gentoo resync : 22.05.2021

17 files changed, 140 insertions, 27 deletions

diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index 8778c0e1caa5..3a310b8d597b 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/autodock_vina/Manifest b/sci-chemistry/autodock_vina/Manifest
index 29a6bdab13b7..d97143eb4ea6 100644
--- a/sci-chemistry/autodock_vina/Manifest
+++ b/sci-chemistry/autodock_vina/Manifest
@@ -2,5 +2,5 @@ AUX 1.1.2-gentoo.patch 2448 BLAKE2B f63add1d0fec8716672672af78fe8f34053bf060044e
 AUX autodock_vina-1.1.2-boost-filesystem.patch 2936 BLAKE2B 70c55e95e9728221ba80177989fde0cc6c93b479779aa0dda45dcad79b97018fe934ea56b4ede4af20ce867b6ed39c3958a5529b8f286aec33ec7ea53d339ada SHA512 4226fb0d7196362a02afa4e0b0616146ef816a439dd63e1bffbfef183975fe7e6260318f919e9d9835d2d47973542b5340e93ad35b070467e42c0990f9a635f7
 AUX autodock_vina-1.1.2-missing-debug-decl.patch 365 BLAKE2B 959b46facdce27850a1f9fd6c66ecc297e4ad089e79896b9fe2127e425bd1bfcfce5d676cf2e4336c47d3a72b0e8319c791fdf1a5807f244cf5b4528de8cbb25 SHA512 ddbdca76fca16b46fd042b57eb941b7ba67f59f46c35dc18428ea6873c8ed5f03051247b8c667a08af8de40fccb0caf851848bb9082536225cacf8eb3e313c98
 DIST autodock_vina_1_1_2.tgz 67366 BLAKE2B dc754bf522795ebfbfcf89a2df4e3761d941c1f0ce05cf56898720c1e855f5dd00fd2a583f5a8d218fa2e738d37e014a9b3239b9aa989b9018a6a33f8f0bd02c SHA512 f704af322ebc192117c49d0cf8a3f217105beccb7b47d6361665470894ef7a9f91fc4b5f07cc9aff56e497bfa80953e40e39090c8394a095c61597756e333ae9
-EBUILD autodock_vina-1.1.2.ebuild 961 BLAKE2B ad31cbddec75c3a632b8c2bb10232c4c5016f7c7d8fa484e7391f56193083745ab5ae1167ad6c10740a807c36a1b6539ab0b1116b17ce63104c5b0d9ede9945c SHA512 2beda21fe701993067864ebc3408e05515b8939c732cf7f01e7a5a033cd1c0f08cd35ed9695bdef841f3c5113707c3792a49733c716f332b5299b33b2af0273b
+EBUILD autodock_vina-1.1.2.ebuild 948 BLAKE2B 4f5bd4de05bd0ad3839df02a8eceb845ac6d87128ebb841f9281a189deb648fc5e542fb0a4f9d6175150c55217eb9fe5aaa42b0f477edb17848f4da099afe565 SHA512 72c931a124bb5532baa934b55e146c859aec7fb5ae8803a2f52b3103adc126a3f4a1d0ee0552974c6aec5a7e13a25976f0a28e2d09711fa840b89c76d3666de8
 MISC metadata.xml 1244 BLAKE2B 7df9f6f260c038c4f6b02a9fe35b54dbdc165975373ece6fb27856893536b3af7218ca1ff487ba908caa8c9beea43dc3f503fc83b6cf685754b8f17e53d771a9 SHA512 121a82bab7f4126fe5afe4ad39bbc9e397483c485e8a5771129d8eff883e87248acb1d689d47a57bf792ea8e1e23e82dec9bde811dae44e9b86a6736944c3484
diff --git a/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild b/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild
index 354d80938d42..19a6a106be73 100644
--- a/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild
+++ b/sci-chemistry/autodock_vina/autodock_vina-1.1.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -33,15 +33,14 @@ src_prepare() {
 }
 
 src_configure() {
-	use debug || c_options="-DNDEBUG"
-	append-cxxflags -DBOOST_FILESYSTEM_VERSION=3
+	append-cxxflags -DBOOST_FILESYSTEM_VERSION=3 -std=c++11
 }
 
 src_compile() {
 	emake \
 		BASE="${EPREFIX}"/usr/ \
 		GPP="$(tc-getCXX)" \
-		C_OPTIONS="${c_options}"
+		C_OPTIONS=$(usex debug '' -DNDEBUG)
 }
 
 src_install() {
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index bd642f2438f8..796f237d7b12 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -16,14 +16,14 @@ DIST regressiontests-2020.5.tar.gz 48541167 BLAKE2B 81f0505090203c970178ca4eba8d
 DIST regressiontests-2020.6.tar.gz 48541232 BLAKE2B dbb405bd9168775984de8c9fb9e3fa2398d2790e2e4de23711c51a01dc3ea570d172a35d4924742ad5eda463eb0a885e6924512801e82b241600ceaefd5db70d SHA512 497a9e7d438b0b7b0734a97cf3683baf480ecc056e96b09f1e143c362ff047a4e51e323216750501c954559579716dc024d3c51319bd2c85fa719466ce4330b2
 DIST regressiontests-2021.1.tar.gz 48516304 BLAKE2B 61e49e7a3ce0856cd22a6adc360f476bd4978650e21ad64074d3cd8db1d6109fb86cb91bcb161d00d1e912cf3fa40dd83c07e5cc873dc2177a11d7fb304e7ecc SHA512 c1158b7890e2ff94c6600e531fdceee439f19ee2d18093b8be68fbd18064aae4b035c697ebda4e9b74d61c68d905c26515a41c34a2ac9f8dd8a29c5348ecbab1
 DIST regressiontests-2021.tar.gz 48513192 BLAKE2B e27898ef3936495fce111c8debdafbdaafae07cd9b27c8591cc27695f681fddda34f083d427e5b3afd2f318ff41201eabc915025f1fddef61ae29ceb13f37557 SHA512 e33578d32b929d516614592d0bf4aac4e518cc4f18fee4048d5b73b11f4373494c6d8aa43442e4e2be632c12c058657bce1064be82c515787d57b449c1241e48
-EBUILD gromacs-2018.8.ebuild 6941 BLAKE2B 84160857aa16b5ae72448939de39b3ca8876be81ced306fbc1f3ecc5de6964daea2fb3c895212e5b6357aaa19f82e5b77f286a11810d286974e266be7ae2ab71 SHA512 a1227cc71d33cb6fb10750c9132d75f1430728ec0e424f501b7c6ea96d7b00ff94c78a574509c68de5a4d19392589f9b74d851d7e4232c7e0f8a45da7575692b
-EBUILD gromacs-2019.6.ebuild 7262 BLAKE2B a4fbc3f39c5969fa9368f0f54311865e8a6d5e8ff309ac7fba3f7bfabea6bb2c0a431b8cb7a3c0cab93dbc335301ffc05ea619420e6e3487580f03f5a8e10971 SHA512 1e6b3b5d81263b6f1614f8e8428a3480bd8c3c0ac82fb560c29ffff540a25ecf5b52b1d71f32cc2655293df489bf16ca74a976f05bcac8256309c9eed27df948
-EBUILD gromacs-2020.4.ebuild 9795 BLAKE2B f4ca74c339366934549d4ae69fe84e30096689f7ebcfc4d6f869fdbe5abc31d47dd0d6d5c012fbb185ba157f37c484e3ce7b3f621237d78d050c1883415f06fb SHA512 7449123e710167fef7b96bdb18f1f719903dc09623c7c8bbadcac5e820e602c4f79dcf737fd105bfa6dc9c41ef27e8df602fac08306d334e91a7395376235888
-EBUILD gromacs-2020.5.ebuild 9798 BLAKE2B b35869bc8fe3a0df94a022d60f38be93a949780b5b40f4c97158ad84a8cd7469684c38bc12d2836c2e4a816b284435cf2ed9d385c128177667b96d391efe72da SHA512 30bf8ab69e895366ee3b288ba03fcbd886d22f712245a4a488983419d0ea0df11c9571609d193ec83613f1491061f3d7702a1d7a66a51ba0edc6e3ec83f5d4f3
-EBUILD gromacs-2020.6.ebuild 9798 BLAKE2B b35869bc8fe3a0df94a022d60f38be93a949780b5b40f4c97158ad84a8cd7469684c38bc12d2836c2e4a816b284435cf2ed9d385c128177667b96d391efe72da SHA512 30bf8ab69e895366ee3b288ba03fcbd886d22f712245a4a488983419d0ea0df11c9571609d193ec83613f1491061f3d7702a1d7a66a51ba0edc6e3ec83f5d4f3
-EBUILD gromacs-2020.9999.ebuild 9798 BLAKE2B b35869bc8fe3a0df94a022d60f38be93a949780b5b40f4c97158ad84a8cd7469684c38bc12d2836c2e4a816b284435cf2ed9d385c128177667b96d391efe72da SHA512 30bf8ab69e895366ee3b288ba03fcbd886d22f712245a4a488983419d0ea0df11c9571609d193ec83613f1491061f3d7702a1d7a66a51ba0edc6e3ec83f5d4f3
-EBUILD gromacs-2021.1.ebuild 10010 BLAKE2B c59a67bf283dc238fe2de9c8d221fdb096c34f7625f843bfcfd7e1ca15727d78b696ab7d893faca1b0f0dddb5cfe58bcb1fef613a9c9c078c78c3d535970ffd3 SHA512 39a9adcea4d81dc56c46788fe516ccf6ab18be021daf6eea959a38e3452a52b1b6e0ae6a6c23d768053ca146f127d211b660fa4ac31cd72c93b035d2178b1280
-EBUILD gromacs-2021.9999.ebuild 9920 BLAKE2B e5e42747bfb0d91070e9c08a9c3f70c506b5f363cd46565ab7da47cda771efd1219d8a24ea5cc92594f86eb2acf076b264edf5cbd53c3824d8daf733adf30ac8 SHA512 42aa5e307f3863614e7048bdd557937003f2f92f8f13a2a980fc3ab7a7bce896cec760b31170961239ef14e4eaba7e5ff086e3380c0d158588ea8fc27acf2616
-EBUILD gromacs-2021.ebuild 9971 BLAKE2B f7d25d846b6beba6e245d0e099d662df821c278d2f01d2dfc50586aa3718ad7928637c27af4f617b450c20c1e143fef89d8708329c706854c4f0bbde291154f6 SHA512 573f606f563c9902d4277277db09f7b8d829fdacef39412fc0f0fa77f681f5f2c5bbc1bcef24a1c4ba7b42bff51b2d2134b417b5f17d843fba1c948a53c2ded6
-EBUILD gromacs-9999.ebuild 9920 BLAKE2B e5e42747bfb0d91070e9c08a9c3f70c506b5f363cd46565ab7da47cda771efd1219d8a24ea5cc92594f86eb2acf076b264edf5cbd53c3824d8daf733adf30ac8 SHA512 42aa5e307f3863614e7048bdd557937003f2f92f8f13a2a980fc3ab7a7bce896cec760b31170961239ef14e4eaba7e5ff086e3380c0d158588ea8fc27acf2616
-MISC metadata.xml 1173 BLAKE2B 768befbbd08adbd39f92bb715798a7ff8d0559bb3dfc3bf58c282ae687d4946f06b32c5a75544dcc33b83e5a874538712021c8ecbee5a989a6f045d752ab359b SHA512 24363e3136b7c81288798ac01f779cf9c06c32482c0b5acd6d1c5f2a66733ddfdf35de661cedb6a23e1a5de08c012b79e6d2903172aee139a675897e5c72e7d3
+EBUILD gromacs-2018.8.ebuild 6944 BLAKE2B a91190e99ed188eeff085d164dee6d65a886906cc4555bbbd61f195e345cb276b5ccfc67e4e356253b11ff2af60af61783be70425292220c5aa5172ece1a21d3 SHA512 5df8545501f57f44a88406da75185fa107fb44446cdbd26bb0ed79086484e9933e0d147de39d7b7797bd6d18f8b2fcdbbe5acda3fc2c39ca29490452d4776082
+EBUILD gromacs-2019.6.ebuild 7265 BLAKE2B 70135e4b38335ccbf51d99a22572dd07bb25df895b4dd50da0297ed7852884bb102e40d94216c04b9503e58473579e8b001f4c94fe8cc164a4d6277b52384f59 SHA512 b95fdca7d93c3817ff820d5e2692b9c396a0fae46e7a700c2aab3e3fcfe29c76099222f61213a7c1e1279fc61dba74dcdb22127b6ada4ee870e813c1d0407e68
+EBUILD gromacs-2020.4.ebuild 9798 BLAKE2B 1b5f2c4d9f095e656c64c5478141dcfca3906640b25aabedf8582e707c6ae3862368b67c4dc79e9244caf5161573fd548169fcd3dbd2129a7d19e54602202d85 SHA512 74ec944c55091fc2ce6923b532e3c9a32a2b73de5329edbbe34f9b4de34efb32d19b85698b7a5fa98053b1ce646ae8c7213386a525abf60ee655313a905b0a34
+EBUILD gromacs-2020.5.ebuild 9801 BLAKE2B b8c3b202bfec4c8073be959a36269465508f342544013b16659ff652f8034a9f2ce18ebb1314564544862549ee4f472ba7afd54d5c4fdd6ecd532c6b5961ff29 SHA512 c6301bc851db9265c8ac1ce65c750b3bfd1e2c36f051002a0bf9f6a3e1fd6642886e0e61d4aa4fc5236fb6f0625aa3606a5494a26a039a20202f599a9670364f
+EBUILD gromacs-2020.6.ebuild 9801 BLAKE2B b8c3b202bfec4c8073be959a36269465508f342544013b16659ff652f8034a9f2ce18ebb1314564544862549ee4f472ba7afd54d5c4fdd6ecd532c6b5961ff29 SHA512 c6301bc851db9265c8ac1ce65c750b3bfd1e2c36f051002a0bf9f6a3e1fd6642886e0e61d4aa4fc5236fb6f0625aa3606a5494a26a039a20202f599a9670364f
+EBUILD gromacs-2020.9999.ebuild 9801 BLAKE2B b8c3b202bfec4c8073be959a36269465508f342544013b16659ff652f8034a9f2ce18ebb1314564544862549ee4f472ba7afd54d5c4fdd6ecd532c6b5961ff29 SHA512 c6301bc851db9265c8ac1ce65c750b3bfd1e2c36f051002a0bf9f6a3e1fd6642886e0e61d4aa4fc5236fb6f0625aa3606a5494a26a039a20202f599a9670364f
+EBUILD gromacs-2021.1.ebuild 10013 BLAKE2B 84d8df2311c84183cdc2e9766048b86eaf664ef40016632b3beffac251596e50c52ebe7cc4add2289ab092323895ef5b419ffa09114e614acc7dd3ca8b9db128 SHA512 0bc4811c4f5e54ff4df13415bdb6b3aaee3c37de5e839f39acf5cd21ded8b1b427470145c1cdae99d891757fa6060af15a29001427bc30018b4a72adf626a71d
+EBUILD gromacs-2021.9999.ebuild 9923 BLAKE2B 29847a40e8a7bc586d04dedbef998eff22388f91459cf364dcea0ff07bd5328e9dc2226237fbd608f96f5511f23d6de067804342c8c2faf95cc0e681403143a5 SHA512 b2ca0e12587d64b0482e026134d43530951b8b8c1df4f082bb85ffda51bc7b347617acf5f002f26e3a4607b29e2d974475fab573ea9d98dea7cf2028673647fc
+EBUILD gromacs-2021.ebuild 9974 BLAKE2B cfb46e429458b38c130ee731af60515ecca1660606ae7ec941dd2da0c5f2e84e8437c141126b859a9dc783c1ffe0b00376faa7535a65ea017a81febb57cb3ea6 SHA512 4c7ee67248e529af4f3f377c8da72e728954a62297b446fc0bc0fe84c3a75bc1ab8d9fdf5ab5e4205471519245a0a2d9f611b940ef641258523b479e3049f0ab
+EBUILD gromacs-9999.ebuild 9923 BLAKE2B 29847a40e8a7bc586d04dedbef998eff22388f91459cf364dcea0ff07bd5328e9dc2226237fbd608f96f5511f23d6de067804342c8c2faf95cc0e681403143a5 SHA512 b2ca0e12587d64b0482e026134d43530951b8b8c1df4f082bb85ffda51bc7b347617acf5f002f26e3a4607b29e2d974475fab573ea9d98dea7cf2028673647fc
+MISC metadata.xml 1149 BLAKE2B c2a231776a6e0e3b62c8ca9e05ee0012b5c90ff3d752034ff1f32e46c0cb5240f1a45a78ad0d8cf62c46ddcdd689aa50f9bbe955547f800baf7c037872295e98 SHA512 0799ce85673f6c8161fe18eeb6303844a0de41ea6c164c6bf16c42e7619c248c8d840dcffd55785699dbfd433d0b086c8982fc36a2414b3fdb687578602b6c83
diff --git a/sci-chemistry/gromacs/gromacs-2018.8.ebuild b/sci-chemistry/gromacs/gromacs-2018.8.ebuild
index dfe7923415e4..7c0c24d883f4 100644
--- a/sci-chemistry/gromacs/gromacs-2018.8.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2018.8.ebuild
@@ -198,7 +198,7 @@ src_compile() {
 src_test() {
 	for x in ${GMX_DIRS}; do
 		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake_src_make check
+			cmake_src_compile check
 	done
 }
 
diff --git a/sci-chemistry/gromacs/gromacs-2019.6.ebuild b/sci-chemistry/gromacs/gromacs-2019.6.ebuild
index 37058195e940..5ba8f9df146a 100644
--- a/sci-chemistry/gromacs/gromacs-2019.6.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2019.6.ebuild
@@ -211,7 +211,7 @@ src_compile() {
 src_test() {
 	for x in ${GMX_DIRS}; do
 		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake_src_make check
+			cmake_src_compile check
 	done
 }
 
diff --git a/sci-chemistry/gromacs/gromacs-2020.4.ebuild b/sci-chemistry/gromacs/gromacs-2020.4.ebuild
index e8417cf59475..3c700bbb99a6 100644
--- a/sci-chemistry/gromacs/gromacs-2020.4.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2020.4.ebuild
@@ -296,7 +296,7 @@ src_compile() {
 src_test() {
 	for x in ${GMX_DIRS}; do
 		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake_src_make check
+			cmake_src_compile check
 	done
 }
 
diff --git a/sci-chemistry/gromacs/gromacs-2020.5.ebuild b/sci-chemistry/gromacs/gromacs-2020.5.ebuild
index 393fdad3162e..ff5aa7c43fdc 100644
--- a/sci-chemistry/gromacs/gromacs-2020.5.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2020.5.ebuild
@@ -296,7 +296,7 @@ src_compile() {
 src_test() {
 	for x in ${GMX_DIRS}; do
 		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake_src_make check
+			cmake_src_compile check
 	done
 }
 
diff --git a/sci-chemistry/gromacs/gromacs-2020.6.ebuild b/sci-chemistry/gromacs/gromacs-2020.6.ebuild
index 393fdad3162e..ff5aa7c43fdc 100644
--- a/sci-chemistry/gromacs/gromacs-2020.6.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2020.6.ebuild
@@ -296,7 +296,7 @@ src_compile() {
 src_test() {
 	for x in ${GMX_DIRS}; do
 		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake_src_make check
+			cmake_src_compile check
 	done
 }
 
diff --git a/sci-chemistry/gromacs/gromacs-2020.9999.ebuild b/sci-chemistry/gromacs/gromacs-2020.9999.ebuild
index 393fdad3162e..ff5aa7c43fdc 100644
--- a/sci-chemistry/gromacs/gromacs-2020.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2020.9999.ebuild
@@ -296,7 +296,7 @@ src_compile() {
 src_test() {
 	for x in ${GMX_DIRS}; do
 		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake_src_make check
+			cmake_src_compile check
 	done
 }
 
diff --git a/sci-chemistry/gromacs/gromacs-2021.1.ebuild b/sci-chemistry/gromacs/gromacs-2021.1.ebuild
index 2a4610540b55..75d52731734e 100644
--- a/sci-chemistry/gromacs/gromacs-2021.1.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2021.1.ebuild
@@ -303,7 +303,7 @@ src_compile() {
 src_test() {
 	for x in ${GMX_DIRS}; do
 		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake_src_make check
+			cmake_src_compile check
 	done
 }
 
diff --git a/sci-chemistry/gromacs/gromacs-2021.9999.ebuild b/sci-chemistry/gromacs/gromacs-2021.9999.ebuild
index dbeed6f4fec5..82fafe89e639 100644
--- a/sci-chemistry/gromacs/gromacs-2021.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2021.9999.ebuild
@@ -298,7 +298,7 @@ src_compile() {
 src_test() {
 	for x in ${GMX_DIRS}; do
 		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake_src_make check
+			cmake_src_compile check
 	done
 }
 
diff --git a/sci-chemistry/gromacs/gromacs-2021.ebuild b/sci-chemistry/gromacs/gromacs-2021.ebuild
index 069792626140..b5e91e41ba15 100644
--- a/sci-chemistry/gromacs/gromacs-2021.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2021.ebuild
@@ -300,7 +300,7 @@ src_compile() {
 src_test() {
 	for x in ${GMX_DIRS}; do
 		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake_src_make check
+			cmake_src_compile check
 	done
 }
 
diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index dbeed6f4fec5..82fafe89e639 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -298,7 +298,7 @@ src_compile() {
 src_test() {
 	for x in ${GMX_DIRS}; do
 		BUILD_DIR="${WORKDIR}/${P}_${x}"\
-			cmake_src_make check
+			cmake_src_compile check
 	done
 }
 
diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml
index 23a4ee60ef76..4235f32ded67 100644
--- a/sci-chemistry/gromacs/metadata.xml
+++ b/sci-chemistry/gromacs/metadata.xml
@@ -1,7 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-	<stabilize-allarches/>
 	<maintainer type="person">
 		<email>alexxy@gentoo.org</email>
 		<name>Alexey Shvetsov</name>
diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
index 3a4f34fe7be6..b87dd02aeb4c 100644
--- a/sci-chemistry/pymol/Manifest
+++ b/sci-chemistry/pymol/Manifest
@@ -1,5 +1,7 @@
 AUX pymol-2.4.0-fix_bug119.patch 1078 BLAKE2B 78ed2953dcb20197de0a06c2c9c4c9f59be79cecbedfc910e7e530e5ad58452aab0da8540f4a4737023a3d56eba51530dfb1f2dfd59cdaf91192b6cd90383610 SHA512 ff4adb6de9c03f165e062698fe6359ab187ccf7cccba05c2e90363b44a53e5d4371e4942f21f26dd89ca8d1b7f9865f48e18f7d9a0214a5c6f453bee0ab49bb7
 DIST pymol-1.8.4.0.png.xz 19528 BLAKE2B f3d23d4cedca3d8bb96b20646a548da4be570697e3346a11b01c5c3599b536ba4697be08472dfa8a4f6533167defc1a37a1de332931a73857319cb28fd42cd2b SHA512 40bb0d3f226476f6e047b5361956aad955232a97641474765eaa5204f0539aee3810e0266213618a45364f9f31f6eb18380b17e0c79f64065f7b62a9016caa7c
 DIST pymol-2.4.0.tar.gz 10552539 BLAKE2B 34e31dce99c1e838b00389c3d7c29657534dd037349769bd6c8cb17028cfaaa856d5729760d3768fd43f61086cac30749a864fb4156c14eda07f9027430f0523 SHA512 2b19294197d58a808bf7bb7fa9f829c2ec582ba47a4380783a2b1eedda2ce4118cd398e01885db8c449e7fd5e4c08a1c40508e679ef42d8e183a6a52b031c02a
+DIST pymol-2.5.0.tar.gz 10470268 BLAKE2B ad3721432001053be93afe755f531ae47348213b042e84dae33cd79580428c9ac3d00629afa0222e4081807dc80e2dd69c3963a457666b5975b6263b988d02d9 SHA512 19f21b8f735fda5314abf202d56f3c81c7251bf6ef0df73ccee534d9c08035f4ef6155ffb68e09d7717a0fb5ba7289bbfa440691bea4cec0de7199c9e858ea91
 EBUILD pymol-2.4.0-r1.ebuild 3106 BLAKE2B ca3e75218437da7eecb7f6cd4feb737386cfed4a002121659cf4147f141fc380dac3d3c18b9a0ea1dd3d614dd05df391545b3cad65905d1d7a52beace3c54b97 SHA512 cd03c112d9210fa24206de44e55dc8ed1bfde7a51c4278902355f01fd5d5846fb12afb3318796c9e4f57b1e5e7cae58812cf81267d9c7f776c5a35f6a0eb3082
+EBUILD pymol-2.5.0.ebuild 3092 BLAKE2B 911add60f71e41659a1bf0754fa1e263ed3b8bb1222b83401ed192db2c4679629b41ec4476e552e23d0c7f85063adcc4380be16cd920a50ce1ba5ef7ee4da1c1 SHA512 2326993a095b2dda7de7b0049d192a57c5a4e28cd323629344e8723090c621fe10b1e767c50c50a3941d2241bb06a7c393210c0093bf0d5810e20419737ca30e
 MISC metadata.xml 439 BLAKE2B 68df7dfc8ca3d4d4b18b419532bade69491f2e9362f10ae2397c804132b7fc9cd08dcf9703c0a89c44588c570e0c0c1bb9bffb7394d51faf1283142dbc5f70b3 SHA512 f5a3eded9b12fa715ba2e6e10b41c75d9bd823ca0dd40acbffc3f5bfc4b36c687f720b1a4e119b4540a31faf849985778cbd72b0b2cd35af8c52ca0f808d71e4
diff --git a/sci-chemistry/pymol/pymol-2.5.0.ebuild b/sci-chemistry/pymol/pymol-2.5.0.ebuild
new file mode 100644
index 000000000000..a7fc5fdc127c
--- /dev/null
+++ b/sci-chemistry/pymol/pymol-2.5.0.ebuild
@@ -0,0 +1,113 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{7..9} )
+DISTUTILS_USE_SETUPTOOLS=no
+
+inherit desktop optfeature flag-o-matic xdg distutils-r1
+
+DESCRIPTION="A Python-extensible molecular graphics system"
+HOMEPAGE="https://www.pymol.org/"
+SRC_URI="
+	https://dev.gentoo.org/~pacho/${PN}/${PN}-1.8.4.0.png.xz
+	https://github.com/schrodinger/pymol-open-source/archive/v${PV}.tar.gz -> ${P}.tar.gz
+	"
+RESTRICT="mirror"
+LICENSE="PSF-2.2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
+IUSE="+netcdf web"
+
+DEPEND="
+	dev-libs/msgpack[cxx]
+	dev-libs/mmtf-cpp
+	dev-python/pyopengl[${PYTHON_USEDEP}]
+	dev-python/PyQt5[opengl,${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/pmw[${PYTHON_USEDEP}]
+	media-libs/freetype:2
+	media-libs/glew:0=
+	media-libs/glm
+	media-libs/libpng:0=
+	media-video/mpeg-tools
+	sys-libs/zlib
+	netcdf? ( sci-libs/netcdf:0= )
+"
+RDEPEND="${DEPEND}
+	sci-chemistry/chemical-mime-data
+"
+
+S="${WORKDIR}"/${PN}-open-source-${PV}
+
+python_prepare_all() {
+	sed \
+		-e "s:\"/usr:\"${EPREFIX}/usr:g" \
+		-e "/ext_comp_args.*+=/s:\[.*\]$:\[\]:g" \
+		-i setup.py || die
+
+	sed \
+		-e "s:/opt/local:${EPREFIX}/usr:g" \
+		-e '/ext_comp_args/s:\[.*\]:[]:g' \
+		-i setup.py || die
+	sed \
+		-e "s:\['msgpackc'\]:\['msgpack'\]:g" \
+		-i setup.py || die
+
+	append-cxxflags -std=c++0x
+
+	use !netcdf && mydistutilsargs=( --no-vmd-plugins )
+
+	distutils-r1_python_prepare_all
+}
+
+python_install() {
+	distutils-r1_python_install \
+		--pymol-path="${EPREFIX}/usr/share/pymol"
+
+# File is not created as apbs was dropped from the tree
+# https://bugs.gentoo.org/790629
+#	sed \
+#		-e '1d' \
+#		-e "/APBS_BINARY_LOCATION/s:None:\"${EPREFIX}/usr/bin/apbs\":g" \
+#		-e "/APBS_PSIZE_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/src/\":g" \
+#		-e "/APBS_PDB2PQR_LOCATION/s:None:\"$(python_get_sitedir)/pdb2pqr/\":g" \
+#		-i "${D}/$(python_get_sitedir)"/pmg_tk/startup/apbs_tools.py || die
+}
+
+python_install_all() {
+	distutils-r1_python_install_all
+
+	sed \
+		-e '1i#!/usr/bin/env python' \
+		"${D}/$(python_get_sitedir)"/pymol/__init__.py > "${T}"/${PN} || die
+
+	python_foreach_impl python_doscript "${T}"/${PN}
+
+	# These environment variables should not go in the wrapper script, or else
+	# it will be impossible to use the PyMOL libraries from Python.
+	cat >> "${T}"/20pymol <<- EOF || die
+		PYMOL_PATH="${EPREFIX}/usr/share/pymol"
+		PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
+		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
+	EOF
+
+	doenvd "${T}"/20pymol
+
+	newicon "${WORKDIR}"/${PN}-1.8.4.0.png ${PN}.png
+	make_desktop_entry ${PN} PyMol ${PN} \
+		"Graphics;Education;Science;Chemistry;" \
+		"MimeType=chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf;"
+
+	if ! use web; then
+		rm -rf "${D}/$(python_get_sitedir)/web" || die
+	fi
+
+	rm -f "${ED}"/usr/share/${PN}/LICENSE || die
+}
+
+#pkg_postinst() {
+#	xdg_pkg_postinst
+#	optfeature "Electrostatic calculations" sci-chemistry/apbs sci-chemistry/pdb2pqr
+#}