claude-turing 4.8.0 → 4.8.1

package/commands/status.md

@@ -10,7 +10,7 @@ Show the current state of the ML training pipeline. This is an observation-only
 
 1. **Run metrics display:**
    ```bash
-   source .venv/bin/activate && python scripts/show_metrics.py --last 10
+   uv run python scripts/show_metrics.py --last 10
    ```
 
 2. **Summarize for the user:**

package/commands/stitch.md

@@ -9,9 +9,9 @@ Decompose your ML pipeline into stages that can be independently varied, cached,
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -23,7 +23,7 @@ Decompose your ML pipeline into stages that can be independently varied, cached,
 
 3. **Run pipeline manager:**
    ```bash
-   python scripts/pipeline_manager.py $ARGUMENTS
+   uv run python scripts/pipeline_manager.py $ARGUMENTS
    ```
 
 4. **Report results:**

package/commands/suggest.md

@@ -2,7 +2,7 @@
 name: suggest
 description: Literature-grounded model selection. Reads the ML task context, searches recent literature, and suggests model architectures worth trying — with citations. Suggestions are auto-queued as hypotheses.
 argument-hint: "[task description override]"
-allowed-tools: Read, Write, Bash(python scripts/*:*, source .venv/bin/activate:*), Grep, Glob, WebSearch, WebFetch
+allowed-tools: Read, Write, Bash(uv run python scripts/*:*, uv sync:*), Grep, Glob, WebSearch, WebFetch
 ---
 
 Suggest model architectures for the current ML task. Supports two strategies:
@@ -25,7 +25,7 @@ cat config.yaml
 ```
 
 ```bash
-source .venv/bin/activate && python scripts/show_metrics.py --last 10 2>/dev/null || echo "No experiments yet"
+uv run python scripts/show_metrics.py --last 10 2>/dev/null || echo "No experiments yet"
 ```
 
 If `$ARGUMENTS` is provided, use that as the task description. Otherwise, infer from `config.yaml` (model type, primary metric, data source, target column).
@@ -66,7 +66,7 @@ From the literature, synthesize **3-5 concrete model architecture suggestions**.
 For each suggestion, add to the hypothesis queue:
 
 ```bash
-source .venv/bin/activate && python scripts/manage_hypotheses.py add "<model>: <rationale> (source: <citation>)" --priority medium --source literature
+uv run python scripts/manage_hypotheses.py add "<model>: <rationale> (source: <citation>)" --priority medium --source literature
 ```
 
 ### 5. Show Results
@@ -105,7 +105,7 @@ Same detection logic as the literature strategy — find `config.yaml` + `train.
 ### 2. Run Tree Search
 
 ```bash
-source .venv/bin/activate && python scripts/treequest_suggest.py \
+uv run python scripts/treequest_suggest.py \
     --log experiments/log.jsonl \
     --config config.yaml \
     --top 5 \
@@ -120,7 +120,7 @@ If TreeQuest is not installed, the script automatically falls back to greedy bes
 For each result from the tree search, queue as a hypothesis:
 
 ```bash
-source .venv/bin/activate && python scripts/manage_hypotheses.py add "<description>" --priority medium --source treequest
+uv run python scripts/manage_hypotheses.py add "<description>" --priority medium --source treequest
 ```
 
 ### 4. Show Results

package/commands/surgery.md

@@ -9,8 +9,8 @@ Programmatic architecture changes with auto warm-start from existing weights.
 
 ## Steps
 
-1. **Activate environment:** `source .venv/bin/activate`
-2. **Run:** `python scripts/architecture_surgery.py $ARGUMENTS`
+1. **Sync environment:** `uv sync`
+2. **Run:** `uv run python scripts/architecture_surgery.py $ARGUMENTS`
 3. **Operations:** add-layer, remove-layer, widen, narrow, swap-activation, add-skip, add-norm, deepen, swap-objective
 4. **For tree models:** deepen (increase max_depth), widen (more estimators), swap-objective
 5. **Report:** operation details, config changes, parameter count delta, warm-start source

package/commands/sweep.md

@@ -2,38 +2,38 @@
 name: sweep
 description: Generate and run a systematic hyperparameter sweep. Computes the cartesian product of configured parameter ranges and processes the queue sequentially with full experiment logging.
 argument-hint: "[sweep_config.yaml]"
-allowed-tools: Read, Write, Edit, Bash(python train.py:*, python scripts/*:*, git:*, source .venv/bin/activate:*, pip:*), Grep, Glob
+allowed-tools: Read, Write, Edit, Bash(uv run python train.py:*, uv run python scripts/*:*, git:*, uv sync:*, uv add:*), Grep, Glob
 ---
 
 Run a systematic hyperparameter sweep using the sweep configuration.
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Resolve config:** Use `$ARGUMENTS` as sweep config path, or default to `sweep_config.yaml`.
 
 3. **Generate queue** (if not already generated):
    ```bash
-   python scripts/sweep.py [sweep_config.yaml]
+   uv run python scripts/sweep.py [sweep_config.yaml]
    ```
 
 4. **Check queue status:**
    ```bash
-   python scripts/sweep.py --status
+   uv run python scripts/sweep.py --status
    ```
 
 5. **Process queue sequentially:**
-   - Get next: `python scripts/sweep.py --next`
+   - Get next: `uv run python scripts/sweep.py --next`
    - Apply config overrides to `config.yaml`
    - Create experiment branch: `git checkout -b exp/NNN-description`
-   - Run training: `python train.py > run.log 2>&1`
+   - Run training: `uv run python train.py > run.log 2>&1`
    - Parse metrics: `grep -A 10 "^---" run.log | head -10`
    - Log the experiment
-   - Mark complete: `python scripts/sweep.py --mark <name> complete`
+   - Mark complete: `uv run python scripts/sweep.py --mark <name> complete`
    - If improved, merge to main. If not, return to main.
    - Repeat until queue is empty
 

package/commands/template.md

@@ -8,8 +8,8 @@ allowed-tools: Read, Bash(*), Grep, Glob
 Turn your best experiment configs into reusable recipes that persist across projects.
 
 ## Steps
-1. **Activate environment:** `source .venv/bin/activate`
-2. **Run:** `python scripts/experiment_templates.py $ARGUMENTS`
+1. **Sync environment:** `uv sync`
+2. **Run:** `uv run python scripts/experiment_templates.py $ARGUMENTS`
 3. **Operations:** save (from experiment), list (all templates), apply (to current project), share (export)
 4. **Stored at:** `~/.turing/templates/` (cross-project)
 

package/commands/train.md

@@ -2,7 +2,7 @@
 name: train
 description: Run the autonomous ML experiment loop. Iteratively hypothesizes, trains, evaluates, and decides — keeping only improvements. Implements the autoresearch pattern with formal convergence detection and git-disciplined rollback.
 argument-hint: "[max_iterations]"
-allowed-tools: Read, Write, Edit, Bash(python train.py:*, python scripts/*:*, git:*, source .venv/bin/activate:*, pip:*), Grep, Glob
+allowed-tools: Read, Write, Edit, Bash(uv run python train.py:*, uv run python scripts/*:*, git:*, uv sync:*, uv add:*), Grep, Glob
 ---
 
 You are an autonomous ML researcher. Your goal: iteratively improve a model by following the experiment loop protocol — the scientific method applied to machine learning.
@@ -26,9 +26,9 @@ Read `program.md` in the ML project directory for the complete protocol. Follow
 
 1. **Restore memory:** Read `.claude/agent-memory/ml-researcher-{project_name}/MEMORY.md` for prior observations and best results.
 2. **Read protocol:** Read `program.md` completely — it defines the experiment loop, constraints, and output format.
-3. **Bootstrap data:** Check for training data at `config.yaml` → `data.source`. If no splits exist, run `python prepare.py`.
-4. **Bootstrap venv:** `test -d .venv || (python3 -m venv .venv && source .venv/bin/activate && pip install -r requirements.txt)`
-5. **Assess state:** `source .venv/bin/activate && python scripts/show_metrics.py --last 5`
+3. **Bootstrap data:** Check for training data at `config.yaml` → `data.source`. If no splits exist, run `uv run python prepare.py`.
+4. **Bootstrap uv environment:** `uv sync`
+5. **Assess state:** `uv run python scripts/show_metrics.py --last 5`
 6. **Begin the loop** from program.md.
 
 ## The Loop
@@ -47,7 +47,7 @@ Use `@ml-evaluator` for analysis tasks. It is read-only (no Write/Edit) and cann
 
 ## Context Management
 
-- Redirect all training output: `python train.py > run.log 2>&1`
+- Redirect all training output: `uv run python train.py > run.log 2>&1`
 - Parse metrics with grep, never read full output
 - Persist observations to MEMORY.md after each experiment
 

package/commands/transfer.md

@@ -9,9 +9,9 @@ Find similar prior projects and surface what worked. "Last time you had tabular
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -22,7 +22,7 @@ Find similar prior projects and surface what worked. "Last time you had tabular
 
 3. **Run knowledge transfer:**
    ```bash
-   python scripts/knowledge_transfer.py $ARGUMENTS
+   uv run python scripts/knowledge_transfer.py $ARGUMENTS
    ```
 
 4. **Report includes:**

package/commands/trend.md

@@ -8,8 +8,8 @@ allowed-tools: Read, Bash(*), Grep, Glob
 See the arc of your research, not just the latest results. Strategic view over 100+ experiments.
 
 ## Steps
-1. **Activate environment:** `source .venv/bin/activate`
-2. **Run:** `python scripts/trend_analysis.py $ARGUMENTS`
+1. **Sync environment:** `uv sync`
+2. **Run:** `uv run python scripts/trend_analysis.py $ARGUMENTS`
 3. **Report:** improvement velocity over time windows, family ROI ranking, diminishing returns prediction, phase transitions
 4. **Saved output:** `experiments/trends/trend-*.yaml`
 

package/commands/try.md

@@ -2,7 +2,7 @@
 name: try
 description: Inject a hypothesis into the agent's experiment queue. This is how research taste reaches the agent — the human selects which coins to flip, the agent flips them.
 argument-hint: "<hypothesis description>"
-allowed-tools: Read, Write, Edit, Bash(python scripts/*:*, source .venv/bin/activate:*), Grep, Glob
+allowed-tools: Read, Write, Edit, Bash(uv run python scripts/*:*, uv sync:*), Grep, Glob
 ---
 
 Inject a human hypothesis into the experiment queue for the next `/turing:train` iteration.
@@ -15,18 +15,18 @@ This is the taste-leverage mechanism: you provide judgment about what's worth tr
 
 2. **Check for archetype syntax.** If the argument starts with `archetype:`, expand it:
    ```bash
-   source .venv/bin/activate && python scripts/manage_hypotheses.py add --archetype <name> --priority high --source human
+   uv run python scripts/manage_hypotheses.py add --archetype <name> --priority high --source human
    ```
 
    Otherwise, use the raw description:
    ```bash
-   source .venv/bin/activate && python scripts/manage_hypotheses.py add "$ARGUMENTS" --priority high --source human
+   uv run python scripts/manage_hypotheses.py add "$ARGUMENTS" --priority high --source human
    ```
 
 3. **Confirm** with the hypothesis ID and instructions:
    - "Queued as hyp-NNN (high priority, human-injected)"
    - "The agent will prioritize this on the next `/turing:train` iteration"
-   - Show current queue: `python scripts/manage_hypotheses.py list --status queued`
+   - Show current queue: `uv run python scripts/manage_hypotheses.py list --status queued`
 
 ## Examples
 

package/commands/update.md

@@ -8,8 +8,8 @@ allowed-tools: Read, Bash(*), Grep, Glob
 Add new data to an existing model without starting from scratch. Detects catastrophic forgetting.
 
 ## Steps
-1. `source .venv/bin/activate`
-2. `python scripts/incremental_update.py $ARGUMENTS`
+1. `uv sync`
+2. `uv run python scripts/incremental_update.py $ARGUMENTS`
 3. **Saved:** `experiments/updates/`
 
 ## Model-specific strategies

package/commands/validate.md

@@ -9,19 +9,19 @@ Validate the stability of the current ML pipeline by running it multiple times a
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Run stability check:**
    ```bash
-   python scripts/validate_stability.py
+   uv run python scripts/validate_stability.py
    ```
 
 3. **If `$ARGUMENTS` contains `--auto`:**
    ```bash
-   python scripts/validate_stability.py --auto
+   uv run python scripts/validate_stability.py --auto
    ```
    This auto-writes `evaluation.n_runs: 3` to `config.yaml` if CV > 5%.
 

package/commands/warm.md

@@ -9,9 +9,9 @@ Take a trained checkpoint and use it as initialization for a new experiment. Aut
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -23,7 +23,7 @@ Take a trained checkpoint and use it as initialization for a new experiment. Aut
 
 3. **Run warm-start planner:**
    ```bash
-   python scripts/warm_start.py $ARGUMENTS
+   uv run python scripts/warm_start.py $ARGUMENTS
    ```
 
 4. **Report results:**

package/commands/watch.md

@@ -9,9 +9,9 @@ Stream metrics during training with early-warning alerts. Catches problems mid-r
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -23,13 +23,13 @@ Stream metrics during training with early-warning alerts. Catches problems mid-r
 
 3. **For post-hoc analysis:**
    ```bash
-   python scripts/training_monitor.py --analyze run.log
+   uv run python scripts/training_monitor.py --analyze run.log
    ```
 
 4. **For live monitoring (inform user):**
    Live monitoring requires a running training process. Suggest the user run in a separate terminal:
    ```bash
-   python scripts/training_monitor.py --log run.log --interval 10
+   uv run python scripts/training_monitor.py --log run.log --interval 10
    ```
 
 5. **Alert types:**

package/commands/whatif.md

@@ -8,8 +8,8 @@ allowed-tools: Read, Bash(*), Grep, Glob
 Answer "what if?" questions using existing experiment data. Routes to the right estimator automatically.
 
 ## Steps
-1. `source .venv/bin/activate`
-2. `python scripts/whatif_engine.py $ARGUMENTS`
+1. `uv sync`
+2. `uv run python scripts/whatif_engine.py $ARGUMENTS`
 3. **Saved:** `experiments/whatif/`
 
 ## Supported question types

package/commands/xray.md

@@ -9,9 +9,9 @@ See inside the model. When it underperforms, the fix depends on *why*.
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -22,7 +22,7 @@ See inside the model. When it underperforms, the fix depends on *why*.
 
 3. **Run model diagnostics:**
    ```bash
-   python scripts/model_xray.py $ARGUMENTS
+   uv run python scripts/model_xray.py $ARGUMENTS
    ```
 
 4. **Diagnostics by model type:**

package/config/commands.yaml

@@ -332,7 +332,7 @@ commands:
     - Glob
     argument_hint: '[--metrics "accuracy,train_seconds,n_params"] [--ascii]'
   init:
-    description: "Initialize a new ML project with the Turing autoresearch harness. Scaffolds the full experiment infrastructure \u2014 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 \u2014 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."
     lifecycle: setup
     invocation_mode: slash_only
     model_invocation: enabled

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "claude-turing",
-  "version": "4.8.0",
+  "version": "4.8.1",
   "type": "module",
   "description": "Autonomous ML research harness for Claude Code. The autoresearch loop as a formal protocol — iteratively trains, evaluates, and improves ML models with structured experiment tracking, convergence detection, immutable evaluation infrastructure, and safety guardrails.",
   "bin": {

package/skills/turing/ablate/SKILL.md

@@ -9,9 +9,9 @@ Run a systematic ablation study to measure the contribution of each model compon
 
 ## 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 systematic ablation study to measure the contribution of each model compon
 
 3. **Run ablation study:**
    ```bash
-   python scripts/ablation_study.py $ARGUMENTS
+   uv run python scripts/ablation_study.py $ARGUMENTS
    ```
 
 4. **Report results:**

package/skills/turing/annotate/SKILL.md

@@ -8,8 +8,8 @@ allowed-tools: Read, Bash(*), Grep, Glob
 Add context that experiment logs can't capture. "This only worked because the data was pre-sorted."
 
 ## Steps
-1. **Activate environment:** `source .venv/bin/activate`
-2. **Run:** `python scripts/experiment_annotations.py $ARGUMENTS`
+1. **Sync environment:** `uv sync`
+2. **Run:** `uv run python scripts/experiment_annotations.py $ARGUMENTS`
 3. **Operations:** add (text + tags), list (per-experiment or all), search (keyword or tag)
 4. **Stored in:** `experiments/annotations.yaml`
 

package/skills/turing/archive/SKILL.md

@@ -8,8 +8,8 @@ allowed-tools: Read, Bash(*), Grep, Glob
 Keep your project directory manageable after 200+ experiments.
 
 ## Steps
-1. **Activate environment:** `source .venv/bin/activate`
-2. **Run:** `python scripts/experiment_archive.py $ARGUMENTS`
+1. **Sync environment:** `uv sync`
+2. **Run:** `uv run python scripts/experiment_archive.py $ARGUMENTS`
 3. **Protected experiments:** Pareto-optimal, current best, recent, top-N by metric
 4. **Report:** archived count, preserved count, space reclaimed
 5. **Saved output:** `experiments/archive/index.yaml`

package/skills/turing/audit/SKILL.md

@@ -9,9 +9,9 @@ A reviewer checklist you run before submitting. Catches methodology mistakes tha
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -21,7 +21,7 @@ A reviewer checklist you run before submitting. Catches methodology mistakes tha
 
 3. **Run methodology audit:**
    ```bash
-   python scripts/methodology_audit.py $ARGUMENTS
+   uv run python scripts/methodology_audit.py $ARGUMENTS
    ```
 
 4. **Checks performed:**

package/skills/turing/baseline/SKILL.md

@@ -9,9 +9,9 @@ Generate trivial baselines so you always know if your model is meaningfully bett
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -21,7 +21,7 @@ Generate trivial baselines so you always know if your model is meaningfully bett
 
 3. **Run baseline generation:**
    ```bash
-   python scripts/generate_baselines.py $ARGUMENTS
+   uv run python scripts/generate_baselines.py $ARGUMENTS
    ```
 
 4. **Baselines generated:**

package/skills/turing/brief/SKILL.md

@@ -2,7 +2,7 @@
 name: brief
 description: Generate a structured research intelligence report from experiment history — what's been learned, what's promising, what's exhausted, and what the human should consider next. Use --deep for literature-grounded suggestions.
 argument-hint: "[ml/project] [--deep]"
-allowed-tools: Read, Bash(python scripts/*:*, source .venv/bin/activate:*), Grep, Glob, WebSearch, WebFetch
+allowed-tools: Read, Bash(uv run python scripts/*:*, uv sync:*), Grep, Glob, WebSearch, WebFetch
 ---
 
 Generate a research briefing that a human can read in 2 minutes and immediately decide what to inject next.
@@ -23,14 +23,14 @@ Before generating the briefing, detect which project to report on:
 
 1. **Generate the briefing:**
    ```bash
-   source .venv/bin/activate && python scripts/generate_brief.py
+   uv run python scripts/generate_brief.py
    ```
 
 2. **Self-critique the briefing** before presenting. Review the generated output and check:
    - **Recommendations specificity:** Are they concrete enough to act on? "Try a different model" is bad. "Try LightGBM with leaf-wise growth because exp-004 showed depth sensitivity" is good. If vague, rewrite them with specific model/hyperparameter suggestions grounded in the experiment data.
    - **Exhausted directions coverage:** Cross-reference the "Model Types Explored" section against `experiments/log.jsonl`. Are there discarded experiments missing from the summary? If so, add them.
    - **Convergence estimate grounding:** If the briefing says "close to convergence" or "further improvement possible", verify against the actual metric trajectory. Is the claim supported by the numbers?
-   - **Metric accuracy:** Spot-check that the "Current Best" metrics match the actual log. Run `python scripts/show_metrics.py --last 1` if uncertain.
+   - **Metric accuracy:** Spot-check that the "Current Best" metrics match the actual log. Run `uv run python scripts/show_metrics.py --last 1` if uncertain.
 
    If any section fails the check, regenerate just that section. Max 1 revision round — don't over-polish.
 
@@ -75,7 +75,7 @@ When `--deep` is requested, add a 7th section: **Literature-Grounded Suggestions
 
 4. **Queue suggestions** as hypotheses:
    ```bash
-   source .venv/bin/activate && python scripts/manage_hypotheses.py add "<technique>: <rationale> (source: <citation>)" --priority medium --source literature
+   uv run python scripts/manage_hypotheses.py add "<technique>: <rationale> (source: <citation>)" --priority medium --source literature
    ```
 
 5. **Format as a section** appended to the briefing.
@@ -83,7 +83,7 @@ When `--deep` is requested, add a 7th section: **Literature-Grounded Suggestions
 ## Saving Briefs
 
 ```bash
-mkdir -p briefs && python scripts/generate_brief.py > briefs/brief-$(date +%Y-%m-%d).md
+mkdir -p briefs && uv run python scripts/generate_brief.py > briefs/brief-$(date +%Y-%m-%d).md
 ```
 
 ## When to Use

package/skills/turing/budget/SKILL.md

@@ -9,9 +9,9 @@ Set a compute ceiling and let the system optimize within it. Prevents runaway ex
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -22,7 +22,7 @@ Set a compute ceiling and let the system optimize within it. Prevents runaway ex
 
 3. **Run budget manager:**
    ```bash
-   python scripts/budget_manager.py $ARGUMENTS
+   uv run python scripts/budget_manager.py $ARGUMENTS
    ```
 
 4. **Actions:**

package/skills/turing/calibrate/SKILL.md

@@ -9,9 +9,9 @@ Make model probabilities trustworthy. Does 80% confidence actually mean 80% corr
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -21,7 +21,7 @@ Make model probabilities trustworthy. Does 80% confidence actually mean 80% corr
 
 3. **Run calibration:**
    ```bash
-   python scripts/calibration.py $ARGUMENTS
+   uv run python scripts/calibration.py $ARGUMENTS
    ```
 
 4. **Report includes:**

package/skills/turing/card/SKILL.md

@@ -1,7 +1,7 @@
 ---
 name: card
 description: Generate a standardized model card documenting the trained model — type, performance, training data, limitations, intended use, and artifact contract.
-allowed-tools: Read, Bash(python scripts/*:*, source .venv/bin/activate:*), Grep, Glob
+allowed-tools: Read, Bash(uv run python scripts/*:*, uv sync:*), Grep, Glob
 ---
 
 You generate a standardized model card from the experiment log, model contract, and config.
@@ -10,12 +10,12 @@ You generate a standardized model card from the experiment log, model contract,
 
 1. **Activate the virtual environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Run the model card generator:**
    ```bash
-   python scripts/generate_model_card.py --config config.yaml --log experiments/log.jsonl --contract model_contract.md --output MODEL_CARD.md
+   uv run python scripts/generate_model_card.py --config config.yaml --log experiments/log.jsonl --contract model_contract.md --output MODEL_CARD.md
    ```
 
 3. **Read and present the generated card:**

package/skills/turing/changelog/SKILL.md

@@ -8,8 +8,8 @@ allowed-tools: Read, Bash(*), Grep, Glob
 Translate experiment logs into a narrative that PMs and stakeholders can read in 2 minutes.
 
 ## Steps
-1. **Activate environment:** `source .venv/bin/activate`
-2. **Run:** `python scripts/generate_changelog.py $ARGUMENTS`
+1. **Sync environment:** `uv sync`
+2. **Run:** `uv run python scripts/generate_changelog.py $ARGUMENTS`
 3. **Audience:** technical (experiment IDs, configs), stakeholder (plain English, percentages)
 4. **Saved output:** `paper/CHANGELOG.md`
 

package/skills/turing/checkpoint/SKILL.md

@@ -9,9 +9,9 @@ Manage model checkpoints intelligently using Pareto dominance.
 
 ## Steps
 
-1. **Activate environment:**
+1. **Sync environment:**
    ```bash
-   source .venv/bin/activate
+   uv sync
    ```
 
 2. **Parse arguments from `$ARGUMENTS`:**
@@ -22,7 +22,7 @@ Manage model checkpoints intelligently using Pareto dominance.
 
 3. **Run checkpoint manager:**
    ```bash
-   python scripts/checkpoint_manager.py $ARGUMENTS
+   uv run python scripts/checkpoint_manager.py $ARGUMENTS
    ```
 
 4. **Report results by action:**

package/skills/turing/cite/SKILL.md

@@ -8,8 +8,8 @@ allowed-tools: Read, Bash(*), Grep, Glob
 Track which papers and methods influenced each experiment. Catch missing citations before submission.
 
 ## Steps
-1. **Activate environment:** `source .venv/bin/activate`
-2. **Run:** `python scripts/citation_manager.py $ARGUMENTS`
+1. **Sync environment:** `uv sync`
+2. **Run:** `uv run python scripts/citation_manager.py $ARGUMENTS`
 3. **Operations:** add (associate citation with experiment), list (group by type), check (audit missing), bib (BibTeX)
 4. **Stored in:** `experiments/citations.yaml`
 

package/skills/turing/compare/SKILL.md

@@ -11,7 +11,7 @@ Compare two ML experiment runs side-by-side to understand what changed and why o
 
 1. **Run comparison:**
    ```bash
-   source .venv/bin/activate && python scripts/compare_runs.py $0 $1
+   uv run python scripts/compare_runs.py $0 $1
    ```
 
 2. **Analyze the delta:**