diff options
Diffstat (limited to 'pkgs/applications/science')
13 files changed, 66 insertions, 47 deletions
diff --git a/pkgs/applications/science/biology/picard-tools/default.nix b/pkgs/applications/science/biology/picard-tools/default.nix index a1616774d5d7..85d92d3af843 100644 --- a/pkgs/applications/science/biology/picard-tools/default.nix +++ b/pkgs/applications/science/biology/picard-tools/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "picard-tools"; - version = "2.22.9"; + version = "2.23.0"; src = fetchurl { url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar"; - sha256 = "0qm32a58b2asiw8rnw1r6vz3bi61vfdan6wyr9f78fj4d07q7n53"; + sha256 = "0yhgfz5jjw55ipgdb32wjdcb01xx2g9ikgvwinnfwswx50iscf5a"; }; nativeBuildInputs = [ makeWrapper ]; diff --git a/pkgs/applications/science/chemistry/jmol/default.nix b/pkgs/applications/science/chemistry/jmol/default.nix index f52621dd71af..45f28c93b380 100644 --- a/pkgs/applications/science/chemistry/jmol/default.nix +++ b/pkgs/applications/science/chemistry/jmol/default.nix @@ -17,14 +17,14 @@ let }; in stdenv.mkDerivation rec { - version = "14.30.2"; + version = "14.31.0"; pname = "jmol"; src = let baseVersion = "${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"; - sha256 = "0f9sxhxyqrd1vvmq566v1zpzzlci37pm9j7alzak766x5dg5yyz1"; + sha256 = "14p823vxb8sfis1dgq8i9kj0rqf3cb8d0l8pspb8nz30fcvp1q7f"; }; patchPhase = '' diff --git a/pkgs/applications/science/chemistry/marvin/default.nix b/pkgs/applications/science/chemistry/marvin/default.nix index 1a22544c270a..c090fbee377b 100644 --- a/pkgs/applications/science/chemistry/marvin/default.nix +++ b/pkgs/applications/science/chemistry/marvin/default.nix @@ -4,12 +4,12 @@ with stdenv.lib; stdenv.mkDerivation rec { pname = "marvin"; - version = "20.12.0"; + version = "20.13.0"; src = fetchurl { name = "marvin-${version}.deb"; url = "http://dl.chemaxon.com/marvin/${version}/marvin_linux_${versions.majorMinor version}.deb"; - sha256 = "1imfr56nbq2mbcyapwa8xmcmj5rjhbjz9r438387s73kd1avd6yl"; + sha256 = "1mbbl7z215l6z4acwdrmqnvlvc2hv4znz4dmng9iw7rrqns3jjlv"; }; nativeBuildInputs = [ dpkg makeWrapper ]; diff --git a/pkgs/applications/science/electronics/eagle/eagle.nix b/pkgs/applications/science/electronics/eagle/eagle.nix index 58bdd5c722da..4cfad20e695f 100644 --- a/pkgs/applications/science/electronics/eagle/eagle.nix +++ b/pkgs/applications/science/electronics/eagle/eagle.nix @@ -13,11 +13,11 @@ let in mkDerivation rec { pname = "eagle"; - version = "9.6.1"; + version = "9.6.2"; src = fetchurl { url = "https://eagle-updates.circuits.io/downloads/${builtins.replaceStrings ["."] ["_"] version}/Autodesk_EAGLE_${version}_English_Linux_64bit.tar.gz"; - sha256 = "1iq4aahrh4g3549vbr7gka5y2h7f17n3yafzl21njc2mkqb12jdw"; + sha256 = "18syygnskl286kn8aqfzzdsyzq59d2w19y1h1ynyxsnrvkyv71h0"; }; desktopItem = makeDesktopItem { diff --git a/pkgs/applications/science/electronics/verilator/default.nix b/pkgs/applications/science/electronics/verilator/default.nix index 189e09f8241b..0613e22bbda0 100644 --- a/pkgs/applications/science/electronics/verilator/default.nix +++ b/pkgs/applications/science/electronics/verilator/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "verilator"; - version = "4.034"; + version = "4.036"; src = fetchurl { url = "https://www.veripool.org/ftp/${pname}-${version}.tgz"; - sha256 = "02xqvl9ic21jpda0xldh4ihqwl4ss8389s8fklgx5d98xq37pval"; + sha256 = "1sy02pgq3kvk8548l57hsh08vfbqdg8dghj8mwlybdi8fdjz4z1h"; }; enableParallelBuilding = true; diff --git a/pkgs/applications/science/logic/abc/default.nix b/pkgs/applications/science/logic/abc/default.nix index a33cc92c7ce7..0bad0046e939 100644 --- a/pkgs/applications/science/logic/abc/default.nix +++ b/pkgs/applications/science/logic/abc/default.nix @@ -4,13 +4,13 @@ stdenv.mkDerivation rec { pname = "abc-verifier"; - version = "2020.03.05"; + version = "2020.04.30"; src = fetchFromGitHub { owner = "berkeley-abc"; repo = "abc"; - rev = "ed90ce20df9c7c4d6e1db5d3f786f9b52e06bab1"; - sha256 = "01sw67pkrb6wzflkxbkxzwsnli3nvp0yxwp3j1ngb3c0j86ri437"; + rev = "fd2c9b1c19216f6b756f88b18f5ca67b759ca128"; + sha256 = "1d18pkpsx0nlzl3a6lyfdnpk4kixjmgswy6cp5fbrkpp4rf1gahi"; }; nativeBuildInputs = [ cmake ]; diff --git a/pkgs/applications/science/logic/boolector/cmake-gtest.patch b/pkgs/applications/science/logic/boolector/cmake-gtest.patch new file mode 100644 index 000000000000..61a64d3abbbf --- /dev/null +++ b/pkgs/applications/science/logic/boolector/cmake-gtest.patch @@ -0,0 +1,16 @@ +diff --git a/cmake/googletest-download.cmake b/cmake/googletest-download.cmake +index 0ec4d558..d0910313 100644 +--- a/cmake/googletest-download.cmake ++++ b/cmake/googletest-download.cmake +@@ -9,10 +9,7 @@ ExternalProject_Add( + googletest + SOURCE_DIR "@GOOGLETEST_DOWNLOAD_ROOT@/googletest-src" + BINARY_DIR "@GOOGLETEST_DOWNLOAD_ROOT@/googletest-build" +- GIT_REPOSITORY +- https://github.com/google/googletest.git +- GIT_TAG +- release-1.10.0 ++ URL REPLACEME + CONFIGURE_COMMAND "" + BUILD_COMMAND "" + INSTALL_COMMAND "" diff --git a/pkgs/applications/science/logic/boolector/default.nix b/pkgs/applications/science/logic/boolector/default.nix index 105e911ed4fd..aedc8e3484a9 100644 --- a/pkgs/applications/science/logic/boolector/default.nix +++ b/pkgs/applications/science/logic/boolector/default.nix @@ -1,37 +1,31 @@ -{ stdenv, fetchFromGitHub, fetchpatch -, cmake, lingeling, btor2tools +{ stdenv, fetchFromGitHub, lib, python3 +, cmake, lingeling, btor2tools, gtest, gmp }: stdenv.mkDerivation rec { pname = "boolector"; - version = "3.0.0"; + version = "3.2.1"; src = fetchFromGitHub { owner = "boolector"; repo = "boolector"; rev = "refs/tags/${version}"; - sha256 = "15i3ni5klss423m57wcy1gx0m5wfrjmglapwg85pm7fb3jj1y7sz"; + sha256 = "0jkmaw678njqgkflzj9g374yk1mci8yqvsxkrqzlifn6bwhwb7ci"; }; - patches = [ - (fetchpatch { - name = "CVE-2019-7560.patch"; - url = "https://github.com/Boolector/boolector/commit/8d979d02e0482c7137c9f3a34e6d430dbfd1f5c5.patch"; - sha256 = "1a1g02mk8b0azzjcigdn5zpshn0dn05fciwi8sd5q38yxvnvpbbi"; - }) - ]; + postPatch = '' + sed s@REPLACEME@file://${gtest.src}@ ${./cmake-gtest.patch} | patch -p1 + ''; nativeBuildInputs = [ cmake ]; - buildInputs = [ lingeling btor2tools ]; + buildInputs = [ lingeling btor2tools gmp ]; cmakeFlags = - [ "-DSHARED=ON" + [ "-DBUILD_SHARED_LIBS=ON" "-DUSE_LINGELING=YES" - "-DBTOR2_INCLUDE_DIR=${btor2tools.dev}/include" - "-DBTOR2_LIBRARIES=${btor2tools.lib}/lib/libbtor2parser.so" - "-DLINGELING_INCLUDE_DIR=${lingeling.dev}/include" - "-DLINGELING_LIBRARIES=${lingeling.lib}/lib/liblgl.a" - ]; + "-DBtor2Tools_INCLUDE_DIR=${btor2tools.dev}/include" + "-DBtor2Tools_LIBRARIES=${btor2tools.lib}/lib/libbtor2parser.so" + ] ++ (lib.optional (gmp != null) "-DUSE_GMP=YES"); installPhase = '' mkdir -p $out/bin $lib/lib $dev/include @@ -39,13 +33,22 @@ stdenv.mkDerivation rec { cp -vr bin/* $out/bin cp -vr lib/* $lib/lib - rm -rf $out/bin/{examples,test} + rm -rf $out/bin/{examples,tests} + # we don't care about gtest related libs + rm -rf $lib/lib/libg* cd ../src find . -iname '*.h' -exec cp --parents '{}' $dev/include \; rm -rf $dev/include/tests ''; + checkInputs = [ python3 ]; + doCheck = true; + preCheck = '' + export LD_LIBRARY_PATH=$(readlink -f lib) + patchShebangs .. + ''; + outputs = [ "out" "dev" "lib" ]; meta = with stdenv.lib; { diff --git a/pkgs/applications/science/logic/btor2tools/default.nix b/pkgs/applications/science/logic/btor2tools/default.nix index 2aedfb1d07ec..714ab49524b0 100644 --- a/pkgs/applications/science/logic/btor2tools/default.nix +++ b/pkgs/applications/science/logic/btor2tools/default.nix @@ -1,24 +1,24 @@ -{ stdenv, fetchFromGitHub }: +{ stdenv, cmake, fetchFromGitHub }: -stdenv.mkDerivation { +stdenv.mkDerivation rec { pname = "btor2tools"; - version = "pre55_8c150b39"; + version = "1.0.0-pre_${src.rev}"; src = fetchFromGitHub { owner = "boolector"; repo = "btor2tools"; - rev = "8c150b39cdbcdef4247344acf465d75ef642365d"; - sha256 = "1r5pid4x567nms02ajjrz3v0zj18k0fi5pansrmc2907rnx2acxx"; + rev = "9831f9909fb283752a3d6d60d43613173bd8af42"; + sha256 = "0mfqmkgvyw8fa2c09kww107dmk180ch1hp98r5kv41vnc04iqb0s"; }; - configurePhase = "./configure.sh -shared"; + nativeBuildInputs = [ cmake ]; installPhase = '' mkdir -p $out $dev/include/btor2parser/ $lib/lib cp -vr bin $out - cp -v src/btor2parser/btor2parser.h $dev/include/btor2parser - cp -v build/libbtor2parser.* $lib/lib + cp -v ../src/btor2parser/btor2parser.h $dev/include/btor2parser + cp -v lib/libbtor2parser.* $lib/lib ''; outputs = [ "out" "dev" "lib" ]; diff --git a/pkgs/applications/science/logic/lean/default.nix b/pkgs/applications/science/logic/lean/default.nix index 451aab6c049a..7fcc4cdd062e 100644 --- a/pkgs/applications/science/logic/lean/default.nix +++ b/pkgs/applications/science/logic/lean/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "lean"; - version = "3.15.0"; + version = "3.16.2"; src = fetchFromGitHub { owner = "leanprover-community"; repo = "lean"; rev = "v${version}"; - sha256 = "0fl8v8n53fr5qdnabici1mj3zpmjrkssx970y3q4m48s68q665v6"; + sha256 = "0fvm7gvbr5kn258sqpnxa7dvzz84iv1dx1n066vih5gz80plz4lh"; }; nativeBuildInputs = [ cmake ]; diff --git a/pkgs/applications/science/logic/symbiyosys/default.nix b/pkgs/applications/science/logic/symbiyosys/default.nix index b180cf307f0f..debdc56f0353 100644 --- a/pkgs/applications/science/logic/symbiyosys/default.nix +++ b/pkgs/applications/science/logic/symbiyosys/default.nix @@ -5,13 +5,13 @@ stdenv.mkDerivation { pname = "symbiyosys"; - version = "2020.03.24"; + version = "2020.05.18"; src = fetchFromGitHub { owner = "YosysHQ"; repo = "SymbiYosys"; - rev = "8a62780b9df4d2584e41cdd42cab92fddcd75b31"; - sha256 = "0ss5mrzwff2dny8kfciqbrz67m6k52yvc1shd7gk3qb99x7g7fp8"; + rev = "13fef4a710d0e2cf0f109ca75a94fb7253ba6838"; + sha256 = "152nyxddiqbxvbd06cmwavvgi931v6i35zj9sh3z04m737grvb3d"; }; buildInputs = [ python3 ]; diff --git a/pkgs/applications/science/math/mxnet/default.nix b/pkgs/applications/science/math/mxnet/default.nix index b006a9dd18d1..3d74421669ea 100644 --- a/pkgs/applications/science/math/mxnet/default.nix +++ b/pkgs/applications/science/math/mxnet/default.nix @@ -17,7 +17,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ cmake perl ]; - buildInputs = [ opencv3 gtest blas ] + buildInputs = [ opencv3 gtest blas.provider ] ++ lib.optionals cudaSupport [ cudatoolkit nvidia_x11 ] ++ lib.optional cudnnSupport cudnn; diff --git a/pkgs/applications/science/misc/sasview/xhtml2pdf.nix b/pkgs/applications/science/misc/sasview/xhtml2pdf.nix index 42b9560d9b8d..41d15e2f1bab 100644 --- a/pkgs/applications/science/misc/sasview/xhtml2pdf.nix +++ b/pkgs/applications/science/misc/sasview/xhtml2pdf.nix @@ -2,7 +2,7 @@ let #xhtml2pdf specifically requires version "1.0b10" of html5lib - html5 = html5lib.overrideAttrs( oldAttrs: rec{ + html5 = html5lib.overrideAttrs( oldAttrs: rec { name = "${oldAttrs.pname}-${version}"; version = "1.0b10"; src = oldAttrs.src.override { |