sage: 8.6 -> 8.7

pkgs/applications/science/math/sage/env-locations.nix

@@ -28,6 +28,7 @@ writeTextFile rec {
     export GPDOCDIR="${pari}/share/pari/doc"
     export SINGULARPATH='${singular}/share/singular'
     export SINGULAR_SO='${singular}/lib/libSingular.so'
+    export GAP_SO='${gap}/lib/libgap.so'
     export SINGULAR_EXECUTABLE='${singular}/bin/Singular'
     export MAXIMA_FAS='${maxima-ecl}/lib/maxima/${maxima-ecl.version}/binary-ecl/maxima.fas'
     export MAXIMA_PREFIX="${maxima-ecl}"

pkgs/applications/science/math/sage/patches/do-not-test-find-library.patch

@@ -0,0 +1,95 @@
+diff --git a/src/sage/env.py b/src/sage/env.py
+index 061b94f3f1..67cd091540 100644
+--- a/src/sage/env.py
++++ b/src/sage/env.py
+@@ -189,88 +189,13 @@ var('MAXIMA_FAS')
+ var('SAGE_BANNER', '')
+ var('SAGE_IMPORTALL', 'yes')
+
+-
+-def _get_shared_lib_filename(libname, *additional_libnames):
+-    """
+-    Return the full path to a shared library file installed in the standard
+-    location for the system within the ``LIBDIR`` prefix (or
+-    ``$SAGE_LOCAL/lib`` in the case of manual build of Sage).
+-
+-    This can also be passed more than one library name (e.g. for cases where
+-    some library may have multiple names depending on the platform) in which
+-    case the first one found is returned.
+-
+-    This supports most *NIX variants (in which ``lib<libname>.so`` is found
+-    under ``$SAGE_LOCAL/lib``), macOS (same, but with the ``.dylib``
+-    extension), and Cygwin (under ``$SAGE_LOCAL/bin/cyg<libname>.dll``,
+-    or ``$SAGE_LOCAL/bin/cyg<libname>-*.dll`` for versioned DLLs).
+-
+-    For distributions like Debian that use a multiarch layout, we also try the
+-    multiarch lib paths (i.e. ``/usr/lib/<arch>/``).
+-
+-    Returns ``None`` if the file does not exist.
+-
+-    EXAMPLES::
+-
+-        sage: import sys
+-        sage: from fnmatch import fnmatch
+-        sage: from sage.env import _get_shared_lib_filename
+-        sage: lib_filename = _get_shared_lib_filename("Singular",
+-        ....:                                         "singular-Singular")
+-        sage: if sys.platform == 'cygwin':
+-        ....:     pattern = "*/cygSingular-*.dll"
+-        ....: elif sys.platform == 'darwin':
+-        ....:     pattern = "*/libSingular.dylib"
+-        ....: else:
+-        ....:     pattern = "*/lib*Singular.so"
+-        sage: fnmatch(lib_filename, pattern)
+-        True
+-        sage: _get_shared_lib_filename("an_absurd_lib") is None
+-        True
+-    """
+-
+-    for libname in (libname,) + additional_libnames:
+-        if sys.platform == 'cygwin':
+-            bindir = sysconfig.get_config_var('BINDIR')
+-            pats = ['cyg{}.dll'.format(libname), 'cyg{}-*.dll'.format(libname)]
+-            filenames = []
+-            for pat in pats:
+-                filenames += glob.glob(os.path.join(bindir, pat))
+-
+-            # Note: This is not very robust, since if there are multi DLL
+-            # versions for the same library this just selects one more or less
+-            # at arbitrary.  However, practically speaking, on Cygwin, there
+-            # will only ever be one version
+-            if filenames:
+-                return filenames[-1]
+-        else:
+-            if sys.platform == 'darwin':
+-                ext = 'dylib'
+-            else:
+-                ext = 'so'
+-
+-            libdirs = [sysconfig.get_config_var('LIBDIR')]
+-            multilib = sysconfig.get_config_var('MULTILIB')
+-            if multilib:
+-                libdirs.insert(0, os.path.join(libdirs[0], multilib))
+-
+-            for libdir in libdirs:
+-                basename = 'lib{}.{}'.format(libname, ext)
+-                filename = os.path.join(libdir, basename)
+-                if os.path.exists(filename):
+-                    return filename
+-
+-    # Just return None if no files were found
+-    return None
+-
+-
+ # locate singular shared object
+ # On Debian it's libsingular-Singular so try that as well
+-SINGULAR_SO = _get_shared_lib_filename('Singular', 'singular-Singular')
++SINGULAR_SO = '/default'
+ var('SINGULAR_SO', SINGULAR_SO)
+
+ # locate libgap shared object
+-GAP_SO= _get_shared_lib_filename('gap','')
++GAP_SO= '/default'
+ var('GAP_SO', GAP_SO)
+
+ # post process

pkgs/applications/science/math/sage/patches/do-not-test-package-manifests.patch

@@ -0,0 +1,26 @@
+diff --git a/src/sage/misc/package.py b/src/sage/misc/package.py
+index 3bca15d53b..7cf04ff8d1 100644
+--- a/src/sage/misc/package.py
++++ b/src/sage/misc/package.py
+@@ -478,16 +478,16 @@ def package_manifest(package):
+
+     EXAMPLES::
+
+-        sage: from sage.misc.package import package_manifest
+-        sage: sagetex_manifest = package_manifest('sagetex')
+-        sage: sagetex_manifest['package_name'] == 'sagetex'
++        sage: from sage.misc.package import package_manifest # optional - buildsystem
++        sage: sagetex_manifest = package_manifest('sagetex') # optional - buildsystem
++        sage: sagetex_manifest['package_name'] == 'sagetex' # optional - buildsystem
+         True
+-        sage: 'files' in sagetex_manifest
++        sage: 'files' in sagetex_manifest # optional - buildsystem
+         True
+
+     Test a nonexistent package::
+
+-        sage: package_manifest('dummy-package')
++        sage: package_manifest('dummy-package') # optional - buildsystem
+         Traceback (most recent call last):
+         ...
+         KeyError: 'dummy-package'

pkgs/applications/science/math/sage/sage-src.nix

@@ -10,14 +10,14 @@
 # all get the same sources with the same patches applied.
 
 stdenv.mkDerivation rec {
-  version = "8.6";
-  name = "sage-src-${version}";
+  version = "8.7";
+  pname = "sage-src";
 
   src = fetchFromGitHub {
     owner = "sagemath";
     repo = "sage";
     rev = version;
-    sha256 = "1vs3pbgbqpg0qnwr018bqsdmm7crgjp310cx8zwh7za3mv1cw5j3";
+    sha256 = "05vvrd6syh0hlmrk6kzjrwd0hpmvxp8vr8p3mkjb0jh5p2kjdd27";
   };
 
   # Patches needed because of particularities of nix or the way this is packaged.
@@ -37,12 +37,6 @@ stdenv.mkDerivation rec {
     # https://github.com/python/cpython/pull/7476
     ./patches/python-5755-hotpatch.patch
 
-    # Revert the commit that made the sphinx build fork even in the single thread
-    # case. For some yet unknown reason, that breaks the docbuild on nix and archlinux.
-    # See https://groups.google.com/forum/#!msg/sage-packaging/VU4h8IWGFLA/mrmCMocYBwAJ.
-    # https://trac.sagemath.org/ticket/26608
-    ./patches/revert-sphinx-always-fork.patch
-
     # Make sure py2/py3 tests are only run when their expected context (all "sage"
     # tests) are also run. That is necessary to test dochtml individually. See
     # https://trac.sagemath.org/ticket/26110 for an upstream discussion.
@@ -59,6 +53,21 @@ stdenv.mkDerivation rec {
       sha256 = "07p9i0fwjgapmfvmi436yn6v60p8pvmxqjc93wsssqgh5kd8qw3n";
       stripLen = 1;
     })
+
+    # Part of the build system. Should become unnecessary with sage 8.8.
+    # Upstream discussion here: https://trac.sagemath.org/ticket/27124#comment:33
+    ./patches/do-not-test-package-manifests.patch
+
+    # Not necessary since library location is set explicitly
+    # https://trac.sagemath.org/ticket/27660#ticket
+    ./patches/do-not-test-find-library.patch
+
+    # https://trac.sagemath.org/ticket/27697#ticket
+    (fetchpatch {
+      name = "pplpy-doc-location-configurable.patch";
+      url = "https://git.sagemath.org/sage.git/patch/?h=c4d966e7cb0c7b87c55d52dc6f46518433a2a0a2";
+      sha256 = "0pqbbsx8mriwny422s9mp3z5d095cnam32sm62q4mxk8g8jb9vm9";
+    })
   ];
 
   # Since sage unfortunately does not release bugfix releases, packagers must
@@ -72,12 +81,6 @@ stdenv.mkDerivation rec {
       url = "https://git.sagemath.org/sage.git/patch?id2=10407524b18659e14e184114b61c043fb816f3c2&id=c9b0cc9d0b8748ab85e568f8f57f316c5e8cbe54";
       sha256 = "0wgp7yvn9sm1ynlhcr4l0hzmvr2n28llg4xc01p6k1zz4im64c17";
     })
-    # https://trac.sagemath.org/ticket/27224
-    (fetchpatch {
-      name = "sig_on_in_matrix_misc.patch";
-      url = "https://git.sagemath.org/sage.git/patch?id=85d25bf2eb73f7d3c6de4ee6222b0c399be43b07";
-      sha256 = "1ciwhh57pnb9b4i8m3vb07wfsibsay5sg0jp5giq1pzc5zc79a4p";
-    })
   ];
 
   # Patches needed because of package updates. We could just pin the versions of
@@ -110,52 +113,12 @@ stdenv.mkDerivation rec {
       stripLen = 1;
     })
 
-    # https://trac.sagemath.org/ticket/26315
-    ./patches/giac-1.5.0.patch
-
-    # https://trac.sagemath.org/ticket/26442
-    (fetchSageDiff {
-      name = "cypari2-2.0.3.patch";
-      base = "8.6.rc1";
-      rev = "cd62d45bcef93fb4f7ed62609a46135e6de07051";
-      sha256 = "08l2b9w0rn1zrha6188j72f7737xs126gkgmydjd31baa6367np2";
-    })
-
-    # https://trac.sagemath.org/ticket/26949
-    (fetchpatch {
-      name = "sphinx-1.8.3-dependency.patch";
-      url = "https://git.sagemath.org/sage.git/patch?id=d305eda0fedc73fdbe0447b5d6d2b520b8d112c4";
-      sha256 = "1x3q5j8lq35vlj893gj5gq9fhzs60szm9r9rx6ri79yiy9apabph";
-    })
     # https://trac.sagemath.org/ticket/26451
-    (fetchpatch {
-      name = "sphinx-1.8.3.patch";
-      url = "https://git.sagemath.org/sage.git/patch?id2=0cb494282d7b4cea50aba7f4d100e7932a4c00b1&id=62b989d5ee1d9646db85ea56053cd22e9ffde5ab";
-      sha256 = "1n5c61mvhalcr2wbp66wzsynwwk59aakvx3xqa5zw9nlkx3rd0h1";
-    })
-
-    # https://trac.sagemath.org/ticket/27061
-    (fetchpatch {
-      name = "numpy-1.16-inline-fortran.patch";
-      url = "https://git.sagemath.org/sage.git/patch?id=a05b6b038e1571ab15464e98f76d1927c0c3fd12";
-      sha256 = "05yq97pq84xi60wb1p9skrad5h5x770gq98ll4frr7hvvmlwsf58";
-    })
-
-    # https://trac.sagemath.org/ticket/27405
-    ./patches/ignore-pip-deprecation.patch
-
-    # https://trac.sagemath.org/ticket/27360
-    (fetchpatch {
-      name = "eclib-20190226.patch";
-      url = "https://git.sagemath.org/sage.git/patch/?id=f570e3a7fc2965764b84c04ce301a88ded2c42df";
-      sha256 = "0l5c4giixkn15v2a06sfzq5mkxila6l67zkjbacirwprrlpcnmmp";
-    })
-
-    # https://trac.sagemath.org/ticket/27420
-    (fetchpatch {
-      name = "cypari-2.1.patch";
-      url = "https://git.sagemath.org/sage.git/patch/?id=e351bf2f2914e683d5e2028597c45ae8d1b7f855";
-      sha256 = "00faa7fl0vaqcqbw0bidkhl78qa8l34d3a07zirbcl0vm74bdn1p";
+    (fetchSageDiff {
+      name = "sphinx-1.8.patch";
+      base = "8.7";
+      rev = "737afd8f314bd1e16feaec562bb4b5efa2effa8b";
+      sha256 = "0n56ss88ds662bp49j23z5c2i6hsn3jynxw13wv76hyl0h7l1hjh";
     })
 
     # https://trac.sagemath.org/ticket/27653
@@ -177,6 +140,12 @@ stdenv.mkDerivation rec {
     echo '#!${runtimeShell}
     python "$@"' > build/bin/sage-python23
 
+    # Make sure sage can at least be imported without setting any environment
+    # variables. It won't be close to feature complete though.
+    sed -i \
+      "s|var('SAGE_LOCAL',.*|var('SAGE_LOCAL', '$out/src')|" \
+      src/sage/env.py
+
     # Do not use sage-env-config (generated by ./configure).
     # Instead variables are set manually.
     echo '# do nothing' >  src/bin/sage-env-config

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

@@ -52,6 +52,9 @@ stdenv.mkDerivation rec {
     export HOME="$TMPDIR/sage_home"
     mkdir -p "$HOME"
 
+    # needed to link them in the sage docs using intersphinx
+    export PPLPY_DOCS=${python.pkgs.pplpy.doc}/share/doc/pplpy
+
     ${sage-with-env}/bin/sage -python -m sage_setup.docbuild \
       --mathjax \
       --no-pdf-links \