From ba0f35d502cc67a8a340f189682da820534c4c07 Mon Sep 17 00:00:00 2001 From: Morgan Helton Date: Mon, 18 Jul 2022 05:24:10 -0500 Subject: [PATCH 01/22] awscli2: 2.7.9 -> 2.7.14 (cherry picked from commit d7dc8c6b6c860537c4f7f588781444088aec0726) --- pkgs/tools/admin/awscli2/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/tools/admin/awscli2/default.nix b/pkgs/tools/admin/awscli2/default.nix index d772d1d16e4f..84df70cc8416 100644 --- a/pkgs/tools/admin/awscli2/default.nix +++ b/pkgs/tools/admin/awscli2/default.nix @@ -29,13 +29,13 @@ let in with py.pkgs; buildPythonApplication rec { pname = "awscli2"; - version = "2.7.9"; # N.B: if you change this, check if overrides are still up-to-date + version = "2.7.14"; # N.B: if you change this, check if overrides are still up-to-date src = fetchFromGitHub { owner = "aws"; repo = "aws-cli"; rev = version; - sha256 = "sha256-6JlBgcHpR2ZfrljS+flxaog/KZQLvPUacJGLMQNsZ5Y="; + sha256 = "sha256-ji/hKoYxM3wag9DXy2e/VsJZVGN5UEebWX/ctOVJ42M="; }; propagatedBuildInputs = [ From 7c8395108b488b00f9e9e8e64fc0580cd7f15c43 Mon Sep 17 00:00:00 2001 From: Morgan Helton Date: Mon, 18 Jul 2022 05:25:13 -0500 Subject: [PATCH 02/22] awscli2: add devusb to maintainers (cherry picked from commit d4ec3b4b0ea45a06b32b6a14af7128e8bb9d6283) --- pkgs/tools/admin/awscli2/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/tools/admin/awscli2/default.nix b/pkgs/tools/admin/awscli2/default.nix index 84df70cc8416..1d4e7a5f2fc2 100644 --- a/pkgs/tools/admin/awscli2/default.nix +++ b/pkgs/tools/admin/awscli2/default.nix @@ -101,6 +101,6 @@ with py.pkgs; buildPythonApplication rec { changelog = "https://github.com/aws/aws-cli/blob/${version}/CHANGELOG.rst"; description = "Unified tool to manage your AWS services"; license = licenses.asl20; - maintainers = with maintainers; [ bhipple davegallant bryanasdev000 ]; + maintainers = with maintainers; [ bhipple davegallant bryanasdev000 devusb ]; }; } From fb0414a693f64f551235e66276eab3234103225a Mon Sep 17 00:00:00 2001 From: natsukium Date: Tue, 19 Jul 2022 12:14:28 +0900 Subject: [PATCH 03/22] libcifpp: init at 4.2.0 (cherry picked from commit a8a4cdb76db3cc272094f24a1a83a2154613d789) --- .../libraries/libcifpp/default.nix | 25 +++++++++++++++++++ pkgs/top-level/all-packages.nix | 2 ++ 2 files changed, 27 insertions(+) create mode 100644 pkgs/development/libraries/libcifpp/default.nix diff --git a/pkgs/development/libraries/libcifpp/default.nix b/pkgs/development/libraries/libcifpp/default.nix new file mode 100644 index 000000000000..22c23f45af86 --- /dev/null +++ b/pkgs/development/libraries/libcifpp/default.nix @@ -0,0 +1,25 @@ +{ lib, stdenv, fetchFromGitHub, boost, cmake, }: + +stdenv.mkDerivation rec { + pname = "libcifpp"; + version = "4.2.0"; + + src = fetchFromGitHub { + owner = "PDB-REDO"; + repo = pname; + rev = "v${version}"; + sha256 = "1hzi6fgbsmy8h8nfwkyfds9jz13nqw72h0x81jqw5516kkvar5iw"; + }; + + nativeBuildInputs = [ cmake ]; + + buildInputs = [ boost ]; + + meta = with lib; { + description = "Manipulate mmCIF and PDB files"; + homepage = "https://github.com/PDB-REDO/libcifpp"; + license = licenses.bsd2; + maintainers = with maintainers; [ natsukium ]; + platforms = platforms.unix; + }; +} diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index f2f187b3ae48..0244d9ec425a 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -18364,6 +18364,8 @@ with pkgs; libchop = callPackage ../development/libraries/libchop { }; + libcifpp = callPackage ../development/libraries/libcifpp { }; + libcint = callPackage ../development/libraries/libcint { }; libclc = callPackage ../development/libraries/libclc { }; From 541a471414f5ecd2c66b55808c620c8ca6f766fd Mon Sep 17 00:00:00 2001 From: natsukium Date: Tue, 19 Jul 2022 12:17:34 +0900 Subject: [PATCH 04/22] dssp: init at 4.0.5 (cherry picked from commit cf0dc604a6097744c8de260ee6f471d322f7d240) --- .../science/biology/dssp/default.nix | 25 +++++++++++++++++++ pkgs/top-level/all-packages.nix | 2 ++ 2 files changed, 27 insertions(+) create mode 100644 pkgs/applications/science/biology/dssp/default.nix diff --git a/pkgs/applications/science/biology/dssp/default.nix b/pkgs/applications/science/biology/dssp/default.nix new file mode 100644 index 000000000000..762b0515e85c --- /dev/null +++ b/pkgs/applications/science/biology/dssp/default.nix @@ -0,0 +1,25 @@ +{ lib, stdenv, fetchFromGitHub, boost, cmake, libcifpp, zlib, }: + +stdenv.mkDerivation rec { + pname = "dssp"; + version = "4.0.5"; + + src = fetchFromGitHub { + owner = "PDB-REDO"; + repo = pname; + rev = "v${version}"; + sha256 = "1x35rdcm4fch66pjbmy73lv0gdb6g9y3v023a66512a6nzsqjsir"; + }; + + nativeBuildInputs = [ cmake ]; + + buildInputs = [ boost libcifpp zlib ]; + + meta = with lib; { + description = "Calculate the most likely secondary structure assignment given the 3D structure of a protein"; + homepage = "https://github.com/PDB-REDO/dssp"; + license = licenses.bsd2; + maintainers = with maintainers; [ natsukium ]; + platforms = platforms.unix; + }; +} diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 0244d9ec425a..567bc9167346 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -32815,6 +32815,8 @@ with pkgs; diamond = callPackage ../applications/science/biology/diamond { }; + dssp = callPackage ../applications/science/biology/dssp { }; + ecopcr = callPackage ../applications/science/biology/ecopcr { }; eggnog-mapper = callPackage ../applications/science/biology/eggnog-mapper { }; From 7d77f7a688283335f54d21e55374514ab76dc22b Mon Sep 17 00:00:00 2001 From: ajs124 Date: Mon, 27 Jun 2022 18:24:40 +0200 Subject: [PATCH 05/22] jitsi-meet-prosody: 1.0.5675 -> 1.0.6260 (cherry picked from commit ecb36a7a6fb365ca0a61835855fa513624fe8b6c) --- pkgs/misc/jitsi-meet-prosody/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/misc/jitsi-meet-prosody/default.nix b/pkgs/misc/jitsi-meet-prosody/default.nix index 4ce79f3b16c2..66f2cdac3cc1 100644 --- a/pkgs/misc/jitsi-meet-prosody/default.nix +++ b/pkgs/misc/jitsi-meet-prosody/default.nix @@ -2,10 +2,10 @@ stdenv.mkDerivation rec { pname = "jitsi-meet-prosody"; - version = "1.0.5675"; + version = "1.0.6260"; src = fetchurl { url = "https://download.jitsi.org/stable/${pname}_${version}-1_all.deb"; - sha256 = "FrafgJcNF3xv985JJ+xOWPtJZFeElIAaIXWdcgheru0="; + sha256 = "ZUfyEYAU4YEYXBoM+tEZ6SAhqlNcsmxnKw8WEv0gy7M="; }; dontBuild = true; From f1876eb1bb8d3e4d5df8d1c1b0e5f3b7415cbab5 Mon Sep 17 00:00:00 2001 From: ajs124 Date: Mon, 27 Jun 2022 18:24:57 +0200 Subject: [PATCH 06/22] jicofo: 1.0-832 -> 1.0-900 (cherry picked from commit cbbdf1bf7ba3f32fecedb2ef5c5292b212f77909) --- pkgs/servers/jicofo/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/servers/jicofo/default.nix b/pkgs/servers/jicofo/default.nix index 71a087afcd93..916e72c90a38 100644 --- a/pkgs/servers/jicofo/default.nix +++ b/pkgs/servers/jicofo/default.nix @@ -2,10 +2,10 @@ let pname = "jicofo"; - version = "1.0-832"; + version = "1.0-900"; src = fetchurl { url = "https://download.jitsi.org/stable/${pname}_${version}-1_all.deb"; - sha256 = "ZSzxD4RCsIkNtB4agBRZkzbJOi6ttzlc4Qw5n0t5syc="; + sha256 = "tAuWhu1DdasOuLIz9/Ox1n1XcFWm5qnTVr6FpdKpwbE="; }; in stdenv.mkDerivation { From b895cbfbd68ee21c9ed2523b673fc23184eed38d Mon Sep 17 00:00:00 2001 From: ajs124 Date: Mon, 27 Jun 2022 18:25:14 +0200 Subject: [PATCH 07/22] jitsi-videobridge: 2.1-595-g3637fda4 -> 2.2-9-g8cded16e (cherry picked from commit bc9c51b90e28c249606458b83ab604d0958aabe2) --- pkgs/servers/jitsi-videobridge/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/servers/jitsi-videobridge/default.nix b/pkgs/servers/jitsi-videobridge/default.nix index a7a6667d6bfa..39629639ad81 100644 --- a/pkgs/servers/jitsi-videobridge/default.nix +++ b/pkgs/servers/jitsi-videobridge/default.nix @@ -2,10 +2,10 @@ let pname = "jitsi-videobridge2"; - version = "2.1-595-g3637fda4"; + version = "2.2-9-g8cded16e"; src = fetchurl { url = "https://download.jitsi.org/stable/${pname}_${version}-1_all.deb"; - sha256 = "vwn9C8M3wwiIqwxAu1MDe2ra2SCQ2Hssco5J/xUFoKM="; + sha256 = "L9h+qYV/W2wPzycfDGC4AXpTl7wlulyt2KryA+Tb/YU="; }; in stdenv.mkDerivation { From c71d718251ee2687014c8c0eabba0af21e056340 Mon Sep 17 00:00:00 2001 From: ajs124 Date: Mon, 27 Jun 2022 18:25:25 +0200 Subject: [PATCH 08/22] jitsi-meet: 1.0.6155 -> 1.0.6260 (cherry picked from commit bf4912f39971c85ed3b359dc3b9554b0f8532b42) --- pkgs/servers/web-apps/jitsi-meet/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/servers/web-apps/jitsi-meet/default.nix b/pkgs/servers/web-apps/jitsi-meet/default.nix index 7be8ac573332..579ffb1a6777 100644 --- a/pkgs/servers/web-apps/jitsi-meet/default.nix +++ b/pkgs/servers/web-apps/jitsi-meet/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "jitsi-meet"; - version = "1.0.6155"; + version = "1.0.6260"; src = fetchurl { url = "https://download.jitsi.org/jitsi-meet/src/jitsi-meet-${version}.tar.bz2"; - sha256 = "baCRVYe1z2uH3vSb5KbWs0y4KyQYO3JpTyoGFZIZQqo="; + sha256 = "Y1ELKdFdbnq20yUt4XoXmstJm8uI8EBGIFOvFWf+5Uw="; }; dontBuild = true; From 611e25c061b309d35fa8e4dce44e1ad4a43a24a5 Mon Sep 17 00:00:00 2001 From: ajs124 Date: Wed, 29 Jun 2022 00:19:39 +0200 Subject: [PATCH 09/22] nixos/jitsi-meet: move prosodyctl calls into prosody preStart (cherry picked from commit aea940da63c27f503915a5ca44cbb9eddf2674f6) --- .../modules/services/web-apps/jitsi-meet.nix | 25 +++++++++++-------- 1 file changed, 14 insertions(+), 11 deletions(-) diff --git a/nixos/modules/services/web-apps/jitsi-meet.nix b/nixos/modules/services/web-apps/jitsi-meet.nix index be0b5b94fb26..8ad92706b064 100644 --- a/nixos/modules/services/web-apps/jitsi-meet.nix +++ b/nixos/modules/services/web-apps/jitsi-meet.nix @@ -253,9 +253,20 @@ in ''; }; }; - systemd.services.prosody.serviceConfig = mkIf cfg.prosody.enable { - EnvironmentFile = [ "/var/lib/jitsi-meet/secrets-env" ]; - SupplementaryGroups = [ "jitsi-meet" ]; + systemd.services.prosody = mkIf cfg.prosody.enable { + preStart = let + videobridgeSecret = if cfg.videobridge.passwordFile != null then cfg.videobridge.passwordFile else "/var/lib/jitsi-meet/videobridge-secret"; + in '' + ${config.services.prosody.package}/bin/prosodyctl register focus auth.${cfg.hostName} "$(cat /var/lib/jitsi-meet/jicofo-user-secret)" + ${config.services.prosody.package}/bin/prosodyctl register jvb auth.${cfg.hostName} "$(cat ${videobridgeSecret})" + ${config.services.prosody.package}/bin/prosodyctl mod_roster_command subscribe focus.${cfg.hostName} focus@auth.${cfg.hostName} + ${config.services.prosody.package}/bin/prosodyctl register jibri auth.${cfg.hostName} "$(cat /var/lib/jitsi-meet/jibri-auth-secret)" + ${config.services.prosody.package}/bin/prosodyctl register recorder recorder.${cfg.hostName} "$(cat /var/lib/jitsi-meet/jibri-recorder-secret)" + ''; + serviceConfig = { + EnvironmentFile = [ "/var/lib/jitsi-meet/secrets-env" ]; + SupplementaryGroups = [ "jitsi-meet" ]; + }; }; users.groups.jitsi-meet = {}; @@ -266,14 +277,12 @@ in systemd.services.jitsi-meet-init-secrets = { wantedBy = [ "multi-user.target" ]; before = [ "jicofo.service" "jitsi-videobridge2.service" ] ++ (optional cfg.prosody.enable "prosody.service"); - path = [ config.services.prosody.package ]; serviceConfig = { Type = "oneshot"; }; script = let secrets = [ "jicofo-component-secret" "jicofo-user-secret" "jibri-auth-secret" "jibri-recorder-secret" ] ++ (optional (cfg.videobridge.passwordFile == null) "videobridge-secret"); - videobridgeSecret = if cfg.videobridge.passwordFile != null then cfg.videobridge.passwordFile else "/var/lib/jitsi-meet/videobridge-secret"; in '' cd /var/lib/jitsi-meet @@ -291,12 +300,6 @@ in chmod 640 secrets-env '' + optionalString cfg.prosody.enable '' - prosodyctl register focus auth.${cfg.hostName} "$(cat /var/lib/jitsi-meet/jicofo-user-secret)" - prosodyctl register jvb auth.${cfg.hostName} "$(cat ${videobridgeSecret})" - prosodyctl mod_roster_command subscribe focus.${cfg.hostName} focus@auth.${cfg.hostName} - prosodyctl register jibri auth.${cfg.hostName} "$(cat /var/lib/jitsi-meet/jibri-auth-secret)" - prosodyctl register recorder recorder.${cfg.hostName} "$(cat /var/lib/jitsi-meet/jibri-recorder-secret)" - # generate self-signed certificates if [ ! -f /var/lib/jitsi-meet.crt ]; then ${getBin pkgs.openssl}/bin/openssl req \ From 99d0f07d751dd3d1d37f1e32b1e7b3630a58d7a6 Mon Sep 17 00:00:00 2001 From: ajs124 Date: Wed, 29 Jun 2022 00:32:53 +0200 Subject: [PATCH 10/22] nixos/tests/jitsi-meet: remove grep for successfull health check afaict, it doesn't log this anymore after https://github.com/jitsi/jitsi-videobridge/pull/1188 (cherry picked from commit 729764a32d6569e692e44620bd98b552a9f72c33) --- nixos/tests/jitsi-meet.nix | 3 --- 1 file changed, 3 deletions(-) diff --git a/nixos/tests/jitsi-meet.nix b/nixos/tests/jitsi-meet.nix index 41d53bc73800..c39cd19e1f0a 100644 --- a/nixos/tests/jitsi-meet.nix +++ b/nixos/tests/jitsi-meet.nix @@ -33,9 +33,6 @@ import ./make-test-python.nix ({ pkgs, ... }: { server.wait_for_unit("nginx.service") server.wait_for_unit("prosody.service") - server.wait_until_succeeds( - "journalctl -b -u jitsi-videobridge2 -o cat | grep -q 'Performed a successful health check'" - ) server.wait_until_succeeds( "journalctl -b -u prosody -o cat | grep -q 'Authenticated as focus@auth.server'" ) From 3707f4a0739f648e47d9c9cb09a03da531367bb7 Mon Sep 17 00:00:00 2001 From: Robin Gloster Date: Wed, 20 Jul 2022 19:37:02 +0200 Subject: [PATCH 11/22] atlassian-crowd: 4.4.0 -> 5.0.1 CVE-2022-26136, CVE-2022-26137 (cherry picked from commit 161e4838fd22dd8fc3eb93f8bdbbf3d5aee2ce62) --- pkgs/servers/atlassian/crowd.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/servers/atlassian/crowd.nix b/pkgs/servers/atlassian/crowd.nix index f62abe805c27..7714fccf5d82 100644 --- a/pkgs/servers/atlassian/crowd.nix +++ b/pkgs/servers/atlassian/crowd.nix @@ -3,11 +3,11 @@ stdenv.mkDerivation rec { pname = "atlassian-crowd"; - version = "4.4.0"; + version = "5.0.1"; src = fetchurl { url = "https://www.atlassian.com/software/crowd/downloads/binary/${pname}-${version}.tar.gz"; - sha256 = "0ipfvdjs8v02y37rmihljy9lkb3ycz5hyc14mcg65ilsscsq3x91"; + sha256 = "sha256-ccXSNuiXP0+b9WObboikqVd0nKH0Fi2gMVEF3+WAx5M="; }; buildPhase = '' From 729d3ce1c66919593908f03c6662c866ccf4a3c8 Mon Sep 17 00:00:00 2001 From: Bernardo Meurer Date: Mon, 18 Jul 2022 18:07:35 -0700 Subject: [PATCH 12/22] nextcloud24: 24.0.2 -> 24.0.3 (cherry picked from commit aea4ab4fd7a89427d4ad2e94c1fb6cba200fa0e9) --- pkgs/servers/nextcloud/default.nix | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pkgs/servers/nextcloud/default.nix b/pkgs/servers/nextcloud/default.nix index a666c3fee358..fe6d43e7175e 100644 --- a/pkgs/servers/nextcloud/default.nix +++ b/pkgs/servers/nextcloud/default.nix @@ -51,10 +51,10 @@ in { }; nextcloud24 = generic { - version = "24.0.2"; - sha256 = "30d6cac1265dff221836bec46a937dcafd7e7d52ee59b939841750b514e5033d"; + version = "24.0.3"; + sha256 = "320c81f9b902922b4bcef3eacf858596a14347fd45bddd26dac198562d212439"; }; - # tip: get she sha with: + # tip: get the sha with: # curl 'https://download.nextcloud.com/server/releases/nextcloud-${version}.tar.bz2.sha256' } From 7dc8a855adbbcc7358e6e5d204424201103db668 Mon Sep 17 00:00:00 2001 From: natsukium Date: Fri, 17 Sep 2021 18:03:44 +0900 Subject: [PATCH 13/22] maintainers: Add natsukium (cherry picked from commit bdf68ddb6af5046dd4880ff077327e72131420f5) --- maintainers/maintainer-list.nix | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/maintainers/maintainer-list.nix b/maintainers/maintainer-list.nix index fff5cb8fff17..e9b0a8c4c24b 100644 --- a/maintainers/maintainer-list.nix +++ b/maintainers/maintainer-list.nix @@ -8976,6 +8976,16 @@ githubId = 818502; name = "Nathan Yong"; }; + natsukium = { + email = "nixpkgs@natsukium.com"; + github = "natsukium"; + githubId = 25083790; + name = "Tomoya Otabi"; + keys = [{ + longkeyid = "ed25519/0x9EA45A31DB994C53"; + fingerprint = "3D14 6004 004C F882 D519 6CD4 9EA4 5A31 DB99 4C53"; + }]; + }; natto1784 = { email = "natto@weirdnatto.in"; github = "natto1784"; From 513072d23fbe71df3fc798dd57e0f43ed6872c55 Mon Sep 17 00:00:00 2001 From: natsukium Date: Fri, 17 Sep 2021 18:08:25 +0900 Subject: [PATCH 14/22] mafft: init at 7.487 (cherry picked from commit ff76ac91562bca8b113df5b3dac946b8fe6877fa) --- .../science/biology/mafft/default.nix | 27 +++++++++++++++++++ pkgs/top-level/all-packages.nix | 2 ++ 2 files changed, 29 insertions(+) create mode 100644 pkgs/applications/science/biology/mafft/default.nix diff --git a/pkgs/applications/science/biology/mafft/default.nix b/pkgs/applications/science/biology/mafft/default.nix new file mode 100644 index 000000000000..3247400bcab7 --- /dev/null +++ b/pkgs/applications/science/biology/mafft/default.nix @@ -0,0 +1,27 @@ +{ lib, stdenv, fetchurl }: + +stdenv.mkDerivation rec { + pname = "mafft"; + version = "7.487"; + + src = fetchurl { + url = "https://mafft.cbrc.jp/alignment/software/mafft-${version}-with-extensions-src.tgz"; + sha256 = "1wcfbpfivi6xx87xdswp0gfksandija8j8hbw1f9506ra5gga1ga"; + }; + + preBuild = '' + cd ./core + make clean + ''; + + makeFlags = [ "CC=${stdenv.cc.targetPrefix}cc" "PREFIX=$(out)" ]; + + meta = with lib; + { + description = "Multiple alignment program for amino acid or nucleotide sequences"; + homepage = "https://mafft.cbrc.jp/alignment/software/"; + license = licenses.bsd3; + maintainers = with maintainers; [ natsukium ]; + platforms = platforms.unix; + }; +} diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 22a40b2958e1..b1ab04bd65e9 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -32865,6 +32865,8 @@ with pkgs; MACS2 = callPackage ../applications/science/biology/MACS2 { }; + mafft = callPackage ../applications/science/biology/mafft { }; + migrate = callPackage ../applications/science/biology/migrate { }; minia = callPackage ../applications/science/biology/minia { }; From 52e3ccfaecce65903188d5518be7c84c5134cd64 Mon Sep 17 00:00:00 2001 From: natsukium Date: Tue, 22 Feb 2022 21:35:45 +0900 Subject: [PATCH 15/22] mafft: 7.487 -> 7.490 (cherry picked from commit 0524e8856b9e72aa436b24e19e14e670a02a97f3) --- pkgs/applications/science/biology/mafft/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/applications/science/biology/mafft/default.nix b/pkgs/applications/science/biology/mafft/default.nix index 3247400bcab7..764a0f0da83a 100644 --- a/pkgs/applications/science/biology/mafft/default.nix +++ b/pkgs/applications/science/biology/mafft/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "mafft"; - version = "7.487"; + version = "7.490"; src = fetchurl { url = "https://mafft.cbrc.jp/alignment/software/mafft-${version}-with-extensions-src.tgz"; - sha256 = "1wcfbpfivi6xx87xdswp0gfksandija8j8hbw1f9506ra5gga1ga"; + sha256 = "0hb5jzcqdnjn3micm5z301lrnyvmn9pnnnxjz4h2wa4yicyz7vnn"; }; preBuild = '' From a8a9eb8b499ee7673f647082f448e1a849d1c84d Mon Sep 17 00:00:00 2001 From: zowoq <59103226+zowoq@users.noreply.github.com> Date: Thu, 21 Jul 2022 12:09:14 +1000 Subject: [PATCH 16/22] ffmpeg: add platforms (cherry picked from commit 643bc7dd2315a038cd609f55a63f9eb220c7e7db) --- pkgs/development/libraries/ffmpeg/generic.nix | 1 + 1 file changed, 1 insertion(+) diff --git a/pkgs/development/libraries/ffmpeg/generic.nix b/pkgs/development/libraries/ffmpeg/generic.nix index 682b1aecf1e4..855586649b74 100644 --- a/pkgs/development/libraries/ffmpeg/generic.nix +++ b/pkgs/development/libraries/ffmpeg/generic.nix @@ -239,6 +239,7 @@ stdenv.mkDerivation rec { ''; license = licenses.gpl3; maintainers = with maintainers; [ ]; + platforms = platforms.all; inherit branch knownVulnerabilities; }; } From 8f48f7c4166154442fb80e7b16f037a4bc5d1a06 Mon Sep 17 00:00:00 2001 From: Filipe Regadas Date: Fri, 3 Jun 2022 16:54:33 +0100 Subject: [PATCH 17/22] metals: 0.11.5 -> 0.11.6 (cherry picked from commit 56048394040202e92c5720a03eace36f1dc8d10b) --- pkgs/development/tools/metals/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/development/tools/metals/default.nix b/pkgs/development/tools/metals/default.nix index 4281a1d9e391..45ea829299a0 100644 --- a/pkgs/development/tools/metals/default.nix +++ b/pkgs/development/tools/metals/default.nix @@ -2,7 +2,7 @@ stdenv.mkDerivation rec { pname = "metals"; - version = "0.11.5"; + version = "0.11.6"; deps = stdenv.mkDerivation { name = "${pname}-deps-${version}"; @@ -16,7 +16,7 @@ stdenv.mkDerivation rec { ''; outputHashMode = "recursive"; outputHashAlgo = "sha256"; - outputHash = "sha256-kw+8688E1b7XjEb7AqOExSVu88NqPprKaCuINWqL2wk="; + outputHash = "sha256-/tFc7xAuUtx2JgEMLhGaq2FXpt7KQNMi82ODr/gTfhM="; }; nativeBuildInputs = [ makeWrapper setJavaClassPath ]; From 9a330e064035a44a0c413b4553ba4e0fbf6c3496 Mon Sep 17 00:00:00 2001 From: Kevin Rauscher Date: Tue, 19 Jul 2022 13:55:33 +0200 Subject: [PATCH 18/22] metals: 0.11.6 -> 0.11.7 (cherry picked from commit e84435878ca0555f927c00c54f83c0de179d0c2a) --- pkgs/development/tools/metals/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/development/tools/metals/default.nix b/pkgs/development/tools/metals/default.nix index 45ea829299a0..4154eb4623ee 100644 --- a/pkgs/development/tools/metals/default.nix +++ b/pkgs/development/tools/metals/default.nix @@ -2,7 +2,7 @@ stdenv.mkDerivation rec { pname = "metals"; - version = "0.11.6"; + version = "0.11.7"; deps = stdenv.mkDerivation { name = "${pname}-deps-${version}"; @@ -16,7 +16,7 @@ stdenv.mkDerivation rec { ''; outputHashMode = "recursive"; outputHashAlgo = "sha256"; - outputHash = "sha256-/tFc7xAuUtx2JgEMLhGaq2FXpt7KQNMi82ODr/gTfhM="; + outputHash = "sha256-Zc/0kod3JM58WpyxwXiyQdixBHOJV7UDGg1YZtHJ3hw="; }; nativeBuildInputs = [ makeWrapper setJavaClassPath ]; From 468695595f0b40015de525c89aae73c2ae52c6b9 Mon Sep 17 00:00:00 2001 From: Kevin Rauscher Date: Tue, 19 Jul 2022 21:51:19 +0200 Subject: [PATCH 19/22] metals: remove client specific wrappers (cherry picked from commit f49a09b5a2effde9bc1cdbab8133935a9ab3b9ea) --- pkgs/development/tools/metals/default.nix | 15 --------------- 1 file changed, 15 deletions(-) diff --git a/pkgs/development/tools/metals/default.nix b/pkgs/development/tools/metals/default.nix index 4154eb4623ee..27e8ec08752a 100644 --- a/pkgs/development/tools/metals/default.nix +++ b/pkgs/development/tools/metals/default.nix @@ -29,23 +29,8 @@ stdenv.mkDerivation rec { installPhase = '' mkdir -p $out/bin - # This variant is not targeted at any particular client, clients are - # expected to declare their supported features in initialization options. makeWrapper ${jre}/bin/java $out/bin/metals \ --add-flags "${extraJavaOpts} -cp $CLASSPATH scala.meta.metals.Main" - - # Further variants targeted at clients with featuresets pre-set. - makeWrapper ${jre}/bin/java $out/bin/metals-emacs \ - --add-flags "${extraJavaOpts} -Dmetals.client=emacs -cp $CLASSPATH scala.meta.metals.Main" - - makeWrapper ${jre}/bin/java $out/bin/metals-vim \ - --add-flags "${extraJavaOpts} -Dmetals.client=coc.nvim -cp $CLASSPATH scala.meta.metals.Main" - - makeWrapper ${jre}/bin/java $out/bin/metals-vim-lsc \ - --add-flags "${extraJavaOpts} -Dmetals.client=vim-lsc -cp $CLASSPATH scala.meta.metals.Main" - - makeWrapper ${jre}/bin/java $out/bin/metals-sublime \ - --add-flags "${extraJavaOpts} -Dmetals.client=sublime -cp $CLASSPATH scala.meta.metals.Main" ''; meta = with lib; { From ab10a971ae5bb40dac58d6536279b01405271eec Mon Sep 17 00:00:00 2001 From: marius david Date: Fri, 27 May 2022 18:22:57 +0200 Subject: [PATCH 20/22] rustdesk: 1.1.8 -> 1.1.9, fix (cherry picked from commit 6bca1a64167f539bef4294fe98fe880e963f4be4) --- .../networking/remote/rustdesk/cargo.patch | 28 +++++++++---------- .../networking/remote/rustdesk/default.nix | 28 ++++++++++++++++--- 2 files changed, 37 insertions(+), 19 deletions(-) diff --git a/pkgs/applications/networking/remote/rustdesk/cargo.patch b/pkgs/applications/networking/remote/rustdesk/cargo.patch index ecf2f4af5beb..e2124f261713 100644 --- a/pkgs/applications/networking/remote/rustdesk/cargo.patch +++ b/pkgs/applications/networking/remote/rustdesk/cargo.patch @@ -1,26 +1,24 @@ diff --git a/Cargo.lock b/Cargo.lock -index c3e139e..b77d8bd 100644 +index fb17c7e..ef157e5 100644 --- a/Cargo.lock +++ b/Cargo.lock -@@ -1761,11 +1761,11 @@ dependencies = [ - +@@ -2332,10 +2332,10 @@ dependencies = [ [[package]] name = "magnum-opus" --version = "0.3.4-2" --source = "git+https://github.com/open-trade/magnum-opus#ad0836164abf4a4df69009b1ee08eabe3a13b33f" -+version = "0.4.0" + version = "0.4.0" +-source = "git+https://github.com/open-trade/magnum-opus#3c3d0b86ae95c84930bebffe4bcb03b3bd83342b" +source = "git+https://github.com/TheRadioGuy/magnum-opus#171e1d021004626f7444d1e39b98f50bc3cb2604" dependencies = [ -- "bindgen 0.59.1", +- "bindgen", - "target_build_utils", + "libc", + "opusic-sys", ] [[package]] -@@ -2188,6 +2188,16 @@ version = "0.1.4" +@@ -2796,6 +2796,16 @@ version = "0.1.5" source = "registry+https://github.com/rust-lang/crates.io-index" - checksum = "28988d872ab76095a6e6ac88d99b54fd267702734fd7ffe610ca27f533ddb95a" + checksum = "ff011a302c396a5197692431fc1948019154afc178baf7d8e37367442a4601cf" +[[package]] +name = "opusic-sys" @@ -33,18 +31,18 @@ index c3e139e..b77d8bd 100644 +] + [[package]] - name = "parity-tokio-ipc" - version = "0.7.2" + name = "os_str_bytes" + version = "6.0.0" diff --git a/Cargo.toml b/Cargo.toml -index 75504a0..43e1624 100644 +index 1b715bd..960e8da 100644 --- a/Cargo.toml +++ b/Cargo.toml -@@ -32,7 +32,7 @@ libc = "0.2" +@@ -35,7 +35,7 @@ libc = "0.2" parity-tokio-ipc = { git = "https://github.com/open-trade/parity-tokio-ipc" } - flexi_logger = "0.17" + flexi_logger = { version = "0.22", features = ["async", "use_chrono_for_offset"] } runas = "0.2" -magnum-opus = { git = "https://github.com/open-trade/magnum-opus" } +magnum-opus = { git = "https://github.com/TheRadioGuy/magnum-opus" } dasp = { version = "0.11", features = ["signal", "interpolate-linear", "interpolate"], optional = true } - rubato = { version = "0.8", optional = true } + rubato = { version = "0.12", optional = true } samplerate = { version = "0.2", optional = true } diff --git a/pkgs/applications/networking/remote/rustdesk/default.nix b/pkgs/applications/networking/remote/rustdesk/default.nix index 2850995bd13c..341cc22976a9 100644 --- a/pkgs/applications/networking/remote/rustdesk/default.nix +++ b/pkgs/applications/networking/remote/rustdesk/default.nix @@ -24,20 +24,21 @@ , libsciter , llvmPackages , wrapGAppsHook +, writeText }: rustPlatform.buildRustPackage rec { pname = "rustdesk"; - version = "1.1.8"; + version = "1.1.9"; src = fetchFromGitHub { owner = "rustdesk"; repo = "rustdesk"; - rev = "0325500ebf331b66220cec6e9078afb83b0e98a7"; - sha256 = "sha256-xglyyoiAjJx3y8+A2OYHZffjqjDkcTjIluPA/J42VVg="; + rev = version; + sha256 = "sha256-IlrfqwNyaSHE9Ct0mn7MUxEg7p1Ku34eOMYelEAYFW8="; }; - cargoSha256 = "sha256-4MQKa54f3X7IHGd29H6RY7v2toeHvTHInIpgXjdotjw="; + cargoSha256 = "sha256-1OMWEk+DerltF7kwdo4d04rbgIFLHBRq3vZaL7jtrdE="; LIBCLANG_PATH="${llvmPackages.libclang.lib}/lib"; @@ -51,10 +52,29 @@ rustPlatform.buildRustPackage rec { # properly. postUnpack = let vcpkg_target = "x64-linux"; + + updates_vcpkg_file = writeText "update_vcpkg_rustdesk" + '' + Package : libyuv + Architecture : ${vcpkg_target} + Version : 1.0 + Status : is installed + + Package : libvpx + Architecture : ${vcpkg_target} + Version : 1.0 + Status : is installed + ''; in '' export VCPKG_ROOT="$TMP/vcpkg"; + mkdir -p $VCPKG_ROOT/.vcpkg-root mkdir -p $VCPKG_ROOT/installed/${vcpkg_target}/lib + mkdir -p $VCPKG_ROOT/installed/vcpkg/updates + ln -s ${updates_vcpkg_file} $VCPKG_ROOT/installed/vcpkg/status + mkdir -p $VCPKG_ROOT/installed/vcpkg/info + touch $VCPKG_ROOT/installed/vcpkg/info/libyuv_1.0_${vcpkg_target}.list + touch $VCPKG_ROOT/installed/vcpkg/info/libvpx_1.0_${vcpkg_target}.list ln -s ${libvpx.out}/lib/* $VCPKG_ROOT/installed/${vcpkg_target}/lib/ ln -s ${libyuv.out}/lib/* $VCPKG_ROOT/installed/${vcpkg_target}/lib/ From e783357d377d97f3302a314fd068a2109c8ba5b2 Mon Sep 17 00:00:00 2001 From: Michael Alan Dorman Date: Sat, 16 Jul 2022 12:41:52 -0400 Subject: [PATCH 21/22] pivy: 0.6.6 -> 0.6.7 When attempting to do certain operations in FreeCAD, I ran into this error: 12:24:32 Traceback (most recent call last): 12:24:32 File "/nix/store/y43dl4mv61lvzpdvwpwpsazj6b3ii87l-freecad-0.20/Mod/Image/ImageTools/_CommandImageScaling.py", line 181, in getmousepoint 12:24:32 event = event_cb.getEvent() 12:24:32 File "/nix/store/dq8yly6isjzq6imm0i0qjxkang5rcq84-python3.10-pivy-0.6.6/lib/python3.10/site-packages/pivy/coin.py", line 49384, in getEvent 12:24:32 return _coin.SoEventCallback_getEvent(self) 12:24:32 SystemError: returned a result with an exception set 12:24:33 12:24:33 SystemError: PY_SSIZE_T_CLEAN macro must be defined for '#' formats 12:24:33 The above exception was the direct cause of the following exception: This macro was defined in https://github.com/coin3d/pivy/commit/2f049c19200ab4a3a1e4740268450496c12359f9, well after 0.6.6 was released, implying that FreeCAD depends on 0.6.7. (cherry picked from commit d5642e3491ff5d79e6836e86944bead8fb7f6022) --- pkgs/development/python-modules/pivy/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/development/python-modules/pivy/default.nix b/pkgs/development/python-modules/pivy/default.nix index 092bcbfcfd9d..d4aee75efe34 100644 --- a/pkgs/development/python-modules/pivy/default.nix +++ b/pkgs/development/python-modules/pivy/default.nix @@ -2,13 +2,13 @@ buildPythonPackage rec { pname = "pivy"; - version = "0.6.6"; + version = "0.6.7"; src = fetchFromGitHub { owner = "coin3d"; repo = "pivy"; rev = version; - sha256 = "1xlynrbq22pb252r37r80b3myzap8hzhvknz4zfznfrsg9ykh8k2"; + sha256 = "mU3QRDJd56gGDWqwcxAN3yUCkAkABP/I9gIBMH2MOXA="; }; dontUseCmakeConfigure = true; From 84fc544332332956e8dcc7b3276088237ef6efe4 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Thu, 21 Jul 2022 15:30:58 -0400 Subject: [PATCH 22/22] [Backport release-22.05] nixos/minecraft-server: let server shutdown cleanly (#182369) (cherry picked from commit e2b34f0f11ed8ad83d9ec9c14260192c3bcccb0d) Co-authored-by: Sofi --- .../services/games/minecraft-server.nix | 30 ++++++++++++++++++- nixos/tests/minecraft-server.nix | 1 + 2 files changed, 30 insertions(+), 1 deletion(-) diff --git a/nixos/modules/services/games/minecraft-server.nix b/nixos/modules/services/games/minecraft-server.nix index 8233962c1a2c..309fe43eaf4c 100644 --- a/nixos/modules/services/games/minecraft-server.nix +++ b/nixos/modules/services/games/minecraft-server.nix @@ -22,6 +22,15 @@ let '' + concatStringsSep "\n" (mapAttrsToList (n: v: "${n}=${cfgToString v}") cfg.serverProperties)); + stopScript = pkgs.writeShellScript "minecraft-server-stop" '' + echo stop > ${config.systemd.sockets.minecraft-server.socketConfig.ListenFIFO} + + # Wait for the PID of the minecraft server to disappear before + # returning, so systemd doesn't attempt to SIGKILL it. + while kill -0 "$1" 2> /dev/null; do + sleep 1s + done + ''; # To be able to open the firewall, we need to read out port values in the # server properties, but fall back to the defaults when those don't exist. @@ -172,16 +181,35 @@ in { }; users.groups.minecraft = {}; + systemd.sockets.minecraft-server = { + bindsTo = [ "minecraft-server.service" ]; + socketConfig = { + ListenFIFO = "/run/minecraft-server.stdin"; + SocketMode = "0660"; + SocketUser = "minecraft"; + SocketGroup = "minecraft"; + RemoveOnStop = true; + FlushPending = true; + }; + }; + systemd.services.minecraft-server = { description = "Minecraft Server Service"; wantedBy = [ "multi-user.target" ]; - after = [ "network.target" ]; + requires = [ "minecraft-server.socket" ]; + after = [ "network.target" "minecraft-server.socket" ]; serviceConfig = { ExecStart = "${cfg.package}/bin/minecraft-server ${cfg.jvmOpts}"; + ExecStop = "${stopScript} $MAINPID"; Restart = "always"; User = "minecraft"; WorkingDirectory = cfg.dataDir; + + StandardInput = "socket"; + StandardOutput = "journal"; + StandardError = "journal"; + # Hardening CapabilityBoundingSet = [ "" ]; DeviceAllow = [ "" ]; diff --git a/nixos/tests/minecraft-server.nix b/nixos/tests/minecraft-server.nix index dbe2cd6d56fe..a51b36ff5308 100644 --- a/nixos/tests/minecraft-server.nix +++ b/nixos/tests/minecraft-server.nix @@ -33,5 +33,6 @@ in import ./make-test-python.nix ({ pkgs, ... }: { assert "${seed}" in server.succeed( "mcrcon -H localhost -P ${toString rcon-port} -p '${rcon-pass}' -c 'seed'" ) + server.succeed("systemctl stop minecraft-server") ''; })