biotonomy 0.2.4 → 0.2.7

package/bt.sh

@@ -1,7 +1,14 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
-BT_VERSION="0.1.0"
+bt_package_version() {
+  local pkg="$BT_ROOT/package.json"
+  if [[ -f "$pkg" ]]; then
+    awk -F '"' '/"version"[[:space:]]*:/ { print $4; exit }' "$pkg"
+    return 0
+  fi
+  return 1
+}
 
 bt_script_dir() {
   local src="${BASH_SOURCE[0]}"
@@ -15,6 +22,8 @@ bt_script_dir() {
 }
 
 BT_ROOT="$(bt_script_dir)"
+BT_VERSION="$(bt_package_version 2>/dev/null || true)"
+BT_VERSION="${BT_VERSION:-0.1.0}"
 
 # shellcheck source=/dev/null
 source "$BT_ROOT/lib/log.sh"
@@ -41,7 +50,7 @@ Usage:
   bt [--target <path>] <command> [args]
 
 Commands:
-  bootstrap  spec  research  implement  review  fix  loop  compound  design  status  gates  reset  pr  ship
+  bootstrap  spec  research  plan-review  implement  review  fix  loop  compound  design  status  gates  reset  pr  ship
 
 Global options:
   -h, --help     Show help
@@ -93,7 +102,26 @@ bt_dispatch() {
   shift || true
 
   case "$cmd" in
-    -h|--help|help) bt_usage; return 0 ;;
+    -h|--help|help)
+      if [[ $# -gt 0 ]]; then
+        # bt help <cmd>
+        cmd="$1"
+        shift
+        local cmd_file="$BT_ROOT/commands/$cmd.sh"
+        if [[ "$cmd" == "ship" ]]; then cmd_file="$BT_ROOT/commands/pr.sh"; fi
+        if [[ -f "$cmd_file" ]]; then
+          # shellcheck source=/dev/null
+          source "$cmd_file"
+          local safe_cmd="${cmd//-/_}"
+          local fn="bt_${safe_cmd}_usage"
+          if [[ "$cmd" == "ship" ]]; then fn="bt_pr_usage"; fi
+          if declare -F "$fn" >/dev/null 2>&1; then
+            "$fn"
+            return 0
+          fi
+        fi
+      fi
+      bt_usage; return 0 ;;
   esac
 
   bt_env_load || true

package/commands/loop.sh

@@ -56,28 +56,39 @@ bt_cmd_loop() {
     return 2
   fi
 
+  feature="$(bt_require_feature "$feature")"
+
   bt_env_load || true
   bt_ensure_dirs
 
   local feat_dir
   feat_dir="$(bt_feature_dir "$feature")"
+
+  # Auto-run plan-review if PLAN_REVIEW.md is missing or unapproved
   local plan_review="$feat_dir/PLAN_REVIEW.md"
   if [[ ! -f "$plan_review" ]] || ! grep -qiE "Verdict:.*(APPROVE_PLAN|APPROVED_PLAN)" "$plan_review"; then
-    bt_err "missing or unapproved $plan_review"
-    bt_err "run: bt plan-review $feature"
-    bt_die "loop hard-fails without approved PLAN_REVIEW verdict before implement/review"
+    bt_info "PLAN_REVIEW missing or unapproved; auto-running plan-review..."
+    # shellcheck source=/dev/null
+    source "$BT_ROOT/commands/plan-review.sh"
+    if ! bt_cmd_plan_review "$feature"; then
+      bt_err "auto plan-review failed for $feature"
+      bt_err "manually run: bt plan-review $feature"
+      bt_die "loop hard-fails without approved PLAN_REVIEW verdict before implement/review"
+    fi
+    # Re-check after auto-run
+    if [[ ! -f "$plan_review" ]] || ! grep -qiE "Verdict:.*(APPROVE_PLAN|APPROVED_PLAN)" "$plan_review"; then
+      bt_err "plan-review ran but did not produce an approved verdict"
+      bt_err "check $plan_review and re-run: bt plan-review $feature"
+      bt_die "loop hard-fails without approved PLAN_REVIEW verdict before implement/review"
+    fi
+    bt_info "plan-review auto-approved; continuing loop"
   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
+  if [[ "${BT_LOOP_REQUIRE_GATES:-0}" == "1" ]]; then
+    if ! bt_run_gates --require-any; then
       bt_err "preflight gates failed (or none configured); aborting before implement/review"
       return 1
     fi
@@ -164,6 +175,7 @@ EOF
   # Ensure subcommands return non-zero instead of exiting the entire loop process.
   export BT_DIE_MODE="return"
 
+
   while [[ "$iter" -lt "$max_iter" ]]; do
     iter=$((iter + 1))
     bt_info "--- Iteration $iter / $max_iter ---"
@@ -221,20 +233,11 @@ 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 (( ${#gate_args[@]} > 0 )); then
-      if ! bt_run_gates "${gate_args[@]}"; then
-        gates_ok=0
-        bt_info "gates: FAIL"
-      else
-        bt_info "gates: PASS"
-      fi
+    if ! bt_run_gates --require-any; then
+      gates_ok=0
+      bt_info "gates: FAIL"
     else
-      if ! bt_run_gates; then
-        gates_ok=0
-        bt_info "gates: FAIL"
-      else
-        bt_info "gates: PASS"
-      fi
+      bt_info "gates: PASS"
     fi
 
     local fix_status="SKIP"

package/commands/plan-review.sh

@@ -29,26 +29,20 @@ EOF
 
   local out="$dir/PLAN_REVIEW.md"
 
-  if bt_codex_available; then
-    bt_info "running codex (full-auto) using prompts/plan-review.md"
-    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 "$BT_ROOT/prompts/plan-review.md"; then
-      :
-    else
-      bt_die "codex failed (plan-review)"
-    fi
-  else
-    # v0.1.0 stub
-    cat <<'EOF' > "$out"
-# Plan Review: Stub Approved
+  if ! bt_codex_available; then
+    bt_die "codex required for plan-review (set BT_CODEX_BIN to a valid codex executable or install codex)"
+  fi
 
-Verdict: APPROVED_PLAN
-EOF
-    bt_info "wrote $out"
+  bt_info "running codex (full-auto) using prompts/plan-review.md"
+  local artifacts_dir codex_logf
+  artifacts_dir="$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" "$out"; then
+    :
+  else
+    bt_die "codex failed (plan-review)"
   fi
 
   if [[ ! -f "$out" ]]; then

package/commands/pr.sh

@@ -161,6 +161,7 @@ bt_cmd_pr() {
     bt_err "feature name is required"
     return 2
   fi
+  feature="$(bt_require_feature "$feature")"
 
   # Ensure BT_PROJECT_ROOT reflects BT_TARGET_DIR / BT_ENV_FILE, and operate within it.
   bt_env_load || true

package/commands/spec.sh

@@ -159,13 +159,19 @@ EOF
   bt_env_load || true
   bt_ensure_dirs
 
-  local feature issue
+  local feature issue url_slug
   issue=""
+  url_slug=""
   if [[ "$arg" =~ ^[0-9]+$ ]]; then
     issue="$arg"
     feature="issue-$arg"
+  elif [[ "$arg" =~ ^https?://github.com/([^/]+/[^/]+)/issues/([0-9]+) ]]; then
+    # support URL format
+    issue="${BASH_REMATCH[2]}"
+    url_slug="${BASH_REMATCH[1]}"
+    feature="issue-$issue"
   else
-    feature="$arg"
+    feature="$(bt_require_feature "$arg")"
   fi
 
   local dir
@@ -186,7 +192,11 @@ EOF
     bt__require_cmd gh
 
     local repo
-    repo="$(bt_repo_resolve "$BT_PROJECT_ROOT")"
+    if [[ -n "$url_slug" ]]; then
+      repo="$url_slug"
+    else
+      repo="$(bt_repo_resolve "$BT_PROJECT_ROOT")"
+    fi
 
     local -a gh_cmd
     gh_cmd=(gh issue view "$issue" -R "$repo" --json "title,body,url")

package/commands/status.sh

@@ -75,7 +75,7 @@ EOF
 
   bt_env_load || true
 
-  echo "bt v0.1.0"
+  echo "bt v${BT_VERSION:-unknown}"
   echo "project_root: $BT_PROJECT_ROOT"
   echo "env_file: ${BT_ENV_FILE:-<none>}"
   echo "specs_dir: $BT_SPECS_DIR"

package/lib/codex.sh

@@ -11,6 +11,7 @@ bt_codex_available() {
 
 bt_codex_exec_full_auto() {
   local prompt_file="$1"
+  local out_file="${2:-}"
   if ! bt_codex_available; then
     bt_warn "codex not found; skipping (set BT_CODEX_BIN or install codex)"
     return 0
@@ -19,7 +20,15 @@ bt_codex_exec_full_auto() {
   bin="$(bt_codex_bin)"
   local log_file
   log_file="${BT_CODEX_LOG_FILE:-/dev/null}"
-  "$bin" exec --full-auto -C "$BT_PROJECT_ROOT" "$(cat "$prompt_file")" 2>&1 | tee -a "$log_file"
+
+  local -a args
+  args=(exec --full-auto -C "$BT_PROJECT_ROOT")
+  if [[ -n "$out_file" ]]; then
+    args+=(-o "$out_file")
+  fi
+  args+=("$(cat "$prompt_file")")
+
+  "$bin" "${args[@]}" 2>&1 | tee -a "$log_file"
   return "${PIPESTATUS[0]}"
 }
 

package/lib/env.sh

@@ -6,6 +6,14 @@ bt__export_kv() {
   local val="$2"
 
   [[ "$key" =~ ^[A-Za-z_][A-Za-z0-9_]*$ ]] || return 0
+
+  # Respect process env: only set if not already present in environment.
+  # This ensures BT_GATE_TEST='echo hi' bt gates works even when .bt.env
+  # contains an empty BT_GATE_TEST= line.  (#38)
+  if [[ -n "${!key+x}" ]]; then
+    return 0
+  fi
+
   # Export without eval; keep value literal even if it contains spaces/symbols.
   export "$key=$val"
 }

package/lib/gates.sh

@@ -76,6 +76,33 @@ 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__gate_script_exists() {
+  # Check if an npm/pnpm/yarn script actually exists in package.json.
+  # Returns 0 if the script exists or if we can't determine (non-npm project).
+  local cmd="$1"
+  local script_name=""
+
+  # Extract script name from common patterns
+  case "$cmd" in
+    "npm run "*)  script_name="${cmd#npm run }" ;;
+    "npm test")   script_name="test" ;;
+    "pnpm "*)     script_name="${cmd#pnpm }" ;;
+    "yarn "*)     script_name="${cmd#yarn }" ;;
+    *)            return 0 ;;  # Not an npm-style command, assume exists
+  esac
+  script_name="${script_name%% *}"  # Take first word only
+
+  local pkg="$BT_PROJECT_ROOT/package.json"
+  [[ -f "$pkg" ]] || return 0  # No package.json, can't check
+
+  # Check if script exists in package.json
+  if command -v node >/dev/null 2>&1; then
+    node -e "const p=require('$pkg'); process.exit(p.scripts && p.scripts['$script_name'] ? 0 : 1)" 2>/dev/null
+    return $?
+  fi
+  return 0  # Can't verify, assume exists
+}
+
 bt_run_gates() {
   local require_any=0
   if [[ "${1:-}" == "--require-any" ]]; then
@@ -93,14 +120,35 @@ bt_run_gates() {
 
   while IFS= read -r line; do
     [[ -n "$line" ]] || continue
-    any=1
     k="${line%%=*}"
     v="${line#*=}"
 
+    # Skip gates explicitly set to "skip" or "" (disabled)
+    if [[ "$v" == "skip" || -z "$v" ]]; then
+      bt_warn "gate disabled: $k"
+      local entry k_json v_json
+      k_json="$(bt__json_escape "$k")"
+      v_json="$(bt__json_escape "$v")"
+      printf -v entry '"%s": {"cmd": "%s", "status": -1, "skipped": true}' "$k_json" "$v_json"
+      if [[ -z "$results_json" ]]; then results_json="$entry"; else results_json="$results_json, $entry"; fi
+      continue
+    fi
+
+    # Skip gates whose scripts don't exist
+    if ! bt__gate_script_exists "$v"; then
+      bt_warn "gate skipped (script missing): $k ($v)"
+      local entry k_json v_json
+      k_json="$(bt__json_escape "$k")"
+      v_json="$(bt__json_escape "$v")"
+      printf -v entry '"%s": {"cmd": "%s", "status": -1, "skipped": true}' "$k_json" "$v_json"
+      if [[ -z "$results_json" ]]; then results_json="$entry"; else results_json="$results_json, $entry"; fi
+      continue
+    fi
+
+    any=1
+
     bt_info "gate: $k ($v)"
     local status=0
-    # Use bash -lc for interactivity if needed, but we typically want it non-interactive.
-    # The original used bash -lc "$v". We'll stick to that but capture status.
     if ! (cd "$BT_PROJECT_ROOT" && bash -lc "$v"); then
       bt_err "gate failed: $k"
       status=1

package/lib/state.sh

@@ -14,10 +14,29 @@ bt_ensure_dirs() {
   mkdir -p "$(bt_specs_path)" "$BT_PROJECT_ROOT/$BT_STATE_DIR"
 }
 
+bt_sanitize_feature() {
+  local s="${1:-}"
+  # Replace characters not in [A-Za-z0-9._-] with underscore
+  s="${s//[^A-Za-z0-9._-]/_}"
+  # Ensure it doesn't start with a dot or dash and isn't empty
+  if [[ "$s" =~ ^[._-] ]]; then
+    s="f$s"
+  fi
+  if [[ -z "$s" ]]; then
+    s="feature"
+  fi
+  printf '%s\n' "$s"
+}
+
 bt_require_feature() {
   local feature="${1:-${BT_FEATURE:-}}"
   [[ -n "$feature" ]] || bt_die "feature required (pass as first arg or set BT_FEATURE)"
 
+  # Apply sanitization if it doesn't already pass validation
+  if [[ "$feature" == *"/"* || "$feature" == *".."* || ! "$feature" =~ ^[A-Za-z0-9][A-Za-z0-9._-]*$ ]]; then
+     feature="$(bt_sanitize_feature "$feature")"
+  fi
+
   # Prevent path traversal and keep on-disk state predictable.
   [[ "$feature" != *"/"* ]] || bt_die "invalid feature (must not contain '/'): $feature"
   [[ "$feature" != *".."* ]] || bt_die "invalid feature (must not contain '..'): $feature"

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "biotonomy",
-  "version": "0.2.4",
+  "version": "0.2.7",
   "description": "Codex-native autonomous development loop CLI",
   "license": "MIT",
   "repository": {