diff options
Diffstat (limited to 'nixpkgs/pkgs/applications/science')
13 files changed, 127 insertions, 122 deletions
diff --git a/nixpkgs/pkgs/applications/science/astronomy/kstars/default.nix b/nixpkgs/pkgs/applications/science/astronomy/kstars/default.nix index ab141666c0aa..5fcd8d95f194 100644 --- a/nixpkgs/pkgs/applications/science/astronomy/kstars/default.nix +++ b/nixpkgs/pkgs/applications/science/astronomy/kstars/default.nix @@ -1,36 +1,86 @@ -{ - lib, mkDerivation, extra-cmake-modules, fetchurl, - - kconfig, kdoctools, kguiaddons, ki18n, kinit, kiconthemes, kio, - knewstuff, kplotting, kwidgetsaddons, kxmlgui, knotifyconfig, - - - qtx11extras, qtwebsockets, qtkeychain, libsecret, - - eigen, zlib, - - cfitsio, indi-full, xplanet, libnova, libraw, gsl, wcslib, stellarsolver +{ lib +, stdenv +, mkDerivation +, extra-cmake-modules +, fetchFromGitHub +, kconfig +, kdoctools +, kguiaddons +, ki18n +, kinit +, kiconthemes +, kio +, knewstuff +, kplotting +, kwidgetsaddons +, kxmlgui +, knotifyconfig +, qtx11extras +, qtwebsockets +, qtkeychain +, qtdatavis3d +, wrapQtAppsHook +, breeze-icons +, libsecret +, eigen +, zlib +, cfitsio +, indi-full +, xplanet +, libnova +, libraw +, gsl +, wcslib +, stellarsolver +, libxisf }: -mkDerivation rec { +stdenv.mkDerivation (finalAttrs: { pname = "kstars"; - version = "3.6.7"; + version = "3.6.9"; - src = fetchurl { - url = "mirror://kde/stable/kstars/kstars-${version}.tar.xz"; - sha256 = "sha256-uEgzvhlHHpXyvi3Djfwg3GmYeZq+r48m7OJFIDARpe4="; + src = fetchFromGitHub { + owner = "KDE"; + repo = "kstars"; + rev = "stable-${finalAttrs.version}"; + hash = "sha256-28RRW+ncMiQcBb/lybEKTeV08ZkF3IqLkeTHNW5nhls="; }; - nativeBuildInputs = [ extra-cmake-modules kdoctools ]; + nativeBuildInputs = [ + extra-cmake-modules + kdoctools + wrapQtAppsHook + ]; buildInputs = [ - kconfig kdoctools kguiaddons ki18n kinit kiconthemes kio - knewstuff kplotting kwidgetsaddons kxmlgui knotifyconfig - - qtx11extras qtwebsockets qtkeychain libsecret - - eigen zlib - - cfitsio indi-full xplanet libnova libraw gsl wcslib stellarsolver + kconfig + kdoctools + kguiaddons + ki18n + kinit + kiconthemes + kio + knewstuff + kplotting + kwidgetsaddons + kxmlgui + knotifyconfig + qtx11extras + qtwebsockets + qtkeychain + qtdatavis3d + breeze-icons + libsecret + eigen + zlib + cfitsio + indi-full + xplanet + libnova + libraw + gsl + wcslib + stellarsolver + libxisf ]; cmakeFlags = [ @@ -51,4 +101,4 @@ mkDerivation rec { platforms = platforms.linux; maintainers = with maintainers; [ timput hjones2199 ]; }; -} +}) diff --git a/nixpkgs/pkgs/applications/science/biology/iqtree/default.nix b/nixpkgs/pkgs/applications/science/biology/iqtree/default.nix index 17b2ba9f9bde..1f00876b5848 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 = "2.2.2.7"; + version = "2.3.1"; src = fetchFromGitHub { owner = "iqtree"; repo = "iqtree2"; rev = "v${version}"; - hash = "sha256-XyjVo5TYMoB+ZOAGc4ivYqFGnEO1M7mhxXrG45TP44Y="; + hash = "sha256-GaNumiTGa6mxvFifv730JFgKrRxG41gJN+ci3imDbzs="; fetchSubmodules = true; }; diff --git a/nixpkgs/pkgs/applications/science/biology/messer-slim/default.nix b/nixpkgs/pkgs/applications/science/biology/messer-slim/default.nix index d4ce4071a274..2e4911d829d1 100644 --- a/nixpkgs/pkgs/applications/science/biology/messer-slim/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/messer-slim/default.nix @@ -1,14 +1,14 @@ { lib, stdenv, fetchFromGitHub, cmake, gcc, gcc-unwrapped }: stdenv.mkDerivation rec { - version = "4.1"; + version = "4.2"; pname = "messer-slim"; src = fetchFromGitHub { owner = "MesserLab"; repo = "SLiM"; rev = "v${version}"; - sha256 = "sha256-mb6xcu28QYAFm2906lRNY0zciQBKSGcz3q/cvOEh/VE="; + sha256 = "sha256-PDIaOMA1QHrJC5xVW+Mzx8ja/YvZBMKvV88MjSoSpfM="; }; nativeBuildInputs = [ cmake gcc gcc-unwrapped ]; diff --git a/nixpkgs/pkgs/applications/science/chemistry/gwyddion/default.nix b/nixpkgs/pkgs/applications/science/chemistry/gwyddion/default.nix index 7c1312f27f25..a4b1cd943e1b 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/gwyddion/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/gwyddion/default.nix @@ -1,5 +1,4 @@ { lib, stdenv, fetchurl, gtk2, pkg-config, fftw, file, - pythonSupport ? false, python2Packages, gnome2, openexrSupport ? true, openexr, libzipSupport ? true, libzip, @@ -15,10 +14,6 @@ openglSupport ? !stdenv.isDarwin, libGL }: -let - inherit (python2Packages) pygtk pygobject2 python; -in - stdenv.mkDerivation rec { pname = "gwyddion"; version = "2.65"; @@ -43,9 +38,6 @@ stdenv.mkDerivation rec { optional libuniqueSupport libunique ++ optional libzipSupport libzip; - propagatedBuildInputs = with lib; - optionals pythonSupport [ pygtk pygobject2 python gnome2.gtksourceview ]; - # This patch corrects problems with python support, but should apply cleanly # regardless of whether python support is enabled, and have no effects if # it is disabled. diff --git a/nixpkgs/pkgs/applications/science/electronics/dataexplorer/default.nix b/nixpkgs/pkgs/applications/science/electronics/dataexplorer/default.nix index aa471d2bfcaf..224d804ee1f6 100644 --- a/nixpkgs/pkgs/applications/science/electronics/dataexplorer/default.nix +++ b/nixpkgs/pkgs/applications/science/electronics/dataexplorer/default.nix @@ -1,26 +1,32 @@ { lib , stdenv , fetchurl -, jdk , ant +, jdk , makeWrapper +, strip-nondeterminism }: -stdenv.mkDerivation rec { +stdenv.mkDerivation (finalAttrs: { pname = "dataexplorer"; version = "3.8.5"; src = fetchurl { - url = "mirror://savannah/dataexplorer/dataexplorer-${version}-src.tar.gz"; - sha256 = "sha256-b68xIZNbzHdPyZwLngcnjcoBtI6AeTdrblz/qx/HbGQ="; + url = "mirror://savannah/dataexplorer/dataexplorer-${finalAttrs.version}-src.tar.gz"; + hash = "sha256-b68xIZNbzHdPyZwLngcnjcoBtI6AeTdrblz/qx/HbGQ="; }; - nativeBuildInputs = [ ant makeWrapper ]; - - buildInputs = [ jdk ]; + nativeBuildInputs = [ + ant + jdk + makeWrapper + strip-nondeterminism + ]; buildPhase = '' + runHook preBuild ant -f build/build.xml dist + runHook postBuild ''; doCheck = false; @@ -30,6 +36,8 @@ stdenv.mkDerivation rec { #''; installPhase = '' + runHook preInstall + ant -Dprefix=$out/share/ -f build/build.xml install # The sources contain a wrapper script in $out/share/DataExplorer/DataExplorer @@ -49,6 +57,14 @@ stdenv.mkDerivation rec { $out/etc/udev/rules.d/50-Junsi-iCharger-USB.rules install -Dvm644 build/misc/GNU_LINUX_SKYRC_UDEV_RULE/50-SkyRC-Charger.rules \ $out/etc/udev/rules.d/50-SkyRC-Charger.rules + + runHook postInstall + ''; + + # manually call strip-nondeterminism because using stripJavaArchivesHook takes + # too long to strip bundled jars + postFixup = '' + strip-nondeterminism --type jar $out/share/DataExplorer/{DataExplorer.jar,devices/*.jar} ''; meta = with lib; { @@ -63,4 +79,4 @@ stdenv.mkDerivation rec { binaryBytecode # contains thirdparty jar files, e.g. javax.json, org.glassfish.json ]; }; -} +}) diff --git a/nixpkgs/pkgs/applications/science/logic/alt-ergo/default.nix b/nixpkgs/pkgs/applications/science/logic/alt-ergo/default.nix index d84aa5b6918a..9d151b947b40 100644 --- a/nixpkgs/pkgs/applications/science/logic/alt-ergo/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/alt-ergo/default.nix @@ -2,11 +2,11 @@ let pname = "alt-ergo"; - version = "2.5.2"; + version = "2.5.3"; src = fetchurl { url = "https://github.com/OCamlPro/alt-ergo/releases/download/v${version}/alt-ergo-${version}.tbz"; - hash = "sha256-9GDBcBH49sheO5AjmDsznMEbw0JSrnSOcIIRN40/aJU="; + hash = "sha256-tmWLZBLfdmfYlCQq+zcUneeueDAE6AJeZMy8kfNCC04="; }; in diff --git a/nixpkgs/pkgs/applications/science/math/gfan/default.nix b/nixpkgs/pkgs/applications/science/math/gfan/default.nix index 11a42d1cfdf8..8fa6da16e336 100644 --- a/nixpkgs/pkgs/applications/science/math/gfan/default.nix +++ b/nixpkgs/pkgs/applications/science/math/gfan/default.nix @@ -14,6 +14,10 @@ stdenv.mkDerivation rec { postPatch = lib.optionalString stdenv.cc.isClang '' substituteInPlace Makefile --replace "-fno-guess-branch-probability" "" + + for f in $(find -name "*.h" -or -name "*.cpp"); do + substituteInPlace "$f" --replace-quiet "log2" "_log2" + done ''; buildFlags = [ "CC=${stdenv.cc.targetPrefix}cc" "CXX=${stdenv.cc.targetPrefix}c++" ]; diff --git a/nixpkgs/pkgs/applications/science/math/gmsh/default.nix b/nixpkgs/pkgs/applications/science/math/gmsh/default.nix index 669d3a3ab8f1..57b20fe12d7c 100644 --- a/nixpkgs/pkgs/applications/science/math/gmsh/default.nix +++ b/nixpkgs/pkgs/applications/science/math/gmsh/default.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, fetchurl, fetchpatch, cmake, blas, lapack, gfortran, gmm, fltk, libjpeg +{ lib, stdenv, fetchurl, cmake, blas, lapack, gfortran, gmm, fltk, libjpeg , zlib, libGL, libGLU, xorg, opencascade-occt , python ? null, enablePython ? false }: @@ -7,11 +7,11 @@ assert enablePython -> (python != null); stdenv.mkDerivation rec { pname = "gmsh"; - version = "4.11.1"; + version = "4.12.2"; src = fetchurl { url = "https://gmsh.info/src/gmsh-${version}-source.tgz"; - sha256 = "sha256-xf4bfL1AOIioFJKfL9D11p4nYAIioYx4bbW3boAFs2U="; + hash = "sha256-E+CdnKgQLlxAFx1u4VDGaHQrmMOmylf4N/e2Th4q9I8="; }; buildInputs = [ @@ -26,19 +26,6 @@ stdenv.mkDerivation rec { patches = [ ./fix-python.patch - - # Pull upstream fix git gcc-13: - # https://gitlab.onelab.info/gmsh/gmsh/-/issues/2416 - (fetchpatch { - name = "gcc-13-p1.patch"; - url = "https://gitlab.onelab.info/gmsh/gmsh/-/commit/fb81a9c9026700e078de947b4522cb39e543a86b.patch"; - hash = "sha256-1GInFqQZvOgflC3eQTjmZ9uBGFASRNCpCwDACN3yTQ4="; - }) - (fetchpatch { - name = "gcc-13-p2.patch"; - url = "https://gitlab.onelab.info/gmsh/gmsh/-/commit/aceb09c807b78ea26555f99fcb16c4f87c31fb5a.patch"; - hash = "sha256-6FI0hIvj8hglCvxoKV0GzT2/F/Wz+ddkxV/TLzzJBLU="; - }) ]; postPatch = '' diff --git a/nixpkgs/pkgs/applications/science/math/gmsh/fix-python.patch b/nixpkgs/pkgs/applications/science/math/gmsh/fix-python.patch index ac07c169c99b..41c5c3b8f976 100644 --- a/nixpkgs/pkgs/applications/science/math/gmsh/fix-python.patch +++ b/nixpkgs/pkgs/applications/science/math/gmsh/fix-python.patch @@ -1,50 +1,13 @@ diff --git a/api/gmsh.py b/api/gmsh.py -index 747acb203..02004da5d 100644 +index f525284..a225c85 100644 --- a/api/gmsh.py +++ b/api/gmsh.py -@@ -44,44 +44,7 @@ moduledir = os.path.dirname(os.path.realpath(__file__)) - parentdir1 = os.path.dirname(moduledir) - parentdir2 = os.path.dirname(parentdir1) +@@ -78,6 +78,8 @@ if not libpath: + else: + libpath = find_library("gmsh") --if platform.system() == "Windows": -- libname = "gmsh-4.11.dll" --elif platform.system() == "Darwin": -- libname = "libgmsh.4.11.dylib" --else: -- libname = "libgmsh.so.4.11" -- --# check if the library is in the same directory as the module... --libpath = os.path.join(moduledir, libname) -- --# ... or in the parent directory or its lib or Lib subdirectory --if not os.path.exists(libpath): -- libpath = os.path.join(parentdir1, libname) --if not os.path.exists(libpath): -- libpath = os.path.join(parentdir1, "lib", libname) --if not os.path.exists(libpath): -- libpath = os.path.join(parentdir1, "Lib", libname) -- --# ... or in the parent of the parent directory or its lib or Lib subdirectory --if not os.path.exists(libpath): -- libpath = os.path.join(parentdir2, libname) --if not os.path.exists(libpath): -- libpath = os.path.join(parentdir2, "lib", libname) --if not os.path.exists(libpath): -- libpath = os.path.join(parentdir2, "Lib", libname) -- --# if we couldn't find it, use ctype's find_library utility... --if not os.path.exists(libpath): -- if platform.system() == "Windows": -- libpath = find_library("gmsh-4.11") -- if not libpath: -- libpath = find_library("gmsh") -- else: -- libpath = find_library("gmsh") -- --# ... and print a warning if everything failed --if not os.path.exists(libpath): -- print("Warning: could not find Gmsh shared library " + libname) +libpath = "@LIBPATH@" - - lib = CDLL(libpath) - ++ + # ... and print a warning if everything failed + if not libpath: + print("Warning: could not find Gmsh shared library " + libname + diff --git a/nixpkgs/pkgs/applications/science/math/sage/sage-env.nix b/nixpkgs/pkgs/applications/science/math/sage/sage-env.nix index 4f179ea3a42b..f95e08c51ff4 100644 --- a/nixpkgs/pkgs/applications/science/math/sage/sage-env.nix +++ b/nixpkgs/pkgs/applications/science/math/sage/sage-env.nix @@ -39,7 +39,6 @@ , ecm , lcalc , rubiks -, flintqs , blas , lapack , flint3 @@ -93,7 +92,6 @@ let ecm lcalc rubiks - flintqs jdk # only needed for `jmol` which may be replaced in the future less # needed to prevent transient test errors until https://github.com/ipython/ipython/pull/11864 is resolved ] diff --git a/nixpkgs/pkgs/applications/science/math/sage/sage-with-env.nix b/nixpkgs/pkgs/applications/science/math/sage/sage-with-env.nix index b2c0843d3100..88c753e89c9d 100644 --- a/nixpkgs/pkgs/applications/science/math/sage/sage-with-env.nix +++ b/nixpkgs/pkgs/applications/science/math/sage/sage-with-env.nix @@ -13,7 +13,6 @@ , gmp , gfan , python3 -, flintqs , eclib , ntl , ecm @@ -40,7 +39,6 @@ let gfan maxima eclib - flintqs ntl ecm ]; diff --git a/nixpkgs/pkgs/applications/science/math/singular/default.nix b/nixpkgs/pkgs/applications/science/math/singular/default.nix index a6c64066d88e..d079134aec76 100644 --- a/nixpkgs/pkgs/applications/science/math/singular/default.nix +++ b/nixpkgs/pkgs/applications/science/math/singular/default.nix @@ -13,12 +13,9 @@ , doxygen , graphviz , latex2html -# upstream generates docs with texinfo 4. later versions of texinfo -# use letters instead of numbers for post-appendix chapters, and we -# want it to match the upstream format because sage depends on it. -, texinfo4 +, texinfo , texliveSmall -, enableDocs ? true +, enableDocs ? !stdenv.isDarwin , enableGfanlib ? true }: @@ -85,7 +82,7 @@ stdenv.mkDerivation rec { doxygen graphviz latex2html - texinfo4 + texinfo texliveSmall ] ++ lib.optionals stdenv.isDarwin [ getconf ]; depsBuildBuild = [ buildPackages.stdenv.cc ]; diff --git a/nixpkgs/pkgs/applications/science/misc/cytoscape/default.nix b/nixpkgs/pkgs/applications/science/misc/cytoscape/default.nix index f4aaac1a3823..1d42600d9770 100644 --- a/nixpkgs/pkgs/applications/science/misc/cytoscape/default.nix +++ b/nixpkgs/pkgs/applications/science/misc/cytoscape/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "cytoscape"; - version = "3.10.1"; + version = "3.10.2"; src = fetchurl { url = "https://github.com/cytoscape/cytoscape/releases/download/${version}/${pname}-unix-${version}.tar.gz"; - sha256 = "sha256-fqxAsnpMYCYj0hW2oxu/NH4PqesRlWPs5eDSeSjy1aU="; + sha256 = "sha256-ArT+g3GbtSxq3FvRi1H4z/kpsmcFCmKhzEJI4bCK44E="; }; patches = [ |