diff options
Diffstat (limited to 'pkgs/applications/science')
8 files changed, 99 insertions, 52 deletions
diff --git a/pkgs/applications/science/astronomy/siril/default.nix b/pkgs/applications/science/astronomy/siril/default.nix index f039d056ec677..569d537172542 100644 --- a/pkgs/applications/science/astronomy/siril/default.nix +++ b/pkgs/applications/science/astronomy/siril/default.nix @@ -1,28 +1,21 @@ -{ 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, 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 wrapGAppsHook3 ]; @@ -30,14 +23,16 @@ stdenv.mkDerivation rec { 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 . + ${meson}/bin/meson setup -Denable-libcurl=yes --buildtype release nixbld . ''; postConfigure = '' diff --git a/pkgs/applications/science/biology/conglomerate/default.nix b/pkgs/applications/science/biology/conglomerate/default.nix index d9092b9eeb11b..0d140914638e7 100644 --- a/pkgs/applications/science/biology/conglomerate/default.nix +++ b/pkgs/applications/science/biology/conglomerate/default.nix @@ -1,20 +1,47 @@ -{ lib, stdenv, fetchFromGitHub, cmake, coreutils, perlPackages, bicpl, libminc, zlib, minc_tools, - makeWrapper }: +{ + lib, + stdenv, + fetchFromGitHub, + cmake, + coreutils, + perlPackages, + bicpl, + libminc, + zlib, + minc_tools, + makeWrapper, +}: stdenv.mkDerivation rec { pname = "conglomerate"; - version = "unstable-2017-09-10"; + version = "unstable-2023-01-19"; src = fetchFromGitHub { - owner = "BIC-MNI"; - repo = pname; - rev = "7343238bc6215942c7ecc885a224f24433a291b0"; - sha256 = "1mlqgmy3jc13bv7d01rjwldxq0p4ayqic85xcl222hhifi3w2prr"; + owner = "BIC-MNI"; + repo = pname; + rev = "6fb26084f2871a85044e2e4afc868982702b40ed"; + hash = "sha256-Inr4b2bxguzkcRQBURObsQQ0Rb3H/Zz6hEzNRd+IX3w="; }; - nativeBuildInputs = [ cmake makeWrapper ]; - buildInputs = [ libminc zlib bicpl ]; - propagatedBuildInputs = [ coreutils minc_tools ] ++ (with perlPackages; [ perl GetoptTabular MNI-Perllib ]); + nativeBuildInputs = [ + cmake + makeWrapper + ]; + buildInputs = [ + libminc + zlib + bicpl + ]; + propagatedBuildInputs = + [ + coreutils + minc_tools + ] + ++ (with perlPackages; [ + perl + GetoptTabular + MNI-Perllib + ]); cmakeFlags = [ "-DLIBMINC_DIR=${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/pkgs/applications/science/biology/migrate/default.nix b/pkgs/applications/science/biology/migrate/default.nix index 31e4eb2fcb42b..7820f177bfb7b 100644 --- a/pkgs/applications/science/biology/migrate/default.nix +++ b/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/pkgs/applications/science/chemistry/jmol/default.nix b/pkgs/applications/science/chemistry/jmol/default.nix index ee3ab5f1f3a56..bafbeb3529c69 100644 --- a/pkgs/applications/science/chemistry/jmol/default.nix +++ b/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-${version}-binary.tar.gz"; - hash = "sha256-zUX3msosz0LNQJuEUbFgT32Hw0Wq4CgW1iHMkvReysU="; + hash = "sha256-zPHh5IFdttliPc0SCgkM/3UQmS4eT2rfi5HqpFjY5hA="; }; patchPhase = '' diff --git a/pkgs/applications/science/logic/alt-ergo/default.nix b/pkgs/applications/science/logic/alt-ergo/default.nix index 9d151b947b406..03787a3a084b1 100644 --- a/pkgs/applications/science/logic/alt-ergo/default.nix +++ b/pkgs/applications/science/logic/alt-ergo/default.nix @@ -2,11 +2,11 @@ let pname = "alt-ergo"; - version = "2.5.3"; + version = "2.5.4"; src = fetchurl { url = "https://github.com/OCamlPro/alt-ergo/releases/download/v${version}/alt-ergo-${version}.tbz"; - hash = "sha256-tmWLZBLfdmfYlCQq+zcUneeueDAE6AJeZMy8kfNCC04="; + hash = "sha256-AsHok5i62vqJ5hK8XRiD8hM6JQaFv3dMxZAcVYEim6w="; }; in diff --git a/pkgs/applications/science/math/eigenmath/default.nix b/pkgs/applications/science/math/eigenmath/default.nix index becf26c61af7a..2f51a00a9b150 100644 --- a/pkgs/applications/science/math/eigenmath/default.nix +++ b/pkgs/applications/science/math/eigenmath/default.nix @@ -7,13 +7,13 @@ stdenv.mkDerivation rec { pname = "eigenmath"; - version = "0-unstable-2024-05-03"; + version = "0-unstable-2024-05-12"; src = fetchFromGitHub { owner = "georgeweigt"; repo = pname; - rev = "69ebfbaa7f328ddc9d97b7c404369818a5febe4a"; - hash = "sha256-lHxVyUXIY9+YIStA6202Bhy/b0xaxJbW/VPI7FbNJk0="; + rev = "978b3bd582a90c8e82079f2e4e4a3a5038cbbe08"; + hash = "sha256-DoGX8nUcWcioTq8ymB+HLsCnt9V6HTKSX4Zs2CQz78Q="; }; checkPhase = let emulator = stdenv.hostPlatform.emulator buildPackages; in '' diff --git a/pkgs/applications/science/math/pynac/default.nix b/pkgs/applications/science/math/pynac/default.nix index 88515b92beaf6..1389a5a77ece9 100644 --- a/pkgs/applications/science/math/pynac/default.nix +++ b/pkgs/applications/science/math/pynac/default.nix @@ -10,15 +10,15 @@ , ncurses }: -stdenv.mkDerivation rec { - version = "0.7.29"; +stdenv.mkDerivation (finalAttrs: { pname = "pynac"; + version = "0.7.29"; src = fetchFromGitHub { owner = "pynac"; repo = "pynac"; - rev = "pynac-${version}"; - sha256 = "sha256-ocR7emXtKs+Xe2f6dh4xEDAacgiolY8mtlLnWnNBS8A="; + rev = "pynac-${finalAttrs.version}"; + hash = "sha256-ocR7emXtKs+Xe2f6dh4xEDAacgiolY8mtlLnWnNBS8A="; }; patches = [ @@ -27,10 +27,16 @@ stdenv.mkDerivation rec { (fetchpatch { name = "realpartloop.patch"; url = "https://git.sagemath.org/sage.git/plain/build/pkgs/pynac/patches/realpartloop.patch?h=9.4.beta5"; - sha256 = "sha256-1nj0xtlFN5fZKEiRLD+tiW/ZtxMQre1ziEGA0OVUGE4="; + hash = "sha256-1nj0xtlFN5fZKEiRLD+tiW/ZtxMQre1ziEGA0OVUGE4="; }) ]; + # Python 3.11 moved this header file, but is now is imported by default + postPatch = '' + substituteInPlace ginac/numeric.cpp \ + --replace-fail "#include <longintrepr.h>" "" + ''; + buildInputs = [ flint gmp @@ -57,4 +63,4 @@ stdenv.mkDerivation rec { maintainers = teams.sage.members; platforms = platforms.unix; }; -} +}) diff --git a/pkgs/applications/science/misc/snakemake/default.nix b/pkgs/applications/science/misc/snakemake/default.nix index bc69b0947e087..1a171f2c7db5d 100644 --- a/pkgs/applications/science/misc/snakemake/default.nix +++ b/pkgs/applications/science/misc/snakemake/default.nix @@ -6,14 +6,14 @@ python3.pkgs.buildPythonApplication rec { pname = "snakemake"; - version = "8.11.3"; + version = "8.11.4"; format = "setuptools"; src = fetchFromGitHub { owner = "snakemake"; repo = pname; rev = "refs/tags/v${version}"; - hash = "sha256-wNs5OW8bM5LU0Ik77VU47dEq2PlrsfNNtl6Zedocnm4="; + 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})"#' |