Fix python version support

aeiwz · aeiwz · commit a1be4da53191 · 2026-06-25T17:48:09.000+07:00
diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml
@@ -44,9 +44,9 @@ jobs:
         python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
 
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v6
+      - uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -58,6 +58,11 @@ jobs:
       - name: Build and install (including C extension)
         run: pip install -e . --no-build-isolation
 
+      - name: Install optional dependencies (best-effort)
+        run: |
+          pip install xgboost || echo "xgboost unavailable for this Python — xgb tests will be skipped"
+          pip install "torch>=2.0" --index-url https://download.pytorch.org/whl/cpu || echo "torch unavailable for this Python — DL tests will be skipped"
+
       - name: Run test suite (excluding slow/perf)
         run: |
           pytest \
@@ -67,14 +72,14 @@ jobs:
 
       - name: Upload test results
         if: always()
-        uses: actions/upload-artifact@v6
+        uses: actions/upload-artifact@v4
         with:
           name: test-results-py${{ matrix.python-version }}
           path: test-results.xml
 
       - name: Upload coverage report
         if: always()
-        uses: actions/upload-artifact@v6
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-py${{ matrix.python-version }}
           path: coverage.xml
@@ -88,9 +93,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v6
+      - uses: actions/setup-python@v5
         with:
           python-version: "3.12"
 
@@ -99,7 +104,7 @@ jobs:
           pip install build
           python -m build --sdist
 
-      - uses: actions/upload-artifact@v6
+      - uses: actions/upload-artifact@v4
         with:
           name: sdist
           path: dist/*.tar.gz
@@ -120,15 +125,15 @@ jobs:
         os: [ubuntu-latest, macos-latest, windows-latest]
 
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v4
 
       - name: Set up QEMU (Linux aarch64 cross-compilation)
         if: matrix.os == 'ubuntu-latest'
         uses: docker/setup-qemu-action@v3
         with:
           platforms: arm64
 
-      - uses: actions/setup-python@v6
+      - uses: actions/setup-python@v5
         with:
           python-version: "3.12"
 
@@ -151,7 +156,7 @@ jobs:
           CIBW_BUILD_VERBOSITY: 1
         run: cibuildwheel --output-dir wheelhouse
 
-      - uses: actions/upload-artifact@v6
+      - uses: actions/upload-artifact@v4
         with:
           name: wheels-${{ matrix.os }}
           path: wheelhouse/*.whl
@@ -165,16 +170,16 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v4
 
       - name: Download source distribution
-        uses: actions/download-artifact@v6
+        uses: actions/download-artifact@v4
         with:
           name: sdist
           path: dist/
 
       - name: Download wheels
-        uses: actions/download-artifact@v6
+        uses: actions/download-artifact@v4
         with:
           pattern: "wheels-*"
           path: dist/
@@ -209,13 +214,13 @@ jobs:
 
     steps:
       - name: Download source distribution
-        uses: actions/download-artifact@v6
+        uses: actions/download-artifact@v4
         with:
           name: sdist
           path: dist/
 
       - name: Download wheels
-        uses: actions/download-artifact@v6
+        uses: actions/download-artifact@v4
         with:
           pattern: "wheels-*"
           path: dist/
@@ -236,7 +241,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -255,13 +260,13 @@ jobs:
           RELEASE_TAG: ${{ env.RELEASE_TAG }}
 
       - name: Download source distribution
-        uses: actions/download-artifact@v6
+        uses: actions/download-artifact@v4
         with:
           name: sdist
           path: release-assets/
 
       - name: Download wheels
-        uses: actions/download-artifact@v6
+        uses: actions/download-artifact@v4
         with:
           pattern: "wheels-*"
           path: release-assets/
diff --git a/Dockerfile.test b/Dockerfile.test
@@ -0,0 +1,39 @@
+# Dockerfile.test — mirrors the GitHub Actions CI test job exactly.
+#
+# Build:
+#   docker build -f Dockerfile.test -t metbit-test .                 # default Python 3.12
+#   docker build -f Dockerfile.test --build-arg PYTHON_VERSION=3.11 -t metbit-test-311 .
+#
+# Run:
+#   docker run --rm metbit-test                      # full suite
+#   docker run --rm metbit-test pytest -k pca        # filter
+#   docker run --rm -it metbit-test bash             # shell
+
+ARG PYTHON_VERSION=3.12
+FROM python:${PYTHON_VERSION}-slim
+
+WORKDIR /src
+
+# System build deps for the C extension
+RUN apt-get update && apt-get install -y --no-install-recommends \
+        gcc g++ make \
+    && rm -rf /var/lib/apt/lists/*
+
+# -- Layer 1: dev tools (cached when requirements-dev.txt unchanged)
+COPY requirements-dev.txt .
+RUN pip install --no-cache-dir --upgrade pip setuptools wheel && \
+    pip install --no-cache-dir -r requirements-dev.txt
+
+# -- Layer 2: optional deps (best-effort — same as CI)
+RUN pip install --no-cache-dir xgboost \
+    || echo "WARNING: xgboost unavailable on this Python — xgb tests will be skipped"
+RUN pip install --no-cache-dir "torch>=2.0" \
+        --index-url https://download.pytorch.org/whl/cpu \
+    || echo "WARNING: torch unavailable on this Python — DL tests will be skipped"
+
+# -- Layer 3: package source + C extension
+COPY . .
+RUN pip install --no-cache-dir -e . --no-build-isolation
+
+# Default command matches the CI release gate exactly
+CMD ["pytest", "-m", "not slow and not perf", "--tb=short", "-q"]
diff --git a/docker-test.sh b/docker-test.sh
@@ -0,0 +1,70 @@
+#!/usr/bin/env bash
+# docker-test.sh — build and run the metbit test container for one or all Python versions.
+#
+# Usage:
+#   ./docker-test.sh                   # test all versions (3.10 → 3.13)
+#   ./docker-test.sh 3.11              # single version
+#   ./docker-test.sh 3.12 -k pca      # filter tests
+#   ./docker-test.sh all               # explicitly test all versions
+#   KEEP=1 ./docker-test.sh 3.12       # keep container after run
+
+set -euo pipefail
+
+ALL_VERSIONS=("3.10" "3.11" "3.12" "3.13")
+
+run_version() {
+    local PY="$1"
+    shift
+    local IMAGE="metbit-test-py${PY//.}"
+
+    echo ""
+    echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━"
+    echo "  Python ${PY}  →  ${IMAGE}"
+    echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━"
+
+    echo "--> Building..."
+    docker build \
+        --build-arg PYTHON_VERSION="${PY}" \
+        -f Dockerfile.test \
+        -t "${IMAGE}" \
+        . \
+        --quiet
+
+    local DOCKER_OPTS="--rm"
+    if [[ "${KEEP:-0}" == "1" ]]; then
+        DOCKER_OPTS=""
+        echo "    (container kept — find it with 'docker ps -a')"
+    fi
+
+    echo "--> Running tests..."
+    if docker run ${DOCKER_OPTS} "${IMAGE}" \
+            pytest -m "not slow and not perf" --tb=short -q "$@"; then
+        echo "✓  Python ${PY} PASSED"
+        return 0
+    else
+        echo "✗  Python ${PY} FAILED"
+        return 1
+    fi
+}
+
+# Determine what to run
+ARG="${1:-all}"
+shift || true
+
+if [[ "$ARG" == "all" ]]; then
+    FAILED=()
+    for PY in "${ALL_VERSIONS[@]}"; do
+        run_version "$PY" "$@" || FAILED+=("$PY")
+    done
+
+    echo ""
+    echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━"
+    if [[ ${#FAILED[@]} -eq 0 ]]; then
+        echo "  All versions PASSED: ${ALL_VERSIONS[*]}"
+    else
+        echo "  FAILED versions: ${FAILED[*]}"
+        exit 1
+    fi
+else
+    run_version "$ARG" "$@"
+fi
diff --git a/metbit/ml/classifiers.py b/metbit/ml/classifiers.py
@@ -451,7 +451,9 @@ def plot_roc(
 
         classes = self.classes_
         n_classes = len(classes)
-        y_bin = label_binarize(self._y, classes=classes)
+        # self._y holds integer-encoded labels (0..n_classes-1); binarize against those
+        int_classes = np.arange(n_classes)
+        y_bin = label_binarize(self._y, classes=int_classes)
         if n_classes == 2:
             y_bin = np.hstack([1 - y_bin, y_bin])
 
diff --git a/tests/test_new_modules.py b/tests/test_new_modules.py
@@ -343,8 +343,12 @@ def test_svm_fit(self, X_y_binary):
         clf = MLClassifier(X, y, model="svm", random_state=0).fit(cv=3)
         assert len(clf.predict(X)) == len(X)
 
-    @pytest.mark.skip(reason="XGBoost segfaults on Python 3.14 — runtime incompatibility")
+    @pytest.mark.skipif(
+        __import__("sys").version_info >= (3, 14),
+        reason="xgboost 3.x segfaults under CPython 3.14 (upstream C-API incompatibility)",
+    )
     def test_xgb_fit(self, X_y_binary):
+        pytest.importorskip("xgboost", reason="xgboost not installed")
         from metbit.ml.classifiers import MLClassifier
         X, y = X_y_binary
         clf = MLClassifier(X, y, model="xgb", random_state=0).fit(cv=3)
@@ -359,6 +363,16 @@ def test_elasticnet_fit(self, X_y_binary):
 
 # ── dl/models ────────────────────────────────────────────────────────────────
 
+try:
+    import torch as _torch_check  # noqa: F401
+    _TORCH_AVAILABLE = True
+except ImportError:
+    _TORCH_AVAILABLE = False
+
+_skip_no_torch = pytest.mark.skipif(not _TORCH_AVAILABLE, reason="torch not installed")
+
+
+@_skip_no_torch
 class TestSpectralAutoencoder:
     def test_fit_encode(self, X_y_binary):
         from metbit.dl.models import SpectralAutoencoder
@@ -399,6 +413,7 @@ def test_plot_loss(self, X_y_binary):
         assert isinstance(fig, go.Figure)
 
 
+@_skip_no_torch
 class TestSpectralMLP:
     def test_fit_predict(self, X_y_binary):
         from metbit.dl.models import SpectralMLP
@@ -448,6 +463,7 @@ def test_get_accuracy(self, X_y_binary):
         assert 0.0 <= acc <= 1.0
 
 
+@_skip_no_torch
 class TestSpectralCNN:
     def test_fit_predict(self, X_y_binary):
         from metbit.dl.models import SpectralCNN
@@ -947,6 +963,7 @@ def test_bootstrap_bad_metric_raises(self, X_y_binary):
             val.bootstrap_ci(metric="invalid_metric")
 
 
+@_skip_no_torch
 class TestDLEdgeCases:
     def test_autoencoder_ndarray(self):
         from metbit.dl.models import SpectralAutoencoder
