-
Notifications
You must be signed in to change notification settings - Fork 70
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
ci workflows support new split htslib. support new wheel. suport wind…
…ows build
- Loading branch information
Showing
13 changed files
with
253 additions
and
107 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -18,43 +18,71 @@ on: | |
|
|
||
| jobs: | ||
| build_wheels: | ||
| name: Build wheels on ${{ matrix.os }} | ||
| runs-on: ${{ matrix.os }}-latest | ||
| name: Build wheels for ${{ matrix.python-version }}-${{ matrix.buildplat[1] }} | ||
| runs-on: ${{ matrix.buildplat[0] }} | ||
| strategy: | ||
| matrix: | ||
| os: [ubuntu, macos] | ||
| python-version: ["3.12"] | ||
| buildplat: | ||
| - [ubuntu-22.04, manylinux_x86_64] | ||
| - [ubuntu-22.04, musllinux_x86_64] | ||
| - [ubuntu-22.04, manylinux_aarch64] | ||
| - [ubuntu-22.04, musllinux_aarch64] | ||
| # macOS build arm64 on x86_64 with cross-compiler | ||
| - [macos-12, macosx_x86_64] | ||
| python-version: [pp310, cp37, cp38, cp39, cp310, cp311, cp312] | ||
| exclude: | ||
| # pp310, cp37, cp38 on musllinux is not support | ||
| - buildplat: [ubuntu-22.04, musllinux_x86_64] | ||
| python-version: cp37 | ||
| - buildplat: [ubuntu-22.04, musllinux_x86_64] | ||
| python-version: cp38 | ||
| - buildplat: [ubuntu-22.04, musllinux_x86_64] | ||
| python-version: pp310 | ||
| - buildplat: [ubuntu-22.04, musllinux_aarch64] | ||
| python-version: cp37 | ||
| - buildplat: [ubuntu-22.04, musllinux_aarch64] | ||
| python-version: cp38 | ||
| - buildplat: [ubuntu-22.04, musllinux_aarch64] | ||
| python-version: pp310 | ||
|
|
||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| with: | ||
| submodules: recursive | ||
| - name: Set up Python ${{ matrix.python-version }} | ||
| uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
|
|
||
| - name: Set up QEMU | ||
| if: runner.os == 'Linux' | ||
| uses: docker/setup-qemu-action@v3 | ||
|
|
||
| - name: Build wheels for Linux | ||
| - name: Build wheels | ||
| uses: pypa/[email protected] | ||
| if: runner.os == 'Linux' | ||
| with: | ||
| package-dir: . | ||
| output-dir: wheelhouse | ||
| config-file: "{package}/pyproject.toml" | ||
| env: | ||
| CIBW_SKIP: "pp* *i686*" | ||
| # select | ||
| CIBW_BUILD: ${{ matrix.python-version }}-${{ matrix.buildplat[1] }} | ||
|
|
||
| # linux | ||
| CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014 | ||
| CIBW_MUSLLINUX_X86_64_IMAGE: musllinux_1_1 | ||
| # manylinux2014 can't build on aarch64 | ||
| CIBW_MANYLINUX_AARCH64_IMAGE: manylinux_2_28 | ||
| CIBW_MUSLLINUX_X86_64_IMAGE: musllinux_1_2 | ||
| CIBW_MUSLLINUX_AARCH64_IMAGE: musllinux_1_2 | ||
| CIBW_ARCHS_LINUX: auto64 aarch64 | ||
| CIBW_BEFORE_BUILD_LINUX: "{project}/ci/linux-deps" | ||
| CIBW_TEST_COMMAND: "{project}/ci/test" | ||
| CIBW_REPAIR_WHEEL_COMMAND_LINUX: 'LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/lib64" && auditwheel repair -w {dest_dir} {wheel}' | ||
|
|
||
| # macos | ||
| CIBW_ARCHS_MACOS: auto64 arm64 | ||
| CIBW_BEFORE_BUILD_MACOS: "{project}/ci/osx-deps" | ||
|
|
||
| # build | ||
| CIBW_ENVIRONMENT: >- | ||
| CYVCF2_HTSLIB_CONFIGURE_OPTIONS="--enable-libcurl --enable-s3 --enable-lzma --enable-bz2 --with-libdeflate" | ||
| CYTHONIZE=1 | ||
| CIBW_TEST_COMMAND: "{project}/ci/test" | ||
|
|
||
| # Enable tmate debugging of manually-triggered workflows if the input option was provided | ||
| - name: Setup tmate session | ||
|
|
@@ -67,7 +95,7 @@ jobs: | |
|
|
||
| build_sdist: | ||
| name: Build source distribution | ||
| runs-on: ubuntu-latest | ||
| runs-on: ubuntu-22.04 | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| with: | ||
|
|
@@ -90,7 +118,7 @@ jobs: | |
|
|
||
| upload_pypi: | ||
| needs: [build_wheels, build_sdist] | ||
| runs-on: ubuntu-latest | ||
| runs-on: ubuntu-22.04 | ||
| # upload to PyPI on every tag starting with 'v' | ||
| if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v') | ||
| steps: | ||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -19,3 +19,4 @@ _templates | |
| setup-requires/* | ||
| .cache/v/cache/lastfailed | ||
| .idea | ||
| **/__pycache__ | ||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,15 @@ | ||
| ARG PYTHON_VERSION=alpine | ||
|
|
||
| FROM python:${PYTHON_VERSION} | ||
|
|
||
| WORKDIR /workspace | ||
|
|
||
| RUN apk add --no-cache build-base autoconf automake git xz-dev curl-dev libdeflate-dev bzip2-dev | ||
|
|
||
| COPY . . | ||
|
|
||
| RUN pip install -r requirements.txt && pip install pytest pytest-cov | ||
|
|
||
| # build cyvcf2 | ||
| RUN CYVCF2_HTSLIB_CONFIGURE_OPTIONS="--enable-libcurl --enable-s3 --enable-lzma --enable-bz2 --with-libdeflate" \ | ||
| CYTHONIZE=1 python setup.py build_ext -i |
File renamed without changes.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file was deleted.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,26 +1,26 @@ | ||
| #!/bin/bash | ||
|
|
||
| set -e | ||
| set -euo pipefail | ||
|
|
||
| git submodule init | ||
| git submodule update | ||
| git submodule update --init --recursive | ||
| export DYLD_LIBRARY_PATH=/usr/local/lib | ||
| # same with python | ||
| export MACOSX_DEPLOYMENT_TARGET=10.9 | ||
|
|
||
| # configure fails with autoconf 2.71, so downgrade | ||
| # see https://github.com/asdf-vm/asdf-erlang/issues/195 | ||
| brew install [email protected] && \ | ||
| brew link --overwrite [email protected] && \ | ||
| autoconf -V | ||
| brew install automake | ||
| brew unlink xz | ||
|
|
||
| curl -L -o libdeflate-v1.8.tar.gz https://github.com/ebiggers/libdeflate/archive/refs/tags/v1.8.tar.gz | ||
| tar xzf libdeflate-v1.8.tar.gz | ||
| cd libdeflate-1.8 | ||
| make | ||
| make install | ||
| cd .. | ||
| # build liblzma and libdelfate for muti arch | ||
|
|
||
| cd htslib | ||
| autoheader | ||
| autoconf | ||
| ./configure --enable-libcurl --enable-s3 --enable-lzma --enable-bz2 | ||
| make | ||
| XZ_VERSION=5.4.5 | ||
| curl -L -o xz-$XZ_VERSION.tar.gz "https://github.com/tukaani-project/xz/releases/download/v$XZ_VERSION/xz-$XZ_VERSION.tar.gz" | ||
| tar -xf xz-$XZ_VERSION.tar.gz | ||
| cd xz-$XZ_VERSION | ||
| cmake -B build && cmake --build build | ||
| cd ./build && make install | ||
|
|
||
| LIBDEFLATE_VERSION=1.19 | ||
| curl -L -o libdeflate-v"$LIBDEFLATE_VERSION".tar.gz https://github.com/ebiggers/libdeflate/archive/refs/tags/v"$LIBDEFLATE_VERSION".tar.gz | ||
| tar xzf libdeflate-v"$LIBDEFLATE_VERSION".tar.gz | ||
| cd libdeflate-"$LIBDEFLATE_VERSION" | ||
| cmake -B build && cmake --build build | ||
| cd ./build && make install |
Oops, something went wrong.