diff options
Diffstat (limited to 'pkgs/applications/science')
69 files changed, 384 insertions, 144 deletions
diff --git a/pkgs/applications/science/astronomy/celestia/default.nix b/pkgs/applications/science/astronomy/celestia/default.nix index d28aa8e62a14..674aa666b7e6 100644 --- a/pkgs/applications/science/astronomy/celestia/default.nix +++ b/pkgs/applications/science/astronomy/celestia/default.nix @@ -68,7 +68,7 @@ stdenv.mkDerivation { meta = { description = "Free space simulation"; - homepage = "http://www.shatters.net/celestia/"; + homepage = http://www.shatters.net/celestia/; license = stdenv.lib.licenses.gpl2; platforms = stdenv.lib.platforms.linux; diff --git a/pkgs/applications/science/astronomy/gravit/default.nix b/pkgs/applications/science/astronomy/gravit/default.nix index eb5506e74908..5903edd337df 100644 --- a/pkgs/applications/science/astronomy/gravit/default.nix +++ b/pkgs/applications/science/astronomy/gravit/default.nix @@ -15,13 +15,13 @@ stdenv.mkDerivation rec { preConfigure = "./autogen.sh"; meta = { - homepage = "http://gravit.slowchop.com"; + homepage = http://gravit.slowchop.com; description = "Beautiful OpenGL-based gravity simulator"; license = stdenv.lib.licenses.gpl2; longDescription = '' Gravit is a gravity simulator which runs under Linux, Windows and - Mac OS X. It uses Newtonian physics using the Barnes-Hut N-body + macOS. It uses Newtonian physics using the Barnes-Hut N-body algorithm. Although the main goal of Gravit is to be as accurate as possible, it also creates beautiful looking gravity patterns. It records the history of each particle so it can animate and diff --git a/pkgs/applications/science/astronomy/stellarium/default.nix b/pkgs/applications/science/astronomy/stellarium/default.nix index da6aa38d746a..886a98f2e6b3 100644 --- a/pkgs/applications/science/astronomy/stellarium/default.nix +++ b/pkgs/applications/science/astronomy/stellarium/default.nix @@ -22,7 +22,7 @@ mkDerivation rec { meta = with lib; { description = "Free open-source planetarium"; - homepage = "http://stellarium.org/"; + homepage = http://stellarium.org/; license = licenses.gpl2; platforms = platforms.linux; # should be mesaPlatforms, but we don't have qt on darwin diff --git a/pkgs/applications/science/biology/bcftools/default.nix b/pkgs/applications/science/biology/bcftools/default.nix index 97e081f908ef..cfd72601d1eb 100644 --- a/pkgs/applications/science/biology/bcftools/default.nix +++ b/pkgs/applications/science/biology/bcftools/default.nix @@ -3,12 +3,12 @@ stdenv.mkDerivation rec { name = "${pname}-${version}"; pname = "bcftools"; - major = "1.4"; + major = "1.5"; version = "${major}.0"; src = fetchurl { url = "https://github.com/samtools/bcftools/releases/download/${major}/bcftools-${major}.tar.bz2"; - sha256 = "0k93mq3lf73dch81p4zxi0bdll567acxfa81qzbzkqflgsjb1ccg"; + sha256 = "0093hkkvxmbwfaa7905s6185jymynvg42kq6sxv7fili11l5mxwz"; }; buildInputs = [ zlib bzip2 lzma perl ]; diff --git a/pkgs/applications/science/biology/igv/default.nix b/pkgs/applications/science/biology/igv/default.nix index 3acf7d965279..a2a40f0acc80 100644 --- a/pkgs/applications/science/biology/igv/default.nix +++ b/pkgs/applications/science/biology/igv/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { name = "igv-${version}"; - version = "2.3.89"; + version = "2.3.98"; src = fetchurl { url = "http://data.broadinstitute.org/igv/projects/downloads/IGV_${version}.zip"; - sha256 = "06bmj9jsnk5010ipv0w4qlcvgw67dy8hsvgcx9l74v3s0zp5di3y"; + sha256 = "1bjdsvx8jsbcry6v7yfclh3vrlsvaw38f3s9587lklj63zj638l2"; }; buildInputs = [ unzip jre ]; @@ -24,7 +24,7 @@ stdenv.mkDerivation rec { ''; meta = with stdenv.lib; { - homepage = "https://www.broadinstitute.org/igv/"; + homepage = https://www.broadinstitute.org/igv/; description = "A visualization tool for interactive exploration of genomic datasets"; license = licenses.lgpl21; platforms = platforms.unix; diff --git a/pkgs/applications/science/biology/plink-ng/default.nix b/pkgs/applications/science/biology/plink-ng/default.nix index eb4d2714a127..06fc1ef641be 100644 --- a/pkgs/applications/science/biology/plink-ng/default.nix +++ b/pkgs/applications/science/biology/plink-ng/default.nix @@ -26,7 +26,7 @@ stdenv.mkDerivation rec { meta = { description = "A comprehensive update to the PLINK association analysis toolset"; - homepage = "https://www.cog-genomics.org/plink2"; + homepage = https://www.cog-genomics.org/plink2; license = stdenv.lib.licenses.gpl3; platforms = stdenv.lib.platforms.all; }; diff --git a/pkgs/applications/science/biology/plink/default.nix b/pkgs/applications/science/biology/plink/default.nix index 009e12aa02f0..cc48a0cb13a9 100644 --- a/pkgs/applications/science/biology/plink/default.nix +++ b/pkgs/applications/science/biology/plink/default.nix @@ -17,7 +17,7 @@ stdenv.mkDerivation { meta = { description = "Whole genome association toolkit"; - homepage = "http://pngu.mgh.harvard.edu/~purcell/plink/"; + homepage = http://pngu.mgh.harvard.edu/~purcell/plink/; license = stdenv.lib.licenses.gpl2; platforms = stdenv.lib.platforms.all; broken = true; diff --git a/pkgs/applications/science/biology/samtools/default.nix b/pkgs/applications/science/biology/samtools/default.nix index 827c1448693a..f8391a2d6b3c 100644 --- a/pkgs/applications/science/biology/samtools/default.nix +++ b/pkgs/applications/science/biology/samtools/default.nix @@ -3,12 +3,12 @@ stdenv.mkDerivation rec { name = "${pname}-${version}"; pname = "samtools"; - major = "1.4"; + major = "1.5"; version = "${major}.0"; src = fetchurl { url = "https://github.com/samtools/samtools/releases/download/${major}/samtools-${major}.tar.bz2"; - sha256 = "1x73c0lxvd58ghrmaqqyp56z7bkmp28a71fk4ap82j976pw5pbls"; + sha256 = "1xidmv0jmfy7l0kb32hdnlshcxgzi1hmygvig0cqrq1fhckdlhl5"; }; buildInputs = [ zlib ncurses ]; diff --git a/pkgs/applications/science/chemistry/gwyddion/default.nix b/pkgs/applications/science/chemistry/gwyddion/default.nix new file mode 100644 index 000000000000..b98af36604a3 --- /dev/null +++ b/pkgs/applications/science/chemistry/gwyddion/default.nix @@ -0,0 +1,31 @@ +{ stdenv, fetchurl, gtk2, pkgconfig }: + +with stdenv.lib; + +stdenv.mkDerivation { + name = "gwyddion"; + version = "2.48"; + src = fetchurl { + url = "http://sourceforge.net/projects/gwyddion/files/gwyddion/2.48/gwyddion-2.48.tar.xz"; + sha256 = "119iw58ac2wn4cas6js8m7r1n4gmmkga6b1y711xzcyjp9hshgwx"; + }; + buildInputs = [ gtk2 pkgconfig ]; + meta = { + homepage = http://gwyddion.net/; + + description = "Scanning probe microscopy data visualization and analysis"; + + longDescription = '' + A modular program for SPM (scanning probe microscopy) data + visualization and analysis. Primarily it is intended for the + analysis of height fields obtained by scanning probe microscopy + techniques (AFM, MFM, STM, SNOM/NSOM) and it supports a lot of + SPM data formats. However, it can be used for general height + field and (greyscale) image processing, for instance for the + analysis of profilometry data or thickness maps from imaging + spectrophotometry. + ''; + license = stdenv.lib.licenses.gpl2; + platforms = stdenv.lib.platforms.linux; + }; +} diff --git a/pkgs/applications/science/chemistry/pymol/default.nix b/pkgs/applications/science/chemistry/pymol/default.nix index ed208014f7d9..39c027706ee3 100644 --- a/pkgs/applications/science/chemistry/pymol/default.nix +++ b/pkgs/applications/science/chemistry/pymol/default.nix @@ -45,7 +45,7 @@ python3Packages.buildPythonApplication { meta = { description = description; - homepage = "https://www.pymol.org/"; + homepage = https://www.pymol.org/; license = licenses.psfl; }; } diff --git a/pkgs/applications/science/electronics/kicad/default.nix b/pkgs/applications/science/electronics/kicad/default.nix index a7dcbb675f5b..506cdcd40371 100644 --- a/pkgs/applications/science/electronics/kicad/default.nix +++ b/pkgs/applications/science/electronics/kicad/default.nix @@ -62,7 +62,7 @@ stdenv.mkDerivation rec { meta = { description = "Free Software EDA Suite"; - homepage = "http://www.kicad-pcb.org/"; + homepage = http://www.kicad-pcb.org/; license = stdenv.lib.licenses.gpl2; maintainers = with stdenv.lib.maintainers; [viric]; platforms = with stdenv.lib.platforms; linux; diff --git a/pkgs/applications/science/electronics/ngspice/default.nix b/pkgs/applications/science/electronics/ngspice/default.nix index dfcdac20ae08..2588ee39addc 100644 --- a/pkgs/applications/science/electronics/ngspice/default.nix +++ b/pkgs/applications/science/electronics/ngspice/default.nix @@ -14,7 +14,7 @@ stdenv.mkDerivation { meta = with stdenv.lib; { description = "The Next Generation Spice (Electronic Circuit Simulator)"; - homepage = "http://ngspice.sourceforge.net"; + homepage = http://ngspice.sourceforge.net; license = with licenses; [ "BSD" gpl2 ]; maintainers = with maintainers; [ viric rongcuid ]; platforms = platforms.linux; diff --git a/pkgs/applications/science/electronics/qfsm/default.nix b/pkgs/applications/science/electronics/qfsm/default.nix index 4b4d21aca006..56bc66eb3caf 100644 --- a/pkgs/applications/science/electronics/qfsm/default.nix +++ b/pkgs/applications/science/electronics/qfsm/default.nix @@ -18,7 +18,7 @@ stdenv.mkDerivation rec { meta = { description = "Graphical editor for finite state machines"; - homepage = "http://qfsm.sourceforge.net/"; + homepage = http://qfsm.sourceforge.net/; license = stdenv.lib.licenses.gpl3Plus; platforms = stdenv.lib.platforms.unix; }; diff --git a/pkgs/applications/science/electronics/tkgate/1.x.nix b/pkgs/applications/science/electronics/tkgate/1.x.nix index 2a3f17b670b4..aca1f9a35898 100644 --- a/pkgs/applications/science/electronics/tkgate/1.x.nix +++ b/pkgs/applications/science/electronics/tkgate/1.x.nix @@ -32,7 +32,7 @@ stdenv.mkDerivation rec { meta = { description = "Event driven digital circuit simulator with a TCL/TK-based graphical editor"; - homepage = "http://www.tkgate.org/"; + homepage = http://www.tkgate.org/; license = stdenv.lib.licenses.gpl2Plus; maintainers = [ stdenv.lib.maintainers.peti ]; hydraPlatforms = stdenv.lib.platforms.linux; diff --git a/pkgs/applications/science/electronics/verilator/default.nix b/pkgs/applications/science/electronics/verilator/default.nix index ed4a430198a1..31c2d4f6475e 100644 --- a/pkgs/applications/science/electronics/verilator/default.nix +++ b/pkgs/applications/science/electronics/verilator/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, perl, flex_2_6_1, bison }: +{ stdenv, fetchurl, perl, flex, bison }: stdenv.mkDerivation rec { name = "verilator-${version}"; @@ -10,7 +10,7 @@ stdenv.mkDerivation rec { }; enableParallelBuilding = true; - buildInputs = [ perl flex_2_6_1 bison ]; + buildInputs = [ perl flex bison ]; postInstall = '' sed -i -e '3a\#!/usr/bin/env perl' -e '1,3d' $out/bin/{verilator,verilator_coverage,verilator_profcfunc} diff --git a/pkgs/applications/science/geometry/tetgen/1.4.nix b/pkgs/applications/science/geometry/tetgen/1.4.nix index 9dd254736834..3a2dbf180ee3 100644 --- a/pkgs/applications/science/geometry/tetgen/1.4.nix +++ b/pkgs/applications/science/geometry/tetgen/1.4.nix @@ -15,7 +15,7 @@ stdenv.mkDerivation rec { meta = { description = "Quality Tetrahedral Mesh Generator and 3D Delaunay Triangulator"; - homepage = "http://tetgen.org/"; + homepage = http://tetgen.org/; license = stdenv.lib.licenses.mit; platforms = stdenv.lib.platforms.linux; }; diff --git a/pkgs/applications/science/geometry/tetgen/default.nix b/pkgs/applications/science/geometry/tetgen/default.nix index 904fb6c7d49e..b655cc48c731 100644 --- a/pkgs/applications/science/geometry/tetgen/default.nix +++ b/pkgs/applications/science/geometry/tetgen/default.nix @@ -17,7 +17,7 @@ stdenv.mkDerivation { meta = { inherit version; description = "Quality Tetrahedral Mesh Generator and 3D Delaunay Triangulator"; - homepage = "http://tetgen.org/"; + homepage = http://tetgen.org/; license = stdenv.lib.licenses.agpl3Plus; platforms = stdenv.lib.platforms.linux; }; diff --git a/pkgs/applications/science/logic/abc/default.nix b/pkgs/applications/science/logic/abc/default.nix index 47fd8e5dbc81..bab9b302d7d1 100644 --- a/pkgs/applications/science/logic/abc/default.nix +++ b/pkgs/applications/science/logic/abc/default.nix @@ -21,7 +21,7 @@ stdenv.mkDerivation rec { ''; meta = { - description = "A tool for squential logic synthesis and ormal verification"; + description = "A tool for squential logic synthesis and formal verification"; homepage = "https://people.eecs.berkeley.edu/~alanmi/abc/abc.htm"; license = stdenv.lib.licenses.mit; platforms = stdenv.lib.platforms.unix; diff --git a/pkgs/applications/science/logic/acgtk/default.nix b/pkgs/applications/science/logic/acgtk/default.nix index 9c8ecd016394..94b292d65887 100644 --- a/pkgs/applications/science/logic/acgtk/default.nix +++ b/pkgs/applications/science/logic/acgtk/default.nix @@ -47,7 +47,7 @@ stdenv.mkDerivation { + " " + optionalString installEmacsMode "install-emacs"; meta = with stdenv.lib; { - homepage = "http://www.loria.fr/equipes/calligramme/acg"; + homepage = http://www.loria.fr/equipes/calligramme/acg; description = "A toolkit for developing ACG signatures and lexicon"; license = licenses.cecill20; platforms = ocaml.meta.platforms or []; diff --git a/pkgs/applications/science/logic/alt-ergo/default.nix b/pkgs/applications/science/logic/alt-ergo/default.nix index 7cf0aeb203de..8cf4bb9b6d25 100644 --- a/pkgs/applications/science/logic/alt-ergo/default.nix +++ b/pkgs/applications/science/logic/alt-ergo/default.nix @@ -5,7 +5,7 @@ stdenv.mkDerivation rec { version = "1.30"; src = fetchurl { - url = "http://alt-ergo.ocamlpro.com/download_manager.php?target=${name}.tar.gz"; + url = "https://alt-ergo.ocamlpro.com/download_manager.php?target=${name}.tar.gz"; name = "${name}.tar.gz"; sha256 = "025pacb4ax864fn5x8k78mw6hiig4jcazblj18gzxspg4f1l5n1g"; }; @@ -15,7 +15,7 @@ stdenv.mkDerivation rec { meta = { description = "High-performance theorem prover and SMT solver"; - homepage = "http://alt-ergo.ocamlpro.com/"; + homepage = "https://alt-ergo.ocamlpro.com/"; license = stdenv.lib.licenses.cecill-c; # LGPL-2 compatible platforms = stdenv.lib.platforms.linux ++ stdenv.lib.platforms.darwin; maintainers = [ stdenv.lib.maintainers.thoughtpolice ]; diff --git a/pkgs/applications/science/logic/boolector/default.nix b/pkgs/applications/science/logic/boolector/default.nix index 37d25c9e9477..2b40995b7433 100644 --- a/pkgs/applications/science/logic/boolector/default.nix +++ b/pkgs/applications/science/logic/boolector/default.nix @@ -1,48 +1,23 @@ -{ stdenv, fetchurl, zlib, useV16 ? false }: +{ stdenv, fetchurl }: -let - v15 = rec { - name = "boolector-${version}"; - version = "1.5.118"; - src = fetchurl { - url = "http://fmv.jku.at/boolector/${name}-with-sat-solvers.tar.gz"; - sha256 = "17j7q02rryvfwgvglxnhx0kv8hxwy8wbhzawn48lw05i98vxlmk9"; - }; +stdenv.mkDerivation rec { + name = "boolector-${version}"; + version = "2.4.1"; + src = fetchurl { + url = "http://fmv.jku.at/boolector/boolector-${version}-with-lingeling-bbc.tar.bz2"; + sha256 = "0mdf7hwix237pvknvrpazcx6s3ininj5k7vhysqjqgxa7lxgq045"; }; - v16 = rec { - name = "boolector-${version}"; - version = "1.6.0"; - src = fetchurl { - url = "http://fmv.jku.at/boolector/${name}-with-sat-solvers.tar.gz"; - sha256 = "0jka4r6bc3i24axgdp6qbq6gjadwz9kvi11s2c5sbwmdnjd7cp85"; - }; - }; - - boolectorPkg = if useV16 then v16 else v15; - license = with stdenv.lib.licenses; if useV16 then unfreeRedistributable else gpl3; -in -stdenv.mkDerivation (boolectorPkg // { - buildInputs = [ - zlib zlib.static (stdenv.lib.getOutput "static" stdenv.cc.libc) - ]; - - enableParallelBuilding = false; - installPhase = '' - mkdir -p $out/bin $out/lib $out/include - cp boolector/boolector $out/bin - cp boolector/deltabtor $out/bin - cp boolector/synthebtor $out/bin - cp boolector/libboolector.a $out/lib - cp boolector/boolector.h $out/include + mkdir $out + mv boolector/bin $out ''; meta = { - inherit license; + license = stdenv.lib.licenses.unfreeRedistributable; description = "An extremely fast SMT solver for bit-vectors and arrays"; homepage = "http://fmv.jku.at/boolector"; platforms = stdenv.lib.platforms.linux; maintainers = [ stdenv.lib.maintainers.thoughtpolice ]; }; -}) +} diff --git a/pkgs/applications/science/logic/coq/8.3.nix b/pkgs/applications/science/logic/coq/8.3.nix index ec4e530ae523..87b847087e34 100644 --- a/pkgs/applications/science/logic/coq/8.3.nix +++ b/pkgs/applications/science/logic/coq/8.3.nix @@ -73,7 +73,7 @@ stdenv.mkDerivation { together with an environment for semi-interactive development of machine-checked proofs. ''; - homepage = "http://coq.inria.fr"; + homepage = http://coq.inria.fr; license = licenses.lgpl21; branch = "8.3"; maintainers = with maintainers; [ roconnor vbgl ]; diff --git a/pkgs/applications/science/logic/coq/8.4.nix b/pkgs/applications/science/logic/coq/8.4.nix index 32007ba45ce3..34505192021c 100644 --- a/pkgs/applications/science/logic/coq/8.4.nix +++ b/pkgs/applications/science/logic/coq/8.4.nix @@ -87,7 +87,7 @@ stdenv.mkDerivation { together with an environment for semi-interactive development of machine-checked proofs. ''; - homepage = "http://coq.inria.fr"; + homepage = http://coq.inria.fr; license = licenses.lgpl21; branch = coq-version; maintainers = with maintainers; [ roconnor thoughtpolice vbgl ]; diff --git a/pkgs/applications/science/logic/coq/HEAD.nix b/pkgs/applications/science/logic/coq/HEAD.nix index 8d3fb19b2638..209cba07c438 100644 --- a/pkgs/applications/science/logic/coq/HEAD.nix +++ b/pkgs/applications/science/logic/coq/HEAD.nix @@ -71,7 +71,7 @@ stdenv.mkDerivation { together with an environment for semi-interactive development of machine-checked proofs. ''; - homepage = "http://coq.inria.fr"; + homepage = http://coq.inria.fr; license = licenses.lgpl21; branch = coq-version; maintainers = with maintainers; [ roconnor thoughtpolice vbgl ]; diff --git a/pkgs/applications/science/logic/coq/default.nix b/pkgs/applications/science/logic/coq/default.nix index fd3655ce9e92..9620140dde4b 100644 --- a/pkgs/applications/science/logic/coq/default.nix +++ b/pkgs/applications/science/logic/coq/default.nix @@ -9,7 +9,7 @@ , ocamlPackages, ncurses , buildIde ? true , csdp ? null -, version ? "8.6" +, version ? "8.6.1" }: let @@ -18,9 +18,10 @@ let "8.5pl2" = "0wyywia0darak2zmc5v0ra9rn0b9whwdfiahralm8v5za499s8w3"; "8.5pl3" = "0fyk2a4fpifibq8y8jhx1891k55qnsnlygglch64sva0bph94nrh"; "8.6" = "1pw1xvy1657l1k69wrb911iqqflzhhp8wwsjvihbgc72r3skqg3f"; + "8.6.1" = "17cg2c40y9lskkiqfhngavp8yw3shpqgkpihh30xx0rlhn9amy1j"; }."${version}"; coq-version = builtins.substring 0 3 version; - camlp5 = ocamlPackages.camlp5_transitional; + camlp5 = ocamlPackages.camlp5_strict; ideFlags = if buildIde then "-lablgtkdir ${ocamlPackages.lablgtk}/lib/ocaml/*/site-lib/lablgtk2 -coqide opt" else ""; csdpPatch = if csdp != null then '' substituteInPlace plugins/micromega/sos.ml --replace "; csdp" "; ${csdp}/bin/csdp" @@ -129,10 +130,10 @@ self = stdenv.mkDerivation { together with an environment for semi-interactive development of machine-checked proofs. ''; - homepage = "http://coq.inria.fr"; + homepage = http://coq.inria.fr; license = licenses.lgpl21; branch = coq-version; - maintainers = with maintainers; [ roconnor thoughtpolice vbgl ]; + maintainers = with maintainers; [ roconnor thoughtpolice vbgl Zimmi48 ]; platforms = platforms.unix; }; }; in self diff --git a/pkgs/applications/science/logic/coq2html/default.nix b/pkgs/applications/science/logic/coq2html/default.nix new file mode 100644 index 000000000000..9687ac66ead1 --- /dev/null +++ b/pkgs/applications/science/logic/coq2html/default.nix @@ -0,0 +1,38 @@ +{ stdenv, lib, make, fetchgit, ocaml }: + +let + version = "20170720"; +in + +stdenv.mkDerivation { + name = "coq2html-${version}"; + + src = fetchgit { + url = "https://github.com/xavierleroy/coq2html"; + rev = "e2b94093c6b9a877717f181765e30577de22439e"; + sha256 = "1x466j0pyjggyz0870pdllv9f5vpnfrgkd0w7ajvm9rkwyp3f610"; + }; + + buildInputs = [ make ocaml ]; + + installPhase = '' + mkdir -p $out/bin + cp coq2html $out/bin + ''; + + meta = with stdenv.lib; { + description = "coq2html is an HTML documentation generator for Coq source files"; + longDescription = '' + coq2html is an HTML documentation generator for Coq source files. It is + an alternative to the standard coqdoc documentation generator + distributed along with Coq. The major feature of coq2html is its ability + to fold proof scripts: in the generated HTML, proof scripts are + initially hidden, but can be revealed one by one by clicking on the + "Proof" keyword. + ''; + homepage = https://github.com/xavierleroy/coq2html; + license = licenses.gpl2; + maintainers = with maintainers; [ jwiegley ]; + platforms = platforms.unix; + }; +} diff --git a/pkgs/applications/science/logic/cryptominisat/default.nix b/pkgs/applications/science/logic/cryptominisat/default.nix index 26efbc5fe723..4d96339149af 100644 --- a/pkgs/applications/science/logic/cryptominisat/default.nix +++ b/pkgs/applications/science/logic/cryptominisat/default.nix @@ -1,18 +1,17 @@ -{ stdenv, fetchFromGitHub, fetchpatch, cmake, python, vim }: +{ stdenv, fetchFromGitHub, fetchpatch, cmake, python, xxd }: stdenv.mkDerivation rec { name = "cryptominisat-${version}"; version = "5.0.1"; src = fetchFromGitHub { - owner = "msoos"; - repo = "cryptominisat"; - rev = version; + owner = "msoos"; + repo = "cryptominisat"; + rev = version; sha256 = "0cpw5d9vplxvv3aaplhnga55gz1hy29p7s4pkw1306knkbhlzvkb"; }; - # vim for xxd binary - buildInputs = [ python vim ]; + buildInputs = [ python xxd ]; nativeBuildInputs = [ cmake ]; patches = [(fetchpatch rec { @@ -23,9 +22,9 @@ stdenv.mkDerivation rec { meta = with stdenv.lib; { description = "An advanced SAT Solver"; + homepage = https://github.com/msoos/cryptominisat; + license = licenses.mit; maintainers = with maintainers; [ mic92 ]; - platforms = platforms.unix; - license = licenses.mit; - homepage = https://github.com/msoos/cryptominisat; + platforms = platforms.unix; }; } diff --git a/pkgs/applications/science/logic/cubicle/default.nix b/pkgs/applications/science/logic/cubicle/default.nix index 9bfbcc3f30df..65a0f72da5eb 100644 --- a/pkgs/applications/science/logic/cubicle/default.nix +++ b/pkgs/applications/science/logic/cubicle/default.nix @@ -12,7 +12,7 @@ stdenv.mkDerivation rec { meta = with stdenv.lib; { description = "An open source model checker for verifying safety properties of array-based systems"; - homepage = "http://cubicle.lri.fr/"; + homepage = http://cubicle.lri.fr/; license = licenses.asl20; platforms = platforms.linux; maintainers = with maintainers; [ lucas8 ]; diff --git a/pkgs/applications/science/logic/cvc3/default.nix b/pkgs/applications/science/logic/cvc3/default.nix index 505d09ef3903..82fad1134bc4 100644 --- a/pkgs/applications/science/logic/cvc3/default.nix +++ b/pkgs/applications/science/logic/cvc3/default.nix @@ -22,7 +22,7 @@ stdenv.mkDerivation rec { [ raskin ]; platforms = platforms.linux; license = licenses.free; - homepage = "http://www.cs.nyu.edu/acsys/cvc3/index.html"; + homepage = http://www.cs.nyu.edu/acsys/cvc3/index.html; }; passthru = { updateInfo = { diff --git a/pkgs/applications/science/logic/hol/default.nix b/pkgs/applications/science/logic/hol/default.nix index e931c6fcf9d5..5eb33daefe80 100644 --- a/pkgs/applications/science/logic/hol/default.nix +++ b/pkgs/applications/science/logic/hol/default.nix @@ -79,7 +79,7 @@ stdenv.mkDerivation { implementing combinations of deduction, execution and property checking. ''; - homepage = "http://hol.sourceforge.net/"; + homepage = http://hol.sourceforge.net/; license = licenses.bsd3; maintainers = with maintainers; [ mudri ]; platforms = with platforms; linux; diff --git a/pkgs/applications/science/logic/iprover/default.nix b/pkgs/applications/science/logic/iprover/default.nix index fe906fbe3578..af225a2961d5 100644 --- a/pkgs/applications/science/logic/iprover/default.nix +++ b/pkgs/applications/science/logic/iprover/default.nix @@ -1,15 +1,15 @@ -{ stdenv, fetchurl, ocaml, eprover }: +{ stdenv, fetchurl, ocaml, eprover, zlib }: stdenv.mkDerivation rec { name = "iprover-${version}"; - version = "0.8.1"; + version = "2.5"; src = fetchurl { - url = "http://iprover.googlecode.com/files/iprover_v${version}.tar.gz"; - sha256 = "15qn523w4l296np5rnkwi50a5x2xqz0kaza7bsh9bkazph7jma7w"; + url = "http://www.cs.man.ac.uk/~korovink/iprover/iprover-v${version}.tar.gz"; + sha256 = "1mbxjczp6nqw0p33glqmw973c268yzy4gxflk1lfiyiihrjdhinb"; }; - buildInputs = [ ocaml eprover ]; + buildInputs = [ ocaml eprover zlib ]; preConfigure = ''patchShebangs .''; @@ -25,12 +25,9 @@ stdenv.mkDerivation rec { meta = with stdenv.lib; { description = "An automated first-order logic theorem prover"; - maintainers = with maintainers; - [ - raskin - ]; + homepage = http://www.cs.man.ac.uk/~korovink/iprover/; + maintainers = with maintainers; [ raskin gebner ]; platforms = platforms.linux; license = licenses.gpl3; - downloadPage = "http://code.google.com/p/iprover/downloads/list"; }; } diff --git a/pkgs/applications/science/logic/logisim/default.nix b/pkgs/applications/science/logic/logisim/default.nix index 50ef1edf63e2..db784237ea91 100644 --- a/pkgs/applications/science/logic/logisim/default.nix +++ b/pkgs/applications/science/logic/logisim/default.nix @@ -20,7 +20,7 @@ stdenv.mkDerivation { ''; meta = { - homepage = "http://ozark.hendrix.edu/~burch/logisim"; + homepage = http://ozark.hendrix.edu/~burch/logisim; description = "Educational tool for designing and simulating digital logic circuits"; license = stdenv.lib.licenses.gpl2Plus; platforms = stdenv.lib.platforms.unix; diff --git a/pkgs/applications/science/logic/minisat/default.nix b/pkgs/applications/science/logic/minisat/default.nix index d980afee7c4e..4b2116680d50 100644 --- a/pkgs/applications/science/logic/minisat/default.nix +++ b/pkgs/applications/science/logic/minisat/default.nix @@ -27,6 +27,6 @@ stdenv.mkDerivation rec { maintainers = with maintainers; [ gebner raskin ]; platforms = platforms.unix; license = licenses.mit; - homepage = "http://minisat.se/"; + homepage = http://minisat.se/; }; } diff --git a/pkgs/applications/science/logic/minisat/unstable.nix b/pkgs/applications/science/logic/minisat/unstable.nix index 9d63f32c5449..f1a42f8215e3 100644 --- a/pkgs/applications/science/logic/minisat/unstable.nix +++ b/pkgs/applications/science/logic/minisat/unstable.nix @@ -18,6 +18,6 @@ stdenv.mkDerivation rec { maintainers = with maintainers; [ mic92 ]; platforms = platforms.unix; license = licenses.mit; - homepage = "http://minisat.se/"; + homepage = http://minisat.se/; }; } diff --git a/pkgs/applications/science/logic/opensmt/default.nix b/pkgs/applications/science/logic/opensmt/default.nix index 6129eaadc891..f9f021b15f07 100644 --- a/pkgs/applications/science/logic/opensmt/default.nix +++ b/pkgs/applications/science/logic/opensmt/default.nix @@ -18,7 +18,7 @@ stdenv.mkDerivation rec { maintainers = [ maintainers.raskin ]; platforms = platforms.linux; license = licenses.gpl3; - homepage = "http://code.google.com/p/opensmt/"; + homepage = http://code.google.com/p/opensmt/; broken = true; downloadPage = "http://code.google.com/p/opensmt/downloads/list"; }; diff --git a/pkgs/applications/science/logic/poly/default.nix b/pkgs/applications/science/logic/poly/default.nix new file mode 100644 index 000000000000..2fdbd87a275c --- /dev/null +++ b/pkgs/applications/science/logic/poly/default.nix @@ -0,0 +1,22 @@ +{stdenv, fetchurl, gmp, cmake, python}: + +let version = "0.1.3"; +in + +stdenv.mkDerivation { + name = "libpoly-${version}"; + + src = fetchurl { + url = "https://github.com/SRI-CSL/libpoly/archive/v${version}.tar.gz"; + sha256 = "0nd90585imnznyp04vg6a5ixxkd3bavhv1437397aj2k3dfc0y2k"; + }; + + buildInputs = [ cmake gmp python ]; + + meta = with stdenv.lib; { + homepage = https://github.com/SRI-CSL/libpoly; + description = "C library for manipulating polynomials"; + license = licenses.lgpl3; + platforms = platforms.all; + }; +} diff --git a/pkgs/applications/science/logic/prover9/default.nix b/pkgs/applications/science/logic/prover9/default.nix index 43c2ae141b7a..74e31d062f48 100644 --- a/pkgs/applications/science/logic/prover9/default.nix +++ b/pkgs/applications/science/logic/prover9/default.nix @@ -31,7 +31,7 @@ stdenv.mkDerivation { ''; meta = { - homepage = "http://www.cs.unm.edu/~mccune/mace4/"; + homepage = http://www.cs.unm.edu/~mccune/mace4/; license = "GPL"; description = "Automated theorem prover for first-order and equational logic"; longDescription = '' diff --git a/pkgs/applications/science/logic/redprl/default.nix b/pkgs/applications/science/logic/redprl/default.nix index 49245c73f2c4..9da2647d1138 100644 --- a/pkgs/applications/science/logic/redprl/default.nix +++ b/pkgs/applications/science/logic/redprl/default.nix @@ -20,7 +20,7 @@ stdenv.mkDerivation { ''; meta = { description = "A proof assistant for Nominal Computational Type Theory"; - homepage = "http://www.redprl.org/"; + homepage = http://www.redprl.org/; license = stdenv.lib.licenses.mit; maintainers = [ stdenv.lib.maintainers.acowley ]; platforms = stdenv.lib.platforms.unix; diff --git a/pkgs/applications/science/logic/satallax/default.nix b/pkgs/applications/science/logic/satallax/default.nix index 6f42ff15a227..c22bff9cdee2 100644 --- a/pkgs/applications/science/logic/satallax/default.nix +++ b/pkgs/applications/science/logic/satallax/default.nix @@ -60,7 +60,7 @@ stdenv.mkDerivation rec { maintainers = [stdenv.lib.maintainers.raskin]; platforms = stdenv.lib.platforms.linux; downloadPage = "http://www.ps.uni-saarland.de/~cebrown/satallax/downloads.php"; - homepage = "http://www.ps.uni-saarland.de/~cebrown/satallax/index.php"; + homepage = http://www.ps.uni-saarland.de/~cebrown/satallax/index.php; updateWalker = true; }; } diff --git a/pkgs/applications/science/logic/yices/default.nix b/pkgs/applications/science/logic/yices/default.nix index cf5114b4a417..c8e20c7260c9 100644 --- a/pkgs/applications/science/logic/yices/default.nix +++ b/pkgs/applications/science/logic/yices/default.nix @@ -1,26 +1,32 @@ -{ stdenv, fetchurl, gmp-static, gperf, autoreconfHook }: +{ stdenv, fetchurl, gmp-static, gperf, autoreconfHook, libpoly }: stdenv.mkDerivation rec { name = "yices-${version}"; - version = "2.5.1"; + version = "2.5.2"; src = fetchurl { - url = "http://yices.csl.sri.com/cgi-bin/yices2-newnewdownload.cgi?file=yices-${version}-src.tar.gz&accept=I+Agree"; - name = "yices-${version}-src.tar.gz"; - sha256 = "1wfq6hcm54h0mqmbs1ip63i0ywlwnciav86sbzk3gafxyzg1nd0c"; + url = "http://yices.csl.sri.com/cgi-bin/yices2-newnewdownload.cgi?file=${name}-src.tar.gz&accept=I+Agree"; + name = "${name}-src.tar.gz"; + sha256 = "18mjnwg0pwc0fx4f99l7hxsi10mb5skkzk0k1m3xv5kx3qfnghs0"; }; patchPhase = ''patchShebangs tests/regress/check.sh''; configureFlags = [ "--with-static-gmp=${gmp-static.out}/lib/libgmp.a" "--with-static-gmp-include-dir=${gmp-static.dev}/include" + "--enable-mcsat" ]; - buildInputs = [ gmp-static gperf autoreconfHook ]; + buildInputs = [ gmp-static gperf autoreconfHook libpoly ]; enableParallelBuilding = true; doCheck = true; - installPhase = ''make install LDCONFIG=true''; + # Includes a fix for the embedded soname being libyices.so.2.5, but + # only installing the libyices.so.2.5.1 file. + installPhase = '' + make install LDCONFIG=true + (cd $out/lib && ln -s -f libyices.so.2.5.2 libyices.so.2.5) + ''; meta = with stdenv.lib; { description = "A high-performance theorem prover and SMT solver"; diff --git a/pkgs/applications/science/math/LiE/default.nix b/pkgs/applications/science/math/LiE/default.nix index 515b7e272899..e0b0bc11f05f 100644 --- a/pkgs/applications/science/math/LiE/default.nix +++ b/pkgs/applications/science/math/LiE/default.nix @@ -9,7 +9,7 @@ stdenv.mkDerivation rec { meta = { description = "A Computer algebra package for Lie group computations"; - homepage = "http://wwwmathlabo.univ-poitiers.fr/~maavl/LiE/"; + homepage = http://wwwmathlabo.univ-poitiers.fr/~maavl/LiE/; license = stdenv.lib.licenses.lgpl3; # see the website longDescription = '' diff --git a/pkgs/applications/science/math/R/default.nix b/pkgs/applications/science/math/R/default.nix index e75ae2222ae9..5adece31370e 100644 --- a/pkgs/applications/science/math/R/default.nix +++ b/pkgs/applications/science/math/R/default.nix @@ -69,7 +69,7 @@ stdenv.mkDerivation rec { setupHook = ./setup-hook.sh; meta = with stdenv.lib; { - homepage = "http://www.r-project.org/"; + homepage = http://www.r-project.org/; description = "Free software environment for statistical computing and graphics"; license = licenses.gpl2Plus; diff --git a/pkgs/applications/science/math/calc/default.nix b/pkgs/applications/science/math/calc/default.nix index b8ed7ffac3cd..ff8a1ff95844 100644 --- a/pkgs/applications/science/math/calc/default.nix +++ b/pkgs/applications/science/math/calc/default.nix @@ -12,11 +12,11 @@ in stdenv.mkDerivation rec { name = "calc-${version}"; - version = "2.12.5.3"; + version = "2.12.6.1"; src = fetchurl { - url = "mirror://sourceforge/calc/${name}.tar.bz2"; - sha256 = "14mnz6smhi3a0rgmwvddk9w3vdisi8khq67i8nqsl47vgs8n1kqg"; + url = "https://github.com/lcn2/calc/releases/download/${version}/${name}.tar.bz2"; + sha256 = "1vy4jmhmpl3gzgpkpv0kqwjv8hn1cza8cn1g8c69gq3inqvr4fvd"; }; buildInputs = [ makeWrapper readline ncurses utillinux ]; diff --git a/pkgs/applications/science/math/eukleides/default.nix b/pkgs/applications/science/math/eukleides/default.nix index 879ad96a9367..6d1c778d1e0e 100644 --- a/pkgs/applications/science/math/eukleides/default.nix +++ b/pkgs/applications/science/math/eukleides/default.nix @@ -19,7 +19,7 @@ stdenv.mkDerivation { meta = { description = "Geometry Drawing Language"; - homepage = "http://www.eukleides.org/"; + homepage = http://www.eukleides.org/; license = stdenv.lib.licenses.gpl2; longDescription = '' diff --git a/pkgs/applications/science/math/geogebra/default.nix b/pkgs/applications/science/math/geogebra/default.nix index b6fdd6f58b9b..ec3d265fb80f 100644 --- a/pkgs/applications/science/math/geogebra/default.nix +++ b/pkgs/applications/science/math/geogebra/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { name = "geogebra-${version}"; - version = "5-0-369-0"; + version = "5-0-377-0"; preferLocalBuild = true; src = fetchurl { url = "http://download.geogebra.org/installers/5.0/GeoGebra-Linux-Portable-${version}.tar.bz2"; - sha256 = "0b5015z1ff3ksnkmyn2hbfwvhqp1572pdn8llpws32k7w1lb0jnk"; + sha256 = "0rvsjpf7pyz8z5yrqmc5ixzq7mnf1pyp00i914qd6wn5bx0apkxv"; }; srcIcon = fetchurl { diff --git a/pkgs/applications/science/math/gfan/default.nix b/pkgs/applications/science/math/gfan/default.nix index dbd28cf9e8ce..05f09e4aedb3 100644 --- a/pkgs/applications/science/math/gfan/default.nix +++ b/pkgs/applications/science/math/gfan/default.nix @@ -19,6 +19,6 @@ stdenv.mkDerivation rec { license = stdenv.lib.licenses.gpl2 ; maintainers = [stdenv.lib.maintainers.raskin]; platforms = stdenv.lib.platforms.linux; - homepage = "http://home.math.au.dk/jensen/software/gfan/gfan.html"; + homepage = http://home.math.au.dk/jensen/software/gfan/gfan.html; }; } diff --git a/pkgs/applications/science/math/ginac/default.nix b/pkgs/applications/science/math/ginac/default.nix index ee67af62bb19..1956ebdcb0f1 100644 --- a/pkgs/applications/science/math/ginac/default.nix +++ b/pkgs/applications/science/math/ginac/default.nix @@ -1,18 +1,20 @@ -{ stdenv, fetchurl, cln, pkgconfig, readline, gmp }: +{ stdenv, fetchurl, cln, pkgconfig, readline, gmp, python }: stdenv.mkDerivation rec { - name = "ginac-1.6.2"; + name = "ginac-1.7.2"; src = fetchurl { url = "${meta.homepage}/${name}.tar.bz2"; - sha256 = "1pivcqqaf142l6vrj2azq6dxrcyzhag4za2dwicb4gsb09ax4d0g"; + sha256 = "1dyq47gc97jn1r5sy0klxs5b4lzhckyjqgsvwcs2a9ybqmhmpdr4"; }; propagatedBuildInputs = [ cln ]; buildInputs = [ readline ] ++ stdenv.lib.optional stdenv.isDarwin gmp; - nativeBuildInputs = [ pkgconfig ]; + nativeBuildInputs = [ pkgconfig python ]; + + preConfigure = "patchShebangs ginsh"; configureFlags = "--disable-rpath"; diff --git a/pkgs/applications/science/math/mathematica/10.nix b/pkgs/applications/science/math/mathematica/10.nix index 4de4a0c261d5..6a49976c86b8 100644 --- a/pkgs/applications/science/math/mathematica/10.nix +++ b/pkgs/applications/science/math/mathematica/10.nix @@ -132,7 +132,7 @@ stdenv.mkDerivation rec { meta = { description = "Wolfram Mathematica computational software system"; - homepage = "http://www.wolfram.com/mathematica/"; + homepage = http://www.wolfram.com/mathematica/; license = stdenv.lib.licenses.unfree; }; } diff --git a/pkgs/applications/science/math/mathematica/9.nix b/pkgs/applications/science/math/mathematica/9.nix index 07a20b4ebe03..c4fd0c384c14 100644 --- a/pkgs/applications/science/math/mathematica/9.nix +++ b/pkgs/applications/science/math/mathematica/9.nix @@ -118,7 +118,7 @@ stdenv.mkDerivation rec { meta = { description = "Wolfram Mathematica computational software system"; - homepage = "http://www.wolfram.com/mathematica/"; + homepage = http://www.wolfram.com/mathematica/; license = stdenv.lib.licenses.unfree; }; } diff --git a/pkgs/applications/science/math/mathematica/default.nix b/pkgs/applications/science/math/mathematica/default.nix index 10737a92f8c2..1e23cfea27fc 100644 --- a/pkgs/applications/science/math/mathematica/default.nix +++ b/pkgs/applications/science/math/mathematica/default.nix @@ -140,7 +140,7 @@ stdenv.mkDerivation rec { meta = { description = "Wolfram Mathematica computational software system"; - homepage = "http://www.wolfram.com/mathematica/"; + homepage = http://www.wolfram.com/mathematica/; license = stdenv.lib.licenses.unfree; }; } diff --git a/pkgs/applications/science/math/maxima/default.nix b/pkgs/applications/science/math/maxima/default.nix index 5a19f73d9cf9..8a84ed78b781 100644 --- a/pkgs/applications/science/math/maxima/default.nix +++ b/pkgs/applications/science/math/maxima/default.nix @@ -4,7 +4,7 @@ tk ? null, gnuplot ? null, ecl ? null, ecl-fasl ? false let name = "maxima"; - version = "5.39.0"; + version = "5.40.0"; searchPath = stdenv.lib.makeBinPath @@ -15,7 +15,7 @@ stdenv.mkDerivation ({ src = fetchurl { url = "mirror://sourceforge/${name}/${name}-${version}.tar.gz"; - sha256 = "1cvignn5y6qzrby6qb885yc8zdcdqdr1d50vcvc3gapw2f0gk3zm"; + sha256 = "15pp35ayglv723bjbqc60gcdv2bm54s6pywsm4i4cwbjsf64dzkl"; }; buildInputs = stdenv.lib.filter (x: x != null) @@ -45,7 +45,7 @@ stdenv.mkDerivation ({ meta = { description = "Computer algebra system"; - homepage = "http://maxima.sourceforge.net"; + homepage = http://maxima.sourceforge.net; license = stdenv.lib.licenses.gpl2; longDescription = '' diff --git a/pkgs/applications/science/math/nauty/default.nix b/pkgs/applications/science/math/nauty/default.nix index 7503c50c6d22..36ac84ece25f 100644 --- a/pkgs/applications/science/math/nauty/default.nix +++ b/pkgs/applications/science/math/nauty/default.nix @@ -19,6 +19,6 @@ stdenv.mkDerivation rec { license = stdenv.lib.licenses.asl20; maintainers = [stdenv.lib.maintainers.raskin]; platforms = stdenv.lib.platforms.linux; - homepage = "http://pallini.di.uniroma1.it/"; + homepage = http://pallini.di.uniroma1.it/; }; } diff --git a/pkgs/applications/science/math/perseus/default.nix b/pkgs/applications/science/math/perseus/default.nix index 55293e6c8a79..2d150d0c30e9 100644 --- a/pkgs/applications/science/math/perseus/default.nix +++ b/pkgs/applications/science/math/perseus/default.nix @@ -32,7 +32,7 @@ stdenv.mkDerivation { around datasets arising from point samples, images, distance matrices and so forth. ''; - homepage = "http://www.sas.upenn.edu/~vnanda/perseus/index.html"; + homepage = http://www.sas.upenn.edu/~vnanda/perseus/index.html; license = stdenv.lib.licenses.gpl3; maintainers = with stdenv.lib.maintainers; [erikryb]; platforms = stdenv.lib.platforms.linux; diff --git a/pkgs/applications/science/math/pssp/default.nix b/pkgs/applications/science/math/pssp/default.nix index e74e17fa44f5..02d24d601b19 100644 --- a/pkgs/applications/science/math/pssp/default.nix +++ b/pkgs/applications/science/math/pssp/default.nix @@ -18,7 +18,7 @@ stdenv.mkDerivation rec { enableParallelBuilding = true; meta = { - homepage = "http://www.gnu.org/software/pspp/"; + homepage = http://www.gnu.org/software/pspp/; description = "A free replacement for SPSS, a program for statistical analysis of sampled data"; license = stdenv.lib.licenses.gpl3Plus; diff --git a/pkgs/applications/science/math/qalculate-gtk/default.nix b/pkgs/applications/science/math/qalculate-gtk/default.nix index 5f49b240fc06..cd89fbbe1871 100644 --- a/pkgs/applications/science/math/qalculate-gtk/default.nix +++ b/pkgs/applications/science/math/qalculate-gtk/default.nix @@ -2,13 +2,19 @@ stdenv.mkDerivation rec { name = "qalculate-gtk-${version}"; - version = "0.9.9"; + version = "1.0.0"; src = fetchurl { url = "https://github.com/Qalculate/qalculate-gtk/archive/v${version}.tar.gz"; - sha256 = "0v9ibycilygmi9zzi7cxif7si56c85lfzdvbqnbf32whg8ydqqkg"; + sha256 = "08sg6kfcfdpxjsl538ba26ncm2cxzc63nlafj99ff4b46wxia57k"; }; + patchPhase = '' + for fn in src/interface.cc src/main.cc; do + substituteInPlace $fn --replace 'getPackageDataDir().c_str()' \"$out/share\" + done + ''; + hardeningDisable = [ "format" ]; nativeBuildInputs = [ intltool pkgconfig autoreconfHook wrapGAppsHook ]; diff --git a/pkgs/applications/science/math/ratpoints/default.nix b/pkgs/applications/science/math/ratpoints/default.nix index 1e99b8782a96..82a6836bd623 100644 --- a/pkgs/applications/science/math/ratpoints/default.nix +++ b/pkgs/applications/science/math/ratpoints/default.nix @@ -15,7 +15,7 @@ stdenv.mkDerivation rec { license = stdenv.lib.licenses.gpl2Plus; maintainers = [stdenv.lib.maintainers.raskin]; platforms = stdenv.lib.platforms.linux; - homepage = "http://www.mathe2.uni-bayreuth.de/stoll/programs/"; + homepage = http://www.mathe2.uni-bayreuth.de/stoll/programs/; updateWalker = true; }; } diff --git a/pkgs/applications/science/math/ripser/default.nix b/pkgs/applications/science/math/ripser/default.nix index 7f94b7408a11..b7453ecb01d4 100644 --- a/pkgs/applications/science/math/ripser/default.nix +++ b/pkgs/applications/science/math/ripser/default.nix @@ -57,7 +57,7 @@ stdenv.mkDerivation { meta = { description = "A lean C++ code for the computation of Vietoris–Rips persistence barcodes"; - homepage = "https://github.com/Ripser/ripser"; + homepage = https://github.com/Ripser/ripser; license = stdenv.lib.licenses.lgpl3; maintainers = with stdenv.lib.maintainers; [erikryb]; platforms = stdenv.lib.platforms.linux; diff --git a/pkgs/applications/science/math/sage/default.nix b/pkgs/applications/science/math/sage/default.nix index e6630815ba16..bf3c7fcea989 100644 --- a/pkgs/applications/science/math/sage/default.nix +++ b/pkgs/applications/science/math/sage/default.nix @@ -34,7 +34,7 @@ stdenv.mkDerivation rec { installPhase = ''DESTDIR=$out make install''; meta = { - homepage = "http://www.sagemath.org"; + homepage = http://www.sagemath.org; description = "A free open source mathematics software system"; license = stdenv.lib.licenses.gpl2Plus; broken = true; diff --git a/pkgs/applications/science/math/scotch/default.nix b/pkgs/applications/science/math/scotch/default.nix index 2e928bc8f344..3b01c684d529 100644 --- a/pkgs/applications/science/math/scotch/default.nix +++ b/pkgs/applications/science/math/scotch/default.nix @@ -27,7 +27,7 @@ stdenv.mkDerivation rec { Scotch is a software package for graph and mesh/hypergraph partitioning, graph clustering, and sparse matrix ordering. ''; - homepage = "http://www.labri.fr/perso/pelegrin/scotch"; + homepage = http://www.labri.fr/perso/pelegrin/scotch; license = stdenv.lib.licenses.cecill-c; maintainers = [ stdenv.lib.maintainers.bzizou ]; platforms = stdenv.lib.platforms.linux; diff --git a/pkgs/applications/science/math/singular/default.nix b/pkgs/applications/science/math/singular/default.nix index 3fe8b542995e..b098da060e07 100644 --- a/pkgs/applications/science/math/singular/default.nix +++ b/pkgs/applications/science/math/singular/default.nix @@ -47,7 +47,7 @@ stdenv.mkDerivation rec { maintainers = with maintainers; [ raskin ]; platforms = subtractLists platforms.i686 platforms.linux; license = licenses.gpl3; # Or GPLv2 at your option - but not GPLv4 - homepage = "http://www.singular.uni-kl.de/index.php"; + homepage = http://www.singular.uni-kl.de/index.php; downloadPage = "http://www.mathematik.uni-kl.de/ftp/pub/Math/Singular/SOURCES/"; }; } diff --git a/pkgs/applications/science/math/symmetrica/default.nix b/pkgs/applications/science/math/symmetrica/default.nix index 0c87beb22dfc..a7212299aa63 100644 --- a/pkgs/applications/science/math/symmetrica/default.nix +++ b/pkgs/applications/science/math/symmetrica/default.nix @@ -24,6 +24,6 @@ stdenv.mkDerivation rec { license = stdenv.lib.licenses.publicDomain; maintainers = [stdenv.lib.maintainers.raskin]; platforms = stdenv.lib.platforms.linux; - homepage = "http://www.symmetrica.de/"; + homepage = http://www.symmetrica.de/; }; } diff --git a/pkgs/applications/science/math/weka/default.nix b/pkgs/applications/science/math/weka/default.nix index cfc63a50165e..18cb26890634 100644 --- a/pkgs/applications/science/math/weka/default.nix +++ b/pkgs/applications/science/math/weka/default.nix @@ -26,7 +26,7 @@ stdenv.mkDerivation rec { ''; meta = { - homepage = "http://www.cs.waikato.ac.nz/ml/weka/"; + homepage = http://www.cs.waikato.ac.nz/ml/weka/; description = "Collection of machine learning algorithms for data mining tasks"; license = stdenv.lib.licenses.gpl2Plus; maintainer = [stdenv.lib.maintainers.mimadrid]; diff --git a/pkgs/applications/science/medicine/aliza/default.nix b/pkgs/applications/science/medicine/aliza/default.nix new file mode 100644 index 000000000000..b0471b80e2f1 --- /dev/null +++ b/pkgs/applications/science/medicine/aliza/default.nix @@ -0,0 +1,52 @@ +{ stdenv, fetchurl, rpmextract, makeWrapper, patchelf, qt4, zlib, libX11, libXt, libSM, libICE, libXext, mesa }: + +with stdenv.lib; +stdenv.mkDerivation { + name = "aliza"; + src = fetchurl { + # Hosted on muoniurn's google drive + url = "https://drive.google.com/uc?export=download&id=0B0s_Yf4jjfZ4WUJaSERHN3FsNFE"; + sha256 = "1nfp3ghjnfxmxiclg76gcn7a3mhvi6h7s5wmd9v9l6w8lfq9vj5h"; + name = "aliza.rpm"; + }; + + buildInputs = [ rpmextract makeWrapper ]; + + unpackCmd = "rpmextract $curSrc"; + + patchPhase = '' + sed -i 's/^Exec.*$/Exec=aliza %F/' share/applications/aliza.desktop + ''; + + installPhase = '' + mkdir -p $out + cp -r bin share $out + + runHook postInstall + ''; + + postInstall = let + libs = stdenv.lib.makeLibraryPath [ qt4 zlib stdenv.cc.cc libSM libICE libX11 libXext libXt mesa ]; + in '' + ${patchelf}/bin/patchelf \ + --interpreter "$(cat $NIX_CC/nix-support/dynamic-linker)" \ + $out/bin/aliza + + ${patchelf}/bin/patchelf \ + --interpreter "$(cat $NIX_CC/nix-support/dynamic-linker)" \ + $out/bin/aliza-vtkvol + + wrapProgram $out/bin/aliza \ + --prefix LD_LIBRARY_PATH : ${libs} + + wrapProgram $out/bin/aliza-vtkvol \ + --prefix LD_LIBRARY_PATH : ${libs} + ''; + + meta = { + description = "Medical imaging software with 2D, 3D and 4D capabilities"; + homepage = http://www.aliza-dicom-viewer.com; + license = licenses.unfreeRedistributable; + maintainers = with maintainers; [ mounium ]; + }; +} diff --git a/pkgs/applications/science/misc/cytoscape/default.nix b/pkgs/applications/science/misc/cytoscape/default.nix index d36b0f0b4d93..d5ffe9cd9ba8 100644 --- a/pkgs/applications/science/misc/cytoscape/default.nix +++ b/pkgs/applications/science/misc/cytoscape/default.nix @@ -25,7 +25,7 @@ stdenv.mkDerivation rec { ''; meta = { - homepage = "http://www.cytoscape.org"; + homepage = http://www.cytoscape.org; description = "A general platform for complex network analysis and visualization"; license = stdenv.lib.licenses.lgpl21; maintainers = [stdenv.lib.maintainers.mimadrid]; diff --git a/pkgs/applications/science/misc/motu-client/default.nix b/pkgs/applications/science/misc/motu-client/default.nix index b5e9fa6a51ee..0d5c79fde900 100644 --- a/pkgs/applications/science/misc/motu-client/default.nix +++ b/pkgs/applications/science/misc/motu-client/default.nix @@ -1,11 +1,11 @@ { python27Packages, fetchurl, lib } : python27Packages.buildPythonApplication rec { name = "motu-client-${version}"; - version = "1.0.8"; + version = "1.4.00"; src = fetchurl { - url = "https://github.com/quiet-oceans/motuclient-setuptools/archive/${name}.tar.gz"; - sha256 = "1naqmav312agn72iad9kyxwscn2lz4v1cfcqqi1qcgvc82vnwkw2"; + url = "https://github.com/quiet-oceans/motuclient-setuptools/archive/${version}.tar.gz"; + sha256 = "0v0h90mylhaamd1vm4nc64q63vmlafhijm47hs0xfam33y1q2yvb"; }; meta = with lib; { diff --git a/pkgs/applications/science/misc/root/default.nix b/pkgs/applications/science/misc/root/default.nix index 8916a9fd1677..cc961c8d392b 100644 --- a/pkgs/applications/science/misc/root/default.nix +++ b/pkgs/applications/science/misc/root/default.nix @@ -4,11 +4,11 @@ stdenv.mkDerivation rec { name = "root-${version}"; - version = "6.10.00"; + version = "6.10.02"; src = fetchurl { url = "https://root.cern.ch/download/root_v${version}.source.tar.gz"; - sha256 = "1rxqcpqf1b3sxig5xbh3mkvarhg9lgj2f0gv0j48klfw8kgfwlsp"; + sha256 = "1ryp9397xpbnxha6s222c10pa50lf2qf5s35n31lc29s90p8s9kc"; }; buildInputs = [ cmake pcre pkgconfig python2 zlib libxml2 lzma gsl ] @@ -71,7 +71,7 @@ stdenv.mkDerivation rec { setupHook = ./setup-hook.sh; meta = { - homepage = "https://root.cern.ch/"; + homepage = https://root.cern.ch/; description = "A data analysis framework"; platforms = stdenv.lib.platforms.unix; maintainers = with stdenv.lib.maintainers; [ veprbl ]; diff --git a/pkgs/applications/science/molecular-dynamics/lammps/default.nix b/pkgs/applications/science/molecular-dynamics/lammps/default.nix index 35ab53483687..9a89b88d7a52 100644 --- a/pkgs/applications/science/molecular-dynamics/lammps/default.nix +++ b/pkgs/applications/science/molecular-dynamics/lammps/default.nix @@ -48,7 +48,7 @@ stdenv.mkDerivation rec { funding from the DOE. It is an open-source code, distributed freely under the terms of the GNU Public License (GPL). ''; - homepage = "http://lammps.sandia.gov"; + homepage = http://lammps.sandia.gov; license = stdenv.lib.licenses.gpl2; platforms = stdenv.lib.platforms.linux; }; diff --git a/pkgs/applications/science/programming/scyther/cli.nix b/pkgs/applications/science/programming/scyther/cli.nix new file mode 100644 index 000000000000..152b71217743 --- /dev/null +++ b/pkgs/applications/science/programming/scyther/cli.nix @@ -0,0 +1,32 @@ +{ stdenv, glibc, flex, bison, cmake +, version, src, meta }: +stdenv.mkDerivation { + name = "scyther-cli-${version}"; + + inherit src meta; + + buildInputs = [ + cmake + glibc.static + flex + bison + ]; + + patchPhase = '' + # Since we're not in a git dir, the normal command this project uses to create this file wouldn't work + printf "%s\n" "#define TAGVERSION \"${version}\"" > src/version.h + ''; + + configurePhase = '' + (cd src && cmakeConfigurePhase) + ''; + + dontUseCmakeBuildDir = true; + cmakeFlags = [ "-DCMAKE_C_FLAGS=-std=gnu89" ]; + + installPhase = '' + mkdir -p "$out/bin" + mv src/scyther-linux "$out/bin/scyther-cli" + ln -s "$out/bin/scyther-cli" "$out/bin/scyther-linux" + ''; +} diff --git a/pkgs/applications/science/programming/scyther/default.nix b/pkgs/applications/science/programming/scyther/default.nix new file mode 100644 index 000000000000..beef26c6032a --- /dev/null +++ b/pkgs/applications/science/programming/scyther/default.nix @@ -0,0 +1,79 @@ +{ stdenv, lib, buildEnv, callPackage_i686, fetchFromGitHub, python27Packages, graphviz +, includeGUI ? true +, includeProtocols ? true +}: +let + version = "1.1.3"; + + src = fetchFromGitHub { + rev = "v${version}"; + sha256 = "0rb4ha5bnjxnwj4f3hciq7kyj96fhw14hqbwl5kr9cdw8q62mx0h"; + owner = "cascremers"; + repo = "scyther"; + }; + + meta = with lib; { + description = "Scyther is a tool for the automatic verification of security protocols."; + homepage = https://www.cs.ox.ac.uk/people/cas.cremers/scyther/; + license = licenses.gpl2; + maintainers = with maintainers; [ infinisil ]; + platforms = platforms.linux; + }; + + cli = callPackage_i686 ./cli.nix { + inherit version src meta; + }; + + gui = stdenv.mkDerivation { + name = "scyther-gui-${version}"; + inherit src meta; + buildInputs = [ + python27Packages.wrapPython + ]; + + patchPhase = '' + file=gui/Scyther/Scyther.py + + # By default the scyther binary is looked for in the directory of the python script ($out/gui), but we want to have it look where our cli package is + substituteInPlace $file --replace "return getMyDir()" "return \"${cli}/bin\"" + + # Removes the Shebang from the file, as this would be wrapped wrongly + sed -i -e "1d" $file + ''; + + dontBuild = true; + + propagatedBuildInputs = [ + python27Packages.wxPython + graphviz + ]; + + installPhase = '' + mkdir -p "$out"/gui "$out"/bin + cp -r gui/* "$out"/gui + ln -s "$out"/gui/scyther-gui.py "$out/bin/scyther-gui" + ''; + + postFixup = '' + wrapPythonProgramsIn "$out/gui" "$out $pythonPath" + ''; + + doInstallCheck = true; + installCheckPhase = '' + "$out/gui/scyther.py" "$src/gui/Protocols/Demo/ns3.spdl" + ''; + }; +in + buildEnv { + name = "scyther-${version}"; + inherit meta; + paths = [ cli ] ++ lib.optional includeGUI gui; + pathsToLink = [ "/bin" ]; + + postBuild = '' + rm "$out/bin/scyther-linux" + '' + lib.optionalString includeProtocols '' + mkdir -p "$out/protocols" + cp -rv ${src}/protocols/* "$out/protocols" + ''; + } |