biotonomy 0.2.2 → 0.2.4

package/commands/loop.sh

@@ -59,15 +59,6 @@ bt_cmd_loop() {
   bt_env_load || true
   bt_ensure_dirs
 
-  bt_info "starting loop for: $feature (max iterations: $max_iter)"
-
-  bt_info "running preflight gates..."
-  if ! bt_run_gates; then
-    bt_err "preflight gates failed; aborting before implement/review"
-    return 1
-  fi
-  bt_info "preflight gates: PASS"
-
   local feat_dir
   feat_dir="$(bt_feature_dir "$feature")"
   local plan_review="$feat_dir/PLAN_REVIEW.md"
@@ -77,6 +68,27 @@ bt_cmd_loop() {
     bt_die "loop hard-fails without approved PLAN_REVIEW verdict before implement/review"
   fi
 
+  bt_info "starting loop for: $feature (max iterations: $max_iter)"
+
+  local -a gate_args=()
+  if [[ "${BT_LOOP_REQUIRE_GATES:-0}" == "1" ]]; then
+    gate_args=(--require-any)
+  fi
+
+  bt_info "running preflight gates..."
+  if (( ${#gate_args[@]} > 0 )); then
+    if ! bt_run_gates "${gate_args[@]}"; then
+      bt_err "preflight gates failed (or none configured); aborting before implement/review"
+      return 1
+    fi
+  else
+    if ! bt_run_gates; then
+      bt_err "preflight gates failed (or none configured); aborting before implement/review"
+      return 1
+    fi
+  fi
+  bt_info "preflight gates: PASS"
+
   # Source required commands so we can call them directly
   # shellcheck source=/dev/null
   source "$BT_ROOT/commands/implement.sh"
@@ -92,10 +104,53 @@ bt_cmd_loop() {
   review_file="$feat_dir/REVIEW.md"
   local history_dir="$feat_dir/history"
   local progress_file="$feat_dir/loop-progress.json"
+  local resume_iter=0
+  local should_resume=0
 
-  # Initialize progress
   mkdir -p "$history_dir"
-  cat > "$progress_file" <<EOF
+  if [[ -f "$progress_file" ]]; then
+    local resume_meta
+    resume_meta="$(python3 - <<PY
+import json
+p = "$progress_file"
+max_iter = $max_iter
+try:
+    with open(p, "r", encoding="utf-8") as f:
+        d = json.load(f)
+except Exception:
+    print("0 0")
+    raise SystemExit(0)
+result = str(d.get("result", ""))
+completed = d.get("completedIterations", 0)
+try:
+    completed = int(completed)
+except Exception:
+    completed = 0
+if result in {"in-progress", "implement-failed"} and completed < max_iter:
+    d["feature"] = "$feature"
+    d["maxIterations"] = max_iter
+    d["completedIterations"] = completed
+    d["result"] = "in-progress"
+    if not isinstance(d.get("iterations"), list):
+        d["iterations"] = []
+    with open(p, "w", encoding="utf-8") as f:
+        json.dump(d, f, indent=2)
+    print(f"1 {completed}")
+else:
+    print("0 0")
+PY
+)"
+    if [[ "$resume_meta" =~ ^1[[:space:]]+([0-9]+)$ ]]; then
+      should_resume=1
+      resume_iter="${BASH_REMATCH[1]}"
+    fi
+  fi
+
+  if [[ "$should_resume" == "1" ]]; then
+    iter="$resume_iter"
+    bt_info "resuming loop from iteration $((iter + 1)) / $max_iter"
+  else
+    cat > "$progress_file" <<EOF
 {
   "feature": "$feature",
   "maxIterations": $max_iter,
@@ -104,6 +159,7 @@ bt_cmd_loop() {
   "iterations": []
 }
 EOF
+  fi
 
   # Ensure subcommands return non-zero instead of exiting the entire loop process.
   export BT_DIE_MODE="return"
@@ -165,11 +221,20 @@ PY
     # bt_cmd_implement/fix return non-zero if gates fail, but we capture the status.
     # We call bt_run_gates here just to be sure of the final state post-review.
     local gates_ok=1
-    if ! bt_run_gates; then
-      gates_ok=0
-      bt_info "gates: FAIL"
+    if (( ${#gate_args[@]} > 0 )); then
+      if ! bt_run_gates "${gate_args[@]}"; then
+        gates_ok=0
+        bt_info "gates: FAIL"
+      else
+        bt_info "gates: PASS"
+      fi
     else
-      bt_info "gates: PASS"
+      if ! bt_run_gates; then
+        gates_ok=0
+        bt_info "gates: FAIL"
+      else
+        bt_info "gates: PASS"
+      fi
     fi
 
     local fix_status="SKIP"

package/commands/plan-review.sh

@@ -31,7 +31,12 @@ EOF
 
   if bt_codex_available; then
     bt_info "running codex (full-auto) using prompts/plan-review.md"
-    if BT_FEATURE="$feature" BT_CODEX_LOG_FILE="/tmp/codex.log" bt_codex_exec_full_auto "$BT_ROOT/prompts/plan-review.md"; then
+    local artifacts_dir codex_logf
+    artifacts_dir="$dir/.artifacts"
+    mkdir -p "$artifacts_dir"
+    codex_logf="$artifacts_dir/codex-plan-review.log"
+    : >"$codex_logf"
+    if BT_FEATURE="$feature" BT_CODEX_LOG_FILE="$codex_logf" bt_codex_exec_full_auto "$BT_ROOT/prompts/plan-review.md"; then
       :
     else
       bt_die "codex failed (plan-review)"

package/commands/pr.sh

@@ -189,20 +189,19 @@ bt_cmd_pr() {
   fi
 
   # 2. Fail-loud preflight for unstaged expected files (before tests/commit flow).
-  if [[ "$commit" == "1" ]]; then
-    local unstaged=""
-    local check_paths=(tests lib commands scripts specs prompts) # Added specs and prompts
-    if git rev-parse --is-inside-work-tree >/dev/null 2>&1; then
-      unstaged="$(git ls-files --others --modified --exclude-standard -- "${check_paths[@]}" 2>/dev/null || true)"
-    else
-      # Outside a git repo, treat present implementation files as unstaged by definition.
-      unstaged="$(find "${check_paths[@]}" -type f 2>/dev/null | LC_ALL=C sort || true)"
-    fi
-    if [[ -n "$unstaged" ]]; then
-      bt_err "Found unstaged files that might be required for this feature:"
-      printf '%s\n' "$unstaged" >&2
-      bt_die "Abort: ship requires all feature files to be staged. Use git add and try again."
-    fi
+  # P0 #18: fail-loud even with --no-commit
+  local unstaged=""
+  if git rev-parse --is-inside-work-tree >/dev/null 2>&1; then
+    # Protect all repo files, not only a fixed allowlist of directories.
+    unstaged="$(git ls-files --others --modified --exclude-standard 2>/dev/null || true)"
+  else
+    # Outside a git repo, treat present files (except .git internals) as unstaged by definition.
+    unstaged="$(find . -path './.git' -prune -o -type f -print 2>/dev/null | sed 's#^\./##' | LC_ALL=C sort || true)"
+  fi
+  if [[ -n "$unstaged" ]]; then
+    bt_err "Found unstaged files that might be required for this feature:"
+    printf '%s\n' "$unstaged" >&2
+    bt_die "Abort: ship requires all feature files to be staged. Use git add and try again."
   fi
 
   if [[ "$run_mode" == "dry-run" ]]; then
@@ -255,14 +254,7 @@ bt_cmd_pr() {
   # 4. Commit changes if requested
   if [[ "$commit" == "1" ]]; then
     bt_info "committing changes..."
-    local unstaged
-    local check_paths=(tests lib commands scripts specs prompts)
-    unstaged="$(git status --porcelain -- "${check_paths[@]}" 2>/dev/null || true)"
-    if [[ -n "$unstaged" ]]; then
-      bt_err "Found unstaged files that might be required for this feature:"
-      printf '%s\n' "$unstaged" >&2
-      bt_die "Abort: ship requires all feature files to be staged. Use git add and try again."
-    fi
+    # (Unstaged check removed here as it is now redundant with global T0 check)
 
     if ! git diff --cached --quiet; then
       git commit -m "feat($feature): ship implementation"

package/commands/spec.sh

@@ -38,6 +38,84 @@ NODE
   )"
 }
 
+bt__stories_from_issue_json() {
+  bt__require_cmd node
+  node -e "$(
+    cat <<'NODE'
+const fs = require("fs");
+const j = JSON.parse(fs.readFileSync(0, "utf8") || "{}");
+
+function clean(s) {
+  return String(s || "").replace(/\s+/g, " ").trim();
+}
+
+const title = clean(j.title);
+const body = String(j.body || "").replace(/\r/g, "");
+const lines = body.split("\n");
+
+let inAcceptance = false;
+const acceptanceBullets = [];
+const allBullets = [];
+for (const rawLine of lines) {
+  const line = rawLine || "";
+  if (/^\s*#{1,6}\s*acceptance\b/i.test(line) || /^\s*acceptance criteria\s*:?\s*$/i.test(line)) {
+    inAcceptance = true;
+    continue;
+  }
+  if (/^\s*#{1,6}\s+/.test(line) && inAcceptance) {
+    inAcceptance = false;
+  }
+
+  const m = line.match(/^\s*[-*]\s+(?:\[[ xX]\]\s*)?(.+?)\s*$/);
+  if (!m) {
+    continue;
+  }
+  const bullet = clean(m[1]);
+  if (!bullet) {
+    continue;
+  }
+  allBullets.push(bullet);
+  if (inAcceptance) {
+    acceptanceBullets.push(bullet);
+  }
+}
+
+const selectedBullets = acceptanceBullets.length > 0 ? acceptanceBullets : allBullets;
+const storyTitles = [];
+if (title) {
+  storyTitles.push(title);
+}
+for (const bullet of selectedBullets) {
+  if (storyTitles.length >= 5) {
+    break;
+  }
+  storyTitles.push(bullet);
+}
+
+if (storyTitles.length === 0) {
+  const fallback = clean(body).slice(0, 120);
+  if (fallback) {
+    storyTitles.push(fallback);
+  } else {
+    storyTitles.push("Capture issue requirements");
+  }
+}
+
+let out = "";
+for (let i = 0; i < storyTitles.length; i += 1) {
+  const id = i + 1;
+  const titleText = storyTitles[i];
+  out += "## [ID:S" + id + "] " + titleText + "\n";
+  out += "- **status:** draft\n";
+  out += "- **priority:** " + (id <= 3 ? 1 : 2) + "\n";
+  out += "- **acceptance:** " + titleText + "\n";
+  out += "- **tests:**\n\n";
+}
+process.stdout.write(out);
+NODE
+  )"
+}
+
 bt_cmd_spec() {
   local force=0
   local arg=""
@@ -132,8 +210,9 @@ EOF
     [[ -n "$title" ]] || title="(untitled)"
     [[ -n "$url" ]] || url="https://github.com/$repo/issues/$issue"
 
-    local summary
+    local summary stories
     summary="$(bt__summarize_body "$body")"
+    stories="$(printf '%s' "$json" | bt__stories_from_issue_json)"
 
     cat >"$spec" <<EOF
 ---
@@ -154,35 +233,7 @@ $summary
 
 # Stories
 
-## [ID:S1] Confirm repo resolution and env fallback
-- **status:** draft
-- **priority:** 1
-- **acceptance:** bt can determine repo slug from git remote origin; otherwise requires BT_REPO
-- **tests:**
-
-## [ID:S2] Fetch issue details via gh
-- **status:** draft
-- **priority:** 1
-- **acceptance:** bt spec <issue#> uses gh to retrieve title/body/url and handles errors clearly
-- **tests:**
-
-## [ID:S3] Generate a SPEC.md with frontmatter + problem summary
-- **status:** draft
-- **priority:** 1
-- **acceptance:** SPEC includes required frontmatter, a Problem section, and a Stories section (3-7 stories)
-- **tests:**
-
-## [ID:S4] Record exact gh commands used in SPEC footer
-- **status:** draft
-- **priority:** 2
-- **acceptance:** SPEC footer includes the exact gh command(s) executed
-- **tests:**
-
-## [ID:S5] Add tests stubbing gh via PATH
-- **status:** draft
-- **priority:** 1
-- **acceptance:** tests run offline and validate SPEC content generation
-- **tests:**
+${stories}
 
 ---
 

package/lib/gates.sh

@@ -77,6 +77,12 @@ bt_get_gate_config() {
 # Runs gates and returns a JSON string fragment with results.
 # Writes logs to stderr. Returns 0 if all gates passed, 1 otherwise.
 bt_run_gates() {
+  local require_any=0
+  if [[ "${1:-}" == "--require-any" ]]; then
+    require_any=1
+    shift
+  fi
+
   local config
   config="$(bt_get_gate_config)"
 
@@ -115,6 +121,9 @@ bt_run_gates() {
   if [[ "$any" == "0" ]]; then
     bt_warn "no gates ran"
     printf '{"ts": "%s", "results": {}}\n' "$(date -u +'%Y-%m-%dT%H:%M:%SZ')"
+    if [[ "$require_any" == "1" ]]; then
+      return 1
+    fi
     return 0
   fi
 

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "biotonomy",
-  "version": "0.2.2",
+  "version": "0.2.4",
   "description": "Codex-native autonomous development loop CLI",
   "license": "MIT",
   "repository": {