diff options
Diffstat (limited to 'nixpkgs/pkgs/applications/science')
41 files changed, 478 insertions, 201 deletions
diff --git a/nixpkgs/pkgs/applications/science/astronomy/gnuastro/default.nix b/nixpkgs/pkgs/applications/science/astronomy/gnuastro/default.nix new file mode 100644 index 000000000000..aed029f9d367 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/astronomy/gnuastro/default.nix @@ -0,0 +1,36 @@ +{ lib, stdenv, fetchurl, libtool +, cfitsio, curl, ghostscript, gsl, libgit2, libjpeg, libtiff, lzlib, wcslib }: + +stdenv.mkDerivation rec { + pname = "gnuastro"; + version = "0.17"; + + src = fetchurl { + url = "mirror://gnu/gnuastro/gnuastro-${version}.tar.gz"; + sha256 = "sha256-xBvtM8wkDOqXg/Q2dNfPR0R0ZgRm4QiPJZoLDKivaPU="; + }; + + nativeBuildInputs = [ libtool ]; + + buildInputs = [ + cfitsio + curl + ghostscript + gsl + libgit2 + libjpeg + libtiff + lzlib + wcslib + ]; + + enableParallelBuilding = true; + + meta = with lib; { + description = "GNU astronomy utilities and library"; + homepage = "https://www.gnu.org/software/gnuastro/"; + license = licenses.gpl3Plus; + platforms = platforms.unix; + maintainers = with maintainers; [ sikmir ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/astronomy/kstars/default.nix b/nixpkgs/pkgs/applications/science/astronomy/kstars/default.nix index 3cd98f1acadc..9f58de432596 100644 --- a/nixpkgs/pkgs/applications/science/astronomy/kstars/default.nix +++ b/nixpkgs/pkgs/applications/science/astronomy/kstars/default.nix @@ -14,11 +14,11 @@ mkDerivation rec { pname = "kstars"; - version = "3.5.7"; + version = "3.5.8"; src = fetchurl { url = "mirror://kde/stable/kstars/kstars-${version}.tar.xz"; - sha256 = "sha256-qo8SLum46BM0QzGR6rJ2w2ERK53Lm8+N+ghR6HoQDQY="; + sha256 = "sha256-Zg2QKDe3q/OBDW4k9y/YTwREopvX1D4YlrGf7OHIjD8="; }; nativeBuildInputs = [ extra-cmake-modules kdoctools ]; diff --git a/nixpkgs/pkgs/applications/science/astronomy/phd2/default.nix b/nixpkgs/pkgs/applications/science/astronomy/phd2/default.nix index 543e6820a763..52049302a27b 100644 --- a/nixpkgs/pkgs/applications/science/astronomy/phd2/default.nix +++ b/nixpkgs/pkgs/applications/science/astronomy/phd2/default.nix @@ -3,13 +3,13 @@ stdenv.mkDerivation rec { pname = "phd2"; - version = "2.6.10"; + version = "2.6.11"; src = fetchFromGitHub { owner = "OpenPHDGuiding"; repo = "phd2"; rev = "v${version}"; - sha256 = "sha256-2ZiPjhlguWXFcC53xG1aqAode7twtoHWszFUMQkK5xU="; + sha256 = "sha256-iautgHOVzdLWYGOVu3wHBDt30uCbaP58mDz/l7buB1k="; }; nativeBuildInputs = [ diff --git a/nixpkgs/pkgs/applications/science/astronomy/siril/default.nix b/nixpkgs/pkgs/applications/science/astronomy/siril/default.nix index b50cb4b71d0d..4a51e88dc3b9 100644 --- a/nixpkgs/pkgs/applications/science/astronomy/siril/default.nix +++ b/nixpkgs/pkgs/applications/science/astronomy/siril/default.nix @@ -6,13 +6,13 @@ stdenv.mkDerivation rec { pname = "siril"; - version = "0.99.10.1"; + version = "1.0.0"; src = fetchFromGitLab { owner = "free-astro"; repo = pname; rev = version; - sha256 = "sha256-gqV+pJNaU+GnYiUo/imofgNdeM+AtDg/pSH7aoqhkYA="; + sha256 = "sha256-yqWFEa1fnSwl0ecN9hMI13QCfj0f69CFqTJlEAhTpJI="; }; nativeBuildInputs = [ diff --git a/nixpkgs/pkgs/applications/science/astronomy/stellarium/default.nix b/nixpkgs/pkgs/applications/science/astronomy/stellarium/default.nix index 0963b4c17e02..7b5f28fbd848 100644 --- a/nixpkgs/pkgs/applications/science/astronomy/stellarium/default.nix +++ b/nixpkgs/pkgs/applications/science/astronomy/stellarium/default.nix @@ -1,25 +1,25 @@ { stdenv, lib, mkDerivation, fetchFromGitHub , cmake, freetype, libpng, libGLU, libGL, openssl, perl, libiconv -, qtscript, qtserialport, qttools +, qtscript, qtserialport, qttools, qtcharts , qtmultimedia, qtlocation, qtbase, wrapQtAppsHook }: mkDerivation rec { pname = "stellarium"; - version = "0.21.3"; + version = "0.22.0"; src = fetchFromGitHub { owner = "Stellarium"; repo = "stellarium"; rev = "v${version}"; - sha256 = "sha256-TQMLy5ziBF7YqPDzPwgjY5FHxxMUe7MXo/TGxQ1nGcg="; + sha256 = "sha256-scG/SS9emEmrZunv6n3Vzcchoh0Cf9rDOkuxAMnxNk4="; }; nativeBuildInputs = [ cmake perl wrapQtAppsHook ]; buildInputs = [ freetype libpng libGLU libGL openssl libiconv qtscript qtserialport qttools - qtmultimedia qtlocation qtbase + qtmultimedia qtlocation qtbase qtcharts ]; preConfigure = lib.optionalString stdenv.isDarwin '' diff --git a/nixpkgs/pkgs/applications/science/biology/flywheel-cli/default.nix b/nixpkgs/pkgs/applications/science/biology/flywheel-cli/default.nix new file mode 100644 index 000000000000..7db8b0066263 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/flywheel-cli/default.nix @@ -0,0 +1,49 @@ +{ lib +, stdenv +, fetchurl +, unzip +}: + +let + inherit (stdenv.targetPlatform) system; + throwSystem = throw "Unsupported system: ${system}"; + + os = { + x86_64-darwin = "darwin"; + x86_64-linux = "linux"; + }.${system} or throwSystem; + + sha256 = { + x86_64-darwin = "sha256-OIyEu3Hsobui9s5+T9nC10SxMw0MhgmTA4SN9Ridyzo="; + x86_64-linux = "sha256-SxBjRd95hoh2zwX6IDnkZnTWVduQafPHvnWw8qTuM78="; + }.${system} or throwSystem; +in +stdenv.mkDerivation rec { + pname = "flywheel-cli"; + version = "16.2.0"; + + src = fetchurl { + url = "https://storage.googleapis.com/flywheel-dist/cli/${version}/fw-${os}_amd64-${version}.zip"; + inherit sha256; + }; + + nativeBuildInputs = [ unzip ]; + + unpackPhase = '' + unzip ${src} + ''; + + installPhase = '' + runHook preInstall + install -Dt $out/bin ./${os}_amd64/fw + runHook postInstall + ''; + + meta = with lib; { + description = "Library and command line interface for interacting with a Flywheel site"; + homepage = "https://gitlab.com/flywheel-io/public/python-cli"; + license = licenses.mit; + maintainers = with maintainers; [ rbreslow ]; + platforms = [ "x86_64-darwin" "x86_64-linux" ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/ncbi-tools/default.nix b/nixpkgs/pkgs/applications/science/biology/ncbi-tools/default.nix index 0e273dbefaac..dff041971ea7 100644 --- a/nixpkgs/pkgs/applications/science/biology/ncbi-tools/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/ncbi-tools/default.nix @@ -8,10 +8,10 @@ # Another note: you may want the older and deprecated C-libs at ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/2008/Mar_17_2008/NCBI_C_Toolkit/ncbi_c--Mar_17_2008.tar.gz stdenv.mkDerivation rec { - name = "ncbi_tools"; - ncbi_version = "Dec_31_2008"; + pname = "ncbi_tools"; + version = "Dec_31_2008"; src = fetchurl { - url = "ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/2008/${ncbi_version}/ncbi_cxx--${ncbi_version}.tar.gz"; + url = "ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/2008/${version}/ncbi_cxx--${version}.tar.gz"; sha256 = "1b2v0dcdqn3bysgdkj57sxmd6s0hc9wpnxssviz399g6plhxggbr"; }; diff --git a/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix b/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix index 3f837edb4c8b..a747b96dd180 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix @@ -25,14 +25,14 @@ let }; in stdenv.mkDerivation rec { - version = "14.32.30"; + version = "14.32.39"; 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-${version}-binary.tar.gz"; - sha256 = "sha256-VpOoduUA0iD+nI83GSQYQDHoK2Snog0NHkHWHfpLqFM="; + sha256 = "sha256-ekwipWWGsXYECJBOmw0+uIWHDpdF8T8jZUo6LeqD6Io="; }; patchPhase = '' diff --git a/nixpkgs/pkgs/applications/science/chemistry/marvin/default.nix b/nixpkgs/pkgs/applications/science/chemistry/marvin/default.nix index 698095715cc5..2b5a1b969509 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/marvin/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/marvin/default.nix @@ -4,12 +4,12 @@ with lib; stdenv.mkDerivation rec { pname = "marvin"; - version = "22.7.0"; + version = "22.8.0"; src = fetchurl { name = "marvin-${version}.deb"; url = "http://dl.chemaxon.com/marvin/${version}/marvin_linux_${versions.majorMinor version}.deb"; - sha256 = "sha256-xK4C+0/Qpc2vXPmsI8KuHuDJLmJ5LXdAfRIREE+gkWA="; + sha256 = "sha256-dmG2p4KqzjLuuVw+wPWaxVoqOqba8Tx5l44PauWpqv4="; }; nativeBuildInputs = [ dpkg makeWrapper ]; diff --git a/nixpkgs/pkgs/applications/science/computer-architecture/qtrvsim/default.nix b/nixpkgs/pkgs/applications/science/computer-architecture/qtrvsim/default.nix index 24d9f642ec56..fc840fe45fbc 100644 --- a/nixpkgs/pkgs/applications/science/computer-architecture/qtrvsim/default.nix +++ b/nixpkgs/pkgs/applications/science/computer-architecture/qtrvsim/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "QtRVSim"; - version = "0.9.1"; + version = "0.9.2"; src = fetchFromGitHub { owner = "cvut"; repo = "qtrvsim"; rev = "refs/tags/v${version}"; - sha256 = "AOksVS0drIBnK4RCxZw40yVxf4E8GjG9kU0rIZsY9gA="; + sha256 = "B1l+ysrodeDbxYfdLLMF8yk4/uPXTcDrTaMtYm89HuU="; }; nativeBuildInputs = [ cmake wrapQtAppsHook ]; diff --git a/nixpkgs/pkgs/applications/science/electronics/caneda/default.nix b/nixpkgs/pkgs/applications/science/electronics/caneda/default.nix index 6a9a491af1ee..1adac4832a13 100644 --- a/nixpkgs/pkgs/applications/science/electronics/caneda/default.nix +++ b/nixpkgs/pkgs/applications/science/electronics/caneda/default.nix @@ -1,4 +1,4 @@ -{ mkDerivation, lib, fetchFromGitHub, cmake, qtbase, qttools, qtsvg, qwt }: +{ mkDerivation, lib, fetchFromGitHub, cmake, qtbase, qttools, qtsvg, qwt6_1}: mkDerivation rec { pname = "caneda"; @@ -12,7 +12,7 @@ mkDerivation rec { }; nativeBuildInputs = [ cmake ]; - buildInputs = [ qtbase qttools qtsvg qwt ]; + buildInputs = [ qtbase qttools qtsvg qwt6_1 ]; meta = { description = "Open source EDA software focused on easy of use and portability"; diff --git a/nixpkgs/pkgs/applications/science/electronics/gaw/default.nix b/nixpkgs/pkgs/applications/science/electronics/gaw/default.nix index 928613737b47..7f0b5625e85a 100644 --- a/nixpkgs/pkgs/applications/science/electronics/gaw/default.nix +++ b/nixpkgs/pkgs/applications/science/electronics/gaw/default.nix @@ -7,11 +7,11 @@ stdenv.mkDerivation rec { pname = "gaw"; - version = "20200922"; + version = "20220315"; src = fetchurl { url = "https://download.tuxfamily.org/gaw/download/gaw3-${version}.tar.gz"; - sha256 = "0qmap11v470a1yj4ypfvdq6wkfni77ijqpknka8b4fndi62sl4wa"; + sha256 = "0j2bqi9444s1mfbr7x9rqp232xf7ab9z7ifsnl305jsklp6qmrbg"; }; nativeBuildInputs = [ pkg-config ]; diff --git a/nixpkgs/pkgs/applications/science/electronics/kicad/versions.nix b/nixpkgs/pkgs/applications/science/electronics/kicad/versions.nix index 364321afbf71..9adfac344b38 100644 --- a/nixpkgs/pkgs/applications/science/electronics/kicad/versions.nix +++ b/nixpkgs/pkgs/applications/science/electronics/kicad/versions.nix @@ -3,45 +3,45 @@ { "kicad" = { kicadVersion = { - version = "6.0.2"; + version = "6.0.4"; src = { - rev = "378541a8ebe8a691b61c8ed1b4012c71343acfbb"; - sha256 = "1lcl25zkqkyj5rvw9rad3n7bklpg10kmhmhkyyrgg8ql7di6wa0f"; + rev = "6f826c9f35a3dc9a104bb24a0a89a2e04b2d9721"; + sha256 = "0lki59ws0ncqkp9wxrhyni1ck2sx5z07mmpkjg0d9jpkync9hx9y"; }; }; libVersion = { - version = "6.0.2"; + version = "6.0.4"; libSources = { - symbols.rev = "80a176076a8f3785a4cd64e55ec87f27f6fcc163"; - symbols.sha256 = "1f57wv5b95iqd64k8ab82fvxnh5q890v7bzclmn019gl6ikisxj5"; - templates.rev = "c9a51b852eacc3e64639548032b50edd80ddb27c"; + symbols.rev = "9d00fbb9373571e54d9f29985b21a03d862795a4"; + symbols.sha256 = "12lyc187337bf2frl3jvwqdwwnd69f7l414k3kxhccs3sa2mcf1y"; + templates.rev = "c4f4fe4b821e062a3ddd275f9313d5d81ff8f8d7"; templates.sha256 = "13h9ly6amiwm7zkwa2fd9730kh295ls8j95fszlfjp9rczv2yyzm"; - footprints.rev = "c81b399054b0d3842094d7e8dfe08eb04310573a"; - footprints.sha256 = "1xmnq2731v2afan1d08xb1qqgl5xd01v5jphi6cdmw28ri555cna"; - packages3d.rev = "75175a21b720c59a26efce9a8c6dba3d032392a9"; - packages3d.sha256 = "10zf8hp85ksi84cbiczsksn0ygvri4ffsa126v73nnkx6irw6nkk"; + footprints.rev = "c48d3dfcfa6ce58ec11e10b7a74878bb69fae580"; + footprints.sha256 = "0px2g9jansky0rvc0bdjylbmv8xwhc0q63g88hd2nzbknqli9f1y"; + packages3d.rev = "b1de0b5c3edc16999602b809a05017da62ff52cc"; + packages3d.sha256 = "0ms9py93qyihxrhh9wm2ziycmdn88m36r8adx22ynjnxixw1f9ja"; }; }; }; "kicad-unstable" = { kicadVersion = { - version = "2022-01-13"; + version = "2022-03-19"; src = { - rev = "33a4c9b08e040a17daefae9069fdf834063555b4"; - sha256 = "1ma0i0vgvdsjrmlfzdi34byly7n1vsaynwp9f1hny4s1m53nirha"; + rev = "58c146a7c00ee64ca07cacbcc594121f40aa2aeb"; + sha256 = "0gcbl11pq0dgp590hdwsh5np7spixk5kgva0v8mx9rqd374z4bdm"; }; }; libVersion = { - version = "2022-01-13"; + version = "2022-03-19"; libSources = { - symbols.rev = "e3b198d827817b79fb8a6df07f0cfc1cb9140edf"; - symbols.sha256 = "1azjx1bmxaz8bniyw75lq60mc8hvay00jn9qdc2zp7isy3c9ibp0"; + symbols.rev = "9b8d3163450172a7f368462c6d005841ad199144"; + symbols.sha256 = "12lyc187337bf2frl3jvwqdwwnd69f7l414k3kxhccs3sa2mcf1y"; templates.rev = "a27d83f0a20f0be0c1ab04b139a0c518da51a5d4"; templates.sha256 = "13h9ly6amiwm7zkwa2fd9730kh295ls8j95fszlfjp9rczv2yyzm"; - footprints.rev = "a939c691f1c515d6830e54cf035a420de3e5a92c"; - footprints.sha256 = "13g6y1l95znz6ixc4dpqsxp3icrzs951xpabnzr5znw42577gm9j"; - packages3d.rev = "196a26294d8e501b0e8b06c1df1abae0ebe23051"; - packages3d.sha256 = "0ywlk00dfwv7hc494finmazdh3g1yx0ir7bvnd8zp6cq4ql0nwl4"; + footprints.rev = "c871df2c81a894bc5e91d2d517b76884d5a918aa"; + footprints.sha256 = "0px2g9jansky0rvc0bdjylbmv8xwhc0q63g88hd2nzbknqli9f1y"; + packages3d.rev = "6ff98426fd51d53c55bc48025d66d3d0b0c5df92"; + packages3d.sha256 = "0ms9py93qyihxrhh9wm2ziycmdn88m36r8adx22ynjnxixw1f9ja"; }; }; }; diff --git a/nixpkgs/pkgs/applications/science/electronics/magic-vlsi/0002-fix-format-security.patch b/nixpkgs/pkgs/applications/science/electronics/magic-vlsi/0002-fix-format-security.patch deleted file mode 100644 index 37ae35195503..000000000000 --- a/nixpkgs/pkgs/applications/science/electronics/magic-vlsi/0002-fix-format-security.patch +++ /dev/null @@ -1,19 +0,0 @@ -diff --git a/database/DBio.c b/database/DBio.c -index 93c4b0b..292ea5f 100644 ---- a/database/DBio.c -+++ b/database/DBio.c -@@ -2378,12 +2378,12 @@ DBCellWriteFile(cellDef, f) - - #define FPRINTF(f,s)\ - {\ -- if (fprintf(f,s) == EOF) goto ioerror;\ -+ if (fprintf(f,"%s",s) == EOF) goto ioerror;\ - DBFileOffset += strlen(s);\ - } - #define FPRINTR(f,s)\ - {\ -- if (fprintf(f,s) == EOF) return 1;\ -+ if (fprintf(f,"%s",s) == EOF) return 1;\ - DBFileOffset += strlen(s);\ - } - diff --git a/nixpkgs/pkgs/applications/science/electronics/magic-vlsi/default.nix b/nixpkgs/pkgs/applications/science/electronics/magic-vlsi/default.nix index 82d8dbd2ddc4..edee5946d946 100644 --- a/nixpkgs/pkgs/applications/science/electronics/magic-vlsi/default.nix +++ b/nixpkgs/pkgs/applications/science/electronics/magic-vlsi/default.nix @@ -13,11 +13,11 @@ stdenv.mkDerivation rec { pname = "magic-vlsi"; - version = "8.3.109"; + version = "8.3.277"; src = fetchurl { url = "http://opencircuitdesign.com/magic/archive/magic-${version}.tgz"; - sha256 = "sha256-ZK4OF5XwjW1OJmOVUFqLklfpM10eIwCILygqIyjRbEQ="; + sha256 = "sha256-cS3KaIVwGN/mMfRKjJxzdY6DeNV7tw2fATIHrFBV0fY="; }; nativeBuildInputs = [ python3 ]; @@ -48,7 +48,6 @@ stdenv.mkDerivation rec { patches = [ ./0001-strip-bin-prefix.patch - ./0002-fix-format-security.patch ]; meta = with lib; { diff --git a/nixpkgs/pkgs/applications/science/electronics/ngspice/default.nix b/nixpkgs/pkgs/applications/science/electronics/ngspice/default.nix index 0eed8b1692aa..f4bf424f1090 100644 --- a/nixpkgs/pkgs/applications/science/electronics/ngspice/default.nix +++ b/nixpkgs/pkgs/applications/science/electronics/ngspice/default.nix @@ -14,11 +14,11 @@ stdenv.mkDerivation rec { pname = "ngspice"; - version = "34"; + version = "36"; src = fetchurl { url = "mirror://sourceforge/ngspice/ngspice-${version}.tar.gz"; - sha256 = "sha256-ImP//GaUdUlyr3By7wHP5irHkIANrWUbwpC/yueb17U="; + sha256 = "sha256-T4GCh++6JFNBBGY1t1eugfh5VJsyakMWtfbml6pRf4w="; }; nativeBuildInputs = [ flex bison ]; diff --git a/nixpkgs/pkgs/applications/science/electronics/xcircuit/default.nix b/nixpkgs/pkgs/applications/science/electronics/xcircuit/default.nix index 68322a191787..eb2a29382e60 100644 --- a/nixpkgs/pkgs/applications/science/electronics/xcircuit/default.nix +++ b/nixpkgs/pkgs/applications/science/electronics/xcircuit/default.nix @@ -1,16 +1,12 @@ { lib, stdenv, fetchurl, autoreconfHook, automake, pkg-config , cairo, ghostscript, ngspice, tcl, tk, xorg, zlib }: -let +stdenv.mkDerivation rec { version = "3.10.12"; - name = "xcircuit-${version}"; - inherit (lib) getBin; - -in stdenv.mkDerivation { - inherit name version; + pname = "xcircuit"; src = fetchurl { - url = "http://opencircuitdesign.com/xcircuit/archive/${name}.tgz"; + url = "http://opencircuitdesign.com/xcircuit/archive/xcircuit-${version}.tgz"; sha256 = "1h1ywc3mr7plvwnhdii2zgnnv5ih2nhyl4qbdjpi83dq0aq1s2mn"; }; @@ -20,7 +16,7 @@ in stdenv.mkDerivation { configureFlags = [ "--with-tcl=${tcl}/lib" "--with-tk=${tk}/lib" - "--with-ngspice=${getBin ngspice}/bin/ngspice" + "--with-ngspice=${lib.getBin ngspice}/bin/ngspice" ]; buildInputs = with xorg; [ cairo ghostscript libSM libXt libICE libX11 libXpm tcl tk zlib ]; diff --git a/nixpkgs/pkgs/applications/science/logic/coq/default.nix b/nixpkgs/pkgs/applications/science/logic/coq/default.nix index 29959be2fa97..a9fb21681586 100644 --- a/nixpkgs/pkgs/applications/science/logic/coq/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/coq/default.nix @@ -47,6 +47,7 @@ let "8.14.0".sha256 = "04y2z0qyvag66zanfyc3f9agvmzbn4lsr0p1l7ck6yjhqx7vbm17"; "8.14.1".sha256 = "0sx78pgx0qw8v7v2r32zzy3l161zipzq95iacda628girim7psnl"; "8.15.0".sha256 = "sha256:1ma76wfrpfsl72yh10w1ys2a0vi0mdc2jc79kdc8nrmxkhpw1nxx"; + "8.15.1".sha256 = "sha256:1dsa04jzkx5pw69pmxn0l55q4w88lg6fvz7clbga0bazzsfnsgd6"; }; releaseRev = v: "V${v}"; fetched = import ../../../../build-support/coq/meta-fetch/default.nix diff --git a/nixpkgs/pkgs/applications/science/logic/isabelle/components/default.nix b/nixpkgs/pkgs/applications/science/logic/isabelle/components/default.nix new file mode 100644 index 000000000000..dd7b605f56af --- /dev/null +++ b/nixpkgs/pkgs/applications/science/logic/isabelle/components/default.nix @@ -0,0 +1,5 @@ +{ callPackage }: + +{ + isabelle-linter = callPackage ./isabelle-linter.nix {}; +} diff --git a/nixpkgs/pkgs/applications/science/logic/isabelle/components/isabelle-linter.nix b/nixpkgs/pkgs/applications/science/logic/isabelle/components/isabelle-linter.nix new file mode 100644 index 000000000000..7fca547f67c8 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/logic/isabelle/components/isabelle-linter.nix @@ -0,0 +1,22 @@ +{ stdenv, lib, fetchFromGitHub, isabelle }: + +stdenv.mkDerivation rec { + pname = "isabelle-linter"; + version = "Isabelle2021-1-v1.0.0"; + + src = fetchFromGitHub { + owner = "isabelle-prover"; + repo = "isabelle-linter"; + rev = version; + sha256 = "0v6scc2rhj6bjv530gzz6i57czzcgpkw7a9iqnfdnm5gvs5qjk7a"; + }; + + installPhase = import ./mkBuild.nix { inherit isabelle; path = "${pname}-${version}"; }; + + meta = with lib; { + description = "Linter component for Isabelle."; + homepage = "https://github.com/isabelle-prover/isabelle-linter"; + maintainers = with maintainers; [ jvanbruegge ]; + license = licenses.mit; + }; +} diff --git a/nixpkgs/pkgs/applications/science/logic/isabelle/components/mkBuild.nix b/nixpkgs/pkgs/applications/science/logic/isabelle/components/mkBuild.nix new file mode 100644 index 000000000000..a05b5196b007 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/logic/isabelle/components/mkBuild.nix @@ -0,0 +1,36 @@ +{ isabelle, path }: + +let + dir = "$out/isabelle/${isabelle.dirname}"; + iDir = "${isabelle}/${isabelle.dirname}"; +in '' + shopt -s extglob + mkdir -p ${dir}/lib/classes + + cDir=$out/${isabelle.dirname}/contrib/${path} + mkdir -p $cDir + cp -r !(isabelle) $cDir + + cd ${dir} + ln -s ${iDir}/!(lib|bin) ./ + ln -s ${iDir}/lib/!(classes) lib/ + ln -s ${iDir}/lib/classes/* lib/classes/ + + mkdir bin/ + cp ${iDir}/bin/* bin/ + + export HOME=$TMP + bin/isabelle components -u $cDir + bin/isabelle scala_build + + cd lib/classes + for f in ${iDir}/lib/classes/*; do + rm $(basename $f) + done + + lDir=$out/${isabelle.dirname}/lib/classes/ + mkdir -p $lDir + cp -r * $lDir + cd $out + rm -rf isabelle +'' diff --git a/nixpkgs/pkgs/applications/science/logic/isabelle/default.nix b/nixpkgs/pkgs/applications/science/logic/isabelle/default.nix index aaac288b615d..6696527cece2 100644 --- a/nixpkgs/pkgs/applications/science/logic/isabelle/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/isabelle/default.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, fetchurl, coreutils, nettools, java, scala, polyml, z3, veriT, vampire, eprover-ho, rlwrap, perl, makeDesktopItem }: +{ lib, stdenv, fetchurl, coreutils, nettools, java, scala, polyml, z3, veriT, vampire, eprover-ho, naproche, rlwrap, perl, makeDesktopItem, isabelle-components, isabelle, symlinkJoin }: # nettools needed for hostname stdenv.mkDerivation rec { @@ -66,7 +66,8 @@ stdenv.mkDerivation rec { ISABELLE_JDK_HOME=${java} EOF - sed -i -e 's/naproche_server : bool = true/naproche_server : bool = false/' contrib/naproche-*/etc/options + rm contrib/naproche-*/x86*/Naproche-SAD + ln -s ${naproche}/bin/Naproche-SAD contrib/naproche-*/x86*/ echo ISABELLE_LINE_EDITOR=${rlwrap}/bin/rlwrap >>etc/settings @@ -152,4 +153,29 @@ stdenv.mkDerivation rec { maintainers = [ maintainers.jwiegley maintainers.jvanbruegge ]; platforms = platforms.linux; }; +} // { + withComponents = f: + let + base = "$out/${isabelle.dirname}"; + components = f isabelle-components; + in symlinkJoin { + name = "isabelle-with-components-${isabelle.version}"; + paths = [ isabelle ] ++ components; + + postBuild = '' + rm $out/bin/* + + cd ${base} + rm bin/* + cp ${isabelle}/${isabelle.dirname}/bin/* bin/ + rm etc/components + cat ${isabelle}/${isabelle.dirname}/etc/components > etc/components + + export HOME=$TMP + bin/isabelle install $out/bin + patchShebangs $out/bin + '' + lib.concatMapStringsSep "\n" (c: '' + echo contrib/${c.pname}-${c.version} >> ${base}/etc/components + '') components; + }; } diff --git a/nixpkgs/pkgs/applications/science/logic/klee/default.nix b/nixpkgs/pkgs/applications/science/logic/klee/default.nix index e0ace7e81c82..612d9fd57c7c 100644 --- a/nixpkgs/pkgs/applications/science/logic/klee/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/klee/default.nix @@ -1,5 +1,5 @@ -{ stdenv -, lib +{ lib +, callPackage , fetchFromGitHub , fetchpatch , cmake @@ -14,13 +14,37 @@ , sqlite , gtest , lit + +# Build KLEE in debug mode. Defaults to false. , debug ? false + +# Include debug info in the build. Defaults to true. +, includeDebugInfo ? true + +# Enable KLEE asserts. Defaults to true, since LLVM is built with them. +, asserts ? true + +# Build the KLEE runtime in debug mode. Defaults to true, as this improves +# stack traces of the software under test. +, debugRuntime ? true + +# Enable runtime asserts. Default false. +, runtimeAsserts ? false + +# Extra klee-uclibc config. +, extraKleeuClibcConfig ? {} }: let + # Python used for KLEE tests. kleePython = python3.withPackages (ps: with ps; [ tabulate ]); + + # The klee-uclibc derivation. + kleeuClibc = callPackage ./klee-uclibc.nix { + inherit clang_9 llvmPackages_9 extraKleeuClibcConfig debugRuntime runtimeAsserts; + }; in -stdenv.mkDerivation rec { +clang_9.stdenv.mkDerivation rec { pname = "klee"; version = "2.2"; src = fetchFromGitHub { @@ -30,11 +54,12 @@ stdenv.mkDerivation rec { sha256 = "Ar3BKfADjJvvP0dI9+x/l3RDs8ncx4jmO7ol4MgOr4M="; }; buildInputs = [ - llvmPackages_9.llvm clang_9 z3 stp cryptominisat + llvmPackages_9.llvm + z3 stp cryptominisat gperftools sqlite ]; nativeBuildInputs = [ - cmake + cmake clang_9 ]; checkInputs = [ gtest @@ -46,14 +71,17 @@ stdenv.mkDerivation rec { ]; cmakeFlags = let - buildType = if debug then "Debug" else "Release"; - in - [ - "-DCMAKE_BUILD_TYPE=${buildType}" - "-DKLEE_RUNTIME_BUILD_TYPE=${buildType}" - "-DENABLE_POSIX_RUNTIME=ON" - "-DENABLE_UNIT_TESTS=ON" - "-DENABLE_SYSTEM_TESTS=ON" + onOff = val: if val then "ON" else "OFF"; + in [ + "-DCMAKE_BUILD_TYPE=${if debug then "Debug" else if !debug && includeDebugInfo then "RelWithDebInfo" else "MinSizeRel"}" + "-DKLEE_RUNTIME_BUILD_TYPE=${if debugRuntime then "Debug" else "Release"}" + "-DKLEE_ENABLE_TIMESTAMP=${onOff false}" + "-DENABLE_KLEE_UCLIBC=${onOff true}" + "-DKLEE_UCLIBC_PATH=${kleeuClibc}" + "-DENABLE_KLEE_ASSERTS=${onOff asserts}" + "-DENABLE_POSIX_RUNTIME=${onOff true}" + "-DENABLE_UNIT_TESTS=${onOff true}" + "-DENABLE_SYSTEM_TESTS=${onOff true}" "-DGTEST_SRC_DIR=${gtest.src}" "-DGTEST_INCLUDE_DIR=${gtest.src}/googletest/include" "-Wno-dev" @@ -66,21 +94,40 @@ stdenv.mkDerivation rec { patchShebangs . ''; - /* This patch is currently necessary for the unit test suite to run correctly. - * See https://www.mail-archive.com/klee-dev@imperial.ac.uk/msg03136.html - * and https://github.com/klee/klee/pull/1458 for more information. - */ patches = map fetchpatch [ + /* This patch is currently necessary for the unit test suite to run correctly. + * See https://www.mail-archive.com/klee-dev@imperial.ac.uk/msg03136.html + * and https://github.com/klee/klee/pull/1458 for more information. + */ { name = "fix-gtest"; sha256 = "F+/6videwJZz4sDF9lnV4B8lMx6W11KFJ0Q8t1qUDf4="; url = "https://github.com/klee/klee/pull/1458.patch"; } + + # This patch fixes test compile issues with glibc 2.33+. + { + name = "fix-glibc-2.33"; + sha256 = "PzxqtFyLy9KF1eA9AAKg1tu+ggRdvu7leuvXifayIcc="; + url = "https://github.com/klee/klee/pull/1385.patch"; + } + + # /etc/mtab doesn't exist in the Nix build sandbox. + { + name = "fix-etc-mtab-in-tests"; + sha256 = "2Yb/rJA791esNNqq8uAXV+MML4YXIjPKkHBOufvyRoQ="; + url = "https://github.com/klee/klee/pull/1471.patch"; + } ]; doCheck = true; checkTarget = "check"; + passthru = { + # Let the user depend on `klee.uclibc` for klee-uclibc + uclibc = kleeuClibc; + }; + meta = with lib; { description = "A symbolic virtual machine built on top of LLVM"; longDescription = '' diff --git a/nixpkgs/pkgs/applications/science/logic/klee/klee-uclibc.nix b/nixpkgs/pkgs/applications/science/logic/klee/klee-uclibc.nix new file mode 100644 index 000000000000..2e3826c50c42 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/logic/klee/klee-uclibc.nix @@ -0,0 +1,98 @@ +{ lib +, fetchurl +, fetchFromGitHub +, which +, linuxHeaders +, clang_9 +, llvmPackages_9 +, python3 +, debugRuntime ? true +, runtimeAsserts ? false +, extraKleeuClibcConfig ? {} +}: + +let + localeSrcBase = "uClibc-locale-030818.tgz"; + localeSrc = fetchurl { + url = "http://www.uclibc.org/downloads/${localeSrcBase}"; + sha256 = "xDYr4xijjxjZjcz0YtItlbq5LwVUi7k/ZSmP6a+uvVc="; + }; + resolvedExtraKleeuClibcConfig = lib.mapAttrsToList (name: value: "${name}=${value}") (extraKleeuClibcConfig // { + "UCLIBC_DOWNLOAD_PREGENERATED_LOCALE_DATA" = "n"; + "RUNTIME_PREFIX" = "/"; + "DEVEL_PREFIX" = "/"; + }); +in +clang_9.stdenv.mkDerivation rec { + pname = "klee-uclibc"; + version = "1.2"; + src = fetchFromGitHub { + owner = "klee"; + repo = "klee-uclibc"; + rev = "klee_uclibc_v${version}"; + sha256 = "qdrGMw+2XwpDsfxdv6swnoaoACcF5a/RWgUxUYbtPrI="; + }; + nativeBuildInputs = [ + clang_9 + llvmPackages_9.llvm + python3 + which + ]; + + # Some uClibc sources depend on Linux headers. + UCLIBC_KERNEL_HEADERS = "${linuxHeaders}/include"; + + # HACK: needed for cross-compile. + # See https://www.mail-archive.com/klee-dev@imperial.ac.uk/msg03141.html + KLEE_CFLAGS = "-idirafter ${clang_9}/resource-root/include"; + + prePatch = '' + patchShebangs ./configure + patchShebangs ./extra + ''; + + # klee-uclibc configure does not support --prefix, so we override configurePhase entirely + configurePhase = '' + ./configure ${lib.escapeShellArgs ( + ["--make-llvm-lib"] + ++ lib.optional (!debugRuntime) "--enable-release" + ++ lib.optional runtimeAsserts "--enable-assertions" + )} + + # Set all the configs we care about. + configs=( + PREFIX=$out + ) + for value in ${lib.escapeShellArgs resolvedExtraKleeuClibcConfig}; do + configs+=("$value") + done + + for configFile in .config .config.cmd; do + for config in "''${configs[@]}"; do + prefix="''${config%%=*}=" + if grep -q "$prefix" "$configFile"; then + sed -i "s"'\001'"''${prefix}"'\001'"#''${prefix}"'\001'"g" "$configFile" + fi + echo "$config" >> "$configFile" + done + done + ''; + + # Link the locale source into the correct place + preBuild = '' + ln -sf ${localeSrc} extra/locale/${localeSrcBase} + ''; + + makeFlags = ["HAVE_DOT_CONFIG=y"]; + + meta = with lib; { + description = "A modified version of uClibc for KLEE."; + longDescription = '' + klee-uclibc is a bitcode build of uClibc meant for compatibility with the + KLEE symbolic virtual machine. + ''; + homepage = "https://klee.github.io/"; + license = licenses.lgpl3; + maintainers = with maintainers; [ numinit ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/logic/lean/default.nix b/nixpkgs/pkgs/applications/science/logic/lean/default.nix index 1eea97a0fd23..b5e5ca8723d4 100644 --- a/nixpkgs/pkgs/applications/science/logic/lean/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/lean/default.nix @@ -2,7 +2,7 @@ stdenv.mkDerivation rec { pname = "lean"; - version = "3.41.0"; + version = "3.42.0"; src = fetchFromGitHub { owner = "leanprover-community"; @@ -11,8 +11,8 @@ stdenv.mkDerivation rec { # from. this is then used to check whether an olean file should be # rebuilt. don't use a tag as rev because this will get replaced into # src/githash.h.in in preConfigure. - rev = "154ac72f4ff674bc4486ac611f926a3d6b999f9f"; - sha256 = "0mpxlfjq460x1vi3v6qzgjv74asg0qlhykd51pj347795x5b1hf1"; + rev = "b35d4695da88139a9168f2ad7acf0782e66dc4f0"; + sha256 = "02rpigw6lnyjw8ccrlp2mcvswawkhl5y6kqa3zq76qp1fdjqjrbp"; }; nativeBuildInputs = [ cmake ]; diff --git a/nixpkgs/pkgs/applications/science/logic/naproche/default.nix b/nixpkgs/pkgs/applications/science/logic/naproche/default.nix new file mode 100644 index 000000000000..5e286a9b57e3 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/logic/naproche/default.nix @@ -0,0 +1,38 @@ +{ lib, fetchFromGitHub, haskellPackages, makeWrapper, eprover }: + +with haskellPackages; mkDerivation { + pname = "Naproche-SAD"; + version = "0.1.0.0"; + + src = fetchFromGitHub { + owner = "naproche"; + repo = "naproche"; + rev = "d39cea85ace04d5b3775fde9972a33886799bfe6"; + sha256 = "1zqrldmxkzbyg9bssrbwb00zic29904igcipaz1m9al0456yjnkf"; + }; + + isExecutable = true; + + buildTools = [ hpack makeWrapper ]; + executableHaskellDepends = [ + base array bytestring containers ghc-prim megaparsec mtl network process + split temporary text threads time transformers uuid + ]; + + prePatch = "hpack"; + + checkPhase = '' + export NAPROCHE_EPROVER=${eprover}/bin/eprover + dist/build/Naproche-SAD/Naproche-SAD examples/cantor.ftl.tex -t 60 --tex=on + ''; + + postInstall = '' + wrapProgram $out/bin/Naproche-SAD \ + --set-default NAPROCHE_EPROVER ${eprover}/bin/eprover + ''; + + homepage = "https://github.com/naproche/naproche#readme"; + description = "Write formal proofs in natural language and LaTeX"; + maintainers = with lib.maintainers; [ jvanbruegge ]; + license = lib.licenses.gpl3Only; +} diff --git a/nixpkgs/pkgs/applications/science/logic/opensmt/default.nix b/nixpkgs/pkgs/applications/science/logic/opensmt/default.nix index ef6f9b157d2f..9f104ab80a63 100644 --- a/nixpkgs/pkgs/applications/science/logic/opensmt/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/opensmt/default.nix @@ -6,13 +6,13 @@ stdenv.mkDerivation rec { pname = "opensmt"; - version = "2.3.0"; + version = "2.3.1"; src = fetchFromGitHub { owner = "usi-verification-and-security"; repo = "opensmt"; rev = "v${version}"; - sha256 = "sha256-5Gw9+J+3LHNUNbcHxsQR/ivWndL2P7yBt/Q35fBMg58="; + sha256 = "sha256-3F4Q/ZWlgkiiW7QVjnaaDLSNLVdfAOSmwYdQo1v9Lv4="; }; nativeBuildInputs = [ cmake bison flex ]; diff --git a/nixpkgs/pkgs/applications/science/logic/why3/with-provers.nix b/nixpkgs/pkgs/applications/science/logic/why3/with-provers.nix index 826473b38e9f..ae0acb1e525c 100644 --- a/nixpkgs/pkgs/applications/science/logic/why3/with-provers.nix +++ b/nixpkgs/pkgs/applications/science/logic/why3/with-provers.nix @@ -12,7 +12,7 @@ let configAwkScript = runCommand "why3-conf.awk" { inherit provers; } ''; in stdenv.mkDerivation { - name = "${why3.name}-with-provers"; + pname = "${why3.pname}-with-provers"; nativeBuildInputs = [ makeWrapper ]; buildInputs = [ why3 ] ++ provers; diff --git a/nixpkgs/pkgs/applications/science/logic/z3/4.4.0.nix b/nixpkgs/pkgs/applications/science/logic/z3/4.4.0.nix index 2fbaa0a28caf..a3d6c16fb7df 100644 --- a/nixpkgs/pkgs/applications/science/logic/z3/4.4.0.nix +++ b/nixpkgs/pkgs/applications/science/logic/z3/4.4.0.nix @@ -1,7 +1,7 @@ { lib, stdenv, fetchFromGitHub, python }: stdenv.mkDerivation rec { - name = "z3-${version}"; + pname = "z3"; version = "4.4.0"; src = fetchFromGitHub { diff --git a/nixpkgs/pkgs/applications/science/math/R/default.nix b/nixpkgs/pkgs/applications/science/math/R/default.nix index 4bd237f87834..f91d72ff3f63 100644 --- a/nixpkgs/pkgs/applications/science/math/R/default.nix +++ b/nixpkgs/pkgs/applications/science/math/R/default.nix @@ -14,11 +14,11 @@ assert (!blas.isILP64) && (!lapack.isILP64); stdenv.mkDerivation rec { pname = "R"; - version = "4.1.2"; + version = "4.1.3"; src = fetchurl { url = "https://cran.r-project.org/src/base/R-${lib.versions.major version}/${pname}-${version}.tar.gz"; - sha256 = "sha256-IDYiXp9yB9TOCX5Ulyrs2qi0DX2ZEc0mSR+sWg+rOK8="; + sha256 = "sha256-Ff9bMzxhCUBgsqUunB2OxVzELdAp45yiKr2qkJUm/tY="; }; dontUseImakeConfigure = true; diff --git a/nixpkgs/pkgs/applications/science/math/cemu/default.nix b/nixpkgs/pkgs/applications/science/math/cemu/default.nix index 35b9200a4774..374b245e2499 100644 --- a/nixpkgs/pkgs/applications/science/math/cemu/default.nix +++ b/nixpkgs/pkgs/applications/science/math/cemu/default.nix @@ -7,7 +7,7 @@ , qtbase , qmake , git -, libpng_apng +, libpng , pkg-config , wrapQtAppsHook , stdenv @@ -37,7 +37,7 @@ stdenv.mkDerivation rec { libarchive libusb-compat-0_1 qtbase - libpng_apng + libpng ]; qmakeFlags = [ diff --git a/nixpkgs/pkgs/applications/science/math/cntk/default.nix b/nixpkgs/pkgs/applications/science/math/cntk/default.nix index ba2225b903fa..eb14982575a2 100644 --- a/nixpkgs/pkgs/applications/science/math/cntk/default.nix +++ b/nixpkgs/pkgs/applications/science/math/cntk/default.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, fetchgit, fetchFromGitHub, cmake +{ lib, stdenv, fetchFromGitHub, cmake , fetchpatch , openblas, blas, lapack, opencv3, libzip, boost, protobuf, mpi , onebitSGDSupport ? false @@ -22,11 +22,12 @@ in stdenv.mkDerivation rec { pname = "CNTK"; version = "2.7"; - # Submodules - src = fetchgit { - url = "https://github.com/Microsoft/CNTK"; + src = fetchFromGitHub { + owner = "Microsoft"; + repo = "CNTK"; rev = "v${version}"; - sha256 = "18l9k7s966a26ywcf7flqyhm61788pcb9fj3wk61jrmgkhy2pcns"; + sha256 = "sha256-2rIrPJyvZhnM5EO6tNhF6ARTocfUHce4N0IZk/SZiaI="; + fetchSubmodules = true; }; patches = [ diff --git a/nixpkgs/pkgs/applications/science/math/fricas/default.nix b/nixpkgs/pkgs/applications/science/math/fricas/default.nix index 79d5664426be..8c2541fe4129 100644 --- a/nixpkgs/pkgs/applications/science/math/fricas/default.nix +++ b/nixpkgs/pkgs/applications/science/math/fricas/default.nix @@ -1,14 +1,11 @@ { lib, stdenv, fetchurl, sbcl, libX11, libXpm, libICE, libSM, libXt, libXau, libXdmcp }: -let +stdenv.mkDerivation rec { + pname = "fricas"; version = "1.3.7"; - name = "fricas-" + version; -in -stdenv.mkDerivation { - inherit name; src = fetchurl { - url = "mirror://sourceforge/fricas/fricas/${version}/${name}-full.tar.bz2"; + url = "mirror://sourceforge/fricas/fricas/${version}/fricas-${version}-full.tar.bz2"; sha256 = "sha256-cOqMvSe3ef/ZeVy5cj/VU/aTRtxgfxZfRbE4lWE5TU4="; }; diff --git a/nixpkgs/pkgs/applications/science/math/nasc/default.nix b/nixpkgs/pkgs/applications/science/math/nasc/default.nix index 2fe027365cdc..3e7a8b56af1c 100644 --- a/nixpkgs/pkgs/applications/science/math/nasc/default.nix +++ b/nixpkgs/pkgs/applications/science/math/nasc/default.nix @@ -48,7 +48,6 @@ stdenv.mkDerivation rec { gtk3 gtksourceview libgee - pantheon.elementary-icon-theme pantheon.granite webkitgtk # We add libqalculate's runtime dependencies because nasc has it as a modified subproject. diff --git a/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix b/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix index 7ba5838faba1..4f68eb6ae78d 100644 --- a/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix +++ b/nixpkgs/pkgs/applications/science/math/qalculate-gtk/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "qalculate-gtk"; - version = "4.0.0"; + version = "4.1.0"; src = fetchFromGitHub { owner = "qalculate"; repo = "qalculate-gtk"; rev = "v${version}"; - sha256 = "sha256-l9lR5MVHWiRz5RG/I/nXRY4GQSSaXXP7PlRNoAu9+yo="; + sha256 = "sha256-EOiExp8JBc3SybSiBVbuRxBqTujzLjysWM0v94goups="; }; hardeningDisable = [ "format" ]; diff --git a/nixpkgs/pkgs/applications/science/math/sage/README.md b/nixpkgs/pkgs/applications/science/math/sage/README.md index 26e91fc63133..c3a81c2109ee 100644 --- a/nixpkgs/pkgs/applications/science/math/sage/README.md +++ b/nixpkgs/pkgs/applications/science/math/sage/README.md @@ -17,7 +17,7 @@ If the build broke as a result of a package update, try those solutions in order - fix the problem yourself. First clone the sagemath source and then check out the sage version you want to patch: ``` -[user@localhost ~]$ git clone git://github.com/sagemath/sage.git +[user@localhost ~]$ git clone https://github.com/sagemath/sage.git [user@localhost ~]$ cd sage [user@localhost sage]$ git checkout 8.2 # substitute the relevant version here ``` @@ -41,7 +41,7 @@ You can [login the sage trac using GitHub](https://trac.sagemath.org/login). You Here's the gist, assuming you want to use ssh key authentication. First, [add your public ssh key](https://trac.sagemath.org/prefs/sshkeys). Then: ``` -[user@localhost ~]$ git clone git://github.com/sagemath/sage.git +[user@localhost ~]$ git clone https://github.com/sagemath/sage.git [user@localhost ~]$ cd sage [user@localhost sage]$ git remote add trac git@trac.sagemath.org:sage.git -t master [user@localhost sage]$ git checkout -b u/gh-<your-github-username>/<your-branch-name> develop diff --git a/nixpkgs/pkgs/applications/science/math/scilab-bin/default.nix b/nixpkgs/pkgs/applications/science/math/scilab-bin/default.nix index 18dba2952cad..65d8c145bef6 100644 --- a/nixpkgs/pkgs/applications/science/math/scilab-bin/default.nix +++ b/nixpkgs/pkgs/applications/science/math/scilab-bin/default.nix @@ -1,11 +1,7 @@ { stdenv, fetchurl, lib, xorg }: let - name = "scilab-bin-${ver}"; - - ver = "6.1.1"; - - badArch = throw "${name} requires i686-linux or x86_64-linux"; + badArch = throw "scilab-bin requires i686-linux or x86_64-linux"; architecture = if stdenv.hostPlatform.system == "i686-linux" then @@ -15,11 +11,12 @@ let else badArch; in -stdenv.mkDerivation { - inherit name; +stdenv.mkDerivation rec { + pname = "scilab-bin"; + version = "6.1.1"; src = fetchurl { - url = "https://www.scilab.org/download/${ver}/scilab-${ver}.bin.linux-${architecture}.tar.gz"; + url = "https://www.scilab.org/download/${version}/scilab-${version}.bin.linux-${architecture}.tar.gz"; sha256 = if stdenv.hostPlatform.system == "i686-linux" then "0fgjc2ak3b2qi6yin3fy50qwk2bcj0zbz1h4lyyic9n1n1qcliib" @@ -43,7 +40,7 @@ stdenv.mkDerivation { sed -i 's|\$(/bin/|$(|g' bin/scilab sed -i 's|/usr/bin/||g' bin/scilab - sci="$out/opt/scilab-${ver}" + sci="$out/opt/scilab-${version}" fullLibPath="$sci/lib/scilab:$sci/lib/thirdparty:$libPath" fullLibPath="$fullLibPath:$sci/lib/thirdparty/redist" @@ -55,31 +52,31 @@ stdenv.mkDerivation { ''; installPhase = '' - mkdir -p "$out/opt/scilab-${ver}" - cp -r . "$out/opt/scilab-${ver}/" + mkdir -p "$out/opt/scilab-${version}" + cp -r . "$out/opt/scilab-${version}/" # Create bin/ dir mkdir "$out/bin" # Creating executable symlinks - ln -s "$out/opt/scilab-${ver}/bin/scilab" "$out/bin/scilab" - ln -s "$out/opt/scilab-${ver}/bin/scilab-cli" "$out/bin/scilab-cli" - ln -s "$out/opt/scilab-${ver}/bin/scilab-adv-cli" "$out/bin/scilab-adv-cli" + ln -s "$out/opt/scilab-${version}/bin/scilab" "$out/bin/scilab" + ln -s "$out/opt/scilab-${version}/bin/scilab-cli" "$out/bin/scilab-cli" + ln -s "$out/opt/scilab-${version}/bin/scilab-adv-cli" "$out/bin/scilab-adv-cli" # Creating desktop config dir mkdir -p "$out/share/applications" # Moving desktop config files - mv $out/opt/scilab-${ver}/share/applications/*.desktop $out/share/applications + mv $out/opt/scilab-${version}/share/applications/*.desktop $out/share/applications # Fixing Exec paths and launching each app with a terminal - sed -i -e "s|Exec=|Exec=$out/opt/scilab-${ver}/bin/|g" \ + sed -i -e "s|Exec=|Exec=$out/opt/scilab-${version}/bin/|g" \ -e "s|Terminal=.*$|Terminal=true|g" $out/share/applications/*.desktop # Moving icons to the appropriate locations - for path in $out/opt/scilab-${ver}/share/icons/hicolor/*/*/* + for path in $out/opt/scilab-${version}/share/icons/hicolor/*/*/* do - newpath=$(echo $path | sed 's|/opt/scilab-${ver}||g') + newpath=$(echo $path | sed 's|/opt/scilab-${version}||g') filename=$(echo $path | sed 's|.*/||g') dir=$(echo $newpath | sed "s|$filename||g") mkdir -p $dir @@ -87,10 +84,10 @@ stdenv.mkDerivation { done # Removing emptied folders - rm -rf $out/opt/scilab-${ver}/share/{applications,icons} + rm -rf $out/opt/scilab-${version}/share/{applications,icons} # Moving other share/ folders - mv $out/opt/scilab-${ver}/share/{appdata,locale,mime} $out/share + mv $out/opt/scilab-${version}/share/{appdata,locale,mime} $out/share ''; meta = { diff --git a/nixpkgs/pkgs/applications/science/misc/fityk/default.nix b/nixpkgs/pkgs/applications/science/misc/fityk/default.nix index 974fd3ece45c..a3d6e1564666 100644 --- a/nixpkgs/pkgs/applications/science/misc/fityk/default.nix +++ b/nixpkgs/pkgs/applications/science/misc/fityk/default.nix @@ -1,12 +1,9 @@ { lib, stdenv, fetchFromGitHub, autoreconfHook, wxGTK30, boost, lua, zlib, bzip2 , xylib, readline, gnuplot, swig3 }: -let - name = "fityk"; +stdenv.mkDerivation rec { + pname = "fityk"; version = "1.3.1"; -in -stdenv.mkDerivation { - name = "${name}-${version}"; src = fetchFromGitHub { owner = "wojdyr"; diff --git a/nixpkgs/pkgs/applications/science/misc/golly/beta.nix b/nixpkgs/pkgs/applications/science/misc/golly/beta.nix deleted file mode 100644 index 9846be8a43a8..000000000000 --- a/nixpkgs/pkgs/applications/science/misc/golly/beta.nix +++ /dev/null @@ -1,50 +0,0 @@ -{lib, stdenv, fetchgit -, wxGTK, perl, python2, zlib, libGLU, libGL, libX11 -, automake, autoconf -}: - -stdenv.mkDerivation rec { - pname = "golly"; - version = "2.8.99.2.20161122"; - #src = fetchurl { - # url="mirror://sourceforge/project/golly/golly/golly-2.8/golly-2.8-src.tar.gz"; - # sha256="0a4vn2hm7h4b47v2iwip1z3n9y8isf79v08aipl2iqms2m3p5204"; - #}; - src = fetchgit { - url = "git://git.code.sf.net/p/golly/code"; - rev = "93495edf3c9639332c6eb43ca7149c69629ee5d8"; - sha256 = "1j308s9zlqkr3wnl1l32s5zk7r3g4ijwawkkysl8j5ik9sibi2gk"; - }; - - setSourceRoot = '' - export sourceRoot="$(echo */gui-wx/configure)" - ''; - - nativeBuildInputs = [autoconf automake]; - - buildInputs = [ - wxGTK perl python2 zlib libGLU libGL libX11 - ]; - - # Link against Python explicitly as it is needed for scripts - makeFlags=[ - "AM_LDFLAGS=" - ]; - NIX_LDFLAGS="-l${python2.libPrefix} -lperl -ldl -lGL"; - preConfigure='' - export NIX_LDFLAGS="$NIX_LDFLAGS -L$(dirname "$(find ${perl} -name libperl.so)")" - export NIX_CFLAGS_COMPILE="$NIX_CFLAGS_COMPILE - -DPYTHON_SHLIB=$(basename "$( - readlink -f ${python2}/lib/libpython*.so)")" - - sh autogen.sh - ''; - - meta = { - description = "Cellular automata simulation program"; - license = lib.licenses.gpl2; - maintainers = [lib.maintainers.raskin]; - platforms = lib.platforms.linux; - downloadPage = "https://sourceforge.net/projects/golly/files/golly"; - }; -} diff --git a/nixpkgs/pkgs/applications/science/misc/simgrid/default.nix b/nixpkgs/pkgs/applications/science/misc/simgrid/default.nix index 888419fbc86f..4867e6c9ed55 100644 --- a/nixpkgs/pkgs/applications/science/misc/simgrid/default.nix +++ b/nixpkgs/pkgs/applications/science/misc/simgrid/default.nix @@ -4,6 +4,7 @@ , buildJavaBindings ? false, openjdk , buildPythonBindings ? true, python3Packages , modelCheckingSupport ? false, libunwind, libevent, elfutils # Inside elfutils: libelf and libdw +, bmfSupport ? true, eigen , minimalBindings ? false , debug ? false , optimize ? (!debug) @@ -19,14 +20,14 @@ in stdenv.mkDerivation rec { pname = "simgrid"; - version = "3.30"; + version = "3.31"; src = fetchFromGitLab { domain = "framagit.org"; owner = pname; repo = pname; rev = "v${version}"; - sha256 = "1dg8ywqif20g0fs8dnd6364n080nvwx7f444zcfwqwz6iax61qv1"; + sha256 = "sha256-K6YkkCMxc2lqxHIwyuLiwcp3m49sqbEtOlwZh4L1YJg="; }; propagatedBuildInputs = [ boost ]; @@ -35,6 +36,7 @@ stdenv.mkDerivation rec { ++ optionals buildJavaBindings [ openjdk ] ++ optionals buildPythonBindings [ python3Packages.pybind11 ] ++ optionals buildDocumentation [ fig2dev ghostscript doxygen ] + ++ optionals bmfSupport [ eigen ] ++ optionals modelCheckingSupport [ libunwind libevent elfutils ]; outputs = [ "out" ] diff --git a/nixpkgs/pkgs/applications/science/robotics/inav-configurator/default.nix b/nixpkgs/pkgs/applications/science/robotics/inav-configurator/default.nix index 40914a8ac1a5..ec605a3a97e9 100644 --- a/nixpkgs/pkgs/applications/science/robotics/inav-configurator/default.nix +++ b/nixpkgs/pkgs/applications/science/robotics/inav-configurator/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "inav-configurator"; - version = "3.0.2"; + version = "4.1.0"; src = fetchurl { url = "https://github.com/iNavFlight/inav-configurator/releases/download/${version}/INAV-Configurator_linux64_${version}.tar.gz"; - sha256 = "0v6dcg634wpp9q4ya3mj00j3pg25g62aq209iq2dsvj0a03afbp2"; + sha256 = "sha256-+rPzytnAQcNGbISFBHb4JS9Nqy0C2i36k+EPBvq/mso="; }; icon = fetchurl { |