commit: 58f023bcae9893f344186cb4474ec86f94653cf7 Author: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org> AuthorDate: Fri Apr 23 11:41:19 2021 +0000 Commit: Alexey Shvetsov <alexxy <AT> gentoo <DOT> org> CommitDate: Fri Apr 23 11:41:19 2021 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=58f023bc
sci-chemistry/gromacs: Update patches Package-Manager: Portage-3.0.18, Repoman-3.0.3 Signed-off-by: Alexey Shvetsov <alexxy <AT> gentoo.org> .../gromacs/files/gromacs-2020-pytest.patch | 35 ++++++++++++++ .../gromacs/files/gromacs-2020_beta1-pytest.patch | 12 ----- .../gromacs/files/gromacs-2021-nblib.patch | 53 ++++++++++++++++++++++ sci-chemistry/gromacs/gromacs-2020.4.ebuild | 2 +- sci-chemistry/gromacs/gromacs-2020.5.ebuild | 2 +- sci-chemistry/gromacs/gromacs-2020.6.ebuild | 2 +- sci-chemistry/gromacs/gromacs-2020.9999.ebuild | 2 +- sci-chemistry/gromacs/gromacs-2021.1.ebuild | 5 +- sci-chemistry/gromacs/gromacs-2021.9999.ebuild | 2 - sci-chemistry/gromacs/gromacs-2021.ebuild | 2 +- sci-chemistry/gromacs/gromacs-9999.ebuild | 2 - 11 files changed, 97 insertions(+), 22 deletions(-) diff --git a/sci-chemistry/gromacs/files/gromacs-2020-pytest.patch b/sci-chemistry/gromacs/files/gromacs-2020-pytest.patch new file mode 100644 index 00000000000..cc7730afecb --- /dev/null +++ b/sci-chemistry/gromacs/files/gromacs-2020-pytest.patch @@ -0,0 +1,35 @@ +From e4e1263776844d660c471e3d1203acf54cdc855f Mon Sep 17 00:00:00 2001 +From: Alexey Shvetsov <[email protected]> +Date: Fri, 23 Apr 2021 13:21:24 +0300 +Subject: [PATCH 2/2] Allow to build python part without build testing enabled + +Signed-off-by: Alexey Shvetsov <[email protected]> +--- + python_packaging/src/CMakeLists.txt | 6 ++++-- + 1 file changed, 4 insertions(+), 2 deletions(-) + +diff --git a/python_packaging/src/CMakeLists.txt b/python_packaging/src/CMakeLists.txt +index c75549fc82..4f983fdd5f 100644 +--- a/python_packaging/src/CMakeLists.txt ++++ b/python_packaging/src/CMakeLists.txt +@@ -1,7 +1,7 @@ + # + # This file is part of the GROMACS molecular simulation package. + # +-# Copyright (c) 2019,2020, by the GROMACS development team, led by ++# Copyright (c) 2019,2020,2021, by the GROMACS development team, led by + # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, + # and including many others, as listed in the AUTHORS file in the + # top-level source directory and at http://www.gromacs.org. +@@ -252,5 +252,7 @@ endif() + # to the `check` target. Normal usage is to first install the Python package, + # then run `pytest` on the `tests` directory. Refer to gmxapi package documentation. + if(NOT GMXAPI_MASTER_PROJECT) +- add_subdirectory(test) ++ if (BUILD_TESTING) ++ add_subdirectory(test) ++ endif() + endif() +-- +2.31.1 + diff --git a/sci-chemistry/gromacs/files/gromacs-2020_beta1-pytest.patch b/sci-chemistry/gromacs/files/gromacs-2020_beta1-pytest.patch deleted file mode 100644 index 452987f38b9..00000000000 --- a/sci-chemistry/gromacs/files/gromacs-2020_beta1-pytest.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -urN gromacs-2020-beta1/python_packaging/src/CMakeLists.txt gromacs-2020-beta1-py/python_packaging/src/CMakeLists.txt ---- gromacs-2020-beta1/python_packaging/src/CMakeLists.txt 2019-09-12 05:48:57.000000000 +0300 -+++ gromacs-2020-beta1-py/python_packaging/src/CMakeLists.txt 2019-10-09 17:01:30.845304765 +0300 -@@ -201,5 +201,7 @@ - # to the `check` target. Normal usage is to first install the Python package, - # then run `pytest` on the `tests` directory. Refer to gmxapi package documentation. - if(NOT GMXAPI_MASTER_PROJECT) -- add_subdirectory(test) -+ if (GMX_BUILD_TESTING) -+ add_subdirectory(test) -+ endif() - endif() diff --git a/sci-chemistry/gromacs/files/gromacs-2021-nblib.patch b/sci-chemistry/gromacs/files/gromacs-2021-nblib.patch new file mode 100644 index 00000000000..67ea6f6f63c --- /dev/null +++ b/sci-chemistry/gromacs/files/gromacs-2021-nblib.patch @@ -0,0 +1,53 @@ +From 5771842a06f483ad52781f4f2cdf5311ddb5cfa1 Mon Sep 17 00:00:00 2001 +From: Alexey Shvetsov <[email protected]> +Date: Fri, 23 Apr 2021 13:15:10 +0300 +Subject: [PATCH 1/2] Allow to build and install nblib without GMX TESTS + enabled + +Without it you'll get error like this: + + CMake Error at api/nblib/CMakeLists.txt:79 (add_dependencies): + Cannot add target-level dependencies to non-existent target "tests". + + The add_dependencies works for top-level logical targets created by the + add_executable, add_library, or add_custom_target commands. If you want to + add file-level dependencies see the DEPENDS option of the add_custom_target + and add_custom_command commands. + +Signed-off-by: Alexey Shvetsov <[email protected]> +--- + api/nblib/CMakeLists.txt | 18 ++++++++++-------- + 1 file changed, 10 insertions(+), 8 deletions(-) + +diff --git a/api/nblib/CMakeLists.txt b/api/nblib/CMakeLists.txt +index a2ce06596e..51211c3d70 100644 +--- a/api/nblib/CMakeLists.txt ++++ b/api/nblib/CMakeLists.txt +@@ -76,14 +76,16 @@ add_custom_target(nblib-tests + ) + # Ensure that "make tests" builds all nblib tests so the top-level + # "make check" will work. +-add_dependencies(tests nblib-tests) +- +-# this allows all nblib tests to be run with "make check-nblib" +-add_custom_target(check-nblib +- COMMAND ${CMAKE_CTEST_COMMAND} --output-on-failure -R NbLib +- COMMENT "Running nblib tests" +- USES_TERMINAL VERBATIM) +-add_dependencies(check-nblib nblib-tests) ++if (BUILD_TESTING) ++ add_dependencies(tests nblib-tests) ++ ++ # this allows all nblib tests to be run with "make check-nblib" ++ add_custom_target(check-nblib ++ COMMAND ${CMAKE_CTEST_COMMAND} --output-on-failure -R NbLib ++ COMMENT "Running nblib tests" ++ USES_TERMINAL VERBATIM) ++ add_dependencies(check-nblib nblib-tests) ++endif() + + set(NBLIB_MAJOR 0) + set(NBLIB_MINOR 1) +-- +2.31.1 + diff --git a/sci-chemistry/gromacs/gromacs-2020.4.ebuild b/sci-chemistry/gromacs/gromacs-2020.4.ebuild index 042897ab6e1..e8417cf5947 100644 --- a/sci-chemistry/gromacs/gromacs-2020.4.ebuild +++ b/sci-chemistry/gromacs/gromacs-2020.4.ebuild @@ -85,7 +85,7 @@ if [[ ${PV} != *9999 ]]; then S="${WORKDIR}/${PN}-${PV/_/-}" fi -PATCHES=( "${FILESDIR}/${PN}-2020_beta1-pytest.patch" ) +PATCHES=( "${FILESDIR}/${PN}-2020-pytest.patch" ) pkg_pretend() { [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" diff --git a/sci-chemistry/gromacs/gromacs-2020.5.ebuild b/sci-chemistry/gromacs/gromacs-2020.5.ebuild index c891ecb0585..393fdad3162 100644 --- a/sci-chemistry/gromacs/gromacs-2020.5.ebuild +++ b/sci-chemistry/gromacs/gromacs-2020.5.ebuild @@ -85,7 +85,7 @@ if [[ ${PV} != *9999 ]]; then S="${WORKDIR}/${PN}-${PV/_/-}" fi -PATCHES=( "${FILESDIR}/${PN}-2020_beta1-pytest.patch" ) +PATCHES=( "${FILESDIR}/${PN}-2020-pytest.patch" ) pkg_pretend() { [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" diff --git a/sci-chemistry/gromacs/gromacs-2020.6.ebuild b/sci-chemistry/gromacs/gromacs-2020.6.ebuild index c891ecb0585..393fdad3162 100644 --- a/sci-chemistry/gromacs/gromacs-2020.6.ebuild +++ b/sci-chemistry/gromacs/gromacs-2020.6.ebuild @@ -85,7 +85,7 @@ if [[ ${PV} != *9999 ]]; then S="${WORKDIR}/${PN}-${PV/_/-}" fi -PATCHES=( "${FILESDIR}/${PN}-2020_beta1-pytest.patch" ) +PATCHES=( "${FILESDIR}/${PN}-2020-pytest.patch" ) pkg_pretend() { [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" diff --git a/sci-chemistry/gromacs/gromacs-2020.9999.ebuild b/sci-chemistry/gromacs/gromacs-2020.9999.ebuild index c891ecb0585..393fdad3162 100644 --- a/sci-chemistry/gromacs/gromacs-2020.9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-2020.9999.ebuild @@ -85,7 +85,7 @@ if [[ ${PV} != *9999 ]]; then S="${WORKDIR}/${PN}-${PV/_/-}" fi -PATCHES=( "${FILESDIR}/${PN}-2020_beta1-pytest.patch" ) +PATCHES=( "${FILESDIR}/${PN}-2020-pytest.patch" ) pkg_pretend() { [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" diff --git a/sci-chemistry/gromacs/gromacs-2021.1.ebuild b/sci-chemistry/gromacs/gromacs-2021.1.ebuild index 6bb2a501176..2a4610540b5 100644 --- a/sci-chemistry/gromacs/gromacs-2021.1.ebuild +++ b/sci-chemistry/gromacs/gromacs-2021.1.ebuild @@ -85,7 +85,10 @@ if [[ ${PV} != *9999 ]]; then S="${WORKDIR}/${PN}-${PV/_/-}" fi -PATCHES=( "${FILESDIR}/${PN}-2020_beta1-pytest.patch" ) +PATCHES=( + "${FILESDIR}/${PN}-2020-pytest.patch" + "${FILESDIR}/${PN}-2021-nblib.patch" +) pkg_pretend() { [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" diff --git a/sci-chemistry/gromacs/gromacs-2021.9999.ebuild b/sci-chemistry/gromacs/gromacs-2021.9999.ebuild index 6bb2a501176..dbeed6f4fec 100644 --- a/sci-chemistry/gromacs/gromacs-2021.9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-2021.9999.ebuild @@ -85,8 +85,6 @@ if [[ ${PV} != *9999 ]]; then S="${WORKDIR}/${PN}-${PV/_/-}" fi -PATCHES=( "${FILESDIR}/${PN}-2020_beta1-pytest.patch" ) - pkg_pretend() { [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" use openmp && ! tc-has-openmp && \ diff --git a/sci-chemistry/gromacs/gromacs-2021.ebuild b/sci-chemistry/gromacs/gromacs-2021.ebuild index 6bb2a501176..06979262614 100644 --- a/sci-chemistry/gromacs/gromacs-2021.ebuild +++ b/sci-chemistry/gromacs/gromacs-2021.ebuild @@ -85,7 +85,7 @@ if [[ ${PV} != *9999 ]]; then S="${WORKDIR}/${PN}-${PV/_/-}" fi -PATCHES=( "${FILESDIR}/${PN}-2020_beta1-pytest.patch" ) +PATCHES=( "${FILESDIR}/${PN}-2020-pytest.patch" ) pkg_pretend() { [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild index 6bb2a501176..dbeed6f4fec 100644 --- a/sci-chemistry/gromacs/gromacs-9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-9999.ebuild @@ -85,8 +85,6 @@ if [[ ${PV} != *9999 ]]; then S="${WORKDIR}/${PN}-${PV/_/-}" fi -PATCHES=( "${FILESDIR}/${PN}-2020_beta1-pytest.patch" ) - pkg_pretend() { [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs" use openmp && ! tc-has-openmp && \
