aboutsummaryrefslogtreecommitdiff
path: root/biology/python-nexus
Commit message (Collapse)AuthorAgeFilesLines
* all: remove explicit versions in USES=python for "3.x+"Rene Ladan2023-06-271-1/+1
| | | | | | | | | | | | | | | | | | | The logic in USES=python will automatically convert this to 3.8+ by itself. Adjust two ports that only had Python 3.7 mentioned but build fine on Python 3.8 too. finance/quickfix: mark BROKEN with PYTHON libtool: compile: c++ -DHAVE_CONFIG_H -I. -I../.. -I -I. -I.. -I../.. -I../C++ -DLIBICONV_PLUG -DPYTHON_MAJOR_VERSION=3 -Wno-unused-variable -Wno-maybe-uninitialized -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -fno-strict-aliasing -DLIBICONV_PLUG -Wall -ansi -Wno-unused-command-line-argument -Wpointer-arith -Wwrite-strings -Wno-overloaded-virtual -Wno-deprecated-declarations -Wno-deprecated -std=c++0x -MT _quickfix_la-QuickfixPython.lo -MD -MP -MF .deps/_quickfix_la-QuickfixPython.Tpo -c QuickfixPython.cpp -fPIC -DPIC -o .libs/_quickfix_la-QuickfixPython.o warning: unknown warning option '-Wno-maybe-uninitialized'; did you mean '-Wno-uninitialized'? [-Wunknown-warning-option] QuickfixPython.cpp:175:11: fatal error: 'Python.h' file not found ^~~~~~~~~~ 1 warning and 1 error generated. Reviewed by: portmgr, vishwin, yuri Differential Revision: <https://reviews.freebsd.org/D40568>
* */*: rename CHEESESHOP to PYPI in MASTER_SITESDmitry Marakasov2023-01-111-1/+1
| | | | | | PR: 267994 Differential revision: D37518 Approved by: bapt
* Remove WWW entries moved into port MakefilesStefan Eßer2022-09-071-2/+0
| | | | | | | | | | Commit b7f05445c00f has added WWW entries to port Makefiles based on WWW: lines in pkg-descr files. This commit removes the WWW: lines of moved-over URLs from these pkg-descr files. Approved by: portmgr (tcberner)
* Add WWW entries to port MakefilesStefan Eßer2022-09-071-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | It has been common practice to have one or more URLs at the end of the ports' pkg-descr files, one per line and prefixed with "WWW:". These URLs should point at a project website or other relevant resources. Access to these URLs required processing of the pkg-descr files, and they have often become stale over time. If more than one such URL was present in a pkg-descr file, only the first one was tarnsfered into the port INDEX, but for many ports only the last line did contain the port specific URL to further information. There have been several proposals to make a project URL available as a macro in the ports' Makefiles, over time. This commit implements such a proposal and moves one of the WWW: entries of each pkg-descr file into the respective port's Makefile. A heuristic attempts to identify the most relevant URL in case there is more than one WWW: entry in some pkg-descr file. URLs that are not moved into the Makefile are prefixed with "See also:" instead of "WWW:" in the pkg-descr files in order to preserve them. There are 1256 ports that had no WWW: entries in pkg-descr files. These ports will not be touched in this commit. The portlint port has been adjusted to expect a WWW entry in each port Makefile, and to flag any remaining "WWW:" lines in pkg-descr files as deprecated. Approved by: portmgr (tcberner)
* biology: remove 'Created by' linesTobias C. Berner2022-07-201-2/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | A big Thank You to the original contributors of these ports: * Aaron Dalton <aaron@FreeBSD.org> * Akinori MUSHA aka knu <knu@idaemons.org> * Andrey Zakhvatov * Bob Zimmermann <rpz@cse.wustl.edu> * Camson Huynh <chuynh@biolateral.com.au> * Dan Siercks <dsiercks@uwm.edu> * Fernan Aguero <fernan@iib.unsam.edu.ar> * Hannes Hauswedell <h2+fbsdports@fsfe.org> * J. Bacon <jwb@FreeBSD.org> * Jason Bacon <jwb@FreeBSD.org> * Jeremy <karlj000@unbc.ca> * Johann Visagie <johann@egenetics.com> * Johann Visagie <wjv@FreeBSD.org> * Mauricio Herrera Cuadra <mauricio@arareko.net> * Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp> * Motomichi Matsuzaki <mzaki@e-mail.ne.jp> * Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp> * Motomichi Matsuzaki <mzaki@niid.go.jp> * Po-Chuan Hsieh <sunpoet@FreeBSD.org> * Razi Khaja <razi@genet.sickkids.on.ca> * Reed A. Cartwright <cartwright@asu.edu> * Ryo MIYAMOTO * Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp> * Sangwoo Shim <sangwoos@gmail.com> * Sunpoet Po-Chuan Hsieh <sunpoet@FreeBSD.org> * Tassilo Philipp <tphilipp@potion-studios.com> * Tony Maher * Tony Maher <tonym@biolateral.com.au> * Wen Heping <wen@FreeBSD.org> * Wen Heping <wenheping@gmail.com> * Yonatan <onatan@gmail.com> * Yuri Victorovich <yuri@rawbw.com> * ballen * barnhart@genetics.wustl.edu * camson@bilateral.com.au * chuynh@biolateral.com.au * dbader@eece.unm.edu * frankch@waru.life.nthu.edu.tw * h2 * lentferj * maho@FreeBSD.org * mzaki@biol.s.u-tokyo.ac.jp * tonym * wen@FreeBSD.org With hat: portmgr
* biology/python-nexus: Fix build with setuptools 58.0.0+Po-Chuan Hsieh2022-03-251-0/+19
| | | | With hat: python
* Remove # $FreeBSD$ from Makefiles.Mathieu Arnold2021-04-061-1/+0
|
* Drop python 2.7 support from a few portsAntoine Brodin2020-12-281-1/+1
| | | | | | | With hat: portmgr Notes: svn path=/head/; revision=559531
* - Update to 1.63Wen Heping2018-09-222-4/+4
| | | | Notes: svn path=/head/; revision=480370
* - Update to 1.61Wen Heping2018-04-012-6/+7
| | | | Notes: svn path=/head/; revision=466142
* Convert Python ports to FLAVORS.Mathieu Arnold2017-11-301-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 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
* - Update to 1.53Wen Heping2017-07-232-4/+4
| | | | Notes: svn path=/head/; revision=446458
* - Update to 1.42Wen Heping2017-03-012-4/+4
| | | | Notes: svn path=/head/; revision=435123
* - Update to 1.35Wen Heping2016-06-082-3/+4
| | | | Notes: svn path=/head/; revision=416534
* - Fix trailing whitespace in pkg-descrs, categories [a-f]*Dmitry Marakasov2016-05-191-1/+1
| | | | | | | Approved by: portmgr blanket Notes: svn path=/head/; revision=415498
* - Update to 1.34Wen Heping2016-02-122-3/+3
| | | | Notes: svn path=/head/; revision=408731
* - Update to 1.32Wen Heping2015-12-113-6/+8
| | | | | | | | - Add LICENSE - Pet portlint Notes: svn path=/head/; revision=403479
* - Convert ports from benchmarks/ and biology/ to new USES=pythonMarcus von Appen2014-10-191-3/+2
| | | | | | | Approved by: portmgr (implicit) Notes: svn path=/head/; revision=371171
* Remove indefinite articles and trailing periods from COMMENT, plusJimmy Olgeni2014-06-091-1/+1
| | | | | | | | | | minor COMMENT typos and surrounding whitespace fixes. Categories A-C. CR: D196 Approved by: portmgr (bapt) Notes: svn path=/head/; revision=357139
* - Convert to PYDISTUTILS_AUTOPLISTMartin Wilke2014-01-312-11/+3
| | | | | | | | - Stage support - Bump PORTREV Notes: svn path=/head/; revision=341983
* Add NO_STAGE all over the place in preparation for the staging support (cat: ↵Baptiste Daroussin2013-09-201-5/+2
| | | | | | | biology) Notes: svn path=/head/; revision=327709
* - Update to 0.87Wen Heping2011-12-233-4/+6
| | | | Notes: svn path=/head/; revision=287905
* - Update to 0.8Wen Heping2011-02-152-4/+3
| | | | Notes: svn path=/head/; revision=269176
* - Update to 0.7Wen Heping2010-02-243-9/+8
| | | | | | | Feature safe: yes Notes: svn path=/head/; revision=250247
* python-nexus is a generic nexus (phylogenetics) file format(.nex, .trees)Wen Heping2009-12-294-0/+34
reader for python. WWW: http://simon.net.nz/articles/python-nexus Notes: svn path=/head/; revision=246859