sci-chemistry/gromacs: Version bump to 2020.2

Also added custom-cflags and fixed bash-completion

Closes: https://bugs.gentoo.org/687920
Closes: https://bugs.gentoo.org/711572
Package-Manager: Portage-2.3.99, Repoman-2.3.22
Signed-off-by: Alexey Shvetsov <alexxy@gentoo.org>

3 files changed, 30 insertions, 22 deletions

diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 7cb4e19f224a..85ca68f29247 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -2,9 +2,9 @@ DIST gromacs-2018.8.tar.gz 29913703 BLAKE2B 8780032305928067fbfe1559efe9eedc4d47
 DIST gromacs-2019.5.tar.gz 33445791 BLAKE2B 1e2e2764b0c8774c878abf4f32c2fa7ddd9b46f464cf1256deb48335433d92ef1b315f5534cdec9f766ae928a71361b5a4dd4a4def638269eb260ff98dbbe8bb SHA512 fdd177e4dfd29629b72bfbb4d61ff7bcdb37279f534883a9df8fd57569212fe1e9f8b8c9cec347fcc607539f31412d604d11ee3c0eb797251960435962b1bec6
 DIST gromacs-2019.6.tar.gz 33446147 BLAKE2B adc21fb6b841b06d499607f8c0166a673645ef5af0b40bd823d0fff5ea24397e6301c5e1e0070986ae1ce1deba8a42052b66da148b071c1e21f2fe3908fee275 SHA512 7c227a9539e5775d5d128ae9e872a24181d79cdcd2852b86453597987e8d7332ecec371da65d089f6e610c54aafbccc8824ce298743383dd6240719ebee692a8
 DIST gromacs-2020.1.tar.gz 29153989 BLAKE2B b1c0313da945c57c74040c2bcd50495b238b0e131cc4ebecd74ae0d01465b47d732ea456a52a2f9d998cd37e2bfdb93d52bd15177328c4b7a14e6b1d8bc00117 SHA512 130394ec70e5d75ea451e9fa77c4ea2dd4adb0c51cc7663ac8579972bab7a0b75d9143d0eebb21802fc93305deca8831393a8cb3f51b6d01f9477f3dadece037
-DIST gromacs-2020.tar.gz 28928068 BLAKE2B 72d4ff8f6b383284e61df9d3b2b53c51300f6961d4c19810670c8ee9ba2f1864d2a325e2774093b9338db785cb91a94461bf93f16cdf4caf0f690298a672d51c SHA512 15f0d58cd8d217eab39ef8e3535dec34127708797eaf6575fb340292cbee2303cd25deb84b3d4417a787076f4ae7be9e4958ec3a347a3aa9aed52ef337a4587c
+DIST gromacs-2020.2.tar.gz 29144614 BLAKE2B cd20b031dcec32d9a797d66f2679779077910c184702f12f12093d92e8417d42e07bfb17a8fe63e9d29a889d5f57461b5f86e11adfc26635f8d2b5a5df19473a SHA512 348c80fad93b34e6703906fec97c6c2294c0803c326d6145776b732e1c33cd58e0967ddb2ec4799e3583542c09e7a6a015e4d084d60cf97b81b3a92253cca76c
 DIST regressiontests-2018.8.tar.gz 67855469 BLAKE2B 34c9b339f6229f483afbb5192ee6ba8b8f72d5c26907a853af9c53dfece0d88739e48f6b44b78d1c010f988f9385d077285300522164f533a5861e9dda879275 SHA512 3642389d27bd1942cd0f091c940ae97b197b94856a387fe581dc516b0d4169480f16551d4ba357f9282b3337d605c286d51dd38112ac87c826dda634904836bb
 DIST regressiontests-2019.5.tar.gz 67643634 BLAKE2B c4d9535d9a8a650869d67544ad5f367324f45e55325bb5074ece9b010f232f2f0dd97c9af97924d3f2368ed63015ca7330baff1cc681310e1439ec330b70ee8d SHA512 7c0917b76e7db35ab4e3271d523d268e0e2d858091e68ead863bfe6d1e56b381e30fdbf44f479f6e065c029e2eb27cfa0dbaa1b243f185144321aaf5084c55ce
 DIST regressiontests-2019.6.tar.gz 67643195 BLAKE2B 1e054e24b187946f7ea28090d4f20cf8e1d79a26253f57ba07d130e0773d8541b8a1552a38023d31a68ce8bc62d8e0af1d98609234bb3e7d3e6d567307ebb386 SHA512 eacf1c55b982515a305c29459fe80a7cd558a8481e5689962aa956148af542568b1d1ce59c6784ecb0afd4768c2b664afa21e12af2d89ae2b06b1ba61ad72036
 DIST regressiontests-2020.1.tar.gz 48541809 BLAKE2B 0fec2f0fb7fad0ad48bb790d7df6487e2c1931a0a2134795bf7da4a9087f0f2a3743288fc4ec057fa6b22412c2d8f312cfa3af38be8c5bea51d7a06afb5ac9f0 SHA512 664d29ce39629ed218de65179ce4a73e479d73d30bc96f5ae57624d7e4447298c6122dc09e7873b8cad458eaee0530866411fab20e009e46bf39b133e0de47e8
-DIST regressiontests-2020.tar.gz 48536146 BLAKE2B 9511db78b5d6a5ea431fdb73782f28dde4b94655139886c0ad519888ef3e435fe81807f158d66c1a4284cb88fe730f62d039ac23549f17d0ce5984764ef35f10 SHA512 5a35aaf6fe2f3b146c7045e9c967dc1c8bf754748cc1f2a7300193ae3f206a9f5058329380ae7b03b181410303bcd434584571e6161a75f99e52bd48f8ba1821
+DIST regressiontests-2020.2.tar.gz 48539492 BLAKE2B 08222ec18e70f551194fc0a060facda394c0d9999e162dace06029aa5f36e7237aeb2468a80d1198257a45fb076f8f633a7279a85976484900bf4154176aa070 SHA512 3066d92a59dafade78807612681d82a7b8a0bd9b74fa7e8784063a908418c55b4427482dc7feb261ff6981fabb2d64a800d3e90ed647ab45e201f4847347bac7
diff --git a/sci-chemistry/gromacs/gromacs-2020-r1.ebuild b/sci-chemistry/gromacs/gromacs-2020.1-r1.ebuild
index a2dcda755c8b..fab120420b28 100644
--- a/sci-chemistry/gromacs/gromacs-2020-r1.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2020.1-r1.ebuild
@@ -5,7 +5,7 @@ EAPI=7
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
-PYTHON_COMPAT=( python3_{6,7} )
+PYTHON_COMPAT=( python3_{6,7,8} )
 
 DISTUTILS_SINGLE_IMPL=1
 
@@ -34,7 +34,7 @@ HOMEPAGE="http://www.gromacs.org/"
 #        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
 LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
 SLOT="0/${PV}"
-IUSE="X blas cuda +doc -double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
+IUSE="X blas cuda +custom-cflags +doc -double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
 
 CDEPEND="
 	X? (
@@ -159,13 +159,17 @@ src_prepare() {
 src_configure() {
 	local mycmakeargs_pre=( ) extra fft_opts=( )
 
-	#go from slowest to fastest acceleration
-	local acce="None"
-	use cpu_flags_x86_sse2 && acce="SSE2"
-	use cpu_flags_x86_sse4_1 && acce="SSE4.1"
-	use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
-	use cpu_flags_x86_avx && acce="AVX_256"
-	use cpu_flags_x86_avx2 && acce="AVX2_256"
+	if use custom-cflags; then
+		#go from slowest to fastest acceleration
+		local acce="None"
+		use cpu_flags_x86_sse2 && acce="SSE2"
+		use cpu_flags_x86_sse4_1 && acce="SSE4.1"
+		use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
+		use cpu_flags_x86_avx && acce="AVX_256"
+		use cpu_flags_x86_avx2 && acce="AVX2_256"
+	else
+		strip-flags
+	fi
 
 	#to create man pages, build tree binaries are executed (bug #398437)
 	[[ ${CHOST} = *-darwin* ]] && \
@@ -320,7 +324,7 @@ src_install() {
 	for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do
 		local n=${x##*/gmx-completion-}
 		n="${n%.bash}"
-		cat "${ED}"/usr/bin/gmx-completion-gmx.bash "$x" > "${T}/${n}" || die
+		cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
 		newbashcomp "${T}"/"${n}" "${n}"
 	done
 	rm "${ED}"/usr/bin/gmx-completion*.bash || die
diff --git a/sci-chemistry/gromacs/gromacs-2020.1.ebuild b/sci-chemistry/gromacs/gromacs-2020.2.ebuild
index a2dcda755c8b..fab120420b28 100644
--- a/sci-chemistry/gromacs/gromacs-2020.1.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2020.2.ebuild
@@ -5,7 +5,7 @@ EAPI=7
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
-PYTHON_COMPAT=( python3_{6,7} )
+PYTHON_COMPAT=( python3_{6,7,8} )
 
 DISTUTILS_SINGLE_IMPL=1
 
@@ -34,7 +34,7 @@ HOMEPAGE="http://www.gromacs.org/"
 #        base,    vmd plugins, fftpack from numpy,  blas/lapck from netlib,        memtestG80 library,  mpi_thread lib
 LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
 SLOT="0/${PV}"
-IUSE="X blas cuda +doc -double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
+IUSE="X blas cuda +custom-cflags +doc -double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
 
 CDEPEND="
 	X? (
@@ -159,13 +159,17 @@ src_prepare() {
 src_configure() {
 	local mycmakeargs_pre=( ) extra fft_opts=( )
 
-	#go from slowest to fastest acceleration
-	local acce="None"
-	use cpu_flags_x86_sse2 && acce="SSE2"
-	use cpu_flags_x86_sse4_1 && acce="SSE4.1"
-	use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
-	use cpu_flags_x86_avx && acce="AVX_256"
-	use cpu_flags_x86_avx2 && acce="AVX2_256"
+	if use custom-cflags; then
+		#go from slowest to fastest acceleration
+		local acce="None"
+		use cpu_flags_x86_sse2 && acce="SSE2"
+		use cpu_flags_x86_sse4_1 && acce="SSE4.1"
+		use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
+		use cpu_flags_x86_avx && acce="AVX_256"
+		use cpu_flags_x86_avx2 && acce="AVX2_256"
+	else
+		strip-flags
+	fi
 
 	#to create man pages, build tree binaries are executed (bug #398437)
 	[[ ${CHOST} = *-darwin* ]] && \
@@ -320,7 +324,7 @@ src_install() {
 	for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do
 		local n=${x##*/gmx-completion-}
 		n="${n%.bash}"
-		cat "${ED}"/usr/bin/gmx-completion-gmx.bash "$x" > "${T}/${n}" || die
+		cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
 		newbashcomp "${T}"/"${n}" "${n}"
 	done
 	rm "${ED}"/usr/bin/gmx-completion*.bash || die