diff --git a/biology/py-orange3-bioinformatics/Makefile b/biology/py-orange3-bioinformatics/Makefile index 714eb7e79afb..7b97466250ce 100644 --- a/biology/py-orange3-bioinformatics/Makefile +++ b/biology/py-orange3-bioinformatics/Makefile @@ -1,34 +1,31 @@ PORTNAME= orange3-bioinformatics DISTVERSION= 4.3.1 CATEGORIES= biology python MASTER_SITES= CHEESESHOP PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} DISTNAME= Orange3-Bioinformatics-${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 expired security/py-keyrings.alt (via msic/orange3) -EXPIRATION_DATE=2022-12-31 - 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} \ ${PYTHON_PKGNAMEPREFIX}requests-cache>0:www/py-requests-cache@${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:3.4+ USE_PYTHON= distutils autoplist NO_ARCH= yes .include diff --git a/biology/py-orange3-single-cell/Makefile b/biology/py-orange3-single-cell/Makefile index a2fd06f80fc4..fa04f5481e29 100644 --- a/biology/py-orange3-single-cell/Makefile +++ b/biology/py-orange3-single-cell/Makefile @@ -1,44 +1,41 @@ PORTNAME= orange3-single-cell DISTVERSION= 0.8.2 PORTREVISION= 3 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 security/py-keyrings.alt (via msic/orange3) -EXPIRATION_DATE=2022-12-31 - 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:3.7+ USE_GITHUB= yes GH_ACCOUNT= biolab USE_PYTHON= distutils autoplist 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 diff --git a/misc/orange3/Makefile b/misc/orange3/Makefile index 98bd9bc21df2..bcf432b6e8ee 100644 --- a/misc/orange3/Makefile +++ b/misc/orange3/Makefile @@ -1,67 +1,64 @@ PORTNAME= orange3 DISTVERSION= 3.29.1 PORTREVISION= 1 CATEGORIES= misc python MAINTAINER= yuri@FreeBSD.org COMMENT= Component-based data mining software WWW= https://orange.biolab.si/ LICENSE= GPLv3 -DEPRECATED= Depends on expired security/py-keyrings.alt -EXPIRATION_DATE=2022-12-31 - BUILD_DEPENDS= ${PYNUMPY} RUN_DEPENDS= ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}AnyQt>=0.0.11:x11-toolkits/py-AnyQt@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}baycomp>=1.0.2:math/py-baycomp@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}bottleneck>=1.0.0:math/py-bottleneck@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}chardet>=3.0.2:textproc/py-chardet@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}docutils>0:textproc/py-docutils@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}joblib>=0.9.4:devel/py-joblib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}httpx>=0.14.0:www/py-httpx@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}keyring>0:security/py-keyring@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}keyrings.alt>0:security/py-keyrings.alt@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}matplotlib>=2.0.0:math/py-matplotlib@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}networkx>0:math/py-networkx@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}openTSNE>=0.6.0:math/py-openTSNE@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}orange-canvas-core>=0.1.19:devel/py-orange-canvas-core@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}orange-widget-base>=4.13.0:devel/py-orange-widget-base@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}openpyxl>0:textproc/py-openpyxl@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pandas>=1.0.0:math/py-pandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pip>=9.0:devel/py-pip@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}PyOpenGL>=0:graphics/py-PyOpenGL@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}python-louvain>=0.13:math/py-python-louvain@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pyqtgraph>=0.11.1:graphics/py-pyqtgraph@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}requests>0:www/py-requests@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scikit-learn>=0.22.0:science/py-scikit-learn@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>=0.16.1:science/py-scipy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}serverfiles>0:misc/py-serverfiles@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}xlrd>=0.9.2:textproc/py-xlrd@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}XlsxWriter>0:textproc/py-xlsxwriter@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}yaml>0:devel/py-yaml@${PY_FLAVOR} USES= python:3.7+ pyqt:5 USE_PYTHON= distutils cython autoplist noflavors USE_PYQT= pyqt5:run webengine:run USE_GITHUB= yes GH_ACCOUNT= biolab CFLAGS+= -DQSORT_R_STYLE_BSD=yes LDFLAGS+= -Xlinker -strip-all # strip, stage-qa doesn't catch that it isn't stripped .include .if ${ARCH} == aarch64 || ${ARCH} == amd64 || ${ARCH} == i386 USE_PYQT+= webengine:run .else USE_PYQT+= webkit:run .endif xpost-install: @${REINPLACE_CMD} -e 's|^"${PREFIX}/|| ; s|"$$||' ${_PYTHONPKGLIST} # https://github.com/biolab/orange3/issues/3060 @${REINPLACE_CMD} -e 's|import sys|& ; from OpenGL import GL|' ${STAGEDIR}${PREFIX}/bin/orange-canvas # https://github.com/biolab/orange3/issues/3062 .include diff --git a/misc/py-orange3-associate/Makefile b/misc/py-orange3-associate/Makefile index bc725546e585..9239fbf85c5a 100644 --- a/misc/py-orange3-associate/Makefile +++ b/misc/py-orange3-associate/Makefile @@ -1,25 +1,22 @@ PORTNAME= orange3-associate DISTVERSION= 1.1.8 CATEGORIES= misc python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Orange 3 add-on: Frequent itemsets and association rules mining WWW= https://github.com/biolab/orange3-associate LICENSE= GPLv3+ -DEPRECATED= Depends on expired security/py-keyrings.alt (via msic/orange3) -EXPIRATION_DATE=2022-12-31 - RUN_DEPENDS= orange3>0:misc/orange3 \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} USES= python:3.4+ USE_PYTHON= distutils autoplist USE_GITHUB= yes GH_ACCOUNT= biolab .include diff --git a/misc/py-orange3-datafusion/Makefile b/misc/py-orange3-datafusion/Makefile index 7836734602e9..31b34f88f861 100644 --- a/misc/py-orange3-datafusion/Makefile +++ b/misc/py-orange3-datafusion/Makefile @@ -1,27 +1,24 @@ PORTNAME= orange3-datafusion DISTVERSIONPREFIX= v DISTVERSION= 0.1.11-7 PORTREVISION= 3 DISTVERSIONSUFFIX= -g69aa51c CATEGORIES= misc python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Data fusion add-on for Orange3 WWW= https://github.com/biolab/orange3-datafusion LICENSE= GPLv3 -DEPRECATED= Depends on expired security/py-keyrings.alt (via msic/orange3) -EXPIRATION_DATE=2022-12-31 - RUN_DEPENDS= orange3>0:misc/orange3 \ ${PYTHON_PKGNAMEPREFIX}scikit-fusion>0:misc/py-scikit-fusion@${PY_FLAVOR} USES= python:3.4+ USE_GITHUB= yes GH_ACCOUNT= biolab USE_PYTHON= distutils autoplist NO_ARCH= yes .include diff --git a/misc/py-orange3-educational/Makefile b/misc/py-orange3-educational/Makefile index c930bbf451b7..fc8fefdf633f 100644 --- a/misc/py-orange3-educational/Makefile +++ b/misc/py-orange3-educational/Makefile @@ -1,28 +1,25 @@ PORTNAME= orange3-educational DISTVERSION= 0.4.0 CATEGORIES= misc education python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Orange add-on: widgets for machine learning and data mining WWW= https://github.com/biolab/orange3-educational LICENSE= CC-BY-3.0 LICENSE_FILE= ${WRKSRC}/LICENSE -DEPRECATED= Depends on expired security/py-keyrings.alt (via msic/orange3) -EXPIRATION_DATE=2022-12-31 - RUN_DEPENDS= orange3>0:misc/orange3 \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}beautifulsoup>0:www/py-beautifulsoup@${PY_FLAVOR} USES= python:3.4+ USE_PYTHON= distutils autoplist USE_GITHUB= yes GH_ACCOUNT= biolab NO_ARCH= yes .include diff --git a/misc/py-orange3-network/Makefile b/misc/py-orange3-network/Makefile index 2fee1ad313b1..45f24ee498c7 100644 --- a/misc/py-orange3-network/Makefile +++ b/misc/py-orange3-network/Makefile @@ -1,29 +1,26 @@ PORTNAME= orange3-network DISTVERSION= 1.5.1.20210224 # the 1.5.1 was forgotten CATEGORIES= misc python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Network analysis add-on for Orange data mining suite WWW= https://github.com/biolab/orange3-network LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/COPYING -DEPRECATED= Depends on expired security/py-keyrings.alt (via msic/orange3) -EXPIRATION_DATE=2022-12-31 - BUILD_DEPENDS= ${PYNUMPY} RUN_DEPENDS= orange3>0:misc/orange3 \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}gensim>0:textproc/py-gensim@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pyqtgraph>=0.9.10:graphics/py-pyqtgraph@${PY_FLAVOR} USES= python:3.4+ USE_PYTHON= distutils cython autoplist USE_GITHUB= yes GH_ACCOUNT= biolab GH_TAGNAME= ec534c9 .include diff --git a/misc/py-orange3-timeseries/Makefile b/misc/py-orange3-timeseries/Makefile index 3f62fc529872..578a215cc116 100644 --- a/misc/py-orange3-timeseries/Makefile +++ b/misc/py-orange3-timeseries/Makefile @@ -1,30 +1,27 @@ PORTNAME= orange3-timeseries DISTVERSION= 0.3.10 CATEGORIES= misc python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Orange add-on for analyzing, visualizing, manipulating time series WWW= https://github.com/biolab/orange3-timeseries LICENSE= CC-BY-3.0 LICENSE_FILE= ${WRKSRC}/LICENSE -DEPRECATED= Depends on expired security/py-keyrings.alt (via msic/orange3) -EXPIRATION_DATE=2022-12-31 - RUN_DEPENDS= orange3>0:misc/orange3 \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}more-itertools>0:devel/py-more-itertools@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pandas>0:math/py-pandas@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pandas-datareader>0:math/py-pandas-datareader@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>=0.17:science/py-scipy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}statsmodels>=0.10.0:math/py-statsmodels@${PY_FLAVOR} USES= python:3.7+ USE_GITHUB= yes GH_ACCOUNT= biolab USE_PYTHON= distutils autoplist NO_ARCH= yes .include diff --git a/textproc/py-orange3-text/Makefile b/textproc/py-orange3-text/Makefile index fc2ea5c31da3..e2b4093bcd37 100644 --- a/textproc/py-orange3-text/Makefile +++ b/textproc/py-orange3-text/Makefile @@ -1,41 +1,38 @@ PORTNAME= orange3-text DISTVERSION= 1.3.1 CATEGORIES= textproc python PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Text Mining add-on for Orange3 WWW= https://github.com/biolab/orange3-text LICENSE= AGPLv3 -DEPRECATED= Depends on expired security/py-keyrings.alt (via msic/orange3) -EXPIRATION_DATE=2022-12-31 - RUN_DEPENDS= orange3>0:misc/orange3 \ ${PYNUMPY} \ ${PYTHON_PKGNAMEPREFIX}beautifulsoup>0:www/py-beautifulsoup@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}biopython>0:biology/py-biopython@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}dateutil>=2.8.0:devel/py-dateutil@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}docx2txt>=0.6:textproc/py-docx2txt@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}gensim>=0.12.3:textproc/py-gensim@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}lxml>0:devel/py-lxml@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}nltk>=3.0.5:textproc/py-nltk@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}odfpy>=1.3.5:devel/py-odfpy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}pdfminer3k>=1.3.1:textproc/py-pdfminer3k@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}scikit-learn>0:science/py-scikit-learn@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}simhash>=1.11:math/py-simhash@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}tweepy>0:net/py-tweepy@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}ufal.udpipe>0:textproc/py-ufal.udpipe@${PY_FLAVOR} \ ${PYTHON_PKGNAMEPREFIX}wikipedia>0:www/py-wikipedia@${PY_FLAVOR} USES= python:3.4+ USE_PYTHON= distutils autoplist USE_GITHUB= yes GH_ACCOUNT= biolab NO_ARCH= yes .include