8 files changed, 138 insertions, 16 deletions
diff --git a/sci-libs/Manifest.gz b/sci-libs/Manifest.gz
index 2cc9c8590375..a5701981f113 100644
--- a/sci-libs/Manifest.gz
+++ b/sci-libs/Manifest.gz
diff --git a/sci-libs/med/Manifest b/sci-libs/med/Manifest
index 00d5b0182d75..2a389a8cbb24 100644
--- a/sci-libs/med/Manifest
+++ b/sci-libs/med/Manifest
@@ -1,5 +1,6 @@
 AUX med-4.1.0-0001-Gentoo-specific-Adjust-install-path-for-build-dir.patch 1412 BLAKE2B 50602ca4a76ba4d15072d6bb96f9ce8576ac819c36b2a2a30268b506e1f453966e2846ea81ab8919d59c47e5f2ca41bc433b9fddee13797834f3a0c11a8fbb0f SHA512 cf810b8f8f2466d0b2bbf6fae1167faf57ce0b01812630ab165401432fee474b6ce80b50e122c36c61f0c347f89a1975cb91ac7ea3939eee2c15bf9e1a1dcdbe
 AUX med-4.1.0-0002-Re-add-option-for-building-Fortran-library.patch 1061 BLAKE2B 1856be8c2189e5d7541f041182e48315d686cadfeb409872eee25a90ff657cf1b6a5c76a4632a6d3d12af29b2f7ee67201d67c40cbc98927702ce1c905aa2509 SHA512 c40235bed175f84615115c899fad9f78a03205a7192bdf68f1b79a1711a7a15c58145102fce9850898f463d6d7ad16bbb89416f689d4013364955036628e7263
+AUX med-4.1.0-0003-build-against-hdf5-1.12.patch 4749 BLAKE2B 3a606c27bce6130e83989dd4e16733ced50da0ef21dd40226ffb6f64abbd5f2eca2174f971b4bbf3204df0e6040b86706c007dbf6b821a5bb287b648078d9113 SHA512 ba2fa24e3aeb2be6fa1e7365d7ac57c9ebd8706dd19de7dba67507baafe1f48b7b00051169f27164b4a9e749816220619490d5f0796a0c02f25644569b26f366
 DIST med-4.1.0.tar.gz 50375039 BLAKE2B 514ca19baf15e349ecbce870b318b37c51bfb57ac9b03c2b2c1b28836fec7fcf2dce573b9ea155f358d5e0bcee120c12a31598cd4f1e44837eca787553bb70d4 SHA512 94d07663c2f6a3cd497f54b480c3d742476d2a25172feb567980c9e75d49f4661aa2c6aaf570470938265997154e348bc1608065b86d42afda52d4e6361fedf8
-EBUILD med-4.1.0.ebuild 3231 BLAKE2B 336bfbfba073d30dd9ef1efb0b00ef5cdc90f53ab3de07002219f3750d433c8aabccdd02c439ef262058cfc3ce9676562e808863ce09af741671b2a107953c73 SHA512 d45cc92458137499e6f735fb4f440d5f823710dd0167c71302dbdea59e0d1938e009fe25d23d60f0aef9eb5df785f9288ea6faedcf30f65c31cda71aa65294c1
+EBUILD med-4.1.0.ebuild 3342 BLAKE2B fde2ce1741442e953a4d141a58b71226cf9e209d7b2941cbb859144dffcf3895740a1aa3b664738b6d0f34a6d450ea2a6f4c87258af557324c21daa694ce1c23 SHA512 8db224906fee79e35308b0445e450e239d34f73717370da0db6bfeb22084b5a99fc4b8fbd6c11fc1cb49352d088aaf74752a8e9b304a63286330d2b9491ee95c
 MISC metadata.xml 635 BLAKE2B 679b3111d148b77df38d08e07223c25390b3e0dbff3661fc1ff88084556979db955b990c9998f84dbc9782773728e73d22c28e534d45a33857d72f36585a7c30 SHA512 f19b5ade75301ed6985a00bbd5e074523bce2601dc992e27a472be17e958f45db4549cb6f88946862204840c2c70bb06e64683716157051769a785763d571908
diff --git a/sci-libs/med/files/med-4.1.0-0003-build-against-hdf5-1.12.patch b/sci-libs/med/files/med-4.1.0-0003-build-against-hdf5-1.12.patch
new file mode 100644
index 000000000000..46d7ed21af8d
--- /dev/null
+++ b/sci-libs/med/files/med-4.1.0-0003-build-against-hdf5-1.12.patch
@@ -0,0 +1,117 @@
+From 5c9c1ce9911290283d39e16b1ed4c1d4ea5a5678 Mon Sep 17 00:00:00 2001
+From: Bernd Waibel <waebbl-gentoo@posteo.net>
+Date: Tue, 24 Aug 2021 08:32:13 +0200
+Subject: [PATCH] build against hdf5-1.12
+
+Signed-off-by: Bernd Waibel <waebbl-gentoo@posteo.net>
+---
+ config/cmake_files/medMacros.cmake | 4 ++--
+ src/ci/MEDfileCompatibility.c      | 2 +-
+ src/hdfi/_MEDfileCreate.c          | 2 +-
+ src/hdfi/_MEDfileOpen.c            | 2 +-
+ src/hdfi/_MEDmemFileOpen.c         | 2 +-
+ src/hdfi/_MEDparFileCreate.c       | 2 +-
+ src/hdfi/_MEDparFileOpen.c         | 2 +-
+ 7 files changed, 8 insertions(+), 8 deletions(-)
+
+diff --git a/config/cmake_files/medMacros.cmake b/config/cmake_files/medMacros.cmake
+index 957c59b..d73c7af 100644
+--- a/config/cmake_files/medMacros.cmake
++++ b/config/cmake_files/medMacros.cmake
+@@ -447,13 +447,13 @@ MACRO(MED_FIND_HDF5)
+     ##
+     ## Requires 1.10.x version
+     ##
+-    IF (NOT HDF_VERSION_MAJOR_REF EQUAL 1 OR NOT HDF_VERSION_MINOR_REF EQUAL 10 OR NOT HDF_VERSION_RELEASE_REF GREATER 1)
++    IF(HDF5_VERSION VERSION_LESS 1.10.2)
+         MESSAGE(FATAL_ERROR "HDF5 version is ${HDF_VERSION_REF}. Only versions >= 1.10.2 are supported.")
+     ENDIF()
+     ##
+     ##
+ 
+-    ADD_DEFINITIONS(-DH5_USE_16_API)  
++    ADD_DEFINITIONS(-DH5_USE_18_API -DH5_USE_16_API)
+     IF(WIN32 AND MEDFILE_BUILD_SHARED_LIBS)
+       ADD_DEFINITIONS(-D_HDF5USEDLL_ -DH5_BUILT_AS_DYNAMIC_LIB=1)   
+     ENDIF()
+diff --git a/src/ci/MEDfileCompatibility.c b/src/ci/MEDfileCompatibility.c
+index 1d6cabf..43b5b50 100644
+--- a/src/ci/MEDfileCompatibility.c
++++ b/src/ci/MEDfileCompatibility.c
+@@ -113,7 +113,7 @@ MEDfileCompatibility(const char* const filename,
+ #if MED_NUM_MAJEUR != 4
+ #error "Don't forget to update the test version here when you change the major version of the library !"
+ #endif
+-#if H5_VERS_MINOR > 10
++#if H5_VERS_MINOR > 12
+ #error "Don't forget to check the compatibility version of the library, depending on the internal hdf model choice !"
+ #error "Cf. _MEDfileCreate ..."
+ #endif
+diff --git a/src/hdfi/_MEDfileCreate.c b/src/hdfi/_MEDfileCreate.c
+index 4bc9551..b670c92 100644
+--- a/src/hdfi/_MEDfileCreate.c
++++ b/src/hdfi/_MEDfileCreate.c
+@@ -159,7 +159,7 @@ med_idt _MEDfileCreate(const char * const filename, const med_access_mode access
+    * En HDF5-1.10.0p1 cela n'a aucun effet ! 
+    * Un test autoconf permet de fixer un intervalle de version HDF à MED.
+    */
+-#if H5_VERS_MINOR > 10
++#if H5_VERS_MINOR > 12
+ #error "Don't forget to change the compatibility version of the library !"
+ #endif
+    
+diff --git a/src/hdfi/_MEDfileOpen.c b/src/hdfi/_MEDfileOpen.c
+index 8ace00e..ebd875b 100644
+--- a/src/hdfi/_MEDfileOpen.c
++++ b/src/hdfi/_MEDfileOpen.c
+@@ -72,7 +72,7 @@ med_idt _MEDfileOpen(const char * const filename,const med_access_mode accessmod
+ 
+    •   The creation order tracking property, H5P_CRT_ORDER_TRACKED, has been set in the group creation property list (see H5Pset_link_creation_order). 
+   */
+-#if H5_VERS_MINOR > 10
++#if H5_VERS_MINOR > 12
+ #error "Don't forget to change the compatibility version of the library !"
+ #endif
+ /* L'avantage de bloquer le modèle interne HDF5 
+diff --git a/src/hdfi/_MEDmemFileOpen.c b/src/hdfi/_MEDmemFileOpen.c
+index ae92ba7..4a929ff 100644
+--- a/src/hdfi/_MEDmemFileOpen.c
++++ b/src/hdfi/_MEDmemFileOpen.c
+@@ -434,7 +434,7 @@ med_idt _MEDmemFileOpen(const char * const filename, med_memfile * const memfile
+     goto ERROR;
+   }
+ 
+-#if H5_VERS_MINOR > 10
++#if H5_VERS_MINOR > 12
+ #error "Don't forget to change the compatibility version of the library !"
+ #endif
+   if ( H5Pset_libver_bounds( _fapl, H5F_LIBVER_18, H5F_LIBVER_18) ) {
+diff --git a/src/hdfi/_MEDparFileCreate.c b/src/hdfi/_MEDparFileCreate.c
+index f0b77be..b7d1b78 100644
+--- a/src/hdfi/_MEDparFileCreate.c
++++ b/src/hdfi/_MEDparFileCreate.c
+@@ -64,7 +64,7 @@ med_idt _MEDparFileCreate(const char * const filename, const med_access_mode acc
+    * En HDF5-1.10.0p1 cela n'a aucun effet ! 
+    * Un test autoconf permet de fixer un intervalle de version HDF à MED.
+    */
+-#if H5_VERS_MINOR > 10
++#if H5_VERS_MINOR > 12
+ #error "Don't forget to change the compatibility version of the library !"
+ #endif
+    
+diff --git a/src/hdfi/_MEDparFileOpen.c b/src/hdfi/_MEDparFileOpen.c
+index 0a9700d..4933692 100644
+--- a/src/hdfi/_MEDparFileOpen.c
++++ b/src/hdfi/_MEDparFileOpen.c
+@@ -55,7 +55,7 @@ med_idt _MEDparFileOpen(const char * const filename,const med_access_mode access
+     MED_ERR_(_fid,MED_ERR_INIT,MED_ERR_PROPERTY,MED_ERR_PARALLEL_MSG);
+     goto ERROR;
+   }
+-#if H5_VERS_MINOR > 10
++#if H5_VERS_MINOR > 12
+ #error "Don't forget to change the compatibility version of the library !"
+ #endif
+   if ( H5Pset_libver_bounds( _fapl, H5F_LIBVER_18, H5F_LIBVER_18 ) ) {
+-- 
+2.32.0
+
diff --git a/sci-libs/med/med-4.1.0.ebuild b/sci-libs/med/med-4.1.0.ebuild
index ab5056e4a4d7..ec6eef42dc1e 100644
--- a/sci-libs/med/med-4.1.0.ebuild
+++ b/sci-libs/med/med-4.1.0.ebuild
@@ -1,11 +1,11 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
 
 FORTRAN_NEEDED=fortran
 
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{8..10} )
 
 inherit cmake fortran-2 python-single-r1
 
@@ -30,9 +30,11 @@ RDEPEND="
 DEPEND="${RDEPEND}"
 BDEPEND="python? ( >=dev-lang/swig-3.0.8 )"
 
+#	"${FILESDIR}/${P}-0003-fix-hdf5-version-check.patch"
 PATCHES=(
 	"${FILESDIR}/${P}-0001-Gentoo-specific-Adjust-install-path-for-build-dir.patch"
 	"${FILESDIR}/${P}-0002-Re-add-option-for-building-Fortran-library.patch"
+	"${FILESDIR}/${P}-0003-build-against-hdf5-1.12.patch"
 )
 
 DOCS=( AUTHORS ChangeLog NEWS README README.CMAKE TODO )
diff --git a/sci-libs/profnet/Manifest b/sci-libs/profnet/Manifest
index ff60d88bc798..b343c4e2d63f 100644
--- a/sci-libs/profnet/Manifest
+++ b/sci-libs/profnet/Manifest
@@ -1,3 +1,3 @@
 DIST profnet-1.0.22.tar.gz 203676 BLAKE2B ecee0347d711784c37b71cc3b0812bbd871d2438716a4fa2fb1e2b9c1fe3a9801073fcff3432203feed226325db36d4246d0be64487c57f2f643a192ae33840e SHA512 11c6d180219b60df7c5e144719354b7fbd5845e4ab6e52027315ee80d820c89fca9bce5b9e9e49314aa64058f93196f0cd35089604b53721fee3c050e45d9555
-EBUILD profnet-1.0.22.ebuild 660 BLAKE2B 2b0c724f2c9d33f14ed7a72e60562f4fa15efcff97f69474073755927726c434e92e81a341eb6af17bf421fab914a4b9e06af313fde06be8ee0ece13d3b3da2f SHA512 89452bb3149a8124ccd60d866ae0afc6c1132126d83d33f2aefe53a3179a4f51fd90885cbf93eda417527ea6874c73daf511eb713cc27d390c0690150517ff94
+EBUILD profnet-1.0.22.ebuild 844 BLAKE2B ad85ec69fb1b95d081ae97a4cae612c82310cc52114cd3c86e9c489e2bd03b837c5f9b59cfc6e7a1f41751832c64dc5f6f0a55ec8af2cb5a5e5b62b87a3cb98a SHA512 d169cd5861636652395a8a83e068ff26ff838637780224137f48e1a3db00ee271e47f11a6d0552c95f061e6a8f83ef41519acdbda705deae56a1ecc90b680d96
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-libs/profnet/profnet-1.0.22.ebuild b/sci-libs/profnet/profnet-1.0.22.ebuild
index df450e7e8d39..5488f1435dec 100644
--- a/sci-libs/profnet/profnet-1.0.22.ebuild
+++ b/sci-libs/profnet/profnet-1.0.22.ebuild
@@ -1,29 +1,30 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-inherit fortran-2 toolchain-funcs
+inherit flag-o-matic fortran-2 toolchain-funcs
 
 DESCRIPTION="Neural network architecture for profacc"
 HOMEPAGE="https://rostlab.org/"
 SRC_URI="ftp://rostlab.org/profnet/${P}.tar.gz"
 
-SLOT="0"
 LICENSE="GPL-3"
+SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
 
 RDEPEND="sys-libs/libunwind"
 DEPEND="${RDEPEND}"
 
 src_prepare() {
+	default
 	sed \
 		-e '/$@/s:-o:$(LDFLAGS) -o:g' \
 		-i src-phd/Makefile || die
 }
 
 src_compile() {
+	append-fflags $(test-flags-FC -fallow-argument-mismatch)
 	emake \
 		F77=$(tc-getF77) \
 		FFLAGS="${FFLAGS}"
@@ -34,4 +35,7 @@ src_install() {
 		DESTDIR="${D}" \
 		prefix="${EPREFIX}/usr" \
 		install
+
+	# Don't install compressed man pages
+	find "${ED}"/usr/share/man -type f -name '*.gz' -exec gzip -d {} \; || die
 }
diff --git a/sci-libs/profphd-utils/Manifest b/sci-libs/profphd-utils/Manifest
index 4418a8171e50..f22b3eace865 100644
--- a/sci-libs/profphd-utils/Manifest
+++ b/sci-libs/profphd-utils/Manifest
@@ -1,3 +1,3 @@
 DIST profphd-utils-1.0.10.tar.gz 388222 BLAKE2B 1985bb9b93a502911f0d3b5c7de9031d633f6060e9ae0b7531d248436b1dacf6f3462bab1bc127add341dc00a8200a88860197dd6515c1430395b840c44b98ca SHA512 c8a777e20bd721e53610ec28da01771300b06f3d284d40b0681ac0e38e8e0b3c7507e1aec7ddc627808d6ce7ccf8d3db94bf87449b958647e00a9c9d98a4300c
-EBUILD profphd-utils-1.0.10-r1.ebuild 570 BLAKE2B 6acb29b2d981d320297858f7ebd0c8fb629576a06f60f19d67d5561e285ba36daf3b5dcfbe939882ccdbec1ee44d45f8099079d8920e5c531e9042c000e88db7 SHA512 9066e8bb37c5b12ed8312e2807470657e63c6b054d3d0f96eb0e52a5fc70c57f836e1f56506ba64123df6c1eda816708f37231c35cd23364599fe027644c8fc8
+EBUILD profphd-utils-1.0.10-r1.ebuild 549 BLAKE2B 9f44502246efdbb5ac63dae09476a96d0e02d22bddb9e14bf48ce563561d66d593ddbd9e7c33af72c8d90d39448d697803e3812ec149c18535efd5f3e3824b2e SHA512 d862b24738f61d6cfd418079a937817ad972d6ca560473762cd7f275aeef3b056225ded19d6b63bb16de1a5ac15a0d3dbd0530c267b1b477d9afbfcae9453871
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-libs/profphd-utils/profphd-utils-1.0.10-r1.ebuild b/sci-libs/profphd-utils/profphd-utils-1.0.10-r1.ebuild
index 83d0f8485e02..288f583f6598 100644
--- a/sci-libs/profphd-utils/profphd-utils-1.0.10-r1.ebuild
+++ b/sci-libs/profphd-utils/profphd-utils-1.0.10-r1.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=8
 
 inherit fortran-2 toolchain-funcs
 
@@ -9,13 +9,11 @@ DESCRIPTION="Additional utils for profphd"
 HOMEPAGE="https://rostlab.org/"
 SRC_URI="ftp://rostlab.org/profphd-utils/${P}.tar.gz"
 
-SLOT="0"
 LICENSE="GPL-3"
+SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
 
-RDEPEND=""
-DEPEND="dev-lang/perl"
+BDEPEND="dev-lang/perl"
 
 src_compile() {
 	emake \