diff options
Diffstat (limited to 'pkgs/applications/science')
40 files changed, 162 insertions, 152 deletions
diff --git a/pkgs/applications/science/astronomy/astrolabe-generator/default.nix b/pkgs/applications/science/astronomy/astrolabe-generator/default.nix index cb3f3131ea1..4a6bdd9d1e9 100644 --- a/pkgs/applications/science/astronomy/astrolabe-generator/default.nix +++ b/pkgs/applications/science/astronomy/astrolabe-generator/default.nix @@ -25,7 +25,7 @@ stdenv.mkDerivation rec { homepage = "https://www.astrolabeproject.com"; description = "A Java-based tool for generating EPS files for constructing astrolabes and related tools"; license = licenses.gpl3; - maintainers = [ maintainers.genesis ]; + maintainers = [ ]; platforms = platforms.all; }; } diff --git a/pkgs/applications/science/biology/igv/default.nix b/pkgs/applications/science/biology/igv/default.nix index 0b990dc541b..86a16c4f047 100644 --- a/pkgs/applications/science/biology/igv/default.nix +++ b/pkgs/applications/science/biology/igv/default.nix @@ -2,10 +2,10 @@ stdenv.mkDerivation rec { pname = "igv"; - version = "2.8.11"; + version = "2.8.12"; src = fetchzip { url = "https://data.broadinstitute.org/igv/projects/downloads/2.8/IGV_${version}.zip"; - sha256 = "1hiwnrrh42qzc7kdc7bypgcgn488pz8g462xzchbhgx7jjdbbwhm"; + sha256 = "0zxmk417j9s5nms0np1fsip7r0jhwkj1d1x424ljr9krcb2zwcyq"; }; installPhase = '' diff --git a/pkgs/applications/science/biology/last/default.nix b/pkgs/applications/science/biology/last/default.nix index 77585293116..0976e5a1080 100644 --- a/pkgs/applications/science/biology/last/default.nix +++ b/pkgs/applications/science/biology/last/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "last"; - version = "1133"; + version = "1145"; src = fetchurl { url = "http://last.cbrc.jp/last-${version}.zip"; - sha256 = "0a600p1fymm1ylaxzjwg46zdwz6ilaaak1f4n8xr3hp3ir9rgfjq"; + sha256 = "0g54nmxxrirgid1i1k5i6rf7vnjpk9548sy06yqb4fj7vdzqgq99"; }; nativeBuildInputs = [ unzip ]; diff --git a/pkgs/applications/science/biology/samblaster/default.nix b/pkgs/applications/science/biology/samblaster/default.nix index 7795ba23736..6846e3c84fa 100644 --- a/pkgs/applications/science/biology/samblaster/default.nix +++ b/pkgs/applications/science/biology/samblaster/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "samblaster"; - version = "0.1.24"; + version = "0.1.26"; src = fetchFromGitHub { owner = "GregoryFaust"; repo = "samblaster"; rev = "v.${version}"; - sha256 = "0iv2ddfw8363vb2x8gr3p8g88whb6mb9m0pf71i2cqsbv6jghap7"; + sha256 = "0g24fq5hplnfgqkh3xqpg3lgx3wmxwnh9c7m6yw7pbi40lmgl1jv"; }; installPhase = '' diff --git a/pkgs/applications/science/chemistry/jmol/default.nix b/pkgs/applications/science/chemistry/jmol/default.nix index cba3f1d0946..9adb8e3674b 100644 --- a/pkgs/applications/science/chemistry/jmol/default.nix +++ b/pkgs/applications/science/chemistry/jmol/default.nix @@ -17,14 +17,14 @@ let }; in stdenv.mkDerivation rec { - version = "14.31.14"; + version = "14.31.17"; pname = "jmol"; src = let baseVersion = "${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 = "1qmy4iqn5xgd4m9hs4w9cn9rzkwmpgdb5azd93cypp05s4nmjsnm"; + sha256 = "1cg3a56bbvlq5wfjgwclg9vsj61kmj6fnqvgf7fdvklhdvnijla2"; }; patchPhase = '' @@ -48,6 +48,6 @@ stdenv.mkDerivation rec { homepage = "https://sourceforge.net/projects/jmol"; license = licenses.lgpl2; platforms = platforms.all; - maintainers = with maintainers; [ timokau mounium ]; + maintainers = with maintainers; [ mounium ] ++ teams.sage.members; }; } diff --git a/pkgs/applications/science/chemistry/marvin/default.nix b/pkgs/applications/science/chemistry/marvin/default.nix index 84a1034849f..ddab526ebe7 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 = "20.19.0"; + version = "20.20.0"; src = fetchurl { name = "marvin-${version}.deb"; url = "http://dl.chemaxon.com/marvin/${version}/marvin_linux_${versions.majorMinor version}.deb"; - sha256 = "0b9a0yl3mxfb2dfdkgs2wphhxsgwixqk6nl2hsn1ly3gz53cws1q"; + sha256 = "1a8b0drb0c95c8arm3aa0z0sbdm9ilj4h1g90i0qyn4g2wk2xsal"; }; nativeBuildInputs = [ dpkg makeWrapper ]; diff --git a/pkgs/applications/science/electronics/appcsxcad/default.nix b/pkgs/applications/science/electronics/appcsxcad/default.nix index d2b7c0d66a1..c2d7cefec9b 100644 --- a/pkgs/applications/science/electronics/appcsxcad/default.nix +++ b/pkgs/applications/science/electronics/appcsxcad/default.nix @@ -27,7 +27,6 @@ mkDerivation { nativeBuildInputs = [ cmake - wrapQtAppsHook ]; buildInputs = [ diff --git a/pkgs/applications/science/electronics/librepcb/default.nix b/pkgs/applications/science/electronics/librepcb/default.nix index 494a5cf2931..4b0a4108ab2 100644 --- a/pkgs/applications/science/electronics/librepcb/default.nix +++ b/pkgs/applications/science/electronics/librepcb/default.nix @@ -1,39 +1,47 @@ -{ lib, mkDerivation, fetchFromGitHub, qtbase, qttools, qmake, wrapQtAppsHook }: +{ stdenv, lib, fetchFromGitHub +, qtbase, qttools, qmake, wrapQtAppsHook +}: -mkDerivation rec { +stdenv.mkDerivation rec { pname = "librepcb"; version = "0.1.5"; src = fetchFromGitHub { - owner = "LibrePCB"; - repo = "LibrePCB"; - fetchSubmodules = true; - rev = version; + owner = pname; + repo = pname; + rev = version; sha256 = "0ag8h3id2c1k9ds22rfrvyhf2vjhkv82xnrdrz4n1hnlr9566vcx"; + fetchSubmodules = true; }; - enableParallelBuilding = true; - nativeBuildInputs = [ qmake qttools wrapQtAppsHook ]; - buildInputs = [ qtbase ]; qmakeFlags = ["-r"]; + enableParallelBuilding = true; postInstall = '' - mkdir -p $out/share/librepcb/fontobene - cp share/librepcb/fontobene/newstroke.bene $out/share/librepcb/fontobene/ - ''; + mkdir -p $out/share/librepcb/fontobene + cp share/librepcb/fontobene/newstroke.bene $out/share/librepcb/fontobene/ + ''; + + # the build system tries to use 'git' at build time to find the HEAD hash. + # that's a no-no, so replace it with a quick hack. NOTE: the # adds a comment + # at the end of the line to remove the git call. + patchPhase = '' + substituteInPlace ./libs/librepcb/common/common.pro \ + --replace 'GIT_COMMIT_SHA' 'GIT_COMMIT_SHA="\\\"${src.rev}\\\"" # ' + ''; preFixup = '' wrapQtApp $out/bin/librepcb ''; - meta = with lib; { + meta = with stdenv.lib; { description = "A free EDA software to develop printed circuit boards"; - homepage = "https://librepcb.org/"; - maintainers = with maintainers; [ luz ]; - license = licenses.gpl3; - platforms = platforms.linux; + homepage = "https://librepcb.org/"; + maintainers = with maintainers; [ luz thoughtpolice ]; + license = licenses.gpl3; + platforms = platforms.linux; }; } diff --git a/pkgs/applications/science/electronics/magic-vlsi/default.nix b/pkgs/applications/science/electronics/magic-vlsi/default.nix index 96849c30029..6667f2be9c3 100644 --- a/pkgs/applications/science/electronics/magic-vlsi/default.nix +++ b/pkgs/applications/science/electronics/magic-vlsi/default.nix @@ -1,16 +1,20 @@ -{ stdenv, fetchurl, m4, tcsh, libX11, tcl, tk, cairo, ncurses, mesa_glu, python3 }: +{ stdenv, fetchurl +, m4, tcsh, libX11, tcl, tk +, cairo, ncurses, mesa_glu, python3 +}: -stdenv.mkDerivation { +stdenv.mkDerivation rec { pname = "magic-vlsi"; - version = "8.3.5"; + version = "8.3.80"; src = fetchurl { - url = "http://opencircuitdesign.com/magic/archive/magic-8.3.5.tgz"; - sha256 = "0wv4zmxlqjfaakgp802icn0cd9f8ylkz2sppix83axq8p5cg90yq"; + url = "http://opencircuitdesign.com/magic/archive/magic-${version}.tgz"; + sha256 = "0a5x4sh5xsr79pqbgv6221jc4fvaxkg2pvrdhy1cs4bmsc1sbm9j"; }; buildInputs = [ m4 tcsh libX11 tcl tk cairo ncurses mesa_glu ]; nativeBuildInputs = [ python3 ]; + enableParallelBuilding = true; configureFlags = [ "--with-tcl=${tcl}" @@ -22,6 +26,8 @@ stdenv.mkDerivation { patchShebangs scripts/* ''; + NIX_CFLAGS_COMPILE = "-Wno-implicit-function-declaration"; + patches = [ ./0001-strip-bin-prefix.patch ./0002-fix-format-security.patch @@ -29,8 +35,8 @@ stdenv.mkDerivation { meta = with stdenv.lib; { description = "VLSI layout tool written in Tcl"; - homepage = "http://opencircuitdesign.com/magic/"; - license = licenses.mit; - maintainers = [ maintainers.anna328p ]; + homepage = "http://opencircuitdesign.com/magic/"; + license = licenses.mit; + maintainers = with maintainers; [ anna328p thoughtpolice ]; }; } diff --git a/pkgs/applications/science/electronics/ngspice/default.nix b/pkgs/applications/science/electronics/ngspice/default.nix index ab2861d53f2..5113dc778f6 100644 --- a/pkgs/applications/science/electronics/ngspice/default.nix +++ b/pkgs/applications/science/electronics/ngspice/default.nix @@ -14,11 +14,11 @@ stdenv.mkDerivation rec { pname = "ngspice"; - version = "32"; + version = "33"; src = fetchurl { url = "mirror://sourceforge/ngspice/ngspice-${version}.tar.gz"; - sha256 = "1wiys30c9mqzxr7iv1sws0jnn4xi0mj3lanhnk2qfvaiji70rn9w"; + sha256 = "1wa1hmpn13spmxqgbb1m7vgy32mwvjqwrxhymzll8z65q5nbd7dr"; }; nativeBuildInputs = [ flex bison ]; diff --git a/pkgs/applications/science/electronics/qcsxcad/default.nix b/pkgs/applications/science/electronics/qcsxcad/default.nix deleted file mode 100644 index c12678c0047..00000000000 --- a/pkgs/applications/science/electronics/qcsxcad/default.nix +++ /dev/null @@ -1,50 +0,0 @@ -{ stdenv -, mkDerivation -, fetchFromGitHub -, cmake -, csxcad -, tinyxml -, vtkWithQt5 -, wrapQtAppsHook -, qtbase -}: - -mkDerivation { - pname = "qcsxcad"; - version = "unstable-2020-01-04"; - - src = fetchFromGitHub { - owner = "thliebig"; - repo = "QCSXCAD"; - rev = "0dabbaf2bc1190adec300871cf309791af842c8e"; - sha256 = "11kbh0mxbdfh7s5azqin3i2alic5ihmdfj0jwgnrhlpjk4cbf9rn"; - }; - - nativeBuildInputs = [ - cmake - wrapQtAppsHook - ]; - - cmakeFlags = [ - "-DCMAKE_INSTALL_PREFIX=${placeholder "out"}" - "-DCSXCAD_ROOT_DIR=${csxcad}" - "-DENABLE_RPATH=OFF" - ]; - - buildInputs = [ - csxcad - tinyxml - vtkWithQt5 - qtbase - ]; - - enableParallelBuilding = true; - - meta = with stdenv.lib; { - description = "Qt library for CSXCAD"; - homepage = "https://github.com/thliebig/QCSXCAD"; - license = licenses.gpl3; - maintainers = with maintainers; [ matthuszagh ]; - platforms = platforms.linux; - }; -} diff --git a/pkgs/applications/science/electronics/verilog/default.nix b/pkgs/applications/science/electronics/verilog/default.nix index df1ce7b7235..6217df2db8f 100644 --- a/pkgs/applications/science/electronics/verilog/default.nix +++ b/pkgs/applications/science/electronics/verilog/default.nix @@ -1,43 +1,45 @@ -{ stdenv, fetchFromGitHub, autoconf, gperf, flex, bison, readline, ncurses -, bzip2, zlib -# Test inputs +{ stdenv +, fetchFromGitHub +, autoconf +, bison +, bzip2 +, flex +, gperf +, ncurses , perl +, readline +, zlib }: let iverilog-test = fetchFromGitHub { - owner = "steveicarus"; - repo = "ivtest"; - rev = "6882cb8ec08926c4e356c6092f0c5f8c23328d5c"; - sha256 = "04sj5nqzwls1y760kgnd9c2whkcrr8kvj9lisd5rvk0w580kjb2x"; + owner = "steveicarus"; + repo = "ivtest"; + rev = "253609b89576355b3bef2f91e90db62223ecf2be"; + sha256 = "18i7jlr2csp7mplcrwjhllwvb6w3v7x7mnx7vdw48nd3g5scrydx"; }; in stdenv.mkDerivation rec { - pname = "iverilog"; - version = "unstable-2020-08-24"; + pname = "iverilog"; + version = "11.0"; src = fetchFromGitHub { - owner = "steveicarus"; - repo = pname; - rev = "d8556e4c86e1465b68bdc8d5ba2056ba95a42dfd"; - sha256 = "sha256-sT9j/0Q2FD5MOGpH/quMGvAuM7t7QavRHKD9lX7Elfs="; + owner = "steveicarus"; + repo = pname; + rev = "v${stdenv.lib.replaceStrings ["."] ["_"] version}"; + sha256 = "0nzcyi6l2zv9wxzsv9i963p3igyjds0n55x0ph561mc3pfbc7aqp"; }; - enableParallelBuilding = true; + nativeBuildInputs = [ autoconf bison flex gperf ]; - preConfigure = '' - chmod +x $PWD/autoconf.sh - $PWD/autoconf.sh - ''; + buildInputs = [ bzip2 ncurses readline zlib ]; - nativeBuildInputs = [ autoconf gperf flex bison ]; + preConfigure = "sh autoconf.sh"; + + enableParallelBuilding = true; - buildInputs = [ readline ncurses bzip2 zlib ]; + doCheck = true; - # tests from .travis.yml - doCheck = true; # runs ``make check`` - # most tests pass, but some that rely on exact text of floating-point numbers fail on aarch64. - doInstallCheck = !stdenv.isAarch64; installCheckInputs = [ perl ]; installCheckPhase = '' @@ -58,9 +60,9 @@ stdenv.mkDerivation rec { meta = with stdenv.lib; { description = "Icarus Verilog compiler"; - homepage = "http://iverilog.icarus.com/"; - license = with licenses; [ gpl2Plus lgpl21Plus] ; - maintainers = with maintainers; [ winden ]; - platforms = platforms.all; + homepage = "http://iverilog.icarus.com/"; # https does not work + license = with licenses; [ gpl2Plus lgpl21Plus ]; + maintainers = with maintainers; [ winden thoughtpolice ]; + platforms = platforms.all; }; } diff --git a/pkgs/applications/science/electronics/vhd2vl/default.nix b/pkgs/applications/science/electronics/vhd2vl/default.nix index 43dfdcabd02..be9e890fc8d 100644 --- a/pkgs/applications/science/electronics/vhd2vl/default.nix +++ b/pkgs/applications/science/electronics/vhd2vl/default.nix @@ -1,5 +1,6 @@ { stdenv , fetchFromGitHub +, fetchpatch , bison , flex , verilog @@ -16,6 +17,15 @@ stdenv.mkDerivation rec { sha256 = "17va2pil4938j8c93anhy45zzgnvq3k71a7glj02synfrsv6fs8n"; }; + patches = stdenv.lib.optionals (!stdenv.isAarch64) [ + # fix build with verilog 11.0 - https://github.com/ldoolitt/vhd2vl/pull/15 + # for some strange reason, this is not needed for aarch64 + (fetchpatch { + url = "https://github.com/ldoolitt/vhd2vl/commit/ce9b8343ffd004dfe8779a309f4b5a594dbec45e.patch"; + sha256 = "1qaqhm2mk66spb2dir9n91b385rarglc067js1g6pcg8mg5v3hhf"; + }) + ]; + nativeBuildInputs = [ bison flex diff --git a/pkgs/applications/science/geometry/antiprism/default.nix b/pkgs/applications/science/geometry/antiprism/default.nix new file mode 100644 index 00000000000..4691291a425 --- /dev/null +++ b/pkgs/applications/science/geometry/antiprism/default.nix @@ -0,0 +1,29 @@ +{ stdenv +, fetchFromGitHub +, autoreconfHook +, libX11 +, libGL +, libGLU +, freeglut }: + +stdenv.mkDerivation rec { + pname = "antiprism"; + version = "0.26"; + + src = fetchFromGitHub { + owner = "antiprism"; + repo = pname; + rev = version; + sha256 = "sha256-5FE6IbYKk7eMT985R9NCX3GDXE8SrdVHFcCpKeJvKtQ="; + }; + + nativeBuildInputs = [ autoreconfHook ]; + buildInputs = [ libX11 libGLU libGL.dev freeglut.dev ]; + + meta = with stdenv.lib; { + homepage = "https://www.antiprism.com"; + description = "A collection of programs for generating, manipulating, transforming and viewing polyhedra"; + license = with licenses; [ mit ]; + maintainers = with maintainers; [ AndersonTorres ]; + }; +} diff --git a/pkgs/applications/science/logic/coq/default.nix b/pkgs/applications/science/logic/coq/default.nix index 946cba41b14..dc9e40912d5 100644 --- a/pkgs/applications/science/logic/coq/default.nix +++ b/pkgs/applications/science/logic/coq/default.nix @@ -35,6 +35,7 @@ let "8.11.1" = "0qriy9dy36dajsv5qmli8gd6v55mah02ya334nw49ky19v7518m0"; "8.11.2" = "0f77ccyxdgbf1nrj5fa8qvrk1cyfy06fv8gj9kzfvlcgn0cf48sa"; "8.12.0" = "18dc7k0piv6v064zgdadpw6mkkxk7j663hb3svgj5236fihjr0cz"; + "8.12.1" = "1rkcyjjrzcqw9xk93hsq0vvji4f8r5iq0f739mghk60bghkpnb7q"; }.${version}; coq-version = stdenv.lib.versions.majorMinor version; versionAtLeast = stdenv.lib.versionAtLeast coq-version; diff --git a/pkgs/applications/science/logic/lean/default.nix b/pkgs/applications/science/logic/lean/default.nix index 749220382c6..88e1b4fbc0e 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 = "3.21.0"; + version = "3.23.0"; src = fetchFromGitHub { owner = "leanprover-community"; repo = "lean"; rev = "v${version}"; - sha256 = "1c7f2x6hdamjkr50761gcb5mg8hhlc75k1mf18vn1k9zsy1gxlgz"; + sha256 = "09mklc1p6ms1jayg2f89hqfmhca3h5744lli936l38ypn1d00sxx"; }; nativeBuildInputs = [ cmake ]; diff --git a/pkgs/applications/science/logic/z3/default.nix b/pkgs/applications/science/logic/z3/default.nix index 88aafcdae22..dd71cf2cb1a 100644 --- a/pkgs/applications/science/logic/z3/default.nix +++ b/pkgs/applications/science/logic/z3/default.nix @@ -22,7 +22,8 @@ stdenv.mkDerivation rec { sha256 = "1hnbzq10d23drd7ksm3c1n2611c3kd0q0yxgz8y78zaafwczvwxx"; }; - buildInputs = [ python fixDarwinDylibNames ] + nativeBuildInputs = optional stdenv.hostPlatform.isDarwin fixDarwinDylibNames; + buildInputs = [ python ] ++ optional javaBindings jdk ++ optionals ocamlBindings [ ocaml findlib zarith ] ; diff --git a/pkgs/applications/science/math/R/default.nix b/pkgs/applications/science/math/R/default.nix index 25ee66e8f75..e4fbe8a7f2d 100644 --- a/pkgs/applications/science/math/R/default.nix +++ b/pkgs/applications/science/math/R/default.nix @@ -113,6 +113,6 @@ stdenv.mkDerivation rec { platforms = platforms.all; hydraPlatforms = platforms.linux; - maintainers = with maintainers; [ peti timokau ]; + maintainers = with maintainers; [ peti ] ++ teams.sage.members; }; } diff --git a/pkgs/applications/science/math/lrcalc/default.nix b/pkgs/applications/science/math/lrcalc/default.nix index 438a84c0e0b..ddd470e621a 100644 --- a/pkgs/applications/science/math/lrcalc/default.nix +++ b/pkgs/applications/science/math/lrcalc/default.nix @@ -34,7 +34,7 @@ stdenv.mkDerivation rec { description = "Littlewood-Richardson calculator"; homepage = "http://math.rutgers.edu/~asbuch/lrcalc/"; license = licenses.gpl2Plus; - maintainers = with maintainers; [ timokau ]; + maintainers = teams.sage.members; platforms = platforms.unix; }; } diff --git a/pkgs/applications/science/math/mathematica/default.nix b/pkgs/applications/science/math/mathematica/default.nix index ace5ee55d7b..d04a89bd884 100644 --- a/pkgs/applications/science/math/mathematica/default.nix +++ b/pkgs/applications/science/math/mathematica/default.nix @@ -144,6 +144,9 @@ stdenv.mkDerivation rec { ''; dontBuild = true; + + # This is primarily an IO bound build; there's little benefit to building remotely. + preferLocalBuild = true; # all binaries are already stripped dontStrip = true; diff --git a/pkgs/applications/science/math/nauty/default.nix b/pkgs/applications/science/math/nauty/default.nix index d75fc9731cd..76e7c796a13 100644 --- a/pkgs/applications/science/math/nauty/default.nix +++ b/pkgs/applications/science/math/nauty/default.nix @@ -33,7 +33,7 @@ stdenv.mkDerivation rec { inherit version; description = ''Programs for computing automorphism groups of graphs and digraphs''; license = licenses.asl20; - maintainers = with maintainers; [ raskin timokau ]; + maintainers = teams.sage.members; platforms = platforms.unix; # I'm not sure if the filename will remain the same for future changelog or # if it will track changes to minor releases. Lets see. Better than nothing diff --git a/pkgs/applications/science/math/palp/default.nix b/pkgs/applications/science/math/palp/default.nix index c383438002f..9ae4fe1ba92 100644 --- a/pkgs/applications/science/math/palp/default.nix +++ b/pkgs/applications/science/math/palp/default.nix @@ -84,7 +84,7 @@ stdenv.mkDerivation rec { # version was released that pointed to gplv2 however, so thats probably # the right license. license = licenses.gpl2; - maintainers = with maintainers; [ timokau ]; + maintainers = teams.sage.members; platforms = platforms.unix; }; } diff --git a/pkgs/applications/science/math/pari/default.nix b/pkgs/applications/science/math/pari/default.nix index bd730a1eaaa..a3e2f99ab27 100644 --- a/pkgs/applications/science/math/pari/default.nix +++ b/pkgs/applications/science/math/pari/default.nix @@ -74,7 +74,7 @@ stdenv.mkDerivation rec { homepage = "http://pari.math.u-bordeaux.fr"; downloadPage = "http://pari.math.u-bordeaux.fr/download.html"; license = licenses.gpl2Plus; - maintainers = with maintainers; [ ertes raskin AndersonTorres timokau ]; + maintainers = with maintainers; [ ertes AndersonTorres ] ++ teams.sage.members; platforms = platforms.linux ++ platforms.darwin; updateWalker = true; }; diff --git a/pkgs/applications/science/math/pari/gp2c.nix b/pkgs/applications/science/math/pari/gp2c.nix index 7726a0d789e..082ff60c3e8 100644 --- a/pkgs/applications/science/math/pari/gp2c.nix +++ b/pkgs/applications/science/math/pari/gp2c.nix @@ -5,11 +5,11 @@ stdenv.mkDerivation rec { pname = "gp2c"; - version = "0.0.11pl4"; + version = "0.0.12"; src = fetchurl { url = "https://pari.math.u-bordeaux.fr/pub/pari/GP2C/${pname}-${version}.tar.gz"; - sha256 = "sha256-QGocEXxTahB5fHhlWtHXgMEl6brQ34LNwScxHNuB1rI="; + sha256 = "039ip7qkwwv46wrcdrz7y12m30kazzkjr44kqbc0h137g4wzd7zf"; }; buildInputs = [ pari perl ]; diff --git a/pkgs/applications/science/math/pynac/default.nix b/pkgs/applications/science/math/pynac/default.nix index 82e33121671..3e6057c9aef 100644 --- a/pkgs/applications/science/math/pynac/default.nix +++ b/pkgs/applications/science/math/pynac/default.nix @@ -42,7 +42,7 @@ stdenv.mkDerivation rec { ''; homepage = "http://pynac.org"; license = licenses.gpl3; - maintainers = with maintainers; [ timokau ]; + maintainers = teams.sage.members; platforms = platforms.unix; }; } diff --git a/pkgs/applications/science/math/qalculate-gtk/default.nix b/pkgs/applications/science/math/qalculate-gtk/default.nix index 133df7c75ac..48c4b77c2cc 100644 --- a/pkgs/applications/science/math/qalculate-gtk/default.nix +++ b/pkgs/applications/science/math/qalculate-gtk/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "qalculate-gtk"; - version = "3.13.0"; + version = "3.14.0"; src = fetchFromGitHub { owner = "qalculate"; repo = "qalculate-gtk"; rev = "v${version}"; - sha256 = "0yrzvsii84r9d2i2hrs4f65wzv3yj24l9d9yqfv3j85881h8wkm2"; + sha256 = "1pff3m5xnw9kai6n110j1grxzcf2r7pxi76jin1lxhm8q8gmnnz1"; }; hardeningDisable = [ "format" ]; diff --git a/pkgs/applications/science/math/sage/flask-oldsessions.nix b/pkgs/applications/science/math/sage/flask-oldsessions.nix index 403dc8708fa..86fe9912c19 100644 --- a/pkgs/applications/science/math/sage/flask-oldsessions.nix +++ b/pkgs/applications/science/math/sage/flask-oldsessions.nix @@ -30,7 +30,7 @@ buildPythonPackage rec { meta = with stdenv.lib; { description = "Provides a session class that works like the one in Flask before 0.10."; license = licenses.bsd2; - maintainers = with maintainers; [ timokau ]; + maintainers = teams.sage.members; homepage = "https://github.com/mitsuhiko/flask-oldsessions"; }; } diff --git a/pkgs/applications/science/math/sage/flask-openid.nix b/pkgs/applications/science/math/sage/flask-openid.nix index 527173dec80..900b033429e 100644 --- a/pkgs/applications/science/math/sage/flask-openid.nix +++ b/pkgs/applications/science/math/sage/flask-openid.nix @@ -22,7 +22,7 @@ buildPythonPackage rec { meta = with stdenv.lib; { description = "Adds openid support to flask applications"; license = licenses.bsd2; - maintainers = with maintainers; [ timokau ]; + maintainers = teams.sage.members; homepage = "https://pythonhosted.org/Flask-OpenID/"; }; } diff --git a/pkgs/applications/science/math/sage/pybrial.nix b/pkgs/applications/science/math/sage/pybrial.nix index 718414126ae..5fc8a4aa6f4 100644 --- a/pkgs/applications/science/math/sage/pybrial.nix +++ b/pkgs/applications/science/math/sage/pybrial.nix @@ -20,6 +20,6 @@ buildPythonPackage rec { meta = with stdenv.lib; { description = "python implementation of BRiAl"; license = licenses.gpl2; - maintainers = with maintainers; [ timokau ]; + maintainers = teams.sage.members; }; } diff --git a/pkgs/applications/science/math/sage/python-openid.nix b/pkgs/applications/science/math/sage/python-openid.nix index 4c7fdadadaf..1e8a908ac79 100644 --- a/pkgs/applications/science/math/sage/python-openid.nix +++ b/pkgs/applications/science/math/sage/python-openid.nix @@ -34,7 +34,7 @@ buildPythonPackage rec { meta = with stdenv.lib; { description = "OpenID library for Python"; license = licenses.asl20; - maintainers = with maintainers; [ timokau ]; + maintainers = teams.sage.members; homepage = "https://github.com/openid/python-openid/"; }; } diff --git a/pkgs/applications/science/math/sage/sage.nix b/pkgs/applications/science/math/sage/sage.nix index 4fa8ae6270b..e2acef7b8eb 100644 --- a/pkgs/applications/science/math/sage/sage.nix +++ b/pkgs/applications/science/math/sage/sage.nix @@ -63,6 +63,6 @@ stdenv.mkDerivation rec { meta = with stdenv.lib; { description = "Open Source Mathematics Software, free alternative to Magma, Maple, Mathematica, and Matlab"; license = licenses.gpl2; - maintainers = with maintainers; [ timokau ]; + maintainers = teams.sage.members; }; } diff --git a/pkgs/applications/science/math/sage/sagenb.nix b/pkgs/applications/science/math/sage/sagenb.nix index 77b2168ad97..ad5c53b6c11 100644 --- a/pkgs/applications/science/math/sage/sagenb.nix +++ b/pkgs/applications/science/math/sage/sagenb.nix @@ -46,7 +46,7 @@ buildPythonPackage rec { meta = with stdenv.lib; { description = "Sage Notebook"; license = licenses.gpl3Plus; - maintainers = with maintainers; [ timokau ]; + maintainers = teams.sage.members; }; # let sagenb use mathjax diff --git a/pkgs/applications/science/math/singular/default.nix b/pkgs/applications/science/math/singular/default.nix index a8c4f6bb9a0..8c5eac2c06d 100644 --- a/pkgs/applications/science/math/singular/default.nix +++ b/pkgs/applications/science/math/singular/default.nix @@ -108,7 +108,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "A CAS for polynomial computations"; - maintainers = with maintainers; [ raskin timokau ]; + maintainers = teams.sage.members; # 32 bit x86 fails with some link error: `undefined reference to `__divmoddi4@GCC_7.0.0'` platforms = subtractLists platforms.i686 platforms.unix; license = licenses.gpl3; # Or GPLv2 at your option - but not GPLv4 diff --git a/pkgs/applications/science/math/symmetrica/default.nix b/pkgs/applications/science/math/symmetrica/default.nix index b363137fb99..ca752259797 100644 --- a/pkgs/applications/science/math/symmetrica/default.nix +++ b/pkgs/applications/science/math/symmetrica/default.nix @@ -29,7 +29,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = ''A collection of routines for representation theory and combinatorics''; license = licenses.isc; - maintainers = with maintainers; [raskin timokau]; + maintainers = teams.sage.members; platforms = platforms.unix; homepage = "https://gitlab.com/sagemath/symmetrica"; }; diff --git a/pkgs/applications/science/misc/foldingathome/control.nix b/pkgs/applications/science/misc/foldingathome/control.nix index 91c3b8c779c..85be61f6686 100644 --- a/pkgs/applications/science/misc/foldingathome/control.nix +++ b/pkgs/applications/science/misc/foldingathome/control.nix @@ -8,7 +8,7 @@ }: let majMin = stdenv.lib.versions.majorMinor version; - version = "7.6.13"; + version = "7.6.21"; python = python2.withPackages ( @@ -25,7 +25,7 @@ stdenv.mkDerivation rec { src = fetchurl { url = "https://download.foldingathome.org/releases/public/release/fahcontrol/debian-stable-64bit/v${majMin}/fahcontrol_${version}-1_all.deb"; - sha256 = "0qfvhwc29cgqkwf2bkhq4gr2d1c4jgccfs58916ss03n4rwz9gng"; + sha256 = "1vfrdqkrvdlyxaw3f6z92w5dllrv6810lmf8yhcmjcwmphipvf71"; }; nativeBuildInputs = [ diff --git a/pkgs/applications/science/misc/foldingathome/viewer.nix b/pkgs/applications/science/misc/foldingathome/viewer.nix index cdeed6536ef..a383de621f2 100644 --- a/pkgs/applications/science/misc/foldingathome/viewer.nix +++ b/pkgs/applications/science/misc/foldingathome/viewer.nix @@ -11,7 +11,7 @@ }: let majMin = stdenv.lib.versions.majorMinor version; - version = "7.6.13"; + version = "7.6.21"; in stdenv.mkDerivation rec { inherit version; @@ -19,7 +19,7 @@ stdenv.mkDerivation rec { src = fetchurl { url = "https://download.foldingathome.org/releases/public/release/fahviewer/debian-stable-64bit/v${majMin}/fahviewer_${version}_amd64.deb"; - sha256 = "09yfvk16j1iwx8h1xg678ks3bc8760gfdn7n32j8r893kd32cwyk"; + sha256 = "00fd00pf6fcpplcaahvy9ir60mk69d9rcmwsyq3jrv9mxqm9aq7p"; }; nativeBuildInputs = [ diff --git a/pkgs/applications/science/misc/rink/default.nix b/pkgs/applications/science/misc/rink/default.nix index b868706a05f..0b1ef2b16ea 100644 --- a/pkgs/applications/science/misc/rink/default.nix +++ b/pkgs/applications/science/misc/rink/default.nix @@ -23,6 +23,6 @@ rustPlatform.buildRustPackage rec { description = "Unit-aware calculator"; homepage = "https://rinkcalc.app"; license = with licenses; [ mpl20 gpl3 ]; - maintainers = with maintainers; [ sb0 filalex77 ]; + maintainers = with maintainers; [ sb0 Br1ght0ne ]; }; } diff --git a/pkgs/applications/science/misc/snakemake/default.nix b/pkgs/applications/science/misc/snakemake/default.nix index 2b7532a9345..a03f7682a51 100644 --- a/pkgs/applications/science/misc/snakemake/default.nix +++ b/pkgs/applications/science/misc/snakemake/default.nix @@ -2,7 +2,7 @@ python3Packages.buildPythonApplication rec { pname = "snakemake"; - version = "5.19.3"; + version = "5.28.0"; propagatedBuildInputs = with python3Packages; [ appdirs @@ -13,6 +13,7 @@ python3Packages.buildPythonApplication rec { jsonschema nbformat psutil + pulp pyyaml ratelimiter requests @@ -22,7 +23,7 @@ python3Packages.buildPythonApplication rec { src = python3Packages.fetchPypi { inherit pname version; - sha256 = "b83f3ef73e25dafcb39b3565030e33fa2f7e80ed70256c535dc7e58ea762305d"; + sha256 = "2367ce91baf7f8fa7738d33aff9670ffdf5410bbac49aeb209f73b45a3425046"; }; doCheck = false; # Tests depend on Google Cloud credentials at ${HOME}/gcloud-service-key.json diff --git a/pkgs/applications/science/physics/xflr5/default.nix b/pkgs/applications/science/physics/xflr5/default.nix index b2e5284796f..5ae56528f96 100644 --- a/pkgs/applications/science/physics/xflr5/default.nix +++ b/pkgs/applications/science/physics/xflr5/default.nix @@ -1,6 +1,6 @@ -{ stdenv, lib, fetchurl, wrapQtAppsHook, qmake }: +{ mkDerivation, lib, fetchurl, qmake }: -stdenv.mkDerivation rec { +mkDerivation rec { pname = "xflr5"; version = "6.47"; @@ -11,9 +11,9 @@ stdenv.mkDerivation rec { enableParallelBuilding = true; - nativeBuildInputs = [ qmake wrapQtAppsHook ]; + nativeBuildInputs = [ qmake ]; - meta = with stdenv.lib; { + meta = with lib; { description = "An analysis tool for airfoils, wings and planes"; homepage = https://sourceforge.net/projects/xflr5/; license = licenses.gpl3; diff --git a/pkgs/applications/science/robotics/mavproxy/default.nix b/pkgs/applications/science/robotics/mavproxy/default.nix index 9c7166afc2a..dcc2114a488 100644 --- a/pkgs/applications/science/robotics/mavproxy/default.nix +++ b/pkgs/applications/science/robotics/mavproxy/default.nix @@ -3,11 +3,11 @@ buildPythonApplication rec { pname = "MAVProxy"; - version = "1.8.22"; + version = "1.8.23"; src = fetchPypi { inherit pname version; - sha256 = "87d7f9c0b8f4f1db3ce3521f67cd244fe3b89ffead797e92f35a7f71bbe8b958"; + sha256 = "46c70e013d3e465daae5523f6a1aad553e6ee0f4db137bb935a3273f7ffcc22e"; }; propagatedBuildInputs = [ |