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* One more small cleanup, forgotten yesterday.Mathieu Arnold2021-04-071-1/+0
| | | | Reported by: lwhsu
* Remove # $FreeBSD$ from Makefiles.Mathieu Arnold2021-04-061-1/+0
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* Update USES=python: math/py-pandas 1.2.0 requires Python 3.7+Sunpoet Po-Chuan Hsieh2021-01-301-1/+1
| | | | | | | PR: 250103 Notes: svn path=/head/; revision=563407
* biology/py-biom-format: Update to version 2.1.10Joseph Mingrone2021-01-112-5/+4
| | | | | | | https://github.com/biocore/biom-format/releases/tag/2.1.10 Notes: svn path=/head/; revision=561187
* biology/py-biom-format: Fix fetch and relax scipy requirementJoseph Mingrone2020-09-262-4/+5
| | | | | | | | | | - The broken fetch was due to a commit error. - The relaxing of the scipy constraint is temporary until scipy can be updated. Notes: svn path=/head/; revision=550141
* biology/py-biom-format: Update to version 2.1.8Joseph Mingrone2020-09-252-15/+7
| | | | | | | | Upstream changes: https://github.com/biocore/biom-format/releases/tag/2.1.8 Notes: svn path=/head/; revision=549977
* biology/py-biom-format: Restore in preparation for an update to v2.1.8Joseph Mingrone2020-09-243-0/+64
| | | | | | | Version 2.1.8 supports python 3 Notes: svn path=/head/; revision=549943
* Remove deprecated ports:Rene Ladan2020-08-153-64/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 2020-08-15 archivers/py-backports.lzma: Uses deprecated version of python 2020-08-15 archivers/py-bup: Uses deprecated version of python 2020-08-15 archivers/py-librtfcomp: Uses deprecated version of python 2020-08-15 audio/blop-lv2: Uses deprecated version of python 2020-08-15 audio/bs2b-lv2: Uses deprecated version of python 2020-08-15 audio/py-gmusicproxy: Uses deprecated version of python 2020-08-15 audio/py-karaoke: Uses deprecated version of python 2020-08-15 audio/py-openal: Uses deprecated version of python 2020-08-15 audio/py-py-jack: Uses deprecated version of python 2020-08-15 audio/py-xmms2: Uses deprecated version of python 2020-08-15 audio/triceratops-lv2: Uses deprecated version of python 2020-08-15 biology/py-biom-format: Uses deprecated version of python 2020-08-15 comms/py-bulksms: Uses deprecated version of python 2020-08-15 comms/py-gammu: Uses deprecated version of python 2020-08-15 databases/py-geoalchemy: Uses deprecated version of python 2020-08-15 databases/py-htsql-mysql: Uses deprecated version of python 2020-08-15 databases/py-htsql-pgsql: Uses deprecated version of python 2020-08-15 databases/py-mysql2pgsql: Uses deprecated version of python 2020-08-15 databases/py-oursql: Uses deprecated version of python 2020-08-15 databases/py-pyPgSQL: Uses deprecated version of python 2020-08-15 databases/py-pyhs: Uses deprecated version of python 2020-08-15 databases/py-pytc: Uses deprecated version of python 2020-08-15 databases/py-riak: Uses deprecated version of python 2020-08-15 databases/py-umemcache: Uses deprecated version of python 2020-08-15 devel/py-Breve: Uses deprecated version of python 2020-08-15 devel/py-PyODE: Uses deprecated version of python 2020-08-15 devel/py-akismet: Uses deprecated version of python 2020-08-15 devel/py-aspects: Uses deprecated version of python 2020-08-15 devel/py-backports.tempfile: Uses deprecated version of python 2020-08-15 devel/py-backports.weakref: Uses deprecated version of python 2020-08-15 devel/py-cfgparse: Uses deprecated version of python 2020-08-15 devel/py-ciphon: Uses deprecated version of python 2020-08-15 devel/py-cjson: Uses deprecated version of python 2020-08-15 devel/py-clonedigger: Uses deprecated version of python 2020-08-15 devel/py-cuisine: Uses deprecated version of python 2020-08-15 devel/py-deliciousapi: Uses deprecated version of python 2020-08-15 devel/py-dialog: Uses deprecated version of python 2020-08-15 devel/py-efl: Uses deprecated version of python 2020-08-15 devel/py-ezpyinline: Uses deprecated version of python 2020-08-15 devel/py-fsm: Uses deprecated 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Uses deprecated version of python 2020-08-15 devel/py-kjbuckets: Uses deprecated version of python 2020-08-15 devel/py-kqueue: Uses deprecated version of python 2020-08-15 devel/py-log4py: Uses deprecated version of python 2020-08-15 devel/py-mwlib.ext: Uses deprecated version of python 2020-08-15 devel/py-mx-experimental: Uses deprecated version of python 2020-08-15 devel/py-option_merge: Uses deprecated version of python 2020-08-15 devel/py-prioritized_methods: Uses deprecated version of python 2020-08-15 devel/py-protocols: Uses deprecated version of python 2020-08-15 devel/py-ptrace: Uses deprecated version of python 2020-08-15 devel/py-pydoop: Uses deprecated version of python 2020-08-15 devel/py-pyke: Uses deprecated version of python 2020-08-15 devel/py-pymtbl: Uses deprecated version of python 2020-08-15 devel/py-pyshapelib: Uses deprecated version of python 2020-08-15 devel/py-pytemplate: Uses deprecated version of python 2020-08-15 devel/py-python2-pythondialog: Uses 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devel/py-trace2html: Uses deprecated version of python 2020-08-15 devel/py-tvrage: Uses deprecated version of python 2020-08-15 devel/py-tw.forms: Uses deprecated version of python 2020-08-15 devel/py-uncompyle2: Uses deprecated version of python 2020-08-15 devel/py-yum-metadata-parser: Uses deprecated version of python 2020-08-15 devel/rubygem-warden127: No longer needed 2020-08-15 dns/py-dnschain: Uses deprecated version of python 2020-08-15 dns/py-idnkit2: Uses deprecated version of python 2020-08-15 games/colobot: Uses deprecated version of python 2020-08-15 games/endgame-singularity: Uses deprecated version of python 2020-08-15 games/katawa-shoujo: Uses deprecated version of RenPy 2020-08-15 games/pyfa: Uses deprecated version of python 2020-08-15 games/renpy6: Uses deprecated version of python 2020-08-15 games/solarwolf: Uses deprecated version of python 2020-08-15 games/thudboard: Uses deprecated version of python 2020-08-15 graphics/djvusmooth: Uses deprecated version of python 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python 2020-08-15 misc/py-socli: Uses deprecated version of python 2020-08-15 misc/py-yolk: Uses deprecated version of python 2020-08-15 multimedia/py-flvlib: Uses deprecated version of python 2020-08-15 net/py-gspreadsheet: Uses deprecated version of python 2020-08-15 net/py-libnet: Uses deprecated version of python 2020-08-15 net/py-netlib: Uses deprecated version of python 2020-08-15 net/py-pynmsg: Uses deprecated version of python 2020-08-15 net/py-rainbowstream: Uses deprecated version of python 2020-08-15 net/py-wolframalpha: Uses deprecated version of python 2020-08-15 net-im/empathy: Uses deprecated version of python 2020-08-15 net-im/farsight2: Uses deprecated version of python 2020-08-15 net-im/py-xmpppy: Uses deprecated version of python 2020-08-15 net-im/telepathy-farsight: Uses deprecated version of python 2020-08-15 net-im/telepathy-python: Uses deprecated version of python 2020-08-15 net-im/telepathy-rakia: Uses deprecated version of python 2020-08-15 net-mgmt/py-pynsca: 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2020-08-15 security/py-sslstrip: Uses deprecated version of python 2020-08-15 security/py-volatility: Uses deprecated version of python 2020-08-15 sysutils/py-analyzemft: Uses deprecated version of python 2020-08-15 sysutils/py-cdmi: Uses deprecated version of python 2020-08-15 sysutils/py-ezjailremote: Uses deprecated version of python 2020-08-15 sysutils/py-gmailfs-fuse: Uses deprecated version of python 2020-08-15 sysutils/py-ploy_ec2: Uses deprecated version of python 2020-08-15 sysutils/py-ploy_fabric: Uses deprecated version of python 2020-08-15 sysutils/py-scriptine: Uses deprecated version of python 2020-08-15 sysutils/py-superlance: Uses deprecated version of python 2020-08-15 textproc/py-bugzillatools: Uses deprecated version of python 2020-08-15 textproc/py-elib.intl: Uses deprecated version of python 2020-08-15 textproc/py-errorhandler: Uses deprecated version of python 2020-08-15 textproc/py-hyperestraier-python: Uses deprecated version of python 2020-08-15 textproc/py-pyes: Uses deprecated version of python 2020-08-15 textproc/py-pyhwp: Uses deprecated version of python 2020-08-15 textproc/py-sphinx_numfig: Uses deprecated version of python 2020-08-15 www/py-HTMLgen: Uses deprecated version of python 2020-08-15 www/py-albatross: Uses deprecated version of python 2020-08-15 www/py-amf: Uses deprecated version of python 2020-08-15 www/py-apachelog: Uses deprecated version of python 2020-08-15 www/py-aws-requests-auth: Uses deprecated version of python 2020-08-15 www/py-clientform: Uses deprecated version of python 2020-08-15 www/py-django-appmedia: Uses deprecated version of python 2020-08-15 www/py-django-evolution: Uses deprecated version of python 2020-08-15 www/py-fedex: Uses deprecated version of python 2020-08-15 www/py-formalchemy: Uses deprecated version of python 2020-08-15 www/py-frappe-bench: Uses deprecated version of python 2020-08-15 www/py-funkload: Uses deprecated version of python 2020-08-15 www/py-goobook: Uses deprecated version of python 2020-08-15 www/py-poster: Uses deprecated version of python 2020-08-15 www/py-pyquery: Uses deprecated version of python 2020-08-15 www/py-pysearch: Uses deprecated version of python 2020-08-15 www/py-pywebdav: Uses deprecated version of python 2020-08-15 www/py-slimmer: Uses deprecated version of python 2020-08-15 www/py-surl: Uses deprecated version of python 2020-08-15 www/py-tmdb3: Uses deprecated version of python 2020-08-15 www/py-trello: Uses deprecated version of python 2020-08-15 www/py-uliweb: Uses deprecated version of python 2020-08-15 www/py-wsgiauth: Uses deprecated version of python 2020-08-15 x11-toolkits/py-wax: Uses deprecated version of python 2020-08-15 x11-toolkits/py-wxPython-common: Uses deprecated version of python 2020-08-15 x11-toolkits/py-wxPython28-common: Uses deprecated version of python Notes: svn path=/head/; revision=544927
* Deprecate a few portsAntoine Brodin2020-02-231-0/+3
| | | | | | | With hat: portmgr Notes: svn path=/head/; revision=526925
* - Limit python version (does not build with 3.7+)Dmitry Marakasov2019-11-081-1/+1
| | | | | | | Approved by: portmgr blanket Notes: svn path=/head/; revision=517051
* Bump PORTREVISION for ports depending on the canonical version of GCCGerald Pfeifer2019-07-261-1/+1
| | | | | | | | | | | | | | | | | | as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3 to GCC 9.1 under most circumstances now after revision 507371. This includes ports - with USE_GCC=yes or USE_GCC=any, - with USES=fortran, - using Mk/bsd.octave.mk which in turn features USES=fortran, and - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang, c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib plus, everything INDEX-11 shows with a dependency on lang/gcc9 now. PR: 238330 Notes: svn path=/head/; revision=507372
* Bump a few PORTREVISIONs after r498529Antoine Brodin2019-04-101-1/+1
| | | | | | | With hat: portmgr Notes: svn path=/head/; revision=498530
* Bump PORTREVISION for ports depending on the canonical version of GCCGerald Pfeifer2018-12-121-0/+1
| | | | | | | | | | | | | | | | | | defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t GCC 8.2 under most circumstances. This includes ports - with USE_GCC=yes or USE_GCC=any, - with USES=fortran, - using Mk/bsd.octave.mk which in turn features USES=fortran, and - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang, c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib plus, as a double check, everything INDEX-11 showed depending on lang/gcc7. PR: 231590 Notes: svn path=/head/; revision=487272
* biology/py-biom-format: Update to version 2.1.7Joseph Mingrone2018-10-062-16/+14
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=481369
* Use PY_FLAVOR for dependencies.Mathieu Arnold2018-06-201-6/+6
| | | | | | | | | | FLAVOR is the current port's flavor, it should not be used outside of this scope. Sponsored by: Absolight Notes: svn path=/head/; revision=472884
* Bump PORTREVISIONs of all users of math/mpc that we just updated toGerald Pfeifer2018-03-101-1/+1
| | | | | | | version 1.1.0 (via revision 464079). Notes: svn path=/head/; revision=464084
* biology/py-biom-format: Add required dependency on math/py-pandas and doJoseph Mingrone2017-12-101-3/+7
| | | | | | | not install tests. Notes: svn path=/head/; revision=455879
* Convert Python ports to FLAVORS.Mathieu Arnold2017-11-301-5/+5
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Ports using USE_PYTHON=distutils are now flavored. They will automatically get flavors (py27, py34, py35, py36) depending on what versions they support. There is also a USE_PYTHON=flavors for ports that do not use distutils but need FLAVORS to be set. A USE_PYTHON=noflavors can be set if using distutils but flavors are not wanted. A new USE_PYTHON=optsuffix that will add PYTHON_PKGNAMESUFFIX has been added to cope with Python ports that did not have the Python PKGNAMEPREFIX but are flavored. USES=python now also exports a PY_FLAVOR variable that contains the current python flavor. It can be used in dependency lines when the port itself is not python flavored. For example, deskutils/calibre. By default, all the flavors are generated. To only generate flavors for the versions in PYTHON2_DEFAULT and PYTHON3_DEFAULT, define BUILD_DEFAULT_PYTHON_FLAVORS in your make.conf. In all the ports with Python dependencies, the *_DEPENDS entries MUST end with the flavor so that the framework knows which to build/use. This is done by appending '@${PY_FLAVOR}' after the origin (or @${FLAVOR} if in a Python module with Python flavors, as the content will be the same). For example: RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}six>0:devel/py-six@${PY_FLAVOR} PR: 223071 Reviewed by: portmgr, python Sponsored by: Absolight Differential Revision: https://reviews.freebsd.org/D12464 Notes: svn path=/head/; revision=455210
* biology/py-biom-format: Update to version 2.1.6Joseph Mingrone2017-04-292-4/+5
| | | | | | | | | Upstream changes: https://github.com/biocore/biom-format/releases/tag/2.1.6 Approved by: swills (mentor, implicit) Notes: svn path=/head/; revision=439751
* Update email address to jrm@FreeBSD.org for ports that I maintainJoseph Mingrone2016-09-231-2/+1
| | | | | | | | | Reviewed by: mat, swills (mentor) Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D7995 Notes: svn path=/head/; revision=422697
* - Fix run-time dependency issuesOlivier Duchateau2016-06-111-2/+13
| | | | | | | | | | - Bump PORTREVISION PR: 209767 Submitted by: Joseph Mingrone (maintainer) Notes: svn path=/head/; revision=416710
* Add final slash in WWW entryOlivier Duchateau2016-05-091-1/+1
| | | | Notes: svn path=/head/; revision=414866
* The BIOM file format (canonically pronounced biome) is designed to be aOlivier Duchateau2016-05-093-0/+47
general-use format for representing biological sample by observation contingency tables. BIOM is a recognized standard for the Earth Microbiome Project and is a Genomics Standards Consortium supported project. The BIOM format is designed for general use in broad areas of comparative -omics. For example, in marker-gene surveys, the primary use of this format is to represent OTU tables: the observations in this case are OTUs and the matrix contains counts corresponding to the number of times each OTU is observed in each sample. With respect to metagenome data, this format would be used to represent metagenome tables: the observations in this case might correspond to SEED subsystems, and the matrix would contain counts corresponding to the number of times each subsystem is observed in each metagenome. Similarly, with respect to genome data, this format may be used to represent a set of genomes: the observations in this case again might correspond to SEED subsystems, and the counts would correspond to the number of times each subsystem is observed in each genome. WWW: http://biom-format.org/ PR: 209193 Submitted by: Joseph Mingrone Notes: svn path=/head/; revision=414865