scikit-survival: Add version 0.28.0

.github/workflows/build-scikit-survival.yml

@@ -0,0 +1,132 @@
+# SPDX-FileCopyrightText: 2026 The RISE Project
+# SPDX-License-Identifier: MIT
+---
+# Based on: https://github.com/sebp/scikit-survival/blob/v0.28.0/.github/workflows/wheels-workflow.yaml
+name: Build scikit-survival wheels (riscv64)
+
+on:
+  workflow_dispatch:
+    inputs:
+      version:
+        description: 'Version glob to (re)build; empty builds every version of docs/packages/scikit-survival.yaml not released yet'
+        required: false
+        default: ''
+  pull_request:
+    branches: [main]
+    paths:
+      - '.github/workflows/build-scikit-survival.yml'
+      - 'docs/packages/scikit-survival.yaml'
+      - 'patches/scikit-survival/**'
+  push:
+    branches: [main]
+    paths:
+      - '.github/workflows/build-scikit-survival.yml'
+      - 'docs/packages/scikit-survival.yaml'
+      - 'patches/scikit-survival/**'
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read  # to fetch code (actions/checkout)
+
+env:
+  MANYLINUX_RISCV64_IMAGE: quay.io/pypa/manylinux_2_39_riscv64
+
+jobs:
+  setup:
+    uses: $/.github/workflows/_setup.yml
+    with:
+      package: scikit-survival
+      version: ${{ inputs.version }}
+
+  build_wheels:
+    needs: [setup]
+    if: needs.setup.outputs.versions != '[]'
+    name: Build scikit-survival ${{ matrix.version }} ${{ matrix.python }}-manylinux_riscv64
+    runs-on: ubuntu-24.04-riscv
+    timeout-minutes: 360
+    strategy:
+      fail-fast: false
+      matrix:
+        version: ${{ fromJSON(needs.setup.outputs.versions) }}
+        # No cp314t: upstream ships none, and pandas (a hard dependency) has no free-threaded wheel.
+        python: ["cp312", "cp313", "cp314"]
+
+    env:
+      SCIKIT_SURVIVAL_VERSION: ${{ matrix.version }}
+
+    steps:
+      - name: Checkout scikit-survival v${{ env.SCIKIT_SURVIVAL_VERSION }}
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
+        with:
+          repository: sebp/scikit-survival
+          ref: v${{ env.SCIKIT_SURVIVAL_VERSION }}
+          submodules: true
+          persist-credentials: false
+
+      - name: Checkout python-wheels
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
+        with:
+          path: python-wheels
+          persist-credentials: false
+
+      - name: Apply patches
+        run: git apply python-wheels/patches/scikit-survival/${{ env.SCIKIT_SURVIVAL_VERSION }}/*.patch
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@1828c10ab37f080699c7b81cea34097c684a7074  # v4.2.0
+        with:
+          only: ${{ matrix.python }}-manylinux_riscv64
+        env:
+          CIBW_MANYLINUX_RISCV64_IMAGE: ${{ env.MANYLINUX_RISCV64_IMAGE }}
+          # Upstream's build[uv] crashes the audit step on the riscv runner (gotcha 13).
+          CIBW_BUILD_FRONTEND: build
+          # The patched tree would otherwise get a dirty setuptools_scm version (gotcha 31).
+          CIBW_ENVIRONMENT: >-
+            PIP_EXTRA_INDEX_URL=https://pypi.riseproject.dev/simple/
+            PIP_ONLY_BINARY=numpy,scipy,scikit-learn,pandas,ecos,osqp,numexpr
+            SETUPTOOLS_SCM_PRETEND_VERSION_FOR_SCIKIT_SURVIVAL=${{ env.SCIKIT_SURVIVAL_VERSION }}
+          CIBW_TEST_GROUPS: test
+          # polars 1.43 (released after 0.28.0) deprecates cat.get_categories(), which the suite's filterwarnings=error turns into failures.
+          CIBW_TEST_REQUIRES: polars<1.43
+          # riscv64 rounding moves a ~2.7e7 cumulative hazard by 6e-13 relative, past this test's 5-decimal absolute check.
+          CIBW_TEST_COMMAND: >-
+            pytest --strict-markers -m 'not slow' -k 'not test_fit_and_predict_linear_regression'
+            --deselect 'tests/test_coxnet.py::TestCoxnetBaselineModel::test_baseline_predict[predict_cumulative_hazard_function-False]'
+            {project}/tests
+
+      - name: Check wheel contents
+        run: |
+          python3 - wheelhouse/*.whl <<'EOF'
+          import sys, zipfile
+          names = zipfile.ZipFile(sys.argv[1]).namelist()
+          exts = {n.split("/")[-1].split(".")[0] for n in names if n.endswith(".so")}
+          assert exts == {"_binarytrees", "_clinical_kernel", "_coxph_loss", "_prsvm", "_minlip", "_criterion", "_coxnet"}, exts
+          licences = {n.rsplit("/", 1)[-1] for n in names if ".dist-info/licenses/" in n} - {""}
+          assert licences == {"COPYING", "COPYING.MPL2", "COPYING.APACHE"}, licences
+          EOF
+
+      - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a  # v7.0.1
+        with:
+          name: scikit-survival-${{ env.SCIKIT_SURVIVAL_VERSION }}-${{ matrix.python }}-manylinux_riscv64
+          path: ./wheelhouse/*.whl
+          if-no-files-found: error
+
+  publish:
+    name: Publish scikit-survival ${{ matrix.version }}
+    needs: [setup, build_wheels]
+    if: needs.setup.outputs.versions != '[]'
+    strategy:
+      fail-fast: false
+      matrix:
+        version: ${{ fromJSON(needs.setup.outputs.versions) }}
+    permissions:
+      contents: write
+      pull-requests: write
+    uses: $/.github/workflows/_publish-wheel.yml
+    secrets:
+      app-private-key: ${{ secrets.RISEPROJECT_APP_PRIVATE_KEY }}
+    with:
+      artifact-pattern: scikit-survival-${{ matrix.version }}-*-manylinux_riscv64

docs/packages/scikit-survival.yaml

@@ -0,0 +1,6 @@
+package-name: scikit-survival
+source-code: https://github.com/sebp/scikit-survival
+license: GPL-3.0-or-later
+versions:
+- version: 0.28.0
+  patched: true

patches/scikit-survival/0.28.0/0001-ship-the-vendored-Eigen-licences-in-the-wheel.patch

@@ -0,0 +1,47 @@
+From 17ec8da55f97261781ede418ee606ed56d6e6b21 Mon Sep 17 00:00:00 2001
+From: Ludovic Henry <git@ludovic.dev>
+Date: Fri, 2 Oct 2026 15:52:22 +0000
+Subject: [PATCH] ship the vendored Eigen licences in the wheel
+
+Upstream-Status: To upstream [not yet submitted; every scikit-survival wheel on PyPI has the same gap, so it needs raising with the maintainer rather than a drive-by PR]
+
+sksurv/linear_model/_coxnet.pyx compiles the sksurv/linear_model/src/eigen
+submodule's Eigen/Core headers (header-only) straight into the
+sksurv.linear_model._coxnet extension. Eigen/Core is MPL-2.0, except
+Eigen/src/Core/arch/Default/BFloat16.h, which Eigen/Core includes
+unconditionally and which carries the TensorFlow Authors' Apache-2.0
+notice. The built wheel ships only scikit-survival's own COPYING:
+`license-files = ["COPYING"]` is an explicit PEP 639 list with no default
+glob behind it, so Eigen's COPYING.* files never reach dist-info/licenses/.
+
+List COPYING.MPL2 and COPYING.APACHE in place from the submodule. The
+other Eigen notices are not reachable from Eigen/Core: Half.h's Fabian
+Giesen notice grants redistribution unconditionally, and the *_BLAS.h /
+*_MKL.h files are only compiled in with EIGEN_USE_BLAS / EIGEN_USE_MKL,
+which scikit-survival never defines.
+
+Signed-off-by: Ludovic Henry <git@ludovic.dev>
+---
+ pyproject.toml | 6 +++++-
+ 1 file changed, 5 insertions(+), 1 deletion(-)
+
+diff --git a/pyproject.toml b/pyproject.toml
+index 5f6fb0b..b16056b 100644
+--- a/pyproject.toml
++++ b/pyproject.toml
+@@ -22,7 +22,11 @@ authors = [
+     {name = "Sebastian Pölsterl", email = "sebp@k-d-w.org"}
+ ]
+ license = "GPL-3.0-or-later"
+-license-files = ["COPYING"]
++license-files = [
++    "COPYING",
++    "sksurv/linear_model/src/eigen/COPYING.MPL2",
++    "sksurv/linear_model/src/eigen/COPYING.APACHE",
++]
+ requires-python = ">=3.11"
+ classifiers = [
+     "Development Status :: 4 - Beta",
+-- 
+2.43.0
+