feat: atom-ids in SMILES for debugging purposes

[r-fedorov]

Summary by Sourcery

Tests:

• Add an integration test to verify that the description includes processed SMILES and corresponding atom IDs.

[sourcery-ai]

Reviewer's guide (collapsed on small PRs)

Reviewer's Guide

Adds inclusion of a processed SMILES sentence with atom IDs to the describer output, and introduces an integration test to verify the new debugging-oriented SMILES/atom-id rendering.

Sequence diagram for updated describer SMILES debugging output

sequenceDiagram
    actor Client
    participant describer_describe as describe
    participant processed_smiles as _processed_smiles_sentence

    Client->>describer_describe: describe(smiles, result)
    describer_describe->>processed_smiles: _processed_smiles_sentence(smiles)
    processed_smiles-->>describer_describe: smiles_sentence
    alt [smiles_sentence]
        describer_describe->>describer_describe: paragraphs.append(smiles_sentence)
    end
    describer_describe-->>Client: description_text

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File-Level Changes

Change	Details	Files
Describer now appends a processed SMILES sentence (including atom IDs when available) to its textual output before decision components.	Calls a new helper _processed_smiles_sentence(smiles) in describe to build a SMILES-related sentence from the input SMILES. Appends the returned SMILES sentence to the paragraphs list immediately after the summary, if the sentence is non-empty.	src/bluenamer/describer.py
Integration test added to ensure the describer output contains the processed SMILES and atom IDs for debugging.	Creates test_describe_includes_processed_smiles_atom_ids that calls describe with a chiral SMILES string and converts the result to text. Asserts the summary line still starts with the expected prefix including the original SMILES. Asserts the output text includes the processed SMILES line, an introductory label for atom IDs, and the expected SMILES annotated with atom indices.	tests/integration/test_describer.py

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[sourcery-ai]

Hey - I've found 1 issue, and left some high level feedback:

• The new integration test tightly couples to the exact textual formatting (including full atom-id sequence and phrasing); consider matching only the key parts (e.g., presence of the processed SMILES and at least one atom-id pattern) to make the test less brittle to minor wording or formatting changes.

Prompt for AI Agents

Please address the comments from this code review:

## Overall Comments
- The new integration test tightly couples to the exact textual formatting (including full atom-id sequence and phrasing); consider matching only the key parts (e.g., presence of the processed SMILES and at least one atom-id pattern) to make the test less brittle to minor wording or formatting changes.

## Individual Comments

### Comment 1
<location path="tests/integration/test_describer.py" line_range="35" />
<code_context>
+    assert d.summary.startswith("The molecule C[C@@H](Cl)C(=O)c1ccccc1 is named")
+    assert "Processed SMILES: C[C@@H](Cl)C(=O)c1ccccc1" in text
+    assert "Atom ids in that SMILES:" in text
+    assert "C{0}[C@@H]{1}(Cl{2})C{3}(=O{4})c{5}1c{6}c{7}c{8}c{9}c{10}1" in text
+
+
</code_context>
<issue_to_address>
**suggestion (testing):** This assertion is quite brittle; consider asserting structure or pattern instead of an exact atom-id string.

Hard-coding the entire atom-id-annotated SMILES makes the test fragile: any harmless change in atom ordering, formatting, or canonicalization will cause a failure. Instead, consider:
- Using a regex to verify the `{id}` pattern on atoms,
- Checking that the count of `{}`-wrapped indices matches the atom count, and/or
- Verifying a few key atom–id mappings rather than the full string.
This keeps the test resilient while still validating the mapping logic.
</issue_to_address>

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[sourcery-ai]

suggestion (testing): This assertion is quite brittle; consider asserting structure or pattern instead of an exact atom-id string.

Hard-coding the entire atom-id-annotated SMILES makes the test fragile: any harmless change in atom ordering, formatting, or canonicalization will cause a failure. Instead, consider:

• Using a regex to verify the {id} pattern on atoms,
• Checking that the count of {}-wrapped indices matches the atom count, and/or
• Verifying a few key atom–id mappings rather than the full string.
  This keeps the test resilient while still validating the mapping logic.