sage: 8.0 -> 8.1, fix sandbox build

The sandboxed build was failing, because it relied heavily on
/usr/bin/env. This is fixed with a lot of shebang patching (both
to system packages and to sage-internal packages).

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

@@ -18,6 +18,7 @@
 # - https://git.archlinux.org/svntogit/community.git/tree/trunk?h=packages/sagemath
 
 { stdenv
+, bash
 , fetchurl
 , perl
 , gfortran
@@ -26,13 +27,17 @@
 , gettext
 , which
 , texlive
+, texinfo
 , hevea
 }:
 
 stdenv.mkDerivation rec {
-  version = "8.0";
+  version = "8.1";
   name = "sage-${version}";
 
+  # Modified version of patchShebangs that patches to the sage-internal version if possible
+  # and falls back to the system version if not.
+  patchSageShebangs = ./patchSageShebangs.sh;
   src = fetchurl {
     # Note that the source is *not* fetched from github, since that doesn't
     # the upstream folder with all the source tarballs of the spkgs.
@@ -70,11 +75,12 @@ stdenv.mkDerivation rec {
       "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";
+    sha256 = "1cpcs1mr0yii64s152xmxyd450bfzjb22jjj0zh9y3n6g9alzpyq";
   };
 
   postPatch = ''
     substituteAllInPlace src/bin/sage-env
+    bash=${bash} substituteAllInPlace build/bin/sage-spkg
   '';
 
   installPhase = ''
@@ -84,14 +90,16 @@ stdenv.mkDerivation rec {
   outputs = [ "out" "doc" ];
 
   buildInputs = [
+    bash # needed for the build
     perl # needed for the build
     python # needed for the build
-    gfortran # needed to build giac
+    gfortran # needed to build giac, openblas
     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
+    texinfo # needed to build maxima
     (texlive.combine { inherit (texlive)
       scheme-basic
       collection-pstricks # needed by giac
@@ -102,18 +110,22 @@ stdenv.mkDerivation rec {
     })
   ];
 
+  nativeBuildInputs = [ gfortran perl which ];
+
   patches = [
     # fix usages of /bin/rm
     ./spkg-singular.patch
     # help python find the crypt library
-    ./spkg-python2.patch
-    ./spkg-python3.patch
+    # patches python3 and indirectly python2, since those installation files are symlinked
+    ./spkg-python.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
+    # adjust wrapper shebang and patch shebangs after each spkg build
+    ./shebangs.patch
   ];
 
   enableParallelBuilding = true;
@@ -144,7 +156,14 @@ stdenv.mkDerivation rec {
   preBuild = ''
     # TODO do this conditionally
     export SAGE_SPKG_INSTALL_DOCS='no'
-    patchShebangs build
+    # symlink python to make sure the shebangs are patched to the sage path
+    # while still being able to use python before building it
+    # (this is important because otherwise sage will try to install python
+    # packages globally later on)
+    ln -s "${python}/bin/python2" $out/bin/python2
+    ln -s "$out/bin/python2" $out/bin/python
+    touch $out/bin/python3
+    bash $patchSageShebangs .
   '';
 
   postBuild = ''
@@ -153,9 +172,12 @@ stdenv.mkDerivation rec {
     rm -rf "$out/sage-root/src/.git"
     rm -r "$out/sage-root/logs"
     # Fix dependency cycle between out and doc
+    rm -f "$out/sage-root/config.log"
     rm -f "$out/sage-root/config.status"
     rm -f "$out/sage-root/build/make/Makefile-auto"
     rm -f "$out/sage-home/.sage/gap/libgap-workspace-"*
+    # Make sure all shebangs are properly patched
+    bash $patchSageShebangs $out
   '';
 
   # TODO there are some doctest failures, which seem harmless.

pkgs/applications/science/math/sage/patchSageShebangs.sh

@@ -0,0 +1,51 @@
+# This is a slightly modified version of nix's default patchShebangs
+
+dir="$1"
+
+echo "patching sage internal script interpreter paths in $( readlink -f "$dir")"
+
+find "$dir" -type f -perm -0100 | while read f; do
+    if [ "$(head -1 "$f" | head -c+2)" != '#!' ]; then
+        # missing shebang => not a script
+        continue
+    fi
+
+    oldInterpreterLine=$(head -1 "$f" | tail -c+3)
+    read -r oldPath arg0 args <<< "$oldInterpreterLine"
+
+    if $(echo "$oldPath" | grep -q "/bin/env$"); then
+        # Check for unsupported 'env' functionality:
+        # - options: something starting with a '-'
+        # - environment variables: foo=bar
+        if $(echo "$arg0" | grep -q -- "^-.*\|.*=.*"); then
+            echo "unsupported interpreter directive \"$oldInterpreterLine\" (set dontPatchShebangs=1 and handle shebang patching yourself)"
+            exit 1
+        fi
+        executable="$arg0"
+    else
+        if [ "$oldPath" = "" ]; then
+            # If no interpreter is specified linux will use /bin/sh. Set
+            # oldpath="/bin/sh" so that we get /nix/store/.../sh.
+            oldPath="/bin/sh"
+        fi
+        executable="$(basename "$oldPath")"
+        args="$arg0 $args"
+    fi
+
+    newPath="$(echo "$out/bin/$executable $args" | sed 's/[[:space:]]*$//')"
+    if [[ ! -x "$newPath" ]] ; then
+        newPath="$(command -v "$executable" || true)"
+    fi
+
+    # Strip trailing whitespace introduced when no arguments are present
+    newInterpreterLine="$(echo "$newPath $args" | sed 's/[[:space:]]*$//')"
+
+    if [ -n "$oldPath" -a "${oldPath:0:${#NIX_STORE}}" != "$NIX_STORE" ]; then
+        if [ -n "$newPath" -a "$newPath" != "$oldPath" ]; then
+            echo "$f: sage interpreter directive changed from \"$oldInterpreterLine\" to \"$newInterpreterLine\""
+            # escape the escape chars so that sed doesn't interpret them
+            escapedInterpreterLine=$(echo "$newInterpreterLine" | sed 's|\\|\\\\|g')
+            sed -i -e "1 s|.*|#\!$escapedInterpreterLine|" "$f"
+        fi
+    fi
+done

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

@@ -0,0 +1,36 @@
+diff --git a/build/bin/sage-spkg b/build/bin/sage-spkg
+index 83e61a7e0d..942ba206c7 100755
+--- a/build/bin/sage-spkg
++++ b/build/bin/sage-spkg
+@@ -648,8 +648,12 @@ if ! sage-apply-patches; then
+     error_msg "Error applying patches"
+     exit 1
+ fi
++
++@bash@/bin/bash @patchSageShebangs@ .
++
+ cd ..
+ 
++
+ ##################################################################
+ # The package has been extracted, prepare for installation
+ ##################################################################
+@@ -671,7 +675,7 @@ write_script_wrapper() {
+     local tmpscript="$(dirname "$script")/.tmp-${script##*/}"
+ 
+     cat > "$tmpscript" <<__EOF__
+-#!/usr/bin/env bash
++#! @bash@/bin/bash
+ 
+ export SAGE_ROOT="$SAGE_ROOT"
+ export SAGE_SRC="$SAGE_SRC"
+@@ -833,6 +837,9 @@ if [ "$UNAME" = "CYGWIN" ]; then
+     sage-rebase.sh "$SAGE_LOCAL" 2>/dev/null
+ fi
+ 
++@bash@/bin/bash @patchSageShebangs@ .
++@bash@/bin/bash @patchSageShebangs@ "$out/bin"
++
+ echo "Successfully installed $PKG_NAME"
+ 
+ if [ "$SAGE_CHECK" = "yes" ]; then

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

@@ -0,0 +1,13 @@
+diff --git a/build/pkgs/python3/spkg-build b/build/pkgs/python3/spkg-build
+index 56db087ae5..b450703c5f 100644
+--- a/build/pkgs/python3/spkg-build
++++ b/build/pkgs/python3/spkg-build
+@@ -27,6 +27,8 @@ fi
+ export EXTRA_CFLAGS="`testcflags.sh -Wno-unused` $CFLAGS"
+ unset CFLAGS
+ 
++export LDFLAGS="$LDFLAGS -lcrypt"
++
+ if [ "$UNAME" = Darwin ]; then
+     PYTHON_CONFIGURE="--disable-toolbox-glue $PYTHON_CONFIGURE"
+ 

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

@@ -1,12 +0,0 @@
---- 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

@@ -1,12 +0,0 @@
---- 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"