fix obsidian always generating, uninstall early return bug, add missing tests

graphify/__main__.py

@@ -171,12 +171,11 @@ def claude_uninstall(project_dir: Path | None = None) -> None:
     ).rstrip()
     if cleaned:
         target.write_text(cleaned + "\n")
+        print(f"graphify section removed from {target.resolve()}")
     else:
         target.unlink()
         print(f"CLAUDE.md was empty after removal - deleted {target.resolve()}")
-        return
 
-    print(f"graphify section removed from {target.resolve()}")
     _uninstall_claude_hook(project_dir or Path("."))
 
 

graphify/skill.md

@@ -411,9 +411,11 @@ print('Report updated with community labels')
 Replace `LABELS_DICT` with the actual dict you constructed (e.g. `{0: "Attention Mechanism", 1: "Training Pipeline"}`).
 Replace INPUT_PATH with the actual path.
 
-### Step 6 - Generate Obsidian vault (default) + optional HTML
+### Step 6 - Generate Obsidian vault (opt-in) + HTML
 
-**Generate HTML always** (unless `--no-viz`). **Obsidian vault only if `--obsidian` was given** — it generates one file per node which creates thousands of files in large repos. Skip it by default.
+**Generate HTML always** (unless `--no-viz`). **Obsidian vault only if `--obsidian` was explicitly given** — skip it otherwise, it generates one file per node.
+
+If `--obsidian` was given:
 
 ```bash
 python3 -c "
@@ -444,7 +446,7 @@ print('  _COMMUNITY_* - overview notes with cohesion scores and dataview queries
 "
 ```
 
-Also generate the HTML graph (always, unless `--no-viz`):
+Generate the HTML graph (always, unless `--no-viz`):
 
 ```bash
 python3 -c "
@@ -631,22 +633,14 @@ rm -f .graphify_detect.json .graphify_extract.json .graphify_ast.json .graphify_
 rm -f graphify-out/.needs_update 2>/dev/null || true
 ```
 
-Tell the user:
+Tell the user (omit the obsidian line unless --obsidian was given):
 ```
-Graph complete. Outputs are in a hidden folder called graphify-out/ inside the directory you ran this on.
+Graph complete. Outputs in PATH_TO_DIR/graphify-out/
 
-The folder is hidden (dot prefix) so it won't show in Finder or a normal ls.
-To see it:
-  Mac/Linux:  ls -la graphify-out/
-  VS Code:    the Explorer panel shows hidden files by default
-  Finder:     Cmd+Shift+. to toggle hidden files
-
-What's inside:
-  graphify-out/obsidian/        - open this folder as a vault in Obsidian (File > Open Vault)
-  graphify-out/GRAPH_REPORT.md  - full audit report, also readable here in Claude
-  graphify-out/graph.json       - persistent graph, query it later with /graphify query "..."
-
-Full path: PATH_TO_DIR/graphify-out/
+  graph.html            - interactive graph, open in browser
+  GRAPH_REPORT.md       - audit report
+  graph.json            - raw graph data
+  obsidian/             - Obsidian vault (only if --obsidian was given)
 ```
 
 Replace PATH_TO_DIR with the actual absolute path of the directory that was processed.

tests/test_claude_md.py

@@ -95,3 +95,42 @@ def test_uninstall_no_op_when_no_file(tmp_path, capsys):
     claude_uninstall(tmp_path)
     out = capsys.readouterr().out
     assert "No CLAUDE.md" in out or "nothing to do" in out
+
+
+# ---------------------------------------------------------------------------
+# settings.json PreToolUse hook
+# ---------------------------------------------------------------------------
+
+def test_install_creates_settings_json(tmp_path):
+    """claude_install also writes .claude/settings.json with PreToolUse hook."""
+    import json
+    claude_install(tmp_path)
+    settings_path = tmp_path / ".claude" / "settings.json"
+    assert settings_path.exists()
+    settings = json.loads(settings_path.read_text())
+    hooks = settings.get("hooks", {}).get("PreToolUse", [])
+    assert any("Glob|Grep" in h.get("matcher", "") for h in hooks)
+
+
+def test_install_settings_json_idempotent(tmp_path):
+    """Running claude_install twice does not duplicate the PreToolUse hook."""
+    import json
+    claude_install(tmp_path)
+    claude_install(tmp_path)
+    settings_path = tmp_path / ".claude" / "settings.json"
+    settings = json.loads(settings_path.read_text())
+    hooks = settings.get("hooks", {}).get("PreToolUse", [])
+    glob_grep_hooks = [h for h in hooks if "Glob|Grep" in h.get("matcher", "")]
+    assert len(glob_grep_hooks) == 1
+
+
+def test_uninstall_removes_settings_hook(tmp_path):
+    """claude_uninstall removes the PreToolUse hook from settings.json."""
+    import json
+    claude_install(tmp_path)
+    claude_uninstall(tmp_path)
+    settings_path = tmp_path / ".claude" / "settings.json"
+    if settings_path.exists():
+        settings = json.loads(settings_path.read_text())
+        hooks = settings.get("hooks", {}).get("PreToolUse", [])
+        assert not any("Glob|Grep" in h.get("matcher", "") for h in hooks)

tests/test_hooks.py

@@ -2,7 +2,7 @@
 import subprocess
 from pathlib import Path
 import pytest
-from graphify.hooks import install, uninstall, status, _HOOK_MARKER
+from graphify.hooks import install, uninstall, status, _HOOK_MARKER, _CHECKOUT_MARKER
 
 
 def _make_git_repo(tmp_path: Path) -> Path:
@@ -78,3 +78,35 @@ def test_status_not_installed(tmp_path):
 def test_no_git_repo_raises(tmp_path):
     with pytest.raises(RuntimeError, match="No git repository"):
         install(tmp_path / "not_a_repo")
+
+
+def test_install_creates_post_checkout_hook(tmp_path):
+    repo = _make_git_repo(tmp_path)
+    install(repo)
+    hook = repo / ".git" / "hooks" / "post-checkout"
+    assert hook.exists()
+    assert _CHECKOUT_MARKER in hook.read_text()
+
+
+def test_install_post_checkout_is_executable(tmp_path):
+    repo = _make_git_repo(tmp_path)
+    install(repo)
+    hook = repo / ".git" / "hooks" / "post-checkout"
+    assert hook.stat().st_mode & 0o111
+
+
+def test_uninstall_removes_post_checkout_hook(tmp_path):
+    repo = _make_git_repo(tmp_path)
+    install(repo)
+    uninstall(repo)
+    hook = repo / ".git" / "hooks" / "post-checkout"
+    assert not hook.exists()
+
+
+def test_status_shows_both_hooks(tmp_path):
+    repo = _make_git_repo(tmp_path)
+    install(repo)
+    result = status(repo)
+    assert "post-commit" in result
+    assert "post-checkout" in result
+    assert result.count("installed") >= 2

tests/test_rationale.py

@@ -0,0 +1,89 @@
+"""Tests for rationale/docstring extraction in extract.py."""
+import textwrap
+from pathlib import Path
+import pytest
+from graphify.extract import extract_python
+
+
+def _write_py(tmp_path: Path, code: str) -> Path:
+    p = tmp_path / "sample.py"
+    p.write_text(textwrap.dedent(code))
+    return p
+
+
+def test_module_docstring_extracted(tmp_path):
+    path = _write_py(tmp_path, '''
+        """This module handles authentication because legacy sessions were insecure."""
+        def login(): pass
+    ''')
+    result = extract_python(path)
+    rationale = [n for n in result["nodes"] if n.get("file_type") == "rationale"]
+    assert len(rationale) >= 1
+    assert any("authentication" in n["label"] for n in rationale)
+
+
+def test_function_docstring_extracted(tmp_path):
+    path = _write_py(tmp_path, '''
+        def process():
+            """We use chunked processing here because the full dataset exceeds RAM."""
+            pass
+    ''')
+    result = extract_python(path)
+    rationale = [n for n in result["nodes"] if n.get("file_type") == "rationale"]
+    assert any("chunked" in n["label"] for n in rationale)
+
+
+def test_class_docstring_extracted(tmp_path):
+    path = _write_py(tmp_path, '''
+        class Cache:
+            """Chosen over Redis because we need zero external dependencies in the test env."""
+            pass
+    ''')
+    result = extract_python(path)
+    rationale = [n for n in result["nodes"] if n.get("file_type") == "rationale"]
+    assert any("Redis" in n["label"] for n in rationale)
+
+
+def test_rationale_comment_extracted(tmp_path):
+    path = _write_py(tmp_path, '''
+        def build():
+            # NOTE: must run before compile() or linker will fail
+            pass
+    ''')
+    result = extract_python(path)
+    rationale = [n for n in result["nodes"] if n.get("file_type") == "rationale"]
+    assert any("NOTE" in n["label"] for n in rationale)
+
+
+def test_rationale_for_edges_present(tmp_path):
+    path = _write_py(tmp_path, '''
+        """Module docstring explaining the why."""
+        def foo():
+            """Function docstring with rationale."""
+            pass
+    ''')
+    result = extract_python(path)
+    rationale_edges = [e for e in result["edges"] if e.get("relation") == "rationale_for"]
+    assert len(rationale_edges) >= 1
+
+
+def test_short_docstring_ignored(tmp_path):
+    """Trivial docstrings under 20 chars should not become rationale nodes."""
+    path = _write_py(tmp_path, '''
+        def foo():
+            """Constructor."""
+            pass
+    ''')
+    result = extract_python(path)
+    rationale = [n for n in result["nodes"] if n.get("file_type") == "rationale"]
+    assert len(rationale) == 0
+
+
+def test_rationale_confidence_is_extracted(tmp_path):
+    path = _write_py(tmp_path, '''
+        """This module exists because we needed a standalone parser."""
+        def parse(): pass
+    ''')
+    result = extract_python(path)
+    rationale_edges = [e for e in result["edges"] if e.get("relation") == "rationale_for"]
+    assert all(e.get("confidence") == "EXTRACTED" for e in rationale_edges)