[gentoo-commits] proj/sci:master commit in: sci-biology/dcm2niix/

[gentoo-commits] proj/sci:master commit in: sci-biology/dcm2niix/

[Horea Christian]

commit:     31edb5fccb73d7f4542f644909527f8a58c56049
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Wed Apr  1 12:04:41 2020 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Wed Apr  1 12:04:41 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=31edb5fc

sci-biology/dcm2niix: new package

Package-Manager: Portage-2.3.96, Repoman-2.3.22
Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 sci-biology/dcm2niix/dcm2niix-1.0.20200331.ebuild | 21 +++++++++++++++++++++
 sci-biology/dcm2niix/metadata.xml                 | 17 +++++++++++++++++
 2 files changed, 38 insertions(+)

diff --git a/sci-biology/dcm2niix/dcm2niix-1.0.20200331.ebuild b/sci-biology/dcm2niix/dcm2niix-1.0.20200331.ebuild
new file mode 100644
index 000000000..b473655b8
--- /dev/null
+++ b/sci-biology/dcm2niix/dcm2niix-1.0.20200331.ebuild
@@ -0,0 +1,21 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake-utils
+
+DESCRIPTION="DICOM to NIfTI converter"
+HOMEPAGE="https://github.com/rordenlab/dcm2niix"
+SRC_URI="https://github.com/rordenlab/dcm2niix/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND=""
+
+pkg_postinst() {
+	optfeature "parallel gzip support" app-arch/pigz
+}

diff --git a/sci-biology/dcm2niix/metadata.xml b/sci-biology/dcm2niix/metadata.xml
new file mode 100644
index 000000000..c5721a2d0
--- /dev/null
+++ b/sci-biology/dcm2niix/metadata.xml
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>chr@chymera.eu</email>
+		<name>Horea Christian</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<longdescription>
+		dcm2niix is a designed to convert neuroimaging data from the DICOM
+		format to the NIfTI format. ICOM provides many ways to store/compress
+		image data, known as transfer syntaxes.
+	</longdescription>
+</pkgmetadata>

[gentoo-commits] proj/sci:master commit in: sci-biology/dcm2niix/

[Andrew Ammerlaan]

commit:     7cddb5d856a4d995ca9ccb57674c827fe2678e32
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sun Jan 24 14:12:13 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sun Jan 24 14:12:13 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=7cddb5d8

sci-biology/dcm2niix: version bump, cmake-utils --> cmake,

fix optfeature

Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 .../{dcm2niix-1.0.20200331.ebuild => dcm2niix-1.0.20201102.ebuild}    | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/dcm2niix/dcm2niix-1.0.20200331.ebuild b/sci-biology/dcm2niix/dcm2niix-1.0.20201102.ebuild
similarity index 86%
rename from sci-biology/dcm2niix/dcm2niix-1.0.20200331.ebuild
rename to sci-biology/dcm2niix/dcm2niix-1.0.20201102.ebuild
index b473655b8..b7f4166f5 100644
--- a/sci-biology/dcm2niix/dcm2niix-1.0.20200331.ebuild
+++ b/sci-biology/dcm2niix/dcm2niix-1.0.20201102.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
 
-inherit cmake-utils
+inherit cmake optfeature
 
 DESCRIPTION="DICOM to NIfTI converter"
 HOMEPAGE="https://github.com/rordenlab/dcm2niix"

[gentoo-commits] proj/sci:master commit in: sci-biology/dcm2niix/

[Andrew Ammerlaan]

commit:     8cde5c549479110f27e426f97ee6011542423ceb
Author:     Lucas Mitrak <lucas <AT> lucasmitrak <DOT> com>
AuthorDate: Fri Jun 11 12:15:47 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Fri Jun 11 12:25:24 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=8cde5c54

sci-biology/dcm2niix: add USE flags, dependencies, src_configure

* Add static system-jpeg +jpeg-ls jpeg2k use flags and implement them

Currently, sci-biology/dcm2niix does not take advantage of many
of the package's potential features. These potential features include
a static runtime, using the system-wide media-libs/libjpeg-turbo
instead of bundled compact NanoJPEG decoder, enabling JPEG-LS using
the bundled CharLS library, and enabling JPEG2000 support. These are
important, especially since the static runtime is enabled by default
and JPEG-LS can be enabled without any downside. This commit adds
these USE flags and their implementation in the dependencies and in
src_configure. The naming of the use flags follow the same naming
convention found elsewhere. For example, system-jpeg is the same
as thunderbird, firefox, and seamonkey. In addition, jpeg-ls is the
only possible name for the JPEG-LS transfer syntaxes. These two
package-specific USE flag names were added to metadata.xml.
With this commit, the use flags will be added to the package.
Without this commit, the package will not have these potential
features.
This commit was tested in a docker image with dev-util/ebuildtester.
This commit was written, tested, and submitted by Lucas Mitrak.
Signed-off-by: Lucas Mitrak <lucas <AT> lucasmitrak.com>
Closes: https://github.com/gentoo/sci/pull/1092

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 sci-biology/dcm2niix/dcm2niix-1.0.20201102.ebuild | 20 ++++++++++++++++++--
 sci-biology/dcm2niix/metadata.xml                 |  5 +++++
 2 files changed, 23 insertions(+), 2 deletions(-)

diff --git a/sci-biology/dcm2niix/dcm2niix-1.0.20201102.ebuild b/sci-biology/dcm2niix/dcm2niix-1.0.20201102.ebuild
index e9d0d7ea0..5ae682ea5 100644
--- a/sci-biology/dcm2niix/dcm2niix-1.0.20201102.ebuild
+++ b/sci-biology/dcm2niix/dcm2niix-1.0.20201102.ebuild
@@ -12,14 +12,30 @@ SRC_URI="https://github.com/rordenlab/dcm2niix/archive/v${PV}.tar.gz -> ${P}.tar
 SLOT="0"
 LICENSE="BSD"
 KEYWORDS="~amd64 ~x86"
+IUSE="static system-jpeg +jpeg-ls jpeg2k"
 
-DEPEND=""
-RDEPEND=""
+DEPEND="
+	system-jpeg? ( media-libs/libjpeg-turbo )
+	jpeg2k? ( media-libs/openjpeg )
+"
+RDEPEND="${DEPEND}"
+BDEPEND="virtual/pkgconfig"
 
 PATCHES=(
 	"${FILESDIR}"/${PN}-disable_find_git.patch
 )
 
+src_configure() {
+	local mycmakeargs=(
+		-DUSE_STATIC_RUNTIME=$(usex static)
+		-DUSE_TURBOJPEG=$(usex system-jpeg)
+		-DUSE_JPEGLS=$(usex jpeg-ls)
+		-DUSE_OPENJPEG=$(usex jpeg2k)
+	)
+
+	cmake_src_configure
+}
+
 pkg_postinst() {
 	optfeature "parallel gzip support" app-arch/pigz
 }

diff --git a/sci-biology/dcm2niix/metadata.xml b/sci-biology/dcm2niix/metadata.xml
index c7c32010c..9c9e19081 100644
--- a/sci-biology/dcm2niix/metadata.xml
+++ b/sci-biology/dcm2niix/metadata.xml
@@ -9,6 +9,11 @@
 		<email>sci@gentoo.org</email>
 		<name>Gentoo Science Project</name>
 	</maintainer>
+	<use>
+	<flag name="system-jpeg">Use the system-wide <pkg>media-libs/libjpeg-turbo</pkg>
+		instead of bundled.</flag>
+	<flag name="jpeg-ls">Supprt for converting DICOM images compressed with the JPEG-LS transfer syntaxes using the bundled CharLS library</flag>
+	</use>
 	<longdescription>
 		dcm2niix is a designed to convert neuroimaging data from the DICOM
 		format to the NIfTI format. ICOM provides many ways to store/compress

[gentoo-commits] proj/sci:master commit in: sci-biology/dcm2niix/

[Andrew Ammerlaan]

commit:     699ded99a805c8d2c23a144efeeacfeb3883b7bd
Author:     Lucas Mitrak <lucas <AT> lucasmitrak <DOT> com>
AuthorDate: Fri Jun 11 14:07:28 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Fri Jun 11 14:51:11 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=699ded99

sci-biology/dcm2niix: add version 1.0.20210317

* sci-biology/dcm2niix version 1.0.20210317 bump to latest

This commit was tested in a docker image with dev-util/ebuildtester.
This commit was written, tested, and submitted by Lucas Mitrak.

Signed-off-by: Lucas Mitrak <lucas <AT> lucasmitrak.com>
Closes: https://github.com/gentoo/sci/pull/1093
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 sci-biology/dcm2niix/dcm2niix-1.0.20210317.ebuild | 41 +++++++++++++++++++++++
 1 file changed, 41 insertions(+)

diff --git a/sci-biology/dcm2niix/dcm2niix-1.0.20210317.ebuild b/sci-biology/dcm2niix/dcm2niix-1.0.20210317.ebuild
new file mode 100644
index 000000000..5ae682ea5
--- /dev/null
+++ b/sci-biology/dcm2niix/dcm2niix-1.0.20210317.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake optfeature
+
+DESCRIPTION="DICOM to NIfTI converter"
+HOMEPAGE="https://github.com/rordenlab/dcm2niix"
+SRC_URI="https://github.com/rordenlab/dcm2niix/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86"
+IUSE="static system-jpeg +jpeg-ls jpeg2k"
+
+DEPEND="
+	system-jpeg? ( media-libs/libjpeg-turbo )
+	jpeg2k? ( media-libs/openjpeg )
+"
+RDEPEND="${DEPEND}"
+BDEPEND="virtual/pkgconfig"
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-disable_find_git.patch
+)
+
+src_configure() {
+	local mycmakeargs=(
+		-DUSE_STATIC_RUNTIME=$(usex static)
+		-DUSE_TURBOJPEG=$(usex system-jpeg)
+		-DUSE_JPEGLS=$(usex jpeg-ls)
+		-DUSE_OPENJPEG=$(usex jpeg2k)
+	)
+
+	cmake_src_configure
+}
+
+pkg_postinst() {
+	optfeature "parallel gzip support" app-arch/pigz
+}