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biology/py-orange3-single-cell: Remove expired port

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2025-06-21 biology/py-orange3-single-cell: Depends on expired math/py-fastdtw and expiring misc/orange3
This commit is contained in:
Rene Ladan
2025-06-23 20:49:24 +02:00
parent 0d81d989c4
commit 8821501c8e
6 changed files with 1 additions and 62 deletions
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MOVED
+1
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@@ -4525,3 +4525,4 @@ devel/py-pytest4-cov||2025-06-23|Has expired: Depends on expiring devel/py-pytes
devel/py-spyder-unittest||2025-06-23|Has expired: Depends on expiring devel/spyder
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/Makefile
-1
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@@ -190,7 +190,6 @@
SUBDIR += py-newick
SUBDIR += py-ont-fast5-api
SUBDIR += py-orange3-bioinformatics
SUBDIR += py-orange3-single-cell
SUBDIR += py-pandas-charm
SUBDIR += py-py2bit
SUBDIR += py-pybigwig
biology/py-orange3-single-cell/Makefile
-46
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@@ -1,46 +0,0 @@
PORTNAME= orange3-single-cell
DISTVERSION= 0.8.2
PORTREVISION= 6
CATEGORIES= biology python
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
MAINTAINER= yuri@FreeBSD.org
COMMENT= Orange add-on for gene expression of single cell data
WWW= https://singlecell.biolab.si/
LICENSE= AGPLv3+
DEPRECATED= Depends on expired math/py-fastdtw and expiring misc/orange3
EXPIRATION_DATE=2025-06-21
RUN_DEPENDS= orange3>0:misc/orange3 \
${PYTHON_PKGNAMEPREFIX}orange3-bioinformatics>0:biology/py-orange3-bioinformatics@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}astropy>0:astro/py-astropy@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}fastdtw>0:math/py-fastdtw@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}joblib>=0.11:devel/py-joblib@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}loompy>=2.0.10:biology/py-loompy@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}networkx>0:math/py-networkx@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}pandas>=0.23:math/py-pandas@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}scikit-learn>0:science/py-scikit-learn@${PY_FLAVOR} \
${PYNUMPY}
# Supports 3.4+ but loompy 3.6+ only.
USES= python
USE_GITHUB= yes
GH_ACCOUNT= biolab
USE_PYTHON= distutils autoplist
NO_ARCH= yes
OPTIONS_DEFINE= DOCS
DOCS_BUILD_DEPENDS= gmake:devel/gmake \
${PYTHON_PKGNAMEPREFIX}sphinx>=0,1:textproc/py-sphinx@${PY_FLAVOR}
pre-build-DOCS-on:
@cd ${WRKSRC}/doc && ${SETENV} ${MAKE_ENV} ${GMAKE} html htmlhelp SPHINXBUILD=${LOCALBASE}/bin/sphinx-build-${PYTHON_VER}
pre-build-DOCS-off:
@${REINPLACE_CMD} "s|^ include_documentation| #include_documentation|" ${WRKSRC}/setup.py
.include <bsd.port.mk>
biology/py-orange3-single-cell/distinfo
-3
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@@ -1,3 +0,0 @@
TIMESTAMP = 1539761270
SHA256 (biolab-orange3-single-cell-0.8.2_GH0.tar.gz) = eebda4303c208951fcbe8f383e0f310b20abedba425b0c68bbe65ae2806cc1bb
SIZE (biolab-orange3-single-cell-0.8.2_GH0.tar.gz) = 5521782
biology/py-orange3-single-cell/files/patch-doc_conf.py
-10
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@@ -1,10 +0,0 @@
# add_stylesheet() deprecated on Sphinx 4.0
# https://www.sphinx-doc.org/en/master/extdev/deprecated.html
--- doc/conf.py.orig 2018-10-15 08:43:14 UTC
+++ doc/conf.py
@@ -288,4 +288,4 @@ texinfo_documents = [
#texinfo_no_detailmenu = False
def setup(app):
- app.add_stylesheet('style.css')
+ app.add_css_file('style.css')
biology/py-orange3-single-cell/pkg-descr
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@@ -1,2 +0,0 @@
The Single Cell add-on for Orange3 adds functionality for analysis of single
cell data.