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05 — Add graph runtime dependencies

• Priority: P1
• Depends on: none
• Size: S (15–30 min)
• Files: pyproject.toml, tests/test_graphify_bridge.py
• PR title: fix: include graph runtime dependencies in extras

Read first

• pyproject.toml, sections [project.optional-dependencies], keys graph (around line 60) and all (around line 80)
• tests/test_graphify_bridge.py, function test_pyproject_has_graph_extra (around line 92)

Problem

The graph extra contains only:

graph = ["graphifyy>=0.4.20"]

But the graph pipeline needs two packages that graphifyy does not declare:

• matplotlib — report and HTML rendering. Without it the graph crashes with ImportError: matplotlib not installed.
• scipy — community detection and analysis. Without it the graph crashes with ModuleNotFoundError: No module named 'scipy'.

Both were installed manually in this environment. A fresh pip install sessionwiki[graph] leaves sessionwiki graph broken: it falls back to the builtin engine with a warning.

Required change

In pyproject.toml update both extras:

graph = [
    "graphifyy>=0.4.20",
    "matplotlib>=3.8",
    "scipy>=1.11",
]
all = [
    "graphifyy>=0.4.20",
    "matplotlib>=3.8",
    "scipy>=1.11",
]

Keep the existing formatting style of the file. Do not add a version pin tighter than the minimums above unless the repository already pins those packages elsewhere.

Test

Update tests/test_graphify_bridge.py::test_pyproject_has_graph_extra:

def test_pyproject_has_graph_extra():
    from sessionwiki import REPO_ROOT

    content = (REPO_ROOT / "pyproject.toml").read_text(encoding="utf-8")
    assert 'graph = [' in content
    assert "graphifyy" in content
    assert "matplotlib" in content
    assert "scipy" in content

The all extra uses the same packages; the test can also assert that the string matplotlib appears at least twice, but a simple presence check is enough.

Verification

.venv/bin/pip install -e '.[graph]'
.venv/bin/python -c "import matplotlib, scipy; print(matplotlib.__version__, scipy.__version__)"
.venv/bin/python -m pytest tests/test_graphify_bridge.py -q
.venv/bin/python -m sessionwiki graph

Expected:

• Both imports succeed.
• The graph command completes without ModuleNotFoundError.
• graphify-out/graph.json is written.

If pip install -e '.[graph]' changes installed versions, record the diff in the PR body. Do not commit a lock file.

Acceptance criteria

• [ ] graph extra lists matplotlib and scipy.
• [ ] all extra lists matplotlib and scipy.
• [ ] The updated test passes.
• [ ] sessionwiki graph completes without a missing-module fallback.
• [ ] CHANGELOG.md updated.

Out of scope

• Updating README.md and docs/configuration.md. The repository rule says new runtime deps need docs; add one line there only if the installation instructions mention the graph extra. If they do, update the same PR.
• Changing graphify itself.
• Adding numpy or other transitive dependencies; graphifyy already declares them.

Rollback

Revert pyproject.toml and the test.