diff options
Diffstat (limited to 'pkgs/applications/science')
17 files changed, 183 insertions, 69 deletions
diff --git a/pkgs/applications/science/biology/igv/default.nix b/pkgs/applications/science/biology/igv/default.nix index 0c9a6bda2c23..2df8b188f785 100644 --- a/pkgs/applications/science/biology/igv/default.nix +++ b/pkgs/applications/science/biology/igv/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { name = "igv-${version}"; - version = "2.4.11"; + version = "2.4.13"; src = fetchurl { url = "https://data.broadinstitute.org/igv/projects/downloads/2.4/IGV_${version}.zip"; - sha256 = "11zbbasqpvf7inbgrk6jzd9pqdfn4v4g4nl149bivg475mmqpnwl"; + sha256 = "0cl6fs1v9rqkzjq4syx0m1pr71hbhvidwa3ym57pvz8ardfs3qa1"; }; buildInputs = [ unzip jre ]; diff --git a/pkgs/applications/science/chemistry/jmol/default.nix b/pkgs/applications/science/chemistry/jmol/default.nix index 4c4278c30faa..d5dae364cc3d 100644 --- a/pkgs/applications/science/chemistry/jmol/default.nix +++ b/pkgs/applications/science/chemistry/jmol/default.nix @@ -1,4 +1,5 @@ { stdenv +, lib , fetchurl , unzip , makeDesktopItem @@ -16,15 +17,15 @@ let }; in stdenv.mkDerivation rec { - version = "${baseVersion}.${patchVersion}"; - baseVersion = "14.29"; - patchVersion = "12"; + version = "14.29.17"; pname = "jmol"; name = "${pname}-${version}"; - src = fetchurl { + 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-${version}-binary.tar.gz"; - sha256 = "1ndq9am75janshrnk26334z1nmyh3k4bp20napvf2zv0lfp8k3bv"; + sha256 = "1dnxbvi8ha9z2ldymkjpxydd216afv6k7fdp3j70sql10zgy0isk"; }; patchPhase = '' diff --git a/pkgs/applications/science/chemistry/octopus/default.nix b/pkgs/applications/science/chemistry/octopus/default.nix index bf8ccee4a635..0d8ab0d0e191 100644 --- a/pkgs/applications/science/chemistry/octopus/default.nix +++ b/pkgs/applications/science/chemistry/octopus/default.nix @@ -1,9 +1,9 @@ { stdenv, fetchurl, symlinkJoin, gfortran, perl, procps -, libyaml, libxc, fftw, openblas, gsl +, libyaml, libxc, fftw, openblas, gsl, netcdf, arpack }: let - version = "7.3"; + version = "8.1"; fftwAll = symlinkJoin { name ="ftw-dev-out"; paths = [ fftw.dev fftw.out ]; }; in stdenv.mkDerivation { @@ -11,11 +11,11 @@ in stdenv.mkDerivation { src = fetchurl { url = "http://www.tddft.org/programs/octopus/down.php?file=${version}/octopus-${version}.tar.gz"; - sha256 = "0hnpqjjxdxh2ggf6ckrsy4hs9iglnazscb4siczddvmysi4kv15d"; + sha256 = "0rxwvcp22364nnhwhqlr38w4rwv1yl60snxi2f8nqdflx1143n10"; }; nativeBuildInputs = [ perl procps fftw.dev ]; - buildInputs = [ libyaml gfortran libxc openblas gsl fftw.out ]; + buildInputs = [ libyaml gfortran libxc openblas gsl fftw.out netcdf arpack ]; configureFlags = '' --with-yaml-prefix=${libyaml} @@ -37,6 +37,8 @@ in stdenv.mkDerivation { patchShebangs testsuite/oct-run_testsuite.sh ''; + enableParallelBuilding = true; + meta = with stdenv.lib; { description = "Real-space time dependent density-functional theory code"; homepage = http://octopus-code.org; diff --git a/pkgs/applications/science/logic/abc/default.nix b/pkgs/applications/science/logic/abc/default.nix index bab9b302d7d1..6e7a3cfc88ac 100644 --- a/pkgs/applications/science/logic/abc/default.nix +++ b/pkgs/applications/science/logic/abc/default.nix @@ -1,20 +1,21 @@ -{ fetchhg, stdenv, readline }: +{ fetchFromGitHub, stdenv, readline, cmake }: stdenv.mkDerivation rec { name = "abc-verifier-${version}"; - version = "20160818"; + version = "2018-07-08"; - src = fetchhg { - url = "https://bitbucket.org/alanmi/abc"; - rev = "a2e5bc66a68a72ccd267949e5c9973dd18f8932a"; - sha256 = "09yvhj53af91nc54gmy7cbp7yljfcyj68a87494r5xvdfnsj11gy"; + src = fetchFromGitHub { + owner = "berkeley-abc"; + repo = "abc"; + rev = "24407e13db4b8ca16c3996049b2d33ec3722de39"; + sha256 = "1rckji7nk81n6v1yajz7daqwipxacv7zlafknvmbiwji30j47sq5"; }; + nativeBuildInputs = [ cmake ]; buildInputs = [ readline ]; - preBuild = '' - export buildFlags="CC=$CC CXX=$CXX LD=$CXX" - ''; + enableParallelBuilding = true; + installPhase = '' mkdir -p $out/bin mv abc $out/bin @@ -22,7 +23,7 @@ stdenv.mkDerivation rec { meta = { description = "A tool for squential logic synthesis and formal verification"; - homepage = "https://people.eecs.berkeley.edu/~alanmi/abc/abc.htm"; + homepage = https://people.eecs.berkeley.edu/~alanmi/abc; license = stdenv.lib.licenses.mit; platforms = stdenv.lib.platforms.unix; maintainers = [ stdenv.lib.maintainers.thoughtpolice ]; diff --git a/pkgs/applications/science/logic/cvc4/default.nix b/pkgs/applications/science/logic/cvc4/default.nix index 222021bb1c9f..cddcbef7a035 100644 --- a/pkgs/applications/science/logic/cvc4/default.nix +++ b/pkgs/applications/science/logic/cvc4/default.nix @@ -35,7 +35,7 @@ stdenv.mkDerivation rec { meta = with stdenv.lib; { description = "A high-performance theorem prover and SMT solver"; - homepage = http://cvc4.cs.nyu.edu/web/; + homepage = http://cvc4.cs.stanford.edu/web/; license = licenses.gpl3; platforms = platforms.unix; maintainers = with maintainers; [ vbgl thoughtpolice gebner ]; diff --git a/pkgs/applications/science/logic/poly/default.nix b/pkgs/applications/science/logic/poly/default.nix index 1b401c927b6e..2f765572f9ad 100644 --- a/pkgs/applications/science/logic/poly/default.nix +++ b/pkgs/applications/science/logic/poly/default.nix @@ -1,17 +1,20 @@ -{stdenv, fetchurl, gmp, cmake, python}: +{stdenv, fetchFromGitHub, gmp, cmake, python}: -let version = "0.1.4"; -in +stdenv.mkDerivation rec { + name = "${pname}-${version}"; + pname = "libpoly"; + version = "0.1.7"; -stdenv.mkDerivation { - name = "libpoly-${version}"; - - src = fetchurl { - url = "https://github.com/SRI-CSL/libpoly/archive/v${version}.tar.gz"; - sha256 = "16x1pk2a3pcb5a0dzyw28ccjwkhmbsck4hy80ss7kx0dd7qgpi7j"; + src = fetchFromGitHub { + owner = "SRI-CSL"; + repo = "libpoly"; + rev = "v${version}"; + sha256 = "0i5ar4lhs88glk0rvkmag656ii434i6i1q5dspx6d0kyg78fii64"; }; - buildInputs = [ cmake gmp python ]; + nativeBuildInputs = [ cmake ]; + + buildInputs = [ gmp python ]; meta = with stdenv.lib; { homepage = https://github.com/SRI-CSL/libpoly; diff --git a/pkgs/applications/science/logic/yices/default.nix b/pkgs/applications/science/logic/yices/default.nix index a607f1066395..3121a83e5b98 100644 --- a/pkgs/applications/science/logic/yices/default.nix +++ b/pkgs/applications/science/logic/yices/default.nix @@ -2,12 +2,12 @@ stdenv.mkDerivation rec { name = "yices-${version}"; - version = "2.5.4"; + version = "2.6.0"; src = fetchurl { url = "https://github.com/SRI-CSL/yices2/archive/Yices-${version}.tar.gz"; name = "${name}-src.tar.gz"; - sha256 = "1k8wmlddi3zv5kgg6xbch3a0s0xqsmsfc7y6z8zrgcyhswl36h7p"; + sha256 = "10ikq7ib8jhx7hlxfm6mp5qg6r8dflqs8242q5zaicn80qixpm12"; }; nativeBuildInputs = [ autoreconfHook ]; @@ -26,9 +26,11 @@ stdenv.mkDerivation rec { # Includes a fix for the embedded soname being libyices.so.2.5, but # only installing the libyices.so.2.5.x file. - installPhase = '' + installPhase = let + ver_XdotY = builtins.concatStringsSep "." (stdenv.lib.take 2 (stdenv.lib.splitString "." version)); + in '' make install LDCONFIG=true - (cd $out/lib && ln -s -f libyices.so.${version} libyices.so.2.5) + ln -sfr $out/lib/libyices.so.{${version},${ver_XdotY}} ''; meta = with stdenv.lib; { diff --git a/pkgs/applications/science/logic/z3/default.nix b/pkgs/applications/science/logic/z3/default.nix index 54c9799a01b8..1cbe914779e6 100644 --- a/pkgs/applications/science/logic/z3/default.nix +++ b/pkgs/applications/science/logic/z3/default.nix @@ -20,6 +20,18 @@ stdenv.mkDerivation rec { cd build ''; + postInstall = '' + mkdir -p $dev $lib $python/lib + + mv $out/lib/python* $python/lib/ + mv $out/lib $lib/lib + mv $out/include $dev/include + + ln -sf $lib/lib/libz3${stdenv.hostPlatform.extensions.sharedLibrary} $python/${python.sitePackages}/z3/lib/libz3${stdenv.hostPlatform.extensions.sharedLibrary} + ''; + + outputs = [ "out" "lib" "dev" "python" ]; + meta = { description = "A high-performance theorem prover and SMT solver"; homepage = "https://github.com/Z3Prover/z3"; diff --git a/pkgs/applications/science/math/bliss/default.nix b/pkgs/applications/science/math/bliss/default.nix index b96aa60da686..1b7a97360079 100644 --- a/pkgs/applications/science/math/bliss/default.nix +++ b/pkgs/applications/science/math/bliss/default.nix @@ -21,11 +21,11 @@ stdenv.mkDerivation rec { ''; installPhase = '' - mkdir -p $out/bin $out/share/doc/bliss $out/lib $out/include + mkdir -p $out/bin $out/share/doc/bliss $out/lib $out/include/bliss mv bliss $out/bin mv html/* COPYING* $out/share/doc/bliss mv *.a $out/lib - mv *.h *.hh $out/include + mv *.h *.hh $out/include/bliss ''; meta = with stdenv.lib; { diff --git a/pkgs/applications/science/math/clp/default.nix b/pkgs/applications/science/math/clp/default.nix index daa9a53c59a1..4899ebe42d77 100644 --- a/pkgs/applications/science/math/clp/default.nix +++ b/pkgs/applications/science/math/clp/default.nix @@ -1,24 +1,22 @@ { stdenv, fetchurl, zlib }: stdenv.mkDerivation rec { - version = "1.16.11"; - name = "clp-${version}"; - src = fetchurl { - url = "https://www.coin-or.org/download/source/Clp/Clp-${version}.tgz"; - sha256 = "0fazlqpp845186nmixa9f1xfxqqkdr1xj4va7q29m8594ca4a9dm"; - }; + version = "1.16.11"; + name = "clp-${version}"; + src = fetchurl { + url = "https://www.coin-or.org/download/source/Clp/Clp-${version}.tgz"; + sha256 = "0fazlqpp845186nmixa9f1xfxqqkdr1xj4va7q29m8594ca4a9dm"; + }; - propagatedBuildInputs = [ zlib ]; + propagatedBuildInputs = [ zlib ]; - doCheck = true; + doCheck = true; - checkTarget = "test"; - - meta = { - license = stdenv.lib.licenses.epl10; - homepage = https://projects.coin-or.org/Clp; - description = "An open-source linear programming solver written in C++"; - platforms = stdenv.lib.platforms.all; - maintainers = [ stdenv.lib.maintainers.vbgl ]; - }; + meta = { + license = stdenv.lib.licenses.epl10; + homepage = https://projects.coin-or.org/Clp; + description = "An open-source linear programming solver written in C++"; + platforms = stdenv.lib.platforms.all; + maintainers = [ stdenv.lib.maintainers.vbgl ]; + }; } diff --git a/pkgs/applications/science/math/gurobi/default.nix b/pkgs/applications/science/math/gurobi/default.nix new file mode 100644 index 000000000000..06d448f6252e --- /dev/null +++ b/pkgs/applications/science/math/gurobi/default.nix @@ -0,0 +1,48 @@ +{ stdenv, fetchurl, autoPatchelfHook, python }: + +stdenv.mkDerivation rec { + name = "gurobi-${version}"; + version = "8.0.1"; + + src = with stdenv.lib; fetchurl { + url = "http://packages.gurobi.com/${versions.majorMinor version}/gurobi${version}_linux64.tar.gz"; + sha256 = "0y3lb0mngnyn7ql4s2n8qxnr1d2xcjdpdhpdjdxc4sc8f2w2ih18"; + }; + + sourceRoot = "gurobi${builtins.replaceStrings ["."] [""] version}/linux64"; + + nativeBuildInputs = [ autoPatchelfHook ]; + buildInputs = [ (python.withPackages (ps: [ ps.gurobipy ])) ]; + + buildPhase = '' + cd src/build + make + cd ../.. + ''; + + installPhase = '' + mkdir -p $out/bin + cp bin/* $out/bin/ + rm $out/bin/gurobi.env + rm $out/bin/gurobi.sh + rm $out/bin/python2.7 + + cp lib/gurobi.py $out/bin/gurobi.sh + + mkdir -p $out/include + cp include/gurobi*.h $out/include/ + + mkdir -p $out/lib + cp lib/libgurobi*.so* $out/lib/ + cp lib/libgurobi*.a $out/lib/ + cp src/build/*.a $out/lib/ + ''; + + meta = with stdenv.lib; { + description = "Optimization solver for mathematical programming"; + homepage = https://www.gurobi.com; + license = licenses.unfree; + platforms = [ "x86_64-linux" ]; + maintainers = with maintainers; [ jfrankenau ]; + }; +} diff --git a/pkgs/applications/science/math/qalculate-gtk/default.nix b/pkgs/applications/science/math/qalculate-gtk/default.nix index 28bd31506874..7990088ffbe9 100644 --- a/pkgs/applications/science/math/qalculate-gtk/default.nix +++ b/pkgs/applications/science/math/qalculate-gtk/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { name = "qalculate-gtk-${version}"; - version = "2.6.0"; + version = "2.6.1"; src = fetchFromGitHub { owner = "qalculate"; repo = "qalculate-gtk"; rev = "v${version}"; - sha256 = "0b2g9ziypcplczsm14b4i2k7vpiw9ll28qskv1fdhyqb0fij3qcx"; + sha256 = "19jw1w29x0r1qq5r8gmqrqr00ml2pfi2w433723vjzxpfg2pp70r"; }; patchPhase = '' diff --git a/pkgs/applications/science/math/sage/default.nix b/pkgs/applications/science/math/sage/default.nix index 9ad112213ffd..afb230cf4287 100644 --- a/pkgs/applications/science/math/sage/default.nix +++ b/pkgs/applications/science/math/sage/default.nix @@ -14,16 +14,6 @@ let cvxopt = super.cvxopt.override { inherit glpk; }; - # https://github.com/sagemath/sagenb/issues/437 - flask-babel = super.flask-babel.overridePythonAttrs (attrs: rec { - version = "0.9"; - src = attrs.src.override { - inherit version; - sha256 = "0k7vk4k54y55ma0nx2k5s0phfqbriwslhy5shh3b0d046q7ibzaa"; - }; - doCheck = false; - }); - # python packages that appear unmaintained and were not accepted into the nixpkgs # tree because of that. These packages are only dependencies of the more-or-less # deprecated sagenb. However sagenb is still a default dependency and the doctests diff --git a/pkgs/applications/science/math/sage/patches/eclib-20180710.patch b/pkgs/applications/science/math/sage/patches/eclib-20180710.patch new file mode 100644 index 000000000000..d06e1e6cedf2 --- /dev/null +++ b/pkgs/applications/science/math/sage/patches/eclib-20180710.patch @@ -0,0 +1,40 @@ +diff --git a/src/sage/interfaces/mwrank.py b/src/sage/interfaces/mwrank.py +index 4417b59276..ae57ca2991 100644 +--- a/src/sage/interfaces/mwrank.py ++++ b/src/sage/interfaces/mwrank.py +@@ -54,8 +54,9 @@ def Mwrank(options="", server=None, server_tmpdir=None): + sage: M = Mwrank('-v 0 -l') + sage: print(M('0 0 1 -1 0')) + Curve [0,0,1,-1,0] : Rank = 1 +- Generator 1 is [0:-1:1]; height 0.0511114082399688 +- Regulator = 0.0511114082399688 ++ Generator 1 is [0:-1:1]; height 0.051111408239969 ++ Regulator = 0.051111408239969 ++ + """ + global instances + try: +diff --git a/src/sage/libs/eclib/wrap.cpp b/src/sage/libs/eclib/wrap.cpp +index 5fd5693b53..d12468faa8 100644 +--- a/src/sage/libs/eclib/wrap.cpp ++++ b/src/sage/libs/eclib/wrap.cpp +@@ -133,8 +133,8 @@ char* Curvedata_isogeny_class(struct Curvedata* E, int verbose) + + + int mw_process(struct Curvedata* curve, struct mw* m, +- const struct bigint* x, const struct bigint* y, +- const struct bigint* z, int sat) ++ const bigint* x, const bigint* y, ++ const bigint* z, int sat) + { + Point P(*curve, *x, *y, *z); + if (!P.isvalid()) +@@ -188,7 +188,7 @@ int mw_rank(struct mw* m) + } + + /* Returns index and unsat long array, which user must deallocate */ +-int mw_saturate(struct mw* m, struct bigint* index, char** unsat, ++int mw_saturate(struct mw* m, bigint* index, char** unsat, + long sat_bd, int odd_primes_only) + { + vector<long> v; diff --git a/pkgs/applications/science/math/sage/sage-src.nix b/pkgs/applications/science/math/sage/sage-src.nix index 2eb7f8100597..d342fba21164 100644 --- a/pkgs/applications/science/math/sage/sage-src.nix +++ b/pkgs/applications/science/math/sage/sage-src.nix @@ -84,6 +84,12 @@ stdenv.mkDerivation rec { ]; packageUpgradePatches = [ + (fetchpatch { + name = "cypari2-1.2.1.patch"; + url = "https://git.sagemath.org/sage.git/patch/?h=62fe6eb15111327d930336d4252d5b23cbb22ab9"; + sha256 = "1xax7vvs8h4xip16xcsp47xdb6lig6f2r3pl8cksvlz8lhgbyxh2"; + }) + # matplotlib 2.2.2 deprecated `normed` (replaced by `density`). # This patch only ignores the warning. It would be equally easy to fix it # (by replacing all mentions of `normed` by `density`), but its better to @@ -170,6 +176,9 @@ stdenv.mkDerivation rec { # https://trac.sagemath.org/ticket/24838 rebased ./patches/pynac-0.7.22.patch + + # https://trac.sagemath.org/ticket/25862 + ./patches/eclib-20180710.patch ]; patches = nixPatches ++ packageUpgradePatches; diff --git a/pkgs/applications/science/math/sage/sagenb.nix b/pkgs/applications/science/math/sage/sagenb.nix index 5ab387ebc5e1..cc883cc24b42 100644 --- a/pkgs/applications/science/math/sage/sagenb.nix +++ b/pkgs/applications/science/math/sage/sagenb.nix @@ -36,6 +36,14 @@ buildPythonPackage rec { # tests depend on sage doCheck = false; + patches = [ + # work with latest flask-babel + (fetchpatch { + url = "https://github.com/sagemath/sagenb/commit/ba065eca63dd34a383e4c7ba7561430a90fcd087.patch"; + sha256 = "1lamzsrgymdd618imrasjp6ivhw2aynh83gkybsd7pm1rzjcq4x8"; + }) + ]; + meta = with stdenv.lib; { description = "Sage Notebook"; license = licenses.gpl3Plus; diff --git a/pkgs/applications/science/misc/golly/default.nix b/pkgs/applications/science/misc/golly/default.nix index 8ecbf656a821..0f0b44ccfa5e 100644 --- a/pkgs/applications/science/misc/golly/default.nix +++ b/pkgs/applications/science/misc/golly/default.nix @@ -1,11 +1,11 @@ {stdenv, fetchurl, wxGTK, perl, python2, zlib, libGLU_combined, libX11}: stdenv.mkDerivation rec { baseName="golly"; - version = "3.1"; + version = "3.2"; name="${baseName}-${version}"; src = fetchurl { - sha256 = "0dn74k3rylhx023n047lz4z6qrqijfcxi0b6jryqklhmm2n532f7"; + sha256 = "0cg9mbwmf4q6qxhqlnzrxh9y047banxdb8pd3hgj3smmja2zf0jd"; url="mirror://sourceforge/project/golly/golly/golly-${version}/golly-${version}-src.tar.gz"; }; |