gentoo auto-resync : 26:10:2024 - 04:04:26

4 files changed, 3 insertions, 44 deletions

diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index 5680eb7a4d15..f3d3e8d96dbc 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index c0e2e17fed77..d2d1863db84d 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -2,7 +2,6 @@ AUX gromacs-2020-pytest.patch 1346 BLAKE2B 4b0b34bf4f46ec1acc3d0088ac11323938ee4
 AUX gromacs-2021-cstdint-include.patch 361 BLAKE2B 98c09c5c82d722fc2fcc320741d8f8ed4f661eed7acd66e72ff1423aa2f0eac316add28f5b2b8b65a3b82c160d36aef6948078d3bad3248ffbd7bd63211980d1 SHA512 decf900c565ad9afed33e9a257a2364b63f0f872a5521dc6de4bdf6c7335e15b1cadaf06041f963573c116f1ffcf289a73d0b482df86740ff0874e0ee598825f
 AUX gromacs-2021-cuda-detection.patch 21849 BLAKE2B 4976321e5f2c5bc9b45feeaa29206d77d04d6148ca910652bd3f7923b6e74b7b10f039b5bcc4430826745f6d64b232c536a8ef75cce61556275942e94945acc0 SHA512 6a1d1f0467d27267d214bc4df95c4b15438fffcae6b84e03763425f869e2551490c0f5e2d28774f9dda2daa07da8b5555617721d46e8b4f067eba2b2b86b353d
 AUX gromacs-2021-musl-stdint.patch 601 BLAKE2B 2e871d22655950ee9b9951229e78bc022f74ce7a8aa8063bafa30e0fd97cd0451e0621ab48f985d813fd5d890c0f2d0c9ced6d4b26d86e9d1f6774c084f169af SHA512 d36497423beb86a26ad011432dd6da7169ae42dc00d15bc90ba14de6ecf5eb3217ac987260dce479e5f92d5f3a40fa28c5eb1b51816a92b6a37745f674581280
-AUX gromacs-9999-Fix-build-with-torch.patch 2090 BLAKE2B aefde1bce2a65653707c8da2732df949d74a06141dd5ba6d26120656cdeeac8b0496a7c837f6f833cd7b82b0e3f6633a56dd40677a7c9db7e1c1bfdc19235ff1 SHA512 8f081544645fb459ed92a5879932b956b91d5f92a97b878bfd03429409e9f3c515c5b8797bacc55382a64f2955300213a61e1f7d3bf8530df7a2839f863cc278
 DIST gromacs-2020.7.tar.gz 29175554 BLAKE2B 98f1aa415946f8eb113febc81105f0c1b0919b96fc3c55a0ab83bf3950ff509b81eade92e645adb0bc2b407df239e20cf3f19828b6e08616437c8693c1fddcc8 SHA512 1d375c44cec38445e56cea252623b5b6c565680268999d4b6c14d6dc38759a27227655b2d29efaab9f9115d3677b446cb555e11cddafa0dc10c4827caaa2477b
 DIST gromacs-2021.7.tar.gz 38028032 BLAKE2B 2dc1b15ca8692ca5cf4ad1c7a266b9e2ced064d34a63cef61fea69e48231dd0310cfd8484d29c56cdb599f795d7655959f40038ac933b46ad2841d57bf2b3646 SHA512 ca478533da3bcb377fda30682660db8eb13beef6456fac6013a1a97ec3be60b5594567412e1e2a31392e484f9a40a22da1f12336f4738cf0422ff4f3e8814609
 DIST gromacs-2022.6.tar.gz 40330705 BLAKE2B fdafbd5b2a92d6022dec3e79e961fef220f1eba42850916e7cb70ef459a8d9c6ebc8c1bbe3c105f5b23161dd5c552ec00505d7c0036649b782cf52c311498743 SHA512 91217394f534ca8f78f73189059712e1c2cd354b658722f23768b12748f7bfaf1a5e95227c5ed1b69c1a9b72c3174e9600a712c157ea2f27156387efb823dd67
@@ -29,5 +28,5 @@ EBUILD gromacs-2023.9999.ebuild 9810 BLAKE2B 29946a30ec5fc7c19233790c48a8e665700
 EBUILD gromacs-2024.3.ebuild 9817 BLAKE2B 65f5ae4402abc5b2b2fac677fb2ca0a62c97ab9c9d7738ca3491d669772a233d65b8e61afa1f441b9b08f1ed31866cb3fed3aa0bd6b76ef894b5f066c7385f7d SHA512 fcc3c48c835590eb96a773981428435e4b048f1a5fbbdc71f8303a89f46257974ed12bfc1649516cb688d8a959f730d4d59dc5555b6982cf7b9fb5595f545a26
 EBUILD gromacs-2024.9999.ebuild 9817 BLAKE2B 65f5ae4402abc5b2b2fac677fb2ca0a62c97ab9c9d7738ca3491d669772a233d65b8e61afa1f441b9b08f1ed31866cb3fed3aa0bd6b76ef894b5f066c7385f7d SHA512 fcc3c48c835590eb96a773981428435e4b048f1a5fbbdc71f8303a89f46257974ed12bfc1649516cb688d8a959f730d4d59dc5555b6982cf7b9fb5595f545a26
 EBUILD gromacs-2024.ebuild 9738 BLAKE2B af8b9cfb076d9bf0d49544cb5a7b2bcec58ccbfd20a74eb3082e818a890901d10734aa1aba3b1425aab0c0999f16afe83423a865a823e24433703380a8ed5153 SHA512 19a573be8b616440e6680a27ad4a43195d39e265142dad103f6d27d952594c8a99410c98ec2fb8792e7d1318e8a58172b0c53dfc6c494a1662793ea123cdc935
-EBUILD gromacs-9999.ebuild 10089 BLAKE2B c141bdd9c2bb7c3fe3dcc4ec8c8d6c22e79809f58f71a1df57b1ef3de5c76378fd8ee660ff667c3ef2ced6160003392e3a2b2b6b17bf71343c62e330a4285062 SHA512 8f9beb4b0f07642b66efcbd62c386bd3795439e940ae0c279958dff629d8387ab32dda49b012de0115ce2bf7f341c90cda3c12046381a63806e013852e3d602c
+EBUILD gromacs-9999.ebuild 10091 BLAKE2B 46b1f7c84e7cab89bfbe933b581fceea1d9a28fc5d733b0b5760297ee820325b5a340ada7f4b6129cf72cd49b378398572701014be9e6d29fcc0df4b9b8a158a SHA512 a62ec593636c8ac1b3ab18aecfa9ce7365dac9bc5c6fbca5b6413e10cf3751fd6b5cf924d8dfffe06e5d5fcea57500fd14b00ddb1b684a4b68c6d2d4c4aa2b14
 MISC metadata.xml 1461 BLAKE2B fa82d5e83fa403fe8c31d076b2cf577d4299b2c97e993b02634c32e8c74088825f8ef61417bc1294947408fddc5b831b983574dafaac5c6975c06af74d890f00 SHA512 ce2b73c332585d9cfb7d1c7cbc49e5fb94f828191c8805463c03e3f215a7137253796ab49718148ea0c5a6ab85b45794b2fe5d213e0d35b2013ea41f6079d484
diff --git a/sci-chemistry/gromacs/files/gromacs-9999-Fix-build-with-torch.patch b/sci-chemistry/gromacs/files/gromacs-9999-Fix-build-with-torch.patch
deleted file mode 100644
index 3a42ba4000ed..000000000000
--- a/sci-chemistry/gromacs/files/gromacs-9999-Fix-build-with-torch.patch
+++ /dev/null
@@ -1,40 +0,0 @@
-From d997978fc0c644784ed929b0c48e153d5c1f1408 Mon Sep 17 00:00:00 2001
-From: Alexey Shvetsov <alexxyum@gmail.com>
-Date: Sat, 19 Oct 2024 21:22:07 +0300
-Subject: [PATCH] Fix build with torch if non default C{XX}_FLAGS set
-MIME-Version: 1.0
-Content-Type: text/plain; charset=UTF-8
-Content-Transfer-Encoding: 8bit
-
-This should fix build colvars with torch if torch was built with non
-default C{,XX}_FLAGS
-
-Erorr info:
-
-FAILED: src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o
-/usr/bin/x86_64-pc-linux-gnu-g++ -DCOLVARS_TORCH -DGMX_DOUBLE=0 -I/usr/include/torch/csrc/api/include  -O2 -pipe -march=skylake -mtune=skylake -std=c++17 -fPIC "-O2 -pipe -march=skylake -mtune=skylake" -D_GLIBCXX_USE_CXX11_ABI=1 -fopenmp -MD -MT src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -MF src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o.d -o src/gromacs/CMakeFiles/colvars_objlib.dir/__/external/colvars/colvar.cpp.o -c /var/tmp/portage/sci-chemistry/gromacs-9999/work/gromacs-9999/src/external/colvars/colvar.cpp
-cc1plus: error: argument to ‘-O’ should be a non-negative integer, ‘g’, ‘s’, ‘z’ or ‘fast’
-
-This caused by doubling quoted C{,XX}_FLAGS
-
-Signed-off-by: Alexey Shvetsov <alexxyum@gmail.com>
----
- cmake/gmxManageColvars.cmake | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/cmake/gmxManageColvars.cmake b/cmake/gmxManageColvars.cmake
-index 509d56e116..f49c820fa0 100644
---- a/cmake/gmxManageColvars.cmake
-+++ b/cmake/gmxManageColvars.cmake
-@@ -52,7 +52,7 @@ function(gmx_manage_colvars)
-             target_link_libraries(colvars_objlib PRIVATE OpenMP::OpenMP_CXX)
-         endif()
-         if(GMX_TORCH)
--            target_compile_options(colvars_objlib PRIVATE ${CMAKE_CXX_FLAGS} ${TORCH_CXX_FLAGS})
-+            target_compile_options(colvars_objlib PRIVATE ${TORCH_CXX_FLAGS})
-             target_include_directories(colvars_objlib PRIVATE ${TORCH_INCLUDE_DIRS})
-             target_compile_definitions(colvars_objlib PRIVATE -DCOLVARS_TORCH)
-         endif()
--- 
-2.47.0
-
diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 9de42117f102..01ebc8ab87b7 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -94,8 +94,6 @@ DOCS=( AUTHORS README )
 
 RESTRICT="!test? ( test )"
 
-PATCHES=( "${FILESDIR}/${P}-Fix-build-with-torch.patch" )
-
 if [[ ${PV} != *9999 ]]; then
 	S="${WORKDIR}/${PN}-${PV/_/-}"
 fi
@@ -286,6 +284,8 @@ src_compile() {
 		einfo "Compiling for ${x} precision"
 		BUILD_DIR="${WORKDIR}/${P}_${x}"\
 			cmake_src_compile
+		BUILD_DIR="${WORKDIR}/${P}_${x}"\
+			cmake_src_compile man
 		if use python; then
 			BUILD_DIR="${WORKDIR}/${P}_${x}"\
 				cmake_src_compile	python_packaging/all