git: e91e2f54bddb - main - biology/py-pydeseq2: Python reimplementation of the DESeq2 R package

The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=e91e2f54bddb6582abde074af8bb48e0462752db

commit e91e2f54bddb6582abde074af8bb48e0462752db
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2025-06-11 14:23:35 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2025-06-11 14:24:15 +0000

    biology/py-pydeseq2: Python reimplementation of the DESeq2 R package
    
    PyDESeq2 is a python implementation of the DESeq2 method for
    differential expression analysis (DEA) with bulk RNA-seq data,
    originally in R. It aims to facilitate DEA experiments for python
    users.
---
 biology/Makefile              |  1 +
 biology/py-pydeseq2/Makefile  | 26 ++++++++++++++++++++++++++
 biology/py-pydeseq2/distinfo  |  3 +++
 biology/py-pydeseq2/pkg-descr |  4 ++++
 4 files changed, 34 insertions(+)

diff --git a/biology/Makefile b/biology/Makefile
index 9f2f693fcfc5..eafb7136ce09 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -195,6 +195,7 @@
     SUBDIR += py-py2bit
     SUBDIR += py-pybigwig
     SUBDIR += py-pyfaidx
+    SUBDIR += py-pydeseq2
     SUBDIR += py-pyrodigal
     SUBDIR += py-pysam
     SUBDIR += py-python-libsbml
diff --git a/biology/py-pydeseq2/Makefile b/biology/py-pydeseq2/Makefile
new file mode 100644
index 000000000000..e31c4eb3d0ab
--- /dev/null
+++ b/biology/py-pydeseq2/Makefile
@@ -0,0 +1,26 @@
+PORTNAME=	pydeseq2
+DISTVERSION=	0.5.1
+CATEGORIES=	biology python
+MASTER_SITES=	PYPI
+PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
+
+MAINTAINER=	jwb@FreeBSD.org
+COMMENT=	Python implementation of the popular DESeq2 R package
+WWW=		https://github.com/owkin/PyDESeq2
+
+LICENSE=	MIT
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}anndata>=0.8.0:devel/py-anndata@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}formulaic>=1.0.2:math/py-formulaic@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}formulaic_contrasts>=0.2.0:math/py-formulaic-contrasts@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}matplotlib>=3.6.2:math/py-matplotlib@${PY_FLAVOR} \
+		${PYNUMPY} \
+		${PYTHON_PKGNAMEPREFIX}pandas>=1.4.0:math/py-pandas@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}scikit-learn>=1.1.0:science/py-scikit-learn@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}scipy>1.11.0:science/py-scipy@${PY_FLAVOR}
+
+USES=		python
+USE_PYTHON=	autoplist distutils
+
+.include <bsd.port.mk>
diff --git a/biology/py-pydeseq2/distinfo b/biology/py-pydeseq2/distinfo
new file mode 100644
index 000000000000..026ce31f8ca4
--- /dev/null
+++ b/biology/py-pydeseq2/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1749586728
+SHA256 (pydeseq2-0.5.1.tar.gz) = 1ec79299f9134748b18bd8242ee4f7f6ccc9407dd18bf32562e051ae5cca626e
+SIZE (pydeseq2-0.5.1.tar.gz) = 51390
diff --git a/biology/py-pydeseq2/pkg-descr b/biology/py-pydeseq2/pkg-descr
new file mode 100644
index 000000000000..5f4c74926b39
--- /dev/null
+++ b/biology/py-pydeseq2/pkg-descr
@@ -0,0 +1,4 @@
+PyDESeq2 is a python implementation of the DESeq2 method for
+differential expression analysis (DEA) with bulk RNA-seq data,
+originally in R. It aims to facilitate DEA experiments for python
+users.