[gentoo-commits] proj/sci:master commit in: sci-biology/pysam/

2021-01-02 Thread Horea Christian 
commit: eeef69fea4f72eb2bd4400a11d80f3a5db0a3d92
Author: Andrew Ammerlaan  riseup  net>
AuthorDate: Sat Jan  2 13:09:32 2021 +
Commit: Horea Christian  gmail  com>
CommitDate: Sun Jan  3 06:25:30 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=eeef69fe

sci-biology/pysam: remove, package is in ::gentoo

Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan  riseup.net>
Signed-off-by: Horea Christian  chymera.eu>

 sci-biology/pysam/metadata.xml| 12 -
 sci-biology/pysam/pysam-0.15.3.ebuild | 46 ---
 2 files changed, 58 deletions(-)

diff --git a/sci-biology/pysam/metadata.xml b/sci-biology/pysam/metadata.xml
deleted file mode 100644
index 6182254bd..0
--- a/sci-biology/pysam/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd;>
-
-  
-sci-biol...@gentoo.org
-Gentoo Biology Project
-  
-  
-pysam
-pysam-developers/pysam
-  
-

diff --git a/sci-biology/pysam/pysam-0.15.3.ebuild 
b/sci-biology/pysam/pysam-0.15.3.ebuild
deleted file mode 100644
index 4224df0be..0
--- a/sci-biology/pysam/pysam-0.15.3.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_6 )
-
-inherit distutils-r1
-
-DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping 
format"
-HOMEPAGE="
-   https://github.com/pysam-developers/pysam
-   https://pypi.org/project/pysam/;
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS=""
-
-# current code wraps 3rd-party code from htslib-1.9, samtools-1.9 and 
bcftools-1.9
-RDEPEND="=sci-libs/htslib-1.9*:="
-DEPEND="${RDEPEND}
-   dev-python/cython[${PYTHON_USEDEP}]
-   dev-python/setuptools[${PYTHON_USEDEP}]"
-
-python_prepare_all() {
-   # unbundle htslib
-   export HTSLIB_MODE="external"
-   export HTSLIB_INCLUDE_DIR="${EPREFIX}"/usr/include
-   export HTSLIB_LIBRARY_DIR="${EPREFIX}"/usr/$(get_libdir)
-   rm -r htslib || die
-
-   # prevent setup.py from adding RPATHs
-   sed -e "/ext\.extra_link_args += \['-Wl,-rpath,\$ORIGIN'\]/d" \
-   -i cy_build.py || die
-   sed -e '/runtime_library_dirs=htslib_library_dirs/d' \
-   -i setup.py || die
-
-   distutils-r1_python_prepare_all
-}
-
-src_compile() {
-   # TODO
-   # empty compile, as the build system runs the whole build again in 
install
-   :
-}

[gentoo-commits] proj/sci:master commit in: sci-biology/pysam/, sci-biology/pysamstats/

2020-01-10 Thread Martin Mokrejs 
commit: b1ad15e7a10105fb9f0905ea5aac0835a62b46f3
Author: Martin Mokrejs  gmail  com>
AuthorDate: Fri Jan 10 16:32:20 2020 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Fri Jan 10 16:52:47 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=b1ad15e7

sci-biology/pysamstats: version bump
sci-biology/pysam: version bump

I am not sure if the path pysam-0.12-fix-buildsystem.patch is still
needed or not. Nevertheless, the modules do not import properly into
python so the ebuild needs more work.

Package-Manager: Portage-2.3.84, Repoman-2.3.20
Signed-off-by: Martin Mokrejs  gmail.com>

 sci-biology/pysam/metadata.xml | 12 ++
 sci-biology/pysam/pysam-0.15.3.ebuild  | 46 ++
 ...stats-0.24.2.ebuild => pysamstats-1.1.2.ebuild} |  9 +++--
 3 files changed, 64 insertions(+), 3 deletions(-)

diff --git a/sci-biology/pysam/metadata.xml b/sci-biology/pysam/metadata.xml
new file mode 100644
index 0..6182254bd
--- /dev/null
+++ b/sci-biology/pysam/metadata.xml
@@ -0,0 +1,12 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+  
+sci-biol...@gentoo.org
+Gentoo Biology Project
+  
+  
+pysam
+pysam-developers/pysam
+  
+

diff --git a/sci-biology/pysam/pysam-0.15.3.ebuild 
b/sci-biology/pysam/pysam-0.15.3.ebuild
new file mode 100644
index 0..4224df0be
--- /dev/null
+++ b/sci-biology/pysam/pysam-0.15.3.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 python3_6 )
+
+inherit distutils-r1
+
+DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping 
format"
+HOMEPAGE="
+   https://github.com/pysam-developers/pysam
+   https://pypi.org/project/pysam/;
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS=""
+
+# current code wraps 3rd-party code from htslib-1.9, samtools-1.9 and 
bcftools-1.9
+RDEPEND="=sci-libs/htslib-1.9*:="
+DEPEND="${RDEPEND}
+   dev-python/cython[${PYTHON_USEDEP}]
+   dev-python/setuptools[${PYTHON_USEDEP}]"
+
+python_prepare_all() {
+   # unbundle htslib
+   export HTSLIB_MODE="external"
+   export HTSLIB_INCLUDE_DIR="${EPREFIX}"/usr/include
+   export HTSLIB_LIBRARY_DIR="${EPREFIX}"/usr/$(get_libdir)
+   rm -r htslib || die
+
+   # prevent setup.py from adding RPATHs
+   sed -e "/ext\.extra_link_args += \['-Wl,-rpath,\$ORIGIN'\]/d" \
+   -i cy_build.py || die
+   sed -e '/runtime_library_dirs=htslib_library_dirs/d' \
+   -i setup.py || die
+
+   distutils-r1_python_prepare_all
+}
+
+src_compile() {
+   # TODO
+   # empty compile, as the build system runs the whole build again in 
install
+   :
+}

diff --git a/sci-biology/pysamstats/pysamstats-0.24.2.ebuild 
b/sci-biology/pysamstats/pysamstats-1.1.2.ebuild
similarity index 77%
rename from sci-biology/pysamstats/pysamstats-0.24.2.ebuild
rename to sci-biology/pysamstats/pysamstats-1.1.2.ebuild
index d6e1350a4..06bb7c69b 100644
--- a/sci-biology/pysamstats/pysamstats-0.24.2.ebuild
+++ b/sci-biology/pysamstats/pysamstats-1.1.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -17,6 +17,9 @@ SLOT="0"
 KEYWORDS="" # needs working pysam, see bug #645060
 IUSE=""
 
-DEPEND="dev-python/cython
-   >=sci-biology/pysam-0.8.4"
+DEPEND="
+   dev-python/cython
+   dev-python/numpy
+   dev-python/pytables
+   >=sci-biology/pysam-0.15.1"
 RDEPEND="${DEPEND}"

[gentoo-commits] proj/sci:master commit in: sci-biology/pysam/, sci-biology/pysam/files/

2017-09-02 Thread David Seifert 
commit: 02fbd9cb160ec37e7a85eb4349717237e120aeeb
Author: David Seifert  gentoo  org>
AuthorDate: Sat Sep  2 12:45:42 2017 +
Commit: David Seifert  gentoo  org>
CommitDate: Sat Sep  2 12:45:42 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=02fbd9cb

sci-biology/pysam: Remove old

 .../pysam/files/pysam-0.8.3-cython-0.23.patch  | 32 --
 sci-biology/pysam/metadata.xml |  8 --
 sci-biology/pysam/pysam-0.7.5.ebuild   | 25 -
 3 files changed, 65 deletions(-)

diff --git a/sci-biology/pysam/files/pysam-0.8.3-cython-0.23.patch 
b/sci-biology/pysam/files/pysam-0.8.3-cython-0.23.patch
deleted file mode 100644
index d14fec5a8..0
--- a/sci-biology/pysam/files/pysam-0.8.3-cython-0.23.patch
+++ /dev/null
@@ -1,32 +0,0 @@
-Patch for building with Cython 0.23
-See also
-https://github.com/pysam-developers/pysam/issues/164
-
 pysam-0.8.3/pysam/chtslib.pxd
-+++ pysam-0.8.3/pysam/chtslib.pxd
-@@ -363,7 +363,7 @@
- hFILE   *hfile
- void*voidp
- 
--ctypedef enum htsFormatCategory:
-+cdef enum htsFormatCategory:
- unknown_category
- sequence_data# Sequence data -- SAM, BAM, CRAM, etc
- variant_data # Variant calling data -- VCF, BCF, etc
-@@ -371,14 +371,14 @@
- region_list  # Coordinate intervals or regions -- BED, etc
- category_maximum
- 
--ctypedef enum htsExactFormat:
-+cdef enum htsExactFormat:
- unknown_format
- binary_format
- text_format
- sam, bam, bai, cram, crai, vcf, bcf, csi, gzi, tbi, bed
- format_maximum
- 
--ctypedef enum htsCompression:
-+cdef enum htsCompression:
- no_compression, gzip, bgzf, custom
- compression_maximum
- 

diff --git a/sci-biology/pysam/metadata.xml b/sci-biology/pysam/metadata.xml
deleted file mode 100644
index 3ff9cd0b0..0
--- a/sci-biology/pysam/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-
-http://www.gentoo.org/dtd/metadata.dtd;>
-
-  
-sci-biol...@gentoo.org
-Gentoo Biology Project
-  
-

diff --git a/sci-biology/pysam/pysam-0.7.5.ebuild 
b/sci-biology/pysam/pysam-0.7.5.ebuild
deleted file mode 100644
index ef596c29d..0
--- a/sci-biology/pysam/pysam-0.7.5.ebuild
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping 
format"
-HOMEPAGE="http://code.google.com/p/pysam http://pypi.python.org/pypi/pysam;
-SRC_URI="http://${PN}.googlecode.com/files/${P}.tar.gz;
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="dev-python/setuptools[${PYTHON_USEDEP}]
-   <=sci-biology/samtools-0.1.19-r2[${PYTHON_USEDEP}]"
-
-python_compile() {
-   python_is_python3 || local -x CFLAGS="${CFLAGS} -fno-strict-aliasing"
-   distutils-r1_python_compile
-}

[gentoo-commits] proj/sci:master commit in: sci-biology/pysam/

2016-04-13 Thread Marius Brehler 
commit: b3b06688c38bc3f28d68be75e5e30ff1adcb1386
Author: David Seifert  gentoo  org>
AuthorDate: Sat Apr  9 22:14:19 2016 +
Commit: Marius Brehler  linux  sungazer  de>
CommitDate: Sat Apr  9 22:14:19 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=b3b06688

sci-biology/pysam: Remove old, latest 0.9.0 in main tree

Package-Manager: portage-2.2.28

 sci-biology/pysam/pysam-0.6-r2.ebuild | 26 --
 sci-biology/pysam/pysam-0.8.3.ebuild  | 29 -
 sci-biology/pysam/pysam-0.8.4.ebuild  | 27 ---
 3 files changed, 82 deletions(-)

diff --git a/sci-biology/pysam/pysam-0.6-r2.ebuild 
b/sci-biology/pysam/pysam-0.6-r2.ebuild
deleted file mode 100644
index 01f86da..000
--- a/sci-biology/pysam/pysam-0.6-r2.ebuild
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="5"
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping 
format"
-HOMEPAGE="http://code.google.com/p/pysam http://pypi.python.org/pypi/pysam;
-SRC_URI="http://${PN}.googlecode.com/files/${P}.tar.gz;
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="dev-python/setuptools[${PYTHON_USEDEP}]
-   <=sci-biology/samtools-0.1.18[${PYTHON_USEDEP}]"
-
-python_compile() {
-   python_is_python3 || local -x CFLAGS="${CFLAGS} -fno-strict-aliasing"
-   distutils-r1_python_compile
-}

diff --git a/sci-biology/pysam/pysam-0.8.3.ebuild 
b/sci-biology/pysam/pysam-0.8.3.ebuild
deleted file mode 100644
index a08855f..000
--- a/sci-biology/pysam/pysam-0.8.3.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="5"
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping 
format"
-HOMEPAGE="https://github.com/pysam-developers/pysam 
http://pypi.python.org/pypi/pysam;
-SRC_URI="https://github.com/pysam-developers/${PN}/archive/v${PV}.tar.gz;
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="dev-python/setuptools[${PYTHON_USEDEP}]
-   >=sci-biology/samtools-1.2[${PYTHON_USEDEP}]
-   >=sci-libs/htslib-1.2.1"
-
-PATCHES=( "${FILESDIR}/${P}-cython-0.23.patch" )
-
-python_compile() {
-   python_is_python3 || local -x CFLAGS="${CFLAGS} -fno-strict-aliasing"
-   distutils-r1_python_compile
-}

diff --git a/sci-biology/pysam/pysam-0.8.4.ebuild 
b/sci-biology/pysam/pysam-0.8.4.ebuild
deleted file mode 100644
index 2b4d3d9..000
--- a/sci-biology/pysam/pysam-0.8.4.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="5"
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping 
format"
-HOMEPAGE="https://github.com/pysam-developers/pysam 
http://pypi.python.org/pypi/pysam;
-SRC_URI="https://github.com/pysam-developers/${PN}/archive/v${PV}.tar.gz -> 
${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="dev-python/setuptools[${PYTHON_USEDEP}]
-   >=sci-biology/samtools-1.2[${PYTHON_USEDEP}]
-   >=sci-libs/htslib-1.2.1"
-
-python_compile() {
-   python_is_python3 || local -x CFLAGS="${CFLAGS} -fno-strict-aliasing"
-   distutils-r1_python_compile
-}

[gentoo-commits] proj/sci:master commit in: sci-biology/pysam/, sci-biology/inGAP-bin/, sci-biology/kallisto/, ...

2016-01-25 Thread Justin Lecher 
commit: 26e6def0b3eb2ebcf04bf0d1a43f84db0a5b1240
Author: Justin Lecher  gentoo  org>
AuthorDate: Mon Jan 25 08:49:16 2016 +
Commit: Justin Lecher  gentoo  org>
CommitDate: Mon Jan 25 08:49:16 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=26e6def0

matadata.xml: Pre Cleanup

Signed-off-by: Justin Lecher  gentoo.org>

 app-benchmarks/numbench/metadata.xml  |  2 +-
 app-doc/root-docs/metadata.xml|  2 +-
 dev-lang/berkeley_upc/metadata.xml|  1 -
 dev-lang/berkeley_upc_translator/metadata.xml |  1 -
 dev-lang/pgi/metadata.xml |  8 
 dev-libs/mxml/metadata.xml|  2 +-
 dev-ml/lacaml/metadata.xml|  2 +-
 dev-perl/BTLib/metadata.xml   |  2 +-
 dev-python/ffc/metadata.xml   |  2 +-
 dev-python/fiat/metadata.xml  |  2 +-
 dev-python/future/metadata.xml|  2 +-
 dev-python/instant/metadata.xml   |  2 +-
 dev-python/metakernel/metadata.xml|  2 +-
 dev-python/metakernel_bash/metadata.xml   |  2 +-
 dev-python/metakernel_python/metadata.xml |  2 +-
 dev-python/pythonqt/metadata.xml  |  2 +-
 dev-python/ufl/metadata.xml   |  2 +-
 dev-tcltk/img_rotate/metadata.xml |  2 +-
 dev-util/VampirTrace/metadata.xml |  2 +-
 media-gfx/brlcad/metadata.xml |  2 +-
 sci-astronomy/mosstack/metadata.xml   |  2 +-
 sci-astronomy/sextractor/metadata.xml |  2 +-
 sci-biology/Atlas2/metadata.xml   |  2 +-
 sci-biology/BBmap/metadata.xml|  2 +-
 sci-biology/BamView/metadata.xml  |  2 +-
 sci-biology/CONTIGuator/metadata.xml  |  2 +-
 sci-biology/EBARDenovo/metadata.xml   |  2 +-
 sci-biology/FLASH/metadata.xml|  2 +-
 sci-biology/IMAGE/metadata.xml|  2 +-
 sci-biology/MeV/metadata.xml  |  2 +-
 sci-biology/NGSTools/metadata.xml |  2 +-
 sci-biology/RSeQC/metadata.xml|  2 +-
 sci-biology/Ray/metadata.xml  |  2 +-
 sci-biology/STAR/metadata.xml |  2 +-
 sci-biology/SolexaQA/metadata.xml |  2 +-
 sci-biology/TransDecoder/metadata.xml |  2 +-
 sci-biology/VarScan/metadata.xml  |  2 +-
 sci-biology/abacas/metadata.xml   |  2 +-
 sci-biology/amos/metadata.xml |  2 +-
 sci-biology/bambus/metadata.xml   |  2 +-
 sci-biology/bru2nii/metadata.xml  |  3 +--
 sci-biology/clview/metadata.xml   |  2 +-
 sci-biology/conifer/metadata.xml  |  2 +-
 sci-biology/cortex_var/metadata.xml   |  2 +-
 sci-biology/estscan/metadata.xml  |  2 +-
 sci-biology/flexbar/metadata.xml  |  2 +-
 sci-biology/fsa/metadata.xml  |  2 +-
 sci-biology/gap2caf/metadata.xml  |  2 +-
 sci-biology/gbrowse/metadata.xml  |  2 +-
 sci-biology/genomeview-bin/metadata.xml   |  2 +-
 sci-biology/glean/metadata.xml|  2 +-
 sci-biology/inGAP-bin/metadata.xml|  2 +-
 sci-biology/jtreeview/metadata.xml|  2 +-
 sci-biology/kallisto/metadata.xml |  2 +-
 sci-biology/lucy/metadata.xml |  2 +-
 sci-biology/manatee-igs/metadata.xml  |  2 +-
 sci-biology/manatee-jcvi/metadata.xml |  2 +-
 sci-biology/mne-python/metadata.xml   |  2 +-
 sci-biology/mricron/metadata.xml  |  3 +--
 sci-biology/parafly/metadata.xml  |  2 +-
 sci-biology/pb-honey/metadata.xml |  2 +-
 sci-biology/pb-jelly/metadata.xml |  2 +-
 sci-biology/psychopy/metadata.xml |  2 +-
 sci-biology/pysam/metadata.xml|  2 +-
 sci-biology/pysurfer/metadata.xml |  2 +-
 sci-biology/quast/metadata.xml|  2 +-
 sci-biology/samstat/metadata.xml  |  2 +-
 sci-biology/scaffold_builder/metadata.xml |  2 +-
 sci-biology/skewer-bin/metadata.xml   |  2 +-
 sci-biology/staden/metadata.xml   |  2 +-
 sci-biology/subread/metadata.xml  |  2 +-
 sci-biology/swissknife/metadata.xml   |  2 +-
 sci-biology/tgicl/metadata.xml|  2 +-
 sci-biology/trowel/metadata.xml   |  2 +-
 sci-biology/wgs-assembler/metadata.xml|  2 +-
 sci-chemistry/NMRdyn/metadata.xml |  2 +-
 sci-chemistry/pesto/metadata.xml  |  2 +-
 sci-chemistry/rosetta-tools/metadata.xml  |  2 +-
 sci-libs/acml/metadata.xml| 10 +-
 sci-libs/elmer-eio/metadata.xml   |  2 +-
 sci-libs/elmer-hutiter/metadata.xml   |  2 +-
 sci-libs/matc/metadata.xml|  2 +-
 sci-libs/nibabel/metadata.xml |  2 +-
 sci-libs/nipype/metadata.xml  |  2 +-

[gentoo-commits] proj/sci:master commit in: sci-biology/pysam/

2015-12-03 Thread Justin Lecher 
commit: 94d90ab3b484a298828765dcccac7416741911d2
Author: Ted Tanberry  gmail  com>
AuthorDate: Thu Dec  3 21:59:00 2015 +
Commit: Justin Lecher  gentoo  org>
CommitDate: Thu Dec  3 21:59:00 2015 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=94d90ab3

sci-biology/pysam: version bump to 0.8.4

Package-Manager: portage-2.2.26

 sci-biology/pysam/ChangeLog  |  5 +
 sci-biology/pysam/pysam-0.8.4.ebuild | 27 +++
 2 files changed, 32 insertions(+)

diff --git a/sci-biology/pysam/ChangeLog b/sci-biology/pysam/ChangeLog
index c4c9a54..492a5fc 100644
--- a/sci-biology/pysam/ChangeLog
+++ b/sci-biology/pysam/ChangeLog
@@ -2,6 +2,11 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Id$
 
+*pysam-0.8.4 (03 Dec 2015)
+
+  03 Dec 2015; Ted Tanberry  +pysam-0.8.4.ebuild:
+  sci-biology/pysam: version bump to 0.8.4
+
   04 May 2015; Marius Brehler  pysam-0.7.5.ebuild:
   Fix deps
 

diff --git a/sci-biology/pysam/pysam-0.8.4.ebuild 
b/sci-biology/pysam/pysam-0.8.4.ebuild
new file mode 100644
index 000..2b4d3d9
--- /dev/null
+++ b/sci-biology/pysam/pysam-0.8.4.ebuild
@@ -0,0 +1,27 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="5"
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit distutils-r1
+
+DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping 
format"
+HOMEPAGE="https://github.com/pysam-developers/pysam 
http://pypi.python.org/pypi/pysam;
+SRC_URI="https://github.com/pysam-developers/${PN}/archive/v${PV}.tar.gz -> 
${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND="dev-python/setuptools[${PYTHON_USEDEP}]
+   >=sci-biology/samtools-1.2[${PYTHON_USEDEP}]
+   >=sci-libs/htslib-1.2.1"
+
+python_compile() {
+   python_is_python3 || local -x CFLAGS="${CFLAGS} -fno-strict-aliasing"
+   distutils-r1_python_compile
+}

[gentoo-commits] proj/sci:master commit in: sci-biology/pysam/files/, sci-biology/pysam/

2015-10-10 Thread Justin Lecher 
commit: 0c71d353954ad0e01c6e1595f4e493ad7857f6dc
Author: Ted Tanberry  gmail  com>
AuthorDate: Sat Oct 10 15:12:58 2015 +
Commit: Justin Lecher  gentoo  org>
CommitDate: Sat Oct 10 15:12:58 2015 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=0c71d353

sci-biology/pysam: version bump to 0.8.3

This also includes a fix for building with
Cython 0.23.

 .../pysam/files/pysam-0.8.3-cython-0.23.patch  | 32 ++
 sci-biology/pysam/pysam-0.8.3.ebuild   | 29 
 2 files changed, 61 insertions(+)

diff --git a/sci-biology/pysam/files/pysam-0.8.3-cython-0.23.patch 
b/sci-biology/pysam/files/pysam-0.8.3-cython-0.23.patch
new file mode 100644
index 000..d14fec5
--- /dev/null
+++ b/sci-biology/pysam/files/pysam-0.8.3-cython-0.23.patch
@@ -0,0 +1,32 @@
+Patch for building with Cython 0.23
+See also
+https://github.com/pysam-developers/pysam/issues/164
+
+--- pysam-0.8.3/pysam/chtslib.pxd
 pysam-0.8.3/pysam/chtslib.pxd
+@@ -363,7 +363,7 @@
+ hFILE   *hfile
+ void*voidp
+ 
+-ctypedef enum htsFormatCategory:
++cdef enum htsFormatCategory:
+ unknown_category
+ sequence_data# Sequence data -- SAM, BAM, CRAM, etc
+ variant_data # Variant calling data -- VCF, BCF, etc
+@@ -371,14 +371,14 @@
+ region_list  # Coordinate intervals or regions -- BED, etc
+ category_maximum
+ 
+-ctypedef enum htsExactFormat:
++cdef enum htsExactFormat:
+ unknown_format
+ binary_format
+ text_format
+ sam, bam, bai, cram, crai, vcf, bcf, csi, gzi, tbi, bed
+ format_maximum
+ 
+-ctypedef enum htsCompression:
++cdef enum htsCompression:
+ no_compression, gzip, bgzf, custom
+ compression_maximum
+ 

diff --git a/sci-biology/pysam/pysam-0.8.3.ebuild 
b/sci-biology/pysam/pysam-0.8.3.ebuild
new file mode 100644
index 000..a08855f
--- /dev/null
+++ b/sci-biology/pysam/pysam-0.8.3.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI="5"
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit distutils-r1
+
+DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping 
format"
+HOMEPAGE="https://github.com/pysam-developers/pysam 
http://pypi.python.org/pypi/pysam;
+SRC_URI="https://github.com/pysam-developers/${PN}/archive/v${PV}.tar.gz;
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND="dev-python/setuptools[${PYTHON_USEDEP}]
+   >=sci-biology/samtools-1.2[${PYTHON_USEDEP}]
+   >=sci-libs/htslib-1.2.1"
+
+PATCHES=( "${FILESDIR}/${P}-cython-0.23.patch" )
+
+python_compile() {
+   python_is_python3 || local -x CFLAGS="${CFLAGS} -fno-strict-aliasing"
+   distutils-r1_python_compile
+}

[gentoo-commits] proj/sci:master commit in: sci-biology/pysam/

2015-05-04 Thread Justin Lecher 
commit: 873670a86527262a39f625944c64be11265f7052
Author: Marius Brehler marbre AT linux DOT sungazer DOT de
AuthorDate: Mon May  4 08:17:56 2015 +
Commit: Justin Lecher jlec AT gentoo DOT org
CommitDate: Mon May  4 08:17:56 2015 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=873670a8

Drop keywords; Fix deps

Package-Manager: portage-2.2.18

 sci-biology/pysam/ChangeLog   | 6 ++
 sci-biology/pysam/pysam-0.6-r2.ebuild | 2 +-
 sci-biology/pysam/pysam-0.7.5.ebuild  | 4 ++--
 3 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/sci-biology/pysam/ChangeLog b/sci-biology/pysam/ChangeLog
index 2fbcbbc..e48ec44 100644
--- a/sci-biology/pysam/ChangeLog
+++ b/sci-biology/pysam/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  04 May 2015; Marius Brehler mar...@linux.sungazer.de pysam-0.7.5.ebuild:
+  Fix deps
+
+  04 May 2015; Marius Brehler mar...@linux.sungazer.de pysam-0.6-r2.ebuild:
+  Drop keywords due to broken deps
+
   02 May 2015; Martin Mokrejs mmokr...@fold.natur.cuni.cz
   pysam-0.6-r2.ebuild, pysam-0.7.5.ebuild:
   added PYTHON_USEDEP

diff --git a/sci-biology/pysam/pysam-0.6-r2.ebuild 
b/sci-biology/pysam/pysam-0.6-r2.ebuild
index 5225a62..ee86039 100644
--- a/sci-biology/pysam/pysam-0.6-r2.ebuild
+++ b/sci-biology/pysam/pysam-0.6-r2.ebuild
@@ -14,7 +14,7 @@ SRC_URI=http://${PN}.googlecode.com/files/${P}.tar.gz;
 
 LICENSE=MIT
 SLOT=0
-KEYWORDS=~amd64 ~x86
+KEYWORDS=
 IUSE=
 
 DEPEND=dev-python/setuptools[${PYTHON_USEDEP}]

diff --git a/sci-biology/pysam/pysam-0.7.5.ebuild 
b/sci-biology/pysam/pysam-0.7.5.ebuild
index 42e24ca..c516382 100644
--- a/sci-biology/pysam/pysam-0.7.5.ebuild
+++ b/sci-biology/pysam/pysam-0.7.5.ebuild
@@ -4,7 +4,7 @@
 
 EAPI=5
 
-PYTHON_COMPAT=( python{2_7,3_3,3_4})
+PYTHON_COMPAT=( python2_7 )
 
 inherit distutils-r1
 
@@ -18,7 +18,7 @@ KEYWORDS=~amd64 ~x86
 IUSE=
 
 DEPEND=dev-python/setuptools[${PYTHON_USEDEP}]
-   =sci-biology/samtools-0.1.19[${PYTHON_USEDEP}]
+   =sci-biology/samtools-0.1.19-r2[${PYTHON_USEDEP}]
 
 python_compile() {
python_is_python3 || local -x CFLAGS=${CFLAGS} -fno-strict-aliasing

[gentoo-commits] proj/sci:master commit in: sci-biology/pysam/

2015-05-02 Thread Martin Mokrejs 
commit: 3ea57834601daea6b91432738e088d0a18428d7b
Author: Martin Mokrejš mmokrejs AT fold DOT natur DOT cuni DOT cz
AuthorDate: Sat May  2 16:28:41 2015 +
Commit: Martin Mokrejs mmokrejs AT fold DOT natur DOT cuni DOT cz
CommitDate: Sat May  2 16:28:41 2015 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=3ea57834

added PYTHON_USEDEP

 sci-biology/pysam/ChangeLog   | 4 
 sci-biology/pysam/pysam-0.6-r2.ebuild | 2 +-
 sci-biology/pysam/pysam-0.7.5.ebuild  | 2 +-
 3 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/sci-biology/pysam/ChangeLog b/sci-biology/pysam/ChangeLog
index 4b24154..2fbcbbc 100644
--- a/sci-biology/pysam/ChangeLog
+++ b/sci-biology/pysam/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  02 May 2015; Martin Mokrejs mmokr...@fold.natur.cuni.cz
+  pysam-0.6-r2.ebuild, pysam-0.7.5.ebuild:
+  added PYTHON_USEDEP
+
 *pysam-0.6-r2 (30 Apr 2015)
 *pysam-0.7.5 (30 Apr 2015)
 

diff --git a/sci-biology/pysam/pysam-0.6-r2.ebuild 
b/sci-biology/pysam/pysam-0.6-r2.ebuild
index d972ba1..5225a62 100644
--- a/sci-biology/pysam/pysam-0.6-r2.ebuild
+++ b/sci-biology/pysam/pysam-0.6-r2.ebuild
@@ -18,7 +18,7 @@ KEYWORDS=~amd64 ~x86
 IUSE=
 
 DEPEND=dev-python/setuptools[${PYTHON_USEDEP}]
-   =sci-biology/samtools-0.1.18
+   =sci-biology/samtools-0.1.18[${PYTHON_USEDEP}]
 
 python_compile() {
python_is_python3 || local -x CFLAGS=${CFLAGS} -fno-strict-aliasing

diff --git a/sci-biology/pysam/pysam-0.7.5.ebuild 
b/sci-biology/pysam/pysam-0.7.5.ebuild
index 888734b..42e24ca 100644
--- a/sci-biology/pysam/pysam-0.7.5.ebuild
+++ b/sci-biology/pysam/pysam-0.7.5.ebuild
@@ -18,7 +18,7 @@ KEYWORDS=~amd64 ~x86
 IUSE=
 
 DEPEND=dev-python/setuptools[${PYTHON_USEDEP}]
-   =sci-biology/samtools-0.1.19
+   =sci-biology/samtools-0.1.19[${PYTHON_USEDEP}]
 
 python_compile() {
python_is_python3 || local -x CFLAGS=${CFLAGS} -fno-strict-aliasing

[gentoo-commits] proj/sci:master commit in: sci-biology/pysam/

2015-04-30 Thread Martin Mokrejs 
commit: 26603b1f757f06f0c7e234390eecd3f5ea6ddfbd
Author: Martin Mokrejš mmokrejs AT fold DOT natur DOT cuni DOT cz
AuthorDate: Thu Apr 30 20:14:31 2015 +
Commit: Martin Mokrejs mmokrejs AT fold DOT natur DOT cuni DOT cz
CommitDate: Thu Apr 30 20:14:31 2015 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=26603b1f

sci-biology/pysam: version bump; noted samtools dependencies as mentioned in 
download page accessible from https://code.google.com/p/pysam/downloads/list ; 
also added PYTHON_COMPAT for python3

Package-Manager: portage-2.2.18

 sci-biology/pysam/ChangeLog   | 12 
 sci-biology/pysam/metadata.xml|  8 
 sci-biology/pysam/pysam-0.6-r2.ebuild | 26 ++
 sci-biology/pysam/pysam-0.7.5.ebuild  | 26 ++
 4 files changed, 72 insertions(+)

diff --git a/sci-biology/pysam/ChangeLog b/sci-biology/pysam/ChangeLog
new file mode 100644
index 000..4b24154
--- /dev/null
+++ b/sci-biology/pysam/ChangeLog
@@ -0,0 +1,12 @@
+# ChangeLog for sci-biology/pysam
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*pysam-0.6-r2 (30 Apr 2015)
+*pysam-0.7.5 (30 Apr 2015)
+
+  30 Apr 2015; Martin Mokrejs mmokr...@fold.natur.cuni.cz +metadata.xml,
+  +pysam-0.6-r2.ebuild, +pysam-0.7.5.ebuild:
+  sci-biology/pysam: version bump; noted samtools dependencies as mentioned in
+  download page accessible from https://code.google.com/p/pysam/downloads/list 
;
+  also added PYTHON_COMPAT for python3

diff --git a/sci-biology/pysam/metadata.xml b/sci-biology/pysam/metadata.xml
new file mode 100644
index 000..49afc3c
--- /dev/null
+++ b/sci-biology/pysam/metadata.xml
@@ -0,0 +1,8 @@
+?xml version=1.0 encoding=UTF-8?
+!DOCTYPE pkgmetadata SYSTEM http://www.gentoo.org/dtd/metadata.dtd;
+pkgmetadata
+  herdsci-biology/herd
+  upstream
+remote-id type=google-codepysam/remote-id
+  /upstream
+/pkgmetadata

diff --git a/sci-biology/pysam/pysam-0.6-r2.ebuild 
b/sci-biology/pysam/pysam-0.6-r2.ebuild
new file mode 100644
index 000..d972ba1
--- /dev/null
+++ b/sci-biology/pysam/pysam-0.6-r2.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/pysam/pysam-0.6-r1.ebuild,v 1.2 
2015/04/13 06:22:56 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit distutils-r1
+
+DESCRIPTION=Python interface for the SAM/BAM sequence alignment and mapping 
format
+HOMEPAGE=http://code.google.com/p/pysam http://pypi.python.org/pypi/pysam;
+SRC_URI=http://${PN}.googlecode.com/files/${P}.tar.gz;
+
+LICENSE=MIT
+SLOT=0
+KEYWORDS=~amd64 ~x86
+IUSE=
+
+DEPEND=dev-python/setuptools[${PYTHON_USEDEP}]
+   =sci-biology/samtools-0.1.18
+
+python_compile() {
+   python_is_python3 || local -x CFLAGS=${CFLAGS} -fno-strict-aliasing
+   distutils-r1_python_compile
+}

diff --git a/sci-biology/pysam/pysam-0.7.5.ebuild 
b/sci-biology/pysam/pysam-0.7.5.ebuild
new file mode 100644
index 000..888734b
--- /dev/null
+++ b/sci-biology/pysam/pysam-0.7.5.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/pysam/pysam-0.6-r1.ebuild,v 1.2 
2015/04/13 06:22:56 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_7,3_3,3_4})
+
+inherit distutils-r1
+
+DESCRIPTION=Python interface for the SAM/BAM sequence alignment and mapping 
format
+HOMEPAGE=http://code.google.com/p/pysam http://pypi.python.org/pypi/pysam;
+SRC_URI=http://${PN}.googlecode.com/files/${P}.tar.gz;
+
+LICENSE=MIT
+SLOT=0
+KEYWORDS=~amd64 ~x86
+IUSE=
+
+DEPEND=dev-python/setuptools[${PYTHON_USEDEP}]
+   =sci-biology/samtools-0.1.19
+
+python_compile() {
+   python_is_python3 || local -x CFLAGS=${CFLAGS} -fno-strict-aliasing
+   distutils-r1_python_compile
+}