diff options
Diffstat (limited to 'pkgs/applications/science')
30 files changed, 65 insertions, 13 deletions
diff --git a/pkgs/applications/science/biology/flywheel-cli/default.nix b/pkgs/applications/science/biology/flywheel-cli/default.nix index 7db8b0066263a..7d74b51f6066f 100644 --- a/pkgs/applications/science/biology/flywheel-cli/default.nix +++ b/pkgs/applications/science/biology/flywheel-cli/default.nix @@ -42,6 +42,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Library and command line interface for interacting with a Flywheel site"; homepage = "https://gitlab.com/flywheel-io/public/python-cli"; + sourceProvenance = with sourceTypes; [ binaryNativeCode ]; license = licenses.mit; maintainers = with maintainers; [ rbreslow ]; platforms = [ "x86_64-darwin" "x86_64-linux" ]; diff --git a/pkgs/applications/science/biology/quast/default.nix b/pkgs/applications/science/biology/quast/default.nix index ed3fc116ddaba..0a33c97673196 100644 --- a/pkgs/applications/science/biology/quast/default.nix +++ b/pkgs/applications/science/biology/quast/default.nix @@ -49,6 +49,10 @@ pythonPackages.buildPythonApplication rec { meta = with lib ; { description = "Evaluates genome assemblies by computing various metrics"; homepage = "https://github.com/ablab/quast"; + sourceProvenance = with sourceTypes; [ + fromSource + binaryNativeCode # source bundles binary dependencies + ]; license = licenses.gpl2; maintainers = [ maintainers.bzizou ]; platforms = platforms.all; diff --git a/pkgs/applications/science/electronics/bitscope/common.nix b/pkgs/applications/science/electronics/bitscope/common.nix index 49415ea048413..2018878773ef0 100644 --- a/pkgs/applications/science/electronics/bitscope/common.nix +++ b/pkgs/applications/science/electronics/bitscope/common.nix @@ -24,6 +24,7 @@ let meta = with lib; { homepage = "http://bitscope.com/software/"; + sourceProvenance = with sourceTypes; [ binaryNativeCode ]; license = licenses.unfree; platforms = [ "x86_64-linux" ]; maintainers = with maintainers; [ diff --git a/pkgs/applications/science/electronics/eagle/eagle.nix b/pkgs/applications/science/electronics/eagle/eagle.nix index 5b4c8eb790fe6..6302c2dbfa384 100644 --- a/pkgs/applications/science/electronics/eagle/eagle.nix +++ b/pkgs/applications/science/electronics/eagle/eagle.nix @@ -73,6 +73,7 @@ let meta = with lib; { description = "Schematic editor and PCB layout tool from Autodesk (formerly CadSoft)"; homepage = "https://www.autodesk.com/products/eagle/overview"; + sourceProvenance = with sourceTypes; [ binaryNativeCode ]; license = licenses.unfree; platforms = [ "x86_64-linux" ]; maintainers = [ ]; diff --git a/pkgs/applications/science/electronics/picoscope/default.nix b/pkgs/applications/science/electronics/picoscope/default.nix index 7db5cceebbaf6..596f220242bb2 100644 --- a/pkgs/applications/science/electronics/picoscope/default.nix +++ b/pkgs/applications/science/electronics/picoscope/default.nix @@ -41,6 +41,7 @@ let ''; meta = with lib; shared_meta lib // { + sourceProvenance = with sourceTypes; [ binaryNativeCode ]; description = "library for picotech oscilloscope software"; }; }) { }; @@ -132,6 +133,7 @@ in stdenv.mkDerivation rec { PicoScope for Linux, PicoScope for macOS and PicoScope for Windows users, or exported in text, CSV and MathWorks MATLAB 4 formats. ''; + sourceProvenance = with sourceTypes; [ binaryBytecode ]; }; } diff --git a/pkgs/applications/science/logic/isabelle/default.nix b/pkgs/applications/science/logic/isabelle/default.nix index 9e5d40be2c6d5..009af3463a25a 100644 --- a/pkgs/applications/science/logic/isabelle/default.nix +++ b/pkgs/applications/science/logic/isabelle/default.nix @@ -47,10 +47,15 @@ in stdenv.mkDerivation rec { sha256 = "0jfaqckhg388jh9b4msrpkv6wrd6xzlw18m0bngbby8k8ywalp9i"; }; - buildInputs = [ polyml z3 veriT vampire eprover-ho ] - ++ lib.optionals (!stdenv.isDarwin) [ nettools java ]; + buildInputs = [ polyml z3 veriT vampire eprover-ho nettools ] + ++ lib.optionals (!stdenv.isDarwin) [ java ]; - sourceRoot = dirname; + sourceRoot = "${dirname}${lib.optionalString stdenv.isDarwin ".app"}"; + + postUnpack = if stdenv.isDarwin then '' + mv $sourceRoot ${dirname} + sourceRoot=${dirname} + '' else null; postPatch = '' patchShebangs . @@ -112,6 +117,9 @@ in stdenv.mkDerivation rec { --replace '"$ML_HOME/" ^ (if ML_System.platform_is_windows then "sha1.dll" else "libsha1.so")' '"${sha1}/lib/libsha1.so"' rm -r heaps + '' + lib.optionalString (stdenv.hostPlatform.system == "x86_64-darwin") '' + substituteInPlace lib/scripts/isabelle-platform \ + --replace 'ISABELLE_APPLE_PLATFORM64=arm64-darwin' "" '' + (if ! stdenv.isLinux then "" else '' arch=${if stdenv.hostPlatform.system == "x86_64-linux" then "x86_64-linux" else "x86-linux"} for f in contrib/*/$arch/{bash_process,epclextract,nunchaku,SPASS,zipperposition}; do @@ -178,9 +186,13 @@ in stdenv.mkDerivation rec { formulas in a logical calculus. ''; homepage = "https://isabelle.in.tum.de/"; + sourceProvenance = with sourceTypes; [ + fromSource + binaryNativeCode # source bundles binary dependencies + ]; license = licenses.bsd3; maintainers = [ maintainers.jwiegley maintainers.jvanbruegge ]; - platforms = platforms.linux; + platforms = platforms.unix; }; } // { withComponents = f: diff --git a/pkgs/applications/science/logic/nuXmv/default.nix b/pkgs/applications/science/logic/nuXmv/default.nix index 710cfdad39a8d..ad40902e92808 100644 --- a/pkgs/applications/science/logic/nuXmv/default.nix +++ b/pkgs/applications/science/logic/nuXmv/default.nix @@ -26,6 +26,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Symbolic model checker for analysis of finite and infinite state systems"; homepage = "https://nuxmv.fbk.eu/pmwiki.php"; + sourceProvenance = with sourceTypes; [ binaryNativeCode ]; license = licenses.unfree; maintainers = with maintainers; [ siraben ]; platforms = [ "x86_64-linux" "x86_64-darwin" ]; diff --git a/pkgs/applications/science/logic/saw-tools/default.nix b/pkgs/applications/science/logic/saw-tools/default.nix index df99d067f08c8..b6291bfae3698 100644 --- a/pkgs/applications/science/logic/saw-tools/default.nix +++ b/pkgs/applications/science/logic/saw-tools/default.nix @@ -51,6 +51,7 @@ stdenv.mkDerivation { meta = { description = "Tools for software verification and analysis"; homepage = "https://saw.galois.com"; + sourceProvenance = with lib.sourceTypes; [ binaryNativeCode ]; license = lib.licenses.bsd3; platforms = lib.platforms.linux; maintainers = [ lib.maintainers.thoughtpolice ]; diff --git a/pkgs/applications/science/logic/tlaplus/toolbox.nix b/pkgs/applications/science/logic/tlaplus/toolbox.nix index 3c53e66c8bd9f..86c3db9942a1e 100644 --- a/pkgs/applications/science/logic/tlaplus/toolbox.nix +++ b/pkgs/applications/science/logic/tlaplus/toolbox.nix @@ -97,6 +97,7 @@ stdenv.mkDerivation rec { ''; # http://lamport.azurewebsites.net/tla/license.html license = with lib.licenses; [ mit ]; + sourceProvenance = with lib.sourceTypes; [ binaryNativeCode ]; platforms = [ "x86_64-linux" ]; maintainers = [ ]; }; diff --git a/pkgs/applications/science/logic/tptp/default.nix b/pkgs/applications/science/logic/tptp/default.nix index 9c91eaddfc47e..5df511ebaa8e7 100644 --- a/pkgs/applications/science/logic/tptp/default.nix +++ b/pkgs/applications/science/logic/tptp/default.nix @@ -44,6 +44,7 @@ stdenv.mkDerivation rec { # Also, it is unclear what is covered by "verbatim" - we will edit configs hydraPlatforms = []; platforms = platforms.all; + sourceProvenance = with sourceTypes; [ binaryNativeCode ]; license = licenses.unfreeRedistributable; }; } diff --git a/pkgs/applications/science/logic/verifast/default.nix b/pkgs/applications/science/logic/verifast/default.nix index c610256ccaef8..a1f5ec65a3be3 100644 --- a/pkgs/applications/science/logic/verifast/default.nix +++ b/pkgs/applications/science/logic/verifast/default.nix @@ -43,6 +43,7 @@ stdenv.mkDerivation rec { meta = { description = "Verification for C and Java programs via separation logic"; homepage = "https://people.cs.kuleuven.be/~bart.jacobs/verifast/"; + sourceProvenance = with lib.sourceTypes; [ binaryNativeCode ]; license = lib.licenses.mit; platforms = [ "x86_64-linux" ]; maintainers = [ lib.maintainers.thoughtpolice ]; diff --git a/pkgs/applications/science/logic/z3/4.4.0.nix b/pkgs/applications/science/logic/z3/4.4.0.nix index a3d6c16fb7df2..857bbbdee5d00 100644 --- a/pkgs/applications/science/logic/z3/4.4.0.nix +++ b/pkgs/applications/science/logic/z3/4.4.0.nix @@ -14,6 +14,8 @@ stdenv.mkDerivation rec { buildInputs = [ python ]; enableParallelBuilding = true; + CXXFLAGS = if stdenv.isDarwin then "-std=gnu++98" else null; + configurePhase = "python scripts/mk_make.py --prefix=$out && cd build"; # z3's install phase is stupid because it tries to calculate the diff --git a/pkgs/applications/science/machine-learning/sc2-headless/default.nix b/pkgs/applications/science/machine-learning/sc2-headless/default.nix index 9438cd972f95b..97cad175ac17f 100644 --- a/pkgs/applications/science/machine-learning/sc2-headless/default.nix +++ b/pkgs/applications/science/machine-learning/sc2-headless/default.nix @@ -51,6 +51,7 @@ in stdenv.mkDerivation rec { meta = { platforms = lib.platforms.linux; description = "Starcraft II headless linux client for machine learning research"; + sourceProvenance = with lib.sourceTypes; [ binaryNativeCode ]; license = { fullName = "BLIZZARD® STARCRAFT® II AI AND MACHINE LEARNING LICENSE"; url = "https://blzdistsc2-a.akamaihd.net/AI_AND_MACHINE_LEARNING_LICENSE.html"; diff --git a/pkgs/applications/science/math/cplex/default.nix b/pkgs/applications/science/math/cplex/default.nix index a570e7e9c6d1e..ddc950b30664b 100644 --- a/pkgs/applications/science/math/cplex/default.nix +++ b/pkgs/applications/science/math/cplex/default.nix @@ -80,6 +80,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Optimization solver for mathematical programming"; homepage = "https://www.ibm.com/be-en/marketplace/ibm-ilog-cplex"; + sourceProvenance = with sourceTypes; [ binaryNativeCode ]; license = licenses.unfree; platforms = [ "x86_64-linux" ]; maintainers = with maintainers; [ bfortz ]; diff --git a/pkgs/applications/science/math/geogebra/default.nix b/pkgs/applications/science/math/geogebra/default.nix index b7eb8b11ecdc8..43d1a3e2068b9 100644 --- a/pkgs/applications/science/math/geogebra/default.nix +++ b/pkgs/applications/science/math/geogebra/default.nix @@ -29,6 +29,10 @@ let homepage = "https://www.geogebra.org/"; maintainers = with maintainers; [ sikmir imsofi ]; license = with licenses; [ gpl3 cc-by-nc-sa-30 geogebra ]; + sourceProvenance = with sourceTypes; [ + binaryBytecode + binaryNativeCode # some jars include native binaries + ]; platforms = with platforms; linux ++ darwin; hydraPlatforms = []; }; diff --git a/pkgs/applications/science/math/geogebra/geogebra6.nix b/pkgs/applications/science/math/geogebra/geogebra6.nix index 76d178b7e490d..e1b5bbaedc2b1 100644 --- a/pkgs/applications/science/math/geogebra/geogebra6.nix +++ b/pkgs/applications/science/math/geogebra/geogebra6.nix @@ -48,7 +48,7 @@ let }; darwinPkg = stdenv.mkDerivation { - inherit pname version meta; + inherit pname version; src = fetchurl { urls = [ @@ -66,6 +66,10 @@ let install -dm755 $out/Applications unzip $src -d $out/Applications ''; + + meta = meta // { + sourceProvenance = with lib.sourceTypes; [ binaryNativeCode ]; + }; }; in if stdenv.isDarwin diff --git a/pkgs/applications/science/math/gurobi/default.nix b/pkgs/applications/science/math/gurobi/default.nix index 574d849d955c2..536d520058a2d 100644 --- a/pkgs/applications/science/math/gurobi/default.nix +++ b/pkgs/applications/science/math/gurobi/default.nix @@ -46,7 +46,10 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Optimization solver for mathematical programming"; homepage = "https://www.gurobi.com"; - sourceProvenance = with sourceTypes; [ binaryBytecode ]; + sourceProvenance = with sourceTypes; [ + binaryBytecode + binaryNativeCode + ]; license = licenses.unfree; platforms = [ "x86_64-linux" ]; maintainers = with maintainers; [ jfrankenau ]; diff --git a/pkgs/applications/science/math/hmetis/default.nix b/pkgs/applications/science/math/hmetis/default.nix index 762216a97a444..1c0152b7bfc77 100644 --- a/pkgs/applications/science/math/hmetis/default.nix +++ b/pkgs/applications/science/math/hmetis/default.nix @@ -36,6 +36,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "hMETIS is a set of programs for partitioning hypergraphs"; homepage = "http://glaros.dtc.umn.edu/gkhome/metis/hmetis/overview"; + sourceProvenance = with sourceTypes; [ binaryNativeCode ]; license = licenses.unfree; platforms = [ "i686-linux" "x86_64-linux" ]; }; diff --git a/pkgs/applications/science/math/mathematica/generic.nix b/pkgs/applications/science/math/mathematica/generic.nix index 0f4819172cea9..b081640c97d5b 100644 --- a/pkgs/applications/science/math/mathematica/generic.nix +++ b/pkgs/applications/science/math/mathematica/generic.nix @@ -121,6 +121,8 @@ in stdenv.mkDerivation { "--set USE_WOLFRAM_LD_LIBRARY_PATH 1" # Fix xkeyboard config path for Qt "--set QT_XKB_CONFIG_ROOT ${xkeyboard_config}/share/X11/xkb" + # wayland isn't supported + "--set QT_QPA_PLATFORM xcb" ] ++ lib.optionals cudaSupport [ "--set CUDA_PATH ${cudaEnv}" "--set NVIDIA_DRIVER_LIBRARY_PATH ${addOpenGLRunpath.driverLink}/lib/libnvidia-tls.so" diff --git a/pkgs/applications/science/math/scilab-bin/default.nix b/pkgs/applications/science/math/scilab-bin/default.nix index 65d8c145bef6f..327472e88c752 100644 --- a/pkgs/applications/science/math/scilab-bin/default.nix +++ b/pkgs/applications/science/math/scilab-bin/default.nix @@ -93,6 +93,7 @@ stdenv.mkDerivation rec { meta = { homepage = "http://www.scilab.org/"; description = "Scientific software package for numerical computations (Matlab lookalike)"; + sourceProvenance = with lib.sourceTypes; [ binaryNativeCode ]; # see http://www.scilab.org/legal_notice license = "Scilab"; }; diff --git a/pkgs/applications/science/math/wolfram-engine/default.nix b/pkgs/applications/science/math/wolfram-engine/default.nix index cf9364ffac174..acb92766910d0 100644 --- a/pkgs/applications/science/math/wolfram-engine/default.nix +++ b/pkgs/applications/science/math/wolfram-engine/default.nix @@ -140,6 +140,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Wolfram Engine computational software system"; homepage = "https://www.wolfram.com/engine/"; + sourceProvenance = with sourceTypes; [ binaryNativeCode ]; license = licenses.unfree; maintainers = with maintainers; [ fbeffa ]; platforms = [ "x86_64-linux" ]; diff --git a/pkgs/applications/science/medicine/aliza/default.nix b/pkgs/applications/science/medicine/aliza/default.nix index 0eb89b63e475f..b08acc77c640c 100644 --- a/pkgs/applications/science/medicine/aliza/default.nix +++ b/pkgs/applications/science/medicine/aliza/default.nix @@ -52,6 +52,7 @@ stdenv.mkDerivation { meta = { description = "Medical imaging software with 2D, 3D and 4D capabilities"; homepage = "https://www.aliza-dicom-viewer.com"; + sourceProvenance = with lib.sourceTypes; [ binaryNativeCode ]; license = licenses.unfreeRedistributable; maintainers = with maintainers; [ mounium ]; platforms = platforms.linux; diff --git a/pkgs/applications/science/misc/boinc/default.nix b/pkgs/applications/science/misc/boinc/default.nix index d0955a4d70c45..702dd3242e649 100644 --- a/pkgs/applications/science/misc/boinc/default.nix +++ b/pkgs/applications/science/misc/boinc/default.nix @@ -3,8 +3,8 @@ libGLU, libGL, libXmu, libXi, freeglut, libjpeg, libtool, wxGTK30, xcbutil, sqlite, gtk2, patchelf, libXScrnSaver, libnotify, libX11, libxcb }: let - majorVersion = "7.18"; - minorVersion = "1"; + majorVersion = "7.20"; + minorVersion = "0"; in stdenv.mkDerivation rec { @@ -16,7 +16,7 @@ stdenv.mkDerivation rec { owner = "BOINC"; repo = "boinc"; rev = "client_release/${majorVersion}/${version}"; - sha256 = "sha256-ijkfWTFwwJXvh6f0P5hkzWODxU+Ugz6iQUK+5jEpWXQ="; + sha256 = "sha256-W8+ALVO2OHxxBi80ZFgc8RxXneGINCHYNeMXimp9TIw="; }; nativeBuildInputs = [ libtool automake autoconf m4 pkg-config ]; diff --git a/pkgs/applications/science/misc/foldingathome/client.nix b/pkgs/applications/science/misc/foldingathome/client.nix index cc3d5445b594d..6ebc72cc7da41 100644 --- a/pkgs/applications/science/misc/foldingathome/client.nix +++ b/pkgs/applications/science/misc/foldingathome/client.nix @@ -52,6 +52,7 @@ buildFHSUserEnv { meta = { description = "Folding@home client"; homepage = "https://foldingathome.org/"; + sourceProvenance = with lib.sourceTypes; [ binaryNativeCode ]; license = lib.licenses.unfree; maintainers = [ lib.maintainers.zimbatm ]; platforms = [ "x86_64-linux" ]; diff --git a/pkgs/applications/science/misc/foldingathome/control.nix b/pkgs/applications/science/misc/foldingathome/control.nix index e5cc02edcfbe6..a64c973914c66 100644 --- a/pkgs/applications/science/misc/foldingathome/control.nix +++ b/pkgs/applications/science/misc/foldingathome/control.nix @@ -1,5 +1,4 @@ { lib, stdenv -, autoPatchelfHook , dpkg , fahviewer , fetchurl diff --git a/pkgs/applications/science/misc/foldingathome/viewer.nix b/pkgs/applications/science/misc/foldingathome/viewer.nix index 75e900a0a72c5..7f28c8d1b1463 100644 --- a/pkgs/applications/science/misc/foldingathome/viewer.nix +++ b/pkgs/applications/science/misc/foldingathome/viewer.nix @@ -48,6 +48,7 @@ stdenv.mkDerivation rec { meta = { description = "Folding@home viewer"; homepage = "https://foldingathome.org/"; + sourceProvenance = with lib.sourceTypes; [ binaryNativeCode ]; license = lib.licenses.unfree; maintainers = [ lib.maintainers.zimbatm ]; platforms = [ "x86_64-linux" ]; diff --git a/pkgs/applications/science/programming/fdr/default.nix b/pkgs/applications/science/programming/fdr/default.nix index bc67c30aa61cf..f7b12342a6659 100644 --- a/pkgs/applications/science/programming/fdr/default.nix +++ b/pkgs/applications/science/programming/fdr/default.nix @@ -63,6 +63,7 @@ stdenv.mkDerivation { homepage = "https://cocotec.io/fdr/"; description = "The CSP refinement checker"; license = licenses.unfreeRedistributable; + sourceProvenance = with sourceTypes; [ binaryNativeCode ]; platforms = platforms.linux; maintainers = with maintainers; [ nickhu ]; }; diff --git a/pkgs/applications/science/robotics/betaflight-configurator/default.nix b/pkgs/applications/science/robotics/betaflight-configurator/default.nix index 5065723995245..271274126b754 100644 --- a/pkgs/applications/science/robotics/betaflight-configurator/default.nix +++ b/pkgs/applications/science/robotics/betaflight-configurator/default.nix @@ -13,10 +13,10 @@ let in stdenv.mkDerivation rec { inherit pname; - version = "10.7.2"; + version = "10.8.0"; src = fetchurl { - url = "https://github.com/betaflight/${pname}/releases/download/${version}/${pname}_${version}_linux64.zip"; - sha256 = "sha256-FDmtFRUupPKiHeF3Xvh/VagqMo+FJi8I7mhTz0VDs3o="; + url = "https://github.com/betaflight/${pname}/releases/download/${version}/${pname}_${version}_linux64-portable.zip"; + sha256 = "sha256-Xn0ga2Z1UKd++TriL47ulV6idVTNBR8uiSW7FnL7r1g="; }; nativeBuildInputs = [ wrapGAppsHook unzip ]; @@ -42,6 +42,7 @@ stdenv.mkDerivation rec { quadcopters, hexacopters, octocopters and fixed-wing aircraft. ''; homepage = "https://github.com/betaflight/betaflight/wiki"; + sourceProvenance = with sourceTypes; [ binaryNativeCode ]; license = licenses.gpl3; maintainers = with maintainers; [ wucke13 ]; platforms = platforms.linux; diff --git a/pkgs/applications/science/robotics/emuflight-configurator/default.nix b/pkgs/applications/science/robotics/emuflight-configurator/default.nix index ca486006fecba..112049d7c0169 100644 --- a/pkgs/applications/science/robotics/emuflight-configurator/default.nix +++ b/pkgs/applications/science/robotics/emuflight-configurator/default.nix @@ -43,6 +43,7 @@ stdenv.mkDerivation rec { The application allows you to configure the Emuflight software running on any supported Emuflight target. ''; homepage = "https://github.com/emuflight/EmuConfigurator"; + sourceProvenance = with sourceTypes; [ binaryNativeCode ]; license = licenses.gpl3Only; maintainers = with maintainers; [ beezow ]; platforms = platforms.linux; diff --git a/pkgs/applications/science/robotics/inav-configurator/default.nix b/pkgs/applications/science/robotics/inav-configurator/default.nix index ec605a3a97e95..a0b694f295415 100644 --- a/pkgs/applications/science/robotics/inav-configurator/default.nix +++ b/pkgs/applications/science/robotics/inav-configurator/default.nix @@ -50,6 +50,7 @@ stdenv.mkDerivation rec { quadcopters, hexacopters, octocopters and fixed-wing aircraft. ''; homepage = "https://github.com/iNavFlight/inav/wiki"; + sourceProvenance = with sourceTypes; [ binaryNativeCode ]; license = licenses.gpl3Only; maintainers = with maintainers; [ tilcreator wucke13 ]; platforms = platforms.linux; |