Add unit-test scaffolding and GitHub Actions CI

.github/workflows/ci.yml

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+name: ci
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+  workflow_dispatch:
+
+concurrency:
+  group: ci-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    name: pytest (py${{ matrix.python }} / ${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        python: ["3.10"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python }}
+
+      - name: Install system libraries
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libcairo2 libxrender1 libglib2.0-0
+
+      - name: Cache pip downloads
+        uses: actions/cache@v4
+        with:
+          path: ~/.cache/pip
+          key: pip-${{ runner.os }}-py${{ matrix.python }}-${{ hashFiles('requirements-ci.txt', 'pyproject.toml') }}
+          restore-keys: |
+            pip-${{ runner.os }}-py${{ matrix.python }}-
+
+      - name: Install CI dependencies
+        run: |
+          python -m pip install --upgrade pip wheel
+          pip install -r requirements-ci.txt
+
+      - name: Install ms_pred (editable, no extra deps)
+        run: pip install -e . --no-deps
+
+      - name: Run pytest
+        run: pytest -ra --durations=10 --maxfail=5

pyproject.toml

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+[build-system]
+requires = ["setuptools>=61", "wheel", "cython>=3", "numpy<2"]
+build-backend = "setuptools.build_meta"

pytest.ini

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+[pytest]
+testpaths = tests
+addopts = -ra --strict-markers
+markers =
+    slow: takes more than 5s; excluded from default CI run
+    gpu: requires CUDA; excluded from CI
+    integration: cross-module / end-to-end
+filterwarnings =
+    ignore::DeprecationWarning:rdkit.*
+    ignore::DeprecationWarning:pkg_resources
+    ignore::UserWarning:dgl.*
+    ignore::FutureWarning:torch.*

requirements-ci.txt

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+# CPU-only dependency set for GitHub Actions CI.
+# Source of truth for the CI install; runtime users should still follow README.
+
+# ---- PyTorch (CPU) ----
+--extra-index-url https://download.pytorch.org/whl/cpu
+torch==2.4.0
+torchvision==0.19.0
+torchaudio==2.4.0
+
+# ---- PyG extension wheels (CPU build) ----
+--find-links https://data.pyg.org/whl/torch-2.4.0+cpu.html
+torch-scatter==2.1.2
+torch-sparse==0.6.18
+torch-geometric
+
+# ---- DGL (CPU build, py3.10 manylinux) ----
+https://data.dgl.ai/wheels/torch-2.4/dgl-2.4.0-cp310-cp310-manylinux1_x86_64.whl
+
+# ---- Pinned for py3.10 compatibility ----
+numpy<2
+scikit-learn>=1.4,<1.8
+
+# ---- Core runtime deps mirrored from requirements.txt + import surface ----
+CairoSVG
+cython>=3
+einops
+h5py
+ipdb
+lightgbm
+matplotlib
+msbuddy
+omegaconf
+packaging
+pandas
+pathos
+pubchempy
+pytorch-lightning>=2.0
+rdkit
+ray[tune]
+seaborn
+tqdm
+
+# pygmtools is a git source; pin to a commit so CI is reproducible
+pygmtools @ git+https://github.com/Thinklab-SJTU/pygmtools.git@main
+
+# ---- Test-only ----
+pytest>=8
+pytest-xdist

tests/conftest.py

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+"""Shared pytest fixtures and global setup for the ms-pred test suite."""
+
+import random
+
+import numpy as np
+import pytest
+
+
+def _seed_all(seed: int = 0) -> None:
+    random.seed(seed)
+    np.random.seed(seed)
+    try:
+        import torch
+    except ImportError:
+        return
+    torch.manual_seed(seed)
+
+
+_seed_all(0)
+
+try:
+    from rdkit import RDLogger
+
+    RDLogger.DisableLog("rdApp.*")
+except ImportError:
+    pass
+
+
+@pytest.fixture(autouse=True)
+def _reseed_each_test():
+    _seed_all(0)
+    yield
+
+
+@pytest.fixture
+def known_molecules():
+    """SMILES, formula, exact monoisotopic mass for a small reference set.
+
+    Masses are RDKit ExactMolWt values rounded to 4 decimals; tests should
+    compare with a tolerance, not by exact equality.
+    """
+    return {
+        "water": ("O", "H2O", 18.0106),
+        "methane": ("C", "CH4", 16.0313),
+        "ethanol": ("CCO", "C2H6O", 46.0419),
+        "glucose": ("OC[C@H]1OC(O)[C@H](O)[C@@H](O)[C@@H]1O", "C6H12O6", 180.0634),
+        "caffeine": ("CN1C=NC2=C1C(=O)N(C)C(=O)N2C", "C8H10N4O2", 194.0804),
+        "aspirin": ("CC(=O)OC1=CC=CC=C1C(=O)O", "C9H8O4", 180.0423),
+        "fluorobenzene": ("Fc1ccccc1", "C6H5F", 96.0375),
+    }
+
+
+@pytest.fixture
+def tiny_spectrum():
+    """A 5-peak spectrum: 2-D array with columns [m/z, intensity]."""
+    return np.array(
+        [
+            [50.0, 0.10],
+            [100.0, 0.80],
+            [150.0, 0.45],
+            [200.0, 1.00],
+            [250.0, 0.20],
+        ],
+        dtype=np.float64,
+    )

tests/test_smoke_imports.py

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+"""Smoke tests: confirm every subpackage's anchor module imports cleanly.
+
+A failure here usually means a dependency rename, a top-level NameError, or
+that one branch's refactor broke the import graph.
+"""
+
+import importlib
+
+import pytest
+
+ANCHOR_MODULES = [
+    "ms_pred",
+    "ms_pred.common",
+    "ms_pred.common.chem_utils",
+    "ms_pred.common.misc_utils",
+    "ms_pred.common.fingerprint",
+    "ms_pred.common.splitter",
+    "ms_pred.common.parallel_utils",
+    "ms_pred.common.plot_utils",
+    "ms_pred.common.denoising_utils",
+    "ms_pred.nn_utils",
+    "ms_pred.nn_utils.form_embedder",
+    "ms_pred.massformer_pred",
+    "ms_pred.dag_pred.dag_data",
+    "ms_pred.ffn_pred.ffn_data",
+    "ms_pred.gnn_pred.gnn_data",
+    "ms_pred.scarf_pred.scarf_data",
+    "ms_pred.marason.dag_data",
+    "ms_pred.magma.fragmentation",
+    "ms_pred.retrieval.bootstrap_metrics",
+    "ms_pred.autoregr_gen.autoregr_data",
+    "ms_pred.graff_ms.graff_ms_data",
+    "ms_pred.molnetms.molnetms_data",
+]
+
+
+@pytest.mark.parametrize("module_name", ANCHOR_MODULES)
+def test_import_anchor_module(module_name: str) -> None:
+    module = importlib.import_module(module_name)
+    assert module is not None