diff options
Diffstat (limited to 'sci-chemistry')
| -rw-r--r-- | sci-chemistry/Manifest.gz | bin | 8209 -> 8211 bytes | |||
| -rw-r--r-- | sci-chemistry/gromacs/Manifest | 3 | ||||
| -rw-r--r-- | sci-chemistry/gromacs/files/gromacs-2025.0-beta-fix-man-build.patch | 41 | ||||
| -rw-r--r-- | sci-chemistry/gromacs/gromacs-2025.0_beta.ebuild | 11 |
4 files changed, 50 insertions, 5 deletions
diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz Binary files differindex 7c72c445ba81..00dacad4d1d0 100644 --- a/sci-chemistry/Manifest.gz +++ b/sci-chemistry/Manifest.gz diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest index 9a2618b30ac5..c9d2a0fcd485 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -1,3 +1,4 @@ +AUX gromacs-2025.0-beta-fix-man-build.patch 1245 BLAKE2B cfb869d4ef7a0b8417e49721b58f6888e86ddf2000079069466743d71c0e8184117538f5f15d1c5e5a29c7533efa42b660d52002bbd8d5b65b9d91461ced6027 SHA512 9ff00cf6ef23332ee63f36d1ca3116f660d0d69cebc375cc1c1212bf0f2a723b09cefeea5f01e9712af2c98eac2a6277dd2aaa7e05d762369883a86f5e02af64 AUX gromacs-gcc-15.patch 1003 BLAKE2B 557d2ca23180c0e7eb8d19518ba1b22a4fde9f1ccf225e05d00f21e3e6afaecc7f34c3614f783ac812fd03f0fe108099985f72dd6f6fa01d01a2daf6c17c0cc7 SHA512 b3c5430c21025b11a4fbb47785de1fe898183b9e5876e47648f3ddb47be69a808fd53bc96aee0f73bdfafefc4784e42a0a16870e57c92541d59063c2d822fa42 DIST gromacs-2023.5.tar.gz 42079310 BLAKE2B e50dbe76396230f4a886280bdebcf7b131506679240e77d2a2263c3b5dbfe7ef754c4265fc04e9acad7932c7691de7f694cc23140a25d0d5be649a4120f45b0c SHA512 f3a34cf0d379d6d4964d7494af6c6617c0c092293ea38a3a248af2dd2a90cae04696d52e68126176065efc480977942b00efa441028e526e1555c7e84551fc0c DIST gromacs-2024.3.tar.gz 42373103 BLAKE2B f45af72ecdf119b423d98b84818eaca1aa2e3f43eaf1aff7435de2a5891079a880f19a654627ee2f43e3a38c9dcfa0638bc6eb6da201b3c9ce89b2dc32fc683b SHA512 13f23e581c2b63f6262e8359e7bed6a1a5f3164047ea38d2b6a44bcd2b20b61332705167435fe2ad30fe6f24f8ab49b982388550cdecb49167e4156e36286d3d @@ -16,7 +17,7 @@ EBUILD gromacs-2023.9999.ebuild 9810 BLAKE2B 29946a30ec5fc7c19233790c48a8e665700 EBUILD gromacs-2024.3.ebuild 9861 BLAKE2B f7fa0c2bf44ebf280967ef0e259d99f5381555965b5fc96707ef0873ebcbaad2f1c5b77bb7307fefb40ef56bae2819b3677a501e478fb5c84f051c285fd90faa SHA512 0975c94642c19ec6d2a2c7a0ea6f55dd758b2b3775b106a09e8839c6f2e124d25610003e24c6a8c82e48575a894be7e5eb0a0309da9fdb8cead2e93121bf34fe EBUILD gromacs-2024.4.ebuild 9863 BLAKE2B 77657c52384762485cc3aa7615b65058dbcd23bd353b8184f99c1a4665c6a17bdf4ddbb62af650f99622e449768cb05d1e8cecefe1a307139ad5e63495c263f2 SHA512 aa550e1f89af67496b00b4a3469f74aff3477e12dd583d9b8ed15f38790b286a7eb90a3a30a8799b4c6258928c91b32e4307d3da9ef236bd6b12cf7da55867d5 EBUILD gromacs-2024.9999.ebuild 9817 BLAKE2B 5ef6b37d8c37ca3109be40e004f959cbad36e7b0334808acdf5711c5f06d22a8e199c0e6cd41aa010401134221ca4539810d7d67865f2d8145bb1669afae4471 SHA512 b288eaf90645a5dcc0904332f0c924fd62adbefd723a8f771d7990f3fdb243eaed13d466e91b4ffae2ec10cbebbbe8edb181136a19b2214fe33d01e2be1a0a94 -EBUILD gromacs-2025.0_beta.ebuild 10141 BLAKE2B f950507f63acc6443e10602d17de77d980585abd611391edec41a84e1d51d4cb9243a4dd3c50ef1078c83961f70d5c520dc199f486e17dc902c3dca0f0b8b502 SHA512 d2f7a2844574f301050f8d83c1e1d73ff04dd66fda56f0b9e916683415f846a3c1ca6b1555630d977e6cb6b3d5b7fa03d0a1e17856cc232a821209e2f7483540 +EBUILD gromacs-2025.0_beta.ebuild 10192 BLAKE2B 7dd93cfced20647ff7d4eed36a4ef3f4d7a9b06ff8236f27a5c6a42c6a43e36299aa754b69b14efdad013b841c6a53ee14504238c80e0a779ddc8c5eec88ab20 SHA512 249a89fe7f00959bb4a087357b97dcba38f81b756f41ccc98bb399bb348c2d0933f48bb6e269c2df9060ad62f2a71fc659c70d42d5e69ebe94bd9453b88fa492 EBUILD gromacs-2025.9999.ebuild 10092 BLAKE2B 15d351a5aa48ac092fc6c969156701f2fd9bec93ffb8c2f26a63e64ec4543dd1af01666cb6cd3b579097c10e23411ac60610db65e3d6106a356989bd4e5537cf SHA512 90d7f60f25b43f349fb0da8dbc62028468bc49e8187d6019a3421877e1c08817dd7186d63883a51c0742510f7f7b27a19fa544dc6bc7c498ba62152652f2e347 EBUILD gromacs-9999.ebuild 10131 BLAKE2B 9e39c3615616ee18584c5778b1faf306c5763af1162b36e28940c65d9c12634cc089f95a1f5098a60a9f087bc35c81375534ff8e6781e31681b187bc728338c4 SHA512 7b3fbf70ce73eacf8c6ed20910be83f4d3083886eda8af3a3546bf2b4ae5b964d31bb93710c0dc2856d00dd1de4cee1ea04f7de2a90a4fbf99e1e09eb99bb380 MISC metadata.xml 1394 BLAKE2B d387fba17fee85119e42ff18968f18d26bcbf5997361b4b1e93eeea1a8df54a9173b614f7d315000ecd0e4fa247becfb1236697825c0579fa7dcaff51a8185e5 SHA512 f8d9ebc33ad1f391dde1b7e056ad9b7860a902b805363c988962743cd4f37af69a0b1acd3323a95b9740ded0abf20904895605d78fecebdf94a4562ccd3ab9e8 diff --git a/sci-chemistry/gromacs/files/gromacs-2025.0-beta-fix-man-build.patch b/sci-chemistry/gromacs/files/gromacs-2025.0-beta-fix-man-build.patch new file mode 100644 index 000000000000..2eb2d45035a2 --- /dev/null +++ b/sci-chemistry/gromacs/files/gromacs-2025.0-beta-fix-man-build.patch @@ -0,0 +1,41 @@ +From 5c9a86c6c6ae3e9202e2feb0e1d33df40818c251 Mon Sep 17 00:00:00 2001 +From: Andrey Alekseenko <al42and@gmail.com> +Date: Tue, 10 Dec 2024 16:21:55 +0100 +Subject: [PATCH] Don't require GMXAPI for building man pages + +Refs #4767 +Fixes #5241 +--- + docs/conf.cmakein.py | 9 +++++++-- + 1 file changed, 7 insertions(+), 2 deletions(-) + +diff --git a/docs/conf.cmakein.py b/docs/conf.cmakein.py +index 577bcba9bd8..46986adbc07 100644 +--- a/docs/conf.cmakein.py ++++ b/docs/conf.cmakein.py +@@ -55,7 +55,12 @@ gmxapi_staging_path = "@GMXAPI_PYTHON_STAGING_DIR@" + if gmxapi_staging_path and os.path.isdir(gmxapi_staging_path): + sys.path.append(gmxapi_staging_path) + +-import gmxapi ++try: ++ import gmxapi ++except ImportError: ++ gmxapi_version_string = "N/A" ++else: ++ gmxapi_version_string = gmxapi.__version__ + + gmx_admin_scripts_path = "@GMX_ADMIN_DIR@" + gmx_containers_path = "@GMX_ADMIN_DIR@/containers" +@@ -277,7 +282,7 @@ rst_epilog += """ + .. |thisyear| replace:: {thisyear_string} + """.format( + gmx_version_string=gmx_version_string, +- gmxapi_version_string=gmxapi.__version__, ++ gmxapi_version_string=gmxapi_version_string, + regressiontest_version=regressiontest_version, + thisyear_string=thisyear_string, + ) +-- +GitLab + diff --git a/sci-chemistry/gromacs/gromacs-2025.0_beta.ebuild b/sci-chemistry/gromacs/gromacs-2025.0_beta.ebuild index 972995fab90d..275d0db9a29b 100644 --- a/sci-chemistry/gromacs/gromacs-2025.0_beta.ebuild +++ b/sci-chemistry/gromacs/gromacs-2025.0_beta.ebuild @@ -94,7 +94,10 @@ DOCS=( AUTHORS README ) RESTRICT="!test? ( test )" -PATCHES=( "${FILESDIR}/${PN}-gcc-15.patch" ) +PATCHES=( + "${FILESDIR}/${PN}-gcc-15.patch" + "${FILESDIR}/${PN}-2025.0-beta-fix-man-build.patch" +) if [[ ${PV} != *9999 ]]; then S="${WORKDIR}/${PN}-${PV/_/-}" @@ -241,7 +244,7 @@ src_configure() { -DGMX_USE_HDF5=off -DGMX_HWLOC=$(usex hwloc) -DGMX_DEFAULT_SUFFIX=off - #-DGMX_BUILD_HELP=on + -DGMX_BUILD_HELP=on -DGMX_SIMD="$acce" -DGMX_NNPOT="$nnpot" -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/" @@ -286,8 +289,8 @@ src_compile() { einfo "Compiling for ${x} precision" BUILD_DIR="${WORKDIR}/${P}_${x}"\ cmake_src_compile - #BUILD_DIR="${WORKDIR}/${P}_${x}"\ - # cmake_src_compile man + BUILD_DIR="${WORKDIR}/${P}_${x}"\ + cmake_src_compile man if use python; then BUILD_DIR="${WORKDIR}/${P}_${x}"\ cmake_src_compile python_packaging/all |