* [gentoo-commits] proj/sci:master commit in: sci-libs/fast5/
@ 2018-01-24 21:08 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2018-01-24 21:08 UTC (permalink / raw
To: gentoo-commits
commit: 7964a3e5fde9e6f2c47e62f8c44d8570a90572f7
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jan 24 21:08:39 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jan 24 21:08:39 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=7964a3e5
sci-libs/fast5: version bump, fix compile paths for hdf5
Package-Manager: Portage-2.3.19, Repoman-2.3.6
sci-libs/fast5/{fast5-0.6.2.ebuild => fast5-0.6.4.ebuild} | 8 ++++----
sci-libs/fast5/fast5-9999.ebuild | 6 +++---
2 files changed, 7 insertions(+), 7 deletions(-)
diff --git a/sci-libs/fast5/fast5-0.6.2.ebuild b/sci-libs/fast5/fast5-0.6.4.ebuild
similarity index 77%
rename from sci-libs/fast5/fast5-0.6.2.ebuild
rename to sci-libs/fast5/fast5-0.6.4.ebuild
index 186c157d4..181c2e593 100644
--- a/sci-libs/fast5/fast5-0.6.2.ebuild
+++ b/sci-libs/fast5/fast5-0.6.4.ebuild
@@ -1,15 +1,15 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
PYTHON_COMPAT=( python{2_7,3_4} )
-inherit distutils-r1
+inherit distutils-r1 multilib
DESCRIPTION="C++ header-only library for reading Oxford Nanopore Fast5 files"
HOMEPAGE="https://github.com/mateidavid/fast5"
-SRC_URI="https://github.com/mateidavid/fast5/archive/v0.6.2.tar.gz -> ${P}.tar.gz"
+SRC_URI="https://github.com/mateidavid/fast5/archive/v${PV}.tar.gz -> ${P}.tar.gz"
LICENSE="MIT"
SLOT="0"
@@ -25,7 +25,7 @@ DEPEND="
RDEPEND="${DEPEND}"
src_compile(){
- emake -C python develop-user
+ emake -C python develop-user HDF5_DIR="${EPREFIX}"/usr HDF5_LIB_DIR="${EPREFIX}"/usr/$(get_libdir)
}
src_install(){
diff --git a/sci-libs/fast5/fast5-9999.ebuild b/sci-libs/fast5/fast5-9999.ebuild
index a36740179..c3b044e61 100644
--- a/sci-libs/fast5/fast5-9999.ebuild
+++ b/sci-libs/fast5/fast5-9999.ebuild
@@ -1,11 +1,11 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
PYTHON_COMPAT=( python{2_7,3_4} )
-inherit distutils-r1 git-r3
+inherit distutils-r1 multilib git-r3
DESCRIPTION="C++ header-only library for reading Oxford Nanopore Fast5 files"
HOMEPAGE="https://github.com/mateidavid/fast5"
@@ -22,5 +22,5 @@ DEPEND="
RDEPEND="${DEPEND}"
src_compile(){
- emake -C python develop-user
+ emake -C python develop-user HDF5_DIR="${EPREFIX}"/usr HDF5_LIB_DIR="${EPREFIX}"/usr/$(get_libdir)
}
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-libs/fast5/
@ 2018-01-24 21:38 Martin Mokrejs
0 siblings, 0 replies; 5+ messages in thread
From: Martin Mokrejs @ 2018-01-24 21:38 UTC (permalink / raw
To: gentoo-commits
commit: 671a509af3620833cc9bea743e7e6bcd828ade93
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jan 24 21:38:46 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jan 24 21:38:46 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=671a509a
sci-libs/fast5: document what is still broken in the ebuild
Package-Manager: Portage-2.3.19, Repoman-2.3.6
sci-libs/fast5/fast5-9999.ebuild | 2 ++
1 file changed, 2 insertions(+)
diff --git a/sci-libs/fast5/fast5-9999.ebuild b/sci-libs/fast5/fast5-9999.ebuild
index c3b044e61..6574116c5 100644
--- a/sci-libs/fast5/fast5-9999.ebuild
+++ b/sci-libs/fast5/fast5-9999.ebuild
@@ -24,3 +24,5 @@ RDEPEND="${DEPEND}"
src_compile(){
emake -C python develop-user HDF5_DIR="${EPREFIX}"/usr HDF5_LIB_DIR="${EPREFIX}"/usr/$(get_libdir)
}
+
+# BUG: python stuff and binaries get installed into "${IMAGEDIR}"/homedir/.local/
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-libs/fast5/
@ 2021-01-05 18:05 Andrew Ammerlaan
0 siblings, 0 replies; 5+ messages in thread
From: Andrew Ammerlaan @ 2021-01-05 18:05 UTC (permalink / raw
To: gentoo-commits
commit: 9eb957c972f24e0852a668ac6b443c7826ff6014
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 5 14:53:36 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 5 18:01:29 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=9eb957c9
sci-libs/fast5: version bump, add keywords, bump py targets
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-libs/fast5/fast5-0.6.4.ebuild | 42 ---------------------------------------
sci-libs/fast5/fast5-0.6.5.ebuild | 36 +++++++++++++++++++++++++++++++++
sci-libs/fast5/fast5-9999.ebuild | 28 --------------------------
3 files changed, 36 insertions(+), 70 deletions(-)
diff --git a/sci-libs/fast5/fast5-0.6.4.ebuild b/sci-libs/fast5/fast5-0.6.4.ebuild
deleted file mode 100644
index 181c2e593..000000000
--- a/sci-libs/fast5/fast5-0.6.4.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python{2_7,3_4} )
-
-inherit distutils-r1 multilib
-
-DESCRIPTION="C++ header-only library for reading Oxford Nanopore Fast5 files"
-HOMEPAGE="https://github.com/mateidavid/fast5"
-SRC_URI="https://github.com/mateidavid/fast5/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="" # the install step is broken (python modules integration, upstream binary code)
-IUSE=""
-
-DEPEND="
- dev-python/cython[${PYTHON_USEDEP}]
- sci-libs/hdf5"
-# TODO: more deps
-# https://github.com/mateidavid/tclap.git
-# https://github.com/mateidavid/hpptools.git
-RDEPEND="${DEPEND}"
-
-src_compile(){
- emake -C python develop-user HDF5_DIR="${EPREFIX}"/usr HDF5_LIB_DIR="${EPREFIX}"/usr/$(get_libdir)
-}
-
-src_install(){
- dobin src/hufftk
- insinto /usr/include
- doins src/*.hpp
- dobin python/bin/* # bindled binaries
- dolib python/fast5.so # bundled library
-}
-
-python_install_all() {
- cd python || die
- distutils-r1_src_install_all
-}
diff --git a/sci-libs/fast5/fast5-0.6.5.ebuild b/sci-libs/fast5/fast5-0.6.5.ebuild
new file mode 100644
index 000000000..38de1b6ff
--- /dev/null
+++ b/sci-libs/fast5/fast5-0.6.5.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{7,8,9} )
+
+DOCS_BUILDER="doxygen"
+DOCS_DIR="${WORKDIR}/${P}"
+
+inherit distutils-r1 docs multilib
+
+DESCRIPTION="C++ header-only library for reading Oxford Nanopore Fast5 files"
+HOMEPAGE="https://github.com/mateidavid/fast5"
+SRC_URI="https://github.com/mateidavid/fast5/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+BDEPEND="sci-libs/hdf5
+ dev-python/cython[${PYTHON_USEDEP}]"
+
+S="${WORKDIR}/${P}/python"
+
+python_compile() {
+ HDF5_DIR="${EPREFIX}"/usr HDF5_LIB_DIR="${EPREFIX}"/usr/$(get_libdir) distutils-r1_python_compile
+}
+
+python_compile_all(){
+ docs_compile
+}
+
+python_install() {
+ HDF5_DIR="${EPREFIX}"/usr HDF5_LIB_DIR="${EPREFIX}"/usr/$(get_libdir) distutils-r1_python_install
+}
diff --git a/sci-libs/fast5/fast5-9999.ebuild b/sci-libs/fast5/fast5-9999.ebuild
deleted file mode 100644
index 6574116c5..000000000
--- a/sci-libs/fast5/fast5-9999.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python{2_7,3_4} )
-
-inherit distutils-r1 multilib git-r3
-
-DESCRIPTION="C++ header-only library for reading Oxford Nanopore Fast5 files"
-HOMEPAGE="https://github.com/mateidavid/fast5"
-EGIT_REPO_URI="https://github.com/mateidavid/fast5.git"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="
- dev-python/cython[${PYTHON_USEDEP}]
- sci-libs/hdf5"
-RDEPEND="${DEPEND}"
-
-src_compile(){
- emake -C python develop-user HDF5_DIR="${EPREFIX}"/usr HDF5_LIB_DIR="${EPREFIX}"/usr/$(get_libdir)
-}
-
-# BUG: python stuff and binaries get installed into "${IMAGEDIR}"/homedir/.local/
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-libs/fast5/
@ 2021-12-16 10:57 Andrew Ammerlaan
0 siblings, 0 replies; 5+ messages in thread
From: Andrew Ammerlaan @ 2021-12-16 10:57 UTC (permalink / raw
To: gentoo-commits
commit: 777c5e71e1132c869c06ac3579cfee9782e02fd6
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Thu Dec 16 10:43:20 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Thu Dec 16 10:43:20 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=777c5e71
sci-libs/fast5: drop UnusedInherits
Package-Manager: Portage-3.0.28, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-libs/fast5/fast5-0.6.5.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-libs/fast5/fast5-0.6.5.ebuild b/sci-libs/fast5/fast5-0.6.5.ebuild
index 38de1b6ff..cf06e1d8d 100644
--- a/sci-libs/fast5/fast5-0.6.5.ebuild
+++ b/sci-libs/fast5/fast5-0.6.5.ebuild
@@ -8,7 +8,7 @@ PYTHON_COMPAT=( python3_{7,8,9} )
DOCS_BUILDER="doxygen"
DOCS_DIR="${WORKDIR}/${P}"
-inherit distutils-r1 docs multilib
+inherit distutils-r1 docs
DESCRIPTION="C++ header-only library for reading Oxford Nanopore Fast5 files"
HOMEPAGE="https://github.com/mateidavid/fast5"
^ permalink raw reply related [flat|nested] 5+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-libs/fast5/
@ 2023-05-02 12:15 Andrew Ammerlaan
0 siblings, 0 replies; 5+ messages in thread
From: Andrew Ammerlaan @ 2023-05-02 12:15 UTC (permalink / raw
To: gentoo-commits
commit: 9aa40cdbee0b33d22cbaad15f3c9de5a5ab4a404
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue May 2 12:12:54 2023 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue May 2 12:15:24 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=9aa40cdb
sci-libs/fast5: treeclean
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-libs/fast5/fast5-0.6.5.ebuild | 36 ------------------------------------
sci-libs/fast5/metadata.xml | 15 ---------------
2 files changed, 51 deletions(-)
diff --git a/sci-libs/fast5/fast5-0.6.5.ebuild b/sci-libs/fast5/fast5-0.6.5.ebuild
deleted file mode 100644
index cf06e1d8d..000000000
--- a/sci-libs/fast5/fast5-0.6.5.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8,9} )
-
-DOCS_BUILDER="doxygen"
-DOCS_DIR="${WORKDIR}/${P}"
-
-inherit distutils-r1 docs
-
-DESCRIPTION="C++ header-only library for reading Oxford Nanopore Fast5 files"
-HOMEPAGE="https://github.com/mateidavid/fast5"
-SRC_URI="https://github.com/mateidavid/fast5/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-BDEPEND="sci-libs/hdf5
- dev-python/cython[${PYTHON_USEDEP}]"
-
-S="${WORKDIR}/${P}/python"
-
-python_compile() {
- HDF5_DIR="${EPREFIX}"/usr HDF5_LIB_DIR="${EPREFIX}"/usr/$(get_libdir) distutils-r1_python_compile
-}
-
-python_compile_all(){
- docs_compile
-}
-
-python_install() {
- HDF5_DIR="${EPREFIX}"/usr HDF5_LIB_DIR="${EPREFIX}"/usr/$(get_libdir) distutils-r1_python_install
-}
diff --git a/sci-libs/fast5/metadata.xml b/sci-libs/fast5/metadata.xml
deleted file mode 100644
index 6f7127e91..000000000
--- a/sci-libs/fast5/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="github">mateidavid/fast5</remote-id>
- </upstream>
-</pkgmetadata>
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