Tests

.dockerignore

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+.git
+.github
+.venv
+venv
+__pycache__
+*.pyc
+*.pyo
+.pytest_cache
+.ruff_cache
+.mypy_cache
+.coverage
+htmlcov
+.hypothesis
+build
+dist
+*.egg-info
+examples
+tests
+docs
+*.md
+!README.md

.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [main, refactor_namer]
+  pull_request:
+    branches: ["**"]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - name: Install ruff
+        run: pip install "ruff==0.15.15"
+      - name: Ruff check
+        run: ruff check src/bluenamer
+      - name: Ruff format check
+        run: ruff format --check src/bluenamer
+
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.11", "3.12"]
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: pip
+
+      - name: Set up JDK (for OPSIN)
+        uses: actions/setup-java@v4
+        with:
+          distribution: temurin
+          java-version: "17"
+
+      - name: Install package
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[dev]"
+
+      - name: Run fast tests
+        run: |
+          pytest -m "not slow and not dataset and not golden" \
+                 --maxfail=20 \
+                 --durations=20
+
+  rdkit-compat:
+    # Strict golden-output regression across RDKit versions. Detects
+    # naming output that drifts with the RDKit upgrade cycle (aromaticity,
+    # kekulisation, H-count perception). Each matrix row pins a specific
+    # rdkit and runs only the `golden` test.
+    runs-on: ubuntu-latest
+    needs: [lint]
+    strategy:
+      fail-fast: false
+      matrix:
+        rdkit-version:
+          - "2024.03.6"
+          - "2024.09.6"
+          - "2025.03.6"
+          - "2025.09.5"
+          - "2026.3.2"
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: pip
+
+      - name: Install package + pinned rdkit
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e ".[dev]"
+          pip install --force-reinstall --no-deps "rdkit==${{ matrix.rdkit-version }}"
+
+      - name: Show installed versions
+        run: |
+          python -c "import rdkit, sys; print('python', sys.version); print('rdkit', rdkit.__version__)"
+
+      - name: Run golden corpus test
+        run: pytest -m golden -v --no-header -rA
+
+  docker:
+    runs-on: ubuntu-latest
+    needs: [lint]
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: docker/setup-buildx-action@v3
+
+      - name: Build image
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          push: false
+          load: true
+          tags: bluenamer:ci
+
+      - name: Smoke-test the image
+        run: |
+          docker run -d --name bluenamer-ci -p 8000:8000 bluenamer:ci
+          for i in $(seq 1 30); do
+            if curl -fsS http://127.0.0.1:8000/healthz > /tmp/health.json; then
+              cat /tmp/health.json
+              exit 0
+            fi
+            sleep 2
+          done
+          docker logs bluenamer-ci
+          exit 1

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# Hatch
+.hatch/
+
+# Unit test / coverage / type checkers
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+.pytest_cache/
+.mypy_cache/
+.ruff_cache/
+htmlcov/
+coverage.xml
+*.cover
+.hypothesis/
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+.python-version
+
+# IDEs
+.vscode/
+.idea/
+*.swp
+*.swo
+.DS_Store
+
+# Notebooks
+.ipynb_checkpoints/
+
+# Project-specific
+*.log
+*.jar
+opsin*.jar
+data/cache/
+.cache/
+
+# Docker
+.docker/

.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-toml
+      - id: check-merge-conflict
+      - id: check-added-large-files
+        args: ["--maxkb=1024"]
+
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.9
+    hooks:
+      - id: ruff
+        args: [--fix]
+      - id: ruff-format

Dockerfile

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+# syntax=docker/dockerfile:1.7
+
+# ----- builder stage -----------------------------------------------------
+FROM python:3.12-slim AS builder
+
+ENV PIP_DISABLE_PIP_VERSION_CHECK=1 \
+    PIP_NO_CACHE_DIR=1 \
+    PYTHONDONTWRITEBYTECODE=1
+
+WORKDIR /build
+
+# Build deps for rdkit wheels: typically just runtime; the manylinux wheels
+# carry their own libs. Keep this stage thin.
+RUN apt-get update -qq \
+ && apt-get install -y --no-install-recommends build-essential \
+ && rm -rf /var/lib/apt/lists/*
+
+COPY pyproject.toml README.md ./
+COPY src ./src
+
+# Install into a clean prefix so we can copy a slim layer into the runtime.
+RUN python -m pip install --upgrade pip \
+ && python -m pip install --prefix=/install ".[web,opsin]"
+
+
+# ----- runtime stage -----------------------------------------------------
+FROM python:3.12-slim AS runtime
+
+ENV PYTHONUNBUFFERED=1 \
+    PYTHONDONTWRITEBYTECODE=1 \
+    PATH="/usr/local/bin:${PATH}"
+
+# Java runtime for OPSIN round-trip verification (py2opsin shells out to java;
+# OPSIN itself requires Java >=8 so the newer JRE is fine).
+RUN apt-get update -qq \
+ && apt-get install -y --no-install-recommends \
+        default-jre-headless \
+        curl \
+        ca-certificates \
+ && rm -rf /var/lib/apt/lists/*
+
+# Bring in the installed package + deps from the builder stage.
+COPY --from=builder /install /usr/local
+
+# Non-root user.
+RUN useradd --create-home --shell /bin/bash bluenamer
+USER bluenamer
+WORKDIR /home/bluenamer
+
+EXPOSE 8000
+
+HEALTHCHECK --interval=30s --timeout=5s --retries=3 \
+  CMD curl -fsS http://127.0.0.1:8000/healthz || exit 1
+
+CMD ["python", "-m", "bluenamer.web", "--host", "0.0.0.0", "--port", "8000"]

LICENSE

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+MIT License
+
+Copyright (c) 2026 lamalab-org
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.