate_logbook.py --since 2026-03-24 --output logbook.html
    ```
 
 2. **Present the result:**

package/commands/merge.md

@@ -9,8 +9,8 @@ Combine model weights (not predictions) into a single, better model with no late
 
 ## Steps
 
-1. **Activate environment:** `source .venv/bin/activate`
-2. **Run:** `python scripts/model_merger.py $ARGUMENTS`
+1. **Sync environment:** `uv sync`
+2. **Run:** `uv run python scripts/model_merger.py $ARGUMENTS`
 3. **Methods:** uniform soup (simple average), greedy soup (include only if improves), TIES (trim+elect+merge), DARE (drop+rescale)
 4. **Report:** compatibility check, per-model metrics, method comparison, improvement delta
 5. **Saved output:** `experiments/merges/merge-*.yaml`

package/commands/mode.md

@@ -20,7 +20,7 @@ Set the research mode for the current project. The mode determines how the novel
 
 2. **Update experiment state:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    python -c "
    import yaml
    from pathlib import Path

package/commands/onboard.md

@@ -8,8 +8,8 @@ allowed-tools: Read, Bash(*), Grep, Glob
 5-minute read that replaces a 1-hour onboarding meeting.
 
 ## Steps
-1. `source .venv/bin/activate`
-2. `python scripts/generate_onboarding.py $ARGUMENTS`
+1. `uv sync`
+2. `uv run python scripts/generate_onboarding.py $ARGUMENTS`
 3. **Saved:** `ONBOARDING.md`
 
 ## Examples

package/commands/paper.md

@@ -9,9 +9,9 @@ Draft paper sections directly from experiment data.
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -20,7 +20,7 @@ Draft paper sections directly from experiment data.
 
 3. **Run paper drafting:**
    ```bash
-   python scripts/draft_paper_sections.py $ARGUMENTS
+   uv run python scripts/draft_paper_sections.py $ARGUMENTS
    ```
 
 4. **Report results:**

package/commands/plan.md

@@ -8,8 +8,8 @@ allowed-tools: Read, Bash(*), Grep, Glob
 Design the next N experiments strategically, not randomly. Allocates budget by expected ROI.
 
 ## Steps
-1. `source .venv/bin/activate`
-2. `python scripts/research_planner.py $ARGUMENTS`
+1. `uv sync`
+2. `uv run python scripts/research_planner.py $ARGUMENTS`
 3. **Saved:** `experiments/plans/`
 
 ## How it works

package/commands/poster.md

@@ -2,7 +2,7 @@
 name: poster
 description: Generate a single-page HTML research poster summarizing the experiment campaign — best result, trajectory, key findings, and methodology. Adapted from posterskill's self-contained HTML architecture.
 argument-hint: "[title override]"
-allowed-tools: Read, Write, Edit, Bash(python scripts/*:*, source .venv/bin/activate:*, mkdir:*, open:*), Grep, Glob
+allowed-tools: Read, Write, Edit, Bash(uv run python scripts/*:*, uv sync:*, mkdir:*, open:*), Grep, Glob
 ---
 
 Generate a research poster summarizing the experiment campaign as a single self-contained HTML file. Adapted from [posterskill](https://github.com/ethanweber/posterskill)'s architecture — no build step, works when opened as `file://`.
@@ -15,8 +15,8 @@ Read the experiment history and project context:
 
 ```bash
 cat config.yaml
-source .venv/bin/activate && python scripts/generate_brief.py
-source .venv/bin/activate && python scripts/show_metrics.py --last 20
+uv run python scripts/generate_brief.py
+uv run python scripts/show_metrics.py --last 20
 cat experiment_state.yaml 2>/dev/null || true
 cat RESEARCH_PLAN.md 2>/dev/null || true
 ```

package/commands/postmortem.md

@@ -8,8 +8,8 @@ allowed-tools: Read, Bash(*), Grep, Glob
 When experiments stop improving, find out why. Diagnoses search space exhaustion, config errors, data issues, metric ceilings, and noise floors.
 
 ## Steps
-1. `source .venv/bin/activate`
-2. `python scripts/failure_postmortem.py $ARGUMENTS`
+1. `uv sync`
+2. `uv run python scripts/failure_postmortem.py $ARGUMENTS`
 3. **Saved:** `experiments/postmortems/`
 
 ## Diagnosis categories

package/commands/preflight.md

@@ -2,28 +2,28 @@
 name: preflight
 description: Pre-flight resource check — estimates VRAM, RAM, and disk requirements before running ML training. Compares against available system resources and issues PASS/WARN/FAIL verdict. Use before training to catch OOM errors before they happen.
 argument-hint: "[--model-type torch] [--params 10M] [--batch-size 32]"
-allowed-tools: Read, Bash(python scripts/*:*, source .venv/bin/activate:*, nvidia-smi:*), Grep, Glob
+allowed-tools: Read, Bash(uv run python scripts/*:*, uv sync:*, nvidia-smi:*), Grep, Glob
 ---
 
 Check whether the current system has enough resources to run the planned experiment.
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Run preflight check:**
 
    If `$ARGUMENTS` is empty (auto-detect from config.yaml):
    ```bash
-   python scripts/preflight.py
+   uv run python scripts/preflight.py
    ```
 
    If `$ARGUMENTS` contains flags:
    ```bash
-   python scripts/preflight.py $ARGUMENTS
+   uv run python scripts/preflight.py $ARGUMENTS
    ```
 
 3. **Interpret the verdict:**

package/commands/present.md

@@ -8,8 +8,8 @@ allowed-tools: Read, Bash(*), Grep, Glob
 Generate presentation-ready figure specifications from experiment data in seconds.
 
 ## Steps
-1. **Activate environment:** `source .venv/bin/activate`
-2. **Run:** `python scripts/generate_figures.py $ARGUMENTS`
+1. **Sync environment:** `uv sync`
+2. **Run:** `uv run python scripts/generate_figures.py $ARGUMENTS`
 3. **Figure types:** training, comparison, ablation, pareto, sensitivity
 4. **Styles:** light (papers), dark (demos), poster (large fonts)
 5. **Saved output:** `paper/figures/`

package/commands/profile.md

@@ -9,9 +9,9 @@ Profile a training run to identify performance bottlenecks.
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -20,7 +20,7 @@ Profile a training run to identify performance bottlenecks.
 
 3. **Run profiling:**
    ```bash
-   python scripts/profile_training.py $ARGUMENTS
+   uv run python scripts/profile_training.py $ARGUMENTS
    ```
 
 4. **Report results:**

package/commands/prune.md

@@ -9,8 +9,8 @@ Remove redundant weights for faster inference and smaller models.
 
 ## Steps
 
-1. **Activate environment:** `source .venv/bin/activate`
-2. **Run:** `python scripts/model_pruning.py $ARGUMENTS`
+1. **Sync environment:** `uv sync`
+2. **Run:** `uv run python scripts/model_pruning.py $ARGUMENTS`
 3. **Methods:** magnitude (zero small weights), structured (remove neurons), lottery (iterative with rewind)
 4. **For tree models:** progressively reduces n_estimators
 5. **Report:** sparsity sweep table, knee point, recommended sparsity

package/commands/quantize.md

@@ -9,8 +9,8 @@ Quantize for production. Lowest-effort optimization: 2-4x speedup, 2-4x memory r
 
 ## Steps
 
-1. **Activate environment:** `source .venv/bin/activate`
-2. **Run:** `python scripts/model_quantization.py $ARGUMENTS`
+1. **Sync environment:** `uv sync`
+2. **Run:** `uv run python scripts/model_quantization.py $ARGUMENTS`
 3. **Precision levels:** FP32 (baseline), FP16 (GPU), INT8 dynamic (simplest), INT8 static (best accuracy)
 4. **Report:** precision comparison table, recommended level, QAT suggestion if needed
 5. **Saved output:** `experiments/quantization/<exp-id>-quantization.yaml`

package/commands/queue.md

@@ -9,9 +9,9 @@ Manage the experiment queue for unattended batch execution.
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -23,7 +23,7 @@ Manage the experiment queue for unattended batch execution.
 
 3. **Run queue manager:**
    ```bash
-   python scripts/experiment_queue.py $ARGUMENTS
+   uv run python scripts/experiment_queue.py $ARGUMENTS
    ```
 
 4. **Report results by action:**

package/commands/registry.md

@@ -8,8 +8,8 @@ allowed-tools: Read, Bash(*), Grep, Glob
 Track which model is production, staging, candidate, or archived. Promotion requires passing gates.
 
 ## Steps
-1. `source .venv/bin/activate`
-2. `python scripts/model_lifecycle.py $ARGUMENTS`
+1. `uv sync`
+2. `uv run python scripts/model_lifecycle.py $ARGUMENTS`
 3. **Registry:** `experiments/registry.yaml`
 
 ## Promotion gates

package/commands/regress.md

@@ -9,9 +9,9 @@ CI for your model. After any change to code, dependencies, or data, verify metri
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -23,7 +23,7 @@ CI for your model. After any change to code, dependencies, or data, verify metri
 
 3. **Run regression gate:**
    ```bash
-   python scripts/regression_gate.py $ARGUMENTS
+   uv run python scripts/regression_gate.py $ARGUMENTS
    ```
 
 4. **Report results:**

package/commands/replay.md

@@ -8,8 +8,8 @@ allowed-tools: Read, Bash(*), Grep, Glob
 Should you revisit old ideas? Infrastructure changes may make failed approaches work now.
 
 ## Steps
-1. **Activate environment:** `source .venv/bin/activate`
-2. **Run:** `python scripts/experiment_replay.py $ARGUMENTS`
+1. **Sync environment:** `uv sync`
+2. **Run:** `uv run python scripts/experiment_replay.py $ARGUMENTS`
 3. **Modes:** default (current code+data), --with-current-data, --with-current-preprocessing
 4. **Report:** original vs replayed metrics, delta, verdict
 5. **Saved output:** `experiments/replays/`

package/commands/report.md

@@ -2,7 +2,7 @@
 name: report
 description: Generate a markdown research report from experiment history — structured for sharing, archiving, or including in documentation. More detailed than a brief, less visual than a poster.
 argument-hint: "[--since YYYY-MM-DD] [--output path]"
-allowed-tools: Read, Bash(python scripts/*:*, source .venv/bin/activate:*, mkdir:*), Grep, Glob
+allowed-tools: Read, Bash(uv run python scripts/*:*, uv sync:*, mkdir:*), Grep, Glob
 ---
 
 Generate a structured markdown research report summarizing the experiment campaign.
@@ -14,12 +14,12 @@ Generate a structured markdown research report summarizing the experiment campai
 Use the logbook generator in markdown mode as the data backbone:
 
 ```bash
-source .venv/bin/activate && python scripts/generate_logbook.py --format markdown
+uv run python scripts/generate_logbook.py --format markdown
 ```
 
 Also gather supplementary data:
 ```bash
-source .venv/bin/activate && python scripts/generate_brief.py
+uv run python scripts/generate_brief.py
 cat experiment_state.yaml 2>/dev/null || true
 cat RESEARCH_PLAN.md 2>/dev/null || true
 ```

package/commands/reproduce.md

@@ -9,9 +9,9 @@ Verify that a logged experiment can be reproduced with consistent results.
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -22,7 +22,7 @@ Verify that a logged experiment can be reproduced with consistent results.
 
 3. **Run reproducibility verification:**
    ```bash
-   python scripts/reproduce_experiment.py $ARGUMENTS
+   uv run python scripts/reproduce_experiment.py $ARGUMENTS
    ```
 
 4. **Report results:**

package/commands/retry.md

@@ -9,9 +9,9 @@ Auto-diagnose and recover from experiment failures.
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -21,7 +21,7 @@ Auto-diagnose and recover from experiment failures.
 
 3. **Run smart retry:**
    ```bash
-   python scripts/smart_retry.py $ARGUMENTS
+   uv run python scripts/smart_retry.py $ARGUMENTS
    ```
 
 4. **Report results:**

package/commands/review.md

@@ -8,8 +8,8 @@ allowed-tools: Read, Bash(*), Grep, Glob
 Simulate a conference reviewer before you submit. Each weakness links to the command that fixes it.
 
 ## Steps
-1. `source .venv/bin/activate`
-2. `python scripts/simulate_review.py $ARGUMENTS`
+1. `uv sync`
+2. `uv run python scripts/simulate_review.py $ARGUMENTS`
 3. **Saved:** `experiments/reviews/`
 
 ## Examples

package/commands/rules/loop-protocol.md

@@ -16,9 +16,9 @@ The autoresearch harness enforces a strict separation between the **hypothesis s
 
 ## Execution Rules
 
-- **ALWAYS redirect training output:** `python train.py > run.log 2>&1`
+- **ALWAYS redirect training output:** `uv run python train.py > run.log 2>&1`
 - **ALWAYS parse metrics with grep** between `---` delimiters: `grep -A 10 "^---" run.log | head -10`
-- **ALWAYS activate the venv first:** `source .venv/bin/activate`
+- **ALWAYS run Python through uv:** `uv run python ...`
 - **NEVER install new packages** without human approval
 
 ## Git Discipline
@@ -40,16 +40,16 @@ The autoresearch harness enforces a strict separation between the **hypothesis s
 
 ## Sweep Workflow
 
-1. Generate queue: `python scripts/sweep.py`
-2. Check status: `python scripts/sweep.py --status`
-3. Get next: `python scripts/sweep.py --next`
+1. Generate queue: `uv run python scripts/sweep.py`
+2. Check status: `uv run python scripts/sweep.py --status`
+3. Get next: `uv run python scripts/sweep.py --next`
 4. Apply overrides, create branch, run training
-5. Mark: `python scripts/sweep.py --mark <name> complete|failed`
+5. Mark: `uv run python scripts/sweep.py --mark <name> complete|failed`
 6. Repeat until queue is empty
 
 ## Logging Rules
 
-- **Log every experiment** to `experiments/log.jsonl` via `python scripts/log_experiment.py` — kept and discarded alike.
+- **Log every experiment** to `experiments/log.jsonl` via `uv run python scripts/log_experiment.py` — kept and discarded alike.
 - **Include all metrics, config, and description** of the hypothesis and its outcome.
 
 ## Convergence Rules
@@ -64,11 +64,11 @@ The researcher agent's Bash access is restricted to a whitelist of necessary com
 
 | Allowed Pattern | Purpose |
 |-----------------|---------|
-| `python train.py:*` | Execute training |
-| `python scripts/*:*` | Run utility scripts (logging, metrics, sweep) |
+| `uv run python train.py:*` | Execute training |
+| `uv run python scripts/*:*` | Run utility scripts (logging, metrics, sweep) |
 | `git:*` | Branch, commit, merge, reset operations |
-| `source .venv/bin/activate:*` | Virtual environment activation |
-| `pip:*` | Package installation (requires human approval) |
+| `uv sync:*` | Virtual environment activation |
+| `uv add:*` | Package installation (requires human approval) |
 
 **Blocked by omission:** `cat`, `head`, `tail`, `less` (prevents reading hidden files via shell), `curl`, `wget` (prevents data exfiltration), arbitrary command execution.
 

package/commands/sanity.md

@@ -9,9 +9,9 @@ Run a battery of fast checks before committing to a full training run. Catches w
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -21,7 +21,7 @@ Run a battery of fast checks before committing to a full training run. Catches w
 
 3. **Run sanity checks:**
    ```bash
-   python scripts/sanity_checks.py $ARGUMENTS
+   uv run python scripts/sanity_checks.py $ARGUMENTS
    ```
 
 4. **Checks performed:**

package/commands/scale.md

@@ -9,9 +9,9 @@ Predict full-scale performance from a handful of small experiments. Answers "is
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -24,11 +24,11 @@ Predict full-scale performance from a handful of small experiments. Answers "is
 3. **Plan or analyze:**
    - **Plan mode (default):** generates scale point configs to run
      ```bash
-     python scripts/scaling_estimator.py --axis data --points 4
+     uv run python scripts/scaling_estimator.py --axis data --points 4
      ```
    - **Analyze mode:** fits power law to completed results
      ```bash
-     python scripts/scaling_estimator.py --analyze experiments/scaling/results.yaml
+     uv run python scripts/scaling_estimator.py --analyze experiments/scaling/results.yaml
      ```
 
 4. **Scaling axes:**

package/commands/search.md

@@ -8,8 +8,8 @@ allowed-tools: Read, Bash(*), Grep, Glob
 Find specific experiments in a large history with natural language and structured filters.
 
 ## Steps
-1. **Activate environment:** `source .venv/bin/activate`
-2. **Run:** `python scripts/experiment_search.py $ARGUMENTS`
+1. **Sync environment:** `uv sync`
+2. **Run:** `uv run python scripts/experiment_search.py $ARGUMENTS`
 3. **Filters:** `accuracy>0.85`, `status:kept`, `family:baseline`, `date:last-week`
 4. **Report:** ranked table of matching experiments
 

package/commands/seed.md

@@ -9,9 +9,9 @@ Run a multi-seed study to verify that experiment results are robust across rando
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -22,7 +22,7 @@ Run a multi-seed study to verify that experiment results are robust across rando
 
 3. **Run seed study:**
    ```bash
-   python scripts/seed_runner.py $ARGUMENTS
+   uv run python scripts/seed_runner.py $ARGUMENTS
    ```
 
 4. **Report results:**

package/commands/sensitivity.md

@@ -9,9 +9,9 @@ Which hyperparameters actually matter? Stop wasting time on the ones that don't.
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -21,7 +21,7 @@ Which hyperparameters actually matter? Stop wasting time on the ones that don't.
 
 3. **Run sensitivity analysis:**
    ```bash
-   python scripts/sensitivity_analysis.py $ARGUMENTS
+   uv run python scripts/sensitivity_analysis.py $ARGUMENTS
    ```
 
 4. **Report includes:**

package/commands/share.md

@@ -8,8 +8,8 @@ allowed-tools: Read, Bash(*), Grep, Glob
 Package experiments for collaborator handoff or paper supplementary material.
 
 ## Steps
-1. `source .venv/bin/activate`
-2. `python scripts/package_experiments.py $ARGUMENTS`
+1. `uv sync`
+2. `uv run python scripts/package_experiments.py $ARGUMENTS`
 3. **Saved:** `exports/packages/<name>/`
 
 ## Examples

package/commands/simulate.md

@@ -8,8 +8,8 @@ allowed-tools: Read, Bash(*), Grep, Glob
 Predict outcomes before spending compute. Ranks proposed configs and recommends which to run vs skip.
 
 ## Steps
-1. `source .venv/bin/activate`
-2. `python scripts/experiment_simulator.py $ARGUMENTS`
+1. `uv sync`
+2. `uv run python scripts/experiment_simulator.py $ARGUMENTS`
 3. **Saved:** `experiments/simulations/`
 
 ## How it works