Merge pull request #105615 from collares/sage-update

sage: 8.9 -> 9.2

36 files changed, 329 insertions, 488 deletions

diff --git a/pkgs/applications/science/math/giac/default.nix b/pkgs/applications/science/math/giac/default.nix
index ea9c921f19e1..b090274919bd 100644
--- a/pkgs/applications/science/math/giac/default.nix
+++ b/pkgs/applications/science/math/giac/default.nix
@@ -9,11 +9,11 @@ assert (!blas.isILP64) && (!lapack.isILP64);
 
 stdenv.mkDerivation rec {
   pname = "giac${lib.optionalString enableGUI "-with-xcas"}";
-  version = "1.5.0-21"; # TODO try to remove preCheck phase on upgrade
+  version = "1.5.0-87"; # TODO try to remove preCheck phase on upgrade
 
   src = fetchurl {
     url = "https://www-fourier.ujf-grenoble.fr/~parisse/debian/dists/stable/main/source/giac_${version}.tar.gz";
-    sha256 = "1b9khiv0mk2xzw1rblm2jy6qsf8y6f9k7qy15sxpb21d72hzzbl2";
+    sha256 = "1d0h1yb7qvh9x7wwv9yrzmcp712f49w1iljkxp4y6g9pzsmg1mmv";
   };
 
   patches = stdenv.lib.optionals (!enableGUI) [
diff --git a/pkgs/applications/science/math/maxima/default.nix b/pkgs/applications/science/math/maxima/default.nix
index 1bf7d16f2904..cdc81a876465 100644
--- a/pkgs/applications/science/math/maxima/default.nix
+++ b/pkgs/applications/science/math/maxima/default.nix
@@ -87,6 +87,10 @@ stdenv.mkDerivation ({
 
   enableParallelBuilding = true;
 
+  passthru = {
+    ecl = ecl;
+  };
+
   meta = {
     description = "Computer algebra system";
     homepage = "http://maxima.sourceforge.net";
diff --git a/pkgs/applications/science/math/nauty/default.nix b/pkgs/applications/science/math/nauty/default.nix
index 76e7c796a138..94b7ad266c45 100644
--- a/pkgs/applications/science/math/nauty/default.nix
+++ b/pkgs/applications/science/math/nauty/default.nix
@@ -7,7 +7,7 @@ stdenv.mkDerivation rec {
   version = "27r1";
   src = fetchurl {
     url = "http://pallini.di.uniroma1.it/nauty${version}.tar.gz";
-    sha256 = "1nym0p2djws8ylkpr0kgpxfa6fxdlh46cmvz0gn5vd02jzgs0aww";
+    sha256 = "0xsfqfcknbd6g6wzpa5l7crmmk3bf3zjh37rhylq6b20dqcmvjkn";
   };
   outputs = [ "out" "dev" ];
   configureFlags = [
diff --git a/pkgs/applications/science/math/pari/default.nix b/pkgs/applications/science/math/pari/default.nix
index a3e2f99ab274..7ec42d11ab14 100644
--- a/pkgs/applications/science/math/pari/default.nix
+++ b/pkgs/applications/science/math/pari/default.nix
@@ -15,7 +15,8 @@ stdenv.mkDerivation rec {
   version = "2.11.4";
 
   src = fetchurl {
-    url = "https://pari.math.u-bordeaux.fr/pub/pari/unix/${pname}-${version}.tar.gz";
+    # Versions with current majorMinor values are at http://pari.math.u-bordeaux.fr/pub/pari/unix/${pname}-${version}.tar.gz
+    url = "https://pari.math.u-bordeaux.fr/pub/pari/OLD/${stdenv.lib.versions.majorMinor version}/${pname}-${version}.tar.gz";
     sha256 = "sha256-v8iPxPc1L0hA5uNSxy8DacvqikVAOxg0piafNwmXCxw=";
   };
 
diff --git a/pkgs/applications/science/math/pynac/default.nix b/pkgs/applications/science/math/pynac/default.nix
index 87fb205174bf..e3474d865e2d 100644
--- a/pkgs/applications/science/math/pynac/default.nix
+++ b/pkgs/applications/science/math/pynac/default.nix
@@ -1,5 +1,6 @@
 { stdenv
 , fetchFromGitHub
+, fetchurl
 , autoreconfHook
 , pkgconfig
 , flint
@@ -33,6 +34,14 @@ stdenv.mkDerivation rec {
     pkgconfig
   ];
 
+  patches = [
+    (fetchurl {
+      name = "py_ssize_t_clean.patch";
+      url = "https://git.sagemath.org/sage.git/plain/build/pkgs/pynac/patches/py_ssize_t_clean.patch?h=9.2";
+      sha256 = "0l3gbg9hc4v671zf4w376krnk3wh8hj3649610nlvzzxckcryzab";
+    })
+  ];
+
   meta = with stdenv.lib; {
     description = "Python is Not a CAS -- modified version of Ginac";
     longDescription = ''
diff --git a/pkgs/applications/science/math/sage/default.nix b/pkgs/applications/science/math/sage/default.nix
index caf51c3da251..416f2b957b7b 100644
--- a/pkgs/applications/science/math/sage/default.nix
+++ b/pkgs/applications/science/math/sage/default.nix
@@ -9,31 +9,13 @@
 let
   inherit (pkgs) symlinkJoin callPackage nodePackages;
 
-  # https://trac.sagemath.org/ticket/15980 for tracking of python3 support
-  python = pkgs.python2.override {
+  python3 = 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;
+        ecl = maxima-ecl.ecl;
         linbox = pkgs.linbox.override { withSage = true; };
         pkg-config = pkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
       };
@@ -59,9 +41,10 @@ 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;
+    ecl = maxima-ecl.ecl;
+    cysignals = python3.pkgs.cysignals;
     three = nodePackages.three;
     mathjax = nodePackages.mathjax;
   };
@@ -69,21 +52,22 @@ let
   # The shell file that gets sourced on every sage start. Will also source
   # the env-locations file.
   sage-env = callPackage ./sage-env.nix {
-    sagelib = python.pkgs.sagelib;
+    sagelib = python3.pkgs.sagelib;
     inherit env-locations;
-    inherit python ecl singular palp flint pynac pythonEnv maxima-ecl;
+    inherit python3 singular palp flint pynac pythonEnv maxima-ecl;
+    ecl = maxima-ecl.ecl;
     pkg-config = pkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
   };
 
   # The documentation for sage, building it takes a lot of ram.
   sagedoc = callPackage ./sagedoc.nix {
     inherit sage-with-env;
-    inherit python maxima-ecl;
+    inherit python3 maxima-ecl;
   };
 
   # sagelib with added wrappers and a dependency on sage-tests to make sure thet tests were run.
   sage-with-env = callPackage ./sage-with-env.nix {
-    inherit pythonEnv;
+    inherit python3 pythonEnv;
     inherit sage-env;
     inherit pynac singular maxima-ecl;
     pkg-config = pkgs.pkgconfig; # not to confuse with pythonPackages.pkgconfig
@@ -100,10 +84,8 @@ let
 
   sage-src = callPackage ./sage-src.nix {};
 
-  pythonRuntimeDeps = with python.pkgs; [
+  pythonRuntimeDeps = with python3.pkgs; [
     sagelib
-    pybrial
-    sagenb
     cvxopt
     networkx
     service-identity
@@ -116,11 +98,10 @@ let
     ipywidgets
     rpy2
     sphinx
-    typing
     pillow
   ];
 
-  pythonEnv = python.buildEnv.override {
+  pythonEnv = python3.buildEnv.override {
     extraLibs = pythonRuntimeDeps;
     ignoreCollisions = true;
   } // { extraLibs = pythonRuntimeDeps; }; # make the libs accessible
@@ -129,8 +110,21 @@ let
 
   singular = pkgs.singular.override { inherit flint; };
 
-  # https://trac.sagemath.org/ticket/26625
-  maxima-ecl = pkgs.maxima-ecl;
+  maxima-ecl = pkgs.maxima-ecl.override {
+    ecl = pkgs.ecl.override {
+      # "echo syntax error | ecl > /dev/full 2>&1" segfaults in
+      # ECL. We apply a patch to fix it (write_error.patch), but it
+      # only works if threads are disabled.  sage 9.2 tests this
+      # (src/sage/interfaces/tests.py) and ships ecl like so.
+      # https://gitlab.com/embeddable-common-lisp/ecl/-/merge_requests/1#note_1657275
+      threadSupport = false;
+
+      # if we don't use the system boehmgc, sending a SIGINT to ecl
+      # can segfault if we it happens during memory allocation.
+      # src/sage/libs/ecl.pyx would intermittently fail in this case.
+      useBoehmgc = true;
+    };
+  };
 
   # *not* to confuse with the python package "pynac"
   pynac = pkgs.pynac.override { inherit singular flint; };
@@ -161,9 +155,6 @@ 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 {
diff --git a/pkgs/applications/science/math/sage/env-locations.nix b/pkgs/applications/science/math/sage/env-locations.nix
index bda2d23b9e52..b1ad0aad9c76 100644
--- a/pkgs/applications/science/math/sage/env-locations.nix
+++ b/pkgs/applications/science/math/sage/env-locations.nix
@@ -44,6 +44,6 @@ writeTextFile rec {
     export JSMOL_DIR="${jmol}/share/jsmol"
     export MATHJAX_DIR="${mathjax}/lib/node_modules/mathjax"
     export THREEJS_DIR="${three}/lib/node_modules/three"
-    export SAGE_INCLUDE_DIRECTORIES="${cysignals}/lib/python2.7/site-packages"
+    export SAGE_INCLUDE_DIRECTORIES="${cysignals}/${cysignals.pythonModule.sitePackages}"
   '';
 }
diff --git a/pkgs/applications/science/math/sage/flask-oldsessions.nix b/pkgs/applications/science/math/sage/flask-oldsessions.nix
deleted file mode 100644
index 86fe9912c19e..000000000000
--- a/pkgs/applications/science/math/sage/flask-oldsessions.nix
+++ /dev/null
@@ -1,36 +0,0 @@
-{ stdenv
-, buildPythonPackage
-, fetchFromGitHub
-, python
-, flask
-}:
-
-buildPythonPackage rec {
-  pname = "Flask-OldSessions";
-  version = "0.10";
-
-  # no artifact on pypi: https://github.com/mitsuhiko/flask-oldsessions/issues/1
-  src = fetchFromGitHub {
-    owner = "mitsuhiko";
-    repo = "flask-oldsessions";
-    rev = version;
-    sha256 = "04b5m8njjiwld9a0zw55iqwvyjgwcpdbhz1cic8nyhgcmypbicqn";
-  };
-
-  propagatedBuildInputs = [
-    flask
-  ];
-
-  # missing module flask.testsuite, probably assumes an old version of flask
-  doCheck = false;
-  checkPhase = ''
-    ${python.interpreter} run-tests.py
-  '';
-
-  meta = with stdenv.lib; {
-    description = "Provides a session class that works like the one in Flask before 0.10.";
-    license = licenses.bsd2;
-    maintainers = teams.sage.members;
-    homepage = "https://github.com/mitsuhiko/flask-oldsessions";
-  };
-}
diff --git a/pkgs/applications/science/math/sage/flask-openid.nix b/pkgs/applications/science/math/sage/flask-openid.nix
deleted file mode 100644
index 900b033429ef..000000000000
--- a/pkgs/applications/science/math/sage/flask-openid.nix
+++ /dev/null
@@ -1,28 +0,0 @@
-{ stdenv
-, buildPythonPackage
-, fetchPypi
-, flask
-, python-openid
-}:
-
-buildPythonPackage rec {
-  pname = "Flask-OpenID";
-  version = "1.2.5";
-
-  src = fetchPypi {
-    inherit pname version;
-    sha256 = "1aycwmwi7ilcaa5ab8hm0bp6323zl8z25q9ha0gwrl8aihfgx3ss";
-  };
-
-  propagatedBuildInputs = [
-    flask
-    python-openid
-  ];
-
-  meta = with stdenv.lib; {
-    description = "Adds openid support to flask applications";
-    license = licenses.bsd2;
-    maintainers = teams.sage.members;
-    homepage = "https://pythonhosted.org/Flask-OpenID/";
-  };
-}
diff --git a/pkgs/applications/science/math/sage/patches/Only-test-py2-py3-optional-tests-when-all-of-sage-is.patch b/pkgs/applications/science/math/sage/patches/Only-test-py2-py3-optional-tests-when-all-of-sage-is.patch
index 8cd80281d0e4..d5c19a54fd96 100644
--- a/pkgs/applications/science/math/sage/patches/Only-test-py2-py3-optional-tests-when-all-of-sage-is.patch
+++ b/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
 
diff --git a/pkgs/applications/science/math/sage/patches/do-not-test-find-library.patch b/pkgs/applications/science/math/sage/patches/do-not-test-find-library.patch
index 3f844e1b1ef5..981759202386 100644
--- a/pkgs/applications/science/math/sage/patches/do-not-test-find-library.patch
+++ b/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
diff --git a/pkgs/applications/science/math/sage/patches/docutils-0.15.patch b/pkgs/applications/science/math/sage/patches/docutils-0.15.patch
deleted file mode 100644
index 63f5d2e146dd..000000000000
--- a/pkgs/applications/science/math/sage/patches/docutils-0.15.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-diff --git a/src/sage/misc/sphinxify.py b/src/sage/misc/sphinxify.py
-index 4849c2bffa..76b7bc8602 100644
---- a/src/sage/misc/sphinxify.py
-+++ b/src/sage/misc/sphinxify.py
-@@ -25,6 +25,7 @@ from __future__ import absolute_import, print_function
- import os
- import re
- import shutil
-+import warnings
- from tempfile import mkdtemp
- from sphinx.application import Sphinx
- 
-@@ -120,7 +121,10 @@ smart_quotes = no""")
-     # buildername, confoverrides, status, warning, freshenv).
-     sphinx_app = Sphinx(srcdir, confdir, outdir, doctreedir, format,
-                         confoverrides, None, None, True)
--    sphinx_app.build(None, [rst_name])
-+    with warnings.catch_warnings():
-+        # Quick and dirty workaround for https://trac.sagemath.org/ticket/28856#comment:19
-+        warnings.simplefilter("ignore")
-+        sphinx_app.build(None, [rst_name])
-     sys.path = old_sys_path
- 
-     # We need to remove "_" from __builtin__ that the gettext module installs
diff --git a/pkgs/applications/science/math/sage/patches/ignore-cmp-deprecation.patch b/pkgs/applications/science/math/sage/patches/ignore-cmp-deprecation.patch
index 11ca74819615..a91ee319b8f0 100644
--- a/pkgs/applications/science/math/sage/patches/ignore-cmp-deprecation.patch
+++ b/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
diff --git a/pkgs/applications/science/math/sage/patches/ignore-werkzeug-immutable-dict-deprecation.patch b/pkgs/applications/science/math/sage/patches/ignore-werkzeug-immutable-dict-deprecation.patch
deleted file mode 100644
index c5f95b498d53..000000000000
--- a/pkgs/applications/science/math/sage/patches/ignore-werkzeug-immutable-dict-deprecation.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff --git a/src/sage/all.py b/src/sage/all.py
-index c87c9372e9..862fca4fcc 100644
---- a/src/sage/all.py
-+++ b/src/sage/all.py
-@@ -306,6 +306,7 @@ warnings.filters.remove(('ignore', None, DeprecationWarning, None, 0))
- # Ignore all deprecations from IPython etc.
- warnings.filterwarnings('ignore', category=DeprecationWarning,
-     module='.*(IPython|ipykernel|jupyter_client|jupyter_core|nbformat|notebook|ipywidgets|storemagic)')
-+warnings.filterwarnings('ignore', category=DeprecationWarning, message=r".*The import 'werkzeug.ImmutableDict' is deprecated")
- # Ignore collections.abc warnings, there are a lot of them but they are
- # harmless.
- warnings.filterwarnings('ignore', category=DeprecationWarning,
diff --git a/pkgs/applications/science/math/sage/patches/pari-stackwarn.patch b/pkgs/applications/science/math/sage/patches/pari-stackwarn.patch
deleted file mode 100644
index 49cdfd189b92..000000000000
--- a/pkgs/applications/science/math/sage/patches/pari-stackwarn.patch
+++ /dev/null
@@ -1,20 +0,0 @@
-diff --git a/src/sage/doctest/parsing.py b/src/sage/doctest/parsing.py
-index 6bdc9a0..31fc780 100644
---- a/src/sage/doctest/parsing.py
-+++ b/src/sage/doctest/parsing.py
-@@ -40,6 +40,7 @@ from .external import available_software
- 
- float_regex = re.compile('\s*([+-]?\s*((\d*\.?\d+)|(\d+\.?))([eE][+-]?\d+)?)')
- optional_regex = re.compile(r'(py2|py3|long time|not implemented|not tested|known bug)|([^ a-z]\s*optional\s*[:-]*((\s|\w)*))')
-+pari_stack_warning_regex = re.compile(r'\s*\*\*\*.*(Warning: increasing stack size to )\d+\.')
- find_sage_prompt = re.compile(r"^(\s*)sage: ", re.M)
- find_sage_continuation = re.compile(r"^(\s*)\.\.\.\.:", re.M)
- random_marker = re.compile('.*random', re.I)
-@@ -935,6 +936,7 @@ class SageOutputChecker(doctest.OutputChecker):
-             <type 'float'>
-         """
-         got = self.human_readable_escape_sequences(got)
-+        got = pari_stack_warning_regex.sub('', got)
-         if isinstance(want, MarkedOutput):
-             if want.random:
-                 return True
diff --git a/pkgs/applications/science/math/sage/patches/pillow-update.patch b/pkgs/applications/science/math/sage/patches/pillow-update.patch
new file mode 100644
index 000000000000..19