gentoo resync : 22.01.2021

3 files changed, 113 insertions, 25 deletions

diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index d839baa00632..d3a5325bddf9 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -1,23 +1,22 @@
 AUX gromacs-2020_beta1-pytest.patch 630 BLAKE2B 1036e06589c24459006f0b579ee89c9d9c4623c7ca32fae90b21646db13280549a23cad717ef7481b03cbf9f2629b6804c0727d4b8c7f3274d0463d2735f976a SHA512 b5880d3a21635892d52b2ac09cbf456194a3db0fa0676bbdd2c2500964da89fbb7f4ebed7ac7843304159bf11f44e279eb505b2af8833127d2e21f10cb254c1e
 DIST gromacs-2018.8.tar.gz 29913703 BLAKE2B 8780032305928067fbfe1559efe9eedc4d47e27ab2f6ab54d6dba39edfcbeefbee4673d8910009048a850620b5a08ba8feb622db652c439cfa50a149ec5f0015 SHA512 6717895942f2ab7b54019511ed2aebadadde8e96d3c4b7414bb9168ffe418432d2dee330192e199f7b9d2f665c71f5d4f1ef0911aa7243d525a2ca182ef5b122
-DIST gromacs-2019.5.tar.gz 33445791 BLAKE2B 1e2e2764b0c8774c878abf4f32c2fa7ddd9b46f464cf1256deb48335433d92ef1b315f5534cdec9f766ae928a71361b5a4dd4a4def638269eb260ff98dbbe8bb SHA512 fdd177e4dfd29629b72bfbb4d61ff7bcdb37279f534883a9df8fd57569212fe1e9f8b8c9cec347fcc607539f31412d604d11ee3c0eb797251960435962b1bec6
 DIST gromacs-2019.6.tar.gz 33446147 BLAKE2B adc21fb6b841b06d499607f8c0166a673645ef5af0b40bd823d0fff5ea24397e6301c5e1e0070986ae1ce1deba8a42052b66da148b071c1e21f2fe3908fee275 SHA512 7c227a9539e5775d5d128ae9e872a24181d79cdcd2852b86453597987e8d7332ecec371da65d089f6e610c54aafbccc8824ce298743383dd6240719ebee692a8
 DIST gromacs-2020.4.tar.gz 29149899 BLAKE2B a07c8efd96137d58c1edf4ac9b5aafeb16d9e65234b9459b71471827032654acacb58ed6ae87ec6e0e593a0acd799683cc4461b06cc883b089d740708619345e SHA512 0c56f058741af70660baf0177724ec940dd984c05ea141ede91ee51ce3744f76d00e31bdb5db907e46fa1639de5dca637b3ace26e89f908c2e74c69f0c21ed3a
-DIST gromacs-2021-beta3.tar.gz 30138154 BLAKE2B 4abea01663c743f70489f6fb874802496605ab1a9bc08f09547409fde370b0388fab826e0d2492e5447654bcb1ae9e5cf22fcdf5e2bd2306e83868b62ef9ec1f SHA512 f36799c5538b0c04d7406a2886c29a95593481e06835885fcd9de2d668a68015d2aeb7865f3050cc0451b1aac37b25b5d41b0b227ac9a33067322cc7ef9ce1c2
+DIST gromacs-2020.5.tar.gz 29148909 BLAKE2B ea439ae95d4af67a77d53182f7ddab702799edab8527c1b6ad20625d21a81f3e3c0cc699fa0b656625bffcca0bdd5a1e104aea4f592ee2db92b4f1a460ad0e80 SHA512 fe38fda36d31aef5ce01a3dbc29c9f50d3cc05b20bb34a9a8f10fda5aecde4f93ca8a3f85433139e1bb88fc23d77916a4aff5a292abaa528bd0e6138e84cba18
+DIST gromacs-2021-rc1.tar.gz 30141045 BLAKE2B 7fca2e8097be35bae3d35aa54d2793e6fa06181a471092930cc21333a11fec97a717e01ea2be494540df05687c06d25d9d2ad8308ac0913fbcfd94b72d380939 SHA512 74512ee4847b114ce6c4420f9b61af067ff9716a2c616d53cf66c6f47c8eb41ed5c566553c16392b5dc233386f1eeade892cb9e01cc9724199cef06ffa794869
 DIST manual-2018.8.pdf 10025023 BLAKE2B afb0a6e6a72d78df743fcb57e7c1716848589e571dd35167b957a9b407ca27978ccfb6cb9e0df9c9439b888f352501a00ba32281ed1e0b4193bd606f1d77152e SHA512 b1972f7ce965bfc9377542993c5943ea4868a8ed23a969d4203264746d6bea3a7a65c6379196ece37fd6d68ec7ec80f827bde87d1049284af7082759a124f1d5
-DIST manual-2019.5.pdf 12702361 BLAKE2B cb80429a59019b190115bf2af689c0df23b0fec6e41a9ebc9eba20977d1b06eed79044c906c41228883767f673140e15d3a5ef947a0c1ec4fe84012089f4fa91 SHA512 baf27961b87e6120c49abc9dc58e25d12a15588b4ac787e1a086748d488692d4a1262229ac66e550d3cca3a6042545fb6ec472a2c98d6a8698b7a18b4397f605
 DIST manual-2019.6.pdf 12702376 BLAKE2B c350127bc06a9eb3dee73da39037c84daeb89500e23cb131bd19a150bf60602d4dde7611e0c6f0f344af4093e96a899303dac71b4df56fd0c44c3a48a56606b7 SHA512 dfdff67c2c1c9ce1f1c236b7686c5331b0fe86951da6c98eddd6a3e748815e0be0a9653ae4318469fcdd913c4e7c355d64a997cc80b9d9fbe6282ef6d98e61eb
 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-2020.4.tar.gz 48542144 BLAKE2B 1dcde67525d40ababa74d9e8ba2dd3fdef1de7d1018491e102edd71d3a622925f213b5a0812e5448882b4cb5fb578317e8e5029bdc4bd53008aa8441a3d9dea1 SHA512 7c71f36a1cef22562f14dcd233e90ad2fe370ae1a7d3b5268727259b374e12d4754253735ac8745d3738bdbc1cc2067780fda5e393be2ff264f632fe4e0c1978
-DIST regressiontests-2021-beta3.tar.gz 48513481 BLAKE2B b39685e7a43dbcd83c0ffc28b15e3aca5c82c18dd817c543262787ac40466c88f72c2a350fd3e945d62e1f9ef6f938db916650315612a5d1e27d4c6b70f8d5e2 SHA512 183bebf3c44805efa5a90ae8b7a34d701ffbe3a5c5b37e80359cbdf61c8492fbe6ca24f10575b8e8061aa1ae38f2a3ea1bac8b723503b1b6ab706faeace9e411
+DIST regressiontests-2020.5.tar.gz 48541167 BLAKE2B 81f0505090203c970178ca4eba8dfd54d942a20970525cad954833481cd79141fa33fc97e8940ca83cee104ef6b017bc0f7bbed9eddc620a86c818760b3fc261 SHA512 aba67542ed00145cae8de040e4a9074a8a359a529135180e6083b2330934962302349d382d6626bddc6971ae6d44e09c8ea44d5df55ca5fcd038055a1c3e5cc3
+DIST regressiontests-2021-rc1.tar.gz 48512759 BLAKE2B 721c495993ded1dd61242014b5dd6bc08be18cebb1c1dd2404b1837bba451189e16cd52c94e842e6052703ec0a2638149ffa7b55b836ee11fcb4378b8e58628a SHA512 41171d1f6e394b10ff426bc0e354cfedc577f75825fc2c31a67761365498a1f2e35e97d66231dd8742a8d836e77e4512dba4238ef0319c9075cfe4231e721b1e
 EBUILD gromacs-2018.8.ebuild 6948 BLAKE2B f7258bdf69131e6eff444b9025573822828e7c073086af2a7b6d59b0e140033e1c6ae5a2bb3d3827cae5e52240366dd53fbac03a447b112993d72ddaf0230793 SHA512 274386cdd1b0b14a16cb785e4399104dc2f7a21718f88ed6fd96117b6606f3249159733dc7eb8afb8def3935f43f026444014f1a64f4ff8ea0af1d4a4fb0155c
-EBUILD gromacs-2019.5-r1.ebuild 7269 BLAKE2B 0767855a053171fbeab635ef2c90725df443d78b4c250cb8ec39ac8e7cc2b77550ca33916db655d08d17bcf9258b47a0f98af07c5f3e391cb82ee3fe501a3058 SHA512 69ca23a3b9599e5f55444e19a7478eb48ea0d48f9bbb98c6f9d237757dac008e5b62868cfe374540a902792b458c1f961e47a1b4bb4545ce412a04e54bcb6599
 EBUILD gromacs-2019.6.ebuild 7269 BLAKE2B 0767855a053171fbeab635ef2c90725df443d78b4c250cb8ec39ac8e7cc2b77550ca33916db655d08d17bcf9258b47a0f98af07c5f3e391cb82ee3fe501a3058 SHA512 69ca23a3b9599e5f55444e19a7478eb48ea0d48f9bbb98c6f9d237757dac008e5b62868cfe374540a902792b458c1f961e47a1b4bb4545ce412a04e54bcb6599
 EBUILD gromacs-2020.4.ebuild 9806 BLAKE2B 01135db92a8255edf64ef01e1c2318834b229186eec17ca36150767d97a65caaff42a09647b773150df99dcd85c9507424ea4b40366190d7a2e097ea6686f52a SHA512 4f66f1936eb632a50b06ec1c6662767e65a51ef17b816f321c6e8cce00a8926c537b4ae3ba50f7edf7b3679b1b8ebb2d683a84404f418be8b33e53ae6e9e2c94
+EBUILD gromacs-2020.5.ebuild 9809 BLAKE2B 63ecf9c00c5d8a67b1378fe24e82a18be87a67c2584baee0daece7e6583aa795be408db0f5c8acf10d136b5003c127b2fef3cfea6624c4951b3d4919a37ee098 SHA512 4f2e53f171f46b8be3372ca4a04b893ea78a81e7241792ae402b75e8a3619aaa8956e5684dc30247e3f19fe01b2b0319b8117b48042cddd9304e57f535b110bc
 EBUILD gromacs-2020.9999.ebuild 9809 BLAKE2B 63ecf9c00c5d8a67b1378fe24e82a18be87a67c2584baee0daece7e6583aa795be408db0f5c8acf10d136b5003c127b2fef3cfea6624c4951b3d4919a37ee098 SHA512 4f2e53f171f46b8be3372ca4a04b893ea78a81e7241792ae402b75e8a3619aaa8956e5684dc30247e3f19fe01b2b0319b8117b48042cddd9304e57f535b110bc
 EBUILD gromacs-2021.9999.ebuild 9982 BLAKE2B 5430b1a73a326a7e69a6193cbcf68195cde80250edfdec33038936318346a02d08fa58fc3bbdb4bf669805be33cfe7156916cfa6479069862bd2a75c4c94fdb5 SHA512 397714718f92fdcce12a6b409a6cc5375720eee92645d38c4580bd522192322ad1ca574fb831a0cbc5c4bca2cb7652a66089f6ebb876c299f8d8ce84f7a2004a
-EBUILD gromacs-2021_beta3.ebuild 9982 BLAKE2B 5430b1a73a326a7e69a6193cbcf68195cde80250edfdec33038936318346a02d08fa58fc3bbdb4bf669805be33cfe7156916cfa6479069862bd2a75c4c94fdb5 SHA512 397714718f92fdcce12a6b409a6cc5375720eee92645d38c4580bd522192322ad1ca574fb831a0cbc5c4bca2cb7652a66089f6ebb876c299f8d8ce84f7a2004a
+EBUILD gromacs-2021_rc1.ebuild 9982 BLAKE2B 5430b1a73a326a7e69a6193cbcf68195cde80250edfdec33038936318346a02d08fa58fc3bbdb4bf669805be33cfe7156916cfa6479069862bd2a75c4c94fdb5 SHA512 397714718f92fdcce12a6b409a6cc5375720eee92645d38c4580bd522192322ad1ca574fb831a0cbc5c4bca2cb7652a66089f6ebb876c299f8d8ce84f7a2004a
 EBUILD gromacs-9999.ebuild 9982 BLAKE2B 5430b1a73a326a7e69a6193cbcf68195cde80250edfdec33038936318346a02d08fa58fc3bbdb4bf669805be33cfe7156916cfa6479069862bd2a75c4c94fdb5 SHA512 397714718f92fdcce12a6b409a6cc5375720eee92645d38c4580bd522192322ad1ca574fb831a0cbc5c4bca2cb7652a66089f6ebb876c299f8d8ce84f7a2004a
 MISC metadata.xml 1173 BLAKE2B 768befbbd08adbd39f92bb715798a7ff8d0559bb3dfc3bf58c282ae687d4946f06b32c5a75544dcc33b83e5a874538712021c8ecbee5a989a6f045d752ab359b SHA512 24363e3136b7c81288798ac01f779cf9c06c32482c0b5acd6d1c5f2a66733ddfdf35de661cedb6a23e1a5de08c012b79e6d2903172aee139a675897e5c72e7d3
diff --git a/sci-chemistry/gromacs/gromacs-2019.5-r1.ebuild b/sci-chemistry/gromacs/gromacs-2020.5.ebuild
index da2db70a9742..bf0d38276e23 100644
--- a/sci-chemistry/gromacs/gromacs-2019.5-r1.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2020.5.ebuild
@@ -5,13 +5,25 @@ EAPI=7
 
 CMAKE_MAKEFILE_GENERATOR="ninja"
 
-inherit bash-completion-r1 cmake cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
-
-SRC_URI="
-	http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
-	doc? ( http://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf )
-	test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
-KEYWORDS="amd64 arm x86 ~amd64-linux ~x86-linux ~x64-macos"
+PYTHON_COMPAT=( python3_{6,7,8,9} )
+
+DISTUTILS_SINGLE_IMPL=1
+
+inherit bash-completion-r1 cmake cuda distutils-r1 eutils flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils
+
+if [[ $PV = *9999* ]]; then
+	EGIT_REPO_URI="
+		https://gitlab.com/gromacs/gromacs.git
+		https://github.com/gromacs/gromacs.git
+		git://git.gromacs.org/gromacs.git"
+	[[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
+	inherit git-r3
+else
+	SRC_URI="
+		http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz
+		test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )"
+	KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+fi
 
 ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
 
@@ -23,7 +35,7 @@ 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 +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +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? (
@@ -41,10 +53,21 @@ CDEPEND="
 	mkl? ( sci-libs/mkl )
 	mpi? ( virtual/mpi )
 	${PYTHON_DEPS}
+	!sci-chemistry/gmxapi
 	"
 BDEPEND="${CDEPEND}
 	virtual/pkgconfig
-	"
+	doc? (
+		app-doc/doxygen
+		$(python_gen_cond_dep '
+			dev-python/sphinx[${PYTHON_MULTI_USEDEP}]
+		')
+		media-gfx/mscgen
+		media-gfx/graphviz
+		dev-texlive/texlive-latex
+		dev-texlive/texlive-latexextra
+		media-gfx/imagemagick
+	)"
 RDEPEND="${CDEPEND}"
 
 REQUIRED_USE="
@@ -58,7 +81,11 @@ DOCS=( AUTHORS README )
 
 RESTRICT="!test? ( test )"
 
-S="${WORKDIR}/${PN}-${PV/_/-}"
+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"
@@ -66,6 +93,24 @@ pkg_pretend() {
 		die "Please switch to an openmp compatible compiler"
 }
 
+pkg_setup() {
+	python-single-r1_pkg_setup
+}
+
+src_unpack() {
+	if [[ ${PV} != *9999 ]]; then
+		default
+	else
+		git-r3_src_unpack
+		if use test; then
+			EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
+			EGIT_BRANCH="${EGIT_BRANCH}" \
+			EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
+				git-r3_src_unpack
+		fi
+	fi
+}
+
 src_prepare() {
 	#notes/todos
 	# -on apple: there is framework support
@@ -88,18 +133,44 @@ src_prepare() {
 	fi
 
 	DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats"
+
+	# try to create policy for imagemagik
+	mkdir -p ${HOME}/.config/ImageMagick
+	cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF
+	<?xml version="1.0" encoding="UTF-8"?>
+	<!DOCTYPE policymap [
+	<!ELEMENT policymap (policy)+>
+	!ATTLIST policymap xmlns CDATA #FIXED ''>
+	<!ELEMENT policy EMPTY>
+	<!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED
+			name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED
+			stealth NMTOKEN #IMPLIED value CDATA #IMPLIED>
+	]>
+	<policymap>
+		<policy domain="coder" rights="read | write" pattern="PS" />
+		<policy domain="coder" rights="read | write" pattern="PS2" />
+		<policy domain="coder" rights="read | write" pattern="PS3" />
+		<policy domain="coder" rights="read | write" pattern="EPS" />
+		<policy domain="coder" rights="read | write" pattern="PDF" />
+		<policy domain="coder" rights="read | write" pattern="XPS" />
+	</policymap>
+	EOF
 }
 
 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)
 	[[ ${CHOST} = *-darwin* ]] && \
@@ -137,6 +208,7 @@ src_configure() {
 		-DGMX_OPENMP=$(usex openmp)
 		-DGMX_COOL_QUOTES=$(usex offensive)
 		-DGMX_USE_TNG=$(usex tng)
+		-DGMX_BUILD_MANUAL=$(usex doc)
 		-DGMX_HWLOC=$(usex hwloc)
 		-DGMX_DEFAULT_SUFFIX=off
 		-DGMX_SIMD="$acce"
@@ -165,11 +237,13 @@ src_configure() {
 			-DGMX_MPI=OFF
 			-DGMX_THREAD_MPI=$(usex threads)
 			-DGMXAPI=$(usex gmxapi)
+			-DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy)
 			"${opencl[@]}"
 			"${cuda[@]}"
 			"$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
 			-DGMX_BINARY_SUFFIX="${suffix}"
 			-DGMX_LIBS_SUFFIX="${suffix}"
+			-DGMX_PYTHON_PACKAGE=$(usex python)
 			)
 		BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure
 		[[ ${CHOST} != *-darwin* ]] || \
@@ -201,6 +275,17 @@ src_compile() {
 		einfo "Compiling for ${x} precision"
 		BUILD_DIR="${WORKDIR}/${P}_${x}"\
 			cmake_src_compile
+		if use python; then
+			BUILD_DIR="${WORKDIR}/${P}_${x}"\
+				cmake_src_compile	python_packaging/all
+			BUILD_DIR="${WORKDIR}/${P}" \
+				distutils-r1_src_compile
+		fi
+		# not 100% necessary for rel ebuilds as available from website
+		if use doc; then
+			BUILD_DIR="${WORKDIR}/${P}_${x}"\
+				cmake_src_compile manual
+		fi
 		use mpi || continue
 		einfo "Compiling for ${x} precision with mpi"
 		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
@@ -219,8 +304,12 @@ src_install() {
 	for x in ${GMX_DIRS}; do
 		BUILD_DIR="${WORKDIR}/${P}_${x}" \
 			cmake_src_install
+		if use python; then
+			BUILD_DIR="${WORKDIR}/${P}_${x}" \
+				cmake_src_install	python_packaging/install
+		fi
 		if use doc; then
-			newdoc "${DISTDIR}/manual-${PV/_/-}.pdf" "${PN}-manual-${PV}.pdf"
+			newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
 		fi
 		use mpi || continue
 		BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
diff --git a/sci-chemistry/gromacs/gromacs-2021_beta3.ebuild b/sci-chemistry/gromacs/gromacs-2021_rc1.ebuild
index 99ee93e05094..99ee93e05094 100644
--- a/sci-chemistry/gromacs/gromacs-2021_beta3.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2021_rc1.ebuild