diff options
author | Vladimír Čunát <vcunat@gmail.com> | 2016-03-08 09:57:58 +0100 |
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committer | Vladimír Čunát <vcunat@gmail.com> | 2016-03-08 09:58:19 +0100 |
commit | 09af15654f0c8091f1b9e0bbb2e523cdee194442 (patch) | |
tree | e648edef1ce4c64c533f2593aa22b8015cf0e506 /pkgs/applications/science | |
parent | f306e67e15bdbe9a8358c9f81319fc4fcbadc2eb (diff) | |
parent | 0ee75214f336474e127c2e3546c0406a0c4d5fa7 (diff) |
Merge master into closure-size
The kde-5 stuff still didn't merge well. I hand-fixed what I saw, but there may be more problems.
Diffstat (limited to 'pkgs/applications/science')
14 files changed, 220 insertions, 36 deletions
diff --git a/pkgs/applications/science/astronomy/stellarium/default.nix b/pkgs/applications/science/astronomy/stellarium/default.nix index e77e848bed2cd..7798b1bef6c10 100644 --- a/pkgs/applications/science/astronomy/stellarium/default.nix +++ b/pkgs/applications/science/astronomy/stellarium/default.nix @@ -1,14 +1,19 @@ -{ stdenv, fetchurl, cmake, freetype, libpng, mesa, gettext, openssl, qt5Full, perl, libiconv }: +{ stdenv, fetchurl, cmake, freetype, libpng, mesa, gettext, openssl, perl, libiconv +, qtscript, qtserialport, qttools +}: stdenv.mkDerivation rec { - name = "stellarium-0.13.3"; + name = "stellarium-0.14.2"; src = fetchurl { url = "mirror://sourceforge/stellarium/${name}.tar.gz"; - sha256 = "1ml6z2xda4vx61agdz54x8fw1b115gwc7rcy0zhz1jh6g5jvf0ij"; + sha256 = "1xxil0rv61zc08znfv83cpsc47y1gjl2f3njhz0pn5zd8jpaa15a"; }; - buildInputs = [ cmake freetype libpng mesa gettext openssl perl libiconv qt5Full ]; + buildInputs = [ + cmake freetype libpng mesa gettext openssl perl libiconv qtscript + qtserialport qttools + ]; enableParallelBuilding = true; diff --git a/pkgs/applications/science/biology/minc-tools/default.nix b/pkgs/applications/science/biology/minc-tools/default.nix new file mode 100644 index 0000000000000..41813dcda1496 --- /dev/null +++ b/pkgs/applications/science/biology/minc-tools/default.nix @@ -0,0 +1,26 @@ +{ stdenv, fetchurl, perl, cmake, flex, bison, libminc }: + +stdenv.mkDerivation rec { + _name = "minc-tools"; + name = "${_name}-2.3.00"; + + src = fetchurl { + url = "https://github.com/BIC-MNI/${_name}/archive/${_name}-2-3-00.tar.gz"; + sha256 = "1d457vrwy2fl6ga2axnwn1cchkx2rmgixfzyb1zjxb06cxkfj1dm"; + }; + + nativeBuildInputs = [ cmake flex bison ] ++ (if doCheck then [ perl ] else [ ]); + buildInputs = [ libminc ]; + + cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" ]; + + checkPhase = "ctest"; + doCheck = true; + + meta = with stdenv.lib; { + homepage = https://github.com/BIC-MNI/minc-tools; + description = "Command-line utilities for working with MINC files"; + maintainers = with maintainers; [ bcdarwin ]; + platforms = platforms.unix; + }; +} diff --git a/pkgs/applications/science/biology/neuron/default.nix b/pkgs/applications/science/biology/neuron/default.nix new file mode 100644 index 0000000000000..33f6d50d8ad84 --- /dev/null +++ b/pkgs/applications/science/biology/neuron/default.nix @@ -0,0 +1,38 @@ +{ stdenv +, fetchurl +, pkgconfig +, ncurses +, mpi ? null +}: + +stdenv.mkDerivation rec { + name = "neuron-7.4"; + buildInputs = [ stdenv pkgconfig ncurses mpi ]; + + src = fetchurl { + url = "http://www.neuron.yale.edu/ftp/neuron/versions/v7.4/nrn-7.4.tar.gz"; + sha256 = "1rid8cmv5mca0vqkgwahm0prkwkbdvchgw2bdwvx4adkn8bbl0ql"; + }; + + + enableParallelBuilding = true; + + configureFlags = [ "--without-x" + "${if mpi != null then "--with-mpi" else "--without-mpi"}" ]; + + meta = with stdenv.lib; { + description = "Simulation environment for empirically-based simulations of neurons and networks of neurons"; + + longDescription = "NEURON is a simulation environment for developing and exercising models of + neurons and networks of neurons. It is particularly well-suited to problems where + cable properties of cells play an important role, possibly including extracellular + potential close to the membrane), and where cell membrane properties are complex, + involving many ion-specific channels, ion accumulation, and second messengers"; + + license = licenses.bsd3; + homepage = http://www.neuron.yale.edu/neuron; + maintainers = [ maintainers.adev ]; + platforms = platforms.all; + }; +} + diff --git a/pkgs/applications/science/electronics/gtkwave/default.nix b/pkgs/applications/science/electronics/gtkwave/default.nix index 36c3b7e899dd8..32d39d8a609dc 100644 --- a/pkgs/applications/science/electronics/gtkwave/default.nix +++ b/pkgs/applications/science/electronics/gtkwave/default.nix @@ -1,10 +1,10 @@ {stdenv, fetchurl, gtk, gperf, pkgconfig, bzip2, tcl, tk, judy, xz}: stdenv.mkDerivation rec { - name = "gtkwave-3.3.66"; + name = "gtkwave-3.3.70"; src = fetchurl { url = "mirror://sourceforge/gtkwave/${name}.tar.gz"; - sha256 = "17mrmgr6zzl1x1qml0wmjjhcbw7bg3w4mqy60rsy0z6gxd8hikh4"; + sha256 = "1akzf1sq8mwarrbrbz5chrvgwlsp444h5za8rg1dfyqk733s7piz"; }; buildInputs = [ gtk gperf pkgconfig bzip2 tcl tk judy xz ]; diff --git a/pkgs/applications/science/logic/eprover/default.nix b/pkgs/applications/science/logic/eprover/default.nix index 97fe7065b85df..1f36858ae3208 100644 --- a/pkgs/applications/science/logic/eprover/default.nix +++ b/pkgs/applications/science/logic/eprover/default.nix @@ -20,7 +20,11 @@ stdenv.mkDerivation { buildInputs = [ which ]; - preConfigure = "sed -e 's@^EXECPATH\\s.*@EXECPATH = '\$out'/bin@' -i Makefile.vars"; + preConfigure = '' + sed -e 's@^EXECPATH\\s.*@EXECPATH = '\$out'/bin@' \ + -e 's/^CC *= gcc$//' \ + -i Makefile.vars + ''; buildPhase = "make install"; @@ -34,6 +38,8 @@ stdenv.mkDerivation { meta = { inherit (s) version; description = "Automated theorem prover for full first-order logic with equality"; + homepage = http://www.eprover.org/; + license = stdenv.lib.licenses.gpl2; maintainers = [stdenv.lib.maintainers.raskin]; platforms = stdenv.lib.platforms.all; }; diff --git a/pkgs/applications/science/logic/isabelle/default.nix b/pkgs/applications/science/logic/isabelle/default.nix index 98b71b7f5007e..6c51fb5192d4d 100644 --- a/pkgs/applications/science/logic/isabelle/default.nix +++ b/pkgs/applications/science/logic/isabelle/default.nix @@ -1,23 +1,23 @@ -{ stdenv, fetchurl, perl, nettools, java, polyml, proofgeneral }: +{ stdenv, fetchurl, perl, nettools, java, polyml }: # nettools needed for hostname let - dirname = "Isabelle2015"; + dirname = "Isabelle2016"; theories = ["HOL" "FOL" "ZF"]; in stdenv.mkDerivation { - name = "isabelle-2015"; + name = "isabelle-2016"; inherit dirname theories; src = if stdenv.isDarwin then fetchurl { - url = http://isabelle.in.tum.de/dist/Isabelle2015.dmg; - sha256 = "1vhm10qc1rn3wy9r12clrl33p64h3q1aj41mcnxkbnsyg2bx03im"; + url = "http://isabelle.in.tum.de/website-${dirname}/dist/${dirname}.dmg"; + sha256 = "0wawf0cjc52h8hif1867p33qhlh6qz0fy5i2kr1gbf7psickd6iw"; } else fetchurl { - url = http://isabelle.in.tum.de/dist/Isabelle2015_linux.tar.gz; - sha256 = "13kqm458d8mw7il1zg5bdb1nfbb869p331d75xzlm2v9xgjxx862"; + url = "http://isabelle.in.tum.de/website-${dirname}/dist/${dirname}_linux.tar.gz"; + sha256 = "0jh1qrsyib13fycymwvw7dq7xfy4iyplwq0s65ash842cdzkbxb4"; }; buildInputs = [ perl polyml ] @@ -34,17 +34,14 @@ stdenv.mkDerivation { --replace /usr/bin/env $ENV sed -i 's|isabelle_java java|${java}/bin/java|g' lib/Tools/java substituteInPlace etc/settings \ - --subst-var-by ML_HOME "${polyml}/bin" \ - --subst-var-by PROOFGENERAL_HOME "${proofgeneral}/share/emacs/site-lisp/ProofGeneral" + --subst-var-by ML_HOME "${polyml}/bin" substituteInPlace contrib/jdk/etc/settings \ --replace ISABELLE_JDK_HOME= '#ISABELLE_JDK_HOME=' substituteInPlace contrib/polyml-*/etc/settings \ - --replace 'ML_HOME="$POLYML_HOME/$ML_PLATFORM"' \ - "ML_HOME=\"${polyml}/bin\"" - ''; - - buildPhase = '' - ISABELLE_JDK_HOME=${java} ./bin/isabelle build -s $theories + --replace '$POLYML_HOME/$ML_PLATFORM' ${polyml}/bin \ + --replace '$POLYML_HOME/$PLATFORM/polyml' ${polyml}/bin/poly + substituteInPlace lib/scripts/run-polyml* lib/scripts/polyml-version \ + --replace '$ML_HOME/poly' ${polyml}/bin/poly ''; installPhase = '' diff --git a/pkgs/applications/science/logic/ltl2ba/default.nix b/pkgs/applications/science/logic/ltl2ba/default.nix index cdadd18ac9f52..f9bdd9a6b3b9f 100644 --- a/pkgs/applications/science/logic/ltl2ba/default.nix +++ b/pkgs/applications/science/logic/ltl2ba/default.nix @@ -9,6 +9,11 @@ stdenv.mkDerivation rec { sha256 = "16z0gc7a9dkarwn0l6rvg5jdhw1q4qyn4501zlchy0zxqddz0sx6"; }; + preConfigure = '' + substituteInPlace Makefile \ + --replace "CC=gcc" "" + ''; + installPhase = '' mkdir -p $out/bin mv ltl2ba $out/bin @@ -18,7 +23,7 @@ stdenv.mkDerivation rec { description = "fast translation from LTL formulae to Buchi automata"; homepage = "http://www.lsv.ens-cachan.fr/~gastin/ltl2ba"; license = stdenv.lib.licenses.gpl2Plus; - platforms = stdenv.lib.platforms.linux; + platforms = stdenv.lib.platforms.darwin ++ stdenv.lib.platforms.linux; maintainers = [ stdenv.lib.maintainers.thoughtpolice ]; }; } diff --git a/pkgs/applications/science/logic/why3/default.nix b/pkgs/applications/science/logic/why3/default.nix index 0313467ed7896..0eb51ff1620bb 100644 --- a/pkgs/applications/science/logic/why3/default.nix +++ b/pkgs/applications/science/logic/why3/default.nix @@ -2,15 +2,20 @@ stdenv.mkDerivation rec { name = "why3-${version}"; - version = "0.86.2"; + version = "0.86.3"; src = fetchurl { - url = https://gforge.inria.fr/frs/download.php/file/35214/why3-0.86.2.tar.gz; - sha256 = "08sa7dmp6yp29xn0m6h98nic4q47vb4ahvaid5drwh522pvwvg10"; + url = https://gforge.inria.fr/frs/download.php/file/35537/why3-0.86.3.tar.gz; + sha256 = "0sph6i4ga9450bk60wpm5cq3psw3g8xprnac7yjfq64iqz1dyz03"; }; - buildInputs = with ocamlPackages; - [ coq coq.camlp5 ocaml findlib lablgtk ocamlgraph zarith menhir ]; + buildInputs = (with ocamlPackages; [ + ocaml findlib lablgtk ocamlgraph zarith menhir ]) ++ + stdenv.lib.optionals (ocamlPackages.ocaml == coq.ocaml ) [ + coq coq.camlp5 + ]; + + installTargets = [ "install" "install-lib" ]; meta = with stdenv.lib; { description = "A platform for deductive program verification"; diff --git a/pkgs/applications/science/math/calc/default.nix b/pkgs/applications/science/math/calc/default.nix new file mode 100644 index 0000000000000..8673d7debd9de --- /dev/null +++ b/pkgs/applications/science/math/calc/default.nix @@ -0,0 +1,45 @@ +{ stdenv, fetchurl, makeWrapper, glibc, readline, ncurses, groff, utillinux }: + +with stdenv.lib; +let + makeFlags = '' + INCDIR=${glibc}/include \ + BINDIR=$out/bin LIBDIR=$out/lib CALC_INCDIR=$out/include/calc CALC_SHAREDIR=$out/share/calc MANDIR=$out/share/man/man1 \ + USE_READLINE=-DUSE_READLINE READLINE_LIB=-lreadline READLINE_EXTRAS='-lhistory -lncurses' \ + TERMCONTROL=-DUSE_TERMIOS \ + NROFF=groff + ''; +in +stdenv.mkDerivation rec { + + name = "calc-${version}"; + version = "2.12.5.3"; + + src = fetchurl { + url = "mirror://sourceforge/calc/${name}.tar.bz2"; + sha256 = "14mnz6smhi3a0rgmwvddk9w3vdisi8khq67i8nqsl47vgs8n1kqg"; + }; + + buildInputs = [ makeWrapper readline ncurses groff utillinux ]; + + configurePhase = '' + sed -i 's/all: check_include/all:/' Makefile + ''; + + buildPhase = '' + make ${makeFlags} + ''; + + installPhase = '' + make install ${makeFlags} + wrapProgram $out/bin/calc --prefix LD_LIBRARY_PATH : $out/lib + ''; + + meta = { + description = "C-style arbitrary precision calculator"; + homepage = http://www.isthe.com/chongo/tech/comp/calc/; + license = licenses.lgpl21; + maintainers = [ ]; + platforms = platforms.all; + }; +} diff --git a/pkgs/applications/science/math/lp_solve/default.nix b/pkgs/applications/science/math/lp_solve/default.nix index 09af2d708c965..7726793fcaf83 100644 --- a/pkgs/applications/science/math/lp_solve/default.nix +++ b/pkgs/applications/science/math/lp_solve/default.nix @@ -32,7 +32,7 @@ stdenv.mkDerivation rec { ''; meta = with stdenv.lib; { - description = "lp_solve is a Mixed Integer Linear Programming (MILP) solver."; + description = "lp_solve is a Mixed Integer Linear Programming (MILP) solver"; homepage = "http://lpsolve.sourceforge.net"; license = licenses.gpl2Plus; maintainers = with maintainers; [ smironov ]; diff --git a/pkgs/applications/science/misc/motu-client/default.nix b/pkgs/applications/science/misc/motu-client/default.nix new file mode 100644 index 0000000000000..b5e9fa6a51ee8 --- /dev/null +++ b/pkgs/applications/science/misc/motu-client/default.nix @@ -0,0 +1,23 @@ +{ python27Packages, fetchurl, lib } : +python27Packages.buildPythonApplication rec { + name = "motu-client-${version}"; + version = "1.0.8"; + + src = fetchurl { + url = "https://github.com/quiet-oceans/motuclient-setuptools/archive/${name}.tar.gz"; + sha256 = "1naqmav312agn72iad9kyxwscn2lz4v1cfcqqi1qcgvc82vnwkw2"; + }; + + meta = with lib; { + homepage = https://github.com/quiet-oceans/motuclient-setuptools; + description = "CLI to query oceanographic data to Motu servers"; + longDescription = '' + Access data from (motu)[http://sourceforge.net/projects/cls-motu/] servers. + This is a refactored fork of the original release in order to simplify integration, + deployment and packaging. Upstream code can be found at + http://sourceforge.net/projects/cls-motu/ . + ''; + license = licenses.lgpl3Plus; + maintainers = [ maintainers.lsix ]; + }; +} diff --git a/pkgs/applications/science/misc/yarp/default.nix b/pkgs/applications/science/misc/yarp/default.nix new file mode 100644 index 0000000000000..2daf5a4b5c7d4 --- /dev/null +++ b/pkgs/applications/science/misc/yarp/default.nix @@ -0,0 +1,26 @@ +{ stdenv, fetchFromGitHub, pkgconfig, cmake, ace +}: + +stdenv.mkDerivation rec { + name = "yarp-${version}"; + version = "2.3.64"; + src = fetchFromGitHub { + owner = "robotology"; + repo = "yarp"; + rev = "v2.3.64"; + sha256 = "0x9sdc8d6rppzf1kx53w0yjlnmz7h75qv62yd3ls09w3cy7nb5x7"; + }; + + buildInputs = [ cmake ace ]; + + enableParallelBuilding = true; + + meta = { + description = "Yet Another Robot Platform"; + homepage = http://yarp.it; + license = stdenv.lib.licenses.lgpl21; + platforms = stdenv.lib.platforms.linux; + maintainers = [ stdenv.lib.maintainers.nico202 ]; + }; +} + diff --git a/pkgs/applications/science/molecular-dynamics/gromacs/default.nix b/pkgs/applications/science/molecular-dynamics/gromacs/default.nix index 43ef4337d5730..5724db9f3069b 100644 --- a/pkgs/applications/science/molecular-dynamics/gromacs/default.nix +++ b/pkgs/applications/science/molecular-dynamics/gromacs/default.nix @@ -1,22 +1,30 @@ { stdenv, fetchurl, cmake, singlePrec ? true, - fftw + mpiEnabled ? false, + fftw, + openmpi }: stdenv.mkDerivation { - name = "gromacs-4.6.5"; + name = "gromacs-4.6.7"; src = fetchurl { - url = "ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.5.tar.gz"; - sha256 = "02ggrplh8fppqib86y3rfk4qm08yddlrb1yjgzl138b3b4qjy957"; + url = "ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.7.tar.gz"; + sha256 = "6afb1837e363192043de34b188ca3cf83db6bd189601f2001a1fc5b0b2a214d9"; }; - buildInputs = [cmake fftw]; + buildInputs = [cmake fftw] + ++ (stdenv.lib.optionals mpiEnabled [ openmpi ]); cmakeFlags = '' ${if singlePrec then "-DGMX_DOUBLE=OFF" else "-DGMX_DOUBLE=ON -DGMX_DEFAULT_SUFFIX=OFF"} + ${if mpiEnabled then "-DGMX_MPI:BOOL=TRUE + -DGMX_CPU_ACCELERATION:STRING=SSE4.1 + -DGMX_OPENMP:BOOL=TRUE + -DGMX_THREAD_MPI:BOOL=FALSE" + else "-DGMX_MPI:BOOL=FALSE" } ''; meta = with stdenv.lib; { diff --git a/pkgs/applications/science/spyder/default.nix b/pkgs/applications/science/spyder/default.nix index 9e74a23323653..73847624e85a6 100644 --- a/pkgs/applications/science/spyder/default.nix +++ b/pkgs/applications/science/spyder/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, unzip, buildPythonPackage, makeDesktopItem +{ stdenv, fetchurl, unzip, buildPythonApplication, makeDesktopItem # mandatory , pyside # recommended @@ -7,7 +7,7 @@ , ipython ? null, pylint ? null, pep8 ? null }: -buildPythonPackage rec { +buildPythonApplication rec { name = "spyder-${version}"; version = "2.3.8"; namePrefix = ""; |