diff options
Diffstat (limited to 'nixpkgs/pkgs/applications/science')
11 files changed, 108 insertions, 85 deletions
diff --git a/nixpkgs/pkgs/applications/science/biology/truvari/default.nix b/nixpkgs/pkgs/applications/science/biology/truvari/default.nix index fffeca2c740c..31c1fc50ee3e 100644 --- a/nixpkgs/pkgs/applications/science/biology/truvari/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/truvari/default.nix @@ -5,15 +5,20 @@ python3Packages.buildPythonApplication rec { pname = "truvari"; - version = "2.0.2"; + version = "2.1.1"; src = fetchFromGitHub { owner = "spiralgenetics"; repo = "truvari"; rev = "v${version}"; - sha256 = "0lp1wnldjv92k4ncga1h0icb0dpjsrx427vggg40x04a7kp9lwx0"; + sha256 = "14nsdbj063qm175xxixs34cihvsiskc9gym8pg7gbwsh13k5a00h"; }; + postPatch = '' + substituteInPlace setup.py \ + --replace 'python-Levenshtein==0.12.1' 'python-Levenshtein>=0.12.1' + ''; + propagatedBuildInputs = with python3Packages; [ pyvcf python-Levenshtein diff --git a/nixpkgs/pkgs/applications/science/chemistry/element/default.nix b/nixpkgs/pkgs/applications/science/chemistry/element/default.nix new file mode 100644 index 000000000000..812272e2fb9b --- /dev/null +++ b/nixpkgs/pkgs/applications/science/chemistry/element/default.nix @@ -0,0 +1,22 @@ +{ lib, buildGoModule, fetchFromGitHub }: + +buildGoModule rec { + pname = "element"; + version = "1.0.0"; + + src = fetchFromGitHub { + owner = "gennaro-tedesco"; + repo = pname; + rev = "v${version}"; + sha256 = "gjdcNvYNnxb6hOE/MQjTezZeYGBWTr4E8/Pt8YQv3lY="; + }; + + vendorSha256 = "A4g2rQTaYrA4/0rqldUv7iuibzNINEvx9StUnaN2/Yg="; + + meta = with lib; { + description = "The periodic table on the command line"; + homepage = "https://github.com/gennaro-tedesco/element"; + license = licenses.asl20; + maintainers = [ maintainers.j0hax ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix b/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix index d8f7bd5eb552..93ec987e2c69 100644 --- a/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix +++ b/nixpkgs/pkgs/applications/science/chemistry/jmol/default.nix @@ -17,14 +17,14 @@ let }; in stdenv.mkDerivation rec { - version = "14.31.38"; + version = "14.31.39"; 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-${version}-binary.tar.gz"; - sha256 = "sha256-yXJ1KtTH3bi24GFiVXu8zzQkreDkqbCxgm7fVoSJepg="; + sha256 = "sha256-ss+QvBsmivqNdjXW45Sv9h/JXuZpryCGmRTsUgcDlRE="; }; patchPhase = '' diff --git a/nixpkgs/pkgs/applications/science/electronics/fritzing/default.nix b/nixpkgs/pkgs/applications/science/electronics/fritzing/default.nix index 79c01d3ec718..30cbd8f92b57 100644 --- a/nixpkgs/pkgs/applications/science/electronics/fritzing/default.nix +++ b/nixpkgs/pkgs/applications/science/electronics/fritzing/default.nix @@ -1,86 +1,75 @@ -{ mkDerivation, lib, fetchpatch, fetchFromGitHub, qmake, pkg-config -, qtbase, qtsvg, qttools, qtserialport, boost, libgit2 +{ mkDerivation +, lib +, fetchFromGitHub +, qmake +, pkg-config +, qtbase +, qtsvg +, qttools +, qtserialport +, boost +, libgit2 }: let # build number corresponding to a release, has no further relation # see https://github.com/fritzing/fritzing-app/releases/tag/CD-498 - fritzingBuild = "498"; + # fritzingBuild = "498"; + # version 0.9.6 is properly tagged, hope it continues + # SHA256 of the fritzing-parts HEAD on the master branch, # which contains the latest stable parts definitions - partsSha = "e79a69765026f3fda8aab1b3e7a4952c28047a62"; + partsSha = "6f04697be286768bc9e4d64f8707e8e40cbcafcb"; in mkDerivation rec { pname = "fritzing"; - version = "0.9.4-${fritzingBuild}"; + version = "0.9.6"; src = fetchFromGitHub { - owner = "fritzing"; + owner = pname; repo = "fritzing-app"; - rev = "CD-${fritzingBuild}"; - sha256 = "0aljj2wbmm1vd64nhj6lh9qy856pd5avlgydsznya2vylyz20p34"; + rev = version; + sha256 = "083nz7vj7a334575smjry6257535h68gglh8a381xxa36dw96aqs"; }; parts = fetchFromGitHub { - owner = "fritzing"; + owner = pname; repo = "fritzing-parts"; name = "fritzing-parts"; rev = partsSha; - sha256 = "0spka33a5qq34aq79j01arw1aly4vh0hzv7mahryhdlcdk22qqvc"; + sha256 = "1f4w0hz44n4iw1rc5vhcgzvlji54rf4yr8bvzkqv99hn2xf5pjgs"; }; buildInputs = [ qtbase qtsvg qtserialport boost libgit2 ]; - nativeBuildInputs = [ qmake pkg-config qttools ]; - patches = [(fetchpatch { - name = "fix-libgit2-version.patch"; - url = "https://github.com/fritzing/fritzing-app/commit/472951243d70eeb40a53b1f7e16e6eab0588d079.patch"; - sha256 = "0v1zi609cjnqac80xgnk23n54z08g1lia37hbzfl8jcq9sn9adak"; - })]; - postPatch = '' substituteInPlace phoenix.pro \ --replace 'LIBGIT_STATIC = true' 'LIBGIT_STATIC = false' - substituteInPlace tools/linux_release_script/release.sh \ - --replace 'git status' 'echo >/dev/null' \ - --replace 'git clean' 'echo >/dev/null' \ - --replace 'git clone' 'echo >/dev/null' \ - --replace 'release_folder="' 'release_folder="$out" #' \ - --replace './Fritzing -db' '# run after fixup' - substituteInPlace src/fapplication.cpp \ --replace 'PartsChecker::getSha(dir.absolutePath());' '"${partsSha}";' - ''; - - buildPhase = '' - bash tools/linux_release_script/release.sh ${version} - ''; - installPhase = '' - rm "$out/Fritzing" # remove script file - mkdir "$out/bin" - mv "$out/lib/Fritzing" "$out/bin/Fritzing" - mkdir --parents "$out/share/applications" "$out/share/metainfo" - mv --target-directory="$out/share/applications" "$out/org.fritzing.Fritzing.desktop" - mv --target-directory="$out/share/metainfo" "$out/org.fritzing.Fritzing.appdata.xml" - cp --recursive --no-target-directory "$parts" "$out/fritzing-parts" + mkdir parts + cp -a ${parts}/* parts/ ''; postFixup = '' # generate the parts.db file - QT_QPA_PLATFORM=offscreen "$out/bin/Fritzing" -db "$out/fritzing-parts/parts.db" -pp "$out/fritzing-parts" -folder "$out" + QT_QPA_PLATFORM=offscreen "$out/bin/Fritzing" \ + -db "$out/share/fritzing/parts/parts.db" \ + -pp "$out/fritzing/parts" \ + -folder "$out/share/fritzing" ''; qmakeFlags = [ "phoenix.pro" ]; - meta = { + meta = with lib; { description = "An open source prototyping tool for Arduino-based projects"; homepage = "https://fritzing.org/"; - license = lib.licenses.gpl3; - maintainers = [ lib.maintainers.robberer ]; - platforms = lib.platforms.linux; + license = with licenses; [ gpl3 cc-by-sa-30 ]; + maintainers = with maintainers; [ robberer ]; + platforms = platforms.linux; }; } diff --git a/nixpkgs/pkgs/applications/science/electronics/horizon-eda/default.nix b/nixpkgs/pkgs/applications/science/electronics/horizon-eda/default.nix index dee0a851bf8c..c1ff99a2c3a3 100644 --- a/nixpkgs/pkgs/applications/science/electronics/horizon-eda/default.nix +++ b/nixpkgs/pkgs/applications/science/electronics/horizon-eda/default.nix @@ -23,13 +23,13 @@ stdenv.mkDerivation rec { pname = "horizon-eda"; - version = "1.4.0"; + version = "2.0.0"; src = fetchFromGitHub { owner = "horizon-eda"; repo = "horizon"; rev = "v${version}"; - sha256 = "0mra6kf1c2qixfzqva6r01qms5kdabbhhblhk5is6h6nq78i8640"; + sha256 = "sha256-FS24B/ySKeF8r7Tro+mf5P0ALtlPwwJCU3YdDNYLe6o="; }; buildInputs = [ diff --git a/nixpkgs/pkgs/applications/science/logic/gappa/default.nix b/nixpkgs/pkgs/applications/science/logic/gappa/default.nix index 73f34f60fc47..c7c5c9c6fa70 100644 --- a/nixpkgs/pkgs/applications/science/logic/gappa/default.nix +++ b/nixpkgs/pkgs/applications/science/logic/gappa/default.nix @@ -1,11 +1,11 @@ { lib, stdenv, fetchurl, gmp, mpfr, boost }: stdenv.mkDerivation { - name = "gappa-1.3.5"; + name = "gappa-1.4.0"; src = fetchurl { - url = "https://gforge.inria.fr/frs/download.php/file/38044/gappa-1.3.5.tar.gz"; - sha256 = "0q1wdiwqj6fsbifaayb1zkp20bz8a1my81sqjsail577jmzwi07w"; + url = "https://gforge.inria.fr/frs/download.php/file/38044/gappa-1.4.0.tar.gz"; + sha256 = "sha256-/IDIf5XnFBqVllgH5GtQ6C8g7vxheaVcXNoZiXlsPGA="; }; buildInputs = [ gmp mpfr boost.dev ]; diff --git a/nixpkgs/pkgs/applications/science/machine-learning/starspace/default.nix b/nixpkgs/pkgs/applications/science/machine-learning/starspace/default.nix index d5a6cb796a71..ca7500cd5c35 100644 --- a/nixpkgs/pkgs/applications/science/machine-learning/starspace/default.nix +++ b/nixpkgs/pkgs/applications/science/machine-learning/starspace/default.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, fetchFromGitHub, boost165 }: +{ lib, stdenv, fetchFromGitHub, boost165, zlib }: stdenv.mkDerivation rec { pname = "starspace"; @@ -11,13 +11,17 @@ stdenv.mkDerivation rec { sha256 = "0sc7a37z1skb9377a1qs8ggwrkz0nmpybx7sms38xj05b702kbvj"; }; - buildInputs = [ boost165 ]; + buildInputs = [ boost165 zlib ]; makeFlags = [ "CXX=${stdenv.cc.targetPrefix}c++" "BOOST_DIR=${boost165.dev}/include" ]; + preBuild = '' + cp makefile_compress makefile + ''; + installPhase = '' mkdir -p $out/bin mv starspace $out/bin diff --git a/nixpkgs/pkgs/applications/science/machine-learning/vowpal-wabbit/default.nix b/nixpkgs/pkgs/applications/science/machine-learning/vowpal-wabbit/default.nix index de6f92129838..d1523b571f4b 100644 --- a/nixpkgs/pkgs/applications/science/machine-learning/vowpal-wabbit/default.nix +++ b/nixpkgs/pkgs/applications/science/machine-learning/vowpal-wabbit/default.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, fetchFromGitHub, cmake, boost169, flatbuffers, fmt, rapidjson, spdlog, zlib }: +{ lib, stdenv, fetchFromGitHub, cmake, boost, flatbuffers, fmt, rapidjson, spdlog, zlib }: stdenv.mkDerivation rec { pname = "vowpal-wabbit"; @@ -14,7 +14,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ cmake ]; buildInputs = [ - boost169 + boost flatbuffers fmt rapidjson diff --git a/nixpkgs/pkgs/applications/science/math/eukleides/default.nix b/nixpkgs/pkgs/applications/science/math/eukleides/default.nix index b5a9fc3fa86d..6b6bfd7d6e5f 100644 --- a/nixpkgs/pkgs/applications/science/math/eukleides/default.nix +++ b/nixpkgs/pkgs/applications/science/math/eukleides/default.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, fetchurl, bison, flex, makeWrapper, texinfo, readline, texLive }: +{ lib, stdenv, fetchurl, bison, flex, makeWrapper, texinfo4, getopt, readline, texlive }: lib.fix (eukleides: stdenv.mkDerivation rec { pname = "eukleides"; @@ -9,12 +9,16 @@ lib.fix (eukleides: stdenv.mkDerivation rec { sha256 = "0s8cyh75hdj89v6kpm3z24i48yzpkr8qf0cwxbs9ijxj1i38ki0q"; }; - # use $CC instead of hardcoded gcc - patches = [ ./use-CC.patch ]; + patches = [ + # use $CC instead of hardcoded gcc + ./use-CC.patch + # allow PostScript transparency in epstopdf call + ./gs-allowpstransparency.patch + ]; - nativeBuildInputs = [ bison flex texinfo makeWrapper ]; + nativeBuildInputs = [ bison flex texinfo4 makeWrapper ]; - buildInputs = [ readline texLive ]; + buildInputs = [ getopt readline ]; preConfigure = '' substituteInPlace Makefile \ @@ -34,19 +38,15 @@ lib.fix (eukleides: stdenv.mkDerivation rec { postInstall = '' wrapProgram $out/bin/euktoeps \ - --set-default TEXINPUTS : \ - --prefix TEXINPUTS : "$tex/tex/latex/eukleides" \ - --prefix PATH : "${texLive}/bin" - wrapProgram $out/bin/euktopdf \ - --set-default TEXINPUTS : \ - --prefix TEXINPUTS : "$tex/tex/latex/eukleides" \ - --prefix PATH : "${texLive}/bin" + --prefix PATH : ${lib.makeBinPath [ getopt ]} ''; outputs = [ "out" "doc" "tex" ]; passthru.tlType = "run"; - passthru.pkgs = [ eukleides.tex ]; + passthru.pkgs = [ eukleides.tex ] + # packages needed by euktoeps, euktopdf and eukleides.sty + ++ (with texlive; collection-pstricks.pkgs ++ epstopdf.pkgs ++ iftex.pkgs ++ moreverb.pkgs); meta = { description = "Geometry Drawing Language"; diff --git a/nixpkgs/pkgs/applications/science/math/eukleides/gs-allowpstransparency.patch b/nixpkgs/pkgs/applications/science/math/eukleides/gs-allowpstransparency.patch new file mode 100644 index 000000000000..aa92e6cc9fa7 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/math/eukleides/gs-allowpstransparency.patch @@ -0,0 +1,10 @@ +--- a/bash/euktopdf ++++ b/bash/euktopdf +@@ -55,6 +55,6 @@ do + exit 1 + fi + dvips -q -E -o $base.eps $base.dvi && +- epstopdf $base.eps && ++ epstopdf --gsopt=-dALLOWPSTRANSPARENCY $base.eps && + rm -f $base.{tex,log,dvi,eps} + done diff --git a/nixpkgs/pkgs/applications/science/math/gurobi/default.nix b/nixpkgs/pkgs/applications/science/math/gurobi/default.nix index 2bfeaa005687..91ee7c1c65e0 100644 --- a/nixpkgs/pkgs/applications/science/math/gurobi/default.nix +++ b/nixpkgs/pkgs/applications/science/math/gurobi/default.nix @@ -1,35 +1,28 @@ -{ stdenv, lib, fetchurl, autoPatchelfHook, python2 }: +{ stdenv, lib, fetchurl, autoPatchelfHook, python3 }: -let - majorVersion = "8.1"; -in stdenv.mkDerivation rec { +stdenv.mkDerivation rec { pname = "gurobi"; - version = "${majorVersion}.0"; + version = "9.1.2"; - src = with lib; fetchurl { - url = "http://packages.gurobi.com/${versions.majorMinor version}/gurobi${version}_linux64.tar.gz"; - sha256 = "1yjqbzqnq4jjkjm616d36bgd3rmqr0a1ii17n0prpdjzmdlq63dz"; + src = fetchurl { + url = "https://packages.gurobi.com/${lib.versions.majorMinor version}/gurobi${version}_linux64.tar.gz"; + sha256 = "7f60bd675f79476bb2b32cd632aa1d470f8246f2b033b7652d8de86f6e7e429b"; }; sourceRoot = "gurobi${builtins.replaceStrings ["."] [""] version}/linux64"; nativeBuildInputs = [ autoPatchelfHook ]; - buildInputs = [ (python2.withPackages (ps: [ ps.gurobipy ])) ]; + buildInputs = [ (python3.withPackages (ps: [ ps.gurobipy ])) ]; strictDeps = true; - buildPhase = '' - cd src/build - make - cd ../.. - ''; + makeFlags = [ "--directory=src/build" ]; installPhase = '' mkdir -p $out/bin cp bin/* $out/bin/ - rm $out/bin/gurobi.env rm $out/bin/gurobi.sh - rm $out/bin/python2.7 + rm $out/bin/python* cp lib/gurobi.py $out/bin/gurobi.sh @@ -48,7 +41,7 @@ in stdenv.mkDerivation rec { ln -s $out/lib/gurobi-javadoc.jar $out/share/java/ ''; - passthru.libSuffix = lib.replaceStrings ["."] [""] majorVersion; + passthru.libSuffix = lib.replaceStrings [ "." ] [ "" ] (lib.versions.majorMinor version); meta = with lib; { description = "Optimization solver for mathematical programming"; |