Conversation
Cython wrapper around htslib (VCF/BCF parsing). htslib (with its htscodecs submodule) is vendored as a git submodule and compiled from source with autoreconf+configure+make, same shape as build-pysam.yml. Drops --enable-libcurl/--enable-s3/--with-libdeflate from upstream's CYVCF2_HTSLIB_CONFIGURE_OPTIONS: no libcurl-devel and no EPEL on the riscv64 manylinux image (as build-pysam.yml/build-pybigwig.yml), and each of those options defaults to a silent "check" in htslib's configure.ac, so dropping them just lets the auto-detect fail closed instead of requesting a feature we cannot build.
test_reader.py/test_writer.py use a package-relative `from ..cyvcf2 import ...` to reach the compiled extension, which needs cyvcf2/ itself to be a proper package (an __init__.py) for pytest to resolve two levels up from cyvcf2.tests. CIBW_TEST_SOURCES only staged cyvcf2/tests (no cyvcf2/__init__.py), so pytest treated the staged tests/ as its own top-level package and the relative import went past it: 'ImportError: attempted relative import beyond top-level package'. Merge the already-installed wheel into the staged cyvcf2/ directory before running pytest (same cp -a pattern as build-dulwich.yml), so the relative import resolves against the compiled wheel directly.
The auditwheel-repaired extension's RPATH is $ORIGIN-relative to a sibling cyvcf2.libs/ (bundled libbz2/liblzma), which the previous fix didn't copy.
This file contains hidden or 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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
cyvcf20.34.0Cython wrapper around a vendored, statically-linked htslib for fast VCF/BCF parsing. Upstream publishes no riscv64 wheel.
Mirrors upstream's
build_wheelsjob ofwheels.yml.Differs from upstream
--enable-libcurl/--enable-s3/--with-libdeflatefromCYVCF2_HTSLIB_CONFIGURE_OPTIONS- no libcurl-devel or EPEL on the riscv64 manylinux image, same gap asbuild-pysam.yml.CIBW_BEFORE_ALL_LINUXinstalls autoconf/automake/libtool/cmake/ninja-build/zlib-bzip2-xz-devel viadnf- none of upstream'sci/linux-depsdistro branches match Rocky 10.Testing
CIBW_TEST_SOURCES/CIBW_TEST_COMMANDinstead of upstream'sci/test(which exercises remote HTTPS reading, unsupported once libcurl is dropped).License: Wheel statically links htslib and its bundled htscodecs (both permissive MIT/BSD), which upstream's own packaging does not ship a licence for; the build adds
LICENSE.htslib/LICENSE.htscodecs.Patches
0001-Add-htslib-htscodecs-LICENSE-files-at-project-root.patch- To upstream. Without it the wheel ships only cyvcf2's own LICENSE despite statically bundling htslib/htscodecs source. Reproduces on any arch.Built on cp312; TBD passed, TBD skipped.