aboutsummaryrefslogtreecommitdiff
path: root/biology/py-biopython
Commit message (Collapse)AuthorAgeFilesLines
* - Update to 1.72Wen Heping2018-08-242-5/+4
| | | | | | | | | PR: 230723 Submitted by: wen@(myself) Approved by: maintainer Notes: svn path=/head/; revision=477931
* Use PY_FLAVOR for dependencies.Mathieu Arnold2018-06-201-1/+1
| | | | | | | | | | 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
* biology/py-biopython: Unbreak on python3; Add licenseYuri Victorovich2018-05-131-2/+9
| | | | | | | | | | | | | | | | | | | | | | Two items prevented python3 compatibility: * Breakage of ASCII codec due to non-ascii characters in README: https://github.com/biopython/biopython/issues/1649 * The outdated dependency: print/py-reportlab1 instead of the modern version 3.X print/py-reportlab Port changes: * USES=python:2.7 -> USES=python * Add pre-configure that clears the README file * Add LICENSE/LICENSE_FILE Testing: * Ran the tutorial testcase http://biopython.org/DIST/docs/tutorial/Tutorial.html, particularly pdf writing through print/py-reportlab worked fine. Asked the upstream to clarify the acceptable dependency version: https://github.com/biopython/biopython/issues/1650 Approved by: portmgr blanket (unbreak for python3; add license) Notes: svn path=/head/; revision=469835
* - Update to 1.71Wen Heping2018-04-092-5/+4
| | | | | | | Approved by: mauricio@arareko.net(maintainer, via email) Notes: svn path=/head/; revision=466835
* 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
* Reduce dependency on the python2 metaportAntoine Brodin2018-02-191-1/+2
| | | | | | | | PR: 225752 Submitted by: Yasuhiro KIMURA Notes: svn path=/head/; revision=462307
* Convert Python ports to FLAVORS.Mathieu Arnold2017-11-301-1/+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 1.70Wen Heping2017-08-182-4/+4
| | | | | | | | | PR: 221443 Submitted by: wen@(myself) Approved by: maintainer Notes: svn path=/head/; revision=448228
* - Update to 1.69Wen Heping2017-05-032-4/+4
| | | | | | | | | PR: 218903 Submitted by: wen@ Approved by: maintainer Notes: svn path=/head/; revision=440010
* - Update to 1.68Wen Heping2016-09-232-3/+4
| | | | | | | | | PR: 212874 Submitted by: wen@(myself) Approved by: maintainer Notes: svn path=/head/; revision=422643
* - Update to 1.66Wen Heping2016-04-172-4/+3
| | | | | | | | | PR: 208825 Submitted by: wen@ Approved by: maintainer Notes: svn path=/head/; revision=413489
* Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.Mathieu Arnold2016-04-011-1/+1
| | | | | | | | With hat: portmgr Sponsored by: Absolight Notes: svn path=/head/; revision=412344
* Update to 1.65.Mathieu Arnold2015-08-052-4/+4
| | | | | | | | | | PR: 201888 Submitted by: brueffer Approved by: maintainer Sponsored by: Absolight Notes: svn path=/head/; revision=393576
* biology/py-biopython:Max Brazhnikov2015-01-191-3/+5
| | | | | | | | | - Convert to options framework Approved by: portmgr blanket Notes: svn path=/head/; revision=377466
* - 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
* Update the default version of GCC in the Ports Collection from GCC 4.7.4Gerald Pfeifer2014-09-101-1/+1
| | | | | | | | | | | | | to GCC 4.8.3. Part II, Bump PORTREVISIONs. PR: 192025 Tested by: antoine (-exp runs) Approved by: portmgr (implicit) Notes: svn path=/head/; revision=367888
* - StageSteve Wills2014-04-272-1138/+2
| | | | | | | | | | | | | - Drop easy_install - Use auto pkg-plist - Delete pkg-plist PR: ports/188818 Submitted by: Bartek Rutkowski <ports@robakdesign.com> Approved by: portmgr@ (blanket) Notes: svn path=/head/; revision=352389
* Update the default version of GCC used in the Ports Collection fromGerald Pfeifer2014-03-101-1/+1
| | | | | | | | | | | | | | GCC 4.6.4 to GCC 4.7.3. This entails updating the lang/gcc port as well as changing the default in Mk/bsd.default-versions.mk. Part II, Bump PORTREVISIONs. PR: 182136 Supported by: Christoph Moench-Tegeder <cmt@burggraben.net> (fixing many ports) Tested by: bdrewery (two -exp runs) Notes: svn path=/head/; revision=347809
* - Repocopy print/py-reportlab to print/py-reportlab1TAKATSU Tomonari2014-02-251-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | to preserve version 1.x and to update to 3.0 print/py-reportlab: - Update print/py-reportlab to 3.0 based on print/py-reportlab2 - Support STAGEDIR - Use PYDISTUTILS_AUTOPLIST * Remove pkg-plist, accordingly - Set CONFLICTS - Add PORTSCOUT - Replace tab with a single space after WWW: in pkg-descr print/py-reportlab1: - Support STAGEDIR - Add PKGNAMESUFFIX not to duplicate ports with the same name - Set CONFLICTS - Use PYDISTUTILS_AUTOPLIST * Remove pkg-plist, accordingly - Make use of PORTDOCS - Set OPTIONS_DEFINE explicitly - Fix include statement - Make docs unconditional to stage - Replace tab with a single space after WWW: in pkg-descr print/py-reportlab2: - Update CONFLICTS - Set PORTSCOUT dependent ports: - Switch dependency from print/py-reportlab to print/py-reportlab1 * biology/py-biopython * deskutils/gourmet * deskutils/griffith * games/pythonsudoku * misc/pdfmap * print/py-trml2pdf * www/py-satchmo PR: ports/186970 Submitted by: tota (myself) Approved by: Muhammad Moinur Rahman (maintainer) Notes: svn path=/head/; revision=345987
* Python cleanup:Rene Ladan2014-01-131-1/+1
| | | | | | | | | | - USE_PYTHON* = 2.X -> USE_PYTHON* = 2 - USE_PYTHON* = 2.X+ -> USE_PYTHON* = yes Reviewed by: python (mva, rm) Approved by: portmgr-lurkers (mat) Notes: svn path=/head/; revision=339634
* Update to libmpc version 1.0.1 which brings the following fixes:Gerald Pfeifer2013-10-261-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Switched to automake 1.11.6, see CVE-2012-3386. - #14669: Fixed extraction of CC from gmp.h. - Fixed case of intermediate zero real or imaginary part in mpc_fma, found by hydra with GMP_CHECK_RANDOMIZE=1346362345. This is on top of the following changes from version 1.0 - Licence change towards LGPLv3+ for the code and GFDLv1.3+ (with no invariant sections) for the documentation. - 100% of all lines are covered by tests - Renamed functions . mpc_mul_2exp to mpc_mul_2ui . mpc_div_2exp to mpc_div_2ui - 0^0, which returned (NaN,NaN) previously, now returns (1,+0). - Removed compatibility with K&R compilers, which was untestable due to lack of such compilers. - New functions . mpc_log10 . mpc_mul_2si, mpc_div_2si - Speed-ups . mpc_fma - Bug fixes . mpc_div and mpc_norm now return a value indicating the effective rounding direction, as the other functions. . mpc_mul, mpc_sqr and mpc_norm now return correct results even if there are over- or underflows during the computation. . mpc_asin, mpc_proj, mpc_sqr: Wrong result when input variable has infinite part and equals output variable is corrected. . mpc_fr_sub: Wrong return value for imaginary part is corrected. Convert to the new LIB_DEPENDS standard and remove hard-coded .so versions from a couple of dependent ports. Bump PORTREVISIONS of all dependent ports. PR: 183141 Approved by: portmgr (bdrewery) Notes: svn path=/head/; revision=331644
* Add NO_STAGE all over the place in preparation for the staging support (cat: ↵Baptiste Daroussin2013-09-201-0/+1
| | | | | | | biology) Notes: svn path=/head/; revision=327709
* - update to 1.60Ruslan Makhmatkhanov2012-09-254-133/+140
| | | | | | | | | | | | | | | | while here: - convert Makefile header into two-line format - update COMMENT (indefinite article removed) - change USE_PYTHON to just -2.7 - remove py-reportlab from BUILD_DEPENDS and kick PYTHON_SITELIBDIR from there - tab -> space change in pkg-descr:WWW PR: 171115 Submitted by: wen Approved by: Mauricio Herrera Cuadra <mauricio at arareko dot net> (maintainer) Notes: svn path=/head/; revision=304822
* - Update to 1.59Wen Heping2012-03-063-1070/+1129
| | | | | | | | | PR: ports/165582 Submitted by: wen@ (myself) Approved by: Mauricio Herrera Cuadra <mauricio@arareko.net> (maintainer, via email) Notes: svn path=/head/; revision=292807
* - remove maintainer tags from pkg-descrEitan Adler2011-10-221-2/+0
| | | | | | | | Approved by: portmgr Approved by: bapt (mentor) Notes: svn path=/head/; revision=284139
* - Update to 1.57Wen Heping2011-05-243-111/+18
| | | | | | | | | PR: ports/156329 Submitted by: Wen Heping (myself) Approved by: maintainer Notes: svn path=/head/; revision=274572
* - Move over to python2.5 or higherMartin Wilke2011-02-242-2/+2
| | | | | | | - While here kick md5 Notes: svn path=/head/; revision=269605
* - Update to 1.54Wen Heping2010-07-023-49/+146
| | | | | | | | | | PR: ports/148274 Submitted by: Ju Pengfei <jupengfei@gmail.com> Approved by: maintainer Feature safe: yes Notes: svn path=/head/; revision=257284
* - Update to 1.53Wen Heping2010-01-063-99/+39
| | | | | | | | | PR: ports/142221 Submitted by: Wen Heping (myself) Approved by: maintainer Notes: svn path=/head/; revision=247241
* - Update to 138038Martin Wilke2009-09-044-444/+152
| | | | | | | | | PR: 138038 Submitted by: Wen Heping <wenheping@gmail.com> Approved by: maintainer Notes: svn path=/head/; revision=240881
* - Update to 1.48Martin Wilke2008-10-113-19/+16
| | | | | | | | | PR: 127776 Submitted by: Wen heping <wenheping@gmail.com> Approved by: maintainer Notes: svn path=/head/; revision=221438
* - Update to 1.47Martin Wilke2008-08-113-53/+92
| | | | | | | | | PR: 125912 Submitted by: Wen heping <wenheping@gmail.com> Approved by: maintainer timeout Notes: svn path=/head/; revision=218425
* - Update to 1.45Beech Rintoul2008-07-043-26/+79
| | | | | | | | | PR: ports/125134 Submitted by: Wen heping <wenheping@gmail.com> Approved by: Mauricio Herrera Cuadra <mauricio@arareko.net> (maintainer) Notes: svn path=/head/; revision=216283
* - Fix typos.Martin Wilke2007-05-311-3/+3
| | | | | | | Reported by: stas@ Notes: svn path=/head/; revision=192436
* - Update to 1.43Martin Wilke2007-05-304-92/+167
| | | | | | | | | PR: 111817 Submitted by: "P.BandieraPaiva" <paiva@unifesp.br> Approved by: maintainer Notes: svn path=/head/; revision=192382
* - Update to 1.42Martin Wilke2006-10-313-121/+90
| | | | | | | | | PR: ports/104635 Submitted by: Thomas Abthorpe <thomas@goodking.ca> Approved by: maintainer Notes: svn path=/head/; revision=175802
* Update to 1.41Marcus Alves Grando2005-11-115-44/+87
| | | | | | | | | | | Take MAINTAINER Add SHA256 PR: 88792 Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net> Notes: svn path=/head/; revision=147871
* Fix build on Python 2.4Hye-Shik Chang2004-12-021-0/+14
| | | | | | | Spotted by: kris Notes: svn path=/head/; revision=122961
* With portmgr hat on, reset inactive maintainer. These ports are now upMark Linimon2004-11-201-1/+1
| | | | | | | for adoption. Notes: svn path=/head/; revision=121990
* - Fix build on amd64 (crude hack to pass -fPIC to c++ compiles)Pav Lucistnik2004-11-061-0/+11
| | | | | | | | Reported by: pointyhat via kris Tested on: arved's box Notes: svn path=/head/; revision=121009
* - Update to 1.30Pav Lucistnik2004-10-273-128/+209
| | | | | | | | | PR: ports/71400 Submitted by: Stefan Walter <sw@gegenunendlich.de> Approved by: maintainer timeout (2 months) Notes: svn path=/head/; revision=120340
* BROKEN: Does not buildKris Kennaway2004-07-021-0/+2
| | | | Notes: svn path=/head/; revision=112742
* SIZEify (maintainer timeout)Trevor Johnson2004-03-311-0/+1
| | | | Notes: svn path=/head/; revision=105747
* Upgrade to 1.23.Dag-Erling Smørgrav2004-02-096-1001/+1125
| | | | | | | Approved by: maintainer timeout Notes: svn path=/head/; revision=100524
* Define USE_PERL5_BUILD, not erroneous USE_PERL.Trevor Johnson2003-11-201-1/+1
| | | | | | | Submitted by: Oliver Eikemeier Notes: svn path=/head/; revision=94477
* Define USE_PERL to make Perl available for (mostly deprecated)Trevor Johnson2003-11-201-0/+1
| | | | | | | "perl -pi -e" construction. Notes: svn path=/head/; revision=94465
* Use the FIND and XARGS macros introduced in bsd.port.mk 1.391.Trevor Johnson2003-11-131-1/+1
| | | | Notes: svn path=/head/; revision=93890
* Cosmetic fix: use %%DOCSDIR%% macro.Sergey A. Osokin2003-10-221-26/+26
| | | | | | | | | | No functionally changes. Submitted by: Oleg Karachevtsev <ok@etrust.ru> A part of PR: 57992 Notes: svn path=/head/; revision=91882
* Fix python version detection routines to cope with python 2.3'sHye-Shik Chang2003-08-011-1/+1
| | | | | | | boolean representation. Notes: svn path=/head/; revision=86153
* Clear moonlight beckons.Ade Lovett2003-03-072-1/+1
| | | | | | | | | | Requiem mors pacem pkg-comment, And be calm ports tree. E Nomini Patri, E Fili, E Spiritu Sancti. Notes: svn path=/head/; revision=77045