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

2021-01-16 Thread Andrew Ammerlaan 
commit: e37cdb85f0e2b068a5d5c65bbd8a4483d0170b19
Author: Andrew Ammerlaan  riseup  net>
AuthorDate: Sat Jan 16 09:14:59 2021 +
Commit: Andrew Ammerlaan  riseup  net>
CommitDate: Sat Jan 16 09:14:59 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=e37cdb85

sci-biology/kat: remove keywords from live ebuild

oops

Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan  riseup.net>

 sci-biology/kat/kat-.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/kat/kat-.ebuild b/sci-biology/kat/kat-.ebuild
index 752dab83c..404f0d0c2 100644
--- a/sci-biology/kat/kat-.ebuild
+++ b/sci-biology/kat/kat-.ebuild
@@ -16,7 +16,7 @@ EGIT_CHECKOUT_DIR="${WORKDIR}"/KAT-Release-"${PV}"
 
 LICENSE="GPL-3+"
 SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS=""
 IUSE="cpu_flags_x86_sse static-libs test"
 
 CDEPEND="

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

2021-01-15 Thread Andrew Ammerlaan 
commit: 0e4a7cec8abd9f06360d25996f05c7d1633f289d
Author: Andrew Ammerlaan  riseup  net>
AuthorDate: Fri Jan 15 20:28:03 2021 +
Commit: Andrew Ammerlaan  riseup  net>
CommitDate: Fri Jan 15 20:28:03 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=0e4a7cec

sci-biology/kat: bump py targets

Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan  riseup.net>

 sci-biology/kat/kat-2.4.2.ebuild | 15 ++-
 sci-biology/kat/kat-.ebuild  | 15 ++-
 2 files changed, 20 insertions(+), 10 deletions(-)

diff --git a/sci-biology/kat/kat-2.4.2.ebuild b/sci-biology/kat/kat-2.4.2.ebuild
index e8f10ad5d..39c4fc6c1 100644
--- a/sci-biology/kat/kat-2.4.2.ebuild
+++ b/sci-biology/kat/kat-2.4.2.ebuild
@@ -1,9 +1,10 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-PYTHON_COMPAT=( python3_{5,6} )
+PYTHON_COMPAT=( python3_{7,8,9} )
+DISTUTILS_USE_SETUPTOOLS=rdepend
 # https://github.com/Ensembl/Bio-DB-HTS/issues/30
 
 inherit flag-o-matic autotools distutils-r1
@@ -23,9 +24,9 @@ CDEPEND="
dev-python/tabulate[${PYTHON_USEDEP}]
dev-python/matplotlib[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
-   dev-python/scipy[${PYTHON_USEDEP}]"
+   dev-python/scipy[${PYTHON_USEDEP}]
+"
 DEPEND="${CDEPEND}
-   dev-python/sphinx
test? ( sys-process/time )"
 RDEPEND="${CDEPEND}"
 # contains bundled and *modified* version of jellyfish-2.2.0
@@ -40,6 +41,9 @@ PATCHES=(
 
 S="${WORKDIR}"/KAT-Release-"${PV}"
 
+distutils_enable_sphinx "${S}/doc/source" --no-autodoc
+distutils_enable_tests pytest
+
 src_prepare(){
default
rm -rf deps/boost || die "Failed to zap bundled boost"
@@ -75,4 +79,5 @@ src_install(){
 
 src_test(){
default
+   python_foreach_impl python_test
 }

diff --git a/sci-biology/kat/kat-.ebuild b/sci-biology/kat/kat-.ebuild
index 961dc9ce8..752dab83c 100644
--- a/sci-biology/kat/kat-.ebuild
+++ b/sci-biology/kat/kat-.ebuild
@@ -1,9 +1,10 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-PYTHON_COMPAT=( python3_{5,6} )
+PYTHON_COMPAT=( python3_{7,8,9} )
+DISTUTILS_USE_SETUPTOOLS=rdepend
 # https://github.com/Ensembl/Bio-DB-HTS/issues/30
 
 inherit flag-o-matic autotools distutils-r1 git-r3
@@ -24,9 +25,9 @@ CDEPEND="
dev-python/tabulate[${PYTHON_USEDEP}]
dev-python/matplotlib[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
-   dev-python/scipy[${PYTHON_USEDEP}]"
+   dev-python/scipy[${PYTHON_USEDEP}]
+"
 DEPEND="${CDEPEND}
-   dev-python/sphinx
test? ( sys-process/time )"
 RDEPEND="${CDEPEND}"
 # contains bundled and *modified* version of jellyfish-2.2.0
@@ -41,6 +42,9 @@ PATCHES=(
 
 S="${WORKDIR}"/KAT-Release-"${PV}"
 
+distutils_enable_sphinx "${S}/doc/source" --no-autodoc
+distutils_enable_tests pytest
+
 src_prepare(){
default
rm -rf deps/boost || die "Failed to zap bundled boost"
@@ -76,4 +80,5 @@ src_install(){
 
 src_test(){
default
+   python_foreach_impl python_test
 }

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

2018-05-07 Thread Martin Mokrejs 
commit: 2ae549fb69309b8ab8537b3e9a8ea158d375cf1d
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Mon May  7 22:33:06 2018 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Mon May  7 22:33:06 2018 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=2ae549fb

sci-biology/kat: removing patches for 2.4.1 version

Package-Manager: Portage-2.3.31, Repoman-2.3.9

 .../kat/files/kat-2.4.1-make_no_pykat.patch| 15 
 .../kat/files/kat-2.4.1-no_static_build.patch  | 43 --
 2 files changed, 58 deletions(-)

diff --git a/sci-biology/kat/files/kat-2.4.1-make_no_pykat.patch 
b/sci-biology/kat/files/kat-2.4.1-make_no_pykat.patch
deleted file mode 100644
index 7ba08010c..0
--- a/sci-biology/kat/files/kat-2.4.1-make_no_pykat.patch
+++ /dev/null
@@ -1,15 +0,0 @@
-diff --git a/Makefile.am b/Makefile.am
-index 5f0f42e..4da6c05 100644
 a/Makefile.am
-+++ b/Makefile.am
-@@ -21,10 +21,6 @@ dist_noinst_SCRIPTS = autogen.sh antigen.sh build_boost.sh
- # SRC DIRS
- make_dirs=deps/jellyfish-2.2.0 deps/seqan-library-2.0.0 lib src tests
- 
--if MAKE_PYKAT
--make_dirs += scripts
--endif
--
- if MAKE_DOCS
- make_dirs += doc
- endif

diff --git a/sci-biology/kat/files/kat-2.4.1-no_static_build.patch 
b/sci-biology/kat/files/kat-2.4.1-no_static_build.patch
deleted file mode 100644
index c8ac6c901..0
--- a/sci-biology/kat/files/kat-2.4.1-no_static_build.patch
+++ /dev/null
@@ -1,43 +0,0 @@
-diff --git a/configure.ac b/configure.ac
-index b68c514..00c8a2e 100644
 a/configure.ac
-+++ b/configure.ac
-@@ -159,11 +159,11 @@ if [[ "${make_pykat}" == "yes" ]]; then
- AM_CPPFLAGS="${ZLIB_CPPFLAGS} ${PYTHON_CPPFLAGS}"
- AM_LIBS="${PTHREAD_CFLAGS} ${ZLIB_LIB} ${RT_LIB} ${PYTHON_EXTRA_LIBS} 
${PYTHON_LIBS}"
- #AM_LDFLAGS="${ZLIB_LDFLAGS} ${PYTHON_EXTRA_LDFLAGS} ${PYTHON_RPATH} 
-static-libstdc++"
--AM_LDFLAGS="${ZLIB_LDFLAGS} -static-libstdc++ ${PYTHON_RPATH}"
-+AM_LDFLAGS="${ZLIB_LDFLAGS} ${PYTHON_RPATH}"
- else
- AM_CPPFLAGS="${ZLIB_CPPFLAGS}"
- AM_LIBS="${PTHREAD_CFLAGS} ${ZLIB_LIB} ${RT_LIB}"
--AM_LDFLAGS="${ZLIB_LDFLAGS} -static-libstdc++"
-+AM_LDFLAGS="${ZLIB_LDFLAGS}"
- fi
- 
- AC_SUBST([AM_CPPFLAGS])
-diff --git a/deps/jellyfish-2.2.0/Makefile.am 
b/deps/jellyfish-2.2.0/Makefile.am
-index 8f6fffd..d6e0a3d 100644
 a/deps/jellyfish-2.2.0/Makefile.am
-+++ b/deps/jellyfish-2.2.0/Makefile.am
-@@ -7,7 +7,7 @@ man1_MANS = doc/kat_jellyfish.man
- pkgconfigdir = $(libdir)/pkgconfig
- pkgconfig_DATA = kat_jellyfish.pc
- 
--AM_LDFLAGS = $(ZLIB_LDFLAGS) $(ZLIB_LIB) -lpthread -static-libstdc++ # 
$(VALGRIND_LIBS)
-+AM_LDFLAGS = $(ZLIB_LDFLAGS) $(ZLIB_LIB) -lpthread # $(VALGRIND_LIBS)
- AM_CPPFLAGS = $(ZLIB_CPPFLAGS) -I$(top_srcdir) -I$(top_srcdir)/include # 
$(VALGRIND_CFLAGS)
- AM_CXXFLAGS = $(ALL_CXXFLAGS) -Wall -Wnon-virtual-dtor 
-Wno-deprecated-declarations
- 
-diff --git a/src/Makefile.am b/src/Makefile.am
-index a2ae071..71def5c 100644
 a/src/Makefile.am
-+++ b/src/Makefile.am
-@@ -19,7 +19,6 @@ kat_CPPFLAGS = \
-   @AM_CPPFLAGS@
- 
- kat_LDFLAGS = \
--  -static \
-   @AM_LDFLAGS@
- 
- kat_LDADD = \

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

2018-05-07 Thread Martin Mokrejs 
commit: f373141b6dd59db5eaf1bce4104e5ba6085958ac
Author: François Bissey  gmail  com>
AuthorDate: Mon Apr 23 08:51:16 2018 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Mon May  7 21:44:57 2018 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f373141b

sci-biology/kat: various fixes for issue #867

  many thanks to @kiwifb and @maplesond for on fixing the package and ebuild

  ax_check_zlib is in use. A hint for zlib location has to be provided
  otherwise system zlib will be used on prefix.

  make sure zlib is a dependency. develop branch has switched to proper
  library detection.

  fixing rpath. enabling python support (but broken right now).

  make sure a suitable python3 is setup at configure time

  bump to 2.4.2

  fix typo in /DEPPEND/DEPEND/, cleanup comments

Closes: https://github.com/gentoo/sci/issues/867
Closes: https://github.com/gentoo/sci/pull/868

Package-Manager: Portage-2.3.31, Repoman-2.3.9

 .../kat/files/kat-2.4.1-do-not-run-setup.py.patch  |  30 --
 .../kat/files/kat-2.4.1-ignore-bundled-deps.patch  | 101 -
 .../kat/files/kat-2.4.1-make_no_pykat.patch|  15 +++
 .../kat/files/kat-2.4.1-no_static_build.patch  |  43 +
 .../kat/files/kat-2.4.2-ignore-bundled-deps.patch  |  79 
 .../kat/files/kat-2.4.2-no_static_build.patch  |  56 
 sci-biology/kat/kat-2.4.1.ebuild   |  69 --
 sci-biology/kat/kat-2.4.2.ebuild   |  78 
 sci-biology/kat/kat-.ebuild|  60 +++-
 sci-biology/kat/metadata.xml   |   4 -
 10 files changed, 307 insertions(+), 228 deletions(-)

diff --git a/sci-biology/kat/files/kat-2.4.1-do-not-run-setup.py.patch 
b/sci-biology/kat/files/kat-2.4.1-do-not-run-setup.py.patch
deleted file mode 100644
index a00c971a6..0
--- a/sci-biology/kat/files/kat-2.4.1-do-not-run-setup.py.patch
+++ /dev/null
@@ -1,30 +0,0 @@
 scripts/Makefile.am.ori2018-04-22 16:02:12.829046527 +0200
-+++ scripts/Makefile.am2018-04-22 16:05:31.444532061 +0200
-@@ -1,27 +1,6 @@
- AUTOMAKE_OPTIONS = subdir-objects
- 
- 
--if MAKE_PYKAT_INSTALL
--
--install-exec-hook:
--  export PYTHONPATH=$(prefix)/lib/python$(PYTHON_VERSION)/site-packages 
&& \
--  mkdir -p $(prefix)/lib/python$(PYTHON_VERSION)/site-packages/ && \
--  python3 setup.py install --prefix=$(prefix) --record install_files.txt
--
--uninstall-hook:
--  cat install_files.txt | xargs rm -rf
--
--else
--
--install-exec-hook:
--  mkdir -p $(prefix)/lib/python$(PYTHON_VERSION)/local/ && \
--  cp -r kat $(prefix)/lib/python$(PYTHON_VERSION)/local
--
--uninstall-hook:
--  rm -rf $(prefix)/lib/python$(PYTHON_VERSION)/local
--
--endif
--
- EXTRA_DIST = \
-   kat/distanalysis.py \
-   kat/plot/__init__.py \

diff --git a/sci-biology/kat/files/kat-2.4.1-ignore-bundled-deps.patch 
b/sci-biology/kat/files/kat-2.4.1-ignore-bundled-deps.patch
deleted file mode 100644
index 649f3ecd8..0
--- a/sci-biology/kat/files/kat-2.4.1-ignore-bundled-deps.patch
+++ /dev/null
@@ -1,101 +0,0 @@
 configure.ac.ori   2018-04-22 12:19:37.318794996 +0200
-+++ configure.ac   2018-04-22 12:20:43.310663598 +0200
-@@ -172,8 +172,8 @@
- 
- 
- AC_CONFIG_HEADERS([config.h])
--AC_CONFIG_FILES([Makefile doc/Makefile doc/source/conf.py lib/kat.pc 
lib/Makefile src/Makefile tests/Makefile tests/compat.sh 
deps/seqan-library-2.0.0/Makefile scripts/setup.py scripts/kat/__init__.py 
scripts/Makefile])
--AC_CONFIG_SUBDIRS([deps/jellyfish-2.2.0])
-+AC_CONFIG_FILES([Makefile doc/Makefile doc/source/conf.py lib/kat.pc 
lib/Makefile src/Makefile tests/Makefile tests/compat.sh 
deps/seqan-library-2.0.0/Makefile scripts/setup.py scripts/kat/__init__.py 
scripts/Makefile])
-+AC_CONFIG_SUBDIRS([deps/jellyfish-2.2.0])
- AC_OUTPUT
- 
- pystr="detected ${PYTHON_VERSION}.  Plotting and downstream analysis enabled."
 lib/Makefile.am.ori2018-04-22 15:30:34.983653065 +0200
-+++ lib/Makefile.am2018-04-22 15:30:46.143961300 +0200
-@@ -7,8 +7,7 @@
- 
- libkat_la_LDFLAGS = \
-   -version-info 2:4:0 \
--  -L../deps/jellyfish-2.2.0 \
--  -L../deps/boost/build/lib
-+  -L../deps/jellyfish-2.2.0
- 
- libkat_la_SOURCES = \
-   src/matrix_metadata_extractor.cc \
-@@ -31,7 +30,6 @@
- 
- libkat_la_CPPFLAGS = \
-   -I$(top_srcdir)/deps/jellyfish-2.2.0/include \
--  -I$(top_srcdir)/deps/boost/build/include \
-   -I$(top_srcdir)/lib/include \
-   -DKAT_SITE_PKGS='"$(libdir)/python$(PYTHON_VERSION)/site-packages"' \
-   @AM_CPPFLAGS@
 src/Makefile.am.ori2018-04-22 15:30:46.203962959 +0200
-+++ src/Makefile.am2018-04-22 15:31:41.385487008 +0200
-@@ -14,7 +14,6 @@
- kat_CPPFLAGS = \
-   -I$(top_srcdir)/deps/seqan-library-2.0.0/include \
-   -I$(top_srcdir)/deps/jellyfish-2.2.0/include \
--  -I$(top_srcdir)/deps/boost/build/include \
-

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

2018-04-22 Thread Martin Mokrejs 
commit: 57485834b37ce2b2da440ee2befb0c92abc725d5
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Sun Apr 22 23:04:03 2018 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Sun Apr 22 23:04:03 2018 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=57485834

sci-biology/kat: properly install python files

Thanks to kiwifb. Drop -, update - and -2.4.1 to
link against system-wide boost.

No ebuilds left which would let the bundled boost slip in as
a static library.

See: https://github.com/TGAC/KAT/issues/94#issuecomment-383385701
Closes: https://github.com/gentoo/sci/issues/867
Package-Manager: Portage-2.3.31, Repoman-2.3.9

 sci-biology/kat/kat-2.4.1.ebuild | 44 -
 sci-biology/kat/kat-.ebuild  | 70 
 sci-biology/kat/kat-.ebuild  | 50 +---
 3 files changed, 59 insertions(+), 105 deletions(-)

diff --git a/sci-biology/kat/kat-2.4.1.ebuild b/sci-biology/kat/kat-2.4.1.ebuild
index 86dd7b5a8..3bd8b7dde 100644
--- a/sci-biology/kat/kat-2.4.1.ebuild
+++ b/sci-biology/kat/kat-2.4.1.ebuild
@@ -6,15 +6,15 @@ EAPI=6
 PYTHON_COMPAT=( python3_{5,6} ) # requires python >= 3.1 but more features 
with >=3.5
 # https://github.com/Ensembl/Bio-DB-HTS/issues/30
 
-inherit python-r1 eutils flag-o-matic
+inherit eutils flag-o-matic autotools distutils-r1
 
 DESCRIPTION="K-mer Analysis Toolkit (histogram, filter, compare sets, plot)"
 HOMEPAGE="https://github.com/TGAC/KAT;
-SRC_URI="https://github.com/TGAC/KAT/archive/Release-${PV}.tar.gz -> 
${P}.tar.gz"
+SRC_URI="https://github.com/TGAC/KAT/archive/Release-2.4.1.tar.gz -> 
${P}.tar.gz"
 
 LICENSE="GPL-3+"
 SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64 ~x86"
 IUSE="cpu_flags_x86_sse doc tex"
 
 DEPEND="
@@ -26,32 +26,44 @@ DEPEND="
doc? ( dev-python/sphinx[${PYTHON_USEDEP}] )
tex? ( dev-tex/latexmk dev-texlive/texlive-formatsextra )"
 RDEPEND="${DEPEND}"
-# contains bundled *modified* version of jellyfish-2.2 which should install 
under different filenames
+# contains bundled a *modified* version of jellyfish-2.2.0 
(libkat_jellyfish.{a,so})
 # contains embedded sci-biology/seqan
 
 S="${WORKDIR}"/KAT-Release-"${PV}"
 
 src_prepare(){
default
-   # autogen.sh
-   test -n "$srcdir" || local srcdir=`dirname "$0"`
-   test -n "$srcdir" || local srcdir=.
-   eautoreconf --force --install --verbose "$srcdir"
+   # keep bundled seqan-library-2.0.0 jellyfish-2.2.0
+   # seqan header do not hurt
+   # jellyfish-2.2.0 is a modified version, "kat_" prefixes are added to 
all binaries
+   # https://github.com/TGAC/KAT/issues/93#issuecomment-383377666
+   rm -rf deps/boost || die "Failed to zap bundled boost"
+   epatch "${FILESDIR}"/kat-2.4.1-ignore-bundled-deps.patch
+   epatch "${FILESDIR}"/kat-2.4.1-do-not-run-setup.py.patch
+   eautoreconf
+   pushd scripts >/dev/null || die
+   distutils-r1_src_prepare
+   popd > /dev/null || die
 }
 
 src_configure(){
local myconf=()
myconf+=( --disable-gnuplot ) # python3 does better image rendering, no 
need for gnuplot
use cpu_flags_x86_sse && myconf+=( $(use_with cpu_flags_x86_sse sse) ) 
# pass down to jellyfish-2.2.0/configure
-   PYTHON_VERSION=3 econf ${myconf[@]}
+   econf ${myconf[@]}
 }
 
 src_compile(){
-   # build_boost.sh
-   cd deps/boost || die
-   ./bootstrap.sh --prefix=build 
--with-libraries=chrono,exception,program_options,timer,filesystem,system,stacktrace
 || die
-   # https://github.com/TGAC/KAT/issues/92#issuecomment-383373418
-   ./b2 headers --ignore-site-config || die
-   ./b2 install --ignore-site-config || die
-   cd ../.. || die
+   emake
+   cd doc && make latexpdf && cd .. || die
+   pushd scripts >/dev/null || die
+   distutils-r1_src_compile
+   popd > /dev/null || die
+}
+
+src_install(){
+   default
+   pushd scripts >/dev/null || die
+   distutils-r1_src_install
+   popd > /dev/null || die
 }

diff --git a/sci-biology/kat/kat-.ebuild b/sci-biology/kat/kat-.ebuild
deleted file mode 100644
index 07c3f57d2..0
--- a/sci-biology/kat/kat-.ebuild
+++ /dev/null
@@ -1,70 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python3_{5,6} ) # requires python >= 3.1 but more features 
with >=3.5
-# https://github.com/Ensembl/Bio-DB-HTS/issues/30
-
-inherit git-r3 eutils flag-o-matic autotools distutils-r1
-
-DESCRIPTION="K-mer Analysis Toolkit (histogram, filter, compare sets, plot)"
-HOMEPAGE="https://github.com/TGAC/KAT;
-EGIT_REPO_URI="https://github.com/TGAC/KAT.git;
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS=""
-IUSE="cpu_flags_x86_sse doc tex"
-
-DEPEND="
-   >=dev-libs/boost-1.52[${PYTHON_USEDEP}]
-   dev-python/tabulate[${PYTHON_USEDEP}]
-

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

2018-04-22 Thread Martin Mokrejs 
commit: 65304d57d4c51cdf0c55740ee37f30e800090a16
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Sun Apr 22 21:17:51 2018 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Sun Apr 22 21:17:51 2018 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=65304d57

sci-biology/kat: add missing DEPENDency

Package-Manager: Portage-2.3.31, Repoman-2.3.9

 sci-biology/kat/kat-2.4.1.ebuild | 5 +++--
 sci-biology/kat/kat-.ebuild  | 2 +-
 sci-biology/kat/kat-.ebuild  | 5 +++--
 3 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/sci-biology/kat/kat-2.4.1.ebuild b/sci-biology/kat/kat-2.4.1.ebuild
index 29f11c9f6..86dd7b5a8 100644
--- a/sci-biology/kat/kat-2.4.1.ebuild
+++ b/sci-biology/kat/kat-2.4.1.ebuild
@@ -15,7 +15,7 @@ 
SRC_URI="https://github.com/TGAC/KAT/archive/Release-${PV}.tar.gz -> ${P}.tar.gz
 LICENSE="GPL-3+"
 SLOT="0"
 KEYWORDS=""
-IUSE="cpu_flags_x86_sse doc"
+IUSE="cpu_flags_x86_sse doc tex"
 
 DEPEND="
>=dev-libs/boost-1.52[${PYTHON_USEDEP}]
@@ -23,7 +23,8 @@ DEPEND="
dev-python/matplotlib[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
sci-libs/scipy[${PYTHON_USEDEP}]
-   doc? ( dev-python/sphinx[${PYTHON_USEDEP}] )"
+   doc? ( dev-python/sphinx[${PYTHON_USEDEP}] )
+   tex? ( dev-tex/latexmk dev-texlive/texlive-formatsextra )"
 RDEPEND="${DEPEND}"
 # contains bundled *modified* version of jellyfish-2.2 which should install 
under different filenames
 # contains embedded sci-biology/seqan

diff --git a/sci-biology/kat/kat-.ebuild b/sci-biology/kat/kat-.ebuild
index a8a776c29..07c3f57d2 100644
--- a/sci-biology/kat/kat-.ebuild
+++ b/sci-biology/kat/kat-.ebuild
@@ -24,7 +24,7 @@ DEPEND="
dev-python/numpy[${PYTHON_USEDEP}]
sci-libs/scipy[${PYTHON_USEDEP}]
doc? ( dev-python/sphinx[${PYTHON_USEDEP}] )
-   tex? ( dev-tex/latexmk )"
+   tex? ( dev-tex/latexmk dev-texlive/texlive-formatsextra )"
 RDEPEND="${DEPEND}"
 # contains bundled a *modified* version of jellyfish-2.2.0 
(libkat_jellyfish.{a,so})
 # contains embedded sci-biology/seqan

diff --git a/sci-biology/kat/kat-.ebuild b/sci-biology/kat/kat-.ebuild
index 8fe79a34b..403a0df59 100644
--- a/sci-biology/kat/kat-.ebuild
+++ b/sci-biology/kat/kat-.ebuild
@@ -15,7 +15,7 @@ EGIT_REPO_URI="https://github.com/TGAC/KAT.git;
 LICENSE="GPL-3+"
 SLOT="0"
 KEYWORDS=""
-IUSE="cpu_flags_x86_sse doc"
+IUSE="cpu_flags_x86_sse doc tex"
 
 DEPEND="
>=dev-libs/boost-1.52
@@ -23,7 +23,8 @@ DEPEND="
dev-python/matplotlib
dev-python/numpy
sci-libs/scipy
-   doc? ( dev-python/sphinx )"
+   doc? ( dev-python/sphinx )
+   tex? ( dev-tex/latexmk dev-texlive/texlive-formatsextra )"
 RDEPEND="${DEPEND}"
 # contains bundled a *modified* version of jellyfish-2.2.0 
(libkat_jellyfish.{a,so})
 # contains embedded sci-biology/seqan

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

2018-04-22 Thread Martin Mokrejs 
commit: e459544d4d91e198e5c5e386a2052dc2600e1286
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Sun Apr 22 18:11:45 2018 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Sun Apr 22 18:11:45 2018 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=e459544d

sci-biology/kat: improve - ebuild

Try call setup.py on our own so that it could receive ${DESTDIR}
contents. This still does not work.

The ebuild drops bundled boost copy but retains bundled seqan
headers and the modified copy of jellyfish. They won't interfere
with with site-wide installed packages of those tools in Gentoo.

The modified jellyfish is linked-in statically and binaries have
'kat_' prefix.

The kat-2.4.1.ebuild and -.ebuild should later get same logic
like appears in -.ebuild. Currently they stick to upstream's
approach of using bundled boost too.

All ebuilds suffer same problem: the python files do not get installed
at all.

Package-Manager: Portage-2.3.28, Repoman-2.3.9

 .../kat/files/kat-2.4.1-do-not-run-setup.py.patch  |  30 
 .../kat/files/kat-2.4.1-ignore-bundled-deps.patch  | 127 +++-
 .../kat/files/kat-2.4.1-rename-jellyfish.patch | 159 -
 sci-biology/kat/kat-2.4.1.ebuild   |  12 +-
 sci-biology/kat/kat-.ebuild|  50 +--
 sci-biology/kat/metadata.xml   |   4 +
 6 files changed, 132 insertions(+), 250 deletions(-)

diff --git a/sci-biology/kat/files/kat-2.4.1-do-not-run-setup.py.patch 
b/sci-biology/kat/files/kat-2.4.1-do-not-run-setup.py.patch
new file mode 100644
index 0..a00c971a6
--- /dev/null
+++ b/sci-biology/kat/files/kat-2.4.1-do-not-run-setup.py.patch
@@ -0,0 +1,30 @@
+--- scripts/Makefile.am.ori2018-04-22 16:02:12.829046527 +0200
 scripts/Makefile.am2018-04-22 16:05:31.444532061 +0200
+@@ -1,27 +1,6 @@
+ AUTOMAKE_OPTIONS = subdir-objects
+ 
+ 
+-if MAKE_PYKAT_INSTALL
+-
+-install-exec-hook:
+-  export PYTHONPATH=$(prefix)/lib/python$(PYTHON_VERSION)/site-packages 
&& \
+-  mkdir -p $(prefix)/lib/python$(PYTHON_VERSION)/site-packages/ && \
+-  python3 setup.py install --prefix=$(prefix) --record install_files.txt
+-
+-uninstall-hook:
+-  cat install_files.txt | xargs rm -rf
+-
+-else
+-
+-install-exec-hook:
+-  mkdir -p $(prefix)/lib/python$(PYTHON_VERSION)/local/ && \
+-  cp -r kat $(prefix)/lib/python$(PYTHON_VERSION)/local
+-
+-uninstall-hook:
+-  rm -rf $(prefix)/lib/python$(PYTHON_VERSION)/local
+-
+-endif
+-
+ EXTRA_DIST = \
+   kat/distanalysis.py \
+   kat/plot/__init__.py \

diff --git a/sci-biology/kat/files/kat-2.4.1-ignore-bundled-deps.patch 
b/sci-biology/kat/files/kat-2.4.1-ignore-bundled-deps.patch
index d1816498e..649f3ecd8 100644
--- a/sci-biology/kat/files/kat-2.4.1-ignore-bundled-deps.patch
+++ b/sci-biology/kat/files/kat-2.4.1-ignore-bundled-deps.patch
@@ -6,51 +6,56 @@
  AC_CONFIG_HEADERS([config.h])
 -AC_CONFIG_FILES([Makefile doc/Makefile doc/source/conf.py lib/kat.pc 
lib/Makefile src/Makefile tests/Makefile tests/compat.sh 
deps/seqan-library-2.0.0/Makefile scripts/setup.py scripts/kat/__init__.py 
scripts/Makefile])
 -AC_CONFIG_SUBDIRS([deps/jellyfish-2.2.0])
-+AC_CONFIG_FILES([Makefile doc/Makefile doc/source/conf.py lib/kat.pc 
lib/Makefile src/Makefile tests/Makefile tests/compat.sh scripts/setup.py 
scripts/kat/__init__.py scripts/Makefile])
-+AC_CONFIG_SUBDIRS([])
++AC_CONFIG_FILES([Makefile doc/Makefile doc/source/conf.py lib/kat.pc 
lib/Makefile src/Makefile tests/Makefile tests/compat.sh 
deps/seqan-library-2.0.0/Makefile scripts/setup.py scripts/kat/__init__.py 
scripts/Makefile])
++AC_CONFIG_SUBDIRS([deps/jellyfish-2.2.0])
  AC_OUTPUT
  
  pystr="detected ${PYTHON_VERSION}.  Plotting and downstream analysis enabled."
 Makefile.am.ori2018-04-22 12:23:58.756197763 +0200
-+++ Makefile.am2018-04-22 12:24:21.176832618 +0200
-@@ -19,7 +19,7 @@
- dist_noinst_SCRIPTS = autogen.sh antigen.sh build_boost.sh
+--- lib/Makefile.am.ori2018-04-22 15:30:34.983653065 +0200
 lib/Makefile.am2018-04-22 15:30:46.143961300 +0200
+@@ -7,8 +7,7 @@
  
- # SRC DIRS
--make_dirs=deps/jellyfish-2.2.0 deps/seqan-library-2.0.0 lib src tests
-+make_dirs=lib src tests
+ libkat_la_LDFLAGS = \
+   -version-info 2:4:0 \
+-  -L../deps/jellyfish-2.2.0 \
+-  -L../deps/boost/build/lib
++  -L../deps/jellyfish-2.2.0
  
- if MAKE_PYKAT
- make_dirs += scripts
 tests/Makefile.am.ori  2018-04-22 12:31:02.738203085 +0200
-+++ tests/Makefile.am  2018-04-22 12:34:15.043648336 +0200
-@@ -29,8 +29,7 @@
+ libkat_la_SOURCES = \
+   src/matrix_metadata_extractor.cc \
+@@ -31,7 +30,6 @@
  
- AM_CPPFLAGS = \
+ libkat_la_CPPFLAGS = \
+   -I$(top_srcdir)/deps/jellyfish-2.2.0/include \
+-  -I$(top_srcdir)/deps/boost/build/include \
-I$(top_srcdir)/lib/include \
--  -I$(top_srcdir)/deps/seqan-library-2.0.0/include \
--

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

2018-04-22 Thread Martin Mokrejs 
commit: fb4f6614269a5413ca8d03aeb6707aabad9ec8cb
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Sun Apr 22 11:56:50 2018 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Sun Apr 22 11:57:19 2018 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=fb4f6614

sci-biology/kat: remove lines commented out

Package-Manager: Portage-2.3.28, Repoman-2.3.9
Signed-off-by: Martin Mokrejs  fold.natur.cuni.cz>

 sci-biology/kat/kat-.ebuild | 12 
 1 file changed, 12 deletions(-)

diff --git a/sci-biology/kat/kat-.ebuild b/sci-biology/kat/kat-.ebuild
index c59669fc5..2c88b2a25 100644
--- a/sci-biology/kat/kat-.ebuild
+++ b/sci-biology/kat/kat-.ebuild
@@ -33,9 +33,6 @@ src_prepare(){
rm -rf deps || die "Failed to zap bundled seqan-library-2.0.0 
jellyfish-2.2.0 boost"
epatch "${FILESDIR}"/kat-2.4.1-ignore-bundled-deps.patch
epatch "${FILESDIR}"/kat-2.4.1-rename-jellyfish.patch
-   # autogen.sh
-   #test -n "$srcdir" || local srcdir=`dirname "$0"`
-   #test -n "$srcdir" || local srcdir=.
eautoreconf --force --install --verbose "$srcdir"
 }
 
@@ -45,12 +42,3 @@ src_configure(){
use cpu_flags_x86_sse && myconf+=( $(use_with cpu_flags_x86_sse sse) ) 
# pass down to jellyfish-2.20/configure
PYTHON_VERSION=3 econf ${myconf[@]}
 }
-
-#src_compile(){
-#  # build_boost.sh
-#  cd deps/boost || die
-#  ./bootstrap.sh --prefix=build 
--with-libraries=chrono,exception,program_options,timer,filesystem,system,stacktrace
 || die
-#  ./b2 headers --prefix=build || die
-#  ./b2 install --prefix=build || die
-#  cd ../.. || die
-#}

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

2018-04-22 Thread Martin Mokrejs 
commit: 8ee8fd95880516f79f8693c728d0ec218fa82277
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Sun Apr 22 11:45:10 2018 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Sun Apr 22 11:45:10 2018 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=8ee8fd95

sci-biology/kat: ignore site-wide boost-build/site-config.jam

Introduce - ebuild which zaps bundled stuff altogether and uses
system-wide boost and jellyfish2 files.

Package-Manager: Portage-2.3.28, Repoman-2.3.9

 .../kat/files/kat-2.4.1-ignore-bundled-deps.patch  | 120 
 .../kat/files/kat-2.4.1-rename-jellyfish.patch | 159 +
 sci-biology/kat/kat-2.4.1.ebuild   |   7 +-
 .../kat/{kat-.ebuild => kat-.ebuild}   |  23 +--
 sci-biology/kat/kat-.ebuild|   7 +-
 5 files changed, 300 insertions(+), 16 deletions(-)

diff --git a/sci-biology/kat/files/kat-2.4.1-ignore-bundled-deps.patch 
b/sci-biology/kat/files/kat-2.4.1-ignore-bundled-deps.patch
new file mode 100644
index 0..d1816498e
--- /dev/null
+++ b/sci-biology/kat/files/kat-2.4.1-ignore-bundled-deps.patch
@@ -0,0 +1,120 @@
+--- configure.ac.ori   2018-04-22 12:19:37.318794996 +0200
 configure.ac   2018-04-22 12:20:43.310663598 +0200
+@@ -172,8 +172,8 @@
+ 
+ 
+ AC_CONFIG_HEADERS([config.h])
+-AC_CONFIG_FILES([Makefile doc/Makefile doc/source/conf.py lib/kat.pc 
lib/Makefile src/Makefile tests/Makefile tests/compat.sh 
deps/seqan-library-2.0.0/Makefile scripts/setup.py scripts/kat/__init__.py 
scripts/Makefile])
+-AC_CONFIG_SUBDIRS([deps/jellyfish-2.2.0])
++AC_CONFIG_FILES([Makefile doc/Makefile doc/source/conf.py lib/kat.pc 
lib/Makefile src/Makefile tests/Makefile tests/compat.sh scripts/setup.py 
scripts/kat/__init__.py scripts/Makefile])
++AC_CONFIG_SUBDIRS([])
+ AC_OUTPUT
+ 
+ pystr="detected ${PYTHON_VERSION}.  Plotting and downstream analysis enabled."
+--- Makefile.am.ori2018-04-22 12:23:58.756197763 +0200
 Makefile.am2018-04-22 12:24:21.176832618 +0200
+@@ -19,7 +19,7 @@
+ dist_noinst_SCRIPTS = autogen.sh antigen.sh build_boost.sh
+ 
+ # SRC DIRS
+-make_dirs=deps/jellyfish-2.2.0 deps/seqan-library-2.0.0 lib src tests
++make_dirs=lib src tests
+ 
+ if MAKE_PYKAT
+ make_dirs += scripts
+--- tests/Makefile.am.ori  2018-04-22 12:31:02.738203085 +0200
 tests/Makefile.am  2018-04-22 12:34:15.043648336 +0200
+@@ -29,8 +29,7 @@
+ 
+ AM_CPPFLAGS = \
+   -I$(top_srcdir)/lib/include \
+-  -I$(top_srcdir)/deps/seqan-library-2.0.0/include \
+-  -I$(top_srcdir)/deps/jellyfish-2.2.0/include \
++  -I$(top_srcdir)/usr/include/seqan-2.2 \
+   -I$(top_srcdir)/deps/boost/build/include \
+   -DDATADIR=\"$(srcdir)/data\" \
+   -DKAT_SITE_PKGS='"$(libdir)/python$(PYTHON_VERSION)/site-packages"' \
+@@ -60,7 +59,6 @@
+   -static \
+   -L. \
+   -L../lib \
+-  -L../deps/jellyfish-2.2.0 \
+   -L../deps/boost/build/lib \
+   @AM_LDFLAGS@
+ 
+@@ -69,11 +67,11 @@
+   -lgtest \
+   -lkat \
+   -lkat_jellyfish \
+-  ../deps/boost/build/lib/libboost_timer.a \
+-../deps/boost/build/lib/libboost_chrono.a \
+-../deps/boost/build/lib/libboost_filesystem.a \
+-../deps/boost/build/lib/libboost_program_options.a \
+-../deps/boost/build/lib/libboost_system.a \
++  -lboost_timer \
++  -lboost_chrono \
++  -lboost_filesystem \
++  -lboost_program_options \
++  -lboost_system \
+   @AM_LIBS@
+ 
+ include gtest.mk
+--- src/Makefile.am.ori2018-04-22 12:34:41.874408065 +0200
 src/Makefile.am2018-04-22 12:36:33.567570728 +0200
+@@ -12,9 +12,7 @@
+   @AM_CXXFLAGS@
+ 
+ kat_CPPFLAGS = \
+-  -I$(top_srcdir)/deps/seqan-library-2.0.0/include \
+-  -I$(top_srcdir)/deps/jellyfish-2.2.0/include \
+-  -I$(top_srcdir)/deps/boost/build/include \
++  -I/usr/include/seqan-2.2 \
+   -I$(top_srcdir)/lib/include \
+   -DKAT_SITE_PKGS='"$(libdir)/python$(PYTHON_VERSION)/site-packages"' \
+   @AM_CPPFLAGS@
+@@ -22,18 +20,16 @@
+ kat_LDFLAGS = \
+   -static \
+   -L../lib \
+-  -L../deps/jellyfish-2.2.0 \
+-  -L../deps/boost/build/lib \
+   @AM_LDFLAGS@
+ 
+ kat_LDADD = \
+   -lkat \
+   -lkat_jellyfish \
+-  ../deps/boost/build/lib/libboost_timer.a \
+-  ../deps/boost/build/lib/libboost_chrono.a \
+-  ../deps/boost/build/lib/libboost_filesystem.a \
+-  ../deps/boost/build/lib/libboost_program_options.a \
+-  ../deps/boost/build/lib/libboost_system.a \
++  -lboost_timer \
++  -lboost_chrono \
++  -lboost_filesystem \
++  -lboost_program_options \
++  -lboost_system \
+   @AM_LIBS@
+ 
+ noinst_HEADERS = \
+--- lib/Makefile.am.ori2018-04-22 12:38:29.680858551 +0200
 lib/Makefile.am2018-04-22 12:38:58.401671799 +0200
+@@ -6,9 +6,7 @@
+ lib_LTLIBRARIES = libkat.la
+ 
+ libkat_la_LDFLAGS = \
+-  -version-info 2:4:0 \
+-

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

2018-04-22 Thread Martin Mokrejs 
commit: aca4c5886f2dc4991a59805666245be2a627f0ea
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Sun Apr 22 08:57:59 2018 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Sun Apr 22 08:57:59 2018 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=aca4c588

sci-biology/kat: execute the build_boost.sh and autogen.sh logic

Execute the commands from within ebuild to ease debugging of errors.

See https://github.com/TGAC/KAT/issues/92

Package-Manager: Portage-2.3.28, Repoman-2.3.9

 sci-biology/kat/kat-2.4.1.ebuild | 15 +--
 sci-biology/kat/kat-.ebuild  | 21 ++---
 2 files changed, 31 insertions(+), 5 deletions(-)

diff --git a/sci-biology/kat/kat-2.4.1.ebuild b/sci-biology/kat/kat-2.4.1.ebuild
index 466b5431e..1df9f4430 100644
--- a/sci-biology/kat/kat-2.4.1.ebuild
+++ b/sci-biology/kat/kat-2.4.1.ebuild
@@ -32,8 +32,10 @@ S="${WORKDIR}"/KAT-Release-"${PV}"
 
 src_prepare(){
default
-   sh build_boost.sh || die
-   sh autogen.sh || die
+   # autogen.sh
+   test -n "$srcdir" || local srcdir=`dirname "$0"`
+   test -n "$srcdir" || local srcdir=.
+   eautoreconf --force --install --verbose "$srcdir"
 }
 
 src_configure(){
@@ -42,3 +44,12 @@ src_configure(){
use cpu_flags_x86_sse && myconf+=( $(use_with cpu_flags_x86_sse sse) ) 
# pass down to jellyfish-2.20/configure
PYTHON_VERSION=3 econf ${myconf[@]}
 }
+
+src_compile(){
+   # build_boost.sh
+   cd deps/boost || die
+   ./bootstrap.sh --prefix=build 
--with-libraries=chrono,exception,program_options,timer,filesystem,system,stacktrace
 || die
+   ./b2 headers || die
+   ./b2 install || die
+   cd ../.. || die
+}

diff --git a/sci-biology/kat/kat-.ebuild b/sci-biology/kat/kat-.ebuild
index 39107167a..d46f6d3e8 100644
--- a/sci-biology/kat/kat-.ebuild
+++ b/sci-biology/kat/kat-.ebuild
@@ -6,7 +6,7 @@ EAPI=6
 PYTHON_COMPAT=( python3_{5,6} ) # requires python >= 3.1 but more features 
with >=3.5
 # https://github.com/Ensembl/Bio-DB-HTS/issues/30
 
-inherit git-r3 eutils flag-o-matic
+inherit git-r3 eutils flag-o-matic autotools
 
 DESCRIPTION="K-mer Analysis Toolkit (histogram, filter, compare sets, plot)"
 HOMEPAGE="https://github.com/TGAC/KAT;
@@ -29,10 +29,25 @@ RDEPEND="${DEPEND}"
 # contains embedded sci-biology/seqan
 
 src_prepare(){
-   sh build_boost.sh || die
-   sh autogen.sh . || die
+   default
+   # autogen.sh
+   test -n "$srcdir" || local srcdir=`dirname "$0"`
+   test -n "$srcdir" || local srcdir=.
+   eautoreconf --force --install --verbose "$srcdir"
+}
+
+src_configure(){
local myconf=()
myconf+=( --disable-gnuplot ) # python3 does better image rendering, no 
need for gnuplot
use cpu_flags_x86_sse && myconf+=( $(use_with cpu_flags_x86_sse sse) ) 
# pass down to jellyfish-2.20/configure
PYTHON_VERSION=3 econf ${myconf[@]}
 }
+
+src_compile(){
+   # build_boost.sh
+   cd deps/boost || die
+   ./bootstrap.sh --prefix=build 
--with-libraries=chrono,exception,program_options,timer,filesystem,system,stacktrace
 || die
+   ./b2 headers || die
+   ./b2 install || die
+   cd ../.. || die
+}

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

2018-04-21 Thread Martin Mokrejs 
commit: 9d6fa783c4d323bddcc63ae47a2c8c3c2d47580e
Author: Martin Mokrejs  fold  natur  cuni  cz>
AuthorDate: Sat Apr 21 15:25:37 2018 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Sat Apr 21 15:25:37 2018 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=9d6fa783

sci-biology/kat: version bump

Lets require >=python-3.5 for best feature availability.

The source code contain bundled sci-libs/boost and
sci-biology/seqan.

It also contain (unfortunately modified) sci-biology/jellyfish-2.2.0

https://github.com/TGAC/KAT/issues/92

Package-Manager: Portage-2.3.28, Repoman-2.3.9

 sci-biology/kat/kat-2.2.0.ebuild | 31 
 sci-biology/kat/kat-2.4.1.ebuild | 44 
 sci-biology/kat/kat-.ebuild  | 18 
 3 files changed, 54 insertions(+), 39 deletions(-)

diff --git a/sci-biology/kat/kat-2.2.0.ebuild b/sci-biology/kat/kat-2.2.0.ebuild
deleted file mode 100644
index 396d9cc4a..0
--- a/sci-biology/kat/kat-2.2.0.ebuild
+++ /dev/null
@@ -1,31 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python{2_7,3_4,3_5} ) # 
https://github.com/Ensembl/Bio-DB-HTS/issues/30
-
-inherit python-r1 eutils flag-o-matic
-
-DESCRIPTION="K-mer Analysis Toolkit (histogram, filter, compare sets, plot)"
-HOMEPAGE="https://github.com/TGAC/KAT;
-SRC_URI="https://github.com/TGAC/KAT/releases/download/Release-${PV}/${P}.tar.gz;
-
-LICENSE="GPL-3+"
-SLOT="0"
-KEYWORDS=""
-IUSE="cpu_flags_x86_sse"
-
-DEPEND="dev-libs/boost:0
-   dev-python/matplotlib
-   sci-visualization/gnuplot"
-RDEPEND="${DEPEND}"
-# contains bundled modified version of jellyfish-2.2 which should install 
under different filenames
-
-src_configure(){
-   local myconf=()
-   myconf+=( --disable-gnuplot ) # python3 does better image rendering, no 
need for gnuplot
-   use cpu_flags_x86_sse && myconf+=( $(use_with cpu_flags_x86_sse sse) ) 
# pass down to jellyfish-2.20/configure
-   PYTHON_VERSION=3 econf ${myconf[@]}
-   eapply_user
-}

diff --git a/sci-biology/kat/kat-2.4.1.ebuild b/sci-biology/kat/kat-2.4.1.ebuild
new file mode 100644
index 0..466b5431e
--- /dev/null
+++ b/sci-biology/kat/kat-2.4.1.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python3_{5,6} ) # requires python >= 3.1 but more features 
with >=3.5
+# https://github.com/Ensembl/Bio-DB-HTS/issues/30
+
+inherit python-r1 eutils flag-o-matic
+
+DESCRIPTION="K-mer Analysis Toolkit (histogram, filter, compare sets, plot)"
+HOMEPAGE="https://github.com/TGAC/KAT;
+SRC_URI="https://github.com/TGAC/KAT/archive/Release-${PV}.tar.gz -> 
${P}.tar.gz"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS=""
+IUSE="cpu_flags_x86_sse doc"
+
+DEPEND="
+   >=dev-libs/boost-1.52
+   dev-python/tabulate
+   dev-python/matplotlib
+   dev-python/numpy
+   sci-libs/scipy
+   doc? ( dev-python/sphinx )"
+RDEPEND="${DEPEND}"
+# contains bundled *modified* version of jellyfish-2.2 which should install 
under different filenames
+# contains embedded sci-biology/seqan
+
+S="${WORKDIR}"/KAT-Release-"${PV}"
+
+src_prepare(){
+   default
+   sh build_boost.sh || die
+   sh autogen.sh || die
+}
+
+src_configure(){
+   local myconf=()
+   myconf+=( --disable-gnuplot ) # python3 does better image rendering, no 
need for gnuplot
+   use cpu_flags_x86_sse && myconf+=( $(use_with cpu_flags_x86_sse sse) ) 
# pass down to jellyfish-2.20/configure
+   PYTHON_VERSION=3 econf ${myconf[@]}
+}

diff --git a/sci-biology/kat/kat-.ebuild b/sci-biology/kat/kat-.ebuild
index 4290739f5..39107167a 100644
--- a/sci-biology/kat/kat-.ebuild
+++ b/sci-biology/kat/kat-.ebuild
@@ -1,9 +1,10 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
 
-PYTHON_COMPAT=( python{3_4,3_5} ) # requires python >= 3.1
+PYTHON_COMPAT=( python3_{5,6} ) # requires python >= 3.1 but more features 
with >=3.5
+# https://github.com/Ensembl/Bio-DB-HTS/issues/30
 
 inherit git-r3 eutils flag-o-matic
 
@@ -14,23 +15,24 @@ EGIT_REPO_URI="https://github.com/TGAC/KAT.git;
 LICENSE="GPL-3+"
 SLOT="0"
 KEYWORDS=""
-IUSE="cpu_flags_x86_sse"
+IUSE="cpu_flags_x86_sse doc"
 
 DEPEND="
-   dev-lang/python:3
>=dev-libs/boost-1.52
+   dev-python/tabulate
dev-python/matplotlib
dev-python/numpy
sci-libs/scipy
-   dev-python/sphinx"
+   doc? ( dev-python/sphinx )"
 RDEPEND="${DEPEND}"
-# contains bundled a modified version of jellyfish-2.2.0 
(libkat_jellyfish.{a,so})
+# contains bundled a *modified* version of jellyfish-2.2.0 
(libkat_jellyfish.{a,so})
+# contains embedded sci-biology/seqan
 
 src_prepare(){
-

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

2016-12-09 Thread Martin Mokrejs 
commit: d8e71f09eab8f04e79adb3f1772e680a0a24
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Fri Dec  9 16:26:07 2016 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Fri Dec  9 16:26:07 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=d8e71f09

sci-biology/kat: respect sse CPU USE flags

Package-Manager: portage-2.3.3

 sci-biology/kat/kat-2.2.0.ebuild | 10 +++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/sci-biology/kat/kat-2.2.0.ebuild b/sci-biology/kat/kat-2.2.0.ebuild
index 38ddae2..fbd3834 100644
--- a/sci-biology/kat/kat-2.2.0.ebuild
+++ b/sci-biology/kat/kat-2.2.0.ebuild
@@ -6,7 +6,7 @@ EAPI=6
 
 PYTHON_COMPAT=( python{2_7,3_4,3_5} ) # 
https://github.com/Ensembl/Bio-DB-HTS/issues/30
 
-inherit python-r1
+inherit python-r1 eutils flag-o-matic
 
 DESCRIPTION="K-mer Analysis Toolkit (histogram, filter, compare sets, plot)"
 HOMEPAGE="https://github.com/TGAC/KAT;
@@ -15,7 +15,7 @@ 
SRC_URI="https://github.com/TGAC/KAT/releases/download/Release-${PV}/${P}.tar.gz
 LICENSE="GPL-3+"
 SLOT="0"
 KEYWORDS=""
-IUSE=""
+IUSE="cpu_flags_x86_sse"
 
 DEPEND="dev-libs/boost:0
dev-python/matplotlib
@@ -24,5 +24,9 @@ RDEPEND="${DEPEND}"
 # contains bundled modified version of jellyfish-2.2 which should install 
under different filenames
 
 src_configure(){
-   econf PYTHON_VERSION="${PYTHON_SINGLE_TARGET}"
+   local myconf=()
+   myconf+=( --disable-gnuplot ) # python3 does better image rendering, no 
need for gnuplot
+   use cpu_flags_x86_sse && myconf+=( $(use_with cpu_flags_x86_sse sse) ) 
# pass down to jellyfish-2.20/configure
+   PYTHON_VERSION=3 econf ${myconf[@]}
+   eapply_user
 }

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

2016-12-09 Thread Martin Mokrejs 
commit: 25e7181982a0e06eab199571be8765db4633591c
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Fri Dec  9 16:24:23 2016 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Fri Dec  9 16:24:23 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=25e71819

sci-biology/kat:

Package-Manager: portage-2.3.3

 sci-biology/kat/kat-.ebuild | 20 ++--
 1 file changed, 14 insertions(+), 6 deletions(-)

diff --git a/sci-biology/kat/kat-.ebuild b/sci-biology/kat/kat-.ebuild
index e8735e4..782d3fc 100644
--- a/sci-biology/kat/kat-.ebuild
+++ b/sci-biology/kat/kat-.ebuild
@@ -6,7 +6,7 @@ EAPI=6
 
 PYTHON_COMPAT=( python{3_4,3_5} ) # requires python >= 3.1
 
-inherit git-r3
+inherit git-r3 eutils flag-o-matic
 
 DESCRIPTION="K-mer Analysis Toolkit (histogram, filter, compare sets, plot)"
 HOMEPAGE="https://github.com/TGAC/KAT;
@@ -15,15 +15,23 @@ EGIT_REPO_URI="https://github.com/TGAC/KAT.git;
 LICENSE="GPL-3+"
 SLOT="0"
 KEYWORDS=""
-IUSE=""
+IUSE="cpu_flags_x86_sse"
 
-DEPEND="dev-libs/boost:0
+DEPEND="
+   dev-lang/python:3
+   >=dev-libs/boost-1.52
dev-python/matplotlib
-   sci-visualization/gnuplot"
+   dev-python/numpy
+   sci-libs/scipy
+   dev-python/sphinx"
 RDEPEND="${DEPEND}"
-# contains bundled a modified version of jellyfish-2.2.0
+# contains bundled a modified version of jellyfish-2.2.0 
(libkat_jellyfish.{a,so})
 
 src_prepare(){
sh ./autogen.sh . || die
-   default
+   local myconf=()
+   myconf+=( --disable-gnuplot ) # python3 does better image rendering, no 
need for gnuplot
+   use cpu_flags_x86_sse && myconf+=( $(use_with cpu_flags_x86_sse sse) ) 
# pass down to jellyfish-2.20/configure
+   PYTHON_VERSION=3 econf ${myconf[@]}
+   eapply_user
 }

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

2016-11-30 Thread Martin Mokrejs 
commit: 1d87d213225badbbf304e163a61815219052cca4
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Wed Nov 30 22:33:40 2016 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Wed Nov 30 22:33:40 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=1d87d213

sci-biology/kat: version bump, blocked by upstream issue #61

Package-Manager: portage-2.3.2

 sci-biology/kat/{kat-2.1.1.ebuild => kat-2.2.0.ebuild} | 10 --
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/sci-biology/kat/kat-2.1.1.ebuild b/sci-biology/kat/kat-2.2.0.ebuild
similarity index 62%
rename from sci-biology/kat/kat-2.1.1.ebuild
rename to sci-biology/kat/kat-2.2.0.ebuild
index 8133fdb..38ddae2 100644
--- a/sci-biology/kat/kat-2.1.1.ebuild
+++ b/sci-biology/kat/kat-2.2.0.ebuild
@@ -4,7 +4,9 @@
 
 EAPI=6
 
-PYTHON_COMPAT=( python{3_4,3_5} ) # requires python >= 3.1
+PYTHON_COMPAT=( python{2_7,3_4,3_5} ) # 
https://github.com/Ensembl/Bio-DB-HTS/issues/30
+
+inherit python-r1
 
 DESCRIPTION="K-mer Analysis Toolkit (histogram, filter, compare sets, plot)"
 HOMEPAGE="https://github.com/TGAC/KAT;
@@ -19,4 +21,8 @@ DEPEND="dev-libs/boost:0
dev-python/matplotlib
sci-visualization/gnuplot"
 RDEPEND="${DEPEND}"
-# contains bundled modified version of jellyfish-2.2.
+# contains bundled modified version of jellyfish-2.2 which should install 
under different filenames
+
+src_configure(){
+   econf PYTHON_VERSION="${PYTHON_SINGLE_TARGET}"
+}

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

2016-10-17 Thread Martin Mokrejs 
commit: 4df5011f6c061f637cfb0cd3629a5f0a8fcc25de
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Mon Oct 17 16:46:05 2016 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Mon Oct 17 16:46:05 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=4df5011f

sci-biology/kat: fix SRC_URI

use SRC_URI for a real release, not for an automatically generated github 
tarball (upstream issue #59)

Package-Manager: portage-2.3.0

 sci-biology/kat/kat-2.1.1.ebuild | 9 +
 1 file changed, 1 insertion(+), 8 deletions(-)

diff --git a/sci-biology/kat/kat-2.1.1.ebuild b/sci-biology/kat/kat-2.1.1.ebuild
index 3a184c9..8133fdb 100644
--- a/sci-biology/kat/kat-2.1.1.ebuild
+++ b/sci-biology/kat/kat-2.1.1.ebuild
@@ -8,7 +8,7 @@ PYTHON_COMPAT=( python{3_4,3_5} ) # requires python >= 3.1
 
 DESCRIPTION="K-mer Analysis Toolkit (histogram, filter, compare sets, plot)"
 HOMEPAGE="https://github.com/TGAC/KAT;
-SRC_URI="https://github.com/TGAC/KAT/archive/Release-${PV}.tar.gz -> 
${P}.tar.gz"
+SRC_URI="https://github.com/TGAC/KAT/releases/download/Release-${PV}/${P}.tar.gz;
 
 LICENSE="GPL-3+"
 SLOT="0"
@@ -20,10 +20,3 @@ DEPEND="dev-libs/boost:0
sci-visualization/gnuplot"
 RDEPEND="${DEPEND}"
 # contains bundled modified version of jellyfish-2.2.
-
-S="${WORKDIR}"/KAT-Release-"${PV}"
-
-src_prepare(){
-   sh ./autogen.sh . || die
-   default
-}

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

2016-10-17 Thread Martin Mokrejs 
commit: 02cb4dded41609783964b8a0f6d01dde60455535
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Mon Oct 17 15:21:39 2016 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Mon Oct 17 15:21:39 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=02cb4dde

sci-biology/kat: new package

Boost library is not found during linking step

Package needs >=python-3.1 as the default python interpreter (for what?)

The bundled jellyfish code seems to result in a renamed library and *.pc
file so probably it will not clash with system-wide jellyfish

Package-Manager: portage-2.3.0

 sci-biology/kat/kat-2.1.1.ebuild | 29 +
 sci-biology/kat/kat-.ebuild  | 29 +
 sci-biology/kat/metadata.xml | 12 
 3 files changed, 70 insertions(+)

diff --git a/sci-biology/kat/kat-2.1.1.ebuild b/sci-biology/kat/kat-2.1.1.ebuild
new file mode 100644
index 000..3a184c9
--- /dev/null
+++ b/sci-biology/kat/kat-2.1.1.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+PYTHON_COMPAT=( python{3_4,3_5} ) # requires python >= 3.1
+
+DESCRIPTION="K-mer Analysis Toolkit (histogram, filter, compare sets, plot)"
+HOMEPAGE="https://github.com/TGAC/KAT;
+SRC_URI="https://github.com/TGAC/KAT/archive/Release-${PV}.tar.gz -> 
${P}.tar.gz"
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="dev-libs/boost:0
+   dev-python/matplotlib
+   sci-visualization/gnuplot"
+RDEPEND="${DEPEND}"
+# contains bundled modified version of jellyfish-2.2.
+
+S="${WORKDIR}"/KAT-Release-"${PV}"
+
+src_prepare(){
+   sh ./autogen.sh . || die
+   default
+}

diff --git a/sci-biology/kat/kat-.ebuild b/sci-biology/kat/kat-.ebuild
new file mode 100644
index 000..e8735e4
--- /dev/null
+++ b/sci-biology/kat/kat-.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+PYTHON_COMPAT=( python{3_4,3_5} ) # requires python >= 3.1
+
+inherit git-r3
+
+DESCRIPTION="K-mer Analysis Toolkit (histogram, filter, compare sets, plot)"
+HOMEPAGE="https://github.com/TGAC/KAT;
+EGIT_REPO_URI="https://github.com/TGAC/KAT.git;
+
+LICENSE="GPL-3+"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="dev-libs/boost:0
+   dev-python/matplotlib
+   sci-visualization/gnuplot"
+RDEPEND="${DEPEND}"
+# contains bundled a modified version of jellyfish-2.2.0
+
+src_prepare(){
+   sh ./autogen.sh . || die
+   default
+}

diff --git a/sci-biology/kat/metadata.xml b/sci-biology/kat/metadata.xml
new file mode 100644
index 000..f68a1b6
--- /dev/null
+++ b/sci-biology/kat/metadata.xml
@@ -0,0 +1,12 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+  
+mmokr...@fold.natur.cuni.cz
+Martin Mokrejs
+  
+  
+sci-biol...@gentoo.org
+Gentoo Biology Project
+  
+