@bastani/atomic 0.6.8 → 0.7.0-1

package/.agents/skills/skill-creator/scripts/run_loop.py

@@ -1,328 +0,0 @@
-#!/usr/bin/env python3
-"""Run the eval + improve loop until all pass or max iterations reached.
-
-Combines run_eval.py and improve_description.py in a loop, tracking history
-and returning the best description found. Supports train/test split to prevent
-overfitting.
-"""
-
-import argparse
-import json
-import random
-import sys
-import tempfile
-import time
-import webbrowser
-from pathlib import Path
-
-from scripts.generate_report import generate_html
-from scripts.improve_description import improve_description
-from scripts.run_eval import find_project_root, run_eval
-from scripts.utils import parse_skill_md
-
-
-def split_eval_set(eval_set: list[dict], holdout: float, seed: int = 42) -> tuple[list[dict], list[dict]]:
-    """Split eval set into train and test sets, stratified by should_trigger."""
-    random.seed(seed)
-
-    # Separate by should_trigger
-    trigger = [e for e in eval_set if e["should_trigger"]]
-    no_trigger = [e for e in eval_set if not e["should_trigger"]]
-
-    # Shuffle each group
-    random.shuffle(trigger)
-    random.shuffle(no_trigger)
-
-    # Calculate split points
-    n_trigger_test = max(1, int(len(trigger) * holdout))
-    n_no_trigger_test = max(1, int(len(no_trigger) * holdout))
-
-    # Split
-    test_set = trigger[:n_trigger_test] + no_trigger[:n_no_trigger_test]
-    train_set = trigger[n_trigger_test:] + no_trigger[n_no_trigger_test:]
-
-    return train_set, test_set
-
-
-def run_loop(
-    eval_set: list[dict],
-    skill_path: Path,
-    description_override: str | None,
-    num_workers: int,
-    timeout: int,
-    max_iterations: int,
-    runs_per_query: int,
-    trigger_threshold: float,
-    holdout: float,
-    model: str,
-    verbose: bool,
-    live_report_path: Path | None = None,
-    log_dir: Path | None = None,
-) -> dict:
-    """Run the eval + improvement loop."""
-    project_root = find_project_root()
-    name, original_description, content = parse_skill_md(skill_path)
-    current_description = description_override or original_description
-
-    # Split into train/test if holdout > 0
-    if holdout > 0:
-        train_set, test_set = split_eval_set(eval_set, holdout)
-        if verbose:
-            print(f"Split: {len(train_set)} train, {len(test_set)} test (holdout={holdout})", file=sys.stderr)
-    else:
-        train_set = eval_set
-        test_set = []
-
-    history = []
-    exit_reason = "unknown"
-
-    for iteration in range(1, max_iterations + 1):
-        if verbose:
-            print(f"\n{'='*60}", file=sys.stderr)
-            print(f"Iteration {iteration}/{max_iterations}", file=sys.stderr)
-            print(f"Description: {current_description}", file=sys.stderr)
-            print(f"{'='*60}", file=sys.stderr)
-
-        # Evaluate train + test together in one batch for parallelism
-        all_queries = train_set + test_set
-        t0 = time.time()
-        all_results = run_eval(
-            eval_set=all_queries,
-            skill_name=name,
-            description=current_description,
-            num_workers=num_workers,
-            timeout=timeout,
-            project_root=project_root,
-            runs_per_query=runs_per_query,
-            trigger_threshold=trigger_threshold,
-            model=model,
-        )
-        eval_elapsed = time.time() - t0
-
-        # Split results back into train/test by matching queries
-        train_queries_set = {q["query"] for q in train_set}
-        train_result_list = [r for r in all_results["results"] if r["query"] in train_queries_set]
-        test_result_list = [r for r in all_results["results"] if r["query"] not in train_queries_set]
-
-        train_passed = sum(1 for r in train_result_list if r["pass"])
-        train_total = len(train_result_list)
-        train_summary = {"passed": train_passed, "failed": train_total - train_passed, "total": train_total}
-        train_results = {"results": train_result_list, "summary": train_summary}
-
-        if test_set:
-            test_passed = sum(1 for r in test_result_list if r["pass"])
-            test_total = len(test_result_list)
-            test_summary = {"passed": test_passed, "failed": test_total - test_passed, "total": test_total}
-            test_results = {"results": test_result_list, "summary": test_summary}
-        else:
-            test_results = None
-            test_summary = None
-
-        history.append({
-            "iteration": iteration,
-            "description": current_description,
-            "train_passed": train_summary["passed"],
-            "train_failed": train_summary["failed"],
-            "train_total": train_summary["total"],
-            "train_results": train_results["results"],
-            "test_passed": test_summary["passed"] if test_summary else None,
-            "test_failed": test_summary["failed"] if test_summary else None,
-            "test_total": test_summary["total"] if test_summary else None,
-            "test_results": test_results["results"] if test_results else None,
-            # For backward compat with report generator
-            "passed": train_summary["passed"],
-            "failed": train_summary["failed"],
-            "total": train_summary["total"],
-            "results": train_results["results"],
-        })
-
-        # Write live report if path provided
-        if live_report_path:
-            partial_output = {
-                "original_description": original_description,
-                "best_description": current_description,
-                "best_score": "in progress",
-                "iterations_run": len(history),
-                "holdout": holdout,
-                "train_size": len(train_set),
-                "test_size": len(test_set),
-                "history": history,
-            }
-            live_report_path.write_text(generate_html(partial_output, auto_refresh=True, skill_name=name))
-
-        if verbose:
-            def print_eval_stats(label, results, elapsed):
-                pos = [r for r in results if r["should_trigger"]]
-                neg = [r for r in results if not r["should_trigger"]]
-                tp = sum(r["triggers"] for r in pos)
-                pos_runs = sum(r["runs"] for r in pos)
-                fn = pos_runs - tp
-                fp = sum(r["triggers"] for r in neg)
-                neg_runs = sum(r["runs"] for r in neg)
-                tn = neg_runs - fp
-                total = tp + tn + fp + fn
-                precision = tp / (tp + fp) if (tp + fp) > 0 else 1.0
-                recall = tp / (tp + fn) if (tp + fn) > 0 else 1.0
-                accuracy = (tp + tn) / total if total > 0 else 0.0
-                print(f"{label}: {tp+tn}/{total} correct, precision={precision:.0%} recall={recall:.0%} accuracy={accuracy:.0%} ({elapsed:.1f}s)", file=sys.stderr)
-                for r in results:
-                    status = "PASS" if r["pass"] else "FAIL"
-                    rate_str = f"{r['triggers']}/{r['runs']}"
-                    print(f"  [{status}] rate={rate_str} expected={r['should_trigger']}: {r['query'][:60]}", file=sys.stderr)
-
-            print_eval_stats("Train", train_results["results"], eval_elapsed)
-            if test_summary:
-                print_eval_stats("Test ", test_results["results"], 0)
-
-        if train_summary["failed"] == 0:
-            exit_reason = f"all_passed (iteration {iteration})"
-            if verbose:
-                print(f"\nAll train queries passed on iteration {iteration}!", file=sys.stderr)
-            break
-
-        if iteration == max_iterations:
-            exit_reason = f"max_iterations ({max_iterations})"
-            if verbose:
-                print(f"\nMax iterations reached ({max_iterations}).", file=sys.stderr)
-            break
-
-        # Improve the description based on train results
-        if verbose:
-            print(f"\nImproving description...", file=sys.stderr)
-
-        t0 = time.time()
-        # Strip test scores from history so improvement model can't see them
-        blinded_history = [
-            {k: v for k, v in h.items() if not k.startswith("test_")}
-            for h in history
-        ]
-        new_description = improve_description(
-            skill_name=name,
-            skill_content=content,
-            current_description=current_description,
-            eval_results=train_results,
-            history=blinded_history,
-            model=model,
-            log_dir=log_dir,
-            iteration=iteration,
-        )
-        improve_elapsed = time.time() - t0
-
-        if verbose:
-            print(f"Proposed ({improve_elapsed:.1f}s): {new_description}", file=sys.stderr)
-
-        current_description = new_description
-
-    # Find the best iteration by TEST score (or train if no test set)
-    if test_set:
-        best = max(history, key=lambda h: h["test_passed"] or 0)
-        best_score = f"{best['test_passed']}/{best['test_total']}"
-    else:
-        best = max(history, key=lambda h: h["train_passed"])
-        best_score = f"{best['train_passed']}/{best['train_total']}"
-
-    if verbose:
-        print(f"\nExit reason: {exit_reason}", file=sys.stderr)
-        print(f"Best score: {best_score} (iteration {best['iteration']})", file=sys.stderr)
-
-    return {
-        "exit_reason": exit_reason,
-        "original_description": original_description,
-        "best_description": best["description"],
-        "best_score": best_score,
-        "best_train_score": f"{best['train_passed']}/{best['train_total']}",
-        "best_test_score": f"{best['test_passed']}/{best['test_total']}" if test_set else None,
-        "final_description": current_description,
-        "iterations_run": len(history),
-        "holdout": holdout,
-        "train_size": len(train_set),
-        "test_size": len(test_set),
-        "history": history,
-    }
-
-
-def main():
-    parser = argparse.ArgumentParser(description="Run eval + improve loop")
-    parser.add_argument("--eval-set", required=True, help="Path to eval set JSON file")
-    parser.add_argument("--skill-path", required=True, help="Path to skill directory")
-    parser.add_argument("--description", default=None, help="Override starting description")
-    parser.add_argument("--num-workers", type=int, default=10, help="Number of parallel workers")
-    parser.add_argument("--timeout", type=int, default=30, help="Timeout per query in seconds")
-    parser.add_argument("--max-iterations", type=int, default=5, help="Max improvement iterations")
-    parser.add_argument("--runs-per-query", type=int, default=3, help="Number of runs per query")
-    parser.add_argument("--trigger-threshold", type=float, default=0.5, help="Trigger rate threshold")
-    parser.add_argument("--holdout", type=float, default=0.4, help="Fraction of eval set to hold out for testing (0 to disable)")
-    parser.add_argument("--model", required=True, help="Model for improvement")
-    parser.add_argument("--verbose", action="store_true", help="Print progress to stderr")
-    parser.add_argument("--report", default="auto", help="Generate HTML report at this path (default: 'auto' for temp file, 'none' to disable)")
-    parser.add_argument("--results-dir", default=None, help="Save all outputs (results.json, report.html, log.txt) to a timestamped subdirectory here")
-    args = parser.parse_args()
-
-    eval_set = json.loads(Path(args.eval_set).read_text())
-    skill_path = Path(args.skill_path)
-
-    if not (skill_path / "SKILL.md").exists():
-        print(f"Error: No SKILL.md found at {skill_path}", file=sys.stderr)
-        sys.exit(1)
-
-    name, _, _ = parse_skill_md(skill_path)
-
-    # Set up live report path
-    if args.report != "none":
-        if args.report == "auto":
-            timestamp = time.strftime("%Y%m%d_%H%M%S")
-            live_report_path = Path(tempfile.gettempdir()) / f"skill_description_report_{skill_path.name}_{timestamp}.html"
-        else:
-            live_report_path = Path(args.report)
-        # Open the report immediately so the user can watch
-        live_report_path.write_text("<html><body><h1>Starting optimization loop...</h1><meta http-equiv='refresh' content='5'></body></html>")
-        webbrowser.open(str(live_report_path))
-    else:
-        live_report_path = None
-
-    # Determine output directory (create before run_loop so logs can be written)
-    if args.results_dir:
-        timestamp = time.strftime("%Y-%m-%d_%H%M%S")
-        results_dir = Path(args.results_dir) / timestamp
-        results_dir.mkdir(parents=True, exist_ok=True)
-    else:
-        results_dir = None
-
-    log_dir = results_dir / "logs" if results_dir else None
-
-    output = run_loop(
-        eval_set=eval_set,
-        skill_path=skill_path,
-        description_override=args.description,
-        num_workers=args.num_workers,
-        timeout=args.timeout,
-        max_iterations=args.max_iterations,
-        runs_per_query=args.runs_per_query,
-        trigger_threshold=args.trigger_threshold,
-        holdout=args.holdout,
-        model=args.model,
-        verbose=args.verbose,
-        live_report_path=live_report_path,
-        log_dir=log_dir,
-    )
-
-    # Save JSON output
-    json_output = json.dumps(output, indent=2)
-    print(json_output)
-    if results_dir:
-        (results_dir / "results.json").write_text(json_output)
-
-    # Write final HTML report (without auto-refresh)
-    if live_report_path:
-        live_report_path.write_text(generate_html(output, auto_refresh=False, skill_name=name))
-        print(f"\nReport: {live_report_path}", file=sys.stderr)
-
-    if results_dir and live_report_path:
-        (results_dir / "report.html").write_text(generate_html(output, auto_refresh=False, skill_name=name))
-
-    if results_dir:
-        print(f"Results saved to: {results_dir}", file=sys.stderr)
-
-
-if __name__ == "__main__":
-    main()

package/.agents/skills/skill-creator/scripts/utils.py

@@ -1,47 +0,0 @@
-"""Shared utilities for skill-creator scripts."""
-
-from pathlib import Path
-
-
-
-def parse_skill_md(skill_path: Path) -> tuple[str, str, str]:
-    """Parse a SKILL.md file, returning (name, description, full_content)."""
-    content = (skill_path / "SKILL.md").read_text()
-    lines = content.split("\n")
-
-    if lines[0].strip() != "---":
-        raise ValueError("SKILL.md missing frontmatter (no opening ---)")
-
-    end_idx = None
-    for i, line in enumerate(lines[1:], start=1):
-        if line.strip() == "---":
-            end_idx = i
-            break
-
-    if end_idx is None:
-        raise ValueError("SKILL.md missing frontmatter (no closing ---)")
-
-    name = ""
-    description = ""
-    frontmatter_lines = lines[1:end_idx]
-    i = 0
-    while i < len(frontmatter_lines):
-        line = frontmatter_lines[i]
-        if line.startswith("name:"):
-            name = line[len("name:"):].strip().strip('"').strip("'")
-        elif line.startswith("description:"):
-            value = line[len("description:"):].strip()
-            # Handle YAML multiline indicators (>, |, >-, |-)
-            if value in (">", "|", ">-", "|-"):
-                continuation_lines: list[str] = []
-                i += 1
-                while i < len(frontmatter_lines) and (frontmatter_lines[i].startswith("  ") or frontmatter_lines[i].startswith("\t")):
-                    continuation_lines.append(frontmatter_lines[i].strip())
-                    i += 1
-                description = " ".join(continuation_lines)
-                continue
-            else:
-                description = value.strip('"').strip("'")
-        i += 1
-
-    return name, description, content

package/.agents/skills/sl-commit/SKILL.md

@@ -1,53 +0,0 @@
----
-name: sl-commit
-description: Create well-formatted commits with conventional commit format using Sapling.
-metadata:
-  provider: atomic
----
-
-# Smart Sapling Commit
-
-Create well-formatted commits following the Conventional Commits specification using Sapling SCM.
-
-<EXTREMELY_IMPORTANT>
-
-> **Windows Note:** Use the full path to `sl.exe` to avoid conflicts with PowerShell's built-in `sl` alias for `Set-Location`.
-> </EXTREMELY_IMPORTANT>
-
-## What This Skill Does
-
-1. Checks which files have changes with `sl status`
-2. If there are untracked files to include, adds them with `sl add`
-3. Performs a `sl diff` to understand what changes are being committed
-4. Analyzes the diff to determine if multiple distinct logical changes are present
-5. If multiple distinct changes are detected, suggests breaking the commit into multiple smaller commits
-6. For each commit, creates a commit message using conventional commit format
-
-## Commands to Use
-
-- `sl status` - Check repository state
-- `sl diff` - View pending changes
-- `sl add <files>` - Add untracked files
-- `sl commit -m "<message>"` - Create commit
-
-## Key Sapling Differences from Git
-
-- **No staging area**: Sapling commits all pending changes directly
-- **Amend with auto-restack**: `sl amend` automatically rebases descendant commits
-- **Stacked Diffs**: Each commit becomes a separate Phabricator diff
-
-## Sapling Commit Commands Reference
-
-| Command                  | Description                                     |
-| ------------------------ | ----------------------------------------------- |
-| `sl commit -m "message"` | Create a new commit with message                |
-| `sl commit -A`           | Add untracked files and commit                  |
-| `sl amend`               | Amend current commit (auto-rebases descendants) |
-| `sl amend --to COMMIT`   | Amend changes to a specific commit in stack     |
-
-## Important Notes
-
-- Follow pre-commit checks if configured
-- Keep commits small and focused - each becomes a separate Phabricator diff
-- Use `sl amend` freely - Sapling handles rebasing automatically
-- Attribute AI-assisted code authorship

package/.agents/skills/sl-submit-diff/SKILL.md

@@ -1,57 +0,0 @@
----
-name: sl-submit-diff
-description: Submit commits as Phabricator diffs for code review using Sapling.
-metadata:
-  provider: atomic
----
-
-# Submit Diff (Sapling + Phabricator)
-
-Submit commits to Phabricator for code review using `jf submit` (Meta).
-
-<EXTREMELY_IMPORTANT>
-
-> **Windows Note:** Use the full path to `sl.exe` to avoid conflicts with PowerShell's built-in `sl` alias for `Set-Location`.
-> </EXTREMELY_IMPORTANT>
-
-## What This Skill Does
-
-1. If there are uncommitted changes, first run `/commit` to create a commit
-2. Submit commits to Phabricator using `jf submit --draft`. Submit for review using DRAFT mode
-3. Each commit in the stack becomes a separate Phabricator diff (D12345)
-4. Commit messages are updated with `Differential Revision:` link
-
-## Commands to Use
-
-- `sl status` - Check for uncommitted changes
-- `jf submit --draft` - Submit commits to Phabricator in DRAFT mode
-- `sl diff --since-last-submit` - View changes since last submission
-
-## Common Operations
-
-| Task                    | Command                         |
-| ----------------------- | ------------------------------- |
-| Submit current commit   | `jf submit --draft`             |
-| Update diff after amend | `sl amend && jf submit --draft` |
-
-## Diff Status Values
-
-- `Needs Review` - Awaiting reviewer feedback
-- `Accepted` - Ready to land
-- `Needs Revision` - Reviewer requested changes
-- `Committed` - Diff has been landed
-- `Abandoned` - Diff was closed without landing
-
-## Stacked Diffs
-
-Sapling naturally supports stacked commits. When submitting:
-
-- Each commit gets its own Phabricator diff (D12345, D12346, D12347)
-- Diffs are linked with proper dependency relationships
-- Reviewers can review each diff independently
-
-## Important Notes
-
-- Unlike GitHub PRs, Phabricator diffs are tied to commits via `Differential Revision:`
-- Use `sl diff --since-last-submit` to see what changed since last submission
-- The ISL (Interactive Smartlog) web UI also supports submitting diffs

package/.agents/skills/tdd/SKILL.md

@@ -1,111 +0,0 @@
----
-name: tdd
-description: Test-driven development with red-green-refactor loop. Use when user wants to build features or fix bugs using TDD, mentions "red-green-refactor", wants integration tests, or asks for test-first development.
-metadata:
-  provider: atomic
----
-
-# Test-Driven Development
-
-## Philosophy
-
-**Core principle**: Tests should verify behavior through public interfaces, not implementation details. Code can change entirely; tests shouldn't.
-
-**Good tests** are integration-style: they exercise real code paths through public APIs. They describe _what_ the system does, not _how_ it does it. A good test reads like a specification - "user can checkout with valid cart" tells you exactly what capability exists. These tests survive refactors because they don't care about internal structure.
-
-**Bad tests** are coupled to implementation. They mock internal collaborators, test private methods, or verify through external means (like querying a database directly instead of using the interface). The warning sign: your test breaks when you refactor, but behavior hasn't changed. If you rename an internal function and tests fail, those tests were testing implementation, not behavior.
-
-See [tests.md](tests.md) for examples and [mocking.md](mocking.md) for mocking guidelines.
-
-## Anti-Pattern: Horizontal Slices
-
-**DO NOT write all tests first, then all implementation.** This is "horizontal slicing" - treating RED as "write all tests" and GREEN as "write all code."
-
-This produces **crap tests**:
-
-- Tests written in bulk test _imagined_ behavior, not _actual_ behavior
-- You end up testing the _shape_ of things (data structures, function signatures) rather than user-facing behavior
-- Tests become insensitive to real changes - they pass when behavior breaks, fail when behavior is fine
-- You outrun your headlights, committing to test structure before understanding the implementation
-
-**Correct approach**: Vertical slices via tracer bullets. One test → one implementation → repeat. Each test responds to what you learned from the previous cycle. Because you just wrote the code, you know exactly what behavior matters and how to verify it.
-
-```
-WRONG (horizontal):
-  RED:   test1, test2, test3, test4, test5
-  GREEN: impl1, impl2, impl3, impl4, impl5
-
-RIGHT (vertical):
-  RED→GREEN: test1→impl1
-  RED→GREEN: test2→impl2
-  RED→GREEN: test3→impl3
-  ...
-```
-
-## Workflow
-
-### 1. Planning
-
-When exploring the codebase, use the project's domain glossary so that test names and interface vocabulary match the project's language, and respect ADRs in the area you're touching.
-
-Before writing any code:
-
-- [ ] Confirm with user what interface changes are needed
-- [ ] Confirm with user which behaviors to test (prioritize)
-- [ ] Identify opportunities for [deep modules](deep-modules.md) (small interface, deep implementation)
-- [ ] Design interfaces for [testability](interface-design.md)
-- [ ] List the behaviors to test (not implementation steps)
-- [ ] Get user approval on the plan
-
-Ask: "What should the public interface look like? Which behaviors are most important to test?"
-
-**You can't test everything.** Confirm with the user exactly which behaviors matter most. Focus testing effort on critical paths and complex logic, not every possible edge case.
-
-### 2. Tracer Bullet
-
-Write ONE test that confirms ONE thing about the system:
-
-```
-RED:   Write test for first behavior → test fails
-GREEN: Write minimal code to pass → test passes
-```
-
-This is your tracer bullet - proves the path works end-to-end.
-
-### 3. Incremental Loop
-
-For each remaining behavior:
-
-```
-RED:   Write next test → fails
-GREEN: Minimal code to pass → passes
-```
-
-Rules:
-
-- One test at a time
-- Only enough code to pass current test
-- Don't anticipate future tests
-- Keep tests focused on observable behavior
-
-### 4. Refactor
-
-After all tests pass, look for [refactor candidates](refactoring.md):
-
-- [ ] Extract duplication
-- [ ] Deepen modules (move complexity behind simple interfaces)
-- [ ] Apply SOLID principles where natural
-- [ ] Consider what new code reveals about existing code
-- [ ] Run tests after each refactor step
-
-**Never refactor while RED.** Get to GREEN first.
-
-## Checklist Per Cycle
-
-```
-[ ] Test describes behavior, not implementation
-[ ] Test uses public interface only
-[ ] Test would survive internal refactor
-[ ] Code is minimal for this test
-[ ] No speculative features added
-```

package/.agents/skills/tdd/deep-modules.md

@@ -1,33 +0,0 @@
-# Deep Modules
-
-From "A Philosophy of Software Design":
-
-**Deep module** = small interface + lots of implementation
-
-```
-┌─────────────────────┐
-│   Small Interface   │  ← Few methods, simple params
-├─────────────────────┤
-│                     │
-│                     │
-│  Deep Implementation│  ← Complex logic hidden
-│                     │
-│                     │
-└─────────────────────┘
-```
-
-**Shallow module** = large interface + little implementation (avoid)
-
-```
-┌─────────────────────────────────┐
-│       Large Interface           │  ← Many methods, complex params
-├─────────────────────────────────┤
-│  Thin Implementation            │  ← Just passes through
-└─────────────────────────────────┘
-```
-
-When designing interfaces, ask:
-
-- Can I reduce the number of methods?
-- Can I simplify the parameters?
-- Can I hide more complexity inside?

package/.agents/skills/tdd/interface-design.md

@@ -1,31 +0,0 @@
-# Interface Design for Testability
-
-Good interfaces make testing natural:
-
-1. **Accept dependencies, don't create them**
-
-   ```typescript
-   // Testable
-   function processOrder(order, paymentGateway) {}
-
-   // Hard to test
-   function processOrder(order) {
-     const gateway = new StripeGateway();
-   }
-   ```
-
-2. **Return results, don't produce side effects**
-
-   ```typescript
-   // Testable
-   function calculateDiscount(cart): Discount {}
-
-   // Hard to test
-   function applyDiscount(cart): void {
-     cart.total -= discount;
-   }
-   ```
-
-3. **Small surface area**
-   - Fewer methods = fewer tests needed
-   - Fewer params = simpler test setup