Date: Thu, 28 May 2026 02:43:10 +0000 From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 5330c42233da - main - science/py-openbabel: update 3.1.1.=?utf-8?Q?1 =E2=86=92 3.?=2.0 Message-ID: <6a17abbe.30018.58acdbac@gitrepo.freebsd.org>
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The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=5330c42233da53353757f008066dd8bf375fb552 commit 5330c42233da53353757f008066dd8bf375fb552 Author: Yuri Victorovich <yuri@FreeBSD.org> AuthorDate: 2026-05-28 02:37:55 +0000 Commit: Yuri Victorovich <yuri@FreeBSD.org> CommitDate: 2026-05-28 02:43:02 +0000 science/py-openbabel: update 3.1.1.1 → 3.2.0 --- science/py-openbabel/Makefile | 28 ++++++++++++---------- science/py-openbabel/distinfo | 6 ++--- science/py-openbabel/files/patch-pyproject.toml | 14 +++++++++++ ...tch-scripts_python_openbabel_____init____.py.in | 19 +++++++++++++++ 4 files changed, 51 insertions(+), 16 deletions(-) diff --git a/science/py-openbabel/Makefile b/science/py-openbabel/Makefile index 16ecbeb51eee..207e25259fdb 100644 --- a/science/py-openbabel/Makefile +++ b/science/py-openbabel/Makefile @@ -1,6 +1,5 @@ PORTNAME= openbabel -DISTVERSION= 3.1.1.1 -PORTREVISION= 1 +DISTVERSION= 3.2.0 CATEGORIES= science # chemistry MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -11,23 +10,26 @@ WWW= https://openbabel.org/wiki/Main_Page LICENSE= GPLv2+ -BUILD_DEPENDS= swig:devel/swig -LIB_DEPENDS= libopenbabel.so:science/openbabel +BUILD_DEPENDS= swig:devel/swig \ + rapidjson>0:devel/rapidjson \ + ${PYTHON_PKGNAMEPREFIX}cmeel-eigen>0:devel/py-cmeel-eigen@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}scikit-build-core>=0.11:devel/py-scikit-build-core@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}setuptools-scm>0:devel/py-setuptools-scm@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}swig>0:devel/py-swig@${PY_FLAVOR} +LIB_DEPENDS= libcoordgen.so:science/coordgenlibs \ + libmaeparser.so:science/maeparser \ + libopenbabel.so:science/openbabel \ + libxml2.so:textproc/libxml2 USES= python -USE_PYTHON= distutils autoplist +USE_PYTHON= pep517 autoplist pytest BINARY_ALIAS= python=${PYTHON_CMD} -.include <bsd.port.options.mk> - -post-patch: -.if ${OPSYS} == FreeBSD - @${REINPLACE_CMD} -e 's|binary_function|__binary_function|g' \ - ${WRKSRC}/openbabel/openbabel-python.i -.endif +TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} +TEST_WRKSRC= ${WRKSRC}/test post-install: - @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/openbabel/_openbabel${PYTHON_TAG}.so + @${STRIP_CMD} ${STAGEDIR}${PYTHON_SITELIBDIR}/openbabel/_openbabel.so .include <bsd.port.mk> diff --git a/science/py-openbabel/distinfo b/science/py-openbabel/distinfo index 0c674328b335..429092c86446 100644 --- a/science/py-openbabel/distinfo +++ b/science/py-openbabel/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1668939398 -SHA256 (openbabel-3.1.1.1.tar.gz) = bb7f8cad15f3a208f4869d7943cbb14eb7125372eba397588f207f8d19e78373 -SIZE (openbabel-3.1.1.1.tar.gz) = 82811 +TIMESTAMP = 1779863957 +SHA256 (openbabel-3.2.0.tar.gz) = 332e6038146e0b69f9c32b8d71d6de153a095d98dce4663972c4a45e55449d01 +SIZE (openbabel-3.2.0.tar.gz) = 36460954 diff --git a/science/py-openbabel/files/patch-pyproject.toml b/science/py-openbabel/files/patch-pyproject.toml new file mode 100644 index 000000000000..15cbdac881a2 --- /dev/null +++ b/science/py-openbabel/files/patch-pyproject.toml @@ -0,0 +1,14 @@ +-- Remove the [project.scripts] entry that installs 'obabel' — that binary is +-- already provided by science/openbabel (a required LIB_DEPENDS), so installing +-- it here would conflict with that package. +--- pyproject.toml.orig 2026-05-27 21:58:16 UTC ++++ pyproject.toml +@@ -41,8 +41,6 @@ Documentation = "https://openbabel.org/docs/" + Repository = "https://github.com/openbabel/openbabel" + Documentation = "https://openbabel.org/docs/" + +-[project.scripts] +-obabel = "openbabel.executable:obabel" + + [tool.scikit-build] + minimum-version = "0.11" diff --git a/science/py-openbabel/files/patch-scripts_python_openbabel_____init____.py.in b/science/py-openbabel/files/patch-scripts_python_openbabel_____init____.py.in new file mode 100644 index 000000000000..e72a42711d1f --- /dev/null +++ b/science/py-openbabel/files/patch-scripts_python_openbabel_____init____.py.in @@ -0,0 +1,19 @@ +-- On FreeBSD, Python loads extension modules with RTLD_LOCAL, which prevents +-- plugin .so files (in BABEL_LIBDIR) from resolving symbols from libopenbabel.so.8 +-- when they are dlopen'd by the plugin loader. Pre-loading libopenbabel.so.8 with +-- RTLD_GLOBAL fixes symbol resolution for all subsequently loaded plugins. +--- scripts/python/openbabel/__init__.py.in.orig 2026-05-27 20:44:02 UTC ++++ scripts/python/openbabel/__init__.py.in +@@ -13,6 +13,12 @@ if "${BUILD_BY_PIP}" == "ON": + if "${BUILD_BY_PIP}" == "ON": + os.environ["BABEL_LIBDIR"] = os.path.join(base_dir, "lib", "openbabel", __version__) + os.environ["BABEL_DATADIR"] = os.path.join(base_dir, "share", "openbabel", __version__) ++ # Load libopenbabel.so with RTLD_GLOBAL so that plugin .so files can resolve ++ # its symbols when they are dlopen'd by the plugin loader. ++ import ctypes as _ctypes ++ _libob = os.path.join(base_dir, "lib", "libopenbabel.so.8") ++ if os.path.exists(_libob): ++ _ctypes.CDLL(_libob, _ctypes.RTLD_GLOBAL) + + from . import openbabel +home | help
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