Merge remote-tracking branch 'refs/remotes/origin/master'

2021-10-01 05:58:00 -04:00 · 2021-10-01 05:58:00 -04:00 · fa58792ab5
parent e987d06dce 9f7263056d
commit fa58792ab5
11 changed files with 295 additions and 4 deletions
--- a/dev-python/click-didyoumean/ChangeLog
+++ b/dev-python/click-didyoumean/ChangeLog
@ -1,3 +1,10 @@
+*click-didyoumean-0.1.0 (01 Oct 2021)
+*click-didyoumean-0.2.0 (01 Oct 2021)
+
+  01 Oct 2021;  <chymera@gentoo.org> +click-didyoumean-0.1.0.ebuild,
+  +click-didyoumean-0.2.0.ebuild, -click-didyoumean-0.0.3.ebuild:
+  dev-python/click-didyoumean: version bump
+
 *click-didyoumean-0.0.3 (27 Sep 2021)

  27 Sep 2021;  <chymera@gentoo.org> +click-didyoumean-0.0.3.ebuild,
--- a/dev-python/click-didyoumean/Manifest
+++ b/dev-python/click-didyoumean/Manifest
@ -1 +1,2 @@
-DIST click-didyoumean-0.0.3.tar.gz 4283 SHA256 ef16f88ac939242400be281d4d5a90303320111a8cc0838ce08f83094f0b1376 SHA512 6e832881817645eb8fa3a40acaab74a7f0dcc798aa984781a011b2ef78da2a4ae71ff2d58907bcbb35adbfc659727223c28c3622788eef05ecbdf758d6ac889d WHIRLPOOL 1f058188e56e2c72ae9368096f133e13141eb36c3685f7716876b405d8074dec0b0f8e8c2fb267c75ad1e69b6c81ebb98ac40a42c9a4ba832ef5d92c5d997aac
+DIST click-didyoumean-0.1.0.tar.gz 2343 SHA256 0d5d412fd670caec17e7c12d053de13c14790b196056082c83e61c5541a3c50a SHA512 5079bcab1701b05767d4b53302baa7f05b59af7f8d4644f6bdad9c4bbcb77673b535828726f401d442b5cb39f45073f75b43204199ddddf3d0ec133eb86b65b7 WHIRLPOOL 65193110e062f1c6f499c9a740b33f57fad23299c2a6d652710aa9c60c21ba591b3e42035752f089db51e18f9abb66aa4312e212f5c3bc5b91d39ae39d09f8db
+DIST click-didyoumean-0.2.0.tar.gz 2413 SHA256 00136c217f7fb2ab2999c272cfbd0c14cd2d6c7a643318a954357e2fc3ea7beb SHA512 1934423a36ef03a3603676b8424cfe619972544fc9d7165f388514d01364872b972069466aee03d696da08cd17653ef4f245dab6acc5f2aba3310da00102ff6a WHIRLPOOL 6746b14375eee12b8bdf813fd53b751a09ce219d806cbcde0926e67c8a36f7dd52954e14be04ca464421323b331e3d7aad22bc2ae2db93e98edefefc2af82b76
--- a/dev-python/click-didyoumean/click-didyoumean-0.1.0.ebuild
+++ b/dev-python/click-didyoumean/click-didyoumean-0.1.0.ebuild
@ -4,17 +4,19 @@
 EAPI=8

 PYTHON_COMPAT=( pypy3 python3_{8..10} )
+DISTUTILS_USE_SETUPTOOLS=pyproject.toml
 inherit distutils-r1

 DESCRIPTION="Enable git-like did-you-mean feature in click"
 HOMEPAGE="https://github.com/click-contrib/click-didyoumean"
-SRC_URI="https://github.com/click-contrib/click-didyoumean/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"

 LICENSE="MIT"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-RESTRICT="test"
-# Issue reported upstream: https://github.com/click-contrib/click-didyoumean/issues/11
+#RESTRICT="test"
+# Tests actually pass, but not included in archive:
+# https://github.com/click-contrib/click-didyoumean/issues/11
 DEPEND="
 	dev-python/click
 "
--- a/dev-python/click-didyoumean/click-didyoumean-0.2.0.ebuild
+++ b/dev-python/click-didyoumean/click-didyoumean-0.2.0.ebuild
@ -0,0 +1,25 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( pypy3 python3_{8..10} )
+inherit distutils-r1
+
+DESCRIPTION="Enable git-like did-you-mean feature in click"
+HOMEPAGE="https://github.com/click-contrib/click-didyoumean"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+#SRC_URI="https://github.com/click-contrib/click-didyoumean/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+#RESTRICT="test"
+# Tests actually pass, but not included in archive:
+# https://github.com/click-contrib/click-didyoumean/issues/11
+DEPEND="
+	dev-python/click
+"
+RDEPEND="${DEPEND}"
+
+distutils_enable_tests pytest
--- a/dev-python/pynwb/ChangeLog
+++ b/dev-python/pynwb/ChangeLog
@ -1,3 +1,6 @@
+  01 Oct 2021;  <chymera@gentoo.org> pynwb-2.0.0.ebuild:
+  dev-python/pynwb: requiring ROS3 support on hdf5
+
 *keyrings_alt-4.1.0 (24 Sep 2021)

  24 Sep 2021;  <chymera@gentoo.org> +keyrings_alt-4.1.0.ebuild, +metadata.xml:
--- a/dev-python/pynwb/pynwb-2.0.0.ebuild
+++ b/dev-python/pynwb/pynwb-2.0.0.ebuild
@ -15,6 +15,7 @@ LICENSE="BSD"
 KEYWORDS="~amd64 ~x86"

 RDEPEND="
+	sci-libs/hdf5[ros3]
 	dev-python/hdmf[${PYTHON_USEDEP}]
 	dev-python/h5py[${PYTHON_USEDEP}]
 	dev-python/numpy[${PYTHON_USEDEP}]
--- a/sci-libs/hdf5/ChangeLog
+++ b/sci-libs/hdf5/ChangeLog
@ -0,0 +1,6 @@
+*hdf5-1.12.1 (01 Oct 2021)
+
+  01 Oct 2021;  <chymera@gentoo.org> +files/hdf5-1.12.1-cmake_installdirs.patch,
+  +hdf5-1.12.1.ebuild, +metadata.xml:
+  sci-libs/hdf5: added ROS3 support (DANDI stack)  Pending:
+  https://github.com/gentoo/gentoo/pull/22455
--- a/sci-libs/hdf5/Manifest
+++ b/sci-libs/hdf5/Manifest
@ -0,0 +1 @@
+DIST hdf5-1.12.1.tar.bz2 9724309 SHA256 aaf9f532b3eda83d3d3adc9f8b40a9b763152218fa45349c3bc77502ca1f8f1c SHA512 158a067ee284ccb9e2c4db12e9d37cf187d90d9ef1bed7a6303e2c3a2fd216d7b13a46c5f46018b097511281c4246156b6f917633ca88872f10f0ad04be285fd WHIRLPOOL 1fa4d86b495652d48a662a955a8d0b384d6d996f83a86e8f23e6f3597fa5795294b10302913a771250ebc1dbc5b5a5619268a549cba594b75bd5d7bc9cad52c3
--- a/sci-libs/hdf5/files/hdf5-1.12.1-cmake_installdirs.patch
+++ b/sci-libs/hdf5/files/hdf5-1.12.1-cmake_installdirs.patch
@ -0,0 +1,103 @@
+--- a/c++/src/CMakeLists.txt
+++ b/c++/src/CMakeLists.txt
+@@ -180,8 +180,8 @@
+ #-----------------------------------------------------------------------------
+ set (_PKG_CONFIG_PREFIX ${CMAKE_INSTALL_PREFIX})
+ set (_PKG_CONFIG_EXEC_PREFIX \${prefix})
+-set (_PKG_CONFIG_LIBDIR \${exec_prefix}/lib)
+-set (_PKG_CONFIG_INCLUDEDIR \${prefix}/include)
+set (_PKG_CONFIG_LIBDIR \${exec_prefix}/${CMAKE_INSTALL_LIBDIR})
+set (_PKG_CONFIG_INCLUDEDIR \${prefix}/${CMAKE_INSTALL_INCLUDEDIR})
+ set (_PKG_CONFIG_LIBNAME "${HDF5_CPP_LIB_CORENAME}")
+ set (_PKG_CONFIG_VERSION "${HDF5_PACKAGE_VERSION}")
+ 
+--- a/CMakeLists.txt
+++ b/CMakeLists.txt
+@@ -46,6 +46,13 @@
+   endif()
+ endif ()
+ 
+include (GNUInstallDirs)
+set (HDF5_INSTALL_BIN_DIR "${CMAKE_INSTALL_FULL_BINDIR}")
+set (HDF5_INSTALL_DATA_DIR "${CMAKE_INSTALL_FULL_DATADIR}")
+set (HDF5_INSTALL_DOC_DIR "${CMAKE_INSTALL_FULL_DOCDIR}")
+set (HDF5_INSTALL_INCLUDE_DIR "${CMAKE_INSTALL_FULL_INCLUDEDIR}")
+set (HDF5_INSTALL_LIB_DIR "${CMAKE_INSTALL_FULL_LIBDIR}")
+
+ #-----------------------------------------------------------------------------
+ # Instructions for use : Sub-Project Build
+ #
+--- a/fortran/src/CMakeLists.txt
+++ b/fortran/src/CMakeLists.txt
+@@ -537,8 +537,8 @@
+ #-----------------------------------------------------------------------------
+ set (_PKG_CONFIG_PREFIX ${CMAKE_INSTALL_PREFIX})
+ set (_PKG_CONFIG_EXEC_PREFIX \${prefix})
+-set (_PKG_CONFIG_LIBDIR \${exec_prefix}/lib)
+-set (_PKG_CONFIG_INCLUDEDIR \${prefix}/include)
+set (_PKG_CONFIG_LIBDIR \${exec_prefix}/${CMAKE_INSTALL_LIBDIR})
+set (_PKG_CONFIG_INCLUDEDIR \${prefix}/${CMAKE_INSTALL_INCLUDEDIR})
+ set (_PKG_CONFIG_LIBNAME "${HDF5_F90_LIB_CORENAME}")
+ set (_PKG_CONFIG_VERSION "${HDF5_PACKAGE_VERSION}")
+ 
+--- a/hl/c++/src/CMakeLists.txt
+++ b/hl/c++/src/CMakeLists.txt
+@@ -91,8 +91,8 @@
+ #-----------------------------------------------------------------------------
+ set (_PKG_CONFIG_PREFIX ${CMAKE_INSTALL_PREFIX})
+ set (_PKG_CONFIG_EXEC_PREFIX \${prefix})
+-set (_PKG_CONFIG_LIBDIR \${exec_prefix}/lib)
+-set (_PKG_CONFIG_INCLUDEDIR \${prefix}/include)
+set (_PKG_CONFIG_LIBDIR \${exec_prefix}/${CMAKE_INSTALL_LIBDIR})
+set (_PKG_CONFIG_INCLUDEDIR \${prefix}/${CMAKE_INSTALL_INCLUDEDIR})
+ set (_PKG_CONFIG_LIBNAME "${HDF5_HL_CPP_LIB_CORENAME}")
+ set (_PKG_CONFIG_VERSION "${HDF5_PACKAGE_VERSION}")
+ 
+--- a/hl/fortran/src/CMakeLists.txt
+++ b/hl/fortran/src/CMakeLists.txt
+@@ -324,8 +324,8 @@
+ #-----------------------------------------------------------------------------
+ set (_PKG_CONFIG_PREFIX ${CMAKE_INSTALL_PREFIX})
+ set (_PKG_CONFIG_EXEC_PREFIX \${prefix})
+-set (_PKG_CONFIG_LIBDIR \${exec_prefix}/lib)
+-set (_PKG_CONFIG_INCLUDEDIR \${prefix}/include)
+set (_PKG_CONFIG_LIBDIR \${exec_prefix}/${CMAKE_INSTALL_LIBDIR})
+set (_PKG_CONFIG_INCLUDEDIR \${prefix}/${CMAKE_INSTALL_INCLUDEDIR})
+ set (_PKG_CONFIG_LIBNAME "${HDF5_HL_F90_LIB_CORENAME}")
+ set (_PKG_CONFIG_VERSION "${HDF5_PACKAGE_VERSION}")
+ 
+--- a/hl/src/CMakeLists.txt
+++ b/hl/src/CMakeLists.txt
+@@ -123,8 +123,8 @@
+ #-----------------------------------------------------------------------------
+ set (_PKG_CONFIG_PREFIX ${CMAKE_INSTALL_PREFIX})
+ set (_PKG_CONFIG_EXEC_PREFIX \${prefix})
+-set (_PKG_CONFIG_LIBDIR \${exec_prefix}/lib)
+-set (_PKG_CONFIG_INCLUDEDIR \${prefix}/include)
+set (_PKG_CONFIG_LIBDIR \${exec_prefix}/${CMAKE_INSTALL_LIBDIR})
+set (_PKG_CONFIG_INCLUDEDIR \${prefix}/${CMAKE_INSTALL_INCLUDEDIR})
+ set (_PKG_CONFIG_LIBNAME "${HDF5_HL_LIB_CORENAME}")
+ set (_PKG_CONFIG_VERSION "${HDF5_PACKAGE_VERSION}")
+ 
+--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
+@@ -1311,8 +1311,8 @@
+ #-----------------------------------------------------------------------------
+ set (_PKG_CONFIG_PREFIX ${CMAKE_INSTALL_PREFIX})
+ set (_PKG_CONFIG_EXEC_PREFIX \${prefix})
+-set (_PKG_CONFIG_LIBDIR \${exec_prefix}/lib)
+-set (_PKG_CONFIG_INCLUDEDIR \${prefix}/include)
+set (_PKG_CONFIG_LIBDIR \${exec_prefix}/${CMAKE_INSTALL_LIBDIR})
+set (_PKG_CONFIG_INCLUDEDIR \${prefix}/${CMAKE_INSTALL_INCLUDEDIR})
+ set (_PKG_CONFIG_LIBNAME "${HDF5_LIB_CORENAME}")
+ set (_PKG_CONFIG_VERSION "${HDF5_PACKAGE_VERSION}")
+ 
+@@ -1419,7 +1419,7 @@
+ #  )
+   install (
+       DIRECTORY ${HDF5_BINARY_DIR}/hdf5lib_docs/html
+-      DESTINATION ${HDF5_INSTALL_DATA_DIR}
+      DESTINATION ${HDF5_INSTALL_DOC_DIR}
+       COMPONENT Documents
+   )
+ 
--- a/sci-libs/hdf5/hdf5-1.12.1.ebuild
+++ b/sci-libs/hdf5/hdf5-1.12.1.ebuild
@ -0,0 +1,123 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+FORTRAN_NEEDED="fortran"
+
+inherit cmake flag-o-matic fortran-2
+
+MY_P="${PN}-${PV/_p/-patch}"
+MAJOR_P="${PN}-$(ver_cut 1-2)"
+
+DESCRIPTION="General purpose library and file format for storing scientific data"
+HOMEPAGE="https://www.hdfgroup.org/HDF5/"
+SRC_URI="https://www.hdfgroup.org/ftp/HDF5/releases/${MAJOR_P}/${MY_P}/src/${MY_P}.tar.bz2"
+
+LICENSE="NCSA-HDF"
+SLOT="0/${PV%%_p*}"
+KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~hppa ~ia64 ~ppc ~ppc64 ~riscv ~sparc ~x86 ~amd64-linux ~x86-linux"
+IUSE="cxx debug doc examples fortran +hl mpi ros3 szip test threads unsupported zlib"
+
+REQUIRED_USE="
+	!unsupported? (
+		mpi? ( !cxx !threads )
+		threads? ( !cxx !fortran !hl )
+	)"
+
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+	mpi? ( virtual/mpi[romio] )
+	ros3? (
+		net-misc/curl
+		dev-libs/openssl
+	)
+	szip? ( virtual/szip )
+	zlib? ( sys-libs/zlib:0= )
+"
+DEPEND="${RDEPEND}"
+BDEPEND="doc? (
+	app-doc/doxygen
+	virtual/latex-base
+)"
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-1.12.1-cmake_installdirs.patch
+)
+
+S="${WORKDIR}/${MY_P}"
+
+pkg_setup() {
+	use fortran && fortran-2_pkg_setup
+
+	if use mpi; then
+		if has_version 'sci-libs/hdf5[-mpi]'; then
+			ewarn "Installing hdf5 with mpi enabled with a previous hdf5 with mpi disabled may fail."
+			ewarn "Try to uninstall the current hdf5 prior to enabling mpi support."
+		fi
+		export CC="mpicc"
+		use fortran && export FC="mpif90"
+		append-libs -lmpi
+	elif has_version 'sci-libs/hdf5[mpi]'; then
+		ewarn "Installing hdf5 with mpi disabled while having hdf5 installed with mpi enabled may fail."
+		ewarn "Try to uninstall the current hdf5 prior to disabling mpi support."
+	fi
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DBUILD_STATIC_LIBS=OFF
+		-DFETCHCONTENT_FULLY_DISCONNECTED=ON
+		-DHDF5_BUILD_EXAMPLES=OFF
+		-DALLOW_UNSUPPORTED=$(usex unsupported)
+		-DBUILD_TESTING=$(usex test)
+		-DHDF5_BUILD_CPP_LIB=$(usex cxx)
+		-DHDF5_BUILD_DOC=$(usex doc)
+		-DHDF5_BUILD_FORTRAN=$(usex fortran)
+		-DHDF5_BUILD_HL_LIB=$(usex hl)
+		-DHDF5_ENABLE_CODESTACK=$(usex debug)
+		-DHDF5_ENABLE_PARALLEL=$(usex mpi)
+		-DHDF5_ENABLE_SZIP_ENCODING=$(usex szip)
+		-DHDF5_ENABLE_SZIP_SUPPORT=$(usex szip)
+		-DHDF5_ENABLE_THREADSAFE=$(usex threads)
+		-DHDF5_ENABLE_Z_LIB_SUPPORT=$(usex zlib)
+		-DHDF5_ENABLE_ROS3_VFD:BOOL=$(usex ros3)
+	)
+	cmake_src_configure
+}
+
+src_install() {
+	cmake_src_install
+
+	# TODO: generate functioning example runners from their respective
+	# .in files - as of version 1.12.1 upstream only has it implemented
+	# for autoconf.
+	if use examples; then
+		# These are all useless outside the source tree
+		rm -f {examples,c++/examples,fortran/examples}/{Makefile*,CMake*}
+		rm -f hl/{examples,c++/examples,fortran/examples}/{Makefile*,CMake*}
+
+		dodoc -r examples
+		if use cxx; then
+			docinto c++
+			dodoc -r c++/examples
+		fi
+		if use fortran; then
+			docinto fortran
+			dodoc -r fortran/examples
+		fi
+		if use hl; then
+			docinto hl
+			dodoc -r hl/examples
+			if use cxx; then
+				docinto hl/c++
+				dodoc -r hl/c++/examples
+			fi
+			if use fortran; then
+				docinto hl/fortran
+				dodoc -r hl/fortran/examples
+			fi
+		fi
+	fi
+}
--- a/sci-libs/hdf5/metadata.xml
+++ b/sci-libs/hdf5/metadata.xml
@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci@gentoo.org</email>
+    <name>Gentoo Science Project</name>
+  </maintainer>
+  <longdescription>
+    HDF5 is a file format and library for storing scientific data. HDF5
+    was designed and implemented to address the deficiencies of HDF4.x. It
+    has a more powerful and flexible data model, supports files larger
+    than 2 GB, and supports parallel I/O.
+  </longdescription>
+  <use>
+    <flag name="hl">Enable high level API (https://support.hdfgroup.org/HDF5/doc/HL/index.html)</flag>
+    <flag name="ros3">Enable support for read-only S3 access (https://portal.hdfgroup.org/display/HDF5/Configuration+and+Setup+for+HDF5+Read+Only+S3+VFD)</flag>
+    <flag name="unsupported">Enable unsupported combinations of configuration options</flag>
+  </use>
+</pkgmetadata>
				`@ -0,0 +1 @@`
				`DIST hdf5-1.12.1.tar.bz2 9724309 SHA256 aaf9f532b3eda83d3d3adc9f8b40a9b763152218fa45349c3bc77502ca1f8f1c SHA512 158a067ee284ccb9e2c4db12e9d37cf187d90d9ef1bed7a6303e2c3a2fd216d7b13a46c5f46018b097511281c4246156b6f917633ca88872f10f0ad04be285fd WHIRLPOOL 1fa4d86b495652d48a662a955a8d0b384d6d996f83a86e8f23e6f3597fa5795294b10302913a771250ebc1dbc5b5a5619268a549cba594b75bd5d7bc9cad52c3`