[WIP] sage: 8.9 -> 9.2

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

@@ -9,30 +9,11 @@
 let
   inherit (pkgs) symlinkJoin callPackage nodePackages;
 
-  # https://trac.sagemath.org/ticket/15980 for tracking of python3 support
-  python = pkgs.python2.override {
+  python = pkgs.python3.override {
     packageOverrides = self: super: {
-      # python packages that appear unmaintained and were not accepted into the nixpkgs
-      # tree because of that. These packages are only dependencies of the more-or-less
-      # deprecated sagenb. However sagenb is still a default dependency and the doctests
-      # depend on it.
-      # See https://github.com/NixOS/nixpkgs/pull/38787 for a discussion.
-      # The dependency on the sage notebook (and therefore these packages) will be
-      # removed in the future:
-      # https://trac.sagemath.org/ticket/25837
-      flask-oldsessions = self.callPackage ./flask-oldsessions.nix {};
-      flask-openid = self.callPackage ./flask-openid.nix {};
-      python-openid = self.callPackage ./python-openid.nix {};
-      sagenb = self.callPackage ./sagenb.nix {
-        mathjax = nodePackages.mathjax;
-      };
-
-      # Package with a cyclic dependency with sage
-      pybrial = self.callPackage ./pybrial.nix {};
-
       # `sagelib`, i.e. all of sage except some wrappers and runtime dependencies
       sagelib = self.callPackage ./sagelib.nix {
-        inherit flint ecl arb;
+        inherit flint arb;
         inherit sage-src env-locations pynac singular;
         linbox = pkgs.linbox.override { withSage = true; };
         pkg-config = pkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
@@ -59,7 +40,7 @@ let
   # A bash script setting various environment variables to tell sage where
   # the files its looking fore are located. Also see `sage-env`.
   env-locations = callPackage ./env-locations.nix {
-    inherit pari_data ecl;
+    inherit pari_data;
     inherit singular maxima-ecl;
     cysignals = python.pkgs.cysignals;
     three = nodePackages.three;
@@ -71,7 +52,7 @@ let
   sage-env = callPackage ./sage-env.nix {
     sagelib = python.pkgs.sagelib;
     inherit env-locations;
-    inherit python ecl singular palp flint pynac pythonEnv maxima-ecl;
+    inherit python singular palp flint pynac pythonEnv maxima-ecl;
     pkg-config = pkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
   };
 
@@ -102,8 +83,6 @@ let
 
   pythonRuntimeDeps = with python.pkgs; [
     sagelib
-    pybrial
-    sagenb
     cvxopt
     networkx
     service-identity
@@ -129,7 +108,6 @@ let
 
   singular = pkgs.singular.override { inherit flint; };
 
-  # https://trac.sagemath.org/ticket/26625
   maxima-ecl = pkgs.maxima-ecl;
 
   # *not* to confuse with the python package "pynac"
@@ -161,9 +139,6 @@ let
       pari-seadata-small
     ];
   };
-
-  # https://trac.sagemath.org/ticket/22191
-  ecl = pkgs.ecl_16_1_2;
 in
 # A wrapper around sage that makes sure sage finds its docs (if they were build).
 callPackage ./sage.nix {

pkgs/applications/science/math/sage/patches/Only-test-py2-py3-optional-tests-when-all-of-sage-is.patch

@@ -1,17 +1,17 @@
-From 8218bd4fdeb4c92de8af0d3aabec55980fc4fb3d Mon Sep 17 00:00:00 2001
+From f5ea42a7aaed7611fb55b65897b9fcf2b7bcf97e Mon Sep 17 00:00:00 2001
 From: Timo Kaufmann <timokau@zoho.com>
 Date: Sun, 21 Oct 2018 17:52:40 +0200
 Subject: [PATCH] Only test py2/py3 optional tests when all of sage is tested
 
 ---
- src/sage/doctest/control.py | 5 +++--
- 1 file changed, 3 insertions(+), 2 deletions(-)
+ src/sage/doctest/control.py | 3 ++-
+ 1 file changed, 2 insertions(+), 1 deletion(-)
 
 diff --git a/src/sage/doctest/control.py b/src/sage/doctest/control.py
-index bf18df8b2b..935c67abf7 100644
+index 2d93841e50..6d156e29a1 100644
 --- a/src/sage/doctest/control.py
 +++ b/src/sage/doctest/control.py
-@@ -362,7 +362,8 @@ class DocTestController(SageObject):
+@@ -375,7 +375,8 @@ class DocTestController(SageObject):
                      if not optionaltag_regex.search(o):
                          raise ValueError('invalid optional tag {!r}'.format(o))
 
@@ -21,15 +21,6 @@ index bf18df8b2b..935c67abf7 100644
 
          self.options = options
 
-@@ -765,7 +766,7 @@ class DocTestController(SageObject):
-             sage: DC = DocTestController(DD, [dirname])
-             sage: DC.expand_files_into_sources()
-             sage: sorted(DC.sources[0].options.optional)  # abs tol 1
--            ['guava', 'magma', 'py2']
-+            ['guava', 'magma']
-
-         We check that files are skipped appropriately::
-
 -- 
-2.18.1
+2.28.0
 

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

@@ -1,17 +1,17 @@
 diff --git a/src/sage/env.py b/src/sage/env.py
-index 061b94f3f1..67cd091540 100644
+index 1ddfc7cfb9..45033d6328 100644
 --- a/src/sage/env.py
 +++ b/src/sage/env.py
-@@ -189,88 +189,13 @@ var('MAXIMA_FAS')
+@@ -203,97 +203,13 @@ var('ARB_LIBRARY',                   'arb')
  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
--    ``$SAGE_LOCAL/lib`` in the case of manual build of Sage).
+-    Return the full path to a shared library file installed in
+-    ``$SAGE_LOCAL/lib`` or the directories associated with the
+-    Python sysconfig.
 -
 -    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
@@ -25,7 +25,7 @@ index 061b94f3f1..67cd091540 100644
 -    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.
+-    This returns ``None`` if the file does not exist.
 -
 -    EXAMPLES::
 -
@@ -48,11 +48,17 @@ index 061b94f3f1..67cd091540 100644
 -
 -    for libname in (libname,) + additional_libnames:
 -        if sys.platform == 'cygwin':
--            bindir = sysconfig.get_config_var('BINDIR')
+-            # Later down we take the last matching DLL found, so search
+-            # SAGE_LOCAL second so that it takes precedence
+-            bindirs = [
+-                sysconfig.get_config_var('BINDIR'),
+-                os.path.join(SAGE_LOCAL, 'bin')
+-            ]
 -            pats = ['cyg{}.dll'.format(libname), 'cyg{}-*.dll'.format(libname)]
 -            filenames = []
--            for pat in pats:
--                filenames += glob.glob(os.path.join(bindir, pat))
+-            for bindir in bindirs:
+-                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
@@ -66,10 +72,13 @@ index 061b94f3f1..67cd091540 100644
 -            else:
 -                ext = 'so'
 -
--            libdirs = [sysconfig.get_config_var('LIBDIR')]
+-            libdirs = [
+-                os.path.join(SAGE_LOCAL, 'lib'),
+-                sysconfig.get_config_var('LIBDIR')
+-            ]
 -            multilib = sysconfig.get_config_var('MULTILIB')
 -            if multilib:
--                libdirs.insert(0, os.path.join(libdirs[0], multilib))
+-                libdirs.insert(1, os.path.join(libdirs[0], multilib))
 -
 -            for libdir in libdirs:
 -                basename = 'lib{}.{}'.format(libname, ext)
@@ -89,7 +98,7 @@ index 061b94f3f1..67cd091540 100644
 
  # locate libgap shared object
 -GAP_SO= _get_shared_lib_filename('gap','')
-+GAP_SO= '/default'
++GAP_SO = '/default'
  var('GAP_SO', GAP_SO)
 
  # post process

pkgs/applications/science/math/sage/patches/ignore-cmp-deprecation.patch

@@ -1,24 +1,24 @@
 diff --git a/src/sage/tests/cmdline.py b/src/sage/tests/cmdline.py
-index bd6b76ab82..ccf1203dec 100644
+index 6e034dcb5a..8ec60ec72b 100644
 --- a/src/sage/tests/cmdline.py
 +++ b/src/sage/tests/cmdline.py
-@@ -837,8 +837,6 @@ def test_executable(args, input="", timeout=100.0, **kwds):
+@@ -660,8 +660,8 @@ def test_executable(args, input="", timeout=100.0, pydebug_ignore_warnings=False
+         sage: with open(input, 'w') as F:
+         ....:     _ = F.write(s)
+         sage: L = ["sage", "--rst2ipynb", input, output]
+-        sage: test_executable(L)                              # optional - rst2ipynb
+-        ('', '', 0)
++        sage: test_executable(L)[2]                           # optional - rst2ipynb
++        0
+         sage: import json                                     # optional - rst2ipynb
+         sage: d = json.load(open(output,'r'))                 # optional - rst2ipynb
+         sage: type(d)                                         # optional - rst2ipynb
+@@ -757,8 +757,6 @@ def test_executable(args, input="", timeout=100.0, pydebug_ignore_warnings=False
          ///
          4
          }}}
--        sage: err # py2
+-        sage: err # py2 # optional -- sagenb
 -        ''
-         sage: ret
+         sage: ret # py2 # optional -- sagenb
          0
 
-@@ -871,8 +869,8 @@ def test_executable(args, input="", timeout=100.0, **kwds):
-         sage: output = tmp_filename(ext='.sws')
-         sage: with open(input, 'w') as F:
-         ....:     _ = F.write(s)
--        sage: test_executable(["sage", "--rst2sws", input, output]) # py2
--        ('', '', 0)
-+        sage: test_executable(["sage", "--rst2sws", input, output])[2] # py2
-+        0
-         sage: import tarfile # py2
-         sage: f = tarfile.open(output, 'r') # py2
-         sage: print(f.extractfile('sage_worksheet/worksheet.html').read()) # py2