From 61936ba06ecc3412e5ad00d298775b4d8acad36a Mon Sep 17 00:00:00 2001 From: Ruben Vorderman Date: Tue, 9 Sep 2025 12:14:47 +0200 Subject: [PATCH 1/3] Fix compile error caused by #pragma pack --- src/sequali/_qcmodule.c | 1 + tox.ini | 4 ++-- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/src/sequali/_qcmodule.c b/src/sequali/_qcmodule.c index fa3fed3..dc61a4d 100644 --- a/src/sequali/_qcmodule.c +++ b/src/sequali/_qcmodule.c @@ -4272,6 +4272,7 @@ struct EstimatorEntry { // 32 bits allows storing 4 billion counts. This should never overflow in practice. uint32_t count; }; +#pragma pack() typedef struct _DedupEstimatorStruct { PyObject_HEAD diff --git a/tox.ini b/tox.ini index d8086d2..5035f69 100644 --- a/tox.ini +++ b/tox.ini @@ -36,7 +36,7 @@ commands = twine check dist/* [testenv:pedantic_compile] -deps= +deps=setuptools skip_install=True setenv= CFLAGS=-Wall -Werror -Wpedantic @@ -46,7 +46,7 @@ commands = bash -c 'CC=clang python setup.py build_ext -f' [testenv:strict_compile] -deps= +deps=setuptools skip_install=True setenv= CFLAGS=-Wall -Werror From 2bfa6e98e15d0d23f96333d940c495d331f51e4d Mon Sep 17 00:00:00 2001 From: Ruben Vorderman Date: Tue, 9 Sep 2025 13:24:33 +0200 Subject: [PATCH 2/3] Update the galaxy wrapper as part of the release procedure --- .github/release_checklist.md | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/.github/release_checklist.md b/.github/release_checklist.md index dd8b23d..d6c0ea8 100644 --- a/.github/release_checklist.md +++ b/.github/release_checklist.md @@ -1,5 +1,5 @@ Release checklist -- [ ] Check outstanding issues on JIRA and Github. +- [ ] Check outstanding issues on JIRA and GitHub. - [ ] Check [latest documentation](https://sequali.readthedocs.io/en/latest) looks fine. - [ ] Create a release branch. @@ -8,9 +8,12 @@ Release checklist - [ ] Merge the release branch into `main`. - [ ] Created an annotated tag with the stable version number. Include changes from CHANGELOG.rst. -- [ ] Push tag to remote. This triggers the wheel/sdist build on github CI. +- [ ] Push tag to remote. This triggers the wheel/sdist build on GitHub CI. - [ ] merge `main` branch back into `develop`. - [ ] Build the new tag on readthedocs. Only build the last patch version of each minor version. So `1.1.1` and `1.2.0` but not `1.1.0`, `1.1.1` and `1.2.0`. -- [ ] Create a new release on github. -- [ ] Update the package on bioconda. +- [ ] Create a new release on GitHub. +- [ ] Update the package on BioConda. +- [ ] Update [Galaxy wrapper]( + https://github.com/galaxyproject/tools-iuc/blob/main/tools/sequali/sequali.xml + ). From ad657e53b366db5097c55daa1859e757389c55d4 Mon Sep 17 00:00:00 2001 From: Ruben Vorderman Date: Tue, 9 Sep 2025 13:25:52 +0200 Subject: [PATCH 3/3] Skip free-threading builds --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 2959e22..51b45fd 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -73,5 +73,5 @@ CFLAGS = "-O3 -DNDEBUG" [tool.cibuildwheel] test-requires = "pytest" test-command = "pytest {project}/tests/" -skip = "*-win32 *-manylinux_i686 pp3*" # Skip 32 bit, pypy +skip = "*-win32 *-manylinux_i686 pp3* cp3??t-*" # Skip 32 bit, pypy build-verbosity = 1 \ No newline at end of file