py-pydeseq2: Python reimplementation of DESeq2 R package

[Jason Bacon (via pkgsrc-wip) <commit-notify%pkgsrc.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Mon Jun 9 17:56:40 2025 -0500
Changeset:	96ff8c6836c209c03d0ff47d1e30c9c6f5e0da20

Modified Files:
	Makefile
Added Files:
	py-pydeseq2/DESCR
	py-pydeseq2/Makefile
	py-pydeseq2/PLIST
	py-pydeseq2/distinfo

Log Message:
py-pydeseq2: Python reimplementation of DESeq2 R package

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=96ff8c6836c209c03d0ff47d1e30c9c6f5e0da20

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 Makefile             |  1 +
 py-pydeseq2/DESCR    |  4 ++++
 py-pydeseq2/Makefile | 32 ++++++++++++++++++++++++++++++++
 py-pydeseq2/PLIST    | 33 +++++++++++++++++++++++++++++++++
 py-pydeseq2/distinfo |  5 +++++
 5 files changed, 75 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index b4c80c18e4..6c470716fe 100644
--- a/Makefile
+++ b/Makefile
@@ -4436,6 +4436,7 @@ SUBDIR+=	py-pybitbucket
 SUBDIR+=	py-pycifrw
 SUBDIR+=	py-pydelay
 SUBDIR+=	py-pydenticon
+SUBDIR+=	py-pydeseq2
 SUBDIR+=	py-pydy
 SUBDIR+=	py-pydy-viz
 SUBDIR+=	py-pyec
diff --git a/py-pydeseq2/DESCR b/py-pydeseq2/DESCR
new file mode 100644
index 0000000000..5f4c74926b
--- /dev/null
+++ b/py-pydeseq2/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.
diff --git a/py-pydeseq2/Makefile b/py-pydeseq2/Makefile
new file mode 100644
index 0000000000..3af94f9c3f
--- /dev/null
+++ b/py-pydeseq2/Makefile
@@ -0,0 +1,32 @@
+# $NetBSD$
+#
+###########################################################
+#                  Generated by fbsd2pkg                  #
+#              Mon Jun  9 16:50:10 CDT 2025               #
+###########################################################
+
+DISTNAME=	pydeseq2-0.5.1
+PKGNAME=	${PYPKGPREFIX}-${DISTNAME}
+CATEGORIES=	biology python
+MASTER_SITES=	${MASTER_SITE_PYPI:=p/pydeseq2/}
+
+OWNER=		bacon%NetBSD.org@localhost
+HOMEPAGE=	https://github.com/owkin/PyDESeq2
+COMMENT=	Python implementation of the popular DESeq2 R package
+LICENSE=	mit
+
+# Doesn't exist yet
+# DEPENDS+=	${PYPKGPREFIX}-anndata>=0.8.0:../../devel/py-anndata
+DEPENDS+=	${PYPKGPREFIX}-numpy>=1.23.0:../../math/py-numpy
+DEPENDS+=	${PYPKGPREFIX}-pandas>=1.23.0:../../math/py-pandas
+DEPENDS+=	${PYPKGPREFIX}-scikit-learn>=1.1.1:../../math/py-scikit-learn
+DEPENDS+=	${PYPKGPREFIX}-scipy>=1.11.0:../../math/py-scipy
+
+# Check these
+PYTHON_VERSIONS_INCOMPATIBLE=	27
+TOOL_DEPENDS+=	${PYPKGPREFIX}-setuptools-[0-9]*:../../devel/py-setuptools
+TOOL_DEPENDS+=	${PYPKGPREFIX}-wheel-[0-9]*:../../devel/py-wheel
+
+# Verify that we shouldn't use distutils.mk or extensions.mk instead.
+.include "../../lang/python/wheel.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/py-pydeseq2/PLIST b/py-pydeseq2/PLIST
new file mode 100644
index 0000000000..335090956e
--- /dev/null
+++ b/py-pydeseq2/PLIST
@@ -0,0 +1,33 @@
+@comment $NetBSD$
+${PYSITELIB}/${WHEEL_INFODIR}/LICENSE
+${PYSITELIB}/${WHEEL_INFODIR}/METADATA
+${PYSITELIB}/${WHEEL_INFODIR}/RECORD
+${PYSITELIB}/${WHEEL_INFODIR}/WHEEL
+${PYSITELIB}/${WHEEL_INFODIR}/top_level.txt
+${PYSITELIB}/pydeseq2/__init__.py
+${PYSITELIB}/pydeseq2/__init__.pyc
+${PYSITELIB}/pydeseq2/__init__.pyo
+${PYSITELIB}/pydeseq2/__version__.py
+${PYSITELIB}/pydeseq2/__version__.pyc
+${PYSITELIB}/pydeseq2/__version__.pyo
+${PYSITELIB}/pydeseq2/dds.py
+${PYSITELIB}/pydeseq2/dds.pyc
+${PYSITELIB}/pydeseq2/dds.pyo
+${PYSITELIB}/pydeseq2/default_inference.py
+${PYSITELIB}/pydeseq2/default_inference.pyc
+${PYSITELIB}/pydeseq2/default_inference.pyo
+${PYSITELIB}/pydeseq2/ds.py
+${PYSITELIB}/pydeseq2/ds.pyc
+${PYSITELIB}/pydeseq2/ds.pyo
+${PYSITELIB}/pydeseq2/grid_search.py
+${PYSITELIB}/pydeseq2/grid_search.pyc
+${PYSITELIB}/pydeseq2/grid_search.pyo
+${PYSITELIB}/pydeseq2/inference.py
+${PYSITELIB}/pydeseq2/inference.pyc
+${PYSITELIB}/pydeseq2/inference.pyo
+${PYSITELIB}/pydeseq2/preprocessing.py
+${PYSITELIB}/pydeseq2/preprocessing.pyc
+${PYSITELIB}/pydeseq2/preprocessing.pyo
+${PYSITELIB}/pydeseq2/utils.py
+${PYSITELIB}/pydeseq2/utils.pyc
+${PYSITELIB}/pydeseq2/utils.pyo
diff --git a/py-pydeseq2/distinfo b/py-pydeseq2/distinfo
new file mode 100644
index 0000000000..125c36c67d
--- /dev/null
+++ b/py-pydeseq2/distinfo
@@ -0,0 +1,5 @@
+$NetBSD$
+
+BLAKE2s (pydeseq2-0.5.1.tar.gz) = b1cad6ab964c8da4d7ab57e992f631a165ba78f4d19f9259d349f852b7dcf3a6
+SHA512 (pydeseq2-0.5.1.tar.gz) = 48778cb79076fac62a87046a95bcbdd55f4daaa3f813fe3e3af35105f4da7297abe4dc2eeba92c56430953e1ad53c417b63020d19a2b6dff3a8e95b4bd555c64
+Size (pydeseq2-0.5.1.tar.gz) = 51390 bytes