sage: 9.5 -> 9.6

8 files changed, 30 insertions, 144 deletions

diff --git a/pkgs/applications/science/math/sage/patches/Only-test-external-software-when-all-of-sage-is.patch b/pkgs/applications/science/math/sage/patches/Only-test-external-software-when-all-of-sage-is.patch
deleted file mode 100644
index a478f50d92e..00000000000
--- a/pkgs/applications/science/math/sage/patches/Only-test-external-software-when-all-of-sage-is.patch
+++ /dev/null
@@ -1,46 +0,0 @@
-diff --git a/src/sage/doctest/control.py b/src/sage/doctest/control.py
-index 01f32fb8e4..4d83dc7b47 100644
---- a/src/sage/doctest/control.py
-+++ b/src/sage/doctest/control.py
-@@ -1253,6 +1253,7 @@ class DocTestController(SageObject):
- 
-             self.log("Using --optional=" + self._optional_tags_string())
-             available_software._allow_external = self.options.optional is True or 'external' in self.options.optional
-+            available_software._autodetect_safe = self.options.optional is True or 'sage' in self.options.optional
-             self.log("Features to be detected: " + ','.join(available_software.detectable()))
-             self.add_files()
-             self.expand_files_into_sources()
-diff --git a/src/sage/doctest/external.py b/src/sage/doctest/external.py
-index 84dae19ea5..badc61466e 100644
---- a/src/sage/doctest/external.py
-+++ b/src/sage/doctest/external.py
-@@ -409,6 +409,7 @@ class AvailableSoftware(object):
-             []
-         """
-         self._allow_external = True
-+        self._autodetect_safe = True
-         # For multiprocessing of doctests, the data self._seen should be
-         # shared among subprocesses. Thus we use Array class from the
-         # multiprocessing module.
-@@ -430,6 +431,8 @@ class AvailableSoftware(object):
-             sage: 'internet' in available_software # random, optional - internet
-             True
-         """
-+        if not self._autodetect_safe:
-+            return False
-         try:
-             idx = self._indices[item]
-         except KeyError:
-diff --git a/src/sage/features/sagemath.py b/src/sage/features/sagemath.py
-index 433338766d..233623b14a 100644
---- a/src/sage/features/sagemath.py
-+++ b/src/sage/features/sagemath.py
-@@ -12,7 +12,7 @@ class sagemath_doc_html(StaticFile):
- 
-     EXAMPLES::
- 
--        sage: from sage.features.sagemath import sagemath_doc_html
-+        sage: from sage.features.sagemath import sagemath_doc_html  # optional - sagemath_doc_html
-         sage: sagemath_doc_html().is_present()  # optional - sagemath_doc_html
-         FeatureTestResult('sagemath_doc_html', True)
-     """
diff --git a/pkgs/applications/science/math/sage/patches/configurationpy-error-verbose.patch b/pkgs/applications/science/math/sage/patches/configurationpy-error-verbose.patch
index e687281ad1a..ca01eba29a2 100644
--- a/pkgs/applications/science/math/sage/patches/configurationpy-error-verbose.patch
+++ b/pkgs/applications/science/math/sage/patches/configurationpy-error-verbose.patch
@@ -13,7 +13,7 @@ index 67d7d2accf..18279581e2 100644
 -    True
 +    sage: print(output)
 +    sage...[False, True]
-+    sage...Exiting Sage ...
++    ...
  """
  
  #*****************************************************************************
diff --git a/pkgs/applications/science/math/sage/patches/docutils-0.18.1-deprecation.patch b/pkgs/applications/science/math/sage/patches/docutils-0.18.1-deprecation.patch
index 94e0488e21e..0a19e7af104 100644
--- a/pkgs/applications/science/math/sage/patches/docutils-0.18.1-deprecation.patch
+++ b/pkgs/applications/science/math/sage/patches/docutils-0.18.1-deprecation.patch
@@ -1,11 +1,11 @@
 diff --git a/src/sage/misc/sagedoc.py b/src/sage/misc/sagedoc.py
-index 4c56aea078..e51a77ae8a 100644
+index 08c4225b87..3a9bbe4ed0 100644
 --- a/src/sage/misc/sagedoc.py
 +++ b/src/sage/misc/sagedoc.py
 @@ -1402,6 +1402,8 @@ class _sage_doc:
              sage: identity_matrix.__doc__ in browse_sage_doc(identity_matrix, 'rst')
              True
-             sage: browse_sage_doc(identity_matrix, 'html', False)             # optional - sphinx
+             sage: browse_sage_doc(identity_matrix, 'html', False)             # optional - sphinx sagemath_doc_html
 +            ...
 +            FutureWarning: The configuration setting "embed_images" will be removed in Docutils 1.2. Use "image_loading: link".
              '...div...File:...Type:...Definition:...identity_matrix...'
diff --git a/pkgs/applications/science/math/sage/patches/sphinx-docbuild-subprocesses.patch b/pkgs/applications/science/math/sage/patches/sphinx-docbuild-subprocesses.patch
index 1ff081b25e0..3e7e37508ff 100644
--- a/pkgs/applications/science/math/sage/patches/sphinx-docbuild-subprocesses.patch
+++ b/pkgs/applications/science/math/sage/patches/sphinx-docbuild-subprocesses.patch
@@ -1,10 +1,10 @@
 diff --git a/src/sage_docbuild/__init__.py b/src/sage_docbuild/__init__.py
-index 8a5c1a19d2..21fd192642 100644
+index b12d56a3c9..df9d949ed1 100644
 --- a/src/sage_docbuild/__init__.py
 +++ b/src/sage_docbuild/__init__.py
-@@ -89,27 +89,6 @@ def builder_helper(type):
+@@ -88,30 +88,6 @@ def builder_helper(type):
      """
-     Returns a function which builds the documentation for
+     Return a function which builds the documentation for
      output type ``type``.
 -
 -    TESTS:
@@ -19,10 +19,13 @@ index 8a5c1a19d2..21fd192642 100644
 -        ....:     raise BaseException("abort pool operation")
 -        sage: original_runsphinx, sage_docbuild.sphinxbuild.runsphinx = sage_docbuild.sphinxbuild.runsphinx, raiseBaseException
 -
+-        sage: from sage.misc.temporary_file import tmp_dir
+-        sage: os.environ['SAGE_DOC'] = tmp_dir()
+-        sage: sage.env.var('SAGE_DOC') # random
 -        sage: from sage_docbuild import builder_helper, build_ref_doc
 -        sage: from sage_docbuild import _build_many as build_many
 -        sage: helper = builder_helper("html")
--        sage: try:
+-        sage: try:  # optional - sagemath_doc_html
 -        ....:     build_many(build_ref_doc, [("docname", "en", "html", {})])
 -        ....: except Exception as E:
 -        ....:     "Non-exception during docbuild: abort pool operation" in str(E)
@@ -30,7 +33,7 @@ index 8a5c1a19d2..21fd192642 100644
      """
      def f(self, *args, **kwds):
          output_dir = self._output_dir(type)
-@@ -131,10 +110,9 @@ def builder_helper(type):
+@@ -139,10 +115,9 @@ def builder_helper(type):
          logger.debug(build_command)
  
          # Run Sphinx with Sage's special logger
@@ -44,10 +47,10 @@ index 8a5c1a19d2..21fd192642 100644
              if ABORT_ON_ERROR:
                  raise
 diff --git a/src/sage_docbuild/sphinxbuild.py b/src/sage_docbuild/sphinxbuild.py
-index d917c3e9d4..551cc8028a 100644
+index a39c99ffe9..73be823684 100644
 --- a/src/sage_docbuild/sphinxbuild.py
 +++ b/src/sage_docbuild/sphinxbuild.py
-@@ -327,3 +327,8 @@ def runsphinx():
+@@ -330,3 +330,8 @@ def runsphinx():
          sys.stderr = saved_stderr
          sys.stdout.flush()
          sys.stderr.flush()
diff --git a/pkgs/applications/science/math/sage/sage-env.nix b/pkgs/applications/science/math/sage/sage-env.nix
index cdff1e8477a..4c22470de91 100644
--- a/pkgs/applications/science/math/sage/sage-env.nix
+++ b/pkgs/applications/science/math/sage/sage-env.nix
@@ -186,7 +186,7 @@ writeTextFile rec {
     export SAGE_EXTCODE='${sagelib.src}/src/sage/ext_data'
 
   # for find_library
-    export DYLD_LIBRARY_PATH="${lib.makeLibraryPath [stdenv.cc.libc singular]}''${DYLD_LIBRARY_PATH:+:}$DYLD_LIBRARY_PATH"
+    export DYLD_LIBRARY_PATH="${lib.makeLibraryPath [stdenv.cc.libc singular giac]}''${DYLD_LIBRARY_PATH:+:}$DYLD_LIBRARY_PATH"
   '';
 } // { # equivalent of `passthru`, which `writeTextFile` doesn't support
   lib = sagelib;
diff --git a/pkgs/applications/science/math/sage/sage-src.nix b/pkgs/applications/science/math/sage/sage-src.nix
index b230b0d42a0..95da9b26e54 100644
--- a/pkgs/applications/science/math/sage/sage-src.nix
+++ b/pkgs/applications/science/math/sage/sage-src.nix
@@ -58,30 +58,19 @@ let
   );
 in
 stdenv.mkDerivation rec {
-  version = "9.5";
+  version = "9.6";
   pname = "sage-src";
 
   src = fetchFromGitHub {
     owner = "sagemath";
     repo = "sage";
     rev = version;
-    sha256 = "sha256-uOsLpsGpcIGs8Xr82X82MElnTB2E908gytyNJ8WVD5w=";
+    sha256 = "sha256-QY8Yga3hD1WhSCtA2/PVry8hHlMmC31J8jCBFtWgIU0=";
   };
 
   # Patches needed because of particularities of nix or the way this is packaged.
   # The goal is to upstream all of them and get rid of this list.
   nixPatches = [
-    # Since https://trac.sagemath.org/ticket/32174, some external features are
-    # marked as "safe" and get auto-detected, in which case the corresponding
-    # optional tests are executed. We disable auto-detection of safe features if
-    # we are doctesting with an "--optional" argument which does not include
-    # "sage", because tests from autodetected features expect context provided
-    # by running basic sage tests. This is necessary to test sagemath_doc_html
-    # separately. See https://trac.sagemath.org/ticket/26110 for a related
-    # upstream discussion (from the time when Sage still had optional py2/py3
-    # tags).
-    ./patches/Only-test-external-software-when-all-of-sage-is.patch
-
     # Fixes a potential race condition which can lead to transient doctest failures.
     ./patches/fix-ecl-race.patch
 
@@ -120,81 +109,13 @@ stdenv.mkDerivation rec {
     # https://trac.sagemath.org/ticket/32959
     ./patches/linbox-1.7-upgrade.patch
 
-    # https://trac.sagemath.org/ticket/33170
-    (fetchSageDiff {
-      base = "9.6.beta5";
-      name = "ipython-8.1-update.patch";
-      rev = "4d2b53f1541375861310af3a7f7109c1c2ed475d";
-      sha256 = "sha256-ELda/VBzsQH7NdFas69fQ35QPUoJCeLx/gxT1j7qGR8=";
-    })
-
-    # https://trac.sagemath.org/ticket/32968
-    (fetchSageDiff {
-      base = "9.5";
-      name = "sphinx-4.3-update.patch";
-      rev = "fc84f82f52b6f05f512cb359ec7c100f93cf8841";
-      sha256 = "sha256-bBbfdcnw/9LUOlY8rHJRbFJEdMXK4shosqTNaobTS1Q=";
-    })
-
-    # https://trac.sagemath.org/ticket/33189
-    (fetchSageDiff {
-      base = "9.5";
-      name = "arb-2.22-update.patch";
-      rev = "53532ddd4e2dc92469c1590ebf0c40f8f69bf579";
-      sha256 = "sha256-6SoSBvIlqvNwZV3jTB6uPdUtaWIOeNmddi2poK/WvGs=";
-    })
-
-    # TODO: This will not be necessary when Sphinx 4.4.1 is released,
-    # since some warnings introduced in 4.4.0 will be disabled by then
-    # (https://github.com/sphinx-doc/sphinx/pull/10126).
-    # https://trac.sagemath.org/ticket/33272
-    (fetchSageDiff {
-      base = "9.5";
-      name = "sphinx-4.4-warnings.patch";
-      rev = "97d7958bed441cf2ccc714d88f83d3a8426bc085";
-      sha256 = "sha256-y1STE0oxswnijGCsBw8eHWWqpmT1XMznIfA0vvX9pFA=";
-    })
-
     # adapted from https://trac.sagemath.org/ticket/23712#comment:22
     ./patches/tachyon-renamed-focallength.patch
 
-    # https://trac.sagemath.org/ticket/33336
-    (fetchSageDiff {
-      base = "9.6.beta2";
-      name = "scipy-1.8-update.patch";
-      rev = "9c8235e44ffb509efa8a3ca6cdb55154e2b5066d";
-      sha256 = "sha256-bfc4ljNOxVnhlmxIuNbjbKl4vJXYq2tlF3Z8bbC8PWw=";
-    })
-
-    # https://trac.sagemath.org/ticket/33495
-    (fetchSageDiff {
-      base = "9.6.beta5";
-      name = "networkx-2.7-update.patch";
-      rev = "8452003846a7303100847d8d0ed642fc642c11d6";
-      sha256 = "sha256-A/XMouPlc2sjFp30L+56fBGJXydS2EtzfPOV98FCDqI=";
-    })
-
-    # https://trac.sagemath.org/ticket/33226
-    (fetchSageDiff {
-      base = "9.6.beta0";
-      name = "giac-1.7.0-45-update.patch";
-      rev = "33ea2adf01e9e2ce9f1e33779f0b1ac0d9d1989c";
-      sha256 = "sha256-DOyxahf3+IaYdkgmAReNDCorRzMgO8+yiVrJ5TW1km0=";
-    })
-
-    # https://trac.sagemath.org/ticket/33398
-    (fetchSageDiff {
-      base = "9.6.beta4";
-      name = "sympy-1.10-update.patch";
-      rev = "6b7c3a28656180e42163dc10f7b4a571b93e5f27";
-      sha256 = "sha256-fnUyM2yjHkCykKRfzQQ4glcUYmCS/fYzDzmCf0nuebk=";
-      # The patch contains a whitespace change to a file that didn't exist in Sage 9.5.
-      excludes = [ "build/*" "src/sage/manifolds/vector_bundle_fiber_element.py" ];
-    })
-
     # docutils 0.18.1 now triggers Sphinx warnings. tolerate them for
-    # now, because patching Sphinx is not feasible.
-    # https://github.com/sphinx-doc/sphinx/issues/9777#issuecomment-1104481271
+    # now, because patching Sphinx is not feasible. remove when Sphinx
+    # 5.0 hits nixpkgs.
+    # https://github.com/sphinx-doc/sphinx/pull/10372
     ./patches/docutils-0.18.1-deprecation.patch
   ];
 
diff --git a/pkgs/applications/science/math/sage/sagedoc.nix b/pkgs/applications/science/math/sage/sagedoc.nix
index 55674719064..67d754caff3 100644
--- a/pkgs/applications/science/math/sage/sagedoc.nix
+++ b/pkgs/applications/science/math/sage/sagedoc.nix
@@ -89,6 +89,10 @@ stdenv.mkDerivation rec {
 
   doCheck = true;
   checkPhase = ''
-    ${sage-with-env}/bin/sage -t --optional=sagemath_doc_html --all
+    # sagemath_doc_html tests assume sage tests are being run, so we
+    # compromise: we run standard tests, but only on files containing
+    # relevant tests. as of Sage 9.6, there are only 4 such files.
+    grep -PRl "#.*optional.*sagemath_doc_html" ${src}/src/sage{,_docbuild} | \
+      xargs ${sage-with-env}/bin/sage -t --optional=sage,sagemath_doc_html
   '';
 }
diff --git a/pkgs/applications/science/math/sage/sagelib.nix b/pkgs/applications/science/math/sage/sagelib.nix
index 92eae35688f..8f864d13692 100644
--- a/pkgs/applications/science/math/sage/sagelib.nix
+++ b/pkgs/applications/science/math/sage/sagelib.nix
@@ -67,7 +67,9 @@
 , pillow
 , ipykernel
 , networkx
-, sphinx # TODO: this is in setup.cfg, bug should we override it?
+, ptyprocess
+, lrcalc-python
+, sphinx # TODO: this is in setup.cfg, should we override it?
 }:
 
 assert (!blas.isILP64) && (!lapack.isILP64);
@@ -157,6 +159,8 @@ buildPythonPackage rec {
     networkx
     jupyter-client
     ipywidgets
+    ptyprocess
+    lrcalc-python
     sphinx
   ];
 
@@ -188,7 +192,7 @@ buildPythonPackage rec {
     # Sage tests already catch any relevant API breakage.
     # according to the discussion at https://trac.sagemath.org/ticket/33520,
     # upper bounds will be less noisy starting from Sage 9.6.
-    sed -i 's/==2.1.0rc1/>=2.1.1/' ../gmpy2/install-requires.txt
+    sed -i 's/==0.5.1/>=0.5.1/' ../ptyprocess/install-requires.txt
     sed -i 's/, <[^, ]*//' ../*/install-requires.txt
 
     for infile in src/*.m4; do