Date: Sat, 30 May 2026 02:32:48 +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: 7bf984b3b478 - main - biology/py-hits: update 0=?utf-8?Q?=2E1 =E2=86=92 0?=.5.1 Message-ID: <6a1a4c50.310e3.6283fbe8@gitrepo.freebsd.org>
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The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=7bf984b3b47837b3bd4aa18c7207b2aed8ad1a21 commit 7bf984b3b47837b3bd4aa18c7207b2aed8ad1a21 Author: Yuri Victorovich <yuri@FreeBSD.org> AuthorDate: 2026-05-29 17:17:17 +0000 Commit: Yuri Victorovich <yuri@FreeBSD.org> CommitDate: 2026-05-30 02:32:42 +0000 biology/py-hits: update 0.1 → 0.5.1 --- biology/py-hits/Makefile | 31 +++++++++++++++++++++++++++--- biology/py-hits/distinfo | 6 +++--- biology/py-hits/files/patch-pyproject.toml | 27 ++++++++++++++++++++++++++ biology/py-hits/files/patch-setup.py | 16 +++++++++++++++ biology/py-hits/pkg-descr | 13 ++++++++++++- 5 files changed, 86 insertions(+), 7 deletions(-) diff --git a/biology/py-hits/Makefile b/biology/py-hits/Makefile index 3ceaf92be25f..3064671389b1 100644 --- a/biology/py-hits/Makefile +++ b/biology/py-hits/Makefile @@ -1,6 +1,5 @@ PORTNAME= hits -PORTVERSION= 0.1 -PORTREVISION= 1 +DISTVERSION= 0.5.1 CATEGORIES= biology python MASTER_SITES= PYPI PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} @@ -11,10 +10,36 @@ WWW= https://github.com/jeffhussmann/hits LICENSE= GPLv3 +BUILD_DEPENDS= ${PY_SETUPTOOLS} \ + ${PYTHON_PKGNAMEPREFIX}setuptools-scm>0:devel/py-setuptools-scm@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}wheel>0:devel/py-wheel@${PY_FLAVOR} +RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}biopython>=1.72:biology/py-biopython@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}bokeh>0:www/py-bokeh@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}ipython>=7.8.0:devel/ipython@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}ipywidgets>=7.4.2:devel/py-ipywidgets@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}matplotlib>=3.0.2:math/py-matplotlib@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}numpy>=1.15.4:math/py-numpy@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}pandas>=0.23.4:math/py-pandas@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}pillow>=5.3.0:graphics/py-pillow@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}pysam>=0.15.1:biology/py-pysam@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}pyyaml>=3.13:devel/py-pyyaml@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}s3fs>=0:filesystems/py-s3fs@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}scipy>=1.2.1:science/py-scipy@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}seaborn>=0.11.0:math/py-seaborn@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}statsmodels>=0.12.1:math/py-statsmodels@${PY_FLAVOR} + USES= python -USE_PYTHON= distutils cython autoplist +USE_PYTHON= pep517 cython autoplist pytest + +TEST_ENV= ${MAKE_ENV} PYTHONPATH=${STAGEDIR}${PYTHONPREFIX_SITELIBDIR} +PYTEST_ARGS= -p no:ruff + +do-test: + @cd ${WRKDIR} && ${SETENV} ${TEST_ENV} ${PYTHON_CMD} -m pytest ${PYTEST_ARGS} ${WRKSRC}/hits/test post-install: @${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/hits/*.so +# tests as of 0.5.1: 11 passed, 1 skipped in 3.87s + .include <bsd.port.mk> diff --git a/biology/py-hits/distinfo b/biology/py-hits/distinfo index 0132c3f476c9..9951c700ba74 100644 --- a/biology/py-hits/distinfo +++ b/biology/py-hits/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1589596183 -SHA256 (hits-0.1.tar.gz) = d522045c7c5f7bb68645c99bf5fde7601ecfb8f13d7c0d94090a5fd84bb86feb -SIZE (hits-0.1.tar.gz) = 1056911 +TIMESTAMP = 1780066404 +SHA256 (hits-0.5.1.tar.gz) = 4c10cf548708a0c64db9abaa551b8da60b994728cc1ecfd4ccfcab2829ac1300 +SIZE (hits-0.5.1.tar.gz) = 1904390 diff --git a/biology/py-hits/files/patch-pyproject.toml b/biology/py-hits/files/patch-pyproject.toml new file mode 100644 index 000000000000..f4ef76bc72a4 --- /dev/null +++ b/biology/py-hits/files/patch-pyproject.toml @@ -0,0 +1,27 @@ +-- Remove ext-modules from pyproject.toml as it is not supported by setuptools < 64. +-- The extension modules are now defined in setup.py. + +--- pyproject.toml.orig 2026-02-23 23:57:10 UTC ++++ pyproject.toml +@@ -13,8 +13,6 @@ readme = "README.md" + ] + description = "Utilities for processing high-throughput sequencing experiments" + readme = "README.md" +-license = "GPL-3.0-or-later" +-license-files = ["LICENSE"] + dynamic = ["version"] + requires-python = ">= 3.12" + dependencies = [ +@@ -45,12 +43,6 @@ packages = [ + 'hits.serialize', + 'hits.visualize', + 'hits.visualize.interactive', +-] +- +-ext-modules = [ +- {name = "hits.adapters_cython", sources = ["hits/adapters_cython.pyx"]}, +- {name = "hits.fastq_cython", sources = ["hits/fastq_cython.pyx"]}, +- {name = "hits.sw_cython", sources = ["hits/sw_cython.pyx"]}, + ] + + [tool.setuptools.dynamic] diff --git a/biology/py-hits/files/patch-setup.py b/biology/py-hits/files/patch-setup.py new file mode 100644 index 000000000000..9438adcc564b --- /dev/null +++ b/biology/py-hits/files/patch-setup.py @@ -0,0 +1,16 @@ +-- Add setup.py to define extension modules. +-- This is needed because the current version of setuptools on FreeBSD does not +-- support defining ext-modules in pyproject.toml. + +--- setup.py.orig 2026-05-29 15:20:01 UTC ++++ setup.py +@@ -0,0 +1,9 @@ ++from setuptools import setup, Extension ++ ++setup( ++ ext_modules=[ ++ Extension("hits.adapters_cython", ["hits/adapters_cython.pyx"]), ++ Extension("hits.fastq_cython", ["hits/fastq_cython.pyx"]), ++ Extension("hits.sw_cython", ["hits/sw_cython.pyx"]), ++ ], ++) diff --git a/biology/py-hits/pkg-descr b/biology/py-hits/pkg-descr index aed78ca0f7fb..d11eaa3d9bc9 100644 --- a/biology/py-hits/pkg-descr +++ b/biology/py-hits/pkg-descr @@ -1 +1,12 @@ -Utilities for processing high-throughput sequencing experiments. +hits is a suite of Python utilities designed for processing high-throughput +sequencing experiments. + +Key features include: +- Tools for read name standardization +- Sequence alignment +- Data visualization + +It is specifically tailored to handle experiments such as ribosome profiling +(Ribo-seq) and RNA-seq, facilitating efficient data analysis and interpretation. +The package streamlines the workflow from raw sequencing data to biological +insights through robust processing pipelines.home | help
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