Merge remote-tracking branch 'upstream/master' into hardened-stdenv

5 files changed, 128 insertions, 5 deletions

diff --git a/pkgs/applications/science/math/LiE/default.nix b/pkgs/applications/science/math/LiE/default.nix
index b448b5114212..515b7e272899 100644
--- a/pkgs/applications/science/math/LiE/default.nix
+++ b/pkgs/applications/science/math/LiE/default.nix
@@ -5,7 +5,7 @@ stdenv.mkDerivation rec {
   version = "2.2.2";
      # The current version of LiE is 2.2.2, which is more or less unchanged
      # since about the year 2000. Minor bugfixes do get applied now and then.
-  name = "LiE-${version}";
+  name = "lie-${version}";
 
   meta = {
     description = "A Computer algebra package for Lie group computations";
@@ -19,7 +19,7 @@ stdenv.mkDerivation rec {
       characteristics, we refer to the following sources of information.
     ''; # take from the website
 
-    platforms = stdenv.lib.platforms.unix;
+    platforms = stdenv.lib.platforms.linux;
     maintainers = [ ]; # this package is probably not going to change anyway
   };
 
diff --git a/pkgs/applications/science/math/geogebra/default.nix b/pkgs/applications/science/math/geogebra/default.nix
new file mode 100644
index 000000000000..fcbd13566657
--- /dev/null
+++ b/pkgs/applications/science/math/geogebra/default.nix
@@ -0,0 +1,58 @@
+{ stdenv, fetchurl, jre, makeDesktopItem, makeWrapper }:
+
+stdenv.mkDerivation rec {
+  name = "geogebra-${version}";
+  version = "5.0.265.0";
+
+  preferLocalBuild = true;
+
+  src = fetchurl {
+    url = "http://download.geogebra.org/installers/5.0/GeoGebra-Linux-Portable-${version}.tar.bz2";
+    sha256 = "74e5abfa098ee0fc464cd391cd3ef6db474ff25e8ea4fbcd82c4b4b5d3d5c459";
+  };
+
+  srcIcon = fetchurl {
+    url = "http://static.geogebra.org/images/geogebra-logo.svg";
+    sha256 = "55ded6b5ec9ad382494f858d8ab5def0ed6c7d529481cd212863b2edde3b5e07";
+  };
+
+  desktopItem = makeDesktopItem {
+    name = "geogebra";
+    exec = "geogebra";
+    icon = "geogebra";
+    desktopName = "Geogebra";
+    genericName = "Geogebra";
+    comment = meta.description;
+    categories = "Education;Science;Math;";
+    mimeType = "application/vnd.geogebra.file;application/vnd.geogebra.tool;";
+  };
+
+  buildInputs = [ makeWrapper ];
+
+  installPhase = ''
+    install -D geogebra/* -t "$out/libexec/geogebra/"
+
+    makeWrapper "$out/libexec/geogebra/geogebra" "$out/bin/geogebra" \
+      --set JAVACMD "${jre}/bin/java" \
+      --set GG_PATH "$out/libexec/geogebra"
+
+    install -Dm644 "${desktopItem}/share/applications/"* \
+      -t $out/share/applications/
+
+    install -Dm644 "${srcIcon}" \
+      "$out/share/icons/hicolor/scalable/apps/geogebra.svg"
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Dynamic mathematics software with graphics, algebra and spreadsheets";
+    longDescription = ''
+      Dynamic mathematics software for all levels of education that brings
+      together geometry, algebra, spreadsheets, graphing, statistics and
+      calculus in one easy-to-use package.
+    '';
+    homepage = https://www.geogebra.org/;
+    license = with licenses; [ gpl3 cc-by-nc-sa-30 geogebra ];
+    platforms = platforms.all;
+    hydraPlatforms = [];
+  };
+}
diff --git a/pkgs/applications/science/math/msieve/default.nix b/pkgs/applications/science/math/msieve/default.nix
index e01b9654711b..4c99b5081cc5 100644
--- a/pkgs/applications/science/math/msieve/default.nix
+++ b/pkgs/applications/science/math/msieve/default.nix
@@ -24,6 +24,6 @@ stdenv.mkDerivation {
     license = stdenv.lib.licenses.publicDomain;
     homepage = http://msieve.sourceforge.net/;
     maintainers = [ stdenv.lib.maintainers.roconnor ];
-    platforms = stdenv.lib.platforms.linux;
+    platforms = [ "x86_64-linux" ];
   };
 }
diff --git a/pkgs/applications/science/math/pari/default.nix b/pkgs/applications/science/math/pari/default.nix
index da10e89855ae..0cda65b32c30 100644
--- a/pkgs/applications/science/math/pari/default.nix
+++ b/pkgs/applications/science/math/pari/default.nix
@@ -1,12 +1,12 @@
 { stdenv, fetchurl, gmp, readline }:
 
 stdenv.mkDerivation rec {
-  version = "2.7.5";
+  version = "2.7.6";
   name = "pari-${version}";
 
   src = fetchurl {
     url = "http://pari.math.u-bordeaux.fr/pub/pari/unix/${name}.tar.gz";
-    sha256 = "0c8l83a0gjq73r9hndsrzkypwxvnnm4pxkkzbg6jm95m80nzwh11";
+    sha256 = "04dqi697czd8mmw8aiwzrkgbvkjassqagg6lfy3lkf1k5qi9g9rr";
   };
 
   buildInputs = [gmp readline];
diff --git a/pkgs/applications/science/math/ripser/default.nix b/pkgs/applications/science/math/ripser/default.nix
new file mode 100644
index 000000000000..7f94b7408a11
--- /dev/null
+++ b/pkgs/applications/science/math/ripser/default.nix
@@ -0,0 +1,65 @@
+{ stdenv, fetchurl, fetchFromGitHub
+, assembleReductionMatrix ? false
+, useCoefficients ? false
+, indicateProgress ? false
+, useGoogleHashmap ? false, sparsehash ? null
+, fileFormat ? "lowerTriangularCsv"
+}:
+
+with stdenv.lib;
+
+assert elem fileFormat ["lowerTriangularCsv" "upperTriangularCsv" "dipha"];
+assert useGoogleHashmap -> sparsehash != null;
+
+let
+  inherit (stdenv.lib) optional;
+in
+stdenv.mkDerivation {
+  name = "ripser";
+  version = "1.0";
+
+  src = fetchFromGitHub {
+    owner = "Ripser";
+    repo = "ripser";
+    rev = "f69c6af6ca6883dd518c48faf41cf8901c379598";
+    sha256 = "1mw2898s7l29hgajsaf75bs9bjn2sn4g2mvmh41a602jpwp9r0rz";
+  };
+
+  #Patch from dev branch to make compilation work.
+  #Will be removed when it gets merged into master.
+  patches = [(fetchurl {
+    url = https://github.com/Ripser/ripser/commit/dc78d8ce73ee35f3828f0aad67a4e53620277ebf.patch;
+    sha256 = "1y93aqpqz8fm1cxxrf90dhh67im3ndkr8dnxgbw5y96296n4r924";
+  })];
+
+  buildInputs = optional useGoogleHashmap sparsehash;
+
+  buildFlags = [
+    "-std=c++11"
+    "-Ofast"
+    "-D NDEBUG"
+  ]
+  ++ optional assembleReductionMatrix "-D ASSEMBLE_REDUCTION_MATRIX"
+  ++ optional useCoefficients "-D USE_COEFFICIENTS"
+  ++ optional indicateProgress "-D INDICATE_PROGRESS"
+  ++ optional useGoogleHashmap "-D USE_GOOGLE_HASHMAP"
+  ++ optional (fileFormat == "lowerTriangularCsv") "-D FILE_FORMAT_LOWER_TRIANGULAR_CSV"
+  ++ optional (fileFormat == "upperTriangularCsv") "-D FILE_FORMAT_UPPER_TRIANGULAR_CSV"
+  ++ optional (fileFormat == "dipha") "-D FILE_FORMAT_DIPHA"
+  ;
+
+  buildPhase = "c++ ripser.cpp -o ripser $buildFlags";
+
+  installPhase = ''
+    mkdir -p $out/bin
+    cp ripser $out/bin
+  '';
+
+  meta = {
+    description = "A lean C++ code for the computation of Vietoris–Rips persistence barcodes";
+    homepage = "https://github.com/Ripser/ripser";
+    license = stdenv.lib.licenses.lgpl3;
+    maintainers = with stdenv.lib.maintainers; [erikryb];
+    platforms = stdenv.lib.platforms.linux;
+  };
+}