diff options
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/Makefile | 2 | ||||
| -rw-r--r-- | biology/py-orange3-bioinformatics/Makefile | 35 | ||||
| -rw-r--r-- | biology/py-orange3-bioinformatics/distinfo | 3 | ||||
| -rw-r--r-- | biology/py-orange3-bioinformatics/pkg-descr | 9 | ||||
| -rw-r--r-- | biology/py-orange3-single-cell/Makefile | 46 | ||||
| -rw-r--r-- | biology/py-orange3-single-cell/distinfo | 3 | ||||
| -rw-r--r-- | biology/py-orange3-single-cell/files/patch-doc_conf.py | 10 | ||||
| -rw-r--r-- | biology/py-orange3-single-cell/pkg-descr | 2 |
8 files changed, 0 insertions, 110 deletions
diff --git a/biology/Makefile b/biology/Makefile index 590109724958..d4ba88800bfe 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -189,8 +189,6 @@ SUBDIR += py-multiqc 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 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. diff --git a/biology/py-orange3-single-cell/Makefile b/biology/py-orange3-single-cell/Makefile deleted file mode 100644 index 54d72a4516fd..000000000000 --- a/biology/py-orange3-single-cell/Makefile +++ /dev/null @@ -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> diff --git a/biology/py-orange3-single-cell/distinfo b/biology/py-orange3-single-cell/distinfo deleted file mode 100644 index ed5f301ce6e1..000000000000 --- a/biology/py-orange3-single-cell/distinfo +++ /dev/null @@ -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 diff --git a/biology/py-orange3-single-cell/files/patch-doc_conf.py b/biology/py-orange3-single-cell/files/patch-doc_conf.py deleted file mode 100644 index a3ecb4c652db..000000000000 --- a/biology/py-orange3-single-cell/files/patch-doc_conf.py +++ /dev/null @@ -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') diff --git a/biology/py-orange3-single-cell/pkg-descr b/biology/py-orange3-single-cell/pkg-descr deleted file mode 100644 index 05cf4bfc5f8a..000000000000 --- a/biology/py-orange3-single-cell/pkg-descr +++ /dev/null @@ -1,2 +0,0 @@ -The Single Cell add-on for Orange3 adds functionality for analysis of single -cell data. |