diff options
Diffstat (limited to 'nixpkgs/pkgs/applications/science')
57 files changed, 315 insertions, 198 deletions
diff --git a/nixpkgs/pkgs/applications/science/astronomy/gpredict/default.nix b/nixpkgs/pkgs/applications/science/astronomy/gpredict/default.nix index 56c5a92460dd..467f478da96b 100644 --- a/nixpkgs/pkgs/applications/science/astronomy/gpredict/default.nix +++ b/nixpkgs/pkgs/applications/science/astronomy/gpredict/default.nix @@ -1,6 +1,6 @@ { lib, stdenv, fetchurl, fetchpatch, pkg-config, intltool , gtk3, glib, curl, goocanvas2, gpsd -, hamlib, wrapGAppsHook +, hamlib, wrapGAppsHook3 }: let @@ -24,7 +24,7 @@ in stdenv.mkDerivation { }) ]; - nativeBuildInputs = [ pkg-config intltool wrapGAppsHook ]; + nativeBuildInputs = [ pkg-config intltool wrapGAppsHook3 ]; buildInputs = [ curl glib gtk3 goocanvas2 gpsd hamlib ]; meta = with lib; { diff --git a/nixpkgs/pkgs/applications/science/astronomy/phd2/default.nix b/nixpkgs/pkgs/applications/science/astronomy/phd2/default.nix index 9c66df83dd4b..b463a2845bdc 100644 --- a/nixpkgs/pkgs/applications/science/astronomy/phd2/default.nix +++ b/nixpkgs/pkgs/applications/science/astronomy/phd2/default.nix @@ -1,5 +1,5 @@ { lib, stdenv, fetchFromGitHub, pkg-config, cmake, gtk3, wxGTK32 -, curl, gettext, glib, indi-full, libnova, wrapGAppsHook }: +, curl, gettext, glib, indi-full, libnova, wrapGAppsHook3 }: stdenv.mkDerivation rec { pname = "phd2"; @@ -15,7 +15,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ cmake pkg-config - wrapGAppsHook + wrapGAppsHook3 ]; buildInputs = [ diff --git a/nixpkgs/pkgs/applications/science/astronomy/siril/default.nix b/nixpkgs/pkgs/applications/science/astronomy/siril/default.nix index 255927d893d2..569d53717254 100644 --- a/nixpkgs/pkgs/applications/science/astronomy/siril/default.nix +++ b/nixpkgs/pkgs/applications/science/astronomy/siril/default.nix @@ -1,43 +1,38 @@ -{ lib, stdenv, fetchFromGitLab, fetchpatch, pkg-config, meson, ninja, cmake +{ lib, stdenv, fetchFromGitLab, pkg-config, meson, ninja, cmake , git, criterion, gtk3, libconfig, gnuplot, opencv, json-glib , fftwFloat, cfitsio, gsl, exiv2, librtprocess, wcslib, ffmpeg -, libraw, libtiff, libpng, libjpeg, libheif, ffms, wrapGAppsHook +, libraw, libtiff, libpng, libjpeg, libheif, ffms, wrapGAppsHook3 +, curl }: stdenv.mkDerivation rec { pname = "siril"; - version = "1.2.0"; + version = "1.2.1"; src = fetchFromGitLab { owner = "free-astro"; repo = "siril"; rev = version; - hash = "sha256-lCoFQ7z6cZbyNPEm5s40DNdvTwFonHK3KCd8RniqQWs="; + hash = "sha256-njvByA8nbG3qHKfv8eX20TrIhngVI0nzIHmhYIN6htE="; }; - patches = [ - (fetchpatch { - name = "siril-1.2-exiv2-0.28.patch"; - url = "https://gitweb.gentoo.org/repo/gentoo.git/plain/sci-astronomy/siril/files/siril-1.2-exiv2-0.28.patch?id=002882203ad6a2b08ce035a18b95844a9f4b85d0"; - hash = "sha256-R1yslW6hzvJHKo0/IqBxkCuqcX6VrdRSz68gpAExxVE="; - }) - ]; - nativeBuildInputs = [ - meson ninja cmake pkg-config git criterion wrapGAppsHook + meson ninja cmake pkg-config git criterion wrapGAppsHook3 ]; buildInputs = [ gtk3 cfitsio gsl exiv2 gnuplot opencv fftwFloat librtprocess wcslib libconfig libraw libtiff libpng libjpeg libheif ffms ffmpeg json-glib + curl ]; # Necessary because project uses default build dir for flatpaks/snaps dontUseMesonConfigure = true; dontUseCmakeConfigure = true; + # Meson fails to find libcurl unless the option is specifically enabled configureScript = '' - ${meson}/bin/meson --buildtype release nixbld . + ${meson}/bin/meson setup -Denable-libcurl=yes --buildtype release nixbld . ''; postConfigure = '' diff --git a/nixpkgs/pkgs/applications/science/astronomy/stellarium/default.nix b/nixpkgs/pkgs/applications/science/astronomy/stellarium/default.nix index 35d6bd8aba92..687c0b3a2dda 100644 --- a/nixpkgs/pkgs/applications/science/astronomy/stellarium/default.nix +++ b/nixpkgs/pkgs/applications/science/astronomy/stellarium/default.nix @@ -4,7 +4,7 @@ , fetchpatch , cmake , perl -, wrapGAppsHook +, wrapGAppsHook3 , wrapQtAppsHook , qtbase , qtcharts @@ -52,7 +52,7 @@ stdenv.mkDerivation (finalAttrs: { nativeBuildInputs = [ cmake perl - wrapGAppsHook + wrapGAppsHook3 wrapQtAppsHook qttools ]; diff --git a/nixpkgs/pkgs/applications/science/biology/conglomerate/default.nix b/nixpkgs/pkgs/applications/science/biology/conglomerate/default.nix index d9092b9eeb11..0d140914638e 100644 --- a/nixpkgs/pkgs/applications/science/biology/conglomerate/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/conglomerate/default.nix @@ -1,20 +1,47 @@ -{ lib, stdenv, fetchFromGitHub, cmake, coreutils, perlPackages, bicpl, libminc, zlib, minc_tools, - makeWrapper }: +{ + lib, + stdenv, + fetchFromGitHub, + cmake, + coreutils, + perlPackages, + bicpl, + libminc, + zlib, + minc_tools, + makeWrapper, +}: stdenv.mkDerivation rec { pname = "conglomerate"; - version = "unstable-2017-09-10"; + version = "unstable-2023-01-19"; src = fetchFromGitHub { - owner = "BIC-MNI"; - repo = pname; - rev = "7343238bc6215942c7ecc885a224f24433a291b0"; - sha256 = "1mlqgmy3jc13bv7d01rjwldxq0p4ayqic85xcl222hhifi3w2prr"; + owner = "BIC-MNI"; + repo = pname; + rev = "6fb26084f2871a85044e2e4afc868982702b40ed"; + hash = "sha256-Inr4b2bxguzkcRQBURObsQQ0Rb3H/Zz6hEzNRd+IX3w="; }; - nativeBuildInputs = [ cmake makeWrapper ]; - buildInputs = [ libminc zlib bicpl ]; - propagatedBuildInputs = [ coreutils minc_tools ] ++ (with perlPackages; [ perl GetoptTabular MNI-Perllib ]); + nativeBuildInputs = [ + cmake + makeWrapper + ]; + buildInputs = [ + libminc + zlib + bicpl + ]; + propagatedBuildInputs = + [ + coreutils + minc_tools + ] + ++ (with perlPackages; [ + perl + GetoptTabular + MNI-Perllib + ]); cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake" @@ -23,15 +50,20 @@ stdenv.mkDerivation rec { postFixup = '' for p in $out/bin/*; do - wrapProgram $p --prefix PERL5LIB : $PERL5LIB --set PATH "${lib.makeBinPath [ coreutils minc_tools ]}"; + wrapProgram $p --prefix PERL5LIB : $PERL5LIB --set PATH "${ + lib.makeBinPath [ + coreutils + minc_tools + ] + }"; done ''; - meta = with lib; { + meta = { homepage = "https://github.com/BIC-MNI/conglomerate"; description = "More command-line utilities for working with MINC files"; - maintainers = with maintainers; [ bcdarwin ]; - platforms = platforms.unix; - license = licenses.hpndUc; + maintainers = with lib.maintainers; [ bcdarwin ]; + platforms = lib.platforms.unix; + license = lib.licenses.hpndUc; }; } diff --git a/nixpkgs/pkgs/applications/science/biology/dssp/default.nix b/nixpkgs/pkgs/applications/science/biology/dssp/default.nix index 6c7157a91764..56eb023805a3 100644 --- a/nixpkgs/pkgs/applications/science/biology/dssp/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/dssp/default.nix @@ -3,39 +3,20 @@ , cmake , eigen , fetchFromGitHub -, fetchpatch , libcifpp , libmcfp , zlib }: -let - libcifpp' = libcifpp.overrideAttrs (oldAttrs: { - # dssp 4.4.3 requires specific version "5.2.0" of libcifpp - version = "5.2.0"; - src = fetchFromGitHub { - inherit (oldAttrs.src) owner repo rev; - hash = "sha256-Sj10j6HxUoUvQ66cd2B8CO7CVBRd7w9CTovxkwPDOvs="; - }; - patches = [ - (fetchpatch { - # https://github.com/PDB-REDO/libcifpp/issues/51 - name = "fix-build-on-darwin.patch"; - url = "https://github.com/PDB-REDO/libcifpp/commit/641f06a7e7c0dc54af242b373820f2398f59e7ac.patch"; - hash = "sha256-eWNfp9nA/+2J6xjZR6Tj+5OM3L5MxdfRi0nBzyaqvS0="; - }) - ]; - }); -in stdenv.mkDerivation (finalAttrs: { pname = "dssp"; - version = "4.4.5"; + version = "4.4.7"; src = fetchFromGitHub { owner = "PDB-REDO"; repo = "dssp"; rev = "refs/tags/v${finalAttrs.version}"; - hash = "sha256-X0aMWqoMhmQVRHWKVm2S6JAOYiBuBBMzMoivMdpNx0M="; + hash = "sha256-qePoZYkzzWuK6j1NM+q6fPuWVRDEe4OkPmXc9Nbqobo="; }; nativeBuildInputs = [ @@ -44,7 +25,7 @@ stdenv.mkDerivation (finalAttrs: { buildInputs = [ eigen - libcifpp' + libcifpp libmcfp zlib ]; diff --git a/nixpkgs/pkgs/applications/science/biology/igv/default.nix b/nixpkgs/pkgs/applications/science/biology/igv/default.nix index ba0114c7b563..219792326b68 100644 --- a/nixpkgs/pkgs/applications/science/biology/igv/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/igv/default.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, fetchzip, jdk17, testers, wrapGAppsHook, igv }: +{ lib, stdenv, fetchzip, jdk17, testers, wrapGAppsHook3, igv }: stdenv.mkDerivation rec { pname = "igv"; @@ -24,7 +24,7 @@ stdenv.mkDerivation rec { chmod +x $out/bin/igv chmod +x $out/bin/igvtools ''; - nativeBuildInputs = [ wrapGAppsHook ]; + nativeBuildInputs = [ wrapGAppsHook3 ]; passthru.tests.version = testers.testVersion { package = igv; diff --git a/nixpkgs/pkgs/applications/science/biology/iqtree/default.nix b/nixpkgs/pkgs/applications/science/biology/iqtree/default.nix index d8e90789f4d5..4dfbaa25b36a 100644 --- a/nixpkgs/pkgs/applications/science/biology/iqtree/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/iqtree/default.nix @@ -10,13 +10,13 @@ stdenv.mkDerivation rec { pname = "iqtree"; - version = "2.3.2"; + version = "2.3.4"; src = fetchFromGitHub { owner = "iqtree"; repo = "iqtree2"; rev = "v${version}"; - hash = "sha256-hAJs48PhIyZSKSRZjQJKQwoJlt6DPRQwaDsuZ00VZII="; + hash = "sha256-dnUFllqcABB3JDYoCwPGtIYD/h5lzX2XKOroDpijPpU="; fetchSubmodules = true; }; diff --git a/nixpkgs/pkgs/applications/science/biology/jbrowse/default.nix b/nixpkgs/pkgs/applications/science/biology/jbrowse/default.nix index c4c8966aa50d..c1025d0b1919 100644 --- a/nixpkgs/pkgs/applications/science/biology/jbrowse/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/jbrowse/default.nix @@ -1,12 +1,12 @@ -{ lib, fetchurl, appimageTools, wrapGAppsHook }: +{ lib, fetchurl, appimageTools, wrapGAppsHook3 }: let pname = "jbrowse"; - version = "2.5.0"; + version = "2.11.1"; src = fetchurl { url = "https://github.com/GMOD/jbrowse-components/releases/download/v${version}/jbrowse-desktop-v${version}-linux.AppImage"; - sha256 = "sha256-YLsyA+RVoFvjE4MfAtglJYdUgic487SxwdUhvolzBPc="; + sha256 = "sha256-/1QNpoJy4u2sSw6907UQpdYX9aFWp31BxsYVTQoDpi4="; }; appimageContents = appimageTools.extractType2 { diff --git a/nixpkgs/pkgs/applications/science/biology/messer-slim/default.nix b/nixpkgs/pkgs/applications/science/biology/messer-slim/default.nix index d463b4fe5366..af3856f04167 100644 --- a/nixpkgs/pkgs/applications/science/biology/messer-slim/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/messer-slim/default.nix @@ -1,14 +1,14 @@ { lib, stdenv, fetchFromGitHub, cmake, gcc, gcc-unwrapped }: stdenv.mkDerivation rec { - version = "4.2.1"; + version = "4.2.2"; pname = "messer-slim"; src = fetchFromGitHub { owner = "MesserLab"; repo = "SLiM"; rev = "v${version}"; - sha256 = "sha256-ba5I/bsDNAhDb1Kq0lWTC6YgpZ1PpeHPmB/vXx/JRK0="; + sha256 = "sha256-TlB7Hj4pVN4p4VanACWjQBeTxP9/DvRvdCdgelrXx60="; }; nativeBuildInputs = [ cmake gcc gcc-unwrapped ]; diff --git a/nixpkgs/pkgs/applications/science/biology/migrate/default.nix b/nixpkgs/pkgs/applications/science/biology/migrate/default.nix index 31e4eb2fcb42..7820f177bfb7 100644 --- a/nixpkgs/pkgs/applications/science/biology/migrate/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/migrate/default.nix @@ -1,18 +1,31 @@ -{ stdenv, lib, gccStdenv, fetchurl, zlib, mpi }: +{ + stdenv, + lib, + fetchurl, + zlib, + mpi, +}: -gccStdenv.mkDerivation rec { - version = "3.7.2"; +stdenv.mkDerivation (finalAttrs: { + version = "5.0.6"; pname = "migrate"; src = fetchurl { - url = "https://peterbeerli.com/migrate-html5/download_version3/${pname}-${version}.src.tar.gz"; - sha256 = "1p2364ffjc56i82snzvjpy6pkf6wvqwvlvlqxliscx2c303fxs8v"; + url = "https://peterbeerli.com/migrate-html5/download_version4/${finalAttrs.pname}-${finalAttrs.version}.src.tar.gz"; + hash = "sha256-twkoR9L6VPUye12OC0B5w0PxcxyKain6RkhCswLEdwg="; }; - buildInputs = [ zlib mpi ]; - setSourceRoot = "sourceRoot=$(echo */src)"; - buildFlags = [ "thread" "mpis" ]; - preInstall = "mkdir -p $out/man/man1"; + sourceRoot = "migrate-${finalAttrs.version}/src"; + + buildInputs = [ + zlib + mpi + ]; + + buildFlags = [ + "thread" + "mpis" + ]; meta = with lib; { broken = stdenv.isDarwin; @@ -21,5 +34,6 @@ gccStdenv.mkDerivation rec { license = licenses.mit; maintainers = [ maintainers.bzizou ]; platforms = platforms.unix; + mainProgram = "migrate-n"; }; -} +}) diff --git a/nixpkgs/pkgs/applications/science/biology/seqkit/default.nix b/nixpkgs/pkgs/applications/science/biology/seqkit/default.nix index 5c46e25f5d6d..0fbda84ccea7 100644 --- a/nixpkgs/pkgs/applications/science/biology/seqkit/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/seqkit/default.nix @@ -5,13 +5,13 @@ buildGoModule rec { pname = "seqkit"; - version = "2.8.1"; + version = "2.8.2"; src = fetchFromGitHub { owner = "shenwei356"; repo = "seqkit"; rev = "v${version}"; - sha256 = "sha256-LtPf99spy2ByTnSMJ5k1mWkh+Nct3Fg4Y9mXARxuXlA="; + sha256 = "sha256-jCzd36ds9YVBpnyR3gDJSX3CCVXzC9WkQWmkcDiDWfM="; }; vendorHash = "sha256-0//kySYhNmfiwiys/Ku0/8RzKpnxO0+byD8pcIkvDY0="; diff --git a/nixpkgs/pkgs/applications/science/chemistry/chemtool/default.nix b/nixpkgs/pkgs/applications/science/chemistry/chemtool/default.nix index fe2d658b5a44..82b183467161 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/chemtool/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/chemtool/default.nix @@ -5,7 +5,7 @@ , libX11 , gtk2 , fig2dev -, wrapGAppsHook +, wrapGAppsHook3 }: stdenv.mkDerivation rec { @@ -17,7 +17,7 @@ stdenv.mkDerivation rec { sha256 = "hhYaBGE4azNKX/sXzfCUpJGUGIRngnL0V0mBNRTdr8s="; }; - nativeBuildInputs = [ pkg-config wrapGAppsHook ]; + nativeBuildInputs = [ pkg-config wrapGAppsHook3 ]; buildInputs = [ libX11 gtk2 diff --git a/nixpkgs/pkgs/applications/science/chemistry/cp2k/default.nix b/nixpkgs/pkgs/applications/science/chemistry/cp2k/default.nix index 42bfc6ffe32e..8a831fe23b74 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/cp2k/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/cp2k/default.nix @@ -64,6 +64,12 @@ stdenv.mkDerivation rec { fetchSubmodules = true; }; + patches = [ + # Remove the build command line from the source. + # This avoids dependencies to .dev inputs + ./remove-compiler-options.patch + ]; + nativeBuildInputs = [ python3 which openssh makeWrapper pkg-config ] ++ lib.optional (gpuBackend == "cuda") cudaPackages.cuda_nvcc; @@ -75,6 +81,7 @@ stdenv.mkDerivation rec { libvori libxc libxsmm + mpi spglib scalapack blas @@ -101,7 +108,7 @@ stdenv.mkDerivation rec { ] ; - propagatedBuildInputs = [ mpi ]; + propagatedBuildInputs = [ (lib.getBin mpi) ]; propagatedUserEnvPkgs = [ mpi ]; makeFlags = [ @@ -149,14 +156,16 @@ stdenv.mkDerivation rec { -D__PLUMED2 -D__HDF5 -D__GSL -D__SIRIUS -D__LIBVDWXC -D__SPFFT -D__SPLA \ ${lib.strings.optionalString (gpuBackend == "cuda") "-D__OFFLOAD_CUDA -D__ACC -D__DBCSR_ACC -D__NO_OFFLOAD_PW"} \ ${lib.strings.optionalString (gpuBackend == "rocm") "-D__OFFLOAD_HIP -D__DBCSR_ACC -D__NO_OFFLOAD_PW"} - CFLAGS = -fopenmp -I${lib.getDev hdf5-fortran}/include -I${lib.getDev gsl}/include + CFLAGS = -fopenmp FCFLAGS = \$(DFLAGS) -O2 -ffree-form -ffree-line-length-none \ -ftree-vectorize -funroll-loops -msse2 \ -std=f2008 \ -fopenmp -ftree-vectorize -funroll-loops \ - -I${lib.getDev libint}/include ${lib.optionalString enableElpa "$(pkg-config --variable=fcflags elpa)"} \ + ${lib.optionalString enableElpa "$(pkg-config --variable=fcflags elpa)"} \ + -I${lib.getDev libint}/include \ -I${lib.getDev sirius}/include/sirius \ - -I${lib.getDev libxc}/include -I${lib.getDev libxsmm}/include \ + -I${lib.getDev libxc}/include \ + -I${lib.getDev libxsmm}/include \ -I${lib.getDev hdf5-fortran}/include \ -fallow-argument-mismatch LIBS = -lfftw3 -lfftw3_threads \ diff --git a/nixpkgs/pkgs/applications/science/chemistry/cp2k/remove-compiler-options.patch b/nixpkgs/pkgs/applications/science/chemistry/cp2k/remove-compiler-options.patch new file mode 100644 index 000000000000..e6cf81494aa3 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/chemistry/cp2k/remove-compiler-options.patch @@ -0,0 +1,37 @@ +diff --git a/src/start/cp2k.F b/src/start/cp2k.F +index f69146ea3..a195f0620 100644 +--- a/src/start/cp2k.F ++++ b/src/start/cp2k.F +@@ -58,8 +58,7 @@ PROGRAM cp2k + USE input_cp2k, ONLY: create_cp2k_root_section + USE input_section_types, ONLY: section_release,& + section_type +- USE iso_fortran_env, ONLY: compiler_options,& +- compiler_version ++ USE iso_fortran_env, ONLY: compiler_version + USE kinds, ONLY: default_path_length + USE machine, ONLY: default_output_unit + #include "../base/base_uses.f90" +@@ -70,7 +69,6 @@ PROGRAM cp2k + arg_att, command + CHARACTER(LEN=default_path_length), & + DIMENSION(:, :), ALLOCATABLE :: initial_variables, initial_variables_tmp +- CHARACTER(LEN=:), ALLOCATABLE :: compiler_options_string + INTEGER :: output_unit, l, i, var_set_sep, inp_var_idx + INTEGER :: ierr, i_arg + LOGICAL :: check, usage, echo_input, command_line_error +@@ -328,14 +326,6 @@ PROGRAM cp2k + WRITE (output_unit, "(T2,A)") cp2k_version, & + "Source code revision "//TRIM(compile_revision), & + TRIM(cp2k_flags()) +- compiler_options_string = compiler_options() +- WRITE (output_unit, "(T2,A,A)") "compiler: ", compiler_version() +- WRITE (output_unit, "(T2,A)") "compiler options:" +- DO i = 0, (LEN(compiler_options_string) - 1)/68 +- WRITE (output_unit, "(T4,A)") & +- compiler_options_string(i*68 + 1:MIN(LEN(compiler_options_string), (i + 1)*68)) +- END DO +- DEALLOCATE (compiler_options_string) + END IF + END IF + diff --git a/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix b/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix index ee3ab5f1f3a5..bafbeb3529c6 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix @@ -25,14 +25,14 @@ let }; in stdenv.mkDerivation rec { - version = "16.1.63"; + version = "16.2.15"; pname = "jmol"; src = let baseVersion = "${lib.versions.major version}.${lib.versions.minor version}"; in fetchurl { url = "mirror://sourceforge/jmol/Jmol/Version%20${baseVersion}/Jmol%20${version}/Jmol-${version}-binary.tar.gz"; - hash = "sha256-zUX3msosz0LNQJuEUbFgT32Hw0Wq4CgW1iHMkvReysU="; + hash = "sha256-zPHh5IFdttliPc0SCgkM/3UQmS4eT2rfi5HqpFjY5hA="; }; patchPhase = '' diff --git a/nixpkgs/pkgs/applications/science/chemistry/octopus/default.nix b/nixpkgs/pkgs/applications/science/chemistry/octopus/default.nix index a3a385802aaa..2e87cf3db51a 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/octopus/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/octopus/default.nix @@ -30,13 +30,13 @@ assert (blas.isILP64 == arpack.isILP64); stdenv.mkDerivation rec { pname = "octopus"; - version = "14.0"; + version = "14.1"; src = fetchFromGitLab { owner = "octopus-code"; repo = "octopus"; rev = version; - sha256 = "sha256-wQ2I+10ZHLKamW3j6AUtq2KZVm6d29+JxYgwvBKz9DU="; + sha256 = "sha256-8wZR+bYdxJFsUPMWbIGYxRdNzjLgHm+KFLjY7fSN7io="; }; nativeBuildInputs = [ diff --git a/nixpkgs/pkgs/applications/science/electronics/gtkwave/default.nix b/nixpkgs/pkgs/applications/science/electronics/gtkwave/default.nix index 584f59ba8b47..3e0f3613ba90 100644 --- a/nixpkgs/pkgs/applications/science/electronics/gtkwave/default.nix +++ b/nixpkgs/pkgs/applications/science/electronics/gtkwave/default.nix @@ -10,7 +10,7 @@ , stdenv , tcl , tk -, wrapGAppsHook +, wrapGAppsHook3 , xz }: @@ -23,7 +23,7 @@ stdenv.mkDerivation rec { sha256 = "sha256-6rPgnnZBEVwHhIv7MPfdDDu+K4y+RQF+leB327pqwDg="; }; - nativeBuildInputs = [ pkg-config wrapGAppsHook ]; + nativeBuildInputs = [ pkg-config wrapGAppsHook3 ]; buildInputs = [ bzip2 glib gperf gtk3 judy tcl tk xz ] ++ lib.optional stdenv.isDarwin gtk-mac-integration; diff --git a/nixpkgs/pkgs/applications/science/electronics/horizon-eda/base.nix b/nixpkgs/pkgs/applications/science/electronics/horizon-eda/base.nix index 8ce75a6ce241..2a37c0265dc3 100644 --- a/nixpkgs/pkgs/applications/science/electronics/horizon-eda/base.nix +++ b/nixpkgs/pkgs/applications/science/electronics/horizon-eda/base.nix @@ -9,12 +9,14 @@ , libgit2 , librsvg , libuuid -, opencascade-occt +, opencascade-occt_7_6 , pkg-config , podofo , sqlite }: - +let + opencascade-occt = opencascade-occt_7_6; +in # This base is used in horizon-eda and python3Packages.horizon-eda rec { pname = "horizon-eda"; diff --git a/nixpkgs/pkgs/applications/science/electronics/horizon-eda/default.nix b/nixpkgs/pkgs/applications/science/electronics/horizon-eda/default.nix index 1fbc92f06115..40a91937f07f 100644 --- a/nixpkgs/pkgs/applications/science/electronics/horizon-eda/default.nix +++ b/nixpkgs/pkgs/applications/science/electronics/horizon-eda/default.nix @@ -4,7 +4,7 @@ , coreutils , libspnav , python3 -, wrapGAppsHook +, wrapGAppsHook3 }: let @@ -24,7 +24,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = base.nativeBuildInputs ++ [ boost.dev - wrapGAppsHook + wrapGAppsHook3 python3 ]; diff --git a/nixpkgs/pkgs/applications/science/electronics/kicad/base.nix b/nixpkgs/pkgs/applications/science/electronics/kicad/base.nix index 209d47875f8d..b5f721c3d772 100644 --- a/nixpkgs/pkgs/applications/science/electronics/kicad/base.nix +++ b/nixpkgs/pkgs/applications/science/electronics/kicad/base.nix @@ -42,7 +42,7 @@ , swig4 , python , wxPython -, opencascade-occt +, opencascade-occt_7_6 , libngspice , valgrind @@ -65,6 +65,7 @@ assert testing -> !stable -> throw "testing implies stable and cannot be used with stable = false"; let + opencascade-occt = opencascade-occt_7_6; inherit (lib) optional optionals optionalString; in stdenv.mkDerivation rec { diff --git a/nixpkgs/pkgs/applications/science/electronics/kicad/default.nix b/nixpkgs/pkgs/applications/science/electronics/kicad/default.nix index 99670eee8a46..1cec011fae33 100644 --- a/nixpkgs/pkgs/applications/science/electronics/kicad/default.nix +++ b/nixpkgs/pkgs/applications/science/electronics/kicad/default.nix @@ -193,14 +193,14 @@ stdenv.mkDerivation rec { "${symbols}/share/kicad/template" ]; }; - # We are emulating wrapGAppsHook, along with other variables to the wrapper + # We are emulating wrapGAppsHook3, along with other variables to the wrapper makeWrapperArgs = with passthru.libraries; [ "--prefix XDG_DATA_DIRS : ${base}/share" "--prefix XDG_DATA_DIRS : ${hicolor-icon-theme}/share" "--prefix XDG_DATA_DIRS : ${gnome.adwaita-icon-theme}/share" "--prefix XDG_DATA_DIRS : ${gtk3}/share/gsettings-schemas/${gtk3.name}" "--prefix XDG_DATA_DIRS : ${gsettings-desktop-schemas}/share/gsettings-schemas/${gsettings-desktop-schemas.name}" - # wrapGAppsHook did these two as well, no idea if it matters... + # wrapGAppsHook3 did these two as well, no idea if it matters... "--prefix XDG_DATA_DIRS : ${cups}/share" "--prefix GIO_EXTRA_MODULES : ${dconf}/lib/gio/modules" # required to open a bug report link in firefox-wayland diff --git a/nixpkgs/pkgs/applications/science/electronics/nvc/default.nix b/nixpkgs/pkgs/applications/science/electronics/nvc/default.nix index 9bab9991baf8..62b62ff15faa 100644 --- a/nixpkgs/pkgs/applications/science/electronics/nvc/default.nix +++ b/nixpkgs/pkgs/applications/science/electronics/nvc/default.nix @@ -15,13 +15,13 @@ stdenv.mkDerivation rec { pname = "nvc"; - version = "1.12.0"; + version = "1.12.2"; src = fetchFromGitHub { owner = "nickg"; repo = "nvc"; rev = "r${version}"; - hash = "sha256-7g4Ki5lhmX/13XCv0on1PgvEthCTfe9wh8EFjMcP1+c="; + hash = "sha256-9nqho+iDqy8oQLSxBppXoafzEuS6AkcUuqEY3xxfFs4="; }; nativeBuildInputs = [ diff --git a/nixpkgs/pkgs/applications/science/electronics/openboardview/default.nix b/nixpkgs/pkgs/applications/science/electronics/openboardview/default.nix index 4eaf29133a44..4aa9ab2b66f2 100644 --- a/nixpkgs/pkgs/applications/science/electronics/openboardview/default.nix +++ b/nixpkgs/pkgs/applications/science/electronics/openboardview/default.nix @@ -9,7 +9,7 @@ , SDL2 , fontconfig , gtk3 -, wrapGAppsHook +, wrapGAppsHook3 , darwin }: @@ -37,7 +37,7 @@ stdenv.mkDerivation rec { }) ]; - nativeBuildInputs = [ cmake pkg-config python3 wrapGAppsHook ]; + nativeBuildInputs = [ cmake pkg-config python3 wrapGAppsHook3 ]; buildInputs = [ SDL2 fontconfig gtk3 ] ++ lib.optionals stdenv.isDarwin [ Cocoa ]; diff --git a/nixpkgs/pkgs/applications/science/logic/alt-ergo/default.nix b/nixpkgs/pkgs/applications/science/logic/alt-ergo/default.nix index 9d151b947b40..03787a3a084b 100644 --- a/nixpkgs/pkgs/applications/science/logic/alt-ergo/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/alt-ergo/default.nix @@ -2,11 +2,11 @@ let pname = "alt-ergo"; - version = "2.5.3"; + version = "2.5.4"; src = fetchurl { url = "https://github.com/OCamlPro/alt-ergo/releases/download/v${version}/alt-ergo-${version}.tbz"; - hash = "sha256-tmWLZBLfdmfYlCQq+zcUneeueDAE6AJeZMy8kfNCC04="; + hash = "sha256-AsHok5i62vqJ5hK8XRiD8hM6JQaFv3dMxZAcVYEim6w="; }; in diff --git a/nixpkgs/pkgs/applications/science/logic/coq/default.nix b/nixpkgs/pkgs/applications/science/logic/coq/default.nix index 37a8aba7d8c7..68b424b32fb4 100644 --- a/nixpkgs/pkgs/applications/science/logic/coq/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/coq/default.nix @@ -11,7 +11,7 @@ , ocamlPackages_4_14 , ncurses , buildIde ? null # default is true for Coq < 8.14 and false for Coq >= 8.14 -, glib, gnome, wrapGAppsHook, makeDesktopItem, copyDesktopItems +, glib, gnome, wrapGAppsHook3, makeDesktopItem, copyDesktopItems , csdp ? null , version, coq-version ? null }@args: @@ -147,7 +147,7 @@ self = stdenv.mkDerivation { nativeBuildInputs = [ pkg-config ] ++ ocamlNativeBuildInputs ++ optional buildIde copyDesktopItems - ++ optional (buildIde && coqAtLeast "8.10") wrapGAppsHook + ++ optional (buildIde && coqAtLeast "8.10") wrapGAppsHook3 ++ optional (!coqAtLeast "8.6") gnumake42; buildInputs = [ ncurses ] ++ optionals buildIde diff --git a/nixpkgs/pkgs/applications/science/logic/eprover/default.nix b/nixpkgs/pkgs/applications/science/logic/eprover/default.nix index d4a8b7a6b2e8..85833940157f 100644 --- a/nixpkgs/pkgs/applications/science/logic/eprover/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/eprover/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "eprover"; - version = "3.0.03"; + version = "3.1"; src = fetchurl { url = "https://wwwlehre.dhbw-stuttgart.de/~sschulz/WORK/E_DOWNLOAD/V_${version}/E.tgz"; - hash = "sha256-cS5zUe2N9Kd9uzbNpeBtvLbgUN0c3N3tGcYczK3KsdQ="; + hash = "sha256-+E2z7JAkiNXhZrWRXFbhI5f9NmB0Q4eixab4GlAFqYY="; }; buildInputs = [ which ]; diff --git a/nixpkgs/pkgs/applications/science/logic/prooftree/default.nix b/nixpkgs/pkgs/applications/science/logic/prooftree/default.nix index adb64f02c14f..d0d95818ff93 100644 --- a/nixpkgs/pkgs/applications/science/logic/prooftree/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/prooftree/default.nix @@ -14,8 +14,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ pkg-config ] ++ (with ocamlPackages; [ ocaml findlib camlp5 ]); buildInputs = [ ncurses ] ++ (with ocamlPackages; [ lablgtk ]); - dontAddPrefix = true; - configureFlags = [ "--prefix" "$(out)" ]; + prefixKey = "--prefix "; meta = with lib; { description = "A program for proof-tree visualization"; diff --git a/nixpkgs/pkgs/applications/science/logic/tlaplus/toolbox.nix b/nixpkgs/pkgs/applications/science/logic/tlaplus/toolbox.nix index 288ddc06806a..1d5cfa5c5d93 100644 --- a/nixpkgs/pkgs/applications/science/logic/tlaplus/toolbox.nix +++ b/nixpkgs/pkgs/applications/science/logic/tlaplus/toolbox.nix @@ -7,7 +7,7 @@ , libXtst , glib , zlib -, wrapGAppsHook +, wrapGAppsHook3 }: let @@ -36,7 +36,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ makeShellWrapper - wrapGAppsHook + wrapGAppsHook3 ]; dontWrapGApps = true; diff --git a/nixpkgs/pkgs/applications/science/logic/why3/default.nix b/nixpkgs/pkgs/applications/science/logic/why3/default.nix index 74659a58f13e..42256ae70aa6 100644 --- a/nixpkgs/pkgs/applications/science/logic/why3/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/why3/default.nix @@ -2,7 +2,7 @@ , ocamlPackages, coqPackages, rubber, hevea, emacs , version ? "1.7.2" , ideSupport ? true -, wrapGAppsHook +, wrapGAppsHook3 }: stdenv.mkDerivation rec { @@ -20,7 +20,7 @@ stdenv.mkDerivation rec { strictDeps = true; nativeBuildInputs = lib.optional ideSupport - wrapGAppsHook + wrapGAppsHook3 ++ (with ocamlPackages; [ ocaml findlib menhir ]) ++ [ diff --git a/nixpkgs/pkgs/applications/science/math/R/default.nix b/nixpkgs/pkgs/applications/science/math/R/default.nix index acfc38686ea4..5ceb413a2421 100644 --- a/nixpkgs/pkgs/applications/science/math/R/default.nix +++ b/nixpkgs/pkgs/applications/science/math/R/default.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, fetchurl, bzip2, gfortran, libX11, libXmu, libXt, libjpeg, libpng +{ lib, stdenv, fetchurl, fetchpatch, bzip2, gfortran, libX11, libXmu, libXt, libjpeg, libpng , libtiff, ncurses, pango, pcre2, perl, readline, tcl, texlive, texliveSmall, tk, xz, zlib , less, texinfo, graphviz, icu, pkg-config, bison, imake, which, jdk, blas, lapack , curl, Cocoa, Foundation, libobjc, libcxx, tzdata @@ -37,6 +37,12 @@ stdenv.mkDerivation (finalAttrs: { patches = [ ./no-usr-local-search-paths.patch + (fetchpatch { + # https://hiddenlayer.com/research/r-bitrary-code-execution/ + name = "CVE-2024-27322.patch"; + url = "https://github.com/r-devel/r-svn/commit/f7c46500f455eb4edfc3656c3fa20af61b16abb7.patch"; + hash = "sha256-CH2mMmie9E96JeGSC7UGm7/roUNhK5xv6HO53N2ixEI="; + }) ]; # Test of the examples for package 'tcltk' fails in Darwin sandbox. See: diff --git a/nixpkgs/pkgs/applications/science/math/eigenmath/default.nix b/nixpkgs/pkgs/applications/science/math/eigenmath/default.nix index feddf92821c6..1ebb93e51630 100644 --- a/nixpkgs/pkgs/applications/science/math/eigenmath/default.nix +++ b/nixpkgs/pkgs/applications/science/math/eigenmath/default.nix @@ -7,13 +7,13 @@ stdenv.mkDerivation rec { pname = "eigenmath"; - version = "0-unstable-2024-04-26"; + version = "0-unstable-2024-05-18"; src = fetchFromGitHub { owner = "georgeweigt"; repo = pname; - rev = "14a55ff60d078b752033b4ae29d332b04b6e8912"; - hash = "sha256-p7wcLmssTqs3LCkZWB9rhCXEc4IVgZJNBvRhS51oH5E="; + rev = "e5fc4a44797549da9d8994203547da63002b3700"; + hash = "sha256-pX8rRIrOq0fQvzVrvAh47ZBzdkS6ZKuXTQ9joa/XJgg="; }; checkPhase = let emulator = stdenv.hostPlatform.emulator buildPackages; in '' diff --git a/nixpkgs/pkgs/applications/science/math/getdp/default.nix b/nixpkgs/pkgs/applications/science/math/getdp/default.nix index d28f59e4be2f..5df35cce8e23 100644 --- a/nixpkgs/pkgs/applications/science/math/getdp/default.nix +++ b/nixpkgs/pkgs/applications/science/math/getdp/default.nix @@ -5,7 +5,7 @@ stdenv.mkDerivation rec { version = "3.6.0"; src = fetchurl { url = "http://getdp.info/src/getdp-${version}-source.tgz"; - sha256 = "sha256-N1cb72W77Dr+TzeHpLgv5FuFb+SJqyGcfn+kOfEvZgA="; + hash = "sha256-nzefwCV+Z9BHDofuTfhR+vhqm3cCSiUT+7cbtn601N8="; }; inherit (petsc) mpiSupport; diff --git a/nixpkgs/pkgs/applications/science/math/gretl/default.nix b/nixpkgs/pkgs/applications/science/math/gretl/default.nix index 2c3963cecec9..552639de6c53 100644 --- a/nixpkgs/pkgs/applications/science/math/gretl/default.nix +++ b/nixpkgs/pkgs/applications/science/math/gretl/default.nix @@ -19,11 +19,11 @@ stdenv.mkDerivation (finalAttrs: { pname = "gretl"; - version = "2023c"; + version = "2024a"; src = fetchurl { url = "mirror://sourceforge/gretl/gretl-${finalAttrs.version}.tar.xz"; - hash = "sha256-vTxCmHrTpYTo9CIPousUCnpcalS6cN1u8bRaOJyu6MI="; + hash = "sha256-6ha0d/n75Xf0hZM0GRHLOnM274P1h2MerB/8SHWTh+o="; }; buildInputs = [ diff --git a/nixpkgs/pkgs/applications/science/math/gurobi/default.nix b/nixpkgs/pkgs/applications/science/math/gurobi/default.nix index 53091e6a84e5..e8f4794d4179 100644 --- a/nixpkgs/pkgs/applications/science/math/gurobi/default.nix +++ b/nixpkgs/pkgs/applications/science/math/gurobi/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "gurobi"; - version = "11.0.1"; + version = "11.0.2"; src = fetchurl { url = "https://packages.gurobi.com/${lib.versions.majorMinor version}/gurobi${version}_linux64.tar.gz"; - hash = "sha256-oZ7Oz22e4k6cVF3TDFxp/pE+RuU+3p/CatTWj1ci5ZY="; + hash = "sha256-9DrIo+25h7mgphRSrNnY2+nrNzaMbafONuUkfLKho2g="; }; sourceRoot = "gurobi${builtins.replaceStrings ["."] [""] version}/linux64"; diff --git a/nixpkgs/pkgs/applications/science/math/lrcalc/default.nix b/nixpkgs/pkgs/applications/science/math/lrcalc/default.nix index 90ee50c68280..0d968e016179 100644 --- a/nixpkgs/pkgs/applications/science/math/lrcalc/default.nix +++ b/nixpkgs/pkgs/applications/science/math/lrcalc/default.nix @@ -1,6 +1,9 @@ { lib, stdenv , fetchFromBitbucket , autoreconfHook + +# Reverse dependency +, sage }: stdenv.mkDerivation rec { @@ -20,6 +23,8 @@ stdenv.mkDerivation rec { autoreconfHook ]; + passthru.tests = { inherit sage; }; + meta = with lib; { description = "Littlewood-Richardson calculator"; homepage = "http://math.rutgers.edu/~asbuch/lrcalc/"; diff --git a/nixpkgs/pkgs/applications/science/math/nasc/default.nix b/nixpkgs/pkgs/applications/science/math/nasc/default.nix index d25f0ad34496..b544d5fc6b14 100644 --- a/nixpkgs/pkgs/applications/science/math/nasc/default.nix +++ b/nixpkgs/pkgs/applications/science/math/nasc/default.nix @@ -15,7 +15,7 @@ , libqalculate , intltool , gnuplot -, wrapGAppsHook +, wrapGAppsHook3 }: stdenv.mkDerivation rec { @@ -39,7 +39,7 @@ stdenv.mkDerivation rec { pkg-config python3 vala - wrapGAppsHook + wrapGAppsHook3 ]; buildInputs = [ diff --git a/nixpkgs/pkgs/applications/science/math/polymake/default.nix b/nixpkgs/pkgs/applications/science/math/polymake/default.nix index 9c2623651517..576a92625d49 100644 --- a/nixpkgs/pkgs/applications/science/math/polymake/default.nix +++ b/nixpkgs/pkgs/applications/science/math/polymake/default.nix @@ -25,13 +25,13 @@ stdenv.mkDerivation rec { pname = "polymake"; - version = "4.11"; + version = "4.12"; src = fetchurl { # "The minimal version is a packager friendly version which omits # the bundled sources of cdd, lrs, libnormaliz, nauty and jReality." url = "https://polymake.org/lib/exe/fetch.php/download/polymake-${version}-minimal.tar.bz2"; - sha256 = "sha256-XfbwrNcAEZvQxLV2Z2KFL/vYV3ZbXcyIgC/10hCK3SM="; + sha256 = "sha256-vVpmf/ykv3641RE0Awzj3zsW3Z0OgA+v2xzoNYZ2QNk="; }; nativeBuildInputs = [ diff --git a/nixpkgs/pkgs/applications/science/math/pynac/default.nix b/nixpkgs/pkgs/applications/science/math/pynac/default.nix index 88515b92beaf..1389a5a77ece 100644 --- a/nixpkgs/pkgs/applications/science/math/pynac/default.nix +++ b/nixpkgs/pkgs/applications/science/math/pynac/default.nix @@ -10,15 +10,15 @@ , ncurses }: -stdenv.mkDerivation rec { - version = "0.7.29"; +stdenv.mkDerivation (finalAttrs: { pname = "pynac"; + version = "0.7.29"; src = fetchFromGitHub { owner = "pynac"; repo = "pynac"; - rev = "pynac-${version}"; - sha256 = "sha256-ocR7emXtKs+Xe2f6dh4xEDAacgiolY8mtlLnWnNBS8A="; + rev = "pynac-${finalAttrs.version}"; + hash = "sha256-ocR7emXtKs+Xe2f6dh4xEDAacgiolY8mtlLnWnNBS8A="; }; patches = [ @@ -27,10 +27,16 @@ stdenv.mkDerivation rec { (fetchpatch { name = "realpartloop.patch"; url = "https://git.sagemath.org/sage.git/plain/build/pkgs/pynac/patches/realpartloop.patch?h=9.4.beta5"; - sha256 = "sha256-1nj0xtlFN5fZKEiRLD+tiW/ZtxMQre1ziEGA0OVUGE4="; + hash = "sha256-1nj0xtlFN5fZKEiRLD+tiW/ZtxMQre1ziEGA0OVUGE4="; }) ]; + # Python 3.11 moved this header file, but is now is imported by default + postPatch = '' + substituteInPlace ginac/numeric.cpp \ + --replace-fail "#include <longintrepr.h>" "" + ''; + buildInputs = [ flint gmp @@ -57,4 +63,4 @@ stdenv.mkDerivation rec { maintainers = teams.sage.members; platforms = platforms.unix; }; -} +}) diff --git a/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix b/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix index 2a2b4617d24b..ab11d833f70c 100644 --- a/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix +++ b/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix @@ -1,19 +1,19 @@ -{ lib, stdenv, fetchFromGitHub, intltool, autoreconfHook, pkg-config, libqalculate, gtk3, curl, wrapGAppsHook, desktopToDarwinBundle }: +{ lib, stdenv, fetchFromGitHub, intltool, autoreconfHook, pkg-config, libqalculate, gtk3, curl, wrapGAppsHook3, desktopToDarwinBundle }: stdenv.mkDerivation (finalAttrs: { pname = "qalculate-gtk"; - version = "5.0.0"; + version = "5.1.0"; src = fetchFromGitHub { owner = "qalculate"; repo = "qalculate-gtk"; rev = "v${finalAttrs.version}"; - hash = "sha256-hlGNL7aMzxBxtATWJBqJTFEQqMv10oC3sRCdtRLHOww="; + hash = "sha256-yI+8TrNZJt4eJnDX5mk6RozBe2ZeP7sTyAjsgiYQPck="; }; hardeningDisable = [ "format" ]; - nativeBuildInputs = [ intltool pkg-config autoreconfHook wrapGAppsHook ] + nativeBuildInputs = [ intltool pkg-config autoreconfHook wrapGAppsHook3 ] ++ lib.optionals stdenv.isDarwin [ desktopToDarwinBundle ]; buildInputs = [ libqalculate gtk3 curl ]; enableParallelBuilding = true; diff --git a/nixpkgs/pkgs/applications/science/math/qalculate-qt/default.nix b/nixpkgs/pkgs/applications/science/math/qalculate-qt/default.nix index 296fc5f783f3..a830c7ddd00e 100644 --- a/nixpkgs/pkgs/applications/science/math/qalculate-qt/default.nix +++ b/nixpkgs/pkgs/applications/science/math/qalculate-qt/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation (finalAttrs: { pname = "qalculate-qt"; - version = "5.0.0"; + version = "5.1.0"; src = fetchFromGitHub { owner = "qalculate"; repo = "qalculate-qt"; rev = "v${finalAttrs.version}"; - hash = "sha256-X7IY2yXpZiyE+T2dl0G4tWpJ5O6MVCy/sOY3v9inma0="; + hash = "sha256-gJfIC5HdA10gb/Dh/yhJbkCZfhUnN0zihqyfDjPv6ow="; }; nativeBuildInputs = [ qmake intltool pkg-config qttools wrapQtAppsHook ]; diff --git a/nixpkgs/pkgs/applications/science/math/rofi-calc/default.nix b/nixpkgs/pkgs/applications/science/math/rofi-calc/default.nix index be126e5fa397..14f8fe734bd6 100644 --- a/nixpkgs/pkgs/applications/science/math/rofi-calc/default.nix +++ b/nixpkgs/pkgs/applications/science/math/rofi-calc/default.nix @@ -7,7 +7,7 @@ , glib , cairo , gobject-introspection -, wrapGAppsHook +, wrapGAppsHook3 }: stdenv.mkDerivation rec { @@ -25,7 +25,7 @@ stdenv.mkDerivation rec { autoreconfHook pkg-config gobject-introspection - wrapGAppsHook + wrapGAppsHook3 ]; buildInputs = [ diff --git a/nixpkgs/pkgs/applications/science/math/sage/sagelib.nix b/nixpkgs/pkgs/applications/science/math/sage/sagelib.nix index 0a2bd8011b0b..1552de773d01 100644 --- a/nixpkgs/pkgs/applications/science/math/sage/sagelib.nix +++ b/nixpkgs/pkgs/applications/science/math/sage/sagelib.nix @@ -6,6 +6,7 @@ , perl , pkg-config , sage-setup +, pythonRelaxDepsHook , gd , iml , libpng @@ -102,6 +103,11 @@ buildPythonPackage rec { pip # needed to query installed packages pkg-config sage-setup + pythonRelaxDepsHook + ]; + + pythonRelaxDeps = [ + "networkx" ]; buildInputs = [ diff --git a/nixpkgs/pkgs/applications/science/math/wxmaxima/default.nix b/nixpkgs/pkgs/applications/science/math/wxmaxima/default.nix index 4d2815d12997..db2ff0c4a844 100644 --- a/nixpkgs/pkgs/applications/science/math/wxmaxima/default.nix +++ b/nixpkgs/pkgs/applications/science/math/wxmaxima/default.nix @@ -1,7 +1,7 @@ { lib , stdenv , fetchFromGitHub -, wrapGAppsHook +, wrapGAppsHook3 , cmake , gettext , maxima @@ -12,13 +12,13 @@ stdenv.mkDerivation (finalAttrs:{ pname = "wxmaxima"; - version = "24.02.2"; + version = "24.05.0"; src = fetchFromGitHub { owner = "wxMaxima-developers"; repo = "wxmaxima"; rev = "Version-${finalAttrs.version}"; - hash = "sha256-ewyg+ZhbRbPjJkYTZFuhbOWMDNZGW7ejmSv38zxcTsw="; + hash = "sha256-pl3sO28HANL9F41aaJznxUsH2Y7W/FO82Rik2/ik2Ag="; }; buildInputs = [ @@ -31,7 +31,7 @@ stdenv.mkDerivation (finalAttrs:{ ]; nativeBuildInputs = [ - wrapGAppsHook + wrapGAppsHook3 cmake gettext ]; diff --git a/nixpkgs/pkgs/applications/science/medicine/xmedcon/default.nix b/nixpkgs/pkgs/applications/science/medicine/xmedcon/default.nix index b09183f71b96..e5c5bf68d53a 100644 --- a/nixpkgs/pkgs/applications/science/medicine/xmedcon/default.nix +++ b/nixpkgs/pkgs/applications/science/medicine/xmedcon/default.nix @@ -6,7 +6,7 @@ , pkg-config , libpng , zlib -, wrapGAppsHook +, wrapGAppsHook3 }: stdenv.mkDerivation rec { @@ -25,7 +25,7 @@ stdenv.mkDerivation rec { zlib ]; - nativeBuildInputs = [ pkg-config wrapGAppsHook ]; + nativeBuildInputs = [ pkg-config wrapGAppsHook3 ]; meta = with lib; { description = "An open source toolkit for medical image conversion "; diff --git a/nixpkgs/pkgs/applications/science/misc/rink/default.nix b/nixpkgs/pkgs/applications/science/misc/rink/default.nix index 1e88047eba72..6b5917e16328 100644 --- a/nixpkgs/pkgs/applications/science/misc/rink/default.nix +++ b/nixpkgs/pkgs/applications/science/misc/rink/default.nix @@ -1,22 +1,22 @@ { lib, stdenv, fetchFromGitHub, rustPlatform, openssl, pkg-config, ncurses -, libiconv, Security }: +, curl, libiconv, Security }: rustPlatform.buildRustPackage rec { - version = "0.7.0"; + version = "0.8.0"; pname = "rink"; src = fetchFromGitHub { owner = "tiffany352"; repo = "rink-rs"; rev = "v${version}"; - sha256 = "sha256-5UrSJ/y6GxDUNaljal57JJY17NuI+2yLwVTwp+xBNxs="; + hash = "sha256-2+ZkyWhEnnO/QgCzWscbMr0u5kwdv2HqPLjtiXDfv/o="; }; - cargoHash = "sha256-G30NcP1ej01ygHzaxZ2OdgfksvXe/SCsmZFwamxlDvA="; + cargoHash = "sha256-j1pQfMjDNu57otOBTVBQEZIx80p4/beEUQdUkAJhvso="; nativeBuildInputs = [ pkg-config ]; buildInputs = [ ncurses ] - ++ (if stdenv.isDarwin then [ libiconv Security ] else [ openssl ]); + ++ (if stdenv.isDarwin then [ curl libiconv Security ] else [ openssl ]); # Some tests fail and/or attempt to use internet servers. doCheck = false; diff --git a/nixpkgs/pkgs/applications/science/misc/root/default.nix b/nixpkgs/pkgs/applications/science/misc/root/default.nix index 59bb9415b37d..afc048cc41ef 100644 --- a/nixpkgs/pkgs/applications/science/misc/root/default.nix +++ b/nixpkgs/pkgs/applications/science/misc/root/default.nix @@ -1,6 +1,7 @@ { stdenv , lib , callPackage +, fetchgit , fetchurl , fetchpatch , makeWrapper @@ -68,6 +69,12 @@ stdenv.mkDerivation rec { hash = "sha256-MA237RtnjtL7ljXKZ1khoZRcfCED2oQAM7STCR9VcAw="; }; + clad_src = fetchgit { + url = "https://github.com/vgvassilev/clad"; + rev = "refs/tags/v1.4"; # Make sure that this is the same tag as in the ROOT build files! + hash = "sha256-OI9PaS7kQ/ewD5Soe3gG5FZdlR6qG6Y3mfHwi5dj1sI="; + }; + nativeBuildInputs = [ makeWrapper cmake pkg-config git ]; propagatedBuildInputs = [ nlohmann_json @@ -131,6 +138,23 @@ stdenv.mkDerivation rec { substituteInPlace cmake/modules/SearchInstalledSoftware.cmake \ --replace 'set(lcgpackages ' '#set(lcgpackages ' + # We have to bypass the connection check, because it would disable clad. + # This should probably be fixed upstream with a flag to disable the + # connectivity check! + substituteInPlace CMakeLists.txt \ + --replace 'if(NO_CONNECTION)' 'if(FALSE)' + substituteInPlace interpreter/cling/tools/plugins/CMakeLists.txt \ + --replace 'if(NOT DEFINED NO_CONNECTION OR NOT NO_CONNECTION)' 'if(TRUE)' + # Make sure that clad is not downloaded when building + substituteInPlace interpreter/cling/tools/plugins/clad/CMakeLists.txt \ + --replace 'UPDATE_COMMAND ""' 'SOURCE_DIR ${clad_src} DOWNLOAD_COMMAND "" UPDATE_COMMAND ""' + # Make sure that clad is finding the right llvm version + substituteInPlace interpreter/cling/tools/plugins/clad/CMakeLists.txt \ + --replace '-DLLVM_DIR=''${LLVM_BINARY_DIR}' '-DLLVM_DIR=${llvm_13.dev}/lib/cmake/llvm' + # Fix that will also be upstream in ROOT 6.32. TODO: remove it when updating to 6.32 + substituteInPlace interpreter/cling/tools/plugins/clad/CMakeLists.txt \ + --replace 'set(_CLAD_LIBRARY_PATH ''${clad_install_dir}/plugins/lib)' 'set(_CLAD_LIBRARY_PATH ''${CMAKE_CURRENT_BINARY_DIR}/clad-prefix/src/clad-build/lib''${LLVM_LIBDIR_SUFFIX})' + substituteInPlace interpreter/llvm-project/clang/tools/driver/CMakeLists.txt \ --replace 'add_clang_symlink(''${link} clang)' "" @@ -151,40 +175,18 @@ stdenv.mkDerivation rec { ''; cmakeFlags = [ - "-Drpath=ON" "-DCMAKE_INSTALL_BINDIR=bin" "-DCMAKE_INSTALL_LIBDIR=lib" "-DCMAKE_INSTALL_INCLUDEDIR=include" "-Dbuiltin_llvm=OFF" - "-Dbuiltin_freetype=OFF" - "-Dbuiltin_gtest=OFF" - "-Dbuiltin_nlohmannjson=OFF" - "-Dbuiltin_openui5=ON" - "-Dclad=OFF" - "-Ddavix=ON" - "-Ddcache=OFF" "-Dfail-on-missing=ON" - "-Dfftw3=OFF" "-Dfitsio=OFF" - "-Dfortran=OFF" "-Dgnuinstall=ON" - "-Dimt=ON" - "-Dgviz=OFF" - "-Dhttp=ON" "-Dmysql=OFF" - "-Dodbc=OFF" - "-Dopengl=ON" "-Dpgsql=OFF" - "-Dpythia8=OFF" - "-Droot7=ON" "-Dsqlite=OFF" - "-Dssl=ON" - "-Dtmva=ON" "-Dtmva-pymva=OFF" "-Dvdt=OFF" - "-Dwebgui=ON" - "-Dxml=ON" - "-Dxrootd=ON" ] ++ lib.optional (stdenv.cc.libc != null) "-DC_INCLUDE_DIRS=${lib.getDev stdenv.cc.libc}/include" ++ lib.optionals stdenv.isDarwin [ @@ -195,6 +197,9 @@ stdenv.mkDerivation rec { "-Druntime_cxxmodules=OFF" ]; + # suppress warnings from compilation of the vendored clang to avoid running into log limits on the Hydra + NIX_CFLAGS_COMPILE = lib.optionals stdenv.cc.isGNU [ "-Wno-shadow" "-Wno-maybe-uninitialized" ]; + postInstall = '' for prog in rootbrowse rootcp rooteventselector rootls rootmkdir rootmv rootprint rootrm rootslimtree; do wrapProgram "$out/bin/$prog" \ @@ -251,7 +256,7 @@ stdenv.mkDerivation rec { setupHook = ./setup-hook.sh; meta = with lib; { - homepage = "https://root.cern.ch/"; + homepage = "https://root.cern/"; description = "A data analysis framework"; platforms = platforms.unix; maintainers = [ maintainers.guitargeek maintainers.veprbl ]; diff --git a/nixpkgs/pkgs/applications/science/misc/root/setup-hook.sh b/nixpkgs/pkgs/applications/science/misc/root/setup-hook.sh index 34c9bfdcebbd..7affd21012eb 100644 --- a/nixpkgs/pkgs/applications/science/misc/root/setup-hook.sh +++ b/nixpkgs/pkgs/applications/science/misc/root/setup-hook.sh @@ -12,8 +12,8 @@ thisroot () { postHooks+=(thisroot) -addRootInludePath() { +addRootIncludePath() { addToSearchPath ROOT_INCLUDE_PATH $1/include } -addEnvHooks "$targetOffset" addRootInludePath +addEnvHooks "$targetOffset" addRootIncludePath diff --git a/nixpkgs/pkgs/applications/science/misc/root/sw_vers.patch b/nixpkgs/pkgs/applications/science/misc/root/sw_vers.patch index 54ad1091392e..2a0fcd757719 100644 --- a/nixpkgs/pkgs/applications/science/misc/root/sw_vers.patch +++ b/nixpkgs/pkgs/applications/science/misc/root/sw_vers.patch @@ -48,7 +48,7 @@ diff a/cmake/modules/SetUpMacOS.cmake b/cmake/modules/SetUpMacOS.cmake #---Set Linker flags---------------------------------------------------------------------- - set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -mmacosx-version-min=${MACOSX_VERSION}") else (CMAKE_SYSTEM_NAME MATCHES Darwin) - MESSAGE(FATAL_ERROR "There is no setup for this this Apple system up to now. Don't know waht to do. Stop cmake at this point.") + MESSAGE(FATAL_ERROR "There is no setup for this this Apple system up to now. Don't know what to do. Stop cmake at this point.") endif (CMAKE_SYSTEM_NAME MATCHES Darwin) diff a/config/root-config.in b/config/root-config.in --- a/config/root-config.in diff --git a/nixpkgs/pkgs/applications/science/misc/snakemake/default.nix b/nixpkgs/pkgs/applications/science/misc/snakemake/default.nix index fa670b85621c..1a171f2c7db5 100644 --- a/nixpkgs/pkgs/applications/science/misc/snakemake/default.nix +++ b/nixpkgs/pkgs/applications/science/misc/snakemake/default.nix @@ -6,14 +6,14 @@ python3.pkgs.buildPythonApplication rec { pname = "snakemake"; - version = "8.11.0"; + version = "8.11.4"; format = "setuptools"; src = fetchFromGitHub { owner = "snakemake"; repo = pname; rev = "refs/tags/v${version}"; - hash = "sha256-bAzhQMGI4t/ftcZnz6h/PmlDlGgMU8vFVHb9QXED/Hw="; + hash = "sha256-nfPA2sQCeRc12A4rrlo17UPpiB8plKYbiumZjS7Yhz8="; # https://github.com/python-versioneer/python-versioneer/issues/217 postFetch = '' sed -i "$out"/snakemake/_version.py -e 's#git_refnames = ".*"#git_refnames = " (tag: v${version})"#' diff --git a/nixpkgs/pkgs/applications/science/physics/crystfel/default.nix b/nixpkgs/pkgs/applications/science/physics/crystfel/default.nix index 33f204360317..e7eb69fb4e1c 100644 --- a/nixpkgs/pkgs/applications/science/physics/crystfel/default.nix +++ b/nixpkgs/pkgs/applications/science/physics/crystfel/default.nix @@ -18,7 +18,7 @@ , pandoc , eigen , pkg-config -, wrapGAppsHook +, wrapGAppsHook3 , flex , bison , doxygen @@ -193,7 +193,7 @@ stdenv.mkDerivation rec { sha256 = "sha256-ogNHWYfbxRmB5TdK8K0JpcCnYOOyXapQGSPh8mfp+Tc="; }; nativeBuildInputs = [ meson pkg-config ninja flex bison doxygen opencl-headers makeWrapper ] - ++ lib.optionals withGui [ wrapGAppsHook ]; + ++ lib.optionals withGui [ wrapGAppsHook3 ]; buildInputs = [ hdf5 gsl diff --git a/nixpkgs/pkgs/applications/science/physics/elmerfem/default.nix b/nixpkgs/pkgs/applications/science/physics/elmerfem/default.nix index e63203a93f28..c3720602d08d 100644 --- a/nixpkgs/pkgs/applications/science/physics/elmerfem/default.nix +++ b/nixpkgs/pkgs/applications/science/physics/elmerfem/default.nix @@ -1,5 +1,23 @@ -{ lib, stdenv, fetchFromGitHub, cmake, git, gfortran, mpi, blas, liblapack, pkg-config, libGL, libGLU, opencascade-occt, libsForQt5, tbb, vtkWithQt5 }: - +{ lib +, stdenv +, fetchFromGitHub +, cmake +, git +, gfortran +, mpi +, blas +, liblapack +, pkg-config +, libGL +, libGLU +, opencascade-occt_7_6 +, libsForQt5 +, tbb +, vtkWithQt5 +}: +let + opencascade-occt = opencascade-occt_7_6; +in stdenv.mkDerivation rec { pname = "elmerfem"; version = "unstable-2023-09-18"; @@ -19,6 +37,7 @@ stdenv.mkDerivation rec { pkg-config libsForQt5.wrapQtAppsHook ]; + buildInputs = [ mpi blas diff --git a/nixpkgs/pkgs/applications/science/physics/xnec2c/default.nix b/nixpkgs/pkgs/applications/science/physics/xnec2c/default.nix index 60afa09ecc8c..ffdd4b6d0b07 100644 --- a/nixpkgs/pkgs/applications/science/physics/xnec2c/default.nix +++ b/nixpkgs/pkgs/applications/science/physics/xnec2c/default.nix @@ -2,7 +2,7 @@ , stdenv , fetchurl , autoreconfHook -, wrapGAppsHook +, wrapGAppsHook3 , pkg-config , which , gtk3 @@ -23,7 +23,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ autoreconfHook - wrapGAppsHook + wrapGAppsHook3 pkg-config which ]; diff --git a/nixpkgs/pkgs/applications/science/robotics/betaflight-configurator/default.nix b/nixpkgs/pkgs/applications/science/robotics/betaflight-configurator/default.nix index 0792d3375d0a..84f94102da13 100644 --- a/nixpkgs/pkgs/applications/science/robotics/betaflight-configurator/default.nix +++ b/nixpkgs/pkgs/applications/science/robotics/betaflight-configurator/default.nix @@ -1,4 +1,4 @@ -{lib, stdenv, fetchurl, unzip, makeDesktopItem, nwjs, wrapGAppsHook, gsettings-desktop-schemas, gtk3 }: +{lib, stdenv, fetchurl, unzip, makeDesktopItem, nwjs, wrapGAppsHook3, gsettings-desktop-schemas, gtk3 }: let pname = "betaflight-configurator"; @@ -24,7 +24,7 @@ stdenv.mkDerivation rec { find -name "lib*.so" -delete ''; - nativeBuildInputs = [ wrapGAppsHook unzip ]; + nativeBuildInputs = [ wrapGAppsHook3 unzip ]; buildInputs = [ gsettings-desktop-schemas gtk3 ]; diff --git a/nixpkgs/pkgs/applications/science/robotics/emuflight-configurator/default.nix b/nixpkgs/pkgs/applications/science/robotics/emuflight-configurator/default.nix index 2c51355eb54f..62592b0cc3fc 100644 --- a/nixpkgs/pkgs/applications/science/robotics/emuflight-configurator/default.nix +++ b/nixpkgs/pkgs/applications/science/robotics/emuflight-configurator/default.nix @@ -1,5 +1,5 @@ {lib, stdenv, fetchurl, unzip, makeDesktopItem, copyDesktopItems, nwjs -, wrapGAppsHook, gsettings-desktop-schemas, gtk3 }: +, wrapGAppsHook3, gsettings-desktop-schemas, gtk3 }: stdenv.mkDerivation rec { pname = "emuflight-configurator"; @@ -10,7 +10,7 @@ stdenv.mkDerivation rec { sha256 = "sha256-e4HNg5yr9V5LyT0hYP6gzw0tZm4dLidJg5MQtH3L3JI="; }; - nativeBuildInputs = [ wrapGAppsHook unzip copyDesktopItems ]; + nativeBuildInputs = [ wrapGAppsHook3 unzip copyDesktopItems ]; buildInputs = [ gsettings-desktop-schemas gtk3 ]; diff --git a/nixpkgs/pkgs/applications/science/robotics/inav-configurator/default.nix b/nixpkgs/pkgs/applications/science/robotics/inav-configurator/default.nix index f5216eaf6c92..1a6f5951ed34 100644 --- a/nixpkgs/pkgs/applications/science/robotics/inav-configurator/default.nix +++ b/nixpkgs/pkgs/applications/science/robotics/inav-configurator/default.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, fetchurl, makeDesktopItem, copyDesktopItems, nwjs, wrapGAppsHook, gsettings-desktop-schemas, gtk3 }: +{ lib, stdenv, fetchurl, makeDesktopItem, copyDesktopItems, nwjs, wrapGAppsHook3, gsettings-desktop-schemas, gtk3 }: stdenv.mkDerivation rec { pname = "inav-configurator"; @@ -14,7 +14,7 @@ stdenv.mkDerivation rec { sha256 = "1i844dzzc5s5cr4vfpi6k2kdn8jiqq2n6c0fjqvsp4wdidwjahzw"; }; - nativeBuildInputs = [ copyDesktopItems wrapGAppsHook ]; + nativeBuildInputs = [ copyDesktopItems wrapGAppsHook3 ]; buildInputs = [ gsettings-desktop-schemas gtk3 ]; diff --git a/nixpkgs/pkgs/applications/science/robotics/mujoco/default.nix b/nixpkgs/pkgs/applications/science/robotics/mujoco/default.nix index 3013ce74a334..76c18a788c30 100644 --- a/nixpkgs/pkgs/applications/science/robotics/mujoco/default.nix +++ b/nixpkgs/pkgs/applications/science/robotics/mujoco/default.nix @@ -12,12 +12,12 @@ let pin = { - # See https://github.com/google-deepmind/mujoco/blob/3.0.0/cmake/MujocoDependencies.cmake#L17-L64 + # See https://github.com/google-deepmind/mujoco/blob/<VERSION>/cmake/MujocoDependencies.cmake#L17-L64 abseil-cpp = fetchFromGitHub { owner = "abseil"; repo = "abseil-cpp"; - rev = "2f9e432cce407ce0ae50676696666f33a77d42ac"; - hash = "sha256-D4E11bICKr3Z5RRah7QkfXVsXtuUg32FMmKpiOGjZDM="; + rev = "d7aaad83b488fd62bd51c81ecf16cd938532cc0a"; + hash = "sha256-eA2/dZpNOlex1O5PNa3XSZhpMB3AmaIoHzVDI9TD/cg="; }; benchmark = fetchFromGitHub { owner = "google"; @@ -70,8 +70,8 @@ let marchingcubecpp = fetchFromGitHub { owner = "aparis69"; repo = "MarchingCubeCpp"; - rev = "5b79e5d6bded086a0abe276a4b5a69fc17ae9bf1"; - hash = "sha256-L0DH1GJZ/3vatQAU/KZj/2xTKE6Fwcw9eQYzLdqX2N4="; + rev = "f03a1b3ec29b1d7d865691ca8aea4f1eb2c2873d"; + hash = "sha256-90ei0lpJA8XuVGI0rGb3md0Qtq8/bdkU7dUCHpp88Bw="; }; tmd = stdenv.mkDerivation rec { @@ -129,7 +129,7 @@ let in stdenv.mkDerivation rec { pname = "mujoco"; - version = "3.1.4"; + version = "3.1.5"; # Bumping version? Make sure to look though the MuJoCo's commit # history for bumped dependency pins! @@ -137,7 +137,7 @@ in stdenv.mkDerivation rec { owner = "google-deepmind"; repo = "mujoco"; rev = "refs/tags/${version}"; - hash = "sha256-VgD6ditMDpHki7l23Gjip2roA8Oi4MGpxl+4gSLTEFs="; + hash = "sha256-XKN489oexHf2/Gv0MVxXUzqyeJJTJXV99+fNi8shdsg="; }; patches = [ ./mujoco-system-deps-dont-fetch.patch ]; |