From 06a0710b7a6719c75afd016cdd7ffab9b02ac12c Mon Sep 17 00:00:00 2001
From: Rene Ladan <rene@FreeBSD.org>
Date: Mon, 23 Jun 2025 21:01:46 +0200
Subject: [PATCH] biology/py-orange3-bioinformatics: Remove expired port

2025-06-21 biology/py-orange3-bioinformatics: Depends on expiring misc/orange3
---
 MOVED                                       |  1 +
 biology/Makefile                            |  1 -
 biology/py-orange3-bioinformatics/Makefile  | 35 ---------------------
 biology/py-orange3-bioinformatics/distinfo  |  3 --
 biology/py-orange3-bioinformatics/pkg-descr |  9 ------
 5 files changed, 1 insertion(+), 48 deletions(-)
 delete mode 100644 biology/py-orange3-bioinformatics/Makefile
 delete mode 100644 biology/py-orange3-bioinformatics/distinfo
 delete mode 100644 biology/py-orange3-bioinformatics/pkg-descr

diff --git a/MOVED b/MOVED
index d793a29c8da3..3eeeb2bd9555 100644
--- a/MOVED
+++ b/MOVED
@@ -4526,3 +4526,4 @@ devel/py-spyder-unittest||2025-06-23|Has expired: Depends on expiring devel/spyd
 comms/py-pynitrokey||2025-06-23|Has expired: Depends on expiring comms/py-spsdk
 devel/bit||2025-06-23|Has expired: Upstream ceased development
 biology/py-orange3-single-cell||2025-06-23|Has expired: Depends on expired math/py-fastdtw and expiring misc/orange3
+biology/py-orange3-bioinformatics||2025-06-23|Has expired: Depends on expiring misc/orange3
diff --git a/biology/Makefile b/biology/Makefile
index 45fce4f6412c..d4ba88800bfe 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -189,7 +189,6 @@
     SUBDIR += py-multiqc
     SUBDIR += py-newick
     SUBDIR += py-ont-fast5-api
-    SUBDIR += py-orange3-bioinformatics
     SUBDIR += py-pandas-charm
     SUBDIR += py-py2bit
     SUBDIR += py-pybigwig
diff --git a/biology/py-orange3-bioinformatics/Makefile b/biology/py-orange3-bioinformatics/Makefile
deleted file mode 100644
index 7904ed980863..000000000000
--- a/biology/py-orange3-bioinformatics/Makefile
+++ /dev/null
@@ -1,35 +0,0 @@
-PORTNAME=	orange3-bioinformatics
-DISTVERSION=	4.8.4
-PORTREVISION=	1
-CATEGORIES=	biology python
-MASTER_SITES=	PYPI
-PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
-DISTNAME=	${PORTNAME:S/-/_/}-${DISTVERSION}
-
-MAINTAINER=	yuri@FreeBSD.org
-COMMENT=	Orange add-on providing common functionality for bioinformatics
-WWW=		https://github.com/biolab/orange3-bioinformatics/
-
-LICENSE=	GPLv3
-LICENSE_FILE=	${WRKSRC}/LICENSE
-
-DEPRECATED=	Depends on expiring misc/orange3
-EXPIRATION_DATE=2025-06-21
-
-BUILD_DEPENDS=	${PYTHON_PKGNAMEPREFIX}setuptools-scm>0:devel/py-setuptools-scm@${PY_FLAVOR}
-RUN_DEPENDS=	orange3>0:misc/orange3 \
-		${PYTHON_PKGNAMEPREFIX}Genesis-PyAPI>0:biology/py-Genesis-PyAPI@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}point-annotator>=2.0:math/py-point-annotator@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}pyclipper>=1.2.0:math/py-pyclipper@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}requests>0:www/py-requests@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}requests-cache0>0:www/py-requests-cache0@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}resdk>0:biology/py-resdk@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}scipy>=1.5.0:science/py-scipy@${PY_FLAVOR} \
-		${PYTHON_PKGNAMEPREFIX}serverfiles>0:misc/py-serverfiles@${PY_FLAVOR}
-
-USES=		python
-USE_PYTHON=	autoplist distutils
-
-NO_ARCH=	yes
-
-.include <bsd.port.mk>
diff --git a/biology/py-orange3-bioinformatics/distinfo b/biology/py-orange3-bioinformatics/distinfo
deleted file mode 100644
index 4b386c48e193..000000000000
--- a/biology/py-orange3-bioinformatics/distinfo
+++ /dev/null
@@ -1,3 +0,0 @@
-TIMESTAMP = 1739870048
-SHA256 (orange3_bioinformatics-4.8.4.tar.gz) = 275a32d3948df5294350c25bb430336b5d4109afaf71edd7ccc76591cb9eeb8b
-SIZE (orange3_bioinformatics-4.8.4.tar.gz) = 3736720
diff --git a/biology/py-orange3-bioinformatics/pkg-descr b/biology/py-orange3-bioinformatics/pkg-descr
deleted file mode 100644
index 8979fa28157a..000000000000
--- a/biology/py-orange3-bioinformatics/pkg-descr
+++ /dev/null
@@ -1,9 +0,0 @@
-Orange Bioinformatics extends Orange, a data mining software package, with
-common functionality for bioinformatics. The provided functionality can be
-accessed as a Python library or through a visual programming interface (Orange
-Canvas). The latter is also suitable for non-programmers.
-
-Orange Bioinformatics provides access to publicly available data, like GEO data
-sets, GO and KEGG. All features can be combined with powerful visualization,
-network exploration and data mining techniques from the Orange data mining
-framework.