diff options
author | Alyssa Ross <hi@alyssa.is> | 2024-01-10 01:11:23 +0100 |
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committer | Alyssa Ross <hi@alyssa.is> | 2024-01-10 01:11:23 +0100 |
commit | c8d05d8abadb244bc4e6cee75d450978d1f09a61 (patch) | |
tree | 2d710425b8e3f78e84d5e46abb3397cb1b34ec18 /nixpkgs/pkgs/by-name | |
parent | ad899504860973e98351c922ecb934595f2c0f19 (diff) | |
parent | 0ed96eed101462bf05e1e99e1bbadcd49b4eb302 (diff) | |
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Merge branch 'nixos-unstable-small' of https://github.com/NixOS/nixpkgs
Diffstat (limited to 'nixpkgs/pkgs/by-name')
15 files changed, 444 insertions, 14 deletions
diff --git a/nixpkgs/pkgs/by-name/as/asn1editor/package.nix b/nixpkgs/pkgs/by-name/as/asn1editor/package.nix index a85d8f53fe6d..07941a7762c4 100644 --- a/nixpkgs/pkgs/by-name/as/asn1editor/package.nix +++ b/nixpkgs/pkgs/by-name/as/asn1editor/package.nix @@ -18,7 +18,7 @@ python3.pkgs.buildPythonApplication rec { propagatedBuildInputs = with python3.pkgs; [ asn1tools coverage - wxPython_4_2 + wxpython ]; pythonImportsCheck = [ "asn1editor" ]; diff --git a/nixpkgs/pkgs/by-name/bi/bitwarden-directory-connector-cli/package.nix b/nixpkgs/pkgs/by-name/bi/bitwarden-directory-connector-cli/package.nix new file mode 100644 index 000000000000..24376014a120 --- /dev/null +++ b/nixpkgs/pkgs/by-name/bi/bitwarden-directory-connector-cli/package.nix @@ -0,0 +1,66 @@ +{ + lib, + buildNpmPackage, + fetchFromGitHub, + buildPackages, + python3, + pkg-config, + libsecret, + nodejs_18, +}: +buildNpmPackage rec { + pname = "bitwarden-directory-connector-cli"; + version = "2023.10.0"; + nodejs = nodejs_18; + + src = fetchFromGitHub { + owner = "bitwarden"; + repo = "directory-connector"; + rev = "v${version}"; + hash = "sha256-PlOtTh+rpTxAv8ajHBDHZuL7yeeLVpbAfKEDPQlejIg="; + }; + + postPatch = '' + ${lib.getExe buildPackages.jq} 'del(.scripts.preinstall)' package.json > package.json.tmp + mv -f package.json{.tmp,} + ''; + + npmDepsHash = "sha256-jBAWWY12qeX2EDhUvT3TQpnQvYXRsIilRrXGpVzxYvw="; + + env.ELECTRON_SKIP_BINARY_DOWNLOAD = "1"; + + makeCacheWritable = true; + npmBuildScript = "build:cli:prod"; + + installPhase = '' + runHook preInstall + mkdir -p $out/libexec/bitwarden-directory-connector + cp -R {build-cli,node_modules} $out/libexec/bitwarden-directory-connector + runHook postInstall + ''; + + # needs to be wrapped with nodejs so that it can be executed + postInstall = '' + chmod +x $out/libexec/bitwarden-directory-connector/build-cli/bwdc.js + mkdir -p $out/bin + ln -s $out/libexec/bitwarden-directory-connector/build-cli/bwdc.js $out/bin/bitwarden-directory-connector-cli + ''; + + buildInputs = [ + libsecret + ]; + + nativeBuildInputs = [ + python3 + pkg-config + ]; + + meta = with lib; { + description = "LDAP connector for Bitwarden"; + homepage = "https://github.com/bitwarden/directory-connector"; + license = licenses.gpl3Only; + maintainers = with maintainers; [Silver-Golden]; + platforms = platforms.linux; + mainProgram = "bitwarden-directory-connector-cli"; + }; +} diff --git a/nixpkgs/pkgs/by-name/br/bruno/package.nix b/nixpkgs/pkgs/by-name/br/bruno/package.nix index 1687065fbd9b..dcacc86071b1 100644 --- a/nixpkgs/pkgs/by-name/br/bruno/package.nix +++ b/nixpkgs/pkgs/by-name/br/bruno/package.nix @@ -17,20 +17,20 @@ buildNpmPackage rec { pname = "bruno"; - version = "1.5.1"; + version = "1.6.1"; src = fetchFromGitHub { owner = "usebruno"; repo = "bruno"; rev = "v${version}"; - hash = "sha256-GgXnsPEUurPHrijf966x5ldp+1lDrgS1iBinU+EkdYU=b"; + hash = "sha256-Vf4UHN13eE9W4rekOEGAWIP3x79cVH3vI9sxuIscv8c="; postFetch = '' ${lib.getExe npm-lockfile-fix} $out/package-lock.json ''; }; - npmDepsHash = "sha256-R5dEL4QbwCSE9+HHCXlf/pYLmjCaD15tmdSSLbZgmt0="; + npmDepsHash = "sha256-pfV9omdJiozJ9VotTImfM/DRsBPNGAEzmSdj3/C//4A="; nativeBuildInputs = [ (writeShellScriptBin "phantomjs" "echo 2.1.1") diff --git a/nixpkgs/pkgs/by-name/cp/cpu-x/package.nix b/nixpkgs/pkgs/by-name/cp/cpu-x/package.nix index aacb3ea75225..8171cfc78f2b 100644 --- a/nixpkgs/pkgs/by-name/cp/cpu-x/package.nix +++ b/nixpkgs/pkgs/by-name/cp/cpu-x/package.nix @@ -16,13 +16,13 @@ stdenv.mkDerivation rec { pname = "cpu-x"; - version = "5.0.2"; + version = "5.0.3"; src = fetchFromGitHub { owner = "X0rg"; repo = "CPU-X"; rev = "v${version}"; - sha256 = "sha256-tdxIbs5jR4sQHt1ZLUmiAYszP2e5SCMqEFq+eW1k7+s="; + sha256 = "sha256-iaqqBeoack41D07Bbr0Fo1JXfF2ksXbqS5V5Ymt6Qvg="; }; nativeBuildInputs = [ cmake pkg-config wrapGAppsHook nasm makeWrapper ]; diff --git a/nixpkgs/pkgs/by-name/ki/kikit/default.nix b/nixpkgs/pkgs/by-name/ki/kikit/default.nix index 886cca973837..c32b89af37d0 100644 --- a/nixpkgs/pkgs/by-name/ki/kikit/default.nix +++ b/nixpkgs/pkgs/by-name/ki/kikit/default.nix @@ -12,7 +12,7 @@ , markdown2 , pytestCheckHook , commentjson -, wxPython_4_2 +, wxpython , pcbnew-transition , pybars3 , versioneer @@ -42,7 +42,7 @@ buildPythonApplication rec { markdown2 commentjson # https://github.com/yaqwsx/KiKit/issues/575 - wxPython_4_2 + wxpython pcbnew-transition pybars3 # https://github.com/yaqwsx/KiKit/issues/574 diff --git a/nixpkgs/pkgs/by-name/la/labwc-menu-generator/package.nix b/nixpkgs/pkgs/by-name/la/labwc-menu-generator/package.nix new file mode 100644 index 000000000000..331936ea5373 --- /dev/null +++ b/nixpkgs/pkgs/by-name/la/labwc-menu-generator/package.nix @@ -0,0 +1,53 @@ +{ lib +, stdenv +, fetchFromGitHub +, glib +, perl +, pkg-config +, unstableGitUpdater +}: + +stdenv.mkDerivation (finalAttrs: { + pname = "labwc-menu-generator"; + version = "unstable-2023-10-31"; + + src = fetchFromGitHub { + owner = "labwc"; + repo = "labwc-menu-generator"; + rev = "d7c81071f8b121ef83da32ae3fa16155d1a2ced9"; + hash = "sha256-gZ0TuSVJwcKW4orawSmRQvoCfrpb8yLXlv81qCR86MU="; + }; + + nativeBuildInputs = [ + pkg-config + ]; + + buildInputs = [ + glib + ]; + + nativeCheckInputs = [ + perl + ]; + + doCheck = true; + + strictDeps = true; + + installPhase = '' + runHook preInstall + install -Dm755 labwc-menu-generator -t $out/bin + runHook postInstall + ''; + + passthru.updateScript = unstableGitUpdater { }; + + meta = { + homepage = "https://github.com/labwc/labwc-menu-generator"; + description = "Menu generator for labwc"; + mainProgram = "labwc-menu-generator"; + license = lib.licenses.gpl2Only; + platforms = lib.platforms.unix; + maintainers = with lib.maintainers; [ AndersonTorres romildo ]; + }; +}) diff --git a/nixpkgs/pkgs/by-name/li/libgff/package.nix b/nixpkgs/pkgs/by-name/li/libgff/package.nix new file mode 100644 index 000000000000..fe3473f2e4df --- /dev/null +++ b/nixpkgs/pkgs/by-name/li/libgff/package.nix @@ -0,0 +1,30 @@ +{ lib +, stdenv +, fetchFromGitHub +, cmake +}: + +stdenv.mkDerivation (finalAttrs: { + pname = "libgff"; + version = "2.0.0"; + + src = fetchFromGitHub { + owner = "COMBINE-lab"; + repo = "libgff"; + rev = "v${finalAttrs.version}"; + hash = "sha256-ZCb3UyuB/+ykrYFQ9E5VytT65gAAULiOzIEu5IXISTc="; + }; + + nativeBuildInputs = [ cmake ]; + + meta = { + description = "A lightweight GTF/GFF parsers exposing a C++ interface"; + homepage = "https://github.com/COMBINE-lab/libgff"; + downloadPage = "https://github.com/COMBINE-lab/libgff/releases"; + changelog = "https://github.com/COMBINE-lab/libgff/releases/tag/" + + "v${finalAttrs.version}"; + license = lib.licenses.boost; + platforms = lib.platforms.all; + maintainers = [ lib.maintainers.kupac ]; + }; +}) diff --git a/nixpkgs/pkgs/by-name/li/libstaden-read/libstaden-install-config-header.patch b/nixpkgs/pkgs/by-name/li/libstaden-read/libstaden-install-config-header.patch new file mode 100644 index 000000000000..39df97a508a3 --- /dev/null +++ b/nixpkgs/pkgs/by-name/li/libstaden-read/libstaden-install-config-header.patch @@ -0,0 +1,12 @@ +diff --git a/Makefile.am b/Makefile.am +index 31286d1..2631af1 100644 +--- a/Makefile.am ++++ b/Makefile.am +@@ -61,6 +61,7 @@ man_MANS = \ + man/man4/Read.4 + + pkginclude_HEADERS = \ ++ io_lib_config.h \ + io_lib/Read.h \ + io_lib/scf_extras.h \ + io_lib/translate.h \ diff --git a/nixpkgs/pkgs/by-name/li/libstaden-read/package.nix b/nixpkgs/pkgs/by-name/li/libstaden-read/package.nix new file mode 100644 index 000000000000..dd2d93ae30a3 --- /dev/null +++ b/nixpkgs/pkgs/by-name/li/libstaden-read/package.nix @@ -0,0 +1,47 @@ +{ lib +, stdenv +, autoreconfHook +, fetchFromGitHub +, bzip2 +, xz +, zlib +}: + +stdenv.mkDerivation (finalAttrs: { + # Same name as the Debian library + pname = "libstaden-read"; + version = "1.15.0"; + + src = fetchFromGitHub { + owner = "jkbonfield"; + repo = "io_lib"; + rev = "io_lib-" + builtins.replaceStrings ["."] ["-"] finalAttrs.version; + fetchSubmodules = true; + hash = "sha256-2Dlx+MXmqar81/Xmf0oE+6lWX461EDYijiZsZf/VD28="; + }; + + patches = [ + # Needed so that the lib can be detected + ./libstaden-install-config-header.patch + ]; + + buildInputs = [ bzip2 xz zlib ]; + nativeBuildInputs = [ autoreconfHook ]; + + # autoreconfHook does not descend into htscodecs folder + preAutoreconf = '' + pushd ./htscodecs + autoreconf --install --force --verbose + pushd + ''; + + meta = { + description = "C library for reading/writing various DNA sequence formats"; + homepage = "https://staden.sourceforge.net"; + downloadPage = "https://github.com/jkbonfield/io_lib/releases"; + changelog = "https://github.com/jkbonfield/io_lib/blob/${finalAttrs.src.rev}/CHANGES"; + license = with lib.licenses; [ bsd3 free ]; + platforms = lib.platforms.all; + maintainers = [ lib.maintainers.kupac ]; + }; +}) diff --git a/nixpkgs/pkgs/by-name/me/memtree/package.nix b/nixpkgs/pkgs/by-name/me/memtree/package.nix index f69c3f8e95d3..528323624805 100644 --- a/nixpkgs/pkgs/by-name/me/memtree/package.nix +++ b/nixpkgs/pkgs/by-name/me/memtree/package.nix @@ -6,14 +6,14 @@ python3Packages.buildPythonApplication { pname = "memtree"; - version = "unstable-2023-11-22"; + version = "unstable-2024-01-04"; pyproject = true; src = fetchFromGitHub { owner = "nbraud"; repo = "memtree"; - rev = "edc09d91dcd72f175d6adc1d08b261dd95cc4fbf"; - hash = "sha256-YLZm0wjkjaTw/lHY5k4cqPXCgINe+49SGPLZq+eRdI4="; + rev = "97615952eabdc5e8e1a4bd590dd1f4971f3c5a24"; + hash = "sha256-Ifp8hwkuyBw57fGer3GbDiJaRjL4TD3hzj+ecGXWqI0="; }; nativeBuildInputs = with python3Packages; [ diff --git a/nixpkgs/pkgs/by-name/ne/neural-amp-modeler-lv2/package.nix b/nixpkgs/pkgs/by-name/ne/neural-amp-modeler-lv2/package.nix new file mode 100644 index 000000000000..a414dc2e65d4 --- /dev/null +++ b/nixpkgs/pkgs/by-name/ne/neural-amp-modeler-lv2/package.nix @@ -0,0 +1,29 @@ +{ lib +, stdenv +, fetchFromGitHub +, cmake +}: + +stdenv.mkDerivation (finalAttrs: { + pname = "neural-amp-modeler-lv2"; + version = "0.1.3"; + + src = fetchFromGitHub { + owner = "mikeoliphant"; + repo = finalAttrs.pname; + rev = finalAttrs.version; + fetchSubmodules = true; + hash = "sha256-sRZngmivNvSWcjkIqcqjjaIgXFH8aMq+/caNroXmzIk="; + }; + + nativeBuildInputs = [ + cmake + ]; + + meta = { + maintainers = [ lib.maintainers.viraptor ]; + description = "Neural Amp Modeler LV2 plugin implementation"; + homepage = finalAttrs.src.meta.homepage; + license = [ lib.licenses.gpl3 ]; + }; +}) diff --git a/nixpkgs/pkgs/by-name/ni/nixseparatedebuginfod/package.nix b/nixpkgs/pkgs/by-name/ni/nixseparatedebuginfod/package.nix new file mode 100644 index 000000000000..faacd2330d3f --- /dev/null +++ b/nixpkgs/pkgs/by-name/ni/nixseparatedebuginfod/package.nix @@ -0,0 +1,49 @@ +{ lib +, fetchFromGitHub +, rustPlatform +, libarchive +, openssl +, sqlite +, pkg-config +, nixosTests +}: + +rustPlatform.buildRustPackage rec { + pname = "nixseparatedebuginfod"; + version = "0.3.2"; + + src = fetchFromGitHub { + owner = "symphorien"; + repo = "nixseparatedebuginfod"; + rev = "v${version}"; + hash = "sha256-XSEHNoc3h21foVeR28KgfiBTRHyUh+GJ52LMD2xFHfA="; + }; + + cargoHash = "sha256-t6W6siHuga/T9kmanA735zH2i9eCOT7vD6v7E5LIp9k="; + + # tests need a working nix install with access to the internet + doCheck = false; + + buildInputs = [ + libarchive + openssl + sqlite + ]; + + nativeBuildInputs = [ pkg-config ]; + + passthru = { + tests = { + inherit (nixosTests) nixseparatedebuginfod; + }; + }; + + meta = with lib; { + description = "Downloads and provides debug symbols and source code for nix derivations to gdb and other debuginfod-capable debuggers as needed"; + homepage = "https://github.com/symphorien/nixseparatedebuginfod"; + license = licenses.gpl3Only; + maintainers = [ maintainers.symphorien ]; + platforms = platforms.linux; + mainProgram = "nixseparatedebuginfod"; + }; +} diff --git a/nixpkgs/pkgs/by-name/qr/qrtool/package.nix b/nixpkgs/pkgs/by-name/qr/qrtool/package.nix index 306950a51532..79791ddb0ca2 100644 --- a/nixpkgs/pkgs/by-name/qr/qrtool/package.nix +++ b/nixpkgs/pkgs/by-name/qr/qrtool/package.nix @@ -8,16 +8,16 @@ rustPlatform.buildRustPackage rec { pname = "qrtool"; - version = "0.10.1"; + version = "0.10.2"; src = fetchFromGitHub { owner = "sorairolake"; repo = "qrtool"; rev = "v${version}"; - sha256 = "sha256-96k3VgxVGuKPLA4rD9B20AigFW03YvedT04UUzzmX38="; + sha256 = "sha256-caQoV0qAj2VXbEaYHsGOqCZCVyb4s1JJbBl7H0X5xEI="; }; - cargoHash = "sha256-nAfW66vasnR0JHhz7n1XGA+OpPavOnGB6D6TfK9cr9Y="; + cargoHash = "sha256-V9TopADUGBR0MdOTIq1Tiee3NEzLa76zRq5bjULoLVI="; nativeBuildInputs = [ asciidoctor installShellFiles ]; diff --git a/nixpkgs/pkgs/by-name/sa/salmon/fetch-pufferfish.patch b/nixpkgs/pkgs/by-name/sa/salmon/fetch-pufferfish.patch new file mode 100644 index 000000000000..7010a1a69fac --- /dev/null +++ b/nixpkgs/pkgs/by-name/sa/salmon/fetch-pufferfish.patch @@ -0,0 +1,60 @@ +diff --git a/scripts/fetchPufferfish.sh b/scripts/fetchPufferfish.sh +index bf2574e0..42582806 100755 +--- a/scripts/fetchPufferfish.sh ++++ b/scripts/fetchPufferfish.sh +@@ -11,10 +11,6 @@ CURR_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd ) + EXTERNAL_DIR=${CURR_DIR}/../external + INSTALL_DIR=${CURR_DIR}/../external/install + +-if [ -d ${EXTERNAL_DIR}/pufferfish ] ; then +- rm -fr ${EXTERNAL_DIR}/pufferfish +-fi +- + if [ -d ${INSTALL_DIR}/include/pufferfish ] ; then + rm -fr ${INSTALL_DIR}/include/pufferfish + fi +@@ -23,42 +19,10 @@ if [ -d ${INSTALL_DIR}/src/pufferfish ] ; then + rm -fr ${INSTALL_DIR}/src/pufferfish + fi + +-SVER=salmon-v1.10.2 +-#SVER=develop +-#SVER=sketch-mode +- +-EXPECTED_SHA256=f225b74833f71dcf767a565345224357fb091f90ce79717abc836814d9ccd101 +- +-mkdir -p ${EXTERNAL_DIR} +-curl -k -L https://github.com/COMBINE-lab/pufferfish/archive/${SVER}.zip -o ${EXTERNAL_DIR}/pufferfish.zip +- +-hashcheck="" +-if exists sha256sum; then +- hashcheck="sha256sum" +-elif exists shasum; then +- hashcheck="shasum -a256" +-else +- unset hashcheck +-fi +- +- +-if [ -z "${hashcheck-}" ]; then +- echo "Couldn't find shasum command; can't verify contents of downloaded pufferfish"; +-else +- +- if [[ $SVER != develop && $SVER != onetbb ]]; then +- echo "${EXPECTED_SHA256} ${EXTERNAL_DIR}/pufferfish.zip" | ${hashcheck} -c - || { echo "pufferfish.zip did not match expected SHA1! Exiting."; exit 1; } +- else +- echo "not testing sha since pulling from develop" +- fi +-fi +- +- +-rm -fr ${EXTERNAL_DIR}/pufferfish +-unzip ${EXTERNAL_DIR}/pufferfish.zip -d ${EXTERNAL_DIR} +-mv ${EXTERNAL_DIR}/pufferfish-${SVER} ${EXTERNAL_DIR}/pufferfish + + mkdir -p ${INSTALL_DIR}/include/pufferfish ++# This is needed later when pufferfish is compiled for Salmon ++cp -r ${pufferFishSrc} ${EXTERNAL_DIR}/pufferfish + + cp ${EXTERNAL_DIR}/pufferfish/include/ProgOpts.hpp ${INSTALL_DIR}/include/pufferfish + cp ${EXTERNAL_DIR}/pufferfish/include/BooPHF.hpp ${INSTALL_DIR}/include/pufferfish diff --git a/nixpkgs/pkgs/by-name/sa/salmon/package.nix b/nixpkgs/pkgs/by-name/sa/salmon/package.nix new file mode 100644 index 000000000000..e4442e96fd6f --- /dev/null +++ b/nixpkgs/pkgs/by-name/sa/salmon/package.nix @@ -0,0 +1,84 @@ +{ lib +, stdenv +, autoreconfHook +, bash +, boost +, bzip2 +, cereal_1_3_2 +, cmake +, curl +, fetchFromGitHub +, jemalloc +, libgff +, libiconv +, libstaden-read +, pkg-config +, tbb_2021_8 +, xz +, zlib +}: + +stdenv.mkDerivation (finalAttrs: { + pname = "salmon"; + version = "1.10.2"; + + pufferFishSrc = fetchFromGitHub { + owner = "COMBINE-lab"; + repo = "pufferfish"; + rev = "salmon-v${finalAttrs.version}"; + hash = "sha256-JKbUFBEsqnENl4vFqve1FCd4TI3n9bRi2RNHC8QGQGc="; + }; + + src = fetchFromGitHub { + owner = "COMBINE-lab"; + repo = "salmon"; + rev = "v${finalAttrs.version}"; + hash = "sha256-kwqoUmVCqjr/xRxJjQKaFjjCQW+MFASHJ2f9OiAumNU="; + }; + + patches = [ + # Use pufferfish source fetched by nix + ./fetch-pufferfish.patch + ]; + + postPatch = "patchShebangs ."; + + buildInputs = [ + (boost.override { enableShared = false; enabledStatic = true; }) + bzip2 + cereal_1_3_2 + curl + jemalloc + libgff + libstaden-read + tbb_2021_8 + xz + zlib + ] ++ lib.optionals stdenv.isDarwin [ libiconv ]; + + nativeBuildInputs = [ cmake pkg-config ]; + + strictDeps = true; + + meta = { + description = + "Tool for quantifying the expression of transcripts using RNA-seq data"; + longDescription = '' + Salmon is a tool for quantifying the expression of transcripts + using RNA-seq data. Salmon uses new algorithms (specifically, + coupling the concept of quasi-mapping with a two-phase inference + procedure) to provide accurate expression estimates very quickly + and while using little memory. Salmon performs its inference using + an expressive and realistic model of RNA-seq data that takes into + account experimental attributes and biases commonly observed in + real RNA-seq data. + ''; + homepage = "https://combine-lab.github.io/salmon"; + downloadPage = "https://github.com/COMBINE-lab/salmon/releases"; + changelog = "https://github.com/COMBINE-lab/salmon/releases/tag/" + + "v${finalAttrs.version}"; + license = lib.licenses.gpl3Only; + platforms = lib.platforms.all; + maintainers = [ lib.maintainers.kupac ]; + }; +}) |