liftover: Add version 1.5.0

Author: luhenry

.github/workflows/build-liftover.yml

@@ -0,0 +1,120 @@
+# SPDX-FileCopyrightText: 2026 The RISE Project
+# SPDX-License-Identifier: MIT
+---
+# This workflow is based on the `build_wheels` job of
+# https://github.com/jeremymcrae/liftover/blob/v1.5.0/.github/workflows/python-package.yml
+name: Build liftover wheels (riscv64)
+
+on:
+  workflow_dispatch:
+    inputs:
+      version:
+        description: 'Version glob to (re)build; empty builds every version of docs/packages/liftover.yaml not released yet'
+        required: false
+        default: ''
+  pull_request:
+    branches: [main]
+    paths:
+      - '.github/workflows/build-liftover.yml'
+      - 'docs/packages/liftover.yaml'
+  push:
+    branches: [main]
+    paths:
+      - '.github/workflows/build-liftover.yml'
+      - 'docs/packages/liftover.yaml'
+
+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: liftover
+      version: ${{ inputs.version }}
+
+  build_wheels:
+    needs: [setup]
+    if: needs.setup.outputs.versions != '[]'
+    name: Build liftover ${{ matrix.version }} ${{ matrix.python }}-manylinux_riscv64
+    runs-on: ubuntu-24.04-riscv
+    timeout-minutes: 60
+    strategy:
+      fail-fast: false
+      matrix:
+        version: ${{ fromJSON(needs.setup.outputs.versions) }}
+        python: ["cp312", "cp313", "cp314", "cp314t"]
+
+    env:
+      LIFTOVER_VERSION: ${{ matrix.version }}
+
+    steps:
+      - name: Checkout liftover v${{ env.LIFTOVER_VERSION }}
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
+        with:
+          repository: jeremymcrae/liftover
+          ref: v${{ env.LIFTOVER_VERSION }}
+          submodules: true
+          persist-credentials: false
+
+      - name: Fetch chain file for tests
+        run: |
+          mkdir -p chain_cache
+          curl --fail --location --retry 5 --retry-all-errors --retry-delay 30 \
+            -o chain_cache/hg19ToHg38.over.chain.gz \
+            https://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz
+          gzip -t chain_cache/hg19ToHg38.over.chain.gz
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@1828c10ab37f080699c7b81cea34097c684a7074  # v4.2.0
+        with:
+          output-dir: wheelhouse/
+          only: ${{ matrix.python }}-manylinux_riscv64
+        env:
+          CIBW_MANYLINUX_RISCV64_IMAGE: ${{ env.MANYLINUX_RISCV64_IMAGE }}
+          CIBW_ENVIRONMENT_LINUX: LIFTOVER_TEST_CACHE=/project/chain_cache
+          CIBW_TEST_COMMAND: python -m unittest discover -s {project}
+
+      - name: Verify the wheel ships the compiled extension and licence
+        run: |
+          python3 - wheelhouse/*.whl <<'EOF'
+          import sys, zipfile
+          names = zipfile.ZipFile(sys.argv[1]).namelist()
+          sos = sorted(n for n in names if n.endswith(".so"))
+          print("\n".join(sos))
+          assert any("liftover/chain_file" in n for n in sos), sos
+
+          lic = sorted(n for n in names if ".dist-info/licenses/" in n and not n.endswith("/"))
+          print("\n".join(lic))
+          assert lic, names
+          EOF
+
+      - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a  # v7.0.1
+        with:
+          name: liftover-${{ env.LIFTOVER_VERSION }}-${{ matrix.python }}-manylinux_riscv64
+          path: wheelhouse/*.whl
+          if-no-files-found: error
+
+  publish:
+    name: Publish liftover ${{ 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: ${{ secrets.RISEPROJECT_APP_PRIVATE_KEY }}
+    with:
+      artifact-pattern: liftover-${{ matrix.version }}-*-manylinux_riscv64

docs/packages/liftover.yaml

@@ -0,0 +1,5 @@
+package-name: liftover
+source-code: https://github.com/jeremymcrae/liftover
+license: MIT
+versions:
+- version: 1.5.0