From c05019d716e2d5aa6f6d05150672c413688b38e3 Mon Sep 17 00:00:00 2001 From: toonn Date: Mon, 19 Jun 2023 14:35:52 +0200 Subject: [PATCH 01/66] PULL_REQUEST_TEMPLATE.md: Update sandboxing check Update the sandboxing check to include the `relaxed` setting for sandboxing. Previously there was no obvious and correct way to convey this intermediate setting between sandboxing being completely disabled and being enforced strictly. --- .github/PULL_REQUEST_TEMPLATE.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index b2ec787313e0..c4ed5c15d41a 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -14,7 +14,9 @@ For new packages please briefly describe the package or provide a link to its ho - [ ] aarch64-linux - [ ] x86_64-darwin - [ ] aarch64-darwin -- [ ] For non-Linux: Is `sandbox = true` set in `nix.conf`? (See [Nix manual](https://nixos.org/manual/nix/stable/command-ref/conf-file.html)) +- For non-Linux: Is sandboxing enabled in `nix.conf`? (See [Nix manual](https://nixos.org/manual/nix/stable/command-ref/conf-file.html)) + - [ ] `sandbox = relaxed` + - [ ] `sandbox = true` - [ ] Tested, as applicable: - [NixOS test(s)](https://nixos.org/manual/nixos/unstable/index.html#sec-nixos-tests) (look inside [nixos/tests](https://github.com/NixOS/nixpkgs/blob/master/nixos/tests)) - and/or [package tests](https://nixos.org/manual/nixpkgs/unstable/#sec-package-tests) From 86f362ce5b9d6606c6b6b832d864a47c45a05aaa Mon Sep 17 00:00:00 2001 From: natsukium Date: Thu, 17 Aug 2023 23:45:27 +0900 Subject: [PATCH 02/66] bioawk: init at unstable-2017-09-11 --- .../science/biology/bioawk/default.nix | 50 +++++++++++++++++++ pkgs/top-level/all-packages.nix | 2 + 2 files changed, 52 insertions(+) create mode 100644 pkgs/applications/science/biology/bioawk/default.nix diff --git a/pkgs/applications/science/biology/bioawk/default.nix b/pkgs/applications/science/biology/bioawk/default.nix new file mode 100644 index 000000000000..cfbb1a551fac --- /dev/null +++ b/pkgs/applications/science/biology/bioawk/default.nix @@ -0,0 +1,50 @@ +{ lib +, stdenv +, fetchFromGitHub +, installShellFiles +, bison +, zlib +}: + +stdenv.mkDerivation { + pname = "bioawk"; + version = "unstable-2017-09-11"; + + src = fetchFromGitHub { + owner = "lh3"; + repo = "bioawk"; + rev = "fd40150b7c557da45e781a999d372abbc634cc21"; + hash = "sha256-WWgz96DPP83J45isWkMbgEvOlibq6WefK//ImV6+AU0="; + }; + + nativeBuildInputs = [ + bison + installShellFiles + ]; + + buildInputs = [ + zlib + ]; + + buildFlags = [ + "CC=${stdenv.cc.targetPrefix}cc" + ]; + + installPhase = '' + runHook preInstall + + install -Dm755 bioawk -t $out/bin + mv awk.1 bioawk.1 + installManPage bioawk.1 + + runHook postInstall + ''; + + meta = with lib; { + description = "BWK awk modified for biological data"; + homepage = "https://github.com/lh3/bioawk"; + license = licenses.hpnd; + maintainers = with maintainers; [ natsukium ]; + platforms = platforms.unix; + }; +} diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 8aed8f81e818..d2f791224a83 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -38671,6 +38671,8 @@ with pkgs; bftools = callPackage ../applications/science/biology/bftools { }; + bioawk = callPackage ../applications/science/biology/bioawk { }; + blast = callPackage ../applications/science/biology/blast { inherit (darwin.apple_sdk.frameworks) ApplicationServices; }; From c814bbda40c688a205050937ade1deb67887efee Mon Sep 17 00:00:00 2001 From: Sergei Trofimovich Date: Mon, 2 Oct 2023 21:31:50 +0100 Subject: [PATCH 03/66] nginx: add missing nginx.8 manpage Without the change "man nginx" does not render any synopsis. Closes: https://github.com/NixOS/nixpkgs/issues/258658 --- pkgs/servers/http/nginx/generic.nix | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/pkgs/servers/http/nginx/generic.nix b/pkgs/servers/http/nginx/generic.nix index 3db19396bee9..1f175c03d8a8 100644 --- a/pkgs/servers/http/nginx/generic.nix +++ b/pkgs/servers/http/nginx/generic.nix @@ -2,7 +2,7 @@ outer@{ lib, stdenv, fetchurl, fetchpatch, openssl, zlib, pcre, libxml2, libxslt , nginx-doc , nixosTests -, substituteAll, removeReferencesTo, gd, geoip, perl +, installShellFiles, substituteAll, removeReferencesTo, gd, geoip, perl , withDebug ? false , withKTLS ? false , withStream ? true @@ -51,15 +51,17 @@ assert lib.assertMsg (lib.unique moduleNames == moduleNames) stdenv.mkDerivation { inherit pname version nginxVersion; - outputs = ["out" "doc"]; + outputs = [ "out" "doc" ]; src = if src != null then src else fetchurl { url = "https://nginx.org/download/nginx-${version}.tar.gz"; inherit hash; }; - nativeBuildInputs = [ removeReferencesTo ] - ++ nativeBuildInputs; + nativeBuildInputs = [ + installShellFiles + removeReferencesTo + ] ++ nativeBuildInputs; buildInputs = [ openssl zlib pcre libxml2 libxslt gd geoip perl ] ++ buildInputs @@ -166,6 +168,12 @@ stdenv.mkDerivation { preInstall = '' mkdir -p $doc cp -r ${nginx-doc}/* $doc + + # TODO: make it unconditional when `openresty` and `nginx` are not + # sharing this code. + if [[ -e man/nginx.8 ]]; then + installManPage man/nginx.8 + fi ''; disallowedReferences = map (m: m.src) modules; From 136c2e9b6f06cf56ccb8acf89c2def562560f48b Mon Sep 17 00:00:00 2001 From: natsukium Date: Wed, 11 Oct 2023 11:28:55 +0900 Subject: [PATCH 04/66] python311Packages.zope-lifecycleevent: rename from zope_lifecycleevent --- .../{zope_lifecycleevent => zope-lifecycleevent}/default.nix | 5 +++-- pkgs/top-level/python-aliases.nix | 1 + pkgs/top-level/python-packages.nix | 2 +- 3 files changed, 5 insertions(+), 3 deletions(-) rename pkgs/development/python-modules/{zope_lifecycleevent => zope-lifecycleevent}/default.nix (89%) diff --git a/pkgs/development/python-modules/zope_lifecycleevent/default.nix b/pkgs/development/python-modules/zope-lifecycleevent/default.nix similarity index 89% rename from pkgs/development/python-modules/zope_lifecycleevent/default.nix rename to pkgs/development/python-modules/zope-lifecycleevent/default.nix index 807deb097feb..31077143f381 100644 --- a/pkgs/development/python-modules/zope_lifecycleevent/default.nix +++ b/pkgs/development/python-modules/zope-lifecycleevent/default.nix @@ -7,11 +7,12 @@ }: buildPythonPackage rec { - pname = "zope.lifecycleevent"; + pname = "zope-lifecycleevent"; version = "4.4"; src = fetchPypi { - inherit pname version; + pname = "zope.lifecycleevent"; + inherit version; hash = "sha256-9ahU6J/5fe6ke/vqN4u77yeJ0uDMkKHB2lfZChzmfLU="; }; diff --git a/pkgs/top-level/python-aliases.nix b/pkgs/top-level/python-aliases.nix index a791b8ccd86c..5f6c543db4c3 100644 --- a/pkgs/top-level/python-aliases.nix +++ b/pkgs/top-level/python-aliases.nix @@ -421,5 +421,6 @@ mapAliases ({ zope_component = zope-component; # added 2023-07-28 zope_deprecation = zope-deprecation; # added 2023-10-07 zope_i18nmessageid = zope-i18nmessageid; # added 2023-07-29 + zope_lifecycleevent = zope-lifecycleevent; # added 2023-10-11 zope_proxy = zope-proxy; # added 2023-10-07 }) diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index 6e845f54927d..f364bd6019a3 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -15918,7 +15918,7 @@ self: super: with self; { zope_interface = callPackage ../development/python-modules/zope_interface { }; - zope_lifecycleevent = callPackage ../development/python-modules/zope_lifecycleevent { }; + zope-lifecycleevent = callPackage ../development/python-modules/zope-lifecycleevent { }; zope_location = callPackage ../development/python-modules/zope_location { }; From 58b0faf3881b01ffb1894fc3c0b0c4dc56c03923 Mon Sep 17 00:00:00 2001 From: natsukium Date: Wed, 11 Oct 2023 12:00:55 +0900 Subject: [PATCH 05/66] python311Packages.zope-lifecycleevent: refactor --- .../python-modules/zope-lifecycleevent/default.nix | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/pkgs/development/python-modules/zope-lifecycleevent/default.nix b/pkgs/development/python-modules/zope-lifecycleevent/default.nix index 31077143f381..619817d41fd2 100644 --- a/pkgs/development/python-modules/zope-lifecycleevent/default.nix +++ b/pkgs/development/python-modules/zope-lifecycleevent/default.nix @@ -2,13 +2,15 @@ , buildPythonPackage , fetchPypi , isPy3k +, setuptools , zope_event -, zope-component +, zope_interface }: buildPythonPackage rec { pname = "zope-lifecycleevent"; version = "4.4"; + pyproject = true; src = fetchPypi { pname = "zope.lifecycleevent"; @@ -16,7 +18,11 @@ buildPythonPackage rec { hash = "sha256-9ahU6J/5fe6ke/vqN4u77yeJ0uDMkKHB2lfZChzmfLU="; }; - propagatedBuildInputs = [ zope_event zope-component ]; + nativeBuildInputs = [ + setuptools + ]; + + propagatedBuildInputs = [ zope_event zope_interface ]; # namespace colides with local directory doCheck = false; @@ -30,8 +36,8 @@ buildPythonPackage rec { meta = with lib; { homepage = "https://github.com/zopefoundation/zope.lifecycleevent"; description = "Object life-cycle events"; - license = licenses.zpl20; + changelog = "https://github.com/zopefoundation/zope.lifecycleevent/blob/${version}/CHANGES.rst"; + license = licenses.zpl21; maintainers = with maintainers; [ goibhniu ]; }; - } From 60995e325c4dcb045fc58395928d2ebf39c7d4c2 Mon Sep 17 00:00:00 2001 From: natsukium Date: Wed, 11 Oct 2023 12:01:41 +0900 Subject: [PATCH 06/66] python311Packages.zope-lifecycleevent: 4.4 -> 5.0 Changelog: https://github.com/zopefoundation/zope.lifecycleevent/blob/5.0/CHANGES.rst --- .../python-modules/zope-lifecycleevent/default.nix | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/pkgs/development/python-modules/zope-lifecycleevent/default.nix b/pkgs/development/python-modules/zope-lifecycleevent/default.nix index 619817d41fd2..fc6b0005ffac 100644 --- a/pkgs/development/python-modules/zope-lifecycleevent/default.nix +++ b/pkgs/development/python-modules/zope-lifecycleevent/default.nix @@ -1,7 +1,7 @@ { lib , buildPythonPackage , fetchPypi -, isPy3k +, pythonOlder , setuptools , zope_event , zope_interface @@ -9,13 +9,15 @@ buildPythonPackage rec { pname = "zope-lifecycleevent"; - version = "4.4"; + version = "5.0"; pyproject = true; + disabled = pythonOlder "3.7"; + src = fetchPypi { pname = "zope.lifecycleevent"; inherit version; - hash = "sha256-9ahU6J/5fe6ke/vqN4u77yeJ0uDMkKHB2lfZChzmfLU="; + hash = "sha256-6tP7SW52FPm1adFtrUt4BSsKwhh1utjWbKNQNS2bb50="; }; nativeBuildInputs = [ @@ -27,8 +29,7 @@ buildPythonPackage rec { # namespace colides with local directory doCheck = false; - # zope uses pep 420 namespaces for python3, doesn't work with nix + python2 - pythonImportsCheck = lib.optionals isPy3k [ + pythonImportsCheck = [ "zope.lifecycleevent" "zope.interface" ]; From f8b06175be9752193c7640ade43ffef743175e72 Mon Sep 17 00:00:00 2001 From: natsukium Date: Wed, 11 Oct 2023 12:47:46 +0900 Subject: [PATCH 07/66] python311Packages.sphinx-pypi-upload: remove It is abandoned and uploading documentation to PyPI has been disabled. --- .../sphinx_pypi_upload/default.nix | 21 ------------------- pkgs/top-level/python-aliases.nix | 1 + pkgs/top-level/python-packages.nix | 2 -- 3 files changed, 1 insertion(+), 23 deletions(-) delete mode 100644 pkgs/development/python-modules/sphinx_pypi_upload/default.nix diff --git a/pkgs/development/python-modules/sphinx_pypi_upload/default.nix b/pkgs/development/python-modules/sphinx_pypi_upload/default.nix deleted file mode 100644 index d2c20e980e7a..000000000000 --- a/pkgs/development/python-modules/sphinx_pypi_upload/default.nix +++ /dev/null @@ -1,21 +0,0 @@ -{ lib -, buildPythonPackage -, fetchPypi -}: - -buildPythonPackage rec { - pname = "Sphinx-PyPI-upload"; - version = "0.2.1"; - - src = fetchPypi { - inherit pname version; - sha256 = "5f919a47ce7a7e6028dba809de81ae1297ac192347cf6fc54efca919d4865159"; - }; - - meta = with lib; { - description = "Setuptools command for uploading Sphinx documentation to PyPI"; - homepage = "https://bitbucket.org/jezdez/sphinx-pypi-upload/"; - license = licenses.bsd0; - }; - -} diff --git a/pkgs/top-level/python-aliases.nix b/pkgs/top-level/python-aliases.nix index a791b8ccd86c..b4b4514a7beb 100644 --- a/pkgs/top-level/python-aliases.nix +++ b/pkgs/top-level/python-aliases.nix @@ -372,6 +372,7 @@ mapAliases ({ somecomfort = throw "somecomfort was removed because Home Assistant switched to aiosomecomfort"; # added 2023-02-01 SPARQLWrapper = sparqlwrapper; sphinx-jquery = sphinxcontrib-jquery; # added 2023-02-24 + sphinx_pypi_upload = throw "sphinx_pypi_upload has been removed since it is abandoned."; # added 2023-10-11 sphinx_rtd_theme = sphinx-rtd-theme; # added 2022-08-03 sphinxcontrib-autoapi = sphinx-autoapi; # added 2023-02=28 sphinxcontrib_plantuml = sphinxcontrib-plantuml; # added 2021-08-02 diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index 6e845f54927d..d1c0b2f62fa4 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -13187,8 +13187,6 @@ self: super: with self; { sphinx-mdinclude = callPackage ../development/python-modules/sphinx-mdinclude { }; - sphinx_pypi_upload = callPackage ../development/python-modules/sphinx_pypi_upload { }; - sphinx-rtd-theme = callPackage ../development/python-modules/sphinx-rtd-theme { }; sphinx-serve = callPackage ../development/python-modules/sphinx-serve { }; From 39e1727f0f01181655f31de474f2fe13b7ce582e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sandro=20J=C3=A4ckel?= Date: Tue, 3 Oct 2023 21:41:57 +0200 Subject: [PATCH 08/66] nixos/dex: fix start with latest systemd update With those settings starting dex crashed with: Oct 03 21:37:51 hydrogen (tart-pre)[11048]: dex.service: Failed to set up mount namespacing: /run/systemd/mount-rootfs/sys/fs/cgroup/system.slice/dex.service/memory.pressure: No such file or directory Oct 03 21:37:51 hydrogen (tart-pre)[11048]: dex.service: Failed at step NAMESPACE spawning /nix/store/q8clp1lm8jznxf9330jd8cwc6mdy6glz-dex-start-pre: No such file or directory --- nixos/modules/services/web-apps/dex.nix | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/nixos/modules/services/web-apps/dex.nix b/nixos/modules/services/web-apps/dex.nix index bd041db007a1..0c4a71c6dfe4 100644 --- a/nixos/modules/services/web-apps/dex.nix +++ b/nixos/modules/services/web-apps/dex.nix @@ -108,8 +108,7 @@ in ProtectClock = true; ProtectHome = true; ProtectHostname = true; - # Would re-mount paths ignored by temporary root - #ProtectSystem = "strict"; + ProtectSystem = "strict"; ProtectControlGroups = true; ProtectKernelLogs = true; ProtectKernelModules = true; @@ -121,9 +120,7 @@ in RestrictSUIDSGID = true; SystemCallArchitectures = "native"; SystemCallFilter = [ "@system-service" "~@privileged @setuid @keyring" ]; - TemporaryFileSystem = "/:ro"; - # Does not work well with the temporary root - #UMask = "0066"; + UMask = "0066"; } // optionalAttrs (cfg.environmentFile != null) { EnvironmentFile = cfg.environmentFile; }; From 2e22b70d8dfe5571fdbeac217d51122230c2587a Mon Sep 17 00:00:00 2001 From: Madoura Date: Thu, 12 Oct 2023 05:04:58 -0500 Subject: [PATCH 09/66] python3Packages.desktop-entry-lib: init at 3.1 --- .../desktop-entry-lib/default.nix | 35 +++++++++++++++++++ pkgs/top-level/python-packages.nix | 2 ++ 2 files changed, 37 insertions(+) create mode 100644 pkgs/development/python-modules/desktop-entry-lib/default.nix diff --git a/pkgs/development/python-modules/desktop-entry-lib/default.nix b/pkgs/development/python-modules/desktop-entry-lib/default.nix new file mode 100644 index 000000000000..5a6d3c00e7f0 --- /dev/null +++ b/pkgs/development/python-modules/desktop-entry-lib/default.nix @@ -0,0 +1,35 @@ +{ lib +, buildPythonPackage +, pythonOlder +, pytestCheckHook +, fetchFromGitea +, setuptools +}: + +buildPythonPackage rec { + pname = "desktop-entry-lib"; + version = "3.1"; + pyproject = true; + disabled = pythonOlder "3.9"; + + # We could use fetchPypi, but then the tests won't run + src = fetchFromGitea { + domain = "codeberg.org"; + owner = "JakobDev"; + repo = pname; + rev = version; + hash = "sha256-+c+FuLv88wc4yVw3iyFFtfbocnWzTCIe2DS0SWoj+VI="; + }; + + nativeBuildInputs = [ setuptools ]; + nativeCheckInputs = [ pytestCheckHook ]; + pythonImportsCheck = [ "desktop_entry_lib" ]; + + meta = with lib; { + description = "Allows reading and writing .desktop files according to the Desktop Entry Specification"; + homepage = "https://codeberg.org/JakobDev/desktop-entry-lib"; + changelog = "https://codeberg.org/JakobDev/desktop-entry-lib/releases/tag/${version}"; + license = licenses.bsd2; + maintainers = with maintainers; [ Madouura ]; + }; +} diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index 831ae4d39def..fd3f6303c242 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -2717,6 +2717,8 @@ self: super: with self; { derpconf = callPackage ../development/python-modules/derpconf { }; + desktop-entry-lib = callPackage ../development/python-modules/desktop-entry-lib { }; + desktop-notifier = callPackage ../development/python-modules/desktop-notifier { }; detect-secrets = callPackage ../development/python-modules/detect-secrets { }; From d894a80537fac33cd2e4cf80dd6902e6e3cf8d58 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Christina=20S=C3=B8rensen?= Date: Sun, 15 Oct 2023 17:27:46 +0200 Subject: [PATCH 10/66] cpufrequtils: add mainProgram `cpufreq-set` MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Christina Sørensen --- pkgs/os-specific/linux/cpufrequtils/default.nix | 1 + 1 file changed, 1 insertion(+) diff --git a/pkgs/os-specific/linux/cpufrequtils/default.nix b/pkgs/os-specific/linux/cpufrequtils/default.nix index d64996c4961e..2bccf5a10020 100644 --- a/pkgs/os-specific/linux/cpufrequtils/default.nix +++ b/pkgs/os-specific/linux/cpufrequtils/default.nix @@ -27,5 +27,6 @@ stdenv.mkDerivation rec { homepage = "http://ftp.be.debian.org/pub/linux/utils/kernel/cpufreq/cpufrequtils.html"; license = licenses.gpl2Only; platforms = [ "x86_64-linux" ]; + mainProgram = "cpufreq-set"; }; } From 38cae8b359c44d9e38d3c294f1975d4bf2c8e698 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Christina=20S=C3=B8rensen?= Date: Sun, 15 Oct 2023 17:29:03 +0200 Subject: [PATCH 11/66] cpufrequtils: change sha256 hash to sri form MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Christina Sørensen --- pkgs/os-specific/linux/cpufrequtils/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/os-specific/linux/cpufrequtils/default.nix b/pkgs/os-specific/linux/cpufrequtils/default.nix index 2bccf5a10020..f62d8463714e 100644 --- a/pkgs/os-specific/linux/cpufrequtils/default.nix +++ b/pkgs/os-specific/linux/cpufrequtils/default.nix @@ -6,7 +6,7 @@ stdenv.mkDerivation rec { src = fetchurl { url = "http://ftp.be.debian.org/pub/linux/utils/kernel/cpufreq/cpufrequtils-${version}.tar.gz"; - sha256 = "127i38d4w1hv2dzdy756gmbhq25q3k34nqb2s0xlhsfhhdqs0lq0"; + hash = "sha256-AFOgcYPQaUg70GJhS8YcuAgMV32mHN9+ExsGThoa8Yg="; }; patches = [ From a9f4d2dd95514d0a05b8d70e062eac8d82d50eb7 Mon Sep 17 00:00:00 2001 From: Mario Rodas Date: Mon, 16 Oct 2023 04:20:00 +0000 Subject: [PATCH 12/66] pgbouncer: 1.20.1 -> 1.21.0 Changelog: https://github.com/pgbouncer/pgbouncer/releases/tag/pgbouncer_1_21_0 --- pkgs/servers/sql/pgbouncer/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/servers/sql/pgbouncer/default.nix b/pkgs/servers/sql/pgbouncer/default.nix index b0f2bcb61626..7f6cfa0f898a 100644 --- a/pkgs/servers/sql/pgbouncer/default.nix +++ b/pkgs/servers/sql/pgbouncer/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "pgbouncer"; - version = "1.20.1"; + version = "1.21.0"; src = fetchurl { url = "https://www.pgbouncer.org/downloads/files/${version}/${pname}-${version}.tar.gz"; - hash = "sha256-JJks9VfXNCbXBIaY3/x7AZ5jZNTYdXriz14kcShqIIg="; + hash = "sha256-fh3WIMjYWoSQr/JQYdUFXXrvnPPov+LZ53GbjuWRFOI="; }; nativeBuildInputs = [ pkg-config ]; From 3ece074bf4828ed1985b881c59c0ff240d7172fb Mon Sep 17 00:00:00 2001 From: natsukium Date: Mon, 16 Oct 2023 15:22:33 +0900 Subject: [PATCH 13/66] python311Packages.opsdroid-get-image-size: rename from opsdroid_get_image_size --- pkgs/applications/networking/opsdroid/default.nix | 2 +- .../default.nix | 5 +++-- pkgs/top-level/python-aliases.nix | 1 + pkgs/top-level/python-packages.nix | 2 +- 4 files changed, 6 insertions(+), 4 deletions(-) rename pkgs/development/python-modules/{opsdroid_get_image_size => opsdroid-get-image-size}/default.nix (84%) diff --git a/pkgs/applications/networking/opsdroid/default.nix b/pkgs/applications/networking/opsdroid/default.nix index 4398c771e535..d4f2a9b26a18 100644 --- a/pkgs/applications/networking/opsdroid/default.nix +++ b/pkgs/applications/networking/opsdroid/default.nix @@ -17,7 +17,7 @@ python3Packages.buildPythonPackage rec { doCheck = false; propagatedBuildInputs = with python3Packages; [ - click babel opsdroid_get_image_size slackclient webexteamssdk bleach + click babel opsdroid-get-image-size slackclient webexteamssdk bleach parse emoji puremagic yamale nbformat websockets pycron nbconvert aiohttp matrix-api-async aioredis aiosqlite arrow pyyaml motor regex mattermostdriver setuptools voluptuous ibm-watson tailer multidict diff --git a/pkgs/development/python-modules/opsdroid_get_image_size/default.nix b/pkgs/development/python-modules/opsdroid-get-image-size/default.nix similarity index 84% rename from pkgs/development/python-modules/opsdroid_get_image_size/default.nix rename to pkgs/development/python-modules/opsdroid-get-image-size/default.nix index 0f33da44145f..c88ce6928b09 100644 --- a/pkgs/development/python-modules/opsdroid_get_image_size/default.nix +++ b/pkgs/development/python-modules/opsdroid-get-image-size/default.nix @@ -2,11 +2,12 @@ }: buildPythonPackage rec { - pname = "opsdroid_get_image_size"; + pname = "opsdroid-get-image-size"; version = "0.2.2"; src = fetchPypi { - inherit pname version; + pname = "opsdroid_get_image_size"; + inherit version; sha256 = "124j2xvfxv09q42qfb8nqlcn55y7f09iayrix3yfyrs2qyzav78a"; }; diff --git a/pkgs/top-level/python-aliases.nix b/pkgs/top-level/python-aliases.nix index 94eeeb99eb80..25fe57b77600 100644 --- a/pkgs/top-level/python-aliases.nix +++ b/pkgs/top-level/python-aliases.nix @@ -241,6 +241,7 @@ mapAliases ({ notifymuch = throw "notifymuch has been promoted to a top-level attribute"; # added 2022-10-02 Nuitka = nuitka; # added 2023-02-19 ntlm-auth = throw "ntlm-auth has been removed, because it relies on the md4 implementation provided by openssl. Use pyspnego instead."; + opsdroid_get_image_size = opsdroid-get-image-size; # added 2023-10-16 ordereddict = throw "ordereddict has been removed because it is only useful on unsupported python versions."; # added 2022-05-28 pafy = throw "pafy has been removed because it is unmaintained and only a dependency of mps-youtube, itself superseded by yewtube"; # Added 2023-01-19 pam = python-pam; # added 2020-09-07. diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index a3b1b0383365..e068e0a98581 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -8502,7 +8502,7 @@ self: super: with self; { opower = callPackage ../development/python-modules/opower { }; - opsdroid_get_image_size = callPackage ../development/python-modules/opsdroid_get_image_size { }; + opsdroid-get-image-size = callPackage ../development/python-modules/opsdroid-get-image-size { }; opt-einsum = callPackage ../development/python-modules/opt-einsum { }; From b5a169004012af311ac4783439028feb7469e880 Mon Sep 17 00:00:00 2001 From: natsukium Date: Mon, 16 Oct 2023 15:28:18 +0900 Subject: [PATCH 14/66] python311Packages.opsdroid-get-image-size: refactor --- .../opsdroid-get-image-size/default.nix | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/pkgs/development/python-modules/opsdroid-get-image-size/default.nix b/pkgs/development/python-modules/opsdroid-get-image-size/default.nix index c88ce6928b09..edd09d2750e2 100644 --- a/pkgs/development/python-modules/opsdroid-get-image-size/default.nix +++ b/pkgs/development/python-modules/opsdroid-get-image-size/default.nix @@ -1,16 +1,24 @@ -{ lib, buildPythonPackage, fetchPypi +{ lib +, buildPythonPackage +, fetchPypi +, setuptools }: buildPythonPackage rec { pname = "opsdroid-get-image-size"; version = "0.2.2"; + pyproject = true; src = fetchPypi { pname = "opsdroid_get_image_size"; inherit version; - sha256 = "124j2xvfxv09q42qfb8nqlcn55y7f09iayrix3yfyrs2qyzav78a"; + hash = "sha256-Cp2tvsdCZ+/86DF7FRNwx5diGcUWLYcFwQns7nYXkog="; }; + nativeBuildInputs = [ + setuptools + ]; + # test data not included on pypi doCheck = false; From 447551520b31cf28738cfaa927f31d73530cdbeb Mon Sep 17 00:00:00 2001 From: Madoura Date: Mon, 16 Oct 2023 08:34:02 -0500 Subject: [PATCH 15/66] kokkos: init at 4.1.00 --- pkgs/by-name/ko/kokkos/package.nix | 44 ++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 pkgs/by-name/ko/kokkos/package.nix diff --git a/pkgs/by-name/ko/kokkos/package.nix b/pkgs/by-name/ko/kokkos/package.nix new file mode 100644 index 000000000000..b6578f4a020f --- /dev/null +++ b/pkgs/by-name/ko/kokkos/package.nix @@ -0,0 +1,44 @@ +{ lib +, stdenv +, fetchFromGitHub +, gitUpdater +, cmake +, python3 +}: + +stdenv.mkDerivation (finalAttrs: { + pname = "kokkos"; + version = "4.1.00"; + + src = fetchFromGitHub { + owner = "kokkos"; + repo = "kokkos"; + rev = finalAttrs.version; + hash = "sha256-bPgXn1Lv+EiiKEHgTVhRFhcELUnZCphaXDlrTYq6cpY="; + }; + + nativeBuildInputs = [ + cmake + python3 + ]; + + cmakeFlags = [ + (lib.cmakeBool "Kokkos_ENABLE_TESTS" true) + ]; + + postPatch = '' + patchShebangs . + ''; + + doCheck = true; + passthru.updateScript = gitUpdater { }; + + meta = with lib; { + description = "C++ Performance Portability Programming EcoSystem"; + homepage = "https://github.com/kokkos/kokkos"; + license = with licenses; [ asl20-llvm ]; + maintainers = with maintainers; [ Madouura ]; + platforms = platforms.unix; + broken = stdenv.isDarwin; + }; +}) From d479580285ed54b392f718c23a2d0cbfd303b62b Mon Sep 17 00:00:00 2001 From: Mario Rodas Date: Mon, 16 Oct 2023 16:20:00 -0500 Subject: [PATCH 16/66] nodejs_21: init at 21.0.0 Changelog: https://github.com/nodejs/node/releases/tag/v21.0.0 --- pkgs/development/web/nodejs/v21.nix | 19 +++++++++++++++++++ pkgs/top-level/all-packages.nix | 10 +++++++--- 2 files changed, 26 insertions(+), 3 deletions(-) create mode 100644 pkgs/development/web/nodejs/v21.nix diff --git a/pkgs/development/web/nodejs/v21.nix b/pkgs/development/web/nodejs/v21.nix new file mode 100644 index 000000000000..6d59e20dfa5f --- /dev/null +++ b/pkgs/development/web/nodejs/v21.nix @@ -0,0 +1,19 @@ +{ callPackage, openssl, python3, enableNpm ? true }: + +let + buildNodejs = callPackage ./nodejs.nix { + inherit openssl; + python = python3; + }; +in +buildNodejs { + inherit enableNpm; + version = "21.0.0"; + sha256 = "sha256-vFYZK5Ua0YNQbcqaz3pNDAJZEUC3/I8lZhN1GZJm8/I="; + patches = [ + ./revert-arm64-pointer-auth.patch + ./disable-darwin-v8-system-instrumentation-node19.patch + ./bypass-darwin-xcrun-node16.patch + ./node-npm-build-npm-package-logic.patch + ]; +} diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index b6f366214a0b..20afeb85a606 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -10295,10 +10295,14 @@ with pkgs; nodejs-slim_20 = callPackage ../development/web/nodejs/v20.nix { enableNpm = false; }; corepack_20 = hiPrio (callPackage ../development/web/nodejs/corepack.nix { nodejs = nodejs_20; }); + nodejs_21 = callPackage ../development/web/nodejs/v21.nix { }; + nodejs-slim_21 = callPackage ../development/web/nodejs/v21.nix { enableNpm = false; }; + corepack_21 = hiPrio (callPackage ../development/web/nodejs/corepack.nix { nodejs = nodejs_21; }); + # Update this when adding the newest nodejs major version! - nodejs_latest = nodejs_20; - nodejs-slim_latest = nodejs-slim_20; - corepack_latest = hiPrio corepack_20; + nodejs_latest = nodejs_21; + nodejs-slim_latest = nodejs-slim_21; + corepack_latest = hiPrio corepack_21; buildNpmPackage = callPackage ../build-support/node/build-npm-package { }; From bc53cc867a7a24ddb1f0fd925f40f37ff56c8f23 Mon Sep 17 00:00:00 2001 From: natsukium Date: Tue, 17 Oct 2023 18:06:43 +0900 Subject: [PATCH 17/66] python311Packages.optuna: 3.3.0 -> 3.4.0 Diff: https://github.com/optuna/optuna/compare/refs/tags/v3.3.0...v3.4.0 Changelog: https://github.com/optuna/optuna/releases/tag/refs/tags/v3.4.0 --- pkgs/development/python-modules/optuna/default.nix | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/pkgs/development/python-modules/optuna/default.nix b/pkgs/development/python-modules/optuna/default.nix index f3b41af02096..7a3b3cca06b0 100644 --- a/pkgs/development/python-modules/optuna/default.nix +++ b/pkgs/development/python-modules/optuna/default.nix @@ -13,6 +13,7 @@ , distributed , fakeredis , fastai +, google-cloud-storage , lightgbm , matplotlib , mlflow @@ -43,7 +44,7 @@ buildPythonPackage rec { pname = "optuna"; - version = "3.3.0"; + version = "3.4.0"; format = "pyproject"; disabled = pythonOlder "3.7"; @@ -52,7 +53,7 @@ buildPythonPackage rec { owner = "optuna"; repo = "optuna"; rev = "refs/tags/v${version}"; - hash = "sha256-uHv8uEJOQO1+AeNSxBtnCt6gDQHLT1RToF4hfolVVX0="; + hash = "sha256-WUjO13NxX0FneOPS4nn6aHq48X95r+GJR/Oxir6n8Pk="; }; nativeBuildInputs = [ @@ -62,7 +63,6 @@ buildPythonPackage rec { propagatedBuildInputs = [ alembic - cmaes colorlog numpy packaging @@ -96,6 +96,8 @@ buildPythonPackage rec { optional = [ boto3 botorch + cmaes + google-cloud-storage matplotlib pandas plotly From dc4d0c3c2a4fa933805c92358d185a5cb1aee34d Mon Sep 17 00:00:00 2001 From: Muhammad Falak R Wani Date: Wed, 18 Oct 2023 22:22:22 +0530 Subject: [PATCH 18/66] redis: 7.2.1 -> 7.2.2 Changelog: https://github.com/redis/redis/raw/7.2.2/00-RELEASENOTES --- pkgs/servers/nosql/redis/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/servers/nosql/redis/default.nix b/pkgs/servers/nosql/redis/default.nix index 25d889694504..b1f3bb7adcc3 100644 --- a/pkgs/servers/nosql/redis/default.nix +++ b/pkgs/servers/nosql/redis/default.nix @@ -12,11 +12,11 @@ stdenv.mkDerivation (finalAttrs: { pname = "redis"; - version = "7.2.1"; + version = "7.2.2"; src = fetchurl { url = "https://download.redis.io/releases/redis-${finalAttrs.version}.tar.gz"; - hash = "sha256-XHbZkKGxxflJvNHu2Q0Mik9wNpvb3LQCiMVh3fiJZ6Q="; + hash = "sha256-ypmb4IgA7cbSZTecTHqvrZLw7kAGkuTi1pgpq0tMPQg="; }; patches = lib.optionals useSystemJemalloc [ From cce349c3fa5b64391cb5a59503515b45fc004cb1 Mon Sep 17 00:00:00 2001 From: "R. Ryantm" Date: Wed, 18 Oct 2023 19:26:33 +0000 Subject: [PATCH 19/66] remind: 04.02.05 -> 04.02.07 --- pkgs/tools/misc/remind/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/tools/misc/remind/default.nix b/pkgs/tools/misc/remind/default.nix index 945e592e848a..97aefe1f8e5c 100644 --- a/pkgs/tools/misc/remind/default.nix +++ b/pkgs/tools/misc/remind/default.nix @@ -15,11 +15,11 @@ let in tcl.mkTclDerivation rec { pname = "remind"; - version = "04.02.05"; + version = "04.02.07"; src = fetchurl { url = "https://dianne.skoll.ca/projects/remind/download/remind-${version}.tar.gz"; - sha256 = "sha256-nOEFhVwZvgUod+j/5ifllFgTS7I8+hOAeMSDlRH4+Ag="; + sha256 = "sha256-A+EtkNmQOcz3Mb4q7qQGNL6pyCnRus4nqNor485tsZA="; }; propagatedBuildInputs = tclLibraries; From 648bef4bc6f3425243e0749c696d8f21cf170c8f Mon Sep 17 00:00:00 2001 From: Vincent Laporte Date: Thu, 19 Oct 2023 07:01:36 +0200 Subject: [PATCH 20/66] =?UTF-8?q?cgal=5F5:=205.5.2=20=E2=86=92=205.5.3?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- pkgs/development/libraries/CGAL/default.nix | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/pkgs/development/libraries/CGAL/default.nix b/pkgs/development/libraries/CGAL/default.nix index 9d9233aad20e..672facdc230c 100644 --- a/pkgs/development/libraries/CGAL/default.nix +++ b/pkgs/development/libraries/CGAL/default.nix @@ -1,5 +1,5 @@ { lib, stdenv -, fetchFromGitHub +, fetchurl , cmake , boost , gmp @@ -8,13 +8,11 @@ stdenv.mkDerivation rec { pname = "cgal"; - version = "5.5.2"; + version = "5.5.3"; - src = fetchFromGitHub { - owner = "CGAL"; - repo = "releases"; - rev = "CGAL-${version}"; - sha256 = "sha256-olMPT/8Q0bf+rooJoNc0k8NrO//O7z0yqBoP8KX39yQ="; + src = fetchurl { + url = "https://github.com/CGAL/cgal/releases/download/v${version}/CGAL-${version}.tar.xz"; + hash = "sha256-CgT2YmkyVjKLBbq/q7XjpbfbL1pY1S48Ug350IKN3XM="; }; # note: optional component libCGAL_ImageIO would need zlib and opengl; From a20c614010580dfb6ac182bdb3661777bbe50955 Mon Sep 17 00:00:00 2001 From: r-vdp Date: Wed, 18 Oct 2023 09:59:02 +0200 Subject: [PATCH 21/66] fzf: fix fish integration Since fzf 0.43.0, the fzf_key_bindings function is only defined when fish is running interactively, see [1]. This caused errors when entering non-interactive fish shells since we called fzf_key_bindings during startup. [1]: https://github.com/junegunn/fzf/commit/7e89458a3b58c047c10494a5cb53d921fb08b4f3 --- pkgs/tools/misc/fzf/default.nix | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/pkgs/tools/misc/fzf/default.nix b/pkgs/tools/misc/fzf/default.nix index 29f87b4ffdd0..be7992f94af5 100644 --- a/pkgs/tools/misc/fzf/default.nix +++ b/pkgs/tools/misc/fzf/default.nix @@ -79,7 +79,10 @@ buildGoModule rec { install -D shell/* -t $out/share/fzf/ install -D shell/key-bindings.fish $out/share/fish/vendor_functions.d/fzf_key_bindings.fish mkdir -p $out/share/fish/vendor_conf.d - echo fzf_key_bindings > $out/share/fish/vendor_conf.d/load-fzf-key-bindings.fish + cat << EOF > $out/share/fish/vendor_conf.d/load-fzf-key-bindings.fish + status is-interactive; or exit 0 + fzf_key_bindings + EOF cat <