feat(cli): wire all commands via Typer (ingest, search, discover, provenance, ask-stub)

- Implement all CLI commands as specified in F-07: ingest, search, and discover subcommands (leads, citing, cited-by, cocited), and provenance subcommands (scan, add-link, links, bib).
- Add ask command stub that exits with code 1 (not yet implemented).
- Implement comprehensive tests with mocked dependencies (no real DB/API calls).

Co-Authored-By: Claude Haiku 4.5 <noreply@anthropic.com>

tests/cli/test_cli.py

@@ -0,0 +1,291 @@
+"""Tests for codex.cli — Typer command-line interface.
+
+All external calls (ingest, DB, embed, discovery, provenance) are mocked
+so the suite runs offline without real API calls.
+"""
+
+from __future__ import annotations
+
+from typing import Any
+from unittest.mock import MagicMock, patch
+
+import numpy as np
+from typer.testing import CliRunner
+
+from codex.cli import app
+from codex.ingest import IngestResult
+from codex.models import CodeLink
+
+runner = CliRunner()
+
+
+class TestIngest:
+    """Tests for `codex ingest` command."""
+
+    def test_ingest_command(self) -> None:
+        """Test basic ingest command with mocked ingest_paper."""
+        with patch("codex.ingest.ingest_paper") as mock_ingest:
+            mock_ingest.return_value = IngestResult(
+                paper_id="2301.07041",
+                chunks_upserted=5,
+                citations_upserted=3,
+            )
+
+            result = runner.invoke(app, ["ingest", "2301.07041"])
+
+            assert result.exit_code == 0
+            assert "2301.07041" in result.stdout
+            assert "5 chunks" in result.stdout
+            assert "3 citations" in result.stdout
+
+
+class TestSearch:
+    """Tests for `codex search` command."""
+
+    def test_search_command(self) -> None:
+        """Test search command with mocked embedder and DB."""
+        with (
+            patch("codex.embed.get_embedder") as mock_embedder,
+            patch("codex.db.get_conn") as mock_get_conn,
+        ):
+            # Mock embedder - return numpy array with one row
+            mock_emb_instance = MagicMock()
+            mock_emb_instance.encode_dense.return_value = np.array([[0.1, 0.2, 0.3]])
+            mock_embedder.return_value = mock_emb_instance
+
+            # Mock DB connection
+            mock_conn = MagicMock()
+            mock_conn.__enter__.return_value = mock_conn
+            mock_conn.__exit__.return_value = None
+            mock_conn.execute.return_value.fetchall.return_value = [
+                {
+                    "id": "2301.07041",
+                    "title": "Test Paper",
+                    "year": 2023,
+                    "distance": 0.123,
+                },
+                {
+                    "id": "2301.07042",
+                    "title": "Another Paper",
+                    "year": 2023,
+                    "distance": 0.456,
+                },
+            ]
+            mock_get_conn.return_value = mock_conn
+
+            result = runner.invoke(app, ["search", "machine learning", "--limit", "2"])
+
+            assert result.exit_code == 0
+            assert "2301.07041" in result.stdout
+            assert "2301.07042" in result.stdout
+            assert "Test Paper" in result.stdout
+            assert "0.123" in result.stdout
+
+
+class TestDiscoverLeads:
+    """Tests for `codex discover leads` command."""
+
+    def test_discover_leads_command(self) -> None:
+        """Test discover leads command with mocked discovery_leads."""
+        with patch("codex.discover.discovery_leads") as mock_leads:
+            mock_leads.return_value = [
+                {"cited_id": "2301.07041", "pull": 5},
+                {"cited_id": "2301.07042", "pull": 3},
+            ]
+
+            result = runner.invoke(app, ["discover", "leads", "--limit", "2"])
+
+            assert result.exit_code == 0
+            assert "2301.07041" in result.stdout
+            assert "2301.07042" in result.stdout
+            assert "5×" in result.stdout
+            assert "3×" in result.stdout
+
+
+class TestDiscoverCiting:
+    """Tests for `codex discover citing` command."""
+
+    def test_discover_citing_command(self) -> None:
+        """Test discover citing command with mocked citing_papers."""
+        with patch("codex.discover.citing_papers") as mock_citing:
+            mock_citing.return_value = ["2301.07041", "2301.07042"]
+
+            result = runner.invoke(app, ["discover", "citing", "2301.07043"])
+
+            assert result.exit_code == 0
+            assert "2301.07041" in result.stdout
+            assert "2301.07042" in result.stdout
+
+
+class TestDiscoverCitedBy:
+    """Tests for `codex discover cited-by` command."""
+
+    def test_discover_cited_by_command(self) -> None:
+        """Test discover cited-by command with mocked cited_by."""
+        with patch("codex.discover.cited_by") as mock_cited:
+            mock_cited.return_value = ["2301.07041", "2301.07042"]
+
+            result = runner.invoke(app, ["discover", "cited-by", "2301.07043"])
+
+            assert result.exit_code == 0
+            assert "2301.07041" in result.stdout
+            assert "2301.07042" in result.stdout
+
+
+class TestDiscoverCocited:
+    """Tests for `codex discover cocited` command."""
+
+    def test_discover_cocited_command(self) -> None:
+        """Test discover cocited command with mocked cocited_papers."""
+        with patch("codex.discover.cocited_papers") as mock_cocited:
+            mock_cocited.return_value = [
+                {"paper_id": "2301.07041", "co_citations": 5},
+                {"paper_id": "2301.07042", "co_citations": 3},
+            ]
+
+            result = runner.invoke(app, ["discover", "cocited", "2301.07043"])
+
+            assert result.exit_code == 0
+            assert "2301.07041" in result.stdout
+            assert "2301.07042" in result.stdout
+            assert "5×" in result.stdout
+            assert "3×" in result.stdout
+
+
+class TestProvScan:
+    """Tests for `codex provenance scan` command."""
+
+    def test_prov_scan_command(self) -> None:
+        """Test provenance scan command with mocked scan_cite_tags."""
+        with patch("codex.provenance.scan_cite_tags") as mock_scan:
+            mock_scan.return_value = [
+                {
+                    "file": "src/main.cpp",
+                    "line": "42",
+                    "symbol": "compute_embedding",
+                    "bibkey": "2301.07041",
+                },
+                {
+                    "file": "src/utils.h",
+                    "line": "10",
+                    "symbol": "helper_func",
+                    "bibkey": "2301.07042",
+                },
+            ]
+
+            result = runner.invoke(app, ["provenance", "scan", "/path/to/src"])
+
+            assert result.exit_code == 0
+            assert "src/main.cpp" in result.stdout
+            assert "2301.07041" in result.stdout
+            assert "compute_embedding" in result.stdout
+
+
+class TestProvAddLink:
+    """Tests for `codex provenance add-link` command."""
+
+    def test_prov_add_link_command(self) -> None:
+        """Test provenance add-link command with mocked add_code_link."""
+        with patch("codex.provenance.add_code_link") as mock_add:
+            mock_link = CodeLink(
+                id=1,
+                symbol="my_func",
+                paper_id="2301.07041",
+                role="core_algorithm",
+                note="Primary reference",
+                added_at="2023-01-01T00:00:00Z",
+            )
+            mock_add.return_value = mock_link
+
+            result = runner.invoke(
+                app,
+                [
+                    "provenance",
+                    "add-link",
+                    "my_func",
+                    "--paper-id",
+                    "2301.07041",
+                    "--role",
+                    "core_algorithm",
+                    "--note",
+                    "Primary reference",
+                ],
+            )
+
+            assert result.exit_code == 0
+            assert "Created code_link" in result.stdout
+            assert "my_func" in result.stdout
+            assert "2301.07041" in result.stdout
+
+
+class TestProvLinks:
+    """Tests for `codex provenance links` command."""
+
+    def test_prov_links_command(self) -> None:
+        """Test provenance links command with mocked list_code_links."""
+        with patch("codex.provenance.list_code_links") as mock_links:
+            mock_links.return_value = [
+                CodeLink(
+                    id=1,
+                    symbol="my_func",
+                    paper_id="2301.07041",
+                    role="core",
+                    note=None,
+                    added_at="2023-01-01T00:00:00Z",
+                ),
+                CodeLink(
+                    id=2,
+                    symbol="another_func",
+                    paper_id="2301.07042",
+                    role="utility",
+                    note=None,
+                    added_at="2023-01-02T00:00:00Z",
+                ),
+            ]
+
+            result = runner.invoke(app, ["provenance", "links"])
+
+            assert result.exit_code == 0
+            assert "[1]" in result.stdout
+            assert "[2]" in result.stdout
+            assert "my_func" in result.stdout
+            assert "another_func" in result.stdout
+
+
+class TestProvBib:
+    """Tests for `codex provenance bib` command."""
+
+    def test_prov_bib_command(self) -> None:
+        """Test provenance bib command with mocked export_bib."""
+        with patch("codex.provenance.export_bib") as mock_export:
+            mock_export.return_value = "@article{2301.07041,\n  title = {Test},\n}"
+
+            result = runner.invoke(app, ["provenance", "bib"])
+
+            assert result.exit_code == 0
+            assert "@article" in result.stdout
+            assert "2301.07041" in result.stdout
+
+    def test_prov_bib_with_output_file(self, tmp_path: Any) -> None:
+        """Test provenance bib command writing to file."""
+        with patch("codex.provenance.export_bib") as mock_export:
+            mock_export.return_value = "@article{2301.07041,\n  title = {Test},\n}"
+
+            output_file = tmp_path / "refs.bib"
+            result = runner.invoke(app, ["provenance", "bib", "--output", str(output_file)])
+
+            assert result.exit_code == 0
+            assert "Wrote" in result.stdout
+            assert output_file.exists()
+            assert "@article" in output_file.read_text()
+
+
+class TestAsk:
+    """Tests for `codex ask` command."""
+
+    def test_ask_command_exits_1(self) -> None:
+        """Test that ask command exits with code 1 (not yet implemented)."""
+        result = runner.invoke(app, ["ask", "what is machine learning?"])
+
+        assert result.exit_code == 1
+        assert "not yet implemented" in result.stdout or "not yet implemented" in result.stderr