diff options
Diffstat (limited to 'pkgs/applications/science')
19 files changed, 64 insertions, 77 deletions
diff --git a/pkgs/applications/science/electronics/eagle/eagle7.nix b/pkgs/applications/science/electronics/eagle/eagle7.nix index 9b8827187b26..d5720440f7cc 100644 --- a/pkgs/applications/science/electronics/eagle/eagle7.nix +++ b/pkgs/applications/science/electronics/eagle/eagle7.nix @@ -17,18 +17,18 @@ stdenv.mkDerivation rec { version = "7.7.0"; src = - if stdenv.system == "i686-linux" then + if stdenv.hostPlatform.system == "i686-linux" then fetchurl { url = "ftp://ftp.cadsoft.de/eagle/program/7.7/eagle-lin32-${version}.run"; sha256 = "16fa66p77xigc7zvzfm7737mllrcs6nrgk2p7wvkjw3p9lvbz7z1"; } - else if stdenv.system == "x86_64-linux" then + else if stdenv.hostPlatform.system == "x86_64-linux" then fetchurl { url = "ftp://ftp.cadsoft.de/eagle/program/7.7/eagle-lin64-${version}.run"; sha256 = "18dcn6wqph1sqh0ah98qzfi05wip8a8ifbkaq79iskbrsi8iqnrg"; } else - throw "Unsupported system: ${stdenv.system}"; + throw "Unsupported system: ${stdenv.hostPlatform.system}"; desktopItem = makeDesktopItem { name = "eagle"; diff --git a/pkgs/applications/science/electronics/verilator/default.nix b/pkgs/applications/science/electronics/verilator/default.nix index 6ee3f3266f8d..fd6240fe1b21 100644 --- a/pkgs/applications/science/electronics/verilator/default.nix +++ b/pkgs/applications/science/electronics/verilator/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { name = "verilator-${version}"; - version = "3.924"; + version = "3.926"; src = fetchurl { url = "https://www.veripool.org/ftp/${name}.tgz"; - sha256 = "0xarifraycmdzjxs0lscpwvrwr59z84p8g8dkyjssc463dqikjvx"; + sha256 = "0f4ajj1gmxskid61qj1ql1rzc3cmn1x2fpgqrbg7x3gszz61c9gr"; }; enableParallelBuilding = true; diff --git a/pkgs/applications/science/logic/isabelle/default.nix b/pkgs/applications/science/logic/isabelle/default.nix index ae04c11d9590..ffe508569553 100644 --- a/pkgs/applications/science/logic/isabelle/default.nix +++ b/pkgs/applications/science/logic/isabelle/default.nix @@ -48,7 +48,7 @@ stdenv.mkDerivation { rm -rf $comp/x86* done '' + (if ! stdenv.isLinux then "" else '' - arch=${if stdenv.system == "x86_64-linux" then "x86_64-linux" else "x86-linux"} + arch=${if stdenv.hostPlatform.system == "x86_64-linux" then "x86_64-linux" else "x86-linux"} for f in contrib/*/$arch/{bash_process,epclextract,eprover,nunchaku,SPASS}; do patchelf --set-interpreter $(cat ${stdenv.cc}/nix-support/dynamic-linker) "$f" done diff --git a/pkgs/applications/science/logic/jonprl/default.nix b/pkgs/applications/science/logic/jonprl/default.nix index 982b5fc8b5fb..a95d1201cbd6 100644 --- a/pkgs/applications/science/logic/jonprl/default.nix +++ b/pkgs/applications/science/logic/jonprl/default.nix @@ -26,7 +26,7 @@ stdenv.mkDerivation rec { based on Brouwer-realizability & meaning explanations. Inspired by Nuprl ''; - homepage = http://www.jonprl.org/; + homepage = https://github.com/jonsterling/JonPRL; license = stdenv.lib.licenses.mit; maintainers = with stdenv.lib.maintainers; [ puffnfresh ]; platforms = stdenv.lib.platforms.linux; diff --git a/pkgs/applications/science/logic/saw-tools/default.nix b/pkgs/applications/science/logic/saw-tools/default.nix index 65d2b4d91c30..32ebdad51d94 100644 --- a/pkgs/applications/science/logic/saw-tools/default.nix +++ b/pkgs/applications/science/logic/saw-tools/default.nix @@ -12,7 +12,7 @@ let url = "https://github.com/GaloisInc/saw-script/releases/download"; saw-bin = - if stdenv.system == "i686-linux" + if stdenv.hostPlatform.system == "i686-linux" then fetchurl { url = url + "/v0.1.1-dev/saw-0.1.1-dev-2015-07-31-CentOS6-32.tar.gz"; sha256 = "126iag5nnvndi78c921z7vjrjfwcspn1hlxwwhzmqm4rvbhhr9v9"; diff --git a/pkgs/applications/science/logic/vampire/default.nix b/pkgs/applications/science/logic/vampire/default.nix index e05839b2a143..8dd8584b9a3c 100644 --- a/pkgs/applications/science/logic/vampire/default.nix +++ b/pkgs/applications/science/logic/vampire/default.nix @@ -8,7 +8,7 @@ stdenv.mkDerivation rec { owner = "vprover"; repo = "vampire"; rev = version; - sha256 = "080zwgmyhn0b2c6hqlhcgaw7n3frz02sh894v5kk68kzxbqr29w2"; + sha256 = "1n0kf0g15yjw3v7z60l51h7fdn880mmvqsbb2szh48vzy20l92il"; fetchSubmodules = true; leaveDotGit = true; }; diff --git a/pkgs/applications/science/math/jags/default.nix b/pkgs/applications/science/math/jags/default.nix index 2925e601e32b..1d1fb96a4739 100644 --- a/pkgs/applications/science/math/jags/default.nix +++ b/pkgs/applications/science/math/jags/default.nix @@ -9,11 +9,11 @@ stdenv.mkDerivation rec { buildInputs = [gfortran openblas]; configureFlags = [ "--with-blas=-lopenblas" "--with-lapack=-lopenblas" ]; - meta = { + meta = with stdenv.lib; { description = "Just Another Gibbs Sampler"; - license = "GPL2"; - homepage = http://www-ice.iarc.fr/~martyn/software/jags/; - maintainers = [stdenv.lib.maintainers.andres]; - platforms = stdenv.lib.platforms.unix; + license = licenses.gpl2; + homepage = http://mcmc-jags.sourceforge.net; + maintainers = [ maintainers.andres ]; + platforms = platforms.unix; }; } diff --git a/pkgs/applications/science/math/mathematica/10.nix b/pkgs/applications/science/math/mathematica/10.nix index 4884ee1f93ab..c6802c3719e9 100644 --- a/pkgs/applications/science/math/mathematica/10.nix +++ b/pkgs/applications/science/math/mathematica/10.nix @@ -18,7 +18,7 @@ let platform = - if stdenv.system == "i686-linux" || stdenv.system == "x86_64-linux" then + if stdenv.hostPlatform.system == "i686-linux" || stdenv.hostPlatform.system == "x86_64-linux" then "Linux" else throw "Mathematica requires i686-linux or x86_64 linux"; @@ -70,7 +70,7 @@ stdenv.mkDerivation rec { ]); ldpath = stdenv.lib.makeLibraryPath buildInputs - + stdenv.lib.optionalString (stdenv.system == "x86_64-linux") + + stdenv.lib.optionalString (stdenv.hostPlatform.system == "x86_64-linux") (":" + stdenv.lib.makeSearchPathOutput "lib" "lib64" buildInputs); phases = "unpackPhase installPhase fixupPhase"; diff --git a/pkgs/applications/science/math/mathematica/9.nix b/pkgs/applications/science/math/mathematica/9.nix index d60feb54695d..1023e7ca3d5c 100644 --- a/pkgs/applications/science/math/mathematica/9.nix +++ b/pkgs/applications/science/math/mathematica/9.nix @@ -16,7 +16,7 @@ let platform = - if stdenv.system == "i686-linux" || stdenv.system == "x86_64-linux" then + if stdenv.hostPlatform.system == "i686-linux" || stdenv.hostPlatform.system == "x86_64-linux" then "Linux" else throw "Mathematica requires i686-linux or x86_64 linux"; @@ -60,7 +60,7 @@ stdenv.mkDerivation rec { ]); ldpath = stdenv.lib.makeLibraryPath buildInputs - + stdenv.lib.optionalString (stdenv.system == "x86_64-linux") + + stdenv.lib.optionalString (stdenv.hostPlatform.system == "x86_64-linux") (":" + stdenv.lib.makeSearchPathOutput "lib" "lib64" buildInputs); phases = "unpackPhase installPhase fixupPhase"; diff --git a/pkgs/applications/science/math/mathematica/default.nix b/pkgs/applications/science/math/mathematica/default.nix index fa4ff8b00687..165a56605579 100644 --- a/pkgs/applications/science/math/mathematica/default.nix +++ b/pkgs/applications/science/math/mathematica/default.nix @@ -69,7 +69,7 @@ stdenv.mkDerivation rec { ]); ldpath = stdenv.lib.makeLibraryPath buildInputs - + stdenv.lib.optionalString (stdenv.system == "x86_64-linux") + + stdenv.lib.optionalString (stdenv.hostPlatform.system == "x86_64-linux") (":" + stdenv.lib.makeSearchPathOutput "lib" "lib64" buildInputs); phases = "unpackPhase installPhase fixupPhase"; diff --git a/pkgs/applications/science/math/sage/default.nix b/pkgs/applications/science/math/sage/default.nix index 7e62f0cf75ee..08e3a752b8b6 100644 --- a/pkgs/applications/science/math/sage/default.nix +++ b/pkgs/applications/science/math/sage/default.nix @@ -21,7 +21,7 @@ let sagelib = self.callPackage ./sagelib.nix { inherit flint ecl arb; - inherit sage-src openblas-blas-pc openblas-cblas-pc openblas-lapack-pc pynac singular; + inherit sage-src pynac singular; linbox = nixpkgs.linbox.override { withSage = true; }; }; @@ -41,13 +41,13 @@ let }; sage-env = self.callPackage ./sage-env.nix { - inherit sage-src python rWrapper openblas-cblas-pc ecl singular palp flint pynac pythonEnv; + inherit sage-src python rWrapper ecl singular palp flint pynac pythonEnv; pkg-config = nixpkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig }; sage-with-env = self.callPackage ./sage-with-env.nix { inherit pythonEnv; - inherit sage-src openblas-blas-pc openblas-cblas-pc openblas-lapack-pc pynac singular; + inherit sage-src pynac singular; pkg-config = nixpkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig three = nodePackages_8_x.three; }; @@ -60,10 +60,6 @@ let }; }; - openblas-blas-pc = callPackage ./openblas-pc.nix { name = "blas"; }; - openblas-cblas-pc = callPackage ./openblas-pc.nix { name = "cblas"; }; - openblas-lapack-pc = callPackage ./openblas-pc.nix { name = "lapack"; }; - sage-src = callPackage ./sage-src.nix {}; pythonRuntimeDeps = with python.pkgs; [ diff --git a/pkgs/applications/science/math/sage/openblas-pc.nix b/pkgs/applications/science/math/sage/openblas-pc.nix deleted file mode 100644 index f4669a6557e9..000000000000 --- a/pkgs/applications/science/math/sage/openblas-pc.nix +++ /dev/null @@ -1,17 +0,0 @@ -{ openblasCompat -, writeTextFile -, name -}: - -writeTextFile { - name = "openblas-${name}-pc-${openblasCompat.version}"; - destination = "/lib/pkgconfig/${name}.pc"; - text = '' - Name: ${name} - Version: ${openblasCompat.version} - - Description: ${name} for SageMath, provided by the OpenBLAS package. - Cflags: -I${openblasCompat}/include - Libs: -L${openblasCompat}/lib -lopenblas - ''; -} diff --git a/pkgs/applications/science/math/sage/sage-env.nix b/pkgs/applications/science/math/sage/sage-env.nix index 317eb6e16c49..74c2e0aa0360 100644 --- a/pkgs/applications/science/math/sage/sage-env.nix +++ b/pkgs/applications/science/math/sage/sage-env.nix @@ -37,7 +37,7 @@ , lcalc , rubiks , flintqs -, openblas-cblas-pc +, openblasCompat , flint , gmp , mpfr @@ -98,9 +98,9 @@ writeTextFile rec { export PKG_CONFIG_PATH='${lib.concatStringsSep ":" (map (pkg: "${pkg}/lib/pkgconfig") [ # This is only needed in the src/sage/misc/cython.py test and I'm not sure if there's really a use-case # for it outside of the tests. However since singular and openblas are runtime dependencies anyways - # and openblas-cblas-pc is tiny, it doesn't really hurt to include. + # it doesn't really hurt to include. singular - openblas-cblas-pc + openblasCompat ]) }' export SAGE_ROOT='${sage-src}' diff --git a/pkgs/applications/science/math/sage/sage-with-env.nix b/pkgs/applications/science/math/sage/sage-with-env.nix index 63b9772b8231..8ccf8b5a4938 100644 --- a/pkgs/applications/science/math/sage/sage-with-env.nix +++ b/pkgs/applications/science/math/sage/sage-with-env.nix @@ -4,9 +4,6 @@ , sage-env , sage-src , openblasCompat -, openblas-blas-pc -, openblas-cblas-pc -, openblas-lapack-pc , pkg-config , three , singular @@ -32,9 +29,6 @@ let makeWrapper pkg-config openblasCompat # lots of segfaults with regular (64 bit) openblas - openblas-blas-pc - openblas-cblas-pc - openblas-lapack-pc singular three pynac diff --git a/pkgs/applications/science/math/sage/sagelib.nix b/pkgs/applications/science/math/sage/sagelib.nix index abcefba5e260..c1dbcf38304e 100644 --- a/pkgs/applications/science/math/sage/sagelib.nix +++ b/pkgs/applications/science/math/sage/sagelib.nix @@ -3,9 +3,6 @@ , buildPythonPackage , arb , openblasCompat -, openblas-blas-pc -, openblas-cblas-pc -, openblas-lapack-pc , brial , cliquer , cypari2 @@ -59,9 +56,7 @@ buildPythonPackage rec { nativeBuildInputs = [ iml perl - openblas-blas-pc - openblas-cblas-pc - openblas-lapack-pc + openblasCompat jupyter_core ]; diff --git a/pkgs/applications/science/math/scilab-bin/default.nix b/pkgs/applications/science/math/scilab-bin/default.nix index dacd3e730736..54b262fe5058 100644 --- a/pkgs/applications/science/math/scilab-bin/default.nix +++ b/pkgs/applications/science/math/scilab-bin/default.nix @@ -10,9 +10,9 @@ let badArch = throw "${name} requires i686-linux or x86_64-linux"; architecture = - if stdenv.system == "i686-linux" then + if stdenv.hostPlatform.system == "i686-linux" then "i686" - else if stdenv.system == "x86_64-linux" then + else if stdenv.hostPlatform.system == "x86_64-linux" then "x86_64" else badArch; @@ -23,9 +23,9 @@ stdenv.mkDerivation rec { src = fetchurl { url = "https://www.scilab.org/download/${ver}/scilab-${ver}.bin.linux-${architecture}.tar.gz"; sha256 = - if stdenv.system == "i686-linux" then + if stdenv.hostPlatform.system == "i686-linux" then "0fgjc2ak3b2qi6yin3fy50qwk2bcj0zbz1h4lyyic9n1n1qcliib" - else if stdenv.system == "x86_64-linux" then + else if stdenv.hostPlatform.system == "x86_64-linux" then "1scswlznc14vyzg0gqa1q9gcpwx05kz1sbn563463mzkdp7nd35d" else badArch; diff --git a/pkgs/applications/science/math/symmetrica/default.nix b/pkgs/applications/science/math/symmetrica/default.nix index a641993b393b..bc971606cd08 100644 --- a/pkgs/applications/science/math/symmetrica/default.nix +++ b/pkgs/applications/science/math/symmetrica/default.nix @@ -57,6 +57,6 @@ stdenv.mkDerivation rec { license = stdenv.lib.licenses.publicDomain; maintainers = [stdenv.lib.maintainers.raskin]; platforms = stdenv.lib.platforms.unix; - homepage = http://www.symmetrica.de/; + homepage = http://www.algorithm.uni-bayreuth.de/en/research/SYMMETRICA/index.html; }; } diff --git a/pkgs/applications/science/molecular-dynamics/lammps/default.nix b/pkgs/applications/science/molecular-dynamics/lammps/default.nix index 9a89b88d7a52..03e37ad9d935 100644 --- a/pkgs/applications/science/molecular-dynamics/lammps/default.nix +++ b/pkgs/applications/science/molecular-dynamics/lammps/default.nix @@ -1,25 +1,37 @@ -{ stdenv, writeText, fetchurl, - libpng, fftw, - mpiSupport ? false, mpi ? null +{ lib +, bash +, stdenv +, writeText +, fetchFromGitHub +, libpng +, gzip +, fftw +, openblas +, mpiSupport ? false, mpi ? null }: assert mpiSupport -> mpi != null; stdenv.mkDerivation rec { # LAMMPS has weird versioning converted to ISO 8601 format - version = "2016-02-16"; + version = "patch_2Aug2018"; name = "lammps-${version}"; - src = fetchurl { - url = "mirror://sourceforge/lammps/lammps-16Feb16.tar.gz"; - sha256 = "1yzfbkxma3xa1288rnn66h4w0smbmjkwq1fx1y60pjiw0prmk105"; + lammps_packages = "asphere body class2 colloid compress coreshell dipole granular kspace manybody mc misc molecule opt peri qeq replica rigid shock snap srd user-reaxc"; + lammps_includes = "-DLAMMPS_EXCEPTIONS -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64"; + + src = fetchFromGitHub { + owner = "lammps"; + repo = "lammps"; + rev = "${version}"; + sha256 = "1ph9pr7s11wgmspmnhxa55bh1pq2cyl8iimfi62lbpbpl9pr1ilc"; }; passthru = { inherit mpi; }; - buildInputs = [ fftw libpng ] + buildInputs = [ fftw libpng openblas gzip bash ] ++ (stdenv.lib.optionals mpiSupport [ mpi ]); # Must do manual build due to LAMMPS requiring a seperate build for @@ -27,13 +39,19 @@ stdenv.mkDerivation rec { builder = writeText "builder.sh" '' source $stdenv/setup - tar xzf $src - cd lammps-*/src - make mode=exe ${if mpiSupport then "mpi" else "serial"} SHELL=$SHELL LMP_INC="-DLAMMPS_GZIP -DLAMMPS_PNG" FFT_PATH=-DFFT_FFTW3 FFT_LIB=-lfftw3 JPG_LIB=-lpng - make mode=shlib ${if mpiSupport then "mpi" else "serial"} SHELL=$SHELL LMP_INC="-DLAMMPS_GZIP -DLAMMPS_PNG" FFT_PATH=-DFFT_FFTW3 FFT_LIB=-lfftw3 JPG_LIB=-lpng + mkdir lammps + cp -r $src/lib $src/src lammps + chmod -R 755 lammps/src/ + cd lammps/src + for pack in ${lammps_packages}; do make "yes-$pack" SHELL=$SHELL; done + make mode=exe ${if mpiSupport then "mpi" else "serial"} SHELL=$SHELL LMP_INC="${lammps_includes}" FFT_PATH=-DFFT_FFTW3 FFT_LIB=-lfftw3 JPG_LIB=-lpng + make mode=shlib ${if mpiSupport then "mpi" else "serial"} SHELL=$SHELL LMP_INC="${lammps_includes}" FFT_PATH=-DFFT_FFTW3 FFT_LIB=-lfftw3 JPG_LIB=-lpng mkdir -p $out/bin - cp -v lmp_* $out/bin/lammps + cp -v lmp_* $out/bin/ + + mkdir -p $out/include + cp -v *.h $out/include/ mkdir -p $out/lib cp -v liblammps* $out/lib/ @@ -51,5 +69,6 @@ stdenv.mkDerivation rec { homepage = http://lammps.sandia.gov; license = stdenv.lib.licenses.gpl2; platforms = stdenv.lib.platforms.linux; + maintainers = with lib.maintainers; [ costrouc ]; }; } diff --git a/pkgs/applications/science/programming/plm/default.nix b/pkgs/applications/science/programming/plm/default.nix index f46f7afb659c..c454ad377686 100644 --- a/pkgs/applications/science/programming/plm/default.nix +++ b/pkgs/applications/science/programming/plm/default.nix @@ -28,9 +28,9 @@ stdenv.mkDerivation rec { meta = with stdenv.lib; { description = "Free cross-platform programming exerciser"; - homepage = http://webloria.loria.fr/~quinson/Teaching/PLM/; license = licenses.gpl3; maintainers = [ ]; platforms = stdenv.lib.platforms.all; + broken = true; }; } |