Merge pull request #31298 from timokau/sage-fix

sage: 6.8 -> 8.0

lib/maintainers.nix

@@ -628,6 +628,7 @@
   ThomasMader = "Thomas Mader <thomas.mader@gmail.com>";
   thoughtpolice = "Austin Seipp <aseipp@pobox.com>";
   timbertson = "Tim Cuthbertson <tim@gfxmonk.net>";
+  timokau = "Timo Kaufmann <timokau@zoho.com>";
   titanous = "Jonathan Rudenberg <jonathan@titanous.com>";
   tnias = "Philipp Bartsch <phil@grmr.de>";
   tohl = "Tomas Hlavaty <tom@logand.com>";

pkgs/applications/science/math/sage/default.nix

@@ -1,42 +1,183 @@
-{ stdenv, fetchurl, m4, perl, gfortran, texlive, ffmpeg, tk, gnused_422
+# TODO
-, imagemagick, liblapack, python, openssl, libpng 
+# - consider writing a script to convert spkgs to nix packages, similar to vim
+#   or cabal2nix. This would allow a more efficient and "cleaner" build, greater
+#   flexibility and the possibility to select which dependencies to add and which
+#   to remove. It would also allow to use system packages for some dependencies
+#   and recompile others (optimized for the system) without recompiling everything.
+# - add optdeps:
+#   - imagemagick
+#   - texlive full for documentation
+#   - ...
+# - further seperate build outputs. Also maybe run `make doc`.
+#   Configure flags like --bindir and --libdir oculd also be used for that, see
+#   ./configure --help`.
+
+# Other resources:
+# - https://wiki.debian.org/DebianScience/Sage
+# - https://github.com/cschwan/sage-on-gentoo
+# - https://git.archlinux.org/svntogit/community.git/tree/trunk?h=packages/sagemath
+
+{ stdenv
+, fetchurl
+, perl
+, gfortran
+, python
+, autoreconfHook
+, gettext
 , which
+, texlive
+, hevea
 }:
 
 stdenv.mkDerivation rec {
-  name = "sage-6.8";
+  version = "8.0";
+  name = "sage-${version}";
 
   src = fetchurl {
-    url = "http://old.files.sagemath.org/src-old/${name}.tar.gz";
+    # Note that the source is *not* fetched from github, since that doesn't
-    sha256 = "102mrzzi215g1xn5zgcv501x9sghwg758jagx2jixvg1rj2jijj9";
+    # the upstream folder with all the source tarballs of the spkgs.
-
+    # If those are not present they are fetched at build time, which breaks
+    # when building in a sandbox (and probably only works if you install the
+    # latest sage version).
+    urls = [
+      "http://mirrors.mit.edu/sage/src/sage-${version}.tar.gz"
+      "ftp://ftp.fu-berlin.de/unix/misc/sage/src/sage-${version}.tar.gz"
+      "http://sagemath.polytechnic.edu.na/src/sage-${version}.tar.gz"
+      "ftp://ftp.sun.ac.za/pub/mirrors/www.sagemath.org/src/sage-${version}.tar.gz"
+      "http://sagemath.mirror.ac.za/src/sage-${version}.tar.gz"
+      "http://ftp.leg.uct.ac.za/pub/packages/sage/src/sage-${version}.tar.gz"
+      "http://mirror.ufs.ac.za/sagemath/src/sage-${version}.tar.gz"
+      "http://mirrors-usa.go-parts.com/sage/sagemath/src/sage-${version}.tar.gz"
+      "http://www.cecm.sfu.ca/sage/src/sage-${version}.tar.gz"
+      "http://files.sagemath.org/src/sage-${version}.tar.gz"
+      "http://mirrors.xmission.com/sage/src/sage-${version}.tar.gz"
+      "http://sagemath.c3sl.ufpr.br/src/sage-${version}.tar.gz"
+      "http://linorg.usp.br/sage/src/sage-${version}.tar.gz"
+      "http://mirror.hust.edu.cn/sagemath/src/sage-${version}.tar.gz"
+      "http://ftp.iitm.ac.in/sage/src/sage-${version}.tar.gz"
+      "http://ftp.kaist.ac.kr/sage/src/sage-${version}.tar.gz"
+      "http://ftp.riken.jp/sagemath/src/sage-${version}.tar.gz"
+      "http://mirrors.tuna.tsinghua.edu.cn/sagemath/src/sage-${version}.tar.gz"
+      "http://mirrors.ustc.edu.cn/sagemath/src/sage-${version}.tar.gz"
+      "http://ftp.tsukuba.wide.ad.jp/software/sage/src/sage-${version}.tar.gz"
+      "http://ftp.yz.yamagata-u.ac.jp/pub/math/sage/src/sage-${version}.tar.gz"
+      "http://mirror.yandex.ru/mirrors/sage.math.washington.edu/src/sage-${version}.tar.gz"
+      "http://mirror.aarnet.edu.au/pub/sage/src/sage-${version}.tar.gz"
+      "http://sage.mirror.garr.it/mirrors/sage/src/sage-${version}.tar.gz"
+      "http://www.mirrorservice.org/sites/www.sagemath.org/src/sage-${version}.tar.gz"
+      "http://mirror.switch.ch/mirror/sagemath/src/sage-${version}.tar.gz"
+      "https://mirrors.up.pt/pub/sage/src/sage-${version}.tar.gz"
+      "http://www-ftp.lip6.fr/pub/math/sagemath/src/sage-${version}.tar.gz"
+      "http://ftp.ntua.gr/pub/sagemath/src/sage-${version}.tar.gz"
+    ];
+    sha256 = "1a9rhb8jby6fdqa2s7n2fl9jwqqlsl7qz7dbpbwvg6jwlrvni7fg";
   };
 
-  buildInputs = [ m4 perl gfortran texlive.combined.scheme-basic ffmpeg gnused_422 tk imagemagick liblapack
+  postPatch = ''
-                  python openssl libpng which ];
+    substituteAllInPlace src/bin/sage-env
+  '';
 
-  patches = [ ./spkg-singular.patch ./spkg-python.patch ./spkg-git.patch ];
+  installPhase = ''
+    # Sage installs during first `make`, `make install` is no-op and just takes time.
+  '';
+
+  outputs = [ "out" "doc" ];
+
+  buildInputs = [
+    perl # needed for the build
+    python # needed for the build
+    gfortran # needed to build giac
+    autoreconfHook # needed to configure sage with prefix
+    gettext # needed to build the singular spkg
+    hevea # needed to build the docs of the giac spkg
+    which # needed in configure of mpir
+    # needed to build the docs of the giac spkg
+    (texlive.combine { inherit (texlive)
+      scheme-basic
+      collection-pstricks # needed by giac
+      times # font needed by giac
+      stmaryrd # needed by giac
+      babel-greek # optional for giac, otherwise throws a bunch of latex command not founds
+      ;
+    })
+  ];
+
+  patches = [
+    # fix usages of /bin/rm
+    ./spkg-singular.patch
+    # help python find the crypt library
+    ./spkg-python2.patch
+    ./spkg-python3.patch
+    # fix usages of /usr/bin/perl
+    ./spkg-git.patch
+    # fix usages of /bin/cp and add necessary argument to function call
+    ./spkg-giac.patch
+    # environment
+    ./env.patch
+  ];
 
   enableParallelBuilding = true;
 
-  hardeningDisable = [ "format" ];
+  hardeningDisable = [
+    "format" # needed to build palp, for lines like `printf(ctime(&_NFL->TIME))`
+    # TODO could be patched with `sed s|printf(ctime(\(.*\)))|%s... or fixed upstream
+  ];
 
   preConfigure = ''
     export SAGE_NUM_THREADS=$NIX_BUILD_CORES
     export SAGE_ATLAS_ARCH=fast
-    mkdir -p $out/sageHome
+
-    export HOME=$out/sageHome
+    export HOME=$out/sage-home
-    export CPPFLAGS="-P"
+    mkdir -p $out/sage-home
+
+    mkdir -p "$out"
+
+    # we need to keep the source around
+    dir="$PWD"
+    cd ..
+    mv "$dir" "$out/sage-root"
+
+    cd "$out/sage-root" # build in target dir, since `make` is also `make install`
   '';
 
-  preBuild = "patchShebangs build";
+  # for reference: http://doc.sagemath.org/html/en/installation/source.html
+  preBuild = ''
+    # TODO do this conditionally
+    export SAGE_SPKG_INSTALL_DOCS='no'
+    patchShebangs build
+  '';
 
-  installPhase = ''DESTDIR=$out make install'';
+  postBuild = ''
+    rm -r "$out/sage-root/upstream" # don't keep the sources of all the spkgs
+    rm -r "$out/sage-root/src/build"
+    rm -rf "$out/sage-root/src/.git"
+    rm -r "$out/sage-root/logs"
+    # Fix dependency cycle between out and doc
+    rm -f "$out/sage-root/config.status"
+    rm -f "$out/sage-root/build/make/Makefile-auto"
+    rm -f "$out/sage-home/.sage/gap/libgap-workspace-"*
+  '';
+
+  # TODO there are some doctest failures, which seem harmless.
+  # We should figure out a way to fix the failures or ignore only those tests.
+  doCheck = false;
+
+  checkTarget = "ptestalllong"; # all long tests in parallell
+  preCheck = ''
+    export SAGE_TIMEOUT=0 # no timeout
+    export SAGE_TIMEOUT_LONG=0 # no timeout
+  '';
 
   meta = {
     homepage = http://www.sagemath.org;
     description = "A free open source mathematics software system";
+    # taken from the homepage
+    longDescription = ''
+      SageMath is a free open-source mathematics software system licensed under the GPL. It builds on top of many existing open-source packages: NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R and many more. Access their combined power through a common, Python-based language or directly via interfaces or wrappers.
+      Mission: Creating a viable free open source alternative to Magma, Maple, Mathematica and Matlab.
+    '';
     license = stdenv.lib.licenses.gpl2Plus;
-    broken = true;
+    platforms = stdenv.lib.platforms.linux;
+    maintainers = with stdenv.lib.maintainers; [ timokau ];
   };
 }

pkgs/applications/science/math/sage/env.patch

@@ -0,0 +1,22 @@
+diff --git a/src/bin/sage-env b/src/bin/sage-env
+index ead308f861..ed8db9f9b7 100644
+--- a/src/bin/sage-env
++++ b/src/bin/sage-env
+@@ -111,6 +111,8 @@ resolvelinks() {
+ }
+ 
+ 
++SAGE_ROOT="@out@/sage-root"
++
+ # New value for SAGE_ROOT: either SAGE_ROOT (if given)
+ # or a guessed value based on pwd.
+ if [ -n "$SAGE_ROOT" ]; then
+@@ -185,6 +187,8 @@ fi
+ export SAGE_ENV_SOURCED=$SAGE_ENV_VERSION
+ 
+ export SAGE_ROOT="$NEW_SAGE_ROOT"
++export SAGE_LOCAL='@out@/'
++export PYTHONPATH="@out@/lib/python2.7/site-packages:$PYTHONPATH"
+ 
+ 
+ # sage-env must know where the Sage's script files are.

pkgs/applications/science/math/sage/fetch-mirrors.sh

@@ -0,0 +1,11 @@
+#! /usr/bin/env nix-shell
+#! nix-shell -i bash -p curl go-pup
+
+# Fetches a list of all available source mirrors from the sage homepage.
+# Note that the list is sorted by country, but fetchurl doesn't offer an option
+# to customize mirror preference.
+
+curl -s http://www.sagemath.org/download-source.html \
+    | pup 'table#mirror'  \
+    | pup 'a attr{href}' \
+    | sed -e 's/index\.html/sage-${version}.tar.gz/'

pkgs/applications/science/math/sage/spkg-giac.patch

@@ -0,0 +1,11 @@
+--- old/build/pkgs/giac/spkg-install	2017-07-21 14:10:00.000000000 -0500
++++ new/build/pkgs/giac/spkg-install	2017-10-15 15:55:55.321237645 -0500
+@@ -4,6 +4,8 @@
+ ## Giac
+ ###########################################
+ 
++find . -type f -exec sed -e 's@/bin/cp@cp@g' -i '{}' ';' && echo "Patching input parser" && find . -iname 'input_parser.cc'
++sed -e 's@yylex (&yylval)@yylex (\&yyval, scanner)@gp' -i 'src/src/input_parser.cc'
+ 
+ if [ "$SAGE_LOCAL" = "" ]; then
+    echo "SAGE_LOCAL undefined ... exiting";

pkgs/applications/science/math/sage/spkg-git.patch

@@ -1,10 +1,12 @@
---- old/build/pkgs/git/spkg-install	2015-07-26 15:34:43.000000000 +0200
+diff --git a/build/pkgs/git/spkg-install b/build/pkgs/git/spkg-install
-+++ new/build/pkgs/git/spkg-install	2015-09-17 08:28:03.586657451 +0200
+index 8469cb58c2..d0dc9a1db9 100755
-@@ -45,6 +45,8 @@
+--- a/build/pkgs/git/spkg-install
-     fi
++++ b/build/pkgs/git/spkg-install
- done
+@@ -35,6 +35,8 @@ fi
  
-+find . -exec sed -e 's@/usr/bin/perl@perl@g' -i '{}' ';'
+ cd src
+ 
++find . -type f -exec sed -e 's@/usr/bin/perl@perl@g' -i '{}' ';'
 +
  # We don't want to think about Fink or Macports
  export NO_FINK=1

pkgs/applications/science/math/sage/spkg-python.patch

@@ -1,11 +0,0 @@
---- old/build/pkgs/python2/spkg-install	2015-07-26 15:34:43.000000000 +0200
-+++ new/build/pkgs/python2/spkg-install	2015-09-16 20:48:51.904555797 +0200
-@@ -32,7 +32,7 @@
- done
- 
- # We are setting LDFLAGS so that we pick up Sage's readline
--LDFLAGS="-L$SAGE_LOCAL/lib $LDFLAGS"
-+LDFLAGS="-L$SAGE_LOCAL/lib -lcrypt $LDFLAGS"
- export LDFLAGS
- 
- if [ "$SAGE_DEBUG" = "yes" ]; then

pkgs/applications/science/math/sage/spkg-python2.patch

@@ -0,0 +1,12 @@
+--- old/build/pkgs/python2/spkg-install	2017-07-21 14:10:00.000000000 -0500
++++ new/build/pkgs/python2/spkg-install	2017-10-15 11:26:54.823134067 -0500
+@@ -22,6 +22,9 @@
+ 
+ cd src
+ 
++LDFLAGS="-lcrypt $LDFLAGS"
++export LDFLAGS
++
+ if [ "$SAGE_DEBUG" = "yes" ]; then
+     echo "Building Python with pydebug"
+     PYTHON_CONFIGURE="$PYTHON_CONFIGURE --with-pydebug"

pkgs/applications/science/math/sage/spkg-python3.patch

@@ -0,0 +1,12 @@
+--- old/build/pkgs/python3/spkg-install	2017-07-21 14:10:00.000000000 -0500
++++ new/build/pkgs/python3/spkg-install	2017-10-15 13:11:17.769261404 -0500
+@@ -22,6 +22,9 @@
+ 
+ cd src
+ 
++LDFLAGS="-lcrypt $LDFLAGS"		
++export LDFLAGS
++
+ if [ "$SAGE_DEBUG" = "yes" ]; then
+     echo "Building Python with pydebug"
+     PYTHON_CONFIGURE="$PYTHON_CONFIGURE --with-pydebug"

pkgs/applications/science/math/sage/spkg-singular.patch

@@ -1,28 +1,12 @@
---- old/build/pkgs/singular/spkg-install	2015-07-26 15:34:43.000000000 +0200
+--- old/build/pkgs/singular/spkg-install	2017-10-15 10:35:41.826540964 -0500
-+++ new/build/pkgs/singular/spkg-install	2015-09-15 20:42:51.716505855 +0200
++++ new/build/pkgs/singular/spkg-install	2017-10-15 10:36:40.613743443 -0500
-@@ -115,6 +115,11 @@
+@@ -4,6 +4,9 @@
-     done
+ ## Singular
- }
+ ###########################################
  
-+nix_nuke_bin_rm()
++find . -type f -exec sed -e 's@/bin/rm@rm@g' -i '{}' ';'
-+{
++#echo '#!/usr/bin/env bash\nIgnoring missing $1' > src/build-aux/missing
-+    find . -exec sed -e 's@/bin/rm@rm@g' -i '{}' ';'
-+}
 +
- remove_old_version()
+ if [ -z "$SAGE_LOCAL" ]; then
- {
+     echo >&2 "Error: SAGE_LOCAL undefined -- exiting..."
-     rm -f "$SAGE_LOCAL"/bin/Singular*
+     echo >&2 "Maybe run 'sage -sh'?"
-@@ -306,11 +311,11 @@
- 
- 
- # Actually run all the functions defined above
--for i in choose_patches apply_patches remove_old_version config \
-+for i in choose_patches apply_patches nix_nuke_bin_rm remove_old_version config \
-   build_singular build_libsingular build_factory build_libfac \
-   create_singular_script install_docs ; do
-     echo "### Singular spkg-install: $i ###"
--    cd "$SRC" && $i
-+    cd "$SRC" && pwd && $i
-     if [ $? -ne 0 ]; then
-         echo >&2 "Error building Singular (error in $i)."
-         exit 1