nexus-cli 0.6.0__tar.gz → 0.7.0__tar.gz

{nexus_cli-0.6.0 → nexus_cli-0.7.0}/.STATUS

@@ -1,12 +1,12 @@
-status: active
-priority: 1
-progress: 80
-next: Merge dev→main release PR, tag v0.6.0, GitHub release (triggers PyPI + homebrew + docs deploy)
+status: deprecated
+priority: 0
+progress: 100
+next: RETIRED (2026-06-21) — absorbed into obsidian-cli-ops (obs) per RFC v2 D1=Option A. Deprecation banner added. Phase 5 remaining: ship v0.7.0 to PyPI with deprecation banner, retire Homebrew formula, archive GitHub repo.
 type: dev
-checkpoint: 2026-06-03 — v0.6.0 release prep: version bumped, CHANGELOG promoted, docs/refcard/tutorials updated. dev→main release PR open.
-version: 0.6.0
-release_date: 2026-06-02
-release_url: https://github.com/Data-Wise/nexus-cli/releases/tag/v0.5.2
+checkpoint: 2026-06-03 — v0.6.1 FULLY SHIPPED (patch: vault.py 78%→98.14%, +34 tests). PR #10 dev→main merged; tagged v0.6.1; PyPI 0.6.1 published (OIDC); GitHub release live; Homebrew formula manually pushed (bc186f9) + brew audit clean; CI green all platforms. Prior: v0.6.0 shipped same day.
+version: 0.6.1
+release_date: 2026-06-03
+release_url: https://github.com/Data-Wise/nexus-cli/releases/tag/v0.6.1
 docs_url: https://data-wise.github.io/nexus-cli/
 planning_doc: ORCHESTRATE-nexus-enhancement.md
 

nexus_cli-0.7.0/.claude/guard-session-counts

@@ -0,0 +1 @@
+edit_existing

{nexus_cli-0.6.0 → nexus_cli-0.7.0}/.github/workflows/homebrew-release.yml

@@ -59,4 +59,10 @@ jobs:
       source_type: pypi
       auto_merge: ${{ github.event.inputs.auto_merge == 'true' || github.event_name == 'workflow_dispatch' }}
     secrets:
+      # Prefer GitHub App auth (short-lived, scoped, no expiry to rotate).
+      # The reusable workflow mints an App token and only falls back to
+      # tap_token (an expiring PAT) when the App secrets are absent.
+      # Matches craft's pattern — see homebrew-tap update-formula.yml.
+      app_id: ${{ secrets.APP_ID }}
+      app_private_key: ${{ secrets.APP_PRIVATE_KEY }}
       tap_token: ${{ secrets.HOMEBREW_TAP_GITHUB_TOKEN }}

{nexus_cli-0.6.0 → nexus_cli-0.7.0}/CLAUDE.md

@@ -13,13 +13,16 @@ Nexus is a **knowledge workflow CLI** for academic researchers. It provides data
 - Teaching materials
 - Manuscripts
 
-**Current Version**: 0.6.0
+**Current Version**: 0.7.0 — **DEPRECATED**
+
+> [!warning] nexus-cli is retired
+> All functionality has been absorbed into `obsidian-cli-ops` (`obs`) as of Phase 1 (PR #37, 2026-06-21). This is the final release (v0.7.0). See the [migration guide](https://data-wise.github.io/obsidian-cli-ops/migration/) for command mappings. Use `obs research` and `obs config` going forward.
 
 ## Quick Start for Claude
 
 ```bash
 # Check installation
-nexus --version              # Should show 0.6.0
+nexus --version              # Should show 0.7.0 (final deprecated release)
 nexus doctor                 # Health check
 
 # Interactive learning system
@@ -463,7 +466,7 @@ echo $PATH | grep ".local/bin"
 ✅ Full type safety (0 mypy errors across 18 source files)
 
 ### Key Metrics
-- **Version**: 0.6.0
+- **Version**: 0.7.0 (DEPRECATED — final release)
 - **Tests**: 719 passing, 1 skipped (87.5% coverage)
 - **Mypy**: 0 errors across 20 source files
 - **Commands**: 50+ across 4 domains

{nexus_cli-0.6.0 → nexus_cli-0.7.0}/PKG-INFO

@@ -1,14 +1,14 @@
 Metadata-Version: 2.4
 Name: nexus-cli
-Version: 0.6.0
-Summary: Knowledge workflow CLI for research, teaching, and writing - Claude's body for academic work
+Version: 0.7.0
+Summary: DEPRECATED — absorbed into obsidian-cli-ops (obs). See https://data-wise.github.io/obsidian-cli-ops/migration/
 Project-URL: Homepage, https://github.com/Data-Wise/nexus-cli
 Project-URL: Documentation, https://data-wise.github.io/nexus-cli
 Project-URL: Repository, https://github.com/Data-Wise/nexus-cli
 Author-email: DT <dt@example.com>
 License: MIT
 Keywords: claude,cli,knowledge-management,obsidian,research,zotero
-Classifier: Development Status :: 3 - Alpha
+Classifier: Development Status :: 7 - Inactive
 Classifier: Environment :: Console
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: MIT License
@@ -39,7 +39,23 @@ Requires-Dist: mkdocs>=1.5.0; extra == 'docs'
 Requires-Dist: mkdocstrings[python]>=0.24.0; extra == 'docs'
 Description-Content-Type: text/markdown
 
-# Nexus CLI
+# Nexus CLI — DEPRECATED
+
+> **⚠️ nexus-cli has been absorbed into [obsidian-cli-ops](https://github.com/Data-Wise/obsidian-cli-ops) (`obs`).**
+>
+> All research, teaching, writing, and vault commands are now available under `obs research …`.
+> This package will no longer receive updates. Please migrate:
+>
+> ```sh
+> brew upgrade data-wise/tap/obsidian-cli-ops
+> # obs research zotero search "query"
+> # obs research manuscript list
+> # obs research course list
+> ```
+>
+> See the [migration guide](https://data-wise.github.io/obsidian-cli-ops/migration/) for the full command mapping.
+
+---
 
 [![CI](https://github.com/Data-Wise/nexus-cli/actions/workflows/ci.yml/badge.svg)](https://github.com/Data-Wise/nexus-cli/actions/workflows/ci.yml)
 [![Documentation](https://github.com/Data-Wise/nexus-cli/actions/workflows/docs.yml/badge.svg)](https://data-wise.github.io/nexus-cli)

{nexus_cli-0.6.0 → nexus_cli-0.7.0}/README.md

@@ -1,4 +1,20 @@
-# Nexus CLI
+# Nexus CLI — DEPRECATED
+
+> **⚠️ nexus-cli has been absorbed into [obsidian-cli-ops](https://github.com/Data-Wise/obsidian-cli-ops) (`obs`).**
+>
+> All research, teaching, writing, and vault commands are now available under `obs research …`.
+> This package will no longer receive updates. Please migrate:
+>
+> ```sh
+> brew upgrade data-wise/tap/obsidian-cli-ops
+> # obs research zotero search "query"
+> # obs research manuscript list
+> # obs research course list
+> ```
+>
+> See the [migration guide](https://data-wise.github.io/obsidian-cli-ops/migration/) for the full command mapping.
+
+---
 
 [![CI](https://github.com/Data-Wise/nexus-cli/actions/workflows/ci.yml/badge.svg)](https://github.com/Data-Wise/nexus-cli/actions/workflows/ci.yml)
 [![Documentation](https://github.com/Data-Wise/nexus-cli/actions/workflows/docs.yml/badge.svg)](https://data-wise.github.io/nexus-cli)

{nexus_cli-0.6.0 → nexus_cli-0.7.0}/docs/adhd-quick-start.md

@@ -8,7 +8,7 @@ The absolute essentials:
 
 ```bash
 nexus doctor                 # Check everything is wired up
-nexus --version              # Confirm install (should show 0.6.0)
+nexus --version              # Confirm install (should show 0.7.0)
 nexus learn                  # See what you can learn
 ```
 

{nexus_cli-0.6.0 → nexus_cli-0.7.0}/docs/changelog.md

@@ -1,3 +1,28 @@
+## [0.7.0] - 2026-06-21
+
+### Changed
+
+- **DEPRECATED**: nexus-cli is now inactive. All functionality has been absorbed into
+  [obsidian-cli-ops (obs)](https://data-wise.github.io/obsidian-cli-ops/). See the
+  [migration guide](https://data-wise.github.io/obsidian-cli-ops/migration/) for the
+  full command mapping.
+- Deprecation banner added to all `nexus` invocations.
+- `Development Status :: 7 - Inactive` PyPI classifier applied.
+- This is the final release. The package will remain on PyPI for existing installs.
+
+---
+
+## [0.6.1] - 2026-06-03
+
+### Changed
+- **Test coverage**: `vault.py` raised from 78% → **98.14%** (+34 tests),
+  meeting the last outstanding v0.6.0 coverage target. New tests cover the
+  ripgrep search fallback (rg-missing, timeout, malformed JSON), `search_files`,
+  template loading/creation, daily notes, invalid-YAML frontmatter handling,
+  missing-vault guards, and the tag-graph node/edge paths.
+
+---
+
 ## [0.6.0] - 2026-06-03
 
 ### Added

{nexus_cli-0.6.0 → nexus_cli-0.7.0}/docs/index.md

@@ -155,7 +155,7 @@ MIT License - see [LICENSE](https://github.com/Data-Wise/nexus-cli/blob/main/LIC
 
 ## Project Stats
 
-**Current Version**: 0.6.0 ✨
+**Current Version**: 0.7.0 (DEPRECATED — see [migration guide](https://data-wise.github.io/obsidian-cli-ops/migration/))
 
 - **Test Coverage**: 87.5% (719 tests passing)
 - **Type Safety**: 0 mypy errors across all 20 source files ✅

{nexus_cli-0.6.0 → nexus_cli-0.7.0}/nexus/__init__.py

@@ -4,5 +4,5 @@ Nexus CLI - Knowledge workflow for research, teaching, and writing.
 Claude is the brain, Nexus is the body.
 """
 
-__version__ = "0.6.0"
+__version__ = "0.7.0"
 __author__ = "DT"

{nexus_cli-0.6.0 → nexus_cli-0.7.0}/nexus/cli.py

@@ -99,7 +99,17 @@ def main(
 
     [dim]Claude is the brain, Nexus is the body.[/]
     """
-    pass
+    console.print(
+        Panel(
+            "[bold yellow]⚠  nexus-cli is deprecated[/]\n\n"
+            "All research, teaching, writing, and vault commands have been absorbed\n"
+            "into [bold cyan]obs[/] (obsidian-cli-ops) under [cyan]obs research …[/].\n\n"
+            "Migration:  [dim]brew upgrade data-wise/tap/obsidian-cli-ops[/]\n"
+            "Guide:      [dim]https://data-wise.github.io/obsidian-cli-ops/migration/[/]",
+            title="[bold red]Deprecated — use obs instead[/]",
+            border_style="yellow",
+        )
+    )
 
 
 @app.command()

{nexus_cli-0.6.0 → nexus_cli-0.7.0}/pyproject.toml

@@ -1,7 +1,7 @@
 [project]
 name = "nexus-cli"
-version = "0.6.0"
-description = "Knowledge workflow CLI for research, teaching, and writing - Claude's body for academic work"
+version = "0.7.0"
+description = "DEPRECATED — absorbed into obsidian-cli-ops (obs). See https://data-wise.github.io/obsidian-cli-ops/migration/"
 readme = "README.md"
 requires-python = ">=3.11"
 license = { text = "MIT" }
@@ -10,7 +10,7 @@ authors = [
 ]
 keywords = ["cli", "research", "knowledge-management", "zotero", "obsidian", "claude"]
 classifiers = [
-    "Development Status :: 3 - Alpha",
+    "Development Status :: 7 - Inactive",
     "Environment :: Console",
     "Intended Audience :: Science/Research",
     "License :: OSI Approved :: MIT License",

nexus_cli-0.7.0/tests/test_vault.py

@@ -0,0 +1,409 @@
+"""Tests for vault management module."""
+
+import subprocess
+from datetime import date
+from unittest.mock import patch
+
+import pytest
+
+from nexus.knowledge.vault import VaultManager
+
+
+class TestVaultManager:
+    """Tests for VaultManager class."""
+
+    def test_vault_exists(self, sample_vault):
+        """Test that vault existence check works."""
+        manager = VaultManager(sample_vault)
+        assert manager.exists() is True
+
+    def test_vault_not_exists(self, temp_dir):
+        """Test non-existent vault."""
+        manager = VaultManager(temp_dir / "nonexistent")
+        assert manager.exists() is False
+
+    def test_note_count(self, sample_vault):
+        """Test counting notes in vault."""
+        manager = VaultManager(sample_vault)
+        count = manager.note_count()
+
+        # Should find the sample notes
+        assert count >= 2
+
+    def test_search_notes(self, sample_vault):
+        """Test searching notes."""
+        manager = VaultManager(sample_vault)
+
+        # Search for mediation
+        results = manager.search("mediation")
+        assert len(results) >= 1
+
+        # Search for something not in notes
+        results = manager.search("xyznonexistent123")
+        assert len(results) == 0
+
+    def test_recent_notes(self, sample_vault):
+        """Test getting recent notes."""
+        manager = VaultManager(sample_vault)
+        recent = manager.recent(limit=5)
+
+        assert len(recent) >= 2
+        assert len(recent) <= 5
+
+    def test_read_note(self, sample_vault):
+        """Test reading a note."""
+        manager = VaultManager(sample_vault)
+        note = manager.read("10-PROJECTS/test-project.md")
+
+        assert note is not None
+        assert "mediation analysis" in note.content
+
+    def test_read_nonexistent_note(self, sample_vault):
+        """Test reading non-existent note raises error."""
+        manager = VaultManager(sample_vault)
+
+        with pytest.raises(FileNotFoundError):
+            manager.read("nonexistent.md")
+
+    def test_backlinks(self, sample_vault):
+        """Test finding backlinks."""
+        manager = VaultManager(sample_vault)
+        backlinks = manager.backlinks("10-PROJECTS/test-project.md")
+
+        # causal-inference.md links to test-project
+        assert len(backlinks) >= 1
+
+    def test_orphans(self, sample_vault):
+        """Test finding orphan notes."""
+        manager = VaultManager(sample_vault)
+
+        # Create an orphan note
+        orphan = sample_vault / "orphan-note.md"
+        orphan.write_text("# Orphan\n\nThis note has no links.")
+
+        orphans = manager.orphans()
+
+        assert "orphan-note.md" in orphans
+
+    def test_graph_generation(self, sample_vault):
+        """Test generating graph data."""
+        manager = VaultManager(sample_vault)
+        graph = manager.graph()
+
+        assert "nodes" in graph
+        assert "edges" in graph
+        assert len(graph["nodes"]) >= 2
+
+        # Check node structure
+        node = graph["nodes"][0]
+        assert "id" in node
+        assert "label" in node
+        assert "path" in node
+        assert "connections" in node
+
+    def test_graph_with_limit(self, sample_vault):
+        """Test graph generation with node limit."""
+        manager = VaultManager(sample_vault)
+        graph = manager.graph(limit=1)
+
+        assert len(graph["nodes"]) <= 1
+
+    def test_graph_with_tags(self, sample_vault):
+        """Test graph generation including tags."""
+        manager = VaultManager(sample_vault)
+        graph = manager.graph(include_tags=True)
+
+        # May or may not have tag nodes depending on sample data
+        tag_nodes = [n for n in graph["nodes"] if n.get("type") == "tag"]
+        assert isinstance(tag_nodes, list)  # Just verify structure
+
+    def test_graph_stats(self, sample_vault):
+        """Test graph statistics calculation."""
+        manager = VaultManager(sample_vault)
+        stats = manager.graph_stats()
+
+        assert "total_notes" in stats
+        assert "total_connections" in stats
+        assert "avg_connections" in stats
+        assert "most_connected" in stats
+        assert "density" in stats
+
+        assert stats["total_notes"] >= 2
+        assert isinstance(stats["avg_connections"], float)
+        assert isinstance(stats["most_connected"], list)
+
+    def test_write_note(self, sample_vault):
+        """Test writing a new note."""
+        manager = VaultManager(sample_vault)
+
+        content = "# New Note\n\nThis is test content."
+        result = manager.write("test-write.md", content)
+
+        assert result is not None
+        assert (sample_vault / "test-write.md").exists()
+
+        # Verify content
+        note = manager.read("test-write.md")
+        assert "test content" in note.content
+
+    def test_write_to_subdirectory(self, sample_vault):
+        """Test writing note to subdirectory."""
+        manager = VaultManager(sample_vault)
+
+        content = "# Nested Note\n\nIn a subdirectory."
+        result = manager.write("10-PROJECTS/nested-note.md", content)
+
+        assert result is not None
+        assert (sample_vault / "10-PROJECTS" / "nested-note.md").exists()
+
+    def test_search_with_limit(self, sample_vault):
+        """Test search with result limit."""
+        manager = VaultManager(sample_vault)
+
+        results = manager.search("", limit=1)
+        assert len(results) <= 1
+
+    def test_search_in_frontmatter(self, sample_vault):
+        """Test searching in frontmatter."""
+        manager = VaultManager(sample_vault)
+
+        results = manager.search("active")
+        # Should find notes with status: active in frontmatter
+        assert len(results) >= 1
+
+    def test_parse_note_with_links(self, sample_vault):
+        """Test parsing note links."""
+        manager = VaultManager(sample_vault)
+        note = manager.read("20-AREAS/causal-inference.md")
+
+        assert len(note.links) >= 1
+        assert "test-project" in note.links
+
+    def test_parse_note_with_tags(self, sample_vault):
+        """Test parsing note tags."""
+        manager = VaultManager(sample_vault)
+        note = manager.read("10-PROJECTS/test-project.md")
+
+        # Tags may or may not be present depending on content
+        assert isinstance(note.tags, list)
+
+    def test_parse_frontmatter(self, sample_vault):
+        """Test frontmatter parsing."""
+        manager = VaultManager(sample_vault)
+        note = manager.read("10-PROJECTS/test-project.md")
+
+        assert "type" in note.frontmatter
+        assert note.frontmatter["type"] == "project"
+
+    def test_backlinks_empty(self, sample_vault):
+        """Test backlinks for note with no incoming links."""
+        manager = VaultManager(sample_vault)
+
+        # Create isolated note
+        isolated = sample_vault / "isolated.md"
+        isolated.write_text("# Isolated\n\nNo one links here.")
+
+        backlinks = manager.backlinks("isolated.md")
+        assert len(backlinks) == 0
+
+    def test_recent_notes_excludes_system(self, sample_vault):
+        """Test that recent notes excludes system folders."""
+        manager = VaultManager(sample_vault)
+
+        # Create a system note
+        system_dir = sample_vault / "_SYSTEM"
+        system_dir.mkdir(exist_ok=True)
+        (system_dir / "config.md").write_text("# System\n\nConfig file.")
+
+        recent = manager.recent(limit=10)
+
+        # Should not include _SYSTEM files
+        assert not any("_SYSTEM" in path for path in recent)
+        assert not any(".obsidian" in path for path in recent)
+
+
+class TestVaultMissing:
+    """Operations on a non-existent vault should degrade gracefully."""
+
+    @pytest.fixture
+    def missing(self, temp_dir):
+        return VaultManager(temp_dir / "no-such-vault")
+
+    def test_note_count_zero(self, missing):
+        assert missing.note_count() == 0
+
+    def test_search_empty(self, missing):
+        assert missing.search("anything") == []
+
+    def test_search_files_empty(self, missing):
+        assert missing.search_files("anything") == []
+
+    def test_recent_empty(self, missing):
+        assert missing.recent() == []
+
+    def test_orphans_empty(self, missing):
+        assert missing.orphans() == []
+
+    def test_graph_empty(self, missing):
+        assert missing.graph() == {"nodes": [], "edges": []}
+
+    def test_graph_stats_empty(self, missing):
+        stats = missing.graph_stats()
+        assert stats["total_notes"] == 0
+        assert stats["total_connections"] == 0
+        assert stats["most_connected"] == []
+
+
+class TestVaultSearchFallback:
+    """Search fallback and error handling when ripgrep misbehaves."""
+
+    def test_fallback_search_direct(self, sample_vault):
+        manager = VaultManager(sample_vault)
+        results = manager._fallback_search("mediation", limit=10)
+        assert len(results) >= 1
+        assert any("mediation" in r.content.lower() for r in results)
+
+    def test_fallback_search_respects_limit(self, sample_vault):
+        manager = VaultManager(sample_vault)
+        results = manager._fallback_search("e", limit=2)
+        assert len(results) <= 2
+
+    def test_search_uses_fallback_when_rg_missing(self, sample_vault):
+        manager = VaultManager(sample_vault)
+        with patch("subprocess.run", side_effect=FileNotFoundError):
+            results = manager.search("mediation")
+        assert len(results) >= 1
+
+    def test_search_returns_empty_on_timeout(self, sample_vault):
+        manager = VaultManager(sample_vault)
+        with patch("subprocess.run", side_effect=subprocess.TimeoutExpired(cmd="rg", timeout=30)):
+            assert manager.search("mediation") == []
+
+    def test_search_skips_malformed_json(self, sample_vault):
+        manager = VaultManager(sample_vault)
+        fake = subprocess.CompletedProcess(
+            args=["rg"], returncode=0, stdout='not json\n\n{"type":"other"}\n', stderr=""
+        )
+        with patch("subprocess.run", return_value=fake):
+            # Malformed/non-match lines are skipped, yielding no results
+            assert manager.search("mediation") == []
+
+    def test_search_files_matches_name(self, sample_vault):
+        manager = VaultManager(sample_vault)
+        matches = manager.search_files("causal")
+        assert any("causal-inference" in m for m in matches)
+
+    def test_search_files_respects_limit(self, sample_vault):
+        manager = VaultManager(sample_vault)
+        matches = manager.search_files(r"\.md", limit=1)
+        assert len(matches) <= 1
+
+
+class TestVaultFrontmatterParsing:
+    """Edge cases in frontmatter parsing."""
+
+    def test_read_invalid_yaml_frontmatter(self, sample_vault):
+        manager = VaultManager(sample_vault)
+        # Unparseable YAML between --- fences: frontmatter falls back to {}
+        (sample_vault / "broken-fm.md").write_text("---\n: : bad: [unclosed\n---\n\n# Body\n")
+        note = manager.read("broken-fm.md")
+        assert note.frontmatter == {}
+        assert "Body" in note.content
+
+
+class TestVaultTemplates:
+    """Template loading and note creation from templates."""
+
+    def test_list_templates_empty_without_dir(self, sample_vault):
+        manager = VaultManager(sample_vault)
+        assert manager.list_templates() == []
+
+    def test_list_templates_strips_tpl_prefix(self, sample_vault):
+        manager = VaultManager(sample_vault)
+        manager.templates_path.mkdir(parents=True, exist_ok=True)
+        (manager.templates_path / "tpl-meeting.md").write_text("# Meeting")
+        (manager.templates_path / "note.md").write_text("# Note")
+        templates = manager.list_templates()
+        assert "meeting" in templates  # tpl- stripped
+        assert "note" in templates
+
+    def test_template_creates_note_with_substitution(self, sample_vault):
+        manager = VaultManager(sample_vault)
+        manager.templates_path.mkdir(parents=True, exist_ok=True)
+        (manager.templates_path / "lit.md").write_text("# {{title}}\n\nBy {{author}} on {{date}}")
+        out = manager.template("lit", "30-RESOURCES/new-lit.md", variables={"title": "Paper", "author": "Smith"})
+        text = out.read_text()
+        assert "# Paper" in text
+        assert "By Smith" in text
+        assert date.today().isoformat() in text
+
+    def test_template_missing_raises(self, sample_vault):
+        manager = VaultManager(sample_vault)
+        with pytest.raises(FileNotFoundError):
+            manager.template("does-not-exist", "dest.md")
+
+    def test_load_template_via_alt_path(self, sample_vault):
+        manager = VaultManager(sample_vault)
+        # Place template in an alternate location (vault/templates/), not _SYSTEM/templates
+        alt = sample_vault / "templates"
+        alt.mkdir(parents=True, exist_ok=True)
+        (alt / "alt-tpl.md").write_text("# Alt template body")
+        loaded = manager._load_template("alt-tpl")
+        assert loaded is not None
+        assert "Alt template body" in loaded
+
+    def test_daily_note_uses_template(self, sample_vault):
+        manager = VaultManager(sample_vault)
+        manager.templates_path.mkdir(parents=True, exist_ok=True)
+        (manager.templates_path / "daily.md").write_text("# {{date}}\n\nWeekday: {{date:dddd}}")
+        target = date(2026, 6, 3)
+        out = manager.daily(target)
+        text = out.read_text()
+        assert "2026-06-03" in text
+        assert "Wednesday" in text  # 2026-06-03 is a Wednesday
+
+    def test_daily_note_default_content(self, sample_vault):
+        manager = VaultManager(sample_vault)
+        target = date(2026, 6, 4)
+        out = manager.daily(target)
+        text = out.read_text()
+        assert "2026-06-04" in text
+        assert "Tasks" in text
+
+
+class TestVaultTagGraph:
+    """Graph generation with inline #tags (tag nodes and tag edges)."""
+
+    @pytest.fixture
+    def tagged_vault(self, sample_vault):
+        # Two notes sharing an inline #stats tag so the tag node qualifies (>1 connection)
+        (sample_vault / "10-PROJECTS" / "a.md").write_text("# A\n\nAbout #stats and #causal methods.\n")
+        (sample_vault / "20-AREAS" / "b.md").write_text("# B\n\nMore #stats here, links [[a]].\n")
+        return sample_vault
+
+    def test_graph_includes_tag_nodes(self, tagged_vault):
+        manager = VaultManager(tagged_vault)
+        graph = manager.graph(include_tags=True)
+        tag_nodes = [n for n in graph["nodes"] if n.get("type") == "tag"]
+        # #stats appears in 2 notes -> should be a tag node
+        assert any(n["id"] == "tag:stats" for n in tag_nodes)
+
+    def test_graph_includes_tag_edges(self, tagged_vault):
+        manager = VaultManager(tagged_vault)
+        graph = manager.graph(include_tags=True)
+        tag_edges = [e for e in graph["edges"] if e.get("type") == "tag"]
+        assert any(e["target"] == "tag:stats" for e in tag_edges)
+
+    def test_graph_stats_counts_tags(self, tagged_vault):
+        manager = VaultManager(tagged_vault)
+        stats = manager.graph_stats()
+        assert stats["total_notes"] >= 2
+        assert "total_tags" in stats
+
+    def test_graph_skips_system_folders(self, sample_vault):
+        manager = VaultManager(sample_vault)
+        sys_dir = sample_vault / "_SYSTEM"
+        sys_dir.mkdir(exist_ok=True)
+        (sys_dir / "secret.md").write_text("# Secret\n\nShould not appear.")
+        node_ids = {n["id"] for n in manager.graph()["nodes"]}
+        assert "secret" not in node_ids

{nexus_cli-0.6.0 → nexus_cli-0.7.0}/uv.lock

@@ -695,7 +695,7 @@ wheels = [
 
 [[package]]
 name = "nexus-cli"
-version = "0.5.2"
+version = "0.6.1"
 source = { editable = "." }
 dependencies = [
     { name = "pydantic" },