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

2016-07-23 Thread Martin Mokrejs 
commit: f301a33fa321175c12de267ecfbf4d1b727be3f0
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Sat Jul 23 07:25:08 2016 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Sat Jul 23 07:25:08 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f301a33f

sci-biology/biopython: version bump with one minor upstream patch

Package-Manager: portage-2.2.28

 sci-biology/biopython/biopython-1.67-r1.ebuild | 60 +++
 .../biopython/files/biopython-1.67-pull-884.patch  | 87 ++
 sci-biology/biopython/metadata.xml |  8 ++
 3 files changed, 155 insertions(+)

diff --git a/sci-biology/biopython/biopython-1.67-r1.ebuild 
b/sci-biology/biopython/biopython-1.67-r1.ebuild
new file mode 100644
index 000..197e265
--- /dev/null
+++ b/sci-biology/biopython/biopython-1.67-r1.ebuild
@@ -0,0 +1,60 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 python3_{3,4,5} pypy )
+
+inherit distutils-r1 eutils
+
+DESCRIPTION="Python modules for computational molecular biology"
+HOMEPAGE="http://www.biopython.org/ https://pypi.python.org/pypi/biopython/;
+SRC_URI="http://www.biopython.org/DIST/${P}.tar.gz;
+
+LICENSE="HPND"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="
+   dev-python/matplotlib[$(python_gen_usedep 'python*')]
+   dev-python/networkx[$(python_gen_usedep 'python*')]
+   dev-python/numpy[$(python_gen_usedep 'python*')]
+   dev-python/rdflib[$(python_gen_usedep 'python*')]
+   dev-python/pygraphviz[$(python_gen_usedep 'python2*')]
+   dev-python/reportlab[$(python_gen_usedep 'python*')]
+   media-gfx/pydot[$(python_gen_usedep 'python2*')]
+   "
+DEPEND="${RDEPEND}
+   sys-devel/flex"
+
+DOCS=( CONTRIB DEPRECATED NEWS README Doc/. )
+
+src_prepare(){
+   epatch "${FILESDIR}"/biopython-1.67-pull-884.patch
+}
+
+python_test() {
+   distutils_install_for_testing
+   cp -r "${S}"/{Doc,Tests} "${TEST_DIR}"/lib/ || die
+   cd "${TEST_DIR}"/lib/Tests || die
+   rm ./test_BioSQL_psycopg2.py ./test_BioSQL_MySQLdb.py 
./test_BioSQL_mysql_connector.py || die
+   ${PYTHON} run_tests.py --offline --verbose || die
+}
+
+python_install_all() {
+   distutils-r1_python_install_all
+
+   dodir /usr/share/${PN}
+   cp -r --preserve=mode Scripts Tests "${ED}"/usr/share/${PN} || die
+}
+
+pkg_postinst() {
+   elog "For database support you need to install:"
+   optfeature "MySQL" dev-python/mysql-python
+   optfeature "PostGreSQL" dev-python/psycopg
+   echo
+   elog "Some applications need extra packages:"
+   optfeature "EMBOSS (The European Molecular Biology Open Software 
Suite)" sci-biology/emboss
+}

diff --git a/sci-biology/biopython/files/biopython-1.67-pull-884.patch 
b/sci-biology/biopython/files/biopython-1.67-pull-884.patch
new file mode 100644
index 000..f2a2537
--- /dev/null
+++ b/sci-biology/biopython/files/biopython-1.67-pull-884.patch
@@ -0,0 +1,87 @@
+--- Bio/SeqRecord.py.old   2016-06-08 15:27:00.0 +0200
 Bio/SeqRecord.py   2016-07-22 17:48:19.620712535 +0200
+@@ -292,19 +292,28 @@
+ >>> sub_record.letter_annotations = {}
+ >>> sub_record.letter_annotations
+ {}
++
++Note that if replacing the record's sequence with a sequence of a
++different length you must first clear the letter_annotations dict.
+ """)
+ 
+ def _set_seq(self, value):
+ # TODO - Add a deprecation warning that the seq should be write only?
+ if self._per_letter_annotations:
+-# TODO - Make this a warning? Silently empty the dictionary?
+-raise ValueError("You must empty the letter annotations first!")
+-self._seq = value
+-try:
+-self._per_letter_annotations = 
_RestrictedDict(length=len(self.seq))
+-except AttributeError:
+-# e.g. seq is None
+-self._per_letter_annotations = _RestrictedDict(length=0)
++if len(self) != len(value):
++# TODO - Make this a warning? Silently empty the dictionary?
++raise ValueError("You must empty the letter annotations 
first!")
++else:
++# Leave the existing per letter annotations unchanged:
++self._seq = value
++else:
++self._seq = value
++# Reset the (empty) letter annotations dict with new length:
++try:
++self._per_letter_annotations = 
_RestrictedDict(length=len(self.seq))
++except AttributeError:
++# e.g. seq is None
++self._per_letter_annotations = _RestrictedDict(length=0)
+ 
+ seq = property(fget=lambda self: self._seq,
+fset=_set_seq,
+@@ -427,10 +436,17 @@
+ if self.seq is

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

2014-05-07 Thread Justin Lecher 
commit: 8f906e56d735e0cb1b85041448dbfadcf6d5e8c8
Author: Justin Lecher jlec AT gentoo DOT org
AuthorDate: Wed May  7 10:29:21 2014 +
Commit: Justin Lecher jlec AT gentoo DOT org
CommitDate: Wed May  7 10:29:21 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=8f906e56

Imported to tree

Signed-off-by: Justin Lecher jlec AT gentoo.org

---
 sci-biology/biopython/ChangeLog| 40 
 sci-biology/biopython/biopython-1.62-r3.ebuild | 53 --
 sci-biology/biopython/biopython-1.62-r4.ebuild | 53 --
 sci-biology/biopython/biopython-1.63-r1.ebuild | 53 --
 .../biopython/files/SffIO_broken_padding.patch | 27 ---
 .../biopython/files/SffIO_error_in_check_eof.patch | 14 --
 .../biopython/files/biopython-1.51-flex.patch  | 21 -
 .../biopython/files/biopython-1.62-SffIO.patch | 36 ---
 sci-biology/biopython/metadata.xml |  5 --
 9 files changed, 302 deletions(-)

diff --git a/sci-biology/biopython/ChangeLog b/sci-biology/biopython/ChangeLog
deleted file mode 100644
index 796f6a9..000
--- a/sci-biology/biopython/ChangeLog
+++ /dev/null
@@ -1,40 +0,0 @@
-# ChangeLog for sci-biology/biopython
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
-  18 Apr 2014; Martin Mokrejs mmokr...@fold.natur.cuni.cz
-  -files/SeqRecord.py.patch, -files/adjust-trimpoints.patch:
-  sci-biology/biopython: ops, taking back my own testing patches
-
-*biopython-1.62-r3 (18 Apr 2014)
-*biopython-1.62-r4 (18 Apr 2014)
-
-  18 Apr 2014; Martin Mokrejs mmokr...@fold.natur.cuni.cz
-  +biopython-1.62-r3.ebuild, +biopython-1.62-r4.ebuild,
-  +files/SeqRecord.py.patch, +files/SffIO_broken_padding.patch,
-  +files/adjust-trimpoints.patch, biopython-1.63-r1.ebuild,
-  files/SffIO_error_in_check_eof.patch, files/biopython-1.51-flex.patch,
-  files/biopython-1.62-SffIO.patch:
-  sci-biology/biopython: upstream patch to downgrade an assert to a warning
-
-  23 Mar 2014; Martin Mokrejs mmokr...@fold.natur.cuni.cz
-  -biopython-1.62-r3.ebuild, -biopython-1.62-r4.ebuild, -biopython-1.63.ebuild,
-  -files/SeqRecord.py.patch, -files/adjust-trimpoints.patch,
-  biopython-1.63-r1.ebuild:
-  sci-biology/biopython-1.63-r1: added missing deps on dev-python/rdflib to 
sync
-  with official sci-biology/biopython-1.63; dropping sci-biology/biopython-1.63
-  from overlay
-
-*biopython-1.62-r3 (23 Mar 2014)
-*biopython-1.62-r4 (23 Mar 2014)
-*biopython-1.63-r1 (23 Mar 2014)
-*biopython-1.63 (23 Mar 2014)
-
-  23 Mar 2014; Martin Mokrejs mmokr...@fold.natur.cuni.cz
-  +biopython-1.62-r3.ebuild, +biopython-1.62-r4.ebuild,
-  +biopython-1.63-r1.ebuild, +biopython-1.63.ebuild, +files/SeqRecord.py.patch,
-  +files/SffIO_error_in_check_eof.patch, +files/adjust-trimpoints.patch,
-  +files/biopython-1.51-flex.patch, +files/biopython-1.62-SffIO.patch,
-  +metadata.xml:
-  sci-biology/biopython-1.63-r1: version bump and an upstream patch to improve
-  error message

diff --git a/sci-biology/biopython/biopython-1.62-r3.ebuild 
b/sci-biology/biopython/biopython-1.62-r3.ebuild
deleted file mode 100644
index 09e6ed7..000
--- a/sci-biology/biopython/biopython-1.62-r3.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: 
/var/cvsroot/gentoo-x86/sci-biology/biopython/biopython-1.62.ebuild,v 1.1 
2013/09/17 16:07:56 jlec Exp $
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_6,2_7} )
-
-inherit distutils-r1 eutils
-
-DESCRIPTION=Python modules for computational molecular biology
-HOMEPAGE=http://www.biopython.org/ http://pypi.python.org/pypi/biopython/;
-SRC_URI=http://www.biopython.org/DIST/${P}.tar.gz;
-
-LICENSE=HPND
-SLOT=0
-KEYWORDS=~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux
-IUSE=mysql postgres
-
-REQUIRED_USE=${PYTHON_REQUIRED_USE}
-
-RDEPEND=${PYTHON_DEPS}
-   dev-python/matplotlib[${PYTHON_USEDEP}]
-   dev-python/networkx[${PYTHON_USEDEP}]
-   dev-python/numpy[${PYTHON_USEDEP}]
-   dev-python/pygraphviz[${PYTHON_USEDEP}]
-   dev-python/reportlab[${PYTHON_USEDEP}]
-   media-gfx/pydot[${PYTHON_USEDEP}]
-   mysql? ( dev-python/mysql-python[${PYTHON_USEDEP}] )
-   postgres? ( dev-python/psycopg[${PYTHON_USEDEP}] )
-DEPEND=${RDEPEND}
-   sys-devel/flex
-
-DOCS=( CONTRIB DEPRECATED NEWS README Doc/. )
-
-src_prepare() {
-   distutils-r1_src_prepare
-   epatch ${FILESDIR}/${PN}-1.62-SffIO.patch
-   epatch ${FILESDIR}/SffIO_error_in_check_eof.patch
-   epatch ${FILESDIR}/SffIO_broken_padding.patch
-}
-
-python_test() {
-   cd Tests || die
-   ${PYTHON} run_tests.py || die
-}
-
-python_install_all() {
-   distutils-r1_python_install_all
-
-   dodir /usr/share/${PN}
-   cp -r --preserve=mode Scripts Tests ${ED}/usr/share/${PN} || die
-}

diff --git

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

2014-04-18 Thread Martin Mokrejs 
commit: 20c8e6ec36a2cdd5af944030720b059fb8d10891
Author: Martin Mokrejš mmokrejs AT fold DOT natur DOT cuni DOT cz
AuthorDate: Fri Apr 18 18:11:59 2014 +
Commit: Martin Mokrejs mmokrejs AT fold DOT natur DOT cuni DOT cz
CommitDate: Fri Apr 18 18:11:59 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=20c8e6ec

sci-biology/biopython: upstream patch to downgrade an assert to a warning

Package-Manager: portage-2.2.7

---
 sci-biology/biopython/ChangeLog|  11 ++
 ...hon-1.63-r1.ebuild = biopython-1.62-r3.ebuild} |   5 +-
 ...hon-1.63-r1.ebuild = biopython-1.62-r4.ebuild} |   5 +-
 sci-biology/biopython/biopython-1.63-r1.ebuild |   3 +-
 sci-biology/biopython/files/SeqRecord.py.patch | 148 +
 .../biopython/files/SffIO_broken_padding.patch |  27 
 .../biopython/files/adjust-trimpoints.patch|  76 +++
 7 files changed, 270 insertions(+), 5 deletions(-)

diff --git a/sci-biology/biopython/ChangeLog b/sci-biology/biopython/ChangeLog
index 037227d..c326c4a 100644
--- a/sci-biology/biopython/ChangeLog
+++ b/sci-biology/biopython/ChangeLog
@@ -2,6 +2,17 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*biopython-1.62-r3 (18 Apr 2014)
+*biopython-1.62-r4 (18 Apr 2014)
+
+  18 Apr 2014; Martin Mokrejs mmokr...@fold.natur.cuni.cz
+  +biopython-1.62-r3.ebuild, +biopython-1.62-r4.ebuild,
+  +files/SeqRecord.py.patch, +files/SffIO_broken_padding.patch,
+  +files/adjust-trimpoints.patch, biopython-1.63-r1.ebuild,
+  files/SffIO_error_in_check_eof.patch, files/biopython-1.51-flex.patch,
+  files/biopython-1.62-SffIO.patch:
+  sci-biology/biopython: upstream patch to downgrade an assert to a warning
+
   23 Mar 2014; Martin Mokrejs mmokr...@fold.natur.cuni.cz
   -biopython-1.62-r3.ebuild, -biopython-1.62-r4.ebuild, -biopython-1.63.ebuild,
   -files/SeqRecord.py.patch, -files/adjust-trimpoints.patch,

diff --git a/sci-biology/biopython/biopython-1.63-r1.ebuild 
b/sci-biology/biopython/biopython-1.62-r3.ebuild
similarity index 90%
copy from sci-biology/biopython/biopython-1.63-r1.ebuild
copy to sci-biology/biopython/biopython-1.62-r3.ebuild
index e99f846..09e6ed7 100644
--- a/sci-biology/biopython/biopython-1.63-r1.ebuild
+++ b/sci-biology/biopython/biopython-1.62-r3.ebuild
@@ -23,7 +23,6 @@ RDEPEND=${PYTHON_DEPS}
dev-python/matplotlib[${PYTHON_USEDEP}]
dev-python/networkx[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
-   dev-python/rdflib[${PYTHON_USEDEP}]
dev-python/pygraphviz[${PYTHON_USEDEP}]
dev-python/reportlab[${PYTHON_USEDEP}]
media-gfx/pydot[${PYTHON_USEDEP}]
@@ -35,8 +34,10 @@ DEPEND=${RDEPEND}
 DOCS=( CONTRIB DEPRECATED NEWS README Doc/. )
 
 src_prepare() {
-   epatch ${FILESDIR}/SffIO_error_in_check_eof.patch
distutils-r1_src_prepare
+   epatch ${FILESDIR}/${PN}-1.62-SffIO.patch
+   epatch ${FILESDIR}/SffIO_error_in_check_eof.patch
+   epatch ${FILESDIR}/SffIO_broken_padding.patch
 }
 
 python_test() {

diff --git a/sci-biology/biopython/biopython-1.63-r1.ebuild 
b/sci-biology/biopython/biopython-1.62-r4.ebuild
similarity index 90%
copy from sci-biology/biopython/biopython-1.63-r1.ebuild
copy to sci-biology/biopython/biopython-1.62-r4.ebuild
index e99f846..09e6ed7 100644
--- a/sci-biology/biopython/biopython-1.63-r1.ebuild
+++ b/sci-biology/biopython/biopython-1.62-r4.ebuild
@@ -23,7 +23,6 @@ RDEPEND=${PYTHON_DEPS}
dev-python/matplotlib[${PYTHON_USEDEP}]
dev-python/networkx[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
-   dev-python/rdflib[${PYTHON_USEDEP}]
dev-python/pygraphviz[${PYTHON_USEDEP}]
dev-python/reportlab[${PYTHON_USEDEP}]
media-gfx/pydot[${PYTHON_USEDEP}]
@@ -35,8 +34,10 @@ DEPEND=${RDEPEND}
 DOCS=( CONTRIB DEPRECATED NEWS README Doc/. )
 
 src_prepare() {
-   epatch ${FILESDIR}/SffIO_error_in_check_eof.patch
distutils-r1_src_prepare
+   epatch ${FILESDIR}/${PN}-1.62-SffIO.patch
+   epatch ${FILESDIR}/SffIO_error_in_check_eof.patch
+   epatch ${FILESDIR}/SffIO_broken_padding.patch
 }
 
 python_test() {

diff --git a/sci-biology/biopython/biopython-1.63-r1.ebuild 
b/sci-biology/biopython/biopython-1.63-r1.ebuild
index e99f846..b600748 100644
--- a/sci-biology/biopython/biopython-1.63-r1.ebuild
+++ b/sci-biology/biopython/biopython-1.63-r1.ebuild
@@ -35,7 +35,8 @@ DEPEND=${RDEPEND}
 DOCS=( CONTRIB DEPRECATED NEWS README Doc/. )
 
 src_prepare() {
-   epatch ${FILESDIR}/SffIO_error_in_check_eof.patch
+   epatch ${FILESDIR}/SffIO_error_in_check_eof.patch
+   epatch ${FILESDIR}/SffIO_broken_padding.patch
distutils-r1_src_prepare
 }
 

diff --git a/sci-biology/biopython/files/SeqRecord.py.patch 
b/sci-biology/biopython/files/SeqRecord.py.patch
new file mode 100644
index 000..ac3785f
--- /dev/null
+++ b/sci-biology/biopython/files/SeqRecord.py.patch
@@

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

2014-04-18 Thread Martin Mokrejs 
commit: 74035c984818c6829c1f82cbcc1f419ff45f93d0
Author: Martin Mokrejš mmokrejs AT fold DOT natur DOT cuni DOT cz
AuthorDate: Fri Apr 18 18:21:20 2014 +
Commit: Martin Mokrejs mmokrejs AT fold DOT natur DOT cuni DOT cz
CommitDate: Fri Apr 18 18:21:20 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=74035c98

sci-biology/biopython: ops, taking back my own testing patches

Package-Manager: portage-2.2.7

---
 sci-biology/biopython/ChangeLog|   4 +
 sci-biology/biopython/files/SeqRecord.py.patch | 148 -
 .../biopython/files/adjust-trimpoints.patch|  76 ---
 3 files changed, 4 insertions(+), 224 deletions(-)

diff --git a/sci-biology/biopython/ChangeLog b/sci-biology/biopython/ChangeLog
index c326c4a..796f6a9 100644
--- a/sci-biology/biopython/ChangeLog
+++ b/sci-biology/biopython/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  18 Apr 2014; Martin Mokrejs mmokr...@fold.natur.cuni.cz
+  -files/SeqRecord.py.patch, -files/adjust-trimpoints.patch:
+  sci-biology/biopython: ops, taking back my own testing patches
+
 *biopython-1.62-r3 (18 Apr 2014)
 *biopython-1.62-r4 (18 Apr 2014)
 

diff --git a/sci-biology/biopython/files/SeqRecord.py.patch 
b/sci-biology/biopython/files/SeqRecord.py.patch
deleted file mode 100644
index ac3785f..000
--- a/sci-biology/biopython/files/SeqRecord.py.patch
+++ /dev/null
@@ -1,148 +0,0 @@
-diff --git a/Bio/SeqIO/SffIO.py b/Bio/SeqIO/SffIO.py
-index 1971dba..43b38fd 100644
 a/Bio/SeqIO/SffIO.py
-+++ b/Bio/SeqIO/SffIO.py
-@@ -539,8 +539,15 @@ _valid_UAN_read_name = re.compile(r'^[a-zA-Z0-9]{14}$')
- 
- 
- def _sff_read_seq_record(handle, number_of_flows_per_read, flow_chars,
-- key_sequence, alphabet, trim=False):
--Parse the next read in the file, return data as a SeqRecord 
(PRIVATE).
-+ key_sequence, alphabet, trim=False, 
interpret_qual_trims=True, interpret_adapter_trims=False):
-+Parse the next read in the file, return data as a SeqRecord (PRIVATE).
-+Allow user to specify which type of clipping values should be applied
-+while reading the SFF stream. To be backwards compatible, we interpret
-+only the quality-based trim points by default. That results in lower-cased
-+sequences in the low-qual region, regardless what adapter-based clip 
points
-+say. This should be the desired behavior. More discussion at
-+https://redmine.open-bio.org/issues/3437
-+
- #Now on to the reads...
- #the read header format (fixed part):
- #read_header_length H
-@@ -589,20 +596,41 @@ def _sff_read_seq_record(handle, 
number_of_flows_per_read, flow_chars,
- warnings.warn(Post quality %i byte padding region contained 
data, SFF data is not broken
-  % padding)
- #Follow Roche and apply most aggressive of qual and adapter clipping.
--#Note Roche seems to ignore adapter clip fields when writing SFF,
--#and uses just the quality clipping values for any clipping.
--clip_left = max(clip_qual_left, clip_adapter_left)
--#Right clipping of zero means no clipping
--if clip_qual_right:
--if clip_adapter_right:
--clip_right = min(clip_qual_right, clip_adapter_right)
-+#Note Roche does not use adapter clip fields when writing SFF files
-+#but instead combines the adapter clipping information with quality-based
-+#values and writes the most aggressive combination into clip fields (as
-+#allowed by SFF specs).
-+
-+if interpret_qual_trims:
-+if interpret_adapter_trims:
-+clip_left = max(clip_qual_left, clip_adapter_left)
-+#Right clipping of zero means no clipping
-+if clip_qual_right:
-+if clip_adapter_right:
-+clip_right = min(clip_qual_right, clip_adapter_right)
-+else:
-+#Typical case with Roche SFF files
-+clip_right = clip_qual_right
-+elif clip_adapter_right:
-+clip_right = clip_adapter_right
-+else:
-+clip_right = seq_len
- else:
--#Typical case with Roche SFF files
--clip_right = clip_qual_right
--elif clip_adapter_right:
--clip_right = clip_adapter_right
-+  clip_left = clip_qual_left
-+  if clip_qual_right:
-+  clip_right = clip_qual_right
-+else:
-+  clip_right = seq_len
-+elif interpret_adapter_trims:
-+clip_left = clip_adapter_left
-+  if clip_adapter_right:
-+  clip_right = clip_adapter_right
-+  else:
-+  clip_right = seq_len
- else:
--clip_right = seq_len
-+clip_left = 0
-+  clip_right = seq_len
-+
- #Now build a SeqRecord
- if trim:
- seq =

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

2014-03-23 Thread Martin Mokrejs 
commit: b6bc96d05888bcfb2a2ebac3a477663d1915c57c
Author: Martin Mokrejš mmokrejs AT fold DOT natur DOT cuni DOT cz
AuthorDate: Sun Mar 23 15:52:18 2014 +
Commit: Martin Mokrejs mmokrejs AT fold DOT natur DOT cuni DOT cz
CommitDate: Sun Mar 23 15:52:18 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b6bc96d0

sci-biology/biopython-1.63-r1: version bump and an upstream patch to improve 
error message

Package-Manager: portage-2.2.7

---
 sci-biology/biopython/ChangeLog|  17 +++
 sci-biology/biopython/biopython-1.62-r3.ebuild |  51 +++
 sci-biology/biopython/biopython-1.62-r4.ebuild |  51 +++
 sci-biology/biopython/biopython-1.63-r1.ebuild |  51 +++
 sci-biology/biopython/biopython-1.63.ebuild|  50 +++
 sci-biology/biopython/files/SeqRecord.py.patch | 148 +
 .../biopython/files/SffIO_error_in_check_eof.patch |  14 ++
 .../biopython/files/adjust-trimpoints.patch|  76 +++
 .../biopython/files/biopython-1.51-flex.patch  |  21 +++
 .../biopython/files/biopython-1.62-SffIO.patch |  36 +
 sci-biology/biopython/metadata.xml |   5 +
 11 files changed, 520 insertions(+)

diff --git a/sci-biology/biopython/ChangeLog b/sci-biology/biopython/ChangeLog
new file mode 100644
index 000..6dfe5e2
--- /dev/null
+++ b/sci-biology/biopython/ChangeLog
@@ -0,0 +1,17 @@
+# ChangeLog for sci-biology/biopython
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*biopython-1.62-r3 (23 Mar 2014)
+*biopython-1.62-r4 (23 Mar 2014)
+*biopython-1.63-r1 (23 Mar 2014)
+*biopython-1.63 (23 Mar 2014)
+
+  23 Mar 2014; Martin Mokrejs mmokr...@fold.natur.cuni.cz
+  +biopython-1.62-r3.ebuild, +biopython-1.62-r4.ebuild,
+  +biopython-1.63-r1.ebuild, +biopython-1.63.ebuild, +files/SeqRecord.py.patch,
+  +files/SffIO_error_in_check_eof.patch, +files/adjust-trimpoints.patch,
+  +files/biopython-1.51-flex.patch, +files/biopython-1.62-SffIO.patch,
+  +metadata.xml:
+  sci-biology/biopython-1.63-r1: version bump and an upstream patch to improve
+  error message

diff --git a/sci-biology/biopython/biopython-1.62-r3.ebuild 
b/sci-biology/biopython/biopython-1.62-r3.ebuild
new file mode 100644
index 000..1eed5a9
--- /dev/null
+++ b/sci-biology/biopython/biopython-1.62-r3.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: 
/var/cvsroot/gentoo-x86/sci-biology/biopython/biopython-1.62.ebuild,v 1.1 
2013/09/17 16:07:56 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit distutils-r1 eutils
+
+DESCRIPTION=Python modules for computational molecular biology
+HOMEPAGE=http://www.biopython.org/ http://pypi.python.org/pypi/biopython/;
+SRC_URI=http://www.biopython.org/DIST/${P}.tar.gz;
+
+LICENSE=HPND
+SLOT=0
+KEYWORDS=~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux
+IUSE=mysql postgres
+
+REQUIRED_USE=${PYTHON_REQUIRED_USE}
+
+RDEPEND=${PYTHON_DEPS}
+   dev-python/matplotlib[${PYTHON_USEDEP}]
+   dev-python/networkx[${PYTHON_USEDEP}]
+   dev-python/numpy[${PYTHON_USEDEP}]
+   dev-python/pygraphviz[${PYTHON_USEDEP}]
+   dev-python/reportlab[${PYTHON_USEDEP}]
+   media-gfx/pydot[${PYTHON_USEDEP}]
+   mysql? ( dev-python/mysql-python[${PYTHON_USEDEP}] )
+   postgres? ( dev-python/psycopg[${PYTHON_USEDEP}] )
+DEPEND=${RDEPEND}
+   sys-devel/flex
+
+DOCS=( CONTRIB DEPRECATED NEWS README Doc/. )
+
+src_prepare() {
+   distutils-r1_src_prepare
+   epatch ${FILESDIR}/${PN}-1.62-SffIO.patch
+}
+
+python_test() {
+   cd Tests || die
+   ${PYTHON} run_tests.py || die
+}
+
+python_install_all() {
+   distutils-r1_python_install_all
+
+   dodir /usr/share/${PN}
+   cp -r --preserve=mode Scripts Tests ${ED}/usr/share/${PN} || die
+}

diff --git a/sci-biology/biopython/biopython-1.62-r4.ebuild 
b/sci-biology/biopython/biopython-1.62-r4.ebuild
new file mode 100644
index 000..1eed5a9
--- /dev/null
+++ b/sci-biology/biopython/biopython-1.62-r4.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: 
/var/cvsroot/gentoo-x86/sci-biology/biopython/biopython-1.62.ebuild,v 1.1 
2013/09/17 16:07:56 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit distutils-r1 eutils
+
+DESCRIPTION=Python modules for computational molecular biology
+HOMEPAGE=http://www.biopython.org/ http://pypi.python.org/pypi/biopython/;
+SRC_URI=http://www.biopython.org/DIST/${P}.tar.gz;
+
+LICENSE=HPND
+SLOT=0
+KEYWORDS=~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux
+IUSE=mysql postgres
+
+REQUIRED_USE=${PYTHON_REQUIRED_USE}
+
+RDEPEND=${PYTHON_DEPS}
+   dev-python/matplotlib[${PYTHON_USEDEP}]
+   dev-python/networkx[${PYTHON_USEDEP}]
+   dev-python/numpy[${PYTHON_USEDEP}]
+