[PythonFZ]

Follow-up to #131 and #132.

What

molify.utils.read_connectivity(atoms) (unexported) reads atoms.info['connectivity'] into native (int, int, float | None) tuples. A valid bond has three entries (i, j, order) with two distinct integer atom indices in 0..len(atoms) - 1; every other bond raises ValueError naming the bond (wrong length, scalar entry, fractional/inf/NaN/None/bool/string index, out of range, self-bond). molify.utils.fragment_indices(atoms) builds on it and groups every atom index into bonded molecules, sorted by first atom.

All five readers go through these helpers: ase2networkx, repeat, pack, iter_fragments and compress(freeze_molecules=True).

Why

The parsing was coded in five places: an inline cast in ase2x.py, a validating loop in repeat.py, raw reads in pack.py and substructure.py, and a hand-rolled union-find in compress.py. One reader gives every site the same types and the same errors.

Behaviour changes

• All five readers raise the same ValueErrors for an invalid bond. Before, ase2networkx added a stray node or a self-loop, pack offset the bond into a neighbouring molecule, compress ignored it, a fractional index such as 1.9 was truncated to 1, True was read as 1, and inf/NaN/None raised bare OverflowError/TypeError.
• pack checks bonds before it runs packmol, and returns native int/float bonds for extxyz-loaded molecules.
• iter_fragments works on extxyz-loaded atoms (it raised IndexError) and yields an unbonded atom, e.g. a Li+ ion, as its own fragment (it dropped it). Fragments come in order of their first atom, with sorted atom indices. Its docstring example now packs water and ethanol and lists the fragment formulas.

Deprecation: find_connected_components

molify.utils.find_connected_components stays importable for zincware/vectra and emits a DeprecationWarning (typing_extensions.deprecated) pointing to fragment_indices(atoms). typing-extensions is now a declared dependency.

Tests

• tests/test_connectivity.py::test_invalid_connectivity: every reader × eleven bad bonds (out of range, negative, self-bond, fractional, inf, NaN, None, bool, string, two entries, scalar), checked against the literal messages. It replaces the per-function copies in test_repeat.py.
• tests/test_substructure.py: iter_fragments on an extxyz-loaded water/ethanol box and on water + Li+.
• tests/test_solvate.py: pack of extxyz-loaded water gives native bonds; an invalid bond raises with a missing packmol executable, so the check runs first.
• compress(freeze_molecules=True) gives positions identical to main on a water/ethanol/Li+ box.
• extxyz_roundtrip is a shared fixture in tests/conftest.py.
• tests/test_utils.py::test_find_connected_components_is_deprecated: the old components plus the warning.
• Full suite: 659 passed; prek --all-files passes.

Follow-up

• iter_fragments and get_substructures fragments keep the parent's connectivity #134: fragments from iter_fragments / get_substructures keep the parent's info['connectivity'].
• compress(freeze_molecules=True) misplaces molecules in triclinic cells #135: compress(freeze_molecules=True) misplaces molecules in triclinic cells.

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📝 Walkthrough

Walkthrough

A shared read_connectivity function normalizes bond entries and rejects out-of-range atom indices and self-links. ASE conversion, packing, and bond tiling now use this function. Tests cover invalid connectivity and extxyz round-trips.

Changes

Connectivity handling

Layer / File(s)	Summary
Normalize and validate connectivity src/molify/utils.py	read_connectivity converts metadata entries to tuples with Python integer indices and floating-point bond orders, while preserving None. It raises ValueError for out-of-range indices and self-links.
Use shared connectivity reader src/molify/ase2x.py, src/molify/pack.py, src/molify/repeat.py, tests/integration/test_ase2x.py, tests/test_solvate.py	ASE conversion, packing, and bond tiling obtain bonds through read_connectivity. Tests check invalid bonds, packed connectivity, and an extxyz round-trip.

Priority: ⬇️ Low

Estimated code review effort: 2 (Simple) | ~12 minutes

Change: Bug fix

Merge Risk: 🟡 Moderate · up to 4199a

Invalid connectivity can silently produce a bond to the wrong atom. Validate endpoints before conversion prior to merging.

Security Architecture Review

Security architecture risk: 🔵 Low · up to 4199a

The change strengthens connectivity validation without adding execution authority. Risk is bounded to changed input rejection and normalization behavior; packing still performs external work before rejecting invalid connectivity.

Retained concerns
No architecture-level concerns identified.

Security review details

Security Blast Radius

• inferred — A caller controlling connectivity metadata can affect graph edges and packed or repeated bond metadata. The inspected change constrains these outputs rather than adding a new sink. No tenant, service, or production exposure model was supplied.

Trust Boundaries and Controls

• observed — Packmol execution remains an existing external-process boundary using a caller-selected executable, argument-list invocation, and a temporary working directory. Connectivity validation does not gate this execution; the PR does not change that authority or ordering.

Resilience and Maintainability Implications

• inferred — Per-call temporary directories contain library-owned packing files and isolate concurrent calls. Ordinary exceptions unwind through cleanup; connectivity rejection occurs after that cleanup. Hard termination and arbitrary executable side effects remain outside the demonstrated containment guarantee.

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 28.57% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 14 functions across 6 files.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly and concisely describes the main change: routing connectivity reads from atoms.info['connectivity'] through one shared helper.

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Actionable comments posted: 1

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Inline comments:
Review comments at @src/molify/utils.py:
- Line 44: Update read_connectivity to validate each original bond endpoint as
finite, integral, and in range before converting it to an integer, preventing
fractional values such as -0.5 from being truncated into valid indices. Add a
test case for a fractional endpoint.

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Configuration used: defaults

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Run ID: 72f8d615-a197-4682-8025-2d11c2976d43

📥 Commits

Reviewing files that changed from the base of the PR and between e06c39c and 4199a21.

📒 Files selected for processing (6)

• src/molify/ase2x.py
• src/molify/pack.py
• src/molify/repeat.py
• src/molify/utils.py
• tests/integration/test_ase2x.py
• tests/test_solvate.py

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