sage: 8.8 -> 8.9

pkgs/applications/science/math/sage/patches/sphinx-docbuild-subprocesses.patch

@@ -1,8 +1,8 @@
 diff --git a/src/sage_setup/docbuild/__init__.py b/src/sage_setup/docbuild/__init__.py
-index 0f2700168a..60f71357d2 100644
+index 73a078e619..059125c59f 100644
 --- a/src/sage_setup/docbuild/__init__.py
 +++ b/src/sage_setup/docbuild/__init__.py
-@@ -86,26 +86,6 @@ def builder_helper(type):
+@@ -86,27 +86,6 @@ def builder_helper(type):
      """
      Returns a function which builds the documentation for
      output type ``type``.
@@ -19,7 +19,8 @@ index 0f2700168a..60f71357d2 100644
 -        ....:     raise BaseException("abort pool operation")
 -        sage: original_runsphinx, sage_setup.docbuild.sphinxbuild.runsphinx = sage_setup.docbuild.sphinxbuild.runsphinx, raiseBaseException
 -
--        sage: from sage_setup.docbuild import builder_helper, build_many, build_ref_doc
+-        sage: from sage_setup.docbuild import builder_helper, build_ref_doc
+-        sage: from sage_setup.docbuild import _build_many as build_many
 -        sage: helper = builder_helper("html")
 -        sage: try:
 -        ....:     build_many(build_ref_doc, [("docname", "en", "html", {})])
@@ -29,7 +30,7 @@ index 0f2700168a..60f71357d2 100644
      """
      def f(self, *args, **kwds):
          output_dir = self._output_dir(type)
-@@ -127,10 +107,9 @@ def builder_helper(type):
+@@ -128,10 +107,9 @@ def builder_helper(type):
          logger.debug(build_command)
 
          # Run Sphinx with Sage's special logger
@@ -43,10 +44,10 @@ index 0f2700168a..60f71357d2 100644
              if ABORT_ON_ERROR:
                  raise
 diff --git a/src/sage_setup/docbuild/sphinxbuild.py b/src/sage_setup/docbuild/sphinxbuild.py
-index 9a2fba79bc..77c8ed3592 100644
+index fe7eba43b2..463790965c 100644
 --- a/src/sage_setup/docbuild/sphinxbuild.py
 +++ b/src/sage_setup/docbuild/sphinxbuild.py
-@@ -318,3 +318,8 @@ def runsphinx():
+@@ -321,3 +321,8 @@ def runsphinx():
          sys.stderr = saved_stderr
          sys.stdout.flush()
          sys.stderr.flush()

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 = "8.8";
+  version = "8.9";
   pname = "sage-src";
 
   src = fetchFromGitHub {
     owner = "sagemath";
     repo = "sage";
     rev = version;
-    sha256 = "0jm7zdkz8wfgrmf6620jfr8kgvprrz3qfl8gzx6rl5z5cm734b6x";
+    sha256 = "1bwga58x3s8z42w5h51c232f91ndsc1861dlb1glhax3pn0rhn3a";
   };
 
   # Patches needed because of particularities of nix or the way this is packaged.
@@ -49,10 +49,6 @@ stdenv.mkDerivation rec {
     # https://trac.sagemath.org/ticket/27660#ticket
     ./patches/do-not-test-find-library.patch
 
-
-    # https://trac.sagemath.org/ticket/28007
-    ./patches/threejs-offline.patch
-
     # Parallelize docubuild using subprocesses, fixing an isolation issue. See
     # https://groups.google.com/forum/#!topic/sage-packaging/YGOm8tkADrE
     ./patches/sphinx-docbuild-subprocesses.patch
@@ -97,14 +93,6 @@ stdenv.mkDerivation rec {
       stripLen = 1;
     })
 
-    # https://trac.sagemath.org/ticket/26932
-    (fetchSageDiff {
-      name = "givaro-4.1.0_fflas-ffpack-2.4.0_linbox-1.6.0.patch";
-      base = "8.8.beta4";
-      rev = "c11d9cfa23ff9f77681a8f12742f68143eed4504";
-      sha256 = "0xzra7mbgqvahk9v45bjwir2mqz73hrhhy314jq5nxrb35ysdxyi";
-    })
-
     # After updating smypow to (https://trac.sagemath.org/ticket/3360) we can
     # now set the cache dir to be withing the .sage directory. This is not
     # strictly necessary, but keeps us from littering in the user's HOME.

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

@@ -138,8 +138,8 @@ buildPythonPackage rec {
     mkdir -p "$SAGE_SHARE/sage/ext/notebook-ipython"
     mkdir -p "var/lib/sage/installed"
 
+    source build/bin/sage-dist-helpers
     cd src
-    source bin/sage-dist-helpers
 
     ${python.interpreter} -u setup.py --no-user-cfg build
   '';

pkgs/development/libraries/science/math/lcalc/makefile.patch

@@ -104,10 +104,10 @@ index 84e4e88..56ca676 100644
 -	cp -rf ../include $(INSTALL_DIR)/include/Lfunction
 +	install -d $(INSTALL_DIR)/bin
 +	install -d $(INSTALL_DIR)/$(LIB_DIR)
-+	install -d $(INSTALL_DIR)/include/libLfunction
++	install -d $(INSTALL_DIR)/include/Lfunction
 +	install lcalc $(INSTALL_DIR)/bin
 +	install libLfunction.so $(INSTALL_DIR)/$(LIB_DIR)
-+	install -m 644 -t $(INSTALL_DIR)/include/libLfunction ../include/*.h
++	install -m 644 -t $(INSTALL_DIR)/include/Lfunction ../include/*.h
 
 
  SRCS = Lcommandline.cc Lcommandline_elliptic.cc Lcommandline_globals.cc Lcommandline_misc.cc Lcommandline_numbertheory.cc Lcommandline_twist.cc Lcommandline_values_zeros.cc Lgamma.cc Lglobals.cc Lmisc.cc Lriemannsiegel.cc Lriemannsiegel_blfi.cc cmdline.c