biology/py-hits: update 0.1 → 0.5.1

2026-06-02 11:08:52 +00:00 · 2026-05-29 10:17:17 -07:00
parent 6c3fbaf906
commit 7bf984b3b4
5 changed files with 86 additions and 7 deletions
@@ -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>
@@ -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
@@ -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]
@@ -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"]),
+    ],
+)
@@ -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.