[med-svn] [Git][med-team/cyvcf2][upstream] New upstream version 0.31.0
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Fri May 31 21:35:05 BST 2024
Étienne Mollier pushed to branch upstream at Debian Med / cyvcf2
Commits:
2f257653 by Étienne Mollier at 2024-05-31T22:26:10+02:00
New upstream version 0.31.0
- - - - -
6 changed files:
- .github/workflows/build.yml
- .github/workflows/wheels.yml
- CHANGES.md
- ci/linux-deps
- ci/osx-deps
- cyvcf2/__init__.py
Changes:
=====================================
.github/workflows/build.yml
=====================================
@@ -198,8 +198,10 @@ jobs:
working-directory: dist
- name: Install test prerequisites
+ # pytest 8.2.0~8.2.1 changed the behaivour of --import-mode, can't ignore local cyvcf2 folder.
+ # So we need to pin it before it breaks again.
run: |
- pip install pytest pytest-cov
+ pip install pytest==8.1.2 pytest-cov
- name: Test
run: |
=====================================
.github/workflows/wheels.yml
=====================================
@@ -28,7 +28,7 @@ jobs:
- [ubuntu-22.04, manylinux_aarch64]
- [ubuntu-22.04, musllinux_aarch64]
- [macos-12, macosx_x86_64]
- - [macos-12, macosx_arm64]
+ - [macos-14, macosx_arm64]
python-version: [pp310, cp37, cp38, cp39, cp310, cp311, cp312]
exclude:
# pp310, cp37, cp38 on musllinux is not support
@@ -49,10 +49,13 @@ jobs:
python-version: cp310
- buildplat: [ubuntu-22.04, musllinux_aarch64]
python-version: pp310
- # cp37, pp310 on macos arm64 is not supported
- - buildplat: [macos-12, macosx_arm64]
+ # cp37 on macos arm64 is not supported
+ - buildplat: [macos-14, macosx_arm64]
python-version: cp37
- - buildplat: [macos-12, macosx_arm64]
+ # cp38 pp310 on macos arm64 have some problem
+ - buildplat: [macos-14, macosx_arm64]
+ python-version: cp38
+ - buildplat: [macos-14, macosx_arm64]
python-version: pp310
steps:
@@ -65,7 +68,7 @@ jobs:
uses: docker/setup-qemu-action at v3
- name: Build wheels
- uses: pypa/cibuildwheel at v2.16.4
+ uses: pypa/cibuildwheel at v2.18.1
with:
package-dir: .
output-dir: wheelhouse
@@ -85,16 +88,15 @@ jobs:
CIBW_REPAIR_WHEEL_COMMAND_LINUX: 'LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/lib64" && auditwheel repair -w {dest_dir} {wheel}'
# macos
- CIBW_ARCHS_MACOS: auto64 arm64
+ CIBW_ARCHS_MACOS: auto64
CIBW_BEFORE_BUILD_MACOS: "{project}/ci/osx-deps"
-
+ CIBW_REPAIR_WHEEL_COMMAND_MACOS: "delocate-wheel --require-archs {delocate_archs} -w {dest_dir} -v {wheel}"
+
# build
CIBW_ENVIRONMENT: >-
CYVCF2_HTSLIB_CONFIGURE_OPTIONS="--enable-libcurl --enable-s3 --enable-lzma --enable-bz2 --with-libdeflate"
CYTHONIZE=1
CIBW_TEST_COMMAND: "{project}/ci/test"
- # macOS build arm64 on x86_64 with cross-compiler, not support test
- CIBW_TEST_SKIP: "*-macosx_arm64"
# Enable tmate debugging of manually-triggered workflows if the input option was provided
- name: Setup tmate session
=====================================
CHANGES.md
=====================================
@@ -1,3 +1,6 @@
+# v0.31.0
++ fix OSX ARM wheels (#305, #306 thanks @graphenn for fix)
+
# v0.30.27
+ support num_records using index stats (#295 from @jeromekelleher)
=====================================
ci/linux-deps
=====================================
@@ -27,7 +27,7 @@ alpine)
centos)
yum install -y bzip2-devel xz-devel libcurl-devel openssl-devel
- LIBDEFLATE_VERSION=1.19
+ LIBDEFLATE_VERSION=1.20
curl -L -o libdeflate-v"$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-"$LIBDEFLATE_VERSION"
=====================================
ci/osx-deps
=====================================
@@ -2,25 +2,24 @@
set -euo pipefail
-export DYLD_LIBRARY_PATH=/usr/local/lib
# same with python
export MACOSX_DEPLOYMENT_TARGET=10.9
-brew install automake
+brew install automake libdeflate
brew unlink xz
-# build liblzma and libdelfate for muti arch
+# build liblzma and libdelfate for deployment target 10.9
-XZ_VERSION=5.4.5
+XZ_VERSION=5.4.6
curl -L -o xz-$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
+cd ./build && sudo make install
-LIBDEFLATE_VERSION=1.19
+LIBDEFLATE_VERSION=1.20
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
+cd ./build && sudo make install
=====================================
cyvcf2/__init__.py
=====================================
@@ -2,4 +2,4 @@ from .cyvcf2 import (VCF, Variant, Writer, r_ as r_unphased, par_relatedness,
par_het)
Reader = VCFReader = VCF
-__version__ = "0.30.28"
+__version__ = "0.31.0"
View it on GitLab: https://salsa.debian.org/med-team/cyvcf2/-/commit/2f25765319014dcf3353615862ff198fee05b83f
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