[gentoo-commits] proj/sci:master commit in: sci-astronomy/sextractor/, sci-astronomy/psfex/, sci-astronomy/sextractor/files/, ...

[Sebastien Fabbro]

commit:     f5d0d9fcf03e7f67c4815305cd00b2cd738f082f
Author:     Sébastien Fabbro <sebfabbro <AT> gmail <DOT> com>
AuthorDate: Mon Nov 28 21:35:17 2011 +0000
Commit:     Sebastien Fabbro <bicatali <AT> gentoo <DOT> org>
CommitDate: Mon Nov 28 21:35:17 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f5d0d9fc

fixed astromatic packages for recent ATLAS

---
 sci-astronomy/psfex/ChangeLog                      |    6 ++
 sci-astronomy/psfex/psfex-3.9.1-r1.ebuild          |   50 ++++++++++++
 sci-astronomy/psfex/psfex-3.9.1.ebuild             |   45 -----------
 sci-astronomy/scamp/ChangeLog                      |   75 +++++++++++++++++
 sci-astronomy/scamp/metadata.xml                   |   13 +++
 sci-astronomy/scamp/scamp-1.7.0-r1.ebuild          |   51 ++++++++++++
 sci-astronomy/sextractor/ChangeLog                 |   48 +++++++++++
 .../sextractor/files/sextractor-configure.patch    |   84 ++++++++++++++++++++
 sci-astronomy/sextractor/metadata.xml              |   13 +++
 .../sextractor/sextractor-2.8.6-r1.ebuild          |   55 +++++++++++++
 10 files changed, 395 insertions(+), 45 deletions(-)

diff --git a/sci-astronomy/psfex/ChangeLog b/sci-astronomy/psfex/ChangeLog
index 194a9b9..24df270 100644
--- a/sci-astronomy/psfex/ChangeLog
+++ b/sci-astronomy/psfex/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*psfex-3.9.1-r1 (28 Nov 2011)
+
+  28 Nov 2011; Sébastien Fabbro <bicatali@g.o> -psfex-3.9.1.ebuild,
+  +psfex-3.9.1-r1.ebuild:
+  Fixed for recent ATLAS. Switch to EAPI4
+
   04 Aug 2011; Sébastien Fabbro <bicatali@g.o> metadata.xml:
   Switched herd to sci-astronomy
 

diff --git a/sci-astronomy/psfex/psfex-3.9.1-r1.ebuild b/sci-astronomy/psfex/psfex-3.9.1-r1.ebuild
new file mode 100644
index 0000000..d94b5c3
--- /dev/null
+++ b/sci-astronomy/psfex/psfex-3.9.1-r1.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=4
+inherit eutils
+
+DESCRIPTION="Extracts models of the Point Spread Function from FITS images"
+HOMEPAGE="http://www.astromatic.net/software/psfex"
+SRC_URI="http://www.astromatic.net/download/${PN}/${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc plplot threads"
+
+RDEPEND="virtual/cblas
+	sci-libs/atlas
+	sci-libs/fftw:3.0
+	plplot? ( sci-libs/plplot )"
+DEPEND="${RDEPEND}
+	dev-util/pkgconfig"
+
+src_prepare() {
+	local mycblas=atlcblas  myclapack=atlclapack
+	if use threads; then
+		[[ -e ${EPREFIX}/usr/$(get_libdir)/libptcblas.so ]] && mycblas=ptcblas
+		[[ -e ${EPREFIX}/usr/$(get_libdir)/libptclapack.so ]] && myclapack=ptclapack
+	fi
+	# fix the configure and not the acx_atlas.m4. the eautoreconf will
+	# produce a configure giving  a wrong install Makefile target (to fix)
+	sed -i \
+		-e "s/-lcblas/-l${mycblas}/g" \
+		-e "s/AC_CHECK_LIB(cblas/AC_CHECK_LIB(${mycblas}/g" \
+		-e "s/-llapack/-l${myclapack}/g" \
+		-e "s/AC_CHECK_LIB(lapack/AC_CHECK_LIB(${myclapack}/g" \
+		configure || die "sed acx_atlas.m4 failed"
+}
+
+src_configure() {
+	econf \
+		--with-atlas-incdir="${EROOT}/usr/include/atlas" \
+		$(use_with plplot) \
+		$(use_enable threads)
+}
+
+src_install () {
+	default
+	use doc && dodoc doc/*.pdf
+}

diff --git a/sci-astronomy/psfex/psfex-3.9.1.ebuild b/sci-astronomy/psfex/psfex-3.9.1.ebuild
deleted file mode 100644
index 3530ea9..0000000
--- a/sci-astronomy/psfex/psfex-3.9.1.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-astronomy/scamp/scamp-1.7.0.ebuild,v 1.1 2010/05/03 21:44:04 bicatali Exp $
-
-EAPI=3
-inherit eutils
-
-DESCRIPTION="Extracts models of the Point Spread Function from FITS images"
-HOMEPAGE="http://www.astromatic.net/software/psfex"
-SRC_URI="http://www.astromatic.net/download/${PN}/${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc plplot threads"
-
-RDEPEND="virtual/cblas
-	sci-libs/lapack-atlas
-	sci-libs/fftw:3.0
-	plplot? ( sci-libs/plplot )"
-DEPEND="${RDEPEND}
-	dev-util/pkgconfig"
-
-src_prepare() {
-	# gentoo uses cblas instead of ptcblas (linked to threaded with eselect)
-	sed -i \
-		-e 's/ptcblas/cblas/g' \
-		configure || die "sed failed"
-}
-
-src_configure() {
-	econf \
-		--with-atlas="${EPREFIX}/usr/$(get_libdir)/lapack/atlas" \
-		$(use_with plplot) \
-		$(use_enable threads)
-}
-
-src_install () {
-	emake DESTDIR="${D}" install || die "emake install failed"
-	dodoc AUTHORS ChangeLog HISTORY README THANKS BUGS
-	if use doc; then
-		insinto /usr/share/doc/${PF}
-		doins doc/*.pdf || die "pdf doc install failed"
-	fi
-}

diff --git a/sci-astronomy/scamp/ChangeLog b/sci-astronomy/scamp/ChangeLog
new file mode 100644
index 0000000..2de8c44
--- /dev/null
+++ b/sci-astronomy/scamp/ChangeLog
@@ -0,0 +1,75 @@
+# ChangeLog for sci-astronomy/scamp
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-astronomy/scamp/ChangeLog,v 1.7 2011/08/04 18:32:22 bicatali Exp $
+
+*scamp-1.7.0-r1 (28 Nov 2011)
+
+  28 Nov 2011; Sébastien Fabbro <bicatali@g.o> +scamp-1.7.0-r1.ebuild,
+  +metadata.xml:
+  Fixed for recent ATLAS. Switch to EAPI4
+
+  04 Aug 2011; Sébastien Fabbro <bicatali@g.o> metadata.xml:
+  Switched herd to sci-astronomy
+
+*scamp-1.7.0 (03 May 2010)
+
+  03 May 2010; Sébastien Fabbro <bicatali@g.o> -scamp-1.5.5.ebuild,
+  +scamp-1.7.0.ebuild:
+  Version bump
+
+*scamp-1.6.2 (04 Nov 2009)
+
+  04 Nov 2009; Sébastien Fabbro <bicatali@g.o> -scamp-1.4.6.ebuild,
+  +scamp-1.6.2.ebuild:
+  Version bump
+
+  28 Jul 2009; Sébastien Fabbro <bicatali@g.o> scamp-1.5.5.ebuild:
+  Updated license to CeCILL-2
+
+*scamp-1.5.5 (28 Jul 2009)
+
+  28 Jul 2009; Sébastien Fabbro <bicatali@g.o> +scamp-1.5.5.ebuild,
+  +files/scamp-1.5.5-autotools.patch:
+  Version bumpp
+
+  05 Mar 2009; Sébastien Fabbro <bicatali@g.o>
+  files/scamp-1.4.6-autotools.patch:
+  More plplot patching
+
+*scamp-1.4.6 (26 Feb 2009)
+
+  26 Feb 2009; Sébastien Fabbro <bicatali@g.o>
+  +files/scamp-1.4.6-autotools.patch, +metadata.xml, +scamp-1.4.6.ebuild:
+  Initial import to the main tree from the sci overlay. Also included
+  autotools from scamp svn public repository for better dependencies
+
+  02 Jul 2008; Sébastien Fabbro <bicatali@g.o>
+  +files/scamp-1.4.6-plplot.patch, -files/scamp-atlas.patch,
+  -scamp-1.4.0.ebuild, +scamp-1.4.6.ebuild:
+  Version bump.
+
+  08 Nov 2007; Sébastien Fabbro <bicatali@g.o>
+  +files/scamp-atlas.patch, -scamp-1.3.11.ebuild, +scamp-1.4.0.ebuild:
+  Version bump
+
+  02 Aug 2007; Sébastien Fabbro <bicatali@g.o> -scamp-1.3.8.ebuild,
+  +scamp-1.3.11.ebuild:
+  Version bump
+
+  18 May 2007; Sébastien Fabbro <bicatali@g.o> -scamp-1.3.5.ebuild,
+  +scamp-1.3.8.ebuild:
+  Version bump
+
+  26 Mar 2007; Sébastien Fabbro <bicatali@g.o>
+  -scamp-1.2.11-r1.ebuild, +scamp-1.3.5.ebuild:
+  Version bump.
+
+  29 Dec 2006; Sebastien Fabbro <seb@×××××××.pt>;
+  Removed icc flag, too buggy.
+	
+  15 Oct 2006; Sebastien Fabbro <seb@×××××××.pt> +scamp-1.2.11-r1.ebuild:
+  Removed flag filtering, some cleaning.
+
+  19 Sep 2006; Sebastien Fabbro <seb@×××××××.pt> +scamp-1.2.11.ebuild:
+  Initial import.
+

diff --git a/sci-astronomy/scamp/metadata.xml b/sci-astronomy/scamp/metadata.xml
new file mode 100644
index 0000000..edd8754
--- /dev/null
+++ b/sci-astronomy/scamp/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci-astronomy</herd>
+<longdescription lang="en">
+  SCAMP computes astrometric and photometric solutions from SExtractor catalogs
+  and stores them in header files. These headers files can be read by SWarp to
+  coadd images.
+</longdescription>
+<use>
+  <flag name="plplot">Build with <pkg>sci-libs/plplot</pkg> to allow diagnostic plots during processing</flag>
+</use>
+</pkgmetadata>

diff --git a/sci-astronomy/scamp/scamp-1.7.0-r1.ebuild b/sci-astronomy/scamp/scamp-1.7.0-r1.ebuild
new file mode 100644
index 0000000..7c1b385
--- /dev/null
+++ b/sci-astronomy/scamp/scamp-1.7.0-r1.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=4
+inherit eutils
+
+DESCRIPTION="Astrometric and photometric solutions for astronomical images"
+HOMEPAGE="http://www.astromatic.net/software/scamp"
+SRC_URI="http://www.astromatic.net/download/${PN}/${P}.tar.gz"
+
+LICENSE="CeCILL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc threads plplot"
+
+RDEPEND=">=sci-astronomy/cdsclient-3.4
+	virtual/cblas
+	sci-libs/atlas
+	sci-libs/fftw:3.0
+	plplot? ( sci-libs/plplot )"
+DEPEND="${RDEPEND}
+	dev-util/pkgconfig"
+
+src_prepare() {
+	local mycblas=atlcblas  myclapack=atlclapack
+	if use threads; then
+		[[ -e ${EPREFIX}/usr/$(get_libdir)/libptcblas.so ]] && mycblas=ptcblas
+		[[ -e ${EPREFIX}/usr/$(get_libdir)/libptclapack.so ]] && myclapack=ptclapack
+	fi
+	# fix the configure and not the acx_atlas.m4. the eautoreconf will
+	# produce a configure giving  a wrong install Makefile target (to fix)
+	sed -i \
+		-e "s/-lcblas/-l${mycblas}/g" \
+		-e "s/AC_CHECK_LIB(cblas/AC_CHECK_LIB(${mycblas}/g" \
+		-e "s/-llapack/-l${myclapack}/g" \
+		-e "s/AC_CHECK_LIB(lapack/AC_CHECK_LIB(${myclapack}/g" \
+		configure || die "sed acx_atlas.m4 failed"
+}
+
+src_configure() {
+	econf \
+		--with-atlas-incdir="${EROOT}/usr/include/atlas" \
+		$(use_with plplot) \
+		$(use_enable threads)
+}
+
+src_install () {
+	default
+	use doc && dodoc doc/*,pdf
+}

diff --git a/sci-astronomy/sextractor/ChangeLog b/sci-astronomy/sextractor/ChangeLog
new file mode 100644
index 0000000..67fe448
--- /dev/null
+++ b/sci-astronomy/sextractor/ChangeLog
@@ -0,0 +1,48 @@
+# ChangeLog for sci-astronomy/sextractor
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-astronomy/sextractor/ChangeLog,v 1.3 2011/08/04 18:32:38 bicatali Exp $
+
+*sextractor-2.8.6-r1 (28 Nov 2011)
+
+  28 Nov 2011; Sébastien Fabbro <bicatali@g.o>
+  +sextractor-2.8.6-r1.ebuild, +files/sextractor-configure.patch,
+  +metadata.xml:
+  Fixed for recent ATLAS. Switch to EAPI4
+
+  04 Aug 2011; Sébastien Fabbro <bicatali@g.o> metadata.xml:
+  Switched herd to sci-astronomy
+
+*sextractor-2.8.6 (28 Jul 2009)
+
+  28 Jul 2009; Sébastien Fabbro <bicatali@g.o>
+  +sextractor-2.8.6.ebuild, +files/sextractor-configure.patch:
+  Version bump
+
+*sextractor-2.5.0 (17 Feb 2009)
+
+  17 Feb 2009; Sébastien Fabbro <bicatali@g.o> +metadata.xml,
+  +sextractor-2.5.0.ebuild:
+  Initial import to the main tree from the sci overlay, closing bug #65684
+
+  02 Aug 2007; Sébastien Fabbro <bicatali@g.o>
+  sextractor-2.5.0-r1.ebuild:
+  filter optim flags
+
+  26 Mar 2007; Sébastien Fabbro <bicatali@g.o>
+  sextractor-2.5.0-r1.ebuild:
+  Cleaning, adapting for new portage.
+
+  29 Dec 2006; Sebastien Fabbro <seb@×××××××.pt>;
+  Removed icc flag, too buggy.
+	
+  15 Oct 2006; Sebastien Fabbro <seb@×××××××.pt> 
+  +sextractor-2.5.0-r1.ebuild -sextractor-2.5.0.ebuild
+  -sextractor-2.4.4.ebuild: removed flag filtering, cleaning,
+  removed old versions.
+
+  06 Sep 2006; Sebastien Fabbro <seb@×××××××.pt> +sextractor-2.5.0.ebuild:
+  Version bump.
+	
+  26 Nov 2005; Sebastien Fabbro <seb@×××××××.pt> +sextractor-2.4.4.ebuild:
+  Initial import. Close bug #65684
+

diff --git a/sci-astronomy/sextractor/files/sextractor-configure.patch b/sci-astronomy/sextractor/files/sextractor-configure.patch
new file mode 100644
index 0000000..dc8957b
--- /dev/null
+++ b/sci-astronomy/sextractor/files/sextractor-configure.patch
@@ -0,0 +1,84 @@
+--- configure.ac.orig	2009-04-09 14:28:38.000000000 +0100
++++ configure.ac	2009-07-28 18:25:38.000000000 +0100
+@@ -22,42 +22,19 @@
+ # Include macros
+ sinclude(acx_atlas.m4)
+ sinclude(acx_fftw.m4)
+-sinclude(acx_prog_cc_optim.m4)
+ sinclude(acx_pthread.m4)
+ sinclude(acx_urbi_resolve_dir.m4)
+ 
+ # Display pakage and version number
+ AC_MSG_RESULT([*********** Configuring:  $PACKAGE $VERSION ($date) **********])
+ 
+-# Initialize the list of compilers to consider
+-cclist="cc gcc"
+-
+-# Backup and reset the input CFLAGS and LDFLAGS
+-mycflags="$CFLAGS"
+-CFLAGS=""
+-myldflags="$LDFLAGS"
+-LDFLAGS=""
+-
+-# Provide special option for the Linux Intel C compiler
+-AC_MSG_CHECKING([for Linux Intel C compiler mode])
+-AC_ARG_ENABLE(icc,
+-	[AC_HELP_STRING([--enable-icc],
+-	[Enable special mode for compilation with the Intel compiler \
+-(off by default)])],
+-        use_icc="yes"
+-        cclist="icc $cclist"
+-	AC_MSG_RESULT([yes]),
+-        use_icc="no"
+-	AC_MSG_RESULT([no]))
+-
+ # Checks for programs.
+ # GCC is chosen last because it is likely to yield less optimized code
+ AC_LANG(C)
+-AC_PROG_CC([$cclist])
++AC_PROG_CC
+ # C Compiler: Check that it is ANSI C and POSIX-compliant
+ AM_PROG_CC_STDC
+ AC_ISC_POSIX
+-ACX_PROG_CC_OPTIM
+ AC_DISABLE_STATIC
+ #AC_DISABLE_SHARED
+ AC_PROG_LIBTOOL
+@@ -160,17 +137,6 @@
+         use_gprof="no"
+ 	AC_MSG_RESULT([no]))
+ 
+-# Enable static linking
+-AC_MSG_CHECKING([static linking])
+-AC_ARG_ENABLE(static,
+-	[AC_HELP_STRING([--enable-static],
+-	[Enable static linking \
+-(off by default)])],
+-        use_static="yes"
+-	AC_MSG_RESULT([yes]),
+-        use_static="no"
+-	AC_MSG_RESULT([no]))
+-
+ ################# Actions to complete in case of multhreading ################
+ AC_DEFINE_UNQUOTED(THREADS_NMAX, $n_pthreads,[Maximum number of POSIX threads])
+ if test "$use_pthreads" = "yes"; then
+@@ -205,19 +171,9 @@
+ 
+ # Link with gprof option
+ if test "$use_gprof" = "yes"; then
+-  if test "$use_icc" = "yes"; then
+-    CFLAGS="$CFLAGS -pq"
+-  else
+-    CFLAGS="$CFLAGS -pg"
+-  fi
+   use_static="no"
+ fi
+ 
+-# Static linking option
+-if test "$use_static" = "yes"; then
+-  LDFLAGS="-static -shared-libgcc $LDFLAGS"
+-fi
+-
+ # Override automatic CFLAGS and LDFLAGS with those of user
+ #if test -n "$mycflags"; then
+ #CFLAGS="$mycflags"

diff --git a/sci-astronomy/sextractor/metadata.xml b/sci-astronomy/sextractor/metadata.xml
new file mode 100644
index 0000000..8b8931e
--- /dev/null
+++ b/sci-astronomy/sextractor/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci-astronomy</herd>
+<longdescription lang="en">
+  SExtractor (Source Extractor) is a program that builds a catalogue of
+  objects from an astronomical image. Although it is particularly
+  oriented towards reduction of large scale galaxy-survey data, it
+  performs rather well on moderately crowded star fields. It has the
+  ability to automatically separate stars and galaxy using neural
+  networks.
+</longdescription>
+</pkgmetadata>

diff --git a/sci-astronomy/sextractor/sextractor-2.8.6-r1.ebuild b/sci-astronomy/sextractor/sextractor-2.8.6-r1.ebuild
new file mode 100644
index 0000000..1db0e06
--- /dev/null
+++ b/sci-astronomy/sextractor/sextractor-2.8.6-r1.ebuild
@@ -0,0 +1,55 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=4
+inherit eutils autotools
+
+DESCRIPTION="Extract catalogs of sources from astronomical FITS images"
+HOMEPAGE="http://www.astromatic.net/software/sextractor"
+SRC_URI="http://www.astromatic.net/download/${PN}/${P}.tar.gz"
+
+LICENSE="CeCILL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc threads"
+
+RDEPEND="virtual/cblas
+	sci-libs/atlas[lapack]
+	sci-libs/fftw:3.0"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PN}-configure.patch
+	local mycblas=atlcblas  myclapack=atlclapack
+	if use threads; then
+		[[ -e ${EPREFIX}/usr/$(get_libdir)/libptcblas.so ]] && mycblas=ptcblas
+		[[ -e ${EPREFIX}/usr/$(get_libdir)/libptclapack.so ]] && myclapack=ptclapack
+	fi
+	sed -i \
+		-e "s/-lcblas/-l${mycblas}/g" \
+		-e "s/AC_CHECK_LIB(cblas/AC_CHECK_LIB(${mycblas}/g" \
+		-e "s/-llapack/-l${myclapack}/g" \
+		-e "s/AC_CHECK_LIB(lapack/AC_CHECK_LIB(${myclapack}/g" \
+		acx_atlas.m4 || die "sed acx_atlas.m4 failed"
+	eautoreconf
+}
+
+src_configure() {
+	econf \
+		--with-atlas-incdir="${EPREFIX}/usr/include/atlas" \
+		$(use_enable threads)
+}
+
+src_install () {
+	default
+	CONFDIR=/usr/share/sextractor
+	insinto ${CONFDIR}
+	doins config/*
+	use doc && dodoc doc/*
+}
+
+pkg_postinst() {
+	elog "SExtractor examples configuration files are located"
+	elog "in ${EROOT}/${CONFDIR} and are not loaded anymore by default."
+}