index: use python3's sqlite3 module, not the sqlite3 CLI (#1329)

.github/scripts/version.mjs

@@ -4,9 +4,10 @@
 //
 // The release version is package.json's `version`. It is repeated in the engine
 // pins (optionalDependencies — each engine package is published under the same
-// version as this one), the vendored parser, and every agent plugin manifest a
-// marketplace reads. A release where they disagree ships a plugin that reports a
-// version nobody can install, or an install that pins engines that were never
+// version as this one) and every agent plugin manifest a marketplace reads. The
+// vendored parser keeps its own version: it moves only when the parser changes.
+// A release where they disagree ships a plugin that reports a version nobody can
+// install, or an install that pins engines that were never
 // published.
 //
 //   node .github/scripts/version.mjs check            every manifest agrees
@@ -24,7 +25,6 @@ const root = join(dirname(fileURLToPath(import.meta.url)), '..', '..');
 // reading the file, so a fifth platform is covered without editing this list.
 const MANIFESTS = [
   'package.json',
-  'parser/package.json',
   'gemini-extension.json',
   'plugins/axiomcode/.claude-plugin/plugin.json',
   'plugins/axiomcode/.codex-plugin/plugin.json',

gemini-extension.json

@@ -1,6 +1,6 @@
 {
   "name": "axiomcode",
-  "version": "0.1.0",
+  "version": "0.1.1",
   "description": "Ask your repository how its code connects: who calls this, what breaks if I change it, which tests an edit reaches, how A reaches B. Answers come from a resolved call graph and are verified against it; nothing is guessed.",
   "contextFileName": "plugins/axiomcode/AGENTS.md",
   "mcpServers": {

package.json

@@ -1,6 +1,6 @@
 {
   "name": "@axiomcode/code-graph",
-  "version": "0.1.0",
+  "version": "0.1.1",
   "description": "AxiomCode Graph: a resolved call graph of your codebase grounded in formal methods, so you and your coding agents can see who calls what, what a change breaks, and which tests it reaches.",
   "repository": {
     "type": "git",
@@ -30,11 +30,11 @@
   ],
   "license": "FSL-1.1-Apache-2.0",
   "optionalDependencies": {
-    "@axiomcode/engine-darwin-arm64": "0.1.0",
-    "@axiomcode/engine-darwin-x64": "0.1.0",
-    "@axiomcode/engine-linux-x64": "0.1.0",
-    "@axiomcode/engine-linux-arm64": "0.1.0",
-    "@axiomcode/engine-win32-x64": "0.1.0"
+    "@axiomcode/engine-darwin-arm64": "0.1.1",
+    "@axiomcode/engine-darwin-x64": "0.1.1",
+    "@axiomcode/engine-linux-x64": "0.1.1",
+    "@axiomcode/engine-linux-arm64": "0.1.1",
+    "@axiomcode/engine-win32-x64": "0.1.1"
   },
   "bin": {
     "axiomcode": "bin/axiomcode.js"

plugins/axiomcode/.claude-plugin/plugin.json

@@ -1,7 +1,7 @@
 {
   "name": "axiomcode",
   "description": "Ask your repository how its code connects: who calls this, what breaks if I change it, which tests an edit reaches, how A reaches B. Answers come from a resolved call graph and are verified against it; nothing is guessed.",
-  "version": "0.1.0",
+  "version": "0.1.1",
   "author": {
     "name": "AxiomCode"
   }

plugins/axiomcode/.codex-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "axiomcode",
-  "version": "0.1.0",
+  "version": "0.1.1",
   "description": "Ask your repository how its code connects: who calls this, what breaks if I change it, which tests an edit reaches, how A reaches B. Answers come from a resolved call graph and are verified against it; nothing is guessed.",
   "author": { "name": "AxiomCode", "url": "https://github.com/AxiomCodeAI/axiomcodegraph" },
   "homepage": "https://github.com/AxiomCodeAI/axiomcodegraph",

plugins/axiomcode/.cursor-plugin/plugin.json

@@ -1,6 +1,6 @@
 {
   "name": "axiomcode",
-  "version": "0.1.0",
+  "version": "0.1.1",
   "description": "Ask your repository how its code connects: who calls this, what breaks if I change it, which tests an edit reaches, how A reaches B. Answers come from a resolved call graph and are verified against it; nothing is guessed. Java, TypeScript, Python, JavaScript.",
   "author": { "name": "AxiomCode" },
   "homepage": "https://github.com/AxiomCodeAI/axiomcodegraph",

plugins/axiomcode/skills/axiomcode/scripts/axiomcode-build

@@ -24,6 +24,9 @@ if [ -z "${AXIOMCODE_ENGINE:-}" ]; then E="$H"; while [ "$E" != "/" ] && [ ! -x
 # not, since it is not in git -- and that clone was taken over the built engine `npm i -g` installed. An
 # unbuilt checkout is still used when nothing else is found, so a developer keeps the "parser not built"
 # advice; an engine named in AXIOMCODE_ENGINE is used as given whenever it is one.
+# python3's sqlite3 module, not the sqlite3 CLI: python3 is a stated requirement, the CLI is not, and stock Ubuntu
+# and Git for Windows ship without it.
+has_symbols() { python3 -c 'import sqlite3, sys; sys.exit(0 if sqlite3.connect(sys.argv[1]).execute("SELECT 1 FROM sqlite_master WHERE name=?", ("symbols",)).fetchone() else 1)' "$1" 2>/dev/null; }
 engine_ok() { [ -x "$1/bin/axiomcode" ] && [ -d "$1/graph" ] && [ -f "$1/package.json" ]; }
 engine_built() { engine_ok "$1" && [ -f "$1/parser/dist/index.js" ]; }
 if ! { if [ -n "$ENGINE_SET" ]; then engine_ok "$AXIOMCODE_ENGINE"; else engine_built "$AXIOMCODE_ENGINE"; fi; }; then
@@ -150,11 +153,11 @@ BASE_SAVED=""
 # from the edit, is. A commit that changed no file moves the stamp, not the graph.
 if [ -f "$OUT/graph.sqlite" ] && [ -f "$OUT/stamp" ] && python3 "$H/ax_fresh.py" uptodate "$REPO" "$LANG_ARG" "${AXIOMCODE_SRC:-}" "${STAMP#"$PREFIX"}"; then
   if [ "$(cat "$OUT/stamp")" != "$STAMP" ]; then echo "$STAMP" > "$OUT/stamp"; INDEXED_TREE="$OLD_INDEXED"; set_base "$OLD_INDEXED"; PREV=""; keep_base_graph; commit_base; fi
-  sqlite3 "$OUT/graph.sqlite" "SELECT 1 FROM sqlite_master WHERE name='symbols'" | grep -q 1 || python3 "$H/axiomcode-index" "$REPO"
+  has_symbols "$OUT/graph.sqlite" || python3 "$H/axiomcode-index" "$REPO"
   echo "graph up to date ($LANG_ARG) at $OUT/graph.sqlite"; exit 0
 fi
 if [ ! -f "$OUT/files.json" ] && [ -f "$OUT/stamp" ] && [ "$(cat "$OUT/stamp")" = "$STAMP" ] && [ -f "$OUT/graph.sqlite" ] && [ -z "$(cd "$REPO" && git status --porcelain 2>/dev/null | head -1)" ]; then
-  sqlite3 "$OUT/graph.sqlite" "SELECT 1 FROM sqlite_master WHERE name='symbols'" | grep -q 1 || python3 "$H/axiomcode-index" "$REPO"
+  has_symbols "$OUT/graph.sqlite" || python3 "$H/axiomcode-index" "$REPO"
   python3 "$H/axiomcode-impact" --warm "$REPO" || true   # export the graph's facts now (~9 s on 1,373 files): the first
 # query pays it otherwise, and for the plugin that first query is inside hooks/changes.py's timeout=14, several at once.
 python3 "$H/dl_program.py" || true   # compile the query rules once, here where ~20 s is noise against the build:
@@ -214,16 +217,28 @@ AXIOMCODE_INDEX_DB="$DB" python3 "$H/axiomcode-index" "$REPO" || { restore; echo
 # the tree and commit it describes. Written before the swap: a write to the live graph later would change its mtime,
 # which keys the impact-facts cache, and cost the next query a re-export.
 REASON="$(printf %s "${AXIOMCODE_REFRESH_REASON:-axiomcode index}" | tr -d "'")"
-sqlite3 "$DB" "DELETE FROM index_meta WHERE key IN ('refreshed_at','refresh_reason','refreshed_tree','refreshed_commit');
-  INSERT INTO index_meta VALUES ('refreshed_at','$(date -u +%Y-%m-%dT%H:%M:%SZ)'),('refresh_reason','$REASON'),('refreshed_tree','$INDEXED_TREE'),('refreshed_commit','$HEAD_SHA');" 2>/dev/null || true
+python3 - "$DB" "$(date -u +%Y-%m-%dT%H:%M:%SZ)" "$REASON" "$INDEXED_TREE" "$HEAD_SHA" <<'PY' 2>/dev/null || true
+import sqlite3, sys
+db, at, reason, tree, commit = sys.argv[1:6]
+with sqlite3.connect(db) as c:
+    c.execute("DELETE FROM index_meta WHERE key IN ('refreshed_at','refresh_reason','refreshed_tree','refreshed_commit')")
+    c.executemany("INSERT INTO index_meta VALUES (?,?)", [('refreshed_at', at), ('refresh_reason', reason),
+                  ('refreshed_tree', tree), ('refreshed_commit', commit)])
+PY
 echo "$STAMP" > "$OUT/stamp"
 if [ -n "$INDEXED_TREE" ]; then echo "$INDEXED_TREE" > "$OUT/indexed-tree"; else rm -f "$OUT/indexed-tree"; fi
 set_base "$INDEXED_TREE"
 point "$DB"; rm -f "$OUT/.live.sqlite"
 if [ -f "$OUT/.files.json.new" ]; then mv "$OUT/.files.json.new" "$OUT/files.json"; else rm -f "$OUT/files.json"; fi
 keep_base_graph; commit_base
 rm -rf "$PREV"
-sqlite3 -column "$OUT/graph.sqlite" "SELECT tier, count(*) AS edges FROM call_edges GROUP BY tier ORDER BY edges DESC;"
+python3 - "$OUT/graph.sqlite" <<'PY'
+import sqlite3, sys
+rows = sqlite3.connect(sys.argv[1]).execute("SELECT tier, count(*) FROM call_edges GROUP BY tier ORDER BY 2 DESC").fetchall()
+w = max([len('tier')] + [len(t) for t, _ in rows])
+print(f"{'tier':<{w}}  edges")
+for t, n in rows: print(f"{t:<{w}}  {n}")
+PY
 python3 "$H/axiomcode-impact" --warm "$REPO" || true   # export the graph's facts now (~9 s on 1,373 files): the first
 # query pays it otherwise, and for the plugin that first query is inside hooks/changes.py's timeout=14, several at once.
 python3 "$H/dl_program.py" || true   # compile the query rules once, here where ~20 s is noise against the build: