Merge branch 'master' into minc_ecosystem

2018-04-21 20:18:27 +01:00
parent 6908f0ce89 0964410b28
commit f7785dd61c
1387 changed files with 23744 additions and 15838 deletions
@@ -45,7 +45,9 @@

 let
  inherit (stdenv.lib) optional optionalString;
-  version = "3.10.3";
+  # Don't upgrade until https://github.com/math-atlas/math-atlas/issues/44
+  # is resolved.
+  version = "3.10.2";
 in

 stdenv.mkDerivation {
@@ -53,7 +55,7 @@ stdenv.mkDerivation {

  src = fetchurl {
    url = "mirror://sourceforge/math-atlas/atlas${version}.tar.bz2";
-    sha256 = "1dyjlq3fiparvm8ypwk6rsmjzmnwk81l88gkishphpvc79ryp216";
+    sha256 = "0bqh4bdnjdyww4mcpg6kn0x7338mfqbdgysn97dzrwwb26di7ars";
  };

  buildInputs = [ gfortran ];
@@ -7,6 +7,7 @@
 , python
 , ocl-icd
 , opencl-headers
+, Accelerate, CoreGraphics, CoreVideo, OpenCL
 , gtest
 }:

@@ -40,11 +41,19 @@ stdenv.mkDerivation rec {
    gfortran
    blas
    python
-    ocl-icd
-    opencl-headers
    boost
    gtest
-  ]; 
+  ] ++ stdenv.lib.optionals (!stdenv.isDarwin) [
+    ocl-icd
+    opencl-headers
+  ] ++ stdenv.lib.optionals stdenv.isDarwin [
+    Accelerate
+    CoreGraphics
+    CoreVideo
+  ];
+  propagatedBuildInputs = stdenv.lib.optionals stdenv.isDarwin [
+    OpenCL
+  ];

  enableParallelBuilding = true;

@@ -56,7 +65,7 @@ stdenv.mkDerivation rec {
    '';
    license = licenses.asl20;
    maintainers = with maintainers; [ artuuge ];
-    platforms = platforms.linux;
+    platforms = platforms.unix;
  };

 }
@@ -0,0 +1,38 @@
+{ stdenv
+, fetchFromGitHub
+, autoreconfHook
+}:
+
+stdenv.mkDerivation rec {
+  version = "1.21";
+  name = "cliquer-${version}";
+
+  # autotoolized version of the original cliquer
+  src = fetchFromGitHub {
+    owner = "dimpase";
+    repo = "autocliquer";
+    rev = "v${version}";
+    sha256 = "180i4qj1a25qfp75ig2d3144xfpb1dgcgpha0iqqghd7di4awg7z";
+  };
+
+  doCheck = true;
+
+  buildInputs = [
+    autoreconfHook
+  ];
+
+  meta = with stdenv.lib; {
+    homepage = https://users.aalto.fi/~pat/cliquer.html;
+    downloadPage = src.meta.homepage; # autocliquer
+    description = "Routines for clique searching";
+    longDescription = ''
+      Cliquer is a set of C routines for finding cliques in an arbitrary weighted graph.
+      It uses an exact branch-and-bound algorithm developed by Patric Östergård.
+      It is designed with the aim of being efficient while still being flexible and
+      easy to use.
+    '';
+    license = licenses.gpl2Plus;
+    maintainers = with maintainers; [ timokau ];
+    platforms = platforms.linux;
+  };
+}
@@ -0,0 +1,30 @@
+{ stdenv
+, fetchFromBitbucket
+, autoreconfHook
+}:
+
+stdenv.mkDerivation rec {
+  version = "20140914";
+  name = "m4ri-${version}";
+
+  src = fetchFromBitbucket {
+    owner = "malb";
+    repo = "m4ri";
+    rev = "release-${version}";
+    sha256 = "0xfg6pffbn8r1s0y7bn9b8i55l00d41dkmhrpf7pwk53qa3achd3";
+  };
+
+  doCheck = true;
+
+  nativeBuildInputs = [
+    autoreconfHook
+  ];
+
+  meta = with stdenv.lib; {
+    homepage = https://malb.bitbucket.io/m4ri/;
+    description = "Library to do fast arithmetic with dense matrices over F_2";
+    license = licenses.gpl2Plus;
+    maintainers = with maintainers; [ timokau ];
+    platforms = platforms.linux;
+  };
+}
@@ -0,0 +1,39 @@
+{ stdenv
+, fetchFromBitbucket
+, autoreconfHook
+, m4ri
+}:
+
+stdenv.mkDerivation rec {
+  version = "20150908";
+  name = "m4rie-${version}";
+
+  src = fetchFromBitbucket {
+    owner = "malb";
+    repo = "m4rie";
+    rev = "release-${version}";
+    sha256 = "0r8lv46qx5mkz5kp3ay2jnsp0mbhlqr5z2z220wdk73wdshcznss";
+  };
+
+  doCheck = true;
+
+  buildInputs = [
+    m4ri
+  ];
+
+  nativeBuildInputs = [
+    autoreconfHook
+  ];
+
+  meta = with stdenv.lib; {
+    homepage = https://malb.bitbucket.io/m4rie/;
+    description = "Library for matrix multiplication, reduction and inversion over GF(2^k) for 2 <= k <= 10";
+    longDescription = ''
+      M4RIE is a library for fast arithmetic with dense matrices over small finite fields of even characteristic.
+      It uses the M4RI library, implementing the same operations over the finite field F2.
+    '';
+    license = licenses.gpl2Plus;
+    maintainers = with maintainers; [ timokau ];
+    platforms = platforms.linux;
+  };
+}
@@ -60,7 +60,7 @@ let
      TARGET = "ATHLON";
      DYNAMIC_ARCH = "1";
      CC = "gcc";
-      USE_OPENMP = "1";
+      USE_OPENMP = if stdenv.hostPlatform.isMusl then "0" else "1";
    };
  };
 in
@@ -0,0 +1,40 @@
+{ stdenv
+, fetchFromGitHub
+, fetchpatch
+, autoreconfHook
+}:
+
+stdenv.mkDerivation rec {
+  pname = "planarity";
+  version = "3.0.0.5";
+  name = "${pname}-${version}";
+
+  src = fetchFromGitHub {
+    owner = "graph-algorithms";
+    repo = "edge-addition-planarity-suite";
+    rev = "Version_${version}";
+    sha256 = "01cm7ay1njkfsdnmnvh5zwc7wg7x189hq1vbfhh9p3ihrbnmqzh8";
+  };
+
+  nativeBuildInputs = [
+    autoreconfHook
+  ];
+
+  doCheck = true;
+
+  patches = [
+    # declare variables declared in headers as extern, not yet merged upstream
+    (fetchpatch {
+      url = "https://github.com/graph-algorithms/edge-addition-planarity-suite/pull/3.patch";
+      sha256 = "1nqjc4clr326imz4jxqxcxv2hgh1sjgzll27k5cwkdin8lnmmil8";
+    })
+  ];
+
+  meta = with stdenv.lib; {
+    homepage = https://github.com/graph-algorithms/edge-addition-planarity-suite;
+    description = "A library for implementing graph algorithms";
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ timokau ];
+    platforms = platforms.unix;
+  };
+}
@@ -0,0 +1,89 @@
+{ stdenv
+, fetchurl
+, fetchpatch
+, makeWrapper
+}:
+
+stdenv.mkDerivation rec {
+  version = "1.018.1";
+  name = "sympow-${version}";
+
+  src = fetchurl {
+    # Original website no longer reachable
+    url = "http://mirrors.mit.edu/sage/spkg/upstream/sympow/sympow-${version}.tar.bz2";
+    sha256 = "0hphs7ia1wr5mydf288zvwj4svrymfpadcg3pi6w80km2yg5bm3c";
+  };
+
+  nativeBuildInputs = [
+    makeWrapper
+  ];
+
+  configurePhase = ''
+    runHook preConfigure
+    ./Configure # doesn't take any options
+    runHook postConfigure
+  '';
+
+  installPhase = ''
+    runHook preInstall
+    install -d datafiles "$out/share/sympow/datafiles"
+    install *.gp "$out/share/sympow/"
+    install -Dm755 sympow "$out/share/sympow/sympow"
+    install -D new_data "$out/bin/new_data"
+
+    makeWrapper "$out/share/sympow/sympow" "$out/bin/sympow" \
+      --run 'export SYMPOW_LOCAL="$HOME/.local/share/sympow"' \
+      --run 'if [ ! -d "$SYMPOW_LOCAL" ]; then
+        mkdir -p "$SYMPOW_LOCAL" 
+        cp -r ${placeholder "out"}/share/sympow/* "$SYMPOW_LOCAL"
+        chmod -R +xw "$SYMPOW_LOCAL"
+    fi' \
+      --run 'cd "$SYMPOW_LOCAL"'
+    runHook postInstall
+  '';
+
+  patches = [
+    # don't hardcode paths
+    (fetchpatch {
+      name = "do_not_hardcode_paths.patch";
+      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/sympow/patches/Configure.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba";
+      sha256 = "1611p8ra8zkxvmxn3gm2l64bd4ma4m6r4vd6vwswcic91k1fci04";
+    })
+
+    # bug on some platforms in combination with a newer gcc:
+    # https://trac.sagemath.org/ticket/11920
+    (fetchpatch {
+      name = "fix_newer_gcc1.patch";
+      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/sympow/patches/fpu.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba";
+      sha256 = "14gfa56w3ddfmd4d5ir9a40y2zi43cj1i4d2l2ij9l0qlqdy9jyx";
+    })
+    (fetchpatch {
+      name = "fix_newer_gcc2.patch";
+      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/sympow/patches/execlp.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba";
+      sha256 = "190gqhgz9wgw4lqwz0nwb1izc9zffx34bazsiw2a2sz94bmgb54v";
+    })
+
+    # fix pointer initialization bug (https://trac.sagemath.org/ticket/22862)
+    (fetchpatch {
+      name = "fix_pointer_initialization1.patch";
+      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/sympow/patches/initialize-tacks.patch?id=07d6c37d18811e2b377a9689790a7c5e24da16ba";
+      sha256 = "02341vdbbidfs39s26vi4n5wigz619sw8fdbl0h9qsmwwhscgf85";
+    })
+    (fetchpatch {
+      name = "fix_pointer_initialization2.patch";
+      url = "https://git.archlinux.org/svntogit/community.git/plain/trunk/sympow-datafiles.patch?h=packages/sympow";
+      sha256 = "1m0vz048layb47r1jjf7fplw650ccc9x0w3l322iqmppzmv3022a";
+    })
+  ];
+
+  meta = with stdenv.lib; {
+    description = "A package to compute special values of symmetric power elliptic curve L-functions";
+    license = {
+      shortName = "sympow";
+      fullName = "Custom, BSD-like. See COPYING file.";
+      free = true;
+    };
+    maintainers = with maintainers; [ timokau ];
+    platforms = platforms.all;
+  };
+}