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* biology/py-pysam: relax python version requirementRuslan Makhmatkhanov2023-12-031-1/+1
| | | | | | | | | According to [1] pysam support Python 3.11 since version 0.21.0 [1] https://github.com/pysam-developers/pysam/releases/tag/v0.21.0 PR: 275494 Approved by: portmgr (blanket)
* biology/py-pysam: update 0.21.0 → 0.22.0Yuri Victorovich2023-10-062-4/+4
| | | | Reported by: portscout
* 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>
* biology/py-pysam: Update 0.20.0 → 0.21.0Yuri Victorovich2023-06-162-6/+5
| | | | Reported by: portscout
* biology/py-pysam: unbundle biology/htslibRobert Clausecker2023-05-251-2/+6
| | | | | | | | | This fixes the build on armv7 by picking up our custom fixed libhts over the bundled unfixed version. The CFLAGS workaround is now no longer required either. Approved by: yuri (maintainer) Differential Revision: https://reviews.freebsd.org/D40251
* */*: rename CHEESESHOP to PYPI in MASTER_SITESDmitry Marakasov2023-01-111-1/+1
| | | | | | PR: 267994 Differential revision: D37518 Approved by: bapt
* biology/py-pysam: Update 0.19.1 -> 0.20.0Yuri Victorovich2022-11-102-11/+12
| | | | Reported by: portscout
* 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/py-pysam: Remove BROKEN linesYuri Victorovich2022-07-191-4/+0
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* biology/py-pysam: Fix on aarch64, riscv6 by backporting of symbols failure fixYuri Victorovich2022-07-192-1/+7
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* biology/py-pysam: Correct BROKEN line; Add commentYuri Victorovich2022-07-191-1/+2
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* biology/py-pysam: Broken on arm64 and riscv64Yuri Victorovich2022-07-151-0/+3
| | | | Reported by: fallout
* biology/py-pysam: Update 0.19.0 -> 0.19.1Yuri Victorovich2022-05-312-4/+4
| | | | Reported by: portscout
* biology/py-pysam: Update 0.18.0 -> 0.19.0Yuri Victorovich2022-04-272-4/+4
| | | | Reported by: portscout
* biology/py-pysam: Update 0.16.0.1 -> 0.18.0Wen Heping2021-12-202-4/+4
| | | | PR: 260556
* biology/py-pysam: limit supported python versionsDmitry Marakasov2021-11-011-1/+1
| | | | | | | pysam/libchtslib.c:1269:15: error: no member named 'use_tracing' in 'struct _ts' tstate->use_tracing = 0; Approved by: portmgr blanket
* 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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* Drop python 2.7 support from a few portsAntoine Brodin2020-12-281-1/+1
| | | | | | | With hat: portmgr Notes: svn path=/head/; revision=559531
* biology/py-pysam: Update 0.16.0 -> 0.16.0.1Yuri Victorovich2020-11-152-4/+4
| | | | Notes: svn path=/head/; revision=555425
* biology/py-pysam: Update 0.15.4 -> 0.16.0Yuri Victorovich2020-06-092-4/+4
| | | | | | | Reported by: potscout Notes: svn path=/head/; revision=538275
* biology/py-pysam: Update 0.15.3 -> 0.15.4Yuri Victorovich2020-01-232-4/+4
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=523862
* biology/py-pysam: Update 0.15.2 -> 0.15.3Yuri Victorovich2019-08-312-4/+4
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=510398
* biology/py-pysam: Update 0.15.1 -> 0.15.2Yuri Victorovich2019-01-262-4/+4
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=491232
* biology/py-pysam: Update 0.15.0 -> 0.15.1Yuri Victorovich2018-09-172-4/+4
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=479938
* biology/py-pysam: Update 0.14.1 -> 0.15.0Yuri Victorovich2018-07-303-8/+5
| | | | | | | | | | | Port changes: * Remove stripping: done by the project now * Update WWW Reported by: portscout Notes: svn path=/head/; revision=475906
* Switch all pypi.python.org WWWs to a new PyPi home pypi.org whereDmitry Marakasov2018-04-251-1/+1
| | | | | | | | | | they now redirect to anyway. All new urls checked to return 200, I've fixed a couple of them in the process. Approved by: portmgr blanket, mat Notes: svn path=/head/; revision=468282
* biology/py-pysam: Update to 0.14.1Yuri Victorovich2018-03-212-5/+5
| | | | | | | | | Also silenced STRIP_CMD. Reported by: portscout Notes: svn path=/head/; revision=465157
* biology/py-pysam: Update to 0.14Yuri Victorovich2018-02-102-4/+4
| | | | | | | | | | | Changelog: https://github.com/pysam-developers/pysam/releases/tag/v0.14 Reported by: portscout Approved by: tcberner (mentor, implicit) Notes: svn path=/head/; revision=461449
* Convert Python ports to FLAVORS.Mathieu Arnold2017-11-301-4/+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
* biology/py-pysam: Update to 0.13Yuri Victorovich2017-11-052-6/+8
| | | | | | | | Approved by: tcberner (mentor) Differential Revision: https://reviews.freebsd.org/D12967 Notes: svn path=/head/; revision=453556
* Update biology/py-pysam to 0.12.0.1Tobias C. Berner2017-10-262-4/+4
| | | | | | | | PR: 223254 Submitted by: Yuri Victorovich <yuri@rawbw.com> (maintainer) Notes: svn path=/head/; revision=452904
* - Update to 0.11.2.2Wen Heping2017-06-102-4/+4
| | | | | | | | PR: 219892 Submitted by: yuri@rawbw.com(maintainer) Notes: svn path=/head/; revision=443056
* - Update to 0.11.2.1Jochen Neumeister2017-05-232-5/+5
| | | | | | | | | | PR: 219396 Submitted by: Yuri Victorovich (Maintainer) <yuri@rawbw.com> Approved by: rene (mentor) Differential Revision: https://reviews.freebsd.org/D10856 Notes: svn path=/head/; revision=441555
* - Update to 0.11.1Martin Wilke2017-05-072-4/+4
| | | | | | | | PR: 219122 Submitted by: maintainer Notes: svn path=/head/; revision=440347
* pysam is a lightweight wrapper of the htslib C-API and provides facilities toMartin Wilke2017-05-064-0/+46
read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ files as well as access to the command line functionality of the samtools and bcftools packages. The module supports compression and random access through indexing. This module provides a low-level wrapper around the htslib C-API as using cython and a high-level API for convenient access to the data within standard genomic file formats. WWW: https://pypi.python.org/pypi/pysam PR: 218745 Submitted by: Yuri Victorovich <yuri@rawbw.com> Notes: svn path=/head/; revision=440231
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