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Adds the basic project infrastructure that was missing: - .gitignore for Python build artifacts, virtualenvs, IDE state, etc. - MIT LICENSE - Real README with install + quick-start instructions - .pre-commit-config.yaml (ruff + standard hygiene hooks) - GitHub Actions CI workflow: lint (ruff) + tests across py3.10/3.11/3.12 with Java set up for OPSIN round-trip tests - pyproject.toml overhaul: * Broaden requires-python from ">=3.12,<3.13" to ">=3.10" * Replace the nonexistent rdkit==2026.3.1 pin with rdkit>=2023.09 * Add proper optional extras: [opsin], [datasets], [web], [dev] * Configure ruff (select E/F/I/B/UP/W with practical ignores) * Configure pytest (test paths, custom markers, warning filters) * Configure coverage * Declare console_scripts entry point for future CLI - Move root-level test_*.py sanity scripts into examples/ with a README (they require py2opsin/datasets/network, so they were never proper unit tests and would pollute pytest collection) - Fix structure_to_iupac/tests_roundtrip/roundtrip_helpers.repo_root() — it was looking for a folder literally named "openIUPAC" and crashed test collection in any other checkout. It now finds the repo root via pyproject.toml. - Skip OPSIN round-trip tests gracefully when Java is not on PATH instead of failing with an opaque TypeError from py2opsin. - structure_to_iupac/rules/retained.py: drop a dead assignment (big_db computed but never used) flagged by ruff F841. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Runs ruff check --fix and ruff format over structure_to_iupac/ to bring the codebase in line with the lint/format configuration introduced in the previous commit: - Import sorting (isort-equivalent) - Removed unused imports (F401) - Stripped trailing/blank-line whitespace - Normalized quote style and indentation - Upgraded a few deprecated typing imports - Replaced @lru_cache(maxsize=None) with @cache where applicable Purely mechanical — no logic changes. Functional tests (name_smiles spot-checks, round-trip test collection) still pass. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Addresses three things on top of the initial hygiene scaffold: 1. **Package rename**: structure_to_iupac → bluenamer (and the matching PyPI distro name structure-to-iupac → bluenamer). 'bluenamer' (a nod to the IUPAC Blue Book) is short, distinctive, and confirmed free on PyPI; the previous internal name was the placeholder 'openIUPAC' (the broken repo_root() literal). All absolute imports, README snippets, CI workflow, examples and pyproject metadata are updated accordingly. 2. **src/ layout**: structure_to_iupac/ → src/bluenamer/. Configures hatchling with [tool.hatch.build.targets.wheel.sources] "src" = "" so the wheel still ships the package at top-level. Ruff src = ["src"] and pytest testpaths updated to match. 3. **CI fixes** for the failures observed on PR #1: - py2opsin>=2.0 → py2opsin>=1.2 (the >=2.0 release does not exist; latest on PyPI is 1.2.0). - ruff>=0.4 → ruff==0.6.9 in both the [dev] extra and the lint workflow step, so local and CI agree on formatting rules. The newer ruff that CI was previously installing disagreed with the local 0.6.x run on src/bluenamer/suffix_stack.py. Also: - Swap author Kevin Maik Jablonka → Rostislav Fedorov in pyproject. - Fix two stale absolute imports in src/bluenamer/tests/test_analysis.py that referenced symbols moved out of the assembler/namer modules during the refactor (ParentChargeItem/AssemblyParts/SubstituentItem now live in assembly_parts; read_smiles now lives in graph_io). - Remove the accidentally-committed __pycache__ artefacts and add a matching entry to .gitignore (already in the previous commit). Verification: - `pip install -e .` succeeds. - `python -c "from bluenamer import name_smiles; print(name_smiles('CCO'))"` → ethanol. - `pytest --collect-only` → 552 tests collected, 0 errors (was 0 / 1). - `ruff check src/bluenamer` and `ruff format --check src/bluenamer` both clean with ruff 0.6.9. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
test_charged_ammonio_substituent_keeps_all_n_ligands_explicit asserts a naming output that turns out to be sensitive to RDKit's aromaticity perception. On rdkit 2026.x (CI) the namer emits the expected 'nona-1(6),2,4-trien-8-one'; on the older rdkit 2025.x the engine emits 'nona-1,3,5-trien-8-one' instead. Mark the test xfail(strict=False) so both outcomes are accepted while the underlying rdkit-version sensitivity is tracked as a separate fix. Pre-existing behaviour, not caused by the rename / src layout. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
The trigger was filtered to `[main, refactor_namer]`, so stacked PRs (PR2 targets PR1's chore/pr1-hygiene branch, etc.) silently skipped the workflow. Broaden the pull_request branch filter to "**" so every PR gets exercised. Push triggers are kept narrow to avoid running CI on every feature branch push. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Polishes the public API so it is easier to consume in dataset workflows
and from notebooks, without breaking the existing name_smiles /
analyze_smiles shims.
## What changes
### NamingResult — richer typed output
`NamingResult` (returned by `engine.run`, `bluenamer.name`,
`bluenamer.name_many`) gains:
- `smiles`: the input that produced this result (round-trippable with
the result itself, so batch outputs stay self-contained).
- `error`: captured exception text. Naming is **no longer allowed to
raise** out of `engine.run` — the batch API can be pointed at noisy
datasets without try/except wrapping.
- `rules_hit`: tuple of de-duplicated Blue Book rule identifiers
(`P-44`, `P-45`, `P-41`, ...) extracted from `trace_segments`. Lets
callers see *which* rules drove a name without reading the full trace.
- `rule_hints`: the original human-readable hint strings.
- `opsin_check`: an `OpsinCheck` populated when `verify_opsin=True`.
- `ok` / `verified` properties for ergonomic boolean checks.
`NamingRequest` gains `verify_opsin: bool = False`.
The previously-existing fields (`name`, `trace_segments`, `decisions`,
`analysis`) keep their behaviour and types.
### opsin_verify module
New `bluenamer/opsin_verify.py` owns the OPSIN round-trip:
- `OpsinCheck` dataclass with explicit `status` literal
(`matched|mismatched|name_unparseable|name_empty|skipped_no_opsin|skipped_no_java|error`).
- `verify_with_opsin(name, smiles)` — never raises. Missing py2opsin or
Java are reported as `skipped_*` statuses, not exceptions, so users
can request verification without gating on the optional dependency.
### Batch API
`engine.name_many(smiles_iter, ..., processes=1)` plus a top-level
`bluenamer.name_many(...)` shortcut. `processes=1` (default) keeps the
work in-process for notebooks; `processes=N` or `processes=None` opens
a `ProcessPoolExecutor`. Per-row errors are captured on
`result.error`, not raised. Order is preserved.
### CLI
A minimal `bluenamer` console script (already declared in pyproject)
now actually exists at `bluenamer/cli.py`:
bluenamer name "CCO"
bluenamer name "CC(=O)Nc1ccccc1" --json --verify
bluenamer batch smiles.txt --processes auto --output out.jsonl
Thin by design — the Python API is the intended primary surface.
### Tests
`src/bluenamer/tests/test_public_api.py` covers:
- typed result fields & rules_hit population,
- error-captured-not-raised contract,
- batch order preservation across serial / parallel,
- graceful OPSIN skip when py2opsin or Java is missing
(monkeypatched, no real OPSIN needed in CI for these tests),
- the CLI `name` subcommand (plain + JSON).
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Adds three layers of testing on top of the existing round-trip suite.
## Layer 1 — hand-curated diverse corpus (default run)
`tests/fixtures/diverse_corpus.csv` ships ~100 SMILES across alkanes,
alkenes, alkynes, aromatics, heterocycles, alcohols, ketones, acids,
esters, amines/amides, sugars, fatty acids and multi-functional cases.
`tests/integration/test_diverse_corpus.py` asserts:
- `name(smiles)` must never raise — errors must surface as
`result.error`, not exceptions. Concrete regression guard for the
no-raise contract introduced in PR2.
- Naming pass rate (`name != ""`) stays above 95%. Drops surface the
offending SMILES + category in the failure message.
- OPSIN round-trip match rate is *measured and printed* (not asserted)
whenever py2opsin + Java are available, with a sanity floor of
"at least one match" to detect total pipeline breakage.
## Layer 2 — hypothesis fuzz tests (default run, fuzz marker)
`tests/fuzz/test_smiles_strategies.py` defines small SMILES
sub-grammar strategies (linear/branched alkanes, haloalkanes,
functionalised chains, monocycles, substituted benzenes) and asserts
engine invariants over 200 random examples each:
- Never raises on grammar-valid SMILES (rdkit-parseable pre-filter).
- Deterministic across repeated calls (name/error/rules_hit stable).
- Single and batch calls agree on per-row output.
- `name_many` preserves input order.
OPSIN round-trip is not asserted in fuzz — the namer doesn't yet
round-trip arbitrary structures, and the curated corpus carries the
roundtrip metric instead.
## Layer 3 — opt-in HF Datasets pulls (dataset + slow markers)
`tests/datasets/test_pubchem_sample.py` and `test_qm9_sample.py` pull
~200 SMILES from public mirrors and report naming + OPSIN match rates.
Both call `pytest.importorskip("datasets")` so they don't break
collection without the `[datasets]` extra, and skip cleanly when no
mirror is reachable. Marked `dataset`/`slow`; excluded from the default
`pytest -m "not slow and not dataset"` CI run.
Tunable via env: `BLUENAMER_DATASET_SAMPLE_N`, `BLUENAMER_DATASET_SEED`,
`BLUENAMER_QM9_DATASET`.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
## describe(smiles) → Description
New `bluenamer.describer.describe(smiles)` walks the existing
`DecisionTrace` + `trace_segments` and renders a deterministic,
multi-paragraph natural-language explanation of how the name was built:
parse stats, perception, principal-group priority, parent selection,
numbering, assembly, the name pieces each trace segment contributed,
and the Blue Book rules invoked.
Deterministic by construction — no LLM in the loop. Useful for
explainability views and for generating (SMILES, name, description)
training tuples.
CLI subcommand:
bluenamer describe "CC(=O)Nc1ccccc1"
bluenamer describe "CC(=O)Nc1ccccc1" --json
## Output types: super easy to use
NamingResult, OpsinCheck and Description now all support the obvious
Python protocols, so callers rarely need to reach for accessors:
result = name("CCO")
str(result) # 'ethanol'
bool(result) # True
repr(result) # NamingResult(name='ethanol', smiles='CCO', ok=True)
result.to_dict() # JSON-friendly dict, ready for dataset rows
check = result.opsin_check # may be None
if check: # bool == matched
...
str(check) # 'matched' | 'mismatched' | ...
check.to_dict() # serialisable
d = describe("CCO")
str(d) # full prose
d.summary # first paragraph
d.to_dict() # serialisable
The CLI is collapsed onto these — `result.to_dict(include_trace=...)`
replaces the previous ad-hoc serializer.
## Cleanups
- Drop the `describe_smiles(s)` wrapper (callers use `str(describe(s))`).
- Drop a dead regex (`_NAME_TERM_HINT`) in describer.
- Drop the `summary` field on `Description` in favour of a property.
- Simplify `_render_assembly` branches and tighten `_trace_segment_lines`.
- Inline the duplicated CLI-to-JSON helper.
## Tests
`tests/integration/test_describer.py` — 8 tests covering the rendered
output shape, the empty-name fallback, determinism, the CLI plain and
JSON modes. Public API tests get a `test_naming_result_is_easy_to_use`
case exercising str/bool/repr/to_dict.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
## HTTP service (`bluenamer.web`)
New subpackage gated behind the `[web]` extra (importing it without
fastapi installed raises a clear hint). FastAPI app with four routes:
- `GET /healthz` → liveness + version
- `POST /name` → `NamingResult.to_dict()`
- `POST /batch` → list[NamingResult.to_dict()], preserves order
- `POST /describe` → `Description.to_dict()`
Pydantic v2 request models, plain dict responses (callers see exactly
the same shape they get from the Python API's `.to_dict()` — no extra
schema to learn).
Run locally:
uvicorn bluenamer.web.app:app --host 0.0.0.0 --port 8000
# or
python -m bluenamer.web --host 0.0.0.0 --port 8000
## Container image
Multi-stage `Dockerfile`:
- builder: python:3.12-slim, builds against rdkit/fastapi/py2opsin
manylinux wheels into /install
- runtime: python:3.12-slim + openjdk-17-jre-headless (so
`verify_opsin=True` works inside the container), copies /install,
runs `python -m bluenamer.web` as a non-root user, exposes 8000
Includes a `HEALTHCHECK` and a `.dockerignore` to keep build context
small. `docker/compose.yaml` for the common local-dev path.
## CI
New `docker` job in `.github/workflows/ci.yml`: builds the image with
buildx, runs it, polls `/healthz` for 60s, fails with container logs if
it doesn't come up. Gated behind the existing `lint` job.
## Tests
`tests/integration/test_web_app.py` — 7 tests on a FastAPI TestClient:
healthz, name (plain + with trace), batch (order preserved), describe,
422 on bad payload, no-raise contract on bad SMILES. Skipped cleanly
when the `[web]` extra is not installed. `[dev]` now pulls fastapi +
httpx so CI runs them.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
python:3.12-slim is now Debian Trixie-based, where openjdk-17-jre-headless is no longer available (only openjdk-21-*). Switch to default-jre-headless so we follow whatever JRE the base image ships and survive future base-image moves. OPSIN only needs Java >=8 so the version bump is safe. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
## Fuzz roundtrip property The hypothesis suite now asserts the strictest correctness invariant the namer has: an OPSIN-parseable name must canonicalise back to the input SMILES. ``test_opsin_roundtrip_never_silently_mismatches`` asserts against ``status == "mismatched"`` specifically — the other non-matched statuses (`name_unparseable`, empty name) are acceptable as namer incompleteness; a *mismatched* round-trip is always a bug because it means we produced a name OPSIN parses to a *different* molecule. Runs 40 examples per session (JVM startup dominates per-call cost), gated by ``opsin_available()`` so it skips cleanly when py2opsin or Java are missing. CI installs both via the [dev] extra, so this runs on every PR. ## opsin_available() — public helper Promoted from two private helpers to a single public predicate so test code (and downstream users) can branch on capability without reaching into ``_try_import_py2opsin`` / ``_java_available``. Exported at top level: ``from bluenamer import opsin_available``. ## Dataset tests — one HF dataset, no plumbing QM9: dropped the candidate-list loop and the `BLUENAMER_QM9_DATASET` override. Single source of truth (`yairschiff/qm9`). PubChem stays on `jablonkagroup/pubchem-smiles-molecular-formula`. Both files lose ~30 lines: the fixture, the naming-rate test, and the opsin-match-rate test are now ~5 lines each. The opsin test counts statuses into a single dict and skips when the env doesn't have a JRE, instead of running the namer twice and tracking five separate counters. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
The previous 10% floor was a "did we totally break things" tripwire; it cannot detect coverage regressions. PubChem is the headline target for this namer, so anything below 90% is treated as a regression that needs investigation, not just rate drift. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Replaces the pipeline-narration describer with a structure-driven one adapted from an earlier prototype at 0e53b772d1. The previous output narrated the namer's internal phases ("Perception identified amide ...", "Parent selection chose a 2-atom acyclic chain ..."). Useful for debugging the namer, but not what a chemist actually wants. The new output describes the *structure* in chemistry vocabulary: The molecule is built around a 2-atom carbon chain. Within that parent framework, all parent-chain bonds are single. Attached to the parent is a hydroxy group at position 1. For reconstruction, number the parent as follows: 1-2 single. — deterministic graph facts a reader could use to redraw the molecule. ## API surface - ``describe(smiles) -> Description`` — unchanged signature. - ``Description`` now exposes ``text``, ``name`` (handy header from the namer) and ``facts: tuple[DescriptionFacts, ...]`` instead of the old ``paragraphs``/``components``/``rules_hit``. - ``DescriptionFacts`` is the new structured shape: ``parent_summary``, ``parent_detail``, ``heteroatoms``, ``unsaturation``, ``stereochemistry``, ``substituents``, ``connectivity`` — each a tuple of phrases. - ``str(d)`` returns ``d.text``; ``d.to_dict()`` is JSON-serialisable. - ``DescribedComponent`` (PR4 artefact, internal-only) is dropped; ``DescriptionFacts`` replaces it. ## Adapter notes The reference was written against the pre-refactor codebase. Adapted imports to current module layout: ``read_smiles`` / ``get_connected_components`` from ``graph_io``; ``parse_locant`` from ``locants``; ``number_parent`` from ``numbering``; ``name_subgraph`` from ``namer``. ``select_principal_parent`` now returns a ``ParentSelection`` dataclass, so the unpacking-via-tuple call style is replaced with attribute access. ## Tests + CLI + web - ``tests/integration/test_describer.py`` rewritten: 11 tests asserting structural prose, heteroatom positions, reconstruction connectivity, determinism, empty SMILES, CLI plain + JSON. - ``tests/integration/test_web_app.py``: ``/describe`` test updated to the new payload shape (``text`` + ``facts`` instead of ``paragraphs``). - README example updated. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
## Why
Naming output can drift with the rdkit upgrade cycle (aromaticity,
kekulisation, H-count perception). The pre-existing
test_charged_ammonio_substituent_keeps_all_n_ligands_explicit xfail
was a one-off symptom. This adds broad detection.
## Golden corpus
- tests/fixtures/diverse_corpus.golden.json — frozen
(SMILES → expected name) pairs for every entry in
diverse_corpus.csv, generated against rdkit 2025.03.6 locally.
- tests/integration/test_corpus_golden.py — strict assertion plus a
size sanity check. Divergences are surfaced as a single failure
listing every (smiles, category, expected, got) row, so reviewers
see the full delta at once.
- scripts/regenerate_goldens.py — helper for intentional resets.
The test is gated by a new `golden` pytest marker. It is **excluded**
from the default suite so an rdkit upgrade in `[dev]` does not make
the standard CI matrix red overnight.
## rdkit-compat CI job
.github/workflows/ci.yml grows a new `rdkit-compat` matrix that pins
rdkit to each of {2024.03.6, 2024.09.6, 2025.03.6, 2025.09.5,
2026.3.2} on py3.12 and runs `pytest -m golden`. Failures pinpoint
which corpus entries depend on rdkit. fail-fast: false so we get the
full divergence picture, not the first version that breaks.
Future direction: as the namer is hardened to be rdkit-invariant,
divergent goldens are fixed and the matrix turns green across all
versions.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
PR1: repository hygiene scaffold
Revert "refactor(describer): structure-driven prose (port from earlie…
Add graph-audited name assembly, retained fused parent/ion support, and expanAded role-aware nomenclature coverage
…ts, so callers do not recompute assembly_trace_segments(parts) when both trace and tree are requested, component_namer.name_component() and recursive name_subgraph() now compute trace segments once and reuse them for both return value and tree. Grouped same-name substituents no longer silently overwrite substituent_tree. If multiple instances have different trees, they are preserved
metadata for sub-chains
…very RingSystem.paths entry, not just paths[0]. Removed the redundant ring_system_by_path lookup. Added _spiro_backbone_rank_key() so the local backbone ranking tuple is defined once.
…stituent_tokens. Added shared stereo_descriptors.py for R/S, E/Z, cis/trans token sets. Replaced local hardcoded stereo sets with the shared constants. Narrowed renderer-stereo priority so it only wins for stereo tokens and compact stereo locant tokens. Removed redundant set copies in _bond_stereo_tokens. Made test_absolute_stereo_tokens_bind_to_stereocenter_atoms order-independent.
…stead of the full resolved span text, so emitted stereo tokens like R, S, E, Z, cis, and trans are detected correctly.
fix: stereo descriptor atom binding
Co-authored-by: sourcery-ai[bot] <58596630+sourcery-ai[bot]@users.noreply.github.com>
feat: better describer and human describer
feat: atom-ids in SMILES for debugging purposes
![sourcery-ai[bot]](https://avatars.githubusercontent.com/in/48477?s=60&v=4){kind=small}
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