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mirror of https://git.FreeBSD.org/ports.git synced 2024-11-22 00:35:15 +00:00
freebsd-ports/biology
Marcus von Appen 900db324a3 Convert the Python framework bits to USES=python.
Please use USES=python instead of USE_PYTHON.

  USE_PYTHON=yes becomes USES=python
  USE_PYTHON=2.7+ becomes USES=python:2.7+
  USE_PYTHON_BUILD=3.3 becomes USES=python:3.3,build
  ...

A new PYTHON_FEATURES variable was added, which enables certain features for a
port and replaces some knobs at the same time;

  PYTHON_FEATURES=distutils replaces USE_PYDISTUTILS
  PYTHON_FEATURES=autoplist replaces PYDISTUTILS_AUTOPLIST
  PYTHON_FEATURES=py3kplist replaces PYTHON_PY3K_PLIST_HACK
  PYTHON_FEATURES=noegginfo replaces PYDISTUTILS_NOEGGINFO
  PYTHON_FEATURES=concurrent replaces PYTHON_CONCURRENT_INSTALL
  PYTHON_FEATURES=pythonprefix replaces USE_PYTHON_PREFIX

Some knobs have been deprecated and are to be removed in the near future:

  PYTHON_MASTER_SITES - use MASTER_SITE_PYTHON instead
  PYTHON_PKGNAMESUFFIX - use PYTHON_PKGNAMEPREFIX instead
  PYDISTUTILS_INSTALLNOSINGLE - deprecated without replacement

Some knobs have been removed completely:

  PYTHON_MASTER_SITE_SUBDIR
  PYTHON_DISTNAME
  PYTHON_WRKSRC

Several variables specific to the Python framework are no longer passed to the
build environment to avoid polluting dependency builds.

  PYTHON_VERSION is not passed to .MAKEFLAGS anymore
  PYTHON_DEFAULT_VERSION,
  PYTHON_DEFAULT_PORTVERSION and
  PYTHONBASE are not passed to the make environment anymore

The conversion required a couple of ports to be updated to fit the changes and
new requirements. Those included "bsd.python.mk" directly or contained checks
in places, for which the USES framework would fail to provide correct values.

Python modules directly using the upstream Python package (such as py-tkinter
or py-sqlite3) were updated to avoid using the now unnecessary and remmoved
knobs from "bsd.python.mk".

Phabric:	D399
exp-run:	167368 192357
PR:		167368 192357
Reviewed by:	antoine, wg
Exp-run award:	antoine
With hat:	python@
Approved by:	portmgr
2014-08-09 15:44:27 +00:00
..
ariadne Convert a bunch of EXTRACT_SUFX=... into USES=tar:... 2014-07-29 19:11:51 +00:00
artemis
avida
babel Rename biology/ patch-xy patches to reflect the files they modify. 2014-07-28 14:22:16 +00:00
biococoa
biojava
blast
blat
boinc-simap
chemeq
clustalw
consed Convert a bunch of EXTRACT_SUFX=... into USES=tar:... 2014-07-29 19:11:51 +00:00
crux Convert a bunch of USE_BZIP2 to USES=tar:bzip2 2014-07-29 18:41:15 +00:00
embassy Reset maintainership for ports not staged with no pending PR 2014-07-23 16:44:27 +00:00
emboss
fasta
fasta3
fastdnaml
fluctuate
garlic biology/garlic: Stage properly to unbreak 2014-07-17 10:13:06 +00:00
gff2ps
gmap
gperiodic
grappa
hmmer
iolib
jalview
lagan
lamarc
libsbml Convert the Python framework bits to USES=python. 2014-08-09 15:44:27 +00:00
linux-foldingathome
mafft Convert a bunch of EXTRACT_SUFX=... into USES=tar:... 2014-07-29 19:11:51 +00:00
mapm3
migrate
molden
mopac - Switch to USES=libtool, drop .la files 2014-08-06 16:05:49 +00:00
mrbayes
mummer biology/mummer: Use OPSYS with OSVERSION 2014-07-19 22:00:16 +00:00
muscle
ncbi-toolkit
njplot
ortep3
p5-AcePerl Rename biology/ patch-xy patches to reflect the files they modify. 2014-07-28 14:22:16 +00:00
p5-Bio-ASN1-EntrezGene Convert a bunch of EXTRACT_SUFX=... into USES=tar:... 2014-07-29 19:11:51 +00:00
p5-Bio-Das
p5-Bio-Das-Lite
p5-Bio-GFF3
p5-Bio-Glite
p5-Bio-Graphics Really fix. 2014-07-25 23:08:58 +00:00
p5-Bio-MAGETAB
p5-Bio-NEXUS
p5-Bio-Phylo
p5-Bio-SCF
p5-bioperl biology/p5-bioperl: fix pkg-descr sidenote link 2014-08-04 04:32:38 +00:00
p5-bioperl-run biology/p5-bioperl-run: 1.6.1 -> 1.6.901, unbreak, stagify 2014-08-04 08:54:10 +00:00
paml Convert a bunch of EXTRACT_SUFX=... into USES=tar:... 2014-07-29 19:11:51 +00:00
phd2fasta Reset maintainership for ports not staged with no pending PR 2014-07-23 16:44:27 +00:00
phrap
phred
phylip
phyml
platon Add a DOCS option. 2014-08-03 21:44:23 +00:00
plink
plinkseq - Switch to USES=libtool, drop .la files 2014-07-22 22:12:15 +00:00
povchem Rename biology/ patch-xy patches to reflect the files they modify. 2014-07-28 14:22:16 +00:00
primer3
protomol Reset maintainership for ports not staged with no pending PR 2014-07-23 16:44:27 +00:00
psi88 Convert a bunch of EXTRACT_SUFX=... into USES=tar:... 2014-07-29 19:11:51 +00:00
py-biopython
pycogent
pyfasta
pymol Convert a bunch of USE_BZIP2 to USES=tar:bzip2 2014-07-29 18:41:15 +00:00
python-nexus
recombine
ruby-bio
seaview
seqan
seqio
seqtools USES=execinfo 2014-08-04 23:06:21 +00:00
sim4
ssaha
t_coffee
tinker
treepuzzle
treeviewx
tRNAscan-SE Convert a bunch of EXTRACT_SUFX=... into USES=tar:... 2014-07-29 19:11:51 +00:00
ugene USES=execinfo 2014-08-04 23:06:21 +00:00
velvet Convert a bunch of EXTRACT_SUFX=... into USES=tar:... 2014-07-29 19:11:51 +00:00
wise
xmolwt
Makefile